git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3674 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/atom.cpp

@@ -52,6 +52,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
   extra_bond_per_atom = 0;
 
   firstgroupname = NULL;
+  sortfreq = 0;
+  maxbin = maxnext = 0;
+  binhead = NULL;
+  next = permute = NULL;
 
   // initialize atom arrays
   // customize by adding new array
@@ -110,13 +114,6 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
   nextra_store = 0;
   extra = NULL;
 
-  // sorting
-
-  sortflag = 0;
-  maxbin = maxnext = 0;
-  binhead = NULL;
-  next = permute = NULL;
-
   // default mapping values and hash table primes
 
   tag_enable = 1;
@@ -146,7 +143,11 @@ Atom::~Atom()
 {
   delete [] atom_style;
   delete avec;
+
   delete [] firstgroupname;
+  memory->sfree(binhead);
+  memory->sfree(next);
+  memory->sfree(permute);
 
   // delete atom arrays
   // customize by adding new array
@@ -211,12 +212,6 @@ Atom::~Atom()
   delete [] dipole;
   delete [] dipole_setflag;
 
-  // delete sorting arrays
-
-  memory->sfree(binhead);
-  memory->sfree(next);
-  memory->sfree(permute);
-
   // delete extra arrays
 
   memory->sfree(extra_grow);
@@ -315,7 +310,7 @@ void Atom::setup()
   // setup for sorting
   // binsize = user setting or 1/2 of neighbor cutoff
 
-  if (sortflag) {
+  if (sortfreq > 0) {
     double binsize;
     if (userbinsize > 0.0) binsize = userbinsize;
     else binsize = 0.5 * neighbor->cutneighmax;
@@ -341,6 +336,8 @@ int Atom::style_match(const char *style)
 
 /* ----------------------------------------------------------------------
    modify parameters of the atom style
+   some options can only be invoked before simulation box is defined
+   first and sort options cannot be used together
 ------------------------------------------------------------------------- */
 
 void Atom::modify_params(int narg, char **arg)
@@ -354,6 +351,8 @@ void Atom::modify_params(int narg, char **arg)
       if (strcmp(arg[iarg+1],"array") == 0) map_style = 1;
       else if (strcmp(arg[iarg+1],"hash") == 0) map_style = 2;
       else error->all("Illegal atom_modify command");
+      if (domain->box_exist) 
+	error->all("Atom_modify map command after simulation box is defined");
       iarg += 2;
     } else if (strcmp(arg[iarg],"first") == 0) {
       if (iarg+2 > narg) error->all("Illegal atom_modify command");
@@ -363,6 +362,7 @@ void Atom::modify_params(int narg, char **arg)
 	firstgroupname = new char[n];
 	strcpy(firstgroupname,arg[iarg+1]);
       }
+      sortfreq = 0;
       iarg += 2;
     } else if (strcmp(arg[iarg],"sort") == 0) {
       if (iarg+3 > narg) error->all("Illegal atom_modify command");
@@ -370,8 +370,9 @@ void Atom::modify_params(int narg, char **arg)
       userbinsize = atof(arg[iarg+2]);
       if (sortfreq < 0 || userbinsize < 0.0)
 	error->all("Illegal atom_modify command");
-      if (sortfreq == 0) sortflag = 0;
+      if (sortfreq >= 0 && firstgroupname) 
-      else sortflag = 1;
+	error->all("Atom_modify sort and first options "
+		   "cannot be used together");
       iarg += 3;
     } else error->all("Illegal atom_modify command");
   }
@@ -1370,7 +1371,7 @@ void Atom::sort()
     permute = (int *) memory->smalloc(maxnext*sizeof(int),"atom:permute");
   }
 
-  // insure one extra location at end of atom arrays
+  // insure there is one extra atom location at end of arrays for swaps
 
   if (nlocal == nmax) avec->grow(0);
 

src/atom.h

@@ -102,7 +102,7 @@ class Atom : protected Pointers {
 
   // spatial sorting of atoms
 
-  int sortflag;             // 0 = off, 1 = on
+  int sortfreq;             // sort atoms every this many steps, 0 = off
   int nextsort;             // next timestep to sort on
 
