From 366c1d1247004815a62d96a2c408ebe98d6b8369 Mon Sep 17 00:00:00 2001
From: Sam Yates <halfflat@gmail.com>
Date: Thu, 23 May 2019 11:11:06 +0200
Subject: [PATCH] Generalized ion names (#749)
* Replace ionKind enumerations with corresponding string values.
* Rename `ion.hpp` as `ion_info.hpp`.
* Re-jig 'nonspecific' current handling in modcc: make explicit the external source of the corresponding current variable, and treat as non-indexed those locals with an external variable that has no data source, as opposed to special-casing the `ionKind::nonspecific` value.
* Add another field in ion dependency information that captures a write to an ionic reversal potential.
Fixes #748.
---
arbor/backends/gpu/mechanism.hpp | 4 +-
arbor/backends/gpu/shared_state.cpp | 7 +--
arbor/backends/gpu/shared_state.hpp | 5 ++-
arbor/backends/multicore/mechanism.hpp | 4 +-
arbor/backends/multicore/shared_state.cpp | 9 ++--
arbor/backends/multicore/shared_state.hpp | 21 ++++-----
arbor/fvm_layout.cpp | 4 +-
arbor/fvm_layout.hpp | 4 +-
arbor/fvm_lowered_cell_impl.hpp | 10 +++--
arbor/include/arbor/cable_cell.hpp | 9 ++--
arbor/include/arbor/ion.hpp | 30 -------------
arbor/include/arbor/ion_info.hpp | 11 +++++
arbor/include/arbor/mechanism.hpp | 1 -
arbor/include/arbor/mechinfo.hpp | 5 +--
modcc/blocks.hpp | 6 +--
modcc/expression.cpp | 8 ++--
modcc/expression.hpp | 44 +++++++++---------
modcc/identifier.hpp | 50 ++-------------------
modcc/module.cpp | 54 +++++++++++++++--------
modcc/module.hpp | 8 ++--
modcc/parser.cpp | 25 +++--------
modcc/printer/cprinter.cpp | 5 +--
modcc/printer/cudaprinter.cpp | 9 ++--
modcc/printer/infoprinter.cpp | 6 +--
modcc/printer/printerutil.cpp | 2 +-
modcc/symdiff.cpp | 1 +
test/unit/test_fvm_layout.cpp | 14 +++---
test/unit/test_fvm_lowered.cpp | 6 +--
28 files changed, 151 insertions(+), 211 deletions(-)
delete mode 100644 arbor/include/arbor/ion.hpp
create mode 100644 arbor/include/arbor/ion_info.hpp
diff --git a/arbor/backends/gpu/mechanism.hpp b/arbor/backends/gpu/mechanism.hpp
index 98e70ce3..94144bf3 100644
--- a/arbor/backends/gpu/mechanism.hpp
+++ b/arbor/backends/gpu/mechanism.hpp
@@ -99,10 +99,10 @@ protected:
using field_default_entry = std::pair<const char*, value_type>;
using mechanism_field_default_table = std::vector<field_default_entry>;
- using ion_state_entry = std::pair<ionKind, ion_state_view*>;
+ using ion_state_entry = std::pair<const char*, ion_state_view*>;
using mechanism_ion_state_table = std::vector<ion_state_entry>;
- using ion_index_entry = std::pair<ionKind, const index_type**>;
+ using ion_index_entry = std::pair<const char*, const index_type**>;
using mechanism_ion_index_table = std::vector<ion_index_entry>;
virtual void nrn_init() = 0;
diff --git a/arbor/backends/gpu/shared_state.cpp b/arbor/backends/gpu/shared_state.cpp
index 1f8c7331..149f0bd5 100644
--- a/arbor/backends/gpu/shared_state.cpp
+++ b/arbor/backends/gpu/shared_state.cpp
@@ -3,7 +3,7 @@
#include <arbor/constants.hpp>
#include <arbor/fvm_types.hpp>
-#include <arbor/ion.hpp>
+#include <arbor/ion_info.hpp>
#include "backends/event.hpp"
#include "backends/gpu/gpu_store_types.hpp"
@@ -132,13 +132,14 @@ shared_state::shared_state(
{}
void shared_state::add_ion(
+ const std::string& ion_name,
ion_info info,
const std::vector<fvm_index_type>& cv,
const std::vector<fvm_value_type>& iconc_norm_area,
const std::vector<fvm_value_type>& econc_norm_area)
{
ion_data.emplace(std::piecewise_construct,
- std::forward_as_tuple(info.kind),
+ std::forward_as_tuple(ion_name),
std::forward_as_tuple(info, cv, iconc_norm_area, econc_norm_area, 1u));
}
@@ -210,7 +211,7 @@ std::ostream& operator<<(std::ostream& o, shared_state& s) {
o << " current " << s.current_density << "\n";
o << " conductivity " << s.conductivity << "\n";
for (auto& ki: s.ion_data) {
- auto kn = to_string(ki.first);
+ auto& kn = ki.first;
auto& i = const_cast<ion_state&>(ki.second);
o << " " << kn << ".current_density " << i.iX_ << "\n";
o << " " << kn << ".reversal_potential " << i.eX_ << "\n";
diff --git a/arbor/backends/gpu/shared_state.hpp b/arbor/backends/gpu/shared_state.hpp
index fe662720..27174810 100644
--- a/arbor/backends/gpu/shared_state.hpp
+++ b/arbor/backends/gpu/shared_state.hpp
@@ -6,7 +6,7 @@
#include <vector>
#include <arbor/fvm_types.hpp>
-#include <arbor/ion.hpp>
+#include <arbor/ion_info.hpp>
#include "backends/gpu/gpu_store_types.hpp"
@@ -80,7 +80,7 @@ struct shared_state {
array conductivity; // Maps CV index to membrane conductivity [kS/m²].
array temperature_degC; // Global temperature [°C] (length 1 array).
