549 lines
18 KiB
C++
549 lines
18 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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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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Steve Plimpton, sjplimp@sandia.gov
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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: Pierre de Buyl (KU Leuven)
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------------------------------------------------------------------------- */
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#include "dump_h5md.h"
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#include "atom.h"
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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 "group.h"
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#include "memory.h"
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#include "output.h"
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#include "update.h"
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#include "version.h"
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#include "ch5md.h"
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#include <climits>
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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#define MYMIN(a,b) ((a) < (b) ? (a) : (b))
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#define MYMAX(a,b) ((a) > (b) ? (a) : (b))
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/** Scan common options for the dump elements
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*/
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static int element_args(int narg, char **arg, int *every)
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{
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int iarg=0;
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while (iarg<narg) {
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if (strcmp(arg[iarg], "every")==0) {
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if (narg<2) return -1;
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*every = atoi(arg[iarg+1]);
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iarg+=2;
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} else {
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break;
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}
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}
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return iarg;
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}
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/* ---------------------------------------------------------------------- */
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DumpH5MD::DumpH5MD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
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{
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if (narg<6) error->all(FLERR,"Illegal dump h5md command");
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if (binary || compressed || multifile || multiproc)
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error->all(FLERR,"Invalid dump h5md filename");
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if (domain->triclinic!=0)
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error->all(FLERR,"Invalid domain for dump h5md. Only triclinic domains supported.");
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size_one = 6;
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sort_flag = 1;
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sortcol = 0;
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format_default = nullptr;
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flush_flag = 0;
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unwrap_flag = 0;
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datafile_from_dump = -1;
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author_name=nullptr;
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every_dump = utils::inumeric(FLERR,arg[3],false,lmp);
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every_position = every_image = -1;
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every_velocity = every_force = every_species = -1;
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every_charge = -1;
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do_box=true;
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create_group=true;
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bool box_is_set, create_group_is_set;
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box_is_set = create_group_is_set = false;
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int iarg=5;
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int n_parsed, default_every;
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size_one=0;
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if (every_dump==0) default_every=0; else default_every=1;
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while (iarg<narg) {
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if (strcmp(arg[iarg], "position")==0) {
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every_position=default_every;
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iarg+=1;
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n_parsed = element_args(narg-iarg, &arg[iarg], &every_position);
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if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
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iarg += n_parsed;
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size_one+=domain->dimension;
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} else if (strcmp(arg[iarg], "image")==0) {
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if (every_position<0) error->all(FLERR, "Illegal dump h5md command");
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iarg+=1;
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size_one+=domain->dimension;
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every_image = every_position;
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} else if (strcmp(arg[iarg], "velocity")==0) {
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every_velocity = default_every;
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iarg+=1;
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n_parsed = element_args(narg-iarg, &arg[iarg], &every_velocity);
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if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
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iarg += n_parsed;
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size_one+=domain->dimension;
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} else if (strcmp(arg[iarg], "force")==0) {
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every_force = default_every;
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iarg+=1;
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n_parsed = element_args(narg-iarg, &arg[iarg], &every_force);
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if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
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iarg += n_parsed;
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size_one+=domain->dimension;
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} else if (strcmp(arg[iarg], "species")==0) {
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every_species=default_every;
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iarg+=1;
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n_parsed = element_args(narg-iarg, &arg[iarg], &every_species);
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if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
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iarg += n_parsed;
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size_one+=1;
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} else if (strcmp(arg[iarg], "charge")==0) {
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if (!atom->q_flag)
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error->all(FLERR, "Requesting non-allocated quantity q in dump_h5md");
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every_charge = default_every;
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iarg+=1;
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n_parsed = element_args(narg-iarg, &arg[iarg], &every_charge);
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if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
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iarg += n_parsed;
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size_one+=1;
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} else if (strcmp(arg[iarg], "file_from")==0) {
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if (iarg+1>=narg) {
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error->all(FLERR, "Invalid number of arguments in dump h5md");
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}
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if (box_is_set||create_group_is_set)
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error->all(FLERR, "Cannot set file_from in dump h5md after box or create_group");
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int idump;
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for (idump = 0; idump < output->ndump; idump++)
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if (strcmp(arg[iarg+1],output->dump[idump]->id) == 0) break;
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if (idump == output->ndump) error->all(FLERR,"Cound not find dump_modify ID");
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datafile_from_dump = idump;
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do_box=false;
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create_group=false;
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iarg+=2;
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} else if (strcmp(arg[iarg], "box")==0) {
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if (iarg+1>=narg) {
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error->all(FLERR, "Invalid number of arguments in dump h5md");
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}
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box_is_set = true;
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do_box = utils::logical(FLERR,arg[iarg+1],false,lmp) == 1;
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iarg+=2;
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} else if (strcmp(arg[iarg], "create_group")==0) {
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if (iarg+1>=narg) {
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error->all(FLERR, "Invalid number of arguments in dump h5md");
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}
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create_group_is_set = true;
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create_group = utils::logical(FLERR,arg[iarg+1],false,lmp) == 1;
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iarg+=2;
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} else if (strcmp(arg[iarg], "author")==0) {
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if (iarg+1>=narg) {
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error->all(FLERR, "Invalid number of arguments in dump h5md");
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}
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if (author_name==nullptr) {
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author_name = new char[strlen(arg[iarg])+1];
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strcpy(author_name, arg[iarg+1]);
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} else {
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error->all(FLERR, "Illegal dump h5md command: author argument repeated");
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}
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iarg+=2;
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} else {
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error->all(FLERR, "Invalid argument to dump h5md");
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}
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}
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// allocate global array for atom coords
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bigint n = group->count(igroup);
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if ((bigint) domain->dimension*n > MAXSMALLINT) error->all(FLERR,"Too many atoms for dump h5md");
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natoms = static_cast<int> (n);
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if (every_position>=0)
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memory->create(dump_position,domain->dimension*natoms,"dump:position");
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if (every_image>=0)
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memory->create(dump_image,domain->dimension*natoms,"dump:image");
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if (every_velocity>=0)
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memory->create(dump_velocity,domain->dimension*natoms,"dump:velocity");
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if (every_force>=0)
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memory->create(dump_force,domain->dimension*natoms,"dump:force");
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if (every_species>=0)
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memory->create(dump_species,natoms,"dump:species");
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if (every_charge>=0)
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memory->create(dump_charge,natoms,"dump:charge");
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openfile();
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ntotal = 0;
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}
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/* ---------------------------------------------------------------------- */
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DumpH5MD::~DumpH5MD()
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{
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if (every_position>=0) {
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memory->destroy(dump_position);
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if (me==0) {
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h5md_close_element(particles_data.position);
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if (do_box)
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h5md_close_element(particles_data.box_edges);
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}
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}
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if (every_image>=0) {
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memory->destroy(dump_image);
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if (me==0) h5md_close_element(particles_data.image);
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}
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if (every_velocity>=0) {
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memory->destroy(dump_velocity);
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if (me==0) h5md_close_element(particles_data.velocity);
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}
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if (every_force>=0) {
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memory->destroy(dump_force);
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if (me==0) h5md_close_element(particles_data.force);
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}
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if (every_species>=0) {
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memory->destroy(dump_species);
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if (me==0) h5md_close_element(particles_data.species);
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}
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if (every_charge>=0) {
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memory->destroy(dump_charge);
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if (me==0) h5md_close_element(particles_data.charge);
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpH5MD::init_style()
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{
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if (sort_flag == 0 || sortcol != 0)
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error->all(FLERR,"Dump h5md requires sorting by atom ID");
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}
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/* ---------------------------------------------------------------------- */
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void DumpH5MD::openfile()
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{
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char *group_name;
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int group_name_length;
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int dims[2];
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char *boundary[3];
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for (int i=0; i<3; i++) {
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boundary[i] = new char[9];
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if (domain->periodicity[i]==1) {
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strcpy(boundary[i], "periodic");
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} else {
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strcpy(boundary[i], "none");
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}
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}
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if (me == 0) {
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if (datafile_from_dump<0) {
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if (author_name==nullptr) {
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datafile = h5md_create_file(filename, "N/A", nullptr, "lammps", LAMMPS_VERSION);
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} else {
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datafile = h5md_create_file(filename, author_name, nullptr, "lammps", LAMMPS_VERSION);
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}
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group_name_length = strlen(group->names[igroup])+1;
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group_name = new char[group_name_length];
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strcpy(group_name, group->names[igroup]);
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if (create_group) {
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particles_data = h5md_create_particles_group(datafile, group_name);
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} else {
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particles_data.group = h5md_open_particles_group(datafile.particles, group_name);
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}
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delete [] group_name;
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dims[0] = natoms;
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dims[1] = domain->dimension;
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if (every_position>0) {
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particles_data.position = h5md_create_time_data(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, nullptr);
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h5md_create_box(&particles_data, dims[1], boundary, true, nullptr, &particles_data.position);
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}
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if (every_image>0)
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particles_data.image = h5md_create_time_data(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, &particles_data.position);
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if (every_velocity>0)
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particles_data.velocity = h5md_create_time_data(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, nullptr);
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if (every_force>0)
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particles_data.force = h5md_create_time_data(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, nullptr);
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if (every_species>0)
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particles_data.species = h5md_create_time_data(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, nullptr);
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if (every_charge>0) {
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particles_data.charge = h5md_create_time_data(particles_data.group, "charge", 1, dims, H5T_NATIVE_DOUBLE, nullptr);
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h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
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}
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} else {
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DumpH5MD* other_dump;
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other_dump=(DumpH5MD*)output->dump[datafile_from_dump];
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datafile = other_dump->datafile;
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group_name_length = strlen(group->names[igroup]);
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group_name = new char[group_name_length];
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strcpy(group_name, group->names[igroup]);
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if (create_group) {
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particles_data = h5md_create_particles_group(datafile, group_name);
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} else {
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particles_data = other_dump->particles_data;
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}
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dims[0] = natoms;
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dims[1] = domain->dimension;
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if (every_position>0) {
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particles_data.position = h5md_create_time_data(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, nullptr);
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h5md_create_box(&particles_data, dims[1], boundary, true, nullptr, &particles_data.position);
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}
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if (every_image>0)
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particles_data.image = h5md_create_time_data(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, &particles_data.position);
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if (every_velocity>0)
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particles_data.velocity = h5md_create_time_data(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, nullptr);
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if (every_force>0)
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particles_data.force = h5md_create_time_data(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, nullptr);
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if (every_species>0)
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particles_data.species = h5md_create_time_data(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, nullptr);
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if (every_charge>0) {
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particles_data.charge = h5md_create_time_data(particles_data.group, "charge", 1, dims, H5T_NATIVE_DOUBLE, nullptr);
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h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
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}
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}
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}
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if (author_name!=nullptr) delete [] author_name;
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for (int i=0; i<3; i++) {
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delete [] boundary[i];
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpH5MD::write_header(bigint /* nbig */)
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{
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return;
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}
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/* ---------------------------------------------------------------------- */
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void DumpH5MD::pack(tagint *ids)
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{
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int m,n;
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tagint *tag = atom->tag;
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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int *species = atom->type;
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double *q = atom->q;
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imageint *image = atom->image;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int dim=domain->dimension;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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m = n = 0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (every_position>=0) {
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int ix = (image[i] & IMGMASK) - IMGMAX;
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int iy = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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int iz = (image[i] >> IMG2BITS) - IMGMAX;
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if (unwrap_flag == 1) {
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buf[m++] = (x[i][0] + ix * xprd);
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buf[m++] = (x[i][1] + iy * yprd);
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if (dim>2) buf[m++] = (x[i][2] + iz * zprd);
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} else {
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buf[m++] = x[i][0];
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buf[m++] = x[i][1];
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if (dim>2) buf[m++] = x[i][2];
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}
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if (every_image>=0) {
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buf[m++] = ix;
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buf[m++] = iy;
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if (dim>2) buf[m++] = iz;
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}
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}
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if (every_velocity>=0) {
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buf[m++] = v[i][0];
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buf[m++] = v[i][1];
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if (dim>2) buf[m++] = v[i][2];
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}
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if (every_force>=0) {
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buf[m++] = f[i][0];
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buf[m++] = f[i][1];
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if (dim>2) buf[m++] = f[i][2];
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}
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if (every_species>=0)
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buf[m++] = species[i];
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if (every_charge>=0)
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buf[m++] = q[i];
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ids[n++] = tag[i];
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpH5MD::write_data(int n, double *mybuf)
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{
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// copy buf atom coords into global array
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int m = 0;
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int dim = domain->dimension;
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int k = dim*ntotal;
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int k_image = dim*ntotal;
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int k_velocity = dim*ntotal;
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int k_force = dim*ntotal;
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int k_species = ntotal;
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int k_charge = ntotal;
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for (int i = 0; i < n; i++) {
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if (every_position>=0) {
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for (int j=0; j<dim; j++) {
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dump_position[k++] = mybuf[m++];
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}
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if (every_image>=0)
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for (int j=0; j<dim; j++) {
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dump_image[k_image++] = mybuf[m++];
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}
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}
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if (every_velocity>=0)
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for (int j=0; j<dim; j++) {
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dump_velocity[k_velocity++] = mybuf[m++];
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}
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if (every_force>=0)
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for (int j=0; j<dim; j++) {
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dump_force[k_force++] = mybuf[m++];
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}
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if (every_species>=0)
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dump_species[k_species++] = mybuf[m++];
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if (every_charge>=0)
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dump_charge[k_charge++] = mybuf[m++];
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ntotal++;
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}
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// if last chunk of atoms in this snapshot, write global arrays to file
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if (ntotal == natoms) {
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if (every_dump>0) {
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write_frame();
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ntotal = 0;
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} else {
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write_fixed_frame();
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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|
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int DumpH5MD::modify_param(int narg, char **arg)
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{
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if (strcmp(arg[0],"unwrap") == 0) {
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if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
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|
unwrap_flag = utils::logical(FLERR, arg[1], false, lmp);
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|
return 2;
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|
}
|
|
return 0;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void DumpH5MD::write_frame()
|
|
{
|
|
int local_step;
|
|
double local_time;
|
|
double edges[3];
|
|
local_step = update->ntimestep;
|
|
local_time = local_step * update->dt;
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|
edges[0] = boxxhi - boxxlo;
|
|
edges[1] = boxyhi - boxylo;
|
|
edges[2] = boxzhi - boxzlo;
|
|
if (every_position>0) {
|
|
if (local_step % (every_position*every_dump) == 0) {
|
|
h5md_append(particles_data.position, dump_position, local_step, local_time);
|
|
h5md_append(particles_data.box_edges, edges, local_step, local_time);
|
|
if (every_image>0)
|
|
h5md_append(particles_data.image, dump_image, local_step, local_time);
|
|
}
|
|
} else {
|
|
if (do_box) h5md_append(particles_data.box_edges, edges, local_step, local_time);
|
|
}
|
|
if (every_velocity>0 && local_step % (every_velocity*every_dump) == 0) {
|
|
h5md_append(particles_data.velocity, dump_velocity, local_step, local_time);
|
|
}
|
|
if (every_force>0 && local_step % (every_force*every_dump) == 0) {
|
|
h5md_append(particles_data.force, dump_force, local_step, local_time);
|
|
}
|
|
if (every_species>0 && local_step % (every_species*every_dump) == 0) {
|
|
h5md_append(particles_data.species, dump_species, local_step, local_time);
|
|
}
|
|
if (every_charge>0 && local_step % (every_charge*every_dump) == 0) {
|
|
h5md_append(particles_data.charge, dump_charge, local_step, local_time);
|
|
}
|
|
}
|
|
|
|
void DumpH5MD::write_fixed_frame()
|
|
{
|
|
double edges[3];
|
|
int dims[2];
|
|
char *boundary[3];
|
|
|
|
for (int i=0; i<3; i++) {
|
|
boundary[i] = new char[9];
|
|
if (domain->periodicity[i]==1) {
|
|
strcpy(boundary[i], "periodic");
|
|
} else {
|
|
strcpy(boundary[i], "none");
|
|
}
|
|
}
|
|
|
|
dims[0] = natoms;
|
|
dims[1] = domain->dimension;
|
|
|
|
edges[0] = boxxhi - boxxlo;
|
|
edges[1] = boxyhi - boxylo;
|
|
edges[2] = boxzhi - boxzlo;
|
|
if (every_position==0) {
|
|
particles_data.position = h5md_create_fixed_data_simple(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, dump_position);
|
|
h5md_create_box(&particles_data, dims[1], boundary, false, edges, nullptr);
|
|
if (every_image==0)
|
|
particles_data.image = h5md_create_fixed_data_simple(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, dump_image);
|
|
}
|
|
if (every_velocity==0)
|
|
particles_data.velocity = h5md_create_fixed_data_simple(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, dump_velocity);
|
|
if (every_force==0)
|
|
particles_data.force = h5md_create_fixed_data_simple(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, dump_force);
|
|
if (every_species==0)
|
|
particles_data.species = h5md_create_fixed_data_simple(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, dump_species);
|
|
if (every_charge==0) {
|
|
particles_data.charge = h5md_create_fixed_data_simple(particles_data.group, "charge", 1, dims, H5T_NATIVE_INT, dump_charge);
|
|
h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
|
|
}
|
|
|
|
for (int i=0; i<3; i++) {
|
|
delete [] boundary[i];
|
|
}
|
|
}
|
|
|