forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14480 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
5d99bf664e
commit
3621171480
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@ -21,10 +21,12 @@
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#include "modify.h"
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#include "force.h"
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#include "fix.h"
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#include "math_const.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace MathConst;
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#define EPSILON 0.001
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@ -37,7 +39,7 @@ AtomVecLine::AtomVecLine(LAMMPS *lmp) : AtomVec(lmp)
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comm_x_only = comm_f_only = 0;
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size_forward = 4;
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size_reverse = 6;
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size_border = 10;
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size_border = 12;
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size_velocity = 6;
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size_data_atom = 8;
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size_data_vel = 7;
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@ -46,7 +48,8 @@ AtomVecLine::AtomVecLine(LAMMPS *lmp) : AtomVec(lmp)
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atom->line_flag = 1;
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atom->molecule_flag = atom->rmass_flag = 1;
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atom->omega_flag = atom->torque_flag = 1;
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atom->radius_flag = atom->omega_flag = atom->torque_flag = 1;
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atom->sphere_flag = 1;
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nlocal_bonus = nghost_bonus = nmax_bonus = 0;
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bonus = NULL;
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@ -93,6 +96,7 @@ void AtomVecLine::grow(int n)
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molecule = memory->grow(atom->molecule,nmax,"atom:molecule");
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rmass = memory->grow(atom->rmass,nmax,"atom:rmass");
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radius = memory->grow(atom->radius,nmax,"atom:radius");
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omega = memory->grow(atom->omega,nmax,3,"atom:omega");
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torque = memory->grow(atom->torque,nmax*comm->nthreads,3,"atom:torque");
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line = memory->grow(atom->line,nmax,"atom:line");
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@ -112,7 +116,7 @@ void AtomVecLine::grow_reset()
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mask = atom->mask; image = atom->image;
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x = atom->x; v = atom->v; f = atom->f;
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molecule = atom->molecule; rmass = atom->rmass;
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omega = atom->omega; torque = atom->torque;
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radius = atom->radius; omega = atom->omega; torque = atom->torque;
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line = atom->line;
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}
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@ -149,6 +153,7 @@ void AtomVecLine::copy(int i, int j, int delflag)
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molecule[j] = molecule[i];
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rmass[j] = rmass[i];
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radius[j] = radius[i];
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omega[j][0] = omega[i][0];
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omega[j][1] = omega[i][1];
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omega[j][2] = omega[i][2];
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@ -212,6 +217,12 @@ void AtomVecLine::set_length(int i, double value)
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nlocal_bonus--;
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line[i] = -1;
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} else bonus[line[i]].length = value;
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// also set radius = half of length
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// unless value = 0.0, then set diameter = 1.0
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radius[i] = 0.5 * value;
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if (value == 0.0) radius[i] = 0.5;
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}
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/* ---------------------------------------------------------------------- */
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@ -482,6 +493,8 @@ int AtomVecLine::pack_border(int n, int *list, double *buf,
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buf[m++] = ubuf(type[j]).d;
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buf[m++] = ubuf(mask[j]).d;
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buf[m++] = ubuf(molecule[j]).d;
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buf[m++] = radius[j];
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buf[m++] = rmass[j];
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if (line[j] < 0) buf[m++] = ubuf(0).d;
