Add gmx dump option for printing parameters

For comparing topologies of the same system with different force
fields it can be very useful to print bonded parameters instead
of the parameter type index.

Change-Id: I06a3b65b695ace4de1491f2d58abb6b7e752693d

diff --git a/src/gromacs/tools/dump.cpp b/src/gromacs/tools/dump.cpp
index 07d1c0fc8d7bb527f58009ffbd2deb0b2c87cad6..1e9da4acfd4cc87d299cd1c7adf3efb7b3692b3d 100644 (file)
--- a/src/gromacs/tools/dump.cpp
+++ b/src/gromacs/tools/dump.cpp
@@ -71,8 +71,11 @@
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/txtdump.h"
 
-static void list_tpx(const char *fn, gmx_bool bShowNumbers, const char *mdpfn,
-                     gmx_bool bSysTop)
+static void list_tpx(const char *fn,
+                     gmx_bool    bShowNumbers,
+                     gmx_bool    bShowParameters,
+                     const char *mdpfn,
+                     gmx_bool    bSysTop)
 {
     FILE         *gp;
     int           indent, i, j, **gcount, atot;
@@ -118,11 +121,11 @@ static void list_tpx(const char *fn, gmx_bool bShowNumbers, const char *mdpfn,
 
             if (!bSysTop)
             {
-                pr_mtop(stdout, indent, "topology", &(mtop), bShowNumbers);
+                pr_mtop(stdout, indent, "topology", &(mtop), bShowNumbers, bShowParameters);
             }
             else
             {
-                pr_top(stdout, indent, "topology", &(top), bShowNumbers);
+                pr_top(stdout, indent, "topology", &(top), bShowNumbers, bShowParameters);
             }
 
             pr_rvecs(stdout, indent, "box", tpx.bBox ? state.box : NULL, DIM);
@@ -623,9 +626,11 @@ int gmx_dump(int argc, char *argv[])
     gmx_output_env_t *oenv;
     /* Command line options */
     static gmx_bool   bShowNumbers = TRUE;
+    static gmx_bool   bShowParams  = FALSE;
     static gmx_bool   bSysTop      = FALSE;
     t_pargs           pa[]         = {
         { "-nr", FALSE, etBOOL, {&bShowNumbers}, "Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)" },
+        { "-param", FALSE, etBOOL, {&bShowParams}, "Show parameters for each bonded interaction (for comparing dumps, it is useful to combine this with -nonr)" },
         { "-sys", FALSE, etBOOL, {&bSysTop}, "List the atoms and bonded interactions for the whole system instead of for each molecule type" }
     };
 
@@ -638,7 +643,7 @@ int gmx_dump(int argc, char *argv[])
 
     if (ftp2bSet(efTPR, NFILE, fnm))
     {
-        list_tpx(ftp2fn(efTPR, NFILE, fnm), bShowNumbers,
+        list_tpx(ftp2fn(efTPR, NFILE, fnm), bShowNumbers, bShowParams,
                  ftp2fn_null(efMDP, NFILE, fnm), bSysTop);
     }
     else if (ftp2bSet(efTRX, NFILE, fnm))

diff --git a/src/gromacs/topology/idef.cpp b/src/gromacs/topology/idef.cpp
index 0ad6cbba67d47f31e0997c5fef4da5a079bf6dfb..4806c2a9ba889416ba5dba0afecc4fbac3f85ecc 100644 (file)
--- a/src/gromacs/topology/idef.cpp
+++ b/src/gromacs/topology/idef.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -303,7 +303,9 @@ void pr_iparams(FILE *fp, t_functype ftype, const t_iparams *iparams)
 }
 
