597 lines
17 KiB
C++
597 lines
17 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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#include "dump_atom.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 "memory.h"
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#include "update.h"
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#include <cstring>
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using namespace LAMMPS_NS;
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#define ONELINE 256
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#define DELTA 1048576
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/* ---------------------------------------------------------------------- */
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DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
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{
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if (narg != 5) error->all(FLERR,"Illegal dump atom command");
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scale_flag = 1;
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image_flag = 0;
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buffer_allow = 1;
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buffer_flag = 1;
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format_default = nullptr;
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::init_style()
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{
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if (image_flag == 0) size_one = 5;
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else size_one = 8;
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// format = copy of default or user-specified line format
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// default depends on image flags
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delete[] format;
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if (format_line_user) {
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format = utils::strdup(std::string(format_line_user) + "\n");
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} else {
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if (image_flag == 0) format = utils::strdup(TAGINT_FORMAT " %d %g %g %g\n");
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else format = utils::strdup(TAGINT_FORMAT " %d %g %g %g %d %d %d\n");
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}
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// setup boundary string
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domain->boundary_string(boundstr);
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// setup column string
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if (scale_flag == 0 && image_flag == 0)
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columns = (char *) "id type x y z";
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else if (scale_flag == 0 && image_flag == 1)
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columns = (char *) "id type x y z ix iy iz";
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else if (scale_flag == 1 && image_flag == 0)
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columns = (char *) "id type xs ys zs";
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else if (scale_flag == 1 && image_flag == 1)
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columns = (char *) "id type xs ys zs ix iy iz";
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// setup function ptrs
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if (binary && domain->triclinic == 0)
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header_choice = &DumpAtom::header_binary;
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else if (binary && domain->triclinic == 1)
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header_choice = &DumpAtom::header_binary_triclinic;
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else if (!binary && domain->triclinic == 0)
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header_choice = &DumpAtom::header_item;
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else if (!binary && domain->triclinic == 1)
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header_choice = &DumpAtom::header_item_triclinic;
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if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 0)
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pack_choice = &DumpAtom::pack_scale_noimage;
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else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 0)
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pack_choice = &DumpAtom::pack_scale_image;
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else if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 1)
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pack_choice = &DumpAtom::pack_scale_noimage_triclinic;
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else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 1)
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pack_choice = &DumpAtom::pack_scale_image_triclinic;
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else if (scale_flag == 0 && image_flag == 0)
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pack_choice = &DumpAtom::pack_noscale_noimage;
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else if (scale_flag == 0 && image_flag == 1)
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pack_choice = &DumpAtom::pack_noscale_image;
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if (image_flag == 0) convert_choice = &DumpAtom::convert_noimage;
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else convert_choice = &DumpAtom::convert_image;
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if (binary) write_choice = &DumpAtom::write_binary;
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else if (buffer_flag == 1) write_choice = &DumpAtom::write_string;
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else if (image_flag == 0) write_choice = &DumpAtom::write_lines_noimage;
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else if (image_flag == 1) write_choice = &DumpAtom::write_lines_image;
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// open single file, one time only
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if (multifile == 0) openfile();
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}
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/* ---------------------------------------------------------------------- */
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int DumpAtom::modify_param(int narg, char **arg)
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{
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if (strcmp(arg[0],"scale") == 0) {
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if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
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scale_flag = utils::logical(FLERR,arg[1],false,lmp);
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return 2;
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} else if (strcmp(arg[0],"image") == 0) {
