examples
peakref (version 1.3 2016100600) started on celesta at 10-Nov-2016 18:18:55
Peakref>
\journal off
The residue definition has been changed (july 2009). Use
resfactor 1 0 0 0 0 1
to redefine to old residue.
- Example 1.
Simple run on ammonium bitartrate
- Example 2.
Two fragments with independent orientation
- Example 3.
Two fragments with dependent orientation
- Example 4.
Incomensurate structure
Peakref>
abort on
Peakref>
show
Simple run on ammonium bitartrate
KappaCCD phi/chi scan.
You may inspect the contents of
example1.rmat and
example1.pk.
First load rmat and pk files
Peakref>
example 1
RMAT 1 example1
RMAT DMAT
0.0118442 -0.1077432 0.0472600 0.6958110 1.4883927 -7.4870992
0.0253138 0.0675984 0.0743739 -6.6553798 4.1747489 0.2107125
-0.1274301 0.0034251 0.0191772 5.8122458 9.1445618 2.3567824
Determinant: 0.1496973E-02 668.0148
cell from rmat: 7.66525 7.85920 11.08872 90.0065 89.9936 89.9951 V= 668.01
pg constrained: 7.66525 7.85920 11.08872 90.0000 90.0000 90.0000 V= 668.01
Sigma 0.0003 0.0003 0.0003 0.003 0.002 0.002 Volume 0.04
Bravais=P pg=mmm
rmatcrit set to 0.11089 0.1 comparecrit set to 0.11089 1.0
orientation-axis -0.40028 0.75298 0.52229 orientation-angle 94.74374
initial orx and ory shift of matrix 1 set to 0.00104
ReadPkData: 710 lines from /global/evalccd/ccd/peakref/example1.pk 500 reflections.
5 experiments.
The cell parameters are extracted from the rmatrix. A new rmatrix
(in a fixed standard orientation) is build from the cell parameters.
Then a rotation axis with a corresponding angle is determined which
will transform the standard rmatrix into the original rmatrix.
(these are the initial values of the orientation parameters
orx,ory and ora).
500 peak positions were read from the file.
To calculate the initial residues the following actions have to be performed:
- index the reflections (reind).
- remove outliers (forbid any).
- calculate and save initial residue
(store initial).
- set constraints. These are the constraints based on the
pointgroup (or the cell parameters).
- disable xtal shifts (lock xtalx/xtaly/xtalz). The possibility to
refine xtal shifts depends on the experiments (see the discussion
at the minxtalangle command).
These actions will be automatically executed after
go,
list,
residue,
save,
savermat and
status.
Peakref>
status
308 reflections with rotation angle. 192 reflections with rotation range.
resfactorvalue 0 all
resfactorvalue 1 mmang rotpartial
res = 1.0*mmAng + 1.0*rotpartial
Rmat 1 setting constraints to orthorhombic.
Reind: no reflections changed indices.
matrix 1: 500 reflections.
SetRot 1.0: 2 out of rot. 500 reflections (498 allowed)
nPg=8 (h,k,l) (-h,-k,l) (h,-k,-l) (-h,k,-l) (-h,-k,-l) (h,k,-l) (-h,k,l) (h,-k,l)
SetupRmatrices matrix 1 rotvec= -0.40028 0.75298 0.52229 AbsVec=1.0 rotang=94.74374 Stored rmat as 1
One matrix. 500 reflections. (forbidden rot:2 total:2)
Used: 498 mm 308 rot
ref current initial change accumulate shift refl
===============================================================
a No 7.66525 7.66525 7.66525 0.01533 498
b No 7.85920 7.85920 7.85920 0.01572 498
c No 11.08872 11.08872 11.08872 0.02218 498
alpha Fix 90.00000 90.00000 90.00000 0.20000 498
beta Fix 90.00000 90.00000 90.00000 0.20000 498
gamma Fix 90.00000 90.00000 90.00000 0.20000 498
orx No -0.40028 -0.40028 -0.40028 0.00104 498
ory No 0.75298 0.75298 0.75298 0.00104 498
ora No 94.74374 94.74374 94.74374 0.20000 498
xtalx No 0.00000 0.00000 0.00000 0.10000 498
xtaly No 0.00000 0.00000 0.00000 0.10000 498
xtalz No 0.00000 0.00000 0.00000 0.10000 498
zerodist No 0.00000 0.00000 0.00000 0.10000 498
zerohor Yes 0.00000 0.00000 0.00000 0.75980 0.10000 498
zerover Yes 0.00000 0.00000 0.00000 0.83320 0.10000 498
detrotx No 0.00000 0.00000 -0.01280 0.20000 498
detroty No 0.00000 0.00000 -0.15910 0.20000 498
detrotz No 0.00000 0.00000 0.05170 0.20000 498
===============================================================
Vol 668.01 668.01 0.00 668.01 498
===============================================================
mm 0.04199 0.04199 0.00000 0.04199 498
mmAng + 0.04556 0.04556 0.00000 0.04556 498
rotpartial + 0.04806 0.04806 0.00000 0.04806 308
rotoutside 0.13998 0.13998 0.00000 0.13998 18
rotinside 0.00000 0.00000 0.00000 0.00000 172
rotall 0.03478 0.03478 0.00000 0.03478 498
res 0.09362 0.09362 0.00000 0.09362
====
- All reflections are indexed.
- The program executes the
command forbid any to reject
reflections with a too great difference between observed and
calculated positions.
2 reflections are rejected.
- The constraints on angles are set to orthorhombic
- And finally the output of status
- The variables (column 1)
- their status (column 2, ref)
(No = will not be refined, Fix = will not be refined,
Yes = will be refined)
- current value (column 3, current).
- The bottom lines show the residues.
- The residue named res is the one used in the refinement.
Start the refinement of the detector positon:
Peakref>
go3
go(1) starting CalcRes: res=0.09362
Refining 2 parameters: Simplex stopped: range/shift (0.06654) < simplexsize (0.1) (rtol=0.00705).
18 evaluations in 9 iterations. residue 0.09296 ====
go(2)
Refining 2 parameters: Simplex stopped: range/shift (0.0907) < simplexsize (0.1) (rtol=0.00141).
16 evaluations in 8 iterations. residue 0.09277 ====
go(3)
Refining 2 parameters: 14 evaluations in 7 iterations. residue 0.09268 ====
starting 0.09362 bestintermediate 0.09268 final 0.09268 diff -0.00093 relative -0.01006 status 1
final residue is best.
One matrix. 500 reflections. (forbidden rot:2 total:2)
Used: 498 mm 308 rot
ref current initial change accumulate shift refl
================================================================
a No 7.66525 7.66525 7.66525 0.01533 498
b No 7.85920 7.85920 7.85920 0.01572 498
c No 11.08872 11.08872 11.08872 0.02218 498
alpha Fix 90.00000 90.00000 90.00000 0.20000 498
beta Fix 90.00000 90.00000 90.00000 0.20000 498
gamma Fix 90.00000 90.00000 90.00000 0.20000 498
orx No -0.40028 -0.40028 -0.40028 0.00104 498
ory No 0.75298 0.75298 0.75298 0.00104 498
ora No 94.74374 94.74374 94.74374 0.20000 498
xtalx No 0.00000 0.00000 0.00000 0.10000 498
xtaly No 0.00000 0.00000 0.00000 0.10000 498
xtalz No 0.00000 0.00000 0.00000 0.10000 498
zerodist No 0.00000 0.00000 0.00000 0.10000 498
zerohor Yes 0.00533 0.00000 0.00533 0.76513 0.10000 498
zerover Yes -0.00386 0.00000 -0.00386 0.82934 0.10000 498
detrotx No 0.00000 0.00000 -0.01280 0.20000 498
detroty No 0.00000 0.00000 -0.15910 0.20000 498
detrotz No 0.00000 0.00000 0.05170 0.20000 498
================================================================
Vol 668.01 668.01 0.00 668.01 498
================================================================
mm 0.04138 0.04199 -0.00062 0.04138 498
mmAng + 0.04462 0.04556 -0.00093 0.04462 498
rotpartial + 0.04806 0.04806 0.00000 0.04806 308
rotoutside 0.13998 0.13998 0.00000 0.13998 18
rotinside 0.00000 0.00000 0.00000 0.00000 172
rotall 0.03478 0.03478 0.00000 0.03478 498
res 0.09268 0.09362 -0.00093 0.09268
- Very small changes.
- The residue is lowered.
- The program will print ==== when a new residue is lower
than the best.
Release the cell parameters and orientation:
Peakref>
free rmat
alpha remains fixed. beta remains fixed. gamma remains fixed.
The angles are constrained to 90°
Another refinement cycle:
Peakref>
go3
go(1) starting CalcRes: res=0.09268
Refining 8 parameters: Simplex stopped: range/shift (0.05005) < simplexsize (0.1) (rtol=0.00286).
108 evaluations in 56 iterations. residue 0.09076 ====
go(2)
Refining 8 parameters: 79 evaluations in 45 iterations. residue 0.09053 ====
go(3)
Refining 8 parameters: 70 evaluations in 36 iterations. residue 0.09049 ====
starting 0.09268 bestintermediate 0.09049 final 0.09049 diff -0.0022 relative -0.02427 status 1
final residue is best.
One matrix. 500 reflections. (forbidden rot:2 total:2)
Used: 498 mm 308 rot
ref current initial change accumulate shift refl
================================================================
a Yes 7.66384 7.66525 -0.00142 7.66384 0.01533 498
b Yes 7.85530 7.85920 -0.00390 7.85530 0.01572 498
c Yes 11.08525 11.08872 -0.00347 11.08525 0.02218 498
alpha Fix 90.00000 90.00000 90.00000 0.20000 498
beta Fix 90.00000 90.00000 90.00000 0.20000 498
gamma Fix 90.00000 90.00000 90.00000 0.20000 498
orx Yes -0.40025 -0.40028 0.00003 -0.40025 0.00104 498
ory Yes 0.75298 0.75298 -0.00001 0.75298 0.00104 498
ora Yes 94.73434 94.74374 -0.00939 94.73434 0.20000 498
xtalx No 0.00000 0.00000 0.00000 0.10000 498
xtaly No 0.00000 0.00000 0.00000 0.10000 498
xtalz No 0.00000 0.00000 0.00000 0.10000 498
zerodist No 0.00000 0.00000 0.00000 0.10000 498
zerohor Yes 0.00742 0.00000 0.00742 0.76722 0.10000 498
zerover Yes -0.00360 0.00000 -0.00360 0.82960 0.10000 498
detrotx No 0.00000 0.00000 -0.01280 0.20000 498
detroty No 0.00000 0.00000 -0.15910 0.20000 498
detrotz No 0.00000 0.00000 0.05170 0.20000 498
================================================================
Vol 667.35 668.01 -0.66 667.35 498
================================================================
mm 0.04141 0.04199 -0.00058 0.04141 498
mmAng + 0.04450 0.04556 -0.00105 0.04450 498
rotpartial + 0.04598 0.04806 -0.00208 0.04598 308
rotoutside 0.16136 0.13998 0.02139 0.16136 16
rotinside 0.00000 0.00000 0.00000 0.00000 174
rotall 0.03362 0.03478 -0.00116 0.03362 498
res 0.09049 0.09362 -0.00313 0.09049
And again, almost no changes. The initial data are almost
perfect. (as a matter of fact, these results are to be expected
on good quality crystals, good quality hardware and good
quality software (the phichi method)).
Save the results (actually, in this case, saving the detector
parameters is not necessary):
Peakref>
save detalign.vic
Created peakref.log
Adding refined zerohor to initial value(0.7598). Adding refined zerover to initial value(0.8332).
