indexing xrd

8/13/2019 Indexing XRD

http://slidepdf.com/reader/full/indexing-xrd 1/22

Indexing XRD-patterns, getting cell parameters

Armel Le Bail

Université du Maine, Laboratoire des Oxydes et Fluorures, Avenue O. Messiaen, 7208 LeMans !edex ", Fran#e $ %mail & alb'#ristal.or( $ )eb & *tt+&---.#ristal.or(

Abstract

ome /eys, *ints and ti+s or t*e su##essul indexin( o a +o-der dira#tion +attern are (ivent*rou(* exam+les, by usin( ex#lusively ree a##ess +ro(rams or a#ademi# resear#*.%ssentially, t*e sam+le *as to #orres+ond to a sin(le +*ase1 t*e +o-der +attern resolutions*ould be maximal, avoidin( +reerred orientation1 t*e tools used or +ea/ +osition *untin(and indexin( s*ould be t*e best on t*e mar/et1 t*e i(ures o merit *ave to be understood soas to be able to save time by dis#ardin( t*e +oor uality su((estions o t*e indexin(

+ro(rams1 urt*er #*e#/in( by +ost$indexin( visuali3ation is re#ommended in #ase o (ooduality multi+le euivalent +ro+ositions1 inally, -*ole +attern ittin( *as to be t*e ultimatetest in order to be #onvin#ed enou(* or attem+tin( t*e stru#ture solution.

Tip-1 : 4ndexin( +o-der dira#tion data is +robably t*e #rystallo(ra+*y to+i# -*ere t*etraditional -ay o s*arin( o+enly #om+uter +ro(rams remains t*e more res+e#ted 546O,6%O, 4!9OL, !:F4%, M#Maille, et#;.

Exercise 1 – starting with a simple case : Y!"

6*e +o-der +attern or t*at exer#ise is available at *tt+&---.#ristal.or(+o-base

5<o-base is a small database o +o-der +attern;, as -ell as t*e ot*ers.

tart )in<LO6, sele#t =File>, t*en sele#t =O+en +attern ile>, sele#t 4?6M@0 in t*elist o =Format o data ile>, a -indo-s allo-s you to sele#t t*e data, ind y2o.dat 5inside o8.3i+ in <o-Base; and o+en it.

http://www.cristal.org/

http://www.cristal.org/



Tip- : 6*e ile y2o.dat is a text ile. Lines startin( by C or D are i(nored by )in<LO6.6*e data ormat #orres+ondin( to 4?6M@0 #orres+onds to a line -it* startin( an(le, ste+and last an(le in de(rees 2θ, t*en ollo- t*e intensities ste+ by ste+ in ree ormat &

15.00 0.01 145.90

25 22 19 21 19 14 23 25

26 21 24 22 33 26 15 21 19 20 20 16 14 17 22 21

17 27 18 30 21 21 21 18

19 22 22 28 19 19 13 30

………..etc

37 33 44 48 55 46 61 48

64 53 72 80 87 122 150 142

150 203 238 256 316 386 453 557

695 762 918 1005 1263 1372 1416 1398

1363 1242 1095 1027 837 761 587 506

384 300 205 199 158 121 123 109

107 82 64 67 42 68 62 59

55 51 45 47 36 31 31 43

32 28 39 27 22 35 25 29

29 17 23 24 18 23 26 29

At t*is sta(e you are ex+e#ted to ma/e use o your #rystallo(ra+*y ex+ertise already. :oumust ans-er to t*e uestion & *i(* or lo- symmetry E !learly, ust by loo/in( at t*e +attern,t*ere are eviden#es or a *i(* symmetry be#ause o t*e uasi #onstant an(ular interval

bet-een t*e +ea/ +ositions. Gee+ t*at +ossibility in mind.

6*en #li#/ on =<oints sele#tion>, and =Automati# +ea/ sear#*>, sele#t =ear#* !u G αG α2 doublets> 5yes, t*is is #onventional laboratory H$ray data -it*out any mono#*romator int*e in#ident beam;. !li#/ on =OG>, t*e result is 2 +ea/s ound i t*e ran(e (oes u+ to"I52θ;. !learly, many +ea/s -it* small intensity -ere not identiied.



Jo ba#/ to =<oints sele#tion>, and =Automati# +ea/ sear#*>, and #*an(e t*e =+ea/t*res*old> to 0.00 instead o 0.02, #li#/ on OG, t*at time 8 +ea/s are dete#ted, #li#/ OG.%ven i some very small +ea/s are not ta/en into a##ount, -e #an try no- to index.

