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modified versions of creating atoms on subset of lattice, ditto for set type/fraction

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This commit is contained in:
Steve Plimpton
2020-01-21 13:31:47 -07:00
parent 4ea679dd54
commit 90ff2eb6c9
13 changed files with 486 additions and 238 deletions
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12
src/read_restart.cpp
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@ -165,6 +165,12 @@ void ReadRestart::command(int narg, char **arg)
atom->allocate_type_arrays();
atom->deallocate_topology();
// allocate atom arrays to size N, rounded up by AtomVec->DELTA
bigint nbig = n;
nbig = atom->avec->roundup(nbig);
n = static_cast<int> (nbig);
atom->avec->grow(n);
n = atom->nmax;
@ -211,13 +217,17 @@ void ReadRestart::command(int narg, char **arg)
memory->create(buf,assignedChunkSize,"read_restart:buf");
mpiio->read((headerOffset+assignedChunkOffset),assignedChunkSize,buf);
mpiio->close();
if (!nextra) { // We can actually calculate number of atoms from assignedChunkSize
// can calculate number of atoms from assignedChunkSize
if (!nextra) {
atom->nlocal = 1; // temporarily claim there is one atom...
int perAtomSize = avec->size_restart(); // ...so we can get its size
atom->nlocal = 0; // restore nlocal to zero atoms
int atomCt = (int) (assignedChunkSize / perAtomSize);
if (atomCt > atom->nmax) avec->grow(atomCt);
}
m = 0;
while (m < assignedChunkSize) m += avec->unpack_restart(&buf[m]);
}