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Fix bug in atom sorting with triclinic boxes #3756

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merged 4 commits into from
Apr 27, 2023
+18 −1
Merged

Fix bug in atom sorting with triclinic boxes #3756

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a4d56b5
Fix bug in atom sorting with triclinic boxes
stanmoore1 Apr 27, 2023
1f54dc3
Port changes to Kokkos
stanmoore1 Apr 27, 2023
c95a349
Small tweak
stanmoore1 Apr 27, 2023
7c3deba
whitespace
stanmoore1 Apr 27, 2023
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11 changes: 10 additions & 1 deletion src/KOKKOS/atom_kokkos.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -165,8 +165,11 @@ void AtomKokkos::sort()

if (nlocal == nmax) avec->grow(0);

// for triclinic, atoms must be in box coords (not lamda) to match bbox

if (domain->triclinic) domain->lamda2x(nlocal);

sync(Host, ALL_MASK);
modified(Host, ALL_MASK);

// bin atoms in reverse order so linked list will be in forward order

Expand Down Expand Up @@ -233,6 +236,12 @@ void AtomKokkos::sort()
//int flagall;
//MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
//if (flagall) errorX->all(FLERR,"Atom sort did not operate correctly");

modified(Host, ALL_MASK);

// convert back to lamda coords

if (domain->triclinic) domain->x2lamda(nlocal);
}

/* ----------------------------------------------------------------------
Expand Down
8 changes: 8 additions & 0 deletions src/atom.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2271,6 +2271,10 @@ void Atom::sort()

for (i = 0; i < nbins; i++) binhead[i] = -1;

// for triclinic, atoms must be in box coords (not lamda) to match bbox

if (domain->triclinic) domain->lamda2x(nlocal);

for (i = nlocal-1; i >= 0; i--) {
ix = static_cast<int> ((x[i][0]-bboxlo[0])*bininvx);
iy = static_cast<int> ((x[i][1]-bboxlo[1])*bininvy);
Expand All @@ -2286,6 +2290,10 @@ void Atom::sort()
binhead[ibin] = i;
}

// convert back to lamda coords

if (domain->triclinic) domain->x2lamda(nlocal);

// permute = desired permutation of atoms
// permute[I] = J means Ith new atom will be Jth old atom

Expand Down