Manual for the xyzxform program
Contents
1. The classification procedure is repeated with increasing class numbers until all the atoms have been classified As a result all the atoms are placed into classes atoms which are members of class N all belong to a cluster in the sense of neighbourhood dictated by cutoff The classes may be inspected by looking at the masses in the output xyze file If you desire to change the names of the atoms to reflect their class membership a combination of tagdef tag mass rename lt name gt tag or rename lt name gt addtag may be used join lt xyz_filename gt Merges the atoms in a xyz file xyz_filename into the system placing them at the bottom indexwise BBox is not altered uniq unique lt tolerance gt For all atoms that occupy the same point in space up to a tolerance along each cartesian direction only the last one is retained In this way duplicates e g resulting from joining several files can be eliminated rename lt speciesl gt any lt species2 gt tag addtag Renames all atoms with a name of species1 to species2 The special name any may be used instead of the source name to rename all atoms The special name tag may be used instead of the target name to change the name of the atoms to their tag character cf working with tags The special name addtag may be used instead of the target name to rename the atoms by the concatenation of their tag character to their current name cf working with tags name lt new_n2. with its periodic image by translating all atoms by a vector that is a xx yy zz tiple of the box BBox is not altered A typical usage would be to subsequently rename the atoms and to join with the original file thus obtaining the original system plus its desired periodic image scale transformations changing the size of the simulation box gt gt stretch lt xx gt lt yy gt lt zz gt Scales stretches the system by a factor of xx along the X axis a factor of yy along the Y axis a factor of zz along the Z axis BBox is not altered Scaling is realized by multiplying all the coordinates by the given factor Because of this care must be taken if the BBox does not begin at 0 0 0 rescaleBBox lt xx gt lt yy gt lt zz gt Scales stretches the BBox by a factor of xx along the X axis a factor of yy along the Y axis a factor of zz along the Z axis The atomic positions remain unchanged Typically used alongside stretch BBox lt x1l gt lt x2 gt lt yl gt lt y2 gt lt zl1l gt lt z2 gt Sets up a new BBox Atomic positions remain unchanged 2009 Jacek Dziedzic jacek dziedzic gmail com Gdansk University of Technology Poland selecting subsets of atoms Warning All the selection operators performed by the select directive described above always replace the system with the new one which contains only the selected atoms Because of this subsequent select operations will always result in
3. selecting smaller and smaller subsets of the original system the intersection of all the selections If you need to obtain a sum of several subsets you will be better off using atom tagging the tag directive The select cylinder directives allow for a selection of atoms contained within a cylinder parallel to one of the cartesian axes X Y or Z If you need to select atoms within a differently oriented cylinder proceed as follows Turn off periodic boundary conditions rotate the system so that the desired cylinder is parallel to one of the cartesian directions select the atoms within the cylinder and rotate the system back gt select cylinder along X lt y gt lt z gt lt r gt Selects atoms lying within an infinintely long cylinder or radius r parallel to the X axis whose axis lies on 00 y z to 0 y z select cylinder along Y lt z gt lt x gt lt r gt Selects atoms lying within an infinintely long cylinder or radius r parallel to the Y axis whose axis lies on x z to x 00 z select cylinder along Z lt x gt lt y gt lt r gt Selects atoms lying within an infinintely long cylinder or radius r parallel to the Z axis whose axis lies on x y 90 to x y 00 select sphere lt x gt lt y gt lt z gt lt r gt Selects atoms lying within a sphere of radius r and a centre at x y z select box lt xl gt lt x2 gt lt yl gt lt y2 gt lt z1 gt lt z2 gt Selects atoms lying within a cuboid whose
4. Cu simulation in a box whose corners are at 0 0 0 and 37 43 37 43 37 43 respectively An extension to the xyz format sometimes termed xyze is often encountered it differs only by an addition of a fifth word often describing the mass or energy of the atom to the description of each atom Several xyz files describing the same system at different time points may be concatenated together to form a multiple frame xyz file Each 2 N line part of this xyz file is then called a frame 2009 Jacek Dziedzic jacek dziedzic gmail com Gdansk University of Technology Poland List of directives input output in lt xyz_filename gt overwrite zap out lt xyz_filename gt framerange lt min gt lt max gt pbc nopbc rotations and translations rotate x lt alpha gt rotate y lt alpha gt rotate z lt alpha gt translate lt x gt lt y gt lt z gt center periodic_image lt xx gt lt yy gt lt zz gt scale transformations changing the size of the simulation box gt stretch lt xx gt lt yy gt lt zz gt gt rescaleBBox lt xx gt lt yy gt lt zz gt gt BBox lt x1 gt lt x2 gt lt yl gt lt y2 gt lt z1 gt lt z2 gt selecting subsets of atoms select cylinder along X lt y gt lt z gt lt r gt select cylinder along Y lt z gt lt x gt lt r gt select cylinder along Z lt x gt lt y gt lt r gt select sphere lt x gt lt y gt lt z gt lt r gt select box lt xl gt lt x2 gt
5. ame gt Changes the name of the system the string in the first line of the frame placed after the BBox namestrip By default the declared name of the system is appended to the previous name along with the previous BBox to preserve a trace of the changes to the system If this is not desired and you want the old names and BBoxes to be left out specify namestrip Other concerns The comment char may be at any time intepreted literally if it is escaped by a backslash Thus the sequence is interpreted as a non comment character 2009 Jacek Dziedzic jacek dziedzic gmail com Gdansk University of Technology Poland Examples of directive files Selects atoms within a sphere with a radius of 12 A centered at 4 3 8 5 Periodic boundary conditions are not applied nopbc zap in input xyz select sphere 4 3 8 5 12 out output xyz Extracts only frames 10 to 19 from the input file f xyz Periodic boundary conditions are not applied nopbc zap in f xyz framerange 10 19 out output xyz Renames all the Au atoms to Pt nopbc zap in input xyz rename Au Pt out output xyz Renames all the Au atoms within a box 0 0 0 10 10 10 to B Periodic boundary conditions are in effect pbc zap in input xyz untag all tagdef B tag box 0 10 0 10 0 10 rename Au addtag tag all out output xyz Stretches the system by 10 along the Z direction Periodic boundary condition
6. ects all atoms thus doing nothing Whereas this makes little sense with the select directive it might be useful to tag alloruntag all see working with tags 2009 Jacek Dziedzic jacek dziedzic gmail com Gdansk University of Technology Poland working with tags Basic usage All the tag directives tag certain atoms those which fulfil a specified condition and the untag directives untag specified atoms The conditions are the same as for the select directive described above In contrast to the application of select the system is not replaced by a new one the atoms that are not tagged still exist they are however not written to the output file when the out directive is encountered Initially all atoms are tagged thus you would normally first untag a subset of atoms or all the atoms untag all By combining multiple tag and untag directives complex subsets of the system may be built Once again it is only the atoms that are tagged that are written out to the output file Advanced usage Atoms may be tagged with differing tags The tag is specified as a single character the default tag being amp the current tag is specified by the tagdef directive Tagging is in general transparent that is the character used to tag an atom does not influence its name location or mass The tag itself is also not written out to the output xyz file the only way to reveal the tag is to use the rename lt name gt tag directive which will
7. l com Gdansk University of Technology Poland Overview of directives input output gt gt in lt xyz_filename gt Declares the name of the input xyz file This directive is mandatory overwrite Forces the output file to be overwritten when outputting every xyz frame This is off by default and subsequent frames are appended to the output file which makes sense if a file containing many frames is transformed When working with a single frame input file it might be desirable to have the output file overwritten every time instead of appending to it This is achieved by using overwrite zap A cousin of overwrite this directive causes the output file to be zapped erased once in the beginning Subsequent writes to the file will append Use zap and not overwrite for multiple frame files out lt xyz_filename gt Declares the name of the output xyz file This directive is mandatory Normally this should be placed as the last directive in the directive file otherwise the output file may be written out before the transforming directives are applied framerange lt min gt lt max gt Forces the program to ignore all the frames whose numbers are not within lt min max gt This allows you to extract ranges of frames from multiple frame xyz files The frames are numbered from 0 Subsequent frames are numbered 1 2 3 regardless of the simulation step or time stored in the frame pbc Turns on periodic boundary condi
