· contents 5 1.20.16 rhono . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ....

Commandreference

D I SC U S

Version 3.2

Reinhard Neder

Institut fur MineralogieUniversitatWurzburg

Am HublandD-97074Wurzburg

GermanyEmail: [email protected]

ThomasProffen

Departmentfor PhysicsandAstronomyMichiganStateUniversity

EastLansing,MI 48824-1116USA

Email: [email protected]

DocumentcreatedMarch4, 1999

Preface

Disclaimer

TheDISCUS softwaredescribedin thisguideis providedwithoutwarrantyof any kind. No liability is takenfor any lossor damages,director indirect,thatmayresultthroughtheuseof DISCUS. No warrantyis madewith respectto thismanual,or theprogramandfunctionstherein.Therearenowarrantiesthattheprogramsarefreeof error, or that they areconsistentwith any standard,or thatthey will meettherequirementfor aparticularapplication.Theprogramsandthemanualhave beenthoroughlychecked. Nevertheless,it cannot beguaranteedthat themanualis correctandup to datein every detail. This manualandtheDISCUSprogrammaybechangedwithoutnotice.DISCUS is intendedasa public domainprogram.It maybeusedfreeof charge. Any commercialuseis,however, notallowedwithoutpermissionof theauthors.

UsingDISCUS

Publicationof resultstotally or partiallyobtainedusingtheprogramDISCUS shouldstatethatDISCUS wasusedandcontainthefollowing reference:

PROFFEN, TH. & NEDER, R.B. (1997) ”DISCUS, a Programfor Diffuse ScatteringandDefectStructureSimulations”J. Appl. Cryst., 30, 171-175

Acknowledgments

Thelist of structurefactorswasadaptedfrom theprogramLazy-Pulverix writtenby K. Yvon,W. Jeitschko& E. Parthe. The randomnumbergeneratorsandinterpolationsroutinesweretaken from the NumericalRecipesby Press,Flannery, Teukolsky & Vetterling,CambridgeUniversityPress,1989. Theroutinesfortheline editingwastakenfrom theprogramGNUPLOT.

1

Contents

1 DISCUScommands 101.1 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101.2 addf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101.3 append . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111.4 asym . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111.5 chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

1.5.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111.5.2 aver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121.5.3 blen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121.5.4 corr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121.5.5 disp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131.5.6 elem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131.5.7 env . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131.5.8 field . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131.5.9 homo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141.5.10 mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141.5.11 neig . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141.5.12 set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141.5.13 show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171.5.14 trans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

1.6 copy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171.7 d2r . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171.8 data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

1.8.1 title . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181.8.2 space. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181.8.3 lattice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181.8.4 atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181.8.5 keywords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

1.9 diff-four . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221.10 find . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221.11 four . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

1.11.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231.11.2 abs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231.11.3 delf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241.11.4 disp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241.11.5 layer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241.11.6 ll . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241.11.7 lots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241.11.8 lr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241.11.9 na . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

2

CONTENTS 3

1.11.10neut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251.11.11no . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251.11.12ord . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251.11.13run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251.11.14scat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251.11.15set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251.11.16show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251.11.17temp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261.11.18ul . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261.11.19wvle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261.11.20xray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

1.12 functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261.13 ins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271.14 internal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271.15 inverse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

1.15.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271.15.2 abs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281.15.3 file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281.15.4 format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281.15.5 layer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291.15.6 ll . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291.15.7 lr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291.15.8 na . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291.15.9 no . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291.15.10ord . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291.15.11rhoabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291.15.12rholayer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291.15.13rholl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301.15.14rholr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301.15.15rhona . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301.15.16rhono . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301.15.17rhoord . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301.15.18rhoul . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301.15.19run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301.15.20scale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301.15.21set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311.15.22show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311.15.23type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311.15.24ul . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

1.16 kick . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321.17 mc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

1.17.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321.17.2 run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331.17.3 set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331.17.4 show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

1.18 micro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351.18.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351.18.2 ang . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361.18.3 asym . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361.18.4 base . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361.18.5 boun . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361.18.6 ccol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

CONTENTS 4

1.18.7 cele . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371.18.8 chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371.18.9 cont . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371.18.10crea . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381.18.11crow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381.18.12dens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381.18.13dist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381.18.14dlu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381.18.15grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381.18.16init . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391.18.17inse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391.18.18log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391.18.19mrow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391.18.20orie . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391.18.21place . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391.18.22radi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401.18.23remo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401.18.24rbase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401.18.25run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401.18.26separation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401.18.27set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401.18.28shift . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411.18.29show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411.18.30sigm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411.18.31six . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411.18.32siy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411.18.33siz . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

1.19 output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411.19.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 421.19.2 format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 421.19.3 input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 431.19.4 outfile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 431.19.5 run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 431.19.6 show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 431.19.7 threshold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 431.19.8 value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

1.20 patterson . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 441.20.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 441.20.2 abs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451.20.3 file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451.20.4 format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451.20.5 layer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461.20.6 ll . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461.20.7 lr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461.20.8 na . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461.20.9 no . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461.20.10ord . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461.20.11rhoabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461.20.12rholayer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461.20.13rholl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461.20.14rholr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471.20.15rhona . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

CONTENTS 5

1.20.16rhono . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471.20.17rhoord . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471.20.18rhoul . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471.20.19run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471.20.20scale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471.20.21set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471.20.22show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 481.20.23type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 481.20.24ul . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

1.21 pdf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 491.21.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 491.21.2 calc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 491.21.3 data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 491.21.4 i/jdese . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 501.21.5 i/jsele . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 501.21.6 run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 501.21.7 save . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 501.21.8 set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 501.21.9 show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

1.22 plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 511.22.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 521.22.2 absc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 521.22.3 asym . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 521.22.4 chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 521.22.5 col . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 531.22.6 des . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 531.22.7 ext . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 531.22.8 hkl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 531.22.9 mdes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 541.22.10mole . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 541.22.11msel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 541.22.12ordi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 541.22.13outfile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 541.22.14prog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 541.22.15run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 551.22.16sel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 551.22.17set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 551.22.18show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 561.22.19thick . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 561.22.20uvw . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 561.22.21type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 561.22.22vector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

1.23 powder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 571.23.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 571.23.2 neut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 571.23.3 run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 571.23.4 show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 571.23.5 set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 571.23.6 xray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

1.24 project . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 591.25 purge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 591.26 r2d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

CONTENTS 6

1.27 read . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 591.27.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 601.27.2 cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 601.27.3 free . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 601.27.4 stru . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

1.28 remove . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 601.29 replace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 611.30 rmc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

1.30.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 611.30.2 data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 611.30.3 dese . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 621.30.4 msel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 621.30.5 mdes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 621.30.6 rese . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 621.30.7 run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 631.30.8 save . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 631.30.9 sele . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 631.30.10set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 641.30.11show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

1.31 save . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 681.31.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 681.31.2 asym . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 681.31.3 chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 681.31.4 des . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 691.31.5 file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 691.31.6 format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 691.31.7 incl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 691.31.8 omit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 701.31.9 run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 701.31.10sel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 701.31.11show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 711.31.12write . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

1.32 seed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 711.33 show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

1.33.1 asym . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 711.33.2 atom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 721.33.3 chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 721.33.4 cdim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 721.33.5 error . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 721.33.6 molecule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 721.33.7 result . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 721.33.8 scat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

1.34 stack . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 731.34.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 731.34.2 aver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 741.34.3 ccol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 741.34.4 cele . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 741.34.5 crea . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 741.34.6 crow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 741.34.7 four . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 741.34.8 layer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 751.34.9 modulus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

CONTENTS 7

1.34.10number . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 751.34.11random . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 751.34.12rese . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 761.34.13rotate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 761.34.14run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 771.34.15set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 771.34.16show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 771.34.17sigma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 771.34.18trans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

1.35 switch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 781.36 symm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

1.36.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 781.36.2 angle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 791.36.3 asym . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 791.36.4 calc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 791.36.5 chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 791.36.6 des . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 791.36.7 hkl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 801.36.8 incl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 801.36.9 mdes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 801.36.10mincl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 801.36.11mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 801.36.12msel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 811.36.13origin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 811.36.14power . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 811.36.15run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 821.36.16sel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 821.36.17show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 821.36.18trans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 831.36.19type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 831.36.20uvw . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

1.37 transform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 831.37.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 831.37.2 anew . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 841.37.3 aold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 841.37.4 asnew . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 841.37.5 asold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 851.37.6 asym . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 851.37.7 bnew . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 851.37.8 bold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 851.37.9 bsnew . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 851.37.10bsold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 851.37.11c2new . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 851.37.12c2old . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 861.37.13csnew . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 861.37.14csold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 861.37.15chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 861.37.16cnew . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 861.37.17cold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 861.37.18des . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 871.37.19incl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 871.37.20onew . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

CONTENTS 8

1.37.21oold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 871.37.22run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 871.37.23sel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 871.37.24show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 881.37.25xnew . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 881.37.26xold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 881.37.27ynew . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 881.37.28yold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 891.37.29znew . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 891.37.30zold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

1.38 ther . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 891.39 variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 891.40 vprod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 911.41 waves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

1.41.1 commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 921.41.2 acco . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 921.41.3 amp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 921.41.4 asym . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 921.41.5 chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 931.41.6 dens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 931.41.7 des . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 931.41.8 func . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 931.41.9 len . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 941.41.10long . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 941.41.11mdes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 941.41.12msel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 941.41.13mrep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 941.41.14rot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 951.41.15opti . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 951.41.16osci . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 951.41.17phase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 951.41.18phigh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 951.41.19plow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 951.41.20repl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 951.41.21run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 961.41.22sel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 961.41.23shift . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 961.41.24show . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 971.41.25tran . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 971.41.26vect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

1.42 bugs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 971.43 errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

1.43.1 appl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 981.43.2 chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1041.43.3 four . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1061.43.4 mc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1061.43.5 pdf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1061.43.6 rmc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

1.44 spacegroups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1081.45 wavelength . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1111.46 atomnames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111

CONTENTS 9

2 Generalcommands 1122.1 # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1122.2 @ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1122.3 = . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1132.4 input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1132.5 break . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1132.6 continue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1132.7 do . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1142.8 echo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1142.9 eval . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1142.10 exit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1142.11 expressions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1142.12 filenames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1152.13 functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1152.14 help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1162.15 if . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1162.16 learn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1172.17 lend . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1172.18 set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1172.19 stop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1182.20 system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1182.21 wait . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1182.22 errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118

2.22.1 comm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1192.22.2 fort . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1192.22.3 i/o . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1212.22.4 macro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1222.22.5 math . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

Getting started

Theprogramis invokedby typing ’discus’at theoperatingsystemor at theshellprompt.Theprogramusesa commandlanguageto interactwith theuser. Thecommand’exit’ or a CTRL Z terminatestheprogram.More informationaboutthesyntax,expressionsetc. of thecommandlanguagecanbeobtainedby typing’command’at thehelpprompt.Help on theprogramis obtainedby typing ”help” or ”help � command� ” to getspecifichelpon thecom-mand � command� . The commandmay be abbreviated. If the abbreviation is not unique,only the firsthelptopic thatmatchesthecommandis listed.Thefirst line of thehelptext givesthesyntaxof thecommandthat is explainedin thefollowing lines. Fora few commandsthesyntaxline is repeatedfor differentsetof possibleparameters.Furtherhelptopicsare:

Chapter 1

DISCUScommands

1.1 Summaryaddf ! Add two files togetherappend ! Append atom to model crystalasym ! Show the contents of the asymmetric unitchem ! Enter CHEMlevel (see chem level for details)copy ! Copy atom or molecule within the crystald2r ! Transform vector from real to reciprocal spacediff-four ! Enter difference Fourier transform levelfind ! Find atoms around a given pointfour ! Enter Fourier transform levelins ! Insert atom or molecule into the crystalinverse ! Enter inverse Fourier transform levelkick ! Insert atom/molecule and possibly remove old atom/mole.mc ! Enter Monte-Carlo simulations levelmicro ! Enter microdomain leveloutput ! Enter output level (save results)patterson ! Enter Patterson levelpdf ! Enter Pair Distribution Function levelplot ! Enter plot level (export crystal for plotting)powder ! Enter powder diffraction levelproject ! Calculate projections in real and reciprocal spacepurge ! Remove VIODs from crystal (DO NOT USE !)r2d ! Transform vector from reciprocal to real spaceread ! Read structure or unit cell from fileremove ! Remove atom or molecule from crystalreplace ! Replace atom(s) or molecule(s) with other typermc ! Enter Reverse-Monte-Carlo levelsave ! Save structureseed ! Set seed for random number generatorshow ! Show various informationstack ! Enter stacking fault levelswitch ! Swap two atoms or molecules within crystalsymm ! Enter symmetry transformation leveltransform ! Enter unit cell transformations leveltherm ! Displace atoms or molecules according to Bvprod ! Calculate vector product in real or reciprocal spacewaves ! Enter modulations level

1.2 addf

addf � resultfile� , � inputfile1 � , � scale� , � inputfile2 � [, � type � ]

Adds two files. The intensityof thesecondinputfile is multiplied by thescaleandaddedto the intensity

10

CHAPTER1. DISCUSCOMMANDS 11

readfrom inputfile 1. Optionallythetypeof the input files canbegiven. It defaultsto ”ni” for files in thestandardformat. typeshouldbe”gnu” for gnuplotfilesand”1d” for one-dimensionalfiles.For standardfiles, the respective headersarecomparedfor consistency. for gnuplotandonedimensionalfiles theh,k,l arecomparedline by line. If anerror is detected,theprocedurestops.Thusit is possiblefortheresultfiles to beincomplete.They arenotdeletedto allow comparisonwith theinputfiles.Any oneof thetwo input filesmaybeidenticalto theresultfile, while thetwo inputfiles mustbedifferentfiles.

1.3 append

appe � name� , � x � , � y � , � z � , � t � , � na � , � ne� , � delx � [, � dely � [, � delz� ]]appe � name� , � x � , � y � , � z � , � t � , � na � , � ne� , - � bondlength�Conditionallyinsertsanatomof type � name� at theposition � x,y,z� in crystalspace.Thetemperaturecoefficient mustbegiven. ’appe’ checkstheposition � x � , � y � , � z � with respectto all atomsnumbered� na� to � ne� . Thenew atomis NOT inserted,if any of theseatomsis within theblock � x � +- � delx� ;� y � +- � dely� ; � z � +- � delz� . If � dely� and/or � delz� arenot given,thenthey default to thevalueof thelast � del.� givenon this ’appe’command.Note,thatthe � del.� arein fractionalcoordinates,NOT in Angstrom.In thealternativeform, theeight’sparameteris interpretedasabonddistance.To distinguishthetwo forms,the bondlengthmustbe lessthanzero. The new atomis inserted,if no atomis lessthan � bondlength�Angstromfrom theposition � x � , � y � , � z � .If thecrystalis empty, i.e. n[1]=0, the ’append’commandignorestheparameters� na� , � ne� , � delx�[, � dely� [, � delz� ]]. Sincethereis no atomwithin thecrystal,thereis no needfor a comparison.Effec-tively, the’append’commandactsjustasanequivalent’insert’ command.

1.4 asym

asym

Shows thecontentof theasymmetricunit. Thenamesof thoseatoms,a numberthat is usedasindex forits scatteringtype, their positionandtemperaturecoefficient arelisted. The numberthat is listed, is thenumberthatrefersto thescatteringcurveof thatatom.It is containedin thevariablem[ � index � ]. If acellwasread,all atomsareconsideredto bedifferent,evenif they arechemicallyidenticalandhave thesametemperaturecoefficient. If a wholestructurewasread,all atomsthatarein theunit cell 0 � = xyz � 1, arechemicallyuniqueandhavea differenttemperaturecoefficientareincludedin theasymmetricunit.

1.5 chem

chem

Entersthe’chem’ sublevel. Hereall kind of statisticsaboutthemodelcrystalcanbeobtainedlike relativeamountof elements,distributionof bond-lengths,...NOTE: TheMC andCHEM sublevel sharesomevariableswhichdefineneighboursetc.andsettingsmadein this sublevel might bealteredwhenusingtheothersublevel. It is alwayssave to repeatsettingswhenenteringthissublevel if bothlevelsareused.Furtherinformationis availablefor commands

1.5.1 commands

Valid commandsat thissublevel are:


@ ! Executes a macro (see main help level)= ! Algebra (see main help level)aver ! Calculates average structure and occupanciesblen ! Calculates distribution of bond lengthscontinue! Continue a stopped macro (see main help level)corr ! Calculates neighbour frequencies/correlationsdisp ! Calculated average distances for given neighboursecho ! Echos a string (see main help level)elem ! Show rel. abundances of elements in crystalenv ! Find neighbours around atom/site or positioneval ! Evaluate an expression (see main help level)exit ! Terminates the chem sublevel.field ! Calculates a correlation fieldhelp ! Gives on-line help for ’chem’ (see main help level)homo ! Calculate concentration/correlation distributionsmode ! Toggles between atoms and molecules modeneig ! Show neighbours for given neighbour definitionset ! Change settings of ’chem’ parametersshow ! Show current parametersstop ! Stops execution of a macro (see main help level)system ! Executes operating system command (see main help)trans ! Transforms between atomindex and unitcell/sitewait ! Waits for user input (see main help level)

1.5.2 aver

aver

Thiscommandallowsto calculatetheaveragestructureof thecurrentmodelcrystal.Theaverageposition,thestandarddeviation andtheoccupancy of every sitewithin theunit cell is given. Theaveragepositionsandsigmasarestoredin thevariablearray’res’.

Warning: This command works only correct, if the structure is givenin the order created by the ’read cell’ command. Appendedatoms are simply ignored ! However, using the PURGEcommandis not recommended when using this commands !!!!

1.5.3 blen

blen � ”all” �� name�� number � ,� ”all” �� name�� number � , [ � filename ]

Thiscommandcalculatesthebondlengthdistributionbetweentheselectedatoms(by � name , � numberor ”all”). Thehistogramis saved to thefile � filename . Thenumberof pointsof thehistogramis givenby ’setbin, � ip ’. Thecalculationmodecanbeswitchedbetween”quick” and”exact”. Themode”exact”calculatesthebondlengthfor EVERY atompairwithin thecrystalwhereasthemode”quick” only looksatneighbouringunit cells. BUT in the”quick” modeerrorscanoccurdueto usingthe”purge” commandorappendingatomsto thestructure.Allowedbondlengthrange,calculationmodeandsigmasfor a neighbourmatchingcriteriaaregivenwith the’set’ command.

1.5.4 corr

corr ”occ”, �� name�� number � , �� name�� number � corr ”disp”, �� name�� number �� ”all” , �� name�� number �� ”a ll” Thiscommandstartsthecalculationof occupational(”occ”) or displacement(”dis”) correlationswithin thecrystal.Theocc.correlationsrequirethenameor numberof two DIFFERENTatomtypesto begiven.Thedisplacementcorrelationcalculationsrequiresatomnamesor ”all” to useall atomtypes. The neighbourdeterminationparametersare set via the commands- ’set neig’ and - ’set vec’. The displacement

directionsusedto calculatedisp. correlationsaresetusingthe - � ’setdir’ command.Correlationvaluescanbe:

correlation > 0 : preferred same neighbours / displacementcorrelation = 0 : random distributioncorrelation < 0 : preferred different neighbours / displacements

Thecorrelationsarecalculatedaccordingto thefollowing equations:

occupational displacement---------------------------------------------------- ------- -------

P(i,j) - theta**2 <x(i)x(j)>c(i,j) = ----------------- c(i,j) = ------------------------

theta * (1-theta) sqrt(<x(i)**2><x(j)**2>)

P(i,j): pair prob. sites i,j x(i): displacement from average pos.theta : concentration <> : average

The resultingcorrelationsarestoredin the variablesres[� i � ] with � i � beingthe numberof the corre-spondingdefinitionfor neighbouringdistancesor vectors.Thevariableres[0]containsasusualthenumberof variablesreturnedby thecommand.

1.5.5 disp

disp �� name�� number �� ”all” � , �� name�� number �� ”a ll” �This commandcalculatesthe averagedistancesandsigmasfor the specifiedpairsof atomtypesfor thegivenneighbours.Theneighbourdeterminationparametersaresetvia thecommands- � ’setneig’ and- �’setvec’.

1.5.6 elem

elem[ � ”on” � ”off ” � ]

Displaysinformationaboutelementsin themodelcrystallike relative abundancesof theelements.’void’standsfor a vacancy. Theresults(range0..1ratherthan%) arestoredin thevariableres[� i � ], with � i �thenumberof theatomtyp.Theoptionalparameter”on” or ”off” controlsif screenoutputis produced.

1.5.7 env

env ”atom”, � ia � , � radius �env ”site”, � nx � , � ny � , � nz � , � site� , � radius �env ”pos”, � x � , � y � , � z � , � radius �Thecommand’env’ allowstheuserto print outall atomswithin adistanceof � radius� A aroundthegivenpositions. This positioncanbe givenby an atomindex � ia � (”atom”), a unit cell � nx � , � ny � , � nz�andsite � site� (”site”) or asabsoluteposition � x � , � y � , � z � in lattice units (”pos”). The neighbourdeterminationmodeandpossibleperiodicboundariescanbedefinedusingthecommand- � ’setmode’.

1.5.8 field

field � ”occ” � ”disp” � , � a1� , � a2� , � file � , � xmin � , � xmax � [, � ymin � , � ymax � ]

This commandallows the calculationof a correlationfield. The first parameterdeterminesthe useof’occupational’or ’displacement’correlations.Thenext two parametersspecifytheatomsto beused.Theycan be specifiedas numberor name(- � corr). The next parameteris the name � file � for the output


graphicsfile that canbe readby the plot programKUPLOT. The last parametersdefinethe rangein x-andy-direction.If no y-valuesaregiven,only a 1-dimensionalfield is calculated.Thevaluesof � xmin � ,� xmax� , � ymin � and � ymax� aremultiplesof theneighbourvectorsdefined.Thefollowing examplewill computethecorrelationfield along � 100� up to the20thneighbour:

discus/chem> set vec,1,1, 1,0,0discus/chem> set neig,vec,1discus/chem> field zr,void,corr.xy,0,20

1.5.9 homo

homo”occ”, � atom � , � file �homo”cor”, � ”occ” � ”dis” , � at1 � , � at2 � , � file �This commandcomputesthe concentrationor correlationdistribution within the crystal. The samplingvolumesaresetusingthe- � ’setlots’ command.Thesizeof theresultinghistogramcanbealteredusingthecommand- � ’setbin’. Thefollowing two optionsareavailable:”occ”: Herethe concentrationdistribution of theatom � atom� is computed.The resultinghistogramiswritten to thefile named� file � .”cor”: Herethecorrelationdistribution for all definedneighboursis computed.Thethird parameterdeter-minesweatheroccupationalor displacementcorrelationsarecomputed.Thenext two parametersspecifiedtheatomtypesandthelastparameterthefilenamefor thehistogramoutput.Notethat*all* definedneigh-bourswill bewritten to thefile. To geta specificcorrelationdistributionuseasingleneighbourdefinition.

1.5.10 mode

mode[ � ”atom” � ”mole” ]

This commanddetermineswhetherCHEM commandsoperateon atomsor on molecules.Notethatwhenworkingwith moleculestheatomnamesor numbersin thecommanddescriptionshaveto bereplacedwithmoleculetypes.Notethatnotall commandsareavailablein moleculemode(e.g.’aver’, ’blen’).

1.5.11 neig

neig � index � , � ic �This commanddeterminesand displaysthe neighbouringatomsor moleculesarounda given atom ormoleculegivenby � index � for theneighbourdefinition � ic � (- � ’setneig’).Theresultingatomor moleculeindicesof thedeterminedneighboursarestoredin thevariableres[i] wherei is thenumberof theneighbour. Thevariableres[0]containsthenumberof foundneighbours.

1.5.12 set

set � subcommand� ,...

This commandsets various parameterswithin the ’chem’ section of the DISCUS program. Valid� subcommands� are:

commands

"blen" : sets range for bond length calculations"bin" : sets number of points for bond length histogram"cryst" : sets crystal dimensions (if wrong determined by read stru)"lots" : sets crystal sampling volumes for ’homo’"mode" : sets calculation mode ("quick"/"exact")"neig" : defines how correlations are calculated"outfile" : redirects screen output to a file"vec" : defines correlation vectors


blen

set”blen”, ! min " , ! max "This commandsetsthe range ! min " to ! max" of the bond-lengthto be calculatedandbinnedto thehistogram.

bin

set”bin”, ! number "Thiscommandsetsthenumberof pointsfor thehistogramscreatedby ’chem’.

cryst

set”cryst”, ! nx " , ! ny " , ! nz " , ! natoms"A bug in the currentversionof DISCUSsometimescauseswrong crystal-dimensions.This commandallows to rewrite thevaluesfor thecrystal-dimension! nx " , ! ny " , ! nz" andnumberof atomsin a unitcell ! natoms" .

lots

lots ”off ”lots # ”box” $ ”ellipsoid” % , ! lx " , ! ly " , ! lz " , ! n " , # ” yes” $ ”no” % ,[ ! fname" ]

This commandallows thedefinitionof ’smallcrystalvolumes’to beusedto checkthehomogeneityof thecrystal(- " ’homo’). For detailsaboutthecommandandits parametersseethehelpfile entryfor - " ’fourlots’.

mode

set”mode”, # ”quick” $ ”exact” % [, # ”period” $ ”normal” % ]This commandswitchesthecalculationmodebetween”quick” and”exact”. In the”quick” modeonly theneighbouringunit cellsarounda certainatomaretakeninto account.If thecommand’purge’ is performedor a structureis readwheretheatomsarenot listedin theDISCUSorderthismodemight fail, becausethecalculationof the index of anatomin a neighouringunit cell canbewrong. In this casethe”exact” modeshouldbeusedwhich takenALL otheratomsinto account.Thesecondoptionalparameterdeterminesis periodicboundariesareused.Notethatthisonly worksif the”quick” modeis selectedandNO extraatomswereaddedto thecrystal.Note that this settingdoesnot affect thecalculationof correlationsdefinedby vectorsusingthe ’setvec’command.

neig

set”neig”, ! subcommand"Thiscommanddetermineshow DISCUScalculatesthecorrelationvalueusingthecommand’corr’. ThesesettingsmightbeoverwrittenwhenusingtheMC sublevel. Thefollowing subcommandsarevalid:

commands

"add" : Adds current definition to list of correlations"dis" : Defines neighbours via distance criteria"dir" : Defines directions for displacement correlation calculations"rese" : Resets list of defined neighbours"vec" : Defines neighbours via given vectors


add set”neig”, ”add”

”Add” addsthecurrentneighbourdefinitionto the list of definitionsexecutedlaterby the- & ’corr’ com-mand.Use’show’ to geta list of definedcorrelationvectors/distances.DISCUSsavesactuallya copy sothatno ”add” is neededafterthelastdefinitionis entered.

dis set”neig”, ”dis”, ' u & , ' v & , ' w & , ' fsig & [, ' wsig& ] [, ( ”sym” ) ”nosym” * ]”Dis” causesDISCUSto determinethe neighboursusedfor the calculationof the correlationsusingthegiven distanceanddirection(optional). Thoseneighbourshaving a distancecorrespondingto the vector' u & , ' v & , ' w & givenin unit cell unitsaretakeninto accountfor thecalculation.Theparameter' fsig &setsthealloweddifferenceof theobserveddistanceto thetheoreticalvalue(+- ' fsig & /2). Thenext optionalparametergivesthealloweddeviationfrom theneighbouringdirectiongivenby ' u & , ' v & , ' w & . Thelastparameterdeterminesif symmetricallyequivalentdirectionsto ' u & , ' v & , ' w & shouldbeusedaswell. Ifthisparameteris omittedALL neighbourswith thecorrectdistancearevalid.

dir set”neig”, ”dir”, ' x1 & , ' y1 & , ' z1& [, ' x2 & , ' y2 & , ' z2& ]set”neig”, ”dir”, ”all”

Thiscommandsetsthedisplacementdirectionsto beusedfor thecalculationof displacementcorrelations.Theparameter”all” will calculatethedisplacementcorrelationsfor displacementsin all directions,i.e. theresultingcorrelationgivesthe correlationof displacementsof two neighbouringatomsregardlessof thedirectionof thedisplacementitself. Onecanalsogivespecificdirections,e.g.if onewantsto determinethecorrelationsof displacementsin z-directionof sitei with theonesin x directionof sitej onewouldenterthecommand’setdir,0,0,1,1,0,0’.Notethattheneighbouringvectorbetweensitesi andj is setby thecommand’setneig’. If ' x2 & , ' y2 & , ' z2& arenotgiventheir valuesaresetto thoseof ' x1 & , ' y1 & , ' z1& .

rese set”neig”, ”r ese”

”Rese”resetsthelist of correlationvector/distancesdefinitions.

vec set”neig”, ”v ec”, ' iv1 & [, ' iv2 & ,..]

”Vec” resultsin DISCUSusingcorrelationvectors' iv & to beusedfor thecalculation.Theparametersarethenumbers' iv & of thecorrelationvectorsdefinedwith ’setvec’.

outfile

set”outfile”, ( ”on” ) ”off ” * ,[ ' filename& ]

Thiscommandallows to redirectthescreenoutputof theresultsof thecommandsin the’chem’ sectiontothefile ' filename& . If nofilenameis given,thedefault ”chem.log” is used.

vec

set”v ec”, ' iv & , ' is1& , ' is2& , ' dx & , ' dy & , ' dz &This commandis usedto definecorrelationvectorsthatmight beusedto calculatecorrelationswithin thecrystal(- & ’setneig’). Thefirst parameter' iv & is thenumberof thevectorto bedefined.Thevariables' is1& and ' is2& givethenumberof thecrystalsiteateachendof thevector. Thevaluesof ' dx & , ' dy &and ' dz& definethevectorin unit cells. Correlationvectorswithin oneunit cell have ' dx & , ' dy & and' dz& settozero.If youwanttodefinecorrelationvectorscrossingtheunit cell boundariesset ' dx & , ' dy &and ' dy & accordingly.


1.5.13 show

show

Thiscommandlists thecurrentsettingsandcorrelationvectordefinitionson thescreen.

1.5.14 trans

trans + atomindex, ortrans + x , , + y , , + z , , + site,This commandallows to transformbetweena givenindex of thestoragearray + atomindex , andthecor-respondingunitcell + x , , + y , , + z , andsite + site, . Theparameternotgivenis calculated...

1.6 copy

copy + s, , + n , , + x , , + y , , + z ,Copiesanatom. If + s, is ”a” theatomnumber + n , is copiedto absolutepositions + x , , + y , , + z , incrystalspace,if + s, is ”r”, a relative motioncopiestheatomnumber + n , to thesumof presentpositionandvector + x , , + y , , + z , .

1.7 d2r

d2r + u , , + v , , + w ,Thiscommandtransformsdirectspacevector + uvw , into its correspondingreciprocalspacecoordinates.See”r2d” for thereversetransformation.Theresultingvectoris storedin ”res[1]”, ”res[2]”, ”res[3]”.

1.8 data

Format of unit cell data file

The unit cell datafile contains3 initial lines andoneline per atomin the unit cell. All lines arein freeformat,beginningin theleft mostcolumn.

Line 1: Title up to 80 charactersline 2: Space group symbol [,origin choice number]line 3: Lattice constants a,b,c,alpha,beta,gamma

andfor eachatoma line with:

Name(4 characters) x y z isotropic B

Emptylinesbein thecell datafile will beignored.Example

Single atom structure of NAPm-3m

5.0 5.0 5.0 90. 90. 90.NA1+ 0.0 0.0 0.0 0.1


!!!!!!!!!!!!!!!!!!! !!! !!! !! !!! !!! !!! !!! !! !!! !!! !!! !!! !!! !! !!! !!! !!! !!! !!!! NEW FORMAT OF DATA FILE, STARTING IN DISCUS-3.10!!!!!!!!!!!!!!!!!!!!! !!! !!! !! !!! !!! !!! !!! !! !!! !!! !!! !!! !!! !! !!! !!! !!! !!! !!

Don’t worry, theold datafile formatis still supported!The new format adoptsa key word controlledstyle of the datafile. Exceptfor the lines containingtheatoms,eachline now containsa keyword in thefirst few characters,followedby theparametersneededforthis keyword. Thefirst line MUST containthekeyword ”title”, thesequenceof theotherkeywordsis notrelevant.ThelastkeywordMUST be”atoms”whichstartsthelist of atoms.Youmayincludecommentariesor emptylinesanywherebetweenthe”title” and”atoms”keyword.Thekeywords”title”, ”spcgr”, ”cell” and”atoms”arerequired,all otherkeywordsareoptional.Example

title Single atom structure of NAspcgr Pm-3msymm 1.00,0.00,0.00,0.123, 0.00,1.0,0.00,0.00, 0.00,0.00,1.00,-0.567cell 5.0,5.0,5.0,90.,90.,90.atomsNA1+ 0.0 0.0 0.0 0.1

Furtherhelptopicsare:

1.8.1 title

Thetitle canbeany characterstringup to 80characterslong

1.8.2 space

Thespacegroupsymbolis usedto generateall atomswithin theunit cell. ThesymbolsusedshouldbetheHermann-Mauguinsymbolsusedin Int. TablesVol.A. A centerof inversionshouldbe givenas”-” signimmediatelyprecedingtheaxis.Latticetypesneedto begivenascapitalcharacters,mirror planesassmallcharacters.Monocliniccell choices2,3or uniquec-axiswill beassumedif thecorrespondingnonstandardHermann-Mauguinsymbolis used.Origin choice2 is indicatedby settingtheoptionalsecondparameterto ”2”.Thelatticeconstantsareusedto distinguishbetweenrhombohedralandhexagonalsettings.Thespacegroupsymbolis checkedfor contradictionswith the latticeconstants.In caseof error, theunitcell is not read.

1.8.3 lattice

Thelatticeconstantsarereadin freeformat - ab c alphabetagamma. All six constantsmustbegiven.Thespacegroupsymbolis checkedfor contradictionswith the latticeconstants.In caseof error, theunitcell is not read.

1.8.4 atoms

If a unit cell is read,only thoseatomsin theasymmetricunit shouldbelisted.For eachof theatomsa linemustbegivenwith the nameof the atom,the fractionalcoordinatesandthe isotropicthermalcoefficientB. Thename(in capitalcharacters)mustbe leftboundin thefirst four columns,thenumericalvaluescanbein freeformat. Optionallychargedatomscanbesymbolizedby e.g. ”NA1+”. Seethehelpentry’atomnames’for a completelist of atomsfor whichscatteringcurvesaresupplied.Emptylinesin thefile areignored.


