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2021-05-03Implement div(B) Cleaning With FDTD (#1829)Gravatar Edoardo Zoni 5-7/+140
* Implement div(B) Cleaning With FDTD * Add CI Test * Clean Up
2021-04-28Fix Two Warnings for Builds Without EB (#1920)Gravatar Edoardo Zoni 2-0/+8
2021-04-27Staircased embedded boundaries in the YEE solver (#1881)Gravatar Lorenzo Giacomel 3-6/+50
* Added staircased embedded boundaris to the YEE solver * adding spherical resonating cavity test * adding functions for fields initialization * style adjustments * fixing tabs * fixed name of analysis script * fixed name of analysis script * fixed a few wrong preprocessor directives * workaround for missing boost * Revert "workaround for missing boost" This reverts commit 601f9eb2ec6f8c2100304379b2bea1c6cf9d1851. * another workaround for missing boost * getting rid of boost by depending on c++17 * Removed a few unused variables * adding USE_EB to addToCompileString for EB testing * removed tabs * fixing the inputs name for EB sphere test * shortened the test * zero padding the names of the images * adjusted two for loops * removed some unused variables * improving the fields initialization * removed the sphere test and implemented the cube test * fixed edges lengths computation and added comments * Fixed the case of all_regular geometries * fixing a bug that was breaking some tests * adding test folder * fixed the default values for the EB cube test * simplified the analysis script * fixed cubic resonator default results * inputting the plot file name from command line * fixing the diag name * Fixed a bug in edges initialization Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Adding comments to the staircased yee solver (thanks Remi) Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * fixed the cube resonator test * removed an unused import Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2021-04-21Fix Silver-Mueller boundary: cell ratio (#1907)Gravatar Remi Lehe 1-2/+2
* Fix typo in the Silver-Mueller boundary conditions * Reset checksum for silver-mueller
2021-04-21Add Silver-Mueller boundaries along z, for the RZ version of the code (#1906)Gravatar Remi Lehe 1-1/+33
* Implement Silver-Mueller boundary conditions in z for RZ * Add automated test and benchmark
2021-03-29Silver Mueller in RZ (#1804)Gravatar Lígia Diana Amorim 1-4/+81
* Added RZ Er, Et, Ez and Br, Bt and Bz * Answered my own question * Making Yee and cells domain check for RZ too * Added relevant coefficients * Derivative in z requires coefsz and n_coefsz * Bt computed with UpwardDz * UpwardDz might require CylindricalYeeAlgorithm.H * Added mode 0 Bz * Added higher-order modes for Bt * Added higher-order modes for Bz * Fix to EOLs * Fix typo * Added cylindrical specific parameters * Fix error of #endif * rmin also needed in RZ parameters * T_Algo needed for RZ -> different initialization in .H * Fix private / public function * Replacing T_Algo by CylindricalYeeAlgorithm * Fix typo * ParallelFor for Br, Bt and Bz separated * Compiled after removing unecessary Br * Changes suggested by reviewer * No need to compute r before if() * Corrected real and imaginary parts of Bz * Remove vscode file Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2021-03-19Warnings: PSATD+RZ & More (#1814)Gravatar Axel Huebl 2-2/+2
* PSATD+RZ: Fix Warnings Fix a couple of warnings in PSATD + RZ. * BesselRoots: Missing Include & using * Kernel & Util: Unused Code & Var
2021-03-18Use Clear Naming Standard for ParmParse Variables (#1809)Gravatar Edoardo Zoni 1-10/+10
2021-03-16Implement Silver Mueller boundary conditions (#1766)Gravatar Remi Lehe 4-0/+163
* Add function definitions for Silver-Mueller boundary condition * Add test file * Implement Silver-Mueller equations * Add equations for Bz * Add equation in the z direction * Add equation for Bx * Add 3D implementation * Add documentation, automated tests, and warnings * Include second automated test and evaluate benchmark * Fix unused variable warning * Fix minor bugs * Update benchmark * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Incorporate review comments * Incorporate more suggestions Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-03-16Add timers in routines that depend on cell-related work (#1692)Gravatar Michael E Rowan 3-20/+73
