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/*************************************************************************
* Copyright (C) 2018-2022 Blue Brain Project
*
* This file is part of NMODL distributed under the terms of the GNU
* Lesser General Public License. See top-level LICENSE file for details.
*************************************************************************/
#include <catch2/catch_test_macros.hpp>
#include "ast/program.hpp"
#include "parser/nmodl_driver.hpp"
#include "test/unit/utils/test_utils.hpp"
#include "visitors/checkparent_visitor.hpp"
#include "visitors/constant_folder_visitor.hpp"
#include "visitors/inline_visitor.hpp"
#include "visitors/local_var_rename_visitor.hpp"
#include "visitors/sympy_conductance_visitor.hpp"
#include "visitors/symtab_visitor.hpp"
#include "visitors/visitor_utils.hpp"
using namespace nmodl;
using namespace visitor;
using namespace test;
using namespace test_utils;
using ast::AstNodeType;
using nmodl::parser::NmodlDriver;
//=============================================================================
// SympyConductance visitor tests
//=============================================================================
std::string run_sympy_conductance_visitor(const std::string& text) {
// construct AST from text
NmodlDriver driver;
const auto& ast = driver.parse_string(text);
// construct symbol table from AST
SymtabVisitor(false).visit_program(*ast);
// run constant folding, inlining & local renaming first
ConstantFolderVisitor().visit_program(*ast);
InlineVisitor().visit_program(*ast);
LocalVarRenameVisitor().visit_program(*ast);
SymtabVisitor(true).visit_program(*ast);
// run SympyConductance on AST
SympyConductanceVisitor().visit_program(*ast);
// check that, after visitor rearrangement, parents are still up-to-date
CheckParentVisitor().check_ast(*ast);
// run lookup visitor to extract results from AST
// return BREAKPOINT block as JSON string
return reindent_text(to_nmodl(collect_nodes(*ast, {AstNodeType::BREAKPOINT_BLOCK}).front()));
}
std::string breakpoint_to_nmodl(const std::string& text) {
// construct AST from text
NmodlDriver driver;
const auto& ast = driver.parse_string(text);
// construct symbol table from AST
SymtabVisitor().visit_program(*ast);
// run lookup visitor to extract results from AST
// return BREAKPOINT block as JSON string
return reindent_text(to_nmodl(collect_nodes(*ast, {AstNodeType::BREAKPOINT_BLOCK}).front()));
}
void run_sympy_conductance_passes(ast::Program& node) {
// construct symbol table from AST
SymtabVisitor v_symtab;
v_symtab.visit_program(node);
// run SympySolver on AST several times
SympyConductanceVisitor v_sympy1;
v_sympy1.visit_program(node);
v_symtab.visit_program(node);
v_sympy1.visit_program(node);
v_symtab.visit_program(node);
