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90 lines
3.1 KiB
Text
90 lines
3.1 KiB
Text
A collection of miscellaneous Python scripts and test cases
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that have been partially tested.
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IMPORTANT:
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Make sure that the directory containing Xrtdb.py is in your PYTHONPATH
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Xrtdb.py - A Tkinter based graphical RTDB editor
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Requires Tkinter support be built into the Python that NWChem
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is linked against. On some machines this also requires linking
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against _tkinter.so which is in the python lib-dynload.
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testxrtb.nw
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Example use of Xrtdb
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nwgeom.py - look in the file for (a little) more documentation
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Defines the procedures
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- coords = geom_get_coords(name)
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- geom_set_coords(name,coords)
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Get/set cartesian coordinates for named geometry
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- bond_length(i,j)
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Compute bond length between atoms i & j for
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default geometry
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- (xmin, fmin) = minimize1d(f, xlo, xhi, xtol, maxeval)
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Fairly robust minimization in 1d ... useful for crude
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localization of saddle points (look in util.py for
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better optimizers, notably quasinr()).
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- results = scan_input(input,start,end,nstep,theory,task)
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Scan parameters from start to end, substituting into
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the NWChem input string and calling the specified
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task(theory), returning results from each step in results.
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util.py - lots of useful python routines for manipulating vectors,
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matrices, and minimizing functions. Look in the file for more
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documentation, and at the end of the file for example usage.
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basopt.nw - example of optimizing the exponents in a primitive basis
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set using the quasi-Newton optimizer quasinr() in util.py
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basopt2.nw - another example of optimizing basis set exponents.
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Uncontracts an STO-3G basis for water and optimizes the exponents.
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(this one will take a few minutes to complete)
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basopt3.nw - yet another example. This time using MP2 for HF to
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optimize the uncontracted sp on H and spd on F in the
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cc-pVDZ basis.
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basopt4.nw - and another example. This optimizes a sequence of
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even tempered primitive basis sets for Be with between 2 and
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twenty s functions and then prints out the summary to demonstrate
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exponential convergence to the Hartree-Fock basis set limit.
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ts_search.nw
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Example use of minimize1d from nwgeom.py
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scanexp.nw
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Example use of scan_input from nwgeom.py
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hcn.nw
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Scans the HCN -> CNH reaction path displaying bond lengths
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and the energy as function of angle using Gnuplot. You
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need Python and the GNUplot and Numeric extensions
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(www.python.org)
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nh3.nw
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Scans the NH3 inversion path displaying bond lengths
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and the energy as function of angle using Gnuplot. You
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need Python and the GNUplot and Numeric extensions
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(www.python.org)
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isdoesmic.nw
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Uses python to compute a reaction energy as a function
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of basis set.
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pes_scan.py
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Python script for use in
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NWchem that is the multidimensional analog of your zcoord scanning
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script. This script can scan a grid of variables in several
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dimensions, covering a parameter "volume", rather than the linear
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track between points done by zcoord.
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Additional documentation and usage notes is in the comments of the
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script itself (from Lev Gelb, gelb@mitre.wustl.edu)
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