set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
-# PROJECT_VERSION should have the following structure:
-# 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!
-# REGRESSIONTEST_VERSION and REGRESSIONTEST_BRANCH should always be
-# defined.
-set(PROJECT_VERSION "5.0.5-dev")
-# If this is a released tarball, "-dev" will not be present in
-# PROJECT_VERSION, and REGRESSIONTEST_VERSION specifies the version
-# number of the regressiontest tarball against which the code tarball
-# can be tested. This will be the version of the last patch release.
-set(REGRESSIONTEST_VERSION "5.0.5-dev")
-# The MD5 checksum of the regressiontest tarball. Only used if "-dev"
-# is not present in the PROJECT_VERSION
-set(REGRESSIONTEST_MD5SUM "81e8ff1600495ce2a57706dca9d73482")
-# If this is not a released tarball, "-dev" will be present in
-# PROJECT_VERSION, and REGRESSIONTEST_BRANCH specifies the name of the
-# gerrit.gromacs.org branch whose HEAD can test this code, *if* this
-# code contains all recent fixes from the corresponding code branch.
-set(REGRESSIONTEST_BRANCH "refs/heads/release-5-0")
-
-set(CUSTOM_VERSION_STRING ""
- CACHE STRING "Custom version string (if empty, use hard-coded default)")
-mark_as_advanced(CUSTOM_VERSION_STRING)
-if (CUSTOM_VERSION_STRING)
- set(PROJECT_VERSION ${CUSTOM_VERSION_STRING})
-endif()
-set(LIBRARY_SOVERSION 0)
-set(LIBRARY_VERSION ${LIBRARY_SOVERSION}.0.0)
-# It is a bit irritating, but this has to be set separately for now!
-SET(CPACK_PACKAGE_VERSION_MAJOR "5")
-SET(CPACK_PACKAGE_VERSION_MINOR "0")
-#SET(CPACK_PACKAGE_VERSION_PATCH "0")
-
-# The numerical gromacs version. It is 40600 for 4.6.0.
-# The #define GMX_VERSION in gromacs/version.h is set to this value.
-math(EXPR NUM_VERSION
- "${CPACK_PACKAGE_VERSION_MAJOR}*10000 + ${CPACK_PACKAGE_VERSION_MINOR}*100")
-if(CPACK_PACKAGE_VERSION_PATCH)
- math(EXPR NUM_VERSION
- "${NUM_VERSION} + ${CPACK_PACKAGE_VERSION_PATCH}")
-endif()
-
-# The API version tracks the numerical Gromacs version (for now).
-# It is potentially different from the Gromacs version in the future, if
-# the programs/libraries diverge from the presumably more stable API.
-# The #define GMX_API_VERSION in version.h is set to this value to
-# provide backward compatibility of software written against the Gromacs API.
-set(API_VERSION ${NUM_VERSION})
+# Set up common version variables, as well as general information about
+# the build tree (whether the build is from a source package or from a git
+# repository). Also declares a few functions that will be used for generating
+# version info files later.
+include(gmxVersionInfo)
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND UNIX)
set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
endif()
include(gmxBuildTypeReference)
+include(gmxBuildTypeProfile)
include(gmxBuildTypeTSAN)
include(gmxBuildTypeASAN)
include(gmxBuildTypeReleaseWithAssert)
if(NOT CMAKE_BUILD_TYPE)
- set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference RelWithAssert." FORCE)
+ set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference RelWithAssert Profile." FORCE)
# There's no need to offer a user the choice of ThreadSanitizer
# Set the possible values of build type for cmake-gui
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
- "MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert")
+ "MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert" "Profile")
endif()
if(CMAKE_CONFIGURATION_TYPES)
# Add appropriate GROMACS-specific build types for the Visual
"List of configuration types"
FORCE)
endif()
-set(build_types_with_explicit_flags RELEASE DEBUG RELWITHDEBINFO RELWITHASSERT MINSIZEREL)
+set(build_types_with_explicit_flags RELEASE DEBUG RELWITHDEBINFO RELWITHASSERT MINSIZEREL PROFILE)
-enable_language(C)
-enable_language(CXX)
set_property(GLOBAL PROPERTY FIND_LIBRARY_USE_LIB64_PATHS ON)
-set(CPACK_PACKAGE_NAME "gromacs")
-set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
-set(CPACK_SOURCE_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}")
-set(CPACK_PACKAGE_VENDOR "gromacs.org")
-set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
-set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
-# Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this...
-set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
-set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt")
-set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$;\\\\.gitattributes;")
-set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
-# CPack source archives include only the directories we list here.
-# This variable is a list of pairs of names of source and destination
-# directories. Most of these are used for content GROMACS generates as
-# part of the configuration or build.
-set(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/src/programs/completion;src/programs/completion;${CMAKE_BINARY_DIR}/docs/man/man1;docs/man/man1;${CMAKE_BINARY_DIR}/docs/man/man7;docs/man/man7;${CMAKE_BINARY_DIR}/docs/old-html/final;docs/old-html/final;${CMAKE_BINARY_DIR}/docs/install-guide/final;/")
-set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org")
-set(CPACK_GMX_BUILD_HELP "${GMX_BUILD_HELP}") #Works even though GMX_BUILD_HELP is defined later because it is off by default.
-
-#must come after all cpack settings!
-include(CPack)
-
# Set a default valgrind suppression file.
# This unfortunately needs to duplicate information from CTest to work as
# expected...
"File that contains suppressions for the memory checker")
include(CTest)
-set(SOURCE_IS_GIT_REPOSITORY OFF)
-set(SOURCE_IS_SOURCE_DISTRIBUTION OFF)
-if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
- set(SOURCE_IS_GIT_REPOSITORY ON)
-endif()
-if(NOT EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
- set(SOURCE_IS_SOURCE_DISTRIBUTION ON)
-endif()
+include(gmxCPackUtilities)
+gmx_cpack_init()
+
+# Variables that accumulate stuff influencing the installed headers
+set(INSTALLED_HEADER_INCLUDE_DIRS "")
+set(INSTALLED_HEADER_DEFINITIONS "")
########################################################################
# Check and warn if cache generated on a different host is being reused
set(REQUIRED_CUDA_COMPUTE_CAPABILITY 2.0)
include(gmxManageGPU)
-if(GMX_CPU_ACCELERATION)
- # Stay compatible with old Jenkins command line options for specific SIMD acceleration
- set(GMX_SIMD "${GMX_CPU_ACCELERATION}" CACHE STRING "SIMD instruction set level and compiler optimization" FORCE)
- message("You set GMX_CPU_ACCELERATION, which is deprecated, and will be removed in a later version of GROMACS. It is replaced by GMX_SIMD. For now, copying the value from GMX_CPU_ACCELERATION to GMX_SIMD.")
