From a2ae832e034fed1813682600aa9f0a70c3ad63b1 Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Tue, 30 Aug 2022 07:48:54 -0700
Subject: [PATCH 01/33] cell center BTD functors for RZ with openpmd

---
 Source/Diagnostics/BTDiagnostics.cpp | 102 +++++++++++++++++++++++++++
 1 file changed, 102 insertions(+)

diff --git a/Source/Diagnostics/BTDiagnostics.cpp b/Source/Diagnostics/BTDiagnostics.cpp
index 90b00a24a08..8b1a79ce2b7 100644
--- a/Source/Diagnostics/BTDiagnostics.cpp
+++ b/Source/Diagnostics/BTDiagnostics.cpp
@@ -523,6 +523,12 @@ BTDiagnostics::InitializeFieldFunctors (int lev)
                   nvars, m_num_buffers, m_varnames);
     }
 
+    // For RZ, initialize field functors RZ for openpmd
+    // This is a specialized call for intializing cell-center functors
+    // such that, all modes of a field component are stored contiguously
+    // For examply, Er0, Er1_real, Er1_imag, etc
+    InitializeFieldFunctorsRZopenPMD(lev);
+
     // Define all cell-centered functors required to compute cell-centere data
     // Fill vector of cell-center functors for all field-components, namely,
     // Ex, Ey, Ez, Bx, By, Bz, jx, jy, jz, and rho are included in the
@@ -695,6 +701,102 @@ BTDiagnostics::AddRZModesToOutputNames (const std::string& field, const int ncom
 #endif
 }
 
+void
+BTDiagnostics::InitializeFieldFunctorsRZopenPMD (int lev)
+{
+#ifdef WARPX_DIM_RZ
+    auto & warpx = WarpX::GetInstance();
+    int ncomp_multimodefab = warpx.get_pointer_Efield_aux(0,0)->nComp();
+    int ncomp = ncomp_multimodefab;
+    // This function may be called multiple times, for different values of `lev`
+    // but the `varnames` need only be updated once.
+    bool update_cellcenter_varnames = (lev == 0);
+    if (update_cellcenter_varnames) {
+        m_cellcenter_varnames.clear();
+        const int n_rz = ncomp * m_cellcenter_varnames.size();
+        m_cellcenter_varnames.reserve(n_rz);
+    }
+
+    // Reset field functors
+    m_cell_center_functors[lev].clear();
+    m_cell_center_functors[lev].resize(m_cellcenter_varnames_fields.size());
+
+    for (int comp=0, n=m_cell_center_functors.at(lev).size(); comp<n; comp++){
+        if        ( m_cellcenter_varnames_fields[comp] == "Er" ){
+            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_Efield_aux(lev, 0), lev, m_crse_ratio, false, ncomp);
+            if (update_cellcenter_varnames) {
+                AddRZModesToOutputNames(std::string("Er"), ncomp, true);
+            }
+        } else if ( m_cellcenter_varnames_fields[comp] == "Et" ){
+            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_Efield_aux(lev, 1), lev, m_crse_ratio, false, ncomp);
+            if (update_cellcenter_varnames) {
+                AddRZModesToOutputNames(std::string("Et"), ncomp, true);
+            }
+        } else if ( m_cellcenter_varnames_fields[comp] == "Ez" ){
+            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_Efield_aux(lev, 2), lev, m_crse_ratio, false, ncomp);
+            if (update_cellcenter_varnames) {
+                AddRZModesToOutputNames(std::string("Ez"), ncomp, true);
+            }
+        } else if ( m_cellcenter_varnames_fields[comp] == "Br" ){
+            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_Bfield_aux(lev, 0), lev, m_crse_ratio, false, ncomp);
+            if (update_cellcenter_varnames) {
+                AddRZModesToOutputNames(std::string("Br"), ncomp, true);
+            }
+        } else if ( m_cellcenter_varnames_fields[comp] == "Bt" ){
+            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_Bfield_aux(lev, 1), lev, m_crse_ratio, false, ncomp);
+            if (update_cellcenter_varnames) {
+                AddRZModesToOutputNames(std::string("Bt"), ncomp, true);
+            }
+        } else if ( m_cellcenter_varnames_fields[comp] == "Bz" ){
+            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_Bfield_aux(lev, 2), lev, m_crse_ratio, false, ncomp);
+            if (update_cellcenter_varnames) {
+                AddRZModesToOutputNames(std::string("Bz"), ncomp, true);
+            }
+        } else if ( m_cellcenter_varnames_fields[comp] == "jr" ){
+            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_current_fp(lev, 0), lev, m_crse_ratio, false, ncomp);
+            if (update_cellcenter_varnames) {
+                AddRZModesToOutputNames(std::string("jr"), ncomp, true);
+            }
+        } else if ( m_cellcenter_varnames_fields[comp] == "jt" ){
+            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_current_fp(lev, 1), lev, m_crse_ratio, false, ncomp);
+            if (update_cellcenter_varnames) {
+                AddRZModesToOutputNames(std::string("jt"), ncomp, true);
+            }
+        } else if ( m_cellcenter_varnames_fields[comp] == "jz" ){
+            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_current_fp(lev, 2), lev, m_crse_ratio, false, ncomp);
+            if (update_cellcenter_varnames) {
+                AddRZModesToOutputNames(std::string("jz"), ncomp, true);
+            }
+        } else if ( m_cellcenter_varnames_fields[comp] == "rho" ){
+            m_cell_center_functors[lev][comp] = std::make_unique<RhoFunctor>(lev, m_crse_ratio, -1, false, ncomp);
+            if (update_cellcenter_varnames) {
+                AddRZModesToOutputNames(std::string("rho"), ncomp, true);
+            }
+        }
+    }
+
+#endif
+    amrex::ignore_unused(lev);
+}
+
+void
+BTDiagnostics::AddRZModesToOutputNames (const std::string& field, const int ncomp, bool cellcenter_data)
+{
+#ifdef WARPX_DIM_RZ
+    // In cylindrical geometry, real and imag part of each mode are also
+    // dumped to file separately, so they need to be added to m_varnames
+    if (cellcenter_data) {
+        m_cellcenter_varnames.push_back( field + "_0_real" );
+        for (int ic=1 ; ic < (ncomp+1)/2 ; ic += 1) {
+            m_cellcenter_varnames.push_back( field + "_" + std::to_string(ic) + "_real" );
+            m_cellcenter_varnames.push_back( field + "_" + std::to_string(ic) + "_imag" );
+        }
+    }
+#else
+    amrex::ignore_unused(field, ncomp, cellcenter_data);
+#endif
+}
+
 void
 BTDiagnostics::PrepareBufferData ()
 {

From 11b6dd71b53cfd1e11e09945f43a25a392d01891 Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Mon, 19 Sep 2022 10:29:38 -0700
Subject: [PATCH 02/33] add RZ modes to output varnames too

---
 Source/Diagnostics/BTDiagnostics.cpp | 55 +++++++++++++++++++++++++---
 1 file changed, 49 insertions(+), 6 deletions(-)

diff --git a/Source/Diagnostics/BTDiagnostics.cpp b/Source/Diagnostics/BTDiagnostics.cpp
index 8b1a79ce2b7..e8b92d43e53 100644
--- a/Source/Diagnostics/BTDiagnostics.cpp
+++ b/Source/Diagnostics/BTDiagnostics.cpp
@@ -482,6 +482,7 @@ BTDiagnostics::DefineCellCenteredMultiFab(int lev)
     amrex::DistributionMapping dmap = warpx.DistributionMap(lev);
     int ngrow = 1;
     int ncomps = static_cast<int>(m_cellcenter_varnames.size());
+    amrex::Print() << " ncomps for CC mf: " << ncomps << "\n";
     m_cell_centered_data[lev] = std::make_unique<amrex::MultiFab>(ba, dmap, ncomps, ngrow);
 
 }
@@ -523,11 +524,6 @@ BTDiagnostics::InitializeFieldFunctors (int lev)
                   nvars, m_num_buffers, m_varnames);
     }
 
-    // For RZ, initialize field functors RZ for openpmd
-    // This is a specialized call for intializing cell-center functors
-    // such that, all modes of a field component are stored contiguously
-    // For examply, Er0, Er1_real, Er1_imag, etc
-    InitializeFieldFunctorsRZopenPMD(lev);
 
     // Define all cell-centered functors required to compute cell-centere data
     // Fill vector of cell-center functors for all field-components, namely,
@@ -708,6 +704,47 @@ BTDiagnostics::InitializeFieldFunctorsRZopenPMD (int lev)
     auto & warpx = WarpX::GetInstance();
     int ncomp_multimodefab = warpx.get_pointer_Efield_aux(0,0)->nComp();
     int ncomp = ncomp_multimodefab;
+
+
+    bool update_varnames = (lev==0);
+    if (update_varnames) {
+        m_varnames.clear();
+        const int n_rz = ncomp * m_varnames.size();
+        m_varnames.reserve(n_rz);
+    }
+    // AddRZ modes to output names for the back-transformed data
+    if (update_varnames) {
+        for (int comp=0, n=m_varnames.size(); comp<n; comp++)
+        {
+            if (m_varnames_fields[comp] == "Er")  AddRZModesToOutputNames(std::string("Er"), ncomp, false);
+            if (m_varnames_fields[comp] == "Et")  AddRZModesToOutputNames(std::string("Et"), ncomp, false);
+            if (m_varnames_fields[comp] == "Ez")  AddRZModesToOutputNames(std::string("Ez"), ncomp, false);
+            if (m_varnames_fields[comp] == "Br")  AddRZModesToOutputNames(std::string("Br"), ncomp, false);
+            if (m_varnames_fields[comp] == "Bt")  AddRZModesToOutputNames(std::string("Bt"), ncomp, false);
+            if (m_varnames_fields[comp] == "Bz")  AddRZModesToOutputNames(std::string("Bz"), ncomp, false);
+            if (m_varnames_fields[comp] == "jr")  AddRZModesToOutputNames(std::string("jr"), ncomp, false);
+            if (m_varnames_fields[comp] == "jt")  AddRZModesToOutputNames(std::string("jt"), ncomp, false);
+            if (m_varnames_fields[comp] == "jz")  AddRZModesToOutputNames(std::string("jz"), ncomp, false);
+            if (m_varnames_fields[comp] == "rho") AddRZModesToOutputNames(std::string("rho"),ncomp, false);
+        }
+    }
+
+    // Clear any pre-existing vector to release stored data
+    // This ensures that when domain is load-balanced, the functors point
+    // to the correct field-data pointers
+    m_all_field_functors[lev].clear();
+    // For back-transformed data, all the components are cell-centered and stored
+    // in a single multifab, m_cell_centered_data.
+    // Therefore, size of functors at all levels is 1
+    int num_BT_functors = 1;
+    m_all_field_functors[lev].resize(num_BT_functors);
+    for (int i = 0; i < num_BT_functors; ++i) {
+        int nvars = static_cast<int>(m_varnames.size());
+        m_all_field_functors[lev][i] = std::make_unique<BackTransformFunctor>(
+                                       m_cell_centered_data[lev].get(), lev,
+                                       nvars, m_num_buffers, m_varnames);
+    }
+
     // This function may be called multiple times, for different values of `lev`
     // but the `varnames` need only be updated once.
     bool update_cellcenter_varnames = (lev == 0);
@@ -717,7 +754,7 @@ BTDiagnostics::InitializeFieldFunctorsRZopenPMD (int lev)
         m_cellcenter_varnames.reserve(n_rz);
     }
 
-    // Reset field functors
+    // Reset field functors for cell-center multifab
     m_cell_center_functors[lev].clear();
     m_cell_center_functors[lev].resize(m_cellcenter_varnames_fields.size());
 
@@ -791,6 +828,12 @@ BTDiagnostics::AddRZModesToOutputNames (const std::string& field, const int ncom
             m_cellcenter_varnames.push_back( field + "_" + std::to_string(ic) + "_real" );
             m_cellcenter_varnames.push_back( field + "_" + std::to_string(ic) + "_imag" );
         }
+    } else {
+        m_varnames.push_back(field + "_0_real");
+        for (int ic=1 ; ic < (ncomp+1)/2 ; ic += 1) {
+            m_varnames.push_back( field + "_" + std::to_string(ic) + "_real" );
+            m_varnames.push_back( field + "_" + std::to_string(ic) + "_imag" );
+        }
     }
 #else
     amrex::ignore_unused(field, ncomp, cellcenter_data);

From 4bd1e384a9ba9065aa69213ca58c4b171c097f3a Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Mon, 19 Sep 2022 17:56:43 -0700
Subject: [PATCH 03/33] update varnames once and set map for RZ fields in
 BTfunctor

---
 Source/Diagnostics/BTDiagnostics.cpp | 146 +--------------------------
 1 file changed, 2 insertions(+), 144 deletions(-)

diff --git a/Source/Diagnostics/BTDiagnostics.cpp b/Source/Diagnostics/BTDiagnostics.cpp
index e8b92d43e53..3ddd2b13ba5 100644
--- a/Source/Diagnostics/BTDiagnostics.cpp
+++ b/Source/Diagnostics/BTDiagnostics.cpp
@@ -237,10 +237,12 @@ BTDiagnostics::ReadParameters ()
         if(m_max_box_size < m_buffer_size) m_max_box_size = m_buffer_size;
     }
 #ifdef WARPX_DIM_RZ
+    pp_diag_name.query("dump_rz_modes", m_dump_rz_modes);
     amrex::Vector< std::string > BTD_varnames_supported = {"Er", "Et", "Ez",
                                                            "Br", "Bt", "Bz",
                                                            "jr", "jt", "jz", "rho"};
 #else
+    amrex::ignore_unused(m_dump_rz_modes);
     amrex::Vector< std::string > BTD_varnames_supported = {"Ex", "Ey", "Ez",
                                                            "Bx", "By", "Bz",
                                                            "jx", "jy", "jz", "rho"};
@@ -482,7 +484,6 @@ BTDiagnostics::DefineCellCenteredMultiFab(int lev)
     amrex::DistributionMapping dmap = warpx.DistributionMap(lev);
     int ngrow = 1;
     int ncomps = static_cast<int>(m_cellcenter_varnames.size());
-    amrex::Print() << " ncomps for CC mf: " << ncomps << "\n";
     m_cell_centered_data[lev] = std::make_unique<amrex::MultiFab>(ba, dmap, ncomps, ngrow);
 
 }
@@ -697,149 +698,6 @@ BTDiagnostics::AddRZModesToOutputNames (const std::string& field, const int ncom
 #endif
 }
 
-void
-BTDiagnostics::InitializeFieldFunctorsRZopenPMD (int lev)
-{
-#ifdef WARPX_DIM_RZ
-    auto & warpx = WarpX::GetInstance();
-    int ncomp_multimodefab = warpx.get_pointer_Efield_aux(0,0)->nComp();
-    int ncomp = ncomp_multimodefab;
-
-
-    bool update_varnames = (lev==0);
-    if (update_varnames) {
-        m_varnames.clear();
-        const int n_rz = ncomp * m_varnames.size();
-        m_varnames.reserve(n_rz);
-    }
-    // AddRZ modes to output names for the back-transformed data
-    if (update_varnames) {
-        for (int comp=0, n=m_varnames.size(); comp<n; comp++)
-        {
-            if (m_varnames_fields[comp] == "Er")  AddRZModesToOutputNames(std::string("Er"), ncomp, false);
-            if (m_varnames_fields[comp] == "Et")  AddRZModesToOutputNames(std::string("Et"), ncomp, false);
-            if (m_varnames_fields[comp] == "Ez")  AddRZModesToOutputNames(std::string("Ez"), ncomp, false);
-            if (m_varnames_fields[comp] == "Br")  AddRZModesToOutputNames(std::string("Br"), ncomp, false);
-            if (m_varnames_fields[comp] == "Bt")  AddRZModesToOutputNames(std::string("Bt"), ncomp, false);
-            if (m_varnames_fields[comp] == "Bz")  AddRZModesToOutputNames(std::string("Bz"), ncomp, false);
-            if (m_varnames_fields[comp] == "jr")  AddRZModesToOutputNames(std::string("jr"), ncomp, false);
-            if (m_varnames_fields[comp] == "jt")  AddRZModesToOutputNames(std::string("jt"), ncomp, false);
-            if (m_varnames_fields[comp] == "jz")  AddRZModesToOutputNames(std::string("jz"), ncomp, false);
-            if (m_varnames_fields[comp] == "rho") AddRZModesToOutputNames(std::string("rho"),ncomp, false);
-        }
-    }
-
-    // Clear any pre-existing vector to release stored data
-    // This ensures that when domain is load-balanced, the functors point
-    // to the correct field-data pointers
-    m_all_field_functors[lev].clear();
-    // For back-transformed data, all the components are cell-centered and stored
-    // in a single multifab, m_cell_centered_data.
-    // Therefore, size of functors at all levels is 1
-    int num_BT_functors = 1;
-    m_all_field_functors[lev].resize(num_BT_functors);
-    for (int i = 0; i < num_BT_functors; ++i) {
-        int nvars = static_cast<int>(m_varnames.size());
-        m_all_field_functors[lev][i] = std::make_unique<BackTransformFunctor>(
-                                       m_cell_centered_data[lev].get(), lev,
-                                       nvars, m_num_buffers, m_varnames);
-    }
-
-    // This function may be called multiple times, for different values of `lev`
-    // but the `varnames` need only be updated once.
-    bool update_cellcenter_varnames = (lev == 0);
-    if (update_cellcenter_varnames) {
-        m_cellcenter_varnames.clear();
-        const int n_rz = ncomp * m_cellcenter_varnames.size();
-        m_cellcenter_varnames.reserve(n_rz);
-    }
-
-    // Reset field functors for cell-center multifab
-    m_cell_center_functors[lev].clear();
-    m_cell_center_functors[lev].resize(m_cellcenter_varnames_fields.size());
-
-    for (int comp=0, n=m_cell_center_functors.at(lev).size(); comp<n; comp++){
-        if        ( m_cellcenter_varnames_fields[comp] == "Er" ){
-            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_Efield_aux(lev, 0), lev, m_crse_ratio, false, ncomp);
-            if (update_cellcenter_varnames) {
-                AddRZModesToOutputNames(std::string("Er"), ncomp, true);
-            }
-        } else if ( m_cellcenter_varnames_fields[comp] == "Et" ){
-            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_Efield_aux(lev, 1), lev, m_crse_ratio, false, ncomp);
-            if (update_cellcenter_varnames) {
-                AddRZModesToOutputNames(std::string("Et"), ncomp, true);
-            }
-        } else if ( m_cellcenter_varnames_fields[comp] == "Ez" ){
-            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_Efield_aux(lev, 2), lev, m_crse_ratio, false, ncomp);
-            if (update_cellcenter_varnames) {
-                AddRZModesToOutputNames(std::string("Ez"), ncomp, true);
-            }
-        } else if ( m_cellcenter_varnames_fields[comp] == "Br" ){
-            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_Bfield_aux(lev, 0), lev, m_crse_ratio, false, ncomp);
-            if (update_cellcenter_varnames) {
-                AddRZModesToOutputNames(std::string("Br"), ncomp, true);
-            }
-        } else if ( m_cellcenter_varnames_fields[comp] == "Bt" ){
-            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_Bfield_aux(lev, 1), lev, m_crse_ratio, false, ncomp);
-            if (update_cellcenter_varnames) {
-                AddRZModesToOutputNames(std::string("Bt"), ncomp, true);
-            }
-        } else if ( m_cellcenter_varnames_fields[comp] == "Bz" ){
-            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_Bfield_aux(lev, 2), lev, m_crse_ratio, false, ncomp);
-            if (update_cellcenter_varnames) {
-                AddRZModesToOutputNames(std::string("Bz"), ncomp, true);
-            }
-        } else if ( m_cellcenter_varnames_fields[comp] == "jr" ){
-            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_current_fp(lev, 0), lev, m_crse_ratio, false, ncomp);
-            if (update_cellcenter_varnames) {
-                AddRZModesToOutputNames(std::string("jr"), ncomp, true);
-            }
-        } else if ( m_cellcenter_varnames_fields[comp] == "jt" ){
-            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_current_fp(lev, 1), lev, m_crse_ratio, false, ncomp);
-            if (update_cellcenter_varnames) {
-                AddRZModesToOutputNames(std::string("jt"), ncomp, true);
-            }
-        } else if ( m_cellcenter_varnames_fields[comp] == "jz" ){
-            m_cell_center_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.get_pointer_current_fp(lev, 2), lev, m_crse_ratio, false, ncomp);
-            if (update_cellcenter_varnames) {
-                AddRZModesToOutputNames(std::string("jz"), ncomp, true);
-            }
-        } else if ( m_cellcenter_varnames_fields[comp] == "rho" ){
-            m_cell_center_functors[lev][comp] = std::make_unique<RhoFunctor>(lev, m_crse_ratio, -1, false, ncomp);
-            if (update_cellcenter_varnames) {
-                AddRZModesToOutputNames(std::string("rho"), ncomp, true);
-            }
-        }
-    }
-
-#endif
-    amrex::ignore_unused(lev);
-}
-
-void
-BTDiagnostics::AddRZModesToOutputNames (const std::string& field, const int ncomp, bool cellcenter_data)
-{
-#ifdef WARPX_DIM_RZ
-    // In cylindrical geometry, real and imag part of each mode are also
-    // dumped to file separately, so they need to be added to m_varnames
-    if (cellcenter_data) {
-        m_cellcenter_varnames.push_back( field + "_0_real" );
-        for (int ic=1 ; ic < (ncomp+1)/2 ; ic += 1) {
-            m_cellcenter_varnames.push_back( field + "_" + std::to_string(ic) + "_real" );
-            m_cellcenter_varnames.push_back( field + "_" + std::to_string(ic) + "_imag" );
-        }
-    } else {
-        m_varnames.push_back(field + "_0_real");
-        for (int ic=1 ; ic < (ncomp+1)/2 ; ic += 1) {
-            m_varnames.push_back( field + "_" + std::to_string(ic) + "_real" );
-            m_varnames.push_back( field + "_" + std::to_string(ic) + "_imag" );
-        }
-    }
-#else
-    amrex::ignore_unused(field, ncomp, cellcenter_data);
-#endif
-}
-
 void
 BTDiagnostics::PrepareBufferData ()
 {

From 9fffba7e661b92099bc155af2cdd365582bae87e Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Mon, 24 Oct 2022 13:27:12 -0700
Subject: [PATCH 04/33] clean commented line

