Run Glossary¶

The run.dat file contains the input for workflow. This includes specifications for

general input (e.g., run/save locations, type of mechanism)

species and reactions numbers of that mechanisms the computations should be done on

the electronic structure tasks to be run and with what options

the transport tasks to be run and with what options

the thermo or k(T, P) tasks to be run and with what options

the information we want to run processing tasks on to output csv and txt files

Glossary of Input Keywords¶

The input block has the following format

input
    run_prefix = My_AutoMech_Database/RUN
    save_prefix = My_AutoMech_Database/SAVE
end input

Input Keywords¶
Input Keyword	Description
run_prefix*	path to run directory
save_prefix*	path to save directory
inp_mech	the type of mechanism in mechanism.dat (chemkin, rmg, etc)
out_mech	the type of mechanism to be outputted (chemkin, rmg, etc)
inp_spc	the format of the species dictionary (csv)
out_spc	the format of outputted species dictionary (csv)

*compulsory keywords

Glossary of SPC/PES Keywords¶

The spc and pes blocks have no keywords. The spc block require only that a species number (or comma seperated list of species numbers) is given that corresponds to the species in the species.csv that the tasks should be performed on. The pes block, similarly, selects for the potential energy surface number in the sorted mechanism to run on, and can be broken down further by selecting specific channels.

pes
    1: 1, 2, 3
end pes

spc
    1,2,3,4,5
end spc

Glossary of Task Keywords¶

The remaining blocks (els, trans, thermo, and ktp) take on a similar format to one another. For instance, an example electronic structure block (els):

els
    spc  init_geom     runlvl=wb97_sto3g
end els

Here els is the block name (compulsory), init_geom is the task keyword (compulsory), spc is the type of molecule (type is compulsory), and runlvl is one of the options of this task keyword (in this case the run level is compulsory, but many options are optional).

The glossary for these tasks is below, where the Task Keyword can be clicked on for more detail. Compulsory information is identified with an asterisk.

Task Keywords¶
Task Keyword	Description	Type to Run on*	Options

els¶
init_geom* *for new species	initialize a geometry for a new species	spc	runlvl*, retryfail, overwrite
conf_samp	search for additional conformers	spc, ts, all	runlvl, inplvl, retryfail, overwrite, cnf_range
conf_opt	runs an optimization job on any number of conformers	spc, ts, all	runlvl, inplvl, retryfail, overwrite, conf_range
conf_energy	runs a single point energy for any number of conformers	spc, ts, all	runlvl, inplvl, retryfail, overwrite, conf_range
conf_grad	runs a gradient computation on any number of conformers	spc, ts, all	runlvl, inplvl, retryfail, overwrite, conf_range
conf_hess	runs a hessian computation on any number of conformers	spc, ts, all	runlvl, inplvl, retryfail, overwrite, conf_range
conf_vpt2	runs an vpt2 anharmonic analysis on any number of conformers	spc, ts, all	runlvl, inplvl, retryfail, overwrite, conf_range
conf_prop		spc, ts, all	runlvl, inplvl, retryfail, overwrite, conf_range
hr_scan	runs a hindered rotor scan on the lowest energy conformer	spc, ts, all	inplvl, runlvl, retryfail, overwrite, tors_model
hr_reopt	runs a geometry optimization for each step of a hindered rotor scan using the geometry optimized at an inplvl of theory for that dihedral angle	spc, ts, all	inplvl, runlvl, retryfail, overwrite, tors_model
hr_grad	runs gradient computations along the steps of a hindered rotor	spc, ts, all	inplvl, runlvl, retryfail, overwrite, tors_model
hr_hess	runs hessian computations along the steps of a hindered rotor	spc, ts, all	inplvl, runlvl, retryfail, overwrite, tors_model
hr_energy	runs single point energy computations along the steps of a hindered rotor	spc, ts, all	inplvl, runlvl, retryfail, overwrite, tors_model
hr_vpt2	runs vpt2 computations along the steps of a hindered rotor	spc, ts, all	inplvl, runlvl, retryfail, overwrite, tors_model
find_ts	search for a transition state	ts	runlvl, inplvl, retryfail, overwrite, nobarrier, var_splvl1, var_splvl2, var_scnlvl
conf_pucker (dev)	search for any ring puckering conformations (in development)	spc, ts	runlvl, inplvl, retryfail, overwrite, conf_range
tau_samp	sample addition configurations that dont need to be local energy minima	spc, ts, all	runlvl, inplvl, retryfail, overwrite
tau_energy	run single point energy for tau geometries	spc, ts, all	runlvl, inplvl, retryfail, overwrite
tau_grad	run gradient computations for tau geometries	spc, ts, all	runlvl, inplvl, retryfail, overwrite
tau_hess	run hessian computations for tau geometries	spc, ts, all	runlvl, inplvl, retryfail, overwrite

trans¶
`onedmin`_		spc, ts, all	inplvl, runlvl, retryfail, overwrite, bath, nsamp, njobs, smin, smax, conf, pot

