Merge branch 'Tim_bgc' into 'main'

Tim bgc

See merge request oceandsl/antlr4-python!3

grammars/dev/BgcDsl.g4

+
+grammar BgcDsl;
+
+import CommonLexerRules;
+
+bgcModel:
+	'model' name=ID
+	'substances' substanceDeclarations+=substanceDeclaration+
+	('parameters' parameterDeclarations+=parameterDeclaration*)?
+	('diagnostics' environments+=environmentVariableDeclaration*)?
+	(compartments+=compartment|connections+=connection)+
+;
+
+substanceDeclaration:
+	type=primitiveTypes name=ID unit
+;
+
+parameterDeclaration:
+	type=primitiveTypes name=ID unit '=' expression=arithmeticExpression
+;
+
+environmentVariableDeclaration:
+	type=primitiveTypes name=ID unit ('=' expression=arithmeticExpression)?
+;
+
+primitiveTypes:
+	'int' | 'float' | 'string'
+;
+
+// type of label "parent": compartment
+compartment:
+	'abstract'? 'compartment' name=ID ('extends' parent = ID)? '{'
+		'states' states+=substanceState+
+		('parameters' constants+=parameterDeclaration*)?
+		('diagnostics' evnironments+=environmentVariableDeclaration*)?
+
+		calculations+=calculation*
+		updateStates+=updateState+
+	'}'
+;
+
+// substance type: substanceDeclaration
+substanceState:
+	substance=ID ('=' expression=arithmeticExpression)?
+;
+
+// state is of type substanceState
+updateState:
+    'update' state=ID '=' expression=arithmeticExpression
+;
+
+// sourceCompartment and targetCompartment are of type compartment
+// substances and substance are of type substanceDeclaration
+connection:
+	'connection' name=ID ('(' substances+=ID (',' substances+=ID)* ')')?
+	'from' sourceCompartment=ID 'to' targetCompartment=ID ('=' expression=arithmeticExpression |
+	'{' (substanceExpressions+=substanceExpression | calculations+=calculation)* '}')
+;
+
+substanceExpression:
+	substance=ID '=' expression=arithmeticExpression
+;
+
+calculation: basicCalculation | alternativeCalculation;
+
+basicCalculation:
+	'calc' name=ID '=' expression=arithmeticExpression
+;
+
+alternativeCalculation:
+	'alternatives' name=ID ':' expression=arithmeticExpression '{'
+		alternatives+=basicCalculation*
+	'}'
+;
+
+// ----------------------
+// Units
+// ----------------------
+
+unit:
+	':' elements+=unitElement+ |
+	'::'
+;
+
+unitElement:
+	prefixUnit | groupUnit
+;
+
+groupUnit: 
+	'(' elements+=unitElement* ')' ('^' exponent=NUMBER)?
+;
+
+// substance is of type substanceDeclaration
+// removed unit-label for UNIT_STRING, here
+prefixUnit:
+	(UNIT_STRING | custom=CUSTOM_STRING) (substance=ID)? ('^' exponent=NUMBER)?
+;
+
+// ----------------------
+// Expression definitions
+// ----------------------
+
+// returns expression
+arithmeticExpression:
+	multiplicationExpression (operator=eAdditionOperator right=arithmeticExpression)?
+;
+
+// returns eAdditionOperator
+eAdditionOperator:
+	ADDITION = '+' |
+	SUBTRACTION = '-'
+;
+
+// returns expression
+multiplicationExpression:
+	powerExpression (operator=eMultiplicationOperator right=multiplicationExpression)?
+;
+
+// returns eMultiplicationOperator
+eMultiplicationOperator:
+	MULTIPLICATION = '*' |
+	DIVISION = '/' |
+	MODULO = '%'
+;
+
+// returns expression
+powerExpression:
+	valueExpression ('^' right=valueExpression)?
+;
+
+
+valueExpression:
+	arrayExpression |
+	functionCallingExpression |
+	literalExpression |
+	parenthesisExpression |
+	termReference
+;
+
+
+arrayExpression:
+	'[' expressions+=arithmeticExpression (',' expressions+=arithmeticExpression)* ']'
+;
+
+functionCallingExpression: type=function '(' expressions+= arithmeticExpression (',' expressions+= arithmeticExpression)* ')';
+
+function:
+	'exp' | 'inverse' | 'max'
+;
+
+literalExpression:
+	value=literal
+;
+
+literal:
+	numberLiteral |
+	stringLiteral
+;
+
+numberLiteral:
+	value=NUMBER
+;
+
+stringLiteral:
+	value='string'
+;
+
+// returns ecore::EBigDecimal
+// changed pre-dot numbers from * to +
+NUMBER:
+	('-')? ('0'..'9')+ ('.' ('0'..'9')+)?
+;
+
+// returns ecore::EString
+CUSTOM_STRING:
+	'#'('A' .. 'Z'|'a'..'z')+
+;
+
+// returns ecore::EString
+UNIT_STRING:
+	('Q'|'R'|'Y'|'Z'|'E'|'P'|'T'|'G'|'M'|'k'|'h'|'da'|'d'|'c'|'m'|'my'|'n'|'p'|'f'|'a'|'z'|'y'|'r'|'q')?('s'|'m'|'g'|'mol'|'cd'|'W'|'J'|'K'|'A')
+;
+
+parenthesisExpression:
+	'(' expression=arithmeticExpression ')'
+;
+
+// sourceCompartment and targetCompartment are of type compartment
+// reference is of type term
+termReference:
+	(sourceCompartment=ID '>')?  (targetCompartment=ID ':')? reference=qualifiedName
+;
+
+// should be moved to documentation
+subterm:
+	updateState | connection | parameterDeclaration | calculation | environmentVariableDeclaration | substanceExpression | substanceState
+;
+
+qualifiedName:
+	ID ('.' ID)*
+;
+
+// returns ecore::EInt
+INT:
+	'this one has been deactivated'
+;

