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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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196
src/atom_vec_line.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
@ -23,12 +22,11 @@
#include "modify.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
using MathConst::MY_PI;
#define EPSILON 0.001
static constexpr double EPSILON = 0.001;
/* ---------------------------------------------------------------------- */
@ -55,18 +53,18 @@ AtomVecLine::AtomVecLine(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 *) "molecule radius rmass omega torque line";
fields_copy = (char *) "molecule radius rmass omega";
fields_comm = (char *) "";
fields_comm_vel = (char *) "omega";
fields_reverse = (char *) "torque";
fields_border = (char *) "molecule radius rmass";
fields_border_vel = (char *) "molecule radius rmass omega";
fields_exchange = (char *) "molecule radius rmass omega";
fields_restart = (char *) "molecule radius rmass omega";
fields_create = (char *) "molecule radius rmass omega line";
fields_data_atom = (char *) "id molecule type line rmass x";
fields_data_vel = (char *) "id v omega";
fields_grow = {"molecule", "radius", "rmass", "omega", "torque", "line"};
fields_copy = {"molecule", "radius", "rmass", "omega"};
fields_comm = {};
fields_comm_vel = {"omega"};
fields_reverse = {"torque"};
fields_border = {"molecule", "radius", "rmass"};
fields_border_vel = {"molecule", "radius", "rmass", "omega"};
fields_exchange = {"molecule", "radius", "rmass", "omega"};
fields_restart = {"molecule", "radius", "rmass", "omega"};
fields_create = {"molecule", "radius", "rmass", "omega", "line"};
fields_data_atom = {"id", "molecule", "type", "line", "rmass", "x"};
fields_data_vel = {"id", "v", "omega"};
setup_fields();
}
@ -85,7 +83,7 @@ void AtomVecLine::init()
AtomVec::init();
if (domain->dimension != 2)
error->all(FLERR,"Atom_style line can only be used in 2d simulations");
error->all(FLERR, "Atom_style line can only be used in 2d simulations");
}
/* ----------------------------------------------------------------------
@ -108,11 +106,9 @@ void AtomVecLine::grow_pointers()
void AtomVecLine::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");
}
/* ----------------------------------------------------------------------
@ -124,7 +120,7 @@ void AtomVecLine::copy_bonus(int i, int j, int delflag)
// if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && line[j] >= 0) {
copy_bonus_all(nlocal_bonus-1,line[j]);
copy_bonus_all(nlocal_bonus - 1, line[j]);
nlocal_bonus--;
}
@ -143,7 +139,7 @@ void AtomVecLine::copy_bonus(int i, int j, int delflag)
void AtomVecLine::copy_bonus_all(int i, int j)
{
line[bonus[i].ilocal] = j;
memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
memcpy(&bonus[j], &bonus[i], sizeof(Bonus));
}
/* ----------------------------------------------------------------------
@ -164,7 +160,7 @@ void AtomVecLine::clear_bonus()
int AtomVecLine::pack_comm_bonus(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
@ -179,7 +175,7 @@ int AtomVecLine::pack_comm_bonus(int n, int *list, double *buf)
void AtomVecLine::unpack_comm_bonus(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
m = 0;
last = first + n;
@ -192,12 +188,13 @@ void AtomVecLine::unpack_comm_bonus(int n, int first, double *buf)
int AtomVecLine::pack_border_bonus(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
if (line[j] < 0) buf[m++] = ubuf(0).d;
if (line[j] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
buf[m++] = bonus[line[j]].length;
@ -212,13 +209,14 @@ int AtomVecLine::pack_border_bonus(int n, int *list, double *buf)
int AtomVecLine::unpack_border_bonus(int n, int first, double *buf)
{
int i,j,m,last;
int i, j, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
