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Merge remote-tracking branch 'github/develop' into collected-small-fixes

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This commit is contained in:
Axel Kohlmeyer
2025-03-07 12:34:08 -05:00
parent 976b73a2f2 a61f67ceb7
commit 0a1e3fa26a
3 changed files with 156 additions and 43 deletions
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14
doc/src/fix_move.rst
View File

@ -35,11 +35,12 @@ Syntax
v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL
* zero or more keyword/value pairs may be appended
* keyword = *units*
* keyword = *units* or *update*
.. parsed-literal::
*units* value = *box* or *lattice*
*update* value = *dipole*
Examples
""""""""
@ -49,7 +50,7 @@ Examples
fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL
fix 3 boundary move transrot 0.1 0.1 0.0 0.0 0.0 0.0 0.0 0.0 1.0 5.0 units box
fix 3 boundary move transrot 0.1 0.1 0.0 0.0 0.0 0.0 0.0 0.0 1.0 5.0 units box update dipole
Description
"""""""""""
@ -217,6 +218,15 @@ been previously used to define the lattice spacing. Each of these 3
quantities may be dependent on the x,y,z dimension, since the lattice
spacings can be different in x,y,z.
.. versionadded:: TBD
If the *update dipole* keyword/value pair is used together with the
*rotate* or *transrot* style, then the orientation of the dipole moment
of each particle is also updated appropriately to correspond with the rotation.
This option should be used for models where a dipole moment is assigned to
finite-size particles, e.g. spheroids via use of the :doc:`atom_style hybrid
sphere dipole <atom_style>` command.
----------
Restart, fix_modify, output, run start/stop, minimize info

182
src/fix_move.cpp
View File

@ -49,9 +49,9 @@ 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");
if (narg < 4) utils::missing_cmd_args(FLERR, "fix move", error);
restart_global = 1;
restart_peratom = 1;
@ -69,7 +69,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
int iarg = 0;
if (strcmp(arg[3], "linear") == 0) {
if (narg < 7) error->all(FLERR, "Illegal fix move command");
if (narg < 7) utils::missing_cmd_args(FLERR, "fix move linear", error);
iarg = 7;
mstyle = LINEAR;
if (strcmp(arg[4], "NULL") == 0)
@ -92,7 +92,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
}
} else if (strcmp(arg[3], "wiggle") == 0) {
if (narg < 8) error->all(FLERR, "Illegal fix move command");
if (narg < 8) utils::missing_cmd_args(FLERR, "fix move wiggle", error);
iarg = 8;
mstyle = WIGGLE;
if (strcmp(arg[4], "NULL") == 0)
@ -114,10 +114,10 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
az = utils::numeric(FLERR, arg[6], false, lmp);
}
period = utils::numeric(FLERR, arg[7], false, lmp);
if (period <= 0.0) error->all(FLERR, "Illegal fix move command");
if (period <= 0.0) error->all(FLERR, 7, "Illegal fix move wiggle period {}", period);
} else if (strcmp(arg[3], "rotate") == 0) {
if (narg < 11) error->all(FLERR, "Illegal fix move command");
if (narg < 11) utils::missing_cmd_args(FLERR, "fix move rotate", error);
iarg = 11;
mstyle = ROTATE;
point[0] = utils::numeric(FLERR, arg[4], false, lmp);
@ -127,10 +127,10 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
axis[1] = utils::numeric(FLERR, arg[8], false, lmp);
axis[2] = utils::numeric(FLERR, arg[9], false, lmp);
period = utils::numeric(FLERR, arg[10], false, lmp);
if (period <= 0.0) error->all(FLERR, "Illegal fix move command");
if (period <= 0.0) error->all(FLERR, 10, "Illegal fix move rotate period {}", period);
} else if (strcmp(arg[3], "transrot") == 0) {
if (narg < 11) error->all(FLERR, "Illegal fix move command");
if (narg < 11) utils::missing_cmd_args(FLERR, "fix move transrot", error);
iarg = 14;
mstyle = TRANSROT;
vxflag = vyflag = vzflag = 1;
@ -144,10 +144,10 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
axis[1] = utils::numeric(FLERR, arg[11], false, lmp);
axis[2] = utils::numeric(FLERR, arg[12], false, lmp);
period = utils::numeric(FLERR, arg[13], false, lmp);
