From d074b48c1dd536e9646fbbf7a167311047aec7cb Mon Sep 17 00:00:00 2001
From: Cheng Li <69489965+chengcli@users.noreply.github.com>
Date: Sun, 13 Aug 2023 10:18:19 -0400
Subject: [PATCH] Fix restart problem (#78)

Initialize IndexMap and Thermodynamics before Mesh. Place global variables in InitUserMeshData
---
 examples/2019-Li-snap/bryan_pgen.cpp | 11 ++++++-----
 src/mesh_setup.cpp                   | 12 ++++++------
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/examples/2019-Li-snap/bryan_pgen.cpp b/examples/2019-Li-snap/bryan_pgen.cpp
index 0a446272..a95a298a 100644
--- a/examples/2019-Li-snap/bryan_pgen.cpp
+++ b/examples/2019-Li-snap/bryan_pgen.cpp
@@ -79,13 +79,18 @@ void MeshBlock::UserWorkBeforeOutput(ParameterInput *pin) {
 }
 
 void Mesh::InitUserMeshData(ParameterInput *pin) {
+  auto pindex = IndexMap::GetInstance();
+
   grav = -pin->GetReal("hydro", "grav_acc1");
   p0 = pin->GetReal("problem", "p0");
+
+  // index
+  iH2O = pindex->GetVaporId("H2O");
+  iH2Oc = pindex->GetCloudId("H2O(c)");
 }
 
 void MeshBlock::ProblemGenerator(ParameterInput *pin) {
   auto pthermo = Thermodynamics::GetInstance();
-  auto pindex = IndexMap::GetInstance();
 
   Real Ps = p0;
   Real Ts = pin->GetReal("problem", "Ts");
@@ -97,10 +102,6 @@ void MeshBlock::ProblemGenerator(ParameterInput *pin) {
   Real dT = pin->GetReal("problem", "dT");
   Real qt = pin->GetReal("problem", "qt");
 
-  // index
-  iH2O = pindex->GetVaporId("H2O");
-  iH2Oc = pindex->GetCloudId("H2O(c)");
-
   AirParcel air(AirParcel::Type::MassFrac);
   air.w[iH2O] = qt;
   air.c[iH2Oc] = 0.;
diff --git a/src/mesh_setup.cpp b/src/mesh_setup.cpp
index 186232d9..ea7f0917 100644
--- a/src/mesh_setup.cpp
+++ b/src/mesh_setup.cpp
@@ -55,6 +55,12 @@ void mesh_setup(ParameterInput*& pinput, Mesh*& pmesh) {
     throw RuntimeError("main", ex.what());
   }
 
+  // index map
+  IndexMap::InitFromAthenaInput(pinput);
+
+  // thermodynamics
+  Thermodynamics::InitFromAthenaInput(pinput);
+
   try {
     if (cli->res_flag == 0) {
       pmesh = new Mesh(pinput, cli->mesh_flag);
@@ -98,12 +104,6 @@ void mesh_setup(ParameterInput*& pinput, Mesh*& pmesh) {
     exit(0);
   }
 
-  // index map
-  IndexMap::InitFromAthenaInput(pinput);
-
-  // thermodynamics
-  Thermodynamics::InitFromAthenaInput(pinput);
-
   // set up additional components
   for (int b = 0; b < pmesh->nblocal; ++b) {
     MeshBlock* pmb = pmesh->my_blocks(b);