!li#/ a(ain on =<oints sele#tion>, t*en on =save as>, t*en on =ave +oints or M#Maille>

5-*at -ere you ex+e#tin(, 4 am t*e aut*or o M#Maille 1$;&

6*en a box is o+ened, ty+e a title 5-*y not :2O;, (ive t*e -avelen(t* 5.K0, yes t*isis G α only no-; and let t*e 3eros*it to be 0, #li#/ OG, t*e +ro(ram says t*at a ile namedy2om#my.dat *as been #reated, #li#/ OG and uit )in<LO6.

Nere is t*e y2om#my.dat ile #ontent &

Y2O3

! Wavelength, zeropont an "#$%& '"#$%&(3) *lac+ *o -oe

1.540560 0.000 3! /t o 2theta poton, ntent '-n.(20

20.50481 1411.71155

29.15784 11198.95700

33.79123 2632.66553

35.91046 531.02966

37.92135 135.21042

39.84880 606.23480

41.70092 118.49068

43.48877 881.15845

46.88918 271.40564

48.52835 4213.47021

50.12016 230.08562

51.68559 66.62399 53.20726 506.43854



54.69715 117.27492

56.16987 404.76215

57.61465 2603.39868

59.03540 563.80334

60.43375 471.21359

61.81146 194.23712

tc

!o+y t*at ile inside o t*e dire#tory -*ere M#Maille is installed and start t*is indexin( +ro(ram 5#li#/ on =M#Maille.exe, and (ive t*e ile name -it*out extension& y2om#my; &

Tip-" & :ou -ill +robably not obtain exa#tly t*is result, be#ause M#Maille uses a Monte!arlo al(orit*m, im+lyin( a seuen#e o +seudo$random number. :ou -ould obtain t*e sameresult i you start exa#tly at t*e same +oint in t*at seuen#e. 6*e startin( +oint is deined inM#Maille by t*e time 5ex+ressed in se#onds sin#e t*e be(innin( o t*e day; at t*e instant-*en you start t*e +ro(ram. At least you s*ould obtain a similar result in a dierent order.

Let us #omment t*ese results. M#Maille is -or/in( in t*e so$#alled =bla#/ box mode>. )e

*ave (iven only very e- inormations & +ea/ +ositions, intensities, -avelen(t*, a null3ero+oint 5t*is is a #onstant an a++roximation $ an(ular s*it due to bot* instrumental i



misali(ned $ and sam+le i not in t*e dira#tin( +lane ee#ts t*at -e s*ould not ne(le#t int*e next exer#ises;. 4n t*at bla#/ box mode, M#Maille ollo-s its o-n strate(y & testin( irstt*e *i(*est symmetries, do-n to tri#lini#, inside o some +redetermined limits o #ell

+arameters and volumes.

Tip-# : All indexin( +ro(rams *ave su#* maximal deault values -*i#* t*e user *as to/no- see t*e manuals $ and s*ould modiy i no result is obtained.

6*e essential t*in(s to see in t*e out+ut ile o any indexin( +ro(ram are t*e FoMs5Fi(ures o Merit;, (enerally noted M20 and F20 or F0. 6*e *i(*er are t*ese FoMs, t*e moret*e #orres+ondin( #ells are +lausible. For t*e deinitions o t*e FoMs, see t*e ex#ellent#*a+ter 7, autoindexin(, -ritten by <er$%ri/ )ernet in t*e boo/ =tru#ture eterminationrom <o-der ira#tion ata.

Tip-$ : eeren#es are at t*e end o t*e tutorial

M#Maille +rovides also t*ese FoMs or sele#ted (ood #ells, but t*e solutions are sorteda##ordin( to a some-*at dierent #riterion noted + -*i#* is euivalent to a ietveld +roilereliability. 6*e +ro(ram -ill not al-ays sto+ li/e it *as done *ere, it may -ell examine allsymmetries do-n to tri#lini#. 4n bla#/ box mode, it -ill sto+ i a solution -it* + P 0.02 isound. 4n t*at #ase, it *as ound an ort*or*ombi# solution -it* + @ 0.0 -it* a very small#ell volume 5K" Q; and very lar(e #onventional FoMs 5M20 @ 280;. A very small + value5P 0.0; means t*at t*e +o-der +attern is -ell itted, t*e smaller -ill be +, t*e lar(er -ill bet*e #onventional FoMs M20 and F20.

But is it t*e (ood #ell E

Tip-% : 6*e ultimate de#ision *as to be made by t*e user, al-aysR

Navin( a (ood ormation in #rystallo(ra+*y -ill *el+ a lot to ma/e t*e de#ision. 4n t*at#ase, solutions -it* small + are also +ro+osed in #ubi# 5 @ 0.02;, *exa(onal 5 @ 0.08;and tetra(onal 5 @ 0.02;.

