Fixed lennardjones error that arises when installing with pip

README

@@ -0,0 +1,278 @@
+[![Build Status](https://travis-ci.org/MaterialsDiscovery/PyChemia.svg?branch=master)](https://travis-ci.org/MaterialsDiscovery/PyChemia)
+[![PyPI version](https://badge.fury.io/py/pychemia.svg)](https://badge.fury.io/py/pychemia)
+[![Coverage Status](https://coveralls.io/repos/github/MaterialsDiscovery/PyChemia/badge.svg?branch=master)](https://coveralls.io/github/MaterialsDiscovery/PyChemia?branch=master)
+[![Documentation Status](https://readthedocs.org/projects/pychemia/badge/?version=latest)](http://pychemia.readthedocs.io/en/latest/?badge=latest)
+[![HitCount](http://hits.dwyl.io/MaterialsDiscovery/PyChemia.svg)](http://hits.dwyl.io/MaterialsDiscovery/PyChemia)
+
+PyChemia, Python Framework for Materials Discovery and Design
+=============================================================
+
+![PyChemia](https://raw.githubusercontent.com/MaterialsDiscovery/PyChemia/master/docs/_static/PyChemia_Small.png)
+
+PyChemia is an open-source Python Library for materials structural
+search. The purpose of the initiative is to create a method agnostic
+framework for materials discovery and design using a variety of methods
+from Minima Hoping to Soft-computing based methods. PyChemia is also a
+library for data-mining, using several methods to discover interesting
+candidates among the materials already processed.
+
+The core of the library is the Structure python class, it is able to
+describe periodic and non-periodic structures. As the focus of this
+library is structural search the class defines extensive capabilities to
+modify atomic structures.
+
+The library includes capability to read and write in several ab-initio
+codes. At the level of DFT, PyChemia support VASP, ABINIT and Octopus.
+At Tight-binding level development is in process to support DFTB+ and
+Fireball. This allows the library to compute electronic-structure
+properties using state-of-the-art ab-initio software packages and
+extract properties from those calculations.
+
+Installation
+============
+
+You can install pychemia in several ways. We are showing 3 ways of
+installing PyChemia inside a Virtual environment. A virtual environment
+is a good way of isolating software packages from the pacakges installed
+with the Operating System. The decision on which method to use
+depends if you want to use the most recent code or the package uploaded
+from time to time to PyPi. The last method is particularly suited for
+developers who want to change the code and get those changes operative without
+an explicit instalation.
+
+
+Installing with pip from pypi.org on a virtual environment 
+----------------------------------------------------------
+
+This method installs PyChemia from the packages uploaded
+to PyPi every month. It will provides a version of 
+PyChemia that is stable.
+
+First, create and activate the virtual environment.
+We are using the name `pychemia_ve`, but that is arbitrary.
+
+```bash
+virtualenv pychemia_ve
+source pychemia_ve/bin/activate
+```
+
+When the virtual environment is activated, your prompt 
+changes to `(pychemia_ve)...$`. Now, install pychemia 
+with pip
+
+```bash
+pip install pychemia
+```
+
+Installing with pip from a cloned repo on a virtual environment
+---------------------------------------------------------------
+
+This method installs PyChemia from the Github repo.
+The method will install PyChemia from the most recent sources.
+
+First, create and activate the virtual environment.
+We are using the name `pychemia_ve`, but that is arbitrary.
+
+```bash
+virtualenv pychemia_ve
+source pychemia_ve/bin/activate
+```
+
+Second, clone the repository from GitHub
+
+```bash
+git clone https://github.com/MaterialsDiscovery/PyChemia.git
+```
+
+Finally, install from the repo folder
+
+```bash
+pip install PyChemia
+```
+
+Using PyChemia from repo folder on a virtual environment
+--------------------------------------------------------
+
+This method is mostly used for development. 
+In this way PyChemia is not actually installed and changes to the code
+will take inmediate effect.
+
+First, create and activate the virtual environment.
+We are using the name `pychemia_ve`, but that is arbitrary.
+
+```bash
+virtualenv pychemia_ve
+source pychemia_ve/bin/activate
+```
+
+Clone the repository
+
+```bash
+git clone https://github.com/MaterialsDiscovery/PyChemia.git
+```
+
+Go to repo folder, install Cython with pip and 
+execute `setup.py` to build the Cython modules.  
+
+```bash
+cd PyChemia
+pip install Cython
+python3 setup.py build_ext --inplace
+python3 setup.py build
+```
+
+Finally, install the packages required for PyChemia to work
+
+```bash
+pip install -r requirements.txt
+```
+
+Set the variable $PYTHONPATH to point to PyChemia folder, in the case of bash it will be:
+
+```bash
+export PYTHONPATH=`path`
+```
+
+On C shell (csh or tcsh)
+
+```csh
+setenv PYTHONPATH `path`
+```
+
+PyChemia requirements
+=====================
+
+PyChemia relies on a number of other python packages to 
+operate. Some of them are mandatory and they must be installed.
+Other packages are optional and their absence will only constrain