8. lt yl gt lt y2 gt lt zl gt lt z2 gt select above below plane through lt x1 gt lt yl gt lt zl gt lt x2 gt lt y2 gt lt z2 gt lt x3 gt lt y3 gt lt z3 gt select species lt speciesl gt any lt species2 gt any select mass lt m1 gt lt m2 gt select indices lt imin gt lt imax gt gt gt gt gt gt gt select above below plane normal lt a gt lt b gt lt c gt lt d gt gt gt gt gt gt select all working with tags tagdef lt tag gt un tag cylinder along X lt y gt lt z gt lt r gt un tag cylinder along Y lt z gt lt x gt lt r gt un tag cylinder along Z lt x gt lt y gt lt r gt un tag sphere lt x gt lt y gt lt z gt lt r gt un tag box lt x1 gt lt x2 gt lt yl gt lt y2 gt lt zl gt lt z2 gt un tag above below plane normal lt a gt lt b gt lt c gt lt d gt un tag above below plane through lt x1 gt lt yl gt lt z1 gt lt x2 gt lt y2 gt lt z2 gt lt x3 gt lt y3 gt lt z3 gt un tag species lt speciesl gt any lt species2 gt any un tag mass lt ml gt lt m2 gt un tag indices lt imin gt lt imax gt un tag all VVVVVVVVVV VV other operations lump lt cutoff gt lt speciesl gt any lt species2 gt any join lt xyz_filename gt uniq unique lt tolerance gt rename lt speciesl gt any lt species2 gt tag addtag name lt new_name gt namestrip 2009 Jacek Dziedzic jacek dziedzic gmai
9. opposite corners are at x1 y1 z1 and x2 y2 z2 select above plane normal lt a gt lt b gt lt c gt lt d gt Selects atoms lying above a plane given by the plane equation axt by cz d 0 that is atoms whose coordinates satisfy axt by cz d gt 0 are selected Geometry reminder The vector a b c is normal to the plane and d controls the offset of the plane along this vector For instance to select atoms lying above a plane parallel to the Z axis one needs to take c 0 and then choose a b tg where 0 is the angle between the plane of interest and the ZX plane NB Depending of what is desired it may be easier to use select above plane through select below plane normal lt a gt lt b gt lt c gt lt d gt As above only atoms whose coordinates satisfy axt by cz d lt 0 are selected select species lt namel gt lt name2 gt Selects atoms of the species name supplied The names must match exactly The special name any may be used to match every possible name Whereas this is pointless for the select directive this may be used with the tag and untag directives select mass lt ml gt lt m2 gt Selects atoms with the specified masses within an absolute tolerance of 1E 10 Of course only xyze files specify atomic masses select indices lt imin gt lt imax gt Selects atoms with the specified indices numbers that is atoms whose numbers lie within lt imin imax gt Atoms are numbered starting from 0 select all Sel
10. rename the atom to its tag or to use the rename lt name gt addtag directive which will concatenate the tag to the name of the atom Example All atoms within a certain cylinder are renamed by adding to their name Other atoms are unaffected nopbc zap in in xyz untag all tagdef tag cylinder along X 0 0 8 rename any addtag tag all so that all atoms are written out out out xyz 2009 Jacek Dziedzic jacek dziedzic gmail com Gdansk University of Technology Poland other operations gt lump lt cutoff gt lt speciesl gt any lt species2 gt any An advanced operation Classifies the atoms into classes basing on their connectivity For atoms of the given species or for all atoms if any was specified the following procedure is performed The atom with the lowest index is chosen and its mass is set to 1 which will be termed the atom belongs to class 1 Then all the neighbours of this atom that is all atoms no further than cutoff from the atom are also placed into class 1 The procedure is repeated for the newly added atoms that is the neighbours of the neighbours their neighbours and so on are all placed into class 1 As a consequence all atoms which may be reached by starting from the initial seed atom by hopping through other atoms no further than cutoff each time If any atoms remain the one with the lowest index is chosen and it is placed into class 2 then the procedure is repeated for class 2