---
 Source/Diagnostics/BTDiagnostics.cpp | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/Source/Diagnostics/BTDiagnostics.cpp b/Source/Diagnostics/BTDiagnostics.cpp
index 3ddd2b13ba5..c2338c84e48 100644
--- a/Source/Diagnostics/BTDiagnostics.cpp
+++ b/Source/Diagnostics/BTDiagnostics.cpp
@@ -270,6 +270,7 @@ bool
 BTDiagnostics::DoDump (int step, int i_buffer, bool force_flush)
 {
     // timestep < 0, i.e., at initialization time when step == -1
+    amrex::Print() << " buffer " << i_buffer << " full ? " << buffer_full(i_buffer) << " snapshot full " << m_snapshot_full[i_buffer] << " empty ? " << buffer_empty(i_buffer) << "\n";
     if (step < 0 )
         return false;
     // Do not call dump if the snapshot is already full and the files are closed.
@@ -954,6 +955,7 @@ BTDiagnostics::GetZSliceInDomainFlag (const int i_buffer, const int lev)
 void
 BTDiagnostics::Flush (int i_buffer)
 {
+    amrex::Print() << " in flush buffer " << i_buffer << "\n";
     auto & warpx = WarpX::GetInstance();
     std::string file_name = m_file_prefix;
     if (m_format=="plotfile") {
@@ -1013,6 +1015,7 @@ BTDiagnostics::Flush (int i_buffer)
             }
         }
     }
+    amrex::Print() << " writing data " << i_buffer <<"\n";
     m_flush_format->WriteToFile(
         m_varnames, m_mf_output[i_buffer], m_geom_output[i_buffer], warpx.getistep(),
         labtime, m_output_species[i_buffer], nlev_output, file_name, m_file_min_digits,

From 96c4f92dd94fbea54d4cfc6b807cb7a957ba3376 Mon Sep 17 00:00:00 2001
From: Revathi  Jambunathan
 <41089244+RevathiJambunathan@users.noreply.github.com>
Date: Fri, 28 Oct 2022 09:44:42 -0700
Subject: [PATCH 05/33] Apply suggestions from code review

From Axels' review

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
---
 Source/Diagnostics/BTDiagnostics.cpp | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/Source/Diagnostics/BTDiagnostics.cpp b/Source/Diagnostics/BTDiagnostics.cpp
index c2338c84e48..e79cb1206d5 100644
--- a/Source/Diagnostics/BTDiagnostics.cpp
+++ b/Source/Diagnostics/BTDiagnostics.cpp
@@ -270,7 +270,7 @@ bool
 BTDiagnostics::DoDump (int step, int i_buffer, bool force_flush)
 {
     // timestep < 0, i.e., at initialization time when step == -1
-    amrex::Print() << " buffer " << i_buffer << " full ? " << buffer_full(i_buffer) << " snapshot full " << m_snapshot_full[i_buffer] << " empty ? " << buffer_empty(i_buffer) << "\n";
+    // amrex::AllPrint() << " buffer " << i_buffer << " full ? " << buffer_full(i_buffer) << " snapshot full " << m_snapshot_full[i_buffer] << " empty ? " << buffer_empty(i_buffer) << "\n";
     if (step < 0 )
         return false;
     // Do not call dump if the snapshot is already full and the files are closed.
@@ -526,7 +526,6 @@ BTDiagnostics::InitializeFieldFunctors (int lev)
                   nvars, m_num_buffers, m_varnames);
     }
 
-
     // Define all cell-centered functors required to compute cell-centere data
     // Fill vector of cell-center functors for all field-components, namely,
     // Ex, Ey, Ez, Bx, By, Bz, jx, jy, jz, and rho are included in the
@@ -955,7 +954,7 @@ BTDiagnostics::GetZSliceInDomainFlag (const int i_buffer, const int lev)
 void
 BTDiagnostics::Flush (int i_buffer)
 {
-    amrex::Print() << " in flush buffer " << i_buffer << "\n";
+    // amrex::AllPrint() << " in flush buffer " << i_buffer << "\n";
     auto & warpx = WarpX::GetInstance();
     std::string file_name = m_file_prefix;
     if (m_format=="plotfile") {
@@ -1015,7 +1014,7 @@ BTDiagnostics::Flush (int i_buffer)
             }
         }
     }
-    amrex::Print() << " writing data " << i_buffer <<"\n";
+    // amrex::AllPrint() << " writing data " << i_buffer <<"\n";
     m_flush_format->WriteToFile(
         m_varnames, m_mf_output[i_buffer], m_geom_output[i_buffer], warpx.getistep(),
         labtime, m_output_species[i_buffer], nlev_output, file_name, m_file_min_digits,

From bb9329ed94d58c32ec0ff9c8c07089c77c6f529b Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Fri, 28 Oct 2022 10:53:11 -0700
Subject: [PATCH 06/33] adding comments, doxygen, and clean-up

---
 Source/Diagnostics/BTDiagnostics.cpp | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/Source/Diagnostics/BTDiagnostics.cpp b/Source/Diagnostics/BTDiagnostics.cpp
index e79cb1206d5..90b00a24a08 100644
--- a/Source/Diagnostics/BTDiagnostics.cpp
+++ b/Source/Diagnostics/BTDiagnostics.cpp
@@ -237,12 +237,10 @@ BTDiagnostics::ReadParameters ()
         if(m_max_box_size < m_buffer_size) m_max_box_size = m_buffer_size;
     }
 #ifdef WARPX_DIM_RZ
-    pp_diag_name.query("dump_rz_modes", m_dump_rz_modes);
     amrex::Vector< std::string > BTD_varnames_supported = {"Er", "Et", "Ez",
                                                            "Br", "Bt", "Bz",
                                                            "jr", "jt", "jz", "rho"};
 #else
-    amrex::ignore_unused(m_dump_rz_modes);
     amrex::Vector< std::string > BTD_varnames_supported = {"Ex", "Ey", "Ez",
                                                            "Bx", "By", "Bz",
                                                            "jx", "jy", "jz", "rho"};
@@ -270,7 +268,6 @@ bool
 BTDiagnostics::DoDump (int step, int i_buffer, bool force_flush)
 {
     // timestep < 0, i.e., at initialization time when step == -1
-    // amrex::AllPrint() << " buffer " << i_buffer << " full ? " << buffer_full(i_buffer) << " snapshot full " << m_snapshot_full[i_buffer] << " empty ? " << buffer_empty(i_buffer) << "\n";
     if (step < 0 )
         return false;
     // Do not call dump if the snapshot is already full and the files are closed.
@@ -954,7 +951,6 @@ BTDiagnostics::GetZSliceInDomainFlag (const int i_buffer, const int lev)
 void
 BTDiagnostics::Flush (int i_buffer)
 {
-    // amrex::AllPrint() << " in flush buffer " << i_buffer << "\n";
     auto & warpx = WarpX::GetInstance();
     std::string file_name = m_file_prefix;
     if (m_format=="plotfile") {
@@ -1014,7 +1010,6 @@ BTDiagnostics::Flush (int i_buffer)
             }
         }
     }
-    // amrex::AllPrint() << " writing data " << i_buffer <<"\n";
     m_flush_format->WriteToFile(
         m_varnames, m_mf_output[i_buffer], m_geom_output[i_buffer], warpx.getistep(),
         labtime, m_output_species[i_buffer], nlev_output, file_name, m_file_min_digits,

From c8db53a480a6328ab6ce3fb8d1e473821ff32961 Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Tue, 25 Oct 2022 13:19:20 -0700
Subject: [PATCH 07/33] adding mulitple modes to RZ BTD

---
 Source/Diagnostics/BTDiagnostics.cpp          | 10 ++-
 .../BackTransformFunctor.H                    |  3 +
 .../BackTransformFunctor.cpp                  | 71 ++++++++++++++++++-
 3 files changed, 78 insertions(+), 6 deletions(-)

diff --git a/Source/Diagnostics/BTDiagnostics.cpp b/Source/Diagnostics/BTDiagnostics.cpp
index 90b00a24a08..150257c8aec 100644
--- a/Source/Diagnostics/BTDiagnostics.cpp
+++ b/Source/Diagnostics/BTDiagnostics.cpp
@@ -198,7 +198,6 @@ BTDiagnostics::ReadParameters ()
         m_crse_ratio == amrex::IntVect(1),
         "Only support for coarsening ratio of 1 in all directions is included for BTD\n"
         );
-    WARPX_ALWAYS_ASSERT_WITH_MESSAGE(WarpX::n_rz_azimuthal_modes==1, "Currently only one mode is supported for BTD");
     // Read list of back-transform diag parameters requested by the user //
     amrex::ParmParse pp_diag_name(m_diag_name);
 
@@ -481,7 +480,11 @@ BTDiagnostics::DefineCellCenteredMultiFab(int lev)
     ba.coarsen(m_crse_ratio);
     amrex::DistributionMapping dmap = warpx.DistributionMap(lev);
     int ngrow = 1;
+#ifdef WARPX_DIM_RZ
+    int ncomps = (2*WarpX::n_rz_azimuthal_modes - 1) * static_cast<int>(m_cellcenter_varnames.size());
+#else
     int ncomps = static_cast<int>(m_cellcenter_varnames.size());
+#endif
     m_cell_centered_data[lev] = std::make_unique<amrex::MultiFab>(ba, dmap, ncomps, ngrow);
 
 }
@@ -520,7 +523,7 @@ BTDiagnostics::InitializeFieldFunctors (int lev)
         int nvars = static_cast<int>(m_varnames.size());
         m_all_field_functors[lev][i] = std::make_unique<BackTransformFunctor>(
                   m_cell_centered_data[lev].get(), lev,
-                  nvars, m_num_buffers, m_varnames);
+                  nvars, m_num_buffers, m_varnames, m_varnames_fields);
     }
 
     // Define all cell-centered functors required to compute cell-centere data
@@ -632,7 +635,8 @@ BTDiagnostics::InitializeFieldFunctorsRZopenPMD (int lev)
         int nvars = static_cast<int>(m_varnames.size());
         m_all_field_functors[lev][i] = std::make_unique<BackTransformFunctor>(
                                        m_cell_centered_data[lev].get(), lev,
-                                       nvars, m_num_buffers, m_varnames);
+                                       nvars, m_num_buffers, m_varnames,
+                                       m_varnames_fields);
     }
 
     // Reset field functors for cell-center multifab
diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.H b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.H
index 35c22908cb3..142bb098da8 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.H
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.H
@@ -47,6 +47,7 @@ public:
     BackTransformFunctor ( const amrex::MultiFab * const mf_src, const int lev,
                            const int ncomp, const int num_buffers,
                            amrex::Vector< std::string > varnames,
+                           amrex::Vector< std::string > varnames_fields,
                            const amrex::IntVect crse_ratio= amrex::IntVect(1));
 
     /** \brief Lorentz-transform mf_src for the ith buffer and write the result in mf_dst.
@@ -118,6 +119,8 @@ private:
     amrex::Vector<int> m_k_index_zlab;
     /** Vector of user-defined field names to be stored in the output multifab */
     amrex::Vector< std::string > m_varnames;
+    /** Vector of user-defined field names without modifications for rz modes */
+    amrex::Vector< std::string > m_varnames_fields;
 
