Code

Geometry upgrade#166

Code

Merged

mrhardman merged 75 commits intomastermabarnes/moment_kinetics:masterfrom geometry-upgrademabarnes/moment_kinetics:geometry-upgradeCopy head branch name to clipboardMar 15, 2024

+2,225-376

Commits

Commits on Dec 4, 2023

• Modifications to the structure of the geometry inputs and how geometric coefficents are used to permit extending to more complex magnetic geometry. Input options (including defaults) are modified b…

  Show description for 6620bf8
  mrhardman

  committed
  6620bf8

  Copy full SHA for 6620bf8

Commits on Dec 6, 2023

• Added advection of vperp by inhomogeneity of the magnetic field, for use in a non-trivial geometry. Untested.

  mrhardman

  committed
  011e598

  Copy full SHA for 011e598

• Added magnetic mirror term for standard drift-kinetic option. Not tested.

  mrhardman

  committed
  d4ecf2f

  Copy full SHA for d4ecf2f

• Address issue #111 by incorporating the true geometric factor in the ExB drift terms. Note that this means that ExB drifts will only be present if bzeta > 0, so the pitch input parameter must be se…

  Show description for 250a324
  mrhardman

  committed
  250a324

  Copy full SHA for 250a324

Commits on Dec 10, 2023

• Merge branch 'merge_fkpl_collisions' into geometry-upgrade to obtain access to the D0 derivative vector for chebyshev grids.

  mrhardman

  committed
  25355e8

  Copy full SHA for 25355e8

Commits on Dec 14, 2023

• Merge branch 'master' into geometry-upgrade

  mrhardman

  committed
  1362835

  Copy full SHA for 1362835

• Merge branch 'master' into geometry-upgrade

  mrhardman

  committed
  b90dec0

  Copy full SHA for b90dec0

• Add a 1D-mirror mock-up of the magnetic field strength, selected with geometry_option='1D-mirror'. Use the parameter DeltaB to set the change in the magnetic field strength from the centre to the e…

  Show description for 80cca93
  mrhardman

  committed
  80cca93

  Copy full SHA for 80cca93

• Bring post_processing.jl up to date.

  mrhardman

  committed
  85aef94

  Copy full SHA for 85aef94

• Example for using the 1D mirror geometry.

  mrhardman

  committed
  3b7bf89

  Copy full SHA for 3b7bf89

Commits on Jan 4, 2024

• Catch for DeltaB too negative.

  mrhardman

  committed
  183c6f9

  Copy full SHA for 183c6f9

• Add struct of symbolic variables for magnetic geometry in the manufactured_solns.jl module.

  mrhardman

  committed
  5c8e587

  Copy full SHA for 5c8e587

• Refactor manufactured solutions module to permit tests with magnetic mirror geometry in 1D and magnetic mirror terms.

  mrhardman

  committed
  3ce44f3

  Copy full SHA for 3ce44f3

• Input file for MMS test with mirror geometry.

  mrhardman

  committed
  a27d84b

  Copy full SHA for a27d84b

• Merge branch 'master' into geometry-upgrade

  mrhardman

  committed
  340eb39

  Copy full SHA for 340eb39

• Parentheses for clarity.

  mrhardman

  committed
  a3331d5

  Copy full SHA for a3331d5

• Correct factor of 2 error in dvpadt.

  mrhardman

  committed
  cc3e837

  Copy full SHA for cc3e837

• Check of the manufactured solutions geometry and correction to magnetic field strength derivative.

  mrhardman

  committed
  c689137

  Copy full SHA for c689137

Commits on Jan 8, 2024

• Try to tidy up the implementation by using the adiabatic invariant mu as a shorthand in the mirror term.

  mrhardman

  committed
  2e0b469

  Copy full SHA for 2e0b469

Commits on Jan 9, 2024

• speculative @views statments.

  mrhardman

  committed
  c6e7401

  Copy full SHA for c6e7401

• Correct several mistakes in the vperp advection implementation. Primarily, to restrict vperp advection to cases with r.n > 1, after relaxing this constraint in time_advance.jl, the remaining bugs i…

  Show description for 57b8b1a
  mrhardman

  committed
  57b8b1a

  Copy full SHA for 57b8b1a

• Safely initialise the advect[is].speed array in the case that the coordinate has coord.n = 1, but the corresponding advect[is].speed array is used in the calculation of another quantity (e.g. r.n =…

  Show description for 868edcc
  mrhardman

  committed
  868edcc

  Copy full SHA for 868edcc

• Use stricter typing in the geometric_coefficients_sym struct.

  mrhardman

  committed
  d338cd7

  Copy full SHA for d338cd7

• Input file showing almost machine precision errors in a manufactured solutions test of a 1D mirror geometry.

  mrhardman

  committed
  073423c

  Copy full SHA for 073423c

Commits on Jan 10, 2024

• Initial addition of a geometry option that will in the future support magnetic drifts. Further work required to make options to determine whether or not r is the cylindrical radial coordinate or a …

  Show description for 965dfae
  mrhardman

  committed
  965dfae

  Copy full SHA for 965dfae

Commits on Jan 24, 2024

• Bring run_MMS_test.jl to a usable state and significant refactoring to permit interactive usage.

  mrhardman

  committed
  89a9aa8

  Copy full SHA for 89a9aa8

• Input files for Mirror MMS test.

  mrhardman

  committed
  7152d22

  Copy full SHA for 7152d22

Commits on Jan 25, 2024

• Added vperp_diffusion flag to advance struct and use this to test when to apply the boundary conditions on vperp, also add a test of the sign of the advection speed to determine when to impose a bo…

  Show description for 9a78fe0
  mrhardman

  committed
  9a78fe0

  Copy full SHA for 9a78fe0

Commits on Jan 26, 2024

• Addition of test of derivative of exp(-y^2) at y = 0.

  mrhardman

  committed
  4b57277

  Copy full SHA for 4b57277

• Fix minor shared-memory bug

  Show description for 3cdff8c
  johnomotani

  committed
  3cdff8c

  Copy full SHA for 3cdff8c

Commits on Jan 28, 2024

• Fix manufactured_solutions() input in makie_post_processing

  johnomotani

  committed
  13330b3

  Copy full SHA for 13330b3

Commits on Jan 30, 2024

• Merge branch 'geometry-upgrade' of https://github.com/mabarnes/moment_kinetics into geometry-upgrade

  mrhardman

  committed
  2d27ea4

  Copy full SHA for 2d27ea4

Commits on Jan 31, 2024

• Correct silly factor of 2 error in the calculation for the vector D0 for d f / d coord at coord = -1 for Radau elements (which avoid the point at x = -1).

  mrhardman

  committed
  a9a26f2

  Copy full SHA for a9a26f2

• Correct error where "gausslegendre_pseudospectral" option was tested by default instead of "chebyshev_pseudospectral" option. discretization is now an optional argument so that this script can be u…

  Show description for ba47914
  mrhardman

  committed
  ba47914

  Copy full SHA for ba47914

• Input files for the mirror manufactured solutions test.

  mrhardman

  committed
  8268c80

  Copy full SHA for 8268c80

• Bring ticks to appropriate values for 1D-mirror MMS test.

  mrhardman

  committed
  cdec9ff

  Copy full SHA for cdec9ff

• Test the 1D mirror geometry with another ngrid.

  mrhardman

  committed
  d29a6a7

  Copy full SHA for d29a6a7

• Permit manufactured solutions testing in a 2D flux tube with a radial domain and the "1D-mirror" geometry. Correct the symbolic distribution function and symbolic upari to reflect the new form of t…

  Show description for f132277
  mrhardman

  committed
  f132277

  Copy full SHA for f132277

Commits on Feb 1, 2024

• Attempt to merge geometry-upgrade and separate-postprocessing-packages.

  mrhardman

  committed
  d588ca3

  Copy full SHA for d588ca3

• Merge branch 'geometry-upgrade' into separate-postprocessing-packages-merge-geometry-upgrade

  johnomotani

  committed
  086dd47

  Copy full SHA for 086dd47

• Don't make bin/julia a symlink when enabling plots_post_processing

  Show description for 054431b
  johnomotani

  committed
  054431b

  Copy full SHA for 054431b

• Restore split into separate get_geometry() and get_composition()

  johnomotani

  committed
  c0bf27f

  Copy full SHA for c0bf27f

Commits on Feb 2, 2024

• Verion of merged code that runsi (and appears to be correct for runs of one core), but which seems to have a bug in the 1D-mirror MMS test for multiple cores (this could be due to compilation issues).

  

  Michael Hardman

  committed
  5b6eb52

  Copy full SHA for 5b6eb52

• Remove print statements.

  

  Michael Hardman

  committed
  2337c89

  Copy full SHA for 2337c89

• Fix export of get_geometry() and get_composition()

  johnomotani

  committed
  6e9e2e3

  Copy full SHA for 6e9e2e3

Commits on Feb 4, 2024

• Modify how run_mms_test() is imported to reflect new package structure.

  

  Michael Hardman

  committed
  e0ef452

  Copy full SHA for e0ef452

• Add option for 2D2V mirror test.

