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        "author": "K. Y. S. Chang",
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        "description": "Python modules for quantum chemistry applications\n=====================================================\nqctoolkit is quantum chemistry tool kit. \nIt meant to provide universal interface to ab initio code\nto test ideas or to produce data reliably. \nThe code includes Abinit, QuantumESPRESSO, Gaussian, NwChem,\nCPMD, BigDFT, ... etc.\nIt also provide some basic molecule operations, including \nrotation, stretching, alignment, bond identification, ... etc,\nand data formatting, including\nxyz files, Gaussian CUBE files, V\\_SIM ascii files, pdb files, ... etc.\n\nIt seems worthwile to put effort to rewrite my bash/perl/python/C \ntools in to an integrated module or package. It should boosts the\nreusability, productivity, and reproducibility of my results \ngenerated during my PhD in Basel.\nMore importantly, every results should be easily reproduced, \nexamined, and especially furthre developed. This package starts as \ncollections of modules of format I/O, analysis, plots.\nHopefully, these modules can one day become a package for general \npurpose chemistry tool kit. \n\n**Installation on Ubuntu 32/64 systems**:\n* __To install__: ```cd /path/to/qctoolkit && python setup.py install --user``` or install by pip using ```pip install qctoolkit --user```. \n* __Install on Amazon Ec2__: It is tested and working on amazon Ec2 ubuntu instances. For a fresh install, all dependencies must be installed\n```\nsudo apt-get update && sudo apt-get install -y gcc g++ gfortran liblapack-dev liblapack-doc-man liblapack-doc liblapack-pic liblapack3 liblapack-test liblapacke liblapacke-dev libgsl0-dev libatlas-base-dev build-essential libffi6 libffi-dev libssl-dev libyaml-dev libpython2.7-dev python-pip python-dev freetype* python-matplotlib cython\n```\nNote that matplotlib and cython are installed through ubuntu repository for convenience. It might be necessary to create temperary swap if the memory run out:\n```\nsudo /bin/dd if=/dev/zero of=/var/swap.1 bs=1M count=1024\nsudo /sbin/mkswap /var/swap.1\nsudo /sbin/swapon /var/swap.1\n```\nThen do pip install ```pip install qctoolkit --user```\nIf temerary swap is added, remove after installation:\n```\nsudo swapoff /var/swap.1\nsudo rm /var/swap.1\n```\n* __To remove__:  Manually remove all created files. List of files can \nbe obtained by the --record flag during install\n```python setup.py install --user --record fileList.txt```\n* **Note** that the ```setup.py``` script depends on python setuptools\n  package. This can be installed by\n```wget https://bootstrap.pypa.io/ez_setup.py --no-check-certificate -O - | python - --user```\n  with superuser priviledge\n* The package depends on [NumPy > 1.11.0](http://www.numpy.org/),\n  [SciPy > 0.16.0](https://www.scipy.org/),\n  [pandas > 0.17.1](http://pandas.pydata.org/), \n  and [matplotlib > 1.5.1](http://matplotlib.org/). \n* **Note** that newer version for many python modules are required. They must __NOT__ \nbe installed via ubuntu repository. When a module is installed \nthrough ubuntu repository as python-modeul (e.g. python-numpy), \nimport path of such module **WILL GET** highest priority. \nIn other words, stable but out-dated versions will always get loaded. \nTo circumvent this, \nthe best solution is to use virtual enviroment and setup dependancy. \nHowever, it is also possible to modify the system behaviour \nby edditing the easy_install path ```/usr/local/lib/python2.7/dist-packages/easy-install.pth```\nSimply comment out the second line ```/usr/lib/python2.7/dist-packages``` \nsupresses the system to insert this path before PYTHONPATH.\nHowever, for some systems this fix is still not working. \nIn that case, one has to modify the python default behaviour of constructing ```sys.path```\nvariable. It can be done via modifying ```/usr/lib/python2.7/site.py```\nand add the following two lines to the end of the file:\n```\n    sys.path.remove('/usr/lib/python2.7/dist-packages')\n    sys.path.append('/usr/lib/python2.7/dist-packages')\n```\n\n* **Note** that all code are writen with **2-space indentation**. \n  To change it according to pep8 standard, use the following command:\n```cd /path/to/qctoolkit && find . -name \"*.py\"|xargs -n 1 autopep8 --in-place```\n  where ```autopep8``` can be installed simply via ```pip install autopep8 --user```\n\n**Dependent Python packages**:\n* numpy 1.11.0\n* scipy 0.16.0\n* pandas 0.17.1\n* matplotlib 1.5.1\n* matplotlib.pyplot\n* PyYAML 3.11\n* cython\n* psutil\n* networkx\n* periodictable\n* mdtraj\n* paramiko (newest version might be problematic, 1.17 works fine)\n* And standard libraries: sys, re, os, glob, math, subprocess, multiprocessing, copy, collections, compiler.ast, shutil, fileinput, operator, inspect, xml.etree.ElementTree\n* pymol is also used for visualization\n* pyscf and horton is optional\n\n**Implemented interfaces to QM codes**:\n* Gaussian basis:\n  - [Gaussian](www.gaussian.com/)\n  - [NWChem](www.nwchem-sw.org/index.php/Main_Page)\n  - [horton](theochem.github.io/horton/)\n  - [pyscf](http://sunqm.github.io/pyscf/)\n* Plane wave basis:\n  - [VASP](www.vasp.at)\n  - [QuantumESPRESSO](www.quantum-espresso.org/)\n  - [CPMD](www.cpmd.org/)\n  - [Abinit](http://www.abinit.org/)\n* Wavelet basis:\n  - [BigDFT](bigdft.org/Wiki/index.php?title=BigDFT_website)\n\n**Required libraries**:\n* OpenMP\n* openmpi\n* gsl\n(GNU Scientific Library)\n* LAPACK\n* libxc-3.0.0\n\n*20150702 KYSC*\n",
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