change to checking timestep for time dumps at start of each step

src/dump.cpp

@@ -330,8 +330,6 @@ void Dump::write()
 
   if (delay_flag && update->ntimestep < delaystep) return;
 
-  printf("DUMP %ld\n",update->ntimestep);
-
   // if file per timestep, open new file
 
   if (multifile) openfile();

src/integrate.cpp

@@ -20,6 +20,7 @@
 #include "kspace.h"
 #include "modify.h"
 #include "pair.h"
+#include "output.h"
 #include "update.h"
 
 using namespace LAMMPS_NS;
@@ -115,7 +116,13 @@ void Integrate::ev_setup()
 
 /* ----------------------------------------------------------------------
    set eflag,vflag for current iteration
-   based on computes that need energy/virial info on this timestep
+   based on
+     (1) computes that need energy/virial info on this timestep
+     (2) time dumps that need unknown per-atom info on this timestep
+     NOTE: could not check time dumps if timestep size is not varying
+           see NOTE in output.cpp
+           also inefficient to add all per-atom eng/virial computes
+           but don't know which ones the dump needs
    invoke matchstep() on all timestep-dependent computes to clear their arrays
    eflag: set any or no bits
      ENERGY_GLOBAL bit for global energy
@@ -133,6 +140,10 @@ void Integrate::ev_set(bigint ntimestep)
 {
   int i,flag;
 
+  int tdflag = 0;
+  if (output->any_time_dumps) 
+    tdflag = output->check_time_dumps(ntimestep);
+
   flag = 0;
   int eflag_global = 0;
   for (i = 0; i < nelist_global; i++)
@@ -143,7 +154,7 @@ void Integrate::ev_set(bigint ntimestep)
   int eflag_atom = 0;
   for (i = 0; i < nelist_atom; i++)
     if (elist_atom[i]->matchstep(ntimestep)) flag = 1;
-  if (flag) eflag_atom = ENERGY_ATOM;
+  if (flag || (tdflag && nelist_atom)) eflag_atom = ENERGY_ATOM;
 
   if (eflag_global) update->eflag_global = ntimestep;
   if (eflag_atom) update->eflag_atom = ntimestep;
@@ -159,13 +170,13 @@ void Integrate::ev_set(bigint ntimestep)
   int vflag_atom = 0;
   for (i = 0; i < nvlist_atom; i++)
     if (vlist_atom[i]->matchstep(ntimestep)) flag = 1;
-  if (flag) vflag_atom = VIRIAL_ATOM;
+  if (flag || (tdflag && nvlist_atom)) vflag_atom = VIRIAL_ATOM;
 
   flag = 0;
   int cvflag_atom = 0;
   for (i = 0; i < ncvlist_atom; i++)
     if (cvlist_atom[i]->matchstep(ntimestep)) flag = 1;
-  if (flag) cvflag_atom = VIRIAL_CENTROID;
+  if (flag || (tdflag && ncvlist_atom)) cvflag_atom = VIRIAL_CENTROID;
 
   if (vflag_global) update->vflag_global = ntimestep;
   if (vflag_atom || cvflag_atom) update->vflag_atom = ntimestep;

src/output.cpp

@@ -133,7 +133,9 @@ void Output::init()
   }
 
   for (int i = 0; i < ndump; i++) dump[i]->init();
-  for (int i = 0; i < ndump; i++)
+  any_time_dumps = 0;
+  for (int i = 0; i < ndump; i++) {
+    if (mode_dump[i]) any_time_dumps = 1;
     if ((mode_dump[i] == 0 && every_dump[i] == 0) ||
         (mode_dump[i] == 1 && every_time_dump[i] == 0.0)) {
       ivar_dump[i] = input->variable->find(var_dump[i]);
@@ -142,6 +144,7 @@ void Output::init()
       if (!input->variable->equalstyle(ivar_dump[i]))
         error->all(FLERR,"Variable for dump every or delta is invalid style");
     }
+  }
 
   if (restart_flag_single && restart_every_single == 0) {
     ivar_restart_single = input->variable->find(var_restart_single);
@@ -176,9 +179,11 @@ void Output::setup(int memflag)
   if (ndump && update->restrict_output == 0) {
     for (int idump = 0; idump < ndump; idump++) {
 
-      // wrap dumps that invoke computes or do variable eval with clear/add
+      // wrap step dumps that invoke computes or do variable eval with clear/add
+      // see NOTE in write() about also wrapping time dumps
 
-      if (dump[idump]->clearstep || var_dump[idump])
+      if (mode_dump[idump] == 0 &&
+          (dump[idump]->clearstep || var_dump[idump]))
         modify->clearstep_compute();
 
       // write a snapshot at setup only if any of these 3 conditions hold
@@ -226,7 +231,8 @@ void Output::setup(int memflag)
       // if dump not written now, use addstep_compute_all() 
       // since don't know what computes the dump will invoke
 
