Merge branch 'Tim_bgc' into 'main'

Merge Tim_bgc into main

See merge request !9

.gitignore

 # src https://www.toptal.com/developers/gitignore/api/intellij
 # src https://www.toptal.com/developers/gitignore/api/python
+# src https://www.toptal.com/developers/gitignore/api/java,macos,maven,eclipse
 
 # Project-specific generated files
 docs/build/
@@ -161,3 +162,14 @@ fabric.properties
 
 # Android studio 3.1+ serialized cache file
 .idea/caches/build_file_checksums.ser
+
+### macOS ###
+**/.DS_Store
+**/.AppleDouble
+**/.LSOverride
+
+# Eclipse Gradle plugin generated files
+# Eclipse Core
+.project
+# JDT-specific (Eclipse Java Development Tools)
+.classpath

bgc-dsl/.vscode/launch.json

@@ -26,6 +26,7 @@
             "justMyCode": false,
             "python": "${command:python.interpreterPath}",
             "cwd": "${workspaceFolder}",
+            "preLaunchTask": "print workspaceFolder",
             "env": {
                 "PYTHONPATH": "${workspaceFolder}:${workspaceFolder}/../antlrLib/"
             }

bgc-dsl/bgcLSPServer/cst/SymbolTableVisitor.py

-"""SymbolTableVisitor module."""
+"""This visitor collects variables and nodes in a SymbolTable."""
 
-__author__ = 'sgu'
+__author__ = 'stu90642'
 
 # util imports
 from typing import TypeVar, Generic, Dict, Optional, Callable, Any
@@ -20,6 +20,8 @@ class SymbolTableVisitor( BgcDslVisitor, Generic[T] ):
     def __init__(self, name: str = '', ):
         super().__init__()
         self._symbolTable = SymbolTable( name, SymbolTableOptions( False ) )
+        # TODO scope marker
+        # self._scope = self._symbolTable.addNewSymbolOfType( ScopedSymbol, None )
         self._scope = None
 
     @property
@@ -29,6 +31,49 @@ class SymbolTableVisitor( BgcDslVisitor, Generic[T] ):
     def defaultResult(self) -> SymbolTable:
         return self._symbolTable
 
+    # 5 mal das gleiche; kann man das kürzer/eleganter schreiben?
+    def visitSubstanceDeclaration(self, ctx:BgcDslParser.SubstanceDeclarationContext):
+        # TODO
+        # save name, type
+        # save unit as node
+        self._symbolTable.addNewSymbolOfType( VariableSymbol, self._scope, ctx.name.text, ctx )
+        return self.visitChildren( ctx )
+
+    def visitParameterDeclaration(self, ctx:BgcDslParser.ParameterDeclarationContext):
+        # TODO
+        # save name, type
+        # save unit, expression as node
+        self._symbolTable.addNewSymbolOfType( VariableSymbol, self._scope, ctx.name.text, ctx )
+        return self.visitChildren( ctx )
+
+    def visitEnvironmentVariableDeclaration(self, ctx:BgcDslParser.EnvironmentVariableDeclarationContext):
+        # TODO
+        # save name, type
+        # save unit, expression as node
+        self._symbolTable.addNewSymbolOfType( VariableSymbol, self._scope, ctx.name.text, ctx )     
+        return self.visitChildren( ctx )
+             
+    # Visit a parse tree produced by BgcDslParser#compartment.
+    def visitCompartment(self, ctx:BgcDslParser.CompartmentContext):
+        # TODO
+        # save name
+        # save node as expression
+        self._symbolTable.addNewSymbolOfType( VariableSymbol, self._scope, ctx.name.text, ctx )
+        return self.visitChildren(ctx)
+    
+    # Visit a parse tree produced by BgcDslParser#connection.
+    def visitConnection(self, ctx:BgcDslParser.ConnectionContext):
+        # TODO
+        # save name
+        # save node as expression
+        # the name needs to be more complex, here:
+        name = ctx.name.text + ' from ' + ctx.sourceCompartment.text + ' to ' + ctx.targetCompartment.text
+        self._symbolTable.addNewSymbolOfType( VariableSymbol, self._scope, name, ctx )
+        return self.visitChildren(ctx)
+
+    # def visitFuncExpr(self, ctx: TestGrammarParser.FuncExprContext):
+    #     return self.withScope( ctx, RoutineSymbol, lambda: self.visitChildren( ctx ), ctx.ID().getText() )
+
     def withScope(self, tree: ParseTree, t: type, action: Callable, *my_args: P.args or None,
                   **my_kwargs: P.kwargs or None) -> T:
         scope = self._symbolTable.addNewSymbolOfType( t, self._scope, *my_args, **my_kwargs )

bgc-dsl/bgcLSPServer/grammars/BgcDsl.g4

-
 grammar BgcDsl;
 
 import CommonLexerRules;

bgc-dsl/bgcLSPServer/other/Main.py

+# Parses from a file (according to BgcDsl.g4)
+# and saves its variables and nodes (context objects) in a SymbolTable.
+
+import sys
+from antlr4 import *
+from BgcDslLexer import BgcDslLexer
+from BgcDslParser import BgcDslParser
+from My_SymbolTableVisitor import My_SymbolTableVisitor
+from SymbolTable import ScopedSymbol, SymbolTable, P, T, VariableSymbol, Symbol, RoutineSymbol, SymbolTableOptions
+
+def main(argv):
+    input_stream = FileStream('example2.bgc')
+    lexer = BgcDslLexer(input_stream)
+    stream = CommonTokenStream(lexer)
+    parser = BgcDslParser(stream)     # returns object of class "Parser"
+
+    tree = parser.bgcModel()  # tree ist ein ctx-objekt
+    symbolTable = My_SymbolTableVisitor('SymbolTableVisitor_1').visit(tree)
+
+    # shows the SymbolTable contents
+    for e in symbolTable.getAllSymbolsSync(Symbol):
+        print('#', e.name, '=', e.value)
+
+main(sys.argv)

