MD-kinetics – Golubev Research Group

This is a short tutorial on how to use MD-kinetics program.

General description

In order to run the program please execute the following command in the terminal.

./MD-kinetics input.inp

1	./MD-kinetics input.inp

Where input.inp is the input file.

Program produces the following files:

cluster.xyz – XYZ trajectory file with atomic positions on each time step.
kinetics.dat – file with the evolution of populations of atomic states and free agents in time.
restart.dat – file with cluster and free agents after propagation. It can be used to run propagation on later timescale.

Moreover, the program prints input and reaction analysis to the output stream.

Available releases

v1.0 are available upon request.

Input

In order to run the MD-kinetics program one needs to provide it with the input file. The following section should be specified in the input.

propagation section (required)

propagation{
   tmin       =  0        \\in [fs]
   tmax       =  100      \\in [fs]
   tsteps     =  100000   \\number of integration steps
   tsubsteps  =  1        \\kinetic equations are solved with substeps on each propagation step
   abserr     =  1.e-5    \\absolute error of integration
   relerr     =  1.e-5    \\relative error of integration
};

propagation{

tmin = 0 \\in [fs]

tmax = 100 \\in [fs]

tsteps = 100000 \\number of integration steps

tsubsteps = 1 \\kinetic equations are solved with substeps on each propagation step

abserr = 1.e-5 \\absolute error of integration

relerr = 1.e-5 \\relative error of integration

};

This section specifies propagation parameters of the integrators.

potentials section (optional)

potentials{
   3p6    3p6    ArgonPotential()
   3p5+   3p5+   CoulombPotential(1.,1.)
};

potentials{

3p6 3p6 ArgonPotential()

3p5+ 3p5+ CoulombPotential(1.,1.)

};

This section specifies interaction potentials between atomic states of the cluster.

reactions section (optional)

reactions{
   1 $atom{A:4s} -1 $atom{A:3p6}  1.4596374871672733e-08
   1 $atom{A:4s}  1 $atom{B:4s} -1 $atom{A:3p6} -1 $atom{B:3p5+} -1 $agent{e_7.6188} 1.2678477902E-01	
};

reactions{

1 $atom{A:4s} -1 $atom{A:3p6} 1.4596374871672733e-08

1 $atom{A:4s} 1 $atom{B:4s} -1 $atom{A:3p6} -1 $atom{B:3p5+} -1 $agent{e_7.6188} 1.2678477902E-01

};

This section specifies chemical reactions between states of atoms. Involved atoms are specified by the following keyword $atom{A:4s} indicating that 4s state of atom A participate in the reaction. When reaction occurs between different atoms, one needs to specify another atom by different id (for example B). Reaction also can include free agents $agent{e_7.6188} which do not belong to any atom. Last number in reaction line is the rate constant.

cluster section (required)

cluster{
   Ar $mass{40.} $pos{0.,0.,0.} $vel{0.,0.,0.} $states{3p6: 0., 4s: 1.0, 3p5+: 0.0}
   Ar $mass{40.} $pos{7.,0.,0.} $vel{0.,0.,0.} $states{3p6: 0., 4s: 1.0, 3p5+: 0.0}				
};

cluster{

Ar $mass{40.} $pos{0.,0.,0.} $vel{0.,0.,0.} $states{3p6: 0., 4s: 1.0, 3p5+: 0.0}

Ar $mass{40.} $pos{7.,0.,0.} $vel{0.,0.,0.} $states{3p6: 0., 4s: 1.0, 3p5+: 0.0}

};

This section specifies atomic cluster. Each line represents atom which has mass, position, velocity and some atomic states with corresponding populations.

agents section (optional)

agents{
   $agent{e_7.6188: 0.000554936}
};

agents{

$agent{e_7.6188: 0.000554936}

};

This section specifies initial concentrations of free reaction agents which do not belong to any atom.