Tip-& : First im+ortant +oint to /ee+ in mind or be#omin( an ex+ert in indexin( & any #ell-it* a *i(* symmetry #an also be indexed in all t*e lo-er symmetries.

4n t*at #ase, i M#Maille *ad not sto++ed at t*e ort*or*ombi# symmetry, it -ould *ave

+rovided #ells also in mono#lini# and tri#lini# symmetries, +ossibly -it* even lo-er +values.

Are all lines indexed E 4n bla#/ box mode, -*atever t*e number o lines (iven, M#Maille-ill -or/ only by usin( t*e irst 20 lines, and *as a toleran#y o unindexed lines. 6*enumber o not indexed lines is +rovided 5+arameter ?ind in t*e i(ure above;. All lines areindexed in #ubi#, tetra(onal and ort*or*ombi# 5?ind @ 0;. Ma/in( t*e ratio 9#ubi#9ort*o(ives "2K8 @ 8R o, very +robably, t*e #ell is #ubi#. M#Maille +re+ares a ne- .dat ileor urt*er investi(ations in manual mode. 6*at ile name is y2om#my$ne-.dat. %dit t*atile &

Y2O3! Wavelength, zeropont, "gr

1.540560 0.0000 0



! oe or --etr

1 0 0 0 0 0 Cubic only

! W, "n

0.300 3

!-n, -a, -n, -a, $-n, $-a, $-are

2. 20. 8. 2000. 0.05 0.25 0.50 Decrease some values here

! "tet, "rn 2000 1

! 2theta %ntent

20.50481 1411.712

29.15784 11198.96

33.79123 2632.666

35.91046 531.0297

37.92135 135.2104

39.84880 606.2348

41.70092 118.4907

43.48877 881.1584

46.88918 271.4056

48.52835 4213.470

50.12016 230.0856

51.68559 66.62399

53.20726 506.4385

54.69715 117.2749

56.16987 404.7621

57.61465 2603.399

59.03540 563.8033

60.43375 471.2136

61.81146 194.2371

63.17843 149.1199

64.53022 288.8621

65.85427 145.6454

69.78623 190.6706

4 you read t*e manual 5donSt believe you #an be#ome an ex+ert in 2 *oursR; you -ill seet*at t*at ile is #oni(ured or a sear#* only in #ubi#, ust ine, t*is is -*at -e -ant to do.A++ly a(ain M#Maille to t*at ile &



Nave a loo/ inside o t*e y2om#my$ne-.im+ ile #ontainin( t*e detailed results &

%":/ :/;< ) '<=:"&:$& &%:=%O"< ) 2n /%"

>$O /:?@&: : @ :/A: @=: #:??:

0.014 1.5406 10.6059 10.6059 10.6059 90.000 90.000 90.000 0.001 0.0000 0.0003 0.0003 0.0003 0.000 0.000 0.000

$%$O:/ // ) 0.09429 0.09429 0.09429 90.000 90.000 90.000

O/;? ':BB3 ) 1193.017

A C / =A'O@< =A>$O =A':/ &%.

