GEOS Utilities

The geos-utils python package defines utilities for all GEOS python packages including a logger, GEOS constants, basic functions, and unit management tools.

API

geos.utils.ConnectionSet module

Defines connection set and connection set collection data structures.

class geos.utils.ConnectionSet.ConnectionSet(cellIdRef, connectedCellIds)

Bases: object

Define connection set data structure.

A ConnectionSet stores information of connection between a reference cell and adjacent cells. Cell information relies on unique ids, and each connected cell is associated with a side according to connection face normal vector.

Parameters:

• cellIdRef (int) – reference cell id.

• connectedCellIds (int) – map of connected cell ids with the side.

addConnectedCells(connectedCellsToAdd)

Add connected cells to the existing map of connected cells.

The addConnectedCells() method adds element(s) to the dictionary if the cell Id is not in the dictionary. If the cell Id is in the dictionary, it updates the cell Id with the new side value.

Parameters:

connectedCellsToAdd (dict[int, bool]) – connected cells to add.

copy()

Create a deep copy of self.

Returns:

copy of ConnectionSet

Return type:

ConnectionSet

getCellIdRef()

Get the reference cell id.

Returns:

reference cell id.

Return type:

int

getConnectedCellIds()

Get connected cell ids.

Returns:

map of connected cell ids with side.

Return type:

int

setCellIdRef(cellIdRef)

Set the reference cell id.

Parameters:

cellIdRef (int) – reference cell id.

setConnectedCellIds(connectedCellIds)

Set the connected cell ids.

Parameters:

connectedCellIds (dict[int, bool]) – map of connected cell ids with side.

class geos.utils.ConnectionSet.ConnectionSetCollection

Bases: MutableSet

Define a collection of ConnectionSet.

Because ConnectionSet relies on cell unique id, the collection imposes uniqueness of reference cell id.

add(item)

Add a ConnectionSet to the collection.

Parameters:

item (ConnectionSet) – ConnectionSet to add.

addMultiple(items)

Add an iterable of ConnectionSet to the collection.

Parameters:

items (Iterable[ConnectionSet]) – list of ConnectionSet to add.

containsCellIdRef(cellIdRef)

Test if a ConnectionSet with cellIdRef is present in the collection.

Parameters:

cellIdRef (int) – reference cell id

Returns:

True if a ConnectionSet is present, False otherwise.

Return type:

bool

containsEqual(item)

Test if a ConnectionSet is present in the collection.

Both th reference cell id and connected cell dictionnary must match the input ConnectionSet.

Parameters:

item (ConnectionSet) – ConnectionSet to add.

discard(item)

Remove a ConnectionSet to the collection.

ConnectionSet is removed if both reference cell id and connected cell dictionnary match an element of the collection.

Parameters:

item (ConnectionSet) – ConnectionSet to remove.

discardCellIdRef(cellIdRef)

Remove a ConnectionSet to the collection using the reference cell id.

Parameters:

cellIdRef (int) – reference cell id to remove.

get(cellIdRef)

Get ConnectionSet from reference cell id.

Parameters:

cellIdRef (int) – reference cell id

Returns:

ConnectionSet with cellIdRef.

Return type:

Optional[ConnectionSet]

getReversedConnectionSetCollection()

Get the set of reversed connection set.

Returns:

reversed collection of ConnectionSet

Return type:

ConnectionSetCollection

replace(item)

Replace a ConnectionSet if another one with the same cellIdRef exists.

Parameters:

item (ConnectionSet) – ConnectionSet to add.

update(item)

Update or add a ConnectionSet to the collection.

Parameters:

item (ConnectionSet) – ConnectionSet

geos.utils.enumUnits module

class geos.utils.enumUnits.Density(value)

Bases: Enum

An enumeration.

G_PER_CUBIC_CENTIMETER = <geos.utils.enumUnits.Unit object>

KG_PER_CUBIC_METER = <geos.utils.enumUnits.Unit object>

POUND_PER_BBL = <geos.utils.enumUnits.Unit object>

class geos.utils.enumUnits.Length(value)

Bases: Enum

An enumeration.

FEET = <geos.utils.enumUnits.Unit object>

KILOMETER = <geos.utils.enumUnits.Unit object>

METER = <geos.utils.enumUnits.Unit object>

MILE = <geos.utils.enumUnits.Unit object>

class geos.utils.enumUnits.Mass(value)

Bases: Enum

An enumeration.

KG = <geos.utils.enumUnits.Unit object>

MEGATON = <geos.utils.enumUnits.Unit object>

POUND = <geos.utils.enumUnits.Unit object>

TON = <geos.utils.enumUnits.Unit object>

class geos.utils.enumUnits.MassRate(value)

Bases: Enum

An enumeration.

KG_PER_DAY = <geos.utils.enumUnits.Unit object>

KG_PER_HOUR = <geos.utils.enumUnits.Unit object>

KG_PER_SECOND = <geos.utils.enumUnits.Unit object>

MTPA = <geos.utils.enumUnits.Unit object>

TON_PER_DAY = <geos.utils.enumUnits.Unit object>

class geos.utils.enumUnits.NoUnit(value)

Bases: Enum

An enumeration.

SAME = <geos.utils.enumUnits.Unit object>

class geos.utils.enumUnits.Permeability(value)

Bases: Enum

An enumeration.

DARCY = <geos.utils.enumUnits.Unit object>

MILLI_DARCY = <geos.utils.enumUnits.Unit object>

SQUARE_METER = <geos.utils.enumUnits.Unit object>

class geos.utils.enumUnits.Pressure(value)

Bases: Enum

An enumeration.

BAR = <geos.utils.enumUnits.Unit object>

GPA = <geos.utils.enumUnits.Unit object>

KPA = <geos.utils.enumUnits.Unit object>

MPA = <geos.utils.enumUnits.Unit object>

PA = <geos.utils.enumUnits.Unit object>

PSI = <geos.utils.enumUnits.Unit object>

class geos.utils.enumUnits.Temperature(value)

Bases: Enum

An enumeration.

CELSIUS = <geos.utils.enumUnits.Unit object>

FAHRENHEIT = <geos.utils.enumUnits.Unit object>

K = <geos.utils.enumUnits.Unit object>

class geos.utils.enumUnits.Time(value)

Bases: Enum

An enumeration.

DAY = <geos.utils.enumUnits.Unit object>

HOUR = <geos.utils.enumUnits.Unit object>

MONTH = <geos.utils.enumUnits.Unit object>

SECOND = <geos.utils.enumUnits.Unit object>

YEAR = <geos.utils.enumUnits.Unit object>

class geos.utils.enumUnits.Unit(conversionMultiplier, conversionAdder, unitLabel)

Bases: object

Unit enumeration.

Parameters:

• conversionMultiplier (float) – conversion multiplier

• conversionAdder (float) – conversion adder

• unitLabel (str) – symbol of the unit.

class geos.utils.enumUnits.Volume(value)

Bases: Enum

An enumeration.

BBL = <geos.utils.enumUnits.Unit object>

CUBIC_FEET = <geos.utils.enumUnits.Unit object>

CUBIC_METER = <geos.utils.enumUnits.Unit object>

class geos.utils.enumUnits.VolumetricRate(value)

Bases: Enum

An enumeration.

BBL_PER_DAY = <geos.utils.enumUnits.Unit object>

CUBIC_METER_PER_DAY = <geos.utils.enumUnits.Unit object>

CUBIC_METER_PER_HOUR = <geos.utils.enumUnits.Unit object>

CUBIC_METER_PER_SECOND = <geos.utils.enumUnits.Unit object>

geos.utils.enumUnits.convert(number, unitObj)

Converts a float number that has SI unit to a specific unit.

Parameters:

• number (float) – Number to convert.

• unitObj (Unit) – Object containing conversion multiplier and adder.

Returns:

number converted to the correct unit.

Return type:

float

geos.utils.enumUnits.enumerationDomainUnit(enumObj)

Get the xml code corresponding to unit enum object for drop down list.

Parameters:

enumObj (Enum) – Unit enum object.

Returns:

xml text.

Return type:

str

geos.utils.enumUnits.getPropertyUnitEnum(propertyName)

Get the Unit enum from property name.

Parameters:

propertyName (str) – name of the property.

Returns:

Unit enum.