line[i] = (int) ubuf(buf[m++]).i;
if (line[i] == 0) line[i] = -1;
if (line[i] == 0)
line[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
@ -242,7 +240,8 @@ int AtomVecLine::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
if (line[i] < 0) buf[m++] = ubuf(0).d;
if (line[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = line[i];
@ -260,7 +259,8 @@ int AtomVecLine::unpack_exchange_bonus(int ilocal, double *buf)
int m = 0;
line[ilocal] = (int) ubuf(buf[m++]).i;
if (line[ilocal] == 0) line[ilocal] = -1;
if (line[ilocal] == 0)
line[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
bonus[nlocal_bonus].length = buf[m++];
@ -284,8 +284,10 @@ int AtomVecLine::size_restart_bonus()
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (line[i] >= 0) n += size_restart_bonus_one;
else n++;
if (line[i] >= 0)
n += size_restart_bonus_one;
else
n++;
}
return n;
@ -301,7 +303,8 @@ int AtomVecLine::pack_restart_bonus(int i, double *buf)
{
int m = 0;
if (line[i] < 0) buf[m++] = ubuf(0).d;
if (line[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = line[i];
@ -321,7 +324,8 @@ int AtomVecLine::unpack_restart_bonus(int ilocal, double *buf)
int m = 0;
line[ilocal] = (int) ubuf(buf[m++]).i;
if (line[ilocal] == 0) line[ilocal] = -1;
if (line[ilocal] == 0)
line[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
bonus[nlocal_bonus].length = buf[m++];
@ -339,31 +343,32 @@ int AtomVecLine::unpack_restart_bonus(int ilocal, double *buf)
void AtomVecLine::data_atom_bonus(int m, const std::vector<std::string> &values)
{
if (line[m]) error->one(FLERR,"Assigning line parameters to non-line atom");
if (line[m]) error->one(FLERR, "Assigning line parameters to non-line atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
int ivalue = 1;
double x1 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double y1 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double x2 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double y2 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double x1 = utils::numeric(FLERR, values[ivalue++], true, lmp);
double y1 = utils::numeric(FLERR, values[ivalue++], true, lmp);
double x2 = utils::numeric(FLERR, values[ivalue++], true, lmp);
double y2 = utils::numeric(FLERR, values[ivalue++], true, lmp);
double dx = x2 - x1;
double dy = y2 - y1;
double length = sqrt(dx*dx + dy*dy);
double length = sqrt(dx * dx + dy * dy);
bonus[nlocal_bonus].length = length;
if (dy >= 0.0) bonus[nlocal_bonus].theta = acos(dx/length);
else bonus[nlocal_bonus].theta = -acos(dx/length);
if (dy >= 0.0)
bonus[nlocal_bonus].theta = acos(dx / length);
else
bonus[nlocal_bonus].theta = -acos(dx / length);
double xc = 0.5*(x1+x2);
double yc = 0.5*(y1+y2);
double xc = 0.5 * (x1 + x2);
double yc = 0.5 * (y1 + y2);
dx = xc - x[m][0];
dy = yc - x[m][1];
double delta = sqrt(dx*dx + dy*dy);
double delta = sqrt(dx * dx + dy * dy);
if (delta/length > EPSILON)
error->one(FLERR,"Inconsistent line segment in data file");
if (delta / length > EPSILON) error->one(FLERR, "Inconsistent line segment in data file");
x[m][0] = xc;
x[m][1] = yc;
@ -385,7 +390,7 @@ void AtomVecLine::data_atom_bonus(int m, const std::vector<std::string> &values)
double AtomVecLine::memory_usage_bonus()
{
double bytes = 0;
bytes += (double)nmax_bonus*sizeof(Bonus);
bytes += (double) nmax_bonus * sizeof(Bonus);
return bytes;
}
@ -398,7 +403,7 @@ void AtomVecLine::create_atom_post(int ilocal)
{
double radius_one = 0.5;
radius[ilocal] = radius_one;
rmass[ilocal] = 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
rmass[ilocal] = 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
line[ilocal] = -1;
}
@ -410,19 +415,22 @@ void AtomVecLine::create_atom_post(int ilocal)
void AtomVecLine::data_atom_post(int ilocal)
{
line_flag = line[ilocal];
if (line_flag == 0) line_flag = -1;
else if (line_flag == 1) line_flag = 0;
else error->one(FLERR,"Invalid line flag in Atoms section of data file");
if (line_flag == 0)
line_flag = -1;
else if (line_flag == 1)
line_flag = 0;
else
error->one(FLERR, "Invalid line flag in Atoms section of data file");
line[ilocal] = line_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");
if (line_flag < 0) {
double radius_one = 0.5;
radius[ilocal] = radius_one;
rmass[ilocal] *= 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
} else radius[ilocal] = 0.0;
rmass[ilocal] *= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
} else
radius[ilocal] = 0.0;
omega[ilocal][0] = 0.0;
omega[ilocal][1] = 0.0;
@ -438,13 +446,16 @@ void AtomVecLine::pack_data_pre(int ilocal)
line_flag = line[ilocal];
rmass_one = rmass[ilocal];
if (line_flag < 0) line[ilocal] = 0;
else line[ilocal] = 1;
if (line_flag < 0)
line[ilocal] = 0;
else
line[ilocal] = 1;
if (line_flag < 0) {
double radius_one = radius[ilocal];
rmass[ilocal] /= 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
} else rmass[ilocal] /= bonus[line_flag].length;
rmass[ilocal] /= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
} else
rmass[ilocal] /= bonus[line_flag].length;
}
/* ----------------------------------------------------------------------
@ -464,9 +475,9 @@ void AtomVecLine::pack_data_post(int ilocal)
int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/)
{
int i,j;
double length,theta;
double xc,yc,x1,x2,y1,y2;
int i, j;
double length, theta;
double xc, yc, x1, x2, y1, y2;
double **x = atom->x;
tagint *tag = atom->tag;
@ -482,15 +493,16 @@ int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/)
theta = bonus[j].theta;
xc = x[i][0];
yc = x[i][1];
x1 = xc - 0.5*cos(theta)*length;
y1 = yc - 0.5*sin(theta)*length;
x2 = xc + 0.5*cos(theta)*length;
y2 = yc + 0.5*sin(theta)*length;
x1 = xc - 0.5 * cos(theta) * length;
y1 = yc - 0.5 * sin(theta) * length;
x2 = xc + 0.5 * cos(theta) * length;
y2 = yc + 0.5 * sin(theta) * length;
buf[m++] = x1;
buf[m++] = y1;
buf[m++] = x2;
buf[m++] = y2;
} else m += size_data_bonus;
} else
m += size_data_bonus;
}
return m;
}
@ -503,8 +515,8 @@ void AtomVecLine::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]);
fmt::print(fp, "{} {} {} {} {}\n", ubuf(buf[i]).i, buf[i + 1], buf[i + 2], buf[i + 3],
buf[i + 4]);
i += size_data_bonus;
}
}
@ -525,10 +537,11 @@ void AtomVecLine::set_length(int i, double value)
bonus[nlocal_bonus].ilocal = i;
line[i] = nlocal_bonus++;
} else if (value == 0.0) {
copy_bonus_all(nlocal_bonus-1,line[i]);
copy_bonus_all(nlocal_bonus - 1, line[i]);
nlocal_bonus--;
line[i] = -1;
} else bonus[line[i]].length = value;
} else
bonus[line[i]].length = value;
// also set radius = half of length
// unless value = 0.0, then set diameter = 1.0
@ -536,40 +549,3 @@ void AtomVecLine::set_length(int i, double value)
radius[i] = 0.5 * value;
if (value == 0.0) radius[i] = 0.5;
}
/* ----------------------------------------------------------------------
check consistency of internal Bonus data structure
n = # of atoms in regular structure to check against
------------------------------------------------------------------------- */
/*
void AtomVecLine::consistency_check(int n, char *str)
{
int iflag = 0;
int count = 0;
for (int i = 0; i < n; i++) {
if (line[i] >= 0) {
count++;
if (line[i] >= nlocal_bonus) iflag++;
if (bonus[line[i]].ilocal != i) iflag++;
//if (comm->me == 1 && update->ntimestep == 873)
// printf("CCHK %s: %d %d: %d %d: %d %d\n",
// str,i,n,line[i],nlocal_bonus,bonus[line[i]].ilocal,iflag);
}
}
if (iflag) {
printf("BAD vecline ptrs: %s: %d %d: %d\n",str,comm->me,
update->ntimestep,iflag);
MPI_Abort(world,1);
}
if (count != nlocal_bonus) {
char msg[128];
printf("BAD vecline count: %s: %d %d: %d %d\n",
str,comm->me,update->ntimestep,count,nlocal_bonus);
MPI_Abort(world,1);
}
}
*/