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Merge pull request #48 from E3SM-Project/develop
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Develop
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@ambrad
ambrad authored Sep 25, 2023
2 parents 0bda7ae + bd60adf commit 0deb504
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Showing 34 changed files with 2,497 additions and 885 deletions.
235 changes: 71 additions & 164 deletions methods/islet/figures/amb3.hy
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
;;; Collection of utils.

;;(require [hy.contrib.walk [let]])
(import sys copy math os re)
(import sys copy math os re [importlib [reload]])

;; when passing kwargs to another function like pl.plot, the dictionary should
;; be like {'option value}, not {:option value}.
Expand All @@ -23,7 +23,6 @@
(defn symbol [string] (HySymbol string))

(defmacro/g! svifn [&rest args]
"setv if none"
`(do ~@(map (fn [e]
`(if (none? ~(first e)) (setv ~(first e) ~(last e))))
(zip (cut args 0 (len args) 2)
Expand Down Expand Up @@ -81,7 +80,7 @@
`(print (.format ~@args) :end "" :file ~fid))

(defmacro prc [sym]
`(prf ~(+ (name sym) " {}") ~sym))
`(print ~sym "|" (eval (read-str ~sym))))

(defmacro mapply [func &rest args]
"Apply func. Works for keyword args, unlike apply. (Probably broken in many
Expand Down Expand Up @@ -149,47 +148,6 @@
(setv last? (= ~g!i ~g!last))
~@body)))

;; Use this instead of macroexpand to get output stripped of the Hy object
;; ctors.
(defn ppme [quoted-form]
(sv sym-dict {} b (Box) b.sym-num 0
b.after-open True)
(defn sym [e]
(unless (in e sym-dict)
(assoc sym-dict e (.format "sym-{:d}" b.sym-num))
(inc! b.sym-num))
(get sym-dict e))
(defn prl [e ldelim rdelim]
(prfno "{:s}" (+ (if b.after-open "" " ") ldelim))
(sv b.after-open True)
(for [li e] (rec li))
(prfno "{:s}" rdelim))
(defn atom? [e]
(in "quote" (first e)))
(defn rec [e]
(setv t (type e))
(case/in t
[[hy.models.HyFloat HyInteger] (print (+ " " (str e)) :end "")]
[[HyExpression]
(if (atom? e)
(for [li e] (rec li))
(prl e "(" ")"))]
[[HyList] (prl e "[" "]")]
[[HyString] (print (.format " \"{:s}\"" e) :end "")]
[:else
(unless b.after-open (print " " :end ""))
(sv b.after-open False)
(cond [(in "keyform" e)
(print (sym e) :end "")]
[(in "quote" e)
(print "'" :end "")
(sv b.after-open True)]
[:else (print e :end "")])]))
(setv h (macroexpand quoted-form))
(print h)
(rec h)
(print))

(defclass Box []
"A box to hold values to be written in closures."
(defn --repr-- [me]
Expand Down Expand Up @@ -357,6 +315,11 @@
(/ (sum (map (fn [e] (** (- e mu) 2)) coll))
(len coll)))

(defn cumsum [coll]
(setv c (list (copy.deepcopy coll)))
(for [i (range 1 (len c))] (+= (get c i) (nth c (dec i))))
c)

(defn cross-prod [x y]
(defn one [i0 i1]
(- (* (get x i0) (get y i1)) (* (get x i1) (get y i0))))
Expand Down Expand Up @@ -397,27 +360,35 @@
(except [e Exception]
(print ln))))

(defn ooa [y &optional [xfac 2] [x None]]
(defn calc-ooa [y &optional [xfac 2] [x None]]
(defn bad [e] (or (npy.isnan e) (npy.isinf e)))
(setv r [])
(for [i (range (dec (len y)))]
(when (or (bad (nth y i)) (bad (nth y (inc i))))
(prf "calc-ooa: i {} y(i) {} y(i+1) {}" i (nth y i) (nth y (inc i))))
(.append r (/ (- (math.log (get y i)) (math.log (get y (inc i))))
(if x
(- (math.log (get x i)) (math.log (get x (inc i))))
(- (math.log (get x (inc i))) (math.log (get x i)))
(math.log xfac)))))
r)

