Merge branch release-2018

[alexxy/gromacs.git] / src / gromacs / fileio / confio.cpp

diff --git a/src/gromacs/fileio/confio.cpp b/src/gromacs/fileio/confio.cpp
index dc7a094e99cbffc1256935973da4504285ce2aaa..5e4bcb961a0e6c2000f0a48e27712471ec748857 100644 (file)
--- a/src/gromacs/fileio/confio.cpp
+++ b/src/gromacs/fileio/confio.cpp
@@ -101,7 +101,7 @@ void write_sto_conf_indexed(const char *outfile, const char *title,
         case efENT:
         case efPQR:
             out = gmx_fio_fopen(outfile, "w");
-            write_pdbfile_indexed(out, title, atoms, x, ePBC, box, ' ', -1, nindex, index, nullptr, TRUE, ftp == efPQR ? TRUE : FALSE);
+            write_pdbfile_indexed(out, title, atoms, x, ePBC, box, ' ', -1, nindex, index, nullptr, TRUE, ftp == efPQR);
             gmx_fio_fclose(out);
             break;
         case efESP:
@@ -111,7 +111,6 @@ void write_sto_conf_indexed(const char *outfile, const char *title,
             break;
         case efTPR:
             gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
-            break;
         default:
             gmx_incons("Not supported in write_sto_conf_indexed");
     }
@@ -162,7 +161,6 @@ void write_sto_conf(const char *outfile, const char *title, const t_atoms *atoms
             break;
         case efTPR:
             gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
-            break;
         default:
             gmx_incons("Not supported in write_sto_conf");
     }
@@ -239,6 +237,7 @@ static void get_stx_coordnum(const char *infile, int *natoms)
     }
 }
 
+// TODO molecule index handling is suspected of being broken here
 static void tpx_make_chain_identifiers(t_atoms *atoms, t_block *mols)
 {
     /* We always assign a new chain number, but save the chain id characters
@@ -351,10 +350,10 @@ static void read_stx_conf(const char *infile,
     }
 }
 
-static void readConfAndAtoms(const char *infile,
-                             t_symtab *symtab, char **name, t_atoms *atoms,
-                             int *ePBC,
-                             rvec **x, rvec **v, matrix box)
+void readConfAndAtoms(const char *infile,
+                      t_symtab *symtab, char **name, t_atoms *atoms,
+                      int *ePBC,
+                      rvec **x, rvec **v, matrix box)
 {
     int natoms;
     get_stx_coordnum(infile, &natoms);
@@ -436,14 +435,11 @@ gmx_bool read_tps_conf(const char *infile, t_topology *top, int *ePBC,
                        rvec **x, rvec **v, matrix box, gmx_bool requireMasses)
 {
     bool        haveTopology;
-    gmx_mtop_t *mtop;
+    gmx_mtop_t  mtop;
 
-    // Note: We should have an initializer instead of relying on snew
-    snew(mtop, 1);
-    readConfAndTopology(infile, &haveTopology, mtop, ePBC, x, v, box);
+    readConfAndTopology(infile, &haveTopology, &mtop, ePBC, x, v, box);
 
-    *top = gmx_mtop_t_to_t_topology(mtop, true);
-    sfree(mtop);
+    *top = gmx_mtop_t_to_t_topology(&mtop, true);
 
     tpx_make_chain_identifiers(&top->atoms, &top->mols);