 void pr_ilist(FILE *fp, int indent, const char *title,
-              const t_functype *functype, const t_ilist *ilist, gmx_bool bShowNumbers)
+              const t_functype *functype, const t_ilist *ilist,
+              gmx_bool bShowNumbers,
+              gmx_bool bShowParameters, const t_iparams *iparams)
 {
     int      i, j, k, type, ftype;
     t_iatom *iatoms;
@@ -320,24 +322,26 @@ void pr_ilist(FILE *fp, int indent, const char *title,
             iatoms = ilist->iatoms;
             for (i = j = 0; i < ilist->nr; )
             {
-#ifndef DEBUG
                 pr_indent(fp, indent+INDENT);
                 type  = *(iatoms++);
                 ftype = functype[type];
-                fprintf(fp, "%d type=%d (%s)",
-                        bShowNumbers ? j : -1, bShowNumbers ? type : -1,
-                        interaction_function[ftype].name);
+                if (bShowNumbers)
+                {
+                    fprintf(fp, "%d type=%d ", j, type);
+                }
                 j++;
+                printf("(%s)", interaction_function[ftype].name);
                 for (k = 0; k < interaction_function[ftype].nratoms; k++)
                 {
-                    fprintf(fp, " %d", *(iatoms++));
+                    fprintf(fp, " %3d", *(iatoms++));
+                }
+                if (bShowParameters)
+                {
+                    fprintf(fp, "  ");
+                    pr_iparams(fp, ftype,  &iparams[type]);
                 }
                 fprintf(fp, "\n");
                 i += 1+interaction_function[ftype].nratoms;
-#else
-                fprintf(fp, "%5d%5d\n", i, iatoms[i]);
-                i++;
-#endif
             }
         }
     }
@@ -406,7 +410,8 @@ void pr_ffparams(FILE *fp, int indent, const char *title,
     pr_cmap(fp, indent, "cmap", &ffparams->cmap_grid, bShowNumbers);
 }
 
-void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef, gmx_bool bShowNumbers)
+void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef,
+             gmx_bool bShowNumbers, gmx_bool bShowParameters)
 {
     int i, j;
 
@@ -430,7 +435,8 @@ void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef, gmx_bo
         for (j = 0; (j < F_NRE); j++)
         {
             pr_ilist(fp, indent, interaction_function[j].longname,
-                     idef->functype, &idef->il[j], bShowNumbers);
+                     idef->functype, &idef->il[j], bShowNumbers,
+                     bShowParameters, idef->iparams);
         }
     }
 }

diff --git a/src/gromacs/topology/idef.h b/src/gromacs/topology/idef.h
index 4446a3f170b3dc82e71ae49dae99bd3d38de18c1..467d7d45f8ad189bf717a5661e1738314a6d836a 100644 (file)
--- a/src/gromacs/topology/idef.h
+++ b/src/gromacs/topology/idef.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -406,10 +406,13 @@ typedef struct t_idef
 
 void pr_iparams(FILE *fp, t_functype ftype, const t_iparams *iparams);
 void pr_ilist(FILE *fp, int indent, const char *title,
-              const t_functype *functype, const t_ilist *ilist, gmx_bool bShowNumbers);
+              const t_functype *functype, const t_ilist *ilist,
+              gmx_bool bShowNumbers,
+              gmx_bool bShowParameters, const t_iparams *iparams);
 void pr_ffparams(FILE *fp, int indent, const char *title,
                  const gmx_ffparams_t *ffparams, gmx_bool bShowNumbers);
-void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef, gmx_bool bShowNumbers);
+void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef,
+             gmx_bool bShowNumbers, gmx_bool bShowParameters);
 
 #ifdef __cplusplus
 }

diff --git a/src/gromacs/topology/topology.cpp b/src/gromacs/topology/topology.cpp
index 27eed7a3c3a2a5d60c8792a495e4015356b5919e..f113900e1364fc4a16b534b5de5581b7234588ec 100644 (file)
--- a/src/gromacs/topology/topology.cpp
+++ b/src/gromacs/topology/topology.cpp
@@ -317,7 +317,7 @@ static void pr_groups(FILE *fp, int indent,
 static void pr_moltype(FILE *fp, int indent, const char *title,
                        const gmx_moltype_t *molt, int n,
                        const gmx_ffparams_t *ffparams,
-                       gmx_bool bShowNumbers)
+                       gmx_bool bShowNumbers, gmx_bool bShowParameters)
 {
     int j;
 
