Merge branch 'jolivet/clang-format-19' into 'main'

clang-format-19

See merge request petsc/petsc!7644

Remove unneeded parentheses

Merge branch 'jolivet/clang-format-18' into 'main'

clang-format version 18

See merge request petsc/petsc!6902

Remove multiple parentheses and extra semicolon

git grep -l -E "\(\([a-zA-Z0-9_]+\)\(\*[a-zA-Z0-9_]+\)[, )]" | xargs sed -r -i'' 's#\(\(([a-zA-Z0-9_]+)\)\(\*([a-zA-Z0-9_]+)\)([, )])#\(\(\1\)\*\2\3#g

Remove multiple parentheses and extra semicolon

git grep -l -E "\(\([a-zA-Z0-9_]+\)\(\*[a-zA-Z0-9_]+\)[, )]" | xargs sed -r -i'' 's#\(\(([a-zA-Z0-9_]+)\)\(\*([a-zA-Z0-9_]+)\)([, )])#\(\(\1\)\*\2\3#g'
git grep -l -E "Petsc(.)*\(\(\*[a-zA-Z0-9_]*\)," | xargs sed -r -i'' 's#Petsc([a-zA-Z0-9_]*)\(\(\*([a-zA-Z0-9_]*)\), #Petsc\1(*\2, #g'
git grep -l -E "([\!\&\~\*\(]|\)\)|\([^,\*\(]+\**\))\(([a-zA-Z0-9_]+((\.|->)[a-zA-Z0-9_]+|\[[a-zA-Z0-9_ \%\+\*\-]+\])+)\)" | xargs sed -r -i'' 's#([\!\&\~\*\(]|\)\)|\([^,\*\(]+\**\))\(([a-zA-Z0-9_]+((\.|->)[a-zA-Z0-9_]+|\[[a-zA-Z0-9_ \%\+\*\-]+\])+)\)#\1\2#g'

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Merge branch 'ilya-fursov/ts-fixevent2' into 'main'

TSEvent: refactor and fix bugs, add TSSetPostEventStep()

See merge request petsc/petsc!6752

TSEvent: refactor and fix bugs, add TSSetPostEventStep()

Refactor the core algorithm for resolution of events: TSEventHandler()
and the helper functions, fixing the existing bugs.

Chang

TSEvent: refactor and fix bugs, add TSSetPostEventStep()

Refactor the core algorithm for resolution of events: TSEventHandler()
and the helper functions, fixing the existing bugs.

Change event indicator functions from PetscScalar to PetscReal.
Change the API of TSSetEventHandler(): in the user `indicator()` callback,
the 'fvalue' argument type changed from PetscScalar[] to PetscReal[].

Add TSSetPostEventStep(), deprecate TSSetPostEventIntervalStep().
Deprecate option -ts_event_post_eventinterval_step.

Fix bugs in interaction of TSEvent with tspan.
Add six new test examples.

Below are the examples of bugs fixed by this patch.
The source codes (ex3.c, ex3span.c, ex4.c, ex5.c) can be found
in src/ts/event/tests. To run them with the older Petsc versions,
one would need to comment out "#define NEW_VERSION".
Behaviour for three library versions is reported below:
* ORIG: current Petsc version, before the proposed patch.
* 6688: independently of the proposed patch, Merge Request 6688 was
developed, which fixed some bugs with zero-crossing directions.
* NEW : the proposed patch.

./ex3 -ts_monitor -ts_event_monitor -ts_view -ts_type beuler \
-ts_adapt_type basic -flg -V 1e9 -ts_adapt_dt_min 1e-6 -change5 1 -dir 1
* ORIG: fails to resolve 5 out of 6 events, and resolves 23 incorrect events.
* 6688: fails to exit the TSEvent iteration via the step size (bracket size)
criterion.
* NEW : ok, resolves all 6 events.

./ex4 -ts_adapt_type basic -ts_type rk -ts_dt 0.25 -ts_event_tol 1e-8 \
-dir 0 -ts_adapt_dt_min 1e-10 -ts_view -ts_monitor -ts_event_monitor
* ORIG: only reaches t = 0.0300236 after 10000 TS steps.
* 6688: only reaches t = 0.0300236 after 10000 TS steps.
* NEW : ok, reaches the final time t = 4.0 after 96 TS steps, resolving
all 16 events.

