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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@254 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-01-30 00:22:05 +00:00
parent 9cdbeaf9f2
commit 209f169cbc
414 changed files with 6935 additions and 10462 deletions
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127
src/read_data.cpp
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@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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
@ -16,6 +16,8 @@
#include "stdlib.h"
#include "read_data.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_hybrid.h"
#include "comm.h"
#include "update.h"
#include "force.h"
@ -26,10 +28,11 @@
#include "dihedral.h"
#include "improper.h"
#include "error.h"
#include "atom_atomic.h"
#include "memory.h"
#include "special.h"
using namespace LAMMPS_NS;
#define MAXLINE 256
#define LB_FACTOR 1.1
#define CHUNK 1024
@ -40,7 +43,7 @@
/* ---------------------------------------------------------------------- */
ReadData::ReadData()
ReadData::ReadData(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
line = new char[MAXLINE];
@ -66,11 +69,8 @@ void ReadData::command(int narg, char **arg)
{
if (narg != 1) error->all("Illegal read_data command");
if (atom == NULL)
error->all("Cannot read_data until atom_style is defined");
if (domain->box_exist)
error->all("Cannot read_data after simulation box is defined");
if (force->dimension == 2 && domain->zperiodic == 0)
error->all("Cannot run 2d simulation with nonperiodic Z dimension");
@ -112,7 +112,7 @@ void ReadData::command(int narg, char **arg)
else n = static_cast<int> (LB_FACTOR * atom->natoms / comm->nprocs);
atom->allocate_type_arrays();
atom->grow(n);
atom->avec->grow(n);
domain->set_initial_box();
domain->set_global_box();
@ -120,35 +120,59 @@ void ReadData::command(int narg, char **arg)
domain->set_local_box();
// read rest of file in free format
// Atoms and Velocities keywords can have trailing hybrid sub-style
int atomflag = 0;
int hybridflag = 0;
if (strcmp(atom->atom_style,"hybrid") == 0) hybridflag = 1;
parse_keyword(1,1);
while (strlen(keyword)) {
if (strcmp(keyword,"Atoms") == 0) {
atoms();
atoms(0);
atomflag = 1;
} else if (hybridflag && strstr(keyword,"Atoms") == keyword) {
strtok(keyword," \t");
char *substyle = strtok(NULL," \t");
AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) atom->avec;
if (substyle == NULL) error->all("Invalid data file section: Atoms");
int ihybrid;
for (ihybrid = 0; ihybrid < avec_hybrid->nstyles; ihybrid++)
if (strcmp(avec_hybrid->keywords[ihybrid],substyle) == 0) break;
atoms(ihybrid);
atomflag = 1;
} else if (strcmp(keyword,"Velocities") == 0) {
if (atomflag == 0) error->all("Must read Atoms before Velocities");
velocities();
velocities(0);
} else if (hybridflag && strstr(keyword,"Velocities") == keyword) {
if (atomflag == 0) error->all("Must read Atoms before Velocities");
strtok(keyword," \t");
char *substyle = strtok(NULL," \t");
AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) atom->avec;
if (substyle == NULL)
error->all("Invalid data file section: Velocities");
int ihybrid;
for (ihybrid = 0; ihybrid < avec_hybrid->nstyles; ihybrid++)
if (strcmp(avec_hybrid->keywords[ihybrid],substyle) == 0) break;
velocities(ihybrid);
} else if (strcmp(keyword,"Bonds") == 0) {
if (atom->bonds_allow == 0)
if (atom->avec->bonds_allow == 0)
error->all("Invalid data file section: Bonds");
if (atomflag == 0) error->all("Must read Atoms before Bonds");
bonds();
} else if (strcmp(keyword,"Angles") == 0) {
if (atom->angles_allow == 0)
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: Angles");
if (atomflag == 0) error->all("Must read Atoms before Angles");
angles();
} else if (strcmp(keyword,"Dihedrals") == 0) {
if (atom->dihedrals_allow == 0)
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: Dihedrals");
if (atomflag == 0) error->all("Must read Atoms before Dihedrals");
dihedrals();
} else if (strcmp(keyword,"Impropers") == 0) {
if (atom->impropers_allow == 0)
if (atom->avec->impropers_allow == 0)
error->all("Invalid data file section: Impropers");
if (atomflag == 0) error->all("Must read Atoms before Impropers");
impropers();
@ -162,76 +186,76 @@ void ReadData::command(int narg, char **arg)
error->all("Must define pair_style before Pair Coeffs");
paircoeffs();
} else if (strcmp(keyword,"Bond Coeffs") == 0) {
if (atom->bonds_allow == 0)
if (atom->avec->bonds_allow == 0)
error->all("Invalid data file section: Bond Coeffs");
if (force->bond == NULL)
error->all("Must define bond_style before Bond Coeffs");
bondcoeffs();
} else if (strcmp(keyword,"Angle Coeffs") == 0) {
if (atom->angles_allow == 0)
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: Angle Coeffs");
if (force->angle == NULL)
error->all("Must define angle_style before Angle Coeffs");
anglecoeffs(0);
} else if (strcmp(keyword,"Dihedral Coeffs") == 0) {
if (atom->dihedrals_allow == 0)
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: Dihedral Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before Dihedral Coeffs");
dihedralcoeffs(0);
} else if (strcmp(keyword,"Improper Coeffs") == 0) {
if (atom->impropers_allow == 0)
if (atom->avec->impropers_allow == 0)
error->all("Invalid data file section: Improper Coeffs");
if (force->improper == NULL)
error->all("Must define improper_style before Improper Coeffs");
impropercoeffs(0);
} else if (strcmp(keyword,"BondBond Coeffs") == 0) {
if (atom->angles_allow == 0)
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: BondBond Coeffs");
if (force->angle == NULL)
error->all("Must define angle_style before BondBond Coeffs");
anglecoeffs(1);
} else if (strcmp(keyword,"BondAngle Coeffs") == 0) {