@@ -330,7 +330,8 @@ static void pr_moltype(FILE *fp, int indent, const char *title,
     for (j = 0; (j < F_NRE); j++)
     {
         pr_ilist(fp, indent, interaction_function[j].longname,
-                 ffparams->functype, &molt->ilist[j], bShowNumbers);
+                 ffparams->functype, &molt->ilist[j],
+                 bShowNumbers, bShowParameters, ffparams->iparams);
     }
 }
 
@@ -357,7 +358,7 @@ static void pr_molblock(FILE *fp, int indent, const char *title,
 }
 
 void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
-             gmx_bool bShowNumbers)
+             gmx_bool bShowNumbers, gmx_bool bShowParameters)
 {
     int mt, mb, j;
 
@@ -380,7 +381,8 @@ void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
             {
                 pr_ilist(fp, indent, interaction_function[j].longname,
                          mtop->ffparams.functype,
-                         &mtop->intermolecular_ilist[j], bShowNumbers);
+                         &mtop->intermolecular_ilist[j],
+                         bShowNumbers, bShowParameters, mtop->ffparams.iparams);
             }
         }
         pr_ffparams(fp, indent, "ffparams", &(mtop->ffparams), bShowNumbers);
@@ -388,13 +390,14 @@ void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
         for (mt = 0; mt < mtop->nmoltype; mt++)
         {
             pr_moltype(fp, indent, "moltype", &mtop->moltype[mt], mt,
-                       &mtop->ffparams, bShowNumbers);
+                       &mtop->ffparams, bShowNumbers, bShowParameters);
         }
         pr_groups(fp, indent, &mtop->groups, bShowNumbers);
     }
 }
 
-void pr_top(FILE *fp, int indent, const char *title, const t_topology *top, gmx_bool bShowNumbers)
+void pr_top(FILE *fp, int indent, const char *title, const t_topology *top,
+            gmx_bool bShowNumbers, gmx_bool bShowParameters)
 {
     if (available(fp, top, indent, title))
     {
@@ -408,7 +411,7 @@ void pr_top(FILE *fp, int indent, const char *title, const t_topology *top, gmx_
         pr_str(fp, indent, "bIntermolecularInteractions",
                gmx::boolToString(top->bIntermolecularInteractions));
         pr_blocka(fp, indent, "excls", &top->excls, bShowNumbers);
-        pr_idef(fp, indent, "idef", &top->idef, bShowNumbers);
+        pr_idef(fp, indent, "idef", &top->idef, bShowNumbers, bShowParameters);
     }
 }
 

diff --git a/src/gromacs/topology/topology.h b/src/gromacs/topology/topology.h
index ed2b5ae7de7303bee75e1cbbccfd79585f9186f5..89c40bfc0816819247c06a9e7423b45ee58c781e 100644 (file)
--- a/src/gromacs/topology/topology.h
+++ b/src/gromacs/topology/topology.h
@@ -160,8 +160,9 @@ bool gmx_mtop_has_atomtypes(const gmx_mtop_t *mtop);
 bool gmx_mtop_has_pdbinfo(const gmx_mtop_t *mtop);
 
 void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
-             gmx_bool bShowNumbers);
-void pr_top(FILE *fp, int indent, const char *title, const t_topology *top, gmx_bool bShowNumbers);
+             gmx_bool bShowNumbers, gmx_bool bShowParameters);
+void pr_top(FILE *fp, int indent, const char *title, const t_topology *top,
+            gmx_bool bShowNumbers, gmx_bool bShowParameters);
 
 void cmp_top(FILE *fp, const t_topology *t1, const t_topology *t2, real ftol, real abstol);
 void cmp_groups(FILE *fp, const gmx_groups_t *g0, const gmx_groups_t *g1,