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Feature/sprkstep #290

Merged
merged 180 commits into from
Jul 19, 2023
Merged

Feature/sprkstep #290

merged 180 commits into from
Jul 19, 2023

Commits on Jun 29, 2023

  1. add kepler problem and try sprk butcher tables

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  2. fix missing return

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  3. optimize rhs

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  4. code working, plot is as it should be

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  5. some upgrades to plotting and example

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  6. switch to one step mode to avoid interpolation

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  7. add increment SPRK algorithm with compensated sums (works for sprk or… 

    …der 1, issue still for more than one stage)
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  8. avoid dense output when we can

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  9. move terr to ark mem

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  10. use tstop instead of compensated sums for tcur

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  11. fix SprkInc implementation

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  12. fix regular sprk implementation

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  13. cleanup

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  14. use sdata

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  15. fix 2nd order table

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  16. update TakeStep_Z to work with sprk

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  17. use less storage in sprk special implementations

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  18. adapt working sort of

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  19. fix methods, add 4th order, adjust adaptivity

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  20. small improvements/fixes

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  21. save work

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  22. sprk stepper compiles and runs, but answer is wrong

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  23. revert changes that were in arkstep

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  24. some minor fixes, still looking for segfault issue

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  25. changes in arkode related to comp summation

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  26. add a bunch more methods

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  27. changes in arkode for compensated sums

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  28. redo incremental formulation

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  29. fix some io options

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  30. fix mc2

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  31. udpates that fix convergence (mostly)

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  32. various cleanup of unused functions

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  33. cleanup the vectors being used

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  34. remove perturbed code

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  35. remove perturbed code

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  36. remove perturbed code

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  37. update example documentation

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  38. format

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  39. updates for adaptivity

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  40. format sprkstep

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  41. add rootfinding

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  42. add missing stdio include

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  43. add hookes law example

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  44. add out files and fix hookes law problem

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  45. order

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  46. use lagrange interpolant

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  47. update plot scripts

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  48. fix adaptive step control (sort-of)

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  49. docs

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  50. finish mathematics section

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  51. cleanup unused functions and add their docs

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  52. automatically use tstop mode if a fixed step is used

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  53. add skeleton

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  54. add example paths to index

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  55. Revert "automatically use tstop mode if a fixed step is used" 

    This reverts commit c9538b2a5d9f8640156f92d6730588353f7c2195.
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  56. add better command line arguments

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  57. add comment regarding SetStopTime use

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  58. add SPRKStep to ARKODE introduction

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  59. cross-verify docs and header/impls

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  60. add support of postprocess functions

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  61. remove inner stepper routine for now

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  62. add SPRK methods to Butcher section

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  63. add stage number to method constants

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  64. ARKodeSPRKMem --> ARKodeSPRKStorage

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  65. add loadbyname function

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  66. add ability to provide method name

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  67. remove adaptivity

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  68. remove remaining adaptivity prototypes

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  69. add SPRK constants to constants table

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  70. clean up plotting scripts

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  71. update cmake to test order

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  72. update answers module to point to staging

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  73. clean up order check

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  74. further updates

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  75. update tarscript

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  76. update defaults

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  77. remove extra script

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  78. add baseline output for examples

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  79. doc and tarscript updates

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  80. update docs

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  81. update examples

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  82. remove extra underscore

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  83. update example header

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  84. clean up

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  85. remove guard on arkGetDky

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  86. bump answers

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  87. update answers

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  88. fix ark profiler reference and tidy

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  89. revert accidental change

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  90. fix warnings

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  91. bump answers

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  92. Apply suggestions from code review 

    Co-authored-by: Daniel R. Reynolds <[email protected]>
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  93. reduce number of output times in ark_kepler

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  94. add more details to changelog

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  95. fix function names

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  96. fix notation

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  97. a bunch of fixes for PR comments

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  98. Update src/arkode/arkode_sprkstep.c 

    Co-authored-by: Daniel R. Reynolds <[email protected]>
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  99. remove controller reference

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  100. check that order is within bounds

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  101. doc updates

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  102. move yerr to SPRKStep

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  103. revert bad change

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  104. compute coefficients directly for 3rd order MacLachlan

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  105. add 6th order Yoshida coefficients for extended precision

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  106. add 8th order McLachlan extended precision coefficients

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  107. Update doc/arkode/guide/source/Mathematics.rst 

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  108. remove unused header

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  109. update McLachlan 8 name

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  110. change ARKODE_SYMPLECTIC to ARKODE_SPRK

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  111. address more PR comments

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  112. update references

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Commits on Jun 30, 2023

  1. add time-dependent example and discuss it in math section

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  2. Update doc/arkode/guide/source/ARKodeSPRKStorage.rst 

    Co-authored-by: Daniel R. Reynolds <[email protected]>
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  3. fix example

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  4. change to time-dependent example

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  5. remove unused macros

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  6. get rid of M_PI

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  7. fix malformed tables

    @balos1
    balos1 committed Jun 30, 2023
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  8. fix reference

    @balos1
    balos1 committed Jun 30, 2023
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  9. give full filenames for out files in tarscript

    @balos1
    balos1 committed Jun 30, 2023
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  10. fix all warnings

    @balos1
    balos1 committed Jun 30, 2023
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  11. fix set but unused warning

    @balos1
    balos1 committed Jun 30, 2023
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Commits on Jul 6, 2023

  1. fix output precisions

    @balos1
    balos1 committed Jul 6, 2023
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  2. add warning about precision for McLachlan 4 and 5