Return type:

Enum

geos.utils.enumUnits.getSIUnits()

Get the dictionary of property Names:Units.

Generates a dict where the keys are meta-properties like pressure, mass etc … and where the values are Unit composed of a conversion factor and its unit associated. Here, the conversion factor will always be 1.0 and the unit will be the SI associate because we work with SI units.

Returns:

dictionary of unit names as keys and Unit enum as value.

Return type:

dict[str, Unit]

geos.utils.geometryFunctions module

Functions to permform geometry calculations.

geos.utils.geometryFunctions.computeCoordinatesInNewBasis(vec, changeOfBasisMatrix)

Computes the coordinates of a matrix from a basis B in the new basis B’.

Parameters:

• vec (npt.NDArray[np.floating[Any]]) – vector to compute the new coordinates

• changeOfBasisMatrix (npt.NDArray[np.floating[Any]]) – Change of basis matrix

Returns:

the new coordinates of the matrix in the basis B’.

Return type:

npt.NDArray[np.floating[Any]]

geos.utils.geometryFunctions.computePlaneFrom3Points(pt1, pt2, pt3)

Compute the 4 coefficients of a plane equation.

Let’s defined a plane from the following equation: ax + by + cz + d = 0. This function determines a, b, c, d from 3 points of the plane.

Parameters:

• pt1 (npt.NDArray[np.floating[Any]]) – 1st point of the plane.

• pt2 (npt.NDArray[np.floating[Any]]) – 2nd point of the plane.

• pt3 (npt.NDArray[np.floating[Any]]) – 3rd point of the plane.

Returns:

tuple of the 4 coefficients.

Return type:

tuple[float, float, float, float]

geos.utils.geometryFunctions.getCellSideAgainstPlane(cellPtsCoords, planePt, planeNormal)

Get the side of input cell against input plane.

Input plane is defined by a point on it and its normal vector.

Parameters:

• cellPtsCoords (npt.NDArray[np.floating[Any]]) – Coordinates of the vertices of the cell to get the side.

• planePt (npt.NDArray[np.floating[Any]]) – Point on the plane.

• planeNormal (npt.NDArray[np.floating[Any]]) – Normal vector to the plane.

Returns:

True if the cell is in the direction of the normal vector, False otherwise.

Return type:

bool

geos.utils.geometryFunctions.getChangeOfBasisMatrix(basisFrom, basisTo)

Get the change of basis matrix from basis basisFrom to basis basisTo.

Let’s define the basis (basisFrom) (b1, b2, b3) and basis (basisTo) (c1, c2, c3) where b1, b2, b3, and c1, c2, c3 are the vectors of the basis in the canonic form. This method returns the change of basis matrix P from basisFrom to basisTo.

The coordinates of a vector Vb(vb1, vb2, vb3) from the basis B in the basis C is then Vc = P.Vb

Parameters:

• basisFrom (tuple[npt.NDArray[np.floating[Any]], npt.NDArray[np.floating[Any]], npt.NDArray[np.floating[Any]]]) – origin basis

• basisTo (tuple[npt.NDArray[np.floating[Any]], npt.NDArray[np.floating[Any]], npt.NDArray[np.floating[Any]]]) – destination basis

Returns:

change of basis matrix.

Return type:

npt.NDArray[np.floating[Any]]

geos.utils.geometryFunctions.getPointSideAgainstPlane(ptCoords, planePt, planeNormal)

Get the side of input point against input plane.

Input plane is defined by a point on it and its normal vector.

Parameters:

• ptCoords (npt.NDArray[np.floating[Any]]) – Coordinates of the point to get the side.

• planePt (npt.NDArray[np.floating[Any]]) – Point on the plane.

• planeNormal (npt.NDArray[np.floating[Any]]) – Normal vector to the plane.

Returns:

True if the point is in the direction of the normal vector, False otherwise.

Return type:

bool

geos.utils.GeosOutputsConstants module

GeosOutputsConstants module defines usefull constant names such as attribute names, domain names, phase types, and the lists of attribute names to process.

Warning

Names may need to be updated when modifications occur in the GEOS code.

