Computational Chemistry

[*] 2 Dimensional Finite Difference Hartree-Fock Program . A Numerical Hartree-Fock Program for Diatomic Molecules by Jacek Kobus, Leif Laaksonen, Dage Sundholm. The program is distributed with source code and sample input and output, however registration is required (the program is not public domain). The program should run without any problems on most unix machines. Authors tested it on Cray, DEC, IBM, SGI and SUN computers.
[CM] ADF is the Amsterdam Density Functional program system for electronic structure calculations. The two main programs are ADF (for molecules) and ADF-BAND - or shortly BAND - for periodic structures: polymers, slabs, crystals. Several smaller programs ("utilities") for pre- and postprocessing data of ADF (molecular) belong to the package. Porting to Linux is on the way (Carles Bo)
[*] AMPAC 4.0 contains the MNDOC, AM1, MINDO/3 and MNDO semiempirical methods along with an extensive set of tools to study molecular structure and chemical reactions. AMPAC 4.0 exclusively features M.J.S. Dewer's new SAM1 semiempirical method, which includes an explicit description of d-orbitals. AMPAC 4.0 has many new features, including a GUI implemented under X-Windows/Motif for rapid input and interpretation of results; more rapid and reliable methods for geometry optimization and SCF convergence; the electrostatic potential (ESP) method for accurate atomic charges; Reed and Weinhold's natural bond order (NBO) population analysis method; an improved method for interpreting vibrational frequencies; more accurate and rapid configuration interaction (CI) calculations; an automated annealing prrocedure for locating multiple minima. Contact: Andrew J. Holder, Semichem, 12715 West 66th Terrace, Shawnee, KS 66216 USA, 913-268-3271, 913-268-3445 (F), aholder@vax1.umkc.edu (e-mail)
[*] New! ARTwork is a program for MD and Monte Carlo simulations based on Effective Medium Theory. The program has built-in interaction potentials based on the effective medium theory (EMT). Alternatively, the user can supply an external program for calculation of the interactions and still take advantage of the setup, dynamics and analysis facilities. The EMT potential that comes with the program allows calculations of Cu, Ag, Au, Ni, Pd, Pt and their alloys and the interaction of oxygen and hydrogen with these metals. The potentials are approximate, but despite their simplicity, they have been shown capable of describing a large number of bulk and surface properties of metals and chemisorption systems very well.
[*] BIGMAC Configurational Bias Monte Carlo (CBMC) is a recent technique to compute thermodynamic properties of flexible molecules. It has been used by several academic groups to study the adsorption behavior of linear and branched alkanes in zeolites and the vapor-liquid equilibrium of linear and branched alkanes. In the new version of Cerius2 there will be a CBMC utility for calculating adsorption properties of linear and brached molecules. However, Cerius2 is platform dependent and quite expensive.
[*] New! CDA (Charge Decomposition Analysis) has been devised to analyze chemical systems which can be described as donor-acceptor complexes. The electronic and energetic charges associated with the formation of a complex consisting of two fragments A and B are partitioned in terms of the familiar Dewar-Chatt-Duncanson model. The energy analysis is feasible within the Hartree-Fock approximation, while the charge decomposition analysis can also be carried out at correlated levels.
[*] Columbus is a collection of programs for high-level ab initio molecular electronic structure calculations. The programs are designed primarily for extended multi-reference (MR) calculations on electronic ground and excited states of atoms and molecules. A variety of methods, including
  • MCSCF
  • MR-CISD (multi-reference configuration interaction with all single and double excitations),
  • MR-ACPF (multi-reference averaged coupled-pair-functional) and
  • MR-AQCC (multi-reference average quadratic coupled-cluster)

are available. An important feature of COLUMBUS is its flexibility. In addition to standard classes of reference wave functions, such as CAS or RAS, calculations can performed with selected reference configurations. Though the multi-reference aspect of COLUMBUS is emphasized, single-reference calculations can also be carried out very efficiently.