+certain capabilities. 
+
+Mandatory
+---------
+
+1.  Python >= 3.6
+    The library is tested on Travis for Python 3.6 and 3.7
+    Support for Python 2.7 has been removed
+
+    https://travis-ci.org/MaterialsDiscovery/PyChemia
+
+2.  [Numpy](http://www.numpy.org/ "Numpy") >= 1.17
+    Fundamental library for numerical intensive computation in Python.
+    Numpy arrays are essential for efficient array manipulation. 
+
+3.  [SciPy](http://scipy.org/ "SciPy") >= 1.3
+    Used mostly for Linear Algebra, FFT and spatial routines.
+
+4.  [Spglib](http://spglib.sourceforge.net/) >= 1.9
+    Used to determine symmetry groups for periodic structures
+
+5.  [Matplotlib](http://matplotlib.org/  "Matplotlib") >= 3.0
+    Used to plot band structures, densities of states and other 2D plots
+
+6.  [PyMongo](http://api.mongodb.org/python/current/) >= 3.9
+    Used for structural search PyChemia relies strongly in MongoDB and its python driver. 
+    For the MongoDB server, any version beyond 3.0 should be fine. 
+    We have tested pychemia on MongoDB 3.4
+
+7.  [psutil](https://github.com/giampaolo/psutil) >= 5.6
+    Cross-platform lib for process and system monitoring in Python
+
+
+Optional
+--------
+
+1.  [nose](https://nose.readthedocs.io/en/latest/) >= 1.3.7 A python
+    library for testing, simply go to the source directory and execute
+
+    nosetests -v
+
+2.  [pytest](https://docs.pytest.org/en/latest/) 
+    Another utility for testing. 
+
+3.  [Pandas](http://pandas.pydata.org/ "Pandas")
+    Library for Data Analysis used by the datamining modules
+
+4.  [PyMC](http://pymc-devs.github.io/pymc/index.html)
+    PyMC is a python module that implements Bayesian statistical models 
+    and fitting algorithms
+    Important for the datamining capabilities of PyChemia
+
+5.  [Mayavi](http://docs.enthought.com/mayavi/mayavi/ "Mayavi") >= 4.1
+    Some basic visualization tools are incorporated using this library
+
+6.  [ScientificPython](http://dirac.cnrs-orleans.fr/plone/software/scientificpython/overview/ "Scientific Python") >2.6
+    This library is used for reading and writing NetCDF files
+
+7.  [pymatgen](http://www.pymatgen.org "pymatgen") >= 2.9
+    pymatgen is an excellent library for materials analysis
+
+8.  [ASE](https://wiki.fysik.dtu.dk/ase/ "Atomic Simulation Environment")
+    Atomic Simulation Environment is another good library for ab-initio calculations.
+    Quite impressive for the number of ab-initio packages supported
+
+9.  [qmpy](http://oqmd.org/static/docs/index.html "qmpy")
+    The Python library behind the [Open Quantum Materials Database](http://oqmd.org).
+    The OQMD is a database of DFT calculated structures.
+    For the time being the database contains more than 300000 structures, with more than
+    90% of them with the electronic ground-state computed.
+
+10. [coverage](https://bitbucket.org/ned/coveragepy) >= 4.0.1
+    Provides code coverage analysis
+
+11. [python-coveralls](https://github.com/z4r/python-coveralls)
+    To submit coverage information to coveralls.io
+
+    https://coveralls.io/github/MaterialsDiscovery/PyChemia
+
+Documentation
+=============
+
+Instructions for installation, using and programming scripts with PyChemia
+can be found on two repositories for documentation:
+
+* Read The Docs:
+
+   http://pychemia.readthedocs.io/en/latest
+
+* Python Hosted:
+
+   http://pythonhosted.org/pychemia
+
+Documentation is hosted on [Read the Docs](https://readthedocs.org/projects/pychemia/) also available with Short URLs [readthedocs](http://pychemia.readthedocs.io) and [rtfd](http://pychemia.rtfd.io)
+
+Documentation is also hosted on [Python Hosted](http://pythonhosted.org/pychemia/index.html)
+
+Sources
+=======
+
+The main repository is on [GitHub](https://github.com/MaterialsDiscovery/PyChemia)
+
+Sources and wheel binaries are also distrubuted on [PyPI](https://pypi.python.org/pypi/pychemia) or [PyPI](https://pypi.org/project/pychemia/)
+
+Structure of the Library
+========================
+
+![PyChemia](https://raw.githubusercontent.com/MaterialsDiscovery/PyChemia/master/docs/_static/PyChemia_code.png)
+
+![PyChemia](https://raw.githubusercontent.com/MaterialsDiscovery/PyChemia/master/docs/_static/PyChemia_workflow.png)
+
+Contributors
+============
+
+1.  Prof. Aldo H. Romero [West Virginia University] (Project Director)
+
+2.  Guillermo Avendaño-Franco [West Virginia University]
+    (Basic Infrastructure)
+
+3.  Adam Payne [West Virginia University] (Bug fixes (Populations,
+    Relaxators, and KPoints) )
+
+4.  Irais Valencia Jaime [West Virginia University] (Simulation
+    and testing)
+
+5.  Sobhit Singh [West Virginia University] (Data-mining)
+
+6.  Francisco Muñoz [Universidad de Chile] (PyPROCAR)
+
+7.  Wilfredo Ibarra Hernandez [West Virginia University] (Interface
+    with MAISE)

pychemia/code/lennardjones/__init__.py

@@ -2,6 +2,8 @@
 Includes class LennardJones and several methods to relax and compute forces and energies from Lennard-Jones clusters
 
 """
+import pyximport
+pyximport.install()
 
 from .lj import LennardJones, lj_compact_evaluate
 from .lj_utils import lj_energy, lj_forces, lj_gradient