-      if (dump[idump]->clearstep || var_dump[idump]) {
+      if (mode_dump[idump] == 0 &&
+          (dump[idump]->clearstep || var_dump[idump])) {
         if (writeflag) modify->addstep_compute(next_dump[idump]);
         else modify->addstep_compute_all(next_dump[idump]);
       }
@@ -304,21 +310,28 @@ void Output::setup(int memflag)
 
    next = MIN(next_dump_any,next_restart);
    next = MIN(next,next_thermo);
-}
+ }
 
-/* ----------------------------------------------------------------------
+ /* ----------------------------------------------------------------------
     perform all output for this timestep
     only perform output if next matches current step and last output doesn't
     do dump/restart before thermo so thermo CPU time will include them
-------------------------------------------------------------------------- */
+ ------------------------------------------------------------------------- */
 
-void Output::write(bigint ntimestep)
-{
+ void Output::write(bigint ntimestep)
+ {
    // perform dump if its next_dump = current ntimestep
    //   but not if it was already written on this step
    // set next_dump and also next_time_dump for mode_dump = 1
    // set next_dump_any to smallest next_dump
-  // wrap dumps that invoke computes or do variable eval with clear/add
+   // wrap step dumps that invoke computes or do variable eval with clear/add
+   // NOTE:
+   //   could wrap time dumps as well, if timestep size did not vary
+   //   if wrap when timestep size varies frequently,
+   //     then can do many unneeded addstep() --> inefficient
+   //   hard to know if timestep varies, since run every could change it
+   //   can't remove an uneeded addstep from a compute, b/c don't know
+   //     what other command may have added it
 
    int writeflag;
 
@@ -327,7 +340,8 @@ void Output::write(bigint ntimestep)
        if (next_dump[idump] == ntimestep) {
          if (last_dump[idump] == ntimestep) continue;
 
-        if (dump[idump]->clearstep || var_dump[idump])
+         if (mode_dump[idump] == 0 && 
+             (dump[idump]->clearstep || var_dump[idump]))
            modify->clearstep_compute();
 
          // perform dump
@@ -337,7 +351,8 @@ void Output::write(bigint ntimestep)
          last_dump[idump] = ntimestep;
          calculate_next_dump(1,idump,ntimestep);
 
-        if (dump[idump]->clearstep || var_dump[idump])
+         if (mode_dump[idump] == 0 && 
+             (dump[idump]->clearstep || var_dump[idump]))
            modify->addstep_compute(next_dump[idump]);
        }
 
@@ -418,22 +433,22 @@ void Output::write(bigint ntimestep)
 
    next = MIN(next_dump_any,next_restart);
    next = MIN(next,next_thermo);
-}
+ }
 
-/* ----------------------------------------------------------------------
+ /* ----------------------------------------------------------------------
     force a snapshot to be written for all dumps
     called from PRD and TAD
-------------------------------------------------------------------------- */
+ ------------------------------------------------------------------------- */
 
-void Output::write_dump(bigint ntimestep)
-{
+ void Output::write_dump(bigint ntimestep)
+ {
    for (int idump = 0; idump < ndump; idump++) {
      dump[idump]->write();
      last_dump[idump] = ntimestep;
    }
-}
+ }
 
-/* ----------------------------------------------------------------------
+ /* ----------------------------------------------------------------------
     calculate when next dump occurs for Dump instance idump
     operates in one of two modes, based on mode_dump flag
     for timestep mode, set next_dump
@@ -442,10 +457,10 @@ void Output::write_dump(bigint ntimestep)
       0 = from setup() at start of run
       1 = from write() during run each time a dump file is written
       2 = from reset_dt() called from fix dt/reset when it changes timestep size
-------------------------------------------------------------------------- */
+ ------------------------------------------------------------------------- */
 
   void Output::calculate_next_dump(int which, int idump, bigint ntimestep)
-{
+ {
    // dump mode is by timestep
    // just set next_dump
 
@@ -533,15 +548,26 @@ void Output::write_dump(bigint ntimestep)
      next_time_dump[idump] = nexttime;
      next_dump[idump] = nextdump;
    }
+ }
+
+/* ---------------------------------------------------------------------- */
+
+int Output::check_time_dumps(bigint ntimestep)
+{
+  int nowflag = 0;
+  for (int i = 0; i < ndump; i++)
+    if (mode_dump[i] && next_dump[i] == ntimestep) nowflag = 1;
+
+  return nowflag;
 }
 
-/* ----------------------------------------------------------------------
+ /* ----------------------------------------------------------------------
     force restart file(s) to be written
     called from PRD and TAD
-------------------------------------------------------------------------- */
+ ------------------------------------------------------------------------- */
 
