strain_step package

Submodules

strain_step.metadata module

This file contains metadata describing the results from the strain step

metadata[“results”] describes the results that this step can produce. It is a dictionary where the keys are the internal names of the results within this step, and the values are a dictionary describing the result. For example:

metadata["results"] = {
    "total_energy": {
        "calculation": [
            "energy",
            "optimization",
        ],
        "description": "The total energy",
        "dimensionality": "scalar",
        "methods": [
            "ccsd",
            "ccsd(t)",
            "dft",
            "hf",
        ],
        "property": "total energy#strain#{model}",
        "type": "float",
        "units": "E_h",
    },
}

The keys for the metadata are the following:

calculation[str]
Optional metadata describing what subtype of the step produces this result. The subtypes are completely arbitrary, but often they are types of calculations which is why this is name calculation. To use this, the step or a substep define self._calculation as a value. That value is used to select only the results with that value in this field.

descriptionstr
A human-readable description of the result.

dimensionalitystr
The dimensions of the data. The value can be “scalar” or an array definition of the form “[dim1, dim2,…]”. Symmetric tringular matrices are denoted “triangular[n,n]”. The dimensions can be integers, other scalar results, or standard parameters such as n_atoms. For example, ‘[3]’, [3, n_atoms], or “triangular[n_aos, n_aos]”.

methodsstr
Optional metadata like the calculation data. methods provides a second level of filtering, often used for the Hamiltionian for ab initio calculations where some properties may or may not be calculated depending on the type of theory.

propertystr
An optional definition of the property for storing this result. Must be one of the standard properties defined either in SEAMM or in this steps property metadata in data/properties.csv.

typestr
The type of the data: string, integer, or float.

unitsstr
Optional units for the result. If present, the value should be in these units.

strain_step.metadata.metadata = {}: Properties that Strain produces.

strain_step.strain module

Non-graphical part of the Strain step in a SEAMM flowchart

class strain_step.strain.Strain(flowchart=None, title='Strain', extension=None, logger=<Logger strain_step.strain (WARNING)>)[source]

Bases: Node

The non-graphical part of a Strain step in a flowchart.

parser

The parser object.

Type:: configargparse.ArgParser

options

It contains a two item tuple containing the populated namespace and the list of remaining argument strings.

Type:: tuple

subflowchart

A SEAMM Flowchart object that represents a subflowchart, if needed.

Type:: seamm.Flowchart

parameters

The control parameters for Strain.

Type:: StrainParameters

See also

TkStrain, Strain, StrainParameters

analyze(indent='', **kwargs)[source]

Do any analysis of the output from this step.

Also print important results to the local step.out file using “printer”.

Parameters:: indent (str) – An extra indentation for the output

description_text(P=None)[source]

Create the text description of what this step will do. The dictionary of control values is passed in as P so that the code can test values, etc.

Parameters:: P (dict) – An optional dictionary of the current values of the control parameters.
Returns:: A description of the current step.
Return type:: str

property git_revision: The git version of this module.

run()[source]

Run a Strain step.

Parameters:: None –
Returns:: The next node object in the flowchart.
Return type:: seamm.Node

property version: The semantic version of this module.

strain_step.strain_parameters module

Control parameters for the Strain step in a SEAMM flowchart.

class strain_step.strain_parameters.StrainParameters(defaults={}, data=None)[source]

Bases: Parameters

The control parameters for Strain.

The developer will add a dictionary of Parameters to this class. The keys are parameters for the current plugin, which themselves might be dictionaries.

You need to replace the “time” example below with one or more definitions of the control parameters for your plugin and application.

parameters{str: {str: str}}: A dictionary containing the parameters for the current step. Each key of the dictionary is a dictionary that contains the the following keys: kind, default, default_units, enumeration, format_string, description and help text.
parameters[“kind”]: custom: Specifies the kind of a variable. While the “kind” of a variable might be a numeric value, it may still have enumerated custom values meaningful to the user. For instance, if the parameter is a convergence criterion for an optimizer, custom values like “normal”, “precise”, etc, might be adequate. In addition, any parameter can be set to a variable of expression, indicated by having “$” as the first character in the field. For example, $OPTIMIZER_CONV.
parameters[“default”]“integer” or “float” or “string” or “boolean” or: “enum” The default value of the parameter, used to reset it.
parameters[“default_units”]str: The default units, used for resetting the value.
parameters[“enumeration”]: tuple: A tuple of enumerated values.
parameters[“format_string”]: str: A format string for “pretty” output.
parameters[“description”]: str: A short string used as a prompt in the GUI.
parameters[“help_text”]: tuple: A longer string to display as help for the user.

