option(GMX_COOL_QUOTES "Enable Gromacs cool quotes" ON)
mark_as_advanced(GMX_COOL_QUOTES)
-if(GMX_GPU OR GMX_FORCE_CXX)
+if(GMX_GPU OR GMX_FORCE_CXX OR GMX_OPENMM)
enable_language(CXX)
endif()
set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
string(TOUPPER ${GMX_FFT_LIBRARY} GMX_FFT_LIBRARY)
set(PKG_FFT "")
set(PKG_FFT_LIBS "")
+set(MKL_LIBRARIES_FORMAT_DESCRIPTION "Use full paths to library files, in the right order, and separated by semicolons.")
+set(MKL_LIBRARIES "" CACHE STRING "List of libraries for linking to MKL. Only used with GMX_FFT_LIBRARY=mkl. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
+set(MKL_INCLUDE_DIR "" CACHE PATH "Path to mkl.h (non-inclusive). Only used with GMX_FFT_LIBRARY=mkl.")
+mark_as_advanced(FORCE MKL_LIBRARIES)
+mark_as_advanced(FORCE MKL_INCLUDE_DIR)
if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
if(GMX_DOUBLE)
set(FFTW fftw)
endif()
elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
-# MESSAGE(STATUS "Using external FFT library - Intel MKL")
- find_package(MKL REQUIRED)
- include_directories(${MKL_INCLUDE_DIR})
- set(FFT_LIBRARIES ${MKL_LIBRARIES})
- set(PKG_FFT_LIBS ${MKL_LIBRARIES})
+ MESSAGE(STATUS "Using external FFT library - Intel MKL")
+
+ # Intel 11 and up makes life somewhat easy if you just want to use
+ # all their stuff. It's not easy if you only want some of their
+ # stuff...
+ if (CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_GREATER "11")
+ # The next line takes care of everything for MKL
+ if (WIN32)
+ set(FFT_LINKER_FLAGS "/Qmkl=sequential")
+ else()
+ set(FFT_LINKER_FLAGS "-mkl=sequential")
+ endif()
+ set(MKL_ERROR_MESSAGE "Make sure you have configured your compiler so that ${FFT_LINKER_FLAGS} will work.")
+ else()
+ # The user will have to provide the set of magic libraries in
+ # MKL_LIBRARIES, which we cache (non-advanced), so that they
+ # don't have to keep specifying it, and can easily see that
+ # CMake is still using that information.
+ set(MKL_LIBRARIES "${MKL_LIBRARIES}" CACHE STRING "User-specified libraries for linking to MKL")
+ mark_as_advanced(CLEAR MKL_LIBRARIES)
+ include_directories(${MKL_INCLUDE_DIR})
+ mark_as_advanced(CLEAR MKL_INCLUDE_DIR)
+ set(FFT_LIBRARIES "${MKL_LIBRARIES}")
+ set(MKL_ERROR_MESSAGE "The include path to mkl.h in MKL_INCLUDE_DIR, and the link libraries in MKL_LIBRARIES=${MKL_LIBRARIES} need to match what the MKL documentation says you need for your system. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
+ # Convert the semi-colon separated list to a list of
+ # command-line linker arguments so that code using our
+ # pkgconfig setup can use it.
+ string(REGEX REPLACE ";" " " PKG_FFT_LIBS "${MKL_LIBRARIES}")
+ endif()
+
+ # Check MKL works. If we were in a non-global scope, we wouldn't
+ # have to play nicely.
+ set(old_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
+ set(CMAKE_REQUIRED_FLAGS "${FFT_LINKER_FLAGS}")
+ set(old_CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
+ set(CMAKE_REQUIRED_LIBRARIES "${FFT_LIBRARIES}")
+
+ check_function_exists(DftiCreateDescriptor TEST_MKL)
+
+ set(CMAKE_REQUIRED_FLAGS "${old_CMAKE_REQUIRED_FLAGS}")
+ set(CMAKE_REQUIRED_LIBRARIES "${old_CMAKE_REQUIRED_LIBRARIES}")
+
+ if(NOT TEST_MKL)
+ # Hack to help the user vary MKL settings until they work.
+ # TODO Make this logic more useful.
+ unset(TEST_MKL CACHE)
+ message(FATAL_ERROR "Linking with MKL was requested, but was not successful. ${MKL_ERROR_MESSAGE}")
+ endif()
+ # Set variables to signal that we have MKL available and should use it for FFTs.
set(GMX_FFT_MKL 1)
- set(HAVE_MKL 1)
+ set(HAVE_LIBMKL 1)
#elseif(${GMX_FFT_LIBRARY} STREQUAL "ACML")
# MESSAGE(STATUS "Using external FFT library - AMD core math library")
set(GMX_EXTERNAL_BLAS TRUE CACHE BOOL "Use external BLAS instead of built-in")
set(GMX_EXTERNAL_LAPACK TRUE CACHE BOOL "Use external LAPACK instead of built-in")
# MKL has BLAS/LAPACK routines
-if(NOT HAVE_MKL AND NOT ACCELERATE_FRAMEWORK)
+if(NOT HAVE_LIBMKL AND NOT ACCELERATE_FRAMEWORK)
if(GMX_EXTERNAL_BLAS)
if (GMX_BLAS_USER)
list(APPEND GMX_EXTRA_LIBRARIES ${GMX_BLAS_USER})
if (NOT GMX_SKIP_DEFAULT_CFLAGS)
set(CMAKE_C_FLAGS "${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${CMAKE_C_FLAGS}")
set(CMAKE_CXX_FLAGS "${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${CMAKE_CXX_FLAGS}")
- set(CMAKE_EXE_LINKER_FLAGS "${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
+ set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
set(CMAKE_SHARED_LINKER_FLAGS "${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
else()
message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
endif()
- message("CMAKE_EXE_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
+ message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
endif()
via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software
packages (and has been). We only ask that proper credit be given to the authors."
-While the rest of Gromacs is GPL, we think it's only fair to give you the same rights to
+While the rest of Gromacs is LGPL, we think it's only fair to give you the same rights to
our modified BLAS files as the original netlib versions, so do what you want with them.
However, be warned that we have only tested that they to the right thing in the cases used
in Gromacs (primarily full & sparse matrix diagonalization), so in most cases it is a much
via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software
packages (and has been). We only ask that proper credit be given to the authors."
-While the rest of Gromacs is GPL, we think it's only fair to give you the same rights to
+While the rest of Gromacs is LGPL, we think it's only fair to give you the same rights to
our modified LAPACK files as the original netlib versions, so do what you want with them.
However, be warned that we have only tested that they to the right thing in the cases used
* * * * *
-GROMACS is free software, distributed under the GNU General Public License.
-However, scientific software is a little special compared to most other
-programs. Both you, we, and all other GROMACS users depend on the quality
-of the code, and when we find bugs (every piece of software has them) it
-is crucial that we can correct it and say that it was fixed in version X of
-the file or package release. For the same reason, it is important that you
-can reproduce other people's result from a certain GROMACS version.
+GROMACS is free software, distributed under the GNU Lesser General
+Public License, version 2.1 However, scientific software is a little
+special compared to most other programs. Both you, we, and all other
+GROMACS users depend on the quality of the code, and when we find bugs
+(every piece of software has them) it is crucial that we can correct
+it and say that it was fixed in version X of the file or package
+release. For the same reason, it is important that you can reproduce
+other people's result from a certain GROMACS version.
The easiest way to avoid this kind of problems is to get your modifications
included in the main distribution. We'll be happy to consider any decent
Name: gromacs-mpi
Version: 4.5
Release: 1
-Copyright: GPL
+Copyright: LGPLv2.1
Group: Applications/Science
Prefix: /usr/local
Buildroot: %{_topdir}/buildroot
Release: 7%{?dist}
Summary: GROMACS binaries
Group: Applications/Engineering
-License: GPLv2+
+License: LGPLv2.1
URL: http://www.gromacs.org
Source0: ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz
Source1: ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf
The GPU support from \gromacs{} version 4.5 using \openmm{}
\url{https://simtk.org/home/openmm} is still contained in the code,
but in the ``user contributions'' section (\verb+src/contrib+). You
-will need to edit \verb+src/contrib/CMakeLists.txt+ to enable it. It
-also requires \cuda{}, and remains the only hardware-based
-acceleration available for implicit solvent simulations in
-\gromacs{} at the moment. However, the long-term plan is to enable
-this functionality in core Gromacs, and not have the OpenMM
-interface supported by the \gromacs team. Right now there are
-some build issues for OpenMM.
+will need to set
+\verb+-DGMX_OPENMM=on -DGMX_GPU=off -DGMX_MPI=off
+-DGMX_THREAD_MPI=off\+ in order to build it. It also requires \cuda{},
+and remains the only hardware-based acceleration available for
+implicit solvent simulations in \gromacs{} at the moment. However, the
+long-term plan is to enable this functionality in core Gromacs, and
+not have the OpenMM interface supported by the \gromacs team.
If you wish to run in parallel on multiple machines across a network,
you will need to have
\subsubsection{\mkl{}}
-Using \mkl{} requires a set of linker flags that \gromacs{} is not
-able to detect for you, so setting up optimal linking is tricky at the
-moment. You will need to consult your compiler documentation and
-use \verb+CMAKE_C_FLAGS+ and \verb+-DCMAKE_EXE_LINKER_FLAGS+
-accordingly.
+Using \mkl{} with \icc{} 11 or higher is very simple. Set up your
+compiler environment correctly, perhaps with a command like
+\verb+source /path/to/compilervars.sh intel64+ (or consult your local
+documentation). Then set \verb+-DGMX_FFT_LIBRARY=mkl+ when you run
+\cmake{}. In this case, \gromacs{} will also use \mkl{} for \blas{}
+and \lapack{} (see \hyperref{linear-algebra}{here}).
+
+Otherwise, you can configure \mkl{} by setting
+\verb+-DGMX_FFT_LIBRARY=mkl
+-DMKL_LIBRARIES="/full/path/to/libone.so;/full/path/to/libtwo.so"
+-DMKL_INCLUDE_DIR="/full/path/to/mkl/include"+,
+where the full list (and order!) of libraries you require are found in
+Intel's \mkl{} documentation for your system.
\subsection{Optional build components}
fine for normal use. If you need to specify a non-standard path to
search, use \verb+-DCMAKE_PREFIX_PATH=/path/to/search+.
+If you are using Intel's \mkl{} for \fft{}, then the \blas{} and
+\lapack{} it provides are used automatically.
+
On Apple platforms where the Accelerate Framework is available, these
will be automatically used for \blas{} and \lapack{}.
#
# This file is part of Gromacs Copyright (c) 2012
-# 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.
-
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org
-
list(LENGTH FFTW_FIND_COMPONENTS FFTW_NUM_COMPONENTS_WANTED)
if(${FFTW_NUM_COMPONENTS_WANTED} LESS 1)
message(FATAL_ERROR "No FFTW component to search given")
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2012,2013, by the GROMACS development team, led by
-# David van der Spoel, Berk Hess, Erik Lindahl, and including many
-# others, as listed in the AUTHORS file in the top-level source
-# directory and at http://www.gromacs.org.
-#
-# GROMACS is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License
-# as published by the Free Software Foundation; either version 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, 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 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.
