CORENRN_ENABLE_LEGACY_UNITS default OFF (#408)

* CORENRN_ENABLE_LEGACY_UNITS default OFF
   - Consistency of units selection for NEURON and CoreNEURON checked
   - Modern units comes from copy of nrnunits-modern.h
      eion.cpp nrn_nernst and nrn_ghk computes according to the units selection.
* Changed CORENRN_LegacyFR to CORENRN_ENABLE_LEGACY_UNITS
* inlined chk_nrnunit_consist
* mod2c_core built in ${CMAKE_BINARY_DIR}/bin
* update mod2c
* Update ring data to version 1.3
* set MOD2C_ENABLE_LEGACY_UNITS from CORENRN_ENABLE_LEGACY_UNITS
* Fix compilation issue for GPU build
  - use set_property with APPEND so that previous flags are not overridden

Author: nrnhines

CMakeLists.txt

@@ -86,6 +86,7 @@ option(CORENRN_ENABLE_CUDA_UNIFIED_MEMORY "Enable CUDA unified memory support" O
 option(CORENRN_ENABLE_UNIT_TESTS "Enable unit tests execution" ON)
 option(CORENRN_ENABLE_GPU "Enable GPU support using OpenACC" OFF)
 option(CORENRN_ENABLE_SHARED "Enable shared library build" ON)
+option(CORENRN_ENABLE_LEGACY_UNITS "Enable legacy FARADAY, R, etc" OFF)
 
 set(CORENRN_NMODL_DIR
     ""
@@ -240,6 +241,13 @@ if(CORENRN_ENABLE_REPORTING)
   include_directories(${sonatareport_INCLUDE_DIR})
 endif()
 
+if(CORENRN_ENABLE_LEGACY_UNITS)
+  set(CORENRN_USE_LEGACY_UNITS 1)
+else()
+  set(CORENRN_USE_LEGACY_UNITS 0)
+endif()
+set(MOD2C_ENABLE_LEGACY_UNITS ${CORENRN_ENABLE_LEGACY_UNITS} CACHE BOOL "" FORCE)
+
 if(MINGW)
   add_definitions("-DMINGW")
 endif()
@@ -275,7 +283,7 @@ if(CORENRN_ENABLE_NMODL)
   separate_arguments(NMODL_EXTRA_FLAGS_LIST UNIX_COMMAND "${CORENRN_NMODL_FLAGS}")
 else()
   include(AddMod2cSubmodule)
-  set(CORENRN_NMODL_BINARY ${CMAKE_BINARY_DIR}/external/mod2c/src/mod2c_core/mod2c_core${CMAKE_EXECUTABLE_SUFFIX})
+  set(CORENRN_NMODL_BINARY ${CMAKE_BINARY_DIR}/bin/mod2c_core${CMAKE_EXECUTABLE_SUFFIX})
   set(CORENRN_NMODL_INCLUDE ${CMAKE_BINARY_DIR}/include)
 endif()
 
@@ -398,6 +406,7 @@ if(cmake_generator_tolower MATCHES "makefile")
     message(STATUS "  INC               | ${MPI_C_INCLUDE_PATH}")
   endif()
   message(STATUS "OpenMP              | ${CORENRN_ENABLE_OPENMP}")
+  message(STATUS "Use legacy units    | ${CORENRN_ENABLE_LEGACY_UNITS}")
   message(STATUS "NMODL               | ${CORENRN_ENABLE_NMODL}")
   if(CORENRN_ENABLE_NMODL)
     message(STATUS "  PATH              | ${CORENRN_NMODL_BINARY}")

coreneuron/CMakeLists.txt

@@ -56,6 +56,11 @@ set(NMODL_UNITS_FILE "${CMAKE_BINARY_DIR}/share/mod2c/nrnunits.lib")
 file(COPY ${CORENEURON_PROJECT_SOURCE_DIR}/coreneuron/mechanism/mech/modfile
      DESTINATION ${CMAKE_BINARY_DIR}/share)
 
+# eion.cpp depends on CORENRN_USE_LEGACY_UNITS
+set(LegacyFR_FILES mechanism/eion.cpp apps/main1.cpp io/global_vars.cpp)
+set_source_files_properties(${LegacyFR_FILES} PROPERTIES COMPILE_FLAGS
+                              "-DCORENRN_USE_LEGACY_UNITS=${CORENRN_USE_LEGACY_UNITS}")
+
 # =============================================================================
 # coreneuron GPU library
 # =============================================================================
@@ -100,6 +105,17 @@ else()
   set(link_cudacoreneuron "")
 endif()
 
+# =============================================================================
+# eion.cpp depends on CORENRN_USE_LEGACY_UNITS
+# =============================================================================
+set(LegacyFR_FILES
+    ${CMAKE_CURRENT_SOURCE_DIR}/mechanism/eion.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/apps/main1.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/io/global_vars.cpp)
+
+set_property(SOURCE ${LegacyFR_FILES} APPEND PROPERTY COMPILE_OPTIONS
+                              "-DCORENRN_USE_LEGACY_UNITS=${CORENRN_USE_LEGACY_UNITS}")
+
 # =============================================================================
 # run KINDERIV_PYTHON_SCRIPT to generate _kinderiv.h
 # =============================================================================

coreneuron/apps/main1.cpp

@@ -70,6 +70,11 @@ const char* corenrn_version() {
     return coreneuron::bbcore_write_version;
 }
 
+// the CORENRN_USE_LEGACY_UNITS determined by CORENRN_ENABLE_LEGACY_UNITS
+bool corenrn_units_use_legacy() {
+    return CORENRN_USE_LEGACY_UNITS;
+}
+
 void (*nrn2core_part2_clean_)();
 
 #ifdef ISPC_INTEROP

coreneuron/io/global_vars.cpp

@@ -9,6 +9,7 @@
 #include "coreneuron/mechanism/membfunc.hpp"
 #include "coreneuron/utils/nrn_assert.h"
 #include "coreneuron/io/nrn2core_direct.h"
+#include "coreneuron/utils/nrnoc_aux.hpp"
 
 void* (*nrn2core_get_global_dbl_item_)(void*, const char*& name, int& size, double*& val);
 int (*nrn2core_get_global_int_item_)(const char* name);
@@ -121,6 +122,12 @@ void set_globals(const char* path, bool cli_global_seed, int cli_global_seed_val
                     secondorder = n;
                 } else if (strcmp(name, "Random123_globalindex") == 0) {
                     nrnran123_set_globalindex((uint32_t)n);
+                } else if (strcmp(name, "_nrnunit_use_legacy_") == 0) {
+                    if (n != CORENRN_USE_LEGACY_UNITS) {
+                        hoc_execerror("CORENRN_ENABLE_LEGACY_UNITS not"
+                            " consistent with NEURON value of"
+                            " nrnunit_use_legacy()", NULL);
+                    }
                 }
             }
         }

coreneuron/mechanism/eion.cpp

@@ -81,7 +81,6 @@ static const char* mechanism[] = {/*just a template*/
 void nrn_init_ion(NrnThread*, Memb_list*, int);
 void nrn_alloc_ion(double*, Datum*, int);
 
-double nrn_nernst(), nrn_ghk();
 static int na_ion, k_ion, ca_ion; /* will get type for these special ions */
 
 int nrn_is_ion(int type) {
@@ -182,8 +181,19 @@ the USEION statement of any model using this ion\n",
     }
 }
 
+#ifndef CORENRN_USE_LEGACY_UNITS
+#define CORENRN_USE_LEGACY_UNITS 0
+#endif
+
+#if CORENRN_USE_LEGACY_UNITS == 1
 #define FARADAY 96485.309
-#define ktf (1000. * 8.3134 * (celsius + 273.15) / FARADAY)
+#define gasconstant 8.3134
+#else
+#include "coreneuron/nrnoc/nrnunits_modern.h"
+#define FARADAY _faraday_codata2018
+#define gasconstant _gasconstant_codata2018
+#endif
+#define ktf (1000. * gasconstant * (celsius + 273.15) / FARADAY)
 
 double nrn_nernst(double ci, double co, double z, double celsius) {
     /*printf("nrn_nernst %g %g %g\n", ci, co, z);*/

coreneuron/nrnoc/nrnunits_modern.h

@@ -0,0 +1,28 @@
+#ifndef nrnunits_modern_h
+#define nrnunits_modern_h
+
+/**
+ NMODL translated MOD files get unit constants typically from
+ share/lib/nrnunits.lib.in. But there were other source files that
+ hardcode some of the constants. Here we gather a few modern units into
+ a single place (but, unfortunately, also in nrnunits.lib.in). Legacy units
+ cannot be gathered here because they can differ slightly from place to place.
+
+ These come from https://physics.nist.gov/cuu/Constants/index.html.
+ Termed the "2018 CODATA recommended values", they became available
+ on 20 May 2019 and replace the 2014 CODATA set.
+
+ See oc/hoc_init.c, nrnoc/eion.c, nrniv/kschan.h
+**/
+
+
+#define _electron_charge_codata2018 1.602176634e-19 /* coulomb exact*/
+#define _avogadro_number_codata2018 6.02214076e+23 /* exact */
+#define _boltzmann_codata2018 1.380649e-23 /* joule/K exact */
+#define _faraday_codata2018 (_electron_charge_codata2018*_avogadro_number_codata2018) /* 96485.33212... coulomb/mol */
+#define _gasconstant_codata2018 (_boltzmann_codata2018*_avogadro_number_codata2018) /* 8.314462618... joule/mol-K */
+
+/* e/k in K/millivolt */
+#define _e_over_k_codata2018 (.001*_electron_charge_codata2018/_boltzmann_codata2018) /* 11.604518... K/mV */
+
+#endif /* nrnunits_modern_h */

coreneuron/utils/nrnoc_aux.cpp

@@ -40,7 +40,7 @@ int v_structure_change;
 int diam_changed;
 #define MAXERRCOUNT 5
 int hoc_errno_count;
-const char* bbcore_write_version = "1.2";
+const char* bbcore_write_version = "1.3"; // globals.dat has _nrnunit_use_legacy_
 
 char* pnt_name(Point_process* pnt) {
     return corenrn.get_memb_func(pnt->_type).sym;

coreneuron/utils/nrnoc_aux.hpp

@@ -55,4 +55,8 @@ extern void hoc_warning(const char*, const char*);
 
 extern double hoc_Exp(double x);
 
+// defined in eion.cpp and this file included in translated mod files.
+extern double nrn_nernst(double ci, double co, double z, double celsius);
+extern double nrn_ghk(double v, double ci, double co, double z);
+
 }  // namespace coreneuron