// also use a second instance of SympySolver
SympyConductanceVisitor v_sympy2;
v_sympy2.visit_program(node);
v_symtab.visit_program(node);
v_sympy1.visit_program(node);
v_symtab.visit_program(node);
v_sympy2.visit_program(node);
v_symtab.visit_program(node);
}
SCENARIO("Addition of CONDUCTANCE using SympyConductance visitor", "[visitor][solver][sympy]") {
// First set of test mod files below all based on:
// nmodldb/models/db/bluebrain/CortexSimplified/mod/Ca.mod
GIVEN("breakpoint block containing VERBATIM statement") {
std::string nmodl_text = R"(
NEURON {
SUFFIX Ca
USEION ca READ eca WRITE ica
RANGE gCabar, gCa, ica
}
BREAKPOINT {
CONDUCTANCE gCa USEION ca
SOLVE states METHOD cnexp
VERBATIM
double z=0;
ENDVERBATIM
gCa = gCabar*m*m*h
ica = gCa*(v-eca)
}
)";
std::string breakpoint_text = R"(
BREAKPOINT {
CONDUCTANCE gCa USEION ca
SOLVE states METHOD cnexp
VERBATIM
double z=0;
ENDVERBATIM
gCa = gCabar*m*m*h
ica = gCa*(v-eca)
}
)";
THEN("Do nothing") {
auto result = run_sympy_conductance_visitor(nmodl_text);
REQUIRE(result == breakpoint_to_nmodl(breakpoint_text));
}
}
GIVEN("breakpoint block containing IF/ELSE block") {
std::string nmodl_text = R"(
NEURON {
SUFFIX Ca
USEION ca READ eca WRITE ica
RANGE gCabar, gCa, ica
}
BREAKPOINT {
CONDUCTANCE gCa USEION ca
SOLVE states METHOD cnexp
IF(gCabar<1){
gCa = gCabar*m*m*h
ica = gCa*(v-eca)
} ELSE {
gCa = 0
ica = 0
}
}
)";
std::string breakpoint_text = R"(
BREAKPOINT {
CONDUCTANCE gCa USEION ca
SOLVE states METHOD cnexp
IF(gCabar<1){
gCa = gCabar*m*m*h
ica = gCa*(v-eca)
} ELSE {
gCa = 0
ica = 0
}
}
)";
THEN("Do nothing") {
auto result = run_sympy_conductance_visitor(nmodl_text);
REQUIRE(result == breakpoint_to_nmodl(breakpoint_text));
}
}
GIVEN("ion current, existing CONDUCTANCE hint & var") {
std::string nmodl_text = R"(
NEURON {
SUFFIX Ca
USEION ca READ eca WRITE ica
RANGE gCabar, gCa, ica
}
UNITS {
(S) = (siemens)
(mV) = (millivolt)
(mA) = (milliamp)
}
PARAMETER {
gCabar = 0.00001 (S/cm2)
}
ASSIGNED {
v (mV)
eca (mV)
ica (mA/cm2)
gCa (S/cm2)
mInf
mTau
mAlpha
mBeta
hInf
hTau
hAlpha
hBeta
}
STATE {
m
h
}
BREAKPOINT {
CONDUCTANCE gCa USEION ca
SOLVE states METHOD cnexp
gCa = gCabar*m*m*h
ica = gCa*(v-eca)
}
DERIVATIVE states {
m' = (mInf-m)/mTau
h' = (hInf-h)/hTau
}
INITIAL{
m = mInf
h = hInf
}
)";
std::string breakpoint_text = R"(
BREAKPOINT {
CONDUCTANCE gCa USEION ca
SOLVE states METHOD cnexp
gCa = gCabar*m*m*h
ica = gCa*(v-eca)
}
)";
THEN("Do nothing") {
auto result = run_sympy_conductance_visitor(nmodl_text);
REQUIRE(result == breakpoint_to_nmodl(breakpoint_text));
}
}
GIVEN("ion current, no CONDUCTANCE hint, existing var") {
std::string nmodl_text = R"(
NEURON {
SUFFIX Ca
USEION ca READ eca WRITE ica
RANGE gCabar, gCa, ica
}
UNITS {
(S) = (siemens)
(mV) = (millivolt)
