Application¶

Modules management¶

PYGAMD is organized by being composed of modules. Application manages and calls modules, and thereby run simulations. Usually, we only define an application object in the context of script. The modules can be added into by add() or removed from by remove() the application before runing run() the simulation.

class application.dynamics(info, dt, sort=True)¶

Constructor of application object.

Parameters:

info – system information
dt – integration time step
sort – if device memory is sorted by Hilbert curve, the default is True.

add(object)¶: adds an object to the application.

remove(object)¶: removes an added object.

run(N)¶: runs the simulation for N time steps.

Example:

app = pygamd.application.dynamics(info=mst, dt=0.001)
# builds up an application.
app.run(10000)
# runs the simulation for 10000 time steps.

Multi-stage simulation¶

An application can have single or multiple stage simulations. The commands in the context of script are executed sequentially. Every stage simulation is achieved with run(). Before a stage of simulation, the modules and parameters can be adjusted. New modules can be added into the applicaitons by add(). The added modules at last stage can be removed from the application, otherwise they will be kept. For example:

First stage simulation:

app = pygamd.application.dynamics(info=mst, dt=0.001)
app.add(lj)
app.add(nvt)
app.run(1000)

Second state simulation:

app.remove(lj)
app.remove(nvt)
app.add(harmonic)
app.add(npt)
app.run(1000)

Two-dimensional simulation¶

Controlling script, i.e. ‘file.py’ script is same for two- and three-dimensional simulations.

2. However, configuration file i.e. MST file should indicate two-dimensional system by:

pointing out dimensions with dimensions=”2”

setting the length of box in Z diretion to zero with lz=”0”

specifying the position of particles in Z direction as 0.0

An example is given:

mst_version 1.0
        num_particles
                8
        timestep
                0
        dimension
                2
        box
                200.0    200.0    0.0
        position
                 28.5678528848   -37.9327360252     0.0000000000
                 28.0019705849   -37.1082499897     0.0000000000
                 29.5648198865   -37.8549105956     0.0000000000
                 28.1367681830   -38.8350474902     0.0000000000
                -37.5589154370   -72.8549398355     0.0000000000
                -38.4958248509   -72.5053675968     0.0000000000
                -36.7877222908   -72.2183386015     0.0000000000
                -37.3931991693   -73.8411133084     0.0000000000
mst_end

3. For molgen script to generate a two-dimensional configuration file, a specification of two dimensions and box size in Z direction as 0.0 is necessary. Such as:

import molgen

mol=molgen.Molecule(4)
mol.setParticleTypes("A,B,B,B")
mol.setTopology("0-1,0-2,0-3")
mol.setBondLength("A","B", 1.0)
mol.setAngleDegree("B", "A", "B", 120)
mol.setInit("B", 1)
mol.setCris("A", 1)


gen=molgen.Generators(200, 200, 0.0) # box size in X, Y, and Z directions
gen.addMolecule(mol, 2000)
gen.setDimension(2)
gen.setMinimumDistance(1.0)
gen.outPutMST("pn2d")