- # TODO remove all references to GMX_CPU_ACCELERATION in master branch
-endif()
-
-if(NOT GMX_TARGET_MIC)
- include(gmxDetectSimd)
- gmx_detect_simd(GMX_SUGGESTED_SIMD)
-else()
- set(GMX_SUGGESTED_SIMD "None")
-endif()
+include(gmxDetectSimd)
+gmx_detect_simd(GMX_SUGGESTED_SIMD)
gmx_option_multichoice(
GMX_SIMD
"SIMD instruction set for CPU kernels and compiler optimization"
"${GMX_SUGGESTED_SIMD}"
- None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 IBM_QPX Sparc64_HPC_ACE Reference)
+ None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 AVX_512F AVX_512ER MIC ARM_NEON ARM_NEON_ASIMD IBM_QPX IBM_VMX IBM_VSX Sparc64_HPC_ACE Reference)
+
+if(GMX_TARGET_MIC)
+ set(GMX_FFT_LIBRARY_DEFAULT "mkl")
+else()
+ set(GMX_FFT_LIBRARY_DEFAULT "fftw3")
+endif()
gmx_option_multichoice(
GMX_FFT_LIBRARY
"FFT library"
- "fftw3"
+ "${GMX_FFT_LIBRARY_DEFAULT}"
fftw3 mkl "fftpack[built-in]")
gmx_dependent_option(
GMX_BUILD_OWN_FFTW
option(GMX_USE_TNG "Use the TNG library for trajectory I/O" ON)
-option(GMX_GIT_VERSION_INFO "Generate git version information" ${SOURCE_IS_GIT_REPOSITORY})
-mark_as_advanced(GMX_GIT_VERSION_INFO)
-
-if(UNIX)
- option(GMX_SYMLINK_OLD_BINARY_NAMES "Create symbolic links for pre-5.0 binary names" ON)
-endif()
option(GMX_BUILD_MDRUN_ONLY "Build and install only the mdrun binary" OFF)
option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
endif()
-
-set(PKG_CFLAGS "")
if(GMX_DOUBLE)
add_definitions(-DGMX_DOUBLE)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
+ list(APPEND INSTALLED_HEADER_DEFINITIONS "-DGMX_DOUBLE")
if(GMX_RELAXED_DOUBLE_PRECISION)
add_definitions(-DGMX_RELAXED_DOUBLE_PRECISION)
endif()
endif()
if(GMX_SOFTWARE_INVSQRT)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
+ list(APPEND INSTALLED_HEADER_DEFINITIONS "-DGMX_SOFTWARE_INVSQRT")
endif()
-if(WIN32 AND NOT CYGWIN)
+if(WIN32)
list(APPEND GMX_EXTRA_LIBRARIES "wsock32")
add_definitions(-DGMX_HAVE_WINSOCK)
endif()
check_include_files(sched.h HAVE_SCHED_H)
check_include_files(regex.h HAVE_POSIX_REGEX)
- check_include_file_cxx(regex HAVE_CXX11_REGEX)
# TODO: It could be nice to inform the user if no regex support is found,
# as selections won't be fully functional.
check_function_exists(rsqrt HAVE_RSQRT)
check_function_exists(rsqrtf HAVE_RSQRTF)
check_function_exists(sqrtf HAVE_SQRTF)
+check_function_exists(nice HAVE_NICE)
include(CheckLibraryExists)
check_library_exists(m sqrt "" HAVE_LIBM)
check_library_exists(rt clock_gettime "" HAVE_CLOCK_GETTIME)
+check_library_exists(m feenableexcept "" HAVE_FEENABLEEXCEPT)
include(TestSchedAffinity)
test_sched_affinity(HAVE_SCHED_AFFINITY)
include(TestBigEndian)
test_big_endian(GMX_INTEGER_BIG_ENDIAN)
+set(GMX_USE_NICE 0)
+if (HAVE_UNISTD_H AND HAVE_NICE)
+ set(GMX_USE_NICE 1)
+endif()
+
# Management of GROMACS options for specific toolchains should go
# here. Because the initial settings for some of the main options have
# already happened, but things like library detection and MPI compiler
# Find external packages #
########################################################################
+ # TNG wants zlib if it is available. And static libxml2 might have a dependency
+ find_package(ZLIB QUIET)
+ include(gmxTestZLib)
+ gmx_test_zlib(HAVE_ZLIB)
+
# Unconditionally find the package, as it is also required for unit
# tests. This exports LIBXML2_FOUND, which we should not use because
# it does not tell us that linking will succeed. Instead, we test that
if(GMX_THREAD_MPI)
# enable MPI functions
tmpi_enable()
- set(GMX_MPI 1)
set(MPI_IN_PLACE_EXISTS 1)
endif()
# If atomics are manually disabled a define is needed because atomics.h doesn't depend on config.h
set(GMX_CYGWIN 1)
endif()
-if(WIN32 AND NOT CYGWIN)
+if(WIN32)
set(GMX_NATIVE_WINDOWS 1)
# This makes windows.h not declare min/max as macros that would break
# C++ code using std::min/std::max.
add_definitions(-DNOMINMAX)
endif()
-# only bother with finding git and using version.h if the source is a git repo
-if(GMX_GIT_VERSION_INFO)
- if (NOT SOURCE_IS_GIT_REPOSITORY)
- message(FATAL_ERROR
- "Cannot generate git version information from source tree not under git. "
- "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
- endif()
- # We need at least git v1.5.3 be able to parse git's date output. If not
- # found or the version is too small, we can't generate version information.
- find_package(Git)
-
- if(NOT GIT_FOUND OR GIT_VERSION_STRING VERSION_LESS "1.5.3")
- message(FATAL_ERROR
- "No compatible git version found (>= 1.5.3 required). "
- "Won't be able to generate development version information. "
- "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
- endif()
-endif()
-
# Detect boost unless GMX_EXTERNAL_BOOST is explicitly OFF
# Used for default if GMX_EXTERNAL_BOOST is not defined (first CMake pass)
if(NOT DEFINED GMX_EXTERNAL_BOOST OR GMX_EXTERNAL_BOOST)
+ if(DEFINED Boost_INCLUDE_DIR)
+ set(Boost_FIND_QUIETLY TRUE)
+ endif()
find_package(Boost 1.44.0)
if(Boost_FOUND AND Boost_VERSION VERSION_LESS "104400")
set(Boost_FOUND FALSE)
"Either set GMX_BUILD_UNITTESTS=OFF or tell CMake how to find a working version of libxml2.")
endif()
- if(GMX_USE_TNG AND NOT GMX_EXTERNAL_TNG)
- # TNG wants zlib if it is available
- find_package(ZLIB QUIET)
- include(gmxTestZLib)
- gmx_test_zlib(HAVE_ZLIB)
- endif()
-########################################################################
-# Generate development version info for cache
-########################################################################
-# set(GEN_VERSION_INFO_INTERNAL "ON")
-# include(gmxGenerateVersionString)
--
########################################################################
# Our own GROMACS tests
########################################################################
include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include)
# Required for config.h, maybe should only be set in src/CMakeLists.txt
include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
-# Required for gmx_header_config_gen.h to be found before installation
-include_directories(BEFORE ${CMAKE_BINARY_DIR}/src/gromacs/utility)
-# Required for now to make old code compile
-include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
include(gmxTestInlineASM)
gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
set(EXTRA_CXX_FLAGS "${EXTRA_CXX_FLAGS} ${GMX_CXX11_FLAGS}")
endif()
+ # Now we can test for CXX11_REGEX include file
+ check_include_file_cxx(regex HAVE_CXX11_REGEX)
include(gmxTestXDR)
gmx_test_xdr(GMX_SYSTEM_XDR)
# Process SIMD instruction settings
##################################################
# This checks what flags to add in order to
-# support the SIMD instructions we need, and sets
-# correct defines for the SIMD instructions supported.
-include(gmxTestSimd)
-gmx_test_simd()
-
+# support the SIMD instructions we need, it sets
+# correct defines for the SIMD instructions supported,
+# and adds advanced options to control accuracy
+# for SIMD math operations.
+include(gmxManageSimd)
+gmx_manage_simd()
# Process QM/MM Settings
if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
set(GMX_USE_PLUGINS OFF)
if(GMX_LOAD_PLUGINS)
- if(CYGWIN OR NOT WIN32)
+ if(NOT WIN32)
# Native Windows does not have, nor need dlopen
- # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
include(gmxTestdlopen)
gmx_test_dlopen(HAVE_DLOPEN)
endif()
# so, should we use plug-ins?
- if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
+ if(WIN32 OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
if(NOT VMD_QUIETLY)
MESSAGE(STATUS "Using dynamic plugins (e.g VMD-supported file formats)")
endif()
if (GMX_NACL)
list(APPEND GMX_EXTRA_LIBRARIES nosys)
set(GMX_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lnosys")
- set(GMX_NO_NICE 1)
+ # TODO: Is this still necessary with the check for its presence?