    @balos1
    balos1 committed Jul 6, 2023
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  3. Merge remote-tracking branch 'origin/develop' into feature/sprkstep

    @balos1
    balos1 committed Jul 6, 2023
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  4. fix unused variable error

    @balos1
    balos1 committed Jul 6, 2023
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  5. gen fortran

    @balos1
    balos1 committed Jul 6, 2023
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  6. bump answers

    @balos1
    balos1 committed Jul 6, 2023
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  7. fix typo

    @balos1
    balos1 committed Jul 6, 2023
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  8. fix out file names

    @balos1
    balos1 committed Jul 6, 2023
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Commits on Jul 8, 2023

  1. update outputs from test machine

    @gardner48
    gardner48 committed Jul 8, 2023
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Commits on Jul 17, 2023

  1. address many PR comments

    @balos1
    balos1 committed Jul 17, 2023
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  2. address more comments

    @balos1
    balos1 committed Jul 17, 2023
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  3. change ARKSPRKStorage to ARKSPRKTable

    @balos1
    balos1 committed Jul 17, 2023
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  4. adress remaining comments

    @balos1
    balos1 committed Jul 17, 2023
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  5. regen fortran

    @balos1
    balos1 committed Jul 17, 2023
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  6. bump answers

    @balos1
    balos1 committed Jul 17, 2023
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  7. fix memory leak

    @balos1
    balos1 committed Jul 17, 2023
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Commits on Jul 18, 2023

  1. fix remaining PR comments

    @balos1
    balos1 committed Jul 18, 2023
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  2. Merge remote-tracking branch 'origin/develop' into feature/sprkstep

    @balos1
    balos1 committed Jul 18, 2023
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  3. remove duplicates from merge

    @balos1
    balos1 committed Jul 18, 2023
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  4. fix table spacing

    @gardner48
    gardner48 committed Jul 18, 2023
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  5. fix reference

    @gardner48
    gardner48 committed Jul 18, 2023
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  6. remove duplicate array end

    @gardner48
    gardner48 committed Jul 18, 2023
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  7. update answers submodule commit

    @gardner48
    gardner48 committed Jul 18, 2023
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  8. add missing ARKSPRKTable_Crate implementation, regen F2003

    @gardner48
    gardner48 committed Jul 18, 2023
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  9. symplectic to sprk in tarscript .out files

    @gardner48
    gardner48 committed Jul 18, 2023
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  10. add Create implementation

    @balos1
    balos1 committed Jul 18, 2023
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  11. regen f2003

    @gardner48
    gardner48 committed Jul 18, 2023
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  12. fix C90 error

    @gardner48
    gardner48 committed Jul 18, 2023
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  13. add sprkstep f2003 files to tarscript

    @gardner48
    gardner48 committed Jul 18, 2023
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  14. install headers for examples

    @balos1
    balos1 committed Jul 18, 2023
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  15. Merge remote-tracking branch 'origin/develop' into feature/sprkstep

    @balos1
    balos1 committed Jul 18, 2023
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  16. various doc formatting fixes

    @gardner48
    gardner48 committed Jul 18, 2023
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  17. install sprk headers

    @gardner48
    gardner48 committed Jul 18, 2023
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Commits on Jul 19, 2023

  1. update output files

    @gardner48
    gardner48 committed Jul 19, 2023
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  2. add into text for SPRK table type

    @gardner48
    gardner48 committed Jul 19, 2023
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  3. storage to table

    @gardner48
    gardner48 committed Jul 19, 2023
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  4. fix signature types in doc

    @gardner48
    gardner48 committed Jul 19, 2023
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  5. add into text for method list

    @gardner48
    gardner48 committed Jul 19, 2023
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  6. move table storage details to table strucutre section

    @gardner48
    gardner48 committed Jul 19, 2023
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  7. remove structure, refer to type

    @gardner48
    gardner48 committed Jul 19, 2023
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  8. remove return in docs for void function

    @gardner48
    gardner48 committed Jul 19, 2023
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  9. minor updates to math section

    @gardner48
    gardner48 committed Jul 19, 2023
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  10. add copyright block

    @gardner48
    gardner48 committed Jul 19, 2023
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  11. structure and storage to table

    @gardner48
    gardner48 committed Jul 19, 2023
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  12. use their for user pronoun

    @gardner48
    gardner48 committed Jul 19, 2023
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  13. fix incomplete sentence

    @gardner48
    gardner48 committed Jul 19, 2023
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  14. fix typo

    @gardner48
    gardner48 committed Jul 19, 2023
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  15. clarify context

    @gardner48
    gardner48 committed Jul 19, 2023
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  16. fix typo

    @gardner48
    gardner48 committed Jul 19, 2023
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  17. remove incorrect comment

    @gardner48
    gardner48 committed Jul 19, 2023
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  18. remove double allocation of a and ahat

    @gardner48
    gardner48 committed Jul 19, 2023
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  19. free table on failure

    @gardner48
    gardner48 committed Jul 19, 2023
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  20. use linear interpolant for first degree method

    @gardner48
    gardner48 committed Jul 19, 2023
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  21. bump answers

    @balos1
    balos1 committed Jul 19, 2023
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  22. bump answers

    @balos1
    balos1 committed Jul 19, 2023
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  23. update double

    @balos1
    balos1 committed Jul 19, 2023
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  24. update answers submodule

    @gardner48
    gardner48 committed Jul 19, 2023
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