Merge pull request #132 from hklion/HSdevmerge_230802

Harris Sheet development merge 230802

.clang-tidy

@@ -3,6 +3,8 @@ Checks: '-*,
     -bugprone-easily-swappable-parameters,
     -bugprone-implicit-widening-of-multiplication-result,
     -bugprone-misplaced-widening-cast,
+    cert-*
+    -cert-err58-cpp,
     cppcoreguidelines-avoid-goto,
     cppcoreguidelines-interfaces-global-init,
     -cppcoreguidelines-avoid-non-const-global-variables,
@@ -12,16 +14,48 @@ Checks: '-*,
     -cppcoreguidelines-no-malloc,
     -cppcoreguidelines-owning-memory,
     misc-const-correctness,
+    misc-misleading-bidirectional,
     modernize-avoid-bind,
     modernize-concat-nested-namespaces,
+    modernize-deprecated-headers,
+    modernize-deprecated-ios-base-aliases,
+    modernize-loop-convert,
+    modernize-make-shared,
+    modernize-make-unique,
+    modernize-pass-by-value,
+    modernize-raw-string-literal,
+    modernize-redundant-void-arg,
+    modernize-replace-auto-ptr,
+    modernize-replace-disallow-copy-and-assign-macro,
+    modernize-replace-random-shuffle,
+    modernize-return-braced-init-list,
+    modernize-shrink-to-fit,
+    modernize-unary-static-assert,
     modernize-use-nullptr,
+    mpi-*,
     performance-faster-string-find,
     performance-for-range-copy,
     performance-implicit-conversion-in-loop,
     performance-inefficient-algorithm,
     performance-inefficient-string-concatenation,
     performance-inefficient-vector-operation,
+    performance-move-const-arg,
+    performance-move-constructor-init,
+    readability-non-const-parameter,
+    readability-simplify-boolean-expr,
+    readability-simplify-subscript-expr,
+    readability-static-accessed-through-instance,
+    readability-static-definition-in-anonymous-namespace,
+    readability-string-compare,
+    readability-suspicious-call-argument,
+    readability-uniqueptr-delete-release,
+    -readability-uppercase-literal-suffix,
+    readability-use-anyofallof,
     readability-non-const-parameter
     '
 
+CheckOptions:
+- key:          modernize-pass-by-value.ValuesOnly
+  value:        'true'
+
 HeaderFilterRegex: 'Source[a-z_A-Z0-9\/]+\.H$'

.github/workflows/cuda.yml

@@ -110,7 +110,7 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach b75dd9d5279263768c418ce19285f87de37209f9 && cd -
+        cd ../amrex && git checkout --detach cf8d9f8e233be2ac68aeb65a95e992adfb483939 && cd -
         make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_PSATD=TRUE USE_CCACHE=TRUE -j 2
 
   build_nvhpc21-11-nvcc:

.pre-commit-config.yaml

@@ -68,7 +68,7 @@ repos:
 
 # Autoremoves unused Python imports
 - repo: https://github.com/hadialqattan/pycln
-  rev: v2.1.6
+  rev: v2.2.0
   hooks:
   - id: pycln
     name: pycln (python)

Docs/source/usage/parameters.rst

@@ -195,8 +195,7 @@ We follow the same naming, but remove the ``SIG`` prefix, e.g., the WarpX signal
    The ``TSTP`` (terminal stop) command is sent interactively from ``Ctrl+Z`` to temporarily send a process to sleep (until send in the background with commands such as ``bg`` or continued with ``fg``), overwriting it would thus disable that functionality.
    The signals ``KILL`` and ``STOP`` cannot be used.
 
-   The ``FPE`` signal should not be overwritten in WarpX, as it is `controlled by AMReX <https://amrex-codes.github.io/amrex/docs_html/Debugging.html#breaking-into-debuggers>`__ for :ref:`debug workflows that catch invalid floating-point operations <debugging_warpx>`.
-
+   The ``FPE`` and ``ILL`` signals should not be overwritten in WarpX, as they are `controlled by AMReX <https://amrex-codes.github.io/amrex/docs_html/Debugging.html#breaking-into-debuggers>`__ for :ref:`debug workflows that catch invalid floating-point operations <debugging_warpx>`.
 .. tip::
 
    For example, the following logic can be added to `Slurm batch scripts <https://docs.gwdg.de/doku.php?id=en:services:application_services:high_performance_computing:running_jobs_slurm:signals>`__ (`signal name to number mapping here <https://en.wikipedia.org/wiki/Signal_(IPC)#Default_action>`__) to gracefully shut down 6 min prior to walltime.

