QCEIMS x MNDO Excited-state molecular dynamics

The MNDO program is used to conduct excited-state molecular dynamics.

The GAMESS program is used to calculate the molecular orbital energy.

The Binary-Encounter-Bethe (BEB) model is used to calculate the ionization cross-section.

Where T is the energy of the impact electrons; B is the electron binding energy of MO_i , U is the kinetic energy of MO_i ; the occupation number N of MO_i is two for ground state molecules.

A modified QCEIMS excutable program is used to conduct EXMD simulation.

Workflow of QCEIMS EXMD

1. The EI spectra are simulated under both ground state and excited state molecular dynamics.
2. The ionization cross section of different electronic state is calculated by BEB model.
3. The hybrid spectrum is generated by mix of different spectra, D₀ and D₁ for example, according to the ionization cross section.

Pipline using SLURM Workload Manager

array.bash

Bash script to generate ground/excited state spectra, respectively.
arry_mix.slurm, folder.slurm and plot_mix.slurm files are needed.

File: array_mix.slurm

Slurm script to conduct ground/excited state MD and generate spectra of each.
The mndo.opt and qceims.in is needed to run this batch command.

To use:

sbatch

--job-name=name
--array=a-b job list
--parsable array_mndo.slurm this slurm file
work path
user name

Exapmle:

sbatch   --job-name=array --array=1-400 --parsable array_molcas.slurm /home/ user1

File: qceims.in

The input file for qceims program
unity: enforces uniform velocity scaling during the vibrational heating phase, which is automatically done if the system is larger than 35 atoms.
MNDOEX: keyword for activating excited-state calculation.

File: mndo.opt

The input file for mndo99 program

Python script for Ionization cross section

File: batch_gms.py

Generate input file for GAMESS program from tmol format coordinate files.

File: BEB.py

Read the log file of GAMESS program to calculate ionization cross section and ratio of spectra under D₀ and D₁ state.

File: ms_correction_batch.py

Generate hybrid spectra from D₀ and D₁ state spectra and ratio from cross section.

User defined command of EXMD (MNDO.opt)

iroot=2 icross=1 ioutci=1 kci=5 ncigrd=1 +

iroot: Total number of lowest CI states computed.
icross: Choice of multi-surface treatment.
icross=1 Calculate energies and gradients for the states specified by ncigrd.
ioutci:Printing flag.
kci: Choice of correlation treatment.
kci=5 General configuration interaction based on the graphical unitary group approach (GUGA-CI).
ncigrd: Number of CI gradients to be computed.

movo=-4 ici1=1 ici2=1 nciref=1 +

movo: Explicit definition of active orbitals.
=-4 Include MOs with highest d-population in active space.
For details see description in GUGA section 3.9.
ici1: Number of active occupied orbitals.
ici2: Number of active unoccupied orbitals.
nciref: Number of reference occupations.
=1: SCF configuration, provided that the spin multiplicity is the same for the SCF and CI calculations.

mciref=0 levexc=2 +

Definition of reference occupations.
= 0 Chosen by default, no further input.

levexc: Maximum excitation level relative to any of the reference configurations. = 1 CIS, only single excitations.
= 2 CISD, up to double excitations.

an input example for mndo99 generated by qceims is listed as inp.