Merge branch 'development' of https://github.com/ECP-WarpX/artemis in…

…to development

.readthedocs.yml

@@ -4,7 +4,19 @@
 #
 # License: BSD-3-Clause-LBNL
 
-requirements_file: Docs/requirements.txt
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+sphinx:
+   configuration: Docs/source/conf.py
+
+python:
+   install:
+   - requirements: Docs/requirements.txt
 
 formats:
   - htmlzip

Examples/Tests/circuits/inputs_resonator

@@ -0,0 +1,132 @@
+################################
+####### GENERAL PARAMETERS ######
+#################################
+
+# do not modify these
+geometry.dims = 3
+warpx.verbose = 1
+amr.max_level = 0
+amr.blocking_factor = 1024
+
+# stop at max_step or 100 periods, whichever occurs first
+max_step = 100000
+stop_time = 100 * wavelength/c
+warpx.cfl = 0.9
+
+# number of cells in each direction
+my_constants.ncells = 40
+amr.n_cell = ncells ncells ncells
+amr.max_grid_size = ncells
+
+# physical size of domain in [m]
+my_constants.Ldomain = 0.02
+geometry.prob_lo = -Ldomain/2 -Ldomain/2 -Ldomain/2
+geometry.prob_hi =  Ldomain/2  Ldomain/2  Ldomain/2
+
+# define grid spacing in each direction
+my_constants.dx = Ldomain/ncells
+my_constants.dy = Ldomain/ncells
+my_constants.dz = Ldomain/ncells
+
+# define a 'small' grid spacing
+my_constants.smalldx = dx/100
+my_constants.smalldy = dy/100
+my_constants.smalldz = dz/100
+
+boundary.field_lo = pml pml pml
+boundary.field_hi = pml pml pml
+
+#################################
+############ NUMERICS ###########
+#################################
+
+algo.em_solver_medium = macroscopic # vacuum/macroscopic
+
+algo.macroscopic_sigma_method = laxwendroff # laxwendroff or backwardeuler
+
+#################################
+############ FIELDS #############
+#################################
+
+# length of cubic cavity
+my_constants.Lcavity = 1.e-2
+
+# thickness of metal
+my_constants.tmetal = 1.e-3
+
+# excitation parameters
+# speed of light
+my_constants.c = 299792458.
+my_constants.wavelength = 1.e-2
+my_constants.f = c/wavelength
+my_constants.BW = 2/f
+my_constants.t0 = 2.e-10
+
+# conductivity of metal
+# 5.8e7 = copper
+my_constants.sigma = 5.8e3
+
+my_constants.pi = 3.14159265359
+my_constants.epsilon_0 = 8.8541878128e-12
+my_constants.mu_0 = 1.25663706212e-06
+
+macroscopic.epsilon_function(x,y,z) = "epsilon_0"
+macroscopic.mu_function(x,y,z) = "mu_0"
+
+macroscopic.sigma_function(x,y,z) = "sigma * (
+( (x>-Lcavity/2-tmetal) * (x<-Lcavity/2) * (y>-Lcavity/2-tmetal) * (y<Lcavity/2+tmetal) * (z>-Lcavity/2-tmetal) * (z<Lcavity/2+tmetal) ) or
+( (x>Lcavity/2) * (x<Lcavity/2+tmetal) * (y>-Lcavity/2-tmetal) * (y<Lcavity/2+tmetal) * (z>-Lcavity/2-tmetal) * (z<Lcavity/2+tmetal) ) or
+( (x>-Lcavity/2-tmetal) * (x<Lcavity/2+tmetal) * (y>-Lcavity/2-tmetal) * (y<-Lcavity/2) * (z>-Lcavity/2-tmetal) * (z<Lcavity/2+tmetal) ) or
+( (x>-Lcavity/2-tmetal) * (x<Lcavity/2+tmetal) * (y>Lcavity/2) * (y<Lcavity/2+tmetal) * (z>-Lcavity/2-tmetal) * (z<Lcavity/2+tmetal) ) or
+( (x>-Lcavity/2-tmetal) * (x<Lcavity/2+tmetal) * (y>-Lcavity/2-tmetal) * (y<Lcavity/2+tmetal) * (z>-Lcavity/2-tmetal) * (z<-Lcavity/2) ) or
+( (x>-Lcavity/2-tmetal) * (x<Lcavity/2+tmetal) * (y>-Lcavity/2-tmetal) * (y<Lcavity/2+tmetal) * (z>Lcavity/2) * (z<Lcavity/2+tmetal) ) )"
+
+# initial E field
+warpx.E_ext_grid_init_style = parse_E_ext_grid_function
+warpx.Ex_external_grid_function(x,y,z) = "0."
+warpx.Ey_external_grid_function(x,y,z) = "0."
+warpx.Ez_external_grid_function(x,y,z) = "0."
+
+# initial B field
+warpx.B_ext_grid_init_style = parse_B_ext_grid_function
+warpx.Bx_external_grid_function(x,y,z) = "0."
+warpx.By_external_grid_function(x,y,z) = "0."
+warpx.Bz_external_grid_function(x,y,z) = "0."
+
+# external E excitation
+warpx.E_excitation_on_grid_style = parse_E_excitation_grid_function
+
+warpx.Ex_excitation_flag_function(x,y,z) = "0."
+warpx.Ey_excitation_flag_function(x,y,z) = "0."
+warpx.Ez_excitation_flag_function(x,y,z) = "0."
+
+warpx.Ex_excitation_grid_function(x,y,z,t) = "0."
+warpx.Ey_excitation_grid_function(x,y,z,t) = "0."
+warpx.Ez_excitation_grid_function(x,y,z,t) = "0."
+
+# external B excitation
+warpx.B_excitation_on_grid_style = parse_B_excitation_grid_function
+
+# 2 = soft source excitation (increment field as opposed to overwrite with a hard source)
+warpx.Bx_excitation_flag_function(x,y,z) = "2 * (x>-smalldx) * (x<smalldx) * (y>0) * (y<dy) * (z>-Lcavity/2) * (z<Lcavity/2)"
+warpx.By_excitation_flag_function(x,y,z) = "0."
+warpx.Bz_excitation_flag_function(x,y,z) = "0."
+
+warpx.Bx_excitation_grid_function(x,y,z,t) = "exp(-(t-t0)*(t-t0)/(BW*BW))*sin(2*pi*f*(t-t0))"
+warpx.By_excitation_grid_function(x,y,z,t) = "0."
+warpx.Bz_excitation_grid_function(x,y,z,t) = "0."
+
+# plotfile diagnostics
+diagnostics.diags_names = plt
+plt.intervals = 100
+plt.fields_to_plot = Ex Ey Ez Bx By Bz
+plt.diag_type = Full
+plt.plot_raw_fields = 0
+
+# output diagnostics
+warpx.reduced_diags_names = Eobs1
+Eobs1.type = RawEFieldReduction
+Eobs1.reduction_type = integral
+Eobs1.integration_type = volume
+Eobs1.intervals = 1
+Eobs1.reduced_function(x,y,z) = (x>Lcavity/4-smalldx) * (x<Lcavity/4+dx/2+smalldx) * (y>Lcavity/4-smalldy) * (y<Lcavity/4+dy/2+smalldy) * (z>Lcavity/4-smalldz) * (z<Lcavity/4+dz/2+smalldz)

Examples/Tests/circuits/inputs_wave_freespace

@@ -0,0 +1,80 @@
+################################
+####### GENERAL PARAMETERS ######
+#################################
+max_step = 250
+amr.n_cell = 32 32 32
+amr.max_grid_size = 32
+amr.blocking_factor = 32
+geometry.dims = 3
+geometry.prob_lo     =  -4.e-6 -4.e-6 -4.e-6
+geometry.prob_hi     =   4.e-6  4.e-6  4.e-6
+amr.max_level = 0
+boundary.field_lo = periodic periodic periodic
+boundary.field_hi = periodic periodic periodic
+
+#################################
+############ NUMERICS ###########
+#################################
+warpx.verbose = 1
+warpx.use_filter = 0
+warpx.cfl = 0.9
+
+algo.em_solver_medium = macroscopic # vacuum/macroscopic
+
+algo.macroscopic_sigma_method = laxwendroff # laxwendroff or backwardeuler
+
+macroscopic.sigma_function(x,y,z) = "sigma_0"
+
+macroscopic.epsilon_function(x,y,z) = "epsilon_0"
+
+macroscopic.mu_function(x,y,z) = "mu_0 "
+
+#################################
+############ FIELDS #############
+#################################
+
+my_constants.pi = 3.14159265359
+my_constants.L = 50.e-6
+my_constants.c = 299792458.
+my_constants.wavelength = 4.e-6
+
+my_constants.sigma_0 = 0.0
+my_constants.epsilon_0 = 8.8541878128e-12
+my_constants.mu_0 = 1.25663706212e-06
+
+warpx.E_ext_grid_init_style = parse_E_ext_grid_function
+warpx.Ex_external_grid_function(x,y,z) = "1.e5*exp(-(y)**2/(L/32)**2)*cos(2*pi*(y)/wavelength)"
+warpx.Ey_external_grid_function(x,y,z) = "0."
+warpx.Ez_external_grid_function(x,y,z) = "0."
+
+warpx.B_ext_grid_init_style = parse_B_ext_grid_function
+warpx.Bx_external_grid_function(x,y,z) = "0."
+warpx.By_external_grid_function(x,y,z) = "0."
+warpx.Bz_external_grid_function(x,y,z) = "(-1.e5*exp(-(y)**2/(L/32)**2)*cos(2*pi*(y)/wavelength)/c)"
+
+warpx.E_excitation_on_grid_style = parse_E_excitation_grid_function
+
+warpx.Ex_excitation_flag_function(x,y,z) = "0."
+warpx.Ey_excitation_flag_function(x,y,z) = "0."
+warpx.Ez_excitation_flag_function(x,y,z) = "0."
+
+warpx.Ex_excitation_grid_function(x,y,z,t) = "0."
+warpx.Ey_excitation_grid_function(x,y,z,t) = "0."
+warpx.Ez_excitation_grid_function(x,y,z,t) = "0."
+
+warpx.B_excitation_on_grid_style = parse_B_excitation_grid_function
+
+warpx.Bx_excitation_flag_function(x,y,z) = "0."
+warpx.By_excitation_flag_function(x,y,z) = "0."
+warpx.Bz_excitation_flag_function(x,y,z) = "0."
+
+warpx.Bx_excitation_grid_function(x,y,z,t) = "0."
+warpx.By_excitation_grid_function(x,y,z,t) = "0."
+warpx.Bz_excitation_grid_function(x,y,z,t) = "0."
+
+# Diagnostics
+diagnostics.diags_names = plt
+plt.intervals = 1
+plt.fields_to_plot = Ex Ey Ez Bx By Bz
+plt.diag_type = Full
+plt.plot_raw_fields = 1

