What is pydynpost?

pydynpost is a set of postprocessing scripts for both ab initio multiple spawning (AIMS) and trajectory surface hopping (TSH) methods. The main motivation of this project is to gather all scripts necessary for data analysis of a previously performed nonadiabatic dynamics in one place. It features a high degree of modularity, allowing for inclusion of new functionality by simply adding a reference to it in the aimsmodandmet.py / tshmodandmet.py dictionary.

What can it do?

The following table

Observables / metrics	AIMS	TSH	Task name (*)
State population	✔️	✔️	population
Incoherent internals	✔️	✔️	internals
Coherent internals	✔️	❓	internals
Molecular population	✔️	✔️	molpop
Comput. complexity & NTBF	✔️	❓	complexity
Stochastic slections	✔️	❓	selection

✔️ = Accesible and implemented

❓ = Unaccesible or trivial

(*) This value is read into the todo variable. See section Input parameters for more information.

Using pydynpost

pydynpost assumes that you are in a directory that contains the outputs of the nonadiabatic dynamics calculations you want to analyse.

• For AIMS and TSH (without repetitions): ./${IC}m/ (${IC} is arbitrary, e.g. geom_; m is an index for the initial condition)
• For AIMSWISS / SSAIMS and TSH (with repetitons): ./${RNG}n/${IC}m/, (${RNG} is arbitrary, e.g. rng; n is an index for the run)

From within this working directory the postprocessing script can be launched by typing

  pydynpost

after which you enter interactive mode, in which the input parameters are parsed. This is handy for quick-and-dirty calculations, but inefficient when done more than once. For this reason pydynpost can also read the input parameters from the dynpost.inp file. This input file may look something like this:

dynMethod       = tsh
code            = ABIN
todo            = population
geomDir         = geom_
nrStates        = 6
nrRNGs          = 0
sampleSize      = 2
maxTime         = 188.19
step            = 0.1

Input parameters

General:

Input variable name	Description	Possible options
dynMethod	Dynamics method	tsh or aims
pckg (only in aims)	Electronic structure interface	tc or molpro
code (only in tsh)	Implementation of TSH	ABIN
todo	Observable / metric to be calcuated	see (*)
sampleSize	Number of intial conditions (ICs)	int
nrRNGs	Number of runs per IC	int
maxTime	Maximum simulation time	float
step	Time between frames	float
duplicatesExist	Ignore certain ICs	y or n
dupList	List of ignored ICs	int, int, ...

Directory names:

Input variable name	Description	Possible options
outputDir (only for aims+molpro)	molpro subdirectory	str
geomDir	initial condition directory	str
RNGDir	rng seed directory	str

Population:

Input variable name	Description
nrStates	Number of electronic states

Internals:

Input variable name	Description	Possible options
internalType	Internal coordinate type	bl, ba, or td
internalName	Name of contributing atoms	a1-a2 (bl) a1-a2-a3 (ba) a1-a2-a3-a4 (td)
expecType (only in aims)	Way of calculating internal	incoherent or coherent

If expecType = coherent then there are additional parameters determining the range and resolution of the nuclear density along the specified internal:

Input variable name	Description	Possible options
expecMin	Minimum value of internal	float
expecMax	Maxmimum value of internal	float
nrBoxes	Number of histogram boxes	int

Molecular population:

Input variable name	Description	Possible options
internalType	Internal coordinate type	bl, ba, or td
dissPartners	Atoms involved in dissociation	a1-a2
thresh	Dissociation threshold	float