Moltools documentation¶

moltools is a package of scripts and modules I use daily in my research as a Ph.D. student to ease setting up and analyzing calculations.

Contents:

Requirements¶

For bug-free performance, and full compatability, the latest source of the core dependencies are recommended.

The only hard-requirement is that python is the 2.7 version.

numpy 1.9.1
scipy 0.15.1
matplotlib 1.4.3
python-nose 1.3.4

Optional dependencies include:

mpl_toolkits
h5py 2.5.0
mayavi2 http://mayavi.sourceforge.net/
DALTON any stable version for Alpha properties. http://www.daltonprogram.org/www/download.html
DALTON (Development version, master branch commit 51601c2 and forward is fine) for Beta properties.

Installation¶

Right now only installation on Linux is supported.

There is currently no plans to port this package to other systems.

Linux¶

Clone the repository git@github.com:fishstamp82/dalton_tools.git
set the PYTHONPATH environment variable to the target dalton_tools/src path.

Modules¶

molecules.py¶

Atom¶

Molecule¶

Water¶

Rotator¶

Property¶

Cluster¶

use_generator.py¶

use_calculator.py¶

template.py¶

class template.Template[source]¶

This class holds data obtained by the LoProp transformation. Each template depends on 5 variables.

Variable	Choices	Type
Model:	TIP3P / OLAV	string
Method:	HF	string
Basis:	PVDZ/ANOPVDZ/ANOPVTZ	string
LoProp:	True/False	bool
Frequency:	Field \(\omega\)	string

>>> temp = Template().get()
>>> print temp ("O1", "charge") 
0.0

>>> temp = Template().get( model = "TIP3P", method = "HF",
        basis = "ANOPVDZ", dist = True, freq = "0.0"  )
>>> print temp ("O1", "charge") 
-0.678

read_dal.py¶

Testing¶

The code uses continous testing with Travis CI.

Unit-tests can be launched by the user by running

$ nosetests

Bugs¶

Bugs can appear in any shape, form or code.

If you find some bugs and want to fix them, it would be greatly appreciated!

Create a pull-request for the github repository.