2 1 1 20.505 20.491 20.495 0.004

2 2 2 29.158 29.144 29.143 0.001

4 0 0 33.791 33.777 33.777 0.000

4 1 1 35.910 35.897 35.893 0.003

4 2 0 37.921 37.907 37.907 0.001

3 3 2 39.849 39.835 39.833 0.002

4 2 2 41.701 41.687 41.685 0.002 4 3 1 43.489 43.475 43.472 0.003

5 2 1 46.889 46.875 46.881 0.006

4 4 0 48.528 48.514 48.515 0.001

4 3 3 50.120 50.106 50.110 0.003

4 4 2 51.686 51.672 51.668 0.004

6 1 1 53.207 53.193 53.193 0.000

6 2 0 54.697 54.683 54.688 0.005

5 4 1 56.170 56.156 56.157 0.001

6 2 2 57.615 57.601 57.600 0.001

6 3 1 59.035 59.022 59.021 0.001

4 4 4 60.434 60.420 60.421 0.001

7 1 0 61.811 61.798 61.801 0.004

6 4 0 63.178 63.165 63.165 0.000 6 3 3 64.530 64.516 64.511 0.005

6 4 2 65.854 65.840 65.843 0.003



7 3 2 69.786 69.772 69.761 0.011

8 0 0 71.059 71.045 71.044 0.001

5 5 4 72.331 72.318 72.318 0.000

8 2 0 73.591 73.577 73.582 0.006

6 5 3 74.859 74.845 74.839 0.006

6 6 0 76.097 76.083 76.087 0.004

7 4 3 77.347 77.333 77.330 0.004 6 6 2 78.580 78.566 78.566 0.000

8 4 0 81.036 81.022 81.023 0.000

8 3 3 82.255 82.241 82.244 0.003

8 4 2 83.480 83.466 83.463 0.003

6 5 5 84.689 84.675 84.678 0.004

7 5 4 87.115 87.101 87.102 0.001

7 6 3 89.529 89.515 89.521 0.006

8 4 4 90.747 90.733 90.730 0.003

9 4 1 91.955 91.941 91.940 0.001

?'20 ( 168.09

'20 ( 151.03 ' 0.0021, 62

6*is loo/s extremely (ood.

)ill any attem+t be t*at easy E !ertainly notR t*is -as t*e irst exer#ise and you arelu#/y.

M#Maille +re+ares a ile or a ietveld$li/e it 5a .+r ile; or t*e best solution -*i#* you#an see by usin( )in<LO6. Let us see t*at y2om#my$ne-.+r ile. tart )in<LO6,#li#/ on =File>, t*en on =O+en ietveld+roile ile>, sele#t =0 & Full+ro <F ile>, #li#/ onOG, and sele#t t*e ile in t*e )indo-s box.



6*e verti#al bars note all lines t*at s*ould be t*ere. A lot are la#/in(. :ou may reali3e, byexaminin( t*e */l indi#es o t*e indexed lines t*at t*ere is a systemati# relation * T / T l @ 2n,and t*us t*e Bravais latti#e is very +robably 4 #entered. M#Maille -ill not do t*atautomati#ally or you.

Tip-' : ome +ro(rams +erorm automati#ally everyt*in( 5indexin(, s+a#e (rou+su((estion, solvin( t*e stru#ture, reinin(, et#;, li/e %H<O200 & use t*ese +ro(rams irst, andi t*ey ail, (o ba#/ to some standalone +ro(rams.

Tip-( : Only solvin( t*e stru#ture #onirm t*e indexin(R but t*is is not t*e s#o+e o t*istutorial.

Tip-1) : you s*ould never try to index -it*out *avin( deined t*e 3ero+ointR

Exercise – A bit m*re di++iclt : -Al"

ot-are or *untin( t*e +ea/ +ositions are numerous 5see session 2 o t*e < 4nternet!ourse & *tt+&sd+d.univ$lemans.rU$<;, ree a##ess 5)in<LO6, <o-derH,%H<O200K, et#; or #ommer#ial 5%9A, Ni(*s#ore, ade, et#;. Let us try <o-derH on t*eτ$AlF +o-der +attern. 4n a#t t*e +attern is #orre#ted or a lar(e 3ero+oint error 50.I C; dueto t*e a#t t*at t*e sam+le -as dusted on t*e sam+le *older or avoidin( +reerred orientation.

Tip–11 : ustin( a sam+le on t*e *older t*rou(* a sieve allo-s or redu#in( +reerredorientation ee#ts. But sin#e t*is enlar(es t*e +ea/ -idt*, it is not re#ommended at t*eindexin( sta(e & +ress t*e sam+le or a better resolution.

Tip-1 : 6y+i#al ex#ellent minimal F)NMs 5Full )idt* at Nal Maximum; are 5or -ell

#rystalli3ed #om+ounds; & 0.0K to 0.0I52θ; or #onventional laboratory instrument and 0.00to 0.0I52θ; or t*ird (eneration syn#*rotron sour#e. ?ote t*at a 0.02I F)NM at asyn#*rotron sour#e -it* a 0.7 Q -avelen(t* is euivalent to 0.0KI in your lab -it* a #o++ertar(etR

Tip-1" : 6*e 3ero+oint #orre#tion #an be done beore indexin( by t-o met*ods & mixin( areeren#e #om+ound -it* t*e sam+le or usin( t*e *armoni#s te#*niue. Let us #onsider t*atyou /no- *o- doin( t*ese =sim+le> t*in(s. 4 not, see sessions 2 and o t*e < 4nternet!ourse.

6*e τ$AlF +o-der +attern is also available in <o-Base 5.dat inside o .3i+;, and #an be

read -it* <o-derH by #li#/in( on =File>, t*en =4m+ort ata>, t*en =4%67> or t*e ormat.6*is is a ormat analo(ous to t*e one read by )in<LO6 54?6M@0;, but you *ave to addK *eader lines 5blan/ i you -is*;. First remove t*e ba#/(round & #li#/ on =ubstra#tBa#/(round> t*en on =*o-> in t*e small box and t*e on =OG> i you are satisied 5ot*er-ise

+lay -it* t*e o+tions, and 3oom to see t*e ee#t;.

http://sdpd.univ-lemans.fr/DU-SDPD/




!li#/ on =Al+*a2 %limination>, #li#/ on =6est>, #li#/ on =Finis*>.

