Update references for working hh.mod (#13)

* Update references for working hh.mod --------- Co-authored-by: Luc Grosheintz <[email protected]>
BlueBrain · May 10, 2024 · 00978a5 · 00978a5
1 parent 247abd6
commit 00978a5
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Showing 11 changed files with 104 additions and 9 deletions.
diff --git a/cnexp_array/neuron/leonhard.cpp b/cnexp_array/neuron/leonhard.cpp
@@ -187,7 +187,14 @@ namespace neuron {
         auto inst = make_instance_leonhard(_lmr);
         auto node_data = make_node_data_leonhard(*_nt, *_ml_arg);
         auto nodecount = _ml_arg->nodecount;
+        auto* const _ml = &_lmr;
+        auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
+            inst.v_unused[id] = v;
             inst.x[id] = 42.0;
             (inst.s+id*2)[static_cast<int>(0)] = 0.1;
             (inst.s+id*2)[static_cast<int>(1)] =  -1.0;
@@ -203,7 +210,13 @@ namespace neuron {
         auto inst = make_instance_leonhard(_lmr);
         auto node_data = make_node_data_leonhard(*_nt, *_ml_arg);
         auto nodecount = _ml_arg->nodecount;
+        auto* const _ml = &_lmr;
+        auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
             inst.x[id] = inst.x[id] + (1.0 - exp(_nt->_dt * ((((inst.s+id*2)[static_cast<int>(0)] + (inst.s+id*2)[static_cast<int>(1)]) * ((inst.z+id*3)[static_cast<int>(0)] * (inst.z+id*3)[static_cast<int>(1)] * (inst.z+id*3)[static_cast<int>(2)])) * (1.0)))) * ( -(0.0) / (((((inst.s+id*2)[static_cast<int>(0)] + (inst.s+id*2)[static_cast<int>(1)])) * (((((inst.z+id*3)[static_cast<int>(0)]) * ((inst.z+id*3)[static_cast<int>(1)])) * ((inst.z+id*3)[static_cast<int>(2)])))) * (1.0)) - inst.x[id]);
         }
     }

diff --git a/cnexp_scalar/neuron/leonhard.cpp b/cnexp_scalar/neuron/leonhard.cpp
@@ -181,7 +181,11 @@ namespace neuron {
         auto* const _ml = &_lmr;
         auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
-            auto& _ppvar = _ml_arg->pdata[id];
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
+            inst.v_unused[id] = v;
             inst.x[id] = 42.0;
         }
     }
@@ -195,6 +199,10 @@ namespace neuron {
         auto* const _ml = &_lmr;
         auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
             inst.x[id] = inst.x[id] + (1.0 - exp(_nt->_dt * ( -1.0))) * ( -(0.0) / ( -1.0) - inst.x[id]);
         }
     }

diff --git a/func_proc/neuron/func_proc.cpp b/func_proc/neuron/func_proc.cpp
@@ -331,20 +331,23 @@ namespace neuron {
 
     inline int set_x_42_test_func_proc(_nrn_mechanism_cache_range* _ml, test_func_proc_Instance& inst, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
         int ret_set_x_42 = 0;
+        auto v = inst.v_unused[id];
         set_x_a_test_func_proc(_ml, inst, id, _ppvar, _thread, _nt, 42.0);
         return ret_set_x_42;
     }
 
 
     inline int set_x_a_test_func_proc(_nrn_mechanism_cache_range* _ml, test_func_proc_Instance& inst, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double a) {
         int ret_set_x_a = 0;
+        auto v = inst.v_unused[id];
         inst.x[id] = a;
         return ret_set_x_a;
     }
 
 
     inline int set_a_x_test_func_proc(_nrn_mechanism_cache_range* _ml, test_func_proc_Instance& inst, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
         int ret_set_a_x = 0;
+        auto v = inst.v_unused[id];
         double a;
         a = inst.x[id];
         return ret_set_a_x;
@@ -353,6 +356,7 @@ namespace neuron {
 