Adding refined detrotx to initial value(-0.0128). Adding refined detroty to initial value(-0.1591).
Adding refined detrotz to initial value(0.0517).
Created detalign.vic detzero 0.0 0.76722 0.8296 detrot -0.0128 -0.1591 0.0517
You may want to save the cell parameters. The angles are now
fixed to 90° and probably this is the cell you are going to use:
Peakref>
savermat 1r.rmat
initial new
0.0118442 -0.1077432 0.0472600 0.0118595 -0.1077995 0.0472784
0.0253138 0.0675984 0.0743739 0.0253508 0.0676277 0.0743913
-0.1274301 0.0034251 0.0191772 -0.1274460 0.0034208 0.0191969
Determinant: 0.1496973E-02 0.1498461E-02
SameRmat=false
Created 1r.rmat
Two fragments with independent orientation
KappaCCD phi/chi scan. Two rough matrices were found using Dirax.
You may inspect the contents of
example2a.rmat and
example2b.rmat and
example2.pk.
The initial orientation matrices are not that well defined.
Be tolerant in comparing axes (1 Å) and angles (1 degree):
Peakref>
rmatcrit 1 1
Peakref>
example 2
removed rmat 1
RMAT 1 example2a
RMAT DMAT
-0.1206187 -0.0361241 0.0165107 -6.8659439 1.8184443 -2.2652709
0.0227663 0.0234710 0.0529414 -2.8333085 1.8326609 6.6595616
-0.0575823 0.1283320 -0.0075446 4.2086668 17.2943363 -1.9783144
Determinant: 0.1015324E-02 984.9076
cell from rmat: 7.45516 7.46566 17.90868 87.1724 86.9801 82.0476 V= 984.91
pg constrained: 7.45516 7.46566 17.90868 87.1724 86.9801 82.0476 V= 984.91
Sigma 0.0023 0.0025 0.0086 0.023 0.033 0.023 Volume 0.48
Bravais=P pg=-1
orientation-axis -0.0036 0.76859 0.63973 orientation-angle 157.0713
initial orx and ory shift of matrix 1 set to 0.00128
RMAT 2 example2b
RMAT DMAT
-0.1170824 -0.0393798 0.0193636 -6.7014790 2.3521936 -2.3192086
0.0323157 0.0138668 0.0526894 -3.0530415 1.4427842 6.7245798
-0.0600903 0.1278541 -0.0025134 4.9136810 17.1567802 -0.3473478
Determinant: 0.1010435E-02 989.6729
cell from rmat: 7.47137 7.52480 17.84993 86.8349 86.4608 81.5536 V= 989.67
pg constrained: 7.47137 7.52480 17.84993 86.8349 86.4608 81.5536 V= 989.67
Sigma 0.0137 0.0104 0.0193 0.147 0.256 0.173 Volume 2.43
Bravais=P pg=-1
cell 1 7.4552 7.4657 17.9087 87.172 86.980 82.048
cell 2 7.4714 7.5248 17.8499 86.835 86.461 81.554
diff 0.0162 0.0591 0.0587 0.338 0.519 0.494
parent=1
orientation-axis 0.01005 0.74182 0.67053 orientation-angle 153.80048
initial orx and ory shift of matrix 1 set to 0.00128
initial orx and ory shift of matrix 2 set to 0.00134
ReadPkData: 448 lines from /global/evalccd/ccd/peakref/example2.pk 280 reflections.
4 experiments.
The output is similar to example1. But now there are two matrices.
The cell parameters of the second matrix are compared to the
first one.
These cell parameters are equal (within the limits set by
rmatcrit)
and will be constrained
to the first matrix. The orientation of the second matrix
will be independent.
Peakref>
status
164 reflections with rotation angle. 116 reflections with rotation range.
resfactorvalue 0 all
resfactorvalue 1 mmang rotpartial
res = 1.0*mmAng + 1.0*rotpartial
Reind: no reflections changed indices. no reflections changed rmat.
matrix 1: 168 reflections. matrix 2: 112 reflections.
SetupRmatrices matrix 1 rotvec= -0.0036 0.76859 0.63974 AbsVec=1.0 rotang=157.0713 Stored rmat as 1
SetupRmatrices matrix 2 rotvec= 0.01005 0.74182 0.67053 AbsVec=1.0 rotang=153.80048 Stored rmat as 2
2 matrices.
rmat 1 168 reflections.
rmat 2 112 reflections.
Used: 280 mm 164 rot
ref current initial change accumulate shift refl
=================================================================
a No 7.45516 7.45516 7.45516 0.01491 280
b No 7.46566 7.46566 7.46566 0.01493 280
c No 17.90868 17.90868 17.90868 0.03582 280
alpha No 87.17242 87.17242 87.17242 0.20000 280
beta No 86.98012 86.98012 86.98012 0.20000 280
gamma No 82.04764 82.04764 82.04764 0.20000 280
orx No -0.00360 -0.00360 -0.00360 0.00128 168
ory No 0.76859 0.76859 0.76859 0.00128 168
ora No 157.07130 157.07130 157.07130 0.20000 168
orx2 No 0.01005 0.01005 0.01005 0.00134 112
ory2 No 0.74182 0.74182 0.74182 0.00134 112
ora2 No 153.80048 153.80048 153.80048 0.20000 112
xtalx No 0.00000 0.00000 0.00000 0.10000 280
xtaly No 0.00000 0.00000 0.00000 0.10000 280
xtalz No 0.00000 0.00000 0.00000 0.10000 280
zerodist No 0.00000 0.00000 0.00000 0.10000 280
zerohor Yes 0.00000 0.00000 0.00000 -1.45530 0.10000 280
zerover Yes 0.00000 0.00000 0.00000 -0.42040 0.10000 280
detrotx No 0.00000 0.00000 0.62960 0.20000 280
detroty No 0.00000 0.00000 0.18030 0.20000 280
detrotz No 0.00000 0.00000 -0.37160 0.20000 280
=================================================================
Vol 984.91 984.91 0.00 984.91 168
Vol2 984.91 984.91 0.00 984.91 112
=================================================================
mm 0.19264 0.04199 0.15065 0.19264 280
mmAng + 0.24851 0.04556 0.20295 0.24851 280
rotpartial + 0.62295 0.04806 0.57489 0.62295 164
rotoutside 7.13813 0.13998 6.99816 7.13813 37
rotinside 0.00000 0.00000 0.00000 0.00000 79
rotall 1.30812 0.03478 1.27334 1.30812 280
res 0.87146 0.09362 0.77784 0.87146
====
- Peaks are indexed by the two available matrices, and
the smallest difference between observed and calculated
impact position determines which matrix is used for each
reflection.
- Peaks with a too great difference between observed and
calculated positions will not be used.
- Peaks with a (possible) overlap in the two lattices are also
not used in the refinement.
- The orientation of the second matrix is available
(orx2, ory2 and ora2).
- The initial residue (bottom line) is not very good.
Start the refinement of the detector positon:
Peakref>
go3
go(1) starting CalcRes: res=0.87146
Refining 2 parameters: 16 evaluations in 8 iterations. residue 0.83319 ====
go(2)
Refining 2 parameters: 6 evaluations in 3 iterations. residue 0.83315 ====
go(3)
Refining 2 parameters: no evaluations in no iterations. residue 0.83315
starting 0.87146 bestintermediate 0.83315 final 0.83315 diff -0.03831 relative -0.04598 status 1
final residue is best.
2 matrices.
rmat 1 168 reflections.
rmat 2 112 reflections.
Used: 280 mm 164 rot
ref current initial change accumulate shift refl
=================================================================
a No 7.45516 7.45516 7.45516 0.01491 280
b No 7.46566 7.46566 7.46566 0.01493 280
c No 17.90868 17.90868 17.90868 0.03582 280
alpha No 87.17242 87.17242 87.17242 0.20000 280
beta No 86.98012 86.98012 86.98012 0.20000 280
gamma No 82.04764 82.04764 82.04764 0.20000 280
orx No -0.00360 -0.00360 -0.00360 0.00128 168
ory No 0.76859 0.76859 0.76859 0.00128 168
ora No 157.07130 157.07130 157.07130 0.20000 168
orx2 No 0.01005 0.01005 0.01005 0.00134 112
ory2 No 0.74182 0.74182 0.74182 0.00134 112
ora2 No 153.80048 153.80048 153.80048 0.20000 112
xtalx No 0.00000 0.00000 0.00000 0.10000 280
xtaly No 0.00000 0.00000 0.00000 0.10000 280
xtalz No 0.00000 0.00000 0.00000 0.10000 280
zerodist No 0.00000 0.00000 0.00000 0.10000 280
zerohor Yes 0.05379 0.00000 0.05379 -1.40151 0.10000 280
zerover Yes 0.07162 0.00000 0.07162 -0.34878 0.10000 280
detrotx No 0.00000 0.00000 0.62960 0.20000 280
detroty No 0.00000 0.00000 0.18030 0.20000 280
detrotz No 0.00000 0.00000 -0.37160 0.20000 280
=================================================================
Vol 984.91 984.91 0.00 984.91 168
Vol2 984.91 984.91 0.00 984.91 112
=================================================================
mm 0.16357 0.04199 0.12158 0.16357 280
mmAng + 0.21020 0.04556 0.16464 0.21020 280
rotpartial + 0.62295 0.04806 0.57489 0.62295 164
rotoutside 7.13813 0.13998 6.99816 7.13813 37
rotinside 0.00000 0.00000 0.00000 0.00000 79
rotall 1.30812 0.03478 1.27334 1.30812 280
res 0.83315 0.09362 0.73953 0.83315
Detector has moved. The residue is lowered.
Release the cell parameters and orientation:
Peakref>
free rmat
Peakref>
go3
go(1) starting CalcRes: res=0.83315
Refining 11 parameters: 147 evaluations in 99 iterations. residue 0.78959 ====
go(2)
Refining 11 parameters: 44 evaluations in 28 iterations. residue 0.78916 ====
go(3)
Refining 11 parameters: no evaluations in no iterations. residue 0.78916
starting 0.83315 bestintermediate 0.78916 final 0.78916 diff -0.04399 relative -0.05574 status 1
final residue is best.
2 matrices.
rmat 1 168 reflections.
rmat 2 112 reflections.
Used: 280 mm 164 rot
ref current initial change accumulate shift refl
==================================================================
a Yes 7.44294 7.45516 -0.01222 7.44294 0.01491 280
b Yes 7.46841 7.46566 0.00276 7.46841 0.01493 280
c Yes 17.88783 17.90868 -0.02085 17.88783 0.03582 280
alpha Yes 87.18228 87.17242 0.00986 87.18228 0.20000 280
beta Yes 87.30386 86.98012 0.32374 87.30386 0.20000 280
gamma Yes 82.16424 82.04764 0.11660 82.16424 0.20000 280
orx Yes -0.00383 -0.00360 -0.00023 -0.00383 0.00128 168
ory Yes 0.76798 0.76859 -0.00060 0.76798 0.00128 168
ora Yes 157.12982 157.07130 0.05851 157.12982 0.20000 168
orx2 No 0.01005 0.01005 0.01005 0.00134 112
ory2 No 0.74182 0.74182 0.74182 0.00134 112
ora2 No 153.80048 153.80048 153.80048 0.20000 112
xtalx No 0.00000 0.00000 0.00000 0.10000 280
xtaly No 0.00000 0.00000 0.00000 0.10000 280
xtalz No 0.00000 0.00000 0.00000 0.10000 280
zerodist No 0.00000 0.00000 0.00000 0.10000 280
zerohor Yes 0.05880 0.00000 0.05880 -1.39650 0.10000 280
zerover Yes 0.07502 0.00000 0.07502 -0.34538 0.10000 280
detrotx No 0.00000 0.00000 0.62960 0.20000 280
detroty No 0.00000 0.00000 0.18030 0.20000 280
detrotz No 0.00000 0.00000 -0.37160 0.20000 280
==================================================================
Vol 983.04 984.91 -1.87 983.04 168
Vol2 983.04 984.91 -1.87 983.04 112
==================================================================
mm 0.16797 0.04199 0.12598 0.16797 280
mmAng + 0.21517 0.04556 0.16961 0.21517 280
rotpartial + 0.57400 0.04806 0.52593 0.57400 164
rotoutside 7.27819 0.13998 7.13821 7.27819 36
rotinside 0.00000 0.00000 0.00000 0.00000 80
rotall 1.27196 0.03478 1.23718 1.27196 280
res 0.78916 0.09362 0.69555 0.78916
No big changes. Let's release the second matrix:
Peakref>
free orient2
Peakref>
go3
go(1) starting CalcRes: res=0.78916
Refining 14 parameters: 326 evaluations in 230 iterations. residue 0.71112 ====
go(2)
Refining 14 parameters: 92 evaluations in 63 iterations. residue 0.70918 ====
go(3)
Refining 14 parameters: 6 evaluations in 4 iterations. residue 0.70898 ====
starting 0.78916 bestintermediate 0.70898 final 0.70898 diff -0.08018 relative -0.11309 status 1
final residue is best.
2 matrices.
rmat 1 168 reflections.
rmat 2 112 reflections.
Used: 280 mm 164 rot
ref current initial change accumulate shift refl
==================================================================
a Yes 7.45188 7.45516 -0.00328 7.45188 0.01491 280
b Yes 7.46961 7.46566 0.00395 7.46961 0.01493 280
c Yes 17.89259 17.90868 -0.01609 17.89259 0.03582 280
alpha Yes 87.12978 87.17242 -0.04264 87.12978 0.20000 280
beta Yes 87.16370 86.98012 0.18359 87.16370 0.20000 280
gamma Yes 82.06363 82.04764 0.01600 82.06363 0.20000 280
orx Yes -0.00343 -0.00360 0.00017 -0.00343 0.00128 168
ory Yes 0.76812 0.76859 -0.00047 0.76812 0.00128 168
ora Yes 157.11543 157.07130 0.04412 157.11543 0.20000 168
orx2 Yes 0.01391 0.01005 0.00386 0.01391 0.00134 112
ory2 Yes 0.74227 0.74182 0.00045 0.74227 0.00134 112
ora2 Yes 153.79279 153.80048 -0.00769 153.79279 0.20000 112
xtalx No 0.00000 0.00000 0.00000 0.10000 280
xtaly No 0.00000 0.00000 0.00000 0.10000 280
xtalz No 0.00000 0.00000 0.00000 0.10000 280
zerodist No 0.00000 0.00000 0.00000 0.10000 280
zerohor Yes 0.06215 0.00000 0.06215 -1.39315 0.10000 280
zerover Yes 0.07820 0.00000 0.07820 -0.34220 0.10000 280
detrotx No 0.00000 0.00000 0.62960 0.20000 280
detroty No 0.00000 0.00000 0.18030 0.20000 280
detrotz No 0.00000 0.00000 -0.37160 0.20000 280
==================================================================
Vol 984.26 984.91 -0.65 984.26 168
Vol2 984.26 984.91 -0.65 984.26 112
==================================================================
mm 0.15685 0.04199 0.11485 0.15685 280
mmAng + 0.20145 0.04556 0.15589 0.20145 280
rotpartial + 0.50754 0.04806 0.45947 0.50754 164
rotoutside 6.84007 0.13998 6.70009 6.84007 38
rotinside 0.00000 0.00000 0.00000 0.00000 78
rotall 1.22557 0.03478 1.19078 1.22557 280
res 0.70898 0.09362 0.61537 0.70898
This helps, but the final residue is still large.
Note the values of zerohor and zerover. They should be
approximately zero. A value of 0.1 for zerover implies a
vertical shift of 1 pixel. So let's save the detector position
Peakref>
save detalign.vic
Adding refined zerohor to initial value(-1.4553). Adding refined zerover to initial value(-0.4204).
Adding refined detrotx to initial value(0.6296). Adding refined detroty to initial value(0.1803).
Adding refined detrotz to initial value(-0.3716).
WARNING: renaming existing file detalign.vic into detalign.vic.~1~
Created detalign.vic detzero 0.0 -1.39315 -0.3422 detrot 0.6296 0.1803 -0.3716
Examine the relation between the two fragments:
The tolerances have been set earlier to 1 Å and 1 degree.
Select the lowest Fom.
Peakref>
comparefomtype
0=smallestangle 1=bestfom 2=unitmatrix[0]
1
and then compare the cells
Peakref>
comparecrit 1 1
Peakref>
compare
2 matrices
a b c alpha beta gamma volume
dmat1 : 7.452 7.470 17.893 87.13 87.16 82.06 984.3
dmat2 : 7.452 7.470 17.893 87.13 87.16 82.06 984.3
Volume ratio = 1.0 Trying 96 solutions
Nr Rotangle Rotvec(xyz) RotVec(hkl) ( angle) RotVec(uvw) ( angle) Fom
1 179.283 0.3973 -0.0480 0.9164 -10.96 11.00 -2.02 ( 0.09) -1.00 1.00 -0.03 ( 2.91) 0.670
2 5.849 0.8034 -0.3248 -0.4990 -4.02 -5.00 -1.01 ( 0.16) -3.01 -4.00 -0.01 ( 0.25) 0.000 U
Selected Solution 2
a b c alpha beta gamma volume
dmat1 : 7.452 7.470 17.893 87.13 87.16 82.06 984.3 <
dmat2 : 7.452 7.470 17.893 87.13 87.16 82.06 984.3 <
H'= +0.994*H -0.001*K +0.032*L
K'= +0.005*H +1.000*K -0.024*L
L'= -0.204*H +0.165*K +0.996*L
Nr Rotangle Rotvec(xyz) RotVec(hkl) ( angle) RotVec(uvw) ( angle) Fom
2 5.849 0.8034 -0.3248 -0.4990 -4.02 -5.00 -1.01 ( 0.16) -3.01 -4.00 -0.01 ( 0.25) 0.000 U<
Two solutions.
Matrix 2 can be found by a rotation
around (0.82 -0.36 -0.45) over almost 6°.
The interpretation of the rotation axis in reciprocal
space (RotVec(hkl)) and direct space (RotVec(uvw)) does
not resemble a nice axis. The two fragments have indeed
a independent orientation.
Save both matrices:
Peakref>
savermat1 2ar
initial new
-0.1206187 -0.0361241 0.0165107 -0.1205947 -0.0360826 0.0164944
0.0227663 0.0234710 0.0529414 0.0232413 0.0230969 0.0530018
-0.0575823 0.1283320 -0.0075446 -0.0575231 0.1283379 -0.0074825
Determinant: 0.1015324E-02 0.1015993E-02
SameRmat=false
Created 2ar.rmat
Peakref>
savermat2 2br
initial new
-0.1170824 -0.0393798 0.0193636 -0.1171980 -0.0393879 0.0193507
0.0323157 0.0138668 0.0526894 0.0340909 0.0144742 0.0525001
-0.0600903 0.1278541 -0.0025134 -0.0591151 0.1286279 -0.0025577
Determinant: 0.1010435E-02 0.1015993E-02
SameRmat=false
Created 2br.rmat
A final note about the cell parameters. The rmat files in this
example describe a primitive lattice. The unit cells could be
transformed into c-centered monoclinic lattices
(use rmatrix example2a.rmat), and the refinement could be
repeated with the angles of alpha and gamma fixed to 90°
Two fragments with dependent orientation
You may inspect the contents of
example3a.rmat and
example3b.rmat and
example3.pk.
The initial orientation matrices are not that well defined.
Be tolerant in comparing axes (1 Å) and angles (1 degree):
Peakref>
pgcrit 1 1
use pgauto to use these values to set pg for existing rmats.
Peakref>
example 3
removed rmat 1 removed rmat 2
RMAT 1 example3a
RMAT DMAT
0.0459509 0.0196275 0.0784559 3.0803876 4.9386539 10.4288425
0.0393564 -0.0572818 0.0156385 4.7773743 -13.9043932 5.1462545
0.0636778 0.0213288 -0.0305794 9.7466917 0.5859708 -7.3955278
Determinant: 0.4603617E-03 2172.205
cell from rmat: 11.94319 15.57689 12.24889 89.8929 107.5899 90.0873 V= 2172.20
pg constrained: 11.94319 15.57689 12.24889 90.0000 107.5899 90.0000 V= 2172.21
Sigma 0.0024 0.0049 0.0059 0.023 0.021 0.021 Volume 1.24
Bravais=P pg=2/m
orientation-axis 0.79255 0.22781 0.56566 orientation-angle 174.60219
initial orx and ory shift of matrix 1 set to 0.00113
RMAT 2 example3b
RMAT DMAT
-0.0024319 -0.0198125 -0.0785923 3.0858576 4.9300828 10.4241095
0.0298162 0.0572270 -0.0157280 -4.7985392 13.9006023 -5.1621284
0.0825498 -0.0212004 0.0307043 -11.6097050 -3.6567850 0.9787763
Determinant: 0.4613548E-03 2167.529
cell from rmat: 11.93693 15.58526 12.21128 90.0525 107.4253 90.0268 V= 2167.53
pg constrained: 11.93693 15.58526 12.21128 90.0000 107.4253 90.0000 V= 2167.53
Sigma 0.0028 0.0057 0.0073 0.040 0.027 0.025 Volume 1.48
Bravais=P pg=2/m
cell 1 11.9432 15.5769 12.2489 89.893 107.590 90.087
cell 2 11.9369 15.5853 12.2113 90.053 107.425 90.027
diff 0.0063 0.0084 0.0376 0.160 0.165 0.060
parent=1
orientation-axis -0.07565 -0.92462 0.3733 orientation-angle 75.16096
initial orx and ory shift of matrix 1 set to 0.00113
initial orx and ory shift of matrix 2 set to 0.00075
ReadPkData: 728 lines from /global/evalccd/ccd/peakref/example3.pk 560 reflections.
4 experiments.
- Parent matrix of rmat2 is 1, so only refinement of orientation
of rmat2.
- Note the pointgroup settings (triclinic for rmat1 and monoclinic
for rmat2). The pointgroup of rmat2 will not be used
(cell parameters of rmat2 are constrained to the cell
parameters of rmat1).
Peakref>
status
209 reflections with rotation angle. 351 reflections with rotation range.
resfactorvalue 0 all
resfactorvalue 1 mmang rotpartial
res = 1.0*mmAng + 1.0*rotpartial
Reind: no reflections changed indices. no reflections changed rmat.
matrix 1: 347 reflections. matrix 2: 213 reflections.
SetupRmatrices matrix 1 rotvec= 0.79255 0.22781 0.56566 AbsVec=1.0 rotang=174.60219 Stored rmat as 1
SetupRmatrices matrix 2 rotvec= -0.07565 -0.92462 0.3733 AbsVec=1.0 rotang=75.16096 Stored rmat as 2
2 matrices.
rmat 1 347 reflections.
rmat 2 213 reflections.
Used: 560 mm 209 rot
ref current initial change accumulate shift refl
=================================================================
a No 11.94319 11.94319 11.94319 0.02389 560
b No 15.57689 15.57689 15.57689 0.03115 560
c No 12.24889 12.24889 12.24889 0.02450 560
alpha No 89.89287 89.89287 89.89287 0.20000 560
beta No 107.58987 107.58987 107.58987 0.20000 560
gamma No 90.08726 90.08726 90.08726 0.20000 560
orx No 0.79255 0.79255 0.79255 0.00113 347
ory No 0.22781 0.22781 0.22781 0.00113 347
ora No 174.60219 174.60219 174.60219 0.20000 347
orx2 No -0.07565 -0.07565 -0.07565 0.00075 213
ory2 No -0.92462 -0.92462 -0.92462 0.00075 213
ora2 No 75.16096 75.16096 75.16096 0.20000 213
xtalx No 0.00000 0.00000 0.00000 0.10000 560
xtaly No 0.00000 0.00000 0.00000 0.10000 560
xtalz No 0.00000 0.00000 0.00000 0.10000 560
zerodist No 0.00000 0.00000 0.00000 0.10000 560
zerohor Yes 0.00000 0.00000 0.00000 -1.45530 0.10000 560
zerover Yes 0.00000 0.00000 0.00000 -0.42040 0.10000 560
detrotx No 0.00000 0.00000 0.62960 0.20000 560
detroty No 0.00000 0.00000 0.18030 0.20000 560
detrotz No 0.00000 0.00000 -0.37160 0.20000 560
=================================================================
Vol 2172.21 2172.21 0.00 2172.21 347
Vol2 2172.20 2172.20 0.00 2172.20 213
=================================================================
mm 0.14318 0.04199 0.10118 0.14318 560
mmAng + 0.12246 0.04556 0.07690 0.12246 560
rotpartial + 0.28712 0.04806 0.23905 0.28712 209
rotoutside 1.79988 0.13998 1.65990 1.79988 85
rotinside 0.00000 0.00000 0.00000 0.00000 266
rotall 0.38035 0.03478 0.34557 0.38035 560
res 0.40957 0.09362 0.31596 0.40957
====
Similar to example 2.
- Peaks with a too great difference between observed and
calculated will not be used.
- Peaks with a (possible) overlap in the two lattices are also not
used in the refinement.
- Note the almost 90° angles. alpha is more than 0.1°
of 90. The lattice is assumed triclinic.
- The initial residue (bottom line) is not very good.
Start the refinement of the detector positon:
Peakref>
go3
go(1) starting CalcRes: res=0.40957
Refining 2 parameters: 12 evaluations in 7 iterations. residue 0.39253 ====
go(2)
Refining 2 parameters: 6 evaluations in 3 iterations. residue 0.39241 ====
go(3)
Refining 2 parameters: no evaluations in no iterations. residue 0.39241
starting 0.40957 bestintermediate 0.39241 final 0.39241 diff -0.01716 relative -0.04374 status 1
final residue is best.
2 matrices.
rmat 1 347 reflections.
rmat 2 213 reflections.
Used: 560 mm 209 rot
ref current initial change accumulate shift refl
==================================================================
a No 11.94319 11.94319 11.94319 0.02389 560
b No 15.57689 15.57689 15.57689 0.03115 560
c No 12.24889 12.24889 12.24889 0.02450 560
alpha No 89.89287 89.89287 89.89287 0.20000 560
beta No 107.58987 107.58987 107.58987 0.20000 560
gamma No 90.08726 90.08726 90.08726 0.20000 560
orx No 0.79255 0.79255 0.79255 0.00113 347
ory No 0.22781 0.22781 0.22781 0.00113 347
ora No 174.60219 174.60219 174.60219 0.20000 347
orx2 No -0.07565 -0.07565 -0.07565 0.00075 213
ory2 No -0.92462 -0.92462 -0.92462 0.00075 213
ora2 No 75.16096 75.16096 75.16096 0.20000 213
xtalx No 0.00000 0.00000 0.00000 0.10000 560
xtaly No 0.00000 0.00000 0.00000 0.10000 560
xtalz No 0.00000 0.00000 0.00000 0.10000 560
zerodist No 0.00000 0.00000 0.00000 0.10000 560
zerohor Yes -0.00907 0.00000 -0.00907 -1.46437 0.10000 560
zerover Yes 0.06717 0.00000 0.06717 -0.35323 0.10000 560
detrotx No 0.00000 0.00000 0.62960 0.20000 560
detroty No 0.00000 0.00000 0.18030 0.20000 560
detrotz No 0.00000 0.00000 -0.37160 0.20000 560
==================================================================
Vol 2172.21 2172.21 0.00 2172.21 347
Vol2 2172.20 2172.20 0.00 2172.20 213
==================================================================
mm 0.12338 0.04199 0.08139 0.12338 560
mmAng + 0.10529 0.04556 0.05974 0.10529 560
rotpartial + 0.28712 0.04806 0.23905 0.28712 209
rotoutside 1.79988 0.13998 1.65990 1.79988 85
rotinside 0.00000 0.00000 0.00000 0.00000 266
rotall 0.38035 0.03478 0.34557 0.38035 560
res 0.39241 0.09362 0.29879 0.39241
Detector has moved. The residue is lowered.
Release the cell parameters and orientation:
Peakref>
free rmat orient2
Peakref>
go3
go(1) starting CalcRes: res=0.39241
Refining 14 parameters: 202 evaluations in 133 iterations. residue 0.37588 ====
go(2)
Refining 14 parameters: 55 evaluations in 31 iterations. residue 0.37563 ====
go(3)
Refining 14 parameters: 22 evaluations in 12 iterations. residue 0.37553 ====
starting 0.39241 bestintermediate 0.37553 final 0.37553 diff -0.01688 relative -0.04495 status 1
final residue is best.
2 matrices.
rmat 1 347 reflections.
rmat 2 213 reflections.
Used: 560 mm 209 rot
ref current initial change accumulate shift refl
==================================================================
a Yes 11.94549 11.94319 0.00229 11.94549 0.02389 560
b Yes 15.57989 15.57689 0.00301 15.57989 0.03115 560
c Yes 12.24212 12.24889 -0.00676 12.24212 0.02450 560
alpha Yes 89.99294 89.89287 0.10007 89.99294 0.20000 560
beta Yes 107.56322 107.58987 -0.02665 107.56322 0.20000 560
gamma Yes 90.01319 90.08726 -0.07407 90.01319 0.20000 560
orx Yes 0.79291 0.79255 0.00036 0.79291 0.00113 347
ory Yes 0.22742 0.22781 -0.00039 0.22742 0.00113 347
ora Yes 174.62660 174.60219 0.02441 174.62660 0.20000 347
orx2 Yes -0.07598 -0.07565 -0.00034 -0.07598 0.00075 213
ory2 Yes -0.92500 -0.92462 -0.00038 -0.92500 0.00075 213
ora2 Yes 75.27427 75.16096 0.11330 75.27427 0.20000 213
xtalx No 0.00000 0.00000 0.00000 0.10000 560
xtaly No 0.00000 0.00000 0.00000 0.10000 560
xtalz No 0.00000 0.00000 0.00000 0.10000 560
zerodist No 0.00000 0.00000 0.00000 0.10000 560
zerohor Yes -0.00886 0.00000 -0.00886 -1.46416 0.10000 560
zerover Yes 0.07540 0.00000 0.07540 -0.34500 0.10000 560
detrotx No 0.00000 0.00000 0.62960 0.20000 560
detroty No 0.00000 0.00000 0.18030 0.20000 560
detrotz No 0.00000 0.00000 -0.37160 0.20000 560
==================================================================
Vol 2172.17 2172.21 -0.04 2172.17 347
Vol2 2172.17 2172.20 -0.04 2172.17 213
==================================================================
mm 0.12158 0.04199 0.07959 0.12158 560
mmAng + 0.10369 0.04556 0.05814 0.10369 560
rotpartial + 0.27184 0.04806 0.22378 0.27184 209
rotoutside 1.91335 0.13998 1.77337 1.91335 80
rotinside 0.00000 0.00000 0.00000 0.00000 271
rotall 0.37479 0.03478 0.34000 0.37479 560
res 0.37553 0.09362 0.28191 0.37553
Almost no changes, and the final residue is still large.
Note the almost 90° values for alpha and gamma.
There are two ways to fix the angles:
Peakref>
pgcrit 0.1 0.1 pgauto
use pgauto to use these values to set pg for existing rmats. laue group set to 2/m
laue group set to 2/m
Rmat 1 setting constraints to monoclinic.
No internal constraints for dependent matrix 2
SetupRmatrices matrix 1 rotvec= 0.79291 0.22742 0.56531 AbsVec=1.0 rotang=174.6266 Stored rmat as 1
SetupRmatrices matrix 2 rotvec= -0.07598 -0.925 0.37229 AbsVec=1.0 rotang=75.27427 Stored rmat as 2
Refine with the new constraints
Peakref>
go3
go(1) starting CalcRes: res=0.37615
Refining 12 parameters: 96 evaluations in 54 iterations. residue 0.37528 ====
go(2)
Refining 12 parameters: 44 evaluations in 24 iterations. residue 0.37513 ====
go(3)
Refining 12 parameters: 16 evaluations in 8 iterations. residue 0.3751 ====
starting 0.37615 bestintermediate 0.3751 final 0.3751 diff -0.00105 relative -0.00281 status 3
final residue is best.
2 matrices.
rmat 1 347 reflections.
rmat 2 213 reflections.
Used: 560 mm 209 rot
ref current initial change accumulate shift refl
==================================================================
a Yes 11.94520 11.94319 0.00200 11.94520 0.02389 560
b Yes 15.57883 15.57689 0.00194 15.57883 0.03115 560
c Yes 12.24159 12.24889 -0.00729 12.24159 0.02450 560
alpha Fix 90.00000 89.89287 90.00000 0.20000 560
beta Yes 107.55914 107.58987 -0.03073 107.55914 0.20000 560
gamma Fix 90.00000 90.08726 90.00000 0.20000 560
orx Yes 0.79295 0.79255 0.00040 0.79295 0.00113 347
ory Yes 0.22733 0.22781 -0.00048 0.22733 0.00113 347
ora Yes 174.63429 174.60219 0.03210 174.63429 0.20000 347
orx2 Yes -0.07614 -0.07565 -0.00049 -0.07614 0.00075 213
ory2 Yes -0.92496 -0.92462 -0.00034 -0.92496 0.00075 213
ora2 Yes 75.27990 75.16096 0.11893 75.27990 0.20000 213
xtalx No 0.00000 0.00000 0.00000 0.10000 560
xtaly No 0.00000 0.00000 0.00000 0.10000 560
xtalz No 0.00000 0.00000 0.00000 0.10000 560
zerodist No 0.00000 0.00000 0.00000 0.10000 560
zerohor Yes -0.00896 0.00000 -0.00896 -1.46426 0.10000 560
zerover Yes 0.07526 0.00000 0.07526 -0.34514 0.10000 560
detrotx No 0.00000 0.00000 0.62960 0.20000 560
detroty No 0.00000 0.00000 0.18030 0.20000 560
detrotz No 0.00000 0.00000 -0.37160 0.20000 560
==================================================================
Vol 2171.92 2172.21 -0.29 2171.92 347
Vol2 2171.92 2172.20 -0.29 2171.92 213
==================================================================
mm 0.12191 0.04199 0.07992 0.12191 560
mmAng + 0.10396 0.04556 0.05840 0.10396 560
rotpartial + 0.27114 0.04806 0.22308 0.27114 209
rotoutside 1.86661 0.13998 1.72663 1.86661 82
rotinside 0.00000 0.00000 0.00000 0.00000 269
rotall 0.37452 0.03478 0.33973 0.37452 560
res 0.37510 0.09362 0.28148 0.37510
Examine the relation between the two fragments:
Select the lowest Fom.
