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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11920 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-05-06 21:10:30 +00:00
parent eaab9700db
commit aa6458d35c
6 changed files with 103 additions and 105 deletions
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61
src/MISC/fix_deposit.cpp
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@ -102,21 +102,22 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
if (mode == MOLECULE) {
for (int i = 0; i < nmol; i++) {
if (onemol[i].xflag == 0)
if (onemols[i]->xflag == 0)
error->all(FLERR,"Fix deposit molecule must have coordinates");
if (onemol[i].typeflag == 0)
if (onemols[i]->typeflag == 0)
error->all(FLERR,"Fix deposit molecule must have atom types");
if (ntype+onemol[i].ntypes <= 0 || ntype+onemol[i].ntypes > atom->ntypes)
if (ntype+onemols[i]->ntypes <= 0 ||
ntype+onemols[i]->ntypes > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix deposit mol command");
if (atom->molecular == 2 && onemol != atom->avec->onemols[0])
if (atom->molecular == 2 && onemols != atom->avec->onemols)
error->all(FLERR,"Fix deposit molecule template ID must be same "
"as atom_style template ID");
onemol[i].check_attributes(0);
onemols[i]->check_attributes(0);
// fix deposit uses geoemetric center of molecule for insertion
onemol[i].compute_center();
onemols[i]->compute_center();
}
}
@ -129,14 +130,14 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
// setup of coords and imageflags array
if (mode == ATOM) natom = 1;
if (mode == ATOM) natom_max = 1;
else {
natom = 0;
natom_max = 0;
for (int i = 0; i < nmol; i++)
natom = MAX(natom,onemol[i].natoms);
natom_max = MAX(natom_max,onemols[i]->natoms);
}
memory->create(coords,natom,3,"deposit:coords");
memory->create(imageflags,natom,"deposit:imageflags");
memory->create(coords,natom_max,3,"deposit:coords");
memory->create(imageflags,natom_max,"deposit:imageflags");
// setup scaling
@ -228,7 +229,7 @@ void FixDeposit::init()
if (ifix < 0) error->all(FLERR,"Fix pour rigid fix does not exist");
fixrigid = modify->fix[ifix];
int tmp;
if (onemol != (Molecule *) fixrigid->extract("onemol",tmp))
if (onemols != (Molecule **) fixrigid->extract("onemol",tmp))
error->all(FLERR,
"Fix deposit and fix rigid/small not using "
"same molecule template ID");
@ -243,7 +244,7 @@ void FixDeposit::init()
if (ifix < 0) error->all(FLERR,"Fix deposit shake fix does not exist");
fixshake = modify->fix[ifix];
int tmp;
if (onemol != (Molecule *) fixshake->extract("onemol",tmp))
if (onemols != (Molecule **) fixshake->extract("onemol",tmp))
error->all(FLERR,"Fix deposit and fix shake not using "
"same molecule template ID");
}
@ -255,7 +256,7 @@ void FixDeposit::init()
void FixDeposit::pre_exchange()
{
int i,j,m,n,nlocalprev,imol,flag,flagall;
int i,j,m,n,nlocalprev,imol,natom,flag,flagall;
double coord[3],lamda[3],delx,dely,delz,rsq;
double r[3],vnew[3],rotmat[3][3],quat[4];
double *newcoord;
@ -363,9 +364,10 @@ void FixDeposit::pre_exchange()
double rng = random->uniform();
imol = 0;
while (rng > molfrac[imol]) imol++;
natom = onemols[imol]->natoms;
if (dimension == 3) {
r[0] = random->uniform() - 0.5;
r[1] = random->uniform() - 0.5;
r[1] = random->uniform() - 0.5
r[2] = random->uniform() - 0.5;
} else {
r[0] = r[1] = 0.0;
@ -376,7 +378,7 @@ void FixDeposit::pre_exchange()
MathExtra::axisangle_to_quat(r,theta,quat);
MathExtra::quat_to_mat(quat,rotmat);
for (i = 0; i < natom; i++) {
MathExtra::matvec(rotmat,onemol[imol].dx[i],coords[i]);
MathExtra::matvec(rotmat,onemols[imol]->dx[i],coords[i]);
coords[i][0] += coord[0];
coords[i][1] += coord[1];
coords[i][2] += coord[2];
@ -459,7 +461,7 @@ void FixDeposit::pre_exchange()
if (flag) {
if (mode == ATOM) atom->avec->create_atom(ntype,coords[m]);
else atom->avec->create_atom(ntype+onemol[imol].type[m],coords[m]);
else atom->avec->create_atom(ntype+onemols[imol]->type[m],coords[m]);
n = atom->nlocal - 1;
atom->tag[n] = maxtag_all + m+1;
if (mode == MOLECULE) {
@ -475,7 +477,7 @@ void FixDeposit::pre_exchange()
atom->v[n][1] = vnew[1];
atom->v[n][2] = vnew[2];
if (mode == MOLECULE)
atom->add_molecule_atom(&onemol[imol],m,n,maxtag_all);
atom->add_molecule_atom(onemols[imol],m,n,maxtag_all);
for (j = 0; j < nfix; j++)
if (fix[j]->create_attribute) fix[j]->set_arrays(n);
}
@ -517,10 +519,10 @@ void FixDeposit::pre_exchange()
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
error->all(FLERR,"Too many total atoms");
if (mode == MOLECULE) {
atom->nbonds += onemol[imol].nbonds;
atom->nangles += onemol[imol].nangles;
atom->ndihedrals += onemol[imol].ndihedrals;
atom->nimpropers += onemol[imol].nimpropers;
atom->nbonds += onemols[imol]->nbonds;
atom->nangles += onemols[imol]->nangles;
atom->ndihedrals += onemols[imol]->ndihedrals;
atom->nimpropers += onemols[imol]->nimpropers;
}
maxtag_all += natom;
if (maxtag_all >= MAXTAGINT)
@ -607,8 +609,8 @@ void FixDeposit::options(int narg, char **arg)
if (imol == -1)
error->all(FLERR,"Molecule template ID for fix deposit does not exist");
mode = MOLECULE;
onemol = atom->molecules[imol];
nmol = onemol->nset;
onemols = &atom->molecules[imol];
nmol = onemols[0]->nset;
delete [] molfrac;
molfrac = new double[nmol];
molfrac[0] = 1.0/nmol;
@ -623,8 +625,7 @@ void FixDeposit::options(int narg, char **arg)
molfrac[i] = molfrac[i-1] + force->numeric(FLERR,arg[iarg+i+1]);
if (molfrac[nmol-1] < 1.0-EPSILON || molfrac[nmol-1] > 1.0+EPSILON)
error->all(FLERR,"Illegal fix deposit command");
if (nmol > 1) molfrac[nmol-1] = 1.0 - molfrac[nmol-2];
else molfrac[nmol-1] = 1.0;
molfrac[nmol-1] = 1.0;
iarg += nmol+1;
} else if (strcmp(arg[iarg],"rigid") == 0) {
@ -766,10 +767,10 @@ void *FixDeposit::extract(const char *str, int &itype)
// find a molecule in template with matching type
for (int i = 0; i < nmol; i++) {
if (itype-ntype > onemol[i].ntypes) continue;
double *radius = onemol[i].radius;
int *type = onemol[i].type;
int natoms = onemol[i].natoms;
if (itype-ntype > onemols[i]->ntypes) continue;
double *radius = onemols[i]->radius;
int *type = onemols[i]->type;
int natoms = onemols[i]->natoms;
// check radii of matching types in Molecule
// default to 0.5, if radii not defined in Molecule