hall-symbols 0.1.0.2 → 0.1.0.3

raw patch · 4 files changed

+86/−20 lines, 4 filesdep ~basePVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependency ranges changed: base

API changes (from Hackage documentation)

Files

• README.md +26/−1
• hall-symbols.cabal +6/−5
• src/Crystallography/HallSymbols.hs +50/−10
• src/Crystallography/HallSymbols/SpacegroupSymbols.hs +4/−4

@@ -2,7 +2,32 @@  Haskell Hall Symbols Library +# Quickstart++```shell+% stack repl+```++```haskell+-- prepare+repl> :set -package matrix-as-xyz+repl> :m Data.Matrix.AsXYZ+repl> :l Crystallography.HallSymbols++-- print general positions+repl> fmap prettyXYZ $ fromHallSymbols' "C -2yc"++ ["x,y,z","x+1/2,y+1/2,z","x,-y,z+1/2","x+1/2,-y+1/2,z+1/2"]++-- print generators+repl> fmap prettyXYZ $ fromHallSymbols'' "C -2yc"++["x,y,z","x+1/2,y+1/2,z","x,-y,z+1/2"]+```+++ ## License -See the [LICENSE](https://github.com/narumij/hall-symbols/LICENSE)+See the [LICENSE](LICENSE) file in the repository.

@@ -1,11 +1,13 @@--- This file has been generated from package.yaml by hpack version 0.28.2.+cabal-version: 1.12++-- This file has been generated from package.yaml by hpack version 0.33.0. -- -- see: https://github.com/sol/hpack ----- hash: d12bbdc0541111541cff37cd9476b103519c83cb6f35480d7c6234e0e14cda37+-- hash: 702da6b77b983eb8b29d4431755b69ea93d2ecadc33590f79090f8406752c85a  name:           hall-symbols-version:        0.1.0.2+version:        0.1.0.3 synopsis:       Symmetry operations generater of Hall Symbols description:    Please see the README on GitHub at <https://github.com/narumij/hall-symbols#readme> category:       Chemistry@@ -17,10 +19,9 @@ license:        BSD3 license-file:   LICENSE build-type:     Simple-cabal-version:  >= 1.10 extra-source-files:-    ChangeLog.md     README.md+    ChangeLog.md  source-repository head   type: git

