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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14480 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2016-01-23 00:49:16 +00:00
parent 5d99bf664e
commit 3621171480
4 changed files with 132 additions and 22 deletions
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70
src/atom_vec_line.cpp
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@ -21,10 +21,12 @@
#include "modify.h"
#include "force.h"
#include "fix.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define EPSILON 0.001
@ -37,7 +39,7 @@ AtomVecLine::AtomVecLine(LAMMPS *lmp) : AtomVec(lmp)
comm_x_only = comm_f_only = 0;
size_forward = 4;
size_reverse = 6;
size_border = 10;
size_border = 12;
size_velocity = 6;
size_data_atom = 8;
size_data_vel = 7;
@ -46,7 +48,8 @@ AtomVecLine::AtomVecLine(LAMMPS *lmp) : AtomVec(lmp)
atom->line_flag = 1;
atom->molecule_flag = atom->rmass_flag = 1;
atom->omega_flag = atom->torque_flag = 1;
atom->radius_flag = atom->omega_flag = atom->torque_flag = 1;
atom->sphere_flag = 1;
nlocal_bonus = nghost_bonus = nmax_bonus = 0;
bonus = NULL;
@ -93,6 +96,7 @@ void AtomVecLine::grow(int n)
molecule = memory->grow(atom->molecule,nmax,"atom:molecule");
rmass = memory->grow(atom->rmass,nmax,"atom:rmass");
radius = memory->grow(atom->radius,nmax,"atom:radius");
omega = memory->grow(atom->omega,nmax,3,"atom:omega");
torque = memory->grow(atom->torque,nmax*comm->nthreads,3,"atom:torque");
line = memory->grow(atom->line,nmax,"atom:line");
@ -112,7 +116,7 @@ void AtomVecLine::grow_reset()
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
molecule = atom->molecule; rmass = atom->rmass;
omega = atom->omega; torque = atom->torque;
radius = atom->radius; omega = atom->omega; torque = atom->torque;
line = atom->line;
}
@ -149,6 +153,7 @@ void AtomVecLine::copy(int i, int j, int delflag)
molecule[j] = molecule[i];
rmass[j] = rmass[i];
radius[j] = radius[i];
omega[j][0] = omega[i][0];
omega[j][1] = omega[i][1];
omega[j][2] = omega[i][2];
@ -212,6 +217,12 @@ void AtomVecLine::set_length(int i, double value)
nlocal_bonus--;
line[i] = -1;
} else bonus[line[i]].length = value;
// also set radius = half of length
// unless value = 0.0, then set diameter = 1.0
radius[i] = 0.5 * value;
if (value == 0.0) radius[i] = 0.5;
}
/* ---------------------------------------------------------------------- */
@ -482,6 +493,8 @@ int AtomVecLine::pack_border(int n, int *list, double *buf,
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = ubuf(molecule[j]).d;
buf[m++] = radius[j];
buf[m++] = rmass[j];
if (line[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
@ -508,6 +521,8 @@ int AtomVecLine::pack_border(int n, int *list, double *buf,
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = ubuf(molecule[j]).d;
buf[m++] = radius[j];
buf[m++] = rmass[j];
if (line[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
@ -543,6 +558,8 @@ int AtomVecLine::pack_border_vel(int n, int *list, double *buf,
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = ubuf(molecule[j]).d;
buf[m++] = radius[j];
buf[m++] = rmass[j];
if (line[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
@ -576,6 +593,8 @@ int AtomVecLine::pack_border_vel(int n, int *list, double *buf,
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = ubuf(molecule[j]).d;
buf[m++] = radius[j];
buf[m++] = rmass[j];
if (line[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
@ -602,6 +621,8 @@ int AtomVecLine::pack_border_vel(int n, int *list, double *buf,
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = ubuf(molecule[j]).d;
buf[m++] = radius[j];
buf[m++] = rmass[j];
if (line[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
@ -641,6 +662,8 @@ int AtomVecLine::pack_border_hybrid(int n, int *list, double *buf)
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(molecule[j]).d;
buf[m++] = radius[j];
buf[m++] = rmass[j];
if (line[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
@ -668,6 +691,8 @@ void AtomVecLine::unpack_border(int n, int first, double *buf)
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
radius[i] = buf[m++];
rmass[i] = buf[m++];
line[i] = (int) ubuf(buf[m++]).i;
if (line[i] == 0) line[i] = -1;
else {
@ -704,6 +729,8 @@ void AtomVecLine::unpack_border_vel(int n, int first, double *buf)
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
radius[i] = buf[m++];
rmass[i] = buf[m++];
line[i] = (int) ubuf(buf[m++]).i;
if (line[i] == 0) line[i] = -1;
else {
@ -739,6 +766,8 @@ int AtomVecLine::unpack_border_hybrid(int n, int first, double *buf)
last = first + n;
for (i = first; i < last; i++) {
molecule[i] = (tagint) ubuf(buf[m++]).i;
radius[i] = buf[m++];
rmass[i] = buf[m++];
line[i] = (int) ubuf(buf[m++]).i;
if (line[i] == 0) line[i] = -1;
else {
@ -775,6 +804,7 @@ int AtomVecLine::pack_exchange(int i, double *buf)
buf[m++] = ubuf(molecule[i]).d;
buf[m++] = rmass[i];
buf[m++] = radius[i];
buf[m++] = omega[i][0];
buf[m++] = omega[i][1];
buf[m++] = omega[i][2];
@ -816,6 +846,7 @@ int AtomVecLine::unpack_exchange(double *buf)
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
rmass[nlocal] = buf[m++];
radius[nlocal] = buf[m++];
omega[nlocal][0] = buf[m++];
omega[nlocal][1] = buf[m++];
omega[nlocal][2] = buf[m++];
@ -851,8 +882,8 @@ int AtomVecLine::size_restart()
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (line[i] >= 0) n += 19;
else n += 17;
if (line[i] >= 0) n += 20;
else n += 18;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
@ -884,6 +915,7 @@ int AtomVecLine::pack_restart(int i, double *buf)
buf[m++] = ubuf(molecule[i]).d;
buf[m++] = rmass[i];
buf[m++] = radius[i];
buf[m++] = omega[i][0];
buf[m++] = omega[i][1];
buf[m++] = omega[i][2];
@ -931,6 +963,7 @@ int AtomVecLine::unpack_restart(double *buf)
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
rmass[nlocal] = buf[m++];
radius[nlocal] = buf[m++];
omega[nlocal][0] = buf[m++];
omega[nlocal][1] = buf[m++];
omega[nlocal][2] = buf[m++];
@ -978,7 +1011,8 @@ void AtomVecLine::create_atom(int itype, double *coord)
v[nlocal][2] = 0.0;
molecule[nlocal] = 0;
rmass[nlocal] = 1.0;
radius[nlocal] = 0.5;
rmass[nlocal] = 4.0*MY_PI/3.0 * radius[nlocal]*radius[nlocal]*radius[nlocal];
omega[nlocal][0] = 0.0;
omega[nlocal][1] = 0.0;
omega[nlocal][2] = 0.0;
@ -1012,6 +1046,12 @@ void AtomVecLine::data_atom(double *coord, imageint imagetmp, char **values)
if (rmass[nlocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (line[nlocal] < 0) {
radius[nlocal] = 0.5;
rmass[nlocal] *= 4.0*MY_PI/3.0 *
radius[nlocal]*radius[nlocal]*radius[nlocal];
} else radius[nlocal] = 0.0;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
@ -1047,6 +1087,12 @@ int AtomVecLine::data_atom_hybrid(int nlocal, char **values)
if (rmass[nlocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (line[nlocal] < 0) {
radius[nlocal] = 0.5;
rmass[nlocal] *= 4.0*MY_PI/3.0 *
radius[nlocal]*radius[nlocal]*radius[nlocal];
} else radius[nlocal] = 0.0;
return 3;
}
@ -1084,9 +1130,10 @@ void AtomVecLine::data_atom_bonus(int m, char **values)
x[m][0] = xc;
x[m][1] = yc;
// reset line mass
// previously stored density in rmass
// reset line radius and mass
// rmass currently holds density
radius[m] = 0.5 * length;
rmass[m] *= length;
bonus[nlocal_bonus].ilocal = m;
@ -1132,7 +1179,8 @@ void AtomVecLine::pack_data(double **buf)
buf[i][2] = ubuf(type[i]).d;
if (line[i] < 0) buf[i][3] = ubuf(0).d;
else buf[i][3] = ubuf(1).d;
if (line[i] < 0) buf[i][4] = rmass[i];
if (line[i] < 0)
buf[i][4] = rmass[i] / (4.0*MY_PI/3.0 * radius[i]*radius[i]*radius[i]);
else buf[i][4] = rmass[i]/bonus[line[i]].length;
buf[i][5] = x[i][0];
buf[i][6] = x[i][1];
@ -1152,7 +1200,8 @@ int AtomVecLine::pack_data_hybrid(int i, double *buf)
buf[0] = ubuf(molecule[i]).d;
if (line[i] < 0) buf[1] = ubuf(0).d;
else buf[1] = ubuf(1).d;
if (line[i] < 0) buf[2] = rmass[i];
if (line[i] < 0)
buf[2] = rmass[i] / (4.0*MY_PI/3.0 * radius[i]*radius[i]*radius[i]);
else buf[2] = rmass[i]/bonus[line[i]].length;
return 3;
}
@ -1255,6 +1304,7 @@ bigint AtomVecLine::memory_usage()
if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
if (atom->memcheck("radius")) bytes += memory->usage(radius,nmax);
if (atom->memcheck("omega")) bytes += memory->usage(omega,nmax,3);
if (atom->memcheck("torque"))
bytes += memory->usage(torque,nmax*comm->nthreads,3);