     /** max grid size used to generate BoxArray to define output MultiFabs */
     int m_max_box_size = 256;
diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
index 10a9ff12a7c..9cf6b48ee53 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
@@ -34,8 +34,10 @@ using namespace amrex;
 BackTransformFunctor::BackTransformFunctor (amrex::MultiFab const * mf_src, int lev,
                                             const int ncomp, const int num_buffers,
                                             amrex::Vector< std::string > varnames,
-                                            const amrex::IntVect crse_ratio)
-    : ComputeDiagFunctor(ncomp, crse_ratio), m_mf_src(mf_src), m_lev(lev), m_num_buffers(num_buffers), m_varnames(varnames)
+                                            amrex::Vector< std::string > varnames_fields,
+                                            const amrex::IntVect crse_ratio
+                                            )
+    : ComputeDiagFunctor(ncomp, crse_ratio), m_mf_src(mf_src), m_lev(lev), m_num_buffers(num_buffers), m_varnames(varnames), m_varnames_fields(varnames_fields)
 {
     InitData();
 }
@@ -112,14 +114,20 @@ BackTransformFunctor::operator ()(amrex::MultiFab& mf_dst, int /*dcomp*/, const
             const Box& tbx = mfi.tilebox();
             amrex::Array4<amrex::Real> src_arr = tmp[mfi].array();
             amrex::Array4<amrex::Real> dst_arr = mf_dst[mfi].array();
+#ifdef WARPX_DIM_RZ
+            const int nrz = WarpX::n_rz_azimuthal_modes;
+#endif
             amrex::ParallelFor( tbx, ncomp_dst,
                 [=] AMREX_GPU_DEVICE(int i, int j, int k, int n)
                 {
                     const int icomp = field_map_ptr[n];
 #if defined(WARPX_DIM_3D)
                     dst_arr(i, j, k_lab, n) = src_arr(i, j, k, icomp);
-#else
+#elif defined(WARPX_DIM_2D)
                     dst_arr(i, k_lab, k, n) = src_arr(i, j, k, icomp);
+#elif defined(WARPX_DIM_RZ)
+                    const int rzcomp = n - static_cast<int>( floor(n/(2.0*nrz-1.0)) ) * (2*nrz-1);
+                    dst_arr(i, k_lab, k, n) = src_arr(i, j, k, icomp*(2*nrz-1)+rzcomp);
 #endif
                 } );
         }
@@ -185,7 +193,12 @@ BackTransformFunctor::InitData ()
 
     for (int i = 0; i < m_varnames.size(); ++i)
     {
+#ifdef WARPX_DIM_RZ
+        const int field_id = i / (WarpX::n_rz_azimuthal_modes*2-1);
+        m_map_varnames[i] = m_possible_fields_to_dump[ m_varnames_fields[field_id] ];
+#else
         m_map_varnames[i] = m_possible_fields_to_dump[ m_varnames[i] ] ;
+#endif
     }
 
 }
@@ -202,6 +215,57 @@ BackTransformFunctor::LorentzTransformZ (amrex::MultiFab& data, amrex::Real gamm
         amrex::Array4< amrex::Real > arr = data[mfi].array();
         amrex::Real clight = PhysConst::c;
         amrex::Real inv_clight = 1.0_rt/clight;
+#ifdef WARPX_DIM_RZ
+        const int n_rz = WarpX::n_rz_azimuthal_modes;
+        amrex::ParallelFor( tbx,
+            [=] AMREX_GPU_DEVICE (int i, int j, int k)
+            {
+            // arr(x,y,z,comp) has (2*num_rz_modes-1)*10 components
+            // If there are 2 components, then Er_0_real, Er_1_real, Er_2_real are the first the components
+            // followed by three components each for Et, Ez, Br, Bt, Bz, jr, jt, jz, and rho
+                for (int imode = 0; imode < n_rz; ++imode) {
+                    int offset = 1;
+                    int ncomp = 2;
+                    if (imode == 0) {
+                        offset = 0;
+                        ncomp = 1;
+                    }
+                    for (int icomp = 0; icomp < ncomp; ++icomp) {
+                        // Back-transform the transverse electric and magnetic fields.
+                        // Note that the z-components, Ez, Bz, are not changed by the transform.
+                        amrex::Real e_lab, b_lab, j_lab, rho_lab;
+                        // Transform Ex_boost (ncomp=0) & By_boost (ncomp=4) to lab-frame
+                        e_lab = gamma_boost * ( arr(i, j, k, n_rz*0 + 2*imode + offset*(icomp-1))
+                                                + beta_boost * clight * arr(i, j, k, n_rz*4+ 2*imode + offset*(icomp-1)) );
+                        b_lab = gamma_boost * ( arr(i, j, k, n_rz*4 + 2*imode + offset*(icomp-1))
+                                                + beta_boost * inv_clight * arr(i, j, k, n_rz*0 + 2*imode + offset*(icomp-1)) );
+                        // Store lab-frame data in-place
+                        arr(i, j, k, n_rz*0 + 2*imode + offset*(icomp-1)) = e_lab;
+                        arr(i, j, k, n_rz*4 + 2*imode + offset*(icomp-1)) = b_lab;
+
+                        // Transform Ey_boost (ncomp=1) & Bx_boost (ncomp=3) to lab-frame
+                        e_lab = gamma_boost * ( arr(i, j, k, n_rz*1 + 2*imode + offset*(icomp-1))
+                                                - beta_boost * clight * arr(i, j, k, n_rz*3 + 2*imode + offset*(icomp-1)) );
+                        b_lab = gamma_boost * ( arr(i, j, k, n_rz*3 + 2*imode + offset*(icomp-1))
+                                                - beta_boost * inv_clight * arr(i, j, k, n_rz*1 + 2*imode + offset*(icomp-1)) );
+                        // Store lab-frame data in-place
+                        arr(i, j, k, n_rz*1 + 2*imode + offset*(icomp-1)) = e_lab;
+                        arr(i, j, k, n_rz*3 + 2*imode + offset*(icomp-1)) = b_lab;
+
+                        // Transform charge density (ncomp=9)
+                        // and z-component of current density (ncomp=8)
+                        j_lab = gamma_boost * ( arr(i, j, k, n_rz*8 + 2*imode + offset*(icomp-1))
+                                                + beta_boost * clight * arr(i, j, k, n_rz*9 + 2*imode + offset*(icomp-1)) );
+                        rho_lab = gamma_boost * ( arr(i, j, k, n_rz*9 + 2*imode + offset*(icomp-1))
+                                                  + beta_boost * inv_clight * arr(i, j, k, n_rz*8 + 2*imode + offset*(icomp-1)) );
+                        // Store lab-frame jz and rho in-place
+                        arr(i, j, k, n_rz*8 + 2*imode + offset*(icomp-1)) = j_lab;
+                        arr(i, j, k, n_rz*9 + 2*imode + offset*(icomp-1)) = rho_lab;
+                    }
+                }
+            }
+        );
+#else
         // arr(x,y,z,comp) has ten-components namely,
         // Ex Ey Ez Bx By Bz jx jy jz rho in that order.
         amrex::ParallelFor( tbx,
@@ -239,6 +303,7 @@ BackTransformFunctor::LorentzTransformZ (amrex::MultiFab& data, amrex::Real gamm
                 arr(i, j, k, 9) = rho_lab;
             }
         );
+#endif
     }
 
 }

From 63c36e0661176b4b5ab9144bc90ef5e414377cb0 Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Wed, 26 Oct 2022 10:16:15 -0700
Subject: [PATCH 08/33] fix comment

---
 .../Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp   | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
index 9cf6b48ee53..317a6e0ff39 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
@@ -221,13 +221,14 @@ BackTransformFunctor::LorentzTransformZ (amrex::MultiFab& data, amrex::Real gamm
             [=] AMREX_GPU_DEVICE (int i, int j, int k)
             {
             // arr(x,y,z,comp) has (2*num_rz_modes-1)*10 components
-            // If there are 2 components, then Er_0_real, Er_1_real, Er_2_real are the first the components
+            // If there are 2 modes, then Er_0_real, Er_1_real, Er_2_real are the first three components
             // followed by three components each for Et, Ez, Br, Bt, Bz, jr, jt, jz, and rho
                 for (int imode = 0; imode < n_rz; ++imode) {
                     int offset = 1;
                     int ncomp = 2;
                     if (imode == 0) {
                         offset = 0;
+                        // Mode 0 has only real part
                         ncomp = 1;
                     }
                     for (int icomp = 0; icomp < ncomp; ++icomp) {

From 9c93329fc28d2e892682c3641224087791e604e2 Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Wed, 26 Oct 2022 21:37:47 -0700
Subject: [PATCH 09/33] fix bug using 2*nrz-1 , instead of nrz

---
 .../BackTransformFunctor.cpp                  | 37 ++++++++++---------
 1 file changed, 19 insertions(+), 18 deletions(-)

diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
index 317a6e0ff39..a6ec98d98d2 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
@@ -217,6 +217,7 @@ BackTransformFunctor::LorentzTransformZ (amrex::MultiFab& data, amrex::Real gamm
         amrex::Real inv_clight = 1.0_rt/clight;
 #ifdef WARPX_DIM_RZ
         const int n_rz = WarpX::n_rz_azimuthal_modes;
+        const int n_rcomps = 2*n_rz - 1;
         amrex::ParallelFor( tbx,
             [=] AMREX_GPU_DEVICE (int i, int j, int k)
             {
@@ -236,32 +237,32 @@ BackTransformFunctor::LorentzTransformZ (amrex::MultiFab& data, amrex::Real gamm
                         // Note that the z-components, Ez, Bz, are not changed by the transform.
                         amrex::Real e_lab, b_lab, j_lab, rho_lab;
                         // Transform Ex_boost (ncomp=0) & By_boost (ncomp=4) to lab-frame
-                        e_lab = gamma_boost * ( arr(i, j, k, n_rz*0 + 2*imode + offset*(icomp-1))
-                                                + beta_boost * clight * arr(i, j, k, n_rz*4+ 2*imode + offset*(icomp-1)) );
-                        b_lab = gamma_boost * ( arr(i, j, k, n_rz*4 + 2*imode + offset*(icomp-1))
-                                                + beta_boost * inv_clight * arr(i, j, k, n_rz*0 + 2*imode + offset*(icomp-1)) );
+                        e_lab = gamma_boost * ( arr(i, j, k, n_rcomps*0 + 2*imode + offset*(icomp-1))
+                                                + beta_boost * clight * arr(i, j, k, n_rcomps*4+ 2*imode + offset*(icomp-1)) );
+                        b_lab = gamma_boost * ( arr(i, j, k, n_rcomps*4 + 2*imode + offset*(icomp-1))
+                                                + beta_boost * inv_clight * arr(i, j, k, n_rcomps*0 + 2*imode + offset*(icomp-1)) );
                         // Store lab-frame data in-place
-                        arr(i, j, k, n_rz*0 + 2*imode + offset*(icomp-1)) = e_lab;
-                        arr(i, j, k, n_rz*4 + 2*imode + offset*(icomp-1)) = b_lab;
+                        arr(i, j, k, n_rcomps*0 + 2*imode + offset*(icomp-1)) = e_lab;
+                        arr(i, j, k, n_rcomps*4 + 2*imode + offset*(icomp-1)) = b_lab;
 
                         // Transform Ey_boost (ncomp=1) & Bx_boost (ncomp=3) to lab-frame
-                        e_lab = gamma_boost * ( arr(i, j, k, n_rz*1 + 2*imode + offset*(icomp-1))
-                                                - beta_boost * clight * arr(i, j, k, n_rz*3 + 2*imode + offset*(icomp-1)) );
-                        b_lab = gamma_boost * ( arr(i, j, k, n_rz*3 + 2*imode + offset*(icomp-1))
-                                                - beta_boost * inv_clight * arr(i, j, k, n_rz*1 + 2*imode + offset*(icomp-1)) );
+                        e_lab = gamma_boost * ( arr(i, j, k, n_rcomps*1 + 2*imode + offset*(icomp-1))
+                                                - beta_boost * clight * arr(i, j, k, n_rcomps*3 + 2*imode + offset*(icomp-1)) );
+                        b_lab = gamma_boost * ( arr(i, j, k, n_rcomps*3 + 2*imode + offset*(icomp-1))
+                                                - beta_boost * inv_clight * arr(i, j, k, n_rcomps*1 + 2*imode + offset*(icomp-1)) );
                         // Store lab-frame data in-place
-                        arr(i, j, k, n_rz*1 + 2*imode + offset*(icomp-1)) = e_lab;
-                        arr(i, j, k, n_rz*3 + 2*imode + offset*(icomp-1)) = b_lab;
+                        arr(i, j, k, n_rcomps*1 + 2*imode + offset*(icomp-1)) = e_lab;
+                        arr(i, j, k, n_rcomps*3 + 2*imode + offset*(icomp-1)) = b_lab;
 