-void Output::write_restart(bigint ntimestep)
-{
+ void Output::write_restart(bigint ntimestep)
+ {
    if (restart_flag_single) {
      std::string file = restart1;
      std::size_t found = file.find('*');
@@ -561,22 +587,22 @@ void Output::write_restart(bigint ntimestep)
    }
 
    last_restart = ntimestep;
-}
+ }
 
-/* ----------------------------------------------------------------------
+ /* ----------------------------------------------------------------------
     timestep is being changed, called by update->reset_timestep()
     for dumps, require that no dump is "active"
       meaning that a snapshot has already been output
-   reset next output values restart and thermo output
+    reset next output values for restart and thermo
     reset to smallest value >= new timestep
     if next timestep set by variable evaluation,
       eval for ntimestep-1, so current ntimestep can be returned if needed
       no guarantee that variable can be evaluated for ntimestep-1
       e.g. if it depends on computes, but live with that rare case for now
-------------------------------------------------------------------------- */
+ ------------------------------------------------------------------------- */
 
-void Output::reset_timestep(bigint ntimestep)
-{
+ void Output::reset_timestep(bigint ntimestep)
+ {
    next_dump_any = MAXBIGINT;
    for (int idump = 0; idump < ndump; idump++)
      if (last_dump[idump] >= 0)
@@ -641,11 +667,13 @@ void Output::reset_timestep(bigint ntimestep)
 
    next = MIN(next_dump_any,next_restart);
    next = MIN(next,next_thermo);
-}
+ }
 
 /* ----------------------------------------------------------------------
-   timestep size is being changed, called by fix dt/reset (at end of step)
+   timestep size is being changed
    reset next output values for dumps which have mode_dump=1
+   called by fix dt/reset (at end of step)
+   or called by timestep command via run every (also at end of step)
 ------------------------------------------------------------------------- */
 
 void Output::reset_dt()
@@ -659,21 +687,10 @@ void Output::reset_dt()
 
       // reset next_dump but do not change next_time_dump, 2 arg for reset_dt()
       // do not invoke for a dump already scheduled for this step
-      // use compute_all() b/c don't know what computes will be needed
+      //   since timestep change affects next step
 
       if (next_dump[idump] != ntimestep) {
         calculate_next_dump(2,idump,update->ntimestep);
-
-        // NOTE: think I should not do this here
-        // for time dumps, calc_next_dump should calc the next timestep
-        //   as one less and not add it to computes
-        // then on that step, write() should not actually write the dump
-        //   but trigger it on next step and addstep_compute_all for that step
-        // b/c when write() is called, the next-step timestep is set
-        // unless run every timestep is invoked in-between!
-
-        //if (dump[idump]->clearstep || var_dump[idump])
-        //  modify->addstep_compute_all(next_dump[idump]);
       }
     }
 
@@ -684,6 +701,7 @@ void Output::reset_dt()
   next = MIN(next,next_thermo);
 }
 
+
 /* ----------------------------------------------------------------------
    add a Dump to list of Dumps
 ------------------------------------------------------------------------- */

src/output.h

@@ -36,6 +36,7 @@ class Output : protected Pointers {
   int ndump;               // # of Dumps defined
   int max_dump;            // max size of Dump list
   bigint next_dump_any;    // next timestep for any Dump
+  int any_time_dumps;      // 1 if any time dump defined
   int *mode_dump;          // 0/1 if write every N timesteps or Delta in sim time
   int *every_dump;         // dump every N timesteps, 0 if variable
   double *every_time_dump; // dump every Delta of sim time, 0.0 if variable
@@ -75,13 +76,14 @@ class Output : protected Pointers {
   void write(bigint);             // output for current timestep
   void write_dump(bigint);        // force output of dump snapshots
   void write_restart(bigint);     // force output of a restart file
-  void reset_timestep(bigint);    // reset output which depeneds on timestep
-  void reset_dt();                // reset output which depends on dt
+  void reset_timestep(bigint);    // reset output which depends on timestep
+  void reset_dt();                // reset output which depends on timestep size
 
   void add_dump(int, char **);       // add a Dump to Dump list
   void modify_dump(int, char **);    // modify a Dump
   void delete_dump(char *);          // delete a Dump from Dump list
   int find_dump(const char *);       // find a Dump ID
+  int check_time_dumps(bigint);      // check if any time dump is output now
 
   void set_thermo(int, char **);        // set thermo output freqquency
   void create_thermo(int, char **);     // create a thermo style

src/verlet.cpp

@@ -252,8 +252,6 @@ void Verlet::run(int n)
     ntimestep = ++update->ntimestep;
     ev_set(ntimestep);
 
-    printf("VERLET %ld: %d %d\n",ntimestep,eflag,vflag);
-
     // initial time integration
 
     timer->stamp();