* Add timers * eol * AtomicAdd * lev argument for getCosts * style * style * wip * eol * .ipynb * passing down lev * eol * passing lev * eol * Update Source/Particles/Collision/PairWiseCoulombCollision.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Add for QED and ionization routines * eol * remove unneeded * mfi-->pti * move cost * eol Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-02-01remove semicolons (#1662)Gravatar Luca Fedeli 1-5/+5
2021-01-21Define: _OPENMP -> AMREX_USE_OMP (#1520)Gravatar Axel Huebl 8-12/+12
* Define: _OPENMP -> AMREX_USE_OMP Replace the define check of `_OPENMP` with the explicit backend control of `AMREX_USE_OMP` for parallel constructs. Doing so avoids that we accidentially turn on OpenMP, e.g. if a dependency pulls it in for linear algebra, I/O, etc. This can led to confusion if the user explicitly requested a serial build. Also, we might want to use OpenMP functionality here and there for auxiliary functions w/o having to use the AMReX OpenMP backend, i.e. because we compile for GPUs. * Add missing amrex::Gpu::notInLaunchRegion
2021-01-11Fix some warnings (#1612)Gravatar Luca Fedeli 1-1/+1
* fixed some warnings * add missing files * fixed bug * fix several other warnings * add missing include * fixed bug * fixed bug * fixed bug * fixed bug
2020-12-23Use PML diagonal components only with div cleaning (#1592)Gravatar Edoardo Zoni 2-16/+50
* Use PML diagonal components only with div cleaning * Apply @RemiLehe's suggestions and simplify allocations
2020-12-14Made sure that n_rz_azimuthal_modes is declared int everywhere (#1571)Gravatar David Grote 1-1/+1
2020-12-11PSATD Runtime Control (#1300)Gravatar Axel Huebl 9-10/+14
* Docs: PSATD Runtime Option * Tests: PSATD Runtime Option Add new runtime option to PSATD regression test matrix. * PICMI: PSATD runtime option * Source: PSATD Runtime Option
2020-12-09Use new parser for more real input parameters (#1564)Gravatar NeilZaim 1-4/+6
2020-12-07material properties are cell-centered. not nodal (#1551)Gravatar Revathi Jambunathan 1-3/+3
2020-12-07fix 2D out of bounds for macroproperty init (#1552)Gravatar Revathi Jambunathan 1-3/+6
2020-10-19Replace wherever possible '.reset(new' with '= make_unique' (#1429)Gravatar Luca Fedeli 1-7/+8
* replace wherever possible .reset(new with = make_unique * fixed bug * fixed bug * revert WarpXOpenPMD.cpp to the original version * removed another .reset(new
2020-09-23[mini-PR] Fix a couple of warnings (#1372)Gravatar Luca Fedeli 1-4/+4
* removed extra ; * fixed unused variable * changed variable name to avoid shadowing * fixed bug
2020-09-18fix warnings in RZ (#1349)Gravatar Luca Fedeli 9-12/+34
2020-09-17Fix few compilation warnings (shift) (#1310)Gravatar Luca Fedeli 1-1/+0
* fix << declaration of galilean_shift shadows a member of WarpX >> * fix << unused mu_stag >> * fix << unused uxp, uyp, uzp >> * renamed galilean_shift (member variable of WarpX class) into m_galilean_shift * renamed v_galilean to m_v_galilean when appropriate * fixed bug introduced in latest commit * fix <<comparison of integer expressions of different signedness>> * Update Source/FieldSolver/FiniteDifferenceSolver/MacroscopicEvolveE.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-09-14Remove The_Managed_Arena (#1313)Gravatar WeiqunZhang 2-6/+6
* Remove the base class of InjectorPoisition, InjectorDensity and InjectorMomentum so that they no longer live in managed memory. * Have both host and device copies of Injector*. * Modify Parser classes so that they can work without unified memory. Add HostDeviceParser that is non-owning and therefore suitable for being value captured by device lambda.
