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Updated to latest LAMMPS

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This commit is contained in:
Aidan Thompson
2022-06-15 19:53:37 -06:00
parent 86034a6277
commit 70f836e275
4 changed files with 88 additions and 45 deletions
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37
src/ML-SNAP/compute_sna_grid.cpp
View File

@ -148,13 +148,13 @@ ComputeSNAGrid::ComputeSNAGrid(LAMMPS *lmp, int narg, char **arg) :
iarg += 2;
} else if (strcmp(arg[iarg],"switchinnerflag") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute snap command");
error->all(FLERR,"Illegal compute sna/grid command");
switchinnerflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"sinner") == 0) {
iarg++;
if (iarg+ntypes > narg)
error->all(FLERR,"Illegal compute snap command");
error->all(FLERR,"Illegal compute sna/grid command");
memory->create(sinnerelem,ntypes+1,"snap:sinnerelem");
for (int i = 0; i < ntypes; i++)
sinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp);
@ -163,7 +163,7 @@ ComputeSNAGrid::ComputeSNAGrid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"dinner") == 0) {
iarg++;
if (iarg+ntypes > narg)
error->all(FLERR,"Illegal compute snap command");
error->all(FLERR,"Illegal compute sna/grid command");
memory->create(dinnerelem,ntypes+1,"snap:dinnerelem");
for (int i = 0; i < ntypes; i++)
dinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp);
@ -201,20 +201,20 @@ ComputeSNAGrid::~ComputeSNAGrid()
void ComputeSNAGrid::init()
{
if (force->pair == nullptr)
error->all(FLERR,"Compute sna/grid requires a pair style be defined");
// if (force->pair == nullptr)
// error->all(FLERR,"Compute sna/grid requires a pair style be defined");
if (cutmax > force->pair->cutforce)
error->all(FLERR,"Compute sna/grid cutoff is longer than pairwise cutoff");
// if (cutmax > force->pair->cutforce)
// error->all(FLERR,"Compute sna/grid cutoff is longer than pairwise cutoff");
// need an occasional full neighbor list
// // 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;
// 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;
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
@ -282,7 +282,8 @@ void ComputeSNAGrid::compute_array()
int jtype = type[j];
int jelem = 0;
if (chemflag)
jelem = map[jtype];
jelem = map[jtype];
if (rsq < cutsq[jtype][jtype] && rsq > 1e-20) {
snaptr->rij[ninside][0] = delx;
snaptr->rij[ninside][1] = dely;
@ -290,7 +291,11 @@ void ComputeSNAGrid::compute_array()
snaptr->inside[ninside] = j;
snaptr->wj[ninside] = wjelem[jtype];
snaptr->rcutij[ninside] = 2.0*radelem[jtype]*rcutfac;
snaptr->element[ninside] = jelem; // element index for multi-element snap
if (switchinnerflag) {
snaptr->sinnerij[ninside] = sinnerelem[jelem];
snaptr->dinnerij[ninside] = dinnerelem[jelem];
}
if (chemflag) snaptr->element[ninside] = jelem;
ninside++;
}
}

36
src/ML-SNAP/compute_sna_grid_local.cpp
View File

@ -148,13 +148,13 @@ ComputeSNAGridLocal::ComputeSNAGridLocal(LAMMPS *lmp, int narg, char **arg) :
iarg += 2;
} else if (strcmp(arg[iarg],"switchinnerflag") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute snap command");
error->all(FLERR,"Illegal compute sna/grid/local command");
switchinnerflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"sinner") == 0) {
iarg++;
if (iarg+ntypes > narg)
error->all(FLERR,"Illegal compute snap command");
error->all(FLERR,"Illegal compute sna/grid/local command");
memory->create(sinnerelem,ntypes+1,"snap:sinnerelem");
for (int i = 0; i < ntypes; i++)
sinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp);
@ -163,7 +163,7 @@ ComputeSNAGridLocal::ComputeSNAGridLocal(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"dinner") == 0) {
iarg++;
if (iarg+ntypes > narg)
error->all(FLERR,"Illegal compute snap command");
error->all(FLERR,"Illegal compute sna/grid/local command");
memory->create(dinnerelem,ntypes+1,"snap:dinnerelem");
for (int i = 0; i < ntypes; i++)
dinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp);
@ -200,20 +200,20 @@ ComputeSNAGridLocal::~ComputeSNAGridLocal()
void ComputeSNAGridLocal::init()
{
if (force->pair == nullptr)
error->all(FLERR,"Compute sna/grid/local requires a pair style be defined");
// if (force->pair == nullptr)
// error->all(FLERR,"Compute sna/grid/local requires a pair style be defined");
if (cutmax > force->pair->cutforce)
error->all(FLERR,"Compute sna/grid/local cutoff is longer than pairwise cutoff");
// if (cutmax > force->pair->cutforce)
// error->all(FLERR,"Compute sna/grid/local cutoff is longer than pairwise cutoff");
// need an occasional full neighbor list
// // 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;
// 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;
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
@ -234,6 +234,7 @@ void ComputeSNAGridLocal::init_list(int /*id*/, NeighList *ptr)
void ComputeSNAGridLocal::compute_local()
{
printf("Entering compute_local()\n");
invoked_array = update->ntimestep;
// compute sna for each gridpoint
@ -290,7 +291,11 @@ void ComputeSNAGridLocal::compute_local()
snaptr->inside[ninside] = j;
snaptr->wj[ninside] = wjelem[jtype];
snaptr->rcutij[ninside] = 2.0*radelem[jtype]*rcutfac;
snaptr->element[ninside] = jelem; // element index for multi-element snap
if (switchinnerflag) {
snaptr->sinnerij[ninside] = sinnerelem[jelem];
snaptr->dinnerij[ninside] = dinnerelem[jelem];
}
if (chemflag) snaptr->element[ninside] = jelem; // element index for multi-element snap
ninside++;
}
}
@ -323,6 +328,7 @@ void ComputeSNAGridLocal::compute_local()
// copy 4d array to 2d array
copy_gridlocal_to_local_array();
printf("Exiting compute_local()\n");
}

