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Merge branch 'compute-snap-apt-2' of github.com:rohskopf/lammps into HEAD

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This commit is contained in:
Aidan Thompson
2022-07-07 11:46:24 -06:00
parent c838c9da6f 0bae7108b5
commit c488db6fe0
3 changed files with 75 additions and 71 deletions
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1
lammps Symbolic link
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@ -0,0 +1 @@
python/lammps/

6
src/ML-SNAP/compute_snap.cpp
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@ -24,7 +24,6 @@
#include "comm.h" #include "comm.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "universe.h" // For MPI
#include <cstring> #include <cstring>
@ -321,6 +320,7 @@ void ComputeSnap::compute_array()
} }
// clear global array // clear global array
for (int irow = 0; irow < size_array_rows; irow++){ for (int irow = 0; irow < size_array_rows; irow++){
for (int icoeff = 0; icoeff < size_array_cols; icoeff++){ for (int icoeff = 0; icoeff < size_array_cols; icoeff++){
snap[irow][icoeff] = 0.0; snap[irow][icoeff] = 0.0;
@ -371,7 +371,9 @@ void ComputeSnap::compute_array()
const int typeoffset_global = nvalues*(itype-1); const int typeoffset_global = nvalues*(itype-1);
if (dgradflag){ if (dgradflag){
// dBi/dRi tags // dBi/dRi tags
snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 0][0] = atom->tag[i]-1; snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 0][0] = atom->tag[i]-1;
snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 0][1] = atom->tag[i]-1; snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 0][1] = atom->tag[i]-1;
snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 0][2] = 0; snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 0][2] = 0;
@ -381,7 +383,9 @@ void ComputeSnap::compute_array()
snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 2][0] = atom->tag[i]-1; snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 2][0] = atom->tag[i]-1;
snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 2][1] = atom->tag[i]-1; snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 2][1] = atom->tag[i]-1;
snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 2][2] = 2; snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 2][2] = 2;
// dBi/dRj tags // dBi/dRj tags
for (int j=0; j<natoms; j++){ for (int j=0; j<natoms; j++){
snap[bik_rows + ((j)*3*natoms) + 3*(atom->tag[i]-1) + 0][0] = atom->tag[i]-1; snap[bik_rows + ((j)*3*natoms) + 3*(atom->tag[i]-1) + 0][0] = atom->tag[i]-1;
snap[bik_rows + ((j)*3*natoms) + 3*(atom->tag[i]-1) + 0][1] = j; snap[bik_rows + ((j)*3*natoms) + 3*(atom->tag[i]-1) + 0][1] = j;

1
src/ML-SNAP/compute_snap.h
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@ -53,7 +53,6 @@ class ComputeSnap : public Compute {
double cutmax; double cutmax;
int quadraticflag; int quadraticflag;
int bikflag, bik_rows, dgradflag, dgrad_rows; int bikflag, bik_rows, dgradflag, dgrad_rows;
int rank;
Compute *c_pe; Compute *c_pe;
Compute *c_virial; Compute *c_virial;