critcatworks.structure package

Submodules

critcatworks.structure.adsorbates module

class critcatworks.structure.adsorbates.GatherPropertyTask(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Task to update database from chunk of calculations. Computes properties of systems. Currently, only reaction energies (adsorption energies) are computed. The ids of the input structures in calc_ids are replaced by the ids of the post-simulation structures from analysis_ids.

Parameters

• chunk_size (int) – number of calculations that are run simulataneously. Default -1 means all calculations are run at once.

• adsite_types (list) – adsorption site types, can contain any combination of “top”, “bridge”, “hollow”

Returns

Firework action, updates fw_spec

Return type

FWAction

optional_params = ['adsite_types']

required_params = ['chunk_size']

run_task(fw_spec)

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

Parameters

fw_spec (dict) – A Firework spec. This comes from the master spec. In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.

Returns

(FWAction)

critcatworks.structure.adsorbates.update_converged_data(chunk_size, adsite_types=['top', 'bridge', 'hollow'])

Updates the internal fw_spec data from chunk of calculations. Computes properties of systems. Currently, only reaction energies (adsorption energies) are computed. The ids of the input structures in calc_ids are replaced by the ids of the post-simulation structures from analysis_ids.

Parameters

• chunk_size (int) – number of calculations that are run simulataneously. Default -1 means all calculations are run at once.

• adsite_types (list) – adsorption site types, can contain any combination of “top”, “bridge”, “hollow”

Returns

Firework GatherPropertyWork

Return type

Firework

critcatworks.structure.coverage module

class critcatworks.structure.coverage.AddRemoveLadderTask(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Firetask in the coverage ladder workflow to either add or remove an adsorbate (at k different positions)

The decision where to add or remove adsorbates is quantified by the ranking_metric, either through a similarity or spatial distance metric.

The bond_length parameters ensures that the positions are not too cramped, hence adsorbates never come too close to each other.

Parameters

• bond_length (float) – distance in angstrom under which two adsorbed atoms are considered bound, hence too close

• k (int) – number of empty candidate sites for adding / adsorbed atoms for removing to consider per step

• ranking_metric (str) – ‘similarity’ or ‘proximity’. Metric based on which to choose k candidates (empty sites / adsorbates)

Returns

Firework action, updates fw_spec

Return type

FWAction

add_adsorbate(simulation, bond_length, db, ranking_metric='proximity', k=7, adsorbate_name='H', reference_id=-1, workflow_id=-1)

Adds one adsorbate to the structure at k different positions, predefined by adsorption sites.

The new structures are added to the simulation collection.

Only supports atomic adsorbates so far.

Parameters

• simulation (dict) – simulation document in custom format

• bond_length (float) – distance in angstrom under which two adsorbed atoms are considered bound, hence too close

• db (pymongo object) – connection to the mongodb database

• k (int) – number of empty candidate sites for adding / adsorbed atoms for removing to consider per step

• ranking_metric (str) – ‘similarity’ or ‘proximity’. Metric based on which to choose k candidates (empty sites / adsorbates)

• adsorbate_name (str) – element symbol of the adsorbed atom

• reference_id (int) – simulation id of the adsorbate reference

• workflow_id (int) – unique identifier of the current workflow

Returns

new simulation ids

Return type

list

get_empty_sites(site_positions, adsorbate_positions, bond_length=1.5)

From a set of predefined adsorption sites, it is reduced to contain only sites which are not too close to existing adsorbate atoms (with respect to parameter bond_length).

Parameters

• site_positions (2D ndarray) – adsorption site positions

• adsorbate_positions (2D ndarray) – positions of all adsorbate atoms

• bond_length (float) – distance criterion up to which a site is considered occupied by neighbouring atoms

Returns

ids of the remaining site positions, ordered by

minimum distance to the adsorbates

Return type

1D ndarray

optional_params = []

remove_adsorbate(simulation, bond_length, db, ranking_metric='similarity', k=7, adsorbate_name='H', workflow_id=-1)

Remove one adsorbate from the structure at k different positions.