+ set(GMX_USE_NICE 0)
set(GMX_NO_RENAME 1)
endif()
mark_as_advanced(GMX_NACL)
include_directories(${COREWRAP_INCLUDE_DIR})
endif()
-option(GMX_BUILD_HELP "Build man pages, HTML help, and completions automatically (requires that compiled binaries can be executed on the build host)" OFF)
+# Value of GMX_BUILD_HELP=AUTO tries to generate things, but will only
+# produce warnings if that fails.
+set(build_help_default AUTO)
+if (SOURCE_IS_SOURCE_DISTRIBUTION OR CMAKE_CROSSCOMPILING)
+ set(build_help_default OFF)
+endif()
+gmx_option_trivalue(GMX_BUILD_HELP "Build completions automatically (requires that compiled binaries can be executed on the build host) and install man pages if built (requires building the 'man' target manually)" ${build_help_default})
mark_as_advanced(GMX_BUILD_HELP)
-if (GMX_BUILD_HELP AND SOURCE_IS_SOURCE_DISTRIBUTION AND
- "${CMAKE_CURRENT_SOURCE_DIR}" STREQUAL "${CMAKE_CURRENT_BINARY_DIR}")
-
+if (GMX_BUILD_HELP AND SOURCE_IS_SOURCE_DISTRIBUTION AND BUILD_IS_INSOURCE)
message(FATAL_ERROR
- "Rebuilding HTML and man pages is not supported for in-source "
- "builds from a source distribution. "
+ "Rebuilding shell completions or man pages is not supported for "
+ "in-source builds from a source distribution. "
"Set GMX_BUILD_HELP=OFF or do an out-of-source build to proceed.")
endif()
set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} ${OpenMP_LINKER_FLAGS})
set(GMX_SHARED_LINKER_FLAGS ${GMX_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS})
endif()
-set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
########################################################################
# Specify install locations
# These variables are used internally to provide a central location for
# customizing the install locations.
-set(LIB_INSTALL_DIR ${GMX_LIB_INSTALL_DIR})
-set(BIN_INSTALL_DIR bin)
-set(DATA_INSTALL_DIR share/${GMX_DATA_INSTALL_DIR})
-set(MAN_INSTALL_DIR share/man)
-set(INCL_INSTALL_DIR include)
-
-# These variables get written into config.h for use in finding the data
+set(LIB_INSTALL_DIR ${GMX_LIB_INSTALL_DIR})
+set(BIN_INSTALL_DIR bin)
+# This variable also gets written into config.h for use in finding the data
# directories.
-set(GMXLIB_SEARCH_DIR share/${GMX_DATA_INSTALL_DIR}/top)
-set(GMXLIB_FALLBACK ${CMAKE_INSTALL_PREFIX}/${DATA_INSTALL_DIR}/top)
+set(DATA_INSTALL_DIR share/${GMX_DATA_INSTALL_DIR})
+set(MAN_INSTALL_DIR share/man)
+# If the nesting level wrt. the installation root is changed,
+# gromacs-config.cmake.cmakein needs to be adapted.
+set(CMAKE_INSTALL_DIR share/cmake)
+# TODO: Make GMXRC adapt if this is changed
+set(PKGCONFIG_INSTALL_DIR ${LIB_INSTALL_DIR}/pkgconfig)
+set(INCL_INSTALL_DIR include)
+
+list(APPEND INSTALLED_HEADER_INCLUDE_DIRS ${INCL_INSTALL_DIR})
# Binary and library suffix options
include(gmxManageSuffixes)
if(GMX_EXTERNAL_BOOST)
include_directories(${Boost_INCLUDE_DIRS})
- set(PKG_CFLAGS "${PKG_CFLAGS} -I${Boost_INCLUDE_DIRS}")
+ list(APPEND INSTALLED_HEADER_INCLUDE_DIRS ${Boost_INCLUDE_DIRS})
else()
include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/boost)
+ list(APPEND INSTALLED_HEADER_INCLUDE_DIRS ${INCL_INSTALL_DIR}/gromacs/external/boost)
+ list(APPEND INSTALLED_HEADED_DEFINITIONS "-DBOOST_NO_TYPEID")
# typeid not supported for minimal internal version
# (would add significant amount of code)
add_definitions(-DBOOST_NO_TYPEID)
- # TODO: Propagate the above settings to the installed CMakeFiles.txt template
- # (from share/template/)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DBOOST_NO_TYPEID -I${CMAKE_INSTALL_PREFIX}/${INCL_INSTALL_DIR}/gromacs/external/boost")
if (NOT GMX_BUILD_MDRUN_ONLY)
install(DIRECTORY ${CMAKE_SOURCE_DIR}/src/external/boost/boost
DESTINATION ${INCL_INSTALL_DIR}/gromacs/external/boost
add_subdirectory(tests)
endif()
+gmx_cpack_write_config()
+
# Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
# Don't bother the user after the first configure pass.
if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
#
# This file is part of the GROMACS molecular simulation package.
#
- # Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ # Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
include(CheckCXXSourceCompiles)
MACRO(GMX_TEST_CXX11 VARIABLE FLAG)
- if(WIN32)
+ if(WIN32 AND NOT MINGW)
set(CXX11_FLAG "/Qstd=c++0x")
elseif(CYGWIN)
set(CXX11_FLAG "-std=gnu++0x") #required for strdup
if(NOT CXXFLAG_STD_CXX0X)
set(CXX11_FLAG "")
endif()
- set(CMAKE_REQUIRED_DEFINITIONS "${CXX11_FLAG}")
+ set(CMAKE_REQUIRED_FLAGS "${CXX11_FLAG}")
check_cxx_source_compiles(
"#include <vector>
#include <memory>
typedef VarList<Tail...> VarListTail;
typedef std::pair<Head, typename VarListTail::ListType> ListType;
};
+class a { explicit operator bool() {return true;} };
int main() {
typedef std::unique_ptr<int> intPointer;
intPointer p(new int(10));
v2.push_back(A()); //requires default move constructor
v2.push_back(A(new int(5))); //detects bug in ICC
}" ${VARIABLE})
- set(CMAKE_REQUIRED_DEFINITIONS "")
+ set(CMAKE_REQUIRED_FLAGS "")
if(${VARIABLE})
set(${FLAG} ${CXX11_FLAG})
endif()
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013,2014, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
\subsection{Modified non-bonded interactions}
\label{sec:mod_nb_int}
In {\gromacs}, the non-bonded potentials can be
- modified by a shift function. The purpose of this is to replace the
+ modified by a shift function, also called a force-switch function,
+ since it switches the force to zero at the cut-off.
+ The purpose of this is to replace the
truncated forces by forces that are continuous and have continuous
derivatives at the \normindex{cut-off} radius. With such forces the
- timestep integration produces much smaller errors and there are no
- such complications as creating charges from dipoles by the truncation
- procedure. In fact, by using shifted forces there is no need for
- charge groups in the construction of neighbor lists. However, the
- shift function produces a considerable modification of the Coulomb
- potential. Unless the ``missing'' long-range potential is properly
- calculated and added (through the use of PPPM, Ewald, or PME), the
- effect of such modifications must be carefully evaluated. The
- modification of the Lennard-Jones dispersion and repulsion is only
- minor, but it does remove the noise caused by cut-off effects.
+ time integration produces smaller errors. But note that for
+ Lennard-Jones interactions these errors are usually smaller than other errors,
+ such as integration errors at the repulsive part of the potential.
+ For Coulomb interactions we advise against using a shifted potential
+ and for use of a reaction field or a proper long-range method such as PME.
There is {\em no} fundamental difference between a switch function
(which multiplies the potential with a function) and a shift function
the {\em force function} $F(r)$, related to the electrostatic or
van der Waals force acting on particle $i$ by particle $j$ as:
\beq
- \ve{F}_i = c F(r_{ij}) \frac{\rvij}{r_{ij}}
+ \ve{F}_i = c \, F(r_{ij}) \frac{\rvij}{r_{ij}}
\eeq
For pure Coulomb or Lennard-Jones interactions
- $F(r)=F_\alpha(r)=r^{-(\alpha+1)}$.
