#Welcome to moltools!
Code purpose: Wrap DALTON LoProp calculation into convinient functions
callable by the Molecule instance using IPython or python scripts.
Features include obtaining LoProp properties for solvent molecules/ligands
or for proteins and polymers that are covalently bonded via the MFCC procedure.
By integrating with the particles module, applequist equations are directly
solvable for a system of classical molecules using damped
charges/dipole-moments directly from QM-obtainable properties.
For localized Beta, this requires the latest development source of
DALTON installed.
git clone git@github.com:fishstamp82/moltools.git
cd moltools
virtualenv -p python2.7 venv2.7
source venv2.7/bin/activate
python setup.py install
Execute the following script if you want to run DALTON computations in parallel using HPC clusters.
For the Linköping HPC triolith, execute:
src/scripts/dalton_run_on_triolith.sh
For Umeå HPC akka, execute:
src/scripts/dalton_run_on_akka.sh
Run:
ipythonin [1]: from molecules import Water, Cluster
in [2]: w1 = Water().get_standard()
in [3]: w2 = Water.get_standard()
in [4]: w2.translate_by_r( [0, 0, 2.5] )
in [5]: c = Cluster( w1, w2 )
in [6]: c.plot()
#See template.py for all available templates
in [8]: c.attach_properties( model = 'tip3p', method = 'HF', basis ='ANOPVDZ' )
Output the atomic/ molecular/ cluster propertiy via the .Property keyword, or via the quick-wrapper .p (.d for dipole, .a alpha .etc )
in [9]: print c.p.a
[ 15.02184 0. 0. 11.48016 0. 13.72182]
Calculate each waters properties from ab-initio using DALTON, and put those properties on each atom using LoProp in one step:
In [10]: c.props_from_qm( tmpdir = '/tmp', dalpath = $PATH_TO_DALTON_SCRIPT )
If the dalton version is the development master branch, localized hyperpolarizabilities are obtainable:
In [11]: c.props_from_qm( method = 'b3lypqua', tmpdir = '/tmp', dalpath = $PATH_TO_DALTON_SCRIPT )
These include uncommenting "#from mayavi import mlab" in
src/pdbreader.py and an installation of mayavi2.
This enables plotting of the beta tensor around molecules and clusters.
######Visit the documentation for the API and more tutorials on the source code. Work in progress and most stuff are outdated.