Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/USER-MOLFILE/reader_molfile.cpp
0241b5ce29e3efficient_neuronet

Last Change
Raw File

reader_molfile.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "math.h"
#include "reader_molfile.h"
#include "atom.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "molfile_interface.h"
#include "math_const.h"
using namespace LAMMPS_NS;
typedef MolfileInterface MFI;
using namespace MathConst;
enum{ID,TYPE,X,Y,Z,VX,VY,VZ};
#define SMALL 1.0e-6
// true if the difference between two floats is "small".
// cannot use fabsf() since it is not fully portable.
static bool is_smalldiff(const float &val1, const float &val2)
{
return (fabs(static_cast<double>(val1-val2)) < SMALL);
}
/* ---------------------------------------------------------------------- */
ReaderMolfile::ReaderMolfile(LAMMPS *lmp) : Reader(lmp)
{
mf = NULL;
coords = NULL;
vels = NULL;
types = NULL;
fieldindex = NULL;
nstep = 0;
needvels = 0;
me = comm->me;
}
/* ---------------------------------------------------------------------- */
ReaderMolfile::~ReaderMolfile()
{
if (me == 0) {
memory->destroy(fieldindex);
memory->destroy(types);
memory->destroy(coords);
memory->destroy(vels);
if (mf) delete mf;
}
}
/* ----------------------------------------------------------------------
pass on settings to find and load the proper plugin
called by all processors.
------------------------------------------------------------------------- */
void ReaderMolfile::settings(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal molfile reader command");
if (me == 0) {
mf = new MolfileInterface(arg[0],MFI::M_READ);
const char *path = (const char *) ".";
if (narg > 1)
path=arg[1];
if (mf->find_plugin(path)!= MFI::E_MATCH)
error->one(FLERR,"No suitable molfile plugin found");
if (screen)
fprintf(screen,"Dump reader uses molfile plugin: %s\n",
mf->get_plugin_name());
if (logfile)
fprintf(logfile,"Dump reader uses molfile plugin: %s\n",
mf->get_plugin_name());
}
}
/* ----------------------------------------------------------------------
try to open given file through plugin interface
only called by proc 0
------------------------------------------------------------------------- */
void ReaderMolfile::open_file(const char *file)
{
int rv;
char str[1024];
// close open file, if needed.
if (mf->is_open()) mf->close();
rv = mf->open(file,&natoms);
if (rv != MFI::E_NONE) {
sprintf(str,"Cannot open file %s",file);
error->one(FLERR,str);
}
if (natoms < 1) {
sprintf(str,"No atoms in file %s",file);
error->one(FLERR,str);
}
memory->create(types,natoms,"reader:types");
memory->create(coords,3*natoms,"reader:coords");
if (mf->has_vels())
memory->create(vels,3*natoms,"reader:vels");
// initialize system properties, if available
if (mf->has_props()) {
mf->structure();
mf->property(MFI::P_TYPE,types);
} else {
for (int i=0; i < natoms; ++i)
types[i] = 1;
}
}
/* ----------------------------------------------------------------------
close current file
only called by proc 0
------------------------------------------------------------------------- */
void ReaderMolfile::close_file()
{
mf->close();
}
/* ----------------------------------------------------------------------
read and return time stamp from dump file
if first read reaches end-of-file, return 1 so caller can open next file
only called by proc 0
------------------------------------------------------------------------- */
int ReaderMolfile::read_time(bigint &ntimestep)
{
int rv;
// try to read in the time step (coordinates, velocities and cell only)
rv = mf->timestep(coords, vels, cell, NULL);
if (rv != 0) return 1;
// we fake time step numbers.
ntimestep = nstep;
nstep++;
return 0;
}
/* ----------------------------------------------------------------------
skip snapshot from timestamp onward
only called by proc 0
------------------------------------------------------------------------- */
void ReaderMolfile::skip()
{
// since we can only signal EOF to the caller in ::read_time(), we
// have to read the entire timestep always there and this is a NOP.
;
}
/* ----------------------------------------------------------------------
read remaining header info:
return natoms
box bounds, triclinic (inferred), fieldflag (1 if any fields not found),
xyz flag = UNSET (not a requested field), SCALED, UNSCALED
if fieldflag set:
match Nfield fields to per-atom column labels
allocate and set fieldindex = which column each field maps to
fieldtype = X,VX,IZ etc
fieldlabel = user-specified label or NULL if use fieldtype default
xyz flag = scaledflag if has fieldlabel name, else set by x,xs,xu,xsu
only called by proc 0
------------------------------------------------------------------------- */
bigint ReaderMolfile::read_header(double box[3][3], int &triclinic,
int fieldinfo, int nfield,
int *fieldtype, char **fieldlabel,
int scaledflag, int &fieldflag,
int &xflag, int &yflag, int &zflag)
{
nid = 0;
// signal that we have no box info at all so far.
triclinic = -1;
// heuristics to determine if we have boxinfo (first if)
// and whether we have an orthogonal box (second if)
if (!is_smalldiff(cell[0]*cell[1]*cell[2], 0.0f)) {
if (is_smalldiff(cell[3],90.0f) && is_smalldiff(cell[4],90.0f) &&
is_smalldiff(cell[5],90.0f)) {
triclinic = 0;
// we have no information about the absolute location
// of the box, so we assume that the origin is in the middle.
