diff --git a/arbor/backends/gpu/shared_state.cpp b/arbor/backends/gpu/shared_state.cpp
index 704ea7f5b89252e8b7d05445dba1ee4bca2786a6..6b8d26e35b6b5487a0fe7d950c1274c48938b680 100644
--- a/arbor/backends/gpu/shared_state.cpp
+++ b/arbor/backends/gpu/shared_state.cpp
@@ -50,20 +50,19 @@ std::pair<fvm_value_type, fvm_value_type> minmax_value_impl(fvm_size_type n, con
ion_state::ion_state(
int charge,
- const std::vector<fvm_index_type>& cv,
- const std::vector<fvm_value_type>& init_iconc,
- const std::vector<fvm_value_type>& init_econc,
- const std::vector<fvm_value_type>& init_erev,
+ const fvm_ion_config& ion_data,
unsigned // alignment/padding ignored.
):
- node_index_(make_const_view(cv)),
- iX_(cv.size(), NAN),
- eX_(cv.size(), NAN),
- Xi_(cv.size(), NAN),
- Xo_(cv.size(), NAN),
- init_Xi_(make_const_view(init_iconc)),
- init_Xo_(make_const_view(init_econc)),
- init_eX_(make_const_view(init_erev)),
+ node_index_(make_const_view(ion_data.cv)),
+ iX_(ion_data.cv.size(), NAN),
+ eX_(ion_data.cv.size(), NAN),
+ Xi_(ion_data.cv.size(), NAN),
+ Xo_(ion_data.cv.size(), NAN),
+ init_Xi_(make_const_view(ion_data.init_iconc)),
+ init_Xo_(make_const_view(ion_data.init_econc)),
+ reset_Xi_(make_const_view(ion_data.reset_iconc)),
+ reset_Xo_(make_const_view(ion_data.reset_econc)),
+ init_eX_(make_const_view(ion_data.init_revpot)),
charge(1u, charge)
{
arb_assert(node_index_.size()==init_Xi_.size());
@@ -82,7 +81,8 @@ void ion_state::zero_current() {
void ion_state::reset() {
zero_current();
- init_concentration();
+ memory::copy(reset_Xi_, Xi_);
+ memory::copy(reset_Xo_, Xo_);
memory::copy(init_eX_, eX_);
}
@@ -120,14 +120,11 @@ shared_state::shared_state(
void shared_state::add_ion(
const std::string& ion_name,
int charge,
- const std::vector<fvm_index_type>& cv,
- const std::vector<fvm_value_type>& init_iconc,
- const std::vector<fvm_value_type>& init_econc,
- const std::vector<fvm_value_type>& init_erev)
+ const fvm_ion_config& ion_info)
{
ion_data.emplace(std::piecewise_construct,
std::forward_as_tuple(ion_name),
- std::forward_as_tuple(charge, cv, init_iconc, init_econc, init_erev, 1u));
+ std::forward_as_tuple(charge, ion_info, 1u));
}
void shared_state::reset() {
diff --git a/arbor/backends/gpu/shared_state.hpp b/arbor/backends/gpu/shared_state.hpp
index 759ed1ca5d1bef2d55de3266707b3bc6088b7f0b..c375aa325f2872c7a426ba8cde2fa373a986665a 100644
--- a/arbor/backends/gpu/shared_state.hpp
+++ b/arbor/backends/gpu/shared_state.hpp
@@ -7,6 +7,8 @@
#include <arbor/fvm_types.hpp>
+#include "fvm_layout.hpp"
+
#include "backends/gpu/gpu_store_types.hpp"
namespace arb {
@@ -33,6 +35,8 @@ struct ion_state {
array init_Xi_; // (mM) area-weighted initial internal concentration
array init_Xo_; // (mM) area-weighted initial external concentration
+ array reset_Xi_; // (mM) area-weighted user-set internal concentration
+ array reset_Xo_; // (mM) area-weighted user-set internal concentration
array init_eX_; // (mM) initial reversal potential
array charge; // charge of ionic species (global, length 1)
@@ -41,10 +45,7 @@ struct ion_state {
ion_state(
int charge,
- const std::vector<fvm_index_type>& cv,
- const std::vector<fvm_value_type>& init_Xi,
- const std::vector<fvm_value_type>& init_Xo,
- const std::vector<fvm_value_type>& init_eX,
+ const fvm_ion_config& ion_data,
unsigned align
);
@@ -97,10 +98,7 @@ struct shared_state {
void add_ion(
const std::string& ion_name,
int charge,
- const std::vector<fvm_index_type>& cv,
- const std::vector<fvm_value_type>& init_iconc,
- const std::vector<fvm_value_type>& init_econc,
- const std::vector<fvm_value_type>& init_erev);
+ const fvm_ion_config& ion_data);
void zero_currents();
diff --git a/arbor/backends/multicore/shared_state.cpp b/arbor/backends/multicore/shared_state.cpp
index d4f98051d8a83c0cfcb2267d13a40ef15634c9bc..10a1295d25b36a5601f9ca35e90e380124f526c1 100644
--- a/arbor/backends/multicore/shared_state.cpp
+++ b/arbor/backends/multicore/shared_state.cpp
@@ -48,21 +48,20 @@ using pad = util::padded_allocator<>;
ion_state::ion_state(
int charge,
- const std::vector<fvm_index_type>& cv,
- const std::vector<fvm_value_type>& init_Xi,
- const std::vector<fvm_value_type>& init_Xo,
- const std::vector<fvm_value_type>& init_eX,
+ const fvm_ion_config& ion_data,
unsigned align
):
alignment(min_alignment(align)),
- node_index_(cv.begin(), cv.end(), pad(alignment)),
- iX_(cv.size(), NAN, pad(alignment)),
- eX_(init_eX.begin(), init_eX.end(), pad(alignment)),
- Xi_(cv.size(), NAN, pad(alignment)),
- Xo_(cv.size(), NAN, pad(alignment)),
- init_Xi_(init_Xi.begin(), init_Xi.end(), pad(alignment)),
- init_Xo_(init_Xo.begin(), init_Xo.end(), pad(alignment)),
- init_eX_(init_eX.begin(), init_eX.end(), pad(alignment)),
+ node_index_(ion_data.cv.begin(), ion_data.cv.end(), pad(alignment)),
+ iX_(ion_data.cv.size(), NAN, pad(alignment)),
+ eX_(ion_data.init_revpot.begin(), ion_data.init_revpot.end(), pad(alignment)),
+ Xi_(ion_data.cv.size(), NAN, pad(alignment)),
+ Xo_(ion_data.cv.size(), NAN, pad(alignment)),
+ init_Xi_(ion_data.init_iconc.begin(), ion_data.init_iconc.end(), pad(alignment)),
+ init_Xo_(ion_data.init_econc.begin(), ion_data.init_econc.end(), pad(alignment)),
+ reset_Xi_(ion_data.reset_iconc.begin(), ion_data.reset_iconc.end(), pad(alignment)),
+ reset_Xo_(ion_data.reset_econc.begin(), ion_data.reset_econc.end(), pad(alignment)),
+ init_eX_(ion_data.init_revpot.begin(), ion_data.init_revpot.end(), pad(alignment)),
charge(1u, charge, pad(alignment))
{
arb_assert(node_index_.size()==init_Xi_.size());
@@ -82,7 +81,8 @@ void ion_state::zero_current() {
void ion_state::reset() {
zero_current();
- init_concentration();
+ std::copy(reset_Xi_.begin(), reset_Xi_.end(), Xi_.begin());
+ std::copy(reset_Xo_.begin(), reset_Xo_.end(), Xo_.begin());
std::copy(init_eX_.begin(), init_eX_.end(), eX_.begin());
}
@@ -134,14 +134,11 @@ shared_state::shared_state(
void shared_state::add_ion(
const std::string& ion_name,
int charge,
- const std::vector<fvm_index_type>& cv,
- const std::vector<fvm_value_type>& init_iconc,
- const std::vector<fvm_value_type>& init_econc,
- const std::vector<fvm_value_type>& init_erev)
+ const fvm_ion_config& ion_info)
{
ion_data.emplace(std::piecewise_construct,
std::forward_as_tuple(ion_name),
- std::forward_as_tuple(charge, cv, init_iconc, init_econc, init_erev, alignment));
+ std::forward_as_tuple(charge, ion_info, alignment));
}
