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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14381 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-12-17 23:05:20 +00:00
parent e37c9faf05
commit 7e9270e813
9 changed files with 161 additions and 22 deletions
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43
src/read_data.cpp
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@ -52,7 +52,7 @@ using namespace LAMMPS_NS;
#define LB_FACTOR 1.1
#define CHUNK 1024
#define DELTA 4 // must be 2 or larger
#define MAXBODY 20 // max # of lines in one body, also in Atom class
#define MAXBODY 32 // max # of lines in one body
// customize for new sections
#define NSECTIONS 25 // change when add to header::section_keywords
@ -73,6 +73,7 @@ ReadData::ReadData(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
line = new char[MAXLINE];
copy = new char[MAXLINE];
keyword = new char[MAXLINE];
style = new char[MAXLINE];
buffer = new char[CHUNK*MAXLINE];
@ -98,6 +99,7 @@ ReadData::ReadData(LAMMPS *lmp) : Pointers(lmp)
ReadData::~ReadData()
{
delete [] line;
delete [] copy;
delete [] keyword;
delete [] style;
delete [] buffer;
@ -1462,12 +1464,12 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
read all body data
variable amount of info per body, described by ninteger and ndouble
to find atoms, must build atom map if not a molecular system
if not firstpass, just read but no processing of data
if not firstpass, just read past data, but no processing of data
------------------------------------------------------------------------- */
void ReadData::bodies(int firstpass)
{
int i,m,nchunk,nline,nmax,ninteger,ndouble,tmp,onebody;
int i,m,nchunk,nline,nmax,ninteger,ndouble,nword,onebody,tmp;
char *eof;
int mapflag = 0;
@ -1498,19 +1500,38 @@ void ReadData::bodies(int firstpass)
sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble);
m += strlen(&buffer[m]);
// read lines one at a time into buffer
// make copy of line and count words
// count to ninteger and ndouble until have enough lines
onebody = 0;
if (ninteger) onebody += (ninteger-1)/10 + 1;
if (ndouble) onebody += (ndouble-1)/10 + 1;
nword = 0;
while (nword < ninteger) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
nword += atom->count_words(&buffer[m],copy);
m += strlen(&buffer[m]);
onebody++;
}
if (nword > ninteger)
error->one(FLERR,"Too many value in body lines in data file");
nword = 0;
while (nword < ndouble) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
nword += atom->count_words(&buffer[m],copy);
m += strlen(&buffer[m]);
onebody++;
}
if (nword > ndouble)
error->one(FLERR,"Too many value in body lines in data file");
if (onebody+1 > MAXBODY)
error->one(FLERR,
"Too many lines in one body in data file - boost MAXBODY");
for (i = 0; i < onebody; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
nchunk++;
nline += onebody+1;
}