if (period <= 0.0) error->all(FLERR, "Illegal fix move command");
if (period <= 0.0) error->all(FLERR, 13, "Illegal fix move rotate period {}", period);
} else if (strcmp(arg[3], "variable") == 0) {
if (narg < 10) error->all(FLERR, "Illegal fix move command");
if (narg < 10) utils::missing_cmd_args(FLERR, "fix move variable", error);
iarg = 10;
mstyle = VARIABLE;
if (strcmp(arg[4], "NULL") == 0)
@ -155,70 +155,83 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
else if (utils::strmatch(arg[4], "^v_")) {
xvarstr = utils::strdup(arg[4] + 2);
} else
error->all(FLERR, "Illegal fix move command");
error->all(FLERR, 4, "Argument must be either NULL or variable reference");
if (strcmp(arg[5], "NULL") == 0)
yvarstr = nullptr;
else if (utils::strmatch(arg[5], "^v_")) {
yvarstr = utils::strdup(arg[5] + 2);
} else
error->all(FLERR, "Illegal fix move command");
error->all(FLERR, 5, "Argument must be either NULL or variable reference");
if (strcmp(arg[6], "NULL") == 0)
zvarstr = nullptr;
else if (utils::strmatch(arg[6], "^v_")) {
zvarstr = utils::strdup(arg[6] + 2);
} else
error->all(FLERR, "Illegal fix move command");
error->all(FLERR, 6, "Argument must be either NULL or variable reference");
if (strcmp(arg[7], "NULL") == 0)
vxvarstr = nullptr;
else if (utils::strmatch(arg[7], "^v_")) {
vxvarstr = utils::strdup(arg[7] + 2);
} else
error->all(FLERR, "Illegal fix move command");
error->all(FLERR, 7, "Argument must be either NULL or variable reference");
if (strcmp(arg[8], "NULL") == 0)
vyvarstr = nullptr;
else if (utils::strmatch(arg[8], "^v_")) {
vyvarstr = utils::strdup(arg[8] + 2);
} else
error->all(FLERR, "Illegal fix move command");
error->all(FLERR, 8, "Argument must be either NULL or variable reference");
if (strcmp(arg[9], "NULL") == 0)
vzvarstr = nullptr;
else if (utils::strmatch(arg[9], "^v_")) {
vzvarstr = utils::strdup(arg[9] + 2);
} else
error->all(FLERR, "Illegal fix move command");
error->all(FLERR, 9, "Argument must be either NULL or variable reference");
} else
error->all(FLERR, "Illegal fix move command");
} else {
error->all(FLERR, 3, "Unknown fix move mode {}", arg[3]);
}
// optional args
int scaleflag = 1;
update_mu_flag = 0;
while (iarg < narg) {
if (strcmp(arg[iarg], "units") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal fix move command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix move units", error);
if (strcmp(arg[iarg + 1], "box") == 0)
scaleflag = 0;
else if (strcmp(arg[iarg + 1], "lattice") == 0)
scaleflag = 1;
else
error->all(FLERR, "Illegal fix move command");
error->all(FLERR, iarg + 1, "Unknown fix move units setting {}", arg[iarg + 1]);
iarg += 2;
} else if (strcmp(arg[iarg], "update") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix move update", error);
if (strcmp(arg[iarg + 1], "dipole") == 0) {
if ((mstyle != ROTATE) && (mstyle != TRANSROT))
error->all(FLERR, 3, "Fix move keyword update dipole requires style rotate or transrot");
if (!atom->mu_flag)
error->all(FLERR, iarg + 1, "Fix move keyword update dipole requires atom attribute mu");
update_mu_flag = 1;
} else
error->all(FLERR, iarg + 1, "Unkown fix move update argument {}", arg[iarg + 1]);
iarg += 2;
} else
error->all(FLERR, "Illegal fix move command");
error->all(FLERR, iarg, "Unknown fix move keyword {}", arg[iarg]);
}
// error checks and warnings
if (domain->dimension == 2) {
if (((mstyle == LINEAR) || (mstyle == TRANSROT)) && vzflag && (vz != 0.0))
error->all(FLERR, "Fix move cannot set linear z motion for 2d problem");
error->all(FLERR, 3, "Fix move cannot set linear z motion for 2d problem");
if (mstyle == WIGGLE && azflag && az != 0.0)
error->all(FLERR, "Fix move cannot set wiggle z motion for 2d problem");
error->all(FLERR, 3, "Fix move cannot set wiggle z motion for 2d problem");
if (((mstyle == ROTATE) || (mstyle == TRANSROT)) && (axis[0] != 0.0 || axis[1] != 0.0))
error->all(FLERR, "Fix move cannot rotate around non z-axis for 2d problem");