!li#/ on =<ea/ ear#*>, t*en on =*o->, modiy t*e intensity limit or t*e dete#tion ot*e -ea/est +ea/s i you -is*, t*en #li#/ on OG.



ave t*e ile ater #onirmation o t*e -avelen(t* &

26*eta d 5A; Nei(*t Area F)NM

2,2"2 7,"KK" ,0 22,2 0,0800,0K0 ,8888 8", K72, 0,007,8 ,0KK8 "0K7, KKKK, 0,002,2K K, K780K, 2K20,K 0,K002,0 ,8KK 82",0 28", 0,K002K, ,078 8, 828,7 0,K002,0" ,K 8"0,K K,0 0,20002,272 ,8"K0 2872,0 227"80,7 0,002,2 ,KK2 K08, KK7,7 0,08002,7K8 ,07 2"0," 08,7 0,080027,K ,222" 28K, K7KK,2 0,80027," ,"K KK, 20K,0 0,08002",02 ,07K07 2K2,0 2082,7 0,002",2K0 ,07" "K,2 2,K 0,08002",K0 ,0KK 28K,2 K20, 0,0002",72" ,0020 7,7 "0",7 0,2000,"K 2,"8K2 8"0, 70, 0,00K,08 2,77 "",2 8," 0,00,2" 2,KK7 "8, K"K, 0,00, 2,K"K K,2 072",8 0,007,2 2,"K" 7",K 2700, 0,00

",0 2,27"K2 2K, "0, 0,K00K0,7 2,22"" 282, 22"K,2 0,K00



K,2 2,728 88," K"2, 0,00

Tip-1# : :ou may also +lay -it* t*e 3ero+oint #orre#tion system inside o <o-derH. 6*ensave t*e ile or 6%O and transorm it into a ile or M#Maille 1$;. :ou *ave to #*an(e t*e#omma into +oints and remove t*e stu at t*e end o t*e ile, rename it as AlF.dat in t*e

M#Maille dire#tory.

Tip-1$ : )*en usin( <o-derH, be #areull t*at t*e -avelen(t* -as ta/en into a##ount,ot*er-ise use only 2θ values, but not d5Q; values.

AlF .K0 0 12.292 6

15.040 348

17.358 360

21.324 905

23.056 729

24.656 224

25.039 111

26.272 544

26.632 8 Remove

26.748 6 Remove

27.634 1000

27.936 12

29.023 482

29.240 18

29.401 5 Remove

29.729 6 Remove

30.394 169

34.038 26

35.239 13 36.355 25

37.523 32

39.501 46

40.567 62

41.526 35

43.515 36

44.450 195

44.727 8 Remove

46.241 145

46.523 10

47.176 251

47.480 9 Remove

49.878 38

emove t*ose -ea/ +ea/s -it* intensity P V o t*e most intense one 5maybe leavin( t*eirst at lo- an(le;.

Tip-1% : <ea/s at lo- an(les are essential even i t*ey are -ea/.

tart M#Maille and see t*e results. !ells -it* #lose to V a++ear in tetra(onal,ort*or*ombi#, mono#lini#, you may sto+ t*e #al#ulation by ty+in( G 5lar(e #*ara#ter;, andt*en t*in/R



)*i#* #ell is t*e (ood one E A(ain t*ere are several +ossibilities. emember t*at any *i(*symmetry #ell #an be +ro+osed in a lo-er symmetry. 4n t*at #ase, t*e tetra(onal #ell -it*smallest volume seems to *ave #*an#es to be t*e #orre#t one. M#Maille +rodu#es iles -it*.#/m extension -*i#* #an be read by t*e !*e/#ell +ro(ram and may *el+ to de#ide.

6*e AlF.#/m ile &

? FoM 9 997 ".28 7K.2K7 .00 7.8 0.20 .0K7 "0.000 "0.0K7 "0.0001& '&.$$ &#'.($# .)) 1).)" 1).1#1 &.1'& ().))) ().))) ().)))

