ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

change energy tally during minimize

Browse Source
This commit is contained in:
Axel Kohlmeyer
2022-06-17 05:31:42 -04:00
parent 7656efe866
commit f05fcaf0d5
3 changed files with 82 additions and 32 deletions
Download Patch File Download Diff File Expand all files Collapse all files

66
src/compute_pe_atom.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -13,30 +12,31 @@
------------------------------------------------------------------------- */
#include "compute_pe_atom.h"
#include <cstring>
#include "atom.h"
#include "update.h"
#include "comm.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "atom.h"
#include "bond.h"
#include "comm.h"
#include "dihedral.h"
#include "error.h"
#include "force.h"
#include "improper.h"
#include "kspace.h"
#include "modify.h"
#include "memory.h"
#include "error.h"
#include "modify.h"
#include "pair.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputePEAtom::ComputePEAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
energy(nullptr)
Compute(lmp, narg, arg), energy(nullptr)
{
if (narg < 3) error->all(FLERR,"Illegal compute pe/atom command");
if (narg < 3) error->all(FLERR, "Illegal compute pe/atom command");
peratom_flag = 1;
size_peratom_cols = 0;
@ -56,14 +56,22 @@ ComputePEAtom::ComputePEAtom(LAMMPS *lmp, int narg, char **arg) :
fixflag = 0;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1;
else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1;
else if (strcmp(arg[iarg],"dihedral") == 0) dihedralflag = 1;
else if (strcmp(arg[iarg],"improper") == 0) improperflag = 1;
else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1;
else if (strcmp(arg[iarg],"fix") == 0) fixflag = 1;
else error->all(FLERR,"Illegal compute pe/atom command");
if (strcmp(arg[iarg], "pair") == 0)
pairflag = 1;
else if (strcmp(arg[iarg], "bond") == 0)
bondflag = 1;
else if (strcmp(arg[iarg], "angle") == 0)
angleflag = 1;
else if (strcmp(arg[iarg], "dihedral") == 0)
dihedralflag = 1;
else if (strcmp(arg[iarg], "improper") == 0)
improperflag = 1;
else if (strcmp(arg[iarg], "kspace") == 0)
kspaceflag = 1;
else if (strcmp(arg[iarg], "fix") == 0)
fixflag = 1;
else
error->all(FLERR, "Illegal compute pe/atom command");
iarg++;
}
}
@ -86,7 +94,7 @@ void ComputePEAtom::compute_peratom()
invoked_peratom = update->ntimestep;
if (update->eflag_atom != invoked_peratom)
error->all(FLERR,"Per-atom energy was not tallied on needed timestep");
error->all(FLERR, "Per-atom energy was not tallied on needed timestep");
// grow local energy array if necessary
// needs to be atom->nmax in length
@ -94,7 +102,7 @@ void ComputePEAtom::compute_peratom()
if (atom->nmax > nmax) {
memory->destroy(energy);
nmax = atom->nmax;
memory->create(energy,nmax,"pe/atom:energy");
memory->create(energy, nmax, "pe/atom:energy");
vector_atom = energy;
}
@ -153,13 +161,11 @@ void ComputePEAtom::compute_peratom()
// add in per-atom contributions from relevant fixes
// always only for owned atoms, not ghost
if (fixflag && modify->n_energy_atom)
modify->energy_atom(nlocal,energy);
if (fixflag && modify->n_energy_atom) modify->energy_atom(nlocal, energy);
// communicate ghost energy between neighbor procs
if (force->newton || (force->kspace && force->kspace->tip4pflag))
comm->reverse_comm(this);
if (force->newton || (force->kspace && force->kspace->tip4pflag)) comm->reverse_comm(this);
// zero energy of atoms not in group
// only do this after comm since ghost contributions must be included
@ -174,7 +180,7 @@ void ComputePEAtom::compute_peratom()
int ComputePEAtom::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
m = 0;
last = first + n;
@ -186,7 +192,7 @@ int ComputePEAtom::pack_reverse_comm(int n, int first, double *buf)
void ComputePEAtom::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
@ -201,6 +207,6 @@ void ComputePEAtom::unpack_reverse_comm(int n, int *list, double *buf)
double ComputePEAtom::memory_usage()
{
double bytes = (double)nmax * sizeof(double);
double bytes = (double) nmax * sizeof(double);
return bytes;
}