NWChem/contrib/python

A collection of miscelaneous Python scripts and test cases 
that have been partially tested.

IMPORTANT:
 Make sure that the directory containing Xrtdb.py is in your PYTHONPATH


Xrtdb.py - A Tkinter based graphical RTDB editor
     Requires Tkinter support be built into the Python that NWChem
     is linked against.  On some machines this also requires linking
     against _tkinter.so which is in the python lib-dynload.

testxrtb.nw
     Example use of Xrtdb

nwgeom.py - look in the file for (a little) more documentation
   Defines the procedures

   - coords = geom_get_coords(name)
   - geom_set_coords(name,coords)
     Get/set cartesian coordinates for named geometry

   - bond_length(i,j)
     Compute bond length between atoms i & j for
     default geometry

   - (xmin, fmin) = minimize1d(f, xlo, xhi, xtol, maxeval)
     Fairly robust minimization in 1d ... useful for crude
     localization of saddle points (look in util.py for
     better optimizers, notably quasinr()).

   - results = scan_input(input,start,end,nstep,theory,task)
     Scan parameters from start to end, substituting into 
     the NWChem input string and calling the specified
     task(theory), returning results from each step in results.

util.py - lots of useful python routines for manipulating vectors,
     matrices, and minimizing functions. Look in the file for more
     documentation, and at the end of the file for example usage.

basopt.nw - example of optimizing the exponents in a primitive basis
     set using the quasi-Newton optimizer quasinr() in util.py

basopt2.nw - another example of optimizing basis set exponents. 
     Uncontracts an STO-3G basis for water and optimizes the exponents.
     (this one will take a few minutes to complete)

basopt3.nw - yet another example. This time using MP2 for HF to 
     optimize the uncontracted sp on H and spd on F in the
     cc-pVDZ basis.

basopt4.nw - and another example.  This optimizes a sequence of
     even tempered primitive basis sets for Be with between 2 and
     twenty s functions and then prints out the summary to demonstrate
     exponential convergence to the Hartree-Fock basis set limit.

ts_search.nw
     Example use of minimize1d from nwgeom.py

scanexp.nw
     Example use of scan_input from nwgeom.py

hcn.nw
     Scans the HCN -> CNH reaction path displaying bond lengths
     and the energy as function of angle using Gnuplot.  You
     need Python and the GNUplot and Numeric extensions
     (www.python.org)

nh3.nw
     Scans the NH3 inversion path displaying bond lengths
     and the energy as function of angle using Gnuplot.  You
     need Python and the GNUplot and Numeric extensions
     (www.python.org)
     
isdoesmic.nw
     Uses python to compute a reaction energy as a function
     of basis set.


pes_scan.py
   Python script for use in
   NWchem that is the multidimensional analog of your zcoord scanning
   script. This script can scan a grid of variables in several
   dimensions, covering a parameter "volume", rather than the linear
   track between points done by zcoord.
   Additional documentation and usage notes is in the comments of the
   script itself  (from Lev Gelb, gelb@mitre.wustl.edu)