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Implement setter for particle director. #4053

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Dec 20, 2020
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12 changes: 8 additions & 4 deletions src/core/particle_data.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -733,13 +733,13 @@ void set_particle_rotational_inertia(int part, double *rinertia) {
#else
constexpr Utils::Vector3d ParticleProperties::rinertia;
#endif

#ifdef ROTATION
void set_particle_rotation(int part, int rot) {
mpi_update_particle_property<uint8_t, &ParticleProperties::rotation>(part,
rot);
}
#endif
#ifdef ROTATION

void rotate_particle(int part, const Utils::Vector3d &axis, double angle) {
mpi_send_update_message(part, UpdateOrientation{axis, angle});
}
Expand All @@ -759,7 +759,6 @@ void set_particle_dip(int part, double const *const dip) {
set_particle_dipm(part, dipm);
set_particle_quat(part, quat.data());
}

#endif

#ifdef VIRTUAL_SITES
Expand Down Expand Up @@ -844,6 +843,12 @@ void set_particle_quat(int part, double *quat) {
part, Utils::Quaternion<double>{quat[0], quat[1], quat[2], quat[3]});
}

void set_particle_director(int part, const Utils::Vector3d &director) {
Utils::Quaternion<double> quat =
convert_director_to_quaternion(director.normalized());
set_particle_quat(part, quat.data());
}

void set_particle_omega_lab(int part, const Utils::Vector3d &omega_lab) {
auto const &particle = get_particle_data(part);

Expand Down Expand Up @@ -1200,7 +1205,6 @@ void pointer_to_omega_body(Particle const *p, double const *&res) {
void pointer_to_quat(Particle const *p, double const *&res) {
res = p->r.quat.data();
}

#endif

void pointer_to_q(Particle const *p, double const *&res) { res = &(p->p.q); }
Expand Down
9 changes: 7 additions & 2 deletions src/core/particle_data.hpp
Original file line number Diff line number Diff line change
Expand Up @@ -194,6 +194,13 @@ void set_particle_mol_id(int part, int mid);
*/
void set_particle_quat(int part, double *quat);

/** Call only on the master node: set particle orientation using director.
* The particle director defines the z-axis in the body-fixed frame.
* @param part the particle.
* @param director its new director vector (will be normalized if necessary)
*/
void set_particle_director(int part, const Utils::Vector3d &director);

/** Call only on the master node: set particle angular velocity from lab frame.
* @param part the particle.
* @param omega_lab its new angular velocity.
Expand All @@ -211,7 +218,6 @@ void set_particle_omega_body(int part, const Utils::Vector3d &omega);
* @param torque_lab its new torque.
*/
void set_particle_torque_lab(int part, const Utils::Vector3d &torque_lab);

#endif

#ifdef DIPOLES
Expand Down Expand Up @@ -366,7 +372,6 @@ void pointer_to_omega_body(Particle const *p, double const *&res);
inline Utils::Vector3d get_torque_body(const Particle &p) { return p.f.torque; }

void pointer_to_quat(Particle const *p, double const *&res);

#endif

void pointer_to_q(Particle const *p, double const *&res);
Expand Down
1 change: 1 addition & 0 deletions src/python/espressomd/particle_data.pxd
Original file line number Diff line number Diff line change
Expand Up @@ -113,6 +113,7 @@ cdef extern from "particle_data.hpp":
IF ROTATION:
void set_particle_quat(int part, double quat[4])
void pointer_to_quat(const particle * p, const double * & res)
void set_particle_director(int part, Vector3d director)
void set_particle_omega_lab(int part, Vector3d omega)
void set_particle_omega_body(int part, Vector3d omega)
void set_particle_torque_lab(int part, Vector3d torque)
Expand Down
27 changes: 21 additions & 6 deletions src/python/espressomd/particle_data.pyx
Original file line number Diff line number Diff line change
Expand Up @@ -411,20 +411,35 @@ cdef class ParticleHandle:
pointer_to_quat(self.particle_data, x)
return array_locked([x[0], x[1], x[2], x[3]])

# Director (z-axis in body fixed frame)
property director:
"""
Director.
The particle director.

The ``director`` defines the the z-axis in the body-fixed frame.
If particle rotations happen, the director, i.e., the body-fixed
coordinate system co-rotates. Properties such as the angular
velocity :attr:`espressomd.particle_data.ParticleHandle.omega_body`
are evaluated in this body-fixed coordinate system.
When using particle dipoles, the dipole moment is co-aligned with
the particle director. Setting the director thus modifies the
dipole moment orientation (:attr:`espressomd.particle_data.ParticleHandle.dip`)
and vice verca.
See also :ref:`Rotational degrees of freedom and particle anisotropy`.

director : (3,) array_like of :obj:`float`

.. note::
Setting the director is not implemented.
This needs the feature ``ROTATION``.

"""

def __set__(self, _q):
raise AttributeError(
"Setting the director is not implemented in the C++-core of ESPResSo.")
def __set__(self, _d):
cdef Vector3d myd
check_type_or_throw_except(
_d, 3, float, "Particle director has to be 3 floats.")
for i in range(3):
myd[i] = _d[i]
set_particle_director(self._id, myd)

def __get__(self):
self.update_particle_data()
Expand Down
17 changes: 15 additions & 2 deletions testsuite/python/particle.py
Original file line number Diff line number Diff line change
Expand Up @@ -120,6 +120,21 @@ def func(self):
test_quat = generateTestForVectorProperty(
"quat", np.array([0.5, 0.5, 0.5, 0.5]))

def test_director(self):
"""
Test `director`. When set, it should get normalized.

"""
sample_vector = np.array([0.5, -0.4, 1.3])
sample_vector_normalized = sample_vector / \
np.linalg.norm(sample_vector)

setattr(self.system.part[self.pid], "director", sample_vector)
np.testing.assert_allclose(
np.array(getattr(self.system.part[self.pid], "director")),
sample_vector_normalized
)

if espressomd.has_features(["LANGEVIN_PER_PARTICLE"]):
if espressomd.has_features(["PARTICLE_ANISOTROPY"]):
test_gamma = generateTestForVectorProperty(
Expand Down Expand Up @@ -147,8 +162,6 @@ def test_gamma_rot_single(self):
else:
test_gamma_rot = generateTestForScalarProperty(
"gamma_rot", 14.23)
# test_director=generateTestForVectorProperty("director",
# np.array([0.5,0.4,0.3]))

if espressomd.has_features(["ELECTROSTATICS"]):
test_charge = generateTestForScalarProperty("q", -19.7)
Expand Down