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Article contents:[[tags:egg]] [[toc:]] == salt A language and code generation tool for equation-based modeling and simulations. == Introduction SALT is an implementation of a domain-specific language for equation-based models. This implementation follows the work of Tom Short and the Julia Sims.jl library [[https://github.com/tshort/Sims.jl]], which is in turn based on David Broman's MKL simulator and the work of George Giorgidze and Henrik Nilsson in functional hybrid modeling. Following Sims.jl, a nodal formulation is used based on David Broman's thesis [[http://www.bromans.com/david/publ/thesis-2010-david-broman.pdf]]: David Broman. Meta-Languages and Semantics for Equation-Based Modeling and Simulation. PhD thesis, Thesis No 1333. Department of Computer and Information Science, Linköping University, Sweden,; 2010. == Library procedures <procedure>parse :: DECLARATIONS -> ASTDECLS</procedure> Parses equation declarations in the syntax described in the next section, and returns an abstract syntax tree structure. <procedure>elaborate :: ASTDECLS -> EQUATIION-SET</procedure> Performs flattening of the given declarations and returns an equation set. The main steps in flattening are: * Creation of a name resolution environment (parameters,fields,externals,constants,variables,functions). * Replacing of fixed initial values. * Flattening models and populating equation, definition, function lists. * Populating list of initials. * Populating event list from event and structural event definitions. * Handles structural events. <procedure>simcreate :: EQUATION-SET -> SIMRUNTIME</procedure> Given an equation set, creates a simulation runtime representation. <procedure>codegen-ODE :: SIMRUNTIME -> ODE LIST</procedure> Given a simulation runtime representation, creates an abstract code representation aimed at ODE solvers. <procedure>codegen-ODE/ML</procedure> Given a simulation runtime representation, creates a code representation aimed at ODE solvers in the Standard ML language. == Model description language === Definitions Definitions serve to define unknowns (state variables), parameters (constants during integration), and units of measurement. (define millivolt = unit Potential (1e-3 * volt)) (define Vinit = parameter (dim Potential) -65.0 * millivolt) (define v = unknown (dim Potential) -65.0 * mV) === Equations Equations serve to define differential and algebraic equations. ((der(u)) = (s - u) / tau) ((s) = b * ((v - a) ^ 3)) === Events (event (v - Vthreshold) ((v := Vreset)) ) == Examples <enscript highlight="scheme"> ;; Van der Pol oscillator (define vdp (parse `( (define x = unknown -0.25) (define y = unknown 1.0) ((der(x)) = (1 - y ^ 2) * x - y ) ((der(y)) = x) ) )) ;; Izhikevich Fast Spiking neuron (define izhfs (parse `( (define millivolt = unit Potential (1e-3 * volt)) (define Isyn = parameter (dim Current) 0.0 * nA) (define Iext = parameter (dim Current) 400.0 * nA) (define k = parameter 1.0) (define Vinit = parameter (dim Potential) -65.0 * millivolt) (define Vpeak = parameter (dim Potential) 25.0 * mV) (define Vt = parameter (dim Potential) -55.0 * mV) (define Vr = parameter (dim Potential) -40.0 * mV) (define Vb = parameter (dim Potential) -55.0 * mV) (define Cm = parameter (dim Capacitance) 20.0 * uF) (define FS_a = parameter 0.2) (define FS_b = parameter (dim Current) 0.025 * nA) (define FS_c = parameter (dim Potential) -45.0 * mV) (define FS_U = parameter (dim Current) FS_b * (Vinit / mV)) (define v = unknown (dim Potential) -65.0 * mV) (define u = unknown (dim Current) FS_U) (define s = unknown (dim Current) 0.0 * nA) ((der(v)) = (((k * (v - Vr) * (v - Vt) / millivolt) + (((- u) + Iext) * megaohm)) / Cm) / megaohm) ((der(u)) = (FS_a * (s - u)) / ms) ((s) = FS_b * ((v - Vb) / mV) ^ 3) (event (v - Vpeak) ((v := FS_c) (u := u) (s := s) ) ) )) ) ;; A routine to generate and compile Standard ML code (define (compile-model name model #!key (solver 'rk4b) (compile #f) (dir "tests")) (pp model) (define elab (elaborate model)) (print "elaborate is done") (pp elab) (define sim (simcreate elab)) (pp sim) (pp (codegen-ODE sim solver)) (let* ((sml-path (make-pathname dir (string-append (->string name) ".sml"))) (mlb-path (make-pathname dir (string-append (->string name) "_run.mlb"))) (port (open-output-file sml-path))) (codegen-ODE/ML sim out: port solver: solver libs: '(interp)) (close-output-port port) (if compile (run (mlton -mlb-path-var ,(sprintf "'SALT_HOME ~A'" SALT-DIR) -mlb-path-var ,(sprintf "'RK_LIB $(SALT_HOME)/sml-lib/rk'") -mlb-path-var ,(sprintf "'DYNAMICS_LIB $(SALT_HOME)/sml-lib/dynamics'") ,mlb-path)))) ) (compile-model 'vdp vdp) (compile-model 'izhfs izhfs) </enscript> == Repository [[https://github.com/iraikov/salt|https://github.com/iraikov/salt]] == Version history * 0.21 : Added step size controller * 0.20 : Support for precise event time interpolation and adaptive solvers * 0.5 : Support for using assigned quantities in external init equations * 0.1 : Initial release == License Copyright 2015-2017 Ivan Raikov This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. A full copy of the GPL license can be found at http://www.gnu.org/licenses/. Description of your changes:

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