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Use lammps memory class in pair_pod

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This commit is contained in:
rohskopf
2022-11-19 16:37:27 -07:00
parent af36dc3df0
commit d8169b02ff
5 changed files with 51 additions and 57 deletions
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2
examples/pod/README.md
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@ -12,7 +12,7 @@ Go to `lammps` directory and build with the POD package:
Go to `lammps/examples/pod/Ta` directory and run
lmp < in.podfit
lmp -n in.podfit
See the README in `lammps/examples/pod/Ta` for instructions on how to run MD with the potential.

4
examples/pod/Ta/README.md
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@ -5,10 +5,10 @@ of the training data taken from [the FitSNAP repo](https://github.com/FitSNAP/Fi
Fit POD with
lmp < in.podfit
lmp -in in.podfit
This creates `coefficients.txt` for the linear model, which we can use to run MD with
lmp < in.pod
lmp -in in.pod

79
src/ML-POD/pair_pod.cpp
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@ -10,8 +10,6 @@
#include "neighbor.h"
#include "tokenizer.h"
#include <glob.h>
#include <cmath>
#include <cstring>
#include <sys/time.h>
@ -27,6 +25,7 @@ CPairPOD::CPairPOD(LAMMPS *lmp) : Pair(lmp)
one_coeff = 1;
manybody_flag = 1;
centroidstressflag = CENTROID_NOTAVAIL;
podptr = nullptr;
}
/* ---------------------------------------------------------------------- */
@ -34,11 +33,11 @@ CPairPOD::CPairPOD(LAMMPS *lmp) : Pair(lmp)
CPairPOD::~CPairPOD()
{
free_memory();
TemplateFree(gd, backend);
TemplateFree(energycoeff, backend);
TemplateFree(forcecoeff, backend);
TemplateFree(podcoeff, backend);
TemplateFree(newpodcoeff, backend);
memory->destroy(podcoeff);
memory->destroy(newpodcoeff);
memory->destroy(gd);
memory->destroy(energycoeff);
memory->destroy(forcecoeff);
delete podptr;
@ -227,11 +226,11 @@ void CPairPOD::InitPairPOD(std::string pod_file, std::string coeff_file)
lammpspairlist = 1;
if (coeff_file != "") {
TemplateMalloc(&podcoeff, podptr->pod.nd, backend);
TemplateMalloc(&newpodcoeff, podptr->pod.nd, backend);
TemplateMalloc(&energycoeff, podptr->pod.nd1234, backend);
TemplateMalloc(&forcecoeff, podptr->pod.nd1234, backend);
TemplateMalloc(&gd, podptr->pod.nd1234, backend);
memory->create(podcoeff, podptr->pod.nd, "pair:podcoeff");
memory->create(newpodcoeff, podptr->pod.nd, "pair:newpodcoeff");
memory->create(energycoeff, podptr->pod.nd1234, "pair:energycoeff");
memory->create(forcecoeff, podptr->pod.nd1234, "pair:forcecoeff");
memory->create(gd, podptr->pod.nd1234, "pair:gd");
podptr->podArrayCopy(podcoeff, podptr->pod.coeff, podptr->pod.nd);
podptr->podArrayCopy(newpodcoeff, podptr->pod.coeff, podptr->pod.nd);
}
@ -240,25 +239,25 @@ void CPairPOD::InitPairPOD(std::string pod_file, std::string coeff_file)
void CPairPOD::free_tempmemory()
{
TemplateFree(rij, backend);
TemplateFree(idxi, backend);
TemplateFree(ai, backend);
TemplateFree(aj, backend);
TemplateFree(ti, backend);
TemplateFree(tj, backend);
TemplateFree(numneighsum, backend);
TemplateFree(typeai, backend);
TemplateFree(tmpmem, backend);
memory->destroy(rij);
memory->destroy(idxi);
memory->destroy(ai);
memory->destroy(aj);
memory->destroy(ti);
memory->destroy(tj);
memory->destroy(numneighsum);
memory->destroy(typeai);
memory->destroy(tmpmem);
}
void CPairPOD::free_atommemory()
{
TemplateFree(forces, backend);
TemplateFree(stress, backend);
memory->destroy(forces);
memory->destroy(stress);
if (atommemory) {
TemplateFree(atomtype, backend);
TemplateFree(pos, backend);
TemplateFree(vel, backend);
memory->destroy(atomtype);
memory->destroy(pos);
memory->destroy(vel);
}
}
@ -270,25 +269,25 @@ void CPairPOD::free_memory()
void CPairPOD::allocate_tempmemory()
{
TemplateMalloc(&rij, dim*nijmax, backend);
TemplateMalloc(&idxi, nijmax, backend);
TemplateMalloc(&ai, nijmax, backend);
TemplateMalloc(&aj, nijmax, backend);
TemplateMalloc(&ti, nijmax, backend);
TemplateMalloc(&tj, nijmax, backend);
TemplateMalloc(&numneighsum, nablockmax+1, backend);
TemplateMalloc(&typeai, nablockmax, backend);
TemplateMalloc(&tmpmem, szd, backend);
memory->create(rij, dim*nijmax, "pair:rij");
memory->create(idxi, nijmax, "pair:idxi");
memory->create(ai, nijmax, "pair:ai");
memory->create(aj, nijmax, "pair:aj");
memory->create(ti, nijmax, "pair:ti");
memory->create(tj, nijmax, "pair:tj");
memory->create(numneighsum, nablockmax+1, "pair:numneighsum");
memory->create(typeai, nablockmax, "pair:typeai");
memory->create(tmpmem, szd, "pair:tmpmem");
}
void CPairPOD::allocate_atommemory()
{
TemplateMalloc(&forces, dim*nmaxatom, backend);
TemplateMalloc(&stress, 9, backend);
memory->create(forces, dim*nmaxatom, "pair:forces");
memory->create(stress, 9, "pair:stress");
if (atommemory) {
TemplateMalloc(&atomtype, nmaxatom, backend);
TemplateMalloc(&pos, dim*nmaxatom, backend);
TemplateMalloc(&vel, dim*nmaxatom, backend);
memory->create(atomtype, nmaxatom, "pair:atomtype");
memory->create(pos, dim*nmaxatom, "pair:pos");
memory->create(vel, dim*nmaxatom, "pair:vel");
}
}

