Coverage for /builds/kinetik161/ase/ase/cli/nebplot.py: 55.00%

1# Note: 

2# Try to avoid module level import statements here to reduce 

3# import time during CLI execution 

4 

5 

6class CLICommand: 

7 """Analyze NEB trajectories by making band plots. 

8 

9 One file: 

10 

11 ase nebplot neb.traj 

12 

13 Multiple files: 

14 

15 ase nebplot neb1.traj neb2.traj 

16 

17 Specify output: 

18 

19 ase nebplot neb1.traj neb2.traj myfile.pdf 

20 """ 

21 

22 @staticmethod 

23 def add_arguments(parser): 

24 add = parser.add_argument 

25 add('filenames', nargs='+', 

26 help='one or more trajectory files to analyze') 

27 add('output', nargs='?', 

28 help='optional name of output file, default=nebplots.pdf') 

29 add('--nimages', dest='n_images', type=int, default=None, 

30 help='number of images per band, guessed if not supplied') 

31 add('--share-x', dest='constant_x', action='store_true', 

32 help='use a single x axis scale for all plots') 

33 add('--share-y', dest='constant_y', action='store_true', 

34 help='use a single y axis scale for all plots') 

35 

36 @staticmethod 

37 def run(args, parser): 

38 from ase.gui.images import Images 

39 from ase.mep import NEBTools 

40 

41 # Nothing will ever be stored in args.output; need to manually find 

42 # if its supplied by checking extensions. 

43 if args.filenames[-1].endswith('.pdf'): 

44 args.output = args.filenames.pop(-1) 

45 else: 

46 args.output = 'nebplots.pdf' 

47 

48 images = Images() 

49 images.read(args.filenames) 

50 nebtools = NEBTools(images=images) 

51 nebtools.plot_bands(constant_x=args.constant_x, 

52 constant_y=args.constant_y, 

53 nimages=args.n_images, 

54 label=args.output[:-4])