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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11192 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-01-08 20:38:38 +00:00
parent 1924cc47bf
commit 21833c99de
8 changed files with 272 additions and 69 deletions
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4
src/GRANULAR/fix_pour.cpp
View File

@ -118,7 +118,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
if (mode == MOLECULE) {
if (atom->molecule_flag == 0)
error->all(FLERR,"Fix pour requires atom attribute molecule");
error->all(FLERR,"Fix pour mol requires atom attribute molecule");
if (onemol->xflag == 0)
error->all(FLERR,"Fix pour molecule must have coordinates");
if (onemol->typeflag == 0)
@ -587,7 +587,7 @@ void FixPour::pre_exchange()
else atom->avec->create_atom(ntype+onemol->type[m],coords[m]);
int n = atom->nlocal - 1;
atom->tag[n] = maxtag_all + m+1;
if (mode == MOLECULE) atom->molecule[n] = maxmol_all;
if (mode == MOLECULE) atom->molecule[n] = maxmol_all+1;
atom->mask[n] = 1 | groupbit;
atom->image[n] = imageflags[m];
atom->v[n][0] = vnew[0];

4
src/MISC/fix_deposit.cpp
View File

@ -100,7 +100,7 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
if (mode == MOLECULE) {
if (atom->molecule_flag == 0)
error->all(FLERR,"Fix deposit requires atom attribute molecule");
error->all(FLERR,"Fix deposit mol requires atom attribute molecule");
if (onemol->xflag == 0)
error->all(FLERR,"Fix deposit molecule must have coordinates");
if (onemol->typeflag == 0)
@ -444,7 +444,7 @@ void FixDeposit::pre_exchange()
else atom->avec->create_atom(ntype+onemol->type[m],coords[m]);
n = atom->nlocal - 1;
atom->tag[n] = maxtag_all + m+1;
if (mode == MOLECULE) atom->molecule[n] = maxmol_all;
if (mode == MOLECULE) atom->molecule[n] = maxmol_all+1;
atom->mask[n] = 1 | groupbit;
atom->image[n] = imageflags[m];
atom->v[n][0] = vnew[0];

11
src/atom.cpp
View File

@ -1205,7 +1205,8 @@ int Atom::find_molecule(char *id)
}
/* ----------------------------------------------------------------------
add info for iatom from molecule template onemol to current atom ilocal
add info to current atom ilocal from molecule template onemol and its iatom
offset = atom ID preceeding IDs of atoms in this molecule
------------------------------------------------------------------------- */
void Atom::add_molecule_atom(Molecule *onemol, int iatom,
@ -1255,7 +1256,15 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom,
}
}
// error check against maxspecial in case user has not done one of these:
// create_box extra/special/per/atom N
// read_data extra special per atom N
// special_bonds extra N
// if explicitly used special_bonds, may not have maintained extra
if (onemol->specialflag) {
if (onemol->maxspecial > maxspecial)
error->one(FLERR,"Molecule file special bond counts are too large");
nspecial[ilocal][0] = onemol->nspecial[iatom][0];
nspecial[ilocal][1] = onemol->nspecial[iatom][1];
int n = nspecial[ilocal][2] = onemol->nspecial[iatom][2];

287
src/create_atoms.cpp
View File

@ -17,22 +17,29 @@
#include "create_atoms.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "comm.h"
#include "irregular.h"
#include "modify.h"
#include "force.h"
#include "fix.h"
#include "domain.h"
#include "lattice.h"
#include "region.h"
#include "random_park.h"
#include "random_mars.h"
#include "math_extra.h"
#include "math_const.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define BIG 1.0e30
#define EPSILON 1.0e-6
enum{BOX,REGION,SINGLE,RANDOM};
enum{ATOM,MOLECULE};
/* ---------------------------------------------------------------------- */
@ -51,9 +58,7 @@ void CreateAtoms::command(int narg, char **arg)
// parse arguments
if (narg < 2) error->all(FLERR,"Illegal create_atoms command");
itype = force->inumeric(FLERR,arg[0]);
if (itype <= 0 || itype > atom->ntypes)
error->all(FLERR,"Invalid atom type in create_atoms command");
ntype = force->inumeric(FLERR,arg[0]);
int iarg;
if (strcmp(arg[1],"box") == 0) {
@ -93,18 +98,19 @@ void CreateAtoms::command(int narg, char **arg)
int scaleflag = 1;
remapflag = 0;
mode = ATOM;
int molseed;
nbasis = domain->lattice->nbasis;
basistype = new int[nbasis];
for (int i = 0; i < nbasis; i++) basistype[i] = itype;
for (int i = 0; i < nbasis; i++) basistype[i] = ntype;
while (iarg < narg) {
if (strcmp(arg[iarg],"basis") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal create_atoms command");
int ibasis = force->inumeric(FLERR,arg[iarg+1]);
itype = force->inumeric(FLERR,arg[iarg+2]);
if (ibasis <= 0 || ibasis > nbasis ||
itype <= 0 || itype > atom->ntypes)
int itype = force->inumeric(FLERR,arg[iarg+2]);
if (ibasis <= 0 || ibasis > nbasis || itype <= 0 || itype > atom->ntypes)
error->all(FLERR,"Invalid basis setting in create_atoms command");
basistype[ibasis-1] = itype;
iarg += 3;
@ -114,6 +120,15 @@ void CreateAtoms::command(int narg, char **arg)
else if (strcmp(arg[iarg+1],"no") == 0) remapflag = 0;
else error->all(FLERR,"Illegal create_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix create_atoms command");
int imol = atom->find_molecule(arg[iarg+1]);
if (imol == -1)
error->all(FLERR,"Molecule ID for create_atoms does not exist");
mode = MOLECULE;
onemol = atom->molecules[imol];
molseed = force->inumeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
@ -125,11 +140,36 @@ void CreateAtoms::command(int narg, char **arg)
// error checks
if (mode == ATOM && (ntype <= 0 || ntype > atom->ntypes))
error->all(FLERR,"Invalid atom type in create_atoms command");
if (style == RANDOM) {
if (nrandom < 0) error->all(FLERR,"Illegal create_atoms command");
if (seed <= 0) error->all(FLERR,"Illegal create_atoms command");
}
// error check and further setup for mode = MOLECULE
ranmol = NULL;
if (mode == MOLECULE) {
if (atom->molecule_flag == 0)
error->all(FLERR,"Create_atoms mol requires atom attribute molecule");
if (onemol->xflag == 0)
error->all(FLERR,"Create_atoms molecule must have coordinates");
if (onemol->typeflag == 0)
error->all(FLERR,"Create_atoms molecule must have atom types");
if (ntype+onemol->maxtype <= 0 || ntype+onemol->maxtype > atom->ntypes)
error->all(FLERR,"Invalid atom type in create_atoms mol command");
// create_atoms uses geoemetric center of molecule for insertion
onemol->compute_center();
// molecule random number generator, same for all procs
ranmol = new RanMars(lmp,molseed+comm->me);
}
// demand non-none lattice be defined for BOX and REGION
// else setup scaling for SINGLE and RANDOM
// could use domain->lattice->lattice2box() to do conversion of
@ -192,7 +232,7 @@ void CreateAtoms::command(int narg, char **arg)
}
}
// add atoms in one of 3 ways
// add atoms/molecules in one of 3 ways
bigint natoms_previous = atom->natoms;
int nlocal_previous = atom->nlocal;
@ -211,16 +251,148 @@ void CreateAtoms::command(int narg, char **arg)
fix->set_arrays(i);
}
// clean up
if (domain->lattice) delete [] basistype;
// new total # of atoms
// new total # of atoms and error check
// for MOLECULE mode, require atom IDs
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
error->all(FLERR,"Too many total atoms");
if (atom->natoms > MAXSMALLINT) {
if (mode == ATOM) {
if (comm->me == 0)
error->warning(FLERR,"Total atom count exceeds ID limit, "
"atoms will not have individual IDs");
atom->tag_enable = 0;
} else error->all(FLERR,"Total atom count exceeds ID limit");
}
// for ATOM mode:
// add IDs for newly created atoms if IDs are still enabled
// if global map exists, reset it
if (mode == ATOM) {
if (atom->natoms <= MAXSMALLINT) atom->tag_extend();
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
}
// for MOLECULE mode:
// set atom and molecule IDs for created atoms
// send atoms to new owning procs via irregular comm
// since not all created atoms will be within my sub-domain
if (mode == MOLECULE) {
// add atom IDs for newly created atoms and reset global map
// global map must exist since atom->molecular is required to be set
atom->tag_extend();
atom->nghost = 0;
atom->map_init();
atom->map_set();
// maxmol = max molecule ID across all procs, for previous atoms
int *molecule = atom->molecule;
int max = 0;
for (int i = 0; i < nlocal_previous; i++) max = MAX(max,molecule[i]);
int maxmol;
MPI_Allreduce(&max,&maxmol,1,MPI_INT,MPI_MAX,world);
// molcreate = # of molecules I created
// moloffset = max molecule ID for all molecules owned by previous procs
// including molecules existing before this creation
int molcreate = (atom->nlocal - nlocal_previous) / onemol->natoms;
int moloffset;
MPI_Scan(&molcreate,&moloffset,1,MPI_INT,MPI_SUM,world);
moloffset = moloffset - molcreate + maxmol;
// loop over molecules I created
// set their molecule ID
// reset their bond,angle,etc and special values
int natoms = onemol->natoms;
int *tag = atom->tag;
int *num_bond = atom->num_bond;
int *num_angle = atom->num_angle;
int *num_dihedral = atom->num_dihedral;
int *num_improper = atom->num_improper;
int **bond_atom = atom->bond_atom;
int **angle_atom1 = atom->angle_atom1;
int **angle_atom2 = atom->angle_atom2;
int **angle_atom3 = atom->angle_atom3;
int **dihedral_atom1 = atom->dihedral_atom1;
int **dihedral_atom2 = atom->dihedral_atom2;
int **dihedral_atom3 = atom->dihedral_atom3;
int **dihedral_atom4 = atom->dihedral_atom4;
int **improper_atom1 = atom->improper_atom1;
int **improper_atom2 = atom->improper_atom2;
int **improper_atom3 = atom->improper_atom3;
int **improper_atom4 = atom->improper_atom4;
int **nspecial = atom->nspecial;
int **special = atom->special;
int ilocal = nlocal_previous;
for (int i = 0; i < molcreate; i++) {
int offset = tag[ilocal]-1;
for (int m = 0; m < natoms; m++) {
molecule[ilocal] = moloffset + i+1;
if (onemol->bondflag)
for (int j = 0; j < num_bond[ilocal]; j++)
bond_atom[ilocal][j] += offset;
if (onemol->angleflag)
for (int j = 0; j < num_angle[ilocal]; j++) {
angle_atom1[ilocal][j] += offset;
angle_atom2[ilocal][j] += offset;
angle_atom3[ilocal][j] += offset;
}
if (onemol->dihedralflag)
for (int j = 0; j < num_dihedral[ilocal]; j++) {
dihedral_atom1[ilocal][j] += offset;
dihedral_atom2[ilocal][j] += offset;
dihedral_atom3[ilocal][j] += offset;
dihedral_atom4[ilocal][j] += offset;
}
if (onemol->improperflag)
for (int j = 0; j < num_improper[ilocal]; j++) {
improper_atom1[ilocal][j] += offset;
improper_atom2[ilocal][j] += offset;
improper_atom3[ilocal][j] += offset;
improper_atom4[ilocal][j] += offset;
}
if (onemol->specialflag)
for (int j = 0; j < nspecial[ilocal][2]; j++)
special[ilocal][j] += offset;
ilocal++;
}
}
// perform irregular comm to migrate atoms to new owning procs
double **x = atom->x;
tagint *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->reset_box();
Irregular *irregular = new Irregular(lmp);
irregular->migrate_atoms();
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
}
// clean up
delete ranmol;
if (domain->lattice) delete [] basistype;
// print status
@ -232,37 +404,6 @@ void CreateAtoms::command(int narg, char **arg)
fprintf(logfile,"Created " BIGINT_FORMAT " atoms\n",
atom->natoms-natoms_previous);
}
// reset simulation now that more atoms are defined
// add tags for newly created atoms if possible
// if global map exists, reset it
// change these to MAXTAGINT when allow tagint = bigint
if (atom->natoms > MAXSMALLINT) {
if (comm->me == 0)
error->warning(FLERR,"Total atom count exceeds ID limit, "
"atoms will not have individual IDs");
atom->tag_enable = 0;
}
if (atom->natoms <= MAXSMALLINT) atom->tag_extend();
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
// if a molecular system, set nspecial to 0 for new atoms
// NOTE: 31May12, don't think this is needed, avec->create_atom() does it
//if (atom->molecular) {
// int **nspecial = atom->nspecial;
// for (int i = nlocal_previous; i < atom->nlocal; i++) {
// nspecial[i][0] = 0;
// nspecial[i][1] = 0;
// nspecial[i][2] = 0;
// }
//}
}
/* ----------------------------------------------------------------------
@ -292,8 +433,10 @@ void CreateAtoms::add_single()
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2])
atom->avec->create_atom(itype,xone);
coord[2] >= sublo[2] && coord[2] < subhi[2]) {
if (mode == ATOM) atom->avec->create_atom(ntype,xone);
else add_molecule(xone);
}
}
@ -372,8 +515,10 @@ void CreateAtoms::add_random()
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2])
atom->avec->create_atom(itype,xone);
coord[2] >= sublo[2] && coord[2] < subhi[2]) {
if (mode == ATOM) atom->avec->create_atom(ntype,xone);
else add_molecule(xone);
}
}
// clean-up
@ -445,7 +590,7 @@ void CreateAtoms::add_lattice()
// iterate on 3d periodic lattice of unit cells using loop bounds
// iterate on nbasis atoms in each unit cell
// convert lattice coords to box coords
// add atom if it meets all criteria
// add atom or molecule (on each basis point) if it meets all criteria
double **basis = domain->lattice->basis;
double x[3],lamda[3];
@ -481,8 +626,46 @@ void CreateAtoms::add_lattice()
coord[1] < sublo[1] || coord[1] >= subhi[1] ||
coord[2] < sublo[2] || coord[2] >= subhi[2]) continue;
// add the atom to my list of atoms
// add the atom or entire molecule to my list of atoms
atom->avec->create_atom(basistype[m],x);
if (mode == ATOM) atom->avec->create_atom(basistype[m],x);
else add_molecule(x);
}
}
/* ----------------------------------------------------------------------
add a randomly rotated molecule with its center at center
------------------------------------------------------------------------- */
void CreateAtoms::add_molecule(double *center)
{
int n;
double r[3],rotmat[3][3],quat[4],xnew[3];
if (domain->dimension == 3) {
r[0] = ranmol->uniform() - 0.5;
r[1] = ranmol->uniform() - 0.5;
r[2] = ranmol->uniform() - 0.5;
} else {
r[0] = r[1] = 0.0;
r[2] = 1.0;
}
double theta = ranmol->uniform() * MY_2PI;
MathExtra::norm3(r);
MathExtra::axisangle_to_quat(r,theta,quat);
MathExtra::quat_to_mat(quat,rotmat);
// create atoms in molecule with atom ID = 0 and mol ID = 0
// reset in caller after all moleclues created by all procs
// pass add_molecule_atom an offset of 0 since don't know
// max tag of atoms in previous molecules at this point
int natoms = onemol->natoms;
for (int m = 0; m < natoms; m++) {
MathExtra::matvec(rotmat,onemol->dx[m],xnew);
MathExtra::add3(xnew,center,xnew);
atom->avec->create_atom(ntype+onemol->type[m],xnew);
n = atom->nlocal - 1;
atom->add_molecule_atom(onemol,m,n,0);
}
}

6
src/create_atoms.h
View File

@ -30,17 +30,21 @@ class CreateAtoms : protected Pointers {
void command(int, char **);
private:
int itype,style,nregion,nbasis,nrandom,seed;
int ntype,style,mode,nregion,nbasis,nrandom,seed;
int *basistype;
double xone[3];
int remapflag;
class Molecule *onemol;
class RanMars *ranmol;
int triclinic;
double sublo[3],subhi[3]; // epsilon-extended proc sub-box for adding atoms
void add_single();
void add_random();
void add_lattice();
void add_molecule(double *);
};
}

20
src/create_box.cpp
View File

@ -108,54 +108,58 @@ void CreateBox::command(int narg, char **arg)
int iarg = 2;
while (iarg < narg) {
if (strcmp(arg[iarg],"bond types") == 0) {
if (strcmp(arg[iarg],"bond/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
if (!atom->avec->bonds_allow)
error->all(FLERR,"No bonds allowed with this atom style");
atom->nbondtypes = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"angle types") == 0) {
} else if (strcmp(arg[iarg],"angle/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
if (!atom->avec->angles_allow)
error->all(FLERR,"No angles allowed with this atom style");
atom->nangletypes = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"dihedral types") == 0) {
} else if (strcmp(arg[iarg],"dihedral/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
if (!atom->avec->dihedrals_allow)
error->all(FLERR,"No dihedrals allowed with this atom style");
atom->ndihedraltypes = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"improper types") == 0) {
} else if (strcmp(arg[iarg],"improper/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
if (!atom->avec->impropers_allow)
error->all(FLERR,"No impropers allowed with this atom style");
atom->nimpropertypes = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"extra bond per atom") == 0) {
} else if (strcmp(arg[iarg],"extra/bond/per/atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
if (!atom->avec->bonds_allow)
error->all(FLERR,"No bonds allowed with this atom style");
atom->bond_per_atom = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"extra angle per atom") == 0) {
} else if (strcmp(arg[iarg],"extra/angle/per/atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
if (!atom->avec->angles_allow)
error->all(FLERR,"No angles allowed with this atom style");
atom->angle_per_atom = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"extra dihedral per atom") == 0) {
} else if (strcmp(arg[iarg],"extra/dihedral/per/atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
if (!atom->avec->dihedrals_allow)
error->all(FLERR,"No dihedrals allowed with this atom style");
atom->dihedral_per_atom = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"extra improper per atom") == 0) {
} else if (strcmp(arg[iarg],"extra/improper/per/atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
if (!atom->avec->impropers_allow)
error->all(FLERR,"No impropers allowed with this atom style");
atom->improper_per_atom = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"extra/special/per/atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
atom->maxspecial = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal create_box command");
}

5
src/molecule.cpp
View File

@ -482,12 +482,13 @@ void Molecule::read(int flag)
error->all(FLERR,"Molecule file bond/angle/etc counts "
"per atom are too large");
// test for maxspecial > atom->maxspecial is done when molecules added
// in Atom::add_molecule_atom()
if ((nspecialflag && !specialflag) || (!nspecialflag && specialflag))
error->all(FLERR,"Molecule file needs both Special Bond sections");
if (specialflag && !bondflag)
error->all(FLERR,"Molecule file has special flags but no bonds");
if (maxspecial > atom->maxspecial)
error->all(FLERR,"Molecule file special bond counts are too large");
if ((shakeflagflag || shakeatomflag || shaketypeflag) && !shakeflag)
error->all(FLERR,"Molecule file shake info is incomplete");

2
src/read_data.cpp
View File

@ -508,6 +508,8 @@ void ReadData::header(int flag)
sscanf(line,"%d",&atom->extra_dihedral_per_atom);
else if (strstr(line,"extra improper per atom"))
sscanf(line,"%d",&atom->extra_improper_per_atom);
else if (strstr(line,"extra special per atom"))
sscanf(line,"%d",&force->special_extra);
else if (strstr(line,"xlo xhi"))
sscanf(line,"%lg %lg",&domain->boxlo[0],&domain->boxhi[0]);