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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14506 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2016-01-27 20:33:55 +00:00
parent dca90d44b7
commit fa7543b714
7 changed files with 150 additions and 50 deletions
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112
src/atom_vec_tri.cpp
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@ -41,7 +41,7 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp)
size_forward = 7;
size_reverse = 6;
size_border = 26;
size_velocity = 6;
size_velocity = 9;
size_data_atom = 8;
size_data_vel = 7;
size_data_bonus = 10;
@ -49,7 +49,9 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp)
atom->tri_flag = 1;
atom->molecule_flag = atom->rmass_flag = 1;
atom->radius_flag = atom->angmom_flag = atom->torque_flag = 1;
atom->radius_flag = atom->omega_flag = atom->angmom_flag = 1;
atom->torque_flag = 1;
atom->sphere_flag = 1;
nlocal_bonus = nghost_bonus = nmax_bonus = 0;
bonus = NULL;
@ -100,6 +102,7 @@ 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");
omega = memory->grow(atom->omega,nmax,3,"atom:omega");
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");
@ -119,7 +122,8 @@ 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;
radius = atom->radius; angmom = atom->angmom; torque = atom->torque;
radius = atom->radius; omega = atom->omega;
angmom = atom->angmom; torque = atom->torque;
tri = atom->tri;
}
@ -158,6 +162,9 @@ void AtomVecTri::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];
angmom[j][0] = angmom[i][0];
angmom[j][1] = angmom[i][1];
angmom[j][2] = angmom[i][2];
@ -343,6 +350,9 @@ int AtomVecTri::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
@ -373,6 +383,9 @@ int AtomVecTri::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
@ -402,6 +415,9 @@ int AtomVecTri::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
@ -479,6 +495,9 @@ void AtomVecTri::unpack_comm_vel(int n, int first, double *buf)
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[i][2] = buf[m++];
angmom[i][0] = buf[m++];
angmom[i][1] = buf[m++];
angmom[i][2] = buf[m++];
@ -728,6 +747,9 @@ int AtomVecTri::pack_border_vel(int n, int *list, double *buf,
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
@ -782,6 +804,9 @@ int AtomVecTri::pack_border_vel(int n, int *list, double *buf,
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
@ -835,6 +860,9 @@ int AtomVecTri::pack_border_vel(int n, int *list, double *buf,
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
@ -1002,6 +1030,9 @@ void AtomVecTri::unpack_border_vel(int n, int first, double *buf)
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[i][2] = buf[m++];
angmom[i][0] = buf[m++];
angmom[i][1] = buf[m++];
angmom[i][2] = buf[m++];
@ -1082,6 +1113,9 @@ int AtomVecTri::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];
buf[m++] = angmom[i][0];
buf[m++] = angmom[i][1];
buf[m++] = angmom[i][2];
@ -1143,6 +1177,9 @@ int AtomVecTri::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++];
angmom[nlocal][0] = buf[m++];
angmom[nlocal][1] = buf[m++];
angmom[nlocal][2] = buf[m++];
@ -1197,8 +1234,8 @@ int AtomVecTri::size_restart()
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (tri[i] >= 0) n += 34;
else n += 18;
if (tri[i] >= 0) n += 37;
else n += 21;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
@ -1231,6 +1268,9 @@ int AtomVecTri::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];
buf[m++] = angmom[i][0];
buf[m++] = angmom[i][1];
buf[m++] = angmom[i][2];
@ -1298,6 +1338,9 @@ int AtomVecTri::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++];
angmom[nlocal][0] = buf[m++];
