Application

Modules management

Usually, we only define an application object in the context of script. The modules can be added add() into or removed remove() from the application before runing run() the simulation.

class Application(all_info, dt)

The constructor of an application object.

Parameters:

  • all_info (AllInfo) – system information

  • dt (float) – integration time step

add(object)

adds an object to the application.

remove(object)

removes an added object.

clear()

removes all objects from the application.

setDt(float dt)

sets integration time step.

run(unsigned int N)

runs the simulation for N time steps.

Example:

dt = 0.001
app = gala.Application(all_info, dt)
# 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:

    dt = 0.001
app = gala.Application(all_info, dt)
app.add(lj)
app.add(nvt)
app.add(xml)
app.run(1000)

  • Second state simulation:

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

Two-dimensional simulation

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

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

  1. pointing out dimensions with dimensions=”2”

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

  3. specifying the position of particles in Z direction as 0.0

An example is given:

<?xml version="1.0" encoding="UTF-8"?>
<galamost_xml version="1.3">
<configuration time_step="0" dimensions="2" natoms="8" >
<box lx="200" ly="200" lz="0"/>
<position num="8">
    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
</position>
</configuration>
</galamost_xml>

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:

#!/usr/bin/python
from poetry 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.outPutXML("pn2d")