git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2189 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/atom.cpp

@@ -1036,6 +1036,8 @@ void Atom::set_mass(const char *str)
 
   mass[itype] = mass_one;
   mass_setflag[itype] = 1;
+
+  if (mass[itype] <= 0.0) error->all("Invalid mass value");
 }
 
 /* ----------------------------------------------------------------------
@@ -1050,6 +1052,8 @@ void Atom::set_mass(int itype, double value)
 
   mass[itype] = value;
   mass_setflag[itype] = 1;
+
+  if (mass[itype] <= 0.0) error->all("Invalid mass value");
 }
 
 /* ----------------------------------------------------------------------
@@ -1068,6 +1072,8 @@ void Atom::set_mass(int narg, char **arg)
   for (int itype = lo; itype <= hi; itype++) {
     mass[itype] = atof(arg[1]);
     mass_setflag[itype] = 1;
+
+    if (mass[itype] <= 0.0) error->all("Invalid mass value");
   }
 }
 
@@ -1116,6 +1122,9 @@ void Atom::set_shape(const char *str)
   shape[itype][1] = 0.5*b;
   shape[itype][2] = 0.5*c;
   shape_setflag[itype] = 1;
+
+  if (shape[itype][0] < 0.0 || shape[itype][1] < 0.0 || shape[itype][2] < 0.0)
+    error->all("Invalid shape value");
 }
 
 /* ----------------------------------------------------------------------
@@ -1139,6 +1148,10 @@ void Atom::set_shape(int narg, char **arg)
     shape[itype][1] = 0.5*atof(arg[2]);
     shape[itype][2] = 0.5*atof(arg[3]);
     shape_setflag[itype] = 1;
+
+    if (shape[itype][0] < 0.0 || shape[itype][1] < 0.0 ||
+	shape[itype][2] < 0.0)
+      error->all("Invalid shape value");
   }
 }
 
@@ -1176,13 +1189,15 @@ void Atom::set_dipole(const char *str)
 {
   if (dipole == NULL) error->all("Cannot set dipole for this atom style");
 
-  int i;
+  int itype;
   double dipole_one;
-  int n = sscanf(str,"%d %lg",&i,&dipole_one);
+  int n = sscanf(str,"%d %lg",&itype,&dipole_one);
-  if (n != 2) error->all("Invalid shape line in data file");
+  if (n != 2) error->all("Invalid dipole line in data file");
 
-  dipole[i] = dipole_one;
+  dipole[itype] = dipole_one;
-  dipole_setflag[i] = 1;
+  dipole_setflag[itype] = 1;
+
+  if (dipole[itype] < 0.0) error->all("Invalid dipole value");
 }
 
 /* ----------------------------------------------------------------------
@@ -1201,6 +1216,8 @@ void Atom::set_dipole(int narg, char **arg)
   for (int itype = lo; itype <= hi; itype++) {
     dipole[itype] = atof(arg[1]);
     dipole_setflag[itype] = 1;
+
+    if (dipole[itype] < 0.0) error->all("Invalid dipole value");
   }
 }
 

src/compute_erotate_sphere.cpp

@@ -66,7 +66,7 @@ void ComputeERotateSphere::init()
     for (int i = 1; i <= atom->ntypes; i++) {
       if (shape[i][0] != shape[i][1] || shape[i][0] != shape[i][2])
 	error->all("Compute erotate/sphere requires spherical particle shapes");
-      inertia[i] = 0.25*shape[i][0]*shape[i][0] * mass[i];
+      inertia[i] = shape[i][0]*shape[i][0] * mass[i];
     }
   }
 }

src/compute_temp_sphere.cpp

@@ -98,7 +98,7 @@ void ComputeTempSphere::init()
     for (int i = 1; i <= atom->ntypes; i++) {
       if (shape[i][0] != shape[i][1] || shape[i][0] != shape[i][2])
 	error->all("Compute temp/sphere requires spherical particle shapes");
-      inertia[i] = INERTIA * 0.25*shape[i][0]*shape[i][0] * mass[i];
+      inertia[i] = INERTIA * shape[i][0]*shape[i][0] * mass[i];
     }
   }
 }

src/verlet.cpp

@@ -221,26 +221,70 @@ void Verlet::force_clear()
 {
   int i;
 
-  // clear global force array
+  // clear force on all particles
-  // nall includes ghosts only if either newton flag is set
+  // if either newton flag is set, also include ghosts
 
-  int nall;
+  if (neighbor->includegroup == 0) {
-  if (force->newton) nall = atom->nlocal + atom->nghost;
+    int nall;
-  else nall = atom->nlocal;
+    if (force->newton) nall = atom->nlocal + atom->nghost;
+    else nall = atom->nlocal;
 
-  double **f = atom->f;
+    double **f = atom->f;
-  for (i = 0; i < nall; i++) {
-    f[i][0] = 0.0;
-    f[i][1] = 0.0;
-    f[i][2] = 0.0;
-  }
-
-  if (torqueflag) {
-    double **torque = atom->torque;
     for (i = 0; i < nall; i++) {
-      torque[i][0] = 0.0;
+      f[i][0] = 0.0;
-      torque[i][1] = 0.0;
+      f[i][1] = 0.0;
-      torque[i][2] = 0.0;
+      f[i][2] = 0.0;
+    }
+    
+    if (torqueflag) {
+      double **torque = atom->torque;
+      for (i = 0; i < nall; i++) {
+	torque[i][0] = 0.0;
+	torque[i][1] = 0.0;
+	torque[i][2] = 0.0;
+      }
+    }
+
+  // neighbor includegroup flag is set
+  // clear force only on initial nfirst particles
+  // if either newton flag is set, also include ghosts
+
+  } else {
+    int nall = atom->nfirst;
+
+    double **f = atom->f;
+    for (i = 0; i < nall; i++) {
+      f[i][0] = 0.0;
+      f[i][1] = 0.0;
+      f[i][2] = 0.0;
+    }
+    
+    if (torqueflag) {
+      double **torque = atom->torque;
+      for (i = 0; i < nall; i++) {
+	torque[i][0] = 0.0;
+	torque[i][1] = 0.0;
+	torque[i][2] = 0.0;
+      }
+    }
+
+    if (force->newton) {
+      nall = atom->nlocal + atom->nghost;
+
+      for (i = atom->nlocal; i < nall; i++) {
+	f[i][0] = 0.0;
+	f[i][1] = 0.0;
+	f[i][2] = 0.0;
+      }
+    
+      if (torqueflag) {
+	double **torque = atom->torque;
+	for (i = atom->nlocal; i < nall; i++) {
+	  torque[i][0] = 0.0;
+	  torque[i][1] = 0.0;
+	  torque[i][2] = 0.0;
+	}
+      }
     }
   }
 }