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## SoftwareWith the rapid development of computer technology and application, especially appearance of the super-large scale integrated circuits and micro-computer, computer graphics (Computer Graphics, CG), computer-aided design (Computer Aided Design, CAD) and computer-aided manufacturing (Computer Aided Manufacturing, CAM) and other new technologies can be very rapid development. CAD, CAM in various fields of electronics, shipbuilding, aviation, aerospace, machinery, construction, automotive and other widely used tools to become the most productive potential shows a bright future, has made tremendous economic benefits. ## Business Software
LS-DYNA is a kind of software for general-purpose explicit dynamic analysis developed by the LSTC Company. Accurately, LS-DYNA is just a solver, then many companies developed special preprocessor and postprocessor for LS-DYNA, such as Visual-Crash for DYNA of the ESI company, the ETA company's FEMB, and LS-PrePost designed by LSTC in recent years, some other company integrated the LS-DYNA to their own simulation environment, such as Ansys company's Ansys LS-DYNA, and MSC company's Dytran, and so on.
CFX is general-purpose computational fluid dynamics analysis software, now has been purchased by Ansys Company, including its preprocessor, solver and postprocessor. CFX has a very strong ability handling the rotating machinery fluid problem. CFX uses the finite volume method based on finite element, which absorbs the numerical accuracy of the finite element method on the base of ensuring the conservation characteristics of the finite volume method. In the application of turbulence models, CFX has been the industry's leading. In addition to the commonly used turbulence models, CFX is the first to use large-eddy simulation (LES) and the detached eddy simulation (DES) turbulence model.
FLUENT is general-purpose computational fluid dynamics analysis software, now has been purchased by Ansys Company. Gambit is its preprocessor. In addition, users can also use other preprocessing software to pre-treatment. FLUENT can be used to simulate complex flows from incompressible to highly compressible. As a result of using a variety of solution methods and multigrid method to accelerate the convergence, FLUENT can achieve the best rate of convergence and accuracy of solution. Because of flexible unstructured grid and adaptive grid based on solution and the appropriate physical model, FLUENT has a widely used in transition and turbulent flow, heat transfer and phase change, chemical reaction and combustion, multiphase flow, rotating machinery, dynamic grid, deformable grid, noise, materials processing, fuel cells and other fields. ## Biomedical Software
NAMD (NAnoscale Molecular Dynamics) is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. The NAMD uses empirical force field, such as Amber, CHARMM, and Dreiding, to calculate the atomic trajectory by solving the equations of motion.
GROMACS is a molecular dynamics package used to study bio-molecular systems. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
The DESMOND developed by DEShaw Research, a relatively new molecular dynamics simulation software, mainly used in biological systems, such as membrane proteins and small molecules. It use different force fields such as CHARMM, AMBER, OPLS, Desmond attaches great importance to the simulation of membrane proteins and can easily build a membrane protein simulation system through using its own tools.
AutoDock is a molecular docking software package, The Scripps Research Institute, Olson research group use the C language to develop these codes and the latest version is 4.2. AutoDock is a software package, which include AutoGrid and AutoDock program. AutoGrid primarily responsible for grid calculation of correlation energy and AutoDock is responsible for the conformational search and evaluation.
DOCK molecular docking program is developed by the UCSF Kuntz team in 1982, the early version is based on rigid docking. It considers the flexibility of the ligand from version 4.0. Like semi-flexible (rigid receptor-flexible ligand docking). ## Chemistry Software
NWChem is computational chemistry software that run in high-performance parallel supercomputers and ordinary workstation cluster, it can use on most computing platforms. NWChem use standard quantum mechanics to describe the electronic wave function or density, to calculate the characteristics of molecules and periodic systems and can also carry out classical molecular dynamics and free energy simulation.
GAMESS is a program for ab initio quantum chemistry. Briefly, GAMESS can compute wave functions ranging from RHF, ROHF, UHF, GVB, and MCSCF, with CI and MP2 energy corrections available for some of these. Analytic gradients are available for these SCF functions, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies. A variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities may be computed. Many basis sets are stored internally, and together with effective core potentials, all elements up to Radon may be included in molecules. Several graphics programs are available for viewing of the final results. Many of the computational functions can be performed using direct techniques, or in parallel on appropriate hardware.
