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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11621 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-03-10 16:43:25 +00:00
parent f7a3672c36
commit 91360a80a8
3 changed files with 111 additions and 26 deletions
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115
src/read_data.cpp
View File

@ -50,6 +50,14 @@ using namespace LAMMPS_NS;
// customize for new sections
#define NSECTIONS 25 // change when add to header::section_keywords
// pair style suffixes to ignore
// when matching Pair Coeffs comment to currently-defined pair style
const char *suffixes[] = {"/cuda","/gpu","/opt","/omp","/kk",
"/coul/cut","/coul/long","/coul/msm",
"/coul/dsf","/coul/debye","/coul/charmm",
NULL};
/* ---------------------------------------------------------------------- */
ReadData::ReadData(LAMMPS *lmp) : Pointers(lmp)
@ -57,6 +65,7 @@ ReadData::ReadData(LAMMPS *lmp) : Pointers(lmp)
MPI_Comm_rank(world,&me);
line = new char[MAXLINE];
keyword = new char[MAXLINE];
style = new char[MAXLINE];
buffer = new char[CHUNK*MAXLINE];
narg = maxarg = 0;
arg = NULL;
@ -80,6 +89,7 @@ ReadData::~ReadData()
{
delete [] line;
delete [] keyword;
delete [] style;
delete [] buffer;
memory->sfree(arg);
@ -218,8 +228,12 @@ void ReadData::command(int narg, char **arg)
if (strcmp(keyword,"Atoms") == 0) {
atomflag = 1;
if (firstpass) atoms();
else skip_lines(atom->natoms);
if (firstpass) {
if (me == 0 && !style_match(style,atom->atom_style))
error->warning(FLERR,"Atom style in data file differs "
"from currently defined atom style");
atoms();
} else skip_lines(atom->natoms);
} else if (strcmp(keyword,"Velocities") == 0) {
if (atomflag == 0)
error->all(FLERR,"Must read Atoms before Velocities");
@ -287,41 +301,65 @@ void ReadData::command(int narg, char **arg)
} else if (strcmp(keyword,"Pair Coeffs") == 0) {
if (force->pair == NULL)
error->all(FLERR,"Must define pair_style before Pair Coeffs");
if (firstpass) paircoeffs();
else skip_lines(atom->ntypes);
if (firstpass) {
if (me == 0 && !style_match(style,force->pair_style))
error->warning(FLERR,"Pair style in data file differs "
"from currently defined pair style");
paircoeffs();
} else skip_lines(atom->ntypes);
} else if (strcmp(keyword,"PairIJ Coeffs") == 0) {
if (force->pair == NULL)
error->all(FLERR,"Must define pair_style before PairIJ Coeffs");
if (firstpass) pairIJcoeffs();
else skip_lines(atom->ntypes*(atom->ntypes+1)/2);
if (firstpass) {
if (me == 0 && !style_match(style,force->pair_style))
error->warning(FLERR,"Pair style in data file differs "
"from currently defined pair style");
pairIJcoeffs();
} else skip_lines(atom->ntypes*(atom->ntypes+1)/2);
} else if (strcmp(keyword,"Bond Coeffs") == 0) {
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Invalid data file section: Bond Coeffs");
if (force->bond == NULL)
error->all(FLERR,"Must define bond_style before Bond Coeffs");
if (firstpass) bondcoeffs();
else skip_lines(atom->nbondtypes);
if (firstpass) {
if (me == 0 && !style_match(style,force->bond_style))
error->warning(FLERR,"Bond style in data file differs "
"from currently defined bond style");
bondcoeffs();
} else skip_lines(atom->nbondtypes);
} else if (strcmp(keyword,"Angle Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
error->all(FLERR,"Invalid data file section: Angle Coeffs");
if (force->angle == NULL)
error->all(FLERR,"Must define angle_style before Angle Coeffs");
if (firstpass) anglecoeffs(0);
else skip_lines(atom->nangletypes);
if (firstpass) {
if (me == 0 && !style_match(style,force->angle_style))
error->warning(FLERR,"Angle style in data file differs "
"from currently defined angle style");
anglecoeffs(0);
} else skip_lines(atom->nangletypes);
} else if (strcmp(keyword,"Dihedral Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Invalid data file section: Dihedral Coeffs");
if (force->dihedral == NULL)
error->all(FLERR,"Must define dihedral_style before Dihedral Coeffs");
if (firstpass) dihedralcoeffs(0);
else skip_lines(atom->ndihedraltypes);
if (firstpass) {
if (me == 0 && !style_match(style,force->dihedral_style))
error->warning(FLERR,"Dihedral style in data file differs "
"from currently defined dihedral style");
dihedralcoeffs(0);
} else skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"Improper Coeffs") == 0) {
if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Invalid data file section: Improper Coeffs");
if (force->improper == NULL)
error->all(FLERR,"Must define improper_style before Improper Coeffs");
if (firstpass) impropercoeffs(0);
else skip_lines(atom->nimpropertypes);
if (firstpass) {
if (me == 0 && !style_match(style,force->improper_style))
error->warning(FLERR,"Improper style in data file differs "
"from currently defined improper style");
impropercoeffs(0);
} else skip_lines(atom->nimpropertypes);
} else if (strcmp(keyword,"BondBond Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
@ -1464,8 +1502,14 @@ void ReadData::open(char *file)
else {
#ifdef LAMMPS_GZIP
char gunzip[128];
sprintf(gunzip,"gunzip -c %s",file);
sprintf(gunzip,"gzip -c -d %s",file);
#ifdef _WIN32
fp = _popen(gunzip,"rb");
#else
fp = popen(gunzip,"r");
#endif
#else
error->one(FLERR,"Cannot open gzipped file");
#endif
@ -1482,6 +1526,7 @@ void ReadData::open(char *file)
grab next keyword
read lines until one is non-blank
keyword is all text on line w/out leading & trailing white space
optional style can be appended after comment char '#'
read one additional line (assumed blank)
if any read hits EOF, set keyword to empty
if first = 1, line variable holds non-blank line that ended header
@ -1519,6 +1564,19 @@ void ReadData::parse_keyword(int first)
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
// store optional "style" following comment char '#' after keyword
char *ptr;
if ((ptr = strchr(line,'#'))) {
*ptr++ = '\0';
while (*ptr == ' ' || *ptr == '\t') ptr++;
int stop = strlen(ptr) - 1;
while (ptr[stop] == ' ' || ptr[stop] == '\t'
|| ptr[stop] == '\n' || ptr[stop] == '\r') stop--;
ptr[stop+1] = '\0';
strcpy(style,ptr);
} else style[0] = '\0';
// copy non-whitespace portion of line into keyword
int start = strspn(line," \t\n\r");
@ -1572,3 +1630,30 @@ void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag)
word = strtok(NULL," \t\n\r\f");
}
}
/* ----------------------------------------------------------------------
compare two style strings if they both exist
one = comment in data file section, two = currently-defined style
ignore suffixes listed in suffixes array at top of file
------------------------------------------------------------------------- */
int ReadData::style_match(const char *one, const char *two)
{
int i,delta,len,len1,len2;
if ((one == NULL) || (two == NULL)) return 1;
len1 = strlen(one);
len2 = strlen(two);
for (i = 0; suffixes[i] != NULL; i++) {
len = strlen(suffixes[i]);
if ((delta = len1 - len) > 0)
if (strcmp(one+delta,suffixes[i]) == 0) len1 = delta;
if ((delta = len2 - len) > 0)
if (strcmp(two+delta,suffixes[i]) == 0) len2 = delta;
}
if ((len1 == 0) || (len1 == len2) || (strncmp(one,two,len1) == 0)) return 1;
return 0;
}

8
src/read_data.h
View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
@ -32,11 +32,10 @@ class ReadData : protected Pointers {
void command(int, char **);
private:
int me;
char *line,*keyword,*buffer;
char *line,*keyword,*buffer,*style;
FILE *fp;
int narg,maxarg,compressed;
char **arg;
int me,narg,maxarg,compressed;
int nfix; // # of extra fixes that process/store info in data file
int *fix_index;
@ -59,6 +58,7 @@ class ReadData : protected Pointers {
void parse_keyword(int);
void skip_lines(bigint);
void parse_coeffs(char *, const char *, int);
int style_match(const char *, const char *);
void atoms();
void velocities();

14
src/write_data.cpp
View File

@ -272,27 +272,27 @@ void WriteData::force_fields()
{
if (force->pair && force->pair->writedata) {
if (pairflag == II) {
fprintf(fp,"\nPair Coeffs\n\n");
fprintf(fp,"\nPair Coeffs # %s\n\n", force->pair_style);
force->pair->write_data(fp);
} else if (pairflag == IJ) {
fprintf(fp,"\nPairIJ Coeffs\n\n");
fprintf(fp,"\nPairIJ Coeffs # %s\n\n", force->pair_style);
force->pair->write_data_all(fp);
}
}
if (force->bond && force->bond->writedata) {
fprintf(fp,"\nBond Coeffs\n\n");
fprintf(fp,"\nBond Coeffs # %s\n\n", force->bond_style);
force->bond->write_data(fp);
}
if (force->angle && force->angle->writedata) {
fprintf(fp,"\nAngle Coeffs\n\n");
fprintf(fp,"\nAngle Coeffs # %s\n\n", force->angle_style);
force->angle->write_data(fp);
}
if (force->dihedral && force->dihedral->writedata) {
fprintf(fp,"\nDihedral Coeffs\n\n");
fprintf(fp,"\nDihedral Coeffs # %s\n\n", force->dihedral_style);
force->dihedral->write_data(fp);
}
if (force->improper && force->improper->writedata) {
fprintf(fp,"\nImproper Coeffs\n\n");
fprintf(fp,"\nImproper Coeffs # %s\n\n", force->improper_style);
force->improper->write_data(fp);
}
}
@ -329,7 +329,7 @@ void WriteData::atoms()
MPI_Request request;
if (me == 0) {
fprintf(fp,"\nAtoms\n\n");
fprintf(fp,"\nAtoms # %s\n\n",atom->atom_style);
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_DOUBLE,iproc,0,world,&request);