git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15250 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/RIGID/compute_rigid_local.cpp

@@ -87,9 +87,10 @@ ComputeRigidLocal::ComputeRigidLocal(LAMMPS *lmp, int narg, char **arg) :
     else error->all(FLERR,"Invalid keyword in compute rigid/local command");
   }
 
-  nmax = 0;
+  ncount = nmax = 0;
   vector = NULL;
   array = NULL;
+  fixrigid = NULL;
 }
 
 /* ---------------------------------------------------------------------- */

src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp

@@ -64,6 +64,7 @@ enum { CONST, EQUAL }; // For treating the variables.
 
 static const char* cite_fix_nve_manifold_rattle =
   "fix nve/manifold/rattle command:\n\n"
+  "@article{paquay-2016,\n"
   "   author        = {Paquay, Stefan and Kusters, Remy},\n"
   "   doi           = {10.1016/j.bpj.2016.02.017},\n"
   "   issn          = {0006-3495},\n"

src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp

@@ -66,6 +66,7 @@ enum {NOBIAS,BIAS};
 
 static const char* cite_fix_nvt_manifold_rattle =
   "fix nvt/manifold/rattle command:\n\n"
+  "@article{paquay-2016,\n"
   "   author        = {Paquay, Stefan and Kusters, Remy},\n"
   "   doi           = {10.1016/j.bpj.2016.02.017},\n"
   "   issn          = {0006-3495},\n"

src/read_data.cpp

@@ -1705,6 +1705,8 @@ void ReadData::pairIJcoeffs()
 
 void ReadData::bondcoeffs()
 {
+  if (!nbondtypes) return;
+
   char *next;
   char *buf = new char[nbondtypes*MAXLINE];
 
@@ -1727,6 +1729,8 @@ void ReadData::bondcoeffs()
 
 void ReadData::anglecoeffs(int which)
 {
+  if (!nangletypes) return;
+
   char *next;
   char *buf = new char[nangletypes*MAXLINE];
 
@@ -1751,6 +1755,8 @@ void ReadData::anglecoeffs(int which)
 
 void ReadData::dihedralcoeffs(int which)
 {
+  if (!ndihedraltypes) return;
+
   char *next;
   char *buf = new char[ndihedraltypes*MAXLINE];
 
@@ -1778,6 +1784,8 @@ void ReadData::dihedralcoeffs(int which)
 
 void ReadData::impropercoeffs(int which)
 {
+  if (!nimpropertypes) return;
+
   char *next;
   char *buf = new char[nimpropertypes*MAXLINE];
 

src/thermo.cpp

@@ -55,7 +55,7 @@ using namespace MathConst;
 
 // customize a new keyword by adding to this list:
 
-// step, elapsed, elaplong, dt, time, cpu, tpcpu, spcpu, cpuremain, part
+// step, elapsed, elaplong, dt, time, cpu, tpcpu, spcpu, cpuremain, part, timeremain
 // atoms, temp, press, pe, ke, etotal, enthalpy
 // evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail
 // vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi, xy, xz, yz,
@@ -672,6 +672,8 @@ void Thermo::parse_fields(char *str)
       addfield("CPULeft",&Thermo::compute_cpuremain,FLOAT);
     } else if (strcmp(word,"part") == 0) {
       addfield("Part",&Thermo::compute_part,INT);
+    } else if (strcmp(word,"timeremain") == 0) {
+      addfield("TimeoutLeft",&Thermo::compute_timeremain,FLOAT);
 
     } else if (strcmp(word,"atoms") == 0) {
       addfield("Atoms",&Thermo::compute_atoms,BIGINT);
@@ -1069,6 +1071,10 @@ int Thermo::evaluate_keyword(char *word, double *answer)
     compute_part();
     dvalue = ivalue;
 
+  } else if (strcmp(word,"timeremain") == 0) {
+    compute_timeremain();
+
+
   } else if (strcmp(word,"atoms") == 0) {
     compute_atoms();
     dvalue = bivalue;
@@ -1598,6 +1604,13 @@ void Thermo::compute_part()
 
 /* ---------------------------------------------------------------------- */
 
+void Thermo::compute_timeremain()
+{
+  dvalue = timer->get_timeout_remain();
+}
+
+/* ---------------------------------------------------------------------- */
+
 void Thermo::compute_atoms()
 {
   bivalue = atom->natoms;

src/thermo.h

@@ -127,6 +127,7 @@ class Thermo : protected Pointers {
   void compute_spcpu();
   void compute_cpuremain();
   void compute_part();
+  void compute_timeremain();
 
   void compute_atoms();
   void compute_temp();

src/timer.cpp

@@ -263,6 +263,12 @@ bool Timer::_check_timeout()
   }
 }
 
+/* ---------------------------------------------------------------------- */
+double Timer::get_timeout_remain()
+{
+  return (_timeout < 0.0) ? 0.0 : _timeout + timeout_start - MPI_Wtime();
+}
+
 /* ----------------------------------------------------------------------
    modify parameters of the Timer class
 ------------------------------------------------------------------------- */

src/timer.h

@@ -66,6 +66,9 @@ class Timer : protected Pointers {
   // trigger enforced timeout
   void force_timeout() { _timeout = 0.0; };
 
+  // get remaining time in seconds. 0.0 if inactive, negative if expired
+  double get_timeout_remain();
+
   // print timeout message
   void print_timeout(FILE *);
 

src/write_data.cpp

@@ -286,19 +286,19 @@ void WriteData::force_fields()
       force->pair->write_data_all(fp);
     }
   }
-  if (force->bond && force->bond->writedata) {
+  if (force->bond && force->bond->writedata && atom->nbondtypes) {
     fprintf(fp,"\nBond Coeffs # %s\n\n", force->bond_style);
     force->bond->write_data(fp);
   }
-  if (force->angle && force->angle->writedata) {
+  if (force->angle && force->angle->writedata && atom->nangletypes) {
     fprintf(fp,"\nAngle Coeffs # %s\n\n", force->angle_style);
     force->angle->write_data(fp);
   }
-  if (force->dihedral && force->dihedral->writedata) {
+  if (force->dihedral && force->dihedral->writedata && atom->ndihedraltypes) {
     fprintf(fp,"\nDihedral Coeffs # %s\n\n", force->dihedral_style);
     force->dihedral->write_data(fp);
   }
-  if (force->improper && force->improper->writedata) {
+  if (force->improper && force->improper->writedata && atom->nimpropertypes) {
     fprintf(fp,"\nImproper Coeffs # %s\n\n", force->improper_style);
     force->improper->write_data(fp);
   }