1.8.5 keywords

Thekeywordcontrolleddatafile will eventuallyreplacethedataformatusedup to version3.0Youmayincludecommentariesor emptylinesanywherebetweenthe”title” and”atoms”keyword.Furtherhelptopicsare:

#

# / comment0You canprovide commandsfor thedatafile by including linesthatstartwith a ”#”. Thecontentof theselinesis ignored.

title

title string

Thestringusedastitle canbeany characterstringup to 80characterslong

spcgrp

spcgrsymbol [,”2”]

The”spcgr” keyworddefinesthespacegroupof thecrystal.Thespacegroupis usedto generateall atomswithin theunit cell. ThesymbolsusedshouldbetheHermann-Mauguinsymbolsusedin Int. TablesVol.A.A centerof inversionshouldbegivenas”-” signimmediatelyprecedingtheaxis. Latticetypesneedto begivenascapitalcharacters,mirror planesassmallcharacters.Monocliniccell choices2,3or uniquec-axiswill beassumedif thecorrespondingnonstandardHermann-Mauguinsymbolis used.Origin choice2 is indicatedby settingtheoptionalsecondparameterto ”2”.Thelatticeconstantsareusedto distinguishbetweenrhombohedralandhexagonalsettings.Thespacegroupsymbolis checkedfor contradictionswith the latticeconstants.In caseof error, theunitcell is not read.

generator

generatorg11,g12,g13,g14,g21,g22,g23,g24,g31,g32,g33,g34

Youcandefineadditionalgeneratorsthroughtheoptional”generator”keyword. Thesegeneratorsactiden-tical to thegeneratorsdefinedthroughthespacegroupsymbol.All previouslygeneratedcopiesof theatomin theasymmetricunit arecopiedby this generator, andwill in turnbecopiedby any generatorsfollowinglater.Sincetheseadditionalgeneratorsareappliedafterthespacegroupgenerators,youcanusethesegeneratorsto createnon-standardgroupsor to createa setof symmetriesthatdoesnot from agroup.Thegeneratorformsthematrixalgebra:( g11g12g13) ( x ) ( g14)( g21g22g23) * ( y ) + ( g24)( g31g32g33) ( z ) ( g34)Thegenerators:

gene 1,0,0,0.5, 0,1,0,0.5, 0,0,1,0.0gene 1,0,0,0.5, 0,1,0,0.0, 0,0,1,0.5

for examplewouldcreatethefollowing copiesof anatomat0,0,0:

0 ,0 ,00.5,0.5,0.00.5,0.0,0.50.0,0.5,0.5


symmetry

symmetry s11,s12,s13,s14,s21,s22,s23,s24,s31,s32,s33,s34

Youcandefineadditionalsymmetryoperationsthroughtheoptional”symmetry”keyword.Thesesymmetryoperationsactdifferentthanthegeneratorsdefinedthroughthespacegroupsymbolor listedasadditionalgenerators.The symmetryoperationscopy only thoseatomscreatedby the generators.The symmetryoperationsdonotactoncopiesof theatomscreatedby previoussymmetryoperations.Sincetheseadditionalsymmetryoperationsareappliedafterthespacegroupgenerators,youcanusethesesymmetryoperationsto createnon-standardgroupsor to createa setof symmetriesthat doesnot from agroup.Thesymmetryoperationformsthematrixalgebra:( s11s12s13) ( x ) ( s14)( s21s22s23) * ( y ) + ( s24)( s31s32s33) ( z ) ( s34)Thesymmetryoperations:

symm 1,0,0,0.5, 0,1,0,0.5, 0,0,1,0.0symm 1,0,0,0.5, 0,1,0,0.0, 0,0,1,0.5

for examplewouldcreatethefollowing copiesof anatomat0,0,0:

0 ,0 ,00.5,0.5,0.00.5,0.0,0.5

cell

cell a,b,c,alpha,beta,gamma

Youcanspecifythelatticeconstantseitherin freeformat 1 ab c alphabetagamma2 or aslist of parametersseparatedby ”,” a,b,c,alpha,beta,gamma.In thelattercasetheparametersareevaluatedandyoumayincludearithmeticexpression.All six constantsmustbegiven.Thespacegroupsymbolis checkedfor contradictionswith the latticeconstants.In caseof error, theunitcell is not read.

ncells

ncellsnx, ny, nz, ncatoms

This commandtells DISCUShow largethecrystalis in termsof unit cellsalongthex,y andz axis. Thisis useful,if you have storedthecrystalcreatedby a previoussimulationandwantto continuework on thiscrystal. In orderfor fastreferencesbetweenatomnumberandthe locationof its correspondingunit cell,DISCUSmustnow how many unit cellswerecreatedby theoriginal== 2 ’read/cell’command.1 ncatoms2is thenumberof atomsin eachunit cell. Youcandeterminethisnumberby typingthecommand”evaln[3]”.If you savedthestructure,usingthekeyword controlledformat,seehelpon the’save’ menu,you cantellDISCUSto save thenumberof unit cellsandnumberof atomsperunit cell valuesfor you.

atoms

atoms

This is thelastkeyword. Now theatomnamesareread,startingin thenext line.If a unit cell is read,only thoseatomsin theasymmetricunit shouldbelisted.For eachof theatomsa linemustbegivenwith the nameof the atom,the fractionalcoordinatesandthe isotropicthermalcoefficientB. Thename(in capitalcharacters)mustbe leftboundin thefirst four columns,thenumericalvaluescanbein freeformat. Optionallychargedatomscanbesymbolizedby e.g. ”NA1+”. Seethehelpentry’atomnames’for a completelist of atomsfor whichscatteringcurvesaresupplied.Emptylinesin thefile areignored.


molecule

molecule

Thiskeywordis allowedanywherebetweentheatomsof theunit cell file. It marksthebeginningof agroupof atomsthataregroupedto form amolecule.

moleculeend

moleculeend

Theparameter”end” signalstheendof a molecule.All atomsstill listed in theunit cell file aretreatedasindividualatoms.

moleculegenerator,g11,g12,g13,g14, g21,g22,g23,g24, g31,g32,g33,g34

moleculegenerator,g11,g12,g13,g14,g21,g22,g23,g24,g31,g32,g33,g34

This parametersignalsthe internal symmetryof the molecule. The generator(s)are internal symmetryoperationsof themolecule.DISCUScomparesthelistsof atomscreatedby thespacegroupandby themoleculegenerator(s).Identicalsectionsarelinkedto onemolecule.Thegeneratorformsthematrixalgebra:( g11g12g13) ( x ) ( g14)( g21g22g23) * ( y ) + ( g24)( g31g32g33) ( z ) ( g34)Thegenerators:

mole gene, -1,0,0,0.0, 0, 1,0,0.0, 0,0,1,0.0mole gene, 1,0,0,0.0, 0,-1,0,0.0, 0,0,1,0.0

for examplewould imply thesymmetrymm2at0,0,0for themolecule.Atomscreatedby othersymmetryoperations(likelatticecentering...)will form anew moleculeof thesametype.Thegenerator(s)of themoleculesymmetryshouldbethegeneratorsthatcreatethesitesymmetry. Seethesectiononsitesymmetryin theInternationalTablesfor furtherdetails.Thefirst atomof any moleculethat lies on a symmetryelementof thespacegroupmustbe locatedat thepoint of highestsymmetryof the molecule. If the structuredoesnot have an atomat this site you mustincludea ”void” on thissite.Thiscouldbethecase.e.g.if youhaveanemptytriangleona threefoldaxis.

moleculesymmetry, s11,s12,s13,s14,s21,s22,s23,s24,s31,s32,s33,s34

moleculesymmetry, s11,s12,s13,s14,s21,s22,s23,s24,s31,s32,s33,s34

This parametersignalsthe internalsymmetryof themolecule.Theseinternalsymmetryoperationsof themoleculeonly createonecopy of eachatomanddo not acton copiescreatedby othermoleculesymmetryoperations.Thusyou coulddefinea moleculewhosesymmetryoperationsdo not form a group! Be verycarefulwhenapplyingthesesymmetryoperations.DISCUScomparesthelistsof atomscreatedby thespacegroupandby themoleculegenerator(s).Identicalsectionsarelinkedto onemolecule.Thesymmetryoperationsform thematrixalgebra:( s11s12s13) ( x ) ( s14)( s21s22s23) * ( y ) + ( s24)( s31s32s33) ( z ) ( s34)Thesymmetryoperations:

mole symm, -1,0,0,0.0, 0, 1,0,0.0, 0,0,1,0.0mole symm, 1,0,0,0.0, 0,-1,0,0.0, 0,0,1,0.0mole symm, -1,0,0,0.0, 0,-1,0,0.0, 0,0,1,0.0

for examplewould imply the symmetrymm2 at 0,0,0 for the molecule. Note that the third symmetryoperationis neededin contrastto thegenerators.


Atoms createdby othersymmetryoperations(like lattice centering...)will form a new moleculeof thesametype. You can defineadditionalsymmetryoperationsthroughthe optional ”symmetry” keyword.Thesesymmetryoperationsact different thanthe generatorsdefinedthroughthe spacegroupsymbolorlistedasadditionalgenerators.Thesymmetryoperationscopy only thoseatomscreatedby thegenerators.Thesymmetryoperationsdonotactoncopiesof theatomscreatedby previoussymmetryoperations.

moleculecontent, 3 type 4 [, 3 number 4 ]

moleculecontent, 3 type 4 [, 3 number 4 ]

This keyword signalsthe beginningof a list of contentfor a molecule.Theparameter3 type4 givesthetypenumberof themolecule.All moleculesof identicaltypecanbereferredto by a numberof DISCUScommands.Theoptional 3 number4 givesthenumberof themoleculein thelist of molecules.Thisnumberis writtenby the== 4 ’save’ command.On input thenumberis ignored!All moleculesreadvia ’moleculecontent’commandsareappendedto thelist of existingmolecule.Themoleculecontentmustbefollowedby == 4 ’moleculeatom’commandsandterminatedby a’moleculeend’command.

moleculeatoms[, 3 i 4 ...]

moleculeatoms[, 3 i 4 ...]

Theatomnumber 3 i 4 is partof themolecule.Thenumber 3 i 4 refersto thenumberof theatomin thecurrentcrystal.Up to 20atomsmaybespecifiedon the’moleculeatom’commandline.Themoleculecontentmustbeterminatedby a ’moleculeend’ command.

1.9 diff-f our

diff

Switchesto thedifferenceFourierlevel of DISCUS.All input parametersareidenticalto ”inverse”seethehelpto ”inverse”for furtherdetails.ThedifferenceFouriercanonlybecalculatedfroma”shelxl” typefile. Theprogramcalculates(Fobs-Fcalc)andthencalculatesthecorrespondinginverseFourier.

1.10 find

find ”env”, 5 ”all” 6�5�3 name4�6�3 number 4�7 [, ...] 7 ,x,y,z,radius

Thiscommandservesto find something.Thefirst parameterdefineswhatDISCUSshallfind.”env”

DISCUSfinds the environmentarounda given position. This environmentconsistsof all atomsthat arecloserthanagivenradius.The last four parametersdefinethe positionwhoseenvironmentis to be found, andthe maximumbondlengthin Angstrom.Thesecondto lastbut four parameter(s)definewhich of thesurroundingatomsaretobeincludedin theenvironment.If thesecondparameteris ”all” all atomsareincludedin theenvironment,elseonly thoseatomsspecifiedby 3 name4 or 3 number4 of thescatteringcurve.The numberof neighbouringatomsis storedin ”env[0]”, the indicesare storedin the next 3 env[0] 4elementsof ”env”. Theresultingbondlengthsarestoredin thefirst 3 env[0] 4 elementsof ”res”. ”res[0]”is setto thesamevalueas”env[0]”.Thus,forexample,it is possibleto searchselectively for the next oxygenatoms,while ignoring all otheratoms.Examples


find all,0,0,0,3.05

Findstheenvironmentconsistingof all atomswithin 3.05Angstromfrom theorigin.

find env,o,n,1.25,-5.25,3.05,2.9

Findsall oxygenandnitrogenatomsthatarewithin 2.9Angstromfrom position1.25,-5.25,3.05

1.11 four

four

This sublevel of DISCUScalculatestheFourier transformof thegivencrystalstructure.Thealgorithmtospeedup the explicit Fourier is basedon the program’diffuse’ by B.D. Butler. Seealso: B.D. Bultler &T.R.Welberry, (1992).J.Appl. Cryst.25,391-399.Theprogramallows to calculateX-ray andneutronscatteringincluding isotropictemperaturefactorsandanomalousscattering.Theprogramalsoallowsto subtractthestructurefactorof theaveragestructurefromthecalculateddiffractionpattern.Furtherhelptopicsare:

1.11.1 commands

Valid commandsat this level are:

@ ! execute a macro file (see main help level)= ! assigns the value to a variable (see main help level)abs ! defines the coordinate of the abscissadelf ! defines the anomalous scattering corrections for an elementdisp ! switches anomalous dispersion on/offcontinue! Continue a stopped macro (see main help level)echo ! echo a string (see main help level)eval ! Evaluates an expression for interactive checkexit ! terminates Fourier levelhelp ! help to Fourier commands (see main help level)layer ! defines the layer in reciprocal space to be calculatedll ! defines the lower left corner in reciprocal spacelots ! defines the crystal volume to be used for the Fourier transformlr ! defines the lower right corner in reciprocal spacena ! defines the number of points along the abscissaneut ! switches to neutron diffractionno ! defines the number of points along the ordinateord ! defines the coordinate of the ordinaterun ! starts the calculationscat ! defines the scattering factor for an elementset ! sets Fourier modeshow ! shows the current settings for the Fourier transformstop ! Stops execution of a macro (see main help level)system ! Executes operating system command (see main help)temp ! defines whether temperature coefficients are to be usedul ! defines the upper left corner in reciprocal spacewait ! Waits for user input (see main help level)wvle ! Defines the wave length to be usedxray ! switches to X-ray calculation

1.11.2 abs

abs 8 switch 9Defineswhich thecomponentof thevectorparallelto theabscissais written to theoutputfile.

1.11.3 delf

delf :�; name<>=�; number <�? , ; f ’ < , ; f ” <Definesfor theelement; name< or thescatteringcurvenumber ; number< thereal ; f ’ < andtheimagi-nary ; f ” < correctiontermsfor thescatteringfactors.

1.11.4 disp

disp [ ; switch < ]

switchesanomalousdispersionon /off. If ; switch< is ”anom” anomalousdispersionwill becalculated,iftheswitchis omitted,noanomalousdispersionis calculated.

1.11.5 layer

layer ; e11,e12,e13,e21,e22,e23,e31,e32,e33,inc1,inc2<setsthelowerleft, lowerright andupperleft cornerof theFourierplaneto becalculatedandsetsthenumberof datapointsalongthehorizontalandthevertical

1.11.6 ll

ll ; e11< , ; e12< , ; e13<Setsthelower left cornerof theFourierplaneto becalculated.

1.11.7 lots

lots ”off ”lots : ”box” = ”ellipsoid” ? , ; lx < , ; ly < , ; lz < , ; n < , : ” yes” = ”no” ?Theprogramallows to Fourier transformlargecrystalsby averagingthescatteringfrom smallervolumesselectedat random.This allows to avoid very long correlationswhich might occurif thecompletecrystalscattersin phase.If thisoptionis notwantedandthecompletecrystalshouldbetransformedatonce,thisoptioncanbeturnedoff by thecommand’ lots off ’. Otherwisethefollowing parametersmustbespecified:First the lot shape.Thechoicesare”box” or ”ellipsoid”. Usually thefirst letterof theparameteris sufficient. The followingparameters; lx < , ; ly < and ; lz < describethesizeof thesubvolumesin unit cells. Theparameter; n <specifiesthenumberof suchvolumesto beaveraged.Thelastparametercanbe”yes” or ”no” andselectsif periodicboundaryconditionsshouldbeapplied.Thelot sizeshouldbeslightly largerthanthelongestcorrelationspresentin themodelcrystalstudied.Thenumberof lotsto beaveragedshouldbesetto avaluethatcompletecrystalwill becoveredonceonaverage.WARNING:

If thecommand’purge’ is performedor a structureis readwheretheatomsarenot listed in theDISCUSorderthiscommandshouldbesetto ’ lotsoff ’.

1.11.8 lr

lr ; e21< , ; e22< , ; e23<Setsthelower right cornerof theFourierplaneto becalculated.


1.11.9 na

na @ inc1 ASetsthenumberof datapointsthatwill becalculatedalongtheabscissa.

1.11.10 neut

neut

Switchesto neutrondiffraction

1.11.11 no

no @ inc2 ASetsthenumberof datapointsthatwill becalculatedalongtheordinate.

1.11.12 ord

ord @ switch ADefineswhich thecomponentof thevectorparallelto theordinateis written to theoutputfile.

1.11.13 run

run

startstheFouriercalculation.Theuseris givena roughestimateof thetime it will take.

1.11.14 scat

scat B�@ nameA�C�@ number A�D , @ a1A , @ b1 A , @ a2A , @ b2 A , @ a3 A , @ b3 A , @ a4A , @ b4 A , @ c ADefinesfor theelement@ nameA or thescatteringcurvenumber @ numberA a new scatteringfactorin theexponentialform.

1.11.15 set

set”aver” [, @ per A ]

TheFourierlevel of DISCUSallows to subtracttheaveragestructurefactor @ F A by settingtheparameter@ perA to a valuenot equalszero. The valueof @ perA setsthe percentageof the crystal to be usedtocalculate@ F A .Theaverageis calculatedby putting @ perA % of thecrystalsatomsinto a singleunit cell which is Fouriertransformedandmultipliedwith theinterferencefunctionof thelot shape.WARNING:

If thecommand’purge’ is performedor a structureis readwheretheatomsarenot listed in theDISCUSordertheaveragestructurewill notbecalculatedcorrectly!

1.11.16 show

show

Showsthecurrentsettingsfor theFouriertransformfile

1.11.17 temp

temp E switch Fsetswhethertemperaturecoefficients are to be usedor not. Valid valuesfor E switchF are ”use” and”ignore”. Thefirst two lettersof theswitcharesufficient.

1.11.18 ul

ul E e31F , E e32F , E e33FSetstheupperleft cornerof theFourierplaneto becalculated.

1.11.19 wvle

wvle G�E nameF�HE valueFJIDefinesthe wave lengthto be used. Anomalousdispersionwill only be calculatedif the wave lengthisgivenassymbol.

1.11.20 xray

xray

Switchesto X-ray calculation

1.12 functions

Thefollowing DISCUSspecificfunctionsexist. For a listing of generalintrinsic functionsseehelpentry’functions’ in the’commandlanguage’sectionof theonlinehelp.

bang(u1,u2,u3,v1,v2,v3[,w1,w2,w3])! Returns the bond angle at the site v

If only vectors u and v are given, theangle between u and v is returned.

blen(u1,u2,u3[,v1,v2,v3]) ! Returns the length of vector v-u.Vector v defaults to zero.

dstar(h1,h2,h2[,k1,k2,k3]) ! Returns the length of reciprocalvector k-h. Vector k defaults to zero.

md_test(u1,u2,u3) ! Returns the number of the microdomainclosest to the position u. if theresult is negative, the position isinside the microdomain, else outside.Additionally this number is stored inthe variable md_next(n[1]+1], i.e. inthe position after the last atom in thelist. The variable md_dist[n[1]+1]receives the distance to the microdomainsurface. If negative the atom is insidethe microdomain, else outside.

rang(h1,h2,h3,k1,k2,k3[,l1,l2,l3])! Returns the angle between vectors

k-h and k-l at reciprocal site k.If l is omitted, the angle between thereciprocal vectors h and k is returned.

gran(val,typ) ! Returns Gaussian distributed pseudorandom number with mean zero an a widthgiven by parameter <val>. If <typ> is"s" <val> is taken as sigma, if <typ>is "f", <val> is taken as FWHM.

gbox(r1,r2,r3) ! Returns pseudo random number with

distribution given by a box centeredat 0 with a width of <r2> and two halfGaussian distributions with individualsigmas of <r1> and <r3> to the left andright, respectively.

Theargumentsto any of thesefunctionsareany arithmeticexpression.

1.13 ins

ins K nameL , K x L , K y L , K z L [,t L ]

Insertsan atom of type K nameL at the position K x,y,zL in crystal space. Optionally the temperaturecoefficientmaybegiven.

1.14 internal

Inter nal storageof the structur e

Whenreadinga new cell, the programstoresthe contentof eachunit cell consecutively. The programalwaysgeneratesa blockof nx * ny * nz unit cells.Theinnermost-fastest-loop is nx, theslowestnz.

1.15 inverse

inverse

branchesto theinverseFouriertransformlevel of DISCUSTheinverseFouriertransformis calculatedfromtwo inputfiles. Thetwo filesmustcontaintheintensity, realor imaginarypartamplitudeor phasein oneofthefollowing combinations:

file a file b-------------------------intensity phaseamplitude phasereal imaginary

TheusermustspecifytheFourierplanethathadbeencalculatedandtherealspaceplaneto becalculated.Furtherhelptopicsare:

1.15.1 commands


@ ! execute a macro file (see main help level)= ! assigns the value to a variable (see main help level)abs ! defines the coordinate of the abscissacontinue! Continue a stopped macro (see main help level)echo ! echo a string (see main help level)eval ! Evaluates an expression (see main help level)exit ! terminates Fourier levelfile ! defines the input file name(s)form ! defines the input file formathelp ! help to Fourier commands (see main help level)layer ! defines the layer in reciprocal space to be calculatedll ! defines the lower left corner in reciprocal spacelr ! defines the lower right corner in reciprocal space


na ! defines the number of points along the abscissano ! defines the number of points along the ordinateord ! defines the coordinate of the ordinaterhoabs ! defines the coordinate of the real space abscissarholayer! defines the layer in real space to be calculatedrholl ! defines the lower left corner in real spacerholr ! defines the lower right corner in real spacerhona ! defines the number of points along the real space abscissarhono ! defines the number of points along the real space ordinaterhoord ! defines the coordinate of the real space ordinaterhoul ! defines the upper left corner in real spacerun ! starts the calculationscale ! defines an overall scale factorset ! sets various parametersshow ! shows the current settings for the inverse Fourier transformstop ! Stops execution of a macro (see main help level)system ! Executes operating system command (see main help)ul ! defines the upper left corner in reciprocal spacewait ! Waits for user input (see main help level)

1.15.2 abs

abs M switch NDefineswhich thecomponentof thevectorparallelto theabscissais written to theoutputfile.

1.15.3 file

file O ”a” P ”b” Q , M filenameNDefinesthefilenamesneededfor theinverseFourier.The inverseFourier transformis calculatedfrom two input files. The two files mustcontainthe intensity,realor imaginarypartamplitudeor phasein oneof thefollowing combinations:

file a file b-------------------------intensityamplitudereal imaginary

If the input format is ’shelxl’ then one input file is sufficient. DISCUS assumesthe input file to be aSHELXL List type5 containing M h NRM k NSM l NTM FobsNRM FcalcNRM phaseanglein degreeN Thefile isreadasfreeformat.

1.15.4 format

form O ”gnu” P ”stan” P ”shelxl” QDefinestheinput formatthatwill beused.Valid parametersare:”gnu”

Setsthe type of the outputfile to gnuplot. The intensitiesarewritten in blocksof intensitiesalongtheabscissa,with anemptyline separatingeachblock. Eachline of eachblockcontains:index alongabscissa,index alongordinate,intensity, third index.”stan”

Setsthe outputto standardfile format,which is usedby KUPL. Theoutputfile containstwo initial linesandthena block for eachdataline separatedby anemptyline. Thefirst line containsthenumberof data


pointsalongtheabscissaandtheordinate,thesecondline theminimumandmaximumvalueof theindicesin reciprocalspacealongtheabscissaandordinaterespectively.”shelxl”

Setsthe input file format to SHELXL. DISCUSassumesthe input file to bea SHLEXL List type5 con-taining U h VWU k V l VWU FobsVXU FcalcVWU phaseanglein degreeV The file is readas free format. Allreflectionsareexpandedby theappropriatesymmetryoperations,includingproperphasetransformation.

1.15.5 layer

layer U e11,e12,e13,e21,e22,e23,e31,e32,e33,inc1,inc2Vsetsthelowerleft, lowerright andupperleft cornerof theFourierplaneto becalculatedandsetsthenumberof datapointsalongthehorizontalandthevertical

1.15.6 ll

ll U e11V , U e12V , U e13VSetsthelower left cornerof theFourierplaneto becalculated.

1.15.7 lr

lr U e21V , U e22V , U e23VSetsthelower right cornerof theFourierplaneto becalculated.

1.15.8 na

na U inc1 VSetsthenumberof datapointsthatwill becalculatedalongtheabscissa.

1.15.9 no

no U inc2 VSetsthenumberof datapointsthatwill becalculatedalongtheordinate.

1.15.10 ord

ord U switch VDefineswhich thecomponentof thevectorparallelto theordinateis written to theoutputfile.

1.15.11 rhoabs

rhoabs U switch VDefineswhich thecomponentof thevectorparallelto therealspaceabscissais written to theoutputfile.

1.15.12 rholayer

rholayer U e11,e12,e13,e21,e22,e23,e31,e32,e33,inc1,inc2Vsetsthe lower left, lower right andupperleft cornerof the real spaceplaneto be calculatedandsetsthenumberof datapointsalongthehorizontalandthevertical


1.15.13 rholl

rholl Y e11Z , Y e12Z , Y e13ZSetsthelower left cornerof therealspaceplaneto becalculated.

1.15.14 rholr

rholr Y e21Z , Y e22Z , Y e23ZSetsthelower right cornerof therealspaceplaneto becalculated.

1.15.15 rhona

rhona Y inc1 ZSetsthenumberof datapointsthatwill becalculatedalongtherealspaceabscissa.

1.15.16 rhono

rhono Y inc2 ZSetsthenumberof datapointsthatwill becalculatedalongtherealspaceordinate.

1.15.17 rhoord

rhoord Y switch ZDefineswhich thecomponentof thevectorparallelto therealspaceordinateis written to theoutputfile.

1.15.18 rhoul

rhoul Y e31Z , Y e32Z , Y e33ZSetstheupperleft cornerof therealspaceplaneto becalculated.

1.15.19 run

run

StartstheinverseFouriercalculation.

1.15.20 scale

scale Y scale-factorZDefinesan overall scalefactor. Togetherwith the automaticscalingby 1/vol(unit cell), this scalefactorservesto put the electrondensityon anabsolutescaleof electronspercubicAngstrom. The scalefactorshouldeffectively multiply theobservedF(000)suchthat it is equalto F(000)calculatedfor oneunit cellof theaveragestructure.Every time you enter”inverse”thescalefactoris calculatedto benumberof atomsin crystal/ numberofatomsin oneunit cell. If you useexperimentaldata,you MUST specifythe scalefactorevery time youenterthe”inverse”submenu.


1.15.21 set

set”accu”, [ ”init” \ ”add” ]set”excl”, [ ”none” \�^ value_�]Setdefinesvariousparameters.”accu”

Setsthemodefor theaccumulationof inverseFouriertransforms.”init”

Theelectrondensityarrayis initialized, i.e. setto zero.”add”

Thenext inverseFourier transformis addedto thepreviousvalue.This way several inverseFouriertrans-formswill contributeto asinglelayerin directspace,which is necessaryto createa inverseFouriersectionratherthana Projectionontothelayer. Seethemanualfor furtherdetails.If you useDISCUSto calculatethe input datafor the inverseFourier, you MUST separatethe loop thatcalculatestheFourierfrom theloop thatcalculatestheinverseFourier!!! Bothpartsof theprogramusethesamevariableto storetheresultsandby mixing theloops,theresultwill beunpredictablenonsense!”excl”

Signalswhethercertaindatapointsshouldbeignored.”none”

All datapointsaretreatedasnormaldatapoints,regardlessof their value. This is thedefault at programstart.^ value_Datapointsthatareequalto ^ value_ areexcludedfrom thePattersontransform.Youcanusethisoptiontomaskoutregionsof theinputdataby settingtheirvaluesto ^ value_ . In thecompanionprogramKUPLOT,datapointsof valueequalto -9999.aretreatedasexcludedregions.

1.15.22 show

show

showsthecurrentsettingsfor theFouriertransformfile

1.15.23 type

type [ ”a” \ ”b” ] ,[ ”intensity” \ ”amplitude” \ ”r eal” \ ”imaginary” \ ”phase” \ ”f obs” \ ” fcalc” ]Definesthecontentof file ”a” or ”b”.The inverseFourier transformis calculatedfrom two input files. The two files mustcontainthe intensity,realor imaginarypartamplitudeor phasein oneof thefollowing combinations:

file a file b-------------------------intensity phaseamplitude phasereal imaginary

If theinput formatis ”shelxl”, DISCUSreadsjustonefile. YoucancalculatetheinverseFourierfrom Fobsor Fcalcdataby choosingtheappropriatefile typefrom oneof thefollowing choices:

file a file b-------------------------amplitude


fobsfcalc

1.15.24 ul

ul ` e31a , ` e32a , ` e33aSetstheupperleft cornerof theFourierplaneto becalculated.

1.16 kick

kick ` namea , ` x a , ` y a , ` z a , ` t a , ` na a , ` nea , ` delx a [, ` dely a [, ` delza ]]kick ` namea , ` x a , ` y a , ` z a , ` t a , ` na a , ` nea , - ` bondlengthaInsertsanatomof type ` namea at theposition ` x,y,z a in crystalspace.Thetemperaturecoefficientmustbegiven. ’kick’ checkstheposition ` x a , ` y a , ` z a with respectto all atomsnumbered naa to ` nea .All atomsthatarewithin theblock ` x a +- ` delxa ; ` y a +- ` delya ; ` z a +- ` delza areremovedfromthestructure.If ` delya and/or ` delza arenot given, thenthey default to the valueof the last ` del.a given on this’kick’ command.Notethatthe ` del.a arein fractionalcoordinates,NOT in Angstrom.In thealternativeform, theeight’sparameteris interpretedasabonddistance.To distinguishthetwo forms,the bondlengthmust be lessthan zero. The new atom is insertedand all atomswithin ` bondlengthaAngstromfrom theposition ` x a , ` y a , ` z a areremoved.

1.17 mc

mc

Enter”Monte Carlo” sectionof DISCUS.This sublevel allows to createdisorderedstructureswith givencorrelationsand/ordisplacementsusingMC simulations.Seehelpentry’commands’for acompletelist ofcommandsavailablein thissublevel.NOTE: TheMC andCHEM sublevel sharesomevariableswhichdefineneighboursetc.andsettingsmadein this sublevel might bealteredwhenusingtheothersublevel. It is alwayssave to repeatsettingswhenenteringthissublevel if bothlevelsareused.

1.17.1 commands


@ ! Executes a macro (see main help)= ! Algebra (see main help)continue! Continue a stopped macro (see main help level)echo ! Echos a string, just for interactive checkeval ! Evaluates an expression (see main help)exit ! Terminates the MC sub level, returns to the main DISCUS level.help ! Gives on-line help for ’mc’ (see main help)run ! Starts MC simulationsave ! Saves structure (see main help -> save)set ! Sets most MC parametersshow ! Shows current settingsstop ! Stops execution of a macro (see main help level)system ! executes operating system command (see main help)wait ! Waits for user input (see main help)


1.17.2 run

run

ThiscommandstartstheMC simulationfor thegivenparametersandnumberof MC moves.

1.17.3 set

set b subcommandcThis commandallows to definethewantedcorrelationsandmostotherparametersfor theMC simulation.Thehelpentry’commands’containsa list of valid subcommandsfor the’set’ command.Furtherhelpcanbefoundfor thefollowing subcommands:

commands

atom : Setting of atom types for MC simulationconst : Setting of interaction constantscyc : Setting of maximum number of MC movesenergy : Setting of MC mode (energy calculation)feed : Setting of display/feedback intervalmode : Setting of MC mode (crystal modification)mole : Setting molecule types for MC simulationmove : Setting size of generated SHIFT movesneig : Setting of the neighbour definitionstarget : Setting of correlations values to be achievedtemp : Setting of MC simulation temperaturevec : Definition of interaction vectors

atom

set”atom”, deb namec�f�b number c�g , d�b namec�fb number c�gThis commandallows theuserto selecttheatomstypesusedfor the MC simulation. They caneitherbespecifiedby b namec (e.g. Zr) or b numberc . Not that differentMC energy definitionshave differentrestrictionson theselectionof theatoms.

const

set”const”, b ic c , b constc [, b fac c ]

Theintroductionof certaincorrelationsdependona givensetof nearneighbourinteractions.Thesevaluesare initially unknown and are adjustedusing a feedbackmethod(- c set feed). This commandallowstheuserto setinitial interactionparametersb constc for thecorrespondinginteraction/correlationb ic c .The optional last parameterb facc is a factorusedin the feedbackprocessandcontrolshow ’f ast’ theinteractionsarechangedin eachfeedbackcycle.

cyc

set”cyc”, b number cThiscommandsetsthenumberof MC moves(i.e. visitedsites)to beexecutedby the’run’ command.Thenumberb numberc actuallydefinesthenumberof ’ tried’ MC moves.Notethatwe referto a MC cycle asthenumberof movesneededto visit everycrystalsiteonceonaverage.

energy

set”energy”, d ”cocc” f ”cdis” f ”disp” g


This commandselectsthetypeof MC energy to beusedfor thesimulation.TheMC sublevel of DISCUScurrentlyallows to introduceoccupationalcorrelations(”cocc”), displacementcorrelations(”cdis”) anddistortions(”disp”). Theenergy for thecorrelationmodesis basedonanIsingmodelwhereasthedistortionsareexpressedusingHookeslaw.

feed

set”feed”, h number iTheinteractionvaluesfor thegivencorrelationstructurearedeterminedby a feedbackprocess.This com-mandsetsthenumberof movesbetweeneachfeedbackrun. Thisvalueis alsousedfor theintervalof screenoutputs.Notethattheenergy mode”disp” doesnotusethefeedbackmechanismandthevalue h numberigivenhereonly determinestheoutputinterval.

mode

set”mode”, j ”shi[ft]” k ”swc[hem]” k ”swd[isp]” k ”ext[er nal]” l ,[ j ”a[ll]” k ”l[ocal]” k ”sl[ocal]” k ”si[te]” l ]Thiscommanddeterminesthetypeof MC moveusedfor modifying thecrystal.Thesettingsareexplainedin theRMC sectionunder- i setmode.

neig

set”neig”, ”add”set”neig”, ”dis”, h u i , h v i , h w i , h fsig i [, h wsigi ] [, j ”sym” k ”nosym” l ]set”neig”, ”dir”, h x1 i , h y1 i , h z1i [, h x2 i , h y2 i , h z2i ]set”neig”, ”r ese”set”neig”, ”v ec”, h iv1 i [, h iv2 i ,..]

