Fix bug in fix_property_*, size_peratom_cols needs to be 1 when using…

… vprop

src/MUTATION/fix_mutate.cpp

@@ -94,7 +94,7 @@ void FixMutate::compute()
     if (mask[i] & groupbit) {
       if (random->uniform() < prob) {
         mask[i] = imutant;
-      }MUT
+      }
     }
   }
 }

src/NUFEB/fix_divide_bacillus.cpp

@@ -108,7 +108,7 @@ void FixDivideBacillus::compute()
         double imass, jmass;
         double ilen, xp1[3], xp2[3];
 
-    //	double phiz = random->uniform() * 2e-8;
+    	// double phiz = random->uniform() * 2e-8;
 
         double vsphere = four_thirds_pi * atom->radius[i]*atom->radius[i]*atom->radius[i];
         double acircle = MY_PI*atom->radius[i]*atom->radius[i];

src/NUFEB/fix_property.cpp

@@ -79,7 +79,7 @@ int FixProperty::modify_param(int narg, char **arg)
 double FixProperty::memory_usage()
 {
   double bytes;
-  if (size_peratom_cols > 0)
+  if (size_peratom_cols > 1)
     bytes = atom->nmax*size_peratom_cols*sizeof(double);
   else
     bytes = atom->nmax*sizeof(double);
@@ -93,7 +93,7 @@ double FixProperty::memory_usage()
 
 void FixProperty::grow_arrays(int nmax)
 {
-  if (size_peratom_cols > 0) {
+  if (size_peratom_cols > 1) {
     memory->grow(aprop,nmax,size_peratom_cols,"fix_property:array");
     array_atom = aprop;
   } else {
@@ -108,7 +108,7 @@ void FixProperty::grow_arrays(int nmax)
 
 void FixProperty::copy_arrays(int i, int j, int /*delflag*/)
 {
-  if (size_peratom_cols > 0) {
+  if (size_peratom_cols > 1) {
     for (int m = 0; m < size_peratom_cols; m++)
       aprop[j][m] = aprop[i][m];
   } else {
@@ -122,7 +122,7 @@ void FixProperty::copy_arrays(int i, int j, int /*delflag*/)
 
 int FixProperty::pack_exchange(int i, double *buf)
 {
-  if (size_peratom_cols > 0) {
+  if (size_peratom_cols > 1) {
     for (int m = 0; m < size_peratom_cols; m++)
       buf[m] = aprop[i][m];
   } else {
@@ -137,7 +137,7 @@ int FixProperty::pack_exchange(int i, double *buf)
 
 int FixProperty::unpack_exchange(int nlocal, double *buf)
 {
-  if (size_peratom_cols > 0) {
+  if (size_peratom_cols > 1) {
     for (int m = 0; m < size_peratom_cols; m++)
       aprop[nlocal][m] = buf[m];
   } else {
@@ -153,7 +153,7 @@ int FixProperty::unpack_exchange(int nlocal, double *buf)
 int FixProperty::pack_restart(int i, double *buf)
 {
   buf[0] = size_peratom_cols + 1;
-  if (size_peratom_cols > 0) {
+  if (size_peratom_cols > 1) {
     for (int m = 0; m < size_peratom_cols; m++)
       buf[m+1] = aprop[i][m];
   } else {
@@ -174,9 +174,9 @@ void FixProperty::unpack_restart(int nlocal, int nth)
   int m = 0;
   for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
   m++;
-  if (size_peratom_cols > 0) {
+  if (size_peratom_cols > 1) {
     for (int i = 0; i < size_peratom_cols; i++)
-      aprop[nlocal][i] = extra[nlocal][m];
+      aprop[nlocal][i] = extra[nlocal][m++];
   } else {
     vprop[nlocal] = extra[nlocal][m];
   }

src/NUFEB/fix_property_ancestor.cpp

@@ -30,8 +30,8 @@ FixPropertyAncestor::FixPropertyAncestor(LAMMPS *lmp, int narg, char **arg) :
   if (narg < 3) error->all(FLERR,"Illegal fix property/nufeb/ancestor command");
 
   create_attribute = 1;
-  // use vprop if size_peratom_cols = 0
-  size_peratom_cols = 0;
+  // use vprop if size_peratom_cols = 1
+  size_peratom_cols = 1;
   grow_arrays(atom->nmax);
 }
 

src/NUFEB/fix_property_cycletime.cpp

@@ -19,14 +19,15 @@
 #include "memory.h"
 #include "error.h"
 #include "update.h"
+#include "random_park.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
 /* ---------------------------------------------------------------------- */
 
 FixPropertyCycletime::FixPropertyCycletime(LAMMPS *lmp, int narg, char **arg) :
-  FixProperty(lmp, narg, arg)
+    FixProperty(lmp, narg, arg)
 {
   if (narg < 3) error->all(FLERR,"Illegal fix nufeb/property/cycletime command");
 
