DYNAMO : Molecular Dynamics structure factor calculation

scale \(F_{{\rm rel}}\) scale factor
transf transformation matrix from archive unit cell to molecular dynamics cell
typinf molecular dynamics data file atom type information
format molecular dynamics data file format
maxhkl maximum and minimum h, k, l and sin \(\theta \) / \(\lambda \)
select [a] select a subset of atoms in the bdf for \(F_{{\rm cal}}\)
omit [a] omit a subset of atoms in the bdf for \(F_{{\rm cal}}\)

[a] Either select lines may be used, or omit lines, but not both.

DYNAMO Option Code Arg   Def
  store Fmd as frel      
    fcal      
  molecular dynamics file name absolute or relative path to file [a]  
  temperature factor mix   mixed iso and aniso  
    iso   isotropic U only  
    ani   anisotropic Uij only  
    ove   overall isotropic, all atoms  
  anom. dispersion dis   apply dispersion terms  
    nod   do not apply dispersion  
  extinction correction noex   do not apply extinction  
    ext   apply extinction correction  
  sin/cos function nos   calculate from library routine  
    sct   use prestored table look-up  
  dataset number dset n use dataset n on bdf 1
  reflection control nlis   produce no hkl listing  
    lis s list hkl with \(F_{{\rm obs}}-F_{{\rm cal}}> s\) 0
    nrej   treat all reflections  
    rej t reject hkl if rcode >= t 2

[a] file should be the last option on the command line

transf 1-9 transformation matrix \(T_{11}, T_{12}, T_{13}, T_{21}, T_{22}, T_{23}, T_{31}, T_{32}, T_{33}\) [a]  

[a] Transformation is \( \alpha '=T\alpha \), \(\alpha \) is a column vector of the unit cell vectors a, b, c.

typinf [a] 1- sequential atom type character code  
  2 number of consecutive sites of atom type in MD file  
  3-4... as for 1-2, up to 15 types per line, to a max of 40 sequences  

[a] Mandatory sub command line for the DYNAMO calculation.

format 1 mol. dynam. file format (3F8.5,24x,I5)

scale 1 \(F_{{\rm rel}}\) scale factor  
  2 scale group 1

maxhkl 1-3 max |h|, |k|, |l|  
  4 min sin \(\theta \) / \(\lambda \) 0
  5 max sin \(\theta \) / \(\lambda \) 2

select [a] 1- atom labels of atoms to be selected  

[a] Any number of atom names may be supplied; those given will be included in the DYNAMO calculation. If no select or omit lines are used, all atoms in the bdf will be used in the calculation.

omit 1- atom labels of atoms to be omitted  


Banner

 Overview
 News
+Example Graphics
 History
-Documentation
   -Xtal Users Manual
      +Preface
      +Primer
      -Program controls
          System
           ABSORB
           ADDATM
           ADDPAT
           ADDREF
           ATABLE
           BAYEST
           BONDAT
           BONDLA
           BUNYIP
           CBAZA
           CHARGE
           CIFIO
           CIFENT
           CONTRS
           CREDUC
           CRILSQ
           CRISP
           CRYLSQ
           DIFDAT
         + DYNAMO  <-
           EXPAND
           FC
           FOURR
           GENEV
           GENSIN
           GENTAN
           GIP
           LATCON
           LISTFC
           LSABS
           LSLS
           LSQPL
           LSRES
           MAPLST
           MAPXCH
           MODEL
           MODHKL
           NEWCEL
           NEWMAN
           ORTEP
           OUTSRC
           PARTN
           PATSEE
           PEKPIK
           PIG
           PLOTX
           POWGEN
           PREABS
           PREPUB
           PREVUE
           REFCAL
           REFM90
           REGFE
           REGWT
           RFOURR
           RIGBOD
           RMAP
           RSCAN
           SCATOM
           SHAPE
           SHELIN
           SIMPEL
           SLANT
           SORTRF
           STARTX
           SURFIN
           VUBDF
           XTINCT
      +Reference Manual
      +Archive
       Symmetry
    FAQ
   +Developer Info
   +Retired Program Info
 Download
+Extra Software
 Support
 Contributors
 Citations
 Year 2000
 Disclaimer

Home Feedback
Copyright © 2005 Xtal System, University of Western Australia.
Prev   Next