Peakref>
comparefomtype
0=smallestangle 1=bestfom 2=unitmatrix[1]
1
Peakref>
comparecrit 1 1
Peakref>
compare
2 matrices
a b c alpha beta gamma volume
dmat1 : 11.945 15.579 12.242 90.00 107.56 90.00 2171.9
dmat2 : 11.945 15.579 12.242 90.00 107.56 90.00 2171.9
Volume ratio = 1.0 Trying 32 solutions
Nr Rotangle Rotvec(xyz) RotVec(hkl) ( angle) RotVec(uvw) ( angle) Fom
1 179.987 0.9158 0.1828 -0.3577 0.00 -0.00 1.00 ( 0.03) 4.02 -0.00 13.00 ( 0.11) 0.000
2 71.955 -0.3072 0.8926 -0.3301 0.00 -1.00 -0.00 ( 0.03) 0.00 -1.00 -0.00 ( 0.03) 4.460
3 108.045 0.3072 -0.8923 0.3308 0.00 1.00 0.00 ( 0.03) 0.00 1.00 0.00 ( 0.03) 4.460
4 179.958 -0.2588 -0.4126 -0.8734 -13.00 0.00 4.02 ( 0.11) -1.00 0.00 0.00 ( 0.02) 0.000 U
Selected Solution 4
a b c alpha beta gamma volume
dmat1 : 11.945 15.579 12.242 90.00 107.56 90.00 2171.9 <
dmat2 : 11.945 15.579 12.242 90.00 107.56 90.00 2171.9 <
H'= +1.000*H -0.000*K -0.001*L
K'= -0.001*H -1.000*K -0.001*L
L'= -0.619*H +0.001*K -1.000*L
Nr Rotangle Rotvec(xyz) RotVec(hkl) ( angle) RotVec(uvw) ( angle) Fom
4 179.958 -0.2588 -0.4126 -0.8734 -13.00 0.00 4.02 ( 0.11) -1.00 0.00 0.00 ( 0.02) 0.000 U<
Four solutions. Matrix 2 can be found by a rotation
around (-0.259 -0.413 -0.873) over
179.958°
The interpretation of the
rotation axis in direct space (RotVec(uvw)) does look promising:
a 180° rotation around a, or in recprocal space
(RotVec(hkl)): a 180° rotation around c*.
Set this constraint by:
Peakref>
twin2
removed rmat 2
parent matrix [1]
<Enter>
xyz/hkl/uvw [hkl]
uvw
uvw indices
1 0 0
v1 1.0 0.0 0.0
Enter angle
180
SetupRmatrices matrix 1 rotvec= 0.79295 0.22733 0.5653 AbsVec=1.0 rotang=174.63429 Stored rmat as 1
SetupRmatrices twin 2 axis(uvw) 1.0 0.0 0.0 axis(lab) 0.25915 0.41259 0.87328 angle 180.0
Stored rmat as 2
RMAT 2 example3a
RMAT DMAT
-0.0025646 -0.0196976 -0.0784659 3.0956275 4.9284592 10.4314451
0.0297109 0.0572886 -0.0156198 -4.7806010 13.9039297 -5.1503892
0.0825878 -0.0212212 0.0306652 -11.6454830 -3.6514418 0.9519727
Determinant: 0.4604222E-03 2171.920
cell from rmat: 11.94519 15.57883 12.24159 90.0000 107.5591 90.0000 V= 2171.92
pg constrained: 11.94519 15.57883 12.24159 90.0000 107.5591 90.0000 V= 2171.92
Sigma 0.0024 0.0049 0.0059 0.023 0.021 0.021 Volume 1.24
Bravais=P pg=2/m
Matrix 2 is now calculated from matrix 1 and the twin relation.
Peakref>
status
Reind:
refl rmat h k l qvp mm ==> rmat h k l qvp mm
22 2 0 5 -2 0.1525 1 0 -5 2 0.1525
52 1 -5 4 3 0.1006 2 -5 -4 0 0.0364
64 1 -5 5 3 0.1077 2 -5 -5 0 0.0341
95 1 -5 7 3 0.1116 2 -5 -7 0 0.0465
102 2 5 7 -4 0.1232 1 5 -7 1 0.0942
105 1 6 -6 0 0.3902 2 6 6 -4 0.3093
110 2 0 9 -4 0.1411 1 0 -9 4 0.1411
113 2 2 9 -4 0.3036 1 2 -9 3 0.2688
120 1 8 -2 -2 0.1238 2 8 2 -3 0.0494
123 1 8 -3 -2 0.2927 2 8 3 -3 0.2645
164 2 0 2 4 0.0410 1 0 -2 -4 0.0410
190 2 0 3 5 0.0436 1 0 -3 -5 0.0436
205 1 0 0 6 0.0337 2 0 0 -6 0.0337
216 1 0 -3 -6 0.2180 2 0 3 6 0.2180
221 2 0 4 6 0.0302 1 0 -4 -6 0.0302
263 1 8 2 -2 0.1251 2 8 -2 -3 0.1191
289 1 0 3 -1 0.0157 2 0 -3 1 0.0157
298 1 -1 -5 1 0.5700 2 -1 5 -1 0.5586
310 2 0 6 -1 0.0815 1 0 -6 1 0.0814
340 2 0 8 -1 0.0908 1 0 -8 1 0.0908
360 2 5 6 0 0.1377 1 5 -6 -3 0.0552
371 1 0 8 -4 0.1040 2 0 -8 4 0.1040
373 1 3 7 -5 0.2347 2 3 -7 3 0.2075
429 2 0 -1 -3 0.1573 1 0 1 3 0.1573
493 2 0 -3 -6 0.1668 1 0 3 6 0.1668
497 1 0 4 6 0.1299 2 0 -4 -6 0.1299
539 1 0 5 7 0.1305 2 0 -5 -7 0.1305
544 2 -8 2 3 0.1246 1 -8 -2 2 0.1187
547 2 0 -1 8 0.0920 1 0 1 -8 0.0920
29 reflections changed indices. 29 reflections changed rmat.
matrix 1: 346 reflections. matrix 2: 214 reflections.
SetMM 1.0: 3 out of position. SetRot 1.0: 26 out of rot. 560 reflections (533 allowed)
SetupRmatrices matrix 1 rotvec= 0.79295 0.22733 0.5653 AbsVec=1.0 rotang=174.63429 Stored rmat as 1
SetupRmatrices twin 2 axis(uvw) 1.0 0.0 0.0 axis(lab) 0.25915 0.41259 0.87328 angle 180.0
Stored rmat as 2
RMAT 2 example3a
RMAT DMAT
-0.0025646 -0.0196976 -0.0784659 3.0956275 4.9284592 10.4314451
0.0297109 0.0572886 -0.0156198 -4.7806010 13.9039297 -5.1503892
0.0825878 -0.0212212 0.0306652 -11.6454830 -3.6514418 0.9519727
Determinant: 0.4604222E-03 2171.920
cell from rmat: 11.94519 15.57883 12.24159 90.0000 107.5591 90.0000 V= 2171.92
pg constrained: 11.94519 15.57883 12.24159 90.0000 107.5591 90.0000 V= 2171.92
Sigma 0.0024 0.0049 0.0059 0.023 0.021 0.021 Volume 1.24
Bravais=P pg=2/m
2 matrices.
rmat 1 346 reflections. (forbidden mm:3 rot:14 total:15)
rmat 2 214 reflections. (forbidden rot:12 total:12)
Used: 533 mm 198 rot
ref current initial change accumulate shift refl
==================================================================
a Yes 11.94520 11.94319 0.00200 11.94520 0.02389 533
b Yes 15.57883 15.57689 0.00194 15.57883 0.03115 533
c Yes 12.24159 12.24889 -0.00729 12.24159 0.02450 533
alpha Fix 90.00000 89.89287 90.00000 0.20000 533
beta Yes 107.55914 107.58987 -0.03073 107.55914 0.20000 533
gamma Fix 90.00000 90.08726 90.00000 0.20000 533
orx Yes 0.79295 0.79255 0.00040 0.79295 0.00113 533
ory Yes 0.22733 0.22781 -0.00048 0.22733 0.00113 533
ora Yes 174.63429 174.60219 0.03210 174.63429 0.20000 533
xtalx No 0.00000 0.00000 0.00000 0.10000 533
xtaly No 0.00000 0.00000 0.00000 0.10000 533
xtalz No 0.00000 0.00000 0.00000 0.10000 533
zerodist No 0.00000 0.00000 0.00000 0.10000 533
zerohor Yes -0.00896 0.00000 -0.00896 -1.46426 0.10000 533
zerover Yes 0.07526 0.00000 0.07526 -0.34514 0.10000 533
detrotx No 0.00000 0.00000 0.62960 0.20000 533
detroty No 0.00000 0.00000 0.18030 0.20000 533
detrotz No 0.00000 0.00000 -0.37160 0.20000 533
==================================================================
Vol 2171.92 2172.21 -0.29 2171.92 331
Vol2 2171.92 2172.21 -0.29 2171.92 202
==================================================================
mm 0.10204 0.12944 -0.02739 0.10204 533
mmAng + 0.08513 0.10898 -0.02385 0.08513 533
rotpartial + 0.19523 0.21526 -0.02003 0.19523 198
rotoutside 0.34006 0.33639 0.00367 0.34006 66
rotinside 0.00000 0.00000 0.00000 0.00000 269
rotall 0.11463 0.12162 -0.00698 0.11463 533
res 0.28036 0.32424 -0.04388 0.28036
====
Due to the twin command, the reflections are reindexed.
The rejections are different compared to before.
Peakref>
go3
go(1) starting CalcRes: res=0.28036
Refining 9 parameters: 79 evaluations in 48 iterations. residue 0.27727 ====
go(2)
Refining 9 parameters: 37 evaluations in 19 iterations. residue 0.27706 ====
go(3)
Refining 9 parameters: 10 evaluations in 5 iterations. residue 0.27702 ====
starting 0.28036 bestintermediate 0.27702 final 0.27702 diff -0.00334 relative -0.01205 status 1
final residue is best.
2 matrices.
rmat 1 346 reflections. (forbidden mm:3 rot:14 total:15)
rmat 2 214 reflections. (forbidden rot:12 total:12)
Used: 533 mm 198 rot
ref current initial change accumulate shift refl
==================================================================
a Yes 11.94204 11.94319 -0.00115 11.94204 0.02389 533
b Yes 15.57360 15.57689 -0.00329 15.57360 0.03115 533
c Yes 12.23942 12.24889 -0.00947 12.23942 0.02450 533
alpha Fix 90.00000 89.89287 90.00000 0.20000 533
beta Yes 107.58274 107.58987 -0.00713 107.58274 0.20000 533
gamma Fix 90.00000 90.08726 90.00000 0.20000 533
orx Yes 0.79280 0.79255 0.00025 0.79280 0.00113 533
ory Yes 0.22750 0.22781 -0.00031 0.22750 0.00113 533
ora Yes 174.65965 174.60219 0.05746 174.65965 0.20000 533
xtalx No 0.00000 0.00000 0.00000 0.10000 533
xtaly No 0.00000 0.00000 0.00000 0.10000 533
xtalz No 0.00000 0.00000 0.00000 0.10000 533
zerodist No 0.00000 0.00000 0.00000 0.10000 533
zerohor Yes -0.01053 0.00000 -0.01053 -1.46583 0.10000 533
zerover Yes 0.07709 0.00000 0.07709 -0.34331 0.10000 533
detrotx No 0.00000 0.00000 0.62960 0.20000 533
detroty No 0.00000 0.00000 0.18030 0.20000 533
detrotz No 0.00000 0.00000 -0.37160 0.20000 533
==================================================================
Vol 2169.95 2172.21 -2.26 2169.95 331
Vol2 2169.95 2172.21 -2.26 2169.95 202
==================================================================
mm 0.10332 0.12944 -0.02612 0.10332 533
mmAng + 0.08609 0.10898 -0.02289 0.08609 533
rotpartial + 0.19094 0.21526 -0.02432 0.19094 198
rotoutside 0.35096 0.33639 0.01457 0.35096 63
rotinside 0.00000 0.00000 0.00000 0.00000 272
rotall 0.11241 0.12162 -0.00921 0.11241 533
res 0.27702 0.32424 -0.04722 0.27702
And now remove 'bad' reflections.
