qctoolkit 0.0.8

quantum chemistry tool kit

Python modules for quantum chemistry applications
=====================================================
It seems worthwile to put effort to rewrite my bash/perl/python/C
tools in to an integrated module or package. It should boosts the
reusability, productivity, and reproducibility of my results
generated during my PhD in Basel.
More importantly, every results should be easily reproduced,
examined, and especially furthre developed. This package starts as
collections of modules of format I/O, analysis, plots.
Hopefully, these modules can one day become a package for general
purpose chemistry tool kit.

**Installation on Ubuntu 32/64 systems**:
* __To install__: ```cd /path/to/qctoolkit && python setup.py install --user```
* __To remove__: Manually remove all created files. List of files can
be obtained by the --record flag during install
```python setup.py install --user --record fileList.txt```
* **Note** that the ```setup.py``` script depends on python setuptools
package. This can be installed by
```wget https://bootstrap.pypa.io/ez_setup.py --no-check-certificate -O - | python - --user```
with superuser priviledge
* The package depends on [NumPy > 1.11.0](http://www.numpy.org/),
[SciPy > 0.16.0](https://www.scipy.org/),
[pandas > 0.17.1](http://pandas.pydata.org/),
and [matplotlib > 1.5.1](http://matplotlib.org/).
* **Note** that newer version for many python modules are required. They must __NOT__
be installed via ubuntu repository. When a module is installed
through ubuntu repository as python-modeul (e.g. python-numpy),
import path of such module **WILL GET** highest priority.
In other words, stable but out-dated versions will always get loaded.
To circumvent this,
the best solution is to use virtual enviroment and setup dependancy.
However, it is also possible to modify the system behaviour
by edditing the easy_install path ```/usr/local/lib/python2.7/dist-packages/easy-install.pth```
Simply comment out the second line ```/usr/lib/python2.7/dist-packages```
supresses the system to insert this path before PYTHONPATH.
* **Note** that all code are writen with **2-space indentation**.
To change it according to pep8 standard, use the following command:
```cd /path/to/qctoolkit && find . -name "*.py"|xargs -n 1 autopep8 --in-place```
where ```autopep8``` can be installed simply via ```pip install autopep8 --user```

**Dependent Python packages**:
* numpy 1.11.0
* scipy 0.16.0
* pandas 0.17.1
* matplotlib 1.5.1
* matplotlib.pyplot
* PyYAML 3.11
* cython
* psutil
* networkx
* periodictable
* mdtraj
* paramiko (newest version might be problematic, 1.17 works fine)
* And standard libraries: sys, re, os, glob, math, subprocess, multiprocessing, copy, collections, compiler.ast, shutil, fileinput, operator, inspect, xml.etree.ElementTree
* pymol is also used for visualization

**Implemented interfaces to QM codes**:
* Gaussian basis:
- [Gaussian](www.gaussian.com/)
- [NWChem](www.nwchem-sw.org/index.php/Main_Page)
- [horton](theochem.github.io/horton/)
* Plane wave basis:
- [VASP](www.vasp.at)
- [QuantumESPRESSO](www.quantum-espresso.org/)
- [CPMD](www.cpmd.org/)
* Wavelet basis:
- [BigDFT](bigdft.org/Wiki/index.php?title=BigDFT_website)

**Required libraries**:
* OpenMP
* openmpi
* gsl
(GNU Scientific Library)
* LAPACK

*20150702 KYSC*