#
# 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.
#
# 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, 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.
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)
- if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 13.99.99)
- GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "/wd3180" GMXC_CFLAGS)
- else()
- GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "/wd161" GMXC_CXXFLAGS)
- endif()
+ 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)
- if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 15.00.00)
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN_OLD /wd193 GMXC_CXXFLAGS)
- endif()
+ #809: exception specification for virtual function X is incompatible with that of overridden function
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/W3 /wd177 /wd271 /wd304 /wd383 /wd424 /wd444 /wd522 /wd593 /wd809 /wd869 /wd981 /wd1418 /wd1419 /wd1572 /wd1599 /wd2259 /wd2415 /wd2547 /wd2557 /wd3280 /wd3346 /wd1782 /wd2282" GMXC_CXXFLAGS)
++ 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
-# Copyright (c) 2016, by the GROMACS development team, led by
+ #
+ # 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()
*
* 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, 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.
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 = NULL;
- char **tpr_names = NULL;
- const char *simulation_tpr = NULL;
- char *deffnm = NULL;
+ char *ExtraArgs = nullptr;
+ char **tpr_names = nullptr;
+ const char *simulation_tpr = nullptr;
+ char *deffnm = nullptr;
int best_npme, best_tpr;
int sim_part = 1; /* For benchmarks with checkpoint files */
char bbuf[STRLEN];
/* We need to allocate one element extra, since we might use
* (unaligned) 4-wide SIMD loads to access rvec entries.
*/
- snew(ems->s.x, ems->s.nalloc + 1);
- snew(ems->f, ems->s.nalloc+1);
- snew(ems->s.v, ems->s.nalloc+1);
- for (i = 0; i < state_global->natoms; i++)
- {
- copy_rvec(state_global->x[i], ems->s.x[i]);
- }
- copy_mat(state_global->box, ems->s.box);
+ ems->s.x.resize(ems->s.natoms + 1);
+ ems->f.resize(ems->s.natoms + 1);
- *top = gmx_mtop_generate_local_top(top_global, ir->efep != efepNO);
-
- setup_bonded_threading(fr, &(*top)->idef);
-
- if (ir->ePBC != epbcNONE && !fr->bMolPBC)
- {
- *graph = mk_graph(fplog, &((*top)->idef), 0, top_global->natoms, FALSE, FALSE);
- }
- else
- {
- *graph = NULL;
- }
-
- atoms2md(top_global, ir, 0, NULL, top_global->natoms, mdatoms);
+ snew(*top, 1);
+ mdAlgorithmsSetupAtomData(cr, ir, top_global, *top, fr,
+ graph, mdatoms,
+ vsite, shellfc ? *shellfc : nullptr);
- update_mdatoms(mdatoms, state_global->lambda[efptFEP]);
-
if (vsite)
{
set_vsite_top(vsite, *top, mdatoms, cr);
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff