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theochem / tinydft

A minimalistic atomic Density Functional Theory (DFT) code
GNU General Public License v3.0
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Uncaught exception of type NSException for Python 3+ #1

Closed yingxingcheng closed 5 years ago

yingxingcheng commented 5 years ago

Hi Prof. Verstraelen:

There is an error when I run python tinydft.py in the Mac operating system, shown as follows:

(tinydft) YingxingdeMacBook-Pro:tinydft yxcheng$ python tinydft.py 
Electronic configuration          1s2 2s2 2p6 3s2 3p6 4s2 3d3
Occupation numbers per ang. mom.  [[2.0, 2.0, 2.0, 2.0], [6.0, 6.0], [3.0]]
Nuclear charge                          23
Number of electrons                   23.0
Maximum ang. mol. quantum number         2

Number of radial grid points           512
Number of basis functions               40
Condition number of the overlap    3.0e-11

Pre-computing some integrals ...

Number of SCF iterations                25
Mixing parameter                     0.500

 It        Total      Rad Kin      Ang Kin      Hartree           XC          Ext
=== ============ ============ ============ ============ ============ ============
  0      (guess)
  1  -146.297775  1000.378965  1098.895851   641.130224   -58.824864 -2827.877951
  2  -416.503845   815.664496   789.082941   504.264268   -48.480019 -2477.035532
  3  -505.716805   746.517142   665.655353   430.078499   -43.233462 -2304.734337
  4  -527.025823   727.102634   630.966259   401.225205   -41.337644 -2244.982276
  5  -529.730362   723.928996   626.288455   395.595669   -40.995804 -2234.547679
  6  -529.937654   723.427688   626.116295   394.867815   -40.962420 -2233.387033
  7  -530.087844   723.156703   625.953212   394.481200   -40.945293 -2232.733666
  8  -530.179460   723.027680   625.861019   394.367285   -40.940645 -2232.494799
  9  -530.240590   722.955912   625.788023   394.311675   -40.937903 -2232.358296
 10  -530.272505   722.921117   625.749141   394.291411   -40.936785 -2232.297389
 11  -530.288290   722.904257   625.729162   394.282042   -40.936216 -2232.267534
 12  -530.295408   722.896581   625.720171   394.278368   -40.935977 -2232.254550
 13  -530.298546   722.893085   625.716188   394.276733   -40.935868 -2232.248685
 14  -530.299874   722.891531   625.714528   394.276064   -40.935822 -2232.246174
 15  -530.300430   722.890837   625.713842   394.275769   -40.935802 -2232.245076
 16  -530.300659   722.890529   625.713568   394.275644   -40.935793 -2232.244606
 17  -530.300752   722.890392   625.713459   394.275589   -40.935790 -2232.244402
 18  -530.300790   722.890330   625.713418   394.275565   -40.935788 -2232.244314
 19  -530.300805   722.890302   625.713402   394.275554   -40.935787 -2232.244275
 20  -530.300811   722.890290   625.713396   394.275549   -40.935787 -2232.244258
 21  -530.300814   722.890284   625.713393   394.275547   -40.935787 -2232.244251
 22  -530.300815   722.890281   625.713393   394.275546   -40.935787 -2232.244247
 23  -530.300815   722.890280   625.713392   394.275545   -40.935787 -2232.244246
 24  -530.300816   722.890279   625.713392   394.275545   -40.935787 -2232.244245
2019-05-20 10:05:05.757 python[15602:7317726] -[NSApplication _setup:]: unrecognized selector sent to instance 0x7f91694f86f0
2019-05-20 10:05:05.764 python[15602:7317726] *** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '-[NSApplication _setup:]: unrecognized selector sent to instance 0x7f91694f86f0'
*** First throw call stack:
(
    0   CoreFoundation                      0x00007fff3ad2acf9 __exceptionPreprocess + 256
    1   libobjc.A.dylib                     0x00007fff658bea17 objc_exception_throw + 48
    2   CoreFoundation                      0x00007fff3ada4b06 -[NSObject(NSObject) __retain_OA] + 0
    3   CoreFoundation                      0x00007fff3accd0ef ___forwarding___ + 1485
    4   CoreFoundation                      0x00007fff3accca98 _CF_forwarding_prep_0 + 120
    5   libtk8.6.dylib                      0x000000061d72c31d TkpInit + 413
    6   libtk8.6.dylib                      0x000000061d68417e Initialize + 2622
    7   _tkinter.cpython-37m-darwin.so      0x000000061d4aca0f _tkinter_create + 1183
    8   python                              0x000000010a104116 _PyMethodDef_RawFastCallKeywords + 230
    9   python                              0x000000010a240e42 call_function + 306
    10  python                              0x000000010a23eaec _PyEval_EvalFrameDefault + 46092
    11  python                              0x000000010a23249e _PyEval_EvalCodeWithName + 414
    12  python                              0x000000010a102de7 _PyFunction_FastCallDict + 231
    13  python                              0x000000010a185381 slot_tp_init + 193
    14  python                              0x000000010a18f361 type_call + 241
    15  python                              0x000000010a103ae3 _PyObject_FastCallKeywords + 179
    16  python                              0x000000010a240ed5 call_function + 453
    17  python                              0x000000010a23ebe0 _PyEval_EvalFrameDefault + 46336
    18  python                              0x000000010a1038d5 function_code_fastcall + 117
    19  python                              0x000000010a240dc7 call_function + 183
    20  python                              0x000000010a23eaec _PyEval_EvalFrameDefault + 46092
    21  python                              0x000000010a23249e _PyEval_EvalCodeWithName + 414
    22  python                              0x000000010a102de7 _PyFunction_FastCallDict + 231
    23  python                              0x000000010a106ce2 method_call + 130
    24  python                              0x000000010a104752 PyObject_Call + 130
    25  python                              0x000000010a23ed58 _PyEval_EvalFrameDefault + 46712
    26  python                              0x000000010a23249e _PyEval_EvalCodeWithName + 414
    27  python                              0x000000010a103fe3 _PyFunction_FastCallKeywords + 195
    28  python                              0x000000010a240dc7 call_function + 183
    29  python                              0x000000010a23eb27 _PyEval_EvalFrameDefault + 46151
    30  python                              0x000000010a1038d5 function_code_fastcall + 117
    31  python                              0x000000010a240dc7 call_function + 183
    32  python                              0x000000010a23eb27 _PyEval_EvalFrameDefault + 46151
    33  python                              0x000000010a1038d5 function_code_fastcall + 117
    34  python                              0x000000010a240dc7 call_function + 183
    35  python                              0x000000010a23eaec _PyEval_EvalFrameDefault + 46092
    36  python                              0x000000010a23249e _PyEval_EvalCodeWithName + 414
    37  python                              0x000000010a103fe3 _PyFunction_FastCallKeywords + 195
    38  python                              0x000000010a240dc7 call_function + 183
    39  python                              0x000000010a23eb27 _PyEval_EvalFrameDefault + 46151
    40  python                              0x000000010a23249e _PyEval_EvalCodeWithName + 414
    41  python                              0x000000010a2959a0 PyRun_FileExFlags + 256
    42  python                              0x000000010a294e17 PyRun_SimpleFileExFlags + 391
    43  python                              0x000000010a2c2d3f pymain_main + 9663
    44  python                              0x000000010a0d666d main + 125
    45  libdyld.dylib                       0x00007fff670ec3d5 start + 1
)
libc++abi.dylib: terminating with uncaught exception of type NSException
Abort trap: 6

