forcefield_step package#

Submodules#

forcefield_step.forcefield module#

A node or step for the forcefield in a flowchart

class forcefield_step.forcefield.Forcefield(flowchart=None, extension=None, logger=<Logger forcefield_step.forcefield (WARNING)>)[source]#

Bases: Node

assign_forcefield(P=None, configuration=None)[source]#

Assign the forcefield to the structure, i.e. find the atom types and charges.

Parameters:

P ({str: Any}) – The final values of the parameters.

Return type:

None

checkpoint_variable(name, value)[source]#

Save the forcefield in the checkpoint as its file and name.

description_text(P=None)[source]#

Return a short description of this step.

Return a nicely formatted string describing what this step will do.

Keyword Arguments:

P – a dictionary of parameter values, which may be variables or final values. If None, then the parameters values will be used as is.

property files#

The files in the forcefield … (short name & full path)

forcefield_names(ff_file)[source]#

The forcefields defined in a forcefield file and the files it includes.

Parameters:

ff_file (str) – The forcefield file, as given in “forcefield_file”, e.g. “oplsaa.frc” or “local:OPLS-AA/my_oplsaa.frc”.

Returns:

The names in the “#define” lines, in order, or [] if the file cannot be found or is not a forcefield file with definitions, e.g. OpenKIM.

Return type:

[str]

property git_revision#

The git version of this module.

list_data_files(local_only=True)[source]#

Returns the forcefield files needed by this step.

restore_variable(name, data)[source]#

Remake the forcefield from the checkpoint when a job resumes.

run()[source]#

Setup the forcefield

setup_forcefield(P=None)[source]#

Setup the forcefield for later use.

Parameters:

P ({str: Any}) – The final values of the parameters.

Return type:

None

uri_handler(path)[source]#

Return the actual file given a path that may have a uri.

Parameters:

path (str or pathlib.Path) – The filename or uri for the file.

Returns:

path – The full path to the file

Return type:

pathlib.Path

Note

Forcefields can be in one of 3 locations:

  1. In the data directory of this Python package. This is where the standard forcefields are stored.

  2. In the SEAMM installation, under <root>/data/Forcefields, and then in the default installation’s ~/SEAMM/data/Forcefields. This allows a site to add or customize forcefields for all users. The user for the SEAMM installation may not be the same as the user running the code! So ‘~/’ may reference a different directory than the next item.

  3. In the users directory at ~/seamm.d/data/Forcefields. This allows the user to add or override any existing forcefield.

When a forcefield is referenced, if it has no URI it is assumed to be in (1), the default location for forcefields shipped with the release.

If it has a URI, i.e. the path starts with ‘local:’, the code searches for it first in the users local data (3). If it is not found, the search continues in site location (2).

Jobs executed by the JobServer are handled a bit differently, because the site and home directories may not exist or may be different on the machine that the JobServer is running on. When a job is submitted to the Dashboard, the code locates the forcefields on the local machine, as outlined above. It then sends copies to the data/Forcefields directory of the job. The path for the job’s data/ directory is changed to its local data/ directory, so the copies sent with the job are used.

property version#

The semantic version of this module.

forcefield_step.forcefield_parameters module#

Control parameters for using forcefields

class forcefield_step.forcefield_parameters.ForcefieldParameters(defaults={}, data=None)[source]#

Bases: Parameters

The control parameters for forcefields

parameters = {'elements': {'default': '', 'default_units': None, 'description': 'Elements:', 'enumeration': None, 'format_string': '', 'help_text': 'The elements to include.', 'kind': 'periodic table'}, 'forcefield': {'default': 'default', 'default_units': '', 'description': 'Forcefield:', 'enumeration': ('default',), 'format_string': 's', 'help_text': "The forcefield in the file to use, e.g. oplsaa+ or oplsaa+-spc_e in oplsaa.frc, or 'default' for the first one in the file.", 'kind': 'string'}, 'forcefield_file': {'default': 'oplsaa.frc', 'default_units': '', 'description': 'Forcefield Repository:', 'enumeration': (), 'format_string': 's', 'help_text': 'The forcefield repository or file to use.', 'kind': 'enumeration'}, 'potentials': {'default': '', 'default_units': '', 'description': 'Interatomic Potentials:', 'enumeration': ('will be replaced',), 'format_string': 's', 'help_text': 'The interatomic potentials to use.', 'kind': 'enumeration'}, 'task': {'default': 'setup forcefield', 'default_units': '', 'description': 'What to do:', 'enumeration': ('setup forcefield', 'assign forcefield to structure'), 'format_string': 's', 'help_text': 'What to do with the forcefield.', 'kind': 'enumeration'}}#

forcefield_step.forcefield_step module#

Helper class needed for the stevedore integration. Needs to provide a description() method that returns a dict containing a description of this node, and a factory() method for creating the graphical and non-graphical nodes.

class forcefield_step.forcefield_step.ForcefieldStep(flowchart=None, gui=None)[source]#

Bases: object

create_node(flowchart=None, **kwargs)[source]#

Return a new node object

create_tk_node(canvas=None, **kwargs)[source]#

Return the graphical Tk node object

description()[source]#

Return a description of what this extension does

classmethod forcefield(model_chemistry, node=None)[source]#

The seamm_ff_util forcefield for a model chemistry from get_model_chemistry_options().

classmethod get_model_chemistry_options(periodic_only=False, mdi_only=False, data_path=None)[source]#

The forcefields in the .frc files the step can find, as model chemistries; data_path is a running flowchart’s data directories. See forcefield_step.model_chemistry.get_model_chemistry_options().

classmethod model_chemistry_data_files(model_chemistry, node, local_only=True)[source]#

The local and personal files a job needs for the model chemistry.

my_description = {'description': 'An interface for the setup and control of the forcefield', 'group': 'Simulations', 'name': 'Forcefield'}#

forcefield_step.ligpargen module#

forcefield_step.ligpargen.add_to_ff(ff, configuration, data)[source]#

Adds the data to the forcefield file

This method adds the data from the .key file to the forcefield file.

Parameters:

  • ff (list) – The list of strings that make up the forcefield file

  • configuration (Configuration) – The configuration object

  • data (dict) – The data read from the .key file

Returns:

The updated forcefield file

Return type:

str

forcefield_step.ligpargen.check_fragment(configuration, data, smarts, match, types)[source]#

Check a fragment’s atom types against the molecule they describe.

A wrong ordering of the types is otherwise silent – it is a permutation, so the charges still sum to the molecular charge and nothing complains until the types are used, if then. These checks catch it at the point it is written.

Parameters:

  • configuration (Configuration) – The configuration the .key file was generated for.

  • data (dict) – The data read from the .key file.

  • smarts (str) – The SMARTS for the fragment.

  • match (tuple(int)) – The configuration’s atom for each position of the SMARTS.

  • types ([str]) – The atom type for each position of the SMARTS.

Raises:

ValueError – If the types do not describe the molecule.

forcefield_step.ligpargen.key_atom_types(configuration, data)[source]#

Get the LigParGen atom type of each atom of the configuration.

LigParGen does not keep the order of the atoms it is given: it perceives the molecule afresh and orders it its own way. The atom records of the .key file are therefore not in the configuration’s order, so they cannot simply be zipped together.

LigParGen does, however, give every atom its own type, which means the bond records – which are in terms of the types – are the molecular graph of its ordering. Matching that graph to the configuration’s gives the mapping exactly, with no reliance on the two orders agreeing.

Parameters:

  • configuration (Configuration) – The configuration the .key file was generated for.

  • data (dict) – The data read from the .key file.

Returns:

The LigParGen atom type of each atom, in the configuration’s order.

Return type:

[str]

forcefield_step.ligpargen.reader(path)[source]#

Reads the .key file and returns the data

This method reads the .key file output by LigParGen and adds the parameters to the local SEAMM forcefield ligpargen.frc file.

Parameters:

path (str or pathlib.Path) – The path to the .key or .xyz files

Note

The .key file is a text file that contains the forcefield parameters for Tinker. It looks like this:

      ##############################
      ##                          ##
      ##  Force Field Definition  ##
      ##                          ##
      ##############################


forcefield              OPLS-AA

vdwindex                TYPE
vdwtype                 LENNARD-JONES
radiusrule              GEOMETRIC
radiustype              SIGMA
radiussize              DIAMETER
epsilonrule             GEOMETRIC
torsionunit             1.0
imptorunit              1.0
vdw-14-scale            2.0
chg-14-scale            2.0
electric                332.06
dielectric              1.0


      #############################
      ##                         ##
      ##  Atom Type Definitions  ##
      ##                         ##
      #############################


atom        800  800    CT    "C00"          6     12.011     4
atom        801  801    CZ    "C01"          6     12.011     2
atom        802  802    NZ    "N02"          7     14.007     1
atom        803  803     F    "F03"          9     18.998     1
atom        804  804    HC    "H04"          1      1.008     1
atom        805  805    HC    "H05"          1      1.008     1



      ################################
      ##                            ##
      ##  Van der Waals Parameters  ##
      ##                            ##
      ################################


vdw         800           3.5000   0.0660
vdw         801           3.3000   0.0660
vdw         802           3.2000   0.1700
...
The interesting keys are:

  • atom: defines the atom types

  • vdw: defines the van der Waals parameters

  • bond: defines the bond parameters

  • angle: defines the angle parameters

  • torsion: defines the torsion parameters

  • imptors: defines the improper torsion parameters

  • charge: defines the charge parameters

forcefield_step.ligpargen.run()[source]#

forcefield_step.model_chemistry module#

The forcefields as model chemistries.

Every forcefield defined in a .frc file the step can find – the package’s, the SEAMM installation’s (local:) and the user’s (personal:) – is offered as a model chemistry: FF@<name> for a classical forcefield (FF@oplsaa+) and ReaxFF@<parameter set> for a ReaxFF one, the names being those the files define. The steps that use a forcefield (LAMMPS, Packmol) build it from the model chemistry with forcefield().

See lammps_step’s campaign of 2026-10-11 (forcefields as model chemistries).

forcefield_step.model_chemistry.RESERVED = ':@/|'#

Characters the model-chemistry grammar reserves

forcefield_step.model_chemistry.TYPES = ('FF', 'ReaxFF')#

The model-chemistry types this package offers

forcefield_step.model_chemistry.data_files(model_chemistry, node, local_only=True)[source]#

The files a job needs for a forcefield model chemistry, as the Forcefield step’s list_data_files: [(uri, path)] of the local: and personal: file and its includes (and the package’s, unless local_only).

forcefield_step.model_chemistry.defined_forcefields(path)[source]#

The names of the forcefields a .frc file defines (#define), in order; the first is the file’s default.

forcefield_step.model_chemistry.forcefield(model_chemistry, node=None)[source]#

The seamm_ff_util forcefield for a model chemistry, ready to use.

Parameters:

  • model_chemistry (dict) – The _model_chemistry wrapper of an FF or ReaxFF model chemistry offered by this package.

  • node (seamm.Node, optional) – The step using it: its data files (a job’s copies of local: and personal: files) and its references, which get the forcefield’s citations.

Return type:

seamm_ff_util.Forcefield

forcefield_step.model_chemistry.forcefield_files(root=None, data_path=None)[source]#

[(spec, path)] of the .frc files, the user’s first.

spec is what the Forcefield step calls the file: personal:<path> or local:<path> relative to its directory, or the path within the package’s data directory. Files that another .frc file includes (#include) are left out: they are parts of that forcefield – e.g. oplsaa.frc includes local:OPLS-AA/ligpargen.frc, whose parameters extend oplsaa+ – not forcefields of their own.

forcefield_step.model_chemistry.get_model_chemistry_options(periodic_only=False, mdi_only=False, root=None, data_path=None)[source]#

The forcefields as model chemistries.

Parameters:

  • periodic_only (bool) – Only those that handle periodic systems – all of them.

  • mdi_only (bool) – Only those launchable as MDI engines – none: LAMMPS evaluates the forcefield itself.

  • root (str or Path, optional) – The SEAMM installation; the current one by default.

  • data_path ([Path], optional) – A flowchart’s data directories (Node.data_path) to search instead of the default ones: in a job, its own copies of the files sent with it.

Returns:

Keyed by the model chemistry (FF@oplsaa+). Each entry has model_chemistry, type, description, file (the file as the Forcefield step names it), path, forcefield (the name in the file), source (personal, local or package), periodic_native, periodic_mdi and mdi_capable. A user’s forcefield of the same name as a bundled one is offered instead of it.

Return type:

dict

forcefield_step.model_chemistry.included_files(path)[source]#

What a .frc file includes, as (where, relative path): local for local: files (the user’s and the installation’s data directories), else package.

forcefield_step.model_chemistry.package_directory()[source]#

The directory of the forcefields shipped with this package.

forcefield_step.model_chemistry.source_directories(root=None, data_path=None)[source]#

[(source, directory)] searched for .frc files, in order.

personal is ~/.seamm.d/data/Forcefields; local the installation’s <root>/data/Forcefields and then the default installation’s ~/SEAMM/data/Forcefields. Given a flowchart’s data_path, the Forcefields directory in each of its directories instead – in a job this starts with the job’s own copies of the files sent with it.

forcefield_step.model_chemistry.type_and_method(name)[source]#

The model-chemistry type and method for a forcefield’s name.

reaxff/<set> is ReaxFF@<set>; any other forcefield is FF@<name> (oplsaa+ is FF@oplsaa+). The grammar’s reserved characters are replaced by - (dreiding/X6 is FF@dreiding-X6).

forcefield_step.model_chemistry.uri_handler(node=None)[source]#

A uri_handler for seamm_ff_util: local: includes are data files.

forcefield_step.tk_forcefield module#

The graphical part of a Forcefield step

class forcefield_step.tk_forcefield.TkForcefield(tk_flowchart=None, node=None, canvas=None, x=None, y=None, w=200, h=50)[source]#

Bases: TkNode

The graphical part of a forcefield step

create_dialog()[source]#

Create the dialog for editing the Forcefield flowchart

edit()[source]#

Present a dialog for editing this step’s parameters. We need to recreate the PeriodicTable for some reason

reset_dialog(widget=None)[source]#

Layout the widgets as needed for the current state

right_click(event)[source]#

Probably need to add our dialog…

update_potentials(elements)[source]#

Update the list of possible OpenKIM potentials as the element selection changes.

Module contents#

forcefield_step A step for choosing the default forcefield.