mods to change_box
This commit is contained in:
Steve Plimpton
@ -19,6 +19,7 @@
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#include "domain.h"
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#include "error.h"
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#include "force.h"
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#include "lattice.h"
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#include "region.h"
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#include "region_prism.h"
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#include "update.h"
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@ -45,40 +46,112 @@ void CreateBox::command(int narg, char **arg)
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// region check
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auto region = domain->get_region_by_id(arg[1]);
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if (!region) error->all(FLERR, "Create_box region {} does not exist", arg[1]);
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if (region->bboxflag == 0) error->all(FLERR, "Create_box region does not support a bounding box");
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Region *region = nullptr;
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int triclinic_general = 0;
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if (strcmp(arg[1],"NULL") == 0) triclinic_general = 1;
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else {
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region = domain->get_region_by_id(arg[1]);
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if (!region) error->all(FLERR, "Create_box region {} does not exist", arg[1]);
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if (region->bboxflag == 0) error->all(FLERR, "Create_box region does not support a bounding box");
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region->init();
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}
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region->init();
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// setup simulation box
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// 3 options: orthogonal, restricted triclinic, general triclinic
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// if region not prism:
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// setup orthogonal domain
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// set simulation domain from region extent
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// if region is prism:
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// seutp triclinic domain
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// set simulation domain params from prism params
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int iarg = 2;
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if (region) {
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// region is not prism
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// setup orthogonal box
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// set simulation domain from region extent
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if (strcmp(region->style, "prism") != 0) {
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domain->triclinic = 0;
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domain->boxlo[0] = region->extent_xlo;
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domain->boxhi[0] = region->extent_xhi;
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domain->boxlo[1] = region->extent_ylo;
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domain->boxhi[1] = region->extent_yhi;
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domain->boxlo[2] = region->extent_zlo;
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domain->boxhi[2] = region->extent_zhi;
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if (strcmp(region->style, "prism") != 0) {
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domain->triclinic = 0;
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domain->boxlo[0] = region->extent_xlo;
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domain->boxhi[0] = region->extent_xhi;
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domain->boxlo[1] = region->extent_ylo;
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domain->boxhi[1] = region->extent_yhi;
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domain->boxlo[2] = region->extent_zlo;
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domain->boxhi[2] = region->extent_zhi;
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// region is prism
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// seutp restricted triclinic box
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// set simulation domain from prism params
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} else {
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domain->triclinic = 1;
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auto prism = dynamic_cast<RegPrism *>(region);
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domain->boxlo[0] = prism->xlo;
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domain->boxhi[0] = prism->xhi;
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domain->boxlo[1] = prism->ylo;
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domain->boxhi[1] = prism->yhi;
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domain->boxlo[2] = prism->zlo;
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domain->boxhi[2] = prism->zhi;
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domain->xy = prism->xy;
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domain->xz = prism->xz;
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domain->yz = prism->yz;
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} else {
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domain->triclinic = 1;
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auto prism = dynamic_cast<RegPrism *>(region);
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domain->boxlo[0] = prism->xlo;
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domain->boxhi[0] = prism->xhi;
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domain->boxlo[1] = prism->ylo;
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domain->boxhi[1] = prism->yhi;
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domain->boxlo[2] = prism->zlo;
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domain->boxhi[2] = prism->zhi;
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domain->xy = prism->xy;
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domain->xz = prism->xz;
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domain->yz = prism->yz;
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}
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// setup general triclinic box (with no region)
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// read next box extent arguments to create ABC edge vectors + origin
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// set_general_triclinic() converts
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// ABC edge vectors + origin to restricted triclinic
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} else if (triclinic_general) {
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if (!domain->lattice->is_custom())
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error->all(FLERR,"Create_box with no region requires custom lattice");
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if (domain->lattice->is_oriented())
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error->all(FLERR,"Create_box with no region requires lattice with default orientation");
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if (iarg + 6 > narg) utils::missing_cmd_args(FLERR, "create_box general triclinic", error);
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double alo = utils::numeric(FLERR, arg[iarg + 0], false, lmp);
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double ahi = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
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double blo = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
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double bhi = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
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double clo = utils::numeric(FLERR, arg[iarg + 4], false, lmp);
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double chi = utils::numeric(FLERR, arg[iarg + 5], false, lmp);
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iarg += 6;
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// use lattice2box() to generate avec, bvec, cvec and origin
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double avec[3],bvec[3],cvec[3],origin[3];
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double px,py,pz;
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px = alo; py = blo; pz = clo;
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domain->lattice->lattice2box(px,py,pz);
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origin[0] = px;
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origin[1] = py;
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origin[2] = pz;
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px = ahi; py = blo; pz = clo;
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domain->lattice->lattice2box(px,py,pz);
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avec[0] = px - origin[0];
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avec[1] = py - origin[1];
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avec[2] = pz - origin[2];
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px = alo; py = bhi; pz = clo;
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domain->lattice->lattice2box(px,py,pz);
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bvec[0] = px - origin[0];
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bvec[1] = py - origin[1];
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bvec[2] = pz - origin[2];
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px = alo; py = blo; pz = chi;
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domain->lattice->lattice2box(px,py,pz);
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cvec[0] = px - origin[0];
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cvec[1] = py - origin[1];
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cvec[2] = pz - origin[2];
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printf("ORIGIN %g %g %g\n",origin[0],origin[1],origin[2]);
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printf("AVEC %g %g %g\n",avec[0],avec[1],avec[2]);
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printf("BVEC %g %g %g\n",bvec[0],bvec[1],bvec[2]);
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printf("CVEC %g %g %g\n",cvec[0],cvec[1],cvec[2]);
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// setup general triclinic box in Domain
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domain->set_general_triclinic(avec,bvec,cvec,origin);
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}
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// if molecular, zero out topology info
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@ -104,7 +177,6 @@ void CreateBox::command(int narg, char **arg)
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// process optional args that can overwrite default settings
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int iarg = 2;
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while (iarg < narg) {
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if (strcmp(arg[iarg], "bond/types") == 0) {
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if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box bond/type", error);
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