(mA) = (milliamp)
}
PARAMETER {
gCabar = 0.00001 (S/cm2)
}
ASSIGNED {
v (mV)
eca (mV)
ica (mA/cm2)
gCa (S/cm2)
mInf
mTau
mAlpha
mBeta
hInf
hTau
hAlpha
hBeta
}
STATE {
m
h
}
BREAKPOINT {
SOLVE states METHOD cnexp
gCa = gCabar*m*m*h
ica = gCa*(v-eca)
}
DERIVATIVE states {
m' = (mInf-m)/mTau
h' = (hInf-h)/hTau
}
INITIAL{
m = mInf
h = hInf
}
)";
std::string breakpoint_text = R"(
BREAKPOINT {
CONDUCTANCE gCa USEION ca
SOLVE states METHOD cnexp
gCa = gCabar*m*m*h
ica = gCa*(v-eca)
}
)";
THEN("Add CONDUCTANCE hint using existing var") {
auto result = run_sympy_conductance_visitor(nmodl_text);
REQUIRE(result == breakpoint_to_nmodl(breakpoint_text));
}
}
GIVEN("ion current, no CONDUCTANCE hint, no existing var") {
std::string nmodl_text = R"(
NEURON {
SUFFIX Ca
USEION ca READ eca WRITE ica
RANGE gCabar, ica
}
UNITS {
(S) = (siemens)
(mV) = (millivolt)
(mA) = (milliamp)
}
PARAMETER {
gCabar = 0.00001 (S/cm2)
}
ASSIGNED {
v (mV)
eca (mV)
ica (mA/cm2)
mInf
mTau
mAlpha
mBeta
hInf
hTau
hAlpha
hBeta
}
STATE {
m
h
}
BREAKPOINT {
SOLVE states METHOD cnexp
ica = (gCabar*m*m*h)*(v-eca)
}
DERIVATIVE states {
m' = (mInf-m)/mTau
h' = (hInf-h)/hTau
}
INITIAL{
m = mInf
h = hInf
}
)";
std::string breakpoint_text = R"(
BREAKPOINT {
LOCAL g_ca_0
CONDUCTANCE g_ca_0 USEION ca
g_ca_0 = gCabar*h*pow(m, 2)
SOLVE states METHOD cnexp
ica = (gCabar*m*m*h)*(v-eca)
}
)";
THEN("Add CONDUCTANCE hint with new local var") {
auto result = run_sympy_conductance_visitor(nmodl_text);
REQUIRE(result == breakpoint_to_nmodl(breakpoint_text));
}
}
GIVEN("2 ion currents, 1 CONDUCTANCE hint, 1 existing var") {
std::string nmodl_text = R"(
NEURON {
SUFFIX Ca
USEION ca READ eca WRITE ica
USEION na READ ena WRITE ina
RANGE gCabar, gNabar, ica, ina
}
UNITS {
(S) = (siemens)
(mV) = (millivolt)
(mA) = (milliamp)
}
PARAMETER {
gCabar = 0.00001 (S/cm2)
gNabar = 0.00005 (S/cm2)
}
ASSIGNED {
v (mV)
eca (mV)
ica (mA/cm2)
ina (mA/cm2)
gCa (S/cm2)
mInf
mTau
mAlpha
mBeta
hInf
hTau
hAlpha
hBeta
}
STATE {
m
h
}
BREAKPOINT {
CONDUCTANCE gCa USEION ca
SOLVE states METHOD cnexp
gCa = gCabar*m*m*h
ica = gCa*(v-eca)
ina = (gNabar*m*h)*(v-eca)
}
DERIVATIVE states {
m' = (mInf-m)/mTau
h' = (hInf-h)/hTau
}
INITIAL{
m = mInf
h = hInf
}
)";
std::string breakpoint_text = R"(
BREAKPOINT {
LOCAL g_na_0
CONDUCTANCE g_na_0 USEION na
g_na_0 = gNabar*h*m
CONDUCTANCE gCa USEION ca
SOLVE states METHOD cnexp
gCa = gCabar*m*m*h
ica = gCa*(v-eca)
ina = (gNabar*m*h)*(v-eca)
}
)";
THEN("Add 1 CONDUCTANCE hint with new local var") {
auto result = run_sympy_conductance_visitor(nmodl_text);
REQUIRE(result == breakpoint_to_nmodl(breakpoint_text));
}
}
GIVEN("2 ion currents, no CONDUCTANCE hints, 1 existing var") {
std::string nmodl_text = R"(
NEURON {
SUFFIX Ca
USEION ca READ eca WRITE ica
USEION na READ ena WRITE ina
RANGE gCabar, gNabar, ica, ina
}
UNITS {
(S) = (siemens)
(mV) = (millivolt)
(mA) = (milliamp)
}
PARAMETER {
gCabar = 0.00001 (S/cm2)
gNabar = 0.00005 (S/cm2)
}
ASSIGNED {
v (mV)
eca (mV)
ica (mA/cm2)
ina (mA/cm2)
gCa (S/cm2)
mInf
mTau
mAlpha
mBeta
hInf
hTau
hAlpha
hBeta
}
STATE {
m
h
}
BREAKPOINT {
SOLVE states METHOD cnexp
gCa = gCabar*m*m*h
ica = gCa*(v-eca)
ina = (gNabar*m*h)*(v-eca)
}
DERIVATIVE states {
m' = (mInf-m)/mTau
h' = (hInf-h)/hTau
}
INITIAL{
m = mInf
h = hInf
}
)";
std::string breakpoint_text = R"(
BREAKPOINT {
LOCAL g_na_0
CONDUCTANCE g_na_0 USEION na
CONDUCTANCE gCa USEION ca
g_na_0 = gNabar*h*m
SOLVE states METHOD cnexp
gCa = gCabar*m*m*h
ica = gCa*(v-eca)
ina = (gNabar*m*h)*(v-eca)
}
)";
THEN("Add 2 CONDUCTANCE hints, 1 with existing var, 1 with new local var") {
auto result = run_sympy_conductance_visitor(nmodl_text);
REQUIRE(result == breakpoint_to_nmodl(breakpoint_text));
}
}
GIVEN("2 ion currents, no CONDUCTANCE hints, no existing vars") {
std::string nmodl_text = R"(
NEURON {
SUFFIX Ca
USEION ca READ eca WRITE ica
USEION na READ ena WRITE ina
RANGE gCabar, gNabar, ica, ina
}
UNITS {
(S) = (siemens)
(mV) = (millivolt)
(mA) = (milliamp)
}
PARAMETER {
gCabar = 0.00001 (S/cm2)
gNabar = 0.00005 (S/cm2)
}
ASSIGNED {
v (mV)
eca (mV)
ica (mA/cm2)
ina (mA/cm2)
gCa (S/cm2)
mInf
mTau
mAlpha
mBeta
hInf
hTau
hAlpha
hBeta
}
STATE {
m
h
}
BREAKPOINT {
SOLVE states METHOD cnexp
ica = (gCabar*m*m*h)*(v-eca)
ina = (gNabar*m*h)*(v-eca)
}
DERIVATIVE states {
m' = (mInf-m)/mTau
h' = (hInf-h)/hTau
}
INITIAL{
m = mInf
h = hInf
}
)";
std::string breakpoint_text = R"(
BREAKPOINT {
LOCAL g_ca_0, g_na_0
CONDUCTANCE g_na_0 USEION na
CONDUCTANCE g_ca_0 USEION ca
g_ca_0 = gCabar*h*pow(m, 2)
g_na_0 = gNabar*h*m
SOLVE states METHOD cnexp
ica = (gCabar*m*m*h)*(v-eca)
ina = (gNabar*m*h)*(v-eca)
}
)";
THEN("Add 2 CONDUCTANCE hints with 2 new local vars") {
auto result = run_sympy_conductance_visitor(nmodl_text);
REQUIRE(result == breakpoint_to_nmodl(breakpoint_text));
}
}
GIVEN("1 ion current, 1 nonspecific current, no CONDUCTANCE hints, no existing vars") {
std::string nmodl_text = R"(
NEURON {
SUFFIX Ca
USEION ca READ eca WRITE ica
NONSPECIFIC_CURRENT ihcn
RANGE gCabar, ica
}
UNITS {
(S) = (siemens)
(mV) = (millivolt)
(mA) = (milliamp)
}
PARAMETER {
gCabar = 0.00001 (S/cm2)
}
ASSIGNED {
v (mV)
eca (mV)
ica (mA/cm2)
ihcn (mA/cm2)
gCa (S/cm2)
mInf
mTau
mAlpha
mBeta
hInf
hTau
hAlpha
hBeta
}
STATE {
m
h
}
BREAKPOINT {
SOLVE states METHOD cnexp
ica = (gCabar*m*m*h)*(v-eca)
ihcn = (0.1235*m*h)*(v-eca)
}
DERIVATIVE states {
m' = (mInf-m)/mTau
h' = (hInf-h)/hTau
}
INITIAL{
m = mInf
h = hInf
}
)";
std::string breakpoint_text = R"(
BREAKPOINT {
LOCAL g_ca_0, g__0
CONDUCTANCE g__0
CONDUCTANCE g_ca_0 USEION ca
g_ca_0 = gCabar*h*pow(m, 2)
