set_cell_step package#

Submodules#

set_cell_step.metadata module#

This file contains metadata describing the results from SetCell

set_cell_step.metadata.metadata = {'results': {'a': {'description': 'The cell parameter a', 'dimensionality': 'scalar', 'type': 'float', 'units': 'Å'}, 'alpha': {'description': 'The cell parameter alpha', 'dimensionality': 'scalar', 'type': 'float', 'units': 'degree'}, 'b': {'description': 'The cell parameter b', 'dimensionality': 'scalar', 'type': 'float', 'units': 'Å'}, 'beta': {'description': 'The cell parameter beta', 'dimensionality': 'scalar', 'type': 'float', 'units': 'degree'}, 'c': {'description': 'The cell parameter c', 'dimensionality': 'scalar', 'type': 'float', 'units': 'Å'}, 'density': {'description': 'The density', 'dimensionality': 'scalar', 'type': 'float', 'units': 'g/mL'}, 'gamma': {'description': 'The cell parameter gamma', 'dimensionality': 'scalar', 'type': 'float', 'units': 'degree'}, 'volume': {'description': 'The volume of the cell', 'dimensionality': 'scalar', 'type': 'float', 'units': 'Å^3'}}}#

Description of the computational models for SetCell.

Hamiltonians, approximations, and basis set or parameterizations, only if appropriate for this code. For example:

metadata["computational models"] = {
    "Hartree-Fock": {
        "models": {
            "PM7": {
                "parameterizations": {
                    "PM7": {
                        "elements": "1-60,62-83",
                        "periodic": True,
                        "reactions": True,
                        "optimization": True,
                        "code": "mopac",
                    },
                    "PM7-TS": {
                        "elements": "1-60,62-83",
                        "periodic": True,
                        "reactions": True,
                        "optimization": False,
                        "code": "mopac",
                    },
                },
            },
        },
    },
}

set_cell_step.set_cell module#

Non-graphical part of the Set Cell step in a SEAMM flowchart

class set_cell_step.set_cell.SetCell(flowchart=None, title='Set Cell', extension=None, logger=<Logger set_cell_step.set_cell (WARNING)>)[source]#

Bases: Node

The non-graphical part of a Set Cell 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 Set Cell.

Type:: SetCellParameters

See also

TkSetCell, SetCell, SetCellParameters

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 Set Cell step.

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

property version#: The semantic version of this module.

set_cell_step.set_cell.move_contents(configuration, parameters, how)[source]#

Set a new cell and move the contents with it.

Parameters:

configuration (molsystem._Configuration) – The periodic structure to change.
parameters ((a, b, c, alpha, beta, gamma)) – The new cell parameters, in Å and degrees.
how (str) – “molecule centers” to make each molecule whole and move it rigidly with its center of mass, keeping its bonds; “atoms” for an affine transformation of every atom.

set_cell_step.set_cell_parameters module#

Control parameters for the Set Cell step in a SEAMM flowchart

class set_cell_step.set_cell_parameters.SetCellParameters(defaults={}, data=None)[source]#

Bases: Parameters

The control parameters for Set Cell.

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#

‘format_string’, description’, help_text’}

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.

Type:: {‘kind’, ‘default’, ‘default_units’, ‘enumeration’,

parameters[]#

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.

Type:: custom

parameters[]#

‘enum’ The default value of the parameter, used to reset it.

Type:: ‘integer’ or ‘float’ or ‘string’ or ‘boolean’ or

parameters[]#

The default units, used for resetting the value.

Type:: str

parameters[]#

A tuple of enumerated values.

Type:: tuple

parameters[]#

A format string for ‘pretty’ output.

Type:: str

parameters[]#

A short string used as a prompt in the GUI.

Type:: str

parameters[]#

A longer string to display as help for the user.

