Sort all includes in src/gromacs

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

diff --git a/src/gromacs/gmxpreprocess/readpull.c b/src/gromacs/gmxpreprocess/readpull.c
index b4ba14531295a4bdf7aa1a7ce1540a32bec5ff91..2e78022c5b1d32b148f31348616f69ab83af7e1a 100644 (file)
--- a/src/gromacs/gmxpreprocess/readpull.c
+++ b/src/gromacs/gmxpreprocess/readpull.c
@@ -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 by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, 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.
@@ -34,29 +34,24 @@
  * 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 <string.h>
 #include <stdlib.h>
-#include "sysstuff.h"
-#include "princ.h"
-#include "gromacs/fileio/futil.h"
-#include "vec.h"
-#include "smalloc.h"
-#include "typedefs.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "index.h"
-#include "symtab.h"
-#include "readinp.h"
-#include "readir.h"
 #include <string.h>
-#include "mdatoms.h"
-#include "pbc.h"
+
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static char pulldim[STRLEN];
@@ -72,7 +67,7 @@ static void string2dvec(const char buf[], dvec nums)
 }
 
 static void init_pull_group(t_pull_group *pg,
-                            const char *wbuf)
+                            const char   *wbuf)
 {
     double d;
     int    n, m;
@@ -98,7 +93,7 @@ static void init_pull_coord(t_pull_coord *pcrd, int eGeom,
     string2dvec(origin_buf, origin);
     if (pcrd->group[0] != 0 && dnorm(origin) > 0)
     {
-        gmx_fatal(FARGS,"The pull origin can only be set with an absolute reference");
+        gmx_fatal(FARGS, "The pull origin can only be set with an absolute reference");
     }
 
     if (eGeom == epullgDIST)
@@ -148,7 +143,7 @@ char **read_pullparams(int *ninp_p, t_inpfile **inp_p,
     RTYPE("pull-r1",          pull->cyl_r1, 1.0);
     CTYPE("Switch from r1 to r0 in case of dynamic reaction force");
     RTYPE("pull-r0",          pull->cyl_r0, 1.5);
-    RTYPE("pull_constr_tol",  pull->constr_tol, 1E-6);
+    RTYPE("pull-constr-tol",  pull->constr_tol, 1E-6);
     EETYPE("pull-start",      *bStart, yesno_names);
     EETYPE("pull-print-reference", pull->bPrintRef, yesno_names);
     ITYPE("pull-nstxout",     pull->nstxout, 10);
@@ -235,7 +230,7 @@ char **read_pullparams(int *ninp_p, t_inpfile **inp_p,
     return grpbuf;
 }
 
-void make_pull_groups(t_pull *pull, 
+void make_pull_groups(t_pull *pull,
                       char **pgnames,
                       const t_blocka *grps, char **gnames)
 {
@@ -251,6 +246,11 @@ void make_pull_groups(t_pull *pull,
     {
         pgrp = &pull->group[g];
 
+        if (strcmp(pgnames[g], "") == 0)
+        {
+            gmx_fatal(FARGS, "Group pull_group%d required by grompp was undefined.", g);
+        }
+
         ig        = search_string(pgnames[g], grps->nr, gnames);
         pgrp->nat = grps->index[ig+1] - grps->index[ig];
 
@@ -395,7 +395,7 @@ void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real l
 
     init_pull(NULL, ir, 0, NULL, mtop, NULL, oenv, lambda, FALSE, 0);
     md = init_mdatoms(NULL, mtop, ir->efep);
-    atoms2md(mtop, ir, 0, NULL, 0, mtop->natoms, md);
+    atoms2md(mtop, ir, 0, NULL, mtop->natoms, md);
     if (ir->efep)
     {
         update_mdatoms(md, lambda);
@@ -413,14 +413,14 @@ void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real l
     {
         pcrd  = &pull->coord[c];
 
-        pgrp0 = &pull->group[pcrd->group[0]]; 
-        pgrp1 = &pull->group[pcrd->group[1]]; 
+        pgrp0 = &pull->group[pcrd->group[0]];
+        pgrp1 = &pull->group[pcrd->group[1]];
         fprintf(stderr, "%8d  %8d  %8d\n",
                 pcrd->group[0], pgrp0->nat, pgrp0->pbcatom+1);
         fprintf(stderr, "%8d  %8d  %8d ",
                 pcrd->group[1], pgrp1->nat, pgrp1->pbcatom+1);
 
-        init = pcrd->init;
+        init       = pcrd->init;
         pcrd->init = 0;
 
         if (pcrd->rate == 0)