g__0 = 0.1235*h*m
SOLVE states METHOD cnexp
ica = (gCabar*m*m*h)*(v-eca)
ihcn = (0.1235*m*h)*(v-eca)
}
)";
THEN("Add 2 CONDUCTANCE hints with 2 new local vars") {
auto result = run_sympy_conductance_visitor(nmodl_text);
REQUIRE(result == breakpoint_to_nmodl(breakpoint_text));
}
}
GIVEN("1 ion current, 1 nonspecific current, no CONDUCTANCE hints, 1 existing var") {
std::string nmodl_text = R"(
NEURON {
SUFFIX Ca
USEION ca READ eca WRITE ica
NONSPECIFIC_CURRENT ihcn
RANGE gCabar, ica, gihcn
}
UNITS {
(S) = (siemens)
(mV) = (millivolt)
(mA) = (milliamp)
}
PARAMETER {
gCabar = 0.00001 (S/cm2)
}
ASSIGNED {
v (mV)
eca (mV)
ica (mA/cm2)
ihcn (mA/cm2)
gCa (S/cm2)
gihcn (S/cm2)
mInf
mTau
mAlpha
mBeta
hInf
hTau
hAlpha
hBeta
}
STATE {
m
h
}
BREAKPOINT {
SOLVE states METHOD cnexp
gihcn = 0.1235*m*h
ica = (gCabar*m*m*h)*(v-eca)
ihcn = gihcn*(v-eca)
}
DERIVATIVE states {
m' = (mInf-m)/mTau
h' = (hInf-h)/hTau
}
INITIAL{
m = mInf
h = hInf
}
)";
std::string breakpoint_text = R"(
BREAKPOINT {
LOCAL g_ca_0
CONDUCTANCE gihcn
CONDUCTANCE g_ca_0 USEION ca
g_ca_0 = gCabar*h*pow(m, 2)
SOLVE states METHOD cnexp
gihcn = 0.1235*m*h
ica = (gCabar*m*m*h)*(v-eca)
ihcn = gihcn*(v-eca)
}
)";
THEN("Add 2 CONDUCTANCE hints, 1 using existing var, 1 with new local var") {
auto result = run_sympy_conductance_visitor(nmodl_text);
REQUIRE(result == breakpoint_to_nmodl(breakpoint_text));
}
}
// based on bluebrain/CortextPlastic/mod/ProbAMPANMDA.mod
GIVEN(
"2 ion currents, 1 nonspecific current, no CONDUCTANCE hints, indirect relation between "
"eqns") {
std::string nmodl_text = R"(
NEURON {
THREADSAFE
POINT_PROCESS ProbAMPANMDA
RANGE tau_r_AMPA, tau_d_AMPA, tau_r_NMDA, tau_d_NMDA
RANGE Use, u, Dep, Fac, u0, mg, NMDA_ratio
RANGE i, i_AMPA, i_NMDA, g_AMPA, g_NMDA, g, e
NONSPECIFIC_CURRENT i, i_AMPA,i_NMDA
POINTER rng
RANGE synapseID, verboseLevel
}
PARAMETER {
tau_r_AMPA = 0.2 (ms) : dual-exponential conductance profile
tau_d_AMPA = 1.7 (ms) : IMPORTANT: tau_r < tau_d
tau_r_NMDA = 0.29 (ms) : dual-exponential conductance profile
tau_d_NMDA = 43 (ms) : IMPORTANT: tau_r < tau_d
Use = 1.0 (1) : Utilization of synaptic efficacy (just initial values! Use, Dep and Fac are overwritten by BlueBuilder assigned values)
Dep = 100 (ms) : relaxation time constant from depression
Fac = 10 (ms) : relaxation time constant from facilitation
e = 0 (mV) : AMPA and NMDA reversal potential
mg = 1 (mM) : initial concentration of mg2+
mggate
gmax = .001 (uS) : weight conversion factor (from nS to uS)
u0 = 0 :initial value of u, which is the running value of Use
NMDA_ratio = 0.71 (1) : The ratio of NMDA to AMPA
synapseID = 0
verboseLevel = 0
}
ASSIGNED {
v (mV)
i (nA)
i_AMPA (nA)
i_NMDA (nA)
g_AMPA (uS)
g_NMDA (uS)
g (uS)
factor_AMPA
factor_NMDA
rng
}
STATE {
A_AMPA : AMPA state variable to construct the dual-exponential profile - decays with conductance tau_r_AMPA
B_AMPA : AMPA state variable to construct the dual-exponential profile - decays with conductance tau_d_AMPA
A_NMDA : NMDA state variable to construct the dual-exponential profile - decays with conductance tau_r_NMDA
B_NMDA : NMDA state variable to construct the dual-exponential profile - decays with conductance tau_d_NMDA
}
BREAKPOINT {
SOLVE state METHOD cnexp
mggate = 1.2
g_AMPA = gmax*(B_AMPA-A_AMPA) :compute time varying conductance as the difference of state variables B_AMPA and A_AMPA
g_NMDA = gmax*(B_NMDA-A_NMDA) * mggate :compute time varying conductance as the difference of state variables B_NMDA and A_NMDA and mggate kinetics
g = g_AMPA + g_NMDA
i_AMPA = g_AMPA*(v-e) :compute the AMPA driving force based on the time varying conductance, membrane potential, and AMPA reversal
i_NMDA = g_NMDA*(v-e) :compute the NMDA driving force based on the time varying conductance, membrane potential, and NMDA reversal
i = i_AMPA + i_NMDA
}
DERIVATIVE state{
A_AMPA' = -A_AMPA/tau_r_AMPA
B_AMPA' = -B_AMPA/tau_d_AMPA
A_NMDA' = -A_NMDA/tau_r_NMDA
B_NMDA' = -B_NMDA/tau_d_NMDA
}
)";
std::string breakpoint_text = R"(
BREAKPOINT {
CONDUCTANCE g
CONDUCTANCE g_NMDA
CONDUCTANCE g_AMPA
SOLVE state METHOD cnexp
mggate = 1.2
g_AMPA = gmax*(B_AMPA-A_AMPA) :compute time varying conductance as the difference of state variables B_AMPA and A_AMPA
g_NMDA = gmax*(B_NMDA-A_NMDA) * mggate :compute time varying conductance as the difference of state variables B_NMDA and A_NMDA and mggate kinetics
g = g_AMPA + g_NMDA
i_AMPA = g_AMPA*(v-e) :compute the AMPA driving force based on the time varying conductance, membrane potential, and AMPA reversal
i_NMDA = g_NMDA*(v-e) :compute the NMDA driving force based on the time varying conductance, membrane potential, and NMDA reversal
i = i_AMPA + i_NMDA
}
)";
THEN("Add 3 CONDUCTANCE hints, using existing vars") {
auto result = run_sympy_conductance_visitor(nmodl_text);
REQUIRE(result == breakpoint_to_nmodl(breakpoint_text));
}
}
// based on neurodamus/bbp/lib/modlib/GluSynapse.mod
GIVEN("1 nonspecific current, no CONDUCTANCE hints, many eqs & a function involved") {
std::string nmodl_text = R"(
NEURON {
GLOBAL tau_r_AMPA, E_AMPA
RANGE tau_d_AMPA, gmax_AMPA
RANGE g_AMPA
GLOBAL tau_r_NMDA, tau_d_NMDA, E_NMDA
RANGE g_NMDA
RANGE Use, Dep, Fac, Nrrp, u
RANGE tsyn, unoccupied, occupied
RANGE ica_NMDA
RANGE volume_CR
GLOBAL ljp_VDCC, vhm_VDCC, km_VDCC, mtau_VDCC, vhh_VDCC, kh_VDCC, htau_VDCC
RANGE gca_bar_VDCC, ica_VDCC
GLOBAL gamma_ca_CR, tau_ca_CR, min_ca_CR, cao_CR
GLOBAL tau_GB, gamma_d_GB, gamma_p_GB, rho_star_GB, tau_Use_GB, tau_effca_GB
RANGE theta_d_GB, theta_p_GB
RANGE rho0_GB
RANGE enable_GB, depress_GB, potentiate_GB
