From 886d49c55cd179c34197fef2880d9623ce37ce22 Mon Sep 17 00:00:00 2001
From: MaxThevenet <mthevenet@lbl.gov>
Date: Thu, 9 May 2019 19:46:35 -0700
Subject: Can select particle quantities to dump

---
 Source/Particles/PhysicalParticleContainer.cpp | 41 +++++++++++++++++---------
 1 file changed, 27 insertions(+), 14 deletions(-)

(limited to 'Source/Particles/PhysicalParticleContainer.cpp')

diff --git a/Source/Particles/PhysicalParticleContainer.cpp b/Source/Particles/PhysicalParticleContainer.cpp
index c6bc92ff6..1bf41816e 100644
--- a/Source/Particles/PhysicalParticleContainer.cpp
+++ b/Source/Particles/PhysicalParticleContainer.cpp
@@ -82,22 +82,35 @@ PhysicalParticleContainer::PhysicalParticleContainer (AmrCore* amr_core, int isp
     pp.query("do_splitting", do_splitting);
     pp.query("split_type", split_type);
     pp.query("do_continuous_injection", do_continuous_injection);
-    {
-        pp.queryarr("plot_vars", plot_vars);
-        if (plot_vars.size() == 0){
-            if (WarpX::do_boosted_frame_diagnostic && WarpX::do_boosted_frame_particles){
-                plot_flags.resize(PIdx::nattribs + 6, 1);
-            } else {
-                plot_flags.resize(PIdx::nattribs, 1);
-            }
-        } else {
-            if (WarpX::do_boosted_frame_diagnostic && WarpX::do_boosted_frame_particles){
-                plot_flags.resize(PIdx::nattribs + 6, 0);
-            } else {
-                plot_flags.resize(PIdx::nattribs, 0);
-            }
 
+    pp.query("plot_species", plot_species);
+    int do_user_plot_vars;
+    do_user_plot_vars = pp.queryarr("plot_vars", plot_vars);
+    if (not do_user_plot_vars){
+        // By default, all particle variables are dumped to plotfiles,
+        // including {x,y,z,ux,uy,uz}old variables when running in a 
+        // boosted frame
+        if (WarpX::do_boosted_frame_diagnostic && WarpX::do_boosted_frame_particles){
+            plot_flags.resize(PIdx::nattribs + 6, 1);
+        } else {
+            plot_flags.resize(PIdx::nattribs, 1);
+        }
+    } else {
+        // Set plot_flag to 0 for all attribs
+        if (WarpX::do_boosted_frame_diagnostic && WarpX::do_boosted_frame_particles){
+            plot_flags.resize(PIdx::nattribs + 6, 0);
+        } else {
+            // Set plot_flags to 1 for data in plot_vars
+            plot_flags.resize(PIdx::nattribs, 0);
+            Print()<<"here2"<<std::endl;
+        }
+        // If not none, set plot_flags values to 1 for elements in plot_vars.
+        if (plot_vars[0] != "none"){
             for (const auto& var : plot_vars){
+                // Return error if var not in PIdx. 
+                AMREX_ALWAYS_ASSERT_WITH_MESSAGE( 
+                    ParticleStringNames::to_index.count(var), 
+                    "<species>.plot_vars argument not in ParticleStringNames");
                 plot_flags[ParticleStringNames::to_index.at(var)] = 1;
             }
         }
-- 
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