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convert more styles to use new neighbor list request API, apply clang-format

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This commit is contained in:
Axel Kohlmeyer
2022-03-05 21:09:19 -05:00
parent ffb367663d
commit 54e667e491
20 changed files with 1083 additions and 1122 deletions
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131
src/compute_coord_atom.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
@ -23,7 +22,6 @@
#include "memory.h"
#include "modify.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "pair.h"
#include "update.h"
@ -33,36 +31,33 @@
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
typelo(nullptr), typehi(nullptr), cvec(nullptr), carray(nullptr),
group2(nullptr), id_orientorder(nullptr), normv(nullptr)
Compute(lmp, narg, arg), typelo(nullptr), typehi(nullptr), cvec(nullptr), carray(nullptr),
group2(nullptr), id_orientorder(nullptr), normv(nullptr)
{
if (narg < 5) error->all(FLERR,"Illegal compute coord/atom command");
if (narg < 5) error->all(FLERR, "Illegal compute coord/atom command");
jgroup = group->find("all");
jgroupbit = group->bitmask[jgroup];
cstyle = NONE;
if (strcmp(arg[3],"cutoff") == 0) {
if (strcmp(arg[3], "cutoff") == 0) {
cstyle = CUTOFF;
double cutoff = utils::numeric(FLERR,arg[4],false,lmp);
cutsq = cutoff*cutoff;
double cutoff = utils::numeric(FLERR, arg[4], false, lmp);
cutsq = cutoff * cutoff;
int iarg = 5;
if ((narg > 6) && (strcmp(arg[5],"group") == 0)) {
if ((narg > 6) && (strcmp(arg[5], "group") == 0)) {
group2 = utils::strdup(arg[6]);
iarg += 2;
jgroup = group->find(group2);
if (jgroup == -1)
error->all(FLERR,"Compute coord/atom group2 ID does not exist");
if (jgroup == -1) error->all(FLERR, "Compute coord/atom group2 ID does not exist");
jgroupbit = group->bitmask[jgroup];
}
ncol = narg-iarg + 1;
ncol = narg - iarg + 1;
int ntypes = atom->ntypes;
typelo = new int[ncol];
typehi = new int[ncol];
@ -74,29 +69,27 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
} else {
ncol = 0;
while (iarg < narg) {
utils::bounds(FLERR,arg[iarg],1,ntypes,typelo[ncol],typehi[ncol],error);
if (typelo[ncol] > typehi[ncol])
error->all(FLERR,"Illegal compute coord/atom command");
utils::bounds(FLERR, arg[iarg], 1, ntypes, typelo[ncol], typehi[ncol], error);
if (typelo[ncol] > typehi[ncol]) error->all(FLERR, "Illegal compute coord/atom command");
ncol++;
iarg++;
}
}
} else if (strcmp(arg[3],"orientorder") == 0) {
} else if (strcmp(arg[3], "orientorder") == 0) {
cstyle = ORIENT;
if (narg != 6) error->all(FLERR,"Illegal compute coord/atom command");
if (narg != 6) error->all(FLERR, "Illegal compute coord/atom command");
id_orientorder = utils::strdup(arg[4]);
int iorientorder = modify->find_compute(id_orientorder);
if (iorientorder < 0)
error->all(FLERR,"Could not find compute coord/atom compute ID");
if (!utils::strmatch(modify->compute[iorientorder]->style,"^orientorder/atom"))
error->all(FLERR,"Compute coord/atom compute ID is not orientorder/atom");
if (iorientorder < 0) error->all(FLERR, "Could not find compute coord/atom compute ID");
if (!utils::strmatch(modify->compute[iorientorder]->style, "^orientorder/atom"))
error->all(FLERR, "Compute coord/atom compute ID is not orientorder/atom");
threshold = utils::numeric(FLERR,arg[5],false,lmp);
threshold = utils::numeric(FLERR, arg[5], false, lmp);
if (threshold <= -1.0 || threshold >= 1.0)
error->all(FLERR,"Compute coord/atom threshold not between -1 and 1");
error->all(FLERR, "Compute coord/atom threshold not between -1 and 1");
ncol = 1;
typelo = new int[ncol];
@ -104,11 +97,14 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
typelo[0] = 1;
typehi[0] = atom->ntypes;
} else error->all(FLERR,"Invalid cstyle in compute coord/atom");
} else
error->all(FLERR, "Invalid cstyle in compute coord/atom");
peratom_flag = 1;
if (ncol == 1) size_peratom_cols = 0;
else size_peratom_cols = ncol;
if (ncol == 1)
size_peratom_cols = 0;
else
size_peratom_cols = ncol;
nmax = 0;
}
@ -119,12 +115,12 @@ ComputeCoordAtom::~ComputeCoordAtom()
{
if (copymode) return;
delete [] group2;
delete [] typelo;
delete [] typehi;
delete[] group2;
delete[] typelo;
delete[] typehi;
memory->destroy(cvec);
memory->destroy(carray);
delete [] id_orientorder;
delete[] id_orientorder;
}
/* ---------------------------------------------------------------------- */
@ -133,30 +129,24 @@ void ComputeCoordAtom::init()
{
if (cstyle == ORIENT) {