My Python environment is:

# Name                    Version                   Build  Channel
autograd                  1.2                        py_1    conda-forge
blas                      1.0                         mkl    defaults
ca-certificates           2019.1.23                     0    defaults
certifi                   2019.3.9                 py37_0    defaults
cycler                    0.10.0                   py37_0    defaults
freetype                  2.9.1                hb4e5f40_0    defaults
future                    0.17.1                   py37_0    defaults
intel-openmp              2019.3                      199    defaults
kiwisolver                1.1.0            py37h0a44026_0    defaults
libcxx                    4.0.1                hcfea43d_1    defaults
libcxxabi                 4.0.1                hcfea43d_1    defaults
libedit                   3.1.20181209         hb402a30_0    defaults
libffi                    3.2.1                h475c297_4    defaults
libgfortran               3.0.1                h93005f0_2    defaults
libpng                    1.6.37               ha441bb4_0    defaults
matplotlib                3.0.3            py37h54f8f79_0    defaults
mkl                       2019.3                      199    defaults
mkl_fft                   1.0.12           py37h5e564d8_0    defaults
mkl_random                1.0.2            py37h27c97d8_0    defaults
ncurses                   6.1                  h0a44026_1    defaults
numpy                     1.16.3           py37hacdab7b_0    defaults
numpy-base                1.16.3           py37h6575580_0    defaults
openssl                   1.1.1b               h1de35cc_1    defaults
pip                       19.1.1                   py37_0    defaults
pyparsing                 2.4.0                      py_0    defaults
python                    3.7.3                h359304d_0    defaults
python-dateutil           2.8.0                    py37_0    defaults
pytz                      2019.1                     py_0    defaults
readline                  7.0                  h1de35cc_5    defaults
scipy                     1.2.1            py37h1410ff5_0    defaults
setuptools                41.0.1                   py37_0    defaults
six                       1.12.0                   py37_0    defaults
sqlite                    3.28.0               ha441bb4_0    defaults
tk                        8.6.8                ha441bb4_0    defaults
tornado                   6.0.2            py37h1de35cc_0    defaults
wheel                     0.33.4                   py37_0    defaults
xz                        5.2.4                h1de35cc_4    defaults
zlib                      1.2.11               h1de35cc_3    defaults
yingxingcheng commented 5 years ago

