From 4e16e62c44e049ab17b777de80aa51117806f1be Mon Sep 17 00:00:00 2001
From: Andy Nonaka <AJNonaka@lbl.gov>
Date: Mon, 12 Aug 2024 17:27:34 -0700
Subject: [PATCH] checkpoint write

---
 src_analysis/StructFact.H   |  2 +-
 src_analysis/StructFact.cpp | 38 ++++++++++++++++++++++++++++++++++++-
 2 files changed, 38 insertions(+), 2 deletions(-)

diff --git a/src_analysis/StructFact.H b/src_analysis/StructFact.H
index 1b82ce08..b651e52a 100644
--- a/src_analysis/StructFact.H
+++ b/src_analysis/StructFact.H
@@ -151,7 +151,7 @@ public:
 
     void WriteCheckPoint(const int& step,
                          const amrex::Real& time,
-                         std::string plotfile_base);
+                         std::string checkfile_base);
 
     const decltype(cov_names)& get_names() const { return cov_names; }
 };
diff --git a/src_analysis/StructFact.cpp b/src_analysis/StructFact.cpp
index 02dacd7f..59269f36 100644
--- a/src_analysis/StructFact.cpp
+++ b/src_analysis/StructFact.cpp
@@ -1946,6 +1946,17 @@ void StructFact::WriteCheckPoint(const int& step,
 
     BoxArray ba = cov_real.boxArray();
 
+    // single level problem
+    int nlevels = 1;
+
+    // ---- prebuild a hierarchy of directories
+    // ---- dirName is built first.  if dirName exists, it is renamed.  then build
+    // ---- dirName/subDirPrefix_0 .. dirName/subDirPrefix_nlevels-1
+    // ---- if callBarrier is true, call ParallelDescriptor::Barrier()
+    // ---- after all directories are built
+    // ---- ParallelDescriptor::IOProcessor() creates the directories
+    amrex::PreBuildDirectorHierarchy(checkpointname, "Level_", nlevels, true);
+
     VisMF::IO_Buffer io_buffer(VisMF::IO_Buffer_Size);
 
     // write Header file
@@ -1973,13 +1984,38 @@ void StructFact::WriteCheckPoint(const int& step,
         // write out time
         HeaderFile << time << "\n";
 
+        // write out misc structure factor member objects
+        HeaderFile << NVAR << "\n";
+        HeaderFile << NVARU << "\n";
+        HeaderFile << NCOV << "\n";
+        HeaderFile << nsamples << "\n";
+        for (int i=0; i<NCOV; ++i) {
+            HeaderFile << scaling[i] << "\n";
+        }
+        for (int i=0; i<NCOV; ++i) {
+            HeaderFile << cov_names[i] << "\n";
+        }
+        for (int i=0; i<NCOV; ++i) {
+            HeaderFile << s_pairA[i] << "\n";
+        }
+        for (int i=0; i<NCOV; ++i) {
+            HeaderFile << s_pairB[i] << "\n";
+        }
+        for (int i=0; i<NVARU; ++i) {
+            HeaderFile << var_u[i] << "\n";
+        }
+
         // write the BoxArray
         ba.writeOn(HeaderFile);
         HeaderFile << '\n';
     }
 
-    // write the MultiFab data to, e.g., chk00010/Level_0/
+    // write the MultiFab data to, e.g., chk_SF00010/Level_0/
     VisMF::Write(cov_real,
                  amrex::MultiFabFileFullPrefix(0, checkpointname, "Level_", "cov_real"));
+    VisMF::Write(cov_imag,
+                 amrex::MultiFabFileFullPrefix(0, checkpointname, "Level_", "cov_imag"));
+    VisMF::Write(cov_mag,
+                 amrex::MultiFabFileFullPrefix(0, checkpointname, "Level_", "cov_mag"));
 
 }