project(Gromacs)
include(Dart)
mark_as_advanced(DART_ROOT)
+
# PROJECT_VERSION should have the following structure:
-# VERSION[-dev-SUFFIX] where the VERSION can have any form and the suffix
-set(PROJECT_VERSION "4.5.1")
+# VERSION-dev[-SUFFIX] where the VERSION should have the for: vMajor.vMinor.vPatch
+#
+# The "-dev" suffix is important to keep because it makes possible to distinguish
+# between a build from official release and a build from git release branch on a
+# machine with no git.
+#
+# NOTE: when releasing the "-dev" suffix needs to be stripped off!
+set(PROJECT_VERSION "4.5.2-dev")
set(CUSTOM_VERSION_STRING ""
CACHE STRING "Custom version string (if empty, use hard-coded default)")
mark_as_advanced(CUSTOM_VERSION_STRING)
# It is a bit irritating, but this has to be set separately for now!
SET(CPACK_PACKAGE_VERSION_MAJOR "4")
SET(CPACK_PACKAGE_VERSION_MINOR "5")
-SET(CPACK_PACKAGE_VERSION_PATCH "1")
+SET(CPACK_PACKAGE_VERSION_PATCH "2")
# Cmake modules/macros are in a subdirectory to keep this file cleaner
option(GMX_THREADS "Build a parallel (thread-based) version of GROMACS (cannot be combined with MPI yet)" ON)
option(GMX_SOFTWARE_INVSQRT "Use GROMACS software 1/sqrt" ON)
mark_as_advanced(GMX_SOFTWARE_INVSQRT)
+option(GMX_POWERPC_INVSQRT "Use PowerPC hardware 1/sqrt" ON)
+mark_as_advanced(GMX_POWERPC_INVSQRT)
option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
mark_as_advanced(GMX_FAHCORE)
option(GMX_OPENMM "Accelerated execution on GPUs through the OpenMM library (rerun cmake after changing to see relevant options)" OFF)
set(GMX_ACCELERATION "auto"
- CACHE STRING "Accelerated kernels. Pick one of: auto, none, SSE, BlueGene, Power6, ia64, altivec")
+ CACHE STRING "Accelerated kernels. Pick one of: auto, none, SSE, BlueGene, Power6, ia64, altivec, fortran")
set(GMX_FFT_LIBRARY "fftw3"
CACHE STRING "FFT library choices: fftw3,fftw2,mkl,fftpack[built-in]")
mark_as_advanced(USE_VERSION_H)
option(GMX_DEFAULT_SUFFIX "Use default suffixes for GROMACS binaries and libs (_d for double, _mpi for MPI; rerun cmake after changing to see relevant options)" ON)
+
+if(UNIX AND NOT APPLE)
+ option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer \".a\" static archives (NOTE: this is enabled only for UNIX (excluding APPLE) platforms but it might not always work!" OFF)
+ mark_as_advanced(GMX_PREFER_STATIC_LIBS)
+endif()
+
+########################################################################
+# Set up binary and library suffixing
+########################################################################
set(GMX_BINARY_SUFFIX "" CACHE STRING "Suffix for GROMACS binaries (default: _d for double, _mpi for MPI, _mpi_d for MPI and double).")
set(GMX_LIBS_SUFFIX ""
CACHE STRING "Suffix for GROMACS libs (default: _d for double, _mpi for MPI, _mpi_d for MPI and double).")
set (GMX_BINARY_SUFFIX "${GMX_BINARY_SUFFIX}_d")
set (GMX_LIBS_SUFFIX "${GMX_LIBS_SUFFIX}_d")
endif(GMX_DOUBLE)
+ if (GMX_OPENMM)
+ set (GMX_BINARY_SUFFIX "-gpu")
+ set (GMX_LIBS_SUFFIX "_gpu")
+ endif(GMX_OPENMM)
mark_as_advanced(FORCE GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
message(STATUS "Using default binary suffix: \"${GMX_BINARY_SUFFIX}\"")
message(STATUS "Using default library suffix: \"${GMX_LIBS_SUFFIX}\"")
set(PKG_CFLAGS "")
if(GMX_DOUBLE)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
+ set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
endif(GMX_DOUBLE)
if(GMX_SOFTWARE_INVSQRT)
set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
endif(GMX_SOFTWARE_INVSQRT)
+if(GMX_POWERPC_INVSQRT)
+ set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_POWERPC_INVSQRT")
+endif(GMX_POWERPC_INVSQRT)
########################################################################
#Process MPI settings
if(GMX_OPENMM)
cmake_minimum_required(VERSION 2.6.4)
# we'll use the built-in fft to avoid unnecessary dependencies
- message(STATUS "No external FFT libraries needed for the OpenMM build, using fftpack!")
- set (GMX_FFT_LIBRARY "fftpack" CACHE STRING
- "No external FFT libraries needed for the OpenMM build, using fftpack!" FORCE)
+ string(TOUPPER ${GMX_FFT_LIBRARY} GMX_FFT_LIBRARY)
+ if(NOT ${GMX_FFT_LIBRARY} STREQUAL "FFTPACK")
+ message(STATUS "No external FFT libraries needed for the OpenMM build, switching to fftpack!")
+ set(GMX_FFT_LIBRARY "fftpack" CACHE STRING
+ "No external FFT libraries needed for the OpenMM build, switching to fftpack!" FORCE)
+ endif()
if(GMX_MPI)
message(FATAL_ERROR "The OpenMM build is not compatible with MPI!")
endif(GMX_MPI)
if(GMX_THREADS)
- message(STATUS "Threads not compatible with OpenMM build, disabled!")
+ message(STATUS "Threads are not compatible with OpenMM build, disabled!")
set(GMX_THREADS OFF CACHE BOOL
- "Threads not compatible with OpenMM build, disabled!" FORCE)
+ "Threads are not compatible with OpenMM build, disabled!" FORCE)
endif(GMX_THREADS)
if(GMX_SOFTWARE_INVSQRT)
- set(GMX_SOFTWARE_INVSQRT OFF FORCE)
+ set(GMX_SOFTWARE_INVSQRT OFF CACHE STRING
+ "The OpenMM build does not need GROMACS software 1/sqrt!" FORCE)
endif(GMX_SOFTWARE_INVSQRT)
- if(NOT GMX_ACCELERATION MATCHES "^(none|None|NONE)")
- message(WARNING "CPU-based acceleration turned off, OpenMM does not support/need any!")
- unset(GMX_ACCELERATION CACHE)
+ string(TOUPPER ${GMX_ACCELERATION} GMX_ACCELERATION)
+ if(NOT GMX_ACCELERATION STREQUAL "NONE")
+ message(STATUS "Switching off CPU-based acceleration, the OpenMM build does not support/need any!")
set(GMX_ACCELERATION "none" CACHE STRING
- "CPU-based acceleration turned off, OpenMM does not support/need any!" FORCE)
+ "Switching off CPU-based acceleration, the OpenMM build does not support/need any!" FORCE)
endif()
if(GMX_FAHCORE)
message(FATAL_ERROR "The OpenMM build does not support FAH build!")
endif(GMX_FAHCORE)
- set(GMX_DOUBLE OFF FORCE )
+ if(GMX_DOUBLE)
+ message(FATAL_ERROR "The OpenMM-build does not support double precision calculations!")
+ endif()
# mark as advanced the unused variables
mark_as_advanced(FORCE GMX_ACCELERATION GMX_MPI GMX_FFT_LIBRARY
GMX_QMMM_PROGRAM GMX_THREADS GMX_DOUBLE)
########################################################################
# Find external packages #
########################################################################
+if(UNIX AND NOT APPLE)
+ if(GMX_PREFER_STATIC_LIBS)
+ SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
+ if(BUILD_SHARED_LIBS)
+ message(WARNING "Static libraries requested, the GROMACS libraries will also be build static (BUILD_SHARED_LIBS=OFF)")
+ set(BUILD_SHARED_LIBS OFF CACHE BOOL "Enable shared libraries (can be problematic with MPI, Windows)" FORCE)
+ endif()
+ endif()
+endif()
find_package(LibXml2)
set(PKG_XML "")
if (${GMX_ACCELERATION} STREQUAL "auto" AND NOT GMX_OPENMM)
if(CMAKE_SYSTEM_PROCESSOR MATCHES "^(i.86|x86|x64|x86_64|AMD64|amd64)")
- set(GMX_ACCELERATION "SSE" CACHE STRING "Accelerated kernels. Pick one of: auto, none, SSE, BlueGene, Power6, ia64, altivec" FORCE)
+ set(GMX_ACCELERATION "SSE" CACHE STRING "Accelerated kernels. Pick one of: auto, none, SSE, BlueGene, Power6, ia64, altivec, fortran" FORCE)
if (GMX_64_BIT)
set(GMX_X86_64_ASM ON CACHE BOOL "Add SSE assembly files for x86_64" FORCE)
# Determine the assembler/compiler to use
else()
- set(GMX_ACCELERATION "none" CACHE STRING "Accelerated kernels. Pick one of: auto, none, SSE, BlueGene, Power6, ia64, altivec" FORCE)
+ set(GMX_ACCELERATION "none" CACHE STRING "Accelerated kernels. Pick one of: auto, none, SSE, BlueGene, Power6, ia64, altivec, fortran" FORCE)
endif()
endif (${GMX_ACCELERATION} STREQUAL "auto" AND NOT GMX_OPENMM)
-
include(gmxTestXDR)
gmx_test_xdr(GMX_SYSTEM_XDR)
if(NOT GMX_SYSTEM_XDR)
set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_INTERNAL_XDR")
endif(NOT GMX_SYSTEM_XDR)
-if(GMX_FORTRAN OR GMX_POWER6)
- enable_language(Fortran)
- include(FortranCInterface)
- discover_fortran_mangling(prefix isupper suffix extra_under_score found)
- if(extra_under_score)
- set(extrasuffix "_")
- endif(extra_under_score)
-
- if(isupper)
- set(F77_FUNCDEF "${prefix} ## NAME ## ${suffix}")
- set(F77_FUNCDEF_ "${prefix} ## NAME ## ${suffix}${extrasuffix}")
- else(isupper)
- set(F77_FUNCDEF "${prefix} ## name ## ${suffix}")
- set(F77_FUNCDEF_ "${prefix} ## name ## ${suffix}${extrasuffix}")
- endif(isupper)
-else(GMX_FORTRAN OR GMX_POWER6)
- set(F77_FUNCDEF "name ## _")
- set(F77_FUNCDEF_ "name ## _")
-endif(GMX_FORTRAN OR GMX_POWER6)
-
-
# Process nonbonded accelerated kernels settings
string(TOUPPER ${GMX_ACCELERATION} ${GMX_ACCELERATION})
if(${GMX_ACCELERATION} STREQUAL "NONE")
if(GMX_DOUBLE)
set(GMX_IA32_SSE2 1)
else()
- set(GMX_IA32_SSE 1)
+ set(GMX_IA32_SSE 1)
endif()
elseif(GMX_X86_64_ASM)
if(GMX_DOUBLE)
- set(GMX_X86_64_SSE2 1)
+ set(GMX_X86_64_SSE2 1)
else()
set(GMX_X86_64_SSE 1)
endif()
elseif(${GMX_ACCELERATION} STREQUAL "FORTRAN")
set(GMX_FORTRAN 1)
+ #these are switch on by default sometimes
+ set(GMX_IA32_ASM 0)
+ set(GMX_GMX_X86_64_ASM 0)
elseif(${GMX_ACCELERATION} STREQUAL "BLUEGENE")
+# GMX_ACCELERATION=BlueGene should be set in the Toolchain-BlueGene?-???.cmake file
+ message(STATUS "Configuring for BlueGene")
set(GMX_BLUEGENE 1)
+ if (${CMAKE_SYSTEM_NAME} STREQUAL "BlueGeneL")
+ set(SHARED_LIBS_DEFAULT OFF CACHE BOOL "Shared libraries not compatible with BlueGene/L, disabled!" FORCE)
+ set(BUILD_SHARED_LIBS OFF CACHE BOOL "Shared libraries not compatible with BlueGene/L, disabled!" FORCE)
+ endif (${CMAKE_SYSTEM_NAME} STREQUAL "BlueGeneL")
+ set(GMX_SOFTWARE_INVSQRT OFF CACHE BOOL "Do not use software reciprocal square root on BlueGene" FORCE)
+ set(GMX_POWERPC_INVSQRT ON CACHE BOOL "Use hardware reciprocal square root on BlueGene" FORCE)
+ set(GMX_X11 OFF CACHE BOOL "X11 not compatible with BlueGene, disabled!" FORCE)
+ set(GMX_THREADS OFF CACHE BOOL "Threads not compatible with BlueGene, disabled!" FORCE)
+ set(GMX_MPI ON CACHE BOOL "Use MPI on BlueGene" FORCE)
+ set(GMX_EXTERNAL_BLAS TRUE CACHE BOOL "Use MASSV for BLAS on BlueGene" FORCE)
+ set(GMX_EXTERNAL_LAPACK TRUE CACHE BOOL "Use MASSV for LAPACK on BlueGene" FORCE)
+ list(APPEND GMX_EXTRA_LIBRARIES massv)
elseif(${GMX_ACCELERATION} STREQUAL "POWER6")
set(GMX_POWER6 1)
+ set(GMX_SOFTWARE_INVSQRT OFF CACHE BOOL "Do not use software reciprocal square root on Power6" FORCE)
+ set(GMX_POWERPC_INVSQRT ON CACHE BOOL "Use hardware reciprocal square root on Power6" FORCE)
elseif(${GMX_ACCELERATION} STREQUAL "IA64")
set(GMX_IA64_ASM 1)
set(DISABLE_WATERWATER_NLIST 1)
MESSAGE(FATAL_ERROR "Unrecognized option for accelerated kernels: ${GMX_ACCELERATION}. Pick one of auto, none, SSE, Fortran, BlueGene, Power6, ia64, altivec")
endif(${GMX_ACCELERATION} STREQUAL "NONE")
+if(GMX_FORTRAN OR GMX_POWER6)
+ if (GMX_THREADS)
+ message(FATAL_ERROR "FORTRAN/POWER6 is incompatible with threads and only provides a speed-up on certain IBM compilers. Disable FORTRAN (or threads if you really want to use FORTRAN kernels).")
+ endif(GMX_THREADS)
+ enable_language(Fortran)
+ include(FortranCInterface)
+ discover_fortran_mangling(prefix isupper suffix extra_under_score found)
+ if(extra_under_score)
+ set(extrasuffix "_")
+ endif(extra_under_score)
+ if(prefix)
+ set(prefix "${prefix} ##")
+ endif(prefix)
-
-
-
-
+ if(isupper)
+ set(F77_FUNCDEF "${prefix} NAME ## ${suffix}")
+ set(F77_FUNCDEF_ "${prefix} NAME ## ${suffix}${extrasuffix}")
+ else(isupper)
+ set(F77_FUNCDEF "${prefix} name ## ${suffix}")
+ set(F77_FUNCDEF_ "${prefix} name ## ${suffix}${extrasuffix}")
+ endif(isupper)
+else(GMX_FORTRAN OR GMX_POWER6)
+ set(F77_FUNCDEF "name ## _")
+ set(F77_FUNCDEF_ "name ## _")
+endif(GMX_FORTRAN OR GMX_POWER6)
# Process QM/MM Settings
string(TOUPPER ${GMX_QMMM_PROGRAM} ${GMX_QMMM_PROGRAM})
########################################################################
# Specify install locations and which subdirectories to process #
########################################################################
-set(LIB_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib)
+if ( DEFINED LIB )
+ set(LIB_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/${LIB}")
+else()
+ set(LIB_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib)
+endif()
set(BIN_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/bin)
set(DATA_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/share/gromacs)
set(MAN_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/share/man)
install-exec-hook:
+if NO_LA_FILES
+ cd $(DESTDIR)$(libdir) && rm -f libmd@LIBSUFFIX@.la libgmx@LIBSUFFIX@.la libgmxpreprocess@LIBSUFFIX@.la libgmxana@LIBSUFFIX@.la
+endif
@echo ""
@echo "GROMACS is installed under $(prefix)."
@echo "Make sure to update your PATH and MANPATH to find the"
(cd $(top_builddir)/src/mdlib && $(MAKE) install ; exit 0)
(cd $(top_builddir)/src/kernel && $(MAKE) install-libLTLIBRARIES ; exit 0)
(cd $(top_builddir)/src/kernel && $(MAKE) install-mdrun ; exit 0)
+if NO_LA_FILES
+ cd $(DESTDIR)$(libdir) && rm -f libmd@LIBSUFFIX@.la libgmx@LIBSUFFIX@.la libgmxpreprocess@LIBSUFFIX@.la libgmxana@LIBSUFFIX@.la
+endif
fahcore:
(cd $(top_builddir)/src/gmxlib && $(MAKE) ; exit 0)
Welcome to the official version of GROMACS!
If you are familiar with unix, it should be fairly trivial to compile and
-install GROMACS. Installation instructions are available in the INSTALL file,
-and a more extended step-by-step guide can be found on http://www.gromacs.org .
+install GROMACS. Installation instructions are available in the INSTALL.*
+files (there is one for automake users, INSTALL.automake and one for cmake
+users, INSTALL.cmake). A more extended step-by-step guide can be found
+on our website http://www.gromacs.org .
Of course we will do our utmost to help you with any problems, but PLEASE
READ THE INSTALLATION INSTRUCTIONS BEFORE CONTACTING US!
CPPFLAGS="$save_CPPFLAGS"
LDFLAGS="$save_LDFLAGS"
LIBS="$save_LIBS"
+ DLOPEN_LIBS="$lt_cv_dlopen_libs"
;;
esac
# Microsoft HPC SDK is automatically added to the system path
# Argonne National Labs MPICH2 sets a registry key that we can use.
+TRY_COMPILE(MPI_FOUND ${CMAKE_BINARY_DIR}
+ "${CMAKE_SOURCE_DIR}/cmake/TestMPI.c"
+ COMPILE_DEFINITIONS )
+
+if(MPI_FOUND)
+ return()
+endif()
+
set(_MPI_PACKAGE_DIR
mpi
mpich
--- /dev/null
+#include <mpi.h>
+
+int main(int argc, char **argv)
+{
+ MPI_Init(&argc,&argv);
+}
--- /dev/null
+# derived from http://cmake.org/Wiki/CmakeBlueGene
+
+# the name of the target operating system
+set(CMAKE_SYSTEM_NAME BlueGeneL CACHE STRING "Cross-compiling for BlueGene/L")
+
+# adjust to suit your machine's versions
+# /bgl/BlueLight/V1R3M2_140_2007-070424/ppc/bglsys
+set(BLRTS_PATH /bgl/BlueLight/V1R3M4_300_2008-080728/ppc/bglsys CACHE STRING "Path to the BlueGene/L system libraries and includes")
+
+# set the compiler
+set(CMAKE_C_COMPILER /opt/ibmcmp/vac/bg/8.0/bin/blrts_xlc)
+set(CMAKE_C_FLAGS "-O3 -qbgl -qarch=auto -qtune=auto -qnoautoconfig -qfloat=norngchk -qhot")
+set(CMAKE_EXE_LINKER_FLAGS "-L${BLRTS_PATH}/lib")
+set(CMAKE_CXX_COMPILER /opt/ibmcmp/vacpp/bg/8.0/bin/blrts_xlC)
+
+set(MPI_LIBRARY mpich.rts CACHE STRING "MPI library for BlueGene" FORCE)
+set(MPI_EXTRA_LIBRARY msglayer.rts devices.rts rts.rts devices.rts CACHE STRING "Extra MPI libraries for BlueGene" FORCE)
+set(MPI_INCLUDE_PATH ${BLRTS_PATH}/include CACHE STRING "MPI include path for BlueGene" FORCE)
+
+# This adds directories that find commands should specifically ignore for cross compiles.
+# Most of these directories are the includeand lib directories for the frontend on BG/P systems.
+# Not ignoring these can cause things like FindX11 to find a frontend PPC version mistakenly.
+# We use this on BG instead of re-rooting because backend libraries are typically strewn about
+# the filesystem, and we can't re-root ALL backend libraries to a single place.
+
+set(CMAKE_SYSTEM_IGNORE_PATH
+ /lib /lib64 /include
+ /usr/lib /usr/lib64 /usr/include
+ /usr/local/lib /usr/local/lib64 /usr/local/include
+ /usr/X11/lib /usr/X11/lib64 /usr/X11/include
+ /usr/lib/X11 /usr/lib64/X11 /usr/include/X11
+ /usr/X11R6/lib /usr/X11R6/lib64 /usr/X11R6/include
+ /usr/X11R7/lib /usr/X11R7/lib64 /usr/X11R7/include
+)
+
+# set the search path for the environment coming with the compiler
+# and a directory where you can install your own compiled software
+set(CMAKE_FIND_ROOT_PATH
+ /bgl/BlueLight/ppcfloor/
+ ${BLRTS_PATH}
+ /opt/ibmcmp/xlmass/bg
+)
+
+# adjust the default behaviour of the FIND_XXX() commands:
+# search headers and libraries in the target environment, search
+# programs in the host environment
+set(CMAKE_FIND_ROOT_PATH_MODE_PROGRAM NEVER)
+set(CMAKE_FIND_ROOT_PATH_MODE_LIBRARY ONLY)
+set(CMAKE_FIND_ROOT_PATH_MODE_INCLUDE ONLY)
+
+set(GMX_ACCELERATION "BlueGene" CACHE STRING "Forcing BlueGene acceleration when using BlueGene toolchain")
#######################################################################
AC_PREREQ(2.50)
-AC_INIT(gromacs, 4.5.1, [gmx-users@gromacs.org])
+
+# The "-dev" suffix is important to keep because it makes possible to distinguish
+# between a build from official release and a build from git release branch on a
+# machine with no git.
+#
+# NOTE: when releasing the "-dev" suffix needs to be stripped off!
+AC_INIT(gromacs, 4.5.2-dev, [gmx-users@gromacs.org])
AC_CONFIG_SRCDIR(src/gmxlib/3dview.c)
AC_CONFIG_AUX_DIR(config)
AC_CANONICAL_HOST
# always use CC for linking:
AC_SUBST(F77LINK,"\$(LINK)")
+#On some systems GNU libtool's la files are more confusing for libtool than helpful due to the
+#hard coded paths/libs in the files. And for better linking we have pkg-config files (.pc).
+AC_ARG_ENABLE(la-files,
+ [AS_HELP_STRING([--disable-la-files],[Do NOT install GNU libtool's la files])],,
+ [enable_la_files=yes])
+AM_CONDITIONAL(NO_LA_FILES,[test "$enable_la_files" = no])
# IBM Power6-specific optimization
AC_ARG_ENABLE(power6,
[AC_HELP_STRING([--enable-power6],
- [Use IBM Pwr6/PPC440/PPC450-specific F77 kernels])],,enable_power6=no)
+ [Use IBM Power6-specific F77 kernels])],,enable_power6=no)
if test "$enable_power6" = "yes"; then
- AC_DEFINE(GMX_POWER6,,[Enable IBM Pwr6/PPC440/PPC450-specific F77 kernels])
+ AC_DEFINE(GMX_POWER6,,[Enable IBM Power6-specific F77 kernels])
fi
AC_ARG_ENABLE(bluegene,
[AC_HELP_STRING([--disable-software-invsqrt],
[No software 1/sqrt (disabled on sgi,ibm,ia64)])],,
[case "${host_cpu}-${host_os}" in
- mips*-irix* | rs6000*-aix* | powerpc*-aix | ia64*-*) enable_software_invsqrt=no ;;
+ mips*-irix* | rs6000*-aix* | powerpc*-aix | powerpc*-none | ia64*-*) enable_software_invsqrt=no ;;
*) enable_software_invsqrt=yes ;;
esac])
if test "$enable_software_invsqrt" = "yes"; then
- AC_DEFINE(GMX_SOFTWARE_INVSQRT,,[Use the GROMACS sGMX_INTERNAL_XDRsqrt(x)])
+ AC_DEFINE(GMX_SOFTWARE_INVSQRT,,[Use the GROMACS software 1/sqrt(x)])
PKG_CFLAGS="$PKG_CFLAGS -DGMX_SOFTWARE_INVSQRT"
fi
AM_CONDITIONAL([GMX_SOFTWARE_INVSQRT],[test "$enable_software_invsqrt" = "yes"])
if test "$with_fft" = "fftw2"; then
AC_MSG_ERROR([fftw2 can't be used with threads. Use fftw3 or mkl.])
fi
+ if test "$enable_fortran" = "yes"; then
+ AC_MSG_ERROR([FORTRAN is incompatible with threads and only provides a speed-up on certain IBM compilers. Use --disable-threads if you really want to use FORTRAN kernels.])
+ fi
AC_CHECK_HEADERS(unistd.h)
AC_CHECK_HEADERS(sys/time.h)
AC_CHECK_HEADERS(sched.h)
AC_PROG_LN_S
AC_PROG_MAKE_SET
AC_LIBTOOL_WIN32_DLL
+AC_LIBTOOL_DLOPEN
AC_PROG_LIBTOOL
AC_SYS_LARGEFILE
#
if test "$enable_bluegene" = "yes"; then
AC_DEFINE(GMX_BLUEGENE,,[Use assembly intrinsics kernels for BlueGene])
+ AC_DEFINE_UNQUOTED(GMX_POWERPC_INVSQRT,,[Use the PowerPC hardware 1/sqrt(x)])
+ PKG_CFLAGS="$PKG_CFLAGS -DGMX_POWERPC_INVSQRT"
fi
if test "$enable_fortran" = "yes"; then
CFLAGS_RET=$CFLAGS
#LDFLAGS="$lt_cv_dlopen_libs $LDFLAGS" #can't make the macro, which is getting lt_cv_dlopen_libs, to work
LDFLAGS_RET=$LDFLAGS
+ LIBS_RET=$LIBS
if test "$enable_all_static" = "yes"; then #make sure we test also whether it works static
LDFLAGS="$LDFLAGS -static"
fi
CFLAGS="-I$srcdir/include -DGMX_DLOPEN $CFLAGS"
- AC_TRY_LINK([#include "$srcdir/src/gmxlib/vmddlopen.c"],,[AC_MSG_RESULT([yes])\
- AC_DEFINE(GMX_DLOPEN,,[Compile with dlopen])],AC_MSG_RESULT([no]))
+ LIBS="$DLOPEN_LIBS $LIBS"
+ AC_TRY_LINK([#include "$srcdir/src/gmxlib/vmddlopen.c"],,[
+ AC_MSG_RESULT([yes])
+ AC_DEFINE(GMX_DLOPEN,,[Compile with dlopen])
+ AC_SUBST(DLOPEN_LIBS)
+ ],[
+ AC_MSG_RESULT([no])
+ AC_SUBST(DLOPEN_LIBS,"")
+ ])
CFLAGS=$CFLAGS_RET
+ LIBS=$LIBS_RET
LDFLAGS=$LDFLAGS_RET
fi
# includes: Nothing to build, just installation
install(DIRECTORY . DESTINATION ${INCL_INSTALL_DIR}/gromacs
+ COMPONENT development
PATTERN "Makefile*" EXCLUDE
PATTERN "CMake*" EXCLUDE
PATTERN "cmake*" EXCLUDE
"Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,",
"Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, ",
"Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, ",
- "Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz, ",
+ "Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, ",
"Michael Shirts, Alfons Sijbers, Peter Tieleman,\n",
"Berk Hess, David van der Spoel, and Erik Lindahl.\n",
"Copyright (c) 1991-2000, University of Groningen, The Netherlands.",
};
#endif
- const __m128d signmask = _mm_castsi128_pd( _mm_set_epi32(0x7FFFFFFF,0xFFFFFFFF,0x7FFFFFFF,0xFFFFFFFF) );
+ const __m128d signmask = gmx_mm_castsi128_pd( _mm_set_epi32(0x7FFFFFFF,0xFFFFFFFF,0x7FFFFFFF,0xFFFFFFFF) );
const __m128d tabscale = _mm_set1_pd(32.0/M_PI);
const __m128d invtabscale = _mm_set1_pd(M_PI/32.0);
const __m128d one = _mm_set1_pd(1.0);
cswapsign = _mm_shuffle_epi32(cswapsign,_MM_SHUFFLE(1,1,0,0));
minusone = _mm_sub_pd(_mm_setzero_pd(),one);
- ssign = _mm_or_pd(_mm_and_pd( _mm_castsi128_pd(sswapsign),minusone ),
- _mm_andnot_pd( _mm_castsi128_pd(sswapsign),one ));
- csign = _mm_or_pd(_mm_and_pd( _mm_castsi128_pd(cswapsign),minusone ),
- _mm_andnot_pd( _mm_castsi128_pd(cswapsign),one ));
+ ssign = _mm_or_pd(_mm_and_pd( gmx_mm_castsi128_pd(sswapsign),minusone ),
+ _mm_andnot_pd( gmx_mm_castsi128_pd(sswapsign),one ));
+ csign = _mm_or_pd(_mm_and_pd( gmx_mm_castsi128_pd(cswapsign),minusone ),
+ _mm_andnot_pd( gmx_mm_castsi128_pd(cswapsign),one ));
/* First lookup into table */
#ifdef _MSC_VER
t_dlist *mk_dlist(FILE *log,
t_atoms *atoms, int *nlist,
gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bHChi,
- int maxchi,int r0,int naa,char **aa);
+ int maxchi, int r0, gmx_residuetype_t rt);
void pr_dlist(FILE *fp,int nl,t_dlist dl[],real dt, int printtype,
gmx_bool bPhi, gmx_bool bPsi,gmx_bool bChi,gmx_bool bOmega, int maxchi);
gmx_bool
gmx_residuetype_is_rna(gmx_residuetype_t rt, const char *resnm);
+int
+gmx_residuetype_get_size(gmx_residuetype_t rt);
+
+int
+gmx_residuetype_get_index(gmx_residuetype_t rt, const char *resnm);
+
+const char *
+gmx_residuetype_get_name(gmx_residuetype_t rt, int index);
+
int nrtp, t_restp rtp[],
t_restp *restp, t_hackblock *hb,
int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
- int *rn, int *rc, gmx_bool bAllowMissing,
+ gmx_bool bAllowMissing,
gmx_bool bVsites, gmx_bool bVsiteAromatics,
const char *ff, const char *ffdir,
real mHmult,
#define GMX_PME_SOLVE (1<<1)
#define GMX_PME_CALC_F (1<<2)
#define GMX_PME_CALC_ENER_VIR (1<<3)
+/* This forces the grid to be backtransformed even without GMX_PME_CALC_F */
+#define GMX_PME_CALC_POT (1<<4)
#define GMX_PME_DO_ALL_F (GMX_PME_SPREAD_Q | GMX_PME_SOLVE | GMX_PME_CALC_F)
int gmx_pme_do(gmx_pme_t pme,
gmx_large_int_t str_to_large_int_t(const char *str, char **endptr);
+#if ((defined WIN32 || defined _WIN32 || defined WIN64 || defined _WIN64) && !defined __CYGWIN__ && !defined __CYGWIN32__)
+#define snprintf _snprintf
+#endif
+
#ifdef __cplusplus
}
#endif
} t_nblists;
/* macros for the cginfo data in forcerec */
-/* The maximum cg size is 255, because we only have space for 8 bits in cginfo,
+/* The maximum cg size in cginfo is 255,
+ * because we only have space for 8 bits in cginfo,
* this cg size entry is actually only read with domain decomposition.
+ * But there is a smaller limit due to the t_excl data structure
+ * which is defined in nblist.h.
*/
-#define MAX_CHARGEGROUP_SIZE 256
#define SET_CGINFO_GID(cgi,gid) (cgi) = (((cgi) & ~65535) | (gid) )
#define GET_CGINFO_GID(cgi) ( (cgi) & 65535)
#define SET_CGINFO_EXCL_INTRA(cgi) (cgi) = ((cgi) | (1<<16))
typedef unsigned long t_excl;
+/* The maximum charge group size because of minimum size of t_excl
+ * could be 32 bits.
+ */
+#define MAX_CHARGEGROUP_SIZE 32
+
/* The maximum charge group size for CG-CG nblists.
* The excl entry in t_nblist uses blocks of this size.
*/
static gmx_inline void mvmul_ur0(matrix a,const rvec src,rvec dest)
{
dest[ZZ]=a[ZZ][XX]*src[XX]+a[ZZ][YY]*src[YY]+a[ZZ][ZZ]*src[ZZ];
- dest[YY]=a[YY][XX]*src[XX]+a[YY][YY];
+ dest[YY]=a[YY][XX]*src[XX]+a[YY][YY]*src[YY];
dest[XX]=a[XX][XX]*src[XX];
}
# Man pages: Nothing to build, just installation
install(DIRECTORY . DESTINATION ${MAN_INSTALL_DIR}
+ COMPONENT data
PATTERN "Makefile*" EXCLUDE
PATTERN "CMake*" EXCLUDE
PATTERN "cmake*" EXCLUDE
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/GMXRC.csh.cmakein ${CMAKE_CURRENT_BINARY_DIR}/GMXRC.csh @ONLY)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/GMXRC.zsh.cmakein ${CMAKE_CURRENT_BINARY_DIR}/GMXRC.zsh @ONLY)
-install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/GMXRC DESTINATION ${BIN_INSTALL_DIR})
-install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/GMXRC.bash DESTINATION ${BIN_INSTALL_DIR})
-install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/GMXRC.zsh DESTINATION ${BIN_INSTALL_DIR})
-install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/GMXRC.csh DESTINATION ${BIN_INSTALL_DIR})
+install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/GMXRC DESTINATION ${BIN_INSTALL_DIR} COMPONENT runtime)
+install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/GMXRC.bash DESTINATION ${BIN_INSTALL_DIR} COMPONENT runtime)
+install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/GMXRC.zsh DESTINATION ${BIN_INSTALL_DIR} COMPONENT runtime)
+install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/GMXRC.csh DESTINATION ${BIN_INSTALL_DIR} COMPONENT runtime)
file(GLOB EXTRA_SCRIPTS completion.*)
-install(FILES ${EXTRA_SCRIPTS} DESTINATION ${BIN_INSTALL_DIR})
+install(FILES ${EXTRA_SCRIPTS} DESTINATION ${BIN_INSTALL_DIR} COMPONENT runtime)
-install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/demux.pl DESTINATION ${BIN_INSTALL_DIR})
-install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/xplor2gmx.pl DESTINATION ${BIN_INSTALL_DIR})
+install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/demux.pl DESTINATION ${BIN_INSTALL_DIR} COMPONENT runtime)
+install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/xplor2gmx.pl DESTINATION ${BIN_INSTALL_DIR} COMPONENT runtime)
tmppath=""
for i in `echo $LD_LIBRARY_PATH | sed "s/:/ /g"`; do
if test "$i" != "$GMXLDLIB"; then
+ if test "${tmppath}" == ""; then
+ tmppath=$i
+ else
tmppath=${tmppath}:$i
fi
+ fi
done
LD_LIBRARY_PATH=$tmppath
tmppath=${tmppath}:$i
fi
done
+if test "$tmppath" == ""; then
+ tmppath=":"
+fi
MANPATH=$tmppath
##########################################################
tmppath=""
for i in `echo $LD_LIBRARY_PATH | sed "s/:/ /g"`; do
if test "$i" != "$GMXLDLIB"; then
+ if test "${tmppath}" == ""; then
+ tmppath=$i
+ else
tmppath=${tmppath}:$i
fi
+ fi
done
LD_LIBRARY_PATH=$tmppath
tmppath=${tmppath}:$i
fi
done
+if test "$tmppath" == ""; then
+ tmppath=":"
+fi
MANPATH=$tmppath
##########################################################
# remove previous gromacs part from ld_library_path
set tmppath = ""
foreach i ( `echo $LD_LIBRARY_PATH | sed "s/:/ /g"` )
- if ( "$i" != "$GMXLDLIB" ) set tmppath = "${tmppath}:$i"
+ if ( "$i" != "$GMXLDLIB" ) then
+ if ("${tmppath}" == "") then
+ set tmppath = "$i"
+ else
+ set tmppath = "${tmppath}:$i"
+ endif
+ endif
end
setenv LD_LIBRARY_PATH $tmppath
foreach i ( `echo $MANPATH | sed "s/:/ /g"` )
if ( "$i" != "$GMXMAN" ) set tmppath = "${tmppath}:$i"
end
+if ("$tmppath" == "") then
+ set tmppath = ":"
+endif
setenv MANPATH $tmppath
##########################################################
# remove previous gromacs part from ld_library_path
set tmppath = ""
foreach i ( `echo $LD_LIBRARY_PATH | sed "s/:/ /g"` )
- if ( "$i" != "$GMXLDLIB" ) set tmppath = "${tmppath}:$i"
+ if ( "$i" != "$GMXLDLIB" ) then
+ if ("${tmppath}" == "") then
+ set tmppath = "$i"
+ else
+ set tmppath = "${tmppath}:$i"
+ endif
+ endif
end
setenv LD_LIBRARY_PATH $tmppath
foreach i ( `echo $MANPATH | sed "s/:/ /g"` )
if ( "$i" != "$GMXMAN" ) set tmppath = "${tmppath}:$i"
end
+if ("$tmppath" == "") then
+ set tmppath = ":"
+endif
setenv MANPATH $tmppath
##########################################################
tmppath=""
for i in `echo $LD_LIBRARY_PATH | sed "s/:/ /g"`; do
if test "$i" != "$GMXLDLIB"; then
+ if test "${tmppath}" = ""; then
+ tmppath=$i
+ else
tmppath=${tmppath}:$i
fi
+ fi
done
LD_LIBRARY_PATH=$tmppath
tmppath=${tmppath}:$i
fi
done
+if test "$tmppath" = ""; then
+ tmppath=":"
+fi
MANPATH=$tmppath
##########################################################
tmppath=""
for i in `echo $LD_LIBRARY_PATH | sed "s/:/ /g"`; do
if test "$i" != "$GMXLDLIB"; then
+ if test "${tmppath}" = ""; then
+ tmppath=$i
+ else
tmppath=${tmppath}:$i
fi
+ fi
done
LD_LIBRARY_PATH=$tmppath
tmppath=${tmppath}:$i
fi
done
+if test "$tmppath" = ""; then
+ tmppath=":"
+fi
MANPATH=$tmppath
##########################################################
# Data: Nothing to build, just installation
install(DIRECTORY . DESTINATION ${DATA_INSTALL_DIR}
+ COMPONENT data
PATTERN "Makefile*" EXCLUDE
PATTERN "CMake*" EXCLUDE
PATTERN "cmake*" EXCLUDE
PATTERN "*~" EXCLUDE
)
-install(FILES template/CMakeLists.txt.template DESTINATION ${DATA_INSTALL_DIR} RENAME template/CMakeLists.txt)
+install(FILES template/CMakeLists.txt.template
+ DESTINATION ${DATA_INSTALL_DIR}
+ RENAME template/CMakeLists.txt
+ COMPONENT data)
nstpcouple, tau_p, compressibility, ref_p, refcoord_scaling)
<li><A HREF="#sa"><b>simulated annealing</b></A> (annealing, annealing_npoints, annealing_time, annealing_temp)
<li><A HREF="#vel"><b>velocity generation</b></A> (gen_vel, gen_temp, gen_seed)
-<li><A HREF="#bond"><b>bonds</b></A> (constraints, constraint_algorithm, unconstrained_start, shake_tol, lincs_order, lincs_iter, lincs_warnangle, morse)
+<li><A HREF="#bond"><b>bonds</b></A> (constraints, constraint_algorithm, continuation, shake_tol, lincs_order, lincs_iter, lincs_warnangle, morse)
<li><A HREF="#egexcl"><b>Energy group exclusions</b></A> (energygrp_excl)
<li><A HREF="#walls"><b>Walls</b></A> (nwall, wall_type, wall_r_linpot, wall_atomtype,
wall_density, wall_ewald_zfac)
SHAKE can not be used with energy minimization.
</dd>
</dl></dd>
-<dt><b>unconstrained_start:</b></dt>
+<dt><b>continuation:</b></dt>
+<dd>This option was formerly known as <tt>unconstrained_start</tt>.</dd>
<dd><dl compact>
<dt><b>no</b></dt>
<dd>apply constraints to the start configuration and reset shells</dd>
When set to <b>2</b> pressure coupling and Ewald summation can be used
(it is usually best to use semiisotropic pressure coupling with
the x/y compressibility set to 0, as otherwise the surface area will change).
+Walls interact wit the rest of the system through an optional <tt>wall_atomtype</tt>.
Energy groups <tt>wall0</tt> and <tt>wall1</tt> (for <b>nwall=2</b>) are
added automatically to monitor the interaction of energy groups
with each wall.
The <A HREF="#run">center of mass motion removal</A> will be turned
off in the z-direction.</dd>
+<dt><b>wall_atomtype:</b></dt>
+<dd>the atom type name in the force field for each wall.
+By (for example) defining a special wall atom type in the topology with its
+own combination rules, this allows for independent tuning of the interaction
+of each atomtype with the walls.</dd>
<dt><b>wall_type:</b></dt>
<dl>
<dt><b>9-3</b></dt>
When the value is ≤0 (<0 for <b>wall_type=table</b>),
a fatal error is generated when atoms are beyond a wall.
</dd>
-<dt><b>wall_atomtype:</b></dt>
-<dd>the atom type name in the force field for each wall, this allows
-for independent tuning of the interaction of each atomtype with the walls</dd>
<dt><b>wall_density: [nm<sup>-3</sup>/nm<sup>-2</sup>]</b></dt>
<dd>the number density of the atoms for each wall for wall types
<b>9-3</b> and <b>10-4</b>
<dt></dt><b>sa_algorithm</b>
<dd><dl compact="compact">
-<dt><b>Ace-approx</b></dt>
+<dt><b>Ace-approximation</b></dt>
<dd>Use an Ace-type approximation (default)</dd>
<dt><b>None</b></dt>
<dd>No non-polar solvation calculation done. For GBSA only the polar part gets
<A HREF="#tc">tc_grps</A><br>
<A HREF="#tc">tcoupl</A><br>
<A HREF="#run">tinit</A><br>
-<A HREF="#bond">unconstrained_start</A><br>
+<A HREF="#bond">continuation</A><br>
<A HREF="#user">user1_grps</A><br>
<A HREF="#user">user2_grps</A><br>
<A HREF="#user">userint1</A><br>
aminoacids.n.tdb dna.rtp forcefield.itp spc.itp \
aminoacids.r2b ffbonded.itp gb.itp tip3p.itp \
aminoacids.rtp ffnabonded.itp ions.itp tip4p.itp \
-spce.itp tips3p.itp watermodels.dat tip5p.itp
+spce.itp tips3p.itp watermodels.dat tip5p.itp \
+dna.hdb dna.n.tdb dna.c.tdb dna.arn \
+rna.hdb rna.n.tdb rna.c.tdb rna.arn \
+rna.r2b
EXTRA_DIST = ${topol_DATA}
LYSN LSN
ASPH ASPP
GLUH GLUP
+HEM HEME
--- /dev/null
+DNA C7 C5M
+DNA H71 H51
+DNA H72 H52
+DNA H73 H53
+DNA OP1 O1P
+DNA OP2 O2P
+DNA H2' H2'1
+DNA H2'' H2'2
+DNA H5' H5'1
+DNA H5'' H5'2
+DNA HO5' H5T
+DNA HO3' H3T
--- /dev/null
+[ None ]
+
+[ 3' ]
+[ replace ]
+C3' C3' CN7 12.011 0.14
+H3' H3' HN7 1.008 0.09
+O3' O3' ON5 15.9994 -0.66
+[ Add ]
+1 2 H3T O3' C3' C4'
+ HN5 1.008 0.43
--- /dev/null
+DA 8
+2 6 H5' C5' O5' C4'
+1 5 H4' C4' C5' O4' C3'
+1 5 H1' C1' O4' N9 C2'
+1 1 H8 C8 N9 N7
+2 3 H6 N6 C6 C5
+1 1 H2 C2 N1 N3
+1 5 H3' C3' C4' C2' O3'
+2 6 H2' C2' C1' C3'
+DT 8
+2 6 H5' C5' O5' C4'
+1 5 H4' C4' C5' O4' C3'
+1 5 H1' C1' O4' N1 C2'
+1 1 H6 C6 N1 C5
+3 4 H5 C5M C5 C6
+1 1 H3 N3 C4 C2
+1 5 H3' C3' C4' C2' O3'
+2 6 H2' C2' C1' C3'
+DG 8
+2 6 H5' C5' O5' C4'
+1 5 H4' C4' C5' O4' C3'
+1 5 H1' C1' O4' N9 C2'
+1 1 H8 C8 N9 N7
+1 1 H1 N1 C6 C2
+2 3 H2 N2 C2 N1
+1 5 H3' C3' C4' C2' O3'
+2 6 H2' C2' C1' C3'
+DC 8
+2 6 H5' C5' O5' C4'
+1 5 H4' C4' C5' O4' C3'
+1 5 H1' C1' O4' N1 C2'
+1 1 H6 C6 N1 C5
+1 1 H5 C5 C6 C4
+2 3 H4 N4 C4 C5
+1 5 H3' C3' C4' C2' O3'
+2 6 H2' C2' C1' C3'
--- /dev/null
+[ None ]
+
+[ 5' ]
+[ delete ]
+ P
+ O1P
+ O2P
+[ replace ]
+O5' O5' ON5 15.9994 -0.66
+C5' C5' CN8B 12.011 0.05
+[ Add ]
+ 1 2 H5T O5' C5' C4'
+ HN5 1.008 0.43
+
+
+
+++ /dev/null
-; rtp residue to rtp building block table
-;GMX Force-field
-DA DA DA5 DA3 -
-DG DG DG5 DG3 -
-DC DC DC5 DC3 -
-DT DT DT5 DT3 -
-
N6 C6 H61 H62
C6 N1 C5 N6
-[ DA5 ]
-; H61 H62;
-; \ /
-; N6
-; |
-; C6
-; // \
-; N1 C5--N7\\
-; | || C8-H8
-; C2 C4--N9/
-; / \\ / \
-; H2 N3 \
-; \
-; \
-; \
-; H5'1H4' O4' \
-; | \ / \ \
-; H5T-O5'-C5'---C4' C1'
-; | \ / \
-; H5'2 C3'--C2' H1'
-; / \ / \
-; O3' H3' H2'1 H2'2
-; |
-;
-;
-[ atoms ]
-H5T HN5 0.43 0
-O5' ON5 -0.66 1
-C5' CN8B 0.05 2
-H5'1 HN8 0.09 3
-H5'2 HN8 0.09 4
-C4' CN7 0.16 5
-H4' HN7 0.09 6
-O4' ON6 -0.50 7
-C1' CN7B 0.16 8
-H1' HN7 0.09 9
-N9 NN2 -0.05 10
-C5 CN5 0.28 11
-N7 NN4 -0.71 12
-C8 CN4 0.34 13
-H8 HN3 0.12 14
-N1 NN3A -0.74 15
-C2 CN4 0.50 16
-H2 HN3 0.13 17
-N3 NN3A -0.75 18
-C4 CN5 0.43 19
-C6 CN2 0.46 20
-N6 NN1 -0.77 21
-H61 HN1 0.38 22
-H62 HN1 0.38 23
-C2' CN8 -0.18 24
-H2'1 HN8 0.09 25
-H2'2 HN8 0.09 26
-C3' CN7 0.01 27
-H3' HN7 0.09 28
-O3' ON2 -0.57 29
-[ bonds ]
-H5T O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N9
-C1' C2'
-N9 C4
-N9 C8
-C4 N3
-C2 N1
-C6 N6
-N6 H61
-N6 H62
-C6 C5
-C5 N7
-C2' C3'
-C3' O3'
-C1' H1'
-C2' H2'1
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C8 H8
-C2 H2
-N1 C6
-C2 N3
-C4 C5
-N7 C8
-[ impropers ]
-N6 C6 H61 H62
-C6 N1 C5 N6
-
-
-[ DA3 ]
-; H61 H62;
-; \ /
-; N6
-; |
-; C6
-; // \
-; N1 C5--N7\\
-; | || C8-H8
-; C2 C4--N9/
-; / \\ / \
-; H2 N3 \
-; \
-; \
-; \
-; O1P H5'1 H4' O4' \
-; | | \ / \ \
-; -P-O5'-C5'---C4' C1'
-; | | \ / \
-; O2P H5'2 C3'--C2' H1'
-; / \ / \
-; O3' H3' H2'1 H2'2
-; |
-; H3T
-
-[ atoms ]
-P P 1.50 0
-O1P ON3 -0.78 1
-O2P ON3 -0.78 2
-O5' ON2 -0.57 3
-C5' CN8B -0.08 4
-H5'1 HN8 0.09 5
-H5'2 HN8 0.09 6
-C4' CN7 0.16 7
-H4' HN7 0.09 8
-O4' ON6 -0.50 9
-C1' CN7B 0.16 10
-H1' HN7 0.09 11
-N9 NN2 -0.05 12
-C5 CN5 0.28 13
-N7 NN4 -0.71 14
-C8 CN4 0.34 15
-H8 HN3 0.12 16
-N1 NN3A -0.74 17
-C2 CN4 0.50 18
-H2 HN3 0.13 19
-N3 NN3A -0.75 20
-C4 CN5 0.43 21
-C6 CN2 0.46 22
-N6 NN1 -0.77 23
-H61 HN1 0.38 24
-H62 HN1 0.38 25
-C2' CN8 -0.18 26
-H2'1 HN8 0.09 27
-H2'2 HN8 0.09 28
-C3' CN7 0.14 29
-H3' HN7 0.09 30
-O3' ON5 -0.66 31
-H3T HN5 0.43 32
-[ bonds ]
--O3' P
-P O1P
-P O2P
-P O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N9
-C1' C2'
-N9 C4
-N9 C8
-C4 N3
-C2 N1
-C6 N6
-N6 H61
-N6 H62
-C6 C5
-C5 N7
-C2' C3'
-C3' O3'
-O3' H3T
-C1' H1'
-C2' H2'1
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C8 H8
-C2 H2
-N1 C6
-C2 N3
-C4 C5
-N7 C8
-[ impropers ]
-N6 C6 H61 H62
-C6 N1 C5 N6
-
;--------------------------------------------------------------------------
[ DC ]
;
C2 CN1 0.52 17
O2 ON1C -0.49 18
N3 NN3 -0.66 19
-C4 CN2 0.65 20
-N4 NN1 -0.75 21
-H41 HN1 0.37 22
-H42 HN1 0.33 23
-C2' CN8 -0.18 24
-H2'1 HN8 0.09 25
-H2'2 HN8 0.09 26
-C3' CN7 0.01 27
-H3' HN7 0.09 28
-O3' ON2 -0.57 29
-[ bonds ]
--O3' P
-P O1P
-P O2P
-P O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N1
-C1' C2'
-N1 C2
-N1 C6
-C2 N3
-C4 N4
-N4 H41
-N4 H42
-C4 C5
-C2' C3'
-C3' O3'
-C1' H1'
-C2' H2'1
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C5 H5
-C6 H6
-C2 O2
-C5 C6
-N3 C4
-[ impropers ]
-C2 N1 N3 O2
-C4 N3 C5 N4
-N4 C4 H41 H42
-
-[ DC5 ]
-;
-; H42 H41
-; \ /
-; N4
-; |
-; C4
-; / \\
-; H5-C5 N3
-; || |
-; H6-C6 C2
-; \ / \\
-; N1 O2
-; \
-; \
-; \
-; H5'1H4' O4' \
-; | \ / \ \
-; H5T-O5'-C5'---C4' C1'
-; | \ / \
-; H5'2 C3'--C2' H1'
-; / \ / \
-; O3' H3' H2'1 H2'2
-; |
-;
-[ atoms ]
-H5T HN5 0.43 0
-O5' ON5 -0.66 1
-C5' CN8B 0.05 2
-H5'1 HN8 0.09 3
-H5'2 HN8 0.09 4
-C4' CN7 0.16 5
-H4' HN7 0.09 6
-O4' ON6 -0.50 7
-C1' CN7B 0.16 8
-H1' HN7 0.09 9
-N1 NN2 -0.13 10
-C6 CN3 0.05 11
-H6 HN3 0.17 12
-C5 CN3 -0.13 13
-H5 HN3 0.07 14
-C2 CN1 0.52 15
-O2 ON1C -0.49 16
-N3 NN3 -0.66 17
-C4 CN2 0.65 18
-N4 NN1 -0.75 19
-H41 HN1 0.37 20
-H42 HN1 0.33 21
-C2' CN8 -0.18 22
-H2'1 HN8 0.09 23
-H2'2 HN8 0.09 24
-C3' CN7 0.01 25
-H3' HN7 0.09 26
-O3' ON2 -0.57 27
-[ bonds ]
-H5T O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N1
-C1' C2'
-N1 C2
-N1 C6
-C2 N3
-C4 N4
-N4 H41
-N4 H42
-C4 C5
-C2' C3'
-C3' O3'
-C1' H1'
-C2' H2'1
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C5 H5
-C6 H6
-C2 O2
-C5 C6
-N3 C4
-[ impropers ]
-C2 N1 N3 O2
-C4 N3 C5 N4
-N4 C4 H41 H42
-
-[ DC3 ]
-;
-; H42 H41
-; \ /
-; N4
-; |
-; C4
-; / \\
-; H5-C5 N3
-; || |
-; H6-C6 C2
-; \ / \\
-; N1 O2
-; \
-; \
-; \
-; O1P H5'1H4' O4' \
-; | | \ / \ \
-; -P-O5'-C5'---C4' C1'
-; | | \ / \
-; O2P H5'2 C3'--C2' H1'
-; / \ / \
-; O3' H3' H2'1 H2'2
-; |
-; H3T
-[ atoms ]
-P P 1.50 0
-O1P ON3 -0.78 1
-O2P ON3 -0.78 2
-O5' ON2 -0.57 3
-C5' CN8B -0.08 4
-H5'1 HN8 0.09 5
-H5'2 HN8 0.09 6
-C4' CN7 0.16 7
-H4' HN7 0.09 8
-O4' ON6 -0.50 9
-C1' CN7B 0.16 10
-H1' HN7 0.09 11
-N1 NN2 -0.13 12
-C6 CN3 0.05 13
-H6 HN3 0.17 14
-C5 CN3 -0.13 15
-H5 HN3 0.07 16
-C2 CN1 0.52 17
-O2 ON1C -0.49 18
-N3 NN3 -0.66 19
-C4 CN2 0.65 20
-N4 NN1 -0.75 21
-H41 HN1 0.37 22
-H42 HN1 0.33 23
-C2' CN8 -0.18 24
-H2'1 HN8 0.09 25
-H2'2 HN8 0.09 26
-C3' CN7 0.14 27
-H3' HN7 0.09 28
-O3' ON5 -0.66 29
-H3T HN5 0.43 30
-[ bonds ]
--O3' P
-P O1P
-P O2P
-P O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N1
-C1' C2'
-N1 C2
-N1 C6
-C2 N3
-C4 N4
-N4 H41
-N4 H42
-C4 C5
-C2' C3'
-C3' O3'
-O3' H3T
-C1' H1'
-C2' H2'1
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C5 H5
-C6 H6
-C2 O2
-C5 C6
-N3 C4
-[ impropers ]
-C2 N1 N3 O2
-C4 N3 C5 N4
-N4 C4 H41 H42
-
-; --------------------------------------------------------------------
-[ DG ]
-; O6
-; ||
-; C6
-; / \
-; H1-N1 C5--N7\\
-; | || C8-H8
-; C2 C4--N9/
-; / \\ / \
-; H21-N2 N3 \
-; | \
-; H22 \
-; \
-; O1P H5'1 H4' O4' \
-; | | \ / \ \
-; -P-O5'-C5'---C4' C1'
-; | | \ / \
-; O2P H5'2 C3'--C2' H1'
-; / \ / \
-; O3' H3' H2'1 H2'2
-; |
-;
-[ atoms ]
-P P 1.50 0
-O1P ON3 -0.78 1
-O2P ON3 -0.78 2
-O5' ON2 -0.57 3
-C5' CN8B -0.08 4
-H5'1 HN8 0.09 5
-H5'2 HN8 0.09 6
-C4' CN7 0.16 7
-H4' HN7 0.09 8
-O4' ON6 -0.50 9
-C1' CN7B 0.16 10
-H1' HN7 0.09 11
-N9 NN2B -0.02 12
-C4 CN5 0.26 13
-N2 NN1 -0.68 14
-H21 HN1 0.32 15
-H22 HN1 0.35 16
-N3 NN3G -0.74 17
-C2 CN2 0.75 18
-N1 NN2G -0.34 19
-H1 HN2 0.26 20
-C6 CN1 0.54 21
-O6 ON1 -0.51 22
-C5 CN5G 0.00 23
-N7 NN4 -0.60 24
-C8 CN4 0.25 25
-H8 HN3 0.16 26
-C2' CN8 -0.18 27
-H2'1 HN8 0.09 28
-H2'2 HN8 0.09 29
-C3' CN7 0.01 30
-H3' HN7 0.09 31
-O3' ON2 -0.57 32
+C4 CN2 0.65 20
+N4 NN1 -0.75 21
+H41 HN1 0.37 22
+H42 HN1 0.33 23
+C2' CN8 -0.18 24
+H2'1 HN8 0.09 25
+H2'2 HN8 0.09 26
+C3' CN7 0.01 27
+H3' HN7 0.09 28
+O3' ON2 -0.57 29
[ bonds ]
-O3' P
P O1P
C4' O4'
C4' C3'
O4' C1'
-C1' N9
+C1' N1
C1' C2'
-N9 C4
-N9 C8
-C4 N3
-C2 N2
-C2 N1
-N2 H21
-N2 H22
-N1 H1
+N1 C2
N1 C6
-C6 C5
-C5 N7
-C2' C3'
-C3' O3'
-C1' H1'
-C2' H2'1
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C8 H8
C2 N3
+C4 N4
+N4 H41
+N4 H42
C4 C5
-N7 C8
-C6 O6
-[ impropers ]
-C2 N3 N1 N2
-C6 N1 C5 O6
-N2 H21 C2 H22
-
-[ DG5 ]
-; O6
-; ||
-; C6
-; / \
-; H1-N1 C5--N7\\
-; | || C8-H8
-; C2 C4--N9/
-; / \\ / \
-; H21-N2 N3 \
-; | \
-; H22 \
-; \
-; H5'1H4' O4' \
-; | \ / \ \
-; H5T-O5'-C5'---C4' C1'
-; | \ / \
-; H5'2 C3'--C2' H1'
-; / \ / \
-; O3' H3' H2'1 H2'2
-; |
-;
-[ atoms ]
-H5T HN5 0.43 0
-O5' ON5 -0.66 1
-C5' CN8B 0.05 2
-H5'1 HN8 0.09 3
-H5'2 HN8 0.09 4
-C4' CN7 0.16 5
-H4' HN7 0.09 6
-O4' ON6 -0.50 7
-C1' CN7B 0.16 8
-H1' HN7 0.09 9
-N9 NN2B -0.02 10
-C4 CN5 0.26 11
-N2 NN1 -0.68 12
-H21 HN1 0.32 13
-H22 HN1 0.35 14
-N3 NN3G -0.74 15
-C2 CN2 0.75 16
-N1 NN2G -0.34 17
-H1 HN2 0.26 18
-C6 CN1 0.54 19
-O6 ON1 -0.51 20
-C5 CN5G 0.00 21
-N7 NN4 -0.60 22
-C8 CN4 0.25 23
-H8 HN3 0.16 24
-C2' CN8 -0.18 25
-H2'1 HN8 0.09 26
-H2'2 HN8 0.09 27
-C3' CN7 0.01 28
-H3' HN7 0.09 29
-O3' ON2 -0.57 30
-[ bonds ]
-H5T O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N9
-C1' C2'
-N9 C4
-N9 C8
-C4 N3
-C2 N2
-C2 N1
-N2 H21
-N2 H22
-N1 H1
-N1 C6
-C6 C5
-C5 N7
C2' C3'
C3' O3'
C1' H1'
C4' H4'
C5' H5'1
C5' H5'2
-C8 H8
-C2 N3
-C4 C5
-N7 C8
-C6 O6
+C5 H5
+C6 H6
+C2 O2
+C5 C6
+N3 C4
[ impropers ]
-C2 N3 N1 N2
-C6 N1 C5 O6
-N2 H21 C2 H22
-
-[ DG3 ]
+C2 N1 N3 O2
+C4 N3 C5 N4
+N4 C4 H41 H42
+
+; --------------------------------------------------------------------
+[ DG ]
; O6
; ||
; C6
; | | \ / \
; O2P H5'2 C3'--C2' H1'
; / \ / \
-; O3' H3' H2'1 H2'2
-; |
-; H3T
+; O3' H3' H2'1 H2'2
+; |
+;
[ atoms ]
P P 1.50 0
O1P ON3 -0.78 1
C2' CN8 -0.18 27
H2'1 HN8 0.09 28
H2'2 HN8 0.09 29
-C3' CN7 0.14 30
+C3' CN7 0.01 30
H3' HN7 0.09 31
-O3' ON5 -0.66 32
-H3T HN5 0.43 33
+O3' ON2 -0.57 32
[ bonds ]
-O3' P
P O1P
C5 N7
C2' C3'
C3' O3'
-O3' H3T
C1' H1'
C2' H2'1
C2' H2'2
C4 N3 C5 O4
C5 C4 C6 C5M
-[ DT5 ]
-; H51 O4
-; | ||
-; H52-C5M C4 H3
-; | \ / \ /
-; H53 C5 N3
-; || |
-; H6-C6 C2
-; \ / \\
-; N1 O2
-; \
-; \
-; \
-; H5'1H4' O4' \
-; | \ / \ \
-; H5T-O5'-C5'---C4' C1'
-; | \ / \
-; H5'2 C3'--C2' H1'
-; / \ / \
-; O3' H3' H2'1 H2'2
-; |
-;
-;
-[ atoms ]
-H5T HN5 0.43 0
-O5' ON5 -0.66 1
-C5' CN8B 0.05 2
-H5'1 HN8 0.09 3
-H5'2 HN8 0.09 4
-C4' CN7 0.16 5
-H4' HN7 0.09 6
-O4' ON6 -0.50 7
-C1' CN7B 0.16 8
-H1' HN7 0.09 9
-N1 NN2B -0.34 10
-C6 CN3 0.17 11
-H6 HN3 0.17 12
-C2 CN1T 0.51 13
-O2 ON1 -0.41 14
-N3 NN2U -0.46 15
-H3 HN2 0.36 16
-C4 CN1 0.50 17
-O4 ON1 -0.45 18
-C5 CN3T -0.15 19
-C5M CN9 -0.11 20
-H51 HN9 0.07 21
-H52 HN9 0.07 22
-H53 HN9 0.07 23
-C2' CN8 -0.18 24
-H2'1 HN8 0.09 25
-H2'2 HN8 0.09 26
-C3' CN7 0.01 27
-H3' HN7 0.09 28
-O3' ON2 -0.57 29
-[ bonds ]
-H5T O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N1
-C1' C2'
-N1 C2
-N1 C6
-C2 N3
-N3 H3
-N3 C4
-C4 C5
-C5 C5M
-C2' C3'
-C3' O3'
-C1' H1'
-C2' H2'1
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C6 H6
-C5M H51
-C5M H52
-C5M H53
-C2 O2
-C4 O4
-C5 C6
-[ impropers ]
-C2 N1 N3 O2
-C4 N3 C5 O4
-C5 C4 C6 C5M
-
-[ DT3 ]
-; H51 O4
-; | ||
-; H52-C5M C4 H3
-; | \ / \ /
-; H53 C5 N3
-; || |
-; H6-C6 C2
-; \ / \\
-; N1 O2
-; \
-; \
-; \
-; O1P H5'1H4' O4' \
-; | | \ / \ \
-; -P-O5'-C5'---C4' C1'
-; | | \ / \
-; O2P H5'2 C3'--C2' H1'
-; / \ / \
-; O3' H3' H2'1 H2'2
-; |
-; H3T
-;
-[ atoms ]
-P P 1.50 0
-O1P ON3 -0.78 1
-O2P ON3 -0.78 2
-O5' ON2 -0.57 3
-C5' CN8B -0.08 4
-H5'1 HN8 0.09 5
-H5'2 HN8 0.09 6
-C4' CN7 0.16 7
-H4' HN7 0.09 8
-O4' ON6 -0.50 9
-C1' CN7B 0.16 10
-H1' HN7 0.09 11
-N1 NN2B -0.34 12
-C6 CN3 0.17 13
-H6 HN3 0.17 14
-C2 CN1T 0.51 15
-O2 ON1 -0.41 16
-N3 NN2U -0.46 17
-H3 HN2 0.36 18
-C4 CN1 0.50 19
-O4 ON1 -0.45 20
-C5 CN3T -0.15 21
-C5M CN9 -0.11 22
-H51 HN9 0.07 23
-H52 HN9 0.07 24
-H53 HN9 0.07 25
-C2' CN8 -0.18 26
-H2'1 HN8 0.09 27
-H2'2 HN8 0.09 28
-C3' CN7 0.14 29
-H3' HN7 0.09 30
-O3' ON5 -0.66 31
-H3T HN5 0.43 32
-[ bonds ]
--O3' P
-P O1P
-P O2P
-P O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N1
-C1' C2'
-N1 C2
-N1 C6
-C2 N3
-N3 H3
-N3 C4
-C4 C5
-C5 C5M
-C2' C3'
-C3' O3'
-O3' H3T
-C1' H1'
-C2' H2'1
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C6 H6
-C5M H51
-C5M H52
-C5M H53
-C2 O2
-C4 O4
-C5 C6
-[ impropers ]
-C2 N1 N3 O2
-C4 N3 C5 O4
-C5 C4 C6 C5M
-
MNH3 0 0.000000 0.00 A 0.0 0.0
MNH2 0 0.000000 0.00 A 0.0 0.0
MCH3 0 0.000000 0.00 A 0.0 0.0
+MCH3S 0 0.000000 0.00 A 0.0 0.0
; Ions and noble gases (useful for tutorials)
Cu2+ 29 63.54600 2.00 A 2.08470e-01 4.76976e+00
Ar 18 39.94800 0.00 A 3.41000e-01 2.74580e-02
HP 0.1 1 1 0.125 0.85 ; H
NY 0.155 1 1.028 0.17063 0.79 ; N
CPT 0.172 0.012 1.554 0.1875 0.72 ; C
- MNH3 0 0 0 0 0 ; vsite (rigid tetrahedrical NH3 group)
- MNH2 0 0 0 0 0 ; vsite
- MCH3 0 0 0 0 0 ; vsite (rigid CH3 group)
\ No newline at end of file
+ MNH3 0 0 0 0 0 ; dummy mass
+ MNH2 0 0 0 0 0 ; dummy mass
+ MCH3 0 0 0 0 0 ; dummy mass
+ MCH3S 0 0 0 0 0 ; dummy mass
--- /dev/null
+RNA OP1 O1P
+RNA OP2 O2P
+RNA H2' H2'1
+RNA H2'' H2'2
+RNA H5' H5'1
+RNA H5'' H5'2
+RNA HO5' H5T
+RNA HO3' H3T
--- /dev/null
+[ None ]
+
+[ 3' ]
+[ replace ]
+C3' C3' CN7 12.011 0.14
+H3' H3' HN7 1.008 0.09
+O3' O3' ON5 15.9994 -0.66
+[ Add ]
+1 2 H3T O3' C3' C4'
+ HN5 1.008 0.43
--- /dev/null
+RA 9
+2 6 H5' C5' O5' C4'
+1 5 H4' C4' C5' O4' C3'
+1 5 H1' C1' O4' N9 C2'
+1 1 H8 C8 N9 N7
+2 3 H6 N6 C6 C5
+1 1 H2 C2 N1 N3
+1 5 H3' C3' C4' C2' O3'
+1 5 H2'2 C2' C1' C3' O2'
+1 2 H2'1 O2' C2' C1'
+RU 9
+2 6 H5' C5' O5' C4'
+1 5 H4' C4' C5' O4' C3'
+1 5 H1' C1' O4' N1 C2'
+1 1 H6 C6 N1 C5
+1 1 H5 C5 C6 C4
+1 1 H3 N3 C4 C2
+1 5 H3' C3' C4' C2' O3'
+1 5 H2'2 C2' C1' C3' O2'
+1 2 H2'1 O2' C2' C1'
+RG 9
+2 6 H5' C5' O5' C4'
+1 5 H4' C4' C5' O4' C3'
+1 5 H1' C1' O4' N9 C2'
+1 1 H8 C8 N9 N7
+1 1 H1 N1 C6 C2
+2 3 H2 N2 C2 N1
+1 5 H3' C3' C4' C2' O3'
+1 5 H2'2 C2' C1' C3' O2'
+1 2 H2'1 O2' C2' C1'
+RC 9
+2 6 H5' C5' O5' C4'
+1 5 H4' C4' C5' O4' C3'
+1 5 H1' C1' O4' N1 C2'
+1 1 H6 C6 N1 C5
+1 1 H5 C5 C6 C4
+2 3 H4 N4 C4 C5
+1 5 H3' C3' C4' C2' O3'
+1 5 H2'2 C2' C1' C3' O2'
+1 2 H2'1 O2' C2' C1'
--- /dev/null
+[ None ]
+
+[ 5' ]
+[ delete ]
+ P
+ O1P
+ O2P
+[ replace ]
+O5' O5' ON5 15.9994 -0.66
+C5' C5' CN8B 12.011 0.05
+[ Add ]
+ 1 2 H5T O5' C5' C4'
+ HN5 1.008 0.43
+
+
+
; rtp residue to rtp building block table
;GMX Force-field
-A RA RA5 RA3 RA
-G RG RG5 RG3 RG
-C RC RC5 RC3 RC
-U RU RU5 RU3 RU
+A RA
+G RG
+C RC
+U RU
N6 C6 H61 H62
C6 N1 C5 N6
-[ RA5 ]
- ; H61 H62;
- ; \ /
- ; N6
- ; |
- ; C6
- ; // \
- ; N1 C5--N7\\
- ; | || C8-H8
- ; C2 C4--N9/
- ; / \\ / \
- ; H2 N3 \
- ; \
- ; \
- ; \
- ; H5'1H4' O4' \
- ; | \ / \ \
- ; H5T-O5'-C5'---C4' C1'
- ; | \ / \
- ; H5'2 C3'--C2' H1'
- ; / \ / \
- ; O3' H3' O2' H2'2
- ; | |
- ; H2'1
- ;
-[ atoms ]
-H5T HN5 0.43 0
-O5' ON5 -0.66 1
-C5' CN8B 0.05 2
-H5'1 HN8 0.09 3
-H5'2 HN8 0.09 4
-C4' CN7 0.16 5
-H4' HN7 0.09 6
-O4' ON6B -0.50 7
-C1' CN7B 0.16 8
-H1' HN7 0.09 9
-N9 NN2 -0.05 10
-C5 CN5 0.28 11
-N7 NN4 -0.71 12
-C8 CN4 0.34 13
-H8 HN3 0.12 14
-N1 NN3A -0.74 15
-C2 CN4 0.50 16
-H2 HN3 0.13 17
-N3 NN3A -0.75 18
-C4 CN5 0.43 19
-C6 CN2 0.46 20
-N6 NN1 -0.77 21
-H61 HN1 0.38 22
-H62 HN1 0.38 23
-C2' CN7B 0.14 24
-H2'2 HN7 0.09 25
-O2' ON5 -0.66 26
-H2'1 HN5 0.43 27
-C3' CN7 0.01 28
-H3' HN7 0.09 29
-O3' ON2 -0.57 30
-[ bonds ]
-H5T O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N9
-C1' C2'
-N9 C4
-N9 C8
-C4 N3
-C2 N1
-C6 N6
-N6 H61
-N6 H62
-C6 C5
-C5 N7
-C2' C3'
-C2' O2'
-O2' H2'1
-C3' O3'
-C1' H1'
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C8 H8
-C2 H2
-N1 C6
-C2 N3
-C4 C5
-N7 C8
-[ impropers ]
-N6 C6 H61 H62
-C6 N1 C5 N6
-
-
-[ RA3 ]
- ; H61 H62;
- ; \ /
- ; N6
- ; |
- ; C6
- ; // \
- ; N1 C5--N7\\
- ; | || C8-H8
- ; C2 C4--N9/
- ; / \\ / \
- ; H2 N3 \
- ; \
- ; \
- ; \
- ; O1P H5'1 H4' O4' \
- ; | | \ / \ \
- ; -P-O5'-C5'---C4' C1'
- ; | | \ / \
- ; O2P H5'2 C3'--C2' H1'
- ; / \ / \
- ; O3' H3' O2' H2'2
- ; | |
- ; H3T H2'1
- ;
-[ atoms ]
-P P 1.50 0
-O1P ON3 -0.78 1
-O2P ON3 -0.78 2
-O5' ON2 -0.57 3
-C5' CN8B -0.08 4
-H5'1 HN8 0.09 5
-H5'2 HN8 0.09 6
-C4' CN7 0.16 7
-H4' HN7 0.09 8
-O4' ON6B -0.50 9
-C1' CN7B 0.16 10
-H1' HN7 0.09 11
-N9 NN2 -0.05 12
-C5 CN5 0.28 13
-N7 NN4 -0.71 14
-C8 CN4 0.34 15
-H8 HN3 0.12 16
-N1 NN3A -0.74 17
-C2 CN4 0.50 18
-H2 HN3 0.13 19
-N3 NN3A -0.75 20
-C4 CN5 0.43 21
-C6 CN2 0.46 22
-N6 NN1 -0.77 23
-H61 HN1 0.38 24
-H62 HN1 0.38 25
-C2' CN7B 0.14 26
-H2'2 HN7 0.09 27
-O2' ON5 -0.66 28
-H2'1 HN5 0.43 29
-C3' CN7 0.14 30
-H3' HN7 0.09 31
-O3' ON5 -0.66 32
-H3T HN5 0.43 33
-[ bonds ]
--O3' P
-P O1P
-P O2P
-P O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N9
-C1' C2'
-N9 C4
-N9 C8
-C4 N3
-C2 N1
-C6 N6
-N6 H61
-N6 H62
-C6 C5
-C5 N7
-C2' C3'
-C2' O2'
-O2' H2'1
-C3' O3'
-O3' H3T
-C1' H1'
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C8 H8
-C2 H2
-N1 C6
-C2 N3
-C4 C5
-N7 C8
-[ impropers ]
-N6 C6 H61 H62
-C6 N1 C5 N6
-
;--------------------------------------------------------------------------
[ RC ]
;
; | |
; H2'1
[ atoms ]
-P P 1.50 0
-O1P ON3 -0.78 1
-O2P ON3 -0.78 2
-O5' ON2 -0.57 3
-C5' CN8B -0.08 4
-H5'1 HN8 0.09 5
-H5'2 HN8 0.09 6
-C4' CN7 0.16 7
-H4' HN7 0.09 8
-O4' ON6B -0.50 9
-C1' CN7B 0.16 10
-H1' HN7 0.09 11
-N1 NN2 -0.13 12
-C6 CN3 0.05 13
-H6 HN3 0.17 14
-C5 CN3 -0.13 15
-H5 HN3 0.07 16
-C2 CN1 0.52 17
-O2 ON1C -0.49 18
-N3 NN3 -0.66 19
-C4 CN2 0.65 20
-N4 NN1 -0.75 21
-H41 HN1 0.37 22
-H42 HN1 0.33 23
-C2' CN7B 0.14 24
-H2'2 HN7 0.09 25
-O2' ON5 -0.66 26
-H2'1 HN5 0.43 27
-C3' CN7 0.01 28
-H3' HN7 0.09 29
-O3' ON2 -0.57 30
-[ bonds ]
--O3' P
-P O1P
-P O2P
-P O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N1
-C1' C2'
-N1 C2
-N1 C6
-C2 N3
-C4 N4
-N4 H41
-N4 H42
-C4 C5
-C2' C3'
-C3' O3'
-C2' O2'
-O2' H2'1
-C1' H1'
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C5 H5
-C6 H6
-C2 O2
-C5 C6
-N3 C4
-[ impropers ]
-C2 N1 N3 O2
-C4 N3 C5 N4
-N4 C4 H41 H42
-
-[ RC5 ]
-;
-; H42 H41
-; \ /
-; N4
-; |
-; C4
-; / \\
-; H5-C5 N3
-; || |
-; H6-C6 C2
-; \ / \\
-; N1 O2
-; \
-; \
-; \
-; H5'1H4' O4' \
-; | \ / \ \
-; H5T-O5'-C5'---C4' C1'
-; | \ / \
-; H5'2 C3'--C2' H1'
-; / \ / \
-; O3' H3' O2' H2'2
-; | |
-; H2'1
-[ atoms ]
-H5T HN5 0.43 0
-O5' ON5 -0.66 1
-C5' CN8B 0.05 2
-H5'1 HN8 0.09 3
-H5'2 HN8 0.09 4
-C4' CN7 0.16 5
-H4' HN7 0.09 6
-O4' ON6B -0.50 7
-C1' CN7B 0.16 8
-H1' HN7 0.09 9
-N1 NN2 -0.13 10
-C6 CN3 0.05 11
-H6 HN3 0.17 12
-C5 CN3 -0.13 13
-H5 HN3 0.07 14
-C2 CN1 0.52 15
-O2 ON1C -0.49 16
-N3 NN3 -0.66 17
-C4 CN2 0.65 18
-N4 NN1 -0.75 19
-H41 HN1 0.37 20
-H42 HN1 0.33 21
-C2' CN7B 0.14 22
-H2'2 HN7 0.09 23
-O2' ON5 -0.66 24
-H2'1 HN5 0.43 25
-C3' CN7 0.01 26
-H3' HN7 0.09 27
-O3' ON2 -0.57 28
-[ bonds ]
-H5T O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N1
-C1' C2'
-N1 C2
-N1 C6
-C2 N3
-C4 N4
-N4 H41
-N4 H42
-C4 C5
-C2' C3'
-C3' O3'
-C2' O2'
-O2' H2'1
-C1' H1'
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C5 H5
-C6 H6
-C2 O2
-C5 C6
-N3 C4
-[ impropers ]
-C2 N1 N3 O2
-C4 N3 C5 N4
-N4 C4 H41 H42
-
-[ RC3 ]
-;
-; H42 H41
-; \ /
-; N4
-; |
-; C4
-; / \\
-; H5-C5 N3
-; || |
-; H6-C6 C2
-; \ / \\
-; N1 O2
-; \
-; \
-; \
-; O1P H5'1H4' O4' \
-; | | \ / \ \
-; -P-O5'-C5'---C4' C1'
-; | | \ / \
-; O2P H5'2 C3'--C2' H1'
-; / \ / \
-; O3' H3' O2' H2'2
-; | |
-; H3T H2'1
-[ atoms ]
-P P 1.50 0
-O1P ON3 -0.78 1
-O2P ON3 -0.78 2
-O5' ON2 -0.57 3
-C5' CN8B -0.08 4
-H5'1 HN8 0.09 5
-H5'2 HN8 0.09 6
-C4' CN7 0.16 7
-H4' HN7 0.09 8
-O4' ON6B -0.50 9
-C1' CN7B 0.16 10
-H1' HN7 0.09 11
-N1 NN2 -0.13 12
-C6 CN3 0.05 13
-H6 HN3 0.17 14
-C5 CN3 -0.13 15
-H5 HN3 0.07 16
-C2 CN1 0.52 17
-O2 ON1C -0.49 18
-N3 NN3 -0.66 19
-C4 CN2 0.65 20
-N4 NN1 -0.75 21
-H41 HN1 0.37 22
-H42 HN1 0.33 23
-C2' CN7B 0.14 24
-H2'2 HN7 0.09 25
-O2' ON5 -0.66 26
-H2'1 HN5 0.43 27
-C3' CN7 0.14 28
-H3' HN7 0.09 29
-O3' ON5 -0.66 30
-H3T HN5 0.43 31
-[ bonds ]
--O3' P
-P O1P
-P O2P
-P O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N1
-C1' C2'
-N1 C2
-N1 C6
-C2 N3
-C4 N4
-N4 H41
-N4 H42
-C4 C5
-C2' C3'
-C3' O3'
-O3' H3T
-C2' O2'
-O2' H2'1
-C1' H1'
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C5 H5
-C6 H6
-C2 O2
-C5 C6
-N3 C4
-[ impropers ]
-C2 N1 N3 O2
-C4 N3 C5 N4
-N4 C4 H41 H42
-
-; --------------------------------------------------------------------
-[ RG ]
-; O6
-; ||
-; C6
-; / \
-; H1-N1 C5--N7\\
-; | || C8-H8
-; C2 C4--N9/
-; / \\ / \
-; H21-N2 N3 \
-; | \
-; H22 \
-; \
-; O1P H5'1 H4' O4' \
-; | | \ / \ \
-; -P-O5'-C5'---C4' C1'
-; | | \ / \
-; O2P H5'2 C3'--C2' H1'
-; / \ / \
-; O3' H3' O2' H2'2
-; | |
-; H2'1
-[ atoms ]
-P P 1.50 0
-O1P ON3 -0.78 1
-O2P ON3 -0.78 2
-O5' ON2 -0.57 3
-C5' CN8B -0.08 4
-H5'1 HN8 0.09 5
-H5'2 HN8 0.09 6
-C4' CN7 0.16 7
-H4' HN7 0.09 8
-O4' ON6B -0.50 9
-C1' CN7B 0.16 10
-H1' HN7 0.09 11
-N9 NN2B -0.02 12
-C4 CN5 0.26 13
-N2 NN1 -0.68 14
-H21 HN1 0.32 15
-H22 HN1 0.35 16
-N3 NN3G -0.74 17
-C2 CN2 0.75 18
-N1 NN2G -0.34 19
-H1 HN2 0.26 20
-C6 CN1 0.54 21
-O6 ON1 -0.51 22
-C5 CN5G 0.00 23
-N7 NN4 -0.60 24
-C8 CN4 0.25 25
-H8 HN3 0.16 26
-C2' CN7B 0.14 27
-H2'2 HN7 0.09 28
-O2' ON5 -0.66 29
-H2'1 HN5 0.43 30
-C3' CN7 0.01 31
-H3' HN7 0.09 32
-O3' ON2 -0.57 33
+P P 1.50 0
+O1P ON3 -0.78 1
+O2P ON3 -0.78 2
+O5' ON2 -0.57 3
+C5' CN8B -0.08 4
+H5'1 HN8 0.09 5
+H5'2 HN8 0.09 6
+C4' CN7 0.16 7
+H4' HN7 0.09 8
+O4' ON6B -0.50 9
+C1' CN7B 0.16 10
+H1' HN7 0.09 11
+N1 NN2 -0.13 12
+C6 CN3 0.05 13
+H6 HN3 0.17 14
+C5 CN3 -0.13 15
+H5 HN3 0.07 16
+C2 CN1 0.52 17
+O2 ON1C -0.49 18
+N3 NN3 -0.66 19
+C4 CN2 0.65 20
+N4 NN1 -0.75 21
+H41 HN1 0.37 22
+H42 HN1 0.33 23
+C2' CN7B 0.14 24
+H2'2 HN7 0.09 25
+O2' ON5 -0.66 26
+H2'1 HN5 0.43 27
+C3' CN7 0.01 28
+H3' HN7 0.09 29
+O3' ON2 -0.57 30
[ bonds ]
-O3' P
P O1P
C4' O4'
C4' C3'
O4' C1'
-C1' N9
+C1' N1
C1' C2'
-N9 C4
-N9 C8
-C4 N3
-C2 N2
-C2 N1
-N2 H21
-N2 H22
-N1 H1
+N1 C2
N1 C6
-C6 C5
-C5 N7
-C2' C3'
-C3' O3'
-C2' O2'
-O2' H2'1
-C1' H1'
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C8 H8
C2 N3
+C4 N4
+N4 H41
+N4 H42
C4 C5
-N7 C8
-C6 O6
-[ impropers ]
-C2 N3 N1 N2
-C6 N1 C5 O6
-N2 H21 C2 H22
-
-[ RG5 ]
-; O6
-; ||
-; C6
-; / \
-; H1-N1 C5--N7\\
-; | || C8-H8
-; C2 C4--N9/
-; / \\ / \
-; H21-N2 N3 \
-; | \
-; H22 \
-; \
-; H5'1H4' O4' \
-; | \ / \ \
-; H5T-O5'-C5'---C4' C1'
-; | \ / \
-; H5'2 C3'--C2' H1'
-; / \ / \
-; O3' H3' O2' H2'2
-; | |
-; H2'1
-[ atoms ]
-H5T HN5 0.43 0
-O5' ON5 -0.66 1
-C5' CN8B 0.05 2
-H5'1 HN8 0.09 3
-H5'2 HN8 0.09 4
-C4' CN7 0.16 5
-H4' HN7 0.09 6
-O4' ON6B -0.50 7
-C1' CN7B 0.16 8
-H1' HN7 0.09 9
-N9 NN2B -0.02 10
-C4 CN5 0.26 11
-N2 NN1 -0.68 12
-H21 HN1 0.32 13
-H22 HN1 0.35 14
-N3 NN3G -0.74 15
-C2 CN2 0.75 16
-N1 NN2G -0.34 17
-H1 HN2 0.26 18
-C6 CN1 0.54 19
-O6 ON1 -0.51 20
-C5 CN5G 0.00 21
-N7 NN4 -0.60 22
-C8 CN4 0.25 23
-H8 HN3 0.16 24
-C2' CN7B 0.14 25
-H2'2 HN7 0.09 26
-O2' ON5 -0.66 27
-H2'1 HN5 0.43 28
-C3' CN7 0.01 29
-H3' HN7 0.09 30
-O3' ON2 -0.57 31
-[ bonds ]
-H5T O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N9
-C1' C2'
-N9 C4
-N9 C8
-C4 N3
-C2 N2
-C2 N1
-N2 H21
-N2 H22
-N1 H1
-N1 C6
-C6 C5
-C5 N7
C2' C3'
C3' O3'
C2' O2'
C4' H4'
C5' H5'1
C5' H5'2
-C8 H8
-C2 N3
-C4 C5
-N7 C8
-C6 O6
+C5 H5
+C6 H6
+C2 O2
+C5 C6
+N3 C4
[ impropers ]
-C2 N3 N1 N2
-C6 N1 C5 O6
-N2 H21 C2 H22
-
-[ RG3 ]
+C2 N1 N3 O2
+C4 N3 C5 N4
+N4 C4 H41 H42
+
+; --------------------------------------------------------------------
+[ RG ]
; O6
; ||
; C6
; / \ / \
; O3' H3' O2' H2'2
; | |
-; H3T H2'1
+; H2'1
[ atoms ]
P P 1.50 0
O1P ON3 -0.78 1
H2'2 HN7 0.09 28
O2' ON5 -0.66 29
H2'1 HN5 0.43 30
-C3' CN7 0.14 31
+C3' CN7 0.01 31
H3' HN7 0.09 32
-O3' ON5 -0.66 33
-H3T HN5 0.43 34
+O3' ON2 -0.57 33
[ bonds ]
-O3' P
P O1P
C5 N7
C2' C3'
C3' O3'
-O3' H3T
C2' O2'
O2' H2'1
C1' H1'
[ impropers ]
C2 N1 N3 O2
C4 N3 C5 O4
-
-[ RU5 ]
- ; O4
- ; ||
- ; C4 H3
- ; / \ /
- ; H5-C5 N3
- ; || |
- ; H6-C6 C2
- ; \ / \\
- ; N1 O2
- ; \
- ; \
- ; \
- ; H5'1 H4' O4' \
- ; | \ / \ \
- ; H5T-O5'-C5'---C4' C1'
- ; | \ / \
- ; H5'2 C3'--C2' H1'
- ; / \ / \
- ; O3' H3' O2' H2'2
- ; | |
- ; H2'1
- ;
-[ atoms ]
-H5T HN5 0.43 0
-O5' ON5 -0.66 1
-C5' CN8B 0.05 2
-H5'1 HN8 0.09 3
-H5'2 HN8 0.09 4
-C4' CN7 0.16 5
-H4' HN7 0.09 6
-O4' ON6B -0.50 7
-C1' CN7B 0.16 8
-H1' HN7 0.09 9
-N1 NN2B -0.34 10
-C6 CN3 0.20 11
-H6 HN3 0.14 12
-C2 CN1T 0.55 13
-O2 ON1 -0.45 14
-N3 NN2U -0.46 15
-H3 HN2 0.36 16
-C4 CN1 0.53 17
-O4 ON1 -0.48 18
-C5 CN3 -0.15 19
-H5 HN3 0.10 20
-C2' CN7B 0.14 21
-H2'2 HN7 0.09 22
-O2' ON5 -0.66 23
-H2'1 HN5 0.43 24
-C3' CN7 0.01 25
-H3' HN7 0.09 26
-O3' ON2 -0.57 27
-[ bonds ]
-H5T O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N1
-C1' C2'
-N1 C2
-N1 C6
-C2 N3
-N3 H3
-N3 C4
-C4 C5
-C2' C3'
-C3' O3'
-C2' O2'
-O2' H2'1
-C1' H1'
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C5 H5
-C6 H6
-C2 O2
-C4 O4
-C5 C6
-[ impropers ]
-C2 N1 N3 O2
-C4 N3 C5 O4
-
-[ RU3 ]
- ; O4
- ; ||
- ; C4 H3
- ; / \ /
- ; H5-C5 N3
- ; || |
- ; H6-C6 C2
- ; \ / \\
- ; N1 O2
- ; \
- ; \
- ; \
- ; O1P H5'1H4' O4' \
- ; | | \ / \ \
- ; -P-O5'-C5'---C4' C1'
- ; | | \ / \
- ; O2P H5'2 C3'--C2' H1'
- ; / \ / \
- ; O3' H3' O2' H2'2
- ; | |
- ; H3T H2'1
- ;
-[ atoms ]
-P P 1.50 0
-O1P ON3 -0.78 1
-O2P ON3 -0.78 2
-O5' ON2 -0.57 3
-C5' CN8B -0.08 4
-H5'1 HN8 0.09 5
-H5'2 HN8 0.09 6
-C4' CN7 0.16 7
-H4' HN7 0.09 8
-O4' ON6B -0.50 9
-C1' CN7B 0.16 10
-H1' HN7 0.09 11
-N1 NN2B -0.34 12
-C6 CN3 0.20 13
-H6 HN3 0.14 14
-C2 CN1T 0.55 15
-O2 ON1 -0.45 16
-N3 NN2U -0.46 17
-H3 HN2 0.36 18
-C4 CN1 0.53 19
-O4 ON1 -0.48 20
-C5 CN3 -0.15 21
-H5 HN3 0.10 22
-C2' CN7B 0.14 23
-H2'2 HN7 0.09 24
-O2' ON5 -0.66 25
-H2'1 HN5 0.43 26
-C3' CN7 0.14 27
-H3' HN7 0.09 28
-O3' ON5 -0.66 29
-H3T HN5 0.43 30
-[ bonds ]
--O3' P
-P O1P
-P O2P
-P O5'
-O5' C5'
-C5' C4'
-C4' O4'
-C4' C3'
-O4' C1'
-C1' N1
-C1' C2'
-N1 C2
-N1 C6
-C2 N3
-N3 H3
-N3 C4
-C4 C5
-C2' C3'
-C3' O3'
-O3' H3T
-C2' O2'
-O2' H2'1
-C1' H1'
-C2' H2'2
-C3' H3'
-C4' H4'
-C5' H5'1
-C5' H5'2
-C5 H5
-C6 H6
-C2 O2
-C4 O4
-C5 C6
-[ impropers ]
-C2 N1 N3 O2
-C4 N3 C5 O4
HISE HISB
LYS LYSH
LYSN LYS
+HEM HEME
[ atomtypes ]
; type mass charge ptype c6 c12
- OMET 15.999 -0.69 A 2.6169e-3 2.5231e-6
+ OMet 15.999 -0.69 A 2.6169e-3 2.5231e-6
OW 15.999 -0.82 A 2.6170e-3 2.6330e-6
- CMET 15.035 0.29 A 8.8758e-3 17.8426e-6
+ CMet 15.035 0.29 A 8.8758e-3 17.8426e-6
H 1.008 0.4 A 0.0 0.0
HW 1.008 0.41 A 0.0 0.0
#endif
[ atoms ]
; nr type resnr residu atom cgnr charge mass
#ifdef _FF_GROMOS96
-1 CMET 1 MeOH Me1 1 0.176 15.035
-2 OMET 1 MeOH O2 1 -0.574 15.999
+1 CMet 1 MeOH Me1 1 0.176 15.035
+2 OMet 1 MeOH O2 1 -0.574 15.999
3 H 1 MeOH H3 1 0.398 1.008
#else
-1 CMET 1 MeOH Me1 1 0.29 15.035
-2 OMET 1 MeOH O2 1 -0.69 15.999
+1 CMet 1 MeOH Me1 1 0.29 15.035
+2 OMet 1 MeOH O2 1 -0.69 15.999
3 H 1 MeOH H3 1 0.40 1.008
#endif
HISE HISB
LYS LYSH
LYSN LYS
+HEM HEME
HISE HISB
LYS LYSH
LYSN LYS
+HEM HEME
HISE HISB
LYS LYSH
LYSN LYS
+HEM HEME
HISE HISB
LYS LYSH
LYSN LYS
+HEM HEME
-363
+364
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+��،ߊ����ߜ���ߋ���ߐ���߆��ߞ��߶ߔ����״���߽����
[ atoms ]
; id at type res nr residu name at name cg nr charge mass
-1 CU2+ 1 CU2+ CU 1 2 63.54600
+1 Cu2+ 1 CU2+ CU 1 2 63.54600
[ moleculetype ]
; molname nrexcl
[ atoms ]
; id at type res nr residu name at name cg nr charge mass
-1 ZN2+ 1 ZN2+ ZN 1 2 65.37000
+1 Zn2+ 1 ZN2+ ZN 1 2 65.37000
[ moleculetype ]
; molname nrexcl
/* Use the GROMACS software 1/sqrt(x) */
#cmakedefine GMX_SOFTWARE_INVSQRT
+/* Use the PowerPC hardware 1/sqrt(x) */
+#cmakedefine GMX_POWERPC_INVSQRT
+
/* Compile with dlopen */
#cmakedefine GMX_DLOPEN
endif()
endif(GMX_X86_64_ASM)
+if(GMX_FORTRAN)
+ if (GMX_DOUBLE)
+ file(GLOB FORTRAN_SOURCES nonbonded/nb_kernel_f77_double/*.[cf])
+ else(GMX_DOUBLE)
+ file(GLOB FORTRAN_SOURCES nonbonded/nb_kernel_f77_single/*.[cf])
+ endif(GMX_DOUBLE)
+endif(GMX_FORTRAN)
+
+if(GMX_POWER6)
+ file(GLOB FORTRAN_SOURCES nonbonded/nb_kernel_power6/*.[cF])
+endif(GMX_POWER6)
+
+if(GMX_BLUEGENE)
+ file(GLOB GMX_BLUEGENE_C_SRC nonbonded/nb_kernel_bluegene/*.c)
+endif(GMX_BLUEGENE)
+
if(NOT GMX_EXTERNAL_BLAS)
file(GLOB BLAS_SOURCES gmx_blas/*.c)
endif(NOT GMX_EXTERNAL_BLAS)
endif(GMX_ASM_USEASM-NASM)
endif(NOT GMX_OPENMM)
-add_library(gmx ${GMXLIB_SOURCES} ${BLAS_SOURCES} ${LAPACK_SOURCES} ${GMX_SSEKERNEL_C_SRC} ${GMX_SSEKERNEL_ASM_SRC} ${THREAD_MPI_SRC})
+add_library(gmx ${GMXLIB_SOURCES} ${BLAS_SOURCES} ${LAPACK_SOURCES} ${GMX_SSEKERNEL_C_SRC} ${GMX_SSEKERNEL_ASM_SRC} ${FORTRAN_SOURCES} ${GMX_BLUEGENE_C_SRC} ${THREAD_MPI_SRC})
target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_LIB})
-add_dependencies(gmx gmx_version)
+if(USE_VERSION_H)
+ add_dependencies(gmx gmx_version)
+endif()
set_target_properties(gmx PROPERTIES OUTPUT_NAME "gmx${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}")
-install(TARGETS gmx DESTINATION ${LIB_INSTALL_DIR})
+install(TARGETS gmx DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libgmx.pc.cmakein ${CMAKE_CURRENT_BINARY_DIR}/libgmx.pc @ONLY)
-install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgmx.pc DESTINATION ${LIB_INSTALL_DIR}/pkgconfig RENAME "libgmx${GMX_LIBS_SUFFIX}.pc")
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgmx.pc
+ DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
+ RENAME "libgmx${GMX_LIBS_SUFFIX}.pc"
+ COMPONENT development)
#
#
-libgmx@LIBSUFFIX@_la_LDFLAGS = -no-undefined -version-info @SHARED_VERSION_INFO@ $(PTHREAD_LIBS)
+libgmx@LIBSUFFIX@_la_LDFLAGS = -no-undefined -version-info @SHARED_VERSION_INFO@ @DLOPEN_LIBS@ $(PTHREAD_LIBS)
libgmx@LIBSUFFIX@_la_SOURCES = \
3dview.c atomprop.c bondfree.c \
int natoms,ngtc,nnhpres,nhchainlength,fflags,flags_eks,flags_enh;
int d;
int ret;
- gmx_file_position_t *outputfiles;
- int nfiles;
- t_fileio *chksum_file;
- FILE* fplog = *pfplog;
- unsigned char digest[16];
+ gmx_file_position_t *outputfiles;
+ int nfiles;
+ t_fileio *chksum_file;
+ FILE* fplog = *pfplog;
+ unsigned char digest[16];
#if !((defined WIN32 || defined _WIN32 || defined WIN64 || defined _WIN64) && !defined __CYGWIN__ && !defined __CYGWIN32__)
- struct flock fl = { 0, SEEK_SET, 0, F_WRLCK, 0 };
+ struct flock fl; /* don't initialize here: the struct order is OS
+ dependent! */
#endif
-
+
const char *int_warn=
- "WARNING: The checkpoint file was generator with integrator %s,\n"
- " while the simulation uses integrator %s\n\n";
+ "WARNING: The checkpoint file was generated with integrator %s,\n"
+ " while the simulation uses integrator %s\n\n";
const char *sd_note=
"NOTE: The checkpoint file was for %d nodes doing SD or BD,\n"
" while the simulation uses %d SD or BD nodes,\n"
" continuation will be exact, except for the random state\n\n";
+#if !((defined WIN32 || defined _WIN32 || defined WIN64 || defined _WIN64) && !defined __CYGWIN__ && !defined __CYGWIN32__)
+ fl.l_type=F_WRLCK;
+ fl.l_whence=SEEK_SET;
+ fl.l_start=0;
+ fl.l_len=0;
+ fl.l_pid=0;
+#endif
+
if (PARTDECOMP(cr))
{
gmx_fatal(FARGS,
if (outputfiles[i].chksum_size != -1)
{
if (gmx_fio_get_file_md5(chksum_file,outputfiles[i].offset,
- digest) != outputfiles[i].chksum_size)
+ digest) != outputfiles[i].chksum_size) /*at the end of the call the file position is at the end of the file*/
{
gmx_fatal(FARGS,"Can't read %d bytes of '%s' to compute checksum. The file has been replaced or its contents has been modified.",
outputfiles[i].chksum_size,
outputfiles[i].filename);
}
}
- else if (i==0) /*log file need to be seeked even when not reading md5*/
+ if (i==0) /*log file needs to be seeked in case we need to truncate (other files are truncated below)*/
{
- gmx_fio_seek(chksum_file,outputfiles[i].offset);
+ if (gmx_fio_seek(chksum_file,outputfiles[i].offset))
+ {
+ gmx_fatal(FARGS,"Seek error! Failed to truncate log-file: %s.", strerror(errno));
+ }
}
#endif
int slen;
char buf[128];
- sprintf(buf,":-) %s (-:",s);
+ snprintf(buf,128,":-) %s (-:",s);
slen=strlen(buf);
space(out,(80-slen)/2);
fprintf(out,"%s\n",buf);
fprintf(out,"\n");
- sprintf(buf,"%s",Program());
+ snprintf(buf,256,"%s",Program());
#ifdef GMX_DOUBLE
strcat(buf," (double precision)");
#endif
"GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation",
"J. Chem. Theory Comput.",
4, 2008, "435-447" },
+ { "Hub2010",
+ "J. S. Hub, B. L. de Groot and D. van der Spoel",
+ "g_wham - A free weighted histogram analysis implementation including robust error and autocorrelation estimates",
+ "J. Chem. Theory Comput.",
+ 0, 2010, "0000-0000"},
{ "In-Chul99a",
"Y. In-Chul and M. L. Berkowitz",
"Ewald summation for systems with slab geometry",
}
break;
default:
- gmx_incons("Unknown block type");
+ gmx_incons("Unknown block type: this file is corrupted or from the future");
}
}
}
}
+static void enx_warning(const char *msg)
+{
+ if (getenv("GMX_ENX_NO_FATAL") != NULL)
+ {
+ gmx_warning(msg);
+ }
+ else
+ {
+ gmx_fatal(FARGS,"%s\n%s",
+ msg,
+ "If you want to use the correct frames before the corrupted frame and avoid this fatal error set the env.var. GMX_ENX_NO_FATAL");
+ }
+}
static void edr_strings(XDR *xdr,gmx_bool bRead,int file_version,
int n,gmx_enxnm_t **nms)
int nre_test,gmx_bool *bWrongPrecision,gmx_bool *bOK)
{
int magic=-7777777;
- real r;
+ real first_real_to_check;
int b,i,zero=0,dum=0;
gmx_bool bRead = gmx_fio_getread(ef->fio);
int tempfix_nr=0;
* (which is the case for for instance the block sizes for variable
* number of blocks, where this number is read before).
