Data files, figures, and scripts for the thermally-corrected NBRA project
ALL scripts must be in the same folder
Tully-Parandekar potential ndof = 2
recipes
This folder contains the pre-defined recipes for different kinds of calculations
main-data-gen.py
generate 1 trajectory, but with all the t-resolved data
DATA-model4-method4-icond2 - Tully-Parandekar, FSSH, istate = 2 etot = 0.14 a.u. DATA-model4-method4-icond0 - Tully-Parandekar, FSSH, istate = 0 etot = 0.061 a.u.
main-namd.py
explicitly run the non-NBRA dynamics with multiple trajectories
NAMD-model4-method4-icond2 - we now start on the second excited state istate = 2 and do explicit dynamics
nbra-standard.py
use the data generated by the main-data-gen.py to do the NBRA calculations
choose options to do NBRA or TC-NBRA calculations
for each case, we can use either DATA-model4-method4-icond2 or DATA-model4-method4-icond2 trajectories
generated in the first step
for the TC option, we choose different options of rescaling and thermostat parameters
plot-all.py
plot the results of the nbra calculations
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Computed results are in three parts of the archive "Calculations.tar.bz2.partaa", "Calculations.tar.bz2.partab" and "Calculations.tar.bz2.partac"
To join them together:
cat Calculations.tar.bz2.parta* > Calculations.tar.bz2
The unpack:
tar -xjf Calculations.tar.bz2
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The folder conv_scripts contains a bit more streamlined codes - so that one could simply run a master script
to produce all the data and then visualize them within the given Jupyter notebook. The results stored in the
included notebook are for alternative guiding trajectories. These are very massive results, so are not included.
Folders NAMD-model4-method4-icond0 and NAMD-model4-method4-icond2 contain the non-NBRA FSSH calculations with
multiple trajectories - just in case some of them aren't included in the previous submission