-#
-# - Find Intel MKL
-# Find the Intel Math Kernel Library, version 6.0 or later
-#
-# MKL_INCLUDE_DIR - where to find mkl_dfti.h
-# MKL_LIBRARIES - List of libraries when using MKL
-# MKL_FOUND - True if MKL was found
-
-if (MKL_INCLUDE_DIR)
- # Already in cache, be silent
- set (MKL_FIND_QUIETLY TRUE)
-endif (MKL_INCLUDE_DIR)
-
-find_path (MKL_INCLUDE_DIR mkl_dfti.h)
-find_library (MKL_LIBRARIES mkl_core)
-
-# handle the QUIETLY and REQUIRED arguments and set MKL_FOUND to TRUE if
-# all listed variables are TRUE
-include (FindPackageHandleStandardArgs)
-find_package_handle_standard_args (MKL DEFAULT_MSG MKL_LIBRARIES MKL_INCLUDE_DIR)
-
-# MKL Libraries change name ALL the time, so the user will have to set these...
-# mark_as_advanced (MKL_LIBRARIES MKL_INCLUDE_DIR)
-
-
# This file is part of Gromacs Copyright (c) 1991-2008
# David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
-# 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.
-
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org
-
-
# The module defines the following variables:
# VMD_EXECUTABLE - path to vmd command
# GMX_VMD_PLUGIN_PATH - path to vmd plugins
+++ /dev/null
-#include <mkl_dfti.h>
-
-int
-main()
-{
- DFTI_DESCRIPTOR *desc;
- MKL_LONG nx = 10;
-
- DftiCreateDescriptor(&desc,DFTI_SINGLE,DFTI_COMPLEX,1,nx);
-}
real dd_cutoff_twobody(gmx_domdec_t *dd);
+GMX_LIBMD_EXPORT
+void get_pme_nnodes(const gmx_domdec_t *dd,
+ int *npmenodes_x, int *npmenodes_y);
+/* Get the number of PME nodes along x and y, can be called with dd=NULL */
+
gmx_bool gmx_pmeonlynode(t_commrec *cr, int nodeid);
/* Return if nodeid in cr->mpi_comm_mysim is a PME-only node */
#undef gmx_add_pr
#undef gmx_sub_pr
#undef gmx_mul_pr
+/* For the FMA macros below, aim for c=d in code, so FMA3 uses 1 instruction */
+/* d = gmx_madd_pr(a,b,c): d = a*b + c, could use FMA3 or FMA4 */
+#undef gmx_madd_pr
+/* d = gmx_nmsub_pr(a,b,c): d = -a*b + c, could use FMA3 or FMA4 */
+#undef gmx_nmsub_pr
#undef gmx_max_pr
#undef gmx_cmplt_pr
/* gmx_blendzero_pr(real a, boolean b) does: (b ? a : 0) */
#undef gmx_or_pr
#undef gmx_andnot_pr
+/* Only used for PBC in bonded interactions, can be avoided */
+#undef gmx_round_pr
/* Not required, only used to speed up the nbnxn tabulated PME kernels */
#undef GMX_HAVE_SIMD_FLOOR
#undef gmx_floor_pr
-/* Not required, only used with when blendv is faster than comparison */
+
+/* Not required, only used when blendv is faster than comparison */
#undef GMX_HAVE_SIMD_BLENDV
#undef gmx_blendv_pr
/* Not required, gmx_anytrue(x) returns if any of the boolean is x is True.
#undef gmx_cvtepi32_pr
#undef gmx_invsqrt_pr
+/* sqrt+inv+sin+cos+acos+atan2 are only used for bonded potentials */
+#undef gmx_sqrt_pr
+#undef gmx_inv_pr
+#undef gmx_sincos_pr
+#undef gmx_acos_pr
+#undef gmx_atan_pr
+
#undef gmx_calc_rsq_pr
#undef gmx_sum4_pr
#undef gmx_pmecorrV_pr
-/* The same SIMD macros, can be translated to SIMD intrinsics, and compiled
- * to instructions for, different SIMD width and float precision.
- * On x86, the gmx_ prefix is replaced by _mm_ or _mm256_ (SSE or AVX).
- * The _pr suffix is replaced by _ps or _pd (single or double precision).
- * Note that compiler settings will decide if 128-bit intrinsics will
+/* Half SIMD-width types and operations only for nbnxn 2xnn search+kernels */
+#undef gmx_mm_hpr
+
+#undef gmx_load_hpr
+#undef gmx_load1_hpr
+#undef gmx_store_hpr
+#undef gmx_add_hpr
+#undef gmx_sub_hpr
+
+#undef gmx_sum4_hpr
+
+#undef gmx_2hpr_to_pr
+
+
+/* The same SIMD macros can be translated to SIMD intrinsics (and compiled
+ * to instructions for) different SIMD width and float precision.
+ *
+ * On x86: The gmx_ prefix is replaced by _mm_ or _mm256_ (SSE or AVX).
+ * The _pr suffix is replaced by _ps or _pd (for single or double precision).
+ * Compiler settings will decide if 128-bit intrinsics will
* be translated into SSE or AVX instructions.
*/
#define gmx_add_pr _mm_add_ps
#define gmx_sub_pr _mm_sub_ps
#define gmx_mul_pr _mm_mul_ps
+#ifdef GMX_X86_AVX_128_FMA
+#define gmx_madd_pr(a, b, c) _mm_macc_ps(a, b, c)
+#define gmx_nmsub_pr(a, b, c) _mm_nmacc_ps(a, b, c)
+#else
+#define gmx_madd_pr(a, b, c) _mm_add_ps(c, _mm_mul_ps(a, b))
+#define gmx_nmsub_pr(a, b, c) _mm_sub_ps(c, _mm_mul_ps(a, b))
+#endif
#define gmx_max_pr _mm_max_ps
#define gmx_cmplt_pr _mm_cmplt_ps
#define gmx_blendzero_pr _mm_and_ps
#define gmx_andnot_pr _mm_andnot_ps
#ifdef GMX_X86_SSE4_1
+#define gmx_round_pr(x) _mm_round_ps(x, 0x0)
#define GMX_HAVE_SIMD_FLOOR
#define gmx_floor_pr _mm_floor_ps
+#else
+#define gmx_round_pr(x) _mm_cvtepi32_ps(_mm_cvtps_epi32(x))
+#endif
+
+#ifdef GMX_X86_SSE4_1
#define GMX_HAVE_SIMD_BLENDV
#define gmx_blendv_pr _mm_blendv_ps
#endif
#define gmx_cvtepi32_pr _mm_cvtepi32_ps
#define gmx_invsqrt_pr gmx_mm_invsqrt_ps
+#define gmx_sqrt_pr gmx_mm_sqrt_ps
+#define gmx_inv_pr gmx_mm_inv_ps
+#define gmx_sincos_pr gmx_mm_sincos_ps
+#define gmx_acos_pr gmx_mm_acos_ps
+#define gmx_atan2_pr gmx_mm_atan2_ps
+
#define gmx_calc_rsq_pr gmx_mm_calc_rsq_ps
#define gmx_sum4_pr gmx_mm_sum4_ps
#define gmx_add_pr _mm_add_pd
#define gmx_sub_pr _mm_sub_pd
#define gmx_mul_pr _mm_mul_pd
+#ifdef GMX_X86_AVX_128_FMA
+#define gmx_madd_pr(a, b, c) _mm_macc_pd(a, b, c)
+#define gmx_nmsub_pr(a, b, c) _mm_nmacc_pd(a, b, c)
+#else
+#define gmx_madd_pr(a, b, c) _mm_add_pd(c, _mm_mul_pd(a, b))
+#define gmx_nmsub_pr(a, b, c) _mm_sub_pd(c, _mm_mul_pd(a, b))
+#endif
#define gmx_max_pr _mm_max_pd
#define gmx_cmplt_pr _mm_cmplt_pd
#define gmx_blendzero_pr _mm_and_pd
#define gmx_andnot_pr _mm_andnot_pd
#ifdef GMX_X86_SSE4_1
+#define gmx_round_pr(x) _mm_round_pd(x, 0x0)
#define GMX_HAVE_SIMD_FLOOR
#define gmx_floor_pr _mm_floor_pd
+#else
+#define gmx_round_pr(x) _mm_cvtepi32_pd(_mm_cvtpd_epi32(x))
+/* gmx_floor_pr is not used in code for pre-SSE4_1 hardware */
+#endif
+
+#ifdef GMX_X86_SSE4_1
#define GMX_HAVE_SIMD_BLENDV
#define gmx_blendv_pr _mm_blendv_pd
#endif
#define gmx_cvtepi32_pr _mm_cvtepi32_pd
#define gmx_invsqrt_pr gmx_mm_invsqrt_pd
+#define gmx_sqrt_pr gmx_mm_sqrt_pd
+#define gmx_inv_pr gmx_mm_inv_pd
+#define gmx_sincos_pr gmx_mm_sincos_pd
+#define gmx_acos_pr gmx_mm_acos_pd
+#define gmx_atan2_pr gmx_mm_atan2_pd
+
#define gmx_calc_rsq_pr gmx_mm_calc_rsq_pd
#define gmx_sum4_pr gmx_mm_sum4_pd
#define gmx_add_pr _mm256_add_ps
#define gmx_sub_pr _mm256_sub_ps
#define gmx_mul_pr _mm256_mul_ps
+#define gmx_madd_pr(a, b, c) _mm256_add_ps(c, _mm256_mul_ps(a, b))
+#define gmx_nmsub_pr(a, b, c) _mm256_sub_ps(c, _mm256_mul_ps(a, b))
#define gmx_max_pr _mm256_max_ps
/* Less-than (we use ordered, non-signaling, but that's not required) */
#define gmx_cmplt_pr(x, y) _mm256_cmp_ps(x, y, 0x11)
#define gmx_or_pr _mm256_or_ps
#define gmx_andnot_pr _mm256_andnot_ps
+#define gmx_round_pr(x) _mm256_round_ps(x, 0x0)
#define GMX_HAVE_SIMD_FLOOR
#define gmx_floor_pr _mm256_floor_ps
+
#define GMX_HAVE_SIMD_BLENDV
#define gmx_blendv_pr _mm256_blendv_ps
#define gmx_cvttpr_epi32 _mm256_cvttps_epi32
#define gmx_invsqrt_pr gmx_mm256_invsqrt_ps
+#define gmx_sqrt_pr gmx_mm256_sqrt_ps
+#define gmx_inv_pr gmx_mm256_inv_ps
+#define gmx_sincos_pr gmx_mm256_sincos_ps
+#define gmx_acos_pr gmx_mm256_acos_ps
+#define gmx_atan2_pr gmx_mm256_atan2_ps
+
#define gmx_calc_rsq_pr gmx_mm256_calc_rsq_ps
#define gmx_sum4_pr gmx_mm256_sum4_ps
#define gmx_add_pr _mm256_add_pd
#define gmx_sub_pr _mm256_sub_pd
#define gmx_mul_pr _mm256_mul_pd
+#define gmx_madd_pr(a, b, c) _mm256_add_pd(c, _mm256_mul_pd(a, b))
+#define gmx_nmsub_pr(a, b, c) _mm256_sub_pd(c, _mm256_mul_pd(a, b))
#define gmx_max_pr _mm256_max_pd
/* Less-than (we use ordered, non-signaling, but that's not required) */
#define gmx_cmplt_pr(x, y) _mm256_cmp_pd(x, y, 0x11)
#define gmx_or_pr _mm256_or_pd
#define gmx_andnot_pr _mm256_andnot_pd
+#define gmx_round_pr(x) _mm256_round_pd(x, 0x0)
#define GMX_HAVE_SIMD_FLOOR
#define gmx_floor_pr _mm256_floor_pd
+
#define GMX_HAVE_SIMD_BLENDV
#define gmx_blendv_pr _mm256_blendv_pd
#define gmx_cvttpr_epi32 _mm256_cvttpd_epi32
#define gmx_invsqrt_pr gmx_mm256_invsqrt_pd
+#define gmx_sqrt_pr gmx_mm256_sqrt_pd
+#define gmx_inv_pr gmx_mm256_inv_pd
+#define gmx_sincos_pr gmx_mm256_sincos_pd
+#define gmx_acos_pr gmx_mm256_acos_pd
+#define gmx_atan2_pr gmx_mm256_atan2_pd
+
#define gmx_calc_rsq_pr gmx_mm256_calc_rsq_pd
#define gmx_sum4_pr gmx_mm256_sum4_pd
* platforms like Microsoft Windows we have created a private version
* of the necessary routines and distribute them with the Gromacs source.