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else {
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buf[m++] = ubuf(1).d;
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@ -508,6 +521,8 @@ int AtomVecLine::pack_border(int n, int *list, double *buf,
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buf[m++] = ubuf(type[j]).d;
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buf[m++] = ubuf(mask[j]).d;
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buf[m++] = ubuf(molecule[j]).d;
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buf[m++] = radius[j];
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buf[m++] = rmass[j];
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if (line[j] < 0) buf[m++] = ubuf(0).d;
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else {
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buf[m++] = ubuf(1).d;
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@ -543,6 +558,8 @@ int AtomVecLine::pack_border_vel(int n, int *list, double *buf,
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buf[m++] = ubuf(type[j]).d;
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buf[m++] = ubuf(mask[j]).d;
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buf[m++] = ubuf(molecule[j]).d;
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buf[m++] = radius[j];
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buf[m++] = rmass[j];
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if (line[j] < 0) buf[m++] = ubuf(0).d;
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else {
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buf[m++] = ubuf(1).d;
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@ -576,6 +593,8 @@ int AtomVecLine::pack_border_vel(int n, int *list, double *buf,
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buf[m++] = ubuf(type[j]).d;
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buf[m++] = ubuf(mask[j]).d;
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buf[m++] = ubuf(molecule[j]).d;
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buf[m++] = radius[j];
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buf[m++] = rmass[j];
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if (line[j] < 0) buf[m++] = ubuf(0).d;
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else {
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buf[m++] = ubuf(1).d;
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@ -602,6 +621,8 @@ int AtomVecLine::pack_border_vel(int n, int *list, double *buf,
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buf[m++] = ubuf(type[j]).d;
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buf[m++] = ubuf(mask[j]).d;
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buf[m++] = ubuf(molecule[j]).d;
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buf[m++] = radius[j];
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buf[m++] = rmass[j];
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if (line[j] < 0) buf[m++] = ubuf(0).d;
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else {
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buf[m++] = ubuf(1).d;
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@ -641,6 +662,8 @@ int AtomVecLine::pack_border_hybrid(int n, int *list, double *buf)
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = ubuf(molecule[j]).d;
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buf[m++] = radius[j];
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buf[m++] = rmass[j];
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if (line[j] < 0) buf[m++] = ubuf(0).d;
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else {
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buf[m++] = ubuf(1).d;
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@ -668,6 +691,8 @@ void AtomVecLine::unpack_border(int n, int first, double *buf)
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type[i] = (int) ubuf(buf[m++]).i;
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mask[i] = (int) ubuf(buf[m++]).i;
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molecule[i] = (tagint) ubuf(buf[m++]).i;
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radius[i] = buf[m++];
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rmass[i] = buf[m++];
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line[i] = (int) ubuf(buf[m++]).i;
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if (line[i] == 0) line[i] = -1;
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else {
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@ -704,6 +729,8 @@ void AtomVecLine::unpack_border_vel(int n, int first, double *buf)
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type[i] = (int) ubuf(buf[m++]).i;
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mask[i] = (int) ubuf(buf[m++]).i;
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molecule[i] = (tagint) ubuf(buf[m++]).i;
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radius[i] = buf[m++];
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rmass[i] = buf[m++];
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line[i] = (int) ubuf(buf[m++]).i;
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if (line[i] == 0) line[i] = -1;
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else {
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@ -739,6 +766,8 @@ int AtomVecLine::unpack_border_hybrid(int n, int first, double *buf)
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last = first + n;
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for (i = first; i < last; i++) {
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molecule[i] = (tagint) ubuf(buf[m++]).i;