void shared_state::reset() {
diff --git a/arbor/backends/multicore/shared_state.hpp b/arbor/backends/multicore/shared_state.hpp
index eb9d3f3086f8b5d80c6992530c392daae3a986ae..df146a5cb7930a533977c1dd2d797bee2636ae24 100644
--- a/arbor/backends/multicore/shared_state.hpp
+++ b/arbor/backends/multicore/shared_state.hpp
@@ -20,6 +20,7 @@
#include "multi_event_stream.hpp"
#include "threshold_watcher.hpp"
+#include "fvm_layout.hpp"
#include "multicore_common.hpp"
namespace arb {
@@ -48,6 +49,8 @@ struct ion_state {
array init_Xi_; // (mM) area-weighted initial internal concentration
array init_Xo_; // (mM) area-weighted initial external concentration
+ array reset_Xi_; // (mM) area-weighted user-set internal concentration
+ array reset_Xo_; // (mM) area-weighted user-set internal concentration
array init_eX_; // (mV) initial reversal potential
array charge; // charge of ionic species (global value, length 1)
@@ -56,10 +59,7 @@ struct ion_state {
ion_state(
int charge,
- const std::vector<fvm_index_type>& cv,
- const std::vector<fvm_value_type>& init_Xi,
- const std::vector<fvm_value_type>& init_Xo,
- const std::vector<fvm_value_type>& init_eX,
+ const fvm_ion_config& ion_data,
unsigned align
);
@@ -115,10 +115,7 @@ struct shared_state {
void add_ion(
const std::string& ion_name,
int charge,
- const std::vector<fvm_index_type>& cv,
- const std::vector<fvm_value_type>& init_iconc,
- const std::vector<fvm_value_type>& init_econc,
- const std::vector<fvm_value_type>& init_erev);
+ const fvm_ion_config& ion_data);
void zero_currents();
diff --git a/arbor/fvm_layout.cpp b/arbor/fvm_layout.cpp
index b10449e17b41a2b59124cfe3a096f4e8135668c5..c0c5a1d8a46af8db9372f4a4096a1d7a01a403ef 100644
--- a/arbor/fvm_layout.cpp
+++ b/arbor/fvm_layout.cpp
@@ -756,6 +756,8 @@ fvm_mechanism_data fvm_build_mechanism_data(const cable_cell_global_properties&
ion_config.init_iconc.resize(ion_config.cv.size());
ion_config.init_econc.resize(ion_config.cv.size());
+ ion_config.reset_iconc.resize(ion_config.cv.size());
+ ion_config.reset_econc.resize(ion_config.cv.size());
ion_config.init_revpot.resize(ion_config.cv.size());
for_each_cv_in_segments(D, keys(seg_ion_data),
@@ -767,6 +769,9 @@ fvm_mechanism_data fvm_build_mechanism_data(const cable_cell_global_properties&
auto& seg_ion_entry = seg_ion_map[seg];
value_type weight = area/D.cv_area[cv];
+ ion_config.reset_iconc[i] += weight*seg_ion_entry.ion_data.init_int_concentration;
+ ion_config.reset_econc[i] += weight*seg_ion_entry.ion_data.init_ext_concentration;
+
if (!seg_ion_entry.mech_writes_iconc) {
ion_config.init_iconc[i] += weight*seg_ion_entry.ion_data.init_int_concentration;
}
diff --git a/arbor/fvm_layout.hpp b/arbor/fvm_layout.hpp
index 213fdcafb0a1e63d5a39bba8b0e278a972087d6e..d02475dae0a0854584dbad5b7d3d0ea9352e678b 100644
--- a/arbor/fvm_layout.hpp
+++ b/arbor/fvm_layout.hpp
@@ -136,8 +136,13 @@ struct fvm_ion_config {
std::vector<value_type> init_iconc;
std::vector<value_type> init_econc;
+ // Normalized area contribution of default concentration contribution in corresponding CV set by users
+ std::vector<value_type> reset_iconc;
+ std::vector<value_type> reset_econc;
+
// Ion-specific (initial) reversal potential per CV.
