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update neighbor list requests and compute style lookups in machine learning packages

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This commit is contained in:
Axel Kohlmeyer
2022-03-09 06:49:07 -05:00
parent 3bb7a247ac
commit e8547af049
11 changed files with 44 additions and 103 deletions
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5
src/ML-HDNNP/pair_hdnnp.cpp
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@ -26,7 +26,6 @@
#include "error.h"
#include "memory.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "update.h"
@ -226,9 +225,7 @@ void PairHDNNP::coeff(int narg, char **arg)
void PairHDNNP::init_style()
{
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->add_request(this, NeighConst::REQ_FULL);
// Return immediately if HDNNP setup is already completed.
if (interface->isInitialized()) return;

28
src/ML-IAP/compute_mliap.cpp
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@ -16,7 +16,7 @@
Contributing author: Aidan Thompson (SNL)
------------------------------------------------------------------------- */
#include <cstring>
#include "compute_mliap.h"
#include "mliap_data.h"
#include "mliap_model_linear.h"
@ -26,17 +26,17 @@
#include "mliap_model_python.h"
#endif
#include "compute_mliap.h"
#include "atom.h"
#include "update.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
@ -151,17 +151,9 @@ void ComputeMLIAP::init()
// need an occasional full neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"mliap") == 0) count++;
if (count > 1 && comm->me == 0)
if (modify->get_compute_by_style("mliap").size() > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute mliap");
// initialize model and descriptor

5
src/ML-IAP/pair_mliap.cpp
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@ -32,7 +32,6 @@
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neigh_request.h"
#include "neighbor.h"
#include <cmath>
@ -314,9 +313,7 @@ void PairMLIAP::init_style()
// need a full neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->add_request(this, NeighConst::REQ_FULL);
}

5
src/ML-PACE/pair_pace.cpp
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@ -35,7 +35,6 @@ Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
#include "math_const.h"
#include "memory.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "update.h"
@ -354,9 +353,7 @@ void PairPACE::init_style()
if (force->newton_pair == 0) error->all(FLERR, "Pair style pACE requires newton pair on");
// request a full neighbor list
int irequest = neighbor->request(this, instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ----------------------------------------------------------------------

7
src/ML-QUIP/pair_quip.cpp
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@ -25,7 +25,6 @@
#include "force.h"
#include "memory.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "potential_file_reader.h"
#include "update.h"
@ -308,10 +307,8 @@ void PairQUIP::init_style()
if (force->newton_pair != 1) error->all(FLERR, "Pair style quip requires newton pair on");
// Initialise neighbor list
int irequest_full = neighbor->request(this);
neighbor->requests[irequest_full]->half = 0;
neighbor->requests[irequest_full]->full = 1;
// request full neighbor list
neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ----------------------------------------------------------------------

28
src/ML-RANN/pair_rann.cpp
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@ -38,7 +38,6 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "tokenizer.h"
#include "update.h"
@ -1253,10 +1252,7 @@ void PairRANN::init_list(int /*which*/, NeighList *ptr)
void PairRANN::init_style()
{
int irequest_full = neighbor->request(this,instance_me);
neighbor->requests[irequest_full]->id = 1;
neighbor->requests[irequest_full]->half = 0;
neighbor->requests[irequest_full]->full = 1;
neighbor->add_request(this, NeighConst::REQ_FULL);
}
@ -1274,34 +1270,34 @@ void PairRANN::errorf(const char *file, int line, const char * message) {
}
int PairRANN::factorial(int n) {
return round(MathSpecial::factorial(n));
return round(MathSpecial::factorial(n));
}
RANN::Fingerprint *PairRANN::create_fingerprint(const char *style)
{
if (strcmp(style,"radial")==0) {
return new RANN::Fingerprint_radial(this);
return new RANN::Fingerprint_radial(this);
}
else if (strcmp(style,"radialscreened")==0) {
return new RANN::Fingerprint_radialscreened(this);
return new RANN::Fingerprint_radialscreened(this);
}
else if (strcmp(style,"radialscreenedspin")==0) {
return new RANN::Fingerprint_radialscreenedspin(this);
return new RANN::Fingerprint_radialscreenedspin(this);
}
else if (strcmp(style,"radialspin")==0) {
return new RANN::Fingerprint_radialspin(this);
return new RANN::Fingerprint_radialspin(this);
}
else if (strcmp(style,"bond")==0) {
return new RANN::Fingerprint_bond(this);
return new RANN::Fingerprint_bond(this);
}
else if (strcmp(style,"bondscreened")==0) {
return new RANN::Fingerprint_bondscreened(this);
return new RANN::Fingerprint_bondscreened(this);
}
else if (strcmp(style,"bondscreenedspin")==0) {
return new RANN::Fingerprint_bondscreenedspin(this);
return new RANN::Fingerprint_bondscreenedspin(this);
}
else if (strcmp(style,"bondspin")==0) {
return new RANN::Fingerprint_bondspin(this);
return new RANN::Fingerprint_bondspin(this);
}
error->one(FLERR,"Unknown fingerprint style {}",style);
return nullptr;
@ -1311,10 +1307,10 @@ RANN::Fingerprint *PairRANN::create_fingerprint(const char *style)
RANN::Activation *PairRANN::create_activation(const char *style)
{
if (strcmp(style,"linear")==0) {
return new RANN::Activation_linear(this);
return new RANN::Activation_linear(this);
}
else if (strcmp(style,"sigI")==0) {
return new RANN::Activation_sigI(this);
return new RANN::Activation_sigI(this);
}
error->one(FLERR,"Unknown activation style {}",style);
return nullptr;