- std::unordered_map<ionKind, ion_state> ion_data;
+ std::unordered_map<std::string, ion_state> ion_data;
deliverable_event_stream deliverable_events;
@@ -94,6 +94,7 @@ struct shared_state {
);
void add_ion(
+ const std::string& ion_name,
ion_info info,
const std::vector<fvm_index_type>& cv,
const std::vector<fvm_value_type>& iconc_norm_area,
diff --git a/arbor/backends/multicore/mechanism.hpp b/arbor/backends/multicore/mechanism.hpp
index f3819ab1..8054c656 100644
--- a/arbor/backends/multicore/mechanism.hpp
+++ b/arbor/backends/multicore/mechanism.hpp
@@ -112,10 +112,10 @@ protected:
using field_default_entry = std::pair<const char*, value_type>;
using mechanism_field_default_table = std::vector<field_default_entry>;
- using ion_state_entry = std::pair<ionKind, ion_state_view*>;
+ using ion_state_entry = std::pair<const char*, ion_state_view*>;
using mechanism_ion_state_table = std::vector<ion_state_entry>;
- using ion_index_entry = std::pair<ionKind, iarray*>;
+ using ion_index_entry = std::pair<const char*, iarray*>;
using mechanism_ion_index_table = std::vector<ion_index_entry>;
virtual void nrn_init() = 0;
diff --git a/arbor/backends/multicore/shared_state.cpp b/arbor/backends/multicore/shared_state.cpp
index 6af8064d..c2917d2f 100644
--- a/arbor/backends/multicore/shared_state.cpp
+++ b/arbor/backends/multicore/shared_state.cpp
@@ -10,7 +10,7 @@
#include <arbor/common_types.hpp>
#include <arbor/constants.hpp>
#include <arbor/fvm_types.hpp>
-#include <arbor/ion.hpp>
+#include <arbor/ion_info.hpp>
#include <arbor/math.hpp>
#include <arbor/simd/simd.hpp>
@@ -149,13 +149,14 @@ shared_state::shared_state(
}
void shared_state::add_ion(
+ const std::string& ion_name,
ion_info info,
const std::vector<fvm_index_type>& cv,
const std::vector<fvm_value_type>& iconc_norm_area,
const std::vector<fvm_value_type>& econc_norm_area)
{
ion_data.emplace(std::piecewise_construct,
- std::forward_as_tuple(info.kind),
+ std::forward_as_tuple(ion_name),
std::forward_as_tuple(info, cv, iconc_norm_area, econc_norm_area, alignment));
}
@@ -266,8 +267,8 @@ std::ostream& operator<<(std::ostream& out, const shared_state& s) {
out << "voltage " << csv(s.voltage) << "\n";
out << "current " << csv(s.current_density) << "\n";
out << "conductivity " << csv(s.conductivity) << "\n";
- for (auto& ki: s.ion_data) {
- auto kn = to_string(ki.first);
+ for (const auto& ki: s.ion_data) {
+ auto& kn = ki.first;
auto& i = const_cast<ion_state&>(ki.second);
out << kn << ".current_density " << csv(i.iX_) << "\n";
out << kn << ".reversal_potential " << csv(i.eX_) << "\n";
diff --git a/arbor/backends/multicore/shared_state.hpp b/arbor/backends/multicore/shared_state.hpp
index be3b5725..bedfaf57 100644
--- a/arbor/backends/multicore/shared_state.hpp
+++ b/arbor/backends/multicore/shared_state.hpp
@@ -10,7 +10,7 @@
#include <arbor/assert.hpp>
#include <arbor/common_types.hpp>
#include <arbor/fvm_types.hpp>
-#include <arbor/ion.hpp>
+#include <arbor/ion_info.hpp>
#include <arbor/simd/simd.hpp>
#include "backends/event.hpp"
@@ -42,15 +42,15 @@ namespace multicore {
struct ion_state {
unsigned alignment = 1; // Alignment and padding multiple.
- iarray node_index_; // Instance to CV map.
- array iX_; // (nA) current
- array eX_; // (mV) reversal potential
- array Xi_; // (mM) internal concentration
- array Xo_; // (mM) external concentration
- array weight_Xi_; // (1) concentration weight internal
- array weight_Xo_; // (1) concentration weight external
+ iarray node_index_; // Instance to CV map.
+ array iX_; // (nA) current
+ array eX_; // (mV) reversal potential
+ array Xi_; // (mM) internal concentration
+ array Xo_; // (mM) external concentration
+ array weight_Xi_; // (1) concentration weight internal
+ array weight_Xo_; // (1) concentration weight external
- int charge; // charge of ionic species
+ int charge; // charge of ionic species
fvm_value_type default_int_concentration; // (mM) default internal concentration
fvm_value_type default_ext_concentration; // (mM) default external concentration
@@ -99,7 +99,7 @@ struct shared_state {
array conductivity; // Maps CV index to membrane conductivity [kS/m²].
fvm_value_type temperature_degC; // Global temperature [°C].
- std::unordered_map<ionKind, ion_state> ion_data;
+ std::unordered_map<std::string, ion_state> ion_data;
deliverable_event_stream deliverable_events;
@@ -113,6 +113,7 @@ struct shared_state {
);
void add_ion(
+ const std::string& ion_name,
ion_info info,
const std::vector<fvm_index_type>& cv,
const std::vector<fvm_value_type>& iconc_norm_area,
diff --git a/arbor/fvm_layout.cpp b/arbor/fvm_layout.cpp
index 1612734b..144aaf5b 100644
--- a/arbor/fvm_layout.cpp
+++ b/arbor/fvm_layout.cpp
@@ -306,10 +306,10 @@ fvm_mechanism_data fvm_build_mechanism_data(const mechanism_catalogue& catalogue
// Record for each stimulus the CV and clamp data.
std::vector<std::pair<size_type, i_clamp>> stimuli;
- // Temporary table for presence of ion channels, mapping ionKind to _sorted_
+ // Temporary table for presence of ion channels, mapping ion name to _sorted_
// collection of segment indices.