The new structures are added to the simulation collection.

Only supports atomic adsorbates so far.

Parameters

• simulation (dict) – simulation document in custom format

• bond_length (float) – distance in angstrom under which two adsorbed atoms are considered bound, hence too close

• db (pymongo object) – connection to the mongodb database

• k (int) – number of empty candidate sites for adding / adsorbed atoms for removing to consider per step

• ranking_metric (str) – ‘similarity’ or ‘proximity’. Metric based on which to choose k candidates (empty sites / adsorbates)

• adsorbate_name (str) – element symbol of the adsorbed atom

• workflow_id (int) – unique identifier of the current workflow

Returns

new simulation ids

Return type

list

required_params = ['bond_length', 'k', 'ranking_metric']

run_task(fw_spec)

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

Parameters

fw_spec (dict) – A Firework spec. This comes from the master spec. In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.

Returns

(FWAction)

split_nanocluster_and_adsorbates(simulation)

Helper function to split a given structure in a simulation document into two ase atoms objects containing only the nanocluster or the adsorbate atoms.

Parameters

simulation (dict) –

Returns

cluster atoms (ase.Atoms),

adsorbate atoms (ase.Atoms), adsorption site ids (list), adsorption site classes (list), reference ids (list), adsorbate ids (list)

Return type

tuple

class critcatworks.structure.coverage.AdsorbateEliminationTask(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Firetask to eliminate too close adsorbate atoms on a covered nanocluster. The adsorbates can be eliminated either based on a minimum distance ‘bond_length’ or the closest ones can be eliminated until only n_remaining adsorbates are left.

The workflow is defused if no adsorbate atoms were removed.

Parameters

• adsorbate_name (str) – element symbol of the adsorbed atom

• bond_length (float) – distance in angstrom under which two adsorbed atoms are considered bound, hence too close

• n_remaining (int) – number of adsorbates which should remain after the first pre-DFT pruning of the adsorbate coverage

Returns

Firework action, updates fw_spec, possible defuses

workflow.

Return type

FWAction

optional_params = ['bond_length', 'n_remaining']

required_params = ['adsorbate_name']

run_task(fw_spec)

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

Parameters

fw_spec (dict) – A Firework spec. This comes from the master spec. In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.

Returns

(FWAction)

class critcatworks.structure.coverage.CoverageLadderTask(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

This Task is at the heart of the coverage ladder workflow. It manages the following steps: - gets lowest energy structures from the previous step - checks if a new root structure has been found - manages branches - computes adsorption free energy - decides upon termination based on parameter d - decides direction of next step

Parameters

• d (int) – maximum depth of the coverage ladder (termination criterion)

• l (int) – number of low-energy structures to carry over to the next step

Returns

Firework action, updates fw_spec, possible defuses

workflow.

Return type

FWAction

check_new_root(is_new_root, branch_dct, lowest_idx, ne_dct, n_adsorbates_root, n_adsorbates, reference_energy=0.0, free_energy_correction=0.0)

Checks if current lowest-energy configuration is eligible for new root. A special check is done after the first step after root. It depends on the direction of the last step and checks the sign of the adsorption free energy. Otherwise, the method level_check_new_root is called.

Parameters

• is_new_root (bool) – if True, the current step is the first step after root

• branch_dct (dict) – parent simulation : list of child simulations

• lowest_idx (int) – lowest-energy simulation id

• ne_dct (dict) – stores total energies of all calculations with respect to the number of adsorbates and their ids

• n_adsorbates_root (int) – number of adsorbates of the root structure

• n_adsorbates (int) – number of adsorbates of the current step

• reference_energy (float) – reference energy for the adsorbate. Can be the total energy of the isolated adsorbate molecule or a different reference point

• free_energy_correction (float) – free energy correction of the adsorption reaction at hand

• Returns –

• bool – new root

compute_dg_diff(idx, branch_dct, ne_dct, reference_energy=0.0, free_energy_correction=0.0)

