This branch of RUQT is an NEGF calculator for pyRUQT. It is not compatible with inputs/datafiles created for the standalone main branch
Rowan University Quantum Transport (RUQT) with JunctionMod included!
RUQT is an in-progress non-equilibrium Green's function (NEGF) based software package focused on studying electron correlation effects in charge transport problems. It is focused on integrating N- and 2-electron methods into the NEGF transport formalism and is the home of the NEGF-RDM and NEGF-PDFT transport methods. As of July 2021, it is capable of performing Landauer NEGF calculations using electronic structure data acquired from separate Hartree-Fock, Density Functional Theory, Multiconfiguration Pair Density Functional Theory, and Parametric 2-Electron Reduced Density Matrix Theory calculations. The code itself is written in Fortran90+ while the supporting scripts are either in Python or Maple. The recommended supporting code JunctionMod is compiled as part of this code and avialable separately here: https://github.com/HoyLab-Rowan/JunctionMod
RUQT currently can read data from the following electronic structure software packages (more methods/package support to come in future):
HF and DFT: Q-Chem, PYSCF, GAMESS, Maple Quantum Chemistry Toolbox, and Molcas (sandx_fock branch) p2-RDM: Maple Quantum Chemistry and GAMESS (Not publically available)
RUQT v1.0 is capable of performing non-self-consistent current and transmission calculations with metal wide band limit electrodes (fixed Fermi level). Additional electrode and calculation types to be added later.
Installation
Required Libraries: Intel MKL
Compiler: GNU or ifort
- Download the code and open the Makefile.
- Set the MKLROOT variable to the location of your MKL library.
- Compiles using Intel fortran compilers by default. Make sure that ifort can find your MKL libraries using the -mkl flag
- To use gfortran uncomment the gfortran line with MKL library links and comment out the ifort line.
- Close Makefile and enter the make command in the terminal.
- This should produce an "RUQT.x" executable for use with external programs.
- If needed, use "make clean" to clear all .mod and .o files from the source and object directories.
How to Use
To run calculations, use either the Maple or Python scripts located in the Hoy Research Group Github: https://github.com/HoyLab-Rowan.
NEGF-RDM
The Maple scripts are available for all methods except MC-PDFT, and Python scripts are available for Q-Chem (HF & DFT), PYSCF (HF & DFT), GAMESS (HF), and Molcas (MC- PDFT) calculations.
The Maple scripts only require an .xyz file with the junction (molecule+electrode) geometry. These can be produced by the JunctionMod code is included in this package and can be used to construct/align molecular junctions. If you use another software package to generate the xyz make sure that the junction is placed along the x-axis.
Using the python scripts requires forming separate electronic structure calculations with specific keywords in the inputs in order to print the Fock, overlap, and T1/T2+MO energies needed by the NEGF-RDM code. Example inputs and outputs for Maple and GAMESS (HF & p2-RDM) can be found in the /examples folder of the source code.
For running p2-RDM calculations, using the Maple Quantum Chemistry Toolbox and related scripts is highly recommended.
The GAMESS p2-RDM code is acquired from the Mazziotti group at UChicago and is not publically available at this time. (Email Dr. Hoy at [email protected] if you need access to the GAMESS p2-RDM code).
NEGF-MCPDFT
In order to run NEGF-MCPDFT calculations, you will need to install the sandx_fock OpenMolcas branch available here (https://gitlab.com/Molcas/OpenMolcas/-/tree/sandx_fock) which generates the FOCK_AO and Overlap files need by RUQT. These contain the MC-PDFT effective Hamilionian and overlap matrices from an OpenMolcas MC-PDFT calculation (see example directory for necessary inputs). These matrices are only available from the sandx_fock branch of OpenMolcas which can be installed according to the regular Openmolcas installation instructions. Use the Junction_Calc.py python script to run the NEGF-MCPDFT code.
If you use this code, cite:
For NEGF-RDM:
Erik P. Hoy, David A. Mazziotti, and Tamar Seideman, “Development and application of a 2-electron reduced density matrix approach to electron transport via molecular junctions” J. Chem. Phys. 147, 184110 (2017).
For NEGF-MCPDFT:
Andrew M. Sand, Justin T. Malme, and Erik P. Hoy, “A multiconfigurational pair-density functional theory approach to molecular junctions”, J. Chem. Phys, 155(11), 114115 (2021). https://doi.org/10.1063/5.0063293