                         // Transform charge density (ncomp=9)
                         // and z-component of current density (ncomp=8)
-                        j_lab = gamma_boost * ( arr(i, j, k, n_rz*8 + 2*imode + offset*(icomp-1))
-                                                + beta_boost * clight * arr(i, j, k, n_rz*9 + 2*imode + offset*(icomp-1)) );
-                        rho_lab = gamma_boost * ( arr(i, j, k, n_rz*9 + 2*imode + offset*(icomp-1))
-                                                  + beta_boost * inv_clight * arr(i, j, k, n_rz*8 + 2*imode + offset*(icomp-1)) );
+                        j_lab = gamma_boost * ( arr(i, j, k, n_rcomps*8 + 2*imode + offset*(icomp-1))
+                                                + beta_boost * clight * arr(i, j, k, n_rcomps*9 + 2*imode + offset*(icomp-1)) );
+                        rho_lab = gamma_boost * ( arr(i, j, k, n_rcomps*9 + 2*imode + offset*(icomp-1))
+                                                  + beta_boost * inv_clight * arr(i, j, k, n_rcomps*8 + 2*imode + offset*(icomp-1)) );
                         // Store lab-frame jz and rho in-place
-                        arr(i, j, k, n_rz*8 + 2*imode + offset*(icomp-1)) = j_lab;
-                        arr(i, j, k, n_rz*9 + 2*imode + offset*(icomp-1)) = rho_lab;
+                        arr(i, j, k, n_rcomps*8 + 2*imode + offset*(icomp-1)) = j_lab;
+                        arr(i, j, k, n_rcomps*9 + 2*imode + offset*(icomp-1)) = rho_lab;
                     }
                 }
             }

From 491defbe16039065c5edb00be92933b5fdd05630 Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Fri, 28 Oct 2022 11:33:04 -0700
Subject: [PATCH 10/33] add comments and clean up

---
 .../BackTransformFunctor.cpp                  | 56 ++++++++++++-------
 1 file changed, 36 insertions(+), 20 deletions(-)

diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
index a6ec98d98d2..cf52966e5c1 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
@@ -116,18 +116,29 @@ BackTransformFunctor::operator ()(amrex::MultiFab& mf_dst, int /*dcomp*/, const
             amrex::Array4<amrex::Real> dst_arr = mf_dst[mfi].array();
 #ifdef WARPX_DIM_RZ
             const int nrz = WarpX::n_rz_azimuthal_modes;
+            const int n_rz_comp = 2*nrz - 1;
 #endif
             amrex::ParallelFor( tbx, ncomp_dst,
                 [=] AMREX_GPU_DEVICE(int i, int j, int k, int n)
                 {
+                    // Field id that corresponds to the nth user-requested component
                     const int icomp = field_map_ptr[n];
 #if defined(WARPX_DIM_3D)
                     dst_arr(i, j, k_lab, n) = src_arr(i, j, k, icomp);
 #elif defined(WARPX_DIM_2D)
                     dst_arr(i, k_lab, k, n) = src_arr(i, j, k, icomp);
 #elif defined(WARPX_DIM_RZ)
-                    const int rzcomp = n - static_cast<int>( floor(n/(2.0*nrz-1.0)) ) * (2*nrz-1);
-                    dst_arr(i, k_lab, k, n) = src_arr(i, j, k, icomp*(2*nrz-1)+rzcomp);
+                    // rzcomp below gives the component id, 0 to (n_rz_comp-1) for a given field
+                    const int rzcomp = n - static_cast<int>( floor(n/(2.0*nrz-1.0)) ) * n_rz_comp;
+                    // Accessing the correct rz component from the cell-centered multifab
+                    // that has back-transformed fields and storing it for the appropriate user-requested field, icomp
+                    // For example, for 2 rz modes, we have three components (n_rz_comp=3) for each field
+                    // If n = 4 gives icomp = 1 (for Et) obtained from field_map_ptr,
+                    //           rzcomp = 4 - int(floor(4/3))*3 = 4 - 3 = 1
+                    // Thus we are accessing real component of mode 1 of Et (note that modes go from 0 to 1)
+                    // Since the fields are stored contiguously in src_arr, icomp*n_rz_comp + rz_comp accesses
+                    // real part of mode 1 for Et (1*3+1) = 4
+                    dst_arr(i, k_lab, k, n) = src_arr(i, j, k, icomp*n_rz_comp+rzcomp);
 #endif
                 } );
         }
@@ -226,43 +237,48 @@ BackTransformFunctor::LorentzTransformZ (amrex::MultiFab& data, amrex::Real gamm
             // followed by three components each for Et, Ez, Br, Bt, Bz, jr, jt, jz, and rho
                 for (int imode = 0; imode < n_rz; ++imode) {
                     int offset = 1;
+                    // number of components for a given mode
                     int ncomp = 2;
                     if (imode == 0) {
                         offset = 0;
-                        // Mode 0 has only real part
+                        // Mode 0 has only real part, thus ncomp = 1
                         ncomp = 1;
                     }
                     for (int icomp = 0; icomp < ncomp; ++icomp) {
                         // Back-transform the transverse electric and magnetic fields.
                         // Note that the z-components, Ez, Bz, are not changed by the transform.
                         amrex::Real e_lab, b_lab, j_lab, rho_lab;
+
+                        // Offset for a given mode, imode, and component, icomp (0-real, 1-imag)
+                        const int mode_comp_offset = 2*imode + offset*(icomp-1);
+
                         // Transform Ex_boost (ncomp=0) & By_boost (ncomp=4) to lab-frame
-                        e_lab = gamma_boost * ( arr(i, j, k, n_rcomps*0 + 2*imode + offset*(icomp-1))
-                                                + beta_boost * clight * arr(i, j, k, n_rcomps*4+ 2*imode + offset*(icomp-1)) );
-                        b_lab = gamma_boost * ( arr(i, j, k, n_rcomps*4 + 2*imode + offset*(icomp-1))
-                                                + beta_boost * inv_clight * arr(i, j, k, n_rcomps*0 + 2*imode + offset*(icomp-1)) );
+                        e_lab = gamma_boost * ( arr(i, j, k, n_rcomps*0 + mode_comp_offset)
+                                                + beta_boost * clight * arr(i, j, k, n_rcomps*4+ mode_comp_offset) );
+                        b_lab = gamma_boost * ( arr(i, j, k, n_rcomps*4 + mode_comp_offset)
+                                                + beta_boost * inv_clight * arr(i, j, k, n_rcomps*0 + mode_comp_offset) );
                         // Store lab-frame data in-place
-                        arr(i, j, k, n_rcomps*0 + 2*imode + offset*(icomp-1)) = e_lab;
-                        arr(i, j, k, n_rcomps*4 + 2*imode + offset*(icomp-1)) = b_lab;
+                        arr(i, j, k, n_rcomps*0 + mode_component_offset) = e_lab;
+                        arr(i, j, k, n_rcomps*4 + mode_component_offset) = b_lab;
 
                         // Transform Ey_boost (ncomp=1) & Bx_boost (ncomp=3) to lab-frame
-                        e_lab = gamma_boost * ( arr(i, j, k, n_rcomps*1 + 2*imode + offset*(icomp-1))
-                                                - beta_boost * clight * arr(i, j, k, n_rcomps*3 + 2*imode + offset*(icomp-1)) );
-                        b_lab = gamma_boost * ( arr(i, j, k, n_rcomps*3 + 2*imode + offset*(icomp-1))
-                                                - beta_boost * inv_clight * arr(i, j, k, n_rcomps*1 + 2*imode + offset*(icomp-1)) );
+                        e_lab = gamma_boost * ( arr(i, j, k, n_rcomps*1 + mode_comp_offset)
+                                                - beta_boost * clight * arr(i, j, k, n_rcomps*3 + mode_comp_offset) );
+                        b_lab = gamma_boost * ( arr(i, j, k, n_rcomps*3 + mode_comp_offset)
+                                                - beta_boost * inv_clight * arr(i, j, k, n_rcomps*1 + mode_comp_offset) );
                         // Store lab-frame data in-place
-                        arr(i, j, k, n_rcomps*1 + 2*imode + offset*(icomp-1)) = e_lab;
-                        arr(i, j, k, n_rcomps*3 + 2*imode + offset*(icomp-1)) = b_lab;
+                        arr(i, j, k, n_rcomps*1 + mode_comp_offset) = e_lab;
+                        arr(i, j, k, n_rcomps*3 + mode_comp_offset) = b_lab;
 
                         // Transform charge density (ncomp=9)
                         // and z-component of current density (ncomp=8)
-                        j_lab = gamma_boost * ( arr(i, j, k, n_rcomps*8 + 2*imode + offset*(icomp-1))
-                                                + beta_boost * clight * arr(i, j, k, n_rcomps*9 + 2*imode + offset*(icomp-1)) );
+                        j_lab = gamma_boost * ( arr(i, j, k, n_rcomps*8 + mode_comp_offset)
+                                                + beta_boost * clight * arr(i, j, k, n_rcomps*9 + mode_comp_offset) );
                         rho_lab = gamma_boost * ( arr(i, j, k, n_rcomps*9 + 2*imode + offset*(icomp-1))
-                                                  + beta_boost * inv_clight * arr(i, j, k, n_rcomps*8 + 2*imode + offset*(icomp-1)) );
+                                                  + beta_boost * inv_clight * arr(i, j, k, n_rcomps*8 + mode_comp_offset) );
                         // Store lab-frame jz and rho in-place
-                        arr(i, j, k, n_rcomps*8 + 2*imode + offset*(icomp-1)) = j_lab;
-                        arr(i, j, k, n_rcomps*9 + 2*imode + offset*(icomp-1)) = rho_lab;
+                        arr(i, j, k, n_rcomps*8 + mode_comp_offset) = j_lab;
+                        arr(i, j, k, n_rcomps*9 + mode_comp_offset) = rho_lab;
                     }
                 }
             }

From 0a5eb916994d869661758fb10424c87a0ea3459d Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Fri, 28 Oct 2022 11:39:45 -0700
Subject: [PATCH 11/33] fix typo

---
 .../Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
index cf52966e5c1..c14e3e2ed51 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
@@ -258,8 +258,8 @@ BackTransformFunctor::LorentzTransformZ (amrex::MultiFab& data, amrex::Real gamm
                         b_lab = gamma_boost * ( arr(i, j, k, n_rcomps*4 + mode_comp_offset)
                                                 + beta_boost * inv_clight * arr(i, j, k, n_rcomps*0 + mode_comp_offset) );
                         // Store lab-frame data in-place
-                        arr(i, j, k, n_rcomps*0 + mode_component_offset) = e_lab;
-                        arr(i, j, k, n_rcomps*4 + mode_component_offset) = b_lab;
+                        arr(i, j, k, n_rcomps*0 + mode_comp_offset) = e_lab;
+                        arr(i, j, k, n_rcomps*4 + mode_comp_offset) = b_lab;
 
                         // Transform Ey_boost (ncomp=1) & Bx_boost (ncomp=3) to lab-frame
                         e_lab = gamma_boost * ( arr(i, j, k, n_rcomps*1 + mode_comp_offset)

From 80a8165d657472726f901ef4fdd80d653fb8a55a Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Mon, 31 Oct 2022 15:23:02 -0700
Subject: [PATCH 12/33] 1D

---
 Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
index c14e3e2ed51..dc6f0efb0e8 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
@@ -139,6 +139,8 @@ BackTransformFunctor::operator ()(amrex::MultiFab& mf_dst, int /*dcomp*/, const
                     // Since the fields are stored contiguously in src_arr, icomp*n_rz_comp + rz_comp accesses
                     // real part of mode 1 for Et (1*3+1) = 4
                     dst_arr(i, k_lab, k, n) = src_arr(i, j, k, icomp*n_rz_comp+rzcomp);
+#else
+                    dst_arr(k_lab, j, k, n) = src_arr(i, j, k, icomp);
 #endif
                 } );
         }

From 033154c98925d858f382683b6b003208fea84d77 Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Mon, 31 Oct 2022 17:18:19 -0700
Subject: [PATCH 13/33] WARPX_DIM_XZ instead of 2D

---
 Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
index dc6f0efb0e8..8522c74d541 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
@@ -125,7 +125,7 @@ BackTransformFunctor::operator ()(amrex::MultiFab& mf_dst, int /*dcomp*/, const
                     const int icomp = field_map_ptr[n];
 #if defined(WARPX_DIM_3D)
                     dst_arr(i, j, k_lab, n) = src_arr(i, j, k, icomp);
-#elif defined(WARPX_DIM_2D)
+#elif defined(WARPX_DIM_XZ)
                     dst_arr(i, k_lab, k, n) = src_arr(i, j, k, icomp);
 #elif defined(WARPX_DIM_RZ)
                     // rzcomp below gives the component id, 0 to (n_rz_comp-1) for a given field

From 55930043442c897e030ff4bd8bdda22e2240bbb3 Mon Sep 17 00:00:00 2001
From: Revathi  Jambunathan
 <41089244+RevathiJambunathan@users.noreply.github.com>
Date: Tue, 1 Nov 2022 10:09:49 -0700
Subject: [PATCH 14/33] Apply suggestions from code review

suggestion from Edoardo

Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
---
 Source/Diagnostics/BTDiagnostics.cpp                        | 2 +-
 .../ComputeDiagFunctors/BackTransformFunctor.cpp            | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/Source/Diagnostics/BTDiagnostics.cpp b/Source/Diagnostics/BTDiagnostics.cpp
index 150257c8aec..0d86d65835f 100644
--- a/Source/Diagnostics/BTDiagnostics.cpp
+++ b/Source/Diagnostics/BTDiagnostics.cpp
@@ -481,7 +481,7 @@ BTDiagnostics::DefineCellCenteredMultiFab(int lev)
     amrex::DistributionMapping dmap = warpx.DistributionMap(lev);
     int ngrow = 1;
 #ifdef WARPX_DIM_RZ
-    int ncomps = (2*WarpX::n_rz_azimuthal_modes - 1) * static_cast<int>(m_cellcenter_varnames.size());
+    int ncomps = WarpX::ncomps * static_cast<int>(m_cellcenter_varnames.size());
 #else
     int ncomps = static_cast<int>(m_cellcenter_varnames.size());
 #endif
diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
index 8522c74d541..ea52d109569 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
@@ -116,7 +116,7 @@ BackTransformFunctor::operator ()(amrex::MultiFab& mf_dst, int /*dcomp*/, const
             amrex::Array4<amrex::Real> dst_arr = mf_dst[mfi].array();
 #ifdef WARPX_DIM_RZ
             const int nrz = WarpX::n_rz_azimuthal_modes;
-            const int n_rz_comp = 2*nrz - 1;
+            const int n_rz_comp = WarpX::ncomps;
 #endif
             amrex::ParallelFor( tbx, ncomp_dst,
                 [=] AMREX_GPU_DEVICE(int i, int j, int k, int n)
@@ -207,7 +207,7 @@ BackTransformFunctor::InitData ()
     for (int i = 0; i < m_varnames.size(); ++i)
     {
 #ifdef WARPX_DIM_RZ
-        const int field_id = i / (WarpX::n_rz_azimuthal_modes*2-1);
+        const int field_id = i / WarpX::ncomps;
         m_map_varnames[i] = m_possible_fields_to_dump[ m_varnames_fields[field_id] ];
 #else
         m_map_varnames[i] = m_possible_fields_to_dump[ m_varnames[i] ] ;
@@ -230,7 +230,7 @@ BackTransformFunctor::LorentzTransformZ (amrex::MultiFab& data, amrex::Real gamm
         amrex::Real inv_clight = 1.0_rt/clight;
 #ifdef WARPX_DIM_RZ
         const int n_rz = WarpX::n_rz_azimuthal_modes;
-        const int n_rcomps = 2*n_rz - 1;
+        const int n_rcomps = WarpX::ncomps;
         amrex::ParallelFor( tbx,
             [=] AMREX_GPU_DEVICE (int i, int j, int k)
             {

From 4575edb78d1e408213e47fc7473fe4b9fdb082df Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Sun, 6 Nov 2022 14:55:44 -0800
Subject: [PATCH 15/33] remove BTD RZ field warning that does not apply anymore

---
 Source/Diagnostics/MultiDiagnostics.cpp | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/Source/Diagnostics/MultiDiagnostics.cpp b/Source/Diagnostics/MultiDiagnostics.cpp
index 62218a17568..1b9f5615ae7 100644
--- a/Source/Diagnostics/MultiDiagnostics.cpp
+++ b/Source/Diagnostics/MultiDiagnostics.cpp
@@ -25,9 +25,6 @@ MultiDiagnostics::MultiDiagnostics ()
             alldiags[i] = std::make_unique<FullDiagnostics>(i, diags_names[i]);
         } else if ( diags_types[i] == DiagTypes::BackTransformed ){
             alldiags[i] = std::make_unique<BTDiagnostics>(i, diags_names[i]);
-#ifdef WARPX_DIM_RZ
-            ablastr::warn_manager::WMRecordWarning("MultiDiagnostics", "BackTransformed diagnostics for fields is not yet fully implemented in RZ. Field output might be incorrect.");
-#endif
         } else if ( diags_types[i] == DiagTypes::BoundaryScraping ){
             alldiags[i] = std::make_unique<BoundaryScrapingDiagnostics>(i, diags_names[i]);
         } else {

From 4ed469c1245a5e1a3d4eb184f32fe16fd4b6198d Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Mon, 7 Nov 2022 13:10:09 -0800
Subject: [PATCH 16/33] BTD rz test for field using laser antenna

---
 Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD | 64 +++++++++++++++++++
 .../Tests/BTD_rz/laser_antenna_compare.py     | 52 +++++++++++++++
 Regression/WarpX-tests.ini                    | 16 +++++
 3 files changed, 132 insertions(+)
 create mode 100644 Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD
 create mode 100644 Examples/Tests/BTD_rz/laser_antenna_compare.py

diff --git a/Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD b/Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD
new file mode 100644
index 00000000000..d2aa789ebcd
--- /dev/null
+++ b/Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD
@@ -0,0 +1,64 @@
+# Maximum number of time steps
+warpx.zmax_plasma_to_compute_max_step = 160e-6
+# number of grid points
+amr.n_cell = 32 256
+
+# Maximum allowable size of each subdomain in the problem domain;
+#    this is used to decompose the domain for parallel calculations.
+amr.max_grid_size = 128
+
+# Maximum level in hierarchy (for now must be 0, i.e., one level in total)
+amr.max_level = 0
+
+# Geometry
+geometry.dims = RZ
+geometry.prob_lo     =  0.e-6 -20.e-6
+geometry.prob_hi     =  40.e-6  0.e-6
+
+boundary.field_lo = none absorbing_silver_mueller
+boundary.field_hi = absorbing_silver_mueller absorbing_silver_mueller
+
+# Boosted frame and moving window
+warpx.do_moving_window = 1
+warpx.moving_window_dir = z
+warpx.moving_window_v = 1.0 # in units of the speed of light
+warpx.gamma_boost = 10.
+warpx.boost_direction = z
+
+
+# Verbosity
+warpx.verbose = 1
+warpx.n_rz_azimuthal_modes = 2
+
+# Algorithms
+warpx.cfl = 1.0
+warpx.use_filter = 0
+
+
+# Order of particle shape factors
+algo.particle_shape = 1
+
+# Laser
+lasers.names        = laser1
+laser1.profile      = Gaussian
+laser1.position     = 0. 0. -1.e-6 # This point is on the laser plane
+laser1.direction    = 0. 0. 1.     # The plane normal direction
+laser1.polarization = 1. 0. 0.     # The main polarization vector
+laser1.a0           = 1.5e1        # Maximum amplitude of the laser field (in V/m)
+laser1.profile_waist = 10.e-6      # The waist of the laser (in meters)
+laser1.profile_duration = 10.e-15  # The duration of the laser (in seconds)
+laser1.profile_t_peak = 20.e-15    # The time at which the laser reaches its peak (in seconds)
+laser1.profile_focal_distance = 1.e-6  # Focal distance from the antenna (in meters)
+laser1.wavelength = 0.8e-6         # The wavelength of the laser (in meters)
+
+# Diagnostics
+diagnostics.diags_names = diag1 back_rz
+diag1.intervals = 50
+diag1.diag_type = Full
+
+back_rz.diag_type = BackTransformed
+back_rz.dt_snapshots_lab = 80.e-15
+back_rz.fields_to_plot = Er Et Ez Br Bt Bz jr jt jz rho
+back_rz.format = openpmd
+back_rz.buffer_size = 32
+back_rz.num_snapshots_lab = 2
diff --git a/Examples/Tests/BTD_rz/laser_antenna_compare.py b/Examples/Tests/BTD_rz/laser_antenna_compare.py
new file mode 100644
index 00000000000..3ea0f498cbd
--- /dev/null
+++ b/Examples/Tests/BTD_rz/laser_antenna_compare.py
@@ -0,0 +1,52 @@
+# Copyright 2022
+# Authors: Revathi Jambunathan, Remi Lehe
+#
+# This file tests if the back-transformed signal is a gaussian
+#
+#
+import os
+import sys
+
+import numpy as np
+from scipy.optimize import curve_fit
+from scipy.constants import c, m_e, e
+from openpmd_viewer import OpenPMDTimeSeries
+import matplotlib.pyplot as plt
+
+def gaussian_laser( z, a0, z0_phase, z0_prop, ctau, lambda0 ):
+    """
+    Returns a Gaussian laser profile
+    """
+    k0 = 2*np.pi/lambda0
+    E0 = a0*m_e*c**2*k0/e
+    return( E0*np.exp( - (z-z0_prop)**2/ctau**2 ) \
+                *np.cos( k0*(z-z0_phase) ) )
+
+# Fit the on-axis profile to extract a0
+def fit_function(z, z0_phase):
+    return( gaussian_laser( z, a0, z0_phase,
+                            z0_b+Lprop_b, ctau0, lambda0 ) )
+
+# The values must be consistent with the values provided in the simulation input
+t_current = 80e-15   # Time of the snapshot1 
+c = 299792458;
+z0_antenna = -1.e-6  # position of laser
+lambda0 = 0.8e-6     # wavelength of the signal
+tau0 = 10e-15        # duration of the signal
+ctau0 = tau0 * c     
+a0 = 15              # amplitude
+t_peak = 20e-15      # Time at which laser reaches its peak
+Lprop_b = c*t_current
+z0_b = z0_antenna - c * t_peak
+
+ts = OpenPMDTimeSeries('./diags/back_rz')
+Ex, info = ts.get_field('E', 'x', iteration=1, slice_across='r')
+
+fit_result = curve_fit( fit_function, info.z, Ex,
+                        p0=np.array([z0_b+Lprop_b]) )
+z0_fit = fit_result[0]
+
+Ex_fit = gaussian_laser( info.z, a0, z0_fit, z0_b+Lprop_b, ctau0, lambda0)
+
+## Check that the a0 agrees within 5% of the predicted value
+assert np.allclose( Ex, Ex_fit, atol=0.18*Ex.max() )
diff --git a/Regression/WarpX-tests.ini b/Regression/WarpX-tests.ini
index cb4cacf00a0..bbcbce4c471 100644
--- a/Regression/WarpX-tests.ini
+++ b/Regression/WarpX-tests.ini
@@ -3715,3 +3715,19 @@ doVis = 0
 compareParticles = 1
 particleTypes = electron ion
 analysisRoutine = Examples/Tests/VayDeposition/analysis.py
+
+[BTD_rz]
+buildDir = .
+inputFile = Examples/Tests/BTZ_rz/inputs_rz_z_boosted_BTD
+runtime_params =
+dim = 2
+addToCompileString = USE_RZ=TRUE
+cmakeSetupOpts = -DWarpX_DIMS=RZ
+restartTest = 0
+useMPI = 1
+numprocs = 2
+useOMP = 1
+numthreads = 1
+compileTest = 0
+doVis = 0
+analysisRoutine = Examples/Tests/SilverMueller/laser_antenna_compare.py

