#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
mark_as_advanced(GMX_BROKEN_CALLOC)
-option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
-mark_as_advanced(GMX_LOAD_PLUGINS)
option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
include(gmxManageLinearAlgebraLibraries)
-# Whether GROMACS will really try to compile support for VMD plugins
-set(GMX_USE_PLUGINS OFF)
+include(gmxManagePluginSupport)
-if(GMX_LOAD_PLUGINS)
- if(NOT WIN32)
- # Native Windows does not have, nor need dlopen
- include(gmxTestdlopen)
- gmx_test_dlopen(HAVE_DLOPEN)
- endif()
-
- # so, should we use plug-ins?
- if(WIN32 OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
- if(NOT VMD_QUIETLY)
- MESSAGE(STATUS "Using dynamic plugins (e.g VMD-supported file formats)")
- endif()
+if (GMX_USE_PLUGINS)
if(NOT GMX_VMD_PLUGIN_PATH)
- find_package(VMD)
+ find_package(VMD)
endif()
- set(GMX_USE_PLUGINS ON)
- list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
- set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
- else()
- set(PKG_DL_LIBS)
- endif()
endif()
-set(VMD_QUIETLY TRUE CACHE INTERNAL "")
# Link real-time library for POSIX timers. The check for clock_gettime
# confirms the linkability of rt.
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
endif()
#Verify FFTW is compiled with fPIC (necessary for shared libraries)
- if (CMAKE_OBJDUMP AND CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64" AND BUILD_SHARED_LIBS AND NOT CYGWIN)
+ if (CMAKE_OBJDUMP AND CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64" AND BUILD_SHARED_LIBS AND NOT CYGWIN AND NOT APPLE)
execute_process(COMMAND ${CMAKE_OBJDUMP} --reloc ${${FFTW}_LIBRARY} OUTPUT_VARIABLE ${FFTW}_OBJDUMP)
if (${${FFTW}_OBJDUMP} MATCHES "R_X86_64" #Should always be true for static libraries. Checks that objdump works properly and that the library isn't dynamic
AND NOT ${${FFTW}_OBJDUMP} MATCHES "R_X86_64_PLT32")
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
GMX_TEST_CXXFLAG(CXXFLAGS_DEBUG "-O0" GMXC_CXXFLAGS_DEBUG)
GMX_TEST_CXXFLAG(CXXFLAGS_FP_RELASSERT "-fp-model except -fp-model precise" GMXC_CXXFLAGS_RELWITHASSERT)
else()
-#809: exception specification for virtual function X is incompatible with that of overridden function
if(NOT GMX_OPENMP)
GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "/wd3180" GMXC_CFLAGS)
endif()
if (GMX_COMPILER_WARNINGS)
-GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/W3 /wd177 /wd383 /wd411 /wd444 /wd809 /wd981 /wd1418 /wd1572 /wd1599 /wd2259 /wd3280 /wd11074 /wd11076 /wd2282" GMXC_CXXFLAGS)
+#809: exception specification for virtual function X is incompatible with that of overridden function
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/W3 /wd177 /wd383 /wd411 /wd444 /wd809 /wd981 /wd1418 /wd1572 /wd1599 /wd2259 /wd3280 /wd11074 /wd11076 /wd2282" GMXC_CXXFLAGS)
endif()
GMX_TEST_CXXFLAG(CXXFLAGS_OPT "/Qip" GMXC_CXXFLAGS_RELEASE)
endif()
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2016,2017, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# 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.
+
+include(gmxOptionUtilities)
+
+# Sets GMX_USE_PLUGINS=ON in the parent scope if the toolchain and
+# user selections permit the build to support plugin loading.
+function(gmx_manage_plugin_support)
+ gmx_option_trivalue(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" AUTO)
+ mark_as_advanced(GMX_LOAD_PLUGINS)
+
+ # Find out if non-Windows builds can support plugins. Native Windows
+ # neither needs nor has library support.
+ if (NOT WIN32)
+ # TODO Make a proper find_package for dlopen to find
+ # dlfcn.h. The CMake variable CMAKE_DL_LIBS works magically
+ # for the library, however.
+ include(gmxTestdlopen)
+ gmx_test_dlopen(HAVE_DLOPEN)
+ endif()
+
+ # Keep the status line quiet unless something relevant has
+ # changed.
