Chemistry

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ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors. Excited states can be computed within the Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory (the GW approximation). In addition to the main ABINIT code, different utility programs are provided.

 

 http://www.abinit.org

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The molecular ADF program can be applied to gas phase molecules, solvated molecules, and molecules in protein environments. It can treat all elements of the periodic table, and contains state-of-the-art relativistic methods (ZORA and spin-orbit coupling) to treat heavy nuclei. ADF is especially suited for transition metal compounds. It is efficient due to a combination of linear scaling and parallelization techniques, and contains many standard methods for studying potential energy surfaces, as well as a wide range of molecular properties.

Chemically relevant analysis methods are available (including bond energy decomposition, fragment orbitals, and charge decomposition). The QM/MM implementation enables the treatment of protein environments with many thousands of atoms. ADF includes the very latest meta-GGA and hybrid exchange-correlation functionals, as well as a full range of standard functionals (including B3LYP).

 

http://www.scm.com/Products/Overview/ADFinfo.html

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BAND is a periodic structure program for the study of bulk crystals, polymers, and surfaces. BAND is often used in heterogeneous catalysis studies. BAND provides the Potential Energy Surface (PES) of, for instance, a chemisorption system or a chemical reaction at a metal surface. New in ADF2008: transition state search, calculation of numerical frequencies, ESR g-tensor and A-tensor.

 

• Bulk crystals, polymers, surfaces (true slab)
• Accuracy and efficiency
  • numerical and Slater atomic orbitals (no pseudo-potentials needed), efficient
• Structure and Reactivity
  • geometry optimization, transition state search
  • numerical frequencies
  • potential energy surface (PES)
• Model hamiltonians
  • LDA, GGA, and meta-GGA density functionals
  • Relativistic methods (ZORA and spin-orbit coupling), important for heavy nuclei
• Time-dependent DFT
  • frequency-dependent dielectric functions (including metals), Vignale-Kohn functional
  • electron energy loss function (EELS)
• ESR Zeeman g-tensor and hyperfine A-tensor
• Analysis
  • analysis of the "bonding" (cohesive) energy in conceptually useful components
  • Mulliken-type population analyses and the charge density Fourier analysis (form factors)
  • densities-of-states (total, partial, population) analyses
  • fragment analysis feature available for decomposition of density-of-states data
    in terms of the molecular orbitals of (molecular) fragments

 

http://www.scm.com/Products/Overview/BANDInfo.html

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Incorporating advanced functionality and the latest analytical algorithms and methods, CHEMKIN-PRO delivers the ultimate in speed, accuracy and solution robustness. Core solver enhancements incorporated in CHEMKIN-PRO cut simulation times from days to hours or hours to minutes for complex models with large mechanisms. As much as 25 times faster than previous versions of CHEMKIN and more than an order of magnitude faster than competing codes in demanding applications.

 

 

To help designers gain key insights into kinetic dependencies, CHEMKIN-PRO includes the Reaction Path Analyzer. Employing an interactive, visual display, the Reaction Path Analyzer provides a clear view of dominant reaction paths, facilitating mechanism development and reduction. The innovative Particle Tracking capability of CHEMKIN-PRO to follow particles through inception, growth and oxidation. Apply number and size statistics to predict soot emissions or to optimize particulate production for carbon-black applications. Enhance simulation results with the ability to calculate error bars based on user-defined input accuracy ranges. CHEMKIN-PRO's Multi-Zone Engine Model simplifies the analysis of key combustion effects including ignition, flame speed, and CO, HC and Soot emissions.

 

 

http://www.reactiondesign.com/products/open/chemkin-pro.html

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CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.

 

CP2K provides state-of-the-art methods for efficient and accurate atomistic simulations, sources are freely available and actively improved. It is therefore easy to give the code a try, and to make modifications as needed.

 

 http://cp2k.berlios.de/

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The main characteristics of the CPMD code include:

 

• wavefunction optimization: direct minimization and diagonalization
• geometry optimization: local optimization and simulated annealing
• molecular dynamics: NVE, NVT, NPT ensembles.
• path integral MD, free-energy path-sampling methods
• response functions and many electronic structure properties
• time-dependent DFT (excitations, molecular dynamics in excited states)
• LDA, LSD and many popular gradient correction schemes
• isolated systems and system with periodic boundary conditions; k-points
• Hybrid quantum mechanical / molecular mechanics calculations (QM/MM)
• coarse-grained non-Markovian meta-dynamics
• works with norm conserving or ultra-soft pseudopotentials

 

 

http://www.cpmd.org/

 

 

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GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package originally developed in the University of Groningen, now maintained and extended at different places, including the University of Uppsala, University of Stockholm and the Max Planck Institute for Polymer Research

 

http://en.wikipedia.org/wiki/GROMACS

 

 

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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.

 

http://www.emsl.pnl.gov/docs/nwchem

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ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.

Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations.

 

http://www.thch.uni-bonn.de/tc/orca/

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Jaguar is a high-performance ab initio package for both gas and solution phase simulations, with particular strength in treating metal containing systems, making it the most practical quantum mechanical tool for solving real-world problems.
Even with tremendous advances in molecular mechanical methods, there remain important research questions that cannot be answered without examining in detail a molecule's electronic structure. Also, molecular mechanics methods are limited by their parametrization. For example, conventional force fields either fail to treat metal containing systems, or experience large errors in computed results. High-level quantum mechanics is still the most accurate and most direct way to study these challenging systems, despite the increased computational cost.

An efficient quantum mechanical program is indispensable to the complete arsenal of any researcher who is interested in reactive chemistry, systems containing transition metals, or phenomena that require precise energetics.

 

• High performance: Jaguar proceeds much faster than conventional ab initio programs, making it possible to carry out many more calculations within the same time frame.
• Real-world systems: Jaguar scales well with molecular size, allowing it to be applied to larger, real-world problems without having to unrealistically reduce the size of the chemical system under study.
• Higher accuracy: Jaguar's performance advantage makes possible the application of higher levels of theory, resulting in more accurate energies and properties. Jaguar models important solvent effects by applying a self-consistent reaction field (SCRF).
• Chemical properties: Jaguar computes a comprehensive array of molecular properties including NMR, IR, pK_a, partial charges, multipole moments, polarizabilities, molecular orbitals, electron density, electrostatic potential, Mulliken population, and NBO analysis.
• Potential energy surface: Jaguar maps reaction coordinates between reactants, products, and transition states; Jaguar also generates potential energy surfaces with respect to variations in internal coordinates.

 

http://www.schrodinger.com/ProductDescription.php?mID=6&sID=9&cID=0