pdf.mac

#                                                                                                                                            
#@setup_pdf
#
read
   stru frozen_500ps.stru
# pound is a comment before and ! for comments after
#can use this section to change B_iso values
#b[1]     = 1.5000 !r[203] !H 
#b[2]     = 0.9000 !r[204] !O 
#b[3]     = 0.4000 !r[205] !Ti
#b[4]     = 0.7000 !r[206] !C
#b[5]     = 0.9000 !r[204] !F
#plot
#   prog dia
#   sel all                
#   ext all                                           
#   outf $1.xyz
#   run
#exit
#
pdf !go into pdf menu
# deselect and reselecting data from file we just read
    ides all
    jdes all
    isel all !can use this to re-select pairs, say only Si-O
    jsel all
#
    set bound, crystal,exact !set boundaries exactly the same as the structure we read in
    set finite,periodic !say i have a finite boundary, but that i have NO PERIODICITY, if you want periodicity, do it in bound instead of periodic 'set bound periodic'
#
    set dens,  0.00  !p_density
    set delta, 0.00  !p_delta r[220]
#    set qalp,  0.021   !0.0191822(NOMAD) 0.007(11IDB) !p_qalp broad
    set qsig,  0.038  !0.017659(NOMAD) 0.0354(11IDB) p_qsig damp
    set qmax,  22.2 !p_qmax
    set rad,   x-ray
    set range, 120.0,0.01 !pdf_range+5.0,pdf_step     is what range, in real space, i want to calculate PDF
#    set srat,  0.1,1.5   !p_srat,1.5 r[221] can be used in addition to delta parameters (if < 1, adds sharpening to peaks below what the 2nd number is)
    set therm, gauss !set thermal effect as described by gaussian distribution, set therm, off will make delta functions representing no thermal fluctuations
#
    set weight,  1.0 !p_scale r[222] is actually a scale factor
#
    calc ! do the calculation
    show ! show the input
    save pdf, model.gr
exit