custEM.misc package
Submodules
custEM.misc.anomaly_expressions module
Created on Mon Jun 13 15:14:20 2016
@author: Rochlitz.R
custEM.misc.misc module
@author: Rochlitz.R
- custEM.misc.misc.block_print()[source]
Supress all prints in the command prompt until enable_print() is called.
- custEM.misc.misc.check_approach_and_file_format(approach, file_format, path, logger)[source]
Utility function that checks if a valid modeling approach is chosen (avoid typos) and if HFD5 format is supported.
Required arguments
- approach, type str
approach specification (see MOD class)
- file_format, type str or None
if None, used h5 if supported, otherwise xml for data export
- path, type str
path to custEM.misc directory, forwarded internally
Returns
- ‘h5 or ‘xml’, type str
file format specification
- custEM.misc.misc.check_if_model_exists(out_name, overwrite, load_existing, logger=None)[source]
Utility function that checks if a finite element model already exists, which can either be overwritten or the calculation can be aborted.
Required arguments
See ‘MOD’ class description
- custEM.misc.misc.dump_csr(fname, values, column_indices, row_pointers, size)[source]
Utility function that dumps a PETSCMatrix as a sparse csr-matrix to the hard disc.
Required arguments
- fname, type str
export name of the matrix without the suffix ‘.csr’
- values, type array
values of matrix elements
- column_indices, type array
column indices
- row_pointers, type array
row_pointers
- size, type int
size (length) of the square matrix
- custEM.misc.misc.enable_print()[source]
Enable prints in the command prompt after block_print() was called.
- custEM.misc.misc.get_coordinates(FS)[source]
Return coordinates of a lagrange VectorFunctionSpace as numpy array.
Required arguments
- FS, type class
FunctionSpaces instance
Returns
- xyz, type numpy array
array or dof coordinates with shape (n, 3)
- custEM.misc.misc.logger_print(logger, lvl, string, val=None, pre_dash=True, post_dash=False, barrier=True, root_only=True)[source]
Utility function that prints only from root process in mpi mode.
Required arguments
- logger, type logger from logging module
default custEM logger
- lvl, type int
debug_level for custEM code
- string, type str
string that should be printed
Keyword arguments
- val = None, various types
a value that should be printed after the “message”
- pre_dash = True, type bool
flag that controls if a dashed line shoul be printed before the “message”
- post_dash = False, type bool
flag that controls if a dashed line shoul be printed before the “message”
- barrier = True, type bool
enable or disable multi-processing barrier (synchronize mpi processes)
- root_only = True, type bool
log “message” only with root process or each single one
- custEM.misc.misc.make_directories(r_dir, m_dir, approach, para_dir=None, m_dir_only=False)[source]
Initialize the export directories if not existing.
Required arguments
see MOD class description
Keyword arguments
- para_dir = None, type str
if None, the default para_dir is ‘m_dir/_para’; otherwise, the parameter directory will be initializied according to specified path
- m_dir_only = False, type bool
initialize only the main mesh directory or also the main results directory
- custEM.misc.misc.mpi_print(string, val=None, pre_dash=True, post_dash=False, barrier=True)[source]
Utility function that prints only from root process in mpi mode.
Required arguments
- string, type str
string that should be printed
Keyword arguments
- val = None, various types
a value that should be printed after the “message”
- pre_dash = True, type bool
Flag that controls if a dashed line shoul be printed before the “message”
- post_dash = False, type bool
Flag that controls if a dashed line shoul be printed before the “message”
- barrier = True, type bool
Enable or disable multi-processing barrier (synchronize all mpi processes)
- custEM.misc.misc.petsc_transfer_function(source_func, target_func, cache=False, q=None)[source]
Build Petsc transfer matrix to interpolate between different meshes in parallel.
Note, this function will crash without error notice if there are more mpi processes used than there are dof in the target mesh.
Required arguments
- source_func, type dolfin function
data function on source interpolation mesh
- target func, tpye dolfin function
data function on target interpolation mesh
Keyword arguments
- fi = 0, type int
iteration index over frequencies
- custEM.misc.misc.read_h5(mpi_comm, var, fname, counter=None, ri='data')[source]
Utility function to write data files in parallel in h5 format.
Required arguments
- mpi_cw, type MPI communicator
communicator attributes for internal usage, FEniCS version dependent
- var, type dolfin function
data which should be imported, e.g., the E-field solution E_t_r
- fname, type str
destination file name, containing also the export path
Keyword arguments
- counter = None, type int
specify the index of the data functions if more than one solution (e.g., multiple Tx or times) should be imported from the same h5 file
- ri = ‘data’, type str
specify a tag to name the data function in the h5 file container; e.g., ‘real’ and ‘imag’ can be used to access both parts of the complex field in the same file, reducing the I/O overhead
- custEM.misc.misc.read_paths(file_name)[source]
Utility function that imports the default ‘r_dir’ and ‘m_dir’ attributes for the ‘MOD’ instance from file.