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if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
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image_flag = utils::logical(FLERR,arg[1],false,lmp);
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return 2;
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}
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return 0;
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::write_header(bigint ndump)
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{
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if (multiproc) (this->*header_choice)(ndump);
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else if (me == 0) (this->*header_choice)(ndump);
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::pack(tagint *ids)
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{
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(this->*pack_choice)(ids);
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}
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/* ---------------------------------------------------------------------- */
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int DumpAtom::convert_string(int n, double *mybuf)
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{
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return (this->*convert_choice)(n,mybuf);
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::write_data(int n, double *mybuf)
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{
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(this->*write_choice)(n,mybuf);
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::format_magic_string_binary()
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{
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// use negative ntimestep as marker for new format
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bigint fmtlen = strlen(MAGIC_STRING);
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bigint marker = -fmtlen;
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fwrite(&marker, sizeof(bigint), 1, fp);
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fwrite(MAGIC_STRING, sizeof(char), fmtlen, fp);
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::format_endian_binary()
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{
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int endian = ENDIAN;
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fwrite(&endian, sizeof(int), 1, fp);
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::format_revision_binary()
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{
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int revision = FORMAT_REVISION;
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fwrite(&revision, sizeof(int), 1, fp);
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::header_unit_style_binary()
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{
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int len = 0;
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if (unit_flag && !unit_count) {
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++unit_count;
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len = strlen(update->unit_style);
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fwrite(&len, sizeof(int), 1, fp);
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fwrite(update->unit_style, sizeof(char), len, fp);
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} else {
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fwrite(&len, sizeof(int), 1, fp);
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::header_columns_binary()
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{
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int len = strlen(columns);
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fwrite(&len, sizeof(int), 1, fp);
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fwrite(columns, sizeof(char), len, fp);
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::header_time_binary()
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{
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char flag = time_flag ? 1 : 0;
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fwrite(&flag, sizeof(char), 1, fp);
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if (time_flag) {
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double t = compute_time();
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fwrite(&t, sizeof(double), 1, fp);
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::header_format_binary()
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{
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format_magic_string_binary();
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format_endian_binary();
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format_revision_binary();
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::header_binary(bigint ndump)
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{
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header_format_binary();
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fwrite(&update->ntimestep,sizeof(bigint),1,fp);
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fwrite(&ndump,sizeof(bigint),1,fp);
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fwrite(&domain->triclinic,sizeof(int),1,fp);
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fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp);
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fwrite(&boxxlo,sizeof(double),1,fp);
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fwrite(&boxxhi,sizeof(double),1,fp);
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fwrite(&boxylo,sizeof(double),1,fp);
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fwrite(&boxyhi,sizeof(double),1,fp);
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fwrite(&boxzlo,sizeof(double),1,fp);
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fwrite(&boxzhi,sizeof(double),1,fp);
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fwrite(&size_one,sizeof(int),1,fp);
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header_unit_style_binary();
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header_time_binary();
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header_columns_binary();
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if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp);
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else fwrite(&nprocs,sizeof(int),1,fp);
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::header_binary_triclinic(bigint ndump)
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{
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header_format_binary();
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fwrite(&update->ntimestep,sizeof(bigint),1,fp);
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fwrite(&ndump,sizeof(bigint),1,fp);
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fwrite(&domain->triclinic,sizeof(int),1,fp);
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fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp);
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fwrite(&boxxlo,sizeof(double),1,fp);
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fwrite(&boxxhi,sizeof(double),1,fp);
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fwrite(&boxylo,sizeof(double),1,fp);
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fwrite(&boxyhi,sizeof(double),1,fp);
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fwrite(&boxzlo,sizeof(double),1,fp);
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fwrite(&boxzhi,sizeof(double),1,fp);
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fwrite(&boxxy,sizeof(double),1,fp);
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fwrite(&boxxz,sizeof(double),1,fp);
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fwrite(&boxyz,sizeof(double),1,fp);
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fwrite(&size_one,sizeof(int),1,fp);
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header_unit_style_binary();
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header_time_binary();
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header_columns_binary();
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if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp);
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else fwrite(&nprocs,sizeof(int),1,fp);
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::header_item(bigint ndump)
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{
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if (unit_flag && !unit_count) {
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++unit_count;
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fmt::print(fp,"ITEM: UNITS\n{}\n",update->unit_style);
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}
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if (time_flag) fmt::print(fp,"ITEM: TIME\n{:.16}\n",compute_time());
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fmt::print(fp,"ITEM: TIMESTEP\n{}\n"
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"ITEM: NUMBER OF ATOMS\n{}\n",
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update->ntimestep, ndump);
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fmt::print(fp,"ITEM: BOX BOUNDS {}\n"
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"{:>1.16e} {:>1.16e}\n"
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"{:>1.16e} {:>1.16e}\n"
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"{:>1.16e} {:>1.16e}\n",
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boundstr,boxxlo,boxxhi,boxylo,boxyhi,boxzlo,boxzhi);
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fmt::print(fp,"ITEM: ATOMS {}\n",columns);
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::header_item_triclinic(bigint ndump)
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{
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if (unit_flag && !unit_count) {
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++unit_count;
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fmt::print(fp,"ITEM: UNITS\n{}\n",update->unit_style);
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}
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if (time_flag) fmt::print(fp,"ITEM: TIME\n{:.16}\n",compute_time());
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fmt::print(fp,"ITEM: TIMESTEP\n{}\n"
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"ITEM: NUMBER OF ATOMS\n{}\n",
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update->ntimestep, ndump);
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fmt::print(fp,"ITEM: BOX BOUNDS xy xz yz {}\n"
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"{:>1.16e} {:>1.16e} {:>1.16e}\n"
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"{:>1.16e} {:>1.16e} {:>1.16e}\n"
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"{:>1.16e} {:>1.16e} {:>1.16e}\n",
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boundstr,boxxlo,boxxhi,boxxy,boxylo,boxyhi,boxxz,boxzlo,boxzhi,boxyz);
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fmt::print(fp,"ITEM: ATOMS {}\n",columns);
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::pack_scale_image(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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int *type = atom->type;
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imageint *image = atom->image;
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int *mask = atom->mask;
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double **x = atom->x;
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int nlocal = atom->nlocal;
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double invxprd = 1.0/domain->xprd;
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double invyprd = 1.0/domain->yprd;
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double invzprd = 1.0/domain->zprd;
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m = n = 00;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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buf[m++] = tag[i];
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buf[m++] = type[i];
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buf[m++] = (x[i][0] - boxxlo) * invxprd;
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buf[m++] = (x[i][1] - boxylo) * invyprd;
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buf[m++] = (x[i][2] - boxzlo) * invzprd;
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buf[m++] = (image[i] & IMGMASK) - IMGMAX;
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buf[m++] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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buf[m++] = (image[i] >> IMG2BITS) - IMGMAX;
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if (ids) ids[n++] = tag[i];
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::pack_scale_noimage(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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int *type = atom->type;
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int *mask = atom->mask;
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double **x = atom->x;
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int nlocal = atom->nlocal;
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double invxprd = 1.0/domain->xprd;
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double invyprd = 1.0/domain->yprd;
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double invzprd = 1.0/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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buf[m++] = tag[i];
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buf[m++] = type[i];
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buf[m++] = (x[i][0] - boxxlo) * invxprd;
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buf[m++] = (x[i][1] - boxylo) * invyprd;
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buf[m++] = (x[i][2] - boxzlo) * invzprd;
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if (ids) ids[n++] = tag[i];
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::pack_scale_image_triclinic(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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int *type = atom->type;
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imageint *image = atom->image;
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int *mask = atom->mask;
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double **x = atom->x;
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int nlocal = atom->nlocal;
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double lamda[3];
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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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buf[m++] = tag[i];
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buf[m++] = type[i];
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domain->x2lamda(x[i],lamda);
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buf[m++] = lamda[0];
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buf[m++] = lamda[1];
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buf[m++] = lamda[2];
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buf[m++] = (image[i] & IMGMASK) - IMGMAX;
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buf[m++] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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buf[m++] = (image[i] >> IMG2BITS) - IMGMAX;
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if (ids) ids[n++] = tag[i];
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::pack_scale_noimage_triclinic(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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int *type = atom->type;
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int *mask = atom->mask;
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double **x = atom->x;
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int nlocal = atom->nlocal;
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double lamda[3];
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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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buf[m++] = tag[i];
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buf[m++] = type[i];
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domain->x2lamda(x[i],lamda);
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buf[m++] = lamda[0];
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buf[m++] = lamda[1];
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buf[m++] = lamda[2];
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if (ids) ids[n++] = tag[i];
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::pack_noscale_image(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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int *type = atom->type;
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imageint *image = atom->image;
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int *mask = atom->mask;
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double **x = atom->x;
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int nlocal = atom->nlocal;
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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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buf[m++] = tag[i];
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buf[m++] = type[i];
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buf[m++] = x[i][0];
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buf[m++] = x[i][1];
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buf[m++] = x[i][2];
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buf[m++] = (image[i] & IMGMASK) - IMGMAX;
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buf[m++] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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buf[m++] = (image[i] >> IMG2BITS) - IMGMAX;
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if (ids) ids[n++] = tag[i];
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::pack_noscale_noimage(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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int *type = atom->type;
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int *mask = atom->mask;
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double **x = atom->x;
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int nlocal = atom->nlocal;
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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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buf[m++] = tag[i];
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buf[m++] = type[i];
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buf[m++] = x[i][0];
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buf[m++] = x[i][1];
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buf[m++] = x[i][2];
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if (ids) ids[n++] = tag[i];
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}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
convert mybuf of doubles to one big formatted string in sbuf
|
|
return -1 if strlen exceeds an int, since used as arg in MPI calls in Dump
|
|
------------------------------------------------------------------------- */
|
|
|
|
int DumpAtom::convert_image(int n, double *mybuf)
|
|
{
|
|
int offset = 0;
|
|
int m = 0;
|
|
for (int i = 0; i < n; i++) {
|
|
if (offset + ONELINE > maxsbuf) {
|
|
if ((bigint) maxsbuf + DELTA > MAXSMALLINT) return -1;
|
|
maxsbuf += DELTA;
|
|
memory->grow(sbuf,maxsbuf,"dump:sbuf");
|
|
}
|
|
|
|
offset += sprintf(&sbuf[offset],format,
|
|
static_cast<tagint> (mybuf[m]),
|
|
static_cast<int> (mybuf[m+1]),
|
|
mybuf[m+2],mybuf[m+3],mybuf[m+4],
|
|
static_cast<int> (mybuf[m+5]),
|
|
static_cast<int> (mybuf[m+6]),
|
|
static_cast<int> (mybuf[m+7]));
|
|
m += size_one;
|
|
}
|
|
|
|
return offset;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int DumpAtom::convert_noimage(int n, double *mybuf)
|
|
{
|
|
int offset = 0;
|
|
int m = 0;
|
|
for (int i = 0; i < n; i++) {
|
|
if (offset + ONELINE > maxsbuf) {
|
|
if ((bigint) maxsbuf + DELTA > MAXSMALLINT) return -1;
|
|
maxsbuf += DELTA;
|
|
memory->grow(sbuf,maxsbuf,"dump:sbuf");
|
|
}
|
|
|
|
offset += sprintf(&sbuf[offset],format,
|
|
static_cast<tagint> (mybuf[m]),
|
|
static_cast<int> (mybuf[m+1]),
|
|
mybuf[m+2],mybuf[m+3],mybuf[m+4]);
|
|
m += size_one;
|
|
}
|
|
|
|
return offset;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void DumpAtom::write_binary(int n, double *mybuf)
|
|
{
|
|
n *= size_one;
|
|
fwrite(&n,sizeof(int),1,fp);
|
|
fwrite(mybuf,sizeof(double),n,fp);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void DumpAtom::write_string(int n, double *mybuf)
|
|
{
|
|
if (mybuf)
|
|
fwrite(mybuf,sizeof(char),n,fp);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void DumpAtom::write_lines_image(int n, double *mybuf)
|
|
{
|
|
int m = 0;
|
|
for (int i = 0; i < n; i++) {
|
|
fprintf(fp,format,
|
|
static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
|
|
mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast<int> (mybuf[m+5]),
|
|
static_cast<int> (mybuf[m+6]), static_cast<int> (mybuf[m+7]));
|
|
m += size_one;
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void DumpAtom::write_lines_noimage(int n, double *mybuf)
|
|
{
|
|
int m = 0;
|
|
for (int i = 0; i < n; i++) {
|
|
fprintf(fp,format,
|
|
static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
|
|
mybuf[m+2],mybuf[m+3],mybuf[m+4]);
|
|
m += size_one;
|
|
}
|
|
}
|