*/
- r = -2e10;
- if (!gmx_fio_do_real(ef->fio, r))
+ first_real_to_check = -2e10;
+ if (!gmx_fio_do_real(ef->fio, first_real_to_check))
{
return FALSE;
}
- if (r > -1e10)
+ if (first_real_to_check > -1e10)
{
/* Assume we are reading an old format */
*file_version = 1;
- fr->t = r;
+ fr->t = first_real_to_check;
if (!gmx_fio_do_int(ef->fio, dum)) *bOK = FALSE;
fr->step = dum;
}
if (!gmx_fio_do_int(ef->fio, magic)) *bOK = FALSE;
if (magic != -7777777)
{
- gmx_fatal(FARGS,"Energy header magic number mismatch, this is not a GROMACS edr file");
+ enx_warning("Energy header magic number mismatch, this is not a GROMACS edr file");
+ *bOK=FALSE;
+ return FALSE;
}
*file_version = enx_version;
if (!gmx_fio_do_int(ef->fio, *file_version)) *bOK = FALSE;
}
if (!gmx_fio_do_int(ef->fio, fr->nblock)) *bOK = FALSE;
+ if (fr->nblock < 0) *bOK=FALSE;
if (ndisre!=0)
{
if (*file_version >= 4)
- gmx_incons("Distance restraint blocks in old style in new style file");
+ {
+ enx_warning("Distance restraint blocks in old style in new style file");
+ *bOK=FALSE;
+ return FALSE;
+ }
fr->nblock+=1;
}
return *bOK;
}
+ /* we now know what these should be, or we've already bailed out because
+ of wrong precision */
+ if ( *file_version==1 && (fr->t < 0 || fr->t > 1e20 || fr->step < 0 ) )
+ {
+ enx_warning("edr file with negative step number or unreasonable time (and without version number).");
+ *bOK=FALSE;
+ return FALSE;
+ }
+
+
if (*bOK && bRead)
+ {
add_blocks_enxframe(fr, fr->nblock);
+ }
startb=0;
if (ndisre>0)
else
{
if (fr->block[b].nsub != 1)
+ {
gmx_incons("Writing an old version .edr file with too many subblocks");
+ }
if (fr->block[b].sub[0].type != dtreal)
{
gmx_incons("Writing an old version .edr file the wrong subblock type");
gmx_enxnm_t *nms=NULL;
int file_version=-1;
t_enxframe *fr;
- gmx_bool bWrongPrecision,bDum=TRUE;
+ gmx_bool bWrongPrecision,bOK=TRUE;
struct ener_file *ef;
snew(ef,1);
gmx_fio_setprecision(ef->fio,FALSE);
do_enxnms(ef,&nre,&nms);
snew(fr,1);
- do_eheader(ef,&file_version,fr,nre,&bWrongPrecision,&bDum);
- if(!bDum)
+ do_eheader(ef,&file_version,fr,nre,&bWrongPrecision,&bOK);
+ if(!bOK)
{
gmx_file("Cannot read energy file header. Corrupt file?");
}
gmx_fio_checktype(ef->fio);
gmx_fio_setprecision(ef->fio,TRUE);
do_enxnms(ef,&nre,&nms);
- do_eheader(ef,&file_version,fr,nre,&bWrongPrecision,&bDum);
- if(!bDum)
+ do_eheader(ef,&file_version,fr,nre,&bWrongPrecision,&bOK);
+ if(!bOK)
{
gmx_file("Cannot write energy file header; maybe you are out of quota?");
}
bOK1=gmx_fio_ndo_string(ef->fio, sub->sval, sub->nr);
break;
default:
- gmx_incons("Reading unknown block type");
+ gmx_incons("Reading unknown block data type: this file is corrupted or from the future");
}
bOK = bOK && bOK1;
}
+++ /dev/null
-/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
- *
- * And Hey:
- * GROningen Mixture of Alchemy and Childrens' Stories
- */
-/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-int ftocstr(char *ds, int dl, char *ss, int sl)
- /* dst, src ptrs */
- /* dst max len */
- /* src len */
-{
- char *p;
-
- p = ss + sl;
- while ( --p >= ss && *p == ' ' );
- sl = p - ss + 1;
- dl--;
- ds[0] = 0;
- if (sl > dl)
- return 1;
- while (sl--)
- (*ds++ = *ss++);
- *ds = '\0';
- return 0;
-}
-
-
-int ctofstr(char *ds, int dl, char *ss)
- /* dest space */
- /* max dest length */
- /* src string (0-term) */
-{
- while (dl && *ss) {
- *ds++ = *ss++;
- dl--;
- }
- while (dl--)
- *ds++ = ' ';
- return 0;
-}
}
else
{
-#if (defined( _WIN32 ) || defined( _WIN64 ) )
- /* windows doesn't do standard C */
-#define snprintf sprintf_s
-#endif
- snprintf(buf, GMX_FIO_BUFLEN, " ; %s %s",
- fio->comment ? fio->comment : "", desc);
+ snprintf(buf, GMX_FIO_BUFLEN, " ; %s %s", fio->comment ? fio->comment : "", desc);
}
return buf;
}
gmx_fio_lock(fio);
if (fio->fp)
{
- gmx_fseek(fio->fp, fpos, SEEK_SET);
+ rc = gmx_fseek(fio->fp, fpos, SEEK_SET);
}
else
{
return rc;
}
+/* Return the size of the arrays */
+int
+gmx_residuetype_get_size(gmx_residuetype_t rt)
+{
+ return rt->n;
+}
+
+/* Search for a residuetype with name resnm within the
+ * gmx_residuetype database. Return the index if found,
+ * otherwise -1.
+ */
+int
+gmx_residuetype_get_index(gmx_residuetype_t rt, const char *resnm)
+{
+ int i,rc;
+
+ rc=-1;
+ for(i=0;i<rt->n && rc;i++)
+ {
+ rc=gmx_strcasecmp(rt->resname[i],resnm);
+ }
+
+ return (0 == rc) ? i-1 : -1;
+}
+
+/* Return the name of the residuetype with the given index, or
+ * NULL if not found. */
+const char *
+gmx_residuetype_get_name(gmx_residuetype_t rt, int index)
+{
+ if(index >= 0 && index < rt->n) {
+ return rt->resname[index];
+ } else {
+ return NULL;
+ }
+}
};
const char *esa_names[esaNR+1] = {
- "Ace-approx", "None", "Still", NULL
+ "Ace-approximation", "None", "Still", NULL
};
const char *ewt_names[ewtNR+1] = {
*/
-/* The optimized version of converts2ints is disabled
+/* The optimized version of converts2ints is disabled on BG/P
* because of issues on BG/P reported in bugzilla 429
*/
-/* #if (defined __IBMC__ || defined __IBMCPP__) */
-#if (0)
+#if defined __blrts__
#define convert2ints(x,xi,conv,i1,i2) \
xi = __fpctiwz(x); \
int * inneriter,
double * work)
{
- int nri,nthreads;
- int n,ii,is3,ii3,k,nj0,nj1,ggid;
- double shX,shY,shZ;
- int jnrA,jnrB;
- int j3A,j3B;
+ int nri,nthreads;
+ int n,ii,is3,ii3,k,nj0,nj1,ggid;
+ double shX,shY,shZ;
+ int jnrA,jnrB;
+ int j3A,j3B;
gmx_gbdata_t *gbdata;
double * gpol;
nri = *p_nri;
- gbfactor = _mm_set1_pd( - ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent)));
- gbtabscale = _mm_load1_pd(p_gbtabscale);
- facel = _mm_load1_pd(p_facel);
-
- nj1 = 0;
- jnrA = jnrB = 0;
- j3A = j3B = 0;
- jx = _mm_setzero_pd();
- jy = _mm_setzero_pd();
- jz = _mm_setzero_pd();
+ gbfactor = _mm_set1_pd( - ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent)));
+ gbtabscale = _mm_load1_pd(p_gbtabscale);
+ facel = _mm_load1_pd(p_facel);
+
+ nj1 = 0;
+ jnrA = jnrB = 0;
+ j3A = j3B = 0;
+ jx = _mm_setzero_pd();
+ jy = _mm_setzero_pd();
+ jz = _mm_setzero_pd();
for(n=0;n<nri;n++)
{
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
- nj0 = jindex[n];
- nj1 = jindex[n+1];
- ii = iinr[n];
- ii3 = 3*ii;
+ is3 = 3*shift[n];
+ shX = shiftvec[is3];
+ shY = shiftvec[is3+1];
+ shZ = shiftvec[is3+2];
+ nj0 = jindex[n];
+ nj1 = jindex[n+1];
+ ii = iinr[n];
+ ii3 = 3*ii;
ix = _mm_set1_pd(shX+pos[ii3+0]);
iy = _mm_set1_pd(shY+pos[ii3+1]);
iz = _mm_set1_pd(shZ+pos[ii3+2]);
-
+
iq = _mm_load1_pd(charge+ii);
iq = _mm_mul_pd(iq,facel);
-
+
isai = _mm_load1_pd(invsqrta+ii);
vctot = _mm_setzero_pd();
j3A = jnrA * 3;
j3B = jnrB * 3;
-
- GMX_MM_LOAD_1RVEC_2POINTERS_PD(pos+j3A,pos+j3B,jx,jy,jz);
+
+ GMX_MM_LOAD_1RVEC_2POINTERS_PD(pos+j3A,pos+j3B,jx,jy,jz);
dx = _mm_sub_pd(ix,jx);
dy = _mm_sub_pd(iy,jy);
dz = _mm_sub_pd(iz,jz);
- rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
-
- rinv = gmx_mm_invsqrt_pd(rsq);
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
rinvsq = _mm_mul_pd(rinv,rinv);
-
+
/***********************************/
/* INTERACTION SECTION STARTS HERE */
/***********************************/
qq = _mm_mul_pd(iq,jq);
vcoul = _mm_mul_pd(qq,rinv);
fscal = _mm_mul_pd(vcoul,rinv);
- vctot = _mm_add_pd(vctot,vcoul);
+ vctot = _mm_add_pd(vctot,vcoul);
/* Polarization interaction */
qq = _mm_mul_pd(qq,_mm_mul_pd(isaprod,gbfactor));
eps = _mm_sub_pd(rtab,_mm_cvtepi32_pd(n0));
nnn = _mm_slli_epi32(n0,2);
- /* the tables are 16-byte aligned, so we can use _mm_load_pd */
- Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1)));
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1))+2);
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_pd(G,eps);
- H = _mm_mul_pd(H, _mm_mul_pd(eps,eps) );
- F = _mm_add_pd(F, _mm_add_pd( G , H ) );
- Y = _mm_add_pd(Y, _mm_mul_pd(F, eps));
- F = _mm_add_pd(F, _mm_add_pd(G , _mm_mul_pd(H,two)));
- vgb = _mm_mul_pd(Y, qq);
- fijGB = _mm_mul_pd(F, _mm_mul_pd(qq,gbscale));
-
- dvdatmp = _mm_mul_pd(_mm_add_pd(vgb, _mm_mul_pd(fijGB,r)) , minushalf);
-
- vgbtot = _mm_add_pd(vgbtot, vgb);
-
- dvdasum = _mm_add_pd(dvdasum, dvdatmp);
- dvdatmp = _mm_mul_pd(dvdatmp, _mm_mul_pd(isaj,isaj));
-
- GMX_MM_INCREMENT_2VALUES_PD(dvda+jnrA,dvda+jnrB,dvdatmp);
-
- fscal = _mm_mul_pd( _mm_sub_pd( fscal, fijGB),rinv );
-
- /***********************************/
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1)));
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1))+2);
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_pd(G,eps);
+ H = _mm_mul_pd(H, _mm_mul_pd(eps,eps) );
+ F = _mm_add_pd(F, _mm_add_pd( G , H ) );
+ Y = _mm_add_pd(Y, _mm_mul_pd(F, eps));
+ F = _mm_add_pd(F, _mm_add_pd(G , _mm_mul_pd(H,two)));
+ vgb = _mm_mul_pd(Y, qq);
+ fijGB = _mm_mul_pd(F, _mm_mul_pd(qq,gbscale));
+
+ dvdatmp = _mm_mul_pd(_mm_add_pd(vgb, _mm_mul_pd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb);
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp);
+ dvdatmp = _mm_mul_pd(dvdatmp, _mm_mul_pd(isaj,isaj));
+
+ GMX_MM_INCREMENT_2VALUES_PD(dvda+jnrA,dvda+jnrB,dvdatmp);
+
+ fscal = _mm_mul_pd( _mm_sub_pd( fscal, fijGB),rinv );
+
+ /***********************************/
/* INTERACTION SECTION ENDS HERE */
/***********************************/
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx);
- ty = _mm_mul_pd(fscal,dy);
- tz = _mm_mul_pd(fscal,dz);
-
- /* Increment i atom force */
- fix = _mm_add_pd(fix,tx);
- fiy = _mm_add_pd(fiy,ty);
- fiz = _mm_add_pd(fiz,tz);
-
- /* Store j forces back */
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_pd(fscal,dx);
+ ty = _mm_mul_pd(fscal,dy);
+ tz = _mm_mul_pd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_pd(fix,tx);
+ fiy = _mm_add_pd(fiy,ty);
+ fiz = _mm_add_pd(fiz,tz);
+
+ /* Store j forces back */
GMX_MM_DECREMENT_1RVEC_2POINTERS_PD(faction+j3A,faction+j3B,tx,ty,tz);
}
{
jnrA = jjnr[k];
j3A = jnrA * 3;
-
- GMX_MM_LOAD_1RVEC_1POINTER_PD(pos+j3A,jx,jy,jz);
-
+
+ GMX_MM_LOAD_1RVEC_1POINTER_PD(pos+j3A,jx,jy,jz);
+
dx = _mm_sub_sd(ix,jx);
dy = _mm_sub_sd(iy,jy);
dz = _mm_sub_sd(iz,jz);
-
- rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
-
- rinv = gmx_mm_invsqrt_pd(rsq);
+
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
rinvsq = _mm_mul_sd(rinv,rinv);
-
+
+ /* These reason for zeroing these variables here is for fixing bug 585
+ * What happens is that __m128d _mm_add_sd(a,b) gives back r0=a[0]+b[0],
+ * and r1=0, but it should be r1=a[1].
+ * This might be a compiler issue (tested with gcc-4.1.3 and -O3).
+ * To work around it, we zero these variables and use _mm_add_pd (**) instead
+ * Note that the only variables that get affected are the energies since
+ * the total sum needs to be correct
+ */
+ vgb = _mm_setzero_pd();
+ vcoul = _mm_setzero_pd();
+ dvdatmp = _mm_setzero_pd();
+
/***********************************/
/* INTERACTION SECTION STARTS HERE */
/***********************************/
GMX_MM_LOAD_1VALUE_PD(charge+jnrA,jq);
GMX_MM_LOAD_1VALUE_PD(invsqrta+jnrA,isaj);
-
+
isaprod = _mm_mul_sd(isai,isaj);
- qq = _mm_mul_sd(iq,jq);
+ qq = _mm_mul_sd(jq,iq);
vcoul = _mm_mul_sd(qq,rinv);
fscal = _mm_mul_sd(vcoul,rinv);
- vctot = _mm_add_sd(vctot,vcoul);
-
- /* Polarization interaction */
+ vctot = _mm_add_pd(vctot,vcoul); /* (**) */
+
+ /* Polarization interaction */
qq = _mm_mul_sd(qq,_mm_mul_sd(isaprod,gbfactor));
gbscale = _mm_mul_sd(isaprod,gbtabscale);
-
+
/* Calculate GB table index */
r = _mm_mul_sd(rsq,rinv);
rtab = _mm_mul_sd(r,gbscale);
-
+
n0 = _mm_cvttpd_epi32(rtab);
eps = _mm_sub_sd(rtab,_mm_cvtepi32_pd(n0));
nnn = _mm_slli_epi32(n0,2);
- /* the tables are 16-byte aligned, so we can use _mm_load_pd */
- Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_sd(G,eps);
- H = _mm_mul_sd(H, _mm_mul_sd(eps,eps) );
- F = _mm_add_sd(F, _mm_add_sd( G , H ) );
- Y = _mm_add_sd(Y, _mm_mul_sd(F, eps));
- F = _mm_add_sd(F, _mm_add_sd(G , _mm_mul_sd(H,two)));
- vgb = _mm_mul_sd(Y, qq);
- fijGB = _mm_mul_sd(F, _mm_mul_sd(qq,gbscale));
-
- dvdatmp = _mm_mul_sd(_mm_add_sd(vgb, _mm_mul_sd(fijGB,r)) , minushalf);
-
- vgbtot = _mm_add_sd(vgbtot, vgb);
-
- dvdasum = _mm_add_sd(dvdasum, dvdatmp);
- dvdatmp = _mm_mul_sd(dvdatmp, _mm_mul_sd(isaj,isaj));
-
- GMX_MM_INCREMENT_1VALUE_PD(dvda+jnrA,dvdatmp);
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_sd(G,eps);
+ H = _mm_mul_sd(H, _mm_mul_sd(eps,eps) );
+ F = _mm_add_sd(F, _mm_add_sd( G , H ) );
+ Y = _mm_add_sd(Y, _mm_mul_sd(F, eps));
+ F = _mm_add_sd(F, _mm_add_sd(G , _mm_mul_sd(H,two)));
+ vgb = _mm_mul_sd(Y, qq);
+ fijGB = _mm_mul_sd(F, _mm_mul_sd(qq,gbscale));
+
+ dvdatmp = _mm_mul_sd(_mm_add_sd(vgb, _mm_mul_sd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb); /* (**) */
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp); /* (**) */
+ dvdatmp = _mm_mul_sd(dvdatmp, _mm_mul_sd(isaj,isaj));
+
+ GMX_MM_INCREMENT_1VALUE_PD(dvda+jnrA,dvdatmp);
- fscal = _mm_mul_sd( _mm_sub_sd( fscal, fijGB),rinv );
-
- /***********************************/
+ fscal = _mm_mul_sd( _mm_sub_sd( fscal, fijGB),rinv );
+
+ /***********************************/
/* INTERACTION SECTION ENDS HERE */
/***********************************/
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_sd(fscal,dx);
- ty = _mm_mul_sd(fscal,dy);
- tz = _mm_mul_sd(fscal,dz);
-
- /* Increment i atom force */
- fix = _mm_add_sd(fix,tx);
- fiy = _mm_add_sd(fiy,ty);
- fiz = _mm_add_sd(fiz,tz);
-
- /* Store j forces back */
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_sd(fscal,dx);
+ ty = _mm_mul_sd(fscal,dy);
+ tz = _mm_mul_sd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_sd(fix,tx);
+ fiy = _mm_add_sd(fiy,ty);
+ fiz = _mm_add_sd(fiz,tz);
+
+ /* Store j forces back */
GMX_MM_DECREMENT_1RVEC_1POINTER_PD(faction+j3A,tx,ty,tz);
}
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai,isai));
- gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,faction+ii3,fshift+is3);
-
- ggid = gid[n];
-
- gmx_mm_update_1pot_pd(vctot,vc+ggid);
- gmx_mm_update_2pot_pd(vgbtot,gpol+ggid,dvdasum,dvda+ii);
- }
+ dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai,isai));
+ gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,faction+ii3,fshift+is3);
+
+ ggid = gid[n];
+ gmx_mm_update_1pot_pd(vctot,vc+ggid);
+ gmx_mm_update_1pot_pd(vgbtot,gpol+ggid);
+ gmx_mm_update_1pot_pd(dvdasum,dvda+ii);
+ }
+
*outeriter = nri;
- *inneriter = nj1;
+ *inneriter = nj1;
}
int * inneriter,
double * work)
{
- int nri,ntype,nthreads;
- int n,ii,is3,ii3,k,nj0,nj1,ggid;
- double shX,shY,shZ;
+ int nri,ntype,nthreads;
+ int n,ii,is3,ii3,k,nj0,nj1,ggid;
+ double shX,shY,shZ;
int offset,nti;
- int jnrA,jnrB;
- int j3A,j3B;
+ int jnrA,jnrB;
+ int j3A,j3B;
int tjA,tjB;
gmx_gbdata_t *gbdata;
double * gpol;
nri = *p_nri;
ntype = *p_ntype;
- gbfactor = _mm_set1_pd( - ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent)));
- gbtabscale = _mm_load1_pd(p_gbtabscale);
- facel = _mm_load1_pd(p_facel);
-
- nj1 = 0;
- jnrA = jnrB = 0;
- j3A = j3B = 0;
- jx = _mm_setzero_pd();
- jy = _mm_setzero_pd();
- jz = _mm_setzero_pd();
- c6 = _mm_setzero_pd();
- c12 = _mm_setzero_pd();
+ gbfactor = _mm_set1_pd( - ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent)));
+ gbtabscale = _mm_load1_pd(p_gbtabscale);
+ facel = _mm_load1_pd(p_facel);
+
+ nj1 = 0;
+ jnrA = jnrB = 0;
+ j3A = j3B = 0;
+ jx = _mm_setzero_pd();
+ jy = _mm_setzero_pd();
+ jz = _mm_setzero_pd();
+ c6 = _mm_setzero_pd();
+ c12 = _mm_setzero_pd();
for(n=0;n<nri;n++)
{
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
- nj0 = jindex[n];
- nj1 = jindex[n+1];
- ii = iinr[n];
- ii3 = 3*ii;
+ is3 = 3*shift[n];
+ shX = shiftvec[is3];
+ shY = shiftvec[is3+1];
+ shZ = shiftvec[is3+2];
+ nj0 = jindex[n];
+ nj1 = jindex[n+1];
+ ii = iinr[n];
+ ii3 = 3*ii;
ix = _mm_set1_pd(shX+pos[ii3+0]);
iy = _mm_set1_pd(shY+pos[ii3+1]);
iz = _mm_set1_pd(shZ+pos[ii3+2]);
-
+
iq = _mm_load1_pd(charge+ii);
iq = _mm_mul_pd(iq,facel);
-
+
isai = _mm_load1_pd(invsqrta+ii);
nti = 2*ntype*type[ii];
j3A = jnrA * 3;
j3B = jnrB * 3;
- GMX_MM_LOAD_1RVEC_2POINTERS_PD(pos+j3A,pos+j3B,jx,jy,jz);
+ GMX_MM_LOAD_1RVEC_2POINTERS_PD(pos+j3A,pos+j3B,jx,jy,jz);
dx = _mm_sub_pd(ix,jx);
dy = _mm_sub_pd(iy,jy);
dz = _mm_sub_pd(iz,jz);
- rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
-
- rinv = gmx_mm_invsqrt_pd(rsq);
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
rinvsq = _mm_mul_pd(rinv,rinv);
-
+
/***********************************/
/* INTERACTION SECTION STARTS HERE */
/***********************************/
GMX_MM_LOAD_2VALUES_PD(charge+jnrA,charge+jnrB,jq);
GMX_MM_LOAD_2VALUES_PD(invsqrta+jnrA,invsqrta+jnrB,isaj);
- /* Lennard-Jones */
- tjA = nti+2*type[jnrA];
+ /* Lennard-Jones */
+ tjA = nti+2*type[jnrA];
tjB = nti+2*type[jnrB];
-
- GMX_MM_LOAD_2PAIRS_PD(vdwparam+tjA,vdwparam+tjB,c6,c12);
+
+ GMX_MM_LOAD_2PAIRS_PD(vdwparam+tjA,vdwparam+tjB,c6,c12);
isaprod = _mm_mul_pd(isai,isaj);
qq = _mm_mul_pd(iq,jq);
vcoul = _mm_mul_pd(qq,rinv);
fscal = _mm_mul_pd(vcoul,rinv);
- vctot = _mm_add_pd(vctot,vcoul);
+ vctot = _mm_add_pd(vctot,vcoul);
- /* Polarization interaction */
+ /* Polarization interaction */
qq = _mm_mul_pd(qq,_mm_mul_pd(isaprod,gbfactor));
gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
+
/* Calculate GB table index */
r = _mm_mul_pd(rsq,rinv);
rtab = _mm_mul_pd(r,gbscale);
eps = _mm_sub_pd(rtab,_mm_cvtepi32_pd(n0));
nnn = _mm_slli_epi32(n0,2);
- /* the tables are 16-byte aligned, so we can use _mm_load_pd */
- Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1)));
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1))+2);
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_pd(G,eps);
- H = _mm_mul_pd(H, _mm_mul_pd(eps,eps) );
- F = _mm_add_pd(F, _mm_add_pd( G , H ) );
- Y = _mm_add_pd(Y, _mm_mul_pd(F, eps));
- F = _mm_add_pd(F, _mm_add_pd(G , _mm_mul_pd(H,two)));
- vgb = _mm_mul_pd(Y, qq);
- fijGB = _mm_mul_pd(F, _mm_mul_pd(qq,gbscale));
-
- dvdatmp = _mm_mul_pd(_mm_add_pd(vgb, _mm_mul_pd(fijGB,r)) , minushalf);
-
- vgbtot = _mm_add_pd(vgbtot, vgb);
-
- dvdasum = _mm_add_pd(dvdasum, dvdatmp);
- dvdatmp = _mm_mul_pd(dvdatmp, _mm_mul_pd(isaj,isaj));
-
- GMX_MM_INCREMENT_2VALUES_PD(dvda+jnrA,dvda+jnrB,dvdatmp);
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1)));
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1))+2);
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_pd(G,eps);
+ H = _mm_mul_pd(H, _mm_mul_pd(eps,eps) );
+ F = _mm_add_pd(F, _mm_add_pd( G , H ) );
+ Y = _mm_add_pd(Y, _mm_mul_pd(F, eps));
+ F = _mm_add_pd(F, _mm_add_pd(G , _mm_mul_pd(H,two)));
+ vgb = _mm_mul_pd(Y, qq);
+ fijGB = _mm_mul_pd(F, _mm_mul_pd(qq,gbscale));
+
+ dvdatmp = _mm_mul_pd(_mm_add_pd(vgb, _mm_mul_pd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb);
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp);
+ dvdatmp = _mm_mul_pd(dvdatmp, _mm_mul_pd(isaj,isaj));
+
+ GMX_MM_INCREMENT_2VALUES_PD(dvda+jnrA,dvda+jnrB,dvdatmp);
rinvsix = _mm_mul_pd(rinvsq,rinvsq);
rinvsix = _mm_mul_pd(rinvsix,rinvsq);
vvdw12 = _mm_mul_pd(c12, _mm_mul_pd(rinvsix,rinvsix));
vvdwtot = _mm_add_pd(vvdwtot,_mm_sub_pd(vvdw12,vvdw6));
- fscal = _mm_sub_pd(_mm_mul_pd(rinvsq,
- _mm_sub_pd(_mm_mul_pd(twelve,vvdw12),
- _mm_mul_pd(six,vvdw6))),
- _mm_mul_pd( _mm_sub_pd( fijGB,fscal),rinv ));
-
- /***********************************/
+ fscal = _mm_sub_pd(_mm_mul_pd(rinvsq,
+ _mm_sub_pd(_mm_mul_pd(twelve,vvdw12),
+ _mm_mul_pd(six,vvdw6))),
+ _mm_mul_pd( _mm_sub_pd( fijGB,fscal),rinv ));
+
+ /***********************************/
/* INTERACTION SECTION ENDS HERE */
/***********************************/
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx);
- ty = _mm_mul_pd(fscal,dy);
- tz = _mm_mul_pd(fscal,dz);
-
- /* Increment i atom force */
- fix = _mm_add_pd(fix,tx);
- fiy = _mm_add_pd(fiy,ty);
- fiz = _mm_add_pd(fiz,tz);
-
- /* Store j forces back */
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_pd(fscal,dx);
+ ty = _mm_mul_pd(fscal,dy);
+ tz = _mm_mul_pd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_pd(fix,tx);
+ fiy = _mm_add_pd(fiy,ty);
+ fiz = _mm_add_pd(fiz,tz);
+
+ /* Store j forces back */
GMX_MM_DECREMENT_1RVEC_2POINTERS_PD(faction+j3A,faction+j3B,tx,ty,tz);
}
jnrA = jjnr[k];
j3A = jnrA * 3;
-
- GMX_MM_LOAD_1RVEC_1POINTER_PD(pos+j3A,jx,jy,jz);
+
+ GMX_MM_LOAD_1RVEC_1POINTER_PD(pos+j3A,jx,jy,jz);
dx = _mm_sub_sd(ix,jx);
dy = _mm_sub_sd(iy,jy);
dz = _mm_sub_sd(iz,jz);
- rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
-
- rinv = gmx_mm_invsqrt_pd(rsq);
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
rinvsq = _mm_mul_sd(rinv,rinv);
-
+
+ /* These reason for zeroing these variables here is for fixing bug 585
+ * What happens is that __m128d _mm_add_sd(a,b) gives back r0=a[0]+b[0],
+ * and r1=0, but it should be r1=a[1].
+ * This might be a compiler issue (tested with gcc-4.1.3 and -O3).
+ * To work around it, we zero these variables and use _mm_add_pd (**) instead
+ * Note that the only variables that get affected are the energies since
+ * the total sum needs to be correct
+ */
+ vgb = _mm_setzero_pd();
+ vcoul = _mm_setzero_pd();
+ dvdatmp = _mm_setzero_pd();
+ vvdw6 = _mm_setzero_pd();
+ vvdw12 = _mm_setzero_pd();
+
/***********************************/
/* INTERACTION SECTION STARTS HERE */
/***********************************/
GMX_MM_LOAD_1VALUE_PD(charge+jnrA,jq);
GMX_MM_LOAD_1VALUE_PD(invsqrta+jnrA,isaj);
-
- /* Lennard-Jones */
- tjA = nti+2*type[jnrA];
-
- GMX_MM_LOAD_1PAIR_PD(vdwparam+tjA,c6,c12);
+
+ /* Lennard-Jones */
+ tjA = nti+2*type[jnrA];
+
+ GMX_MM_LOAD_1PAIR_PD(vdwparam+tjA,c6,c12);
isaprod = _mm_mul_sd(isai,isaj);
- qq = _mm_mul_sd(iq,jq);
+ qq = _mm_mul_sd(jq,iq);
vcoul = _mm_mul_sd(qq,rinv);
fscal = _mm_mul_sd(vcoul,rinv);
- vctot = _mm_add_sd(vctot,vcoul);
-
- /* Polarization interaction */
+ vctot = _mm_add_pd(vctot,vcoul); /* (**) */
+
+ /* Polarization interaction */
qq = _mm_mul_sd(qq,_mm_mul_sd(isaprod,gbfactor));
gbscale = _mm_mul_sd(isaprod,gbtabscale);
-
+
/* Calculate GB table index */
r = _mm_mul_sd(rsq,rinv);
rtab = _mm_mul_sd(r,gbscale);
eps = _mm_sub_sd(rtab,_mm_cvtepi32_pd(n0));
nnn = _mm_slli_epi32(n0,2);
- /* the tables are 16-byte aligned, so we can use _mm_load_pd */
- Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_sd(G,eps);
- H = _mm_mul_sd(H, _mm_mul_sd(eps,eps) );
- F = _mm_add_sd(F, _mm_add_sd( G , H ) );
- Y = _mm_add_sd(Y, _mm_mul_sd(F, eps));
- F = _mm_add_sd(F, _mm_add_sd(G , _mm_mul_sd(H,two)));
- vgb = _mm_mul_sd(Y, qq);
- fijGB = _mm_mul_sd(F, _mm_mul_sd(qq,gbscale));
-
- dvdatmp = _mm_mul_sd(_mm_add_sd(vgb, _mm_mul_sd(fijGB,r)) , minushalf);
-
- vgbtot = _mm_add_sd(vgbtot, vgb);
-
- dvdasum = _mm_add_sd(dvdasum, dvdatmp);
- dvdatmp = _mm_mul_sd(dvdatmp, _mm_mul_sd(isaj,isaj));
-
- GMX_MM_INCREMENT_1VALUE_PD(dvda+jnrA,dvdatmp);
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_sd(G,eps);
+ H = _mm_mul_sd(H, _mm_mul_sd(eps,eps) );
+ F = _mm_add_sd(F, _mm_add_sd( G , H ) );
+ Y = _mm_add_sd(Y, _mm_mul_sd(F, eps));
+ F = _mm_add_sd(F, _mm_add_sd(G , _mm_mul_sd(H,two)));
+ vgb = _mm_mul_sd(Y, qq);
+ fijGB = _mm_mul_sd(F, _mm_mul_sd(qq,gbscale));
+
+ dvdatmp = _mm_mul_sd(_mm_add_sd(vgb, _mm_mul_sd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb); /* (**) */
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp); /* (**) */
+ dvdatmp = _mm_mul_sd(dvdatmp, _mm_mul_sd(isaj,isaj));
+
+ GMX_MM_INCREMENT_1VALUE_PD(dvda+jnrA,dvdatmp);
rinvsix = _mm_mul_sd(rinvsq,rinvsq);
rinvsix = _mm_mul_sd(rinvsix,rinvsq);
vvdw6 = _mm_mul_sd(c6,rinvsix);
vvdw12 = _mm_mul_sd(c12, _mm_mul_sd(rinvsix,rinvsix));
- vvdwtot = _mm_add_sd(vvdwtot,_mm_sub_sd(vvdw12,vvdw6));
-
- fscal = _mm_sub_sd(_mm_mul_sd(rinvsq,
- _mm_sub_sd(_mm_mul_sd(twelve,vvdw12),
- _mm_mul_sd(six,vvdw6))),
- _mm_mul_sd( _mm_sub_sd( fijGB,fscal),rinv ));
-
- /***********************************/
+ vvdwtot = _mm_add_pd(vvdwtot,_mm_sub_sd(vvdw12,vvdw6)); /* (**) */
+
+ fscal = _mm_sub_sd(_mm_mul_sd(rinvsq,
+ _mm_sub_sd(_mm_mul_sd(twelve,vvdw12),
+ _mm_mul_sd(six,vvdw6))),
+ _mm_mul_sd( _mm_sub_sd( fijGB,fscal),rinv ));
+
+ /***********************************/
/* INTERACTION SECTION ENDS HERE */
/***********************************/
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_sd(fscal,dx);
- ty = _mm_mul_sd(fscal,dy);
- tz = _mm_mul_sd(fscal,dz);
-
- /* Increment i atom force */
- fix = _mm_add_sd(fix,tx);
- fiy = _mm_add_sd(fiy,ty);
- fiz = _mm_add_sd(fiz,tz);
-
- /* Store j forces back */
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_sd(fscal,dx);
+ ty = _mm_mul_sd(fscal,dy);
+ tz = _mm_mul_sd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_sd(fix,tx);
+ fiy = _mm_add_sd(fiy,ty);
+ fiz = _mm_add_sd(fiz,tz);
+
+ /* Store j forces back */
GMX_MM_DECREMENT_1RVEC_1POINTER_PD(faction+j3A,tx,ty,tz);
}
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai,isai));
- gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,faction+ii3,fshift+is3);
-
- ggid = gid[n];
-
- gmx_mm_update_2pot_pd(vctot,vc+ggid,vvdwtot,vvdw+ggid);
- gmx_mm_update_2pot_pd(vgbtot,gpol+ggid,dvdasum,dvda+ii);
+ dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai,isai));
+ gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,faction+ii3,fshift+is3);
+
+ ggid = gid[n];
+
+ gmx_mm_update_1pot_pd(vctot,vc+ggid);
+ gmx_mm_update_1pot_pd(vgbtot,gpol+ggid);
+ gmx_mm_update_1pot_pd(dvdasum,dvda+ii);
+ gmx_mm_update_1pot_pd(vvdwtot,vvdw+ggid);
+
}
-
+
*outeriter = nri;
- *inneriter = nj1;
+ *inneriter = nj1;
}
int * inneriter,
double * work)
{
- int nri,ntype,nthreads;
- int n,ii,is3,ii3,k,nj0,nj1,ggid;
- double shX,shY,shZ;
+ int nri,ntype,nthreads;
+ int n,ii,is3,ii3,k,nj0,nj1,ggid;
+ double shX,shY,shZ;
int offset,nti;
- int jnrA,jnrB;
- int j3A,j3B;
+ int jnrA,jnrB;
+ int j3A,j3B;
int tjA,tjB;
gmx_gbdata_t *gbdata;
double * gpol;
__m128d vcoul,fscal,gbscale,c6,c12;
__m128d rinvsq,r,rtab;
__m128d eps,Y,F,G,H;
- __m128d VV,FF,Fp;
+ __m128d VV,FF,Fp;
__m128d vgb,fijGB,dvdatmp;
__m128d rinvsix,vvdw6,vvdw12,vvdwtmp;
__m128d facel,gbtabscale,dvdaj;
- __m128d fijD,fijR;
- __m128d xmm1,tabscale,eps2;
+ __m128d fijD,fijR;
+ __m128d xmm1,tabscale,eps2;
__m128i n0, nnn;
nri = *p_nri;
ntype = *p_ntype;
- gbfactor = _mm_set1_pd( - ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent)));
- gbtabscale = _mm_load1_pd(p_gbtabscale);
- facel = _mm_load1_pd(p_facel);
- tabscale = _mm_load1_pd(p_tabscale);
-
- nj1 = 0;
- jnrA = jnrB = 0;
- j3A = j3B = 0;
- jx = _mm_setzero_pd();
- jy = _mm_setzero_pd();
- jz = _mm_setzero_pd();
- c6 = _mm_setzero_pd();
- c12 = _mm_setzero_pd();
+ gbfactor = _mm_set1_pd( - ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent)));
+ gbtabscale = _mm_load1_pd(p_gbtabscale);
+ facel = _mm_load1_pd(p_facel);
+ tabscale = _mm_load1_pd(p_tabscale);
+
+ nj1 = 0;
+ jnrA = jnrB = 0;
+ j3A = j3B = 0;
+ jx = _mm_setzero_pd();
+ jy = _mm_setzero_pd();
+ jz = _mm_setzero_pd();
+ c6 = _mm_setzero_pd();
+ c12 = _mm_setzero_pd();
for(n=0;n<nri;n++)
{
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
- nj0 = jindex[n];
- nj1 = jindex[n+1];
- ii = iinr[n];
- ii3 = 3*ii;
+ is3 = 3*shift[n];
+ shX = shiftvec[is3];
+ shY = shiftvec[is3+1];
+ shZ = shiftvec[is3+2];
+ nj0 = jindex[n];
+ nj1 = jindex[n+1];
+ ii = iinr[n];
+ ii3 = 3*ii;
ix = _mm_set1_pd(shX+pos[ii3+0]);
iy = _mm_set1_pd(shY+pos[ii3+1]);
iz = _mm_set1_pd(shZ+pos[ii3+2]);
-
+
iq = _mm_load1_pd(charge+ii);
iq = _mm_mul_pd(iq,facel);
-
+
isai = _mm_load1_pd(invsqrta+ii);
-
+
nti = 2*ntype*type[ii];
vctot = _mm_setzero_pd();
j3A = jnrA * 3;
j3B = jnrB * 3;
- GMX_MM_LOAD_1RVEC_2POINTERS_PD(pos+j3A,pos+j3B,jx,jy,jz);
+ GMX_MM_LOAD_1RVEC_2POINTERS_PD(pos+j3A,pos+j3B,jx,jy,jz);
dx = _mm_sub_pd(ix,jx);
dy = _mm_sub_pd(iy,jy);
dz = _mm_sub_pd(iz,jz);
- rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
-
- rinv = gmx_mm_invsqrt_pd(rsq);
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
rinvsq = _mm_mul_pd(rinv,rinv);
-
+
/***********************************/
/* INTERACTION SECTION STARTS HERE */
/***********************************/
GMX_MM_LOAD_2VALUES_PD(charge+jnrA,charge+jnrB,jq);
GMX_MM_LOAD_2VALUES_PD(invsqrta+jnrA,invsqrta+jnrB,isaj);
- /* Lennard-Jones */
- tjA = nti+2*type[jnrA];
+ /* Lennard-Jones */
+ tjA = nti+2*type[jnrA];
tjB = nti+2*type[jnrB];
-
- GMX_MM_LOAD_2PAIRS_PD(vdwparam+tjA,vdwparam+tjB,c6,c12);
+
+ GMX_MM_LOAD_2PAIRS_PD(vdwparam+tjA,vdwparam+tjB,c6,c12);
isaprod = _mm_mul_pd(isai,isaj);
qq = _mm_mul_pd(iq,jq);
vcoul = _mm_mul_pd(qq,rinv);
fscal = _mm_mul_pd(vcoul,rinv);
- vctot = _mm_add_pd(vctot,vcoul);
-
- /* Polarization interaction */
+ vctot = _mm_add_pd(vctot,vcoul);
+
+ /* Polarization interaction */
qq = _mm_mul_pd(qq,_mm_mul_pd(isaprod,gbfactor));
gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
+
/* Calculate GB table index */
r = _mm_mul_pd(rsq,rinv);
rtab = _mm_mul_pd(r,gbscale);
eps = _mm_sub_pd(rtab,_mm_cvtepi32_pd(n0));
nnn = _mm_slli_epi32(n0,2);
- /* the tables are 16-byte aligned, so we can use _mm_load_pd */
- Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1)));
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1))+2);
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_pd(G,eps);
- H = _mm_mul_pd(H, _mm_mul_pd(eps,eps) );
- F = _mm_add_pd(F, _mm_add_pd( G , H ) );
- Y = _mm_add_pd(Y, _mm_mul_pd(F, eps));
- F = _mm_add_pd(F, _mm_add_pd(G , _mm_mul_pd(H,two)));
- vgb = _mm_mul_pd(Y, qq);
- fijGB = _mm_mul_pd(F, _mm_mul_pd(qq,gbscale));
-
- dvdatmp = _mm_mul_pd(_mm_add_pd(vgb, _mm_mul_pd(fijGB,r)) , minushalf);
-
- vgbtot = _mm_add_pd(vgbtot, vgb);
-
- dvdasum = _mm_add_pd(dvdasum, dvdatmp);
- dvdatmp = _mm_mul_pd(dvdatmp, _mm_mul_pd(isaj,isaj));
-
- GMX_MM_INCREMENT_2VALUES_PD(dvda+jnrA,dvda+jnrB,dvdatmp);
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1)));
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1))+2);
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_pd(G,eps);
+ H = _mm_mul_pd(H, _mm_mul_pd(eps,eps) );
+ F = _mm_add_pd(F, _mm_add_pd( G , H ) );
+ Y = _mm_add_pd(Y, _mm_mul_pd(F, eps));
+ F = _mm_add_pd(F, _mm_add_pd(G , _mm_mul_pd(H,two)));
+ vgb = _mm_mul_pd(Y, qq);
+ fijGB = _mm_mul_pd(F, _mm_mul_pd(qq,gbscale));
+
+ dvdatmp = _mm_mul_pd(_mm_add_pd(vgb, _mm_mul_pd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb);
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp);
+ dvdatmp = _mm_mul_pd(dvdatmp, _mm_mul_pd(isaj,isaj));
+
+ GMX_MM_INCREMENT_2VALUES_PD(dvda+jnrA,dvda+jnrB,dvdatmp);
- /* Calculate VDW table index */
+ /* Calculate VDW table index */
rtab = _mm_mul_pd(r,tabscale);
n0 = _mm_cvttpd_epi32(rtab);
eps = _mm_sub_pd(rtab,_mm_cvtepi32_pd(n0));
eps2 = _mm_mul_pd(eps,eps);
nnn = _mm_slli_epi32(n0,3);
- /* Dispersion */
- Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1)));
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1))+2);
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_pd(G,eps);
+ /* Dispersion */
+ Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1)));
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1))+2);
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_pd(G,eps);
H = _mm_mul_pd(H,eps2);
Fp = _mm_add_pd(F,G);
Fp = _mm_add_pd(Fp,H);
vvdw6 = _mm_mul_pd(c6,VV);
fijD = _mm_mul_pd(c6,FF);
-
- /* Dispersion */
- Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+4);
- F = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1))+4);
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+6);
- H = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1))+6);
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_pd(G,eps);
+
+ /* Dispersion */
+ Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+4);
+ F = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1))+4);
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+6);
+ H = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1))+6);
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_pd(G,eps);
H = _mm_mul_pd(H,eps2);
Fp = _mm_add_pd(F,G);
Fp = _mm_add_pd(Fp,H);
vvdwtmp = _mm_add_pd(vvdw12,vvdw6);
vvdwtot = _mm_add_pd(vvdwtot,vvdwtmp);
-
+
xmm1 = _mm_add_pd(fijD,fijR);
xmm1 = _mm_mul_pd(xmm1,tabscale);
xmm1 = _mm_add_pd(xmm1,fijGB);
xmm1 = _mm_sub_pd(xmm1,fscal);
fscal = _mm_mul_pd(xmm1,neg);
fscal = _mm_mul_pd(fscal,rinv);
-
- /***********************************/
+
+ /***********************************/
/* INTERACTION SECTION ENDS HERE */
/***********************************/
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx);
- ty = _mm_mul_pd(fscal,dy);
- tz = _mm_mul_pd(fscal,dz);
-
- /* Increment i atom force */
- fix = _mm_add_pd(fix,tx);
- fiy = _mm_add_pd(fiy,ty);
- fiz = _mm_add_pd(fiz,tz);
-
- /* Store j forces back */
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_pd(fscal,dx);
+ ty = _mm_mul_pd(fscal,dy);
+ tz = _mm_mul_pd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_pd(fix,tx);
+ fiy = _mm_add_pd(fiy,ty);
+ fiz = _mm_add_pd(fiz,tz);
+
+ /* Store j forces back */
GMX_MM_DECREMENT_1RVEC_2POINTERS_PD(faction+j3A,faction+j3B,tx,ty,tz);
}
{
jnrA = jjnr[k];
j3A = jnrA * 3;
-
- GMX_MM_LOAD_1RVEC_1POINTER_PD(pos+j3A,jx,jy,jz);
-
+
+ GMX_MM_LOAD_1RVEC_1POINTER_PD(pos+j3A,jx,jy,jz);
+
dx = _mm_sub_sd(ix,jx);
dy = _mm_sub_sd(iy,jy);
dz = _mm_sub_sd(iz,jz);
- rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
-
- rinv = gmx_mm_invsqrt_pd(rsq);
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
rinvsq = _mm_mul_sd(rinv,rinv);
-
- /***********************************/
+
+ /* These reason for zeroing these variables here is for fixing bug 585
+ * What happens is that __m128d _mm_add_sd(a,b) gives back r0=a[0]+b[0],
+ * and r1=0, but it should be r1=a[1].
+ * This might be a compiler issue (tested with gcc-4.1.3 and -O3).
