file arg = filename
filename = name of file to output time averages to
diff -Naur lammps-19Nov09/doc/fix_ave_time.txt lammps-20Nov09/doc/fix_ave_time.txt
--- lammps-19Nov09/doc/fix_ave_time.txt 2008-07-03 08:59:09.000000000 -0600
+++ lammps-20Nov09/doc/fix_ave_time.txt 2009-11-19 09:18:14.000000000 -0700
@@ -26,7 +26,7 @@
v_name = global value calculated by an equal-style variable with name :pre
zero or more keyword/arg pairs may be appended :l
-keyword = {file} or {ave} :l
+keyword = {file} or {ave} or {start} :l
{file} arg = filename
filename = name of file to output time averages to
{ave} args = {one} or {running} or {window M}
diff -Naur lammps-19Nov09/doc/fix_wall.html lammps-20Nov09/doc/fix_wall.html
--- lammps-19Nov09/doc/fix_wall.html 2009-11-18 09:14:23.000000000 -0700
+++ lammps-20Nov09/doc/fix_wall.html 2009-11-18 09:55:58.000000000 -0700
@@ -197,7 +197,8 @@
Related commands:
->fix wall/reflect wall/gran
+
fix wall/reflect, fix
+wall/gran
Default:
diff -Naur lammps-19Nov09/doc/fix_wall.txt lammps-20Nov09/doc/fix_wall.txt
--- lammps-19Nov09/doc/fix_wall.txt 2009-11-18 09:14:23.000000000 -0700
+++ lammps-20Nov09/doc/fix_wall.txt 2009-11-18 09:55:58.000000000 -0700
@@ -187,7 +187,8 @@
[Related commands:]
-"fix wall/reflect"_fix_wall_reflect.html wall/gran"_fix_wall_gran.html
+"fix wall/reflect"_fix_wall_reflect.html, "fix
+wall/gran"_fix_wall_gran.html
[Default:]
diff -Naur lammps-19Nov09/src/COLLOID/fix_wall_colloid.cpp lammps-20Nov09/src/COLLOID/fix_wall_colloid.cpp
--- lammps-19Nov09/src/COLLOID/fix_wall_colloid.cpp 2009-11-17 17:59:12.000000000 -0700
+++ lammps-20Nov09/src/COLLOID/fix_wall_colloid.cpp 2009-11-19 09:00:00.000000000 -0700
@@ -101,10 +101,11 @@
int dim = m/2;
int side = m % 2;
+ if (side == 0) side = -1;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (side == 0) delta = x[i][dim] - coord;
+ if (side < 0) delta = x[i][dim] - coord;
else delta = coord - x[i][dim];
if (delta <= 0.0) continue;
if (delta > cutoff[m]) continue;
@@ -119,10 +120,10 @@
r2inv = rinv*rinv;
r4inv = r2inv*r2inv;
r8inv = r4inv*r4inv;
- fwall = (coeff1[m]*(rad8*rad + 27.0*rad4*rad2*rad*pow(delta,2.0)
- + 63.0*rad4*rad*pow(delta,4.0)
- + 21.0*rad2*rad*pow(delta,6.0))*r8inv -
- new_coeff2*r2inv) * side;
+ fwall = side * (coeff1[m]*(rad8*rad + 27.0*rad4*rad2*rad*pow(delta,2.0)
+ + 63.0*rad4*rad*pow(delta,4.0)
+ + 21.0*rad2*rad*pow(delta,6.0))*r8inv -
+ new_coeff2*r2inv);
f[i][dim] -= fwall;
r2 = 0.5*diam - delta;
rinv2 = 1.0/r2;
diff -Naur lammps-19Nov09/src/PRD/prd.cpp lammps-20Nov09/src/PRD/prd.cpp
--- lammps-19Nov09/src/PRD/prd.cpp 2009-10-30 10:43:07.000000000 -0600
+++ lammps-20Nov09/src/PRD/prd.cpp 2009-11-19 09:15:19.000000000 -0700
@@ -52,16 +52,8 @@
PRD::PRD(LAMMPS *lmp) : Pointers(lmp) {}
-/* ---------------------------------------------------------------------- */
-
-PRD::~PRD()
-{
- delete [] loop_setting;
- delete [] dist_setting;
-}
-
/* ----------------------------------------------------------------------
- perform PRD
+ perform PRD simulation on one or more replicas
------------------------------------------------------------------------- */
void PRD::command(int narg, char **arg)
diff -Naur lammps-19Nov09/src/PRD/prd.h lammps-20Nov09/src/PRD/prd.h
--- lammps-19Nov09/src/PRD/prd.h 2009-10-30 10:43:07.000000000 -0600
+++ lammps-20Nov09/src/PRD/prd.h 2009-11-19 09:15:19.000000000 -0700
@@ -21,7 +21,7 @@
class PRD : protected Pointers {
public:
PRD(class LAMMPS *);
- ~PRD();
+ ~PRD() {}
void command(int, char **);
private:
diff -Naur lammps-19Nov09/src/dump.cpp lammps-20Nov09/src/dump.cpp
--- lammps-19Nov09/src/dump.cpp 2009-09-04 13:39:53.000000000 -0600
+++ lammps-20Nov09/src/dump.cpp 2009-11-19 09:14:29.000000000 -0700
@@ -66,6 +66,7 @@
// else if ends in .gz = gzipped text file
// else ASCII text file
+ fp = NULL;
singlefile_opened = 0;
compressed = 0;
binary = 0;
diff -Naur lammps-19Nov09/src/fix_rdf.cpp lammps-20Nov09/src/fix_rdf.cpp
--- lammps-19Nov09/src/fix_rdf.cpp 2009-08-11 17:10:03.000000000 -0600
+++ lammps-20Nov09/src/fix_rdf.cpp 2009-11-19 09:00:00.000000000 -0700
@@ -283,7 +283,8 @@
nideal = constant*nrdfatoms[j] *
(rupper*rupper*rupper - rlower*rlower*rlower);
irdf = rdfpair[i][j] - 1;
- if (nrdfatoms[i]*nideal != 0.0) gr = hist_all[irdf][bin] / (nrdfatoms[i]*nideal);
+ if (nrdfatoms[i]*nideal != 0.0)
+ gr = hist_all[irdf][bin] / (nrdfatoms[i]*nideal);
else gr = 0.0;
ncoord[irdf] += gr*nideal;
fprintf(fp,"%f %f ",gr,ncoord[irdf]);