Merge release-5-0 into master

[alexxy/gromacs.git] / src / gromacs / gmxpreprocess / toppush.c

diff --git a/src/gromacs/gmxpreprocess/toppush.c b/src/gromacs/gmxpreprocess/toppush.c
index bc7f299e551dd888f80cf00673cd510384c3abbb..8272b7787ecf3f2dad111040e9d2ca76dca6b884 100644 (file)
--- a/src/gromacs/gmxpreprocess/toppush.c
+++ b/src/gromacs/gmxpreprocess/toppush.c
@@ -34,28 +34,27 @@
  * 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 "toppush.h"
+
+#include <assert.h>
 #include <ctype.h>
 #include <math.h>
-#include <assert.h>
-
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
+#include <stdlib.h>
+
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
-#include "names.h"
-#include "toputil.h"
-#include "toppush.h"
-#include "topdirs.h"
-#include "readir.h"
-#include "symtab.h"
-#include "gmx_fatal.h"
-#include "warninp.h"
-#include "gpp_atomtype.h"
-#include "gpp_bond_atomtype.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 void generate_nbparams(int comb, int ftype, t_params *plist, gpp_atomtype_t atype,
                        warninp_t wi)
@@ -95,7 +94,7 @@ void generate_nbparams(int comb, int ftype, t_params *plist, gpp_atomtype_t atyp
                     break;
 
                 case eCOMB_ARITHMETIC:
-                    /* c0 and c1 are epsilon and sigma */
+                    /* c0 and c1 are sigma and epsilon */
                     for (i = k = 0; (i < nr); i++)
                     {
                         for (j = 0; (j < nr); j++, k++)
@@ -104,14 +103,21 @@ void generate_nbparams(int comb, int ftype, t_params *plist, gpp_atomtype_t atyp
                             cj0                  = get_atomtype_nbparam(j, 0, atype);
                             ci1                  = get_atomtype_nbparam(i, 1, atype);
                             cj1                  = get_atomtype_nbparam(j, 1, atype);
-                            plist->param[k].c[0] = (ci0+cj0)*0.5;
+                            plist->param[k].c[0] = (fabs(ci0) + fabs(cj0))*0.5;
+                            /* Negative sigma signals that c6 should be set to zero later,
+                             * so we need to propagate that through the combination rules.
+                             */
+                            if (ci0 < 0 || cj0 < 0)
+                            {
+                                plist->param[k].c[0] *= -1;
+                            }
                             plist->param[k].c[1] = sqrt(ci1*cj1);
                         }
                     }
 
                     break;
                 case eCOMB_GEOM_SIG_EPS:
-                    /* c0 and c1 are epsilon and sigma */
+                    /* c0 and c1 are sigma and epsilon */
                     for (i = k = 0; (i < nr); i++)
                     {
                         for (j = 0; (j < nr); j++, k++)
@@ -120,7 +126,14 @@ void generate_nbparams(int comb, int ftype, t_params *plist, gpp_atomtype_t atyp
                             cj0                  = get_atomtype_nbparam(j, 0, atype);
                             ci1                  = get_atomtype_nbparam(i, 1, atype);
                             cj1                  = get_atomtype_nbparam(j, 1, atype);
-                            plist->param[k].c[0] = sqrt(ci0*cj0);
+                            plist->param[k].c[0] = sqrt(fabs(ci0*cj0));
+                            /* Negative sigma signals that c6 should be set to zero later,
+                             * so we need to propagate that through the combination rules.
+                             */
+                            if (ci0 < 0 || cj0 < 0)
+                            {
+                                plist->param[k].c[0] *= -1;
+                            }
                             plist->param[k].c[1] = sqrt(ci1*cj1);
                         }
                     }
@@ -586,9 +599,11 @@ static void push_bondtype(t_params     *       bt,
                     {
                         sprintf(errbuf, "Overriding %s parameters.%s",
                                 interaction_function[ftype].longname,
-                                (ftype == F_PDIHS) ? "\nUse dihedraltype 4 to allow several multiplicity terms." : "");
+                                (ftype == F_PDIHS) ?
+                                "\nUse dihedraltype 9 to allow several multiplicity terms. Only consecutive lines are combined. Non-consective lines overwrite each other."
+                                : "");
                         warning(wi, errbuf);
-                        fprintf(stderr, "  old:");
+                        fprintf(stderr, "  old:                                         ");
                         for (j = 0; (j < nrfp); j++)
                         {
                             fprintf(stderr, " %g", bt->param[i].c[j]);