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@11918 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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

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;
}