thermo¶
`write_mess_thermo`_	write the MESS partition function input file for each species	no type prefix for this section	kin_model, spc_model, overwrite
`run_mess_thermo`_	run MESS for each species	no type prefix for this section	kin_model, spc_model, overwrite, inpname
`run_fits_thermo`_	produce NASA polynomials and CHEMKIN style inputs for each speices	no type prefix for this section	kin_model

ktp¶
`write_mess`_	write the MESS rate constant input file for each connected PES	no type prefix for this section	kin_model, spc_model, overwrite
`run_mess`_	run MESS for each connected PES	no type prefix for this section	kin_model, spc_model, overwrite, inpname
`run_fits`_	produce Arhennius fits and CHEMKIN style input for the rate constants	no type prefix for this section	kin_model

process¶
`freqs`_	produce a csv file of frequencies	spc, ts, vdw, all	geolvl, proplvl, nconfs, econfs, scale
`energy`_	produce a csv file of energies	spc, ts, vdw, all	geolvl, proplvl, nconfs, econfs
`geo`_	produce a txt file of geometries	spc, ts, vdw, all	geolvl, proplvl, nconfs, econfs
`zmatrix`_	produce a txt file of zmatrices	spc, ts, vdw, all	geolvl, proplvl, nconfs, econfs
`enthalpy`_	produce a csv file of 0 K heats of formation	spc, ts, vdw, all	geolvl, proplvl, nconfs, econfs
`coeffs`_	produce a csv file of the reference molecules required for a heat of fomration calculation	spc, ts, vdw, all	None

Detailed Description of Task Keywords¶

init_geom¶

This tasks initializes a geometry for your species based on a geometry built from the default force fields from, on first attempt, RDKit, and on second attempt, OpenBabel. It then optimizes it with the level of theory specified by runlvl. This is a key that connects it to a theory in the theory.dat file. The geometry is then saved in the filesystem

Option Keyword	Description	Values	Default
runlvl*	the task will be performed at this level of theory	<theory level key> as defined in theory.dat	No Default
retryfail	if the electronic structure job fails, reads the failed output, processes why it may have failed, and resubmits it.	True or False	False
overwrite	overwrite any existing or running data saved for this molecule and level of theory in the filesystem	True or False	False

Example:

els
    spc  init_geom     runlvl=wb97_sto3g
end els

Check out our (some sort of theory manual) to see how to set up wb97_sto3g as a theory key in theory.dat.

conf_samp¶

This tasks runs a monte carlo sampling over the torsional coordinates of a molecule to produce geometry samples that are then optimized at the runlvl of theory. The starting geometry to generate new conformers is a stored geometry that was optimized at inplvl of theory already. If no such geometry is saved in the saved filesystems, the user needs to have run init_geom for this quantum chemistry method and basis set. The number of samples is set with the cnf_range keyword.

Option Keyword	Description	Values	Default
inplvl*	the starting geometry is from prior optimization at this level of theory	<theory level key> as defined in theory.dat	No Default
runlvl*	the task will be performed at this level of theory	<theory level key> as defined in theory.dat	No Default
retryfail	if the electronic structure job fails, reads the failed output, processes why it may have failed, and resubmits it.	True or False	False
overwrite	overwrite any existing or running data saved for this molecule and level of theory in the filesystem	True or False	False
cnf_range	the number of geometries to generated by the stochastic sampling routine. The value can be either an integer, and that exact number of samples will be optimized or an array of [a, b, c, d] which will take N (the number of torsions) and use the formula nsamp = min(d, a + ( b * c^N))	<int> or <[int, int, int, int]>	[3, 1, 3, 100]

Example:

els
    spc  init_geom     runlvl=wb97_sto3g
    spc  conf_samp     runlvl=m062x_ccpvdz inplvl=wb97_sto3g  cnf_range=[6,1,3,200]
end els

Check out our (some sort of theory manual) to see how to set up wb97_sto3g as a theory key in theory.dat.

conf_opt¶

This task runs geometry optimizations on a set of conformers for a molecule, specified by conf_range, at the runlvl of theory, where the starting geometries and sorting is done based on the inplvl of theory.

Option Keyword	Description	Values	Default
inplvl*	the starting geometry is from prior optimization at this level of theory	<theory level key> as defined in theory.dat	No Default
runlvl*	the task will be performed at this level of theory	<theory level key> as defined in theory.dat	No Default
retryfail	if the electronic structure job fails, reads the failed output, processes why it may have failed, and resubmits it.	True or False	False
overwrite	overwrite any existing or running data saved for this molecule and level of theory in the filesystem	True or False	False
cnf_range	the conformers to run the task on, sorted using the inplvl of theory	min: the lowest energy conformer n <int>: the lowest <int> number of conformers e <float>: any conformers within <float> kcal/mol of the lowest energy conformer	min

Example:

els
    spc  init_geom     runlvl=wb97_sto3g
    spc  conf_samp     runlvl=wb97_sto3g   inplvl=wb97_sto3g
    spc  conf_opt       runlvl=m062x_ccpvdz inplvl=wb97_sto3g  cnf_range=n5
end els

conf_energy¶

This task runs single point energies on a set of conformers for a molecule, specified by conf_range, at the runlvl of theory, where the starting geometries and sorting is done based on the inplvl of theory.

