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

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

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

76
src/GRANULAR/fix_pour.cpp
View File

@ -118,21 +118,22 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
if (mode == MOLECULE) { if (mode == MOLECULE) {
for (int i = 0; i < nmol; i++) { for (int i = 0; i < nmol; i++) {
if (onemol[i].xflag == 0) if (onemols[i]->xflag == 0)
error->all(FLERR,"Fix pour molecule must have coordinates"); error->all(FLERR,"Fix pour molecule must have coordinates");
if (onemol[i].typeflag == 0) if (onemols[i]->typeflag == 0)
error->all(FLERR,"Fix pour molecule must have atom types"); error->all(FLERR,"Fix pour 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 pour mol command"); error->all(FLERR,"Invalid atom type in fix pour mol command");
if (atom->molecular == 2 && onemol != atom->avec->onemols[0]) if (atom->molecular == 2 && onemols != atom->avec->onemols)
error->all(FLERR,"Fix pour molecule template ID must be same " error->all(FLERR,"Fix pour molecule template ID must be same "
"as atom style template ID"); "as atom style template ID");
onemol[i].check_attributes(0); onemols[i]->check_attributes(0);
// fix pour uses geoemetric center of molecule for insertion // fix pour uses geoemetric center of molecule for insertion
onemol[i].compute_center(); onemols[i]->compute_center();
} }
} }
@ -145,14 +146,14 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
// setup of coords and imageflags array // setup of coords and imageflags array
if (mode == ATOM) natom = 1; if (mode == ATOM) natom_max = 1;
else { else {
natom = 0; natom_max = 0;
for (int i = 0; i < nmol; i++) 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,4,"pour:coords"); memory->create(coords,natom_max,4,"pour:coords");
memory->create(imageflags,natom,"pour:imageflags"); memory->create(imageflags,natom_max,"pour:imageflags");
// find current max atom and molecule IDs if necessary // find current max atom and molecule IDs if necessary
@ -220,7 +221,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
molradius_max = 0.0; molradius_max = 0.0;
if (mode == MOLECULE) { if (mode == MOLECULE) {
for (int i = 0; i < nmol; i++) for (int i = 0; i < nmol; i++)
molradius_max = MAX(molradius_max,onemol[i].molradius); molradius_max = MAX(molradius_max,onemols[i]->molradius);
} }
if (domain->dimension == 3) { if (domain->dimension == 3) {
@ -340,7 +341,7 @@ void FixPour::init()
if (ifix < 0) error->all(FLERR,"Fix pour rigid fix does not exist"); if (ifix < 0) error->all(FLERR,"Fix pour rigid fix does not exist");
fixrigid = modify->fix[ifix]; fixrigid = modify->fix[ifix];
int tmp; int tmp;
if (onemol != (Molecule *) fixrigid->extract("onemol",tmp)) if (onemols != (Molecule **) fixrigid->extract("onemol",tmp))
error->all(FLERR, error->all(FLERR,
"Fix pour and fix rigid/small not using " "Fix pour and fix rigid/small not using "
"same molecule template ID"); "same molecule template ID");
@ -355,7 +356,7 @@ void FixPour::init()
if (ifix < 0) error->all(FLERR,"Fix pour shake fix does not exist"); if (ifix < 0) error->all(FLERR,"Fix pour shake fix does not exist");
fixshake = modify->fix[ifix]; fixshake = modify->fix[ifix];
int tmp; int tmp;
if (onemol != (Molecule *) fixshake->extract("onemol",tmp)) if (onemols != (Molecule **) fixshake->extract("onemol",tmp))
error->all(FLERR,"Fix pour and fix shake not using " error->all(FLERR,"Fix pour and fix shake not using "
"same molecule template ID"); "same molecule template ID");
} }
@ -367,7 +368,7 @@ void FixPour::init()