Todo

If possible, link GEOS names directly with GEOS code instead of redefining them here.

class geos.utils.GeosOutputsConstants.AttributeEnum(value)

Bases: Enum

An enumeration.

Define the enumeration to store attrbute properties.

Parameters:

• attributeName (str) – name of the attribute

• nbComponent (int) – number of component: 1 is scalar attribute, >1 is vectorial attribute

• onPoints (bool) – location of the attribute: on Points (True) or on Cells (False)

class geos.utils.GeosOutputsConstants.ComponentNameEnum(value)

Bases: Enum

An enumeration.

NONE = ('',)

NORMAL_TANGENTS = ('normal', 'tangent1', 'tangent2', 'T1T2', 'NT2', 'NT1')

XYZ = ('XX', 'YY', 'ZZ', 'YZ', 'XZ', 'XY')

class geos.utils.GeosOutputsConstants.FluidPrefixEnum(value)

Bases: Enum

Define usual names used for the fluid phase.

FLUID = 'fluid'

GAS = 'gas'

WATER = 'water'

class geos.utils.GeosOutputsConstants.GeosDomainNameEnum(value)

Bases: Enum

Name of the nodes in the MultiBlock data tree.

FAULT_DOMAIN_NAME = 'SurfaceElementRegion'

VOLUME_DOMAIN_NAME = 'CellElementRegion'

WELL_DOMAIN_NAME = 'WellElementRegion'

class geos.utils.GeosOutputsConstants.GeosLogOutputsEnum(value)

Bases: Enum

Define the keywords in Geos log.

PHASE = 'phase'

class geos.utils.GeosOutputsConstants.GeosMeshOutputsEnum(value)

Bases: AttributeEnum

Attribute names that come from Geos.

Define the names of Geos outputs, the number of components for vectorial attributes, and the location (Point or Cell) in the mesh

Define the enumeration to store attrbute properties.

Parameters:

• attributeName (str) – name of the attribute

• nbComponent (int) – number of component: 1 is scalar attribute, >1 is vectorial attribute

• onPoints (bool) – location of the attribute: on Points (True) or on Cells (False)

BULK_MODULUS = ('bulkModulus', 1, False)

CELL_ID = ('Cell ID', 1, False)

DELTA_PRESSURE = ('deltaPressure', 1, False)

DISPLACEMENT_JUMP = ('displacementJump', 3, False)

ELEMENT_CENTER = ('elementCenter', 1, False)

GRAIN_BULK_MODULUS = ('bulkModulusGrains', 1, False)

MASS = ('mass', 1, False)

PERMEABILITY = ('permeability', 1, False)

POINT = ('Points', 3, True)

POINTS_ID = ('Point ID', 1, True)

POROSITY = ('porosity', 1, False)

POROSITY_INI = ('porosityInitial', 1, False)

PRESSURE = ('pressure', 1, False)

ROCK_DENSITY = ('density', 1, False)

SHEAR_MODULUS = ('shearModulus', 1, False)

STRESS_EFFECTIVE = ('stressEffective', 6, False)

TOTAL_DISPLACEMENT = ('totalDisplacement', 4, True)

TRACTION = ('traction', 3, False)

VTK_ORIGINAL_CELL_ID = ('vtkOriginalCellIds', 1, False)

WATER_DENSITY = ('water_density', 1, False)

class geos.utils.GeosOutputsConstants.GeosMeshSuffixEnum(value)

Bases: Enum

Define the suffix of attributes in Geos output mesh.

BIOT_COEFFICIENT_SUFFIX = '_biotCoefficient'

BULK_MODULUS_SUFFIX = '_bulkModulus'

DENSITY_SUFFIX = '_density'

GRAIN_BULK_MODULUS_SUFFIX = '_grainBulkModulus'

PERMEABILITY_SUFFIX = '_permeability'

PHASE_DENSITY_SUFFIX = '_phaseDensity'

PHASE_FRACTION_SUFFIX = '_phaseFraction'

PHASE_MASS_DENSITY_SUFFIX = '_phaseMassDensity'

PHASE_VISCOSITY_SUFFIX = '_phaseViscosity'

POROSITY_REF_SUFFIX = '_referencePorosity'

POROSITY_SUFFIX = '_porosity'

SHEAR_MODULUS_SUFFIX = '_shearModulus'

STRAIN_SUFFIX = 'strain'

STRESS_SUFFIX = '_stress'

SURFACE_MINUS_SUFFIX = '_Minus'

SURFACE_PLUS_SUFFIX = '_Plus'

class geos.utils.GeosOutputsConstants.OutputObjectEnum(value)

Bases: Enum

Kind of objects present in GEOS pvd output.

FAULTS = 'Faults'

VOLUME = 'Volume'

WELLS = 'Wells'

geos.utils.GeosOutputsConstants.PHASE_SEP = '_'

Phase separator in Geos output log file.

class geos.utils.GeosOutputsConstants.PhaseTypeEnum(value)

Bases: Enum

An enumeration.

Define the main phases and associated property suffix.

Parameters:

• phaseType (str) – name of the type of phase

• attributes (tuple[str,...]) – list of attributes

FLUID = ('Fluid', ('_phaseDensity', '_phaseViscosity', '_phaseFraction', '_phaseMassDensity'))

ROCK = ('Rock', ('_density', '_stress', '_bulkModulus', '_shearModulus', '_porosity', '_referencePorosity', '_permeability'))

UNKNOWN = ('Other', ())

class geos.utils.GeosOutputsConstants.PostProcessingOutputsEnum(value)

Bases: AttributeEnum

Compute attributes enumeration.

Define the names of post-processing outputs, the number of components for vectorial attributes, and the location (Point or Cell) in the mesh

Define the enumeration to store attrbute properties.

Parameters:

• attributeName (str) – name of the attribute

• nbComponent (int) – number of component: 1 is scalar attribute, >1 is vectorial attribute

• onPoints (bool) – location of the attribute: on Points (True) or on Cells (False)

ADJACENT_CELL_SIDE = ('SurfaceAdjacentCells', 1, False)

BIOT_COEFFICIENT = ('biotCoefficient', 1, False)

BIOT_COEFFICIENT_INITIAL = ('biotCoefficientInitial', 1, False)

BLOCK_INDEX = ('blockIndex', 1, False)

BULK_MODULUS_INITIAL = ('bulkModulusInitial', 1, False)

COMPRESSIBILITY = ('compressibilityCoefficient', 1, False)

COMPRESSIBILITY_OED = ('compressibilityCoefficient_oed', 1, False)

COMPRESSIBILITY_REAL = ('compressibilityCoefficient_real', 1, False)

CRITICAL_PORE_PRESSURE = ('porePressureCritical_real', 1, False)

CRITICAL_PORE_PRESSURE_THRESHOLD = ('porePressureThreshold_real', 1, False)

CRITICAL_TOTAL_STRESS_RATIO = ('totalStressRatioCritical_real', 1, False)

LITHOSTATIC_STRESS = ('stressLithostatic', 1, False)

OEDOMETRIC_MODULUS = ('oedometricModulus', 1, False)

POISSON_RATIO = ('poissonRatio', 1, False)

POISSON_RATIO_INITIAL = ('poissonRatioInitial', 1, False)

RSP_OED = ('rsp_oed', 1, False)

RSP_REAL = ('rsp_real', 6, False)

SCU = ('SCU', 1, False)

SHEAR_MODULUS_INITIAL = ('shearModulusInitial', 1, False)

SPECIFIC_GRAVITY = ('specificGravity', 1, False)

STRAIN_ELASTIC = ('strainElastic', 6, False)

STRESS_EFFECTIVE_INITIAL = ('stressEffectiveInitial', 6, False)

STRESS_EFFECTIVE_RATIO_OED = ('stressEffectiveRatio_oed', 6, False)

STRESS_EFFECTIVE_RATIO_REAL = ('stressEffectiveRatio_real', 6, False)

STRESS_TOTAL = ('stressTotal', 6, False)

STRESS_TOTAL_DELTA = ('deltaStressTotal', 6, False)

STRESS_TOTAL_INITIAL = ('stressTotalInitial', 6, False)

STRESS_TOTAL_RATIO_REAL = ('stressTotalRatio_real', 6, False)

TOTAL_STRESS_RATIO_THRESHOLD = ('totalStressRatioThreshold_real', 1, False)

YOUNG_MODULUS = ('youngModulus', 1, False)

YOUNG_MODULUS_INITIAL = ('youngModulusInitial', 1, False)

geos.utils.GeosOutputsConstants.getAttributeToConvertFromLocalToXYZ()

Get the list of attribute names to convert from local to xyz basis.

Returns:

list of attributes to convert

Return type:

list[str]

geos.utils.GeosOutputsConstants.getAttributeToTransferFromInitialTime()

Get the list of attributes to copy from initial time step.

Returns:

dictionary where attribute names are keys and copied names are values

Return type:

dict[str,str]

geos.utils.GeosOutputsConstants.getRockSuffixRenaming()

Get the list of attributes to rename according to suffix.

Returns:

dictionary where suffix are keys and new names are values

Return type:

dict[str,str]

geos.utils.algebraFunctions module

GeosUtils module defines usefull methods to process GEOS outputs according to GEOS conventions.

geos.utils.algebraFunctions.getAttributeMatrixFromVector(attrArray)

Get the matrix of attribute values from the vector.

Matrix to vector conversion is the following:

• if input vector size is 3:

  \[\begin{split}(v1, v2, v3) => \begin{bmatrix} v0 & 0 & 0 \\ 0 & v1 & 0 \\ 0 & 0 & v2 \end{bmatrix}\end{split}\]

• if input vector size is 6:

  \[\begin{split}(v1, v2, v3, v4, v5, v6) => \begin{bmatrix} v1 & v6 & v5 \\ v6 & v2 & v4 \\ v5 & v4 & v3 \end{bmatrix}\end{split}\]

Warning

Input vector must be of size 3 or 6.

Parameters:

attrArray (npt.NDArray[np.float64]) – Vector of attribute values.

Returns:

matrix of attribute values

Return type:

npt.NDArray[np.float64]

geos.utils.algebraFunctions.getAttributeVectorFromMatrix(attrMatrix, size)

Get the vector of attribute values from the matrix.

Matrix to vector conversion is the following:

• 3x3 diagonal matrix:

  \[\begin{split}\begin{bmatrix} M00 & 0 & 0 \\ 0 & M11 & 0 \\ 0 & 0 & M22 \end{bmatrix} => (M00, M11, M22)\end{split}\]

• otherwise:

  \[\begin{split}\begin{bmatrix} M00 & M01 & M02 \\ M01 & M11 & M12 \\ M02 & M12 & M22 \end{bmatrix} => (M00, M11, M22, M12, M02, M01)\end{split}\]

Parameters:

• attrMatrix (npt.NDArray[np.float64]) – Matrix of attribute values.

• size (int) – Size of the final vector.

Returns:

vector of attribute values

Return type:

npt.NDArray[np.float64]

geos.utils.Logger module

Logger module manages logging tools.

Code was modified from <https://stackoverflow.com/questions/384076/how-can-i-color-python-logging-output>

class geos.utils.Logger.CustomLoggerFormatter(fmt=None, datefmt=None, style='%', validate=True, *, defaults=None)

Bases: Formatter

Custom formatter for the logger.

Warning

Colors do not work in the ouput message window of Paraview.

To use it:

logger = logging.getLogger("Logger name")
ch = logging.StreamHandler()
ch.setFormatter(CustomLoggerFormatter())
logger.addHandler(ch)

Initialize the formatter with specified format strings.

Initialize the formatter either with the specified format string, or a default as described above. Allow for specialized date formatting with the optional datefmt argument. If datefmt is omitted, you get an ISO8601-like (or RFC 3339-like) format.

Use a style parameter of ‘%’, ‘{’ or ‘$’ to specify that you want to use one of %-formatting, str.format() ({}) formatting or string.Template formatting in your format string.

Changed in version 3.2: Added the style parameter.

FORMATS = {10: '\x1b[38;20m%(asctime)s - %(name)s - %(levelname)s - %(message)s (%(filename)s:%(lineno)d)\x1b[0m', 20: '\x1b[38;20m%(asctime)s - %(name)s - %(levelname)s - %(message)s\x1b[0m', 30: '\x1b[33;20m%(asctime)s - %(name)s - %(levelname)s - %(message)s\x1b[0m', 40: '\x1b[31;20m%(asctime)s - %(name)s - %(levelname)s - %(message)s\x1b[0m', 50: '\x1b[31;1m%(asctime)s - %(name)s - %(levelname)s - %(message)s (%(filename)s:%(lineno)d)\x1b[0m'}

format for each logger output type

FORMATS_PV = {10: '%(asctime)s - %(name)s - %(levelname)s - %(message)s (%(filename)s:%(lineno)d)', 20: '%(asctime)s - %(name)s - %(levelname)s - %(message)s', 30: '%(asctime)s - %(name)s - %(levelname)s - %(message)s', 40: '%(asctime)s - %(name)s - %(levelname)s - %(message)s', 50: '%(asctime)s - %(name)s - %(levelname)s - %(message)s (%(filename)s:%(lineno)d)'}

same without colors

bold_red = '\x1b[31;1m'

format(record)

Return the format according to input record.

Parameters:

record (logging.LogRecord) – record

Returns:

format as a string

Return type:

str

format1 = '%(asctime)s - %(name)s - %(levelname)s - %(message)s'

format2 = '%(asctime)s - %(name)s - %(levelname)s - %(message)s (%(filename)s:%(lineno)d)'

grey = '\x1b[38;20m'

red = '\x1b[31;20m'

reset = '\x1b[0m'

yellow = '\x1b[33;20m'

class geos.utils.Logger.Logger(name, level=0)

Bases: Filterer

Instances of the Logger class represent a single logging channel. A “logging channel” indicates an area of an application. Exactly how an “area” is defined is up to the application developer. Since an application can have any number of areas, logging channels are identified by a unique string. Application areas can be nested (e.g. an area of “input processing” might include sub-areas “read CSV files”, “read XLS files” and “read Gnumeric files”). To cater for this natural nesting, channel names are organized into a namespace hierarchy where levels are separated by periods, much like the Java or Python package namespace. So in the instance given above, channel names might be “input” for the upper level, and “input.csv”, “input.xls” and “input.gnu” for the sub-levels. There is no arbitrary limit to the depth of nesting.

Initialize the logger with a name and an optional level.

addHandler(hdlr)

Add the specified handler to this logger.

callHandlers(record)

Pass a record to all relevant handlers.

Loop through all handlers for this logger and its parents in the logger hierarchy. If no handler was found, output a one-off error message to sys.stderr. Stop searching up the hierarchy whenever a logger with the “propagate” attribute set to zero is found - that will be the last logger whose handlers are called.

critical(msg, *args, **kwargs)

Log ‘msg % args’ with severity ‘CRITICAL’.

To pass exception information, use the keyword argument exc_info with a true value, e.g.

logger.critical(“Houston, we have a %s”, “major disaster”, exc_info=1)

debug(msg, *args, **kwargs)

Log ‘msg % args’ with severity ‘DEBUG’.

To pass exception information, use the keyword argument exc_info with a true value, e.g.

logger.debug(“Houston, we have a %s”, “thorny problem”, exc_info=1)

error(msg, *args, **kwargs)

Log ‘msg % args’ with severity ‘ERROR’.

To pass exception information, use the keyword argument exc_info with a true value, e.g.

logger.error(“Houston, we have a %s”, “major problem”, exc_info=1)

exception(msg, *args, exc_info=True, **kwargs)

Convenience method for logging an ERROR with exception information.

fatal(msg, *args, **kwargs)

Don’t use this method, use critical() instead.

findCaller(stack_info=False, stacklevel=1)

Find the stack frame of the caller so that we can note the source file name, line number and function name.

getChild(suffix)

Get a logger which is a descendant to this one.

This is a convenience method, such that

logging.getLogger(‘abc’).getChild(‘def.ghi’)

is the same as

logging.getLogger(‘abc.def.ghi’)

It’s useful, for example, when the parent logger is named using __name__ rather than a literal string.

getEffectiveLevel()

Get the effective level for this logger.

Loop through this logger and its parents in the logger hierarchy, looking for a non-zero logging level. Return the first one found.

handle(record)

Call the handlers for the specified record.

This method is used for unpickled records received from a socket, as well as those created locally. Logger-level filtering is applied.

hasHandlers()

See if this logger has any handlers configured.