*
- * Although the rest of Gromacs is GPL, you can copy and use the XDR
+ * Although the rest of Gromacs is LGPL, you can copy and use the XDR
* routines in any way you want as long as you obey Sun's license:
*
* Sun RPC is a product of Sun Microsystems, Inc. and is provided for
/* Abstract type for PME <-> PP communication */
typedef struct gmx_pme_pp *gmx_pme_pp_t;
+GMX_LIBMD_EXPORT
+void gmx_pme_check_restrictions(int pme_order,
+ int nkx, int nky, int nkz,
+ int nnodes_major,
+ int nnodes_minor,
+ gmx_bool bUseThreads,
+ gmx_bool bFatal,
+ gmx_bool *bValidSettings);
+/* Check restrictions on pme_order and the PME grid nkx,nky,nkz.
+ * With bFatal=TRUE, a fatal error is generated on violation,
+ * bValidSettings=NULL can be passed.
+ * With bFatal=FALSE, *bValidSettings reports the validity of the settings.
+ * bUseThreads tells if any MPI rank doing PME uses more than 1 threads.
+ * If at calling you bUseThreads is unknown, pass TRUE for conservative
+ * checking.
+ */
+
gmx_pme_pp_t gmx_pme_pp_init(t_commrec *cr);
/* Initialize the PME-only side of the PME <-> PP communication */
/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS development team,
+ * Copyright (c) 2001-2009,2010,2012, 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
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * 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.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, 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 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.
*/
#include <gromacs/copyrite.h>
#include <gromacs/filenm.h>
/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2009, 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
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * 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.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 http://www.gromacs.org.
*
- * For more info, check our website 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.
*/
/*! \dir share/template
* \brief Template code for writing analysis programs.
# 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)
+add_library(openmm_api_wrapper STATIC ${CMAKE_SOURCE_DIR}/src/contrib/openmm_wrapper.cpp)
target_link_libraries(openmm_api_wrapper ${OpenMM_LIBRARIES})
-list(APPEND GMX_EXTRA_LIBRARIES openmm_api_wrapper ${OpenMM_LIBRARIES})
-list(REMOVE_ITEM MDRUN_SOURCES mdrun.c)
+list(REMOVE_ITEM MDRUN_SOURCES mdrun.c runner.c)
list(APPEND MDRUN_SOURCES
- ${CMAKE_CURRENT_SOURCE_DIR}/src/contrib/md_openmm.c
- ${CMAKE_CURRENT_SOURCE_DIR}/src/contrib/mdrun_openmm.c)
+ ${CMAKE_SOURCE_DIR}/src/contrib/md_openmm.c
+ ${CMAKE_SOURCE_DIR}/src/contrib/mdrun_openmm.c
+ ${CMAKE_SOURCE_DIR}/src/contrib/runner_openmm.c
+ )
# this is to circumvent the following MSVC error:
# warning LNK4098: defaultlib 'LIBCMT' conflicts with use of other libs
message(FATAL_ERROR "The OpenMM build is not compatible with the native GPU build")
endif()
- enable_language(CXX)
- set (GMX_BINARY_SUFFIX "-openmm")
- set (GMX_LIBS_SUFFIX "_openmm")
+ # These won't actually do anything unless they precede the
+ # definition of these options elsewhere. However, they can't be
+ # FORCE-d either.
+ set(GMX_BINARY_SUFFIX "-openmm" CACHE STRING "Suffix to distinguish OpenMM build from normal")
+ set(GMX_LIBS_SUFFIX "_openmm" CACHE STRING "Suffix to distinguish OpenMM build from normal")
#######################################################################
# Check for options incompatible with OpenMM build #
if(CMAKE_BUILD_TYPE STREQUAL "DEBUG")
set(CUDA_VERBOSE_BUILD ON)
endif()
- list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/contrib)
- find_package(OpenMM)
# mark as advanced the unused variables
mark_as_advanced(FORCE GMX_CPU_ACCELERATION GMX_MPI GMX_FFT_LIBRARY
{ efXVG, "-tpi", "tpi", ffOPTWR },
{ efXVG, "-tpid", "tpidist", ffOPTWR },
{ efEDI, "-ei", "sam", ffOPTRD },
- { efEDO, "-eo", "sam", ffOPTWR },
+ { efXVG, "-eo", "sam", ffOPTWR },
{ efGCT, "-j", "wham", ffOPTRD },
{ efGCT, "-jo", "bam", ffOPTWR },
{ efXVG, "-ffout", "gct", ffOPTWR },
{ NULL, "interleave", "pp_pme", "cartesian", NULL };
const char *dddlb_opt[] =
{ NULL, "auto", "no", "yes", NULL };
+ const char *thread_aff_opt[threadaffNR+1] =
+ { NULL, "auto", "no", "yes", NULL };
const char *nbpu_opt[] =
{ NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL };
real rdd=0.0,rconstr=0.0,dlb_scale=0.8,pforce=-1;
"Number of OpenMP threads per MPI process/thread to start (0 is guess)" },
{ "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
"Number of OpenMP threads per MPI process/thread to start (0 is -ntomp)" },
- { "-pin", FALSE, etBOOL, {&hw_opt.bThreadPinning},
+ { "-pin", FALSE, etBOOL, {thread_aff_opt},
"Pin OpenMP threads to cores" },
- { "-pinht", FALSE, etBOOL, {&hw_opt.bPinHyperthreading},
- "Always pin threads to Hyper-Threading cores" },
{ "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
"Core offset for pinning (for running multiple mdrun processes on a single physical node)" },
+ { "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
+ "Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
{ "-gpu_id", FALSE, etSTR, {&hw_opt.gpu_id},
"List of GPU id's to use" },
{ "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
if (MULTISIM(cr) && MASTER(cr))
{
- check_multi_int(stdout,cr->ms,sim_part,"simulation part");
+ check_multi_int(stdout,cr->ms,sim_part,"simulation part", TRUE);
}
}
else
*
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2010, The GROMACS development team,
+ * Copyright (c) 2001-2010, 2013, 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
+ * modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
#include "mdrun.h"
#include "physics.h"
#include "string2.h"
+#include "openmm_gpu_utils.h"
#include "gpu_utils.h"
#include "mtop_util.h"
#include "force.h"
#include "nonbonded.h"
-#if !defined GMX_DOUBLE && defined GMX_X86_SSE2
-#include "gmx_x86_simd_single.h"
-#define SSE_PROPER_DIHEDRALS
+#ifdef GMX_X86_SSE2
+#define SIMD_BONDEDS
+
+#include "gmx_simd_macros.h"
#endif
/* Find a better place for this? */
}
}
+#ifdef SIMD_BONDEDS
+
+/* Below are 3 SIMD vector operations.
+ * Currently these are only used here, but they should be moved to
+ * a general SIMD include file when used elsewhere.
+ */
+
+/* SIMD inner-product of multiple vectors */
+static gmx_inline gmx_mm_pr
+gmx_iprod_pr(gmx_mm_pr ax, gmx_mm_pr ay, gmx_mm_pr az,
+ gmx_mm_pr bx, gmx_mm_pr by, gmx_mm_pr bz)
+{
+ gmx_mm_pr ret;
+
+ ret = gmx_mul_pr(ax, bx);
+ ret = gmx_madd_pr(ay, by, ret);
+ ret = gmx_madd_pr(az, bz, ret);
+
+ return ret;
+}
+
+/* SIMD norm squared of multiple vectors */
+static gmx_inline gmx_mm_pr
+gmx_norm2_pr(gmx_mm_pr ax, gmx_mm_pr ay, gmx_mm_pr az)
+{
+ gmx_mm_pr ret;
+
+ ret = gmx_mul_pr(ax, ax);
+ ret = gmx_madd_pr(ay, ay, ret);
+ ret = gmx_madd_pr(az, az, ret);
+
+ return ret;
+}
+
+/* SIMD cross-product of multiple vectors */
+static gmx_inline void
+gmx_cprod_pr(gmx_mm_pr ax, gmx_mm_pr ay, gmx_mm_pr az,
+ gmx_mm_pr bx, gmx_mm_pr by, gmx_mm_pr bz,
+ gmx_mm_pr *cx, gmx_mm_pr *cy, gmx_mm_pr *cz)
+{
+ *cx = gmx_mul_pr(ay, bz);
+ *cx = gmx_nmsub_pr(az, by, *cx);
+
+ *cy = gmx_mul_pr(az, bx);
+ *cy = gmx_nmsub_pr(ax, bz, *cy);
+
+ *cz = gmx_mul_pr(ax, by);
+ *cz = gmx_nmsub_pr(ay, bx, *cz);
+}
+
+/* SIMD PBC data structure, containing 1/boxdiag and the box vectors */
+typedef struct {
+ gmx_mm_pr inv_bzz;
+ gmx_mm_pr inv_byy;
+ gmx_mm_pr inv_bxx;
+ gmx_mm_pr bzx;
+ gmx_mm_pr bzy;
+ gmx_mm_pr bzz;
+ gmx_mm_pr byx;
+ gmx_mm_pr byy;
+ gmx_mm_pr bxx;
+} pbc_simd_t;
+
+/* Set the SIMD pbc data from a normal t_pbc struct */
+static void set_pbc_simd(const t_pbc *pbc, pbc_simd_t *pbc_simd)
+{
+ rvec inv_bdiag;
+ int d;
+
+ /* Setting inv_bdiag to 0 effectively turns off PBC */
+ clear_rvec(inv_bdiag);
+ if (pbc != NULL)
+ {
+ for (d = 0; d < pbc->ndim_ePBC; d++)
+ {
+ inv_bdiag[d] = 1.0/pbc->box[d][d];
+ }
+ }
+
+ pbc_simd->inv_bzz = gmx_set1_pr(inv_bdiag[ZZ]);
+ pbc_simd->inv_byy = gmx_set1_pr(inv_bdiag[YY]);
+ pbc_simd->inv_bxx = gmx_set1_pr(inv_bdiag[XX]);
+
+ if (pbc != NULL)
+ {
+ pbc_simd->bzx = gmx_set1_pr(pbc->box[ZZ][XX]);
+ pbc_simd->bzy = gmx_set1_pr(pbc->box[ZZ][YY]);
+ pbc_simd->bzz = gmx_set1_pr(pbc->box[ZZ][ZZ]);
+ pbc_simd->byx = gmx_set1_pr(pbc->box[YY][XX]);
+ pbc_simd->byy = gmx_set1_pr(pbc->box[YY][YY]);
+ pbc_simd->bxx = gmx_set1_pr(pbc->box[XX][XX]);
+ }
+ else
+ {
+ pbc_simd->bzx = gmx_setzero_pr();
+ pbc_simd->bzy = gmx_setzero_pr();
+ pbc_simd->bzz = gmx_setzero_pr();
+ pbc_simd->byx = gmx_setzero_pr();
+ pbc_simd->byy = gmx_setzero_pr();
+ pbc_simd->bxx = gmx_setzero_pr();
+ }
+}
+
+/* Correct distance vector *dx,*dy,*dz for PBC using SIMD */
+static gmx_inline void
+pbc_dx_simd(gmx_mm_pr *dx, gmx_mm_pr *dy, gmx_mm_pr *dz,
+ const pbc_simd_t *pbc)
+{
+ gmx_mm_pr sh;
+
+ sh = gmx_round_pr(gmx_mul_pr(*dz, pbc->inv_bzz));
+ *dx = gmx_nmsub_pr(sh, pbc->bzx, *dx);
+ *dy = gmx_nmsub_pr(sh, pbc->bzy, *dy);
+ *dz = gmx_nmsub_pr(sh, pbc->bzz, *dz);
+
+ sh = gmx_round_pr(gmx_mul_pr(*dy, pbc->inv_byy));
+ *dx = gmx_nmsub_pr(sh, pbc->byx, *dx);
+ *dy = gmx_nmsub_pr(sh, pbc->byy, *dy);
+
+ sh = gmx_round_pr(gmx_mul_pr(*dx, pbc->inv_bxx));
+ *dx = gmx_nmsub_pr(sh, pbc->bxx, *dx);
+}
+
+#endif /* SIMD_BONDEDS */
+
/*
* Morse potential bond by Frank Everdij
*
return vtot;
}
+#ifdef SIMD_BONDEDS
+
+/* As angles, but using SIMD to calculate many dihedrals at once.
