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22 Introduction and usage of CMRimport cmr . . .c a l c = GPAW( ) . . .cmr params = {” db keywords ” : [ ”ABO3” , ”CsZnO3 ” ] ,” d b s c r i p t s ” : [ ” CsZnO3 . py ” ] ,” d b f i l e s ” : [ ” CsZnO3 . t x t ” ] ,”name ” : ” CsZnO3” ,”A” : ” Cs ” ,”B” : ” Zn” ,”X” : ”O3”}c a l c . w r i t e ( ” . db ” , cmr params=cmr params )Figure 2.3: A small python script to add an arbitrary result to the db-file repository.GPAW provides the ability to use its native write function.new so-called fields which are name–value pairs. The last field in the examplefor example has the name “X” with the value “O3”. Some of the informationcarried by the fields or keywords are in this example somehow redundant. It is ofcourse possible just from the identity of the atoms and their positions to recoverwhich metal atom is in fact the “A” atom in the perovskite structure, but itmay be convenient sometimes to add the information explicitly for fast and easyretrieval. If other programs than GPAW are used or if one wants to “manually”add information to the db-files this can be done as shown in figure 2.4.importcmrcmr params = {” input ” : ” CsZnO3 . xxx ” ,” output ” : ” . db ” ,” db keywords ” : [ ”ABO3” , ”CsZnO3” , ” hof ” ] ,” d b s c r i p t s ” : [ ” CsZnO3 . py ” ] ,” d b f i l e s ” : [ ” CsZnO3 . t x t ” ] ,”name ” : ”CsZnKO3” ,”A” : ” Cs ” ,”B” : ” Zn” ,”X” : ”O3”}cmr . c o n v e r t ( cmr params )Figure 2.4: A small python script to add an arbitrary result to the db-file repository.All extra fields and keywords are defined in a python dictionary and passedas an extra argument to cmr.convert. ”input” specifies the file that shouldbe imported and ”output” the name of the output file - using ”.db” as a namesignals that we are not interested in a real filename and would like the outputto be written directly to the db-file repository (from where it will be added tothe database). ”db keywords” is a list of keywords that identify this calculation,db scripts and db files take a list of filenames that will be included - and finally
2.2 Step by Step 23”A”, ”B” and ”X” are user defined fields.The calculation of the heats of formation require input from several differentGPAW calculations. The link between different calculations in CMR is establishedby creating so-called groups of calculations: The resulting calculated energy,E hof,CsZnO3 , will be linked to a group containing the calculations for CsZnO 3 ,Cs, Zn, and O. When loading the data into CMR they have been equipped withkeywords and fields as illustrated in figure 2.3, so the A- and B-metal atoms in agiven perovskite calculation can be referred to using the fields “A” and “B”. Thekeywords make finding a result easier - there are no file and directory names in adatabase that provide hints. When choosing keywords and fields, it is importantto assure that results can be identified uniquely. The above proposed fields aresufficient for the presented example, but if there would be reference calculationsfor AO 2 , they could not be distinguished from the calculations of A: looking forthe keyword ”reference” and A=Cu would return both of the results. In thatcase one would have to either add another keyword (e.g. bulk, oxide) or add anew field (e.g. type=”bulk”, type=”oxide”) to distinguish them. Alternatively,the atoms entering the calculation could be directly analyzed.The easiest way to visualize the relevant grouping, is to use the PHP/HTMLinterface which provides an intuitive way to write queries. A screen shot is shownin figure 2.5 on page 24. The query that was used is ABO3 A=Cs and shows allresults having the keyword ”ABO3” and containing a field “A” with the value“Cs”. The rest of the query columns=... in the figure selects the columns anddefines to display the atoms, that should be displayed. These argument areoptional, but convenient when viewing a data set with custom fields.Now we would like to calculate the heat of formation (hof) by finding matchingcalculations. To make the syntax easier we denote in the following ABO 3 asthe calculation of ABO 3 and ABO 3 .PotentialEnergy as the potential energy ofABO 3 . The hof is evaluated asE hof =ABO 3 .P otentialEnergy − A.P otentialEnergy/A.nA− B.P otentialEnergy/B.nA − X.P otentialEnergywhere A.nA denotes the number of atoms of type A. We therefore need to findthe four calculations in order to perform the computation.The combination criteria can be written as three equations and be passed onto the GroupingAgent.• ABO 3 .A = A.A• ABO 3 .B = B.A• ABO 3 .X = X.AThe items A, B, X and ABO 3 are identified by the keywords. We also includethe user name (db user=ivca) to prevent confusions - other users might haveused the same keywords and fields for other purposes and we don’t want to mixresults:A, B and X are identified with• keyword: reference• name-value: db user=ivca
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90 BIBLIOGRAPHY[11] Anubhav Jain, G
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