Unable to create custom multispheres

[fcgrogan]

I'm trying to create custom non-spherical particles using multispheres. When I run compaction.py (replacing the original species parameters with the line below)

'species': ({'material': organic, 'style': 'multisphere', 'args': ('nspheres 2', 'ntry 1000000 spheres', '0. 0. 0. 0.0002   0. 0. 0.0002 0.0002', 'type 1')}, ),

I get the following stack trace:

Traceback (most recent call last):
  File "multisphere_from_compaction.py", line 53, in <module>
    run(**params)
  File "multisphere_from_compaction.py", line 33, in run
    sim = simulation.DEM(**params)
  File "/home/<user>/.local/lib/python3.6/site-packages/PyGran/simulation/PyGranSim/dem.py", line 192, in __init__
    self.initialize()
  File "/home/<user>/.local/lib/python3.6/site-packages/PyGran/simulation/PyGranSim/dem.py", line 270, in initialize
    self.dem.initialize()
  File "/home/<user>/.local/lib/python3.6/site-packages/PyGran/simulation/PyGranSim/engine_liggghts.py", line 974, in initialize
    self.setupParticles()
  File "/home/<user>/.local/lib/python3.6/site-packages/PyGran/simulation/PyGranSim/engine_liggghts.py", line 530, in setupParticles
    if radius[0] == 'constant':
UnboundLocalError: local variable 'radius' referenced before assignment

On another note, I noticed you put up a new multisphere.py example, but it seems like template_multisphere() is not quite fully functional yet?

Traceback (most recent call last):
  File "multisphere.py", line 68, in <module>
    run(**params)
  File "multisphere.py", line 47, in run
    sim = simulation.DEM(**params)
  File "/home/<user>/.local/lib/python3.6/site-packages/PyGran/simulation/PyGranSim/dem.py", line 70, in __init__
    pargs = pargs['model'](**pargs).params
  File "/home/<user>/.local/lib/python3.6/site-packages/PyGran/simulation/PyGranSim/models.py", line 558, in __init__
    super(SpringDashpot, self).__init__(**params)
  File "/home/<user>/.local/lib/python3.6/site-packages/PyGran/simulation/PyGranSim/models.py", line 242, in __init__
    ss['args'] = template_tablet(ss['nspheres'], ss['radius'], ss['length'])
KeyError: 'nspheres'

I was wondering if this more general template was going to be added to PyGranSim/models.py in the near future.

[anabiman]

Your code should work just fine. Can you please specify which version of PyGran you're using? The recently added "multisphere.py" example also works without any problems in v1.2.2 and above.

[fcgrogan]

I'm using v1.2.1 on Ubuntu 18.04.

I just noticed in "CHANGELOG.md" it says "New interface for user-defined functions used in multisphere particles" under v1.2.2. I updated PyGran according to the instructions you provided on another issue (or at least thought I did) as the final step pip3 install . --upgrade gave me the following

Processing /home/<user>/PyGran
Collecting numpy (from PyGran==1.2.2)
  Using cached https://files.pythonhosted.org/packages/62/20/4d43e141b5bc426ba38274933ef8e76e85c7adea2c321ecf9ebf7421cedf/numpy-1.18.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting scipy (from PyGran==1.2.2)
  Using cached https://files.pythonhosted.org/packages/dc/29/162476fd44203116e7980cfbd9352eef9db37c49445d1fec35509022f6aa/scipy-1.4.1-cp36-cp36m-manylinux1_x86_64.whl
Installing collected packages: numpy, scipy, PyGran
  Running setup.py install for PyGran ... done
Successfully installed PyGran-1.2.2 numpy-1.18.1 scipy-1.4.1

However, "multisphere.py" still failed in the same way, and when I checked

import PyGran._version
PyGran._version.__version__

it still said I had v1.2.1. I'm assuming this means I messed up the upgrade and am still only on v1.2.1. However, I'm still unable to get "multisphere.py" to work on v1.2.1 (stack trace the same as the above post).

[anabiman]

I see where the problem is right now. v1.2.2 is still experimental, i.e. I have not yet packaged it via pypi. It's only available from github for now. Plz try to remove pygran completely via: "pip uninstall pygran". Then clone the pygran repo and run from the source dir: "pip install . --user".

[anabiman]

pip uninstall pygran
git clone https://github.com/Andrew-AbiMansour/PyGran
cd PyGran
git submodule init
git submodule update
pip install . --user

[fcgrogan]

Thank you for your help! I upgraded to v1.2.2 and was able to run 'multisphere.py' (it did give me "WARNING: Energy calculated for multisphere particles is currently not correct (../fix_multisphere.cpp:1312)", but this is from LIGGGHTS.log, not PyGran).

[anabiman]

Yup that's a feature still in the works in LIGGGHTS v3.8.0. If you encounter any other problems, plz feel free to report them as new issues.