[ase-users] bug in read traj file

[GENG SUN]

Dear ASE users,

I encounter a problem when read the traj file generated by two different
versions of python ase.

The struct.traj is generated by python-3.7.3 and ase-3.19.0b1 ( I don't
know why conda installed this version for me).

Then when I move the file "struct.traj" to another computer (which has
python3.6 and ase 3.18.1 installed), and try to read it by simply:

from ase.io import read
atoms=read("struct.traj")

The line complains that:

Traceback (most recent call last):
  File "read_traj.py", line 2, in <module>
    atoms=read("struct.traj")
  File
"/home/gengsun/anaconda3/envs/py36/lib/python3.6/site-packages/ase/io/formats.py",
line 498, in read
    parallel=parallel, **kwargs))
  File
"/home/gengsun/anaconda3/envs/py36/lib/python3.6/site-packages/ase/io/formats.py",
line 556, in _iread
    for dct in io.read(fd, *args, **kwargs):
  File
"/home/gengsun/anaconda3/envs/py36/lib/python3.6/site-packages/ase/io/trajectory.py",
line 356, in read_traj
    yield trj[i]
  File
"/home/gengsun/anaconda3/envs/py36/lib/python3.6/site-packages/ase/io/trajectory.py",
line 256, in __getitem__
    atoms = read_atoms(b)
  File
"/home/gengsun/anaconda3/envs/py36/lib/python3.6/site-packages/ase/io/trajectory.py",
line 319, in read_atoms
    for d in decode(constraints)],
  File
"/home/gengsun/anaconda3/envs/py36/lib/python3.6/site-packages/ase/io/trajectory.py",
line 319, in <listcomp>
    for d in decode(constraints)],
  File
"/home/gengsun/anaconda3/envs/py36/lib/python3.6/site-packages/ase/constraints.py",
line 20, in dict2constraint
    return globals()[dct['name']](**dct['kwargs'])

* File
"/home/gengsun/anaconda3/envs/py36/lib/python3.6/site-packages/ase/constraints.py",
line 138, in __init__    srt = np.sort(indices)*
  File "<__array_function__ internals>", line 6, in sort
  File
"/home/gengsun/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/fromnumeric.py",
line 970, in sort
    a.sort(axis=axis, kind=kind, order=order)


Then I print the "indices" before the line of "srt=np.sort(indices)"
and I found that the value of "indices" are:

{'__ndarray__': [array([120]), 'int64', array([  0,   1,   2,   3,   4,
5,   6,   7,   8,   9,  10,  11,  17,
        16,  15,  14,  13,  12,  18,  19,  20,  21,  22,  23,  35,  33,
        32,  31,  30,  34,  28,  27,  26,  25,  29,  24,  47,  46,  45,
        44,  43,  42,  41,  40,  39,  38,  37,  36,  58,  59,  57,  56,
        55,  54,  49,  52,  51,  50,  48,  53,  60,  61,  62,  63,  64,
        65,  70,  71,  69,  67,  66,  68,  82,  72,  73,  74,  75,  76,
        77,  78,  79,  80,  81,  83,  89,  87,  88,  85,  84,  86,  97,
       101,  99,  98,  96, 100,  94,  93,  92,  91,  90,  95, 113, 109,
       112, 111, 110, 108, 102, 106, 105, 104, 103, 107, 118, 117, 119,
       115, 114, 116])]}

It seems that "indices" here is a dictionary rather than a numpy array.

I wonder how to fix this problem?
Since I already have quite a lot of data from the ase 3.19.0b1, hence I
would like to find a method to make them compatible.


Thanks so much.

Best,

Geng
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