From ce8f0898592a056a0fe2993b2c00b2732a0c0f3e Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Sat, 19 May 2012 00:34:04 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8105
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/fix.h | 4 ++
src/read_data.cpp | 113 +++++++++++++++++++++++++++++++++++++++++++++-
src/read_data.h | 7 +++
3 files changed, 123 insertions(+), 1 deletion(-)
diff --git a/src/fix.h b/src/fix.h
index f507cb5752..5919ed882e 100644
--- a/src/fix.h
+++ b/src/fix.h
@@ -146,6 +146,10 @@ class Fix : protected Pointers {
virtual void reset_target(double) {}
virtual void reset_dt() {}
+ virtual void read_data_header(char *) {}
+ virtual void read_data_section(char *, int, char *) {}
+ virtual int read_data_skip_lines(char *) {}
+
virtual int modify_param(int, char **) {return 0;}
virtual double memory_usage() {return 0.0;}
diff --git a/src/read_data.cpp b/src/read_data.cpp
index 73cc47b81a..2862c5d07a 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -25,6 +25,8 @@
#include "atom_vec_tri.h"
#include "comm.h"
#include "update.h"
+#include "modify.h"
+#include "fix.h"
#include "force.h"
#include "pair.h"
#include "domain.h"
@@ -82,13 +84,46 @@ ReadData::~ReadData()
void ReadData::command(int narg, char **arg)
{
- if (narg != 1) error->all(FLERR,"Illegal read_data command");
+ if (narg < 1) error->all(FLERR,"Illegal read_data command");
if (domain->box_exist)
error->all(FLERR,"Cannot read_data after simulation box is defined");
if (domain->dimension == 2 && domain->zperiodic == 0)
error->all(FLERR,"Cannot run 2d simulation with nonperiodic Z dimension");
+ // fixes that process data file info
+
+ nfix = 0;
+ fix_index = NULL;
+ fix_header = NULL;
+ fix_section = NULL;
+
+ int iarg = 1;
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"fix") == 0) {
+ if (iarg+4 > narg)
+ error->all(FLERR,"Illegal read_data command");
+ memory->grow(fix_index,nfix+1,"read_data:fix_index");
+ fix_header = (char **)
+ memory->srealloc(fix_header,(nfix+1)*sizeof(char *),
+ "read_data:fix_header");
+ fix_section = (char **)
+ memory->srealloc(fix_section,(nfix+1)*sizeof(char *),
+ "read_data:fix_section");
+ fix_index[nfix] = modify->find_fix(arg[iarg+1]);
+ if (fix_index[nfix] < 0)
+ error->all(FLERR,"Fix ID for Read_data does not exist");
+ int n = strlen(arg[iarg+2]) + 1;
+ fix_header[nfix] = new char[n];
+ strcpy(fix_header[nfix],arg[iarg+2]);
+ n = strlen(arg[iarg+3]) + 1;
+ fix_section[nfix] = new char[n];
+ strcpy(fix_section[nfix],arg[iarg+3]);
+ nfix++;
+ iarg += 4;
+ } else error->all(FLERR,"Illegal read_data command");
+ }
+
// scan data file to determine max topology needed per atom
// allocate initial topology arrays
@@ -146,6 +181,21 @@ void ReadData::command(int narg, char **arg)
int atomflag = 0;
while (strlen(keyword)) {
+
+ // allow special fixes first chance to match and process the section
+ // if fix matches, continue to next section
+
+ if (nfix) {
+ for (n = 0; n < nfix; n++)
+ if (strstr(line,fix_section[n])) {
+ int nlines = modify->fix[fix_index[n]]->read_data_skip_lines(keyword);
+ fix(n,keyword,nlines);
+ parse_keyword(0,1);
+ break;
+ }
+ if (n < nfix) continue;
+ }
+
if (strcmp(keyword,"Atoms") == 0) {
atoms();
atomflag = 1;
@@ -370,6 +420,18 @@ void ReadData::header(int flag)
if (ptr = strchr(line,'#')) *ptr = '\0';
if (strspn(line," \t\n\r") == strlen(line)) continue;
+ // allow special fixes first chance to match and process the line
+ // if fix matches, continue to next header line
+
+ if (nfix) {
+ for (n = 0; n < nfix; n++)
+ if (strstr(line,fix_header[n])) {
+ modify->fix[fix_index[n]]->read_data_header(line);
+ break;
+ }
+ if (n < nfix) continue;
+ }
+
// search line for header keyword and set corresponding variable
if (strstr(line,"atoms")) sscanf(line,BIGINT_FORMAT,&atom->natoms);
@@ -1028,6 +1090,38 @@ void ReadData::impropercoeffs(int which)
delete [] original;
}
+/* ----------------------------------------------------------------------
+ read fix section, pass lines to fix to process
+ n = index of fix
+------------------------------------------------------------------------- */
+
+void ReadData::fix(int ifix, char *line, int nlines)
+{
+ int i,m,nchunk;
+
+ bigint nread = 0;
+
+ while (nread < nlines) {
+ if (nlines-nread > CHUNK) nchunk = CHUNK;
+ else nchunk = nlines-nread;
+ if (me == 0) {
+ char *eof;
+ m = 0;
+ for (i = 0; i < nchunk; i++) {
+ eof = fgets(&buffer[m],MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ m += strlen(&buffer[m]);
+ }
+ m++;
+ }
+ MPI_Bcast(&m,1,MPI_INT,0,world);
+ MPI_Bcast(buffer,m,MPI_CHAR,0,world);
+
+ modify->fix[ifix]->read_data_section(line,nchunk,buffer);
+ nread += nchunk;
+ }
+}
+
/* ----------------------------------------------------------------------
proc 0 scans the data file for topology maximums
------------------------------------------------------------------------- */
@@ -1060,6 +1154,23 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
while (strlen(keyword)) {
+ // allow special fixes first chance to match and process the section
+ // if fix matches, continue to next section
+
+ if (nfix) {
+ for (i = 0; i < nfix; i++) {
+ printf("LINE SECTION %s %s\n",line,fix_section[i]);
+ if (strstr(line,fix_section[i])) {
+ int n = modify->fix[fix_index[i]]->read_data_skip_lines(keyword);
+ printf("NLINES SKIP %d\n",n);
+ skip_lines(n);
+ parse_keyword(0,0);
+ break;
+ }
+ }
+ if (i < nfix) continue;
+ }
+
if (strcmp(keyword,"Masses") == 0) skip_lines(atom->ntypes);
else if (strcmp(keyword,"Atoms") == 0) skip_lines(natoms);
else if (strcmp(keyword,"Velocities") == 0) skip_lines(natoms);
diff --git a/src/read_data.h b/src/read_data.h
index cc5d413468..2d29fc8fcc 100644
--- a/src/read_data.h
+++ b/src/read_data.h
@@ -38,6 +38,11 @@ class ReadData : protected Pointers {
int narg,maxarg,compressed;
char **arg;
+ int nfix; // # of extra fixes that process/store info in data file
+ int *fix_index;
+ char **fix_header;
+ char **fix_section;
+
bigint nellipsoids;
class AtomVecEllipsoid *avec_ellipsoid;
bigint nlines;
@@ -68,6 +73,8 @@ class ReadData : protected Pointers {
void anglecoeffs(int);
void dihedralcoeffs(int);
void impropercoeffs(int);
+
+ void fix(int, char *, int);
};
}
--
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