DL_Software training - General information.

 

DL_Software Training Workshop

General Information

This is an introductory course for new and current users of molecular simulation software (DL_Software) developed at Daresbury Laboratory given by the principal developers of these packages. The course will give an overview of the scientific capabilities of the packages by describing in detail their capabilities, functionality and I/O files. It will outline the performance and scaling of the different packages and give the Attendees the opportunity to install and run their own copies of the software. Finally, it will also offer hands-on sessions where the Attendees could practice the application of their newly gained knowledge and give them the opportunity to interact with the authors. Attendees are also given opportunity to ask for advice how DL_Software can be used for their projects.

DL_Software is the collective term that refers to the computational chemistry software suites developed at Daresbury Laboratory. Below lists the available software suites for training. Note that not all software suites are made available in every training event. Users are adviced to refer to any particular on-coming training event before filling up the registration page.

DL_POLY is a general purpose molecular dynamics simulation package developed at Daresbury Laboratory by I.T. Todorov and W. Smith under the auspices of EPSRC and in support of CCP5. It can be used to simulate a wide variety of molecular systems including simple liquids, ionic liquids and solids, small polar and non-polar molecular systems, bio- and synthetic polymers, ionic polymers and glasses, solutions, simple metals and alloys. It is a widely used package in the UK and worldwide (see Molecular Simulation, 28 (2002), pp 385). It is supplied with its own Java-based Graphical User Interface (GUI) and is capable of both serial and parallel execution.

DL_FIELD is a computer program package written in C that primarily serves as a support application software tool for DL_POLY molecular dynamics simulation package. DL_FIELD is developed at Daresbury Laboratory by C.W. Yong under the auspices of EPSRC and in support of CCP5. The primary function of the Program is to convert users' atom models, in particular those of large complex bio molecular systems for a wide range of force fields (CHARMM, AMBER, OPLS, DREIDING, PCFF, CVFF, INORGANIC), into file formats that are recognisable by, and ready to run using, DL_POLY with minimum intervention by the user. The DL_FIELD operates with a minimum set of directive and, without having to learn any scripting languages, users can also easily fine tune force field models and set up their own force field library.

ChemShell is a computational chemistry scripting environment for quantum mechanical and classical force field calculations, with a focus on hybrid QM/MM methods. ChemShell interfaces with a range of QM and MM codes to perform energy evaluations while handling communication, data handling and higher-level tasks such as geometry optimisation and molecular dynamics.

DL_MESO is a general purpose mesoscale simulation package developed at Daresbury Laboratory by M.A. Seaton under the auspices of EPSRC and in support of CCP5. It is written in Fortran90 and C++ and supports both Lattice Boltzmann Equation (LBE) and Dissipative Particle Dynamics (DPD) methods. It is supplied with its own Java-based Graphical User Interface (GUI) and is capable of both serial and parallel execution.

DL_CGMAP is a tool chain program for systematic coarse graining of atomistic models developed at Daresbury Laboratory and University of Bath by A. Brukhno under the auspices of EPSRC and in support of CCP5.

DL_MONTE is a general purpose atomistic Monte Carlo simulation package developed at Daresbury Laboratory by J.A. Purton under the auspices of EPSRC and in support of CCP5. It is written in Fortran90 and supports a wide range of of common potentials in a DL_POLY force-field form. The MC method is free from the restrictions of solving motion as in MD which allows for cleverness in the proposal of moves that generate trial configurations within the statistical mechanics ensemble of choice. Although these moves may be nontrivial, they lead to faster time to solution than MD in the sampling of equilibrium properties. Specific Monte Carlo moves can also be combined in a simulation allowing the modeller great flexibility in the approach to a specific problem. This flexiblity leads to capabilities beyond what classical MD could such as Grand and Semi-Grand Canonical ensembles.

DL_AKMC is a general purpose adaptive kinetic Monte Carlo (aKMC) simulation package developed at Daresbury Laboratory by David S.D. Gunn and John A. Purton. It is written in Fortran90 and supports a variety of common potentials in a DL_POLY force-field form. The AKMC method uses saddle-point searches and harmonic transition state theory to model rare-event, state-to-state dynamics in systems of interest. The dynamical events can be complex, involve many atoms and are not constrained to a grid, relaxing many of the conditions of regular KMC, making the code more versatile and useful in situations where the state transitions are not known a priori.

Course Pre-requisites

Please, note that the Attendees MUST bring with them a laptop:

  • enabled with a wireless adaptor in order to be able to download course notes and browse manual pages, and

  • capable of emulating linux like environment with the following components:

    • C, C++ and Fortran90 compilers (eg. gnu compiler suite),

    • the GNU make file management utility and

    • the Java Virtual Machine and possibly the Java Development Toolkit;

    • the above are routinely available in any linux distro, please consul the administrator of your machine if you are in trouble. On an Apple computer you need to install first XCode from apple store, then use macports or homebrew to get up to date version of compilers and mpi libraries. Native Windows compilation is also possible but more tricky and supported only with cmake, a windows binary will be provided in case of need. You can emulate a linux like environment in Windows by using cygwin . 

    • optional but desirable cmake (above version 3) and a modern mpi library (e.g. openmpi version 2 or above)

    • a recent version of vmdaten or vesta for visualisation of CONFIG/HISTORY files. 

    in order to carry out the course exercises!

WIFI can be accessed via Eudoroam. Note that the host organisers will provide the registered Attendees wireless access to the internet as a backup in case you do not have access to Eudoroam.

At times these Workshops can be oversubscribed, so please fill in the registration page early to avoid dissapointment!

 

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