Move read_tps_conf() to confio.h

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_genion.c

diff --git a/src/gromacs/gmxana/gmx_genion.c b/src/gromacs/gmxana/gmx_genion.c
index 6b03ea738b616fea6f89d93ebadff13593efc0f2..c7d980eee99a68d5b8a266427d420ef520f95c5b 100644 (file)
--- a/src/gromacs/gmxana/gmx_genion.c
+++ b/src/gromacs/gmxana/gmx_genion.c
@@ -34,32 +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 <ctype.h>
+#include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "gromacs/fileio/confio.h"
 #include "gromacs/commandline/pargs.h"
-#include "pbc.h"
-#include "force.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/math/utilities.h"
-#include "macros.h"
-#include "vec.h"
-#include "gromacs/fileio/tpxio.h"
-#include "mdrun.h"
-#include "main.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/random/random.h"
-#include "index.h"
-#include "mtop_util.h"
-#include "gmx_ana.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void insert_ion(int nsa, int *nwater,
                        gmx_bool bSet[], int repl[], atom_id index[],
@@ -126,7 +121,7 @@ static char *aname(const char *mname)
     char *str;
     int   i;
 
-    str = strdup(mname);
+    str = gmx_strdup(mname);
     i   = strlen(str)-1;
     while (i > 1 && (isdigit(str[i]) || (str[i] == '+') || (str[i] == '-')))
     {
@@ -180,14 +175,14 @@ void sort_ions(int nsa, int nw, int repl[], atom_id index[],
         if (np)
         {
             snew(pptr, 1);
-            pptr[0] = strdup(p_name);
+            pptr[0] = gmx_strdup(p_name);
             snew(paptr, 1);
             paptr[0] = aname(p_name);
         }
         if (nn)
         {
             snew(nptr, 1);
-            nptr[0] = strdup(n_name);
+            nptr[0] = gmx_strdup(n_name);
             snew(naptr, 1);
             naptr[0] = aname(n_name);
         }
@@ -296,7 +291,7 @@ static void update_topol(const char *topinout, int p_num, int n_num,
             }
             /* Store this molecules section line */
             srenew(mol_line, nmol_line+1);
-            mol_line[nmol_line] = strdup(buf);
+            mol_line[nmol_line] = gmx_strdup(buf);
             nmol_line++;
         }
     }
@@ -383,7 +378,7 @@ int gmx_genion(int argc, char *argv[])
         { "-rmin",  FALSE, etREAL, {&rmin},  "Minimum distance between ions" },
         { "-seed",  FALSE, etINT,  {&seed},  "Seed for random number generator" },
         { "-conc",  FALSE, etREAL, {&conc},
-          "Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input [TT].tpr[tt] file. Overrides the [TT]-np[tt] and [TT]-nn[tt] options." },
+          "Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input [REF].tpr[ref] file. Overrides the [TT]-np[tt] and [TT]-nn[tt] options." },
         { "-neutral", FALSE, etBOOL, {&bNeutral}, "This option will add enough ions to neutralize the system. These ions are added on top of those specified with [TT]-np[tt]/[TT]-nn[tt] or [TT]-conc[tt]. "}
     };
     t_topology         top;
@@ -400,14 +395,14 @@ int gmx_genion(int argc, char *argv[])
     output_env_t       oenv;
     gmx_rng_t          rng;
     t_filenm           fnm[] = {
-        { efTPX, NULL,  NULL,      ffREAD  },
+        { efTPR, NULL,  NULL,      ffREAD  },
         { efNDX, NULL,  NULL,      ffOPTRD },
         { efSTO, "-o",  NULL,      ffWRITE },
         { efTOP, "-p",  "topol",   ffOPTRW }
     };
 #define NFILE asize(fnm)
 
-    if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
+    if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
                            asize(desc), desc, asize(bugs), bugs, &oenv))
     {
         return 0;
@@ -425,7 +420,7 @@ int gmx_genion(int argc, char *argv[])
     }
 
     /* Read atom positions and charges */
-    read_tps_conf(ftp2fn(efTPX, NFILE, fnm), title, &top, &ePBC, &x, &v, box, FALSE);
+    read_tps_conf(ftp2fn(efTPR, NFILE, fnm), title, &top, &ePBC, &x, &v, box, FALSE);
     atoms = top.atoms;
 
     /* Compute total charge */