Helper function to compute the adsorption free energy

In the case of hydrogen the property is: dGdiff(nH) = G(nH) - G(nH-1)) - 0.5 G(H2)

Parameters

• idx (int) – simulation id

• branch_dct (dict) – parent simulation : list of child simulations

• ne_dct (dict) – stores total energies of all calculations with respect to the number of adsorbates and their ids

• reference_energy (float) – reference energy for the adsorbate. Can be the total energy of the isolated adsorbate molecule or a different reference point

• free_energy_correction (float) – free energy correction of the adsorption reaction at hand

• Returns –

• tuple – adsorption free energy (float), assignment of property to ‘parent’ or ‘child’ simulation

decide_next_branch(open_branches, ne_dct)

The next branch from the collected possible branches is picked. The first element is removed from the list which contains information about direction and parent simulation ids

Parameters

• open_branches (list) – each element is a tuple containing parent simulation ids and direction

• ne_dct (dict) – stores total energies of all calculations with respect to the number of adsorbates and their ids

Returns

direction (bool),

simulation ids (list), updated number of adsorbates (int)

Return type

tuple

find_lowest_energy_structures(l, calc_ids, energies)

Finds the l lowest energy structures based on the given total energies.

Parameters

• l (int) – number of lowest-energy structures

• calc_ids (list) – simulation ids

• energies (list) – total energies of the systems

Returns

list of l calc_ids, list of l total energies

Return type

tuple

level_check_new_root(idx, ne_dct, n_adsorbates_root, n_adsorbates)

Has to compare with root, if it is on the same coverage level. The new structure becomes the new root if its total energy is lower.

optional_params = []

required_params = ['l', 'd']

run_task(fw_spec)

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

Parameters

fw_spec (dict) – A Firework spec. This comes from the master spec. In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.

Returns

(FWAction)

class critcatworks.structure.coverage.GatherLadderTask(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Firetask for Gathering properties for coverage ladder. Update database from previous calculations. Computes properties of systems. Currently, only reaction energies (adsorption energies) are computed. The ids of the input structures in calc_ids are replaced by the ids of the post-simulation structures from analysis_ids.

Args:

Returns

Firework action, updates fw_spec

Return type

FWAction

optional_params = []

required_params = []

run_task(fw_spec)

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

Parameters

fw_spec (dict) – A Firework spec. This comes from the master spec. In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.

Returns

(FWAction)

class critcatworks.structure.coverage.NewLadderRootTask(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Task to start CoverageLadder Workflow. It initiates a few fw_spec[“temp”] entries: -“step_history” -“root_history” -“is_return” -“start_id” -“is_new_root” -“n_adsorbates” -“n_adsorbates_root” -“branch_dct” -“open_branches” -“ne_dct” -“direction” -“calc_ids” -“reference_energy” -“free_energy_correction”

Parameters

• start_ids (list) – unique identifiers of the simulations collection which are used to start the workflow

• reference_energy (float) – reference energy for the adsorbate. Can be the total energy of the isolated adsorbate molecule or a different reference point

• free_energy_correction (float) – free energy correction of the adsorption reaction at hand

• initial_direction (bool) – True will force the initial step to add an adsorbate, False will force the initial step to remove an adsorbate

Returns

Firework action, updates fw_spec

Return type

FWAction

optional_params = ['initial_direction']

required_params = ['start_ids', 'reference_energy', 'free_energy_correction']

run_task(fw_spec)

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

Parameters

fw_spec (dict) – A Firework spec. This comes from the master spec. In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.

Returns

(FWAction)

class critcatworks.structure.coverage.PerTypeCoverageCreationTask(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Task to cover cluster fully with adsorbates based on a type of site.

Additionally, a reference simulation document is created and the descriptors of the sites are stored.

Parameters

• reference_energy (float) – reference energy of the adsorbate

• adsorbate_name (str) – Adsorbate atom name to be placed on all sites found.

• adsite_types (list of str) – Can be “top”, “bridge” or “hollow”.

Returns

Firework action, updates fw_spec

Return type

FWAction

optional_params = []

required_params = ['reference_energy', 'adsorbate_name', 'adsite_types']

run_task(fw_spec)

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

Parameters

fw_spec (dict) – A Firework spec. This comes from the master spec. In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.

Returns

(FWAction)

critcatworks.structure.coverage.add_remove_adsorbate(bond_length, k=7, ranking_metric='similarity')

Firework in the coverage ladder workflow to either add or remove an adsorbate (at k different positions)

The decision where to add or remove adsorbates is quantified by the ranking_metric, either through a similarity or spatial distance metric.

The bond_length parameters ensures that the positions are not too cramped, hence adsorbates never come too close to each other.

Parameters

• bond_length (float) – distance in angstrom under which two adsorbed atoms are considered bound, hence too close

• k (int) – number of empty candidate sites for adding / adsorbed atoms for removing to consider per step

• ranking_metric (str) – ‘similarity’ or ‘proximity’. Metric based on which to choose k candidates (empty sites / adsorbates)

Returns

Firework AddRemoveLadderWork

Return type

Firework

critcatworks.structure.coverage.eliminate_closest(adsorbate_name, n_remaining)

Firework to eliminate too close adsorbate atoms on a covered nanocluster. The adsorbates closest to each other are eliminated until only n_remaining adsorbates are left.

The workflow is defused if no adsorbate atoms were removed.

Parameters

• adsorbate_name (str) – element symbol of the adsorbed atom

• n_remaining (int) – number of adsorbates which should remain after the first pre-DFT pruning of the adsorbate coverage

Returns

Firework AdsorbateEliminationWork

Return type

Firework

critcatworks.structure.coverage.eliminate_pairs(adsorbate_name, bond_length)

Firework to eliminate too close adsorbate atoms on a covered nanocluster. The adsorbates closest to each other are eliminated based on a minimum distance ‘bond_length’.

The workflow is defused if no adsorbate atoms were removed.

Parameters

• adsorbate_name (str) – element symbol of the adsorbed atom

• bond_length (float) – distance in angstrom under which two adsorbed atoms are considered bound, hence too close

Returns

Firework AdsorbateEliminationWork

Return type

Firework

critcatworks.structure.coverage.gather_ladder()

Firework for Gathering properties for coverage ladder. Update database from previous calculations. Computes properties of systems. Currently, only reaction energies (adsorption energies) are computed. The ids of the input structures in calc_ids are replaced by the ids of the post-simulation structures from analysis_ids.

Args:

Returns

Firework GatherLadderWork

Return type

Firework

critcatworks.structure.coverage.get_per_type_coverage(reference_energy=0.0, adsorbate_name='H', adsite_types=['top', 'bridge', 'hollow'], descriptor='soap', descriptor_params={'crossover': True, 'lmax': 6, 'nmax': 9, 'rcut': 5.0, 'sparse': False})

Firework to cover cluster fully with adsorbates based on a type of site.

Additionally, a reference simulation document is created and the descriptors of the sites are stored.

Parameters

• reference_energy (float) – reference energy of the adsorbate

• adsorbate_name (str) – Adsorbate atom name to be placed on all sites found.

• adsite_types (list of str) – Can be “top”, “bridge” or “hollow”.

• descriptor (str) – type of descriptor to be used. For a list of descriptors, see the documentation of dscribe Defaults to ‘soap’

• descriptor_params (dict) – descriptor parameters

Returns

Firework PerTypeCoverageCreationWork

Return type

Firework

critcatworks.structure.coverage.start_coverage_ladder(start_ids, initial_direction=1, reference_energy=0.0, free_energy_correction=0.0)

Firework to start CoverageLadder Workflow. It initiates a few fw_spec[“temp”] entries: -“step_history” -“root_history” -“is_return” -“start_id” -“is_new_root” -“n_adsorbates” -“n_adsorbates_root” -“branch_dct” -“open_branches” -“ne_dct” -“direction” -“calc_ids” -“reference_energy” -“free_energy_correction”

Parameters

• start_ids (list) – unique identifiers of the simulations collection which are used to start the workflow

• reference_energy (float) – reference energy for the adsorbate. Can be the total energy of the isolated adsorbate molecule or a different reference point

• free_energy_correction (float) – free energy correction of the adsorption reaction at hand

• initial_direction (bool) – True will force the initial step to add an adsorbate, False will force the initial step to remove an adsorbate

Returns

Firework NewLadderRootWork

Return type

Firework

critcatworks.structure.coverage.step_coverage_ladder(l=2, d=4)

This Firework is at the heart of the coverage ladder workflow. It manages the following steps: - gets lowest energy structures from the previous step - checks if a new root structure has been found - manages branches - computes adsorption free energy - decides upon termination based on parameter d - decides direction of next step

Parameters

• d (int) – maximum depth of the coverage ladder (termination criterion)

• l (int) – number of low-energy structures to carry over to the next step

Returns

Firework CoverageLadderWork

Return type

Firework

critcatworks.structure.coverage.x2_to_x(points, bondlength=1.5)

Helper function to determine the points closest to all other points. It ranks them removing one by one until no points are closer than the specified parameter bondlength.

Parameters

• points (2D ndarray) – Points in n-dimensional space

• bondlength (float) – criterion up to which points should be removed.

Returns

ids of the remaining points, ordered by minimum

distance

Return type

1D ndarray

critcatworks.structure.nanoclusters module

class critcatworks.structure.nanoclusters.NCGenerationTask(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Firetask to generate binary nanoclusters of defined size and shape. For each binary element combination, for each composition, n_configurations maximally dissimilar structures are created and uploaded to the simulations collection of the mongodb database. For further information on the generation algorithm, consult the documentation of cluskit.

The new structures are added to the simulation collection of the mongodb database.

Parameters

• n_initial_configurations (int) – number of initial configurations per composition to choose from (higher number will make the grid finer)

• n_configurations (int) – number of configurations per composition (chosen based on maximally different structural features)

• shape (str) – determines shape of nanoclusters. ‘ico’, ‘octa’ and ‘wulff’

• nanocluster_size (int) – determines nanocluster size. Meaning depends on shape

• compositions (list) – each element determines the amount of atoms of type 1.

• elements (list) – elements (str) to iterate over

• generate_pure_nanoclusters (bool) – if set to True, also pure nanoclusters are generated

• bondlength_dct (dict) – bond lengths to use for specific elements. Some default bond lenghts are provided for common elements

Returns

Firework action, updates fw_spec

Return type

FWAction

generate(n_initial_configurations, n_configurations, shape, nanocluster_size, compositions, elements, generate_pure_nanoclusters=True, bondlength_dct={}, db=None, workflow_id=-1)

Generates binary nanoclusters. For further information, consult the documentation of cluskit

Parameters

• n_initial_configurations (int) – number of initial configurations per composition to choose from (higher number will make the grid finer)

• n_configurations (int) – number of configurations per composition (chosen based on maximally different structural features)

• shape (str) – determines shape of nanoclusters. ‘ico’, ‘octa’ and ‘wulff’

• nanocluster_size (int) – determines nanocluster size. Meaning depends on shape

• compositions (list) – each element determines the amount of atoms of type 1.

• elements (list) – elements (str) to iterate over

• generate_pure_nanoclusters (bool) – if set to True, also pure nanoclusters are generated

• bondlength_dct (dict) – bond lengths to use for specific elements. Some default bond lenghts are provided for common elements

• db (pymongo object) – connection to the mongodb database

• workflow_id (int) – unique identifier of the current workflow

Returns

list of nanocluster ase.Atoms objects,

list of simulation ids

Return type

tuple

optional_params = ['generate_pure_nanoclusters', 'bondlength_dct']

required_params = ['n_initial_configurations', 'n_configurations', 'shape', 'nanocluster_size', 'compositions', 'elements']

run_task(fw_spec)

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

Parameters

fw_spec (dict) – A Firework spec. This comes from the master spec. In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.

