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Dirac Crystal Editor User GuideXianlong WangDirac Scientific Computing LLC21 Gaopeng Rd, High-Tech ZoneChengdu, 610041Sichuan, ChinaTel: ＋86-28-85333110Fax: ＋86-28-85333113.604Email: www@, chem.wang@URL: 1. IntroductionThis user guide gives a brief introduction on the Mathematica package, DiracCrystal. The package is designed to be a general-purpose editor for molecular crystals. A comprehensive list of useful functions are defined. However, only the examples for the basic usage of the package are given in this guide. For more information on the advanced usage, the users are advised to contact the author.à1.1 PurposeThe package, DiracCrystal, is designed for editing molecular crystal structure. The following tasks can be fulfilled with assistance of the package: parsing a STAR (Self-Defining Text Archive and Retrieval) file or a CIF (Crystallo-graphic Information File) file, visualizing molecular structures, building a crystal structure from scratch, cutting a crystal structure to build a cluster, writing the molecule structure to a POV ray tracer file, preparing a Gaussian input file (PBC or molecule job, Cartesian or Z-Matrix format), and many more...à1.2 ComponentsThe package includes the following components.1. Init.m, the master declaration file.2. Dict.m, the dictionary file for symmetry operations, atom parameters, Pov file header and default settings,Gaussian file headers and default settings.3. Math.m, a collection of some math functions.4. Tools.m, a collection of some utility functions.5. StarParser.m, the parser for STAR format files without nested loops. The parser is general-purpose. The stringmatching technique is used. Several additional reserved words are used for parsing purpose besides the STAR reserved. It is assumed that those reserved words would never appear in a normal STAR file.6. CifParser.m, the parser for CIF format files. This parser is an in-depth parser for the data item names and valuesin the StarParser parsing result, based on the information in Dict.m.7. CrystalEditor.m, a collection of crystal editing functions.8. Test folder. It includes this guide, some example CIF files and output files.2Dirac Scientific Computing LLCà1.3 RequirementsThe package was created in Mathematica 5.2. It has also been tested on Mathematica 6.0 and 4.0, but only par-tially.2. Basic UsageThe following sections present a step-by-step guide to use DiracCrystal for some specific tasks.à2.1 InitiationLoad the package.Set the The directory paths on Mac OS X, Linux and other operating systems may be in a different format.à2.2 CIF file ParsingImport a CIF file.ShadowParseCIF@s D parses the string,s,in the STARformat at a shadow level.The string s representsa data file in conform with the STAR H CIF L formatand multiple data blocks may be contained in.Further parse the content at a deeper level with the info defined in Dict.m. The returned result, cifFile, is the main data source for the following examples.DictParseCIF@data_List D parsesthe data list with the definitions in theDiracCrystal`Dict`.The data list format shouldbe in conform with the output of ShadowParseCIF.à2.3 VisualizationExtract the molecules information from the data, cifFile. In this example, there are two molecules in the unit cell.Each molecule is considered as a set of bonds. A bond is considered as a set of two molecule sites.getMolSet@cif D returns the molecule set information.The returned value is in the format,8molecule<,where molecule is in the format8bond<andbond is in the format8site1,site2<.If thereare multiple datablocks,only the moleculeset info in the first data block is returned.Draw the molecules. The function, DrawMolecules, has several options to control the presentation effect.DrawMolecules@data_,opts___D,draw a molecule set.The following options can be used.Here is the default setting.Show bonds only...NOTE: In order to rotate the 3-D graph freely, one may use an undisclosed package of Mathematica, Needs["Real-Time3D`"]. However, this is not recommended.