* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include <math.h>
+#include <stdlib.h>
#include <string.h>
#include <time.h>
-#include <math.h>
-#include "sysstuff.h"
-#include "network.h"
-#include "gromacs/utility/smalloc.h"
-#include "nrnb.h"
-#include "chargegroup.h"
-#include "force.h"
-#include "macros.h"
-#include "names.h"
-#include "gromacs/utility/fatalerror.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "update.h"
-#include "constr.h"
-#include "vec.h"
-#include "tgroup.h"
-#include "mdebin.h"
-#include "vsite.h"
-#include "force.h"
-#include "mdrun.h"
-#include "domdec.h"
-#include "gromacs/random/random.h"
-#include "physics.h"
-#include "xvgr.h"
-#include "mdatoms.h"
-#include "ns.h"
-#include "mtop_util.h"
-#include "pme.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static void global_max(t_commrec *cr, int *n)
{
real bU_bin_limit = 50;
real bU_logV_bin_limit = bU_bin_limit + 10;
+ if (inputrec->cutoff_scheme == ecutsVERLET)
+ {
+ gmx_fatal(FARGS, "TPI does not work (yet) with the Verlet cut-off scheme");
+ }
+
nnodes = cr->nnodes;
top = gmx_mtop_generate_local_top(top_global, inputrec);
snew(leg, 4+nener);
e = 0;
sprintf(str, "-kT log(<Ve\\S-\\betaU\\N>/<V>)");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
sprintf(str, "f. -kT log<e\\S-\\betaU\\N>");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
sprintf(str, "f. <e\\S-\\betaU\\N>");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
sprintf(str, "f. V");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
sprintf(str, "f. <Ue\\S-\\betaU\\N>");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
for (i = 0; i < ngid; i++)
{
sprintf(str, "f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
*(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
}
if (bDispCorr)
{
sprintf(str, "f. <U\\sdisp c\\Ne\\S-\\betaU\\N>");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
}
if (bCharge)
{
{
sprintf(str, "f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
*(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
}
if (bRFExcl)
{
sprintf(str, "f. <U\\sRF excl\\Ne\\S-\\betaU\\N>");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
}
if (EEL_FULL(fr->eeltype))
{
sprintf(str, "f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
}
}
xvgr_legend(fp_tpi, 4+nener, (const char**)leg, oenv);
bNS = FALSE;
/* Calculate long range corrections to pressure and energy */
- calc_dispcorr(fplog, inputrec, fr, step, top_global->natoms, state->box,
+ calc_dispcorr(inputrec, fr, top_global->natoms, state->box,
lambda, pres, vir, &prescorr, &enercorr, &dvdlcorr);
/* figure out how to rearrange the next 4 lines MRS 8/4/2009 */
enerd->term[F_DISPCORR] = enercorr;