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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11918 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-05-06 17:37:44 +00:00
parent 7cdef3fd61
commit 7785c98703
9 changed files with 223 additions and 120 deletions
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127
src/GRANULAR/fix_pour.cpp
View File

@ -117,21 +117,23 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Cannot use fix_pour unless atoms have IDs");
if (mode == MOLECULE) {
if (onemol->xflag == 0)
error->all(FLERR,"Fix pour molecule must have coordinates");
if (onemol->typeflag == 0)
error->all(FLERR,"Fix pour molecule must have atom types");
if (ntype+onemol->ntypes <= 0 || ntype+onemol->ntypes > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix pour mol command");
for (int i = 0; i < nmol; i++) {
if (onemol[i].xflag == 0)
error->all(FLERR,"Fix pour molecule must have coordinates");
if (onemol[i].typeflag == 0)
error->all(FLERR,"Fix pour molecule must have atom types");
if (ntype+onemol[i].ntypes <= 0 || ntype+onemol[i].ntypes > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix pour mol command");
if (atom->molecular == 2 && onemol != atom->avec->onemols[0])
error->all(FLERR,"Fix pour molecule template ID must be same "
"as atom style template ID");
onemol[i].check_attributes(0);
if (atom->molecular == 2 && onemol != atom->avec->onemols[0])
error->all(FLERR,"Fix pour molecule template ID must be same "
"as atom style template ID");
onemol->check_attributes(0);
// fix pour uses geoemetric center of molecule for insertion
// fix pour uses geoemetric center of molecule for insertion
onemol->compute_center();
onemol[i].compute_center();
}
}
if (rigidflag && mode == ATOM)
@ -144,7 +146,11 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
// setup of coords and imageflags array
if (mode == ATOM) natom = 1;
else natom = onemol->natoms;
else {
natom = 0;
for (int i = 0; i < nmol; i++)
natom = MAX(natom,onemol[i].natoms);
}
memory->create(coords,natom,4,"pour:coords");
memory->create(imageflags,natom,"pour:imageflags");
@ -211,6 +217,12 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
double volume,volume_one;
molradius_max = 0.0;
if (mode == MOLECULE) {
for (int i = 0; i < nmol; i++)
molradius_max = MAX(molradius_max,onemol[i].molradius);
}
if (domain->dimension == 3) {
if (region_style == 1) {
double dy = yhi - ylo;
@ -218,8 +230,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
volume = (xhi-xlo) * dy * (zhi-zlo);
} else volume = MY_PI*rc*rc * (zhi-zlo);
if (mode == MOLECULE) {
double molradius = onemol->molradius;
volume_one = 4.0/3.0 * MY_PI * molradius*molradius*molradius;
volume_one = 4.0/3.0 * MY_PI * molradius_max*molradius_max*molradius_max;
} else if (dstyle == ONE || dstyle == RANGE) {
volume_one = 4.0/3.0 * MY_PI * radius_max*radius_max*radius_max;
} else if (dstyle == POLY) {
@ -231,8 +242,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
} else {
volume = (xhi-xlo) * (yhi-ylo);
if (mode == MOLECULE) {
double molradius = onemol->molradius;
volume_one = MY_PI * molradius*molradius;