+ * To work around it, we zero these variables and use _mm_add_pd (**) instead
+ * Note that the only variables that get affected are the energies since
+ * the total sum needs to be correct
+ */
+ vgb = _mm_setzero_pd();
+ vcoul = _mm_setzero_pd();
+ dvdatmp = _mm_setzero_pd();
+ vvdw6 = _mm_setzero_pd();
+ vvdw12 = _mm_setzero_pd();
+
+ /***********************************/
/* INTERACTION SECTION STARTS HERE */
/***********************************/
GMX_MM_LOAD_1VALUE_PD(charge+jnrA,jq);
GMX_MM_LOAD_1VALUE_PD(invsqrta+jnrA,isaj);
- /* Lennard-Jones */
- tjA = nti+2*type[jnrA];
-
- GMX_MM_LOAD_1PAIR_PD(vdwparam+tjA,c6,c12);
+ /* Lennard-Jones */
+ tjA = nti+2*type[jnrA];
+
+ GMX_MM_LOAD_1PAIR_PD(vdwparam+tjA,c6,c12);
isaprod = _mm_mul_sd(isai,isaj);
- qq = _mm_mul_sd(iq,jq);
+ qq = _mm_mul_sd(jq,iq);
vcoul = _mm_mul_sd(qq,rinv);
fscal = _mm_mul_sd(vcoul,rinv);
- vctot = _mm_add_sd(vctot,vcoul);
-
- /* Polarization interaction */
+ vctot = _mm_add_pd(vctot,vcoul); /* (**) */
+
+ /* Polarization interaction */
qq = _mm_mul_sd(qq,_mm_mul_sd(isaprod,gbfactor));
gbscale = _mm_mul_sd(isaprod,gbtabscale);
-
+
/* Calculate GB table index */
r = _mm_mul_sd(rsq,rinv);
rtab = _mm_mul_sd(r,gbscale);
eps = _mm_sub_sd(rtab,_mm_cvtepi32_pd(n0));
nnn = _mm_slli_epi32(n0,2);
- /* the tables are 16-byte aligned, so we can use _mm_load_pd */
- Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_sd(G,eps);
- H = _mm_mul_sd(H, _mm_mul_sd(eps,eps) );
- F = _mm_add_sd(F, _mm_add_sd( G , H ) );
- Y = _mm_add_sd(Y, _mm_mul_sd(F, eps));
- F = _mm_add_sd(F, _mm_add_sd(G , _mm_mul_sd(H,two)));
- vgb = _mm_mul_sd(Y, qq);
- fijGB = _mm_mul_sd(F, _mm_mul_sd(qq,gbscale));
-
- dvdatmp = _mm_mul_sd(_mm_add_sd(vgb, _mm_mul_sd(fijGB,r)) , minushalf);
-
- vgbtot = _mm_add_sd(vgbtot, vgb);
-
- dvdasum = _mm_add_sd(dvdasum, dvdatmp);
- dvdatmp = _mm_mul_sd(dvdatmp, _mm_mul_sd(isaj,isaj));
-
- GMX_MM_INCREMENT_1VALUE_PD(dvda+jnrA,dvdatmp);
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_sd(G,eps);
+ H = _mm_mul_sd(H, _mm_mul_sd(eps,eps) );
+ F = _mm_add_sd(F, _mm_add_sd( G , H ) );
+ Y = _mm_add_sd(Y, _mm_mul_sd(F, eps));
+ F = _mm_add_sd(F, _mm_add_sd(G , _mm_mul_sd(H,two)));
+ vgb = _mm_mul_sd(Y, qq);
+ fijGB = _mm_mul_sd(F, _mm_mul_sd(qq,gbscale));
+
+ dvdatmp = _mm_mul_sd(_mm_add_sd(vgb, _mm_mul_sd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb); /* (**) */
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp); /* (**) */
+ dvdatmp = _mm_mul_sd(dvdatmp, _mm_mul_sd(isaj,isaj));
+
+ GMX_MM_INCREMENT_1VALUE_PD(dvda+jnrA,dvdatmp);
- /* Calculate VDW table index */
+ /* Calculate VDW table index */
rtab = _mm_mul_sd(r,tabscale);
n0 = _mm_cvttpd_epi32(rtab);
eps = _mm_sub_sd(rtab,_mm_cvtepi32_pd(n0));
eps2 = _mm_mul_sd(eps,eps);
nnn = _mm_slli_epi32(n0,3);
- /* Dispersion */
- Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_sd(G,eps);
+ /* Dispersion */
+ Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_sd(G,eps);
H = _mm_mul_sd(H,eps2);
Fp = _mm_add_sd(F,G);
Fp = _mm_add_sd(Fp,H);
vvdw6 = _mm_mul_sd(c6,VV);
fijD = _mm_mul_sd(c6,FF);
-
- /* Dispersion */
- Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+4);
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+6);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_sd(G,eps);
+
+ /* Dispersion */
+ Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+4);
+ F = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+6);
+ H = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_sd(G,eps);
H = _mm_mul_sd(H,eps2);
Fp = _mm_add_sd(F,G);
Fp = _mm_add_sd(Fp,H);
fijR = _mm_mul_sd(c12,FF);
vvdwtmp = _mm_add_sd(vvdw12,vvdw6);
- vvdwtot = _mm_add_sd(vvdwtot,vvdwtmp);
+ vvdwtot = _mm_add_pd(vvdwtot,vvdwtmp); /* (**) */
xmm1 = _mm_add_sd(fijD,fijR);
xmm1 = _mm_mul_sd(xmm1,tabscale);
fscal = _mm_mul_sd(xmm1,neg);
fscal = _mm_mul_sd(fscal,rinv);
- /***********************************/
+ /***********************************/
/* INTERACTION SECTION ENDS HERE */
/***********************************/
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_sd(fscal,dx);
- ty = _mm_mul_sd(fscal,dy);
- tz = _mm_mul_sd(fscal,dz);
-
- /* Increment i atom force */
- fix = _mm_add_sd(fix,tx);
- fiy = _mm_add_sd(fiy,ty);
- fiz = _mm_add_sd(fiz,tz);
-
- /* Store j forces back */
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_sd(fscal,dx);
+ ty = _mm_mul_sd(fscal,dy);
+ tz = _mm_mul_sd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_sd(fix,tx);
+ fiy = _mm_add_sd(fiy,ty);
+ fiz = _mm_add_sd(fiz,tz);
+
+ /* Store j forces back */
GMX_MM_DECREMENT_1RVEC_1POINTER_PD(faction+j3A,tx,ty,tz);
}
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai,isai));
- gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,faction+ii3,fshift+is3);
-
- ggid = gid[n];
-
- gmx_mm_update_2pot_pd(vctot,vc+ggid,vvdwtot,vvdw+ggid);
- gmx_mm_update_2pot_pd(vgbtot,gpol+ggid,dvdasum,dvda+ii);
- }
+ dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai,isai));
+ gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,faction+ii3,fshift+is3);
+ ggid = gid[n];
+
+ gmx_mm_update_1pot_pd(vctot,vc+ggid);
+ gmx_mm_update_1pot_pd(vgbtot,gpol+ggid);
+ gmx_mm_update_1pot_pd(dvdasum,dvda+ii);
+ gmx_mm_update_1pot_pd(vvdwtot,vvdw+ggid);
+
+ }
+
*outeriter = nri;
- *inneriter = nj1;
+ *inneriter = nj1;
}
pmask1 = prologue_mask[i+1];
emask0 = epilogue_mask[i];
emask1 = epilogue_mask[i+1];
- imask_SSE0 = _mm_load1_pd((double *)(imask+i));
+ imask_SSE0 = _mm_load1_pd((double *)(imask+2*i));
imask_SSE1 = _mm_load1_pd((double *)(imask+2*i+2));
for(j=nj0; j<nj1; j+=UNROLLJ)
#include<math.h>
#include<vec.h>
-
#include <xmmintrin.h>
#include <emmintrin.h>
#include "../nb_kerneltype.h"
-
void nb_kernel400_sse2_double(int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- double * shiftvec,
- double * fshift,
- int * gid,
- double * pos,
- double * faction,
- double * charge,
- double * p_facel,
- double * p_krf,
- double * p_crf,
- double * Vc,
- int * type,
- int * p_ntype,
- double * vdwparam,
- double * Vvdw,
- double * p_tabscale,
- double * VFtab,
- double * invsqrta,
- double * dvda,
- double * p_gbtabscale,
- double * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- double * work)
+ int * iinr,
+ int * jindex,
+ int * jjnr,
+ int * shift,
+ double * shiftvec,
+ double * fshift,
+ int * gid,
+ double * pos,
+ double * faction,
+ double * charge,
+ double * p_facel,
+ double * p_krf,
+ double * p_crf,
+ double * vc,
+ int * type,
+ int * p_ntype,
+ double * vdwparam,
+ double * vvdw,
+ double * p_tabscale,
+ double * VFtab,
+ double * invsqrta,
+ double * dvda,
+ double * p_gbtabscale,
+ double * GBtab,
+ int * p_nthreads,
+ int * count,
+ void * mtx,
+ int * outeriter,
+ int * inneriter,
+ double * work)
{
- int nri,ntype,nthreads,offset;
- int n,ii,is3,ii3,k,nj0,nj1,jnr1,jnr2,j13,j23,ggid;
- double facel,krf,crf,tabscl,gbtabscl,vct,vgbt;
- double shX,shY,shZ,isai_d,dva;
+ int nri,nthreads;
+ int n,ii,is3,ii3,k,nj0,nj1,ggid;
+ double shX,shY,shZ;
+ int jnrA,jnrB;
+ int j3A,j3B;
gmx_gbdata_t *gbdata;
- float * gpol;
-
- __m128d ix,iy,iz,jx,jy,jz;
- __m128d dx,dy,dz,t1,t2,t3;
- __m128d fix,fiy,fiz,rsq11,rinv,r,fscal,rt,eps,eps2;
- __m128d q,iq,qq,isai,isaj,isaprod,vcoul,gbscale,dvdai,dvdaj;
- __m128d Y,F,G,H,Fp,VV,FF,vgb,fijC,dvdatmp,dvdasum,vctot,vgbtot,n0d;
- __m128d xmm0,xmm1,xmm2,xmm3,xmm4,xmm5,xmm6,xmm7,xmm8;
- __m128d fac,tabscale,gbtabscale;
- __m128i n0,nnn;
+ double * gpol;
+
+ __m128d iq,qq,jq,isai;
+ __m128d ix,iy,iz;
+ __m128d jx,jy,jz;
+ __m128d dx,dy,dz;
+ __m128d vctot,vgbtot,dvdasum,gbfactor;
+ __m128d fix,fiy,fiz,tx,ty,tz,rsq;
+ __m128d rinv,isaj,isaprod;
+ __m128d vcoul,fscal,gbscale;
+ __m128d rinvsq,r,rtab;
+ __m128d eps,Y,F,G,H;
+ __m128d vgb,fijGB,dvdatmp;
+ __m128d facel,gbtabscale,dvdaj;
+ __m128i n0, nnn;
- const __m128d neg = {-1.0,-1.0};
- const __m128d zero = {0.0,0.0};
- const __m128d half = {0.5,0.5};
- const __m128d two = {2.0,2.0};
- const __m128d three = {3.0,3.0};
+ const __m128d neg = _mm_set1_pd(-1.0);
+ const __m128d zero = _mm_set1_pd(0.0);
+ const __m128d minushalf = _mm_set1_pd(-0.5);
+ const __m128d two = _mm_set1_pd(2.0);
gbdata = (gmx_gbdata_t *)work;
gpol = gbdata->gpol;
-
+
nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = (*p_facel) * ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent));
- krf = *p_krf;
- crf = *p_crf;
- tabscl = *p_tabscale;
- gbtabscl = *p_gbtabscale;
- nj1 = 0;
-
- /* Splat variables */
- fac = _mm_load1_pd(&facel);
- tabscale = _mm_load1_pd(&tabscl);
- gbtabscale = _mm_load1_pd(&gbtabscl);
-
- /* Keep compiler happy */
- dvdatmp = _mm_setzero_pd();
- vgb = _mm_setzero_pd();
- dvdaj = _mm_setzero_pd();
- isaj = _mm_setzero_pd();
- vcoul = _mm_setzero_pd();
- t1 = _mm_setzero_pd();
- t2 = _mm_setzero_pd();
- t3 = _mm_setzero_pd();
-
- jnr1=jnr2=0;
- j13=j23=0;
+
+ gbfactor = _mm_set1_pd( - ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent)));
+ gbtabscale = _mm_load1_pd(p_gbtabscale);
+ facel = _mm_load1_pd(p_facel);
+
+ nj1 = 0;
+ jnrA = jnrB = 0;
+ j3A = j3B = 0;
+ jx = _mm_setzero_pd();
+ jy = _mm_setzero_pd();
+ jz = _mm_setzero_pd();
for(n=0;n<nri;n++)
{
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- nj0 = jindex[n];
- nj1 = jindex[n+1];
- offset = (nj1-nj0)%2;
+ is3 = 3*shift[n];
+ shX = shiftvec[is3];
+ shY = shiftvec[is3+1];
+ shZ = shiftvec[is3+2];
+ nj0 = jindex[n];
+ nj1 = jindex[n+1];
+ ii = iinr[n];
+ ii3 = 3*ii;
- ii = iinr[n];
- ii3 = ii*3;
-
- ix = _mm_set1_pd(shX+pos[ii3+0]);
- iy = _mm_set1_pd(shX+pos[ii3+1]);
- iz = _mm_set1_pd(shX+pos[ii3+2]);
- q = _mm_set1_pd(charge[ii]);
-
- iq = _mm_mul_pd(fac,q);
- isai_d = invsqrta[ii];
- isai = _mm_load1_pd(&isai_d);
-
- fix = _mm_setzero_pd();
- fiy = _mm_setzero_pd();
- fiz = _mm_setzero_pd();
- dvdasum = _mm_setzero_pd();
- vctot = _mm_setzero_pd();
- vgbtot = _mm_setzero_pd();
-
- for(k=nj0;k<nj1-offset; k+=2)
+ ix = _mm_set1_pd(shX+pos[ii3+0]);
+ iy = _mm_set1_pd(shY+pos[ii3+1]);
+ iz = _mm_set1_pd(shZ+pos[ii3+2]);
+
+ iq = _mm_load1_pd(charge+ii);
+ iq = _mm_mul_pd(iq,facel);
+
+ isai = _mm_load1_pd(invsqrta+ii);
+
+ vctot = _mm_setzero_pd();
+ vgbtot = _mm_setzero_pd();
+ dvdasum = _mm_setzero_pd();
+ fix = _mm_setzero_pd();
+ fiy = _mm_setzero_pd();
+ fiz = _mm_setzero_pd();
+
+ for(k=nj0;k<nj1-1; k+=2)
{
- jnr1 = jjnr[k];
- jnr2 = jjnr[k+1];
-
- j13 = jnr1 * 3;
- j23 = jnr2 * 3;
-
- /* Load coordinates */
- xmm1 = _mm_loadu_pd(pos+j13); /* x1 y1 */
- xmm2 = _mm_loadu_pd(pos+j23); /* x2 y2 */
-
- xmm5 = _mm_load_sd(pos+j13+2); /* z1 - */
- xmm6 = _mm_load_sd(pos+j23+2); /* z2 - */
-
- /* transpose */
- jx = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0));
- jy = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1));
- jz = _mm_shuffle_pd(xmm5,xmm6,_MM_SHUFFLE2(0,0));
-
- /* distances */
- dx = _mm_sub_pd(ix,jx);
- dy = _mm_sub_pd(iy,jy);
- dz = _mm_sub_pd(iz,jz);
-
- rsq11 = _mm_add_pd( _mm_add_pd( _mm_mul_pd(dx,dx) , _mm_mul_pd(dy,dy) ) , _mm_mul_pd(dz,dz) );
- rinv = gmx_mm_invsqrt_pd(rsq11);
-
- /* Load invsqrta */
- isaj = _mm_loadl_pd(isaj,invsqrta+jnr1);
- isaj = _mm_loadh_pd(isaj,invsqrta+jnr2);
- isaprod = _mm_mul_pd(isai,isaj);
-
- /* Load charges */
- q = _mm_loadl_pd(q,charge+jnr1);
- q = _mm_loadh_pd(q,charge+jnr2);
- qq = _mm_mul_pd(iq,q);
-
- vcoul = _mm_mul_pd(qq,rinv);
- fscal = _mm_mul_pd(vcoul,rinv);
- qq = _mm_mul_pd(isaprod,qq);
- qq = _mm_mul_pd(qq,neg);
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Load dvdaj */
- dvdaj = _mm_loadl_pd(dvdaj, dvda+jnr1);
- dvdaj = _mm_loadh_pd(dvdaj, dvda+jnr2);
-
- r = _mm_mul_pd(rsq11,rinv);
- rt = _mm_mul_pd(r,gbscale);
- n0 = _mm_cvttpd_epi32(rt);
- n0d = _mm_cvtepi32_pd(n0);
- eps = _mm_sub_pd(rt,n0d);
- eps2 = _mm_mul_pd(eps,eps);
-
- nnn = _mm_slli_epi64(n0,2);
-
- xmm1 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,0))); /* Y1 F1 */
- xmm2 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,1))); /* Y2 F2 */
- xmm3 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,0))+2); /* G1 H1 */
- xmm4 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,1))+2); /* G2 H2 */
-
- Y = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0)); /* Y1 Y2 */
- F = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1)); /* F1 F2 */
- G = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(0,0)); /* G1 G2 */
- H = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(1,1)); /* H1 H2 */
-
- G = _mm_mul_pd(G,eps);
- H = _mm_mul_pd(H,eps2);
- Fp = _mm_add_pd(F,G);
- Fp = _mm_add_pd(Fp,H);
- VV = _mm_mul_pd(Fp,eps);
- VV = _mm_add_pd(Y,VV);
- H = _mm_mul_pd(two,H);
- FF = _mm_add_pd(Fp,G);
- FF = _mm_add_pd(FF,H);
- vgb = _mm_mul_pd(qq,VV);
- fijC = _mm_mul_pd(qq,FF);
- fijC = _mm_mul_pd(fijC,gbscale);
-
- dvdatmp = _mm_mul_pd(fijC,r);
- dvdatmp = _mm_add_pd(vgb,dvdatmp);
- dvdatmp = _mm_mul_pd(dvdatmp,neg);
- dvdatmp = _mm_mul_pd(dvdatmp,half);
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
-
- xmm1 = _mm_mul_pd(dvdatmp,isaj);
- xmm1 = _mm_mul_pd(xmm1,isaj);
- dvdaj = _mm_add_pd(dvdaj,xmm1);
-
- /* store dvda */
- _mm_storel_pd(dvda+jnr1,dvdaj);
- _mm_storeh_pd(dvda+jnr2,dvdaj);
-
- vctot = _mm_add_pd(vctot,vcoul);
- vgbtot = _mm_add_pd(vgbtot,vgb);
-
- fscal = _mm_sub_pd(fijC,fscal);
- fscal = _mm_mul_pd(fscal,neg);
- fscal = _mm_mul_pd(fscal,rinv);
-
- /* calculate partial force terms */
- t1 = _mm_mul_pd(fscal,dx);
- t2 = _mm_mul_pd(fscal,dy);
- t3 = _mm_mul_pd(fscal,dz);
-
- /* update the i force */
- fix = _mm_add_pd(fix,t1);
- fiy = _mm_add_pd(fiy,t2);
- fiz = _mm_add_pd(fiz,t3);
-
- /* accumulate forces from memory */
- xmm1 = _mm_loadu_pd(faction+j13); /* fx1 fy1 */
- xmm2 = _mm_loadu_pd(faction+j23); /* fx2 fy2 */
-
- xmm5 = _mm_load1_pd(faction+j13+2); /* fz1 fz1 */
- xmm6 = _mm_load1_pd(faction+j23+2); /* fz2 fz2 */
-
- /* transpose */
- xmm7 = _mm_shuffle_pd(xmm5,xmm6,_MM_SHUFFLE2(0,0)); /* fz1 fz2 */
- xmm5 = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0)); /* fx1 fx2 */
- xmm6 = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1)); /* fy1 fy2 */
-
- /* subtract partial forces */
- xmm5 = _mm_sub_pd(xmm5,t1);
- xmm6 = _mm_sub_pd(xmm6,t2);
- xmm7 = _mm_sub_pd(xmm7,t3);
-
- xmm1 = _mm_shuffle_pd(xmm5,xmm6,_MM_SHUFFLE2(0,0)); /* fx1 fy1 */
- xmm2 = _mm_shuffle_pd(xmm5,xmm6,_MM_SHUFFLE2(1,1)); /* fy1 fy2 */
-
- /* store fx and fy */
- _mm_storeu_pd(faction+j13,xmm1);
- _mm_storeu_pd(faction+j23,xmm2);
-
- /* .. then fz */
- _mm_storel_pd(faction+j13+2,xmm7);
- _mm_storeh_pd(faction+j23+2,xmm7);
+ jnrA = jjnr[k];
+ jnrB = jjnr[k+1];
+
+ j3A = jnrA * 3;
+ j3B = jnrB * 3;
+
+ GMX_MM_LOAD_1RVEC_2POINTERS_PD(pos+j3A,pos+j3B,jx,jy,jz);
+
+ dx = _mm_sub_pd(ix,jx);
+ dy = _mm_sub_pd(iy,jy);
+ dz = _mm_sub_pd(iz,jz);
+
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
+ rinvsq = _mm_mul_pd(rinv,rinv);
+
+ /***********************************/
+ /* INTERACTION SECTION STARTS HERE */
+ /***********************************/
+ GMX_MM_LOAD_2VALUES_PD(charge+jnrA,charge+jnrB,jq);
+ GMX_MM_LOAD_2VALUES_PD(invsqrta+jnrA,invsqrta+jnrB,isaj);
+
+ isaprod = _mm_mul_pd(isai,isaj);
+ qq = _mm_mul_pd(iq,jq);
+ vcoul = _mm_mul_pd(qq,rinv);
+ fscal = _mm_mul_pd(vcoul,rinv);
+ vctot = _mm_add_pd(vctot,vcoul);
+
+ /* Polarization interaction */
+ qq = _mm_mul_pd(qq,_mm_mul_pd(isaprod,gbfactor));
+ gbscale = _mm_mul_pd(isaprod,gbtabscale);
+
+ /* Calculate GB table index */
+ r = _mm_mul_pd(rsq,rinv);
+ rtab = _mm_mul_pd(r,gbscale);
+
+ n0 = _mm_cvttpd_epi32(rtab);
+ eps = _mm_sub_pd(rtab,_mm_cvtepi32_pd(n0));
+ nnn = _mm_slli_epi32(n0,2);
+
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1)));
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1))+2);
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_pd(G,eps);
+ H = _mm_mul_pd(H, _mm_mul_pd(eps,eps) );
+ F = _mm_add_pd(F, _mm_add_pd( G , H ) );
+ Y = _mm_add_pd(Y, _mm_mul_pd(F, eps));
+ F = _mm_add_pd(F, _mm_add_pd(G , _mm_mul_pd(H,two)));
+ vgb = _mm_mul_pd(Y, qq);
+ fijGB = _mm_mul_pd(F, _mm_mul_pd(qq,gbscale));
+
+ dvdatmp = _mm_mul_pd(_mm_add_pd(vgb, _mm_mul_pd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb);
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp);
+ dvdatmp = _mm_mul_pd(dvdatmp, _mm_mul_pd(isaj,isaj));
+
+ GMX_MM_INCREMENT_2VALUES_PD(dvda+jnrA,dvda+jnrB,dvdatmp);
+
+ fscal = _mm_mul_pd( _mm_sub_pd( fscal, fijGB),rinv );
+
+ /***********************************/
+ /* INTERACTION SECTION ENDS HERE */
+ /***********************************/
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_pd(fscal,dx);
+ ty = _mm_mul_pd(fscal,dy);
+ tz = _mm_mul_pd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_pd(fix,tx);
+ fiy = _mm_add_pd(fiy,ty);
+ fiz = _mm_add_pd(fiz,tz);
+
+ /* Store j forces back */
+ GMX_MM_DECREMENT_1RVEC_2POINTERS_PD(faction+j3A,faction+j3B,tx,ty,tz);
}
/* In double precision, offset can only be either 0 or 1 */
- if(offset!=0)
+ if(k<nj1)
{
- jnr1 = jjnr[k];
- j13 = jnr1*3;
-
- jx = _mm_load_sd(pos+j13);
- jy = _mm_load_sd(pos+j13+1);
- jz = _mm_load_sd(pos+j13+2);
-
- isaj = _mm_load_sd(invsqrta+jnr1);
- isaprod = _mm_mul_sd(isai,isaj);
- dvdaj = _mm_load_sd(dvda+jnr1);
- q = _mm_load_sd(charge+jnr1);
- qq = _mm_mul_sd(iq,q);
-
- dx = _mm_sub_sd(ix,jx);
- dy = _mm_sub_sd(iy,jy);
- dz = _mm_sub_sd(iz,jz);
-
- rsq11 = _mm_add_pd( _mm_add_pd( _mm_mul_pd(dx,dx) , _mm_mul_pd(dy,dy) ) , _mm_mul_pd(dz,dz) );
- rinv = gmx_mm_invsqrt_pd(rsq11);
-
- vcoul = _mm_mul_sd(qq,rinv);
- fscal = _mm_mul_sd(vcoul,rinv);
- qq = _mm_mul_sd(isaprod,qq);
- qq = _mm_mul_sd(qq,neg);
- gbscale = _mm_mul_sd(isaprod,gbtabscale);
-
- r = _mm_mul_sd(rsq11,rinv);
- rt = _mm_mul_sd(r,gbscale);
- n0 = _mm_cvttpd_epi32(rt);
- n0d = _mm_cvtepi32_pd(n0);
- eps = _mm_sub_sd(rt,n0d);
- eps2 = _mm_mul_sd(eps,eps);
-
- nnn = _mm_slli_epi64(n0,2);
-
- xmm1 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,0)));
- xmm2 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,1)));
- xmm3 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,0))+2);
- xmm4 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,1))+2);
-
- Y = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0));
- F = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1));
- G = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(0,0));
- H = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(1,1));
-
- G = _mm_mul_sd(G,eps);
- H = _mm_mul_sd(H,eps2);
- Fp = _mm_add_sd(F,G);
- Fp = _mm_add_sd(Fp,H);
- VV = _mm_mul_sd(Fp,eps);
- VV = _mm_add_sd(Y,VV);
- H = _mm_mul_sd(two,H);
- FF = _mm_add_sd(Fp,G);
- FF = _mm_add_sd(FF,H);
- vgb = _mm_mul_sd(qq,VV);
- fijC = _mm_mul_sd(qq,FF);
- fijC = _mm_mul_sd(fijC,gbscale);
-
- dvdatmp = _mm_mul_sd(fijC,r);
- dvdatmp = _mm_add_sd(vgb,dvdatmp);
- dvdatmp = _mm_mul_sd(dvdatmp,neg);
- dvdatmp = _mm_mul_sd(dvdatmp,half);
- dvdasum = _mm_add_sd(dvdasum,dvdatmp);
-
- xmm1 = _mm_mul_sd(dvdatmp,isaj);
- xmm1 = _mm_mul_sd(xmm1,isaj);
- dvdaj = _mm_add_sd(dvdaj,xmm1);
-
- /* store dvda */
- _mm_storel_pd(dvda+jnr1,dvdaj);
-
- vctot = _mm_add_sd(vctot,vcoul);
- vgbtot = _mm_add_sd(vgbtot,vgb);
-
- fscal = _mm_sub_sd(fijC,fscal);
- fscal = _mm_mul_sd(fscal,neg);
- fscal = _mm_mul_sd(fscal,rinv);
-
- /* calculate partial force terms */
- t1 = _mm_mul_sd(fscal,dx);
- t2 = _mm_mul_sd(fscal,dy);
- t3 = _mm_mul_sd(fscal,dz);
-
- /* update the i force */
- fix = _mm_add_sd(fix,t1);
- fiy = _mm_add_sd(fiy,t2);
- fiz = _mm_add_sd(fiz,t3);
-
- /* accumulate forces from memory */
- xmm5 = _mm_load_sd(faction+j13); /* fx */
- xmm6 = _mm_load_sd(faction+j13+1); /* fy */
- xmm7 = _mm_load_sd(faction+j13+2); /* fz */
-
- /* subtract partial forces */
- xmm5 = _mm_sub_sd(xmm5,t1);
- xmm6 = _mm_sub_sd(xmm6,t2);
- xmm7 = _mm_sub_sd(xmm7,t3);
-
- /* store forces */
- _mm_store_sd(faction+j13,xmm5);
- _mm_store_sd(faction+j13+1,xmm6);
- _mm_store_sd(faction+j13+2,xmm7);
+ jnrA = jjnr[k];
+ j3A = jnrA * 3;
+
+ GMX_MM_LOAD_1RVEC_1POINTER_PD(pos+j3A,jx,jy,jz);
+
+ dx = _mm_sub_sd(ix,jx);
+ dy = _mm_sub_sd(iy,jy);
+ dz = _mm_sub_sd(iz,jz);
+
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
+ rinvsq = _mm_mul_sd(rinv,rinv);
+
+ /* These reason for zeroing these variables here is for fixing bug 585
+ * What happens is that __m128d _mm_add_sd(a,b) gives back r0=a[0]+b[0],
+ * and r1=0, but it should be r1=a[1].
+ * This might be a compiler issue (tested with gcc-4.1.3 and -O3).
+ * To work around it, we zero these variables and use _mm_add_pd (**) instead
+ * Note that the only variables that get affected are the energies since
+ * the total sum needs to be correct
+ */
+ vgb = _mm_setzero_pd();
+ vcoul = _mm_setzero_pd();
+ dvdatmp = _mm_setzero_pd();
+
+ /***********************************/
+ /* INTERACTION SECTION STARTS HERE */
+ /***********************************/
+ GMX_MM_LOAD_1VALUE_PD(charge+jnrA,jq);
+ GMX_MM_LOAD_1VALUE_PD(invsqrta+jnrA,isaj);
+
+ isaprod = _mm_mul_sd(isai,isaj);
+ qq = _mm_mul_sd(jq,iq);
+ vcoul = _mm_mul_sd(qq,rinv);
+ fscal = _mm_mul_sd(vcoul,rinv);
+ vctot = _mm_add_pd(vctot,vcoul); /* (**) */
+
+ /* Polarization interaction */
+ qq = _mm_mul_sd(qq,_mm_mul_sd(isaprod,gbfactor));
+ gbscale = _mm_mul_sd(isaprod,gbtabscale);
+
+ /* Calculate GB table index */
+ r = _mm_mul_sd(rsq,rinv);
+ rtab = _mm_mul_sd(r,gbscale);
+
+ n0 = _mm_cvttpd_epi32(rtab);
+ eps = _mm_sub_sd(rtab,_mm_cvtepi32_pd(n0));
+ nnn = _mm_slli_epi32(n0,2);
+
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_sd(G,eps);
+ H = _mm_mul_sd(H, _mm_mul_sd(eps,eps) );
+ F = _mm_add_sd(F, _mm_add_sd( G , H ) );
+ Y = _mm_add_sd(Y, _mm_mul_sd(F, eps));
+ F = _mm_add_sd(F, _mm_add_sd(G , _mm_mul_sd(H,two)));
+ vgb = _mm_mul_sd(Y, qq);
+ fijGB = _mm_mul_sd(F, _mm_mul_sd(qq,gbscale));
+
+ dvdatmp = _mm_mul_sd(_mm_add_sd(vgb, _mm_mul_sd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb); /* (**) */
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp); /* (**) */
+ dvdatmp = _mm_mul_sd(dvdatmp, _mm_mul_sd(isaj,isaj));
+
+ GMX_MM_INCREMENT_1VALUE_PD(dvda+jnrA,dvdatmp);
+
+ fscal = _mm_mul_sd( _mm_sub_sd( fscal, fijGB),rinv );
+
+ /***********************************/
+ /* INTERACTION SECTION ENDS HERE */
+ /***********************************/
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_sd(fscal,dx);
+ ty = _mm_mul_sd(fscal,dy);
+ tz = _mm_mul_sd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_sd(fix,tx);
+ fiy = _mm_add_sd(fiy,ty);
+ fiz = _mm_add_sd(fiz,tz);
+
+ /* Store j forces back */
+ GMX_MM_DECREMENT_1RVEC_1POINTER_PD(faction+j3A,tx,ty,tz);
}
- /* fix/fiy/fiz now contain four partial terms, that all should be
- * added to the i particle forces
- */
- t1 = _mm_unpacklo_pd(t1,fix);
- t2 = _mm_unpacklo_pd(t2,fiy);
- t3 = _mm_unpacklo_pd(t3,fiz);
-
- fix = _mm_add_pd(fix,t1);
- fiy = _mm_add_pd(fiy,t2);
- fiz = _mm_add_pd(fiz,t3);
-
- fix = _mm_shuffle_pd(fix,fix,_MM_SHUFFLE2(1,1));
- fiy = _mm_shuffle_pd(fiy,fiy,_MM_SHUFFLE2(1,1));
- fiz = _mm_shuffle_pd(fiz,fiz,_MM_SHUFFLE2(1,1));
-
- /* Load i forces from memory */
- xmm1 = _mm_load_sd(faction+ii3);
- xmm2 = _mm_load_sd(faction+ii3+1);
- xmm3 = _mm_load_sd(faction+ii3+2);
-
- /* Add to i force */
- fix = _mm_add_sd(fix,xmm1);
- fiy = _mm_add_sd(fiy,xmm2);
- fiz = _mm_add_sd(fiz,xmm3);
-
- /* store i forces to memory */
- _mm_store_sd(faction+ii3,fix);
- _mm_store_sd(faction+ii3+1,fiy);
- _mm_store_sd(faction+ii3+2,fiz);
-
- /* now do dvda */
- dvdatmp = _mm_unpacklo_pd(dvdatmp,dvdasum);
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- _mm_storeh_pd(&dva,dvdasum);
- dvda[ii] = dvda[ii] + dva*isai_d*isai_d;
-
- ggid = gid[n];
-
- /* Coulomb potential */
- vcoul = _mm_unpacklo_pd(vcoul,vctot);
- vctot = _mm_add_pd(vctot,vcoul);
- _mm_storeh_pd(&vct,vctot);
- Vc[ggid] = Vc[ggid] + vct;
-
- /* GB potential */
- vgb = _mm_unpacklo_pd(vgb,vgbtot);
- vgbtot = _mm_add_pd(vgbtot,vgb);
- _mm_storeh_pd(&vgbt,vgbtot);
- gpol[ggid] = gpol[ggid] + vgbt;
- }
-
- *outeriter = nri;
- *inneriter = nj1;
-}
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel400nf
- * Coulomb interaction: Generalized-Born
- * VdW interaction: Not calculated
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel400nf_sse2_double(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- double * shiftvec,
- double * fshift,
- int * gid,
- double * pos,
- double * faction,
- double * charge,
- double * p_facel,
- double * p_krf,
- double * p_crf,
- double * Vc,
- int * type,
- int * p_ntype,
- double * vdwparam,
- double * Vvdw,
- double * p_tabscale,
- double * VFtab,
- double * invsqrta,
- double * dvda,
- double * p_gbtabscale,
- double * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- double * work)
-{
- int nri,ntype,nthreads;
- double facel,krf,crf,tabscale,gbtabscale,vgb,fgb;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- double shX,shY,shZ;
- double iq;
- double qq,vcoul,vctot;
- double r,rt,eps,eps2;
- int n0,nnn;
- double Y,F,Geps,Heps2,Fp,VV;
- double isai,isaj,isaprod,gbscale;
- double ix1,iy1,iz1;
- double jx1,jy1,jz1;
- double dx11,dy11,dz11,rsq11,rinv11;
- const int fractshift = 12;
- const int fractmask = 8388607;
- const int expshift = 23;
- const int expmask = 2139095040;
- const int explsb = 8388608;
- double lu;
- int iexp,addr;
- union { unsigned int bval; double fval; } bitpattern,result;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
- gbtabscale = *p_gbtabscale;
- nj1 = 0;
+ dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai,isai));
+ gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,faction+ii3,fshift+is3);
- for(n=0; (n<nri); n++)
- {
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
- nj0 = jindex[n];
- nj1 = jindex[n+1];
- ii = iinr[n];
- ii3 = 3*ii;
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- iq = facel*charge[ii];
- isai = invsqrta[ii];
- vctot = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
- jnr = jjnr[k];
- j3 = 3*jnr;
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- bitpattern.fval = rsq11;
- iexp = (((bitpattern.bval)&expmask)>>expshift);
- addr = (((bitpattern.bval)&(fractmask|explsb))>>fractshift);
- result.bval = gmx_invsqrt_exptab[iexp] | gmx_invsqrt_fracttab[addr];
- lu = result.fval;
- rinv11 = (0.5*lu*(3.0-((rsq11*lu)*lu)));
- isaj = invsqrta[jnr];
- isaprod = isai*isaj;
- qq = iq*charge[jnr];
- vcoul = qq*rinv11;
- qq = isaprod*(-qq);
- gbscale = isaprod*gbtabscale;
- r = rsq11*rinv11;
- rt = r*gbscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
- Y = GBtab[nnn];
- F = GBtab[nnn+1];
- Geps = eps*GBtab[nnn+2];
- Heps2 = eps2*GBtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vgb = qq*VV;
- vctot = vctot + vcoul;
- }
-
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- }
+ ggid = gid[n];
- *outeriter = nri;
- *inneriter = nj1;
+ gmx_mm_update_1pot_pd(vctot,vc+ggid);
+ gmx_mm_update_1pot_pd(vgbtot,gpol+ggid);
+ gmx_mm_update_1pot_pd(dvdasum,dvda+ii);
+ }
+
+ *outeriter = nri;
+ *inneriter = nj1;
}
-
-
#include "../nb_kerneltype.h"
+
void nb_kernel410_sse2_double(int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- double * shiftvec,
- double * fshift,
- int * gid,
- double * pos,
- double * faction,
- double * charge,
- double * p_facel,
- double * p_krf,
- double * p_crf,
- double * Vc,
- int * type,
- int * p_ntype,
- double * vdwparam,
- double * Vvdw,
- double * p_tabscale,
- double * VFtab,
- double * invsqrta,
- double * dvda,
- double * p_gbtabscale,
- double * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- double * work)
+ int * iinr,
+ int * jindex,
+ int * jjnr,
+ int * shift,
+ double * shiftvec,
+ double * fshift,
+ int * gid,
+ double * pos,
+ double * faction,
+ double * charge,
+ double * p_facel,
+ double * p_krf,
+ double * p_crf,
+ double * vc,
+ int * type,
+ int * p_ntype,
+ double * vdwparam,
+ double * vvdw,
+ double * p_tabscale,
+ double * VFtab,
+ double * invsqrta,
+ double * dvda,
+ double * p_gbtabscale,
+ double * GBtab,
+ int * p_nthreads,
+ int * count,
+ void * mtx,
+ int * outeriter,
+ int * inneriter,
+ double * work)
{
- int nri,ntype,nthreads,offset,tj,tj2,nti;
- int n,ii,is3,ii3,k,nj0,nj1,jnr1,jnr2,j13,j23,ggid;
- double facel,krf,crf,tabscl,gbtabscl,vct,vdwt,nt1,nt2;
- double shX,shY,shZ,isai_d,dva,vgbt;
+ int nri,ntype,nthreads;
+ int n,ii,is3,ii3,k,nj0,nj1,ggid;
+ double shX,shY,shZ;
+ int offset,nti;
+ int jnrA,jnrB;
+ int j3A,j3B;
+ int tjA,tjB;
gmx_gbdata_t *gbdata;
- float * gpol;
-
- __m128d ix,iy,iz,jx,jy,jz;
- __m128d dx,dy,dz,t1,t2,t3;
- __m128d fix,fiy,fiz,rsq11,rinv,r,fscal,rt,eps,eps2;
- __m128d q,iq,qq,isai,isaj,isaprod,vcoul,gbscale,dvdai,dvdaj;
- __m128d Y,F,G,H,Fp,VV,FF,vgb,fijC,dvdatmp,dvdasum,vctot,vgbtot,n0d;
- __m128d xmm0,xmm1,xmm2,xmm3,xmm4,xmm5,xmm6,xmm7,xmm8;
- __m128d c6,c12,Vvdw6,Vvdw12,Vvdwtmp,Vvdwtot,rinvsq,rinvsix;
- __m128d fac,tabscale,gbtabscale;
- __m128i n0,nnn;
+ double * gpol;
+
+ __m128d iq,qq,jq,isai;
+ __m128d ix,iy,iz;
+ __m128d jx,jy,jz;
+ __m128d dx,dy,dz;
+ __m128d vctot,vvdwtot,vgbtot,dvdasum,gbfactor;
+ __m128d fix,fiy,fiz,tx,ty,tz,rsq;
+ __m128d rinv,isaj,isaprod;
+ __m128d vcoul,fscal,gbscale,c6,c12;
+ __m128d rinvsq,r,rtab;
+ __m128d eps,Y,F,G,H;
+ __m128d vgb,fijGB,dvdatmp;
+ __m128d rinvsix,vvdw6,vvdw12;
+ __m128d facel,gbtabscale,dvdaj;
+ __m128i n0, nnn;
- const __m128d neg = {-1.0,-1.0};
- const __m128d zero = {0.0,0.0};
- const __m128d half = {0.5,0.5};
- const __m128d two = {2.0,2.0};
- const __m128d three = {3.0,3.0};
- const __m128d six = {6.0,6.0};
- const __m128d twelwe = {12.0,12.0};
+ const __m128d neg = _mm_set1_pd(-1.0);
+ const __m128d zero = _mm_set1_pd(0.0);
+ const __m128d minushalf = _mm_set1_pd(-0.5);
+ const __m128d two = _mm_set1_pd(2.0);
+ const __m128d six = _mm_set1_pd(6.0);
+ const __m128d twelve = _mm_set1_pd(12.0);
gbdata = (gmx_gbdata_t *)work;
gpol = gbdata->gpol;
-
+
nri = *p_nri;
ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = (*p_facel) * ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent));
- krf = *p_krf;
- crf = *p_crf;
- tabscl = *p_tabscale;
- gbtabscl = *p_gbtabscale;
- nj1 = 0;
-
- /* Splat variables */
- fac = _mm_load1_pd(&facel);
- tabscale = _mm_load1_pd(&tabscl);
- gbtabscale = _mm_load1_pd(&gbtabscl);
-
- /* Keep compiler happy */
- Vvdwtmp = _mm_setzero_pd();
- Vvdwtot = _mm_setzero_pd();
- dvdatmp = _mm_setzero_pd();
- dvdaj = _mm_setzero_pd();
- isaj = _mm_setzero_pd();
- vcoul = _mm_setzero_pd();
- vgb = _mm_setzero_pd();
- t1 = _mm_setzero_pd();
- t2 = _mm_setzero_pd();
- t3 = _mm_setzero_pd();
- xmm1 = _mm_setzero_pd();
- xmm2 = _mm_setzero_pd();
- xmm3 = _mm_setzero_pd();
- xmm4 = _mm_setzero_pd();
- jnr1 = jnr2 = 0;
- j13 = j23 = 0;
+
+ gbfactor = _mm_set1_pd( - ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent)));
+ gbtabscale = _mm_load1_pd(p_gbtabscale);
+ facel = _mm_load1_pd(p_facel);
+
+ nj1 = 0;
+ jnrA = jnrB = 0;
+ j3A = j3B = 0;
+ jx = _mm_setzero_pd();
+ jy = _mm_setzero_pd();
+ jz = _mm_setzero_pd();
+ c6 = _mm_setzero_pd();
+ c12 = _mm_setzero_pd();
for(n=0;n<nri;n++)
{
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- nj0 = jindex[n];
- nj1 = jindex[n+1];
- offset = (nj1-nj0)%2;
-
- ii = iinr[n];
- ii3 = ii*3;
-
- ix = _mm_set1_pd(shX+pos[ii3+0]);
- iy = _mm_set1_pd(shX+pos[ii3+1]);
- iz = _mm_set1_pd(shX+pos[ii3+2]);
- q = _mm_set1_pd(charge[ii]);
+ is3 = 3*shift[n];
+ shX = shiftvec[is3];
+ shY = shiftvec[is3+1];
+ shZ = shiftvec[is3+2];
+ nj0 = jindex[n];
+ nj1 = jindex[n+1];
+ ii = iinr[n];
+ ii3 = 3*ii;
- iq = _mm_mul_pd(fac,q);
- isai_d = invsqrta[ii];
- isai = _mm_load1_pd(&isai_d);
-
- nti = 2*ntype*type[ii];
-
- fix = _mm_setzero_pd();
- fiy = _mm_setzero_pd();
- fiz = _mm_setzero_pd();
- dvdasum = _mm_setzero_pd();
- vctot = _mm_setzero_pd();
- vgbtot = _mm_setzero_pd();
- Vvdwtot = _mm_setzero_pd();
+ ix = _mm_set1_pd(shX+pos[ii3+0]);
+ iy = _mm_set1_pd(shY+pos[ii3+1]);
+ iz = _mm_set1_pd(shZ+pos[ii3+2]);
+
+ iq = _mm_load1_pd(charge+ii);
+ iq = _mm_mul_pd(iq,facel);
+
+ isai = _mm_load1_pd(invsqrta+ii);
+
+ nti = 2*ntype*type[ii];
- for(k=nj0;k<nj1-offset; k+=2)
+ vctot = _mm_setzero_pd();
+ vvdwtot = _mm_setzero_pd();
+ vgbtot = _mm_setzero_pd();
+ dvdasum = _mm_setzero_pd();
+ fix = _mm_setzero_pd();
+ fiy = _mm_setzero_pd();
+ fiz = _mm_setzero_pd();
+
+ for(k=nj0;k<nj1-1; k+=2)
{
- jnr1 = jjnr[k];
- jnr2 = jjnr[k+1];
-
- j13 = jnr1 * 3;
- j23 = jnr2 * 3;
-
- /* Load coordinates */
- xmm1 = _mm_loadu_pd(pos+j13); /* x1 y1 */
- xmm2 = _mm_loadu_pd(pos+j23); /* x2 y2 */
-
- xmm5 = _mm_load_sd(pos+j13+2); /* z1 - */
- xmm6 = _mm_load_sd(pos+j23+2); /* z2 - */
-
- /* transpose */
- jx = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0));
- jy = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1));
- jz = _mm_shuffle_pd(xmm5,xmm6,_MM_SHUFFLE2(0,0));
-
- /* distances */
- dx = _mm_sub_pd(ix,jx);
- dy = _mm_sub_pd(iy,jy);
- dz = _mm_sub_pd(iz,jz);
-
- rsq11 = _mm_add_pd( _mm_add_pd( _mm_mul_pd(dx,dx) , _mm_mul_pd(dy,dy) ) , _mm_mul_pd(dz,dz) );
- rinv = gmx_mm_invsqrt_pd(rsq11);
-
- /* Load invsqrta */
- isaj = _mm_loadl_pd(isaj,invsqrta+jnr1);
- isaj = _mm_loadh_pd(isaj,invsqrta+jnr2);
- isaprod = _mm_mul_pd(isai,isaj);
-
- /* Load charges */
- q = _mm_loadl_pd(q,charge+jnr1);
- q = _mm_loadh_pd(q,charge+jnr2);
- qq = _mm_mul_pd(iq,q);
-
- vcoul = _mm_mul_pd(qq,rinv);
- fscal = _mm_mul_pd(vcoul,rinv);
- qq = _mm_mul_pd(isaprod,qq);
- qq = _mm_mul_pd(qq,neg);
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Load VdW parameters */
- tj = nti+2*type[jnr1];
- tj2 = nti+2*type[jnr2];
+ jnrA = jjnr[k];
+ jnrB = jjnr[k+1];
- xmm1 = _mm_loadu_pd(vdwparam+tj);
- xmm2 = _mm_loadu_pd(vdwparam+tj2);
- c6 = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0));
- c12 = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1));
-
- rinvsq = _mm_mul_pd(rinv,rinv);
-
- /* Load dvdaj */
- dvdaj = _mm_loadl_pd(dvdaj, dvda+jnr1);
- dvdaj = _mm_loadh_pd(dvdaj, dvda+jnr2);
-
- r = _mm_mul_pd(rsq11,rinv);
- rt = _mm_mul_pd(r,gbscale);
- n0 = _mm_cvttpd_epi32(rt);
- n0d = _mm_cvtepi32_pd(n0);
- eps = _mm_sub_pd(rt,n0d);
- eps2 = _mm_mul_pd(eps,eps);
-
- nnn = _mm_slli_epi64(n0,2);
-
- xmm1 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,0))); /* Y1 F1 */
- xmm2 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,1))); /* Y2 F2 */
- xmm3 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,0))+2); /* G1 H1 */
- xmm4 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,1))+2); /* G2 H2 */
-
- Y = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0)); /* Y1 Y2 */
- F = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1)); /* F1 F2 */
- G = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(0,0)); /* G1 G2 */
- H = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(1,1)); /* H1 H2 */
-
- G = _mm_mul_pd(G,eps);
- H = _mm_mul_pd(H,eps2);
- Fp = _mm_add_pd(F,G);
- Fp = _mm_add_pd(Fp,H);
- VV = _mm_mul_pd(Fp,eps);
- VV = _mm_add_pd(Y,VV);
- H = _mm_mul_pd(two,H);
- FF = _mm_add_pd(Fp,G);
- FF = _mm_add_pd(FF,H);
- vgb = _mm_mul_pd(qq,VV);
- fijC = _mm_mul_pd(qq,FF);
- fijC = _mm_mul_pd(fijC,gbscale);
-
- dvdatmp = _mm_mul_pd(fijC,r);
- dvdatmp = _mm_add_pd(vgb,dvdatmp);
- dvdatmp = _mm_mul_pd(dvdatmp,neg);
- dvdatmp = _mm_mul_pd(dvdatmp,half);
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
-
- xmm1 = _mm_mul_pd(dvdatmp,isaj);
- xmm1 = _mm_mul_pd(xmm1,isaj);
- dvdaj = _mm_add_pd(dvdaj,xmm1);
-
- /* store dvda */
- _mm_storel_pd(dvda+jnr1,dvdaj);
- _mm_storeh_pd(dvda+jnr2,dvdaj);
-
- vctot = _mm_add_pd(vctot,vcoul);
- vgbtot = _mm_add_pd(vgbtot,vgb);
-
- /* VdW interaction */
- rinvsix = _mm_mul_pd(rinvsq,rinvsq);
- rinvsix = _mm_mul_pd(rinvsix,rinvsq);
-
- Vvdw6 = _mm_mul_pd(c6,rinvsix);
- Vvdw12 = _mm_mul_pd(c12,rinvsix);
- Vvdw12 = _mm_mul_pd(Vvdw12,rinvsix);
- Vvdwtmp = _mm_sub_pd(Vvdw12,Vvdw6);
- Vvdwtot = _mm_add_pd(Vvdwtot,Vvdwtmp);
-
- xmm1 = _mm_mul_pd(twelwe,Vvdw12);
- xmm2 = _mm_mul_pd(six,Vvdw6);
- xmm1 = _mm_sub_pd(xmm1,xmm2);
- xmm1 = _mm_mul_pd(xmm1,rinvsq);
-
- /* Scalar force */
- fscal = _mm_sub_pd(fijC,fscal);
- fscal = _mm_mul_pd(fscal,rinv);
- fscal = _mm_sub_pd(xmm1,fscal);
-
- /* calculate partial force terms */
- t1 = _mm_mul_pd(fscal,dx);
- t2 = _mm_mul_pd(fscal,dy);
- t3 = _mm_mul_pd(fscal,dz);
-
- /* update the i force */
- fix = _mm_add_pd(fix,t1);
- fiy = _mm_add_pd(fiy,t2);
- fiz = _mm_add_pd(fiz,t3);
-
- /* accumulate forces from memory */
- xmm1 = _mm_loadu_pd(faction+j13); /* fx1 fy1 */
- xmm2 = _mm_loadu_pd(faction+j23); /* fx2 fy2 */
-
- xmm5 = _mm_load1_pd(faction+j13+2); /* fz1 fz1 */
- xmm6 = _mm_load1_pd(faction+j23+2); /* fz2 fz2 */
-
- /* transpose */
- xmm7 = _mm_shuffle_pd(xmm5,xmm6,_MM_SHUFFLE2(0,0)); /* fz1 fz2 */
- xmm5 = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0)); /* fx1 fx2 */
- xmm6 = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1)); /* fy1 fy2 */
-
- /* subtract partial forces */
- xmm5 = _mm_sub_pd(xmm5,t1);
- xmm6 = _mm_sub_pd(xmm6,t2);
- xmm7 = _mm_sub_pd(xmm7,t3);
-
- xmm1 = _mm_shuffle_pd(xmm5,xmm6,_MM_SHUFFLE2(0,0)); /* fx1 fy1 */
- xmm2 = _mm_shuffle_pd(xmm5,xmm6,_MM_SHUFFLE2(1,1)); /* fy1 fy2 */
-
- /* store fx and fy */
- _mm_storeu_pd(faction+j13,xmm1);
- _mm_storeu_pd(faction+j23,xmm2);
-
- /* .. then fz */
- _mm_storel_pd(faction+j13+2,xmm7);
- _mm_storeh_pd(faction+j23+2,xmm7);
+ j3A = jnrA * 3;
+ j3B = jnrB * 3;
+
+ GMX_MM_LOAD_1RVEC_2POINTERS_PD(pos+j3A,pos+j3B,jx,jy,jz);
+
+ dx = _mm_sub_pd(ix,jx);
+ dy = _mm_sub_pd(iy,jy);
+ dz = _mm_sub_pd(iz,jz);
+
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
+ rinvsq = _mm_mul_pd(rinv,rinv);
+
+ /***********************************/
+ /* INTERACTION SECTION STARTS HERE */
+ /***********************************/
+ GMX_MM_LOAD_2VALUES_PD(charge+jnrA,charge+jnrB,jq);
+ GMX_MM_LOAD_2VALUES_PD(invsqrta+jnrA,invsqrta+jnrB,isaj);
+
+ /* Lennard-Jones */
+ tjA = nti+2*type[jnrA];
+ tjB = nti+2*type[jnrB];
+
+ GMX_MM_LOAD_2PAIRS_PD(vdwparam+tjA,vdwparam+tjB,c6,c12);
+
+ isaprod = _mm_mul_pd(isai,isaj);
+ qq = _mm_mul_pd(iq,jq);
+ vcoul = _mm_mul_pd(qq,rinv);
+ fscal = _mm_mul_pd(vcoul,rinv);
+ vctot = _mm_add_pd(vctot,vcoul);
+
+ /* Polarization interaction */
+ qq = _mm_mul_pd(qq,_mm_mul_pd(isaprod,gbfactor));
+ gbscale = _mm_mul_pd(isaprod,gbtabscale);
+
+ /* Calculate GB table index */
+ r = _mm_mul_pd(rsq,rinv);
+ rtab = _mm_mul_pd(r,gbscale);
+
+ n0 = _mm_cvttpd_epi32(rtab);
+ eps = _mm_sub_pd(rtab,_mm_cvtepi32_pd(n0));
+ nnn = _mm_slli_epi32(n0,2);
+
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1)));
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1))+2);
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_pd(G,eps);
+ H = _mm_mul_pd(H, _mm_mul_pd(eps,eps) );
+ F = _mm_add_pd(F, _mm_add_pd( G , H ) );
+ Y = _mm_add_pd(Y, _mm_mul_pd(F, eps));
+ F = _mm_add_pd(F, _mm_add_pd(G , _mm_mul_pd(H,two)));
+ vgb = _mm_mul_pd(Y, qq);
+ fijGB = _mm_mul_pd(F, _mm_mul_pd(qq,gbscale));
+
+ dvdatmp = _mm_mul_pd(_mm_add_pd(vgb, _mm_mul_pd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb);
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp);
+ dvdatmp = _mm_mul_pd(dvdatmp, _mm_mul_pd(isaj,isaj));
+
+ GMX_MM_INCREMENT_2VALUES_PD(dvda+jnrA,dvda+jnrB,dvdatmp);
+
+ rinvsix = _mm_mul_pd(rinvsq,rinvsq);
+ rinvsix = _mm_mul_pd(rinvsix,rinvsq);
+
+ vvdw6 = _mm_mul_pd(c6,rinvsix);
+ vvdw12 = _mm_mul_pd(c12, _mm_mul_pd(rinvsix,rinvsix));
+ vvdwtot = _mm_add_pd(vvdwtot,_mm_sub_pd(vvdw12,vvdw6));
+
+ fscal = _mm_sub_pd(_mm_mul_pd(rinvsq,
+ _mm_sub_pd(_mm_mul_pd(twelve,vvdw12),
+ _mm_mul_pd(six,vvdw6))),
+ _mm_mul_pd( _mm_sub_pd( fijGB,fscal),rinv ));
+
+ /***********************************/
+ /* INTERACTION SECTION ENDS HERE */
+ /***********************************/
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_pd(fscal,dx);
+ ty = _mm_mul_pd(fscal,dy);
+ tz = _mm_mul_pd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_pd(fix,tx);
+ fiy = _mm_add_pd(fiy,ty);
+ fiz = _mm_add_pd(fiz,tz);
+
+ /* Store j forces back */
+ GMX_MM_DECREMENT_1RVEC_2POINTERS_PD(faction+j3A,faction+j3B,tx,ty,tz);
}
/* In double precision, offset can only be either 0 or 1 */
- if(offset!=0)
+ if(k<nj1)
{
- jnr1 = jjnr[k];
- j13 = jnr1*3;
-
- jx = _mm_load_sd(pos+j13);
- jy = _mm_load_sd(pos+j13+1);
- jz = _mm_load_sd(pos+j13+2);
-
- isaj = _mm_load_sd(invsqrta+jnr1);
- isaprod = _mm_mul_sd(isai,isaj);
- dvdaj = _mm_load_sd(dvda+jnr1);
- q = _mm_load_sd(charge+jnr1);
- qq = _mm_mul_sd(iq,q);
-
- dx = _mm_sub_sd(ix,jx);
- dy = _mm_sub_sd(iy,jy);
- dz = _mm_sub_sd(iz,jz);
-
- rsq11 = _mm_add_pd( _mm_add_pd( _mm_mul_pd(dx,dx) , _mm_mul_pd(dy,dy) ) , _mm_mul_pd(dz,dz) );
- rinv = gmx_mm_invsqrt_pd(rsq11);
-
- vcoul = _mm_mul_sd(qq,rinv);
- fscal = _mm_mul_sd(vcoul,rinv);
- qq = _mm_mul_sd(isaprod,qq);
- qq = _mm_mul_sd(qq,neg);
- gbscale = _mm_mul_sd(isaprod,gbtabscale);
-
- /* Load VdW parameters */
- tj = nti+2*type[jnr1];
-
- c6 = _mm_load_sd(vdwparam+tj);
- c12 = _mm_load_sd(vdwparam+tj+1);
-
- rinvsq = _mm_mul_sd(rinv,rinv);
-
- r = _mm_mul_sd(rsq11,rinv);
- rt = _mm_mul_sd(r,gbscale);
- n0 = _mm_cvttpd_epi32(rt);
- n0d = _mm_cvtepi32_pd(n0);
- eps = _mm_sub_sd(rt,n0d);
- eps2 = _mm_mul_sd(eps,eps);
-
- nnn = _mm_slli_epi64(n0,2);
-
- xmm1 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,0)));
- xmm2 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,1)));
- xmm3 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,0))+2);
- xmm4 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,1))+2);
-
- Y = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0));
- F = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1));
- G = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(0,0));
- H = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(1,1));
-
- G = _mm_mul_sd(G,eps);
- H = _mm_mul_sd(H,eps2);
- Fp = _mm_add_sd(F,G);
- Fp = _mm_add_sd(Fp,H);
- VV = _mm_mul_sd(Fp,eps);
- VV = _mm_add_sd(Y,VV);
- H = _mm_mul_sd(two,H);
- FF = _mm_add_sd(Fp,G);
- FF = _mm_add_sd(FF,H);
- vgb = _mm_mul_sd(qq,VV);
- fijC = _mm_mul_sd(qq,FF);
- fijC = _mm_mul_sd(fijC,gbscale);
-
- dvdatmp = _mm_mul_sd(fijC,r);
- dvdatmp = _mm_add_sd(vgb,dvdatmp);
- dvdatmp = _mm_mul_sd(dvdatmp,neg);
- dvdatmp = _mm_mul_sd(dvdatmp,half);
- dvdasum = _mm_add_sd(dvdasum,dvdatmp);
-
- xmm1 = _mm_mul_sd(dvdatmp,isaj);
- xmm1 = _mm_mul_sd(xmm1,isaj);
- dvdaj = _mm_add_sd(dvdaj,xmm1);
-
- /* store dvda */
- _mm_storel_pd(dvda+jnr1,dvdaj);
-
- vctot = _mm_add_sd(vctot,vcoul);
- vgbtot = _mm_add_sd(vgbtot,vgb);
-
- /* VdW interaction */
- rinvsix = _mm_mul_sd(rinvsq,rinvsq);
- rinvsix = _mm_mul_sd(rinvsix,rinvsq);
-
- Vvdw6 = _mm_mul_sd(c6,rinvsix);
- Vvdw12 = _mm_mul_sd(c12,rinvsix);
- Vvdw12 = _mm_mul_sd(Vvdw12,rinvsix);
- Vvdwtmp = _mm_sub_sd(Vvdw12,Vvdw6);
- Vvdwtot = _mm_add_sd(Vvdwtot,Vvdwtmp);
-
- xmm1 = _mm_mul_sd(twelwe,Vvdw12);
- xmm2 = _mm_mul_sd(six,Vvdw6);
- xmm1 = _mm_sub_sd(xmm1,xmm2);
- xmm1 = _mm_mul_sd(xmm1,rinvsq);
-
- /* Scalar force */
- fscal = _mm_sub_sd(fijC,fscal);
- fscal = _mm_mul_sd(fscal,rinv);
- fscal = _mm_sub_sd(xmm1,fscal);
-
- /* calculate partial force terms */
- t1 = _mm_mul_sd(fscal,dx);
- t2 = _mm_mul_sd(fscal,dy);
- t3 = _mm_mul_sd(fscal,dz);
-
- /* update the i force */
- fix = _mm_add_sd(fix,t1);
- fiy = _mm_add_sd(fiy,t2);
- fiz = _mm_add_sd(fiz,t3);
-
- /* accumulate forces from memory */
- xmm5 = _mm_load_sd(faction+j13); /* fx */
- xmm6 = _mm_load_sd(faction+j13+1); /* fy */
- xmm7 = _mm_load_sd(faction+j13+2); /* fz */
-
- /* subtract partial forces */
- xmm5 = _mm_sub_sd(xmm5,t1);
- xmm6 = _mm_sub_sd(xmm6,t2);
- xmm7 = _mm_sub_sd(xmm7,t3);
-
- /* store forces */
- _mm_store_sd(faction+j13,xmm5);
- _mm_store_sd(faction+j13+1,xmm6);
- _mm_store_sd(faction+j13+2,xmm7);
+ jnrA = jjnr[k];
+
+ j3A = jnrA * 3;
+
+ GMX_MM_LOAD_1RVEC_1POINTER_PD(pos+j3A,jx,jy,jz);
+
+ dx = _mm_sub_sd(ix,jx);
+ dy = _mm_sub_sd(iy,jy);
+ dz = _mm_sub_sd(iz,jz);
+
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
+ rinvsq = _mm_mul_sd(rinv,rinv);
+
+ /* These reason for zeroing these variables here is for fixing bug 585
+ * What happens is that __m128d _mm_add_sd(a,b) gives back r0=a[0]+b[0],
+ * and r1=0, but it should be r1=a[1].
+ * This might be a compiler issue (tested with gcc-4.1.3 and -O3).
+ * To work around it, we zero these variables and use _mm_add_pd (**) instead
+ * Note that the only variables that get affected are the energies since
+ * the total sum needs to be correct
+ */
+ vgb = _mm_setzero_pd();
+ vcoul = _mm_setzero_pd();
+ dvdatmp = _mm_setzero_pd();
+ vvdw6 = _mm_setzero_pd();
+ vvdw12 = _mm_setzero_pd();
+
+ /***********************************/
+ /* INTERACTION SECTION STARTS HERE */
+ /***********************************/
+ GMX_MM_LOAD_1VALUE_PD(charge+jnrA,jq);
+ GMX_MM_LOAD_1VALUE_PD(invsqrta+jnrA,isaj);
+
+ /* Lennard-Jones */
+ tjA = nti+2*type[jnrA];
+
+ GMX_MM_LOAD_1PAIR_PD(vdwparam+tjA,c6,c12);
+
+ isaprod = _mm_mul_sd(isai,isaj);
+ qq = _mm_mul_sd(jq,iq);
+ vcoul = _mm_mul_sd(qq,rinv);
+ fscal = _mm_mul_sd(vcoul,rinv);
+ vctot = _mm_add_pd(vctot,vcoul); /* (**) */
+
+ /* Polarization interaction */
+ qq = _mm_mul_sd(qq,_mm_mul_sd(isaprod,gbfactor));
+ gbscale = _mm_mul_sd(isaprod,gbtabscale);
+
+ /* Calculate GB table index */
+ r = _mm_mul_sd(rsq,rinv);
+ rtab = _mm_mul_sd(r,gbscale);
+
+ n0 = _mm_cvttpd_epi32(rtab);
+ eps = _mm_sub_sd(rtab,_mm_cvtepi32_pd(n0));
+ nnn = _mm_slli_epi32(n0,2);
+
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_sd(G,eps);
+ H = _mm_mul_sd(H, _mm_mul_sd(eps,eps) );
+ F = _mm_add_sd(F, _mm_add_sd( G , H ) );
+ Y = _mm_add_sd(Y, _mm_mul_sd(F, eps));
+ F = _mm_add_sd(F, _mm_add_sd(G , _mm_mul_sd(H,two)));
+ vgb = _mm_mul_sd(Y, qq);
+ fijGB = _mm_mul_sd(F, _mm_mul_sd(qq,gbscale));
+
+ dvdatmp = _mm_mul_sd(_mm_add_sd(vgb, _mm_mul_sd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb); /* (**) */
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp); /* (**) */
+ dvdatmp = _mm_mul_sd(dvdatmp, _mm_mul_sd(isaj,isaj));
+
+ GMX_MM_INCREMENT_1VALUE_PD(dvda+jnrA,dvdatmp);
+
+ rinvsix = _mm_mul_sd(rinvsq,rinvsq);
+ rinvsix = _mm_mul_sd(rinvsix,rinvsq);
+
+ vvdw6 = _mm_mul_sd(c6,rinvsix);
+ vvdw12 = _mm_mul_sd(c12, _mm_mul_sd(rinvsix,rinvsix));
+ vvdwtot = _mm_add_pd(vvdwtot,_mm_sub_sd(vvdw12,vvdw6)); /* (**) */
+
+ fscal = _mm_sub_sd(_mm_mul_sd(rinvsq,
+ _mm_sub_sd(_mm_mul_sd(twelve,vvdw12),
+ _mm_mul_sd(six,vvdw6))),
+ _mm_mul_sd( _mm_sub_sd( fijGB,fscal),rinv ));
+
+ /***********************************/
+ /* INTERACTION SECTION ENDS HERE */
+ /***********************************/
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_sd(fscal,dx);
+ ty = _mm_mul_sd(fscal,dy);
+ tz = _mm_mul_sd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_sd(fix,tx);
+ fiy = _mm_add_sd(fiy,ty);
+ fiz = _mm_add_sd(fiz,tz);
+
+ /* Store j forces back */
+ GMX_MM_DECREMENT_1RVEC_1POINTER_PD(faction+j3A,tx,ty,tz);
}
- /* fix/fiy/fiz now contain four partial terms, that all should be
- * added to the i particle forces
- */
- t1 = _mm_unpacklo_pd(t1,fix);
- t2 = _mm_unpacklo_pd(t2,fiy);
- t3 = _mm_unpacklo_pd(t3,fiz);
-
- fix = _mm_add_pd(fix,t1);
- fiy = _mm_add_pd(fiy,t2);
- fiz = _mm_add_pd(fiz,t3);
-
- fix = _mm_shuffle_pd(fix,fix,_MM_SHUFFLE2(1,1));
- fiy = _mm_shuffle_pd(fiy,fiy,_MM_SHUFFLE2(1,1));
- fiz = _mm_shuffle_pd(fiz,fiz,_MM_SHUFFLE2(1,1));
-
- /* Load i forces from memory */
- xmm1 = _mm_load_sd(faction+ii3);
- xmm2 = _mm_load_sd(faction+ii3+1);
- xmm3 = _mm_load_sd(faction+ii3+2);
-
- /* Add to i force */
- fix = _mm_add_sd(fix,xmm1);
- fiy = _mm_add_sd(fiy,xmm2);
- fiz = _mm_add_sd(fiz,xmm3);
-
- /* store i forces to memory */
- _mm_store_sd(faction+ii3,fix);
- _mm_store_sd(faction+ii3+1,fiy);
- _mm_store_sd(faction+ii3+2,fiz);
-
- /* now do dvda */
- dvdatmp = _mm_unpacklo_pd(dvdatmp,dvdasum);
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- _mm_storeh_pd(&dva,dvdasum);
- dvda[ii] = dvda[ii] + dva*isai_d*isai_d;
-
- ggid = gid[n];
-
- /* Coulomb potential */
- vcoul = _mm_unpacklo_pd(vcoul,vctot);
- vctot = _mm_add_pd(vctot,vcoul);
- _mm_storeh_pd(&vct,vctot);
- Vc[ggid] = Vc[ggid] + vct;
-
- /* VdW potential */
- Vvdwtmp = _mm_unpacklo_pd(Vvdwtmp,Vvdwtot);
- Vvdwtot = _mm_add_pd(Vvdwtot,Vvdwtmp);
- _mm_storeh_pd(&vdwt,Vvdwtot);
- Vvdw[ggid] = Vvdw[ggid] + vdwt;
-
- /* GB potential */
- vgb = _mm_unpacklo_pd(vgb,vgbtot);
- vgbtot = _mm_add_pd(vgbtot,vgb);
- _mm_storeh_pd(&vgbt,vgbtot);
- gpol[ggid] = gpol[ggid] + vgbt;
+ dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai,isai));
+ gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,faction+ii3,fshift+is3);
+
+ ggid = gid[n];
+
+ gmx_mm_update_1pot_pd(vctot,vc+ggid);
+ gmx_mm_update_1pot_pd(vgbtot,gpol+ggid);
+ gmx_mm_update_1pot_pd(dvdasum,dvda+ii);
+ gmx_mm_update_1pot_pd(vvdwtot,vvdw+ggid);
+
}
-
+
*outeriter = nri;
- *inneriter = nj1;
+ *inneriter = nj1;
}
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel410nf
- * Coulomb interaction: Generalized-Born
- * VdW interaction: Lennard-Jones
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel410nf_sse2_double(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- double * shiftvec,
- double * fshift,
- int * gid,
- double * pos,
- double * faction,
- double * charge,
- double * p_facel,
- double * p_krf,
- double * p_crf,
- double * Vc,
- int * type,
- int * p_ntype,
- double * vdwparam,
- double * Vvdw,
- double * p_tabscale,
- double * VFtab,
- double * invsqrta,
- double * dvda,
- double * p_gbtabscale,
- double * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- double * work)
-{
- int nri,ntype,nthreads;
- double facel,krf,crf,tabscale,gbtabscale,vgb,fgb;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- double shX,shY,shZ;
- double rinvsq;
- double iq;
- double qq,vcoul,vctot;
- int nti;
- int tj;
- double rinvsix;
- double Vvdw6,Vvdwtot;
- double Vvdw12;
- double r,rt,eps,eps2;
- int n0,nnn;
- double Y,F,Geps,Heps2,Fp,VV;
- double isai,isaj,isaprod,gbscale;
- double ix1,iy1,iz1;
- double jx1,jy1,jz1;
- double dx11,dy11,dz11,rsq11,rinv11;
- double c6,c12;
- const int fractshift = 12;
- const int fractmask = 8388607;
- const int expshift = 23;
- const int expmask = 2139095040;
- const int explsb = 8388608;
- double lu;
- int iexp,addr;
- union { unsigned int bval; double fval; } bitpattern,result;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
- gbtabscale = *p_gbtabscale;
- nj1 = 0;
-
- for(n=0; (n<nri); n++)
- {
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
- nj0 = jindex[n];
- nj1 = jindex[n+1];
- ii = iinr[n];
- ii3 = 3*ii;
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- iq = facel*charge[ii];
- isai = invsqrta[ii];
- nti = 2*ntype*type[ii];
- vctot = 0;
- Vvdwtot = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
- jnr = jjnr[k];
- j3 = 3*jnr;
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- bitpattern.fval = rsq11;
- iexp = (((bitpattern.bval)&expmask)>>expshift);
- addr = (((bitpattern.bval)&(fractmask|explsb))>>fractshift);
- result.bval = gmx_invsqrt_exptab[iexp] | gmx_invsqrt_fracttab[addr];
- lu = result.fval;
- rinv11 = (0.5*lu*(3.0-((rsq11*lu)*lu)));
- isaj = invsqrta[jnr];
- isaprod = isai*isaj;
- qq = iq*charge[jnr];
- vcoul = qq*rinv11;
- qq = isaprod*(-qq);
- gbscale = isaprod*gbtabscale;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
- r = rsq11*rinv11;
- rt = r*gbscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
- Y = GBtab[nnn];
- F = GBtab[nnn+1];
- Geps = eps*GBtab[nnn+2];
- Heps2 = eps2*GBtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vgb = qq*VV;
- vctot = vctot + vcoul;
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- }
-
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
- }
-
- *outeriter = nri;
- *inneriter = nj1;
-}
-
-
#include<math.h>
#include<vec.h>
-
#include <xmmintrin.h>
#include <emmintrin.h>
/* get gmx_gbdata_t */
#include "../nb_kerneltype.h"
-
+#include "nb_kernel430_x86_64_sse2.h"
void nb_kernel430_sse2_double(int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- double * shiftvec,
- double * fshift,
- int * gid,
- double * pos,
- double * faction,
- double * charge,
- double * p_facel,
- double * p_krf,
- double * p_crf,
- double * Vc,
- int * type,
- int * p_ntype,
- double * vdwparam,
- double * Vvdw,
- double * p_tabscale,
- double * VFtab,
- double * invsqrta,
- double * dvda,
- double * p_gbtabscale,
- double * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- double * work)
+ int * iinr,
+ int * jindex,
+ int * jjnr,
+ int * shift,
+ double * shiftvec,
+ double * fshift,
+ int * gid,
+ double * pos,
+ double * faction,
+ double * charge,
+ double * p_facel,
+ double * p_krf,
+ double * p_crf,
+ double * vc,
+ int * type,
+ int * p_ntype,
+ double * vdwparam,
+ double * vvdw,
+ double * p_tabscale,
+ double * VFtab,
+ double * invsqrta,
+ double * dvda,
+ double * p_gbtabscale,
+ double * GBtab,
+ int * p_nthreads,
+ int * count,
+ void * mtx,
+ int * outeriter,
+ int * inneriter,
+ double * work)
{
- int nri,ntype,nthreads,offset,tj,tj2,nti;
- int n,ii,is3,ii3,k,nj0,nj1,jnr1,jnr2,j13,j23,ggid;
- double facel,krf,crf,tabscl,gbtabscl,vct,vdwt,vgbt,nt1,nt2;
- double shX,shY,shZ,isai_d,dva;
+ int nri,ntype,nthreads;
+ int n,ii,is3,ii3,k,nj0,nj1,ggid;
+ double shX,shY,shZ;
+ int offset,nti;
+ int jnrA,jnrB;
+ int j3A,j3B;
+ int tjA,tjB;
gmx_gbdata_t *gbdata;
- float * gpol;
-
- __m128d ix,iy,iz,jx,jy,jz;
- __m128d dx,dy,dz,t1,t2,t3;
- __m128d fix,fiy,fiz,rsq11,rinv,r,fscal,rt,eps,eps2;
- __m128d q,iq,qq,isai,isaj,isaprod,vcoul,gbscale,dvdai,dvdaj;
- __m128d Y,F,G,H,Fp,VV,FF,vgb,fijC,fijD,fijR,dvdatmp,dvdasum,vctot,n0d;
- __m128d xmm0,xmm1,xmm2,xmm3,xmm4,xmm5,xmm6,xmm7,xmm8;
- __m128d c6,c12,Vvdw6,Vvdw12,Vvdwtmp,Vvdwtot,vgbtot,rinvsq,rinvsix;
- __m128d fac,tabscale,gbtabscale;
- __m128i n0,nnn;
-
- const __m128d neg = {-1.0,-1.0};
- const __m128d zero = {0.0,0.0};
- const __m128d half = {0.5,0.5};
- const __m128d two = {2.0,2.0};
- const __m128d three = {3.0,3.0};
- const __m128d six = {6.0,6.0};
- const __m128d twelwe = {12.0,12.0};
+ double * gpol;
+
+ __m128d iq,qq,jq,isai;
+ __m128d ix,iy,iz;
+ __m128d jx,jy,jz;
+ __m128d dx,dy,dz;
+ __m128d vctot,vvdwtot,vgbtot,dvdasum,gbfactor;
+ __m128d fix,fiy,fiz,tx,ty,tz,rsq;
+ __m128d rinv,isaj,isaprod;
+ __m128d vcoul,fscal,gbscale,c6,c12;
+ __m128d rinvsq,r,rtab;
+ __m128d eps,Y,F,G,H;
+ __m128d VV,FF,Fp;
+ __m128d vgb,fijGB,dvdatmp;
+ __m128d rinvsix,vvdw6,vvdw12,vvdwtmp;
+ __m128d facel,gbtabscale,dvdaj;
+ __m128d fijD,fijR;
+ __m128d xmm1,tabscale,eps2;
+ __m128i n0, nnn;
+
- const __m128i four = _mm_set_epi32(4,4,4,4);
+ const __m128d neg = _mm_set1_pd(-1.0);
+ const __m128d zero = _mm_set1_pd(0.0);
+ const __m128d minushalf = _mm_set1_pd(-0.5);
+ const __m128d two = _mm_set1_pd(2.0);
gbdata = (gmx_gbdata_t *)work;
gpol = gbdata->gpol;
-
+
nri = *p_nri;
ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = (*p_facel) * ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent));
- krf = *p_krf;
- crf = *p_crf;
- tabscl = *p_tabscale;
- gbtabscl = *p_gbtabscale;
- nj1 = 0;
-
- /* Splat variables */
- fac = _mm_load1_pd(&facel);
- tabscale = _mm_load1_pd(&tabscl);
- gbtabscale = _mm_load1_pd(&gbtabscl);
-
- /* Keep compiler happy */
- Vvdwtmp = _mm_setzero_pd();
- Vvdwtot = _mm_setzero_pd();
- dvdatmp = _mm_setzero_pd();
- dvdaj = _mm_setzero_pd();
- isaj = _mm_setzero_pd();
- vcoul = _mm_setzero_pd();
- vgb = _mm_setzero_pd();
- t1 = _mm_setzero_pd();
- t2 = _mm_setzero_pd();
- t3 = _mm_setzero_pd();
- xmm1 = _mm_setzero_pd();
- xmm2 = _mm_setzero_pd();
- xmm3 = _mm_setzero_pd();
- xmm4 = _mm_setzero_pd();
- jnr1 = jnr2 = 0;
- j13 = j23 = 0;
+
+ gbfactor = _mm_set1_pd( - ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent)));
+ gbtabscale = _mm_load1_pd(p_gbtabscale);
+ facel = _mm_load1_pd(p_facel);
+ tabscale = _mm_load1_pd(p_tabscale);
+
+ nj1 = 0;
+ jnrA = jnrB = 0;
+ j3A = j3B = 0;
+ jx = _mm_setzero_pd();
+ jy = _mm_setzero_pd();
+ jz = _mm_setzero_pd();
+ c6 = _mm_setzero_pd();
+ c12 = _mm_setzero_pd();
for(n=0;n<nri;n++)
{
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- nj0 = jindex[n];
- nj1 = jindex[n+1];
- offset = (nj1-nj0)%2;
-
- ii = iinr[n];
- ii3 = ii*3;
-
- ix = _mm_set1_pd(shX+pos[ii3+0]);
- iy = _mm_set1_pd(shX+pos[ii3+1]);
- iz = _mm_set1_pd(shX+pos[ii3+2]);
- q = _mm_set1_pd(charge[ii]);
-
- iq = _mm_mul_pd(fac,q);
- isai_d = invsqrta[ii];
- isai = _mm_load1_pd(&isai_d);
+ is3 = 3*shift[n];
+ shX = shiftvec[is3];
+ shY = shiftvec[is3+1];
+ shZ = shiftvec[is3+2];
+ nj0 = jindex[n];
+ nj1 = jindex[n+1];
+ ii = iinr[n];
+ ii3 = 3*ii;
- nti = 2*ntype*type[ii];
-
- fix = _mm_setzero_pd();
- fiy = _mm_setzero_pd();
- fiz = _mm_setzero_pd();
- dvdasum = _mm_setzero_pd();
- vctot = _mm_setzero_pd();
- vgbtot = _mm_setzero_pd();
- Vvdwtot = _mm_setzero_pd();
+ ix = _mm_set1_pd(shX+pos[ii3+0]);
+ iy = _mm_set1_pd(shY+pos[ii3+1]);
+ iz = _mm_set1_pd(shZ+pos[ii3+2]);
+
+ iq = _mm_load1_pd(charge+ii);
+ iq = _mm_mul_pd(iq,facel);
+
+ isai = _mm_load1_pd(invsqrta+ii);
+
+ nti = 2*ntype*type[ii];
- for(k=nj0;k<nj1-offset; k+=2)
+ vctot = _mm_setzero_pd();
+ vvdwtot = _mm_setzero_pd();
+ vgbtot = _mm_setzero_pd();
+ dvdasum = _mm_setzero_pd();
+ fix = _mm_setzero_pd();
+ fiy = _mm_setzero_pd();
+ fiz = _mm_setzero_pd();
+
+ for(k=nj0;k<nj1-1; k+=2)
{
- jnr1 = jjnr[k];
- jnr2 = jjnr[k+1];
-
- j13 = jnr1 * 3;
- j23 = jnr2 * 3;
-
- /* Load coordinates */
- xmm1 = _mm_loadu_pd(pos+j13); /* x1 y1 */
- xmm2 = _mm_loadu_pd(pos+j23); /* x2 y2 */
-
- xmm5 = _mm_load_sd(pos+j13+2); /* z1 - */
- xmm6 = _mm_load_sd(pos+j23+2); /* z2 - */
-
- /* transpose */
- jx = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0));
- jy = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1));
- jz = _mm_shuffle_pd(xmm5,xmm6,_MM_SHUFFLE2(0,0));
-
- /* distances */
- dx = _mm_sub_pd(ix,jx);
- dy = _mm_sub_pd(iy,jy);
- dz = _mm_sub_pd(iz,jz);
-
- rsq11 = _mm_add_pd( _mm_add_pd( _mm_mul_pd(dx,dx) , _mm_mul_pd(dy,dy) ) , _mm_mul_pd(dz,dz) );
- rinv = gmx_mm_invsqrt_pd(rsq11);
-
- /* Load invsqrta */
- isaj = _mm_loadl_pd(isaj,invsqrta+jnr1);
- isaj = _mm_loadh_pd(isaj,invsqrta+jnr2);
- isaprod = _mm_mul_pd(isai,isaj);
-
- /* Load charges */
- q = _mm_loadl_pd(q,charge+jnr1);
- q = _mm_loadh_pd(q,charge+jnr2);
- qq = _mm_mul_pd(iq,q);
-
- vcoul = _mm_mul_pd(qq,rinv);
- fscal = _mm_mul_pd(vcoul,rinv);
- qq = _mm_mul_pd(isaprod,qq);
- qq = _mm_mul_pd(qq,neg);
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Load VdW parameters */
- tj = nti+2*type[jnr1];
- tj2 = nti+2*type[jnr2];
-
- xmm1 = _mm_loadu_pd(vdwparam+tj);
- xmm2 = _mm_loadu_pd(vdwparam+tj2);
- c6 = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0));
- c12 = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1));
-
- /* Load dvdaj */
- dvdaj = _mm_loadl_pd(dvdaj, dvda+jnr1);
- dvdaj = _mm_loadh_pd(dvdaj, dvda+jnr2);
-
- /* Calculate GB table index */
- r = _mm_mul_pd(rsq11,rinv);
- rt = _mm_mul_pd(r,gbscale);
- n0 = _mm_cvttpd_epi32(rt);
- n0d = _mm_cvtepi32_pd(n0);
- eps = _mm_sub_pd(rt,n0d);
- eps2 = _mm_mul_pd(eps,eps);
-
- nnn = _mm_slli_epi64(n0,2);
-
- xmm1 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,0))); /* Y1 F1 */
- xmm2 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,1))); /* Y2 F2 */
- xmm3 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,0))+2); /* G1 H1 */
- xmm4 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,1))+2); /* G2 H2 */
-
- Y = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0)); /* Y1 Y2 */
- F = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1)); /* F1 F2 */
- G = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(0,0)); /* G1 G2 */
- H = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(1,1)); /* H1 H2 */
-
- G = _mm_mul_pd(G,eps);
- H = _mm_mul_pd(H,eps2);
- Fp = _mm_add_pd(F,G);
- Fp = _mm_add_pd(Fp,H);
- VV = _mm_mul_pd(Fp,eps);
- VV = _mm_add_pd(Y,VV);
- H = _mm_mul_pd(two,H);
- FF = _mm_add_pd(Fp,G);
- FF = _mm_add_pd(FF,H);
- vgb = _mm_mul_pd(qq,VV);
- fijC = _mm_mul_pd(qq,FF);
- fijC = _mm_mul_pd(fijC,gbscale);
-
- dvdatmp = _mm_mul_pd(fijC,r);
- dvdatmp = _mm_add_pd(vgb,dvdatmp);
- dvdatmp = _mm_mul_pd(dvdatmp,neg);
- dvdatmp = _mm_mul_pd(dvdatmp,half);
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
-
- xmm1 = _mm_mul_pd(dvdatmp,isaj);
- xmm1 = _mm_mul_pd(xmm1,isaj);
- dvdaj = _mm_add_pd(dvdaj,xmm1);
-
- /* store dvda */
- _mm_storel_pd(dvda+jnr1,dvdaj);
- _mm_storeh_pd(dvda+jnr2,dvdaj);
-
- vctot = _mm_add_pd(vctot,vcoul);
- vgbtot = _mm_add_pd(vgbtot,vgb);
-
- /* Calculate VDW table index */
- rt = _mm_mul_pd(r,tabscale);
- n0 = _mm_cvttpd_epi32(rt);
- n0d = _mm_cvtepi32_pd(n0);
- eps = _mm_sub_pd(rt,n0d);
+ jnrA = jjnr[k];
+ jnrB = jjnr[k+1];
+
+ j3A = jnrA * 3;
+ j3B = jnrB * 3;
+
+ GMX_MM_LOAD_1RVEC_2POINTERS_PD(pos+j3A,pos+j3B,jx,jy,jz);
+
+ dx = _mm_sub_pd(ix,jx);
+ dy = _mm_sub_pd(iy,jy);
+ dz = _mm_sub_pd(iz,jz);
+
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
+ rinvsq = _mm_mul_pd(rinv,rinv);
+
+ /***********************************/
+ /* INTERACTION SECTION STARTS HERE */
+ /***********************************/
+ GMX_MM_LOAD_2VALUES_PD(charge+jnrA,charge+jnrB,jq);
+ GMX_MM_LOAD_2VALUES_PD(invsqrta+jnrA,invsqrta+jnrB,isaj);
+
+ /* Lennard-Jones */
+ tjA = nti+2*type[jnrA];
+ tjB = nti+2*type[jnrB];
+
+ GMX_MM_LOAD_2PAIRS_PD(vdwparam+tjA,vdwparam+tjB,c6,c12);
+
+ isaprod = _mm_mul_pd(isai,isaj);
+ qq = _mm_mul_pd(iq,jq);
+ vcoul = _mm_mul_pd(qq,rinv);
+ fscal = _mm_mul_pd(vcoul,rinv);
+ vctot = _mm_add_pd(vctot,vcoul);
+
+ /* Polarization interaction */
+ qq = _mm_mul_pd(qq,_mm_mul_pd(isaprod,gbfactor));
+ gbscale = _mm_mul_pd(isaprod,gbtabscale);
+
+ /* Calculate GB table index */
+ r = _mm_mul_pd(rsq,rinv);
+ rtab = _mm_mul_pd(r,gbscale);
+
+ n0 = _mm_cvttpd_epi32(rtab);
+ eps = _mm_sub_pd(rtab,_mm_cvtepi32_pd(n0));
+ nnn = _mm_slli_epi32(n0,2);
+
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1)));
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1))+2);
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_pd(G,eps);
+ H = _mm_mul_pd(H, _mm_mul_pd(eps,eps) );
+ F = _mm_add_pd(F, _mm_add_pd( G , H ) );
+ Y = _mm_add_pd(Y, _mm_mul_pd(F, eps));
+ F = _mm_add_pd(F, _mm_add_pd(G , _mm_mul_pd(H,two)));
+ vgb = _mm_mul_pd(Y, qq);
+ fijGB = _mm_mul_pd(F, _mm_mul_pd(qq,gbscale));
+
+ dvdatmp = _mm_mul_pd(_mm_add_pd(vgb, _mm_mul_pd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb);
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp);
+ dvdatmp = _mm_mul_pd(dvdatmp, _mm_mul_pd(isaj,isaj));
+
+ GMX_MM_INCREMENT_2VALUES_PD(dvda+jnrA,dvda+jnrB,dvdatmp);
+
+ /* Calculate VDW table index */
+ rtab = _mm_mul_pd(r,tabscale);
+ n0 = _mm_cvttpd_epi32(rtab);
+ eps = _mm_sub_pd(rtab,_mm_cvtepi32_pd(n0));
eps2 = _mm_mul_pd(eps,eps);
nnn = _mm_slli_epi32(n0,3);
- /* Tabulated VdW interaction - dispersion */
- xmm1 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,0))); /* Y1 F1 */
- xmm2 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,1))); /* Y2 F2 */
- xmm3 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,0))+2); /* G1 H1 */
- xmm4 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,1))+2); /* G2 H2 */
-
- Y = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0)); /* Y1 Y2 */
- F = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1)); /* F1 F2 */
- G = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(0,0)); /* G1 G2 */
- H = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(1,1)); /* H1 H2 */
-
- G = _mm_mul_pd(G,eps);
+ /* Dispersion */
+ Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1)));
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1))+2);
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_pd(G,eps);
H = _mm_mul_pd(H,eps2);
Fp = _mm_add_pd(F,G);
Fp = _mm_add_pd(Fp,H);
FF = _mm_add_pd(Fp,G);
FF = _mm_add_pd(FF,xmm1);
- Vvdw6 = _mm_mul_pd(c6,VV);
+ vvdw6 = _mm_mul_pd(c6,VV);
fijD = _mm_mul_pd(c6,FF);
-
- /* Tabulated VdW interaction - repulsion */
- nnn = _mm_add_epi32(nnn,four);
-
- xmm1 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,0))); /* Y1 F1 */
- xmm2 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,1))); /* Y2 F2 */
- xmm3 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,0))+2); /* G1 H1 */
- xmm4 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,1))+2); /* G2 H2 */
-
- Y = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0)); /* Y1 Y2 */
- F = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1)); /* F1 F2 */
- G = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(0,0)); /* G1 G2 */
- H = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(1,1)); /* H1 H2 */
-
- G = _mm_mul_pd(G,eps);
+
+ /* Dispersion */
+ Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+4);
+ F = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1))+4);
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+6);
+ H = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1))+6);
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_pd(G,eps);
H = _mm_mul_pd(H,eps2);
Fp = _mm_add_pd(F,G);
Fp = _mm_add_pd(Fp,H);
FF = _mm_add_pd(Fp,G);
FF = _mm_add_pd(FF,xmm1);
- Vvdw12 = _mm_mul_pd(c12,VV);
+ vvdw12 = _mm_mul_pd(c12,VV);
fijR = _mm_mul_pd(c12,FF);
- Vvdwtmp = _mm_add_pd(Vvdw12,Vvdw6);
- Vvdwtot = _mm_add_pd(Vvdwtot,Vvdwtmp);
-
+ vvdwtmp = _mm_add_pd(vvdw12,vvdw6);
+ vvdwtot = _mm_add_pd(vvdwtot,vvdwtmp);
+
xmm1 = _mm_add_pd(fijD,fijR);
xmm1 = _mm_mul_pd(xmm1,tabscale);
- xmm1 = _mm_add_pd(xmm1,fijC);
+ xmm1 = _mm_add_pd(xmm1,fijGB);
xmm1 = _mm_sub_pd(xmm1,fscal);
fscal = _mm_mul_pd(xmm1,neg);
fscal = _mm_mul_pd(fscal,rinv);
-
- /* calculate partial force terms */
- t1 = _mm_mul_pd(fscal,dx);
- t2 = _mm_mul_pd(fscal,dy);
- t3 = _mm_mul_pd(fscal,dz);
-
- /* update the i force */
- fix = _mm_add_pd(fix,t1);
- fiy = _mm_add_pd(fiy,t2);
- fiz = _mm_add_pd(fiz,t3);
-
- /* accumulate forces from memory */
- xmm1 = _mm_loadu_pd(faction+j13); /* fx1 fy1 */
- xmm2 = _mm_loadu_pd(faction+j23); /* fx2 fy2 */
-
- xmm5 = _mm_load1_pd(faction+j13+2); /* fz1 fz1 */
- xmm6 = _mm_load1_pd(faction+j23+2); /* fz2 fz2 */
-
- /* transpose */
- xmm7 = _mm_shuffle_pd(xmm5,xmm6,_MM_SHUFFLE2(0,0)); /* fz1 fz2 */
- xmm5 = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0)); /* fx1 fx2 */
- xmm6 = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1)); /* fy1 fy2 */
-
- /* subtract partial forces */
- xmm5 = _mm_sub_pd(xmm5,t1);
- xmm6 = _mm_sub_pd(xmm6,t2);
- xmm7 = _mm_sub_pd(xmm7,t3);
-
- xmm1 = _mm_shuffle_pd(xmm5,xmm6,_MM_SHUFFLE2(0,0)); /* fx1 fy1 */
- xmm2 = _mm_shuffle_pd(xmm5,xmm6,_MM_SHUFFLE2(1,1)); /* fy1 fy2 */
-
- /* store fx and fy */
- _mm_storeu_pd(faction+j13,xmm1);
- _mm_storeu_pd(faction+j23,xmm2);
-
- /* .. then fz */
- _mm_storel_pd(faction+j13+2,xmm7);
- _mm_storel_pd(faction+j23+2,xmm7);
+
+ /***********************************/
+ /* INTERACTION SECTION ENDS HERE */
+ /***********************************/
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_pd(fscal,dx);
+ ty = _mm_mul_pd(fscal,dy);
+ tz = _mm_mul_pd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_pd(fix,tx);
+ fiy = _mm_add_pd(fiy,ty);
+ fiz = _mm_add_pd(fiz,tz);
+
+ /* Store j forces back */
+ GMX_MM_DECREMENT_1RVEC_2POINTERS_PD(faction+j3A,faction+j3B,tx,ty,tz);
}
/* In double precision, offset can only be either 0 or 1 */
- if(offset!=0)
+ if(k<nj1)
{
- jnr1 = jjnr[k];
- j13 = jnr1*3;
-
- jx = _mm_load_sd(pos+j13);
- jy = _mm_load_sd(pos+j13+1);
- jz = _mm_load_sd(pos+j13+2);
-
- isaj = _mm_load_sd(invsqrta+jnr1);
- isaprod = _mm_mul_sd(isai,isaj);
- dvdaj = _mm_load_sd(dvda+jnr1);
- q = _mm_load_sd(charge+jnr1);
- qq = _mm_mul_sd(iq,q);
-
- dx = _mm_sub_sd(ix,jx);
- dy = _mm_sub_sd(iy,jy);
- dz = _mm_sub_sd(iz,jz);
-
- rsq11 = _mm_add_pd( _mm_add_pd( _mm_mul_pd(dx,dx) , _mm_mul_pd(dy,dy) ) , _mm_mul_pd(dz,dz) );
- rinv = gmx_mm_invsqrt_pd(rsq11);
-
- vcoul = _mm_mul_sd(qq,rinv);
- fscal = _mm_mul_sd(vcoul,rinv);
- qq = _mm_mul_sd(isaprod,qq);
- qq = _mm_mul_sd(qq,neg);
- gbscale = _mm_mul_sd(isaprod,gbtabscale);
-
- /* Load VdW parameters */
- tj = nti+2*type[jnr1];
-
- c6 = _mm_load_sd(vdwparam+tj);
- c12 = _mm_load_sd(vdwparam+tj+1);
-
- /* Calculate GB table index */
- r = _mm_mul_sd(rsq11,rinv);
- rt = _mm_mul_sd(r,gbscale);
- n0 = _mm_cvttpd_epi32(rt);
- n0d = _mm_cvtepi32_pd(n0);
- eps = _mm_sub_sd(rt,n0d);
- eps2 = _mm_mul_sd(eps,eps);
-
- nnn = _mm_slli_epi64(n0,2);
-
- xmm1 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,0)));
- xmm2 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,1)));
- xmm3 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,0))+2);
- xmm4 = _mm_load_pd(GBtab+(gmx_mm_extract_epi64(nnn,1))+2);
-
- Y = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0));
- F = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1));
- G = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(0,0));
- H = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(1,1));
-
- G = _mm_mul_sd(G,eps);
- H = _mm_mul_sd(H,eps2);
- Fp = _mm_add_sd(F,G);
- Fp = _mm_add_sd(Fp,H);
- VV = _mm_mul_sd(Fp,eps);
- VV = _mm_add_sd(Y,VV);
- H = _mm_mul_sd(two,H);
- FF = _mm_add_sd(Fp,G);
- FF = _mm_add_sd(FF,H);
- vgb = _mm_mul_sd(qq,VV);
- fijC = _mm_mul_sd(qq,FF);
- fijC = _mm_mul_sd(fijC,gbscale);
-
- dvdatmp = _mm_mul_sd(fijC,r);
- dvdatmp = _mm_add_sd(vgb,dvdatmp);
- dvdatmp = _mm_mul_sd(dvdatmp,neg);
- dvdatmp = _mm_mul_sd(dvdatmp,half);
- dvdasum = _mm_add_sd(dvdasum,dvdatmp);
-
- xmm1 = _mm_mul_sd(dvdatmp,isaj);
- xmm1 = _mm_mul_sd(xmm1,isaj);
- dvdaj = _mm_add_sd(dvdaj,xmm1);
-
- /* store dvda */
- _mm_storel_pd(dvda+jnr1,dvdaj);
-
- vctot = _mm_add_sd(vctot,vcoul);
- vgbtot = _mm_add_sd(vgbtot,vgb);
-
- /* Calculate VDW table index */
- rt = _mm_mul_sd(r,tabscale);
- n0 = _mm_cvttpd_epi32(rt);
- n0d = _mm_cvtepi32_pd(n0);
- eps = _mm_sub_sd(rt,n0d);
+ jnrA = jjnr[k];
+ j3A = jnrA * 3;
+
+ GMX_MM_LOAD_1RVEC_1POINTER_PD(pos+j3A,jx,jy,jz);
+
+ dx = _mm_sub_sd(ix,jx);
+ dy = _mm_sub_sd(iy,jy);
+ dz = _mm_sub_sd(iz,jz);
+
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
+ rinvsq = _mm_mul_sd(rinv,rinv);
+
+ /* These reason for zeroing these variables here is for fixing bug 585
+ * What happens is that __m128d _mm_add_sd(a,b) gives back r0=a[0]+b[0],
+ * and r1=0, but it should be r1=a[1].