See also

Strain, TkStrain, Strain, StrainParameters, StrainStep

Examples

parameters = {
    "time": {
        "default": 100.0,
        "kind": "float",
        "default_units": "ps",
        "enumeration": tuple(),
        "format_string": ".1f",
        "description": "Simulation time:",
        "help_text": ("The time to simulate in the dynamics run.")
    },
}

parameters = {'strain_xx': {'default': 0.0, 'default_units': '', 'description': 'ε(xx) = ε₁:', 'enumeration': (), 'format_string': '.3f', 'help_text': 'Strain in the XX direction.', 'kind': 'float'}, 'strain_xy': {'default': 0.0, 'default_units': '', 'description': '2ε(xy) = ε₆:', 'enumeration': (), 'format_string': '.3f', 'help_text': 'Strain in the XY direction.', 'kind': 'float'}, 'strain_xz': {'default': 0.0, 'default_units': '', 'description': '2ε(xz) = ε₅:', 'enumeration': (), 'format_string': '.3f', 'help_text': 'Strain in the XZ direction.', 'kind': 'float'}, 'strain_yy': {'default': 0.0, 'default_units': '', 'description': 'ε(yy) = ε₂:', 'enumeration': (), 'format_string': '.3f', 'help_text': 'Strain in the YY direction.', 'kind': 'float'}, 'strain_yz': {'default': 0.0, 'default_units': '', 'description': '2ε(yz) = ε₄:', 'enumeration': (), 'format_string': '.3f', 'help_text': 'Strain in the YZ direction.', 'kind': 'float'}, 'strain_zz': {'default': 0.0, 'default_units': '', 'description': 'ε(zz) = ε₃:', 'enumeration': (), 'format_string': '.3f', 'help_text': 'Strain in the ZZ direction.', 'kind': 'float'}}

strain_step.strain_step module

class strain_step.strain_step.StrainStep(flowchart=None, gui=None)[source]

Bases: object

Helper class needed for the stevedore integration.

This must provide a description() method that returns a dict containing a description of this node, and create_node() and create_tk_node() methods for creating the graphical and non-graphical nodes.

my_description{description, group, name}: A human-readable description of this step. It can be several lines long, and needs to be clear to non-expert users. It contains the following keys: description, group, name.
my_description[“description”]tuple: A description of the Strain step. It must be clear to non-experts.
my_description[“group”]str: Which group in the menus to put this step. If the group does not exist it will be created. Common groups are “Building”, “Calculations”, “Control” and “Data”.
my_description[“name”]str: The name of this step, to be displayed in the menus.

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

Create and return the new node object.

Parameters:

flowchart (seamm.Node) – A non-graphical SEAMM node
**kwargs (keyworded arguments) – Various keyworded arguments such as title, namespace or extension representing the title displayed in the flowchart, the namespace for the plugins of a subflowchart and the extension, respectively.

Return type:

Strain

See also

Strain

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

Create and return the graphical Tk node object.

Parameters:

canvas (tk.Canvas) – The Tk Canvas widget
**kwargs (keyworded arguments) – Various keyworded arguments such as tk_flowchart, node, x, y, w, h representing a graphical flowchart object, a non-graphical node for a step, and dimensions of the graphical node.

Return type:

TkStrain

See also

TkStrain

description()[source]: Return a description of what this extension does.

my_description = {'description': 'A plug-in for straining systems', 'group': 'Building', 'name': 'Strain'}

strain_step.tk_strain module

The graphical part of a Strain step

class strain_step.tk_strain.TkStrain(tk_flowchart=None, node=None, canvas=None, x=None, y=None, w=200, h=50)[source]

Bases: TkNode

The graphical part of a Strain step in a flowchart.

tk_flowchart

The flowchart that we belong to.

Type:: TkFlowchart = None

node

The corresponding node of the non-graphical flowchart

Type:: Node = None

namespace

The namespace of the current step.

Type:: str

tk_subflowchart

A graphical Flowchart representing a subflowchart

Type:: TkFlowchart

canvas

The Tk Canvas to draw on

Type:: tkCanvas = None

dialog

The Pmw dialog object

Type:: Dialog

x

The x-coordinate of the center of the picture of the node

Type:: int = None

y

The y-coordinate of the center of the picture of the node

Type:: int = None

w

The width in pixels of the picture of the node

Type:: int = 200

h

The height in pixels of the picture of the node

Type:: int = 50

self[widget]

A dictionary of tk widgets built using the information contained in Strain_parameters.py

Type:: dict

See also

Strain, TkStrain, StrainParameters

create_dialog()[source]

Create the dialog. A set of widgets will be chosen by default based on what is specified in the Strain_parameters module.

Parameters:: None –
Return type:: None

See also

TkStrain.reset_dialog

edit()[source]

Present a dialog for editing the Strain input

Parameters:: None –
Return type:: None

See also

TkStrain.right_click

handle_dialog(result)[source]

Handle the closing of the edit dialog

What to do depends on the button used to close the dialog. If the user closes it by clicking the “x” of the dialog window, None is returned, which we take as equivalent to cancel.

Parameters:: result (None or str) – The value of this variable depends on what the button the user clicked.
Return type:: None

handle_help()[source]

Shows the help to the user when click on help button.

Parameters:: None –
Return type:: None

reset_dialog(widget=None)[source]

Layout the widgets in the dialog.

The widgets are chosen by default from the information in Strain_parameter.

This function simply lays them out row by row with aligned labels. You may wish a more complicated layout that is controlled by values of some of the control parameters. If so, edit or override this method

Parameters:: widget (Tk Widget = None) –
Return type:: None

See also

TkStrain.create_dialog

right_click(event)[source]

Handles the right click event on the node.

Parameters:: event (Tk Event) –
Return type:: None

See also

TkStrain.edit

Module contents

strain_step A SEAMM plug-in for straining periodic systems