Car–Parrinello molecular dynamics or CPMD usually refers to either the computational chemistry software package CPMD, a parallelized plane wave / pseudopotential implementation of density functional theory, particularly designed for ab initio molecular dynamics,[1] or the underlying theory known as the Car–Parrinello method,[2] which is related to the more-common Born–Oppenheimer molecular dynamics (BOMD) method in that the quantum mechanical effect of the electrons is included in the calculation of energy and forces for the classical motion of the nuclei, but whereas BOMD treats the electronic structure problem within the time-independent Schr?dinger equation, CPMD explicitly includes the electrons as active degrees of freedom, via (fictitious) dynamical variables. ## Materials Science
LAMMPS ("Large-scale Atomic/Molecular Massively Parallel Simulator") is a molecular dynamics program from Sandia National Laboratories.. LAMMPS makes use of MPI for parallel communication and is free, open-source software, distributed under the terms of the GNU General Public License. LAMMPS was originally developed under a Cooperative Research and Development Agreement (CRADA) between two laboratories from United States Department of Energy and three other laboratories from private sector firms.[1] It is currently maintained and distributed by researchers at the Sandia National Laboratories.
DL_POLY is a general purpose serial and parallel molecular dynamics simulation package developed at Daresbury Laboratory by W. Smith, T.R. Forester and I.T. Todorov. The current version of DL_POLY is DL_POLY_4.
SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is an original method and a software implementation for performing electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. It uses a density functional theory code that predicts the physical properties of a collection of atoms. Properties that can be predicted using the code include Kohn-Sham band-structures, electron density, and Mulliken populations.
GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). The focus of the code is on analytical solutions, through the use of lattice dynamics, where possible, rather than on molecular dynamics. A variety of force fields can be used within GULP spanning the shell model for ionic materials, molecular mechanics for organic systems, the embedded atom model for metals and the reactive REBO potential for hydrocarbons. Analytic derivatives are included up to at least second order for most force fields, and to third order for many.
PWscf (Plane-Wave Self-Consistent Field) is a computer code for electronic-structure calculations within Density-Functional Theory and Density-Functional Perturbation Theory, using pseudopotentials and a plane-wave basis set. PWscf is part of the Quantum ESPRESSO distribution of codes for the quantum simulation of matter at the atomic scale. PWscf is released under the GNU General Public License.
ABINIT is an open-source suite of programs for materials science, distributed under the GNU General Public License. ABINIT implements density functional theory, using a plane wave basis set and pseudopotentials, to compute the electronic density and derived properties of materials ranging from molecules to surfaces to solids. It is developed collaboratively by researchers throughout the world. ## Meteorology Software
GRAPES is a new generation of static / non-static multi-scale numerical prediction models developed by the numerical prediction research center of the Chinese Academy of Meteorological Sciences. This mode adopts a standardized and modular software architecture which developed in terms of the requirement of software engineering, including parallel computing. According to the testing result, the design and completion of software framework of GRAPES mode is satisfied with request of mode development and it lays the good foundation for the sustainable development of numerical climate forecast system of China.
The WRF, which is a climate mode, was developed By the U.S. Centers for Environmental Prediction (NCEP), U.S. National Center for Atmospheric Research (NCAR) and other research institutes in 2000. The WRF model is fully compressible and non-hydrostatic model and it was programmed with F90 language. The horizontal direction uses the Arakawa C (Arakawa C) grid points and the vertical direction uses the coordinate with quality terrain. WRF mode uses the third-order or fourth-order Runge-Kutta algorithm in the time-integrating. WRF model could be used for the case of real weather simulation.
The fifth-generation mesoscale mode is a mesoscale numerical prediction mode developed by the U.S. Center for Atmospheric Research (NCAR) and the United States Binzhou University (PSU) based-on the mm4 in recent years. It has been wide used in various mesoscale phenomena. MM5 has made many changes in the previous mode based on the following points: 1) The nesting feature of the recombination zone, 2) the expansion of non-hydrostatic part, 3) four data assimilation capabilities, and a more physical parameterization can convenient, widely used in a variety of computing platforms. Limited area numerical weather prediction system has been built in China. Both the Beijing Meteorological Bureau and the Tianjin Meteorological Bureau have adopted this model as a business model. MM5 is a non-linear change partial differential equations based on changes of weather so that it could handle the large density of data and complex calculations. ## GPU Software
Intel Compiler 11.1 CUDA 4.0 Tianhe MPI |