coreneuron.hpp

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/*
# =============================================================================
# Copyright (c) 2016 - 2021 Blue Brain Project/EPFL
#
# See top-level LICENSE file for details.
# =============================================================================.
*/
#pragma once
 
/***
 * Includes all headers required to communicate and run all methods
 * described in CoreNEURON, neurox, and mod2c C-generated mechanisms
 * functions.
 **/
 
 
#include <cstdio>
#include <cstdlib>
#include <cmath>
#include <string.h>
#include <vector>
#include <array>
 
#include "coreneuron/utils/randoms/nrnran123.h"     //Random Number Generator
#include "coreneuron/sim/scopmath/newton_struct.h"  //Newton Struct
#include "coreneuron/membrane_definitions.h"        //static definitions
#include "coreneuron/mechanism/mechanism.hpp"       //Memb_list and mechs info
 
#include "coreneuron/utils/memory.h"  //Memory alignments and padding
#include "coreneuron/nrnconf.h"
#include "coreneuron/sim/multicore.hpp"
#include "coreneuron/mechanism/mech_mapping.hpp"
 
namespace coreneuron {
 
// from nrnoc/capac.c
extern void nrn_init_capacitance(NrnThread*, Memb_list*, int);
extern void nrn_cur_capacitance(NrnThread* _nt, Memb_list* ml, int type);
extern void nrn_alloc_capacitance(double* data, Datum* pdata, int type);
 
// from nrnoc/eion.c
extern void nrn_init_ion(NrnThread*, Memb_list*, int);
extern void nrn_cur_ion(NrnThread* _nt, Memb_list* ml, int type);
extern void nrn_alloc_ion(double* data, Datum* pdata, int type);
extern void second_order_cur(NrnThread* _nt, int secondorder);
 
using DependencyTable = std::vector<std::vector<int>>;
 
/**
 * A class representing the CoreNEURON state, holding pointers to the various data structures
 *
 * The pointers to "global" data such as the NrnThread, Memb_list and Memb_func data structures
 * are managed here. they logically share their lifetime and runtime scope with instances of
 * this class.
 */
class CoreNeuron {
    /**
     * map if mech is a point process
     * In the future only a field of Mechanism class
     */
    std::vector<char> pnt_map; /* so prop_free can know its a point mech*/
 
    /** Vector mapping the types (IDs) of different mechanisms of mod files between NEURON and
     * CoreNEURON
     */
    std::vector<int> different_mechanism_type;
 
    /**
     * dependency helper filled by calls to hoc_register_dparam_semantics
     * used when nrn_mech_depend is called
     * vector-of-vector DS. First idx is the mech, second idx is the dependent mech.
     */
    DependencyTable ion_write_dependency;
 
    std::vector<Memb_func> memb_funcs;
 
    /**
     * Net send / Net receive
     * only used in CoreNEURON for book keeping synapse mechs, should go into CoreNEURON class
     */
    std::vector<std::pair<NetBufReceive_t, int>> net_buf_receive;
    std::vector<int> net_buf_send_type;
 
    /**
     * before-after-blocks from nmodl are registered here as function pointers
     */
    std::array<BAMech*, BEFORE_AFTER_SIZE> bamech;
 
    /**
     * Internal lookup tables. Number of float and int variables in each mechanism and memory layout
     * future --> mech class
     */
    std::vector<int> nrn_prop_param_size;
    std::vector<int> nrn_prop_dparam_size;
    std::vector<int> nrn_mech_data_layout; /* 1 AoS (default), 0 SoA */
    /* array is parallel to memb_func. All are 0 except 1 for ARTIFICIAL_CELL */
    std::vector<short> nrn_artcell_qindex;
    std::vector<bool> nrn_is_artificial;
 
    /**
     * Net Receive function pointer lookup tables
     */
    std::vector<pnt_receive_t> pnt_receive; /* for synaptic events. */
    std::vector<pnt_receive_t> pnt_receive_init;
    std::vector<short> pnt_receive_size;
 
    /**
     * Holds function pointers for WATCH callback
     */
    std::vector<nrn_watch_check_t> nrn_watch_check;
 
    /**
     * values are type numbers of mechanisms which do net_send call
     * related to NMODL net_event()
     *
     */
    std::vector<int> nrn_has_net_event;
 
    /**
     * inverse of nrn_has_net_event_ maps the values of nrn_has_net_event_ to the index of
     * ptntype2presyn
     */
    std::vector<int> pnttype2presyn;
 
 
    std::vector<bbcore_read_t> nrn_bbcore_read;
    std::vector<bbcore_write_t> nrn_bbcore_write;
 
  public:
    auto& get_memb_funcs() {
        return memb_funcs;
    }
 
    auto& get_memb_func(size_t idx) {
        return memb_funcs[idx];
    }
 
    auto& get_different_mechanism_type() {
        return different_mechanism_type;
    }
 
    auto& get_pnt_map() {
        return pnt_map;
    }
 
    auto& get_ion_write_dependency() {
        return ion_write_dependency;
    }
 
    auto& get_net_buf_receive() {
        return net_buf_receive;
    }
 
    auto& get_net_buf_send_type() {
        return net_buf_send_type;
    }
 
    auto& get_bamech() {
        return bamech;
    }
 
    auto& get_prop_param_size() {
        return nrn_prop_param_size;
    }
 
    auto& get_prop_dparam_size() {
        return nrn_prop_dparam_size;
    }
 
    auto& get_mech_data_layout() {
        return nrn_mech_data_layout;
    }
 
    auto& get_is_artificial() {
        return nrn_is_artificial;
    }
 
    auto& get_artcell_qindex() {
        return nrn_artcell_qindex;
    }
 
    auto& get_pnt_receive() {
        return pnt_receive;
    }
 
    auto& get_pnt_receive_init() {
        return pnt_receive_init;
    }
 
    auto& get_pnt_receive_size() {
        return pnt_receive_size;
    }
 
    auto& get_watch_check() {
        return nrn_watch_check;
    }
 
    auto& get_has_net_event() {
        return nrn_has_net_event;
    }
 
    auto& get_pnttype2presyn() {
        return pnttype2presyn;
    }
 
    auto& get_bbcore_read() {
        return nrn_bbcore_read;
    }
 
    auto& get_bbcore_write() {
        return nrn_bbcore_write;
    }
};
 
extern CoreNeuron corenrn;
 
}  // namespace coreneuron