     inline double x_plus_a_test_func_proc(_nrn_mechanism_cache_range* _ml, test_func_proc_Instance& inst, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double a) {
         double ret_x_plus_a = 0.0;
+        auto v = inst.v_unused[id];
         ret_x_plus_a = inst.x[id] + a;
         return ret_x_plus_a;
     }
@@ -366,7 +370,11 @@ namespace neuron {
         auto* const _ml = &_lmr;
         auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
-            auto& _ppvar = _ml_arg->pdata[id];
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
+            inst.v_unused[id] = v;
             set_a_x_test_func_proc(_ml, inst, id, _ppvar, _thread, _nt);
         }
     }

diff --git a/func_proc_pnt/neuron/func_proc_pnt.cpp b/func_proc_pnt/neuron/func_proc_pnt.cpp
@@ -265,20 +265,23 @@ namespace neuron {
 
     inline int set_x_42_test_func_proc_pnt(_nrn_mechanism_cache_range* _ml, test_func_proc_pnt_Instance& inst, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
         int ret_set_x_42 = 0;
+        auto v = inst.v_unused[id];
         inst.x[id] = 42.0;
         return ret_set_x_42;
     }
 
 
     inline int set_x_a_test_func_proc_pnt(_nrn_mechanism_cache_range* _ml, test_func_proc_pnt_Instance& inst, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double a) {
         int ret_set_x_a = 0;
+        auto v = inst.v_unused[id];
         inst.x[id] = a;
         return ret_set_x_a;
     }
 
 
     inline double x_plus_a_test_func_proc_pnt(_nrn_mechanism_cache_range* _ml, test_func_proc_pnt_Instance& inst, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double a) {
         double ret_x_plus_a = 0.0;
+        auto v = inst.v_unused[id];
         ret_x_plus_a = inst.x[id] + a;
         return ret_x_plus_a;
     }
@@ -292,7 +295,11 @@ namespace neuron {
         auto* const _ml = &_lmr;
         auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
-            auto& _ppvar = _ml_arg->pdata[id];
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
+            inst.v_unused[id] = v;
         }
     }
 

diff --git a/global_breakpoint/neuron/leonhard.cpp b/global_breakpoint/neuron/leonhard.cpp
@@ -182,7 +182,11 @@ namespace neuron {
         auto* const _ml = &_lmr;
         auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
-            auto& _ppvar = _ml_arg->pdata[id];
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
+            inst.v_unused[id] = v;
             inst.x[id] = 42.0;
         }
     }
@@ -196,6 +200,10 @@ namespace neuron {
         auto* const _ml = &_lmr;
         auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
             inst.x[id] = inst.global->c;
         }
     }

diff --git a/hodgkin_huxley/neuron/hodhux.cpp b/hodgkin_huxley/neuron/hodhux.cpp
@@ -212,10 +212,12 @@ namespace neuron {
         Prop * na_prop = need_memb(na_sym);
         _ppvar[0] = _nrn_mechanism_get_param_handle(na_prop, 0);
         _ppvar[1] = _nrn_mechanism_get_param_handle(na_prop, 3);
+        _ppvar[2] = _nrn_mechanism_get_param_handle(na_prop, 4);
         Symbol * k_sym = hoc_lookup("k_ion");
         Prop * k_prop = need_memb(k_sym);
         _ppvar[3] = _nrn_mechanism_get_param_handle(k_prop, 0);
         _ppvar[4] = _nrn_mechanism_get_param_handle(k_prop, 3);
+        _ppvar[5] = _nrn_mechanism_get_param_handle(k_prop, 4);
     }
 
 
@@ -377,6 +379,7 @@ namespace neuron {
 
     inline int states_hodhux(_nrn_mechanism_cache_range* _ml, hodhux_Instance& inst, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
         int ret_states = 0;
+        auto v = inst.v_unused[id];
         rates_hodhux(_ml, inst, id, _ppvar, _thread, _nt, v);
         inst.m[id] = inst.m[id] + inst.mexp[id] * (inst.minf[id] - inst.m[id]);
         inst.h[id] = inst.h[id] + inst.hexp[id] * (inst.hinf[id] - inst.h[id]);
@@ -411,6 +414,7 @@ namespace neuron {
 
