From c3ec12daa78b17bb007a5acb68db5079b12e58ae Mon Sep 17 00:00:00 2001
From: Ioannis Magkanaris <iomagkanaris@gmail.com>
Date: Fri, 25 Feb 2022 12:35:06 +0100
Subject: [PATCH] Fixed initialization of global variables

---
 coreneuron/apps/main1.cpp     | 24 ++++--------------------
 coreneuron/io/global_vars.cpp |  6 +++++-
 2 files changed, 9 insertions(+), 21 deletions(-)

diff --git a/coreneuron/apps/main1.cpp b/coreneuron/apps/main1.cpp
index ef02f96f9..9e3f0e348 100644
--- a/coreneuron/apps/main1.cpp
+++ b/coreneuron/apps/main1.cpp
@@ -508,36 +508,21 @@ extern "C" void mk_mech_init(int argc, char** argv) {
         out.close();
     }
 
-    // Not working
     // initialise default coreneuron parameters
     initnrn();
-    printf("CoreNEURON Global Vars after initnrn(): second order=%d t=%g dt=%g rev_dt=%d celsius=%lf\n", secondorder, t, dt, rev_dt, celsius);
 
     // set global variables
     // precedence is: set by user, globals.dat, 34.0
     celsius = corenrn_param.celsius;
-    printf("CoreNEURON Global Vars after corenrn_param: second order=%d t=%g dt=%g rev_dt=%d celsius=%lf\n", secondorder, t, dt, rev_dt, celsius);
 
     // read the global variable names and set their values from globals.dat
+    // some global variables need to be read before the ion_reg to initialize
+    // properly the in-built ion mechanisms
     set_globals(corenrn_param.datpath.c_str(), (corenrn_param.seed >= 0), corenrn_param.seed);
-    printf("CoreNEURON Global Vars after set_globals(): second order=%d t=%g dt=%g rev_dt=%d celsius=%lf\n", secondorder, t, dt, rev_dt, celsius);
     
     // reads mechanism information from bbcore_mech.dat
     mk_mech((corenrn_param.datpath).c_str());
 
-    // // Not working
-    // // initialise default coreneuron parameters
-    // initnrn();
-    // printf("CoreNEURON Global Vars after initnrn(): second order=%d t=%g dt=%g rev_dt=%d celsius=%lf\n", secondorder, t, dt, rev_dt, celsius);
-
-    // // set global variables
-    // // precedence is: set by user, globals.dat, 34.0
-    // celsius = corenrn_param.celsius;
-    // printf("CoreNEURON Global Vars after corenrn_param: second order=%d t=%g dt=%g rev_dt=%d celsius=%lf\n", secondorder, t, dt, rev_dt, celsius);
-
-    // // read the global variable names and set their values from globals.dat
-    // set_globals(corenrn_param.datpath.c_str(), (corenrn_param.seed >= 0), corenrn_param.seed);
-    // printf("CoreNEURON Global Vars after set_globals(): second order=%d t=%g dt=%g rev_dt=%d celsius=%lf\n", secondorder, t, dt, rev_dt, celsius);
 }
 
 extern "C" int run_solve_core(int argc, char** argv) {
@@ -549,10 +534,9 @@ extern "C" int run_solve_core(int argc, char** argv) {
     bool reports_needs_finalize = false;
 
 
-    // read the global variable names and set their values from globals.dat
+    // read agin the global variables to set the global variables defined by
+    // the mod files' mechanisms
     set_globals(corenrn_param.datpath.c_str(), (corenrn_param.seed >= 0), corenrn_param.seed);
-    printf("CoreNEURON Global Vars after set_globals(): second order=%d t=%g dt=%g rev_dt=%d celsius=%lf\n", secondorder, t, dt, rev_dt, celsius);
-
 
     if (!corenrn_param.is_quiet()) {
         report_mem_usage("After mk_mech");
diff --git a/coreneuron/io/global_vars.cpp b/coreneuron/io/global_vars.cpp
index 7b40b8766..3976d6831 100644
--- a/coreneuron/io/global_vars.cpp
+++ b/coreneuron/io/global_vars.cpp
@@ -77,6 +77,9 @@ void set_globals(const char* path, bool cli_global_seed, int cli_global_seed_val
                         }
                     }
                 }
+                if (static_cast<std::string>(name).find("ion") != std::string::npos) {
+                    nrn_ion_init[name] = *val;
+                }
                 delete[] val;
                 val = nullptr;
             }
@@ -116,7 +119,8 @@ void set_globals(const char* path, bool cli_global_seed, int cli_global_seed_val
                 if (it != n2v->end()) {
                     nrn_assert(it->second.first == 0);
                     *(it->second.second) = val;
-                } else if (static_cast<std::string>(name).find("ion") != std::string::npos) {
+                }
+                if (static_cast<std::string>(name).find("ion") != std::string::npos) {
                     nrn_ion_init[name] = val;
                 }
             } else if (sscanf(line, "%[^[][%d]\n", name, &n) == 2) {