Description:
The DPD force consists of pair‐wise conservative, dissipative and random terms.
\begin{eqnarray*} \vec{F}_{ij}^{C}&=&\alpha\left(1-\frac{r_{ij}}{r_{cut}}\right)\vec{e}_{ij} \\ \vec{F}_{ij}^{D}&=&-\gamma\omega^{D}(r_{ij})(\vec{e}_{ij} \cdot \vec{v}_{ij} )\vec{e}_{ij} \\ \vec{F}_{ij}^{R}&=&T\sigma\omega^{R}(r_{ij})\xi_{ij}\vec{e}_{ij} \\ \end{eqnarray*}
- \gamma=\sigma^{2}/2k_{B}T
- \omega^{D}(r_{ij})=[\omega^{R}(r_{ij})]^2=(1-r_{ij}/r_{cut})^2
- \xi_{ij} - a random number with zero mean and unit variance
- T - temperature - optional: defaults to 1.0
- r_{cut} - r_cut (in distance units) - optional: defaults to 1.0
The following coefficients must be set per unique pair of particle types:
- \alpha - alpha (in energy units)
- \sigma - sigma (unitless)
.. py:class:: force.dpd(info, rcut=1.0)
Constructor of a DPD interaction object.
:param info: system information.
:param rcut: the cut-off radius of interactions.
.. py:function:: setParams(type_i, type_j, alpha, sigma)
specifies the DPD interaction parameters between two types of particles.
Example::
fn = pygamd.force.dpd(info=mst, rcut=1.0)
fn.setParams(type_i="A", type_j="A", alpha=25.0, sigma=3.0)
app.add(fn)
Description:
Integration algorithm.
\begin{eqnarray*} &v_i^0&\leftarrow v_i+ \lambda\frac{1}{m}(F_i^c \Delta t + F_i^d \Delta t + F_i^r \sqrt{\Delta t})\\ &v_i&\leftarrow v_i+ \frac{1}{2}\frac{1}{m}(F_i^c \Delta t + F_i^d \Delta t + F_i^r \sqrt{\Delta t})\\ &r_i&\leftarrow r_i+ v_i \Delta t\\ &&Calculate \quad F_i^c\{r_j\}, F_i^d\{r_j, v_j^0\}, F_i^r\{r_j\}\\ &v_i&\leftarrow v_i+ \frac{1}{2}\frac{1}{m}(F_i^c \Delta t + F_i^d \Delta t + F_i^r \sqrt{\Delta t}) \end{eqnarray*}
- \lambda - lambda (unitless) - optional: defaults to 0.65
.. py:class:: integration.gwvv(info, group)
Constructor of a GWVV NVT thermostat for a group of DPD particles.
:param info: system information.
:param group: a group of particles.
Example::
gw = pygamd.integration.gwvv(info=mst, group='all')
app.add(gw)