- The shifted force $F_s(r)$ can generally be written as:
+ $F(r) = F_\alpha(r) = \alpha \, r^{-(\alpha+1)}$.
+ The switched force $F_s(r)$ can generally be written as:
\beq
\begin{array}{rcl}
\vspace{2mm}
\end{array}
\eeq
When $r_1=0$ this is a traditional shift function, otherwise it acts as a
- switch function. The corresponding shifted coulomb potential then reads:
+ switch function. The corresponding shifted potential function then reads:
\beq
- V_s(r_{ij}) = f \Phi_s (r_{ij}) q_i q_j
- \eeq
- where $\Phi(r)$ is the potential function
- \beq
- \Phi_s(r) = \int^{\infty}_r~F_s(x)\, dx
+ V_s(r) = \int^{\infty}_r~F_s(x)\, dx
\eeq
- The {\gromacs} shift function should be smooth at the boundaries, therefore
- the following boundary conditions are imposed on the shift function:
+ The {\gromacs} force switch function should be smooth at the boundaries, therefore
+ the following boundary conditions are imposed on the switch function:
\beq
\begin{array}{rcl}
S(r_1) &=&0 \\
\beq
\begin{array}{rcl}
\vspace{2mm}
- A &~=~& -\displaystyle
+ A &~=~& -\alpha \, \displaystyle
\frac{(\alpha+4)r_c~-~(\alpha+1)r_1} {r_c^{\alpha+2}~(r_c-r_1)^2} \\
- B &~=~& \displaystyle
+ B &~=~& \alpha \, \displaystyle
\frac{(\alpha+3)r_c~-~(\alpha+1)r_1}{r_c^{\alpha+2}~(r_c-r_1)^3}
\end{array}
\eeq
\eeq
and the potential function reads:
\beq
- \Phi(r) = \frac{1}{r^\alpha} - \frac{A}{3} (r-r_1)^3 - \frac{B}{4} (r-r_1)^4 - C
+ V_s(r) = \frac{1}{r^\alpha} - \frac{A}{3} (r-r_1)^3 - \frac{B}{4} (r-r_1)^4 - C
\eeq
where
\beq
C = \frac{1}{r_c^\alpha} - \frac{A}{3} (r_c-r_1)^3 - \frac{B}{4} (r_c-r_1)^4
\eeq
- When $r_1$ = 0, the modified Coulomb force function is
- \beq
- F_s(r) = \frac{1}{r^2} - \frac{5 r^2}{r_c^4} + \frac{4 r^3}{r_c^5}
- \eeq
- which is identical to the {\em \index{parabolic force}}
- function recommended to be used as a short-range function in
- conjunction with a \swapindex{Poisson}{solver}
- for the long-range part~\cite{Berendsen93a}.
- The modified Coulomb potential function is:
- \beq
- \Phi(r) = \frac{1}{r} - \frac{5}{3r_c} + \frac{5r^3}{3r_c^4} - \frac{r^4}{r_c^5}
- \eeq
- See also \figref{shift}.
-
- \begin{figure}
- \centerline{\includegraphics[width=10cm]{plots/shiftf}}
- \caption[The Coulomb Force, Shifted Force and Shift Function
- $S(r)$,.]{The Coulomb Force, Shifted Force and Shift Function $S(r)$,
- using r$_1$ = 2 and r$_c$ = 4.}
- \label{fig:shift}
- \end{figure}
-
\subsection{Modified short-range interactions with Ewald summation}
When Ewald summation\index{Ewald sum} or \seeindex{particle-mesh
Ewald}{PME}\index{Ewald, particle-mesh} is used to calculate the
long-range interactions, the
- short-range Coulomb potential must also be modified, similar to the
- switch function above. In this case the short range potential is given
- by:
+ short-range Coulomb potential must also be modified. Here the potential
+ is switched to (nearly) zero at the cut-off, instead of the force.
+ In this case the short range potential is given by:
\beq
V(r) = f \frac{\mbox{erfc}(\beta r_{ij})}{r_{ij}} q_i q_j,
\eeq
\beq
d_g(\ve{r}_i;\ve{R}_i) = |\ve{r}_i-\ve{R}_i|
\eeq
-{\bfseries Cylinder} ($g=2$): The particle is kept in a cylinder of given radius
-parallel to the $z$-axis. The force from the flat-bottomed potential acts
-towards the axis of the cylinder. The $z$-component of the force is zero.
+{\bfseries Cylinder} ($g=6,7,8$): The particle is kept in a cylinder of given radius
+parallel to the $x$ ($g=6$), $y$ ($g=7$), or $z$-axis ($g=8$). For backwards compatibility, setting
+$g=2$ is mapped to $g=8$ in the code so that old {\tt .tpr} files and topologies work.
+The force from the flat-bottomed potential acts towards the axis of the cylinder.
+The component of the force parallel to the cylinder axis is zero.
+For a cylinder aligned along the $z$-axis:
\beq
d_g(\ve{r}_i;\ve{R}_i) = \sqrt{ (x_i-X_i)^2 + (y_i - Y_i)^2 }
\eeq
\subsubsection{Constraints}
\label{subsubsec:constraints}
-\newcommand{\clam}{C_{\lambda}}
The constraints are formally part of the Hamiltonian, and therefore
they give a contribution to the free energy. In {\gromacs} this can be
calculated using the \normindex{LINCS} or the \normindex{SHAKE} algorithm.
-If we have a number of constraint equations $g_k$:
+If we have $k = 1 \ldots K$ constraint equations $g_k$ for LINCS, then
\beq
-g_k = \ve{r}_{k} - d_{k}
+g_k = |\ve{r}_{k}| - d_{k}
\eeq
-where $\ve{r}_k$ is the distance vector between two particles and
-$d_k$ is the constraint distance between the two particles, we can write
-this using a $\LAM$-dependent distance as
+where $\ve{r}_k$ is the displacement vector between two particles and
+$d_k$ is the constraint distance between the two particles. We can express
+the fact that the constraint distance has a $\LAM$ dependency by
\beq
-g_k = \ve{r}_{k} - \left(\LL d_{k}^A + \LAM d_k^B\right)
+d_k = \LL d_{k}^A + \LAM d_k^B
\eeq
-the contribution $\clam$
-to the Hamiltonian using Lagrange multipliers $\lambda$:
+
+Thus the $\LAM$-dependent constraint equation is
+\beq
+g_k = |\ve{r}_{k}| - \left(\LL d_{k}^A + \LAM d_k^B\right).
+\eeq
+
+The (zero) contribution $G$ to the Hamiltonian from the constraints
+(using Lagrange multipliers $\lambda_k$, which are logically distinct
+from the free-energy $\LAM$) is
\bea
-\clam &=& \sum_k \lambda_k g_k \\
-\dvdl{\clam} &=& \sum_k \lambda_k \left(d_k^B-d_k^A\right)
+G &=& \sum^K_k \lambda_k g_k \\
+\dvdl{G} &=& \frac{\partial G}{\partial d_k} \dvdl{d_k} \\
+ &=& - \sum^K_k \lambda_k \left(d_k^B-d_k^A\right)
\eea
+For SHAKE, the constraint equations are
+\beq
+g_k = \ve{r}_{k}^2 - d_{k}^2
+\eeq
+with $d_k$ as before, so
+\bea
+\dvdl{G} &=& -2 \sum^K_k \lambda_k \left(d_k^B-d_k^A\right)
+\eea
\subsection{Soft-core interactions\index{soft-core interactions}}
\begin{figure}
For both Coulomb and van der Waals interactions there are interaction
type selectors (termed {\tt vdwtype} and {\tt coulombtype}) and two
parameters, for a total of six non-bonded interaction parameters. See
-\secref{mdpopt} for a complete description of these parameters.
+the User Guide for a complete description of these parameters.
The neighbor searching (NS) can be performed using a single-range, or a twin-range
approach. Since the former is merely a special case of the latter, we will
% LocalWords: fc ravdisre nstdisreout dipolar lll ccc orientational MSD const
% LocalWords: orire fitgrp nstorireout Drude intra Noskov et al fecalc coulrf
% LocalWords: polarizabilities parameterized sigeps Ek sc softcore GROMOS NBF
-% LocalWords: hydrogens alkane vdwtype coulombtype mdpopt rlist rcoulomb rvdw
+% LocalWords: hydrogens alkane vdwtype coulombtype rlist rcoulomb rvdw
% LocalWords: nstlist virial funcparm VdW jk jl fvsite fd vsites lcr vsitetop
% LocalWords: vsite lclllll lcl parameterize parameterization enercorr avcsix
% LocalWords: pcorr ecorr totalcoulomb dir fourierspacing ewald rtol Darden gz
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <math.h>
+#include "gmxpre.h"
-/*#define HAVE_NN_LOOPS*/
+#include "config.h"
-#include "gromacs/commandline/pargs.h"
-#include "copyrite.h"
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "physics.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "index.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "gstat.h"
-#include "gromacs/utility/cstringutil.h"
-#include "pbc.h"
-#include "correl.h"
-#include "gmx_ana.h"
-#include "geminate.h"
+#include <math.h>
-#include "gromacs/fileio/futil.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/correlationfunctions/autocorr.h"
+#include "gromacs/correlationfunctions/crosscorr.h"
+#include "gromacs/correlationfunctions/expfit.h"
+#include "gromacs/correlationfunctions/integrate.h"
#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/geminate.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/snprintf.h"
+
+#include "geminate.h"
+
+/*#define HAVE_NN_LOOPS*/
typedef short int t_E;
typedef int t_EEst;
{
int i;
- if (ISDON(datable[id]) || !datable)
+ if (!datable || ISDON(datable[id]))
{
if (ddd->dptr[id] == NOTSET) /* New donor */
{
}
void pbc_correct_gem(rvec dx, matrix box, rvec hbox);
+ void pbc_in_gridbox(rvec dx, matrix box);
static void build_grid(t_hbdata *hb, rvec x[], rvec xshell,
gmx_bool bBox, matrix box, rvec hbox,
{
copy_rvec(x[ad[i]], xtemp);
}
- pbc_correct_gem(x[ad[i]], box, hbox);
- }
- for (m = DIM-1; m >= 0; m--)
- {
- if (TRUE || !hb->bGem)
+ pbc_in_gridbox(x[ad[i]], box);
+
+ for (m = DIM-1; m >= 0; m--)
+ { /* determine grid index of atom */
+ grididx[m] = x[ad[i]][m]*invdelta[m];
+ grididx[m] = (grididx[m]+ngrid[m]) % ngrid[m];
+ }
+ if (hb->bGem)
{
- /* put atom in the box */
- while (x[ad[i]][m] < 0)
- {
- rvec_inc(x[ad[i]], box[m]);
- }
- while (x[ad[i]][m] >= box[m][m])
- {
- rvec_dec(x[ad[i]], box[m]);
- }
+ copy_rvec(xtemp, x[ad[i]]); /* copy back */
}
- /* determine grid index of atom */
- grididx[m] = x[ad[i]][m]*invdelta[m];
- grididx[m] = (grididx[m]+ngrid[m]) % ngrid[m];
- }
- if (hb->bGem)
- {
- copy_rvec(xtemp, x[ad[i]]); /* copy back */
}
+
gx = grididx[XX];
gy = grididx[YY];
gz = grididx[ZZ];
}
}
+ void pbc_in_gridbox(rvec dx, matrix box)
+ {
+ int m;
+ gmx_bool bDone = FALSE;
+ while (!bDone)
+ {
+ bDone = TRUE;
+ for (m = DIM-1; m >= 0; m--)
+ {
+ if (dx[m] < 0)
+ {
+ bDone = FALSE;
+ rvec_inc(dx, box[m]);
+ }
+ if (dx[m] >= box[m][m])
+ {
+ bDone = FALSE;
+ rvec_dec(dx, box[m]);
+ }
+ }
+ }
+ }
+
/* Added argument r2cut, changed contact and implemented
* use of second cut-off.
* - Erik Marklund, June 29, 2006
integral += x1;
}
integral *= dt;
- gmx_ffclose(fp);
+ xvgrclose(fp);
printf("%s lifetime = %.2f ps\n", bContact ? "Contact" : "HB", integral);
printf("Note that the lifetime obtained in this manner is close to useless\n");
printf("Use the -ac option instead and check the Forward lifetime\n");
static void smooth_tail(int n, real t[], real c[], real sigma_c[], real start,
const output_env_t oenv)
{
- FILE *fp;
- real e_1, fitparm[4];
- int i;
+ FILE *fp;
+ real e_1;
+ double fitparm[4];
+ int i;
e_1 = exp(-1);
for (i = 0; (i < n); i++)
fitparm[0] = 10;
}
fitparm[1] = 0.95;
- do_lmfit(n, c, sigma_c, 0, t, start, t[n-1], oenv, bDebugMode(), effnEXP2, fitparm, 0);
+ do_lmfit(n, c, sigma_c, 0, t, start, t[n-1], oenv, bDebugMode(),
+ effnEXP2, fitparm, 0);
}
void analyse_corr(int n, real t[], real ct[], real nt[], real kt[],
static void normalizeACF(real *ct, real *gt, int nhb, int len)
{
- real ct_fac, gt_fac;
+ real ct_fac, gt_fac = 0;
int i;
/* Xu and Berne use the same normalization constant */
ct_fac = 1.0/ct[0];
- gt_fac = (nhb == 0) ? 0 : 1.0/(real)nhb;
+ if (nhb != 0)
+ {
+ gt_fac = 1.0/(real)nhb;
+ }
printf("Normalization for c(t) = %g for gh(t) = %g\n", ct_fac, gt_fac);
for (i = 0; i < len; i++)
fprintf(fp, "%10g %10g %10g %10g %10g\n",
hb->time[j]-hb->time[0], ct[j], cct[j], ght[j], kt[j]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
analyse_corr(nn, hb->time, ct, ght, kt, NULL, NULL, NULL,
fit_start, temp, smooth_tail_start, oenv);
/*set_hb(hb->hbmap[i][j]->h[m],nframes-hb->hbmap[i][j]->n0,HB_NO);*/
}
-static void analyse_donor_props(const char *fn, t_hbdata *hb, int nframes, real t,
- const output_env_t oenv)
+static FILE *open_donor_properties_file(const char *fn,
+ t_hbdata *hb,
+ const output_env_t oenv)
{
- static FILE *fp = NULL;
- const char *leg[] = { "Nbound", "Nfree" };
