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Impl ordinary diff equation solver #77

Merged
merged 328 commits into from
Mar 8, 2024
Merged

Impl ordinary diff equation solver #77

merged 328 commits into from
Mar 8, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Feb 5, 2024

  1. Fix bugs in explicit RK nd ODE solver

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  2. [wip] Add sample ODE

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  3. Fix sample

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  4. Add test

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  5. [Important] Rename parameters

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    cpmech committed Feb 5, 2024
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  6. [wip] Organize parameters

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  7. Rename files

    @cpmech
    cpmech committed Feb 5, 2024
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  8. Rename Params

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  9. Rename Solver

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    cpmech committed Feb 5, 2024
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  10. Rename System

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    cpmech committed Feb 5, 2024
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  11. Fix doc

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    cpmech committed Feb 5, 2024
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  12. Remove unused files

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    cpmech committed Feb 5, 2024
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  13. Improve doc

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    cpmech committed Feb 5, 2024
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  14. Improve params checks and comments

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    cpmech committed Feb 5, 2024
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  15. Fix check

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Commits on Feb 6, 2024

  1. Improve Params

    @cpmech
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  2. Improve test

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    cpmech committed Feb 6, 2024
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  3. [wip] Radau5

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    cpmech committed Feb 6, 2024
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  4. Remove phantom data

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  5. [wip] Radau5

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  6. [sparse] Impl Symmetry::No and remove Option<Symmetry>

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Commits on Feb 8, 2024

  1. Remove use of rmp-serde in tests

    @cpmech
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  2. [sparse] Impl serialize for enums

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  3. Make CooMatrix generic

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  4. [sparse] Fix bug: mat_vec_mul needs to use alpha in symmetric case

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  5. Add tests

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  6. [wip] Important: Impl COO to CSC directly

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  7. [wip] Coo to Csc matrix

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Commits on Feb 9, 2024

  1. Save Coo to Csc temp vectors in CscMatrix

    @cpmech
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  2. Improve comments

    @cpmech
    cpmech committed Feb 9, 2024
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  3. Improve comment

    @cpmech
    cpmech committed Feb 9, 2024
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  4. Remove unnecessary cast

    @cpmech
    cpmech committed Feb 9, 2024
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  5. [sparse] Use samples in tests

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  6. [sparse] Use samples in tests

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  7. [sparse] Add tests

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  8. [sparse] Add tests

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  9. [sparse] Add tests

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  10. [sparse] Add aux code

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  11. [sparse] Fix comment in sample

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  12. [sparse] Shuffle sample data

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  13. [sparse] Improve comment

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  14. [sparse] Important: replace Coo to Csr with Davis' code

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  15. [sparse] Improve comments

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  16. [sparse] Remove unused comment

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  17. [sparse] Impl serialize + deserialize for Csc and Csr matrices

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  18. [sparse] Improve sorting in Coo to Csr conversion

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    cpmech committed Feb 9, 2024
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  19. [sparse] Improve comments

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  20. Improve comments about types

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  21. [sparse] Make CSC and CSR matrices generic. Working on Complex numbers

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  22. [sparse] Fix doc

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Commits on Feb 10, 2024

  1. [sparse] Add tests

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  2. [sparse] Add sample

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  3. [sparse] Add tests

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  4. [sparse] Add sample

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  5. [sparse] Add sample

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  6. [sparse] Add tests

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  7. [sparse] Add tests

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  8. [sparse] Add dup and shuffle samples

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Commits on Feb 11, 2024

  1. [sparse] Fix grammar

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  2. [sparse] Impl serialize for SparseMatrix

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    cpmech committed Feb 11, 2024
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  3. [sparse] Use unwrap where an error cannot happen

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  4. [sparse] Add tests

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  5. [sparse] Make SparseMatrix generic

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Commits on Feb 12, 2024

  1. Merge branch 'main' into impl-ordinary-diff-equation-solver

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  2. Merge branch 'main' into impl-ordinary-diff-equation-solver

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  3. [ode] Fix dep version

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    cpmech committed Feb 12, 2024
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  4. [wip] Impl real and imag parts of the mantissa in stats

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Commits on Feb 13, 2024

  1. [lab] Impl complex vec norm and update

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  2. [lab] Replace http with https for netlib links

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  3. [lab] Impl complex_mat_update

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  4. [lab] Fix doc tests

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    cpmech committed Feb 13, 2024
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  5. [sparse] Impl complex option in VerifyLinSys

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  6. [sparse] Rename method from of VerifyLinSys

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  7. [sparse] Fix doc test

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Commits on Feb 14, 2024

  1. [sparse] [wip] Complex UMFPACK

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  2. [lab] Impl complex mat copy and inverse

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  3. [sparse] Add sample

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  4. [sparse] [wip] Add test

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  5. [lab] Add test

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  6. [sparse] Improve sample

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  7. [sparse] Fix test

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  8. [sparse] Add sample

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  9. [sparse] Add test

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  10. [sparse] Add tests

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  11. [sparse] Add tests

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  12. [sparse] Improve tests