+ * This might be a compiler issue (tested with gcc-4.1.3 and -O3).
+ * To work around it, we zero these variables and use _mm_add_pd (**) instead
+ * Note that the only variables that get affected are the energies since
+ * the total sum needs to be correct
+ */
+ vgb = _mm_setzero_pd();
+ vcoul = _mm_setzero_pd();
+ dvdatmp = _mm_setzero_pd();
+ vvdw6 = _mm_setzero_pd();
+ vvdw12 = _mm_setzero_pd();
+
+ /***********************************/
+ /* INTERACTION SECTION STARTS HERE */
+ /***********************************/
+ GMX_MM_LOAD_1VALUE_PD(charge+jnrA,jq);
+ GMX_MM_LOAD_1VALUE_PD(invsqrta+jnrA,isaj);
+
+ /* Lennard-Jones */
+ tjA = nti+2*type[jnrA];
+
+ GMX_MM_LOAD_1PAIR_PD(vdwparam+tjA,c6,c12);
+
+ isaprod = _mm_mul_sd(isai,isaj);
+ qq = _mm_mul_sd(jq,iq);
+ vcoul = _mm_mul_sd(qq,rinv);
+ fscal = _mm_mul_sd(vcoul,rinv);
+ vctot = _mm_add_pd(vctot,vcoul); /* (**) */
+
+ /* Polarization interaction */
+ qq = _mm_mul_sd(qq,_mm_mul_sd(isaprod,gbfactor));
+ gbscale = _mm_mul_sd(isaprod,gbtabscale);
+
+ /* Calculate GB table index */
+ r = _mm_mul_sd(rsq,rinv);
+ rtab = _mm_mul_sd(r,gbscale);
+
+ n0 = _mm_cvttpd_epi32(rtab);
+ eps = _mm_sub_sd(rtab,_mm_cvtepi32_pd(n0));
+ nnn = _mm_slli_epi32(n0,2);
+
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_sd(G,eps);
+ H = _mm_mul_sd(H, _mm_mul_sd(eps,eps) );
+ F = _mm_add_sd(F, _mm_add_sd( G , H ) );
+ Y = _mm_add_sd(Y, _mm_mul_sd(F, eps));
+ F = _mm_add_sd(F, _mm_add_sd(G , _mm_mul_sd(H,two)));
+ vgb = _mm_mul_sd(Y, qq);
+ fijGB = _mm_mul_sd(F, _mm_mul_sd(qq,gbscale));
+
+ dvdatmp = _mm_mul_sd(_mm_add_sd(vgb, _mm_mul_sd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb); /* (**) */
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp); /* (**) */
+ dvdatmp = _mm_mul_sd(dvdatmp, _mm_mul_sd(isaj,isaj));
+
+ GMX_MM_INCREMENT_1VALUE_PD(dvda+jnrA,dvdatmp);
+
+ /* Calculate VDW table index */
+ rtab = _mm_mul_sd(r,tabscale);
+ n0 = _mm_cvttpd_epi32(rtab);
+ eps = _mm_sub_sd(rtab,_mm_cvtepi32_pd(n0));
eps2 = _mm_mul_sd(eps,eps);
nnn = _mm_slli_epi32(n0,3);
- /* Tabulated VdW interaction - dispersion */
- xmm1 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,0))); /* Y1 F1 */
- xmm2 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,1))); /* Y2 F2 */
- xmm3 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,0))+2); /* G1 H1 */
- xmm4 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,1))+2); /* G2 H2 */
-
- Y = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0)); /* Y1 Y2 */
- F = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1)); /* F1 F2 */
- G = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(0,0)); /* G1 G2 */
- H = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(1,1)); /* H1 H2 */
-
- G = _mm_mul_sd(G,eps);
+ /* Dispersion */
+ Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_sd(G,eps);
H = _mm_mul_sd(H,eps2);
Fp = _mm_add_sd(F,G);
Fp = _mm_add_sd(Fp,H);
FF = _mm_add_sd(Fp,G);
FF = _mm_add_sd(FF,xmm1);
- Vvdw6 = _mm_mul_sd(c6,VV);
+ vvdw6 = _mm_mul_sd(c6,VV);
fijD = _mm_mul_sd(c6,FF);
-
- /* Tabulated VdW interaction - repulsion */
- nnn = _mm_add_epi32(nnn,four);
-
- xmm1 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,0))); /* Y1 F1 */
- xmm2 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,1))); /* Y2 F2 */
- xmm3 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,0))+2); /* G1 H1 */
- xmm4 = _mm_load_pd(VFtab+(gmx_mm_extract_epi64(nnn,1))+2); /* G2 H2 */
-
- Y = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(0,0)); /* Y1 Y2 */
- F = _mm_shuffle_pd(xmm1,xmm2,_MM_SHUFFLE2(1,1)); /* F1 F2 */
- G = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(0,0)); /* G1 G2 */
- H = _mm_shuffle_pd(xmm3,xmm4,_MM_SHUFFLE2(1,1)); /* H1 H2 */
-
- G = _mm_mul_sd(G,eps);
+
+ /* Dispersion */
+ Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+4);
+ F = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+6);
+ H = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_sd(G,eps);
H = _mm_mul_sd(H,eps2);
Fp = _mm_add_sd(F,G);
Fp = _mm_add_sd(Fp,H);
FF = _mm_add_sd(Fp,G);
FF = _mm_add_sd(FF,xmm1);
- Vvdw12 = _mm_mul_sd(c12,VV);
+ vvdw12 = _mm_mul_sd(c12,VV);
fijR = _mm_mul_sd(c12,FF);
- Vvdwtmp = _mm_add_sd(Vvdw12,Vvdw6);
- Vvdwtot = _mm_add_sd(Vvdwtot,Vvdwtmp);
-
+ vvdwtmp = _mm_add_sd(vvdw12,vvdw6);
+ vvdwtot = _mm_add_pd(vvdwtot,vvdwtmp); /* (**) */
+
xmm1 = _mm_add_sd(fijD,fijR);
xmm1 = _mm_mul_sd(xmm1,tabscale);
- xmm1 = _mm_add_sd(xmm1,fijC);
+ xmm1 = _mm_add_sd(xmm1,fijGB);
xmm1 = _mm_sub_sd(xmm1,fscal);
fscal = _mm_mul_sd(xmm1,neg);
fscal = _mm_mul_sd(fscal,rinv);
-
- /* calculate partial force terms */
- t1 = _mm_mul_sd(fscal,dx);
- t2 = _mm_mul_sd(fscal,dy);
- t3 = _mm_mul_sd(fscal,dz);
-
- /* update the i force */
- fix = _mm_add_sd(fix,t1);
- fiy = _mm_add_sd(fiy,t2);
- fiz = _mm_add_sd(fiz,t3);
-
- /* accumulate forces from memory */
- xmm5 = _mm_load_sd(faction+j13); /* fx */
- xmm6 = _mm_load_sd(faction+j13+1); /* fy */
- xmm7 = _mm_load_sd(faction+j13+2); /* fz */
-
- /* subtract partial forces */
- xmm5 = _mm_sub_sd(xmm5,t1);
- xmm6 = _mm_sub_sd(xmm6,t2);
- xmm7 = _mm_sub_sd(xmm7,t3);
-
- /* store forces */
- _mm_store_sd(faction+j13,xmm5);
- _mm_store_sd(faction+j13+1,xmm6);
- _mm_store_sd(faction+j13+2,xmm7);
+
+ /***********************************/
+ /* INTERACTION SECTION ENDS HERE */
+ /***********************************/
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_sd(fscal,dx);
+ ty = _mm_mul_sd(fscal,dy);
+ tz = _mm_mul_sd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_sd(fix,tx);
+ fiy = _mm_add_sd(fiy,ty);
+ fiz = _mm_add_sd(fiz,tz);
+
+ /* Store j forces back */
+ GMX_MM_DECREMENT_1RVEC_1POINTER_PD(faction+j3A,tx,ty,tz);
}
- /* fix/fiy/fiz now contain four partial terms, that all should be
- * added to the i particle forces
- */
- t1 = _mm_unpacklo_pd(t1,fix);
- t2 = _mm_unpacklo_pd(t2,fiy);
- t3 = _mm_unpacklo_pd(t3,fiz);
-
- fix = _mm_add_pd(fix,t1);
- fiy = _mm_add_pd(fiy,t2);
- fiz = _mm_add_pd(fiz,t3);
-
- fix = _mm_shuffle_pd(fix,fix,_MM_SHUFFLE2(1,1));
- fiy = _mm_shuffle_pd(fiy,fiy,_MM_SHUFFLE2(1,1));
- fiz = _mm_shuffle_pd(fiz,fiz,_MM_SHUFFLE2(1,1));
-
- /* Load i forces from memory */
- xmm1 = _mm_load_sd(faction+ii3);
- xmm2 = _mm_load_sd(faction+ii3+1);
- xmm3 = _mm_load_sd(faction+ii3+2);
-
- /* Add to i force */
- fix = _mm_add_sd(fix,xmm1);
- fiy = _mm_add_sd(fiy,xmm2);
- fiz = _mm_add_sd(fiz,xmm3);
-
- /* store i forces to memory */
- _mm_store_sd(faction+ii3,fix);
- _mm_store_sd(faction+ii3+1,fiy);
- _mm_store_sd(faction+ii3+2,fiz);
-
- /* now do dvda */
- dvdatmp = _mm_unpacklo_pd(dvdatmp,dvdasum);
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- _mm_storeh_pd(&dva,dvdasum);
- dvda[ii] = dvda[ii] + dva*isai_d*isai_d;
-
- ggid = gid[n];
-
- /* Coulomb potential */
- vcoul = _mm_unpacklo_pd(vcoul,vctot);
- vctot = _mm_add_pd(vctot,vcoul);
- _mm_storeh_pd(&vct,vctot);
- Vc[ggid] = Vc[ggid] + vct;
-
- /* VdW potential */
- Vvdwtmp = _mm_unpacklo_pd(Vvdwtmp,Vvdwtot);
- Vvdwtot = _mm_add_pd(Vvdwtot,Vvdwtmp);
- _mm_storeh_pd(&vdwt,Vvdwtot);
- Vvdw[ggid] = Vvdw[ggid] + vdwt;
-
- /* GB potential */
- vgb = _mm_unpacklo_pd(vgb,vgbtot);
- vgbtot = _mm_add_pd(vgbtot,vgb);
- _mm_storeh_pd(&vgbt,vgbtot);
- gpol[ggid] = gpol[ggid] + vgbt;
- }
-
- *outeriter = nri;
- *inneriter = nj1;
-}
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel430nf
- * Coulomb interaction: Generalized-Born
- * VdW interaction: Tabulated
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel430nf_sse2_double(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- double * shiftvec,
- double * fshift,
- int * gid,
- double * pos,
- double * faction,
- double * charge,
- double * p_facel,
- double * p_krf,
- double * p_crf,
- double * Vc,
- int * type,
- int * p_ntype,
- double * vdwparam,
- double * Vvdw,
- double * p_tabscale,
- double * VFtab,
- double * invsqrta,
- double * dvda,
- double * p_gbtabscale,
- double * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- double * work)
-{
- int nri,ntype,nthreads;
- double facel,krf,crf,tabscale,gbtabscale,vgb,fgb;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- double shX,shY,shZ;
- double iq;
- double qq,vcoul,vctot;
- int nti;
- int tj;
- double Vvdw6,Vvdwtot;
- double Vvdw12;
- double r,rt,eps,eps2;
- int n0,nnn;
- double Y,F,Geps,Heps2,Fp,VV;
- double isai,isaj,isaprod,gbscale;
- double ix1,iy1,iz1;
- double jx1,jy1,jz1;
- double dx11,dy11,dz11,rsq11,rinv11;
- double c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
- gbtabscale = *p_gbtabscale;
- nj1 = 0;
+ dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai,isai));
+ gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,faction+ii3,fshift+is3);
- for(n=0; (n<nri); n++)
- {
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
- nj0 = jindex[n];
- nj1 = jindex[n+1];
- ii = iinr[n];
- ii3 = 3*ii;
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- iq = facel*charge[ii];
- isai = invsqrta[ii];
- nti = 2*ntype*type[ii];
- vctot = 0;
- Vvdwtot = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
- jnr = jjnr[k];
- j3 = 3*jnr;
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- rinv11 = gmx_invsqrt(rsq11);
- isaj = invsqrta[jnr];
- isaprod = isai*isaj;
- qq = iq*charge[jnr];
- vcoul = qq*rinv11;
- qq = isaprod*(-qq);
- gbscale = isaprod*gbtabscale;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- r = rsq11*rinv11;
- rt = r*gbscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
- Y = GBtab[nnn];
- F = GBtab[nnn+1];
- Geps = eps*GBtab[nnn+2];
- Heps2 = eps2*GBtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vgb = qq*VV;
- vctot = vctot + vcoul;
- r = rsq11*rinv11;
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- }
-
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
- }
+ ggid = gid[n];
+
+ gmx_mm_update_1pot_pd(vctot,vc+ggid);
+ gmx_mm_update_1pot_pd(vgbtot,gpol+ggid);
+ gmx_mm_update_1pot_pd(dvdasum,dvda+ii);
+ gmx_mm_update_1pot_pd(vvdwtot,vvdw+ggid);
- *outeriter = nri;
- *inneriter = nj1;
+ }
+
+ *outeriter = nri;
+ *inneriter = nj1;
}
-
/* get gmx_gbdata_t */
#include "../nb_kerneltype.h"
-#include "nb_kernel400_sse2_single.h"
-
-
void nb_kernel400_sse2_single(int * p_nri,
int * iinr,
fix = _mm_setzero_ps();
fiy = _mm_setzero_ps();
fiz = _mm_setzero_ps();
-
+
for(k=nj0; k<nj1-7; k+=8)
{
jnrA = jjnr[k];
rB = _mm_mul_ps(rsqB,rinvB);
rtab = _mm_mul_ps(r,gbscale);
rtabB = _mm_mul_ps(rB,gbscaleB);
-
+
n0 = _mm_cvttps_epi32(rtab);
n0B = _mm_cvttps_epi32(rtabB);
eps = _mm_sub_ps(rtab , _mm_cvtepi32_ps(n0) );
FB = _mm_add_ps(FB, _mm_add_ps(GB , _mm_mul_ps(HB,two)));
vgbB = _mm_mul_ps(YB, qqB);
fijGBB = _mm_mul_ps(FB, _mm_mul_ps(qqB,gbscaleB));
-
-
+
dvdatmp = _mm_mul_ps(_mm_add_ps(vgb, _mm_mul_ps(fijGB,r)) , minushalf);
dvdatmpB = _mm_mul_ps(_mm_add_ps(vgbB, _mm_mul_ps(fijGBB,rB)) , minushalf);
/* Calculate GB table index */
r = _mm_mul_ps(rsq,rinv);
rtab = _mm_mul_ps(r,gbscale);
-
+
n0 = _mm_cvttps_epi32(rtab);
eps = _mm_sub_ps(rtab , _mm_cvtepi32_ps(n0) );
nnn = _mm_slli_epi32(n0,2);
F = _mm_add_ps(F, _mm_add_ps(G , _mm_mul_ps(H,two)));
vgb = _mm_mul_ps(Y, qq);
fijGB = _mm_mul_ps(F, _mm_mul_ps(qq,gbscale));
-
+
dvdatmp = _mm_mul_ps(_mm_add_ps(vgb, _mm_mul_ps(fijGB,r)) , minushalf);
vgbtot = _mm_add_ps(vgbtot, vgb);
/* Calculate GB table index */
r = _mm_mul_ps(rsq,rinv);
rtab = _mm_mul_ps(r,gbscale);
-
+
n0 = _mm_cvttps_epi32(rtab);
eps = _mm_sub_ps(rtab , _mm_cvtepi32_ps(n0) );
nnn = _mm_slli_epi32(n0,2);
F = _mm_add_ps(F, _mm_add_ps(G , _mm_mul_ps(H,two)));
vgb = _mm_mul_ps(Y, qq);
fijGB = _mm_mul_ps(F, _mm_mul_ps(qq,gbscale));
-
+
dvdatmp = _mm_mul_ps(_mm_add_ps(vgb, _mm_mul_ps(fijGB,r)) , minushalf);
vgbtot = _mm_add_ps(vgbtot, vgb);
* water optimization: No
* Calculate forces: no
*/
-void nb_kernel400nf_sse2_single(
+void nb_kernel400nf_x86_64_sse(
int * p_nri,
int * iinr,
int * jindex,
/* get gmx_gbdata_t */
#include "../nb_kerneltype.h"
-#include "nb_kernel410_sse2_single.h"
-
-
void nb_kernel410_sse2_single(int * p_nri,
int * iinr,
__m128i n0, nnn;
__m128i n0B, nnnB;
- const __m128 neg = {-1.0f,-1.0f,-1.0f,-1.0f};
- const __m128 zero = {0.0f,0.0f,0.0f,0.0f};
- const __m128 minushalf = {-0.5f,-0.5f,-0.5f,-0.5f};
- const __m128 two = {2.0f,2.0f,2.0f,2.0f};
- const __m128 six = {6.0f,6.0f,6.0f,6.0f};
- const __m128 twelve = {12.0f,12.0f,12.0f,12.0f};
+ const __m128 neg = _mm_set1_ps(-1.0f);
+ const __m128 zero = _mm_set1_ps(0.0f);
+ const __m128 minushalf = _mm_set1_ps(-0.5f);
+ const __m128 two = _mm_set1_ps(2.0f);
+ const __m128 six = _mm_set1_ps(6.0f);
+ const __m128 twelve = _mm_set1_ps(12.0f);
gbdata = (gmx_gbdata_t *)work;
gpol = gbdata->gpol;
* water optimization: No
* Calculate forces: no
*/
-void nb_kernel410nf_sse2_single(
+void nb_kernel410nf_x86_64_sse(
int * p_nri,
int * iinr,
int * jindex,
#include <xmmintrin.h>
#include <emmintrin.h>
+
#include <gmx_sse2_single.h>
/* get gmx_gbdata_t */
#include "../nb_kerneltype.h"
-#include "nb_kernel430_sse2_single.h"
-
-/* to extract single integers from a __m128i datatype */
-#define _mm_extract_epi32(x, imm) \
-_mm_cvtsi128_si32(_mm_srli_si128((x), 4 * (imm)))
void nb_kernel430_sse2_single(int * p_nri,
int * iinr,
__m128 fac_sse,tabscale_sse,gbtabscale_sse;
__m128i n0, nnn;
- const __m128 neg = {-1.0f,-1.0f,-1.0f,-1.0f};
- const __m128 zero = {0.0f,0.0f,0.0f,0.0f};
- const __m128 half = {0.5f,0.5f,0.5f,0.5f};
- const __m128 two = {2.0f,2.0f,2.0f,2.0f};
- const __m128 three = {3.0f,3.0f,3.0f,3.0f};
- const __m128 six = {6.0f,6.0f,6.0f,6.0f};
- const __m128 twelwe = {12.0f,12.0f,12.0f,12.0f};
+ const __m128 neg = _mm_set1_ps(-1.0f);
+ const __m128 zero = _mm_set1_ps(0.0f);
+ const __m128 half = _mm_set1_ps(0.5f);
+ const __m128 two = _mm_set1_ps(2.0f);
+ const __m128 three = _mm_set1_ps(3.0f);
+ const __m128 six = _mm_set1_ps(6.0f);
+ const __m128 twelwe = _mm_set1_ps(12.0f);
- __m128i four = _mm_set_epi32(4,4,4,4);
+ __m128i four = _mm_set1_epi32(4);
__m128i maski = _mm_set_epi32(0, 0xffffffff, 0xffffffff, 0xffffffff);
__m128i mask = _mm_set_epi32(0, 0xffffffff, 0xffffffff, 0xffffffff);
gpol = gbdata->gpol;
nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = (*p_facel) * ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent));
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
- gbtabscale = *p_gbtabscale;
- nj1 = 0;
+ ntype = *p_ntype;
+ nthreads = *p_nthreads;
+ facel = (*p_facel) * ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent));
+ krf = *p_krf;
+ crf = *p_crf;
+ tabscale = *p_tabscale;
+ gbtabscale = *p_gbtabscale;
+ nj1 = 0;
/* Splat variables */
fac_sse = _mm_load1_ps(&facel);
nnn = _mm_slli_epi32(n0,2);
/* the tables are 16-byte aligned, so we can use _mm_load_ps */
- xmm1 = _mm_load_ps(GBtab+(_mm_extract_epi32(nnn,0))); /* Y1,F1,G1,H1 */
- xmm2 = _mm_load_ps(GBtab+(_mm_extract_epi32(nnn,1))); /* Y2,F2,G2,H2 */
- xmm3 = _mm_load_ps(GBtab+(_mm_extract_epi32(nnn,2))); /* Y3,F3,G3,H3 */
- xmm4 = _mm_load_ps(GBtab+(_mm_extract_epi32(nnn,3))); /* Y4,F4,G4,H4 */
+ xmm1 = _mm_load_ps(GBtab+(gmx_mm_extract_epi32(nnn,0))); /* Y1,F1,G1,H1 */
+ xmm2 = _mm_load_ps(GBtab+(gmx_mm_extract_epi32(nnn,1))); /* Y2,F2,G2,H2 */
+ xmm3 = _mm_load_ps(GBtab+(gmx_mm_extract_epi32(nnn,2))); /* Y3,F3,G3,H3 */
+ xmm4 = _mm_load_ps(GBtab+(gmx_mm_extract_epi32(nnn,3))); /* Y4,F4,G4,H4 */
/* transpose 4*4 */
xmm5 = _mm_unpacklo_ps(xmm1,xmm2); /* Y1,Y2,F1,F2 */
nnn = _mm_slli_epi32(n0,3);
/* Tabulated VdW interaction - disperion */
- xmm1 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,0))); /* Y1,F1,G1,H1 */
- xmm2 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,1))); /* Y2,F2,G2,H2 */
- xmm3 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,2))); /* Y3,F3,G3,H3 */
- xmm4 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,3))); /* Y4,F4,G4,H4 */
+ xmm1 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,0))); /* Y1,F1,G1,H1 */
+ xmm2 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,1))); /* Y2,F2,G2,H2 */
+ xmm3 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,2))); /* Y3,F3,G3,H3 */
+ xmm4 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,3))); /* Y4,F4,G4,H4 */
/* transpose 4*4 */
xmm5 = _mm_unpacklo_ps(xmm1,xmm2); /* Y1,Y2,F1,F2 */
/* Tabulated VdW interaction - repulsion */
nnn = _mm_add_epi32(nnn,four);
- xmm1 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,0))); /* Y1,F1,G1,H1 */
- xmm2 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,1))); /* Y2,F2,G2,H2 */
- xmm3 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,2))); /* Y3,F3,G3,H3 */
- xmm4 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,3))); /* Y4,F4,G4,H4 */
+ xmm1 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,0))); /* Y1,F1,G1,H1 */
+ xmm2 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,1))); /* Y2,F2,G2,H2 */
+ xmm3 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,2))); /* Y3,F3,G3,H3 */
+ xmm4 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,3))); /* Y4,F4,G4,H4 */
/* transpose 4*4 */
xmm5 = _mm_unpacklo_ps(xmm1,xmm2); /* Y1,Y2,F1,F2 */
nnn = _mm_slli_epi32(n0,2);
/* the tables are 16-byte aligned, so we can use _mm_load_ps */
- xmm1 = _mm_load_ps(GBtab+(_mm_extract_epi32(nnn,0))); /* Y1,F1,G1,H1 */
- xmm2 = _mm_load_ps(GBtab+(_mm_extract_epi32(nnn,1))); /* Y2,F2,G2,H2 */
- xmm3 = _mm_load_ps(GBtab+(_mm_extract_epi32(nnn,2))); /* Y3,F3,G3,H3 */
- xmm4 = _mm_load_ps(GBtab+(_mm_extract_epi32(nnn,3))); /* Y4,F4,G4,H4 */
+ xmm1 = _mm_load_ps(GBtab+(gmx_mm_extract_epi32(nnn,0))); /* Y1,F1,G1,H1 */
+ xmm2 = _mm_load_ps(GBtab+(gmx_mm_extract_epi32(nnn,1))); /* Y2,F2,G2,H2 */
+ xmm3 = _mm_load_ps(GBtab+(gmx_mm_extract_epi32(nnn,2))); /* Y3,F3,G3,H3 */
+ xmm4 = _mm_load_ps(GBtab+(gmx_mm_extract_epi32(nnn,3))); /* Y4,F4,G4,H4 */
/* transpose 4*4 */
xmm5 = _mm_unpacklo_ps(xmm1,xmm2); /* Y1,Y2,F1,F2 */
nnn = _mm_slli_epi32(n0,3);
/* Tabulated VdW interaction - disperion */
- xmm1 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,0))); /* Y1,F1,G1,H1 */
- xmm2 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,1))); /* Y2,F2,G2,H2 */
- xmm3 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,2))); /* Y3,F3,G3,H3 */
- xmm4 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,3))); /* Y4,F4,G4,H4 */
+ xmm1 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,0))); /* Y1,F1,G1,H1 */
+ xmm2 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,1))); /* Y2,F2,G2,H2 */
+ xmm3 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,2))); /* Y3,F3,G3,H3 */
+ xmm4 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,3))); /* Y4,F4,G4,H4 */
/* transpose 4*4 */
xmm5 = _mm_unpacklo_ps(xmm1,xmm2); /* Y1,Y2,F1,F2 */
/* Tabulated VdW interaction - repulsion */
nnn = _mm_add_epi32(nnn,four);
- xmm1 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,0))); /* Y1,F1,G1,H1 */
- xmm2 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,1))); /* Y2,F2,G2,H2 */
- xmm3 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,2))); /* Y3,F3,G3,H3 */
- xmm4 = _mm_load_ps(VFtab+(_mm_extract_epi32(nnn,3))); /* Y4,F4,G4,H4 */
+ xmm1 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,0))); /* Y1,F1,G1,H1 */
+ xmm2 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,1))); /* Y2,F2,G2,H2 */
+ xmm3 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,2))); /* Y3,F3,G3,H3 */
+ xmm4 = _mm_load_ps(VFtab+(gmx_mm_extract_epi32(nnn,3))); /* Y4,F4,G4,H4 */
/* transpose 4*4 */
xmm5 = _mm_unpacklo_ps(xmm1,xmm2); /* Y1,Y2,F1,F2 */
* water optimization: No
* Calculate forces: no
*/
-void nb_kernel430nf_sse2_single(
+void nb_kernel430nf_x86_64_sse(
int * p_nri,
int * iinr,
int * jindex,
dy11 = iy1 - jy1;
dz11 = iz1 - jz1;
rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- rinv11 = gmx_mm_invsqrt(rsq11);
+ rinv11 = gmx_invsqrt(rsq11);
isaj = invsqrta[jnr];
isaprod = isai*isaj;
qq = iq*charge[jnr];
int * inneriter,
double * work)
{
- int nri,nthreads;
- int n,ii,is3,ii3,k,nj0,nj1,ggid;
- double shX,shY,shZ;
- int jnrA,jnrB;
- int j3A,j3B;
+ int nri,nthreads;
+ int n,ii,is3,ii3,k,nj0,nj1,ggid;
+ double shX,shY,shZ;
+ int jnrA,jnrB;
+ int j3A,j3B;
gmx_gbdata_t *gbdata;
double * gpol;
nri = *p_nri;
- gbfactor = _mm_set1_pd( - ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent)));
- gbtabscale = _mm_load1_pd(p_gbtabscale);
- facel = _mm_load1_pd(p_facel);
-
- nj1 = 0;
- jnrA = jnrB = 0;
- j3A = j3B = 0;
- jx = _mm_setzero_pd();
- jy = _mm_setzero_pd();
- jz = _mm_setzero_pd();
+ gbfactor = _mm_set1_pd( - ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent)));
+ gbtabscale = _mm_load1_pd(p_gbtabscale);
+ facel = _mm_load1_pd(p_facel);
+
+ nj1 = 0;
+ jnrA = jnrB = 0;
+ j3A = j3B = 0;
+ jx = _mm_setzero_pd();
+ jy = _mm_setzero_pd();
+ jz = _mm_setzero_pd();
for(n=0;n<nri;n++)
{
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
- nj0 = jindex[n];
- nj1 = jindex[n+1];
- ii = iinr[n];
- ii3 = 3*ii;
+ is3 = 3*shift[n];
+ shX = shiftvec[is3];
+ shY = shiftvec[is3+1];
+ shZ = shiftvec[is3+2];
+ nj0 = jindex[n];
+ nj1 = jindex[n+1];
+ ii = iinr[n];
+ ii3 = 3*ii;
ix = _mm_set1_pd(shX+pos[ii3+0]);
iy = _mm_set1_pd(shY+pos[ii3+1]);
iz = _mm_set1_pd(shZ+pos[ii3+2]);
-
+
iq = _mm_load1_pd(charge+ii);
iq = _mm_mul_pd(iq,facel);
-
+
isai = _mm_load1_pd(invsqrta+ii);
vctot = _mm_setzero_pd();
j3A = jnrA * 3;
j3B = jnrB * 3;
-
- GMX_MM_LOAD_1RVEC_2POINTERS_PD(pos+j3A,pos+j3B,jx,jy,jz);
+
+ GMX_MM_LOAD_1RVEC_2POINTERS_PD(pos+j3A,pos+j3B,jx,jy,jz);
dx = _mm_sub_pd(ix,jx);
dy = _mm_sub_pd(iy,jy);
dz = _mm_sub_pd(iz,jz);
- rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
-
- rinv = gmx_mm_invsqrt_pd(rsq);
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
rinvsq = _mm_mul_pd(rinv,rinv);
-
+
/***********************************/
/* INTERACTION SECTION STARTS HERE */
/***********************************/
qq = _mm_mul_pd(iq,jq);
vcoul = _mm_mul_pd(qq,rinv);
fscal = _mm_mul_pd(vcoul,rinv);
- vctot = _mm_add_pd(vctot,vcoul);
+ vctot = _mm_add_pd(vctot,vcoul);
/* Polarization interaction */
qq = _mm_mul_pd(qq,_mm_mul_pd(isaprod,gbfactor));
eps = _mm_sub_pd(rtab,_mm_cvtepi32_pd(n0));
nnn = _mm_slli_epi32(n0,2);
- /* the tables are 16-byte aligned, so we can use _mm_load_pd */
- Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1)));
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1))+2);
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_pd(G,eps);
- H = _mm_mul_pd(H, _mm_mul_pd(eps,eps) );
- F = _mm_add_pd(F, _mm_add_pd( G , H ) );
- Y = _mm_add_pd(Y, _mm_mul_pd(F, eps));
- F = _mm_add_pd(F, _mm_add_pd(G , _mm_mul_pd(H,two)));
- vgb = _mm_mul_pd(Y, qq);
- fijGB = _mm_mul_pd(F, _mm_mul_pd(qq,gbscale));
-
- dvdatmp = _mm_mul_pd(_mm_add_pd(vgb, _mm_mul_pd(fijGB,r)) , minushalf);
-
- vgbtot = _mm_add_pd(vgbtot, vgb);
-
- dvdasum = _mm_add_pd(dvdasum, dvdatmp);
- dvdatmp = _mm_mul_pd(dvdatmp, _mm_mul_pd(isaj,isaj));
-
- GMX_MM_INCREMENT_2VALUES_PD(dvda+jnrA,dvda+jnrB,dvdatmp);
-
- fscal = _mm_mul_pd( _mm_sub_pd( fscal, fijGB),rinv );
-
- /***********************************/
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1)));
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1))+2);
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_pd(G,eps);
+ H = _mm_mul_pd(H, _mm_mul_pd(eps,eps) );
+ F = _mm_add_pd(F, _mm_add_pd( G , H ) );
+ Y = _mm_add_pd(Y, _mm_mul_pd(F, eps));
+ F = _mm_add_pd(F, _mm_add_pd(G , _mm_mul_pd(H,two)));
+ vgb = _mm_mul_pd(Y, qq);
+ fijGB = _mm_mul_pd(F, _mm_mul_pd(qq,gbscale));
+
+ dvdatmp = _mm_mul_pd(_mm_add_pd(vgb, _mm_mul_pd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb);
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp);
+ dvdatmp = _mm_mul_pd(dvdatmp, _mm_mul_pd(isaj,isaj));
+
+ GMX_MM_INCREMENT_2VALUES_PD(dvda+jnrA,dvda+jnrB,dvdatmp);
+
+ fscal = _mm_mul_pd( _mm_sub_pd( fscal, fijGB),rinv );
+
+ /***********************************/
/* INTERACTION SECTION ENDS HERE */
/***********************************/
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx);
- ty = _mm_mul_pd(fscal,dy);
- tz = _mm_mul_pd(fscal,dz);
-
- /* Increment i atom force */
- fix = _mm_add_pd(fix,tx);
- fiy = _mm_add_pd(fiy,ty);
- fiz = _mm_add_pd(fiz,tz);
-
- /* Store j forces back */
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_pd(fscal,dx);
+ ty = _mm_mul_pd(fscal,dy);
+ tz = _mm_mul_pd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_pd(fix,tx);
+ fiy = _mm_add_pd(fiy,ty);
+ fiz = _mm_add_pd(fiz,tz);
+
+ /* Store j forces back */
GMX_MM_DECREMENT_1RVEC_2POINTERS_PD(faction+j3A,faction+j3B,tx,ty,tz);
}
{
jnrA = jjnr[k];
j3A = jnrA * 3;
-
- GMX_MM_LOAD_1RVEC_1POINTER_PD(pos+j3A,jx,jy,jz);
-
+
+ GMX_MM_LOAD_1RVEC_1POINTER_PD(pos+j3A,jx,jy,jz);
+
dx = _mm_sub_sd(ix,jx);
dy = _mm_sub_sd(iy,jy);
dz = _mm_sub_sd(iz,jz);
-
- rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
-
- rinv = gmx_mm_invsqrt_pd(rsq);
+
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
rinvsq = _mm_mul_sd(rinv,rinv);
-
+
+ /* These reason for zeroing these variables here is for fixing bug 585
+ * What happens is that __m128d _mm_add_sd(a,b) gives back r0=a[0]+b[0],
+ * and r1=0, but it should be r1=a[1].
+ * This might be a compiler issue (tested with gcc-4.1.3 and -O3).
+ * To work around it, we zero these variables and use _mm_add_pd (**) instead
+ * Note that the only variables that get affected are the energies since
+ * the total sum needs to be correct
+ */
+ vcoul = _mm_setzero_pd();
+ dvdatmp = _mm_setzero_pd();
+ vgb = _mm_setzero_pd();
+
/***********************************/
/* INTERACTION SECTION STARTS HERE */
/***********************************/
GMX_MM_LOAD_1VALUE_PD(charge+jnrA,jq);
GMX_MM_LOAD_1VALUE_PD(invsqrta+jnrA,isaj);
-
+
isaprod = _mm_mul_sd(isai,isaj);
- qq = _mm_mul_sd(iq,jq);
- vcoul = _mm_mul_sd(qq,rinv);
- fscal = _mm_mul_sd(vcoul,rinv);
- vctot = _mm_add_sd(vctot,vcoul);
-
- /* Polarization interaction */
+ /* Since we need _mm_add_pd below, the order here og jq,iq becomes important */
+ qq = _mm_mul_sd(jq,iq);
+ vcoul = _mm_mul_sd(qq,rinv);
+ fscal = _mm_mul_sd(vcoul,rinv);
+ vctot = _mm_add_pd(vctot,vcoul); /* (**) */
+
+ /* Polarization interaction */
qq = _mm_mul_sd(qq,_mm_mul_sd(isaprod,gbfactor));
gbscale = _mm_mul_sd(isaprod,gbtabscale);
-
+
/* Calculate GB table index */
r = _mm_mul_sd(rsq,rinv);
rtab = _mm_mul_sd(r,gbscale);
-
+
n0 = _mm_cvttpd_epi32(rtab);
eps = _mm_sub_sd(rtab,_mm_cvtepi32_pd(n0));
nnn = _mm_slli_epi32(n0,2);
- /* the tables are 16-byte aligned, so we can use _mm_load_pd */
- Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_sd(G,eps);
- H = _mm_mul_sd(H, _mm_mul_sd(eps,eps) );
- F = _mm_add_sd(F, _mm_add_sd( G , H ) );
- Y = _mm_add_sd(Y, _mm_mul_sd(F, eps));
- F = _mm_add_sd(F, _mm_add_sd(G , _mm_mul_sd(H,two)));
- vgb = _mm_mul_sd(Y, qq);
- fijGB = _mm_mul_sd(F, _mm_mul_sd(qq,gbscale));
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(G,H);
- dvdatmp = _mm_mul_sd(_mm_add_sd(vgb, _mm_mul_sd(fijGB,r)) , minushalf);
-
- vgbtot = _mm_add_sd(vgbtot, vgb);
-
- dvdasum = _mm_add_sd(dvdasum, dvdatmp);
- dvdatmp = _mm_mul_sd(dvdatmp, _mm_mul_sd(isaj,isaj));
-
- GMX_MM_INCREMENT_1VALUE_PD(dvda+jnrA,dvdatmp);
+ G = _mm_mul_sd(G,eps);
+ H = _mm_mul_sd(H, _mm_mul_sd(eps,eps) );
+ F = _mm_add_sd(F, _mm_add_sd( G , H ) );
+ Y = _mm_add_sd(Y, _mm_mul_sd(F, eps));
+ F = _mm_add_sd(F, _mm_add_sd(G , _mm_mul_sd(H,two)));
+ vgb = _mm_mul_sd(Y, qq);
+ fijGB = _mm_mul_sd(F, _mm_mul_sd(qq,gbscale));
+ dvdatmp = _mm_mul_sd(_mm_add_sd(vgb, _mm_mul_sd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb); /* (**) */
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp); /* (**) */
+ dvdatmp = _mm_mul_sd(dvdatmp, _mm_mul_sd(isaj,isaj));
+
+ GMX_MM_INCREMENT_1VALUE_PD(dvda+jnrA,dvdatmp);
- fscal = _mm_mul_sd( _mm_sub_sd( fscal, fijGB),rinv );
-
- /***********************************/
+ fscal = _mm_mul_sd( _mm_sub_sd( fscal, fijGB),rinv );
+
+ /***********************************/
/* INTERACTION SECTION ENDS HERE */
/***********************************/
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_sd(fscal,dx);
- ty = _mm_mul_sd(fscal,dy);
- tz = _mm_mul_sd(fscal,dz);
-
- /* Increment i atom force */
- fix = _mm_add_sd(fix,tx);
- fiy = _mm_add_sd(fiy,ty);
- fiz = _mm_add_sd(fiz,tz);
-
- /* Store j forces back */
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_sd(fscal,dx);
+ ty = _mm_mul_sd(fscal,dy);
+ tz = _mm_mul_sd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_sd(fix,tx);
+ fiy = _mm_add_sd(fiy,ty);
+ fiz = _mm_add_sd(fiz,tz);
+
+ /* Store j forces back */
GMX_MM_DECREMENT_1RVEC_1POINTER_PD(faction+j3A,tx,ty,tz);
}
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai,isai));
- gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,faction+ii3,fshift+is3);
-
- ggid = gid[n];
-
- gmx_mm_update_1pot_pd(vctot,vc+ggid);
- gmx_mm_update_2pot_pd(vgbtot,gpol+ggid,dvdasum,dvda+ii);
- }
+ dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai,isai));
+ gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,faction+ii3,fshift+is3);
+ ggid = gid[n];
+
+ gmx_mm_update_1pot_pd(vctot,vc+ggid);
+ gmx_mm_update_1pot_pd(vgbtot,gpol+ggid);
+ gmx_mm_update_1pot_pd(dvdasum,dvda+ii);
+ }
+
*outeriter = nri;
- *inneriter = nj1;
+ *inneriter = nj1;
}
int * inneriter,
double * work)
{
- int nri,ntype,nthreads;
- int n,ii,is3,ii3,k,nj0,nj1,ggid;
- double shX,shY,shZ;
+ int nri,ntype,nthreads;
+ int n,ii,is3,ii3,k,nj0,nj1,ggid;
+ double shX,shY,shZ;
int offset,nti;
- int jnrA,jnrB;
- int j3A,j3B;
+ int jnrA,jnrB;
+ int j3A,j3B;
int tjA,tjB;
gmx_gbdata_t *gbdata;
double * gpol;
-
+
__m128d iq,qq,jq,isai;
__m128d ix,iy,iz;
__m128d jx,jy,jz;
nri = *p_nri;
ntype = *p_ntype;
- gbfactor = _mm_set1_pd( - ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent)));
- gbtabscale = _mm_load1_pd(p_gbtabscale);
- facel = _mm_load1_pd(p_facel);
-
- nj1 = 0;
- jnrA = jnrB = 0;
- j3A = j3B = 0;
- jx = _mm_setzero_pd();
- jy = _mm_setzero_pd();
- jz = _mm_setzero_pd();
- c6 = _mm_setzero_pd();
- c12 = _mm_setzero_pd();
+ gbfactor = _mm_set1_pd( - ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent)));
+ gbtabscale = _mm_load1_pd(p_gbtabscale);
+ facel = _mm_load1_pd(p_facel);
+
+ nj1 = 0;
+ jnrA = jnrB = 0;
+ j3A = j3B = 0;
+ jx = _mm_setzero_pd();
+ jy = _mm_setzero_pd();
+ jz = _mm_setzero_pd();
+ c6 = _mm_setzero_pd();
+ c12 = _mm_setzero_pd();
for(n=0;n<nri;n++)
{
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
- nj0 = jindex[n];
- nj1 = jindex[n+1];
- ii = iinr[n];
- ii3 = 3*ii;
+ is3 = 3*shift[n];
+ shX = shiftvec[is3];
+ shY = shiftvec[is3+1];
+ shZ = shiftvec[is3+2];
+ nj0 = jindex[n];
+ nj1 = jindex[n+1];
+ ii = iinr[n];
+ ii3 = 3*ii;
ix = _mm_set1_pd(shX+pos[ii3+0]);
iy = _mm_set1_pd(shY+pos[ii3+1]);
iz = _mm_set1_pd(shZ+pos[ii3+2]);
-
+
iq = _mm_load1_pd(charge+ii);
iq = _mm_mul_pd(iq,facel);
-
+
isai = _mm_load1_pd(invsqrta+ii);
nti = 2*ntype*type[ii];
j3A = jnrA * 3;
j3B = jnrB * 3;
- GMX_MM_LOAD_1RVEC_2POINTERS_PD(pos+j3A,pos+j3B,jx,jy,jz);
+ GMX_MM_LOAD_1RVEC_2POINTERS_PD(pos+j3A,pos+j3B,jx,jy,jz);
dx = _mm_sub_pd(ix,jx);
dy = _mm_sub_pd(iy,jy);
dz = _mm_sub_pd(iz,jz);
- rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
-
- rinv = gmx_mm_invsqrt_pd(rsq);
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
rinvsq = _mm_mul_pd(rinv,rinv);
-
+
/***********************************/
/* INTERACTION SECTION STARTS HERE */
/***********************************/
GMX_MM_LOAD_2VALUES_PD(charge+jnrA,charge+jnrB,jq);
GMX_MM_LOAD_2VALUES_PD(invsqrta+jnrA,invsqrta+jnrB,isaj);
- /* Lennard-Jones */
- tjA = nti+2*type[jnrA];
+ /* Lennard-Jones */
+ tjA = nti+2*type[jnrA];
tjB = nti+2*type[jnrB];
-
- GMX_MM_LOAD_2PAIRS_PD(vdwparam+tjA,vdwparam+tjB,c6,c12);
+
+ GMX_MM_LOAD_2PAIRS_PD(vdwparam+tjA,vdwparam+tjB,c6,c12);
isaprod = _mm_mul_pd(isai,isaj);
qq = _mm_mul_pd(iq,jq);
vcoul = _mm_mul_pd(qq,rinv);
fscal = _mm_mul_pd(vcoul,rinv);
- vctot = _mm_add_pd(vctot,vcoul);
+ vctot = _mm_add_pd(vctot,vcoul);
- /* Polarization interaction */
+ /* Polarization interaction */
qq = _mm_mul_pd(qq,_mm_mul_pd(isaprod,gbfactor));
gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
+
/* Calculate GB table index */
r = _mm_mul_pd(rsq,rinv);
rtab = _mm_mul_pd(r,gbscale);
eps = _mm_sub_pd(rtab,_mm_cvtepi32_pd(n0));
nnn = _mm_slli_epi32(n0,2);
- /* the tables are 16-byte aligned, so we can use _mm_load_pd */
- Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1)));
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1))+2);
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_pd(G,eps);
- H = _mm_mul_pd(H, _mm_mul_pd(eps,eps) );
- F = _mm_add_pd(F, _mm_add_pd( G , H ) );
- Y = _mm_add_pd(Y, _mm_mul_pd(F, eps));
- F = _mm_add_pd(F, _mm_add_pd(G , _mm_mul_pd(H,two)));
- vgb = _mm_mul_pd(Y, qq);
- fijGB = _mm_mul_pd(F, _mm_mul_pd(qq,gbscale));
-
- dvdatmp = _mm_mul_pd(_mm_add_pd(vgb, _mm_mul_pd(fijGB,r)) , minushalf);
-
- vgbtot = _mm_add_pd(vgbtot, vgb);
-
- dvdasum = _mm_add_pd(dvdasum, dvdatmp);
- dvdatmp = _mm_mul_pd(dvdatmp, _mm_mul_pd(isaj,isaj));
-
- GMX_MM_INCREMENT_2VALUES_PD(dvda+jnrA,dvda+jnrB,dvdatmp);
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1)));
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1))+2);
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_pd(G,eps);
+ H = _mm_mul_pd(H, _mm_mul_pd(eps,eps) );
+ F = _mm_add_pd(F, _mm_add_pd( G , H ) );
+ Y = _mm_add_pd(Y, _mm_mul_pd(F, eps));
+ F = _mm_add_pd(F, _mm_add_pd(G , _mm_mul_pd(H,two)));
+ vgb = _mm_mul_pd(Y, qq);
+ fijGB = _mm_mul_pd(F, _mm_mul_pd(qq,gbscale));
+
+ dvdatmp = _mm_mul_pd(_mm_add_pd(vgb, _mm_mul_pd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb);
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp);
+ dvdatmp = _mm_mul_pd(dvdatmp, _mm_mul_pd(isaj,isaj));
+
+ GMX_MM_INCREMENT_2VALUES_PD(dvda+jnrA,dvda+jnrB,dvdatmp);
rinvsix = _mm_mul_pd(rinvsq,rinvsq);
rinvsix = _mm_mul_pd(rinvsix,rinvsq);
vvdw12 = _mm_mul_pd(c12, _mm_mul_pd(rinvsix,rinvsix));
vvdwtot = _mm_add_pd(vvdwtot,_mm_sub_pd(vvdw12,vvdw6));
- fscal = _mm_sub_pd(_mm_mul_pd(rinvsq,
- _mm_sub_pd(_mm_mul_pd(twelve,vvdw12),
- _mm_mul_pd(six,vvdw6))),
- _mm_mul_pd( _mm_sub_pd( fijGB,fscal),rinv ));
-
- /***********************************/
+ fscal = _mm_sub_pd(_mm_mul_pd(rinvsq,
+ _mm_sub_pd(_mm_mul_pd(twelve,vvdw12),
+ _mm_mul_pd(six,vvdw6))),
+ _mm_mul_pd( _mm_sub_pd( fijGB,fscal),rinv ));
+
+ /***********************************/
/* INTERACTION SECTION ENDS HERE */
/***********************************/
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx);
- ty = _mm_mul_pd(fscal,dy);
- tz = _mm_mul_pd(fscal,dz);
-
- /* Increment i atom force */
- fix = _mm_add_pd(fix,tx);
- fiy = _mm_add_pd(fiy,ty);
- fiz = _mm_add_pd(fiz,tz);
-
- /* Store j forces back */
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_pd(fscal,dx);
+ ty = _mm_mul_pd(fscal,dy);
+ tz = _mm_mul_pd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_pd(fix,tx);
+ fiy = _mm_add_pd(fiy,ty);
+ fiz = _mm_add_pd(fiz,tz);
+
+ /* Store j forces back */
GMX_MM_DECREMENT_1RVEC_2POINTERS_PD(faction+j3A,faction+j3B,tx,ty,tz);
}
jnrA = jjnr[k];
j3A = jnrA * 3;
-
- GMX_MM_LOAD_1RVEC_1POINTER_PD(pos+j3A,jx,jy,jz);
+
+ GMX_MM_LOAD_1RVEC_1POINTER_PD(pos+j3A,jx,jy,jz);
dx = _mm_sub_sd(ix,jx);
dy = _mm_sub_sd(iy,jy);
dz = _mm_sub_sd(iz,jz);
- rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
-
- rinv = gmx_mm_invsqrt_pd(rsq);
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
rinvsq = _mm_mul_sd(rinv,rinv);
-
+
+ /* These reason for zeroing these variables here is for fixing bug 585
+ * What happens is that __m128d _mm_add_sd(a,b) gives back r0=a[0]+b[0],
+ * and r1=0, but it should be r1=a[1].
+ * This might be a compiler issue (tested with gcc-4.1.3 and -O3).
+ * To work around it, we zero these variables and use _mm_add_pd (**) instead
+ * Note that the only variables that get affected are the energies since
+ * the total sum needs to be correct
+ */
+ vgb = _mm_setzero_pd();
+ vcoul = _mm_setzero_pd();
+ dvdatmp = _mm_setzero_pd();
+ vvdw6 = _mm_setzero_pd();
+ vvdw12 = _mm_setzero_pd();
+
/***********************************/
/* INTERACTION SECTION STARTS HERE */
/***********************************/
GMX_MM_LOAD_1VALUE_PD(charge+jnrA,jq);
GMX_MM_LOAD_1VALUE_PD(invsqrta+jnrA,isaj);
-
- /* Lennard-Jones */
- tjA = nti+2*type[jnrA];
-
- GMX_MM_LOAD_1PAIR_PD(vdwparam+tjA,c6,c12);
+
+ /* Lennard-Jones */
+ tjA = nti+2*type[jnrA];
+
+ GMX_MM_LOAD_1PAIR_PD(vdwparam+tjA,c6,c12);
isaprod = _mm_mul_sd(isai,isaj);
- qq = _mm_mul_sd(iq,jq);
+ qq = _mm_mul_sd(jq,iq);
vcoul = _mm_mul_sd(qq,rinv);
fscal = _mm_mul_sd(vcoul,rinv);
- vctot = _mm_add_sd(vctot,vcoul);
-
- /* Polarization interaction */
+ vctot = _mm_add_pd(vctot,vcoul); /* (**) */
+
+ /* Polarization interaction */
qq = _mm_mul_sd(qq,_mm_mul_sd(isaprod,gbfactor));
gbscale = _mm_mul_sd(isaprod,gbtabscale);
-
+
/* Calculate GB table index */
r = _mm_mul_sd(rsq,rinv);
rtab = _mm_mul_sd(r,gbscale);
eps = _mm_sub_sd(rtab,_mm_cvtepi32_pd(n0));
nnn = _mm_slli_epi32(n0,2);
- /* the tables are 16-byte aligned, so we can use _mm_load_pd */
- Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_sd(G,eps);
- H = _mm_mul_sd(H, _mm_mul_sd(eps,eps) );
- F = _mm_add_sd(F, _mm_add_sd( G , H ) );
- Y = _mm_add_sd(Y, _mm_mul_sd(F, eps));
- F = _mm_add_sd(F, _mm_add_sd(G , _mm_mul_sd(H,two)));
- vgb = _mm_mul_sd(Y, qq);
- fijGB = _mm_mul_sd(F, _mm_mul_sd(qq,gbscale));
-
- dvdatmp = _mm_mul_sd(_mm_add_sd(vgb, _mm_mul_sd(fijGB,r)) , minushalf);
-
- vgbtot = _mm_add_sd(vgbtot, vgb);
-
- dvdasum = _mm_add_sd(dvdasum, dvdatmp);
- dvdatmp = _mm_mul_sd(dvdatmp, _mm_mul_sd(isaj,isaj));
-
- GMX_MM_INCREMENT_1VALUE_PD(dvda+jnrA,dvdatmp);
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_sd(G,eps);
+ H = _mm_mul_sd(H, _mm_mul_sd(eps,eps) );
+ F = _mm_add_sd(F, _mm_add_sd( G , H ) );
+ Y = _mm_add_sd(Y, _mm_mul_sd(F, eps));
+ F = _mm_add_sd(F, _mm_add_sd(G , _mm_mul_sd(H,two)));
+ vgb = _mm_mul_sd(Y, qq);
+ fijGB = _mm_mul_sd(F, _mm_mul_sd(qq,gbscale));
+
+ dvdatmp = _mm_mul_sd(_mm_add_sd(vgb, _mm_mul_sd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb); /* (**) */
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp); /* (**) */
+ dvdatmp = _mm_mul_sd(dvdatmp, _mm_mul_sd(isaj,isaj));
+
+ GMX_MM_INCREMENT_1VALUE_PD(dvda+jnrA,dvdatmp);
rinvsix = _mm_mul_sd(rinvsq,rinvsq);
rinvsix = _mm_mul_sd(rinvsix,rinvsq);
vvdw6 = _mm_mul_sd(c6,rinvsix);
vvdw12 = _mm_mul_sd(c12, _mm_mul_sd(rinvsix,rinvsix));
- vvdwtot = _mm_add_sd(vvdwtot,_mm_sub_sd(vvdw12,vvdw6));
-
- fscal = _mm_sub_sd(_mm_mul_sd(rinvsq,
- _mm_sub_sd(_mm_mul_sd(twelve,vvdw12),
- _mm_mul_sd(six,vvdw6))),
- _mm_mul_sd( _mm_sub_sd( fijGB,fscal),rinv ));
-
- /***********************************/
+ vvdwtot = _mm_add_pd(vvdwtot,_mm_sub_sd(vvdw12,vvdw6)); /* (**) */
+
+ fscal = _mm_sub_sd(_mm_mul_sd(rinvsq,
+ _mm_sub_sd(_mm_mul_sd(twelve,vvdw12),
+ _mm_mul_sd(six,vvdw6))),
+ _mm_mul_sd( _mm_sub_sd( fijGB,fscal),rinv ));
+
+ /***********************************/
/* INTERACTION SECTION ENDS HERE */
/***********************************/
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_sd(fscal,dx);
- ty = _mm_mul_sd(fscal,dy);
- tz = _mm_mul_sd(fscal,dz);
-
- /* Increment i atom force */
- fix = _mm_add_sd(fix,tx);
- fiy = _mm_add_sd(fiy,ty);
- fiz = _mm_add_sd(fiz,tz);
-
- /* Store j forces back */
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_sd(fscal,dx);
+ ty = _mm_mul_sd(fscal,dy);
+ tz = _mm_mul_sd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_sd(fix,tx);
+ fiy = _mm_add_sd(fiy,ty);
+ fiz = _mm_add_sd(fiz,tz);
+
+ /* Store j forces back */
GMX_MM_DECREMENT_1RVEC_1POINTER_PD(faction+j3A,tx,ty,tz);
}
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai,isai));
- gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,faction+ii3,fshift+is3);
-
- ggid = gid[n];
-
- gmx_mm_update_2pot_pd(vctot,vc+ggid,vvdwtot,vvdw+ggid);
- gmx_mm_update_2pot_pd(vgbtot,gpol+ggid,dvdasum,dvda+ii);
+ dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai,isai));
+ gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,faction+ii3,fshift+is3);
+
+ ggid = gid[n];
+
+ gmx_mm_update_1pot_pd(vctot,vc+ggid);
+ gmx_mm_update_1pot_pd(vgbtot,gpol+ggid);
+ gmx_mm_update_1pot_pd(dvdasum,dvda+ii);
+ gmx_mm_update_1pot_pd(vvdwtot,vvdw+ggid);
+
}
-
+
*outeriter = nri;
- *inneriter = nj1;
+ *inneriter = nj1;
}
int * inneriter,
double * work)
{
- int nri,ntype,nthreads;
- int n,ii,is3,ii3,k,nj0,nj1,ggid;
- double shX,shY,shZ;
+ int nri,ntype,nthreads;
+ int n,ii,is3,ii3,k,nj0,nj1,ggid;
+ double shX,shY,shZ;
int offset,nti;
- int jnrA,jnrB;
- int j3A,j3B;
+ int jnrA,jnrB;
+ int j3A,j3B;
int tjA,tjB;
gmx_gbdata_t *gbdata;
double * gpol;
__m128d vcoul,fscal,gbscale,c6,c12;
__m128d rinvsq,r,rtab;
__m128d eps,Y,F,G,H;
- __m128d VV,FF,Fp;
+ __m128d VV,FF,Fp;
__m128d vgb,fijGB,dvdatmp;
__m128d rinvsix,vvdw6,vvdw12,vvdwtmp;
__m128d facel,gbtabscale,dvdaj;
- __m128d fijD,fijR;
- __m128d xmm1,tabscale,eps2;
+ __m128d fijD,fijR;
+ __m128d xmm1,tabscale,eps2;
__m128i n0, nnn;
nri = *p_nri;
ntype = *p_ntype;
- gbfactor = _mm_set1_pd( - ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent)));
- gbtabscale = _mm_load1_pd(p_gbtabscale);
- facel = _mm_load1_pd(p_facel);
- tabscale = _mm_load1_pd(p_tabscale);
-
- nj1 = 0;
- jnrA = jnrB = 0;
- j3A = j3B = 0;
- jx = _mm_setzero_pd();
- jy = _mm_setzero_pd();
- jz = _mm_setzero_pd();
- c6 = _mm_setzero_pd();
- c12 = _mm_setzero_pd();
+ gbfactor = _mm_set1_pd( - ((1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent)));
+ gbtabscale = _mm_load1_pd(p_gbtabscale);
+ facel = _mm_load1_pd(p_facel);
+ tabscale = _mm_load1_pd(p_tabscale);
+
+ nj1 = 0;
+ jnrA = jnrB = 0;
+ j3A = j3B = 0;
+ jx = _mm_setzero_pd();
+ jy = _mm_setzero_pd();
+ jz = _mm_setzero_pd();
+ c6 = _mm_setzero_pd();
+ c12 = _mm_setzero_pd();
for(n=0;n<nri;n++)
{
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
- nj0 = jindex[n];
- nj1 = jindex[n+1];
- ii = iinr[n];
- ii3 = 3*ii;
+ is3 = 3*shift[n];
+ shX = shiftvec[is3];
+ shY = shiftvec[is3+1];
+ shZ = shiftvec[is3+2];
+ nj0 = jindex[n];
+ nj1 = jindex[n+1];
+ ii = iinr[n];
+ ii3 = 3*ii;
ix = _mm_set1_pd(shX+pos[ii3+0]);
iy = _mm_set1_pd(shY+pos[ii3+1]);
iz = _mm_set1_pd(shZ+pos[ii3+2]);
-
+
iq = _mm_load1_pd(charge+ii);
iq = _mm_mul_pd(iq,facel);
-
+
isai = _mm_load1_pd(invsqrta+ii);
-
+
nti = 2*ntype*type[ii];
vctot = _mm_setzero_pd();
j3A = jnrA * 3;
j3B = jnrB * 3;
- GMX_MM_LOAD_1RVEC_2POINTERS_PD(pos+j3A,pos+j3B,jx,jy,jz);
+ GMX_MM_LOAD_1RVEC_2POINTERS_PD(pos+j3A,pos+j3B,jx,jy,jz);
dx = _mm_sub_pd(ix,jx);
dy = _mm_sub_pd(iy,jy);
dz = _mm_sub_pd(iz,jz);
- rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
-
- rinv = gmx_mm_invsqrt_pd(rsq);
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
rinvsq = _mm_mul_pd(rinv,rinv);
-
+
/***********************************/
/* INTERACTION SECTION STARTS HERE */
/***********************************/
GMX_MM_LOAD_2VALUES_PD(charge+jnrA,charge+jnrB,jq);
GMX_MM_LOAD_2VALUES_PD(invsqrta+jnrA,invsqrta+jnrB,isaj);
- /* Lennard-Jones */
- tjA = nti+2*type[jnrA];
+ /* Lennard-Jones */
+ tjA = nti+2*type[jnrA];
tjB = nti+2*type[jnrB];
-
- GMX_MM_LOAD_2PAIRS_PD(vdwparam+tjA,vdwparam+tjB,c6,c12);
+
+ GMX_MM_LOAD_2PAIRS_PD(vdwparam+tjA,vdwparam+tjB,c6,c12);
isaprod = _mm_mul_pd(isai,isaj);
qq = _mm_mul_pd(iq,jq);
vcoul = _mm_mul_pd(qq,rinv);
fscal = _mm_mul_pd(vcoul,rinv);
- vctot = _mm_add_pd(vctot,vcoul);
-
- /* Polarization interaction */
+ vctot = _mm_add_pd(vctot,vcoul);
+
+ /* Polarization interaction */
qq = _mm_mul_pd(qq,_mm_mul_pd(isaprod,gbfactor));
gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
+
/* Calculate GB table index */
r = _mm_mul_pd(rsq,rinv);
rtab = _mm_mul_pd(r,gbscale);
eps = _mm_sub_pd(rtab,_mm_cvtepi32_pd(n0));
nnn = _mm_slli_epi32(n0,2);
- /* the tables are 16-byte aligned, so we can use _mm_load_pd */
- Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1)));
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1))+2);
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_pd(G,eps);
- H = _mm_mul_pd(H, _mm_mul_pd(eps,eps) );
- F = _mm_add_pd(F, _mm_add_pd( G , H ) );
- Y = _mm_add_pd(Y, _mm_mul_pd(F, eps));
- F = _mm_add_pd(F, _mm_add_pd(G , _mm_mul_pd(H,two)));
- vgb = _mm_mul_pd(Y, qq);
- fijGB = _mm_mul_pd(F, _mm_mul_pd(qq,gbscale));
-
- dvdatmp = _mm_mul_pd(_mm_add_pd(vgb, _mm_mul_pd(fijGB,r)) , minushalf);
-
- vgbtot = _mm_add_pd(vgbtot, vgb);
-
- dvdasum = _mm_add_pd(dvdasum, dvdatmp);
- dvdatmp = _mm_mul_pd(dvdatmp, _mm_mul_pd(isaj,isaj));
-
- GMX_MM_INCREMENT_2VALUES_PD(dvda+jnrA,dvda+jnrB,dvdatmp);
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1)));
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,1))+2);
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_pd(G,eps);
+ H = _mm_mul_pd(H, _mm_mul_pd(eps,eps) );
+ F = _mm_add_pd(F, _mm_add_pd( G , H ) );
+ Y = _mm_add_pd(Y, _mm_mul_pd(F, eps));
+ F = _mm_add_pd(F, _mm_add_pd(G , _mm_mul_pd(H,two)));
+ vgb = _mm_mul_pd(Y, qq);
+ fijGB = _mm_mul_pd(F, _mm_mul_pd(qq,gbscale));
+
+ dvdatmp = _mm_mul_pd(_mm_add_pd(vgb, _mm_mul_pd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb);
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp);
+ dvdatmp = _mm_mul_pd(dvdatmp, _mm_mul_pd(isaj,isaj));
+
+ GMX_MM_INCREMENT_2VALUES_PD(dvda+jnrA,dvda+jnrB,dvdatmp);
- /* Calculate VDW table index */
+ /* Calculate VDW table index */
rtab = _mm_mul_pd(r,tabscale);
n0 = _mm_cvttpd_epi32(rtab);
eps = _mm_sub_pd(rtab,_mm_cvtepi32_pd(n0));
eps2 = _mm_mul_pd(eps,eps);
nnn = _mm_slli_epi32(n0,3);
- /* Dispersion */
- Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1)));
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1))+2);
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_pd(G,eps);
+ /* Dispersion */
+ Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1)));
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1))+2);
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_pd(G,eps);
H = _mm_mul_pd(H,eps2);
Fp = _mm_add_pd(F,G);
Fp = _mm_add_pd(Fp,H);
vvdw6 = _mm_mul_pd(c6,VV);
fijD = _mm_mul_pd(c6,FF);
-
- /* Dispersion */
- Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+4);
- F = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1))+4);
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+6);
- H = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1))+6);
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_pd(G,eps);
+
+ /* Dispersion */
+ Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+4);
+ F = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1))+4);
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+6);
+ H = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,1))+6);
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_pd(G,eps);
H = _mm_mul_pd(H,eps2);
Fp = _mm_add_pd(F,G);
Fp = _mm_add_pd(Fp,H);
vvdwtmp = _mm_add_pd(vvdw12,vvdw6);
vvdwtot = _mm_add_pd(vvdwtot,vvdwtmp);
-
+
xmm1 = _mm_add_pd(fijD,fijR);
xmm1 = _mm_mul_pd(xmm1,tabscale);
xmm1 = _mm_add_pd(xmm1,fijGB);
xmm1 = _mm_sub_pd(xmm1,fscal);
fscal = _mm_mul_pd(xmm1,neg);
fscal = _mm_mul_pd(fscal,rinv);
-
- /***********************************/
+
+ /***********************************/
/* INTERACTION SECTION ENDS HERE */
/***********************************/
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx);
- ty = _mm_mul_pd(fscal,dy);
- tz = _mm_mul_pd(fscal,dz);
-
- /* Increment i atom force */
- fix = _mm_add_pd(fix,tx);
- fiy = _mm_add_pd(fiy,ty);
- fiz = _mm_add_pd(fiz,tz);
-
- /* Store j forces back */
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_pd(fscal,dx);
+ ty = _mm_mul_pd(fscal,dy);
+ tz = _mm_mul_pd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_pd(fix,tx);
+ fiy = _mm_add_pd(fiy,ty);
+ fiz = _mm_add_pd(fiz,tz);
+
+ /* Store j forces back */
GMX_MM_DECREMENT_1RVEC_2POINTERS_PD(faction+j3A,faction+j3B,tx,ty,tz);
}
{
jnrA = jjnr[k];
j3A = jnrA * 3;
-
- GMX_MM_LOAD_1RVEC_1POINTER_PD(pos+j3A,jx,jy,jz);
-
+
+ GMX_MM_LOAD_1RVEC_1POINTER_PD(pos+j3A,jx,jy,jz);
+
dx = _mm_sub_sd(ix,jx);
dy = _mm_sub_sd(iy,jy);
dz = _mm_sub_sd(iz,jz);
- rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
-
- rinv = gmx_mm_invsqrt_pd(rsq);
+ rsq = gmx_mm_calc_rsq_pd(dx,dy,dz);
+
+ rinv = gmx_mm_invsqrt_pd(rsq);
rinvsq = _mm_mul_sd(rinv,rinv);
-
- /***********************************/
+
+ /* These reason for zeroing these variables here is for fixing bug 585
+ * What happens is that __m128d _mm_add_sd(a,b) gives back r0=a[0]+b[0],
+ * and r1=0, but it should be r1=a[1].
+ * This might be a compiler issue (tested with gcc-4.1.3 and -O3).
+ * To work around it, we zero these variables and use _mm_add_pd (**) instead
+ * Note that the only variables that get affected are the energies since
+ * the total sum needs to be correct
+ */
+ vgb = _mm_setzero_pd();
+ vcoul = _mm_setzero_pd();
+ dvdatmp = _mm_setzero_pd();
+ vvdw6 = _mm_setzero_pd();
+ vvdw12 = _mm_setzero_pd();
+
+ /***********************************/
/* INTERACTION SECTION STARTS HERE */
/***********************************/
GMX_MM_LOAD_1VALUE_PD(charge+jnrA,jq);
GMX_MM_LOAD_1VALUE_PD(invsqrta+jnrA,isaj);
- /* Lennard-Jones */
- tjA = nti+2*type[jnrA];
-
- GMX_MM_LOAD_1PAIR_PD(vdwparam+tjA,c6,c12);
+ /* Lennard-Jones */
+ tjA = nti+2*type[jnrA];
+
+ GMX_MM_LOAD_1PAIR_PD(vdwparam+tjA,c6,c12);
isaprod = _mm_mul_sd(isai,isaj);
- qq = _mm_mul_sd(iq,jq);
+ qq = _mm_mul_sd(jq,iq);
vcoul = _mm_mul_sd(qq,rinv);
fscal = _mm_mul_sd(vcoul,rinv);
- vctot = _mm_add_sd(vctot,vcoul);
-
- /* Polarization interaction */
+ vctot = _mm_add_pd(vctot,vcoul); /* (**) */
+
+ /* Polarization interaction */
qq = _mm_mul_sd(qq,_mm_mul_sd(isaprod,gbfactor));
gbscale = _mm_mul_sd(isaprod,gbtabscale);
-
+
/* Calculate GB table index */
r = _mm_mul_sd(rsq,rinv);
rtab = _mm_mul_sd(r,gbscale);
eps = _mm_sub_sd(rtab,_mm_cvtepi32_pd(n0));
nnn = _mm_slli_epi32(n0,2);
- /* the tables are 16-byte aligned, so we can use _mm_load_pd */
- Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_sd(G,eps);
- H = _mm_mul_sd(H, _mm_mul_sd(eps,eps) );
- F = _mm_add_sd(F, _mm_add_sd( G , H ) );
- Y = _mm_add_sd(Y, _mm_mul_sd(F, eps));
- F = _mm_add_sd(F, _mm_add_sd(G , _mm_mul_sd(H,two)));
- vgb = _mm_mul_sd(Y, qq);
- fijGB = _mm_mul_sd(F, _mm_mul_sd(qq,gbscale));
-
- dvdatmp = _mm_mul_sd(_mm_add_sd(vgb, _mm_mul_sd(fijGB,r)) , minushalf);
-
- vgbtot = _mm_add_sd(vgbtot, vgb);
-
- dvdasum = _mm_add_sd(dvdasum, dvdatmp);
- dvdatmp = _mm_mul_sd(dvdatmp, _mm_mul_sd(isaj,isaj));
-
- GMX_MM_INCREMENT_1VALUE_PD(dvda+jnrA,dvdatmp);
+ /* the tables are 16-byte aligned, so we can use _mm_load_pd */
+ Y = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(GBtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_sd(G,eps);
+ H = _mm_mul_sd(H, _mm_mul_sd(eps,eps) );
+ F = _mm_add_sd(F, _mm_add_sd( G , H ) );
+ Y = _mm_add_sd(Y, _mm_mul_sd(F, eps));
+ F = _mm_add_sd(F, _mm_add_sd(G , _mm_mul_sd(H,two)));
+ vgb = _mm_mul_sd(Y, qq);
+ fijGB = _mm_mul_sd(F, _mm_mul_sd(qq,gbscale));
+
+ dvdatmp = _mm_mul_sd(_mm_add_sd(vgb, _mm_mul_sd(fijGB,r)) , minushalf);
+
+ vgbtot = _mm_add_pd(vgbtot, vgb); /* (**) */
+
+ dvdasum = _mm_add_pd(dvdasum, dvdatmp); /* (**) */
+ dvdatmp = _mm_mul_sd(dvdatmp, _mm_mul_sd(isaj,isaj));
+
+ GMX_MM_INCREMENT_1VALUE_PD(dvda+jnrA,dvdatmp);
- /* Calculate VDW table index */
+ /* Calculate VDW table index */
rtab = _mm_mul_sd(r,tabscale);
n0 = _mm_cvttpd_epi32(rtab);
eps = _mm_sub_sd(rtab,_mm_cvtepi32_pd(n0));
eps2 = _mm_mul_sd(eps,eps);
nnn = _mm_slli_epi32(n0,3);
- /* Dispersion */
- Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0)));
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_sd(G,eps);
+ /* Dispersion */
+ Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0)));
+ F = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+2);
+ H = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_sd(G,eps);
H = _mm_mul_sd(H,eps2);
Fp = _mm_add_sd(F,G);
Fp = _mm_add_sd(Fp,H);
vvdw6 = _mm_mul_sd(c6,VV);
fijD = _mm_mul_sd(c6,FF);
-
- /* Dispersion */
- Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+4);
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+6);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
-
- G = _mm_mul_sd(G,eps);
+
+ /* Dispersion */
+ Y = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+4);
+ F = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(Y,F);
+ G = _mm_load_pd(VFtab+(gmx_mm_extract_epi32(nnn,0))+6);
+ H = _mm_setzero_pd();
+ GMX_MM_TRANSPOSE2_PD(G,H);
+
+ G = _mm_mul_sd(G,eps);
H = _mm_mul_sd(H,eps2);
Fp = _mm_add_sd(F,G);
Fp = _mm_add_sd(Fp,H);
fijR = _mm_mul_sd(c12,FF);
vvdwtmp = _mm_add_sd(vvdw12,vvdw6);
- vvdwtot = _mm_add_sd(vvdwtot,vvdwtmp);
+ vvdwtot = _mm_add_pd(vvdwtot,vvdwtmp); /* (**) */
xmm1 = _mm_add_sd(fijD,fijR);
xmm1 = _mm_mul_sd(xmm1,tabscale);
fscal = _mm_mul_sd(xmm1,neg);
fscal = _mm_mul_sd(fscal,rinv);
- /***********************************/
+ /***********************************/
/* INTERACTION SECTION ENDS HERE */
/***********************************/
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_sd(fscal,dx);
- ty = _mm_mul_sd(fscal,dy);
- tz = _mm_mul_sd(fscal,dz);
-
- /* Increment i atom force */
- fix = _mm_add_sd(fix,tx);
- fiy = _mm_add_sd(fiy,ty);
- fiz = _mm_add_sd(fiz,tz);
-
- /* Store j forces back */
+
+ /* Calculate temporary vectorial force */
+ tx = _mm_mul_sd(fscal,dx);
+ ty = _mm_mul_sd(fscal,dy);
+ tz = _mm_mul_sd(fscal,dz);
+
+ /* Increment i atom force */
+ fix = _mm_add_sd(fix,tx);
+ fiy = _mm_add_sd(fiy,ty);
+ fiz = _mm_add_sd(fiz,tz);
+
+ /* Store j forces back */
GMX_MM_DECREMENT_1RVEC_1POINTER_PD(faction+j3A,tx,ty,tz);
}
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai,isai));
- gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,faction+ii3,fshift+is3);
-
- ggid = gid[n];
-
- gmx_mm_update_2pot_pd(vctot,vc+ggid,vvdwtot,vvdw+ggid);
- gmx_mm_update_2pot_pd(vgbtot,gpol+ggid,dvdasum,dvda+ii);
- }
+ dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai,isai));
+ gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,faction+ii3,fshift+is3);
+ ggid = gid[n];
+
+ gmx_mm_update_1pot_pd(vctot,vc+ggid);
+ gmx_mm_update_1pot_pd(vgbtot,gpol+ggid);
+ gmx_mm_update_1pot_pd(dvdasum,dvda+ii);
+ gmx_mm_update_1pot_pd(vvdwtot,vvdw+ggid);
+
+ }
+
*outeriter = nri;
- *inneriter = nj1;
+ *inneriter = nj1;
}
pmask1 = prologue_mask[i+1];
emask0 = epilogue_mask[i];
emask1 = epilogue_mask[i+1];
- imask_SSE0 = _mm_load1_pd((double *)(imask+i));
+ imask_SSE0 = _mm_load1_pd((double *)(imask+2*i));
imask_SSE1 = _mm_load1_pd((double *)(imask+2*i+2));
for(j=nj0; j<nj1; j+=UNROLLJ)
}
}
}
+ /* Clear the values for dynamic output to avoid valgrind warnings. */
+ if ((sel->flags & SEL_DYNAMIC) && sel->v.type == REAL_VALUE)
+ {
+ int i;
+
+ for (i = 0; i < sel->v.nr; ++i)
+ {
+ sel->v.u.r[i] = 0.0;
+ }
+ }
}
return 0;
if (left->mempool)
{
_gmx_selvalue_setstore(&left->v, sel->v.u.ptr);
- rc = _gmx_selelem_mempool_reserve(right, g->isize);
- if (rc != 0)
+ if (right)
{
- return rc;
+ rc = _gmx_selelem_mempool_reserve(right, g->isize);
+ if (rc != 0)
+ {
+ return rc;
+ }
}
}
- else if (right->mempool)
+ else if (right && right->mempool)
{
_gmx_selvalue_setstore(&right->v, sel->v.u.ptr);
}
if (left->mempool)
{
_gmx_selvalue_setstore(&left->v, NULL);
- _gmx_selelem_mempool_release(right);
+ if (right)
+ {
+ _gmx_selelem_mempool_release(right);
+ }
}
- else if (right->mempool)
+ else if (right && right->mempool)
{
_gmx_selvalue_setstore(&right->v, NULL);
}
OR = 286,
AND = 287,
NOT = 288,
- UNARY_NEG = 289
+ UNARY_NEG = 289,
+ NUM_REDUCT = 290
};
#endif
/* Tokens. */
#define AND 287
#define NOT 288
#define UNARY_NEG 289
+#define NUM_REDUCT 290
struct t_selexpr_param *param;
}
/* Line 187 of yacc.c. */
-#line 212 "parser.c"
+#line 214 "parser.c"
YYSTYPE;
# define yystype YYSTYPE /* obsolescent; will be withdrawn */
# define YYSTYPE_IS_DECLARED 1
/* Line 216 of yacc.c. */
-#line 225 "parser.c"
+#line 227 "parser.c"
#ifdef short
# undef short
/* YYFINAL -- State number of the termination state. */
#define YYFINAL 2
/* YYLAST -- Last index in YYTABLE. */
-#define YYLAST 329
+#define YYLAST 417
/* YYNTOKENS -- Number of terminals. */
-#define YYNTOKENS 44
+#define YYNTOKENS 49
/* YYNNTS -- Number of nonterminals. */
-#define YYNNTS 20
+#define YYNNTS 26
/* YYNRULES -- Number of rules. */
-#define YYNRULES 76
+#define YYNRULES 91
/* YYNRULES -- Number of states. */
-#define YYNSTATES 125
+#define YYNSTATES 150
/* YYTRANSLATE(YYLEX) -- Bison symbol number corresponding to YYLEX. */
#define YYUNDEFTOK 2
-#define YYMAXUTOK 289
+#define YYMAXUTOK 290
#define YYTRANSLATE(YYX) \
((unsigned int) (YYX) <= YYMAXUTOK ? yytranslate[YYX] : YYUNDEFTOK)
2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
- 41, 42, 36, 34, 43, 35, 2, 37, 2, 2,
+ 42, 43, 36, 34, 45, 35, 2, 37, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
- 2, 40, 2, 2, 2, 2, 2, 2, 2, 2,
+ 2, 41, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
- 2, 2, 2, 2, 39, 2, 2, 2, 2, 2,
- 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
+ 2, 44, 2, 46, 39, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
+ 2, 2, 2, 47, 2, 48, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 1, 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
- 25, 26, 27, 28, 29, 30, 31, 32, 33, 38
+ 25, 26, 27, 28, 29, 30, 31, 32, 33, 38,
+ 40
};
#if YYDEBUG
/* YYPRHS[YYN] -- Index of the first RHS symbol of rule number YYN in
YYRHS. */
-static const yytype_uint8 yyprhs[] =
+static const yytype_uint16 yyprhs[] =
{
0, 0, 3, 4, 7, 10, 13, 14, 16, 18,
20, 22, 25, 29, 33, 37, 39, 41, 44, 47,
- 49, 51, 55, 59, 61, 63, 65, 67, 70, 74,
- 78, 82, 86, 89, 92, 94, 96, 99, 103, 107,
- 111, 113, 115, 118, 122, 126, 130, 134, 138, 141,
- 145, 149, 151, 154, 162, 166, 169, 173, 175, 177,
- 179, 181, 184, 185, 188, 191, 192, 194, 196, 199,
- 203, 205, 207, 209, 211, 215, 219
+ 49, 51, 55, 59, 61, 64, 66, 69, 71, 73,
+ 75, 77, 80, 84, 88, 92, 96, 99, 102, 104,
+ 106, 109, 113, 117, 121, 123, 125, 128, 132, 136,
+ 140, 144, 148, 151, 155, 159, 161, 164, 172, 176,
+ 179, 183, 185, 187, 189, 191, 194, 195, 198, 201,
+ 202, 204, 208, 210, 213, 217, 219, 223, 225, 228,
+ 232, 234, 236, 238, 240, 242, 244, 246, 248, 250,
+ 254, 258
};
/* YYRHS -- A `-1'-separated list of the rules' RHS. */
static const yytype_int8 yyrhs[] =
{
- 45, 0, -1, -1, 45, 46, -1, 47, 10, -1,
- 1, 10, -1, -1, 48, -1, 6, -1, 52, -1,
- 50, -1, 52, 50, -1, 9, 40, 53, -1, 9,
- 40, 55, -1, 9, 40, 57, -1, 4, -1, 49,
- -1, 4, 5, -1, 49, 5, -1, 57, -1, 53,
- -1, 41, 50, 42, -1, 50, 23, 58, -1, 6,
- -1, 7, -1, 8, -1, 9, -1, 33, 53, -1,
- 53, 32, 53, -1, 53, 31, 53, -1, 41, 53,
- 42, -1, 55, 28, 55, -1, 11, 52, -1, 11,
- 6, -1, 24, -1, 18, -1, 54, 19, -1, 54,
- 17, 62, -1, 54, 16, 62, -1, 54, 21, 58,
- -1, 6, -1, 7, -1, 54, 16, -1, 54, 20,
- 58, -1, 55, 34, 55, -1, 55, 35, 55, -1,
- 55, 36, 55, -1, 55, 37, 55, -1, 35, 55,
- -1, 55, 39, 55, -1, 41, 55, 42, -1, 52,
- -1, 54, 17, -1, 41, 51, 43, 51, 43, 51,
- 42, -1, 41, 57, 42, -1, 22, 58, -1, 18,
- 27, 53, -1, 14, -1, 13, -1, 15, -1, 59,
- -1, 59, 26, -1, -1, 59, 60, -1, 25, 61,
- -1, -1, 62, -1, 63, -1, 62, 63, -1, 62,
- 43, 63, -1, 53, -1, 57, -1, 55, -1, 56,
- -1, 6, 12, 6, -1, 6, 12, 7, -1, 7,
- 12, 51, -1
+ 50, 0, -1, -1, 50, 51, -1, 52, 10, -1,
+ 1, 10, -1, -1, 53, -1, 6, -1, 59, -1,
+ 55, -1, 59, 55, -1, 9, 41, 60, -1, 9,
+ 41, 62, -1, 9, 41, 64, -1, 4, -1, 54,
+ -1, 4, 5, -1, 54, 5, -1, 64, -1, 60,
+ -1, 42, 55, 43, -1, 55, 23, 65, -1, 6,
+ -1, 35, 6, -1, 7, -1, 35, 7, -1, 56,
+ -1, 57, -1, 8, -1, 9, -1, 33, 60, -1,
+ 60, 32, 60, -1, 60, 31, 60, -1, 42, 60,
+ 43, -1, 62, 28, 62, -1, 11, 59, -1, 11,
+ 6, -1, 24, -1, 18, -1, 61, 19, -1, 61,
+ 17, 70, -1, 61, 16, 70, -1, 61, 21, 65,
+ -1, 6, -1, 7, -1, 61, 16, -1, 61, 20,
+ 65, -1, 62, 34, 62, -1, 62, 35, 62, -1,
+ 62, 36, 62, -1, 62, 37, 62, -1, 35, 62,
+ -1, 62, 39, 62, -1, 42, 62, 43, -1, 59,
+ -1, 61, 17, -1, 44, 58, 45, 58, 45, 58,
+ 46, -1, 42, 64, 43, -1, 22, 65, -1, 18,
+ 27, 60, -1, 14, -1, 13, -1, 15, -1, 66,
+ -1, 66, 26, -1, -1, 66, 67, -1, 25, 68,
+ -1, -1, 69, -1, 47, 69, 48, -1, 72, -1,
+ 69, 72, -1, 69, 45, 72, -1, 71, -1, 47,
+ 71, 48, -1, 73, -1, 71, 73, -1, 71, 45,
+ 73, -1, 60, -1, 64, -1, 62, -1, 63, -1,
+ 74, -1, 56, -1, 57, -1, 59, -1, 74, -1,
+ 56, 12, 56, -1, 56, 12, 57, -1, 57, 12,
+ 58, -1
};
/* YYRLINE[YYN] -- source line where rule number YYN was defined. */
static const yytype_uint16 yyrline[] =
{
- 0, 178, 178, 179, 188, 189, 209, 213, 214, 223,
- 233, 235, 237, 239, 241, 247, 248, 251, 252, 256,
- 257, 262, 263, 274, 275, 278, 279, 287, 293, 299,
- 311, 315, 323, 329, 337, 338, 342, 347, 352, 360,
- 372, 379, 389, 394, 402, 404, 406, 408, 410, 412,
- 414, 421, 428, 440, 445, 449, 457, 468, 472, 476,
- 485, 487, 492, 493, 498, 505, 506, 510, 511, 513,
- 517, 519, 521, 523, 525, 530, 535
+ 0, 182, 182, 183, 192, 193, 213, 217, 218, 227,
+ 237, 239, 241, 243, 245, 251, 252, 255, 256, 260,
+ 261, 266, 267, 279, 280, 284, 285, 288, 289, 292,
+ 293, 301, 307, 313, 325, 329, 337, 343, 351, 352,
+ 356, 361, 366, 374, 386, 393, 403, 408, 416, 418,
+ 420, 422, 424, 426, 428, 435, 442, 454, 459, 463,
+ 471, 482, 486, 490, 499, 501, 506, 507, 512, 519,
+ 520, 521, 525, 526, 528, 533, 534, 538, 539, 541,
+ 545, 547, 549, 551, 553, 557, 562, 567, 572, 576,
+ 581, 586
};
#endif
"KEYWORD_STR", "KEYWORD_POS", "KEYWORD_GROUP", "METHOD_NUMERIC",
"METHOD_GROUP", "METHOD_POS", "MODIFIER", "EMPTY_POSMOD", "PARAM",
"END_OF_METHOD", "OF", "CMP_OP", "PARAM_REDUCT", "XOR", "OR", "AND",
- "NOT", "'+'", "'-'", "'*'", "'/'", "UNARY_NEG", "'^'", "'='", "'('",
- "')'", "','", "$accept", "commands", "command", "cmd_plain",
- "help_request", "help_topic", "selection", "number", "string",
+ "NOT", "'+'", "'-'", "'*'", "'/'", "UNARY_NEG", "'^'", "NUM_REDUCT",
+ "'='", "'('", "')'", "'['", "','", "']'", "'{'", "'}'", "$accept",
+ "commands", "command", "cmd_plain", "help_request", "help_topic",
+ "selection", "integer_number", "real_number", "number", "string",
"sel_expr", "pos_mod", "num_expr", "str_expr", "pos_expr",
"method_params", "method_param_list", "method_param", "value_list",
- "value_list_nonempty", "value_item", 0
+ "value_list_contents", "basic_value_list", "basic_value_list_contents",
+ "value_item", "basic_value_item", "value_item_range", 0
};
#endif
265, 266, 267, 268, 269, 270, 271, 272, 273, 274,
275, 276, 277, 278, 279, 280, 281, 282, 283, 284,
285, 286, 287, 288, 43, 45, 42, 47, 289, 94,
- 61, 40, 41, 44
+ 290, 61, 40, 41, 91, 44, 93, 123, 125
};
# endif
/* YYR1[YYN] -- Symbol number of symbol that rule YYN derives. */
static const yytype_uint8 yyr1[] =
{
- 0, 44, 45, 45, 46, 46, 47, 47, 47, 47,
- 47, 47, 47, 47, 47, 48, 48, 49, 49, 50,
- 50, 50, 50, 51, 51, 52, 52, 53, 53, 53,
- 53, 53, 53, 53, 54, 54, 53, 53, 53, 53,
- 55, 55, 55, 55, 55, 55, 55, 55, 55, 55,
- 55, 56, 56, 57, 57, 57, 57, 53, 55, 57,
- 58, 58, 59, 59, 60, 61, 61, 62, 62, 62,
- 63, 63, 63, 63, 63, 63, 63
+ 0, 49, 50, 50, 51, 51, 52, 52, 52, 52,
+ 52, 52, 52, 52, 52, 53, 53, 54, 54, 55,
+ 55, 55, 55, 56, 56, 57, 57, 58, 58, 59,
+ 59, 60, 60, 60, 60, 60, 60, 60, 61, 61,
+ 60, 60, 60, 60, 62, 62, 62, 62, 62, 62,
+ 62, 62, 62, 62, 62, 63, 63, 64, 64, 64,
+ 64, 60, 62, 64, 65, 65, 66, 66, 67, 68,
+ 68, 68, 69, 69, 69, 70, 70, 71, 71, 71,
+ 72, 72, 72, 72, 72, 73, 73, 73, 73, 74,
+ 74, 74
};
/* YYR2[YYN] -- Number of symbols composing right hand side of rule YYN. */
{
0, 2, 0, 2, 2, 2, 0, 1, 1, 1,
1, 2, 3, 3, 3, 1, 1, 2, 2, 1,
- 1, 3, 3, 1, 1, 1, 1, 2, 3, 3,
- 3, 3, 2, 2, 1, 1, 2, 3, 3, 3,
- 1, 1, 2, 3, 3, 3, 3, 3, 2, 3,
- 3, 1, 2, 7, 3, 2, 3, 1, 1, 1,
- 1, 2, 0, 2, 2, 0, 1, 1, 2, 3,
- 1, 1, 1, 1, 3, 3, 3
+ 1, 3, 3, 1, 2, 1, 2, 1, 1, 1,
+ 1, 2, 3, 3, 3, 3, 2, 2, 1, 1,
+ 2, 3, 3, 3, 1, 1, 2, 3, 3, 3,
+ 3, 3, 2, 3, 3, 1, 2, 7, 3, 2,
+ 3, 1, 1, 1, 1, 2, 0, 2, 2, 0,
+ 1, 3, 1, 2, 3, 1, 3, 1, 2, 3,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 3,
+ 3, 3
};
/* YYDEFACT[STATE-NAME] -- Default rule to reduce with in state
means the default is an error. */
static const yytype_uint8 yydefact[] =
{
- 2, 0, 1, 0, 15, 40, 41, 25, 26, 0,
- 58, 57, 59, 35, 62, 34, 0, 0, 0, 3,
- 0, 7, 16, 10, 9, 20, 0, 0, 19, 5,
- 17, 0, 33, 26, 32, 0, 55, 60, 40, 35,
- 0, 27, 0, 0, 48, 40, 41, 0, 0, 20,
- 0, 19, 4, 18, 62, 11, 0, 0, 42, 0,
- 36, 62, 62, 0, 0, 0, 0, 0, 0, 0,
- 12, 13, 14, 56, 65, 61, 63, 0, 0, 42,
- 21, 0, 30, 50, 54, 22, 29, 28, 40, 41,
- 51, 70, 0, 72, 73, 71, 38, 67, 37, 43,
- 39, 31, 44, 45, 46, 47, 49, 0, 64, 66,
- 23, 24, 0, 0, 0, 52, 0, 68, 0, 74,
- 75, 76, 69, 0, 53
+ 2, 0, 1, 0, 15, 44, 45, 29, 30, 0,
+ 62, 61, 63, 39, 66, 38, 0, 0, 0, 0,
+ 3, 0, 7, 16, 10, 9, 20, 0, 0, 19,
+ 5, 17, 0, 37, 30, 36, 0, 59, 64, 44,
+ 39, 0, 31, 0, 0, 52, 0, 20, 0, 19,
+ 23, 25, 0, 27, 28, 0, 4, 18, 66, 11,
+ 0, 0, 46, 0, 40, 66, 66, 0, 0, 0,
+ 0, 0, 0, 0, 12, 13, 14, 60, 69, 65,
+ 67, 0, 0, 46, 21, 34, 54, 58, 24, 26,
+ 0, 22, 33, 32, 0, 85, 86, 87, 42, 75,
+ 77, 88, 41, 47, 43, 35, 48, 49, 50, 51,
+ 53, 0, 44, 45, 0, 0, 0, 0, 55, 80,
+ 0, 82, 83, 81, 68, 70, 72, 84, 0, 0,
+ 0, 0, 0, 78, 44, 45, 0, 56, 0, 73,
+ 0, 76, 89, 90, 91, 79, 71, 74, 0, 57
};
/* YYDEFGOTO[NTERM-NUM]. */
static const yytype_int8 yydefgoto[] =
{
- -1, 1, 19, 20, 21, 22, 23, 48, 90, 91,
- 26, 93, 94, 95, 36, 37, 76, 108, 98, 97
+ -1, 1, 20, 21, 22, 23, 24, 95, 96, 55,
+ 97, 119, 27, 28, 122, 123, 37, 38, 80, 124,
+ 125, 102, 99, 126, 100, 101
};
/* YYPACT[STATE-NUM] -- Index in YYTABLE of the portion describing
STATE-NUM. */
-#define YYPACT_NINF -87
+#define YYPACT_NINF -93
static const yytype_int16 yypact[] =
{
- -87, 124, -87, -1, 6, 8, -87, -87, 12, 56,
- -87, -87, -87, 17, -87, -87, 278, 288, 200, -87,
- 53, -87, 75, 66, 225, 0, 133, 84, -87, -87,
- -87, 239, -87, -87, -87, 278, -87, 57, -87, -87,
- 278, -87, 288, -14, 55, 54, 58, -16, 63, -18,
- 68, 69, -87, -87, -87, 66, 278, 278, 186, 186,
- -87, -87, -87, 288, 288, 288, 288, 288, 288, 264,
- 0, 84, -87, 0, 186, -87, -87, -18, 51, -87,
- -87, 102, -87, -87, -87, -87, 83, -87, 110, 114,
- -87, 0, 164, 19, -87, -87, 155, -87, 155, -87,
- -87, 19, 38, 38, 55, 55, 55, 69, -87, 155,
- -87, -87, 93, 107, 102, 186, 186, -87, 102, -87,
- -87, -87, -87, 85, -87
+ -93, 155, -93, 10, 19, 26, -93, -93, -3, 73,
+ -93, -93, -93, 22, -93, -93, 356, 372, 317, 11,
+ -93, 79, -93, 86, 70, 317, 29, 384, 180, -93,
+ -93, -93, 342, -93, -93, -93, 356, -93, 6, -93,
+ -93, 356, -93, 372, -10, 57, -20, -17, 256, 54,
+ -93, -93, 88, -93, -93, 55, -93, -93, -93, 70,
+ 356, 356, 197, 174, -93, -93, -93, 372, 372, 372,
+ 372, 372, 372, 342, 29, 180, -93, 29, 221, -93,
+ -93, -17, 223, -93, -93, -93, -93, -93, -93, -93,
+ 11, -93, 69, -93, 78, 90, 94, -93, -93, 244,
+ -93, -93, -93, -93, -93, 267, 36, 36, 57, 57,
+ 57, 54, 95, 96, 375, 303, 90, 94, -93, 29,
+ 392, 267, -93, -93, -93, 263, -93, -93, 71, 35,
+ 11, 11, 78, -93, 105, 106, 178, 174, 303, -93,
+ 11, -93, -93, -93, -93, -93, -93, -93, 80, -93
};
/* YYPGOTO[NTERM-NUM]. */
static const yytype_int8 yypgoto[] =
{
- -87, -87, -87, -87, -87, -87, 15, -78, 28, 60,
- -17, 3, -87, 4, -46, -87, -87, -87, -57, -86
+ -93, -93, -93, -93, -93, -93, -13, 0, 14, -81,
+ -1, 87, -4, -16, -93, 3, -36, -93, -93, -93,
+ 12, 81, 39, -91, -92, -67
};
/* YYTABLE[YYPACT[STATE-NUM]]. What to do in state STATE-NUM. If
positive, shift that token. If negative, reduce the rule which
number is the opposite. If zero, do what YYDEFACT says.
If YYTABLE_NINF, syntax error. */
-#define YYTABLE_NINF -25
-static const yytype_int8 yytable[] =
+#define YYTABLE_NINF -27
+static const yytype_int16 yytable[] =
{
- 43, 96, 79, 112, 27, 28, 61, 54, 85, 29,
- 117, 30, 117, 56, 57, 99, 100, 109, -8, 27,
- 44, 50, 51, 117, 82, 43, 80, 27, 28, 24,
- 122, 56, 57, 47, 71, 72, 121, 34, 27, 55,
- 123, 92, 92, 50, 35, 78, 43, 43, 43, 43,
- 43, 43, 31, 64, 65, 66, 67, 92, 68, 27,
- 27, 25, 32, 52, 7, 33, 101, 102, 103, 104,
- 105, 106, 50, 107, 66, 67, 41, 68, 49, 92,
- 53, 92, 74, 75, 25, 64, 65, 66, 67, 54,
- 68, 70, 92, 83, 68, 73, 63, -23, 92, 92,
- 77, -24, 64, 65, 66, 67, 81, 68, 110, 111,
- 83, 84, 63, 119, 120, 57, 86, 87, 64, 65,
- 66, 67, 113, 68, 2, 3, 114, 124, 4, 77,
- 5, 6, 7, 8, -6, 9, 118, 10, 11, 12,
- 0, 0, 13, 0, 0, 0, 14, 0, 15, 58,
- 59, 0, 60, 61, 62, 0, 0, 16, 0, 17,
- 0, 88, 89, 7, 33, 18, 9, 0, 10, 11,
+ 25, 45, 48, 58, 29, 46, 83, 133, 35, 128,
+ 65, 127, 59, 44, 60, 61, 75, 50, 51, 53,
+ 30, 49, 91, 84, 31, 48, 85, 82, 29, 103,
+ 104, 78, 79, 54, 139, 76, -8, 133, 32, 44,
+ 145, 50, 51, 7, 34, 139, 52, 147, 127, 36,
+ 144, 105, 106, 107, 108, 109, 110, 48, 127, 148,
+ 60, 61, 121, 44, 44, 44, 44, 44, 44, 127,
+ 52, 127, 70, 71, 120, 72, 111, 118, 116, 33,
+ 132, 7, 34, 141, 50, 51, 7, 34, 26, 56,
+ 53, 57, 117, 58, 88, 89, 72, 87, 45, 121,
+ 90, 61, 130, 42, 54, 47, 131, -23, -25, 121,
+ 44, 120, 26, 52, 118, 116, 140, -24, -26, 74,
+ 121, 120, 121, 77, 118, 116, 149, 136, 81, 117,
+ 142, 53, 120, 129, 120, 118, 116, 118, 116, 117,
+ 53, 0, 0, 98, 143, 54, 0, 92, 93, 0,
+ 117, 0, 117, 0, 54, 2, 3, 0, 0, 4,
+ 81, 5, 6, 7, 8, -6, 9, 0, 10, 11,
12, 0, 0, 13, 0, 0, 0, 14, 0, 15,
- 58, 115, 0, 60, 61, 62, 0, 0, 16, 0,
- 17, 0, 88, 89, 7, 33, 69, 9, 116, 10,
- 11, 12, 0, 0, 13, 0, 45, 46, 14, 0,
- 15, 9, 0, 10, 11, 12, 0, 0, 13, 16,
- 0, 17, 14, 0, 15, 0, 0, 69, 0, 0,
- 0, 38, 6, 16, 0, 17, 9, 0, 10, 11,
- 12, 18, 0, 13, 0, 38, 6, 14, 0, 15,
- 9, 0, 10, 11, 12, 0, 0, 13, 16, 0,
- 17, 14, 0, 15, 0, 0, 18, 0, 0, 0,
- 45, 46, 16, 0, 17, 9, 0, 10, 11, 12,
- 69, 0, 13, 0, 38, 6, 14, 0, 15, 9,
- 0, 10, 11, 0, 38, 6, 39, 16, 0, 17,
- 0, 10, 15, 0, 0, 69, 39, 0, 0, 0,
- 0, 16, 15, 17, 0, 0, 0, 0, 0, 40,
- 0, 0, 0, 17, 0, 0, 0, 0, 0, 42
+ 50, 51, 7, 34, 112, 113, 7, 34, 16, 9,
+ 17, 10, 11, 12, 0, 0, 13, 18, 0, 19,
+ 14, 0, 15, 50, 51, 7, 34, 0, 67, 52,
+ 0, 16, 0, 114, 68, 69, 70, 71, 0, 72,
+ 73, 94, 19, 138, 0, 0, 146, 112, 113, 7,
+ 34, 0, 9, 0, 10, 11, 12, 0, 0, 13,
+ 0, 0, 0, 14, 94, 15, 0, 0, 0, 0,
+ 50, 51, 7, 34, 16, 0, 114, 68, 69, 70,
+ 71, 0, 72, 73, 0, 19, 86, 0, 115, 112,
+ 113, 7, 34, 0, 9, 0, 10, 11, 12, 52,
+ 0, 13, 0, 0, 67, 14, 0, 15, 0, 132,
+ 68, 69, 70, 71, 0, 72, 16, 0, 114, 86,
+ 0, 68, 69, 70, 71, 73, 72, 19, 138, 112,
+ 113, 7, 34, 0, 9, 0, 10, 11, 12, 0,
+ 0, 13, 0, 39, 6, 14, 0, 15, 9, 0,
+ 10, 11, 12, 0, 0, 13, 16, 0, 114, 14,
+ 0, 15, 0, 0, 0, 73, 0, 19, 39, 6,
+ 16, 0, 17, 9, 0, 10, 11, 12, 0, 18,
+ 13, 19, 39, 6, 14, 0, 15, 9, 0, 10,
+ 11, 0, 0, 0, 40, 16, 0, 17, 39, 6,
+ 15, 134, 135, 0, 73, 10, 19, 0, 10, 16,
+ 40, 17, 0, 40, 0, 0, 15, 0, 41, 15,
+ 62, 63, 0, 64, 65, 66, 0, 17, 62, 137,
+ 17, 64, 65, 66, 43, 0, 0, 43
};
-static const yytype_int8 yycheck[] =
+static const yytype_int16 yycheck[] =
{
- 17, 58, 16, 81, 1, 1, 20, 23, 54, 10,
- 96, 5, 98, 31, 32, 61, 62, 74, 10, 16,
- 17, 18, 18, 109, 42, 42, 42, 24, 24, 1,
- 116, 31, 32, 18, 31, 31, 114, 9, 35, 24,
- 118, 58, 59, 40, 27, 42, 63, 64, 65, 66,
- 67, 68, 40, 34, 35, 36, 37, 74, 39, 56,
- 57, 1, 6, 10, 8, 9, 63, 64, 65, 66,
- 67, 68, 69, 69, 36, 37, 16, 39, 18, 96,
- 5, 98, 25, 26, 24, 34, 35, 36, 37, 23,
- 39, 31, 109, 42, 39, 35, 28, 43, 115, 116,
- 40, 43, 34, 35, 36, 37, 43, 39, 6, 7,
- 42, 42, 28, 6, 7, 32, 56, 57, 34, 35,
- 36, 37, 12, 39, 0, 1, 12, 42, 4, 69,
- 6, 7, 8, 9, 10, 11, 43, 13, 14, 15,
- -1, -1, 18, -1, -1, -1, 22, -1, 24, 16,
- 17, -1, 19, 20, 21, -1, -1, 33, -1, 35,
- -1, 6, 7, 8, 9, 41, 11, -1, 13, 14,
+ 1, 17, 18, 23, 1, 18, 16, 99, 9, 90,
+ 20, 78, 25, 17, 31, 32, 32, 6, 7, 19,
+ 10, 18, 58, 43, 5, 41, 43, 43, 25, 65,
+ 66, 25, 26, 19, 125, 32, 10, 129, 41, 43,
+ 132, 6, 7, 8, 9, 136, 35, 138, 115, 27,
+ 131, 67, 68, 69, 70, 71, 72, 73, 125, 140,
+ 31, 32, 78, 67, 68, 69, 70, 71, 72, 136,
+ 35, 138, 36, 37, 78, 39, 73, 78, 78, 6,
+ 45, 8, 9, 48, 6, 7, 8, 9, 1, 10,
+ 90, 5, 78, 23, 6, 7, 39, 43, 114, 115,
+ 45, 32, 12, 16, 90, 18, 12, 12, 12, 125,
+ 114, 115, 25, 35, 115, 115, 45, 12, 12, 32,
+ 136, 125, 138, 36, 125, 125, 46, 115, 41, 115,
+ 130, 131, 136, 94, 138, 136, 136, 138, 138, 125,
+ 140, -1, -1, 62, 130, 131, -1, 60, 61, -1,
+ 136, -1, 138, -1, 140, 0, 1, -1, -1, 4,
+ 73, 6, 7, 8, 9, 10, 11, -1, 13, 14,
15, -1, -1, 18, -1, -1, -1, 22, -1, 24,
- 16, 17, -1, 19, 20, 21, -1, -1, 33, -1,
- 35, -1, 6, 7, 8, 9, 41, 11, 43, 13,
- 14, 15, -1, -1, 18, -1, 6, 7, 22, -1,
- 24, 11, -1, 13, 14, 15, -1, -1, 18, 33,
- -1, 35, 22, -1, 24, -1, -1, 41, -1, -1,
- -1, 6, 7, 33, -1, 35, 11, -1, 13, 14,
- 15, 41, -1, 18, -1, 6, 7, 22, -1, 24,
- 11, -1, 13, 14, 15, -1, -1, 18, 33, -1,
- 35, 22, -1, 24, -1, -1, 41, -1, -1, -1,
- 6, 7, 33, -1, 35, 11, -1, 13, 14, 15,
- 41, -1, 18, -1, 6, 7, 22, -1, 24, 11,
- -1, 13, 14, -1, 6, 7, 18, 33, -1, 35,
- -1, 13, 24, -1, -1, 41, 18, -1, -1, -1,
- -1, 33, 24, 35, -1, -1, -1, -1, -1, 41,
- -1, -1, -1, 35, -1, -1, -1, -1, -1, 41
+ 6, 7, 8, 9, 6, 7, 8, 9, 33, 11,
+ 35, 13, 14, 15, -1, -1, 18, 42, -1, 44,
+ 22, -1, 24, 6, 7, 8, 9, -1, 28, 35,
+ -1, 33, -1, 35, 34, 35, 36, 37, -1, 39,
+ 42, 47, 44, 45, -1, -1, 48, 6, 7, 8,
+ 9, -1, 11, -1, 13, 14, 15, -1, -1, 18,
+ -1, -1, -1, 22, 47, 24, -1, -1, -1, -1,
+ 6, 7, 8, 9, 33, -1, 35, 34, 35, 36,
+ 37, -1, 39, 42, -1, 44, 43, -1, 47, 6,
+ 7, 8, 9, -1, 11, -1, 13, 14, 15, 35,
+ -1, 18, -1, -1, 28, 22, -1, 24, -1, 45,
+ 34, 35, 36, 37, -1, 39, 33, -1, 35, 43,
+ -1, 34, 35, 36, 37, 42, 39, 44, 45, 6,
+ 7, 8, 9, -1, 11, -1, 13, 14, 15, -1,
+ -1, 18, -1, 6, 7, 22, -1, 24, 11, -1,
+ 13, 14, 15, -1, -1, 18, 33, -1, 35, 22,
+ -1, 24, -1, -1, -1, 42, -1, 44, 6, 7,
+ 33, -1, 35, 11, -1, 13, 14, 15, -1, 42,
+ 18, 44, 6, 7, 22, -1, 24, 11, -1, 13,
+ 14, -1, -1, -1, 18, 33, -1, 35, 6, 7,
+ 24, 6, 7, -1, 42, 13, 44, -1, 13, 33,
+ 18, 35, -1, 18, -1, -1, 24, -1, 42, 24,
+ 16, 17, -1, 19, 20, 21, -1, 35, 16, 17,
+ 35, 19, 20, 21, 42, -1, -1, 42
};
/* YYSTOS[STATE-NUM] -- The (internal number of the) accessing
symbol of state STATE-NUM. */
static const yytype_uint8 yystos[] =
{
- 0, 45, 0, 1, 4, 6, 7, 8, 9, 11,
- 13, 14, 15, 18, 22, 24, 33, 35, 41, 46,
- 47, 48, 49, 50, 52, 53, 54, 55, 57, 10,
- 5, 40, 6, 9, 52, 27, 58, 59, 6, 18,
- 41, 53, 41, 54, 55, 6, 7, 50, 51, 53,
- 55, 57, 10, 5, 23, 50, 31, 32, 16, 17,
- 19, 20, 21, 28, 34, 35, 36, 37, 39, 41,
- 53, 55, 57, 53, 25, 26, 60, 53, 55, 16,
- 42, 43, 42, 42, 42, 58, 53, 53, 6, 7,
- 52, 53, 54, 55, 56, 57, 62, 63, 62, 58,
- 58, 55, 55, 55, 55, 55, 55, 57, 61, 62,
- 6, 7, 51, 12, 12, 17, 43, 63, 43, 6,
- 7, 51, 63, 51, 42
+ 0, 50, 0, 1, 4, 6, 7, 8, 9, 11,
+ 13, 14, 15, 18, 22, 24, 33, 35, 42, 44,
+ 51, 52, 53, 54, 55, 59, 60, 61, 62, 64,
+ 10, 5, 41, 6, 9, 59, 27, 65, 66, 6,
+ 18, 42, 60, 42, 61, 62, 55, 60, 62, 64,
+ 6, 7, 35, 56, 57, 58, 10, 5, 23, 55,
+ 31, 32, 16, 17, 19, 20, 21, 28, 34, 35,
+ 36, 37, 39, 42, 60, 62, 64, 60, 25, 26,
+ 67, 60, 62, 16, 43, 43, 43, 43, 6, 7,
+ 45, 65, 60, 60, 47, 56, 57, 59, 70, 71,
+ 73, 74, 70, 65, 65, 62, 62, 62, 62, 62,
+ 62, 64, 6, 7, 35, 47, 56, 57, 59, 60,
+ 61, 62, 63, 64, 68, 69, 72, 74, 58, 71,
+ 12, 12, 45, 73, 6, 7, 69, 17, 45, 72,
+ 45, 48, 56, 57, 58, 73, 48, 72, 58, 46
};
#define yyerrok (yyerrstatus = 0)
switch (yytype)
{
case 5: /* "HELP_TOPIC" */
-#line 158 "parser.y"
+#line 161 "parser.y"
{ free((yyvaluep->str)); };
-#line 1274 "parser.c"
+#line 1317 "parser.c"
break;
case 8: /* "STR" */
-#line 158 "parser.y"
+#line 161 "parser.y"
{ free((yyvaluep->str)); };
-#line 1279 "parser.c"
+#line 1322 "parser.c"
break;
case 9: /* "IDENTIFIER" */
-#line 158 "parser.y"
+#line 161 "parser.y"
{ free((yyvaluep->str)); };
-#line 1284 "parser.c"
+#line 1327 "parser.c"
break;
case 25: /* "PARAM" */
-#line 159 "parser.y"
+#line 162 "parser.y"
{ if((yyvaluep->str)) free((yyvaluep->str)); };
-#line 1289 "parser.c"
+#line 1332 "parser.c"
break;
case 28: /* "CMP_OP" */
-#line 158 "parser.y"
+#line 161 "parser.y"
{ free((yyvaluep->str)); };
-#line 1294 "parser.c"
+#line 1337 "parser.c"
break;
- case 46: /* "command" */
-#line 160 "parser.y"
+ case 51: /* "command" */
+#line 163 "parser.y"
{ if((yyvaluep->sel)) _gmx_selelem_free((yyvaluep->sel)); };
-#line 1299 "parser.c"
+#line 1342 "parser.c"
break;
- case 47: /* "cmd_plain" */
-#line 160 "parser.y"
+ case 52: /* "cmd_plain" */
+#line 163 "parser.y"
{ if((yyvaluep->sel)) _gmx_selelem_free((yyvaluep->sel)); };
-#line 1304 "parser.c"
+#line 1347 "parser.c"
break;
- case 50: /* "selection" */
-#line 161 "parser.y"
+ case 55: /* "selection" */
+#line 164 "parser.y"
{ _gmx_selelem_free_chain((yyvaluep->sel)); };
-#line 1309 "parser.c"
+#line 1352 "parser.c"
break;
- case 52: /* "string" */
-#line 158 "parser.y"
+ case 59: /* "string" */
+#line 161 "parser.y"
{ free((yyvaluep->str)); };
-#line 1314 "parser.c"
+#line 1357 "parser.c"
break;
- case 53: /* "sel_expr" */
-#line 162 "parser.y"
+ case 60: /* "sel_expr" */
+#line 165 "parser.y"
{ _gmx_selelem_free((yyvaluep->sel)); };
-#line 1319 "parser.c"
+#line 1362 "parser.c"
break;
- case 55: /* "num_expr" */
-#line 162 "parser.y"
+ case 62: /* "num_expr" */
+#line 165 "parser.y"
{ _gmx_selelem_free((yyvaluep->sel)); };
-#line 1324 "parser.c"
+#line 1367 "parser.c"
break;
- case 56: /* "str_expr" */
-#line 162 "parser.y"
+ case 63: /* "str_expr" */
+#line 165 "parser.y"
{ _gmx_selelem_free((yyvaluep->sel)); };
-#line 1329 "parser.c"
+#line 1372 "parser.c"
break;
- case 57: /* "pos_expr" */
-#line 162 "parser.y"
+ case 64: /* "pos_expr" */
+#line 165 "parser.y"
{ _gmx_selelem_free((yyvaluep->sel)); };
-#line 1334 "parser.c"
+#line 1377 "parser.c"
break;
- case 58: /* "method_params" */
-#line 163 "parser.y"
+ case 65: /* "method_params" */
+#line 166 "parser.y"
{ _gmx_selexpr_free_params((yyvaluep->param)); };
-#line 1339 "parser.c"
+#line 1382 "parser.c"
break;
- case 59: /* "method_param_list" */
-#line 163 "parser.y"
+ case 66: /* "method_param_list" */
+#line 166 "parser.y"
{ _gmx_selexpr_free_params((yyvaluep->param)); };
-#line 1344 "parser.c"
+#line 1387 "parser.c"
break;
- case 60: /* "method_param" */
-#line 163 "parser.y"
+ case 67: /* "method_param" */
+#line 166 "parser.y"
{ _gmx_selexpr_free_params((yyvaluep->param)); };
-#line 1349 "parser.c"
+#line 1392 "parser.c"
break;
- case 61: /* "value_list" */
-#line 164 "parser.y"
+ case 68: /* "value_list" */
+#line 167 "parser.y"
{ _gmx_selexpr_free_values((yyvaluep->val)); };
-#line 1354 "parser.c"
+#line 1397 "parser.c"
break;
- case 62: /* "value_list_nonempty" */
-#line 164 "parser.y"
+ case 69: /* "value_list_contents" */
+#line 167 "parser.y"
{ _gmx_selexpr_free_values((yyvaluep->val)); };
-#line 1359 "parser.c"
+#line 1402 "parser.c"
break;
- case 63: /* "value_item" */
-#line 164 "parser.y"
+ case 70: /* "basic_value_list" */
+#line 168 "parser.y"
+ { _gmx_selexpr_free_values((yyvaluep->val)); };
+#line 1407 "parser.c"
+ break;
+ case 71: /* "basic_value_list_contents" */
+#line 168 "parser.y"
+ { _gmx_selexpr_free_values((yyvaluep->val)); };
+#line 1412 "parser.c"
+ break;
+ case 72: /* "value_item" */
+#line 167 "parser.y"
+ { _gmx_selexpr_free_values((yyvaluep->val)); };
+#line 1417 "parser.c"
+ break;
+ case 73: /* "basic_value_item" */
+#line 168 "parser.y"
+ { _gmx_selexpr_free_values((yyvaluep->val)); };
+#line 1422 "parser.c"
+ break;
+ case 74: /* "value_item_range" */
+#line 167 "parser.y"
{ _gmx_selexpr_free_values((yyvaluep->val)); };
-#line 1364 "parser.c"
+#line 1427 "parser.c"
break;
default:
switch (yyn)
{
case 2:
-#line 178 "parser.y"
+#line 182 "parser.y"
{ (yyval.sel) = NULL ;}
break;
case 3:
-#line 180 "parser.y"
+#line 184 "parser.y"
{
(yyval.sel) = _gmx_sel_append_selection((yyvsp[(2) - (2)].sel), (yyvsp[(1) - (2)].sel), scanner);
if (_gmx_sel_parser_should_finish(scanner))
break;
case 4:
-#line 188 "parser.y"
+#line 192 "parser.y"
{ (yyval.sel) = (yyvsp[(1) - (2)].sel); ;}
break;
case 5:
-#line 190 "parser.y"
+#line 194 "parser.y"
{
(yyval.sel) = NULL;
_gmx_selparser_error("invalid selection '%s'",
break;
case 6:
-#line 209 "parser.y"
+#line 213 "parser.y"
{
(yyval.sel) = NULL;
_gmx_sel_handle_empty_cmd(scanner);
break;
case 7:
-#line 213 "parser.y"
+#line 217 "parser.y"
{ (yyval.sel) = NULL; ;}
break;
case 8:
-#line 215 "parser.y"
+#line 219 "parser.y"
{
t_selelem *s, *p;
s = _gmx_sel_init_group_by_id((yyvsp[(1) - (1)].i), scanner);
break;
case 9:
-#line 224 "parser.y"
+#line 228 "parser.y"
{
t_selelem *s, *p;
s = _gmx_sel_init_group_by_name((yyvsp[(1) - (1)].str), scanner);
break;
case 10:
-#line 234 "parser.y"
+#line 238 "parser.y"
{ (yyval.sel) = _gmx_sel_init_selection(NULL, (yyvsp[(1) - (1)].sel), scanner); ;}
break;
case 11:
-#line 236 "parser.y"
+#line 240 "parser.y"
{ (yyval.sel) = _gmx_sel_init_selection((yyvsp[(1) - (2)].str), (yyvsp[(2) - (2)].sel), scanner); ;}
break;
case 12:
-#line 238 "parser.y"
+#line 242 "parser.y"
{ (yyval.sel) = _gmx_sel_assign_variable((yyvsp[(1) - (3)].str), (yyvsp[(3) - (3)].sel), scanner); ;}
break;
case 13:
-#line 240 "parser.y"
+#line 244 "parser.y"
{ (yyval.sel) = _gmx_sel_assign_variable((yyvsp[(1) - (3)].str), (yyvsp[(3) - (3)].sel), scanner); ;}
break;
case 14:
-#line 242 "parser.y"
+#line 246 "parser.y"
{ (yyval.sel) = _gmx_sel_assign_variable((yyvsp[(1) - (3)].str), (yyvsp[(3) - (3)].sel), scanner); ;}
break;
case 15:
-#line 247 "parser.y"
+#line 251 "parser.y"
{ _gmx_sel_handle_help_cmd(NULL, scanner); ;}
break;
case 17:
-#line 251 "parser.y"
+#line 255 "parser.y"
{ _gmx_sel_handle_help_cmd((yyvsp[(2) - (2)].str), scanner); ;}
break;
case 18:
-#line 252 "parser.y"
+#line 256 "parser.y"
{ _gmx_sel_handle_help_cmd((yyvsp[(2) - (2)].str), scanner); ;}
break;
case 19:
-#line 256 "parser.y"
+#line 260 "parser.y"
{ (yyval.sel) = (yyvsp[(1) - (1)].sel); ;}
break;
case 20:
-#line 258 "parser.y"
+#line 262 "parser.y"
{
(yyval.sel) = _gmx_sel_init_position((yyvsp[(1) - (1)].sel), NULL, scanner);
if ((yyval.sel) == NULL) YYERROR;
break;
case 21:
-#line 262 "parser.y"
+#line 266 "parser.y"
{ (yyval.sel) = (yyvsp[(2) - (3)].sel); ;}
break;
case 22:
-#line 264 "parser.y"
+#line 268 "parser.y"
{
(yyval.sel) = _gmx_sel_init_modifier((yyvsp[(2) - (3)].meth), (yyvsp[(3) - (3)].param), (yyvsp[(1) - (3)].sel), scanner);
if ((yyval.sel) == NULL) YYERROR;
break;
case 23:
-#line 274 "parser.y"
+#line 279 "parser.y"
{ (yyval.r) = (yyvsp[(1) - (1)].i); ;}
break;
case 24:
-#line 275 "parser.y"
- { (yyval.r) = (yyvsp[(1) - (1)].r); ;}
+#line 280 "parser.y"
+ { (yyval.r) = -(yyvsp[(2) - (2)].i); ;}
break;
case 25:
-#line 278 "parser.y"
- { (yyval.str) = (yyvsp[(1) - (1)].str); ;}
+#line 284 "parser.y"
+ { (yyval.r) = (yyvsp[(1) - (1)].r); ;}
break;
case 26:
-#line 279 "parser.y"
- { (yyval.str) = (yyvsp[(1) - (1)].str); ;}
+#line 285 "parser.y"
+ { (yyval.r) = -(yyvsp[(2) - (2)].r); ;}
break;
case 27:
#line 288 "parser.y"
+ { (yyval.r) = (yyvsp[(1) - (1)].r); ;}
+ break;
+
+ case 28:
+#line 289 "parser.y"
+ { (yyval.r) = (yyvsp[(1) - (1)].r); ;}
+ break;
+
+ case 29:
+#line 292 "parser.y"
+ { (yyval.str) = (yyvsp[(1) - (1)].str); ;}
+ break;
+
+ case 30:
+#line 293 "parser.y"
+ { (yyval.str) = (yyvsp[(1) - (1)].str); ;}
+ break;
+
+ case 31:
+#line 302 "parser.y"
{
(yyval.sel) = _gmx_selelem_create(SEL_BOOLEAN);
(yyval.sel)->u.boolt = BOOL_NOT;
;}
break;
- case 28:
-#line 294 "parser.y"
+ case 32:
+#line 308 "parser.y"
{
(yyval.sel) = _gmx_selelem_create(SEL_BOOLEAN);
(yyval.sel)->u.boolt = BOOL_AND;
;}
break;
- case 29:
-#line 300 "parser.y"
+ case 33:
+#line 314 "parser.y"
{
(yyval.sel) = _gmx_selelem_create(SEL_BOOLEAN);
(yyval.sel)->u.boolt = BOOL_OR;
;}
break;
- case 30:
-#line 311 "parser.y"
+ case 34:
+#line 325 "parser.y"
{ (yyval.sel) = (yyvsp[(2) - (3)].sel); ;}
break;
- case 31:
-#line 316 "parser.y"
+ case 35:
+#line 330 "parser.y"
{
(yyval.sel) = _gmx_sel_init_comparison((yyvsp[(1) - (3)].sel), (yyvsp[(3) - (3)].sel), (yyvsp[(2) - (3)].str), scanner);
if ((yyval.sel) == NULL) YYERROR;
;}
break;
- case 32:
-#line 324 "parser.y"
+ case 36:
+#line 338 "parser.y"
{
(yyval.sel) = _gmx_sel_init_group_by_name((yyvsp[(2) - (2)].str), scanner);
free((yyvsp[(2) - (2)].str));
;}
break;
- case 33:
-#line 330 "parser.y"
+ case 37:
+#line 344 "parser.y"
{
(yyval.sel) = _gmx_sel_init_group_by_id((yyvsp[(2) - (2)].i), scanner);
if ((yyval.sel) == NULL) YYERROR;
;}
break;
- case 34:
-#line 337 "parser.y"
+ case 38:
+#line 351 "parser.y"
{ (yyval.str) = NULL; ;}
break;
- case 35:
-#line 338 "parser.y"
+ case 39:
+#line 352 "parser.y"
{ (yyval.str) = (yyvsp[(1) - (1)].str); ;}
break;
- case 36:
-#line 343 "parser.y"
+ case 40:
+#line 357 "parser.y"
{
(yyval.sel) = _gmx_sel_init_keyword((yyvsp[(2) - (2)].meth), NULL, (yyvsp[(1) - (2)].str), scanner);
if ((yyval.sel) == NULL) YYERROR;
;}
break;
- case 37:
-#line 348 "parser.y"
+ case 41:
+#line 362 "parser.y"
{
(yyval.sel) = _gmx_sel_init_keyword((yyvsp[(2) - (3)].meth), process_value_list((yyvsp[(3) - (3)].val), NULL), (yyvsp[(1) - (3)].str), scanner);
if ((yyval.sel) == NULL) YYERROR;
;}
break;
- case 38:
-#line 353 "parser.y"
+ case 42:
+#line 367 "parser.y"
{
(yyval.sel) = _gmx_sel_init_keyword((yyvsp[(2) - (3)].meth), process_value_list((yyvsp[(3) - (3)].val), NULL), (yyvsp[(1) - (3)].str), scanner);
if ((yyval.sel) == NULL) YYERROR;
;}
break;
- case 39:
-#line 361 "parser.y"
+ case 43:
+#line 375 "parser.y"
{
(yyval.sel) = _gmx_sel_init_method((yyvsp[(2) - (3)].meth), (yyvsp[(3) - (3)].param), (yyvsp[(1) - (3)].str), scanner);
if ((yyval.sel) == NULL) YYERROR;
;}
break;
- case 40:
-#line 373 "parser.y"
+ case 44:
+#line 387 "parser.y"
{
(yyval.sel) = _gmx_selelem_create(SEL_CONST);
_gmx_selelem_set_vtype((yyval.sel), INT_VALUE);
;}
break;
- case 41:
-#line 380 "parser.y"
+ case 45:
+#line 394 "parser.y"
{
(yyval.sel) = _gmx_selelem_create(SEL_CONST);
_gmx_selelem_set_vtype((yyval.sel), REAL_VALUE);
;}
break;
- case 42:
-#line 390 "parser.y"
+ case 46:
+#line 404 "parser.y"
{
(yyval.sel) = _gmx_sel_init_keyword((yyvsp[(2) - (2)].meth), NULL, (yyvsp[(1) - (2)].str), scanner);
if ((yyval.sel) == NULL) YYERROR;
;}
break;
- case 43:
-#line 395 "parser.y"
+ case 47:
+#line 409 "parser.y"
{
(yyval.sel) = _gmx_sel_init_method((yyvsp[(2) - (3)].meth), (yyvsp[(3) - (3)].param), (yyvsp[(1) - (3)].str), scanner);
if ((yyval.sel) == NULL) YYERROR;
;}
break;
- case 44:
-#line 403 "parser.y"
+ case 48:
+#line 417 "parser.y"
{ (yyval.sel) = _gmx_sel_init_arithmetic((yyvsp[(1) - (3)].sel), (yyvsp[(3) - (3)].sel), '+', scanner); ;}
break;
- case 45:
-#line 405 "parser.y"
+ case 49:
+#line 419 "parser.y"
{ (yyval.sel) = _gmx_sel_init_arithmetic((yyvsp[(1) - (3)].sel), (yyvsp[(3) - (3)].sel), '-', scanner); ;}
break;
- case 46:
-#line 407 "parser.y"
+ case 50:
+#line 421 "parser.y"
{ (yyval.sel) = _gmx_sel_init_arithmetic((yyvsp[(1) - (3)].sel), (yyvsp[(3) - (3)].sel), '*', scanner); ;}
break;
- case 47:
-#line 409 "parser.y"
+ case 51:
+#line 423 "parser.y"
{ (yyval.sel) = _gmx_sel_init_arithmetic((yyvsp[(1) - (3)].sel), (yyvsp[(3) - (3)].sel), '/', scanner); ;}
break;
- case 48:
-#line 411 "parser.y"
+ case 52:
+#line 425 "parser.y"
{ (yyval.sel) = _gmx_sel_init_arithmetic((yyvsp[(2) - (2)].sel), NULL, '-', scanner); ;}
break;
- case 49:
-#line 413 "parser.y"
+ case 53:
+#line 427 "parser.y"
{ (yyval.sel) = _gmx_sel_init_arithmetic((yyvsp[(1) - (3)].sel), (yyvsp[(3) - (3)].sel), '^', scanner); ;}
break;
- case 50:
-#line 414 "parser.y"
+ case 54:
+#line 428 "parser.y"
{ (yyval.sel) = (yyvsp[(2) - (3)].sel); ;}
break;
- case 51:
-#line 422 "parser.y"
+ case 55:
+#line 436 "parser.y"
{
(yyval.sel) = _gmx_selelem_create(SEL_CONST);
_gmx_selelem_set_vtype((yyval.sel), STR_VALUE);
;}
break;
- case 52:
-#line 429 "parser.y"
+ case 56:
+#line 443 "parser.y"
{
(yyval.sel) = _gmx_sel_init_keyword((yyvsp[(2) - (2)].meth), NULL, (yyvsp[(1) - (2)].str), scanner);
if ((yyval.sel) == NULL) YYERROR;
;}
break;
- case 53:
-#line 441 "parser.y"
+ case 57:
+#line 455 "parser.y"
{ (yyval.sel) = _gmx_sel_init_const_position((yyvsp[(2) - (7)].r), (yyvsp[(4) - (7)].r), (yyvsp[(6) - (7)].r)); ;}
break;
- case 54:
-#line 445 "parser.y"
+ case 58:
+#line 459 "parser.y"
{ (yyval.sel) = (yyvsp[(2) - (3)].sel); ;}
break;
- case 55:
-#line 450 "parser.y"
+ case 59:
+#line 464 "parser.y"
{
(yyval.sel) = _gmx_sel_init_method((yyvsp[(1) - (2)].meth), (yyvsp[(2) - (2)].param), NULL, scanner);
if ((yyval.sel) == NULL) YYERROR;
;}
break;
- case 56:
-#line 458 "parser.y"
+ case 60:
+#line 472 "parser.y"
{
(yyval.sel) = _gmx_sel_init_position((yyvsp[(3) - (3)].sel), (yyvsp[(1) - (3)].str), scanner);
if ((yyval.sel) == NULL) YYERROR;
;}
break;
- case 57:
-#line 469 "parser.y"
+ case 61:
+#line 483 "parser.y"
{ (yyval.sel) = _gmx_sel_init_variable_ref((yyvsp[(1) - (1)].sel)); ;}
break;
- case 58:
-#line 473 "parser.y"
+ case 62:
+#line 487 "parser.y"
{ (yyval.sel) = _gmx_sel_init_variable_ref((yyvsp[(1) - (1)].sel)); ;}
break;
- case 59:
-#line 477 "parser.y"
+ case 63:
+#line 491 "parser.y"
{ (yyval.sel) = _gmx_sel_init_variable_ref((yyvsp[(1) - (1)].sel)); ;}
break;
- case 60:
-#line 486 "parser.y"
+ case 64:
+#line 500 "parser.y"
{ (yyval.param) = process_param_list((yyvsp[(1) - (1)].param)); ;}
break;
- case 61:
-#line 488 "parser.y"
+ case 65:
+#line 502 "parser.y"
{ (yyval.param) = process_param_list((yyvsp[(1) - (2)].param)); ;}
break;
- case 62:
-#line 492 "parser.y"
+ case 66:
+#line 506 "parser.y"
{ (yyval.param) = NULL; ;}
break;
- case 63:
-#line 494 "parser.y"
+ case 67:
+#line 508 "parser.y"
{ (yyvsp[(2) - (2)].param)->next = (yyvsp[(1) - (2)].param); (yyval.param) = (yyvsp[(2) - (2)].param); ;}
break;
- case 64:
-#line 499 "parser.y"
+ case 68:
+#line 513 "parser.y"
{
(yyval.param) = _gmx_selexpr_create_param((yyvsp[(1) - (2)].str));
(yyval.param)->value = process_value_list((yyvsp[(2) - (2)].val), &(yyval.param)->nval);
;}
break;
- case 65:
-#line 505 "parser.y"
+ case 69:
+#line 519 "parser.y"
{ (yyval.val) = NULL; ;}
break;
- case 66:
-#line 506 "parser.y"
+ case 70:
+#line 520 "parser.y"
{ (yyval.val) = (yyvsp[(1) - (1)].val); ;}
break;
- case 67:
-#line 510 "parser.y"
+ case 71:
+#line 521 "parser.y"
+ { (yyval.val) = (yyvsp[(2) - (3)].val); ;}
+ break;
+
+ case 72:
+#line 525 "parser.y"
{ (yyval.val) = (yyvsp[(1) - (1)].val); ;}
break;
- case 68:
-#line 512 "parser.y"
+ case 73:
+#line 527 "parser.y"
{ (yyvsp[(2) - (2)].val)->next = (yyvsp[(1) - (2)].val); (yyval.val) = (yyvsp[(2) - (2)].val); ;}
break;
- case 69:
-#line 514 "parser.y"
+ case 74:
+#line 529 "parser.y"
{ (yyvsp[(3) - (3)].val)->next = (yyvsp[(1) - (3)].val); (yyval.val) = (yyvsp[(3) - (3)].val); ;}
break;
- case 70:
-#line 518 "parser.y"
+ case 75:
+#line 533 "parser.y"
+ { (yyval.val) = (yyvsp[(1) - (1)].val); ;}
+ break;
+
+ case 76:
+#line 534 "parser.y"
+ { (yyval.val) = (yyvsp[(2) - (3)].val); ;}
+ break;
+
+ case 77:
+#line 538 "parser.y"
+ { (yyval.val) = (yyvsp[(1) - (1)].val); ;}
+ break;
+
+ case 78:
+#line 540 "parser.y"
+ { (yyvsp[(2) - (2)].val)->next = (yyvsp[(1) - (2)].val); (yyval.val) = (yyvsp[(2) - (2)].val); ;}
+ break;
+
+ case 79:
+#line 542 "parser.y"
+ { (yyvsp[(3) - (3)].val)->next = (yyvsp[(1) - (3)].val); (yyval.val) = (yyvsp[(3) - (3)].val); ;}
+ break;
+
+ case 80:
+#line 546 "parser.y"
{ (yyval.val) = _gmx_selexpr_create_value_expr((yyvsp[(1) - (1)].sel)); ;}
break;
- case 71:
-#line 520 "parser.y"
+ case 81:
+#line 548 "parser.y"
{ (yyval.val) = _gmx_selexpr_create_value_expr((yyvsp[(1) - (1)].sel)); ;}
break;
- case 72:
-#line 522 "parser.y"
+ case 82:
+#line 550 "parser.y"
{ (yyval.val) = _gmx_selexpr_create_value_expr((yyvsp[(1) - (1)].sel)); ;}
break;
- case 73:
-#line 524 "parser.y"
+ case 83:
+#line 552 "parser.y"
{ (yyval.val) = _gmx_selexpr_create_value_expr((yyvsp[(1) - (1)].sel)); ;}
break;
- case 74:
-#line 526 "parser.y"
+ case 84:
+#line 553 "parser.y"
+ { (yyval.val) = (yyvsp[(1) - (1)].val); ;}
+ break;
+
+ case 85:
+#line 558 "parser.y"
{
(yyval.val) = _gmx_selexpr_create_value(INT_VALUE);
- (yyval.val)->u.i.i1 = (yyvsp[(1) - (3)].i); (yyval.val)->u.i.i2 = (yyvsp[(3) - (3)].i);
+ (yyval.val)->u.i.i1 = (yyval.val)->u.i.i2 = (yyvsp[(1) - (1)].r);
;}
break;
- case 75:
-#line 531 "parser.y"
+ case 86:
+#line 563 "parser.y"
{
(yyval.val) = _gmx_selexpr_create_value(REAL_VALUE);
- (yyval.val)->u.r.r1 = (yyvsp[(1) - (3)].i); (yyval.val)->u.r.r2 = (yyvsp[(3) - (3)].r);
+ (yyval.val)->u.r.r1 = (yyval.val)->u.r.r2 = (yyvsp[(1) - (1)].r);
;}
break;
- case 76:
-#line 536 "parser.y"
+ case 87:
+#line 568 "parser.y"
+ {
+ (yyval.val) = _gmx_selexpr_create_value(STR_VALUE);
+ (yyval.val)->u.s = (yyvsp[(1) - (1)].str);
+ ;}
+ break;
+
+ case 88:
+#line 572 "parser.y"
+ { (yyval.val) = (yyvsp[(1) - (1)].val); ;}
+ break;
+
+ case 89:
+#line 577 "parser.y"
+ {
+ (yyval.val) = _gmx_selexpr_create_value(INT_VALUE);
+ (yyval.val)->u.i.i1 = (yyvsp[(1) - (3)].r); (yyval.val)->u.i.i2 = (yyvsp[(3) - (3)].r);
+ ;}
+ break;
+
+ case 90:
+#line 582 "parser.y"
+ {
+ (yyval.val) = _gmx_selexpr_create_value(REAL_VALUE);
+ (yyval.val)->u.r.r1 = (yyvsp[(1) - (3)].r); (yyval.val)->u.r.r2 = (yyvsp[(3) - (3)].r);
+ ;}
+ break;
+
+ case 91:
+#line 587 "parser.y"
{
(yyval.val) = _gmx_selexpr_create_value(REAL_VALUE);
(yyval.val)->u.r.r1 = (yyvsp[(1) - (3)].r); (yyval.val)->u.r.r2 = (yyvsp[(3) - (3)].r);
/* Line 1267 of yacc.c. */
-#line 2162 "parser.c"
+#line 2309 "parser.c"
default: break;
}
YY_SYMBOL_PRINT ("-> $$ =", yyr1[yyn], &yyval, &yyloc);
}
-#line 542 "parser.y"
+#line 593 "parser.y"
static t_selexpr_value *
OR = 286,
AND = 287,
NOT = 288,
- UNARY_NEG = 289
+ UNARY_NEG = 289,
+ NUM_REDUCT = 290
};
#endif
/* Tokens. */
#define AND 287
#define NOT 288
#define UNARY_NEG 289
+#define NUM_REDUCT 290
struct t_selexpr_param *param;
}
/* Line 1489 of yacc.c. */
-#line 129 "parser.h"
+#line 131 "parser.h"
YYSTYPE;
# define yystype YYSTYPE /* obsolescent; will be withdrawn */
# define YYSTYPE_IS_DECLARED 1
%left '*' '/'
%right UNARY_NEG /* Dummy token for unary negation precedence */
%right '^'
+%nonassoc NUM_REDUCT /* Dummy token for numerical keyword reduction precedence */
/* Simple non-terminals */
-%type <r> number
+%type <r> integer_number
+%type <r> real_number number
%type <str> string
%type <str> pos_mod
/* Parameter/value non-terminals */
%type <param> method_params method_param_list method_param
-%type <val> value_list value_list_nonempty value_item
+%type <val> value_list value_list_contents value_item value_item_range
+%type <val> basic_value_list basic_value_list_contents basic_value_item
%destructor { free($$); } HELP_TOPIC STR IDENTIFIER CMP_OP string
%destructor { if($$) free($$); } PARAM
%destructor { _gmx_selelem_free_chain($$); } selection
%destructor { _gmx_selelem_free($$); } sel_expr num_expr str_expr pos_expr
%destructor { _gmx_selexpr_free_params($$); } method_params method_param_list method_param
-%destructor { _gmx_selexpr_free_values($$); } value_list value_list_nonempty value_item
+%destructor { _gmx_selexpr_free_values($$); } value_list value_list_contents value_item value_item_range
+%destructor { _gmx_selexpr_free_values($$); } basic_value_list basic_value_list_contents basic_value_item
-%expect 91
+%expect 50
%debug
%pure-parser
* BASIC NON-TERMINAL SYMBOLS
********************************************************************/
-number: TOK_INT { $$ = $1; }
- | TOK_REAL { $$ = $1; }
+integer_number:
+ TOK_INT { $$ = $1; }
+ | '-' TOK_INT { $$ = -$2; }
+;
+
+real_number:
+ TOK_REAL { $$ = $1; }
+ | '-' TOK_REAL { $$ = -$2; }
+;
+
+number: integer_number { $$ = $1; }
+ | real_number { $$ = $1; }
;
string: STR { $$ = $1; }
$$ = _gmx_sel_init_keyword($2, NULL, $1, scanner);
if ($$ == NULL) YYERROR;
}
- | pos_mod KEYWORD_STR value_list_nonempty
+ | pos_mod KEYWORD_STR basic_value_list
{
$$ = _gmx_sel_init_keyword($2, process_value_list($3, NULL), $1, scanner);
if ($$ == NULL) YYERROR;
}
- | pos_mod KEYWORD_NUMERIC value_list_nonempty
+ | pos_mod KEYWORD_NUMERIC basic_value_list
{
$$ = _gmx_sel_init_keyword($2, process_value_list($3, NULL), $1, scanner);
if ($$ == NULL) YYERROR;
;
/* Numeric selection methods */
-num_expr: pos_mod KEYWORD_NUMERIC
+num_expr: pos_mod KEYWORD_NUMERIC %prec NUM_REDUCT
{
$$ = _gmx_sel_init_keyword($2, NULL, $1, scanner);
if ($$ == NULL) YYERROR;
********************************************************************/
/* Constant position expressions */
-pos_expr: '(' number ',' number ',' number ')'
+pos_expr: '[' number ',' number ',' number ']'
{ $$ = _gmx_sel_init_const_position($2, $4, $6); }
;
}
;
-value_list: /* empty */ { $$ = NULL; }
- | value_list_nonempty { $$ = $1; }
+value_list: /* empty */ { $$ = NULL; }
+ | value_list_contents { $$ = $1; }
+ | '{' value_list_contents '}' { $$ = $2; }
;
-value_list_nonempty:
+value_list_contents:
value_item { $$ = $1; }
- | value_list_nonempty value_item
+ | value_list_contents value_item
{ $2->next = $1; $$ = $2; }
- | value_list_nonempty ',' value_item
+ | value_list_contents ',' value_item
+ { $3->next = $1; $$ = $3; }
+;
+
+basic_value_list:
+ basic_value_list_contents { $$ = $1; }
+ | '{' basic_value_list_contents '}' { $$ = $2; }
+;
+
+basic_value_list_contents:
+ basic_value_item { $$ = $1; }
+ | basic_value_list_contents basic_value_item
+ { $2->next = $1; $$ = $2; }
+ | basic_value_list_contents ',' basic_value_item
{ $3->next = $1; $$ = $3; }
;
{ $$ = _gmx_selexpr_create_value_expr($1); }
| str_expr %prec PARAM_REDUCT
{ $$ = _gmx_selexpr_create_value_expr($1); }
- | TOK_INT TO TOK_INT
+ | value_item_range { $$ = $1; }
+;
+
+basic_value_item:
+ integer_number %prec PARAM_REDUCT
+ {
+ $$ = _gmx_selexpr_create_value(INT_VALUE);
+ $$->u.i.i1 = $$->u.i.i2 = $1;
+ }
+ | real_number %prec PARAM_REDUCT
+ {
+ $$ = _gmx_selexpr_create_value(REAL_VALUE);
+ $$->u.r.r1 = $$->u.r.r2 = $1;
+ }
+ | string %prec PARAM_REDUCT
+ {
+ $$ = _gmx_selexpr_create_value(STR_VALUE);
+ $$->u.s = $1;
+ }
+ | value_item_range { $$ = $1; }
+;
+
+value_item_range:
+ integer_number TO integer_number
{
$$ = _gmx_selexpr_create_value(INT_VALUE);
$$->u.i.i1 = $1; $$->u.i.i2 = $3;
}
- | TOK_INT TO TOK_REAL
+ | integer_number TO real_number
{
$$ = _gmx_selexpr_create_value(REAL_VALUE);
$$->u.r.r1 = $1; $$->u.r.r2 = $3;
}
- | TOK_REAL TO number
+ | real_number TO number
{
$$ = _gmx_selexpr_create_value(REAL_VALUE);
$$->u.r.r1 = $1; $$->u.r.r2 = $3;
flex_int32_t yy_verify;
flex_int32_t yy_nxt;
};
-static yyconst flex_int16_t yy_accept[93] =
+static yyconst flex_int16_t yy_accept[89] =
{ 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 27, 25, 23, 6, 20, 25, 1, 25, 25, 25,
- 2, 6, 21, 25, 22, 25, 24, 22, 22, 22,
- 22, 22, 22, 25, 22, 22, 22, 22, 22, 11,
- 8, 10, 10, 9, 23, 21, 0, 4, 0, 1,
- 17, 0, 0, 3, 3, 2, 24, 24, 22, 5,
- 22, 22, 22, 18, 15, 22, 18, 16, 13, 22,
- 12, 22, 22, 8, 9, 0, 0, 0, 3, 17,
- 22, 20, 19, 13, 22, 3, 0, 3, 22, 7,
- 14, 0
-
+ 27, 25, 23, 6, 20, 25, 1, 25, 25, 2,
+ 6, 21, 25, 22, 25, 24, 22, 22, 22, 22,
+ 22, 22, 25, 22, 22, 22, 22, 22, 11, 8,
+ 10, 10, 9, 23, 21, 0, 4, 0, 1, 17,
+ 3, 3, 2, 24, 24, 22, 5, 22, 22, 22,
+ 18, 15, 22, 18, 16, 13, 22, 12, 22, 22,
+ 8, 9, 0, 0, 3, 17, 22, 20, 19, 13,
+ 22, 0, 3, 3, 22, 7, 14, 0
} ;
static yyconst flex_int32_t yy_ec[256] =
1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 2, 4, 5, 6, 1, 1, 7, 1, 1,
- 1, 1, 8, 1, 9, 10, 1, 11, 11, 11,
- 11, 11, 11, 11, 11, 11, 11, 1, 12, 13,
- 14, 13, 1, 1, 15, 15, 15, 15, 16, 15,
- 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
- 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
- 1, 17, 1, 1, 18, 1, 19, 15, 15, 20,
-
- 21, 22, 23, 24, 15, 15, 15, 25, 15, 26,
- 27, 28, 15, 29, 30, 31, 32, 15, 15, 33,
- 34, 15, 1, 35, 1, 1, 1, 1, 1, 1,
+ 1, 1, 8, 1, 8, 9, 1, 10, 10, 10,
+ 10, 10, 10, 10, 10, 10, 10, 1, 11, 12,
+ 13, 12, 1, 1, 14, 14, 14, 14, 15, 14,
+ 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+ 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+ 1, 16, 1, 1, 17, 1, 18, 14, 14, 19,
+
+ 20, 21, 22, 23, 14, 14, 14, 24, 14, 25,
+ 26, 27, 14, 28, 29, 30, 31, 14, 14, 32,
+ 33, 14, 1, 34, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1
} ;
-static yyconst flex_int32_t yy_meta[36] =
+static yyconst flex_int32_t yy_meta[35] =
{ 0,
- 1, 1, 2, 1, 1, 1, 1, 1, 1, 3,
- 4, 1, 1, 1, 4, 4, 1, 4, 4, 4,
+ 1, 1, 2, 1, 1, 1, 1, 1, 3, 4,
+ 1, 1, 1, 4, 4, 1, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 1
+ 4, 4, 4, 1
} ;
-static yyconst flex_int16_t yy_base[98] =
+static yyconst flex_int16_t yy_base[94] =
{ 0,
- 0, 0, 144, 143, 10, 12, 145, 144, 46, 0,
- 167, 172, 164, 172, 151, 77, 0, 157, 30, 152,
- 74, 172, 148, 147, 0, 157, 149, 132, 128, 129,
- 126, 127, 126, 117, 64, 124, 70, 129, 128, 172,
- 146, 172, 172, 0, 145, 172, 83, 172, 141, 0,
- 172, 134, 87, 90, 91, 94, 134, 108, 0, 172,
- 123, 115, 110, 0, 0, 111, 172, 0, 108, 116,
- 0, 107, 111, 133, 0, 34, 112, 123, 103, 0,
- 97, 0, 0, 0, 97, 111, 98, 80, 61, 0,
- 0, 172, 123, 127, 129, 83, 79
+ 0, 0, 131, 130, 10, 12, 132, 131, 45, 0,
+ 153, 158, 150, 158, 138, 75, 0, 143, 139, 72,
+ 158, 135, 134, 0, 143, 136, 119, 115, 116, 113,
+ 114, 113, 104, 62, 111, 68, 116, 115, 158, 132,
+ 158, 158, 0, 131, 158, 79, 158, 127, 0, 158,
+ 84, 87, 91, 122, 31, 0, 158, 111, 103, 98,
+ 0, 0, 99, 158, 0, 96, 104, 0, 95, 99,
+ 120, 0, 34, 107, 76, 0, 82, 0, 0, 0,
+ 83, 99, 98, 95, 76, 0, 0, 158, 111, 115,
+ 117, 94, 84
} ;
-static yyconst flex_int16_t yy_def[98] =
+static yyconst flex_int16_t yy_def[94] =
{ 0,
- 92, 1, 1, 1, 1, 1, 1, 1, 92, 9,
- 92, 92, 92, 92, 92, 93, 94, 92, 92, 92,
- 95, 92, 92, 92, 96, 92, 95, 96, 96, 96,
- 96, 96, 96, 92, 96, 96, 96, 96, 96, 92,
- 92, 92, 92, 97, 92, 92, 93, 92, 92, 94,
- 92, 92, 92, 92, 92, 95, 95, 95, 96, 92,
- 96, 96, 96, 96, 96, 96, 92, 96, 96, 96,
- 96, 96, 96, 92, 97, 92, 92, 92, 95, 96,
- 96, 96, 96, 96, 96, 92, 92, 92, 96, 96,
- 96, 0, 92, 92, 92, 92, 92
+ 88, 1, 1, 1, 1, 1, 1, 1, 88, 9,
+ 88, 88, 88, 88, 88, 89, 90, 88, 88, 91,
+ 88, 88, 88, 92, 88, 91, 92, 92, 92, 92,
+ 92, 92, 88, 92, 92, 92, 92, 92, 88, 88,
+ 88, 88, 93, 88, 88, 89, 88, 88, 90, 88,
+ 88, 88, 91, 91, 91, 92, 88, 92, 92, 92,
+ 92, 92, 92, 88, 92, 92, 92, 92, 92, 92,
+ 88, 93, 88, 88, 91, 92, 92, 92, 92, 92,
+ 92, 88, 88, 88, 92, 92, 92, 0, 88, 88,
+ 88, 88, 88
} ;
-static yyconst flex_int16_t yy_nxt[208] =
+static yyconst flex_int16_t yy_nxt[193] =
{ 0,
12, 13, 14, 15, 16, 17, 18, 12, 19, 20,
- 21, 22, 23, 24, 25, 25, 26, 27, 28, 25,
- 25, 25, 29, 25, 25, 30, 31, 25, 25, 25,
- 32, 25, 33, 25, 34, 36, 37, 36, 37, 52,
- 53, 78, 78, 38, 86, 38, 40, 41, 42, 40,
- 40, 40, 40, 40, 40, 40, 40, 43, 40, 40,
- 44, 44, 40, 40, 44, 44, 44, 44, 44, 44,
- 44, 44, 44, 44, 44, 44, 44, 44, 44, 44,
- 40, 48, 75, 55, 56, 68, 59, 48, 91, 58,
- 88, 70, 64, 49, 58, 71, 55, 53, 64, 49,
-
- 54, 54, 76, 55, 56, 77, 77, 76, 88, 58,
- 77, 77, 92, 79, 58, 78, 78, 92, 79, 87,
- 87, 86, 88, 47, 90, 47, 47, 50, 89, 50,
- 50, 57, 57, 86, 74, 85, 71, 84, 82, 83,
- 82, 81, 80, 92, 54, 47, 45, 74, 73, 72,
- 69, 67, 66, 65, 64, 63, 62, 61, 92, 60,
- 46, 46, 54, 51, 46, 45, 92, 39, 39, 35,
- 35, 11, 92, 92, 92, 92, 92, 92, 92, 92,
- 92, 92, 92, 92, 92, 92, 92, 92, 92, 92,
- 92, 92, 92, 92, 92, 92, 92, 92, 92, 92,
-
- 92, 92, 92, 92, 92, 92, 92
+ 21, 22, 23, 24, 24, 25, 26, 27, 24, 24,
+ 24, 28, 24, 24, 29, 30, 24, 24, 24, 31,
+ 24, 32, 24, 33, 35, 36, 35, 36, 74, 88,
+ 75, 82, 37, 83, 37, 39, 40, 41, 39, 39,
+ 39, 39, 39, 39, 39, 42, 39, 39, 43, 43,
+ 39, 39, 43, 43, 43, 43, 43, 43, 43, 43,
+ 43, 43, 43, 43, 43, 43, 43, 43, 39, 47,
+ 52, 53, 65, 47, 88, 75, 55, 72, 67, 61,
+ 48, 55, 68, 51, 48, 61, 51, 56, 73, 52,
+
+ 53, 73, 87, 73, 84, 55, 73, 83, 83, 86,
+ 55, 46, 85, 46, 46, 49, 84, 49, 49, 54,
+ 54, 71, 81, 68, 80, 78, 79, 78, 77, 76,
+ 88, 46, 44, 71, 70, 69, 66, 64, 63, 62,
+ 61, 60, 59, 58, 88, 57, 45, 45, 51, 50,
+ 45, 44, 88, 38, 38, 34, 34, 11, 88, 88,
+ 88, 88, 88, 88, 88, 88, 88, 88, 88, 88,
+ 88, 88, 88, 88, 88, 88, 88, 88, 88, 88,
+ 88, 88, 88, 88, 88, 88, 88, 88, 88, 88,
+ 88, 88
+
} ;
-static yyconst flex_int16_t yy_chk[208] =
+static yyconst flex_int16_t yy_chk[193] =
{ 0,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1, 5, 5, 6, 6, 19,
- 19, 76, 76, 5, 76, 6, 9, 9, 9, 9,
+ 1, 1, 1, 1, 5, 5, 6, 6, 55, 55,
+ 55, 73, 5, 73, 6, 9, 9, 9, 9, 9,
9, 9, 9, 9, 9, 9, 9, 9, 9, 9,
9, 9, 9, 9, 9, 9, 9, 9, 9, 9,
- 9, 9, 9, 9, 9, 9, 9, 9, 9, 9,
- 9, 16, 97, 21, 21, 35, 96, 47, 89, 21,
- 88, 37, 35, 16, 21, 37, 53, 53, 37, 47,
-
- 54, 55, 53, 56, 56, 54, 55, 53, 87, 56,
- 54, 55, 79, 79, 56, 58, 58, 58, 58, 77,
- 77, 86, 77, 93, 85, 93, 93, 94, 81, 94,
- 94, 95, 95, 78, 74, 73, 72, 70, 69, 66,
- 63, 62, 61, 57, 52, 49, 45, 41, 39, 38,
- 36, 34, 33, 32, 31, 30, 29, 28, 27, 26,
- 24, 23, 20, 18, 15, 13, 11, 8, 7, 4,
- 3, 92, 92, 92, 92, 92, 92, 92, 92, 92,
- 92, 92, 92, 92, 92, 92, 92, 92, 92, 92,
- 92, 92, 92, 92, 92, 92, 92, 92, 92, 92,
-
- 92, 92, 92, 92, 92, 92, 92
+ 9, 9, 9, 9, 9, 9, 9, 9, 9, 16,
+ 20, 20, 34, 46, 75, 75, 20, 93, 36, 34,
+ 16, 20, 36, 51, 46, 36, 52, 92, 51, 53,
+
+ 53, 52, 85, 51, 84, 53, 52, 83, 82, 81,
+ 53, 89, 77, 89, 89, 90, 74, 90, 90, 91,
+ 91, 71, 70, 69, 67, 66, 63, 60, 59, 58,
+ 54, 48, 44, 40, 38, 37, 35, 33, 32, 31,
+ 30, 29, 28, 27, 26, 25, 23, 22, 19, 18,
+ 15, 13, 11, 8, 7, 4, 3, 88, 88, 88,
+ 88, 88, 88, 88, 88, 88, 88, 88, 88, 88,
+ 88, 88, 88, 88, 88, 88, 88, 88, 88, 88,
+ 88, 88, 88, 88, 88, 88, 88, 88, 88, 88,
+ 88, 88
+
} ;
/* The intent behind this definition is that it'll catch
-#line 575 "scanner.c"
+#line 571 "scanner.c"
#define INITIAL 0
#define matchof 1
}
-#line 838 "scanner.c"
+#line 834 "scanner.c"
if ( !yyg->yy_init )
{
while ( yy_chk[yy_base[yy_current_state] + yy_c] != yy_current_state )
{
yy_current_state = (int) yy_def[yy_current_state];
- if ( yy_current_state >= 93 )
+ if ( yy_current_state >= 89 )
yy_c = yy_meta[(unsigned int) yy_c];
}
yy_current_state = yy_nxt[yy_base[yy_current_state] + (unsigned int) yy_c];
++yy_cp;
}
- while ( yy_current_state != 92 );
+ while ( yy_current_state != 88 );
yy_cp = yyg->yy_last_accepting_cpos;
yy_current_state = yyg->yy_last_accepting_state;
#line 156 "scanner.l"
YY_FATAL_ERROR( "flex scanner jammed" );
YY_BREAK
-#line 1064 "scanner.c"
+#line 1060 "scanner.c"
case YY_STATE_EOF(INITIAL):
case YY_STATE_EOF(matchof):
case YY_STATE_EOF(matchbool):
while ( yy_chk[yy_base[yy_current_state] + yy_c] != yy_current_state )
{
yy_current_state = (int) yy_def[yy_current_state];
- if ( yy_current_state >= 93 )
+ if ( yy_current_state >= 89 )
yy_c = yy_meta[(unsigned int) yy_c];
}
yy_current_state = yy_nxt[yy_base[yy_current_state] + (unsigned int) yy_c];
while ( yy_chk[yy_base[yy_current_state] + yy_c] != yy_current_state )
{
yy_current_state = (int) yy_def[yy_current_state];
- if ( yy_current_state >= 93 )
+ if ( yy_current_state >= 89 )
yy_c = yy_meta[(unsigned int) yy_c];
}
yy_current_state = yy_nxt[yy_base[yy_current_state] + (unsigned int) yy_c];
- yy_is_jam = (yy_current_state == 92);
+ yy_is_jam = (yy_current_state == 88);
return yy_is_jam ? 0 : yy_current_state;
}
DSEQ ([[:digit:]]+)
FRAC (([[:digit:]]*"."{DSEQ})|{DSEQ}".")
