thermochemistry_step package#

Submodules#

thermochemistry_step.metadata module#

This file contains metadata describing the results from Thermochemistry

thermochemistry_step.metadata.metadata = {'results': {'E thermal': {'description': 'the thermal correction to the electronic energy', 'dimensionality': '[nPs*[nTs]]', 'format': '.6f', 'type': 'float', 'units': 'kJ/mol'}, 'G': {'description': 'The free energy of the system', 'dimensionality': 'scalar', 'format': '.6f', 'property': 'G#Thermochemistry#{model}', 'type': 'float', 'units': 'kJ/mol'}, 'G thermal': {'description': 'the free energy correction to the electronic energy', 'dimensionality': '[nPs*[nTs]]', 'format': '.6f', 'type': 'float', 'units': 'kJ/mol'}, 'H': {'description': 'The enthalpy of the system', 'dimensionality': 'scalar', 'format': '.6f', 'property': 'H#Thermochemistry#{model}', 'type': 'float', 'units': 'kJ/mol'}, 'H 0': {'description': 'the electronic energy plus ZPE', 'dimensionality': 'scalar', 'format': '.6f', 'property': 'H(0 K)#Thermochemistry#{model}', 'type': 'float', 'units': 'kJ/mol'}, 'H thermal': {'description': 'the enthalpy correction to the electronic energy', 'dimensionality': '[nPs*[nTs]]', 'format': '.6f', 'type': 'float', 'units': 'kJ/mol'}, 'N saddle modes': {'description': 'Number of saddle point modes', 'dimensionality': 'scalar', 'format': '', 'property': 'number of saddle modes#Thermochemistry#{model}', 'type': 'integer'}, 'P': {'description': 'Pressure', 'dimensionality': '[nPs]', 'format': '.2f', 'property': 'P#Thermochemistry#{model}', 'type': 'float', 'units': 'atm'}, 'S': {'description': 'The entropy of the system', 'dimensionality': 'scalar', 'format': '.6f', 'property': 'S#Thermochemistry#{model}', 'type': 'float', 'units': 'kJ/mol/K'}, 'T': {'description': 'Temperature', 'dimensionality': '[nTs]', 'format': '.2f', 'property': 'T#Thermochemistry#{model}', 'type': 'float', 'units': 'K'}, 'U': {'description': 'the internal energy', 'dimensionality': 'scalar', 'format': '.6f', 'property': 'U#Thermochemistry#{model}', 'type': 'float', 'units': 'kJ/mol'}, 'ZPE': {'description': 'the zero point energy', 'dimensionality': 'scalar', 'format': '.6f', 'property': 'ZPE#Thermochemistry#{model}', 'type': 'float', 'units': 'kJ/mol'}, 'symmetry number': {'description': 'Symmetry number', 'dimensionality': 'scalar', 'format': '', 'type': 'integer'}, 'total_energy': {'description': 'The total energy', 'dimensionality': 'scalar', 'property': 'total energy#Thermochemistry#{model}', 'type': 'float', 'units': 'E_h'}, 'transition state frequency': {'description': 'Transition state curvature', 'dimensionality': 'scalar', 'format': '.1f', 'property': 'transition state frequency#Thermochemistry#{model}', 'type': 'float', 'units': 'cm^-1'}, 'vibrational frequencies': {'description': 'Vibrational frequencies', 'dimensionality': '[nvibs]', 'format': '.1f', 'property': 'vibrational frequencies#Thermochemistry#{model}', 'type': 'float', 'units': 'cm^-1'}}}#

Description of the computational models for Thermochemistry.

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

thermochemistry_step.thermochemistry module#

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

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

Bases: Node, ASE_mixin

The non-graphical part of a Thermochemistry 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 Thermochemistry.

Type:: ThermochemistryParameters

See also

TkThermochemistry, Thermochemistry, ThermochemistryParameters

analyze(_P, 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

description_text(P=None, short=False, natoms=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 Thermochemistry 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.

thermochemistry_step.thermochemistry_parameters module#

Control parameters for the Thermochemistry step in a SEAMM flowchart

class thermochemistry_step.thermochemistry_parameters.ThermochemistryParameters(defaults={}, data=None)[source]#

Bases: Parameters

The control parameters for Thermochemistry.

