ogstools.ogs6py package

class ogstools.ogs6py.Project

Bases: object

Class for handling an OGS6 project.

In this class everything for an OGS6 project can be specified.

Parameters

output_filestr, optional

Filename of the output project file Default: default.prj

input_filestr, optional

Filename of the input project file

xml_stringstr,optional

String containing the XML tree

OMP_NUM_THREADSint, optional

Sets the environmentvariable before OGS execution to restrict number of OMP Threads

verbosebool, optional

Default: False

__init__(**args)

add_element(parent_xpath='./', tag=None, text=None, attrib_list=None, attrib_value_list=None)

General method to add an Entry.

An element is a single tag containing ‘text’, attributes and anttribute values.

Parameters

parent_xpathstr, optional

XPath of the parent tag

tagstr

tag name

textstr, int or float

content

attribstr

attribute keyword

attrib_valuestr, int or float

value of the attribute keyword

add_include(parent_xpath='./', file='')

Add include element.

Parameters

parent_xpathstr, optional

XPath of the parent tag

filestr

file name

add_block(blocktag, block_attrib=None, parent_xpath='./', taglist=None, textlist=None)

General method to add a Block.

A block consists of an enclosing tag containing a number of subtags retaining a key-value structure.

Parameters

blocktagstr

name of the enclosing tag

block_attrib‘dict’, optional

attributes belonging to the blocktag

parent_xpathstr, optional

XPath of the parent tag

taglistlist

list of strings containing the keys

textlistlist

list of strings, ints or floats retaining the corresponding values

deactivate_property(name, mediumid=0, phase=None)

Replaces MPL properties by a comment.

Parameters

mediumidint

id of the medium

phasestr

name of the phase

namestr

property name

deactivate_parameter(name)

Replaces parameters by a comment.

Parameters

namestr

property name

remove_element(xpath, tag=None, text=None)

Removes an element.

Parameters

xpath : str tag : str text : str

replace_text(value, xpath='.', occurrence=-1)

General method for replacing text between opening and closing tags.

Parameters

valuestr/any

Text

xpathstr, optional

XPath of the tag

occurrenceint, optional

Easy way to address nonunique XPath addresses by their occurrence from the top of the XML file Default: -1

replace_block_by_include(xpath='./', filename='include.xml', occurrence=0)

General method for replacing a block by an include.

Parameters

xpathstr, optional

XPath of the tag

filenamestr, optional

name of the include file

occurrenceint, optional

Addresses nonunique XPath by their occurece

replace_mesh(oldmesh, newmesh)

Method to replace meshes.

Parameters

oldmesh : str newmesh : str

replace_parameter(name='', parametertype='', taglist=None, textlist=None)

Replacing parametertypes and values.

Parameters

namestr

parametername

parametertypestr

parametertype

taglistlist

list of tags needed for parameter spec

textlistlist

values of parameter

replace_parameter_value(name='', value=0, valuetag='value')

Replacing parameter values.

Parameters

namestr

parametername

valuestr

value

parametertypestr

parameter type

valuetagstr, optional

name of the tag containing the value, e.g., values Default: value

replace_phase_property_value(mediumid=0, phase='AqueousLiquid', component=None, name='', value=0, propertytype='Constant', valuetag='value')

Replaces properties in medium phases.

Parameters

mediumidint

id of the medium

phasestr

name of the phase

componentstr

name of the component

namestr

property name

valuestr/any

value

propertytypestr

type of the property

valuetagstr/any

name of the tag containing the value, e.g., values Default: value

replace_medium_property_value(mediumid=0, name='', value=0, propertytype='Constant', valuetag='value')

Replaces properties in medium (not belonging to any phase).

Parameters

mediumidint

id of the medium

namestr

property name

valuestr/any

value

propertytypestr

type of the property

valuetagstr/any

name of the tag containing the value, e.g., values Default: value

set(**args)

Sets directly a uniquely defined property. List of properties is given in the dictory below.

restart(restart_suffix='_restart', t_initial=None, t_end=None, zero_displacement=False)

Prepares the project file for a restart.

Takes the last time step from the PVD file mentioned in the PRJ file. Sets initial conditions accordingly.

Parameters

restart_suffixstr,

suffix by which the output prefix is appended

t_initialfloat, optional

first time step, takes the last from previous simulation if None

t_endfloat, optional

last time step, the same as in previous run if None

zero_displacement: bolean, False

sets the initial displacement to zero if True

run_model(logfile=Path('out.log'), path=None, args=None, container_path=None, wrapper=None, write_logs=True, write_prj_to_pvd=True)

Command to run OGS.

Runs OGS with the project file specified as output_file.

Parameters

logfilestr, optional

Name of the file to write STDOUT of ogs Default: out

pathstr, optional

Path of the directory in which the ogs executable can be found. If container_path is given: Path to the directory in which the Singularity executable can be found.

argsstr, optional

additional arguments for the ogs executable

container_pathstr, optional

Path of the OGS container file.

wrapperstr, optional

add a wrapper command. E.g. mpirun

write_logs: bolean, optional

set False to omit logging

write_input(keep_includes=False)

Writes the projectfile to disk.

Parameters

keep_includes : boolean, optional

property_dataframe(mediamapping=None)

Returns a dataframe containing most properties defined in the Material Property (MPL) section of the input file.

Parameters

mediamapping : dict, optional

Return type:

DataFrame

write_property_latextable(latexfile=Path('property_dataframe.tex'), mediamapping=None, float_format='{:.2e}')

Write material properties to disc as latex table.

Parameters

latexfile : str mediamapping : dict, optional float_format : str

Submodules

• ogstools.ogs6py.build_tree module
  • BuildTree
    • BuildTree.__init__()
    • BuildTree.populate_tree()
    • BuildTree.get_child_tag()
    • BuildTree.get_child_tag_for_type()
• ogstools.ogs6py.curves module
  • Curves
    • Curves.__init__()
    • Curves.add_curve()
• ogstools.ogs6py.display module
  • Display
    • Display.__init__()
• ogstools.ogs6py.geo module
  • Geo
    • Geo.__init__()
    • Geo.add_geometry()
• ogstools.ogs6py.linsolvers module
  • LinSolvers
    • LinSolvers.__init__()
    • LinSolvers.add_lin_solver()
• ogstools.ogs6py.local_coordinate_system module
  • LocalCoordinateSystem
    • LocalCoordinateSystem.__init__()
    • LocalCoordinateSystem.add_basis_vec()
• ogstools.ogs6py.media module
  • Media
    • Media.__init__()
    • Media.add_property()
• ogstools.ogs6py.mesh module
  • Mesh
    • Mesh.__init__()
    • Mesh.add_mesh()
• ogstools.ogs6py.nonlinsolvers module
  • NonLinSolvers
    • NonLinSolvers.__init__()
    • NonLinSolvers.add_non_lin_solver()
• ogstools.ogs6py.parameters module
  • Parameters
    • Parameters.__init__()
    • Parameters.add_parameter()
• ogstools.ogs6py.processes module
  • Processes
    • Processes.__init__()
    • Processes.add_process_variable()
    • Processes.add_secondary_variable()
    • Processes.set_process()
    • Processes.set_constitutive_relation()
    • Processes.add_bhe_type()
    • Processes.add_bhe_component()
    • Processes.add_surfaceflux()
• ogstools.ogs6py.processvars module
  • ProcessVars
    • ProcessVars.__init__()
    • ProcessVars.set_ic()
    • ProcessVars.add_bc()
    • ProcessVars.add_st()
• ogstools.ogs6py.project module
  • Project
    • Project.__init__()
    • Project.add_element()
    • Project.add_include()
    • Project.add_block()
    • Project.deactivate_property()
    • Project.deactivate_parameter()
    • Project.remove_element()
    • Project.replace_text()
    • Project.replace_block_by_include()
    • Project.replace_mesh()
    • Project.replace_parameter()
    • Project.replace_parameter_value()
    • Project.replace_phase_property_value()
    • Project.replace_medium_property_value()
    • Project.set()
    • Project.restart()
    • Project.run_model()
    • Project.write_input()
    • Project.property_dataframe()
    • Project.write_property_latextable()
• ogstools.ogs6py.properties module
  • Value
    • Value.medium
    • Value.value
    • Value.__init__()
  • Property
    • Property.title
    • Property.symbol
    • Property.unit
    • Property.value
    • Property.__init__()
  • PropertySet
    • PropertySet.property
    • PropertySet.__init__()
• ogstools.ogs6py.python_script module
  • PythonScript
    • PythonScript.__init__()
    • PythonScript.set_pyscript()
• ogstools.ogs6py.timeloop module
  • TimeLoop
    • TimeLoop.__init__()
    • TimeLoop.add_process()
    • TimeLoop.set_stepping()
    • TimeLoop.add_output()
    • TimeLoop.add_time_stepping_pair()
    • TimeLoop.add_output_pair()
    • TimeLoop.add_global_process_coupling()