// also we cannot tell periodicity. we assume, yes.
box[0][0] = -0.5*static_cast<double>(cell[0]);
box[0][1] = 0.5*static_cast<double>(cell[0]);
box[0][2] = 0.0;
box[1][0] = -0.5*static_cast<double>(cell[1]);
box[1][1] = 0.5*static_cast<double>(cell[1]);
box[1][2] = 0.0;
box[2][0] = -0.5*static_cast<double>(cell[2]);
box[2][1] = 0.5*static_cast<double>(cell[2]);
box[2][2] = 0.0;
} else {
triclinic = 1;
const double la = static_cast<double>(cell[0]);
const double lb = static_cast<double>(cell[1]);
const double lc = static_cast<double>(cell[2]);
const double alpha = static_cast<double>(cell[3]);
const double beta = static_cast<double>(cell[4]);
const double gamma = static_cast<double>(cell[5]);
const double lx = la;
const double xy = lb * cos(gamma/90.0*MY_PI2);
const double xz = lc * cos(beta/90.0*MY_PI2);
const double ly = sqrt(lb*lb - xy*xy);
const double yz = (fabs(ly) > SMALL) ?
(lb*lc*cos(alpha/90.0*MY_PI2) - xy*xz) / ly : 0.0;
const double lz = sqrt(lc*lc - xz*xz - yz*yz);
/* go from box length to boundary */
double xbnd;
xbnd = 0.0;
xbnd = (xy < xbnd) ? xy : xbnd;
xbnd = (xz < xbnd) ? xz : xbnd;
xbnd = (xy+xz < xbnd) ? (xy + xz) : xbnd;
box[0][0] = -0.5*lx + xbnd;
xbnd = 0.0;
xbnd = (xy > xbnd) ? xy : xbnd;
xbnd = (xz > xbnd) ? xz : xbnd;
xbnd = (xy+xz > xbnd) ? (xy + xz) : xbnd;
box[0][1] = 0.5*lx+xbnd;
box[0][2] = xy;
xbnd = 0.0;
xbnd = (yz < xbnd) ? yz : xbnd;
box[1][0] = -0.5*ly+xbnd;
xbnd = 0.0;
xbnd = (yz > xbnd) ? yz : xbnd;
box[1][1] = 0.5*ly+xbnd;
box[1][2] = xz;
box[2][0] = -0.5*lz;
box[2][1] = 0.5*lz;
box[2][2] = yz;
}
}
// if no field info requested, just return
if (!fieldinfo) return natoms;
memory->create(fieldindex,nfield,"read_dump:fieldindex");
// we know nothing about the scaling style of coordinates,
// so the caller has to set the proper flag.
xflag = scaledflag;
yflag = scaledflag;
zflag = scaledflag;
// copy fieldtype list for supported fields
fieldflag = 0;
needvels = 0;
for (int i = 0; i < nfield; i++) {
if ( (fieldtype[i] == X) ||
(fieldtype[i] == Y) ||
(fieldtype[i] == Z) ||
(fieldtype[i] == ID) ||
(fieldtype[i] == TYPE) ) {
fieldindex[i] = fieldtype[i];
} else if ( (fieldtype[i] == VX) ||
(fieldtype[i] == VY) ||
(fieldtype[i] == VZ) ) {
fieldindex[i] = fieldtype[i];
needvels = 1;
} else {
fieldflag = 1;
}
}
if ((needvels > 0) && (!mf->has_vels()))
error->one(FLERR,"Molfile plugin does not support reading velocities");
return natoms;
}
/* ----------------------------------------------------------------------
read N atom lines from dump file
stores appropriate values in fields array
return 0 if success, 1 if error
only called by proc 0
------------------------------------------------------------------------- */
void ReaderMolfile::read_atoms(int n, int nfield, double **fields)
{
int i,m,mytype;
char buf[16];
for (i = 0; i < n; i++) {
++nid;
if (mf->property(MFI::P_TYPE,nid-1,buf) != MFI::P_NONE) {
mytype = atoi(buf);
} else mytype = 0;
for (m = 0; m < nfield; m++) {
switch (fieldindex[m]) {
case X:
fields[i][m] = static_cast<double>(coords[3*nid-3]);
break;
case Y:
fields[i][m] = static_cast<double>(coords[3*nid-2]);
break;
case Z:
fields[i][m] = static_cast<double>(coords[3*nid-1]);
break;
case VX:
fields[i][m] = static_cast<double>(vels[3*nid-3]);
break;
case VY:
fields[i][m] = static_cast<double>(vels[3*nid-2]);
break;
case VZ:
fields[i][m] = static_cast<double>(vels[3*nid-1]);
break;
case ID:
fields[i][m] = nid;
break;
case TYPE:
fields[i][m] = mytype;
break;
}
}
}
}
c4science · Help