2020-09-09Variation of macroscopic properties for E-update (#1016)Gravatar Revathi Jambunathan 7-83/+447
* Adding macro-E Push and new file * Add macroEvolveE, call it, and include algo selection in utils * fix eol * Fixing bug in macroE for sigma method 1 * changing MacroEvolveE to MacroscopicEvolveE * add class for macroscopicproperties and an object in WarpX class * fix eol * adding templated ckc call with comment that EvolveE is same for yee and ckc * add header file pointing to ckc algorithm * adding obejct m_macroscopic_properties to access sigma,eps,mu * some cleaning * Adding comments * adding documentation * spelling wandroff to wendroff * fixing eol * eol * const in the right place. Thanks bot! * profiler for macroscopic evolveE * MultiFab macroproperties with constant init, templated macroEvolveE, * call macroparameter init * eol fix * add parser for macroscopic properties * fix eol * adding input file * __device__ lambda cannot be private in class * fix grown tilebox declaration for init data * [skip ci] some more merge conflicts * some comments * removing redundant calls to Macroscopic EvolveE * [skip ci] fix growntilebox for initializing macro mf * clean and fix BackwardEuler call for ckc * commenting out old alpha and beta implementations * temporarily commiting local changes with calls in Interp. * fixing a typo * clean and add documentation * remove the test input file * fix typo * eol fix * Update Docs/source/running_cpp/parameters.rst Co-authored-by: Andy Nonaka <AJNonaka@lbl.gov> * PR suggestions * Update Source/FieldSolver/WarpXPushFieldsEM.cpp Co-authored-by: Andy Nonaka <AJNonaka@lbl.gov> * removing unnecessary includes * adding 2D initialization for stag arrays * removing init_style input parameter for material properties * eol fix * Adding dE/dt eq curl of (B/mu) * PhysConst ep0 and mu0 * Add functor for field access for macro and vacuum (B/mu) * fix eol * Update Source/FieldSolver/FiniteDifferenceSolver/FiniteDifferenceAlgorithms/FieldAccessorFunctors.H Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Apply suggestions from code review Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Source/FieldSolver/FiniteDifferenceSolver/FiniteDifferenceAlgorithms/CartesianCKCAlgorithm.H Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Apply suggestions from code review Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * fixing compilation errors and removing Gpu ManagedVector Co-authored-by: Andy Nonaka <AJNonaka@lbl.gov> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2020-09-03Remove ManagedVector from finite-difference solver (#1269)Gravatar WeiqunZhang 6-21/+51
2020-09-01 Fix 🩹(almost) all warnings ⚠️ with default configuration in 2D ↵Gravatar Luca Fedeli 1-0/+3
(DIM=2, openMP+MPI, double precision, no advanced solvers, no QED, native output) (#1264) Depends on #1263
2020-08-31Fix 🩹 (almost) all warnings ⚠️ with default configuration (DIM=3, ↵Gravatar Luca Fedeli 2-1/+6
openMP+MPI, double precision, no advanced solvers, no QED, native output) (#1263) This PR should fix almost all the compilation warnings in the default configuration (DIM=3, openMP+MPI, double precision, no advanced solvers, no QED, native output...). Or at least it does that on my system (my compiler is `g++ (Ubuntu 9.3.0-10ubuntu2) 9.3.0` ). I have just two residual warnings: ### 1 ``` [ 89%] Building CXX object CMakeFiles/WarpX.dir/Source/Parser/wp_parser.lex.cpp.o wp_parser.lex.c:1356:17: warning: ‘void yyunput(int, char*)’ defined but not used [-Wunused-function] ``` I don't know if `yyunput(int, char*)` is there for a reason, even if it is not used. So I didn't do anything. ### 2 ``` [ 96%] Building CXX object CMakeFiles/WarpX.dir/Source/Utils/CoarsenIO.cpp.o /home/luca/Projects/warpx_dir/WarpX/Source/Particles/WarpXParticleContainer.cpp: In member function ‘void WarpXParticleContainer::AddNParticles(int, int, const ParticleReal*, const ParticleReal*, const ParticleReal*, const ParticleReal*, const ParticleReal*, const ParticleReal*, int, const ParticleReal*, int, int)’: /home/luca/Projects/warpx_dir/WarpX/Source/Particles/WarpXParticleContainer.cpp:102:44: warning: unused parameter ‘nattr’ [-Wunused-parameter] 102 | int nattr, const ParticleReal* attr, int uniqueparticles, int id) ``` The first line of `AddNParticles` is `BL_ASSERT(nattr == 1); //! @fixme nattr is unused below: false sense of safety` . So I thought that there might be something to fix here and I didn't do anything.