(defn ooa-from-file [fname fieldno &optional anchor]
(defn ooa-from-file [fname xanchor xfldno yanchor yfldno]
"Read text from file fname, optionally scan for lines beginning with anchor,
and read symbol fieldno, starting from 0. Return a list of OOAs."
(sv txt (.split (readall fname) "\n")
errs [])
x [] y [])
(for [ln txt]
(unless (none? anchor)
(when (or (< (len ln) (len anchor))
(!= anchor (cut ln 0 (len anchor))))
(continue)))
(.append errs (float (get (.split ln) fieldno))))
(, errs (ooa errs)))
(cond [(and (>= (len ln) (len xanchor))
(= xanchor (cut ln 0 (len xanchor))))
(.append x (float (get (.split ln) xfldno)))]
[(and (>= (len ln) (len yanchor))
(= yanchor (cut ln 0 (len yanchor))))
(.append y (float (get (.split ln) yfldno)))]))
(, x y (ooa y :x x)))

(defn sypd [procs calls time &optional [calls-per-day 48]]
(/ (/ calls procs calls-per-day 365)
(/ time (* 24 3600))))

(defn single? [coll]
(or (not (coll? coll))
Expand Down Expand Up @@ -521,8 +492,10 @@
(do
(import [numpy :as npy] ctypes)

(defmacro getc [vs i] `(get ~vs (, (s-all) ~i)))

(defn array-range [&rest args]
(npy.array (list (apply range args)) :dtype int))
(npy.array (list (range #*args)) :dtype int))

(defn array-if-not [A &optional [dtype float]]
(unless (= (type A) npy.ndarray)
Expand All @@ -540,6 +513,10 @@
(defn ones-row-vec [n] (npy.ones (, 1 (pod-or-len n))))
(defn ones-col-vec [n] (npy.ones (, (pod-or-len n) 1)))

(defn xy->XY [x y]
(, (npy.dot (col-vec (npy.ones (len y))) (row-vec x))
(npy.dot (col-vec y) (row-vec (npy.ones (len x))))))

(defn sort-with-p [ai]
"Return sorted ai and permutation array. Each entry of a must have the same
type."
Expand Down Expand Up @@ -651,6 +628,28 @@

(defn antidiag [v]
(get (npy.diag (get (npy.array v) (s-all-rev))) (s-all-rev)))

(defn get-row-2norms [vs]
(assert (and (= (len vs.shape) 2)))
(sv nrm (second vs.shape)
den 0)
(for [i (range nrm)]
(+= den (** (getc vs i) 2)))
(sv den (npy.sqrt den))
den)

(defn scale-rows! [scale vs]
(assert (and (< (len scale.shape) 2)
(= (len scale) (len vs))
(= (len vs.shape) 2)))
(sv dim (second vs.shape))
(for [i (range dim)]
(sv (getc vs i) (* scale (getc vs i))))
vs)

(defn normalize-rows! [vs]
(scale-rows! (/ (get-row-2norms vs)) vs))

)
(except []
(do
Expand All @@ -663,9 +662,9 @@
(do
(import matplotlib [matplotlib.pyplot :as pl])

(defn my-grid [&optional ls zorder]
(svifn ls "-" zorder -1)
(pl.grid True :lw 0.5 :ls ls :color (, 0.8 0.8 0.8) :zorder zorder
(defn my-grid [&optional ls]
(svifn ls "-")
(pl.grid True :lw 0.5 :ls ls :color (, 0.8 0.8 0.8) :zorder -1
:which "both")
(.set_axisbelow (pl.gca) True))