- std::unordered_map<ionKind, std::set<size_type>> ion_segments;
+ std::unordered_map<std::string, std::set<size_type>> ion_segments;
auto update_paramset_and_validate =
[&catalogue]
diff --git a/arbor/fvm_layout.hpp b/arbor/fvm_layout.hpp
index 459fb513..e470a719 100644
--- a/arbor/fvm_layout.hpp
+++ b/arbor/fvm_layout.hpp
@@ -133,8 +133,8 @@ struct fvm_mechanism_data {
// Mechanism config, indexed by mechanism name.
std::unordered_map<std::string, fvm_mechanism_config> mechanisms;
- // Ion config, indexed by ionKind.
- std::unordered_map<ionKind, fvm_ion_config> ions;
+ // Ion config, indexed by ion name.
+ std::unordered_map<std::string, fvm_ion_config> ions;
// Total number of targets (point-mechanism points)
std::size_t ntarget = 0;
diff --git a/arbor/fvm_lowered_cell_impl.hpp b/arbor/fvm_lowered_cell_impl.hpp
index c3e1d8da..2e5574fc 100644
--- a/arbor/fvm_lowered_cell_impl.hpp
+++ b/arbor/fvm_lowered_cell_impl.hpp
@@ -18,7 +18,6 @@
#include <arbor/assert.hpp>
#include <arbor/common_types.hpp>
-#include <arbor/ion.hpp>
#include <arbor/recipe.hpp>
#include "builtin_mechanisms.hpp"
@@ -404,10 +403,13 @@ void fvm_lowered_cell_impl<B>::initialize(
// Instantiate mechanisms and ions.
for (auto& i: mech_data.ions) {
- ionKind kind = i.first;
+ const std::string& ion_name = i.first;
- if (auto ion = value_by_key(global_props.ion_default, to_string(kind))) {
- state_->add_ion(ion.value(), i.second.cv, i.second.iconc_norm_area, i.second.econc_norm_area);
+ if (auto ion = value_by_key(global_props.ion_default, ion_name)) {
+ state_->add_ion(ion_name, ion.value(), i.second.cv, i.second.iconc_norm_area, i.second.econc_norm_area);
+ }
+ else {
+ throw cable_cell_error("unrecognized ion '"+ion_name+"' in mechanism");
}
}
diff --git a/arbor/include/arbor/cable_cell.hpp b/arbor/include/arbor/cable_cell.hpp
index dd865de8..14be4c23 100644
--- a/arbor/include/arbor/cable_cell.hpp
+++ b/arbor/include/arbor/cable_cell.hpp
@@ -7,7 +7,7 @@
#include <arbor/arbexcept.hpp>
#include <arbor/common_types.hpp>
#include <arbor/constants.hpp>
-#include <arbor/ion.hpp>
+#include <arbor/ion_info.hpp>
#include <arbor/mechcat.hpp>
#include <arbor/morphology.hpp>
#include <arbor/segment.hpp>
@@ -81,11 +81,10 @@ struct cable_cell_global_properties {
//
// Defaults below chosen to match NEURON.
- // Ion species currently limited to just "ca", "na", "k".
std::unordered_map<std::string, ion_info> ion_default = {
- {"ca", { ionKind::ca, 2, 5e-5, 2. }},
- {"na", { ionKind::na, 1, 10., 140.}},
- {"k", { ionKind::k, 1, 54.4, 2.5 }}
+ {"ca", { 2, 5e-5, 2. }},
+ {"na", { 1, 10., 140.}},
+ {"k", { 1, 54.4, 2.5 }}
};
double temperature_K = constant::hh_squid_temp; // [K]
diff --git a/arbor/include/arbor/ion.hpp b/arbor/include/arbor/ion.hpp
deleted file mode 100644
index b0bd0c3c..00000000
--- a/arbor/include/arbor/ion.hpp
+++ /dev/null
@@ -1,30 +0,0 @@
-#pragma once
-
-#include <stdexcept>
-#include <string>
-
-namespace arb {
-
-// Fixed set of ion species (to be generalized in the future):
-
-enum class ionKind {ca, na, k};
-inline std::string to_string(ionKind k) {
- switch (k) {
- case ionKind::ca: return "ca";
- case ionKind::na: return "na";
- case ionKind::k: return "k";
- default: throw std::out_of_range("unknown ionKind");
- }
-}
-
-// Ion (species) description
-
-struct ion_info {
- ionKind kind;
- int charge; // charge of ionic species
- double default_int_concentration; // (mM) default internal concentration
- double default_ext_concentration; // (mM) default external concentration
-};
-
-} // namespace arb
-
diff --git a/arbor/include/arbor/ion_info.hpp b/arbor/include/arbor/ion_info.hpp
new file mode 100644
index 00000000..a3e97263
--- /dev/null
+++ b/arbor/include/arbor/ion_info.hpp
@@ -0,0 +1,11 @@
+#pragma once
+
+namespace arb {
+
+struct ion_info {
+ int charge; // charge of ionic species
+ double default_int_concentration; // (mM) default internal concentration
+ double default_ext_concentration; // (mM) default external concentration
+};
+
+} // namespace arb
diff --git a/arbor/include/arbor/mechanism.hpp b/arbor/include/arbor/mechanism.hpp
index 8e17ad66..0fe32db4 100644
--- a/arbor/include/arbor/mechanism.hpp
+++ b/arbor/include/arbor/mechanism.hpp
@@ -5,7 +5,6 @@
#include <vector>
#include <arbor/fvm_types.hpp>
-#include <arbor/ion.hpp>
#include <arbor/mechinfo.hpp>
namespace arb {
diff --git a/arbor/include/arbor/mechinfo.hpp b/arbor/include/arbor/mechinfo.hpp
index dce3c70d..5e23e2ea 100644
--- a/arbor/include/arbor/mechinfo.hpp
+++ b/arbor/include/arbor/mechinfo.hpp
@@ -10,8 +10,6 @@
#include <utility>
#include <vector>
-#include <arbor/ion.hpp>
-
namespace arb {
struct mechanism_field_spec {
@@ -34,6 +32,7 @@ struct mechanism_field_spec {
struct ion_dependency {
bool write_concentration_int;
bool write_concentration_ext;
+ bool write_reversal_potential;
};
// A hash of the mechanism dynamics description is used to ensure that offline-compiled
@@ -57,7 +56,7 @@ struct mechanism_info {
std::unordered_map<std::string, mechanism_field_spec> state;
// Ion dependencies.