error->all(FLERR, 3, "Fix move cannot rotate around non z-axis for 2d problem");
if (mstyle == VARIABLE && (zvarstr || vzvarstr))
error->all(FLERR, "Fix move cannot define z or vz variable for 2d problem");
error->all(FLERR, 3, "Fix move cannot define z or vz variable for 2d problem");
}
// setup scaling and apply scaling factors to velocity & amplitude
@ -283,7 +296,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
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 || update_mu_flag) extra_flag = 1;
// perform initial allocation of atom-based array
// register with Atom class
@ -304,6 +317,7 @@ 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 +376,18 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
}
}
if (update_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 +414,7 @@ FixMove::~FixMove()
memory->destroy(xoriginal);
memory->destroy(toriginal);
memory->destroy(qoriginal);
memory->destroy(muoriginal);
memory->destroy(displace);
memory->destroy(velocity);
@ -426,63 +453,83 @@ void FixMove::init()
if (mstyle == VARIABLE) {
if (xvarstr) {
xvar = input->variable->find(xvarstr);
if (xvar < 0) error->all(FLERR, "Variable name for fix move does not exist");
if (xvar < 0)
error->all(FLERR, Error::NOLASTLINE, "Variable name {} for fix move does not exist",
xvarstr);
if (input->variable->equalstyle(xvar))
xvarstyle = EQUAL;
else if (input->variable->atomstyle(xvar))
xvarstyle = ATOM;
else
error->all(FLERR, "Variable for fix move is invalid style");
error->all(FLERR, Error::NOLASTLINE, "Variable name {} for fix move is invalid style",
xvarstr);
}
if (yvarstr) {
yvar = input->variable->find(yvarstr);
if (yvar < 0) error->all(FLERR, "Variable name for fix move does not exist");
if (yvar < 0)
error->all(FLERR, Error::NOLASTLINE, "Variable name {} for fix move does not exist",
yvarstr);
if (input->variable->equalstyle(yvar))
yvarstyle = EQUAL;
else if (input->variable->atomstyle(yvar))
yvarstyle = ATOM;
else
error->all(FLERR, "Variable for fix move is invalid style");
error->all(FLERR, Error::NOLASTLINE, "Variable name {} for fix move is invalid style",
yvarstr);
}
if (zvarstr) {
zvar = input->variable->find(zvarstr);
if (zvar < 0) error->all(FLERR, "Variable name for fix move does not exist");
if (zvar < 0)
error->all(FLERR, Error::NOLASTLINE, "Variable name {} for fix move does not exist",
zvarstr);
if (input->variable->equalstyle(zvar))
zvarstyle = EQUAL;
else if (input->variable->atomstyle(zvar))
zvarstyle = ATOM;
else
error->all(FLERR, "Variable for fix move is invalid style");
error->all(FLERR, Error::NOLASTLINE, "Variable name {} for fix move is invalid style",
zvarstr);
}
if (vxvarstr) {
vxvar = input->variable->find(vxvarstr);
if (vxvar < 0) error->all(FLERR, "Variable name for fix move does not exist");
if (vxvar < 0)
error->all(FLERR, Error::NOLASTLINE, "Variable name {} for fix move does not exist",
vxvarstr);
if (input->variable->equalstyle(vxvar))
vxvarstyle = EQUAL;
else if (input->variable->atomstyle(vxvar))
vxvarstyle = ATOM;
else
error->all(FLERR, "Variable for fix move is invalid style");
error->all(FLERR, Error::NOLASTLINE, "Variable name {} for fix move is invalid style",
vxvarstr);
}
if (vyvarstr) {
vyvar = input->variable->find(vyvarstr);
if (vyvar < 0) error->all(FLERR, "Variable name for fix move does not exist");
if (vyvar < 0)
error->all(FLERR, Error::NOLASTLINE, "Variable name {} for fix move does not exist",
vyvarstr);
if (input->variable->equalstyle(vyvar))
vyvarstyle = EQUAL;
else if (input->variable->atomstyle(vyvar))
vyvarstyle = ATOM;
else
error->all(FLERR, "Variable for fix move is invalid style");
error->all(FLERR, Error::NOLASTLINE, "Variable name {} for fix move is invalid style",
vyvarstr);
}
if (vzvarstr) {
vzvar = input->variable->find(vzvarstr);
if (vzvar < 0) error->all(FLERR, "Variable name for fix move does not exist");
if (vzvar < 0)
error->all(FLERR, Error::NOLASTLINE, "Variable name {} for fix move does not exist",
vzvarstr);
