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more work on read_data and write_data

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This commit is contained in:
Steve Plimpton
2023-09-13 13:29:37 -06:00
parent c7e794146f
commit e5f3fcbbf4
18 changed files with 488 additions and 14 deletions
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87
src/atom_vec_ellipsoid.cpp
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@ -18,6 +18,7 @@
#include "atom_vec_ellipsoid.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "math_const.h"
@ -48,6 +49,8 @@ AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp) : AtomVec(lmp)
nlocal_bonus = nghost_bonus = nmax_bonus = 0;
bonus = nullptr;
quat_hold = nullptr;
// strings with peratom variables to include in each AtomVec method
// strings cannot contain fields in corresponding AtomVec default strings
// order of fields in a string does not matter
@ -457,6 +460,90 @@ void AtomVecEllipsoid::data_atom_post(int ilocal)
angmom[ilocal][2] = 0.0;
}
/* ----------------------------------------------------------------------
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 bonus quat
------------------------------------------------------------------------- */
void AtomVecEllipsoid::read_data_general_to_restricted(int nlocal_previous, int nlocal)
{
AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal);
double quat[4];
double *bquat;
for (int i = nlocal_previous; i < nlocal; i++) {
if (ellipsoid[i] < 0) continue;
bquat = bonus[ellipsoid[i]].quat;
MathExtra::quatquat(domain->quat_g2r,bquat,quat);
bquat[0] = quat[0];
bquat[1] = quat[1];
bquat[2] = quat[2];
bquat[3] = quat[3];
MathExtra::qnormalize(bquat);
}
}
/* ----------------------------------------------------------------------
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 bonus quat
------------------------------------------------------------------------- */
void AtomVecEllipsoid::write_data_restricted_to_general()
{
AtomVec::write_data_restricted_to_general();
double quat[4],quat_r2g[4];
double *bquat;
memory->create(quat_hold,nlocal_bonus,4,"atomvec:quat_hold");
MathExtra::qconjugate(domain->quat_g2r,quat_r2g);
for (int i = 0; i < nlocal_bonus; i++) {
bquat = bonus[i].quat;
quat_hold[i][0] = bquat[0];
quat_hold[i][1] = bquat[1];
quat_hold[i][2] = bquat[2];
quat_hold[i][3] = bquat[3];
MathExtra::quatquat(quat_r2g,bquat,quat);
bquat[0] = quat[0];
bquat[1] = quat[1];
bquat[2] = quat[2];
bquat[3] = quat[3];
MathExtra::qnormalize(bquat);
}
}
/* ----------------------------------------------------------------------
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 bonus quat
------------------------------------------------------------------------- */
void AtomVecEllipsoid::write_data_restore_restricted()
{
AtomVec::write_data_restore_restricted();
if (!quat_hold) return;
double *bquat;
for (int i = 0; i < nlocal_bonus; i++) {
bquat = bonus[i].quat;
bquat[0] = quat_hold[i][0];
bquat[1] = quat_hold[i][1];
bquat[2] = quat_hold[i][2];
bquat[3] = quat_hold[i][3];
}
memory->destroy(quat_hold);
quat_hold = nullptr;
}
/* ----------------------------------------------------------------------
modify values for AtomVec::pack_data() to pack
------------------------------------------------------------------------- */