add region2vmd command
This commit is contained in:
Axel Kohlmeyer
198
src/EXTRA-COMMAND/region2vmd.cpp
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198
src/EXTRA-COMMAND/region2vmd.cpp
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/* -*- c++ -*--------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Axel Kohlmeyer (Temple U)
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------------------------------------------------------------------------- */
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#include "region2vmd.h"
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#include "atom.h"
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#include "comm.h"
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#include "domain.h"
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#include "error.h"
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#include "region.h"
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#include "region_block.h"
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#include "region_cone.h"
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#include "region_cylinder.h"
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#include "region_sphere.h"
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#include <cmath>
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using namespace LAMMPS_NS;
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static constexpr double SMALL = 1.0e-10;
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/* ---------------------------------------------------------------------- */
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void Region2VMD::command(int narg, char **arg)
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{
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FILE *fp = nullptr;
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if (narg < 2) utils::missing_cmd_args(FLERR, "region2vmd", error);
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if (comm->me == 0) {
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fp = fopen(arg[0], "w");
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if (fp == nullptr) {
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error->one(FLERR, Error::ARGZERO, "Cannot open file {} for writing: {}", arg[0],
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utils::getsyserror());
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} else {
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utils::logmesg(lmp, "Writing region visualizations to VMD Tcl script file {}:\n", arg[0]);
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fputs("# save old top molecule index\nset oldtop [molinfo top]\n", fp);
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}
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}
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for (int iarg = 1; iarg < narg; ++iarg) {
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auto *region = domain->get_region_by_id(arg[iarg]);
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if (!region) {
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if (fp) fclose(fp);
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error->all(FLERR, iarg, "Region {} does not exist", arg[iarg]);
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} else {
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write_region(fp, region);
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}
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}
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// done, close file
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if (comm->me == 0) {
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// reset views and restore previous top molecule
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fputs("display resetview\nif {$oldtop >= 0} {mol top $oldtop}\n", fp);
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fclose(fp);
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}
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}
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/* ----------------------------------------------------------------------
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write out one region using VMD graphics primitives
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fp is non-NULL only on MPI rank 0
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---------------------------------------------------------------------- */
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void Region2VMD::write_region(FILE *fp, Region *region)
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{
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if (!fp || !region) return;
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if (region->dynamic_check()) {
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utils::logmesg(lmp, "Cannot (yet) handle moving or rotating region {}. Skipping... ",
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region->id);
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return;
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}
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// create a new (empty) VMD molecule to hold the graphics for this specific region.
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utils::logmesg(lmp, " writing region {} ...", region->id);
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utils::print(fp, "\n# region {} of style {}\n", region->id, region->style);
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fputs("# create new empty VMD molecule to store the graphics primitives\n"
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"set gfxmol [mol new]\nmol top $gfxmol\n",
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fp);
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utils::print(fp, "mol rename $gfxmol {{LAMMPS region {}}}\n", region->id);
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fputs("# set color to desired value. Use 'gray' by default\n"
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"graphics $gfxmol color gray\n",
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fp);
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fputs("# set material to desired choice\n"
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"graphics $gfxmol material Transparent\n",
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fp);
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// translate compatible regions to VMD graphics primitives, skip others.
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const std::string regstyle = region->style;
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if (regstyle == "block") {
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const auto block = dynamic_cast<RegBlock *>(region);
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if (!block) {
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error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'block'", region->id);
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} else {
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// a block is represented by 12 triangles
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utils::print(fp,
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"draw triangle {{{0} {2} {4}}} {{{0} {2} {5}}} {{{0} {3} {4}}}\n"
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"draw triangle {{{0} {3} {4}}} {{{0} {3} {5}}} {{{0} {2} {5}}}\n"
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"draw triangle {{{0} {2} {4}}} {{{0} {2} {5}}} {{{1} {2} {4}}}\n"
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"draw triangle {{{1} {2} {4}}} {{{1} {2} {5}}} {{{0} {2} {5}}}\n"
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"draw triangle {{{1} {2} {4}}} {{{1} {2} {5}}} {{{1} {3} {4}}}\n"
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"draw triangle {{{1} {3} {4}}} {{{1} {3} {5}}} {{{1} {2} {5}}}\n"
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"draw triangle {{{0} {2} {4}}} {{{1} {2} {4}}} {{{1} {3} {4}}}\n"
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"draw triangle {{{0} {2} {4}}} {{{0} {3} {4}}} {{{1} {3} {4}}}\n"
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"draw triangle {{{0} {2} {5}}} {{{1} {2} {5}}} {{{1} {3} {5}}}\n"
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"draw triangle {{{0} {2} {5}}} {{{0} {3} {5}}} {{{1} {3} {5}}}\n"
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"draw triangle {{{0} {3} {4}}} {{{0} {3} {5}}} {{{1} {3} {5}}}\n"
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"draw triangle {{{0} {3} {4}}} {{{1} {3} {4}}} {{{1} {3} {5}}}\n",
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block->xlo, block->xhi, block->ylo, block->yhi, block->zlo, block->zhi);
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}
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} else if (regstyle == "cone") {
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const auto cone = dynamic_cast<RegCone *>(region);
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if (!cone) {
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error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'cone'", region->id);
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} else {
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// The VMD cone primitive requires one radius set to zero
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if (cone->radiuslo < SMALL) {
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// a cone uses a single cone primitive
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if (cone->axis == 'x') {
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utils::print(fp, "draw cone {{{1} {2} {3}}} {{{0} {2} {3}}} radius {4} resolution 20\n",
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cone->lo, cone->hi, cone->c1, cone->c2, cone->radiushi);
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} else if (cone->axis == 'y') {
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utils::print(fp, "draw cone {{{2} {1} {3}}} {{{2} {0} {3}}} radius {4} resolution 20\n",
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cone->lo, cone->hi, cone->c1, cone->c2, cone->radiushi);
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} else if (cone->axis == 'z') {
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utils::print(fp, "draw cone {{{2} {3} {1}}} {{{2} {3} {0}}} radius {4} resolution 20\n",
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cone->lo, cone->hi, cone->c1, cone->c2, cone->radiushi);
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}
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} else if (cone->radiushi < SMALL) {
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// a cone uses a single cone primitive
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if (cone->axis == 'x') {
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utils::print(fp, "draw cone {{{0} {2} {3}}} {{{1} {2} {3}}} radius {4} resolution 20\n",
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cone->lo, cone->hi, cone->c1, cone->c2, cone->radiuslo);
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} else if (cone->axis == 'y') {
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utils::print(fp, "draw cone {{{2} {0} {3}}} {{{2} {1} {3}}} radius {4} resolution 20\n",
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cone->lo, cone->hi, cone->c1, cone->c2, cone->radiuslo);
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} else if (cone->axis == 'z') {
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utils::print(fp, "draw cone {{{2} {3} {0}}} {{{2} {3} {1}}} radius {4} resolution 20\n",
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cone->lo, cone->hi, cone->c1, cone->c2, cone->radiuslo);
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}
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} else {
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utils::logmesg(lmp,
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"Cannot (yet) translate a truncated cone to VMD graphics. Skipping...\n");
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}
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}
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} else if (regstyle == "cylinder") {
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const auto cylinder = dynamic_cast<RegCylinder *>(region);
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if (!cylinder) {
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error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'cylinder'", region->id);
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} else {
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// a cylinder uses a single cylinder primitive
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if (cylinder->axis == 'x') {
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utils::print(fp, "draw cylinder {{{0} {2} {3}}} {{{1} {2} {3}}} radius {4} resolution 20\n",
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cylinder->lo, cylinder->hi, cylinder->c1, cylinder->c2, cylinder->radius);
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} else if (cylinder->axis == 'y') {
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utils::print(fp, "draw cylinder {{{2} {0} {3}}} {{{2} {1} {3}}} radius {4} resolution 20\n",
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cylinder->lo, cylinder->hi, cylinder->c1, cylinder->c2, cylinder->radius);
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} else if (cylinder->axis == 'z') {
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utils::print(fp, "draw cylinder {{{2} {3} {0}}} {{{2} {3} {1}}} radius {4} resolution 20\n",
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cylinder->lo, cylinder->hi, cylinder->c1, cylinder->c2, cylinder->radius);
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}
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}
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} else if (regstyle == "sphere") {
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const auto sphere = dynamic_cast<RegSphere *>(region);
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if (!sphere) {
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error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'sphere'", region->id);
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} else {
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// a sphere uses a single sphere primitive
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utils::print(fp, "draw sphere {{{} {} {}}} radius {} resolution 20\n", sphere->xc, sphere->yc,
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sphere->zc, sphere->radius);
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}
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} else {
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utils::logmesg(lmp,
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"Cannot (yet) translate region {} of style {} to VMD graphics. Skipping... ",
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region->id, region->style);
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}
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utils::logmesg(lmp, " done\n");
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}
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41
src/EXTRA-COMMAND/region2vmd.h
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41
src/EXTRA-COMMAND/region2vmd.h
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@ -0,0 +1,41 @@
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/* -*- c++ -*-----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef COMMAND_CLASS
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// clang-format off
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CommandStyle(region2vmd,Region2VMD);
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// clang-format on
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#else
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#ifndef LMP_REGION2VMD_H
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#define LMP_REGION2VMD_H
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#include "command.h"
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namespace LAMMPS_NS {
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class Region;
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class Region2VMD : public Command {
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public:
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Region2VMD(class LAMMPS *lmp) : Command(lmp) {};
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void command(int, char **) override;
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protected:
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void write_region(FILE *, Region *);
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};
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} // namespace LAMMPS_NS
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#endif
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#endif
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