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;;;; in opt.lsp

;;; Given argument forms to an arbitrary arity arithmetic function,
;;; return new arguments with all constants folded together.
;;; FIXME: handler-case, return original arguments
;;;  if there's an error (e.g. overflow).
(defun fold-constants (function argforms env)
  (loop for form in argforms
        when (constantp form env)
          collect (ext:constant-form-value form env) into constants

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(define-method-combination machine ()
  ((start (:start))
   (rest *))
  (let ((qualifiers (mapcar #'method-qualifiers rest))
        (tags (mapcar (lambda (m) (declare (ignore m)) (gensym)) rest)))
    `(prog (switch)
        (setf switch
              (lambda (state)
                (cond ((equal state nil) (go nil))
                      ,@(loop for qualifier in qualifiers

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;;;; public domain, by Bike
;;;; Gillespie, Daniel T. (1977). "Exact Stochastic Simulation of Coupled Chemical Reactions". The Journal of Physical Chemistry 81 (25): 2340–2361. doi:10.1021/j100540a008.

(defun gillespie (species reactions
		  &key (stop-time 0d0 st-p) (stop-reactions 0 sr-p)
		    (rpd 0 rpd-p))
  ;; SPECIES is a vector of N positive integers, molecule counts.
  ;; REACTIONS is a vector of M lists
  ;;  The first of each list is the rate constant for that reaction.
  ;;  The second is a vector of N nonnegative integers describing the substrates.