Hi,
I'm trying to install a python source
https://github.com/peteboyd/lammps_interface
when I run the example test I receive this error
AttributeError: 'NoneType' object has no attribute 'copy'
How could I fix it?
regards
lammps-interface
/home/alberto/Scaricati/lammps_interface-master/test_struct/IRMOF-1.cif
fatal: Not a git repository (or any of the parent directories): .git
No bonds reported in cif file - computing bonding..
Molecules found in the framework, separating.
Traceback (most recent call last):
File "/usr/local/bin/lammps-interface", line 4, in <module>
__import__('pkg_resources').run_script('lammps-interface==0.1.1',
'lammps-interface')
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 719, in
run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1504,
in run_script
exec(code, namespace, namespace)
File
"/usr/local/lib/python3.5/dist-packages/lammps_interface-0.1.1-py3.5.egg/EGG-INFO/scripts/lammps-interface",
line 13, in <module>
sim.split_graph()
File
"/usr/local/lib/python3.5/dist-packages/lammps_interface-0.1.1-py3.5.egg/lammps_interface/lammps_main.py",
line 398, in split_graph
sg = self.cut_molecule(molecule)
File
"/usr/local/lib/python3.5/dist-packages/lammps_interface-0.1.1-py3.5.egg/lammps_interface/lammps_main.py",
line 1535, in cut_molecule
mgraph.distance_matrix = self.graph.distance_matrix.copy()
AttributeError: 'NoneType' object has no attribute 'copy'
the installetion seems completed correctly
sudo python3 setup.py install
/usr/lib/python3.5/distutils/dist.py:261: UserWarning: Unknown distribution
option: 'long_description_content_type'
warnings.warn(msg)
running install
Checking .pth file support in /usr/local/lib/python3.5/dist-packages/
/usr/bin/python3 -E -c pass
TEST PASSED: /usr/local/lib/python3.5/dist-packages/ appears to support .pth
files
running bdist_egg
running egg_info
creating lammps_interface.egg-info
writing requirements to lammps_interface.egg-info/requires.txt
writing dependency_links to lammps_interface.egg-info/dependency_links.txt
writing lammps_interface.egg-info/PKG-INFO
writing top-level names to lammps_interface.egg-info/top_level.txt
writing manifest file 'lammps_interface.egg-info/SOURCES.txt'
reading manifest file 'lammps_interface.egg-info/SOURCES.txt'
writing manifest file 'lammps_interface.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/lammps_interface
copying lammps_interface/mof_sbus.py -> build/lib/lammps_interface
copying lammps_interface/Dubbeldam.py -> build/lib/lammps_interface
copying lammps_interface/gas_models.py -> build/lib/lammps_interface
copying lammps_interface/lammps_main.py -> build/lib/lammps_interface
copying lammps_interface/structure_data.py -> build/lib/lammps_interface
copying lammps_interface/Molecules.py -> build/lib/lammps_interface
copying lammps_interface/water_models.py -> build/lib/lammps_interface
copying lammps_interface/lammps_potentials.py -> build/lib/lammps_interface
copying lammps_interface/BTW.py -> build/lib/lammps_interface
copying lammps_interface/dreiding.py -> build/lib/lammps_interface
copying lammps_interface/CIFIO.py -> build/lib/lammps_interface
copying lammps_interface/__init__.py -> build/lib/lammps_interface
copying lammps_interface/generic_raspa.py -> build/lib/lammps_interface
copying lammps_interface/atomic.py -> build/lib/lammps_interface
copying lammps_interface/ccdc.py -> build/lib/lammps_interface
copying lammps_interface/uff_nonbonded.py -> build/lib/lammps_interface
copying lammps_interface/MOFFF.py -> build/lib/lammps_interface
copying lammps_interface/uff.py -> build/lib/lammps_interface
copying lammps_interface/InputHandler.py -> build/lib/lammps_interface
copying lammps_interface/uff4mof.py -> build/lib/lammps_interface
copying lammps_interface/ForceFields.py -> build/lib/lammps_interface
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/mof_sbus.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/Dubbeldam.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/gas_models.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/lammps_main.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/structure_data.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/Molecules.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/water_models.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/lammps_potentials.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/BTW.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/dreiding.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/CIFIO.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/__init__.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/generic_raspa.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/atomic.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/ccdc.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/uff_nonbonded.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/MOFFF.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/uff.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/InputHandler.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/uff4mof.py ->
build/bdist.linux-x86_64/egg/lammps_interface
copying build/lib/lammps_interface/ForceFields.py ->
build/bdist.linux-x86_64/egg/lammps_interface
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/mof_sbus.py to
mof_sbus.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/Dubbeldam.py to
Dubbeldam.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/gas_models.py to
gas_models.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/lammps_main.py to