+ * This routines does not calculate energies and shift forces.
+ */
+static gmx_inline void
+angles_noener_simd(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[],
+ const t_pbc *pbc, const t_graph *g,
+ real lambda,
+ const t_mdatoms *md, t_fcdata *fcd,
+ int *global_atom_index)
+{
+#define UNROLL GMX_SIMD_WIDTH_HERE
+ const int nfa1 = 4;
+ int i, iu, s, m;
+ int type, ai[UNROLL], aj[UNROLL], ak[UNROLL];
+ real coeff_array[2*UNROLL+UNROLL], *coeff;
+ real dr_array[2*DIM*UNROLL+UNROLL], *dr;
+ real f_buf_array[6*UNROLL+UNROLL], *f_buf;
+ gmx_mm_pr k_S, theta0_S;
+ gmx_mm_pr rijx_S, rijy_S, rijz_S;
+ gmx_mm_pr rkjx_S, rkjy_S, rkjz_S;
+ gmx_mm_pr one_S;
+ gmx_mm_pr rij_rkj_S;
+ gmx_mm_pr nrij2_S, nrij_1_S;
+ gmx_mm_pr nrkj2_S, nrkj_1_S;
+ gmx_mm_pr cos_S, sin_S;
+ gmx_mm_pr theta_S;
+ gmx_mm_pr st_S, sth_S;
+ gmx_mm_pr cik_S, cii_S, ckk_S;
+ gmx_mm_pr f_ix_S, f_iy_S, f_iz_S;
+ gmx_mm_pr f_kx_S, f_ky_S, f_kz_S;
+ pbc_simd_t pbc_simd;
+
+ /* Ensure register memory alignment */
+ coeff = gmx_simd_align_real(coeff_array);
+ dr = gmx_simd_align_real(dr_array);
+ f_buf = gmx_simd_align_real(f_buf_array);
+
+ set_pbc_simd(pbc,&pbc_simd);
+
+ one_S = gmx_set1_pr(1.0);
+
+ /* nbonds is the number of angles times nfa1, here we step UNROLL angles */
+ for (i = 0; (i < nbonds); i += UNROLL*nfa1)
+ {
+ /* Collect atoms for UNROLL angles.
+ * iu indexes into forceatoms, we should not let iu go beyond nbonds.
+ */
+ iu = i;
+ for (s = 0; s < UNROLL; s++)
+ {
+ type = forceatoms[iu];
+ ai[s] = forceatoms[iu+1];
+ aj[s] = forceatoms[iu+2];
+ ak[s] = forceatoms[iu+3];
+
+ coeff[s] = forceparams[type].harmonic.krA;
+ coeff[UNROLL+s] = forceparams[type].harmonic.rA*DEG2RAD;
+
+ /* If you can't use pbc_dx_simd below for PBC, e.g. because
+ * you can't round in SIMD, use pbc_rvec_sub here.
+ */
+ /* Store the non PBC corrected distances packed and aligned */
+ for (m = 0; m < DIM; m++)
+ {
+ dr[s + m *UNROLL] = x[ai[s]][m] - x[aj[s]][m];
+ dr[s + (DIM+m)*UNROLL] = x[ak[s]][m] - x[aj[s]][m];
+ }
+
+ /* At the end fill the arrays with identical entries */
+ if (iu + nfa1 < nbonds)
+ {
+ iu += nfa1;
+ }
+ }
+
+ k_S = gmx_load_pr(coeff);
+ theta0_S = gmx_load_pr(coeff+UNROLL);
+
+ rijx_S = gmx_load_pr(dr + 0*UNROLL);
+ rijy_S = gmx_load_pr(dr + 1*UNROLL);
+ rijz_S = gmx_load_pr(dr + 2*UNROLL);
+ rkjx_S = gmx_load_pr(dr + 3*UNROLL);
+ rkjy_S = gmx_load_pr(dr + 4*UNROLL);
+ rkjz_S = gmx_load_pr(dr + 5*UNROLL);
+
+ pbc_dx_simd(&rijx_S, &rijy_S, &rijz_S, &pbc_simd);
+ pbc_dx_simd(&rkjx_S, &rkjy_S, &rkjz_S, &pbc_simd);
+
+ rij_rkj_S = gmx_iprod_pr(rijx_S, rijy_S, rijz_S,
+ rkjx_S, rkjy_S, rkjz_S);
+
+ nrij2_S = gmx_norm2_pr(rijx_S, rijy_S, rijz_S);
+ nrkj2_S = gmx_norm2_pr(rkjx_S, rkjy_S, rkjz_S);
+
+ nrij_1_S = gmx_invsqrt_pr(nrij2_S);
+ nrkj_1_S = gmx_invsqrt_pr(nrkj2_S);
+
+ cos_S = gmx_mul_pr(rij_rkj_S, gmx_mul_pr(nrij_1_S, nrkj_1_S));
+
+ theta_S = gmx_acos_pr(cos_S);
+
+ sin_S = gmx_invsqrt_pr(gmx_max_pr(gmx_sub_pr(one_S, gmx_mul_pr(cos_S, cos_S)),
+ gmx_setzero_pr()));
+ st_S = gmx_mul_pr(gmx_mul_pr(k_S, gmx_sub_pr(theta0_S, theta_S)),
+ sin_S);
+ sth_S = gmx_mul_pr(st_S, cos_S);
+
+ cik_S = gmx_mul_pr(st_S, gmx_mul_pr(nrij_1_S, nrkj_1_S));
+ cii_S = gmx_mul_pr(sth_S, gmx_mul_pr(nrij_1_S, nrij_1_S));
+ ckk_S = gmx_mul_pr(sth_S, gmx_mul_pr(nrkj_1_S, nrkj_1_S));
+
+ f_ix_S = gmx_mul_pr(cii_S, rijx_S);
+ f_ix_S = gmx_nmsub_pr(cik_S, rkjx_S, f_ix_S);
+ f_iy_S = gmx_mul_pr(cii_S, rijy_S);
+ f_iy_S = gmx_nmsub_pr(cik_S, rkjy_S, f_iy_S);
+ f_iz_S = gmx_mul_pr(cii_S, rijz_S);
+ f_iz_S = gmx_nmsub_pr(cik_S, rkjz_S, f_iz_S);
+ f_kx_S = gmx_mul_pr(ckk_S, rkjx_S);
+ f_kx_S = gmx_nmsub_pr(cik_S, rijx_S, f_kx_S);
+ f_ky_S = gmx_mul_pr(ckk_S, rkjy_S);
+ f_ky_S = gmx_nmsub_pr(cik_S, rijy_S, f_ky_S);
+ f_kz_S = gmx_mul_pr(ckk_S, rkjz_S);
+ f_kz_S = gmx_nmsub_pr(cik_S, rijz_S, f_kz_S);
+
+ gmx_store_pr(f_buf + 0*UNROLL, f_ix_S);
+ gmx_store_pr(f_buf + 1*UNROLL, f_iy_S);
+ gmx_store_pr(f_buf + 2*UNROLL, f_iz_S);
+ gmx_store_pr(f_buf + 3*UNROLL, f_kx_S);
+ gmx_store_pr(f_buf + 4*UNROLL, f_ky_S);
+ gmx_store_pr(f_buf + 5*UNROLL, f_kz_S);
+
+ iu = i;
+ s = 0;
+ do
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ f[ai[s]][m] += f_buf[s + m*UNROLL];
+ f[aj[s]][m] -= f_buf[s + m*UNROLL] + f_buf[s + (DIM+m)*UNROLL];
+ f[ak[s]][m] += f_buf[s + (DIM+m)*UNROLL];
+ }
+ s++;
+ iu += nfa1;
+ }
+ while (s < UNROLL && iu < nbonds);
+ }
+#undef UNROLL
+}
+
+#endif /* SIMD_BONDEDS */
+
real linear_angles(int nbonds,
const t_iatom forceatoms[], const t_iparams forceparams[],
const rvec x[], rvec f[], rvec fshift[],
}
-#ifdef SSE_PROPER_DIHEDRALS
-
-/* x86 SIMD inner-product of 4 float vectors */
-#define GMX_MM_IPROD_PS(ax, ay, az, bx, by, bz) \
- _mm_add_ps(_mm_add_ps(_mm_mul_ps(ax, bx), _mm_mul_ps(ay, by)), _mm_mul_ps(az, bz))
-
-/* x86 SIMD norm^2 of 4 float vectors */
-#define GMX_MM_NORM2_PS(ax, ay, az) GMX_MM_IPROD_PS(ax, ay, az, ax, ay, az)
+#ifdef SIMD_BONDEDS
-/* x86 SIMD cross-product of 4 float vectors */
-#define GMX_MM_CPROD_PS(ax, ay, az, bx, by, bz, cx, cy, cz) \
- { \
- cx = _mm_sub_ps(_mm_mul_ps(ay, bz), _mm_mul_ps(az, by)); \
- cy = _mm_sub_ps(_mm_mul_ps(az, bx), _mm_mul_ps(ax, bz)); \
- cz = _mm_sub_ps(_mm_mul_ps(ax, by), _mm_mul_ps(ay, bx)); \
- }
-
-/* load 4 rvec's into 3 x86 SIMD float registers */
-#define load_rvec4(r0, r1, r2, r3, rx_SSE, ry_SSE, rz_SSE) \
- { \
- __m128 tmp; \
- rx_SSE = _mm_load_ps(r0); \
- ry_SSE = _mm_load_ps(r1); \
- rz_SSE = _mm_load_ps(r2); \
- tmp = _mm_load_ps(r3); \
- _MM_TRANSPOSE4_PS(rx_SSE, ry_SSE, rz_SSE, tmp); \
- }
-
-#define store_rvec4(rx_SSE, ry_SSE, rz_SSE, r0, r1, r2, r3) \
- { \
- __m128 tmp = _mm_setzero_ps(); \
- _MM_TRANSPOSE4_PS(rx_SSE, ry_SSE, rz_SSE, tmp); \
- _mm_store_ps(r0, rx_SSE); \
- _mm_store_ps(r1, ry_SSE); \
- _mm_store_ps(r2, rz_SSE); \
- _mm_store_ps(r3, tmp ); \
- }
-
-/* An rvec in a structure which can be allocated 16-byte aligned */
-typedef struct {
- rvec v;
- float f;
-} rvec_sse_t;
-
-/* As dih_angle above, but calculates 4 dihedral angles at once using SSE,
+/* As dih_angle above, but calculates 4 dihedral angles at once using SIMD,
* also calculates the pre-factor required for the dihedral force update.
