Merge remote-tracking branch 'upstream/master' into introduce_heat_sources

Author: masterleinad

CONTRIBUTING.md

@@ -0,0 +1,6 @@
+# Contributing
+
+Contributing to adamantine is easy. Just send us a [pullrequest](https://help.github.com/articles/using-pull-requests/).
+When you send your request, make `master` the destination branch on the [adamantine repository](https://github.com/adamantine-sim/adamantine).
+
+Your pull request must pass adamantine's tests before being merged into the `master` branch. These tests are (usually) performed automatically through the continuous integration (CI) testing integrated into adamantine's GitHub repository.

README.md

@@ -150,6 +150,7 @@ The following options are available:
   * beam\_X.scan\_path\_file: scan path filename (required)
   * beam\_X.scan\_path\_file\_format: format of the scan path: segment or
   event\_series (required)
+  * beam\_X.max\_power: maximum power of the beam in watts (required)
   * beam\_X.depth: maximum depth reached by the electron beam in meters (required)
   * beam\_X.absorption\_efficiency: absorption efficiency of the beam equivalent
   to energy\_conversion\_efficiency * control\_efficiency for electon beam. Number
@@ -276,3 +277,7 @@ The first entry of the file is the dimension the problem: 2 or 3.
 ## Questions
 If you have any question, find a bug, or have feature request please open an
 issue.
+
+## Contributing
+We encourage you to contribute to adamantine! Please check out the
+[guidelines](CONTRIBUTING.md) about how to proceed.

application/adamantine.cc

@@ -106,7 +106,7 @@ get_p_order_and_n_material_states(boost::property_tree::ptree &database)
 
   // Sanity check
   adamantine::ASSERT_THROW(
-      p_order >= 0 && p_order < 5,
+      p_order < 5,
       "Error when computing the polynomial order of the material properties");
   adamantine::ASSERT_THROW(
       n_material_states > 0 && n_material_states < 4,

application/adamantine.hh

@@ -37,6 +37,7 @@
 #include <deal.II/lac/vector_operation.h>
 #include <deal.II/numerics/error_estimator.h>
 
+#include <boost/algorithm/string.hpp>
 #include <boost/archive/text_iarchive.hpp>
 #include <boost/archive/text_oarchive.hpp>
 #include <boost/property_tree/ptree.hpp>
@@ -759,6 +760,7 @@ run(MPI_Comm const &communicator, boost::property_tree::ptree const &database,
   std::unique_ptr<adamantine::ThermalPhysicsInterface<dim, MemorySpaceType>>
       thermal_physics;
   adamantine::HeatSources<dim, MemorySpaceType> heat_sources;
+  std::vector<std::pair<double, bool>> scan_path_end;
   if (use_thermal_physics)
   {
     // PropertyTreeInput discretization.thermal.fe_degree
@@ -771,6 +773,13 @@ run(MPI_Comm const &communicator, boost::property_tree::ptree const &database,
         fe_degree, quadrature_type, communicator, database, geometry,
         material_properties);
     heat_sources = thermal_physics->get_heat_sources();
+    // Store the current end time of each heat source and set a flag that the
+    // scan path has changed
+    for (auto const &source : heat_sources)
+    {
+      scan_path_end.emplace_back(
+          source->get_scan_path().get_segment_list().back().end_time, true);
+    }
     post_processor_database.put("thermal_output", true);
   }
 
@@ -1001,6 +1010,43 @@ run(MPI_Comm const &communicator, boost::property_tree::ptree const &database,
     if (time > activation_time_end)
     {
       double const eps = time_step / 1e10;
+
+      // We may need to check if the scan path has been updated. We don't want
+      // to keep reading the file if it's not going to be updated. Once we
+      // reach the end of the scan path, we reread the scan path file. If it was
+      // not updated, we won't try to read it again.
+      bool scan_path_updated = false;
+      for (unsigned int s = 0; s < scan_path_end.size(); ++s)
+      {
+        if ((time > scan_path_end[s].first - eps) && (scan_path_end[s].second))
+        {
+          scan_path_updated = true;
+          break;
+        }
+      }
+      if (scan_path_updated)
+      {
+        for (unsigned int s = 0; s < scan_path_end.size(); ++s)
+        {
+          // Read the scan path file
+          heat_sources[s]->get_scan_path().read_file();
+
+          // Update scan_path_end
+          double new_end_time = heat_sources[s]
+                                    ->get_scan_path()
+                                    .get_segment_list()
+                                    .back()
+                                    .end_time;
+          scan_path_end[s].second = scan_path_end[s].first != new_end_time;
+          scan_path_end[s].first = new_end_time;
+        }
+
+        std::tie(material_deposition_boxes, deposition_times, deposition_cos,
+                 deposition_sin) =
+            adamantine::create_material_deposition_boxes<dim>(geometry_database,
+                                                              heat_sources);
+      }
+
       auto activation_start =
           std::lower_bound(deposition_times.begin(), deposition_times.end(),
                            time - eps) -

cmake/SetupDealII.cmake

@@ -3,26 +3,19 @@ find_package(deal.II 9.5 REQUIRED PATHS ${DEAL_II_DIR})
 
 deal_ii_initialize_cached_variables()
 
