Change-Id: I7efefc3835d1a5974886ef680a9fb0ddce11ee3e
52 files changed:
-#include "gromacs/commandline/cmdlinemodulemanager.h"
#include "gromacs/commandline/cmdlineinit.h"
#include "gromacs/commandline/cmdlineinit.h"
+#include "gromacs/commandline/cmdlinemodulemanager.h"
#include "gromacs/selection/selhelp.h"
#include "gromacs/trajectoryanalysis/modules.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/selection/selhelp.h"
#include "gromacs/trajectoryanalysis/modules.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/commandline/cmdlinemodule.h"
#include "gromacs/commandline/cmdlinemodulemanager.h"
#include "gromacs/commandline/cmdlinemodule.h"
#include "gromacs/commandline/cmdlinemodulemanager.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxpreprocess/genconf.h"
#include "gromacs/gmxpreprocess/grompp.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxpreprocess/genconf.h"
#include "gromacs/gmxpreprocess/grompp.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/vcm.h"
-#include "gromacs/legacyheaders/mdebin.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/mdoutf.h"
+#include "gromacs/fileio/trajectory_writing.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/gmxpreprocess/compute_io.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/bonded-threading.h"
#include "gromacs/legacyheaders/calcmu.h"
#include "gromacs/legacyheaders/calcmu.h"
-#include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/domdec_network.h"
+#include "gromacs/legacyheaders/force.h"
#include "gromacs/legacyheaders/md_logging.h"
#include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/mdrun.h"
#include "gromacs/legacyheaders/names.h"
#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
#include "gromacs/legacyheaders/orires.h"
#include "gromacs/legacyheaders/pme.h"
#include "gromacs/legacyheaders/orires.h"
#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "repl_ex.h"
-#include "deform.h"
#include "gromacs/legacyheaders/qmmm.h"
#include "gromacs/legacyheaders/qmmm.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/legacyheaders/domdec_network.h"
-#include "gromacs/legacyheaders/coulomb.h"
-#include "gromacs/legacyheaders/constr.h"
#include "gromacs/legacyheaders/shellfc.h"
#include "gromacs/legacyheaders/shellfc.h"
-#include "gromacs/gmxpreprocess/compute_io.h"
-#include "gromacs/legacyheaders/checkpoint.h"
-#include "gromacs/topology/mtop_util.h"
#include "gromacs/legacyheaders/sighandler.h"
#include "gromacs/legacyheaders/txtdump.h"
#include "gromacs/legacyheaders/sighandler.h"
#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/utility/cstringutil.h"
-#include "pme_loadbal.h"
-#include "gromacs/legacyheaders/bonded-threading.h"
-#include "membed.h"
-#include "gromacs/legacyheaders/types/nlistheuristics.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/vcm.h"
+#include "gromacs/legacyheaders/vsite.h"
#include "gromacs/legacyheaders/types/iteratedconstraints.h"
#include "gromacs/legacyheaders/types/iteratedconstraints.h"
+#include "gromacs/legacyheaders/types/nlistheuristics.h"
+#include "gromacs/math/vec.h"
#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
-
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/mdoutf.h"
-#include "gromacs/fileio/trajectory_writing.h"
-#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/xtcio.h"
-#include "gromacs/imd/imd.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/swap/swapcoords.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/swap/swapcoords.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/smalloc.h"
+#include "deform.h"
+#include "membed.h"
+#include "pme_loadbal.h"
+#include "repl_ex.h"
+
#ifdef GMX_FAHCORE
#include "corewrap.h"
#endif
#ifdef GMX_FAHCORE
#include "corewrap.h"
#endif
-#include "mdrun_main.h"
-
#include "config.h"
#include <stdio.h>
#include <string.h>
#include "config.h"
#include <stdio.h>
#include <string.h>
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/filenm.h"
#include "gromacs/legacyheaders/checkpoint.h"
#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/checkpoint.h"
#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/readinp.h"
#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/legacyheaders/readinp.h"
#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/types/commrec.h"
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/filenm.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/fatalerror.h"
+#include "mdrun_main.h"
+
static bool is_multisim_option_set(int argc, const char *const argv[])
{
for (int i = 0; i < argc; ++i)
static bool is_multisim_option_set(int argc, const char *const argv[])
{
for (int i = 0; i < argc; ++i)
#include <signal.h>
#include <stdlib.h>
#include <signal.h>
#include <stdlib.h>
+
+#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/readinp.h"
#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/utility/smalloc.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/index.h"
#include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/names.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/mtop_util.h"
-#include "gromacs/fileio/tpxio.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/cstringutil.h"
-#include "membed.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/readinp.h"
-#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
/* information about scaling center */
typedef struct {
/* information about scaling center */
typedef struct {
#ifndef _gmx_membed_h
#define _gmx_membed_h
#ifndef _gmx_membed_h
#define _gmx_membed_h
+#include "gromacs/fileio/filenm.h"
#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/types/membedt.h"
#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/types/membedt.h"
-#include "gromacs/fileio/filenm.h"
#ifdef __cplusplus
extern "C" {
#ifdef __cplusplus
extern "C" {
+#include "pme_loadbal.h"
+
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/network.h"
#include "gromacs/legacyheaders/calcgrid.h"
#include "gromacs/legacyheaders/calcgrid.h"
-#include "gromacs/legacyheaders/pme.h"
#include "gromacs/legacyheaders/domdec.h"
#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
#include "gromacs/legacyheaders/force.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/md_logging.h"
#include "gromacs/legacyheaders/force.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/md_logging.h"
-#include "pme_loadbal.h"
-
-#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/pme.h"
#include "gromacs/legacyheaders/sim_util.h"
#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/random/random.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/units.h"
#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/names.h"
#include "gromacs/legacyheaders/domdec.h"
#include "gromacs/legacyheaders/main.h"
#include "gromacs/legacyheaders/domdec.h"
#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
#include "gromacs/random/random.h"
+#include "gromacs/utility/smalloc.h"
#define PROBABILITYCUTOFF 100
/* we don't bother evaluating if events are more rare than exp(-100) = 3.7x10^-44 */
#define PROBABILITYCUTOFF 100
/* we don't bother evaluating if events are more rare than exp(-100) = 3.7x10^-44 */
#include <assert.h>
#include <signal.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <signal.h>
#include <stdlib.h>
#include <string.h>
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/gmxpreprocess/calc_verletbuf.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/domdec.h"
#include "gromacs/legacyheaders/force.h"
#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/gmx_detect_hardware.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/gmx_thread_affinity.h"
+#include "gromacs/legacyheaders/inputrec.h"
+#include "gromacs/legacyheaders/main.h"
#include "gromacs/legacyheaders/md_logging.h"
#include "gromacs/legacyheaders/md_support.h"
#include "gromacs/legacyheaders/md_logging.h"
#include "gromacs/legacyheaders/md_support.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/mvdata.h"
#include "gromacs/legacyheaders/names.h"
#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/oenv.h"
#include "gromacs/legacyheaders/orires.h"
#include "gromacs/legacyheaders/pme.h"
#include "gromacs/legacyheaders/orires.h"
#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "repl_ex.h"
-#include "deform.h"
#include "gromacs/legacyheaders/qmmm.h"
#include "gromacs/legacyheaders/qmmm.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/legacyheaders/coulomb.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/mvdata.h"
-#include "gromacs/legacyheaders/checkpoint.h"
-#include "gromacs/topology/mtop_util.h"
#include "gromacs/legacyheaders/sighandler.h"
#include "gromacs/legacyheaders/txtdump.h"
#include "gromacs/legacyheaders/sighandler.h"
#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/gmx_detect_hardware.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/gmxpreprocess/calc_verletbuf.h"
-#include "membed.h"
-#include "gromacs/legacyheaders/gmx_thread_affinity.h"
-#include "gromacs/legacyheaders/inputrec.h"
-#include "gromacs/legacyheaders/main.h"
-
-#include "gromacs/essentialdynamics/edsam.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vec.h"
-#include "gromacs/mdlib/nbnxn_search.h"
#include "gromacs/mdlib/nbnxn_consts.h"
#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_search.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/pulling/pull_rotation.h"
#include "gromacs/swap/swapcoords.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/pulling/pull_rotation.h"
#include "gromacs/swap/swapcoords.h"
#include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/smalloc.h"
+#include "deform.h"
+#include "membed.h"
+#include "repl_ex.h"
+
#ifdef GMX_FAHCORE
#include "corewrap.h"
#endif
#ifdef GMX_FAHCORE
#include "corewrap.h"
#endif
-#include "moduletest.h"
-#include <gtest/gtest.h>
+
+#include <gtest/gtest.h>
+
#include "gromacs/options/filenameoption.h"
#include "gromacs/tools/check.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/tools/check.h"
#include "testutils/cmdlinetest.h"
#include "testutils/cmdlinetest.h"
+#include "moduletest.h"
+
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/file.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/file.h"
#include "programs/mdrun/mdrun_main.h"
#include "programs/mdrun/mdrun_main.h"
+#include "testutils/cmdlinetest.h"
#include "testutils/integrationtests.h"
#include "testutils/testoptions.h"
#include "testutils/integrationtests.h"
#include "testutils/testoptions.h"
-#include "testutils/cmdlinetest.h"
#ifndef GMX_MDRUN_TESTS_MODULETEST_H
#define GMX_MDRUN_TESTS_MODULETEST_H
#ifndef GMX_MDRUN_TESTS_MODULETEST_H
#define GMX_MDRUN_TESTS_MODULETEST_H
-#include "testutils/integrationtests.h"
-
#include "testutils/cmdlinetest.h"
#include "testutils/cmdlinetest.h"
+#include "testutils/integrationtests.h"
#include "gromacs/utility/path.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/path.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/stringutil.h"
#include "programs/mdrun/mdrun_main.h"
#include "testutils/cmdlinetest.h"
#include "programs/mdrun/mdrun_main.h"
#include "testutils/cmdlinetest.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/filenameoption.h"
#include "testutils/cmdlinetest.h"
#include "testutils/cmdlinetest.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/utility/stringutil.h"
-#include "mdrun/mdrun_main.h"
-
#include "gromacs/commandline/cmdlinemodulemanager.h"
#include "gromacs/commandline/cmdlinemodulemanager.h"
+#include "mdrun/mdrun_main.h"
+
int main(int argc, char *argv[])
{
return gmx::CommandLineModuleManager::runAsMainCMain(argc, argv, &gmx_mdrun);
int main(int argc, char *argv[])
{
return gmx::CommandLineModuleManager::runAsMainCMain(argc, argv, &gmx_mdrun);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, 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.
* 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
#include <X11/Xlib.h>
#endif
#include <X11/Xlib.h>
+#include <X11/Xresource.h>
#include <X11/cursorfont.h>
#include <X11/cursorfont.h>
-#include <X11/Xresource.h>
#ifdef _acc_
typedef unsigned char bmchar;
#ifdef _acc_
typedef unsigned char bmchar;
#include <stdlib.h>
#include <string.h>
#include <stdlib.h>
#include <string.h>
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
-#include "x11.h"
-#include "xutil.h"
-#include "buttons.h"
-
-#include "stop_ani.bm"
-#include "play.bm"
+#include "stop_ani.bm"
+#include "x11.h"
+#include "xutil.h"
static void move_bbox(t_x11 *x11, t_butbox *bbox)
{
static void move_bbox(t_x11 *x11, t_butbox *bbox)
{
#include <unistd.h> // for fork()
#endif
#include <unistd.h> // for fork()
#endif
-#include "gromacs/legacyheaders/macros.h"
-#include "x11.h"
-#include "xdlghi.h"
-#include "xmb.h"
-#include "gromacs/legacyheaders/names.h"
-#include "nmol.h"
-#include "manager.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
+#include "manager.h"
+#include "nmol.h"
+#include "x11.h"
+#include "xdlghi.h"
+#include "xmb.h"
+
#define MBFLAGS /* MB_APPLMODAL | */ MB_DONTSHOW
void write_gmx(t_x11 *x11, t_gmx *gmx, int mess)
#define MBFLAGS /* MB_APPLMODAL | */ MB_DONTSHOW
void write_gmx(t_x11 *x11, t_gmx *gmx, int mess)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, 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.
* 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.
#ifndef _dialogs_h
#define _dialogs_h
#ifndef _dialogs_h
#define _dialogs_h
-#include "xdlg.h"
-#include "pulldown.h"
-#include "manager.h"
+#include "manager.h"
+#include "pulldown.h"
+#include "xdlg.h"
typedef struct {
bool bMapped;
typedef struct {
bool bMapped;
#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/smalloc.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/topology/index.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/topology/index.h"
-#include "xdlghi.h"
-#include "dialogs.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "dialogs.h"
+#include "xdlghi.h"
t_filter *init_filter(t_atoms *atoms, const char *fn, int natom_trx)
{
t_filter *init_filter(t_atoms *atoms, const char *fn, int natom_trx)
{
-#include "gromacs/legacyheaders/macros.h"
-#include "xutil.h"
-#include "Xstuff.h"
#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
+#include "Xstuff.h"
+#include "xutil.h"
+
typedef struct {
int x, y, rad;
unsigned long *col;
typedef struct {
int x, y, rad;
unsigned long *col;
#include <unistd.h> // for usleep()
#endif
#include <unistd.h> // for usleep()
#endif
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/tpxio.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/smalloc.h"
#include "3dview.h"
#include "gromacs/utility/smalloc.h"
#include "3dview.h"
#include "nmol.h"
static void add_object(t_manager *man, eObject eO, atom_id ai, atom_id aj)
#include "nmol.h"
static void add_object(t_manager *man, eObject eO, atom_id ai, atom_id aj)
-#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/pbcutil/rmpbc.h"
#include "3dview.h"
#include "gromacs/pbcutil/rmpbc.h"
#include "3dview.h"
#include <stdlib.h>
#include <string.h>
#include <stdlib.h>
#include <string.h>
-#include "gromacs/legacyheaders/macros.h"
-
#include "gromacs/fileio/writeps.h"
#include "gromacs/fileio/writeps.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/smalloc.h"
#include "3dview.h"
#include "gromacs/utility/smalloc.h"
#include "3dview.h"
#include <string.h>
#include <algorithm>
#include <string.h>
#include <algorithm>
-#include "gromacs/legacyheaders/types/rgb.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/types/rgb.h"
#include "gromacs/utility/smalloc.h"
#include "buttons.h"
#include "gromacs/utility/smalloc.h"
#include "buttons.h"
typedef struct {
const char *tp;
typedef struct {
const char *tp;
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/txtdump.h"
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/pbcutil/pbc.h"
-
#include "gromacs/math/vec.h"
#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "3dview.h"
#include "buttons.h"
#include "manager.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "3dview.h"
#include "buttons.h"
#include "manager.h"
#include "xutil.h"
#define MSIZE 4
#include "xutil.h"
#define MSIZE 4
#ifndef _nmol_h
#define _nmol_h
#ifndef _nmol_h
#define _nmol_h
-#include "programs/view/manager.h"
#include "x11.h"
#include "xutil.h"
#include "x11.h"
#include "xutil.h"
#include <math.h>
#include <string.h>
#include <math.h>
#include <string.h>
#include "x11.h"
#include "xutil.h"
#include "x11.h"
#include "xutil.h"
bool ChildCallBack(t_x11 *x11, XEvent *event, Window w, void *data)
{
bool ChildCallBack(t_x11 *x11, XEvent *event, Window w, void *data)
{
#include <string.h>
#include <algorithm>
#include <string.h>
#include <algorithm>
-#include "gromacs/utility/smalloc.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/smalloc.h"
static bool PDCallBack(t_x11 *x11, XEvent *event, Window w, void *data)
{
static bool PDCallBack(t_x11 *x11, XEvent *event, Window w, void *data)
{
#include <stdio.h>
#include <string.h>
#include <stdio.h>
#include <string.h>
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/tpxio.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#ifdef GMX_X11
#include "gromacs/fileio/writeps.h"
#include "Xstuff.h"
#ifdef GMX_X11
#include "gromacs/fileio/writeps.h"
#include "Xstuff.h"
-#include "gromacs.bm"
-#include "xutil.h"
#include "molps.h"
#include "nmol.h"
#include "molps.h"
#include "nmol.h"
static void dump_it(t_manager *man)
{
static void dump_it(t_manager *man)
{
#include <stdlib.h>
#include <string.h>
#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
#include <stdlib.h>
#include <string.h>
#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
/* These colours will be mapped to black on a monochrome screen */
unsigned long BLACK, BLUE, GREEN, CYAN, RED, BROWN, GREY, DARKGREY;
/* These colours will be mapped to black on a monochrome screen */
unsigned long BLACK, BLUE, GREEN, CYAN, RED, BROWN, GREY, DARKGREY;
#define _x11_h
#include <stdio.h>
#define _x11_h
#include <stdio.h>
#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/typedefs.h"
#include "Xstuff.h"
/* These colours will be mapped to black on a monochrome screen */
#include "Xstuff.h"
/* These colours will be mapped to black on a monochrome screen */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include "gromacs/utility/cstringutil.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/smalloc.h"
-#include "xutil.h"
-#include "xdlg.h"
-#include "gromacs/utility/fatalerror.h"
/*****************************
*
* Helpful routines
/*****************************
*
* Helpful routines
#include <stdlib.h>
#include <string.h>
#include <algorithm>
#include "gromacs/legacyheaders/macros.h"
#include <stdlib.h>
#include <string.h>
#include <algorithm>
#include "gromacs/legacyheaders/macros.h"
-#include "xutil.h"
-#include "xdlghi.h"
-#include "fgrid.h"
-
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
+#include "fgrid.h"
+#include "xutil.h"
+
t_dlgitem **CreateRadioButtonGroup(t_x11 *x11, char *szTitle,
t_id GroupID, int nrb, t_id rb[],
int nSelect,
t_dlgitem **CreateRadioButtonGroup(t_x11 *x11, char *szTitle,
t_id GroupID, int nrb, t_id rb[],
int nSelect,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, 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.
