References for 'BlueBrain/nmodl#1444'.

net_receive/coreneuron/for_netcons_syn.cpp

@@ -0,0 +1,362 @@
+/*********************************************************
+Model Name      : ForNetconsSyn
+Filename        : for_netcons_syn.mod
+NMODL Version   : 7.7.0
+Vectorized      : true
+Threadsafe      : true
+Created         : DATE
+Simulator       : CoreNEURON
+Backend         : C++ (api-compatibility)
+NMODL Compiler  : VERSION
+*********************************************************/
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include <coreneuron/gpu/nrn_acc_manager.hpp>
+#include <coreneuron/mechanism/mech/mod2c_core_thread.hpp>
+#include <coreneuron/mechanism/register_mech.hpp>
+#include <coreneuron/nrnconf.h>
+#include <coreneuron/nrniv/nrniv_decl.h>
+#include <coreneuron/sim/multicore.hpp>
+#include <coreneuron/sim/scopmath/newton_thread.hpp>
+#include <coreneuron/utils/ivocvect.hpp>
+#include <coreneuron/utils/nrnoc_aux.hpp>
+#include <coreneuron/utils/randoms/nrnran123.h>
+
+
+namespace coreneuron {
+    #ifndef NRN_PRCELLSTATE
+    #define NRN_PRCELLSTATE 0
+    #endif
+
+
+    /** channel information */
+    static const char *mechanism_info[] = {
+        "7.7.0",
+        "ForNetconsSyn",
+        0,
+        "a0",
+        0,
+        0,
+        0
+    };
+
+
+    /** all global variables */
+    struct ForNetconsSyn_Store {
+        int point_type{};
+        int reset{};
+        int mech_type{};
+    };
+    static_assert(std::is_trivially_copy_constructible_v<ForNetconsSyn_Store>);
+    static_assert(std::is_trivially_move_constructible_v<ForNetconsSyn_Store>);
+    static_assert(std::is_trivially_copy_assignable_v<ForNetconsSyn_Store>);
+    static_assert(std::is_trivially_move_assignable_v<ForNetconsSyn_Store>);
+    static_assert(std::is_trivially_destructible_v<ForNetconsSyn_Store>);
+    ForNetconsSyn_Store ForNetconsSyn_global;
+
+
+    /** all mechanism instance variables and global variables */
+    struct ForNetconsSyn_Instance  {
+        double* a0{};
+        double* v_unused{};
+        double* tsave{};
+        const double* node_area{};
+        const int* point_process{};
+        int* fornetcon_data{};
+        ForNetconsSyn_Store* global{&ForNetconsSyn_global};
+    };
+
+
+    /** connect global (scalar) variables to hoc -- */
+    static DoubScal hoc_scalar_double[] = {
+        {nullptr, nullptr}
+    };
+
+
+    /** connect global (array) variables to hoc -- */
+    static DoubVec hoc_vector_double[] = {
+        {nullptr, nullptr, 0}
+    };
+
+
+    static inline int first_pointer_var_index() {
+        return -1;
+    }
+
+
+    static inline int first_random_var_index() {
+        return -1;
+    }
+
+
+    static inline int num_net_receive_args() {
+        return 2;
+    }
+
+
+    static inline int float_variables_size() {
+        return 3;
+    }
+
+
+    static inline int int_variables_size() {
+        return 3;
+    }
+
+
+    static inline int get_mech_type() {
+        return ForNetconsSyn_global.mech_type;
+    }
+
+
+    static inline Memb_list* get_memb_list(NrnThread* nt) {
+        if (!nt->_ml_list) {
+            return nullptr;
+        }
+        return nt->_ml_list[get_mech_type()];
+    }
+
+
+    static inline void* mem_alloc(size_t num, size_t size, size_t alignment = 64) {
+        size_t aligned_size = ((num*size + alignment - 1) / alignment) * alignment;
+        void* ptr = aligned_alloc(alignment, aligned_size);
+        memset(ptr, 0, aligned_size);
+        return ptr;
+    }
+
+
+    static inline void mem_free(void* ptr) {
+        free(ptr);
+    }
+
+
+    static inline void coreneuron_abort() {
+        abort();
+    }
+
+    // Allocate instance structure
+    static void nrn_private_constructor_ForNetconsSyn(NrnThread* nt, Memb_list* ml, int type) {
+        assert(!ml->instance);
+        assert(!ml->global_variables);
+        assert(ml->global_variables_size == 0);
+        auto* const inst = new ForNetconsSyn_Instance{};
+        assert(inst->global == &ForNetconsSyn_global);
+        ml->instance = inst;
+        ml->global_variables = inst->global;
