From 31731fd1cef1391d8c5a23ec6886a3f32962c50f Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Tue, 20 Jan 2015 23:17:36 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12977
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/XTC/dump_xtc.cpp | 28 ++++++++++++++++++++++++----
 src/XTC/dump_xtc.h   |  2 +-
 src/create_bonds.cpp |  2 +-
 src/update.cpp       |  2 +-
 4 files changed, 27 insertions(+), 7 deletions(-)

diff --git a/src/XTC/dump_xtc.cpp b/src/XTC/dump_xtc.cpp
index cd86e2dbac..f2709f431f 100644
--- a/src/XTC/dump_xtc.cpp
+++ b/src/XTC/dump_xtc.cpp
@@ -76,10 +76,18 @@ DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
   memory->create(coords,3*natoms,"dump:coords");
 
   // sfactor = conversion of coords to XTC units
-  // GROMACS standard is nanometers, not Angstroms
+  // tfactor = conversion of simulation time to XTC units
+  // GROMACS standard is nanometers and picoseconds
 
-  sfactor = 0.1;
-  if (strcmp(update->unit_style,"lj") == 0) sfactor = 1.0;
+  sfactor = 0.1 / force->angstrom;
+  tfactor = 0.001 / force->femtosecond;
+
+  // in reduced units we do not scale anything
+  if (strcmp(update->unit_style,"lj") == 0) {
+    sfactor = tfactor = 1.0;
+    error->warning(FLERR,"No automatic unit conversion to XTC file "
+                   "format conventions possible for 'units lj'");
+  }
 
   openfile();
   nevery_save = 0;
@@ -160,7 +168,7 @@ void DumpXTC::write_header(bigint nbig)
   xdr_int(&xd,&tmp);
   xdr_int(&xd,&n);
   xdr_int(&xd,&ntimestep);
-  float time_value = ntimestep * update->dt;
+  float time_value = ntimestep * tfactor * update->dt;
   xdr_float(&xd,&time_value);
 
   // cell basis vectors
@@ -280,6 +288,18 @@ int DumpXTC::modify_param(int narg, char **arg)
         (fabs(precision-1000000.0) > EPS))
       error->all(FLERR,"Illegal dump_modify command");
     return 2;
+  } else if (strcmp(arg[0],"sfactor") == 0) {
+    if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
+    sfactor = force->numeric(FLERR,arg[1]);
+    if (sfactor <= 0.0)
+      error->all(FLERR,"Illegal dump_modify sfactor value (must be >0.0)");
+    return 2;
+  } else if (strcmp(arg[0],"tfactor") == 0) {
+    if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
+    tfactor = force->numeric(FLERR,arg[1]);
+    if (tfactor <= 0.0)
+      error->all(FLERR,"Illegal dump_modify tfactor value (must be >0.0)");
+    return 2;
   }
   return 0;
 }
diff --git a/src/XTC/dump_xtc.h b/src/XTC/dump_xtc.h
index f1e960af6c..0c1eed5204 100644
--- a/src/XTC/dump_xtc.h
+++ b/src/XTC/dump_xtc.h
@@ -42,7 +42,7 @@ class DumpXTC : public Dump {
   int unwrap_flag;            // 1 if atom coords are unwrapped, 0 if no
   float precision;            // user-adjustable precision setting
   float *coords;
-  double sfactor;
+  double sfactor,tfactor;     // scaling factors for positions and time unit 
   XDR xd;
 
   void init_style();
diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp
index 3de639c30a..c56adbfd13 100644
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@@ -101,7 +101,7 @@ void CreateBonds::command(int narg, char **arg)
   if (force->special_lj[1] != 0.0 || force->special_coul[1] != 0.0)
     error->all(FLERR,"Create_bonds command requires "
                "special_bonds 1-2 weights be 0.0");
-  if (force->kspace_style)
+  if (force->kspace)
     error->all(FLERR,"Create_bonds command requires "
                "no kspace_style be defined");
 
diff --git a/src/update.cpp b/src/update.cpp
index 610cce1abd..ac5318578b 100644
--- a/src/update.cpp
+++ b/src/update.cpp
@@ -235,7 +235,7 @@ void Update::set_units(const char *style)
     force->hhmrr2e = 0.0;
     force->mvh2r = 0.0;
     force->angstrom = 1.88972612;
-    force->femtosecond = 0.0241888428;
+    force->femtosecond = 41.34137413;
     force->qelectron = 1.0;
 
     dt = 0.001;