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radius[i] = buf[m++];
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rmass[i] = buf[m++];
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line[i] = (int) ubuf(buf[m++]).i;
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if (line[i] == 0) line[i] = -1;
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else {
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@ -775,6 +804,7 @@ int AtomVecLine::pack_exchange(int i, double *buf)
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buf[m++] = ubuf(molecule[i]).d;
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buf[m++] = rmass[i];
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buf[m++] = radius[i];
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buf[m++] = omega[i][0];
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buf[m++] = omega[i][1];
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buf[m++] = omega[i][2];
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@ -816,6 +846,7 @@ int AtomVecLine::unpack_exchange(double *buf)
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molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
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rmass[nlocal] = buf[m++];
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radius[nlocal] = buf[m++];
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omega[nlocal][0] = buf[m++];
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omega[nlocal][1] = buf[m++];
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omega[nlocal][2] = buf[m++];
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@ -851,8 +882,8 @@ int AtomVecLine::size_restart()
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int n = 0;
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int nlocal = atom->nlocal;
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for (i = 0; i < nlocal; i++)
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if (line[i] >= 0) n += 19;
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else n += 17;
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if (line[i] >= 0) n += 20;
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else n += 18;
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if (atom->nextra_restart)
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for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
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@ -884,6 +915,7 @@ int AtomVecLine::pack_restart(int i, double *buf)
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buf[m++] = ubuf(molecule[i]).d;
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buf[m++] = rmass[i];
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buf[m++] = radius[i];
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buf[m++] = omega[i][0];
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buf[m++] = omega[i][1];
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buf[m++] = omega[i][2];
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@ -931,6 +963,7 @@ int AtomVecLine::unpack_restart(double *buf)
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molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
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rmass[nlocal] = buf[m++];
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radius[nlocal] = buf[m++];
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omega[nlocal][0] = buf[m++];
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omega[nlocal][1] = buf[m++];
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omega[nlocal][2] = buf[m++];
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@ -978,7 +1011,8 @@ void AtomVecLine::create_atom(int itype, double *coord)
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v[nlocal][2] = 0.0;
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molecule[nlocal] = 0;
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rmass[nlocal] = 1.0;
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radius[nlocal] = 0.5;
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rmass[nlocal] = 4.0*MY_PI/3.0 * radius[nlocal]*radius[nlocal]*radius[nlocal];
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omega[nlocal][0] = 0.0;
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omega[nlocal][1] = 0.0;
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omega[nlocal][2] = 0.0;
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@ -1012,6 +1046,12 @@ void AtomVecLine::data_atom(double *coord, imageint imagetmp, char **values)
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if (rmass[nlocal] <= 0.0)
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error->one(FLERR,"Invalid density in Atoms section of data file");
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if (line[nlocal] < 0) {
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radius[nlocal] = 0.5;
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rmass[nlocal] *= 4.0*MY_PI/3.0 *
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radius[nlocal]*radius[nlocal]*radius[nlocal];
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} else radius[nlocal] = 0.0;
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x[nlocal][0] = coord[0];
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x[nlocal][1] = coord[1];
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x[nlocal][2] = coord[2];
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@ -1047,6 +1087,12 @@ int AtomVecLine::data_atom_hybrid(int nlocal, char **values)
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if (rmass[nlocal] <= 0.0)
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error->one(FLERR,"Invalid density in Atoms section of data file");