- std::unordered_map<ionKind, ion_dependency> ions;
+ std::unordered_map<std::string, ion_dependency> ions;
mechanism_fingerprint fingerprint;
diff --git a/modcc/blocks.hpp b/modcc/blocks.hpp
index 868f60bd..118077df 100644
--- a/modcc/blocks.hpp
+++ b/modcc/blocks.hpp
@@ -11,9 +11,6 @@
// describes a relationship with an ion channel
struct IonDep {
- ionKind kind() const {
- return to_ionKind(name);
- }
std::string name; // name of ion channel
std::vector<Token> read; // name of channels parameters to write
std::vector<Token> write; // name of channels parameters to read
@@ -40,6 +37,9 @@ struct IonDep {
bool writes_concentration_ext() const {
return writes_variable(name+"o");
};
+ bool writes_rev_potential() const {
+ return writes_variable("e"+name);
+ };
bool reads_variable(const std::string& name) const {
return std::find_if(read.begin(), read.end(),
diff --git a/modcc/expression.cpp b/modcc/expression.cpp
index 960339f8..2d4accd1 100644
--- a/modcc/expression.cpp
+++ b/modcc/expression.cpp
@@ -265,8 +265,8 @@ std::string VariableExpression::to_string() const {
+ colorize("write", is_writeable() ? stringColor::green : stringColor::red) + ", "
+ colorize("read", is_readable() ? stringColor::green : stringColor::red) + ", "
+ (is_range() ? "range" : "scalar") + ", "
- + "ion" + colorize(::to_string(ion_channel()),
- (ion_channel()==ionKind::none) ? stringColor::red : stringColor::green) + ", "
+ + "ion" + (is_ion()? colorize(ion_channel(), stringColor::green)
+ : colorize("none", stringColor::red)) + ", "
+ "vis " + ::to_string(visibility()) + ", "
+ "link " + ::to_string(linkage()) + ", "
+ colorize("state", is_state() ? stringColor::green : stringColor::red) + ")";
@@ -278,11 +278,11 @@ std::string VariableExpression::to_string() const {
*******************************************************************************/
std::string IndexedVariable::to_string() const {
- auto ch = ::to_string(ion_channel());
return
blue("indexed") + " " + yellow(name()) + "->" + yellow(index_name()) + "("
+ (is_write() ? " write-only" : " read-only")
- + ", ion" + (ion_channel()==ionKind::none ? red(ch) : green(ch)) + ") ";
+ + ", ion" + (is_ion()? colorize(ion_channel(), stringColor::green)
+ : colorize("none", stringColor::red)) + ") ";
}
/*******************************************************************************
diff --git a/modcc/expression.hpp b/modcc/expression.hpp
index 12b9fc5f..2157d396 100644
--- a/modcc/expression.hpp
+++ b/modcc/expression.hpp
@@ -9,8 +9,8 @@
#include "error.hpp"
#include "identifier.hpp"
-#include "memop.hpp"
#include "scope.hpp"
+#include "token.hpp"
#include "io/pprintf.hpp"
@@ -455,8 +455,8 @@ public:
void range(rangeKind r) {
range_kind_ = r;
}
- void ion_channel(ionKind i) {
- ion_channel_ = i;
+ void ion_channel(std::string i) {
+ ion_channel_ = std::move(i);
}
void state(bool s) {
is_state_ = s;
@@ -474,7 +474,7 @@ public:
linkageKind linkage() const {
return linkage_;
}
- ionKind ion_channel() const {
+ const std::string& ion_channel() const {
return ion_channel_;
}
@@ -482,7 +482,7 @@ public:
return shadows_;
}
- bool is_ion() const {return ion_channel_ != ionKind::none;}
+ bool is_ion() const {return !ion_channel_.empty();}
bool is_state() const {return is_state_;}
bool is_range() const {return range_kind_ == rangeKind::range;}
bool is_scalar() const {return !is_range();}
@@ -507,7 +507,7 @@ protected:
visibilityKind visibility_ = visibilityKind::local;
linkageKind linkage_ = linkageKind::external;
rangeKind range_kind_ = rangeKind::range;
- ionKind ion_channel_ = ionKind::none;
+ std::string ion_channel_ = "";
double value_ = std::numeric_limits<double>::quiet_NaN();
Symbol* shadows_ = nullptr;
};
@@ -521,11 +521,11 @@ public:
sourceKind data_source,
accessKind acc,
tok o=tok::eq,
- ionKind channel=ionKind::none)
+ std::string channel="")
: Symbol(std::move(loc), std::move(lookup_name), symbolKind::indexed_variable),
access_(acc),
- ion_channel_(channel),
- index_name_(index_name), // (TODO: deprecate/remove this...)
