remove old versions of read_dump and rerun w/o parallel reading support
This commit is contained in:
Axel Kohlmeyer
1011
src/read_dump2.cpp
1011
src/read_dump2.cpp
File diff suppressed because it is too large
Load Diff
172
src/read_dump2.h
172
src/read_dump2.h
@ -1,172 +0,0 @@
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, 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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Contributed by Timothy Sirk
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------------------------------------------------------------------------- */
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#ifdef COMMAND_CLASS
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CommandStyle(read_dump2,ReadDump2)
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#else
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#ifndef LMP_READ_DUMP2_H
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#define LMP_READ_DUMP2_H
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#include <cstdio>
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#include "pointers.h"
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namespace LAMMPS_NS {
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class ReadDump2 : protected Pointers {
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public:
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ReadDump2(class LAMMPS *);
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~ReadDump2();
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void command(int, char **);
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void store_files(int, char **);
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void setup_reader(int, char **);
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bigint seek(bigint, int);
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void header(int);
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bigint next(bigint, bigint, int, int);
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void atoms();
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int fields_and_keywords(int, char **);
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private:
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int me,nprocs;
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FILE *fp;
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int dimension;
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int triclinic;
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int nfile; // # of dump files to process
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char **files; // list of file names
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int currentfile; // currently open file
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int boxflag; // overwrite simulation with dump file box params
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int replaceflag,addflag; // flags for processing dump snapshot atoms
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int trimflag,purgeflag;
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int scaleflag; // user 0/1 if dump file coords are unscaled/scaled
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int wrapflag; // user 0/1 if dump file coords are unwrapped/wrapped
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char *readerstyle; // style of dump files to read
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int nfield; // # of fields to extract from dump file
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int *fieldtype; // type of each field = X,VY,IZ,etc
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char **fieldlabel; // user specified label for field
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double **fields; // per-atom field values
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int scaled; // 0/1 if dump file coords are unscaled/scaled
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int wrapped; // 0/1 if dump file coords are unwrapped/wrapped
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double box[3][3]; // dump file box parameters
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double xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz; // dump snapshot box params
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double xprd,yprd,zprd;
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bigint nsnapatoms; // # of atoms in dump file shapshot
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int npurge,nreplace,ntrim,nadd; // stats on processed atoms
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int addproc; // proc that should add next atom
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int yindex,zindex; // field index for Y,Z coords
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int *uflag; // set to 1 if snapshot atom matches owned atom
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int *ucflag,*ucflag_all; // set to 1 if snapshot chunk atom was processed
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class Reader *reader; // class that reads dump file
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int whichtype(char *);
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void process_atoms(int);
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void delete_atoms();
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double xfield(int, int);
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double yfield(int, int);
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double zfield(int, int);
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Read_dump command before simulation box is defined
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The read_dump command cannot be used before a read_data, read_restart,
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or create_box command.
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Dump file does not contain requested snapshot
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Self-explanatory.
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E: Unknown dump reader style
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The choice of dump reader style via the format keyword is unknown.
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E: No box information in dump, must use 'box no'
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UNDOCUMENTED
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E: Read_dump triclinic status does not match simulation
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Both the dump snapshot and the current LAMMPS simulation must
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be using either an orthogonal or triclinic box.
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E: Read_dump field not found in dump file
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Self-explanatory.
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E: Read_dump xyz fields do not have consistent scaling/wrapping
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Self-explanatory.
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E: All read_dump x,y,z fields must be specified for scaled, triclinic coords
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For triclinic boxes and scaled coordinates you must specify all 3 of
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the x,y,z fields, else LAMMPS cannot reconstruct the unscaled
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coordinates.
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E: Too many total atoms
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See the setting for bigint in the src/lmptype.h file.
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E: Read dump of atom property that isn't allocated
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Self-explanatory.
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E: Duplicate fields in read_dump command
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Self-explanatory.
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E: If read_dump purges it cannot replace or trim
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These operations are not compatible. See the read_dump doc
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page for details.
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E: Read_dump cannot use 'add keep' without atom IDs
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UNDOCUMENTED
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E: Cannot add atoms if dump file does not store atom type
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UNDOCUMENTED
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U: No box information in dump. You have to use 'box no'
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Self-explanatory.
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*/
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193
src/rerun2.cpp
193
src/rerun2.cpp
@ -1,193 +0,0 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, 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 <cstdlib>
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#include <cstring>
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#include "rerun2.h"
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#include "read_dump2.h"
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#include "domain.h"
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#include "update.h"
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#include "integrate.h"
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#include "modify.h"
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#include "output.h"
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#include "finish.h"
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#include "timer.h"
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#include "error.h"
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#include "force.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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Rerun2::Rerun2(LAMMPS *lmp) : Pointers(lmp) {}
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/* ---------------------------------------------------------------------- */
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void Rerun2::command(int narg, char **arg)
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{
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if (domain->box_exist == 0)
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error->all(FLERR,"Rerun command before simulation box is defined");
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if (narg < 2) error->all(FLERR,"Illegal rerun command");
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// list of dump files = args until a keyword
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int iarg = 0;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"first") == 0) break;
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if (strcmp(arg[iarg],"last") == 0) break;
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if (strcmp(arg[iarg],"every") == 0) break;
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if (strcmp(arg[iarg],"skip") == 0) break;
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if (strcmp(arg[iarg],"start") == 0) break;
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if (strcmp(arg[iarg],"stop") == 0) break;
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if (strcmp(arg[iarg],"dump") == 0) break;
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iarg++;
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}
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int nfile = iarg;
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if (nfile == 0 || nfile == narg) error->all(FLERR,"Illegal rerun command");
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// parse optional args up until "dump"
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// use MAXBIGINT -1 so Output can add 1 to it and still be a big int
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bigint first = 0;
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bigint last = MAXBIGINT - 1;
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int nevery = 0;
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int nskip = 1;
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int startflag = 0;
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int stopflag = 0;
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bigint start = -1;
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bigint stop = -1;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"first") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
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first = force->bnumeric(FLERR,arg[iarg+1]);
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if (first < 0) error->all(FLERR,"Illegal rerun command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"last") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
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last = force->bnumeric(FLERR,arg[iarg+1]);
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if (last < 0) error->all(FLERR,"Illegal rerun command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"every") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
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nevery = force->inumeric(FLERR,arg[iarg+1]);
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if (nevery < 0) error->all(FLERR,"Illegal rerun command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"skip") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
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nskip = force->inumeric(FLERR,arg[iarg+1]);
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if (nskip <= 0) error->all(FLERR,"Illegal rerun command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"start") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
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startflag = 1;
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start = force->bnumeric(FLERR,arg[iarg+1]);
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if (start < 0) error->all(FLERR,"Illegal rerun command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"stop") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
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stopflag = 1;
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stop = force->bnumeric(FLERR,arg[iarg+1]);
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if (stop < 0) error->all(FLERR,"Illegal rerun command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"dump") == 0) {
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break;
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} else error->all(FLERR,"Illegal rerun command");
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}
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int nremain = narg - iarg - 1;
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if (nremain <= 0) error->all(FLERR,"Illegal rerun command");
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if (first > last) error->all(FLERR,"Illegal rerun command");
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if (startflag && stopflag && start > stop)
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error->all(FLERR,"Illegal rerun command");
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// pass list of filenames to ReadDump
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// along with post-"dump" args and post-"format" args
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ReadDump2 *rd = new ReadDump2(lmp);
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rd->store_files(nfile,arg);
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if (nremain)
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nremain = rd->fields_and_keywords(nremain,&arg[narg-nremain]);
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else nremain = rd->fields_and_keywords(0,NULL);
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if (nremain) rd->setup_reader(nremain,&arg[narg-nremain]);
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else rd->setup_reader(0,NULL);
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// perform the pseudo run
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// invoke lmp->init() only once
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// read all relevant snapshots
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// use setup_minimal() since atoms are already owned by correct procs
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// addstep_compute_all() insures energy/virial computed on every snapshot
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update->whichflag = 1;
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if (startflag) update->beginstep = update->firststep = start;
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else update->beginstep = update->firststep = first;
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if (stopflag) update->endstep = update->laststep = stop;
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else update->endstep = update->laststep = last;
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int firstflag = 1;
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int ndump = 0;
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lmp->init();
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timer->init();
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timer->barrier_start();
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bigint ntimestep = rd->seek(first,0);
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if (ntimestep < 0)
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error->all(FLERR,"Rerun dump file does not contain requested snapshot");
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while (1) {
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ndump++;
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rd->header(firstflag);
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update->reset_timestep(ntimestep);
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rd->atoms();
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modify->init();
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update->integrate->setup_minimal(1);
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modify->end_of_step();
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if (firstflag) output->setup();
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else if (output->next) output->write(ntimestep);
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firstflag = 0;
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ntimestep = rd->next(ntimestep,last,nevery,nskip);
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if (stopflag && ntimestep > stop)
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error->all(FLERR,"Read rerun dump file timestep > specified stop");
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if (ntimestep < 0) break;
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}
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// insure thermo output on last dump timestep
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output->next_thermo = update->ntimestep;
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output->write(update->ntimestep);
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timer->barrier_stop();
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update->integrate->cleanup();
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// set update->nsteps to ndump for Finish stats to print
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update->nsteps = ndump;
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Finish finish(lmp);
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finish.end(1);
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update->whichflag = 0;
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update->firststep = update->laststep = 0;
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update->beginstep = update->endstep = 0;
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// clean-up
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delete rd;
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}
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59
src/rerun2.h
59
src/rerun2.h
@ -1,59 +0,0 @@
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
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||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
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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CommandStyle(rerun2,Rerun2)
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#else
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#ifndef LMP_RERUN2_H
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#define LMP_RERUN2_H
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#include "pointers.h"
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namespace LAMMPS_NS {
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class Rerun2 : protected Pointers {
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public:
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Rerun2(class LAMMPS *);
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void command(int, char **);
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Rerun command before simulation box is defined
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The rerun command cannot be used before a read_data, read_restart, or
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create_box command.
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E: Illegal ... command
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||||
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||||
Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
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E: Rerun dump file does not contain requested snapshot
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Self-explanatory.
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E: Read rerun dump file timestep > specified stop
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Self-explanatory.
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*/
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Reference in New Issue
Block a user