Code for CTRAMER v 1.0
Software is divided in five modules, each of which focus on a specific calculation:
- Module 1: Molecule-level electronic structure calculations a) RUN_DFTFUNC.sh calculates ground state charges for each molecule
- Module 2: Condensed-phase molecular dynamics simulations a) Contruct_layers.sh constructs semi-random condensed-phase systems by tessellating individual molecules b) Generate_gs_prmtop.sh assigns the parameters and topology from Module 1 to each molecule in 2a. c) Run_md.sh generates multiple parallel production runs for the system after equilibration.
- Module 3: Molecular pair-level electronic structure calculations a) RUN_DFTFUNC.sh calculates excited state characteristics for each pair selected from Module 2 b) Analyze_states.py selects the important states and transitions from 3a.
- Module 4: Fixed pair molecular dynamics simulations a) Generate_prmtop.sh creates the files necessary for MD for each state from Module 3 b) Recalculate_ex.sh i) ct_trajectory creates a trajectory for each donor state in selected transitions with the chosen pair fixed ii) ct_recalculate recalculates the energy at each step for each state in the transition
- Module 5: Linear semi-classical rate constant approximation a) Calculate_corrections.sh calculates the energy correction term for each state b) km_calc.sh calculates the rate constants for each transition
Please consult the following paper for a more detailed description of the features, architecture, guidelines for usage, and scientific justification of CTRAMER. When using CTRAMER, please cite:
Jacob Tinnin, Huseyin Aksu, Zhengqing Tong, Pengzhi Zhang, Eitan Geva, Barry D. Dunietz, Xiang Sun, and Margaret S. Cheung , "CTRAMER: An open-source software package for correlating interfacial charge transfer rate constants with donor/acceptor geometries in organic photovoltaic materials", The Journal of Chemical Physics 154, 214108 (2021) https://doi.org/10.1063/5.0050574