This class is a PLAMS style job class that can run an ACErxn calculation, and return a reaction network.
ACErxnJob(reactant, products, known_intermediates=None, name='acerxn', **kwargs)¶
Class representing the ACErxn computational task.
List of constructor arguments :
reactant– Reactant object
products– List of lists of PLAMS
Moleculeobjects, one list for each possible product with the same stoichiometry as the reactant, and each
Moleculeobject for each product summolecule. Can also be a single list of product molecules.
known_intermediates– Optional list of lists of PLAMS
Moleculeobjects, each list representing an intermediate with the same stoichiometry as the reactant, and each
Moleculeobject representing one of the intermediate submolecules.
settings– A PLAMS
Settingsobject with ACE keywords
This class derives from the PLAMS
The ACErxn procedure consists of three steps, that by default will be performed consecutively.
Intermediate generation: A set of intermediates is generated by enumeratively breaking and forming bonds in the reactant molecules.
Network creation: The intermediates are connected by elementary reactions, using filters based on the number of broken and formed bonds.
Network minimization: The most likely mechanisms from reactant to product are extracted, using shortest path algorithms.
After running ACErxn the reaction network info and the intermediates are stored as RKF files in a results folder. Like any PLAMS SingleJob ACErxn generates a working folder with the default name plams_workdir. After running a single ACErxn job, the results folder is located inside this working folder, as plams_workdir/acerxn/acerxn.results.
A simple example of use, for a unimolecular reaction:
>>> from scm.plams import Molecule, Settings >>> from scm.plams import init, finish >>> from scm.acerxn import Reactant, ACErxnJob, default_settings >>> reactant_filenames = ['reactant.xyz'] >>> product_filenames = ['product.xyz'] >>> # Some user supplied info on the reactants >>> molcharges =  >>> active_atoms = [[0,12,13,15]] >>> # Create the reactant molecules and the Reactant object >>> reactants = [Molecule(fn) for fn in reactant_filenames] >>> reactant = Reactant(reactants, active_atoms, molcharges) >>> reactant.guess_fragments() >>> # Create the product molecules >>> products = [Molecule(fn) for fn in product_filenames] >>> # Set up the ACE job >>> job = ACErxnJob(reactant, products) >>> # Now run the first step >>> init() >>> result = job.run() >>> finish()
In the above examples all the default settings were used. It is also possible to provide them as a PLAMS
>>> # Create the settings object >>> settings = default_settings() >>> settings.BasicOptions.MaxJobs = 4 # Maximum number of parallel processes >>> settings.RunInfo.Steps = 'All' >>> # QM engine settings >>> engine_settings = Settings() >>> engine_settings.Mopac.Model = 'PM6' >>> settings.qmengine = engine_settings >>> # Set up the ACE job >>> job = ACErxnJob(reactant, products, settings=settings)
Generate the runscript. Abstract method.
This method should return a single string with the runscript contents. It can process information stored in
runscriptbranch of job settings. In general the full runscript has the following form:
[first line defined by job.settings.runscript.shebang] [contents of job.settings.runscript.pre, when present] [value returned by get_runscript()] [contents of job.settings.runscript.post, when present]
When overridden, this method should pay attention to
.runscript.stdout_redirectkey in job’s
Put together a complete input file in AMS format
Read an ACErxn job from and AMS style input file
‘’infile’’ – Can be either a file object, or a file name
reactant– A complete Reactant object (including fragment data)
load_external(path, settings=None, finalize=False, fmt='acerxn')¶
Load an external job from path.
In this context an “external job” is an execution of some external binary that was not managed by PLAMS, and hence does not have a
.dillfile. Here it is expected to be an RKF file created by ACErxnJob
path– Can be either the folder containsing all the acerxn result RKF files, or the path to the main ams.rkf file
fmt– The format of the file to be found. Can currently only be ‘acerxn’, which means that RKF files created by ACErxnJob are expected