Regression/WarpX-GPU-tests.ini

@@ -60,7 +60,7 @@ emailBody = Check https://ccse.lbl.gov/pub/GpuRegressionTesting/WarpX/ for more
 
 [AMReX]
 dir = /home/regtester/git/amrex/
-branch = b75dd9d5279263768c418ce19285f87de37209f9
+branch = cf8d9f8e233be2ac68aeb65a95e992adfb483939
 
 [source]
 dir = /home/regtester/git/WarpX

Regression/WarpX-tests.ini

@@ -59,7 +59,7 @@ emailBody = Check https://ccse.lbl.gov/pub/RegressionTesting/WarpX/ for more det
 
 [AMReX]
 dir = /home/regtester/AMReX_RegTesting/amrex/
-branch = b75dd9d5279263768c418ce19285f87de37209f9
+branch = cf8d9f8e233be2ac68aeb65a95e992adfb483939
 
 [source]
 dir = /home/regtester/AMReX_RegTesting/warpx

Source/BoundaryConditions/PML.cpp

@@ -58,7 +58,7 @@ using namespace amrex;
 
 namespace
 {
-    static void FillLo (Sigma& sigma, Sigma& sigma_cumsum,
+    void FillLo (Sigma& sigma, Sigma& sigma_cumsum,
                         Sigma& sigma_star, Sigma& sigma_star_cumsum,
                         const int olo, const int ohi, const int glo, Real fac,
                         const amrex::Real v_sigma)
@@ -87,7 +87,7 @@ namespace
         });
     }
 
-    static void FillHi (Sigma& sigma, Sigma& sigma_cumsum,
+    void FillHi (Sigma& sigma, Sigma& sigma_cumsum,
                         Sigma& sigma_star, Sigma& sigma_star_cumsum,
                         const int olo, const int ohi, const int ghi, Real fac,
                         const amrex::Real v_sigma)
@@ -115,7 +115,7 @@ namespace
     }
 
 #if (AMREX_SPACEDIM != 1)
-    static void FillZero (Sigma& sigma, Sigma& sigma_cumsum,
+    void FillZero (Sigma& sigma, Sigma& sigma_cumsum,
                           Sigma& sigma_star, Sigma& sigma_star_cumsum,
                           const int olo, const int ohi)
     {

Source/BoundaryConditions/WarpX_PEC.H

@@ -166,23 +166,22 @@ using namespace amrex;
                 // For 2D : for icomp==1, (Ey in XZ, Etheta in RZ),
                 //          icomp=1 is tangential to both x and z boundaries
                 //          The logic below ensures that the flags are set right for 2D
-                const bool is_tangent_to_PEC = ( (icomp == AMREX_SPACEDIM*idim)
-                                             ? false : true );
+                const bool is_tangent_to_PEC = (icomp != AMREX_SPACEDIM*idim);
 #elif (defined WARPX_DIM_1D_Z)
                 // For 1D : icomp=0 and icomp=1 (Ex and Ey are tangential to the z boundary)
                 //          The logic below ensures that the flags are set right for 1D
-                const bool is_tangent_to_PEC = ( ( icomp == idim+2) ? false : true );
+                const bool is_tangent_to_PEC = (icomp != idim+2);
 #else
-                const bool is_tangent_to_PEC = ( ( icomp == idim) ? false : true );
+                const bool is_tangent_to_PEC = (icomp != idim);
 #endif
-                if (isPECBoundary == true) {
+                if (isPECBoundary) {
                     // grid point ijk_vec is ig number of points pass the
                     // domain boundary in direction, idim
                     const int ig = get_cell_count_to_boundary(
                         dom_lo, dom_hi, ijk_vec, is_nodal, idim, iside);
 