void FixPour::pre_exchange() void FixPour::pre_exchange()
{ {
int i,j,m,flag,nlocalprev,imol; int i,j,m,flag,nlocalprev,imol,natom;
double r[3],rotmat[3][3],quat[4],vnew[3]; double r[3],rotmat[3][3],quat[4],vnew[3];
double *newcoord; double *newcoord;
@ -410,7 +411,7 @@ void FixPour::pre_exchange()
double **xmine,**xnear; double **xmine,**xnear;
memory->create(xmine,ncount,4,"fix_pour:xmine"); memory->create(xmine,ncount,4,"fix_pour:xmine");
memory->create(xnear,nprevious+nnew*natom,4,"fix_pour:xnear"); memory->create(xnear,nprevious+nnew*natom_max,4,"fix_pour:xnear");
int nnear = nprevious; int nnear = nprevious;
// setup for allgatherv // setup for allgatherv
@ -467,11 +468,11 @@ void FixPour::pre_exchange()
double *sublo = domain->sublo; double *sublo = domain->sublo;
double *subhi = domain->subhi; double *subhi = domain->subhi;
int nsuccess = 0;
int attempt = 0; int attempt = 0;
int maxiter = nnew * maxattempt; int maxiter = nnew * maxattempt;
int ntotal = nprevious + nnew*natom;
while (nnear < ntotal) { while (nsuccess < nnew) {
rn = random->uniform(); rn = random->uniform();
h = hi_current - rn*rn * (hi_current-lo_current); h = hi_current - rn*rn * (hi_current-lo_current);
if (mode == ATOM) radtmp = radius_sample(); if (mode == ATOM) radtmp = radius_sample();
@ -492,6 +493,7 @@ void FixPour::pre_exchange()
double rng = random->uniform(); double rng = random->uniform();
imol = 0; imol = 0;
while (rng > molfrac[imol]) imol++; while (rng > molfrac[imol]) imol++;
natom = onemols[imol]->natoms;
if (dimension == 3) { if (dimension == 3) {
r[0] = random->uniform() - 0.5; r[0] = random->uniform() - 0.5;
r[1] = random->uniform() - 0.5; r[1] = random->uniform() - 0.5;
@ -505,7 +507,7 @@ void FixPour::pre_exchange()
MathExtra::axisangle_to_quat(r,theta,quat); MathExtra::axisangle_to_quat(r,theta,quat);
MathExtra::quat_to_mat(quat,rotmat); MathExtra::quat_to_mat(quat,rotmat);
for (i = 0; i < natom; i++) { 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][0] += coord[0];
coords[i][1] += coord[1]; coords[i][1] += coord[1];
coords[i][2] += coord[2]; coords[i][2] += coord[2];
@ -514,7 +516,8 @@ void FixPour::pre_exchange()
// default to 0.5, if radii not defined in Molecule // default to 0.5, if radii not defined in Molecule
// same as atom->avec->create_atom(), invoked below // same as atom->avec->create_atom(), invoked below
if (onemol[imol].radiusflag) coords[i][3] = onemol[imol].radius[i]; if (onemols[imol]->radiusflag)
coords[i][3] = onemols[imol]->radius[i];
else coords[i][3] = 0.5; else coords[i][3] = 0.5;
imageflags[i] = ((imageint) IMGMAX << IMG2BITS) | imageflags[i] = ((imageint) IMGMAX << IMG2BITS) |
@ -548,6 +551,7 @@ void FixPour::pre_exchange()
// proceed with insertion // proceed with insertion
nsuccess++;
nlocalprev = atom->nlocal; nlocalprev = atom->nlocal;
// add all atoms in particle to xnear // add all atoms in particle to xnear
@ -603,7 +607,7 @@ void FixPour::pre_exchange()
if (flag) { if (flag) {
if (mode == ATOM) atom->avec->create_atom(ntype,coords[m]); 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]);
int n = atom->nlocal - 1; int n = atom->nlocal - 1;
atom->tag[n] = maxtag_all + m+1; atom->tag[n] = maxtag_all + m+1;
if (mode == MOLECULE) { if (mode == MOLECULE) {
@ -622,7 +626,7 @@ void FixPour::pre_exchange()
radtmp = newcoord[3]; radtmp = newcoord[3];
atom->radius[n] = radtmp; atom->radius[n] = radtmp;
atom->rmass[n] = 4.0*MY_PI/3.0 * radtmp*radtmp*radtmp * denstmp; atom->rmass[n] = 4.0*MY_PI/3.0 * radtmp*radtmp*radtmp * denstmp;
} else atom->add_molecule_atom(&onemol[imol],m,n,maxtag_all); } else atom->add_molecule_atom(onemols[imol],m,n,maxtag_all);
