References for 'BlueBrain/nmodl#1364'.

BlueBrain · Oct 8, 2024 · e8c05cf · e8c05cf
1 parent 1b84e18
commit e8c05cf
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diff --git a/at_time/neuron/example.cpp b/at_time/neuron/example.cpp
@@ -144,6 +144,9 @@ namespace neuron {
 
     /* Mechanism procedures and functions */
     inline double f_example(_nrn_mechanism_cache_range& _lmc, example_Instance& inst, example_NodeData& node_data, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* nt, double _lx);
+    static void _apply_diffusion_function(ldifusfunc2_t _f, const _nrn_model_sorted_token& _sorted_token, NrnThread& _nt) {
+    }
+
     /* Neuron setdata functions */
     extern void _nrn_setdata_reg(int, void(*)(Prop*));
     static void _setdata(Prop* _prop) {
@@ -226,11 +229,11 @@ namespace neuron {
 
 
     void nrn_init_example(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_example(_lmc);
         auto node_data = make_node_data_example(*nt, *_ml_arg);
-        auto nodecount = _ml_arg->nodecount;
         auto* _thread = _ml_arg->_thread;
+        auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
             auto* _ppvar = _ml_arg->pdata[id];
             int node_id = node_data.nodeindices[id];
@@ -240,9 +243,10 @@ namespace neuron {
 
 
     static void nrn_jacob_example(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_example(_lmc);
         auto node_data = make_node_data_example(*nt, *_ml_arg);
+        auto* _thread = _ml_arg->_thread;
         auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
         }

diff --git a/builtin_functions/neuron/compile_only.cpp b/builtin_functions/neuron/compile_only.cpp
@@ -144,6 +144,9 @@ namespace neuron {
 
     /* Mechanism procedures and functions */
     inline double call_nrn_ghk_compile_only(_nrn_mechanism_cache_range& _lmc, compile_only_Instance& inst, compile_only_NodeData& node_data, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* nt);
+    static void _apply_diffusion_function(ldifusfunc2_t _f, const _nrn_model_sorted_token& _sorted_token, NrnThread& _nt) {
+    }
+
     /* Neuron setdata functions */
     extern void _nrn_setdata_reg(int, void(*)(Prop*));
     static void _setdata(Prop* _prop) {
@@ -226,11 +229,11 @@ namespace neuron {
 
 
     void nrn_init_compile_only(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_compile_only(_lmc);
         auto node_data = make_node_data_compile_only(*nt, *_ml_arg);
-        auto nodecount = _ml_arg->nodecount;
         auto* _thread = _ml_arg->_thread;
+        auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
             auto* _ppvar = _ml_arg->pdata[id];
             int node_id = node_data.nodeindices[id];
@@ -240,9 +243,10 @@ namespace neuron {
 
 
     static void nrn_jacob_compile_only(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_compile_only(_lmc);
         auto node_data = make_node_data_compile_only(*nt, *_ml_arg);
+        auto* _thread = _ml_arg->_thread;
         auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
         }

diff --git a/constant/neuron/constant.cpp b/constant/neuron/constant.cpp
@@ -149,6 +149,9 @@ namespace neuron {
 
     /* Mechanism procedures and functions */
     inline double foo_constant_mod(_nrn_mechanism_cache_range& _lmc, constant_mod_Instance& inst, constant_mod_NodeData& node_data, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* nt);
+    static void _apply_diffusion_function(ldifusfunc2_t _f, const _nrn_model_sorted_token& _sorted_token, NrnThread& _nt) {
+    }
+
     /* Neuron setdata functions */
     extern void _nrn_setdata_reg(int, void(*)(Prop*));
     static void _setdata(Prop* _prop) {
@@ -231,11 +234,11 @@ namespace neuron {
 
 
     void nrn_init_constant_mod(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_constant_mod(_lmc);
         auto node_data = make_node_data_constant_mod(*nt, *_ml_arg);
-        auto nodecount = _ml_arg->nodecount;
         auto* _thread = _ml_arg->_thread;
+        auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
             auto* _ppvar = _ml_arg->pdata[id];
             int node_id = node_data.nodeindices[id];
@@ -245,9 +248,10 @@ namespace neuron {
 
 
     static void nrn_jacob_constant_mod(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_constant_mod(_lmc);
         auto node_data = make_node_data_constant_mod(*nt, *_ml_arg);
+        auto* _thread = _ml_arg->_thread;
         auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
         }

diff --git a/constructor/neuron/art_ctor.cpp b/constructor/neuron/art_ctor.cpp
@@ -187,6 +187,9 @@ namespace neuron {
 
