md.bond¶

Overview

 Bond Constructs the bond potential. FENE FENE bond potential. Harmonic Harmonic bond potential.

Details

Bond potentials.

class hoomd.md.bond.Bond

Constructs the bond potential.

Note

Bond is the base class for all bond potentials. Users should not instantiate this class directly.

class hoomd.md.bond.FENE

FENE bond potential.

FENE specifies a FENE potential energy between the two particles in each defined bond.

$V(r) = - \frac{1}{2} k r_0^2 \ln \left( 1 - \left( \frac{r - \Delta}{r_0} \right)^2 \right) + V_{\mathrm{WCA}}(r)$

where $$\vec{r}$$ is the vector pointing from one particle to the other in the bond, $$\Delta = (d_i + d_j)/2 - 1$$, $$d_i$$ is the diameter of particle $$i$$, and

\begin{eqnarray*} V_{\mathrm{WCA}}(r) = & 4 \varepsilon \left[ \left( \frac{\sigma}{r - \Delta} \right)^{12} - \left( \frac{\sigma}{r - \Delta} \right)^{6} \right] + \varepsilon & r-\Delta < 2^{\frac{1}{6}}\sigma\\ = & 0 & r-\Delta \ge 2^{\frac{1}{6}}\sigma \end{eqnarray*}
params

The parameter of the FENE potential bonds. The dictionary has the following keys:

• k (float, required) - attractive force strength (in units of energy/distance^2)

• r0 (float, required) - size parameter (in units distance)

• epsilon (float, required) - repulsive force strength (in units of energy)

• sigma (float, required) - repulsive force interaction distance (in units of distance)

Type

TypeParameter[bond type, dict]

Examples:

bond_potential = bond.FENE()
bond_potential.params['molecule'] = dict(k=3.0, r0=2.38, epsilon=1.0, sigma=1.0)
bond_potential.params['backbone'] = dict(k=10.0, r0=1.0, epsilon=0.8, sigma=1.2)

class hoomd.md.bond.Harmonic

Harmonic bond potential.

Harmonic specifies a harmonic potential energy between the two particles in each defined bond.

$V(r) = \frac{1}{2} k \left( r - r_0 \right)^2$

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

params

The parameter of the harmonic bonds for each particle type. The dictionary has the following keys:

Type

TypeParameter[bond type, dict]

Examples:

harmonic = bond.Harmonic()
harmonic.params['polymer'] = dict(k=3.0, r0=2.38)
harmonic.params['backbone'] = dict(k=10.0, r0=1.0)