git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@371 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -54,8 +54,8 @@ void CreateAtoms::command(int narg, char **arg)
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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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regionflag = -1;
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nhybrid = 0;
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int regionflag = -1;
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int nhybrid = 0;
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int iarg = 1;
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while (iarg < narg) {
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@ -93,30 +93,42 @@ void CreateAtoms::command(int narg, char **arg)
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// convert 8 corners of my sub-box from box coords to lattice coords
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// min to max = bounding box around the pts in lattice space
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subxlo = domain->subxlo;
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subxhi = domain->subxhi;
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subylo = domain->subylo;
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subyhi = domain->subyhi;
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subzlo = domain->subzlo;
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subzhi = domain->subzhi;
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int triclinic = domain->triclinic;
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double *bboxlo,*bboxhi;
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if (triclinic == 0) {
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bboxlo = domain->sublo;
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bboxhi = domain->subhi;
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} else {
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bboxlo = domain->sublo_bound;
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bboxhi = domain->subhi_bound;
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}
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double xmin,ymin,zmin,xmax,ymax,zmax;
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xmin = ymin = zmin = BIG;
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xmax = ymax = zmax = -BIG;
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domain->lattice->bbox(1,subxlo,subylo,subzlo,xmin,ymin,zmin,xmax,ymax,zmax);
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domain->lattice->bbox(1,subxhi,subylo,subzlo,xmin,ymin,zmin,xmax,ymax,zmax);
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domain->lattice->bbox(1,subxlo,subyhi,subzlo,xmin,ymin,zmin,xmax,ymax,zmax);
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domain->lattice->bbox(1,subxhi,subyhi,subzlo,xmin,ymin,zmin,xmax,ymax,zmax);
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domain->lattice->bbox(1,subxlo,subylo,subzhi,xmin,ymin,zmin,xmax,ymax,zmax);
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domain->lattice->bbox(1,subxhi,subylo,subzhi,xmin,ymin,zmin,xmax,ymax,zmax);
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domain->lattice->bbox(1,subxlo,subyhi,subzhi,xmin,ymin,zmin,xmax,ymax,zmax);
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domain->lattice->bbox(1,subxhi,subyhi,subzhi,xmin,ymin,zmin,xmax,ymax,zmax);
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domain->lattice->bbox(1,bboxlo[0],bboxlo[1],bboxlo[2],
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xmin,ymin,zmin,xmax,ymax,zmax);
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domain->lattice->bbox(1,bboxhi[0],bboxlo[1],bboxlo[2],
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xmin,ymin,zmin,xmax,ymax,zmax);
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domain->lattice->bbox(1,bboxlo[0],bboxhi[1],bboxlo[2],
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xmin,ymin,zmin,xmax,ymax,zmax);
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domain->lattice->bbox(1,bboxhi[0],bboxhi[1],bboxlo[2],
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xmin,ymin,zmin,xmax,ymax,zmax);
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domain->lattice->bbox(1,bboxlo[0],bboxlo[1],bboxhi[2],
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xmin,ymin,zmin,xmax,ymax,zmax);
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domain->lattice->bbox(1,bboxhi[0],bboxlo[1],bboxhi[2],
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xmin,ymin,zmin,xmax,ymax,zmax);
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domain->lattice->bbox(1,bboxlo[0],bboxhi[1],bboxhi[2],
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xmin,ymin,zmin,xmax,ymax,zmax);
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domain->lattice->bbox(1,bboxhi[0],bboxhi[1],bboxhi[2],
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xmin,ymin,zmin,xmax,ymax,zmax);
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// ilo:ihi,jlo:jhi,klo:khi = loop bounds for lattice overlap of my sub-box
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// overlap = any part of a unit cell (face,edge,pt) in common with my sub-box
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// in lattice space, sub-box is a tilted box
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// but bbox of sub-box is aligned with lattice axes
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// ilo:ihi,jlo:jhi,klo:khi = loop bounds for lattice overlap of my subbox
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// overlap = any part of a unit cell (face,edge,pt) in common with my subbox
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// in lattice space, subbox is a tilted box
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// but bbox of subbox is aligned with lattice axes
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// so ilo:khi unit cells should completely tile bounding box
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// decrement lo values if min < 0, since static_cast(-1.5) = -1
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@ -132,25 +144,84 @@ void CreateAtoms::command(int narg, char **arg)
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if (ymin < 0.0) jlo--;
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if (zmin < 0.0) klo--;
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// set bounds for my proc
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// if periodic and I am lo/hi proc, adjust bounds by EPSILON
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// on lower boundary, allows triclinic atoms just outside box to be added
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// on upper boundary, prevents atoms with lower images from being added
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double sublo[3],subhi[3];
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if (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 (domain->xperiodic) {
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if (triclinic && comm->myloc[0] == 0) sublo[0] -= EPSILON;
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if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= EPSILON;
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}
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if (domain->yperiodic) {
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if (triclinic && comm->myloc[1] == 0) sublo[1] -= EPSILON;
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if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= EPSILON;
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}
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if (domain->zperiodic) {
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if (triclinic && comm->myloc[2] == 0) sublo[2] -= EPSILON;
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if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= EPSILON;
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}
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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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// add_atom converts lattice coords to box coords, checks if in my sub-box
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boxxhi = domain->boxxhi;
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boxyhi = domain->boxyhi;
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boxzhi = domain->boxzhi;
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// converts 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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int i,j,k,m;
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for (k = klo; k <= khi; k++)
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for (j = jlo; j <= jhi; j++)
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for (i = ilo; i <= ihi; i++)
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for (m = 0; m < nbasis; m++)
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add_atom(basistype[m],i+basis[m][0],j+basis[m][1],k+basis[m][2]);
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for (m = 0; m < nbasis; m++) {
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x[0] = i + basis[m][0];
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x[1] = j + basis[m][1];
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x[2] = k + basis[m][2];
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// convert from lattice coords to box coords
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domain->lattice->lattice2box(x[0],x[1],x[2]);
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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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// test if atom is in my subbox
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if (triclinic) {
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domain->x2lamda(x,lamda);
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coord = lamda;
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} else coord = x;
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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]) continue;
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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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}
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// clean up
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delete [] basistype;
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@ -189,36 +260,3 @@ void CreateAtoms::command(int narg, char **arg)
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}
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}
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}
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/* ----------------------------------------------------------------------
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add an atom of type at lattice coords x,y,z if it meets all criteria
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------------------------------------------------------------------------- */
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void CreateAtoms::add_atom(int ntype, double x, double y, double z)
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{
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// convert from lattice coords to box coords
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domain->lattice->lattice2box(x,y,z);
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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,y,z)) return;
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// test if atom is in my subbox
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if (x < subxlo || x >= subxhi ||
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y < subylo || y >= subyhi ||
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z < subzlo || z >= subzhi) return;
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// don't put atoms within EPSILON of upper periodic boundary
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// else may overlap image atom at lower boundary
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if (domain->xperiodic && fabs(x-boxxhi) < EPSILON) return;
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if (domain->yperiodic && fabs(y-boxyhi) < EPSILON) return;
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if (domain->zperiodic && fabs(z-boxzhi) < EPSILON) return;
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// add the atom to my list of atoms
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atom->avec->create_atom(ntype,x,y,z,nhybrid);
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}
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