This commandis usedto definetheneighboursusedto determinethecorrelations.Thesubcommand’dis’usesthedistanceasa criterionwhereas’vec’ usesdefinedinteractionvectors(- i setvec). Thesubcom-mands’add’ and’rese’allow thestorageandresetof thelist of definitions.Thedetailsof thesecommandsaregivenin theonlinehelpfor thesamecommand’setneig’ in theCHEM sublevel.

mole

set”mole”, h typ1 i , h typ2 iThis commandallows theuserto selectthemoleculetypesusedfor theMC simulation.Not thatdifferentMC energy definitionshavedifferentrestrictionson theselectionof themoleculetypes.

move

set”move”, j ”all” k�h namei�kh number iml , h sxi , h syi , h sziSetsanuserdefinedsigmafor thegeneratesmoves.ThecreatedshiftsareGaussiandistributed.Thedefaultis a sigmaof 0.2 unit cell. Note that thevaluesof h sxi , h syi and h szi aregiven in unit cell units tospeedup theMC runs. In casemoleculesareselectedh numberi specifiesthemoleculetype,otherwiseatomsareaddressedby their h numberi or h namei .

range

target

set”tar get”, h ic i , h valueiset”tar get”, h ic i , j�h number ink�h nameimk ”all” l ,


o�pnumber q�r p nameq�r ”all” s , p dist q

Thefirst commandsetsthedesiredcorrelationvaluep

valueq for modes”cocc” and”cdis” for theneigh-bourdefinition

pic q .

Thesecondversionof thecommandsetsthedesireddistancebetweenthegivenatomtypestop

distq A.Thissettingis usedfor mode”disp”. If

pdispq is setto zerothecorrespondingatompair is notusedin the

MC simulation.

temp

set”temp”,p

kt qThis commandsetsthe temperature

pkt q usedfor the MC simulation. In order to be able to usethe

feedbackprocedureto determinetheinteractionenergiesthevalueofp

kt q shouldbesetto 1.0 (default).As a resultthe interactionenergieswill be in unitsof kT. If no feedbackis used,

pkT q canbesetto the

desiredsimulationtemperature.

vec

set”v ec”,p

iv q ,p

is1q ,p

is2q ,p

dx q ,p

dy q ,p

dz qThis commandis usedto definecorrelationvectorsthatmight beusedto calculatecorrelationswithin thecrystal(- q ’setcorr’). Thecompletedescriptionis givenin theCHEM sectionof theonlinehelp (- q setvec).

1.17.4 show

show

Thiscommandlistsall currentsettingsfor theMC simulationpartof DISCUSon thescreen.

1.18 micro

micro

Switchesto themicrodomaincalculationlevel of discus.Furtherhelptopicsare:

1.18.1 commands


@ ! Executes a macro (see main help level)= ! assigns the value to a variable (see main help level)ang ! Sets the current units to Angstromasym ! Displays the content of the asymmetric unitbase ! Defines the super latticeboun ! Sets the current boundary typeccol ! Reads a single column of the correlation matrixchem ! Displays the different atoms that are present in the crystalcele ! Reads a single element of the correlation matrixcontinue! Continue a stopped macro (see main help level)content ! Sets the current content type for the microdomainscrea ! Creates the list of microdomainscrow ! Reads a single row of the correlation matrixdens ! Sets the density of randomly distributed microdomainsdist ! Sets the distribution type of the microdomainsdlu ! Sets the current units to direct lattice unitsecho ! Echos a string (see main help level)


eval ! Evaluates an expression for interactive checkexit ! Terminates the microdomain sublevelhelp ! Gives on line help for micro (see main help level)grid ! Sets the fitting of microdomain origins to the host latticeini ! Initializes the microdomain menuins ! Inserts the currently defined microdomain parameters into the listlog ! Turns log of microdomain positions on/offmrow ! Read a single row of the orientation matrixorie ! Sets the default value for the orientation matrix numberplace ! Places a single microdomain into the crystalradi ! Sets the current radius and its sigma for the microdomainsremo ! Removes all or a single microdomain type from the listrbase ! Defines the super lattice in reciprocal spacerun ! Starts the calculation of the microdomain distributionseparate! Defines minimum interatomic distance for "fuzzy" microdomainsset ! Sets some general variablesshift ! Constant shift of all microdomain origins.show ! Shows the current settings for microsigm ! Defines the FWHMfor Gaussian distributionssix ! Defines the FWHMfor Gaussian distributions along the

! x axis of the superlatticesiy ! Defines the FWHMfor Gaussian distributions along the

! y axis of the superlatticesiz ! Defines the FWHMfor Gaussian distributions along the

! z axis of the superlatticestop ! Stops execution of a macro (see main help level)system ! Executes operating system command (see main help)wait ! Waits for user input (see main help level)

1.18.2 ang

ang

Setsthecurrentunit to Angstrom.All radii readfrom now onwill beunderstoodasgivenin Angstrom.

1.18.3 asym

asym

Shows thecontentof theasymmetricunit. Thenamesof thoseatoms,a numberthat is usedasindex forits scatteringtype, their positionandtemperaturecoefficient arelisted. The numberthat is listed, is thenumberthatrefersto thescatteringcurveof thatatom.It is containedin thevariablem[ t index u ]. If acellwasread,all atomsareconsideredto bedifferent,evenif they arechemicallyidenticalandhave thesametemperaturecoefficient. If a wholestructurewasread,all atomsthatarein theunit cell 0 t = xyz t 1, arechemicallyuniqueandhavea differenttemperaturecoefficientareincludedin theasymmetricunit.

1.18.4 base

base t b11u , t b12u , t b13u , t b21u , t b22u , t b23u , t b31 u , t b32 u , t b33 uDefinesthebasevectorsof thesuperlatticeon which themicrodomainsarelocated.Theindicesareto begivenasmultiplesof thebasevectorsof thehostcrystal. t b1* u givestheaaxisof thesuperlattice,t b2* utheb and t b3* u thec axis.

1.18.5 boun

boun v ”block” w ”face”, t h u , t k u , t l uxw ”fuzzy” w ”sphere” ySetstheboundarytypeof thenext microdomaintype.Thethreeoptionsaremutuallyexclusive.

"block": The microdomains are limited by {100} (as if cubic).The radii of the faces are determined by the size ofthe structure file read.

"face,<h>,<k>,<l>": The microdomain is limited by (several) faces withindices <h>,<k>,<l>. The distance of this face fromthe origin of the microdomain is taken from thecurrent radius. The set of faces must form a closedshape in real space.

"fuzzy" The microdomain is defined only through the atomsthat are read from the input file. Only those hostatoms, whose distance to any microdomain atom is lessthan the separation defined by the command:sep fuzzy,<dist>are replaced by the microdomain.

"sphere": The microdomain is limited by a sphere with radiusas defined by the ==> ’radius’ command.

1.18.6 ccol

ccol z nr { , z c1nr { , z c2nr { ,...,z cmdtypenr {Reada singlecolumn z nr { of thecorrelationmatrix. Following theindex z nr { , asmany parametersastherearemicrodomaintypesmustfollow. Thesumof any columnneednotbeequalto one.Thenumberofarrayelementsrequestedby ’ccol’ is equalto thenumberof new microdomaintypesintroducedsincethelast== { ’crea’ command.

1.18.7 cele

cele z i { , z j { , z value{Readsthevalue z value{ thatis storedin elementz i { , z j { of thecorrelationmatrix.

1.18.8 chem

chem

Shows thetypeof all atomspresentin thecrystal.For eachdifferentatompresent,its identifying number,its nameandits temperaturecoefficient arelisted. The list containsall the atomsin the asymmetricunitplusany atomsaddedto thestructure.If atomsareremovedfrom thestructure,theprogramdoesnotcheckwhetherthereareany atomsof this type left. If a particulartypeof atomis completelyremovedfrom thestructure,it will remainin thelist of differentatoms,andwill bedisplayedby ’chem’.

1.18.9 cont

cont | ”cell”, z file {>} ”fr ee” } ”structur e”, z file {n~Definesthecontentof amicrodomaintype.Theparametersaremutuallyexclusive.

"cell",<file> : Under development"free" : The structure of the microdomain can freely be

modified by the user. For each atom the number ofthe closest microdomain is stored in the variable==> "md_next[]". If this is negative, the atom isinside the microdomain, else outside. The distance tothe nearest surface is stored in md_dist[]. Again,if this is negative or zero the atom is inside themicrodomain.

"structure",<file> : The structure read from file <file> is used tofill the microdomain.

1.18.10 crea

crea

Createsthelist of microdomainorigins. No changesaredoneto theactualstructure,this is performedbythecommand== � ’run’. Thelist of originsmaybeeditedby theuser.

1.18.11 crow

crow � nr � , � cnr � 1, � cnr � 2,...,� cnrmdtype �Readasinglerow � nr � of thecorrelationmatrix. Following theindex � nr � , asmany parametersastherearemicrodomaintypesmust follow. The sumof any row neednot be equalto one,as long asthe sumof all rows is identical. Thenumberof arrayelementsrequestedby ’ccol’ is equalto thenumberof newmicrodomaintypesintroducedsincethelast== � ’crea’ command.

1.18.12 dens

dens � rho �Definesthe densityof microdomainsin microdomainsper unit cell. This is usedin caseof a randomdistributionof microdomains.

1.18.13 dist

dist � ”lattice” � ”para” � ”random” � ”file”, � infile �J�Definesthetypeof distribution to beused.

"lattice" : The origins of all microdomains are located on the nodes ofa perfect lattice defined by the base.

"para": The microdomains are distributed on a paracrystalline lattice.The average separation of two microdomain origins is definedby the base vectors. The length and direction of each individualseparation is Gaussian distributed with the mean valuegiven by ==> ’base’ and the sigma given by ==> ’si..’.

"random" : The origins are randomly distributed with a density of==> ’dens’ microdomains per unit cell.

"file" : DISCUS reads the data file <infile> and interprets theatom positions as microdomain origins. The scattering typeof the atom gives the microdomain type. All atoms whosescattering curve type is zero are omitted. This allows youto replace atoms in the model crystal by voids which arenot used as microdomain origins.

1.18.14 dlu

dlu

Setsthe currentunit to direct lattice units. All radii readfrom now on will be understoodas given inmultiplesof thelatticeconstanta of thehostlattice.

1.18.15 grid

grid � ”host” � ”fr ee” �Definesthefitting of themicrodomainoriginsto thenodesof thehostlattice.

"host" : The microdomain origins are forced to be integermultiples of the host lattice, including any centeringpositions.


"free" : The microdomain origins may assume any value, in effectcreating an incoherent intergrowth of the two structures.

1.18.16 init

init

Initializesthemicrodomaindistribution. Thenumberof microdomaintypes,microdomainoriginsis settozero.Theactualcrystalis notmodifiedby thiscommand,norareany previousmodificationsundone.

1.18.17 inse

inse

Insertsa microdomaintypewith thecurrentparametersinto thelist of microdomaintypes.

1.18.18 log

log ”pos” , � ”off ” � ”on” �Determineswhetherthe list of microdomainorigins is written to files ”fort.97”, ”fort.98” and”fort.99”.This commandservesmainly for testing. Files ”fort.97” and”fort.99” containsthe list of microdomainorigins in a form identicalto thestructurefiles of DISCUS.Eachsite is denotedby a point scatterer”E1-”. This file canbereadandits Fourier transformbecalculated.File ”fort.98” containsjust a list of x,y,zpositionsto be displayedby a suitablegraphicsprogram. ”fort.98” and ”fort.99” containthe list of allmicrodomainscreatedby the== � ’crea’ command,while ”fort.97” containsonly thosemicrodomainsthatareat leastpartially insidethecrystal.

1.18.19 mrow

mrow � nr � , � mnr � 1, � mnr � 2, � mnr3 � , � mnr4 �Reada singlerow � nr � of the orientationmatrix. Following the index � nr � , the four elementsof theorientationmatrix areread. As soonasthe first threerows of the orientationmatrix have beenread,thematrix is stored.

1.18.20 orie

orie � nr �Setsthedefaultfor theorientationmatrixnumber. All followingmicrodomainsinserteduntil thenext ”orie”commandwill have theorientationspecifiedby theorientationmatrix � nr � .

1.18.21 place

place � x � , � y � , � z � , � type �With this commandan individual microdomaincanbe placedinto the crystal. The microdomainof type� type� is placedat coordinates� x � , � y � , � z � and the structureof the crystalmodifiedaccordingtothe microdomaintype � type� . The type mustbe a previously definedmicrodomaintype. The currentdistributiontypehasnoeffectonthepositionof themicrodomain.Thefitting to thehostgrid is determinedby thecurrentvaluesetby == � ’grid’.


1.18.22 radi

radi � value� [, � sig� ]

Setsthe currentradiusfor microdomains.In caseof boundarytype ”sphere”,this is theactualradius,incaseof boundarytype ”f ace” it is the distancefrom the origin of the microdomainto the boundaryface.Theradius � value� is interpretedaccordingto thecurrentunit == � ’dlu’ and’ang’. If theoptionalvalue� sig� is given,theradii of theindividualmicrodomainsaredistributedaccordingto aGaussiandistributionwith sigma � sig� .

1.18.23 remo

remo � ”all” �� number ��Removesall microdomaintypesor a specifiedmicrodomaintypefrom thelist of microdomaintypes.Onlythosemicrodomaintypescanberemovedthathavebeendefinedby == � ’inse’ but whoseoriginshavenotyetbeendistributedthroughoutthecrystalwith the== � ’crea’ command.

1.18.24 rbase

rbase � b11� , � b12� , � b13� , � b21 � , � b22 � , � b23 � , � b31 � , � b32 � , � b33 �Definesthereciprocalbasevectorsof thesuperlatticeon which themicrodomainsarelocated.Theindicesareto begivenasmultiplesof thereciprocalbasevectorsof thehostcrystal. � b1* � givesthea* axisofthesuperlattice,� b2* � theb* and � b3* � thec* axis.

1.18.25 run

run

Startsthecalculationof themodificationof thestructure.Theoriginal atomsof thehostthatareinsideamicrodomainareremoved. If thecontenttypeof themicrodomainis ”free”, theatomsaremarkedbut notremoved.Thestructurereadfrom thecontentfile is usedto fill theavailablespace.If this commandis notused,nomodificationsof thestructuretakeeffect.

1.18.26 separation

sepfuzzy, � distance�Definesthe maximumseparationbetweenhostatomsandmicrodomainatomsthat are insidea ”fuzzy”microdomain.All hostatomsareremoved, if their distanceto any microdomainatomis lessor equalto� distance� .

1.18.27 set

setoverlap, � ”err or” � ”war ning” �If microdomainsarelarge,comparedto thebasevectors,themicrodomainsmight overlap.Thestatusflag”overlap”signalsDISCUShow toproceedonceit findssuchanoverlap.If theflagis setto ”error”, DISCUSstopsmakingthemicrodomainsandprintsanerrormessagethatinformsyouwhichatomsis in at leasttwomicrodomains.If theflag is setto ”warning”,only themessageis displayedandDISCUScontinues.WARNING: If DISCUSstopsdueto the”error” flag,partof thecrystalwill alreadyhavebeenaltered!Theold atomsinsidethemicrodomainswill alreadyhave beenremovedandnew atomsareprobablyaddedtothecrystalaswell. Proceedwith caution!WARNING: If you instructDISCUSto proceeddespitean overlap,many atomsfrom two differentmi-crodomainsmightendup to betooclosetogether. Becarefulwheninterpretingtheresults!


1.18.28 shift

shift � x � , � y � , � z �Thevectorxyz is addedto all microdomainorigins,exceptfor arandomdistribution.Thustwo distributionswith thesamelatticecanbegeneratedthatareshiftedwith respectto eachotherby thevectorxyz.

1.18.29 show

show [ � ”def ” � ”dist” � ”type” � ”corr” � ”orie” � ]

Shows the currentsettingsfor micro. If no parameteris given, all information is shown, elseonly theinformationfor thespecificparameteris shown:

"def" : Shows the current default values for the nextmicrodomain type.

"dist" : Shows the parameters describing the microdomaindistribution.

"type" : Shows the microdomain type inserted so far."corr" : Shows the correlation matrix."orie" : Shows the orientation matrices that have been defined.

1.18.30 sigm

sigm � s11� , � s12� , � s13� , � s21 � , � s22 � , � s23� , � s31� , � s32� , � s33�Definesthe SIGMA’s of the Gaussiandistribution. � sii � are the SIGMA’s along the basevectors,the� sij � give theSIGMA of theGaussiandistribution in directionof basevectorj at theendof basevectori.

1.18.31 six

six � s11� , � s12� , � s13�DefinestheSIGMA’s of theGaussiandistribution alongthebasevectorx. � sii � aretheSIGMA’s alongthebasevectors,the � sij � givetheSIGMA of theGaussiandistribution in directionof basevectorj at theendof basevectori.

1.18.32 siy

siy � s11� , � s12� , � s13�DefinestheSIGMA’s of theGaussiandistribution alongthebasevectory. � sii � aretheSIGMA’s alongthebasevectors,the � sij � givetheSIGMA of theGaussiandistribution in directionof basevectorj at theendof basevectori.

1.18.33 siz

siz � s11� , � s12� , � s13�DefinestheSIGMA’s of theGaussiandistribution alongthebasevectorz. � sii � aretheSIGMA’s alongthebasevectors,the � sij � givetheSIGMA of theGaussiandistribution in directionof basevectorj at theendof basevectori.

1.19 output

output

Switchesto theoutputlevel of discus.All Fourieroutputis written at this level. Severalgraphicformatsareavailable.


Furtherhelptopicsare:

1.19.1 commands@ ! Execute a macro file (see main help)= ! assigns the value to a variable (see main help)continue! Continue a stopped macro (see main help level)echo ! Echo a string (see main help)eval ! Evaluates an expression for interactive check (see main help)exit ! Returns to the main discus levelform ! Defines the output format to be usedhelp ! Gives help for the output level (see main help)input ! reads an old data fileoutfile ! sets name of output filerun ! Starts writing of outputshow ! Shows the current settingsthre ! Sets the thresholds used for bitmap outputvalu ! Sets the value that is written to filestop ! Stops execution of a macro (see main help level)system ! Executes operating system command (see main help)wait ! Waits for user input (see main help)

1.19.2 format

form � ”gnu” � ”pgm” � ”ppm” � ”powder” � ”post” � ”shel” � ”stan” �Definestheoutputformatthatwill beused.Valid parametersare:”gnu”

Setsthe type of the outputfile to gnuplot. The intensitiesarewritten in blocksof intensitiesalongtheabscissa,with anemptyline separatingeachblock. Eachline of eachblockcontains:index alongabscissa,index alongordinate,intensity, third index.”pgm”

Setsthetypeof theoutputto portablegrey map.A bitmapof theintensityis written in portablegrey mapstyle.All valuesbelow theminimumthresholdaresetto thisvalue,all valuesabovethemaximumthresholdaresetto thismaximumvalue.”ppm”

Setsthe typeof theoutputto portableany-map. A bitmapof the intensityis written in portableany-mapstyle. Thecolor schemeis readfrom file ”color.map”. All valuesbelow theminimumthresholdaresettothisvalue,all valuesabovethemaximumthresholdaresetto thismaximumvalue.”powder”

Setsthe outputformat to powder. You musthave calculateda powderdiffractionpatternusingthe == �’powder’ menuof DISCUS.DISCUSwrites a two collumn output,with 2-Thetaandthe intensityin thetwo collumns.”post”

Setsthetypeof theoutputto color postscript.A bitmapof theintensityis written in color postscript.Thecolor schemeis readfrom file ”color.map”. All valuesbelow theminimumthresholdaresetto this value,all valuesabovethemaximumthresholdaresetto thismaximumvalue.”shel”

Setstheoutputformatto SHELX data.Thedataarewritten in format3I4,2F8.2.Thehkl areconvertedbyan”int” commandto integers.Theuserhasto make surethat the incrementsusedin theFourierresultedin integerspacing.Usethe== � ’value’ ”intensity” or ”amplitude” for theoutput.DISCUScalculatesthevalueof I(000) or F(000)respectively andscalesthedatasuchthatI(000) is lessthan10**6 to fit into theformat.Thesigmais just thesquarerootof thefinal intensityafterscaling.”stan”

Setstheoutputto standardfile format,which is usedby KUPLOT. Theoutputfile containstwo initial linesandthena block for eachdataline separatedby anemptyline. Thefirst line containsthenumberof datapointsalongtheabszissaandtheordinate,thesecondline theminimumandmaximumvalueof theindicesin reciprocalspacealongtheabscissaandordinaterespectively.

1.19.3 input

input

Readsanold datafile

1.19.4 outfile

outfile � filename�Setsthenameof theoutputfile, to which theintensitiesarewritten.

1.19.5 run

run

Startswriting theoutputfile. Without thiscommandtheoutputfile is notwritten!

1.19.6 show

show

Showsthecurrentsettings

1.19.7 threshold

thr esh � ”high” � ”lo w” � ”sigma” � ”zmin” � ”zmax” �� value�This commandsetsthe thresholdthat is usedwhen writing BITMAP output. All valueslessthan theminimumthresholdaresetto zero,all valueshigherthanthemaximumthresholdaresetto themaximumthreshold.Thevaluesin betweenarelinearlyscaledfrom zeroto 255.Dependingon thefirst parameter, thesecondparameteris interpretedin fivedifferentways:

"high" : Sets maximum threshold for BITMAP in percent of the maximumdiffuse intensity.

"low" : Sets minimum threshold for BITMAP in percent of the maximumdiffuse intensity.

"sigma" : Sets threshold for BITMAP to average diffuse intensity+- <value> times standard deviation of diffuse intensity.

"zmax" : Sets maximum threshold for BITMAP"zmin" : Sets minimum threshold for BITMAP

1.19.8 value

valu � ”int” � ”amp” � ”pha” [,”random”] � ”r eal” � ”imag” �valu � ” � int � ” � ” � amp � ” � ” � pha � ” [,”random”] � ” � real� ” � ” � imag � ” �Setswhat valueis written to the outputfile. The keyword given in �� correspondsto the valueof theaveragestructurefactor � F � whereastheplainwordstandsfor theresultingvalueof theFouriertransformwhichcanbeFor F- � F � dependingontheselectedmodus.Thecommand’valueint’ will savetheresultingintensitywhereas’value � int � ’ will give the intensityof the averagestructure. The allowed valuesaresummedup in thefollowing list:


"int" : intensity I(hkl)"amp" : modulus of structure factor |F(hkl)|"pha" : phase angle in degrees

If the optional second parameter is given as "random",the phases for integer HKL are written as calculated.All other phases are assigned a random number between-180 and +180 degrees.

"real": real part of structure factor"imag": imaginary part of structure factor

Thefile nameis notadaptedautomatically!

1.20 patterson

patterson

branchesto thePattersontransformlevel of DISCUSThePattersontransformis calculatedfrom two inputfiles. Thetwo files mustcontaintheintensity, realor imaginarypart,or amplitudein oneof thefollowingcombinations:


TheusermustspecifytheFourierplanethathadbeencalculatedandtherealspaceplaneto becalculated.Furtherhelptopicsare:

1.20.1 commands


@ ! execute a macro file (see main help)= ! assigns the value to a variable (see main help)abs ! defines the coordinate of the abscissacontinue! Continue a stopped macro (see main help level)echo ! echo a string (see main help)eval ! Evaluates an expression for interactive check (see main help)exit ! terminates Fourier levelfile ! defines the input file name(s)form ! defines the input file formathelp ! help to Fourier commands (see main help)layer ! defines the layer in reciprocal space to be calculatedll ! defines the lower left corner in reciprocal spacelr ! defines the lower right corner in reciprocal spacena ! defines the number of points along the abscissano ! defines the number of points along the ordinateord ! defines the coordinate of the ordinaterhoabs ! defines the coordinate of the real space abscissarholayer! defines the layer in real space to be calculatedrholl ! defines the lower left corner in real spacerholr ! defines the lower right corner in real spacerhona ! defines the number of points along the real space abscissarhono ! defines the number of points along the real space ordinaterhoord ! defines the coordinate of the real space ordinaterhoul ! defines the upper left corner in real spacerun ! starts the calculationscale ! defines an overall scale factorset ! sets various parameters

show ! shows the current settings for the inverse Fourier transformstop ! Stops execution of a macro (see main help level)system ! Executes operating system command (see main help)type ! defines the file type (intensity, amplitude ...)ul ! defines the upper left corner in reciprocal spacewait ! Waits for user input (see main help)

1.20.2 abs

abs � switch �Defineswhich thecomponentof thevectorparallelto theabscissais written to theoutputfile.

1.20.3 file

file ”a” ¡ ”b” ¢ , � filename�Definesthefilenamesneededfor thepatterson.ThePattersontransformis calculatedfrom oneor two input files. Thetwo files mustcontaintheintensity,realor imaginarypart,or amplitudein oneof thefollowing combinations:


If the input format is ’shelxl’ then one input file is sufficient. DISCUS assumesthe input file to be aSHLEXL List type5 containing� h �n� k � l �� Fobs�x� Fcalc�n� phaseanglein degree� Thefile is readasfreeformat.

1.20.4 format

form ”gnu” ¡ ”stan” ¡ ”shelxl” ¢Definestheinput formatthatwill beused.Valid parametersare:”gnu”

Setsthe type of the outputfile to gnuplot. The intensitiesarewritten in blocksof intensitiesalongtheabscissa,with anemptyline separatingeachblock. Eachline of eachblockcontains:index alongabscissa,index alongordinate,intensity, third index.”stan”

Setsthe outputto standardfile format,which is usedby KUPL. Theoutputfile containstwo initial linesandthena block for eachdataline separatedby anemptyline. Thefirst line containsthenumberof datapointsalongtheabscissaandtheordinate,thesecondline theminimumandmaximumvalueof theindicesin reciprocalspacealongtheabscissaandordinaterespectively.”shelxl”

Setstheinputfile formatto SHELXL. DISCUSassumestheinputfile to beaSHLEXL List type5 contain-ing

<h> <k> l> <Fobs> <Fcalc> <phase angle in degree>

Thefile is readasfreeformat.All reflectionsareexpandedby theappropriatesymmetryoperations,includ-ing properphasetransformation.


1.20.5 layer

layer £ e11,e12,e13,e21,e22,e23,e31,e32,e33,inc1,inc2¤setsthelowerleft, lowerright andupperleft cornerof theFourierplaneto becalculatedandsetsthenumberof datapointsalongthehorizontalandthevertical

1.20.6 ll

ll £ e11¤ , £ e12¤ , £ e13¤Setsthelower left cornerof theFourierplaneto becalculated.

1.20.7 lr

lr £ e21¤ , £ e22¤ , £ e23¤Setsthelower right cornerof theFourierplaneto becalculated.

1.20.8 na

na £ inc1 ¤Setsthenumberof datapointsthatwill becalculatedalongtheabscissa.

1.20.9 no

no £ inc2 ¤Setsthenumberof datapointsthatwill becalculatedalongtheordinate.

1.20.10 ord

ord £ switch ¤Defineswhich thecomponentof thevectorparallelto theordinateis written to theoutputfile.

1.20.11 rhoabs

rhoabs £ switch ¤Defineswhich thecomponentof thevectorparallelto therealspaceabscissais written to theoutputfile.

1.20.12 rholayer

rholayer £ e11,e12,e13,e21,e22,e23,e31,e32,e33,inc1,inc2¤setsthe lower left, lower right andupperleft cornerof the real spaceplaneto be calculatedandsetsthenumberof datapointsalongthehorizontalandthevertical

1.20.13 rholl

rholl £ e11¤ , £ e12¤ , £ e13¤Setsthelower left cornerof therealspaceplaneto becalculated.


1.20.14 rholr

rholr ¥ e21¦ , ¥ e22¦ , ¥ e23¦Setsthelower right cornerof therealspaceplaneto becalculated.

1.20.15 rhona

rhona ¥ inc1 ¦Setsthenumberof datapointsthatwill becalculatedalongtherealspaceabscissa.

1.20.16 rhono

rhono ¥ inc2 ¦Setsthenumberof datapointsthatwill becalculatedalongtherealspaceordinate.

1.20.17 rhoord

rhoord ¥ switch ¦Defineswhich thecomponentof thevectorparallelto therealspaceordinateis written to theoutputfile.

1.20.18 rhoul

rhoul ¥ e31¦ , ¥ e32¦ , ¥ e33¦Setstheupperleft cornerof therealspaceplaneto becalculated.

1.20.19 run

run

StartsthePattersoncalculation.

1.20.20 scale

scale ¥ scale-factor¦Definesan overall scalefactor. Togetherwith the automaticscalingby 1/vol(unit cell), this scalefactorservesto put the electrondensityon anabsolutescaleof electronspercubicAngstrom. The scalefactorshouldeffectively multiply theobservedF(000)suchthat it is equalto F(000)calculatedfor oneunit cellof theaveragestructure.Every time you enter”patterson”thescalefactoris calculatedto benumberof atomsin crystal/ numberof atomsin oneunit cell. If you useexperimentaldata,you MUST specifythescalefactorevery time youenterthe”patterson”submenu.

1.20.21 set

set”accu”, § ”init” ¨ ”add” ©set”9999”, § ”excl” ¨ ”incl” ©Setdefinesvariousparameters.”accu”

Setsthemodefor theaccumulationof Pattersontransforms.”init”


Theelectrondensityarrayis initialized, i.e. setto zero.”add”

The next Pattersontransformis addedto the previousvalue. This way several Pattersontransformswillcontribute to a singlelayer in direct space,which is necessaryto createa Pattersonsectionratherthanaprojectionontothelayer. Seethemanualfor furtherdetails.If youuseDISCUSto calculatetheinputdatafor thePatterson,youMUST separatetheloopthatcalculatestheFourierfrom theloop thatcalculatesthePatterson!!!Bothpartsof theprogramusethesamevariabletostoretheresultsandby mixing theloops,theresultwill beunpredictablenonsense!”9999”

Signalswhatto dowith datavaluesthatareequalto -9999.In thecompanionprogramKUPLOT, thesearetreatedasexcludedregions.”excl”

Datapointsthatareequalto -9999.areexcludedfrom thePattersontransform.”incl”

Datapointsthatareequalto -9999.aretreatedasnormaldatapoints.This is thedefaultat programstart.

1.20.22 show

show

showsthecurrentsettingsfor theFouriertransformfile

1.20.23 type

type ª ”a” « ”b” ¬ ,ª ”intensity” « ”amplitude” « ”r eal” « ”imaginary” « ”phase” « ”f obs” « ” fcalc” ¬Definesthecontentof file ”a” or ”b”.ThePattersontransformis calculatedfrom oneor two input files. Thetwo files mustcontaintheintensity,realor imaginarypart,or amplitudein oneof thefollowing combinations:


If theinput formatis ”shelxl”, DISCUSreadsjustonefile. YoucancalculatetheinverseFourierfrom Fobsor Fcalcdataby choosingtheappropriatefile typefrom oneof thefollowing choices:

file a file b-------------------------amplitudefobsfcalc

1.20.24 ul

ul e31® , e32® , e33®Setstheupperleft cornerof theFourierplaneto becalculated.


1.21 pdf

pdf

This commandswitchesto the PDF modeof DISCUS.PDF standsfor Pair-Distribution-Function. Thefunctionactuallyusedin DISCUSis theso-calledreducedradialdistributionfunctionG(r) whichis definedas

G(r) = 4 pi r ( rho(r) - rho(0) )

Thevalueof ”rho(r)” is the probabilitydensityof finding anatomat thedistance”r” from a givenatom.BesidescalculatingG(r) from a givenstructure,thestructurecanbemodifiedto matcha observedG(r) viatheRMC method.Note,thatthissublevel usedmany RMC commandsandwill overwritepossiblesettingsmadein theRMC segment.All commandsarelistedin thehelpentry’commands’.Only commandsuniqueto this level aredescribedbelow.

1.21.1 commands


@ ! Executes a macro (see main help)= ! Algebra (see main help)

calc! CalculatesPDFfor currentstructure

data ! reads observed PDF for RMCrefinementdese ! Deselects used atomtypes (see RMClevel)continue! Continue a stopped macro (see main help level)echo ! Echos a string, just for interactive checkeval ! Evaluates an expression (see main help)exit ! Terminates the PDF sub levelhelp ! Gives on-line help for ’pdf’ (see main help)i/jdese ! Deselect atoms (i/j) for PDF calculationi/jsele ! Select atoms (i/j) for PDF calculationmdes ! Deselects molecules (see RMClevel)msel ! Selects molecules for refinement (see RMClevel)run ! start PDF refinementsave ! saves structure or PDF to given filesele ! selects used atomtypes (see RMClevel)set ! sets most PDF parametersshow ! show current PDF settingsstop ! Stops execution of a macro (see main help level)system ! executes operating system command (see main help)wait ! Waits for user input (see main help)

1.21.2 calc

calc

This commandwill calculatethePDFof the currentstructure.Note that the resultis NOT automaticallysaved.Thismustbedoneusingthecommand’save’ (- ¯ save).

1.21.3 data

data ° file ¯Thiscommandwill readanobservedPDFfrom thefile ° file ¯ . Thefile needsto beASCII formatwith thefollowing informationon eachline: r G dr w(G). Here’r’ is thedistanceandG theobservedvalueof thereducedradialdistributionfunctionG(r). Thevalue’dr’ is ignoredandthelastvaluegivestheweightw(G)of G(r) to beusedin therefinement(e.g.1/(errorof G)).


1.21.4 i/jdese

idese ± ”all” ²³ name�²�³ number ´�µ , [ ... ]jdese ± ”all” ²�³ name�²³ number ´�µ , [ ... ]

This commanddeselectsatomtypesgiveneitherby ³ name or ³ number for thePDFcalculation.Thetwo commandsallow oneto deselectatomtypesfor eachatomin a pair ’ij’ contributing to thePDFcalcu-lation.

1.21.5 i/jsele

isele ± ”all” ²³ name�²�³ number ´�µ , [ ... ]jsele ± ”all” ²�³ name>²³ number ´�µ , [ ... ]

This commandselectsatomtypesgiven eitherby ³ name or ³ number for the PDF calculation. Allotheratomsareignored. This allows the calculationof differentialor partial PDFs. The two commandsallow oneto selectatomtypesfor eachatomin a pair ’ij’ contributingto thePDFcalculation.

1.21.6 run

run

ThiscommandstartstheRMC refinementto matchthecalculatedPDFwith theobservedone.

1.21.7 save

save ± ”pdf ” ² ”stru” µ , ³ file ´This commandallows to save either the currentPDF (”pdf”) or the currentstructure(”stru”) to the filenamed³ file ´ .