+ gmx_check_if_changed(EMIT_STATUS_MESSAGES GMX_LOAD_PLUGINS BUILD_SHARED_LIBS HAVE_DLOPEN)
+
+ # Whether GROMACS will really try to compile support for VMD
+ # plugins.
+ set(GMX_USE_PLUGINS OFF)
+
+ # Plugins are supported natively on Windows
+ if (WIN32 OR (BUILD_SHARED_LIBS AND HAVE_DLOPEN))
+ set(GMX_USE_PLUGINS ${GMX_LOAD_PLUGINS})
+ elseif(GMX_LOAD_PLUGINS)
+ # Can't support plugins for some reason. If the user required
+ # plugins, emit fatal errors. Otherwise, emit status messages
+ # for AUTO and be silent for OFF.
+ set(message "")
+ if (NOT HAVE_DLOPEN)
+ set(message "${message}dlopen() support for using dynamic plugins for VMD-supported file formats is missing. ")
+ endif()
+ if(NOT BUILD_SHARED_LIBS)
+ set(message "${message}GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) ")
+ endif()
+ if (GMX_LOAD_PLUGINS_FORCE)
+ message(FATAL_ERROR "${message}Cannot build with GMX_LOAD_PLUGINS=${GMX_LOAD_PLUGINS}.")
+ endif()
+ if (GMX_LOAD_PLUGINS_AUTO AND EMIT_STATUS_MESSAGES)
+ message(STATUS "${message}")
+ endif()
+ endif()
+
+ if(EMIT_STATUS_MESSAGES)
+ if(GMX_USE_PLUGINS)
+ MESSAGE(STATUS "Using dynamic plugins (e.g VMD-supported file formats)")
+ else()
+ MESSAGE(STATUS "Not using dynamic plugins (e.g VMD-supported file formats)")
+ endif()
+ endif()
+ set(GMX_USE_PLUGINS ${GMX_USE_PLUGINS} PARENT_SCOPE)
+endfunction()
+
+gmx_manage_plugin_support()
+
+if(GMX_USE_PLUGINS)
+ list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
+ set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
+endif()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
int main() {
// Test nullptr
double *x = nullptr;
+ (void)x; // Suppressing unused variable warning
// Test range-based for loops
int array[5] = { 1, 2, 3, 4, 5 };
for (int& x : array)
/* Position restraints need an additional treatment */
if (ftype == F_POSRES || ftype == F_FBPOSRES)
{
- int nposres = dest->il[ftype].nr/2;
- if (nposres > dest->iparams_posres_nalloc)
+ int nposres = dest->il[ftype].nr/2;
+ // TODO: Simplify this code using std::vector
+ t_iparams * &iparams_dest = (ftype == F_POSRES ? dest->iparams_posres : dest->iparams_fbposres);
+ int &posres_nalloc = (ftype == F_POSRES ? dest->iparams_posres_nalloc : dest->iparams_fbposres_nalloc);
+ if (nposres > posres_nalloc)
{
- dest->iparams_posres_nalloc = over_alloc_large(nposres);
- srenew(dest->iparams_posres, dest->iparams_posres_nalloc);
+ posres_nalloc = over_alloc_large(nposres);
+ srenew(iparams_dest, posres_nalloc);
}
+
/* Set nposres to the number of original position restraints in dest */
for (int s = 1; s < nsrc; s++)
{
nposres -= src[s].idef.il[ftype].nr/2;
}
+
for (int s = 1; s < nsrc; s++)
{
- if (ftype == F_POSRES)
- {
- for (int i = 0; i < src[s].idef.il[ftype].nr/2; i++)
- {
- /* Correct the index into iparams_posres */
- dest->il[ftype].iatoms[nposres*2] = nposres;
- /* Copy the position restraint force parameters */
- dest->iparams_posres[nposres] = src[s].idef.iparams_posres[i];
- nposres++;
- }
- }
- else
+ const t_iparams *iparams_src = (ftype == F_POSRES ? src[s].idef.iparams_posres : src[s].idef.iparams_fbposres);
+
+ for (int i = 0; i < src[s].idef.il[ftype].nr/2; i++)
{
- for (int i = 0; i < src[s].idef.il[ftype].nr/2; i++)
- {
- /* Correct the index into iparams_fbposres */
- dest->il[ftype].iatoms[nposres*2] = nposres;
- /* Copy the position restraint force parameters */
- dest->iparams_fbposres[nposres] = src[s].idef.iparams_fbposres[i];
- nposres++;
- }
+ /* Correct the index into iparams_posres */
+ dest->il[ftype].iatoms[nposres*2] = nposres;
+ /* Copy the position restraint force parameters */
+ iparams_dest[nposres] = iparams_src[i];
+ nposres++;
}
}
}