* 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.
#define _xdlghi_h
#include <stdarg.h>
#define _xdlghi_h
#include <stdarg.h>
#include "Xstuff.h"
#include "x11.h"
#include "xdlg.h"
#include "Xstuff.h"
#include "x11.h"
#include "xdlg.h"
#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
#include <algorithm>
#include "gromacs/legacyheaders/macros.h"
#include <algorithm>
#include "gromacs/legacyheaders/macros.h"
-#include "Xstuff.h"
-#include "xdlgitem.h"
-
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#define BUFSIZE 16
static t_dlgitem *newitem(void)
#define BUFSIZE 16
static t_dlgitem *newitem(void)
#define _xdlgitem_h
#include "Xstuff.h"
#define _xdlgitem_h
#include "Xstuff.h"
typedef enum {
edlgBN, edlgRB, edlgGB, edlgCB, edlgPM, edlgST, edlgET, edlgNR
typedef enum {
edlgBN, edlgRB, edlgGB, edlgCB, edlgPM, edlgST, edlgET, edlgNR
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/macros.h"
-#include "Xstuff.h"
-#include "x11.h"
-#include "xutil.h"
-#include "xdlg.h"
-#include "xmb.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/fatalerror.h"
+
+#include "Xstuff.h"
+#include "alert.bm"
+#include "stop.bm"
+#include "x11.h"
+#include "xdlg.h"
+#include "xutil.h"
#define ID_BOX -3
#define ID_ICON -2
#define ID_BOX -3
#define ID_ICON -2
#ifndef _xmb_h
#define _xmb_h
#ifndef _xmb_h
#define _xmb_h
-#include "programs/view/manager.h"
-#include "programs/view/x11.h"
-#include "programs/view/xdlg.h"
-#include "programs/view/xmb.h"
+#include "manager.h"
+#include "x11.h"
+#include "xdlg.h"
+#include "xmb.h"
#define MB_OK 1
#define MB_CANCEL (1<<1)
#define MB_OK 1
#define MB_CANCEL (1<<1)
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
+
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "xutil.h"
#include "Xstuff.h"
int CheckWin(Window win, const char *file, int line)
#include "Xstuff.h"
int CheckWin(Window win, const char *file, int line)
#include <cstdlib>
#include <cstring>
#include <cstdlib>
#include <cstring>
#include <vector>
#include "gromacs/commandline/cmdlineprogramcontext.h"
#include <vector>
#include "gromacs/commandline/cmdlineprogramcontext.h"
#include "integrationtests.h"
#include "integrationtests.h"
-#include "testutils/testoptions.h"
-#include "gromacs/utility/stringutil.h"
-#include "gromacs/utility/exceptions.h"
-#include "gromacs/options/options.h"
+#include "config.h"
+
+#include <stdio.h>
+#include <stdlib.h>
+
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/options.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/file.h"
#include "gromacs/utility/file.h"
-#include <stdlib.h>
-#include <stdio.h>
+#include "gromacs/utility/stringutil.h"
+#include "testutils/testoptions.h"
#include "mpi-printer.h"
#include "config.h"
#include "mpi-printer.h"
#include "config.h"
#include "gromacs/utility/gmxmpi.h"
#ifdef GMX_LIB_MPI
#include "gromacs/utility/gmxmpi.h"
#ifdef GMX_LIB_MPI
-#include "testutils/stringtest.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, 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.
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <boost/scoped_ptr.hpp>
#include <gtest/gtest.h>
#include <boost/scoped_ptr.hpp>
#include <gtest/gtest.h>
+#include "testutils/refdata.h"
-#include "testutils/testasserts.h"
+#include "testasserts.h"
-#include "gromacs/options/options.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/options.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/path.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/path.h"
#include "gromacs/utility/file.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/file.h"
#include "gromacs/utility/programcontext.h"
-#include "refdata.h"
-#include "testfilemanager.h"
-#include "mpi-printer.h"
+#include "testutils/mpi-printer.h"
+#include "testutils/refdata.h"
+#include "testutils/testfilemanager.h"
* \code
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
* \code
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
#include "testutils/testoptions.h"
namespace gmx
#include "testutils/testoptions.h"
namespace gmx
-#include <gtest/gtest.h>
#include <gtest/gtest-spi.h>
#include <gtest/gtest-spi.h>
+#include <gtest/gtest.h>