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/*************************************************************************
* Copyright (C) 2019-2022 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 "codegen/codegen_helper_visitor.hpp"
#include "parser/nmodl_driver.hpp"
#include "visitors/kinetic_block_visitor.hpp"
#include "visitors/neuron_solve_visitor.hpp"
#include "visitors/solve_block_visitor.hpp"
#include "visitors/steadystate_visitor.hpp"
#include "visitors/symtab_visitor.hpp"
using namespace nmodl;
using namespace visitor;
using namespace codegen;
using nmodl::parser::NmodlDriver;
//=============================================================================
// Helper for codegen related visitor
//=============================================================================
std::string run_codegen_helper_visitor(const std::string& text) {
NmodlDriver driver;
const auto& ast = driver.parse_string(text);
/// construct symbol table and run codegen helper visitor
SymtabVisitor().visit_program(*ast);
CodegenHelperVisitor v;
/// symbols/variables are collected in info object
const auto& info = v.analyze(*ast);
/// semicolon separated list of variables
std::string variables;
/// range variables in order of code generation
for (const auto& var: info.range_parameter_vars) {
variables += var->get_name() + ";";
}
for (const auto& var: info.range_assigned_vars) {
variables += var->get_name() + ";";
}
for (const auto& var: info.range_state_vars) {
variables += var->get_name() + ";";
}
for (const auto& var: info.assigned_vars) {
variables += var->get_name() + ";";
}
return variables;
}
SCENARIO("unusual / failing mod files", "[codegen][var_order]") {
GIVEN("cal_mig.mod : USEION variables declared as RANGE") {
std::string nmodl_text = R"(
PARAMETER {
gcalbar=.003 (mho/cm2)
ki=.001 (mM)
cai = 50.e-6 (mM)
cao = 2 (mM)
q10 = 5
USEGHK=1
}
NEURON {
SUFFIX cal
USEION ca READ cai,cao WRITE ica
RANGE gcalbar, cai, ica, gcal, ggk
RANGE minf, tau
GLOBAL USEGHK
}
STATE {
m
}
ASSIGNED {
ica (mA/cm2)
gcal (mho/cm2)
minf
tau (ms)
ggk
}
DERIVATIVE state {
rate(v)
m' = (minf - m)/tau
}
)";
THEN("ionic current variable declared as RANGE appears first") {
std::string expected = "gcalbar;ica;gcal;minf;tau;ggk;m;cai;cao;";
auto result = run_codegen_helper_visitor(nmodl_text);
REQUIRE(result == expected);
}
}
GIVEN("CaDynamics_E2.mod : USEION variables declared as STATE variable") {
std::string nmodl_text = R"(
NEURON {
SUFFIX CaDynamics_E2
USEION ca READ ica WRITE cai
RANGE decay, gamma, minCai, depth
}
PARAMETER {
gamma = 0.05 : percent of free calcium (not buffered)
decay = 80 (ms) : rate of removal of calcium
depth = 0.1 (um) : depth of shell
minCai = 1e-4 (mM)
}
ASSIGNED {ica (mA/cm2)}
STATE {
cai (mM)
}
DERIVATIVE states {
cai' = -(10000)*(ica*gamma/(2*FARADAY*depth)) - (cai - minCai)/decay
}
)";
THEN("ion state variable is ordered after parameter and assigned ionic current") {
std::string expected = "gamma;decay;depth;minCai;ica;cai;";
auto result = run_codegen_helper_visitor(nmodl_text);
REQUIRE(result == expected);
}
}
GIVEN("cadyn.mod : same USEION variables used for read as well as write") {
std::string nmodl_text = R"(
NEURON {
SUFFIX cadyn
USEION ca READ cai,ica WRITE cai
RANGE ca
GLOBAL depth,cainf,taur
}
PARAMETER {
depth = .1 (um)
taur = 200 (ms) : rate of calcium removal
cainf = 50e-6(mM) :changed oct2
cai (mM)
}
ASSIGNED {
ica (mA/cm2)
drive_channel (mM/ms)
}
STATE {
ca (mM)
}
BREAKPOINT {
SOLVE state METHOD euler
}
DERIVATIVE state {
ca' = drive_channel/18 + (cainf -ca)/taur*11
cai = ca
}
)";
THEN("ion variables are ordered correctly") {
std::string expected = "ca;cai;ica;drive_channel;";
auto result = run_codegen_helper_visitor(nmodl_text);
REQUIRE(result == expected);
}
}
}
SCENARIO("Check global variable setup", "[codegen][global_variables]") {
GIVEN("SH_na8st.mod: modfile from reduced_dentate model") {
std::string const nmodl_text{R"(
NEURON {
SUFFIX na8st
}
STATE { c1 c2 }
BREAKPOINT {
SOLVE kin METHOD derivimplicit
}
INITIAL {
SOLVE kin STEADYSTATE derivimplicit
}
KINETIC kin {
~ c1 <-> c2 (a1, b1)
}
)"};
NmodlDriver driver;
const auto ast = driver.parse_string(nmodl_text);
/// construct symbol table and run codegen helper visitor
SymtabVisitor{}.visit_program(*ast);
KineticBlockVisitor{}.visit_program(*ast);
SymtabVisitor{}.visit_program(*ast);
SteadystateVisitor{}.visit_program(*ast);
SymtabVisitor{}.visit_program(*ast);
NeuronSolveVisitor{}.visit_program(*ast);
SolveBlockVisitor{}.visit_program(*ast);
SymtabVisitor{true}.visit_program(*ast);
CodegenHelperVisitor v;
const auto info = v.analyze(*ast);
// See https://github.com/BlueBrain/nmodl/issues/736
THEN("Checking that primes_size and prime_variables_by_order have the expected size") {
REQUIRE(info.primes_size == 2);
REQUIRE(info.prime_variables_by_order.size() == 2);
}
}
}
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