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:

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

and the potential $U(r)$ is:

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

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: $F = -\frac{\partial U}{\partial r}$.

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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...

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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...

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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