# NOTE: when releasing the "-dev" suffix needs to be stripped off!
# REGRESSIONTEST_VERSION and REGRESSIONTEST_BRANCH should always be
# defined.
-set(PROJECT_VERSION "5.0-rc1-dev")
+set(PROJECT_VERSION "5.1-dev")
# If this is a released tarball, "-dev" will not be present in
# PROJECT_VERSION, and REGRESSIONTEST_VERSION specifies the version
# number of the regressiontest tarball against which the code tarball
# PROJECT_VERSION, and REGRESSIONTEST_BRANCH specifies the name of the
# gerrit.gromacs.org branch whose HEAD can test this code, *if* this
# code contains all recent fixes from the corresponding code branch.
-set(REGRESSIONTEST_BRANCH "refs/heads/release-5-0")
+set(REGRESSIONTEST_BRANCH "refs/heads/master")
set(CUSTOM_VERSION_STRING ""
CACHE STRING "Custom version string (if empty, use hard-coded default)")
set(LIBRARY_VERSION ${LIBRARY_SOVERSION}.0.0)
# It is a bit irritating, but this has to be set separately for now!
SET(CPACK_PACKAGE_VERSION_MAJOR "5")
-SET(CPACK_PACKAGE_VERSION_MINOR "0")
+SET(CPACK_PACKAGE_VERSION_MINOR "1")
#SET(CPACK_PACKAGE_VERSION_PATCH "0")
# The numerical gromacs version. It is 40600 for 4.6.0.
mark_as_advanced(GMX_INSTALL_PREFIX)
include(gmxBuildTypeReference)
-include(gmxBuildTypeThreadSanitizer)
+include(gmxBuildTypeProfile)
+include(gmxBuildTypeTSAN)
+include(gmxBuildTypeASAN)
include(gmxBuildTypeReleaseWithAssert)
if(NOT CMAKE_BUILD_TYPE)
- set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference RelWithAssert." FORCE)
+ set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference RelWithAssert Profile." FORCE)
# There's no need to offer a user the choice of ThreadSanitizer
# Set the possible values of build type for cmake-gui
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
- "MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert")
+ "MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert" "Profile")
endif()
if(CMAKE_CONFIGURATION_TYPES)
# Add appropriate GROMACS-specific build types for the Visual
"List of configuration types"
FORCE)
endif()
-set(build_types_with_explicit_flags RELEASE DEBUG RELWITHDEBUGINFO RELWITHASSERT MINSIZEREL)
+set(build_types_with_explicit_flags RELEASE DEBUG RELWITHDEBUGINFO RELWITHASSERT MINSIZEREL PROFILE)
enable_language(C)
enable_language(CXX)
if(GMX_CPU_ACCELERATION)
# Stay compatible with old Jenkins command line options for specific SIMD acceleration
set(GMX_SIMD "${GMX_CPU_ACCELERATION}" CACHE STRING "SIMD instruction set level and compiler optimization" FORCE)
+ message("You set GMX_CPU_ACCELERATION, which is deprecated, and will be removed in a later version of GROMACS. It is replaced by GMX_SIMD. For now, copying the value from GMX_CPU_ACCELERATION to GMX_SIMD.")
+ # TODO remove all references to GMX_CPU_ACCELERATION in master branch
endif()
if(NOT GMX_TARGET_MIC)
# Note: it's better to not use the later set value of GMX_SIMD because
# it reflects the system's capability of both compiling and running AVX code.
# TODO: After merge with 5.0 one could implement a cache variable dependency
- # such that GMX_USE_RDTSCP can change if GMX_CPU_ACCELERATION is changed to AVX
+ # such that GMX_USE_RDTSCP can change if GMX_SIMD is changed to AVX
# after the first cmake pass.
if (BUILD_CPU_FEATURES MATCHES "rdtscp" OR GMX_SIMD MATCHES "AVX")
set(GMX_USE_RDTSCP_DEFAULT_VALUE ON)
- 399
-401
++402
If You Want Something Done You Have to Do It Yourself_(Highlander II)
I Live the Life They Wish They Did_(Tricky)
Jesus Built My Hotrod_(Ministry)
It was something to at least have a choice of nightmares_(Joseph Conrad)
You fight, work, sweat, nearly kill yourself, sometimes you do kill yourself, trying to accomplish something - and you can't._(Joseph Conrad)
And after some more talk we agreed that the wisdom of rats had been grossly overrated, being in fact no greater than that of men_(Joseph Conrad)
+It's an easy game, just don't let the ball past!_(Szilard Pall)
+ The soul? There's nothing but chemistry here_(Breaking Bad)
+ You got one part of that wrong. This is not meth._(Breaking Bad)
+ It's easy to remember: a half a kT is equal to five fourths of a kJ/mol._(Anders Gabrielsson)
#include <config.h>
#endif
-#include <string.h>
#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "copyrite.h"
#include "macros.h"
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/tngio_for_tools.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/confio.h"
#include "names.h"
#include "index.h"
-#include "vec.h"
+#include "gromacs/math/vec.h"
#include "gromacs/fileio/xtcio.h"
-#include "rmpbc.h"
-#include "pbc.h"
#include "viewit.h"
-#include "xvgr.h"
#include "gmx_ana.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/math/do_fit.h"