volume_one = MY_PI * molradius_max*molradius_max;
} else if (dstyle == ONE || dstyle == RANGE) {
volume_one = MY_PI * radius_max*radius_max;
} else if (dstyle == POLY) {
@ -264,6 +274,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
FixPour::~FixPour()
{
delete random;
delete [] molfrac;
delete [] idrigid;
delete [] idshake;
delete [] radius_poly;
@ -356,7 +367,7 @@ void FixPour::init()
void FixPour::pre_exchange()
{
int i,j,m,flag,nlocalprev;
int i,j,m,flag,nlocalprev,imol;
double r[3],rotmat[3][3],quat[4],vnew[3];
double *newcoord;
@ -478,6 +489,9 @@ void FixPour::pre_exchange()
imageflags[0] = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
} else {
double rng = random->uniform();
imol = 0;
while (rng > molfrac[imol]) imol++;
if (dimension == 3) {
r[0] = random->uniform() - 0.5;
r[1] = random->uniform() - 0.5;
@ -491,7 +505,7 @@ void FixPour::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->dx[i],coords[i]);
MathExtra::matvec(rotmat,onemol[imol].dx[i],coords[i]);
coords[i][0] += coord[0];
coords[i][1] += coord[1];
coords[i][2] += coord[2];
@ -500,7 +514,7 @@ void FixPour::pre_exchange()
// default to 0.5, if radii not defined in Molecule
// same as atom->avec->create_atom(), invoked below
if (onemol->radiusflag) coords[i][3] = onemol->radius[i];
if (onemol[imol].radiusflag) coords[i][3] = onemol[imol].radius[i];
else coords[i][3] = 0.5;
imageflags[i] = ((imageint) IMGMAX << IMG2BITS) |
@ -589,7 +603,7 @@ void FixPour::pre_exchange()
if (flag) {
if (mode == ATOM) atom->avec->create_atom(ntype,coords[m]);
else atom->avec->create_atom(ntype+onemol->type[m],coords[m]);
else atom->avec->create_atom(ntype+onemol[imol].type[m],coords[m]);
int n = atom->nlocal - 1;
atom->tag[n] = maxtag_all + m+1;
if (mode == MOLECULE) {
@ -608,7 +622,7 @@ void FixPour::pre_exchange()
radtmp = newcoord[3];
atom->radius[n] = radtmp;
atom->rmass[n] = 4.0*MY_PI/3.0 * radtmp*radtmp*radtmp * denstmp;
} else atom->add_molecule_atom(onemol,m,n,maxtag_all);
} else atom->add_molecule_atom(&onemol[imol],m,n,maxtag_all);
for (j = 0; j < nfix; j++)
if (fix[j]->create_attribute) fix[j]->set_arrays(n);
}
@ -619,9 +633,9 @@ void FixPour::pre_exchange()
// FixShake::set_molecule stores shake info for molecule
if (rigidflag)
fixrigid->set_molecule(nlocalprev,maxtag_all,coord,vnew,quat);
fixrigid->set_molecule(nlocalprev,maxtag_all,imol,coord,vnew,quat);
else if (shakeflag)
fixshake->set_molecule(nlocalprev,maxtag_all,coord,vnew,quat);
fixshake->set_molecule(nlocalprev,maxtag_all,imol,coord,vnew,quat);
maxtag_all += natom;
if (mode == MOLECULE && atom->molecule_flag) maxmol_all++;
@ -645,10 +659,10 @@ void FixPour::pre_exchange()
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
error->all(FLERR,"Too many total atoms");
if (mode == MOLECULE) {
atom->nbonds += onemol->nbonds * ninserted_mols;
atom->nangles += onemol->nangles * ninserted_mols;
atom->ndihedrals += onemol->ndihedrals * ninserted_mols;
atom->nimpropers += onemol->nimpropers * ninserted_mols;
atom->nbonds += onemol[imol].nbonds * ninserted_mols;
atom->nangles += onemol[imol].nangles * ninserted_mols;
atom->ndihedrals += onemol[imol].ndihedrals * ninserted_mols;
atom->nimpropers += onemol[imol].nimpropers * ninserted_mols;
}
if (maxtag_all >= MAXTAGINT)
error->all(FLERR,"New atom IDs exceed maximum allowed ID");
@ -696,7 +710,7 @@ void FixPour::find_maxid()
check if particle i could overlap with a particle inserted into region
return 1 if yes, 0 if no
for ATOM mode, use delta with maximum size for inserted atoms
for MOLECULE mode, use delta with radius of inserted molecules
for MOLECULE mode, use delta with max radius of inserted molecules
account for PBC in overlap decision via outside() and minimum_image()
------------------------------------------------------------------------- */
@ -704,7 +718,7 @@ int FixPour::overlap(int i)
{
double delta;
if (mode == ATOM) delta = atom->radius[i] + radius_max;
else delta = atom->radius[i] + onemol->molradius;
else delta = atom->radius[i] + molradius_max;
double *x = atom->x[i];
@ -835,6 +849,7 @@ void FixPour::options(int narg, char **arg)
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1) error->all(FLERR,"Fix pour region ID does not exist");
iarg += 2;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix pour command");
int imol = atom->find_molecule(arg[iarg+1]);
@ -845,7 +860,26 @@ void FixPour::options(int narg, char **arg)
"fix pour has multiple molecules");
mode = MOLECULE;
onemol = atom->molecules[imol];
nmol = onemol->nset;
delete [] molfrac;
molfrac = new double[nmol];
molfrac[0] = 1.0/nmol;
for (int i = 1; i < nmol-1; i++) molfrac[i] = molfrac[i-1] + 1.0/nmol;
molfrac[nmol-1] = 1.0;
iarg += 2;
} else if (strcmp(arg[iarg],"molfrac") == 0) {
if (mode != MOLECULE) error->all(FLERR,"Illegal fix deposit command");
if (iarg+nmol+1 > narg) error->all(FLERR,"Illegal fix deposit command");
molfrac[0] = force->numeric(FLERR,arg[iarg+1]);
for (int i = 1; i < nmol; i++)
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;
iarg += nmol+1;
} else if (strcmp(arg[iarg],"rigid") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix pour command");
int n = strlen(arg[iarg+1]) + 1;
@ -960,21 +994,28 @@ void *FixPour::extract(const char *str, int &itype)
if (mode == ATOM) {
if (itype == ntype) oneradius = radius_max;
else oneradius = 0.0;
} else {
double *radius = onemol->radius;
int *type = onemol->type;
int natoms = onemol->natoms;
// check radii of matching types in Molecule
// default to 0.5, if radii not defined in Molecule
// same as atom->avec->create_atom(), invoked in pre_exchange()
// find a molecule in template with matching type
oneradius = 0.0;
for (int i = 0; i < natoms; i++)
if (type[i] == itype-ntype) {
if (radius) oneradius = MAX(oneradius,radius[i]);
else oneradius = 0.5;
}
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;
// check radii of matching types in Molecule
// default to 0.5, if radii not defined in Molecule
// same as atom->avec->create_atom(), invoked in pre_exchange()
oneradius = 0.0;
for (int i = 0; i < natoms; i++)
if (type[i] == itype-ntype) {
if (radius) oneradius = MAX(oneradius,radius[i]);
else oneradius = 0.5;
}
}
}
itype = 0;
return &oneradius;

4
src/GRANULAR/fix_pour.h
View File

@ -52,7 +52,9 @@ class FixPour : public Fix {
char *idrigid,*idshake;
class Molecule *onemol;
int natom; // # of atoms per inserted particle
int natom,nmol;
double molradius_max;
double *molfrac;
double **coords;
imageint *imageflags;
class Fix *fixrigid,*fixshake;

118
src/MISC/fix_deposit.cpp
View File

@ -38,6 +38,8 @@ using namespace MathConst;
enum{ATOM,MOLECULE};
#define EPSILON 1.0e6
/* ---------------------------------------------------------------------- */
FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
@ -99,21 +101,23 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Cannot use fix_deposit unless atoms have IDs");
if (mode == MOLECULE) {
if (onemol->xflag == 0)
error->all(FLERR,"Fix deposit molecule must have coordinates");
if (onemol->typeflag == 0)
error->all(FLERR,"Fix deposit molecule must have atom types");
if (ntype+onemol->ntypes <= 0 || ntype+onemol->ntypes > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix deposit mol command");
for (int i = 0; i < nmol; i++) {
if (onemol[i].xflag == 0)
error->all(FLERR,"Fix deposit molecule must have coordinates");
if (onemol[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)
error->all(FLERR,"Invalid atom type in fix deposit mol command");
if (atom->molecular == 2 && onemol != atom->avec->onemols[0])
error->all(FLERR,"Fix deposit molecule template ID must be same "
"as atom_style template ID");
onemol[i].check_attributes(0);
if (atom->molecular == 2 && onemol != atom->avec->onemols[0])
error->all(FLERR,"Fix deposit molecule template ID must be same "
"as atom_style template ID");
onemol->check_attributes(0);
// fix deposit uses geoemetric center of molecule for insertion
onemol->compute_center();
// fix deposit uses geoemetric center of molecule for insertion
onemol[i].compute_center();
}
}
if (rigidflag && mode == ATOM)
@ -126,7 +130,11 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
// setup of coords and imageflags array
if (mode == ATOM) natom = 1;
else natom = onemol->natoms;
else {
natom = 0;
for (int i = 0; i < nmol; i++)
natom = MAX(natom,onemol[i].natoms);
}
memory->create(coords,natom,3,"deposit:coords");
memory->create(imageflags,natom,"deposit:imageflags");
@ -184,6 +192,7 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
FixDeposit::~FixDeposit()
{
delete random;
delete [] molfrac;
delete [] idrigid;
delete [] idshake;
delete [] idregion;
@ -246,7 +255,7 @@ void FixDeposit::init()
void FixDeposit::pre_exchange()
{
int i,j,m,n,nlocalprev,flag,flagall;
int i,j,m,n,nlocalprev,imol,flag,flagall;
double coord[3],lamda[3],delx,dely,delz,rsq;
double r[3],vnew[3],rotmat[3][3],quat[4];
double *newcoord;
@ -351,6 +360,9 @@ void FixDeposit::pre_exchange()
imageflags[0] = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
} else {
double rng = random->uniform();
imol = 0;
while (rng > molfrac[imol]) imol++;
if (dimension == 3) {
r[0] = random->uniform() - 0.5;
r[1] = random->uniform() - 0.5;
@ -364,7 +376,7 @@ 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->dx[i],coords[i]);
MathExtra::matvec(rotmat,onemol[imol].dx[i],coords[i]);
coords[i][0] += coord[0];
coords[i][1] += coord[1];
coords[i][2] += coord[2];
@ -447,7 +459,7 @@ void FixDeposit::pre_exchange()
if (flag) {
if (mode == ATOM) atom->avec->create_atom(ntype,coords[m]);
else atom->avec->create_atom(ntype+onemol->type[m],coords[m]);
else atom->avec->create_atom(ntype+onemol[imol].type[m],coords[m]);
n = atom->nlocal - 1;
atom->tag[n] = maxtag_all + m+1;
if (mode == MOLECULE) {
@ -462,7 +474,8 @@ void FixDeposit::pre_exchange()
atom->v[n][0] = vnew[0];
atom->v[n][1] = vnew[1];
atom->v[n][2] = vnew[2];
if (mode == MOLECULE) atom->add_molecule_atom(onemol,m,n,maxtag_all);
if (mode == MOLECULE)
atom->add_molecule_atom(&onemol[imol],m,n,maxtag_all);
for (j = 0; j < nfix; j++)
if (fix[j]->create_attribute) fix[j]->set_arrays(n);
}
@ -473,9 +486,9 @@ void FixDeposit::pre_exchange()
// FixShake::set_molecule stores shake info for molecule
if (rigidflag)
fixrigid->set_molecule(nlocalprev,maxtag_all,coord,vnew,quat);
fixrigid->set_molecule(nlocalprev,maxtag_all,imol,coord,vnew,quat);
else if (shakeflag)
fixshake->set_molecule(nlocalprev,maxtag_all,coord,vnew,quat);
fixshake->set_molecule(nlocalprev,maxtag_all,imol,coord,vnew,quat);
// old code: unsuccessful if no proc performed insertion of an atom
// don't think that check is necessary
@ -504,10 +517,10 @@ void FixDeposit::pre_exchange()
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
error->all(FLERR,"Too many total atoms");
if (mode == MOLECULE) {
atom->nbonds += onemol->nbonds;
atom->nangles += onemol->nangles;
atom->ndihedrals += onemol->ndihedrals;
atom->nimpropers += onemol->nimpropers;
atom->nbonds += onemol[imol].nbonds;
atom->nangles += onemol[imol].nangles;
atom->ndihedrals += onemol[imol].ndihedrals;
atom->nimpropers += onemol[imol].nimpropers;
}
maxtag_all += natom;
if (maxtag_all >= MAXTAGINT)
@ -561,6 +574,7 @@ void FixDeposit::options(int narg, char **arg)
iregion = -1;
idregion = NULL;
mode = ATOM;
molfrac = NULL;
rigidflag = 0;
idrigid = NULL;
shakeflag = 0;
@ -586,17 +600,33 @@ void FixDeposit::options(int narg, char **arg)
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
int imol = atom->find_molecule(arg[iarg+1]);
if (imol == -1)
error->all(FLERR,"Molecule template ID for fix deposit does not exist");
if (atom->molecules[imol]->nset > 1 && comm->me == 0)
error->warning(FLERR,"Molecule template for "
"fix deposit has multiple molecules");
mode = MOLECULE;
onemol = atom->molecules[imol];
nmol = onemol->nset;
delete [] molfrac;
molfrac = new double[nmol];
molfrac[0] = 1.0/nmol;
for (int i = 1; i < nmol-1; i++) molfrac[i] = molfrac[i-1] + 1.0/nmol;
molfrac[nmol-1] = 1.0;
iarg += 2;
} else if (strcmp(arg[iarg],"molfrac") == 0) {
if (mode != MOLECULE) error->all(FLERR,"Illegal fix deposit command");
if (iarg+nmol+1 > narg) error->all(FLERR,"Illegal fix deposit command");
molfrac[0] = force->numeric(FLERR,arg[iarg+1]);
for (int i = 1; i < nmol; i++)
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;
iarg += nmol+1;
} else if (strcmp(arg[iarg],"rigid") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
int n = strlen(arg[iarg+1]) + 1;
@ -730,24 +760,32 @@ void *FixDeposit::extract(const char *str, int &itype)
if (mode == ATOM) {
if (itype == ntype) oneradius = 0.5;
else oneradius = 0.0;
} else {
double *radius = onemol->radius;
int *type = onemol->type;
int natoms = onemol->natoms;
// check radii of matching types in Molecule
// default to 0.5, if radii not defined in Molecule
// same as atom->avec->create_atom(), invoked in pre_exchange()
// find a molecule in template with matching type
oneradius = 0.0;
for (int i = 0; i < natoms; i++)
if (type[i] == itype-ntype) {
if (radius) oneradius = MAX(oneradius,radius[i]);
else oneradius = 0.5;
}
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;
// check radii of matching types in Molecule
// default to 0.5, if radii not defined in Molecule
// same as atom->avec->create_atom(), invoked in pre_exchange()
oneradius = 0.0;
for (int i = 0; i < natoms; i++)
if (type[i] == itype-ntype) {
if (radius) oneradius = MAX(oneradius,radius[i]);
else oneradius = 0.5;
}
}
}
itype = 0;
return &oneradius;
}
return NULL;
}

3
src/MISC/fix_deposit.h
View File

@ -48,7 +48,8 @@ class FixDeposit : public Fix {
char *idrigid,*idshake;
class Molecule *onemol;
int natom;
int natom,nmol;
double *molfrac;
double **coords;
imageint *imageflags;
class Fix *fixrigid,*fixshake;

67
src/RIGID/fix_rigid_small.cpp
View File

@ -178,6 +178,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
error->warning(FLERR,"Molecule template for "
"fix rigid/small has multiple molecules");
onemol = atom->molecules[imol];
nmol = onemol->nset;
iarg += 2;
} else if (strcmp(arg[iarg],"temp") == 0) {
@ -300,17 +301,19 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
// error check and further setup for Molecule template
if (onemol) {
if (onemol->xflag == 0)
error->all(FLERR,"Fix rigid/small molecule must have coordinates");
if (onemol->typeflag == 0)
error->all(FLERR,"Fix rigid/small molecule must have atom types");
for (int i = 0; i < nmol; i++) {
if (onemol[i].xflag == 0)
error->all(FLERR,"Fix rigid/small molecule must have coordinates");
if (onemol[i].typeflag == 0)
error->all(FLERR,"Fix rigid/small molecule must have atom types");
// fix rigid/small uses center, masstotal, COM, inertia of molecule
onemol->compute_center();
onemol->compute_mass();
onemol->compute_com();
onemol->compute_inertia();
// fix rigid/small uses center, masstotal, COM, inertia of molecule
onemol[i].compute_center();
onemol[i].compute_mass();
onemol[i].compute_com();
onemol[i].compute_inertia();
}
}
// set pstat_flag
@ -1549,7 +1552,10 @@ void FixRigidSmall::create_bodies()
MPI_Allreduce(&rsqfar,&maxextent,1,MPI_DOUBLE,MPI_MAX,world);
maxextent = sqrt(maxextent);
if (onemol) maxextent = MAX(maxextent,onemol->maxextent);
if (onemol) {
for (int i = 0; i < nmol; i++)
maxextent = MAX(maxextent,onemol[i].maxextent);
}
// clean up
@ -1716,8 +1722,17 @@ void FixRigidSmall::setup_bodies_static()
}
// extended = 1 if using molecule template with finite-size particles
// require all molecules in template to have consistent radiusflag
if (onemol && onemol->radiusflag) extended = 1;
if (onemol) {
int radiusflag = onemol->radiusflag;
for (i = 1; i < nmol; i++) {
if (onemol->radiusflag != radiusflag)
error->all(FLERR,"Inconsistent use of finite-size particles "
"by molecule template molecules");
}
if (radiusflag) extended = 1;
}
// grow extended arrays and set extended flags for each particle
// orientflag = 4 if any particle stores ellipsoid or tri orientation
@ -2579,7 +2594,7 @@ void FixRigidSmall::set_arrays(int i)
relative to template in Molecule class
------------------------------------------------------------------------- */
void FixRigidSmall::set_molecule(int nlocalprev, tagint tagprev,
void FixRigidSmall::set_molecule(int nlocalprev, tagint tagprev, int imol,
double *xgeom, double *vcm, double *quat)
{
int m;
@ -2592,16 +2607,16 @@ void FixRigidSmall::set_molecule(int nlocalprev, tagint tagprev,
tagint *tag = atom->tag;
for (int i = nlocalprev; i < nlocal; i++) {
bodytag[i] = tagprev + onemol->comatom;
if (tag[i]-tagprev == onemol->comatom) bodyown[i] = nlocal_body;
bodytag[i] = tagprev + onemol[imol].comatom;
if (tag[i]-tagprev == onemol[imol].comatom) bodyown[i] = nlocal_body;
m = tag[i] - tagprev-1;
displace[i][0] = onemol->dxbody[m][0];
displace[i][1] = onemol->dxbody[m][1];
displace[i][2] = onemol->dxbody[m][2];
displace[i][0] = onemol[imol].dxbody[m][0];
displace[i][1] = onemol[imol].dxbody[m][1];
displace[i][2] = onemol[imol].dxbody[m][2];
eflags[i] = 0;
if (onemol->radiusflag) {
if (onemol[imol].radiusflag) {
eflags[i] |= SPHERE;
eflags[i] |= OMEGA;
eflags[i] |= TORQUE;
@ -2610,27 +2625,27 @@ void FixRigidSmall::set_molecule(int nlocalprev, tagint tagprev,
if (bodyown[i] >= 0) {
if (nlocal_body == nmax_body) grow_body();
Body *b = &body[nlocal_body];
b->mass = onemol->masstotal;
b->mass = onemol[imol].masstotal;
// new COM = Q (onemol->xcm - onemol->center) + xgeom
// new COM = Q (onemol[imol].xcm - onemol[imol].center) + xgeom
// Q = rotation matrix associated with quat
MathExtra::quat_to_mat(quat,rotmat);
MathExtra::sub3(onemol->com,onemol->center,ctr2com);
MathExtra::sub3(onemol[imol].com,onemol[imol].center,ctr2com);
MathExtra::matvec(rotmat,ctr2com,ctr2com_rotate);
MathExtra::add3(ctr2com_rotate,xgeom,b->xcm);
b->vcm[0] = vcm[0];
b->vcm[1] = vcm[1];
b->vcm[2] = vcm[2];
b->inertia[0] = onemol->inertia[0];
b->inertia[1] = onemol->inertia[1];
b->inertia[2] = onemol->inertia[2];
b->inertia[0] = onemol[imol].inertia[0];
b->inertia[1] = onemol[imol].inertia[1];
b->inertia[2] = onemol[imol].inertia[2];
// final quat is product of insertion quat and original quat
// true even if insertion rotation was not around COM
MathExtra::quatquat(quat,onemol->quat,b->quat);
MathExtra::quatquat(quat,onemol[imol].quat,b->quat);
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;

3
src/RIGID/fix_rigid_small.h
View File

@ -48,7 +48,7 @@ class FixRigidSmall : public Fix {
void grow_arrays(int);
void copy_arrays(int, int, int);
void set_arrays(int);
void set_molecule(int, tagint, double *, double *, double *);
void set_molecule(int, tagint, int, double *, double *, double *);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
@ -171,6 +171,7 @@ class FixRigidSmall : public Fix {
// molecules added on-the-fly as rigid bodies
class Molecule *onemol;
int nmol;
// class data used by ring communication callbacks

16
src/RIGID/fix_shake.cpp
View File

@ -161,14 +161,18 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
error->warning(FLERR,"Molecule template for "
"fix shake has multiple molecules");
onemol = atom->molecules[imol];
nmol = onemol->nset;
iarg += 2;
} else error->all(FLERR,"Illegal fix shake command");
}
// error check for Molecule template
if (onemol && onemol->shakeflag == 0)
error->all(FLERR,"Fix shake molecule template must have shake info");
if (onemol) {
for (int i = 0; i < nmol; i++)
if (onemol[i].shakeflag == 0)
error->all(FLERR,"Fix shake molecule template must have shake info");
}
// allocate bond and angle distance arrays, indexed from 1 to n
@ -2456,7 +2460,7 @@ void FixShake::update_arrays(int i, int atom_offset)
xgeom,vcm,quat ignored
------------------------------------------------------------------------- */
void FixShake::set_molecule(int nlocalprev, tagint tagprev,
void FixShake::set_molecule(int nlocalprev, tagint tagprev, int imol,
double *xgeom, double *vcm, double *quat)
{
int m,flag;
@ -2465,13 +2469,13 @@ void FixShake::set_molecule(int nlocalprev, tagint tagprev,
if (nlocalprev == nlocal) return;
tagint *tag = atom->tag;
tagint **mol_shake_atom = onemol->shake_atom;
int **mol_shake_type = onemol->shake_type;
tagint **mol_shake_atom = onemol[imol].shake_atom;
int **mol_shake_type = onemol[imol].shake_type;
for (int i = nlocalprev; i < nlocal; i++) {
m = tag[i] - tagprev-1;
flag = shake_flag[i] = onemol->shake_flag[m];
flag = shake_flag[i] = onemol[imol].shake_flag[m];
if (flag == 1) {
shake_atom[i][0] = mol_shake_atom[m][0] + tagprev;

3
src/RIGID/fix_shake.h
View File

@ -40,7 +40,7 @@ class FixShake : public Fix {
void copy_arrays(int, int, int);
void set_arrays(int);
void update_arrays(int, int);
void set_molecule(int, tagint, double *, double *, double *);
void set_molecule(int, tagint, int, double *, double *, double *);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
@ -105,6 +105,7 @@ class FixShake : public Fix {
class Molecule **onemols; // atom style template pointer
class Molecule *onemol; // molecule added on-the-fly
int nmol;
void find_clusters();
int masscheck(double);

2
src/fix.h
View File

@ -125,7 +125,7 @@ class Fix : protected Pointers {
virtual void copy_arrays(int, int, int) {}
virtual void set_arrays(int) {}
virtual void update_arrays(int, int) {}
virtual void set_molecule(int, tagint, double *, double *, double *) {}
virtual void set_molecule(int, tagint, int, double *, double *, double *) {}
virtual int pack_border(int, int *, double *) {return 0;}
virtual int unpack_border(int, int, double *) {return 0;}