diff -Naur lammps-8Apr08/doc/compute_centro_atom.html lammps-9Apr08/doc/compute_centro_atom.html --- lammps-8Apr08/doc/compute_centro_atom.html 2008-01-03 17:56:10.000000000 -0700 +++ lammps-9Apr08/doc/compute_centro_atom.html 2008-04-07 09:58:34.000000000 -0600 @@ -39,10 +39,10 @@
where the 12 nearest neighbors are found and Ri and Ri+6 are the -vectors from the central atom to the opposite pair of nearest -neighbors. Atoms not in the group are included in the 12 neighbors -used in this calculation. +
where the 12 nearest neighbors are found (for fcc lattices) and Ri and +Ri+6 are the vectors from the central atom to the opposite pair of +nearest neighbors. Atoms not in the group are included in the 12 +neighbors used in this calculation.
The neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms diff -Naur lammps-8Apr08/doc/compute_centro_atom.txt lammps-9Apr08/doc/compute_centro_atom.txt --- lammps-8Apr08/doc/compute_centro_atom.txt 2008-01-03 17:56:10.000000000 -0700 +++ lammps-9Apr08/doc/compute_centro_atom.txt 2008-04-07 09:58:34.000000000 -0600 @@ -36,10 +36,10 @@ :c,image(Eqs/centro_symmetry.jpg) -where the 12 nearest neighbors are found and Ri and Ri+6 are the -vectors from the central atom to the opposite pair of nearest -neighbors. Atoms not in the group are included in the 12 neighbors -used in this calculation. +where the 12 nearest neighbors are found (for fcc lattices) and Ri and +Ri+6 are the vectors from the central atom to the opposite pair of +nearest neighbors. Atoms not in the group are included in the 12 +neighbors used in this calculation. The neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms diff -Naur lammps-8Apr08/doc/compute_temp_asphere.html lammps-9Apr08/doc/compute_temp_asphere.html --- lammps-8Apr08/doc/compute_temp_asphere.html 2008-03-20 18:45:02.000000000 -0600 +++ lammps-9Apr08/doc/compute_temp_asphere.html 2008-04-07 09:58:34.000000000 -0600 @@ -85,6 +85,10 @@ be altered using the extra option of the compute_modify command.
+See this howto section of the manual for a +discussion of different ways to compute temperature and perform +thermostatting. +
Output info:
The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-8Apr08/doc/compute_temp_asphere.txt lammps-9Apr08/doc/compute_temp_asphere.txt
--- lammps-8Apr08/doc/compute_temp_asphere.txt 2008-03-20 18:45:02.000000000 -0600
+++ lammps-9Apr08/doc/compute_temp_asphere.txt 2008-04-07 09:58:34.000000000 -0600
@@ -82,6 +82,10 @@
be altered using the {extra} option of the
"compute_modify"_compute_modify.html command.
+See "this howto section"_Section_howto.html#4_16 of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
[Output info:]
The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-8Apr08/src/MOLECULE/dump_bond.cpp lammps-9Apr08/src/MOLECULE/dump_bond.cpp
--- lammps-8Apr08/src/MOLECULE/dump_bond.cpp 2007-10-03 10:16:14.000000000 -0600
+++ lammps-9Apr08/src/MOLECULE/dump_bond.cpp 2008-04-08 07:58:15.000000000 -0600
@@ -59,11 +59,13 @@
void DumpBond::write_header(int ndump)
{
- fprintf(fp,"ITEM: TIMESTEP\n");
- fprintf(fp,"%d\n",update->ntimestep);
- fprintf(fp,"ITEM: NUMBER OF BONDS\n");
- fprintf(fp,"%d\n",ndump);
- fprintf(fp,"ITEM: BONDS\n");
+ if (me == 0) {
+ fprintf(fp,"ITEM: TIMESTEP\n");
+ fprintf(fp,"%d\n",update->ntimestep);
+ fprintf(fp,"ITEM: NUMBER OF BONDS\n");
+ fprintf(fp,"%d\n",ndump);
+ fprintf(fp,"ITEM: BONDS\n");
+ }
}
/* ---------------------------------------------------------------------- */
diff -Naur lammps-8Apr08/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp lammps-9Apr08/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
--- lammps-8Apr08/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp 2008-01-02 12:24:46.000000000 -0700
+++ lammps-9Apr08/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp 2008-04-07 14:21:05.000000000 -0600
@@ -441,7 +441,8 @@
double factor_coul, double factor_lj,
double &fforce)
{
- double r2inv,r6inv,switch1,switch2,forcecoul,forcelj,phicoul,philj;
+ double r2inv,r6inv,forcecoul,forcelj,phicoul,philj;
+ double switch1,switch2;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
@@ -454,6 +455,7 @@
forcecoul *= switch1 + switch2;
}
} else forcecoul = 0.0;
+
if (rsq < cut_ljsq) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
@@ -466,6 +468,7 @@
forcelj = forcelj*switch1 + philj*switch2;
}
} else forcelj = 0.0;
+
fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
double eng = 0.0;
diff -Naur lammps-8Apr08/src/XTC/dump_xtc.cpp lammps-9Apr08/src/XTC/dump_xtc.cpp
--- lammps-8Apr08/src/XTC/dump_xtc.cpp 2008-02-08 13:06:26.000000000 -0700
+++ lammps-9Apr08/src/XTC/dump_xtc.cpp 2008-04-08 07:58:15.000000000 -0600
@@ -151,7 +151,7 @@
void DumpXTC::write_header(int n)
{
- // realloc coords if necessary
+ // all procs realloc types & coords if necessary
if (n != natoms) {
memory->sfree(coords);
@@ -161,6 +161,10 @@
coords = (float *) memory->smalloc(3*natoms*sizeof(float),"dump:coords");
}
+ // only proc 0 writes header
+
+ if (me != 0) return;
+
int tmp = XTC_MAGIC;
xdr_int(&xd,&tmp);
xdr_int(&xd,&n);
diff -Naur lammps-8Apr08/src/atom.cpp lammps-9Apr08/src/atom.cpp
--- lammps-8Apr08/src/atom.cpp 2008-03-17 17:37:19.000000000 -0600
+++ lammps-9Apr08/src/atom.cpp 2008-04-08 07:58:15.000000000 -0600
@@ -602,7 +602,7 @@
/* ----------------------------------------------------------------------
check if atom tags are consecutive from 1 to Natoms
- return 0 if any tag <= 0 or maxtag > Natoms
+ return 0 if any tag <= 0 or maxtag != Natoms
return 1 if OK (doesn't actually check if all tag values are used)
------------------------------------------------------------------------- */
@@ -620,7 +620,7 @@
}
MPI_Allreduce(check,check_all,2,MPI_INT,MPI_MAX,world);
- if (check_all[0] || check_all[1] > natoms) return 0;
+ if (check_all[0] || check_all[1] != static_cast