bgc-dsl/bgcLSPServer/other/my server old.py

+# altered, to react to bgc-file opening (not done, yet)
+
+import asyncio
+import json
+import re
+import time
+import uuid
+from json import JSONDecodeError
+from typing import Optional
+from antlr4 import InputStream, CommonTokenStream     
+
+from lsprotocol.types import (TEXT_DOCUMENT_COMPLETION, TEXT_DOCUMENT_DID_CHANGE,
+                               TEXT_DOCUMENT_DID_CLOSE, TEXT_DOCUMENT_DID_OPEN,
+                               TEXT_DOCUMENT_SEMANTIC_TOKENS_FULL)
+from lsprotocol.types import (CompletionItem, CompletionList, CompletionOptions,
+                              CompletionParams, ConfigurationItem,
+                              Diagnostic,
+                              DidChangeTextDocumentParams,
+                              DidCloseTextDocumentParams,
+                              DidOpenTextDocumentParams, MessageType, Position,
+                              Range, Registration, RegistrationParams,
+                              SemanticTokens, SemanticTokensLegend, SemanticTokensParams,
+                              Unregistration, UnregistrationParams,
+                              WorkDoneProgressBegin, WorkDoneProgressEnd,
+                              WorkDoneProgressReport,
+                              WorkspaceConfigurationParams)
+from pygls.server import LanguageServer
+
+COUNT_DOWN_START_IN_SECONDS = 10
+COUNT_DOWN_SLEEP_IN_SECONDS = 1
+
+
+class BgcDslLanguageServer(LanguageServer):
+    CMD_COUNT_DOWN_BLOCKING = 'countDownBlocking'
+    CMD_COUNT_DOWN_NON_BLOCKING = 'countDownNonBlocking'
+    CMD_PROGRESS = 'progress'
+    CMD_REGISTER_COMPLETIONS = 'registerCompletions'
+    CMD_SHOW_CONFIGURATION_ASYNC = 'showConfigurationAsync'
+    CMD_SHOW_CONFIGURATION_CALLBACK = 'showConfigurationCallback'
+    CMD_SHOW_CONFIGURATION_THREAD = 'showConfigurationThread'
+    CMD_UNREGISTER_COMPLETIONS = 'unregisterCompletions'
+
+    CONFIGURATION_SECTION = 'BgcDslServer'
+
+    def __init__(self, *args):
+        super().__init__(*args)
+
+#######
+
+def main():
+    print('###########test')
+    # a = BgcDslLanguageServer()
+    # _validate_bgc(a, params)
+
+######
+
+bgcDsl_server = BgcDslLanguageServer('pygls-BgcDsl-example', 'v0.1')
+
+# ls steht für BgcDslLanguageServer (siehe main branch)
+def _validate(ls, params):
+    ls.show_message_log('Validating bgc-file...')
+
+    text_doc = ls.workspace.get_document(params.text_document.uri)
+
+    source = text_doc.source
+    diagnostics = _validate_bgc(ls, source) if source else []
+
+    ls.publish_diagnostics(text_doc.uri, diagnostics)
+
+# copied from example from main branch
+def _validate_bgc(ls: BgcDslLanguageServer, source: str):
+    """Validates file format."""
+    # get input stream of characters for lexer
+    input_stream: InputStream = InputStream( source )
+
+    # set the input stream and reset the lexer/parser/listener
+    ls.error_listener.reset()
+    ls.lexer.inputStream = input_stream
+    ls.tokenStream = CommonTokenStream( ls.lexer )
+    ls.parser.setInputStream( ls.tokenStream )
+
+    try:
+        # launch parser by invoking top-level rule
+        ls.parser.stat()
+    except OSError as err:
+        # TODO add exception
+        msg = err.filename.msg
+
+        ls.error_listener.diagnostics.append( msg )
+
+    # return diagnostics
+    return ls.error_listener.diagnostics
+
+# def _validate_bgc(source):
+#     """Validates bgc-file."""
+#     diagnostics = []
+
+#     try:
+#         # hier muss noch an bgc angepasst werden, incl parser
+#         # alt: json.loads(source)
+#         # hinweis: ls.parser.stat()
+
+#         input_stream = InputStream(source)   # old: FileStream('example2.bgc')
+#         lexer = BgcDslLexer(input_stream)
+#         stream = CommonTokenStream(lexer)
+#         parser = BgcDslParser(stream)     # returns object of class "Parser"
+
+#         tree = parser.bgcModel()  # tree ist ein ctx-objekt
+#         # symbolTable = My_SymbolTableVisitor('SymbolTableVisitor_1').visit(tree)
+
+#     # unnötig?
+#     except OSError as err:
+#         msg = err.msg
+#         col = err.colno
+#         line = err.lineno
+
+#         d = Diagnostic(
+#             range=Range(
+#                 start=Position(line=line - 1, character=col - 1),
+#                 end=Position(line=line - 1, character=col)
+#             ),
+#             message=msg,
+#             source=type(bgcDsl_server).__name__
+#         )
+
+#         diagnostics.append(d)
+
+#     return diagnostics
+
+
+@bgcDsl_server.feature(TEXT_DOCUMENT_DID_CHANGE)
+def did_change(ls, params: DidChangeTextDocumentParams):
+    """Text document did change notification."""
+    _validate(ls, params)
+
+
+@bgcDsl_server.feature(TEXT_DOCUMENT_DID_CLOSE)
+def did_close(server: BgcDslLanguageServer, params: DidCloseTextDocumentParams):
+    """Text document did close notification."""
+    server.show_message('Text Document Did Close')
+
+
+@bgcDsl_server.feature(TEXT_DOCUMENT_DID_OPEN)
+async def did_open(ls, params: DidOpenTextDocumentParams):
+    """Text document did open notification."""
+    ls.show_message('Text Document Did Open')
+    _validate(ls, params)
+
+main()
\ No newline at end of file

bgc-dsl/bgcLSPServer/other/test.py

+a = [1,2,3]
+a = map(lambda x: x + 1, a)
+b = list(a)
+print(a)
+print(b)
\ No newline at end of file

bgc-dsl/bgcLSPServer/other/test_sample.py

+#
+#
+# # # an example to try PyTest
+#
+# import unittest
+#
+# #
+# # def func(x):
+# #     return x + 1
+# #
+#
+# class TestClass(unittest.TestCase):    # wenn ich eine klasse verwende, dann muss ihr name mit "Test" beginnen.
+#
+#     def test_1(self):   # namen von test-funktionen müssen mit "test_" beginnen, oder auf "_test" enden.
+#         self.assertEqual(3, 11)
+#
+#     # def test_answer(self):
+#     #     assert func(3) == 5

bgc-dsl/bgcLSPServer/other/test_symbolTableVisitor.py

+
+from antlr4 import *
+from BgcDslLexer import BgcDslLexer
+from BgcDslParser import BgcDslParser
+from My_SymbolTableVisitor import My_SymbolTableVisitor
+from SymbolTable_copy import ScopedSymbol, SymbolTable, P, T, VariableSymbol, Symbol, RoutineSymbol, SymbolTableOptions
+import unittest
+
+# tests My_SymbolTableVisitor
+def prepare():
+    input_stream = FileStream('example1_shortened.bgc')
+    lexer = BgcDslLexer(input_stream)
+    stream = CommonTokenStream(lexer)
+    parser = BgcDslParser(stream)     # returns object of class "Parser"
+
+    tree = parser.bgcModel()  # tree ist ein ctx-objekt
+    my_SymbolTableVisitor = My_SymbolTableVisitor('SymbolTableVisitor_1')  # parse tree an My_SymbolTableVisitor übergeben
+    symbolTable = my_SymbolTableVisitor.visit(tree)
+    return symbolTable
+
+# # tests SymbolTable
+# def prepare():
+#     st1 = SymbolTable('SymbolTable_1', SymbolTableOptions( allowDuplicateSymbols = False ))
+#     st1.addNewSymbolOfType(VariableSymbol, None, 'A', 123)
+#     st1.addNewSymbolOfType(VariableSymbol, None, 'B', 111)
+#     return st1
+
+class TestSTVisitor(unittest.TestCase):    # wenn ich eine klasse verwende, dann muss ihr name mit "Test" beginnen.
+
+    def test_amount(self):   # namen von test-funktionen müssen mit "test_" beginnen, oder auf "_test" enden.
+        symbolTable = prepare()
+        self.assertEqual(len(symbolTable.getAllSymbolsSync(Symbol)), 2)
+
+    # tests whether this variable is in the ST
+    def test_variable1(self):
+        symbolTable = prepare()
+        self.assertIsNotNone(symbolTable.resolveSync('N'))  # resolveSync returns a VariableSymbol object
+
+    def test_variable2(self):
+        symbolTable = prepare()
+        self.assertIsNotNone(symbolTable.resolveSync('C'))  # resolveSync returns a VariableSymbol object
+
+
+    # def test_variableC(self):
+    #     symbolTable = prepare()
+    #     self.assertIsNotNone(symbolTable.resolveSync('C'))

bgc-dsl/client/src/extension.ts

@@ -61,7 +61,7 @@ function startLangServerTCP(addr: number): LanguageClient {
 
     return new LanguageClient(
         `tcp lang server (port ${addr})`,
-        serverOptions,
+        serverOptioMy_Sns,
         getClientOptions()
     );
 }

bgc-dsl/input/example1_no_dup_vars.bgc

+// out-commented duplicate variables
+
+model cnp_recom
+
+substances
+	float N : mmol
+	float C : mmol
+	float P : mmol
+	float Chl : mmol
+	float DIN : mmol N m^-3
+	float DIP ::
+	float DIC ::
+	float _TA ::
+
+parameters
+	float Q_r_C_N : mmol C (mmol N)^-1 = 5.5   //
+	float Q_r_N_P :  mmol N (mmol P)^-1 = 16.0  //
+
+	float T_ref : K = 283.15
+
+	float sigma_N_C : (mmol N)^2 (mmol C)^-2 = 100.0
+	float sigma_P_N  : (mmol P)^2 (mmol N)^-2 = 50.0
+	float g_max:: = 0.3
+
+	float T_f :: = 0
+
+	float epsilon :: = 0.78
+	float A_E :: = 0.75
+	float Omega :: = 0
+
+	float Q_1_N_C : mmol N (mmol C)^-1 = 0.043
+	float Q_2_N_C : mmol N (mmol C)^-1 = 0.171
+	float Q_1_P_N : mmol P (mmol N)^-1 = 0.02
+	float Q_2_P_N : mmol P (mmol N)^-1 = 0.2
+	float Q_u_N_C : mmol N (mmol C)^-1 = 0.171
+	float Q_u_P_N : mmol P (mmol N)^-1 = 0.014
+
+	float Zeta_DIN : mmol C (mmol N)^-1 = 2.3
+	float Zeta_N_2 : mmol C (mmol N)^-1 = 4.2
+
+	float Psi_max :: = 0.8
+	string criteria :: = option_a
+
+diagnostics
+	float T_K : K = 0
+	float I : W m^-2
+
+	float q_C_P ::
+	float q_N_P ::
+	float q_C_N : mmol C (mmol N)^-1
+	float q_N_C : mmol N (mmol C)^-1
+	float q_P_N : mmol P (mmol N)^-1
+
+compartment Phy {
+	states
+		Chl = 0
+		C = 0
+		N = 0
+		P = 0
+
+	parameters
+		float r_0 :: = 0.01
+		float Ar :: = 4000
+
+		float alpha : mmol C (mg Chl)^-1 m^2 W^-1 #d^-1 = 0.6
+		float my_max : #d^-1 = 2.6
+		float gamma_C : #d^-1 = 0.08
+		float gamma_Chl : #d^-1 = 0.01
+		float gamma : #d^-1 = 0.06
+		float Phi :  m^3 (mmol N)^-1 #d^-1 = 0.02
+		float Theta_2_N : mg Chl (mmol N)^-1 = 2.4
+
+	diagnostics
+		float Theta_C : mg Chl (mmol C)^-1
+		float Theta_N : mg Chl (mmol N)^-1
+
+	calc Psi = max(0, Psi_max * ( 1 - q_N_C/Q_2_N_C))
+
+	calc R_P = 1 - Q_1_P_N / q_P_N
+	calc R_C = (1 + exp(-1 * sigma_N_C * (Q_2_N_C - q_N_C)))^-1
+	calc R_N = (1 + exp(-1 * sigma_P_N * (Q_2_P_N - q_P_N)))^-1
+	calc T_f = exp (-1*Ar * (T_K^-1 - T_K^-1))
+
+	calc phot_max = my_max * T_f * (q_N_C - Q_1_N_C)/(Q_2_N_C - Q_1_N_C)
+	calc phot_DIC = phot_max * (1 - exp( -1 * alpha * Theta_C * I / phot_max ))
+
+	calc assim_DIN = Q_u_N_C * my_max * T_f * R_P * R_C * Nutrients.DIN / (Nutrients.K_DIN + Nutrients.DIN)
+	calc assim_DIP = Q_u_P_N * my_max * T_f * R_N * Nutrients.DIP/(Nutrients.K_DIP + Nutrients.DIP)
+
+	calc degr_Chl = gamma_Chl
+	calc synth_Chl = assim_DIN * Theta_2_N * phot_DIC / (alpha * Theta_C * I)
+
+	update C = phot_DIC * C - (respiration + gamma_C + aggregation) * C - Phy>grazing * q_C_N
+	update N = assim_DIN * C - (r_0 * T_f + gamma + aggregation) * N - Phy>grazing
+	update P = assim_DIP * N - (r_0 * T_f + gamma + aggregation) * P - Phy>grazing * q_P_N
+	update Chl = synth_Chl * C - (degr_Chl + aggregation) * Chl - Phy>grazing * Theta_N
+}
+
+compartment N_2 {
+	states
+		N = 0
+
+	update N = 0
+}
+
+compartment Nutrients {
+	states
+		DIN = 0
+		DIP = 0
+		DIC = 0
+		_TA = 0
+
+	parameters
+		float K_DIP : mmol P m^-3 = 0
+		float K_DIN : mmol N m^-3 = 0
+
+		float rho_C :: = 0
+		float rho_N :: = 0
+		float rho_P :: = 0
+
+	update DIC = T_f * (rho_C * LDOM.C + MG.rho * MG.C)
+		+ respiration * Phy.C
+		+ respiration * Nif.C
+		+ (Het:respiration + epsilon * (1 - Omega) * Het:mortality) * Het.C
+		- Phy.phot_DIC * Phy.C - Nif.phot_DIC * Nif.C
+	update DIN = T_f * (rho_N * LDOM.N + MG.rho * MG.N)
+		+ Phy.r_0 * Phy.T_f * Phy.N
+		+ Nif.r_0 * Nif.T_f * Nif.N
+		+ epsilon * (Het:excretion.N + (1 - Omega) * Het:mortality) * Het.N
+		- Phy:assimilation - Nif.assim_DIN * Nif.C - denitrification
+	update DIP = T_f * rho_P * LDOM.P
+		+ Phy.r_0 * Phy.T_f * Phy.P
+		+ Nif.r_0 * Nif.T_f * Nif.P
+		+ epsilon * (Het:excretion.P + ( 1-Omega) * Het:mortality) * Het.P - Phy.assim_DIP * Phy.N - Nif.assim_DIP * Nif.N
+	update _TA = Phy.assim_DIN * Phy.C + Phy.assim_DIP * Phy.N
+		+ assimilation.C + assimilation.N
+		- Phy.r_0 * Phy.T_f * Phy.N - Nif.r_0 * Nif.T_f * Nif.N
+		- Phy.r_0 * Phy.T_f * Phy.P - Nif.r_0 * Nif.T_f * Nif.P
+		- epsilon * (Het:excretion.N + (1-Omega) * Het:mortality) * Het.N
+		- epsilon * (Het:excretion.P + (1-Omega) * Het:mortality) * Het.P
+		- T_f * (rho_N * LDOM.N - MG.rho * MG.N - rho_P * LDOM.P)
+		+ denitrification
+}
+
+compartment Het {
+	states
+		C = 0
+		N = 0
+		P = 0
+
+	parameters
+		float K_N : mmol N m^-3 = 1.0
+		//float r_0 : #d^-1 = 0.01    // duplicate variable
+		float tau : #d^-1 = 0.5
+		// float gamma : m^3 (mmol N)^-1 #d^-1 = 0.3      // dupl
+
+	update C = A_E * (Phy:grazing * q_C_N + Nif:grazing * q_C_N) - (respiration + mortality) * C
+	update N = A_E * (Phy:grazing + Nif:grazing) - (excretion.N + mortality) * N
+	update P = A_E * (Phy:grazing * q_P_N + Nif:grazing * q_P_N) - (excretion.P + mortality) * P
+}
+
+compartment Det {
+	states
+		C = 0
+		N = 0
+		P = 0
+
+	parameters
+		//float Phi : m^3 (mmol N)^-1 #d^-1 = 0.02
+		//float Omega :: = 0
+
+	calc omega_C = 0
+	calc omega_N = 0
+	calc omega_P = 0
+
+	// could add a sink
+	calc sedimentation_C = 0
+	calc sedimentation_N = 0
+	calc sedimentation_P = 0
+
+	update C = Phy:aggregation * Phy.C
+		+ aggregation * Nif.C
+		+ MG.Phi * N * MG.C
+		+ (1-A_E) * (Phy:grazing * q_C_N + Phy:grazing * q_C_N)
+		+ Omega * Het:mortality * Het.C - degradation.C - sedimentation_C
+	update N = Phy:aggregation * Phy.N
+		+ Nif:aggregation * Nif.N
+		+ MG.Phi * N * MG.N
+		+ (1-A_E) * (Phy:grazing + Nif:grazing) + Omega * Het:mortality * Het.N - degradation.N - sedimentation_N
+	update P = Phy:aggregation * Phy.P
+		+ Nif:aggregation * Nif.P
+		+ (1-A_E) * (Phy:grazing * q_P_N + Nif:grazing * q_P_N)
+		+ Omega * Het:mortality * Het.P - degradation.P - sedimentation_P
+}
+
+
+compartment dCCHO {
+	states C = 0
+
+	parameters
+		float Phi_TEPC :: = 0
+		//float Phi :: = 0
+
+	update C = Phy.Psi * Phy.gamma_C * Phy.C + Nif.Psi * Nif.gamma_C * Nif.C - coagulation * C
+}
+
+
+compartment MG {
+	states
+		C = 0
+		N = 0
+
+	parameters
+		//float Phi :: = 0
+		float rho :: = 0
+		float Xi :: = 0
+
+	update C = coagulation * dCCHO.C - aggregation * C
+	update N = Xi * C * LDOM.N - (rho * T_f + Phi * Det.N) * N
+}
+
+
+compartment LDOM {
+	states
+		C = 0
+		N = 0
+		P = 0
+
+	parameters
+		float omega_C :: = 0
+		float omega_N :: = 0
+		float omega_P :: = 0
+		//float Omega :: = 0
+		//float rho_C :: = 0
+		//float rho_N :: = 0
+		//float rho_P :: = 0
+
+	update C = degradation.C
+		+ (1 - Phy.Psi) * Phy.gamma_C * Phy.C
+		+ (1 - Nif.Psi) * Nif.gamma_C * Nif.C
+		+ (1-epsilon) * (1-Omega) * mortality * Het.C - rho_C * T_f * C
+	update N = degradation.N
+		+ Phy.gamma * Phy.N + Nif.gamma * Nif.N
+		+ (1-epsilon) * excretion.N * Het.N
+		+ (1-epsilon) * (1-Omega) * mortality * Het.N - (rho_N * T_f + MG.Xi * MG.C) * N
+	update P = degradation.P
+		- Phy.gamma * Phy.P + Nif.gamma * Nif.P
+		+ (1-epsilon) * (excretion.P + (1-Omega) * mortality) * Het.P - rho_P * T_f * P
+}
+
+
+compartment Nif {
+	states
+		Chl = 0
+		C = 0
+		N = 0
+		P = 0
+
+	parameters
+		//float Q_1_N_C : mmol N (mmol C)^-1 = 0.043
+		//float Q_2_N_C : mmol N (mmol C)^-1 = 0.171
+		//float Q_u_N_C : mmol N (mmol C)^-1 = 0.171
+		float Q_u2_N_C : mmol N (mmol C)^-1 = 0.09
+		//float Q_1_P_N : mmol P (mmol N)^-1 = 0.02
+		//float Q_2_P_N : mmol P (mmol N)^-1 = 0.2
+		//float Q_u_P_N : mmol P (mmol N)^-1 = 0.025
+
+		float theta_2_N : mg Chl (mmol N)^-1 = 1.2
+
+		//float alpha : mmol C (mg Chl)^-1 m^2 W^-1 #d^-1 = 0.6
+		// float r_0 : #d^-1 = 0.01       // duplicate variable
+		//float my_max : #d^-1 = 1.0     // d^-1
+
+		//float Ar :: = 1500        // -
+		//float gamma_C : #d^-1 = 0.08   // d^-1
+		//float gamma_Chl : #d^-1 = 0.01 // d^-1
+		//float gamma : #d^-1 = 0.06     // d^-1
+		//float Phi : m^3 (mmol N)^-1 #d^-1 = 0.002      // m^3 (mmol N)^-1 d^-1
+
+	diagnostics
+		float theta_C ::
+		float theta_N ::
+
+	calc Psi = max(0, Psi_max * (1 - q_N_C / Q_2_N_C))
+
+	calc phot_max = my_max * T_f * (q_N_C - Q_1_N_C)/(Q_2_N_C  - Q_1_N_C)
+	calc phot_DIC = phot_max * (1 - exp ((-1*alpha * theta_C * I)/phot_max))
+
+	calc T_f = exp(-1 * Ar * (1/T_K - 1/T_ref))
+
+	calc gamma = 0
+	calc degr_Chl = 0
+
+	calc R_P = 1 - Q_1_P_N / q_P_N
+	calc R_C = (1 + exp(-1 * sigma_N_C * (Q_2_N_C - q_N_C)))^-1
+	calc R_N = (1 + exp(-1 *sigma_P_N * (Q_2_P_N - q_P_N)))^-1
+
+	calc assim_DIN = Q_u_N_C * (1 - f_N2) * my_max * T_f * R_P * R_C
+	calc assim_N_2 = Q_u2_N_C * f_N2 * my_max * T_f * R_P * R_C
+	calc assim_DIP = Q_u_P_N * my_max * T_f * R_N * Nutrients.DIP / (Nutrients.K_DIP + Nutrients.DIP)
+
+	calc f_N2 = 0
+	calc synth_Chl = (assim_DIN + assim_N_2) * theta_2_N * phot_DIC / (alpha * theta_C * I)
+
+	update C = phot_DIC * C - (respiration + gamma + aggregation) * C
+	update N = (assim_DIN + assim_N_2) * C - ( r_0 * T_f + gamma + aggregation) * N - Phy:grazing
+	update P = assim_DIP * N - (r_0 * T_f + gamma + aggregation) * P - Phy:grazing * q_P_N
+	update Chl = synth_Chl * C - (degr_Chl + aggregation) * Chl - Phy:grazing * theta_N
+}
+
+connection absorption from LDOM to MG = 0 // to MG
+
+connection aggregation from Phy to Det = Phy.Phi * Phy.N + Det.Phi * Det.N
+connection aggregation from MG to Det = (MG.rho * T_f + MG.Phi * Det.N) // to Det
+connection aggregation from Nif to Det = Nif.Phi * Nif.N + Det.Phi * Det.N
+
+connection assimilation from Nutrients to Phy = Phy.assim_DIN * Phy.C // to phy
+
+connection assimilation(N,C) from Nutrients to Nif {
+	N = Nif.assim_DIP * Nif.N
+	C = Nif.assim_DIN * Nif.C
+}
+
+connection coagulation from dCCHO to MG = (dCCHO.Phi * dCCHO.C + dCCHO.Phi_TEPC * MG.C)  // connection to MG
+
+connection degradation(C,N,P) from Det to LDOM {
+	C = Det.omega_C * Det.C
+	N = Det.omega_N * Det.N
+	P = Det.omega_P * Det.P
+}
+
+connection denitrification from Nutrients to N_2 = 0
+
+connection exudation from Phy to dCCHO = 0 // to dCCHO
+connection exudation from Phy to LDOM = 0 // to LDOM
+connection exudation from Nif to LDOM = 0 // to LDOM
+
+connection excretion(N,P) from Het to LDOM {
+	N = Het.tau * (max(0, 1 - q_C_N/Q_r_C_N, 1 - Q_r_N_P/q_N_P))^2  // to LDOM
+	P = Het.tau * (max(0, 1 - q_C_P/(Q_r_C_N * Q_r_N_P), 1-q_N_P/Q_r_N_P)) // to LDOM
+}
+
+connection grazing from Phy to Het = g_max * Phy.T_f * Phy.N^2/(Het.K_N^2 + Nif.N^2+Nif.N^2) * Het.N
+connection grazing from Nif to Het = g_max * T_f * (Nif.N^2 / (Het.K_N^2 + Phy.N^2 + Nif.N^2) * Het.N)
+
+connection mortality from Het to Det = Het.gamma * Het.N  // to Det
+
+connection nitrification from N_2 to Nif = 0 // connection to Nif
+
+connection remineralization from MG to Nutrients = 0 // to Nutrients
+connection remineralization from LDOM to Nutrients = 0 // to Nutrients
+
+connection respiration from Phy to Nutrients = Phy.r_0 * Phy.T_f + Zeta_DIN * Phy.assim_DIN
+connection respiration from Het to Nutrients = T_f * Het.r_0
+		+ Het.tau * (max(0, 1 - Q_r_C_N/q_C_N, 1 - Q_r_C_N * Q_r_N_P / q_C_P))^2
+connection respiration from Nif to Nutrients = Nif.r_0 * T_f + Zeta_DIN * Nif.assim_DIN + Zeta_N_2 * Nif.assim_N_2