Use reject 5 to reject reflections
with a delmm>5*resmm and
delrot>5*resrot.
Peakref>
reject 5
using mm residue mm and rotation residue rotpartial
Peakref>
go3
SetMM 0.51659: 14 out of position. SetRot 0.95468: 31 out of rot. 560 reflections (525 allowed)
SetupRmatrices matrix 1 rotvec= 0.7928 0.2275 0.56543 AbsVec=1.0 rotang=174.65965 Stored rmat as 1
SetupRmatrices twin 2 axis(uvw) 1.0 0.0 0.0 axis(lab) 0.25868 0.41257 0.87342 angle 180.0
Stored rmat as 2
RMAT 2 example3a
RMAT DMAT
-0.0026389 -0.0197332 -0.0784884 3.0892019 4.9269004 10.4304724
0.0296936 0.0573003 -0.0156779 -4.7860379 13.8974333 -5.1470590
0.0826286 -0.0212217 0.0306516 -11.6413116 -3.6596839 0.9433658
Determinant: 0.4608403E-03 2169.949
cell from rmat: 11.94204 15.57360 12.23942 90.0000 107.5827 90.0000 V= 2169.95
pg constrained: 11.94204 15.57360 12.23942 90.0000 107.5827 90.0000 V= 2169.95
Sigma 0.0024 0.0049 0.0059 0.023 0.021 0.021 Volume 1.24
Bravais=P pg=2/m
go(1) starting CalcRes: res=0.25155
Refining 9 parameters: 76 evaluations in 42 iterations. residue 0.25161 ====
go(2)
Refining 9 parameters: 50 evaluations in 27 iterations. residue 0.25146 ====
go(3)
Refining 9 parameters: 21 evaluations in 11 iterations. residue 0.25144 ====
starting 0.25155 bestintermediate 0.25144 final 0.25144 diff -0.00012 relative -0.00046 status 3
final residue is best.
2 matrices.
rmat 1 346 reflections. (forbidden mm:9 rot:15 total:19)
rmat 2 214 reflections. (forbidden mm:5 rot:16 total:16)
Used: 525 mm 192 rot
ref current initial change accumulate shift refl
==================================================================
a Yes 11.94068 11.94319 -0.00251 11.94068 0.02389 525
b Yes 15.57093 15.57689 -0.00595 15.57093 0.03115 525
c Yes 12.23948 12.24889 -0.00941 12.23948 0.02450 525
alpha Fix 90.00000 89.89287 90.00000 0.20000 525
beta Yes 107.58369 107.58987 -0.00617 107.58369 0.20000 525
gamma Fix 90.00000 90.08726 90.00000 0.20000 525
orx Yes 0.79277 0.79255 0.00022 0.79277 0.00113 525
ory Yes 0.22754 0.22781 -0.00027 0.22754 0.00113 525
ora Yes 174.66228 174.60219 0.06008 174.66228 0.20000 525
xtalx No 0.00000 0.00000 0.00000 0.10000 525
xtaly No 0.00000 0.00000 0.00000 0.10000 525
xtalz No 0.00000 0.00000 0.00000 0.10000 525
zerodist No 0.00000 0.00000 0.00000 0.10000 525
zerohor Yes -0.00971 0.00000 -0.00971 -1.46501 0.10000 525
zerover Yes 0.07735 0.00000 0.07735 -0.34305 0.10000 525
detrotx No 0.00000 0.00000 0.62960 0.20000 525
detroty No 0.00000 0.00000 0.18030 0.20000 525
detrotz No 0.00000 0.00000 -0.37160 0.20000 525
==================================================================
Vol 2169.33 2172.21 -2.88 2169.33 327
Vol2 2169.33 2172.21 -2.88 2169.33 198
==================================================================
mm 0.09926 0.12565 -0.02638 0.09926 525
mmAng + 0.08228 0.10544 -0.02316 0.08228 525
rotpartial + 0.16916 0.19585 -0.02670 0.16916 192
rotoutside 0.34209 0.32934 0.01275 0.34209 62
rotinside 0.00000 0.00000 0.00000 0.00000 271
rotall 0.10226 0.11240 -0.01014 0.10226 525
res 0.25144 0.30129 -0.04986 0.25144
detector position and matrices can now be saved using
save,
savermat1 and
savermat2,
Incomensurate structure
You may inspect the contents of
example4.rmat and
example4.pk.
example4.rmat constains four
qvectors (QVEC) with a user defined
set of qvector combinations (QVC)
first, reset the reject parameters
Peakref>
maxmismm 1
Peakref>
maxmisrot 1
get the data
Peakref>
example 4
removed rmat 1 removed rmat 2
RMAT 1 example4
RMAT DMAT
0.1372836 0.2920939 0.0116994 -0.1319185 -3.8726881 0.1954563
-0.2636430 -0.0127565 0.0026720 3.3636947 1.7923243 -0.7255700
-0.0148209 -0.0556102 0.0608381 3.0425107 0.6948735 15.8214626
Determinant: 0.4756656E-02 210.2317
cell from rmat: 3.87986 3.87986 16.12633 90.0001 90.0000 120.0000 V= 210.23
pg constrained: 3.87986 3.87986 16.12633 90.0000 90.0000 120.0000 V= 210.23
Bravais=P pg=-3
Qvectype=2 MODULATED
ActiveQvecRadius=0.36056
QVEC dh dk dl Order
1 0.3000 -0.1000 0.0000 1
2 0.3000 -0.2000 0.0000 1
3 -0.1000 0.3000 0.0000 1
4 -0.2000 0.3000 0.0000 1
13 explicit QV Combinations
orientation-axis 0.1151 -0.06923 0.99094 orientation-angle -92.7446
initial orx and ory shift of matrix 1 set to 0.00198
ReadPkData: 2763 lines from /global/evalccd/ccd/peakref/example4.pk 2399 reflections.
47 experiments.
Peakref>
status
no reflections with rotation angle. 2399 reflections with rotation range.
resfactorvalue 0 all
resfactorvalue 1 mmang rotall
res = 1.0*mmAng + 1.0*rotall
Reind: 2 not-indexed reflections. no reflections changed indices.
matrix 1: 2397 reflections. 0 main 2397 satellite.
SetMM 1.0: 777 out of position. SetRot 1.0: 1070 out of rot. 2399 reflections (1106 allowed)
SetupRmatrices matrix 1 rotvec= 0.1151 -0.06923 0.99094 AbsVec=1.0 rotang=-92.7446 Stored rmat as 1
Saving 4 qvecs Stored rmat as 1
One matrix. 2399 reflections. (forbidden index:2 mm:777 rot:1070 total:1293)
Used: 1106 mm 1106 rot
ref current initial change accumulate shift refl
=================================================================
a No 3.87986 3.87986 3.87986 0.00776 1106
b No 3.87986 3.87986 3.87986 0.00776 1106
c No 16.12633 16.12633 16.12633 0.03225 1106
alpha No 90.00005 90.00005 90.00005 0.20000 1106
beta No 89.99998 89.99998 89.99998 0.20000 1106
gamma No 120.00001 120.00001 120.00001 0.20000 1106
orx No 0.11510 0.11510 0.11510 0.00198 1106
ory No -0.06923 -0.06923 -0.06923 0.00198 1106
ora No -92.74460 -92.74460 -92.74460 0.20000 1106
xtalx No 0.00000 0.00000 0.00000 0.10000 1106
xtaly No 0.00000 0.00000 0.00000 0.10000 1106
xtalz No 0.00000 0.00000 0.00000 0.10000 1106
zerodist No 0.00000 0.00000 0.00000 0.10000 1106
zerohor Yes 0.00000 0.00000 0.00000 0.51200 0.10000 1106
zerover Yes 0.00000 0.00000 0.00000 -0.80210 0.10000 1106
detrotx No 0.00000 0.00000 -0.10280 0.20000 1106
detroty No 0.00000 0.00000 0.09980 0.20000 1106
detrotz No 0.00000 0.00000 0.06290 0.20000 1106
qvx1 No 0.30000 0.30000 0.30000 0.01000 290
qvy1 No -0.10000 -0.10000 -0.10000 0.01000 290
qvz1 No 0.00000 0.00000 0.00000 0.01000 290
qvx2 No 0.30000 0.30000 0.30000 0.01000 282
qvy2 No -0.20000 -0.20000 -0.20000 0.01000 282
qvz2 No 0.00000 0.00000 0.00000 0.01000 282
qvx3 No -0.10000 -0.10000 -0.10000 0.01000 271
qvy3 No 0.30000 0.30000 0.30000 0.01000 271
qvz3 No 0.00000 0.00000 0.00000 0.01000 271
qvx4 No -0.20000 -0.20000 -0.20000 0.01000 312
qvy4 No 0.30000 0.30000 0.30000 0.01000 312
qvz4 No 0.00000 0.00000 0.00000 0.01000 312
=================================================================
Vol 210.23 210.23 0.00 210.23 1106
=================================================================
mm 0.17963 0.17963 0.00000 0.17963 1106
mmAng + 0.27032 0.27032 0.00000 0.27032 1106
rotoutside 0.33424 0.33424 0.00000 0.33424 324
rotinside 0.00000 0.00000 0.00000 0.00000 782
rotall + 0.09792 0.09792 0.00000 0.09792 1106
res 0.36823 0.36823 0.00000 0.36823
====
- The qvector variables are shown.
- 1293 peaks are not used in the calculations.
- The peaksearch program was invoked with very tolerant parameters
and delivered a lot of peaks. We know we have to add more
qvector combinations.
Peakref>
go3
go(1) starting CalcRes: res=0.36823
Refining 2 parameters: 18 evaluations in 9 iterations. residue 0.31737 ====
go(2)
Refining 2 parameters: 6 evaluations in 3 iterations. residue 0.31735 ====
go(3)
Refining 2 parameters: no evaluations in no iterations. residue 0.31735
starting 0.36823 bestintermediate 0.31735 final 0.31735 diff -0.05088 relative -0.16033 status 1
final residue is best.
