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Re: [sdpd] Soft distance constraints in Fullprof
>is it possible to constrain specific
>bond lenghts within given values? in the case, how can I do?
Yep !
See the manual :
Line 11-2 :
NDIST = number of distance constraints
and then :
Line 11-15*: NDIST number of lines of distance constraints
A .pcr file is below, from the sample 1 of the SDPDRR-2
:http://www.cristal.org/sdpdrr2/results/P000-2-1.pdf
The system for coding the pairs of atoms is reputed
to be difficult (not that difficult with some experience),
an example for two C atoms you wish to be at 1.47 A,
these 2 C atoms being in fact the same C1 at two positions :
C1 C1 -1 1.00000 0.00000 1.00000 1.47000 0.01500
Any big error in the code will produce divergence in the refinement...
Best wishes...
Armel
This example uses 51 soft distance contraints :
COMM SDPDRR-2 Sample 1 - with H atoms and constraints on distances
...
! Current global Chi2 (Bragg contrib.) = 2.683
! Files => DAT-file: saupoudre, PCR-file: saupoudre
!Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut
0 5 2 20 2 0 0 1 1 0 1 0 0 0 0 0 0 0 0
!
!Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 NLI Prf Ins Rpa Sym Hkl Fou Sho Ana
0 0 1 0 2 0 0 0 0 1 0 -1 1 2 2 1 0
!
! lambda1
Lambda2 Ratio Bkpos Wdt Cthm muR AsyLim Rpolarz ->Patt# 1
1.540560 1.544390 0.4970 0.000 7.0000 0.7998 0.0000 25.00 0.0000
!
!NCY Eps R_at R_an R_pr R_gl Thmin Step Thmax PSD
Sent0
80 0.01 0.25 0.25 0.25 0.25 10.0000 0.0200 120.0000
0.000 0.000
!
!2Theta/TOF/E(Kev) Background for Pattern# 1
10.294 894.377 761.000
12.302 929.728 771.000
14.144 1110.868 781.000
16.320 1381.319 791.000
18.664 1751.063 801.000
19.669 1962.021 811.000
21.761 2287.531 821.000
22.431 2380.573 831.000
24.440 2491.739 841.000
26.198 2357.910 851.000
28.709 2164.223 861.000
32.392 1864.333 871.000
33.815 1625.587 881.000
35.656 1429.595 891.000
38.502 1109.854 901.000
39.674 1186.229 911.000
50.974 936.557 921.000
58.759 941.494 931.000
71.709 753.291 941.000
79.900 622.835 951.000
!
! Excluded regions (LowT HighT) for Pattern# 1
0.00 10.00
80.00 150.00
!
!
96 !Number of refined parameters
!
! Zero Code Sycos Code Sysin Code Lambda Code MORE
->Patt# 1
-0.01047 431.00 0.00000 0.00 0.00000 0.00 0.000000 0.00 0
!-------------------------------------------------------------------------------
! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 7.87
!-------------------------------------------------------------------------------
phase tetra
insaturée
!
!Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More
22 51 0 0.0 0.0 1.0 0 0 0 0 0 744.08 0 5 0
!
