Merge release-4-5-patches into release-4-6

[alexxy/gromacs.git] / src / kernel / md.c

diff --git a/src/kernel/md.c b/src/kernel/md.c
index c5dd33da726eb6538a5f982390a9e56998b96f24..92792d1fbb13b97c5ab6ed963283c7dae9372cad 100644 (file)
--- a/src/kernel/md.c
+++ b/src/kernel/md.c
@@ -37,11 +37,6 @@
 #include <config.h>
 #endif
 
-#if ((defined WIN32 || defined _WIN32 || defined WIN64 || defined _WIN64) && !defined __CYGWIN__ && !defined __CYGWIN32__)
-/* _isnan() */
-#include <float.h>
-#endif
-
 #include "typedefs.h"
 #include "smalloc.h"
 #include "sysstuff.h"
@@ -69,7 +64,6 @@
 #include "disre.h"
 #include "orires.h"
 #include "dihre.h"
-#include "pppm.h"
 #include "pme.h"
 #include "mdatoms.h"
 #include "repl_ex.h"
@@ -91,7 +85,7 @@
 #ifdef GMX_LIB_MPI
 #include <mpi.h>
 #endif
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
 #include "tmpi.h"
 #endif
 
@@ -168,7 +162,7 @@ double do_md(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
     gmx_bool        bAppend;
     gmx_bool        bResetCountersHalfMaxH=FALSE;
     gmx_bool        bVV,bIterations,bFirstIterate,bTemp,bPres,bTrotter;
-    real        temp0,mu_aver=0,dvdl;
+    real        mu_aver=0,dvdl;
     int         a0,a1,gnx=0,ii;
     atom_id     *grpindex=NULL;
     char        *grpname;
@@ -298,13 +292,13 @@ double do_md(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
 
     if (DEFORM(*ir))
     {
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
         tMPI_Thread_mutex_lock(&deform_init_box_mutex);
 #endif
         set_deform_reference_box(upd,
                                  deform_init_init_step_tpx,
                                  deform_init_box_tpx);
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
         tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
 #endif
     }
@@ -507,7 +501,6 @@ double do_md(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
         enerd->term[F_TEMP] *= 2; /* result of averages being done over previous and current step,
                                      and there is no previous step */
     }
-    temp0 = enerd->term[F_TEMP];
     
     /* if using an iterative algorithm, we need to create a working directory for the state. */
     if (bIterations) 
@@ -535,7 +528,10 @@ double do_md(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
                     "RMS relative constraint deviation after constraining: %.2e\n",
                     constr_rmsd(constr,FALSE));
         }
-        fprintf(fplog,"Initial temperature: %g K\n",enerd->term[F_TEMP]);
+        if (EI_STATE_VELOCITY(ir->eI))
+        {
+            fprintf(fplog,"Initial temperature: %g K\n",enerd->term[F_TEMP]);
+        }
         if (bRerunMD)
         {
             fprintf(stderr,"starting md rerun '%s', reading coordinates from"
@@ -1311,7 +1307,7 @@ double do_md(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
 
         /* Check whether everything is still allright */    
         if (((int)gmx_get_stop_condition() > handled_stop_condition)
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
             && MASTER(cr)
 #endif
             )