ncad023a
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Makefile,
RCS,
README,
cl-nogui.lsp,
compile.lsp,
config.lsp,
contrib,
diamondoid,
feedback-317,
forces.scm,
gambit.scm,
gui-1.scm,
gui-2.lsp,
gui-2.mrd,
gui-2.tcl,
hackv.scm,
helper,
lisp.lsp,
lispd.lsp,
make-tgz,
make-zip,
methane,
mred.scm,
mz-nogui.scm,
ncad023.scm,
propane,
run-clisp.lsp,
run-mred.scm,
scheme.scm,
test.scm,
trial,
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;#if defined(SCHEME)
;#if defined(GAMBIT)
;; Gambit configuration file for NanoCAD
;#else
;; MzScheme/MrEd configuration file for NanoCAD
;#endif /* defined (GAMBIT) */
;#else
;; Common Lisp configuration file for NanoCAD
;#endif /* defined (SCHEME) */
;#ifdef SCHEME
;#define DEFCONST(x,y) (define x y)
;#define TRUE #t
;#define FALSE #f
;#else
;#define DEFCONST(x,y) (defconstant x y)
;#define TRUE t
;#define FALSE nil
(defmacro define (name-args &rest body)
(cond ((listp name-args)
`(defun ,(car name-args) ,(cdr name-args) ,@body))
(t
`(defvar ,name-args ,@body))))
;#endif
DEFCONST(true, TRUE)
DEFCONST(false, FALSE)
;#ifdef DEBUG
DEFCONST(debugging, TRUE)
;#else
DEFCONST(debugging, FALSE)
;#endif
;#ifdef USE_MRED
DEFCONST(use-mred, TRUE)
;#else
DEFCONST(use-mred, FALSE)
;#endif
;#if defined(SCHEME)
;#if defined(GAMBIT)
(define-macro (make-lambda args . body) `(lambda ,args ,@body))
(define-macro (funcall lexp . args) `(,lexp ,@args))
(define-macro (func x) x)
(define-macro (mapcar f lst) `(map ,f ,lst))
(define-macro (qsort x y) `(quicksort ,x ,y))
(define-macro (labels defns . body)
`(let
,(map
(lambda (x)
(list (car x) (cons 'lambda (cdr x))))
defns)
,@body))
(define-macro (dolist args . body)
`(do ((local-list ,(cadr args) (cdr local-list))
(,(car args) '()))
((null? local-list))
(set! ,(car args) (car local-list))
,@body))
(define-macro (dotimes args . body)
`(do ((,(car args) 0 (+ 1 ,(car args)))
(iteration-limit ,(cadr args)))
((>= ,(car args) iteration-limit))
,@body))
;#ifdef DEBUG
(define-macro (dbgprintf x . y) `(printf ,x ,@y))
(define-macro (entering name) `(printf "Entering ~s~%" ,name))
;#else
(define-macro (dbgprintf x . y) '())
(define-macro (entering name) '())
;#endif
;#else /* !defined(GAMBIT) */
(define-macro make-lambda
(lambda (args . body) `(lambda ,args ,@body)))
(define-macro funcall
(lambda (lexp . args) `(,lexp ,@args)))
(define-macro func
(lambda (x) x))
(define-macro mapcar
(lambda (f lst) `(map ,f ,lst)))
(define-macro qsort
(lambda (x y) `(quicksort ,x ,y)))
(define-macro labels
(lambda (defns . body)
`(let
,(map
(lambda (x)
(list (car x) (cons 'lambda (cdr x))))
defns)
,@body)))
(define-macro dolist
(lambda (args . body)
`(do ((local-list ,(cadr args) (cdr local-list))
(,(car args) '()))
((null? local-list))
(set! ,(car args) (car local-list))
,@body)))
(define-macro dotimes
(lambda (args . body)
`(do ((,(car args) 0 (+ 1 ,(car args)))
(iteration-limit ,(cadr args)))
((>= ,(car args) iteration-limit))
,@body)))
;#ifdef DEBUG
(define-macro dbgprintf
(lambda (x . y) `(printf ,x ,@y)))
(define-macro entering
(lambda (name) `(printf "Entering ~s~%" ,name)))
;#else
(define-macro dbgprintf
(lambda (x . y) '()))
(define-macro entering
(lambda (name) '()))
;#endif
;#endif /* defined(GAMBIT) */
;#else /* !defined(SCHEME) */
(defconstant else t)
(defmacro list-ref (lst n) `(nth ,n ,lst))
(defmacro make-lambda (args &rest body) `#'(lambda ,args ,@body))
(defmacro func (x) `#',x)
(defmacro real-part (x) x)
(defmacro printf (fmt &rest args) `(format t ,fmt ,@args))
(defmacro set! (var value) `(setf ,var ,value))
(defmacro equal? (x y) `(equal ,x ,y))
(defmacro null? (x) `(null ,x))
(defmacro vector-ref (v n) `(svref ,v ,n))
(defmacro vector-set! (v n value) `(setf (svref ,v ,n) ,value))
(defmacro defined? (x) `(boundp ,x))
(defmacro qsort (x y) `(sort ,x ,y))