Option Keyword	Description	Values	Default
inplvl*	the starting geometry is from prior optimization at this level of theory	<theory level key> as defined in theory.dat	No Default
runlvl*	the task will be performed at this level of theory	<theory level key> as defined in theory.dat	No Default
retryfail	if the electronic structure job fails, reads the failed output, processes why it may have failed, and resubmits it.	True or False	False
overwrite	overwrite any existing or running data saved for this molecule and level of theory in the filesystem	True or False	False
cnf_range	the conformers to run the task on, sorted using the inplvl of theory	min: the lowest energy conformer n <int>: the lowest <int> number of conformers e <float>: any conformers within <float> kcal/mol of the lowest energy conformer	min

Example:

els
    spc  init_geom     runlvl=wb97_sto3g
    spc  conf_samp     runlvl=wb97_sto3g   inplvl=wb97_sto3g
    spc  conf_energy   runlvl=m062x_ccpvdz inplvl=wb97_sto3g  cnf_range=n5
end els

conf_grad¶

This task runs gradients on a set of conformers for a molecule, specified by conf_range, at the runlvl of theory, where the starting geometries and sorting is done based on the inplvl of theory.

Option Keyword	Description	Values	Default
inplvl*	the starting geometry is from prior optimization at this level of theory	<theory level key> as defined in theory.dat	No Default
runlvl*	the task will be performed at this level of theory	<theory level key> as defined in theory.dat	No Default
retryfail	if the electronic structure job fails, reads the failed output, processes why it may have failed, and resubmits it.	True or False	False
overwrite	overwrite any existing or running data saved for this molecule and level of theory in the filesystem	True or False	False
cnf_range	the conformers to run the task on, sorted using the inplvl of theory	min: the lowest energy conformer n <int>: the lowest <int> number of conformers e <float>: any conformers within <float> kcal/mol of the lowest energy conformer	min

Example:

els
    spc  init_geom     runlvl=wb97_sto3g
    spc  conf_samp     runlvl=wb97_sto3g   inplvl=wb97_sto3g
    spc  conf_grad     runlvl=wb97_sto3g   inplvl=wb97_sto3g  cnf_range=n5
end els

conf_hess¶

This task runs hessians on a set of conformers for a molecule, specified by conf_range, at the runlvl of theory, where the starting geometries and sorting is done based on the inplvl of theory.

Option Keyword	Description	Values	Default
inplvl*	the starting geometry is from prior optimization at this level of theory	<theory level key> as defined in theory.dat	No Default
runlvl*	the task will be performed at this level of theory	<theory level key> as defined in theory.dat	No Default
retryfail	if the electronic structure job fails, reads the failed output, processes why it may have failed, and resubmits it.	True or False	False
overwrite	overwrite any existing or running data saved for this molecule and level of theory in the filesystem	True or False	False
cnf_range	the conformers to run the task on, sorted using the inplvl of theory	min: the lowest energy conformer n <int>: the lowest <int> number of conformers e <float>: any conformers within <float> kcal/mol of the lowest energy conformer	min

Example:

els
    spc  init_geom     runlvl=wb97_sto3g
    spc  conf_samp     runlvl=wb97_sto3g   inplvl=wb97_sto3g
    spc  conf_hess     runlvl=wb97_sto3g   inplvl=wb97_sto3g  cnf_range=n5
end els

conf_vpt2¶

lalala

conf_prop¶

lalala

conf_pucker¶

lalala

hr_scan¶

Runs a hindered rotor scan on either a species (at an energy minima) or a transition state (at a saddle point). The hindered rotor scans can be run with multiple models, which are described in the options table below.

Option Keyword

Description

Values

inplvl

the starting geometry comes from this level of theory

<theory level> as defined in theory.dat

runlvl

the task will be performed at this level of theory

<theory level> as defined in theory.dat

tors_model

the type of optimization run at each step along the torsional profile

1dhr: Scans are along one torsional coordinate at a time, that coordinate is frozen, and all other coordinates are optimized

1dhrfa: Scans are along one torsional coordinate at a time, all coordinates are frozen

1dhrf: ?????????????????

mdhr: 2 or 3 torsional coordinates are scanned together to define a rotor, those coordinates are frozen, and all other coordinates are optimized

Run Glossary¶

Glossary of Input Keywords¶

Glossary of SPC/PES Keywords¶

Glossary of Task Keywords¶

Detailed Description of Task Keywords¶

init_geom¶

conf_samp¶

conf_opt¶

conf_energy¶

conf_grad¶

conf_hess¶

conf_vpt2¶

conf_prop¶

conf_pucker¶

hr_scan¶

hr_grad¶

hr_hess¶

hr_energy¶

hr_vpt2¶

hr_opt¶

find_ts¶

tau_samp¶

tau_grad¶

tau_energy¶

tau_hess¶

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