- * Note that bv and buf should be 16-byte aligned.
+ * Note that bv and buf should be register aligned.
*/
-static void
-dih_angle_sse(const rvec *x,
- int ai[4], int aj[4], int ak[4], int al[4],
- const t_pbc *pbc,
- int t1[4], int t2[4], int t3[4],
- rvec_sse_t *bv,
- real *buf)
+static gmx_inline void
+dih_angle_simd(const rvec *x,
+ const int *ai, const int *aj, const int *ak, const int *al,
+ const pbc_simd_t *pbc,
+ real *dr,
+ gmx_mm_pr *phi_S,
+ gmx_mm_pr *mx_S, gmx_mm_pr *my_S, gmx_mm_pr *mz_S,
+ gmx_mm_pr *nx_S, gmx_mm_pr *ny_S, gmx_mm_pr *nz_S,
+ gmx_mm_pr *nrkj_m2_S,
+ gmx_mm_pr *nrkj_n2_S,
+ real *p,
+ real *q)
{
- int s;
- __m128 rijx_SSE, rijy_SSE, rijz_SSE;
- __m128 rkjx_SSE, rkjy_SSE, rkjz_SSE;
- __m128 rklx_SSE, rkly_SSE, rklz_SSE;
- __m128 mx_SSE, my_SSE, mz_SSE;
- __m128 nx_SSE, ny_SSE, nz_SSE;
- __m128 cx_SSE, cy_SSE, cz_SSE;
- __m128 cn_SSE;
- __m128 s_SSE;
- __m128 phi_SSE;
- __m128 ipr_SSE;
- int signs;
- __m128 iprm_SSE, iprn_SSE;
- __m128 nrkj2_SSE, nrkj_1_SSE, nrkj_2_SSE, nrkj_SSE;
- __m128 nrkj_m2_SSE, nrkj_n2_SSE;
- __m128 p_SSE, q_SSE;
- __m128 fmin_SSE = _mm_set1_ps(GMX_FLOAT_MIN);
-
- for (s = 0; s < 4; s++)
+#define UNROLL GMX_SIMD_WIDTH_HERE
+ int s, m;
+ gmx_mm_pr rijx_S, rijy_S, rijz_S;
+ gmx_mm_pr rkjx_S, rkjy_S, rkjz_S;
+ gmx_mm_pr rklx_S, rkly_S, rklz_S;
+ gmx_mm_pr cx_S, cy_S, cz_S;
+ gmx_mm_pr cn_S;
+ gmx_mm_pr s_S;
+ gmx_mm_pr ipr_S;
+ gmx_mm_pr iprm_S, iprn_S;
+ gmx_mm_pr nrkj2_S, nrkj_1_S, nrkj_2_S, nrkj_S;
+ gmx_mm_pr p_S, q_S;
+ gmx_mm_pr fmin_S = gmx_set1_pr(GMX_FLOAT_MIN);
+ /* Using -0.0 should lead to only the sign bit being set */
+ gmx_mm_pr sign_mask_S = gmx_set1_pr(-0.0);
+
+ for (s = 0; s < UNROLL; s++)
{
- t1[s] = pbc_rvec_sub(pbc, x[ai[s]], x[aj[s]], bv[0+s].v);
- t2[s] = pbc_rvec_sub(pbc, x[ak[s]], x[aj[s]], bv[4+s].v);
- t3[s] = pbc_rvec_sub(pbc, x[ak[s]], x[al[s]], bv[8+s].v);
+ /* If you can't use pbc_dx_simd below for PBC, e.g. because
+ * you can't round in SIMD, use pbc_rvec_sub here.
+ */
+ for (m = 0; m < DIM; m++)
+ {
+ dr[s + (0*DIM + m)*UNROLL] = x[ai[s]][m] - x[aj[s]][m];
+ dr[s + (1*DIM + m)*UNROLL] = x[ak[s]][m] - x[aj[s]][m];
+ dr[s + (2*DIM + m)*UNROLL] = x[ak[s]][m] - x[al[s]][m];
+ }
}
- load_rvec4(bv[0].v, bv[1].v, bv[2].v, bv[3].v, rijx_SSE, rijy_SSE, rijz_SSE);
- load_rvec4(bv[4].v, bv[5].v, bv[6].v, bv[7].v, rkjx_SSE, rkjy_SSE, rkjz_SSE);
- load_rvec4(bv[8].v, bv[9].v, bv[10].v, bv[11].v, rklx_SSE, rkly_SSE, rklz_SSE);
+ rijx_S = gmx_load_pr(dr + 0*UNROLL);
+ rijy_S = gmx_load_pr(dr + 1*UNROLL);
+ rijz_S = gmx_load_pr(dr + 2*UNROLL);
+ rkjx_S = gmx_load_pr(dr + 3*UNROLL);
+ rkjy_S = gmx_load_pr(dr + 4*UNROLL);
+ rkjz_S = gmx_load_pr(dr + 5*UNROLL);
+ rklx_S = gmx_load_pr(dr + 6*UNROLL);
+ rkly_S = gmx_load_pr(dr + 7*UNROLL);
+ rklz_S = gmx_load_pr(dr + 8*UNROLL);
- GMX_MM_CPROD_PS(rijx_SSE, rijy_SSE, rijz_SSE,
- rkjx_SSE, rkjy_SSE, rkjz_SSE,
- mx_SSE, my_SSE, mz_SSE);
+ pbc_dx_simd(&rijx_S, &rijy_S, &rijz_S, pbc);
+ pbc_dx_simd(&rkjx_S, &rkjy_S, &rkjz_S, pbc);
+ pbc_dx_simd(&rklx_S, &rkly_S, &rklz_S, pbc);
- GMX_MM_CPROD_PS(rkjx_SSE, rkjy_SSE, rkjz_SSE,
- rklx_SSE, rkly_SSE, rklz_SSE,
- nx_SSE, ny_SSE, nz_SSE);
+ gmx_cprod_pr(rijx_S, rijy_S, rijz_S,
+ rkjx_S, rkjy_S, rkjz_S,
+ mx_S, my_S, mz_S);
- GMX_MM_CPROD_PS(mx_SSE, my_SSE, mz_SSE,
- nx_SSE, ny_SSE, nz_SSE,
- cx_SSE, cy_SSE, cz_SSE);
+ gmx_cprod_pr(rkjx_S, rkjy_S, rkjz_S,
+ rklx_S, rkly_S, rklz_S,
+ nx_S, ny_S, nz_S);
- cn_SSE = gmx_mm_sqrt_ps(GMX_MM_NORM2_PS(cx_SSE, cy_SSE, cz_SSE));
+ gmx_cprod_pr(*mx_S, *my_S, *mz_S,
+ *nx_S, *ny_S, *nz_S,
+ &cx_S, &cy_S, &cz_S);
- s_SSE = GMX_MM_IPROD_PS(mx_SSE, my_SSE, mz_SSE, nx_SSE, ny_SSE, nz_SSE);
+ cn_S = gmx_sqrt_pr(gmx_norm2_pr(cx_S, cy_S, cz_S));
- phi_SSE = gmx_mm_atan2_ps(cn_SSE, s_SSE);
- _mm_store_ps(buf+16, phi_SSE);
+ s_S = gmx_iprod_pr(*mx_S, *my_S, *mz_S, *nx_S, *ny_S, *nz_S);
- ipr_SSE = GMX_MM_IPROD_PS(rijx_SSE, rijy_SSE, rijz_SSE,
- nx_SSE, ny_SSE, nz_SSE);
+ /* Determine the dihedral angle, the sign might need correction */
+ *phi_S = gmx_atan2_pr(cn_S, s_S);
- signs = _mm_movemask_ps(ipr_SSE);
+ ipr_S = gmx_iprod_pr(rijx_S, rijy_S, rijz_S,
+ *nx_S, *ny_S, *nz_S);
- for (s = 0; s < 4; s++)
- {
- if (signs & (1<<s))
- {
- buf[16+s] = -buf[16+s];
- }
- }
+ iprm_S = gmx_norm2_pr(*mx_S, *my_S, *mz_S);
+ iprn_S = gmx_norm2_pr(*nx_S, *ny_S, *nz_S);
- iprm_SSE = GMX_MM_NORM2_PS(mx_SSE, my_SSE, mz_SSE);
- iprn_SSE = GMX_MM_NORM2_PS(nx_SSE, ny_SSE, nz_SSE);
-
- /* store_rvec4 messes with the input, don't use it after this! */
- store_rvec4(mx_SSE, my_SSE, mz_SSE, bv[0].v, bv[1].v, bv[2].v, bv[3].v);
- store_rvec4(nx_SSE, ny_SSE, nz_SSE, bv[4].v, bv[5].v, bv[6].v, bv[7].v);
-
- nrkj2_SSE = GMX_MM_NORM2_PS(rkjx_SSE, rkjy_SSE, rkjz_SSE);
+ nrkj2_S = gmx_norm2_pr(rkjx_S, rkjy_S, rkjz_S);
/* Avoid division by zero. When zero, the result is multiplied by 0
* anyhow, so the 3 max below do not affect the final result.
*/
- nrkj2_SSE = _mm_max_ps(nrkj2_SSE, fmin_SSE);
- nrkj_1_SSE = gmx_mm_invsqrt_ps(nrkj2_SSE);
- nrkj_2_SSE = _mm_mul_ps(nrkj_1_SSE, nrkj_1_SSE);
- nrkj_SSE = _mm_mul_ps(nrkj2_SSE, nrkj_1_SSE);
-
- iprm_SSE = _mm_max_ps(iprm_SSE, fmin_SSE);
- iprn_SSE = _mm_max_ps(iprn_SSE, fmin_SSE);
- nrkj_m2_SSE = _mm_mul_ps(nrkj_SSE, gmx_mm_inv_ps(iprm_SSE));
- nrkj_n2_SSE = _mm_mul_ps(nrkj_SSE, gmx_mm_inv_ps(iprn_SSE));
-
- _mm_store_ps(buf+0, nrkj_m2_SSE);
- _mm_store_ps(buf+4, nrkj_n2_SSE);
+ nrkj2_S = gmx_max_pr(nrkj2_S, fmin_S);
+ nrkj_1_S = gmx_invsqrt_pr(nrkj2_S);
+ nrkj_2_S = gmx_mul_pr(nrkj_1_S, nrkj_1_S);
+ nrkj_S = gmx_mul_pr(nrkj2_S, nrkj_1_S);
+
+ iprm_S = gmx_max_pr(iprm_S, fmin_S);
+ iprn_S = gmx_max_pr(iprn_S, fmin_S);
+ *nrkj_m2_S = gmx_mul_pr(nrkj_S, gmx_inv_pr(iprm_S));
+ *nrkj_n2_S = gmx_mul_pr(nrkj_S, gmx_inv_pr(iprn_S));
+
+ /* Set sign of the angle with the sign of ipr_S.
+ * Since phi is currently positive, we can use OR instead of XOR.