grammars/dev/BgcDsl.xtext

+
+grammar org.oceandsl.BgcDsl with org.eclipse.xtext.common.Terminals
+generate bgcDsl "http://www.oceandsl.org/BgcDsl"
+import "http://www.eclipse.org/emf/2002/Ecore" as ecore
+
+BgcModel:
+	{BgcModel}
+	'model' name=ID
+	'substances' substanceDeclarations+=SubstanceDeclaration+
+	('parameters' parameterDeclarations+=ParameterDeclaration*)?
+	('diagnostics' evnironments+=EnvironmentVariableDeclaration*)?
+	(compartments+=Compartment|connections+=Connection)+
+;
+
+SubstanceDeclaration:
+	type=PrimitiveTypes name=ID unit=Unit
+;
+
+ParameterDeclaration:
+	type=PrimitiveTypes name=ID unit=Unit "=" expression=ArithmeticExpression
+;
+
+EnvironmentVariableDeclaration:
+	type=PrimitiveTypes name=ID unit=Unit ("=" expression=ArithmeticExpression)?
+;
+
+PrimitiveTypes:
+	"int" | "float" | "string"
+;
+
+Compartment: 
+	(abstract?='abstract')? 'compartment' name=ID ('extends' parent=[Compartment|ID])? '{'
+		'states' states+=SubstanceState+
+		('parameters' constants+=ParameterDeclaration*)?
+		('diagnostics' evnironments+=EnvironmentVariableDeclaration*)?
+		
+		calculations+=Calculation*
+		updateStates+=UpdateState+
+	'}'
+;
+
+SubstanceState:
+	substance=[SubstanceDeclaration|ID] ("=" expression=ArithmeticExpression)?
+;
+
+UpdateState:
+    'update' state=[SubstanceState|ID] "=" expression=ArithmeticExpression
+;
+
+Connection:
+	'connection' name=ID ('(' substances+=[SubstanceDeclaration|ID] (',' substances+=[SubstanceDeclaration|ID])* ')')? 
+	'from' sourceCompartment=[Compartment|ID] 'to' targetCompartment=[Compartment|ID] ("=" expression=ArithmeticExpression | 
+	'{' (substanceExpressions+=SubstanceExpression | calculations+=Calculation)* '}')
+;
+
+SubstanceExpression:
+	substance=[SubstanceDeclaration|ID] '=' expression=ArithmeticExpression
+;
+
+Calculation: BasicCalculation | AlternativeCalculation;
+
+BasicCalculation:
+	'calc' name=ID "=" expression=ArithmeticExpression
+;
+
+AlternativeCalculation:
+	'alternatives' name=ID ':' expression=ArithmeticExpression '{'
+		alternatives+=BasicCalculation*
+	'}'
+;
+
+// ----------------------
+// Units
+// ----------------------
+
+Unit: 
+	':' elements+=UnitElement+ | 
+	{Unit} '::'
+;
+
+UnitElement:
+	PrefixUnit | GroupUnit
+;
+
+GroupUnit: {GroupUnit}
+	'(' elements+=UnitElement* ')' ("^" exponent=NUMBER)?
+;
+
+PrefixUnit:
+	(unit=UNIT_STRING | custom=CUSTOM_STRING) (substance=[SubstanceDeclaration|ID])? ("^" exponent=NUMBER)?
+;
+
+// ----------------------
+// Expression definitions
+// ----------------------
+
+ArithmeticExpression returns Expression:
+	MultiplicationExpression ->({ArithmeticExpression.left=current} operator=EAdditionOperator right=ArithmeticExpression)?
+;
+
+enum EAdditionOperator returns EAdditionOperator:
+	ADDITION = "+" |
+	SUBTRACTION = "-"
+;
+
+MultiplicationExpression returns Expression:
+	PowerExpression ->({MultiplicationExpression.left=current} operator=EMultiplicationOperator right=MultiplicationExpression)?
+;
+
+enum EMultiplicationOperator returns EMultiplicationOperator:
+	MULTIPLICATION = "*" |
+	DIVISION = "/" |
+	MODULO = "%" 
+;
+
+PowerExpression returns Expression:
+	ValueExpression ->({PowerExpression.left=current} "^" right=ValueExpression)?
+;
+
+
+ValueExpression: 
+	ArrayExpression |
+	FunctionCallingExpression |
+	LiteralExpression |
+	ParenthesisExpression |
+	TermReference 	
+;
+
+
+ArrayExpression:
+	'[' expressions+=ArithmeticExpression (',' expressions+=ArithmeticExpression)* ']'
+;
+
+FunctionCallingExpression: type=EFunction '(' expressions+= ArithmeticExpression(',' expressions+= ArithmeticExpression)* ')'; 
+enum EFunction:
+	exp = 'exp' | inverse = 'inverse' | max = 'max'
+;
+
+LiteralExpression:
+	value=Literal
+;
+
+Literal:
+	NumberLiteral | 
+	StringLiteral
+;
+	
+NumberLiteral:
+	value=NUMBER 
+;
+
+StringLiteral:
+	value=STRING
+;
+
+terminal NUMBER returns ecore::EBigDecimal:
+	("-")?('0'..'9')* ('.' ('0'..'9')+)?
+;
+	
+terminal CUSTOM_STRING returns ecore::EString:
+	"#"('A' .. 'Z'|'a'..'z')+	
+;
+
+terminal UNIT_STRING returns ecore::EString:
+	("Q"|"R"|"Y"|"Z"|"E"|"P"|"T"|"G"|"M"|"k"|"h"|"da"|"d"|"c"|"m"|"my"|"n"|"p"|"f"|"a"|"z"|"y"|"r"|"q")?("s"|"m"|"g"|"mol"|"cd"|"W"|"J"|"K"|"A")
+;
+
+ParenthesisExpression:
+	'(' expression=ArithmeticExpression ')'
+;
+
+TermReference:
+	(sourceCompartment=[Compartment | ID] '>')?  (targetCompartment=[Compartment | ID] ':')? reference=[Term | QualifiedName]
+;
+
+Term: 
+	name=ID
+; 
+
+Subterm returns Term: 
+	UpdateState | Connection | ParameterDeclaration | Calculation | EnvironmentVariableDeclaration | SubstanceExpression | SubstanceState
+; 
+
+QualifiedName:
+	ID ('.' ID)*
+;
+
+@Override
+terminal INT returns ecore::EInt:
+	'this one has been deactivated';

grammars/dev/CommonLexerRules.g4

@@ -4,12 +4,13 @@
 grammar CommonLexerRules;
 
 // lexer rules with uppercase letters
-ID      :   [a-zA-Z]+ ;                                 // match identifiers <label id="code.tour.expr.3"/>
+ID      :   [a-zA-Z_0-9]+ ;                                 // added id-characters; before: match identifiers <label id="code.tour.expr.3"/>
 NUM     :   '-'? ('.' DIG+ | DIG+ ('.' DIG*)? EXP? ) ;  // match numbers
 /** fragments generate no lexer tokens */
 fragment INT :   '0' | [1-9] DIG* ;                     // fragment match integers without leading zeros
 fragment EXP :   [eE] [+\-]? INT ;                      // fragment match exponent
 fragment DIG :   [0-9] ;                                // fragment match digits
 
-NEWLINE :   '\r'? '\n' ;                                // return newlines to parser (is end-statement signal)
-WS      :   [ \t]+ -> skip ;                            // suppress the generation of the spaces and tabs token
\ No newline at end of file
+//NEWLINE :   '\r'? '\n' ;                                // causes errors: return newlines to parser (is end-statement signal)
+WS      :   [ \t\n]+ -> skip ;                            // suppress the generation of the spaces and tabs token
+COMMENT : '//' .*? '\n'-> channel(HIDDEN) ;               // hide / ignore comments

grammars/dev/Tim_bgc_test.g4

+// das ist eine versuchs-grammatik.
+
+grammar Tim_bgc_test;	// grammar name
+
+// regeln
+
+regel1: ding*
+      ;	// regeln müssen klein sein
+
+ding: '#' regel1
+    | INT
+    | CHAR
+    ;	// hier muss '#' oder was anderes stehen, sonst gibts n problem mit left recursive.
+
+
+// Token
+
+INT:  [0-9]+;	// muss hier def werden; keine Ahnung warum das außerhalb muss
+CHAR: [a-z]+;
+
+Ignore: [ \n]+ -> skip;	// ignores spaces (here is one explicit space char) and next lines
\ No newline at end of file

grammars/dev/example.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_N ::
+	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
+	float q_C_N ::
+	float q_N_C ::
+	float q_P_N ::
+
+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
+		float tau : #d^-1 = 0.5
+		float gamma : m^3 (mmol N)^-1 #d^-1 = 0.3
+
+	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       //
+		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

grammars/dev/example2.bgc

+model bgc
+
+substances
+    float N ::
+    float P ::
+
+compartment Phy {
+    states N P
+
+    update N = assimilation.N
+    update P = assimilation.P
+}
+
+compartment Ki {
+    states N
+
+    update N = 0
+}
+
+connection assimilation(N, P) from Phy to Ki {
+    N = Phy.N + Ki.N
+    P = Phy.P + 1
+}