Expand Down Expand Up @@ -753,118 +752,26 @@

(defn make-reference-slope-triangle [x-span y-span slope pattern
&optional [kwargs-plot None]
[kwargs-text None]
[opposite None]]
[kwargs-text None]]
(assert (= 2 (len x-span)))
(assert (= 2 (len y-span)))
(svifn kwargs-plot {})
(svifn kwargs-text {})
(svifn opposite False)
(sv (, x0 x1) x-span (, y0 y1) y-span
dx (- x1 x0) dy (- y1 y0))
(if opposite
(do (sv x [x0 x1 x1 x0]
y [y1 y1 y0 y1]))
(do (sv x [x0 x1 x0 x0]
y [y0 y0 y1 y0])))
dx (- x1 x0) dy (- y1 y0)
x [x0 x1 x0 x0] y [y0 y0 y1 y0])
(pl.plot #*[x y pattern] #**kwargs-plot)
(when opposite
(if (none? kwargs-text) (sv kwargs-text {}))
(assoc kwargs-text "horizontalalignment" "right" "verticalalignment" "top"))
(pl.text #*[(if opposite (- x1 (* 0.1 dx)) (+ x0 (* 0.1 dx)))
(if opposite (- y1 (* 0.1 dy)) (+ y0 (* 0.1 dy))) (str slope)]
(pl.text #*[(+ x0 (* 0.1 dx)) (+ y0 (* 0.1 dy)) (str slope)]
#**kwargs-text))

) (except [] ))
(defn frame-init []
(pl.show :block False))
(defn frame-flip [U &optional [clim None] [pause 0.05]]
(pl.clf)
(pl.imshow U :interpolation "none" :origin "lower")
(unless (none? clim)
(pl.clim clim))
(pl.tight-layout)
(pl.pause pause))

;;; More extensive unit tests.
(if-main
(expect
(case/eq 'hi
('hit 'nope)
('hi 'bark 'yep))
'yep)
(expect
(case/in 'hello
['(bye hello) 'nope]
('(hi) 'yep)
('(4) 'another-nope))
'nope)
(expect
(case/in 'hi
('(bye hello) 'nope)
('(hi) 'yep)
('(4) 'another-nope))
'yep)
(expect
(case/in 'hi
('(bye hello) 'nope)
('hi 'yep)
('(4) 'another-nope))
'yep)
(expect
(case/test in 'hi
('(bye hello) 'nope)
('hi 'yep)
('(4) 'another-nope))
'yep)
(expect (case/eq 4 [5 'bye] [4 'hi])
'hi)
(expect
(case/in 'hi
('(bye hello) 'nope))
None)
(expect
(case/in 'hi
('(bye hello) 'nope)
(:else 'woot))
'woot)
(expect
(sdo (setv key 'hi)
(case/in key
('(bye hello) 'nope)
([key] 'yup)))
'yup)

(expect
(do
(sv a None b 4 c "hi" d None)
(svifn a "hi" b 3 c "bye")
(and (= a "hi") (= b 4) (= c "hi") (none? d))))
(expect
(do
(sv a None)
(svifn a "hi")
(= a "hi")))
(expect
(do
(sv a 5)
(svifn a "hi")
(= a 5)))

(expect
(do (sv a 1 b "hi" c 'd)
(svb (ab 1) (bb "hi") (cb 'd))
(and (= a ab) (= b bb) (= c cb))))

(when-inp ["test-pretty-print"]
(ppme '(case/in 'hi
(['hi 'bye] 'hi)
('[foo] (for [d dinos]
(print (.format "{:s} goes {:d}"
d.name d.sound))))
('[bar]
(defn axis-tight-pad [&optional [pad 0.05] [mult False]
[foo 3]]
(pl.axis "tight")
(setv xl (pl.xlim) yl (pl.ylim))
(pl.xlim (pad-lim xl pad mult))
(pl.ylim (pad-lim yl pad mult)))
(axis-tight-pad)))))

(when-inp ["ooa-from-file" {:fname str :anchor str :fieldno int}]
(sv (, errs ooas) (ooa-from-file fname fieldno :anchor anchor))
(for [i (range (len errs))]
(prf "{:10.3e} {}" (get errs i)
(if (zero? i) " n/a" (.format "{:6.3f}" (get ooas (dec i)))))))
)
) (except [] ))
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