16
src/ML-SNAP/compute_sna_atom.cpp
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@ -13,7 +13,6 @@
------------------------------------------------------------------------- */
#include "compute_sna_atom.h"
#include <cstring>
#include "sna.h"
#include "atom.h"
@ -21,13 +20,14 @@
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include <cstring>
using namespace LAMMPS_NS;
ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
@ -172,17 +172,9 @@ void ComputeSNAAtom::init()
// need an occasional full neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"sna/atom") == 0) count++;
if (count > 1 && comm->me == 0)
if (modify->get_compute_by_style("sna/atom").size() > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute sna/atom");
snaptr->init();
}

16
src/ML-SNAP/compute_snad_atom.cpp
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@ -13,7 +13,6 @@
------------------------------------------------------------------------- */
#include "compute_snad_atom.h"
#include <cstring>
#include "sna.h"
#include "atom.h"
@ -21,13 +20,14 @@
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include <cstring>
using namespace LAMMPS_NS;
ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
@ -174,17 +174,9 @@ void ComputeSNADAtom::init()
// need an occasional full neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"snad/atom") == 0) count++;
if (count > 1 && comm->me == 0)
if (modify->get_compute_by_style("snad/atom").size() > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute snad/atom");
snaptr->init();
}

16
src/ML-SNAP/compute_snap.cpp
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@ -13,7 +13,6 @@
------------------------------------------------------------------------- */
#include "compute_snap.h"
#include <cstring>
#include "sna.h"
#include "atom.h"
@ -21,13 +20,14 @@
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include <cstring>
using namespace LAMMPS_NS;
enum{SCALAR,VECTOR,ARRAY};
@ -197,17 +197,9 @@ void ComputeSnap::init()
// need an occasional full neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"snap") == 0) count++;
if (count > 1 && comm->me == 0)
if (modify->get_compute_by_style("snap").size() > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute snap");
snaptr->init();

16
src/ML-SNAP/compute_snav_atom.cpp
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@ -13,7 +13,6 @@
------------------------------------------------------------------------- */
#include "compute_snav_atom.h"
#include <cstring>
#include "sna.h"
#include "atom.h"
@ -21,12 +20,13 @@
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include <cstring>
using namespace LAMMPS_NS;
ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
@ -170,17 +170,9 @@ void ComputeSNAVAtom::init()
// need an occasional full neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"snav/atom") == 0) count++;
if (count > 1 && comm->me == 0)
if (modify->get_compute_by_style("snav/atom").size() > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute snav/atom");
snaptr->init();
}

5
src/ML-SNAP/pair_snap.cpp
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@ -20,7 +20,6 @@
#include "force.h"
#include "memory.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "sna.h"
#include "tokenizer.h"
@ -435,9 +434,7 @@ void PairSNAP::init_style()
// need a full neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->add_request(this, NeighConst::REQ_FULL);
snaptr->init();