  

  Michael Hardman

  committed
  d8a6f0f

  Copy full SHA for d8a6f0f

• Input files for MMS test with a 1D mirror geometry and a radial dimension.

  

  Michael Hardman

  committed
  5142847

  Copy full SHA for 5142847

• Attempt to merge the two separate-package and geometry-upgrade merge branches.

  mrhardman

  committed
  c6aadcc

  Copy full SHA for c6aadcc

Commits on Feb 5, 2024

• Fokker Planck relaxation example with the same resolutions as used for the ExCALIBUR report.

  

  Michael Hardman

  committed
  0acbf8c

  Copy full SHA for 0acbf8c

• Expected scaling for 2D2V plot.

  

  Michael Hardman

  committed
  9ff5669

  Copy full SHA for 9ff5669

• Merge branch 'geometry-upgrade-separate-packages' of https://github.com/mabarnes/moment_kinetics into geometry-upgrade-separate-packages

  

  Michael Hardman

  committed
  f5c4c8d

  Copy full SHA for f5c4c8d

Commits on Feb 6, 2024

• Remove unnecessary packages.

  

  Michael Hardman

  committed
  5abac5e

  Copy full SHA for 5abac5e

• Change the specification of the magnetic geometry to add a finite bzeta to the 1D mirror option to allow a nonzero ExB drift to emerge in 2D simulations.

  

  Michael Hardman

  committed
  9330f25

  Copy full SHA for 9330f25

• Change comment to reflect correct definition of Jacobian.

  

  Michael Hardman

  committed
  d9b5aab

  Copy full SHA for d9b5aab

Commits on Feb 7, 2024

• Merge pull request #179 from mabarnes/geometry-upgrade-separate-packages

  Show description for 4c1415d
  

  mrhardman

  authored
  4c1415d

  Copy full SHA for 4c1415d

Commits on Mar 13, 2024

• Create API docs page for geo module

  johnomotani

  committed
  d91aca7

  Copy full SHA for d91aca7

• Check for removed options: error telling user to update input file

  Show description for b52f943
  johnomotani

  committed
  b52f943

  Copy full SHA for b52f943

• Error if dBdz!=0 for moment-kinetic modes

  Show description for b3ad10b
  johnomotani

  committed
  b3ad10b

  Copy full SHA for b3ad10b

• Remove debug print

  johnomotani

  committed
  347ff6b

  Copy full SHA for 347ff6b

• Simplify 1D geometry check

  johnomotani

  committed
  9489a2f

  Copy full SHA for 9489a2f

• Tidy up setting of advance flags

  johnomotani

  committed
  5e821b2

  Copy full SHA for 5e821b2

• Use one-liner instead of defining geofac

  Show description for 0718045
  johnomotani

  committed
  0718045

  Copy full SHA for 0718045

• Remove commented-out lines

  johnomotani

  committed
  90c1027

  Copy full SHA for 90c1027

• Remove uses of Bzed and Bmag in example inputs and test scripts

  Show description for 842bee5
  johnomotani

  committed
  842bee5

  Copy full SHA for 842bee5

• Improve comment regarding updating vperp_advect.

  mrhardman

  committed
  8605909

  Copy full SHA for 8605909

• Merge branch 'geometry-upgrade' of https://github.com/mabarnes/moment_kinetics into geometry-upgrade

  mrhardman

  committed
  8af9553

  Copy full SHA for 8af9553

• Fix geometry check for moment-kinetic cases

  johnomotani

  committed
  7173367

  Copy full SHA for 7173367

• Create geometry.md

  Show description for 0b1190e
  

  mrhardman

  authored
  0b1190e

  Copy full SHA for 0b1190e

• Merge branch 'master' into geometry-upgrade

  johnomotani

  authored
  b3bf060

  Copy full SHA for b3bf060

• Add toml namelist [geometry] to the input files and modify existing input files to be compatible with this change. This changes is not backwards compatible.

  mrhardman

  committed
  7709ab4

  Copy full SHA for 7709ab4

Commits on Mar 14, 2024

• Update geometry.md

  Show description for df1cff5
  

  mrhardman

  authored
  df1cff5

  Copy full SHA for df1cff5

• Merge branch 'master' into geometry-upgrade

  mrhardman

  committed
  70b6409

  Copy full SHA for 70b6409

• Update geo.jl

  Show description for a13f9a0
  

  mrhardman

  authored
  a13f9a0

  Copy full SHA for a13f9a0

• Update debug_test inputs for changes to geometry input

  johnomotani

  committed
  b6b7df0

  Copy full SHA for b6b7df0