git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8201 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
@ -148,7 +148,52 @@ void CreateAtoms::command(int narg, char **arg)
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xone[2] *= domain->lattice->zlattice;
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}
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// add atoms
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// set bounds for my proc in sublo[3] & subhi[3]
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// if periodic:
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// should create exactly 1 atom when 2 images are both "on" the boundary
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// either image may be slightly inside/outside true box due to round-off
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// if I am lo proc, decrement lower bound by EPSILON
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// this will insure lo image is created
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// if I am hi proc, decrement upper bound by 2.0*EPSILON
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// this will insure hi image is not created
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// thus insertion box is EPSILON smaller than true box
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// and is shifted away from true boundary
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// which is where atoms are likely to be generated
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triclinic = domain->triclinic;
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double epsilon[3];
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if (triclinic) epsilon[0] = epsilon[1] = epsilon[2] = EPSILON;
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else {
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epsilon[0] = domain->prd[0] * EPSILON;
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epsilon[1] = domain->prd[1] * EPSILON;
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epsilon[2] = domain->prd[2] * EPSILON;
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}
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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 (comm->myloc[0] == 0) sublo[0] -= epsilon[0];
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if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= 2.0*epsilon[0];
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}
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if (domain->yperiodic) {
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if (comm->myloc[1] == 0) sublo[1] -= epsilon[1];
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if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= 2.0*epsilon[1];
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}
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if (domain->zperiodic) {
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if (comm->myloc[2] == 0) sublo[2] -= epsilon[2];
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if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= 2.0*epsilon[2];
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}
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// add atoms in one of 3 ways
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bigint natoms_previous = atom->natoms;
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int nlocal_previous = atom->nlocal;
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@ -222,8 +267,6 @@ void CreateAtoms::command(int narg, char **arg)
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void CreateAtoms::add_single()
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{
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double *sublo,*subhi;
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// remap atom if requested
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if (remapflag) {
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@ -231,20 +274,10 @@ void CreateAtoms::add_single()
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domain->remap(xone,imagetmp);
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}
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// sub-domain bounding box, in lamda units if triclinic
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if (domain->triclinic == 0) {
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sublo = domain->sublo;
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subhi = domain->subhi;
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} else {
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sublo = domain->sublo_lamda;
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subhi = domain->subhi_lamda;
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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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if (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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@ -266,7 +299,7 @@ void CreateAtoms::add_random()
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{
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double xlo,ylo,zlo,xhi,yhi,zhi,zmid;
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double lamda[3],*coord;
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double *sublo,*subhi,*boxlo,*boxhi;
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double *boxlo,*boxhi;
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// random number generator, same for all procs
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@ -276,7 +309,7 @@ void CreateAtoms::add_random()
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// in real units, even if triclinic
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// only limit bbox by region if its bboxflag is set (interior region)
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if (domain->triclinic == 0) {
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if (triclinic == 0) {
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xlo = domain->boxlo[0]; xhi = domain->boxhi[0];
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ylo = domain->boxlo[1]; yhi = domain->boxhi[1];
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zlo = domain->boxlo[2]; zhi = domain->boxhi[2];
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@ -286,6 +319,8 @@ void CreateAtoms::add_random()
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ylo = domain->boxlo_bound[1]; yhi = domain->boxhi_bound[1];
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zlo = domain->boxlo_bound[2]; zhi = domain->boxhi_bound[2];
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zmid = zlo + 0.5*(zhi-zlo);
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boxlo = domain->boxlo_lamda;
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boxhi = domain->boxhi_lamda;
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}
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if (nregion >= 0 && domain->regions[nregion]->bboxflag) {
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@ -297,18 +332,6 @@ void CreateAtoms::add_random()
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zhi = MIN(zhi,domain->regions[nregion]->extent_zhi);
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}
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// sub-domain bounding box, in lamda units if triclinic
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if (domain->triclinic == 0) {
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sublo = domain->sublo;
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subhi = domain->subhi;
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} else {
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sublo = domain->sublo_lamda;
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subhi = domain->subhi_lamda;
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boxlo = domain->boxlo_lamda;
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boxhi = domain->boxhi_lamda;
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}
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// generate random positions for each new atom within bounding box
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// iterate until atom is within region and triclinic simulation box
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// if final atom position is in my subbox, create it
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@ -325,7 +348,7 @@ void CreateAtoms::add_random()
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if (nregion >= 0 &&
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domain->regions[nregion]->match(xone[0],xone[1],xone[2]) == 0)
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valid = 0;
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if (domain->triclinic) {
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if (triclinic) {
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domain->x2lamda(xone,lamda);
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coord = lamda;
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if (coord[0] < boxlo[0] || coord[0] >= boxhi[0] ||
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@ -360,7 +383,6 @@ void CreateAtoms::add_lattice()
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// for triclinic, use bounding box of my subbox
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// xyz min to max = bounding box around the domain corners in lattice space
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int triclinic = domain->triclinic;
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double bboxlo[3],bboxhi[3];
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if (triclinic == 0) {
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@ -411,50 +433,6 @@ void CreateAtoms::add_lattice()
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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:
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// should create exactly 1 atom when 2 images are both "on" the boundary
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// either image may be slightly inside/outside true box due to round-off
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// if I am lo proc, decrement lower bound by EPSILON
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// this will insure lo image is created
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// if I am hi proc, decrement upper bound by 2.0*EPSILON
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// this will insure hi image is not created
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// thus insertion box is EPSILON smaller than true box
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// and is shifted away from true boundary
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// which is where atoms are likely to be generated
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double epsilon[3];
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if (triclinic) epsilon[0] = epsilon[1] = epsilon[2] = EPSILON;
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else {
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epsilon[0] = domain->prd[0] * EPSILON;
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epsilon[1] = domain->prd[1] * EPSILON;
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epsilon[2] = domain->prd[2] * EPSILON;
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}
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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 (comm->myloc[0] == 0) sublo[0] -= epsilon[0];
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if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= 2.0*epsilon[0];
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}
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if (domain->yperiodic) {
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if (comm->myloc[1] == 0) sublo[1] -= epsilon[1];
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if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= 2.0*epsilon[1];
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}
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if (domain->zperiodic) {
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if (comm->myloc[2] == 0) sublo[2] -= epsilon[2];
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if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= 2.0*epsilon[2];
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}
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// iterate on 3d periodic lattice of unit cells using loop bounds
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// iterate on nbasis atoms in each unit cell
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// convert lattice coords to box coords
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