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

changes for body particles in general triclinic

Browse Source
This commit is contained in:
Steve Plimpton
2023-11-14 17:03:56 -07:00
parent 4da49c6d85
commit a0a21fab64
7 changed files with 137 additions and 19 deletions
Download Patch File Download Diff File Expand all files Collapse all files

83
src/atom_vec_body.cpp
View File

@ -597,6 +597,15 @@ void AtomVecBody::pack_data_pre(int ilocal)
body[ilocal] = 1;
}
/* ----------------------------------------------------------------------
unmodify values packed by AtomVec::pack_data()
------------------------------------------------------------------------- */
void AtomVecBody::pack_data_post(int ilocal)
{
body[ilocal] = body_flag;
}
/* ----------------------------------------------------------------------
pack bonus body info for writing to data file
if buf is nullptr, just return buffer size
@ -631,12 +640,80 @@ void AtomVecBody::write_data_bonus(FILE *fp, int n, double *buf, int /*flag*/)
}
/* ----------------------------------------------------------------------
unmodify values packed by AtomVec::pack_data()
convert read_data file info from general to restricted triclinic
parent class operates on data from Velocities section of data file
child class operates on body quaternion
------------------------------------------------------------------------- */
void AtomVecBody::pack_data_post(int ilocal)
void AtomVecBody::read_data_general_to_restricted(int nlocal_previous, int nlocal)
{
body[ilocal] = body_flag;
int j;
AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal);
// quat_g2r = quat that rotates from general to restricted triclinic
// quat_new = body quat converted to restricted triclinic
double quat_g2r[4],quat_new[4];
MathExtra::mat_to_quat(domain->rotate_g2r,quat_g2r);
for (int i = nlocal_previous; i < nlocal; i++) {
if (body[i] < 0) continue;
j = body[i];
MathExtra::quatquat(quat_g2r,bonus[j].quat,quat_new);
bonus[j].quat[0] = quat_new[0];
bonus[j].quat[1] = quat_new[1];
bonus[j].quat[2] = quat_new[2];
bonus[j].quat[3] = quat_new[3];
}
}
/* ----------------------------------------------------------------------
convert info output by write_data from restricted to general triclinic
parent class operates on x and data from Velocities section of data file
child class operates on body quaternion
------------------------------------------------------------------------- */
void AtomVecBody::write_data_restricted_to_general()
{
AtomVec::write_data_restricted_to_general();
memory->create(quat_hold,nlocal_bonus,4,"atomvec:quat_hold");
for (int i = 0; i < nlocal_bonus; i++)
memcpy(quat_hold[i],bonus[i].quat,4*sizeof(double));
// quat_r2g = quat that rotates from restricted to general triclinic
// quat_new = ellipsoid quat converted to general triclinic
double quat_r2g[4],quat_new[4];
MathExtra::mat_to_quat(domain->rotate_r2g,quat_r2g);
for (int i = 0; i < nlocal_bonus; i++) {
MathExtra::quatquat(quat_r2g,bonus[i].quat,quat_new);
bonus[i].quat[0] = quat_new[0];
bonus[i].quat[1] = quat_new[1];
bonus[i].quat[2] = quat_new[2];
bonus[i].quat[3] = quat_new[3];
}
}
/* ----------------------------------------------------------------------
restore info output by write_data to restricted triclinic
original data is in "hold" arrays
parent class operates on x and data from Velocities section of data file
child class operates on body quaternion
------------------------------------------------------------------------- */
void AtomVecBody::write_data_restore_restricted()
{
AtomVec::write_data_restore_restricted();
for (int i = 0; i < nlocal_bonus; i++)
memcpy(bonus[i].quat,quat_hold[i],4*sizeof(double));
memory->destroy(quat_hold);
quat_hold = nullptr;
}
/* ----------------------------------------------------------------------