@@ -23,7 +23,8 @@   fromHallSymbols,   fromHallSymbols',   hallSymbols,-  hallSymbols',+--  hallSymbols',+  parser,   LatticeSymbol,   MatrixSymbol,   OriginShift,@@ -110,8 +111,8 @@ space' = oneOf " _"  -- | Primitive parser-hallSymbols' :: CharParser () ( LatticeSymbol, [MatrixSymbol], OriginShift )-hallSymbols' = do+parser :: CharParser () ( LatticeSymbol, [MatrixSymbol], OriginShift )+parser = do   l   <- latticeSymbol   nat <- many1 (try ms)   v   <- option (0,0,0) os@@ -124,15 +125,21 @@       space'       originShift --- | Parser with convert+-- | Parse and make Generators.+generators :: CharParser () [Matrix Rational]+generators = do+  raw <- parser+  return $ decodeSymbols raw++-- | Parse and make General Positions. hallSymbols :: CharParser () [Matrix Rational] hallSymbols = do-  raw <- hallSymbols'+  g <- generators   -- Step 1: Decode space-group symbols   -- decodeSymbols関数で省略された軸情報を復元し、seiz matrixを生成します   -- Step 2: Generate symmetry operators   -- generate関数で得られたseiz matrixをgeneratorとして、一般点を生成します-  let equivalentPositions = generate . decodeSymbols $ raw+  let equivalentPositions = generate g   -- generate関数が計算に失敗すると空の配列を返すので、その場合パースエラーとして処理します   if null equivalentPositions     then@@ -141,9 +148,29 @@       -- 正常に終了すると、一般座標の行列を返します。       return equivalentPositions +-- | Parse and make General Positions.+generateLikeITC :: CharParser () [Matrix Rational]+generateLikeITC = do+  raw <- parser+  let equivalentPositions = likeITC raw+  if null equivalentPositions+    then+      fail "something happen when decode or generate process."+    else+      -- 正常に終了すると、一般座標の行列を返します。+      return equivalentPositions++likeITC :: ( LatticeSymbol, [MatrixSymbol], OriginShift ) -> [Matrix Rational]+likeITC raw = if null h then [] else r            +  where+    constructMatrices' (l,nat,v) = fmap (mapOriginShfit v) [lattice l, map matrix nat]+    [a,b] = constructMatrices' . restoreDefaultAxis $ raw+    h = generate $ [identity] ++ b+    r = generate $ h ++ a+ -- | Generate general equivalent positions by 4x4 matrix fromHallSymbols :: String -> Either ParseError [Matrix Rational]-fromHallSymbols s = parse hallSymbols ("while reading " ++ show s) s+fromHallSymbols s = parse generateLikeITC ("while reading " ++ show s) s  -- | Generate general equivalent positions by 4x4 matrix (unsafe version) fromHallSymbols' :: String -> [Matrix Rational]@@ -151,7 +178,20 @@   Left e -> error $ show e   Right mm -> mm --- パーズした簡約記号からseiz matrixを復元します+-- | Generate Generators by 4x4 matrix (unsafe version)+fromHallSymbols'' :: String -> [Matrix Rational]+fromHallSymbols'' s = case gg s of+  Left e -> error $ show e+  Right mm -> mm+  where+    gg s = parse generators ("while reading " ++ show s) s++-- | Generate general equivalent positions by 4x4 matrix+-- same as old version fromHallSymbols+fromHallSymbols''' :: String -> Either ParseError [Matrix Rational]+fromHallSymbols''' s = parse hallSymbols ("while reading " ++ show s) s++-- パースした簡約記号からseiz matrixを復元します decodeSymbols :: ( LatticeSymbol, [MatrixSymbol], OriginShift ) -> [Matrix Rational] decodeSymbols = constructMatrices . restoreDefaultAxis @@ -223,11 +263,11 @@ -- 注意点として、恒等操作が二つあるなどしただけで、計算結果が変化するようである。 -- このため、計算に供する行列はジェネレーターの組み合わせとして正しいかどうか配慮する必要がある。 gn :: Int -> [Matrix Rational] -> [Matrix Rational] -> [Matrix Rational]-gn n s m | length m == length mm = m+gn n s m | length (nub m) == length mm = mm          -- 計算が収束しなかった場合、空の配列を返し終了する.          -- 既存の空間群の対称操作の生成が最大4回の繰り返しで足りるので、なんとなくで10回にしています          | n > 10 = []-         | otherwise = gn (succ n) s mm+         | otherwise = gn (succ n) (nub s) mm   where     mm = nub . map (modulus1 . foldl1 multStd) . sequenceA $ [s,m] 

@@ -171,7 +171,7 @@   (  "28:cab",  "P 2 m b",  "P -2b 2"  ),   (  "28:-cba",  "P 2 c m",  "P -2c 2"  ),   (  "28:bca",  "P c 2 m",  "P -2c -2c"  ),-  (  "28:a-c",  "b   P m 2 a",  "P -2a -2a"  ),+  (  "28:a-cb",  "P m 2 a",  "P -2a -2a"  ),   (  "29",  "P c a 21",  "P 2c -2ac"  ),   (  "29:ba-c",  "P b c 21",  "P 2c -2b"  ),   (  "29:cab",  "P 21 a b",  "P -2b 2a"  ),@@ -396,7 +396,7 @@   (  "88:1",  "I 41/a:1",  "I 4bw -1bw"  ),   (  "88:2",  "I 41/a:2",  "-I 4ad"  ),   (  "89",  "P 4 2 2",  "P 4 2"  ),-  (  "90",  "P 42 1 2",  "P 4ab 2ab"  ),+  (  "90",  "P 4 21 2",  "P 4ab 2ab"  ),   (  "91",  "P 41 2 2",  "P 4w 2c"  ),   (  "92",  "P 41 21 2",  "P 4abw 2nw"  ),   (  "93",  "P 42 2 2",  "P 4c 2"  ),@@ -473,8 +473,8 @@   (  "152",  "P 31 2 1",  "P 31 2\""  ),   (  "153",  "P 32 1 2",  "P 32 2c (0 0 -1)"  ),   (  "154",  "P 32 2 1",  "P 32 2\""  ),-  (  "155:H",  "R 32:H",  "R 3 2\""  ),-  (  "155:R",  "R 32:R",  "P 3* 2"  ),+  (  "155:H",  "R 3 2:H",  "R 3 2\""  ),+  (  "155:R",  "R 3 2:R",  "P 3* 2"  ),   (  "156",  "P 3 m 1",  "P 3 -2\""  ),   (  "157",  "P 3 1 m",  "P 3 -2"  ),   (  "158",  "P 3 c 1",  "P 3 -2\"c"  ),