lammps_main.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/structure_data.py
to structure_data.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/Molecules.py to
Molecules.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/water_models.py to
water_models.cpython-35.pyc
byte-compiling
build/bdist.linux-x86_64/egg/lammps_interface/lammps_potentials.py to
lammps_potentials.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/BTW.py to
BTW.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/dreiding.py to
dreiding.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/CIFIO.py to
CIFIO.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/__init__.py to
__init__.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/generic_raspa.py
to generic_raspa.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/atomic.py to
atomic.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/ccdc.py to
ccdc.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/uff_nonbonded.py
to uff_nonbonded.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/MOFFF.py to
MOFFF.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/uff.py to
uff.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/InputHandler.py to
InputHandler.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/uff4mof.py to
uff4mof.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/lammps_interface/ForceFields.py to
ForceFields.cpython-35.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-3.5
copying and adjusting lammps-interface -> build/scripts-3.5
changing mode of build/scripts-3.5/lammps-interface from 644 to 755
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.5/lammps-interface ->
build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/lammps-interface
to 755
copying lammps_interface.egg-info/PKG-INFO ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying lammps_interface.egg-info/SOURCES.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying lammps_interface.egg-info/dependency_links.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying lammps_interface.egg-info/requires.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying lammps_interface.egg-info/top_level.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
lammps_interface.__pycache__.InputHandler.cpython-35: module references __file__
creating dist
creating 'dist/lammps_interface-0.1.1-py3.5.egg' and adding
'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing lammps_interface-0.1.1-py3.5.egg
removing
'/usr/local/lib/python3.5/dist-packages/lammps_interface-0.1.1-py3.5.egg' (and
everything under it)
creating /usr/local/lib/python3.5/dist-packages/lammps_interface-0.1.1-py3.5.egg
Extracting lammps_interface-0.1.1-py3.5.egg to
/usr/local/lib/python3.5/dist-packages
lammps-interface 0.1.1 is already the active version in easy-install.pth
Installing lammps-interface script to /usr/local/bin
Installed
/usr/local/lib/python3.5/dist-packages/lammps_interface-0.1.1-py3.5.egg
Processing dependencies for lammps-interface==0.1.1
Searching for matplotlib==3.0.3
Best match: matplotlib 3.0.3
Processing matplotlib-3.0.3-py3.5-linux-x86_64.egg
matplotlib 3.0.3 is already the active version in easy-install.pth
Using
/usr/local/lib/python3.5/dist-packages/matplotlib-3.0.3-py3.5-linux-x86_64.egg
Searching for networkx==2.4
Best match: networkx 2.4
Processing networkx-2.4-py3.5.egg
networkx 2.4 is already the active version in easy-install.pth
Using /usr/local/lib/python3.5/dist-packages/networkx-2.4-py3.5.egg
Searching for scipy==1.3.3
Best match: scipy 1.3.3
Adding scipy 1.3.3 to easy-install.pth file
Using /home/alberto/.local/lib/python3.5/site-packages
Searching for numpy==1.17.4
Best match: numpy 1.17.4
Processing numpy-1.17.4-py3.5-linux-x86_64.egg
numpy 1.17.4 is already the active version in easy-install.pth
Installing f2py3 script to /usr/local/bin
Installing f2py3.5 script to /usr/local/bin
Installing f2py script to /usr/local/bin
Using /usr/local/lib/python3.5/dist-packages/numpy-1.17.4-py3.5-linux-x86_64.egg
Searching for python-dateutil==2.4.2
Best match: python-dateutil 2.4.2
python-dateutil 2.4.2 is already the active version in easy-install.pth
Using /usr/lib/python3/dist-packages
Searching for pyparsing==2.0.3
Best match: pyparsing 2.0.3
pyparsing 2.0.3 is already the active version in easy-install.pth
Using /usr/lib/python3/dist-packages
Searching for kiwisolver==1.1.0
Best match: kiwisolver 1.1.0
Processing kiwisolver-1.1.0-py3.5-linux-x86_64.egg
kiwisolver 1.1.0 is already the active version in easy-install.pth
Using
/usr/local/lib/python3.5/dist-packages/kiwisolver-1.1.0-py3.5-linux-x86_64.egg
Searching for cycler==0.10.0
Best match: cycler 0.10.0
Processing cycler-0.10.0-py3.5.egg
Removing cycler 0.9.0 from easy-install.pth file
cycler 0.10.0 is already the active version in easy-install.pth
Using /usr/local/lib/python3.5/dist-packages/cycler-0.10.0-py3.5.egg
Searching for decorator==4.4.1
Best match: decorator 4.4.1
Processing decorator-4.4.1-py3.5.egg
decorator 4.4.1 is already the active version in easy-install.pth
Using /usr/local/lib/python3.5/dist-packages/decorator-4.4.1-py3.5.egg
Searching for setuptools==20.7.0
Best match: setuptools 20.7.0
Adding setuptools 20.7.0 to easy-install.pth file
Installing easy_install script to /usr/local/bin
Using /usr/lib/python3/dist-packages
Searching for six==1.10.0
Best match: six 1.10.0
six 1.10.0 is already the active version in easy-install.pth
Using /usr/lib/python3/dist-packages
Finished processing dependencies for lammps-interface==0.1.1
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