for (j = 0; j < nfix; j++) for (j = 0; j < nfix; j++)
if (fix[j]->create_attribute) fix[j]->set_arrays(n); if (fix[j]->create_attribute) fix[j]->set_arrays(n);
} }
@ -659,10 +663,10 @@ void FixPour::pre_exchange()
if (atom->natoms < 0 || atom->natoms > MAXBIGINT) if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
error->all(FLERR,"Too many total atoms"); error->all(FLERR,"Too many total atoms");
if (mode == MOLECULE) { if (mode == MOLECULE) {
atom->nbonds += onemol[imol].nbonds * ninserted_mols; atom->nbonds += onemols[imol]->nbonds * ninserted_mols;
atom->nangles += onemol[imol].nangles * ninserted_mols; atom->nangles += onemols[imol]->nangles * ninserted_mols;
atom->ndihedrals += onemol[imol].ndihedrals * ninserted_mols; atom->ndihedrals += onemols[imol]->ndihedrals * ninserted_mols;
atom->nimpropers += onemol[imol].nimpropers * ninserted_mols; atom->nimpropers += onemols[imol]->nimpropers * ninserted_mols;
} }
if (maxtag_all >= MAXTAGINT) if (maxtag_all >= MAXTAGINT)
error->all(FLERR,"New atom IDs exceed maximum allowed ID"); error->all(FLERR,"New atom IDs exceed maximum allowed ID");
@ -828,6 +832,7 @@ void FixPour::options(int narg, char **arg)
iregion = -1; iregion = -1;
mode = ATOM; mode = ATOM;
molfrac = NULL;
rigidflag = 0; rigidflag = 0;
idrigid = NULL; idrigid = NULL;
shakeflag = 0; shakeflag = 0;
@ -855,12 +860,9 @@ void FixPour::options(int narg, char **arg)
int imol = atom->find_molecule(arg[iarg+1]); int imol = atom->find_molecule(arg[iarg+1]);
if (imol == -1) if (imol == -1)
error->all(FLERR,"Molecule template ID for fix pour does not exist"); error->all(FLERR,"Molecule template ID for fix pour does not exist");
if (atom->molecules[imol]->nset > 1 && comm->me == 0)
error->warning(FLERR,"Molecule template for "
"fix pour has multiple molecules");
mode = MOLECULE; mode = MOLECULE;
onemol = atom->molecules[imol]; onemols = &atom->molecules[imol];
nmol = onemol->nset; nmol = onemols[0]->nset;
delete [] molfrac; delete [] molfrac;
molfrac = new double[nmol]; molfrac = new double[nmol];
molfrac[0] = 1.0/nmol; molfrac[0] = 1.0/nmol;
@ -875,11 +877,9 @@ void FixPour::options(int narg, char **arg)
molfrac[i] = molfrac[i-1] + force->numeric(FLERR,arg[iarg+i+1]); 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) if (molfrac[nmol-1] < 1.0-EPSILON || molfrac[nmol-1] > 1.0+EPSILON)
error->all(FLERR,"Illegal fix deposit command"); error->all(FLERR,"Illegal fix deposit command");
if (nmol > 1) molfrac[nmol-1] = 1.0 - molfrac[nmol-2]; molfrac[nmol-1] = 1.0;
else molfrac[nmol-1] = 1.0;
iarg += nmol+1; iarg += nmol+1;
} else if (strcmp(arg[iarg],"rigid") == 0) { } else if (strcmp(arg[iarg],"rigid") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix pour command"); if (iarg+2 > narg) error->all(FLERR,"Illegal fix pour command");
int n = strlen(arg[iarg+1]) + 1; int n = strlen(arg[iarg+1]) + 1;
@ -1000,10 +1000,10 @@ void *FixPour::extract(const char *str, int &itype)
// find a molecule in template with matching type // find a molecule in template with matching type
for (int i = 0; i < nmol; i++) { for (int i = 0; i < nmol; i++) {
if (itype-ntype > onemol[i].ntypes) continue; if (itype-ntype > onemols[i]->ntypes) continue;
double *radius = onemol[i].radius; double *radius = onemols[i]->radius;
int *type = onemol[i].type; int *type = onemols[i]->type;
int natoms = onemol[i].natoms; int natoms = onemols[i]->natoms;
// check radii of matching types in Molecule // check radii of matching types in Molecule
// default to 0.5, if radii not defined in Molecule // default to 0.5, if radii not defined in Molecule

