The Fiesta-MEScal QC-Exciton Workflow

Summary

The Fiesta + MEScal QC-Exciton Workflow is designed to determine the charged and neutral excitations of any molecule or cluster (the QM part) in the presence of an environment described by the Molecular Mechanics (MM) cluster. There are four functional blocks:

  1. The NWChem block consists of two WaNos. The first WaNo (Fiesta-NWChem) takes the atomistic structure of the QM part as an input and yields the DFT Kohn-Sham eigenstates. The post processing WaNo (Fiesta-NWChem-Post) converts the Kohn-Sham states into the proper format to be used in the following Fiesta WaNos.
  2. The Fiesta-MEScal WaNo determines the reaction field in order to take care of the screening effect by the environment. The reaction field is passed to later WaNos.
  3. The Fiesta-GW WaNo determines the charged excitation energies, namely the occupied and empty energy levels associated with the QM part, both in the gas phase and in the presence of the environment. The gas and bulk HOMO-LUMO gap is obtained.
  4. The neutral (optical) excitation states are determined by the Fiesta-BSE (Bethe-Salpeter equation) WaNo. The hole-averaged electron wave function and electron-averaged hole wave function of an excitation state can be plotted and give the indication if such state is a charge transfer state or a Frenkel excitation. In the end of the workflow, the charged excitation energies (HOMO, LUMO and gap) and optical excitation energies are summarized in a PDF file for the convenience of the user.

The QC-Exciton workflow opened inside the workflow client. Right: The four functional blocks and their intermediate results.

Tutorial: Calculation of energy levels of F4TCNQ inside a Pentacene cluster

For this tutorial, we calculate a system of one F4TCNQ molecule (QM part) embedded in 6 Pentacene molecules (MM cluster). The system is shown in Fig. 4a. The tutorial is setup to execute on 16 CPU cores.

  1. In the Fiesta-NWChem WaNo, we put the “F4TCNQ.xyz” file, which contains the atomistic structure of the molecule. The 6-311g* basis and the functional pbe0 are chosen for DFT.
  2. In the Fiesta-MEScal WaNo, we put the “MMstr.pdb” file, which contains the structure of the 6 pentacenes. There are two types of pentacene molecules among the 6, they are named “PC1” and “PC2”. Therefore, we specify the two types of molecules and their micro-electrostatics input files (MEI files) in the graphical user interface. The default SCF control parameters are used.
  3. In the Fiesta-GW WaNo, the parallelization parameters are set to 1x1x16. For this example, only HOMO and LUMO levels are computed by 3 iterations using the default energy grid.
  4. In the Fiesta-BSE WaNo, the parallelization parameters are set to 4x4. We use 40 iterations to determine the first 10 optical excitation states with the “energy cut” at 20 eV. At the end of the simulation, the summary PDF file (Fig. 4b) can be obtained from the Fiesta-BSE WaNo.

(a) The system simulated for the tutorial: One F4TCNQ molecule (the QM part) is considered surrounded by six Pentacene molecules (MM cluster) (b) The summary PDF file, which contains the charged excitation states from the GW calculation and the neutral excitation states from BSE. (c) The comparison of the HOMO and LUMO levels in the Kohn-Sham states, in GW with and without embedding and the lowest neutral excitation state, which is from the HOMO to LUMO transition.

Parameter explanations of the QC-Exciton workflow

The graphical user interface of the WaNos is shown below. The following gives the description of input parameters.

The user interfaces of the four WaNos of the QC-Exciton workflow.

Fiesta-NWChem

Molecule The atomistic structure of the QM molecules, which will be computed, in *.xyz file format.

DFT parameters

  • Basis Selects the basis used in DFT calculation.
  • Functional Selects the functional used in DFT calculation.

Partial Charge Analysis

  • Mulliken charges If ticked, Mulliken charge analysis will be performed in the DFT calculation performed by the Fiesta-NWChem WaNo.
  • ESP fit If ticked, Electrostatic Potential Fitted Charges (ESP) will be determined in the DFT calculation performed by the Fiesta-NWChem WaNo.

Fiesta-MEScal

MM Structure The atomistic structure of the molecule cluster in *.PDB file format.

Molecular species

In this segment parameters for each molecular species inside the provided MM Structure file have to be provided.

  • Molecular type The type of molecule as specified in the MM structure.
  • MEI file The micro-electrostatics input file for this type of molecule.

SCF control

  • Energy tolerance Required energy tolerance in eV.
  • Max. number of iterations Maximum number of iterations carried out by the WaNo
  • Damping Damping factor in the iterative solution update. Accepted values are between 0 (no damping) and 1 (no update). Large damping leads to safer convergence but requires more iterations.
  • Max. energy Maximum energy per molecule allowed in eV. The Fiesta-MEScal WaNo stops its execution if absolute value of the maximum energy per molecule exceeds the specified value.

Fiesta-GW

Parallelization Parameters

The Fiesta-GW code is parallelized in three dimensions. The total number of cores is the product of the three following parameters.

  • Number of columns Together with “Number of rows”, a matrix will be partitioned into blocks and located to corresponding processor. Generally, small number is recommended, such as 1, 2 or 4.
  • Number of rows Together with “Number of columns”, a matrix will be partitioned into blocks and located to corresponding processor. Generally, small number is recommended, such as 1, 2 or 4.
  • Number of slices Wave-functions of the QM cluster will be partitioned into the number of slices. Parallelization on Wave-functions is recommended, therefore large number if preferable.

GW

  • Number of iterations Number of GW iterations. If set to 1, G0W0 will be performed.
  • Number of bands to correct The number of bands to correct by GW, scissors will be applied to other bands.
  • Occupied bands The number of occupied bands to correct. Set to 1 to correct only HOMO level.
  • Unoccupied bands The number of unoccupied bands to correct. Set to 1 to correct only LUMO level.

Energy Grid

The GW values are interpolated based on an energy grid centered at previous GW values (if already iterated) or the Kohn-Sham energy for the first iteration.

  • Number of Grid point The number of points in the energy grid.
  • Step of Grid The step size (in eV) of the energy grid.

Initial guess change in HOMO/LUMO

  • Delta HOMO A shift of the grid (in eV) will be applied for occupied states at the first iteration.
  • Delta LUMO A shift of the grid (in eV) will be applied for unoccupied states at the first iteration.

Fiesta-BSE

Parallelization Parameters

The Fiesta-BSE code is parallelized in two dimensions. It is recommended to set the number of columns and the number of rows equally.

  • Number of columns Together with the parameter “Number of rows”, a matrix will be partitioned into blocks and computed on its own processor.
  • Number of rows Together with the parameter “Number of columns”, a matrix will be partitioned into blocks and computed on its own processor.

BSE

  • Number of iterations The number of iterations to perform in the BSE calculation.
  • Number of excitons The number of neutral excited states to determine.
  • Energy Cut The cutoff energy in eV. Only bands within the energy window, from the energy of HOMO – Energy_cut to the energy of LUMO + Energy_cut, are considered.
  • Tamm Dancoff Approximation If ticked, Tamm Dancoff approximation is used.
  • Triplet If ticked, the calculation is performed for triplet states, otherwise for singlet states.

The results of the search are