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

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

diff --git a/src/kernel/mdrun.c b/src/kernel/mdrun.c
index 085e35020fb3d2e86e5878ed770def40bea88a13..012a330c92d6932f9bfa8f52ed32286c15c62f47 100644 (file)
--- a/src/kernel/mdrun.c
+++ b/src/kernel/mdrun.c
@@ -49,7 +49,7 @@
 #include "mdrun.h"
 #include "xmdrun.h"
 #include "checkpoint.h"
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
 #include "thread_mpi.h"
 #endif
 
@@ -362,6 +362,7 @@ int main(int argc,char *argv[])
     { efXVG, "-dhdl",   "dhdl",     ffOPTWR },
     { efXVG, "-field",  "field",    ffOPTWR },
     { efXVG, "-table",  "table",    ffOPTRD },
+    { efXVG, "-tabletf", "tabletf",    ffOPTRD },
     { efXVG, "-tablep", "tablep",   ffOPTRD },
     { efXVG, "-tableb", "table",    ffOPTRD },
     { efTRX, "-rerun",  "rerun",    ffOPTRD },
@@ -376,6 +377,10 @@ int main(int argc,char *argv[])
     { efXVG, "-runav",  "runaver",  ffOPTWR },
     { efXVG, "-px",     "pullx",    ffOPTWR },
     { efXVG, "-pf",     "pullf",    ffOPTWR },
+    { efXVG, "-ro",     "rotation", ffOPTWR },
+    { efLOG, "-ra",     "rotangles",ffOPTWR },
+    { efLOG, "-rs",     "rotslabs", ffOPTWR },
+    { efLOG, "-rt",     "rottorque",ffOPTWR },
     { efMTX, "-mtx",    "nm",       ffOPTWR },
     { efNDX, "-dn",     "dipole",   ffOPTWR },
     { efRND, "-multidir",NULL,      ffOPTRDMULT}
@@ -425,7 +430,7 @@ int main(int argc,char *argv[])
       "Use particle decompostion" },
     { "-dd",      FALSE, etRVEC,{&realddxyz},
       "Domain decomposition grid, 0 is optimize" },
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
     { "-nt",      FALSE, etINT, {&nthreads},
       "Number of threads to start (0 is guess)" },
 #endif
@@ -541,7 +546,7 @@ int main(int argc,char *argv[])
   dd_node_order = nenum(ddno_opt);
   cr->npmenodes = npme;
 
-#ifndef GMX_THREADS
+#ifndef GMX_THREAD_MPI
   nthreads=1;
 #endif
 
@@ -561,7 +566,7 @@ int main(int argc,char *argv[])
       gmx_fatal(FARGS,"Need at least two replicas for replica exchange (option -multi)");
 
   if (nmultisim > 1) {
-#ifndef GMX_THREADS
+#ifndef GMX_THREAD_MPI
     gmx_bool bParFn = (multidir == NULL);
     init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
 #else