notes on model-files.txt

note on gfrd model files:

known issules:
	file should have unix style line terminators, that is a LF, (0x0A or \n) or parser will fail on linux
	last line of model-file should have a LF (or that line is not parsed)


speciestype names:
	conform regex "[a-zA-Z][\w\-*_']*"

variable names:
	conform regex "[a-zA-Z][a-zA-Z0-9_]*"

particle placement:
	conform regex "(\(([^,]+),([^,]+),([^,]+)\)\s*(?:,\s*(.+))*)"
		=> exact position in form (x, y, z) [,N] 
		   with N is amount of particles (as number or expression), x,y,z, should also be expressions, use following loop parameters:
				n = 0..N-1 or x = 0..1 or xx = -1..+1
		   when N is omitted a single particle is placed at the specified coordinate
	non conform: specifies number or expression for random placement of N particles.
	
	
expressions: as described in exprtk (case sensitive, NO enhanced_features, break_continue, return_statement, rtl_io_file, rtl_vecops, control_structures)


declared variables are evaluated and assigned in order of the model file (lines from top to bottom). 
variables assigned on the command-line (-d argument) take precedence over the model-file.


build in functions:  

		// Calculate the number of particles in a volume (in liter or dm^3) with a concentration (in molar or mol/dm3).
		concentration( mol , volume) -> number of particles
					
		// Convert a reaction rate from units 'per nanomolar per second' to units 'meter^3 per second'
		per_nM_per_sec_to_m3_per_sec(rate) -> rate

		More to follow: ? k_D(), k_a(), k_d(), ...
		
build in constants:  

		pi, e, inf, NA, 
		
		More to follow: ? kb, ... 
		
text variables:
		
		declare with $ prefix, 
		example: 
			dir = $ '~/data_out/'
			file = $ dir + 'file.abc'
		
		
		
Mode flags: 
	definition
		On = whole simulation (pre-run and main-run)
		Run = main-run only (not in pre-run)
		Off = Not at all

	Default mode for sections (no need to specify)
		CopyNumbers = Run
		ParticlePosition = Run
		Particles = On
		Progress = On
		ReactionRecord = Run
		ReactionRule = On