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"stringify" and "vectorize" processing of per-atom attributs in AtomVec classes

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This commit is contained in:
Axel Kohlmeyer
2022-04-14 11:06:10 -04:00
parent 1755d06870
commit b16d48aa41
37 changed files with 1596 additions and 1832 deletions
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137
src/atom_vec_ellipsoid.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
@ -26,10 +25,8 @@
#include "memory.h"
#include "modify.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
using MathConst::MY_PI;
/* ---------------------------------------------------------------------- */
@ -54,18 +51,18 @@ AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "rmass angmom torque ellipsoid";
fields_copy = (char *) "rmass angmom";
fields_comm = (char *) "";
fields_comm_vel = (char *) "angmom";
fields_reverse = (char *) "torque";
fields_border = (char *) "rmass";
fields_border_vel = (char *) "rmass angmom";
fields_exchange = (char *) "rmass angmom";
fields_restart = (char *) "rmass angmom";
fields_create = (char *) "rmass angmom ellipsoid";
fields_data_atom = (char *) "id type ellipsoid rmass x";
fields_data_vel = (char *) "id v angmom";
fields_grow = {"rmass", "angmom", "torque", "ellipsoid"};
fields_copy = {"rmass", "angmom"};
fields_comm = {};
fields_comm_vel = {"angmom"};
fields_reverse = {"torque"};
fields_border = {"rmass"};
fields_border_vel = {"rmass", "angmom"};
fields_exchange = {"rmass", "angmom"};
fields_restart = {"rmass", "angmom"};
fields_create = {"rmass", "angmom", "ellipsoid"};
fields_data_atom = {"id", "type", "ellipsoid", "rmass", "x"};
fields_data_vel = {"id", "v", "angmom"};
setup_fields();
}
@ -96,11 +93,9 @@ void AtomVecEllipsoid::grow_pointers()
void AtomVecEllipsoid::grow_bonus()
{
nmax_bonus = grow_nmax_bonus(nmax_bonus);
if (nmax_bonus < 0)
error->one(FLERR,"Per-processor system is too big");
if (nmax_bonus < 0) error->one(FLERR, "Per-processor system is too big");
bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
"atom:bonus");
bonus = (Bonus *) memory->srealloc(bonus, nmax_bonus * sizeof(Bonus), "atom:bonus");
}
/* ----------------------------------------------------------------------
@ -112,7 +107,7 @@ void AtomVecEllipsoid::copy_bonus(int i, int j, int delflag)
// if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && ellipsoid[j] >= 0) {
copy_bonus_all(nlocal_bonus-1,ellipsoid[j]);
copy_bonus_all(nlocal_bonus - 1, ellipsoid[j]);
nlocal_bonus--;
}
@ -131,7 +126,7 @@ void AtomVecEllipsoid::copy_bonus(int i, int j, int delflag)
void AtomVecEllipsoid::copy_bonus_all(int i, int j)
{
ellipsoid[bonus[i].ilocal] = j;
memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
memcpy(&bonus[j], &bonus[i], sizeof(Bonus));
}
/* ----------------------------------------------------------------------
@ -152,7 +147,7 @@ void AtomVecEllipsoid::clear_bonus()
int AtomVecEllipsoid::pack_comm_bonus(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
double *quat;
m = 0;
@ -174,7 +169,7 @@ int AtomVecEllipsoid::pack_comm_bonus(int n, int *list, double *buf)
void AtomVecEllipsoid::unpack_comm_bonus(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
double *quat;
m = 0;
@ -194,13 +189,14 @@ void AtomVecEllipsoid::unpack_comm_bonus(int n, int first, double *buf)
int AtomVecEllipsoid::pack_border_bonus(int n, int *list, double *buf)
{
int i,j,m;
double *shape,*quat;
int i, j, m;
double *shape, *quat;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d;
