Read species distribution from OPMD - part 3 (#883)

* Added <species>.profile=external_file and .profile_file

* Added description of input parameters to Docs

* Changed from profile to injection option for external file

* Fix typo in amrex abort message (due to copy paste)

* Added the OpenPMD use amrex abort message

* Minor fix - not sure how to remove EOL issue

* Tried to add AddExternalFileBeam functon to PhysicalParticleContainer

* Trued to fix EOL white space issue

* Added read/print species name from OPMD file

* Fixed OpenPMD charge and mass read

* Added number of particles in species

* Added nparts and converted charge/mass units to SI

* Fix to nr of particles

* Added q_tot parameter to determine part weight

* Added macroparticle's weight

* Fixed std::int typo - use only int

* Added read x,y and z + ifdef 3D

* Added velocity of particles and stored in container

* Converted velocities to SI

* No need to specfy momentum distribution if external file is used

* Update Source/Initialization/PlasmaInjector.cpp

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

* Update Source/Particles/PhysicalParticleContainer.cpp

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

* Update Source/Particles/PhysicalParticleContainer.cpp

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.cpp

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

* No need to include openPMD header yet

* Fixed const in AddExternalFileBeam

* Fix compatibility with read_opmd and read_opmd_2

* Corrected position and charge units/sign

* Added Doc note and abort message for RZ

* Fix typo and EOL

* Minor fixes

* Fixed details. Added fix to EOL - testing

* Changed to physical_charge and explained it in Docs

* Fix header extra openPMD include files

* Removed additional debugging comments

* Try doxygen again

* Fix plasmainjector physical_q_tot

* Change apart to auto (not long as in gaussian beam injection style)

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

* Correct for new type of npart

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

* Removed Geant4 renormalization

* Read openPMD file and checked its units

* Trying to correct momentum information in plotfiles

* Compilation error - > SegFault 11

* Added unitSI() to each position/momentum direction. Compilation SegFault

* Re-structured code to use only once series.flush()

* Commented out amrex::Print() s

* Path to fix issue

* Update after review

* Chanegd <physical_q_tot> to <q_tot> and made it optional

* Fixed documentation typo and re-organized it

* Added const to npart as per reviewer recommendation

* Fixed issue with velocity - which became momentum

* Fixed 2D and 3D options + documentation

* Implemented fixes from past reviewsand fixed duplicate entry in Docs

* Fix auto in iterator in for loop

* Added fixes according to reviewer

* Revert "Added fixes according to reviewer"

This reverts commit 0a485d83c28014c8b6f53a30f26719f23f89bad5.

* Fixed IO block and reordered logic with Axel

* Fix spaces

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

1 files changed, 12 insertions, 3 deletions

diff --git a/Source/Initialization/PlasmaInjector.cpp b/Source/Initialization/PlasmaInjector.cpp
index ec2c454e2..e34447411 100644
--- a/Source/Initialization/PlasmaInjector.cpp
+++ b/Source/Initialization/PlasmaInjector.cpp
@@ -229,10 +229,14 @@ PlasmaInjector::PlasmaInjector (int ispecies, const std::string& name)
         parseDensity(pp);
         parseMomentum(pp);
     } else if (part_pos_s == "external_file") {
+#ifdef WARPX_DIM_RZ
+        amrex::Abort("The option of reading particle data from an external "
+                     "file has not been implemented nor tested in RZ geometry");
+#endif
 #ifdef WARPX_USE_OPENPMD
         external_file = true;
-        pp.get("injection_file",str_injection_file);
-        pp.get("q_tot",q_tot);
+        pp.get("injection_file", str_injection_file);
+        pp.query("q_tot", q_tot);
 #else
         amrex::Abort("WarpX has to be compiled with USE_OPENPMD=TRUE to be able"
                      " to read the external openPMD file with species data");
@@ -398,7 +402,12 @@ void PlasmaInjector::parseMomentum (ParmParse& pp)
                                            makeParser(str_momentum_function_uy,{"x","y","z"}),
                                            makeParser(str_momentum_function_uz,{"x","y","z"})));
     } else {
-        StringParseAbortMessage("Momentum distribution type", mom_dist_s);
+        //No need for momentum definition if external file is used
+        std::string s_inj_style;
+        pp.query("injection_style", s_inj_style);
+        if (s_inj_style != "external_file") {
+            StringParseAbortMessage("Momentum distribution type", mom_dist_s);
+        }
     }
 }