ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
Download Patch File Download Diff File Expand all files Collapse all files

448
src/atom_vec_tri.cpp
View File

@ -130,7 +130,7 @@ void AtomVecTri::grow_bonus()
error->one(FLERR,"Per-processor system is too big");
bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
"atom:bonus");
"atom:bonus");
}
/* ----------------------------------------------------------------------
@ -256,7 +256,7 @@ void AtomVecTri::set_equilateral(int i, double size)
/* ---------------------------------------------------------------------- */
int AtomVecTri::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@ -270,11 +270,11 @@ int AtomVecTri::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][1];
buf[m++] = x[j][2];
if (tri[j] >= 0) {
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
}
} else {
@ -293,11 +293,11 @@ int AtomVecTri::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
if (tri[j] >= 0) {
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
}
}
@ -308,7 +308,7 @@ int AtomVecTri::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecTri::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@ -322,11 +322,11 @@ int AtomVecTri::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = x[j][1];
buf[m++] = x[j][2];
if (tri[j] >= 0) {
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
@ -347,52 +347,52 @@ int AtomVecTri::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
if (tri[j] >= 0) {
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
if (tri[j] >= 0) {
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
if (tri[j] >= 0) {
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
if (tri[j] >= 0) {
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
}
}
@ -565,7 +565,7 @@ int AtomVecTri::unpack_reverse_hybrid(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecTri::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@ -584,28 +584,28 @@ int AtomVecTri::pack_border(int n, int *list, double *buf,
buf[m++] = molecule[j];
if (tri[j] < 0) buf[m++] = 0;
else {
buf[m++] = 1;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
buf[m++] = 1;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
}
}
} else {
@ -629,28 +629,28 @@ int AtomVecTri::pack_border(int n, int *list, double *buf,
buf[m++] = molecule[j];
if (tri[j] < 0) buf[m++] = 0;
else {
buf[m++] = 1;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
buf[m++] = 1;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
}
}
}
@ -660,7 +660,7 @@ int AtomVecTri::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecTri::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@ -679,28 +679,28 @@ int AtomVecTri::pack_border_vel(int n, int *list, double *buf,
buf[m++] = molecule[j];
if (tri[j] < 0) buf[m++] = 0;
else {
buf[m++] = 1;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
buf[m++] = 1;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
@ -721,96 +721,96 @@ int AtomVecTri::pack_border_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
if (tri[j] < 0) buf[m++] = 0;
else {
buf[m++] = 1;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
if (tri[j] < 0) buf[m++] = 0;
else {
buf[m++] = 1;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
if (tri[j] < 0) buf[m++] = 0;
else {
buf[m++] = 1;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
}
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
if (tri[j] < 0) buf[m++] = 0;
else {
buf[m++] = 1;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
}
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
}
}
@ -1012,7 +1012,7 @@ int AtomVecTri::unpack_border_hybrid(int n, int first, double *buf)
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecTri::pack_exchange(int i, double *buf)
@ -1063,7 +1063,7 @@ int AtomVecTri::pack_exchange(int i, double *buf)
}
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
@ -1125,9 +1125,9 @@ int AtomVecTri::unpack_exchange(double *buf)
}
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@ -1149,9 +1149,9 @@ int AtomVecTri::size_restart()
else n += 17;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
@ -1159,7 +1159,7 @@ int AtomVecTri::size_restart()
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecTri::pack_restart(int i, double *buf)
@ -1210,7 +1210,7 @@ int AtomVecTri::pack_restart(int i, double *buf)
}
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
@ -1469,7 +1469,7 @@ void AtomVecTri::data_atom_bonus(int m, char **values)
int ierror = MathExtra::jacobi(tensor,bonus[nlocal_bonus].inertia,evectors);
if (ierror) error->one(FLERR,"Insufficient Jacobi rotations for triangle");
double ex_space[3],ey_space[3],ez_space[3];
ex_space[0] = evectors[0][0];
ex_space[1] = evectors[1][0];
@ -1488,7 +1488,7 @@ void AtomVecTri::data_atom_bonus(int m, char **values)
if (MathExtra::dot3(norm,ez_space) < 0.0) MathExtra::negate3(ez_space);
// create initial quaternion
MathExtra::exyz_to_q(ex_space,ey_space,ez_space,bonus[nlocal_bonus].quat);
// bonus c1,c2,c3 = displacement of c1,c2,c3 from centroid
@ -1497,13 +1497,13 @@ void AtomVecTri::data_atom_bonus(int m, char **values)
double disp[3];
MathExtra::sub3(c1,centroid,disp);
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
disp,bonus[nlocal_bonus].c1);
disp,bonus[nlocal_bonus].c1);
MathExtra::sub3(c2,centroid,disp);
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
disp,bonus[nlocal_bonus].c2);
disp,bonus[nlocal_bonus].c2);
MathExtra::sub3(c3,centroid,disp);
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
disp,bonus[nlocal_bonus].c3);
disp,bonus[nlocal_bonus].c3);
bonus[nlocal_bonus].ilocal = m;
tri[m] = nlocal_bonus++;
@ -1536,7 +1536,7 @@ int AtomVecTri::data_vel_hybrid(int m, char **values)
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecTri::memory_usage()