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# PyQuante - Python Quantum Chemistry [Rick Muller](mailto:firstname.lastname@example.org) v1.5.0 ## What is PyQuante? [PyQuante](http://pyquante.sourceforge.net/) ([Download Site](http://sourceforge.net/projects/pyquante) [User Guide](userguide.html)) is an open-source suite of programs for developing quantum chemistry methods. The program is written in the [Python](http://www.python.org) programming language, but has many "rate-determining" modules also written in C for speed. The resulting code is not nearly as fast as [Jaguar](http://www.schrodinger.com/Products/jaguar.html), [NWChem](http://www.emsl.pnl.gov/docs/nwchem/nwchem.html), [Gaussian](http://www.gaussian.com/), or [GAMESS](http://www.msg.ameslab.gov/GAMESS/GAMESS.html), but the resulting code is much easier to understand and modify. The goal of this software is not necessarily to provide a working quantum chemistry program (although it will hopefully do that), but rather to provide a well-engineered set of tools so that scientists can construct their own quantum chemistry programs without going through the tedium of having to write every low-level routine. More information, including links to the download page, is available at [the PyQuante Home Page](http://pyquante.sourceforge.net). Here is an example of what closed-shell Hartree-Fock scripts look like: def rhf(atoms,**opts): "General wrapper for restricted closed-shell hartree fock" ConvCriteria = opts.get('ConvCriteria',1e-5) MaxIter = opts.get('MaxIter',20) basis = opts.get('basis',None) bfs = getbasis(atoms,basis) S,h,Ints = getints(bfs,atoms) orbs = get_guess(h,S) nel = atoms.get_nel() enuke = atoms.get_enuke() nclosed,nopen = divmod(nel,2) eold = 0. for i in range(MaxIter): D = mkdens(evecs,0,nocc) G = get2JmK(Ints,D) F = h+G evals,evecs = GHeigenvectors(F,S) energy = get_energy(h,F,D,enuke) print energy if abs(energy-eold) < ConvCriteria: break eold = energy return energy Even without knowing any Python, it is easy to see what the various steps in the program are doing. ## Current features - Hartree-Fock: Restriced closed-shell HF and unrestricted open-shell HF; - DFT: LDA (SVWN, Xalpha) and GGA (BLYP, PBE) functionals; - Two electron integrals computed using Huzinaga, Rys, or Head-Gordon/Pople techniques. C and Python interfaces to all of these programs. - MINDO/3 semiempirical energies and forces - CI-Singles excited states - DIIS convergence acceleration - Second-order Moller-Plesset (MP2) perturbation theory Upcoming release road map (your suggestions are welcome: [Email Me](mailto:email@example.com)): - Spin polarized (aka unrestricted spin) DFT - Divide-and-conquer linear scaling Hamiltonians - Restricted open-shell Hartree-Fock and GVB - Forces - Hybrid functionals - CI/MCSCF - MPn/CCSD ## Programming Philosophy I always strive for simplicity over speed. Data structures change more often than functions. My aim here is to be more rigid about functional interfaces than data interfaces. Which means that I only program functions in C, not data structures themselves, which I keep in python so I can change them as the needs of the code evolve. I believe that the first mistake people make in object-oriented programming is to make a very rigid object structure that cannot evolve with the code. Currently the only C routines are the integral code and the NumPy routines. This may change out of necessity if there appear to be huge bottlenecks keeping some of this in python, but I'd rather keep as much code in python and only put routines in C if I really, really need to. ## License The software is released under the modified BSD license, which means that everyone is free to download, use, and modify the code without charge. ## Obtaining the Code The program is available in tarball form from the [PyQuante Download Page](http://sourceforge.net/projects/pyquante). The CVS archive for the program is also at Sourceforge, and is recommended for anyone wanting to stay on the bleeding edge; information on how to access the CVS archive is available [here](http://sourceforge.net/cvs/?group_id=43213). ##Building the Code Much of the code is written in python, and thus is platform independent. The rest of the code now uses the python distutils procedures for building the C modules. Type % sudo python setup.py install and the code should build and install properly. I've tested this on Linux, Windows/Cygwin, and Macintosh OS X. Getting Started --------------- There is a [User Guide](userguide.html) and other documentation in the Doc subdirectory, and tests in the Tests subdirectory. Subscription to the [mailing list](http://lists.sourceforge.net/lists/listinfo/pyquante-users) is highly recommended for further support. [Email me](mailto:firstname.lastname@example.org) if you need additional help. Contributors ------------ - Konrad Hinsen helped with the original setup.py file - Tom Manz wrote the Epstein-Nesbet pair correlation theory that is distributed in the EN2.py module - Daniel Rohr has written and debugged the EXX density functional code - Nigel Moriarty has made contributions to the semiempirical code - Huub Van Dam was very helpful in implementing gradient-corrected functionals. His http://www.cse.clrc.ac.uk/qcg/dft/[Density Functional Repository Web Site] is an essential reference for anyone trying to implement density functionals. ## Changelog - 1.6.2: 2009-02-24 * Removed the shebangs because they made the FC installation barf * Fixed a problem with MINDO in the TessSuite.py - 1.5.0: 2005-12-19 * A User's Guide * EXX density functionals * Gradient-corrected density functionals * Fermi-Dirac finite-temperature occupations in DFT and HF * Minor interface improvements in the software routines - 1.4.0: 2005-10-25 * Fixed a serious bug in the AtomicGrid staggering (the spingrid=True) functions. * Made charge a property of Molecule, and removed it from the arguments in hartree_fock.py and dft.py. * Started a major interface change where all non-essential arguments to functions will be passed in keyword argument dictionaries, since this provides *much* more flexibility. - 1.3.1: 2005-07-07 * Moved the cints, crys, chgp routines into the PyQuante subdirectory. * Renamed chgp.index to chgp.iiindex, which fixed a compile error under gcc 4.0 (I think). - 1.3.0: 2005-06-01 * Added a capability to do three-center integrals over Gaussians, which is useful for EXX and OEP. * Fixed a bug in cints.binomial() where the return type was incorrectly specified. * Made the typing slightly stronger in CGBF and PGBF * Fixed a bug in mopac_doverlap submitted by Andrew Ryzhkov - 1.2: 2004-10-19 * Relicensed the code under the modified BSD license. - 1.1.1: 2003-04-14 * Got MP2 working, so I decided to release a new version of the code. - 1.1.0: 2003-04-09 * Got Pulay's DIIS convergence acceleration working; this is now the default converger in both hartree_fock and dft. * Got a simple version of Configuration-Interaction Singles working. * Made the test suite a little bit more robust; hopefully the variations in the results that other people complained about are now fixed. - 1.0.5: 2002-12-12 * Added a MINDO3.py module, which performs semi-empirical calculations using Dewar's MINDO/3 Hamiltonian * Added a Dynamics.py module to run molecular dynamics. Currently only the MINDO3.py module supplies forces. * Added a Minimizers.py module with a steepest descent minimizer currently resides. - 1.0.4: 2002-09-28 * Fixed a bug whereby the different integral modules cints, chgp, and crys could not be imported at the same time. Reported by Konrad Hinsen. * Fixed a bug in crys related to the Rys polynomials. Reported by Pat Nichols. - 1.0.3: 2002-09-09 * Fixed an underflow bug in DFunctionals.py * Slightly improved the test suite - 1.0.2: 2002-09-08 * Fixed a bug in CGBF/contr_coulomb where the return values were multiplied by the wrong normalization constants (all a.norm()). * Wrote a test suite (Tests/TessSweet.py), that also contains the expected result of each program. * Put additional comments in MolecularGrid.py, AtomicGrid.py, and DFunctionals.py on the methods these are based upon. - 1.0.1: 2002-09-01 * Rearranged the files according to the "proper" Python distutils module, according to Konrad Hinson's suggestions. - 1.0.0: 2002-07-22 * Original PyQuante release, naively called "1.0".