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[WIP] Implement new gridless model#157

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AngelFP wants to merge 142 commits intodevAngelFP/Wake-T:devfrom feature/new_gridless_modelAngelFP/Wake-T:feature/new_gridless_modelCopy head branch name to clipboard

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Commits on Mar 28, 2023

• Implement new QS model with ions

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• Speed up calculation of psi and dr_psi

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Commits on Mar 29, 2023

• Speed up calculation of dxi_psi

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• Don't push plasma particles after last iteration

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Commits on Mar 30, 2023

• Precalculate logarithms

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• Ensure that leftmost neighboring point is not 0

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• Improve efficiency of plasma particle deposition

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Commits on Jun 16, 2023

• Split calculation of a_i, b_i in several methods

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• Remove unnecessary if

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• Do not use lists in plasma pusher

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• Use jitted PlasmaParticles class

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• Reduce number of arrays

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• Make arrays contiguous

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Commits on Jun 18, 2023

• Reorder spec and remove unnecessary code

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• Move methods into PlasmaParticles class

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• Formatting

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• Make use of max_gamma

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Commits on Jul 4, 2023

• Rename method

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Commits on Jul 6, 2023

• Fix bug in array indexing and ion push

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• Initialize rho_e and rho_i arrays in base class

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• Make use of rho_e and rho_i in new solver

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• Pass ion (instead of electron) array to method

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• Reset plasma electrons also when ion_motion=True

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• Implement smarter boundary condition for psi

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• Fix bug with indexing of right neighbor

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• Always deposit electron and ion density

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• Define species_rho_diags in base RZWakefield

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• Expose mass and charge of plasma particles to user

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Commits on Jul 10, 2023

• Add option to store history of plasma particles

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Commits on Jul 14, 2023

• Allow fields to save species (also in rz)

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• Pass bunch name when gathering fields

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• Add geometry attribute to bunch diags

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• Improvements to plasma particles:

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Commits on Jul 17, 2023

• Implement AdaptiveGrid class

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• Move calculate_bunch_source to dedicated module

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• Split gathering of laser and bunch sources

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• Update source gathering in PlasmaParticles

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• Update solver and wakefield

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Commits on Jul 18, 2023

• Implement radially-dependent ppc

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Commits on Jul 19, 2023

• Speed-up plasma pusher

  AngelFP

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• Upgrade to openpmd-API 0.15

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• Merge branch 'dev' into ion_motion

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• Allow choosing which diagnostics to save

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• Gather laser field and deposit chi only if needed

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• Fix crash when when no bunches are tracked

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• Create bunch sources only when there are bunches

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• Store no particle diagnostics by default

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Commits on Jul 21, 2023

• Calculate psi and derivatives in single method

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• Remove unused code + formatting

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Commits on Jul 22, 2023

• Implement single method to calculate b_theta

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• Divide by radial volume in deposition methods

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• Use numpy error model

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• Implement utils.py

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• Implement non-jitted PlasmaParticles

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• Switch to AB2 pusher

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• Rename file

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Commits on Jul 23, 2023

• Fix bug in diagnostics

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Commits on Jul 24, 2023

• Implement faster gradient

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• Add test

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• Allow deposit_3d_distribution to be jitted

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• Improve efficiency of b_theta and psi calculation

  AngelFP

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• Implement faster bunch source calculation

  AngelFP

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• Reduce overhead of wakefield calculation

  AngelFP

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Commits on Jul 25, 2023

• Improve efficiency of particle history

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• Improve docstrings

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Commits on Aug 4, 2023

• Implement arbitrary radial density profile

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Commits on Aug 11, 2023

• Merge branch 'dev' into ion_motion

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• Improve numba compatibility

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Commits on Aug 25, 2023

• Fix bug in plasma pusher

  AngelFP

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• Merge branch 'ion_motion' of https://github.com/AngelFP/Wake-T into ion_motion

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• Merge branch 'dev' into ion_motion

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Commits on Aug 28, 2023

• Include 'a' as default field diag

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Commits on Aug 31, 2023

• Improve radial gradient on axis

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• Improve docstring

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• Merge branch 'dev' into ion_motion

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Commits on Sep 1, 2023

• Rename plasma species diagnostics

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• Calculate adaptive grid fields on wakefield update

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• Calculate adaptive grid fields only if needed

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Commits on Sep 6, 2023

• Allow some bunches to not use an adaptive grid

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Commits on Sep 12, 2023

• Merge branch 'dev' into ion_motion

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Commits on Sep 14, 2023

• Add guard cells to adaptive grids

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• Add guard cells to nr

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• Fix wrong symbol

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Commits on Sep 15, 2023

• Implement fixed radial extent of adaptive grids

  AngelFP

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• Use new gradient functions in adaptive grid

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Commits on Oct 17, 2023

• Merge branch 'dev' into ion_motion

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Commits on Oct 25, 2023

• Fix bug causing the grid to continuously update

  AngelFP

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• Merge branch 'ion_motion' of https://github.com/AngelFP/Wake-T into ion_motion

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• Small fixes

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Commits on Nov 1, 2023

• Do not recalculate dxi and dr on _gather

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Commits on Nov 2, 2023

• Improve 3d deposition methods for adaptive grids

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• Improve bunch source gathering for adaptive grids

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• Calculate bunch source also on guard cells

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• Improved plasma field gathering for adaptive grids

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• Radial limit for AGs and gather/deposit multigrid

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• Remove unused attribute

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• Add tests for adaptive grids

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• Merge branch 'dev' into ion_motion

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Commits on Mar 14, 2024

• Merge branch 'dev' into ion_motion

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• Implement conversion from r to x in plasma particle diagnostics

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Commits on Mar 25, 2024

• Add bunch charge density to total density array

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Commits on Mar 28, 2024

• Implement new solver without neighbors, using q_center

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Commits on Apr 19, 2024

• Fix bug

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• Fix bug

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Commits on Apr 20, 2024

• Update test

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• Update test data

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• Update test

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• Update docstring

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Commits on Apr 30, 2024

• Merge branch 'dev' into ion_motion_new

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• Merge branch 'dev' into ion_motion_new

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• Add backwards compatibility with parabolic coefficient

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• Merge branch 'dev' into ion_motion_new_pc

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  02a133e

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• Fix bug

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• Improve backwards compatibility of plasma pusher

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• Prevent psi from going above 1

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Commits on May 2, 2024

• Merge branch 'dev' into ion_motion_new

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• Fix typo

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• Add deprecation warnings

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• Move backward compatibility checks to the top

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Commits on May 3, 2024

• Add final spot size check

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• Merge branch 'dev' into ion_motion_new

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• Shorten docstrings

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Commits on May 10, 2024

• Separate q into q and w, make q_species a float

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Commits on May 15, 2024

• Remove unused code

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• Merge branch 'dev' into feature/new_gridless_model

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Commits on Jun 3, 2024

• added id as a dictionary element in the output of get_openpmd_diagnostics_data in the particle bunch

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• added the particle tags to the copy routine

  rob-shalloo

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• added if statement to prevent tags getting added if they dont exist

  rob-shalloo

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• added the tags to the id output for the open pmd diagnostics

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Commits on Jun 18, 2024

• Formatting

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• Merge methods

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• Formatting

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• Formatting

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Commits on Jul 5, 2024

• Enable the use of auto_dt_bunch in FieldElement and PlasmaStage.

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• Change the syntax a bit.

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Commits on Jul 8, 2024

• Increase a bit the tolerance to let the test pass.

  delaossa

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• Increase a bit the tolerance to let the tess pass (2).

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Commits on Oct 1, 2024

• Merge pull request #158 from rob-shalloo/origin/trackingParticles

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• Merge pull request #159 from delaossa/feature/auto_dt_bunch

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• Merge pull request #160 from delaossa/feature/new_gridless_model

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• Rename tag to id

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• Fix test

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