bgc-dsl/visitor/.idea/.gitignore

+# Default ignored files
+/shelf/
+/workspace.xml

bgc-dsl/visitor/.idea/Tim_visitor.iml

+<?xml version="1.0" encoding="UTF-8"?>
+<module type="JAVA_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>
\ No newline at end of file

bgc-dsl/visitor/.idea/misc.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectRootManager">
+    <output url="file://$PROJECT_DIR$/out" />
+  </component>
+</project>
\ No newline at end of file

bgc-dsl/visitor/.idea/modules.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/Tim_visitor.iml" filepath="$PROJECT_DIR$/.idea/Tim_visitor.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file

bgc-dsl/visitor/.idea/vcs.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$/../../.." vcs="Git" />
+  </component>
+</project>
\ No newline at end of file

bgc-dsl/visitor/.vscode/launch.json

+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Current File",
+            "type": "python",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal",
+            "justMyCode": true
+        }
+    ]
+}
\ No newline at end of file

bgc-dsl/visitor/.vscode/settings.json

+{
+    "python.defaultInterpreterPath": "./env/bin/python"
+}

bgc-dsl/visitor/example1.bgc

+model cnp_recom
+
+substances
+	float N : mmol
+	float C : mmol
+	float P : mmol
+	float Chl : mmol
+	float DIN : mmol N m^-3
+	float DIP ::
+	float DIC ::
+	float _TA ::
+
+parameters
+	float Q_r_C_N : mmol C (mmol N)^-1 = 5.5   //
+	float Q_r_N_P :  mmol N (mmol P)^-1 = 16.0  //
+
+	float T_ref : K = 283.15
+
+	float sigma_N_C : (mmol N)^2 (mmol C)^-2 = 100.0
+	float sigma_P_N  : (mmol P)^2 (mmol N)^-2 = 50.0
+	float g_max:: = 0.3
+
+	float T_f :: = 0
+
+	float epsilon :: = 0.78
+	float A_E :: = 0.75
+	float Omega :: = 0
+
+	float Q_1_N_C : mmol N (mmol C)^-1 = 0.043
+	float Q_2_N_C : mmol N (mmol C)^-1 = 0.171
+	float Q_1_P_N : mmol P (mmol N)^-1 = 0.02
+	float Q_2_P_N : mmol P (mmol N)^-1 = 0.2
+	float Q_u_N_C : mmol N (mmol C)^-1 = 0.171
+	float Q_u_P_N : mmol P (mmol N)^-1 = 0.014
+
+	float Zeta_DIN : mmol C (mmol N)^-1 = 2.3
+	float Zeta_N_2 : mmol C (mmol N)^-1 = 4.2
+
+	float Psi_max :: = 0.8
+	string criteria :: = option_a
+
+diagnostics
+	float T_K : K = 0
+	float I : W m^-2
+
+	float q_C_P ::
+	float q_N_P ::
+	float q_C_N : mmol C (mmol N)^-1
+	float q_N_C : mmol N (mmol C)^-1
+	float q_P_N : mmol P (mmol N)^-1
+
+compartment Phy {
+	states
+		Chl = 0
+		C = 0
+		N = 0
+		P = 0
+
+	parameters
+		float r_0 :: = 0.01
+		float Ar :: = 4000
+
+		float alpha : mmol C (mg Chl)^-1 m^2 W^-1 #d^-1 = 0.6
+		float my_max : #d^-1 = 2.6
+		float gamma_C : #d^-1 = 0.08
+		float gamma_Chl : #d^-1 = 0.01
+		float gamma : #d^-1 = 0.06
+		float Phi :  m^3 (mmol N)^-1 #d^-1 = 0.02
+		float Theta_2_N : mg Chl (mmol N)^-1 = 2.4
+
+	diagnostics
+		float Theta_C : mg Chl (mmol C)^-1
+		float Theta_N : mg Chl (mmol N)^-1
+
+	calc Psi = max(0, Psi_max * ( 1 - q_N_C/Q_2_N_C))
+
+	calc R_P = 1 - Q_1_P_N / q_P_N
+	calc R_C = (1 + exp(-1 * sigma_N_C * (Q_2_N_C - q_N_C)))^-1
+	calc R_N = (1 + exp(-1 * sigma_P_N * (Q_2_P_N - q_P_N)))^-1
+	calc T_f = exp (-1*Ar * (T_K^-1 - T_K^-1))
+
+	calc phot_max = my_max * T_f * (q_N_C - Q_1_N_C)/(Q_2_N_C - Q_1_N_C)
+	calc phot_DIC = phot_max * (1 - exp( -1 * alpha * Theta_C * I / phot_max ))
+
+	calc assim_DIN = Q_u_N_C * my_max * T_f * R_P * R_C * Nutrients.DIN / (Nutrients.K_DIN + Nutrients.DIN)
+	calc assim_DIP = Q_u_P_N * my_max * T_f * R_N * Nutrients.DIP/(Nutrients.K_DIP + Nutrients.DIP)
+
+	calc degr_Chl = gamma_Chl
+	calc synth_Chl = assim_DIN * Theta_2_N * phot_DIC / (alpha * Theta_C * I)
+
+	update C = phot_DIC * C - (respiration + gamma_C + aggregation) * C - Phy>grazing * q_C_N
+	update N = assim_DIN * C - (r_0 * T_f + gamma + aggregation) * N - Phy>grazing
+	update P = assim_DIP * N - (r_0 * T_f + gamma + aggregation) * P - Phy>grazing * q_P_N
+	update Chl = synth_Chl * C - (degr_Chl + aggregation) * Chl - Phy>grazing * Theta_N
+}
+
+compartment N_2 {
+	states
+		N = 0
+
+	update N = 0
+}
+
+compartment Nutrients {
