This repository contains all the input files used to study the effect of charge carrier concentration on electron-hole recombination dynamics in C3N4 monolayers by performing NA-MD calculations in the extended tight-binding (xTB) framework.
More details on how to run the code are brought in Libra CompChemCyberTraining repository. Detailed explanations about installation and running the CP2K inputs can be found in here.
Below you can find the details about how we use these inputs to perform NA-MD for electron-hole recombination dynamics in C3N4 monolayers with up to 5600 atoms using xTB method.
This folder contains CP2K inputs for molecular dynamics simulations along with compressed trajectory xyz files. To uncompress the tar.bz2 files that contain the trajectories that are splitted into multiple parts, you can do this in these folders:
cat *.tar.bz2.part* > file.tar.gz.joined
tar xvf file.tar.gz.joined
The detialed explanation about different inputs used in this folder for computing the molecular overlaps and time-overlaps using CP2K and Libra are brought in here.
This folder also contains all the VMD input files that can be used to plot multiple molecular orbitals on the same geometry using together_mode keyword.
The computation of the NACs requires the correct path to molecular orbitals overlaps and time-overlaps. Detailed explanation about the parameters used in the step3.py files are brought in thislink. The NACs are computed between excited states in mixed electron and hole excitation basis that are ordered based on their identities.
The inputs in this folder are used to perform electron-hole recombination dynamics using NA-MD and are adapted to the most recent version of Libra v5.3.0.
Below, we explain only about the parameters that you we need to change to perform electron-hole recombination dynamics, such as longer trajectories by repeating the Hamiltonian matrices, defined with user_nsteps. Other parameters are fully explained in details in this link.
path_to_npz_files: The full path to the folder where the NAC were computed.
istep: The index of the initial step for reading the NAC files.
fstep: The index of the final step for reading the NAC files.
igeo: The initial geometry to start the dynamics from the read files from istep to fstep. For example, if you set igeo = 10, it will start the dynamics from the istep+10th step.
power: With this parameter, one can scale the NAC values by a factor of sqrt(2)^power which is equal to 2^(power/2). We do not scale the NAC in this study, using power=0.
nfiles: The number of files that were read. This value is fstep-istep.
active_space: The active space means that which states you want to involve in the dynamics. For example, to include only the ground state and the first excited state, you can set it to range(0,2). You can include more states in the dynamics as desired. In this study, we choose an active space which includes all excited states with ~0.2 eV above the first excited state that differs for each monolayer size.
user_nsteps: This parameter is dependent on how long you want to do the dynamics. If this value is larger than nfiles, it will use a repeating Hamiltonian approach. So, you can set it to an arbitrary positive integer value. For example, you can run 10 ps dynamics using the 2 ps Hamiltonian files.
isNBRA: This keyword, in the params_nbra, is used only for FSSH, ID-A, and mSDM type of calculations. If it is set to 1, the Hamiltonian related properties are only computed for one of the trajectories. This is good for nanoscale structures and for dynamics that involve a high number of states and trajectories. For DISH scheme, this value should be set to 0. Currently, large number of states with a large number of trajectories cannot be used for DISH.
After setting up your input, you can submit the jobs through slurm for multiple geometries using sh exe.sh. If you do not have access to multiple nodes, you can uncomment # for icond in range(igeo,fgeo): line and set your geometries as desired (don't forget to uncomment for icond in [igeo]:!).
The results will be stored for each scaling factor power and initial geometry in power_namd_res_igeo folders for each initial state, scheme, and batch.
We perform the electron-hole recombination dynamics in the spin adapted configuration basis (SAC) basis by multiplying the NAC values by sqrt(2) which can be done using:
hvib_im[:,0] *= np.sqrt(2)
hvib_im[0,:] *= np.sqrt(2)
The Python files in folder 5_plot_properties are multiple files that are used for analyzing and plotting the properties of the generated data from previous steps. The e-h-recom_res.py file is used for fitting the NA-MD results and plot_timescales.py file is used for plotting the fitted timescales but before running that, ones needs to run sh extract_data.sh to generate the average timescales with their error bars. plot_electronic_properties.py file is used for plotting the electronic structure poperties such as PDOS, energy vs time, NAC maps, and generating NAC distribution hdf files. The user can modify these scripts as desired. One of the most important libraries that we use is glob which can be used to find files with specific names. For example, for finding the imaginary part of the Hamiltonians, one can use glob.glob('/path/to/nac/folder/*im*') and use the found files for plotting the average NAC maps.