#!/usr/bin/env python
# coding: utf-8

# # Test your pyiron installation
# The goal of this notebooks is to evaluate your pyiron installation - to identify which components are working and which are might need some additional configuration.

# # Your operation system
# 

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import sys
sys.platform  # ['linux', 'darwin', 'win32']


# # Test pyiron 
# Install pyiron from conda-forge: 
# ```
# conda install -c conda-forge pyiron
# ```

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get_ipython().system(' conda list pyiron')


# ## Install location
# List where conda is installed:

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import pyiron
pyiron.__file__  # location where pyiron is installed 


# ## Your .pyiron configuration 
# Check pyiron configuration, if pyiron is not configured, configure it using: 
# ```
# python
# >>> import pyiron
# >>> pyiron.install()
# ```

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from pyiron.base.settings.generic import Settings
s = Settings()
s._configuration


# ## Your pyiron working directory 
# pyiron restricts the users to execute notebooks only in the `project_paths`. We check if the current working directory is part of the `project_paths`.

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from pyiron import Project
pr = Project('.')


# # NGLview for visualizing atomistic structures
# NGLView is used for visualisation of atomistic structures. First we check if NGLview was installed using conda: 

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get_ipython().system(' conda list nglview')


# For jupyter notebooks nglview can be installed using: 
# 
# ```
# conda install -c conda-forge nglview
# jupyter nbextension install nglview --py --sys-prefix
# jupyter nbextension enable nglview --py --sys-prefix
# ```
# 
# For jupyterlab the installation is slightly different: 
# ```
# conda install -c conda-forge nodejs nglview
# jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build
# jupyter labextension install nglview-js-widgets
# ```

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import nglview
nglview.demo()  # You should see a molecule which you can rotate in 3D 


# # Simulation codes
# pyiron does not include any simulation codes, these have to be installed separatley:

# ## Lammps 
# We start with installing Lammps directly from Anaconda (the conda-forge channel provides the executables for Linux and Mac Os X): 
# ```
# conda install -c conda-forge lammps 
# ```
# For windows Lammps is available from the pyiron conda channel: 
# ```
# conda install -c pyiron lammps 
# ```

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get_ipython().system(' conda list lammps')


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from pyiron import Project
pr = Project('lammps')
pr.remove_jobs(recursive=True)
lmp = pr.create_job(pr.job_type.Lammps, 'static')
lmp.structure = pr.create_structure('Fe', 'bcc', 2.55)
lmp.potential = 'Fe_C_Hepburn_Ackland_eam'
lmp.run()  # The job static was saved and received the ID: 1


# ## Lammps interactive 
# The conda-forge channel includes the Lammps executables as well as the Lammps library, unfortunatley this is not available for windows. Therefore for Windows we recommend installing pyiron using the Linux subsystem.

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from pyiron import Project
pr = Project('lammps')
pr.remove_jobs(recursive=True)
lmp = pr.create_job(pr.job_type.Lammps, 'interactive')
lmp.structure = pr.create_structure('Fe', 'bcc', 2.55)
lmp.potential = 'Fe_C_Hepburn_Ackland_eam'
lmp.server.run_mode.interactive = True
lmp.run()  # The job interactive was saved and received the ID: 1
print(lmp.output.energy_tot)  # [-6.38884508]
lmp.run()
print(lmp.output.energy_tot) # [-6.38884508 -6.38884508]
lmp.interactive_close()  


# ## Sphinx 
# The Sphinx DFT code is developed at the MPIE and it can be installed for Linux using the conda-forge channel: 
# ```
# conda install -c conda-forge sphinxdft
# ```

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get_ipython().system(' conda list sphinxdft')


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from pyiron import Project
pr = Project('sphinx')
pr.remove_jobs(recursive=True)
lmp = pr.create_job(pr.job_type.Sphinx, 'static')
lmp.structure = pr.create_structure('Fe', 'bcc', 2.55)
lmp.run()  # The job static was saved and received the ID: 2


# ## GPAW 
# Besides Sphinx is GPAW a second opensource DFT code available for pyiron. For both Mac Os X and Linux GPAW is available from conda-forge available: 
# ```
# conda install -c conda-forge 
# ```

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get_ipython().system(' conda list gpaw')


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from pyiron import Project
pr = Project('gpaw')
pr.remove_jobs(recursive=True)
lmp = pr.create_job(pr.job_type.GpawJob, 'static')
lmp.structure = pr.create_structure('Fe', 'bcc', 2.55)
lmp.run()  # The job static was saved and received the ID: 3


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