hoomd.hpmc.external.field#
Overview
Base class external field. |
|
Restrain particle positions and orientations with harmonic springs. |
Details
Apply external fields to HPMC simulations.
- class hoomd.hpmc.external.field.ExternalField#
Bases:
Base class external field.
Provides common methods for all external field subclasses.
Note
Users should use the subclasses and not instantiate
ExternalField
directly.
- class hoomd.hpmc.external.field.Harmonic(reference_positions, reference_orientations, k_translational, k_rotational, symmetries)#
Bases:
ExternalField
Restrain particle positions and orientations with harmonic springs.
- Parameters:
reference_positions ((N_particles, 3)
numpy.ndarray
offloat
) – the reference positions to which particles are restrained \([\mathrm{length}]\).reference_orientations ((N_particles, 4)
numpy.ndarray
offloat
) – the reference orientations to which particles are restrained \([\mathrm{dimensionless}]\).k_translational (hoomd.variant.variant_like) – translational spring constant \([\mathrm{energy} \cdot \mathrm{length}^{-2}]\).
k_rotational (hoomd.variant.variant_like) – rotational spring constant \([\mathrm{energy}]\).
symmetries ((N_symmetries, 4)
numpy.ndarray
offloat
) – the orientations that are equivalent through symmetry, i.e., the rotation quaternions that leave the particles unchanged. At a minimum, the identity quaternion ([1, 0, 0, 0]
) must be included here \([\mathrm{dimensionless}]\).
Harmonic
computes harmonic spring energies between the particle positions/orientations and given reference positions/orientations:\[\begin{split}U_{\mathrm{external},i} & = U_{\mathrm{translational},i} + U_{\mathrm{rotational},i} \\ U_{\mathrm{translational},i} & = \frac{1}{2} k_{translational} \cdot (\vec{r}_i-\vec{r}_{0,i})^2 \\ U_{\mathrm{rotational},i} & = \frac{1}{2} k_{rotational} \cdot \min_j \left[ (\mathbf{q}_i-\mathbf{q}_{0,i} \cdot \mathbf{q}_{\mathrm{symmetry},j})^2 \right]\end{split}\]where \(k_{translational}\) and \(k_{rotational}\) correspond to the parameters
k_translational
andk_rotational
, respectively, \(\vec{r}_i\) and \(\mathbf{q}_i\) are the position and orientation of particle \(i\), the \(0\) subscripts denote the given reference quantities, and \(\mathbf{q}_{\mathrm{symmetry}}\) is the given set of symmetric orientations from thesymmetries
parameter.Note
Harmonic
does not support execution on GPUs.- k_translational#
The translational spring constant \([\mathrm{energy} \cdot \mathrm{length}^{-2}]\).
- Type:
- k_rotational#
The rotational spring constant \([\mathrm{energy}]\).
- Type:
- reference_positions#
The reference positions to which particles are restrained \([\mathrm{length}]\).
- Type:
(N_particles, 3)
numpy.ndarray
offloat
- reference_orientations#
The reference orientations to which particles are restrained \([\mathrm{dimensionless}]\).
- Type:
(N_particles, 4)
numpy.ndarray
offloat
- symmetries#
The orientations that are equivalent through symmetry, i.e., the rotation quaternions that leave the particles unchanged \([\mathrm{dimensionless}]\).
- Type:
(N_symmetries, 4)
numpy.ndarray
offloat
- property energy#
The total energy of the harmonic field \([\mathrm{energy}]\).
\[\sum_{i=0}^\mathrm{N_particles-1} U_{\mathrm{external},i}\](
Loggable
: category=”scalar”)- Type: