Read twice the global data to fill the global variables of coreneuron and the mod files

Author: iomaganaris

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();
@@ -236,6 +226,8 @@ void nrn_init_and_load_data(int argc,
 
     rev_dt = (int) (1. / dt);
 
+    printf("CoreNEURON Global Vars before editing: second order=%d t=%g dt=%g rev_dt=%d celsius=%lf\n", secondorder, t, dt, rev_dt, celsius);
+
     if (corenrn_param.celsius != -1000.) {  // command line arg highest precedence
         celsius = corenrn_param.celsius;
     } else if (celsius == -1000.) {  // not on command line and no celsius in globals.dat
@@ -247,6 +239,8 @@ void nrn_init_and_load_data(int argc,
     // for ispc backend
     ispc_celsius = celsius;
 
+    printf("CoreNEURON Global Vars after editing: second order=%d t=%g dt=%g rev_dt=%d celsius=%lf\n", secondorder, t, dt, rev_dt, celsius);
+
     // create net_cvode instance
     mk_netcvode();
 
@@ -514,9 +508,36 @@ extern "C" void mk_mech_init(int argc, char** argv) {
         out.close();
     }
 
-    // reads mechanism information from bbcore_mech.dat
+    // 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);
+    
+    // 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) {
@@ -527,6 +548,12 @@ 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 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);
+
+
     if (!corenrn_param.is_quiet()) {
         report_mem_usage("After mk_mech");
     }

coreneuron/io/global_vars.cpp

@@ -62,6 +62,7 @@ void set_globals(const char* path, bool cli_global_seed, int cli_global_seed_val
             // will be processed before exit from loop.
             if (val) {
                 N2V::iterator it = n2v->find(name);
+                printf("Passing from NEURON %s %d %g\n", name, size, *val);
                 if (it != n2v->end()) {
                     if (size == 0) {
                         nrn_assert(it->second.first == 0);

coreneuron/mechanism/eion.cpp

@@ -109,16 +109,19 @@ void ion_reg(const char* name, double valence) {
         sprintf(buf[1], "%so0_%s", name, buf[0]);
         if (strcmp("na", name) == 0) {
             na_ion = mechtype;
+            printf("Setting global_conci(na) to %lf and global_conco(na) to %lf\n", DEF_nai, DEF_nao);
             global_conci(mechtype) = DEF_nai;
             global_conco(mechtype) = DEF_nao;
             global_charge(mechtype) = 1.;
         } else if (strcmp("k", name) == 0) {
             k_ion = mechtype;
+            printf("Setting global_conci(k) to %lf and global_conco(k) to %lf\n",DEF_ki, DEF_ko);
             global_conci(mechtype) = DEF_ki;
             global_conco(mechtype) = DEF_ko;
             global_charge(mechtype) = 1.;
         } else if (strcmp("ca", name) == 0) {
             ca_ion = mechtype;
+            printf("Setting global_conci(ca) to %lf and global_conco(ca) to %lf\n", DEF_cai, DEF_cao);
             global_conci(mechtype) = DEF_cai;
             global_conco(mechtype) = DEF_cao;
             global_charge(mechtype) = 2.;