4
src/GRANULAR/fix_pour.h
View File

@ -51,8 +51,8 @@ class FixPour : public Fix {
double grav; double grav;
char *idrigid,*idshake; char *idrigid,*idshake;
class Molecule *onemol; class Molecule **onemols;
int natom,nmol; int nmol,natom_max;
double molradius_max; double molradius_max;
double *molfrac; double *molfrac;
double **coords; double **coords;

61
src/MISC/fix_deposit.cpp
View File

@ -102,21 +102,22 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
if (mode == MOLECULE) { if (mode == MOLECULE) {
for (int i = 0; i < nmol; i++) { 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"); 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"); 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"); 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 " error->all(FLERR,"Fix deposit molecule template ID must be same "
"as atom_style template ID"); "as atom_style template ID");
onemol[i].check_attributes(0); onemols[i]->check_attributes(0);
// fix deposit uses geoemetric center of molecule for insertion // 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 // setup of coords and imageflags array
if (mode == ATOM) natom = 1; if (mode == ATOM) natom_max = 1;
else { else {
natom = 0; natom_max = 0;
for (int i = 0; i < nmol; i++) 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(coords,natom_max,3,"deposit:coords");
memory->create(imageflags,natom,"deposit:imageflags"); memory->create(imageflags,natom_max,"deposit:imageflags");
// setup scaling // setup scaling
@ -228,7 +229,7 @@ void FixDeposit::init()
if (ifix < 0) error->all(FLERR,"Fix pour rigid fix does not exist"); if (ifix < 0) error->all(FLERR,"Fix pour rigid fix does not exist");
fixrigid = modify->fix[ifix]; fixrigid = modify->fix[ifix];
int tmp; int tmp;
if (onemol != (Molecule *) fixrigid->extract("onemol",tmp)) if (onemols != (Molecule **) fixrigid->extract("onemol",tmp))
error->all(FLERR, error->all(FLERR,
"Fix deposit and fix rigid/small not using " "Fix deposit and fix rigid/small not using "
"same molecule template ID"); "same molecule template ID");
@ -243,7 +244,7 @@ void FixDeposit::init()
if (ifix < 0) error->all(FLERR,"Fix deposit shake fix does not exist"); if (ifix < 0) error->all(FLERR,"Fix deposit shake fix does not exist");
fixshake = modify->fix[ifix]; fixshake = modify->fix[ifix];
int tmp; 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 " error->all(FLERR,"Fix deposit and fix shake not using "
"same molecule template ID"); "same molecule template ID");
} }
@ -255,7 +256,7 @@ void FixDeposit::init()
void FixDeposit::pre_exchange() 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 coord[3],lamda[3],delx,dely,delz,rsq;
double r[3],vnew[3],rotmat[3][3],quat[4]; double r[3],vnew[3],rotmat[3][3],quat[4];
double *newcoord; double *newcoord;
@ -363,9 +364,10 @@ void FixDeposit::pre_exchange()
double rng = random->uniform(); double rng = random->uniform();
imol = 0; imol = 0;
while (rng > molfrac[imol]) imol++; while (rng > molfrac[imol]) imol++;
natom = onemols[imol]->natoms;
if (dimension == 3) { if (dimension == 3) {
r[0] = random->uniform() - 0.5; r[0] = random->uniform() - 0.5;
r[1] = random->uniform() - 0.5; r[1] = random->uniform() - 0.5
r[2] = random->uniform() - 0.5; r[2] = random->uniform() - 0.5;
} else { } else {
r[0] = r[1] = 0.0; r[0] = r[1] = 0.0;
@ -376,7 +378,7 @@ void FixDeposit::pre_exchange()
MathExtra::axisangle_to_quat(r,theta,quat); MathExtra::axisangle_to_quat(r,theta,quat);
MathExtra::quat_to_mat(quat,rotmat); MathExtra::quat_to_mat(quat,rotmat);
for (i = 0; i < natom; i++) { 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][0] += coord[0];
coords[i][1] += coord[1]; coords[i][1] += coord[1];
coords[i][2] += coord[2]; coords[i][2] += coord[2];
@ -459,7 +461,7 @@ void FixDeposit::pre_exchange()
if (flag) { if (flag) {
if (mode == ATOM) atom->avec->create_atom(ntype,coords[m]); 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; n = atom->nlocal - 1;
atom->tag[n] = maxtag_all + m+1; atom->tag[n] = maxtag_all + m+1;
if (mode == MOLECULE) { if (mode == MOLECULE) {
@ -475,7 +477,7 @@ void FixDeposit::pre_exchange()
atom->v[n][1] = vnew[1]; atom->v[n][1] = vnew[1];
atom->v[n][2] = vnew[2]; atom->v[n][2] = vnew[2];
if (mode == MOLECULE) 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++) for (j = 0; j < nfix; j++)
if (fix[j]->create_attribute) fix[j]->set_arrays(n); 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) if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
error->all(FLERR,"Too many total atoms"); error->all(FLERR,"Too many total atoms");
if (mode == MOLECULE) { if (mode == MOLECULE) {
atom->nbonds += onemol[imol].nbonds; atom->nbonds += onemols[imol]->nbonds;
atom->nangles += onemol[imol].nangles; atom->nangles += onemols[imol]->nangles;
atom->ndihedrals += onemol[imol].ndihedrals; atom->ndihedrals += onemols[imol]->ndihedrals;
atom->nimpropers += onemol[imol].nimpropers; atom->nimpropers += onemols[imol]->nimpropers;
} }
maxtag_all += natom; maxtag_all += natom;
if (maxtag_all >= MAXTAGINT) if (maxtag_all >= MAXTAGINT)
@ -607,8 +609,8 @@ void FixDeposit::options(int narg, char **arg)
if (imol == -1) if (imol == -1)
error->all(FLERR,"Molecule template ID for fix deposit does not exist"); error->all(FLERR,"Molecule template ID for fix deposit does not exist");
mode = MOLECULE; mode = MOLECULE;
onemol = atom->molecules[imol]; onemols = &atom->molecules[imol];
nmol = onemol->nset; nmol = onemols[0]->nset;
delete [] molfrac; delete [] molfrac;
molfrac = new double[nmol]; molfrac = new double[nmol];
molfrac[0] = 1.0/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]); 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) if (molfrac[nmol-1] < 1.0-EPSILON || molfrac[nmol-1] > 1.0+EPSILON)
error->all(FLERR,"Illegal fix deposit command"); error->all(FLERR,"Illegal fix deposit command");
if (nmol > 1) molfrac[nmol-1] = 1.0 - molfrac[nmol-2]; molfrac[nmol-1] = 1.0;
else molfrac[nmol-1] = 1.0;
iarg += nmol+1; iarg += nmol+1;
} else if (strcmp(arg[iarg],"rigid") == 0) { } 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 // find a molecule in template with matching type
for (int i = 0; i < nmol; i++) { for (int i = 0; i < nmol; i++) {
if (itype-ntype > onemol[i].ntypes) continue; if (itype-ntype > onemols[i]->ntypes) continue;
double *radius = onemol[i].radius; double *radius = onemols[i]->radius;
int *type = onemol[i].type; int *type = onemols[i]->type;
int natoms = onemol[i].natoms; int natoms = onemols[i]->natoms;
// check radii of matching types in Molecule // check radii of matching types in Molecule
// default to 0.5, if radii not defined in Molecule // default to 0.5, if radii not defined in Molecule

4
src/MISC/fix_deposit.h
View File

@ -47,8 +47,8 @@ class FixDeposit : public Fix {
char *idregion; char *idregion;
char *idrigid,*idshake; char *idrigid,*idshake;
class Molecule *onemol; class Molecule **onemols;
int natom,nmol; int nmol,natom_max;
double *molfrac; double *molfrac;
double **coords; double **coords;
imageint *imageflags; imageint *imageflags;

61
src/RIGID/fix_rigid_small.cpp
View File

@ -126,7 +126,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
int seed; int seed;
langflag = 0; langflag = 0;
infile = NULL; infile = NULL;
onemol = NULL; onemols = NULL;
tstat_flag = 0; tstat_flag = 0;
pstat_flag = 0; pstat_flag = 0;
@ -174,11 +174,8 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
if (imol == -1) if (imol == -1)
error->all(FLERR,"Molecule template ID for " error->all(FLERR,"Molecule template ID for "
"fix rigid/small does not exist"); "fix rigid/small does not exist");
if (atom->molecules[imol]->nset > 1 && comm->me == 0) onemols = &atom->molecules[imol];
error->warning(FLERR,"Molecule template for " nmol = onemols[0]->nset;
"fix rigid/small has multiple molecules");
onemol = atom->molecules[imol];
nmol = onemol->nset;
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"temp") == 0) { } else if (strcmp(arg[iarg],"temp") == 0) {
@ -300,19 +297,19 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
// error check and further setup for Molecule template // error check and further setup for Molecule template
if (onemol) { if (onemols) {
for (int i = 0; i < nmol; i++) { for (int i = 0; i < nmol; i++) {
if (onemol[i].xflag == 0) if (onemols[i]->xflag == 0)
error->all(FLERR,"Fix rigid/small molecule must have coordinates"); error->all(FLERR,"Fix rigid/small molecule must have coordinates");
if (onemol[i].typeflag == 0) if (onemols[i]->typeflag == 0)
error->all(FLERR,"Fix rigid/small molecule must have atom types"); error->all(FLERR,"Fix rigid/small molecule must have atom types");
// fix rigid/small uses center, masstotal, COM, inertia of molecule // fix rigid/small uses center, masstotal, COM, inertia of molecule
onemol[i].compute_center(); onemols[i]->compute_center();
onemol[i].compute_mass(); onemols[i]->compute_mass();
onemol[i].compute_com(); onemols[i]->compute_com();
onemol[i].compute_inertia(); onemols[i]->compute_inertia();
} }
} }
@ -1552,9 +1549,9 @@ void FixRigidSmall::create_bodies()
MPI_Allreduce(&rsqfar,&maxextent,1,MPI_DOUBLE,MPI_MAX,world); MPI_Allreduce(&rsqfar,&maxextent,1,MPI_DOUBLE,MPI_MAX,world);
maxextent = sqrt(maxextent); maxextent = sqrt(maxextent);
if (onemol) { if (onemols) {
for (int i = 0; i < nmol; i++) for (int i = 0; i < nmol; i++)
maxextent = MAX(maxextent,onemol[i].maxextent); maxextent = MAX(maxextent,onemols[i]->maxextent);
} }
// clean up // clean up
@ -1724,10 +1721,10 @@ void FixRigidSmall::setup_bodies_static()
// extended = 1 if using molecule template with finite-size particles // extended = 1 if using molecule template with finite-size particles
// require all molecules in template to have consistent radiusflag // require all molecules in template to have consistent radiusflag
if (onemol) { if (onemols) {
int radiusflag = onemol->radiusflag; int radiusflag = onemols[0]->radiusflag;
for (i = 1; i < nmol; i++) { for (i = 1; i < nmol; i++) {
if (onemol->radiusflag != radiusflag) if (onemols[i]->radiusflag != radiusflag)
error->all(FLERR,"Inconsistent use of finite-size particles " error->all(FLERR,"Inconsistent use of finite-size particles "
"by molecule template molecules"); "by molecule template molecules");
} }
@ -2607,16 +2604,16 @@ void FixRigidSmall::set_molecule(int nlocalprev, tagint tagprev, int imol,
tagint *tag = atom->tag; tagint *tag = atom->tag;
for (int i = nlocalprev; i < nlocal; i++) { for (int i = nlocalprev; i < nlocal; i++) {