     inline double vtrap_hodhux(_nrn_mechanism_cache_range* _ml, hodhux_Instance& inst, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double x, double y) {
         double ret_vtrap = 0.0;
+        auto v = inst.v_unused[id];
         if (fabs(x / y) < 1e-6) {
             ret_vtrap = y * (1.0 - x / y / 2.0);
         } else {
@@ -425,7 +429,14 @@ namespace neuron {
         auto inst = make_instance_hodhux(_lmr);
         auto node_data = make_node_data_hodhux(*_nt, *_ml_arg);
         auto nodecount = _ml_arg->nodecount;
+        auto* const _ml = &_lmr;
+        auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
+            inst.v_unused[id] = v;
             inst.ena[id] = (*inst.ion_ena[id]);
             inst.ek[id] = (*inst.ion_ek[id]);
             rates_hodhux(_ml, inst, id, _ppvar, _thread, _nt, v);
@@ -454,6 +465,8 @@ namespace neuron {
         auto inst = make_instance_hodhux(_lmr);
         auto node_data = make_node_data_hodhux(*_nt, *_ml_arg);
         auto nodecount = _ml_arg->nodecount;
+        auto* const _ml = &_lmr;
+        auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
             int node_id = node_data.nodeindices[id];
             double v = node_data.node_voltages[node_id];
@@ -481,7 +494,13 @@ namespace neuron {
         auto inst = make_instance_hodhux(_lmr);
         auto node_data = make_node_data_hodhux(*_nt, *_ml_arg);
         auto nodecount = _ml_arg->nodecount;
+        auto* const _ml = &_lmr;
+        auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
             inst.ena[id] = (*inst.ion_ena[id]);
             inst.ek[id] = (*inst.ion_ek[id]);
             rates_hodhux(_ml, inst, id, _ppvar, _thread, _nt, v);

diff --git a/net_receive/neuron/snapsyn.cpp b/net_receive/neuron/snapsyn.cpp
@@ -210,7 +210,11 @@ namespace neuron {
         auto* const _ml = &_lmr;
         auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
-            auto& _ppvar = _ml_arg->pdata[id];
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
+            inst.v_unused[id] = v;
             inst.g[id] = 0.0;
         }
     }
@@ -257,6 +261,10 @@ namespace neuron {
         auto* const _ml = &_lmr;
         auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
         }
     }
 

diff --git a/nonspecific_current/neuron/leonhard.cpp b/nonspecific_current/neuron/leonhard.cpp
@@ -181,7 +181,11 @@ namespace neuron {
         auto* const _ml = &_lmr;
         auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
-            auto& _ppvar = _ml_arg->pdata[id];
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
+            inst.v_unused[id] = v;
         }
     }
 
@@ -224,6 +228,10 @@ namespace neuron {
         auto* const _ml = &_lmr;
         auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
         }
     }
 

diff --git a/parameter/neuron/neuron_variables.cpp b/parameter/neuron/neuron_variables.cpp
@@ -180,7 +180,11 @@ namespace neuron {
         auto* const _ml = &_lmr;
         auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
-            auto& _ppvar = _ml_arg->pdata[id];
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
+            inst.v_unused[id] = v;
         }
     }
 
@@ -193,6 +197,10 @@ namespace neuron {
         auto* const _ml = &_lmr;
         auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
             inst.range_celsius[id] = *(inst.celsius);
         }
     }

diff --git a/parameter/neuron/test_parameter.cpp b/parameter/neuron/test_parameter.cpp
@@ -201,7 +201,11 @@ namespace neuron {
         auto* const _ml = &_lmr;
         auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
-            auto& _ppvar = _ml_arg->pdata[id];
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
+            inst.v_unused[id] = v;
         }
     }
 

diff --git a/point_process/neuron/test_pp.cpp b/point_process/neuron/test_pp.cpp
@@ -197,7 +197,11 @@ namespace neuron {
         auto* const _ml = &_lmr;
         auto* _thread = _ml_arg->_thread;
         for (int id = 0; id < nodecount; id++) {
-            auto& _ppvar = _ml_arg->pdata[id];
+
+            int node_id = node_data.nodeindices[id];
+            auto* _ppvar = _ml_arg->pdata[id];
+            auto v = node_data.node_voltages[node_id];
+            inst.v_unused[id] = v;
         }
     }