Type:: tuple

See also

SetCell, TkSetCell, SetCell, SetCellParameters, Set

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 = {'a': {'applies_when': {'method': 'cell parameters'}, 'default': '10', 'default_units': 'Å', 'description': 'a:', 'enumeration': None, 'format_string': '.2f', 'help_text': 'The length of the first side of the cell.', 'kind': 'float'}, 'alpha': {'applies_when': {'method': 'cell parameters'}, 'default': 90.0, 'default_units': 'degree', 'description': 'alpha:', 'enumeration': None, 'format_string': '.1f', 'help_text': 'The angle between a and b.', 'kind': 'float'}, 'b': {'applies_when': {'method': 'cell parameters'}, 'default': '10', 'default_units': 'Å', 'description': 'b:', 'enumeration': None, 'format_string': '.2f', 'help_text': 'The length of the second side of the cell.', 'kind': 'float'}, 'beta': {'applies_when': {'method': 'cell parameters'}, 'default': 90.0, 'default_units': 'degree', 'description': 'beta:', 'enumeration': None, 'format_string': '.1f', 'help_text': 'The angle between a and c.', 'kind': 'float'}, 'c': {'applies_when': {'method': 'cell parameters'}, 'default': '10', 'default_units': 'Å', 'description': 'c:', 'enumeration': None, 'format_string': '.2f', 'help_text': 'The length of the third side of the cell.', 'kind': 'float'}, 'density': {'applies_when': {'method': 'density'}, 'default': '1', 'default_units': 'g/mL', 'description': 'Density:', 'enumeration': (), 'format_string': '.3f', 'help_text': 'The target density of the cell.', 'kind': 'float'}, 'expansion': {'applies_when': {'method': 'uniform contraction/expansion'}, 'default': '1%', 'default_units': None, 'description': 'Percent contraction (-)/expansion(+):', 'enumeration': (), 'format_string': '', 'help_text': 'The amount to contract (negative value) or expand (positive value). The change is proportional to current cell lengths and does not affect the angles.', 'kind': 'str'}, 'gamma': {'applies_when': {'method': 'cell parameters'}, 'default': 90.0, 'default_units': 'degree', 'description': 'gamma:', 'enumeration': None, 'format_string': '.1f', 'help_text': 'The angle between b and c.', 'kind': 'float'}, 'method': {'default': 'density', 'default_units': None, 'description': 'Adjust cell by:', 'enumeration': ('density', 'volume', 'the mean volume of the last NPT run', 'cell parameters', 'uniform contraction/expansion'), 'format_string': '', 'help_text': 'How to adjust the cell: to a density or volume, which may be variables; to the mean volume of the last NPT run earlier in the flowchart, over its equilibrated part; to given cell parameters; or by a uniform contraction or expansion.', 'kind': 'enumeration'}, 'scaling': {'default': 'automatic', 'default_units': None, 'description': 'Move the contents by:', 'enumeration': ('automatic', 'molecule centers', 'atoms'), 'format_string': '', 'help_text': "How the contents follow the cell. 'molecule centers' moves each molecule rigidly with its center of mass, as a liquid of molecules needs: scaling the atoms would stretch the bonds. 'atoms' scales every atom with the cell (an affine transformation), as for a solid. 'automatic' moves the molecules' centers when the system is made of separate molecules, none spanning the cell, and the atoms otherwise.", 'kind': 'enumeration'}, 'volume': {'applies_when': {'method': 'volume'}, 'default': '1000', 'default_units': 'Å^3', 'description': 'Volume:', 'enumeration': (), 'format_string': '.3f', 'help_text': 'The target volume of the cell.', 'kind': 'float'}}#

set_cell_step.set_cell_step module#

class set_cell_step.set_cell_step.SetCellStep(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#

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.

Type:: {description, group, name}

my_description[]#

A description of the Set Cell step. It must be clear to non-experts.

Type:: tuple

my_description[]#

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’.

Type:: str

my_description[]#

The name of this step, to be displayed in the menus.

Type:: str

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:

SetCell

See also

SetCell

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:

TkSetCell

See also

TkSetCell

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

my_description = {'description': 'An interface for Set Cell', 'group': 'Building', 'name': 'Set Cell'}#

set_cell_step.tk_set_cell module#

The graphical part of a Set Cell step

class set_cell_step.tk_set_cell.TkSetCell(tk_flowchart=None, node=None, canvas=None, x=None, y=None, w=200, h=50)[source]#

Bases: TkNode

The graphical part of a Set Cell 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

sub_tk_flowchart#

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 Set Cell_parameters.py

Type:: dict

See also

SetCell, TkSetCell, SetCellParameters

create_dialog()[source]#

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

Parameters:: None
Return type:: None

See also

TkSetCell.reset_dialog

edit()[source]#

Present a dialog for editing the Set Cell input

Parameters:: None
Return type:: None

See also

TkSetCell.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 Set Cell_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

TkSetCell.create_dialog

right_click(event)[source]#

Handles the right click event on the node.

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

See also

TkSetCell.edit

Module contents#

set_cell_step A plug-in for setting the periodic (unit) cell in a SEAMM flowchart