Returns

(FWAction)

class critcatworks.structure.nanoclusters.NCStabilityTask(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Task to compare the stability of clusters using cohesive or total energy. Cohesive energy requires atomic total energies.

Writes a file called cohesive_energy.json where the energies are summarized split by nanocluster composition.

Parameters

atomic_energies (list) – atomic energies provided using the same simulation parameters

Returns

Firework action, updates fw_spec

Return type

FWAction

optional_params = ['atomic_energies']

required_params = []

run_task(fw_spec)

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

Parameters

fw_spec (dict) – A Firework spec. This comes from the master spec. In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.

Returns

(FWAction)

critcatworks.structure.nanoclusters.compare_nanoclusters(atomic_energies={})

Firework to compare the stability of clusters using cohesive or total energy. Cohesive energy requires atomic total energies.

Writes a file called cohesive_energy.json where the energies are summarized split by nanocluster composition.

Parameters

atomic_energies (list) – atomic energies provided using the same simulation parameters

Returns

Firework NCStabilityWork

Return type

Firework

critcatworks.structure.nanoclusters.generate_nanoclusters(n_initial_configurations, n_configurations, shape, nanocluster_size, compositions, elements, generate_pure_nanoclusters=True, bondlength_dct={})

Firework to generate binary nanoclusters of defined size and shape. For each binary element combination, for each composition, n_configurations maximally dissimilar structures are created and uploaded to the simulations collection of the mongodb database. For further information on the generation algorithm, consult the documentation of cluskit.

The new structures are added to the simulation collection of the mongodb database.

Parameters

• n_initial_configurations (int) – number of initial configurations per composition to choose from (higher number will make the grid finer)

• n_configurations (int) – number of configurations per composition (chosen based on maximally different structural features)

• shape (str) – determines shape of nanoclusters. ‘ico’, ‘octa’ and ‘wulff’

• nanocluster_size (int) – determines nanocluster size. Meaning depends on shape

• compositions (list) – each element determines the amount of atoms of type 1.

• elements (list) – elements (str) to iterate over

• generate_pure_nanoclusters (bool) – if set to True, also pure nanoclusters are generated

• bondlength_dct (dict) – bond lengths to use for specific elements. Some default bond lenghts are provided for common elements

Returns

Firework NCGenerationWork

Return type

Firework

critcatworks.structure.singlesites module

class critcatworks.structure.singlesites.AdsiteCreationTask(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Firetask to determine adsorption site structures. The adsorbate can only be a single atom. For a molecular adsorbate (binding to only one site), please use the Firetask MonodentateAdsiteCreationTask. On a set of nanoclusters, a combination of top/bridge/hollow sites is classified and populated. Hence, the simulation collection of the mongodb database is updated with structures which each contain a single adsorbate on a nanocluster.

Besides, a descriptor matrix is written to a file for later use.

Parameters

• reference_energy (float) – reference energy for the adsorbate. Can be the total energy of the isolated adsorbate molecule or a different reference point

• adsorbate_name (str) – element symbold of the adsorbed atom

• adsite_types (list) – adsorption site types, can contain any combination of “top”, “bridge”, “hollow”

Returns

Firework action, updates fw_spec

Return type

FWAction

optional_params = []

required_params = ['reference_energy', 'adsorbate_name', 'adsite_types']

run_task(fw_spec)

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

Parameters

fw_spec (dict) – A Firework spec. This comes from the master spec. In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.

Returns

(FWAction)

class critcatworks.structure.singlesites.AdsiteRankTask(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Firetask to determine ranking of adsorption site structures. Based on a previously calculated descriptor matrix (in the fw_spec as a path to a file), the adsorbate structure sites are ranked are ranked for their dissimilarity.

Hence, the calc_ids, the structures to be simulated are reordered.

Besides, the descriptor matrix is reordered and written to a file for later use.