P 2/C <--Space group symbol
!Atom Typ X Y Z Biso Occ In Fin N_t Spc /Codes
AL1 AL+3 0.00000 0.50000 0.50000 5.92971 0.50000 0 0 0 0
0.00 0.00 0.00 441.00 0.00
AL2 AL+3 0.00000 0.00000 0.50000 5.92971 0.50000 0 0 0 0
0.00 0.00 0.00 441.00 0.00
F1 F-1 0.24034 0.47648 0.53631 5.60527 1.00000 0 0 0 0
31.00 41.00 51.00 451.00 0.00
F2 F-1 0.02539 0.25397 0.48835 5.60527 1.00000 0 0 0 0
61.00 71.00 81.00 451.00 0.00
F3 F-1 0.11373 0.46882 0.65783 5.60527 1.00000 0 0 0 0
91.00 101.00 111.00 451.00 0.00
F4 F-1 0.02195 0.02060 0.37202 5.60527 1.00000 0 0 0 0
121.00 131.00 141.00 451.00 0.00
F5 F-1 0.26972 0.01887 0.61796 5.60527 1.00000 0 0 0 0
151.00 161.00 171.00 451.00 0.00
C1 C 0.49725 0.09114 0.51912 11.10444 1.00000 0 0 0 0
181.00 191.00 201.00 461.00 0.00
C2 C 0.59251 0.24048 0.62736 11.10444 1.00000 0 0 0 0
211.00 221.00 231.00 461.00 0.00
C3 C 0.35101 0.17865 0.38704 11.10444 1.00000 0 0 0 0
241.00 251.00 261.00 461.00 0.00
N1 N 0.78427 0.28155 0.65027 11.10444 1.00000 0 0 0 0
271.00 281.00 291.00 461.00 0.00
N2 N 0.44666 0.24595 0.32804 11.10444 1.00000 0 0 0 0
301.00 311.00 321.00 461.00 0.00
H1 H 0.75324 0.35105 0.58359 11.10444 1.00000 0 0 0 0
471.00 481.00 491.00 461.00 0.00
H2 H 0.86659 0.34267 0.72306 11.10444 1.00000 0 0 0 0
501.00 511.00 521.00 461.00 0.00
H3 H 0.83862 0.17969 0.65012 11.10444 1.00000 0 0 0 0
531.00 541.00 551.00 461.00 0.00
H4 H 0.27580 0.09307 0.32451 11.10444 1.00000 0 0 0 0
561.00 571.00 581.00 461.00 0.00
H5 H 0.52921 0.24978 0.66065 11.10444 1.00000 0 0 0 0
591.00 601.00 611.00 461.00 0.00
H6 H 0.49028 0.15515 0.30968 11.10444 1.00000 0 0 0 0
621.00 631.00 641.00 461.00 0.00
H7 H 0.35323 0.30865 0.25566 11.10444 1.00000 0 0 0 0
651.00 661.00 671.00 461.00 0.00
H8 H 0.54341 0.32439 0.38303 11.10444 1.00000 0 0 0 0
681.00 691.00 701.00 461.00 0.00
H9 H 0.72146 0.20744 0.69316 11.10444 1.00000 0 0 0 0
711.00 721.00 731.00 461.00 0.00
H10 H 0.25230 0.24050 0.38461 11.10444 1.00000 0 0 0 0
741.00 751.00 21.00 461.00 0.00
!-------> Profile Parameters for Pattern # 1
! Scale Shape1 Bov Str1 Str2 Str3 Strain-Model
0.19206E-02 0.79775 0.00000 0.00000 0.00000 0.00000 0
11.00000 331.000 0.000 0.000 0.000 0.000
! U V W X Y GauSiz
LorSiz Size-Model
0.013620 0.065752 0.004578 0.000000 0.000000 0.000000
0.000000 0
0.000 961.000 341.000 0.000 0.000 0.000 0.000
! a b c alpha beta gamma
8.527951 7.393794 13.236815 90.000000 128.777084 90.000000
351.00000 361.00000 371.00000 0.00000 381.00000 0.00000
! Pref1 Pref2 Asy1 Asy2 Asy3 Asy4
0.00000 0.00000 0.00439 0.00542 0.00000 0.00000
0.00 0.00 411.00 421.00 0.00 0.00
! Soft distance constraints:
AL1 F1 1 0.00000 0.00000 0.00000 1.81000 0.01500
AL1 F2 1 0.00000 0.00000 0.00000 1.81000 0.01500
AL1 F3 1 0.00000 0.00000 0.00000 1.81000 0.01500
AL2 F2 1 0.00000 0.00000 0.00000 1.81000 0.01500
AL2 F4 1 0.00000 0.00000 0.00000 1.81000 0.01500
AL2 F5 1 0.00000 0.00000 0.00000 1.81000 0.01500
F1 F2 1 0.00000 0.00000 0.00000 2.40000 0.01500
F1 F3 -1 0.00000 1.00000 1.00000 2.40000 0.01500
F1 F3 1 0.00000 0.00000 0.00000 2.40000 0.01500
