Coverage for ase / gui / ag.py: 53.85%

1# fmt: off 

2 

3# Copyright 2008, 2009 

4# CAMd (see accompanying license files for details). 

5import warnings 

6 

7 

8class CLICommand: 

9 """ASE's graphical user interface. 

10 

11 ASE-GUI. See the online manual 

12 (https://ase-lib.org/ase/gui/gui.html) 

13 for more information. 

14 """ 

15 

16 @staticmethod 

17 def add_arguments(parser): 

18 add = parser.add_argument 

19 add('filenames', nargs='*', 

20 help='Files to open. Append @SLICE to a filename to pick ' 

21 'a subset of images from that file. See --image-number ' 

22 'for SLICE syntax.') 

23 add('-n', '--image-number', metavar='SLICE', default=':', 

24 help='Pick individual image or slice from each of the files. ' 

25 'SLICE can be a number or a Python slice-like expression ' 

26 'such as :STOP, START:STOP, or START:STOP:STEP, ' 

27 'where START, STOP, and STEP are integers. ' 

28 'Indexing counts from 0. ' 

29 'Negative numbers count backwards from last image. ' 

30 'Using @SLICE syntax for a filename overrides this option ' 

31 'for that file.') 

32 add('-r', '--repeat', 

33 default='1', 

34 help='Repeat unit cell. Use "-r 2" or "-r 2,3,1".') 

35 add('-R', '--rotations', default='', 

36 help='Examples: "-R -90x", "-R 90z,-30x".') 

37 add('-o', '--output', metavar='FILE', 

38 help='Write configurations to FILE.') 

39 add('-g', '--graph', 

40 # TRANSLATORS: EXPR abbreviates 'expression' 

41 metavar='EXPR', 

42 help='Plot x,y1,y2,... graph from configurations or ' 

43 'write data to sdtout in terminal mode. Use the ' 

44 'symbols: i, s, d, fmax, e, ekin, A, R, E and F. See ' 

45 'https://ase-lib.org/ase/gui/gui.html' 

46 '#plotting-data for more details.') 

47 add('-t', '--terminal', 

48 action='store_true', 

49 default=False, 

50 help='Run in terminal window - no GUI.') 

51 add('--interpolate', 

52 type=int, metavar='N', 

53 help='Interpolate N images between 2 given images.') 

54 add('-b', '--bonds', 

55 action='store_true', 

56 default=False, 

57 help='Draw bonds between atoms.') 

58 add('-s', '--scale', dest='radii_scale', metavar='FLOAT', 

59 default=None, type=float, 

60 help='Scale covalent radii.') 

61 

62 @staticmethod 

63 def run(args): 

64 from ase.atoms import Atoms 

65 from ase.gui.images import Images 

66 

67 images = Images() 

68 

69 if args.filenames: 

70 images.read(args.filenames, args.image_number) 

71 else: 

72 images.initialize([Atoms()]) 

73 

74 if args.interpolate: 

75 images.interpolate(args.interpolate) 

76 

77 if args.repeat != '1': 

78 r = args.repeat.split(',') 

79 if len(r) == 1: 

80 r = 3 * r 

81 images.repeat_images([int(c) for c in r]) 

82 

83 if args.radii_scale: 

84 images.scale_radii(args.radii_scale) 

85 

86 if args.output is not None: 

87 warnings.warn('You should be using "ase convert ..." instead!') 

88 images.write(args.output, rotations=args.rotations) 

89 args.terminal = True 

90 

91 if args.terminal: 

92 if args.graph is not None: 

93 data = images.graph(args.graph) 

94 for line in data.T: 

95 for x in line: 

96 print(x, end=' ') 

97 print() 

98 else: 

99 import os 

100 

101 import matplotlib 

102 

103 from ase.gui.gui import GUI 

104 

105 # When using Jupyter or some other interactive interpreter, 

106 # matplotlib is set up to use an inline backend such as: 

107 # 'inline' 

108 # 'module://ipykernel.pylab.backend_inline' 

109 # 'module://matplotlib_inline.backend_inline' 

110 # However, these would cause plots in the GUI to break so 

111 # we need to switch to Tk 

112 backend = matplotlib.get_backend() 

113 if 'inline' in backend: 

114 os.environ['MPLBACKEND'] = 'TkAgg' 

115 

116 gui = GUI(images, args.rotations, args.bonds, args.graph) 

117 gui.run() 

118 

119 # Reinstate the backend used before the GUI was opened 

120 os.environ['MPLBACKEND'] = backend