Loop through all handlers for this logger and its parents in the logger hierarchy. Return True if a handler was found, else False. Stop searching up the hierarchy whenever a logger with the “propagate” attribute set to zero is found - that will be the last logger which is checked for the existence of handlers.

info(msg, *args, **kwargs)

Log ‘msg % args’ with severity ‘INFO’.

To pass exception information, use the keyword argument exc_info with a true value, e.g.

logger.info(“Houston, we have a %s”, “interesting problem”, exc_info=1)

isEnabledFor(level)

Is this logger enabled for level ‘level’?

log(level, msg, *args, **kwargs)

Log ‘msg % args’ with the integer severity ‘level’.

To pass exception information, use the keyword argument exc_info with a true value, e.g.

logger.log(level, “We have a %s”, “mysterious problem”, exc_info=1)

makeRecord(name, level, fn, lno, msg, args, exc_info, func=None, extra=None, sinfo=None)

A factory method which can be overridden in subclasses to create specialized LogRecords.

manager = <logging.Manager object>

removeHandler(hdlr)

Remove the specified handler from this logger.

root = <RootLogger root (WARNING)>

setLevel(level)

Set the logging level of this logger. level must be an int or a str.

warn(msg, *args, **kwargs)

warning(msg, *args, **kwargs)

Log ‘msg % args’ with severity ‘WARNING’.

To pass exception information, use the keyword argument exc_info with a true value, e.g.

logger.warning(“Houston, we have a %s”, “bit of a problem”, exc_info=1)

geos.utils.Logger.getLogger(title)

Return the Logger with pre-defined configuration.

Example:

# module import
import Logger

# logger instanciation
logger :Logger.Logger = Logger.getLogger("My application")

# logger use
logger.debug("debug message")
logger.info("info message")
logger.warning("warning message")
logger.error("error message")
logger.critical("critical message")

Parameters:

title (str) – Name of the logger.

Returns:

logger

Return type:

Logger

geos.utils.PhysicalConstants module

Define default values of usefull physical constants.

geos.utils.PhysicalConstants.DEFAULT_FRICTION_ANGLE_DEG = 10.0

default friction angle (deg)

geos.utils.PhysicalConstants.DEFAULT_FRICTION_ANGLE_RAD = 0.17453292519943295

default friction angle (rad)

geos.utils.PhysicalConstants.DEFAULT_GRAIN_BULK_MODULUS = 38000000000.0

default grain bulk modulus is that of Quartz (Pa)

geos.utils.PhysicalConstants.DEFAULT_ROCK_COHESION = 0.0

default rock cohesion - fractured case - (Pa)

geos.utils.PhysicalConstants.EPSILON = 1e-06

epsilon

geos.utils.PhysicalConstants.GRAVITY = 9.81

gravity (m/s)

geos.utils.PhysicalConstants.WATER_DENSITY = 1000.0

water density (kg/m³)

geos.utils.PhysicalConstants.WATER_DYNAMIC_VISCOSITY = 0.001

water dynamic viscosity (kg.m^-1/s^-1 = Pa.s)

geos.utils.PhysicalConstants.WATER_KINEMATIC_VISCOSITY = 1e-06

water kinematic viscosity (m²/s)

geos.utils.UnitRepository module

class geos.utils.UnitRepository.UnitRepository(userPropertiesUnitChoice=None)

Bases: object

Unit repository.

• Input example : { “pressure”: 4, “bhp”: 4,”stress”: 3, “length”: 2, …}

• Output example{ “pressure”: Pressure.BAR.value, “bhp”: Pressure.BAR.value,

  “stress”: Pressure.MPA.value, “length”: Lenght.FEET.value, … }

These Pressure.BAR.value corresponds to Unit objects that have a conversion multiplier and a conversion adder, and also a unit label.

Parameters:

userPropertiesUnitChoice (dict[str, int], Optional) –

dictionary of unit user choices.

Defaults {}.

getPropertiesUnit()

Access the m_propertiesUnit attribute.

Returns:

dictionary of unit as values for each property as keys.

Return type:

dict[str, Unit]

initPropertiesUnit()

Initialize the attribute m_propertiesUnit.