From fbf6690458de5d8bbe080c2d1bc75a0b2826f653 Mon Sep 17 00:00:00 2001
From: Michael Buehlmann <buehlmann.michi@gmail.com>
Date: Thu, 28 Apr 2022 13:13:51 -0500
Subject: [PATCH 1/2] add missing HACC/GenericIO fields

---
 src/plugins/output_genericio.cc | 38 ++++++++++++++++-----------------
 1 file changed, 18 insertions(+), 20 deletions(-)

diff --git a/src/plugins/output_genericio.cc b/src/plugins/output_genericio.cc
index f77bef8..9e4a850 100644
--- a/src/plugins/output_genericio.cc
+++ b/src/plugins/output_genericio.cc
@@ -16,6 +16,7 @@ protected:
     std::vector<float> vx, vy, vz;
     std::vector<float> mass, hh, uu;
     std::vector<float> mu, phi, rho;
+    std::vector<float> zmet, yhe;
     std::vector<uint16_t> mask;
 
 public:
@@ -85,12 +86,16 @@ public:
         vy.reserve(vy.size() + npart);
         vz.reserve(vz.size() + npart);
         ids.reserve(ids.size() + npart);
-        
+        mask.reserve(mask.size() + npart);
+        // phi doesn't need to be initialized, just needs to be present in data
+        phi.resize(phi.size() + npart, 0.0f);
+
+
         auto _pos = reinterpret_cast<const float*>(pc.get_pos32_ptr());
         auto _vel = reinterpret_cast<const float*>(pc.get_vel32_ptr());
         auto _ids = reinterpret_cast<const uint64_t*>(pc.get_ids64_ptr());
         auto _mass = reinterpret_cast<const float*>(pc.get_mass32_ptr());
-        
+
         for(size_t i=0; i<npart; ++i) {
             xx.push_back(fmod(_pos[3*i + 0]+lunit_, lunit_));
             yy.push_back(fmod(_pos[3*i + 1]+lunit_, lunit_));
@@ -98,16 +103,15 @@ public:
             vx.push_back(_vel[3*i + 0]);
             vy.push_back(_vel[3*i + 1]);
             vz.push_back(_vel[3*i + 2]);
+            mask.push_back(s == cosmo_species::baryon ? 1<<2 : 0);
         }
 
-        // phi doesn't need to be initialized, just needs to be present in data
-        phi.resize(phi.size() + npart);
         std::copy(_ids, _ids+npart, std::back_inserter(ids));
 
         if(hacc_hydro_) {
             size_t prev_size = mass.size();
             size_t new_size = prev_size + npart;
-            
+
             if(pc.bhas_individual_masses_) {
                 std::copy(_mass, _mass+npart, std::back_inserter(mass));
             } else {
@@ -115,20 +119,12 @@ public:
                 std::fill(mass.begin() + prev_size, mass.end(), particle_mass);
             }
 
-            mask.resize(new_size);
-            std::fill(mask.begin() + prev_size, mask.end(), s == cosmo_species::baryon ? 1<<2 : 0);
-
-            hh.resize(new_size);
-            std::fill(hh.begin() + prev_size, hh.end(), hh_value_);
-
-            uu.resize(new_size);
-            std::fill(uu.begin() + prev_size, uu.end(), s == cosmo_species::baryon ? uu_value_ : 0.0f);
-
-            rho.resize(new_size);
-            std::fill(rho.begin() + prev_size, rho.end(), rho_value_);
-
-            mu.resize(new_size);
-            std::fill(mu.begin() + prev_size, mu.end(), s == cosmo_species::baryon ? mu_value_ : 0.0f);
+            hh.resize(new_size, hh_value_);
+            uu.resize(new_size, s == cosmo_species::baryon ? uu_value_ : 0.0f);
+            rho.resize(new_size, rho_value_);
+            mu.resize(new_size, s == cosmo_species::baryon ? mu_value_ : 0.0f);
+            zmet.resize(new_size, 0.0f);
+            yhe.resize(new_size, 0.0f);
         }
     }
 
@@ -145,13 +141,15 @@ public:
         writer.addVariable("vz", vz);
         writer.addVariable("id", ids);
         writer.addVariable("phi", phi);
+        writer.addVariable("mask", mask);
         if(hacc_hydro_) {
             writer.addVariable("mass", mass);
-            writer.addVariable("mask", mask);
             writer.addVariable("hh", hh);
             writer.addVariable("uu", uu);
             writer.addVariable("rho", rho);
             writer.addVariable("mu", mu);
+            writer.addVariable("zmet", zmet);
+            writer.addVariable("yhe", yhe);
         }
         writer.write();
         MPI_Barrier(MPI_COMM_WORLD);

From 82237a0c1c38352160451c9463cd59e0d6cf1290 Mon Sep 17 00:00:00 2001
From: Oliver Hahn <oliverjhahn@gmail.com>
Date: Thu, 10 Nov 2022 11:16:28 +0100
Subject: [PATCH 2/2] removed compilation problems with GCC 12

---
 include/general.hh   | 1 +
 include/math/vec3.hh | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/include/general.hh b/include/general.hh
index 05feb0a..dcf4388 100644
--- a/include/general.hh
+++ b/include/general.hh
@@ -20,6 +20,7 @@
 
 #include <complex>
 #include <map>
+#include <memory>
 
 #if defined(USE_MPI)
 #include <mpi.h>
diff --git a/include/math/vec3.hh b/include/math/vec3.hh
index bbaffbc..593c725 100644
--- a/include/math/vec3.hh
+++ b/include/math/vec3.hh
@@ -30,7 +30,7 @@ public:
 
     //! empty constructor
     vec3_t()
-    : x(data_[0]),y(data_[1]),z(data_[2]){}
+    : data_{{T(0),T(0),T(0)}},x(data_[0]),y(data_[1]),z(data_[2]){}
 
     //! copy constructor
     vec3_t( const vec3_t<T> &v)