if (atom->angles_allow == 0)
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: BondAngle Coeffs");
if (force->angle == NULL)
error->all("Must define angle_style before BondAngle Coeffs");
anglecoeffs(2);
} else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) {
if (atom->dihedrals_allow == 0)
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: MiddleBondTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before MiddleBondTorsion Coeffs");
dihedralcoeffs(1);
} else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
if (atom->dihedrals_allow == 0)
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: EndBondTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before EndBondTorsion Coeffs");
dihedralcoeffs(2);
} else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
if (atom->dihedrals_allow == 0)
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: AngleTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before AngleTorsion Coeffs");
dihedralcoeffs(3);
} else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
if (atom->dihedrals_allow == 0)
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: AngleAngleTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before AngleAngleTorsion Coeffs");
dihedralcoeffs(4);
} else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
if (atom->dihedrals_allow == 0)
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: BondBond13 Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before BondBond13 Coeffs");
dihedralcoeffs(5);
} else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
if (atom->impropers_allow == 0)
if (atom->avec->impropers_allow == 0)
error->all("Invalid data file section: AngleAngle Coeffs");
if (force->improper == NULL)
error->all("Must define improper_style before AngleAngle Coeffs");
@ -257,7 +281,7 @@ void ReadData::command(int narg, char **arg)
// create bond topology now that system is defined
if (atom->molecular) {
Special special;
Special special(lmp);
special.build();
}
}
@ -337,13 +361,17 @@ void ReadData::header(int flag)
// error check on consistency of header values
if ((atom->nbonds || atom->nbondtypes) && atom->bonds_allow == 0)
if ((atom->nbonds || atom->nbondtypes) &&
atom->avec->bonds_allow == 0)
error->one("No bonds allowed with this atom style");
if ((atom->nangles || atom->nangletypes) && atom->angles_allow == 0)
if ((atom->nangles || atom->nangletypes) &&
atom->avec->angles_allow == 0)
error->one("No angles allowed with this atom style");
if ((atom->ndihedrals || atom->ndihedraltypes) && atom->dihedrals_allow == 0)
if ((atom->ndihedrals || atom->ndihedraltypes) &&
atom->avec->dihedrals_allow == 0)
error->one("No dihedrals allowed with this atom style");
if ((atom->nimpropers || atom->nimpropertypes) && atom->impropers_allow == 0)
if ((atom->nimpropers || atom->nimpropertypes) &&
atom->avec->impropers_allow == 0)
error->one("No impropers allowed with this atom style");
if (atom->nbonds > 0 && atom->nbondtypes <= 0)
@ -361,27 +389,16 @@ void ReadData::header(int flag)
}
/* ----------------------------------------------------------------------
read all atoms
read all atoms of a sub-style ihybrid (0 if not atom style hybrid)
to find atoms, must build atom map if not a molecular system
accumulate nread in double precision to allow natoms > 2^31
------------------------------------------------------------------------- */
void ReadData::atoms()
void ReadData::atoms(int ihybrid)
{
int i,m,nchunk;
if (me == 0) {
char *eof = fgets(buffer,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
m = strlen(buffer) + 1;
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
if (atom->parse_data(buffer))
error->all("Incorrect atom format in data file");
atom->unpack_data(1,buffer);
double nread = 1.0;
double nread = 0.0;
double natoms = atom->natoms;
while (nread < natoms) {
@ -400,7 +417,7 @@ void ReadData::atoms()
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
atom->unpack_data(nchunk,buffer);
atom->data_atoms(nchunk,buffer,ihybrid);
nread += nchunk;
}
@ -453,12 +470,12 @@ void ReadData::atoms()
}
/* ----------------------------------------------------------------------
read all velocities
read all velocities of a sub-style ihybrid (0 if not atom style hybrid)
to find atoms, must build atom map if not a molecular system
accumulate nread in double precision to allow natoms > 2^31
------------------------------------------------------------------------- */
void ReadData::velocities()
void ReadData::velocities(int ihybrid)
{
int i,m,nchunk;
@ -471,7 +488,7 @@ void ReadData::velocities()
}
double nread = 0.0;
double natoms = static_cast<int> (atom->natoms);
double natoms = atom->natoms;
while (nread < natoms) {
if (natoms-nread > CHUNK) nchunk = CHUNK;
@ -489,7 +506,7 @@ void ReadData::velocities()
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
atom->unpack_vels(nchunk,buffer);
atom->data_vels(nchunk,buffer,ihybrid);
nread += nchunk;
}
@ -526,7 +543,7 @@ void ReadData::bonds()
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
atom->unpack_bonds(nchunk,buffer);
atom->data_bonds(nchunk,buffer);
nread += nchunk;
}
@ -568,7 +585,7 @@ void ReadData::angles()
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
atom->unpack_angles(nchunk,buffer);
atom->data_angles(nchunk,buffer);
nread += nchunk;
}
@ -610,7 +627,7 @@ void ReadData::dihedrals()
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
atom->unpack_dihedrals(nchunk,buffer);
atom->data_dihedrals(nchunk,buffer);
nread += nchunk;
}
@ -653,7 +670,7 @@ void ReadData::impropers()
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
atom->unpack_impropers(nchunk,buffer);
atom->data_impropers(nchunk,buffer);
nread += nchunk;
}