Changelog¶
recent versions¶
v0.12.0 : Survey & Simulation¶
2020-07-25
This is a big release with many new features, and unfortunately not completely backwards compatible. The main new features are the new Survey and Simulation classes, as well as some initial work for optimization (misfit, gradient). Also, a Model can now be a resistivity model, a conductivity model, or the logarithm (natural or base 10) therefore. Receivers can now be arbitrarily rotated, just as the sources. In addition to the existing soft-dependencies empymod, discretize, and h5py there are the new soft-dependencies xarray and tqm; discretize is now much tighter integrated. For the new survey and simulation classes xarray is a required dependency. However, the only hard dependency remain scipy and numba, if you use emg3d purely as a solver. Data reading and writing has new a JSON-backend, in addition to the existing HDF5 and NumPy-backends.
In more detail:
- Modules:
- surveys (new; requires xarray):
- Class surveys.Survey, which combines sources, receivers, and data.
- Class surveys.Dipole, which defines electric or magnetic point dipoles and finite length dipoles.
- simulations (new; requires xarray; soft-dependency tqdm):
- Class simulations.Simulation, which combines a survey with a model. A simulation computes the e-field (and h-field) asynchronously using concurrent.futures. This class will include automatic, source- and frequency-dependent gridding in the future. If tqdm is installed it displays a progress bar for the asynchronous computation. Note that the simulation class has still some limitations, consult the class documentation.
- models:
- Model instances take new the parameters property_{x;y;z} instead of res_{x;y;z}. The properties can be either resistivity, conductivity, or log_{e;10} thereof. What is actually provided has to be defined with the parameter mapping. By default, it remains resistivity, as it was until now. The keywords res_{x;y;z} are deprecated, but still accepted at the moment. The attributes model.res_{x;y;z} are still available too, but equally deprecated. However, it is no longer possible to assign values to these attributes, which is a backwards incompatible change.
- A model knows now how to interpolate itself from its grid to another grid (interpolate2grid).
- maps:
- New mappings for models.Model instances: The mappings take care of how to transform the investigation variable to conductivity and back, and how it affects its derivative.
- New interpolation routine edges2cellaverages.
- fields:
- Function get_receiver_response (new), which returns the response for arbitrarily rotated receivers.
- Improvements to Field and SourceField:
- _sval and _smu0 not stored any longer, derived from _freq.
- SourceField is now using the copy() and from_dict() from its parents class Field.
- io:
- File-format json (new), writes to a hierarchical, plain json file.
- Deprecated the use of backend, it uses the file extension of fname instead.
- This means .npz (instead of numpy), .h5 (instead of h5py), and new .json.
- New parameter collect_classes, which can be used to switch-on collection of the main classes in root-level dictionaries. By default, they are no longer collected (changed).
- meshes:
- meshes.TensorMesh new inherits from discretize if installed.
- Added __eq__ to models.TensorMesh to compare meshes.
- optimize (new)
- Functionalities related to inversion (data misfit, gradient, data weighting, and depth weighting). This module is in an early stage, and the API will likely change in the future. Current functions are misfit, gradient (using the adjoint-state method), and data_weighting. These functionalities are best accessed through the Simulation class.
- surveys (new; requires xarray):
- Dependencies:
- empymod is now a soft dependency (no longer a hard dependency), only required for utils.Fourier (time-domain modelling).
- Existing soft dependency discretize is now baked straight into meshes.
- New soft dependency xarray for the Survey class (and therefore also for the Simulation class and the optimize module).
- New soft dependency tqdm for nice progress bars in asynchronous computation.
- Deprecations and removals:
- Removed deprecated functions data_write and data_read.
- Removed all deprecated functions from utils.
- Miscellaneous:
- Re-organise API-docs.
- Much bookkeeping (improve error raising and checking; chaining errors, numpy types, etc).
v0.11.0 : Refactor¶
2020-05-05
Grand refactor with new internal layout. Mainly splitting-up utils into smaller bits. Most functionalities (old names) are currently retained in utils and it should be mostly backwards compatible for now, but they are deprecated and will eventually be removed. Some previously deprecated functions were removed, however.
- Removed deprecated functions:
- emg3d.solver.solver (use emg3d.solver.solve instead).
- Aliases of emg3d.io.data_write and emg3d.io.data_read in emg3d.utils.
- Changes:
- SourceField has now the same signature as Field (this might break your code if you called SourceField directly, with positional arguments, and not through get_source_field).
- More functions and classes in the top namespace.
- Replaced core.l2norm with scipy.linalg.norm, as SciPy 1.4 got the following PR: https://github.com/scipy/scipy/pull/10397 (reason to raise minimum SciPy to 1.4).
- Increased minimum required versions of dependencies to
- scipy>=1.4.0 (raised from 1.1, see note above)
- empymod>=2.0.0 (no min requirement before)
- numba>=0.45.0 (raised from 0.40)
- New layout
- njitted -> core.
- utils split in fields, meshes, models, maps, and utils.
- Bugfixes:
- Fixed to_dict, from_dict, and copy for the SourceField.
- Fixed io for SourceField, that was not implemented properly.
v0.8.0 - v0.10.x¶
v0.10.1 : Zero Source¶
2020-04-29
- Bug fixes:
- Checks now if provided source-field is zero, and exists gracefully if so, returning a zero electric field. Until now it failed with a division-by-zero error.
- Improvements:
- Warnings: If
verb=1
it prints a warning in case it did not converge (it finished silently until now). - Improvements to docs (figures-scaling; intersphinx).
- Adjust
Fields.pha
andFields.amp
in accordance withempymod v2
:.pha
and.amp
are now methods; uses directlyempymod.utils.EMArray
. - Adjust tests for
empymod v2
(Fields, Fourier).
- Warnings: If
v0.10.0 : Data persistence¶
2020-03-25
- New:
- New functions
emg3d.save
andemg3d.load
to save and load all sort ofemg3d
instances. The currently implemented backends areh5py
for.h5
-files (default, but requiresh5py
to be installed) andnumpy
for.npz
-files. - Classes
emg3d.utils.Field
,emg3d.utils.Model
, andemg3d.utils.TensorMesh
have new methods.copy()
,.to_dict()
, and.from_dict()
. emg3d.utils.Model
: Possible to create new models by adding or subtracting existing models, and comparing two models (+
,-
,==
and!=
). New attributesshape
andsize
.emg3d.utils.Model
does not store the volume any longer (justvnC
).
- New functions
- Deprecations:
- Deprecated
data_write
anddata_read
.
- Deprecated
- Internal and bug fixes:
- All I/O-related stuff moved to its own file io.py.
- Change from
NUMBA_DISABLE_JIT
to usepy_func
for testing and coverage. - Bugfix:
emg3d.njitted.restrict
did not store the {x;y;z}-field ifsc_dir
was {4;5;6}, respectively.
v0.9.3 : Sphinx gallery¶
2020-02-11
- Rename
solver.solver
tosolver.solve
; loadsolve
also into the main namespace asemg3d.solve
. - Adjustment to termination criterion for STAGNATION: The current error is now compared to the last error of the same cycle type. Together with this the workaround for sslsolver when called with an initial efield introduced in v0.8.0 was removed.
- Adjustment to
utils.get_hx_h0
(this might change your boundaries): The computation domain is now computed so that the distance for the signal travelling from the source to the boundary and back to the most remote receiver is at least two wavelengths away. If this is within the provided domain, then now extra buffer is added around the domain. Additionally, the function has a new parametermax_domain
, which is the maximum distance from the center to the boundary; defaults to 100 km. - New parameter
log
forutils.grid2grid
; ifTrue
, then the interpolation is carried out on a log10-scale. - Change from the notebook-based
emg3d-examples
-repo to thesphinx
-basedemg3d-gallery
-repo.
v0.9.2 : Complex sources¶
2019-12-26
- Strength input for
get_source_field
can now be complex; it also stores now the source location and its strength and moment. get_receiver
can now take entireField
instances, and returns in that case (fx
,fy
,fz
) at receiver locations.- Krylov subspace solvers:
- Solver now finishes in the middle of preconditioning cycles if tolerance is reached.
- Solver now aborts if solution diverges or stagnates also for the SSL solvers; it fails and returns a zero field.
- Removed
gmres
andlgmres
from the supported SSL solvers; they do not work nice for this problem. Supported remainbicgstab
(default),cgs
, andgcrotmk
.
- Various small things:
- New attribute
Field.is_electric
, so the field knows if it is electric or magnetic. - New
verb
-possibility:verb=-1
is a continuously updated one-liner, ideal to monitor large sets of computations or in inversions. - The returned
info
dictionary contains new keys:runtime_at_cycle
: accumulated total runtime at each cycle;error_at_cycle
: absolute error at each cycle.
- Simple
__repr__
forTensorMesh
,Model
,Fourier
,Time
.
- New attribute
- Bugfixes:
- Related to
get_hx_h0
,data_write
, printing inFourier
.
- Related to
v0.9.1 : VolumeModel¶
2019-11-13
- New class
VolumeModel
; changes inModel
:Model
now only contains resistivity, magnetic permeability, and electric permittivity.VolumeModel
contains the volume-averaged values eta and zeta; called from withinemg3d.solver.solver
.- Full wave equation is enabled again, via
epsilon_r
; by default it is set to None, hence diffusive approximation. - Model parameters are now internally stored as 1D arrays.
- An {isotropic, VTI, HTI} initiated model can be changed by providing the missing resistivities.
- Bugfix: Up and till version 0.8.1 there was a bug. If resistivity was set
with slices, e.g.,
model.res[:, :, :5]=1e10
, it DID NOT update the corresponding eta. This bug was unintentionally fixed in 0.9.0, but only realised now. - Various:
- The log now lists the version of emg3d.
- PEP8: internal imports now use absolute paths instead of relative ones.
- Move from conda-channel
prisae
toconda-forge
. - Automatic deploy for PyPi and conda-forge.
v0.9.0 : Fourier¶
2019-11-07
- New routine:
emg3d.utils.Fourier
, a class to handle Fourier-transform related stuff for time-domain modelling. See the example notebooks for its usage.
- Utilities:
Fields
and returned receiver-arrays (EMArray
) both have amplitude (.amp
) and phase (.pha
) attributes.Fields
have attributes containing frequency-information (freq
,smu0
).- New class
SourceField
; a subclass ofField
, addingvector
andv{x,y,z}
attributes for the real valued source vectors. - The
Model
is not frequency-dependent any longer and does NOT take afreq
-parameter any more (currently it still takes it, but it is deprecated and will be removed in the future). data_write
automatically removes_vol
fromTensorMesh
instances and_eta_{x,y,z}
,_zeta
fromModel
instances. This makes the archives smaller, and they are not required, as they are simply reconstructed if needed.
- Internal changes:
- The multigrid method, as implemented, only works for the diffusive
approximation. Nevertheless, we always used
\sigma-i\omega\epsilon
, hence a complex number. This is now changed and\epsilon
set to 0, leaving only\sigma
. - Change time convention from
exp(-iwt)
toexp(iwt)
, as used inempymod
and commonly in CSEM. Removed the parameterconjugate
from the solver, to simplify. - Change own private class variables from
__
to_
. res
andmu_r
are now checked to ensure they are >0;freq
is checked to ensure !=0.
- The multigrid method, as implemented, only works for the diffusive
approximation. Nevertheless, we always used
- New dependencies and maintenance:
empymod
is a new dependency.- Travis now checks all the url’s in the documentation, so there should be no broken links down the road. (Check is allowed to fail, it is visual QC.)
- Bugfixes:
- Fixes to the
setuptools_scm
-implementation (MANIFEST.in
).
- Fixes to the
v0.8.1 : setuptools_scm¶
2019-10-22
- Implement
setuptools_scm
for versioning (adds git hashes for dev-versions).
v0.8.0 : Laplace¶
2019-10-04
- Laplace-domain computation: By providing a negative
freq
-value toutils.get_source_field
andutils.Model
, the computation is carried out in the real Laplace domains = freq
instead of the complex frequency domains = 2i*pi*freq
. - New meshing helper routines (particularly useful for transient modelling
where frequency-dependent/adaptive meshes are inevitable):
utils.get_hx_h0
to get cell widths and origin for given parameters including a few fixed interfaces (center plus two, e.g. top anomaly, sea-floor, and sea-surface).utils.get_cell_numbers
to get good values of number of cells for given primes.
- Speed-up
njitted.volume_average
significantly thanks to @jcapriot. - Bugfixes and other minor things:
- Abort if l2-norm is NaN (only works for MG).
- Workaround for the case where a
sslsolver
is used together with a provided initialefield
. - Changed parameter
rho
tores
for consistency reasons inutils.get_domain
. - Changed parameter
h_min
tomin_width
for consistency reasons inutils.get_stretched_h
.
v0.1.0 - v0.7.x¶
v0.7.1 : JOSS article¶
2019-07-17
- Version of the JOSS article, https://doi.org/10.21105/joss.01463 .
- New function
utils.grid2grid
to move from one grid to another. Both functions (utils.get_receiver
andutils.grid2grid
) can be used for fields and model parameters (with or without extrapolation). They are very similar, the former taking coordinates (x, y, z) as new points, the latter one another TensorMesh instance. - New jitted function
njitted.volume_average
for interpolation using the volume-average technique. - New parameter
conjugate
insolver.solver
to permit both Fourier transform conventions. - Added
exit_status
andexit_message
toinfo_dict
. - Add section
Related ecosystem
to documentation.
v0.7.0 : H-field¶
2019-07-05
- New routines:
utils.get_h_field
: Small routine to compute the magnetic field from the electric field using Faraday’s law.utils.get_receiver
: Small wrapper to interpolate a field at receiver positions. Added 3D spline interpolation; is the new default.
- Re-implemented the possibility to define isotropic magnetic permeabilities in
utils.Model
. Magnetic permeability is not tri-axially included in the solver currently; however, it would not be too difficult to include if there is a need. - CPU-graph added on top of RAM-graph.
- Expand
utils.Field
to work with pickle/shelve. - Jit
np.linalg.norm
(njitted.l2norm
). - Use
scooby
(soft dependency) for versioning, renameVersion
toReport
(backwards incompatible). - Bug fixes:
- Small bugfix introduced in ebd2c9d5:
sc_cycle
andlr_cycle
was not updated any longer at the end of a cycle (only affectedsslsolver=True
. - Small bugfix in
utils.get_hx
.
- Small bugfix introduced in ebd2c9d5:
v0.6.2 : CPU & RAM¶
2019-06-03
Further speed and memory improvements:
- Add CPU & RAM-page to documentation.
- Change loop-order from x-z-y to z-x-y in Gauss-Seidel smoothing with line relaxation in y-direction. Hence reversed lexicographical order. This results in a significant speed-up, as x is the fastest changing axis.
- Move total residual computation from
solver.residual
intonjitted.amat_x
. - Simplifications in
utils
:- Simplify
utils.get_source_field
. - Simplify
utils.Model
. - Removed unused timing-stuff from early development.
- Simplify
v0.6.1 : Memory¶
2019-05-28
Memory and speed improvements:
- Only compute residual and l2-norm when absolutely necessary.
- Inplace computations for
np.conjugate
insolver.solver
andnp.subtract
insolver.residual
.
v0.6.0 : RegularGridInterpolator¶
2019-05-26
- Replace
scipy.interpolate.RegularGridInterpolator
with a custom tailored version of it (solver.RegularGridProlongator); results in twice as fast prolongation. - Simplify the fine-grid computation in
prolongation
without usinggridE*
; memory friendlier. - Submission to JOSS.
- Add Multi-what?-page to documentation.
- Some major refactoring, particularly in
solver
. - Removed
discretize
as hard dependency. - Rename
rdir
andldir
(and relatedp*dir
;*cycle
) to the more descriptivesc_dir
andlr_dir
.
v0.5.0 : Accept any grid size¶
2019-05-01
- First open-source version.
- Include RTD, Travis, Coveralls, Codacy, and Zenodo. No benchmarks yet.
- Accepts now any grid size (warns if a bad grid size for MG is provided).
- Coarsens now to the lowest level of each dimension, not only to the coarsest level of the smallest dimension.
- Combined
restrict_rx
,restrict_ry
, andrestrict_rz
torestrict
. - Improve speed by passing pre-allocated arrays to jitted functions.
- Store
res_y
,res_z
and correspondingeta_y
,eta_z
only ifres_y
,res_z
were provided in initial call toutils.model
. - Change
zeta
tov_mu_r
. - Include rudimentary
TensorMesh
-class inutils
; removes hard dependency ondiscretize
. - Bugfix: Take a provided
efield
into account; don’t return if provided.
v0.4.0 : Cholesky¶
2019-03-29
- Use
solve_chol
for everything, removesolve_zlin
. - Moved
mesh.py
and some functionalities fromsolver.py
intoutils.py
. - New mesh-tools. Should move to
discretize
eventually. - Improved source generation tool. Might also move to
discretize
. printversion
is now included inutils
.- Many bug fixes.
- Lots of improvements to tests.
- Lots of improvements to documentation. Amongst other, moved docs from
__init__.py
into the docs rst.
v0.3.0 : Semicoarsening¶
2019-01-18
- Semicoarsening option.
- Number of cells must still be 2^n, but n can be different in the x-, y-, and z-directions.
- Many other iterative solvers from
scipy.sparse.linalg
can be used. It seems to work fine with the following methods:scipy.sparse.linalg.bicgstab()
: BIConjugate Gradient STABilize;scipy.sparse.linalg.cgs()
: Conjugate Gradient Squared;scipy.sparse.linalg.gmres()
: Generalized Minimal RESidual;scipy.sparse.linalg.lgmres()
: Improvement of GMRES using alternating residual vectors;scipy.sparse.linalg.gcrotmk()
: GCROT: Generalized Conjugate Residual with inner Orthogonalization and Outer Truncation.
- The SciPy-solver or MG can be used all in combination or on its own, hence only MG, SciPy-solver with MG preconditioning, only SciPy-solver.
v0.1.0 : Initial¶
2018-12-28
- Standard multigrid with or without BiCGSTAB.
- Tri-axial anisotropy.
- Number of cells must be 2^n, and n has to be the same in the x-, y-, and z-directions.