"of both files will be used unless [TT]-first[tt] and [TT]-last[tt]",
"have been set explicitly.[PAR]",
- "When [TT]-v[tt], [TT]-eig[tt], [TT]-v2[tt] and [TT]-eig2[tt] are given,",
- "a single number for the overlap between the covariance matrices is",
- "generated. The formulas are::",
+ "When [TT]-v[tt] and [TT]-v2[tt] are given, a single number for the",
+ "overlap between the covariance matrices is generated. Note that the",
+ "eigenvalues are by default read from the timestamp field in the",
+ "eigenvector input files, but when [TT]-eig[tt], or [TT]-eig2[tt] are",
+ "given, the corresponding eigenvalues are used instead. The formulas are::",
"",
" difference = sqrt(tr((sqrt(M1) - sqrt(M2))^2))",
" normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))",
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"the reference structure for the fit is written first with t=-1.",
"The average (or reference when [TT]-ref[tt] is used) structure is",
"written with t=0, the eigenvectors",
- "are written as frames with the eigenvector number as timestamp.",
+ "are written as frames with the eigenvector number and eigenvalue",
+ "as step number and timestamp, respectively.",
"[PAR]",
"The eigenvectors can be analyzed with [gmx-anaeig].",
"[PAR]",
int i, n;
gmx_bool found;
+ if (n_bfac > atoms->nres)
+ {
+ peratom = TRUE;
+ }
+
bfac_max = -1e10;
bfac_min = 1e10;
for (i = 0; (i < n_bfac); i++)
{
- if (bfac_nr[i] - 1 >= atoms->nres)
- {
- peratom = TRUE;
- }
/* if ((bfac_nr[i]-1<0) || (bfac_nr[i]-1>=atoms->nr))
gmx_fatal(FARGS,"Index of B-Factor %d is out of range: %d (%g)",
i+1,bfac_nr[i],bfac[i]); */
"from a file with with following format: first line states number of",
"entries in the file, next lines state an index",
"followed by a B-factor. The B-factors will be attached per residue",
- "unless an index is larger than the number of residues or unless the",
+ "unless the number of B-factors is larger than the number of the residues or unless the",
"[TT]-atom[tt] option is set. Obviously, any type of numeric data can",
"be added instead of B-factors. [TT]-legend[tt] will produce",
"a row of CA atoms with B-factors ranging from the minimum to the",
"which can be calculated with [gmx-mdrun].",
"The eigenvectors are written to a trajectory file ([TT]-v[tt]).",
"The structure is written first with t=0. The eigenvectors",
- "are written as frames with the eigenvector number as timestamp.",
+ "are written as frames with the eigenvector number and eigenvalue",
+ "written as step number and timestamp, respectively.",
"The eigenvectors can be analyzed with [gmx-anaeig].",
"An ensemble of structures can be generated from the eigenvectors with",
"[gmx-nmens]. When mass weighting is used, the generated eigenvectors",
real rcoulomb = -1.0; /* Coulomb radius as set in .tpr file */
gmx_bool bScaleRvdw = TRUE;
gmx_int64_t bench_nsteps = BENCHSTEPS;
- gmx_int64_t new_sim_nsteps = -1; /* -1 indicates: not set by the user */
- gmx_int64_t cpt_steps = 0; /* Step counter in .cpt input file */
- int presteps = 100; /* Do a full cycle reset after presteps steps */
+ gmx_int64_t new_sim_nsteps = -1; /* -1 indicates: not set by the user */
+ gmx_int64_t cpt_steps = 0; /* Step counter in .cpt input file */
+ int presteps = 1500; /* Do a full cycle reset after presteps steps */
gmx_bool bOverwrite = FALSE, bKeepTPR;
gmx_bool bLaunch = FALSE;
char *ExtraArgs = nullptr;
graph, mdatoms,
vsite, shellfc ? *shellfc : nullptr);
- update_mdatoms(mdatoms, state_global->lambda[efptFEP]);
-
if (vsite)
{
set_vsite_top(vsite, *top, mdatoms, cr);
}
}
+ update_mdatoms(mdatoms, state_global->lambda[efptMASS]);
+
if (constr)
{
if (ir->eConstrAlg == econtSHAKE &&
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff