Intermolecular bonded interaction support added

[alexxy/gromacs.git] / src / gromacs / fileio / tpxio.c

diff --git a/src/gromacs/fileio/tpxio.c b/src/gromacs/fileio/tpxio.c
index cf77d95e6b27cf4f7624769bd01a7bd3aa31985e..26aed407ee010b92645dc3e7d5cd4ca2e541692d 100644 (file)
--- a/src/gromacs/fileio/tpxio.c
+++ b/src/gromacs/fileio/tpxio.c
@@ -92,7 +92,8 @@ enum tpxv {
     tpxv_InteractiveMolecularDynamics,                       /**< interactive molecular dynamics (IMD) */
     tpxv_RemoveObsoleteParameters1,                          /**< remove optimize_fft, dihre_fc, nstcheckpoint */
     tpxv_PullCoordTypeGeom,                                  /**< add pull type and geometry per group and flat-bottom */
-    tpxv_PullGeomDirRel                                      /**< add pull geometry direction-relative */
+    tpxv_PullGeomDirRel,                                     /**< add pull geometry direction-relative */
+    tpxv_IntermolecularBondeds                               /**< permit inter-molecular bonded interactions in the topology */
 };
 
 /*! \brief Version number of the file format written to run input
@@ -106,7 +107,7 @@ enum tpxv {
  *
  * When developing a feature branch that needs to change the run input
  * file format, change tpx_tag instead. */
-static const int tpx_version = tpxv_PullGeomDirRel;
+static const int tpx_version = tpxv_IntermolecularBondeds;
 
 
 /* This number should only be increased when you edit the TOPOLOGY section
@@ -3024,16 +3025,19 @@ static void add_posres_molblock(gmx_mtop_t *mtop)
 
 static void set_disres_npair(gmx_mtop_t *mtop)
 {
-    int        mt, i, npair;
-    t_iparams *ip;
-    t_ilist   *il;
-    t_iatom   *a;
+    t_iparams            *ip;
+    gmx_mtop_ilistloop_t  iloop;
+    t_ilist              *ilist, *il;
+    int                   nmol, i, npair;
+    t_iatom              *a;
 
     ip = mtop->ffparams.iparams;
 
-    for (mt = 0; mt < mtop->nmoltype; mt++)
+    iloop     = gmx_mtop_ilistloop_init(mtop);
+    while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
     {
-        il = &mtop->moltype[mt].ilist[F_DISRES];
+        il = &ilist[F_DISRES];
+
         if (il->nr > 0)
         {
             a     = il->iatoms;
@@ -3122,6 +3126,23 @@ static void do_mtop(t_fileio *fio, gmx_mtop_t *mtop, gmx_bool bRead,
         mtop->molblock[0].nposres_xB = 0;
     }
 
+    if (file_version >= tpxv_IntermolecularBondeds)
+    {
+        gmx_fio_do_gmx_bool(fio, mtop->bIntermolecularInteractions);
+        if (mtop->bIntermolecularInteractions)
+        {
+            if (bRead)
+            {
+                snew(mtop->intermolecular_ilist, F_NRE);
+            }
+            do_ilists(fio, mtop->intermolecular_ilist, bRead, file_version);
+        }
+    }
+    else
+    {
+        mtop->bIntermolecularInteractions = FALSE;
+    }
+
     do_atomtypes (fio, &(mtop->atomtypes), bRead, file_version);
     if (bRead && debug)
     {