thermomechanical_step package#

Submodules#

thermomechanical_step.metadata module#

This file contains metadata describing the results from Thermomechanical step

thermomechanical_step.metadata.metadata = {'results': {'A - U0': {'description': 'Helmholtz free energy', 'dimensionality': 'nTs', 'property': 'A - U0#Thermomechanical#{model}', 'type': 'json', 'units': 'kJ/mol'}, 'Cij': {'description': 'elastic constants', 'dimensionality': '[6][6]', 'type': 'float', 'units': 'GPa'}, 'Cv': {'description': 'Constant volume heat capacity', 'dimensionality': 'nTs', 'property': 'Cv#Thermomechanical#{model}', 'type': 'json', 'units': 'J/mol/K'}, 'Eh': {'description': 'Hill Young modulus', 'dimensionality': 'scalar', 'property': 'Young modulus#Thermomechanical#{model}', 'type': 'float', 'units': 'GPa'}, 'Er': {'description': 'Reuss Young modulus', 'dimensionality': 'scalar', 'type': 'float', 'units': 'GPa'}, 'Ev': {'description': 'Voigt Young modulus', 'dimensionality': 'scalar', 'type': 'float', 'units': 'GPa'}, 'Gh': {'description': 'Hill shear modulus', 'dimensionality': 'scalar', 'property': 'shear modulus#Thermomechanical#{model}', 'type': 'float', 'units': 'GPa'}, 'Gr': {'description': 'Reuss shear modulus', 'dimensionality': 'scalar', 'type': 'float', 'units': 'GPa'}, 'Gruneisen parameter': {'description': 'Gruneisen parameter', 'dimensionality': 'scalar', 'property': 'Gruneisen parameter#Thermomechanical#{model}', 'type': 'float', 'units': ''}, 'Gv': {'description': 'Voigt shear modulus', 'dimensionality': 'scalar', 'type': 'float', 'units': 'GPa'}, 'Hv_chen': {'description': 'Vickers hardness [Chen]', 'dimensionality': 'scalar', 'property': 'Vickers hardness [Chen]#Thermomechanical#{model}', 'type': 'float', 'units': ''}, 'Hv_tian': {'description': 'Vickers hardness [Tian]', 'dimensionality': 'scalar', 'property': 'Vickers hardness [Tian]#Thermomechanical#{model}', 'type': 'float', 'units': ''}, 'Kh': {'description': 'Hill bulk modulus', 'dimensionality': 'scalar', 'property': 'bulk modulus#Thermomechanical#{model}', 'type': 'float', 'units': 'GPa'}, 'Kr': {'description': 'Reuss bulk modulus', 'dimensionality': 'scalar', 'type': 'float', 'units': 'GPa'}, 'Kv': {'description': 'Voigt bulk modulus', 'dimensionality': 'scalar', 'type': 'float', 'units': 'GPa'}, 'P': {'description': 'Pressure', 'dimensionality': '[nPs]', 'format': '.2f', 'property': 'P#Thermomechanical#{model}', 'type': 'float', 'units': 'atm'}, 'Pcauchy': {'description': 'Cauchy pressure', 'dimensionality': 'scalar', 'property': 'Pcauchy#Thermomechanical#{model}', 'type': 'float', 'units': 'GPa'}, 'S': {'description': 'Entropy', 'dimensionality': 'nTs', 'property': 'S#Thermomechanical#{model}', 'type': 'json', 'units': 'J/mol/K'}, 'Sij': {'description': 'compliance matrix', 'dimensionality': '[6][6]', 'type': 'float', 'units': '1/GPa'}, 'T': {'description': 'Temperature', 'dimensionality': '[nTs]', 'format': '.2f', 'property': 'T#Thermomechanical#{model}', 'type': 'float', 'units': 'K'}, 'Td': {'description': 'Debye temperature', 'dimensionality': 'scalar', 'property': 'Debye temperature#Thermomechanical#{model}', 'type': 'float', 'units': 'K'}, 'U - U0': {'description': 'Internal energy', 'dimensionality': 'nTs', 'property': 'U - U0#Thermomechanical#{model}', 'type': 'json', 'units': 'kJ/mol'}, 'alpha': {'description': 'Linear coefficient of thermal expansion', 'dimensionality': 'nTs', 'property': 'alpha#Thermomechanical#{model}', 'type': 'json', 'units': '1/K'}, 'alpha(V)': {'description': 'volumetric coefficient of thermal expansion', 'dimensionality': 'scalar', 'format': '.2g', 'type': 'float', 'units': '1/K'}, 'alpha(a)': {'description': 'linear coefficient of thermal expansion in cell a', 'dimensionality': 'scalar', 'format': '.2g', 'type': 'float', 'units': '1/K'}, 'alpha(b)': {'description': 'linear coefficient of thermal expansion in cell b', 'dimensionality': 'scalar', 'format': '.2g', 'type': 'float', 'units': '1/K'}, 'alpha(c)': {'description': 'linear coefficient of thermal expansion in cell c', 'dimensionality': 'scalar', 'format': '.2g', 'type': 'float', 'units': '1/K'}, 'k_pugh': {'description': "Pugh's ductility criterion", 'dimensionality': 'scalar', 'property': "Pugh's ductility criterion#Thermomechanical#{model}", 'type': 'float', 'units': ''}, 'mu_h': {'description': 'Hill Poisson ratio', 'dimensionality': 'scalar', 'property': 'Poisson ratio#Thermomechanical#{model}', 'type': 'float', 'units': ''}, 'mu_r': {'description': 'Reuss Poisson ratio', 'dimensionality': 'scalar', 'type': 'float', 'units': ''}, 'mu_v': {'description': 'Voigt Poisson ratio', 'dimensionality': 'scalar', 'type': 'float', 'units': ''}, 'stress': {'description': 'stress', 'dimensionality': '[6]', 'type': 'float', 'units': 'GPa'}, 'vl': {'description': 'longitudinal sound velocity', 'dimensionality': 'scalar', 'property': 'longitudinal sound velocity#Thermomechanical#{model}', 'type': 'float', 'units': 'm/s'}, 'vm': {'description': 'mean sound velocity', 'dimensionality': 'scalar', 'property': 'mean sound velocity#Thermomechanical#{model}', 'type': 'float', 'units': 'm/s'}, 'vt': {'description': 'transverse sound velocity', 'dimensionality': 'scalar', 'property': 'transverse sound velocity#Thermomechanical#{model}', 'type': 'float', 'units': 'm/s'}}}#