if (ellipsoid[j] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
shape = bonus[ellipsoid[j]].shape;
@ -222,14 +218,15 @@ int AtomVecEllipsoid::pack_border_bonus(int n, int *list, double *buf)
int AtomVecEllipsoid::unpack_border_bonus(int n, int first, double *buf)
{
int i,j,m,last;
double *shape,*quat;
int i, j, m, last;
double *shape, *quat;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
ellipsoid[i] = (int) ubuf(buf[m++]).i;
if (ellipsoid[i] == 0) ellipsoid[i] = -1;
if (ellipsoid[i] == 0)
ellipsoid[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
@ -260,7 +257,8 @@ int AtomVecEllipsoid::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
if (ellipsoid[i] < 0) buf[m++] = ubuf(0).d;
if (ellipsoid[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = ellipsoid[i];
@ -285,7 +283,8 @@ int AtomVecEllipsoid::unpack_exchange_bonus(int ilocal, double *buf)
int m = 0;
ellipsoid[ilocal] = (int) ubuf(buf[m++]).i;
if (ellipsoid[ilocal] == 0) ellipsoid[ilocal] = -1;
if (ellipsoid[ilocal] == 0)
ellipsoid[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *shape = bonus[nlocal_bonus].shape;
@ -316,8 +315,10 @@ int AtomVecEllipsoid::size_restart_bonus()
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (ellipsoid[i] >= 0) n += size_restart_bonus_one;
else n++;
if (ellipsoid[i] >= 0)
n += size_restart_bonus_one;
else
n++;
}
return n;
@ -333,7 +334,8 @@ int AtomVecEllipsoid::pack_restart_bonus(int i, double *buf)
{
int m = 0;
if (ellipsoid[i] < 0) buf[m++] = ubuf(0).d;
if (ellipsoid[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = ellipsoid[i];
@ -358,7 +360,8 @@ int AtomVecEllipsoid::unpack_restart_bonus(int ilocal, double *buf)
int m = 0;
ellipsoid[ilocal] = (int) ubuf(buf[m++]).i;
if (ellipsoid[ilocal] == 0) ellipsoid[ilocal] = -1;
if (ellipsoid[ilocal] == 0)
ellipsoid[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *shape = bonus[nlocal_bonus].shape;
@ -381,32 +384,31 @@ int AtomVecEllipsoid::unpack_restart_bonus(int ilocal, double *buf)
unpack one line from Ellipsoids section of data file
------------------------------------------------------------------------- */
void AtomVecEllipsoid::data_atom_bonus(int m, const std::vector<std::string> & values)
void AtomVecEllipsoid::data_atom_bonus(int m, const std::vector<std::string> &values)
{
if (ellipsoid[m])
error->one(FLERR,"Assigning ellipsoid parameters to non-ellipsoid atom");
if (ellipsoid[m]) error->one(FLERR, "Assigning ellipsoid parameters to non-ellipsoid atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *shape = bonus[nlocal_bonus].shape;
int ivalue = 1;
shape[0] = 0.5 * utils::numeric(FLERR,values[ivalue++],true,lmp);
shape[1] = 0.5 * utils::numeric(FLERR,values[ivalue++],true,lmp);
shape[2] = 0.5 * utils::numeric(FLERR,values[ivalue++],true,lmp);
shape[0] = 0.5 * utils::numeric(FLERR, values[ivalue++], true, lmp);
shape[1] = 0.5 * utils::numeric(FLERR, values[ivalue++], true, lmp);
shape[2] = 0.5 * utils::numeric(FLERR, values[ivalue++], true, lmp);
if (shape[0] <= 0.0 || shape[1] <= 0.0 || shape[2] <= 0.0)
error->one(FLERR,"Invalid shape in Ellipsoids section of data file");
error->one(FLERR, "Invalid shape in Ellipsoids section of data file");
double *quat = bonus[nlocal_bonus].quat;
quat[0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
quat[1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
quat[2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
quat[3] = utils::numeric(FLERR,values[ivalue++],true,lmp);