+ */
+ *phi_S = gmx_or_pr(*phi_S, gmx_and_pr(ipr_S, sign_mask_S));
- p_SSE = GMX_MM_IPROD_PS(rijx_SSE, rijy_SSE, rijz_SSE,
- rkjx_SSE, rkjy_SSE, rkjz_SSE);
- p_SSE = _mm_mul_ps(p_SSE, nrkj_2_SSE);
+ p_S = gmx_iprod_pr(rijx_S, rijy_S, rijz_S,
+ rkjx_S, rkjy_S, rkjz_S);
+ p_S = gmx_mul_pr(p_S, nrkj_2_S);
- q_SSE = GMX_MM_IPROD_PS(rklx_SSE, rkly_SSE, rklz_SSE,
- rkjx_SSE, rkjy_SSE, rkjz_SSE);
- q_SSE = _mm_mul_ps(q_SSE, nrkj_2_SSE);
+ q_S = gmx_iprod_pr(rklx_S, rkly_S, rklz_S,
+ rkjx_S, rkjy_S, rkjz_S);
+ q_S = gmx_mul_pr(q_S, nrkj_2_S);
- _mm_store_ps(buf+8, p_SSE);
- _mm_store_ps(buf+12, q_SSE);
+ gmx_store_pr(p, p_S);
+ gmx_store_pr(q, q_S);
+#undef UNROLL
}
-#endif /* SSE_PROPER_DIHEDRALS */
+#endif /* SIMD_BONDEDS */
void do_dih_fup(int i, int j, int k, int l, real ddphi,
}
/* As do_dih_fup_noshiftf above, but with pre-calculated pre-factors */
-static void
-do_dih_fup_noshiftf_precalc(int i, int j, int k, int l, real ddphi,
- real nrkj_m2, real nrkj_n2,
+static gmx_inline void
+do_dih_fup_noshiftf_precalc(int i, int j, int k, int l,
real p, real q,
- rvec m, rvec n, rvec f[])
+ real f_i_x, real f_i_y, real f_i_z,
+ real mf_l_x, real mf_l_y, real mf_l_z,
+ rvec f[])
{
rvec f_i, f_j, f_k, f_l;
- rvec uvec, vvec, svec, dx_jl;
- real a, b, toler;
- ivec jt, dt_ij, dt_kj, dt_lj;
-
- a = -ddphi*nrkj_m2;
- svmul(a, m, f_i);
- b = ddphi*nrkj_n2;
- svmul(b, n, f_l);
+ rvec uvec, vvec, svec;
+
+ f_i[XX] = f_i_x;
+ f_i[YY] = f_i_y;
+ f_i[ZZ] = f_i_z;
+ f_l[XX] = -mf_l_x;
+ f_l[YY] = -mf_l_y;
+ f_l[ZZ] = -mf_l_z;
svmul(p, f_i, uvec);
svmul(q, f_l, vvec);
rvec_sub(uvec, vvec, svec);
}
-#ifdef SSE_PROPER_DIHEDRALS
+#ifdef SIMD_BONDEDS
-/* As pdihs_noner above, but using SSE to calculate 4 dihedrals at once */
+/* As pdihs_noner above, but using SIMD to calculate many dihedrals at once */
static void
-pdihs_noener_sse(int nbonds,
- const t_iatom forceatoms[], const t_iparams forceparams[],
- const rvec x[], rvec f[],
- const t_pbc *pbc, const t_graph *g,
- real lambda,
- const t_mdatoms *md, t_fcdata *fcd,
- int *global_atom_index)
+pdihs_noener_simd(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[],
+ const t_pbc *pbc, const t_graph *g,
+ real lambda,
+ const t_mdatoms *md, t_fcdata *fcd,
+ int *global_atom_index)
{
- int i, i4, s;
- int type, ai[4], aj[4], ak[4], al[4];
- int t1[4], t2[4], t3[4];
- int mult[4];
- real cp[4], mdphi[4];
- real ddphi;
- rvec_sse_t rs_array[13], *rs;
- real buf_array[24], *buf;
- __m128 mdphi_SSE, sin_SSE, cos_SSE;
-
- /* Ensure 16-byte alignment */
- rs = (rvec_sse_t *)(((size_t)(rs_array +1)) & (~((size_t)15)));
- buf = (float *)(((size_t)(buf_array+3)) & (~((size_t)15)));
-
- for (i = 0; (i < nbonds); i += 20)
- {
- /* Collect atoms quadruplets for 4 dihedrals */
- i4 = i;
- for (s = 0; s < 4; s++)
- {
- ai[s] = forceatoms[i4+1];
- aj[s] = forceatoms[i4+2];
- ak[s] = forceatoms[i4+3];
- al[s] = forceatoms[i4+4];
- /* At the end fill the arrays with identical entries */
- if (i4 + 5 < nbonds)
- {
- i4 += 5;
- }
- }
+#define UNROLL GMX_SIMD_WIDTH_HERE
+ const int nfa1 = 5;
+ int i, iu, s;
+ int type, ai[UNROLL], aj[UNROLL], ak[UNROLL], al[UNROLL];
+ int t1[UNROLL], t2[UNROLL], t3[UNROLL];
+ real ddphi;
+ real dr_array[3*DIM*UNROLL+UNROLL], *dr;
+ real buf_array[7*UNROLL+UNROLL], *buf;
+ real *cp, *phi0, *mult, *phi, *p, *q, *sf_i, *msf_l;
+ gmx_mm_pr phi0_S, phi_S;
+ gmx_mm_pr mx_S, my_S, mz_S;
+ gmx_mm_pr nx_S, ny_S, nz_S;
+ gmx_mm_pr nrkj_m2_S, nrkj_n2_S;
+ gmx_mm_pr cp_S, mdphi_S, mult_S;
+ gmx_mm_pr sin_S, cos_S;
+ gmx_mm_pr mddphi_S;
+ gmx_mm_pr sf_i_S, msf_l_S;
+ pbc_simd_t pbc_simd;
+
+ /* Ensure SIMD register alignment */
+ dr = gmx_simd_align_real(dr_array);
+ buf = gmx_simd_align_real(buf_array);
+
+ /* Extract aligned pointer for parameters and variables */
+ cp = buf + 0*UNROLL;
+ phi0 = buf + 1*UNROLL;
+ mult = buf + 2*UNROLL;
+ p = buf + 3*UNROLL;
+ q = buf + 4*UNROLL;
+ sf_i = buf + 5*UNROLL;
+ msf_l = buf + 6*UNROLL;
+
+ set_pbc_simd(pbc, &pbc_simd);
+
+ /* nbonds is the number of dihedrals times nfa1, here we step UNROLL dihs */
+ for (i = 0; (i < nbonds); i += UNROLL*nfa1)
+ {
+ /* Collect atoms quadruplets for UNROLL dihedrals.
+ * iu indexes into forceatoms, we should not let iu go beyond nbonds.
+ */
+ iu = i;
+ for (s = 0; s < UNROLL; s++)
+ {
+ type = forceatoms[iu];
+ ai[s] = forceatoms[iu+1];
+ aj[s] = forceatoms[iu+2];
+ ak[s] = forceatoms[iu+3];
+ al[s] = forceatoms[iu+4];
- /* Caclulate 4 dihedral angles at once */
- dih_angle_sse(x, ai, aj, ak, al, pbc, t1, t2, t3, rs, buf);
+ cp[s] = forceparams[type].pdihs.cpA;
+ phi0[s] = forceparams[type].pdihs.phiA*DEG2RAD;
+ mult[s] = forceparams[type].pdihs.mult;
- i4 = i;
- for (s = 0; s < 4; s++)
- {
- if (i4 < nbonds)
- {
- /* Calculate the coefficient and angle deviation */
- type = forceatoms[i4];
- dopdihs_mdphi(forceparams[type].pdihs.cpA,
- forceparams[type].pdihs.cpB,
- forceparams[type].pdihs.phiA,
- forceparams[type].pdihs.phiB,
- forceparams[type].pdihs.mult,
- buf[16+s], lambda, &cp[s], &buf[16+s]);
- mult[s] = forceparams[type].pdihs.mult;
- }
- else
+ /* At the end fill the arrays with identical entries */
+ if (iu + nfa1 < nbonds)
{
- buf[16+s] = 0;
+ iu += nfa1;
}
- i4 += 5;
}
- /* Calculate 4 sines at once */
- mdphi_SSE = _mm_load_ps(buf+16);
- gmx_mm_sincos_ps(mdphi_SSE, &sin_SSE, &cos_SSE);
- _mm_store_ps(buf+16, sin_SSE);
-
- i4 = i;
+ /* Caclulate UNROLL dihedral angles at once */
+ dih_angle_simd(x, ai, aj, ak, al, &pbc_simd,
+ dr,
+ &phi_S,
+ &mx_S, &my_S, &mz_S,
+ &nx_S, &ny_S, &nz_S,
+ &nrkj_m2_S,
+ &nrkj_n2_S,
+ p, q);
+
+ cp_S = gmx_load_pr(cp);
+ phi0_S = gmx_load_pr(phi0);
+ mult_S = gmx_load_pr(mult);
+
+ mdphi_S = gmx_sub_pr(gmx_mul_pr(mult_S, phi_S), phi0_S);
+
+ /* Calculate UNROLL sines at once */
+ gmx_sincos_pr(mdphi_S, &sin_S, &cos_S);
+ mddphi_S = gmx_mul_pr(gmx_mul_pr(cp_S, mult_S), sin_S);
+ sf_i_S = gmx_mul_pr(mddphi_S, nrkj_m2_S);
+ msf_l_S = gmx_mul_pr(mddphi_S, nrkj_n2_S);
+
+ /* After this m?_S will contain f[i] */
+ mx_S = gmx_mul_pr(sf_i_S, mx_S);
+ my_S = gmx_mul_pr(sf_i_S, my_S);
+ mz_S = gmx_mul_pr(sf_i_S, mz_S);
+
+ /* After this m?_S will contain -f[l] */
+ nx_S = gmx_mul_pr(msf_l_S, nx_S);
+ ny_S = gmx_mul_pr(msf_l_S, ny_S);
+ nz_S = gmx_mul_pr(msf_l_S, nz_S);
+
+ gmx_store_pr(dr + 0*UNROLL, mx_S);
+ gmx_store_pr(dr + 1*UNROLL, my_S);
+ gmx_store_pr(dr + 2*UNROLL, mz_S);
+ gmx_store_pr(dr + 3*UNROLL, nx_S);
+ gmx_store_pr(dr + 4*UNROLL, ny_S);
+ gmx_store_pr(dr + 5*UNROLL, nz_S);
+
+ iu = i;
s = 0;
do
{
- ddphi = -cp[s]*mult[s]*buf[16+s];
-
- do_dih_fup_noshiftf_precalc(ai[s], aj[s], ak[s], al[s], ddphi,
- buf[ 0+s], buf[ 4+s],
- buf[ 8+s], buf[12+s],
- rs[0+s].v, rs[4+s].v,
+ do_dih_fup_noshiftf_precalc(ai[s], aj[s], ak[s], al[s],
+ p[s], q[s],
+ dr[ XX *UNROLL+s],
+ dr[ YY *UNROLL+s],
+ dr[ ZZ *UNROLL+s],
+ dr[(DIM+XX)*UNROLL+s],
+ dr[(DIM+YY)*UNROLL+s],
+ dr[(DIM+ZZ)*UNROLL+s],
f);
s++;
- i4 += 5;
+ iu += nfa1;
}
- while (s < 4 && i4 < nbonds);
+ while (s < UNROLL && iu < nbonds);
}
+#undef UNROLL
}
-#endif /* SSE_PROPER_DIHEDRALS */
+#endif /* SIMD_BONDEDS */
real idihs(int nbonds,
pbc, g, lambda[efptFTYPE], &(dvdl[efptFTYPE]),
md, fcd, global_atom_index);
}
+#ifdef SIMD_BONDEDS
+ else if (ftype == F_ANGLES &&
+ !bCalcEnerVir && fr->efep == efepNO)
+ {
+ /* No energies, shift forces, dvdl */
+ angles_noener_simd(nbn, idef->il[ftype].iatoms+nb0,
+ idef->iparams,
+ (const rvec*)x, f,
+ pbc, g, lambda[efptFTYPE], md, fcd,
+ global_atom_index);
+ v = 0;
+ }
+#endif
else if (ftype == F_PDIHS &&
!bCalcEnerVir && fr->efep == efepNO)
{
/* No energies, shift forces, dvdl */
-#ifndef SSE_PROPER_DIHEDRALS
+#ifndef SIMD_BONDEDS
pdihs_noener
#else
- pdihs_noener_sse
+ pdihs_noener_simd
#endif
(nbn, idef->il[ftype].iatoms+nb0,
idef->iparams,
v = do_nonbonded_listed(ftype, nbn, iatoms+nb0, idef->iparams, (const rvec*)x, f, fshift,
pbc, g, lambda, dvdl, md, fr, grpp, global_atom_index);
- enerd->dvdl_nonlin[efptCOUL] += dvdl[efptCOUL];
- enerd->dvdl_nonlin[efptVDW] += dvdl[efptVDW];
-
if (bPrintSepPot)
{
fprintf(fplog, " %-5s + %-15s #%4d dVdl %12.5e\n",
#define NCR (int)asize(CopyrightText)
/* TODO: Is this exception still needed? */
#ifdef GMX_FAHCORE
-#define NLICENSE 0 /*FAH has an exception permission from GPL to allow digital signatures in Gromacs*/
+#define NLICENSE 0 /*FAH has an exception permission from LGPL to allow digital signatures in Gromacs*/
#else
#define NLICENSE (int)asize(LicenseText)
#endif
}
#ifdef HAVE_LIBMKL
/* MKL might be used for LAPACK/BLAS even if FFTs use FFTW, so keep it separate */
- fprintf(fp, "Linked with Intel MKL version %s.%s.%s.\n",
+ fprintf(fp, "Linked with Intel MKL version %d.%d.%d.\n",
__INTEL_MKL__, __INTEL_MKL_MINOR__, __INTEL_MKL_UPDATE__);
#endif
#ifdef GMX_GPU
via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software
packages (and has been). We only ask that proper credit be given to the authors."
