Gator is a program for computational spectroscopy and calculations of molecular properties, currently using the algebraic diagrammatic construction (ADC) scheme for the polarization propagator.

Installation

We recommend installation via the conda package manager via the command

conda install -c gator gator

which will install Gator together with all its dependencies. Afterwards, Gator can be run via

gator input.inp

or be alternatively imported as a Python module.

Features

Calculations using ADC(2), ADC(2)-x, and ADC(3) are available via adcc, also with the core-valence separation (CVS) for computations in the X-ray region. The VeloxChem program serves as SCF driver and provides all the necessary integrals.

Absorption cross sections are implemented using the complex polarization propagator (CPP) approach via the respondo library.

Furthermore, Gator provides a hybrid OpenMP/MPI-parallelized implementation (HPC-QC) for MP2 energies and ADC(2) excitation energies, which can be run on multiple cluster nodes using distributed memory.

Example Python Scripts

Gator can simply be used as a Python module, e.g., using the following script for computing and plotting the X-ray absorption spectrum of water:

import gator
import matplotlib.pyplot as plt

water = gator.get_molecule("""
O   0.0    0.0  0.12
H  -0.7532 0.0 -0.475
H   0.7532 0.0 -0.475
""")

basis = gator.get_molecular_basis(water, '6-311++G**')
scf   = gator.run_scf(water, basis, verbose=False)
xas   = gator.run_adc(water, basis, scf, method='cvs-adc2', singlets=5, core_orbitals=1)

# plot spectrum
plt.figure(figsize=(4, 5))
xas.plot_spectrum()
plt.tight_layout()
plt.show()

In the background, Gator runs the SCF via VeloxChem and then dispatches the SCF results to adcc, which computes the CVS-ADC(2) eigenstates. The resulting spectrum can be directly visualized using the plot_spectrum function provided by adcc. Of course, the calculation can also be run in a Jupyter notebook.

Example Input Files

An example input file for the computation of five singlet excited states of water is shown below:

@jobs
task: adc
@end

@adc
method: adc2 
singlets: 5
@end

@method settings
basis: cc-pvdz
@end

@molecule
charge: 0
multiplicity: 1
units: au
xyz:  
O 0 0 0
H 0 0 1.795239827225189
H 1.693194615993441 0 -0.599043184453037
@end

This job will first run the SCF in VeloxChem and then hand over control to adcc, which computes the ADC(2) eigenstates.

A more advanced example is the computation of the one-photon absorption cross section with the CPP approach:

@jobs
task: adc
@end

@adc
method: cvs-adc2 (cpp)
frequencies: 20
damping: 0.001
core_orbitals: 1
@end

@method settings
basis: cc-pvdz
@end

@molecule
charge: 0
multiplicity: 1
units: au
xyz:  
O 0 0 0
H 0 0 1.795239827225189
H 1.693194615993441 0 -0.599043184453037
@end 

Here, the cross section is determined by solving the response equation for the complex polarizability at a frequency of 20 a.u. with a damping parameter of 0.001. This calculation also makes use of the CVS approximation to guarantee smooth convergence of the response function in the X-ray regime.

HPC-QC input file

To run the OpenMP/MPI-parallelized implementation for ADC(2) excitation energies for water, the following input file is required:

@jobs
task: adc2
@end

@adc2
nstates: 5
@end

@method settings
basis: cc-pvdz
@end

@molecule
charge: 0
multiplicity: 1
units: au
xyz:  
O 0 0 0
H 0 0 1.795239827225189
H 1.693194615993441 0 -0.599043184453037
@end