quat[0] = utils::numeric(FLERR, values[ivalue++], true, lmp);
quat[1] = utils::numeric(FLERR, values[ivalue++], true, lmp);
quat[2] = utils::numeric(FLERR, values[ivalue++], true, lmp);
quat[3] = utils::numeric(FLERR, values[ivalue++], true, lmp);
MathExtra::qnormalize(quat);
// reset ellipsoid mass
// previously stored density in rmass
rmass[m] *= 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2];
rmass[m] *= 4.0 * MY_PI / 3.0 * shape[0] * shape[1] * shape[2];
bonus[nlocal_bonus].ilocal = m;
ellipsoid[m] = nlocal_bonus++;
@ -419,7 +421,7 @@ void AtomVecEllipsoid::data_atom_bonus(int m, const std::vector<std::string> & v
double AtomVecEllipsoid::memory_usage_bonus()
{
double bytes = 0;
bytes += nmax_bonus*sizeof(Bonus);
bytes += nmax_bonus * sizeof(Bonus);
return bytes;
}
@ -441,13 +443,15 @@ void AtomVecEllipsoid::create_atom_post(int ilocal)
void AtomVecEllipsoid::data_atom_post(int ilocal)
{
ellipsoid_flag = ellipsoid[ilocal];
if (ellipsoid_flag == 0) ellipsoid_flag = -1;
else if (ellipsoid_flag == 1) ellipsoid_flag = 0;
else error->one(FLERR,"Invalid ellipsoid flag in Atoms section of data file");
if (ellipsoid_flag == 0)
ellipsoid_flag = -1;
else if (ellipsoid_flag == 1)
ellipsoid_flag = 0;
else
error->one(FLERR, "Invalid ellipsoid flag in Atoms section of data file");
ellipsoid[ilocal] = ellipsoid_flag;
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");
angmom[ilocal][0] = 0.0;
angmom[ilocal][1] = 0.0;
@ -465,12 +469,14 @@ void AtomVecEllipsoid::pack_data_pre(int ilocal)
ellipsoid_flag = atom->ellipsoid[ilocal];
rmass_one = atom->rmass[ilocal];
if (ellipsoid_flag < 0) ellipsoid[ilocal] = 0;
else ellipsoid[ilocal] = 1;
if (ellipsoid_flag < 0)
ellipsoid[ilocal] = 0;
else
ellipsoid[ilocal] = 1;
if (ellipsoid_flag >= 0) {
shape = bonus[ellipsoid_flag].shape;
rmass[ilocal] /= 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2];
rmass[ilocal] /= 4.0 * MY_PI / 3.0 * shape[0] * shape[1] * shape[2];
}
}
@ -491,7 +497,7 @@ void AtomVecEllipsoid::pack_data_post(int ilocal)
int AtomVecEllipsoid::pack_data_bonus(double *buf, int /*flag*/)
{
int i,j;
int i, j;
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
@ -502,14 +508,15 @@ int AtomVecEllipsoid::pack_data_bonus(double *buf, int /*flag*/)
if (buf) {
buf[m++] = ubuf(tag[i]).d;
j = ellipsoid[i];
buf[m++] = 2.0*bonus[j].shape[0];
buf[m++] = 2.0*bonus[j].shape[1];
buf[m++] = 2.0*bonus[j].shape[2];
buf[m++] = 2.0 * bonus[j].shape[0];
buf[m++] = 2.0 * bonus[j].shape[1];
buf[m++] = 2.0 * bonus[j].shape[2];
buf[m++] = bonus[j].quat[0];
buf[m++] = bonus[j].quat[1];
buf[m++] = bonus[j].quat[2];
buf[m++] = bonus[j].quat[3];
} else m += size_data_bonus;
} else
m += size_data_bonus;
}
return m;
@ -523,8 +530,8 @@ void AtomVecEllipsoid::write_data_bonus(FILE *fp, int n, double *buf, int /*flag
{
int i = 0;
while (i < n) {
fmt::print(fp,"{} {} {} {} {} {} {} {}\n",ubuf(buf[i]).i,
buf[i+1],buf[i+2],buf[i+3],buf[i+4],buf[i+5],buf[i+6],buf[i+7]);
fmt::print(fp, "{} {} {} {} {} {} {} {}\n", ubuf(buf[i]).i, buf[i + 1], buf[i + 2], buf[i + 3],
buf[i + 4], buf[i + 5], buf[i + 6], buf[i + 7]);
i += size_data_bonus;
}
}
@ -552,7 +559,7 @@ void AtomVecEllipsoid::set_shape(int i, double shapex, double shapey, double sha
bonus[nlocal_bonus].ilocal = i;
ellipsoid[i] = nlocal_bonus++;
} else if (shapex == 0.0 && shapey == 0.0 && shapez == 0.0) {
copy_bonus_all(nlocal_bonus-1,ellipsoid[i]);
copy_bonus_all(nlocal_bonus - 1, ellipsoid[i]);
nlocal_bonus--;
ellipsoid[i] = -1;
} else {