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Merge branch 'master' into lammps-icms

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This commit is contained in:
Axel Kohlmeyer
2010-11-30 08:35:42 -05:00
parent 189735810b 0e72c6f0e5
commit e42d61f775
8 changed files with 29 additions and 35 deletions
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10
doc/fix_ave_spatial.html
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@ -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
self-explanatory. Note that other atom attributes can be used as
inputs to this fix by using the <A HREF = "compute_property_atom.html">compute
<P>The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
Note that other atom attributes (including atom postitions x,y,z) can
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>

10
doc/fix_ave_spatial.txt
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@ -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
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name :l
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
self-explanatory. Note that other atom attributes can be used as
inputs to this fix by using the "compute
The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
Note that other atom attributes (including atom postitions x,y,z) can
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.

6
python/examples/pizza/vmd.py
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@ -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", \

7
src/MANYBODY/pair_tersoff.cpp
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@ -47,8 +47,7 @@ PairTersoff::PairTersoff(LAMMPS *lmp) : Pair(lmp)
nelements = 0;
elements = NULL;
nparams = 0;
maxparam = 0;
nparams = 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

21
src/fix_ave_spatial.cpp
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@ -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) {
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) {
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;
else if (which[m] == V) attribute = atom->v;
if (which[m] == V) attribute = atom->v;
else attribute = atom->f;
if (regionflag == 0) {

2
src/input.cpp
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@ -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

4
src/variable.cpp
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@ -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++;

2
src/version.h
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@ -1 +1 @@
#define LAMMPS_VERSION "1 Dec 2010"
#define LAMMPS_VERSION "3 Dec 2010"