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Material for the Introduction to kmos hands-on session

Python 100.00%

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mieand cristinagrosutum mseibt zqhuang2014 meelod

intro2kmos's Issues

error with kmos view command

Expected behavior

run thekMC model about CO adsorption and desorption according to the tutorials: A first kMC Model- the API way (http://kmos.readthedocs.io/en/latest/tutorials/index.html)

Actual behavior

I installed the kmos and the dependencies on ubuntu 16.04, and learn the tutorials "A first kMC Model-the API way"

while, after I export the xml, and try to view the model, it rised an TypeError, the error info is shown as followed:

abel@Abel:~/CL-SMR-KMC/kmos-learn/myfirst_kmc_local_smart$ kmos view
Traceback (most recent call last):
  File "/usr/local/bin/kmos", line 21, in <module>
    main()
  File "/home/abel/.local/lib/python2.7/site-packages/kmos/cli.py", line 426, in main
    view.main(steps_per_frame=options.steps_per_frame)
  File "/home/abel/.local/lib/python2.7/site-packages/kmos/view.py", line 452, in main
    viewer = KMC_Viewer(model, steps_per_frame=steps_per_frame)
  File "/home/abel/.local/lib/python2.7/site-packages/kmos/view.py", line 398, in __init__
    self.vbox, self.window)
  File "/home/abel/.local/lib/python2.7/site-packages/kmos/view.py", line 174, in __init__
    View.__init__(self, self.vbox, rotations)
TypeError: __init__() takes exactly 2 arguments (3 given)

It seems to be related to the ase.view, but I don't know how to deal with it.
How could I fix this problem? Did I do something wrong in installation?
Looking forward to your solution and suggestion.

//: # (Besides the text description, include any screenshot(s) that help us visualize the issue you're facing)

abel@Abel:~/CL-SMR-KMC/kmos-learn/myfirst_kmc_local_smart$ kmos view
Traceback (most recent call last):
  File "/usr/local/bin/kmos", line 21, in <module>
    main()
  File "/home/abel/.local/lib/python2.7/site-packages/kmos/cli.py", line 426, in main
    view.main(steps_per_frame=options.steps_per_frame)
  File "/home/abel/.local/lib/python2.7/site-packages/kmos/view.py", line 452, in main
    viewer = KMC_Viewer(model, steps_per_frame=steps_per_frame)
  File "/home/abel/.local/lib/python2.7/site-packages/kmos/view.py", line 398, in __init__
    self.vbox, self.window)
  File "/home/abel/.local/lib/python2.7/site-packages/kmos/view.py", line 174, in __init__
    View.__init__(self, self.vbox, rotations)
TypeError: __init__() takes exactly 2 arguments (3 given)

Steps to reproduce the issue

System information

result of kmos version, operating system, version, python version, possibly link to model file

gfortran version (4:5.3.1-1ubuntu1).
python-dev iversion (2.7.11-1).
python-glade2 version (2.24.0-4ubuntu1).
python-lxml version (3.5.0-1build1).
python-numpy version (1:1.11.0-1ubuntu1).
python-kiwi version (1.9.22-4).
python-matplotlib version (1.5.1-1ubuntu1).
python-pygoocanvas version (0.14.1-1.1ubuntu1).
gazpacho version (0.7.2-3).

abel@Abel:~/CL-SMR-KMC/kmos-learn/myfirst_kmc_local_smart$ ase info
platform        Linux-4.4.0-21-generic-x86_64-with-Ubuntu-16.04-xenial
python-2.7.12   /usr/bin/python
ase-3.15.0b1    /usr/local/lib/python2.7/dist-packages/ase-3.15.0b1-py2.7.egg/ase/
numpy-1.11.0    /usr/lib/python2.7/dist-packages/numpy/
scipy-0.17.0    /usr/lib/python2.7/dist-packages/scipy/

LGD running error

Dear sir,
I tried to run the exapmle "render_LGD.py", while there is a error in shell as followed:

kmos view
14:13:04 environ              No zh_CN translation found for domain kiwi
/usr/lib/python2.7/dist-packages/matplotlib/axes/_axes.py:519: UserWarning: No labelled objects found. Use label='...' kwarg on individual plots.
  warnings.warn("No labelled objects found. "
 +------------------------------------------------------------+
 |                                                            |
 | This kMC Model 'ion_diffusion_model' was written by        |
 |                                                            |
 |           Juan M. Lorenzi ([email protected])            |
 |                                                            |
 | and implemented with the help of kmos,                     |
 | which is distributed under GNU/GPL Version 3               |
 | (C) Max J. Hoffmann [email protected]                   |
 |                                                            |
 | kmos is distributed in the hope that it will be useful     |
 | but WIHTOUT ANY WARRANTY; without even the implied         |
 | waranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR     |
 | PURPOSE. See the GNU General Public License for more       |
 | details.                                                   |
 |                                                            |
 | If using kmos for a publication, attribution is            |
 | greatly appreciated.                                       |
 | Hoffmann, M. J., Matera, S., & Reuter, K. (2014).          |
 | kmos: A lattice kinetic Monte Carlo framework.             |
 | Computer Physics Communications, 185(7), 2138-2150.        |
 |                                                            |
 | Development http://mhoffman.github.org/kmos                |
 | Documentation http://kmos.readthedocs.org                  |
 | Reference http://dx.doi.org/10.1016/j.cpc.2014.04.003      |
 |                                                            |
 +------------------------------------------------------------+
 


 
 
 ERROR: interval_search_real can't find available process
 This usually means one of the following:
  - you forgot to define rate constants
  - you create a dead-lock: e.g. adsorption without corresponding desorption.
  - you started the model in an initial state without transitions

The GUI window also didn't show atoms, Did I set something wrong?

On the other hand, I tried to replace the ASE with older version as you told me, now it works!
Thank you for you help!

Errors in SOS_adsdes (task 10)

I got the following error message when the Solid-on-Solid crystal growth model (Task 10) was tested.

ERROR: interval_search_real can't find available process
This usually means one of the following:

you forgot to define rate constants
you create a dead-lock: e.g. adsorption without corresponding desorption.
you started the model in an initial state without transitions

I try to simplify this 3D case into a 2D case then everything goes well.

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