7 87.2 7"." .02 .8KK 0.8K 7.2 "0.000 00.22 "0.0007 8.8 7K.K0 .00 .K0K 7.8" .0 "0.000 .0 "0.0008 8.00 7"."" .02 .8K 0.77 8.882 "0.000 8. "0.0007 8.K 7K.K7 .00 0.202 7.87 .0K "0.000 "0.00 "0.0008 8K." 2.7" .00 .20 7.87 0.202 "0.000 "0.000 "0.0007 8. 7K.K8K .00 .070 7.872 0.202 "0.000 "0.000 "0.0007 82. 02. .K 7.07 0." .8K87 "0.000 0".K2 "0.0007 80.7 08.28 0.82 K.208K 0.20 7.8KK "0.000 .20 "0.0007 80.2 KK.K .8 7.K87 0."" .0087 "0.000 0.27 "0.000

7 7". 08.88 0.82 K.208 0.2022 7.2 "0.000 "8.8 "0.0007 7.28 ".78 2."" 2.K887 8.787" 0.202 "0.000 "0.000 "0.0007 7.K K." 0." 7.2 0.207 K.87 "0.000 "K.722 "0.000



7 7. 8."2 0." K.0 0.2002 7.0K "0.000 ""." "0.000" 7. 8." K.8" K.70 2.K8"7 0.2020 "0.000 "0.000 "0.0007 7K.7 8."22 0." 7."8 0."" K.0 "0.000 .K "0.0007 7.0 02.2 .K 7. 0."70 .827 "0.000 0".K7 "0.0007 72.K8 2"".72 8.00 K.K70 K.K70 K.72 "0.000 "0.000 "0.00020 72.K 2"".7 8.00 0.208 0.208 28.7K7 "0.000 "0.000 "0.0008 8." .200 0."0 7."8 0.20 K.8K "0.000 K.722 "0.0008 8.K 7.8 0."" 0.8 .0KK 7.8K "0.000 "0.22 "0.000" 7. 208. .2 K.2227 0.202" 8.27 "0.000 "0.000 "0.0008 7. K70.27 .2 .K70 0.202 7.K "0.000 0.K "0.0007 K. K2"."0 . 7.2"7 0.20 .828 "0.000 ""."78 "0.0007 ." 2.82 0."7 K."K7 0.20" 7." "0.000 "2.K" "0.0001& %".( &#'.("$ .)) 1).)'$ 1).)'$ &.1'%$ ().))) ().))) ().)))

7 .2 8.0"" 0."0 7.08 0." K.008 "0.000 "".K" "0.000

Most o t*e #ells -it* t*e *i(*est FoMs *ave volumes multi+le o 7K Q.

tart !*e/#ell. !li#/ on =File>, t*en =O+en>, t*en =ira#tion ata File>, t*en =ietveldFormat>, s+e#iy t*e -avelen(t* -*en as/ed by t*e +ro(ram, t*e +attern s*ould a++ear 5t*edata ile must *ave K *eader lines;, 3oom eventually.

6*en, o+en t*e .#/m ile & #li#/ on =File>, =O+en>, =!ell File>, =!rysire ummary File>,sear#* or t*e .#/m o+tion and sele#t it, ind AlF.#/m 5note t*at sub$iles or dierentsymmetries are also built u+ by M#Maille; &



6*ere is a #*an#e t*at t*e #ell -ould be tetra(onal -it* #ell +arameters a @ 0.2 and # @7.2 Q. One intense im+urity line is obvious 5t*is is α$AlF;.

Tip-1& : )*ole +roile ittin( 5<a-ley o Le Bail met*ods; -ould +rovide t*e ultimate#onvin#in( ar(uments 5a +ere#t itR; and allo- to de#ide or some s+a#e (rou+ +ossibilities.

Exercise " – /'0#!' snchr*tr*n data - E2en m*re di++iclt 3

6*e +o-der +attern or t*at sam+le is also inside o <o-Base 5see 8".dat in 8".3i+;. Let us#ome ba#/ to )in<LO6 or t*e +ea/ +osition extra#tion. )avelen(t* & λ @ .02 Q.

Tip-1' : in +rin#i+le, syn#*rotron data #orres+onds to +arallel beamline so t*at t*ere is no

3ero+oint. 4n +ra#ti#e, but veriyR

Use t*e automati# +ea/ sear#* o+tion as in t*e exer#ise , de#rease t*e +ea/ t*res*old to0.00 in order to lo#ate some o t*e -ea/est +ea/s and save t*e ile or M#Maille &



tart M#Maille, and durin( t*e #al#ulations, save also t*e results or 6%O &

o not or(et to #*an(e t*e -avelen(t* and in#rease t*e limit o t*e FoM to 0 & t*is issyn#*rotron data, you may ex+e#t *i(* FoMs.