   // functions
@@ -203,7 +203,6 @@ class Atom : protected Pointers {
   int *permute;                   // permutation vector
   double userbinsize;             // sorting bin size
   double bininv;
-  int sortfreq;
 
   int memlength;                  // allocated size of memstr
   char *memstr;                   // string of array names already counted

src/compute_pressure.cpp

@@ -172,7 +172,7 @@ double ComputePressure::compute_scalar()
 
   double t;
   if (keflag) {
-    if (temperature->invoked_scalar == update->ntimestep)
+    if (temperature->invoked_scalar != update->ntimestep)
       t = temperature->compute_scalar();
     else t = temperature->scalar;
   }
@@ -209,7 +209,7 @@ void ComputePressure::compute_vector()
   if (update->vflag_global != invoked_vector)
     error->all("Virial was not tallied on needed timestep");
 
-  // invoke temperature it it hasn't been already
+  // invoke temperature if it hasn't been already
 
   double *ke_tensor;
   if (keflag) {

src/input.cpp

@@ -691,8 +691,6 @@ void Input::angle_style()
 
 void Input::atom_modify()
 {
-  if (domain->box_exist) 
-    error->all("Atom_modify command after simulation box is defined");
   atom->modify_params(narg,arg);
 }
 

src/modify.cpp

@@ -192,12 +192,20 @@ void Modify::init()
   list_init_compute();
 
   // init each compute
+  // set invoked_scalar,vector,etc to -1 to force new run to re-compute them
   // add initial timestep to all computes that store invocation times
   //   since any of them may be invoked by initial thermo
   // do not clear out invocation times stored within a compute,
   //   b/c some may be holdovers from previous run, like for ave fixes
 
-  for (i = 0; i < ncompute; i++) compute[i]->init();
+  for (i = 0; i < ncompute; i++) {
+    compute[i]->init();
+    compute[i]->invoked_scalar = -1;
+    compute[i]->invoked_vector = -1;
+    compute[i]->invoked_array = -1;
+    compute[i]->invoked_peratom = -1;
+    compute[i]->invoked_local = -1;
+  }
   addstep_compute_all(update->ntimestep);
 
   // warn if any particle is time integrated more than once

src/update.cpp

@@ -222,7 +222,8 @@ void Update::create_minimize(int narg, char **arg)
    do not allow any timestep-dependent fixes to be defined
    do not allow any dynamic regions to be defined
    reset eflag/vflag global so nothing will think eng/virial are current
-   reset invoked flags of computes, so nothing will think they are current
+   reset invoked flags of computes,
+     so nothing will think they are current between runs
    clear timestep list of computes that store future invocation times
 ------------------------------------------------------------------------- */
 
@@ -249,6 +250,7 @@ void Update::reset_timestep(int narg, char **arg)
   for (int i = 0; i < modify->ncompute; i++) {
     modify->compute[i]->invoked_scalar = -1;
     modify->compute[i]->invoked_vector = -1;
+    modify->compute[i]->invoked_array = -1;
     modify->compute[i]->invoked_peratom = -1;
     modify->compute[i]->invoked_local = -1;
   }

src/verlet.cpp

@@ -92,7 +92,7 @@ void Verlet::setup()
   comm->setup();
   if (neighbor->style) neighbor->setup_bins();
   comm->exchange();
-  if (atom->sortflag) atom->sort();
+  if (atom->sortfreq > 0) atom->sort();
   comm->borders();
   if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
   neighbor->build();
@@ -178,7 +178,7 @@ void Verlet::setup_minimal(int flag)
 
 void Verlet::run(int n)
 {
-  int nflag,ntimestep;
+  int nflag,ntimestep,sortflag;
 
   int n_post_integrate = modify->n_post_integrate;
   int n_pre_exchange = modify->n_pre_exchange;
@@ -186,7 +186,9 @@ void Verlet::run(int n)
   int n_pre_force = modify->n_pre_force;
   int n_post_force = modify->n_post_force;
   int n_end_of_step = modify->n_end_of_step;
-  int sortflag = atom->sortflag;
+
+  if (atom->sortfreq > 0) sortflag = 1;
+  else sortflag = 0;
 
   for (int i = 0; i < n; i++) {
 
@@ -217,7 +219,7 @@ void Verlet::run(int n)
       }
       timer->stamp();
       comm->exchange();
-      if (sortflag && ntimestep > atom->nextsort) atom->sort();
+      if (sortflag && ntimestep >= atom->nextsort) atom->sort();
       comm->borders();
       if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
       timer->stamp(TIME_COMM);