-While the rest of Gromacs is GPL, we think it's only fair to give you the same rights to
+While the rest of Gromacs is LGPL, we think it's only fair to give you the same rights to
our modified BLAS files as the original netlib versions, so do what you want with them.
However, be warned that we have only tested that they to the right thing in the cases used
in Gromacs (primarily full & sparse matrix diagonalization), so in most cases it is a much
via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software
packages (and has been). We only ask that proper credit be given to the authors."
-While the rest of Gromacs is GPL, we think it's only fair to give you the same rights to
+While the rest of Gromacs is LGPL, we think it's only fair to give you the same rights to
our modified LAPACK files as the original netlib versions, so do what you want with them.
However, be warned that we have only tested that they to the right thing in the cases used
* platforms like Microsoft Windows we have created a private version
* of the necessary routines and distribute them with the Gromacs source.
*
- * Although the rest of Gromacs is GPL, you can copy and use the XDR
+ * Although the rest of Gromacs is LGPL, you can copy and use the XDR
* routines in any way you want as long as you obey Sun's license:
*
* Sun RPC is a product of Sun Microsystems, Inc. and is provided for
ip->restraint.up2A != ip->restraint.up2B ||
ip->restraint.kA != ip->restraint.kB);
break;
+ case F_UREY_BRADLEY:
+ bPert = (ip->u_b.thetaA != ip->u_b.thetaB ||
+ ip->u_b.kthetaA != ip->u_b.kthetaB ||
+ ip->u_b.r13A != ip->u_b.r13B ||
+ ip->u_b.kUBA != ip->u_b.kUBB);
+ break;
case F_PDIHS:
case F_PIDIHS:
case F_ANGRES:
fr->bStep = FALSE;
fr->bTime = FALSE;
fr->bLambda = FALSE;
+ fr->bFepState = FALSE;
fr->bAtoms = FALSE;
fr->bPrec = FALSE;
fr->bX = FALSE;
fr->step = 0;
fr->time = 0;
fr->lambda = 0;
+ fr->fep_state = 0;
fr->atoms = NULL;
fr->prec = 0;
fr->x = NULL;
# Even though the OpenMM build has "moved to contrib", many things
# have be be done from within the scope of the CMakeLists.txt that
# builds its mdrun, and that is here
- include(../contrib/BuildMdrunOpenMM)
+ list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/src/contrib)
+ find_package(OpenMM)
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR})
+ include(${CMAKE_SOURCE_DIR}/src/contrib/BuildMdrunOpenMM.cmake)
endif(GMX_OPENMM)
if(GMX_GPU OR GMX_FORCE_CXX)
target_link_libraries(mdrun gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS})
set_target_properties(mdrun PROPERTIES OUTPUT_NAME "mdrun${GMX_BINARY_SUFFIX}" COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+if(GMX_OPENMM)
+ target_link_libraries(mdrun openmm_api_wrapper)
+endif()
+
# Construct component groups for installation; note that a component may
# belong to only one group
foreach(PROGRAM ${GMX_KERNEL_PROGRAMS})
#define PME_LB_ACCEL_TOL 1.02
enum {
- epmelblimNO, epmelblimBOX, epmelblimDD, epmelblimNR
+ epmelblimNO, epmelblimBOX, epmelblimDD, epmelblimPMEGRID, epmelblimNR
};
const char *pmelblim_str[epmelblimNR] =
-{ "no", "box size", "domain decompostion" };
+{ "no", "box size", "domain decompostion", "PME grid restriction" };
struct pme_load_balancing {
int nstage; /* the current maximum number of stages */
}
static gmx_bool pme_loadbal_increase_cutoff(pme_load_balancing_t pme_lb,
- int pme_order)
+ int pme_order,
+ const gmx_domdec_t *dd)
{
pme_setup_t *set;
+ int npmenodes_x, npmenodes_y;
real fac, sp;
real tmpr_coulomb, tmpr_vdw;
int d;
+ gmx_bool grid_ok;
/* Try to add a new setup with next larger cut-off to the list */
pme_lb->n++;
set = &pme_lb->setup[pme_lb->n-1];
set->pmedata = NULL;
+ get_pme_nnodes(dd, &npmenodes_x, &npmenodes_y);
+
fac = 1;
do
{
+ /* Avoid infinite while loop, which can occur at the minimum grid size.
+ * Note that in practice load balancing will stop before this point.
+ * The factor 2.1 allows for the extreme case in which only grids
+ * of powers of 2 are allowed (the current code supports more grids).
+ */
+ if (fac > 2.1)
+ {
+ pme_lb->n--;
+
+ return FALSE;
+ }
+
fac *= 1.01;
clear_ivec(set->grid);
sp = calc_grid(NULL, pme_lb->box_start,
&set->grid[YY],
&set->grid[ZZ]);
- /* In parallel we can't have grids smaller than 2*pme_order,
- * and we would anyhow not gain much speed at these grid sizes.
+ /* As here we can't easily check if one of the PME nodes
+ * uses threading, we do a conservative grid check.
+ * This means we can't use pme_order or less grid lines
+ * per PME node along x, which is not a strong restriction.
*/
- for (d = 0; d < DIM; d++)
- {
- if (set->grid[d] <= 2*pme_order)
- {
- pme_lb->n--;
-
- return FALSE;
- }
- }
+ gmx_pme_check_restrictions(pme_order,
+ set->grid[XX], set->grid[YY], set->grid[ZZ],
+ npmenodes_x, npmenodes_y,
+ TRUE,
+ FALSE,
+ &grid_ok);
}
- while (sp <= 1.001*pme_lb->setup[pme_lb->cur].spacing);
+ while (sp <= 1.001*pme_lb->setup[pme_lb->cur].spacing || !grid_ok);
set->rcut_coulomb = pme_lb->cut_spacing*sp;
{
char buf[STRLEN], sbuf[22];
- sprintf(buf, "step %4s: the %s limited the PME load balancing to a coulomb cut-off of %.3f",
+ sprintf(buf, "step %4s: the %s limits the PME load balancing to a coulomb cut-off of %.3f",
gmx_step_str(step, sbuf),
pmelblim_str[pme_lb->elimited],
pme_lb->setup[pme_loadbal_end(pme_lb)-1].rcut_coulomb);
else
{
/* Find the next setup */
- OK = pme_loadbal_increase_cutoff(pme_lb, ir->pme_order);
+ OK = pme_loadbal_increase_cutoff(pme_lb, ir->pme_order, cr->dd);
+
+ if (!OK)
+ {
+ pme_lb->elimited = epmelblimPMEGRID;
+ }
}
if (OK && ir->ePBC != epbcNONE)
return pmenode;
}
+void get_pme_nnodes(const gmx_domdec_t *dd,
+ int *npmenodes_x, int *npmenodes_y)
+{
+ if (dd != NULL)
+ {
+ *npmenodes_x = dd->comm->npmenodes_x;
+ *npmenodes_y = dd->comm->npmenodes_y;
+ }
+ else
+ {
+ *npmenodes_x = 1;
+ *npmenodes_y = 1;
+ }
+}
+
gmx_bool gmx_pmeonlynode(t_commrec *cr, int sim_nodeid)
{
gmx_bool bPMEOnlyNode;
/* The SIMD width here is actually independent of that in the kernels,
* but we use the same width for simplicity (usually optimal anyhow).
*/
-#if GMX_NBNXN_SIMD_BITWIDTH == 128
-#define GMX_MM128_HERE
-#endif
-#if GMX_NBNXN_SIMD_BITWIDTH == 256
-#define GMX_MM256_HERE
+#ifdef GMX_NBNXN_HALF_WIDTH_SIMD
+#define GMX_USE_HALF_WIDTH_SIMD_HERE
#endif
#include "gmx_simd_macros.h"
gmx_store_pr(dest+i, dest_SSE);
}
}
-
-#undef GMX_MM128_HERE
-#undef GMX_MM256_HERE
#endif
}
} nbnxn_grid_t;
#ifdef GMX_NBNXN_SIMD
-#if GMX_NBNXN_SIMD_BITWIDTH == 128
-#define GMX_MM128_HERE
-#else
-#if GMX_NBNXN_SIMD_BITWIDTH == 256
-#define GMX_MM256_HERE
-#else
-#error "unsupported GMX_NBNXN_SIMD_BITWIDTH"
-#endif
+#ifdef GMX_NBNXN_HALF_WIDTH_SIMD
+#define GMX_USE_HALF_WIDTH_SIMD_HERE
#endif
#include "gmx_simd_macros.h"
static gmx_icell_set_x_t icell_set_x_supersub_sse8;
#endif
-#undef GMX_MM128_HERE
-#undef GMX_MM256_HERE
-
/* Local cycle count struct for profiling */
typedef struct {
int count;
return work;
}
-static void
-gmx_pme_check_grid_restrictions(FILE *fplog, char dim, int nnodes, int *nk)
+void gmx_pme_check_restrictions(int pme_order,
+ int nkx, int nky, int nkz,
+ int nnodes_major,
+ int nnodes_minor,
+ gmx_bool bUseThreads,
+ gmx_bool bFatal,
+ gmx_bool *bValidSettings)
{
- int nk_new;
-
- if (*nk % nnodes != 0)
+ if (pme_order > PME_ORDER_MAX)
{
- nk_new = nnodes*(*nk/nnodes + 1);
+ if (!bFatal)
+ {
+ *bValidSettings = FALSE;
+ return;
+ }
+ gmx_fatal(FARGS, "pme_order (%d) is larger than the maximum allowed value (%d). Modify and recompile the code if you really need such a high order.",
+ pme_order, PME_ORDER_MAX);
+ }
- if (2*nk_new >= 3*(*nk))
+ if (nkx <= pme_order*(nnodes_major > 1 ? 2 : 1) ||
+ nky <= pme_order*(nnodes_minor > 1 ? 2 : 1) ||
+ nkz <= pme_order)
+ {
+ if (!bFatal)
{
- gmx_fatal(FARGS, "The PME grid size in dim %c (%d) is not divisble by the number of nodes doing PME in dim %c (%d). The grid size would have to be increased by more than 50%% to make the grid divisible. Change the total number of nodes or the number of domain decomposition cells in x or the PME grid %c dimension (and the cut-off).",
- dim, *nk, dim, nnodes, dim);
+ *bValidSettings = FALSE;
+ return;
}
+ gmx_fatal(FARGS, "The PME grid sizes need to be larger than pme_order (%d) and for dimensions with domain decomposition larger than 2*pme_order",
+ pme_order);
+ }
- if (fplog != NULL)
+ /* Check for a limitation of the (current) sum_fftgrid_dd code.
