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Resources_and_technology
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* [[JUMBO-Converters]] (Java) for legacy2CML and other transformations * [[Lensfield2]] build system with dependencies * [[http://quixote.wikispot.org/Resources_and_technology|RESTful]] system for uploading and aggregation * [[http://quixote.wikispot.org/Resources_and_technology|Greenchain]] server on virtual machine at Cambridge - allows free upload (ca 25 GB available) * [[Chempound]] a standalone database server for archiving the outputs of computational chemistry calculations.
* [[ANTLR]] technology for parsing (QB and Weerapong developing).
* [[http://www.oracle.com/technetwork/java/javase/downloads/index.html|Java 1.5 JDK]] * [[http://quixote.wikispot.org/Tutorials_and_problems#Maven|Maven]] for resolving Java dependencies. Check [[Maven]] for a basic tutorial and known problems. * [[http://mercurial.selenic.com/|Mercurial]] for interacting with software repositories. Check [[Mercurial]] for a basic tutorial and known problems. * [[http://sourceforge.net/projects/avogadro/files/avogadro/1.0.1/|Avogadro]] for visualizing the parsed output. Check [[Avogadro]] for instructions about how to install it.
* [[NWChem]] - a powerful Opensource electronic structure code. * [[http://avogadro.openmolecules.net/|Avogadro]] - an Opensource molecular modelling environment
* Embed calls in the code. Current libraries include:
1. [[FoX]] (FORTRAN95, Toby White).
1. [[JUMBO]]/[[CMLXOM]] (Java, Peter Murray-Rust)
1. [[http://www.codalogic.com/lmx/|LMX]] (move to another section if I am wrong)
* Write scripts or programs that read files and convert into semantic form:
1. [[JUMBO-Converters]]
1. [[Openbabel]]
1. [[http://cclib.sourceforge.net/wiki/index.php/Main_Page|cclib]]
* Write high-level parsers:
1. [[ANTLR]]
The current approach adopted by the Quixote Project is to use the JUMBO-Converters.
- NB:** we are currently working this out the prototype on the Prototype_data page.
- Metadata:**
* author email in logfile (e.g. through title) (is this normally in the logfile or it would be a good practice) * datacite DOI in logfile (pre-publication) * publication associated to the logfile (if published)
- Definition of the system:**
* geometry/structure/nuclear coordinates (its all the same thing, size n) * charge/spin/state (from my point of view, the spin and the state go in the provenance section, they are constraints to the wavefunction)
- Provenance (type of calculation):**
* level of the theory (RHF, B3LYP, MP2, AM1, etc.) * basis set (either with an agreed-upon name, as in BSSE, or custom basis sets) * additional details to the level of the theory (frozen core, etc.) * convergence parameters for SCF, CC iterations, etc. * initial guess for the iterative procedures (e.g., Hückel guess for SCF) * algorithm used for the iterative procedures
- Results of the calculation (observables):**
* energy * energy gradient (size n) * energy hessian (size n^2^) * wave function (size n) * density matrix (size n^2^) * Mulliken charges (or some other type) (size n) * Normal Modes; hessian eigenvalues, eigenvectors
- Performance of the calculation:**
* wall-clock time * CPU time * number of cores it ran into * total RAM used * scratch space in disk used * code exited successfully or unsuccessfully
- CML examples:**
* [[http://cml.svn.sourceforge.net/viewvc/cml/schema2/trunk/examples/complex/calcite1.xml?revision=161|GULP ouptut]] * [[http://cml.svn.sourceforge.net/viewvc/cml/schema2/trunk/examples/complex/castep2.xml?revision=161|CASTEP output (shows use of properties)]] * [[http://cml.svn.sourceforge.net/viewvc/cml/schema2/trunk/examples/complex/castep3.xml?revision=161|similar CASTEP output]] * [[http://cml.svn.sourceforge.net/viewvc/cml/schema2/trunk/examples/complex/dlpoly.xml?revision=161|DLPOLY output]]
* [[Dictionaries_examples]] * [[Creating_dictionaries]]
* [[CML]] * [[http://www.hdfgroup.org/HDF5/|HDF5]] * [[http://abigrid.cineca.it/abigrid/the-docs-archive/q5cost/index_html|Q5cost]]
* CMLcomp: [[http://cml.sourceforge.net/schema/cmlComp/HTMLDOCS/cmlcomp.pdf|Old schema]], [[http://como.cheng.cam.ac.uk/preprints/c4e-Preprint-97.pdf|Newer preprint]]
Some of the codes we intend to support
* [[DALTON]] * [[Gaussian]] * [[GAMESS]] * [[GAMESS-UK]] * [[MOLCAS]] * [[MOLDEN]] * [[MOLPRO]] * [[MPQC]] * [[MOPAC7]] * [[NWChem]] * [[ORCA]] * [[QChem]] * [[TURBOMOLE]]
A long list of quantum chemistry and solid state physics codes: http://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid_state_physics_software
Please edit the pages that these point to. Add:
* any home page(s) * examples of files * notes on any already existing parsers * person of contact
* [[Pablo_Echenique's_dataset]] * [[cclib_test_set]] * [[http://www.oci.uzh.ch/group.pages/baldridge/efiles/UZH_GC3_M06_O3ADD6.tgz|Mark Monroe's dataset]] * [[Three_NWChem_6.0_single-points]]
We expect a variety of approaches to upload and download as people try out different mechanisms. Here we describe the simple REST approach.
We have set up a server at http://greenchain.ch.cam.ac.uk/patents/quixote/ (The "patents" is historical - we may be able to rename it). This server is wide open in all respects so please don't advertise it to spammers. We may tackle security later -if the server is hacked or damaged we simply close it and start again.
You can use a REST-based approach to:
* upload files to server * download files/URLs from server * list files in a server "directory" * delete files/URLs on server
The URL structure reflects the local files hierarchy directly so I shall often simply call the webpages "files" and "directories"
The power of REST is:
* its simplicitly * the library support * the warm feeling you get from doing something really simply that works exactly as you want.
The current HTTP commands are:
* PUT (or possibly POST) puts a file * GET gets a file * DELETE delete a file
That's it.
REST is supported in almost ball languages (I don't know about FORTRAN and I wouldn't use it anyway for this). We shall use Java from: http://bitbucket.org/petermr/lensfieldjumbo. Check this out (if you haven't done already). The code (if you need it) is in: . The routines we shall use are:
* }
*
*
* [[http://harmful.cat-v.org/software/xml/soap/simple|The S stands for Simple]] Why PMR uses REST, not SOAP * [[http://rest.elkstein.org/|Learn REST: A Tutorial (by M. Elkstein)]]