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

Thermochemistry, TkThermochemistry, Thermochemistry, ThermochemistryParameters, ThermochemistryStep

parameters = {'# imaginary modes': {'default': 'perceive', 'default_units': '', 'description': 'Number of imaginary modes:', 'enumeration': ('perceive', 'transition state'), 'format_string': '', 'help_text': 'The number of imaginary modes to ignore.', 'kind': 'integer'}, 'P': {'default': '1.0', 'default_units': 'bar', 'description': 'Pressures:', 'enumeration': (), 'format_string': '', 'help_text': 'The pressures for the thermodynamic functions.', 'kind': 'string'}, 'T': {'default': '200, 250, 298.15, 300:1000:50', 'default_units': 'K', 'description': 'Temperatures:', 'enumeration': (), 'format_string': '', 'help_text': 'The temperatures for the thermodynamic functions.', 'kind': 'string'}, 'approach': {'default': 'Harmonic approximation', 'default_units': '', 'description': 'Approach:', 'enumeration': ('Harmonic approximation',), 'format_string': '', 'help_text': 'The approach or method for determining the thermochemistry.', 'kind': 'enum'}, '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'}, 'print frequencies': {'default': 'all', 'default_units': '', 'description': 'Maximum frequencies to print:', 'enumeration': ('all', 'none'), 'format_string': '', 'help_text': 'Whether to print the frequencies of vibration.', 'kind': 'integer'}, 'results': {'default': {}, 'default_units': None, 'description': 'results', 'enumeration': (), 'format_string': '', 'help_text': 'The results to save to variables or in tables.', 'kind': 'dictionary'}, 'spin multiplicity': {'default': 'from system', 'default_units': '', 'description': 'Spin multiplicity:', 'enumeration': ('from system', 'singlet', 'doublet', 'triplet', 'quartet', 'quintet', 'sextet', 'septet', 'octet'), 'format_string': '', 'help_text': 'The spin multiplicity of the system as word or integer.', 'kind': 'string'}, 'step size': {'default': 0.01, 'default_units': 'Å', 'description': 'Step size:', 'enumeration': (), 'format_string': '.g', 'help_text': 'The size of the step for finite differences.', 'kind': 'float'}, 'symmetry number': {'default': 'from system', 'default_units': '', 'description': 'Symmetry number:', 'enumeration': ('from system',), 'format_string': '', 'help_text': 'The symmetry number of the system.', 'kind': 'integer'}}#

thermochemistry_step.thermochemistry_step module#

class thermochemistry_step.thermochemistry_step.ThermochemistryStep(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 Thermochemistry 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:

Thermochemistry

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:

TkThermochemistry

description()[source]#

Return a description of what this step does.

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

my_description = {'description': 'An step for predicting thermochemistry', 'group': 'Properties', 'name': 'Thermochemistry'}#

thermochemistry_step.tk_thermochemistry module#

The graphical part of a Thermochemistry step

class thermochemistry_step.tk_thermochemistry.TkThermochemistry(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 Thermochemistry 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 Thermochemistry_parameters.py

Type:: dict

See also

Thermochemistry, TkThermochemistry, ThermochemistryParameters

create_dialog()[source]#

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

Parameters:: None
Return type:: None

See also

TkThermochemistry.reset_dialog

reset_dialog(widget=None)[source]#

Layout the widgets in the dialog.

The widgets are chosen by default from the information in Thermochemistry 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

TkThermochemistry.create_dialog

reset_thermochemistry_frame(widget=None)[source]#: Layout the widgets in the thermochemistry 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

TkThermochemistry.edit

Module contents#

thermochemistry_step A SEAMM plug-in for Thermochemistry

thermochemistry_step package#

Submodules#

thermochemistry_step.metadata module#

thermochemistry_step.thermochemistry module#

thermochemistry_step.thermochemistry_parameters module#

thermochemistry_step.thermochemistry_step module#

thermochemistry_step.tk_thermochemistry module#

Module contents#

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