RANGE Use_d_GB, Use_p_GB
GLOBAL p_gen_RW, p_elim0_RW, p_elim1_RW
RANGE enable_RW, synstate_RW
GLOBAL mg, scale_mg, slope_mg
RANGE vsyn, NMDA_ratio, synapseID, selected_for_report, verbose
NONSPECIFIC_CURRENT i
}
UNITS {
(nA) = (nanoamp)
(mV) = (millivolt)
(uS) = (microsiemens)
(nS) = (nanosiemens)
(pS) = (picosiemens)
(umho) = (micromho)
(um) = (micrometers)
(mM) = (milli/liter)
(uM) = (micro/liter)
FARADAY = (faraday) (coulomb)
PI = (pi) (1)
R = (k-mole) (joule/degC)
}
ASSIGNED {
g_AMPA (uS)
g_NMDA (uS)
ica_NMDA (nA)
ica_VDCC (nA)
depress_GB (1)
potentiate_GB (1)
v (mV)
vsyn (mV)
i (nA)
}
FUNCTION nernst(ci(mM), co(mM), z) (mV) {
nernst = (1000) * R * (celsius + 273.15) / (z*FARADAY) * log(co/ci)
}
BREAKPOINT {
LOCAL Eca_syn, mggate, i_AMPA, gmax_NMDA, i_NMDA, Pf_NMDA, gca_bar_abs_VDCC, gca_VDCC
g_AMPA = (1e-3)*gmax_AMPA*(B_AMPA-A_AMPA)
i_AMPA = g_AMPA*(v-E_AMPA)
gmax_NMDA = gmax_AMPA*NMDA_ratio
mggate = 1 / (1 + exp(slope_mg * -(v)) * (mg / scale_mg))
g_NMDA = (1e-3)*gmax_NMDA*mggate*(B_NMDA-A_NMDA)
i_NMDA = g_NMDA*(v-E_NMDA)
Pf_NMDA = (4*cao_CR) / (4*cao_CR + (1/1.38) * 120 (mM)) * 0.6
ica_NMDA = Pf_NMDA*g_NMDA*(v-40.0)
gca_bar_abs_VDCC = gca_bar_VDCC * 4(um2)*PI*(3(1/um3)/4*volume_CR*1/PI)^(2/3)
gca_VDCC = (1e-3) * gca_bar_abs_VDCC * m_VDCC * m_VDCC * h_VDCC
Eca_syn = FARADAY*nernst(cai_CR, cao_CR, 2)
ica_VDCC = gca_VDCC*(v-Eca_syn)
vsyn = v
i = i_AMPA + i_NMDA + ica_VDCC
}
)";
std::string breakpoint_text = R"(
BREAKPOINT {
LOCAL Eca_syn, mggate, i_AMPA, gmax_NMDA, i_NMDA, Pf_NMDA, gca_bar_abs_VDCC, gca_VDCC, nernst_in_0, g__0
CONDUCTANCE g__0
g__0 = (0.001*gmax_NMDA*mg*scale_mg*slope_mg*(A_NMDA-B_NMDA)*(E_NMDA-v)*exp(slope_mg*v)-0.001*gmax_NMDA*scale_mg*(A_NMDA-B_NMDA)*(mg+scale_mg*exp(slope_mg*v))*exp(slope_mg*v)+(g_AMPA+gca_VDCC)*pow(mg+scale_mg*exp(slope_mg*v), 2))/pow(mg+scale_mg*exp(slope_mg*v), 2)
g_AMPA = 1e-3*gmax_AMPA*(B_AMPA-A_AMPA)
i_AMPA = g_AMPA*(v-E_AMPA)
gmax_NMDA = gmax_AMPA*NMDA_ratio
mggate = 1/(1+exp(slope_mg*-v)*(mg/scale_mg))
g_NMDA = 1e-3*gmax_NMDA*mggate*(B_NMDA-A_NMDA)
i_NMDA = g_NMDA*(v-E_NMDA)
Pf_NMDA = (4*cao_CR)/(4*cao_CR+0.7246376811594204*120(mM))*0.6
ica_NMDA = Pf_NMDA*g_NMDA*(v-40.0)
gca_bar_abs_VDCC = gca_bar_VDCC*4(um2)*PI*(3(1/um3)/4*volume_CR*1/PI)^0.6666666666666666
gca_VDCC = 1e-3*gca_bar_abs_VDCC*m_VDCC*m_VDCC*h_VDCC
{
LOCAL ci_in_0, co_in_0, z_in_0
ci_in_0 = cai_CR
co_in_0 = cao_CR
z_in_0 = 2
nernst_in_0 = 1000*R*(celsius+273.15)/(z_in_0*FARADAY)*log(co_in_0/ci_in_0)
}
Eca_syn = FARADAY*nernst_in_0
ica_VDCC = gca_VDCC*(v-Eca_syn)
vsyn = v
i = i_AMPA+i_NMDA+ica_VDCC
}
)";
THEN("Add 1 CONDUCTANCE hint using new var") {
auto result = run_sympy_conductance_visitor(nmodl_text);
REQUIRE(result == breakpoint_to_nmodl(breakpoint_text));
}
}
}
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