GayBerne¶
- class hoomd.md.pair.aniso.GayBerne(nlist, default_r_cut=None, mode='none')¶
Bases:
AnisotropicPairGay-Berne anisotropic pair force.
- Parameters:
nlist (hoomd.md.nlist.NeighborList) – Neighbor list
default_r_cut (float) – Default cutoff radius \([\mathrm{length}]\).
mode (str) – energy shifting/smoothing mode.
GayBernecomputes the Gay-Berne anisotropic pair force on every particle in the simulation state. This version of the Gay-Berne force supports identical pairs of uniaxial ellipsoids, with orientation-independent energy-well depth. The potential comes from the following paper Allen et. al. 2006.\[\begin{split}U(\vec r, \vec e_i, \vec e_j) = \begin{cases} 4 \varepsilon \left[ \zeta^{-12} - \zeta^{-6} \right] & \zeta < \zeta_{\mathrm{cut}} \\ 0 & \zeta \ge \zeta_{\mathrm{cut}} \\ \end{cases}\end{split}\]where
\[ \begin{align}\begin{aligned}\zeta &= \left(\frac{r-\sigma+\sigma_{\mathrm{min}}} {\sigma_{\mathrm{min}}}\right),\\\sigma^{-2} &= \frac{1}{2} \hat{\vec{r}} \cdot \vec{H^{-1}} \cdot \hat{\vec{r}},\\\vec{H} &= 2 \ell_\perp^2 \vec{1} + (\ell_\parallel^2 - \ell_\perp^2) (\vec{e_i} \otimes \vec{e_i} + \vec{e_j} \otimes \vec{e_j}),\end{aligned}\end{align} \]and \(\sigma_{\mathrm{min}} = 2 \min(\ell_\perp, \ell_\parallel)\). The parallel direction is aligned with z axis in the particle’s reference frame.
The cut-off parameter \(r_{\mathrm{cut}}\) is defined for two particles oriented parallel along the long axis, i.e. \(\zeta_{\mathrm{cut}} = \left(\frac{r-\sigma_{\mathrm{max}} + \sigma_{\mathrm{min}}}{\sigma_{\mathrm{min}}}\right)\) where \(\sigma_{\mathrm{max}} = 2 \max(\ell_\perp, \ell_\parallel)\) .
The quantities \(\ell_\parallel\) and \(\ell_\perp\) denote the semi-axis lengths parallel and perpendicular to particle orientation.
Example:
nl = nlist.Cell() gay_berne = md.pair.aniso.GayBerne(nlist=nl, default_r_cut=2.5) gay_berne.params[('A', 'A')] = dict(epsilon=1.0, lperp=0.45, lpar=0.5) gay_berne.r_cut[('A', 'B')] = 2 ** (1.0 / 6.0)
Members inherited from
AutotunedObject:- property kernel_parameters¶
Kernel parameters.
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- property is_tuning_complete¶
Check if kernel parameter tuning is complete.
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- tune_kernel_parameters()¶
Start tuning kernel parameters.
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Members inherited from
Force:- additional_energy¶
Additional energy term.
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- additional_virial¶
Additional virial tensor term \(W_\mathrm{additional}\).
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- cpu_local_force_arrays¶
Local force arrays on the CPU.
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- energies¶
Energy contribution \(U_i\) from each particle.
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- energy¶
The potential energy \(U\) of the system from this force.
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- forces¶
The force \(\vec{F}_i\) applied to each particle.
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- gpu_local_force_arrays¶
Local force arrays on the GPU.
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- torques¶
The torque \(\vec{\tau}_i\) applied to each particle.
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- virials¶
Virial tensor contribution \(W_i\) from each particle.
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Members inherited from
Pair:- nlist¶
Neighbor list used to compute the pair force.
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- mode¶
Energy smoothing/cutoff mode.
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- r_cut¶
Cuttoff radius beyond which the energy and force are 0.
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- r_on¶
Radius at which the XPLOR smoothing function starts.
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- compute_energy()¶
Compute the energy between two sets of particles.
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Members defined in
GayBerne:- params¶
The Gay-Berne potential parameters. The dictionary has the following keys:
epsilon(float, required) - \(\varepsilon\) \([\mathrm{energy}]\)lperp(float, required) - \(\ell_\perp\) \([\mathrm{length}]\)lpar(float, required) - \(\ell_\parallel\) \([\mathrm{length}]\)
Type:
TypeParameter[tuple[particle_type,particle_type],dict]