+ ion_channel_(std::move(channel)),
+ index_name_(std::move(index_name)), // (TODO: deprecate/remove this...)
data_source_(data_source),
op_(o)
{
@@ -558,12 +558,13 @@ public:
std::string to_string() const override;
accessKind access() const { return access_; }
- ionKind ion_channel() const { return ion_channel_; }
+ std::string ion_channel() const { return ion_channel_; }
sourceKind data_source() const { return data_source_; }
+ void data_source(sourceKind k) { data_source_ = k; }
std::string const& index_name() const { return index_name_; }
tok op() const { return op_; }
- bool is_ion() const { return ion_channel_ != ionKind::none; }
+ bool is_ion() const { return !ion_channel_.empty(); }
bool is_read() const { return access_ == accessKind::read; }
bool is_write() const { return access_ == accessKind::write; }
@@ -573,7 +574,7 @@ public:
~IndexedVariable() {}
protected:
accessKind access_;
- ionKind ion_channel_;
+ std::string ion_channel_;
std::string index_name_; // hint to printer only
sourceKind data_source_;
tok op_;
@@ -597,12 +598,11 @@ public :
}
bool is_indexed() const {
- return external_!=nullptr && ion_channel()!=ionKind::nonspecific;
+ return external_!=nullptr && external_->data_source()!=sourceKind::no_source;
}
- ionKind ion_channel() const {
- if(external_) return external_->ion_channel();
- return ionKind::none;
+ std::string ion_channel() const {
+ return external_? external_->ion_channel(): "";
}
bool is_read() const {
@@ -695,20 +695,20 @@ public:
ConductanceExpression(
Location loc,
std::string name,
- ionKind channel)
- : Expression(loc), name_(std::move(name)), ion_channel_(channel)
+ std::string channel)
+ : Expression(loc), name_(std::move(name)), ion_channel_(std::move(channel))
{}
std::string to_string() const override {
return blue("conductance") + "(" + yellow(name_) + ", "
- + green(::to_string(ion_channel_)) + ")";
+ + green(ion_channel_.empty()? "none": ion_channel_) + ")";
}
std::string const& name() const {
return name_;
}
- ionKind ion_channel() const {
+ std::string const& ion_channel() const {
return ion_channel_;
}
@@ -725,7 +725,7 @@ public:
private:
/// pointer to the variable symbol for the state variable to be solved for
std::string name_;
- ionKind ion_channel_;
+ std::string ion_channel_;
};
////////////////////////////////////////////////////////////////////////////////
@@ -1041,8 +1041,6 @@ protected:
class APIMethod : public ProcedureExpression {
public:
- using memop_type = MemOp<Symbol>;
-
APIMethod( Location loc,
std::string name,
std::vector<expression_ptr>&& args,
diff --git a/modcc/identifier.hpp b/modcc/identifier.hpp
index 891e6f49..58aea569 100644
--- a/modcc/identifier.hpp
+++ b/modcc/identifier.hpp
@@ -33,15 +33,6 @@ enum class linkageKind {
external
};
-/// ion channel that the variable belongs to
-enum class ionKind {
- none, ///< not an ion variable
- nonspecific, ///< nonspecific current
- Ca, ///< calcium ion
- Na, ///< sodium ion
- K ///< potassium ion
-};
-
/// possible external data source for indexed variables
enum class sourceKind {
voltage,
@@ -64,25 +55,6 @@ inline std::string yesno(bool val) {
// to_string functions convert types
// to strings for printing diagnostics
////////////////////////////////////////////
-inline std::string to_string(ionKind i) {
- switch(i) {
- case ionKind::Ca : return std::string("ca");
- case ionKind::Na : return std::string("na");
- case ionKind::K : return std::string("k");
- case ionKind::none : return std::string("none");
- case ionKind::nonspecific : return std::string("nonspecific");
- }
- throw std::runtime_error("unknown ionKind");
-}
-
-inline ionKind to_ionKind(const std::string& s) {
- if(s=="k") return ionKind::K;
- if(s=="na") return ionKind::Na;
- if(s=="ca") return ionKind::Ca;
- if(s=="none") return ionKind::Ca;
- if(s=="nonspecific") return ionKind::nonspecific;
- throw std::runtime_error("invalid ion description string");
-}
inline std::string to_string(visibilityKind v) {
switch(v) {
@@ -101,9 +73,6 @@ inline std::string to_string(linkageKind v) {
}
// ostream writers
-inline std::ostream& operator<< (std::ostream& os, ionKind i) {
- return os << to_string(i);
-}
inline std::ostream& operator<< (std::ostream& os, visibilityKind v) {
return os << to_string(v);
@@ -115,25 +84,12 @@ inline std::ostream& operator<< (std::ostream& os, linkageKind l) {
/// ion variable to data source kind
-inline sourceKind ion_source(ionKind i, const std::string& var) {
- std::string ion = to_string(i);
- if (var=="i"+ion) return sourceKind::ion_current;
+inline sourceKind ion_source(const std::string& ion, const std::string& var) {
+ if (ion.empty()) return sourceKind::no_source;
+ else if (var=="i"+ion) return sourceKind::ion_current;
else if (var=="e"+ion) return sourceKind::ion_revpot;
else if (var==ion+"i") return sourceKind::ion_iconc;
else if (var==ion+"e") return sourceKind::ion_econc;
else return sourceKind::no_source;
}
-// TODO: deprecate; back-end dependent.
-inline std::string ion_store(ionKind k) {
- switch(k) {
- case ionKind::Ca:
- return "ion_ca";
- case ionKind::Na:
- return "ion_na";
- case ionKind::K:
- return "ion_k";
- default:
- return "";
- }
-}
diff --git a/modcc/module.cpp b/modcc/module.cpp
index 97debcad..3c86d0de 100644
--- a/modcc/module.cpp
+++ b/modcc/module.cpp
@@ -26,15 +26,20 @@ class NrnCurrentRewriter: public BlockRewriterBase {
return id(name, loc_);
}
- static ionKind is_ion_update(Expression* e) {
+ static sourceKind current_update(Expression* e) {
if(auto a = e->is_assignment()) {
if(auto sym = a->lhs()->is_identifier()->symbol()) {
if(auto var = sym->is_local_variable()) {
- return var->ion_channel();
+ if(auto ext = var->external_variable()) {
+ sourceKind src = ext->data_source();
+ if (src==sourceKind::current || src==sourceKind::ion_current) {
+ return src;
+ }
+ }
}
}
}
- return ionKind::none;
+ return sourceKind::no_source;
}
bool has_current_update_ = false;
@@ -81,12 +86,20 @@ public:
statements_.push_back(e->clone());
auto loc = e->location();
- auto update_kind = is_ion_update(e);
- if (update_kind!=ionKind::none) {
- if (update_kind!=ionKind::nonspecific) {
+ sourceKind current_source = current_update(e);
+ if (current_source != sourceKind::no_source) {
+ has_current_update_ = true;
+
+ if (current_source==sourceKind::ion_current) {
ion_current_vars_.insert(e->lhs()->is_identifier()->name());
}
- has_current_update_ = true;
+ else {
+ // A 'nonspecific' current contribution.
+ // Remove data source; currents accumulated into `current_` instead.
+
+ e->lhs()->is_identifier()->symbol()->is_local_variable()
+ ->external_variable()->data_source(sourceKind::no_source);
+ }
linear_test_result L = linear_test(e->rhs(), {"v"});
if (!L.is_linear) {
@@ -497,7 +510,7 @@ void Module::add_variables_to_symbols() {
// add indexed variables to the table
auto create_indexed_variable = [this]
(std::string const& name, std::string const& indexed_name, sourceKind data_source,
- tok op, accessKind acc, ionKind ch, Location loc) -> symbol_ptr&
+ tok op, accessKind acc, std::string ch, Location loc) -> symbol_ptr&
{
if(symbols_.count(name)) {
throw compiler_exception(
@@ -508,13 +521,13 @@ void Module::add_variables_to_symbols() {
};
create_indexed_variable("current_", "vec_i", sourceKind::current, tok::plus,
- accessKind::write, ionKind::none, Location());
+ accessKind::write, "", Location());
create_indexed_variable("conductivity_", "vec_g", sourceKind::conductivity, tok::plus,
- accessKind::write, ionKind::none, Location());
+ accessKind::write, "", Location());
create_indexed_variable("v", "vec_v", sourceKind::voltage, tok::eq,
- accessKind::read, ionKind::none, Location());
+ accessKind::read, "", Location());
create_indexed_variable("dt", "vec_dt", sourceKind::dt, tok::eq,
- accessKind::read, ionKind::none, Location());
+ accessKind::read, "", Location());
// If we put back support for accessing cell time again from NMODL code,
// add indexed_variable also for "time" with appropriate cell-index based
@@ -537,7 +550,7 @@ void Module::add_variables_to_symbols() {
if (id.name() == "celsius") {
create_indexed_variable("celsius", "celsius",
- sourceKind::temperature, tok::eq, accessKind::read, ionKind::none, Location());
+ sourceKind::temperature, tok::eq, accessKind::read, "", Location());
}
else {
// Parameters are scalar by default, but may later be changed to range.
@@ -575,7 +588,7 @@ void Module::add_variables_to_symbols() {
// first the ION channels
// add ion channel variables
auto update_ion_symbols = [this, create_indexed_variable]
- (Token const& tkn, accessKind acc, ionKind channel)
+ (Token const& tkn, accessKind acc, const std::string& channel)
{
std::string name = tkn.spelling;
sourceKind data_source = ion_source(channel, name);
@@ -610,18 +623,23 @@ void Module::add_variables_to_symbols() {
}
};
- // check for nonspecific current
+ // Nonspecific current variables are represented by an indexed variable
+ // with a 'current' data source. Assignments in the NrnCurrent block will
+ // later be rewritten so that these contributions are accumulated in `current_`
+ // (potentially saving some weight multiplications); at that point the
+ // data source for the nonspecific current variable will be reset to 'no_source'.
+
if( neuron_block_.has_nonspecific_current() ) {
auto const& i = neuron_block_.nonspecific_current;
- update_ion_symbols(i, accessKind::write, ionKind::nonspecific);
+ create_indexed_variable(i.spelling, "", sourceKind::current, tok::plus, accessKind::write, "", i.location);
}
for(auto const& ion : neuron_block_.ions) {
for(auto const& var : ion.read) {
- update_ion_symbols(var, accessKind::read, ion.kind());
+ update_ion_symbols(var, accessKind::read, ion.name);
}
for(auto const& var : ion.write) {
- update_ion_symbols(var, accessKind::write, ion.kind());
+ update_ion_symbols(var, accessKind::write, ion.name);
}
}
diff --git a/modcc/module.hpp b/modcc/module.hpp
index dbe8c1ff..4cf5e6ac 100644
--- a/modcc/module.hpp
+++ b/modcc/module.hpp
@@ -91,16 +91,16 @@ public:
// Perform semantic analysis pass.
bool semantic();
- auto find_ion(ionKind k) -> decltype(ion_deps().begin()) {
+ auto find_ion(const std::string& ion_name) -> decltype(ion_deps().begin()) {
auto& ions = neuron_block().ions;
return std::find_if(
ions.begin(), ions.end(),
- [k](IonDep const& d) {return d.kind()==k;}
+ [&ion_name](IonDep const& d) {return d.name==ion_name;}
);
};
- bool has_ion(ionKind k) {
- return find_ion(k) != neuron_block().ions.end();
+ bool has_ion(const std::string& ion_name) {
+ return find_ion(ion_name) != neuron_block().ions.end();
};
bool is_linear() const { return linear_; }
diff --git a/modcc/parser.cpp b/modcc/parser.cpp
index 1598711a..d2fd3a02 100644
--- a/modcc/parser.cpp
+++ b/modcc/parser.cpp
@@ -304,16 +304,10 @@ void Parser::parse_neuron_block() {
get_token();
// check this is an identifier token
if(token_.type != tok::identifier) {
- error(pprintf("invalid name for an ion chanel '%'",
- token_.spelling));
- return;
- }
- // check that the ion type is valid (insist on lower case?)
- if(!(token_.spelling == "k" || token_.spelling == "ca" || token_.spelling == "na")) {
- error(pprintf("invalid ion type % must be on eof 'k' 'ca' or 'na'",
- yellow(token_.spelling)));
+ error(pprintf("invalid name for an ion chanel '%'", token_.spelling));
return;
}
+
ion.name = token_.spelling;
get_token(); // consume the ion name
@@ -1464,7 +1458,7 @@ expression_ptr Parser::parse_conductance() {
int line = location_.line;
Location loc = location_; // solve location for expression
std::string name;
- ionKind channel;
+ std::string channel;
get_token(); // consume the CONDUCTANCE keyword
@@ -1473,20 +1467,11 @@ expression_ptr Parser::parse_conductance() {
name = token_.spelling; // save name of variable
get_token(); // consume the variable identifier
- if(token_.type != tok::useion) { // no ion channel was provided
- // we set nonspecific not none because ionKind::none marks
- // any variable that is not associated with an ion channel
- channel = ionKind::nonspecific;
- }
- else {
+ if(token_.type == tok::useion) {
get_token(); // consume the USEION keyword
if(token_.type!=tok::identifier) goto conductance_statement_error;
- if (token_.spelling == "na") channel = ionKind::Na;
- else if(token_.spelling == "ca") channel = ionKind::Ca;
- else if(token_.spelling == "k") channel = ionKind::K;
- else goto conductance_statement_error;
-
+ channel = token_.spelling;
get_token(); // consume the ion channel type
}
// check that the rest of the line was empty
diff --git a/modcc/printer/cprinter.cpp b/modcc/printer/cprinter.cpp
index 1c1ce229..5560ff22 100644
--- a/modcc/printer/cprinter.cpp
+++ b/modcc/printer/cprinter.cpp
@@ -216,7 +216,6 @@ std::string emit_cpp_source(const Module& module_, const printer_options& opt) {
out <<
"\n" << popindent <<
"protected:\n" << indent <<
- "using ionKind = ::arb::ionKind;\n\n"
"std::size_t object_sizeof() const override { return sizeof(*this); }\n";
io::separator sep("\n", ",\n");
@@ -280,14 +279,14 @@ std::string emit_cpp_source(const Module& module_, const printer_options& opt) {
sep.reset();
for (const auto& dep: ion_deps) {
- out << sep << "{ionKind::" << dep.name << ", &" << ion_state_field(dep.name) << "}";
+ out << sep << "{\"" << dep.name << "\", &" << ion_state_field(dep.name) << "}";
}
out << popindent << "\n};" << popindent << "\n}\n";
sep.reset();
out << "mechanism_ion_index_table ion_index_table() override {\n" << indent << "return {" << indent;
for (const auto& dep: ion_deps) {
- out << sep << "{ionKind::" << dep.name << ", &" << ion_state_index(dep.name) << "}";
+ out << sep << "{\"" << dep.name << "\", &" << ion_state_index(dep.name) << "}";
}
out << popindent << "\n};" << popindent << "\n}\n";
}
diff --git a/modcc/printer/cudaprinter.cpp b/modcc/printer/cudaprinter.cpp
index e84200f2..91f69c03 100644
--- a/modcc/printer/cudaprinter.cpp
+++ b/modcc/printer/cudaprinter.cpp
@@ -40,11 +40,11 @@ std::string make_ppack_name(const std::string& module_name) {
return make_class_name(module_name)+"_pp_";
}
-static std::string ion_state_field(std::string ion_name) {
+static std::string ion_state_field(const std::string& ion_name) {
return "ion_"+ion_name+"_";
}
-static std::string ion_state_index(std::string ion_name) {
+static std::string ion_state_index(const std::string& ion_name) {
return "ion_"+ion_name+"_index_";
}
@@ -117,7 +117,6 @@ std::string emit_cuda_cpp_source(const Module& module_, const printer_options& o
out << popindent <<
"protected:\n" << indent <<
- "using ionKind = ::arb::ionKind;\n\n"
"std::size_t object_sizeof() const override { return sizeof(*this); }\n"
"::arb::gpu::mechanism_ppack_base* ppack_ptr() { return &pp_; }\n\n";
@@ -183,14 +182,14 @@ std::string emit_cuda_cpp_source(const Module& module_, const printer_options& o
sep.reset();
for (const auto& dep: ion_deps) {
- out << sep << "{ionKind::" << dep.name << ", &pp_." << ion_state_field(dep.name) << "}";
+ out << sep << "{\"" << dep.name << "\", &pp_." << ion_state_field(dep.name) << "}";
}
out << popindent << "\n};" << popindent << "\n}\n";
sep.reset();
out << "mechanism_ion_index_table ion_index_table() override {\n" << indent << "return {" << indent;
for (const auto& dep: ion_deps) {
- out << sep << "{ionKind::" << dep.name << ", &pp_." << ion_state_index(dep.name) << "}";
+ out << sep << "{\"" << dep.name << "\", &pp_." << ion_state_index(dep.name) << "}";
}
out << popindent << "\n};" << popindent << "\n}\n";
}
diff --git a/modcc/printer/infoprinter.cpp b/modcc/printer/infoprinter.cpp
index 7c69918e..5e9fe0b9 100644