16
src/ML-POD/pair_pod.h
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@ -61,20 +61,10 @@ namespace LAMMPS_NS {
data.filenames = filenames;
}
void freememory(int backend)
{
TemplateFree(lattice, backend);
TemplateFree(energy, backend);
TemplateFree(stress, backend);
TemplateFree(position, backend);
TemplateFree(velocity, backend);
TemplateFree(force, backend);
TemplateFree(atomtype, backend);
}
};
datastruct data;
class CPOD *podptr;
//class CPOD *podptr;
CPairPOD(class LAMMPS *);
~CPairPOD() override;
@ -89,7 +79,6 @@ namespace LAMMPS_NS {
void InitPairPOD(std::string pod_file, std::string coeff_file);
int backend=1;
int dim = 3;
int atommemory = 0;
int podpairlist=0;
@ -156,6 +145,9 @@ namespace LAMMPS_NS {
int nijmax=0; // maximum number of atom pairs
int szd=0; // size of tmpmem
class CPOD *podptr;
// class SNA *snaptr; // why does this work, but commenting #include pod.h causes the above line to fail?
// temporary arrays for computation blocks
double *tmpmem=NULL; // temporary memory

7
src/ML-POD/pod.h
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@ -4,8 +4,11 @@
Contributing authors: Ngoc-Cuong Nguyen (cuongng@mit.edu, exapde@gmail.com)
***************************************************************************/
#ifndef __POD_H__
#define __POD_H__
#ifndef LMP_POD_H__
#define LMP_POD_H__
//#ifndef LMP_SNA_H
//#define LMP_SNA_H
#include "podcommon.h"
#include "pointers.h"