Note, these attributes are always overwritten if the keyword arguments ‘r_dir’ or ‘m_dir’ are set manually by initializing the ‘MOD’ instance with theses keyword arguments.
Required arguments
- file_name, type str
file name of the file which contains the paths, forwarded internally
Returns
- results_dir, type str
main results directory
- mesh_dir, type str
main mesh directory
- custEM.misc.misc.resort_coordinates(c1, c2)[source]
Resort two arrays with overall identical row entries but different order.
Required arguments
- c1/c2, type numpy_arrays
two data arrays of shape (n, 3)
Returns
- c1_sort and c2_sort, type numpy_arrays
index arrays which can be used to resort data from array 1 to array 2 and vice versa.
- custEM.misc.misc.root_write(writing_function)[source]
Utility function that stores data to file only from root process in mpi mode.
Required arguments
- writing_function, type python function
a function for writing e.g. data or json files
- custEM.misc.misc.run_multiple_serial(script_name, *serial_args)[source]
Utility function which is nearly identical to run_serial. The only difference is that a communicator object ic is returned that can be used for multi-threading of several serial runs.
A synchronisation with all communicators can be foreced from the root process in mpi mode by collecting all communicator objects in a list and by using the “Barrier” and “Disconnect” mpi4py methods before continuing.
Required arguments
- script_name, type str
name of the python script that should be called in serial
- *serial_args, type python list
list of input console arguments for the python script
Returns
- ic, type MPI intercommunicator object
communicator object to communicate with spawned process
- custEM.misc.misc.run_serial(script_name, *serial_args)[source]
Utility function that calls a script in serial from root process in mpi mode.
Required arguments
- script_name, type str
name of the python script that should be called in serial
- *serial_args, type python list
list of input console arguments for the python script
- custEM.misc.misc.specify_td_export_strings(FE)[source]
Utility function for specifying time-domain export names.
Required arguments
- FE, type class
FE approach instance (e.g., E_vector)
Returns
- E_str, H_str, mode, type str
data name suffixes to differ between shut-on and shut-off processes and impulse or step-response modeling with the implicite Euler method
- custEM.misc.misc.write_h5(mpi_comm, var, fname, counter=None, new=True, append=False, close=True, f=None, ri='data')[source]
Utility function to write data files in parallel in ‘h5’ format.
Required arguments
- mpi_cw, type MPI communicator
communicator attributes for internal usage, FEniCS version dependent
- var, type dolfin function
data which should be exported, e.g., the E-field solution E_t_r
- fname, type str
destination file name, containing also the export path
Keyword arguments
- counter = None, type int
specify the index of the data functions if more than one solution (e.g., multiple Tx or times) should be stored in the same h5 file.
- new = True, type bool
open new h5 file, otherwise, continue writing into f
- close = True, type bool
close h5 file or leave it open for writing further solutions
- f = None, type str
filename to continue writing in an opened, existing file; this makes only sense if counter is not None or 0
- ri = ‘data’, type str
specify a tag to name the data function in the h5 file container; e.g., ‘real’ and ‘imag’ can be used to store both parts of the complex field in one file, reducing the I/O overhead
Returns
- f, type str
file name of export file if not closed
custEM.misc.profiler module
@author: Rochlitz.R
- custEM.misc.profiler.export_config_file(PP)[source]
Write model parameters - mainly MP and FE instance dictionaries - to file in the specified export directory (out_dir) using JSON.
Required arguments
- PP, type class
PostProcessing instance
- custEM.misc.profiler.export_resource_file(PP)[source]
Write consumed computational resources and times to file in the specified export directory (out_dir) using JSON.
Required arguments
- PP, type class
PostProcessing instance
- custEM.misc.profiler.get_logger(log_level, profiler, out_path)[source]
Initialize logger for all custEM prints during simulations. The information in the command promt will be printed corresponding to the specified debug_level level in the MOD class. Furthermore, a log file is stored in the export directory of the results if profiler=True, using always the debug level for the log files.
Required arguments
- log_level, type str or int
specify log_level, see MOD class description
- profiler, type bool
flag to set if log-field should be created or not
- out_path, type bool
path where log-file should be created
- custEM.misc.profiler.max_mem(total=True, to_store=False, logger=None, fmt='GiB')[source]
Print the maximum memory requirements, either for each MPI process or in total.
Keyword arguments
- total=True, type bool
Flag if memory consumption should be printed in total or per process
- to_store = False, type bool
set True if value should be returned
custEM.misc.pyhed_calculations module
@author: Rochlitz.R
- class custEM.misc.pyhed_calculations.PHC(config_file)[source]
Bases:
objectPyhedCalculations (PHC) class for reference solution calculated with pyhed sub-module of COMET library.
Methods
- calc_reference()
calucalte semi-analytic reference solution for given 1D CSEM setup-
Usage
Load a config file (JSON format) from a custEM modeling to obtain the Tx information and calculate results for E and/or H on specified coordinates.
>>> from custEM.misc import pyhed_calculations as ph >>> calculator = ph.PHC("CONFIG_FILE") >>> calculator.calc_reference(np.array([0., 100., 0.]), 'EH', max_procs=4)
- calc_reference(coords, EH, freq=None, max_procs=1)[source]
Calculate semi-analytic reference solution for 1D CSEm setups.
Required arguments
- coords, type array of shape (:, 3)
array of target coordinates
- EH, type str
specify either ‘E’ for electric or ‘H’ for magnetic fields
Keyword arguments
- max_procs = 1, type int
allowed number of processes for pyhed internal multiprocessing
custEM.misc.synthetic_definitions module
@author: Rochlitz.R
- custEM.misc.synthetic_definitions.almost_flat_topo(x, y, h=0.1)[source]
Almost flat topo specified as function for mesh generation tests.
- custEM.misc.synthetic_definitions.anti_cone_bathy(x, y, h=1000.0, z=0.0)[source]
Example topography with a cone hole for testing bathy-tools.
- custEM.misc.synthetic_definitions.borehole_tx()[source]
Description of Tx grounded in two different boreholes.
- custEM.misc.synthetic_definitions.cone_bathy(x, y, h=1000.0, z=0.0)[source]
Example topography with a cone hill for testing bathy-tools.
- custEM.misc.synthetic_definitions.double_cone_bathy(x, y, h=1000.0, sigma=1.0, zl=0.0)[source]
Example topography with two cones for testing bathy-tools.
- custEM.misc.synthetic_definitions.example_2_loop_tx()[source]
Crooked loop Tx description for frequency-domain example 2
- custEM.misc.synthetic_definitions.example_4_topo_cos_sin(x, y, h=200.0)[source]
Example topography for frequency-domain example 4, x- and y-directed cosine/sine topography.
- custEM.misc.synthetic_definitions.flat_topo(x, y, h=0.0)[source]
Flat topo specified as function for implementation tests.
- custEM.misc.synthetic_definitions.gaussian_topo(x, y, h=3000000000.0, sigma=1000.0, z=0.0, x_off=0.0, y_off=0.0)[source]
Example topography with hill descriped as gaussian function.
- custEM.misc.synthetic_definitions.gaussian_topo_hole(x, y, h=3000000000.0, sigma=1000.0, x_off=0.0, y_off=0.0)[source]
Example topography with hole descriped as gaussian function.
- custEM.misc.synthetic_definitions.pyramid_topo(x, y, h=1000.0, slope=1.0, z_off=0.0, x_off=0.0, y_off=0.0)[source]
Pyramid-shaped topography.
- custEM.misc.synthetic_definitions.roof_topo(x, y, h=1000.0, slope=1.0, z_off=0.0, x_off=0.0, ylim=[-1000.0, 1000.0])[source]
Pyramid-shaped topography with cutted top (roof).
- custEM.misc.synthetic_definitions.sample_topo_func(x, y, h=100.0)[source]
Example sine topography for test scripts.
- custEM.misc.synthetic_definitions.subtopo_func1(x, y, h=200.0)[source]
Example sine-shaped subsurface topography in x-direction.
- custEM.misc.synthetic_definitions.subtopo_func2(x, y, h=0.1)[source]
Slope of subsurface layer in y-direction.
- custEM.misc.synthetic_definitions.surface_anomly_outcrop_1()[source]
Example outcrop polygon for surface anomaly.
- custEM.misc.synthetic_definitions.surface_anomly_outcrop_2()[source]
Example outcrop polygon for surface anomaly.
- custEM.misc.synthetic_definitions.surface_anomly_outcrop_3()[source]
Example outcrop polygon for surface anomaly.
- custEM.misc.synthetic_definitions.topo_func1(x, y, h=100.0)[source]
Example cosine-topography in y-direction.
- custEM.misc.synthetic_definitions.topo_func3(x, y, h=200.0)[source]
Example sine-topography in y-direction.
Module contents
misc
Submodules:
misc for general utility functions used in all submodules
profiler for analysing model and performance statistics
pyhed_calculations for calling pyhed
synthetic_definitions for defining supporting python functions
anomaly_expressions for defining anomalies with FEniCS, deprecated