One matrix. 2399 reflections. (forbidden index:2 mm:777 rot:1070 total:1293)
Used: 1106 mm 1106 rot
ref current initial change accumulate shift refl
==================================================================
a No 3.87986 3.87986 3.87986 0.00776 1106
b No 3.87986 3.87986 3.87986 0.00776 1106
c No 16.12633 16.12633 16.12633 0.03225 1106
alpha No 90.00005 90.00005 90.00005 0.20000 1106
beta No 89.99998 89.99998 89.99998 0.20000 1106
gamma No 120.00001 120.00001 120.00001 0.20000 1106
orx No 0.11510 0.11510 0.11510 0.00198 1106
ory No -0.06923 -0.06923 -0.06923 0.00198 1106
ora No -92.74460 -92.74460 -92.74460 0.20000 1106
xtalx No 0.00000 0.00000 0.00000 0.10000 1106
xtaly No 0.00000 0.00000 0.00000 0.10000 1106
xtalz No 0.00000 0.00000 0.00000 0.10000 1106
zerodist No 0.00000 0.00000 0.00000 0.10000 1106
zerohor Yes 0.09457 0.00000 0.09457 0.60657 0.10000 1106
zerover Yes 0.02311 0.00000 0.02311 -0.77899 0.10000 1106
detrotx No 0.00000 0.00000 -0.10280 0.20000 1106
detroty No 0.00000 0.00000 0.09980 0.20000 1106
detrotz No 0.00000 0.00000 0.06290 0.20000 1106
qvx1 No 0.30000 0.30000 0.30000 0.01000 290
qvy1 No -0.10000 -0.10000 -0.10000 0.01000 290
qvz1 No 0.00000 0.00000 0.00000 0.01000 290
qvx2 No 0.30000 0.30000 0.30000 0.01000 282
qvy2 No -0.20000 -0.20000 -0.20000 0.01000 282
qvz2 No 0.00000 0.00000 0.00000 0.01000 282
qvx3 No -0.10000 -0.10000 -0.10000 0.01000 271
qvy3 No 0.30000 0.30000 0.30000 0.01000 271
qvz3 No 0.00000 0.00000 0.00000 0.01000 271
qvx4 No -0.20000 -0.20000 -0.20000 0.01000 312
qvy4 No 0.30000 0.30000 0.30000 0.01000 312
qvz4 No 0.00000 0.00000 0.00000 0.01000 312
==================================================================
Vol 210.23 210.23 0.00 210.23 1106
==================================================================
mm 0.14875 0.17963 -0.03088 0.14875 1106
mmAng + 0.21944 0.27032 -0.05088 0.21944 1106
rotoutside 0.33424 0.33424 0.00000 0.33424 324
rotinside 0.00000 0.00000 0.00000 0.00000 782
rotall + 0.09792 0.09792 0.00000 0.09792 1106
res 0.31735 0.36823 -0.05088 0.31735
Peakref>
free rmat
Peakref>
go3
go(1) starting CalcRes: res=0.31735
Refining 11 parameters: 92 evaluations in 55 iterations. residue 0.31651 ====
go(2)
Refining 11 parameters: 42 evaluations in 25 iterations. residue 0.31652
go(3)
Refining 11 parameters: 5 evaluations in 3 iterations. residue 0.31646 ====
starting 0.31735 bestintermediate 0.31646 final 0.31646 diff -0.00089 relative -0.0028 status 3
final residue is best.
One matrix. 2399 reflections. (forbidden index:2 mm:777 rot:1070 total:1293)
Used: 1106 mm 1106 rot
ref current initial change accumulate shift refl
==================================================================
a Yes 3.87870 3.87986 -0.00116 3.87870 0.00776 1106
b Yes 3.87920 3.87986 -0.00066 3.87920 0.00776 1106
c Yes 16.12652 16.12633 0.00019 16.12652 0.03225 1106
alpha Yes 90.00749 90.00005 0.00744 90.00749 0.20000 1106
beta Yes 89.97677 89.99998 -0.02322 89.97677 0.20000 1106
gamma Yes 120.02465 120.00001 0.02464 120.02465 0.20000 1106
orx Yes 0.11525 0.11510 0.00015 0.11525 0.00198 1106
ory Yes -0.06902 -0.06923 0.00020 -0.06902 0.00198 1106
ora Yes -92.73322 -92.74460 0.01139 -92.73322 0.20000 1106
xtalx No 0.00000 0.00000 0.00000 0.10000 1106
xtaly No 0.00000 0.00000 0.00000 0.10000 1106
xtalz No 0.00000 0.00000 0.00000 0.10000 1106
zerodist No 0.00000 0.00000 0.00000 0.10000 1106
zerohor Yes 0.08564 0.00000 0.08564 0.59764 0.10000 1106
zerover Yes 0.02215 0.00000 0.02215 -0.77995 0.10000 1106
detrotx No 0.00000 0.00000 -0.10280 0.20000 1106
detroty No 0.00000 0.00000 0.09980 0.20000 1106
detrotz No 0.00000 0.00000 0.06290 0.20000 1106
qvx1 No 0.30000 0.30000 0.30000 0.01000 290
qvy1 No -0.10000 -0.10000 -0.10000 0.01000 290
qvz1 No 0.00000 0.00000 0.00000 0.01000 290
qvx2 No 0.30000 0.30000 0.30000 0.01000 282
qvy2 No -0.20000 -0.20000 -0.20000 0.01000 282
qvz2 No 0.00000 0.00000 0.00000 0.01000 282
qvx3 No -0.10000 -0.10000 -0.10000 0.01000 271
qvy3 No 0.30000 0.30000 0.30000 0.01000 271
qvz3 No 0.00000 0.00000 0.00000 0.01000 271
qvx4 No -0.20000 -0.20000 -0.20000 0.01000 312
qvy4 No 0.30000 0.30000 0.30000 0.01000 312
qvz4 No 0.00000 0.00000 0.00000 0.01000 312
==================================================================
Vol 210.08 210.23 -0.15 210.08 1106
==================================================================
mm 0.14838 0.17963 -0.03125 0.14838 1106
mmAng + 0.21922 0.27032 -0.05110 0.21922 1106
rotoutside 0.33717 0.33424 0.00293 0.33717 319
rotinside 0.00000 0.00000 0.00000 0.00000 787
rotall + 0.09725 0.09792 -0.00067 0.09725 1106
res 0.31646 0.36823 -0.05177 0.31646
Now release the qvector variables.
Peakref>
free qvx* qvy*
Peakref>
go3
go(1) starting CalcRes: res=0.31646
Refining 19 parameters: 297 evaluations in 206 iterations. residue 0.23266 ====
go(2)
Refining 19 parameters: 106 evaluations in 65 iterations. residue 0.23253 ====
go(3)
Refining 19 parameters: 16 evaluations in 9 iterations. residue 0.23258
starting 0.31646 bestintermediate 0.23253 final 0.23258 diff -0.08393 relative -0.36096 status 2
intermediate residue is best.
One matrix. 2399 reflections. (forbidden index:2 mm:777 rot:1070 total:1293)
Used: 1106 mm 1106 rot
ref current initial change accumulate shift refl
==================================================================
a Yes 3.88080 3.87986 0.00094 3.88080 0.00776 1106
b Yes 3.87954 3.87986 -0.00032 3.87954 0.00776 1106
c Yes 16.12758 16.12633 0.00126 16.12758 0.03225 1106
alpha Yes 89.98964 90.00005 -0.01042 89.98964 0.20000 1106
beta Yes 89.98232 89.99998 -0.01767 89.98232 0.20000 1106
gamma Yes 119.99731 120.00001 -0.00270 119.99731 0.20000 1106
orx Yes 0.11517 0.11510 0.00006 0.11517 0.00198 1106
ory Yes -0.06893 -0.06923 0.00030 -0.06893 0.00198 1106
ora Yes -92.73539 -92.74460 0.00921 -92.73539 0.20000 1106
xtalx No 0.00000 0.00000 0.00000 0.10000 1106
xtaly No 0.00000 0.00000 0.00000 0.10000 1106
xtalz No 0.00000 0.00000 0.00000 0.10000 1106
zerodist No 0.00000 0.00000 0.00000 0.10000 1106
zerohor Yes 0.08799 0.00000 0.08799 0.59999 0.10000 1106
zerover Yes 0.02001 0.00000 0.02001 -0.78209 0.10000 1106
detrotx No 0.00000 0.00000 -0.10280 0.20000 1106
detroty No 0.00000 0.00000 0.09980 0.20000 1106
detrotz No 0.00000 0.00000 0.06290 0.20000 1106
qvx1 Yes 0.30096 0.30000 0.00096 0.30096 0.01000 290
qvy1 Yes -0.11441 -0.10000 -0.01441 -0.11441 0.01000 290
qvz1 No 0.00000 0.00000 0.00000 0.01000 290
qvx2 Yes 0.30349 0.30000 0.00349 0.30349 0.01000 282
qvy2 Yes -0.18593 -0.20000 0.01407 -0.18593 0.01000 282
qvz2 No 0.00000 0.00000 0.00000 0.01000 282
qvx3 Yes -0.11422 -0.10000 -0.01422 -0.11422 0.01000 271
qvy3 Yes 0.29957 0.30000 -0.00043 0.29957 0.01000 271
qvz3 No 0.00000 0.00000 0.00000 0.01000 271
qvx4 Yes -0.18767 -0.20000 0.01233 -0.18767 0.01000 312
qvy4 Yes 0.30436 0.30000 0.00436 0.30436 0.01000 312
qvz4 No 0.00000 0.00000 0.00000 0.01000 312
==================================================================
Vol 210.29 210.23 0.06 210.29 1106
==================================================================
mm 0.11509 0.17963 -0.06454 0.11509 1106
mmAng + 0.17026 0.27032 -0.10006 0.17026 1106
rotoutside 0.41242 0.33424 0.07818 0.41242 167
rotinside 0.00000 0.00000 0.00000 0.00000 939
rotall + 0.06227 0.09792 -0.03564 0.06227 1106
res 0.23253 0.36823 -0.13570 0.23253
The qvector variables are refined independently.
The final values suggest a possible relation between the numbers.
- qvx1 = qvx2 = qvy3 = qvy4 = 0.3
- qvx3 = qvy1 = -0.11
- qvx4 = qvy2 = -0.19
- 0.3 = 0.11 + 0.19
Let's define these constraints using free variables.
- fvar1 will be set to -0.10
- fvar2 will be set to -0.20
- fvar3 will be constrained to -fvar1-fvar2
Peakref>
set fvar1 -0.1
Peakref>
set fvar2 -0.2
Peakref>
shift fvar1 0.01
Peakref>
shift fvar2 0.01
Peakref>
constraint fvar3 -[fvar1]-[fvar2]
Note the use of the square brackets.
