TGA – Golubev Research Group

This is a short manual on how to use the Thawed Gaussian Approximation program.

The program is intended to perform semiclassical reconstruction of the wave function based on the classical molecular dynamics trajectory. It consists a library and a set of scripts which can be used to analyze different dynamical properties of a system by approximating the nuclear wave packet by a single Gaussian function.

The source code is available at the bitbucket.org. In order to download repository you should be included in the list of developers.

Input file description

The TGA program uses the input file to specify parameters of calculations. Here we present an example of input file with description of parameter which can be modified by user.

# comments start with '#' character
# this section is required
[system]
  coordinate = Cartesian     # (required) - Coordinate system
  natoms = 7                 # (required) - Number of atoms in a molecule
  initial_state = file_name  # (required) - Path to file with initial state.

# this section is required
[propagation]
  method = VelocityVerlet    # (optional; default is VelocityVerlet) - Method of integration.
  dt = float number          # (required) - Propagation time step in fs.
  steps = integer_number     # (required) - Number of propagation steps.

# this section is required
[trajectory]
  state1 = state1/           # (required) - Path to MD trajectory on first state.
  state2 = state3/           # (required) - Path to MD trajectory on second state.
  popul = float_number       # (required) - Population of first state.

# this is optional section
[output]
  output = file_name         # (optional; default is output.dat) - Name of output file.

# comments start with '#' character

# this section is required

[system]

coordinate = Cartesian # (required) - Coordinate system

natoms = 7 # (required) - Number of atoms in a molecule

initial_state = file_name # (required) - Path to file with initial state.

# this section is required

[propagation]

method = VelocityVerlet # (optional; default is VelocityVerlet) - Method of integration.

dt = float number # (required) - Propagation time step in fs.

steps = integer_number # (required) - Number of propagation steps.

# this section is required

[trajectory]

state1 = state1/ # (required) - Path to MD trajectory on first state.

state2 = state3/ # (required) - Path to MD trajectory on second state.

popul = float_number # (required) - Population of first state.

# this is optional section

[output]

output = file_name # (optional; default is output.dat) - Name of output file.

Initial state file

This file is used to construct initial Gaussian which then will be propagated on specified states.

The structure of this file should be the following

$geom
  ... [vector of XYZ coordinates in angstroms]
$END
$atomic mass
  ... [vector of atomic masses in amu]
$END
$potential
  ... [single number in Hartree]
$END
$hessian
  ... [matrix of XYZ Hessian in Hartree/bohr^2]
$END

$geom

... [vector of XYZ coordinates in angstroms]

$END

$atomic mass

... [vector of atomic masses in amu]

$END

$potential

... [single number in Hartree]

$END

$hessian

... [matrix of XYZ Hessian in Hartree/bohr^2]

$END

Trajectory files

The program approximates the wave function by a single Gaussian wave packet which center is propagated according to the classical molecular dynamics trajectory. The width and the phase of the wave packet is reconstructed from the Hessian of the PES. The MD trajectory should be generated by external software (e.g., one can use the OTF-MD program). User should specify path to the directory which has the following structure: step_$i/step_$i.dat, i.e. it contains trajectory files, each placed in a separate directory and $i is the time step.

The step_$i.dat files should have the following structure

$geom
  ... [vector of XYZ coordinates in angstroms]
$END
$atomic mass
  ... [vector of atomic masses in amu]
$END
$potential
  ... [single number in Hartree]
$END
$force
  ... [vector of XYZ forces in Hartree/bohr]
$END
$hessian
  ... [matrix of XYZ Hessian in Hartree/bohr^2]
$END