Haystack: The compuational chemistry notebook
------------------------

Quantum chemistry inside an IPython notebook.

Based on the atomic simulaton environment for constructon of ab-initio calculations
JSMol for visualisaton
cclib for extracting data

Offers a local Gaussian calculator object that can send calculations to be executed remotely on a pbs-torque cluster

Install from anaconda via:

  conda install --channel https://conda.binstar.org/Clyde_Fare cc-notebook
  conda install --channel https://conda.binstar.org/Clyde_Fare gausspy
  cc_notebook_init

If you are using an old operating system (as many computational clusters do) then you may have an old version 
of libc6 in this case you will want to use the install commands below that make use of a slightly older version of numpy (1.8):

  conda install --channel https://conda.binstar.org/Clyde_Fare cc-notebook numpy=1.8
  conda install --channel https://conda.binstar.org/Clyde_Fare gausspy numpy=1.8
  cc_notebook_init

a .cc_notebook.ini file is created by the cc_notebook_init command and placed in your home directory.

Details particular to your setup need to be filled in.

The ase_home and ase_scratch directories need to be set to the directory the notebook server will be run in.
The gauss_home and gauss_scratch directories need to be set to the equivalent directory on the cluster

To run calculations remotely on a PBS server, Haystack must also be installed and initialised on the cluster.
The .cc_notebook.ini file on the cluster should have ase_home and ase_scratch set to the cluster's directories
(i.e. to the gauss_home and gauss_scratch values on the local machines .cc_notebook.ini file.