à2.4 Cut and ClustersThe function, CrystalCut, can be used to cut a crystal with a sphere. NOTE: This function may take a few seconds or longer.CrystalCut@cif_List,center_,radius_,8a_Integer,b_Integer,c_Integer<D,cut a crystal with asphere which is centered at the center and theradius is radius.8a,b,c<is used to createa supercell for cut.The returned value isin the format,888x,y,z<,81,2<<<.And,centercan be a site,or8x,y,z<,or an integer whichdesignates the atom site in the unit cell.Manually sort the cluster directives to make the center molecule to be the first one.buildCluster@molSet_List,molPos_List,transM_List D, build a cluster according to the given molecule set and the molecules position designation.unitCell is in the format of molSet and molPos is in the format, 888x,y,z<,81,2<<<,where8x,y,z<is the translation vector,81,2<are the molecule numbering in the unit cell.The vectors are in the fractional coordinates.getTransMatrix@cif D returns the transformation matrix from the fractional coordinates tocartesian coordinates of the CIF file.Ifthere are multiple databalocks present,theoperation is for the first datablock only.getMolSet@cif D returns the molecule set information.The returned value is in the format,8molecule<,where molecule is in the format8bond<andbond is in the format8site1,site2<.If thereare multiple datablocks,only the moleculeset info in the first data block is returned.i k j j C1C2i k j j C1C2y{z zi k j j C1C2y{z zi k j j C1C2y{z zi k j j C1C2y{z zi k j j C1C2i k j j C1C2i k j j C1C2y {z z i k j j C1C2i k j j C1C2Now, we may take a look at the cluster structure. NOTE: Although there are four molcules in the returned value by CrystalCut, only two of them are unique. This is seen in the above list information, and more obviously in the following graph. This is because of the inversion symmetry in this crystal.To remove the repeated data, we apply the function, Union[], on the results.ikj jC1C2y{z z ikj jC1C2y{z z ikj jC1C2y{z z ikj jC1C2ikj jC1C2y{z z ikj jC1C2ikj jC1C2ikj jC1C2ikj jC1C2y{z z ikj jC1C2In the above example, the center, 1, refers to the first atom in the cifFile. Alternatively, center can also be an atom site, or an arbitrary point in the form, {x, y, z}.The atom site information can be obtained with the following information.getAtomSiteCart@cif D returns the atomsite info in the cartesian coordinates.If there are multiple datablocks,only theinfo for the first data block is returned.Here is a cluster cut by a sphere located at the original point with a radius of 7.0.à2.5 Conversion to Gaussian Input FilesThe molecule set information can be output as a Gaussian input file. Two kinds of jobs, PBC (Periodic Boundary Condition Calculation) calculation and regular molecular calculations, are supported. NOTE: The output file needs to be edited for your specific needs.First, we output the result in a Gaussian PBC job. NOTE: You need to created the molecule set information first.For some CIF files, the molecule set derived from the fractional coordinates may lay outside of the unit cell.WriteGaussianPBC@data_List,transMatrix_List D,write the molecule set info in the GaussianPBC job format.The input data can be amoleclue set,a molecule or an atom site set.WriteGaussianPBCtoFile@fileName_String,molSet_List,transMatrix_List D,output the molcule set in theGaussian PBC job format.The input data can bea moleclue set,a molecule or an atom site set.Now, we output the cluster information to a Gaussian molecule calculation job. The output data can be either in the cartesian coordinates or in the Z-matrix format. The default is the cartesian coordinates. The Z-matrix is generated by a z-matrix index, which can be supplied as an option, zlist. But before the conversion, we need to relabel the atoms.RelabelAtoms@data_List D The input data set needs to bein the format8site<and where site is inthe format,8atom label,atom symbol,x,y,z<In this example, it is more convenient to write the methyl group in the z-matrix format, if we want to study its rotation. To do so, we need to supply a z-matrix index list as an option for the function, WriteGaussianMol or WriteGaussianMoltoFile.zlist,option of WriteGaussianMol,the z−matrix indexlist.It is in the format,8z−matrix index<,where thez−matrix index is a list of1,2,3or4atom labels.WriteGaussianMol@data,options D,write themolecule set info in the Gaussian job inputfile format.The data can be a molecule set,amolecule or an atom site.The option,zlist,canbe added to direct the z−matrix output format.。