angmom[nlocal][1] = buf[m++];
angmom[nlocal][2] = buf[m++];
@ -1366,6 +1409,9 @@ void AtomVecTri::create_atom(int itype, double *coord)
molecule[nlocal] = 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;
angmom[nlocal][0] = 0.0;
angmom[nlocal][1] = 0.0;
angmom[nlocal][2] = 0.0;
@ -1415,6 +1461,9 @@ void AtomVecTri::data_atom(double *coord, imageint imagetmp, char **values)
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
omega[nlocal][0] = 0.0;
omega[nlocal][1] = 0.0;
omega[nlocal][2] = 0.0;
angmom[nlocal][0] = 0.0;
angmom[nlocal][1] = 0.0;
angmom[nlocal][2] = 0.0;
@ -1591,21 +1640,27 @@ void AtomVecTri::data_vel(int m, char **values)
v[m][0] = atof(values[0]);
v[m][1] = atof(values[1]);
v[m][2] = atof(values[2]);
angmom[m][0] = atof(values[3]);
angmom[m][1] = atof(values[4]);
angmom[m][2] = atof(values[5]);
omega[m][0] = atof(values[3]);
omega[m][1] = atof(values[4]);
omega[m][2] = atof(values[5]);
angmom[m][0] = atof(values[6]);
angmom[m][1] = atof(values[7]);
angmom[m][2] = atof(values[8]);
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one tri in Velocities section of data file
unpack hybrid quantities from one line in Velocities section of data file
------------------------------------------------------------------------- */
int AtomVecTri::data_vel_hybrid(int m, char **values)
{
angmom[m][0] = atof(values[0]);
angmom[m][1] = atof(values[1]);
angmom[m][2] = atof(values[2]);
return 3;
omega[m][0] = atof(values[0]);
omega[m][1] = atof(values[1]);
omega[m][2] = atof(values[2]);
angmom[m][0] = atof(values[3]);
angmom[m][1] = atof(values[4]);
angmom[m][2] = atof(values[5]);
return 6;
}
/* ----------------------------------------------------------------------
@ -1703,9 +1758,12 @@ void AtomVecTri::pack_vel(double **buf)
buf[i][1] = v[i][0];
buf[i][2] = v[i][1];
buf[i][3] = v[i][2];
buf[i][4] = angmom[i][0];
buf[i][5] = angmom[i][1];
buf[i][6] = angmom[i][2];
buf[i][4] = omega[i][0];
buf[i][5] = omega[i][1];
buf[i][6] = omega[i][2];
buf[i][7] = angmom[i][0];
buf[i][8] = angmom[i][1];
buf[i][9] = angmom[i][2];
}
}
@ -1715,10 +1773,13 @@ void AtomVecTri::pack_vel(double **buf)
int AtomVecTri::pack_vel_hybrid(int i, double *buf)
{
buf[0] = angmom[i][0];
buf[1] = angmom[i][1];
buf[2] = angmom[i][2];
return 3;
buf[0] = omega[i][0];
buf[1] = omega[i][1];
buf[2] = omega[i][2];
buf[3] = angmom[i][0];
buf[4] = angmom[i][1];
buf[5] = angmom[i][2];
return 6;
}
/* ----------------------------------------------------------------------
@ -1729,9 +1790,10 @@ void AtomVecTri::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT
" %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n",
" %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "
"%-1.16e %-1.16e %-1.16e\n",
(tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
buf[i][4],buf[i][5],buf[i][6]);
buf[i][4],buf[i][5],buf[i][6],buf[i][7],buf[i][8],buf[i][9]);
}
/* ----------------------------------------------------------------------
@ -1740,8 +1802,9 @@ void AtomVecTri::write_vel(FILE *fp, int n, double **buf)
int AtomVecTri::write_vel_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %-1.16e %-1.16e %-1.16e",buf[0],buf[1],buf[2]);
return 3;
fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",
buf[0],buf[1],buf[2],buf[3],buf[4],buf[5]);
return 6;
}
/* ----------------------------------------------------------------------
@ -1763,6 +1826,7 @@ 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("omega")) bytes += memory->usage(omega,nmax,3);
if (atom->memcheck("angmom")) bytes += memory->usage(angmom,nmax,3);
if (atom->memcheck("torque")) bytes +=
memory->usage(torque,nmax*comm->nthreads,3);