; Meep Tutorial: TE transmission and reflection through a cavity; formed by a periodic sequence of holes in a dielectric waveguide,; with a defect formed by a larger spacing between one pair of holes.; This structure is based on one analyzed in:;    S. Fan, J. N. Winn, A. Devenyi, J. C. Chen, R. D. Meade, and;    J. D. Joannopoulos, "Guided and defect modes in periodic dielectric;    waveguides," J. Opt. Soc. Am. B, 12 (7), 1267-1272 (1995).; Some parameters to describe the geometry:(define-param eps 13) ; dielectric constant of waveguide(define-param w 1.2) ; width of waveguide(define-param r 0.36) ; radius of holes(define-param d 1.4) ; defect spacing (ordinary spacing = 1)(define-param N 3) ; number of holes on either side of defect; The cell dimensions(define-param sy 6) ; size of cell in y direction (perpendicular to wvg.)(define-param pad 2) ; padding between last hole and PML edge(define-param dpml 1) ; PML thickness(define sx (+ (* 2 (+ pad dpml N)) d -1)) ; size of cell in x direction(set! geometry-lattice (make lattice (size sx sy no-size)))(set! geometry      (append ; combine lists of objects:       (list (make block (center 0 0) (size infinity w infinity)		   (material (make dielectric (epsilon eps)))))       (geometric-object-duplicates (vector3 1 0) 0 (- N 1)	(make cylinder (center (/ d 2) 0) (radius r) (height infinity)	      (material air)))       (geometric-object-duplicates (vector3 -1 0) 0 (- N 1)	(make cylinder (center (/ d -2) 0) (radius r) (height infinity)	      (material air)))))(set! pml-layers (list (make pml (thickness dpml))))(set-param! resolution 20)(define-param fcen 0.25) ; pulse center frequency                            (define-param df 0.2)  ; pulse width (in frequency) (define-param nfreq 500) ; number of frequencies at which to compute flux; false = transmission spectrum, true = resonant modes:(define-param compute-mode? false)(if compute-mode?    (begin      (set! sources (list		     (make source		       (src (make gaussian-src (frequency fcen) (fwidth df)))		       (component Hz) (center 0 0))))      (set! symmetries	    (list (make mirror-sym (direction Y) (phase -1))		  (make mirror-sym (direction X) (phase -1))))      (run-sources+ 400		    (at-beginning output-epsilon)		    (after-sources (harminv Hz (vector3 0) fcen df)))      (run-until (/ 1 fcen) (at-every (/ 1 fcen 20) output-hfield-z))            )    (begin      (set! sources (list		     (make source		       (src (make gaussian-src (frequency fcen) (fwidth df)))		       (component Ey)		       (center (+ dpml (* -0.5 sx)) 0)		       (size 0 w))))      (set! symmetries (list (make mirror-sym (direction Y) (phase -1))))            (define trans ; transmitted flux	(add-flux fcen df nfreq		  (make flux-region		    (center (- (* 0.5 sx) dpml 0.5) 0) (size 0 (* w 2)))))            (run-sources+ (stop-when-fields-decayed 		     50 Ey		     (vector3 (- (* 0.5 sx) dpml 0.5) 0)		     1e-3)		    (at-beginning output-epsilon)		    (during-sources                     (in-volume (volume (center 0 0) (size sx 0))                     (to-appended "hz-slice" (at-every 0.4 output-hfield-z)))))            (display-fluxes trans) ; print out the flux spectrum      ))