Description of the computational models for Thermomechanical.

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",
                    },
                },
            },
        },
    },
}

thermomechanical_step.thermomechanical module#

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

class thermomechanical_step.thermomechanical.Thermomechanical(flowchart=None, title='Thermomechanical', namespace='org.molssi.seamm', extension=None, logger=<Logger thermomechanical_step.thermomechanical (WARNING)>)[source]#

Bases: Node

The non-graphical part of a Thermomechanical 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 Thermomechanical.

Type:: ThermomechanicalParameters

See also

TkThermomechanical, Thermomechanical, ThermomechanicalParameters

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

create_parser()[source]#: Setup the command-line / config file parser

debye_model(Td, Ts, N=1)[source]#: Compute the thermodynamic functions from the Debye model

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 the Thermomechanical step.

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

set_id(node_id=())[source]#: Sequentially number the subnodes

set_subids(node_id=())[source]#: Set the ids of the nodes in the subflowchart

property version#: The semantic version of this module.

thermomechanical_step.thermomechanical.round_value(value, digits=3)[source]#: Round a value to the given number of digits accuracy

thermomechanical_step.thermomechanical_parameters module#

Control parameters for the Thermomechanical step in a SEAMM flowchart

class thermomechanical_step.thermomechanical_parameters.ThermomechanicalParameters(defaults={}, data=None)[source]#

Bases: Parameters

The control parameters for Thermomechanical.

You need to replace the “time” entry in dictionary below these comments with the definitions of parameters to control this step. The keys are parameters for the current plugin,the values are dictionaries as outlined below.

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{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:

parameters[“default”] :

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

parameters[“kind”]enum()

Specifies the kind of a variable. One of “integer”, “float”, “string”, “boolean”, or “enum”

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_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”]str

A longer string to display as help for the user.

