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Merge pull request #2486 from tomswinburne/master

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Very minor bug fix for NEB
This commit is contained in:
Richard Berger
2020-11-30 12:55:21 -05:00
committed by GitHub
parent e0c87fc0b6 dde42a5bd0
commit e2e86bbffa
1 changed files with 15 additions and 16 deletions
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31
src/REPLICA/neb.cpp
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@ -69,9 +69,7 @@ NEB::NEB(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in,
MPI_Comm_rank(world,&me);
// generate linear interpolate replica
double fraction = ireplica/(nreplica-1.0);
double **x = atom->x;
int nlocal = atom->nlocal;
@ -465,13 +463,12 @@ void NEB::readfile(char *file, int flag)
// adjust atom coord based on replica fraction
// for flag = 0, interpolate for intermediate and final replicas
// for flag = 1, replace existing coord with new coord
// ignore image flags of final x
// for interpolation:
// new x is displacement from old x via minimum image convention
// if final x is across periodic boundary:
// new x may be outside box
// will be remapped back into box when simulation starts
// its image flags will then be adjusted
// ignore image flags of replica x
// displacement from first replica is via minimum image convention
// if x of some replica is across periodic boundary:
// new x may be outside box
// will be remapped back into box when simulation starts
// its image flags will then be adjusted
tag = ATOTAGINT(values[0]);
m = atom->map(tag);
@ -481,18 +478,20 @@ void NEB::readfile(char *file, int flag)
yy = atof(values[2]);
zz = atof(values[3]);
delx = xx - x[m][0];
dely = yy - x[m][1];
delz = zz - x[m][2];
domain->minimum_image(delx,dely,delz);
if (flag == 0) {
delx = xx - x[m][0];
dely = yy - x[m][1];
delz = zz - x[m][2];
domain->minimum_image(delx,dely,delz);
x[m][0] += fraction*delx;
x[m][1] += fraction*dely;
x[m][2] += fraction*delz;
} else {
x[m][0] = xx;
x[m][1] = yy;
x[m][2] = zz;
x[m][0] += delx;
x[m][1] += dely;
x[m][2] += delz;
}
}