md.bond¶
Overview
Constructs the bond potential. |
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FENE bond potential. |
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Harmonic bond potential. |
Details
Bond potentials.
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class
hoomd.md.bond.
Bond
¶ Bases:
hoomd.md.force.Force
Constructs the bond potential.
Note
Bond
is the base class for all bond potentials. Users should not instantiate this class directly.
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class
hoomd.md.bond.
FENE
¶ Bases:
hoomd.md.bond.Bond
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)
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class
hoomd.md.bond.
Harmonic
¶ Bases:
hoomd.md.bond.Bond
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.
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params
¶ The parameter of the harmonic bonds for each particle type. The dictionary has the following keys:
k
(float
, required) - potential constant (in units of energy/distance^2)r0
(float
, required) - rest length (in units distance)
- 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)
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