ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Fixed recent segfault in fix gcmc and added mcmoves keyword

Browse Source
This commit is contained in:
Aidan Thompson
2018-01-17 13:45:15 -07:00
parent 5e9d257ec2
commit 9bb7f1ddf6
3 changed files with 229 additions and 160 deletions
Download Patch File Download Diff File Expand all files Collapse all files

244
src/MC/fix_gcmc.cpp
View File

@ -64,15 +64,16 @@ using namespace MathConst;
#define MAXENERGYTEST 1.0e50
enum{ATOM,MOLECULE};
enum{EXCHATOM,EXCHMOL}; // exchmode
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), atom_coord(NULL), random_equal(NULL), random_unequal(NULL),
coords(NULL), imageflags(NULL), fixrigid(NULL), fixshake(NULL), idrigid(NULL), idshake(NULL)
grouptypebits(NULL), grouptypes(NULL), local_gas_list(NULL), molcoords(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");
@ -161,9 +162,9 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
static_cast<double> (attempts);
}
// error check and further setup for mode = MOLECULE
// error check and further setup for exchmode = EXCHMOL
if (mode == MOLECULE) {
if (exchmode == EXCHMOL) {
if (onemols[imol]->xflag == 0)
error->all(FLERR,"Fix gcmc molecule must have coordinates");
if (onemols[imol]->typeflag == 0)
@ -182,9 +183,9 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
if (charge_flag && atom->q == NULL)
error->all(FLERR,"Fix gcmc atom has charge, but atom style does not");
if (rigidflag && mode == ATOM)
if (rigidflag && exchmode == EXCHATOM)
error->all(FLERR,"Cannot use fix gcmc rigid and not molecule");
if (shakeflag && mode == ATOM)
if (shakeflag && exchmode == EXCHATOM)
error->all(FLERR,"Cannot use fix gcmc shake and not molecule");
if (rigidflag && shakeflag)
error->all(FLERR,"Cannot use fix gcmc rigid and shake");
@ -193,13 +194,13 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
if (shakeflag && (nmcmoves > 0))
error->all(FLERR,"Cannot use fix gcmc shake with MC moves");
// setup of coords and imageflags array
if (mode == ATOM) natoms_per_molecule = 1;
// setup of array of coordinates for molecule insertion
// also used by rotation moves for any molecule
if (exchmode == EXCHATOM) natoms_per_molecule = 1;
else natoms_per_molecule = onemols[imol]->natoms;
memory->create(coords,natoms_per_molecule,3,"gcmc:coords");
memory->create(imageflags,natoms_per_molecule,"gcmc:imageflags");
memory->create(atom_coord,natoms_per_molecule,3,"gcmc:atom_coord");
nmaxmolcoords = natoms_per_molecule;
memory->create(molcoords,nmaxmolcoords,3,"gcmc:molcoords");
// compute the number of MC cycles that occur nevery timesteps
@ -235,7 +236,12 @@ void FixGCMC::options(int narg, char **arg)
// defaults
mode = ATOM;
exchmode = EXCHATOM;
movemode = MOVEATOM;
patomtrans = 0.0;
pmoltrans = 0.0;
pmolrotate = 0.0;
pmctot = 0.0;
max_rotation_angle = 10*MY_PI/180;
regionflag = 0;
iregion = -1;
@ -277,10 +283,21 @@ void FixGCMC::options(int narg, char **arg)
if (atom->molecules[imol]->nset > 1 && comm->me == 0)
error->warning(FLERR,"Molecule template for "
"fix gcmc has multiple molecules");
mode = MOLECULE;
exchmode = EXCHMOL;
onemols = atom->molecules;
nmol = onemols[imol]->nset;
iarg += 2;
} else if (strcmp(arg[iarg],"mcmoves") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix gcmc command");
patomtrans = force->numeric(FLERR,arg[iarg+1]);
pmoltrans = force->numeric(FLERR,arg[iarg+2]);
pmolrotate = force->numeric(FLERR,arg[iarg+3]);
if (patomtrans < 0 || pmoltrans < 0 || pmolrotate < 0)
error->all(FLERR,"Illegal fix gcmc command");
pmctot = patomtrans + pmoltrans + pmolrotate;
if (pmctot <= 0)
error->all(FLERR,"Illegal fix gcmc command");
iarg += 4;
} else if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
iregion = domain->find_region(arg[iarg+1]);
@ -387,9 +404,7 @@ FixGCMC::~FixGCMC()
delete random_unequal;
memory->destroy(local_gas_list);
memory->destroy(atom_coord);
memory->destroy(coords);
memory->destroy(imageflags);
memory->destroy(molcoords);
delete [] idrigid;
delete [] idshake;
@ -430,6 +445,30 @@ void FixGCMC::init()
triclinic = domain->triclinic;
// set probabilities for MC moves
if (pmctot == 0.0)
if (exchmode == EXCHATOM) {
movemode = MOVEATOM;
patomtrans = 1.0;
pmoltrans = 0.0;
pmolrotate = 0.0;
} else {
movemode = MOVEMOL;
patomtrans = 0.0;
pmoltrans = 0.5;
pmolrotate = 0.5;
}
else {
if (pmoltrans == 0.0 && pmolrotate == 0.0)
movemode = MOVEATOM;
else
movemode = MOVEMOL;
patomtrans /= pmctot;
pmoltrans /= pmctot;
pmolrotate /= pmctot;
}
// decide whether to switch to the full_energy option
if (!full_flag) {
@ -454,14 +493,14 @@ void FixGCMC::init()
int *type = atom->type;
if (mode == ATOM) {
if (exchmode == EXCHATOM) {
if (ngcmc_type <= 0 || ngcmc_type > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix gcmc command");
}
// if mode == ATOM, warn if any deletable atom has a mol ID
// if atoms are exchanged, warn if any deletable atom has a mol ID
if ((mode == ATOM) && atom->molecule_flag) {
if ((exchmode == EXCHATOM) && atom->molecule_flag) {
tagint *molecule = atom->molecule;
int flag = 0;
for (int i = 0; i < atom->nlocal; i++)
@ -474,9 +513,9 @@ void FixGCMC::init()
"Fix gcmc cannot exchange individual atoms belonging to a molecule");
}
// if mode == MOLECULE, check for unset mol IDs
// if molecules are exchanged are moves, check for unset mol IDs
if (mode == MOLECULE) {
if (exchmode == EXCHMOL || movemode == MOVEMOL) {
tagint *molecule = atom->molecule;
int *mask = atom->mask;
int flag = 0;
@ -490,11 +529,11 @@ void FixGCMC::init()
"All mol IDs should be set for fix gcmc group atoms");
}
if (((mode == MOLECULE) && (atom->molecule_flag == 0)) ||
((mode == MOLECULE) && (!atom->tag_enable || !atom->map_style)))
error->all(FLERR,
"Fix gcmc molecule command requires that "
"atoms have molecule attributes");
if (exchmode == EXCHMOL || movemode == MOVEMOL)
if (atom->molecule_flag == 0 || !atom->tag_enable || !atom->map_style)
error->all(FLERR,
"Fix gcmc molecule command requires that "
"atoms have molecule attributes");
// if rigidflag defined, check for rigid/small fix
// its molecule template must be same as this one
@ -566,7 +605,7 @@ void FixGCMC::init()
// create a new group for temporary use with selected molecules
if (mode == MOLECULE) {
if (exchmode == EXCHMOL || movemode == MOVEMOL) {
char **group_arg = new char*[3];
// create unique group name for atoms to be rotated
int len = strlen(id) + 30;
@ -586,10 +625,10 @@ void FixGCMC::init()
delete [] group_arg;
}
// get all of the needed molecule data if mode == MOLECULE,
// otherwise just get the gas mass
// get all of the needed molecule data if exchanging
// or moving molecules, otherwise just get the gas mass
if (mode == MOLECULE) {
if (exchmode == EXCHMOL || movemode == MOVEMOL) {
onemols[imol]->compute_mass();
onemols[imol]->compute_com();
@ -713,27 +752,21 @@ void FixGCMC::pre_exchange()
error->warning(FLERR,"Energy of old configuration in "
"fix gcmc is > MAXENERGYTEST.");
if (mode == MOLECULE) {
for (int i = 0; i < ncycles; i++) {
int random_int_fraction =
static_cast<int>(random_equal->uniform()*ncycles) + 1;
if (random_int_fraction <= nmcmoves) {
if (random_equal->uniform() < 0.5) attempt_molecule_translation_full();
else attempt_molecule_rotation_full();
} else {
if (random_equal->uniform() < 0.5) attempt_molecule_deletion_full();