std::vector<value_type> init_revpot;
+
};
struct fvm_mechanism_data {
diff --git a/arbor/fvm_lowered_cell_impl.hpp b/arbor/fvm_lowered_cell_impl.hpp
index 429104e81fbae687c9da24b7c35bf818e6dcd20d..f7e70f86f4c2e0e1b4a84c25a1b1e79a2a6c6caf 100644
--- a/arbor/fvm_lowered_cell_impl.hpp
+++ b/arbor/fvm_lowered_cell_impl.hpp
@@ -164,6 +164,18 @@ void fvm_lowered_cell_impl<Backend>::reset() {
update_ion_state();
+ state_->zero_currents();
+
+ // Note: mechanisms must be initialized again after the ion state is updated,
+ // as mechanisms can read/write the ion_state within the initialize block
+ for (auto& m: revpot_mechanisms_) {
+ m->initialize();
+ }
+
+ for (auto& m: mechanisms_) {
+ m->initialize();
+ }
+
// NOTE: Threshold watcher reset must come after the voltage values are set,
// as voltage is implicitly read by watcher to set initial state.
threshold_watcher_.reset();
@@ -422,7 +434,7 @@ void fvm_lowered_cell_impl<B>::initialize(
const std::string& ion_name = i.first;
if (auto charge = value_by_key(global_props.ion_species, ion_name)) {
- state_->add_ion(ion_name, *charge, i.second.cv, i.second.init_iconc, i.second.init_econc, i.second.init_revpot);
+ state_->add_ion(ion_name, *charge, i.second);
}
else {
throw cable_cell_error("unrecognized ion '"+ion_name+"' in mechanism");
diff --git a/test/unit/CMakeLists.txt b/test/unit/CMakeLists.txt
index 6791ccabe9b9de6c12e0a218787edeff5c31020d..3e557a08a44667baa0f9861184e02ad6e2bd1da6 100644
--- a/test/unit/CMakeLists.txt
+++ b/test/unit/CMakeLists.txt
@@ -25,6 +25,8 @@ set(test_mechanisms
read_eX
write_multiple_eX
write_eX
+ read_cai_init
+ write_cai_breakpoint
)
include(${PROJECT_SOURCE_DIR}/mechanisms/BuildModules.cmake)
diff --git a/test/unit/mod/read_cai_init.mod b/test/unit/mod/read_cai_init.mod
new file mode 100644
index 0000000000000000000000000000000000000000..0dd8a3375829410bde448d4e44e3282457432d09
--- /dev/null
+++ b/test/unit/mod/read_cai_init.mod
@@ -0,0 +1,27 @@
+: Test mechanism with linear response to ica.
+
+NEURON {
+ SUFFIX read_cai_init
+ USEION ca READ cai VALENCE 2
+}
+
+PARAMETER {}
+
+ASSIGNED {}
+
+STATE {
+ s
+}
+
+INITIAL {
+ s = cai
+}
+
+BREAKPOINT {
+ SOLVE states
+}
+
+DERIVATIVE states {
+ s = cai
+}
+
diff --git a/test/unit/mod/write_cai_breakpoint.mod b/test/unit/mod/write_cai_breakpoint.mod
new file mode 100644
index 0000000000000000000000000000000000000000..89eda1fa3fbd2eb362f6d7eac8e36564b314e12d
--- /dev/null
+++ b/test/unit/mod/write_cai_breakpoint.mod
@@ -0,0 +1,24 @@
+: Test mechanism with linear response to ica.