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  13. [sparse] c_code: set determinant data to zero

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  14. [sparse] Make MUMPS methods pub(crate)

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  15. [sparse] Improve var name in test

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  16. [sparse] Improve samples

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  17. [sparse] Impl Complex solver MUMPS

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  18. [sparse] Add tests

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  19. [sparse] Add tests

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Commits on Feb 15, 2024

  1. [sparse] Organize tests: MUMPS

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  2. [sparse] Improve test

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  3. [sparse] Add example

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  4. [sparse] Improve memcheck

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Commits on Feb 16, 2024

  1. [sparse] [Important] Enforce Send on the C-wrapped structures

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  2. [sparse] Impl augment in CooMatrix

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  3. [sparse] Impl augment for Sparse Matrix

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  4. [sparse] Improve comment

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  5. [sparse] Impl assign and augment for complex COO

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  6. [lab] Improve complex zip methods

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  7. [lab] Impl complex_mat_unzip

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  8. [lab] Impl complex_vec_unzip

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  9. [lab] Improve doc tests

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  10. [lab] Fix mod.rs

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  11. [sparse] [wip] Impl Radau5

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  12. [ode] Improve OdeSolver

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  13. [ode] Rename ode solver files

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  14. [ode] Rename OdeSolverTrait

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  15. [ode] Rename OdeSolver

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Commits on Feb 17, 2024

  1. [lab] Fix test name

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  2. [lab] Fix test name

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  3. [ode] [wip] Radau5

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  4. [ode] Improve params for Radau5

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  5. [sparse] Impl assign method of Coo and Sparse matrices

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  6. [ode] [wip] Radau5 (working)

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Commits on Feb 18, 2024

  1. [ode] Rewrite test function

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Commits on Feb 19, 2024

  1. [ode] Organize params

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  2. [ode] Rename first accept step variable

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  3. [lab] Impl format fortran number

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  4. [ode] Add check for x == x1

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Commits on Feb 20, 2024

  1. [ode] Remove new line in display bench

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  2. [ode] Ignore log txt file

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  3. [ode] Rename success flag in BwEuler

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  4. [ode] Add fortran radau5.f reference results

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  5. [ode] Impl summary for Benchmark

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  6. [ode] Fix radau5 and improve tests

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  7. [ode] Improve tests

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  8. [wip] Impl dense output for Radau5

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  9. [wip] Impl dense output for Radau5

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  10. [wip] Impl Output for Ode Solver

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  11. [ode] Rename push_step method

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Commits on Feb 21, 2024

  1. [ode] Improve dense output comments. Add assert to radau5

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  2. [ode] Improve Output

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  3. [ode] Add prelude

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  4. [ode] Fix dense output

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  5. [ode] Handle unavailable dense output cases

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  6. [ode] Fix saving of optimal stepsize. Improve tests

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  7. [ode] Fix saving accepted steps in dense output

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  8. [ode] Remove redundant step stat. Fix tests

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  9. [ode] Organize tests

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  10. [ode] Rename log files

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  11. [ode] Remove the last three lines of the log files

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  12. [ode] Improve compare script

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  13. [ode] Simplify comparison script

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  14. [ode] Rename debug test files

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  15. [ode] Rename test debug functions

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  16. [ode] Rename test files

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  17. [ode] Rename test functions

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  18. [ode] Fix comment about fortran file

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  19. [ode] Split dopri5 test files

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  20. [ode] [wip] Impl ERK Dense Output

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Commits on Feb 22, 2024

  1. [ode] Improve params

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  2. [ode] Improve doc comments

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    cpmech committed Feb 22, 2024
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  3. [ode] Add comments in Radau5

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  4. [ode] Impl logging in Explicit Runge-Kutta

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  5. [ode] Rename script

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  6. [ode] Print method description in Benchmark

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  7. [ode] Check DoPri5

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  8. [ode] Rename variable

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    cpmech committed Feb 22, 2024
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  9. [ode] Show log for reject steps in ERK

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Commits on Feb 23, 2024

  1. [ode] Important: simplify the main loop. Save h_accepted instead of o… 

    …ptimal
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  2. [ode] Add test

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  3. [ode] Add DoPri8 test

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  4. [ode] Improve doc comment

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  5. [ode] Check for small stepsize. Impl Robertson's equation

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  6. [ode] Remove use of unzip in Radau5

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Commits on Feb 24, 2024

  1. [ode] Improve doc comments

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  2. [ode] Fix x1 in Robertson's equation

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  3. [ode] Add robertson's test

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  4. [ode] Fix robertson's test

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  5. [ode] Remove unnecessary output in robertson's test

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  6. [ode] [wip] Amplifier problem

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Commits on Feb 26, 2024

  1. [lab] Impl matrix conversion to BLAS band format

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  2. [ode] Add the Amplifier test

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Commits on Feb 27, 2024

  1. [ode] Remove stiffness detection temporarily

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  2. [ode] Organize ERK code

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  3. [ode] Simplify ERK dense output struct

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  4. [ode] [wip] Stiffness detection

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  5. [ode] Important: Organize parameters

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  6. [ode] Add tests

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  7. [ode] Rename debug flag

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    cpmech committed Feb 27, 2024
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  8. [ode] Add test: VDP equation with DoPri8

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  9. [ode] Remove temporary stiff detect in ERK

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  10. [ode] Improve comment

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  11. [ode] [wip] Impl stiffness detection

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Commits on Feb 28, 2024

  1. [ode] Improve stiffness detection

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  2. [ode] Simplify detect_stiffness function

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  3. [ode] Debug DoPri8 stiffness detection

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  4. [ode] Add test

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  5. Increase tol to make tests work on different machines

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  6. Increase tol of test for Intel MKL

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  7. Remove unnecessary pub use command

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    cpmech committed Feb 28, 2024
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Commits on Mar 2, 2024

  1. [ode] Improve samples

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  2. [ode] Improve doc comments

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    cpmech committed Mar 2, 2024
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  3. [ode] Improve test script

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  4. [ode] Improve comments

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  5. [ode] Organize tests

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  6. [ode] Improve tests

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  7. [ode] Improve tests

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    cpmech committed Mar 2, 2024
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  8. [ode] Improve test

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  9. [ode] Simplify test

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  10. [ode] Add test

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  11. [ode] Add test

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  12. [ode] Add test

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  13. [ode] Add test

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Commits on Mar 4, 2024

  1. [ode] Rename sample

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  2. [ode] Update Mathematica reference results

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  3. [ode] Add Mathematica code to example

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  4. [ode] Add Mathematica code to test

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  5. [ode] Add Mathematica code to test

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  6. [ode] Rename sample equation

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  7. [ode] Remove sample eq

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  8. [ode] Add sample problem

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Commits on Mar 5, 2024

  1. [ode] Run initialize inside step in Radau5. Simplify BwEuler. Remove … 

    …initialize from Trait
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  2. [ode] Fix handling of unavailable dense output in ERK

    @cpmech
    cpmech committed Mar 5, 2024
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  3. [ode] Improve handling of (un)availability of dense output

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    cpmech committed Mar 5, 2024
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  4. [ode] Fix comment in test

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    cpmech committed Mar 5, 2024
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  5. [ode] Improve test

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  6. [ode] Add test

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  7. [ode] Add test

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  8. [ode] Add test

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  9. [ode] Add test

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  10. [ode] Add test

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  11. [ode] Use unwrap in Samples put command

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  12. [ode] Test num Jacobian in BwEuler

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  13. [ode] Add test

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  14. [ode] Use unwrap where error cannot occur (Radau5)

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  15. [ode] Improve test

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    cpmech committed Mar 5, 2024
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  16. [ode] Rename NoArgs type

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  17. [ode] Add sample ODE

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    cpmech committed Mar 5, 2024
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  18. [ode] Improve handling of final step. Add tests

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    cpmech committed Mar 5, 2024
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  19. [ode] Improve small step checking

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    cpmech committed Mar 5, 2024
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  20. [ode] Remove unnecessary error return in dense_output function (becau… 

    …se it's internal)
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    cpmech committed Mar 5, 2024
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  21. [ode] Improve ErkDenseOut

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    cpmech committed Mar 5, 2024
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Commits on Mar 6, 2024

  1. [ode] Rename sample amplifier to amplifier2t (two-transistors)

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    cpmech committed Mar 6, 2024
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  2. [ode] Impl sample: one-transistor amplifier

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    cpmech committed Mar 6, 2024
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  3. [lab] Impl format scientific

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    cpmech committed Mar 6, 2024
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  4. [ode] Add missing semicolon

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    cpmech committed Mar 6, 2024
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  5. [ode] Test one-transistor amplifier with Radau5

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    cpmech committed Mar 6, 2024
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  6. [ode] Remove two-transistor amplifier example

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    cpmech committed Mar 6, 2024
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Commits on Mar 7, 2024

  1. [ode] Simplify ERK a little

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    cpmech committed Mar 7, 2024
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  2. [sparse] Increase tol of test for Intel MKL

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    cpmech committed Mar 7, 2024
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  3. [ode] Add comments about RK constants

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    cpmech committed Mar 7, 2024
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Commits on Mar 8, 2024

  1. [ode] [Important] Store the mass matrix in System. Use Fn instead of … 

    …FnMut for F and J
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    cpmech committed Mar 8, 2024
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  2. [sparse] [Important] Remove the one_based flag. Store Fortran indices… 

    … in MUMPS struct directly
    @cpmech
    cpmech committed Mar 8, 2024
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  3. [sparse] Fix tests that use intel mkl feature

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    cpmech committed Mar 8, 2024
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  4. [ode] Add tests

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    cpmech committed Mar 8, 2024
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