Set the initial values of ions properly in direct and file mode transfer

coreneuron/apps/main1.cpp

@@ -185,13 +185,6 @@ void nrn_init_and_load_data(int argc,
         report_mem_usage("After MPI_Init");
     }
 
-    // initialise default coreneuron parameters
-    initnrn();
-
-    // set global variables
-    // precedence is: set by user, globals.dat, 34.0
-    celsius = corenrn_param.celsius;
-
 #if CORENEURON_ENABLE_GPU
     if (!corenrn_param.gpu && corenrn_param.cell_interleave_permute == 2) {
         fprintf(stderr,
@@ -218,9 +211,6 @@ void nrn_init_and_load_data(int argc,
     // full path of files.dat file
     std::string filesdat(corenrn_param.datpath + "/" + corenrn_param.filesdat);
 
-    // 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);
-
     // set global variables for start time, timestep and temperature
     if (!corenrn_embedded) {
         t = checkPoints.restore_time();
@@ -514,8 +504,19 @@ extern "C" void mk_mech_init(int argc, char** argv) {
         out.close();
     }
 
-    // reads mechanism information from bbcore_mech.dat
+    // initialise default coreneuron parameters
+    initnrn();
+
+    // set global variables
+    // precedence is: set by user, globals.dat, 34.0
+    celsius = corenrn_param.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);
 
+    // reads mechanism information from bbcore_mech.dat
     mk_mech((corenrn_param.datpath).c_str());
 }
 
@@ -527,6 +528,11 @@ extern "C" int run_solve_core(int argc, char** argv) {
     std::vector<std::pair<std::string, int>> spikes_population_name_offset;
     bool reports_needs_finalize = false;
 
+
+    // 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);
+
     if (!corenrn_param.is_quiet()) {
         report_mem_usage("After mk_mech");
     }

coreneuron/io/global_vars.cpp

@@ -11,6 +11,7 @@
 #include <map>
 #include <string>
 #include <algorithm>
+#include <unordered_map>
 
 #include "coreneuron/utils/randoms/nrnran123.h"
 #include "coreneuron/nrnconf.h"
@@ -28,6 +29,8 @@ using N2V = std::map<std::string, PSD>;
 
 static N2V* n2v;
 
+extern std::unordered_map<std::string, double> nrn_ion_init;
+
 void hoc_register_var(DoubScal* ds, DoubVec* dv, VoidFunc*) {
     if (!n2v) {
         n2v = new N2V();
@@ -74,6 +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;
             }
@@ -114,6 +120,9 @@ void set_globals(const char* path, bool cli_global_seed, int cli_global_seed_val
                     nrn_assert(it->second.first == 0);
                     *(it->second.second) = val;
                 }
+                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) {
                 if (strcmp(name, "0") == 0) {
                     break;

coreneuron/mechanism/eion.cpp

@@ -60,6 +60,15 @@ double nrn_ion_charge(int type) {
     return global_charge(type);
 }
 
+std::unordered_map<std::string, double> nrn_ion_init = {
+    {"nai0_na_ion", DEF_nai},
+    {"nao0_na_ion", DEF_nao},
+    {"ki0_k_ion", DEF_ki},
+    {"ko0_k_ion", DEF_ko},
+    {"cai0_ca_ion", DEF_cai},
+    {"cao0_ca_ion", DEF_cao},
+};
+
 void ion_reg(const char* name, double valence) {
     char buf[7][50];
 #define VAL_SENTINAL -10000.
@@ -109,22 +118,30 @@ void ion_reg(const char* name, double valence) {
         sprintf(buf[1], "%so0_%s", name, buf[0]);
         if (strcmp("na", name) == 0) {
             na_ion = mechtype;
-            global_conci(mechtype) = DEF_nai;
-            global_conco(mechtype) = DEF_nao;
+            global_conci(mechtype) = nrn_ion_init["nai0_na_ion"];
+            global_conco(mechtype) = nrn_ion_init["nao0_na_ion"];
             global_charge(mechtype) = 1.;
         } else if (strcmp("k", name) == 0) {
             k_ion = mechtype;
-            global_conci(mechtype) = DEF_ki;
-            global_conco(mechtype) = DEF_ko;
+            global_conci(mechtype) = nrn_ion_init["ki0_k_ion"];
+            global_conco(mechtype) = nrn_ion_init["ko0_k_ion"];
             global_charge(mechtype) = 1.;
         } else if (strcmp("ca", name) == 0) {
             ca_ion = mechtype;
-            global_conci(mechtype) = DEF_cai;
-            global_conco(mechtype) = DEF_cao;
+            global_conci(mechtype) = nrn_ion_init["cai0_ca_ion"];
+            global_conco(mechtype) = nrn_ion_init["cao0_ca_ion"];
             global_charge(mechtype) = 2.;
         } else {
-            global_conci(mechtype) = DEF_ioni;
-            global_conco(mechtype) = DEF_iono;
+            if (nrn_ion_init[static_cast<std::string>(buf[0])]) {
+                global_conci(mechtype) = nrn_ion_init[static_cast<std::string>(buf[0])];
+            } else {
+                global_conci(mechtype) = DEF_ioni;
+            }
+            if (nrn_ion_init[static_cast<std::string>(buf[1])]) {
+                global_conco(mechtype) = nrn_ion_init[static_cast<std::string>(buf[1])];
+            } else {
+                global_conco(mechtype) = DEF_iono;
+            }
             global_charge(mechtype) = VAL_SENTINAL;
         }
     }