F2 F3 1 0.00000 0.00000 0.00000 2.40000 0.01500
F2 F4 1 0.00000 0.00000 0.00000 2.40000 0.01500
F2 F5 1 0.00000 0.00000 0.00000 2.40000 0.01500
F4 F5 1 0.00000 0.00000 0.00000 2.40000 0.01500
C1 C1 -1 1.00000 0.00000 1.00000 1.47000 0.01500
C1 C2 1 0.00000 0.00000 0.00000 1.50500 0.01500
C1 C3 1 0.00000 0.00000 0.00000 1.50500 0.01500
C1 H4 1 0.00000 0.00000 0.00000 2.04000 0.01500
C1 H5 1 0.00000 0.00000 0.00000 2.04000 0.01500
C1 H9 1 0.00000 0.00000 0.00000 2.04000 0.01500
C1 H10 1 0.00000 0.00000 0.00000 2.04000 0.01500
C1 N1 1 0.00000 0.00000 0.00000 2.48500 0.01500
C1 N2 1 0.00000 0.00000 0.00000 2.48500 0.01500
C2 N1 1 0.00000 0.00000 0.00000 1.50000 0.01500
C2 H9 1 0.00000 0.00000 0.00000 0.90000 0.01500
C2 H5 1 0.00000 0.00000 0.00000 0.90000 0.01500
C2 H1 1 0.00000 0.00000 0.00000 1.98000 0.01500
C2 H2 1 0.00000 0.00000 0.00000 1.98000 0.01500
C2 H3 1 0.00000 0.00000 0.00000 1.98000 0.01500
C2 C3 1 0.00000 0.00000 0.00000 2.54000 0.01500
C3 N2 1 0.00000 0.00000 0.00000 1.50000 0.01500
C3 H4 1 0.00000 0.00000 0.00000 0.90000 0.01500
C3 H10 1 0.00000 0.00000 0.00000 0.90000 0.01500
C3 H6 1 0.00000 0.00000 0.00000 1.98000 0.01500
C3 H7 1 0.00000 0.00000 0.00000 1.98000 0.01500
C3 H8 1 0.00000 0.00000 0.00000 1.98000 0.01500
N1 H1 1 0.00000 0.00000 0.00000 0.90000 0.01500
N1 H2 1 0.00000 0.00000 0.00000 0.90000 0.01500
N1 H3 1 0.00000 0.00000 0.00000 0.90000 0.01500
N2 H6 1 0.00000 0.00000 0.00000 0.90000 0.01500
N2 H7 1 0.00000 0.00000 0.00000 0.90000 0.01500
N2 H8 1 0.00000 0.00000 0.00000 0.90000 0.01500
H1 H2 1 0.00000 0.00000 0.00000 1.45000 0.01500
H1 H3 1 0.00000 0.00000 0.00000 1.45000 0.01500
H2 H3 1 0.00000 0.00000 0.00000 1.45000 0.01500
H4 H10 1 0.00000 0.00000 0.00000 1.45000 0.01500
H5 H9 1 0.00000 0.00000 0.00000 1.45000 0.01500
H6 H7 1 0.00000 0.00000 0.00000 1.45000 0.01500
H6 H8 1 0.00000 0.00000 0.00000 1.45000 0.01500
H7 H8 1 0.00000 0.00000 0.00000 1.45000 0.01500
H1 H2 1 0.00000 0.00000 0.00000 1.45000 0.01500
H1 H2 1 0.00000 0.00000 0.00000 1.45000 0.01500
!-------------------------------------------------------------------------------
! Data for PHASE number: 2 ==> Current R_Bragg for Pattern# 1: 4.76
!-------------------------------------------------------------------------------
Pyrochlore
!
!Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More
0 0 0 0.0 0.0 1.0 2 2 0 0 0 1343.63 0 5 0
!
F D 3 M <--Space group symbol
!-------> Profile Parameters for Pattern # 1
! Scale Shape1 Bov Str1 Str2 Str3 Strain-Model
0.22597E-04 0.85606 0.00000 0.00000 0.00000 0.00000 0
0.00000 391.000 0.000 0.000 0.000 0.000
! U V W X Y GauSiz
LorSiz Size-Model
0.013620 0.065752 0.004578 0.000000 0.000000 0.000000
0.000000 0
0.000 961.000 341.000 0.000 0.000 0.000 0.000
! a b c alpha beta gamma
9.819705 9.819705 9.819705 90.000000 90.000000 90.000000
401.00000 401.00000 401.00000 0.00000 0.00000 0.00000
! Pref1 Pref2 Asy1 Asy2 Asy3 Asy4
0.00000 0.00000 0.00439 0.00542 0.00000 0.00000
0.00 0.00 411.00 421.00 0.00 0.00
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