else attempt_molecule_insertion_full();
}
}
} else {
for (int i = 0; i < ncycles; i++) {
int random_int_fraction =
static_cast<int>(random_equal->uniform()*ncycles) + 1;
if (random_int_fraction <= nmcmoves) {
attempt_atomic_translation_full();
} else {
if (random_equal->uniform() < 0.5) attempt_atomic_deletion_full();
for (int i = 0; i < ncycles; i++) {
int ixm = static_cast<int>(random_equal->uniform()*ncycles) + 1;
if (ixm <= nmcmoves) {
double xmcmove = random_equal->uniform();
if (xmcmove < patomtrans) attempt_atomic_translation_full();
else if (xmcmove < patomtrans+pmoltrans) attempt_molecule_translation_full();
else attempt_molecule_rotation_full();
} else {
double xgcmc = random_equal->uniform();
if (exchmode == EXCHATOM) {
if (xgcmc < 0.5) attempt_atomic_deletion_full();
else attempt_atomic_insertion_full();
} else {
if (xgcmc < 0.5) attempt_molecule_deletion_full();
else attempt_molecule_insertion_full();
}
}
}
@ -746,27 +779,21 @@ void FixGCMC::pre_exchange()
} else {
if (mode == MOLECULE) {
for (int i = 0; i < ncycles; i++) {
int random_int_fraction =
static_cast<int>(random_equal->uniform()*ncycles) + 1;
if (random_int_fraction <= nmcmoves) {
if (random_equal->uniform() < 0.5) attempt_molecule_translation();
else attempt_molecule_rotation();
} else {
if (random_equal->uniform() < 0.5) attempt_molecule_deletion();
else attempt_molecule_insertion();
}
}
} else {
for (int i = 0; i < ncycles; i++) {
int random_int_fraction =
static_cast<int>(random_equal->uniform()*ncycles) + 1;
if (random_int_fraction <= nmcmoves) {
attempt_atomic_translation();
} else {
if (random_equal->uniform() < 0.5) attempt_atomic_deletion();
for (int i = 0; i < ncycles; i++) {
int ixm = static_cast<int>(random_equal->uniform()*ncycles) + 1;
if (ixm <= nmcmoves) {
double xmcmove = random_equal->uniform();
if (xmcmove < patomtrans) attempt_atomic_translation();
else if (xmcmove < patomtrans+pmoltrans) attempt_molecule_translation();
else attempt_molecule_rotation();
} else {
double xgcmc = random_equal->uniform();
if (exchmode == EXCHATOM) {
if (xgcmc < 0.5) attempt_atomic_deletion();
else attempt_atomic_insertion();
} else {
if (xgcmc < 0.5) attempt_molecule_deletion();
else attempt_molecule_insertion();
}
}
}
@ -1116,14 +1143,21 @@ void FixGCMC::attempt_molecule_rotation()
"fix gcmc is > MAXENERGYTEST.");
int *mask = atom->mask;
int nmolcoords = 0;
for (int i = 0; i < atom->nlocal; i++) {
if (atom->molecule[i] == rotation_molecule) {
mask[i] |= molecule_group_bit;
nmolcoords++;
} else {
mask[i] &= molecule_group_inversebit;
}
}
if (nmolcoords > nmaxmolcoords) {
nmaxmolcoords = nmolcoords;
molcoords = memory->grow(molcoords,nmaxmolcoords,3,"gcmc:molcoords");
}
double com[3];
com[0] = com[1] = com[2] = 0.0;
group->xcm(molecule_group,gas_mass,com);
@ -1156,13 +1190,13 @@ void FixGCMC::attempt_molecule_rotation()
xtmp[0] -= com[0];
xtmp[1] -= com[1];
xtmp[2] -= com[2];
MathExtra::matvec(rotmat,xtmp,atom_coord[n]);
atom_coord[n][0] += com[0];
atom_coord[n][1] += com[1];
atom_coord[n][2] += com[2];
xtmp[0] = atom_coord[n][0];
xtmp[1] = atom_coord[n][1];
xtmp[2] = atom_coord[n][2];
MathExtra::matvec(rotmat,xtmp,molcoords[n]);
molcoords[n][0] += com[0];
molcoords[n][1] += com[1];
molcoords[n][2] += com[2];
xtmp[0] = molcoords[n][0];
xtmp[1] = molcoords[n][1];
xtmp[2] = molcoords[n][2];
domain->remap(xtmp);
if (!domain->inside(xtmp))
error->one(FLERR,"Fix gcmc put atom outside box");
@ -1181,9 +1215,9 @@ void FixGCMC::attempt_molecule_rotation()
for (int i = 0; i < atom->nlocal; i++) {
if (mask[i] & molecule_group_bit) {
image[i] = imagezero;
x[i][0] = atom_coord[n][0];
x[i][1] = atom_coord[n][1];