+        ml->global_variables_size = sizeof(ForNetconsSyn_Store);
+    }
+
+    // Deallocate the instance structure
+    static void nrn_private_destructor_ForNetconsSyn(NrnThread* nt, Memb_list* ml, int type) {
+        auto* const inst = static_cast<ForNetconsSyn_Instance*>(ml->instance);
+        assert(inst);
+        assert(inst->global);
+        assert(inst->global == &ForNetconsSyn_global);
+        assert(inst->global == ml->global_variables);
+        assert(ml->global_variables_size == sizeof(ForNetconsSyn_Store));
+        delete inst;
+        ml->instance = nullptr;
+        ml->global_variables = nullptr;
+        ml->global_variables_size = 0;
+    }
+
+    /** initialize mechanism instance variables */
+    static inline void setup_instance(NrnThread* nt, Memb_list* ml) {
+        auto* const inst = static_cast<ForNetconsSyn_Instance*>(ml->instance);
+        assert(inst);
+        assert(inst->global);
+        assert(inst->global == &ForNetconsSyn_global);
+        assert(inst->global == ml->global_variables);
+        assert(ml->global_variables_size == sizeof(ForNetconsSyn_Store));
+        int pnodecount = ml->_nodecount_padded;
+        Datum* indexes = ml->pdata;
+        inst->a0 = ml->data+0*pnodecount;
+        inst->v_unused = ml->data+1*pnodecount;
+        inst->tsave = ml->data+2*pnodecount;
+        inst->node_area = nt->_data;
+        inst->point_process = ml->pdata;
+        inst->fornetcon_data = ml->pdata;
+    }
+
+
+
+    static void nrn_alloc_ForNetconsSyn(double* data, Datum* indexes, int type) {
+        // do nothing
+    }
+
+
+    void nrn_constructor_ForNetconsSyn(NrnThread* nt, Memb_list* ml, int type) {
+        #ifndef CORENEURON_BUILD
+        int nodecount = ml->nodecount;
+        int pnodecount = ml->_nodecount_padded;
+        const int* node_index = ml->nodeindices;
+        double* data = ml->data;
+        const double* voltage = nt->_actual_v;
+        Datum* indexes = ml->pdata;
+        ThreadDatum* thread = ml->_thread;
+        auto* const inst = static_cast<ForNetconsSyn_Instance*>(ml->instance);
+
+        #endif
+    }
+
+
+    void nrn_destructor_ForNetconsSyn(NrnThread* nt, Memb_list* ml, int type) {
+        #ifndef CORENEURON_BUILD
+        int nodecount = ml->nodecount;
+        int pnodecount = ml->_nodecount_padded;
+        const int* node_index = ml->nodeindices;
+        double* data = ml->data;
+        const double* voltage = nt->_actual_v;
+        Datum* indexes = ml->pdata;
+        ThreadDatum* thread = ml->_thread;
+        auto* const inst = static_cast<ForNetconsSyn_Instance*>(ml->instance);
+
+        #endif
+    }
+
+
+    /** initialize block for net receive */
+    static void net_init(Point_process* pnt, int weight_index, double flag) {
+        int tid = pnt->_tid;
+        int id = pnt->_i_instance;
+        double v = 0;
+        NrnThread* nt = nrn_threads + tid;
+        Memb_list* ml = nt->_ml_list[pnt->_type];
+        int nodecount = ml->nodecount;
+        int pnodecount = ml->_nodecount_padded;
+        double* data = ml->data;
+        double* weights = nt->weights;
+        Datum* indexes = ml->pdata;
+        ThreadDatum* thread = ml->_thread;
+        auto* const inst = static_cast<ForNetconsSyn_Instance*>(ml->instance);
+
+        double* a = weights + weight_index + 1;
+        (*a) = inst->a0[id];
+        auto& nsb = ml->_net_send_buffer;
+    }
+
+
+    static inline void net_receive_kernel_ForNetconsSyn(double t, Point_process* pnt, ForNetconsSyn_Instance* inst, NrnThread* nt, Memb_list* ml, int weight_index, double flag) {
+        int tid = pnt->_tid;
+        int id = pnt->_i_instance;
+        double v = 0;
+        int nodecount = ml->nodecount;
+        int pnodecount = ml->_nodecount_padded;
+        double* data = ml->data;
+        double* weights = nt->weights;
+        Datum* indexes = ml->pdata;
+        ThreadDatum* thread = ml->_thread;
+
+        double* a = weights + weight_index + 1;
+        inst->tsave[id] = t;
+        {
+            const size_t offset = 2*pnodecount + id;
+            const size_t for_netcon_start = nt->_fornetcon_perm_indices[indexes[offset]];
