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adjust compute cnp/atom to match the documentation. need to skip atoms not in compute group.

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This commit is contained in:
Axel Kohlmeyer
2017-06-10 16:55:42 -04:00
parent 2b3c124e61
commit a849f35dcd
2 changed files with 17 additions and 13 deletions
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6
doc/src/compute_cnp_atom.txt
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@ -29,9 +29,9 @@ around an atom and can be used to characterize whether the
atom is part of a perfect lattice, a local defect (e.g. a dislocation
or stacking fault), or at a surface.
The value of the CNP parameter will be 0.0 for atoms not
in the specified compute group. Note that normally a CNP calculation should only be
performed on mono-component systems.
The value of the CNP parameter will be 0.0 for atoms not in the
specified compute group. Note that normally a CNP calculation should
only be performed on single component systems.
This parameter is computed using the following formula from
"(Tsuzuki)"_#Tsuzuki2

24
src/USER-MISC/compute_cnp_atom.cpp
View File

@ -117,7 +117,7 @@ void ComputeCNPAtom::compute_peratom()
int i,j,k,ii,jj,kk,m,n,inum,jnum,inear,jnear;
int firstflag,ncommon;
int *ilist,*jlist,*numneigh,**firstneigh;
int cnp[MAXNEAR][4],onenearest[MAXNEAR];
int onenearest[MAXNEAR];
int common[MAXCOMMON];
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double xjtmp,yjtmp,zjtmp,rjkx,rjky,rjkz;
@ -204,8 +204,12 @@ void ComputeCNPAtom::compute_peratom()
ytmp = x[i][1];
ztmp = x[i][2];
// reset cnpv
cnpv[i] = 0.0;
cnpv[i] = 0.0;
// skip computation of cnpv for atoms outside the compute group
if (!(mask[i] & groupbit)) continue;
// loop over nearest neighbors of I to build cnp data structure
// cnp[k][NCOMMON] = # of common neighbors of I with each of its neighbors
for (m = 0; m < nnearest[i]; m++) {
@ -265,12 +269,12 @@ void ComputeCNPAtom::compute_peratom()
firstflag = 0;
}
}
}
}
// Calculate and update sum |Rik+Rjk|ˆ2
rjkx = 0.0;
rjky = 0.0;
rjkz = 0.0;
rjkz = 0.0;
for (kk = 0; kk < ncommon; kk++) {
k = common[kk];
rjkx += 2.0*x[k][0] - xjtmp - xtmp;
@ -279,16 +283,16 @@ void ComputeCNPAtom::compute_peratom()
}
// update cnpv with summed (valuejk)
cnpv[i] += rjkx*rjkx + rjky*rjky + rjkz*rjkz;
// end of loop over j atoms
}
// normalize cnp by the number of nearest neighbors
cnpv[i] = cnpv[i] / nnearest[i];
// end of loop over i atoms
}
}
// warning message
MPI_Allreduce(&nerror,&nerrorall,1,MPI_INT,MPI_SUM,world);
if (nerrorall && comm->me == 0) {