Args:

Returns

Firework action, updates fw_spec

Return type

FWAction

optional_params = []

required_params = []

run_task(fw_spec)

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

Parameters

fw_spec (dict) – A Firework spec. This comes from the master spec. In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.

Returns

(FWAction)

class critcatworks.structure.singlesites.MonodentateAdsiteCreationTask(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Firetask to determine adsorption site structures. The adsorbate is specified as a molecule with an anchor X which binds to only one site. The position of the binding atom is exactly determined by the adsorption vector of the adsorption site and the bond length between X and the closest, later binding, atom. On a set of nanoclusters, a combination of top/bridge/hollow sites is classified and populated. Hence, the simulation collection of the mongodb database is updated with structures which each contain a single adsorbate on a nanocluster.

Besides, a descriptor matrix is written to a file for later use.

Parameters

• reference_energy (float) – reference energy for the adsorbate. Can be the total energy of the isolated adsorbate molecule or a different reference point

• adsorbate (dict) – adsorbed molecule as atoms dict. Contains an “X” dummy atom which indicates the anchor point to the nanocluster

• adsite_types (list) – adsorption site types, can contain any combination of “top”, “bridge”, “hollow”

Returns

Firework action, updates fw_spec

Return type

FWAction

optional_params = []

required_params = ['reference_energy', 'adsorbate', 'adsite_types']

run_task(fw_spec)

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

Parameters

fw_spec (dict) – A Firework spec. This comes from the master spec. In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.

Returns

(FWAction)

class critcatworks.structure.singlesites.MonodentateUniqueAdsiteCreationTask(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Firetask to determine unique adsorption site structures. The adsorbate is specified as a molecule with an anchor X which binds to only one site. The position of the binding atom is exactly determined by the adsorption vector of the adsorption site and the bond length between X and the closest, later binding, atom. On a set of nanoclusters, a combination of top/bridge/hollow sites is classified. The sites are ranked for their dissimilarity based on a local descriptor (default soap), then uniqueness is defined by a threshold parameter. Only the unique sites are kept and populated with the adsorbate.

Hence, the simulation collection of the mongodb database is updated with structures which each contain a single adsorbate on a nanocluster.

Besides, a descriptor matrix is written to a file for later use.

Parameters

• reference_energy (float) – reference energy for the adsorbate. Can be the total energy of the isolated adsorbate molecule or a different reference point

• adsorbate (dict) – adsorbed molecule as atoms dict. Contains an “X” dummy atom which indicates the anchor point to the nanocluster

• adsite_types (list) – adsorption site types, can contain any combination of “top”, “bridge”, “hollow”

• threshold (float) – threshold of similarity metric between the local structures of the adsorption sites. Only sites which are more dissimilar than the given threshold are computed

Returns

Firework action, updates fw_spec

Return type

FWAction

optional_params = []

required_params = ['reference_energy', 'adsorbate', 'adsite_types', 'threshold']

run_task(fw_spec)

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

Parameters

fw_spec (dict) – A Firework spec. This comes from the master spec. In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.

Returns

(FWAction)

critcatworks.structure.singlesites.get_adsites(reference_energy=0.0, adsorbate_name='H', adsite_types=['top', 'bridge', 'hollow'], descriptor='soap', descriptor_params={'crossover': True, 'lmax': 6, 'nmax': 9, 'rcut': 5.0, 'sparse': False})

Firetask to determine adsorption site structures. The adsorbate can only be a single atom. For a molecular adsorbate (binding to only one site), please use the Firetask MonodentateAdsiteCreationTask. On a set of nanoclusters, a combination of top/bridge/hollow sites is classified and populated. Hence, the simulation collection of the mongodb database is updated with structures which each contain a single adsorbate on a nanocluster.

Besides, a descriptor matrix is written to a file for later use.