EXP ([eE][+-]?{DSEQ})
-REAL ("-"?(({FRAC}{EXP}?)|({DSEQ}{EXP})))
+REAL (({FRAC}{EXP}?)|({DSEQ}{EXP}))
STRING (\"([^\"\\\n]|(\\\"))*\")
IDENTIFIER ([[:alpha:]][_[:alnum:]]*)
CMPOP (([<>]=?)|([!=]=))
"remaining expressions are not evaluated at all.",
"This can be used to optimize the selections: you should write the",
"most restrictive and/or the most inexpensive expressions first in",
- "gmx_boolean expressions.",
+ "boolean expressions.",
"The relative ordering between dynamic and static expressions does not",
"matter: all static expressions are evaluated only once, before the first",
"frame, and the result becomes the leftmost expression.[PAR]",
"of groups of three or four atoms).",
"For such programs, it is up to the user to provide a proper selection",
"expression that always returns such positions.",
+ "[PAR]",
+
+ "Due to technical reasons, having a negative value as the first value in",
+ "expressions like[BR]",
+ "[TT]charge -1 to -0.7[tt][BR]",
+ "result in a syntax error. A workaround is to write[BR]",
+ "[TT]charge {-1 to -0.7}[tt][BR]",
+ "instead.",
};
static const char *help_positions[] = {
"Possible ways of specifying positions in selections are:[PAR]",
- "1. A constant position can be defined as [TT](XX, YY, ZZ)[tt], where",
+ "1. A constant position can be defined as [TT][XX, YY, ZZ][tt], where",
"[TT]XX[tt], [TT]YY[tt] and [TT]ZZ[tt] are real numbers.[PAR]",
"2. [TT]com of ATOM_EXPR [pbc][tt] or [TT]cog of ATOM_EXPR [pbc][tt]",
#endif
fr->bX = 1;
+ fr->bBox = 1;
vec[0] = .1*ts.A; vec[1] = .1*ts.B; vec[2] = .1*ts.C;
angle[0] = ts.alpha; angle[1] = ts.beta; angle[2] = ts.gamma;
matrix_convert(fr->box,vec,angle);
- fr->bTime = 1;
- fr->time = ts.physical_time;
-
+ if (fr->vmdplugin.api->abiversion>10)
+ {
+ fr->bTime = TRUE;
+ fr->time = ts.physical_time;
+ }
+ else
+ {
+ fr->bTime = FALSE;
+ }
return 1;
return 0;
}
- if (fr->natoms < 1) {
- fprintf(stderr, "\nNo atoms found by VMD plugin in %s.\n"
- "Or format does not record number of atoms.\n", fn );
+ if (fr->natoms == MOLFILE_NUMATOMS_UNKNOWN) {
+ fprintf(stderr, "\nFormat of file %s does not record number of atoms.\n", fn);
+ return 0;
+ } else if (fr->natoms == MOLFILE_NUMATOMS_NONE) {
+ fprintf(stderr, "\nNo atoms found by VMD plugin in file %s.\n", fn );
+ return 0;
+ } else if (fr->natoms < 1) { /*should not be reached*/
+ fprintf(stderr, "\nUnknown number of atoms %d for VMD plugin opening file %s.\n",
+ fr->natoms, fn );
return 0;
}
snew(fr->x,fr->natoms);
fr->vmdplugin.bV = 0;
- if (fr->vmdplugin.api->read_timestep_metadata)
+ if (fr->vmdplugin.api->abiversion > 10 && fr->vmdplugin.api->read_timestep_metadata)
{
fr->vmdplugin.api->read_timestep_metadata(fr->vmdplugin.handle, metadata);
fr->vmdplugin.bV = metadata->has_velocities;
add_library(gmxpreprocess ${GMXPREPROCESS_SOURCES})
target_link_libraries(gmxpreprocess md)
set_target_properties(gmxpreprocess PROPERTIES OUTPUT_NAME "gmxpreprocess${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}")
-set_target_properties(md PROPERTIES OUTPUT_NAME "md${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}")
if(GMX_OPENMM)
add_subdirectory(gmx_gpu_utils)
include_directories(./gmx_gpu_utils ${OpenMM_INCLUDE_DIR})
link_directories(${OpenMM_LIBRARY_DIR})
- # only define if this is a local build not a release
- # we assume that the auto-generated version is not used &&
- # version string does not contain "-dev" => it's a release build
- if(NOT USE_VERSION_H AND NOT PROJECT_VERSION MATCHES ".*-dev.*")
- add_definitions( -DOPENMM_PLUGIN_DIR="${OpenMM_PLUGIN_DIR}" )
- else()
- add_definitions( -DOPENMM_PLUGIN_DIR="" )
- endif()
- add_library(openmm_api_wrapper openmm_wrapper.cpp)
- target_link_libraries(openmm_api_wrapper gmx gmx_gpu_utils ${OpenMM_LIBRARIES})
-# remove_definitions( -DOPENMM_PLUGIN_DIR="${OpenMM_PLUGIN_DIR}" ) # TODO where should this go?!
+ # with this define no evn.var. is needed with OPENMM_PLUGIN_DIR
+ # if the same OpenMM installation is used for running and building
+ add_definitions( -DOPENMM_PLUGIN_DIR="${OpenMM_PLUGIN_DIR}" )
+ file(TO_CMAKE_PATH ${OpenMM_PLUGIN_DIR} _path)
+ add_library(openmm_api_wrapper STATIC openmm_wrapper.cpp)
+ target_link_libraries(openmm_api_wrapper gmx_gpu_utils ${OpenMM_LIBRARIES})
set(GMX_OPENMM_LIBRARIES openmm_api_wrapper gmx_gpu_utils ${OpenMM_LIBRARIES})
- install(TARGETS openmm_api_wrapper DESTINATION ${LIB_INSTALL_DIR})
endif(GMX_OPENMM)
if(GMX_FAHCORE)
add_executable(mdrun ${MDRUN_SOURCES})
target_link_libraries(mdrun ${GMX_EXTRA_LIBRARIES} ${GMX_OPENMM_LIBRARIES})
-# set binary name to mdrun-gpu
-if(GMX_OPENMM)
- set(_mdrun_exec_name "mdrun-gpu")
-else()
- set(_mdrun_exec_name "mdrun${GMX_BINARY_SUFFIX}")
-endif()
-set_target_properties(mdrun PROPERTIES OUTPUT_NAME "${_mdrun_exec_name}")
+set_target_properties(mdrun PROPERTIES OUTPUT_NAME "mdrun${GMX_BINARY_SUFFIX}")
# this is to circumvent the following MSVC error:
# warning LNK4098: defaultlib 'LIBCMT' conflicts with use of other libs
endif()
+install(TARGETS gmxpreprocess DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries)
+install(TARGETS mdrun DESTINATION ${BIN_INSTALL_DIR} COMPONENT mdrun)
install(TARGETS
grompp
tpbconv
gmxdump
g_x2top
gmxcheck
- mdrun
- gmxpreprocess DESTINATION ${LIB_INSTALL_DIR}
+ COMPONENT runtime
RUNTIME DESTINATION ${BIN_INSTALL_DIR})
-
-get_target_property(MDRUN_PATH mdrun LOCATION)
-add_custom_target(install-mdrun
- COMMAND ${CMAKE_COMMAND} -E copy "${MDRUN_PATH}"
- "${CMAKE_INSTALL_PREFIX}/bin/${_mdrun_exec_name}"
- DEPENDS mdrun
+# Create the custom install-mdrun target
+if (BUILD_SHARED_LIBS)
+ # If shared libraries are used, we need to install the libraries in
+ # addition to the mdrun binary.
+ add_custom_target(install-mdrun
+ COMMAND ${CMAKE_COMMAND} -DCOMPONENT=libraries
+ -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+ COMMAND ${CMAKE_COMMAND} -DCOMPONENT=mdrun
+ -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+ COMMENT "Installing mdrun")
+else (BUILD_SHARED_LIBS)
+ add_custom_target(install-mdrun
+ COMMAND ${CMAKE_COMMAND} -DCOMPONENT=mdrun
+ -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
COMMENT "Installing mdrun")
+endif (BUILD_SHARED_LIBS)
+add_dependencies(install-mdrun mdrun)
endif(GMX_FAHCORE)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libgmxpreprocess.pc.cmakein ${CMAKE_CURRENT_BINARY_DIR}/libgmxpreprocess.pc @ONLY)
-install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgmxpreprocess.pc DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
- RENAME "libgmxpreprocess${GMX_LIBS_SUFFIX}.pc")
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgmxpreprocess.pc
+ DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
+ RENAME "libgmxpreprocess${GMX_LIBS_SUFFIX}.pc"
+ COMPONENT development)
CUDA_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
set(CUDA_ATTACH_VS_BUILD_RULE_TO_CUDA_FILE OFF)
if(CMAKE_BUILD_TYPE STREQUAL "DEBUG")
- CUDA_ADD_LIBRARY(gmx_gpu_utils
- gmx_gpu_utils.cu
- memtestG80_core.cu
+ CUDA_ADD_LIBRARY(gmx_gpu_utils STATIC
+ gmx_gpu_utils.cu memtestG80_core.cu
OPTIONS ${_os_def}
- DEBUG -g -D_DEBUG_=1
- )
+ DEBUG -g -D_DEBUG_=1 )
else()
- CUDA_ADD_LIBRARY(gmx_gpu_utils
- gmx_gpu_utils.cu
- memtestG80_core.cu
- OPTIONS ${_os_def}
- )
+ CUDA_ADD_LIBRARY(gmx_gpu_utils STATIC
+ gmx_gpu_utils.cu memtestG80_core.cu
+ OPTIONS ${_os_def} )
endif()
CUDA_BUILD_CLEAN_TARGET()
-
-target_link_libraries(gmx_gpu_utils gmx)
-install(TARGETS gmx_gpu_utils DESTINATION ${LIB_INSTALL_DIR})
-
{
maxsize = max(maxsize,cgs->index[cg+1]-cgs->index[cg]);
}
-
- if (maxsize > 10)
+
+ if (maxsize > MAX_CHARGEGROUP_SIZE)
+ {
+ gmx_fatal(FARGS,"The largest charge group contains %d atoms. The maximum is %d.",maxsize,MAX_CHARGEGROUP_SIZE);
+ }
+ else if (maxsize > 10)
{
set_warning_line(wi,topfn,-1);
sprintf(warn_buf,
}
}
+static void check_bonds_timestep(gmx_mtop_t *mtop,double dt,warninp_t wi)
+{
+ /* This check is not intended to ensure accurate integration,
+ * rather it is to signal mistakes in the mdp settings.
+ * A common mistake is to forget to turn on constraints
+ * for MD after energy minimization with flexible bonds.
+ * This check can also detect too large time steps for flexible water
+ * models, but such errors will often be masked by the constraints
+ * mdp options, which turns flexible water into water with bond constraints,
+ * but without an angle constraint. Unfortunately such incorrect use
+ * of water models can not easily be detected without checking
+ * for specific model names.
+ *
+ * The stability limit of leap-frog or velocity verlet is 4.44 steps
+ * per oscillational period.
+ * But accurate bonds distributions are lost far before that limit.
+ * To allow relatively common schemes (although not common with Gromacs)
+ * of dt=1 fs without constraints and dt=2 fs with only H-bond constraints
+ * we set the note limit to 10.
+ */
+ int min_steps_warn=5;
+ int min_steps_note=10;
+ t_iparams *ip;
+ int molt;
+ gmx_moltype_t *moltype,*w_moltype;
+ t_atom *atom;
+ t_ilist *ilist,*ilb,*ilc,*ils;
+ int ftype;
+ int i,a1,a2,w_a1,w_a2,j;
+ real twopi2,limit2,fc,re,m1,m2,period2,w_period2;
+ gmx_bool bFound,bWater,bWarn;
+ char warn_buf[STRLEN];
+
+ ip = mtop->ffparams.iparams;
+
+ twopi2 = sqr(2*M_PI);
+
+ limit2 = sqr(min_steps_note*dt);
+
+ w_a1 = w_a2 = -1;
+ w_period2 = -1.0;
+
+ w_moltype = NULL;
+ for(molt=0; molt<mtop->nmoltype; molt++)
+ {
+ moltype = &mtop->moltype[molt];
+ atom = moltype->atoms.atom;
+ ilist = moltype->ilist;
+ ilc = &ilist[F_CONSTR];
+ ils = &ilist[F_SETTLE];
+ for(ftype=0; ftype<F_NRE; ftype++)
+ {
+ if (!(ftype == F_BONDS || ftype == F_G96BONDS || ftype == F_HARMONIC))
+ {
+ continue;
+ }
+
+ ilb = &ilist[ftype];
+ for(i=0; i<ilb->nr; i+=3)
+ {
+ fc = ip[ilb->iatoms[i]].harmonic.krA;
+ re = ip[ilb->iatoms[i]].harmonic.rA;
+ if (ftype == F_G96BONDS)
+ {
+ /* Convert squared sqaure fc to harmonic fc */
+ fc = 2*fc*re;
+ }
+ a1 = ilb->iatoms[i+1];
+ a2 = ilb->iatoms[i+2];
+ m1 = atom[a1].m;
+ m2 = atom[a2].m;
+ if (fc > 0 && m1 > 0 && m2 > 0)
+ {
+ period2 = twopi2*m1*m2/((m1 + m2)*fc);
+ }
+ else
+ {
+ period2 = GMX_FLOAT_MAX;
+ }
+ if (debug)
+ {
+ fprintf(debug,"fc %g m1 %g m2 %g period %g\n",
+ fc,m1,m2,sqrt(period2));
+ }
+ if (period2 < limit2)
+ {
+ bFound = FALSE;
+ for(j=0; j<ilc->nr; j+=3)
+ {
+ if ((ilc->iatoms[j+1] == a1 && ilc->iatoms[j+2] == a2) ||
+ (ilc->iatoms[j+1] == a2 && ilc->iatoms[j+2] == a1))
+ {
+ bFound = TRUE;
+ }
+ }
+ for(j=0; j<ils->nr; j+=2)
+ {
+ if ((a1 >= ils->iatoms[j+1] && a1 < ils->iatoms[j+1]+3) &&
+ (a2 >= ils->iatoms[j+1] && a2 < ils->iatoms[j+1]+3))
+ {
+ bFound = TRUE;
+ }
+ }
+ if (!bFound &&
+ (w_moltype == NULL || period2 < w_period2))
+ {
+ w_moltype = moltype;
+ w_a1 = a1;
+ w_a2 = a2;
+ w_period2 = period2;
+ }
+ }
+ }
+ }
+ }
+
+ if (w_moltype != NULL)
+ {
+ bWarn = (w_period2 < sqr(min_steps_warn*dt));
+ /* A check that would recognize most water models */
+ bWater = ((*w_moltype->atoms.atomname[0])[0] == 'O' &&
+ w_moltype->atoms.nr <= 5);
+ sprintf(warn_buf,"The bond in molecule-type %s between atoms %d %s and %d %s has an estimated oscillational period of %.1e ps, which is less than %d times the time step of %.1e ps.\n"
+ "%s",
+ *w_moltype->name,
+ w_a1+1,*w_moltype->atoms.atomname[w_a1],
+ w_a2+1,*w_moltype->atoms.atomname[w_a2],
+ sqrt(w_period2),bWarn ? min_steps_warn : min_steps_note,dt,
+ bWater ?
+ "Maybe you asked for fexible water." :
+ "Maybe you forgot to change the constraints mdp option.");
+ if (bWarn)
+ {
+ warning(wi,warn_buf);
+ }
+ else
+ {
+ warning_note(wi,warn_buf);
+ }
+ }
+}
+
static void check_vel(gmx_mtop_t *mtop,rvec v[])
{
gmx_mtop_atomloop_all_t aloop;
return count;
}
+static void check_gbsa_params_charged(gmx_mtop_t *sys, gpp_atomtype_t atype)
+{
+ int i,nmiss,natoms,mt;
+ real q;
+ const t_atoms *atoms;
+
+ nmiss = 0;
+ for(mt=0;mt<sys->nmoltype;mt++)
+ {
+ atoms = &sys->moltype[mt].atoms;
+ natoms = atoms->nr;
+
+ for(i=0;i<natoms;i++)
+ {
+ q = atoms->atom[i].q;
+ if ((get_atomtype_radius(atoms->atom[i].type,atype) == 0 ||
+ get_atomtype_vol(atoms->atom[i].type,atype) == 0 ||
+ get_atomtype_surftens(atoms->atom[i].type,atype) == 0 ||
+ get_atomtype_gb_radius(atoms->atom[i].type,atype) == 0 ||
+ get_atomtype_S_hct(atoms->atom[i].type,atype) == 0) &&
+ q != 0)
+ {
+ fprintf(stderr,"\nGB parameter(s) zero for atom type '%s' while charge is %g\n",
+ get_atomtype_name(atoms->atom[i].type,atype),q);
+ nmiss++;
+ }
+ }
+ }
+
+ if (nmiss > 0)
+ {
+ gmx_fatal(FARGS,"Can't do GB electrostatics; the implicit_genborn_params section of the forcefield has parameters with value zero for %d atomtypes that occur as charged atoms.",nmiss);
+ }
+}
+
+
static void check_gbsa_params(t_inputrec *ir,gpp_atomtype_t atype)
{
int nmiss,i;
get_atomtype_gb_radius(i,atype) < 0 ||
get_atomtype_S_hct(i,atype) < 0)
{
- fprintf(stderr,"GB parameter(s) missing or negative for atom type '%s'\n",
+ fprintf(stderr,"\nGB parameter(s) missing or negative for atom type '%s'\n",
get_atomtype_name(i,atype));
nmiss++;
}
if (nmiss > 0)
{
- gmx_fatal(FARGS,"Can't do GB electrostatics; the forcefield is missing %d values for\n"
- "atomtype radii, or they might be negative\n.",nmiss);
+ gmx_fatal(FARGS,"Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for %d atomtypes or they might be negative.",nmiss);
}
}
char warn_buf[STRLEN];
t_filenm fnm[] = {
- { efMDP, NULL, NULL, ffOPTRD },
+ { efMDP, NULL, NULL, ffREAD },
{ efMDP, "-po", "mdout", ffWRITE },
{ efSTX, "-c", NULL, ffREAD },
{ efSTX, "-r", NULL, ffOPTRD },
{
/* Now we have renumbered the atom types, we can check the GBSA params */
check_gbsa_params(ir,atype);
+
+ /* Check that all atoms that have charge and/or LJ-parameters also have
+ * sensible GB-parameters
+ */
+ check_gbsa_params_charged(sys,atype);
}
/* PELA: Copy the atomtype data to the topology atomtype list */
check_cg_sizes(ftp2fn(efTOP,NFILE,fnm),&sys->moltype[i].cgs,wi);
}
+ if (EI_DYNAMICS(ir->eI) && ir->eI != eiBD)
+ {
+ check_bonds_timestep(sys,ir->delta_t,wi);
+ }
+
check_warning_error(wi,FARGS);
if (bVerbose)
bStartingFromCpt = FALSE;
/* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
- /* Complicated conditional when bGStatEveryStep=FALSE.
- * We can not just use bGStat, since then the simulation results
- * would depend on nstenergy and nstlog or step_nscheck.
+ /* With all integrators, except VV, we need to retain the pressure
+ * at the current step for coupling at the next step.
*/
- if (((state->flags & (1<<estPRES_PREV)) ||
- (state->flags & (1<<estSVIR_PREV)) ||
- (state->flags & (1<<estFVIR_PREV))) &&
+ if ((state->flags & (1<<estPRES_PREV)) &&
(bGStatEveryStep ||
- (ir->nstlist > 0 && step % ir->nstlist == 0) ||
- (ir->nstlist < 0 && nlh.nabnsb > 0) ||
- (ir->nstlist == 0 && bGStat)))
+ (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
{
/* Store the pressure in t_state for pressure coupling
* at the next MD step.
*/
- if (state->flags & (1<<estPRES_PREV))
- {
- copy_mat(pres,state->pres_prev);
- }
+ copy_mat(pres,state->pres_prev);
}
/* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
const char *ommOptions = NULL;
void *openmmData;
+#ifdef GMX_DOUBLE
+ /* Checks in cmake should prevent the compilation in double precision
+ * with OpenMM, but just to be sure we check here.
+ */
+ gmx_fatal(FARGS,"Compilation was performed in double precision, but OpenMM only supports single precision. If you want to use to OpenMM, compile in single precision.");
+#endif
+
bAppend = (Flags & MD_APPENDFILES);
check_ir_old_tpx_versions(cr,fplog,ir,top_global);
openmm_copy_state(openmmData, state, &t, f, enerd, bX, bV, bF, do_ene);
- upd_mdebin(mdebin, FALSE,TRUE,
+ upd_mdebin(mdebin,FALSE,TRUE,
t,mdatoms->tmass,enerd,state,lastbox,
shake_vir,force_vir,total_vir,pres,
ekind,mu_tot,constr);
}
/* macro set at build time */
-#ifdef OpenMM_PLUGIN_DIR
+#ifdef OPENMM_PLUGIN_DIR
if (!hasLoadedPlugins)
{
loadedPlugins = Platform::loadPluginsFromDirectory(OPENMM_PLUGIN_DIR);
int nid_used;
int this_chainstart;
int prev_chainstart;
+ gmx_bool bMerged;
gmx_atomprop_t aps;
this_chainstart = 0;
pdb_ch=NULL;
+ bMerged = FALSE;
for (i=0; (i<natom); i++)
{
ri = &pdba_all.resinfo[pdba_all.atom[i].resind];
prev_resnum = this_resnum;
prev_chainid = this_chainid;
prev_chainnumber = this_chainnumber;
- prev_chainstart = this_chainstart;
+ if (!bMerged)
+ {
+ prev_chainstart = this_chainstart;
+ }
this_atomname = *pdba_all.atomname[i];
this_atomnum = (pdba_all.pdbinfo != NULL) ? pdba_all.pdbinfo[i].atomnr : i+1;
select[0] = 'n';
}
- if (select[0] == 'y')
+ bMerged = (select[0] == 'y');
+ if (bMerged)
{
pdb_ch[nch-1].chainstart[pdb_ch[nch-1].nterpairs] =
- pdba_all.atom[i].resind - prev_chainstart;
+ pdba_all.atom[i].resind - prev_chainstart;
pdb_ch[nch-1].nterpairs++;
srenew(pdb_ch[nch-1].chainstart,pdb_ch[nch-1].nterpairs+1);
}
bHisMan,bArgMan,bGlnMan,angle,distance,&symtab,
nrtprename,rtprename);
- for(i=0; i<cc->nterpairs; i++) {
-
- cc->chainstart[cc->nterpairs] = pdba->nres;
-
- find_nc_ter(pdba,cc->chainstart[i],cc->chainstart[i+1],
- &(cc->r_start[i]),&(cc->r_end[i]),rt);
+ cc->chainstart[cc->nterpairs] = pdba->nres;
+ j = 0;
+ for(i=0; i<cc->nterpairs; i++)
+ {
+ find_nc_ter(pdba,cc->chainstart[i],cc->chainstart[i+1],
+ &(cc->r_start[j]),&(cc->r_end[j]),rt);
-
- if ( (cc->r_start[i]<0) || (cc->r_end[i]<0) ) {
- printf("Problem with chain definition, or missing terminal residues.\n"
- "This chain does not appear to contain a recognized chain molecule.\n"
- "If this is incorrect, you can edit residuetypes.dat to modify the behavior.\n");
-
- cc->nterpairs = i;
- break;
- }
- }
+ if (cc->r_start[j] >= 0 && cc->r_end[j] >= 0)
+ {
+ j++;
+ }
+ }
+ cc->nterpairs = j;
+ if (cc->nterpairs == 0)
+ {
+ printf("Problem with chain definition, or missing terminal residues.\n"
+ "This chain does not appear to contain a recognized chain molecule.\n"
+ "If this is incorrect, you can edit residuetypes.dat to modify the behavior.\n");
+ }
/* Check for disulfides and other special bonds */
nssbonds = mk_specbonds(pdba,x,bCysMan,&ssbonds,bVerbose);
{
if(bTerMan && ntdblist>1)
{
- cc->ntdb[i] = choose_ter(ntdblist,tdblist,"Select start terminus type");
+ sprintf(select,"Select start terminus type for %s-%d",
+ *pdba->resinfo[cc->r_start[i]].name,
+ pdba->resinfo[cc->r_start[i]].nr);
+ cc->ntdb[i] = choose_ter(ntdblist,tdblist,select);
}
else
{
cc->ntdb[i] = tdblist[0];
}
- printf("Start terminus: %s\n",(cc->ntdb[i])->name);
+ printf("Start terminus %s-%d: %s\n",
+ *pdba->resinfo[cc->r_start[i]].name,
+ pdba->resinfo[cc->r_start[i]].nr,
+ (cc->ntdb[i])->name);
sfree(tdblist);
}
}
{
if(bTerMan && ntdblist>1)
{
- cc->ctdb[i] = choose_ter(ntdblist,tdblist,"Select end terminus type");
+ sprintf(select,"Select end terminus type for %s-%d",
+ *pdba->resinfo[cc->r_end[i]].name,
+ pdba->resinfo[cc->r_end[i]].nr);
+ cc->ctdb[i] = choose_ter(ntdblist,tdblist,select);
}
else
{
cc->ctdb[i] = tdblist[0];
}
- printf("End terminus: %s\n",(cc->ctdb[i])->name);
+ printf("End terminus %s-%d: %s\n",
+ *pdba->resinfo[cc->r_end[i]].name,
+ pdba->resinfo[cc->r_end[i]].nr,
+ (cc->ctdb[i])->name);
sfree(tdblist);
}
}
pdb2top(top_file2,posre_fn,molname,pdba,&x,atype,&symtab,
nrtp,restp,
restp_chain,hb_chain,
- cc->nterpairs,cc->ntdb,cc->ctdb,cc->r_start,cc->r_end,bAllowMissing,
+ cc->nterpairs,cc->ntdb,cc->ctdb,bAllowMissing,
bVsites,bVsiteAromatics,forcefield,ffdir,
mHmult,nssbonds,ssbonds,
long_bond_dist,short_bond_dist,bDeuterate,bChargeGroups,bCmap,
int nrtp, t_restp rtp[],
t_restp *restp, t_hackblock *hb,
int nterpairs,t_hackblock **ntdb, t_hackblock **ctdb,
- int *rn, int *rc, gmx_bool bAllowMissing,
+ gmx_bool bAllowMissing,
gmx_bool bVsites, gmx_bool bVsiteAromatics,
const char *ff, const char *ffdir,
real mHmult,
* not be zero at the cut-off.
*/
if (EVDW_IS_ZERO_AT_CUTOFF(ir->vdwtype) &&
- rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
+ rvdw1 + rvdw2 > ir->rlist - ir->rvdw)
{
- sprintf(warn_buf,"The sum of the two largest charge group radii (%f) is larger than %s (%f) - rvdw (%f)\n",
+ sprintf(warn_buf,"The sum of the two largest charge group radii (%f) is larger than rlist (%f) - rvdw (%f)\n",
rvdw1+rvdw2,
- ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
ir->rlist,ir->rvdw);
if (ir_NVE(ir))
{
/* PME, if used, is done on all nodes with 1D decomposition */
cr->npmenodes = 0;
cr->duty = (DUTY_PP | DUTY_PME);
- npme_major = cr->nnodes;
+ npme_major = 1;
npme_minor = 1;
+ if (!EI_TPI(inputrec->eI))
+ {
+ npme_major = cr->nnodes;
+ }
if (inputrec->ePBC == epbcSCREW)
{
add_library(md ${MDLIB_SOURCES})
target_link_libraries(md gmx ${GMX_EXTRA_LIBRARIES} ${FFT_LIBRARIES} ${XML_LIBRARIES})
-set_target_properties(md PROPERTIES OUTPUT_NAME "md${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION})
+set_target_properties(md PROPERTIES OUTPUT_NAME "md${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}")
-install(TARGETS md DESTINATION ${LIB_INSTALL_DIR})
+install(TARGETS md DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libmd.pc.cmakein ${CMAKE_CURRENT_BINARY_DIR}/libmd.pc @ONLY)
-install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libmd.pc DESTINATION ${LIB_INSTALL_DIR}/pkgconfig RENAME "libmd${GMX_LIBS_SUFFIX}.pc")
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libmd.pc
+ DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
+ RENAME "libmd${GMX_LIBS_SUFFIX}.pc"
+ COMPONENT development)
{
cconerr(cr->dd,lincsd->nc,lincsd->bla,lincsd->bllen,xprime,pbc_null,
&ncons_loc,&p_ssd,&p_max,&p_imax);
- lincsd->rmsd_data[0] = ncons_loc;
/* Check if we are doing the second part of SD */
if (ir->eI == eiSD2 && v == NULL)
{
lincsd->rmsd_data[0] = ncons_loc;
lincsd->rmsd_data[i] = p_ssd;
}
+ else
+ {
+ lincsd->rmsd_data[0] = 0;
+ lincsd->rmsd_data[1] = 0;
+ lincsd->rmsd_data[2] = 0;
+ }
if (bLog && fplog && lincsd->nc > 0)
{
fprintf(fplog,
static real vrescale_gamdev(int ia, gmx_rng_t rng)
/* Gamma distribution, adapted from numerical recipes */
{
- int j;
- real am,e,s,v1,v2,x,y;
-
- if (ia < 6) {
- x = 1.0;
- for(j=1; j<=ia; j++) {
- x *= gmx_rng_uniform_real(rng);
+ int j;
+ real am,e,s,v1,v2,x,y;
+
+ if (ia < 6)
+ {
+ do
+ {
+ x = 1.0;
+ for(j=1; j<=ia; j++)
+ {
+ x *= gmx_rng_uniform_real(rng);
+ }
+ }
+ while (x == 0);
+ x = -log(x);
+ }
+ else
+ {
+ do
+ {
+ do
+ {
+ do
+ {
+ v1 = gmx_rng_uniform_real(rng);
+ v2 = 2.0*gmx_rng_uniform_real(rng)-1.0;
+ }
+ while (v1*v1 + v2*v2 > 1.0 ||
+ v1*v1*GMX_REAL_MAX < 3.0*ia);
+ /* The last check above ensures that both x (3.0 > 2.0 in s)
+ * and the pre-factor for e do not go out of range.
+ */
+ y = v2/v1;
+ am = ia - 1;
+ s = sqrt(2.0*am + 1.0);
+ x = s*y + am;
+ }
+ while (x <= 0.0);
+ e = (1.0 + y*y)*exp(am*log(x/am) - s*y);
+ }
+ while (gmx_rng_uniform_real(rng) > e);
}
- x = -log(x);
- } else {
- do {
- do {
- do {
- v1 = gmx_rng_uniform_real(rng);
- v2 = 2.0*gmx_rng_uniform_real(rng)-1.0;
- } while (v1*v1 + v2*v2 > 1.0);
- y = v2/v1;
- am = ia - 1;
- s = sqrt(2.0*am + 1.0);
- x = s*y + am;
- } while (x <= 0.0);
- e = (1.0 + y*y)*exp(am*log(x/am) - s*y);
- } while (gmx_rng_uniform_real(rng) > e);
- }
- return x;
+ return x;
}
static real vrescale_sumnoises(int nn,gmx_rng_t rng)
char buf[30];
rc = 0;
-
+
if (index < 0)
{
gmx_fatal(FARGS,"Invalid index in pr_ebin: %d",index);
{
nener = index + nener;
}
- for(i=index; (i<nener) && rc>=0; ) {
- if (bPrHead)
+ for(i=index; (i<nener) && rc>=0; )
+ {
+ if (bPrHead)
{
- i0=i;
- for(j=0; (j<nperline) && (i<nener) && rc>=0; j++,i++)
+ i0=i;
+ for(j=0; (j<nperline) && (i<nener) && rc>=0; j++,i++)
{
if (strncmp(eb->enm[i].name,"Pres",4) == 0)
{
rc = fprintf(fp,"%15s",eb->enm[i].name);
}
}
-
- if (rc >= 0)
+
+ if (rc >= 0)
{
- rc = fprintf(fp,"\n");
+ rc = fprintf(fp,"\n");
}
-
- i=i0;
- }
- for(j=0; (j<nperline) && (i<nener) && rc>=0; j++,i++)
+
+ i=i0;
+ }
+ for(j=0; (j<nperline) && (i<nener) && rc>=0; j++,i++)
{
switch (prmode) {
- case eprNORMAL: ee = eb->e[i].e; break;
- case eprAVER: ee = eb->e_sim[i].esum/eb->nsum_sim; break;
- default: gmx_fatal(FARGS,"Invalid print mode %d in pr_ebin",prmode);
+ case eprNORMAL: ee = eb->e[i].e; break;
+ case eprAVER: ee = eb->e_sim[i].esum/eb->nsum_sim; break;
+ default: gmx_fatal(FARGS,"Invalid print mode %d in pr_ebin",
+ prmode);
}
-
- rc = fprintf(fp," %12.5e",ee);
- }
- if (rc >= 0)
+
+ rc = fprintf(fp," %12.5e",ee);
+ }
+ if (rc >= 0)
{
- rc = fprintf(fp,"\n");
+ rc = fprintf(fp,"\n");
}
- }
- if (rc < 0)
- {
- gmx_fatal(FARGS,"Cannot write to logfile; maybe you are out of quota?");
- }
+ }
+ if (rc < 0)
+ {
+ gmx_fatal(FARGS,"Cannot write to logfile; maybe you are out of quota?");
+ }
}
#ifdef DEBUGEBIN
{
pme_flags |= GMX_PME_CALC_ENER_VIR;
}
+ if (fr->n_tpi > 0)
+ {
+ /* We don't calculate f, but we do want the potential */
+ pme_flags |= GMX_PME_CALC_POT;
+ }
wallcycle_start(wcycle,ewcPMEMESH);
status = gmx_pme_do(fr->pmedata,
md->start,md->homenr - fr->n_tpi,
void set_avcsixtwelve(FILE *fplog,t_forcerec *fr,const gmx_mtop_t *mtop)
{
- const t_atoms *atoms;
+ const t_atoms *atoms,*atoms_tpi;
const t_blocka *excl;
int mb,nmol,nmolc,i,j,tpi,tpj,j1,j2,k,n,nexcl,q;
#if (defined SIZEOF_LONG_LONG_INT) && (SIZEOF_LONG_LONG_INT >= 8)
/* Only correct for the interaction of the test particle
* with the rest of the system.
*/
- atoms = &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].atoms;
- if (q == 0)
- {
- tpi = atoms->atom[atoms->nr-1].type;
- }
- else
- {
- tpi = atoms->atom[atoms->nr-1].typeB;
- }
+ atoms_tpi =
+ &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].atoms;
+
npair = 0;
for(mb=0; mb<mtop->nmolblock; mb++) {
nmol = mtop->molblock[mb].nmol;
/* Remove the interaction of the test charge group
* with itself.
*/
- if (mb == mtop->nmolblock-1 && j >= atoms->nr - fr->n_tpi)
+ if (mb == mtop->nmolblock-1)
{
nmolc--;
+
+ if (mb == 0 && nmol == 1)
+ {
+ gmx_fatal(FARGS,"Old format tpr with TPI, please generate a new tpr file");
+ }
}
if (q == 0)
{
{
tpj = atoms->atom[j].typeB;
}
- if (bBHAM)
- {
- csix += nmolc*BHAMC(nbfp,ntp,tpi,tpj);
- }
- else
+ for(i=0; i<fr->n_tpi; i++)
{
- csix += nmolc*C6 (nbfp,ntp,tpi,tpj);
- ctwelve += nmolc*C12(nbfp,ntp,tpi,tpj);
+ if (q == 0)
+ {
+ tpi = atoms_tpi->atom[i].type;
+ }
+ else
+ {
+ tpi = atoms_tpi->atom[i].typeB;
+ }
+ if (bBHAM)
+ {
+ csix += nmolc*BHAMC(nbfp,ntp,tpi,tpj);
+ }
+ else
+ {
+ csix += nmolc*C6 (nbfp,ntp,tpi,tpj);
+ ctwelve += nmolc*C12(nbfp,ntp,tpi,tpj);
+ }
+ npair += nmolc;
}
- npair += nmolc;
}
}
}
return 0;
}
-typedef union {
- real numlog;
- int exp;
-} u_table;
-
-void fill_log_table(const int n, real *table)
-{
- u_table log_table;
- real logfactor;
- int i;
-
- int incr = 1 << (23-n);
- int p=pow(2,n);
-
- logfactor = 1.0/log(2.0);
-
- log_table.exp = 0x3F800000;
-
- for(i=0;i<p;++i)
- {
- /* log2(numlog)=log(numlog)/log(2.0) */
- table[i]=log(log_table.numlog)*logfactor;
- log_table.exp+=incr;
- }
-}
-
-
-real table_log(real val, const real *table, const int n)
-{
- int *const exp_ptr = ((int*)&val);
- int x = *exp_ptr;
- const int log_2 = ((x>>23) & 255) - 127;
- x &= 0x7FFFFF;
- x = x >> (23-n);
- val = table[x];
- return ((val+log_2)*0.69314718);
-}
void gb_pd_send(t_commrec *cr, real *send_data, int nr)
{
return 0;
}
-
-
-#define LOG_TABLE_ACCURACY 15 /* Accuracy of the table logarithm */
-
-
/* Initialize all GB datastructs and compute polarization energies */
int init_gb(gmx_genborn_t **p_born,
const t_commrec *cr, t_forcerec *fr, const t_inputrec *ir,
snew(born,1);
*p_born = born;
- born->nr = fr->natoms_force;
born->nr = natoms;
snew(born->drobc, natoms);
}
}
- /* Init the logarithm table */
- p=pow(2,LOG_TABLE_ACCURACY);
- snew(born->log_table, p);
-
- fill_log_table(LOG_TABLE_ACCURACY, born->log_table);
-
/* Allocate memory for work arrays for temporary use */
snew(born->work,natoms+4);
snew(born->count,natoms);
{
ai = nl->iinr[i];
- nj0 = nl->jindex[ai];
- nj1 = nl->jindex[ai+1];
+ nj0 = nl->jindex[i];
+ nj1 = nl->jindex[i+1];
/* Load shifts for this list */
shift = nl->shift[i];
sk2_rinv = sk2*rinv;
prod = 0.25*sk2_rinv;
- /* log_term = table_log(uij*lij_inv,born->log_table,
- LOG_TABLE_ACCURACY); */
log_term = log(uij*lij_inv);
tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term +
log_term = log(uij*lij_inv);
- /* log_term = table_log(uij*lij_inv,born->log_table,LOG_TABLE_ACCURACY); */
tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term + prod*(-diff2);
if(rai < sk-dr)
n = 0;
rb = born->work;
-
- n0 = md->start;
- n1 = md->start+md->homenr+1+natoms/2;
-
+ n0 = 0;
+ n1 = natoms;
+
if(gb_algorithm==egbSTILL)
{
for(i=n0;i<n1;i++)
{
- k = i % natoms;
- rbi = born->bRad[k];
- rb[k] = (2 * rbi * rbi * dvda[k])/ONE_4PI_EPS0;
+ rbi = born->bRad[i];
+ rb[i] = (2 * rbi * rbi * dvda[i])/ONE_4PI_EPS0;
}
}
else if(gb_algorithm==egbHCT)
{
for(i=n0;i<n1;i++)
{
- k = i % natoms;
- rbi = born->bRad[k];
- rb[k] = rbi * rbi * dvda[k];
+ rbi = born->bRad[i];
+ rb[i] = rbi * rbi * dvda[i];
}
}
else if(gb_algorithm==egbOBC)
{
for(i=n0;i<n1;i++)
{
- k = i % natoms;
- rbi = born->bRad[k];
- rb[k] = rbi * rbi * born->drobc[k] * dvda[k];
+ rbi = born->bRad[i];
+ rb[i] = rbi * rbi * born->drobc[i] * dvda[i];
}
}
#if ( defined(GMX_IA32_SSE2) || defined(GMX_X86_64_SSE2) || (defined(GMX_DOUBLE) && defined(GMX_SSE2)) )
if(fr->UseOptimizedKernels)
{
- calc_gb_chainrule_sse2_double(born->nr, &(fr->gblist), fr->dadx, fr->dvda,
+ calc_gb_chainrule_sse2_double(fr->natoms_force, &(fr->gblist), fr->dadx, fr->dvda,
x[0], f[0], fr->fshift[0], fr->shift_vec[0],
gb_algorithm, born, md);
}
else
{
- calc_gb_chainrule(born->nr, &(fr->gblist), fr->dadx, fr->dvda,
+ calc_gb_chainrule(fr->natoms_force, &(fr->gblist), fr->dadx, fr->dvda,
x, f, fr->fshift, fr->shift_vec, gb_algorithm, born, md);
}
#else
- calc_gb_chainrule(born->nr, &(fr->gblist), fr->dadx, fr->dvda,
+ calc_gb_chainrule(fr->natoms_force, &(fr->gblist), fr->dadx, fr->dvda,
x, f, fr->fshift, fr->shift_vec, gb_algorithm, born, md);
#endif
/* x86 or x86-64 with GCC inline assembly and/or SSE intrinsics */
if(fr->UseOptimizedKernels)
{
- calc_gb_chainrule_sse2_single(born->nr, &(fr->gblist), fr->dadx, fr->dvda,
+ calc_gb_chainrule_sse2_single(fr->natoms_force, &(fr->gblist), fr->dadx, fr->dvda,
x[0], f[0], fr->fshift[0], fr->shift_vec[0],
gb_algorithm, born, md);
}
else
{
- calc_gb_chainrule(born->nr, &(fr->gblist), fr->dadx, fr->dvda,
+ calc_gb_chainrule(fr->natoms_force, &(fr->gblist), fr->dadx, fr->dvda,
x, f, fr->fshift, fr->shift_vec, gb_algorithm, born, md);
}
#else
/* Calculate the forces due to chain rule terms with non sse code */
- calc_gb_chainrule(born->nr, &(fr->gblist), fr->dadx, fr->dvda,
+ calc_gb_chainrule(fr->natoms_force, &(fr->gblist), fr->dadx, fr->dvda,
x, f, fr->fshift, fr->shift_vec, gb_algorithm, born, md);
#endif
#endif
natoms = mdatoms->nr;
ni0 = mdatoms->start;
- ni1 = mdatoms->homenr;
+ ni1 = mdatoms->start+mdatoms->homenr;
factor = 0.5*ONE_4PI_EPS0;
n = 0;
natoms = mdatoms->nr;
ni0 = mdatoms->start;
- ni1 = mdatoms->homenr;
+ ni1 = mdatoms->start+mdatoms->homenr;
n = 0;
prod = 0;
natoms = mdatoms->nr;
ni0 = mdatoms->start;
- ni1 = mdatoms->homenr;
+ ni1 = mdatoms->start+mdatoms->homenr;
dadx = fr->dadx;
aadata = (gmx_allvsallgb2_data_t *)work;
rb = born->work;
- jjnr = nl->jjnr;
-
+ jjnr = nl->jjnr;
+
/* Loop to get the proper form for the Born radius term, sse style */
- n0 = md->start;
- n1 = md->start+md->homenr+1+natoms/2;
+ n0 = 0;
+ n1 = natoms;
if(gb_algorithm==egbSTILL)
{
for(i=n0;i<n1;i++)
{
- k = i % natoms;
- rbi = born->bRad[k];
- rb[k] = (2 * rbi * rbi * dvda[k])/ONE_4PI_EPS0;
+ rbi = born->bRad[i];
+ rb[i] = (2 * rbi * rbi * dvda[i])/ONE_4PI_EPS0;
}
}
else if(gb_algorithm==egbHCT)
{
for(i=n0;i<n1;i++)
{
- k = i % natoms;
- rbi = born->bRad[k];
- rb[k] = rbi * rbi * dvda[k];
+ rbi = born->bRad[i];
+ rb[i] = rbi * rbi * dvda[i];
}
}
else if(gb_algorithm==egbOBC)
{
for(i=n0;i<n1;i++)
{
- k = i % natoms;
- rbi = born->bRad[k];
- rb[k] = rbi * rbi * born->drobc[k] * dvda[k];
+ rbi = born->bRad[k];
+ rb[i] = rbi * rbi * born->drobc[i] * dvda[i];
}
}
- jz = _mm_setzero_pd();
-
- n = j3A = j3B = 0;
-
+ jz = _mm_setzero_pd();
+
+ n = j3A = j3B = 0;
+
for(i=0;i<nl->nri;i++)
{
- ii = nl->iinr[i];
+ ii = nl->iinr[i];
ii3 = ii*3;
- is3 = 3*nl->shift[i];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
- nj0 = nl->jindex[i];
- nj1 = nl->jindex[i+1];
-
- ix = _mm_set1_pd(shX+x[ii3+0]);
+ is3 = 3*nl->shift[i];
+ shX = shiftvec[is3];
+ shY = shiftvec[is3+1];
+ shZ = shiftvec[is3+2];
+ nj0 = nl->jindex[i];
+ nj1 = nl->jindex[i+1];
+
+ ix = _mm_set1_pd(shX+x[ii3+0]);
iy = _mm_set1_pd(shY+x[ii3+1]);
iz = _mm_set1_pd(shZ+x[ii3+2]);
-
+
rbai = _mm_load1_pd(rb+ii);
fix = _mm_setzero_pd();
fiy = _mm_setzero_pd();
fiz = _mm_setzero_pd();
+
-
- for(k=nj0;k<nj1-1;k+=2)
+ for(k=nj0;k<nj1-1;k+=2)
{
jnrA = jjnr[k];
jnrB = jjnr[k+1];
-
- j3A = 3*jnrA;
+
+ j3A = 3*jnrA;
j3B = 3*jnrB;
- GMX_MM_LOAD_1RVEC_2POINTERS_PD(x+j3A,x+j3B,jx,jy,jz);
-
+ GMX_MM_LOAD_1RVEC_2POINTERS_PD(x+j3A,x+j3B,jx,jy,jz);
+
dx = _mm_sub_pd(ix,jx);
dy = _mm_sub_pd(iy,jy);
dz = _mm_sub_pd(iz,jz);
-
- GMX_MM_LOAD_2VALUES_PD(rb+jnrA,rb+jnrB,rbaj);
-
+
+ GMX_MM_LOAD_2VALUES_PD(rb+jnrA,rb+jnrB,rbaj);
+
/* load chain rule terms for j1-4 */
f_gb = _mm_load_pd(dadx);
dadx += 2;
f_gb_ai = _mm_load_pd(dadx);
dadx += 2;
- /* calculate scalar force */
- f_gb = _mm_mul_pd(f_gb,rbai);
- f_gb_ai = _mm_mul_pd(f_gb_ai,rbaj);
- f_gb = _mm_add_pd(f_gb,f_gb_ai);
-
- tx = _mm_mul_pd(f_gb,dx);
- ty = _mm_mul_pd(f_gb,dy);
- tz = _mm_mul_pd(f_gb,dz);
-
- fix = _mm_add_pd(fix,tx);
- fiy = _mm_add_pd(fiy,ty);
- fiz = _mm_add_pd(fiz,tz);
-
- GMX_MM_DECREMENT_1RVEC_2POINTERS_PD(f+j3A,f+j3B,tx,ty,tz);
+ /* calculate scalar force */
+ f_gb = _mm_mul_pd(f_gb,rbai);
+ f_gb_ai = _mm_mul_pd(f_gb_ai,rbaj);
+ f_gb = _mm_add_pd(f_gb,f_gb_ai);
+
+ tx = _mm_mul_pd(f_gb,dx);
+ ty = _mm_mul_pd(f_gb,dy);
+ tz = _mm_mul_pd(f_gb,dz);
+
+ fix = _mm_add_pd(fix,tx);
+ fiy = _mm_add_pd(fiy,ty);
+ fiz = _mm_add_pd(fiz,tz);
+
+ GMX_MM_DECREMENT_1RVEC_2POINTERS_PD(f+j3A,f+j3B,tx,ty,tz);
}
-
+
/*deal with odd elements */
if(k<nj1)
{
- jnrA = jjnr[k];
- j3A = 3*jnrA;
-
- GMX_MM_LOAD_1RVEC_1POINTER_PD(x+j3A,jx,jy,jz);
-
- dx = _mm_sub_sd(ix,jx);
- dy = _mm_sub_sd(iy,jy);
- dz = _mm_sub_sd(iz,jz);
-
- GMX_MM_LOAD_1VALUE_PD(rb+jnrA,rbaj);
-
- /* load chain rule terms */
- f_gb = _mm_load_pd(dadx);
- dadx += 2;
- f_gb_ai = _mm_load_pd(dadx);
- dadx += 2;
-
- /* calculate scalar force */
- f_gb = _mm_mul_sd(f_gb,rbai);
- f_gb_ai = _mm_mul_sd(f_gb_ai,rbaj);
- f_gb = _mm_add_sd(f_gb,f_gb_ai);
-
- tx = _mm_mul_sd(f_gb,dx);
- ty = _mm_mul_sd(f_gb,dy);
- tz = _mm_mul_sd(f_gb,dz);
-
- fix = _mm_add_sd(fix,tx);
- fiy = _mm_add_sd(fiy,ty);
- fiz = _mm_add_sd(fiz,tz);
-
- GMX_MM_DECREMENT_1RVEC_1POINTER_PD(f+j3A,tx,ty,tz);
+ jnrA = jjnr[k];
+ j3A = 3*jnrA;
+
+ GMX_MM_LOAD_1RVEC_1POINTER_PD(x+j3A,jx,jy,jz);
+
+ dx = _mm_sub_sd(ix,jx);
+ dy = _mm_sub_sd(iy,jy);
+ dz = _mm_sub_sd(iz,jz);
+
+ GMX_MM_LOAD_1VALUE_PD(rb+jnrA,rbaj);
+
+ /* load chain rule terms */
+ f_gb = _mm_load_pd(dadx);
+ dadx += 2;
+ f_gb_ai = _mm_load_pd(dadx);
+ dadx += 2;
+
+ /* calculate scalar force */
+ f_gb = _mm_mul_sd(f_gb,rbai);
+ f_gb_ai = _mm_mul_sd(f_gb_ai,rbaj);
+ f_gb = _mm_add_sd(f_gb,f_gb_ai);
+
+ tx = _mm_mul_sd(f_gb,dx);
+ ty = _mm_mul_sd(f_gb,dy);
+ tz = _mm_mul_sd(f_gb,dz);
+
+ fix = _mm_add_sd(fix,tx);
+ fiy = _mm_add_sd(fiy,ty);
+ fiz = _mm_add_sd(fiz,tz);
+
+ GMX_MM_DECREMENT_1RVEC_1POINTER_PD(f+j3A,tx,ty,tz);
}
-
+
/* fix/fiy/fiz now contain four partial force terms, that all should be
- * added to the i particle forces and shift forces.
- */
+ * added to the i particle forces and shift forces.
+ */
gmx_mm_update_iforce_1atom_pd(&fix,&fiy,&fiz,f+ii3,fshift+is3);
}
-
+
return 0;
}
/* Loop to get the proper form for the Born radius term, sse style */
offset=natoms%4;
- n0 = md->start;
- n1 = md->start+md->homenr+1+natoms/2;
-
+ n0 = 0;
+ n1 = natoms;
+
if(gb_algorithm==egbSTILL)
{
for(i=n0;i<n1;i++)
{
- k = i % natoms;
- rbi = born->bRad[k];
- rb[k] = (2 * rbi * rbi * dvda[k])/ONE_4PI_EPS0;
+ rbi = born->bRad[i];
+ rb[i] = (2 * rbi * rbi * dvda[i])/ONE_4PI_EPS0;
}
}
else if(gb_algorithm==egbHCT)
{
for(i=n0;i<n1;i++)
{
- k = i % natoms;
- rbi = born->bRad[k];
- rb[k] = rbi * rbi * dvda[k];
+ rbi = born->bRad[i];
+ rb[i] = rbi * rbi * dvda[i];
}
}
else if(gb_algorithm==egbOBC)
{
for(i=n0;i<n1;i++)
{
- k = i % natoms;
- rbi = born->bRad[k];
- rb[k] = rbi * rbi * born->drobc[k] * dvda[k];
+ rbi = born->bRad[i];
+ rb[i] = rbi * rbi * born->drobc[i] * dvda[i];
}
}
#define FFTW_UNLOCK
#endif /* GMX_THREADS */
+/* We assume here that aligned memory starts at multiple of 16 bytes and unaligned memory starts at multiple of 8 bytes. The later is guranteed for all malloc implementation.
+ Consequesences:
+ - It is not allowed to use these FFT plans from memory which doesn't have a starting address as a multiple of 8 bytes.
+ This is OK as long as the memory directly comes from malloc and is not some subarray within alloated memory.
+ - This has to be fixed if any future architecute requires memory to be aligned to multiples of 32 bytes.
+*/
+
struct gmx_fft
{
/* Three alternatives (unaligned/aligned, out-of-place/in-place, forward/backward)
void * in_data,
void * out_data)
{
- int aligned = (((size_t)in_data & (size_t)out_data & 0xf)==0);
+ int aligned = ((((size_t)in_data | (size_t)out_data) & 0xf)==0);
int inplace = (in_data == out_data);
int isforward = (dir == GMX_FFT_FORWARD);
void * in_data,
void * out_data)
{
- int aligned = (((size_t)in_data & (size_t)out_data & 0xf)==0);
+ int aligned = ((((size_t)in_data | (size_t)out_data) & 0xf)==0);
int inplace = (in_data == out_data);
int isforward = (dir == GMX_FFT_REAL_TO_COMPLEX);
void * in_data,
void * out_data)
{
- int aligned = (((size_t)in_data & (size_t)out_data & 0xf)==0);
+ int aligned = ((((size_t)in_data | (size_t)out_data) & 0xf)==0);
int inplace = (in_data == out_data);
int isforward = (dir == GMX_FFT_FORWARD);
void * in_data,
void * out_data)
{
- int aligned = (((size_t)in_data & (size_t)out_data & 0xf)==0);
+ int aligned = ((((size_t)in_data | (size_t)out_data) & 0xf)==0);
int inplace = (in_data == out_data);
int isforward = (dir == GMX_FFT_REAL_TO_COMPLEX);
void * in_data,
void * out_data)
{
- int aligned = (((size_t)in_data & (size_t)out_data & 0xf)==0);
+ int aligned = ((((size_t)in_data | (size_t)out_data) & 0xf)==0);
int inplace = (in_data == out_data);
int isforward = (dir == GMX_FFT_FORWARD);
void * in_data,
void * out_data)
{
- int aligned = (((size_t)in_data & (size_t)out_data & 0xf)==0);
+ int aligned = ((((size_t)in_data | (size_t)out_data) & 0xf)==0);
int inplace = (in_data == out_data);
int isforward = (dir == GMX_FFT_REAL_TO_COMPLEX);
#else
int
-gmx_fft_fftw2_empty;
-#endif /* GMX_FFT_FFTW2 */
+gmx_fft_fftw3_empty;
+#endif /* GMX_FFT_FFTW3 */
}
static void print_cycles(FILE *fplog, double c2t, const char *name, int nnodes,
- int n, gmx_cycles_t c, gmx_cycles_t tot)
+ int n, double c, double tot)
{
- char num[11];
+ char num[11];
- if (c > 0) {
- if (n > 0)
- sprintf(num,"%10d",n);
- else
- sprintf(num," ");
- fprintf(fplog," %-19s %4d %10s %12.3f %10.1f %5.1f\n",
- name,nnodes,num,c*1e-9,c*c2t,100*(double)c/(double)tot);
- }
+ if (c > 0)
+ {
+ if (n > 0)
+ {
+ sprintf(num,"%10d",n);
+ }
+ else
+ {
+ sprintf(num," ");
+ }
+ fprintf(fplog," %-19s %4d %10s %12.3f %10.1f %5.1f\n",
+ name,nnodes,num,c*1e-9,c*c2t,100*c/tot);
+ }
}
static gmx_bool subdivision(int ewc)
}
void wallcycle_print(FILE *fplog, int nnodes, int npme, double realtime,
- gmx_wallcycle_t wc, double cycles[])
+ gmx_wallcycle_t wc, double cycles[])
{
double c2t,tot,sum;
int i,j,npp;
static const char *boxs_nm[] = { "Box-X", "Box-Y", "Box-Z" };
-static const char *tricl_boxs_nm[] = { "Box-XX", "Box-YX", "Box-YY",
- "Box-ZX", "Box-ZY", "Box-ZZ" };
+static const char *tricl_boxs_nm[] = {
+ "Box-XX", "Box-YY", "Box-ZZ",
+ "Box-YX", "Box-ZX", "Box-ZY"
+};
static const char *vol_nm[] = { "Volume" };
md->bEInd[i]=FALSE;
}
- for(i=0; i<F_NRE; i++) {
+#ifndef GMX_OPENMM
+ for(i=0; i<F_NRE; i++)
+ {
md->bEner[i] = FALSE;
if (i == F_LJ)
md->bEner[i] = !bBHAM;
else
md->bEner[i] = (gmx_mtop_ftype_count(mtop,i) > 0);
}
+#else
+ /* OpenMM always produces only the following 4 energy terms */
+ md->bEner[F_EPOT] = TRUE;
+ md->bEner[F_EKIN] = TRUE;
+ md->bEner[F_ETOT] = TRUE;
+ md->bEner[F_TEMP] = TRUE;
+#endif
md->f_nre=0;
for(i=0; i<F_NRE; i++)
}
if (md->bDynBox)
{
- md->ib = get_ebin_space(md->ebin, md->bTricl ? NTRICLBOXS :
- NBOXS, md->bTricl ? tricl_boxs_nm : boxs_nm,
+ md->ib = get_ebin_space(md->ebin,
+ md->bTricl ? NTRICLBOXS : NBOXS,
+ md->bTricl ? tricl_boxs_nm : boxs_nm,
unit_length);
md->ivol = get_ebin_space(md->ebin, 1, vol_nm, unit_volume);
md->idens = get_ebin_space(md->ebin, 1, dens_nm, unit_density_SI);
}
if (md->bDynBox)
{
+ int nboxs;
if(md->bTricl)
{
bs[0] = box[XX][XX];
- bs[1] = box[YY][XX];
- bs[2] = box[YY][YY];
- bs[3] = box[ZZ][XX];
- bs[4] = box[ZZ][YY];
- bs[5] = box[ZZ][ZZ];
+ bs[1] = box[YY][YY];
+ bs[2] = box[ZZ][ZZ];
+ bs[3] = box[YY][XX];
+ bs[4] = box[ZZ][XX];
+ bs[5] = box[ZZ][YY];
+ nboxs=NTRICLBOXS;
}
else
{
bs[0] = box[XX][XX];
bs[1] = box[YY][YY];
bs[2] = box[ZZ][ZZ];
+ nboxs=NBOXS;
}
vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
}
}
}
- add_ebin(md->ebin,md->ib ,NBOXS,bs ,bSum);
+
+ add_ebin(md->ebin,md->ib ,nboxs,bs ,bSum);
add_ebin(md->ebin,md->ivol ,1 ,&vol ,bSum);
add_ebin(md->ebin,md->idens,1 ,&dens,bSum);
add_ebin(md->ebin,md->ipv ,1 ,&pv ,bSum);
order = pme->pme_order;
- thx = atc->theta[XX];
- thy = atc->theta[YY];
- thz = atc->theta[ZZ];
energy = 0;
for(n=0; (n<atc->n); n++) {
pme->nnodes_minor = nnodes_minor;
#ifdef GMX_MPI
- if (PAR(cr))
+ if (nnodes_major*nnodes_minor > 1 && PAR(cr))
{
pme->mpi_comm = cr->mpi_comm_mygroup;
MPI_Comm_rank(pme->mpi_comm,&pme->nodeid);
MPI_Comm_size(pme->mpi_comm,&pme->nnodes);
+ if (pme->nnodes != nnodes_major*nnodes_minor)
+ {
+ gmx_incons("PME node count mismatch");
+ }
}
#endif
/* We only use the A-charges grid */
grid = pme->pmegridA;
- spread_on_grid(pme,atc,grid,TRUE,FALSE);
+ spread_on_grid(pme,atc,NULL,TRUE,FALSE);
*V = gather_energy_bsplines(pme,grid,atc);
}
}
atc->maxshift = (atc->dimind==0 ? maxshift_x : maxshift_y);
}
+ else
+ {
+ /* This could be necessary for TPI */
+ pme->atc[0].n = homenr;
+ }
for(q=0; q<(pme->bFEP ? 2 : 1); q++) {
if (q == 0) {
inc_nrnb(nrnb,eNR_SOLVEPME,loop_count);
}
- if (flags & GMX_PME_CALC_F)
+ if ((flags & GMX_PME_CALC_F) ||
+ (flags & GMX_PME_CALC_POT))
{
/* do 3d-invfft */
where();
unwrap_periodic_pmegrid(pme,grid);
-
+ }
+
+ if (flags & GMX_PME_CALC_F)
+ {
/* interpolate forces for our local atoms */
GMX_BARRIER(cr->mpi_comm_mygroup);
GMX_MPE_LOG(ev_gather_f_bsplines_start);
endforeach(PROG)
install(TARGETS ${NGMX_PROGRAMS}
+ COMPONENT ngmx
RUNTIME DESTINATION ${BIN_INSTALL_DIR})
endif(X11_FOUND)
g_helixorient g_principal g_dipoles g_disre g_dist
g_dyndom g_enemat g_energy g_lie g_filter g_gyrate
g_h2order g_hbond g_helix g_mindist g_msd g_morph g_nmeig
- g_nmens g_order g_polystat g_potential g_rama g_rdf g_rms
+ g_nmens g_order g_kinetics g_polystat g_potential g_rama g_rdf g_rms
g_rmsf g_rotacf g_saltbr g_sas g_select g_sgangle g_sham g_sorient
g_spol g_spatial g_tcaf g_traj g_tune_pme g_vanhove
g_velacc g_clustsize g_mdmat g_wham g_sigeps g_bar
endforeach(TOOL ${GMX_TOOLS_PROGRAMS})
+install(TARGETS gmxana DESTINATION ${LIB_INSTALL_DIR} COMPONENT runtime)
install(TARGETS ${GMX_TOOLS_PROGRAMS}
- gmxana DESTINATION ${LIB_INSTALL_DIR}
- RUNTIME DESTINATION ${BIN_INSTALL_DIR})
+ DESTINATION ${BIN_INSTALL_DIR}
+ COMPONENT runtime)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libgmxana.pc.cmakein ${CMAKE_CURRENT_BINARY_DIR}/libgmxana.pc @ONLY)
-install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgmxana.pc DESTINATION ${LIB_INSTALL_DIR}/pkgconfig RENAME "libgmxana${GMX_LIBS_SUFFIX}.pc")
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgmxana.pc
+ DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
+ RENAME "libgmxana${GMX_LIBS_SUFFIX}.pc"
+ COMPONENT development)
g_enemat g_energy g_lie g_filter \
g_gyrate g_h2order g_hbond g_helix \
g_mindist g_msd g_morph g_nmeig \
- g_nmens g_order \
+ g_nmens g_order g_kinetics \
g_polystat g_potential g_rama \
g_rdf g_rms g_rmsdist g_rmsf \
g_rotacf g_rotmat g_saltbr g_sas \
#include "smalloc.h"
#include "gstat.h"
#include "gmx_fatal.h"
+#include "index.h"
t_dlist *mk_dlist(FILE *log,
t_atoms *atoms, int *nlist,
gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bHChi,
- int maxchi,int r0,int naa,char **aa)
+ int maxchi, int r0, gmx_residuetype_t rt)
{
int ires,i,j,k,ii;
t_dihatms atm,prev;
}
if ((atm.minC != -1) && (atm.minO != -1))
nc[6]++;
- for(k=0; (k<naa); k++) {
- if (gmx_strcasecmp(aa[k],thisres) == 0)
- break;
- }
- dl[nl].index=k;
+ dl[nl].index=gmx_residuetype_get_index(rt,thisres);
sprintf(dl[nl].name,"%s%d",thisres,ires+r0);
nl++;
(blk->sub[0].nr < 1) ||
(blk->sub[1].nr < 1) )
{
- gmx_fatal(FARGS, "Unexpected block data in file %s", filename);
+ gmx_fatal(FARGS,
+ "Unexpected/corrupted block data in file %s around time %g.",
+ filename, start_time);
}
derivative = blk->sub[0].ival[0];
( (derivative!=0) != (s->derivative!=0) ) )
{
fprintf(stderr, "Got foreign lambda=%g, expected: %g\n",
- s->foreign_lambda, foreign_lambda);
- fprintf(stderr, "Got derivative=%d, derivative: %d\n",
+ foreign_lambda, s->foreign_lambda);
+ fprintf(stderr, "Got derivative=%d, expected: %d\n",
derivative, s->derivative);
- gmx_fatal(FARGS, "Inconsistent data in file %s around t=%g", filename,
- start_time);
+ gmx_fatal(FARGS, "Corrupted data in file %s around t=%g.",
+ filename, start_time);
}
/* make room for the data */
(blk->sub[0].nr < 2) ||
(blk->sub[1].nr < 2) )
{
- gmx_fatal(FARGS, "Unexpected block data in file %s", filename);
+ gmx_fatal(FARGS,
+ "Unexpected/corrupted block data in file %s around time %g",
+ filename, start_time);
}
nhist=blk->nsub-2;
}
if (nhist > 2)
{
- gmx_fatal(FARGS, "Unexpected block data in file %s", filename);
+ gmx_fatal(FARGS,
+ "Unexpected/corrupted block data in file %s around time %g",
+ filename, start_time);
}
snew(s, 1);
return j ;
}
-static void histogramming(FILE *log,int nbin, int naa,char **aa,
+static void histogramming(FILE *log,int nbin,gmx_residuetype_t rt,
int nf,int maxchi,real **dih,
int nlist,t_dlist dlist[],
atom_id index[],
gmx_bool bBfac,bOccup;
char hisfile[256],hhisfile[256],sshisfile[256],title[256],*ss_str=NULL;
char **leg;
-
+ const char *residue_name;
+ int rt_size;
+
+ rt_size = gmx_residuetype_get_size(rt);
if (bSSHisto) {
fp = ffopen(ssdump,"r");
if(1 != fscanf(fp,"%d",&nres))
/* Four dimensional array... Very cool */
snew(his_aa_ss,3);
for(i=0; (i<3); i++) {
- snew(his_aa_ss[i],naa+1);
- for(j=0; (j<=naa); j++) {
+ snew(his_aa_ss[i],rt_size+1);
+ for(j=0; (j<=rt_size); j++) {
snew(his_aa_ss[i][j],edMax);
for(Dih=0; (Dih<edMax); Dih++)
snew(his_aa_ss[i][j][Dih],nbin+1);
}
snew(his_aa,edMax);
for(Dih=0; (Dih<edMax); Dih++) {
- snew(his_aa[Dih],naa+1);
- for(i=0; (i<=naa); i++) {
+ snew(his_aa[Dih],rt_size+1);
+ for(i=0; (i<=rt_size); i++) {
snew(his_aa[Dih][i],nbin+1);
}
}
/* finished -jc stuff */
snew(normhisto,nbin);
- for(i=0; (i<naa); i++) {
+ for(i=0; (i<rt_size); i++) {
for(Dih=0; (Dih<edMax); Dih++){
/* First check whether something is in there */
for(j=0; (j<nbin); j++)
if (bNormalize)
normalize_histo(nbin,his_aa[Dih][i],(360.0/nbin),normhisto);
+ residue_name = gmx_residuetype_get_name(rt,i);
switch (Dih) {
case edPhi:
- sprintf(hisfile,"histo-phi%s",aa[i]);
- sprintf(title,"\\xf\\f{} Distribution for %s",aa[i]);
+ sprintf(hisfile,"histo-phi%s",residue_name);
+ sprintf(title,"\\xf\\f{} Distribution for %s",residue_name);
break;
case edPsi:
- sprintf(hisfile,"histo-psi%s",aa[i]);
- sprintf(title,"\\xy\\f{} Distribution for %s",aa[i]);
+ sprintf(hisfile,"histo-psi%s",residue_name);
+ sprintf(title,"\\xy\\f{} Distribution for %s",residue_name);
break;
case edOmega:
- sprintf(hisfile,"histo-omega%s",aa[i]);
- sprintf(title,"\\xw\\f{} Distribution for %s",aa[i]);
+ sprintf(hisfile,"histo-omega%s",residue_name);
+ sprintf(title,"\\xw\\f{} Distribution for %s",residue_name);
break;
default:
- sprintf(hisfile,"histo-chi%d%s",Dih-NONCHI+1,aa[i]);
+ sprintf(hisfile,"histo-chi%d%s",Dih-NONCHI+1,residue_name);
sprintf(title,"\\xc\\f{}\\s%d\\N Distribution for %s",
- Dih-NONCHI+1,aa[i]);
+ Dih-NONCHI+1,residue_name);
}
strcpy(hhisfile,hisfile);
strcat(hhisfile,".xvg");
if (bSSHisto) {
/* Four dimensional array... Very cool */
for(i=0; (i<3); i++) {
- for(j=0; (j<=naa); j++) {
+ for(j=0; (j<=rt_size); j++) {
for(Dih=0; (Dih<edMax); Dih++)
sfree(his_aa_ss[i][j][Dih]);
sfree(his_aa_ss[i][j]);
};
FILE *log;
- int natoms,nlist,naa,idum,nbin;
+ int natoms,nlist,idum,nbin;
t_atoms atoms;
rvec *x;
int ePBC;
matrix box;
char title[256],grpname[256];
t_dlist *dlist;
- char **aa;
gmx_bool bChi,bCorr,bSSHisto;
gmx_bool bDo_rt, bDo_oh, bDo_ot, bDo_jc ;
real dt=0, traj_t_ns;
output_env_t oenv;
+ gmx_residuetype_t rt;
atom_id isize,*index;
int ndih,nactdih,nf;
read_stx_conf(ftp2fn(efSTX,NFILE,fnm),title,&atoms,x,NULL,&ePBC,box);
fprintf(log,"Title: %s\n",title);
- naa=get_strings("aminoacids.dat",&aa);
- dlist=mk_dlist(log,&atoms,&nlist,bPhi,bPsi,bChi,bHChi,maxchi,r0,naa,aa);
+ gmx_residuetype_init(&rt);
+ dlist=mk_dlist(log,&atoms,&nlist,bPhi,bPsi,bChi,bHChi,maxchi,r0,rt);
fprintf(stderr,"%d residues with dihedrals found\n", nlist);
if (nlist == 0)
dump_em_all(nlist,dlist,nf,time,dih,maxchi,bPhi,bPsi,bChi,bOmega,bRAD,oenv);
/* Histogramming & J coupling constants & calc of S2 order params */
- histogramming(log,nbin,naa,aa,nf,maxchi,dih,nlist,dlist,index,
+ histogramming(log,nbin,rt,nf,maxchi,dih,nlist,dlist,index,
bPhi,bPsi,bOmega,bChi,
bNormHisto,bSSHisto,ftp2fn(efDAT,NFILE,fnm),bfac_max,&atoms,
bDo_jc,opt2fn("-jc",NFILE,fnm),oenv);
if (bCorr)
do_view(oenv,opt2fn("-corr",NFILE,fnm),"-nxy");
+ gmx_residuetype_destroy(rt);
+
thanx(stderr);
return 0;
int gmx_density(int argc,char *argv[])
{
const char *desc[] = {
- "Compute partial densities across the box, using an index file. Densities",
- "in kg/m^3, number densities or electron densities can be",
+ "Compute partial densities across the box, using an index file.[PAR]",
+ "For the total density of NPT simulations, use [TT]g_energy[tt] instead.",
+ "[PAR]",
+ "Densities in kg/m^3, number densities or electron densities can be",
"calculated. For electron densities, a file describing the number of",
"electrons for each type of atom should be provided using [TT]-ei[tt].",
"It should look like:[BR]",
void sort_molecule(t_atoms **atoms_solvt,rvec *x,rvec *v,real *r)
{
- int atnr,i,j,moltp=0,nrmoltypes,resnr;
+ int atnr,i,j,moltp=0,nrmoltypes,resi_o,resi_n,resnr;
t_moltypes *moltypes;
- int *tps;
t_atoms *atoms,*newatoms;
rvec *newx, *newv=NULL;
real *newr;
atoms = *atoms_solvt;
/* copy each residue from *atoms to a molecule in *molecule */
- snew(tps,atoms->nr);
moltypes=NULL;
nrmoltypes=0;
atnr=0;
}
moltypes[moltp].nmol++;
}
- tps[i]=moltp;
}
fprintf(stderr,"Found %d%s molecule type%s:\n",
if (v) snew(newv,atoms->nr);
snew(newr,atoms->nr);
- for (i=0; i<atoms->nr; i++) {
- resnr = moltypes[tps[i]].res0 +
- (moltypes[tps[i]].i-moltypes[tps[i]].i0) / moltypes[tps[i]].natoms;
- newatoms->atom[moltypes[tps[i]].i].resind = resnr;
- newatoms->resinfo[resnr] = atoms->resinfo[atoms->atom[i].resind];
- newatoms->resinfo[resnr].nr = resnr + 1;
- newatoms->atomname[moltypes[tps[i]].i] = atoms->atomname[i];
- newatoms->atom[moltypes[tps[i]].i] = atoms->atom[i];
- copy_rvec(x[i],newx[moltypes[tps[i]].i]);
- if (v) copy_rvec(v[i],newv[moltypes[tps[i]].i]);
- newr[moltypes[tps[i]].i] = r[i];
- moltypes[tps[i]].i++;
+ resi_n = 0;
+ resnr = 1;
+ j = 0;
+ for(moltp=0; moltp<nrmoltypes; moltp++) {
+ i = 0;
+ while (i < atoms->nr) {
+ resi_o = atoms->atom[i].resind;
+ if (strcmp(*atoms->resinfo[resi_o].name,moltypes[moltp].name) == 0) {
+ /* Copy the residue info */
+ newatoms->resinfo[resi_n] = atoms->resinfo[resi_o];
+ newatoms->resinfo[resi_n].nr = resnr;
+ /* Copy the atom info */
+ do {
+ newatoms->atom[j] = atoms->atom[i];
+ newatoms->atomname[j] = atoms->atomname[i];
+ newatoms->atom[j].resind = resi_n;
+ copy_rvec(x[i],newx[j]);
+ if (v != NULL) {
+ copy_rvec(v[i],newv[j]);
+ }
+ newr[j] = r[i];
+ i++;
+ j++;
+ } while (i < atoms->nr && atoms->atom[i].resind == resi_o);
+ /* Increase the new residue counters */
+ resi_n++;
+ resnr++;
+ } else {
+ /* Skip this residue */
+ do {
+ i++;
+ } while (i < atoms->nr && atoms->atom[i].resind == resi_o);
+ }
+ }
}
/* put them back into the original arrays and throw away temporary arrays */
srenew(hb0->h[0],4+nnframes/hb->wordlen);
srenew(hb0->g[0],4+nnframes/hb->wordlen);
}
- clearPshift(&(hb->per->pHist[a1][a2]));
+ if (NULL != hb->per->pHist)
+ {
+ clearPshift(&(hb->per->pHist[a1][a2]));
+ }
/* Copy temp array to target array */
for(m=0; (m<=nnframes); m++) {
trrStatus = (read_next_x(oenv,status,&t,natoms,x,box));
nframes++; /* + */
} /* + */
-#ifdef HAVE_OPENMP /* ++++++++++++++++� */
+#ifdef HAVE_OPENMP /* +++++++++++++++++ */
#pragma omp barrier
#endif
} while (trrStatus);
bStartingFromCpt = FALSE;
/* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
- /* Complicated conditional when bGStatEveryStep=FALSE.