From 25d1e8ccd185de656eff32791792e7493dd1377f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 7 Nov 2022 21:12:14 +0000
Subject: [PATCH 17/33] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 Examples/Tests/BTD_rz/laser_antenna_compare.py | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/Examples/Tests/BTD_rz/laser_antenna_compare.py b/Examples/Tests/BTD_rz/laser_antenna_compare.py
index 3ea0f498cbd..2646b77c19d 100644
--- a/Examples/Tests/BTD_rz/laser_antenna_compare.py
+++ b/Examples/Tests/BTD_rz/laser_antenna_compare.py
@@ -4,14 +4,13 @@
 # This file tests if the back-transformed signal is a gaussian
 #
 #
-import os
-import sys
 
+import matplotlib.pyplot as plt
 import numpy as np
-from scipy.optimize import curve_fit
-from scipy.constants import c, m_e, e
 from openpmd_viewer import OpenPMDTimeSeries
-import matplotlib.pyplot as plt
+from scipy.constants import c, e, m_e
+from scipy.optimize import curve_fit
+
 
 def gaussian_laser( z, a0, z0_phase, z0_prop, ctau, lambda0 ):
     """
@@ -28,12 +27,12 @@ def fit_function(z, z0_phase):
                             z0_b+Lprop_b, ctau0, lambda0 ) )
 
 # The values must be consistent with the values provided in the simulation input
-t_current = 80e-15   # Time of the snapshot1 
+t_current = 80e-15   # Time of the snapshot1
 c = 299792458;
 z0_antenna = -1.e-6  # position of laser
 lambda0 = 0.8e-6     # wavelength of the signal
 tau0 = 10e-15        # duration of the signal
-ctau0 = tau0 * c     
+ctau0 = tau0 * c
 a0 = 15              # amplitude
 t_peak = 20e-15      # Time at which laser reaches its peak
 Lprop_b = c*t_current

From f18d5b3f7f32679f72ff6a2f5d9789eed8d2667a Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Mon, 7 Nov 2022 13:19:39 -0800
Subject: [PATCH 18/33] file starts with analysis

---
 .../{laser_antenna_compare.py => analysis_BTD_laser_antenna.py}   | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename Examples/Tests/BTD_rz/{laser_antenna_compare.py => analysis_BTD_laser_antenna.py} (100%)

diff --git a/Examples/Tests/BTD_rz/laser_antenna_compare.py b/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py
similarity index 100%
rename from Examples/Tests/BTD_rz/laser_antenna_compare.py
rename to Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py

From 440ad31ecdabd328a735ce3c0cda7a4db661a2d7 Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Mon, 7 Nov 2022 13:21:15 -0800
Subject: [PATCH 19/33] change analysis

---
 Regression/WarpX-tests.ini | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Regression/WarpX-tests.ini b/Regression/WarpX-tests.ini
index bbcbce4c471..54166fc00f5 100644
--- a/Regression/WarpX-tests.ini
+++ b/Regression/WarpX-tests.ini
@@ -3730,4 +3730,4 @@ useOMP = 1
 numthreads = 1
 compileTest = 0
 doVis = 0
-analysisRoutine = Examples/Tests/SilverMueller/laser_antenna_compare.py
+analysisRoutine = Examples/Tests/SilverMueller/analysis_BTD_laser_antenna.py

From 954513abd707185e00d8841191d8b6012847fced Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Mon, 7 Nov 2022 13:26:00 -0800
Subject: [PATCH 20/33] fix typo

---
 Regression/WarpX-tests.ini | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Regression/WarpX-tests.ini b/Regression/WarpX-tests.ini
index 54166fc00f5..25fb765d573 100644
--- a/Regression/WarpX-tests.ini
+++ b/Regression/WarpX-tests.ini
@@ -3718,7 +3718,7 @@ analysisRoutine = Examples/Tests/VayDeposition/analysis.py
 
 [BTD_rz]
 buildDir = .
-inputFile = Examples/Tests/BTZ_rz/inputs_rz_z_boosted_BTD
+inputFile = Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD
 runtime_params =
 dim = 2
 addToCompileString = USE_RZ=TRUE

From ad6ebe9859a7a5b80fefa6aa51827c2529e5496f Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Wed, 9 Nov 2022 16:10:48 -0800
Subject: [PATCH 21/33] fix rz input so all snapshots are filled

---
 Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD b/Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD
index d2aa789ebcd..edcc51ed5b0 100644
--- a/Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD
+++ b/Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD
@@ -1,5 +1,5 @@
 # Maximum number of time steps
-warpx.zmax_plasma_to_compute_max_step = 160e-6
+warpx.zmax_plasma_to_compute_max_step = 500e-6
 # number of grid points
 amr.n_cell = 32 256
 

From 305d5cddeb5378d845ed52a190911f4ae9d5404a Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Wed, 9 Nov 2022 16:12:10 -0800
Subject: [PATCH 22/33] remove plt from analysis script

---
 Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py b/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py
index 2646b77c19d..801073fd6cf 100644
--- a/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py
+++ b/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py
@@ -5,7 +5,6 @@
 #
 #
 
-import matplotlib.pyplot as plt
 import numpy as np
 from openpmd_viewer import OpenPMDTimeSeries
 from scipy.constants import c, e, m_e

From fb9c65c7d04405a46291c01d7993fc734b33c829 Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Wed, 16 Nov 2022 11:16:25 -0800
Subject: [PATCH 23/33] initialize cell-centered data to 0 so that guard cells
 are initialized

---
 Source/Diagnostics/BTDiagnostics.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Source/Diagnostics/BTDiagnostics.cpp b/Source/Diagnostics/BTDiagnostics.cpp
index 0d86d65835f..f641b493c21 100644
--- a/Source/Diagnostics/BTDiagnostics.cpp
+++ b/Source/Diagnostics/BTDiagnostics.cpp
@@ -486,6 +486,7 @@ BTDiagnostics::DefineCellCenteredMultiFab(int lev)
     int ncomps = static_cast<int>(m_cellcenter_varnames.size());
 #endif
     m_cell_centered_data[lev] = std::make_unique<amrex::MultiFab>(ba, dmap, ncomps, ngrow);
+    m_cell_centered_data[lev]->setVal(0.);
 
 }
 

From 049610424e21e99616045ddd913bd7b9b49643e6 Mon Sep 17 00:00:00 2001
From: Revathi  Jambunathan
 <41089244+RevathiJambunathan@users.noreply.github.com>
Date: Wed, 16 Nov 2022 11:28:58 -0800
Subject: [PATCH 24/33] Remi's suggestions

Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
---
 Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py        | 7 +++++--
 Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD              | 2 +-
 .../ComputeDiagFunctors/BackTransformFunctor.cpp           | 4 ++--
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py b/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py
index 801073fd6cf..8c914b5c0b2 100644
--- a/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py
+++ b/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py
@@ -1,7 +1,10 @@
 # Copyright 2022
 # Authors: Revathi Jambunathan, Remi Lehe
 #
-# This file tests if the back-transformed signal is a gaussian
+# This tests checks the backtransformed diagnostics by emitting a laser 
+# (with the antenna) in the boosted-frame and then checking that the 
+# fields recorded by the backtransformed diagnostics have the right amplitude,
+# wavelength, and envelope (i.e. gaussian envelope with the right duration.
 #
 #
 
@@ -20,7 +23,7 @@ def gaussian_laser( z, a0, z0_phase, z0_prop, ctau, lambda0 ):
     return( E0*np.exp( - (z-z0_prop)**2/ctau**2 ) \
                 *np.cos( k0*(z-z0_phase) ) )
 
-# Fit the on-axis profile to extract a0
+# Fit the on-axis profile to extract the phase (a.k.a. CEP)
 def fit_function(z, z0_phase):
     return( gaussian_laser( z, a0, z0_phase,
                             z0_b+Lprop_b, ctau0, lambda0 ) )
diff --git a/Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD b/Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD
index edcc51ed5b0..a2bdc8089c1 100644
--- a/Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD
+++ b/Examples/Tests/BTD_rz/inputs_rz_z_boosted_BTD
@@ -44,7 +44,7 @@ laser1.profile      = Gaussian
 laser1.position     = 0. 0. -1.e-6 # This point is on the laser plane
 laser1.direction    = 0. 0. 1.     # The plane normal direction
 laser1.polarization = 1. 0. 0.     # The main polarization vector
-laser1.a0           = 1.5e1        # Maximum amplitude of the laser field (in V/m)
+laser1.a0           = 1.5e1        # Maximum amplitude of the laser field
 laser1.profile_waist = 10.e-6      # The waist of the laser (in meters)
 laser1.profile_duration = 10.e-15  # The duration of the laser (in seconds)
 laser1.profile_t_peak = 20.e-15    # The time at which the laser reaches its peak (in seconds)
diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
index ea52d109569..ca23ce85a93 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
@@ -234,8 +234,8 @@ BackTransformFunctor::LorentzTransformZ (amrex::MultiFab& data, amrex::Real gamm
         amrex::ParallelFor( tbx,
             [=] AMREX_GPU_DEVICE (int i, int j, int k)
             {
-            // arr(x,y,z,comp) has (2*num_rz_modes-1)*10 components
-            // If there are 2 modes, then Er_0_real, Er_1_real, Er_2_real are the first three components
+            // arr(x,y,z,comp) has n_rcomps*10 components
+            // If there are 2 modes, then Er_0_real, Er_1_real, Er_1_imag are the first three components
             // followed by three components each for Et, Ez, Br, Bt, Bz, jr, jt, jz, and rho
                 for (int imode = 0; imode < n_rz; ++imode) {
                     int offset = 1;

From 123eea6c6b290007223b2a318b1768da0a26baa3 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 16 Nov 2022 19:29:20 +0000
Subject: [PATCH 25/33] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py b/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py
index 8c914b5c0b2..e9b4dfab817 100644
--- a/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py
+++ b/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py
@@ -1,8 +1,8 @@
 # Copyright 2022
 # Authors: Revathi Jambunathan, Remi Lehe
 #
-# This tests checks the backtransformed diagnostics by emitting a laser 
-# (with the antenna) in the boosted-frame and then checking that the 
+# This tests checks the backtransformed diagnostics by emitting a laser
+# (with the antenna) in the boosted-frame and then checking that the
 # fields recorded by the backtransformed diagnostics have the right amplitude,
 # wavelength, and envelope (i.e. gaussian envelope with the right duration.
 #

From fd1102668301a7d96951b3a80718b6b5793e8b1b Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Wed, 16 Nov 2022 12:03:09 -0800
Subject: [PATCH 26/33] AllocInitMultifab to add mf to maps of mfs

---
 Source/Diagnostics/BTDiagnostics.cpp | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Source/Diagnostics/BTDiagnostics.cpp b/Source/Diagnostics/BTDiagnostics.cpp
index f641b493c21..2b4efcb5ed8 100644
--- a/Source/Diagnostics/BTDiagnostics.cpp
+++ b/Source/Diagnostics/BTDiagnostics.cpp
@@ -485,8 +485,7 @@ BTDiagnostics::DefineCellCenteredMultiFab(int lev)
 #else
     int ncomps = static_cast<int>(m_cellcenter_varnames.size());
 #endif
-    m_cell_centered_data[lev] = std::make_unique<amrex::MultiFab>(ba, dmap, ncomps, ngrow);
-    m_cell_centered_data[lev]->setVal(0.);
+    WarpX::AllocInitMultiFab(m_cell_centered_data[lev], ba, dmap, ncomps, amrex::IntVect(ngrow), "cellcentered_BTD",0._rt);
 
 }
 

From fed982be2309f18d13ddfec268d761d7b8ef1219 Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Wed, 16 Nov 2022 14:31:42 -0800
Subject: [PATCH 27/33] fix path to analysis script

---
 Regression/WarpX-tests.ini | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Regression/WarpX-tests.ini b/Regression/WarpX-tests.ini
index 25fb765d573..9934fb64c4a 100644
--- a/Regression/WarpX-tests.ini
+++ b/Regression/WarpX-tests.ini
@@ -3730,4 +3730,4 @@ useOMP = 1
 numthreads = 1
 compileTest = 0
 doVis = 0
-analysisRoutine = Examples/Tests/SilverMueller/analysis_BTD_laser_antenna.py
+analysisRoutine = Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py

From 5c5b2e5b1d023c3aa210ac050406c42ae74df370 Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Wed, 16 Nov 2022 14:55:28 -0800
Subject: [PATCH 28/33]  analysis script executable

---
 Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py

diff --git a/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py b/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py
old mode 100644
new mode 100755

From 5e31a4ddfae1f5003e68f829ff6740432dd8c646 Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Wed, 16 Nov 2022 15:01:42 -0800
Subject: [PATCH 29/33] a better and succint for loop

---
 .../BackTransformFunctor.cpp                  | 73 +++++++------------
 1 file changed, 28 insertions(+), 45 deletions(-)

diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
index ca23ce85a93..59647ae9270 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
@@ -234,54 +234,37 @@ BackTransformFunctor::LorentzTransformZ (amrex::MultiFab& data, amrex::Real gamm
         amrex::ParallelFor( tbx,
             [=] AMREX_GPU_DEVICE (int i, int j, int k)
             {
-            // arr(x,y,z,comp) has n_rcomps*10 components
-            // If there are 2 modes, then Er_0_real, Er_1_real, Er_1_imag are the first three components
-            // followed by three components each for Et, Ez, Br, Bt, Bz, jr, jt, jz, and rho
-                for (int imode = 0; imode < n_rz; ++imode) {
-                    int offset = 1;
-                    // number of components for a given mode
-                    int ncomp = 2;
-                    if (imode == 0) {
-                        offset = 0;
-                        // Mode 0 has only real part, thus ncomp = 1
-                        ncomp = 1;
-                    }
-                    for (int icomp = 0; icomp < ncomp; ++icomp) {
-                        // Back-transform the transverse electric and magnetic fields.
-                        // Note that the z-components, Ez, Bz, are not changed by the transform.
-                        amrex::Real e_lab, b_lab, j_lab, rho_lab;
+                for (int mode_comp = 0; mode_comp < n_rcomps; ++mode_comp) {
+                    // Back-transform the transverse electric and magnetic fields.
+                    // Note that the z-components, Ez, Bz, are not changed by the transform.
+                    amrex::Real e_lab, b_lab, j_lab, rho_lab;
 
-                        // Offset for a given mode, imode, and component, icomp (0-real, 1-imag)
-                        const int mode_comp_offset = 2*imode + offset*(icomp-1);
+                    // Transform Er_boost & Bt_boost to lab-frame for corresponding mode (mode_comp)
+                    e_lab = gamma_boost * ( arr(i, j, k, n_rcomps*0 + mode_comp)
+                                            + beta_boost * clight * arr(i, j, k, n_rcomps*4+ mode_comp) );
+                    b_lab = gamma_boost * ( arr(i, j, k, n_rcomps*4 + mode_comp)
+                                            + beta_boost * inv_clight * arr(i, j, k, n_rcomps*0 + mode_comp) );
+                    // Store lab-frame data in-place
+                    arr(i, j, k, n_rcomps*0 + mode_comp) = e_lab;
+                    arr(i, j, k, n_rcomps*4 + mode_comp) = b_lab;
 
-                        // Transform Ex_boost (ncomp=0) & By_boost (ncomp=4) to lab-frame
-                        e_lab = gamma_boost * ( arr(i, j, k, n_rcomps*0 + mode_comp_offset)
-                                                + beta_boost * clight * arr(i, j, k, n_rcomps*4+ mode_comp_offset) );
-                        b_lab = gamma_boost * ( arr(i, j, k, n_rcomps*4 + mode_comp_offset)
-                                                + beta_boost * inv_clight * arr(i, j, k, n_rcomps*0 + mode_comp_offset) );
-                        // Store lab-frame data in-place
-                        arr(i, j, k, n_rcomps*0 + mode_comp_offset) = e_lab;
-                        arr(i, j, k, n_rcomps*4 + mode_comp_offset) = b_lab;
+                    // Transform Et_boost & Br_boost to lab-frame for corresponding mode (mode_comp)
+                    e_lab = gamma_boost * ( arr(i, j, k, n_rcomps*1 + mode_comp)
+                                            - beta_boost * clight * arr(i, j, k, n_rcomps*3 + mode_comp) );
+                    b_lab = gamma_boost * ( arr(i, j, k, n_rcomps*3 + mode_comp)
+                                            - beta_boost * inv_clight * arr(i, j, k, n_rcomps*1 + mode_comp) );
+                    // Store lab-frame data in-place
+                    arr(i, j, k, n_rcomps*1 + mode_comp) = e_lab;
+                    arr(i, j, k, n_rcomps*3 + mode_comp) = b_lab;
 
-                        // Transform Ey_boost (ncomp=1) & Bx_boost (ncomp=3) to lab-frame
-                        e_lab = gamma_boost * ( arr(i, j, k, n_rcomps*1 + mode_comp_offset)
-                                                - beta_boost * clight * arr(i, j, k, n_rcomps*3 + mode_comp_offset) );
-                        b_lab = gamma_boost * ( arr(i, j, k, n_rcomps*3 + mode_comp_offset)
-                                                - beta_boost * inv_clight * arr(i, j, k, n_rcomps*1 + mode_comp_offset) );
-                        // Store lab-frame data in-place
-                        arr(i, j, k, n_rcomps*1 + mode_comp_offset) = e_lab;
-                        arr(i, j, k, n_rcomps*3 + mode_comp_offset) = b_lab;
-
-                        // Transform charge density (ncomp=9)
-                        // and z-component of current density (ncomp=8)
-                        j_lab = gamma_boost * ( arr(i, j, k, n_rcomps*8 + mode_comp_offset)
-                                                + beta_boost * clight * arr(i, j, k, n_rcomps*9 + mode_comp_offset) );
-                        rho_lab = gamma_boost * ( arr(i, j, k, n_rcomps*9 + 2*imode + offset*(icomp-1))
-                                                  + beta_boost * inv_clight * arr(i, j, k, n_rcomps*8 + mode_comp_offset) );
-                        // Store lab-frame jz and rho in-place
-                        arr(i, j, k, n_rcomps*8 + mode_comp_offset) = j_lab;
-                        arr(i, j, k, n_rcomps*9 + mode_comp_offset) = rho_lab;
-                    }
+                    // Transform charge density z-component of current density
+                    j_lab = gamma_boost * ( arr(i, j, k, n_rcomps*8 + mode_comp)
+                                            + beta_boost * clight * arr(i, j, k, n_rcomps*9 + mode_comp) );
+                    rho_lab = gamma_boost * ( arr(i, j, k, n_rcomps*9 + mode_comp)
+                                              + beta_boost * inv_clight * arr(i, j, k, n_rcomps*8 + mode_comp) );
+                    // Store lab-frame jz and rho in-place
+                    arr(i, j, k, n_rcomps*8 + mode_comp) = j_lab;
+                    arr(i, j, k, n_rcomps*9 + mode_comp) = rho_lab;
                 }
             }
         );

From dec5a1788330015ed8b4598026239b46e3fc3d3c Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Wed, 16 Nov 2022 15:09:15 -0800
Subject: [PATCH 30/33] unused var

---
 Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
index 59647ae9270..a57b61b666f 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
@@ -229,7 +229,6 @@ BackTransformFunctor::LorentzTransformZ (amrex::MultiFab& data, amrex::Real gamm
         amrex::Real clight = PhysConst::c;
         amrex::Real inv_clight = 1.0_rt/clight;
 #ifdef WARPX_DIM_RZ
-        const int n_rz = WarpX::n_rz_azimuthal_modes;
         const int n_rcomps = WarpX::ncomps;
         amrex::ParallelFor( tbx,
             [=] AMREX_GPU_DEVICE (int i, int j, int k)

From 8e14707e533c45ae51b744031a6cdc04e6b931b3 Mon Sep 17 00:00:00 2001
From: Revathi  Jambunathan
 <41089244+RevathiJambunathan@users.noreply.github.com>
Date: Wed, 16 Nov 2022 15:24:56 -0800
Subject: [PATCH 31/33] Update
 Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp

Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
---
 Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
index a57b61b666f..0cc1530266c 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
@@ -129,7 +129,7 @@ BackTransformFunctor::operator ()(amrex::MultiFab& mf_dst, int /*dcomp*/, const
                     dst_arr(i, k_lab, k, n) = src_arr(i, j, k, icomp);
 #elif defined(WARPX_DIM_RZ)
                     // rzcomp below gives the component id, 0 to (n_rz_comp-1) for a given field
-                    const int rzcomp = n - static_cast<int>( floor(n/(2.0*nrz-1.0)) ) * n_rz_comp;
+                    const int rzcomp = n % n_rz_comp;
                     // Accessing the correct rz component from the cell-centered multifab
                     // that has back-transformed fields and storing it for the appropriate user-requested field, icomp
                     // For example, for 2 rz modes, we have three components (n_rz_comp=3) for each field

From bc10eed4699e0780eac5a7e677866865f5caf34f Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Wed, 16 Nov 2022 15:45:34 -0800
Subject: [PATCH 32/33] fix unused var

---
 Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
index 0cc1530266c..3678e03f0c2 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp
@@ -115,7 +115,6 @@ BackTransformFunctor::operator ()(amrex::MultiFab& mf_dst, int /*dcomp*/, const
             amrex::Array4<amrex::Real> src_arr = tmp[mfi].array();
             amrex::Array4<amrex::Real> dst_arr = mf_dst[mfi].array();
 #ifdef WARPX_DIM_RZ
-            const int nrz = WarpX::n_rz_azimuthal_modes;
             const int n_rz_comp = WarpX::ncomps;
 #endif
             amrex::ParallelFor( tbx, ncomp_dst,

From 37c9587c41944eea09c58a3143272dcf240adac6 Mon Sep 17 00:00:00 2001
From: RevathiJambunathan <revanathan@gmail.com>
Date: Wed, 16 Nov 2022 16:36:26 -0800
Subject: [PATCH 33/33] add python path

---
 Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py b/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py
index e9b4dfab817..5b5f8c94bf3 100755
--- a/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py
+++ b/Examples/Tests/BTD_rz/analysis_BTD_laser_antenna.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 # Copyright 2022
 # Authors: Revathi Jambunathan, Remi Lehe
 #
@@ -5,8 +7,6 @@
 # (with the antenna) in the boosted-frame and then checking that the
 # fields recorded by the backtransformed diagnostics have the right amplitude,
 # wavelength, and envelope (i.e. gaussian envelope with the right duration.
-#
-#
 
 import numpy as np
 from openpmd_viewer import OpenPMDTimeSeries