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if (line[nlocal] < 0) {
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radius[nlocal] = 0.5;
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rmass[nlocal] *= 4.0*MY_PI/3.0 *
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radius[nlocal]*radius[nlocal]*radius[nlocal];
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} else radius[nlocal] = 0.0;
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return 3;
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}
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@ -1084,9 +1130,10 @@ void AtomVecLine::data_atom_bonus(int m, char **values)
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x[m][0] = xc;
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x[m][1] = yc;
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// reset line mass
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// previously stored density in rmass
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// reset line radius and mass
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// rmass currently holds density
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radius[m] = 0.5 * length;
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rmass[m] *= length;
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bonus[nlocal_bonus].ilocal = m;
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@ -1132,7 +1179,8 @@ void AtomVecLine::pack_data(double **buf)
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buf[i][2] = ubuf(type[i]).d;
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if (line[i] < 0) buf[i][3] = ubuf(0).d;
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else buf[i][3] = ubuf(1).d;
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if (line[i] < 0) buf[i][4] = rmass[i];
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if (line[i] < 0)
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buf[i][4] = rmass[i] / (4.0*MY_PI/3.0 * radius[i]*radius[i]*radius[i]);
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else buf[i][4] = rmass[i]/bonus[line[i]].length;
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buf[i][5] = x[i][0];
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buf[i][6] = x[i][1];
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@ -1152,7 +1200,8 @@ int AtomVecLine::pack_data_hybrid(int i, double *buf)
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buf[0] = ubuf(molecule[i]).d;
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if (line[i] < 0) buf[1] = ubuf(0).d;
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else buf[1] = ubuf(1).d;
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if (line[i] < 0) buf[2] = rmass[i];
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if (line[i] < 0)
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buf[2] = rmass[i] / (4.0*MY_PI/3.0 * radius[i]*radius[i]*radius[i]);
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else buf[2] = rmass[i]/bonus[line[i]].length;
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return 3;
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}
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@ -1255,6 +1304,7 @@ bigint AtomVecLine::memory_usage()
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if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
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if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
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if (atom->memcheck("radius")) bytes += memory->usage(radius,nmax);
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if (atom->memcheck("omega")) bytes += memory->usage(omega,nmax,3);
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if (atom->memcheck("torque"))
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bytes += memory->usage(torque,nmax*comm->nthreads,3);
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@ -89,7 +89,7 @@ class AtomVecLine : public AtomVec {
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imageint *image;
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double **x,**v,**f;
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tagint *molecule;
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double *rmass;
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double *rmass,*radius;
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double **omega,**torque;
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int *line;
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@ -22,10 +22,12 @@
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#include "modify.h"
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#include "force.h"
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#include "fix.h"
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#include "math_const.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace MathConst;
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#define EPSILON 0.001
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@ -38,7 +40,7 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp)
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comm_x_only = comm_f_only = 0;
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size_forward = 7;
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size_reverse = 6;
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size_border = 24;
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size_border = 26;
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size_velocity = 6;
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size_data_atom = 8;
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size_data_vel = 7;
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@ -47,10 +49,13 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp)
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atom->tri_flag = 1;
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atom->molecule_flag = atom->rmass_flag = 1;
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atom->angmom_flag = atom->torque_flag = 1;
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atom->radius_flag = atom->angmom_flag = atom->torque_flag = 1;
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nlocal_bonus = nghost_bonus = nmax_bonus = 0;
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bonus = NULL;
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if (domain->dimension != 3)
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error->all(FLERR,"Atom_style tri can only be used in 3d simulations");
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}
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/* ---------------------------------------------------------------------- */
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@ -94,6 +99,7 @@ void AtomVecTri::grow(int n)
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molecule = memory->grow(atom->molecule,nmax,"atom:molecule");
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rmass = memory->grow(atom->rmass,nmax,"atom:rmass");
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radius = memory->grow(atom->radius,nmax,"atom:radius");
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angmom = memory->grow(atom->angmom,nmax,3,"atom:angmom");
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torque = memory->grow(atom->torque,nmax*comm->nthreads,3,"atom:torque");
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tri = memory->grow(atom->tri,nmax,"atom:tri");
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@ -113,7 +119,7 @@ void AtomVecTri::grow_reset()
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mask = atom->mask; image = atom->image;
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x = atom->x; v = atom->v; f = atom->f;
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molecule = atom->molecule; rmass = atom->rmass;
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angmom = atom->angmom; torque = atom->torque;
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radius = atom->radius; angmom = atom->angmom; torque = atom->torque;
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tri = atom->tri;
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}
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@ -151,6 +157,7 @@ void AtomVecTri::copy(int i, int j, int delflag)
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molecule[j] = molecule[i];
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rmass[j] = rmass[i];
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radius[j] = radius[i];
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angmom[j][0] = angmom[i][0];
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angmom[j][1] = angmom[i][1];
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angmom[j][2] = angmom[i][2];
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@ -202,6 +209,9 @@ void AtomVecTri::clear_bonus()
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void AtomVecTri::set_equilateral(int i, double size)
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{
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// also set radius = distance from center to corner-pt = len(c1)
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// unless size = 0.0, then set diameter = 1.0
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if (tri[i] < 0) {
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if (size == 0.0) return;
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if (nlocal_bonus == nmax_bonus) grow_bonus();
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@ -226,9 +236,11 @@ void AtomVecTri::set_equilateral(int i, double size)
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inertia[0] = sqrt(3.0)/96.0 * size*size*size*size;
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inertia[1] = sqrt(3.0)/96.0 * size*size*size*size;
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inertia[2] = sqrt(3.0)/48.0 * size*size*size*size;
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radius[i] = MathExtra::len3(c1);
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bonus[nlocal_bonus].ilocal = i;
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tri[i] = nlocal_bonus++;
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} else if (size == 0.0) {
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radius[i] = 0.5;
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copy_bonus(nlocal_bonus-1,tri[i]);
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nlocal_bonus--;
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tri[i] = -1;
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@ -249,6 +261,7 @@ void AtomVecTri::set_equilateral(int i, double size)
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inertia[0] = sqrt(3.0)/96.0 * size*size*size*size;
|
||||
inertia[1] = sqrt(3.0)/96.0 * size*size*size*size;
|
||||
inertia[2] = sqrt(3.0)/48.0 * size*size*size*size;
|
||||
radius[i] = MathExtra::len3(c1);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -581,6 +594,8 @@ int AtomVecTri::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 (tri[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
|
|
@ -626,6 +641,8 @@ int AtomVecTri::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 (tri[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
|
|
@ -681,6 +698,8 @@ int AtomVecTri::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 (tri[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
|
|
@ -733,6 +752,8 @@ int AtomVecTri::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 (tri[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
|
|
@ -778,6 +799,8 @@ int AtomVecTri::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 (tri[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
|
|
@ -837,6 +860,8 @@ int AtomVecTri::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 (tri[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
|
|
@ -884,6 +909,8 @@ void AtomVecTri::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++];
|
||||
tri[i] = (int) ubuf(buf[m++]).i;
|
||||
if (tri[i] == 0) tri[i] = -1;
|
||||
else {
|
||||
|
|
@ -940,6 +967,8 @@ void AtomVecTri::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++];
|
||||
tri[i] = (int) ubuf(buf[m++]).i;
|
||||
if (tri[i] == 0) tri[i] = -1;
|
||||
else {
|
||||
|
|
@ -995,6 +1024,8 @@ int AtomVecTri::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++];
|
||||
tri[i] = (int) ubuf(buf[m++]).i;
|
||||
if (tri[i] == 0) tri[i] = -1;
|
||||
else {
|
||||
|
|
@ -1050,6 +1081,7 @@ int AtomVecTri::pack_exchange(int i, double *buf)
|
|||
|
||||
buf[m++] = ubuf(molecule[i]).d;
|
||||
buf[m++] = rmass[i];
|
||||
buf[m++] = radius[i];
|
||||
buf[m++] = angmom[i][0];
|
||||
buf[m++] = angmom[i][1];
|
||||
buf[m++] = angmom[i][2];
|
||||
|
|
@ -1110,6 +1142,7 @@ int AtomVecTri::unpack_exchange(double *buf)
|
|||
|
||||
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
|
||||
rmass[nlocal] = buf[m++];
|
||||
radius[nlocal] = buf[m++];
|
||||
angmom[nlocal][0] = buf[m++];
|
||||
angmom[nlocal][1] = buf[m++];
|
||||
angmom[nlocal][2] = buf[m++];
|
||||
|
|
@ -1164,8 +1197,8 @@ int AtomVecTri::size_restart()
|
|||
int n = 0;
|
||||
int nlocal = atom->nlocal;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (tri[i] >= 0) n += 33;
|
||||
else n += 17;
|
||||
if (tri[i] >= 0) n += 34;
|
||||
else n += 18;
|
||||
|
||||
if (atom->nextra_restart)
|
||||
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
|
||||
|
|
@ -1197,6 +1230,7 @@ int AtomVecTri::pack_restart(int i, double *buf)
|
|||
|
||||
buf[m++] = ubuf(molecule[i]).d;
|
||||
buf[m++] = rmass[i];
|
||||
buf[m++] = radius[i];
|
||||
buf[m++] = angmom[i][0];
|
||||
buf[m++] = angmom[i][1];
|
||||
buf[m++] = angmom[i][2];
|
||||
|
|
@ -1263,6 +1297,7 @@ int AtomVecTri::unpack_restart(double *buf)
|
|||
|
||||
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
|
||||
rmass[nlocal] = buf[m++];
|
||||
radius[nlocal] = buf[m++];
|
||||
angmom[nlocal][0] = buf[m++];
|
||||
angmom[nlocal][1] = buf[m++];
|
||||
angmom[nlocal][2] = buf[m++];
|
||||
|
|
@ -1329,7 +1364,8 @@ void AtomVecTri::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];
|
||||
angmom[nlocal][0] = 0.0;
|
||||
angmom[nlocal][1] = 0.0;
|
||||
angmom[nlocal][2] = 0.0;
|
||||
|
|
@ -1363,6 +1399,12 @@ void AtomVecTri::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 (tri[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];
|
||||
|
|
@ -1398,6 +1440,12 @@ int AtomVecTri::data_atom_hybrid(int nlocal, char **values)
|
|||
if (rmass[nlocal] <= 0.0)
|
||||
error->one(FLERR,"Invalid density in Atoms section of data file");
|
||||
|
||||
if (tri[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;
|
||||
}
|
||||
|
||||
|
|
@ -1457,10 +1505,19 @@ void AtomVecTri::data_atom_bonus(int m, char **values)
|
|||
x[m][1] = centroid[1];
|
||||
x[m][2] = centroid[2];
|
||||
|
||||
// reset tri mass
|
||||
// previously stored density in rmass
|
||||
// reset tri radius and mass
|
||||
// rmass currently holds density
|
||||
// tri area = 0.5 len(U x V), where U,V are edge vectors from one vertex
|
||||
|
||||
double c4[3];
|
||||
MathExtra::sub3(c1,centroid,c4);
|
||||
radius[m] = MathExtra::lensq3(c4);
|
||||
MathExtra::sub3(c2,centroid,c4);
|
||||
radius[m] = MAX(radius[m],MathExtra::lensq3(c4));
|
||||
MathExtra::sub3(c3,centroid,c4);
|
||||
radius[m] = MAX(radius[m],MathExtra::lensq3(c4));
|
||||
radius[m] = sqrt(radius[m]);
|
||||
|
||||
double norm[3];
|
||||
MathExtra::cross3(c2mc1,c3mc1,norm);
|
||||
double area = 0.5 * MathExtra::len3(norm);
|
||||
|
|
@ -1567,7 +1624,8 @@ void AtomVecTri::pack_data(double **buf)
|
|||
buf[i][2] = ubuf(type[i]).d;
|
||||
if (tri[i] < 0) buf[i][3] = ubuf(0).d;
|
||||
else buf[i][3] = ubuf(1).d;
|
||||
if (tri[i] < 0) buf[i][4] = rmass[i];
|
||||
if (tri[i] < 0)
|
||||
buf[i][4] = rmass[i] / (4.0*MY_PI/3.0 * radius[i]*radius[i]*radius[i]);
|
||||
else {
|
||||
MathExtra::sub3(bonus[tri[i]].c2,bonus[tri[i]].c1,c2mc1);
|
||||
MathExtra::sub3(bonus[tri[i]].c3,bonus[tri[i]].c1,c3mc1);
|
||||
|
|
@ -1593,7 +1651,8 @@ int AtomVecTri::pack_data_hybrid(int i, double *buf)
|
|||
buf[0] = ubuf(molecule[i]).d;
|
||||
if (tri[i] < 0) buf[1] = ubuf(0).d;
|
||||
else buf[1] = ubuf(1).d;
|
||||
if (tri[i] < 0) buf[2] = rmass[i];
|
||||
if (tri[i] < 0)
|
||||
buf[2] = rmass[i] / (4.0*MY_PI/3.0 * radius[i]*radius[i]*radius[i]);
|
||||
else {
|
||||
double c2mc1[3],c3mc1[3],norm[3];
|
||||
MathExtra::sub3(bonus[tri[i]].c2,bonus[tri[i]].c1,c2mc1);
|
||||
|
|
@ -1703,6 +1762,7 @@ bigint AtomVecTri::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("angmom")) bytes += memory->usage(angmom,nmax,3);
|
||||
if (atom->memcheck("torque")) bytes +=
|
||||
memory->usage(torque,nmax*comm->nthreads,3);
|
||||
|
|
|
|||
|
|
@ -91,7 +91,7 @@ class AtomVecTri : public AtomVec {
|
|||
imageint *image;
|
||||
double **x,**v,**f;
|
||||
tagint *molecule;
|
||||
double *rmass;
|
||||
double *rmass,*radius;
|
||||
double **angmom,**torque;
|
||||
int *tri;
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue