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Dfn transport #219

Merged
merged 108 commits into from
Feb 21, 2019
Merged

Dfn transport #219

merged 108 commits into from
Feb 21, 2019

Commits on Nov 20, 2018

  1. error fix in the importer dfn_3d_from_fab, probably due to an old imp… 

    …lementation
    @alessiofumagalli
    alessiofumagalli committed Nov 20, 2018
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  2. fix the ndof for the upwind coupler, this is not really an error but … 

    …an aesthetic fix
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    alessiofumagalli committed Nov 20, 2018
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  3. introduce a first example for a dfn_transport, it compute flux with d… 

    …arcy and then a advection+diffusion with tpfa and upwind
    @alessiofumagalli
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  4. update example1 by make the bc easier to define in the dfn_transport

    @alessiofumagalli
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  5. add discretization for the mass matrix, used in the time dependent part

    @alessiofumagalli
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  6. add second example of a dfn with flow and time dependent advection+di… 

    …ffusion
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    alessiofumagalli committed Nov 20, 2018
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Commits on Nov 26, 2018

  1. Merge branch 'develop' into dfn_transport

    @alessiofumagalli
    alessiofumagalli committed Nov 26, 2018
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  2. add a tolerance in the rotation of the grid, to overwrite default val… 

    …ue. for method mvem/rt0
    @alessiofumagalli
    alessiofumagalli committed Nov 26, 2018
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  3. in the comp_geom.map_grid propagate the input tolerance into the proj… 

    …ect_plane_matrix and project_line_matrix
    @alessiofumagalli
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  4. add a new example in the dfn_transport

    @alessiofumagalli
    alessiofumagalli committed Nov 26, 2018
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Commits on Nov 27, 2018

  1. dfn transport: example 3. Add extra parameters in the data useful for… 

    … the exporting
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  2. add post_process script to summarise data

    @alessiofumagalli
    alessiofumagalli committed Nov 27, 2018
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  3. add example 4 for the dfn transport test case

    @alessiofumagalli
    alessiofumagalli committed Nov 27, 2018
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Commits on Nov 28, 2018

  1. in dfn_transport rename a folder which will be not included in a poss… 

    …ible publication
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  2. in dfn_transport rename a second folder which will be not included in… 

    … a possible publication
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  3. in dfn_transport rename a folder where the example is now the possibl… 

    …e second
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  4. in dfn_transport rename a folder where the example is now the possibl… 

    …e third
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  5. add a function to compute the flux jump on each trace, useful for the… 

    … dfn_transport
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    alessiofumagalli committed Nov 28, 2018
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Commits on Dec 3, 2018

  1. Merge branch 'develop' into dfn_transport

    @alessiofumagalli
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  2. in the dfn_transport examples: adapt the discretization setup to the … 

    …new implementation,
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  3. in dfn_transport, add first example and update example 2

    @alessiofumagalli
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  4. in the dfn_transport remove useless data file, now it's handled in a … 

    …consistent way among examples
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    alessiofumagalli committed Dec 3, 2018
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Commits on Dec 4, 2018

  1. dfn transport - update the main file

    @alessiofumagalli
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  2. dfn transport, add the geometries

    @alessiofumagalli
    alessiofumagalli committed Dec 4, 2018
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  3. dfn transport, the first example loops on all the considered geometries

    @alessiofumagalli
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  4. consider the 1d with (almost) empty volume, this is just a temporal fix

    @alessiofumagalli
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  5. dfn transport, define two scenarios (boundary conditions related) for… 

    … the example 3
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Commits on Dec 5, 2018

  1. dfn transport: in the mass discretization fix the behavior for the lo… 

    …wer dimensional objects
    @alessiofumagalli
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Commits on Dec 6, 2018

  1. Merge branch 'develop' into dfn_transport 

    Conflicts:
    src/porepy/numerics/interface_laws/elliptic_interface_laws.py
    @alessiofumagalli
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  2. dfn transport, allow the exporting of the P0 velocity

    @alessiofumagalli
    alessiofumagalli committed Dec 6, 2018
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  3. dfn transport, update test case of complex geometry

    @alessiofumagalli
    alessiofumagalli committed Dec 6, 2018
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  4. allow to cut the dfn while importing by giving a box

    @alessiofumagalli
    alessiofumagalli committed Dec 6, 2018
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  5. dfn transport, add extra variables for post process

    @alessiofumagalli
    alessiofumagalli committed Dec 6, 2018
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  6. remove debug point

    @alessiofumagalli
    alessiofumagalli committed Dec 6, 2018
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  7. dfn transport, add post process script for example 1

    @alessiofumagalli
    alessiofumagalli committed Dec 6, 2018
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  8. dfn transport, add outflow computation

    @alessiofumagalli
    alessiofumagalli committed Dec 6, 2018
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  9. dfn transport, update post process and plot-over-time example 1

    @alessiofumagalli
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Commits on Dec 11, 2018

  1. Merge branch 'develop' into dfn_transport 

    Conflicts:
	src/porepy/fracs/meshing.py
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  2. dfn transport, remove useless dfn geometry

    @alessiofumagalli
    alessiofumagalli committed Dec 11, 2018
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  3. dfn transport, rename file according to the order of the examples

    @alessiofumagalli
    alessiofumagalli committed Dec 11, 2018
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  4. dfn transport, rename file according to the order of the examples

    @alessiofumagalli
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  5. dfn transport, remove useless dfn geometries

    @alessiofumagalli
    alessiofumagalli committed Dec 11, 2018
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  6. dfn transport, update the geometry of example 3 by cutting the domain

    @alessiofumagalli
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  7. dfn transport, consider an already cut dfn instead of using a box arg… 

    …ument
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  8. dfn transport, add the possibility to impose a different boundary con… 

    …dition value in the complex dfn example
    @alessiofumagalli
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  9. Merge branch 'dfn_transport' of github.com:pmgbergen/porepy into dfn_… 

    …transport
    @alessiofumagalli
    alessiofumagalli committed Dec 11, 2018
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Commits on Dec 12, 2018

  1. dfn trasnport, add more time steps and increase the pressure gradient

    @alessiofumagalli
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  2. dfn transport, add the possibility to define physical parameters for … 

    …the simulation
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    alessiofumagalli committed Dec 12, 2018
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  3. dfn transport, add the possibility to impose the initial condition

    @alessiofumagalli
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Commits on Jan 9, 2019

  1. in rt0 consider a custom tolerance (with a default value) in the mapp… 

    …ing of the grid
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  2. in mpfa consider a custom tolerance (with a default value) in the map… 

    …ping of the grid
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  3. in the extract_flux and extract_pressure for the dual_elliptic remove… 

    … the default value for the data
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  4. in mvem consider a custom tolerance (with a default value) in the map… 

    …ping of the grid
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  5. update the computation of extract flux for fv scheme by using the new… 

    … interface with DISCRETIZATION_MATRICES and PARAMETERS
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  6. in the example of dfn_transport, update the list of discretization an… 

    …d make the flow and flow_data general
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  7. dfn_transport, adapt the main files of the example with the new inter… 

    …face
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Commits on Jan 11, 2019

  1. dfn_transport, in the tests consider the outflow without the flux

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  2. dfn_transport, update the post process files

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Commits on Jan 14, 2019

  1. dfn_transport, update outflow computation

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  2. dfn_transport, update post process computation

    @alessiofumagalli
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  3. dfn_transport, avoid mpfa in the solvers

    @alessiofumagalli
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  4. dfn_transport, for the mvem consider the coarsening with the same num… 

    …ber of elements
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Commits on Jan 16, 2019

  1. dfn_trasnport, update definition of mesh size for example 1

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Commits on Jan 17, 2019

  1. dfn_transport, extract the flux and the pressure

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Commits on Jan 21, 2019

  1. dfn_transport, fix computation of flux

    @alessiofumagalli
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  2. dfn_tranport, example 1 fix the grid size for the examples

    @alessiofumagalli
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  3. dfn_transport, add the export of the grids for the MVEM case

    @alessiofumagalli
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  4. dfn_transport, update the post process script

    @alessiofumagalli
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  5. dfn_transport, update the plot over time script

    @alessiofumagalli
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  6. dfn_transport, update the plot over time script

    @alessiofumagalli
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  7. Merge branch 'dfn_transport' of github.com:pmgbergen/porepy into dfn_… 

    …transport
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Commits on Jan 23, 2019

  1. during the coarsening keep track of the new mapping also for the face… 

    …_cells
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  2. dfn_transport, since we couple MVEM with primal VEM (from Torino) no … 

    …need to run the transport
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  3. bug fix, when computing the cell center of a star shaped cell shift t… 

    …he coordinate first. The problem was related on 2d fractures.
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  4. dfn_transport, small fix in discretization

    @alessiofumagalli
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Commits on Jan 24, 2019

  1. add to the exporting also the face boundary tag

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Commits on Jan 29, 2019

  1. dfn_transport, after a bug fixed reactivate the mvem simulation

    @alessiofumagalli
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Commits on Feb 5, 2019

  1. dfn_transport, set up mvem coarse grid for case 2

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  2. dfn_trasnport, update post process example 1

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Commits on Feb 6, 2019

  1. dfn_transport, consider Aavatsmark way of computing transmissibilitie… 

    …s for the TPFA
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Commits on Feb 18, 2019

  1. Merge branch 'develop' into dfn_transport

    @alessiofumagalli
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  2. remove useless functions, use now the new interface

    @alessiofumagalli
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  3. dfn_transport, remove unused mpfa scheme

    @alessiofumagalli
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  4. dfn_transport, change name from PressureTrace to EmptyDiscretization … 

    …to handle a discretization scheme on the traces
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  5. dfn_transport, consider the time step explicitly after the creation o… 

    …f the mass matrix
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  6. dfn_transport, remove useless intersection files

    @alessiofumagalli
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  7. dfn_transport, in the example use the new interface to create the grids

    @alessiofumagalli
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  8. dfn_transport, remove unused examples

    @alessiofumagalli
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  9. fix default value for the extract pressure and flux

    @alessiofumagalli
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  10. in the mpfa set the default value for the tolerance to 1e-5, the one … 

    …default in the function used in comp_geom
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  11. change name from EmptyDiscretization to Cell_dof_face_dof_map

    @alessiofumagalli
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  12. remove unused files

    @alessiofumagalli
    alessiofumagalli committed Feb 18, 2019
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  13. remove useless import and logger

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    alessiofumagalli committed Feb 18, 2019
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  14. re-introduce the inverter for mpfa that was deleted, not sure why

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    alessiofumagalli committed Feb 18, 2019
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  15. dfn tranport, add post process file

    @alessiofumagalli
    alessiofumagalli committed Feb 18, 2019
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  16. dfn transport, introduce a reaction and source term in the discretiza… 

    …tion of the heat equation
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    alessiofumagalli committed Feb 18, 2019
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  17. dfn transport, update example3 to consider the reaction and source term

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    alessiofumagalli committed Feb 18, 2019
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  18. change the name of Integral to ScalarSource, the new implementation h… 

    …andle only scalar source term in primal formulation (currently tpfa, mpfa)
    @alessiofumagalli
    alessiofumagalli committed Feb 18, 2019
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  19. dfn transport, update post process plot over time

    @alessiofumagalli
    alessiofumagalli committed Feb 18, 2019
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Commits on Feb 19, 2019

  1. fix pytest, from Integral to ScalarSource

    @alessiofumagalli
    alessiofumagalli committed Feb 19, 2019
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  2. modifications according to codacy

    @alessiofumagalli
    alessiofumagalli committed Feb 19, 2019
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  3. fix other suggestions from codacy

    @alessiofumagalli
    alessiofumagalli committed Feb 19, 2019
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Commits on Feb 20, 2019

  1. change name from Cell_dof_face_dof_map to CellDofFaceDofMap

    @alessiofumagalli
    alessiofumagalli committed Feb 20, 2019
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  2. add comments to the function star_shape_cell_centers

    @alessiofumagalli
    alessiofumagalli committed Feb 20, 2019
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  3. change from tol to deviation_from_plane_tol + additional comments

    @alessiofumagalli
    alessiofumagalli committed Feb 20, 2019
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  4. remove useless -------- line

    @alessiofumagalli
    alessiofumagalli committed Feb 20, 2019
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  5. run black on the modified files of the branch dfn_transport

    @alessiofumagalli
    alessiofumagalli committed Feb 20, 2019
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Commits on Feb 21, 2019

  1. revert a part of the code to a previous status in elliptic interface … 

    …laws
    @alessiofumagalli
    alessiofumagalli committed Feb 21, 2019
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