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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8258 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-06-11 22:31:06 +00:00
parent b1723e1714
commit 9de3aecca1
7 changed files with 125 additions and 40 deletions
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1
src/Make.sh
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@ -60,6 +60,7 @@ if (test $1 = "style") then
style KSPACE_CLASS "" kspace force
style MINIMIZE_CLASS min_ minimize update
style PAIR_CLASS pair_ pair force pair_hybrid
style READER_CLASS reader_ reader read_dump
style REGION_CLASS region_ region domain
# edit Makefile.lib

36
src/read_dump.cpp
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@ -20,7 +20,8 @@
#include "string.h"
#include "stdlib.h"
#include "read_dump.h"
#include "read_dump_native.h"
#include "reader.h"
#include "style_reader.h"
#include "atom.h"
#include "atom_vec.h"
#include "update.h"
@ -39,7 +40,6 @@ using namespace LAMMPS_NS;
enum{ID,TYPE,X,Y,Z,VX,VY,VZ,IX,IY,IZ};
enum{UNSET,UNSCALED,SCALED};
enum{NATIVE};
/* ---------------------------------------------------------------------- */
@ -59,6 +59,10 @@ ReadDump::ReadDump(LAMMPS *lmp) : Pointers(lmp)
fieldlabel = NULL;
fields = NULL;
int n = strlen("native") + 1;
readerstyle = new char[n];
strcpy(readerstyle,"native");
reader = NULL;
fp = NULL;
}
@ -72,6 +76,7 @@ ReadDump::~ReadDump()
for (int i = 0; i < nfield; i++) delete [] fieldlabel[i];
delete [] fieldlabel;
delete [] fieldtype;
delete [] readerstyle;
memory->destroy(fields);
delete reader;
@ -169,14 +174,24 @@ void ReadDump::store_files(int nstr, char **str)
void ReadDump::setup_reader()
{
// create reader class
// could make this a parent class and customize with other readers
if (format == NATIVE) reader = new ReadDumpNative(lmp);
// allocate snapshot field buffer
memory->create(fields,CHUNK,nfield,"read_dump:fields");
// create reader class
// match readerstyle to options in style_reader.h
if (0) return; // dummy line to enable else-if macro expansion
#define READER_CLASS
#define ReaderStyle(key,Class) \
else if (strcmp(readerstyle,#key) == 0) reader = new Class(lmp);
#include "style_reader.h"
#undef READER_CLASS
// unrecognized style
else error->all(FLERR,"Invalid dump reader style");
}
/* ----------------------------------------------------------------------
@ -558,7 +573,6 @@ void ReadDump::fields_and_keywords(int narg, char **arg)
addflag = 0;
for (int i = 0; i < nfield; i++) fieldlabel[i] = NULL;
scaledflag = UNSCALED;
format = NATIVE;
while (iarg < narg) {
if (strcmp(arg[iarg],"box") == 0) {
@ -609,8 +623,10 @@ void ReadDump::fields_and_keywords(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
if (strcmp(arg[iarg+1],"native") == 0) format = NATIVE;
else error->all(FLERR,"Illegal read_dump command");
delete [] readerstyle;
int n = strlen(arg[iarg+1]) + 1;
readerstyle = new char[n];
strcpy(readerstyle,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal read_dump command");
}

4
src/read_dump.h
View File

@ -57,8 +57,8 @@ private:
int trimflag,purgeflag;
int scaledflag; // user setting for coordinate scaling
int scaled; // actual setting for coordinate scaling
int format; // style of dump file
int compressed; // flag for dump file compression
char *readerstyle; // style of dump files to read
int nfield; // # of fields to extract from dump file
int *fieldtype; // type of each field = X,VY,IZ,etc
@ -78,7 +78,7 @@ private:
int *uflag; // set to 1 if snapshot atom matches owned atom
int *ucflag,*ucflag_all; // set to 1 if snapshot chunk atom was processed
class ReadDumpNative *reader; // class that reads native dump file
class Reader *reader; // class that reads dump file
void process_atoms(int);
void delete_atoms();

31
src/reader.cpp Normal file
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@ -0,0 +1,31 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include "stdio.h"
#include "reader.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
Reader::Reader(LAMMPS *lmp) : Pointers(lmp) {}
/* ----------------------------------------------------------------------
set file ptr
caller opens/closes dump files
------------------------------------------------------------------------- */
void Reader::file(FILE *fpcaller)
{
fp = fpcaller;
}

43
src/reader.h Normal file
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@ -0,0 +1,43 @@
/* ----------------------------------------------------------------------
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.
Contributed by Timothy Sirk
------------------------------------------------------------------------- */
#ifndef LMP_READER_H
#define LMP_READER_H
#include "stdio.h"
#include "pointers.h"
namespace LAMMPS_NS {
class Reader : protected Pointers {
public:
Reader(class LAMMPS *);
virtual ~Reader() {}
virtual int read_time(bigint &) = 0;
virtual void skip() = 0;
virtual bigint read_header(double [3][3], int &, int, int, int *, char **,
int, int &, int &, int &, int &) = 0;
virtual void read_atoms(int, int, double **) = 0;
void file(FILE *);
protected:
FILE *fp; // pointer to file opened by caller
};
}
#endif

28
src/read_dump_native.cpp → src/reader_native.cpp
View File

@ -13,7 +13,7 @@
#include "string.h"
#include "stdlib.h"
#include "read_dump_native.h"
#include "reader_native.h"
#include "atom.h"
#include "memory.h"
#include "error.h"
@ -27,7 +27,7 @@ enum{UNSET,UNSCALED,SCALED};
/* ---------------------------------------------------------------------- */
ReadDumpNative::ReadDumpNative(LAMMPS *lmp) : Pointers(lmp)
ReaderNative::ReaderNative(LAMMPS *lmp) : Reader(lmp)
{
line = new char[MAXLINE];
words = NULL;
@ -36,30 +36,20 @@ ReadDumpNative::ReadDumpNative(LAMMPS *lmp) : Pointers(lmp)
/* ---------------------------------------------------------------------- */
ReadDumpNative::~ReadDumpNative()
ReaderNative::~ReaderNative()
{
delete [] line;
delete [] words;
memory->destroy(fieldindex);
}
/* ----------------------------------------------------------------------
set file ptr
caller opens/closes dump files
------------------------------------------------------------------------- */
void ReadDumpNative::file(FILE *fpcaller)
{
fp = fpcaller;
}
/* ----------------------------------------------------------------------
read and return time stamp from dump file
if first read reaches end-of-file, return 1 so caller can open next file
only called by proc 0
------------------------------------------------------------------------- */
int ReadDumpNative::read_time(bigint &ntimestep)
int ReaderNative::read_time(bigint &ntimestep)
{
char *eof = fgets(line,MAXLINE,fp);
if (eof == NULL) return 1;
@ -77,7 +67,7 @@ int ReadDumpNative::read_time(bigint &ntimestep)
only called by proc 0
------------------------------------------------------------------------- */
void ReadDumpNative::skip()
void ReaderNative::skip()
{
read_lines(2);
bigint natoms;
@ -110,7 +100,7 @@ void ReadDumpNative::skip()
only called by proc 0
------------------------------------------------------------------------- */
bigint ReadDumpNative::read_header(double box[3][3], int &triclinic,
bigint ReaderNative::read_header(double box[3][3], int &triclinic,
int fieldinfo, int nfield,
int *fieldtype, char **fieldlabel,
int scaledflag, int &fieldflag,
@ -284,7 +274,7 @@ bigint ReadDumpNative::read_header(double box[3][3], int &triclinic,
only called by proc 0
------------------------------------------------------------------------- */
void ReadDumpNative::read_atoms(int n, int nfield, double **fields)
void ReaderNative::read_atoms(int n, int nfield, double **fields)
{
int i,m;
char *eof;
@ -311,7 +301,7 @@ void ReadDumpNative::read_atoms(int n, int nfield, double **fields)
return index of match or -1 if no match
------------------------------------------------------------------------- */
int ReadDumpNative::find_label(const char *label, int n, char **labels)
int ReaderNative::find_label(const char *label, int n, char **labels)
{
for (int i = 0; i < n; i++)
if (strcmp(label,labels[i]) == 0) return i;
@ -325,7 +315,7 @@ int ReadDumpNative::find_label(const char *label, int n, char **labels)
only called by proc 0
------------------------------------------------------------------------- */
void ReadDumpNative::read_lines(int n)
void ReaderNative::read_lines(int n)
{
char *eof;
for (int i = 0; i < n; i++) eof = fgets(line,MAXLINE,fp);

22
src/read_dump_native.h → src/reader_native.h
View File

@ -13,20 +13,24 @@
Contributed by Timothy Sirk
------------------------------------------------------------------------- */
#ifndef LMP_READ_DUMP_NATIVE_H
#define LMP_READ_DUMP_NATIVE_H
#ifdef READER_CLASS
#include "stdio.h"
#include "pointers.h"
ReaderStyle(native,ReaderNative)
#else
#ifndef LMP_READER_NATIVE_H
#define LMP_READER_NATIVE_H
#include "reader.h"
namespace LAMMPS_NS {
class ReadDumpNative : protected Pointers {
class ReaderNative : public Reader {
public:
ReadDumpNative(class LAMMPS *);
~ReadDumpNative();
ReaderNative(class LAMMPS *);
~ReaderNative();
void file(FILE *);
int read_time(bigint &);
void skip();
bigint read_header(double [3][3], int &, int, int, int *, char **,
@ -34,7 +38,6 @@ class ReadDumpNative : protected Pointers {
void read_atoms(int, int, double **);
private:
FILE *fp; // pointer to file opened by caller
char *line; // line read from dump file
int nwords; // # of per-atom columns in dump file
@ -48,3 +51,4 @@ private:
}
#endif
#endif