Parameters

• reference_energy (float) – reference energy for the adsorbate. Can be the total energy of the isolated adsorbate molecule or a different reference point

• adsorbate_name (str) – element symbold of the adsorbed atom

• adsite_types (list) – adsorption site types, can contain any combination of “top”, “bridge”, “hollow”

• descriptor (str) – type of descriptor to be used. For a list of descriptors, see the documentation of dscribe Defaults to ‘soap’

• descriptor_params (dict) – descriptor parameters

Returns

Firework action, updates fw_spec

Return type

FWAction

critcatworks.structure.singlesites.get_monodentate_adsites(reference_energy=0.0, adsorbate={}, adsite_types=['top', 'bridge', 'hollow'], descriptor='soap', descriptor_params={'crossover': True, 'lmax': 6, 'nmax': 9, 'rcut': 5.0, 'sparse': False})

Firetask to determine adsorption site structures. The adsorbate is specified as a molecule with an anchor X which binds to only one site. The position of the binding atom is exactly determined by the adsorption vector of the adsorption site and the bond length between X and the closest, later binding, atom. On a set of nanoclusters, a combination of top/bridge/hollow sites is classified and populated. Hence, the simulation collection of the mongodb database is updated with structures which each contain a single adsorbate on a nanocluster.

Besides, a descriptor matrix is written to a file for later use.

Parameters

• reference_energy (float) – reference energy for the adsorbate. Can be the total energy of the isolated adsorbate molecule or a different reference point

• adsorbate (dict) – adsorbed molecule as atoms dict. Contains an “X” dummy atom which indicates the anchor point to the nanocluster

• adsite_types (list) – adsorption site types, can contain any combination of “top”, “bridge”, “hollow”

• descriptor (str) – type of descriptor to be used. For a list of descriptors, see the documentation of dscribe Defaults to ‘soap’

• descriptor_params (dict) – descriptor parameters

Returns

Firework MonodentateAdsiteCreationWork

Return type

Firework

critcatworks.structure.singlesites.get_monodentate_unique_adsites(reference_energy=0.0, adsorbate={}, adsite_types=['top', 'bridge', 'hollow'], threshold=0.001, descriptor='soap', descriptor_params={'crossover': True, 'lmax': 6, 'nmax': 9, 'rcut': 5.0, 'sparse': False})

Firework to determine unique adsorption site structures. The adsorbate is specified as a molecule with an anchor X which binds to only one site. The position of the binding atom is exactly determined by the adsorption vector of the adsorption site and the bond length between X and the closest, later binding, atom. On a set of nanoclusters, a combination of top/bridge/hollow sites is classified. The sites are ranked for their dissimilarity based on a local descriptor (default soap), then uniqueness is defined by a threshold parameter. Only the unique sites are kept and populated with the adsorbate.

Hence, the simulation collection of the mongodb database is updated with structures which each contain a single adsorbate on a nanocluster.

Besides, a descriptor matrix is written to a file for later use.

Parameters

• reference_energy (float) – reference energy for the adsorbate. Can be the total energy of the isolated adsorbate molecule or a different reference point

• adsorbate (dict) – adsorbed molecule as atoms dict. Contains an “X” dummy atom which indicates the anchor point to the nanocluster

• adsite_types (list) – adsorption site types, can contain any combination of “top”, “bridge”, “hollow”

• threshold (float) – threshold of similarity metric between the local structures of the adsorption sites. Only sites which are more dissimilar than the given threshold are computed

• descriptor (str) – type of descriptor to be used. For a list of descriptors, see the documentation of dscribe Defaults to ‘soap’

• descriptor_params (dict) – descriptor parameters

Returns

Firework MonodentateUniqueAdsiteCreationWork

Return type

Firework

critcatworks.structure.singlesites.rank_adsites()

Firework to determine ranking of adsorption site structures. Based on a previously calculated descriptor matrix (in the fw_spec as a path to a file), the adsorbate structure sites are ranked are ranked for their dissimilarity.

Hence, the calc_ids, the structures to be simulated are reordered.

Besides, the descriptor matrix is reordered and written to a file for later use.

Args:

Returns

Firework AdsiteRankWork

Return type

Firework

Module contents