(defmacro eq? (x y) `(eq ,x ,y))
(defmacro fprintf (f &rest args)
`(format ,f ,@args))
(defmacro define-structure (name &rest stuff)
`(defstruct ,name ,@stuff))
(defun make-vector (n) (make-array (list n)))
(defun open-input-file (name)
(open name))
(defun open-output-file (name)
(open name :direction :output :if-exists :supersede))
(defun close-input-port (name)
(close name))
(defun close-output-port (name)
(close name))
;#ifdef DEBUG
(defmacro dbgprintf (x &rest y)
`(format t ,x ,@y))
(defmacro entering (name)
`(format t "Entering ~s~%" ,name))
;#else
(defmacro dbgprintf (x &rest y) nil)
(defmacro entering (name) nil)
;#endif
;#endif /* defined(SCHEME) */
;#if defined(GAMBIT) || !defined(SCHEME)
(define-structure atm element species position velocity force)
(define (create-atm e p)
(let ((s (lookup-species (element-name e)
(element-initial-hybridization e))))
;#if defined(GAMBIT)
(make-atm e s p '#(0.0 0.0 0.0) '#(0.0 0.0 0.0))
;#else
(make-atm :element e :species s :position p
:velocity '#(0.0 0.0 0.0) :force '#(0.0 0.0 0.0))
;#endif
))
;#ifdef GAMBIT
(define (atm-set-species a s) (atm-species-set! a s))
(define (atm-add-pos a x)
(atm-position-set! a
(vplus x (atm-position a))))
(define (atm-set-pos a s) (atm-position-set! a s))
(define (atm-add-velocity a v)
(atm-velocity-set! a
(vplus v (atm-velocity a))))
(define (atm-set-velocity a s) (atm-velocity-set! a s))
(define (atm-zero-velocity a) (atm-velocity-set! a '#(0.0 0.0 0.0)))
(define (atm-zero-force a) (atm-force-set! a '#(0.0 0.0 0.0)))
(define (atm-add-force a v)
(atm-force-set! a
(vplus v (atm-force a))))
;#else
(define (atm-set-species a s) (set! (atm-species a) s))
(define (atm-add-pos a x)
(set! (atm-position a)
(vplus x (atm-position a))))
(define (atm-set-pos a s) (set! (atm-position a) s))
(define (atm-add-velocity a v)
(set! (atm-velocity a)
(vplus v (atm-velocity a))))
(define (atm-set-velocity a s) (set! (atm-velocity a) s))
(define (atm-zero-velocity a) (set! (atm-velocity a) '#(0.0 0.0 0.0)))
(define (atm-zero-force a) (set! (atm-force a) '#(0.0 0.0 0.0)))
(define (atm-add-force a v)
(set! (atm-force a)
(vplus v (atm-force a))))
;#endif
(define-structure bond order first second)
;#if defined(GAMBIT)
(define (create-bond ord f s)
(make-bond ord f s))
;#else
(define (create-bond ord f s)
(make-bond :order ord :first f :second s))
;#endif
(define-structure element
name rvdw mass total-bonds initial-hybridization how-to-hybridize)
;#if defined(GAMBIT)
(define (create-element name rvdw mass bonds init-hybrid ch-hybrid)
(make-element name rvdw mass bonds init-hybrid ch-hybrid))
;#else
(define (create-element name rvdw mass bonds init-hybrid ch-hybrid)
(make-element :name name :rvdw rvdw :mass mass :total-bonds bonds
:initial-hybridization init-hybrid
:how-to-hybridize ch-hybrid))
;#endif
(define-structure species name hybridization evdw mm2index)
;#if defined(GAMBIT)
(define (create-species name hybrid evdw mm2)
(make-species name hybrid evdw mm2))
;#else
(define (create-species name hybrid evdw mm2)
(make-species :name name :hybridization hybrid :evdw evdw :mm2index mm2))
;#endif
(define-structure bond-count singles doubles triples total-bonds)
(define (create-bond-count n)
(let ((b1 0) (b2 0) (b3 0))
(do ((BL bond-list (cdr BL)))
((null? BL))
(if (or (= n (bond-first (car BL))) (= n (bond-second (car BL))))
(cond ((= (bond-order (car BL)) 1) (set! b1 (+ b1 1)))
((= (bond-order (car BL)) 2) (set! b2 (+ b1 1)))
(else (set! b2 (+ b1 1))))))
(let ((total (+ b1 (* 2 b2) (* 3 b3))))
;#if defined(GAMBIT)
(make-bond-count b1 b2 b3 total)
;#else
(make-bond-count :singles b1 :doubles b2 :triples b3 :total-bonds total)
;#endif
)))
(define-structure dd diff dist)
(define (create-diff-dist m n)
(let ((dif (vdiff (atm-position m) (atm-position n))))
;#ifdef GAMBIT
(make-dd dif (vlen dif))
#else
(make-dd :diff dif :dist (vlen dif))
#endif
))
;#else /* ! (defined(GAMBIT) || !defined(SCHEME)) */
(define (create-atm elem pos)
(entering "make-atm")
(let ((velocity '#(0.0 0.0 0.0))
(force '#(0.0 0.0 0.0))
(species (lookup-species (funcall elem 'name)
(funcall elem 'initial-hybridization))))
(make-lambda (x y)
(case x
('element elem)
('species species)
('set-species (set! species y))
('position pos)
('add-pos (set! pos (vplus pos y)))
('set-pos (set! pos y))
('velocity velocity)
('add-velocity (set! velocity (vplus velocity y)))
('set-velocity (set! velocity y))
('zero-velocity (set! velocity '#(0.0 0.0 0.0)))
('force force)
('zero-force (set! force '#(0.0 0.0 0.0)))
('add-force (set! force (vplus force y)))
(else
(printf "Atom trouble, args: ~s, ~s~%" x y))))))
(define (atm-element a) (funcall a 'element '()))
(define (atm-species a) (funcall a 'species '()))
(define (atm-set-species a s) (funcall a 'set-species s))
(define (atm-position a) (funcall a 'position '()))
(define (atm-add-pos a x) (funcall a 'add-pos x))
(define (atm-set-pos a x) (funcall a 'set-pos x))
(define (atm-velocity a) (funcall a 'velocity '()))
(define (atm-add-velocity a v) (funcall a 'add-velocity v))
(define (atm-set-velocity a v) (funcall a 'set-velocity v))
(define (atm-zero-velocity a) (funcall a 'zero-velocity '()))
(define (atm-force a) (funcall a 'force '()))
(define (atm-zero-force a) (funcall a 'zero-force '()))
(define (atm-add-force a x) (funcall a 'add-force x))
(define (create-bond order first second)
(entering "make-bond")
(make-lambda (x)
(case x
('order order)
('first first)
('second second))))
(define (bond-order b) (funcall b 'order))
(define (bond-first b) (funcall b 'first))
(define (bond-second b) (funcall b 'second))
(define (create-element name rvdw mass bonds init-hybrid ch-hybrid)
(entering "make-element")
(make-lambda (x)
(case x
('name name)
('rvdw rvdw)
('mass mass)
('total-bonds bonds)
('initial-hybridization init-hybrid)
('how-to-hybridize ch-hybrid))))
(define (element-name e) (funcall e 'name))
(define (element-rvdw e) (funcall e 'rvdw))
(define (element-mass e) (funcall e 'mass))
(define (element-total-bonds e) (funcall e 'total-bonds))
(define (element-initial-hybridization e) (funcall e 'initial-hybridization))
(define (element-how-to-hybridize e) (funcall e 'how-to-hybridize))
(define (create-species name hybrid evdw mm2)
(entering "make-species")
(make-lambda (x)
(case x
('name name)
('hybridization hybrid)
('evdw evdw)
('mm2index mm2))))
(define (species-name s) (funcall s 'name))
(define (species-hybridization s) (funcall s 'hybridization))
(define (species-evdw s) (funcall s 'evdw))
(define (species-mm2index s) (funcall s 'mm2index))
(define (create-bond-count n)
(entering "make-bond-count")
(let ((singles 0)
(doubles 0)
(triples 0))
(dolist (bond bond-list)
(if (or (= n (bond-first bond)) (= n (bond-second bond)))
(case (bond-order bond)
(1 (set! singles (+ singles 1)))
(2 (set! doubles (+ doubles 1)))
(else (set! triples (+ triples 1))))))
(make-lambda (x)
(case x
('singles singles)
('doubles doubles)
('triples triples)
('total-bonds (+ singles (* 2 doubles) (* 3 triples)))))))
(define (bond-count-singles bc) (funcall bc 'singles))
(define (bond-count-doubles bc) (funcall bc 'doubles))
(define (bond-count-triples bc) (funcall bc 'triples))
(define (bond-count-total-bonds bc) (funcall bc 'total-bonds))
(define (create-diff-dist m n)
(let* ((ma (atm-position m))
(na (atm-position n))
(diff (vdiff ma na))
(dist (vlen diff)))
(make-lambda (x)
(case x
('diff diff)
('distance dist)))))
(define (dd-diff dd) (funcall dd 'diff))
(define (dd-dist dd) (funcall dd 'distance))
;#endif /* defined(USE_STRUCTS) */
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