C A6A F4L%& 8".datC 4?6M& 0 !28N2KO8 K."8" 28.8072 8.088" ".""00 K72.K 7.KK0 .8K K72.K870 .808 K.2077 20.2782 2.2"8"7



K.K2KK 2K.02"7 27.7822 K.8000 277.K80 K.00K8 .0" 0.88" ".8777 .72 K02.""7K 0."7 .K2K2 87."K7 0.08

8.K0 20.0K770 7.7K7KK 8.707 02.07K0 .272 8.82" 20.7 ."02 20.082 ".7802 2.7" 2.K"77 78.88 K"."027 2.70K8" 2"02.22KK 7.88" 2.8"08 7.28K ."8 22.7" K"7.0"2 7.K 22.8072 K8.K728 .8" 22."07 K.K0 7.802 2.72K2K 2K.8K0 08.8K7

2K.KKK72 0.278 "".K028 2K."82K7 22."278 "0.2 2.7K2 2".028 82.88 28.02" 7."K80 7.28"2 28.727 0.22" 7.02 2"."787K 0.807" 7.7887 0.2" K"0.878 8.808 0."K 222.K8 8.727 2.008 K.8 ".0"0 2.2 8.88K2 "2."07 2."802 "K.28 82."K2 . 7.K 80.22 ."708 KK.8K07 7.K70K

!NO4!%@, )A9%@ .02, [email protected], 9OL@ 00., !%M@ 20., M%46@ 0., %?W

Maybe t*ere are too mu#* data.

Tip-1( & (enerally, t*e irst 20 lines o a +o-der +attern are sui#ient or indexin(. Usin(more may even obs#ure t*e resultsR

And run 6%O inside o )in<LO6 &



4nside o )in<LO6, 6%O +rodu#es also iles or !N%G!%LL.

Tip-) : t*e statement WWWWW :OU NA9% JO6 A? 4?6%%64?J %UL6 CCC WWWWWis (iven only i M520; is better t*an your s+e#ii#ations, (enerally it announ#es a #orre#tsolution.

Tip-1 : 6%O runs mu#* aster t*an M#MailleR 4t is better to a++ly it irst.

?o- (o ba#/ to t*e M#Maille s#reen, and sto+ t*e #al#ulations by ty+in( G 5#a+ital letter;.Maybe it *ad enou(* time to ind t*at mono#lini# solution as -ell E

Exercise # – Tetraccline 0dr*chl*ride – 4nchr*tr*n data

Use t*e ile tetrasyn#.dat in <o-Base 5do-nload 7.3i+; -it* -avelen(t* & λ @ 0."2 Q.6*is is a #a+illary measurement 5ex+lainin( t*e amor+*ous #om+onent;.

Let us try a(ain )in<LO6 &



Let us save t*e data or 4!9OL0K &

Tip- : 4!9OL0K is (enerally mu#* aster t*an M#Maille but is a bit lon(er t*an6%O or lo- symmetries 5mono#lini# and tri#lini#;, in (eneral, so, start -it* 6%O, t*en4!9OL0K, t*en M#Maille, t*en !:F4%.

Tip-" : Usin( irst 6%O and 4!9OL #an be sui#ient and #onvin#in( enou(* ornot a++lyin( any ot*er indexin( sot-are.



D 4n+ut ile or )4!9OL0K 5#reated by )in<LO6;D #reated by )in<LO6& 22$0$200 at K&K0&"C A6A F4L%& tetrasyn#.datC 4?6M& 0 6etra#y#line Nydro#*loride

20 2 0 C ?,46:<%,!,6,N,O,M,62.0 2.0 2.0 0.0 200.0 "0.0 2.0 C AMAH, BMAH, !MAH, 9OLM4?, 9OLMAH,

B%M4?, B%MAH 0."200 0.000 0.000 0.000 C )A9%,<O4MOL,%?,%L%? 0.00 20.000 0 C %<,FOM, ?4M<, X%Osear#*, X%Oreinement, 4U< ."8" K.K800 02.200 K.K08 K888."K0 0.K7270 K.7K 2"07.2700 002.7770 .0K28 K.02K0 8.00 .80K K"8.8K770 82.K20 ." 282K.0"K0 02.8"K0

.200 0K88.20"0 20.0"0 .7000 788."0 22K.80 ."070 K82."770 K."020 7.K" 77.K0 2.0K"0 7.82 802.70"0 787.K20 7."7" 808.0 K2"8.07K0 8.28 K80.K00 K822.0720 8.77 K.K0 7K8."0 8."88 K"."K80 77".20"0 ".K2 K"22.K00 87"."0 ". 2"8".77K0 ""."0 ".0K7 .2780 20"K.K7270 ".777 2"K8.20 200.0K0 ".8K0 K20"."0"0 20K88.700 0.0"KK 2K"K.20 "272.2820 0.2K7 2KK02.7"K"0 "K"K.780 0.K20" 80K."K0 207.22270 0.KK0 22"K.K80 20K87.2820 0.7"2 "77.020 200.K0 0.""0 K".870 20K.K0 .07 8K.78"0 20".8K00

."72 2"".00 ""72.8870 2.27 K2."2"0 20K0.87"0



6ry also -it* 6%O and M#Maille.