+            const size_t for_netcon_end = nt->_fornetcon_perm_indices[indexes[offset] + 1];
+            for (auto i = for_netcon_start; i < for_netcon_end; ++i) {
+                weights[1 + nt->_fornetcon_weight_perm[i]] = 2.0 * weights[1 + nt->_fornetcon_weight_perm[i]];
+            }
+
+        }
+    }
+
+
+    static void net_receive_ForNetconsSyn(Point_process* pnt, int weight_index, double flag) {
+        NrnThread* nt = nrn_threads + pnt->_tid;
+        Memb_list* ml = get_memb_list(nt);
+        NetReceiveBuffer_t* nrb = ml->_net_receive_buffer;
+        if (nrb->_cnt >= nrb->_size) {
+            realloc_net_receive_buffer(nt, ml);
+        }
+        int id = nrb->_cnt;
+        nrb->_pnt_index[id] = pnt-nt->pntprocs;
+        nrb->_weight_index[id] = weight_index;
+        nrb->_nrb_t[id] = nt->_t;
+        nrb->_nrb_flag[id] = flag;
+        nrb->_cnt++;
+    }
+
+
+    void net_buf_receive_ForNetconsSyn(NrnThread* nt) {
+        Memb_list* ml = get_memb_list(nt);
+        if (!ml) {
+            return;
+        }
+
+        NetReceiveBuffer_t* nrb = ml->_net_receive_buffer;
+        auto* const inst = static_cast<ForNetconsSyn_Instance*>(ml->instance);
+        int count = nrb->_displ_cnt;
+        #pragma omp simd
+        #pragma ivdep
+        for (int i = 0; i < count; i++) {
+            int start = nrb->_displ[i];
+            int end = nrb->_displ[i+1];
+            for (int j = start; j < end; j++) {
+                int index = nrb->_nrb_index[j];
+                int offset = nrb->_pnt_index[index];
+                double t = nrb->_nrb_t[index];
+                int weight_index = nrb->_weight_index[index];
+                double flag = nrb->_nrb_flag[index];
+                Point_process* point_process = nt->pntprocs + offset;
+                net_receive_kernel_ForNetconsSyn(t, point_process, inst, nt, ml, weight_index, flag);
+            }
+        }
+        nrb->_displ_cnt = 0;
+        nrb->_cnt = 0;
+    }
+
+
+    /** initialize channel */
+    void nrn_init_ForNetconsSyn(NrnThread* nt, Memb_list* ml, int type) {
+        int nodecount = ml->nodecount;
+        int pnodecount = ml->_nodecount_padded;
+        const int* node_index = ml->nodeindices;
+        double* data = ml->data;
+        const double* voltage = nt->_actual_v;
+        Datum* indexes = ml->pdata;
+        ThreadDatum* thread = ml->_thread;
+
+        setup_instance(nt, ml);
+        auto* const inst = static_cast<ForNetconsSyn_Instance*>(ml->instance);
+
+        if (_nrn_skip_initmodel == 0) {
+            #pragma omp simd
+            #pragma ivdep
+            for (int id = 0; id < nodecount; id++) {
+                inst->tsave[id] = -1e20;
+                int node_id = node_index[id];
+                double v = voltage[node_id];
+                #if NRN_PRCELLSTATE
+                inst->v_unused[id] = v;
+                #endif
+            }
+        }
+    }
+
+
+    /** register channel with the simulator */
+    void _for_netcons_syn_reg() {
+
+        int mech_type = nrn_get_mechtype("ForNetconsSyn");
+        ForNetconsSyn_global.mech_type = mech_type;
+        if (mech_type == -1) {
+            return;
+        }
+
+        _nrn_layout_reg(mech_type, 0);
+        point_register_mech(mechanism_info, nrn_alloc_ForNetconsSyn, nullptr, nullptr, nullptr, nrn_init_ForNetconsSyn, nrn_private_constructor_ForNetconsSyn, nrn_private_destructor_ForNetconsSyn, first_pointer_var_index(), nullptr, nullptr, 1);
+
+        hoc_register_prop_size(mech_type, float_variables_size(), int_variables_size());
+        hoc_register_dparam_semantics(mech_type, 0, "area");
+        hoc_register_dparam_semantics(mech_type, 1, "pntproc");
+        hoc_register_dparam_semantics(mech_type, 2, "fornetcon");
+        hoc_register_net_receive_buffering(net_buf_receive_ForNetconsSyn, mech_type);
+        set_pnt_receive(mech_type, net_receive_ForNetconsSyn, net_init, num_net_receive_args());
+        add_nrn_fornetcons(mech_type, 2);
+        hoc_register_var(hoc_scalar_double, hoc_vector_double, NULL);
+    }
+}