bodytag[i] = tagprev + onemol[imol].comatom; bodytag[i] = tagprev + onemols[imol]->comatom;
if (tag[i]-tagprev == onemol[imol].comatom) bodyown[i] = nlocal_body; if (tag[i]-tagprev == onemols[imol]->comatom) bodyown[i] = nlocal_body;
m = tag[i] - tagprev-1; m = tag[i] - tagprev-1;
displace[i][0] = onemol[imol].dxbody[m][0]; displace[i][0] = onemols[imol]->dxbody[m][0];
displace[i][1] = onemol[imol].dxbody[m][1]; displace[i][1] = onemols[imol]->dxbody[m][1];
displace[i][2] = onemol[imol].dxbody[m][2]; displace[i][2] = onemols[imol]->dxbody[m][2];
eflags[i] = 0; eflags[i] = 0;
if (onemol[imol].radiusflag) { if (onemols[imol]->radiusflag) {
eflags[i] |= SPHERE; eflags[i] |= SPHERE;
eflags[i] |= OMEGA; eflags[i] |= OMEGA;
eflags[i] |= TORQUE; eflags[i] |= TORQUE;
@ -2625,27 +2622,27 @@ void FixRigidSmall::set_molecule(int nlocalprev, tagint tagprev, int imol,
if (bodyown[i] >= 0) { if (bodyown[i] >= 0) {
if (nlocal_body == nmax_body) grow_body(); if (nlocal_body == nmax_body) grow_body();
Body *b = &body[nlocal_body]; Body *b = &body[nlocal_body];
b->mass = onemol[imol].masstotal; b->mass = onemols[imol]->masstotal;
// new COM = Q (onemol[imol].xcm - onemol[imol].center) + xgeom // new COM = Q (onemols[imol]->xcm - onemols[imol]->center) + xgeom
// Q = rotation matrix associated with quat // Q = rotation matrix associated with quat
MathExtra::quat_to_mat(quat,rotmat); MathExtra::quat_to_mat(quat,rotmat);
MathExtra::sub3(onemol[imol].com,onemol[imol].center,ctr2com); MathExtra::sub3(onemols[imol]->com,onemols[imol]->center,ctr2com);
MathExtra::matvec(rotmat,ctr2com,ctr2com_rotate); MathExtra::matvec(rotmat,ctr2com,ctr2com_rotate);
MathExtra::add3(ctr2com_rotate,xgeom,b->xcm); MathExtra::add3(ctr2com_rotate,xgeom,b->xcm);
b->vcm[0] = vcm[0]; b->vcm[0] = vcm[0];
b->vcm[1] = vcm[1]; b->vcm[1] = vcm[1];
b->vcm[2] = vcm[2]; b->vcm[2] = vcm[2];
b->inertia[0] = onemol[imol].inertia[0]; b->inertia[0] = onemols[imol]->inertia[0];
b->inertia[1] = onemol[imol].inertia[1]; b->inertia[1] = onemols[imol]->inertia[1];
b->inertia[2] = onemol[imol].inertia[2]; b->inertia[2] = onemols[imol]->inertia[2];
// final quat is product of insertion quat and original quat // final quat is product of insertion quat and original quat
// true even if insertion rotation was not around COM // true even if insertion rotation was not around COM
MathExtra::quatquat(quat,onemol[imol].quat,b->quat); MathExtra::quatquat(quat,onemols[imol]->quat,b->quat);
MathExtra::q_to_exyz(b->quat,b->ex_space,b->ey_space,b->ez_space); MathExtra::q_to_exyz(b->quat,b->ex_space,b->ey_space,b->ez_space);
b->angmom[0] = b->angmom[1] = b->angmom[2] = 0.0; b->angmom[0] = b->angmom[1] = b->angmom[2] = 0.0;
@ -3194,7 +3191,7 @@ void *FixRigidSmall::extract(const char *str, int &dim)
if (strcmp(str,"onemol") == 0) { if (strcmp(str,"onemol") == 0) {
dim = 0; dim = 0;
return onemol; return onemols;
} }
// return vector of rigid body masses, for owned+ghost bodies // return vector of rigid body masses, for owned+ghost bodies

2
src/RIGID/fix_rigid_small.h
View File

@ -170,7 +170,7 @@ class FixRigidSmall : public Fix {
// molecules added on-the-fly as rigid bodies // molecules added on-the-fly as rigid bodies
class Molecule *onemol; class Molecule **onemols;
int nmol; int nmol;
// class data used by ring communication callbacks // class data used by ring communication callbacks