TKY2 Result failure with gather

リンクされた結果アーカイブを使って失敗を再現し、その後 openfecli/commands/gather.py の _write_dg_mle から開始して、cinnabar/stats.py:mle への呼び出しを追跡してください。ゼロ除算の警告と SVD の失敗を調査してください。現在の未処理例外を発生させずに gather パスがこの入力を処理するか、明確に報告できれば完了です。

/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:207: RuntimeWarning: divide by zero encountered in scalar power
  F_matrix[i, j] = -df_ij[i, j] ** (-2)
/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:208: RuntimeWarning: divide by zero encountered in scalar power
  F_matrix[j, i] = -df_ij[i, j] ** (-2)
/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:228: RuntimeWarning: divide by zero encountered in scalar power
  z[i] += f_ij[i, j] * df_ij[i, j] ** (-2)
/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:229: RuntimeWarning: divide by zero encountered in scalar power
  z[j] += f_ij[j, i] * df_ij[j, i] ** (-2)
/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:228: RuntimeWarning: invalid value encountered in scalar add
  z[i] += f_ij[i, j] * df_ij[i, j] ** (-2)
/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:229: RuntimeWarning: invalid value encountered in scalar add
  z[j] += f_ij[j, i] * df_ij[j, i] ** (-2)
Traceback (most recent call last):
  File "/usr/local/bin/openfe", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/usr/local/lib/python3.10/site-packages/openfecli/commands/gather.py", line 376, in gather
    writing_func(legs, writer, allow_partial)
  File "/usr/local/lib/python3.10/site-packages/openfecli/commands/gather.py", line 259, in _write_dg_mle
    f_i, df_i = mle(g, factor='calc_DDG')
  File "/usr/local/lib/python3.10/site-packages/cinnabar/stats.py", line 232, in mle
    Finv = np.linalg.pinv(F_matrix)
  File "/usr/local/lib/python3.10/site-packages/numpy/linalg/linalg.py", line 2022, in pinv
    u, s, vt = svd(a, full_matrices=False, hermitian=hermitian)
  File "/usr/local/lib/python3.10/site-packages/numpy/linalg/linalg.py", line 1681, in svd
    u, s, vh = gufunc(a, signature=signature, extobj=extobj)
  File "/usr/local/lib/python3.10/site-packages/numpy/linalg/linalg.py", line 121, in _raise_linalgerror_svd_nonconvergence
    raise LinAlgError("SVD did not converge")
numpy.linalg.LinAlgError: SVD did not converge

This is with https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2024/results_tyk2_transformations_openfe_1.0.0rc0_uc_2.tar.gz