- int i, j, k, nbound, nb, nhtot;
+ FILE *fp = NULL;
+ const char *leg[] = { "Nbound", "Nfree" };
- if (!fn)
+ if (!fn || !hb)
{
- return;
+ return NULL;
}
- if (!fp)
+
+ fp = xvgropen(fn, "Donor properties", output_env_get_xvgr_tlabel(oenv), "Number", oenv);
+ xvgr_legend(fp, asize(leg), leg, oenv);
+
+ return fp;
+}
+
+static void analyse_donor_properties(FILE *fp, t_hbdata *hb, int nframes, real t)
+{
+ int i, j, k, nbound, nb, nhtot;
+
+ if (!fp || !hb)
{
- fp = xvgropen(fn, "Donor properties", output_env_get_xvgr_tlabel(oenv), "Number", oenv);
- xvgr_legend(fp, asize(leg), leg, oenv);
+ return;
}
nbound = 0;
nhtot = 0;
for (i = 0; i < isize[grp]; i++)
{
fprintf(fp, (i%15) ? " " : "\n");
- fprintf(fp, " %4u", index[grp][i]+1);
+ fprintf(fp, " %4d", index[grp][i]+1);
}
fprintf(fp, "\n");
/*
{
for (j = 0; (j < hb->d.nhydro[i]); j++)
{
- fprintf(fp, " %4u %4u", hb->d.don[i]+1,
+ fprintf(fp, " %4d %4d", hb->d.don[i]+1,
hb->d.hydro[i][j]+1);
}
fprintf(fp, "\n");
if (hb->a.grp[i] == grp)
{
fprintf(fp, (i%15 && !first) ? " " : "\n");
- fprintf(fp, " %4u", hb->a.acc[i]+1);
+ fprintf(fp, " %4d", hb->a.acc[i]+1);
first = FALSE;
}
}
sprintf(as, "%s", mkatomname(atoms, aaa));
if (bContact)
{
- fprintf(fp, " %6u %6u\n", ddd+1, aaa+1);
+ fprintf(fp, " %6d %6d\n", ddd+1, aaa+1);
if (fplog)
{
fprintf(fplog, "%12s %12s\n", ds, as);
{
hhh = hb->d.hydro[i][m];
sprintf(hs, "%s", mkatomname(atoms, hhh));
- fprintf(fp, " %6u %6u %6u\n", ddd+1, hhh+1, aaa+1);
+ fprintf(fp, " %6d %6d %6d\n", ddd+1, hhh+1, aaa+1);
if (fplog)
{
fprintf(fplog, "%12s %12s %12s\n", ds, hs, as);
/* "It is also possible to analyse specific hydrogen bonds with",
"[TT]-sel[tt]. This index file must contain a group of atom triplets",
- "Donor Hydrogen Acceptor, in the following way:[PAR]",
+ "Donor Hydrogen Acceptor, in the following way::",
+ "",
+ "[ selected ]",
+ " 20 21 24",
+ " 25 26 29",
+ " 1 3 6",
+ "",
+ "Note that the triplets need not be on separate lines.",
+ "Each atom triplet specifies a hydrogen bond to be analyzed,",
+ "note also that no check is made for the types of atoms.[PAR]",
*/
- "[TT]",
- "[ selected ][BR]",
- " 20 21 24[BR]",
- " 25 26 29[BR]",
- " 1 3 6[BR]",
- "[tt][BR]",
- "Note that the triplets need not be on separate lines.",
- "Each atom triplet specifies a hydrogen bond to be analyzed,",
- "note also that no check is made for the types of atoms.[PAR]",
-
- "[BB]Output:[bb][BR]",
- "[TT]-num[tt]: number of hydrogen bonds as a function of time.[BR]",
- "[TT]-ac[tt]: average over all autocorrelations of the existence",
- "functions (either 0 or 1) of all hydrogen bonds.[BR]",
- "[TT]-dist[tt]: distance distribution of all hydrogen bonds.[BR]",
- "[TT]-ang[tt]: angle distribution of all hydrogen bonds.[BR]",
- "[TT]-hx[tt]: the number of n-n+i hydrogen bonds as a function of time",
- "where n and n+i stand for residue numbers and i ranges from 0 to 6.",
- "This includes the n-n+3, n-n+4 and n-n+5 hydrogen bonds associated",
- "with helices in proteins.[BR]",
- "[TT]-hbn[tt]: all selected groups, donors, hydrogens and acceptors",
- "for selected groups, all hydrogen bonded atoms from all groups and",
- "all solvent atoms involved in insertion.[BR]",
- "[TT]-hbm[tt]: existence matrix for all hydrogen bonds over all",
- "frames, this also contains information on solvent insertion",
- "into hydrogen bonds. Ordering is identical to that in [TT]-hbn[tt]",
- "index file.[BR]",
- "[TT]-dan[tt]: write out the number of donors and acceptors analyzed for",
- "each timeframe. This is especially useful when using [TT]-shell[tt].[BR]",
- "[TT]-nhbdist[tt]: compute the number of HBonds per hydrogen in order to",
- "compare results to Raman Spectroscopy.",
- "[PAR]",
+
+ "[BB]Output:[bb]",
+ "",
+ " * [TT]-num[tt]: number of hydrogen bonds as a function of time.",
+ " * [TT]-ac[tt]: average over all autocorrelations of the existence",
+ " functions (either 0 or 1) of all hydrogen bonds.",
+ " * [TT]-dist[tt]: distance distribution of all hydrogen bonds.",
+ " * [TT]-ang[tt]: angle distribution of all hydrogen bonds.",
+ " * [TT]-hx[tt]: the number of n-n+i hydrogen bonds as a function of time",
+ " where n and n+i stand for residue numbers and i ranges from 0 to 6.",
+ " This includes the n-n+3, n-n+4 and n-n+5 hydrogen bonds associated",
+ " with helices in proteins.",
+ " * [TT]-hbn[tt]: all selected groups, donors, hydrogens and acceptors",
+ " for selected groups, all hydrogen bonded atoms from all groups and",
+ " all solvent atoms involved in insertion.",
+ " * [TT]-hbm[tt]: existence matrix for all hydrogen bonds over all",
+ " frames, this also contains information on solvent insertion",
+ " into hydrogen bonds. Ordering is identical to that in [TT]-hbn[tt]",
+ " index file.",
+ " * [TT]-dan[tt]: write out the number of donors and acceptors analyzed for",
+ " each timeframe. This is especially useful when using [TT]-shell[tt].",
+ " * [TT]-nhbdist[tt]: compute the number of HBonds per hydrogen in order to",
+ " compare results to Raman Spectroscopy.",
+ "",
"Note: options [TT]-ac[tt], [TT]-life[tt], [TT]-hbn[tt] and [TT]-hbm[tt]",
"require an amount of memory proportional to the total numbers of donors",
"times the total number of acceptors in the selected group(s)."
