* 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 "grompp.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "grompp.h"
-#include <sys/types.h>
-#include <math.h>
-#include <string.h>
+#include <assert.h>
#include <errno.h>
#include <limits.h>
-#include <assert.h>
+#include <math.h>
+#include <string.h>
+
+#include <sys/types.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "readir.h"
-#include "toputil.h"
-#include "topio.h"
-#include "gromacs/fileio/confio.h"
-#include "readir.h"
-#include "symtab.h"
-#include "names.h"
-#include "grompp-impl.h"
-#include "gromacs/random/random.h"
-#include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
-#include "vec.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/commandline/pargs.h"
-#include "splitter.h"
-#include "gromacs/gmxpreprocess/sortwater.h"
-#include "convparm.h"
-#include "gmx_fatal.h"
-#include "warninp.h"
-#include "index.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/trxio.h"
-#include "vsite_parm.h"
-#include "txtdump.h"
-#include "calcgrid.h"
-#include "add_par.h"
-#include "gromacs/fileio/enxio.h"
-#include "perf_est.h"
-#include "compute_io.h"
-#include "gpp_atomtype.h"
-#include "mtop_util.h"
-#include "genborn.h"
-#include "calc_verletbuf.h"
-#include "tomorse.h"
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/convparm.h"
+#include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/gmxpreprocess/sortwater.h"
+#include "gromacs/gmxpreprocess/tomorse.h"
+#include "gromacs/gmxpreprocess/topio.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/gmxpreprocess/vsite_parm.h"
#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/calcgrid.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/perf_est.h"
+#include "gromacs/legacyheaders/splitter.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/calc_verletbuf.h"
+#include "gromacs/mdlib/compute_io.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/random/random.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
-
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/snprintf.h"
static int rm_interactions(int ifunc, int nrmols, t_molinfo mols[])
{
}
}
+/* TODO Decide whether this function can be consolidated with
+ * gmx_mtop_ftype_count */
static gmx_bool nint_ftype(gmx_mtop_t *mtop, t_molinfo *mi, int ftype)
{
int nint, mb;
nmismatch, (nmismatch == 1) ? "" : "s", topfile, confin);
warning(wi, buf);
}
+
+ /* Do more checks, mostly related to constraints */
if (bVerbose)
{
fprintf(stderr, "double-checking input for internal consistency...\n");
}
- double_check(ir, state->box, nint_ftype(sys, molinfo, F_CONSTR), wi);
+ {
+ int bHasNormalConstraints = 0 < (nint_ftype(sys, molinfo, F_CONSTR) +
+ nint_ftype(sys, molinfo, F_CONSTRNC));
+ int bHasAnyConstraints = bHasNormalConstraints || 0 < nint_ftype(sys, molinfo, F_SETTLE);
+ double_check(ir, state->box,
+ bHasNormalConstraints,
+ bHasAnyConstraints,
+ wi);
+ }
}
if (bGenVel)
/* Set the relative box lengths for preserving the box shape.
* Note that this call can lead to differences in the last bit
- * with respect to using gmx convert-tpr to create a [TT].tpx[tt] file.
+ * with respect to using gmx convert-tpr to create a [REF].tpx[ref] file.
*/
set_box_rel(ir, state);
"only the atom types are used for generating interaction parameters.[PAR]",
"[THISMODULE] uses a built-in preprocessor to resolve includes, macros, ",
- "etc. The preprocessor supports the following keywords:[PAR]",
- "#ifdef VARIABLE[BR]",
- "#ifndef VARIABLE[BR]",
- "#else[BR]",
- "#endif[BR]",
- "#define VARIABLE[BR]",
- "#undef VARIABLE[BR]"
- "#include \"filename\"[BR]",
- "#include <filename>[PAR]",
+ "etc. The preprocessor supports the following keywords::",
+ "",
+ " #ifdef VARIABLE",
+ " #ifndef VARIABLE",
+ " #else",
+ " #endif",
+ " #define VARIABLE",
+ " #undef VARIABLE",
+ " #include \"filename\"",
+ " #include <filename>",
+ "",
"The functioning of these statements in your topology may be modulated by",
- "using the following two flags in your [TT].mdp[tt] file:[PAR]",
- "[TT]define = -DVARIABLE1 -DVARIABLE2[BR]",
- "include = -I/home/john/doe[tt][BR]",
+ "using the following two flags in your [REF].mdp[ref] file::",
+ "",
+ " define = -DVARIABLE1 -DVARIABLE2",
+ " include = -I/home/john/doe",
+ "",
"For further information a C-programming textbook may help you out.",
"Specifying the [TT]-pp[tt] flag will get the pre-processed",
"topology file written out so that you can verify its contents.[PAR]",
- /* cpp has been unnecessary for some time, hasn't it?
- "If your system does not have a C-preprocessor, you can still",
- "use [TT]grompp[tt], but you do not have access to the features ",
- "from the cpp. Command line options to the C-preprocessor can be given",
- "in the [TT].mdp[tt] file. See your local manual (man cpp).[PAR]",
- */
-
"When using position restraints a file with restraint coordinates",
"can be supplied with [TT]-r[tt], otherwise restraining will be done",
"with respect to the conformation from the [TT]-c[tt] option.",
"unless the [TT]-time[tt] option is used. Only if this information",
"is absent will the coordinates in the [TT]-c[tt] file be used.",
"Note that these velocities will not be used when [TT]gen_vel = yes[tt]",
- "in your [TT].mdp[tt] file. An energy file can be supplied with",
+ "in your [REF].mdp[ref] file. An energy file can be supplied with",
"[TT]-e[tt] to read Nose-Hoover and/or Parrinello-Rahman coupling",
"variables.[PAR]",
"You then supply the old checkpoint file directly to [gmx-mdrun]",
"with [TT]-cpi[tt]. If you wish to change the ensemble or things",
"like output frequency, then supplying the checkpoint file to",
- "[THISMODULE] with [TT]-t[tt] along with a new [TT].mdp[tt] file",
+ "[THISMODULE] with [TT]-t[tt] along with a new [REF].mdp[ref] file",
"with [TT]-f[tt] is the recommended procedure.[PAR]",
"By default, all bonded interactions which have constant energy due to",
{ efNDX, NULL, NULL, ffOPTRD },
{ efTOP, NULL, NULL, ffREAD },
{ efTOP, "-pp", "processed", ffOPTWR },
- { efTPX, "-o", NULL, ffWRITE },
+ { efTPR, "-o", NULL, ffWRITE },
{ efTRN, "-t", NULL, ffOPTRD },
{ efEDR, "-e", NULL, ffOPTRD },
/* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
}
}
- if (ir->ePull != epullNO)
+ if (ir->bPull)
{
- set_pull_init(ir, sys, state->x, state->box, state->lambda[efptMASS], oenv, opts->pull_start);
+ set_pull_init(ir, sys, state->x, state->box, state->lambda[efptMASS], oenv);
}
if (ir->bRot)
}
done_warning(wi, FARGS);
- write_tpx_state(ftp2fn(efTPX, NFILE, fnm), ir, state, sys);
+ write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, state, sys);
/* Output IMD group, if bIMD is TRUE */
write_IMDgroup_to_file(ir->bIMD, ir, state, sys, NFILE, fnm);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff