make 2 copy of old read_dump and rerun for comparison to new
This commit is contained in:
Steve Plimpton
1011
src/read_dump2.cpp
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1011
src/read_dump2.cpp
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File diff suppressed because it is too large
Load Diff
172
src/read_dump2.h
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172
src/read_dump2.h
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@ -0,0 +1,172 @@
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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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@ -31,11 +31,13 @@ class ReadRestart : protected Pointers {
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void command(int, char **);
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void command(int, char **);
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private:
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private:
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int me,nprocs,nprocs_file,multiproc_file;
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int me,nprocs;
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FILE *fp;
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FILE *fp;
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int multiproc; // 0 = proc 0 writes for all
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int multiproc; // 0 = restart file is a single file
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// else # of procs writing files
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// 1 = restart file is parallel (multiple files)
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int multiproc_file; // # of parallel files in restart
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int nprocs_file; // total # of procs that wrote restart file
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// MPI-IO values
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// MPI-IO values
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@ -18,6 +18,8 @@
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using namespace LAMMPS_NS;
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using namespace LAMMPS_NS;
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// only proc 0 calls methods of this class, except for constructor/destructor
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/* ---------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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Reader::Reader(LAMMPS *lmp) : Pointers(lmp)
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Reader::Reader(LAMMPS *lmp) : Pointers(lmp)
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193
src/rerun2.cpp
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193
src/rerun2.cpp
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@ -0,0 +1,193 @@
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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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||||||
|
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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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|
|
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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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|
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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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|
|
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|
ReadDump2 *rd = new ReadDump2(lmp);
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|
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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
|
||||||
|
// 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
|
||||||
|
// addstep_compute_all() insures energy/virial computed on every snapshot
|
||||||
|
|
||||||
|
update->whichflag = 1;
|
||||||
|
|
||||||
|
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;
|
||||||
|
int ndump = 0;
|
||||||
|
|
||||||
|
lmp->init();
|
||||||
|
|
||||||
|
timer->init();
|
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|
timer->barrier_start();
|
||||||
|
|
||||||
|
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);
|
||||||
|
update->reset_timestep(ntimestep);
|
||||||
|
rd->atoms();
|
||||||
|
modify->init();
|
||||||
|
update->integrate->setup_minimal(1);
|
||||||
|
modify->end_of_step();
|
||||||
|
if (firstflag) output->setup();
|
||||||
|
else if (output->next) output->write(ntimestep);
|
||||||
|
|
||||||
|
firstflag = 0;
|
||||||
|
ntimestep = rd->next(ntimestep,last,nevery,nskip);
|
||||||
|
if (stopflag && ntimestep > stop)
|
||||||
|
error->all(FLERR,"Read rerun dump file timestep > specified stop");
|
||||||
|
if (ntimestep < 0) break;
|
||||||
|
}
|
||||||
|
|
||||||
|
// insure thermo output on last dump timestep
|
||||||
|
|
||||||
|
output->next_thermo = update->ntimestep;
|
||||||
|
output->write(update->ntimestep);
|
||||||
|
|
||||||
|
timer->barrier_stop();
|
||||||
|
|
||||||
|
update->integrate->cleanup();
|
||||||
|
|
||||||
|
// set update->nsteps to ndump for Finish stats to print
|
||||||
|
|
||||||
|
update->nsteps = ndump;
|
||||||
|
|
||||||
|
Finish finish(lmp);
|
||||||
|
finish.end(1);
|
||||||
|
|
||||||
|
update->whichflag = 0;
|
||||||
|
update->firststep = update->laststep = 0;
|
||||||
|
update->beginstep = update->endstep = 0;
|
||||||
|
|
||||||
|
// clean-up
|
||||||
|
|
||||||
|
delete rd;
|
||||||
|
}
|
||||||
59
src/rerun2.h
Normal file
59
src/rerun2.h
Normal file
@ -0,0 +1,59 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef COMMAND_CLASS
|
||||||
|
|
||||||
|
CommandStyle(rerun2,Rerun2)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_RERUN2_H
|
||||||
|
#define LMP_RERUN2_H
|
||||||
|
|
||||||
|
#include "pointers.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class Rerun2 : protected Pointers {
|
||||||
|
public:
|
||||||
|
Rerun2(class LAMMPS *);
|
||||||
|
void command(int, char **);
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Rerun command before simulation box is defined
|
||||||
|
|
||||||
|
The rerun command cannot be used before a read_data, read_restart, or
|
||||||
|
create_box command.
|
||||||
|
|
||||||
|
E: Illegal ... command
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script syntax and compare to the
|
||||||
|
documentation for the command. You can use -echo screen as a
|
||||||
|
command-line option when running LAMMPS to see the offending line.
|
||||||
|
|
||||||
|
E: Rerun dump file does not contain requested snapshot
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Read rerun dump file timestep > specified stop
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
*/
|
||||||
Reference in New Issue
Block a user