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)")
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
#
# 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")
# 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
* 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
gmx_bool bNEMD;
int ngtc; /* The number of T-coupling groups */
t_grp_tcstat *tcstat; /* T-coupling data */
- tensor **ekin_work_alloc; /* Allocated locations of ekin_work */
+ tensor **ekin_work_alloc; /* Allocated locations for *_work members */
tensor **ekin_work; /* Work arrays for tcstat per thread */
+ real **dekindl_work; /* Work location for dekindl per thread */
int ngacc; /* The number of acceleration groups */
t_grp_acc *grpstat; /* Acceleration data */
tensor ekin; /* overall kinetic energy */
/*
+ * 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"
#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
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})
/* could this be done more readably/compactly? */
switch (i)
{
+ case (efptMASS):
+ index = F_DKDL;
+ break;
case (efptCOUL):
index = F_DVDL_COUL;
break;
case (efptRESTRAINT):
index = F_DVDL_RESTRAINT;
break;
- case (efptMASS):
- index = F_DKDL;
- break;
default:
index = F_DVDL;
break;
so we don't need to add anything to the
enerd->enerpart_lambda[0] */
- /* we don't need to worry about dvdl contributions to the current lambda, because
- it's automatically zero */
-
- /* first kinetic energy term */
- dlam = (fepvals->all_lambda[efptMASS][i] - lambda[efptMASS]);
-
- enerd->enerpart_lambda[i+1] += enerd->term[F_DKDL]*dlam;
+ /* we don't need to worry about dvdl_lin contributions to dE at
+ current lambda, because the contributions to the current
+ lambda are automatically zeroed */
for (j = 0; j < efptNR; j++)
{
- if (j == efptMASS)
- {
- continue;
- } /* no other mass term to worry about */
-
+ /* Note that this loop is over all dhdl components, not just the separated ones */
dlam = (fepvals->all_lambda[j][i]-lambda[j]);
enerd->enerpart_lambda[i+1] += dlam*enerd->dvdl_lin[j];
if (debug)
gmx_bool bEner, bPres, bTemp, bVV;
gmx_bool bRerunMD, bStopCM, bGStat, bIterate,
bFirstIterate, bReadEkin, bEkinAveVel, bScaleEkin, bConstrain;
- real ekin, temp, prescorr, enercorr, dvdlcorr;
+ real ekin, temp, prescorr, enercorr, dvdlcorr, dvdl_ekin;
/* translate CGLO flags to gmx_booleans */
bRerunMD = flags & CGLO_RERUNMD;
bSaveEkinOld: If TRUE (in the case of iteration = bIterate is TRUE), we don't reset the ekinscale_nhc.
If FALSE, we go ahead and erase over it.
*/
- enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, &(enerd->term[F_DKDL]),
+ enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, &dvdl_ekin,
bEkinAveVel, bIterate, bScaleEkin);
+ enerd->dvdl_lin[efptMASS] = (double) dvdl_ekin;
enerd->term[F_EKIN] = trace(ekind->ekin);
}
snew(ekind->ekin_work_alloc, nthread);
snew(ekind->ekin_work, nthread);
+ snew(ekind->dekindl_work, nthread);
#pragma omp parallel for num_threads(nthread) schedule(static)
for (thread = 0; thread < nthread; thread++)
{
- /* Allocate 2 elements extra on both sides,
- * so in single precision we have 2*3*3*4=72 bytes buffer
- * on both sides to avoid cache pollution.
+#define EKIN_WORK_BUFFER_SIZE 2
+ /* Allocate 2 extra elements on both sides, so in single
+ * precision we have
+ * EKIN_WORK_BUFFER_SIZE*DIM*DIM*sizeof(real) = 72/144 bytes
+ * buffer on both sides to avoid cache pollution.
*/
- snew(ekind->ekin_work_alloc[thread], ekind->ngtc+4);
- ekind->ekin_work[thread] = ekind->ekin_work_alloc[thread] + 2;
+ snew(ekind->ekin_work_alloc[thread], ekind->ngtc+2*EKIN_WORK_BUFFER_SIZE);
+ ekind->ekin_work[thread] = ekind->ekin_work_alloc[thread] + EKIN_WORK_BUFFER_SIZE;
+ /* Nasty hack so we can have the per-thread accumulation
+ * variable for dekindl in the same thread-local cache lines
+ * as the per-thread accumulation tensors for ekin[fh],
+ * because they are accumulated in the same loop. */
+ ekind->dekindl_work[thread] = &(ekind->ekin_work[thread][ekind->ngtc][0][0]);
+#undef EKIN_WORK_BUFFER_SIZE
}
ekind->ngacc = opts->ngacc;
}
}
else
-
{
/* Calculate the full step Ekin as the average of the half steps */
for (j = 0; (j < DIM); j++)
}
if (dekindlambda)
{
- *dekindlambda = 0.5*(ekind->dekindl + ekind->dekindl_old);
+ if (bEkinAveVel)
+ {
+ *dekindlambda = ekind->dekindl;
+ }
+ else
+ {
+ *dekindlambda = 0.5*(ekind->dekindl + ekind->dekindl_old);
+ }
}
return T;
}
end_t = md->start + ((thread+1)*md->homenr)/nthread;
ekin_sum = ekind->ekin_work[thread];
- dekindl_sum = &ekind->ekin_work[thread][opts->ngtc][0][0];
+ dekindl_sum = ekind->dekindl_work[thread];
for (gt = 0; gt < opts->ngtc; gt++)
{
clear_mat(ekin_sum[gt]);
}
+ *dekindl_sum = 0.0;
ga = 0;
gt = 0;
}
if (md->nMassPerturbed && md->bPerturbed[n])
{
- *dekindl_sum -=
+ *dekindl_sum +=
0.5*(md->massB[n] - md->massA[n])*iprod(v_corrt, v_corrt);
}
}
}
}
- ekind->dekindl += ekind->ekin_work[thread][opts->ngtc][0][0];
+ ekind->dekindl += *ekind->dekindl_work[thread];
}
inc_nrnb(nrnb, eNR_EKIN, md->homenr);
}
if (md->nPerturbed && md->bPerturbed[n])
{
- dekindl -= 0.5*(md->massB[n] - md->massA[n])*iprod(v_corrt, v_corrt);
+ dekindl += 0.5*(md->massB[n] - md->massA[n])*iprod(v_corrt, v_corrt);
}
}
ekind->dekindl = dekindl;
/*
- *
- * 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>
/*
+ * 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