PS: for ubuntu, there are no these problems.

yingxingcheng commented 5 years ago

PS: for window, it does work both for Python 2+ and Python 3+ as well.

tovrstra commented 5 years ago

Thanks for bringing this up. It can be fixed by configuring matplotlib to use the agg backend. Can you try putting the following line in ~/.config/matplotlib/matplotlibrc (can be created if needed):

backend: agg
yingxingcheng commented 5 years ago

Yes and no, the configuration directory you provided is not suited for my case, but I use the line below to find the configuration directory, and after this, it works! Many thanks.

First, one should obtain the correct matplotlib configuration directory:

>>> import matplotlib as mpl
>>> print(mpl.get_configdir())
>>> '/Users/yxcheng/.matplotlib'

Then, one should create a matplotlibrc file if it doesn't exist and add the line backend : agg:

echo 'backend : agg' >> /Users/yxcheng/.matplotlib/matplotlibrc

Finally, the output of python tinydft.py is:

(tinydft) YingxingdeMacBook-Pro:tinydft yxcheng$ python tinydft.py
Electronic configuration          1s2 2s2 2p6 3s2 3p6 4s2 3d3
Occupation numbers per ang. mom.  [[2.0, 2.0, 2.0, 2.0], [6.0, 6.0], [3.0]]
Nuclear charge                          23
Number of electrons                   23.0
Maximum ang. mol. quantum number         2

Number of radial grid points           512
Number of basis functions               40
Condition number of the overlap    3.0e-11

Pre-computing some integrals ...

Number of SCF iterations                25
Mixing parameter                     0.500

 It        Total      Rad Kin      Ang Kin      Hartree           XC          Ext
=== ============ ============ ============ ============ ============ ============
  0      (guess)
  1  -146.297775  1000.378965  1098.895851   641.130224   -58.824864 -2827.877951
  2  -416.503845   815.664496   789.082941   504.264268   -48.480019 -2477.035532
  3  -505.716805   746.517142   665.655353   430.078499   -43.233462 -2304.734337
  4  -527.025823   727.102634   630.966259   401.225205   -41.337644 -2244.982276
  5  -529.730362   723.928996   626.288455   395.595669   -40.995804 -2234.547679
  6  -529.937654   723.427688   626.116295   394.867815   -40.962420 -2233.387033
  7  -530.087844   723.156703   625.953212   394.481200   -40.945293 -2232.733666
  8  -530.179460   723.027680   625.861019   394.367285   -40.940645 -2232.494799
  9  -530.240590   722.955912   625.788023   394.311675   -40.937903 -2232.358296
 10  -530.272505   722.921117   625.749141   394.291411   -40.936785 -2232.297389
 11  -530.288290   722.904257   625.729162   394.282042   -40.936216 -2232.267534
 12  -530.295408   722.896581   625.720171   394.278368   -40.935977 -2232.254550
 13  -530.298546   722.893085   625.716188   394.276733   -40.935868 -2232.248685
 14  -530.299874   722.891531   625.714528   394.276064   -40.935822 -2232.246174
 15  -530.300430   722.890837   625.713842   394.275769   -40.935802 -2232.245076
 16  -530.300659   722.890529   625.713568   394.275644   -40.935793 -2232.244606
 17  -530.300752   722.890392   625.713459   394.275589   -40.935790 -2232.244402
 18  -530.300790   722.890330   625.713418   394.275565   -40.935788 -2232.244314
 19  -530.300805   722.890302   625.713402   394.275554   -40.935787 -2232.244275
 20  -530.300811   722.890290   625.713396   394.275549   -40.935787 -2232.244258
 21  -530.300814   722.890284   625.713393   394.275547   -40.935787 -2232.244251
 22  -530.300815   722.890281   625.713393   394.275546   -40.935787 -2232.244247
 23  -530.300815   722.890280   625.713392   394.275545   -40.935787 -2232.244246
 24  -530.300816   722.890279   625.713392   394.275545   -40.935787 -2232.244245
tovrstra commented 5 years ago

This problem is fixed with matplotlib version 3.1.0 (or newer), which are available on pip and (recently) also on conda.