if (input->variable->equalstyle(vzvar))
vzvarstyle = EQUAL;
else if (input->variable->atomstyle(vzvar))
vzvarstyle = ATOM;
else
error->all(FLERR, "Variable for fix move is invalid style");
error->all(FLERR, Error::NOLASTLINE, "Variable name {} for fix move is invalid style",
vzvarstr);
}
if (xvarstr && xvarstyle == ATOM) displaceflag = 1;
@ -533,6 +580,7 @@ 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 +724,8 @@ void FixMove::initial_integrate(int /*vflag*/)
qrotate[2] = runit[1] * qsine;
qrotate[3] = runit[2] * qsine;
double rotmat[3][3], g[3]; // for dipole rotation
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
xold[0] = x[i][0];
@ -775,6 +825,15 @@ void FixMove::initial_integrate(int /*vflag*/)
} else if (quat_atom_flag) {
MathExtra::quatquat(qrotate, qoriginal[i], quat_atom[i]);
}
if (update_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 +868,8 @@ void FixMove::initial_integrate(int /*vflag*/)
qrotate[2] = runit[1] * qsine;
qrotate[3] = runit[2] * qsine;
double rotmat[3][3], g[3]; // for dipole rotation
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
xold[0] = x[i][0];
@ -908,6 +969,15 @@ void FixMove::initial_integrate(int /*vflag*/)
} else if (quat_atom_flag) {
MathExtra::quatquat(qrotate, qoriginal[i], quat_atom[i]);
}
if (update_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 +1318,7 @@ 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 (update_mu_flag) memory->grow(muoriginal, nmax, 4, "move:muoriginal");
array_atom = xoriginal;
}
@ -1267,6 +1338,12 @@ void FixMove::copy_arrays(int i, int j, int /*delflag*/)
qoriginal[j][2] = qoriginal[i][2];
qoriginal[j][3] = qoriginal[i][3];
}
if (update_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];
}
}
/* ----------------------------------------------------------------------
@ -1302,7 +1379,8 @@ void FixMove::set_arrays(int i)
// backup particle to time_origin
if (mstyle == VARIABLE) error->all(FLERR, "Cannot add atoms to fix move variable");
if (mstyle == VARIABLE)
error->all(FLERR, Error::NOLASTLINE, "Cannot add atoms with fix move style variable");
domain->unmap(x[i], image[i], xoriginal[i]);
double delta = (update->ntimestep - time_origin) * update->dt;
@ -1461,6 +1539,12 @@ int FixMove::pack_exchange(int i, double *buf)
buf[n++] = qoriginal[i][2];
buf[n++] = qoriginal[i][3];
}
if (update_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 +1565,12 @@ int FixMove::unpack_exchange(int nlocal, double *buf)
qoriginal[nlocal][2] = buf[n++];
qoriginal[nlocal][3] = buf[n++];
}
if (update_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 +1591,12 @@ int FixMove::pack_restart(int i, double *buf)
buf[n++] = qoriginal[i][2];
buf[n++] = qoriginal[i][3];
}
if (update_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 +1627,12 @@ void FixMove::unpack_restart(int nlocal, int nth)
qoriginal[nlocal][2] = extra[nlocal][m++];
qoriginal[nlocal][3] = extra[nlocal][m++];
}
if (update_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++];
}
}
/* ----------------------------------------------------------------------
@ -1555,5 +1657,5 @@ int FixMove::size_restart(int /*nlocal*/)
void FixMove::reset_dt()
{
error->all(FLERR, "Resetting timestep size is not allowed with fix move");
error->all(FLERR, Error::NOLASTLINE, "Resetting timestep size is not allowed with fix move");
}

3
src/fix_move.h
View File

@ -62,13 +62,14 @@ class FixMove : public Fix {
int xvarstyle, yvarstyle, zvarstyle, vxvarstyle, vyvarstyle, vzvarstyle;
int extra_flag, omega_flag, angmom_flag;
int radius_flag, ellipsoid_flag, line_flag, tri_flag, body_flag, quat_atom_flag;
int theta_flag, quat_flag;
int theta_flag, quat_flag, update_mu_flag;
int nlevels_respa, nrestart;
int time_origin;
double **xoriginal; // original coords of atoms
double *toriginal; // original theta of atoms
double **qoriginal; // original quat of atoms
double **muoriginal; // original mu of atoms
int displaceflag, velocityflag;
int maxatom;
double **displace, **velocity;