{ "-smooth", FALSE, etREAL, {&smooth_tail_start},
"If >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/[GRK]tau[grk])" },
{ "-dump", FALSE, etINT, {&nDump},
- "Dump the first N hydrogen bond ACFs in a single [TT].xvg[tt] file for debugging" },
+ "Dump the first N hydrogen bond ACFs in a single [REF].xvg[ref] file for debugging" },
{ "-max_hb", FALSE, etREAL, {&maxnhb},
"Theoretical maximum number of hydrogen bonds used for normalizing HB autocorrelation function. Can be useful in case the program estimates it wrongly" },
{ "-merge", FALSE, etBOOL, {&bMerge},
};
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
/* { efNDX, "-sel", "select", ffOPTRD },*/
{ efXVG, "-num", "hbnum", ffWRITE },
int grp, nabin, nrbin, bin, resdist, ihb;
char **leg;
t_hbdata *hb, *hbptr;
- FILE *fp, *fpins = NULL, *fpnhb = NULL;
+ FILE *fp, *fpins = NULL, *fpnhb = NULL, *donor_properties = NULL;
t_gridcell ***grid;
t_ncell *icell, *jcell, *kcell;
ivec ngrid;
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE, NFILE, fnm, npargs,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, npargs,
ppa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
hb = mk_hbdata(bHBmap, opt2bSet("-dan", NFILE, fnm), bMerge || bContact, bGem, gemmode);
/* get topology */
- read_tpx_top(ftp2fn(efTPX, NFILE, fnm), &ir, box, &natoms, NULL, NULL, NULL, &top);
+ read_tpx_top(ftp2fn(efTPR, NFILE, fnm), &ir, box, &natoms, NULL, NULL, NULL, &top);
snew(grpnames, grNR);
snew(index, grNR);
/*if (bSelected)
snew(donors[gr0D], dons[gr0D].nrd);*/
+ donor_properties = open_donor_properties_file(opt2fn_null("-don", NFILE, fnm), hb, oenv);
+
if (bHBmap)
{
printf("Making hbmap structure...");
#pragma omp barrier
#pragma omp single
{
- if (hb != NULL)
- {
- analyse_donor_props(opt2fn_null("-don", NFILE, fnm), hb, k, t, oenv);
- }
+ analyse_donor_properties(donor_properties, hb, k, t);
}
#pragma omp single
free_grid(ngrid, &grid);
close_trj(status);
+
+ if (donor_properties)
+ {
+ xvgrclose(donor_properties);
+ }
+
if (fpnhb)
{
- gmx_ffclose(fpnhb);
+ xvgrclose(fpnhb);
}
/* Compute maximum possible number of different hbonds */
aver_nhb += hb->nhb[i];
aver_dist += hb->ndist[i];
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
aver_nhb /= nframes;
aver_dist /= nframes;
/* Print HB distance distribution */
{
fprintf(fp, "%10g %10g\n", (i+0.5)*rbin, rdist[i]/(rbin*(real)sum));
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
/* Print HB angle distribution */
{
fprintf(fp, "%10g %10g\n", (i+0.5)*abin, adist[i]/(abin*(real)sum));
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
/* Print HB in alpha-helix */
}
fprintf(fp, "\n");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
if (!bNN)
{
gmx_fatal(FARGS, "Could not initiate t_gemParams params.");
}
}
- gemstring = strdup(gemType[hb->per->gemtype]);
+ gemstring = gmx_strdup(gemType[hb->per->gemtype]);
do_hbac(opt2fn("-ac", NFILE, fnm), hb, nDump,
bMerge, bContact, fit_start, temp, r2cut > 0, smooth_tail_start, oenv,
gemstring, nThreads, NN, bBallistic, bGemFit);
{
t_matrix mat;
int id, ia, hh, x, y;
+ mat.flags = mat.y0 = 0;
if ((nframes > 0) && (hb->nrhb > 0))
{
if (USE_THIS_GROUP(j) )
{
sprintf(buf, "Donors %s", grpnames[j]);
- legnames[i++] = strdup(buf);
+ legnames[i++] = gmx_strdup(buf);
sprintf(buf, "Acceptors %s", grpnames[j]);
- legnames[i++] = strdup(buf);
+ legnames[i++] = gmx_strdup(buf);
}
}
if (i != nleg)
}
fprintf(fp, "\n");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
return 0;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
/* This file is completely threadsafe - please keep it that way! */
+#include "gromacs/legacyheaders/txtdump.h"
+
#include <stdio.h>
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "names.h"
-#include "txtdump.h"
-#include "vec.h"
-#include "macros.h"
-
-#include "gmx_fatal.h"
+#include <stdlib.h>
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
int pr_indent(FILE *fp, int n)
fprintf(fp, "pull-coord %d:\n", c);
PI("group[0]", pcrd->group[0]);
PI("group[1]", pcrd->group[1]);
+ if (pcrd->eGeom == epullgDIRRELATIVE)
+ {
+ PI("group[2]", pcrd->group[2]);
+ PI("group[3]", pcrd->group[3]);
+ }
+ PS("type", EPULLTYPE(pcrd->eType));
+ PS("geometry", EPULLGEOM(pcrd->eGeom));
+ pr_ivec(fp, indent, "dim", pcrd->dim, DIM, TRUE);
pr_rvec(fp, indent, "origin", pcrd->origin, DIM, TRUE);
pr_rvec(fp, indent, "vec", pcrd->vec, DIM, TRUE);
+ PS("start", EBOOL(pcrd->bStart));
PR("init", pcrd->init);
PR("rate", pcrd->rate);
PR("k", pcrd->k);
{
int g;
- PS("pull-geometry", EPULLGEOM(pull->eGeom));
- pr_ivec(fp, indent, "pull-dim", pull->dim, DIM, TRUE);
- PR("pull-r1", pull->cyl_r1);
- PR("pull-r0", pull->cyl_r0);
+ PR("pull-cylinder-r", pull->cylinder_r);
PR("pull-constr-tol", pull->constr_tol);
- PS("pull-print-reference", EBOOL(pull->bPrintRef));
+ PS("pull-print-COM1", EBOOL(pull->bPrintCOM1));
+ PS("pull-print-COM2", EBOOL(pull->bPrintCOM2));
+ PS("pull-print-ref-value", EBOOL(pull->bPrintRefValue));
+ PS("pull-print-components", EBOOL(pull->bPrintComp));
PI("pull-nstxout", pull->nstxout);
PI("pull-nstfout", pull->nstfout);
PI("pull-ngroups", pull->ngroup);
PR("gb-obc-beta", ir->gb_obc_beta);
PR("gb-obc-gamma", ir->gb_obc_gamma);
PR("gb-dielectric-offset", ir->gb_dielectric_offset);
- PS("sa-algorithm", ESAALGORITHM(ir->gb_algorithm));
+ PS("sa-algorithm", ESAALGORITHM(ir->sa_algorithm));
PR("sa-surface-tension", ir->sa_surface_tension);
/* Options for weak coupling algorithms */
PR("wall-ewald-zfac", ir->wall_ewald_zfac);
/* COM PULLING */
- PS("pull", EPULLTYPE(ir->ePull));
- if (ir->ePull != epullNO)
+ PS("pull", EBOOL(ir->bPull));
+ if (ir->bPull)
{
pr_pull(fp, indent, ir->pull);
}
j++;
for (k = 0; k < interaction_function[ftype].nratoms; k++)
{
- (void) fprintf(fp, " %u", *(iatoms++));
+ (void) fprintf(fp, " %d", *(iatoms++));
}
(void) fprintf(fp, "\n");
i += 1+interaction_function[ftype].nratoms;
for (i = 0; i <= block->nr; i++)
{
(void) pr_indent(fp, indent+INDENT);
- (void) fprintf(fp, "%s->index[%d]=%u\n",
+ (void) fprintf(fp, "%s->index[%d]=%d\n",
title, bShowNumbers ? i : -1, block->index[i]);
}
for (i = 0; i < block->nra; i++)
{
(void) pr_indent(fp, indent+INDENT);
- (void) fprintf(fp, "%s->a[%d]=%u\n",
+ (void) fprintf(fp, "%s->a[%d]=%d\n",
title, bShowNumbers ? i : -1, block->a[i]);
}
}
(void) fprintf(fp, "\n");
size = pr_indent(fp, indent+INDENT);
}
- size += fprintf(fp, "%u", block->a[j]);
+ size += fprintf(fp, "%d", block->a[j]);
}
(void) fprintf(fp, "}\n");
start = end;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "toputil.h"
#include <assert.h>
#include <math.h>
#include <string.h>
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "macros.h"
-#include "topdirs.h"
-#include "toputil.h"
-#include "symtab.h"
-#include "gmx_fatal.h"
-#include "gpp_atomtype.h"
/* UTILITIES */
}
else
{
- gmx_fatal(FARGS, "Increase MAXSLEN in include/grompp-impl.h to at least %d,"
+ gmx_fatal(FARGS, "Increase MAXSLEN in the grompp code to at least %d,"
" or shorten your definition of bonds like %s to at most %d",
strlen(s)+1, s, MAXSLEN-1);
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <assert.h>
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "update.h"
-#include "vec.h"
-#include "macros.h"
-#include "physics.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "txtdump.h"
-#include "nrnb.h"
+#include <algorithm>
+
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
-#include "update.h"
-#include "mdrun.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#define NTROTTERPARTS 3
{
/* general routine for both barostat and thermostat nose hoover chains */
- int i, j, mi, mj, jmax;
+ int i, j, mi, mj;
double Ekin, Efac, reft, kT, nd;
double dt;
t_grp_tcstat *tcstat;
{
iQinv = &(MassQ->QPinv[i*nh]);
nd = 1.0; /* THIS WILL CHANGE IF NOT ISOTROPIC */
- reft = max(0.0, opts->ref_t[0]);
+ reft = std::max<real>(0, opts->ref_t[0]);
Ekin = sqr(*veta)/MassQ->Winv;
}
else
iQinv = &(MassQ->Qinv[i*nh]);
tcstat = &ekind->tcstat[i];
nd = opts->nrdf[i];
- reft = max(0.0, opts->ref_t[i]);
+ reft = std::max<real>(0, opts->ref_t[i]);
if (bEkinAveVel)
{
Ekin = 2*trace(tcstat->ekinf)*tcstat->ekinscalef_nhc;
real pscal;
double alpha;
- int i, j, d, n, nwall;
- real T, GW, vol;
- tensor Winvm, ekinmod, localpres;
+ int nwall;
+ real GW, vol;
+ tensor ekinmod, localpres;
/* The heat bath is coupled to a separate barostat, the last temperature group. In the
2006 Tuckerman et al paper., the order is iL_{T_baro} iL {T_part}
* The pressure and compressibility always occur as a product,
* therefore the pressure unit drops out.
*/
- maxl = max(box[XX][XX], box[YY][YY]);
- maxl = max(maxl, box[ZZ][ZZ]);
+ maxl = std::max(box[XX][XX], box[YY][YY]);
+ maxl = std::max(maxl, box[ZZ][ZZ]);
for (d = 0; d < DIM; d++)
{
for (n = 0; n < DIM; n++)
{
int d, n;
real scalar_pressure, xy_pressure, p_corr_z;
- char *ptr, buf[STRLEN];
+ char buf[STRLEN];
/*
* Calculate the scaling matrix mu
t_nrnb *nrnb)
{
ivec *nFreeze = ir->opts.nFreeze;
- int n, d, g = 0;
+ int n, d;
+ int nthreads gmx_unused;
+
+#ifndef __clang_analyzer__
+ // cppcheck-suppress unreadVariable
+ nthreads = gmx_omp_nthreads_get(emntUpdate);
+#endif
/* Scale the positions */
+#pragma omp parallel for num_threads(nthreads) schedule(static)
for (n = start; n < start+nr_atoms; n++)
{
- if (cFREEZE)
+ int g;
+
+ if (cFREEZE == NULL)
+ {
+ g = 0;
+ }
+ else
{
g = cFREEZE[n];
}
if ((opts->tau_t[i] > 0) && (T > 0.0))
{
- reft = max(0.0, opts->ref_t[i]);
+ reft = std::max<real>(0, opts->ref_t[i]);
lll = sqrt(1.0 + (dt/opts->tau_t[i])*(reft/T-1.0));
- ekind->tcstat[i].lambda = max(min(lll, 1.25), 0.8);
+ ekind->tcstat[i].lambda = std::max<real>(std::min<real>(lll, 1.25), 0.8);
}
else
{
}
if (randomize[gc])
{
- if (ir->etc == etcANDERSEN)
+ if (ir->etc == etcANDERSENMASSIVE)
{
+ /* Randomize particle always */
bRandomize = TRUE;
}
else
{
+ /* Randomize particle probabilistically */
double uniform[2];
gmx_rng_cycle_2uniform(step*2, ng, ir->andersen_seed, RND_SEED_ANDERSEN, uniform);
for (i = 0; (i < opts->ngtc); i++)
{
- reft = max(0.0, opts->ref_t[i]);
+ reft = std::max<real>(0, opts->ref_t[i]);
oldvxi = vxi[i];
vxi[i] += dt*MassQ->Qinv[i]*(ekind->tcstat[i].Th - reft);
xi[i] += dt*(oldvxi + vxi[i])*0.5;
t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno)
{
- int n, i, j, d, ntgrp, ngtc, gc = 0;
+ int n, i, d, ngtc, gc = 0;
t_grp_tcstat *tcstat;
t_grpopts *opts;
gmx_int64_t step_eff;
- real ecorr, pcorr, dvdlcorr;
- real bmass, qmass, reft, kT, dt, nd;
- tensor dumpres, dumvir;
+ real dt;
double *scalefac, dtc;
int *trotter_seq;
- rvec sumv = {0, 0, 0}, consk;
+ rvec sumv = {0, 0, 0};
gmx_bool bCouple;
if (trotter_seqno <= ettTSEQ2)
extern void init_npt_masses(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bInit)
{
- int n, i, j, d, ntgrp, ngtc, nnhpres, nh, gc = 0;
- t_grp_tcstat *tcstat;
+ int n, i, j, d, ngtc, nh;
t_grpopts *opts;
- real ecorr, pcorr, dvdlcorr;
- real bmass, qmass, reft, kT, dt, ndj, nd;
- tensor dumpres, dumvir;
+ real reft, kT, ndj, nd;
opts = &(ir->opts); /* just for ease of referencing */
ngtc = ir->opts.ngtc;
- nnhpres = state->nnhpres;
nh = state->nhchainlength;
if (ir->eI == eiMD)
{
if ((opts->tau_t[i] > 0) && (opts->ref_t[i] > 0))
{
- reft = max(0.0, opts->ref_t[i]);
+ reft = std::max<real>(0, opts->ref_t[i]);
nd = opts->nrdf[i];
kT = BOLTZ*reft;
for (j = 0; j < nh; j++)
}
else
{
- reft = 0.0;
for (j = 0; j < nh; j++)
{
MassQ->Qinv[i*nh+j] = 0.0;
int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bTrotter)
{
- int n, i, j, d, ntgrp, ngtc, nnhpres, nh, gc = 0;
- t_grp_tcstat *tcstat;
+ int i, j, nnhpres, nh;
t_grpopts *opts;
- real ecorr, pcorr, dvdlcorr;
- real bmass, qmass, reft, kT, dt, ndj, nd;
- tensor dumpres, dumvir;
+ real bmass, qmass, reft, kT;
int **trotter_seq;
opts = &(ir->opts); /* just for ease of referencing */
- ngtc = state->ngtc;
nnhpres = state->nnhpres;
nh = state->nhchainlength;
/* barostat temperature */
if ((ir->tau_p > 0) && (opts->ref_t[0] > 0))
{
- reft = max(0.0, opts->ref_t[0]);
+ reft = std::max<real>(0, opts->ref_t[0]);
kT = BOLTZ*reft;
for (i = 0; i < nnhpres; i++)
{
real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ)
{
- int i, j, nd, ndj, bmass, qmass, ngtcall;
- real ener_npt, reft, eta, kT, tau;
+ int i, j;
+ real nd, ndj;
+ real ener_npt, reft, kT;
double *ivxi, *ixi;
double *iQinv;
- real vol, dbaro, W, Q;
+ real vol;
int nh = state->nhchainlength;
ener_npt = 0;
ivxi = &state->nhpres_vxi[i*nh];
ixi = &state->nhpres_xi[i*nh];
iQinv = &(MassQ->QPinv[i*nh]);
- reft = max(ir->opts.ref_t[0], 0); /* using 'System' temperature */
+ reft = std::max<real>(ir->opts.ref_t[0], 0.0); /* using 'System' temperature */
kT = BOLTZ * reft;
for (j = 0; j < nh; j++)
iQinv = &(MassQ->Qinv[i*nh]);
nd = ir->opts.nrdf[i];
- reft = max(ir->opts.ref_t[i], 0);
+ reft = std::max<real>(ir->opts.ref_t[i], 0);
kT = BOLTZ * reft;
- if (nd > 0)
+ if (nd > 0.0)
{
if (IR_NVT_TROTTER(ir))
{
}
else
{
- ndj = 1;
+ ndj = 1.0;
}
ener_npt += ndj*ixi[j]*kT;
}
case eannPERIODIC:
/* calculate time modulo the period */
pert = opts->anneal_time[i][npoints-1];
- n = t / pert;
+ n = static_cast<int>(t / pert);
thist = t - n*pert; /* modulo time */
/* Make sure rounding didn't get us outside the interval */
if (fabs(thist-pert) < GMX_REAL_EPS*100)
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff