git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@622 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -17,7 +17,6 @@
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#include "create_atoms.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "atom_vec_hybrid.h"
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#include "comm.h"
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#include "domain.h"
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#include "lattice.h"
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@ -30,6 +29,8 @@ using namespace LAMMPS_NS;
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#define BIG 1.0e30
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#define EPSILON 1.0e-6
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enum{BOX,REGION,SINGLE};
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/* ---------------------------------------------------------------------- */
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CreateAtoms::CreateAtoms(LAMMPS *lmp) : Pointers(lmp) {}
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@ -40,36 +41,48 @@ void CreateAtoms::command(int narg, char **arg)
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{
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if (domain->box_exist == 0)
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error->all("Create_atoms command before simulation box is defined");
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if (domain->lattice == NULL)
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error->all("Cannot create atoms with undefined lattice");
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// parse arguments
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int nbasis = domain->lattice->nbasis;
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int *basistype = new int[nbasis];
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if (narg < 1) error->all("Illegal create_atoms command");
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int itype = atoi(arg[0]);
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if (narg < 2) error->all("Illegal create_atoms command");
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itype = atoi(arg[0]);
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if (itype <= 0 || itype > atom->ntypes)
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error->all("Invalid atom type in create_atoms command");
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for (int i = 0; i < nbasis; i++) basistype[i] = itype;
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int regionflag = -1;
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int nhybrid = 0;
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int iarg;
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if (strcmp(arg[1],"box") == 0) {
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style = BOX;
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iarg = 2;
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} else if (strcmp(arg[1],"region") == 0) {
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style = REGION;
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if (narg < 3) error->all("Illegal create_atoms command");
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int iregion = domain->find_region(arg[2]);
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if (iregion == -1) error->all("Create_atoms region ID does not exist");
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iarg = 3;;
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} else if (strcmp(arg[1],"single") == 0) {
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style = SINGLE;
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if (narg < 5) error->all("Illegal create_atoms command");
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xone[0] = atof(arg[2]);
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xone[1] = atof(arg[3]);
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xone[2] = atof(arg[4]);
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iarg = 5;
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} else error->all("Illegal create_atoms command");
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// process optional keywords
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int scaleflag = 1;
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if (domain->lattice) {
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nbasis = domain->lattice->nbasis;
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basistype = new int[nbasis];
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for (int i = 0; i < nbasis; i++) basistype[i] = itype;
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}
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int iarg = 1;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"region") == 0) {
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if (iarg+2 > narg) error->all("Illegal create_atoms command");
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int iregion;
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for (iregion = 0; iregion < domain->nregion; iregion++)
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if (strcmp(arg[iarg+1],domain->regions[iregion]->id) == 0) break;
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if (iregion == domain->nregion)
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error->all("Create_atoms region ID does not exist");
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regionflag = iregion;
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iarg += 2;
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} else if (strcmp(arg[iarg],"basis") == 0) {
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if (strcmp(arg[iarg],"basis") == 0) {
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if (iarg+3 > narg) error->all("Illegal create_atoms command");
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if (domain->lattice == NULL)
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error->all("Cannot create atoms with undefined lattice");
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int ibasis = atoi(arg[iarg+1]);
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itype = atoi(arg[iarg+2]);
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if (ibasis <= 0 || ibasis > nbasis ||
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@ -77,19 +90,121 @@ void CreateAtoms::command(int narg, char **arg)
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error->all("Illegal create_atoms command");
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basistype[ibasis-1] = itype;
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iarg += 3;
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} else if (strcmp(arg[iarg],"hybrid") == 0) {
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if (iarg+3 > narg) error->all("Illegal create_atoms command");
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AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) atom->avec;
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int ihybrid;
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for (ihybrid = 0; ihybrid < avec_hybrid->nstyles; ihybrid++)
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if (strcmp(avec_hybrid->keywords[ihybrid],arg[iarg+1]) == 0) break;
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if (ihybrid == avec_hybrid->nstyles)
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error->all("Create atoms hybrid sub-style does not exist");
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nhybrid = ihybrid;
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iarg += 3;
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} else if (strcmp(arg[iarg],"units") == 0) {
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if (iarg+2 > narg) error->all("Illegal create_atoms command");
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if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
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else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
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else error->all("Illegal create_atoms command");
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iarg += 2;
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} else error->all("Illegal create_atoms command");
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}
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// demand lattice be defined
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// else setup scaling for single atom
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// could use domain->lattice->lattice2box() to do conversion of
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// lattice to box, but not consistent with other uses of units=lattice
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// triclinic remapping occurs in add_single()
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if (style == BOX || style == REGION) {
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if (domain->lattice == NULL)
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error->all("Cannot create atoms with undefined lattice");
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} else if (scaleflag == 1) {
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if (domain->lattice == NULL)
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error->all("Cannot create atoms with undefined lattice");
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xone[0] *= domain->lattice->xlattice;
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xone[1] *= domain->lattice->ylattice;
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xone[2] *= domain->lattice->zlattice;
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}
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// add atoms
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double natoms_previous = atom->natoms;
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int nlocal_previous = atom->nlocal;
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if (style == SINGLE) add_single();
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else add_many();
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// clean up
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if (domain->lattice) delete [] basistype;
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// new total # of atoms
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double rlocal = atom->nlocal;
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MPI_Allreduce(&rlocal,&atom->natoms,1,MPI_DOUBLE,MPI_SUM,world);
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// print status
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if (comm->me == 0) {
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if (screen)
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fprintf(screen,"Created %.15g atoms\n",atom->natoms-natoms_previous);
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if (logfile)
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fprintf(logfile,"Created %.15g atoms\n",atom->natoms-natoms_previous);
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}
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// reset simulation now that more atoms are defined
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// add tags for newly created atoms if possible
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// if global map exists, reset it
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// if a molecular system, set nspecial to 0 for new atoms
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if (atom->natoms > MAXATOMS) atom->tag_enable = 0;
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if (atom->natoms <= MAXATOMS) atom->tag_extend();
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if (atom->map_style) {
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atom->map_init();
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atom->map_set();
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}
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if (atom->molecular) {
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int **nspecial = atom->nspecial;
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for (int i = nlocal_previous; i < atom->nlocal; i++) {
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nspecial[i][0] = 0;
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nspecial[i][1] = 0;
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nspecial[i][2] = 0;
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}
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}
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}
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/* ----------------------------------------------------------------------
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add single atom with coords at xone if it's in my sub-box
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if triclinic, xone is in lamda coords
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------------------------------------------------------------------------- */
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void CreateAtoms::add_single()
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{
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double sublo[3],subhi[3];
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if (domain->triclinic == 0) {
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sublo[0] = domain->sublo[0]; subhi[0] = domain->subhi[0];
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sublo[1] = domain->sublo[1]; subhi[1] = domain->subhi[1];
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sublo[2] = domain->sublo[2]; subhi[2] = domain->subhi[2];
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} else {
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sublo[0] = domain->sublo_lamda[0]; subhi[0] = domain->subhi_lamda[0];
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sublo[1] = domain->sublo_lamda[1]; subhi[1] = domain->subhi_lamda[1];
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sublo[2] = domain->sublo_lamda[2]; subhi[2] = domain->subhi_lamda[2];
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}
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// if triclinic, convert to lamda coords (0-1)
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double lamda[3],*coord;
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if (domain->triclinic) {
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domain->x2lamda(xone,lamda);
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coord = lamda;
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} else coord = xone;
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// if atom is in my subbox, create it
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if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
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coord[1] >= sublo[1] && coord[1] < subhi[1] &&
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coord[2] >= sublo[2] && coord[2] < subhi[2])
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atom->avec->create_atom(itype,xone);
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}
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/* ----------------------------------------------------------------------
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add many atoms by looping over lattice
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------------------------------------------------------------------------- */
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void CreateAtoms::add_many()
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{
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// convert 8 corners of my subdomain from box coords to lattice coords
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// for orthogonal, use corner pts of my subbox
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// for triclinic, use bounding box of my subbox
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@ -176,12 +291,9 @@ void CreateAtoms::command(int narg, char **arg)
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// iterate on 3d periodic lattice using loop bounds
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// invoke add_atom for nbasis atoms in each unit cell
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// converts lattice coords to box coords
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// convert lattice coords to box coords
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// add atom if it meets all criteria
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double natoms_previous = atom->natoms;
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int nlocal_previous = atom->nlocal;
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double **basis = domain->lattice->basis;
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double x[3],lamda[3];
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double *coord;
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@ -202,8 +314,8 @@ void CreateAtoms::command(int narg, char **arg)
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// if a region was specified, test if atom is in it
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if (regionflag >= 0)
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if (!domain->regions[regionflag]->match(x[0],x[1],x[2])) continue;
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if (style == REGION)
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if (!domain->regions[iregion]->match(x[0],x[1],x[2])) continue;
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// test if atom is in my subbox
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@ -218,45 +330,6 @@ void CreateAtoms::command(int narg, char **arg)
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// add the atom to my list of atoms
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atom->avec->create_atom(basistype[m],x,nhybrid);
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atom->avec->create_atom(basistype[m],x);
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}
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// clean up
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delete [] basistype;
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// new total # of atoms
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double rlocal = atom->nlocal;
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MPI_Allreduce(&rlocal,&atom->natoms,1,MPI_DOUBLE,MPI_SUM,world);
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// print status
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if (comm->me == 0) {
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if (screen)
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fprintf(screen,"Created %.15g atoms\n",atom->natoms-natoms_previous);
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if (logfile)
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fprintf(logfile,"Created %.15g atoms\n",atom->natoms-natoms_previous);
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}
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// reset simulation now that more atoms are defined
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// add tags for newly created atoms if possible
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// if global map exists, reset it
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// if a molecular system, set nspecial to 0 for new atoms
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if (atom->natoms > MAXATOMS) atom->tag_enable = 0;
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if (atom->natoms <= MAXATOMS) atom->tag_extend();
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if (atom->map_style) {
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atom->map_init();
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atom->map_set();
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}
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if (atom->molecular) {
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int **nspecial = atom->nspecial;
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for (i = nlocal_previous; i < atom->nlocal; i++) {
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nspecial[i][0] = 0;
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nspecial[i][1] = 0;
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nspecial[i][2] = 0;
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}
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}
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}
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