Table

class hoomd.md.bond.Table(width)

Bases: Bond

Tabulated bond force.

Parameters:

width (int) – Number of points in the table.

Table computes computes forces, virials, and energies on all bonds in the simulation given the user defined tables \(U\) and \(F\).

Note

For potentials that diverge near r=0, to set r_min to a non-zero value.

The force \(\vec{F}\) is:

\[\begin{split}\vec{F}(\vec{r}) = \begin{cases} 0 & r < r_{\mathrm{min}} \\ F_\mathrm{table}(r)\hat{r} & r_{\mathrm{min}} \le r < r_{\mathrm{max}} \\ 0 & r \ge r_{\mathrm{max}} \\ \end{cases}\end{split}\]

and the potential \(U(r)\) is:

\[\begin{split}U(r) = \begin{cases} 0 & r < r_{\mathrm{min}} \\ U_\mathrm{table}(r) & r_{\mathrm{min}} \le r < r_{\mathrm{max}} \\ 0 & r \ge r_{\mathrm{max}} \\ \end{cases}\end{split}\]

where \(\vec{r}\) is the vector pointing from one particle to the other in the bond.

Warning

Bonds that stretch to a length \(r \ge r_{\mathrm{max}}\) result in an error.

Provide \(F_\mathrm{table}(r)\) and \(U_\mathrm{table}(r)\) on evenly spaced grid points points between \(r_{\mathrm{min}}\) and \(r_{\mathrm{max}}\). Table linearly interpolates values when \(r\) lies between grid points and between the last grid point and \(r=r_{\mathrm{max}}\). The force must be commensurate with the potential: \(F = -\frac{\partial U}{\partial r}\).

Members inherited from AutotunedObject:

property kernel_parameters

Kernel parameters. Read more...

property is_tuning_complete

Check if kernel parameter tuning is complete. Read more...

tune_kernel_parameters()

Start tuning kernel parameters. Read more...

Members inherited from Force:

additional_energy

Additional energy term. Read more...

additional_virial

Additional virial tensor term \(W_\mathrm{additional}\). Read more...

cpu_local_force_arrays

Local force arrays on the CPU. Read more...

energies

Energy contribution \(U_i\) from each particle. Read more...

energy

The potential energy \(U\) of the system from this force. Read more...

forces

The force \(\vec{F}_i\) applied to each particle. Read more...

gpu_local_force_arrays

Local force arrays on the GPU. Read more...

torques

The torque \(\vec{\tau}_i\) applied to each particle. Read more...

virials

Virial tensor contribution \(W_i\) from each particle. Read more...

Members defined in Table:

params

The potential parameters. The dictionary has the following keys:

  • r_min (float, required) - the minimum distance to apply the tabulated potential, corresponding to the first element of the energy and force arrays \([\mathrm{length}]\).

  • r_max (float, required) - the minimum distance to apply the tabulated potential, corresponding to the first element of the energy and force arrays \([\mathrm{length}]\).

  • U ((width,) numpy.ndarray of float, required) - the tabulated energy values \([\mathrm{energy}]\). Must have a size equal to width.

  • F ((width,) numpy.ndarray of float, required) - the tabulated force values \([\mathrm{force}]\). Must have a size equal to width.

Type:

TypeParameter [bond type, dict]

width

Number of points in the table.

Type:

int