Sort all includes in src/gromacs

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

diff --git a/src/gromacs/fileio/tngio.cpp b/src/gromacs/fileio/tngio.cpp
index 7a2cb969dac3c8ac159bb30c71b7a8c406c70f18..1303872d3d8364a0ee2a3405b1efc82a2d0c9ee8 100644 (file)
--- a/src/gromacs/fileio/tngio.cpp
+++ b/src/gromacs/fileio/tngio.cpp
@@ -32,24 +32,23 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
+#include "gmxpre.h"
+
 #include "tngio.h"
 
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "config.h"
 
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
 
 #ifdef GMX_USE_TNG
-#include "../../external/tng_io/include/tng_io.h"
+#include "tng/tng_io.h"
 #endif
 
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/types/ifunc.h"
-
-#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/topology/topology.h"
@@ -61,21 +60,24 @@
 
 static const char *modeToVerb(char mode)
 {
+    const char *p;
     switch (mode)
     {
         case 'r':
-            return "reading";
+            p = "reading";
             break;
         case 'w':
-            return "writing";
+            p = "writing";
             break;
         case 'a':
-            return "appending";
+            p = "appending";
             break;
         default:
             gmx_fatal(FARGS, "Invalid file opening mode %c", mode);
-            return "";
+            p = "";
+            break;
     }
+    return p;
 }
 
 void gmx_tng_open(const char       *filename,
@@ -147,12 +149,14 @@ void gmx_tng_open(const char       *filename,
 //             tng_last_program_name_set(*tng, programInfo);
 //         }
 
-#ifdef HAVE_UNISTD_H
+#if defined(HAVE_UNISTD_H) && !defined(__MINGW32__)
         char username[256];
-        getlogin_r(username, 256);
-        if (mode == 'w')
+        if (!getlogin_r(username, 256))
         {
-            tng_first_user_name_set(*tng, username);
+            if (mode == 'w')
+            {
+                tng_first_user_name_set(*tng, username);
+            }
         }
 /* TODO: This should be implemented when the above fixme is done (adding data to
  * the header). */
@@ -192,6 +196,9 @@ static void addTngMoleculeFromTopology(tng_trajectory_t     tng,
                                        gmx_int64_t          numMolecules,
                                        tng_molecule_t      *tngMol)
 {
+    tng_chain_t      tngChain = NULL;
+    tng_residue_t    tngRes   = NULL;
+
     if (tng_molecule_add(tng, moleculeName, tngMol) != TNG_SUCCESS)
     {
         gmx_file("Cannot add molecule to TNG molecular system.");
@@ -208,24 +215,32 @@ static void addTngMoleculeFromTopology(tng_trajectory_t     tng,
         {
             const t_resinfo *resInfo        = &atoms->resinfo[at->resind];
             char             chainName[2]   = {resInfo->chainid, 0};
-            tng_chain_t      tngChain       = NULL;
-            tng_residue_t    tngRes         = NULL;
             tng_atom_t       tngAtom        = NULL;
+            t_atom          *prevAtom;
 
-            if (tng_molecule_chain_find (tng, *tngMol, chainName,
-                                         (gmx_int64_t)-1, &tngChain) !=
-                TNG_SUCCESS)
+            if (atomIndex > 0)
             {
-                tng_molecule_chain_add (tng, *tngMol, chainName,
-                                        &tngChain);
+                prevAtom = &atoms->atom[atomIndex - 1];
+            }
+            else
+            {
+                prevAtom = 0;
             }
 
-            /* FIXME: When TNG supports both residue index and residue
-             * number the latter should be used. Wait for TNG 2.0*/
-            if (tng_chain_residue_find(tng, tngChain, *resInfo->name,
-                                       at->resind + 1, &tngRes)
-                != TNG_SUCCESS)
+            /* If this is the first atom or if the residue changed add the
+             * residue to the TNG molecular system. */
+            if (!prevAtom || resInfo != &atoms->resinfo[prevAtom->resind])
             {
+                /* If this is the first atom or if the chain changed add
+                 * the chain to the TNG molecular system. */
+                if (!prevAtom || resInfo->chainid !=
+                    atoms->resinfo[prevAtom->resind].chainid)
+                {
+                    tng_molecule_chain_add(tng, *tngMol, chainName,
+                                           &tngChain);
+                }
+                /* FIXME: When TNG supports both residue index and residue
+                 * number the latter should be used. Wait for TNG 2.0*/
                 tng_chain_residue_add(tng, tngChain, *resInfo->name, &tngRes);
             }
             tng_residue_atom_add(tng, tngRes, *(atoms->atomname[atomIndex]), *(atoms->atomtype[atomIndex]), &tngAtom);