Jo ba#/ to +revious exer#ises and try t*e +ro(rams t*at -ere not already a++lied. <aly-it* !*e/#ell.

Tip-# : A sim+le -ay to deal -it* lar(e #ells -it*out #*an(in( t*e deault values o t*eindexin( +ro(ram is to (ive a i#titious -avelen(t* bein( 2, or 0 times 5+roteins; smaller

t*an t*e real one. 6*en, t*e obtained #ell +arameters -ill be 2, or 0 times smaller t*at t*eee#tive ones.

Additi*nal n*tes

?ot obtainin( results -it* 6%O, 4!9OL0K or M#Maille, you may #onsider tryin(-it* !:F4% 5see session o t*e < 4nternet !ourse, or t*e !!<K )eb site;.!onsider also to use ?$6%O 5eit*er standalone or inside o %H<O200K; instead o6%O. 9isit t*e 4ndexin( Ben#*mar/s )eb +a(es #om+arin( t*e +erorman#es o manyindexin( +ro(rams, and see -*y usin( 46O may not be very interestin(.



Re+erences

5se+l 6eb address :

!!<K & *tt+&---.##+K.a#.u/

4ndexin( Ben#*mar/s & *tt+&sd+d.univ$lemans.ru++-ben#*mar/s

< 4nternet !ourse & *tt+&sd+d.univ$lemans.rU$<

7*st recent re2iew papers ab*t indexing :

<.$%. )erner in =tru#ture etermination rom <o-der ira#tion ata>, %dited by ).4.Favid, G. *an/land, L.B. M#!us/er and !*. Baerlo#*er, Oxord #ien#e <ubli#ations,!*a+ter 7 & =Autoindexin(>, 2002, 8$.

. *irley, =Overvie- o +o-der$indexin( +ro(ram al(orit*ms 5*istory and stren(*ts and-ea/nesses;. 4U!r !om+utin( !ommission ?e-sletter 2 5200; K8$K.

. Ber(mann, A. Le Bail, . *irley and 9. Xlo/a3ov, =ene-ed interest in +o-derdira#tion data indexin(>, X. Gristallo(r. 2" 5200K; 78$7"0.

8r*grams :

/he9cell : . Lau(ier Y B. Bo#*u, *tt+&---.in+(.rLMJ< 5and !!<K;

/RY4IRE : . *irley, =6*e !rysire 2002 system or automati# +o-der indexin(& userSsmanual. Latti#e <ress& Juilord, UG 52002;.

DI/!;)#: A. Boulti Y . LouZr, =<o-der +attern indexin( -it* t*e di#*otomy met*od>,. A++l. !rystallo(r. 7 5200K; 72K$72.

7c7aille : A. Le Bail, =Monte !arlo indexin( -it* M#Maille>, <o-der ira#tion ",200K, 2K"$2K. *tt+&---.#ristal.or(M#Maille

<-TRE!R : A. Altomare, !. Jia#ova33o, A. Jua(liardi, A.J.J. Moliterni, . i33i Y <.$%.)erner,=?e- te#*niues or indexin( & ?$6%O in %H<O>, . A++l. !rystallo(r. 52000;

80$8.

8*wderX : !. on(, =<o-derH& )indo-s$"$based +ro(ram or +o-der H$ray dira#tiondata +ro#essin(>, . A++l. !rystallo(r. 2 5"""; 88.

TRE!R: <.$%. )erner, L. %ri/sson Y M. )estda*l, =6%O, a semi$ex*austive trial$and$error +o-der indexin( +ro(ram or all symmetries>, . A++l. !ryst. 8 5"8; 7$70.

6in8;!TR & 6. oisnel Y . odri(ue3$!arvaal,http:==www-llb.cea.+r=+llweb=winpl*tr=winpl*tr.htm

http://www.ccp14.ac.uk/

http://sdpd.univ-lemans.fr/uppw/benchmarks/


http://www.cristal.org/McMaille/

http://www-llb.cea.fr/fullweb/winplotr/winplotr.htm

http://www.ccp14.ac.uk/

http://sdpd.univ-lemans.fr/uppw/benchmarks/


http://www.cristal.org/McMaille/

http://www-llb.cea.fr/fullweb/winplotr/winplotr.htm

indexing xrd

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