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OSCHINA-MIRROR/helloyesterday-mindsponge

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xrd

Предстоит сделать
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Создано  
30.11.2024
$ python3 tutorial_xrd.py 
[MindSPONGE] Started simulation at 2024-07-30 15:20:42
[MindSPONGE] Step: 200, E_pot: -2466.971, E_kin: 812.4643, E_tot: -1654.5066, Temperature: 341.07153, Pressure: -9770.434, Volume: 2.1168654
[MindSPONGE] Step: 400, E_pot: -1634.615, E_kin: 1344.8087, E_tot: -289.80627, Temperature: 564.5491, Pressure: -1524.2262, Volume: 2.1168654
[MindSPONGE] Step: 600, E_pot: 2462.2605, E_kin: 6197.043, E_tot: 8659.304, Temperature: 2601.5112, Pressure: -11050.308, Volume: 2.1168654
[MindSPONGE] Step: 800, E_pot: -1832.9491, E_kin: 1303.2518, E_tot: -529.69727, Temperature: 547.1036, Pressure: -7776.9336, Volume: 2.1168654
[MindSPONGE] Step: 1000, E_pot: nan, E_kin: nan, E_tot: nan, Temperature: nan, Pressure: nan, Volume: 2.1168654
[MindSPONGE] Finished simulation at 2024-07-30 15:21:22
[MindSPONGE] Simulation time: 39.19 seconds.
--------------------------------------------------------------------------------
../../sponge/colvar/xrd.py:79: RuntimeWarning: divide by zero encountered in true_divide
  fft_fijk = scalor * 1. / pi2ijk*(np.exp(-0.25/self.att_coeff*(pi2ijk_2 - rk0)) - np.exp(-0.25/self.att_coeff*(pi2ijk_2 + rk0))) / (np.real(fft_B_spline))**2
../../sponge/colvar/xrd.py:79: RuntimeWarning: invalid value encountered in multiply
  fft_fijk = scalor * 1. / pi2ijk*(np.exp(-0.25/self.att_coeff*(pi2ijk_2 - rk0)) - np.exp(-0.25/self.att_coeff*(pi2ijk_2 + rk0))) / (np.real(fft_B_spline))**2
Traceback (most recent call last):
  File "tutorial_xrd.py", line 42, in <module>
    we2 = WithEnergyCell(system, ff, metad)
  File "../../sponge/core/simulation/energy.py", line 132, in __init__
    system, cutoff, exclude_index=self.exclude_index)
  File "../../sponge/partition/neighbourlist.py", line 195, in __init__
    index, mask = self.calculate(self.coordinate, self.pbc_box)
  File "../../sponge/partition/neighbourlist.py", line 318, in calculate
    coordinate, pbc_box, self.atom_mask, self.exclude_index)
  File "/usr/local/python-3.7.5/lib/python3.7/site-packages/mindspore/nn/cell.py", line 705, in __call__
    raise err
  File "/usr/local/python-3.7.5/lib/python3.7/site-packages/mindspore/nn/cell.py", line 701, in __call__
    output = self._run_construct(args, kwargs)
  File "/usr/local/python-3.7.5/lib/python3.7/site-packages/mindspore/nn/cell.py", line 482, in _run_construct
    output = self.construct(*cast_inputs, **kwargs)
  File "/usr/local/python-3.7.5/lib/python3.7/site-packages/mindspore/common/api.py", line 718, in staging_specialize
    out = _MindsporeFunctionExecutor(func, hash_obj, input_signature, process_obj, jit_config)(*args, **kwargs)
  File "/usr/local/python-3.7.5/lib/python3.7/site-packages/mindspore/common/api.py", line 121, in wrapper
    results = fn(*arg, **kwargs)
  File "/usr/local/python-3.7.5/lib/python3.7/site-packages/mindspore/common/api.py", line 350, in __call__
    raise err
  File "/usr/local/python-3.7.5/lib/python3.7/site-packages/mindspore/common/api.py", line 344, in __call__
    phase = self.compile(self.fn.__name__, *args_list, **kwargs)
  File "/usr/local/python-3.7.5/lib/python3.7/site-packages/mindspore/common/api.py", line 443, in compile
    is_compile = self._graph_executor.compile(self.obj, compile_args, kwargs, phase, True)
  File "/usr/local/python-3.7.5/lib/python3.7/site-packages/mindspore/ops/operations/array_ops.py", line 2516, in __infer__
    multiple, "multiples[%d]" % i, self.name)
  File "/usr/local/python-3.7.5/lib/python3.7/site-packages/mindspore/_checkparam.py", line 327, in check_positive_int
    return _check_number(arg_value, 0, GT, int, arg_name, prim_name)
  File "/usr/local/python-3.7.5/lib/python3.7/site-packages/mindspore/_checkparam.py", line 219, in _check_number
    _check_param()
  File "/usr/local/python-3.7.5/lib/python3.7/site-packages/mindspore/_checkparam.py", line 217, in _check_param
    raise ValueError(msg)
ValueError: For 'Tile', the 'multiples[2]' must be int and must > 0, but got '0' with type 'int'.

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