-#include "gmx_fatal.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#ifdef HAVE_UNISTD_H
#include <unistd.h>
{
/* check if velocities are possible in input and output files */
ftpin = fn2ftp(in_file);
- bVels = (ftp == efTRR || ftp == efTRJ || ftp == efGRO || ftp == efG96)
- && (ftpin == efTRR || ftpin == efTRJ || ftpin == efGRO || ftpin == efG96 ||
- ftpin == efCPT);
+ bVels = (ftp == efTRR || ftp == efTRJ || ftp == efGRO ||
+ ftp == efG96 || ftp == efTNG)
+ && (ftpin == efTRR || ftpin == efTRJ || ftpin == efGRO ||
+ ftpin == efG96 || ftpin == efTNG || ftpin == efCPT);
}
if (bSeparate || bSplit)
{
#include <config.h>
#endif
+#include <assert.h>
+#include <ctype.h>
+#include <errno.h>
#include <math.h>
-#include <sys/types.h>
#include <stdio.h>
+#include <stdlib.h>
#include <string.h>
-#include <errno.h>
-#include <ctype.h>
-#include <assert.h>
-#include "gromacs/fileio/futil.h"
-#include "sysstuff.h"
+#include <sys/types.h>
+
+#include "gromacs/utility/futil.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "gromacs/fileio/gmxfio.h"
#include "txtdump.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
#include "macros.h"
#include "names.h"
#include "gromacs/utility/cstringutil.h"
-#include "symtab.h"
-#include "gmx_fatal.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/fatalerror.h"
#include "warninp.h"
#include "vsite_parm.h"
char buf[256];
int i, mb, nmol, ri, pt;
double q;
- real m;
+ real m, mB;
t_atoms *atoms;
/* Check mass and charge */
{
q += nmol*atoms->atom[i].q;
m = atoms->atom[i].m;
+ mB = atoms->atom[i].mB;
pt = atoms->atom[i].ptype;
/* If the particle is an atom or a nucleus it must have a mass,
* else, if it is a shell, a vsite or a bondshell it can have mass zero
*/
- if ((m <= 0.0) && ((pt == eptAtom) || (pt == eptNucleus)))
+ if (((m <= 0.0) || (mB <= 0.0)) && ((pt == eptAtom) || (pt == eptNucleus)))
{
ri = atoms->atom[i].resind;
- sprintf(buf, "atom %s (Res %s-%d) has mass %g\n",
+ sprintf(buf, "atom %s (Res %s-%d) has mass %g (state A) / %g (state B)\n",
*(atoms->atomname[i]),
*(atoms->resinfo[ri].name),
atoms->resinfo[ri].nr,
- m);
+ m, mB);
warning_error(wi, buf);
}
else
- if ((m != 0) && (pt == eptVSite))
+ if (((m != 0) || (mB != 0)) && (pt == eptVSite))
{
ri = atoms->atom[i].resind;
- sprintf(buf, "virtual site %s (Res %s-%d) has non-zero mass %g\n"
+ sprintf(buf, "virtual site %s (Res %s-%d) has non-zero mass %g (state A) / %g (state B)\n"
" Check your topology.\n",
*(atoms->atomname[i]),
*(atoms->resinfo[ri].name),
atoms->resinfo[ri].nr,
- m);
+ m, mB);
warning_error(wi, buf);
/* The following statements make LINCS break! */
/* atoms->atom[i].m=0; */
j = 0;
while (j < molt->ilist[i].nr)
{
- bexcl = FALSE;
a1 = molt->ilist[i].iatoms[j+1];
a2 = molt->ilist[i].iatoms[j+2];
bexcl = ((bQMMM[a1] && bQMMM[a2]) ||
#include "types/commrec.h"
#include "gromacs/utility/smalloc.h"
#include "update.h"
-#include "vec.h"
+#include "gromacs/math/vec.h"
#include "macros.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
#include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "txtdump.h"
#include "nrnb.h"
#include "gromacs/random/random.h"
Ek_new = vrescale_resamplekin(Ek, Ek_ref, opts->nrdf[i],
opts->tau_t[i]/dt,
- ir->ld_seed, step);
+ step, ir->ld_seed);
/* Analytically Ek_new>=0, but we check for rounding errors */
if (Ek_new <= 0)
#include <config.h>
#endif
+#include <assert.h>
+#include <math.h>
#include <stdio.h>
#include <string.h>
-#include <math.h>
-#include <assert.h>
-#include "main.h"
+
#include "macros.h"
-#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "txtdump.h"
-#include "gmx_fatal.h"
-#include "gromacs/utility/smalloc.h"
#include "names.h"
#include "txtdump.h"
-#include "gromacs/gmxpreprocess/gmxcpp.h"
#include "checkpoint.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/fileio/xtcio.h"
#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/tngio.h"
#include "gromacs/fileio/tngio_for_tools.h"
#include <unistd.h>
#endif
-#include "gromacs/linearalgebra/mtxio.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/mtxio.h"
+#include "gromacs/gmxpreprocess/gmxcpp.h"
#include "gromacs/linearalgebra/sparsematrix.h"
-
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static void list_tpx(const char *fn, gmx_bool bShowNumbers, const char *mdpfn,
gmx_bool bSysTop)
/* Can't write any output because we don't know what
arrays are valid. */
fprintf(stderr, "\nWARNING: Incomplete frame at time %g, will not write output\n", frame_time);
+ }
+ else
+ {
list_tng_inner(fn, (0 == i), values, step, frame_time,
n_values_per_frame, n_atoms, prec, nframe, block_name);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff