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

Update fix_move.cpp

Browse Source
This commit is contained in:
Gabriel Alkuino
2025-03-04 15:27:16 -05:00
committed by GitHub
parent ac2214e5f2
commit 61daafca62
1 changed files with 71 additions and 2 deletions
Download Patch File Download Diff File Expand all files Collapse all files

73
src/fix_move.cpp
View File

@ -49,7 +49,7 @@ static constexpr double INERTIA = 0.2; // moment of inertia prefactor for ell
FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), xvarstr(nullptr), yvarstr(nullptr), zvarstr(nullptr), vxvarstr(nullptr),
vyvarstr(nullptr), vzvarstr(nullptr), xoriginal(nullptr), toriginal(nullptr),
qoriginal(nullptr), displace(nullptr), velocity(nullptr)
qoriginal(nullptr), muoriginal(nullptr), displace(nullptr), velocity(nullptr)
{
if (narg < 4) error->all(FLERR, "Illegal fix move command");
@ -277,13 +277,14 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
tri_flag = atom->tri_flag;
body_flag = atom->body_flag;
quat_atom_flag = atom->quat_flag;
mu_flag = atom->mu_flag;
theta_flag = quat_flag = 0;
if (line_flag) theta_flag = 1;
if (ellipsoid_flag || tri_flag || body_flag || quat_atom_flag) quat_flag = 1;
extra_flag = 0;
if (omega_flag || angmom_flag || theta_flag || quat_flag) extra_flag = 1;
if (omega_flag || angmom_flag || theta_flag || quat_flag || mu_flag) extra_flag = 1;
// perform initial allocation of atom-based array
// register with Atom class
@ -304,6 +305,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
// xoriginal = initial unwrapped positions of atoms
// toriginal = initial theta of lines
// qoriginal = initial quat of extended particles
// muoriginal = initial dipole moment of extended particles
double **x = atom->x;
imageint *image = atom->image;
@ -362,6 +364,18 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
}
}
if (mu_flag) {
double **mu = atom->mu;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
muoriginal[i][0] = mu[i][0];
muoriginal[i][1] = mu[i][1];
muoriginal[i][2] = mu[i][2];
muoriginal[i][3] = mu[i][3];
}
}
}
// nrestart = size of per-atom restart data
// nrestart = 1 + xorig + torig + qorig
@ -388,6 +402,7 @@ FixMove::~FixMove()
memory->destroy(xoriginal);
memory->destroy(toriginal);
memory->destroy(qoriginal);
memory->destroy(muoriginal);
memory->destroy(displace);
memory->destroy(velocity);
@ -533,6 +548,7 @@ void FixMove::initial_integrate(int /*vflag*/)
double *rmass = atom->rmass;
double *mass = atom->mass;
double **quat_atom = atom->quat;
double **mu = atom->mu;
int *type = atom->type;
int *ellipsoid = atom->ellipsoid;
int *line = atom->line;
@ -676,6 +692,8 @@ void FixMove::initial_integrate(int /*vflag*/)
qrotate[2] = runit[1] * qsine;
qrotate[3] = runit[2] * qsine;
double rotmat[3][3], g[3]; // for dipole rotations
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
xold[0] = x[i][0];
@ -775,6 +793,15 @@ void FixMove::initial_integrate(int /*vflag*/)
} else if (quat_atom_flag) {
MathExtra::quatquat(qrotate, qoriginal[i], quat_atom[i]);
}
if (mu_flag && mu[i][3] > 0.0) {
MathExtra::quat_to_mat(qrotate, rotmat);
MathExtra::matvec(rotmat, muoriginal[i], g);
mu[i][0] = g[0];
mu[i][1] = g[1];
mu[i][2] = g[2];
// mu[i][3] = sqrt(g[0] * g[0] + g[1] * g[1] + g[2] * g[2]);
}
}
domain->remap_near(x[i], xold);
@ -809,6 +836,8 @@ void FixMove::initial_integrate(int /*vflag*/)
qrotate[2] = runit[1] * qsine;
qrotate[3] = runit[2] * qsine;
double rotmat[3][3], g[3]; // for dipole rotations
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
xold[0] = x[i][0];
@ -908,6 +937,15 @@ void FixMove::initial_integrate(int /*vflag*/)
} else if (quat_atom_flag) {
MathExtra::quatquat(qrotate, qoriginal[i], quat_atom[i]);
}
if (mu_flag && mu[i][3] > 0.0) {
MathExtra::quat_to_mat(qrotate, rotmat);
MathExtra::matvec(rotmat, muoriginal[i], g);
mu[i][0] = g[0];
mu[i][1] = g[1];
mu[i][2] = g[2];
// mu[i][3] = sqrt(g[0] * g[0] + g[1] * g[1] + g[2] * g[2]);
}
}
v[i][0] += vx;
@ -1248,6 +1286,7 @@ void FixMove::grow_arrays(int nmax)
memory->grow(xoriginal, nmax, 3, "move:xoriginal");
if (theta_flag) memory->grow(toriginal, nmax, "move:toriginal");
if (quat_flag) memory->grow(qoriginal, nmax, 4, "move:qoriginal");
if (mu_flag) memory->grow(muoriginal, nmax, 4, "move:muoriginal");
array_atom = xoriginal;
}
@ -1267,6 +1306,12 @@ void FixMove::copy_arrays(int i, int j, int /*delflag*/)
qoriginal[j][2] = qoriginal[i][2];
qoriginal[j][3] = qoriginal[i][3];
}
if (mu_flag) {
muoriginal[j][0] = muoriginal[i][0];
muoriginal[j][1] = muoriginal[i][1];
muoriginal[j][2] = muoriginal[i][2];
muoriginal[j][3] = muoriginal[i][3];
}
}
/* ----------------------------------------------------------------------
@ -1461,6 +1506,12 @@ int FixMove::pack_exchange(int i, double *buf)
buf[n++] = qoriginal[i][2];
buf[n++] = qoriginal[i][3];
}
if (mu_flag) {
buf[n++] = muoriginal[i][0];
buf[n++] = muoriginal[i][1];
buf[n++] = muoriginal[i][2];
buf[n++] = muoriginal[i][3];
}
return n;
}
@ -1481,6 +1532,12 @@ int FixMove::unpack_exchange(int nlocal, double *buf)
qoriginal[nlocal][2] = buf[n++];
qoriginal[nlocal][3] = buf[n++];
}
if (mu_flag) {
muoriginal[nlocal][0] = buf[n++];
muoriginal[nlocal][1] = buf[n++];
muoriginal[nlocal][2] = buf[n++];
muoriginal[nlocal][3] = buf[n++];
}
return n;
}
@ -1501,6 +1558,12 @@ int FixMove::pack_restart(int i, double *buf)
buf[n++] = qoriginal[i][2];
buf[n++] = qoriginal[i][3];
}
if (mu_flag) {
buf[n++] = muoriginal[i][0];
buf[n++] = muoriginal[i][1];
buf[n++] = muoriginal[i][2];
buf[n++] = muoriginal[i][3];
}
// pack buf[0] this way because other fixes unpack it
buf[0] = n;
return n;
@ -1531,6 +1594,12 @@ void FixMove::unpack_restart(int nlocal, int nth)
qoriginal[nlocal][2] = extra[nlocal][m++];
qoriginal[nlocal][3] = extra[nlocal][m++];
}
if (mu_flag) {
muoriginal[nlocal][0] = extra[nlocal][m++];
muoriginal[nlocal][1] = extra[nlocal][m++];
muoriginal[nlocal][2] = extra[nlocal][m++];
muoriginal[nlocal][3] = extra[nlocal][m++];
}
}
/* ----------------------------------------------------------------------