+	states
+		DIN = 0
+		DIP = 0
+		DIC = 0
+		_TA = 0
+
+	parameters
+		float K_DIP : mmol P m^-3 = 0
+		float K_DIN : mmol N m^-3 = 0
+
+		float rho_C :: = 0
+		float rho_N :: = 0
+		float rho_P :: = 0
+
+	update DIC = T_f * (rho_C * LDOM.C + MG.rho * MG.C)
+		+ respiration * Phy.C
+		+ respiration * Nif.C
+		+ (Het:respiration + epsilon * (1 - Omega) * Het:mortality) * Het.C
+		- Phy.phot_DIC * Phy.C - Nif.phot_DIC * Nif.C
+	update DIN = T_f * (rho_N * LDOM.N + MG.rho * MG.N)
+		+ Phy.r_0 * Phy.T_f * Phy.N
+		+ Nif.r_0 * Nif.T_f * Nif.N
+		+ epsilon * (Het:excretion.N + (1 - Omega) * Het:mortality) * Het.N
+		- Phy:assimilation - Nif.assim_DIN * Nif.C - denitrification
+	update DIP = T_f * rho_P * LDOM.P
+		+ Phy.r_0 * Phy.T_f * Phy.P
+		+ Nif.r_0 * Nif.T_f * Nif.P
+		+ epsilon * (Het:excretion.P + ( 1-Omega) * Het:mortality) * Het.P - Phy.assim_DIP * Phy.N - Nif.assim_DIP * Nif.N
+	update _TA = Phy.assim_DIN * Phy.C + Phy.assim_DIP * Phy.N
+		+ assimilation.C + assimilation.N
+		- Phy.r_0 * Phy.T_f * Phy.N - Nif.r_0 * Nif.T_f * Nif.N
+		- Phy.r_0 * Phy.T_f * Phy.P - Nif.r_0 * Nif.T_f * Nif.P
+		- epsilon * (Het:excretion.N + (1-Omega) * Het:mortality) * Het.N
+		- epsilon * (Het:excretion.P + (1-Omega) * Het:mortality) * Het.P
+		- T_f * (rho_N * LDOM.N - MG.rho * MG.N - rho_P * LDOM.P)
+		+ denitrification
+}
+
+compartment Het {
+	states
+		C = 0
+		N = 0
+		P = 0
+
+	parameters
+		float K_N : mmol N m^-3 = 1.0
+		//float r_0 : #d^-1 = 0.01    // duplicate variable
+		float tau : #d^-1 = 0.5
+		// float gamma : m^3 (mmol N)^-1 #d^-1 = 0.3      // dupl
+
+	update C = A_E * (Phy:grazing * q_C_N + Nif:grazing * q_C_N) - (respiration + mortality) * C
+	update N = A_E * (Phy:grazing + Nif:grazing) - (excretion.N + mortality) * N
+	update P = A_E * (Phy:grazing * q_P_N + Nif:grazing * q_P_N) - (excretion.P + mortality) * P
+}
+
+compartment Det {
+	states
+		C = 0
+		N = 0
+		P = 0
+
+	parameters
+		//float Phi : m^3 (mmol N)^-1 #d^-1 = 0.02
+		//float Omega :: = 0
+
+	calc omega_C = 0
+	calc omega_N = 0
+	calc omega_P = 0
+
+	// could add a sink
+	calc sedimentation_C = 0
+	calc sedimentation_N = 0
+	calc sedimentation_P = 0
+
+	update C = Phy:aggregation * Phy.C
+		+ aggregation * Nif.C
+		+ MG.Phi * N * MG.C
+		+ (1-A_E) * (Phy:grazing * q_C_N + Phy:grazing * q_C_N)
+		+ Omega * Het:mortality * Het.C - degradation.C - sedimentation_C
+	update N = Phy:aggregation * Phy.N
+		+ Nif:aggregation * Nif.N
+		+ MG.Phi * N * MG.N
+		+ (1-A_E) * (Phy:grazing + Nif:grazing) + Omega * Het:mortality * Het.N - degradation.N - sedimentation_N
+	update P = Phy:aggregation * Phy.P
+		+ Nif:aggregation * Nif.P
+		+ (1-A_E) * (Phy:grazing * q_P_N + Nif:grazing * q_P_N)
+		+ Omega * Het:mortality * Het.P - degradation.P - sedimentation_P
+}
+
+
+compartment dCCHO {
+	states C = 0
+
+	parameters
+		float Phi_TEPC :: = 0
+		//float Phi :: = 0
+
+	update C = Phy.Psi * Phy.gamma_C * Phy.C + Nif.Psi * Nif.gamma_C * Nif.C - coagulation * C
+}
+
+
+compartment MG {
+	states
+		C = 0
+		N = 0
+
+	parameters
+		//float Phi :: = 0
+		float rho :: = 0
+		float Xi :: = 0
+
+	update C = coagulation * dCCHO.C - aggregation * C
+	update N = Xi * C * LDOM.N - (rho * T_f + Phi * Det.N) * N
+}
+
+
+compartment LDOM {
+	states
+		C = 0
+		N = 0
+		P = 0
+
+	parameters
+		float omega_C :: = 0
+		float omega_N :: = 0
+		float omega_P :: = 0
+		//float Omega :: = 0
+		//float rho_C :: = 0
+		//float rho_N :: = 0
+		//float rho_P :: = 0
+
+	update C = degradation.C
+		+ (1 - Phy.Psi) * Phy.gamma_C * Phy.C
+		+ (1 - Nif.Psi) * Nif.gamma_C * Nif.C
+		+ (1-epsilon) * (1-Omega) * mortality * Het.C - rho_C * T_f * C
+	update N = degradation.N
+		+ Phy.gamma * Phy.N + Nif.gamma * Nif.N
+		+ (1-epsilon) * excretion.N * Het.N
+		+ (1-epsilon) * (1-Omega) * mortality * Het.N - (rho_N * T_f + MG.Xi * MG.C) * N
+	update P = degradation.P
+		- Phy.gamma * Phy.P + Nif.gamma * Nif.P
+		+ (1-epsilon) * (excretion.P + (1-Omega) * mortality) * Het.P - rho_P * T_f * P
+}
+
+
+compartment Nif {
+	states
+		Chl = 0
