Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F82624849
ntopo_dihedral_template.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Thu, Sep 12, 12:15
Size
4 KB
Mime Type
text/x-c
Expires
Sat, Sep 14, 12:15 (1 d, 21 h)
Engine
blob
Format
Raw Data
Handle
20722147
Attached To
rLAMMPS lammps
ntopo_dihedral_template.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.
------------------------------------------------------------------------- */
#include <mpi.h>
#include "ntopo_dihedral_template.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "domain.h"
#include "update.h"
#include "output.h"
#include "thermo.h"
#include "molecule.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
NTopoDihedralTemplate::NTopoDihedralTemplate(LAMMPS *lmp) :
NTopo(lmp)
{
allocate_dihedral();
}
/* ---------------------------------------------------------------------- */
void NTopoDihedralTemplate::build()
{
int i,m,atom1,atom2,atom3,atom4;
int imol,iatom;
tagint tagprev;
int *num_dihedral;
tagint **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
int **dihedral_type;
Molecule **onemols = atom->avec->onemols;
tagint *tag = atom->tag;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
int lostbond = output->thermo->lostbond;
int nmissing = 0;
ndihedrallist = 0;
for (i = 0; i < nlocal; i++) {
if (molindex[i] < 0) continue;
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
num_dihedral = onemols[imol]->num_dihedral;
dihedral_atom1 = onemols[imol]->dihedral_atom1;
dihedral_atom2 = onemols[imol]->dihedral_atom2;
dihedral_atom3 = onemols[imol]->dihedral_atom3;
dihedral_atom4 = onemols[imol]->dihedral_atom4;
dihedral_type = onemols[imol]->dihedral_type;
for (m = 0; m < num_dihedral[iatom]; m++) {
atom1 = atom->map(dihedral_atom1[iatom][m]+tagprev);
atom2 = atom->map(dihedral_atom2[iatom][m]+tagprev);
atom3 = atom->map(dihedral_atom3[iatom][m]+tagprev);
atom4 = atom->map(dihedral_atom4[iatom][m]+tagprev);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
if (lostbond == ERROR) {
char str[128];
sprintf(str,"Dihedral atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
dihedral_atom1[iatom][m]+tagprev,
dihedral_atom2[iatom][m]+tagprev,
dihedral_atom3[iatom][m]+tagprev,
dihedral_atom4[iatom][m]+tagprev,
me,update->ntimestep);
error->one(FLERR,str);
}
continue;
}
atom1 = domain->closest_image(i,atom1);
atom2 = domain->closest_image(i,atom2);
atom3 = domain->closest_image(i,atom3);
atom4 = domain->closest_image(i,atom4);
if (newton_bond ||
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (ndihedrallist == maxdihedral) {
maxdihedral += DELTA;
memory->grow(dihedrallist,maxdihedral,5,"neigh_topo:dihedrallist");
}
dihedrallist[ndihedrallist][0] = atom1;
dihedrallist[ndihedrallist][1] = atom2;
dihedrallist[ndihedrallist][2] = atom3;
dihedrallist[ndihedrallist][3] = atom4;
dihedrallist[ndihedrallist][4] = dihedral_type[iatom][m];
ndihedrallist++;
}
}
}
if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
if (lostbond == IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
if (all) {
char str[128];
sprintf(str,
"Dihedral atoms missing at step " BIGINT_FORMAT,update->ntimestep);
if (me == 0) error->warning(FLERR,str);
}
}
Event Timeline
Log In to Comment