-if(NOT DEAL_II_WITH_CXX17)
-  message(FATAL_ERROR "deal.II needs to be configured with C++17 support.")
-endif()
+set(DEAL_II_REQUIRED_FEATURES ARBORX CXX17 MPI P4EST TRILINOS)
 
-if(NOT DEAL_II_WITH_MPI)
-  message(FATAL_ERROR "deal.II needs to be configured with MPI support.")
-endif()
+foreach(FEATURE ${DEAL_II_REQUIRED_FEATURES})
+  if(NOT DEAL_II_WITH_${FEATURE})
+    list(APPEND DEAL_II_MISSING_FEATURES ${FEATURE})
+  endif()
+endforeach()
 
-if(NOT DEAL_II_WITH_ARBORX)
-  message(FATAL_ERROR "deal.II needs to be configured with ArborX support.")
+if(DEAL_II_MISSING_FEATURES)
+  string(REPLACE ";"  ", " DEAL_II_MISSING_FEATURES "${DEAL_II_MISSING_FEATURES}")
+  message(FATAL_ERROR "deal.II wasn't configured with all required dependencies. The missing dependencies are ${DEAL_II_MISSING_FEATURES}.")
 endif()
 
 if(NOT DEAL_II_ARBORX_WITH_MPI)
   message(FATAL_ERROR "ArborX needs to be configured with MPI support.")
 endif()
-
-if(NOT DEAL_II_WITH_P4EST)
-  message(FATAL_ERROR "deal.II needs to be configured with P4EST support.")
-endif()
-
-if(NOT DEAL_II_WITH_TRILINOS)
-  message(FATAL_ERROR "deal.II needs to be configured with Trilinos support.")
-endif()

source/ElectronBeamHeatSource.hh

@@ -1,4 +1,4 @@
-/* Copyright (c) 2020 - 2022, the adamantine authors.
+/* Copyright (c) 2020 - 2024, the adamantine authors.
  *
  * This file is subject to the Modified BSD License and may not be distributed
  * without copyright and license information. Please refer to the file LICENSE
@@ -11,6 +11,8 @@
 #include <BeamHeatSourceProperties.hh>
 #include <ScanPath.hh>
 
+#include <limits>
+
 namespace adamantine
 {
 /**
@@ -70,7 +72,7 @@ public:
 
 private:
   dealii::Point<3> _beam_center;
-  double _alpha;
+  double _alpha = std::numeric_limits<double>::signaling_NaN();
   BeamHeatSourceProperties _beam;
   ScanPath<MemorySpaceType> _scan_path;
 };

source/GoldakHeatSource.hh

@@ -1,4 +1,4 @@
-/* Copyright (c) 2020 - 2022, the adamantine authors.
+/* Copyright (c) 2020 - 2024, the adamantine authors.
  *
  * This file is subject to the Modified BSD License and may not be distributed
  * without copyright and license information. Please refer to the file LICENSE
@@ -11,6 +11,8 @@
 #include <BeamHeatSourceProperties.hh>
 #include <ScanPath.hh>
 
+#include <limits>
+
 namespace adamantine
 {
 /**
@@ -70,7 +72,7 @@ public:
 
 private:
   dealii::Point<3> _beam_center;
-  double _alpha;
+  double _alpha = std::numeric_limits<double>::signaling_NaN();
   BeamHeatSourceProperties _beam;
 
   ScanPath<MemorySpaceType> _scan_path;

source/MaterialProperty.hh

@@ -56,13 +56,6 @@ public:
       dealii::parallel::distributed::Triangulation<dim> const &tria,
       boost::property_tree::ptree const &database);
 
-  /**
-   * Copy constructor. It should only be called by KOKKOS_CLASS_LAMBDA. The
-   * copy constructor does not copy all the member variables of the class.
-   */
-  MaterialProperty(MaterialProperty<dim, p_order, MaterialStates,
-                                    MemorySpaceType> const &other);
-
   /**
    * Return true if the material properties are given in table format.
    * Return false if they are given in polynomial format.