2020-08-24Fix some warnings (#1239)Gravatar Luca Fedeli 3-12/+36
This PR fixes the source of several compilation warnings. Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-08-03Fix bug in imaginary part of divE (#1233)Gravatar Edoardo Zoni 1-1/+1
2020-07-24Fix -Wextra-semi (#1207)Gravatar Axel Huebl 4-19/+19
Remove unnecessary semicolons (fix compiler warnings).
2020-07-22Cleaner calculation of the simulation timestep (#1031)Gravatar Remi Lehe 4-0/+82
* Cleaner calculation of the simulation timestep * Fix compilation errors * Remove specification of CKC solver in PSATD test * Correct calculation of dt * Fix compilation error * Cleaner calculation of the simulation timestep * Fix compilation errors * Remove specification of CKC solver in PSATD test * Correct calculation of dt * Fix compilation error * Cleanup for cylindrical * Change input of automated tests to preserve previous results * Fix import statement for cylindrical * Preserve dt for PML test * Move function documentation to WarpX.H * Update CMakeList * Update CFL in some tests * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Fix compilation errors * Revert "Fix compilation errors" This reverts commit 56ef67f228269b266876629f49789d3afdbbc00b. * Fix compilation error * Add cmath headers Add directly used header files. * Fix Include Order Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-06-12Add CMake Scripts (#759)Gravatar Axel Huebl 2-0/+18
* [skip travis] CMake: Add CMake Scripts This add CMake scripts for the CMake build system generator. * CUDA Support Achieved Fastest compile via: cmake .. -DENABLE_CUDA=ON -DCUDA_ARCH=6.0 * CMake: openPMD & QED * CMake: Dimension Support WarpX_DIMS=2,3,RZ * CCache & Out-of-Source Enable CCache when found and prevent in-root builds (in-source okay-ish). * CMake: CUDA C++ Language Minimum * Add new Files * CI: Migrate macOS to CMake * Fortran: Enable Because Transitive ... for now :) * CI: Migrate Linux ICC to CMake * CI: Verbose Make * CMake: Add Missing PSATD Sources * CMake: PSATD, Compute, Precision, Clean
2020-05-29Macroscopic EvolveE with constant properties (#991)Gravatar Revathi Jambunathan 6-0/+241
* Adding macro-E Push and new file * Add macroEvolveE, call it, and include algo selection in utils * fix eol * Fixing bug in macroE for sigma method 1 * changing MacroEvolveE to MacroscopicEvolveE * add class for macroscopicproperties and an object in WarpX class * fix eol * adding templated ckc call with comment that EvolveE is same for yee and ckc * add header file pointing to ckc algorithm * adding obejct m_macroscopic_properties to access sigma,eps,mu * some cleaning * Adding comments * adding documentation * spelling wandroff to wendroff * fixing eol * eol * const in the right place. Thanks bot! * profiler for macroscopic evolveE * re-introduced deleted line when fixing conflict to declare templated EvolveBPMLCartesian function * fixing if-else statement for RZ in MAcroscopicEvolveE.cpp * adding suggestions and corrections made in PR review. * fixing grammar in docs * fix eol whitespace * fix typo
2020-05-22Use C++ templates for the PML field pusher (#808)Gravatar Remi Lehe 5-0/+488
* Allow to pass component in stencil templates * Define and use enum to address PML components * Start implementing PML equations * Implement EvolveEPML * Implemented EvolveBPML * Added interface for pml_has_particles * Added interface for pml_has_particles * [skip ci] Add update expressions for E * [skip ci] Fix compilation * Call new PML pusher for B field * Fix compilation errors * Fix more typos * Abort code if `do_pml` is used in cylindrical geometry * Add contribution from F in EvolveEPML * Remove unused function for CKC coefficients * Remove unneeded ExchangeF * Add damping for J * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Revert "Apply suggestions from code review" This reverts commit 08f262a676ba5e5b44b9118b8daba1b03c08b64b. * Remove sanity checks for nodal * Implement dive cleaning in PML * Implement push F in the PML * Clean-up unused code Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-05-13Allow to pass component in stencil templates (#1012)Gravatar Remi Lehe 3-70/+70
2020-04-06replace ixType().ixType() with ixType().toIntVect() for clarity (#895)Gravatar MaxThevenet 4-16/+16
2020-04-02Includes: Only From `Source/` (#873)Gravatar Axel Huebl 3-5/+4
* Includes: Only From `Source/` Avoid adding all directories to include paths: - automatically structure includes more clearly, e.g. a util include with a short name is clearly seen as such - should have some small positive impact on compile time, since the compiler has to search less directories for an include file * Includes: Fix Non-Local Paths Add missing prefix relative to `Source/` for WarpX-local includes.