See also

Thermomechanical, TkThermomechanical, Thermomechanical, ThermomechanicalParameters, ThermomechanicalStep

parameters = {'P': {'default': '1.0', 'default_units': 'atm', 'description': 'Pressures:', 'enumeration': (), 'format_string': '', 'help_text': 'The pressures for the thermomechanical properties.', 'kind': 'string'}, 'T': {'default': '298.15', 'default_units': 'K', 'description': 'Temperatures:', 'enumeration': (), 'format_string': '', 'help_text': 'The temperatures for the thermomechanical properties.', 'kind': 'string'}, 'elastic constants': {'default': 'no', 'default_units': '', 'description': 'Calculate elastic constants:', 'enumeration': ('yes', 'no'), 'format_string': '', 'help_text': 'Whether to calculate the elastic constants.', 'kind': 'boolean'}, 'on error': {'default': 'keep all subdirectories', 'default_units': '', 'description': 'On error:', 'enumeration': ('keep last subdirectory', 'keep all subdirectories', 'delete all subdirectories'), 'format_string': '', 'help_text': 'Which subdirectories to keep if there is an error.', 'kind': 'enum'}, 'on success': {'default': 'keep last subdirectory', 'default_units': '', 'description': 'On success:', 'enumeration': ('keep last subdirectory', 'keep all subdirectories', 'delete all subdirectories'), 'format_string': '', 'help_text': 'Which subdirectories to keep.', 'kind': 'enum'}, 'results': {'default': {}, 'default_units': None, 'description': 'results', 'enumeration': (), 'format_string': '', 'help_text': 'The results to save to variables or in tables.', 'kind': 'dictionary'}, 'state point definition': {'default': 'as given', 'default_units': '', 'description': 'Enter state points as:', 'enumeration': ('as given', 'lists of Ps and Ts', 'list of P, T pairs'), 'format_string': '', 'help_text': 'How the state points will be defined', 'kind': 'enum'}, 'state points': {'default': '(298.15 K, 1 atm)', 'default_units': '', 'description': 'Temperatures:', 'enumeration': (), 'format_string': '', 'help_text': 'The temperatures for the thermomechanical properties.', 'kind': 'string'}, 'step size': {'default': 0.01, 'default_units': '', 'description': 'Strain step:', 'enumeration': (), 'format_string': '.2f', 'help_text': 'The size of the step in strain for elastic constants.', 'kind': 'float'}, 'thermochemistry Ts': {'default': '1:10,20:100:10,125:275:25,298.15,300:1000:50,1100:3000:100', 'default_units': '', 'description': 'Temperatures for thermochemistry (K):', 'enumeration': (), 'format_string': '', 'help_text': 'The temperatures for the thermochemistry properties.', 'kind': 'string'}}#

thermomechanical_step.thermomechanical_step module#

class thermomechanical_step.thermomechanical_step.ThermomechanicalStep(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.

The dictionary for the description is the class variable just below these comments. The felds are as follows:

my_description{str, str}
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 Thermomechanical 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”, “Control”, “Custom”, “Data”, and “Simulations”.

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 (keyword arguments) – Various keyword 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:

Thermomechanical

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

Create and return the graphical Tk node object.

Parameters:

canvas (tk.Canvas) – The Tk Canvas widget
**kwargs (keyword arguments) – Various keyword 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:

TkThermomechanical

description()[source]#

Return a description of what this step does.

Returns:: description
Return type:: dict(str, str)

my_description = {'description': 'An interface for calculating thermomechanical properties', 'group': 'Properties', 'name': 'Thermomechanical'}#

thermomechanical_step.tk_thermomechanical module#

The graphical part of a Thermomechanical step

class thermomechanical_step.tk_thermomechanical.TkThermomechanical(tk_flowchart=None, node=None, namespace='org.molssi.seamm.tk', canvas=None, x=None, y=None, w=200, h=50)[source]#

Bases: TkNode

The graphical part of a Thermomechanical 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

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 Thermomechanical_parameters.py

Type:: dict

See also

Thermomechanical, TkThermomechanical, ThermomechanicalParameters

create_dialog()[source]#

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

Parameters:: None
Return type:: None

See also

TkThermomechanical.reset_dialog

reset_dialog(widget=None)[source]#

Layout the widgets in the dialog.

The widgets are chosen by default from the information in Thermomechanical parameters.

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

TkThermomechanical.create_dialog

reset_thermomechanical_frame(widget=None)[source]#: Layout the widgets in the thermomechanical frame as needed for the current state

right_click(event)[source]#

Handles the right click event on the node.

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

See also

TkThermomechanical.edit

Module contents#

thermomechanical_step A SEAMM plug-in for calculating thermomechanical properties

thermomechanical_step package#

Submodules#

thermomechanical_step.metadata module#

thermomechanical_step.thermomechanical module#

thermomechanical_step.thermomechanical_parameters module#

thermomechanical_step.thermomechanical_step module#

thermomechanical_step.tk_thermomechanical module#

Module contents#

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