int iorientorder = modify->find_compute(id_orientorder);
c_orientorder = (ComputeOrientOrderAtom*)(modify->compute[iorientorder]);
c_orientorder = (ComputeOrientOrderAtom *) (modify->compute[iorientorder]);
cutsq = c_orientorder->cutsq;
l = c_orientorder->qlcomp;
// communicate real and imaginary 2*l+1 components of the normalized vector
comm_forward = 2*(2*l+1);
comm_forward = 2 * (2 * l + 1);
if (!(c_orientorder->qlcompflag))
error->all(FLERR,"Compute coord/atom requires components "
"option in compute orientorder/atom");
error->all(FLERR,
"Compute coord/atom requires components option in compute orientorder/atom");
}
if (force->pair == nullptr)
error->all(FLERR,"Compute coord/atom requires a pair style be defined");
error->all(FLERR, "Compute coord/atom requires a pair style be defined");
if (sqrt(cutsq) > force->pair->cutforce)
error->all(FLERR,
"Compute coord/atom cutoff is longer than pairwise cutoff");
error->all(FLERR, "Compute coord/atom cutoff is longer than pairwise cutoff");
// 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);
}
/* ---------------------------------------------------------------------- */
@ -170,9 +160,9 @@ void ComputeCoordAtom::init_list(int /*id*/, NeighList *ptr)
void ComputeCoordAtom::compute_peratom()
{
int i,j,m,ii,jj,inum,jnum,jtype,n;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
int i, j, m, ii, jj, inum, jnum, jtype, n;
double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
int *ilist, *jlist, *numneigh, **firstneigh;
double *count;
invoked_peratom = update->ntimestep;
@ -183,12 +173,12 @@ void ComputeCoordAtom::compute_peratom()
if (ncol == 1) {
memory->destroy(cvec);
nmax = atom->nmax;
memory->create(cvec,nmax,"coord/atom:cvec");
memory->create(cvec, nmax, "coord/atom:cvec");
vector_atom = cvec;
} else {
memory->destroy(carray);
nmax = atom->nmax;
memory->create(carray,nmax,ncol,"coord/atom:carray");
memory->create(carray, nmax, ncol, "coord/atom:carray");
array_atom = carray;
}
}
@ -242,14 +232,14 @@ void ComputeCoordAtom::compute_peratom()
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0])
n++;
rsq = delx * delx + dely * dely + delz * delz;
if (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0]) n++;
}
}
cvec[i] = n;
} else cvec[i] = 0.0;
} else
cvec[i] = 0.0;
}
} else {
@ -265,7 +255,6 @@ void ComputeCoordAtom::compute_peratom()
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
@ -274,11 +263,10 @@ void ComputeCoordAtom::compute_peratom()
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
rsq = delx * delx + dely * dely + delz * delz;
if (rsq < cutsq) {
for (m = 0; m < ncol; m++)
if (jtype >= typelo[m] && jtype <= typehi[m])
count[m] += 1.0;
if (jtype >= typelo[m] && jtype <= typehi[m]) count[m] += 1.0;
}
}
}
@ -303,31 +291,30 @@ void ComputeCoordAtom::compute_peratom()
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
rsq = delx * delx + dely * dely + delz * delz;
if (rsq < cutsq) {
double dot_product = 0.0;
for (m=0; m < 2*(2*l+1); m++) {
dot_product += normv[i][nqlist+m]*normv[j][nqlist+m];
for (m = 0; m < 2 * (2 * l + 1); m++) {
dot_product += normv[i][nqlist + m] * normv[j][nqlist + m];
}
if (dot_product > threshold) n++;
}
}
cvec[i] = n;
} else cvec[i] = 0.0;
} else
cvec[i] = 0.0;
}
}
}
/* ---------------------------------------------------------------------- */
int ComputeCoordAtom::pack_forward_comm(int n, int *list, double *buf,
int /*pbc_flag*/, int * /*pbc*/)
int ComputeCoordAtom::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/,
int * /*pbc*/)
{
int i,m=0,j;
int i, m = 0, j;
for (i = 0; i < n; ++i) {
for (j = nqlist; j < nqlist + 2*(2*l+1); ++j) {
buf[m++] = normv[list[i]][j];
}
for (j = nqlist; j < nqlist + 2 * (2 * l + 1); ++j) { buf[m++] = normv[list[i]][j]; }
}
return m;
@ -337,12 +324,10 @@ int ComputeCoordAtom::pack_forward_comm(int n, int *list, double *buf,
void ComputeCoordAtom::unpack_forward_comm(int n, int first, double *buf)
{
int i,last,m=0,j;
int i, last, m = 0, j;
last = first + n;
for (i = first; i < last; ++i) {
for (j = nqlist; j < nqlist + 2*(2*l+1); ++j) {
normv[i][j] = buf[m++];
}
for (j = nqlist; j < nqlist + 2 * (2 * l + 1); ++j) { normv[i][j] = buf[m++]; }
}
}
@ -352,6 +337,6 @@ void ComputeCoordAtom::unpack_forward_comm(int n, int first, double *buf)
double ComputeCoordAtom::memory_usage()
{
double bytes = (double)ncol*nmax * sizeof(double);
double bytes = (double) ncol * nmax * sizeof(double);
return bytes;
}