2020-03-31Make Build System: No Public Includes (#870)Gravatar Axel Huebl 1-1/+0
Remove the listing of all header-files from the Make-buildsystem. Listing public header files here tells the AMReX Makefile build system to install those in an install step after build. WarpX is currently not building a public library which can be consumed by users for their projects and only an executable.
2020-03-30Remove compiler warnings (#843)Gravatar Edoardo Zoni 2-2/+6
* Fix compiler warnings with DIM=2 * Fix compiler warnings with USE_RZ=TRUE * Fix compiler warnings with USE_PSATD=TRUE and DIM=2 * Fix compiler warnings with USE_PSATD=TRUE and DIM=3 * Fix bug: discard only return value when calling DefineAndReturnParticleTile * Remove unused variables not triggering warnings
2020-03-16Use C++ templates for the `EvolveF` and `ComputeDivE` function (#753)Gravatar Remi Lehe 4-0/+423
* Prepare EvolveE * Cartesian equations without current * Implement Cartesian EvolveE * Progress towards cylindrical solver * Correct typo * Implement cylindrical solver (without on-axis condition) * Fix compilation errors * Add regularization for RZ solver * Added correction term for F * Remove file for nodal stencil * Apply stylistic changes to EvolveE * Fix compilation errors * Correction to avoid out of bound * Remove references to old file * Correct bug in EvolveB * Implement correction on axis for Et * Remove previous field update functions * Implement EvolveF in Cartesian * Add missing file * Update on-axis condition * Correct typo * Add theta derivative for divE calculation * Fix rho component * Fix compilation error * Use C++ templates in computation of divE * Update Source/FieldSolver/FiniteDifferenceSolver/ComputeDivE.cpp Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * Apply suggestions from code review Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * Use comparisons to 0 again Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
2020-03-13Fixed FDTD coefficients of E push from F (#804)Gravatar David Grote 1-13/+13
2020-03-02EvolveE: Update Includes (#761)Gravatar Axel Huebl 1-2/+3
Generalize includes to base path.
2020-02-28fixing bug in ckc (#760)Gravatar Revathi Jambunathan 1-10/+10
2020-02-26Use C++ templates in `EvolveE` function (#676)Gravatar Remi Lehe 3-0/+369
* Prepare EvolveE * Cartesian equations without current * Implement Cartesian EvolveE * Progress towards cylindrical solver * Correct typo * Implement cylindrical solver (without on-axis condition) * Fix compilation errors * Add regularization for RZ solver * Added correction term for F * Remove file for nodal stencil * Apply stylistic changes to EvolveE * Fix compilation errors * Correction to avoid out of bound * Remove references to old file * Correct bug in EvolveB * Implement correction on axis for Et * Remove previous field update functions * Remove unused code
2020-02-25Includes: Clean Up (#743)Gravatar Axel Huebl 2-2/+2
- Use `""` for WarpX-local includes - Order: WarpX `""`, AMReX `<>`, other third party includes `<>` - Add dir prefixes for WarpX Add order to includes by including from `Source/` onward and keeping directory prefixes of non-local includes for clarity.
2020-02-25FDTD: Real Literals and Formatting (#736)Gravatar Axel Huebl 4-149/+176
Clean up `amrex::Real` literals (aka "numbers"). This avoids calculating a line in double precision and casting it down to `Real` on assignment. Also fixes some formatting issues. (Commit credited to Remi.) Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2020-02-06Add Doxygen commentsGravatar Remi Lehe 6-10/+28
2020-02-06Correct errors in CKCGravatar Remi Lehe 1-0/+5
2020-02-06Prepend class members with "m_"Gravatar Remi Lehe 3-19/+19
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