1.21.8 set

set”subcommand”

Thiscommandallowsto setmostof thePDFparameters.Someof thecommandsareexplainedin theRMCsection(- ´ rmc). Thefollowing ”subcommands”arevalid:

commands

Valid subcommandsare:

"cycl" : sets number of cycles to be calculated (see RMClevel)"disp" : sets output interval (see RMClevel)"frange" : sets the range in r used for the refinement"mdis" : sets minimal allowed distances between atoms (see RMClevel)"mode" : sets RMCmode (relaxation/switch atoms) (see RMClevel)"move" : sets sigma for generated RMCshifts (see RMClevel)"qmax" : sets maximal Q value used for termination correction"qsig" : sets SIGMA Q for resolution correction"rad" : sets radiation used to calculate PDF"range" : sets r range for PDF calculation"sigm" : sets SIGMA for CHI2 calculation (see RMClevel)

frange

set”frange”, ³ rmin ´ , ³ rmax ´Thiscommandsetstherangein ”r” thatwill beusedfor therefinement.Therangeof thePDFthatwill besavedusingthecommand’save’ is alsodeterminedby thesesettings.


qmax

set”qmax”, ¶ qmax ·Sincewecanonly measurethescatteringup to a maximumvaluein Q, theresultingPDFwill show termi-nationripples.In orderto accountfor these,terminationripplescanbecalculatedfor thecomputedPDF. Inorderto do this theactualmaximumQ value ¶ qmax· in A**-1 mustbeentered.If thevalueis zeroNOterminationcorrectionwill beapplied.

qsig

set”qsig”, ¶ qsig·This allows to entera value ¶ qsig· for the correctionof the limited resolutionof the experiment. Thisresultsin a dampeningof theG(r) functionwith increasingvaluesof r. Again if theenteredvalueis zero,nocorrectionwill beapplied.

rad

set”rad”, ”neutr on”set”rad”, ”xray” [, ¶ qx · ]

This commandselectstheradiationusedto calculatethePDF. Theweightingfactorfor eachatompair isB(i)*B(j)/ ¶ B**2 · . In caseof neutrons(”neutron”), thevaluesB(i) aresimply thescatteringlengthof theindividualelements.For Xrays(”xray”) thesituationis morecomplicatedsincethescatteringpowervariesasafunctionof Q. As anapproximationthescatteringpoweratagiveQ value ¶ qx · in A**-1 is used.Thevalue ¶ qx · canbe takenaszero(default) in which casethenumberof electronsdeterminesthe weight.Oneothercommonway is to usetheQ of thefirst peakin thediffractionpattern.

range

set”range”, ¶ rmax · , ¶ dr ·This commandallows to set the maximumr andthe stepwidth usedto calculatethe PDF. Note that ifobserveddataareused,thesevaluesaresetto thecorrespondingvaluesof thereaddatefile. All valuesareenteredin unitsof A.

1.21.9 show

show [ ¸ ”all” ¹ ”pdf ” ¹ ”mode” ¹ ”atom” º ]This commandshows thevarioussettings.If thecommandis enteredwithout furtherparameters,thePDFsettingsareshown similar to the situationwhen the parameteris ”pdf”. The parameter”mode” resultsin the outputof the currentRMC mode. Note that somesettingsarelisted that arenot usedby the PDFRMC refinement.Theparameter”atom” correspondsto thelisting of parameterslike selectedatoms,sizesof movesandminimal allowed distancesbetweenatomtypes. Finally the parameter”all” will causeallsettingsto beprintedon thescreen.

1.22 plot

plot

Switchesto thestructureplottingsubmenu.Thestructurecanbewritten in a formatsuitablefor plottingbyseveralstructureplottingprogramssuchasKUPL, GNUPLOT.Furtherhelptopicsare:


1.22.1 commands


@ ! Executes a macro (see main help)= ! assigns the value to a variable (see main help)absc ! Defines the abscissa of the plotasym ! Lists the content of the asymmetric unitchem ! Lists all type of atoms present in the crystalcol ! Defines the sequence in which the xy and z coordinates are written.continue! Coninue a stopped macro (see main help level)des ! Deselects atoms or microdomainsecho ! Echos a string, just for interactive check (see main help)exit ! Terminates the plot sub level, returns to the main DISCUS level.ext ! Sets the extend of crystal space to be plottedhelp ! Gives on-line help for ’plot’ (see main help)hkl ! Sets reciprocal space direction normal to plot sliceordi ! Defines the ordinate of the plotoutfile ! Name of output file to which the structure is writtenprog ! Selects the plotting programrun ! Starts writing of the structuresel ! Selects which atoms are to be included in the plotset ! Sets type, color and size of atom in plot fileshow ! Shows settings for the plotting parametersthick ! Sets the half thickness of the plot sliceuvw ! Sets direct space direction normal to plot slicestop ! Stops execution of a macro (see main help level)system ! Executes operating system command (see main help)type ! Sets type of output - crystal or unit cell projectionwait ! Waits for user input (see main help)vec ! Sets a point inside plot slice

1.22.2 absc

abscissa» x ¼ , » y ¼ , » z ¼Definestheabscissaof theplot. Insteadof usingtheatomcoordinateswith respectto thecrystallographicaxes,theatomsaretransformedinto thesystembasedon theabscissa,the== ¼ ’ordinate’ andthenormalto theplot slice== ¼ ’uvw’, ’hkl’. Usethesecommandsto plot theprojectionontoany plainotherthanthexy-, xz- or yz-plane.

1.22.3 asym

asym

Shows thecontentof theasymmetricunit. Thenamesof thoseatoms,a numberthat is usedasindex forits scatteringtype, their positionandtemperaturecoefficient arelisted. The numberthat is listed, is thenumberthatrefersto thescatteringcurveof thatatom.It is containedin thevariablem[ » index ¼ ]. If acellwasread,all atomsareconsideredto bedifferent,evenif they arechemicallyidenticalandhave thesametemperaturecoefficient. If a wholestructurewasread,all atomsthatarein theunit cell 0 » = xyz » 1, arechemicallyuniqueandhavea differenttemperaturecoefficientareincludedin theasymmetricunit.

1.22.4 chem

chem

Shows thetypeof all atomspresentin thecrystal.For eachdifferentatompresent,its identifying number,its nameandits temperaturecoefficient arelisted. The list containsall the atomsin the asymmetricunitplusany atomsaddedto thestructure.If atomsareremovedfrom thestructure,theprogramdoesnotcheckwhetherthereareany atomsof this type left. If a particulartypeof atomis completelyremovedfrom thestructure,it will remainin thelist of differentatoms,andwill bedisplayedby ’chem’.

1.22.5 col

col ½ ”xyz” ¾ ”yzx” ¾ ”zxy” ¾ ”zyx” ¾ ”yxz” ¾ ”xzy” ¿Definesthesequencein which thexy andz coordinatesof theatomsarewritten. If the ’prog’ ”gnuplot”is used,this will allow the userto view the structurefrom differentdirections. For ”kupl” this will giveprojectionsof thestructurealongthelastdirection.If you plot theprojectionalonga vectorselectedby == À ’uvw’, ’hkl’ the interpretationof thecoordinatetripletstakesadifferentmeaning:x representsthecoordinatealongthe== À abscissay representsthecoor-dinatealongthe== À ordinatez representsthecoordinatealongthe== À ’uvw’ directionThecoordinatesare,in this case,written as: 1.coordinate2.coordinate3. coordinatexyz abscissaordinateuvw zxy uvwabscissaordinateyzx ordinateuvw abscissayxz ordinateabscissauvw xzy abscissauvw ordinatezyx uvwordinateabscissaFor ”xyz” theplot will show theprojectionalonguvw ontotheplaneof theabscissaandordinate.For ”zxy”theplot will show theprojectionalongtheordinateonto the planeof theuvw-directionandtheabscissa.etc.Sincethethicknessof theslicewill oftenbelimited by the== À ’ thick’ command,thesequence’xyz’ wouldbethemostusefulone.

1.22.6 des

dese½ ”all” ¾Á nameÀ�¾�Á number À�¿ [ , Á nameÀ>¾�Á number À�¿ ... ]dese”mic”

Deselectstheatoms.

"all" All atoms are deselected, no atom will be plotted."mic" The microdomain status is set back to include the host structure

and any microdomains.<name> Only the atom specified by <name> is deselected.<number> Only the atom specified by the scattering type <number> is

deselected.

More thanoneatomcanbedeselectedby thecommand.

1.22.7 ext

ext ½ ”all” ¾ ”x”, Á xmin À , Á xmax ÀJ¾ ”y”, Á ymin À , Á ymax Àx¾ ”z”, Á zmin À , Á zmaxÀÂ¿Setstheextendof crystalspaceto beplotted.

"all" The whole crystal is written to the plot file."x" The extend along the x direction is limited to (including)

<xmin> and <xmax>."y" The extend along the y direction is limited to (including)

<ymin> and <ymax>."z" The extend along the z direction is limited to (including)

<zmin> and <zmax>.

If any of the parameters”x”, ”y”, ”z” is used,theextendalongtheotherdirectionsis not changed,even ifpreviouslysetwith the”all” command.

1.22.8 hkl

hkl Á h À , Á k À , Á l ÀSetsthereciprocalspacedirectionnormalto theplot slice. thecorrespondingdirectspacedirection== À’uvw’ is calculatedautomatically. If Á hkl À is setto ”000”, all atomsareplotted,otherwiseall atomsare

written to the output file, if they arewithin a slice normal to the Ã hkl Ä (and Ã uvw Ä ) direction. Thethicknessof theplot sliceis definedby the== Ä ’ thick’ command,while the== Ä ’vec’ commanddefinesapoint thatrepresentsthecenterof theslice. Furtherrestrictionson theatomsto beincludedcanbeappliedby the== Ä ’sel’ andthe== Ä ’exte’ commands.

1.22.9 mdes

mdes Å ”all” Æ�Ã number Ä�Ç [ , Ã number Ä ...]

Thiscommanddeselectsall or individualmoleculetypesusedfor theplottingoutput.

1.22.10 mole

mole Å ”all” Æ ”origin” ÇThiscommandallowstheuserto specifywhetherall (”all”) atomsof amoleculeshouldbeusedin theplotor only theorigin (”origin”) of themoleculeshouldbeused.

1.22.11 msel

msel Å ”all” Æ�Ã number Ä�Ç [ , Ã number Ä ...]

This commandallows to selectthe moleculetypesto be usedfor the plotting output. By using ’msel’the atomselectionbecomesinvalid. The parameter”all” will selectALL moleculetypes. AlternativelyindividualmoleculetypescanbeselectedusingthecorrespondingÃ numberÄ . In orderto useatomsagain,usethe’sele’command.

1.22.12 ordi

ordinate Ã x Ä , Ã y Ä , Ã z ÄDefinestheordinateof theplot. Insteadof usingtheatomcoordinateswith respectto thecrystallographicaxes,theatomsaretransformedinto thesystembasedon the== Ä ’abscissa’,’ordinate’ andthenormaltotheplot slice== Ä ’uvw’, ’hkl’. Usethesecommandsto plot theprojectionontoany plain otherthanthexy-, xz- or yz-plane.

1.22.13 outfile

outfile Ã filenameÄSetsthenameof theoutputfile to which thestructureis written.

1.22.14 prog

prog Å ”gnuplot” Æ ”kuplot” ÇSelectstheplottingprogramfor which theoutputis to beformatted.

"gnuplot" The xyz coordinates of all selected atoms are written in thesequence defined by the ==> ’col’ command.

"kuplot" The xyz coordinates of all selected atoms are written in thesequence defined by the ==> ’col’ command. A projection of thestructure along the third direction of the ’col’ parameter isplotted. The file contains the typ, color and size code setwith the ==> ’set’ command. Use ’load cr,<file>’ to read thefile with KUPLOT.

1.22.15 run

run

Startswriting of thestructure.If no outputfilenamehasbeenprovidedor no atomsbeenselected,anerrormessageis given.

1.22.16 sel

sel È ”all” ÉÊ nameË�É�Ê number Ë�Ì [ , È�Ê nameË�ÉÊ number ËmÌ ...]sel”mic”, È ”all” É ”eve” É ”none” ÉÊ number Ë�ÌDefineswhich atomsare includedin the output. Possiblevaluesfor the first mandatoryparameteraremutuallyexclusively:

"all" all atoms of the crystal are included.

This includesthe”voids” in thestructure,whicharestoredasscatteringcurvenumberzero.

<name> all the atoms called <name> of the crystal are included.This includes symmetrically not equivalent atoms.

<number> all atoms of the crystal that are of scattering type <number>are included.

"mic" selects the microdomain status. This status defines whether atomsthat are inside a microdomain are to be plotted or not.The kind of atoms to be included have to be chosen by anadditional ’sel’ command.Second parameter:"all" atoms inside any microdomain are selected, all atoms

outside all microdomains are not included."eve" Disregard microdomain status of an atom. Atoms in the

host structure and inside any microdomain are plottedalike.

<number> Only atoms inside microdomain type <number> are selected."none" Only atoms outside all microdomains are selected.

Theselectionmadestayvalid until explicitly deselected!

1.22.17 set

set È�Ê nameË>ÉÊ number Ë�Ì , Ê typ Ë , Ê col Ë , Ê sizeËThis commandallows to setthemarker type Ê typ Ë , its color Ê col Ë andsize Ê sizeË for thegivenatomor molecule. In caseof atoms,the input canbe given by its name Ê nameË or scatteringtype numberÊ numberË . For moleculesonly Ê numberË asthemoleculetype is a valid input. Theresultingfile willcontainsthecoordinatesof the atomandtyp, color andsizein a row. This file canbe readby KUPLOTusingthecommand

load cr,<file>

Thepossiblevaluesfor Ê typ Ë are:

0 : no marker 5 : filled square 10 : line (/)1 : dot 6 : empty triangle 11 : line (\)2 : empty circle 7 : cross (x) 12 : line (-)3 : filled circle 8 : cross (+) 13 : vertical line4 : empty square 9 : line (|) from y-axis

Thepossiblevaluesfor thecolors Ê col Ë are:


1 : red 4 : purple2 : green 5 : yellow3 : blue 6 : black

Thesizeof themarkers Í sizeÎ is givenrelative to themarkersizesetin theplot programKUPLOT, i.e. avalueof 1.0will resultin thefull markersizewhereas0.5will reducethesizeby 50%.If youareusing’gnuplot’ asprogramtyp (- Î ’prog’) thesettingswill beignored.

1.22.18 show

show

Showsthesettingsfor theplottingparameters.

1.22.19 thick

thic Í valueÎSetsthe half thicknessof the plot slice in Angstrom. All atomsarewritten to the outputfile, if they arewithin a slice of thickness2* Í valueÎ that containsthe direct spacepoint definedby == Î ’vec’ and isnormalto thedirectiondefinedby == Î ’hkl’ or ’uvw’. Furtherrestrictionson theatomsto beincludedcanbeappliedby the== Î ’sel’ andthe== Î ’exte’ commands.

1.22.20 uvw

uvw Í u Î , Í v Î , Í w ÎSetsthedirectspacedirectionnormalto theplot slice.Thecorrespondingreciprocalspacedirection Í hkl Îis calculatedautomatically. If Í hkl Î is setto ”000”, all atomsareplotted,otherwiseall atomsarewrittento theoutputfile, if they arewithin a slicenormalto the Í uvw Î (and Í hkl) direction. The thicknessoftheplot slice is definedby the== Î ’ thick’ command,while the== Î ’vec’ commanddefinesa point thatrepresentsthecenterof theslice.Furtherrestrictionsontheatomsto beincludedcanbeappliedby the== Î’sel’ andthe== Î ’exte’ commands.

1.22.21 type

typ Ï ”crystal” Ð ”pr ojection” ÑThis commandswitchesbetweento plot modes.The typ ”crystal” will write theatomcoordinatesof theselected(- Î ’sele’)atomsona file. Thetype”projection” will removethetranslationandall atomswill beprojectedin a singleunit cell. Thesecondtypecanbereadwith KUPLOT using’ loadcr, Í file Î ’ or ’ loadde,Í file Î , Í dx Î , Í dy Î ’ . SeetheKUPLOT onlinehelpfor moredetailson thedifferentfile formats.

1.22.22 vector

vec Í v1 Î , Í v1 Î , Í v3 ÎSetsthevectorthat representsthecenterof theplot slice. All atomsarewritten to theoutputfile, if theyarewithin a slicethat is normalto the Í hkl Î (and Í uvw Î ) directionandcontainsthedirectspacevectorÍ v1 ,v2,v3 Î . Thethicknessof theplot sliceis definedby the== Î ’ thick’ command,while the== Î ’vec’commanddefinesa point that representsthe centerof the slice. Furtherrestrictionson the atomsto beincludedcanbeappliedby the== Î ’sel’ andthe== Î ’exte’ commands.


1.23 powder

Switchesto thepowderdiffractionsublevel of DISCUS.Presentlythis is averycrudestartingpoint for thedevelopments.Bugsandproblemscouldbepresent.Thecalculationhasnotyet beenoptimizedfor speed.DISCUScalculatesthepowderdiffractionpatternbetweena lowerandupperlimit of 2-Theta.

1.23.1 commands


@ ! Executes a macro (see main help)= ! assigns the value to a variable (see main help)asym ! Lists the content of the asymmetric unitchem ! Lists all type of atoms present in the crystalcontinue! Coninue a stopped macro (see main help level)echo ! Echos a string, just for interactive check (see main help)exit ! Terminates the plot sub level, returns to the main DISCUS level.help ! Gives on-line help for ’plot’ (see main help)run ! Starts writing of the structureset ! Sets Theta limits, grid in reciprocal space, ...show ! Shows settings for the plotting parametersstop ! Stops execution of a macro (see main help level)system ! Executes operating system command (see main help)wait ! Waits for user input (see main help)

1.23.2 neut

neut

Switchesto neutrondiffraction.

1.23.3 run

run

Startsthecalculationof thepowderdiffractionpattern.

1.23.4 show

show

Showsthecurrentsettingsrelevantto thecalculationof a powderpattern.

1.23.5 set

Setsvariousparametersfor powderdiffraction.

disp

setdisp,[ Ò switch Ó ]

switchesanomalousdispersionon /off. If Ò switchÓ is ”anom” anomalousdispersionwill becalculated,iftheswitchis omitted,noanomalousdispersionis calculated.


dtth

setdtth, Ô valueÕThepowderpatternis printedat2-Thetastepsof Ô valueÕ . All reciprocalpointsarebinnedto agrid along2-Thetawith intervalsof Ô valueÕ

dh

setdh, Ô valueÕThecalculationis carriedout in reciprocalspaceintervalsof Ô valueÕ long theh00direction.

dk

setdk, Ô valueÕThecalculationis carriedout in reciprocalspaceintervalsof Ô valueÕ long the0k0direction.

dl

setdl, Ô valueÕThecalculationis carriedout in reciprocalspaceintervalsof Ô valueÕ long the00l direction.

four

setfour, Ö ”f our” × ”stack” ØSetsthe switch for the Fourier calculationmode. For all normalcrystalsthis shouldbe setto ”four”. Ifyou createda crystalusingthe== Õ ’stack”menu,you canspeedup TheFouriercalculationby settingtheswitchto ”stack”. Seethestackingfault informationregardingthedetailsof thisFouriermode.

tthmin

settthmin, Ô valueÕSetsthelower limit for 2-Theta.

tthmax

settthmax, Ô valueÕSetstheupperlimit for 2-Theta.Thepowderpatternis calculatedup to this2-Thetavalue.

temp

settemp,Ô switch Õsetswhethertemperaturecoefficients are to be usedor not. Valid valuesfor Ô switchÕ are ”use” and”ignore”. Thefirst two lettersof theswitcharesufficient.

wvle

setwvle,ÖÙÔ nameÕ>×�Ô valueÕxØDefinesthe wave lengthto be used. Anomalousdispersionwill only be calculatedif the wave lengthisgivenassymbol.


1.23.6 xray

xray

Switchesto X-ray calculation.

1.24 project

project Ú u1 Û , Ú v1 Û , Ú w1 Û , Ú u2 Û , Ú v2 Û , Ú w2 Û [ , Ú flag Û ]

This commandcalculatesthe projectionof vector Ú uvw 1 Û onto the secondvector Ú uvw 2 Û and theprojectionof the first vectoronto the planenormalto the secondvector. The Ú flagÛ is a string of fourcharactersthat indicateswhetherthe input vectorsor the outputvectorsaregiven in direct or reciprocalspacecoordinates.

The four characters correspond to:

first input vector,second input vector,projection of vector 1 onto vector 2,projection of vector 1 onto the plane normal to vector 2.

"drdd" means: vector one is given in direct space coordinates, vector 2is in reciprocal space coordinates (hkl) and the twoprojections are to be given in direct space coordinates.

Any combination of "d" and "r" is allowed.

The two output vectors are stored in the result variable:

"res[1]","res[2]","res[3]" projection of vector 1 onto vector 2"res[4]","res[5]","res[6]" projection of vector 1 onto plane normal to

vector 2

1.25 purge

purge

deletesall vacanciesin thestructurearray, thusspeedsupFouriercalculation.

1.26 r2d

r2d Ú u Û , Ú v Û , Ú w ÛThis commandtransformsreciprocalspacevector Ú uvw Û into its correspondingcoordinatesin directspace.See”r2d” for thereversetransformation.Theresultingvectoris storedin ”res[1]”, ”res[2]”, ”res[3]”.

1.27 read

read

Branchesto readinglevel of DISCUS.At this level a new unit cell or structuremay be read. The oldstructureis lost ! If necessarysave it with the– Û ”save” command.Furtherhelptopicsare:


1.27.1 commands

Valid commandsat this level:

@ ! Execute a macro file (see main help)cell ! reads a single unit cell from fileecho ! Echo a string (see main help)exit ! Exits read sublevelfree ! Allow free modification of a structure.help ! help to read (see main help)stru ! reads a file containing a whole crystalwait ! waits for user input (see main help)

1.27.2 cell

cell Ü nameÝ [, Ü nx Ý [, Ü ny Ý [, Ü nz Ý ]]]

readsthecontentsof asingleasymmetricunit fromfile Ü nameÝ andthengeneratestheunit cell. Optionallythenumberof unit cellsalongx,y,z canbegivento generatedthewholecrystal. Thenumberof unit cellsdefault to 1. Theunit cellsarearrangedsymmetricallyaroundtheorigin, .i.e. from -nx/2to +nx/2etc.Aftertheunit cell hasbeenreadtheprogramreturnsto themainDISCUSlevel.

1.27.3 fr ee

fr ee[ Ü a Ý , Ü b Ý , Ü c Ý , Ü alpha Ý , Ü beta Ý , Ü gammaÝ ]

No structureis read.Thespacegroupis setto ”P1”. Thelatticeconstantsaresetto theoptionalvaluesonthecommandline. Defaultvaluesare1,1,1Angstromand90,90,90degrees.Thestructuredoesnotcontainany atoms.

1.27.4 stru

stru Ü nameÝreadsa whole structurefrom file Ü nameÝ . The spacegroupinformation is ignored,nor is a checkforconsistency of spacegroupandlatticeconstantsperformed.

1.28 remove

remove Ü start Ý [, Ü endÝ ]remove Ü start Ý [, Ü endÝ ] , ”mole” [ ,”type”, Ü t start Ý [, Ü t endÝ ]]

TheparametersÜ startÝ and Ü t startÝ cantakeoneof thefollowing values: Þ�Ü startÝ>ß ”all” ß ”last” àRemovesatom(s)numberÜ startÝ to Ü endÝ from thestructure.If you usethekeyword ”all”, all atomsareremoved. If you usethekeyword ”last”, only the lastatomisremoved.Internally, this commandonly setsthe scatteringtype of theseatom(s)to zero. Otherwisethe atom(s)istreatedasif present.Specifically, in thearraycontainingthestructurethesequenceof atomsis notchanged.Thesecondform of thecommandremovesatomsthatarepartof themolecule(s)Ü startÝ through Ü endÝ .Optionallyyou canspecifywhich moleculetypewill be removed. Only thosemoleculesof a type in therangeÜ t startÝ through Ü t endÝ will beremoved.Thedefault for thisoptionis all typeof molecules.If you usethekeyword ”all”, all moleculetypesareremoved. If you usethekeyword ”last”, only the lastmoleculetypeis removed.


1.29 replace

replace á index â , á at â [, á dbw â ]replace á at1 â , á at2 â , ã ”all” ä�á siteâJå , á prob âreplace á mo1â , á mo2â ,”mol”replace á mtyp â , á mol â ,”mol”, á prob âThis commandallows to replaceatomsandmolecules. The first two variationsoperateon atoms. Thefirst variationreplacesthe atomat index á index â with atomname(or number) á atâ . It the atomtypdoesnotalreadyexist in thecrystal,thetemperaturefactor á dbwâ hasto begivenasadditionalparameter.Alternatively theatomtype á at1â canbereplacedby á at2â within thecompletecrystalwith aprobabilityof á probâ . Thisworksmuch(!!) fasterthanreplacingusingDISCUSloops.Thethird parameterspecifiesif all ”all” occurringatomsof type á at1â mightbereplacedor just thoseon thegivensite á siteâ .Thelasttwo variationsof the’replace’commandoperateonmolecules.Thethird variantreplacesmoleculeá mo1â by á mo2â . Thepositionsareexchangedrelative to theorigin of themolecule(atom1) andbothmoleculesMUST have thesamelength. Thelastvariationworksthesameway, just all moleculesof typeá mtypâ will bereplacedwith moleculeá mol â with thegivenprobabilityof á probâ .

1.30 rmc

rmc

Enter”reverseMonteCarlo” sectionof discus.Thispartof theprogramallows to ”fit” a modelatomcon-figurationto measureddiffusescatteringdata. Thedifferencebetweencalculatedscatteringandobservedscatteringis minimized. Movesminimizing this differencearealwaysaccepted,othermovedonly with aprobabilityof exp (-diff**2).(Nield etal.,ActaCrystA51 (1995),763-771for moreinformation)

1.30.1 commands


@ ! Executes a macro (see main help)= ! Algebra (see main help)data ! read experimental data for RMCfitdese ! Deselects the atomtypes allowed for RMCmoves/switches (-> sele)continue! Coninue a stopped macro (see main help level)echo ! Echos a string, just for interactive checkeval ! Evaluates an expression (see main help)exit ! Terminates the rmc sub level, returns to the main DISCUS level.help ! Gives on-line help for ’rmc’ (see main help)mdes ! Deselects moleculesmsel ! Selects molecules for RMCrefinementrese ! reset RMCsettings (i.e. reset plane counter)run ! start RMCfitsave ! saves structure or intensity to given filesele ! selects the atomtypes allowed for RMCmoves/switches (-> dese)set ! sets most RMCparametersshow ! show current RMCsettingsstop ! Stops execution of a macro (see main help level)system ! executes operating system command (see main help)wait ! Waits for user input (see main help)

1.30.2 data

data ã ”x-ray” ä ”neutr on” å , ã�á nameâ�ä�á value â�å , á file â , á wic â ,á e11â , á e12â , á e13â , á e21â , á e22 â , á e23 â , á e31â , á e32 â , á e33 â

This commandreadsthe experimentaldatastoredin æ file ç . The parameter”x-ray” / ”neutron” selectswhatkind of scatteringdataarestoredin thefile. Thesecondparameteris the wavelengthwhich canbegivenas æ nameç (like cua1..) or asvalue(line 1.23).After thefilenameæ file ç theweightingschemetobeusedcanbespecified.Theparameteræ wic ç cantake thefollowing values:

"one" : w(Int) = 1.0 "squa" : w(Int) = Int**2"sqrt" : w(Int) = SQRT(Int) "inv" : w(Int) = 1/Int"log" : w(Int) = LOG(Int) "isq" : w(Int) = 1/SQRT(Int)"lin" : w(Int) = Int

All othervaluesfor æ wic ç aretakenasthenameof afile containingtheweights.Thisfile andthedatafilehaveto bethesametype! Finally thethreecornersof theinputdataplanearegivenin thefollowing order:

<e11>,<e12>,<e13> : hkl’s of the lower left corner<e21>,<e22>,<e23> : hkl’s of the lower right corner<e31>,<e32>,<e33> : hkl’s of the upper left corner

The formatof the input file is setby the ’setdata’ command.For moreinformationaboutthe supporteddatafile formatsseehelpfor the’setdata’command.By repeatingthedatacommandyou canreadseveralplaneswith exp. datafor theRMC fit. To startagainusethe’rese’command.

1.30.3 dese

deseè ”all” éæ nameç�é�æ number ç�ê , [ ... ]

Thiscommanddeselectsatomtypesgiveneitherby æ nameç or æ numberç for theRMC moves,i.e. ’dese’thoseatomtypeswhichshouldnotbemovedor switched.

1.30.4 msel

msel è ”all” é�æ number ç�ê [ , æ number ç ...]

This commandallows to selectthe moleculetypesto be usedfor the RMC refinement.By using’msel’the atomselectionbecomesinvalid. The parameter”all” will selectALL moleculetypes. Alternativelyindividualmoleculetypescanbeselectedusingthecorrespondingæ numberç . In orderto useatomsagain,usethe’sele’command.

1.30.5 mdes

mdes è ”all” é�æ number ç�ê [ , æ number ç ...]

Thiscommanddeselectsall or individualmoleculetypesusedin theRMC refinement.

1.30.6 rese

rese

This commandresetstheRMC parameters.In this versiononly the ’planecounter’is resetandthe ’data’commandwill startreadingplane1 again.


1.30.7 run

run

StarttheRMC fit. After therun is finished,thefollowing valuesarestoredin theres[i] variables:

res[1] : last value of CHI2res[2] : number of tried movesres[3] : number of accepted ’good’ movesres[4] : number of accepted ’bad’ movesres[5] : DELTA CHI2 average during the last runres[6] : DELTA CHI2 standard deviation during the last runres[7] : DELTA CHI2 maximum value during the last runres[8] : elapsed time / cycle in seconds

1.30.8 save

save ë subcommandìThiscommandis for saving thecalculatedintensitiesor theresultingstructure.Valid subcommandsare:

lots

save”lots”, ë nameìThiscommandsavesthecurrentsetof lot originsto thefile namedë nameì . Theselot originscanbeusedasdefault in subsequentrefinementratherthancreatinganew setof randomlots (- ì ’setlots,..’).

stru

save”stru”, ë nameìThis commandsavesthe currentstructureto the file namedë nameì . The format is identicalto theunitcell or structurefile. Eachatomis written in formatA4,3(2X,F11.6),5X,F6.4.Thefilenamecanbecreatedby anformatstringandoneor morenumbers- ì filenames.

scat

save”scat”, ë planeì , ë nameìsave ”scat” saves the current computed intensities of plane ë planeì in the following format:h,k,l,skal*(a**2+b**2)+back (= intensity).

sym

save”sym”, ë planeì , ë symì , ë nameìDoesthesameas’save scat,..’, but theusercansave alsotheresultingintensitiesof symmetricequivalentplanesby giving thenumberof thesym.-transformation(1=datacorrespondingto inputdata).

1.30.9 sele

sele í ”all” î�ë nameì�î�ë number ì�ï , [ ... ]

This commandselectsatomtypesgiveneitherby ë nameì or ë numberì for theRMC moves,i.e. ’sele’thoseatomtypeswhichshouldbemovedor switchedduringtheRMC cycles.

1.30.10 set

set”subcommand”

Thiscommandallowsto setmostof theRMC parameters.Thefollowing ”subcommands”arevalid:

commands

Valid subcommandsare:

"aver" : sets the portion of the crystal to be used for <F> calc."back" : controls if background is calculated during RMCcycles"const" : sets possible constrains for scaling factor/background"cycl" : sets number of RMCcycles to be calculated"data" : sets data type of input/output diffuse scattering files"dbw" : ignore/use temperature factor"disp" : sets output interval"log" : controls if "rmc.log" will be created during calculation"mdis" : sets minimal allowed distances between atoms"mode" : sets RMCmode (relaxation/switch atoms)"move" : sets sigma for generated RMCshifts"range" : sets Q-range of data used for RMCrefinement"scal" : controls if scaling factor is calculated during RMCcycles"sigm" : sets SIGMA for CHI2 calculation"sym" : controls if symmetric equivalent planes of input data should

be used for RMCcalculations.

aver

set”aver”, ð per ñThiscommandsetstheportionof thecrystal,thatshouldbeusedto calculateð F ñ . Thevariable ð perñ isgivenin %. Theaveragestructurefactor ð F ñ is calculatedandsubtractedfrom theoverallstructurefactorcalculatedat the beginning of the RMC refinement.Startingfrom thesevaluesthe contributionsof thechangesatomsduringtheRMC cyclesarecalculatedandthestructurefactoradjusted.Thereis no checkweatherð F ñ changessignificantlyduringtherefinement.To switch the useof ð F ñ off, just setthe valueof ð perñ to zero. After settingthe valueof ð perñ thestructurefactorwill be recalculated.This canalsobe usedto recalculatethe Fourier transformandtheaveragefrom timeto timeduringtheRMC refinementif theaveragestructureis changing.

back

set”back”, ò ”on” ó ”off ” ô ,[ ð valueñ ], [ ð planeñ ]

This commandcontrolsif a backgroundparametershouldbe calculatedand usedfor the RMC fits. Ifthecalculationof thebackgroundparameteris switchedoff its valuecanbesetto ð valueñ otherwisethedefault is 0. Thesecondoptionalparameterallows to specifytheplanethecurrentvalueof ð valueñ is setfor. If theparameterð planeñ is omitted,thevalueof ð valueñ is setfor ALL experimentaldataplanes.

const

set”const”, ð p1 ñ , ð p2 ñThiscommandallowsto constrainthescalingfactorandbackgroundparameterof thetwo inputdataplanesnumberð p1ñ and ð p2ñ . If ð p1ñ and ð p2ñ areequal,noconstrainis set,andtheplaneshavetheir indi-vidualscalingfactor/background.If two planesshouldhavethesamevaluesfor scalingfactor/background,theconstrainis setby ð p1ñ notequal ð p2ñ . Thevalueof ð p1ñ is theplanewhichshouldtakethevaluesfor scalingfactor/backgroundof plane ð p2ñ . Not, thatthevalueof ð p1ñ hasto besmallerthan ð p2ñ .If for examplescalingfactor/backgroundfor plane2 shouldbethesameasfor plane1, usethecommand’setconst,2,1’.If therearemorethantwo planesto constrainusethecommandseveraltimes.Plane1 to 3


canbeconstrainedby ’setconst,2,1’and’setconst,3,2’.to unconstraintheplanesagaintype’setconst1,1’,’setconst,2,2’and’setconst,3,3’.

cycl

set”cycl”, õ icyc öThis commandsetsthenumberof RMC movesto bedoneafterthe’run’ command.Notethatthenumbergiven is the actualnumberof RMC movesto be tried and*NOT* the numberof RMC cycles,which isnormallydefinedasthenumberof movesnecessaryto visit everycrystalsiteonceonaverage.

data

set”data”, ÷ ”nipl” ø ”pgm” ùThiscommandssetsthedatatypeof theexperimentaldatafilesusedasinput for RMC andthecorrespond-ing outputfiles. Therearecurrentlytwo file formatssupported:

"nipl" : An ASCII file containing the Z-values in the following format:

nx ny ! # pixels in x- and y directionxmin xmax ymin ymax ! dimensions in x- and y-direction (ignored)data ! ny rows of nx intensity values

"pgm" : PGMfile (pbmplus package). In the current version, onlyASCII PGMfiles are supported. To convert the binary filesinto the ASCII PGMversion, use the ’pnmnoraw’ program,which is part of the ’pbmplus’ package.

disp

set”disp”, õ id öThiscommandsetstheupdateinterval of theoutput.

dbw

set”dbw”, ÷ ”on” ø ”off ” ù [, õ planeö ,...]