- * We can not just use bGStat, since then the simulation results
- * would depend on nstenergy and nstlog or step_nscheck.
+ /* With all integrators, except VV, we need to retain the pressure
+ * at the current step for coupling at the next step.
*/
- if (((state->flags & (1<<estPRES_PREV)) ||
- (state->flags & (1<<estSVIR_PREV)) ||
- (state->flags & (1<<estFVIR_PREV))) &&
+ if ((state->flags & (1<<estPRES_PREV)) &&
(bGStatEveryStep ||
- (ir->nstlist > 0 && step % ir->nstlist == 0) ||
- (ir->nstlist < 0 && nlh.nabnsb > 0) ||
- (ir->nstlist == 0 && bGStat)))
+ (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
{
/* Store the pressure in t_state for pressure coupling
* at the next MD step.
*/
- if (state->flags & (1<<estPRES_PREV))
- {
- copy_mat(pres,state->pres_prev);
- }
+ copy_mat(pres,state->pres_prev);
}
/* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
for (n = 0; n < nr_grps; n++)
{
+ /* Check whether we actually have all positions of the requested index
+ * group in the trajectory file */
+ if (gnx[n] > natoms)
+ {
+ gmx_fatal(FARGS, "You selected a group with %d atoms, but only %d atoms\n"
+ "were found in the trajectory.\n", gnx[n], natoms);
+ }
for (i = 0; i < gnx[n]; i++) /* loop over all atoms in index file */
{
if (bSpherical)
for (n = 0; n < nr_grps; n++)
{
fprintf(pot," %20.16g", potential[n][slice]);
- fprintf(fie," %20.16g", field[n][slice]);
+ fprintf(fie," %20.16g", field[n][slice]/1e9); /* convert to V/nm */
fprintf(cha," %20.16g", charge[n][slice]);
}
fprintf(pot,"\n");
#include <config.h>
#endif
+
+#include <time.h>
+#ifdef HAVE_SYS_TIME_H
+#include <sys/time.h>
+#endif
+
+
+
#include "statutil.h"
#include "typedefs.h"
#include "smalloc.h"
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL,&oenv);
- if (bMol)
- bTPS = bM || ftp2bSet(efTPS,NFILE,fnm) || !ftp2bSet(efNDX,NFILE,fnm);
+ if (bMol || bM) {
+ bTPS = ftp2bSet(efTPS,NFILE,fnm) || !ftp2bSet(efNDX,NFILE,fnm);
+ }
if (bTPS) {
bTop=read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,NULL,NULL,box,
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*- */
/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* Green Red Orange Magenta Azure Cyan Skyblue
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
-
-
#include <stdio.h>
#include "statutil.h"
#include "statutil.h"
#include "tpxio.h"
#include "names.h"
+#include "gmx_random.h"
#include "gmx_ana.h"
-
#ifndef HAVE_STRDUP
#define HAVE_STRDUP
#endif
#include "xvgr.h"
+#define WHAM_MAXFILELEN 2048
+
/* enum for energy units */
enum { enSel, en_kJ, en_kCal, en_kT, enNr };
/* enum for type of input files (pdos, tpr, or pullf) */
enum { whamin_unknown, whamin_tpr, whamin_pullxf, whamin_pdo };
-/* enum for methods to make profile cyclic/periodic */
-enum { enCycl, enCycl_no, enCycl_yes, enCycl_weighted, enCycl_nr};
+/* enum for bootstrapping method (
+ - bootstrap complete histograms with continuous weights (Bayesian bootstrap)
+ - bootstrap complete histograms
+ - bootstrap trajectories from given umbrella histograms
+ - bootstrap trajectories from Gaussian with mu/sigam computed from
+ the respective histogram
+
+ ********************************************************************
+ FOR MORE DETAILS ON THE BOOTSTRAP METHODS (INCLUDING EXAMPLES), SEE
+ JS Hub, BL de Groot, D van der Spoel
+ g_wham - A free weighted histogram analysis implementation including
+ robust error and autocorrelation estimates,
+ J Chem Theory Comput, accepted (2010)
+ ********************************************************************
+ */
+enum { bsMethod_unknown, bsMethod_BayesianHist, bsMethod_hist,
+ bsMethod_traj, bsMethod_trajGauss };
+
-typedef struct
+typedef struct
{
- /* umbrella with pull code of gromacs 4 */
+ /* umbrella with pull code of gromacs 4.x */
int npullgrps; /* nr of pull groups in tpr file */
int pull_geometry; /* such as distance, position */
ivec pull_dim; /* pull dimension with geometry distance */
int pull_ndim; /* nr of pull_dim != 0 */
real *k; /* force constants in tpr file */
rvec *init_dist; /* reference displacements */
- real *umbInitDist; /* referebce displacement in umbrella direction */
-
+ real *umbInitDist; /* reference displacement in umbrella direction */
+
/* From here, old pdo stuff */
- int nSkip;
+ int nSkip;
char Reference[256];
int nPull;
int nDim;
char PullName[4][256];
double UmbPos[4][3];
double UmbCons[4][3];
- gmx_bool Flipped[4];
} t_UmbrellaHeader;
-typedef struct
+typedef struct
{
- int nPull;
- int nBin;
- double **Histo,**cum;
- double *k;
- double *pos;
- double *z;
- double * N, *Ntot;
- gmx_bool * Flipped;
- double dt;
- gmx_bool **bContrib;
+ int nPull; /* nr of pull groups in this pdo or pullf/x file */
+ double **Histo,**cum; /* nPull histograms and nPull cumulative distr. funct */
+ int nBin; /* nr of bins. identical to opt->bins */
+ double *k; /* force constants for the nPull groups */
+ double *pos; /* umbrella positions for the nPull groups */
+ double *z; /* z=(-Fi/kT) for the nPull groups. These values are
+ iteratively computed during wham */
+ double *N, *Ntot; /* nr of data points in nPull histograms. N and Ntot
+ only differ if bHistEq==TRUE */
+
+ double *g,*tau,*tausmooth; /* g = 1 + 2*tau[int]/dt where tau is the integrated
+ autocorrelation time. Compare, e.g.
+ Ferrenberg/Swendsen, PRL 63:1195 (1989)
+ Kumar et al, J Comp Chem 13, 1011-1021 (1992), eq. 28 */
+
+ double dt; /* timestep in the input data. Can be adapted with
+ g_wham option -dt */
+ gmx_bool **bContrib; /* TRUE, if any data point of the histogram is within min
+ and max, otherwise FALSE. */
+ real **ztime; /* input data z(t) as a function of time. Required to
+ compute ACTs */
+ real *forceAv; /* average force estimated from average displacement, fAv=dzAv*k
+ Used for integration to guess the potential. */
+ real *aver,*sigma; /* average and stddev of histograms */
+ double *bsWeight; /* for bootstrapping complete histograms with continuous weights */
} t_UmbrellaWindow;
-typedef struct
+
+typedef struct
{
- const char *fnTpr,*fnPullf,*fnPdo,*fnPullx;
- gmx_bool bTpr,bPullf,bPdo,bPullx;
- int bins,cycl;
- gmx_bool verbose,bShift,bAuto,bBoundsOnly;
- gmx_bool bFlipProf;
- real tmin, tmax, dt;
- real Temperature,Tolerance;
- int nBootStrap,histBootStrapBlockLength;
- real dtBootStrap,zProfZero,alpha;
- int bsSeed,stepchange;
- gmx_bool bHistBootStrap,bWeightedCycl,bHistOutOnly;
- gmx_bool bAutobounds,bNoprof;
+ /* INPUT STUFF */
+ const char *fnTpr,*fnPullf;
+ const char *fnPdo,*fnPullx; /* file names of input */
+ gmx_bool bTpr,bPullf,bPdo,bPullx;/* input file types given? */
+ real tmin, tmax, dt; /* only read input within tmin and tmax with dt */
+
+ gmx_bool bInitPotByIntegration; /* before WHAM, guess potential by force integration. Yields
+ 1.5 to 2 times faster convergence */
+ int stepUpdateContrib; /* update contribution table every ... iterations. Accelerates
+ WHAM. */
+
+ /* BASIC WHAM OPTIONS */
+ int bins; /* nr of bins, min, max, and dz of profile */
real min,max,dz;
- gmx_bool bLog;
- int unit;
- real zProf0;
- gmx_bool bProf0Set,bs_verbose;
- gmx_bool bHistEq, bTab;
+ real Temperature,Tolerance; /* temperature, converged when probability changes less
+ than Tolerance */
+ gmx_bool bCycl; /* generate cyclic (periodic) PMF */
+
+ /* OUTPUT CONTROL */
+ gmx_bool bLog; /* energy output (instead of probability) for profile */
+ int unit; /* unit for PMF output kJ/mol or kT or kCal/mol */
+ gmx_bool bSym; /* symmetrize PMF around z=0 after WHAM, useful for
+ membranes etc. */
+ real zProf0; /* after wham, set prof to zero at this z-position
+ When bootstrapping, set zProf0 to a "stable" reference
+ position. */
+ gmx_bool bProf0Set; /* setting profile to 0 at zProf0? */
+
+ gmx_bool bBoundsOnly,bHistOnly; /* determine min and max, or write histograms and exit */
+ gmx_bool bAuto; /* determine min and max automatically but do not exit */
+
+ gmx_bool verbose; /* more noisy wham mode */
+ int stepchange; /* print maximum change in prof after how many interations */
+ output_env_t oenv; /* xvgr options */
+
+ /* AUTOCORRELATION STUFF */
+ gmx_bool bTauIntGiven,bCalcTauInt;/* IACT given or should be calculated? */
+ real sigSmoothIact; /* sigma of Gaussian to smooth ACTs */
+ gmx_bool bAllowReduceIact; /* Allow to reduce ACTs during smoothing. Otherwise
+ ACT are only increased during smoothing */
+ real acTrestart; /* when computing ACT, time between restarting points */
+ gmx_bool bHistEq; /* Enforce the same weight for each umbella window, that is
+ calculate with the same number of data points for
+ each window. That can be reasonable, if the histograms
+ have different length, but due to autocorrelation,
+ a longer simulation should not have larger weightin wham. */
+
+ /* BOOTSTRAPPING STUFF */
+ int nBootStrap; /* nr of bootstraps (50 is usually enough) */
+ int bsMethod; /* if == bsMethod_hist, consider complete histograms as independent
+ data points and, hence, only mix complete histograms.
+ if == bsMethod_BayesianHist, consider complete histograms
+ as independent data points, but assign random weights
+ to the histograms during the bootstrapping ("Bayesian bootstrap")
+ In case of long correlations (e.g., inside a channel), these
+ will yield a more realistic error.
+ if == bsMethod_traj(Gauss), generate synthetic histograms
+ for each given
+ histogram by generating an autocorrelated random sequence
+ that is distributed according to the respective given
+ histogram. With bsMethod_trajGauss, bootstrap from a Gaussian
+ (instead of from the umbrella histogram) to generate a new
+ histogram
+ */
+ real tauBootStrap; /* autocorrelation time (ACT) used to generate synthetic
+ histograms. If ==0, use calculated ACF */
+ int histBootStrapBlockLength; /* when mixing histograms, mix only histograms withing blocks
+ long the reaction coordinate xi. Avoids gaps along xi. */
+ int bsSeed; /* random seed for bootstrapping */
+ gmx_bool bs_verbose; /* Write cumulative distribution functions (CDFs) of histograms
+ and write the generated histograms for each bootstrap */
+
+ /* tabulated umbrella potential stuff */
+ gmx_bool bTab;
double *tabX,*tabY,tabMin,tabMax,tabDz;
int tabNbins;
+
+ gmx_rng_t rng; /* gromacs random number generator */
} t_UmbrellaOptions;
+t_UmbrellaWindow * initUmbrellaWindows(int nwin)
+{
+ t_UmbrellaWindow *win;
+ int i;
+ snew(win,nwin);
+ for (i=0; i<nwin; i++)
+ {
+ win[i].Histo = win[i].cum = 0;
+ win[i].k = win[i].pos = win[i].z =0;
+ win[i].N = win[i].Ntot = 0;
+ win[i].g = win[i].tau = win[i].tausmooth = 0;
+ win[i].bContrib=0;
+ win[i].ztime=0;
+ win[i].forceAv=0;
+ win[i].aver = win[i].sigma = 0;
+ win[i].bsWeight = 0;
+ }
+ return win;
+}
+
+void freeUmbrellaWindows(t_UmbrellaWindow *win, int nwin)
+{
+ int i,j;
+ for (i=0; i<nwin; i++)
+ {
+ if (win[i].Histo)
+ for (j=0;j<win[i].nPull;j++)
+ sfree(win[i].Histo[j]);
+ if (win[i].cum)
+ for (j=0;j<win[i].nPull;j++)
+ sfree(win[i].cum[j]);
+ if (win[i].bContrib)
+ for (j=0;j<win[i].nPull;j++)
+ sfree(win[i].bContrib[j]);
+ sfree(win[i].Histo);
+ sfree(win[i].cum);
+ sfree(win[i].k);
+ sfree(win[i].pos);
+ sfree(win[i].z);
+ sfree(win[i].N);
+ sfree(win[i].Ntot);
+ sfree(win[i].g);
+ sfree(win[i].tau);
+ sfree(win[i].tausmooth);
+ sfree(win[i].bContrib);
+ sfree(win[i].ztime);
+ sfree(win[i].forceAv);
+ sfree(win[i].aver);
+ sfree(win[i].sigma);
+ sfree(win[i].bsWeight);
+ }
+ sfree(win);
+}
+
/* Return j such that xx[j] <= x < xx[j+1] */
void searchOrderedTable(double xx[], int n, double x, int *j)
{
int ju,jm,jl;
int ascending;
-
-
+
jl=-1;
ju=n;
ascending=(xx[n-1] > xx[0]);
- while (ju-jl > 1)
+ while (ju-jl > 1)
{
jm=(ju+jl) >> 1;
if ((x >= xx[jm]) == ascending)
else *j=jl;
}
-
/* Read and setup tabulated umbrella potential */
void setup_tab(const char *fn,t_UmbrellaOptions *opt)
{
int i,ny,nl;
double **y;
-
-
+
printf("Setting up tabulated potential from file %s\n",fn);
nl=read_xvg(fn,&y,&ny);
opt->tabNbins=nl;
opt->tabDz=(opt->tabMax-opt->tabMin)/(nl-1);
if (opt->tabDz<=0)
gmx_fatal(FARGS,"The tabulated potential in %s must be provided in \n"
- "ascending z-direction",fn);
+ "ascending z-direction",fn);
for (i=0;i<nl-1;i++)
if (fabs(y[0][i+1]-y[0][i]-opt->tabDz) > opt->tabDz/1e6)
gmx_fatal(FARGS,"z-values in %s are not equally spaced.\n",ny,fn);
snew(opt->tabY,nl);
snew(opt->tabX,nl);
- for (i=0;i<nl;i++){
+ for (i=0;i<nl;i++)
+ {
opt->tabX[i]=y[0][i];
opt->tabY[i]=y[1][i];
}
printf("Found equally spaced tabulated potential from %g to %g, spacing %g\n",
- opt->tabMin,opt->tabMax,opt->tabDz);
+ opt->tabMin,opt->tabMax,opt->tabDz);
}
-
-void read_pdo_header(FILE * file,t_UmbrellaHeader * header,
- t_UmbrellaOptions *opt)
+void read_pdo_header(FILE * file,t_UmbrellaHeader * header, t_UmbrellaOptions *opt)
{
- char Buffer0[256];
- char Buffer1[256];
- char Buffer2[256];
- char Buffer3[256];
- char Buffer4[256];
- int i,j;
-
-
+ char line[2048];
+ char Buffer0[256], Buffer1[256], Buffer2[256], Buffer3[256], Buffer4[256];
+ int i;
+
/* line 1 */
- if(3 != fscanf(file,"%s%s%s",Buffer0,Buffer1,Buffer2))
- {
- gmx_fatal(FARGS,"Error reading header from pdo file");
- }
- if(strcmp(Buffer1,"UMBRELLA"))
- gmx_fatal(FARGS,"This does not appear to be a valid pdo file. Found %s, expected %s",
- Buffer1, "UMBRELLA");
+ if (fgets(line,2048,file) == NULL)
+ gmx_fatal(FARGS,"Error reading header from pdo file\n");
+ sscanf(line,"%s%s%s",Buffer0,Buffer1,Buffer2);
+ if(strcmp(Buffer1,"UMBRELLA"))
+ gmx_fatal(FARGS,"This does not appear to be a valid pdo file. Found %s, expected %s\n"
+ "(Found in first line: `%s')\n",
+ Buffer1, "UMBRELLA",line);
if(strcmp(Buffer2,"3.0"))
gmx_fatal(FARGS,"This does not appear to be a version 3.0 pdo file");
-
+
/* line 2 */
- if(6 != fscanf(file,"%s%s%s%d%d%d",Buffer0,Buffer1,Buffer2,
- &(header->Dims[0]),&(header->Dims[1]),&(header->Dims[2])))
- {
- gmx_fatal(FARGS,"Error reading dimensions in header from pdo file");
- }
-
+ if (fgets(line,2048,file) == NULL)
+ gmx_fatal(FARGS,"Error reading header from pdo file\n");
+ sscanf(line,"%s%s%s%d%d%d",Buffer0,Buffer1,Buffer2,
+ &(header->Dims[0]),&(header->Dims[1]),&(header->Dims[2]));
+
/* printf("%d %d %d\n", header->Dims[0],header->Dims[1],header->Dims[2]); */
-
+
header->nDim = header->Dims[0] + header->Dims[1] + header->Dims[2];
if(header->nDim!=1)
gmx_fatal(FARGS,"Currently only supports one dimension");
-
+
/* line3 */
- if(3 != fscanf(file,"%s%s%d",Buffer0,Buffer1,&(header->nSkip)))
- {
- gmx_fatal(FARGS,"Error reading header from pdo file");
- }
-
- /* line 4 */
- if(4 != fscanf(file,"%s%s%s%s",Buffer0,Buffer1,Buffer2,header->Reference))
- {
- gmx_fatal(FARGS,"Error reading header from pdo file");
- }
-
+ if (fgets(line,2048,file) == NULL)
+ gmx_fatal(FARGS,"Error reading header from pdo file\n");
+ sscanf(line,"%s%s%d",Buffer0,Buffer1,&(header->nSkip));
+
+ /* line 4 */
+ if (fgets(line,2048,file) == NULL)
+ gmx_fatal(FARGS,"Error reading header from pdo file\n");
+ sscanf(line,"%s%s%s%s",Buffer0,Buffer1,Buffer2,header->Reference);
+
/* line 5 */
- if(6 != fscanf(file,"%s%s%s%s%s%d",Buffer0,Buffer1,Buffer2,Buffer3,Buffer4,&(header->nPull)))
- {
- gmx_fatal(FARGS,"Error reading header from pdo file");
- }
-
+ if (fgets(line,2048,file) == NULL)
+ gmx_fatal(FARGS,"Error reading header from pdo file\n");
+ sscanf(line,"%s%s%s%s%s%d",Buffer0,Buffer1,Buffer2,Buffer3,Buffer4,&(header->nPull));
+
if (opt->verbose)
- printf("Found nPull=%d , nSkip=%d, ref=%s\n",header->nPull,header->nSkip,
- header->Reference);
-
- for(i=0;i<header->nPull;++i)
+ printf("\tFound nPull=%d , nSkip=%d, ref=%s\n",header->nPull,header->nSkip,
+ header->Reference);
+
+ for(i=0;i<header->nPull;++i)
{
- if(4 != fscanf(file,"%s%s%s%s",Buffer0,Buffer1,Buffer2,header->PullName[i]))
- {
- gmx_fatal(FARGS,"Error reading header from pdo file");
- }
+ if (fgets(line,2048,file) == NULL)
+ gmx_fatal(FARGS,"Error reading header from pdo file\n");
+ sscanf(line,"%*s%*s%*s%s%*s%*s%lf%*s%*s%lf",header->PullName[i]
+ ,&(header->UmbPos[i][0]),&(header->UmbCons[i][0]));
if (opt->verbose)
- printf("pullgroup %d, pullname = %s\n",i,header->PullName[i]);
- for(j=0;j<header->nDim;++j)
- {
- if(6 != fscanf(file,"%s%s%lf%s%s%lf",Buffer0,Buffer1,&(header->UmbPos[i][j]),
- Buffer2,Buffer3,&(header->UmbCons[i][j])))
- {
- gmx_fatal(FARGS,"Error reading header from pdo file");
- }
-
- if (opt->bFlipProf)
- {
- /* We want to combine both halves of a profile into one */
- if(header->UmbPos[i][j]<0)
- {
- header->UmbPos[i][j]= -header->UmbPos[i][j];
- header->Flipped[i]=TRUE;
- }
- }
- else header->Flipped[i]=FALSE;
- /*printf("%f\t%f\n",header->UmbPos[i][j],header->UmbCons[i][j]);*/
- }
- }
-
- if(1 != fscanf(file,"%s",Buffer3))
- {
- gmx_fatal(FARGS,"Error reading header from pdo file");
+ printf("\tpullgroup %d, pullname = %s, UmbPos = %g, UmbConst = %g\n",
+ i,header->PullName[i],header->UmbPos[i][0],header->UmbCons[i][0]);
}
-
+
+ if (fgets(line,2048,file) == NULL)
+ gmx_fatal(FARGS,"Cannot read from file\n");
+ sscanf(line,"%s",Buffer3);
if (strcmp(Buffer3,"#####") != 0)
gmx_fatal(FARGS,"Expected '#####', found %s. Hick.\n",Buffer3);
}
{
char *p;
int slen;
-
-
+
if (fgets(ptr,*len-1,fp) == NULL)
return NULL;
p = ptr;
- while ((strchr(ptr,'\n') == NULL) && (!feof(fp)))
+ while ((strchr(ptr,'\n') == NULL) && (!feof(fp)))
{
/* This line is longer than len characters, let's increase len! */
*len += STRLEN;
slen = strlen(ptr);
if (ptr[slen-1] == '\n')
ptr[slen-1] = '\0';
-
+
return ptr;
}
-
void read_pdo_data(FILE * file, t_UmbrellaHeader * header,
- int fileno, t_UmbrellaWindow * win,
- t_UmbrellaOptions *opt,
- gmx_bool bGetMinMax,real *mintmp,real *maxtmp)
+ int fileno, t_UmbrellaWindow * win,
+ t_UmbrellaOptions *opt,
+ gmx_bool bGetMinMax,real *mintmp,real *maxtmp)
{
- int i,inttemp,bins,count;
- real min,max,minfound,maxfound;
+ int i,inttemp,bins,count,ntot;
+ real min,max,minfound=1e20,maxfound=-1e20;
double temp,time,time0=0,dt;
- char *ptr;
+ char *ptr=0;
t_UmbrellaWindow * window=0;
gmx_bool timeok,dt_ok=1;
- char *tmpbuf,fmt[256],fmtign[256];
- int len=STRLEN,dstep=1;
-
- minfound=1e20;
- maxfound=-1e20;
-
+ char *tmpbuf=0,fmt[256],fmtign[256];
+ int len=STRLEN,dstep=1;
+ const int blocklen=4096;
+ int *lennow=0;
+
if (!bGetMinMax)
{
bins=opt->bins;
min=opt->min;
max=opt->max;
-
+
window=win+fileno;
/* Need to alocate memory and set up structure */
window->nPull=header->nPull;
window->nBin=bins;
-
+
snew(window->Histo,window->nPull);
snew(window->z,window->nPull);
snew(window->k,window->nPull);
snew(window->pos,window->nPull);
- snew(window->Flipped,window->nPull);
snew(window->N, window->nPull);
snew(window->Ntot, window->nPull);
-
- for(i=0;i<window->nPull;++i)
+ snew(window->g, window->nPull);
+ snew(window->bsWeight, window->nPull);
+
+ window->bContrib=0;
+
+ if (opt->bCalcTauInt)
+ snew(window->ztime, window->nPull);
+ else
+ window->ztime=0;
+ snew(lennow,window->nPull);
+
+ for(i=0;i<window->nPull;++i)
{
window->z[i]=1;
+ window->bsWeight[i]=1.;
snew(window->Histo[i],bins);
window->k[i]=header->UmbCons[i][0];
window->pos[i]=header->UmbPos[i][0];
- window->Flipped[i]=header->Flipped[i];
window->N[i]=0;
window->Ntot[i]=0;
+ window->g[i]=1.;
+ if (opt->bCalcTauInt)
+ window->ztime[i]=0;
}
+
/* Done with setup */
}
else
maxfound=-1e20;
min=max=bins=0; /* Get rid of warnings */
}
-
+
count=0;
snew(tmpbuf,len);
while ( (ptr=fgets3(file,tmpbuf,&len)) != NULL)
{
trim(ptr);
-
+
if (ptr[0] == '#' || strlen(ptr)<2)
continue;
-
+
/* Initiate format string */
fmtign[0] = '\0';
strcat(fmtign,"%*s");
-
+
sscanf(ptr,"%lf",&time); /* printf("Time %f\n",time); */
/* Round time to fs */
time=1.0/1000*( (int) (time*1000+0.5) );
-
+
/* get time step of pdo file */
if (count==0)
time0=time;
dt=time-time0;
if (opt->dt>0.0)
{
- dstep=(int)(opt->dt/dt+0.5);
+ dstep=(int)(opt->dt/dt+0.5);
if (dstep==0)
dstep=1;
}
window->dt=dt*dstep;
}
count++;
-
+
dt_ok=((count-1)%dstep == 0);
timeok=(dt_ok && time >= opt->tmin && time <= opt->tmax);
/* if (opt->verbose)
- printf(" time = %f, (tmin,tmax)=(%e,%e), dt_ok=%d timeok=%d\n",
- time,opt->tmin, opt->tmax, dt_ok,timeok); */
-
+ printf(" time = %f, (tmin,tmax)=(%e,%e), dt_ok=%d timeok=%d\n",
+ time,opt->tmin, opt->tmax, dt_ok,timeok); */
+
if (timeok)
{
- for(i=0;i<header->nPull;++i)
+ for(i=0;i<header->nPull;++i)
{
strcpy(fmt,fmtign);
strcat(fmt,"%lf"); /* Creating a format stings such as "%*s...%*s%lf" */
strcat(fmtign,"%*s"); /* ignoring one more entry in the next loop */
- if(sscanf(ptr,fmt,&temp))
+ if(sscanf(ptr,fmt,&temp))
{
- if(opt->bFlipProf)
- {
- if(header->Flipped[i]) temp=-temp;
- }
-
temp+=header->UmbPos[i][0];
- if (bGetMinMax){
+ if (bGetMinMax)
+ {
if (temp<minfound)
minfound=temp;
if (temp>maxfound)
maxfound=temp;
}
- else
- {
+ else{
+ if (opt->bCalcTauInt)
+ {
+ /* save time series for autocorrelation analysis */
+ ntot=window->Ntot[i];
+ if (ntot>=lennow[i])
+ {
+ lennow[i]+=blocklen;
+ srenew(window->ztime[i],lennow[i]);
+ }
+ window->ztime[i][ntot]=temp;
+ }
+
temp-=min;
temp/=(max-min);
temp*=bins;
temp=floor(temp);
-
+
inttemp = (int)temp;
- if (opt->cycl==enCycl_yes)
+ if (opt->bCycl)
{
if (inttemp < 0)
inttemp+=bins;
else if (inttemp >= bins)
inttemp-=bins;
}
-
- if(inttemp >= 0 && inttemp < bins)
+
+ if(inttemp >= 0 && inttemp < bins)
{
- window->Histo[i][inttemp]+=1;
+ window->Histo[i][inttemp]+=1.;
window->N[i]++;
}
window->Ntot[i]++;
}
- }
+ }
}
}
if (time>opt->tmax)
break;
}
}
-
+
if (bGetMinMax)
{
*mintmp=minfound;
*maxtmp=maxfound;
}
+
+ sfree(lennow);
+ sfree(tmpbuf);
}
-
void enforceEqualWeights(t_UmbrellaWindow * window,int nWindows)
{
int i,k,j,NEnforced;
double ratio;
-
-
+
NEnforced=window[0].Ntot[0];
printf("\nFound -hist-eq. Enforcing equal weights for all histograms, \ni.e. doing a "
- "non-weighted histogram analysis method. Ndata = %d\n",NEnforced);
+ "non-weighted histogram analysis method. Ndata = %d\n",NEnforced);
/* enforce all histograms to have the same weight as the very first histogram */
-
+
for(j=0;j<nWindows;++j)
- for(k=0;k<window[j].nPull;++k)
+ {
+ for(k=0;k<window[j].nPull;++k)
{
ratio=1.0*NEnforced/window[j].Ntot[k];
for(i=0;i<window[0].nBin;++i)
+ {
window[j].Histo[k][i]*=ratio;
- window[j].N[k]=(int)(ratio*window[j].N[k]+0.5);
+ }
+ window[j].N[k]=(int)(ratio*window[j].N[k] + 0.5);
}
+ }
}
-
/* Simple linear interpolation between two given tabulated points */
double tabulated_pot(double dist, t_UmbrellaOptions *opt)
{
int jl,ju;
double pl,pu,dz,dp;
-
jl=floor((dist-opt->tabMin)/opt->tabDz);
ju=jl+1;
if (jl<0 || ju>=opt->tabNbins)
+ {
gmx_fatal(FARGS,"Distance %f out of bounds of tabulated potential (jl=%d, ju=%d).\n"
- "Provide an extended table.",dist,jl,ju);
+ "Provide an extended table.",dist,jl,ju);
+ }
pl=opt->tabY[jl];
pu=opt->tabY[ju];
dz=dist-opt->tabX[jl];
/* Don't worry, that routine does not mean we compute the PMF in limited precision.
- After rapid convergence (using only substiantal contributions), we always switch to
+ After rapid convergence (using only substiantal contributions), we always switch to
full precision. */
-#define WHAM_CONTRIB_LIM 1e-10
-void setup_acc_wham(t_UmbrellaWindow * window,int nWindows, t_UmbrellaOptions *opt)
+void setup_acc_wham(double *profile,t_UmbrellaWindow * window,int nWindows,
+ t_UmbrellaOptions *opt)
{
- int i,j,k;
- double U,min=opt->min,dz=opt->dz,temp,ztot_half,distance,ztot,contrib;
+ int i,j,k,nGrptot=0,nContrib=0,nTot=0;
+ double U,min=opt->min,dz=opt->dz,temp,ztot_half,distance,ztot,contrib1,contrib2;
gmx_bool bAnyContrib;
-
-
+ static int bFirst=1;
+ static double wham_contrib_lim;
+
+ if (bFirst)
+ {
+ for(i=0;i<nWindows;++i)
+ {
+ nGrptot+=window[i].nPull;
+ }
+ wham_contrib_lim=opt->Tolerance/nGrptot;
+ }
+
ztot=opt->max-opt->min;
ztot_half=ztot/2;
-
- for(i=0;i<nWindows;++i)
+
+ for(i=0;i<nWindows;++i)
{
- snew(window[i].bContrib,window[i].nPull);
- for(j=0;j<window[i].nPull;++j)
+ if ( ! window[i].bContrib)
+ {
+ snew(window[i].bContrib,window[i].nPull);
+ }
+ for(j=0;j<window[i].nPull;++j)
{
- snew(window[i].bContrib[j],opt->bins);
+ if ( ! window[i].bContrib[j])
+ snew(window[i].bContrib[j],opt->bins);
bAnyContrib=FALSE;
- for(k=0;k<opt->bins;++k)
+ for(k=0;k<opt->bins;++k)
{
temp=(1.0*k+0.5)*dz+min;
distance = temp - window[i].pos[j]; /* distance to umbrella center */
- if (opt->cycl==enCycl_yes)
+ if (opt->bCycl)
{ /* in cyclic wham: */
if (distance > ztot_half) /* |distance| < ztot_half */
distance-=ztot;
else if (distance < -ztot_half)
distance+=ztot;
}
+ /* Note: there are two contributions to bin k in the wham equations:
+ i) N[j]*exp(- U/(8.314e-3*opt->Temperature) + window[i].z[j])
+ ii) exp(- U/(8.314e-3*opt->Temperature))
+ where U is the umbrella potential
+ If any of these number is larger wham_contrib_lim, I set contrib=TRUE
+ */
+
if (!opt->bTab)
U=0.5*window[i].k[j]*sqr(distance); /* harmonic potential assumed. */
else
U=tabulated_pot(distance,opt); /* Use tabulated potential */
-
- contrib=exp(- U/(8.314e-3*opt->Temperature));
- window[i].bContrib[j][k] = (contrib > WHAM_CONTRIB_LIM);
+
+ contrib1=profile[k]*exp(- U/(8.314e-3*opt->Temperature));
+ contrib2=window[i].N[j]*exp(- U/(8.314e-3*opt->Temperature) + window[i].z[j]);
+ window[i].bContrib[j][k] = (contrib1 > wham_contrib_lim || contrib2 > wham_contrib_lim);
bAnyContrib = (bAnyContrib | window[i].bContrib[j][k]);
+ if (window[i].bContrib[j][k])
+ nContrib++;
+ nTot++;
}
/* If this histo is far outside min and max all bContrib may be FALSE,
- * causing a floating point exception later on. To avoid that, switch
- * them all to true.*/
+ causing a floating point exception later on. To avoid that, switch
+ them all to true.*/
if (!bAnyContrib)
for(k=0;k<opt->bins;++k)
window[i].bContrib[j][k]=TRUE;
}
}
- printf("Initialized rapid wham stuff.\n");
+ if (bFirst)
+ printf("Initialized rapid wham stuff (contrib tolerance %g)\n"
+ "Evaluating only %d of %d expressions.\n\n",wham_contrib_lim,nContrib, nTot);
+
+ if (opt->verbose)
+ printf("Updated rapid wham stuff. (evaluating only %d of %d contributions)\n",
+ nContrib,nTot);
+ bFirst=0;
}
-void calc_profile(double *profile,t_UmbrellaWindow * window, int nWindows, t_UmbrellaOptions *opt,
- gmx_bool bExact)
+void calc_profile(double *profile,t_UmbrellaWindow * window, int nWindows,
+ t_UmbrellaOptions *opt, gmx_bool bExact)
{
int i,k,j;
double num,ztot_half,ztot,distance,min=opt->min,dz=opt->dz;
- double denom,U=0,temp=0;
-
-
+ double denom,U=0,temp=0,invg;
+
ztot=opt->max-opt->min;
- ztot_half=ztot/2;
-
-
- for(i=0;i<opt->bins;++i)
+ ztot_half=ztot/2;
+
+ for(i=0;i<opt->bins;++i)
{
- num=denom=0;
- for(j=0;j<nWindows;++j)
+ num=denom=0.;
+ for(j=0;j<nWindows;++j)
{
- for(k=0;k<window[j].nPull;++k)
+ for(k=0;k<window[j].nPull;++k)
{
- temp=(1.0*i+0.5)*dz+min;
- num+=window[j].Histo[k][i];
-
+ invg = 1.0/window[j].g[k] * window[j].bsWeight[k];
+ temp = (1.0*i+0.5)*dz+min;
+ num += invg*window[j].Histo[k][i];
+
if (! (bExact || window[j].bContrib[k][i]))
continue;
distance = temp - window[j].pos[k]; /* distance to umbrella center */
- if (opt->cycl==enCycl_yes){ /* in cyclic wham: */
+ if (opt->bCycl)
+ { /* in cyclic wham: */
if (distance > ztot_half) /* |distance| < ztot_half */
distance-=ztot;
else if (distance < -ztot_half)
distance+=ztot;
}
-
+
if (!opt->bTab)
U=0.5*window[j].k[k]*sqr(distance); /* harmonic potential assumed. */
else
U=tabulated_pot(distance,opt); /* Use tabulated potential */
- denom+=window[j].N[k]*exp(- U/(8.314e-3*opt->Temperature) + window[j].z[k]);
+ denom+=invg*window[j].N[k]*exp(- U/(8.314e-3*opt->Temperature) + window[j].z[k]);
}
}
profile[i]=num/denom;
}
-double calc_z(double * profile,t_UmbrellaWindow * window, int nWindows, t_UmbrellaOptions *opt,
- gmx_bool bExact)
+double calc_z(double * profile,t_UmbrellaWindow * window, int nWindows,
+ t_UmbrellaOptions *opt, gmx_bool bExact)
{
- int i,j,k;
- double U=0,min=opt->min,dz=opt->dz,temp,ztot_half,distance,ztot;
+ int i,j,k,binMax=-1;
+ double U=0,min=opt->min,dz=opt->dz,temp,ztot_half,distance,ztot,totalMax;
double MAX=-1e20, total=0;
-
-
+
ztot=opt->max-opt->min;
ztot_half=ztot/2;
-
- for(i=0;i<nWindows;++i)
+
+ for(i=0;i<nWindows;++i)
{
- for(j=0;j<window[i].nPull;++j)
+ for(j=0;j<window[i].nPull;++j)
{
total=0;
- for(k=0;k<window[i].nBin;++k)
+ for(k=0;k<window[i].nBin;++k)
{
if (! (bExact || window[i].bContrib[j][k]))
continue;
temp=(1.0*k+0.5)*dz+min;
distance = temp - window[i].pos[j]; /* distance to umbrella center */
- if (opt->cycl==enCycl_yes)
+ if (opt->bCycl)
{ /* in cyclic wham: */
if (distance > ztot_half) /* |distance| < ztot_half */
distance-=ztot;
else if (distance < -ztot_half)
distance+=ztot;
}
-
+
if (!opt->bTab)
U=0.5*window[i].k[j]*sqr(distance); /* harmonic potential assumed. */
else
U=tabulated_pot(distance,opt); /* Use tabulated potential */
-
+
total+=profile[k]*exp(-U/(8.314e-3*opt->Temperature));
}
- if (total > 0.0)
+ /* Avoid floating point exception if window is far outside min and max */
+ if (total != 0.0)
total = -log(total);
else
total = 1000.0;
temp = fabs(total - window[i].z[j]);
- if(temp > MAX) MAX=temp;
+ if(temp > MAX){
+ MAX=temp;
+ binMax=k;
+ totalMax=total;
+ }
window[i].z[j] = total;
}
}
return MAX;
}
-
-void cyclicProfByWeightedCorr(double *profile,t_UmbrellaWindow *window,
- int nWindows, t_UmbrellaOptions * opt,
- gmx_bool bAppendCorr2File, const char *fn,
- const output_env_t oenv)
+void symmetrizeProfile(double* profile,t_UmbrellaOptions *opt)
{
- int i,j,k,bins=opt->bins;
- static int first=1;
- double *weight,sum=0.,diff,*histsum,*corr,sumCorr=0.,dCorr;
- FILE *fp;
- char buf[256];
-
- if (first)
- {
- printf("\nEnforcing a periodic profile by a sampling wheighted correction.");
- please_cite(stdout,"Hub2008");
- }
-
- snew(weight,bins-1);
- snew(histsum,bins);
- snew(corr,bins-1);
-
- /* generate weights proportional to 1/(n(i)*n(i+1))^alpha
- where n(i) is the total nur of data points in bin i from all histograms */
- for(i=0;i<nWindows;++i)
- for(j=0;j<window[i].nPull;++j)
- for(k=0;k<bins;++k)
- histsum[k]+=window[i].Histo[j][k];
-
- for(k=0,sum=0.;k<bins-1;++k)
- {
- weight[k]=1./pow(histsum[k]*histsum[k+1],opt->alpha);
- sum+=weight[k];
- }
- for(k=0;k<bins-1;++k)
- weight[k]/=sum;
-
- /* difference between last and first bin */
- diff=profile[bins-1]-profile[0];
- printf("Distributing %f between adjacent bins to enforce a cyclic profile\n",diff);
-
- for (i=0;i<bins-1;i++)
- {
- dCorr=weight[i]*diff;
- sumCorr+=dCorr;
- corr[i]=sumCorr;
- }
-
- for (i=0;i<bins-1;i++)
- profile[i+1]-=corr[i];
-
- if (bAppendCorr2File)
+ int i,j;
+ double *prof2,bins=opt->bins,min=opt->min,max=opt->max,dz=opt->dz,zsym,deltaz,profsym;
+ double z,z1;
+
+ if (min>0. || max<0.)
+ gmx_fatal(FARGS,"Cannot symmetrize profile around z=0 with min=%f and max=%f\n",
+ opt->min,opt->max);
+
+ snew(prof2,bins);
+
+ for (i=0;i<bins;i++)
{
- fp=xvgropen(fn,"Corrections to enforce periodicity","z",
- "\\f{12}D\\f{}G(z)",oenv);
- sprintf(buf,"corrections propotional to 1/(n\\si\\Nn\\si+1\\N)\\S%.2f",
- opt->alpha);
- xvgr_subtitle(fp,buf,oenv);
- for (i=0;i<bins-1;i++)
- fprintf(fp,"%g %g\n",opt->min+opt->dz*(i+1),-corr[i]);
- ffclose(fp);
+ z=min+(i+0.5)*dz;
+ zsym=-z;
+ /* bin left of zsym */
+ j=floor((zsym-min)/dz-0.5);
+ if (j>=0 && (j+1)<bins)
+ {
+ /* interpolate profile linearly between bins j and j+1 */
+ z1=min+(j+0.5)*dz;
+ deltaz=zsym-z1;
+ profsym=profile[j] + (profile[j+1]-profile[j])/dz*deltaz;
+ /* average between left and right */
+ prof2[i]=0.5*(profsym+profile[i]);
+ }
+ else
+ {
+ prof2[i]=profile[i];
+ }
}
-
- sfree(histsum);
- sfree(corr);
- sfree(weight);
- first=0;
+
+ memcpy(profile,prof2,bins*sizeof(double));
+ sfree(prof2);
}
-
void prof_normalization_and_unit(double * profile, t_UmbrellaOptions *opt)
{
int i,bins,imin;
double unit_factor=1., R_MolarGasConst, diff;
-
-
+
R_MolarGasConst=8.314472e-3; /* in kJ/(mol*K) */
bins=opt->bins;
-
- /* No log? Nothing to do! */
+
+ /* Not log? Nothing to do! */
if (!opt->bLog)
return;
-
+
/* Get profile in units of kT, kJ/mol, or kCal/mol */
if (opt->unit == en_kT)
unit_factor=1.0;
else if (opt->unit == en_kCal)
unit_factor=R_MolarGasConst*opt->Temperature/4.1868;
else
- gmx_fatal(FARGS,"Sorry I don't know this energy unit.");
-
+ gmx_fatal(FARGS,"Sorry, I don't know this energy unit.");
+
for (i=0;i<bins;i++)
if (profile[i]>0.0)
profile[i]=-log(profile[i])*unit_factor;
-
+
/* shift to zero at z=opt->zProf0 */
if (!opt->bProf0Set)
+ {
diff=profile[0];
- else{
- /* Get bin with shortest distance to opt->zProf0 */
- imin=(int)((opt->zProf0-opt->min)/opt->dz);
+ }
+ else
+ {
+ /* Get bin with shortest distance to opt->zProf0
+ (-0.5 from bin position and +0.5 from rounding cancel) */
+ imin=(int)((opt->zProf0-opt->min)/opt->dz);
if (imin<0)
imin=0;
else if (imin>=bins)
imin=bins-1;
diff=profile[imin];
}
-
+
/* Shift to zero */
for (i=0;i<bins;i++)
profile[i]-=diff;
}
-
-void getRandomIntArray(int nPull,int blockLength,int* randomArray)
+void getRandomIntArray(int nPull,int blockLength,int* randomArray,gmx_rng_t rng)
{
int ipull,blockBase,nr,ipullRandom;
-
-
+
if (blockLength==0)
blockLength=nPull;
-
+
for (ipull=0; ipull<nPull; ipull++)
{
blockBase=(ipull/blockLength)*blockLength;
- do{ /* make sure nothing bad happens in the last block */
- nr=(int)((1.0*rand()/RAND_MAX)*blockLength);
+ do
+ { /* make sure nothing bad happens in the last block */
+ nr=(int)(gmx_rng_uniform_real(rng)*blockLength);
ipullRandom = blockBase + nr;
} while (ipullRandom >= nPull);
if (ipullRandom<0 || ipullRandom>=nPull)
gmx_fatal(FARGS,"Ups, random iWin = %d, nPull = %d, nr = %d, "
- "blockLength = %d, blockBase = %d\n",
- ipullRandom,nPull,nr,blockLength,blockBase);
+ "blockLength = %d, blockBase = %d\n",
+ ipullRandom,nPull,nr,blockLength,blockBase);
randomArray[ipull]=ipullRandom;
}
/*for (ipull=0; ipull<nPull; ipull++)
- printf("%d ",randomArray[ipull]); printf("\n"); */
+ printf("%d ",randomArray[ipull]); printf("\n"); */
}
-
void copy_pullgrp_to_synthwindow(t_UmbrellaWindow *synthWindow,
- t_UmbrellaWindow *thisWindow,int pullid)
+ t_UmbrellaWindow *thisWindow,int pullid)
{
synthWindow->N [0]=thisWindow->N [pullid];
synthWindow->Histo [0]=thisWindow->Histo [pullid];
synthWindow->z [0]=thisWindow->z [pullid];
synthWindow->k [0]=thisWindow->k [pullid];
synthWindow->bContrib[0]=thisWindow->bContrib [pullid];
+ synthWindow->g [0]=thisWindow->g [pullid];
+ synthWindow->bsWeight[0]=thisWindow->bsWeight [pullid];
}
-
-/* Calculate cummulative of all histograms. They allow to create random numbers
+/* Calculate cumulative distribution function of of all histograms. They
+ allow to create random number sequences
which are distributed according to the histograms. Required to generate
the "synthetic" histograms for the Bootstrap method */
-void calc_cummulants(t_UmbrellaWindow *window,int nWindows,
- t_UmbrellaOptions *opt,const char *fnhist,
- const output_env_t oenv)
+void calc_cumulatives(t_UmbrellaWindow *window,int nWindows,
+ t_UmbrellaOptions *opt,const char *fnhist)
{
int i,j,k,nbin;
double last;
char *fn=0,*buf=0;
FILE *fp=0;
-
-
+
if (opt->bs_verbose)
{
snew(fn,strlen(fnhist)+10);
snew(buf,strlen(fnhist)+10);
sprintf(fn,"%s_cumul.xvg",strncpy(buf,fnhist,strlen(fnhist)-4));
- fp=xvgropen(fn,"Cummulants of umbrella histograms","z","cummulant",
- oenv);
+ fp=xvgropen(fn,"CDFs of umbrella windows","z","CDF",opt->oenv);
}
-
+
nbin=opt->bins;
for (i=0; i<nWindows; i++)
{
window[i].cum[j][0]=0.;
for (k=1; k<=nbin; k++)
window[i].cum[j][k] = window[i].cum[j][k-1]+window[i].Histo[j][k-1];
-
- /* normalize cummulant. Ensure cum[nbin]==1 */
+
+ /* normalize CDFs. Ensure cum[nbin]==1 */
last = window[i].cum[j][nbin];
for (k=0; k<=nbin; k++)
window[i].cum[j][k] /= last;
}
}
-
- printf("Cumulants of all histograms created.\n");
+
+ printf("Cumulative distriubtion functions of all histograms created.\n");
if (opt->bs_verbose)
{
for (k=0; k<=nbin; k++)
fprintf(fp,"%g\t",window[i].cum[j][k]);
fprintf(fp,"\n");
}
- printf("Wrote cumulants to %s\n",fn);
+ printf("Wrote cumulative distribution functions to %s\n",fn);
ffclose(fp);
sfree(fn);
sfree(buf);
/* Return j such that xx[j] <= x < xx[j+1] */
-void searchCummulant(double xx[], int n, double x, int *j)
+void searchCumulative(double xx[], int n, double x, int *j)
{
int ju,jm,jl;
-
-
+
jl=-1;
ju=n;
- while (ju-jl > 1)
+ while (ju-jl > 1)
{
jm=(ju+jl) >> 1;
if (x >= xx[jm])
*j=jl;
}
-
-void create_synthetic_histo(t_UmbrellaWindow *synthWindow,
- t_UmbrellaWindow *thisWindow,
+void create_synthetic_histo(t_UmbrellaWindow *synthWindow, t_UmbrellaWindow *thisWindow,
int pullid,t_UmbrellaOptions *opt)
{
- int nsynth,N,i,nbins,r_index;
- double r;
- static gmx_bool bWarnout=0;
-
-
+ int N,i,nbins,r_index,ibin;
+ double r,tausteps=0.0,a,ap,dt,x,invsqrt2,g,y,sig=0.,z,mu=0.;
+ char errstr[1024];
+
N=thisWindow->N[pullid];
+ dt=thisWindow->dt;
nbins=thisWindow->nBin;
-
- /* nsynth = nr of data points in synthetic histo */
- if (opt->dtBootStrap==0.0)
- nsynth=N;
- else
+
+ /* tau = autocorrelation time */
+ if (opt->tauBootStrap>0.0)
+ tausteps=opt->tauBootStrap/dt;
+ else if (opt->bTauIntGiven || opt->bCalcTauInt)
{
- nsynth=(int)(thisWindow->N[pullid]*thisWindow->dt/opt->dtBootStrap+0.5);
- if (nsynth>N)
- nsynth=N;
+ /* calc tausteps from g=1+2tausteps */
+ g=thisWindow->g[pullid];
+ tausteps=(g-1)/2;
}
-
- if (!bWarnout && nsynth<10)
+ else
{
- printf("\n++++ WARNING ++++\n\tOnly %d data points per synthetic histogram!\n"
- "\tYou may want to consider option -bs-dt.\n\n",nsynth);
- bWarnout=1;
+ sprintf(errstr,
+ "When generating hypothetical trajctories from given umbrella histograms,\n"
+ "autocorrelation times (ACTs) are required. Otherwise the statistical error\n"
+ "cannot be predicted. You have 3 options:\n"
+ "1) Make g_wham estimate the ACTs (options -ac and -acsig).\n"
+ "2) Calculate the ACTs by yourself (e.g. with g_analyze) and provide them\n");
+ strcat(errstr,
+ " with option -iiact for all umbrella windows.\n"
+ "3) If all ACTs are identical and know, you can define them with -bs-tau.\n"
+ " Use option (3) only if you are sure what you're doing, you may severely\n"
+ " underestimate the error if a too small ACT is given.\n");
+ gmx_fatal(FARGS,errstr);
}
- synthWindow->N [0]=nsynth;
+ synthWindow->N [0]=N;
synthWindow->pos [0]=thisWindow->pos[pullid];
synthWindow->z [0]=thisWindow->z[pullid];
synthWindow->k [0]=thisWindow->k[pullid];
synthWindow->bContrib[0]=thisWindow->bContrib[pullid];
-
+ synthWindow->g [0]=thisWindow->g [pullid];
+ synthWindow->bsWeight[0]=thisWindow->bsWeight[pullid];
+
for (i=0;i<nbins;i++)
synthWindow->Histo[0][i]=0.;
-
- for (i=0;i<nsynth;i++)
+
+ if (opt->bsMethod==bsMethod_trajGauss)
+ {
+ sig = thisWindow->sigma [pullid];
+ mu = thisWindow->aver [pullid];
+ }
+
+ /* Genrate autocorrelated Gaussian random variable with autocorrelation time tau
+ Use the following:
+ If x and y are random numbers from N(0,1) (Gaussian with average 0 and sigma=1),
+ then
+ z = a*x + sqrt(1-a^2)*y
+ is also from N(0,1), and cov(z,x) = a. Thus, by gerenating a sequence
+ x' = a*x + sqrt(1-a^2)*y, the sequnce x(t) is from N(0,1) and has an autocorrelation
+ function
+ C(t) = exp(-t/tau) with tau=-1/ln(a)
+
+ Then, use error function to turn the Gaussian random variable into a uniformly
+ distributed one in [0,1]. Eventually, use cumulative distribution function of
+ histogram to get random variables distributed according to histogram.
+ Note: The ACT of the flat distribution and of the generated histogram is not
+ 100% exactly tau, but near tau (my test was 3.8 instead of 4).
+ */
+ a=exp(-1.0/tausteps);
+ ap=sqrt(1-a*a);
+ invsqrt2=1./sqrt(2.0);
+
+ /* init random sequence */
+ x=gmx_rng_gaussian_table(opt->rng);
+
+ if (opt->bsMethod==bsMethod_traj)
+ {
+ /* bootstrap points from the umbrella histograms */
+ for (i=0;i<N;i++)
+ {
+ y=gmx_rng_gaussian_table(opt->rng);
+ x=a*x+ap*y;
+ /* get flat distribution in [0,1] using cumulative distribution function of Gauusian
+ Note: CDF(Gaussian) = 0.5*{1+erf[x/sqrt(2)]}
+ */
+ r=0.5*(1+gmx_erf(x*invsqrt2));
+ searchCumulative(thisWindow->cum[pullid],nbins+1 ,r,&r_index);
+ synthWindow->Histo[0][r_index]+=1.;
+ }
+ }
+ else if (opt->bsMethod==bsMethod_trajGauss)
+ {
+ /* bootstrap points from a Gaussian with the same average and sigma
+ as the respective umbrella histogram. The idea was, that -given
+ limited sampling- the bootstrapped histograms are otherwise biased
+ from the limited sampling of the US histos. However, bootstrapping from
+ the Gaussian seems to yield a similar estimate. */
+ i=0;
+ while (i<N)
+ {
+ y=gmx_rng_gaussian_table(opt->rng);
+ x=a*x+ap*y;
+ z = x*sig+mu;
+ ibin=floor((z-opt->min)/opt->dz);
+ if (opt->bCycl)
+ {
+ if (ibin<0)
+ while ( (ibin+=nbins) < 0);
+ else if (ibin>=nbins)
+ while ( (ibin-=nbins) >= nbins);
+ }
+
+ if (ibin>=0 && ibin<nbins)
+ {
+ synthWindow->Histo[0][ibin]+=1.;
+ i++;
+ }
+ }
+ }
+ else
{
- r=1.0*rand()/RAND_MAX;
- searchCummulant(thisWindow->cum[pullid],nbins+1 ,r,&r_index);
- synthWindow->Histo[0][r_index]+=1.;
+ gmx_fatal(FARGS,"Unknown bsMethod (id %d). That should not happen.\n",opt->bsMethod);
}
}
-void print_histograms(const char *fnhist, t_UmbrellaWindow * window,
- int nWindows, int bs_index,t_UmbrellaOptions *opt,
- const output_env_t oenv)
+void print_histograms(const char *fnhist, t_UmbrellaWindow * window, int nWindows,
+ int bs_index,t_UmbrellaOptions *opt)
{
- char *fn;
- char *buf=0,title[256];
+ char *fn=0,*buf=0,title[256];
FILE *fp;
int bins,l,i,j;
-
-
+
if (bs_index<0)
{
fn=strdup(fnhist);
}
else
{
- snew(fn,strlen(fnhist)+6);
+ snew(fn,strlen(fnhist)+10);
snew(buf,strlen(fnhist)+1);
sprintf(fn,"%s_bs%d.xvg",strncpy(buf,fnhist,strlen(fnhist)-4),bs_index);
sprintf(title,"Umbrella histograms. Bootstrap #%d",bs_index);
}
-
- fp=xvgropen(fn,title,"z","count",oenv);
+
+ fp=xvgropen(fn,title,"z","count",opt->oenv);
bins=opt->bins;
-
+
/* Write histograms */
- for(l=0;l<bins;++l)
+ for(l=0;l<bins;++l)
{
fprintf(fp,"%e\t",(double)(l+0.5)*opt->dz+opt->min);
- for(i=0;i<nWindows;++i)
+ for(i=0;i<nWindows;++i)
{
- for(j=0;j<window[i].nPull;++j)
+ for(j=0;j<window[i].nPull;++j)
{
fprintf(fp,"%e\t",window[i].Histo[j][l]);
}
}
fprintf(fp,"\n");
}
-
+
ffclose(fp);
printf("Wrote %s\n",fn);
if (buf)
}
}
+int func_wham_is_larger(const void *a, const void *b)
+{
+ double *aa,*bb;
+ aa=(double*)a;
+ bb=(double*)b;
+ if (*aa < *bb)
+ return -1;
+ else if (*aa > *bb)
+ return 1;
+ else
+ return 0;
+}
+
+
+void setRandomBsWeights(t_UmbrellaWindow *synthwin,int nAllPull, t_UmbrellaOptions *opt)
+{
+ int i;
+ double *r;
+
+ snew(r,nAllPull);
+
+ /* generate ordered random numbers between 0 and nAllPull */
+ for (i=0; i<nAllPull-1; i++)
+ {
+ r[i] = gmx_rng_uniform_real(opt->rng) * nAllPull;
+ }
+ qsort((void *)r,nAllPull-1, sizeof(double), &func_wham_is_larger);
+ r[nAllPull-1]=1.0*nAllPull;
+
+ synthwin[0].bsWeight[0]=r[0];
+ for (i=1; i<nAllPull; i++)
+ {
+ synthwin[i].bsWeight[0]=r[i]-r[i-1];
+ }
+
+ /* avoid to have zero weight by adding a tiny value */
+ for (i=0; i<nAllPull; i++)
+ if (synthwin[i].bsWeight[0] < 1e-5)
+ synthwin[i].bsWeight[0] = 1e-5;
+
+ sfree(r);
+}
-void do_bootstrapping(const char *fnres, const char* fnprof,
- const char *fnhist, char* ylabel, double *profile,
- t_UmbrellaWindow * window, int nWindows,
- t_UmbrellaOptions *opt, const output_env_t oenv)
+void do_bootstrapping(const char *fnres, const char* fnprof, const char *fnhist,
+ char* ylabel, double *profile,
+ t_UmbrellaWindow * window, int nWindows, t_UmbrellaOptions *opt)
{
t_UmbrellaWindow * synthWindow;
double *bsProfile,*bsProfiles_av, *bsProfiles_av2,maxchange=1e20,tmp,stddev;
int iAllPull,nAllPull,*allPull_winId,*allPull_pullId;
FILE *fp;
gmx_bool bExact=FALSE;
-
-
- /* init random */
+
+ /* init random generator */
if (opt->bsSeed==-1)
- srand(time(NULL));
+ opt->rng=gmx_rng_init(gmx_rng_make_seed());
else
- srand(opt->bsSeed);
-
+ opt->rng=gmx_rng_init(opt->bsSeed);
+
snew(bsProfile, opt->bins);
snew(bsProfiles_av, opt->bins);
snew(bsProfiles_av2,opt->bins);
-
+
/* Create array of all pull groups. Note that different windows
- may have different nr of pull groups
- First: Get total nr of pull groups */
+ may have different nr of pull groups
+ First: Get total nr of pull groups */
nAllPull=0;
for (i=0;i<nWindows;i++)
nAllPull+=window[i].nPull;
iAllPull=0;
/* Setup one array of all pull groups */
for (i=0;i<nWindows;i++)
+ {
for (j=0;j<window[i].nPull;j++)
{
allPull_winId[iAllPull]=i;
allPull_pullId[iAllPull]=j;
iAllPull++;
}
-
+ }
+
/* setup stuff for synthetic windows */
snew(synthWindow,nAllPull);
for (i=0;i<nAllPull;i++)
synthWindow[i].nPull=1;
synthWindow[i].nBin=opt->bins;
snew(synthWindow[i].Histo,1);
- if (!opt->bHistBootStrap)
+ if (opt->bsMethod == bsMethod_traj || opt->bsMethod == bsMethod_trajGauss)
snew(synthWindow[i].Histo[0],opt->bins);
snew(synthWindow[i].N,1);
snew(synthWindow[i].pos,1);
snew(synthWindow[i].z,1);
snew(synthWindow[i].k,1);
snew(synthWindow[i].bContrib,1);
+ snew(synthWindow[i].g,1);
+ snew(synthWindow[i].bsWeight,1);
}
-
- if (opt->bHistBootStrap)
+
+ switch(opt->bsMethod)
{
+ case bsMethod_hist:
snew(randomArray,nAllPull);
printf("\n\nWhen computing statistical errors by bootstrapping entire histograms:\n");
please_cite(stdout,"Hub2006");
+ break;
+ case bsMethod_BayesianHist :
+ /* just copy all histogams into synthWindow array */
+ for (i=0;i<nAllPull;i++)
+ {
+ winid =allPull_winId [i];
+ pullid=allPull_pullId[i];
+ copy_pullgrp_to_synthwindow(synthWindow+i,window+winid,pullid);
+ }
+ break;
+ case bsMethod_traj:
+ case bsMethod_trajGauss:
+ calc_cumulatives(window,nWindows,opt,fnhist);
+ break;
+ default:
+ gmx_fatal(FARGS,"Unknown bootstrap method. That should not have happened.\n");
}
- else
- {
- calc_cummulants(window,nWindows,opt,fnhist,oenv);
- }
-
+
/* do bootstrapping */
- fp=xvgropen(fnprof,"Boot strap profiles","z",ylabel,oenv);
+ fp=xvgropen(fnprof,"Boot strap profiles","z",ylabel,opt->oenv);
for (ib=0;ib<opt->nBootStrap;ib++)
{
printf(" *******************************************\n"
- " ******** Start bootstrap nr %d ************\n"
- " *******************************************\n",ib+1);
-
- if (opt->bHistBootStrap)
+ " ******** Start bootstrap nr %d ************\n"
+ " *******************************************\n",ib+1);
+
+ switch(opt->bsMethod)
{
- /* only mix given histos */
- getRandomIntArray(nAllPull,opt->histBootStrapBlockLength,randomArray);
- for (i=0;i<nAllPull;i++)
- {
+ case bsMethod_hist:
+ /* bootstrap complete histograms from given histograms */
+ getRandomIntArray(nAllPull,opt->histBootStrapBlockLength,randomArray,opt->rng);
+ for (i=0;i<nAllPull;i++){
winid =allPull_winId [randomArray[i]];
pullid=allPull_pullId[randomArray[i]];
copy_pullgrp_to_synthwindow(synthWindow+i,window+winid,pullid);
}
- }
- else
- {
- /* create new histos from given histos */
+ break;
+ case bsMethod_BayesianHist:
+ /* keep histos, but assign random weights ("Bayesian bootstrap") */
+ setRandomBsWeights(synthWindow,nAllPull,opt);
+ break;
+ case bsMethod_traj:
+ case bsMethod_trajGauss:
+ /* create new histos from given histos, that is generate new hypothetical
+ trajectories */
for (i=0;i<nAllPull;i++)
{
winid=allPull_winId[i];
- pullid=allPull_pullId[i];
+ pullid=allPull_pullId[i];
create_synthetic_histo(synthWindow+i,window+winid,pullid,opt);
}
+ break;
}
-
- /* print histos in case of verbose output */
+
+ /* write histos in case of verbose output */
if (opt->bs_verbose)
- print_histograms(fnhist,synthWindow,nAllPull,ib,opt,oenv);
-
+ print_histograms(fnhist,synthWindow,nAllPull,ib,opt);
+
/* do wham */
i=0;
bExact=FALSE;
maxchange=1e20;
memcpy(bsProfile,profile,opt->bins*sizeof(double)); /* use profile as guess */
- do {
+ do
+ {
+ if ( (i%opt->stepUpdateContrib) == 0)
+ setup_acc_wham(bsProfile,synthWindow,nAllPull,opt);
if (maxchange<opt->Tolerance)
bExact=TRUE;
if (((i%opt->stepchange) == 0 || i==1) && !i==0)
i++;
} while( (maxchange=calc_z(bsProfile, synthWindow, nAllPull, opt,bExact)) > opt->Tolerance || !bExact);
printf("\tConverged in %d iterations. Final maximum change %g\n",i,maxchange);
-
+
if (opt->bLog)
prof_normalization_and_unit(bsProfile,opt);
- /* Force cyclic profile by wheighted correction */
- if (opt->cycl==enCycl_weighted)
- cyclicProfByWeightedCorr(bsProfile,synthWindow,nAllPull,opt,
- FALSE, 0,oenv);
-
+
+ /* symmetrize profile around z=0 */
+ if (opt->bSym)
+ symmetrizeProfile(bsProfile,opt);
+
/* save stuff to get average and stddev */
for (i=0;i<opt->bins;i++)
{
fprintf(fp,"&\n");
}
ffclose(fp);
-
+
/* write average and stddev */
- fp=ffopen(fnres,"w");
- fprintf(fp,"@ title \"%s\"\n","Average and stddev from bootstrapping");
- fprintf(fp,"@ xaxis label \"%s\"\n","z");
- fprintf(fp,"@ yaxis label \"%s\"\n",ylabel);
+ fp=xvgropen(fnres,"Average and stddev from bootstrapping","z",ylabel,opt->oenv);
fprintf(fp,"@TYPE xydy\n");
for (i=0;i<opt->bins;i++)
{
printf("Wrote boot strap result to %s\n",fnres);
}
-
-int whaminFileType(const char *fn)
+int whaminFileType(char *fn)
{
int len;
len=strlen(fn);
return whamin_unknown;
}
-
void read_wham_in(const char *fn,char ***filenamesRet, int *nfilesRet,
t_UmbrellaOptions *opt)
{
- char **filename,tmp[STRLEN];
- int nread,sizenow,i,block=10;
+ char **filename=0,tmp[STRLEN];
+ int nread,sizenow,i,block=1;
FILE *fp;
-#define MAXFILELEN 512
-
-
+
fp=ffopen(fn,"r");
- sizenow=block;
- snew(filename,sizenow);
- for (i=0;i<sizenow;i++)
- snew(filename[i],MAXFILELEN);
nread=0;
+ sizenow=0;
while (fscanf(fp,"%s",tmp) != EOF)
{
- if (strlen(tmp)>=MAXFILELEN)
- gmx_fatal(FARGS,"Filename too long. Only %d characters allowed\n",MAXFILELEN);
- strcpy(filename[nread],tmp);
- if (opt->verbose)
- printf("Found file %s in %s\n",filename[nread],fn);
- nread++;
+ if (strlen(tmp)>=WHAM_MAXFILELEN)
+ gmx_fatal(FARGS,"Filename too long. Only %d characters allowed\n",WHAM_MAXFILELEN);
if (nread>=sizenow)
{
sizenow+=block;
srenew(filename,sizenow);
for (i=sizenow-block;i<sizenow;i++)
- snew(filename[i],MAXFILELEN);
+ snew(filename[i],WHAM_MAXFILELEN);
}
+ strcpy(filename[nread],tmp);
+ if (opt->verbose)
+ printf("Found file %s in %s\n",filename[nread],fn);
+ nread++;
}
*filenamesRet=filename;
*nfilesRet=nread;
}
-FILE *pdo_open_file(const char *fn)
+FILE *open_pdo_pipe(const char *fn, t_UmbrellaOptions *opt,gmx_bool *bPipeOpen)
{
char Buffer[1024],gunzip[1024],*Path=0;
- FILE *fp;
-
- if (!gmx_fexist(fn))
- {
- gmx_fatal(FARGS,"File %s does not exist.\n",fn);
- }
-
+ FILE *pipe=0;
+ static gmx_bool bFirst=1;
+
/* gzipped pdo file? */
- if (strcmp(fn+strlen(fn)-3,".gz")==0)
+ if ((strcmp(fn+strlen(fn)-3,".gz")==0))
{
-#ifdef HAVE_PIPES
+ /* search gunzip executable */
if(!(Path=getenv("GMX_PATH_GZIP")))
- sprintf(gunzip,"%s","/bin/gunzip");
+ {
+ if (gmx_fexist("/bin/gunzip"))
+ sprintf(gunzip,"%s","/bin/gunzip");
+ else if (gmx_fexist("/usr/bin/gunzip"))
+ sprintf(gunzip,"%s","/usr/bin/gunzip");
+ else
+ gmx_fatal(FARGS,"Cannot find executable gunzip in /bin or /usr/bin.\n"
+ "You may want to define the path to gunzip "
+ "with the environment variable GMX_PATH_GZIP.",gunzip);
+ }
else
+ {
sprintf(gunzip,"%s/gunzip",Path);
- if (!gmx_fexist(gunzip))
- gmx_fatal(FARGS,"Cannot find executable %s. You may want to define the path to gunzip "
- "with the environment variable GMX_PATH_GZIP.",gunzip);
- sprintf(Buffer,"%s -c < %s",gunzip,fn);
- if((fp=popen(Buffer,"r"))==NULL)
- {
- gmx_fatal(FARGS,"Unable to open pipe to `%s'\n",Buffer);
- }
+ if (!gmx_fexist(gunzip))
+ gmx_fatal(FARGS,"Cannot find executable %s. Please define the path to gunzip"
+ " in the environmental varialbe GMX_PATH_GZIP.",gunzip);
+ }
+ if (bFirst)
+ {
+ printf("Using gunzig executable %s\n",gunzip);
+ bFirst=0;
+ }
+ if (!gmx_fexist(fn))
+ {
+ gmx_fatal(FARGS,"File %s does not exist.\n",fn);
+ }
+ sprintf(Buffer,"%s -c < %s",gunzip,fn);
+ if (opt->verbose)
+ printf("Executing command '%s'\n",Buffer);
+#ifdef HAVE_PIPES
+ if((pipe=popen(Buffer,"r"))==NULL)
+ {
+ gmx_fatal(FARGS,"Unable to open pipe to `%s'\n",Buffer);
+ }
#else
- gmx_fatal(FARGS,"Cannot open a compressed file on platform without pipe support");
+ gmx_fatal(FARGS,"Cannot open a compressed file on platform without pipe support");
#endif
+ *bPipeOpen=TRUE;
+ }
+ else{
+ pipe=ffopen(fn,"r");
+ *bPipeOpen=FALSE;
+ }
+
+ return pipe;
+}
+
+
+FILE *open_pdo_pipe_gmx(const char *fn)
+{
+ char *fnNoGz=0;
+ FILE *pipe;
+
+ /* gzipped pdo file? */
+ if (strcmp(fn+strlen(fn)-3,".gz")==0)
+ {
+ snew(fnNoGz,strlen(fn));
+ strncpy(fnNoGz,fn,strlen(fn)-3);
+ fnNoGz[strlen(fn)-3]='\0';
+ if (gmx_fexist(fnNoGz) && gmx_fexist(fn))
+ gmx_fatal(FARGS,"Found file %s and %s. That confuses me. Please remove one of them\n",
+ fnNoGz,fn);
+ pipe=ffopen(fnNoGz,"r");
+ sfree(fnNoGz);
}
else
- {
- if((fp=ffopen(fn,"r"))==NULL)
- {
- gmx_fatal(FARGS,"Unable to open file %s\n",fn);
- }
- }
- return fp;
+ {
+ pipe=ffopen(fn,"r");
+ }
+
+ return pipe;
}
-void
-pdo_close_file(FILE *fp)
+void pdo_close_file(FILE *fp)
{
#ifdef HAVE_PIPES
pclose(fp);
#endif
}
+
/* Reading pdo files */
void read_pdo_files(char **fn, int nfiles, t_UmbrellaHeader* header,
- t_UmbrellaWindow **window, t_UmbrellaOptions *opt)
+ t_UmbrellaWindow *window, t_UmbrellaOptions *opt)
{
- FILE * file;
- real mintmp,maxtmp;
+ FILE *file;
+ real mintmp,maxtmp,done=0.;
int i;
-
-
+ gmx_bool bPipeOpen;
+ /* char Buffer0[1000]; */
+
if(nfiles<1)
gmx_fatal(FARGS,"No files found. Hick.");
-
+
/* if min and max are not given, get min and max from the input files */
if (opt->bAuto)
{
printf("Automatic determination of boundaries from %d pdo files...\n",nfiles);
opt->min=1e20;
opt->max=-1e20;
- for(i=0;i<nfiles;++i)
+ for(i=0;i<nfiles;++i)
{
- file=pdo_open_file(fn[i]);
- printf("\rOpening %s ...",fn[i]); fflush(stdout);
+ file=open_pdo_pipe(fn[i],opt,&bPipeOpen);
+ /*fgets(Buffer0,999,file);
+ fprintf(stderr,"First line '%s'\n",Buffer0); */
+ done=100.0*(i+1)/nfiles;
+ printf("\rOpening %s ... [%2.0f%%]",fn[i],done); fflush(stdout);
if (opt->verbose)
printf("\n");
read_pdo_header(file,header,opt);
opt->max=maxtmp;
if (mintmp<opt->min)
opt->min=mintmp;
- pdo_close_file(file);
+ if (bPipeOpen)
+ pdo_close_file(file);
+ else
+ ffclose(file);
}
printf("\n");
printf("\nDetermined boundaries to %f and %f\n\n",opt->min,opt->max);
}
/* store stepsize in profile */
opt->dz=(opt->max-opt->min)/opt->bins;
-
- snew(*window,nfiles);
-
+
/* Having min and max, we read in all files */
/* Loop over all files */
- for(i=0;i<nfiles;++i)
+ for(i=0;i<nfiles;++i)
{
- printf("\rOpening %s ...",fn[i]); fflush(stdout);
+ done=100.0*(i+1)/nfiles;
+ printf("\rOpening %s ... [%2.0f%%]",fn[i],done); fflush(stdout);
if (opt->verbose)
printf("\n");
- file=pdo_open_file(fn[i]);
- /* read in the headers */
+ file=open_pdo_pipe(fn[i],opt,&bPipeOpen);
read_pdo_header(file,header,opt);
/* load data into window */
- read_pdo_data(file,header,i,*window,opt,FALSE,NULL,NULL);
- pdo_close_file(file);
+ read_pdo_data(file,header,i,window,opt,FALSE,NULL,NULL);
+ if ((window+i)->Ntot[0] == 0.0)
+ fprintf(stderr,"\nWARNING, no data points read from file %s (check -b option)\n", fn[i]);
+ if (bPipeOpen)
+ pdo_close_file(file);
+ else
+ ffclose(file);
}
printf("\n");
+ for(i=0;i<nfiles;++i)
+ sfree(fn[i]);
+ sfree(fn);
}
-
#define int2YN(a) (((a)==0)?("N"):("Y"))
-void read_tpr_header(const char *fn,t_UmbrellaHeader* header,
- t_UmbrellaOptions *opt)
+void read_tpr_header(const char *fn,t_UmbrellaHeader* header,t_UmbrellaOptions *opt)
{
t_inputrec ir;
- int i,ngrp,d;
+ int i,ngrp,d;
t_state state;
static int first=1;
-
-
+
/* printf("Reading %s \n",fn); */
read_tpx_state(fn,&ir,&state,NULL,NULL);
-
+
if (ir.ePull != epullUMBRELLA)
- gmx_fatal(FARGS,"This is not a tpr of an umbrella simulation. Found ir.ePull = %s\n",
- epull_names[ir.ePull]);
-
+ gmx_fatal(FARGS,"This is not a tpr of an umbrella simulation. Found pull type \"%s\" "
+ " (ir.ePull = %d)\n", epull_names[ir.ePull],ir.ePull);
+
/* nr of pull groups */
ngrp=ir.pull->ngrp;
if (ngrp < 1)
gmx_fatal(FARGS,"This is not a tpr of umbrella simulation. Found only %d pull groups\n",ngrp);
-
+
header->npullgrps=ir.pull->ngrp;
header->pull_geometry=ir.pull->eGeom;
copy_ivec(ir.pull->dim,header->pull_dim);
header->pull_ndim=header->pull_dim[0]+header->pull_dim[1]+header->pull_dim[2];
if (header->pull_geometry==epullgPOS && header->pull_ndim>1)
+ {
gmx_fatal(FARGS,"Found pull geometry 'position' and more than 1 pull dimension (%d).\n"
- "Hence, the pull potential does not correspond to a one-dimensional umbrella potential.\n"
- "If you have some special umbrella setup you may want to write your own pdo files\n"
- "and feed them into g_wham. Check g_wham -h !\n",header->pull_ndim);
+ "Hence, the pull potential does not correspond to a one-dimensional umbrella potential.\n"
+ "If you have some special umbrella setup you may want to write your own pdo files\n"
+ "and feed them into g_wham. Check g_wham -h !\n",header->pull_ndim);
+ }
snew(header->k,ngrp);
snew(header->init_dist,ngrp);
snew(header->umbInitDist,ngrp);
+
+ /* only z-direction with epullgCYL? */
+ if (header->pull_geometry == epullgCYL)
+ {
+ if (header->pull_dim[XX] || header->pull_dim[YY] || (!header->pull_dim[ZZ]))
+ gmx_fatal(FARGS,"With pull geometry 'cylinder', expected pulling in Z direction only.\n"
+ "However, found dimensions [%s %s %s]\n",
+ int2YN(header->pull_dim[XX]),int2YN(header->pull_dim[YY]),
+ int2YN(header->pull_dim[ZZ]));
+ }
for (i=0;i<ngrp;i++)
{
header->k[i]=ir.pull->grp[i+1].k;
if (header->k[i]==0.0)
gmx_fatal(FARGS,"Pull group %d has force constant of of 0.0 in %s.\n"
- "That doesn't seem to be an Umbrella tpr.\n",
- i,fn);
+ "That doesn't seem to be an Umbrella tpr.\n",
+ i,fn);
copy_rvec(ir.pull->grp[i+1].init,header->init_dist[i]);
- header->Flipped[i]=opt->bFlipProf;
-
+
/* initial distance to reference */
switch(header->pull_geometry)
{
if (header->pull_dim[d])
header->umbInitDist[i]=header->init_dist[i][d];
break;
+ case epullgCYL:
+ /* umbrella distance stored in init_dist[i][0] for geometry cylinder (not in ...[i][ZZ]) */
case epullgDIST:
+ case epullgDIR:
+ case epullgDIRPBC:
header->umbInitDist[i]=header->init_dist[i][0];
break;
default:
gmx_fatal(FARGS,"Pull geometry %s not supported\n",epullg_names[header->pull_geometry]);
}
}
-
+
if (opt->verbose || first)
{
printf("File %s, %d groups, geometry \"%s\", dimensions [%s %s %s], (%d dimensions)\n",
- fn,header->npullgrps,epullg_names[header->pull_geometry],
- int2YN(header->pull_dim[0]),int2YN(header->pull_dim[1]),int2YN(header->pull_dim[2]),
- header->pull_ndim);
+ fn,header->npullgrps,epullg_names[header->pull_geometry],
+ int2YN(header->pull_dim[0]),int2YN(header->pull_dim[1]),int2YN(header->pull_dim[2]),
+ header->pull_ndim);
for (i=0;i<ngrp;i++)
- printf("\tgrp %d) k = %.3f inittial distance = %g\n",i,header->k[i],header->umbInitDist[i]);
+ printf("\tgrp %d) k = %-5g position = %g\n",i,header->k[i],header->umbInitDist[i]);
}
+ if (!opt->verbose && first)
+ printf("\tUse option -v to see this output for all input tpr files\n");
+
first=0;
}
{
int i;
double r2=0.;
-
-
for (i=0;i<ndim;i++)
r2+=sqr(dx[i][line]);
-
return sqrt(r2);
}
-
-void read_pull_xf(const char *fn, const char *fntpr,
- t_UmbrellaHeader * header, t_UmbrellaWindow * window,
- t_UmbrellaOptions *opt, gmx_bool bGetMinMax,real *mintmp,
- real *maxtmp)
+void read_pull_xf(const char *fn, const char *fntpr, t_UmbrellaHeader * header,
+ t_UmbrellaWindow * window,
+ t_UmbrellaOptions *opt,
+ gmx_bool bGetMinMax,real *mintmp,real *maxtmp)
{
- double **y,pos=0.,t,force,time0=0.,dt;
- int ny,nt,bins,ibin,i,g,dstep=1,nColPerGrp,nColRef,nColExpect;
- real min,max,minfound,maxfound;
+ double **y=0,pos=0.,t,force,time0=0.,dt;
+ int ny,nt,bins,ibin,i,g,dstep=1,nColPerGrp,nColRefOnce,nColRefEachGrp,nColExpect,ntot;
+ real min,max,minfound=1e20,maxfound=-1e20;
gmx_bool dt_ok,timeok,bHaveForce;
const char *quantity;
+ const int blocklen=4096;
+ int *lennow=0;
+
+ /*
+ in force output pullf.xvg:
+ No reference, one column per pull group
+ in position output pullx.xvg (not cylinder)
+ ndim reference, ndim columns per pull group
+ in position output pullx.xvg (in geometry cylinder):
+ ndim*2 columns per pull group (ndim for ref, ndim for group)
+ */
- minfound=1e20;
- maxfound=-1e20;
-
- /*
- in force output pullf.xvg: No reference, one column per pull group
- in position output pullx.xvg: ndim reference, ndim columns per pull group
- */
nColPerGrp = opt->bPullx ? header->pull_ndim : 1;
- nColRef = opt->bPullx ? header->pull_ndim : 0;
quantity = opt->bPullx ? "position" : "force";
- nColExpect = 1 + nColRef + header->npullgrps*nColPerGrp;
+
+ if (opt->bPullx)
+ {
+ if (header->pull_geometry == epullgCYL)
+ {
+ /* Geometry cylinder -> reference group before each pull group */
+ nColRefEachGrp=header->pull_ndim;
+ nColRefOnce=0;
+ }
+ else
+ {
+ /* Geometry NOT cylinder -> reference group only once after time column */
+ nColRefEachGrp=0;
+ nColRefOnce=header->pull_ndim;
+ }
+ }
+ else /* read forces, no reference groups */
+ {
+ nColRefEachGrp=0;
+ nColRefOnce=0;
+ }
+ nColExpect = 1 + nColRefOnce + header->npullgrps*(nColRefEachGrp+nColPerGrp);
bHaveForce = opt->bPullf;
-
+
+ /* With geometry "distance" or "distance_periodic", only force reading is supported so far.
