Commit 36211714 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14480 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 5d99bf66

src/atom_vec_line.cpp

+60 −10
Original line number Diff line number Diff line
@@ -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);

src/atom_vec_line.h

+1 −1
Original line number Diff line number Diff line
@@ -89,7 +89,7 @@ class AtomVecLine : public AtomVec { 
  imageint *image;

  double **x,**v,**f;

  tagint *molecule;

  double *rmass;

  double *rmass,*radius;

  double **omega,**torque;

  int *line;

src/atom_vec_tri.cpp

+70 −10
Original line number Diff line number Diff line
@@ -22,10 +22,12 @@ 
#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
@@ -38,7 +40,7 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp) 
  comm_x_only = comm_f_only = 0;

  size_forward = 7;

  size_reverse = 6;

  size_border = 24;

  size_border = 26;

  size_velocity = 6;

  size_data_atom = 8;

  size_data_vel = 7;
@@ -47,10 +49,13 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp) 


  atom->tri_flag = 1;

  atom->molecule_flag = atom->rmass_flag = 1;

  atom->angmom_flag = atom->torque_flag = 1;

  atom->radius_flag = atom->angmom_flag = atom->torque_flag = 1;



  nlocal_bonus = nghost_bonus = nmax_bonus = 0;

  bonus = NULL;



  if (domain->dimension != 3)

    error->all(FLERR,"Atom_style tri can only be used in 3d simulations");

}



/* ---------------------------------------------------------------------- */
@@ -94,6 +99,7 @@ void AtomVecTri::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");

  angmom = memory->grow(atom->angmom,nmax,3,"atom:angmom");

  torque = memory->grow(atom->torque,nmax*comm->nthreads,3,"atom:torque");

  tri = memory->grow(atom->tri,nmax,"atom:tri");
@@ -113,7 +119,7 @@ void AtomVecTri::grow_reset() 
  mask = atom->mask; image = atom->image;

  x = atom->x; v = atom->v; f = atom->f;

  molecule = atom->molecule; rmass = atom->rmass;

  angmom = atom->angmom; torque = atom->torque;

  radius = atom->radius; angmom = atom->angmom; torque = atom->torque;

  tri = atom->tri;

}
@@ -151,6 +157,7 @@ void AtomVecTri::copy(int i, int j, int delflag) 


  molecule[j] = molecule[i];

  rmass[j] = rmass[i];

  radius[j] = radius[i];

  angmom[j][0] = angmom[i][0];

  angmom[j][1] = angmom[i][1];

  angmom[j][2] = angmom[i][2];
@@ -202,6 +209,9 @@ void AtomVecTri::clear_bonus() 


void AtomVecTri::set_equilateral(int i, double size)

{

  // also set radius = distance from center to corner-pt = len(c1)

  // unless size = 0.0, then set diameter = 1.0



  if (tri[i] < 0) {

    if (size == 0.0) return;

    if (nlocal_bonus == nmax_bonus) grow_bonus();
@@ -226,9 +236,11 @@ void AtomVecTri::set_equilateral(int i, double size) 
    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);

    bonus[nlocal_bonus].ilocal = i;

    tri[i] = nlocal_bonus++;

  } else if (size == 0.0) {

    radius[i] = 0.5;

    copy_bonus(nlocal_bonus-1,tri[i]);

    nlocal_bonus--;

    tri[i] = -1;
@@ -249,6 +261,7 @@ void AtomVecTri::set_equilateral(int i, double size) 
    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);

src/atom_vec_tri.h

+1 −1
Original line number Diff line number Diff line
@@ -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;

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