Usage

With a prepared script, you could run pygamd MD engine for obtaining trajectory.

Examples:

python3 yourscript.py --gpu=0 >a.log&

Where you could specify the GPU id (default value is 0) with the --gpu= option and output the screen information into a.log file.

Here is an example of script for DPD simulation.

Firstly, importing the pygamd module installed as a package of python3 and reading system information by snapshot.read from a mst file

Examples:

import pygamd
mst = pygamd.snapshot.read("AB.mst")

After that, we need to build up an application by application.dynamics which will call defined and added objects.

Examples:

app = pygamd.application.dynamics(info=mst, dt=0.04)

Further, we should define objects by the classes of pygamd and pass them to the application, such as the following example: DPD force force.dpd , NVT thermostat with GWVV algorithm integration.gwvv, and th dump of system collective information dump.data.

Examples:

fn = pygamd.force.dpd(info=mst, rcut=1.0)
fn.setParams(type_i="A", type_j="A", alpha=25.0, sigma=3.0)
fn.setParams(type_i="A", type_j="B", alpha=40.0, sigma=3.0)
fn.setParams(type_i="B", type_j="B", alpha=25.0, sigma=3.0)
app.add(fn)


gw = pygamd.integration.gwvv(info=mst, group='all')
app.add(gw)

di = pygamd.dump.data(info=mst, group='all', file='data.log', period=500)
app.add(di)

Finally, running the simulation with the number of time steps.

Examples:

app.run(10000)