Add QED particle creaction routines (#698)

* Initial work to add back QED particle generation

* Work in progress: port old QED routines

* Add two distinct CopyFuncs

* modified getMFItInfo and CopyFunc (not working)

* bugfixing & work to add back QED particle creation routines

* bugfixing

* added back quantum photon emission

* bugfixing

* bugfixing

* added back pair generation (still some bugs in photon emission)

* removed unwanted check

* bugfixing

* bugfixing

* bugfixing

* Moved QED folder

* added comments + some refactoring

* added comments

* remove some virtual functions to make lgtm happy

* updated tests

* added PhysicalParticleType

* bugfixing

* added copyright

* improved comments

* improved comments

* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* moved inclusion of QEDInternals folder

* moved some inclusion directives between Make files

* moved some inclusion directives between Make files (forgot to add a file)

* Update Source/Particles/PhysicalParticleContainer.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/PhysicalParticleContainer.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/PhysicalParticleContainer.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/PhysicalParticleContainer.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/PhysicalParticleContainer.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/MultiParticleContainer.cpp

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/MultiParticleContainer.cpp

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* Update Source/Particles/MultiParticleContainer.cpp

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Update Source/Particles/MultiParticleContainer.cpp

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* Update Source/Particles/MultiParticleContainer.cpp

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* Update Source/Particles/MultiParticleContainer.cpp

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* Update Source/Particles/MultiParticleContainer.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* corrected alignment

* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* removed some unnecessary amrex::

* add missing comment

* Replaced BL_PROFILE with WARPX_PROFILE

* bugfixing and making some variables const

* removed some moves

* removed some moves

* started to change tau into optical_depth_BW or optical_depth_QSR

* Using initialization policy to initialize optical depth

* bugfixing

* forgot to add a file

* fixed bug

* Revert "fixed bug"

This reverts commit a3fb98d10cc30327635aeaa71451a05ca2229ff4.

* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* Update Source/Particles/MultiParticleContainer.cpp

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* Added doQEDEvents to OneStep_sub1

* add a bunch of const

* add _rt suffix

* Update Source/Particles/MultiParticleContainer.cpp

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* added path to included files

* Introduced a templated AmIA<something> function using physical_species

* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* added paths to included headers

* updated documentation

* updated examples

* bugfixing

* bugfixing

* fixing examples

* fixed example

* fixed example

* correct a misprint in error message

* fixed issue related to 1./mass for photons

* Update Source/Particles/MultiParticleContainer.cpp

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* Update Source/Particles/MultiParticleContainer.cpp

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* Update Source/Particles/MultiParticleContainer.cpp

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* make the use of energy_threshold more transparent

* remove unnecessary checks

* bigfixing

* added comment

* separate checks for QED processes

* added a CheckIonizationProductSpecies for consistency

* bugfixing

* now using a new variable for photon energy creation threshold

* removed unwanted comment

* added option to set a user-defined threshold for photon creation

* bugfixing

* updated documentation

* updated example to include new option

* updated doc

* fixed merge conflict

* correct bug in example

* reorganized function

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>

1 files changed, 96 insertions, 0 deletions

diff --git a/Source/Particles/ElementaryProcess/QEDInternals/QedTableParserHelperFunctions.H b/Source/Particles/ElementaryProcess/QEDInternals/QedTableParserHelperFunctions.H
new file mode 100644
index 000000000..dd66f626f
--- /dev/null
+++ b/Source/Particles/ElementaryProcess/QEDInternals/QedTableParserHelperFunctions.H
@@ -0,0 +1,96 @@
+/* Copyright 2019 Luca Fedeli, Maxence Thevenet
+ *
+ * This file is part of WarpX.
+ *
+ * License: BSD-3-Clause-LBNL
+ */
+#ifndef WARPX_amrex_qed_table_parser_helper_functions_h_
+#define WARPX_amrex_qed_table_parser_helper_functions_h_
+
+/**
+ * This header contains helper functions to safely extract data
+ * (e.g. integers, floating point numbers) from raw binary data
+ * (i.e. a char*) and to convert arrays into raw binary data.
+ */
+
+#include <AMReX_Vector.H>
+#include <tuple>
+
+namespace QedUtils{
+    /**
+    * This function safely extracts an amrex::Vector<T> from raw binary data.
+    * T must be a simple datatype (e.g. an int, a float, a double...).
+    *
+    * @param[in] p_data a pointer to the binary stream
+    * @param[in] how_many how many T should be read from stream
+    * @param[in] p_last a pointer to the last element of the char* array
+    * @return {a tuple containing
+    * 1) flag (which is false if p_last is exceeded)
+    * 2) a Vector of T
+    * 3) a pointer to a new location of the binary data (after having read how_many T)}
+    */
+    template <class T>
+    std::tuple<bool, amrex::Vector<T>, const char*>parse_raw_data_vec(
+        const char* p_data, size_t how_many, const char* const p_last)
+    {
+        amrex::Vector<T> res;
+        if(p_data + sizeof(T)*how_many > p_last)
+            return std::make_tuple(false, res, nullptr);
+
+        auto r_data = reinterpret_cast<const T*>(p_data);
+
+        res.assign(r_data, r_data + how_many);
+
+        p_data += sizeof(T)*how_many;
+        return std::make_tuple(true, res, p_data);
+    }
+
+    /**
+    * This function safely extracts a T from raw binary data.
+    * T must be a simple datatype (e.g. an int, a float, a double...).
+    *
+    * @param[in] p_data a pointer to the binary stream
+    * @param[in] p_last a pointer to the last element of the char* array
+    * @return {a tuple containing
+    * 1) flag (which is false if p_last is exceeded)
+    * 2) a T
+    * 3) a pointer to a new location of the binary data (after having read 1 T)}
+    */
+    template <class T>
+    std::tuple<bool, T, const char*> parse_raw_data(
+        const char* p_data, const char* const p_last)
+    {
+        T res;
+        if(p_data + sizeof(T) > p_last)
+            return std::make_tuple(false, res, nullptr);
+
+        auto r_data = reinterpret_cast<const T*>(p_data);
+
+        res = *r_data;
+
+        p_data += sizeof(T);
+        return std::make_tuple(true, res, p_data);
+    }
+
+    /**
+    * This function converts a C-style array of T into
+    * a Vector<char> (i.e. raw binary data) and adds it
+    * to an existing Vector<char> passed by reference
+    * @param[in] p_data a pointer to the beginning of the array
+    * @param[in] how_many number of elements of type T in the array
+    * @param[in,out] raw_data data will be appended to this vector
+    */
+    template <class T>
+    void add_data_to_vector_char (
+        const T* p_data, size_t how_many, amrex::Vector<char>& raw_data)
+    {
+        raw_data.insert(
+            raw_data.end(),
+            reinterpret_cast<const char*>(p_data),
+            reinterpret_cast<const char*>(p_data) +
+            sizeof(T)*how_many
+        );
+    }
+};
+
+#endif //WARPX_amrex_qed_table_parser_helper_functions_h_