x[i][2] = atom_coord[n][2];
x[i][0] = molcoords[n][0];
x[i][1] = molcoords[n][1];
x[i][2] = molcoords[n][2];
domain->remap(x[i],image[i]);
n++;
}
@ -1303,18 +1337,18 @@ void FixGCMC::attempt_molecule_insertion()
bool procflag[natoms_per_molecule];
for (int i = 0; i < natoms_per_molecule; i++) {
MathExtra::matvec(rotmat,onemols[imol]->x[i],atom_coord[i]);
atom_coord[i][0] += com_coord[0];
atom_coord[i][1] += com_coord[1];
atom_coord[i][2] += com_coord[2];
MathExtra::matvec(rotmat,onemols[imol]->x[i],molcoords[i]);
molcoords[i][0] += com_coord[0];
molcoords[i][1] += com_coord[1];
molcoords[i][2] += com_coord[2];
// use temporary variable for remapped position
// so unmapped position is preserved in atom_coord
// so unmapped position is preserved in molcoords
double xtmp[3];
xtmp[0] = atom_coord[i][0];
xtmp[1] = atom_coord[i][1];
xtmp[2] = atom_coord[i][2];
xtmp[0] = molcoords[i][0];
xtmp[1] = molcoords[i][1];
xtmp[2] = molcoords[i][2];
domain->remap(xtmp);
if (!domain->inside(xtmp))
error->one(FLERR,"Fix gcmc put atom outside box");
@ -1372,7 +1406,7 @@ void FixGCMC::attempt_molecule_insertion()
for (int i = 0; i < natoms_per_molecule; i++) {
if (procflag[i]) {
atom->avec->create_atom(onemols[imol]->type[i],atom_coord[i]);
atom->avec->create_atom(onemols[imol]->type[i],molcoords[i]);
int m = atom->nlocal - 1;
// add to groups
@ -1772,14 +1806,21 @@ void FixGCMC::attempt_molecule_rotation_full()
double energy_before = energy_stored;
int *mask = atom->mask;
int nmolcoords = 0;
for (int i = 0; i < atom->nlocal; i++) {
if (atom->molecule[i] == rotation_molecule) {
mask[i] |= molecule_group_bit;
nmolcoords++;
} else {
mask[i] &= molecule_group_inversebit;
}
}
if (nmolcoords > nmaxmolcoords) {
nmaxmolcoords = nmolcoords;
molcoords = memory->grow(molcoords,nmaxmolcoords,3,"gcmc:molcoords");
}
double com[3];
com[0] = com[1] = com[2] = 0.0;
group->xcm(molecule_group,gas_mass,com);
@ -1807,9 +1848,9 @@ void FixGCMC::attempt_molecule_rotation_full()
int n = 0;
for (int i = 0; i < atom->nlocal; i++) {
if (mask[i] & molecule_group_bit) {
atom_coord[n][0] = x[i][0];
atom_coord[n][1] = x[i][1];
atom_coord[n][2] = x[i][2];
molcoords[n][0] = x[i][0];
molcoords[n][1] = x[i][1];
molcoords[n][2] = x[i][2];
image_orig[n] = image[i];
double xtmp[3];
domain->unmap(x[i],image[i],xtmp);
@ -1840,9 +1881,9 @@ void FixGCMC::attempt_molecule_rotation_full()
int n = 0;
for (int i = 0; i < atom->nlocal; i++) {
if (mask[i] & molecule_group_bit) {
x[i][0] = atom_coord[n][0];
x[i][1] = atom_coord[n][1];
x[i][2] = atom_coord[n][2];
x[i][0] = molcoords[n][0];
x[i][1] = molcoords[n][1];
x[i][2] = molcoords[n][2];
image[i] = image_orig[n];
n++;
}
@ -2140,7 +2181,7 @@ double FixGCMC::energy(int i, int itype, tagint imolecule, double *coord)
for (int j = 0; j < nall; j++) {
if (i == j) continue;
if (mode == MOLECULE)
if (exchmode == EXCHMOL || movemode == MOVEMOL)
if (imolecule == molecule[j]) continue;
delx = coord[0] - x[j][0];
@ -2212,9 +2253,10 @@ double FixGCMC::energy_full()
tagint *molecule = atom->molecule;
int nall = atom->nlocal + atom->nghost;
for (int i = 0; i < atom->nlocal; i++) {
if (mode == MOLECULE) imolecule = molecule[i];
if (exchmode == EXCHMOL || movemode == MOVEMOL)
imolecule = molecule[i];
for (int j = i+1; j < nall; j++) {
if (mode == MOLECULE)
if (exchmode == EXCHMOL || movemode == MOVEMOL)
if (imolecule == molecule[j]) continue;
delx = x[i][0] - x[j][0];
@ -2352,7 +2394,7 @@ void FixGCMC::update_gas_atoms_list()
if (regionflag) {
if (mode == MOLECULE) {
if (exchmode == EXCHMOL || movemode == MOVEMOL) {
tagint maxmol = 0;
for (int i = 0; i < nlocal; i++) maxmol = MAX(maxmol,molecule[i]);