Source/Evolve/WarpXEvolve.cpp

@@ -184,7 +184,7 @@ WarpX::Evolve (int numsteps)
         // ionization, Coulomb collisions, QED
         doFieldIonization();
         ExecutePythonCallback("beforecollisions");
-        mypc->doCollisions( cur_time, dt[0] );
+        //mypc->doCollisions( cur_time, dt[0] );
         ExecutePythonCallback("aftercollisions");
 #ifdef WARPX_QED
         doQEDEvents();

Source/Initialization/WarpXInitData.cpp

@@ -394,12 +394,18 @@ WarpX::InitData ()
         ComputeDt();
         WarpX::PrintDtDxDyDz();
         InitFromScratch();
+        if (WarpX::em_solver_medium==1) {
+            m_macroscopic_properties->InitData();
+        }
         InitDiagnostics();
     }
     else
     {
         InitFromCheckpoint();
         WarpX::PrintDtDxDyDz();
+        if (WarpX::em_solver_medium==1) {
+            m_macroscopic_properties->InitData();
+        }
         PostRestart();
         reduced_diags->InitData();
     }
@@ -414,9 +420,6 @@ WarpX::InitData ()
 
     BuildBufferMasks();
 
-    if (WarpX::em_solver_medium==1) {
-        m_macroscopic_properties->InitData();
-    }
 
     if (WarpX::yee_coupled_solver_algo == CoupledYeeSolver::MaxwellLondon) {
         amrex::Print() << " calling london \n";

Source/Particles/Make.package

@@ -15,7 +15,7 @@ include $(WARPX_HOME)/Source/Particles/Gather/Make.package
 include $(WARPX_HOME)/Source/Particles/Sorting/Make.package
 include $(WARPX_HOME)/Source/Particles/ParticleCreation/Make.package
 include $(WARPX_HOME)/Source/Particles/ElementaryProcess/Make.package
-include $(WARPX_HOME)/Source/Particles/Collision/Make.package
+#include $(WARPX_HOME)/Source/Particles/Collision/Make.package
 include $(WARPX_HOME)/Source/Particles/Filter/Make.package
 include $(WARPX_HOME)/Source/Particles/Resampling/Make.package
 

Source/Particles/MultiParticleContainer.H

@@ -172,7 +172,7 @@ public:
                             const amrex::MultiFab& Ex, const amrex::MultiFab& Ey, const amrex::MultiFab& Ez,
                             const amrex::MultiFab& Bx, const amrex::MultiFab& By, const amrex::MultiFab& Bz);
 
-    void doCollisions (amrex::Real cur_time, amrex::Real dt);
+    //void doCollisions (amrex::Real cur_time, amrex::Real dt);
 
     /**
     * \brief This function loops over all species and performs resampling if appropriate.
@@ -357,7 +357,7 @@ protected:
 
     std::vector<std::string> lasers_names;
 
-    std::unique_ptr<CollisionHandler> collisionhandler;
+    //std::unique_ptr<CollisionHandler> collisionhandler;
 
     //! instead of depositing (current, charge) on the finest patch level, deposit to the coarsest grid
     std::vector<bool> m_deposit_on_main_grid;

Source/Particles/MultiParticleContainer.cpp

@@ -120,7 +120,7 @@ MultiParticleContainer::MultiParticleContainer (AmrCore* amr_core)
     pc_tmp = std::make_unique<PhysicalParticleContainer>(amr_core);
 
     // Setup particle collisions
-    collisionhandler = std::make_unique<CollisionHandler>(this);
+    //collisionhandler = std::make_unique<CollisionHandler>(this);
 
 }
 
@@ -933,12 +933,14 @@ MultiParticleContainer::doFieldIonization (int lev,
     }
 }
 
+/*
 void
 MultiParticleContainer::doCollisions ( Real cur_time, amrex::Real dt )
 {
     WARPX_PROFILE("MultiParticleContainer::doCollisions()");
     collisionhandler->doCollisions(cur_time, dt, this);
 }
+*/
 
 void MultiParticleContainer::doResampling (const int timestep)
 {