Input files and raw data for publication publication "First-principles treatment of solvent effects on electronic excitations in alizarin"
Zuehlsdorff, Tim J.
University of Cambridge
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Zuehlsdorff, T. J. (2015). Input files and raw data for publication publication "First-principles treatment of solvent effects on electronic excitations in alizarin" [Dataset]. https://www.repository.cam.ac.uk/handle/1810/252337
This file was created by Tim J. Zuehlsdorff on the 15th of October 2015. It contains all input files necessary to reproduce the results of the publication "First-principles treatment of solvent effects on electronic excitations in alizarin". The data in this file is organised as follows. The folders alizarin_frame1 to alizarin_frame5 contain the input files associated with the MD snapshots that are referred to as frame 1 to frame 5 in the publication. The subfolders labelled NWChem contain the NWChem input files for the vacuum, the implicit solvent and the 4 angstrom calculation. All ONETEP input files are labelled with a .dat file label. Note that the ONETEP calculations making use of implicit solvation were all performed in several stages. First a calculation in vacuum and open BC was performed. Then the resulting density was used to define a cavitiy for the dielectric medium felt by the system and a ground state, conduction optimisation and LR_TDDFT calculation was perfomed sequentially. Please refer to the user manuals on the ONETEP website (www.onetep.org) for further details regarding how to perform these calculations. For frame 1, frame 3 and frame 5, the atoms in the 8ang, 10ang and 12ang .dat files are labelled in such a way that waters to within 7 ang are denoted with a H1 and O1 label, while in the 6 ang .dat file, waters within the 4 ang region are denoted in the same way. This labelling enables the performance of TDDFT calculaions using a truncated density matrix in order to reproduce Fig. 5 (please again refer to the manuals on the ONETEP website for further details). The frame5 folder contains 2 additional files where atoms beyond the 7ang and 4ang region are replaced by cassical charges. These files can be used to obtain the black data points in the lower part of figure 5. The folder raw_data/ contains all the raw data used to generate the plots in this work. The NWChem calculations performed in this work were carried out unsing version 6.3, while all ONETEP calculations were performed using version 188.8.131.52
Alizarin, DFT, TDDFT
Publication Reference: https://doi.org/10.1021/acs.jctc.5b01014
This work was supported by the EPSRC [grant numbers EP/J017639/1 and EP/J015059/1] and the ARCHER eCSE programme.
This record's URL: https://www.repository.cam.ac.uk/handle/1810/252337
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Licence URL: http://creativecommons.org/licenses/by-sa/2.0/uk/
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