This commandcontrolswhethertheDebye-Waller factoris ignoredor usedwhenthescatteringamplitudeis calculated.If noparameterõ planeö is given,thesettingaffectsALL readdataplanes.

log

set”log”, ÷ ”on” ø ”off ” ùThis commandcontrols if in the RMC main loop the screenoutput shouldalso be logged to the file”rmc.log”. This file containsonly the last outputandshouldgive the possibility to watch the programsprogressbecausecachedoutputredirectionmightnotupdateoftenenough.

lots

lots ”off ”lots ÷ ”box” ø ”ellipsoid” ù , õ lx ö , õ ly ö , õ lz ö , õ n ö , ÷ ” yes” ø ”no” ù ,[ õ fnameö ]

This commandallows to usethe ’ lot’ optionduringtheRMC refinement.For detailsaboutthecommandandits parametersseethehelpfile entryfor ’four lots’.Theoptionallastparameteris a filenamefor a file containinga predefinedsetof lot origins. This file canbecreatedusing’save lots,..’ aftera RMC refinementwascarriedout. If no filename õ fnameö is given,DISCUScreatesa new randomsetof lots for theRMC fit.


Theadvantageof usinglots is thecombinationof a smoothcalculateddiffractionpatternasaverageof theFouriertransformof smallcrystalvolumes(lots). This forcesRMC ona ’ local’ scalein realspacewithouttheproblemof largeerrorsandnoisypatternsasfor smallcrystalsizes.It is importantto subtracttheaveragestructurefactor(- ú setaver)whenusingthis modeevenif ”periodicboundaryconditions”arefulfilled, becausetheFouriertransformof thelotsshapeneedsto besubtractedaswell as û F ú . Thiscanbedoneusingthecommand’setaver ..’.

mdis

set”mdis”, ü ”all” ýû nameú�ýû number ú�þ ,ü ”all” ý�û nameú�ý�û number ú�þ , û dist úThis commandsetsthe minimal allowed distancebetweentwo atomtypesto the valueof û distú A. Ageneratedmove will only be acceptedif the moved atom is not closerthan û distú to the others. Theatomtypesto be selectedcanbe specifiedby eithernameor numberor all atomtypescanbe selectedbytyping ”all”.

mode

set”mode”, ü ”shi[ft]” ý ”swc[hem]” ý ”swd[isp]” ý ”ext[er nal]” þ ,[ ü ”a[ll]” ý ”l[ocal]” ý ”sl[ocal]” ý ”si[te]” þ ]Thiscommandallowsto selectoneof thethreeRMC operationmodes:

"shift" : The selected atoms are displaced by a random move. Themax. size of a move can be specified via "set move .."command.

"swchem" : Here two atoms are selected at random and their chemistryis switched (if the atoms are selected via "sel" command).If your structure consists of only ONE atom type this modewill just waste computer time :-)

"swdisp" : Here the displacement from the average structure of twoselected atoms of the SAME type are switched. The modecan only properly work, if there are initial displacementsgenerated e.g. by the "therm" command.

"external" : The modification of the structure for each RMCmove is doneusing an user supplied external subroutine. Check thesource file ’extrmc.f’ for details how to supply such asubroutine.

The secondoptional parameterspecifiesif the pair of the atomsto be selectedfor the SWCHEM andSWDISPmodeshouldbe restrictedin any way. The following settingsarevalid, the setting”all” is thedefault,whichwill betakenif nosecondparameteris entered.

"all" : Any atom within the crystal can be chosen as second atom."local" : Only atoms within +-1 unit cell from the first selected

atom will be chosen."slocal" : Same as "local" only the second atom must be on the same

site within the unit cell as the first one."site" : Atom on the same site in any unit cell are allowed as

second atom.

move

set”move”, ü ”all” ý�û nameú�ýû number úmþ , û sxú , û syú , û szúSetsanuserdefinedsigmafor thegeneratesmoves.ThecreatedshiftsareGaussiandistributed.Thedefaultis a sigmaof 0.2 unit cell. Note that thevaluesof û sxú , û syú and û szú aregiven in unit cell units to


speedup theRMC runs. In casemoleculesareselectedÿ number� specifiesthemoleculetype,otherwiseatomsareaddressedby their ÿ number� or ÿ name� .

range

set”range”, ”all”set”range”, ÿ qmin � , ÿ qmax �set”range”, ÿ hmin � , ÿ kmin � , ÿ lmin � , ÿ hmax � , ÿ kmax � , ÿ lmax �This commandallows to seta rangein Q which will beusedfor theRMC refinements.This canbeusefulif e.g. occupationaldisordershouldonly berefinedbasedon thelow Q partof the input datawhereasthedisplacementsshouldberefinedusingthecompletediffusescatteringdataset.Thereare3 waysto specifytheQ range:”all” will usethecompleteinput datasetfor thefit. TheQ-rangecanbegivenas ÿ qmin� , ÿ qmax� ( in reciprocalA) or ashkl’s ( ÿ hmin� ,...,ÿ lmax� ).

scal

set”scal”, � ”on” � ”off ” � ,[ ÿ value� ], [ ÿ plane� ]

Thiscommandcontrolsif ascalingfactorshouldbecalculatedandusedfor theRMC fits. If thecalculationof thescalingfactoris switchedoff it canbesetto thevaluegivenby ÿ value� . If no valueis given,thedefault is 1. Thesecondoptionalparameterallows to specifytheplanethecurrentvalueof ÿ value� is setfor. If theparameterÿ plane� is omitted,thevalueof ÿ value� is setfor ALL experimentaldataplanes.

sigm

set”sigm”, ÿ sigma�Thiscommandsetsthevaluefor SIGMA. CHI2 is calculatedbyCHI2 = SUM (Fobs-Fcalc)**2/SIGMA**2

Thevalueof SIGMA is importantfor thecalculation.A too largevaluewill allow nearlyevery move anda too small valuewill drive thefit in thenearestlocal minimum. Thedefault valueis 0.01If thevalueofSIGMA is setto zero,only movedimproving thefit will beaccepted.For testanddebugrunsa settingof SIGMA to -9999.will resultin theacceptanceof ALL moves.

sym

set”sym”, � ”on” � ”off ” �This commandscontrolstheuseof symmetricequivalentplanesto thereaddata-planesfor theRMC cal-culations.If this flag is setto ”off”, only theexperimentaldataareusedfor CHI2 calculation,if theflag is”on” thesymmetryof themeasureddatais takeninto account.

1.30.11 show

show [ ÿ subcommand� ]

Shows thecurrentparametersettingsof theRMC subsection.Thefollowing subcommandsallow to selectcertainparametersof interest.Theallowedsubcommandsare:

"all" : show all settings (same as calling ’show’ without parameter)"atom" : show selected atoms, minimal distances, ..."data" : show information about experimental data"mode" : show general RMCcalculation settings"rval" : show R-values for current refinement"sym" : show information about using symmetry information of read planes


1.31 save

save � name�savesthecurrentstructureto file � name�The format is identical to the unit cell or structure file. Each atom is written in formatA4,3(2X,F11.6),5X,F6.4If the’save’ commandis usedwith oneparameter, theparameteris interpretedasoutputfile name.Seetheentry== � ’filenames’underthecommandlanguageentry in themainhelpsectionon informationaboutvalid file namesandfile namesubstitution.Thesave menuis executedusingthecurrentdefault valuesandthestandardDISCUSpromptreturns.If the’save’ commandis usedwithoutparameter, thesave menuis called.At thismenuyou candefinetheoutputformatof thestructurefile, its name,which informationandwhichatomsto include.

1.31.1 commands

Valid commandsat this level are

@ ! Execute a macro file (see main help)= ! assigns the value to a variable (see main help)asym ! Shows asymmetric unitchem ! Shows the atoms present in the crystalcontinue! Coninue a stopped macro (see main help level)des ! deselects atomsecho ! echo a string (see main help)eval ! Evaluates an expression for interactive check (see main help)exit ! terminates ’save’file ! Defines the file name to which the structure is writtenformat ! Defines the format of the structure filehelp ! gives on line help for saving the structure (see main help)omit ! Defines which information to omit from the filerun ! starts the saving of the structuresel ! selects atoms to be included in the structure fileshow ! shows the current parametersstop ! Stops execution of a macro (see main help level)system ! Executes operating system command (see main help)wait ! Waits for user input (see main help)write ! Defines which information to write to the file

1.31.2 asym

asym

Shows thecontentof theasymmetricunit. Thenamesof thoseatoms,a numberthat is usedasindex forits scatteringtype, their positionandtemperaturecoefficient arelisted. The numberthat is listed, is thenumberthatrefersto thescatteringcurveof thatatom.It is containedin thevariablem[ � index � ]. If acellwasread,all atomsareconsideredto bedifferent,evenif they arechemicallyidenticalandhave thesametemperaturecoefficient. If a wholestructurewasread,all atomsthatarein theunit cell 0 � = xyz � 1, arechemicallyuniqueandhavea differenttemperaturecoefficientareincludedin theasymmetricunit.

1.31.3 chem

chem

Displaysthe type of atomspresentin the crystal. For eachtype of atom, its scatteringcurve number,its nameandits temperaturefactorarelisted. Warning,even, if all atomsof a particulartype have beendeleted,its scatteringtypewill remainin thelist. This list couldthereforeincludemoretypesof atomsthanareactuallypresentin thecrystal.

1.31.4 des

des � ”all” �� name�� number � [ , �� name�� number � ...]des”mic”

Deselectschoicesmadeby == ’sel’ . Possiblevaluesfor theparameteraremutuallyexclusively:

"all" all atoms of the crystal are deselected."mic" The selection of atoms that are inside a microdomain is canceled.<name> all the atoms called <name> of the crystal are deselected.

This includes symmetrically not equivalent atoms.<number> all atoms of the crystal that are of scattering type <number>

are deselected.

More thanoneatommaybedeselectedatonce.

1.31.5 file

file � filenameSetsthenameof theoutputfile to which thestructureis written.

1.31.6 format

format � ”k eyword” � ”nok eyword” �The keyword controlledformat useskeywords analogousto the commandsof DISCUSto describetheinformationin thestructurefile. Seethehelpon ”data” at themainhelp level for a completelisting of allkeywords. A flexible numberof keywordscanbe includedat theheaderof thestructurefile == ’write’and’omit’.Thenon-keywordcontrolledformatwritesasimplifiedfile thatcontainsonly thefollowing information:

Line 1: Title up to 80 charactersline 2: Space group symbol [,origin choice number]line 3: Lattice constants a,b,c,alpha,beta,gamma

andfor eachatoma line with:

Name(4 characters) x y z isotropic B

1.31.7 incl

incl �� start , � end � ”all” �Theunit cell transformationincludesall atomsnumbered� start to � end inclusively. All otheratomsareignored. If, insteadof explicit numbers,theparameter”all” is given,theunit cell transformationwillincludeall atomsof thecrystal.This holdseven,if at a latertime you includefurtheratomsin thecrystal.Thus,you candefinea setupfor the unit cell transformationsearly in a lengthymacro,thenmodify thecrystaland just run the unit cell transformationlater on. In additionyou candefinethe atomsthat areaffectedby theunit cell transformationoperationwith the== ’sele’and’dese’commands.

1.31.8 omit

omit � ”all” � ”generator” � ”ncell” � ”symmetry” � ”molecule” �Thekeywordcontrolledformatincludesthemandatorylines: title spcgrpcell atomsAll otherkeywordsareoptional.”all” All optionalkeywordsareomittedfrom thestructurefile.”generator”The additionalgeneratorsare omitted from the structurefile, while the statusof the otherkeyword is notchanged.”ncell” Thenumberof unit cellsandthenumberof atomsin eachunit cell areomittedfrom thestructurefile, while thestatusof theotherkeyword is notchanged.”symmetry” Theadditionalsymmetryoperatorsareomittedfrom thestructurefile, while thestatusof theotherkeyword is notchanged.”molecule” Althoughthecrystalcontainsmoleculestheir typeandcontentis not written to theendof thestructurefile. WARNING: All informationaboutmoleculesis lost!

1.31.9 run

run

Startsthetransformationoperation.

1.31.10 sel

sel � ”all” �� name�� number � � [ , �� name�� number �� ...]sel”mic”, � ”all” � ”eve” � ”non” �� number ��Thiscommandexecutestwo differentfunctions.It servesto selectthoseatomsthatwill bemodifiedby theunit cell transformationandsecondlyit cansetthemicrodomainstatus.First function:Defineswhich atomsare includedin unit cell transformations.Possiblevaluesfor the first mandatoryparameteraremutuallyexclusively:





More thanoneatommaybeselectedatonce.Secondfunction:Defineshow atomsinsideany microdomainsareto betreated.Thesecondparameterservesto distinguishdifferentpossiblevaluesof thestatus.

"mic" selects whether atoms that are inside a microdomain are to bemodified by the unit cell transformation operation or not.The kind of atoms to be included are to be chosen by anadditional ’sel’ command.Second parameter:"all" atoms inside any microdomain are selected, all atoms


host structure and inside any microdomain are includedalike.

"none" Only atoms outside all microdomains are selected.<number> Only atoms inside microdomain type <number> are selected.



1.31.11 show

show

Showsthecurrentparametersof thetransformationoperation.

1.31.12 write

write � ”all” � ”generator” � ”ncell” � ”symmetry” � ”molecule” �Thekeywordcontrolledformatincludesthemandatorylines: title spcgrpcell atomsAll otherkeywordsareoptional.”all” All optionalkeywordsarewritten to thestructurefile.”generator”If additionalgeneratorswerereadfrom theinputfile they will bewrittento thestructurefile aswell.”ncell” Thenumberof unit cellsandthenumberof atomsin eachunit cell arewritten to thestructurefile.Thenumberof unit cellscorrespondsto theparameterusedfor the ’read/cell’command.Thesenumbersareneededfor a fastassociationbetweenatomnumberandits unit cell insidea largecrystal.Warning!!!!If you purged”voids” from thecrystal,thenumberof atomsperunit cell is no longerconstantthroughoutthecrystalandnofixedassociationexistsbetweenatomnumberandthecorrespondingunit cell. Useof thepurgecommandis discouraged!!!!!!”symmetry” If additionalsymmetryoperatorswere readfrom the input file they will be written to thestructurefile aswell.”molecule” If thecrystalcontainsmoleculestheir typeandcontentis writtento theendof thestructurefile.

1.32 seed

seed[ � value� ]

Reinitializesthepseudorandomgenerator. Theseedpassedto therandomgeneratoris -abs(nint(value)).Ifthe � value� is omitted,therandomgeneratorwill bepassedthenumberof hundredthof secondspassedsincemidnight,essentiallyinitializing thesequenceataunknown fairly randompoint.

1.33 show

show � subcommand� ,..

Thiscommandallowsto obtainvariousinformationaboutthemodelcrystal,DISCUSsettingsetc.Valid subcommandsare:

1.33.1 asym

show ”asym”

hows the contentof the asymmetricunit. The namesof thoseatoms,a numberthat is usedasindex forits scatteringtype, their positionandtemperaturecoefficient arelisted. The numberthat is listed, is thenumberthatrefersto thescatteringcurveof thatatom.It is containedin thevariablem[ � index � ]. If acellwasread,all atomsareconsideredto bedifferent,evenif they arechemicallyidenticalandhave thesametemperaturecoefficient. If a wholestructurewasread,all atomsthatarein theunit cell 0 � = xyz � 1, arechemicallyuniqueandhavea differenttemperaturecoefficientareincludedin theasymmetricunit.


1.33.2 atom

show ”atom”, � number � [, � end� ]show ”atom”, ”all”show ”atom”, ”last”

Thetype,positionandisotropicB of atomnumber� number� areshown. If theoptionalsecondparameter� end� is given,all atomsin therange � number� to � end� areshown. If thesecondparameteris ”all”,all atomsin thecrystalareshown. WARNING, this couldlasta while :-) If thesecondparameteris ”last”,only thelastatomof thecrystalis shown. This is identicalto settingthesecondparameterto ”n[1]”, whichcontainsthenumberof atomsin thecrystal.If � number� is higherthanthenumberof atomsin thecrystal,nothingis shown andno errormessageisdisplayed.If � end� is higherthanthenumberof atomsin thecrystal, � end� is resetto the lastatominthecrystal.

1.33.3 chem

show ”chem”

Displaysthe type of atomspresentin the crystal. For eachtype of atom, its scatteringcurve number,its nameandits temperaturefactorarelisted. Warning,even, if all atomsof a particulartype have beendeleted,its scatteringtypewill remainin thelist. This list couldthereforeincludemoretypesof atomsthanareactuallypresentin thecrystal.A shortinformationaboutthecontentof theasymmetricunit is printed.

1.33.4 cdim

show ”cdim”

Printsthecurrentcrystaldimensions.Thesmallestandlargestcoordinatesof any atomalongx,y andz areprinted.

1.33.5 error

show ”err or”

Theerrorstatusof DISCUSis displayed.

1.33.6 molecule

show ”molecule”, � ”all” � ”last” show ”molecule”, � number � [, � end� ]

For eachmoleculein therange� number� to � end� thetype,numberof theatomin thecrystal,positionandisotropicB of all atomin themoleculeareshown.If thesecondparameteris ”all”, all moleculesin thecrystalareshown. WARNING, this couldlasta while:-) If thesecondparameteris ”last”, only thelastmoleculesof thecrystalis shown.If � number� is higherthanthenumberof moleculesin thecrystal,nothingis shown andnoerrormessageis displayed.If � end� is higherthanthe numberof moleculesin the crystal, � end� is resetto the lastatomin thecrystal.

1.33.7 result

show ”r esult”

Theresultarrayis shownonscreen.Thenumberof valuesshowndependsonthelastcalculationperformed.Furtherinformationaboutthecrystal,its compositionetccanbeobtainedby evaluatingthecorresponding== � variable.


1.33.8 scat

show ”scat”, !" name#%$&" number #%' [, !" name#%$" number # ' ...]Shows thescatteringcurve of theselectedatomtypes,which maybegivenasthescatteringnumberof astheelementname.

1.34 stack

stack

Switchesto the stackingfault submenuof DISCUS.At this sub menuyou createa crystal containingstackingfaults.Severaltypesof layerscanbestackedon topof eachother. At presenttheselayersarereadfrom file. In future releasesyou will beableto call a macrothatcreatesthe layer. A layercouldbea 2-dimensionallayerof atomsor unit cellsof any thicknessor a1-dimensionalrow of atomsor unit cells.Thetranslationvectorsfrom onelayer typeto thenext canbedefinedandneednot beexactvaluesbut canbeGaussiandistributed.A correlationmatrixdefinestheprobabilitiesof layersequences.Theseprobabilitiesonly includefirst neighborinteractions.Alternatively to thestackingfaultsruledby thecorrelations,youcanincluderandomstackingfaults.Thesestackingfaultschooseat randomthenext layertypeandthetranslationvector.Youcancreatethecrystalfollowing two alternatechoices:1) Theorigin of thecurrentlayeris thesumof thepreviousorigin andthetranslationvector2) Theaboveorigin is takenmodulothemodulusvectors.By usingthefirstoption,thecrystalcontinuouslygrowsin onedirectionasgivenby thetranslationvector(s).By usingthesecondoptiontheoriginsarerestrictedto a finite rangearoundtheaveragetranslationvector,which resultsin azig-zagshapedcrystal.Themenuincludesanew approachto calculatetheFouriertransformthatsavesconsiderablecomputationaltime.Furtherhelptopicsare

1.34.1 commands


@ ! Execute a macro file (see main help)= ! assigns the value to a variable (see main help)aver ! Sets the intended average translationccol ! Reads a single column of the correlation matrixcele ! Reads a single element of the correlation matrixcontinue! Coninue a stopped macro (see main help level)crea ! Creates the list of microdomainscrow ! Reads a single row of the correlation matrixecho ! echo a string (see main help)eval ! Evaluates an expression for interactive check (see main help)exit ! terminates ’stack’ (see main help)four ! calculates the Fourier transform in quick modehelp ! gives on line help for symmetry operations (see main help)layer ! Reads the name of a file that contains a layermodulus ! Reads the modulus vector of the translationnumber ! Reads the number of layers to be createdrandom ! Sets values for random stacking faultsrese ! Resets the number of layers to zerorotate ! Set values for rotational disorder of the layersrun ! Decorates the list of origins with atoms to create the crystalset ! Sets parametersshow ! Shows the current settingssigma ! Reads the sigmas for the translation vectorsstop ! Stops execution of a macro (see main help level)system ! Executes operating system command (see main help)


trans ! Reads the translation vectorswait ! Waits for user input (see main help)

1.34.2 aver

aver ( u ) , ( v ) , ( w )Setsthe intendedaveragetranslation.If themodulusis switchedon == ) ’setmodulus’,andthemodeofthetranslation== ) ’settrans’is setto ”fix ed”, thisvectoris used.

1.34.3 ccol

ccol ( nr ) , ( c1nr ) , ( c2nr ) ,...,( cmdtypenr )Reada singlecolumn ( nr ) of thecorrelationmatrix. Following theindex ( nr ) , asmany parametersastherearelayertypesmustfollow. Thesumof any columnneednotbeequalto one.

1.34.4 cele

cele ( i ) , ( j ) , ( value)Readsthevalue ( value) thatis storedin element( i ) , ( j ) of thecorrelationmatrix.

1.34.5 crea

crea

Createsthe list of layer origins. No changesaredoneto the actualstructure,this is performedby thecommand== ) ’run’.

1.34.6 crow

crow ( nr ) , ( cnr ) 1, ( cnr ) 2,...,( cnrmdtype )Readasinglerow ( nr ) of thecorrelationmatrix. Following theindex ( nr ) , asmany parametersastherearelayertypesmustfollow. Thesumof any row neednotbeequalto one,aslongasthesumof all rows isidentical.

1.34.7 four

four

A crystalwith stackingfaultscanbecreatedin thefollowing stepwisemanner:

1. Create the distribution of layer origins.2. Convolute each origin with the corresponding layer.

At this point, the convolution theoremsavesa lot of computationtime sincethe Fourier transformof aconvolution is equalto theproductof the individual Fourier transforms.TheFourier transformapproachrealizedin thestackingfaultmenuoperatesby thefollowing steps:

0. The current parameters of the ==> ’fourier’ menu are used.1. For each layer type calculate the Fourier transform of the

list of origins.Calculate the Fourier transform of the actual atoms in the layer.Multiply the resulting complex amplitudes and store the resultsin temporary files.

2. Add the complex amplitudes from all layer types and store theresult in internal memory.


Theusercanthenwrite any desiredoutputvalueusingthe== * ’output’ submenu.Note:

In orderto calculatetheFourier transformof eachlayer type theatomsin thecorrespondingfile arereadinto the internalstructurearray. A previousstructureis lost! If necessarysave this structureto file by the== * ’save’ command.Note:

DISCUSdoesnot comparethespacegroupor latticeconstantsin thedifferentlayerfiles. You mustmakesurethattheseareidentical.

1.34.8 layer

layer + filename*Definesa new layer type. Thefile + filename* mustbea standardDISCUSinput file thatcontainsa listof atoms.No restrictionsapplyto thepositionandtypesof atomsin thelayer. Youhave to createthelayerbeforehandusingthetoolsof DISCUS.

1.34.9 modulus

modulus + x1 * , + y1 * , + z1* , + x2 * , + y2 * , + z2*Setsthe two moduli vectorsthat are usedto restrict the origins to a finite volume aroundthe averagetranslationvector. Theplanedefinedby thesetwo vectorsneednot to benormalto theaveragetranslation.

==> ’set mod’==> ’set tran’==> ’aver’

Youcancreatethecrystalfollowing two alternatechoices:

1) The origin of the current layer is the sum of the previous originand the translation vector

2) The above origin is taken modulo the modulus vector.

By usingthefirstoption,thecrystalcontinuouslygrowsin onedirectionasgivenby thetranslationvector(s).By usingthesecondoptiononeor two coordinatescanbeconstrainedto a finite range,which resultsin azig-zagshapedcrystal. If any of theparametersis not equalto zero,thecorrespondingcoordinateof theorigin is takenmodulothisparameter.DISCUSdoesNOT checkwhetherthemoduli vectorsaretranslationvectorsof thecurrentspacegroup!

1.34.10 number

number + n *Readsthenumberof layersto becreated.

1.34.11 random

random prob, + value*random offset,+ u * , + v * , + w *random sigma, + su* , + sv* , + sw*This commandsetsvaluesfor the randomstackingfaults. The programselectsthe next layer type byweightedrandomchoice.Theweightsarechosenaccordingto theoverallprobabilitiesfor eachlayertype.Thenext layer is thenshiftedby thecorrespondingtranslationvectorbetweentheresultingneighbors.In


additionarandomfractionof thetwo modulivectorsis added,whichresultsin a randomdistributionof thenext layerorigin.random prob, , value-Setstheprobabilityfor randomstackingfaults. , value- mustbebetweenzeroandone.Settheprobabilityto zeroto excluderandomstackingfaults.random offset,, u - , , v - , , w -If specifiedthis vectoris addedto thetranslationvector. You canusethisoffsetto forceanincreasedlayerseparationfor randomfaultscomparedto regularstackingfaults.random sigma, , su- , , sv- , , sw-Specifiesthesigma’s for aGaussiandistributionappliedto thecomponentsof theoffset.

1.34.12 rese

rese

Setsthenumberof layersandlayertypesbackto zero.

1.34.13 rotate

rotateaxis, ”normal”, , u - , , v - , , w - [ ”d” . ”r” ]rotateaxis, ”mod1”, , u - , , v - , , w - [ ”d” . ”r” ]rotateaxis, ”mod2”, , u - , , v - , , w - [ ”d” . ”r” ]rotatemode,[ ”all” . ”fault” ]rotatesigma,”normal”, , snormal -rotatesigma,”mod1”, , smod1-rotatesigma,”mod2”, , smod2-rotatestatus,[ ”on” . ”off ” ]

Thiscommandsetsvaluesfor rotationaldisorderof thestackingfaults.Thelayersarerotatedaroundthreeaxes,which aredefinedby the ’axis’ command.Theangleof rotationis Gaussiandistributedwith meanvaluezeroandsigmadefinedby the’sigma’command.rotateaxis, ”normal”, , u - , , v - , , w - [ ”d” . ”r” ]rotateaxis, ”mod1”, , u - , , v - , , w - [ ”d” . ”r” ]rotateaxis, ”mod2”, , u - , , v - , , w - [ ”d” . ”r” ]

Theparameter”axis” definesthethreeaxesaroundwhich you canrotatethelayers.Theaxiscanbegivenin realspacecoordinates”d” or reciprocalspacecoordinates”r”. Default is realspace.DISCUSdoesnotmakeany assumptionsaboutthethreeaxes.Thelayeris rotatedfirst aroundthe”normal” axis,thenaround”mod1” andfinally around”mod2”. It is suggestedto define”normal” as the axis perpendicularto thelayersand”mod1” and”mod2” within theplaneof thelayers.Attention!! If youtilt thelayeraround”mod1” or ”mod2” theoutersectionsof thelayermightoverlapwiththepreviouslayer!rotatemode,[ ”all” . ”fault” ]

Therotationaldisordercanaffect all layersindividually, regardlesswhethertheprevious layerwasof thesametype asthe currentlayer or not. Alternatively, a new rotationangleis computedonly at a stackingfault, i.e. if thecurrentlayertypeis differentthanthepreviouslayertype.All following layersof identicaltypeupto thenext stackingfaultarerotatedby thesameangle.rotatesigma,”normal”, , snormal -rotatesigma,”mod1”, , smod1-rotatesigma,”mod2”, , smod2-Therotationis Gaussiandistributedwith individualsigmafor eachaxis.Themeanvalueof thedistributionis zero.Eachnew angleis calculatedindividually from a Gaussiandistribution irrespectiveof theprevious


value.This forcestheaveragelayerorientationsto remainconstantthroughoutthecrystal.A sigmaof zerofixestherotationsaroundtherespectiveaxisto zero.rotatestatus,[ ”on” / ”off ” ]

Therotationaldisorderis only effective if its statusis switched”on”.

1.34.14 run

run

Decoratestheoriginswith thecorrespondingatomdistribution. Any previouslyexistingstructureis lost.

1.34.15 set

set”aver”, 0 value1set”modulus” , 2 ”off ” / ”on” 3set”trans” , 2 ”calculate” / ”fixed” 3set”aver”, 0 value1If thevalueof 0 value1 is notequalto zero,theaverage0 F 1 is subtractedfrom theactualstructurefactorF. Otherwisetheaverage0 F 1 is calculatedusingthewholecrystalandsubtractedfrom theactualF.

==> "four"==> "discus four set aver"

set”modulus” , 2 ”off ” / ”on” 3If themodulusis set”off”, eachorigin is calculatedby addingthecorrespondingtranslationvectorto theprevious origin. This way the crystalgrows alongthe averagetranslationvector. The resultingaveragetranslationvectoris thesumof all translationvectorsweightedby thecorrespondingprobabilityasstoredin thecorrelationmatrix. If themodulusis set”on”, eachorigin is calculatedasabove. Theorigin is thenexpressedasmultiplesof thetwo moduli vectorsandtheaveragetranslation.If any of thetwo multiplierscorrespondingto thetwo moduli vectorsis largerthan / 1 / , themoduli vectoris subtractedfrom theorigin.This hasthe effect that all origins are no further than the moduli vectorsfrom the averagetranslation.Eventhoughall translationvectorsmightpoint in onedirection,youcanrestrictthecrystalto any arbitrarydirectionby definingtheaveragevector== 1 ’settrans’,== 1 ’aver’.set”trans” , 2 ”calculate” / ”fixed” 3You have two choicesto restrict the crystalgrowth oncethe modulusis seton. The averagetranslationcan be fixed to the value given by == 1 ’aver’ by settingthe parameterof the ’set trans’ commandto”fix ed”. Alternatively theaveragetranslationis computedusingthearrayof thetranslationvectorsandthecorrelationmatrix.

1.34.16 show

show

Showsthecurrentsettings.

1.34.17 sigma

sigma 0 i 1 , 0 j 1 , 0 sx1 , 0 sy1 , 0 sz1Readthe sigmasof the translationvectorbetweenlayer type 0 i 1 and 0 j 1 . The currentorigin of anylayer is calculatedby addingthe translationvector== 1 ’ trans’betweenlayer types 0 i 1 and 0 j 1 to thepreviousorigin. If any sigmais non-zero,a Gaussiandistributedvaluewith meanvalueof zerois addedtothecorrespondingvectorcomponent.


1.34.18 trans

trans 4 i 5 , 4 j 5 , 4 tx 5 , 4 ty 5 , 4 tz 5Readsthe componentsof the translationvectorbetweenlayers 4 i 5 and 4 j 5 . The currentorigin of anylayeris calculatedby addingthetranslationvectorbetweenlayertypes 4 i 5 and 4 j 5 to thepreviousorigin.

1.35 switch

switch 4 atom15 , 4 atom25switch 4 mole15 , 4 mole25 ,”mol”

Theatomsnumber 4 atom15 and 4 atom25 switchposition. Internally, thechemistryof thetwo atomsisswitched,while thepositionsremainasbefore.If ’mol’ is givenasa third parameter, molecules4 mole15 and 4 mole25 areinterchanged.Theorigin ofthetwo molecules(positionof atom1) areunchanged.

1.36 symm

symm

Switchesto thesymmetrysubmenuof DISCUS.You candefinea generalsymmetryoperationin triclinicspacesuchasa rotationaroundageneralaxisby ageneralangle.DISCUSperformsasymmetryoperationin generaltriclinic spaceaccordingto thematrixnotation:

r’ = S*r + t

Here,r is theoriginal position,r’ its image,S thesymmetrymatrix andt thetranslationvector. Thereareno restrictionson thedirectionof thesymmetryaxis, therotationangleor the translationalpart. You canusethis featureto createa twinnedcrystal,to rotatea groupof atomsaroundageneralaxisetc.Furtherhelptopicsare:

1.36.1 commands


@ ! Execute a macro file (see main help)= ! assigns the value to a variable (see main help)angle ! sets the angle of a rotation axisasym ! Shows asymmetric unitcalc ! Calculates the symmetry transformation for a single pointchem ! Shows the atoms present in the crystalcontinue! Coninue a stopped macro (see main help level)des ! deselects atomsecho ! echo a string (see main help)eval ! Evaluates an expression for interactive check (see main help)exit ! terminates ’symm’help ! gives on line help for symmetry operations (see main help)hkl ! sets the symmetry axis in reciprocal space coordinatesincl ! sets the range of atoms to be included in the symmetry operationmdes ! deselects moleculesmincl ! sets the range of atoms to be included in the symmetry operationmode ! allows choice of creating a copy or replacing the atommsel ! selects molecules to be included in the symmetry operationsorigin ! sets the origin for the symmetry operationpower ! sets the power of the symmetry operationrun ! starts the calculation of the symmetry operationssel ! selects atoms to be included in the symmetry operations


show ! shows the current parametersstop ! Stops execution of a macro (see main help level)system ! Executes operating system command (see main help)trans ! sets the translational part of the symmetry operationtype ! Allows choice between proper and improper rotationsuvw ! sets the symmetry axis in direct space coordinateswait ! Waits for user input (see main help)

1.36.2 angle

angle 6 value7Setsthe angleof the symmetryoperation. The anglemustbe given in degrees. No limit appliesto thenumericalvalue.

1.36.3 asym

asym

Shows thecontentof theasymmetricunit. Thenamesof thoseatoms,a numberthat is usedasindex forits scatteringtype, their positionandtemperaturecoefficient arelisted. The numberthat is listed, is thenumberthatrefersto thescatteringcurveof thatatom.It is containedin thevariablem[ 6 index 7 ]. If acellwasread,all atomsareconsideredto bedifferent,evenif they arechemicallyidenticalandhave thesametemperaturecoefficient. If a wholestructurewasread,all atomsthatarein theunit cell 0 6 = xyz 6 1, arechemicallyuniqueandhavea differenttemperaturecoefficientareincludedin theasymmetricunit.

1.36.4 calc

calcx,y,z [,”d” 8 ”r” ]

Calculatesthesymmetrytransformationfor a singlepoint 6 x,y,z7 . Thecurrentsettingsfor thesymmetryoperationareusedto transformthevector 6 x,y,z7 . Theresultis displayedandstoredin the resultarray”res”. By default, or if the optionalfourth parameteris setto ”d”, DISCUSassumesthat the vectoris arealspacevector.i If theoptionalfourthparameteris setto ”r” thevectoris interpretedasareciprocalspacevectorandthecorrespondingsymmetrymatrix in reciprocalspaceis used.

1.36.5 chem

chem


1.36.6 des

des 9 ”all” 86 name7�86 number 7 : [ , 9�6 name7�86 number 7 : ...]des”mic”

Deselectschoicesmadeby == 7 ’sel’ . Possiblevaluesfor theparameteraremutuallyexclusively:



are deselected.

1.36.7 hkl

hkl ; h < , ; k < , ; l <Specifiesthedirectionof thesymmetryaxisin reciprocalspacecoordinates.Thecorrespondingdirectspacecoordinatesarecalculatedby theprogram.Alternatively you mayspecifythedirectionin directspacebythe== < ’uvw” command.