                     if (ig == 0) {
-                        if (is_tangent_to_PEC == true and is_nodal[idim] == 1) {
+                        if (is_tangent_to_PEC && is_nodal[idim] == 1) {
                             OnPECBoundary = true;
                         }
                     } else if (ig > 0) {
@@ -192,15 +191,15 @@ using namespace amrex;
                                         : (dom_hi[idim] + 1 - ig));
                         GuardCell = true;
                         // tangential components are inverted across PEC boundary
-                        if (is_tangent_to_PEC == true) sign *= -1._rt;
+                        if (is_tangent_to_PEC) sign *= -1._rt;
                     }
                 } // is PEC boundary
             } // loop over iside
         } // loop over dimensions
-        if (OnPECBoundary == true) {
+        if (OnPECBoundary) {
             // if ijk_vec is on a PEC boundary in any direction, set Etangential to 0.
             Efield(ijk_vec,n) = 0._rt;
-        } else if (GuardCell == true) {
+        } else if (GuardCell) {
             Efield(ijk_vec,n) = sign * Efield(ijk_mirror,n);
         }
     }
@@ -288,19 +287,18 @@ using namespace amrex;
                 const bool isPECBoundary = ( (iside == 0 )
                                         ? is_boundary_PEC(fbndry_lo, idim)
                                         : is_boundary_PEC(fbndry_hi, idim) );
-                if (isPECBoundary == true) {
+                if (isPECBoundary) {
 #if (defined WARPX_DIM_XZ) || (defined WARPX_DIM_RZ)
                     // For 2D : for icomp==1, (By in XZ, Btheta in RZ),
                     //          icomp=1 is not normal to x or z boundary
                     //          The logic below ensures that the flags are set right for 2D
-                    const bool is_normal_to_PEC = ( (icomp == AMREX_SPACEDIM*idim)
-                                                ? true : false );
+                    const bool is_normal_to_PEC = (icomp == (AMREX_SPACEDIM*idim));
 #elif (defined WARPX_DIM_1D_Z)
                     // For 1D : icomp=0 and icomp=1 (Bx and By are not normal to the z boundary)
                     //          The logic below ensures that the flags are set right for 1D
-                    const bool is_normal_to_PEC = ( ( icomp == idim+2) ? true : false );
+                    const bool is_normal_to_PEC = (icomp == (idim+2));
 #else
-                    const bool is_normal_to_PEC = ( ( icomp == idim) ? true : false );
+                    const bool is_normal_to_PEC = (icomp == idim);
 #endif
 
                     // grid point ijk_vec is ig number of points pass the
@@ -310,7 +308,7 @@ using namespace amrex;
 
                     if (ig == 0) {
                         // Only normal component is set to 0
-                        if (is_normal_to_PEC == true and is_nodal[idim]==1) {
+                        if (is_normal_to_PEC && is_nodal[idim]==1) {
                             OnPECBoundary = true;
                         }
                     } else if ( ig > 0) {
@@ -321,16 +319,16 @@ using namespace amrex;
                                         : (dom_hi[idim] + 1 - ig));
                         GuardCell = true;
                         // Sign of the normal component in guard cell is inverted
-                        if (is_normal_to_PEC == true) sign *= -1._rt;
+                        if (is_normal_to_PEC) sign *= -1._rt;
                     }
                 } // if PEC Boundary
             } // loop over sides
         } // loop of dimensions
 
-        if (OnPECBoundary == true) {
+        if (OnPECBoundary) {
             // if ijk_vec is on a PEC boundary in any direction, set Bnormal to 0.
             Bfield(ijk_vec,n) = 0._rt;
-        } else if (GuardCell == true) {
+        } else if (GuardCell) {
             // Bnormal and Btangential is set opposite and equal to the value
             // in the mirror location, respectively.
             Bfield(ijk_vec,n) = sign * Bfield(ijk_mirror,n);

Source/BoundaryConditions/WarpX_PEC.cpp

@@ -361,15 +361,14 @@ PEC::ApplyPECtoJfield(amrex::MultiFab* Jx, amrex::MultiFab* Jy,
 #if (defined WARPX_DIM_1D_Z)
             // For 1D : icomp=0 and icomp=1 (Ex and Ey are tangential to the z boundary)
             //          The logic below ensures that the flags are set right for 1D
-            is_tangent_to_bndy[icomp][idim] = ( ( icomp == idim+2) ? false : true );
+            is_tangent_to_bndy[icomp][idim] = (icomp != (idim+2));
 #elif (defined WARPX_DIM_XZ) || (defined WARPX_DIM_RZ)
             // For 2D : for icomp==1, (Ey in XZ, Etheta in RZ),
             //          icomp=1 is tangential to both x and z boundaries
             //          The logic below ensures that the flags are set right for 2D
-            is_tangent_to_bndy[icomp][idim] = ( (icomp == AMREX_SPACEDIM*idim)
-                                            ? false : true );
+            is_tangent_to_bndy[icomp][idim] = (icomp != AMREX_SPACEDIM*idim);
 #else
-            is_tangent_to_bndy[icomp][idim] = ( ( icomp == idim) ? false : true );
+            is_tangent_to_bndy[icomp][idim] = (icomp != idim);
 #endif
 