./ex5 -ts_monitor -ts_event_monitor -ts_type rk -ts_adapt_type basic \
-ts_view -ts_dt 0.25 -flg -dir 0
* ORIG: only reaches t = 4.0 after 10000 TS steps, erroneously reports
event at t = 4.0 around 5000 times.
* 6688: only reaches t = 4.0 after 10000 TS steps.
* NEW : ok, reaches the final time t = 10.0 after 99 TS steps, resolving
all 34 events.

./ex5 -ts_monitor -ts_event_monitor -ts_type rk -ts_adapt_type basic \
-ts_view -ts_dt 0.25 -flg -dir 1
* ORIG: fails, starts taking negative time steps, no events are correctly
resolved.
* 6688: ok, but slower: 90 TS steps to resolve all 17 events.
* NEW : ok, and faster: 48 TS steps to resolve all 17 events.

./ex5 -ts_monitor -ts_event_monitor -ts_type rk -ts_adapt_type basic \
-ts_view -ts_dt 0.25 -flg -dir -1
* ORIG: fails, starts taking 'nan' time steps.
* 6688: mostly fails, only reaches t = 4.99993 after 10000 TS steps.
* NEW : ok, reaches the final time t = 10.0 after 74 TS steps, resolving
all 17 events.

The same run in parallel:
mpirun -n 2 ./ex5 -ts_monitor -ts_event_monitor -ts_type rk \
-ts_adapt_type basic -ts_view -ts_dt 0.25 -flg -dir -1
* ORIG: fails, starts taking negative time steps, exits with runtime error.
* 6688: mostly fails, only reaches t = 3, besides, the parallel run is not
consistent with the serial run (see above).
* NEW : ok, reaches the final time t = 10.0 after 74 TS steps, resolving
all 17 events.

./ex3span -ts_monitor -ts_event_monitor
* ORIG: (confused by events) misses tspan points: 4.02, 4.21, 4.98, 5.01,
5.21, 5.98, 6, 6.01, 6.02, 6.21, 6.99, 7.21, 8.01, 8.21, 9.01.
* 6688: (confused by events) misses tspan points: 4.02, 4.21, 4.98, 5.01,
5.21, 5.98, 6, 6.01, 6.02, 6.21, 6.99, 7.21, 8.01, 8.21, 9.01.
* NEW : ok.

./ex3span -ts_monitor -ts_event_monitor -ts_event_post_event_step 0.5
* ORIG: misses the majority of tspan points (except 0.01 and 0.21),
and also resolves the last event location at wrong time t = 9.21.
* 6688: misses the majority of tspan points (except 0.01 and 0.21),
and also resolves the last event location at wrong time t = 9.21.
* NEW : ok.

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Merge branch 'jeremy/less-strcpy-strcat' into 'main'

Use Petsc[Strncpy,Strlcat,Memcpy] over Petsc[Strcpy,Strcat]

Closes #1332

See merge request petsc/petsc!6115

Clean up PETSc str ops to use more secure implementations where possible. These include:

- Use PetscStrncpy()/PetscStrlcat()/PetscMemcpy() over PetscStrcpy()/PetscStrcat()
- Use PetscArraycpy() over

Clean up PETSc str ops to use more secure implementations where possible. These include:

- Use PetscStrncpy()/PetscStrlcat()/PetscMemcpy() over PetscStrcpy()/PetscStrcat()
- Use PetscArraycpy() over PetscMemcpy() as appropriate for string buffer copying
- Use built in string from name over hardcoding
- Use sizeof over hardcoded length
- Replace some Strlcat with Strncpy when offset is known

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Merge branch 'jacobf/2022-12-10/petscerrorcode-nodiscard' into 'main'

Feature: Non-discardable PetscErrorCode

See merge request petsc/petsc!5923

Make PetscErrorCode a non-discardable enum

Merge branch 'jacobf/2022-09-21/2-bike-2-shed' into 'main'

Feature: Bicycle Storage Facility 2

See merge request petsc/petsc!5661

source code format changes due to .clang-format changes

Merge branch 'barry/2022-08-21/clang-format-source' into 'main'

format repository with clang-format

See merge request petsc/petsc!5541

clang-format: convert PETSc sources to comply with clang-format

Merge branch 'barry/2022-07-23/add-petscbeginuser' into 'main'

Add PetscFunctionBeginUser to all PETSc C/C++ examples

See merge request petsc/petsc!5470

Add PetscFunctionBeginUser to all PETSc C/C++ examples

Now the stack frames will contain the main program and the correct line numbers in them

git ls-files | egrep "(tutorials|tests)" | xargs sed -

Add PetscFunctionBeginUser to all PETSc C/C++ examples

Now the stack frames will contain the main program and the correct line numbers in them

git ls-files | egrep "(tutorials|tests)" | xargs sed -i "s?\(PetscCall(PetscInitialize(&argc\)?PetscFunctionBeginUser;\n \1?g"

Commit-type: error-checking, testing-fix
/spend 15m

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Merge branch 'jacobf/2022-04-05/petscattrformat-all-the-rest' into 'main'

Enable PETSC_ATTRIBUTE_FORMAT()

See merge request petsc/petsc!5085

Enable PETSC_ATTRIBUTE_FORMAT()

Merge branch 'barry/2022-04-01/fix-petsc-options-begin-end/release' into 'main'

Remove bogus error returns from Begin/End() macros

See merge request petsc/petsc!5069

Cleanup of introduction of PetscCall()

* remove bogus error flags from XXXBegin()/End() macros such as PetscOptionsBegin()/End()

* rename for consistency certain XXXBegin()/End() macros such as Mat

Cleanup of introduction of PetscCall()

* remove bogus error flags from XXXBegin()/End() macros such as PetscOptionsBegin()/End()

* rename for consistency certain XXXBegin()/End() macros such as MatPreallocateInitialize()/Finalize()

* fix many lingering ierr = XXX that arose from multiline function calls

* sync slepc/hpddm - to use snapshots with the same changes

Commit-type: error-checking, style-fix
/spend 8h

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Merge branch 'jacobf/2022-02-23/variadic-chkerr' into 'main'

Variadic CHKERRQ()

See merge request petsc/petsc!4889

The great renaming:

- CHKERRQ() -> PetscCall()
- CHKERRV() -> PetscCallVoid()
- CHKERRMPI() -> PetscCallMPI()
- CHKERRABORT() -> PetscCallAbort()
- CHKERRCONTINUE() -> PetscCallContinue()
- CHKERRXX

The great renaming:

- CHKERRQ() -> PetscCall()
- CHKERRV() -> PetscCallVoid()
- CHKERRMPI() -> PetscCallMPI()
- CHKERRABORT() -> PetscCallAbort()
- CHKERRCONTINUE() -> PetscCallContinue()
- CHKERRXX() -> PetscCallThrow()
- CHKERRCXX() -> PetscCallCXX()
- CHKERRCUDA() -> PetscCallCUDA()
- CHKERRCUBLAS() -> PetscCallCUBLAS()
- CHKERRCUSPARSE() -> PetscCallCUSPARSE()
- CHKERRCUSOLVER() -> PetscCallCUSOLVER()
- CHKERRCUFFT() -> PetscCallCUFFT()
- CHKERRCURAND() -> PetscCallCURAND()
- CHKERRHIP() -> PetscCallHIP()
- CHKERRHIPBLAS() -> PetscCallHIPBLAS()
- CHKERRHIPSOLVER() -> PetscCallHIPSOLVER()
- CHKERRQ_CEED() -> PetscCallCEED()
- CHKERR_FORTRAN_VOID_FUNCTION() -> PetscCallFortranVoidFunction()
- CHKERRMKL() -> PetscCallMKL()
- CHKERRMMG() -> PetscCallMMG()
- CHKERRMMG_NONSTANDARD() -> PetscCallMMG_NONSTANDARD()
- CHKERRCGNS() -> PetscCallCGNS()
- CHKERRPTSCOTCH() -> PetscCallPTSCOTCH()
- CHKERRSTR() -> PetscCallSTR()
- CHKERRTC() -> PetscCallTC()

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PetscInitialize() and PetscFinalize() wrapped:

- ierr = PetscInitialize();if (ierr) return ierr;
+ CHKERRQ(PetscInitialize());

- ierr = PetscFinalize();
- return ierr;
+ CHKERRQ(PetscFinalize());
+

PetscInitialize() and PetscFinalize() wrapped:

- ierr = PetscInitialize();if (ierr) return ierr;
+ CHKERRQ(PetscInitialize());

- ierr = PetscFinalize();
- return ierr;
+ CHKERRQ(PetscFinalize());
+ return 0;

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chkerr and friends wrapped

Merge branch 'jolivet/fix-some-missing-chkerr' into 'main'

Some missing CHKERR[Q|MPI]

See merge request petsc/petsc!4190