Merge release-4-6 into master

[alexxy/gromacs.git] / src / tools / gmx_covar.c

diff --git a/src/tools/gmx_covar.c b/src/tools/gmx_covar.c
index 66d2085f26c75025c05c9ae2f1992382983ca764..e3668a6283ca768fbbcfda991ff6936a0d65f205 100644 (file)
--- a/src/tools/gmx_covar.c
+++ b/src/tools/gmx_covar.c
@@ -35,7 +35,7 @@
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
-#include "gmx_header_config.h"
+
 #include <math.h>
 #include <string.h>
 #include <time.h>
@@ -44,12 +44,6 @@
 #include <sys/time.h>
 #endif
 
-
-#ifdef GMX_NATIVE_WINDOWS
-#include <direct.h>
-#include <io.h>
-#endif
-
 #include "statutil.h"
 #include "sysstuff.h"
 #include "typedefs.h"
@@ -70,11 +64,12 @@
 #include "txtdump.h"
 #include "matio.h"
 #include "eigio.h"
-#include "eigensolver.h"
 #include "physics.h"
 #include "gmx_ana.h"
 #include "string2.h"
 
+#include "gromacs/linearalgebra/eigensolver.h"
+
 /* Portable version of ctime_r implemented in src/gmxlib/string2.c, but we do not want it declared in public installed headers */
 char *
 gmx_ctime_r(const time_t *clock,char *buf, int n);
@@ -488,15 +483,7 @@ int gmx_covar(int argc,char *argv[])
   fprintf(out,"Covariance analysis log, written %s\n",timebuf);
     
   fprintf(out,"Program: %s\n",argv[0]);
-#ifdef GMX_NATIVE_WINDOWS
-  pcwd=_getcwd(str,STRLEN);
-#else
-  pcwd=getcwd(str,STRLEN);
-#endif
-  if(NULL==pcwd)
-  {
-      gmx_fatal(FARGS,"Current working directory is undefined");
-  }
+  gmx_getcwd(str, STRLEN);
 
   fprintf(out,"Working directory: %s\n\n",str);