@@ -35,6 +36,37 @@ FixPropertyCycletime::FixPropertyCycletime(LAMMPS *lmp, int narg, char **arg) :
   // use aprop if size_peratom_cols > 0
   size_peratom_cols = 2;
   grow_arrays(atom->nmax);
+
+  seed = 0;
+  max_time = 0;
+  ran_flag = 0;
+
+  int iarg = 3;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg], "seed") == 0) {
+      seed = utils::inumeric(FLERR,arg[iarg+1],true,lmp);
+      random = new RanPark(lmp, seed);
+      ran_flag = 1;
+      iarg += 2;
+    } else if (strcmp(arg[iarg], "max_time") == 0 ) {
+      max_time = utils::numeric(FLERR,arg[iarg+1],true,lmp);
+      iarg += 2;
+    } else {
+      error->all(FLERR, "Illegal fix nufeb/property/cycletime command");
+    }
+  }
+
+  for (int i = 0; i < atom->nlocal; i++) {
+    if (atom->mask[i] & groupbit) {
+      if (ran_flag > 0) {
+        aprop[i][0] = random->uniform() * max_time;
+        aprop[i][1] = aprop[i][0];
+      } else {
+        aprop[i][0] = 0.0;
+        aprop[i][1] = 0.0;
+      }
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -46,16 +78,6 @@ int FixPropertyCycletime::setmask()
   return mask;
 }
 
-/* ---------------------------------------------------------------------- */
-
-void FixPropertyCycletime::init()
-{
-  for (int i = 0; i < atom->nlocal; i++) {
-    aprop[i][0] = 0.0;
-    aprop[i][1] = 0.0;
-  }
-}
-
 /* ----------------------------------------------------------------------
    update cell age
 ------------------------------------------------------------------------- */
@@ -67,6 +89,7 @@ void FixPropertyCycletime::biology_nufeb()
   for (int i = 0; i < atom->nlocal; i++) {
     if (atom->mask[i] & groupbit) {
       aprop[i][0] += update->dt;
+      aprop[i][1] += update->dt;
     }
   }
 }
@@ -78,7 +101,6 @@ void FixPropertyCycletime::biology_nufeb()
 void FixPropertyCycletime::set_arrays(int j)
 {
   aprop[j][0] = 0.0;
-  aprop[j][1] = 0.0;
 }
 
 /* ----------------------------------------------------------------------
@@ -87,10 +109,9 @@ void FixPropertyCycletime::set_arrays(int j)
 ------------------------------------------------------------------------- */
 void FixPropertyCycletime::update_arrays(int i, int j)
 {
-  // no need to update j here as this has been done in set_arrary
   // when cell divides, record cell cycle time and reset to 0
-  aprop[i][1] = aprop[i][0];
   aprop[i][0] = 0.0;
+  aprop[j][1] = aprop[i][1];
 }
 
 /* ----------------------------------------------------------------------

src/NUFEB/fix_property_cycletime.h

@@ -25,17 +25,27 @@ FixStyle(nufeb/property/cycletime,FixPropertyCycletime)
 namespace LAMMPS_NS {
 
 class FixPropertyCycletime : public FixProperty {
- public:
+public:
 
   FixPropertyCycletime(class LAMMPS *, int, char **);
   virtual ~FixPropertyCycletime() {};
 
-  void init();
   int setmask();
   void biology_nufeb();
   void set_arrays(int);
   void update_arrays(int, int);
   double compute_scalar();
+
+//  int pack_restart(int, double *);
+//  void unpack_restart(int, int);
+//  int size_restart(int);
+//  int maxsize_restart();
+
+protected:
+  int seed, ran_flag;
+  double max_time;
+
+  class RanPark *random;
 };
 
 }

src/NUFEB/fix_property_generation.cpp

@@ -31,8 +31,8 @@ FixPropertyGeneration::FixPropertyGeneration(LAMMPS *lmp, int narg, char **arg)
   if (narg < 3) error->all(FLERR,"Illegal fix nufeb/property/generation command");
 
   create_attribute = 1;
-  // use vprop if size_peratom_cols = 0
-  size_peratom_cols = 0;
+  // use vprop if size_peratom_cols = 1
+  size_peratom_cols = 1;
   grow_arrays(atom->nmax);
 }
 
@@ -68,9 +68,7 @@ void FixPropertyGeneration::set_arrays(int j)
 ------------------------------------------------------------------------- */
 void FixPropertyGeneration::update_arrays(int i, int j)
 {
-  if (atom->mask[i] & groupbit)
     vprop[i]++;
-  if (atom->mask[j] & groupbit)
     vprop[j] = vprop[i];
 }
 

src/PLASMID/fix_property_plasmid.cpp

@@ -78,7 +78,7 @@ FixPropertyPlasmid::FixPropertyPlasmid(LAMMPS *lmp, int narg, char **arg) :
   if (plm_init > plm_max) error->all(FLERR,"Illegal fix nufeb/property/plasmid command: "
       "initial plasmid cannot be more than maximum plasmid number");
 
-  size_peratom_cols = 0;
+  size_peratom_cols = 1;
   fila_max = plm_max * (plm_max - 1) / 2;
 
   grow_arrays(atom->nmax);