+		C = 0
+		N = 0
+		P = 0
+
+	parameters
+		//float Q_1_N_C : mmol N (mmol C)^-1 = 0.043
+		//float Q_2_N_C : mmol N (mmol C)^-1 = 0.171
+		//float Q_u_N_C : mmol N (mmol C)^-1 = 0.171
+		float Q_u2_N_C : mmol N (mmol C)^-1 = 0.09
+		//float Q_1_P_N : mmol P (mmol N)^-1 = 0.02
+		//float Q_2_P_N : mmol P (mmol N)^-1 = 0.2
+		//float Q_u_P_N : mmol P (mmol N)^-1 = 0.025
+
+		float theta_2_N : mg Chl (mmol N)^-1 = 1.2
+
+		//float alpha : mmol C (mg Chl)^-1 m^2 W^-1 #d^-1 = 0.6
+		// float r_0 : #d^-1 = 0.01       // duplicate variable
+		//float my_max : #d^-1 = 1.0     // d^-1
+
+		//float Ar :: = 1500        // -
+		//float gamma_C : #d^-1 = 0.08   // d^-1
+		//float gamma_Chl : #d^-1 = 0.01 // d^-1
+		//float gamma : #d^-1 = 0.06     // d^-1
+		//float Phi : m^3 (mmol N)^-1 #d^-1 = 0.002      // m^3 (mmol N)^-1 d^-1
+
+	diagnostics
+		float theta_C ::
+		float theta_N ::
+
+	calc Psi = max(0, Psi_max * (1 - q_N_C / Q_2_N_C))
+
+	calc phot_max = my_max * T_f * (q_N_C - Q_1_N_C)/(Q_2_N_C  - Q_1_N_C)
+	calc phot_DIC = phot_max * (1 - exp ((-1*alpha * theta_C * I)/phot_max))
+
+	calc T_f = exp(-1 * Ar * (1/T_K - 1/T_ref))
+
+	calc gamma = 0
+	calc degr_Chl = 0
+
+	calc R_P = 1 - Q_1_P_N / q_P_N
+	calc R_C = (1 + exp(-1 * sigma_N_C * (Q_2_N_C - q_N_C)))^-1
+	calc R_N = (1 + exp(-1 *sigma_P_N * (Q_2_P_N - q_P_N)))^-1
+
+	calc assim_DIN = Q_u_N_C * (1 - f_N2) * my_max * T_f * R_P * R_C
+	calc assim_N_2 = Q_u2_N_C * f_N2 * my_max * T_f * R_P * R_C
+	calc assim_DIP = Q_u_P_N * my_max * T_f * R_N * Nutrients.DIP / (Nutrients.K_DIP + Nutrients.DIP)
+
+	calc f_N2 = 0
+	calc synth_Chl = (assim_DIN + assim_N_2) * theta_2_N * phot_DIC / (alpha * theta_C * I)
+
+	update C = phot_DIC * C - (respiration + gamma + aggregation) * C
+	update N = (assim_DIN + assim_N_2) * C - ( r_0 * T_f + gamma + aggregation) * N - Phy:grazing
+	update P = assim_DIP * N - (r_0 * T_f + gamma + aggregation) * P - Phy:grazing * q_P_N
+	update Chl = synth_Chl * C - (degr_Chl + aggregation) * Chl - Phy:grazing * theta_N
+}
+
+connection absorption from LDOM to MG = 0 // to MG
+
+connection aggregation from Phy to Det = Phy.Phi * Phy.N + Det.Phi * Det.N
+connection aggregation from MG to Det = (MG.rho * T_f + MG.Phi * Det.N) // to Det
+connection aggregation from Nif to Det = Nif.Phi * Nif.N + Det.Phi * Det.N
+
+connection assimilation from Nutrients to Phy = Phy.assim_DIN * Phy.C // to phy
+
+connection assimilation(N,C) from Nutrients to Nif {
+	N = Nif.assim_DIP * Nif.N
+	C = Nif.assim_DIN * Nif.C
+}
+
+connection coagulation from dCCHO to MG = (dCCHO.Phi * dCCHO.C + dCCHO.Phi_TEPC * MG.C)  // connection to MG
+
+connection degradation(C,N,P) from Det to LDOM {
+	C = Det.omega_C * Det.C
+	N = Det.omega_N * Det.N
+	P = Det.omega_P * Det.P
+}
+
+connection denitrification from Nutrients to N_2 = 0
+
+connection exudation from Phy to dCCHO = 0 // to dCCHO
+connection exudation from Phy to LDOM = 0 // to LDOM
+connection exudation from Nif to LDOM = 0 // to LDOM
+
+connection excretion(N,P) from Het to LDOM {
+	N = Het.tau * (max(0, 1 - q_C_N/Q_r_C_N, 1 - Q_r_N_P/q_N_P))^2  // to LDOM
+	P = Het.tau * (max(0, 1 - q_C_P/(Q_r_C_N * Q_r_N_P), 1-q_N_P/Q_r_N_P)) // to LDOM
+}
+
+connection grazing from Phy to Het = g_max * Phy.T_f * Phy.N^2/(Het.K_N^2 + Nif.N^2+Nif.N^2) * Het.N
+connection grazing from Nif to Het = g_max * T_f * (Nif.N^2 / (Het.K_N^2 + Phy.N^2 + Nif.N^2) * Het.N)
+
+connection mortality from Het to Det = Het.gamma * Het.N  // to Det
+
+connection nitrification from N_2 to Nif = 0 // connection to Nif
+
+connection remineralization from MG to Nutrients = 0 // to Nutrients
+connection remineralization from LDOM to Nutrients = 0 // to Nutrients
+
+connection respiration from Phy to Nutrients = Phy.r_0 * Phy.T_f + Zeta_DIN * Phy.assim_DIN
+connection respiration from Het to Nutrients = T_f * Het.r_0
+		+ Het.tau * (max(0, 1 - Q_r_C_N/q_C_N, 1 - Q_r_C_N * Q_r_N_P / q_C_P))^2
+connection respiration from Nif to Nutrients = Nif.r_0 * T_f + Zeta_DIN * Nif.assim_DIN + Zeta_N_2 * Nif.assim_N_2