+
+NEURON {
+ SUFFIX write_cai_breakpoint
+ USEION ca WRITE cai READ ica VALENCE 2
+}
+
+PARAMETER {}
+
+ASSIGNED {}
+
+STATE {
+ cai
+}
+
+INITIAL {}
+
+BREAKPOINT {
+ SOLVE states
+}
+
+DERIVATIVE states {
+ cai = 5.2e-4
+}
\ No newline at end of file
diff --git a/test/unit/test_fvm_lowered.cpp b/test/unit/test_fvm_lowered.cpp
index 191249958991bbd5eb60680beeca7d8086e1fa20..434e74245fc896418e9ea673ae5fb4f810493d46 100644
--- a/test/unit/test_fvm_lowered.cpp
+++ b/test/unit/test_fvm_lowered.cpp
@@ -21,6 +21,7 @@
#include "execution_context.hpp"
#include "fvm_lowered_cell.hpp"
#include "fvm_lowered_cell_impl.hpp"
+#include "mech_private_field_access.hpp"
#include "sampler_map.hpp"
#include "util/meta.hpp"
#include "util/maputil.hpp"
@@ -543,6 +544,68 @@ TEST(fvm_lowered, read_valence) {
}
// Test correct scaling of ionic currents in reading and writing
+TEST(fvm_lowered, ionic_concentrations) {
+ auto cat = make_unit_test_catalogue();
+
+ // one cell, one CV:
+ fvm_size_type ncell = 1;
+ fvm_size_type ncv = 1;
+ std::vector<fvm_index_type> cv_to_intdom(ncv, 0);
+ std::vector<fvm_value_type> temp(ncv, 23);
+ std::vector<fvm_value_type> diam(ncv, 1.);
+ std::vector<fvm_value_type> vinit(ncv, -65);
+ std::vector<fvm_gap_junction> gj = {};
+
+ fvm_ion_config ion_config;
+ mechanism_layout layout;
+ mechanism_overrides overrides;
+
+ layout.weight.assign(ncv, 1.);
+ for (fvm_size_type i = 0; i<ncv; ++i) {
+ layout.cv.push_back(i);
+ ion_config.cv.push_back(i);
+ }
+ ion_config.init_revpot.assign(ncv, 0.);
+ ion_config.init_econc.assign(ncv, 0.);
+ ion_config.init_iconc.assign(ncv, 0.);
+ ion_config.reset_econc.assign(ncv, 0.);
+ ion_config.reset_iconc.assign(ncv, 2.3e-4);
+
+ auto read_cai = cat.instance<backend>("read_cai_init");
+ auto write_cai = cat.instance<backend>("write_cai_breakpoint");
+
+ auto& read_cai_mech = read_cai.mech;
+ auto& write_cai_mech = write_cai.mech;
+
+ auto shared_state = std::make_unique<typename backend::shared_state>(
+ ncell, cv_to_intdom, gj, vinit, temp, diam, read_cai_mech->data_alignment());
+ shared_state->add_ion("ca", 2, ion_config);
+
+ read_cai_mech->instantiate(0, *shared_state, overrides, layout);
+ write_cai_mech->instantiate(1, *shared_state, overrides, layout);
+
+ shared_state->reset();
+
+ // expect 2.3 value in state 's' in read_cai_init after init:
+ read_cai_mech->initialize();
+ write_cai_mech->initialize();
+
+ std::vector<fvm_value_type> expected_s_values(ncv, 2.3e-4);
+
+ EXPECT_EQ(expected_s_values, mechanism_field(read_cai_mech.get(), "s"));
+
+ // expect 5.2 + 2.3 value in state 's' in read_cai_init after state update:
+ read_cai_mech->nrn_state();
+ write_cai_mech->nrn_state();
+
+ read_cai_mech->write_ions();
+ write_cai_mech->write_ions();
+
+ read_cai_mech->nrn_state();
+
+ expected_s_values.assign(ncv, 7.5e-4);
+ EXPECT_EQ(expected_s_values, mechanism_field(read_cai_mech.get(), "s"));
+}
TEST(fvm_lowered, ionic_currents) {
soma_cell_builder b(6);
diff --git a/test/unit/unit_test_catalogue.cpp b/test/unit/unit_test_catalogue.cpp
index e68bbdfbc056b62a83d861adadffb8fe32e8066d..0d893f288939b4ec65796e413c1f134429b57a0d 100644
--- a/test/unit/unit_test_catalogue.cpp
+++ b/test/unit/unit_test_catalogue.cpp
@@ -31,6 +31,8 @@
#include "mechanisms/read_eX.hpp"
#include "mechanisms/write_multiple_eX.hpp"
#include "mechanisms/write_eX.hpp"
+#include "mechanisms/read_cai_init.hpp"
+#include "mechanisms/write_cai_breakpoint.hpp"
#include "../gtest.h"
@@ -74,6 +76,8 @@ mechanism_catalogue make_unit_test_catalogue() {
ADD_MECH(cat, read_eX)
ADD_MECH(cat, write_multiple_eX)
ADD_MECH(cat, write_eX)
+ ADD_MECH(cat, read_cai_init)
+ ADD_MECH(cat, write_cai_breakpoint)
return cat;
}