1.36.8 incl

incl =; start < , ; end<?> ”all” @Thesymmetryoperationincludesall atomsnumbered; start< to ; end< inclusively. All otheratomsareignored.If, insteadof explicit numbers,theparameter”all” is given,thesymmetryoperationwill includeall atomsof thecrystal.Thisholdseven,if atalatertimeyouincludefurtheratomsin thecrystal.Thus,youcandefinea setupfor thesymmetryoperationsearly in a lengthymacro,thenmodify thecrystalandjustrunthesymmetryoperationlateron. In additionyoucandefinetheatomsthatareaffectedby thesymmetryoperationwith the== < ’sele’and’dese’commands.

1.36.9 mdes

mdes = ”all” >; name<%>; number < @ [ , =�; name<�>; number < @ ...]mdes”mic”

Deselectschoicesmadeby == < ’msel’ . Possiblevaluesfor theparameteraremutuallyexclusively:

"all" all molecules of the crystal are deselected."mic" The selection of molecules that are inside a microdomain

is canceled.<number> all molecules of the crystal that are of type <number>

are deselected.

More thanonemoleculetypemaybedeselectedatonce.

1.36.10 mincl

mincl =; start < , ; end<?> ”all” @The symmetryoperationincludesall moleculesnumbered ; start< to ; end< inclusively. All othermoleculesareignored.If, insteadof explicit numbers,theparameter”all” is given,thesymmetryoperationwill includeall moleculesof thecrystal.Thisholdseven,if at a latertimeyou includefurthermoleculesinthecrystal.Thus,youcandefineasetupfor thesymmetryoperationsearlyin a lengthymacro,thenmodifythecrystalandjust run thesymmetryoperationlateron. In additionyou candefinethemoleculesthatareaffectedby thesymmetryoperationwith the== < ’msele’and’mdese’commands.

1.36.11 mode

mode = ”copy” > ”r epl” @ [ , = ”new” > ”old” @ ]

The symmetryoperationcan have two different effects on the currentatom. In the ”copy” mode, thesymmetryoperationcreatesa copy of thecurrentatom.In the”repl” mode,thesymmetryoperationmovesthecurrentatomfrom its old positionto thenew position.Theoptionalsecondparameterhasonly aneffect if moleculesareused.It determinesif thenew moleculecreatedby the symmetryoperationhasis of the sametype asthe original (”old”) or is treatedasa newmoleculetype(”new”).

1.36.12 msel

msel A ”all” BC number D E [ , C number D ...]msel”mic”, A ”all” B ”eve” B ”non” BC number D EThiscommandexecutestwo differentfunctions.It servesto selectthosemoleculesthatwill bemodifiedbythesymmetryoperationandsecondlyit cansetthemicrodomainstatus.First function:Defineswhich moleculesareincludedin symmetryoperation.Possiblevaluesfor thefirst mandatorypa-rameteraremutuallyexclusively:

"all" all molecules of the crystal are included.This includes the empty molecules in the structure, which arestored as scattering curve number zero.

<number> all molecules of the crystal that are of type <number>are included.

More thanoneatommaybeselectedatonce.Secondfunction:Defineshow moleculesinsideany microdomainsareto betreated.Thesecondparameterservesto distin-guishdifferentpossiblevaluesof thestatus.

"mic" selects whether molecules that are inside a microdomain are to bemodified by the symmetry operation or not.The kind of molecules to be included are to be chosen by anadditional ’sel’ command.Second parameter:"all" molecules inside any microdomain are selected, all

molecules outside all microdomains are not included."eve" Disregard microdomain status of an molecule. Molecules

in the host structure and inside any microdomain areincluded alike.

"none" Only molecules outside all microdomains are selected.<number> Only molecules inside microdomain type <number> are

selected.

Theselectionsmadestayvalid until explicitly deselected!Theselectionof moleculesby ’msel’ andatomsby ’sel’ aremutuallyexclusive. Thesymmetryoperationuseseitheratomsor molecules.

1.36.13 origin

origin C x D , C y D , C z D [, A ”mol” B ”cryst” E ]

Specifiestheorigin of the symmetryoperationin direct spacecoordinates.Thesymmetryaxis intersectsthis pointandhasthedirectionspecifiedby == D ’hkl’ or ’uvw’. If thesymmetryoperationis animproperrotation,thecenterof symmetryis at C x D , C y D , C z D .In caseof moleculesto betransformed,theoptionallastparameterspecifiesif thegivenorigin is relative totheorigin of themolecule(”mol”) or thecrystal(”cryst”). Notethatthefirst atomwithin a moleculehastobeon themoleculesorigin (seemanual).

1.36.14 power

power C n D A , ”multiple” B ”single” ESetsthepowerof thesymmetryoperation.Thesymmetryoperationis applied C n D times.If the== D ’mode’of thesymmetryoperationis ”repl”, thesecondparameteris meaningless.Thesymmetryoperationthatappliesin thiscaseis :


n nr’ = S * r + t

Theatomis movedto thenew positionthatresultsfrom an F n G fold applicationof thesymmetryoperation.If the== G ’mode’ of thesymmetryoperationis ”copy”, F n G new atomsarecreated.Thepositionof thefirst atomresultsfrom a singleapplicationof the symmetryoperation,the positionof the secondfrom atwofold applicationetc.

1.36.15 run

run

Startsthesymmetryoperation.

1.36.16 sel

sel H ”all” I�F nameG�IF number G J [ , H�F nameG�I�F number G�J ...]sel”mic”, H ”all” I ”eve” I ”non” I�F number G�JThiscommandexecutestwo differentfunctions.It servesto selectthoseatomsthatwill bemodifiedby thesymmetryoperationandsecondlyit cansetthemicrodomainstatus.First function:Defineswhichatomsareincludedin symmetryoperation.Possiblevaluesfor thefirst mandatoryparameteraremutuallyexclusively:






"mic" selects whether atoms that are inside a microdomain are to bemodified by the symmetry operation or not.The kind of atoms to be included are to be chosen by anadditional ’sel’ command.Second parameter:"all" atoms inside any microdomain are selected, all atoms





1.36.17 show

show

Showsthecurrentparametersof thesymmetryoperation.


1.36.18 trans

trans K t1 L , K t2 L , K t3 LSetsthetranslationalpartof thesymmetryoperation.Thetranslationis appliedaftertherotationaccordingto thematrixnotation:

r’ = S*r + t

Here,r is theoriginalposition,r’ its image,S thesymmetrymatrixandt thetranslationvector.

1.36.19 type

type M ”pr oper” N ”impr oper” OA generalrotationmaybeeithera ”proper” or an ”improper” rotation. An improperrotationis a normalrotationfollowedby an inversion. To create,for example,a mirror operationspecifya 180 degreeangleandanimproperrotation.

1.36.20 uvw

uvw K h L , K k L , K l LSpecifiesthedirectionof thesymmetryaxisin directspacecoordinates.Thecorrespondingreciprocalspacecoordinatesarecalculatedby theprogram.Alternatively you mayspecifythedirectionin reciprocalspaceby the== L ’hkl” command.terminates’wave’ returnsto thenormaldiscusprompt

1.37 transform

tran

Switchesto theunit cell transformationsubmenuof DISCUS.At this sublevel you candefinetherelation-ship betweenan old anda new unit cell andperformthe transformationof the atomsin the crystal. Aninteractive transformationallows to calculatethe result for any singlereal andreciprocalspacevectorinbothdirections:old == L new andnew == L old.Youcanspecifytherelationshipbetweenthetwo unit cellsin any of four possibleoptions:definethenewbasevectorsa,b,cin termsof theold basedefinetheold basevectorsa,b,cin termsof thenew basedefinethe new coordinatesx,y,z in termsof the old coordinatesdefinethe old coordinatesx,y,z in termsof thenew coordinatesdefinethenew basevectorsa*,b*,c* in termsof theold reciprocalbasedefinetheold basevectorsa*,b*,c* in termsof thenew reciprocalbaseIndependentof thechoiceabove,youcandefineanoptionalshift of theorigin by: definingthecoordinatesof thenew origin in termsof theold basedefiningthecoordinatesof theold origin in termsof thenew baseIf all atomsin the crystalaretransformedto the new basevectors,thenthe unit cell dimensionsandthemetric tensorsare transformedas well. The spacegroup is set to ”P1” to prevent erroneoussymmetryoperationsoncethepresentcrystalis savedto file andreadagain.

1.37.1 commands


@ ! Execute a macro file (see main help)= ! assigns the value to a variable (see main help)anew ! sets the new base vector "a" in terms of the old baseaold ! sets the old base vector "a" in terms of the new baseasnew ! sets the new reciprocal base vector "a" in terms of the old base


asold ! sets the old reciprocal base vector "a" in terms of the new baseasym ! Shows asymmetric unitbnew ! sets the new base vector "b" in terms of the old basebold ! sets the old base vector "b" in terms of the new basebsnew ! sets the new reciprocal base vector "b" in terms of the old basebsold ! sets the old reciprocal base vector "b" in terms of the new basec2new ! Calculates the transformation to "new" for a single vectorc2old ! Calculates the transformation to "old" for a single vectorchem ! Shows the atoms present in the crystalcnew ! sets the new base vector "c" in terms of the old basecold ! sets the old base vector "c" in terms of the new basecsnew ! sets the new reciprocal base vector "c" in terms of the old basecsold ! sets the old reciprocal base vector "c" in terms of the new basecontinue! Coninue a stopped macro (see main help level)des ! deselects atomsecho ! echo a string (see main help)eval ! Evaluates an expression for interactive check (see main help)exit ! terminates ’tran’help ! gives on line help for unit cell transformations (see main help)incl ! sets the range of atoms to be included in the transformationonew ! sets the new origin in terms of the old baseoold ! sets the old origin in terms of the new baserun ! starts the transformation for the selected atomssel ! selects atoms to be included in the transformationshow ! shows the current parametersstop ! Stops execution of a macro (see main help level)system ! Executes operating system command (see main help)wait ! Waits for user input (see main help)xnew ! sets the new coordinate "x" in terms of the old x,y,zxold ! sets the old coordinate "x" in terms of the new x,y,zynew ! sets the new coordinate "y" in terms of the old x,y,zyold ! sets the old coordinate "y" in terms of the new x,y,zznew ! sets the new coordinate "z" in terms of the old x,y,zzold ! sets the old coordinate "z" in terms of the new x,y,z

1.37.2 anew

anewa,b,c

Definesthe new basevector”a” in termsof multiples P aQ , P b Q , P c Q of the old basevectors. If youchoosethis definitionof theunit cell transformation,you MUST defineall three== Q ’anew’,’bnew’ and’cnew’.

1.37.3 aold

aold a,b,c

Definesthe old basevector”a” in termsof multiples P aQ , P b Q , P c Q of the new basevectors. If youchoosethis definition of the unit cell transformation,you MUST defineall three== Q ’aold’,’bold’ and’cold’.

1.37.4 asnew

asnewa,b,c

Definesthe new reciprocalbasevector”a” in termsof multiples P aQ , P b Q , P c Q of the old reciprocalbasevectors.If you choosethis definitionof theunit cell transformation,you MUST defineall three== Q’asnew’,’bsnew’ and’csnew’.


1.37.5 asold

asolda,b,c

Definesthe old reciprocalbasevector”a” in termsof multiples R aS , R b S , R c S of the new reciprocalbasevectors.If you choosethis definitionof theunit cell transformation,you MUST defineall three== S’asold’,’bsold’ and’csold’.

1.37.6 asym

asym

Shows thecontentof theasymmetricunit. Thenamesof thoseatoms,a numberthat is usedasindex forits scatteringtype, their positionandtemperaturecoefficient arelisted. The numberthat is listed, is thenumberthatrefersto thescatteringcurveof thatatom.It is containedin thevariablem[ R index S ]. If acellwasread,all atomsareconsideredto bedifferent,evenif they arechemicallyidenticalandhave thesametemperaturecoefficient. If a wholestructurewasread,all atomsthatarein theunit cell 0 R = xyz R 1, arechemicallyuniqueandhavea differenttemperaturecoefficientareincludedin theasymmetricunit.

1.37.7 bnew

bnewa,b,c

Definesthe new basevector”b” in termsof multiples R aS , R b S , R c S of the old basevectors. If youchoosethis definitionof theunit cell transformation,you MUST defineall three== S ’anew’,’bnew’ and’cnew’.

1.37.8 bold

bold a,b,c

Definesthe old basevector”b” in termsof multiples R aS , R b S , R c S of the new basevectors. If youchoosethis definition of the unit cell transformation,you MUST defineall three== S ’aold’,’bold’ and’cold’.

1.37.9 bsnew

bsnewa,b,c

Definesthe new reciprocalbasevector”b” in termsof multiples R aS , R b S , R c S of the old reciprocalbasevectors.If you choosethis definitionof theunit cell transformation,you MUST defineall three== S’asnew’,’bsnew’ and’csnew’.

1.37.10 bsold

bsolda,b,c

Definesthe old reciprocalbasevector”b” in termsof multiples R aS , R b S , R c S of the new reciprocalbasevectors.If you choosethis definitionof theunit cell transformation,you MUST defineall three== S’asold’,’bsold’ and’csold’.

1.37.11 c2new

c2newx,y,z [, [”d” T ”r” U ]

Calculatesthe transformationfrom the old coordinatesystemto the new systemfor a single vectorR x S , R y S , R z S . Default is a direct spacevector, the fourth optional parameterallows you to define


V x W , V y W , V z W asa reciprocalspacevector. The resultof the transformationis displayedon thescreenandstoredin thefirst threeelementsof theresultarray”res[i]”.

1.37.12 c2old

c2oldx,y,z [, [”d” X ”r” Y ]

Calculatesthe transformationfrom the new coordinatesystemto the old systemfor a single vectorV x W , V y W , V z W . Default is a direct spacevector, the fourth optional parameterallows you to defineV x W , V y W , V z W asa reciprocalspacevector. The resultof the transformationis displayedon thescreenandstoredin thefirst threeelementsof theresultarray”res[i]”.

1.37.13 csnew

csnewa,b,c

Definesthe new reciprocalbasevector”c” in termsof multiples V aW , V b W , V c W of the old reciprocalbasevectors.If you choosethis definitionof theunit cell transformation,you MUST defineall three== W’asnew’,’bsnew’ and’csnew’.

1.37.14 csold

csolda,b,c

Definesthe old reciprocalbasevector”c” in termsof multiples V aW , V b W , V c W of the new reciprocalbasevectors.If you choosethis definitionof theunit cell transformation,you MUST defineall three== W’asold’,’bsold’ and’csold’.

1.37.15 chem

chem


1.37.16 cnew

cnewa,b,c

Definesthe new basevector”c” in termsof multiples V aW , V b W , V c W of the old basevectors. If youchoosethis definitionof theunit cell transformation,you MUST defineall three== W ’anew’,’bnew’ and’cnew’.

1.37.17 cold

cold a,b,c

Definesthe old basevector”c” in termsof multiples V aW , V b W , V c W of the new basevectors. If youchoosethis definition of the unit cell transformation,you MUST defineall three== W ’aold’,’bold’ and’cold’.


1.37.18 des

des Z ”all” [\ name]�[\ number ] ^ [ , Z�\ name]�[\ number ] ^ ...]des”mic”

Deselectschoicesmadeby == ] ’sel’ . Possiblevaluesfor theparameteraremutuallyexclusively:



are deselected.


1.37.19 incl

incl Z�\ start ] , \ end] [ ”all” ^Theunit cell transformationincludesall atomsnumbered\ start] to \ end] inclusively. All otheratomsareignored. If, insteadof explicit numbers,theparameter”all” is given,theunit cell transformationwillincludeall atomsof thecrystal.This holdseven,if at a latertime you includefurtheratomsin thecrystal.Thus,you candefinea setupfor the unit cell transformationsearly in a lengthymacro,thenmodify thecrystaland just run the unit cell transformationlater on. In additionyou candefinethe atomsthat areaffectedby theunit cell transformationoperationwith the== ] ’sele’and’dese’commands.

1.37.20 onew

onewa,b,c

Definesthepositionof thenew origin in termsof multiples \ a] , \ b ] , \ c ] of theold basevectors.Thedefaultat programstartupis 0.0,0.0,0.0

1.37.21 oold

oold a,b,c

Definesthepositionof theold origin in termsof multiples \ a] , \ b ] , \ c ] of thenew basevectors.Thedefaultat programstartupis 0.0,0.0,0.0

1.37.22 run

run

Startsthetransformationoperation.

1.37.23 sel

sel Z ”all” [�\ name]�[\ number ] ^ [ , Z�\ name]�[�\ number ]�^ ...]sel”mic”, Z ”all” [ ”eve” [ ”non” [�\ number ]�^Thiscommandexecutestwo differentfunctions.It servesto selectthoseatomsthatwill bemodifiedby theunit cell transformationandsecondlyit cansetthemicrodomainstatus.First function:Defineswhich atomsare includedin unit cell transformations.Possiblevaluesfor the first mandatoryparameteraremutuallyexclusively:







"mic" selects whether atoms that are inside a microdomain are to bemodified by the unit cell transformation operation or not.The kind of atoms to be included are to be chosen by anadditional ’sel’ command.Second parameter:"all" atoms inside any microdomain are selected, all atoms





1.37.24 show

show

Showsthecurrentparametersof thetransformationoperation.

1.37.25 xnew

xnewa,b,c

Definesthetransformationthroughtherelationshipbetweenthenew ”x” coordinateof anatomin termsofmultiples _ x ` , _ y ` , _ z ` of theold coordinatesof theatom.If youchoosethisdefinitionof theunit celltransformation,you MUST defineall three== ` ’xnew’,’ynew’ and’znew’.

1.37.26 xold

xold a,b,c

Definesthetransformationthroughtherelationshipbetweentheold ”x” coordinateof anatomin termsofmultiples _ x ` , _ y ` , _ z ` of thenew coordinatesof theatom.If youchoosethisdefinitionof theunit celltransformation,you MUST defineall three== ` ’xold’, ’yold’ and’zold’.

1.37.27 ynew

ynewa,b,c

Definesthetransformationthroughtherelationshipbetweenthenew ”y” coordinateof anatomin termsofmultiples _ x ` , _ y ` , _ z ` of theold coordinatesof theatom.If youchoosethisdefinitionof theunit celltransformation,you MUST defineall three== ` ’xnew’,’ynew’ and’znew’.


1.37.28 yold

yold a,b,c

Definesthetransformationthroughtherelationshipbetweentheold ”y” coordinateof anatomin termsofmultiples a x b , a y b , a z b of thenew coordinatesof theatom.If youchoosethisdefinitionof theunit celltransformation,you MUST defineall three== b ’xold’, ’yold’ and’zold’.

1.37.29 znew

znewa,b,c

Definesthetransformationthroughtherelationshipbetweenthenew ”z” coordinateof anatomin termsofmultiples a x b , a y b , a z b of theold coordinatesof theatom.If youchoosethisdefinitionof theunit celltransformation,you MUST defineall three== b ’xnew’,’ynew’ and’znew’.

1.37.30 zold

zold a,b,c

Definesthetransformationthroughtherelationshipbetweentheold ”z” coordinateof anatomin termsofmultiples a x b , a y b , a z b of thenew coordinatesof theatom.If youchoosethisdefinitionof theunit celltransformation,you MUST defineall three== b ’xold’, ’yold’ and’zold’.

1.38 ther

ther [ c ”all” d ”2d” e ]ther ”mol”,[ c ”all” d ”2d” e ]Randomlydisplacesall atomsaccordingto their respective isotropicthermalcoefficient. The directionsof the displacementsaredistributed in uniform randomdistribution, the amplitudeof the displacementsareGaussiandistributedwith FWHM calculatedfrom the isotropicB. As default the displacementsareperformedin all 3 dimensions.For 2dsimulationshowever, thedisplacementin all directionscorrespondingto a sizeof oneunit cell canbeswitchedoff by theparameter”2d”. Thevalue”all” is equalto thedefault.If thesecondparameteris setto ”mol”, thecompleterigid moleculeis displacedaccordingto thetempera-turefactorof theatomat theorigin of themolecule.

1.39 variables

Theprogramrecognizesfreevariables:

"i[ ]" integer variables"r[ ]" real variables

Thecurrentimplementationallows10 freevariables[0] through[59] each.

"res[ ]" Result of several calculations that return more than onevalue.res[0] contains the number of values returned, res[1] tores[res[0]] contain the actual values.The values of "res" change every time, a command is appliedthat returns more than one value. The old values are lost !

Severalothervariablesarelinkedto structuralvalues:

"x[]","y[]" and"z[]" are the fractional coordinates of the atom number .

"m[]" is the number of the scattering curve for atom 

"n[1]" is the total number of atoms in the crystal, this variableis read only.

"n[2]" is the total number of different scattering curves in thecrystal, this variable is read only.

"n[3]" is the total number of atoms in the original unit cell,this variable is read only.

"n[4]" is the total number of molecules in the crystal, this variableis read only.

"n[5]" is the total number of different molecule types in thecrystal, this variable is read only.

"n[6]" is the total number of molecules in the original unit cell,this variable is read only.

"cdim[1,1]" lowest x coordinate of any atom in the crystal."cdim[1,2]" highest x coordinate of any atom in the crystal."cdim[2,1]" lowest y coordinate of any atom in the crystal."cdim[2,2]" highest y coordinate of any atom in the crystal."cdim[3,1]" lowest z coordinate of any atom in the crystal."cdim[3,2]" highest z coordinate of any atom in the crystal.

Thevariable”cdim” is readonly.

"env[]" Index of neighbouring atoms as found by==> "find""env[0]" is the number of neighbours.

"md_num[1]" Number of different microdomain types, read only

"md_cre[1]" Number of different microdomain types that have beencreated with the ’create’ command but not yet used tomodify the crystal with the ’run’ command. read only

"mc_num[1]" Number of microdomains whose origins have been distributedthroughout the crystal with the ’create’ command.read only

"md_rad[,<j>]" Radius of microdomain type .If the type is "block", <j> = 6 always.If the type is "sphere", <j> = 1 gives the radius.If the type is "face", <j> gives the radius of face

number <j>.If the type is "fuzzy", <j> = 6 always.The radius of microdomains type "block" and "fuzzy"is determined automatically by the ==>’run’ command.read only.

"mc_run[1]" Number of microdomains that have been used to modify thecrystal with the ’run’ command.read only

"mc_type[]" Number specifying the type of microdomain number .read only

"mc_orig[1,] x coordinate of microdomain "mc_orig[2,] y coordinate of microdomain "mc_orig[3,] z coordinate of microdomain 

Read only for microdomains that have been used to modifythe crystal, i.e. for which the ’run’ command has been used.Read/write for microdomains whose origins have been

created with ’create’ but not yet used to modify thecrystal with ’run’.

"mc_rad[]" Individual radius for microdomain . This radius isadded to the microdomain radius for a Gaussian distribution.Read only for microdomains that have been used to modifythe crystal, i.e. for which the ’run’ command has been used.Read/write for microdomains whose origins have beencreated with ’create’ but not yet used to modify the

"md_next[]" Number of the closest microdomain. If "md_next" isnegative, the atom is inside the microdomain,else outside.

"md_dist[]" Distance of the atom to the closest microdomain.If "md_next" is negative, the atom is inside the

microdomain, else outside.

Thevariablescanbeassignedconstantnumbers:

i[0] = 1 ! Integer variable no 0 is set to "1"r[4] = 1.5 ! Real variable no 4 is set to "1.5"x[5] = -2.7888 ! x-coordinate of atom 5 is set to "-2.7888"

Arithmeticexpressionsmaybeusedon theright handside:

i[i[4]+2] = 2.0*(i[2]+i[0])/(i[2]**2)m[i[0]+50] = m[i[0]] ! The atom 50 atoms down the line from

atom no <i[0]> is assigned the samescattering curve, thus essentially switchingits chemistry around !

As shown in theexampleabove,arithmeticoperationscanbenestedandgroupedby brackets”(” and”)”.

1.40 vprod

vprod f u1 g , f v1 g , f w1 g , f u2 g , f v2 g , f w2 g [ , f flag g ]

This commandcalculatesthe vector product f uvw 1 g X f uvw 2 g . The f flagg is a string of threecharactersthat indicateswhetherthe input vectorsor the output vectoraregiven in direct or reciprocalspacecoordinates.Thethreecharacterscorrespondto:

first input vector,second input vectorresulting vector

"drd" means: vector one is given in direct space coordinates, vector 2is in reciprocal space coordinates (hkl) and theresulting vector product is to be given in direct spacecoordinates

Any combinationof ”d” and”r” is allowed.Theoutputvectoris storedin theresultvariable:”res[1]”,”res[2]”,”res[3]” vectorproductof vector1 andvector2


1.41 waves

wave

displacestheatomsalongawave. It generatessublevel with prompt”discus/wave h ”.Furtherhelptopicsare:

1.41.1 commands


@ ! Execute a macro file (see main help)= ! Assigns the value to a variable (see main help)acco ! Sets the wave type to acousticamp ! Sets the amplitude in Angstromasym ! Shows asymmetric unitchem ! Shows the atoms present in the crystalcontinue! Coninue a stopped macro (see main help level)dens ! Sets the wave type to density wavedes ! Deselects atomsecho ! Echo a string (see main help)eval ! Evaluates an expression for interactive check (see main help)exit ! Terminates ’wave’func ! Sets the wave functionhelp ! Gives on line help for waves (see main help)len ! Sets the wave length in Angstromlong ! Sets the wave type to longitudinalmdese ! Deselects molecule typesmrepl ! Selects molecules to be replaced by density wavemsel ! Selects molecule typesopti ! Sets the wave type to opticalosci ! Oscillation vector for transverse wavesphase ! Sets the phase of the wave at 0,0,0 in direct spacephigh ! Sets the high probability for density wavesplow ! Sets the low probability for density wavesrepl ! Selects atoms to be replaced by a density waverot ! Sets type to rotational wave (molecules only)run ! Starts the calculation of the wavesel ! Selects atoms to be included in the waveshift ! Allows a constant shift to be added to the displacementshow ! Show current settingsstop ! Stops execution of a macro (see main help level)system ! Executes operating system command (see main help)tran ! Sets the wave type to transversevect ! Sets wave vectorwait ! Waits for user input (see main help)

1.41.2 acco

acco

Setsthewave typeto acoustic,atomsof oppositechargearedisplacedin thesamedirection.

1.41.3 amp

amp i valuehsetstheamplitudein Angstrom

1.41.4 asym

asym

Shows thecontentof theasymmetricunit. Thenamesof thoseatoms,a numberthat is usedasindex forits scatteringtype, their positionandtemperaturecoefficient arelisted. The numberthat is listed, is thenumberthatrefersto thescatteringcurveof thatatom.It is containedin thevariablem[ j index k ]. If acellwasread,all atomsareconsideredto bedifferent,evenif they arechemicallyidenticalandhave thesametemperaturecoefficient. If a wholestructurewasread,all atomsthatarein theunit cell 0 j = xyz j 1, arechemicallyuniqueandhavea differenttemperaturecoefficientareincludedin theasymmetricunit.

1.41.5 chem

chem


1.41.6 dens

dens

Setsthetypeof thewave to bea densitywave. All atomsselectedby ’sel’ or ’repl’ will bemodulatedbythewave. Theprobabilitywith whichanatomis presentoscillatesbetween’plow’ and’phigh’.

1.41.7 des

des l ”all” mj namek�mj number k n [ , l�j namek�mj number k n ...]des”mic”

Deselectschoicesmadeby == k ’sel’ or == k ’repl’. Possiblevaluesfor theparameteraremutuallyexclu-sively:



are deselected.


1.41.8 func

func ”box” [, j delta k ]func ”sinus”func ”triang”

Setsthetypeof wave functionused.Theparametercanbeany of thestringslisted.A) displacementwaves:

"box" : A box shaped wave function is used. The function issymmetrical around the origin. This, however, can bechanged by changing the phase at the origin, see command==> ’phase’. The default is a symmetrical box function,i.e. a value of <delta> of 0.5. The value of <delta>can be given as additional parameter to us an asymmetricbox function, i.e. maxima and minima have different widths.

"sinus" : A sinusoidal wave function is used. The displacement is givenby amp*SIN(arg).

"triang": A triangular displacement is applied. The displacement linearlyincreases from zero to amp and drops back to zero at the endof the wave. The point at 0/4 = 4/4 wave length has displacementzero.

Theconstantshift is addedto thesedisplacements.B) replacementwaves:

"box" : A box shaped wave function is used. The occupation probabilityof the original atom, see ==> ’repl’, is equal to <plow> alonghalf the wave length and <phigh> else. Other details weregiven above.

"sinus" : A sinusoidal wave function is used. The occupation probabilityis given by

amp * SIN(arg) + amp0, whereamp = 0.5*( phigh-plow)amp0= 0.5*( phigh+plow)

This will give a sinusoidal wave with minimum at <plow> andmaximum value at <phigh>.

"triang": A triangular occupation probability is applied. The occupationprobability linearly increases from <plow> to <phigh> and dropsback to zero at the end of the wave.The point at 0/4 = 4/4 wave length has the occupationprobability of <plow>.

1.41.9 len

len o valuepSetsthewave lengthin Angstrom

1.41.10 long

long

Setsthewave typeto longitudinal

1.41.11 mdes

mdes q ”all” ro number p s [ , o number p ...]

Thiscommanddeselectsall or individualmoleculetypesusedfor theplottingoutput.

1.41.12 msel

msel q ”all” ro number p s [ , o number p ...]

This commandallows to selectthe moleculetypesto be usedfor the plotting output. By using ’msel’the atomselectionbecomesinvalid. The parameter”all” will selectALL moleculetypes. Alternativelyindividualmoleculetypescanbeselectedusingthecorrespondingo numberp . In orderto useatomsagain,usethe’sele’command.

1.41.13 mrep

mrep o typ1 p , o typ2 pThis commandselectsthemoleculesthatwill be replacedby a densityfunction. Theparametero typ1pspecifiesthemoleculetypeto eventuallybereplacedby type o typ2p . Repeatthecommandto selectmorethanonemoleculetype. To deselectuse’mdes’. To remove themoleculesratherthanreplacingthem,seto typ2p to zero.

1.41.14 rot

rot t u u , t v u , t w u [, t x u , t y u , t z u ]

This commandselectstherotationalwave modewhich is only availablewhenusingmolecules.Thewaveamplitudeis hereusedasrotationangleratherthanasdisplacementor probabilityasfor theothermodes.The parameterst u u , t v u , t w u definethe rotationaxis in real space.The origin of the rotationaxis istheorigin of themolecule.However, anoffset t x u , t y u , t z u for this origin canbespecifiedasoptionalparameters.

1.41.15 opti

opti

Setsthewave typeto optical,atomsof oppositechargearedisplacedin oppositedirections.

1.41.16 osci

osci t x,y,z uSetsthedirectionof theoscillationvectorfor transversewaves.

1.41.17 phase

phase v�t valueu%w ”random” xSetsthe phaseof the wave at 0,0,0in direct spacein degrees.The initial phaseis zero. With phase= 0,a sinewave results,with phase= 90 a cosinewave. Thephasetype”random” causesa randomphaseforeachmicrodomain.

1.41.18 phigh

phigh t valueuSetstheupperprobabilitylimit, with whichanatomis retainedbyadensitywave.Themaximumoccupancyof theatomreachest valueu .

1.41.19 plow

plow t valueuSetsthelowerprobabilitylimit, with whichanatomis retainedby adensitywave.Theminimumoccupancyof theatomreachest valueu .

1.41.20 repl

repl v ”all” wt nameu%w�t number u x , v�t nameu�w&t number u xThis commandselectsthoseatomsthatwill bereplacedby a densityfunction. Possiblevaluesfor thefirstmandatoryparameteraremutuallyexclusively:

"all" all atoms of the crystal are replaced by the atom definedby the second parameter.

<name> all the atoms called <name> of the crystal are replaced bythe atom defined by the second parameter. This includessymmetrically not equivalent atoms.

<number> all atoms of the crystal that are of scattering type <name>are replaced by the atom defined by the second parameter.


The secondparameterdefinesthe atom,the original is replacedby. If a nameis given, it neednot to bepresentin the original crystal. A new scatteringtype is automaticallyaddedto the table. If a numberisgiven,to whichnocorrespondingatomexists,anerrormessageis displayed.Usethecommand’sele’to alterthemicrodomainselectstatus.

1.41.21 run

run

Startsthecalculationof thewave

1.41.22 sel

sel y ”all” z�{ name|�z{ number | } [ , y�{ name|�z�{ number |�} ...]sel”mic”, y ”all” z ”eve” z ”non” z�{ number |�}This commandexecutestwo differentfunctions.It servesto selectthoseatomsthatwill bemodifiedby awave functionandsecondlyit cansetthemicrodomainstatus.First function:Defineswhichatomsareincludedin awave. Possiblevaluesfor thefirst mandatoryparameteraremutuallyexclusively:






"mic" selects whether atoms that are inside a microdomain are to bemodified by the wave or not.The kind of atoms to be included are to be chosen by anadditional ’sel’ command.Second parameter:"all" atoms inside any microdomain are selected, all atoms





1.41.23 shift

shift { amount |A constantshift { amount| is addedto thedisplacementof theatoms

1.41.24 show

show

showsthecurrentsettingsfor thewave.

1.41.25 tran

tran

setsthewave typeto transverse

1.41.26 vect

vect ~ x,y,z�setsthe directionof thewave vectorin units of the latticeconstants.The wave lengthhasto be setwith== � ”len”.

1.42 bugs

Known bugs

Hereis a list of known bugsof DISCUSwhichareonour ’repairlist’:

- DISCUS hangs if the input is redirected from a file (’discus < file’)and the prompt status is ON if command line editing is used.Use ’set prompt,off’ or ’set prompt,redirect’ in the firstline of the file to be redirected to avoid the problem.

1.43 errors

Theprogramhasbeenwritten suchthat it shouldhandlealmostany typing errorwhengiving commandsandhopefullyall errorsthat resultfrom calculationwith erroneousdata.Whenanerror is foundanerrormessageisdisplayedthatshouldgetyoubackontrack.Seethemanualfor acompletelist of errormessages.Error messagesconcerningthecommandlanguageareexplainedin the- � commandlanguagesectionoftheonlinehelp.Applicationspecificcommandsaredescribedhereandaregroupedasfollows:

APPL Errors specific to DISCUS usageCHEM Errors at the chemistry sublevelFOUR Errors related to Fourier TransformMC Errors at the Monte Carlo levelPDF Errors at the PDF levelRMC Errors at the Reverse Monte Carlo level

Eacherror messageis displayedtogetherwith thecorrespondingcategory ~ cccc� andthe error number~ numb� in theform:****CCCC****message **** numb ****

Typehelperror ~ cccc�%~ numb� to getanexplanationfor theerrormessageandhintsfor possiblestepsto correctthesituation.In the default modeDISCUSreturnsthe standardpromptandyou cancontinuethe executionfrom thispoint. Youcansettheerrorstatusto ”exit” by the== � ’set’command.In thiscaseDISCUSterminatesif anerroris detected.Thisoptionis usefulto terminatea faultysequenceof commandswhenrunningDISCUSin thebatchmodeof youroperatingsystem.


1.43.1 appl

ThiscategorylistserrormessagesthatarespecifictoDISCUSusage.Youwill finderrormessagesregardingimproperusageof atoms,spacegroupviolations,improperusageof microdomainsetc.

Err or : -1 : Maximumnumberof Orient.matricesreadThemaximumnumberof orientationmatricesthatcanbeusedfor microdomainsis limitedby theparameter”MAX MD ORI” in thefile ”microdis.inc”. If necessaryadjustthisparameterandrecompiletheprogram.

Err or : -2 : Improperlimits for atomnumberEither of the upperor lower limits usedon the ’append’commandis outsidethe rangeof atomspresentin the crystal. Checkwhetherthe limits areboth positive, the upperlimit is higheror equalto the lowerlimit andwhetherbothlimits arelessor equalto thenumberof atomspresentin thecrystal.Thenumberofatomsin thecrystalcanbecheckedwith thecommand:”eval n[1]”.

Err or : -3 : No atomsselectedyetTheplot andwavescanonly berun for selectedatoms.Usethe’select’commandto selectindividualatomtypesor to selectall atomspresentin thecrystal.

Err or : -4 : Extendof plotspaceis zeroThedimensionsof thespacefrom whichatomsareto beplottedis zero.Checkthevaluesdisplayedby theplot ’show’ commandandusethe’exte’ commandto giveappropriatevalues.

Err or : -5 : Toomany microdomainswithin crystalDISCUS storesall microdomainpositionsin an array. The size of this array is definedby parameterMC MAXMICRO in file ”microdis.inc”. If necessaryreadjustthe valueof this parameterandrecompiletheprogram.

Err or : -6 : Unknown microdomaintypeThe microdomaintype numberusedwith the ’place’ commanddoesnot correspondto an existing mi-crodomaintypein thelist. Checkwith ’show types’for a list of microdomaintypesthathavebeeninsertedinto thelist of availablemicrodomains.

Err or : -7 : Unknown spacegroupsymbolThe crystalfile containsan unknown spacegroup. Checkthe spellingof the spacegroupsymbol. Theallowedspacegroupsareall 230spacegroupsin theInt. Tablesfor Crystallographyplusthespacegroupsgivenfor alternative settingsandcell choicesof themonoclinicspacegroups.Referto appendixA of themanualfor acompletelisting of spacegroupsymbols.

Err or : -8 : Toomany pointsin reciprocallayerThenumberof pointsin reciprocalspacethatcanbecalculatedby theFouriertransformis limited by theparameter”MAXQXY” in thefile ”qspace.inc”.Checkthattheproductof � na� and � no� is lessor equalto ”MAXQXY”. If necessaryadjusttheparameter”MAXQXY” andrecompiletheprogram.

Err or : -9 : Unknown OutputFormatAn unknown outputformatwasdefinedfor theoutputlevel. Checkthateitherof: ”stan”, ”gnu”, ”pgm” or”post” wasusedasoutputformatwith the’format’ command.

Err or : -10 : Toomany Atomsin crystalThemaximumnumberof atomsthatcanbestoredin thestructureis determinedby theparameterMAX-ATOMS in the file ”crystal.inc”. By insertingnew atomsor by definingtoo largea crystalon the ’read’command,this numberwasexceeded.If necessary, changethevalueof theparameterMAXATOMS andrecompiletheprogram.


Err or : -11 : Unknown thresholdtypeTheparametergivenonthe’ thresh’commanddoesnotcorrespondto a valid entry. Checkthespellingof theparameter.

Err or : -12 : Numberof pointsmustbe � zeroThevalueof theparametergivenon the’abs’ or ’ord’ commandis lessthanone.Thisvaluerepresentsthenumberof datapointscalculatedalongtherespectivedirection.Thevaluemustbeat leastoneor higher.

Err or : -13 : Correlationmatrix index outsidelimitsTheindex of thecorrelationmatrix element(s)is eitherlessthanoneor higherthanthenumberof definedmicrodomaintypes.Checkthe’ccol’, ’crow’ and’cele’ commandsfor propernumberof parameters.Usethe’show type’ commandat ’microdomain’sublevel to seethenumberof microdomainscurrentlydefined.

Err or : -14 : Invalid spacegroup& latticeconstantsWhile readinga new cell the programchecksthe spacegroupand the lattice constantsfor consistency.Eithera spacegroupwasgiventhatis not includedin theprogram,or thelatticeconstantsdonot fulfill theconstraintsimposedby thespacegroup. Checkthespacegroupsymbolandthe latticeconstantsgivenintheinputfile.

Err or : -15 : No microdomaininputfile namedefinedAn attemptwasmadeto inserta microdomaintypewithout specifyingthe input file name.With the ex-ceptionof contenttype’free’ all microdomainsrequireaninputfile from which thenew atompositionsareread.Checkthecurrentdefaultsby ’show def’ andtheparametersgivenonthen’cont’ command.

Err or : -16 : Statusfor log mustbe: ”on” or ”off”Thesecondparameterfor the’ log’ commandmustbeeither”on” or ”off”.

Err or : -17 : Index of matrixoutsidelimitsThefirst parameteron the’mrow’ commandis the index of therow that is to beinserted.Allowedvaluesareone,two or three.

Err or : -18 : No orientationwith thisnumberexistsTheorientationmatrix requestedasparameteron the ’orie’ commanddoesnot exist. Usethe ’show orie’commandto view the list of definedorientationmatrices.Checkwhetherthree’mrow’ commandswereusedfor eachorientationmatrix thatyou intendedto setup.

Err or : -19 : Atom numberoutsidelimitsThenumberof theatomis eitherlessthanone,larger thanthecurrentnumberof atomsin the crystalorevenlarger thanthemaximumnumberof atomsallowed in your implementation.Checkthevalueof theparameter(s)on the’remove’ and’switch’ commandsor checktheindex of thevariables”m”, ”x”, ”y” or”z”. Checkthenumberof atomspresentin thecrystalby thecommand:’eval n[1]’.

Err or : -20 : Unknown element,noFouriercalculatedAn elementwasdetectedin the list of atomsfor which thereis no scatteringcurve available. TheFouriertransformis not calculatedat all. Checkthenameof all atomspresentin thecrystalusingthe’asym’ and’chem’ commands.If a chargedion wasgiven, this valencemight not be presentin the list of scatteringcurves. Referto Appendixb of themanualfor a list of internallystorednames.If the ’scat’and/or’delf’commandswereused,any namemaybeused.Checkwhetherthecommandswereusedproperly.

Err or : -21 : No elementpresent,noFouriercalculatedThereareno elementspresentat all in the crystal. The Fourier transformis not calculatedat all. Mostlikely, theFourierwascalledbeforeastructureor unit cell wasread,or anerroroccurredduringthereadingof thestructureor unit cell.

Err or : -22 : Incompatiblestandardfile sizes


While attemptingto addtwo Standardfiles,DISCUSencountereddifferentlengthof rowsor columnsin thetwo inputfiles. Theaddingis interruptedat thisstage.Theindicesalongtheabscissaandordinateatwhichtheerroroccurred,is displayedaswell, checktheinputfile for erroneouscontent.Also check,whethertheparametersnx,ny in the two input files areidenticalaswell asthexmin,xmax,yminandymaxparametersin thesecondline of bothinputfiles.

Err or : -23 : IncompatibleGNUPLOT file sizesWhile attemptingto addtwo GNUPLOT files,DISCUSencountereddifferentlengthof rowsor columnsinthetwo inputfiles. Theaddingis interruptedat this stage.Theline numberin which theerroroccurred,isdisplayedaswell, checktheinputfile for erroneouscontent.

Err or : -24 : Differentcoordinatesin GNUPLOT filesWhile attemptingto addtwo GNUPLOT files,DISCUSencountereddifferentcoordinatesin thetwo inputfiles. Theaddingis interruptedat this stage.Theline numberin which theerroroccurred,is displayedaswell, checktheinputfile for erroneouscontent.

Err or : -25 : Differentcoordinatesin 1-dimfilesWhile attemptingto addtwo 1-dim files,DISCUSencountereddifferentcoordinatesin thetwo input files.Theaddingis interruptedat this stage.Theline numberin which theerror occurred,is displayedaswell,checktheinputfile for erroneouscontent.

Err or : -26 : Toomany differentatomsin crystalThe maximumnumberof differentatomsallowed in your implementationwasexceeded.No morenewtypesof atomscanbe insertedinto the structure.Checkthechemistryof your crystalby the ’asym’ and’chem’ commands.All atomsareconsidereddifferenttypesthat arechemicallydifferent,have differentchargeor adifferenttemperaturecoefficient. If all typesareneeded,modify theparameter”maxscat”in thefile ”param.inc”andrecompiletheprogram.Seechapter9.1of themanualfor furtherinformation.

Err or : -27 : No atomof this typepresentin crystalAn atomwasselectedfor displacementby a wave or for plotting that doesnot exist within the crystal.Checkthespellingof theatomname,andthechemistryof thecrystalby the’asym’ and’chem’ commands.

Err or : -28 : Inputparametersmustbe � zeroThis function/commandrequiresnon-negative parameters.Checkthe valuesof the parametersand theexplanationfor thefunctionor commandusedfor valid rangesof numericalinput.

Err or : -29 : Toomany differentmicrodomaintypesThe maximumnumberof microdomaintypes is definedby the parameterMAX MD TY in file ”mi-crodis.inc”.If necessaryadjustthisparameterandrecompiletheprogram.

Err or : -30 : Unknown boundarytypeTheboundarytypeof microdomainsis notsetto eitherof ”block”, ”f ace”,”fuzzy” or ”sphere”.Checkthe’boundary’commandatsublevel ’microdomains’for properspelling.

Err or : -31 : Unknown distributionmodeThedistribution typefor microdomainsis not setto eitherof ”lattice”, ”paracrystal”or ”random”. Checkthe’distribution’ commandatsublevel ’microdomains’for properspelling.

Err or : -32 : Lengthof vectoris zeroAn attemptwasmadeto calculatetheanglebetweentwo vectorswhile oneof themis of lengthzero.Checktheparametersgivenon the’bang’ or ’rang’commandfor propernumbers.

Err or : -33 : No microdomaintypesdefinedyet


An attemptwasmadeto usethe’create’or ’run’ commandbeforeany microdomainsweredefinedby the’insert’ command.Checkfor propersequenceof commandsandmissingor misspelled’insert’ commands.

Err or : -34 : Formdoesnotappearto beclosedA microdomaintype of boundarytype ’f ace’ was definedfor which the form suppliedby the ’bound’commanddoesappearnot to beclosed.DISCUScheckswhethertheorigin of themicrodomainis insidethemicrodomainandthepositionsat1.0*10**9 alongeachof thebasevectorsis outsidethemicrodomain.If oneof theseconditionsis not met,theerrormessageis given. Checkthe’boundary’commandsusedtodefinethemicrodomaintype.

Err or : -35 : Volumeof unit cell � = zeroThevolumeof theunit cell wascalculatedaszeroor a negativevalue.Checkthelatticeparametersgivenin theinputfile. Are thereany accidental”-” signs? Do theanglesform animpossibleshape?

Err or : -36 : Unsuitablefile typesfor inverseFourierNot everycombinationof file typesis allowedfor aninverseFouriersynthesis.Allowedfile combinationsare:

file a file bintensity phaseamplitude phasereal part imaginary part

Err or : -37 : No filenamedefinedyetAn attemptwasmadeto write outputto or readfrom a file without defininga file name. DISCUSdoesnot providedefault namesfor theoutputof the’plot’ commandor theinput filenames.Checkthe’outfile’commandatsublevels’output’ and’plot’ or the’content’commandatsublevel ’microdomains’.

Err or : -38 : Unsuitablefile typesfor PattersonNot everycombinationof file typesis allowedfor a Pattersonsynthesis.Allowedfile combinationsare:

file a file bintensity any file typeamplitude any file typereal part imaginary part

Err or : -39 : All elementsof correlationmatrixzeroSincethe correlationmatrix givesthe probabilitiesfor existenceof a microdomaintype,not all elementsmaybeequalto zero. Thedefault valuesat startupare1 for thediagonalelementsandzerofor all otherelements.displaythe correlationmatrix with the command’show corr’ andcheckthe ’ccol’, ’cele’ and’crow’ commandsfor propervalues.

Err or : -40 : MicrodomaintypecannotberemovedDISCUScanonly remove thosemicrodomaintypesfrom the list of typesthat have not yet beenusedbythe’create’command,i.e. only thosemicrodomaintypesthathavebeeninsertedinto thelist by the’insert’commandafterthelast’create’command.

Err or : -41 : File specifiermustbe”a” or ”b”Thetwo files for inverseFourierandPattersonsynthesisarereferredto by ”a” and”b”. Thefirst parameteron the’file’ andthe’ type’ commandsmustbeeither”a” or ”b”.

Err or : -42 : Typemustbe: inten,ampl,phase,real,imagThefile typefor inverseFourierandPattersonsynthesismustbespecifiedasoneof thefollowing strings:”intensity”,”amplitude”,”phase”,”real”,”imaginary” They maybeabbreviatedto auniquestring.Checkthespellingof theparameter.


Err or : -43 : Not enoughparameterfor filenameformatAn attemptwasmadeto generatea file namefrom a string like ”text%dtext” without supplyingenoughnumericalparameters.Checkthatthespellingof thestingwithin ” ” is correct.Are thereany unwanted%dcombinations?.Checkthenumberandtypeof parametersfollowing thefile name.

Err or : -44 : Rightquotationmarkmissingin formatAn attemptwasmadeto generatea file namefrom a string like ”text%dtext” without supplyingthe rightquotationmark.Checktheline andprovidethemissing”.

Err or : -45 : Toomany atomsin environmentTheindicesof all atomsfoundarestoredin theinternalvariable”res”. Moreatomswerefoundthatfit intothedimensionsof ”res”. Restrictthesearchfor theenvironmentto asmallershellor changethedimensionof ”res para”in file ”param.inc”.

Err or : -46 : Error readingtitle of structureAn erroroccurredwhile readingthetitle line of astructureor unit cell file. Checkthefile for any garbage.

Err or : -47 : Error readingspacegroupsymbolAn erroroccurredwhile readingthespacegroupline of a structureor unit cell file. Checkthefile for anygarbage.

Err or : -48 : Error readinglatticeconstantsAn erroroccurredwhile readingthe latticeconstantsof a structureor unit cell file. Checkthefile for anygarbageor accidentalletters.

Err or : -49 : Error readingatomcoordinatesAn erroroccurredwhile readingtheatomcoordinatesof theatomlisted.Checkthefile for any garbage.Istheline of thetypeNamex y z B Are therelettersamongthenumericalvalues?

Err or : -50 : Wrongformatfor 1-dimensionaldataYou tried to write a one-dimensionalsectionof spaceaseitherPostscript,PGM or PPM Bitmap. One-dimensionaldatacanonly bewrittenas”gnuplot” or ”standard”format.

Err or : -51 : Unsuitablefile typefor SHELXL formatIf thefile formatis setto ”shelxl” to calculatetheinverseFourierof Pattersonform SHELXL data,thefiletypemustbesetto eitherof ”fobs” or ”fcalc”.Checkthe’ type’ commandfor erroneousinput.

Err or : -52 : Unsuitableinputvaluefor SHELXL formatIf the file format is set to ”shelxl” to calculatethe inverseFourier of Pattersonform SHELXL data,theoptionalsecondparametermustbeeitherof ”fobs” or ”fcalc”. Checktheinputline for the’form’ command.

Err or : -53 : Toomany differentlayertypesYou tried to definetoomany differentlayertypesfor a crystalwith stackingfaults.If necessarymodify thevalueof ”ST MAXTYPE” in file ”stack.inc”andcompiletheprogram.

Err or : -54 : Index outsidelimitsThe valuegiven is outsidethe properlimits allowedby this command.This usuallymeansthat an arrayelementis outsidethecurrentdimensionof anarray, for examplea correlationmatrix or you aretrying toincludetoomany atomsin thecrystal.Checkthesectionondimensionsin themanual.

Err or : -55 : No layerscreatedatallDuring thecreationof thestackingfaults,noneof thelayertypesmettheconditionsimposedby thecorre-lationmatrix. Checkthecorrelationmatrix for propervalues.


Err or : -56 : Av. Transl.in planeof moduli vectorsTheaveragetranslationvector, - calculatedfrom thematrixof translationvectorsandthecorrelationmatrixor readvia the ’aver’ commandis in theplanedefinedby the two moduli vectorthatwerereadusingthe’modu’ command.Usethe’show’ commandto checkthevaluesof thevectors.Correctthevectorsby the’aver’, ’modu’ commands.

Err or : -57 : Av. Translationis zeroTheaveragetranslationvectoris avectorof lengthzero.Usethe’show’ commandto checkthevaluesof thevector. If theaveragevectoris setexplicitly by == � ’settrans,fixed’, thencorrectthevectorby the’aver’command.If theaveragevectoris calculatedfrom thetranslationandcorrelationmatrix, theweightedsumof translationvectorsis equalto zero. Usethe ’show’ commandto checkthevaluesof the two matrices.Correctthevaluesby the== � ’ trans’,’crow’, ’ccol’, ’cele’ commands.

Err or : -58 : No atomswritten to fileNo atomswerewrittento theplot file aftertheruncommand.Checkthesettingsusingthecommand’show’andchecktheonlinehelpfor furtherdetails.Themostcommonproblemis a toosmallvaluefor ’ thick’.

Err or : -59 : Invalid coloror typ selectedfor atomThecoloror typeselectedfor plottingatomsis invalid. Checktheonlinehelpfor a list of valid numbers.

Err or : -60 : OutputvalueNOT allowedusinglotsYoucalculatedtheFourierusing== � ’ lots’. In thiscaseyoucanwrite intensitiesonly asoutput.

Err or : -61 : Toomany additionalgeneratorsYou tried to specifytoo many additionalgeneratorsthroughthe”generator”key word in thestructurefile.Themaximumnumberof generatorsis specifiedin thefile ”gen add.inc”. If necessary, increasethevalueandcompileDISCUS.

Err or : -62 : Toomany additionalsymmetryoperatorsYoutriedto specifytoomany additionalsymmetryoperatorsthroughthe”symmetry”key wordin thestruc-turefile. Themaximumnumberof symmetryoperatorsis specifiedin thefile ”gen add.inc”. If necessary,increasethevalueandcompileDISCUS.

Err or : -63 : MoleculenumberoutsidelimitsYou tried to selecta moleculenumberthat is lessthanzeroor higherthanthenumberof moleculesin thecrystal.Or theupperlimit of a rangeof numberscouldbelessthanthelower limit.

Err or : -64 : MoleculetypeoutsidelimitsYou tried to selectamoleculetypethatis lessthanzeroor higherthanthenumberof moleculetypesin thecrystal.Or theupperlimit of a rangeof numberscouldbelessthanthelower limit.

Err or : -65 : Toomany moleculescreatedYoucreatedmoremoleculesthanfit into thecorrespondingarrays.Checkthesizeof thecrystalor thelimitsof loopsusedto createthe molecules.If necessaryadjustthe maximumnumberof moleculesin the file”molecule.inc”andcompileDISCUS.

Err or : -66 : Toomany moleculestypescreatedYoucreatedmoremoleculetypesthanfit into thecorrespondingarrays.Checkthenumberof moleculesinthecrystalfile or thelimits of loopsusedto createthemolecules.If necessaryadjustthemaximumnumberof moleculetypesin thefile ”molecule.inc”andcompileDISCUS.

Err or : -67 : Moleculeshavedifferentnumberof atomsYou tried to swaptwo moleculesof differentlength. This modeis possiblefor moleculesof equallengthonly.

Err or : -68 : Modeonly availablefor molecules


Rotationalwavesarecanactonly ontomolecules,notontoindividualatoms

Err or : -69 : MicrodomainsoverlapAn atom was found that is insideat leasttwo microdomains. The atom numberand the microdomainnumbersarewritten onto the screen.Checkthe distribution of the microdomainsandthe correspondingmicrodomainradii. Eitherthetwo microdomainsaretoocloseto eachotheror theradiiof themicrodomainsaretoo large.

Err or : -70 : Deltavaluemustbein interval 0 - � 1A wave functionof type ”box” waschosen.Theoptionalsecondparametergivesthe width of the lowerhalf of thebox in multiplesof thewave length.Thisvaluemustbein therange0 - � 1. Thevalues0 and1arenotallowedeither.

Err or : -71 : Toomany pointsin directspacelayerThe numberof datapointsyou selectedwith the ’rhona’ and ’rhono’ commandsexceedsthe maximumnumberof datapointsDISCUScanhandle.Themaximumvalueis definedin thevariableMAXQXY inthefile ”config.inc”. If necessaryadjustthisparameterandcompileDISCUSagain.

1.43.2 chem

Errorsat thechemistrylevel of DISCUS

Err or : -1 : Toomany pointsfor histogramThenumberof pointsyou specifiedfor thehistogramexceedsthedimensionsof thearray. Checkwhetheryouneedthismany points.If soenlargethevalueof ”chem max bin” in thefile ”chem.inc”

Err or : -2 : Can’t storeall informationin variableRESThenumberof itemsproducedby thecommandexceedsthedimensionof theresultarray.

Err or : -3 : Invalid rangefor bond-lengthhistogramTheminimumvalueof thebondlengthsis +0.01,andthemaximumvalue(parameter#2) mustbegreaterthantheminimumvalue.Checktheparameterson the== � ’setbl’ command.

Err or : -4 : Invalid SIGMA enteredThesigmasmustall belargerthanzero.Checktheparameterson the== � ’setfs’, ’setwsig’ commands.

Err or : -5 : Toomany differentatomsonONEsiteThenumberof differentatomsfoundononesitein theunit cell exceedsthedimensionsof thearray.Youhaveto setthevalueof ”chem max ave” to a largervalueandcompileDISCUSagain.

Err or : -6 : Atom nameALL notallowedfor thiscommandThe== � ’corr’ commandrequiresexplicit atomnames.Youcannotusetheatomname”ALL”.

Err or : -7 : Atomsneedto bedifferentThe== � ’corr’ commandrequiresthe two atomtypesto bedifferent. Theself correlationof atom1withitself is storedby the’freq’ commandaswell. If you know thatthereareno otheratomtypesin thegivendirection,setthesecondatomtypeto ”void”.

Err or : -8 : No neighbouringatomsfoundThe’freq’ commandfoundno neighbouringatomsfor thegivendistanceanddirection. Checktheonlinehelpfor moreinformationon ’neig’.

Err or : -9 : Invalid correlationvectorindex givenThegivencorrelationvectorindex wasinvalid. Checkyour input.

Err or : -10 : Invalid crystalsitegiven


A invalid sitenumberfor thecurrentcrystalwasentered.Checkthat thestructureis loadedandyour sitenumberis valid.

Err or : -11 : No correlationsselectedBeforeyoucancalculatecorrelationsyouneedto definethecalculationmoreusingthe’setneig’ commandin the’chem’ sublevel.

Err or : -12 : Toomany correlationdefinitionsThecommand’setcorr,add’wasexecutedbut thereis nomorespacefor theadditionalcorrelationdefinition.Use’setcorr,rese’to discardpreviousdefinitionsor adjustthevalueof CHEM MAX CORin ’chem.inc’andrecompileDISCUS.

Err or : -13 : CorrelationdirectioninvalidTheentereddirectionfor thecalculationof thedisplacementcorrelationsis invalid (e.g.lengthzero),checkyour input.

Err or : -14 : Toomany displacementdirectionsYou have enteredtoo many displacementdirectionsfor thecalculationof displacementcorrelations.Use’setdir,rese’to discardthe previous input our adjustthe parameterCHEM MAX DIR in ’chem.inc’ andrecompileDISCUS.

Err or : -15 : No displacementdirectionsselectedYou have tried to calculatedisplacementcorrelationsbut thereareno directionsdefinedthat areusedtoobtainthedisplacement.Usethecommand’setdir,..’ to enterthedesiredvalues.

Err or : -16 : Failedto applyperiodicboundariesDISCUSis notableto applyperiodiccrystalboundaries(shouldnothappen).

Err or : -17 : CorrelationfieldsrequiresamemodeTo calculatecorrelationfields,all neighbourdefinitionsmustbemadeusingthesamemode,i.e. ’dist’ or’vec’. Redefinethe neighboursto be usedvia the command’setneig’. This condition is only valid for2-dimensionalcorrelationfields.

Err or : -18 : Correlationfieldsrequiresame# vectorsIf working with neighbouringvectordefinitionsto determinea 2D correlationfield, thenumberof vectorsmustbethesamefor bothdirections.

Err or : -19 : No neighbouringmoleculesfoundFor thecurrentneighbourdefinitionsnoneighbouringmoleculeswerefound.Checkyour input.

Err or : -20 : No moleculespresentin crystalYoucannotusethe’molecule’modewithouthaving at leastonemoleculewithin themodelcrystal.Checkthemanualhow to definemolecules.

Err or : -21 : Moleculetypesneedto bedifferentIn orderto executetheselectedoperation(e.g.determinecorrelations),theselectedmoleculetypesneedtobedifferent.Checkyour input.

Err or : -22 : Commandnotavailablein moleculemodeThisparticularcommand(e.g.aver) is notavailablein ’molecule’mode.Switchto ’atoms’modeusingthecommand’modeatom’andreenterthedesiredcommand.

Err or : -23 : Toomany neighbouringatoms/moleculesThecurrentoperationhasfoundtoo many neighbouringatomsor molecules.Eitherrestricttheneighbourdefinitionsof adjustthevariableCHEM MAX NEIG in thefile ’config.inc’ andrecompileDISCUS.


1.43.3 four

Thesearethepossibleerrormessagesrelatedto thecalculationof theFourierTransform

Err or : -2 : Invalid lot shapeselectedTheonly two supportedlot shapesare’eli’ and’box’ ! Selectapropershape.

Err or : -3 : SIN(THETA)/LAMBD A � lookuptablelimitsTo speed up the calculation of the Fourier Transform, DISCUS uses a lookup table forSIN(THETA)/LAMBD A. You needto adjustthe maximumh,k,l or the wave length. Alternatively, thevaluesCFPKT andCFINC in the file ’config.inc’ might be adjustedto the specificneedsandDISCUSrecompiled.

Err or : -4 : Componentof incrementvectoris zeroThecornersof theplanein reciprocalspaceto becalculatedareinvalid sincetwo or morecornersarethesame.Adjustyour input.

1.43.4 mc

Thesearetheerrormessagesof theMC sectionof DISCUS

Err or : -1 : Invalid or noenergy typeselectedBeforerunninga MC simulation,a valid energy definition (e.g. occupationalcorrelationsor distortions)mustbeselectedusingthe’setenergy’ command.

Err or : -2 : No valid moveafter1000cyclesAfter 1000cyclesNO valid MC move wasgeneratedandDISCUShasterminatedthesimulation.Checkyour input.

Err or : -3 : Invalid modeselectedfor COCCMC runOccupationalorderingrequirestheSWCHEMmodeto beselected.Usethecommand’setmode’to selectthecorrectmodeandrestartthesimulation.

1.43.5 pdf

Errorsat thePDFLevel

Err or : -1 : Toomany pointsin PDFThespecifiedrangeandgrid sizefor thePDFresultsin toomany points.Eitheradjustyour inputor changetheparameterMAXDAT in ’config.inc’ andrecompileDISCUS.

Err or : -2 : Cannotextendr-rangefor corr. convolutionIn orderto carryout theconvolutionwith theSINCfunctiondefinedby thevalueof Q(max),thecalculationrangefor the PDF needsto be extended.This error messageoccurswhenthereis not enoughspacefortheadditionaldatapoints. Eitheradjustyour input or changetheparameterMAXDAT in ’config.inc’ andrecompileDISCUS.

Err or : -3 : Crystaltoo largeto createperiodicbound.Thesizeof thecrystalis too largefor theperiodicboundaryarrayDISCUSusesfor rapidcalculationof thePDF. Eitherusea smallermodelcrystalor changetheparameterMAXBND in ’config.inc’ andrecompileDISCUS.

1.43.6 rmc

Errorsat theReverseMonteCarloLevel


Err or : -1 : Toomany experimentaldataplanesThis messageappearsif the usertries to readan additionalplaneof experimental dataandthe maximalnumberof planesis exceeded.If thatmany dataplanesarereallyneeded,thevariableRMC MAX PLANEShasto beadjustedin thefile ’config.inc’ andDISCUSmustberecompiled.

Err or : -2 : Toomany experimentaldatapointsTheexperimentaldatafile containstoo many datapoints. In orderto beableto usetheparticulardatafilethevariableRMC MAX Q mustbealteredin ’config.inc’ andDISCUSmustberecompiled.

Err or : -3 : No atomspresentin modelcrystalThecommand’run’ wasenteredbut thereis no modelcrystalpresent.Thestartingstructurehasto besetupbeforeenteringtheRMC sublevel.

Err or : -4 : No experimentaldatapresentThecommand’run’ wasenteredbut noexperimentaldataarepresent.Usethecommand’data’to readtheexperimentaldata.

Err or : -5 : Invalid method(x,n) selectedWhenusingthe’data’commandaninvalid scatteringmethodwasused.Thepresentversionof theprogramrecognizes”neutron” and”x-ray” data. The methodparametercanbe abbreviatedto a singleletter. Theinput is notcasesensitive.

Err or : -7 : Invalid planeselectedAn invalid dataplanewasselected.Usethecommand’show’ for a list of loadeddataplanes.

Err or : -8 : Invalid symmetrynumberselectedTheselectedsymmetrynumberis invalid. Usethecommand’show’ for a list of thecurrentsettings.

Err or : -9 : Invalid RMC modeselectedAn invalid RMC modewasselected.Checktheonlinehelpentryfor ’setmode’in theRMC sublevel for alist of allowedRMC moves.

Err or : -10 : No atomtypesselectedfor RMC runNo atomswereselectedfor theRMC refinement.Usethecommand’sele’ to selectthe atomtypesto beusedfor theRMC run.

Err or : -11 : Only ONEatomtypepresentin SWCHEMmodeTheRMC modeSWCHEMrequirestwo differentatomtypesto beselected.Vacanciesareto beselectedasVOID.

Err or : -12 : Displacementstoosmallfor SWDISPmodeThedisplacementspresentin thestartingstructurearetoo smallto usetheSWDISPmode.Thelimit is setin ’rmc.f’ if thereis any needto changethat.

Err or : -13 : Toomany symmetricallyequivalentplanesThenumberof symmetricallyequivalentplanesexceedsthelimit setby RMC MAX SYM in ’config.inc’.You caneitheradjustthatvalueandrecompileDISCUSor setthespacegroupsymbolin thestructurefileto P1if you don’t wantto usethesymmetryinformation.

Err or : -14 : No experimentaldatawithin givenq limitsThereareno experimentaldatain thegivesq limits. Checkthecurrentsettingswith ’show’ andadjustthelimits usingthecommand’setrange’in theRMC sublevel.

Err or : -15 : Invalid datatypeselectedDISCUScanreadPGM andNIPL files asinput data.You selecteda nonsupporteddatatype. Checktheonlinehelpfor ’data’for a descriptionof thevalid dataformats.


Err or : -16 : Invalid weightingschemeor weightingfileThe enteredweightingschemeis invalid. Checkthe online help for ’data’ for a descriptionof the validweightingschemes.

Err or : -17 : Dataandweightfile havedifferentsizesIf youreadweightsfrom a file, datafile andweightfile MUST have thesamesize.

Err or : -18 : Datafile is notanASCII PGMfileIn thepresentversion,DISCUScanonly readASCII PGM files with thecodeP2in thefirst line. Usethetool ’pnmnoraw’ to transformfrom abinaryto anASCII versionof your inputfile. Thetool ’pnmnoraw’ ispartof the’netpbm’package.

Err or : -19 : Invalid constrainenteredTheenteredconstrainis invalid. Checktheonlinehelpfor moreinformation.

Err or : -20 : No valid moveafter1000displayintervalsAfter 1000displayintervals,DISCUShasnotgeneratedasinglevalidmove.Checkthesettingsfor minimalallowedatomdistancesandall otherRMC settings.

Err or : -21 : Numberof LOTSexceedsmaximumThenumberof ’ lots’ (crystalvolumesto beaveraged)exceedsthemaximumnumberRMC MAX LOTSdefinedin ’config.inc’.

1.44 spacegroups

List of allowedSpacegroups

a)Standardspacegroupssettings

# 1 : P1 # 2 : P-1

# 3 : P2 # 4 : P21 # 5 : C2 # 6 : Pm# 7 : Pc # 8 : Cm # 9 : Cc # 10 : P2/m# 11 : P21/m # 12 : C2/m # 13 : P2/c # 14 : P21/c# 15 : C2/c

# 16 : P222 # 17 : P2221 # 18 : P21212 # 19 : P212121# 20 : C2221 # 21 : C222 # 22 : F222 # 23 : I222# 24 : I212121 # 25 : Pmm2 # 26 : Pmc21 # 27 : Pcc2# 28 : Pma2 # 29 : Pca21 # 30 : Pnc2 # 31 : Pmn21# 32 : Pba2 # 33 : Pna21 # 34 : Pnn2 # 35 : Cmm2# 36 : Cmc21 # 37 : Ccc2 # 38 : Amm2 # 39 : Abm2# 40 : Ama2 # 41 : Aba2 # 42 : Fmm2 # 43 : Fdd2# 44 : Imm2 # 45 : Iba2 # 46 : Ima2 # 47 : Pmmm# 48 : Pnnn # 49 : Pccm # 50 : Pban # 51 : Pmma# 52 : Pnna # 53 : Pmna # 54 : Pcca # 55 : Pbam# 56 : Pccn # 57 : Pbcm # 58 : Pnnm # 59 : Pmmn# 60 : Pbcn # 61 : Pbca # 62 : Pnma # 63 : Cmcm# 64 : Cmca # 65 : Cmmm # 66 : Cccm # 67 : Cmma# 68 : Ccca # 69 : Fmmm # 70 : Fddd # 71 : Immm# 72 : Ibam # 73 : Ibca # 74 : Imma

# 75 : P4 # 76 : P41 # 77 : P42 # 78 : P43# 79 : I4 # 80 : I41 # 81 : P-4 # 82 : I-4# 83 : P4/m # 84 : P42/m # 85 : P4/n # 86 : P42/n# 87 : I4/m # 88 : I41/a # 89 : P422 # 90 : P4212# 91 : P4122 # 92 : P41212 # 93 : P4222 # 94 : P42212# 95 : P4322 # 96 : P43212 # 97 : I422 # 98 : I4122# 99 : P4mm # 100 : P4bm # 101 : P42cm # 102 : P42nm# 103 : P4cc # 104 : P4nc # 105 : P42mc # 106 : P42bc


# 107 : I4mm # 108 : I4cm # 109 : I41md # 110 : I41cd# 111 : P-42m # 112 : P-42c # 113 : P-421m # 114 : P-421c# 115 : P-4m2 # 116 : P-4c2 # 117 : P-4b2 # 118 : P-4n2# 119 : I-4m2 # 120 : I-4c2 # 121 : I-42m # 122 : I-42d# 123 : P4/mmm # 124 : P4/mcc # 125 : P4/nbm # 126 : P4/nnc# 127 : P4/mbm # 128 : P4/mnc # 129 : P4/nmm # 130 : P4/ncc# 131 : P42/mmc # 132 : P42/mcm # 133 : P42/nbc # 134 : P42/nnn# 135 : P42/mbc # 136 : P42/mnm # 137 : P42/nmc # 138 : P42/ncm# 139 : I4/mmm # 140 : I4/mcm # 141 : I41/amd # 142 : I41/acd

# 143 : P3# 144 : P31 # 145 : P32# 146 : R3: hexagonal axes # 147 : P-3# 148 : R-3: hexagonal axes # 149 : P312# 150 : P321 # 151 : P3112# 152 : P3121 # 153 : P3212# 154 : P3221 # 155 : R32: hexagonal axes# 156 : P3m1 # 157 : P31m# 158 : P3c1 # 159 : P31c# 160 : R3m: hexagonal axes # 161 : R3c: hexagonal axes# 162 : P-31m # 163 : P-31c# 164 : P-3m1 # 165 : P-3c1# 166 : R-3m: hexagonal axes # 167 : R-3c: hexagonal axes

# 168 : P6 # 169 : P61 # 170 : P65 # 171 : P62# 172 : P64 # 173 : P63 # 174 : P-6 # 175 : P6/m# 176 : P63/m # 177 : P622 # 178 : P6122 # 179 : P6522# 180 : P6222 # 181 : P6422 # 182 : P6322 # 183 : P6mm# 184 : P6cc # 185 : P63cm # 186 : P63mc # 187 : P-6m2# 188 : P-6c2 # 189 : P-62m # 190 : P-62c # 191 : P6/mmm# 192 : P6/mcc # 193 : P63/mcm # 194 : P63/mmc

# 195 : P23 # 196 : F23 # 197 : I23 # 198 : P213# 199 : I213 # 200 : Pm-3 # 201 : Pn-3 # 202 : Fm-3# 203 : Fd-3 # 204 : Im-3 # 205 : Pa-3 # 206 : Ia-3# 207 : P432 # 208 : P4232 # 209 : F432 # 210 : F4132# 211 : I432 # 212 : P4332 # 213 : P4132 # 214 : I4132# 215 : P-43m # 216 : F-43m # 217 : I-43m # 218 : P-43n# 219 : F-43c # 220 : I-43d # 221 : Pm-3m # 222 : Pn-3n# 223 : Pm-3n # 224 : Pn-3m # 225 : Fm-3m # 226 : Fm-3c# 227 : Fd-3m # 228 : Fd-3c # 229 : Im-3m # 230 : Ia-3d

b) nonstandardsettingsof spacegroups

# 231 : P112: # 3: P2 : unique c axis# 232 : P1121: # 4: P21 : unique c axis# 233 : A121: # 5: C2 : unique b axis: cell choice 2# 234 : I121: # 5: C2 : unique b axis: cell choice 3# 235 : A112: # 5: C2 : unique c axis: cell choice 1# 236 : B112: # 5: C2 : unique c axis: cell choice 2# 237 : I112: # 5: C2 : unique c axis: cell choice 3# 238 : P11m: # 6: Pm : unique c axis# 239 : P1n1: # 7: Pc : unique b axis: cell choice 2# 240 : P1a1: # 7: Pc : unique b axis: cell choice 3# 241 : P11a: # 7: Pc : unique c axis: cell choice 1# 242 : P11n: # 7: Pc : unique c axis: cell choice 2# 243 : P11b: # 7: Pc : unique c axis: cell choice 3# 244 : A1m1: # 8: Cm : unique b axis: cell choice 2# 245 : I1m1: # 8: Cm : unique b axis: cell choice 3# 246 : A11m: # 8: Cm : unique c axis: cell choice 1# 247 : B11m: # 8: Cm : unique c axis: cell choice 2# 248 : I11m: # 8: Cm : unique c axis: cell choice 3# 249 : A1n1: # 9: Cc : unique b axis: cell choice 2


# 250 : I1a1: # 9: Cc : unique b axis: cell choice 3# 251 : A11a: # 9: Cc : unique c axis: cell choice 1# 252 : B11n: # 9: Cc : unique c axis: cell choice 2# 253 : I11b: # 9: Cc : unique c axis: cell choice 3# 254 : P112/m: # 10: P2/m : unique c axis# 255 : P1121/m: # 11: P21/m : unique c axis# 256 : A12/m1: # 12: C2/m : unique b axis: cell choice 2# 257 : I12/m1: # 12: C2/m : unique b axis: cell choice 3# 258 : A112/m: # 12: C2/m : unique c axis: cell choice 1# 259 : B112/m: # 12: C2/m : unique c axis: cell choice 2# 260 : I112/m: # 12: C2/m : unique c axis: cell choice 3# 261 : P12/n1: # 13: P2/c : unique b axis: cell choice 2# 262 : P12/a1: # 13: P2/c : unique b axis: cell choice 3# 263 : P112/a: # 13: P2/c : unique c axis: cell choice 1# 264 : P112/n: # 13: P2/c : unique c axis: cell choice 2# 265 : P112/b: # 13: P2/c : unique c axis: cell choice 3# 266 : P121/n1: # 14: P21/c : unique b axis: cell choice 2# 267 : P121/a1: # 14: P21/c : unique b axis: cell choice 3# 268 : P1121/a: # 14: P21/c : unique c axis: cell choice 1# 269 : P1121/n: # 14: P21/c : unique c axis: cell choice 2# 270 : P1121/b: # 14: P21/c : unique c axis: cell choice 3# 271 : A12/n1: # 15: C2/c : unique b axis: cell choice 2# 272 : I12/a1: # 15: C2/c : unique b axis: cell choice 3# 273 : A112/a: # 15: C2/c : unique c axis: cell choice 1# 274 : B112/n: # 15: C2/c : unique c axis: cell choice 2# 275 : I112/b: # 15: C2/c : unique c axis: cell choice 3

# 276 : Pnnn: # 48: origin choice 2# 277 : Pban: # 50: origin choice 2# 278 : Pmmn: # 59: origin choice 2# 279 : Ccca: # 68: origin choice 2# 280 : Fddd: # 70: origin choice 2

# 281 : P4/n: # 85: origin choice 2# 282 : P42/n: # 86: origin choice 2# 283 : I41/a: # 88: origin choice 2# 284 : P4/nbm: # 125: origin choice 2# 285 : P4/nnc: # 126: origin choice 2# 286 : P4/nmm: # 129: origin choice 2# 287 : P4/ncc: # 130: origin choice 2# 288 : P42/nbc: # 133: origin choice 2# 289 : P42/nnn: # 134: origin choice 2# 290 : P42/nmc: # 137: origin choice 2# 291 : P42/ncm: # 138: origin choice 2# 292 : I41/amd: # 141: origin choice 2# 293 : I41/acd: # 142: origin choice 2

# 294 : R3: # 146 rhombohedral axes# 295 : R-3: # 148 rhombohedral axes# 296 : R32: # 155 rhombohedral axes# 297 : R3m: # 160 rhombohedral axes# 298 : R3c: # 161 rhombohedral axes# 299 : R-3m: # 166 rhombohedral axes# 300 : R-3c: # 167 rhombohedral axes

# 301 : Pn-3: # 201: origin choice 2# 302 : Fd-3: # 203: origin choice 2# 303 : Pn-3n: # 222: origin choice 2# 304 : Pn-3m: # 224: origin choice 2# 305 : Fd-3m: # 227: origin choice 2# 306 : Fd-3c: # 228: origin choice 2

# 307 : Pbnm: # 62: Pnma non-standard orientation


1.45 wavelength

List of allowedwavelengthsymbols

CRA1 2.28970 CRA2 2.29361 CRB 2.0848 CR 2.2909FEA1 1.193604 FEA2 1.93998 FEB 1.75653 FE 1.9373CUA1 1.54056 CUA2 1.54439 CUB 1.39217 CU 1.5418MOA1 0.709309 MOA2 0.71335 MOB 0.63225 MO 0.7107AGA1 0.55941 AGA2 0.56380 AGB 0.49701 AG 0.5608

1.46 atom names

List of allowedatom names

H H. H1- D. HE LI LI1 BE BE2+ B C. N O O1-O2-. F F1- NE NA NA1+ MG MG2+ AL AL3+ SI SI. SI4+ SP CL CL1- AR K K1+ CA CA2+ SC SC3+ TI TI2+ TI3+ TI4+V V2+ V3+ V5+ CR CR2+ CR3+ MN MN2+ MN3+ MN4+ FE FE+ FE3+CO CO2+ CO3+ NI NI2+ NI3+ CU CU1+ CU2+ ZN ZN2+ GA GA3+ GEGE4+ AS SE BR BR1- KR RB RB1+ SR SR2+ Y Y3+ ZR ZR4+NB NB3+ NB5+ MO MO3+ MO5+ MO6+ TC RU RU3+ RU+ RH RH3+ RH4+PD PD2+ PD4+ AG AG1+ AG2+ CD CD2+ IN IN3+ SN SN2+ SN4+ SBSB3+ SB5+ TE I I1- XE CS CS1+ BA BA2+ LA LA3+ CE CE3+CE4+ PR PR3+ PR4+ ND ND3+ PM PM3+ SM SM3+ EU EU2+ EU3+ GDGD3+ TB TB3+ DY DY3+ HO HO3+ ER ER3+ TM TM3+ YB YB2+ YB3+LU LU3+ HF HF4+ TA TA5+ W W6+ RE OS OS4+ IR IR3+ IR4+PT PT2+ PT4+ AU AU1+ AU3+ HG HG1+ HG2+ TL TL1+ TL3+ PB PB2+PB4+ BI BI3+ BI5+ PO AT RN FR RA RA2+ AC AC3+ THE TH4+PA U U3+ U4+ U6+ NP NP3+ NP4+ NP6+ PU PU3+ PU4+ PU6+ AMCM BK CF

Thesymbolsendingwith aperiodhavespecialmeaningsaslisted:

H. Hydrogen HF scattering factorC. Carbon HF scattering factorSI. Silicon HF scattering factorD. Deuterium (for neutron diffraction only)O2-. Oxygen, taken from Acta Cryst. 19, p 486 (1965).

Otherspecialnames:

E1- Single electron with form factor =1 independent of sin( )/

Othernamesmaybeusedaswell, if scatteringcurvesaresuppliedfor thesenames.Seethe’delf, and’scat’commandsat ’fourier’ sublevel for details.

Chapter 2

Generalcommands

All commandsconsistof a commandverb,optionallyfollowedby oneor moreparameters.All parametersmustbeseparatedfrom oneanotherby acomma”,”. Thereis nopredefinedneedfor any specificsequenceof commands.Commandsare casesensitive, all commandsand alphabeticparametersMUST be typed in lower caseletters.Only the first four lettersof any commandverb aresignificant,all commandsmay be abbreviatedevenfurther. At leasta singlespaceis neededbetweenthecommandverbandthefirst parameter. No commaisto precedethefirst parameter. Thecommandverbitself MAY NOT beprecededby any blanks.ThewordPROGin thispartof thehelpsectionis to bereplacedby DISCUSor KUPLOT dependingwhichprogramyouareusing.Furtherhelptopicsare:

2.1 #

# � comment�Any line beginningwith a ”#” is regardedascomment.

2.2 @

@� filename� [ � argument� ...]

Any list of valid commandscanbewritten to anASCII file andandindirectlyby thecommand:

prompt > @<name>

Thecommandsmuststartin the left mostcolumnof thefile andareotherwiseexecutedastyped. Macrofiles maycall othermacrofiles up to a level definedat installation.This is not a call in thesenseof callinga function.All variablesareidenticalatall levelsof macrofile nesting.Macro files canbe written by any editor on your systemor be generatedby the == � ’ learn’ command.’ learn’ startsto rememberall the commandsthat follow andsavestheminto the file givenon the ’ learn’command.Thelearnsequenceis terminatedby the’ lend’ command.Thedefaultextensionis ”.mac”Optionallyargumentscanbelistedon thecommandline. Theseargumentswill replacetheformalparame-tersinsidethemacro.Theformal parametersmustbegivenas”$1”, ”$2” ... Thestring � argument� willreplacethestring”$1”. ”$1” is thefirst argumenton thecommandline, ”$2” thesecondandsoon. If therearenotenoughcommandline arguments,anerrormessageis displayed.

112

CHAPTER2. GENERALCOMMANDS 113

2.3 =� variable � = � expression�Theexpressionon theright of theequalsignis evaluatedandits resultstoredin variable � variable� .

2.4 input

Input editing functions

If theprogramwascompiledwith -DREADLINE, thefollowing basiceditingfunctionsareavailableat theprogramprompt:

Â : moves to the beginning of the lineˆB : moves back a single characterÊ : moves to the end of the lineˆF : moves forward a single characterˆK : kills from current position to the end of lineˆP or arrow up : moves back through historyˆN or arrow down : moves forward through historyˆH and DEL : delete the previous characterˆD : deletes the current characterˆL/ˆR : redraw line in case it gets trashedÛ : kills the entire lineˆW : kills last word

Furthermoreyoucanmovewithin theline usingthearrow keys.NOTE:

If you redirect the input for executedPROG using ’prog � infile’ you MUST use the command’setprompt,off ’ or ’set prompt,redirect’in the first line to avoid that the program’hangs’ at the end of thefile. (- � setprompt)

2.5 break

break � levels�The’break’ commandstopstheexecutionof thecurrentblockstructureandadvancesto thenext commandfollowing theblockstructure.With � levels� equalto 1 only thecurrentblockstructureis interrupted,withany highernumberthe � levels� innermostblock structuresareinterrupted.The’break’ commandcanbeusedonly insidea blockstructure.

2.6 continue

continue[ ”pr og” ]

Thiscommandis effectiveonly while PROGis in theinteruptedmacromodeor insideinterrupteddo-loopor if-statements,whichservesasadebugmodefor lengthymacrosor blockstructuresMake sureyou havereturnedto the samesubmenuebeforeyou continue!

Without parametersPROG resumesthe executionof a macroor block structurein the line following the’stop’command.If youhadstartedanothermacrowhile debuggingamacro,andthisnew macrocontaineda ’stop’ commandaswell, the’continue’commandwill run theremaininglinesin thenew macroandthenstopagainat thepositionof the’stop’ commandin theoutermacro.By providing the ’prog’ parameter, PROG immediatelyinteruptsall macrosand returnsto the normalprompt.

2.7 do

Loopscanbeprogrammedwith the’do’ command.Thecommandmaytake thefollowing forms:

a)do <variable> = <start>,<end> [,<increment>]

<commands to be repeated>enddo

b)do while (<logical expression>)

<commands to be repeated>enddo

c)do

<commands to be repeated>enddo until (<logical expression>)

Typea)loopsmaycontainconstantsor arithmeticexpressionsfor � start� , � end� , and � increment� . Theinternaltypeof thevariablesis real. Theloopcounteris evaluatedfrom ( � end� - � start� )/ � increment�=1 . If this is negative,theloop is notexecutedatall.Typeb) loopsareexecutedwhile � logicalexpression� is true.Thus,they maynotbeexecutedatall.Typec) loops,however, arealwaysexecutedonce,andrepeateduntil � logicalexpression� is true.If anerroroccurresduringexecutionof theloop,theloop is interrupted.

2.8 echo

echo[ � string � ]echo[ ”string%dstring”, � integer expression� ]

The string � string� is echoedto the default outputdevice astyped. This commandservesasa markerinside long macrofiles. It gives the usera chanceto includeeasyto find messagesin order to followlengthyor nestedstructures.The alternative commandformat allows to echoformattedstringsto the screen.Each”%d” is replacedby the valueof the correspondingparameter. The sequenceof ”%d” correspondsto the sequenceof theparameters.Theseparameterscanconsistof any integerexpression.

2.9 eval

eval � expr �Evaluatestheexpressionanddisplaysthe result. The resultis not stored,this commandis for interactivedisplayonly.

2.10 exit

exit

Terminatestheprogramandgetsyoubackto yourshell.

2.11 expressions

Arithmeticexpressionscanbeevaluatedin aFORTRAN style.Fivebasicoperatorsaredefined:

"+" Addition"-" Subtraction"*" Multiplication"/" Division"**" Exponentiation

Theusualhierarchyof operatorsholds.Thepartsof theexpressioncanbegroupedwith parentheses”(”, ”)”in orderto circumventthestandardhierarchySeveralintrinsic functionshavebeendefined,see”functions” for a full listing.Examplesof valid expressionsare:

11+3*(sin(3.14*r[1]))x[1]*0.155asind(0.5)

2.12 filenames

Usually, file namesareunderstoodastyped,includingcapitalletters. Unix operatingsystemsdistinguishbetweenupperandlowercasetyping !Additionally (integer) numerical input can be written into the filename. The syntax for this is:”string%dstring”,� integerexpression�Thefile formatMUST beenclosedin quotationmarks.Thepositionof eachintegermustbecharacterisedby a”%d”. Thesequenceof stringsand”%d”’ scanbemixedatwill. Thecorrespondingintegerexpressionsmustfollow aftertheclosingquotationmark.If thecommandline requiresfurtherparameter(like”addfile”for example)they mustbegivenaftertheformat-parameters.Theinterpretationof the”%d”’ s follows theC syntax.Up to 10numberscanbewritten into a filename.Examples:

1)i[5]=1outfile a1.1outfile "a%d.%d",1,1outfile "a%d.%d",4-3,i[5]

All theaboveexampleswill resultin thefile name”a1.1”.

2)do i[1]=1,11...outfile "data%d.calc",i[1]...enddo

Theoutputis written to thefiles ”data1.calc”through”data11.calc”

2.13 functions

Thefollowing intrinsic functionsexist:

asin(<arg>) !acos(<arg>) !atan(<arg>) !asind(<arg>) ! Result in degreesacosd(<arg>) ! Result in degreesatand(<arg>) ! Result in degrees

sin(<arg>) !cos(<arg>) !tan(<arg>) !sind(<arg>) ! Argument in degreescosd(<arg>) ! Argument in degreestand(<arg>) ! Argument in degrees

sinh(<arg>) ! Hyperbolic functionscosh(<arg>) !tanh(<arg>) !

sqrt(<arg>) ! Square root of <arg>exp(<arg>) ! exponential (base e)ln(<arg>) ! natural logarithm of <arg>abs(<arg>) ! Absolute value of <arg>

int(<arg>) ! Convert argument to integernint(<arg>) ! Convert argument to nearest integermod(<arg1>,<arg2>) ! Modulo <arg1> of <arg2>, real argumentsfrac(<arg>) ! Returns fractional part of <arg>

ran(<arg>) ! Returns uniformly distributed pseudorandom value 0<= r < 1.

Theargumentsto any of thesefunctionsareany arithmeticexpression.

2.14 help

help [ � command� [, � subcommand� ] ]

The ’help’ commandis usedto display on-line help messages.They are short noteson the command� command� . Thecommandmaybeabbreviated.If theabbreviationis notunique,only thefirst helptopicthatmatchesthecommandis listed.Thefirst line of thehelptext givesthesyntaxof thecommandthat is explainedin thefollowing lines. Fora few commandsthesyntaxline is repeatedfor differentsetof possibleparameters.After thetext is displayed,youarein theHELPsublevel of DISCUSandtherearethefollowing commandspossible:

<command> : Display help for <command> of current help level.".." : Go up one help level."?" : Prints list of help entries of the current level.<RETURN> : Exit help sublevel.

2.15 if

Theif-control structuretakesthefollowing form:

if ( <logical expression> ) then<conditional commands>

[elseif ( <logical expression>) then<conditional commands>]

[else<conditional commands>]

endif

Thelogicalexpressionsmaycontainnumericalcomparisonswith syntax:

<arithmetic expression> <operator> <arithmetic comparison>

Thefollowing operatorsareallowed:

.lt. ! less than

.le. ! less or equal

.gt. ! greater than

.ge. ! greater or equal

.eq. ! equal

.ne. ! not equal

Logicalexpressionscanbecombinedby logicaloperators:

.not. ! negation of the following expression

.and. ! logical and

.or. ! logical or

Logicaloperationsmaybenestedandgroupedby brackets”(” and”)”.

2.16 learn

learn [ � name� ]

Startsa learn sequence. All following commandsare saved as typed in file � name� . defaults to” � prog� .mac”.== � lendfinishesthelearnsequence.

2.17 lend

lend

Finishesthelearnsequencestartedby == � learn.

2.18 set

setprompt, � ”on” � ”off ” � ”r edirect” �Setsthe statusof the PROG prompt. The default is ”on”, i.e. PROG promptsfor the next commandbywriting ”discus � ”. You canturn this promptoff. This is useful,if you arerunninga long macroanddonot want to getall thepromptswritten into theoutput. By usingthis optionyou canconsiderablyshortentheoutputwrittenby PROGinto a redirectedlog file. If youareusingPROGonaUNIX platform,youcanstarttheprogramwith redirectedinputby thecommand:

"prog < inputfile"

By default,PROGwill write theprompt”discus � ” into theoutputfile,expectingaRETURNfrom thekey-board.Verylonglinesin theoutputfile will result.To avoid thissituationinserttheline ”setoutput,redirect”asfirst line in theinputfile to forcediscusto echothelinesfrom file inputfile.seterror , � ”cont” � ”exit” �Setstheerrorstatus.


"cont" PROGreturns the normal prompt after the display of the errormessage. You can continue the input of commands.

"exit" PROGterminates after the display of the error message.This option is useful if you run PROGin the batch mode of youroperating system. Instead of continuing with a faulty calculationPROGstops and you can immediately check the error.

setdebug, � ”on” � ”off ” �Thiscommandallws theuserto enablevariousDEBUG outputs...

2.19 stop

stop

Thiscommandis activeonly while readingfrom amacrofile or in interactivemodeinsideablockstructure(do-loopsand/orif ’s).Thecurrentmacrofile is interuptedandyoucantypecommandsasin thenormalinputmode.Youcanusethewholerangeof PROG commands,includingthe’@’ macrocommand.The’stop’ commandsprovidesa convenientmodeto debuga macroby settingabreakpointatwhichyoucancheckthevalueof variablesor setnew values,runanadditionalmacroetc.To continueexecutionof themacroor to continuewith thenormalPROG mode,usethe== � ’continue’command.If includedin a block structurestatement(do-loopsand/orif ’s) in both,macroandinteractive mode,theprogramcontinuesreadingall statementsthatbelongto theblockstructure.Duringexecutionof thestruc-ture,PROGinteruptsthisexecutionif it encountersa ’stop’command.Youcanissueany PROGcommandexceptfurtherdoor if commands.To continueexecutionof thestructureor to continuewith thenormalPROGmode,usethe== � ’continue’command.

2.20 system

system � com�Executesthesingleshellcommand� com� .

2.21 wait

wait [ � ”r eturn” � ”input” � ]This commandwaits for userinput. Without a parameteror with ”return”, theprogramwaits for a simple� RETURN� . If thefirst parameteris ”input”, theprogramexpectstheuserto entera realnumber, whichis storesin thevariableres[1].Thiscommandallowsto write quasiinteractivemacros,demomacrosandtutorials.

2.22 errors

Theprogramhasbeenwritten suchthat it shouldhandlealmostany typing errorwhengiving commandsandhopefullyall errorsthat resultfrom calculationwith erroneousdata.Whenanerror is foundanerrormessageisdisplayedthatshouldgetyoubackontrack.Seethemanualfor acompletelist of errormessages.In thispartwe referto theprogramyouareusingasDISCUSfor convenience.Theerrormessagesconcerningtheuseof thecommandlanguagearegroupedin thefollowing categories:


COMM Command language errorsFORT Fortran interpreter errorsI/O Errors regarding input/outputMACR Errors related to macrosMATH General mathematical errors

Eacherror messageis displayedtogetherwith thecorrespondingcategory � cccc� andthe error number� numb� in theform:****CCCC****message **** numb ****

In the default modeDISCUSreturnsthe standardpromptandyou cancontinuethe executionfrom thispoint. Youcansettheerrorstatusto ”exit” by the== � ’set’command.In thiscaseDISCUSterminatesif anerroris detected.Thisoptionis usefulto terminatea faultysequenceof commandswhenrunningDISCUSin thebatchmodeof youroperatingsystem.

2.22.1 comm

CommandlanguageerrorsThesemessagesdescribeillegal usageof the commandlanguage,suchasun-known commands,impropernumbersof parameters.

Err or : -1 : DISCUSdirectorynotdefinedTheenvironmentvariableDISCUSDIR wasnot defined.Checkthechapteron installationfor your plat-form for theappropriatedefinition.

Err or : -5 : Error in operatingsystemcommandTheoperatingsystem/shellreturnedanerrormessage.Checktheappropriatesystemmanualsfor details.

Err or : -6 : Missingor wrongparametersfor commandEitherthecommandneedsmoreparametersthanwereprovided,or theparametersareincorrect.Checkthenumberandtypeof parameters.Is thesequenceof numericalandcharacterparameterscorrect?

Err or : -8 : Unknown commandThe commandinterpreterreadan unknown command. Checkthe spelling of the commandor check,whetherthiscommandis allowedat thecurrentsublevel.

Err or : -11 : Error in subroutineMoreor lessasystemerrormessage,ignorethismessage.

Err or : -17 : Toomany parametersMore parametershave beenprovidedthanarerequiredby thecommand.Checkthenumber, andtypeofparameterssupplied,or theoccurrenceof additional’,’.

2.22.2 fort

FortraninterpretererrorsThesemessagesdescribeerroneousmathematicalcalculationsandimproperusageof controlstructures(do,if, ...).

Err or : -1 : NonnumericalParametersin expressionThe interpreterfound a nonnumericalstring wherea numberis expected. If an intrinsic function or avariablewasintended,checkfor missingparentheses.

Err or : -2 : Unknown VariableTheexpressioncontainsa referenceto anunknown variable. Checkthespellingof thevariable. Chapter3.7.1 of the manualand the help entry ”variables”containsa list of allowed variables. Checkwhetherthevariableis a read-onlyvariableandwasusedon the left sideof anexpression.Someof thevariablesassociatedwith microdomainsareread-onlydependingof thecircumstances!


Err or : -3 : Unknown intrinsic functionTheexpressioncontainsa referenceto anunknown intrinsic function. Checkthespellingof the function.Chapter3.7.4of thegeneralpartin themanualandthehelpentry”functions’ containa completelist of theallowedintrinsic functions.

Err or : -4 : Divisionby zero’An attemptwasmadeto divide by zero. Checkthe valueof the argumentandcorrectthe algorithmthatcalculatestheargument.

Err or : -5 : Squarerootof negativenumberAn attemptwasmadeto calculatethesquarerootof anegativeargument.Checkthevalueof theargumentandcorrectthealgorithmthatcalculatestheargument.

Err or : -6 : Missingor wrongParametersfor commandEitherthefunctionor variablereferencedneedsmoreparametersthanwereprovided,or theparametersareincorrect.Checkthenumberandtypeof parameters.Is thesequenceof numericalandcharacterparameterscorrect?

Err or : -7 : Argumentfor asin,acosgreater1An attemptwasmadeto calculateasinor acoswith an argumentgreaterthan1. Checkthe valueof theargumentandcorrectthealgorithmthatcalculatestheargument.

Err or : -8 : Index outsidearraylimitsThe index suppliedfor the variableis outsidethe limits of this variable. Checkthe generalpart for thedimensionsof thevariables.

Err or : -9 : Numberof bracketsis notmatchingThenumberof openingandclosingbrackets”[” and”]” doesnot matchor is illegally nestedwith paren-theses”(”, ”)” or otheroperators.Checkthe string usedin the expressionand correctit following theFORTRAN rules.

Err or : -10 : Index for arrayelementis missingYou have useda string like ”i[]”, wherethe openingandclosingbracketsdo not containany expression.Checkthestringusedin theexpressionandcorrectit following theFORTRAN rules.

Err or : -11 : Numberof parenthesesis notmatchingThe numberof openingand closing parentheses”(” and ”)” doesnot matchor is illegally nestedwithbrackets”[”, ”]” or otheroperators.Checkthe string usedin the expressionandcorrectit following theFORTRAN rules.

Err or : -12 : Expressionbetween() is missingYouhave useda stringlike ”()”, wheretheopeningandclosingparentheses”(” and”)” do not containanyexpression.Checkthestringusedin theexpressionandcorrectit following theFORTRAN rules.

Err or : -13 : Wrongnumberof indizesfor arrayThenumberof indicesgivenfor theenteredparameteris wrong. Checkthehelpentry ’variables’for thepropernumberof indices.

Err or : -14 : Index of DO-loopcounteris missingHeretheindex for theloopcounterof a do-loopis missing.Checktheonlinehelpfor thecorrectsyntaxofsuchloops.

Err or : -15 : Toomany commandsTheprogramstoresall commandswithin a controlblock in anarray. Themaximumnumberof commandsthat canbe storedin this arrayis given by the parameterMAXCOM in file ”doloop.inc”. The macroor


runusedmorecommandsthancurrentlyallowedby thisparameter. Rewrite themacroor list of commandssuchthatlesscommandsaresufficient,or changethevalueof theparameterandrecompiletheprogram.

Err or : -16 : Toodeeplyleveled(do,if) constructionTheprogramstoresall commandswithin a controlblock in anarray. Themaximumnumberof levels forthis array is given by the parameterMAXLEV in file ”doloop.inc”. The macroor run usedmorelevelsthancurrentlyallowedby this parameter. Rewrite themacroor list of commandssuchthat lesslevelsaresufficient,or changethevalueof theparameterandrecompiletheprogram.

Err or : -18 : UnresolvableconditionAn erroroccurredwhile trying to calculatethevalueof anarithmeticor logicalexpression.Checkthatthereis no illegaloperation/(divisionby zero.../ no typingerrors,all parenthesesareproperlymatched.

Err or : -19 : Illegalnestingof controlcommandsDo loops and/or if constructionshave beennestedwith overlappingsegments,missingenddoor endifstatementsor similar causes.Checkfor spellingerrorson the control statements,andthat eachcontrolstatementis properlyterminatedby a correspondingenddoor endif statementthat is not enclosedwithinanothercontrolblock.

Err or : -20 : Illigal argumentfor ln(x) functionTheargumentfor theln mustbepositiv, largerthanzero.Checkthevalueof theargumentor thevalueoftheexpressionthatservesasargument

Err or : -28 : ToodeeplyleveledbreakcommandIllegaluseof thebreakcommand.Theparameteron thebreakcommandsignalshow many blockstructurelevelsaretobeexited. Checkthevalueof thisparameterwith regardto thenestingof do-loopsandif-blocks.

2.22.3 i/o

Errorsrelatedto input / outputAn erroroccuredwhile attemptingto read/writefrom a file

Err or : -1 : File doesnotexistDISCUScouldnotfind thefile. Checkthespellingandthepath.

Err or : -2 : ErroropeningfileDISCUScouldnotopena file. Thefile mightbein useby anotherprocess.

Err or : -3 : Error readingfileAn erroroccurredwhile DISCUSwasreadinga file. Checkwhetherthecontentsof thefile is correct.

Err or : -4 : File alreadyexistsAn attemptwasmadeto overwriteanexistingfile. Renameor deletethefile in question.

Err or : -5 : No suchentryin onlinehelpYouhavetried to obtainhelpfor a stringthatdoesnothavea matchingentryin thehelpfile.Checkthe spellingof the string. Are you at the right sublevel? Usethe ’?’ commandto get a listing ofavailablehelpentries.

Err or : -6 : Unexpectedendof fileDISCUShasencounteredthe endof a file, but is still expectingdata. Checkthe file(s) involved, to seewhetherthedataarecompleteor whethererroneousdataarepresent.

Err or : -7 : Learningsequencealreadyin progressYou have tried to starta learningsequenceby == � ’ learn’ without closingthe active learningsequence.Closethecurrentlearningsequenceby == � ’ lend’ beforestartingto recorda new macro.


Err or : -8 : Nothinglearned- nomacrowrittenYou did not typeany commandssincethe== � ’ learn’ command.No commandsarewritten to themacrofile. Youneedto giveat leastonecommandbeforeclosinga learnsequence.

Err or : -9 : Error readinguserinputAn error occuredwhile readingthe last input. Doesthe stringcontainany characterswherea numberisexpected,or any controlor escapesequences.

2.22.4 macro

Errorsrelatedto macroThesemessagesdescribesituationsthat result from missingmacrofiles,missingmacroparameters...

Err or : -1 : Toomany macroparametersgivenThe numberof parametersgivenon the macrocommandline is higherthanallowed in your installation.The maximumnumberof parametersallowed is definedby the parameterMAC MAX PARA in the filemacro.inc.Checkthemacrocommandline for any additional”,” or rewrite themacrotouselessparameters.If necessaryadjustthevalueof theparameterMAC MAX PARA andrecompiletheprogram.

Err or : -12 : Macronot foundThefile givenonthe@ name� commanddoesnotexist. Checkthespellingof name� andthepath.

Err or : -13 : Macrofilenameis missingon thecommandlineThecommand’@’ to executea macrowascalledwithout any macrofile name.Thefile namemuststartimmediatlyafterthe”@”. Checkthe’@’ commandfor completenessandblanksafterthe”@”.

Err or : -35 : ToodeeplyleveledmacrosThe maximumlevel at which macrosmay be nestedis definedin the file macro.incin the parameterMAC MAX LEVEL. Checkthenestingof macrofile for thelevel of nestingor possiblerecursivenestingwithout propertermination.Rewrite themacrosto uselessnesting,or changethevalueof theparameterandrecompiletheprogram.

Err or : -36 : UnexpectedEOFin macrofileWhenDISCUSfinds a ’@’ commandinsidea macro,it storesthe currentmacroname,the line numberinsidethecurrentmacroandclosesthecurrentmacrofile. After completionof thenew macro,thepreviousmacrois readagainup to thepositionstored.Theerrormessageis displayedwhenanendof file is foundbeforethepositionis reached.Checkwhetherthemacrofile wasdamaged,or accidentallydeletedduringexecutionof thenestedmacro.

Err or : -41 : Not enoughmacroparametersgivenDISCUSreadaparameternumberinsideamacrofile thatis higherthanthenumberof parametersgivenonthecommandline of themacro.Checktheparametersinsidethemacrofor correctnumberingandspelling.Checkthenumberof parameterssuppliedon thecommandandcheckwhetherany ”,” is missingbetweenparameters.

2.22.5 math

Errorsfrom generalusageof mathematicaltreatments

Singular Matrix

DISCUS/KUPLOT tried to calculatethe inverseof a matrix that is singular. Readinga cell file: Are yourlatticeconstantsin error, i.e. a lengthof zero,anangleof 0 or 180degrees? MicrodomainsIs thematrixofthebasevectorscorrect?

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