--- a/modcc/printer/infoprinter.cpp
+++ b/modcc/printer/infoprinter.cpp
@@ -44,9 +44,10 @@ std::ostream& operator<<(std::ostream& out, const ion_dep_info& wrap) {
const char* boolalpha[2] = {"false", "true"};
const IonDep& ion = wrap.ion;
- return out << "{ionKind::" << ion.name << ", {"
+ return out << "{\"" << ion.name << "\", {"
<< boolalpha[ion.writes_concentration_int()] << ", "
- << boolalpha[ion.writes_concentration_ext()] << "}}";
+ << boolalpha[ion.writes_concentration_ext()] << ", "
+ << boolalpha[ion.writes_rev_potential()] << "}}";
}
std::string build_info_header(const Module& m, const printer_options& opt) {
@@ -73,7 +74,6 @@ std::string build_info_header(const Module& m, const printer_options& opt) {
"\n"
"inline const ::arb::mechanism_info& mechanism_" << name << "_info() {\n"
<< indent <<
- "using ::arb::ionKind;\n"
"using spec = ::arb::mechanism_field_spec;\n"
"static mechanism_info info = {\n"
<< indent <<
diff --git a/modcc/printer/printerutil.cpp b/modcc/printer/printerutil.cpp
index f5f95cf5..ca42489c 100644
--- a/modcc/printer/printerutil.cpp
+++ b/modcc/printer/printerutil.cpp
@@ -118,7 +118,7 @@ indexed_variable_info decode_indexed_variable(IndexedVariable* sym) {
std::string index_var = "node_index_";
if (sym->is_ion()) {
- ion_pfx = "ion_"+to_string(sym->ion_channel())+"_";
+ ion_pfx = "ion_"+sym->ion_channel()+"_";
index_var = ion_pfx+"index_";
}
diff --git a/modcc/symdiff.cpp b/modcc/symdiff.cpp
index f9f6a4bc..75a1b76a 100644
--- a/modcc/symdiff.cpp
+++ b/modcc/symdiff.cpp
@@ -8,6 +8,7 @@
#include "error.hpp"
#include "expression.hpp"
#include "symdiff.hpp"
+#include "util.hpp"
#include "visitor.hpp"
class FindIdentifierVisitor: public Visitor {
diff --git a/test/unit/test_fvm_layout.cpp b/test/unit/test_fvm_layout.cpp
index 0b9496a0..a4a1541f 100644
--- a/test/unit/test_fvm_layout.cpp
+++ b/test/unit/test_fvm_layout.cpp
@@ -324,12 +324,12 @@ TEST(fvm_layout, mech_index) {
// There should be a K and Na ion channel associated with each
// hh mechanism node.
- ASSERT_EQ(1u, M.ions.count(ionKind::na));
- ASSERT_EQ(1u, M.ions.count(ionKind::k));
- EXPECT_EQ(0u, M.ions.count(ionKind::ca));
+ ASSERT_EQ(1u, M.ions.count("na"s));
+ ASSERT_EQ(1u, M.ions.count("k"s));
+ EXPECT_EQ(0u, M.ions.count("ca"s));
- EXPECT_EQ(ivec({0,5}), M.ions.at(ionKind::na).cv);
- EXPECT_EQ(ivec({0,5}), M.ions.at(ionKind::k).cv);
+ EXPECT_EQ(ivec({0,5}), M.ions.at("na"s).cv);
+ EXPECT_EQ(ivec({0,5}), M.ions.at("k"s).cv);
}
TEST(fvm_layout, coalescing_synapses) {
@@ -755,8 +755,8 @@ TEST(fvm_layout, ion_weights) {
fvm_discretization D = fvm_discretize(cells);
fvm_mechanism_data M = fvm_build_mechanism_data(global_default_catalogue(), cells, D);
- ASSERT_EQ(1u, M.ions.count(ionKind::ca));
- auto& ca = M.ions.at(ionKind::ca);
+ ASSERT_EQ(1u, M.ions.count("ca"s));
+ auto& ca = M.ions.at("ca"s);
EXPECT_EQ(expected_ion_cv[run], ca.cv);
EXPECT_TRUE(testing::seq_almost_eq<fvm_value_type>(expected_iconc_norm_area[run], ca.iconc_norm_area));
diff --git a/test/unit/test_fvm_lowered.cpp b/test/unit/test_fvm_lowered.cpp
index cdc09371..59fa34d1 100644
--- a/test/unit/test_fvm_lowered.cpp
+++ b/test/unit/test_fvm_lowered.cpp
@@ -58,7 +58,7 @@ arb::mechanism* find_mechanism(fvm_cell& fvcell, const std::string& name) {
using mechanism_global_table = std::vector<std::pair<const char*, arb::fvm_value_type*>>;
using mechanism_field_table = std::vector<std::pair<const char*, arb::fvm_value_type**>>;
-using mechanism_ion_index_table = std::vector<std::pair<arb::ionKind, backend::iarray*>>;
+using mechanism_ion_index_table = std::vector<std::pair<const char*, backend::iarray*>>;
ACCESS_BIND(\
mechanism_global_table (arb::multicore::mechanism::*)(),\
@@ -534,7 +534,7 @@ TEST(fvm_lowered, weighted_write_ion) {
fvcell.initialize({0}, cable1d_recipe(c), cell_to_intdom, targets, probe_map);
auto& state = *(fvcell.*private_state_ptr).get();
- auto& ion = state.ion_data.at(ionKind::ca);
+ auto& ion = state.ion_data.at("ca"s);
ion.default_int_concentration = con_int;
ion.default_ext_concentration = con_ext;
ion.init_concentration();
@@ -553,7 +553,7 @@ TEST(fvm_lowered, weighted_write_ion) {
ASSERT_TRUE(opt_cai_ptr);
auto& test_ca_cai = *opt_cai_ptr.value();
- auto opt_ca_index_ptr = util::value_by_key((test_ca->*private_ion_index_table_ptr)(), ionKind::ca);
+ auto opt_ca_index_ptr = util::value_by_key((test_ca->*private_ion_index_table_ptr)(), "ca"s);
ASSERT_TRUE(opt_ca_index_ptr);
auto& test_ca_ca_index = *opt_ca_index_ptr.value();
--
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