             if (is_tangent_to_bndy[icomp][idim]){

Source/Diagnostics/BTD_Plotfile_Header_Impl.cpp

@@ -7,7 +7,8 @@
 #include "BTD_Plotfile_Header_Impl.H"
 
 #include "Utils/TextMsg.H"
-#include "WarpX.H"
+
+#include <ablastr/utils/text/StreamUtils.H>
 
 #include <AMReX.H>
 #include <AMReX_FileSystem.H>
@@ -21,7 +22,7 @@
 using namespace amrex::literals;
 
 BTDPlotfileHeaderImpl::BTDPlotfileHeaderImpl (std::string const & Headerfile_path)
-    : m_Header_path(Headerfile_path)
+    : m_Header_path{Headerfile_path}
 {
 
 }
@@ -71,7 +72,7 @@ BTDPlotfileHeaderImpl::ReadHeaderData ()
     for (int idim = 0; idim < m_spacedim; ++idim) {
         is >> m_prob_hi[idim];
     }
-    WarpX::GotoNextLine(is);
+    ablastr::utils::text::goto_next_line(is);
 
     is >> m_prob_domain;
 
@@ -177,7 +178,7 @@ BTDPlotfileHeaderImpl::WriteHeader ()
 
 
 BTDMultiFabHeaderImpl::BTDMultiFabHeaderImpl (std::string const & Headerfile_path)
-    : m_Header_path(Headerfile_path)
+    : m_Header_path{Headerfile_path}
 {
 
 }
@@ -232,7 +233,7 @@ BTDMultiFabHeaderImpl::ReadMultiFabHeader ()
     for (int ifab = 0; ifab < m_ba.size(); ++ifab) {
         is >> m_FabOnDiskPrefix[ifab] >> m_fabname[ifab] >> m_fabhead[ifab];
     }
-    WarpX::GotoNextLine(is);
+    ablastr::utils::text::goto_next_line(is);
     char ch;
     is >> in_hash >> ch >> in_hash;
     m_minval.resize(m_ba.size());
@@ -243,7 +244,7 @@ BTDMultiFabHeaderImpl::ReadMultiFabHeader ()
             if( ch != ',' ) amrex::Error("Expected a ',' got something else");
         }
     }
-    WarpX::GotoNextLine(is);
+    ablastr::utils::text::goto_next_line(is);
     is >> in_hash >> ch >> in_hash;
     m_maxval.resize(m_ba.size());
     for (int ifab = 0; ifab < m_ba.size(); ++ifab) {
@@ -353,7 +354,7 @@ BTDMultiFabHeaderImpl::CopyVec(amrex::Vector<amrex::Real>& dst,
 
 
 BTDSpeciesHeaderImpl::BTDSpeciesHeaderImpl (std::string const & Headerfile_path, std::string const& species_name)
-    : m_Header_path(Headerfile_path), m_species_name(species_name)
+    : m_Header_path{Headerfile_path}, m_species_name{species_name}
 {
 
 }

Source/Diagnostics/BTDiagnostics.H

@@ -148,7 +148,7 @@ private:
      */
     bool m_do_back_transformed_particles = true;
 
-    /** m_gamma_boost, is a copy of warpx.gamma_boost
+    /** m_gamma_boost, is a copy of WarpX::gamma_boost
      *  That is, the Lorentz factor of the boosted frame in which the simulation is run.
      *  The direction for Lorentz transformation is assumed to be along
      *  ``warpx.boost_direction``, which is the same as the moving window direction.
@@ -157,7 +157,7 @@ private:
      */
     amrex::Real m_gamma_boost;
     amrex::Real m_beta_boost;
-    /** m_moving_window_dir is a copy of warpx.moving_window_dir
+    /** m_moving_window_dir is a copy of WarpX::moving_window_dir
      *  Currently, back-transformed diagnostics only works if moving window is
      *  in z-direction for both 2D and 3D simulations in the Cartesian frame of reference.
      */