Merge branch 'master' into lammps-icms

doc/fix_ave_spatial.html

@@ -33,9 +33,9 @@
 </PRE>
 <LI>one or more input values can be listed 
 
-<LI>value = x, y, z, vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name 
+<LI>value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name 
 
-<PRE>  x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
+<PRE>  vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
   density/number, density/mass = number or mass density
   c_ID = per-atom vector calculated by a compute with ID
   c_ID[I] = Ith column of per-atom array calculated by a compute with ID
@@ -176,9 +176,9 @@ to <I>reduced</I> when using a triclinic simulation box, as noted below.
 </P>
 <HR>
 
-<P>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
+<P>The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
-self-explanatory.  Note that other atom attributes can be used as
+Note that other atom attributes (including atom postitions x,y,z) can
-inputs to this fix by using the <A HREF = "compute_property_atom.html">compute
+be used as inputs to this fix by using the <A HREF = "compute_property_atom.html">compute
 property/atom</A> command and then specifying
 an input value from that compute.
 </P>

doc/fix_ave_spatial.txt

@@ -22,8 +22,8 @@ dim, origin, delta can be repeated 1, 2, or 3 times for 1d, 2d, or 3d bins :l
   origin = {lower} or {center} or {upper} or coordinate value (distance units)
   delta = thickness of spatial bins in dim (distance units) :pre
 one or more input values can be listed :l
-value = x, y, z, vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name :l
+value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name :l
-  x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
+  vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
   density/number, density/mass = number or mass density
   c_ID = per-atom vector calculated by a compute with ID
   c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID
@@ -161,9 +161,9 @@ to {reduced} when using a triclinic simulation box, as noted below.
 
 :line
 
-The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
+The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
-self-explanatory.  Note that other atom attributes can be used as
+Note that other atom attributes (including atom postitions x,y,z) can
-inputs to this fix by using the "compute
+be used as inputs to this fix by using the "compute
 property/atom"_compute_property_atom.html command and then specifying
 an input value from that compute.
 

python/examples/pizza/vmd.py

@@ -54,6 +54,12 @@ except: PIZZA_VMDDEV = "win"
 try: from DEFAULTS import PIZZA_VMDARCH
 except: PIZZA_VMDARCH = "LINUX"
 
+# try these settings for a Mac
+#PIZZA_VMDNAME = "vmd"
+#PIZZA_VMDDIR = "/Applications/VMD\ 1.8.7.app/Contents/vmd"
+#PIZZA_VMDDEV = "win"
+#PIZZA_VMDARCH = "MACOSXX86"
+
 try: import pexpect
 except: 
   print "pexpect from http://pypi.python.org/pypi/pexpect", \

src/MANYBODY/pair_tersoff.cpp

@@ -47,8 +47,7 @@ PairTersoff::PairTersoff(LAMMPS *lmp) : Pair(lmp)
 
   nelements = 0;
   elements = NULL;
-  nparams = 0;
+  nparams = maxparam = 0;
-  maxparam = 0;
   params = NULL;
   elem2param = NULL;
 }
@@ -369,9 +368,9 @@ void PairTersoff::read_file(char *file)
   int params_per_line = 17;
   char **words = new char*[params_per_line+1];
 
-  if (params) delete [] params;
+  if (params) memory->sfree(params);
   params = NULL;
-  nparams = 0;
+  nparams = maxparam = 0;
 
   // open file on proc 0
 

src/fix_ave_spatial.cpp

@@ -34,7 +34,7 @@
 using namespace LAMMPS_NS;
 
 enum{LOWER,CENTER,UPPER,COORD};
-enum{X,V,F,DENSITY_NUMBER,DENSITY_MASS,COMPUTE,FIX,VARIABLE};
+enum{V,F,DENSITY_NUMBER,DENSITY_MASS,COMPUTE,FIX,VARIABLE};
 enum{SAMPLE,ALL};
 enum{BOX,LATTICE,REDUCED};
 enum{ONE,RUNNING,WINDOW};
@@ -102,17 +102,7 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
   while (iarg < narg) {
     ids[nvalues] = NULL;
 
-    if (strcmp(arg[iarg],"x") == 0) {
+    if (strcmp(arg[iarg],"vx") == 0) {
-      which[nvalues] = X;
-      argindex[nvalues++] = 0;
-    } else if (strcmp(arg[iarg],"y") == 0) {
-      which[nvalues] = X;
-      argindex[nvalues++] = 1;
-    } else if (strcmp(arg[iarg],"z") == 0) {
-      which[nvalues] = X;
-      argindex[nvalues++] = 2;
-
-    } else if (strcmp(arg[iarg],"vx") == 0) {
       which[nvalues] = V;
       argindex[nvalues++] = 0;
     } else if (strcmp(arg[iarg],"vy") == 0) {
@@ -554,12 +544,11 @@ void FixAveSpatial::end_of_step()
     n = value2index[m];
     j = argindex[m];
 
-    // X,V,F adds coords,velocities,forces to values
+    // V,F adds velocities,forces to values
 
-    if (which[m] == X || which[m] == V || which[m] == F) {
+    if (which[m] == V || which[m] == F) {
       double **attribute;
-      if (which[m] == X) attribute = x;
+      if (which[m] == V) attribute = atom->v;
-      else if (which[m] == V) attribute = atom->v;
       else attribute = atom->f;
       
       if (regionflag == 0) {

src/input.cpp

@@ -529,7 +529,7 @@ void Input::echo()
 
 void Input::ifthenelse()
 {
-  if (narg < 4) error->all("Illegal if command");
+  if (narg < 3) error->all("Illegal if command");
 
   // substitute for variables in Boolean expression for "if"
   // in case expression was enclosed in quotes

src/variable.cpp

@@ -3163,13 +3163,13 @@ double Variable::evaluate_boolean(char *str)
     // number: push value onto stack
     // ----------------
       
-    } else if (isdigit(onechar) || onechar == '.') {
+    } else if (isdigit(onechar) || onechar == '.' || onechar == '-') {
       if (expect == OP) error->all("Invalid Boolean syntax in if command");
       expect = OP;
       
       // istop = end of number, including scientific notation
       
-      int istart = i;
+      int istart = i++;
       while (isdigit(str[i]) || str[i] == '.') i++;
       if (str[i] == 'e' || str[i] == 'E') {
 	i++;

src/version.h

@@ -1 +1 @@
-#define LAMMPS_VERSION "1 Dec 2010"
+#define LAMMPS_VERSION "3 Dec 2010"