+ That avoids the somewhat tedious extraction of the right columns from the pullx files
+ to compute the distances projection on the vector. Sorry for the laziness. */
+ if ( (header->pull_geometry==epullgDIR || header->pull_geometry==epullgDIRPBC)
+ && opt->bPullx)
+ {
+ gmx_fatal(FARGS,"With pull geometries \"direction\" and \"direction_periodic\", only pull force "
+ "reading \n(option -if) is supported at present, "
+ "not pull position reading (options -ix).\nMake sure mdrun writes the pull "
+ "forces (pullf.xvg files)\nand provide them to g_wham with option -if.",
+ epullg_names[header->pull_geometry]);
+ }
+
nt=read_xvg(fn,&y,&ny);
/* Check consistency */
if (nt<1)
+ {
gmx_fatal(FARGS,"Empty pull %s file %s\n",quantity,fn);
+ }
if (ny != nColExpect)
+ {
gmx_fatal(FARGS,"Found %d pull groups in %s,\n but %d data columns in %s (expected %d)\n",
- header->npullgrps,fntpr,ny-1,fn,nColExpect-1);
-
+ header->npullgrps,fntpr,ny-1,fn,nColExpect-1);
+ }
+
if (opt->verbose)
printf("Found %d times and %d %s sets %s\n",nt,(ny-1)/nColPerGrp,quantity,fn);
-
+
if (!bGetMinMax)
{
bins=opt->bins;
min=opt->min;
max=opt->max;
if (nt>1)
+ {
window->dt=y[0][1]-y[0][0];
- else if (opt->nBootStrap && opt->dtBootStrap!=0.0)
+ }
+ else if (opt->nBootStrap && opt->tauBootStrap!=0.0)
+ {
fprintf(stderr,"\n *** WARNING, Could not determine time step in %s\n",fn);
-
+ }
+
/* Need to alocate memory and set up structure */
window->nPull=header->npullgrps;
window->nBin=bins;
-
+
snew(window->Histo,window->nPull);
snew(window->z,window->nPull);
snew(window->k,window->nPull);
snew(window->pos,window->nPull);
- snew(window->Flipped,window->nPull);
snew(window->N, window->nPull);
snew(window->Ntot, window->nPull);
+ snew(window->g, window->nPull);
+ snew(window->bsWeight, window->nPull);
+ window->bContrib=0;
- for(g=0;g<window->nPull;++g)
+ if (opt->bCalcTauInt)
+ snew(window->ztime,window->nPull);
+ else
+ window->ztime=NULL;
+ snew(lennow,window->nPull);
+
+ for(g=0;g<window->nPull;++g)
{
window->z[g]=1;
+ window->bsWeight[g]=1.;
snew(window->Histo[g],bins);
window->k[g]=header->k[g];
- window->Flipped[g]=header->Flipped[g];
window->N[g]=0;
window->Ntot[g]=0;
+ window->g[g]=1.;
window->pos[g]=header->umbInitDist[g];
+ if (opt->bCalcTauInt)
+ window->ztime[g]=NULL;
}
+
}
else
- {
- /* only determine min and max */
+ { /* only determine min and max */
minfound=1e20;
maxfound=-1e20;
min=max=bins=0; /* Get rid of warnings */
}
- if(header->Flipped[0])
- gmx_fatal(FARGS,"Sorry, flipping not supported for gmx4 output\n");
-
for (i=0;i<nt;i++)
{
/* Do you want that time frame? */
- t=1.0/1000*((int)(0.5+y[0][i]*1000)); /* round time to fs */
-
+ t=1.0/1000*( (int) ((y[0][i]*1000) + 0.5)); /* round time to fs */
+
/* get time step of pdo file and get dstep from opt->dt */
if (i==0)
+ {
time0=t;
+ }
else if (i==1)
{
dt=t-time0;
if (!bGetMinMax)
window->dt=dt*dstep;
}
-
+
dt_ok=(i%dstep == 0);
timeok=(dt_ok && t >= opt->tmin && t <= opt->tmax);
/*if (opt->verbose)
- printf(" time = %f, (tmin,tmax)=(%e,%e), dt_ok=%d timeok=%d\n",
- t,opt->tmin, opt->tmax, dt_ok,timeok); */
-
+ printf(" time = %f, (tmin,tmax)=(%e,%e), dt_ok=%d timeok=%d\n",
+ t,opt->tmin, opt->tmax, dt_ok,timeok); */
+
if (timeok)
{
- for(g=0;g<header->npullgrps;++g)
+ for(g=0;g<header->npullgrps;++g)
{
if (bHaveForce)
{
switch (header->pull_geometry)
{
case epullgDIST:
- /* y has 1 time column y[0] and nColPerGrps columns per pull group;
- Distance to reference: */
- pos=dist_ndim(y+1+nColRef+g*nColPerGrp,header->pull_ndim,i);
+ /* y has 1 time column y[0] and nColPerGrps columns per pull group;
+ Distance to reference: */
+ /* pos=dist_ndim(y+1+nColRef+g*nColPerGrp,header->pull_ndim,i); gmx 4.0 */
+ pos=dist_ndim(y + 1 + nColRefOnce + g*nColPerGrp,header->pull_ndim,i);
break;
case epullgPOS:
- /* with geometry==position, we have always one column per group;
- Distance to reference: */
- pos=y[1+nColRef+g][i];
+ case epullgCYL:
+ /* with geometry==position, we have the reference once (nColRefOnce==ndim), but
+ no extra reference group columns before each group (nColRefEachGrp==0)
+ with geometry==cylinder, we have no initial ref group column (nColRefOnce==0),
+ but ndim ref group colums before every group (nColRefEachGrp==ndim)
+ Distance to reference: */
+ pos=y[1 + nColRefOnce + g*(nColRefEachGrp+nColPerGrp)][i];
break;
default:
gmx_fatal(FARGS,"Bad error, this error should have been catched before. Ups.\n");
}
}
-
+
/* printf("grp %d dpos %f poseq %f pos %f \n",g,dpos,poseq,pos); */
if (bGetMinMax)
{
}
else
{
+ if (opt->bCalcTauInt && !bGetMinMax)
+ {
+ /* save time series for autocorrelation analysis */
+ ntot=window->Ntot[g];
+ /* printf("i %d, ntot %d, lennow[g] = %d\n",i,ntot,lennow[g]); */
+ if (ntot>=lennow[g])
+ {
+ lennow[g]+=blocklen;
+ srenew(window->ztime[g],lennow[g]);
+ }
+ window->ztime[g][ntot]=pos;
+ }
+
ibin=(int) floor((pos-min)/(max-min)*bins);
- if (opt->cycl==enCycl_yes)
+ if (opt->bCycl)
{
if (ibin<0)
while ( (ibin+=bins) < 0);
else if (ibin>=bins)
while ( (ibin-=bins) >= bins);
- }
- if(ibin >= 0 && ibin < bins)
+ }
+ if(ibin >= 0 && ibin < bins)
{
window->Histo[g][ibin]+=1.;
window->N[g]++;
break;
}
}
-
+
if (bGetMinMax)
{
*mintmp=minfound;
*maxtmp=maxfound;
}
+ sfree(lennow);
+ for (i=0;i<ny;i++)
+ sfree(y[i]);
}
-
-void read_tpr_pullxf_files(char **fnTprs,char **fnPull,
- int nfiles, t_UmbrellaHeader* header,
- t_UmbrellaWindow **window, t_UmbrellaOptions *opt)
+void read_tpr_pullxf_files(char **fnTprs,char **fnPull,int nfiles,
+ t_UmbrellaHeader* header,
+ t_UmbrellaWindow *window, t_UmbrellaOptions *opt)
{
int i;
real mintmp,maxtmp;
-
-
- printf("Reading %d tpr and pullf files\n",nfiles);
-
+
+ printf("Reading %d tpr and pullf files\n",nfiles/2);
+
/* min and max not given? */
if (opt->bAuto)
{
read_tpr_header(fnTprs[i],header,opt);
if (whaminFileType(fnPull[i]) != whamin_pullxf)
gmx_fatal(FARGS,"Expected the %d'th file in input file to be a xvg (pullx/pullf) file\n",i);
- read_pull_xf(fnPull[i],fnTprs[i],header,NULL,opt,TRUE,&mintmp,&maxtmp);
+ read_pull_xf(fnPull[i],fnTprs[i],header,NULL,opt,TRUE,&mintmp,&maxtmp);
if (maxtmp>opt->max)
opt->max=maxtmp;
if (mintmp<opt->min)
opt->min=mintmp;
}
printf("\nDetermined boundaries to %f and %f\n\n",opt->min,opt->max);
- if (opt->bBoundsOnly){
+ if (opt->bBoundsOnly)
+ {
printf("Found option -boundsonly, now exiting.\n");
exit (0);
}
/* store stepsize in profile */
opt->dz=(opt->max-opt->min)/opt->bins;
- snew(*window,nfiles);
for (i=0;i<nfiles; i++)
{
if (whaminFileType(fnTprs[i]) != whamin_tpr)
read_tpr_header(fnTprs[i],header,opt);
if (whaminFileType(fnPull[i]) != whamin_pullxf)
gmx_fatal(FARGS,"Expected the %d'th file in input file to be a xvg (pullx/pullf) file\n",i);
- read_pull_xf(fnPull[i],fnTprs[i],header,*window+i,opt,FALSE,NULL,NULL);
+ read_pull_xf(fnPull[i],fnTprs[i],header,window+i,opt,FALSE,NULL,NULL);
+ if (window[i].Ntot[0] == 0.0)
+ fprintf(stderr,"\nWARNING, no data points read from file %s (check -b option)\n", fnPull[i]);
+ }
+
+ for (i=0;i<nfiles; i++)
+ {
+ sfree(fnTprs[i]);
+ sfree(fnPull[i]);
+ }
+ sfree(fnTprs);
+ sfree(fnPull);
+}
+
+/* Note: Here we consider tau[int] := int_0^inf ACF(t) as the integrated autocorrelation time.
+ The factor `g := 1 + 2*tau[int]` subsequently enters the uncertainty.
+*/
+void readIntegratedAutocorrelationTimes(t_UmbrellaWindow *window,int nwins,t_UmbrellaOptions *opt,
+ const char* fn)
+{
+ int nlines,ny,i,ig;
+ double **iact;
+
+ printf("Readging Integrated autocorrelation times from %s ...\n",fn);
+ nlines=read_xvg(fn,&iact,&ny);
+ if (nlines!=nwins)
+ gmx_fatal(FARGS,"Found %d lines with integrated autocorrelation times in %s.\nExpected %d",
+ nlines,fn,nwins);
+ for (i=0;i<nlines;i++){
+ if (window[i].nPull != ny)
+ gmx_fatal(FARGS,"You are providing autocorrelation times with option -iiact and the\n"
+ "number of pull groups is different in different simulations. That is not\n"
+ "supported yet. Sorry.\n");
+ for (ig=0;ig<window[i].nPull;ig++){
+ /* compare Kumar et al, J Comp Chem 13, 1011-1021 (1992) */
+ window[i].g[ig]=1+2*iact[ig][i]/window[i].dt;
+
+ if (iact[ig][i] <= 0.0)
+ fprintf(stderr,"\nWARNING, IACT = %f (window %d, group %d)\n", iact[ig][i],i,ig);
+ }
}
}
+/* Smooth autocorreltion times along the reaction coordinate. This is useful
+ if the ACT is subject to high uncertainty in case if limited sampling. Note
+ that -in case of limited sampling- the ACT may be severely underestimated.
+ Note: the g=1+2tau are overwritten.
+ if opt->bAllowReduceIact==FALSE, the ACTs are never reduced, only increased
+ by the smoothing
+*/
+void smoothIact(t_UmbrellaWindow *window,int nwins,t_UmbrellaOptions *opt)
+{
+ int i,ig,j,jg;
+ double pos,dpos2,siglim,siglim2,gaufact,invtwosig2,w,weight,tausm;
+
+ /* only evaluate within +- 3sigma of the Gausian */
+ siglim=3.0*opt->sigSmoothIact;
+ siglim2=dsqr(siglim);
+ /* pre-factor of Gaussian */
+ gaufact=1.0/(sqrt(2*M_PI)*opt->sigSmoothIact);
+ invtwosig2=0.5/dsqr(opt->sigSmoothIact);
+
+ for (i=0;i<nwins;i++)
+ {
+ snew(window[i].tausmooth,window[i].nPull);
+ for (ig=0;ig<window[i].nPull;ig++)
+ {
+ tausm=0.;
+ weight=0;
+ pos=window[i].pos[ig];
+ for (j=0;j<nwins;j++)
+ {
+ for (jg=0;jg<window[j].nPull;jg++)
+ {
+ dpos2=dsqr(window[j].pos[jg]-pos);
+ if (dpos2<siglim2){
+ w=gaufact*exp(-dpos2*invtwosig2);
+ weight+=w;
+ tausm+=w*window[j].tau[jg];
+ /*printf("Weight %g dpos2=%g pos=%g gaufact=%g invtwosig2=%g\n",
+ w,dpos2,pos,gaufact,invtwosig2); */
+ }
+ }
+ }
+ tausm/=weight;
+ if (opt->bAllowReduceIact || tausm>window[i].tau[ig])
+ window[i].tausmooth[ig]=tausm;
+ else
+ window[i].tausmooth[ig]=window[i].tau[ig];
+ window[i].g[ig] = 1+2*tausm/window[i].dt;
+ }
+ }
+}
+
+/* try to compute the autocorrelation time for each umbrealla window */
+#define WHAM_AC_ZERO_LIMIT 0.05
+void calcIntegratedAutocorrelationTimes(t_UmbrellaWindow *window,int nwins,
+ t_UmbrellaOptions *opt, const char *fn)
+{
+ int i,ig,ncorr,ntot,j,k,*count,restart;
+ real *corr,c0,dt,timemax,tmp;
+ real *ztime,av,tausteps;
+ FILE *fp,*fpcorr=0;
+
+ if (opt->verbose)
+ fpcorr=xvgropen("hist_autocorr.xvg","Autocorrelation functions of umbrella windows",
+ "time [ps]","autocorrelation function",opt->oenv);
+
+ printf("\n");
+ for (i=0;i<nwins;i++)
+ {
+ printf("\rEstimating integrated autocorreltion times ... [%2.0f%%] ...",100.*(i+1)/nwins);
+ fflush(stdout);
+ ntot=window[i].Ntot[0];
+
+ /* using half the maximum time as length of autocorrelation function */
+ ncorr=ntot/2;
+ if (ntot<10)
+ gmx_fatal(FARGS,"Tryig to estimtate autocorrelation time from only %d"
+ " points. Provide more pull data!",ntot);
+ snew(corr,ncorr);
+ /* snew(corrSq,ncorr); */
+ snew(count,ncorr);
+ dt=window[i].dt;
+ timemax=dt*ncorr;
+ snew(window[i].tau,window[i].nPull);
+ restart=(int)(opt->acTrestart/dt+0.5);
+ if (restart==0)
+ restart=1;
+
+ for (ig=0;ig<window[i].nPull;ig++)
+ {
+ if (ntot != window[i].Ntot[ig])
+ gmx_fatal(FARGS,"Encountered different nr of frames in different pull groups.\n"
+ "That should not happen. (%d and %d)\n", ntot,window[i].Ntot[ig]);
+ ztime=window[i].ztime[ig];
+
+ /* calc autocorrelation function C(t) = < [z(tau)-<z>]*[z(tau+t)-<z>]> */
+ for(j=0, av=0; (j<ntot); j++)
+ av+=ztime[j];
+ av/=ntot;
+ for(k=0; (k<ncorr); k++)
+ {
+ corr[k]=0.;
+ count[k]=0;
+ }
+ for(j=0; (j<ntot); j+=restart)
+ for(k=0; (k<ncorr) && (j+k < ntot); k++)
+ {
+ tmp=(ztime[j]-av)*(ztime[j+k]-av);
+ corr [k] += tmp;
+ /* corrSq[k] += tmp*tmp; */
+ count[k]++;
+ }
+ /* divide by nr of frames for each time displacement */
+ for(k=0; (k<ncorr); k++)
+ {
+ /* count probably = (ncorr-k+(restart-1))/restart; */
+ corr[k] = corr[k]/count[k];
+ /* variance of autocorrelation function */
+ /* corrSq[k]=corrSq[k]/count[k]; */
+ }
+ /* normalize such that corr[0] == 0 */
+ c0=1./corr[0];
+ for(k=0; (k<ncorr); k++)
+ {
+ corr[k]*=c0;
+ /* corrSq[k]*=c0*c0; */
+ }
+
+ /* write ACFs in verbose mode */
+ if (fpcorr)
+ {
+ for(k=0; (k<ncorr); k++)
+ fprintf(fpcorr,"%g %g\n",k*dt,corr[k]);
+ fprintf(fpcorr,"&\n");
+ }
+
+ /* esimate integrated correlation time, fitting is too unstable */
+ tausteps = 0.5*corr[0];
+ /* consider corr below WHAM_AC_ZERO_LIMIT as noise */
+ for(j=1; (j<ncorr) && (corr[j]>WHAM_AC_ZERO_LIMIT); j++)
+ tausteps += corr[j];
+
+ /* g = 1+2*tau, see. Ferrenberg/Swendsen, PRL 63:1195 (1989) or
+ Kumar et al, eq. 28 ff. */
+ window[i].tau[ig] = tausteps*dt;
+ window[i].g[ig] = 1+2*tausteps;
+ /* printf("win %d, group %d, estimated correlation time = %g ps\n",i,ig,window[i].tau[ig]); */
+ } /* ig loop */
+ sfree(corr);
+ sfree(count);
+ }
+ printf(" done\n");
+ if (fpcorr)
+ ffclose(fpcorr);
+
+ /* plot IACT along reaction coordinate */
+ fp=xvgropen(fn,"Integrated autocorrelation times","z","IACT [ps]",opt->oenv);
+ fprintf(fp,"@ s0 symbol 1\n@ s0 symbol size 0.5\n@ s0 line linestyle 0\n");
+ fprintf(fp,"# WIN tau(gr1) tau(gr2) ...\n");
+ for (i=0;i<nwins;i++)
+ {
+ fprintf(fp,"# %3d ",i);
+ for (ig=0;ig<window[i].nPull;ig++)
+ fprintf(fp," %11g",window[i].tau[ig]);
+ fprintf(fp,"\n");
+ }
+ for (i=0;i<nwins;i++)
+ for (ig=0;ig<window[i].nPull;ig++)
+ fprintf(fp,"%8g %8g\n",window[i].pos[ig],window[i].tau[ig]);
+ if (opt->sigSmoothIact > 0.0)
+ {
+ printf("Smoothing autocorrelation times along reaction coordinate with Gaussian of sig = %g\n",
+ opt->sigSmoothIact);
+ /* smooth IACT along reaction coordinate and overwrite g=1+2tau */
+ smoothIact(window,nwins,opt);
+ fprintf(fp,"&\n@ s1 symbol 1\n@ s1 symbol size 0.5\n@ s1 line linestyle 0\n");
+ fprintf(fp,"@ s1 symbol color 2\n");
+ for (i=0;i<nwins;i++)
+ for (ig=0;ig<window[i].nPull;ig++)
+ fprintf(fp,"%8g %8g\n",window[i].pos[ig],window[i].tausmooth[ig]);
+ }
+ ffclose(fp);
+ printf("Wrote %s\n",fn);
+}
+
+/* compute average and sigma of each umbrella window */
+void averageSigma(t_UmbrellaWindow *window,int nwins,t_UmbrellaOptions *opt)
+{
+ int i,ig,ntot,k;
+ real av,sum2,sig,diff,*ztime,nSamplesIndep;
+
+ for (i=0;i<nwins;i++)
+ {
+ snew(window[i].aver, window[i].nPull);
+ snew(window[i].sigma,window[i].nPull);
+
+ ntot=window[i].Ntot[0];
+ for (ig=0;ig<window[i].nPull;ig++)
+ {
+ ztime=window[i].ztime[ig];
+ for (k=0, av=0.; k<ntot; k++)
+ av+=ztime[k];
+ av/=ntot;
+ for (k=0, sum2=0.; k<ntot; k++)
+ {
+ diff=ztime[k]-av;
+ sum2+=diff*diff;
+ }
+ sig=sqrt(sum2/ntot);
+ window[i].aver[ig]=av;
+
+ /* Note: This estimate for sigma is biased from the limited sampling.
+ Correct sigma by n/(n-1) where n = number of independent
+ samples. Only possible if IACT is known.
+ */
+ if (window[i].tau)
+ {
+ nSamplesIndep=window[i].N[ig]/(window[i].tau[ig]/window[i].dt);
+ window[i].sigma[ig]=sig * nSamplesIndep/(nSamplesIndep-1);
+ }
+ else
+ window[i].sigma[ig]=sig;
+ printf("win %d, aver = %f sig = %f\n",i,av,window[i].sigma[ig]);
+ }
+ }
+}
+
+
+/* Use histograms to compute average force on pull group.
+ In addition, compute the sigma of the histogram.
+*/
+void computeAverageForce(t_UmbrellaWindow *window,int nWindows,t_UmbrellaOptions *opt)
+{
+ int i,j,bins=opt->bins,k;
+ double dz,min=opt->min,max=opt->max,displAv,displAv2,temp,distance,ztot,ztot_half,w,weight;
+ double posmirrored;
+
+ dz=(max-min)/bins;
+ ztot=opt->max-min;
+ ztot_half=ztot/2;
+
+ /* Compute average displacement from histograms */
+ for(j=0;j<nWindows;++j)
+ {
+ snew(window[j].forceAv,window[j].nPull);
+ for(k=0;k<window[j].nPull;++k)
+ {
+ displAv = 0.0;
+ displAv2 = 0.0;
+ weight = 0.0;
+ for(i=0;i<opt->bins;++i)
+ {
+ temp=(1.0*i+0.5)*dz+min;
+ distance = temp - window[j].pos[k];
+ if (opt->bCycl)
+ { /* in cyclic wham: */
+ if (distance > ztot_half) /* |distance| < ztot_half */
+ distance-=ztot;
+ else if (distance < -ztot_half)
+ distance+=ztot;
+ }
+ w=window[j].Histo[k][i]/window[j].g[k];
+ displAv += w*distance;
+ displAv2 += w*sqr(distance);
+ weight+=w;
+ /* Are we near min or max? We are getting wron forces from the histgrams since
+ the histigrams are zero outside [min,max). Therefore, assume that the position
+ on the other side of the histomgram center is equally likely. */
+ if (!opt->bCycl)
+ {
+ posmirrored=window[j].pos[k]-distance;
+ if (posmirrored>=max || posmirrored<min)
+ {
+ displAv += -w*distance;
+ displAv2 += w*sqr(-distance);
+ weight+=w;
+ }
+ }
+ }
+ displAv /= weight;
+ displAv2 /= weight;
+
+ /* average force from average displacement */
+ window[j].forceAv[k] = displAv*window[j].k[k];
+ /* sigma from average square displacement */
+ /* window[j].sigma [k] = sqrt(displAv2); */
+ /* printf("Win %d, sigma = %f\n",j,sqrt(displAv2)); */
+ }
+ }
+}
+
+/* Check if the complete reaction coordinate is covered by the histograms */
+void checkReactionCoordinateCovered(t_UmbrellaWindow *window,int nwins,
+ t_UmbrellaOptions *opt)
+{
+ int i,ig,j,bins=opt->bins,bBoundary;
+ real avcount=0,z,relcount,*count;
+ snew(count,opt->bins);
+
+ for(j=0;j<opt->bins;++j)
+ {
+ for (i=0;i<nwins;i++){
+ for (ig=0;ig<window[i].nPull;ig++)
+ count[j]+=window[i].Histo[ig][j];
+ }
+ avcount+=1.0*count[j];
+ }
+ avcount/=bins;
+ for(j=0;j<bins;++j)
+ {
+ relcount=count[j]/avcount;
+ z=(j+0.5)*opt->dz+opt->min;
+ bBoundary=( j<bins/20 || (bins-j)>bins/20 );
+ /* check for bins with no data */
+ if (count[j] == 0)
+ fprintf(stderr, "\nWARNING, no data point in bin %d (z=%g) !\n"
+ "You may not get a reasonable profile. Check your histograms!\n",j,z);
+ /* and check for poor sampling */
+ else if (relcount<0.005 && !bBoundary)
+ fprintf(stderr, "Warning, poor sampling bin %d (z=%g). Check your histograms!\n",j,z);
+ }
+ sfree(count);
+}
+
+
+void guessPotByIntegration(t_UmbrellaWindow *window,int nWindows,t_UmbrellaOptions *opt,
+ char *fn)
+{
+ int i,j,ig,bins=opt->bins,nHist,winmin,groupmin;
+ double dz,min=opt->min,*pot,pos,hispos,dist,diff,fAv,distmin,*f;
+ FILE *fp;
+
+ dz=(opt->max-min)/bins;
+
+ printf("Getting initial potential by integration.\n");
+
+ /* Compute average displacement from histograms */
+ computeAverageForce(window,nWindows,opt);
+
+ /* Get force for each bin from all histograms in this bin, or, alternatively,
+ if no histograms are inside this bin, from the closest histogram */
+ snew(pot,bins);
+ snew(f,bins);
+ for(j=0;j<opt->bins;++j)
+ {
+ pos=(1.0*j+0.5)*dz+min;
+ nHist=0;
+ fAv=0.;
+ distmin=1e20;
+ groupmin=winmin=0;
+ for (i=0;i<nWindows;i++)
+ {
+ for (ig=0;ig<window[i].nPull;ig++)
+ {
+ hispos=window[i].pos[ig];
+ dist=fabs(hispos-pos);
+ /* average force within bin */
+ if (dist < dz/2)
+ {
+ nHist++;
+ fAv+=window[i].forceAv[ig];
+ }
+ /* at the same time, rememer closest histogram */
+ if (dist<distmin){
+ winmin=i;
+ groupmin=ig;
+ distmin=dist;
+ }
+ }
+ }
+ /* if no histogram found in this bin, use closest histogram */
+ if (nHist>0)
+ fAv=fAv/nHist;
+ else{
+ fAv=window[winmin].forceAv[groupmin];
+ }
+ f[j]=fAv;
+ }
+ for(j=1;j<opt->bins;++j)
+ pot[j] = pot[j-1] - 0.5*dz*(f[j-1]+f[j]);
+
+ /* cyclic wham: linearly correct possible offset */
+ if (opt->bCycl)
+ {
+ diff=(pot[bins-1]-pot[0])/(bins-1);
+ for(j=1;j<opt->bins;++j)
+ pot[j]-=j*diff;
+ }
+ if (opt->verbose)
+ {
+ fp=xvgropen("pmfintegrated.xvg","PMF from force integration","z","PMF [kJ/mol]",opt->oenv);
+ for(j=0;j<opt->bins;++j)
+ fprintf(fp,"%g %g\n",(j+0.5)*dz+opt->min,pot[j]);
+ ffclose(fp);
+ printf("verbose mode: wrote %s with PMF from interated forces\n","pmfintegrated.xvg");
+ }
+
+ /* get initial z=exp(-F[i]/kT) from integrated potential, where F[i] denote the free
+ energy offsets which are usually determined by wham
+ First: turn pot into probabilities:
+ */
+ for(j=0;j<opt->bins;++j)
+ pot[j]=exp(-pot[j]/(8.314e-3*opt->Temperature));
+ calc_z(pot,window,nWindows,opt,TRUE);
+
+ sfree(pot);
+ sfree(f);
+}
+
+
int gmx_wham(int argc,char *argv[])
{
const char *desc[] = {
- "This is an analysis program that implements the Weighted",
- "Histogram Analysis Method (WHAM). It is intended to analyze",
- "output files generated by umbrella sampling simulations to ",
- "compute a potential of mean force (PMF). [PAR]",
- "At present, three input modes are supported:[BR]",
- "[TT]*[tt] With option [TT]-it[tt], the user provides a file which contains the",
- " filenames of the umbrella simulation run-input files (tpr files),",
- " AND, with option -ix, a file which contains filenames of",
- " the pullx mdrun output files. The tpr and pullx files must",
- " be in corresponding order, i.e. the first tpr created the",
- " first pullx, etc.[BR]",
- "[TT]*[tt] Same as the previous input mode, except that the the user",
- " provides the pull force ouput file names (pullf.xvg) with option -if.",
- " From the pull force the position in the ubrella potential is",
- " computed. This does not work with tabulated umbrella potentials.",
- "[TT]*[tt] With option [TT]-ip[tt], the user provides filenames of (gzipped) pdo files, i.e.",
- " the gromacs 3.3 umbrella output files. If you have some unusual",
- " reaction coordinate you may also generate your own pdo files and",
- " feed them with the -ip option into to g_wham. The pdo file header",
- " must be similar to the folowing:[BR]",
- "[TT]# UMBRELLA 3.0[BR]",
- "# Component selection: 0 0 1[BR]",
- "# nSkip 1[BR]",
- "# Ref. Group 'TestAtom'[BR]",
- "# Nr. of pull groups 2[BR]",
- "# Group 1 'GR1' Umb. Pos. 5.0 Umb. Cons. 1000.0[BR]",
- "# Group 2 'GR2' Umb. Pos. 2.0 Umb. Cons. 500.0[BR]",
- "#####[tt][BR]",
- " Nr of pull groups, umbrella positions, force constants, and names",
- " may (of course) differ. Following the header, a time column and",
- " a data columns for each pull group follow (i.e. the displacement",
- " with respect to the umbrella center). Up to four pull groups are possible",
- " at present.[PAR]",
- "By default, the output files are[BR]",
- " [TT]-o[tt] PMF output file[BR]",
- " [TT]-hist[tt] histograms output file[PAR]",
- "The umbrella potential is assumed to be harmonic and the force constants are ",
- "read from the tpr or pdo files. If a non-harmonic umbrella force was applied ",
- "a tabulated potential can be provied with -tab.[PAR]",
- "WHAM OPTIONS[PAR]",
- " [TT]-bins[tt] Nr of bins used in analysis[BR]",
- " [TT]-temp[tt] Temperature in the simulations[BR]",
- " [TT]-tol[tt] Stop iteration if profile (probability) changed less than tolerance[BR]",
- " [TT]-auto[tt] Automatic determination of boudndaries[BR]",
- " [TT]-min,-max[tt] Boundaries of the profile [BR]",
- "The data points which are used ",
- "to compute the profile can be restricted with options -b, -e, and -dt. ",
- "Play particularly with -b to ensure sufficient equilibration in each ",
- "umbrella window![PAR]",
- "With -log (default) the profile is written in energy units, otherwise (-nolog) as ",
- "probability. The unit can be specified with -unit. With energy output, ",
- "the energy in the first bin is defined to be zero. If you want the free energy at a different ",
- "position to be zero, choose with -zprof0 (useful with bootstrapping, see below).[PAR]",
- "For cyclic (or periodic) reaction coordinates (dihedral angle, channel PMF",
- "without osmotic gradient), -cycl is useful.[BR]",
- "[TT]-cycl yes[tt] min and max are assumed to",
- "be neighboring points and histogram points outside min and max are mapped into ",
- "the interval [min,max] (compare histogram output). [BR]",
- "[TT]-cycl weighted[tt] First, a non-cyclic profile is computed. Subsequently, ",
- "periodicity is enforced by adding corrections dG(i) between neighboring bins",
- "i and i+1. The correction is chosen proportional to 1/[n(i)*n(i+1)]^alpha, where",
- "n(i) denotes the total nr of data points in bin i as collected from all histograms.",
- "alpha is defined with -alpha. The corrections are written to the file defined by -wcorr.",
- " (Compare Hub and de Groot, PNAS 105:1198 (2008))[PAR]",
- "ERROR ANALYSIS[BR]",
- "Statistical errors may be estimated with bootstrap analysis. Use it with care, ",
- "otherwise the statistical error may be substantially undererstimated !![BR]",
- "[TT]-nBootstrap[tt] defines the nr of bootstraps. Two bootstrapping modes are supported.[BR]",
- "[TT]-histbs[tt] Complete histograms are considered as independent data points (default). For each",
- "bootstrap, N histograms are randomly chosen from the N given histograms (allowing duplication).",
- "To avoid gaps without data along the reaction coordinate blocks of histograms (-histbs-block)",
- "may be defined. In that case, the given histograms are divided into blocks and ",
- "only histograms within each block are mixed. Note that the histograms",
- "within each block must be representative for all possible histograms, otherwise the",
- "statistical error is undererstimated![BR]",
- "[TT]-nohistbs[tt] The given histograms are used to generate new random histograms,",
- "such that the generated data points are distributed according the given histograms. The number",
- "of points generated for each bootstrap histogram can be controlled with -bs-dt.",
- "Note that one data point should be generated for each *independent* point in the given",
- "histograms. With the long autocorrelations in MD simulations, this procedure may ",
- "easily understimate the error![BR]",
- "Bootstrapping output:[BR]",
- "[TT]-bsres[tt] Average profile and standard deviations[BR]",
- "[TT]-bsprof[tt] All bootstrapping profiles[BR]",
- "With [TT]-vbs[tt] (verbose bootstrapping), the histograms of each bootstrap are written, and, ",
- "with [TT]-nohistBS[tt], the cummulants of the histogram.",
+ "This is an analysis program that implements the Weighted",
+ "Histogram Analysis Method (WHAM). It is intended to analyze",
+ "output files generated by umbrella sampling simulations to ",
+ "compute a potential of mean force (PMF). [PAR] ",
+ "At present, three input modes are supported.[BR]",
+ "[TT]*[tt] With option [TT]-it[tt], the user provides a file which contains the[BR]",
+ " file names of the umbrella simulation run-input files (tpr files),[BR]",
+ " AND, with option [TT]-ix[tt], a file which contains file names of [BR]",
+ " the pullx mdrun output files. The tpr and pullx files must [BR]",
+ " be in corresponding order, i.e. the first tpr created the [BR]",
+ " first pullx, etc.[BR]",
+ "[TT]*[tt] Same as the previous input mode, except that the the user [BR]",
+ " provides the pull force output file names (pullf.xvg) with option [TT]-if[tt].[BR]",
+ " From the pull force the position in the umbrella potential is [BR]",
+ " computed. This does not work with tabulated umbrella potentials.[BR]"
+ "[TT]*[tt] With option [TT]-ip[tt], the user provides file names of (gzipped) pdo files, i.e.[BR]",
+ " the gromacs 3.3 umbrella output files. If you have some unusual[BR]"
+ " reaction coordinate you may also generate your own pdo files and [BR]",
+ " feed them with the [TT]-ip[tt] option into to g_wham. The pdo file header [BR]",
+ " must be similar to the following:[BR]",
+ "[TT]# UMBRELLA 3.0[BR]",
+ "# Component selection: 0 0 1[BR]",
+ "# nSkip 1[BR]",
+ "# Ref. Group 'TestAtom'[BR]",
+ "# Nr. of pull groups 2[BR]",
+ "# Group 1 'GR1' Umb. Pos. 5.0 Umb. Cons. 1000.0[BR]",
+ "# Group 2 'GR2' Umb. Pos. 2.0 Umb. Cons. 500.0[BR]",
+ "#####[tt][BR]",
+ "Nr of pull groups, umbrella positions, force constants, and names ",
+ "may (of course) differ. Following the header, a time column and ",
+ "a data columns for each pull group follows (i.e. the displacement",
+ "with respect to the umbrella center). Up to four pull groups are possible ",
+ "per pdo file at present.[PAR]",
+ "By default, the output files are[BR]",
+ " [TT]-o[tt] PMF output file[BR]",
+ " [TT]-hist[tt] histograms output file[BR]",
+ "Always check whether the histograms sufficiently overlap![PAR]",
+ "The umbrella potential is assumed to be harmonic and the force constants are ",
+ "read from the tpr or pdo files. If a non-harmonic umbrella force was applied ",
+ "a tabulated potential can be provided with [TT]-tab[tt].[PAR]",
+ "WHAM OPTIONS[BR]------------[BR]",
+ " [TT]-bins[tt] Nr of bins used in analysis[BR]",
+ " [TT]-temp[tt] Temperature in the simulations[BR]",
+ " [TT]-tol[tt] Stop iteration if profile (probability) changed less than tolerance[BR]",
+ " [TT]-auto[tt] Automatic determination of boundaries[BR]",
+ " [TT]-min,-max[tt] Boundaries of the profile [BR]",
+ "The data points which are used ",
+ "to compute the profile can be restricted with options [TT]-b[tt], [TT]-e[tt], and [TT]-dt[tt]. ",
+ "Play particularly with [TT]-b[tt] to ensure sufficient equilibration in each ",
+ "umbrella window![PAR]",
+ "With [TT]-log[tt] (default) the profile is written in energy units, otherwise ([TT]-nolog[tt]) as ",
+ "probability. The unit can be specified with [TT]-unit[tt]. With energy output, ",
+ "the energy in the first bin is defined to be zero. If you want the free energy at a different ",
+ "position to be zero, choose with [TT]-zprof0[tt] (useful with bootstrapping, see below).[PAR]",
+ "For cyclic (or periodic) reaction coordinates (dihedral angle, channel PMF",
+ "without osmotic gradient), the option [TT]-cycl[tt] is useful. g_wham will make use of the ",
+ "periodicity of the system and generate a periodic PMF. The first and the last bin of the",
+ "reaction coordinate will assumed be be neighbors[PAR]",
+ "Option [TT]-sym[tt] symmetrizes the profile around z=0 before output (useful for membrane etc.)[PAR]",
+ "AUTOCORRELATIONS[BR]----------------[BR]",
+ "With [TT]-ac[tt], g_wham estimates the integrated autocorrelation time (IACT) tau for each ",
+ "umbrella window and weights the respective window with 1/[1+2*tau/dt]. The IACTs are written ",
+ "to the file defined with [TT]-oiact[tt]. In verbose mode, all autocorrelation functions (ACFs) are",
+ "written to hist_autocorr.xvg. Because the IACTs can be severely underestimated in case of ",
+ "limited sampling, option [TT]-acsig[tt] allows to smooth the IACTs along the reaction coordinate ",
+ "with a Gaussian (sigma provided with [TT]-acsig[tt], see output in iact.xvg). Note that the ",
+ "IACTs are estimated by simple integration of the ACFs while the ACFs are larger 0.05.",
+ "If you prefer to compute the IACTs by a more sophisticated (but possibly less robust) method ",
+ "such as fitting to a double exponential, you can compute the IACTs with g_analyze and provide",
+ "them to g_wham with the file iact-in.dat (option [TT]-iiact[tt]). iact-in.dat should contain ",
+ "one line per input file (pdo or pullx/f file) and one column per pull group in the respective file.[PAR]"
+ "ERROR ANALYSIS[BR]--------------[BR]",
+ "Statistical errors may be estimated with bootstrap analysis. Use it with care, ",
+ "otherwise the statistical error may be substantially underestimated !![BR]",
+ "More background and examples for the bootstrap technique can be found in ",
+ "Hub, de Groot and Van der Spoel, JCTC (2010)[BR]",
+ "-nBootstrap defines the nr of bootstraps (use, e.g., 100). Four bootstrapping methods are supported and ",
+ "selected with [TT]-bs-method[tt].[BR]",
+ " (1) [TT]b-hist[tt] Default: complete histograms are considered as independent data points, and ",
+ " the bootstrap is carried out by assigning random weights to the histograms (\"Bayesian bootstrap\").",
+ " Note that each point along the reaction coordinate",
+ "must be covered by multiple independent histograms (e.g. 10 histograms), otherwise the ",
+ "statistical error is underestimated![BR]",
+ " (2) [TT]hist[tt] Complete histograms are considered as independent data points. For each",
+ "bootstrap, N histograms are randomly chosen from the N given histograms (allowing duplication, i.e. ",
+ "sampling with replacement).",
+ "To avoid gaps without data along the reaction coordinate blocks of histograms ([TT]-histbs-block[tt])",
+ "may be defined. In that case, the given histograms are divided into blocks and ",
+ "only histograms within each block are mixed. Note that the histograms",
+ "within each block must be representative for all possible histograms, otherwise the",
+ "statistical error is underestimated![BR]",
+ " (3) [TT]traj[tt] The given histograms are used to generate new random trajectories,",
+ "such that the generated data points are distributed according the given histograms ",
+ "and properly autocorrelated. The ",
+ "autocorrelation time (ACT) for each window must be known, so use [TT]-ac[tt] or provide the ACT",
+ "with [TT]-iiact[TT]. If the ACT of all windows are identical (and known), you can also ",
+ "provide them with [TT]-bs-tau[tt]. Note that this method may severely underestimate the error ",
+ "in case of limited sampling, that is if individual histograms do not represent the complete",
+ "phase space at the respective positions.[BR]",
+ " (4) [TT]traj-gauss[tt] The same as Method [TT]traj[tt], but the trajectories are not bootstrapped ",
+ "from the umbrella histograms but from Gaussians with the average and width of the umbrella ",
+ "histograms. That method yields similar error estimates like method [TT]traj[tt].[BR]"
+ "Bootstrapping output:[BR]",
+ " [TT]-bsres[tt] Average profile and standard deviations[BR]",
+ " [TT]-bsprof[tt] All bootstrapping profiles[BR]",
+ "With [TT]-vbs[tt] (verbose bootstrapping), the histograms of each bootstrap are written, and, ",
+ "with bootstrap method [TT]traj[tt], the cumulative distribution functions of the histograms.",
};
- static t_UmbrellaOptions opt;
- static gmx_bool bHistOnly=FALSE;
-
const char *en_unit[]={NULL,"kJ","kCal","kT",NULL};
- const char *en_unit_label[]={"","E (kJ mol\\S-1\\N)","E (kcal mol\\S-1\\N)","E (kT)",};
- const char *en_cycl[]={NULL,"no","yes","weighted",NULL};
-
+ const char *en_unit_label[]={"","E (kJ mol\\S-1\\N)","E (kcal mol\\S-1\\N)","E (kT)",NULL};
+ const char *en_bsMethod[]={ NULL,"b-hist", "hist", "traj", "traj-gauss", NULL };
+
+ static t_UmbrellaOptions opt;
+
t_pargs pa[] = {
- { "-min", FALSE, etREAL, {&opt.min},
- "Minimum coordinate in profile"},
- { "-max", FALSE, etREAL, {&opt.max},
- "Maximum coordinate in profile"},
- { "-auto", FALSE, etBOOL, {&opt.bAuto},
- "determine min and max automatically"},
- { "-bins",FALSE, etINT, {&opt.bins},
- "Number of bins in profile"},
- { "-temp", FALSE, etREAL, {&opt.Temperature},
- "Temperature"},
- { "-tol", FALSE, etREAL, {&opt.Tolerance},
- "Tolerance"},
- { "-v", FALSE, etBOOL, {&opt.verbose},
- "verbose mode"},
- { "-b", FALSE, etREAL, {&opt.tmin},
- "first time to analyse (ps)"},
- { "-e", FALSE, etREAL, {&opt.tmax},
- "last time to analyse (ps)"},
- { "-dt", FALSE, etREAL, {&opt.dt},
- "Analyse only every dt ps"},
- { "-histonly", FALSE, etBOOL, {&bHistOnly},
- "Write histograms and exit"},
- { "-boundsonly", FALSE, etBOOL, {&opt.bBoundsOnly},
- "Determine min and max and exit (with -auto)"},
- { "-log", FALSE, etBOOL, {&opt.bLog},
- "Calculate the log of the profile before printing"},
- { "-unit", FALSE, etENUM, {en_unit},
- "energy unit in case of log output" },
- { "-zprof0", FALSE, etREAL, {&opt.zProf0},
- "Define profile to 0.0 at this position (with -log)"},
- { "-cycl", FALSE, etENUM, {en_cycl},
- "Create cyclic/periodic profile. Assumes min and max are the same point."},
- { "-alpha", FALSE, etREAL, {&opt.alpha},
- "for '-cycl weighted', set parameter alpha"},
- { "-flip", FALSE, etBOOL, {&opt.bFlipProf},
- "Combine halves of profile (not supported)"},
- { "-hist-eq", FALSE, etBOOL, {&opt.bHistEq},
- "Enforce equal weight for all histograms. (Non-Weighed-HAM)"},
- { "-nBootstrap", FALSE, etINT, {&opt.nBootStrap},
- "nr of bootstraps to estimate statistical uncertainty" },
- { "-bs-dt", FALSE, etREAL, {&opt.dtBootStrap},
- "timestep for synthetic bootstrap histograms (ps). Ensure independent data points!"},
- { "-bs-seed", FALSE, etINT, {&opt.bsSeed},
- "seed for bootstrapping. (-1 = use time)"},
- { "-histbs", FALSE, etBOOL, {&opt.bHistBootStrap},
- "In bootstrapping, consider complete histograms as one data point. "
- "Accounts better for long autocorrelations."},
- { "-histbs-block", FALSE, etINT, {&opt.histBootStrapBlockLength},
- "when mixin histograms only mix within blocks of -histBS_block."},
- { "-vbs", FALSE, etBOOL, {&opt.bs_verbose},
- "verbose bootstrapping. Print the cummulants and a histogram file for each bootstrap."},
+ { "-min", FALSE, etREAL, {&opt.min},
+ "Minimum coordinate in profile"},
+ { "-max", FALSE, etREAL, {&opt.max},
+ "Maximum coordinate in profile"},
+ { "-auto", FALSE, etBOOL, {&opt.bAuto},
+ "determine min and max automatically"},
+ { "-bins",FALSE, etINT, {&opt.bins},
+ "Number of bins in profile"},
+ { "-temp", FALSE, etREAL, {&opt.Temperature},
+ "Temperature"},
+ { "-tol", FALSE, etREAL, {&opt.Tolerance},
+ "Tolerance"},
+ { "-v", FALSE, etBOOL, {&opt.verbose},
+ "verbose mode"},
+ { "-b", FALSE, etREAL, {&opt.tmin},
+ "first time to analyse (ps)"},
+ { "-e", FALSE, etREAL, {&opt.tmax},
+ "last time to analyse (ps)"},
+ { "-dt", FALSE, etREAL, {&opt.dt},
+ "Analyse only every dt ps"},
+ { "-histonly", FALSE, etBOOL, {&opt.bHistOnly},
+ "Write histograms and exit"},
+ { "-boundsonly", FALSE, etBOOL, {&opt.bBoundsOnly},
+ "Determine min and max and exit (with -auto)"},
+ { "-log", FALSE, etBOOL, {&opt.bLog},
+ "Calculate the log of the profile before printing"},
+ { "-unit", FALSE, etENUM, {en_unit},
+ "energy unit in case of log output" },
+ { "-zprof0", FALSE, etREAL, {&opt.zProf0},
+ "Define profile to 0.0 at this position (with -log)"},
+ { "-cycl", FALSE, etBOOL, {&opt.bCycl},
+ "Create cyclic/periodic profile. Assumes min and max are the same point."},
+ { "-sym", FALSE, etBOOL, {&opt.bSym},
+ "symmetrize profile around z=0"},
+ { "-hist-eq", FALSE, etBOOL, {&opt.bHistEq},
+ "HIDDENEnforce equal weight for all histograms. (Non-Weighed-HAM)"},
+ { "-ac", FALSE, etBOOL, {&opt.bCalcTauInt},
+ "calculate integrated autocorrelation times and use in wham"},
+ { "-acsig", FALSE, etREAL, {&opt.sigSmoothIact},
+ "Smooth autocorrelation times along reaction coordinate with Gaussian of this sigma"},
+ { "-ac-trestart", FALSE, etREAL, {&opt.acTrestart},
+ "When computing autocorrelation functions, restart computing every .. (ps)"},
+ { "-acred", FALSE, etBOOL, {&opt.bAllowReduceIact},
+ "HIDDENWhen smoothing the ACTs, allow to reduce ACTs. Otherwise, only increase ACTs "
+ "during smoothing"},
+ { "-nBootstrap", FALSE, etINT, {&opt.nBootStrap},
+ "nr of bootstraps to estimate statistical uncertainty (e.g., 200)" },
+ { "-bs-method", FALSE, etENUM, {en_bsMethod},
+ "bootstrap method" },
+ { "-bs-tau", FALSE, etREAL, {&opt.tauBootStrap},
+ "Autocorrelation time (ACT) assumed for all histograms. Use option -ac if ACT is unknown."},
+ { "-bs-seed", FALSE, etINT, {&opt.bsSeed},
+ "seed for bootstrapping. (-1 = use time)"},
+ { "-histbs-block", FALSE, etINT, {&opt.histBootStrapBlockLength},
+ "when mixing histograms only mix within blocks of -histbs-block."},
+ { "-vbs", FALSE, etBOOL, {&opt.bs_verbose},
+ "verbose bootstrapping. Print the CDFs and a histogram file for each bootstrap."},
+ { "-stepout", FALSE, etINT, {&opt.stepchange},
+ "HIDDENWrite maximum change every ... (set to 1 with -v)"},
+ { "-updateContr", FALSE, etINT, {&opt.stepUpdateContrib},
+ "HIDDENUpdate table with significan contributions to WHAM every ... iterations"},
};
-
+
t_filenm fnm[] = {
- { efDAT, "-ix","pullx-files",ffOPTRD}, /* wham input: pullf.xvg's and tprs */
- { efDAT, "-if","pullf-files",ffOPTRD}, /* wham input: pullf.xvg's and tprs */
- { efDAT, "-it","tpr-files",ffOPTRD}, /* wham input: tprs */
- { efDAT, "-ip","pdo-files",ffOPTRD}, /* wham input: pdo files (gmx3 style) */
- { efXVG, "-o", "profile", ffWRITE }, /* output file for profile */
- { efXVG, "-hist","histo", ffWRITE}, /* output file for histograms */
- { efXVG, "-bsres","bsResult", ffOPTWR}, /* average and errors of bootstrap analysis */
- { efXVG, "-bsprof","bsProfs", ffOPTWR}, /* output file for bootstrap profiles */
- { efDAT, "-tab","umb-pot",ffOPTRD}, /* Tabulated umbrella potential (if not harmonic) */
- { efXVG, "-wcorr","cycl-corr",ffOPTRD}, /* Corrections to profile in case -cycl weighted */
+ { efDAT, "-ix","pullx-files",ffOPTRD}, /* wham input: pullf.xvg's and tprs */
+ { efDAT, "-if","pullf-files",ffOPTRD}, /* wham input: pullf.xvg's and tprs */
+ { efDAT, "-it","tpr-files",ffOPTRD}, /* wham input: tprs */
+ { efDAT, "-ip","pdo-files",ffOPTRD}, /* wham input: pdo files (gmx3 style) */
+ { efXVG, "-o", "profile", ffWRITE }, /* output file for profile */
+ { efXVG, "-hist","histo", ffWRITE}, /* output file for histograms */
+ { efXVG, "-oiact","iact",ffOPTWR}, /* writing integrated autocorrelation times */
+ { efDAT, "-iiact","iact-in",ffOPTRD}, /* reading integrated autocorrelation times */
+ { efXVG, "-bsres","bsResult", ffOPTWR}, /* average and errors of bootstrap analysis */
+ { efXVG, "-bsprof","bsProfs", ffOPTWR}, /* output file for bootstrap profiles */
+ { efDAT, "-tab","umb-pot",ffOPTRD}, /* Tabulated umbrella potential (if not harmonic) */
};
-
+
int i,j,l,nfiles,nwins,nfiles2;
t_UmbrellaHeader header;
t_UmbrellaWindow * window=NULL;
char **fninTpr,**fninPull,**fninPdo;
const char *fnPull;
FILE *histout,*profout;
- char ylabel[256],title[256];
- output_env_t oenv;
+ char ylabel[256],title[256];
+
+#define NFILE asize(fnm)
+
+ CopyRight(stderr,argv[0]);
opt.bins=200;
opt.verbose=FALSE;
- opt.cycl=enCycl_no;
+ opt.bHistOnly=FALSE;
+ opt.bCycl=FALSE;
opt.tmin=50;
opt.tmax=1e20;
opt.dt=0.0;
- opt.bShift=TRUE;
- opt.nBootStrap=0;
- opt.dtBootStrap=0.0;
- opt.bsSeed=-1;
- opt.bHistBootStrap=TRUE;
- opt.histBootStrapBlockLength=12;
- opt.zProfZero=0.0;
- opt.bWeightedCycl=FALSE;
- opt.alpha=2;
- opt.bHistOutOnly=FALSE;
opt.min=0;
opt.max=0;
- opt.bLog=TRUE;
- opt.unit=en_kJ;
- opt.zProf0=0.0;
+ opt.bAuto=TRUE;
+
+ /* bootstrapping stuff */
opt.nBootStrap=0;
+ opt.bsMethod=bsMethod_hist;
+ opt.tauBootStrap=0.0;
opt.bsSeed=-1;
- opt.bHistBootStrap=TRUE;
opt.histBootStrapBlockLength=8;
opt.bs_verbose=FALSE;
+
+ opt.bLog=TRUE;
+ opt.unit=en_kJ;
+ opt.zProf0=0.;
opt.Temperature=298;
- opt.bFlipProf=FALSE;
opt.Tolerance=1e-6;
- opt.bAuto=TRUE;
opt.bBoundsOnly=FALSE;
+ opt.bSym=FALSE;
+ opt.bCalcTauInt=FALSE;
+ opt.sigSmoothIact=0.0;
+ opt.bAllowReduceIact=TRUE;
+ opt.bInitPotByIntegration=TRUE;
+ opt.acTrestart=1.0;
+ opt.stepchange=100;
+ opt.stepUpdateContrib=100;
-
-#define NFILE asize(fnm)
-
- CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_BE_NICE,
- NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
-
+ NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&opt.oenv);
+
opt.unit=nenum(en_unit);
- opt.cycl=nenum(en_cycl);
+ opt.bsMethod=nenum(en_bsMethod);
opt.bProf0Set=opt2parg_bSet("-zprof0", asize(pa), pa);
-
+
opt.bTab=opt2bSet("-tab",NFILE,fnm);
opt.bPdo=opt2bSet("-ip",NFILE,fnm);
opt.bTpr=opt2bSet("-it",NFILE,fnm);
opt.bPullx=opt2bSet("-ix",NFILE,fnm);
opt.bPullf=opt2bSet("-if",NFILE,fnm);
+ opt.bTauIntGiven=opt2bSet("-iiact",NFILE,fnm);
if (opt.bTab && opt.bPullf)
gmx_fatal(FARGS,"Force input does not work with tabulated potentials. "
- "Provide pullx.xvg or pdo files!");
+ "Provide pullx.xvg or pdo files!");
-#define BOOLXOR(a,b) ( ((!(a))&&(b)) || ((a)&&(!(b))))
- if (!opt.bPdo && !BOOLXOR(opt.bPullx,opt.bPullf))
+#define WHAMBOOLXOR(a,b) ( ((!(a))&&(b)) || ((a)&&(!(b))))
+ if (!opt.bPdo && !WHAMBOOLXOR(opt.bPullx,opt.bPullf))
gmx_fatal(FARGS,"Give either pullx (-ix) OR pullf (-if) data. Not both.");
if ( !opt.bPdo && !(opt.bTpr || opt.bPullf || opt.bPullx))
gmx_fatal(FARGS,"g_wham supports three input modes, pullx, pullf, or pdo file input."
- "\n\n Check g_wham -h !");
-
+ "\n\n Check g_wham -h !");
+
opt.fnPdo=opt2fn("-ip",NFILE,fnm);
opt.fnTpr=opt2fn("-it",NFILE,fnm);
opt.fnPullf=opt2fn("-if",NFILE,fnm);
opt.bAuto=FALSE;
}
+ if (opt.bTauIntGiven && opt.bCalcTauInt)
+ gmx_fatal(FARGS,"Either read (option -iiact) or calculate (option -ac) the\n"
+ "the autocorrelation times. Not both.");
+
+ if (opt.tauBootStrap>0.0 && opt2parg_bSet("-ac",asize(pa), pa))
+ gmx_fatal(FARGS,"Either compute autocorrelation times (ACTs) (option -ac) or "
+ "provide it with -bs-tau for bootstrapping. Not Both.\n");
+ if (opt.tauBootStrap>0.0 && opt2bSet("-iiact",NFILE,fnm))
+ gmx_fatal(FARGS,"Either provide autocorrelation times (ACTs) with file iact-in.dat "
+ "(option -iiact) or define all ACTs with -bs-tau for bootstrapping\n. Not Both.");
+
+
/* Reading gmx4 pull output and tpr files */
if (opt.bTpr || opt.bPullf || opt.bPullx)
{
read_wham_in(opt.fnTpr,&fninTpr,&nfiles,&opt);
-
+
fnPull=opt.bPullf ? opt.fnPullf : opt.fnPullx;
read_wham_in(fnPull,&fninPull,&nfiles2,&opt);
printf("Found %d tpr and %d pull %s files in %s and %s, respectively\n",
- nfiles,nfiles2,opt.bPullf ? "force" : "position",opt.fnTpr,fnPull);
+ nfiles,nfiles2,opt.bPullf ? "force" : "position",opt.fnTpr,fnPull);
if (nfiles!=nfiles2)
gmx_fatal(FARGS,"Found %d file names in %s, but %d in %s\n",nfiles,
- opt.fnTpr,nfiles2,fnPull);
- read_tpr_pullxf_files(fninTpr,fninPull,nfiles, &header, &window, &opt);
+ opt.fnTpr,nfiles2,fnPull);
+ window=initUmbrellaWindows(nfiles);
+ read_tpr_pullxf_files(fninTpr,fninPull,nfiles, &header, window, &opt);
}
else
- {
- /* reading pdo files */
+ { /* reading pdo files */
read_wham_in(opt.fnPdo,&fninPdo,&nfiles,&opt);
printf("Found %d pdo files in %s\n",nfiles,opt.fnPdo);
- read_pdo_files(fninPdo,nfiles, &header, &window, &opt);
+ window=initUmbrellaWindows(nfiles);
+ read_pdo_files(fninPdo,nfiles, &header, window, &opt);
}
- nwins=nfiles;
+ nwins=nfiles;
/* enforce equal weight for all histograms? */
if (opt.bHistEq)
/* write histograms */
histout=xvgropen(opt2fn("-hist",NFILE,fnm),"Umbrella histograms",
- "z","count",oenv);
- for(l=0;l<opt.bins;++l)
+ "z","count",opt.oenv);
+ for(l=0;l<opt.bins;++l)
{
fprintf(histout,"%e\t",(double)(l+0.5)/opt.bins*(opt.max-opt.min)+opt.min);
- for(i=0;i<nwins;++i)
- {
- for(j=0;j<window[i].nPull;++j)
+ for(i=0;i<nwins;++i)
+ {
+ for(j=0;j<window[i].nPull;++j)
{
fprintf(histout,"%e\t",window[i].Histo[j][l]);
}
fprintf(histout,"\n");
}
ffclose(histout);
- if (bHistOnly)
+ printf("Wrote %s\n",opt2fn("-hist",NFILE,fnm));
+ if (opt.bHistOnly)
{
printf("Wrote histograms to %s, now exiting.\n",opt2fn("-hist",NFILE,fnm));
return 0;
/* Using tabulated umbrella potential */
if (opt.bTab)
setup_tab(opt2fn("-tab",NFILE,fnm),&opt);
-
- setup_acc_wham(window,nwins,&opt);
+
+ /* Integrated autocorrelation times provided ? */
+ if (opt.bTauIntGiven)
+ readIntegratedAutocorrelationTimes(window,nwins,&opt,opt2fn("-iiact",NFILE,fnm));
+
+ /* Compute integrated autocorrelation times */
+ if (opt.bCalcTauInt)
+ calcIntegratedAutocorrelationTimes(window,nwins,&opt,opt2fn("-oiact",NFILE,fnm));
+
+ /* calc average and sigma for each histogram
+ (maybe required for bootstrapping. If not, this is fast anyhow) */
+ if (opt.nBootStrap && opt.bsMethod==bsMethod_trajGauss)
+ averageSigma(window,nwins,&opt);
+
+ /* Get initial potential by simple integration */
+ if (opt.bInitPotByIntegration)
+ guessPotByIntegration(window,nwins,&opt,0);
+
+ /* Check if complete reaction coordinate is covered */
+ checkReactionCoordinateCovered(window,nwins,&opt);
/* Calculate profile */
- snew(profile,opt.bins);
- opt.stepchange=(opt.verbose)? 1 : 100;
+ snew(profile,opt.bins);
+ if (opt.verbose)
+ opt.stepchange=1;
i=0;
- do {
+ do
+ {
+ if ( (i%opt.stepUpdateContrib) == 0)
+ setup_acc_wham(profile,window,nwins,&opt);
if (maxchange<opt.Tolerance)
{
bExact=TRUE;
if (((i%opt.stepchange) == 0 || i==1) && !i==0)
printf("\t%4d) Maximum change %e\n",i,maxchange);
i++;
- } while( (maxchange=calc_z(profile, window, nwins, &opt,bExact)) > opt.Tolerance || !bExact);
+ } while ( (maxchange=calc_z(profile, window, nwins, &opt,bExact)) > opt.Tolerance || !bExact);
printf("Converged in %d iterations. Final maximum change %g\n",i,maxchange);
+ /* calc error from Kumar's formula */
+ /* Unclear how the error propagates along reaction coordinate, therefore
+ commented out */
+ /* calc_error_kumar(profile,window, nwins,&opt); */
+
/* Write profile in energy units? */
if (opt.bLog)
{
strcpy(ylabel,"Density of states");
strcpy(title,"Density of states");
}
- /* Force cyclic profile by wheighted correction? */
- if (opt.cycl==enCycl_weighted)
- cyclicProfByWeightedCorr(profile,window,nwins,&opt,TRUE,
- opt2fn("-wcorr",NFILE,fnm),oenv);
+
+ /* symmetrize profile around z=0? */
+ if (opt.bSym)
+ symmetrizeProfile(profile,&opt);
- profout=xvgropen(opt2fn("-o",NFILE,fnm),title,"z",ylabel,oenv);
+ /* write profile or density of states */
+ profout=xvgropen(opt2fn("-o",NFILE,fnm),title,"z",ylabel,opt.oenv);
for(i=0;i<opt.bins;++i)
- fprintf(profout,"%e\t%e\n",
- (double)(i+0.5)/opt.bins*(opt.max-opt.min)+opt.min,profile[i]);
+ fprintf(profout,"%e\t%e\n",(double)(i+0.5)/opt.bins*(opt.max-opt.min)+opt.min,profile[i]);
ffclose(profout);
printf("Wrote %s\n",opt2fn("-o",NFILE,fnm));
-
+
/* Bootstrap Method */
if (opt.nBootStrap)
- do_bootstrapping(opt2fn("-bsres",NFILE,fnm),opt2fn("-bsprof",NFILE,fnm),
- opt2fn("-hist",NFILE,fnm),
- ylabel, profile, window, nwins, &opt,oenv);
+ do_bootstrapping(opt2fn("-bsres",NFILE,fnm),opt2fn("-bsprof",NFILE,fnm),
+ opt2fn("-hist",NFILE,fnm),
+ ylabel, profile, window, nwins, &opt);
+
+ sfree(profile);
+ freeUmbrellaWindows(window,nfiles);
+
+ printf("\nIn case you use results from g_wham for a publication, please cite:\n");
+ please_cite(stdout,"Hub2010");
thanx(stderr);
return 0;
static gmx_bool check_have_atoms(t_atoms *atoms, char *string)
{
if ( atoms==NULL ) {
- printf("Can not process '%s' without atoms info\n", string);
+ printf("Can not process '%s' without atom info, use option -f\n", string);
return FALSE;
} else
return TRUE;
extern t_dlist *mk_dlist(FILE *log,
t_atoms *atoms, int *nlist,
gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, int maxchi,
- int r0,int naa,char **aa);
+ int r0, gmx_residuetype_t rt);
extern void pr_dlist(FILE *fp,int nl,t_dlist dl[],real dt, int printtype,
gmx_bool bPhi, gmx_bool bPsi,gmx_bool bChi,gmx_bool bOmega, int maxchi);
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff