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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2330 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2009-01-05 22:26:08 +00:00
parent e1f72f6d3a
commit 0cc1d090f4
90 changed files with 1129 additions and 779 deletions
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87
src/read_data.cpp
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@ -38,6 +38,8 @@ using namespace LAMMPS_NS;
#define CHUNK 1024
#define DELTA 4
#define NSECTIONS 22 // change when add to header::section_keywords
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
@ -82,14 +84,17 @@ void ReadData::command(int narg, char **arg)
if (screen) fprintf(screen,"Scanning data file ...\n");
open(arg[0]);
header(0);
scan(&atom->bond_per_atom,&atom->angle_per_atom,
&atom->dihedral_per_atom,&atom->improper_per_atom);
scan(atom->bond_per_atom,atom->angle_per_atom,
atom->dihedral_per_atom,atom->improper_per_atom);
fclose(fp);
atom->bond_per_atom += atom->extra_bond_per_atom;
}
MPI_Bcast(&atom->bond_per_atom,1,MPI_INT,0,world);
MPI_Bcast(&atom->angle_per_atom,1,MPI_INT,0,world);
MPI_Bcast(&atom->dihedral_per_atom,1,MPI_INT,0,world);
MPI_Bcast(&atom->improper_per_atom,1,MPI_INT,0,world);
} else
atom->bond_per_atom = atom->angle_per_atom =
atom->dihedral_per_atom = atom->improper_per_atom = 0;
@ -122,9 +127,9 @@ void ReadData::command(int narg, char **arg)
domain->set_local_box();
// read rest of file in free format
// if add a section keyword, add to header::section_keywords and NSECTIONS
int atomflag = 0;
parse_keyword(1,1);
while (strlen(keyword)) {
if (strcmp(keyword,"Atoms") == 0) {
@ -242,7 +247,7 @@ void ReadData::command(int narg, char **arg)
} else {
char str[128];
sprintf(str,"Unknown section in data file: %s",keyword);
sprintf(str,"Unknown identifier in data file: %s",keyword);
error->all(str);
}
@ -281,6 +286,15 @@ void ReadData::header(int flag)
int n;
char *ptr;
char *section_keywords[NSECTIONS] =
{"Atoms","Velocities","Bonds","Angles","Dihedrals","Impropers",
"Masses","Shapes","Dipoles",
"Pair Coeffs","Bond Coeffs","Angle Coeffs",
"Dihedral Coeffs","Improper Coeffs",
"BondBond Coeffs","BondAngle Coeffs","MiddleBondTorsion Coeffs",
"EndBondTorsion Coeffs","AngleTorsion Coeffs",
"AngleAngleTorsion Coeffs","BondBond13 Coeffs","AngleAngle Coeffs"};
// skip 1st line of file
if (me == 0) {
@ -322,6 +336,7 @@ void ReadData::header(int flag)
else if (strstr(line,"angles")) sscanf(line,"%d",&atom->nangles);
else if (strstr(line,"dihedrals")) sscanf(line,"%d",&atom->ndihedrals);
else if (strstr(line,"impropers")) sscanf(line,"%d",&atom->nimpropers);
else if (strstr(line,"atom types")) sscanf(line,"%d",&atom->ntypes);
else if (strstr(line,"bond types")) sscanf(line,"%d",&atom->nbondtypes);
else if (strstr(line,"angle types")) sscanf(line,"%d",&atom->nangletypes);
@ -329,6 +344,10 @@ void ReadData::header(int flag)
sscanf(line,"%d",&atom->ndihedraltypes);
else if (strstr(line,"improper types"))
sscanf(line,"%d",&atom->nimpropertypes);
else if (strstr(line,"extra bond per atom"))
sscanf(line,"%d",&atom->extra_bond_per_atom);
else if (strstr(line,"xlo xhi"))
sscanf(line,"%lg %lg",&domain->boxlo[0],&domain->boxhi[0]);
else if (strstr(line,"ylo yhi"))
@ -341,6 +360,17 @@ void ReadData::header(int flag)
} else break;
}
// check that exiting string is a valid section keyword
parse_keyword(1,flag);
for (n = 0; n < NSECTIONS; n++)
if (strcmp(keyword,section_keywords[n]) == 0) break;
if (n == NSECTIONS) {
char str[128];
sprintf(str,"Unknown identifier in data file: %s",keyword);
error->all(str);
}
// error check on consistency of header values
if ((atom->nbonds || atom->nbondtypes) &&
@ -914,15 +944,14 @@ void ReadData::impropercoeffs(int which)
proc 0 scans the data file for topology maximums
------------------------------------------------------------------------- */
void ReadData::scan(int *pbond_per, int *pangle_per,
int *pdihedral_per, int *pimproper_per)
void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
int &dihedral_per_atom, int &improper_per_atom)
{
int i,tmp1,tmp2,atom1,atom2,atom3,atom4;
int bond_per,angle_per,dihedral_per,improper_per;
char *eof;
int natoms = static_cast<int> (atom->natoms);
bond_per = angle_per = dihedral_per = improper_per = 0;
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
// allocate topology counting vector
// initially, array length = 1 to natoms
@ -931,8 +960,6 @@ void ReadData::scan(int *pbond_per, int *pangle_per,
int cmax = natoms + 1;
int *count = (int *) memory->smalloc(cmax*sizeof(int),"read_data:count");
parse_keyword(1,0);
while (strlen(keyword)) {
if (strcmp(keyword,"Masses") == 0) skip_lines(atom->ntypes);
@ -1050,9 +1077,9 @@ void ReadData::scan(int *pbond_per, int *pangle_per,
count[atom1]++;
count[atom2]++;
}
for (i = 1; i < cmax; i++) bond_per = MAX(bond_per,count[i]);
if (screen) fprintf(screen," %d = max bonds/atom\n",bond_per);
if (logfile) fprintf(logfile," %d = max bonds/atom\n",bond_per);
for (i = 1; i < cmax; i++) bond_per_atom = MAX(bond_per_atom,count[i]);
if (screen) fprintf(screen," %d = max bonds/atom\n",bond_per_atom);
if (logfile) fprintf(logfile," %d = max bonds/atom\n",bond_per_atom);
} else if (strcmp(keyword,"Angles") == 0) {
@ -1077,9 +1104,9 @@ void ReadData::scan(int *pbond_per, int *pangle_per,
count[atom2]++;
count[atom3]++;
}
for (i = 1; i < cmax; i++) angle_per = MAX(angle_per,count[i]);
if (screen) fprintf(screen," %d = max angles/atom\n",angle_per);
if (logfile) fprintf(logfile," %d = max angles/atom\n",angle_per);
for (i = 1; i < cmax; i++) angle_per_atom = MAX(angle_per_atom,count[i]);
if (screen) fprintf(screen," %d = max angles/atom\n",angle_per_atom);
if (logfile) fprintf(logfile," %d = max angles/atom\n",angle_per_atom);
} else if (strcmp(keyword,"Dihedrals") == 0) {
@ -1108,11 +1135,12 @@ void ReadData::scan(int *pbond_per, int *pangle_per,
count[atom3]++;
count[atom4]++;
}
for (i = 1; i < cmax; i++) dihedral_per = MAX(dihedral_per,count[i]);
for (i = 1; i < cmax; i++)
dihedral_per_atom = MAX(dihedral_per_atom,count[i]);
if (screen)
fprintf(screen," %d = max dihedrals/atom\n",dihedral_per);
fprintf(screen," %d = max dihedrals/atom\n",dihedral_per_atom);
if (logfile)
fprintf(logfile," %d = max dihedrals/atom\n",dihedral_per);
fprintf(logfile," %d = max dihedrals/atom\n",dihedral_per_atom);
} else if (strcmp(keyword,"Impropers") == 0) {
for (i = 1; i < cmax; i++) count[i] = 0;
@ -1140,11 +1168,12 @@ void ReadData::scan(int *pbond_per, int *pangle_per,
count[atom3]++;
count[atom4]++;
}
for (i = 1; i < cmax; i++) improper_per = MAX(improper_per,count[i]);
for (i = 1; i < cmax; i++)
improper_per_atom = MAX(improper_per_atom,count[i]);
if (screen)
fprintf(screen," %d = max impropers/atom\n",improper_per);
fprintf(screen," %d = max impropers/atom\n",improper_per_atom);
if (logfile)
fprintf(logfile," %d = max impropers/atom\n",improper_per);
fprintf(logfile," %d = max impropers/atom\n",improper_per_atom);
} else {
char str[128];
@ -1161,17 +1190,11 @@ void ReadData::scan(int *pbond_per, int *pangle_per,
// error check that topology was specified in file
if ((atom->nbonds && !bond_per) || (atom->nangles && !angle_per) ||
(atom->ndihedrals && !dihedral_per) ||
(atom->nimpropers && !improper_per))
if ((atom->nbonds && !bond_per_atom) ||
(atom->nangles && !angle_per_atom) ||
(atom->ndihedrals && !dihedral_per_atom) ||
(atom->nimpropers && !improper_per_atom))
error->one("Needed topology not in data file");
// return values
*pbond_per = bond_per;
*pangle_per = angle_per;
*pdihedral_per = dihedral_per;
*pimproper_per = improper_per;
}
/* ----------------------------------------------------------------------