+ * We only allow multiple communication pulses in dim 1, not in dim 0.
+ */
+ if (bUseThreads && (nkx < nnodes_major*pme_order &&
+ nkx != nnodes_major*(pme_order - 1)))
+ {
+ if (!bFatal)
{
- fprintf(fplog, "\nNOTE: The PME grid size in dim %c (%d) is not divisble by the number of nodes doing PME in dim %c (%d). Increasing the PME grid size in dim %c to %d. This will increase the accuracy and will not decrease the performance significantly on this number of nodes. For optimal performance change the total number of nodes or the number of domain decomposition cells in x or the PME grid %c dimension (and the cut-off).\n\n",
- dim, *nk, dim, nnodes, dim, nk_new, dim);
+ *bValidSettings = FALSE;
+ return;
}
+ gmx_fatal(FARGS, "The number of PME grid lines per node along x is %g. But when using OpenMP threads, the number of grid lines per node along x should be >= pme_order (%d) or = pmeorder-1. To resolve this issue, use less nodes along x (and possibly more along y and/or z) by specifying -dd manually.",
+ nkx/(double)nnodes_major, pme_order);
+ }
- *nk = nk_new;
+ if (bValidSettings != NULL)
+ {
+ *bValidSettings = TRUE;
}
+
+ return;
}
int gmx_pme_init(gmx_pme_t * pmedata,
pme->pme_order = ir->pme_order;
pme->epsilon_r = ir->epsilon_r;
- if (pme->pme_order > PME_ORDER_MAX)
- {
- gmx_fatal(FARGS, "pme_order (%d) is larger than the maximum allowed value (%d). Modify and recompile the code if you really need such a high order.",
- pme->pme_order, PME_ORDER_MAX);
- }
-
- /* Currently pme.c supports only the fft5d FFT code.
- * Therefore the grid always needs to be divisible by nnodes.
- * When the old 1D code is also supported again, change this check.
- *
- * This check should be done before calling gmx_pme_init
- * and fplog should be passed iso stderr.
- *
- if (pme->ndecompdim >= 2)
- */
- if (pme->ndecompdim >= 1)
- {
- /*
- gmx_pme_check_grid_restrictions(pme->nodeid==0 ? stderr : NULL,
- 'x',nnodes_major,&pme->nkx);
- gmx_pme_check_grid_restrictions(pme->nodeid==0 ? stderr : NULL,
- 'y',nnodes_minor,&pme->nky);
- */
- }
-
- if (pme->nkx <= pme->pme_order*(pme->nnodes_major > 1 ? 2 : 1) ||
- pme->nky <= pme->pme_order*(pme->nnodes_minor > 1 ? 2 : 1) ||
- pme->nkz <= pme->pme_order)
- {
- gmx_fatal(FARGS, "The PME grid sizes need to be larger than pme_order (%d) and for dimensions with domain decomposition larger than 2*pme_order", pme->pme_order);
- }
+ /* If we violate restrictions, generate a fatal error here */
+ gmx_pme_check_restrictions(pme->pme_order,
+ pme->nkx, pme->nky, pme->nkz,
+ pme->nnodes_major,
+ pme->nnodes_minor,
+ pme->bUseThreads,
+ TRUE,
+ NULL);
if (pme->nnodes > 1)
{
pme->nky,
(div_round_up(pme->nkx, pme->nnodes_major)+pme->pme_order+1)*pme->nkz);
- /* Check for a limitation of the (current) sum_fftgrid_dd code.
- * We only allow multiple communication pulses in dim 1, not in dim 0.
+ /* Double-check for a limitation of the (current) sum_fftgrid_dd code.
+ * Note that gmx_pme_check_restrictions checked for this already.
*/
- if (pme->bUseThreads && (pme->overlap[0].noverlap_nodes > 1 ||
- pme->nkx < pme->nnodes_major*pme->pme_order))
+ if (pme->bUseThreads && pme->overlap[0].noverlap_nodes > 1)
{
- gmx_fatal(FARGS, "The number of PME grid lines per node along x is %g. But when using OpenMP threads, the number of grid lines per node along x and should be >= pme_order (%d). To resolve this issue, use less nodes along x (and possibly more along y and/or z) by specifying -dd manually.",
- pme->nkx/(double)pme->nnodes_major, pme->pme_order);
+ gmx_incons("More than one communication pulse required for grid overlap communication along the major dimension while using threads");
}
snew(pme->bsp_mod[XX], pme->nkx);
}
}
+ if (inputrec->bRot)
+ {
+ /* Enforced rotation has its own cycle counter that starts after the collective
+ * coordinates have been communicated. It is added to ddCyclF to allow
+ * for proper load-balancing */
+ wallcycle_start(wcycle, ewcROT);
+ do_rotation(cr, inputrec, box, x, t, step, wcycle, bNS);
+ wallcycle_stop(wcycle, ewcROT);
+ }
+
/* Start the force cycle counter.
* This counter is stopped in do_forcelow_level.
* No parallel communication should occur while this counter is running,
f, vir_force, mdatoms, enerd, lambda, t);
}
+ /* Add the forces from enforced rotation potentials (if any) */
+ if (inputrec->bRot)
+ {
+ wallcycle_start(wcycle, ewcROTadd);
+ enerd->term[F_COM_PULL] += add_rot_forces(inputrec->rot, f, cr, step, t);
+ wallcycle_stop(wcycle, ewcROTadd);
+ }
+
if (PAR(cr) && !(cr->duty & DUTY_PME))
{
/* In case of node-splitting, the PP nodes receive the long-range
/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.0
- *
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2001
* BIOSON Research Institute, Dept. of Biophysical Chemistry
* University of Groningen, The Netherlands
- *
- * 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
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
- *
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 http://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.
- *
- * Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
- *
- * And Hey:
- * GROup of MAchos and Cynical Suckers
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifndef _alert_bm
/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.0
- *
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2001
* BIOSON Research Institute, Dept. of Biophysical Chemistry
* University of Groningen, The Netherlands
- *
- * 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
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
- *
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 http://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.
- *
- * Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
- *
- * And Hey:
- * GROup of MAchos and Cynical Suckers
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifndef _ff_bm
/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.0
- *
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2001
* BIOSON Research Institute, Dept. of Biophysical Chemistry
* University of Groningen, The Netherlands
- *
- * 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
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
- *
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 http://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.
- *
- * Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
- *
- * And Hey:
- * GROup of MAchos and Cynical Suckers
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.0
- *
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2001
* BIOSON Research Institute, Dept. of Biophysical Chemistry
* University of Groningen, The Netherlands
- *
- * 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
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
- *
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 http://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.
- *
- * Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
- *
- * And Hey:
- * GROup of MAchos and Cynical Suckers
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifndef _info_bm
/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.0
- *
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2001
* BIOSON Research Institute, Dept. of Biophysical Chemistry
* University of Groningen, The Netherlands
- *
- * 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
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
- *
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 http://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.
- *
- * Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
- *
- * And Hey:
- * GROup of MAchos and Cynical Suckers
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifndef _play_bm
/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.0
- *
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2001
* BIOSON Research Institute, Dept. of Biophysical Chemistry
* University of Groningen, The Netherlands
- *
- * 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
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
- *
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 http://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.
- *
- * Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
- *
- * And Hey:
- * GROup of MAchos and Cynical Suckers
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#define rama_width 48
/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.0
- *
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2001
* BIOSON Research Institute, Dept. of Biophysical Chemistry
* University of Groningen, The Netherlands
- *
- * 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
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
- *
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 http://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.
- *
- * Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
- *
- * And Hey:
- * GROup of MAchos and Cynical Suckers
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifndef _rewind_bm
#define _rewind_bm
/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.0
- *
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2001
* BIOSON Research Institute, Dept. of Biophysical Chemistry
* University of Groningen, The Netherlands
- *
- * 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
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
- *
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 http://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.
- *
- * Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
- *
- * And Hey:
- * GROup of MAchos and Cynical Suckers
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifndef _stop_bm
/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.0
- *
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2001
* BIOSON Research Institute, Dept. of Biophysical Chemistry
* University of Groningen, The Netherlands
- *
- * 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
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
- *
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 http://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.
- *
- * Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
- *
- * And Hey:
- * GROup of MAchos and Cynical Suckers
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifndef _stop_ani_bm
/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * 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
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * 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.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, 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 http://www.gromacs.org.
*
- * And Hey:
- * Green Red Orange Magenta Azure Cyan Skyblue
+ * 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>
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * 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
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * 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.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, 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 http://www.gromacs.org.
*
- * And Hey:
- * Green Red Orange Magenta Azure Cyan Skyblue
+ * 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>
snew(skmol, maxidx);
/* Must init pbc every step because of pressure coupling */
+ set_pbc(&pbc,ePBC,box);
gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms, box);
gmx_rmpbc(gpbc, natoms, box, x);
/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
*
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- *
- * The make_edi program was generously contributed by Oliver Lange, based
- * on the code from g_anaeig. You can reach him as olange@gwdg.de.
- *
- * 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
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * 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.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, 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 http://www.gromacs.org.
*
- * And Hey:
- * Gromacs Runs One Microsecond At Cannonball Speeds
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/* The make_edi program was generously contributed by Oliver Lange, based
+ * on the code from g_anaeig. You can reach him as olange@gwdg.de. He
+ * probably also holds copyright to the following code.
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * 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
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * 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.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, 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 http://www.gromacs.org.
*
- * And Hey:
- * Green Red Orange Magenta Azure Cyan Skyblue
+ * 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>
/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * 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
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * 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.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, 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 http://www.gromacs.org.
*
- * And Hey:
- * Green Red Orange Magenta Azure Cyan Skyblue
+ * 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>
/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * 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
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * 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.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, 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 http://www.gromacs.org.
*
- * And Hey:
- * Good gRace! Old Maple Actually Chews Slate
+ * 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>
/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * 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
+ * Copyright (c) 2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * 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.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, 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 http://www.gromacs.org.
*
- * And Hey:
- * Green Red Orange Magenta Azure Cyan Skyblue
+ * 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>
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff