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Added warning to discourage use of group all and fixed some segfault cases

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This commit is contained in:
Aidan Thompson
2018-02-05 13:29:14 -07:00
parent fa4c7fc664
commit 1d403b2aa3
5 changed files with 66 additions and 28 deletions
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55
src/MC/fix_gcmc.cpp
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@ -72,7 +72,8 @@ enum{MOVEATOM,MOVEMOL}; // movemode
FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
idregion(NULL), full_flag(0), ngroups(0), groupstrings(NULL), ngrouptypes(0), grouptypestrings(NULL),
grouptypebits(NULL), grouptypes(NULL), local_gas_list(NULL), molcoords(NULL), random_equal(NULL), random_unequal(NULL),
grouptypebits(NULL), grouptypes(NULL), local_gas_list(NULL), molcoords(NULL), molq(NULL), molimage(NULL),
random_equal(NULL), random_unequal(NULL),
fixrigid(NULL), fixshake(NULL), idrigid(NULL), idshake(NULL)
{
if (narg < 11) error->all(FLERR,"Illegal fix gcmc command");
@ -199,8 +200,8 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
if (exchmode == EXCHATOM) natoms_per_molecule = 1;
else natoms_per_molecule = onemols[imol]->natoms;
nmaxmolcoords = natoms_per_molecule;
memory->create(molcoords,nmaxmolcoords,3,"gcmc:molcoords");
nmaxmolatoms = natoms_per_molecule;
grow_molecule_arrays(nmaxmolatoms);
// compute the number of MC cycles that occur nevery timesteps
@ -513,7 +514,7 @@ void FixGCMC::init()
"Fix gcmc cannot exchange individual atoms belonging to a molecule");
}
// if molecules are exchanged are moves, check for unset mol IDs
// if molecules are exchanged or moved, check for unset mol IDs
if (exchmode == EXCHMOL || movemode == MOVEMOL) {
tagint *molecule = atom->molecule;
@ -683,6 +684,12 @@ void FixGCMC::init()
imagezero = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
// warning if group id is "all"
if (groupbit & 1)
error->warning(FLERR, "Fix gcmc is being applied "
"to the default group all");
// construct group bitmask for all new atoms
// aggregated over all group keywords
@ -1153,10 +1160,8 @@ void FixGCMC::attempt_molecule_rotation()
}
}
if (nmolcoords > nmaxmolcoords) {
nmaxmolcoords = nmolcoords;
molcoords = memory->grow(molcoords,nmaxmolcoords,3,"gcmc:molcoords");
}
if (nmolcoords > nmaxmolatoms)
grow_molecule_arrays(nmolcoords);
double com[3];
com[0] = com[1] = com[2] = 0.0;
@ -1816,10 +1821,8 @@ void FixGCMC::attempt_molecule_rotation_full()
}
}
if (nmolcoords > nmaxmolcoords) {
nmaxmolcoords = nmolcoords;
molcoords = memory->grow(molcoords,nmaxmolcoords,3,"gcmc:molcoords");
}
if (nmolcoords > nmaxmolatoms)
grow_molecule_arrays(nmolcoords);
double com[3];
com[0] = com[1] = com[2] = 0.0;
@ -1844,14 +1847,14 @@ void FixGCMC::attempt_molecule_rotation_full()
double **x = atom->x;
imageint *image = atom->image;
imageint image_orig[natoms_per_molecule];
int n = 0;
for (int i = 0; i < atom->nlocal; i++) {
if (mask[i] & molecule_group_bit) {
molcoords[n][0] = x[i][0];
molcoords[n][1] = x[i][1];
molcoords[n][2] = x[i][2];
image_orig[n] = image[i];
molimage[n] = image[i];
double xtmp[3];
domain->unmap(x[i],image[i],xtmp);
xtmp[0] -= com[0];
@ -1884,7 +1887,7 @@ void FixGCMC::attempt_molecule_rotation_full()
x[i][0] = molcoords[n][0];
x[i][1] = molcoords[n][1];
x[i][2] = molcoords[n][2];
image[i] = image_orig[n];
image[i] = molimage[n];
n++;
}
}
@ -1906,8 +1909,17 @@ void FixGCMC::attempt_molecule_deletion_full()
double energy_before = energy_stored;
// check nmolq, grow arrays if necessary
int nmolq = 0;
for (int i = 0; i < atom->nlocal; i++)
if (atom->molecule[i] == deletion_molecule)
if (atom->q_flag) nmolq++;
if (nmolq > nmaxmolatoms)
grow_molecule_arrays(nmolq);
int m = 0;
double q_tmp[natoms_per_molecule];
int tmpmask[atom->nlocal];
for (int i = 0; i < atom->nlocal; i++) {
if (atom->molecule[i] == deletion_molecule) {
@ -1915,7 +1927,7 @@ void FixGCMC::attempt_molecule_deletion_full()
atom->mask[i] = exclusion_group_bit;
toggle_intramolecular(i);
if (atom->q_flag) {
q_tmp[m] = atom->q[i];
molq[m] = atom->q[i];
m++;
atom->q[i] = 0.0;
}
@ -1948,7 +1960,7 @@ void FixGCMC::attempt_molecule_deletion_full()
atom->mask[i] = tmpmask[i];
toggle_intramolecular(i);
if (atom->q_flag) {
atom->q[i] = q_tmp[m];
atom->q[i] = molq[m];
m++;
}
}
@ -2521,3 +2533,10 @@ void FixGCMC::restart(char *buf)
next_reneighbor = static_cast<int> (list[n++]);
}
void FixGCMC::grow_molecule_arrays(int nmolatoms) {
nmaxmolatoms = nmolatoms;
molcoords = memory->grow(molcoords,nmaxmolatoms,3,"gcmc:molcoords");
molq = memory->grow(molq,nmaxmolatoms,"gcmc:molq");
molimage = memory->grow(molimage,nmaxmolatoms,"gcmc:molimage");
}