The Computational Materials Repository

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46 Introduction and usage of CMRatom 1atom 2ase chemical symbols N Nase positions [0.0, 0.0, 0.499..] [0.0, 0.0, -0.499..]ase masses 14.0067 14.0067ase tags 0 0... ... ...Figure 2.25: Aligning the ASE arrays shown in Fig. 2.24 allows to identify the propertiesfor each individual atom.view ( data )or the ASE command line tool agag N2 . dbMost of the discussed content should contain sufficient information for mostof the users. For more advanced usages the db-file stores also most of the fieldsavailable in the original data files with the original variable names (if possible)and units. In general some of the big matrices are ignored in order to keep thesize of the db-file small. For GPAW all variables are stored except the followingparameters: Projections, AtomicDensityMatrices, NonLocalPartOfHamiltonian,PseudoElectronDensity, PseudoPotential, PseudoWaveFunctions.
2.9 Advanced Task 47People often wonder what the name of the extracted data fields are in detail.It is out of the scope of this work to document these fields that are mostly usedby code developers only, but a list of the currently extracted ones is shown inthe Appendix 4.1.2.9 Advanced Task2.9.1 Publishing results with CMRThe PHP/HTML interface can be used to share data with the public or collaborators.For certain data sets it is useful to restrict the parameters with thepurpose of providing a view with specially tailored parameter choices. Examplesof such a customization can be found at http://cmr.fysik.dtu.dk. Currentlyit shows the dataset of the case study described in paper [19]. In order to performsuch a customization some knowledge in PHP and Javascript are required.2.9.2 Using a MappingWhen working with different codes it is common that some fields have the samemeaning, but a different names. In this case a mapping can be applied to anindividual db-file or to a collection of db-files. (The mapping does currently notsupport to custom defined fields.) Fig. 2.26 shows a complete example scriptthat retrieves some data and maps the name of TotalEnergy to e tot and theunits from eV to hartree. As shown, a dictionary defines the items that shouldbe mapped. The mapping can then be applied to a DataCollection object.2.9.3 Supporting a new file formatThis section explains how to add support for a new file format and implementit as a CMR plug-in. Please note that this section is meant for developers anddoes not explain all source code in detail. Nevertheless it should be possible tocreate a converter by following these instructions.In order to understand how to create a new file format you have to know thatCMR supports plug-ins (Fig. 2.27). Plug-ins allow to add functionality to CMRwithout modifying the CMR source code. In this tutorial we are going to createa converter and a schema plug-in.2.9.3.1 Step 1: create a converterWe assume that we would like to create db-files from a file format that storesatoms, positions and a identifier. We call the file format newc. An example isshown here:atoms = [ 6 , 8 , 8 ]p o s i t i o n s = [ [ 0 , 0 , 0 ] , [ 0 , 0 , 1 . 1 7 8 6 5 8 ] , [ 0 , 0 , −1.178658]]name = CO2
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