[*] CRYSTAL 98 solved the Hartree-Fock and Kohn-Sham equations for periodic systems (polymers, slabs, crystals) and computed the ground state energy and many related properties. See also http://www.ch.unito.it/ifm/teorica/crystal.html
[*] Dalton The Dalton Quantum Chemistry Program represents a powerful quantum chemistry program for the calculation of molecular properties with SCF, MP2 or MCSCF wave functions. The strengths of the program are mainly in the areas of magnetic and (frequency-dependent) electric properties, and for studies of molecular potential energy surfaces, both for static and dynamical investigations.
[*] DeFT is a quantum mechanical computational software. It uses density functional theory and Gaussian density function als. DeFT is designed to run faster than the conventional ab initio software.
[*] Fenske-Hall program. An Hartree-Fock SCF method (STO Basis Set), with special optimization, suitable to perform calculations (especially ionization energies) of large inorganic and organometallic compounds. The original fortran source is compiled by f2c. (Ask to Carlo Nervi)
[*] GAMESS package is ready to compile on linux. GAMESS (General Atomic and Molecular Electronic Structure System) perform ab-initio calculations, and is available only on request, but it is free. Details can be found on GAMESS Home Page.
[CM] GAUSSIAN 94 is now available for Linux platform. It is designed to model a broad range of molecular systems under a variety of conditions, performing its computations starting from the basic laws of quantum mechanics. Please direct your information requests to info@gaussian.com
[CM] Jaguar is a comprehensive electronic structure program suite. Jaguar's unique numerical methods enable rapid evaluations of gas-phase and solvated DFT, HF, MP2 and GVB wavefunctions, energies, structures, vibrational frequencies, atomic charges, hyperpolarizabilities, and thermochemical properties.
[*] Lennard-Jones Gas Simulation by molecular simulation.
[GPL] MOISS (Molecular Integration and Sampling Software). is a n-particle, n-dimensions Monte Carlo Schroedinger equation integrator. It implements multiple educational and research potentials. Our goal is to implement a freely available general purpose QMC program released under the GNU/GPL program.
[CM] MOLCAS is a quantum chemistry software developed by scientists to be used by scientists. The basic philosophy behind Molcas is to develop methods that will allow an accurate Molcas ab initio treatment of very general electronic structure problems for molecular systems in both ground and excited states.
[*] MOLPRO (quantum chemistry package) is a complete system of ab initio programs for molecular electronic structure calculations, written and maintained by H.-J. Werner and P. J. Knowles, and containing contributions from a number of other authors. As distinct from other commonly used quantum chemistry packages, the emphasis is on highly accurate computations for small molecules, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods.
The heart of the program consists of the multiconfiguration SCF and multireference CI modules, and these are accompanied by a full set of supporting programs. The package comprises
[*] MOLSCAT is a code for quantum mechanical (coupled channel) solution of the nonreactive molecular scattering problem. Code is implemented for various types of collision partners. In addition to the essentially exact close coupling method several approximate methods, including the Coupled States and Infinite Order Sudden approximations, are provided. The code is in near standard FORTRAN 77 and has been ported to a large number of platforms. The source code supplied here is currently running at this site on an IBM RS/6000 and also on IBM and compatible mainframes. It should work on most other machines; for the Cray, however, modifications to run in single precision should be made.
[*] MPQC (Massively Parallel Quantum Chemistry Program) computes properties of atoms and molecules from first principles using the time independent Schrodinger equation. It runs on a wide range of architectures ranging from individual workstations to symmetric multiprocessors to massively parallel computers. Its design is object oriented, using the C++ programming language.
[*] NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources. NWChem has been developed by the High-performance Computational Chemistry group of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). Most of the implementation has been funded by the EMSL Construction Project
[*] ORAC is a program for running classical simulations of biomolecules in the NVE, NPT, NHP, and NVT thermodynamic ensembles. The integration of the equations of motion in the NVE ensemble can be carried out with the r-RESPA multiple time step integrator and electrostatic interactions can be handled with the Smooth Particle Mesh Ewald method in any ensemble.
[*] PIMM (Pi-SCF-Molecular Mechanics Program) is a combined SCF/molecular mechanics program for organic molecules and complexes, with parameters for compounds of C,H,N,O,S,P,Si,F,Cl,Br and ions of Li, Na, K, Mg, Ca, Fe, Co, Ni, Cu, Zn, Ce, In, Zr, Th.
[*] Q-Chem A system that brings together a variety of advanced computational methods and tools in an integrated ab initio software package. Q-Chem is the first commercially available quantum chemistry program that is capable of treating large molecules in a practical amount of time, extending the boundaries of application with each new release. Q-Chem software products are discounted by user type.
[*] QCDMPI is a pure QCD (Quantum Chromo Dynamics) Monte Carlo simulation code with MPI. Lattice QCD and its Monte Carlo simulation is a powerful tool to analyze the non-perturbative aspects of QCD. In order to get reliable and stable results from lattice QCD, huge computational power is required. QCDMPI allows the simulation to be performed in parallel while keeping the portability through MPI interface.
[*] TheRate (Theoretical Rates) allows thermal and vibrational-state selected rate constants of unimolecular and bimolecular gas-phase reactions to be calculated directly from an ab initio and/or densitiy functional electronic structure theory. The calculations are based on variational transition state theory augmented by several multidimensional semiclassical tunneling approximations. TheRate was designed to be an advanced research tool, as well as a teaching tool for courses in applied quantum chemistry and kinetics.
[CM] TURBOMOLE is a program package for ab initio electronic structure calculations. It uses SCF, DFT, RIDFT, MP2, RIMP2 for closed and open shells (UHF), and has DFT functionals such as: S-VWN, BP, B-LYP, B3-LYP, Becke Half-and-half. TURBOMOLE consists of a series of modules; their use is facilitated by various tools.
[CM] VASP VAMP/VASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in VAMP/VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing. These techniques avoid all problems occurring in the original Car-Parrinello method which is based on the simultaneous integration of electronic and ionic equations of motion. The interaction between ions and electrons is described using ultrasoft Vanderbilt pseudopotentials (US-PP). These pseudopotentials allow a considerable reduction of the necessary number of plane-waves per atom for transition metals and first row elements. Forces and stress can be easily calculated with VAMP/VASP and used to relax atoms into their instantaneous groundstate VASP is not free. Contact Prof. Hafner
[CM] WIEN97 This program package allows you to perform electronic structure calculations of solids using the full-potential linearized-augmented-plane-wave (LAPW) method, one among the most accurate schemes for band structure calculations. It is based on density functional theory and uses the local (spin) density approximation (LDA) or the improved version of the generalized gradient approximation (GGA). It is an all-electron scheme including relativistic effects.
[*] XCrySDen (X-Window Crystalline Structures and Densities). Program Purpose:
  • molecular and crystalline structure render program
  • property analyzer
  • graphical user interface (GUI) for the program CRYSTAL95/98
  • yields visualization of crystalline structures, 2D/3D electron densities and generates k-mesh for band structure plots for WIEN97 program
By Tone Kokalj.
[*] XNBC v8 is a simulation tool for the neuroscientists interested in simulating biological neural networks using a user friendly tool. XNBC is a software package for simulating biological neural networks. Two neuron models are available, a leaky integrator model and an ion-conductance based model. Inputs to the simulated neurons can be provided by experimental data stored in files, allowing the creation of "hybrid" networks.