57
src/ML-SNAP/pair_sna_grid.cpp
View File

@ -59,15 +59,16 @@ void PairSNAGrid::init_style()
if (force->newton_pair == 0)
error->all(FLERR,"Pair style sna/grid requires newton pair on");
// need a full neighbor list
// // need a full neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
// int irequest = neighbor->request(this,instance_me);
// neighbor->requests[irequest]->half = 0;
// neighbor->requests[irequest]->full = 1;
snaptr = new SNA(lmp, rfac0, twojmax,
rmin0, switchflag, bzeroflag,
chemflag, bnormflag, wselfallflag, nelements);
chemflag, bnormflag, wselfallflag,
nelements, switchinnerflag);
ncoeff = snaptr->ncoeff;
ndesc = ndesc_base + ncoeff;
snaptr->init();
@ -213,8 +214,8 @@ void PairSNAGrid::compute(int eflag, int vflag)
const double rsq = delx*delx + dely*dely + delz*delz;
int jtype = type[j];
int jelem = 0;
if (chemflag)
jelem = map[jtype];
jelem = map[jtype];
if (rsq < cutsq[jtype][jtype] && rsq > 1e-20) {
snaptr->rij[ninside][0] = delx;
snaptr->rij[ninside][1] = dely;
@ -222,7 +223,11 @@ void PairSNAGrid::compute(int eflag, int vflag)
snaptr->inside[ninside] = j;
snaptr->wj[ninside] = wjelem[jtype];
snaptr->rcutij[ninside] = 2.0*radelem[jtype]*rcutfac;
snaptr->element[ninside] = jelem; // element index for multi-element snap
if (switchinnerflag) {
snaptr->sinnerij[ninside] = 0.5*(sinnerelem[ielem]+sinnerelem[jelem]);
snaptr->dinnerij[ninside] = 0.5*(dinnerelem[ielem]+dinnerelem[jelem]);
}
if (chemflag) snaptr->element[ninside] = jelem;
ninside++;
}
}
@ -243,12 +248,7 @@ void PairSNAGrid::compute(int eflag, int vflag)
for (int jj = 0; jj < ninside; jj++) {
int j = snaptr->inside[jj];
if (chemflag)
snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
snaptr->rcutij[jj],jj, snaptr->element[jj]);
else
snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
snaptr->rcutij[jj],jj, 0);
snaptr->compute_duidrj(jj);
snaptr->compute_deidrj(fij);
@ -326,6 +326,7 @@ void PairSNAGrid::settings(int narg, char ** arg)
chemflag = 0;
bnormflag = 0;
wselfallflag = 0;
switchinnerflag = 0;
nelements = 1;
// process required arguments
@ -357,6 +358,11 @@ void PairSNAGrid::settings(int narg, char ** arg)
}
}
// set local input checks
int sinnerflag = 0;
int dinnerflag = 0;
// process optional args
int iarg = nargmin;
@ -405,6 +411,29 @@ void PairSNAGrid::settings(int narg, char ** arg)
error->all(FLERR,"Illegal pair sna/grid command");
wselfallflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"switchinnerflag") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal pair sna/grid command");
switchinnerflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"sinner") == 0) {
iarg++;
if (iarg+ntypes > narg)
error->all(FLERR,"Illegal pair sna/grid command");
memory->create(sinnerelem,ntypes+1,"snap:sinnerelem");
for (int i = 0; i < ntypes; i++)
sinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp);
sinnerflag = 1;
iarg += ntypes;
} else if (strcmp(arg[iarg],"dinner") == 0) {
iarg++;
if (iarg+ntypes > narg)
error->all(FLERR,"Illegal pair sna/grid command");
memory->create(dinnerelem,ntypes+1,"snap:dinnerelem");
for (int i = 0; i < ntypes; i++)
dinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp);
dinnerflag = 1;
iarg += ntypes;
} else error->all(FLERR,"Illegal pair sna/grid command");
}

3
src/ML-SNAP/pair_sna_grid.h
View File

@ -45,6 +45,9 @@ class PairSNAGrid : public PairGrid {
int quadraticflag;
int twojmax, switchflag, bzeroflag, bnormflag;
int chemflag, wselfallflag;
int switchinnerflag;
double *sinnerelem;
double *dinnerelem;
double rfac0, rmin0;
};