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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2948 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-07-02 15:17:08 +00:00
parent fd7945cabc
commit ddd61344db
2 changed files with 36 additions and 17 deletions
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49
src/fix_rigid.cpp
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@ -418,6 +418,8 @@ void FixRigid::init()
// extended = 1 if any particle in a rigid body is finite size
extended = dorientflag = qorientflag = 0;
double *radius = atom->radius;
double *rmass = atom->rmass;
double *mass = atom->mass;
@ -1357,51 +1359,68 @@ int FixRigid::dof(int igroup)
{
int groupbit = group->bitmask[igroup];
// nall = # of atoms in each rigid body that are also in temperature group
// nall = # of point particles in each rigid body
// mall = # of finite-size particles in each rigid body
// particles must also be in temperature group
int *mask = atom->mask;
int nlocal = atom->nlocal;
int *ncount = new int[nbody];
for (int ibody = 0; ibody < nbody; ibody++) ncount[ibody] = 0;
int *mcount = new int[nbody];
for (int ibody = 0; ibody < nbody; ibody++)
ncount[ibody] = mcount[ibody] = 0;
for (int i = 0; i < nlocal; i++)
if (body[i] >= 0 && mask[i] & groupbit) ncount[body[i]]++;
if (body[i] >= 0 && mask[i] & groupbit) {
if (extended && eflags[i]) mcount[body[i]]++;
else ncount[body[i]]++;
}
int *nall = new int[nbody];
int *mall = new int[nbody];
MPI_Allreduce(ncount,nall,nbody,MPI_INT,MPI_SUM,world);
MPI_Allreduce(mcount,mall,nbody,MPI_INT,MPI_SUM,world);
// warn if nall != nrigid for any body included in temperature group
// warn if nall+mall != nrigid for any body included in temperature group
int flag = 0;
for (int ibody = 0; ibody < nbody; ibody++) {
if (nall[ibody] && nall[ibody] != nrigid[ibody]) flag = 1;
if (nall[ibody]+mall[ibody] > 0 &&
nall[ibody]+mall[ibody] != nrigid[ibody]) flag = 1;
}
if (flag && comm->me == 0)
error->warning("Computing temperature of portions of rigid bodies");
// remove appropriate DOFs for each rigid body wholly in temperature group
// each has 3N (3d) or 2N (2d) to start with
// 3d N>2 rigid body should have 6 dof, so remove 3N-6 dof
// 3d N=2 rigid dimer should have 5 dof, so remove 1 dof
// 2d N>=2 rigid body should have 3 dof, so remove 2N-3 dof
// N = # of point particles in body
// M = # of finite-size particles in body
// 3d body has 3N + 6M dof to start with
// 2d body has 2N + 3M dof to start with
// 3d point-particle body with all non-zero I should have 6 dof, remove 3N-6
// 3d point-particle body (linear) with a 0 I should have 5 dof, remove 3N-5
// 2d point-particle body should have 3 dof, remove 2N-3
// 3d body with any finite-size M should have 6 dof, remove (3N+6M) - 6
// 2d body with any finite-size M should have 3 dof, remove (2N+3M) - 3
int n = 0;
if (domain->dimension == 3) {
for (int ibody = 0; ibody < nbody; ibody++)
if (nall[ibody] == nrigid[ibody]) {
n += 3*nrigid[ibody] - 6;
if (nrigid[ibody] == 2) n++;
if (nall[ibody]+mall[ibody] == nrigid[ibody]) {
n += 3*nall[ibody] + 6*mall[ibody] - 6;
if (inertia[ibody][0] == 0.0 || inertia[ibody][1] == 0.0 ||
inertia[ibody][2] == 0.0) n++;
}
} else if (domain->dimension == 2) {
for (int ibody = 0; ibody < nbody; ibody++)
if (nall[ibody] == nrigid[ibody]) {
n += 2*nrigid[ibody] - 3;
}
if (nall[ibody]+mall[ibody] == nrigid[ibody])
n += 2*nall[ibody] + 3*mall[ibody] - 3;
}
delete [] ncount;
delete [] mcount;
delete [] nall;
delete [] mall;
return n;
}

4
src/fix_shake.cpp
View File

@ -532,8 +532,8 @@ int FixShake::dof(int igroup)
int *tag = atom->tag;
int nlocal = atom->nlocal;
// count dof in a cluster if and only if the central atom is in group
// and this atom i is the central atom
// count dof in a cluster if and only if
// the central atom is in group and atom i is the central atom
int n = 0;
for (int i = 0; i < nlocal; i++) {