 
     /* Mechanism procedures and functions */
+    static void _apply_diffusion_function(ldifusfunc2_t _f, const _nrn_model_sorted_token& _sorted_token, NrnThread& _nt) {
+    }
+
     /* Point Process specific functions */
     static void* _hoc_create_pnt(Object* _ho) {
         return create_point_process(_pointtype, _ho);
@@ -262,22 +265,22 @@ namespace neuron {
 
 
     void nrn_init_art_ctor(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_art_ctor(_lmc);
-        auto node_data = make_node_data_art_ctor(*nt, *_ml_arg);
-        auto nodecount = _ml_arg->nodecount;
         auto* _thread = _ml_arg->_thread;
         auto _thread_vars = art_ctor_ThreadVariables(_thread[0].get<double*>());
+        auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
             auto* _ppvar = _ml_arg->pdata[id];
         }
     }
 
 
     static void nrn_jacob_art_ctor(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_art_ctor(_lmc);
-        auto node_data = make_node_data_art_ctor(*nt, *_ml_arg);
+        auto* _thread = _ml_arg->_thread;
+        auto _thread_vars = art_ctor_ThreadVariables(_thread[0].get<double*>());
         auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
         }

diff --git a/constructor/neuron/ctor.cpp b/constructor/neuron/ctor.cpp
@@ -187,6 +187,9 @@ namespace neuron {
 
 
     /* Mechanism procedures and functions */
+    static void _apply_diffusion_function(ldifusfunc2_t _f, const _nrn_model_sorted_token& _sorted_token, NrnThread& _nt) {
+    }
+
     /* Point Process specific functions */
     static void* _hoc_create_pnt(Object* _ho) {
         return create_point_process(_pointtype, _ho);
@@ -262,12 +265,12 @@ namespace neuron {
 
 
     void nrn_init_ctor(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_ctor(_lmc);
         auto node_data = make_node_data_ctor(*nt, *_ml_arg);
-        auto nodecount = _ml_arg->nodecount;
         auto* _thread = _ml_arg->_thread;
         auto _thread_vars = ctor_ThreadVariables(_thread[0].get<double*>());
+        auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
             auto* _ppvar = _ml_arg->pdata[id];
             int node_id = node_data.nodeindices[id];
@@ -277,9 +280,11 @@ namespace neuron {
 
 
     static void nrn_jacob_ctor(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_ctor(_lmc);
         auto node_data = make_node_data_ctor(*nt, *_ml_arg);
+        auto* _thread = _ml_arg->_thread;
+        auto _thread_vars = ctor_ThreadVariables(_thread[0].get<double*>());
         auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
         }

diff --git a/electrode_current/neuron/leonhard.cpp b/electrode_current/neuron/leonhard.cpp
@@ -152,6 +152,9 @@ namespace neuron {
 
 
     /* Mechanism procedures and functions */
+    static void _apply_diffusion_function(ldifusfunc2_t _f, const _nrn_model_sorted_token& _sorted_token, NrnThread& _nt) {
+    }
+
     /* Neuron setdata functions */
     extern void _nrn_setdata_reg(int, void(*)(Prop*));
     static void _setdata(Prop* _prop) {
@@ -191,11 +194,11 @@ namespace neuron {
 
 
     void nrn_init_leonhard(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_leonhard(_lmc);
         auto node_data = make_node_data_leonhard(*nt, *_ml_arg);
-        auto nodecount = _ml_arg->nodecount;
         auto* _thread = _ml_arg->_thread;
+        auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
             auto* _ppvar = _ml_arg->pdata[id];
             int node_id = node_data.nodeindices[id];
@@ -214,11 +217,11 @@ namespace neuron {
 
     /** update current */
     void nrn_cur_leonhard(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_leonhard(_lmc);
         auto node_data = make_node_data_leonhard(*nt, *_ml_arg);
-        auto nodecount = _ml_arg->nodecount;
         auto* _thread = _ml_arg->_thread;
+        auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
             int node_id = node_data.nodeindices[id];
             double v = node_data.node_voltages[node_id];
@@ -234,11 +237,11 @@ namespace neuron {
 
 
     void nrn_state_leonhard(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_leonhard(_lmc);
         auto node_data = make_node_data_leonhard(*nt, *_ml_arg);
-        auto nodecount = _ml_arg->nodecount;
         auto* _thread = _ml_arg->_thread;
+        auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
             int node_id = node_data.nodeindices[id];
             auto* _ppvar = _ml_arg->pdata[id];
@@ -248,9 +251,10 @@ namespace neuron {
 
 
     static void nrn_jacob_leonhard(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_leonhard(_lmc);
         auto node_data = make_node_data_leonhard(*nt, *_ml_arg);
+        auto* _thread = _ml_arg->_thread;
         auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
             int node_id = node_data.nodeindices[id];

diff --git a/external/neuron/dst.cpp b/external/neuron/dst.cpp
@@ -148,6 +148,9 @@ namespace neuron {
     /* Mechanism procedures and functions */
     inline double get_gbl_dst(_nrn_mechanism_cache_range& _lmc, dst_Instance& inst, dst_NodeData& node_data, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* nt);
     inline double get_param_dst(_nrn_mechanism_cache_range& _lmc, dst_Instance& inst, dst_NodeData& node_data, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* nt);
+    static void _apply_diffusion_function(ldifusfunc2_t _f, const _nrn_model_sorted_token& _sorted_token, NrnThread& _nt) {
+    }
+
     /* Neuron setdata functions */
     extern void _nrn_setdata_reg(int, void(*)(Prop*));
     static void _setdata(Prop* _prop) {
@@ -273,11 +276,11 @@ namespace neuron {
 
 
     void nrn_init_dst(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_dst(_lmc);
         auto node_data = make_node_data_dst(*nt, *_ml_arg);
-        auto nodecount = _ml_arg->nodecount;
         auto* _thread = _ml_arg->_thread;
+        auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
             auto* _ppvar = _ml_arg->pdata[id];
             int node_id = node_data.nodeindices[id];
@@ -287,9 +290,10 @@ namespace neuron {
 
 
     static void nrn_jacob_dst(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_dst(_lmc);
         auto node_data = make_node_data_dst(*nt, *_ml_arg);
+        auto* _thread = _ml_arg->_thread;
         auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
         }

diff --git a/external/neuron/src.cpp b/external/neuron/src.cpp
@@ -152,6 +152,9 @@ namespace neuron {
 
 
     /* Mechanism procedures and functions */
+    static void _apply_diffusion_function(ldifusfunc2_t _f, const _nrn_model_sorted_token& _sorted_token, NrnThread& _nt) {
+    }
+
     /* Neuron setdata functions */
     extern void _nrn_setdata_reg(int, void(*)(Prop*));
     static void _setdata(Prop* _prop) {
@@ -193,11 +196,11 @@ namespace neuron {
 
 
     void nrn_init_src(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_src(_lmc);
         auto node_data = make_node_data_src(*nt, *_ml_arg);
-        auto nodecount = _ml_arg->nodecount;
         auto* _thread = _ml_arg->_thread;
+        auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
             auto* _ppvar = _ml_arg->pdata[id];
             int node_id = node_data.nodeindices[id];
@@ -207,9 +210,10 @@ namespace neuron {
 
 
     static void nrn_jacob_src(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_src(_lmc);
         auto node_data = make_node_data_src(*nt, *_ml_arg);
+        auto* _thread = _ml_arg->_thread;
         auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
         }

diff --git a/function/neuron/artificial_functions.cpp b/function/neuron/artificial_functions.cpp
@@ -170,6 +170,9 @@ namespace neuron {
     /* Mechanism procedures and functions */
     inline double x_plus_a_art_functions(_nrn_mechanism_cache_range& _lmc, art_functions_Instance& inst, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* nt, double _la);
     inline double identity_art_functions(_nrn_mechanism_cache_range& _lmc, art_functions_Instance& inst, size_t id, Datum* _ppvar, Datum* _thread, NrnThread* nt, double _lv);
+    static void _apply_diffusion_function(ldifusfunc2_t _f, const _nrn_model_sorted_token& _sorted_token, NrnThread& _nt) {
+    }
+
     /* Point Process specific functions */
     static void* _hoc_create_pnt(Object* _ho) {
         return create_point_process(_pointtype, _ho);
@@ -282,11 +285,10 @@ namespace neuron {
 
 
     void nrn_init_art_functions(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_art_functions(_lmc);
-        auto node_data = make_node_data_art_functions(*nt, *_ml_arg);
-        auto nodecount = _ml_arg->nodecount;
         auto* _thread = _ml_arg->_thread;
+        auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
             auto* _ppvar = _ml_arg->pdata[id];
             inst.z[id] = inst.global->z0;
@@ -297,9 +299,9 @@ namespace neuron {
 
 
     static void nrn_jacob_art_functions(const _nrn_model_sorted_token& _sorted_token, NrnThread* nt, Memb_list* _ml_arg, int _type) {
-        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};
+        _nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _ml_arg->type()};
         auto inst = make_instance_art_functions(_lmc);
-        auto node_data = make_node_data_art_functions(*nt, *_ml_arg);
+        auto* _thread = _ml_arg->_thread;
         auto nodecount = _ml_arg->nodecount;
         for (int id = 0; id < nodecount; id++) {
         }