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"stringify" and "vectorize" processing of per-atom attributs in AtomVec classes

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This commit is contained in:
Axel Kohlmeyer
2022-04-14 11:06:10 -04:00
parent 1755d06870
commit b16d48aa41
37 changed files with 1596 additions and 1832 deletions
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76
src/AWPMD/atom_vec_wavepacket.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -20,8 +19,6 @@
#include "atom.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
@ -32,33 +29,29 @@ AtomVecWavepacket::AtomVecWavepacket(LAMMPS *lmp) : AtomVec(lmp)
molecular = Atom::ATOMIC;
forceclearflag = 1;
atom->wavepacket_flag = 1;
atom->electron_flag = 1; // compatible with eff
atom->q_flag = atom->spin_flag = atom->eradius_flag =
atom->ervel_flag = atom->erforce_flag = 1;
atom->cs_flag = atom->csforce_flag =
atom->vforce_flag = atom->ervelforce_flag = atom->etag_flag = 1;
atom->wavepacket_flag = atom->q_flag = atom->spin_flag = atom->eradius_flag = 1;
atom->ervel_flag = atom->erforce_flag = atom->cs_flag = atom->csforce_flag = 1;
atom->vforce_flag = atom->ervelforce_flag = atom->etag_flag = 1;
// strings with peratom variables to include in each AtomVec method
// strings cannot contain fields in corresponding AtomVec default strings
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *)
"q spin eradius ervel erforce cs csforce "
"vforce ervelforce etag";
fields_copy = (char *) "q spin eradius ervel cs etag";
fields_comm = (char *) "eradius";
fields_comm_vel = (char *) "eradius ervel cs";
fields_reverse = (char *) "erforce ervelforce vforce csforce";
fields_border = (char *) "q spin eradius etag";
fields_border_vel = (char *) "q spin eradius etag ervel cs";
fields_exchange = (char *) "q spin eradius ervel etag cs";
fields_restart = (char *) "q spin eradius ervel etag cs";
fields_create = (char *) "q spin eradius ervel etag cs";
fields_data_atom = (char *) "id type q spin eradius etag cs x";
fields_data_vel = (char *) "id v ervel";
fields_grow = {"q", "spin", "eradius", "ervel", "erforce",
"cs", "csforce", "vforce", "ervelforce", "etag"};
fields_copy = {"q", "spin", "eradius", "ervel", "cs", "etag"};
fields_comm = {"eradius"};
fields_comm_vel = {"eradius", "ervel", "cs"};
fields_reverse = {"erforce", "ervelforce", "vforce", "csforce"};
fields_border = {"q", "spin", "eradius", "etag"};
fields_border_vel = {"q", "spin", "eradius", "etag", "ervel", "cs"};
fields_exchange = {"q", "spin", "eradius", "ervel", "etag", "cs"};
fields_restart = {"q", "spin", "eradius", "ervel", "etag", "cs"};
fields_create = {"q", "spin", "eradius", "ervel", "etag", "cs"};
fields_data_atom = {"id", "type", "q", "spin", "eradius", "etag", "cs", "x"};
fields_data_vel = {"id", "v", "ervel"};
setup_fields();
}
@ -84,7 +77,7 @@ void AtomVecWavepacket::grow_pointers()
void AtomVecWavepacket::force_clear(int n, size_t nbytes)
{
memset(&erforce[n],0,nbytes);
memset(&erforce[n], 0, nbytes);
}
/* ----------------------------------------------------------------------
@ -114,10 +107,10 @@ void AtomVecWavepacket::data_atom_post(int ilocal)
int AtomVecWavepacket::property_atom(char *name)
{
if (strcmp(name,"spin") == 0) return 0;
if (strcmp(name,"eradius") == 0) return 1;
if (strcmp(name,"ervel") == 0) return 2;
if (strcmp(name,"erforce") == 0) return 3;
if (strcmp(name, "spin") == 0) return 0;
if (strcmp(name, "eradius") == 0) return 1;
if (strcmp(name, "ervel") == 0) return 2;
if (strcmp(name, "erforce") == 0) return 3;
return -1;
}
@ -126,34 +119,41 @@ int AtomVecWavepacket::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecWavepacket::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
void AtomVecWavepacket::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
{
int nlocal = atom->nlocal;
int n = 0;
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = spin[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = spin[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = eradius[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = eradius[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 2) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = ervel[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = ervel[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 3) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = erforce[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = erforce[i];
else
buf[n] = 0.0;
n += nvalues;
}
}