11. s are not applied nopbc zap in input xyz stretch 111 1 rescaleBBox 1 1 1 1 out output xyz 2009 Jacek Dziedzic jacek dziedzic gmail com Gdansk University of Technology Poland
12. tions When on during every operation all the atoms that are outside the simulation box BBox will be put back inside the box by the employment of periodic boundary conditions nopbc Turns off periodic boundary conditions Atoms remaining outside the simulation box BBox will not be put back inside the box Exactly one of pbc or nopbc is mandatory rotations and translations gt rotate x lt alpha gt Rotates the system about the X axis by an angle alpha expressed in degrees BBox is not altered Rotating about an axis parallel to the X axis is possible by a combination of rotation and translation rotate y lt alpha gt Rotates the system about the Y axis by an angle alpha expressed in degrees BBox is not altered Rotating about an axis parallel to the Y axis is possible by a combination of rotation and translation rotate z lt alpha gt Rotates the system about the Z axis by an angle alpha expressed in degrees BBox is not altered Rotating about an axis parallel to the Z axis is possible by a combination of rotation and translation translate lt x gt lt y gt lt z gt Translates the system all atoms by a vector x y z BBox is not altered center Translates the system all atoms in such a way that the centre of mass is at 0 0 0 NB The current version assumes that all atoms have the same mass BBox is not altered periodic_image lt xx gt lt yy gt lt zz gt Replaces the system all atoms
13. ucture of xyz files is very simple An xyz file describes the a system of N atoms Each atom is described by a row line containing four words the name of the atom its x coordinate its y coordinate and its z coordinate expressed in A For example a gold atom at 8 5 12 35 4 2 may be described as Au 8 5000 12 3500 4 2000 The number of spaces between the words and the decimal precision is not significant here four decimal digits were used Scientific notation where 1 543x10 would be written as 1 543z 04 may also be used Thus the same gold atom could be described with for instance Au 8 5E 00 1 235E 01 4 2E 00 The name of the atom is usually limited to eight characters The xyz file contains N lines each describing one of the N atoms The atoms are usually numbered indexed from 0 to N 1 A two line header is placed at the very front of the file The first line contains N the number of atoms The second line contains a description of the contents of the file and acts like a comment Several utilities assume that the description begins with a fixed phrase the word BBox followed by six numbers The numbers are interpreted as the coordinates of two points that are the opposite corners of the simulation box to which the xyz file pertains For example the following header 4000 BBox 0 0 37 43 0 0 37 43 0 0 37 43 liquid Cu at 7 97 g cm3 tells us that the xyz file contains 4000 atoms of Cu from a liquid
14. xyzxform A utility for the manipulation of xyz files v2 32 C 2005 2009 Jacek Dziedzic User s Manual Synopsis The xyzxform utility is used to manipulate xyz files An xyz file describes the positions of N atoms termed a system By applying the xyzxform utility transformations such as rotations translations scaling selections of subsets of the original system joining two systems and other may be performed The input and output files and the operations to be undertaken are specified in a directive file The xyzxform program is then invoked with the name of the directive file as an argument Consider a simple example a file named test xform containing the following directives A simple directive file nopbc zap in input xyz rotate 0 30 0 out output xyz To execute the operations the xyzxform program is then invoked as follows xyzxform test xform Anything following the character in a directive file up to the end of line is considered a comment and is ignored The first line in the above directive file is an example of a comment The example directive file realizes a rotation of the system read from input xyz by 30 degrees about the Y axis The output is written to output xyz The directives nopbe and zap tell xyzxform that periodic boundary conditions should not be applied and that the output file should be zapped erased before anything is written to it Structure of xyz files The str
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