Now the relations between the qvector variables and these free variables:
Peakref>
constraint qvx1 [fvar3]
Peakref>
constraint qvy1 [fvar1]
Peakref>
constraint qvx2 [fvar3]
Peakref>
constraint qvy2 [fvar2]
Peakref>
constraint qvx3 [fvar1]
Peakref>
constraint qvy3 [fvar3]
Peakref>
constraint qvx4 [fvar2]
Peakref>
constraint qvy4 [fvar3]
Peakref>
status
One matrix. 2399 reflections. (forbidden index:2 mm:777 rot:1070 total:1293)
Used: 1106 mm 1106 rot
ref current initial change accumulate shift refl
==================================================================
a Yes 3.88080 3.87986 0.00094 3.88080 0.00776 1106
b Yes 3.87954 3.87986 -0.00032 3.87954 0.00776 1106
c Yes 16.12758 16.12633 0.00126 16.12758 0.03225 1106
alpha Yes 89.98964 90.00005 -0.01042 89.98964 0.20000 1106
beta Yes 89.98232 89.99998 -0.01767 89.98232 0.20000 1106
gamma Yes 119.99731 120.00001 -0.00270 119.99731 0.20000 1106
orx Yes 0.11517 0.11510 0.00006 0.11517 0.00198 1106
ory Yes -0.06893 -0.06923 0.00030 -0.06893 0.00198 1106
ora Yes -92.73539 -92.74460 0.00921 -92.73539 0.20000 1106
xtalx No 0.00000 0.00000 0.00000 0.10000 1106
xtaly No 0.00000 0.00000 0.00000 0.10000 1106
xtalz No 0.00000 0.00000 0.00000 0.10000 1106
zerodist No 0.00000 0.00000 0.00000 0.10000 1106
zerohor Yes 0.08799 0.00000 0.08799 0.59999 0.10000 1106
zerover Yes 0.02001 0.00000 0.02001 -0.78209 0.10000 1106
detrotx No 0.00000 0.00000 -0.10280 0.20000 1106
detroty No 0.00000 0.00000 0.09980 0.20000 1106
detrotz No 0.00000 0.00000 0.06290 0.20000 1106
fvar1 No -0.10000 0.00000 -0.10000 0.01000 1106
fvar2 No -0.20000 0.00000 -0.20000 0.01000 1106
fvar3 Con 0.30000 0.00000 0.30000 0.10000 1106
qvx1 Con 0.30000 0.30000 0.30000 0.01000 290
qvy1 Con -0.10000 -0.10000 -0.10000 0.01000 290
qvz1 No 0.00000 0.00000 0.00000 0.01000 290
qvx2 Con 0.30000 0.30000 0.30000 0.01000 282
qvy2 Con -0.20000 -0.20000 -0.20000 0.01000 282
qvz2 No 0.00000 0.00000 0.00000 0.01000 282
qvx3 Con -0.10000 -0.10000 -0.10000 0.01000 271
qvy3 Con 0.30000 0.30000 0.30000 0.01000 271
qvz3 No 0.00000 0.00000 0.00000 0.01000 271
qvx4 Con -0.20000 -0.20000 -0.20000 0.01000 312
qvy4 Con 0.30000 0.30000 0.30000 0.01000 312
qvz4 No 0.00000 0.00000 0.00000 0.01000 312
==================================================================
Vol 210.29 210.23 0.06 210.29 1106
==================================================================
mm 0.14916 0.17963 -0.03047 0.14916 1106
mmAng + 0.22003 0.27032 -0.05029 0.22003 1106
rotoutside 0.33407 0.33424 -0.00017 0.33407 323
rotinside 0.00000 0.00000 0.00000 0.00000 783
rotall + 0.09756 0.09792 -0.00035 0.09756 1106
res 0.31759 0.36823 -0.05064 0.31759
fvar3 depends on fvar1 and fvar2. Every time fvar1 and or fvar2 change,
fvar3 will be re-evaluated. And every time the free variables
fvar1, fvar2 and/or fvar3 change, the constraint variables
qvx1, qvy1, qvx2, qvy2, qvx3, qvy3, qvx4 and qvy4 will be updated.
Let's examine all constraints
Peakref>
list constraint
fvar3 constrained to -[fvar1]-[fvar2]
qvx1 constrained to [fvar3]
qvy1 constrained to [fvar1]
qvx2 constrained to [fvar3]
qvy2 constrained to [fvar2]
qvx3 constrained to [fvar1]
qvy3 constrained to [fvar3]
qvx4 constrained to [fvar2]
qvy4 constrained to [fvar3]
9 constraints
First refine detector and rmat to accomodate to these
new (not refined) qvectors.
Peakref>
go3
go(1) starting CalcRes: res=0.31759
Refining 11 parameters: 85 evaluations in 47 iterations. residue 0.31667
go(2)
Refining 11 parameters: 53 evaluations in 31 iterations. residue 0.31656
go(3)
Refining 11 parameters: 6 evaluations in 3 iterations. residue 0.31649
starting 0.31759 bestintermediate 0.31649 final 0.31649 diff -0.0011 relative -0.00349 status 3
final residue is best.
One matrix. 2399 reflections. (forbidden index:2 mm:777 rot:1070 total:1293)
Used: 1106 mm 1106 rot
ref current initial change accumulate shift refl
==================================================================
a Yes 3.87890 3.87986 -0.00097 3.87890 0.00776 1106
b Yes 3.87919 3.87986 -0.00067 3.87919 0.00776 1106
c Yes 16.12687 16.12633 0.00054 16.12687 0.03225 1106
alpha Yes 90.00150 90.00005 0.00145 90.00150 0.20000 1106
beta Yes 89.96806 89.99998 -0.03192 89.96806 0.20000 1106
gamma Yes 120.02273 120.00001 0.02272 120.02273 0.20000 1106
orx Yes 0.11528 0.11510 0.00017 0.11528 0.00198 1106
ory Yes -0.06896 -0.06923 0.00027 -0.06896 0.00198 1106
ora Yes -92.72638 -92.74460 0.01822 -92.72638 0.20000 1106
xtalx No 0.00000 0.00000 0.00000 0.10000 1106
xtaly No 0.00000 0.00000 0.00000 0.10000 1106
xtalz No 0.00000 0.00000 0.00000 0.10000 1106
zerodist No 0.00000 0.00000 0.00000 0.10000 1106
zerohor Yes 0.08786 0.00000 0.08786 0.59986 0.10000 1106
zerover Yes 0.01873 0.00000 0.01873 -0.78337 0.10000 1106
detrotx No 0.00000 0.00000 -0.10280 0.20000 1106
detroty No 0.00000 0.00000 0.09980 0.20000 1106
detrotz No 0.00000 0.00000 0.06290 0.20000 1106
fvar1 No -0.10000 0.00000 -0.10000 0.01000 1106
fvar2 No -0.20000 0.00000 -0.20000 0.01000 1106
fvar3 Con 0.30000 0.00000 0.30000 0.10000 1106
qvx1 Con 0.30000 0.30000 0.30000 0.01000 290
qvy1 Con -0.10000 -0.10000 -0.10000 0.01000 290
qvz1 No 0.00000 0.00000 0.00000 0.01000 290
qvx2 Con 0.30000 0.30000 0.30000 0.01000 282
qvy2 Con -0.20000 -0.20000 -0.20000 0.01000 282
qvz2 No 0.00000 0.00000 0.00000 0.01000 282
qvx3 Con -0.10000 -0.10000 -0.10000 0.01000 271
qvy3 Con 0.30000 0.30000 0.30000 0.01000 271
qvz3 No 0.00000 0.00000 0.00000 0.01000 271
qvx4 Con -0.20000 -0.20000 -0.20000 0.01000 312
qvy4 Con 0.30000 0.30000 0.30000 0.01000 312
qvz4 No 0.00000 0.00000 0.00000 0.01000 312
==================================================================
Vol 210.10 210.23 -0.13 210.10 1106
==================================================================
mm 0.14847 0.17963 -0.03116 0.14847 1106
mmAng + 0.21928 0.27032 -0.05104 0.21928 1106
rotoutside 0.33917 0.33424 0.00493 0.33917 317
rotinside 0.00000 0.00000 0.00000 0.00000 789
rotall + 0.09721 0.09792 -0.00070 0.09721 1106
res 0.31649 0.36823 -0.05174 0.31649
And now release the 2 free variables.
Peakref>
free fvar1 fvar2
Peakref>
go3
go(1) starting CalcRes: res=0.31649
Refining 13 parameters: 194 evaluations in 124 iterations. residue 0.23466
go(2)
Refining 13 parameters: 74 evaluations in 43 iterations. residue 0.23453
go(3)
Refining 13 parameters: 25 evaluations in 14 iterations. residue 0.23448
starting 0.31649 bestintermediate 0.23448 final 0.23448 diff -0.08201 relative -0.34974 status 1
final residue is best.
One matrix. 2399 reflections. (forbidden index:2 mm:777 rot:1070 total:1293)
Used: 1106 mm 1106 rot
ref current initial change accumulate shift refl
==================================================================
a Yes 3.88088 3.87986 0.00102 3.88088 0.00776 1106
b Yes 3.87946 3.87986 -0.00040 3.87946 0.00776 1106
c Yes 16.12747 16.12633 0.00114 16.12747 0.03225 1106
alpha Yes 89.95480 90.00005 -0.04525 89.95480 0.20000 1106
beta Yes 90.02059 89.99998 0.02061 90.02059 0.20000 1106
gamma Yes 119.99596 120.00001 -0.00406 119.99596 0.20000 1106
orx Yes 0.11499 0.11510 -0.00011 0.11499 0.00198 1106
ory Yes -0.06899 -0.06923 0.00023 -0.06899 0.00198 1106
ora Yes -92.74393 -92.74460 0.00066 -92.74393 0.20000 1106
xtalx No 0.00000 0.00000 0.00000 0.10000 1106
xtaly No 0.00000 0.00000 0.00000 0.10000 1106
xtalz No 0.00000 0.00000 0.00000 0.10000 1106
zerodist No 0.00000 0.00000 0.00000 0.10000 1106
zerohor Yes 0.09047 0.00000 0.09047 0.60247 0.10000 1106
zerover Yes 0.02139 0.00000 0.02139 -0.78071 0.10000 1106
detrotx No 0.00000 0.00000 -0.10280 0.20000 1106
detroty No 0.00000 0.00000 0.09980 0.20000 1106
detrotz No 0.00000 0.00000 0.06290 0.20000 1106
fvar1 Yes -0.11522 0.00000 -0.11522 -0.11522 0.01000 1106
fvar2 Yes -0.18756 0.00000 -0.18756 -0.18756 0.01000 1106
fvar3 Con 0.30278 0.00000 0.30278 0.10000 1106
qvx1 Con 0.30278 0.30000 0.30278 0.01000 290
qvy1 Con -0.11522 -0.10000 -0.11522 0.01000 290
qvz1 No 0.00000 0.00000 0.00000 0.01000 290
qvx2 Con 0.30278 0.30000 0.30278 0.01000 282
qvy2 Con -0.18756 -0.20000 -0.18756 0.01000 282
qvz2 No 0.00000 0.00000 0.00000 0.01000 282
qvx3 Con -0.11522 -0.10000 -0.11522 0.01000 271
qvy3 Con 0.30278 0.30000 0.30278 0.01000 271
qvz3 No 0.00000 0.00000 0.00000 0.01000 271
qvx4 Con -0.18756 -0.20000 -0.18756 0.01000 312
qvy4 Con 0.30278 0.30000 0.30278 0.01000 312
qvz4 No 0.00000 0.00000 0.00000 0.01000 312
==================================================================
Vol 210.29 210.23 0.06 210.29 1106
==================================================================
mm 0.11535 0.17963 -0.06428 0.11535 1106
mmAng + 0.17081 0.27032 -0.09951 0.17081 1106
rotoutside 0.46027 0.33424 0.12603 0.46027 153
rotinside 0.00000 0.00000 0.00000 0.00000 953
rotall + 0.06367 0.09792 -0.03424 0.06367 1106
res 0.23448 0.36823 -0.13375 0.23448
show the cell results
Peakref>
list rmat
independent matrix 1
RMAT 1 example4
RMAT DMAT
0.1372270 0.2920920 0.0116771 -0.1320145 -3.8736854 0.1959534
-0.2635745 -0.0127728 0.0026796 3.3637283 1.7918119 -0.7245525
-0.0147425 -0.0557148 0.0608376 3.0484982 0.7022412 15.8211489
Determinant: 0.4755359E-02 210.2891
cell from rmat: 3.88088 3.87946 16.12747 89.9548 90.0206 119.9960 V= 210.29
pg constrained: 3.88017 3.88017 16.12747 90.0000 90.0000 120.0000 V= 210.28
Bravais=P pg=-3
Qvectype=2 MODULATED
ActiveQvecRadius=0.36056
QVEC dh dk dl Order
1 0.3028 -0.1152 0.0000 1
2 0.3028 -0.1876 0.0000 1
3 -0.1152 0.3028 0.0000 1
4 -0.1876 0.3028 0.0000 1
13 explicit QV Combinations
Peakref>
exit
peakref ended at 10-Nov-2016 18:19:07 CPU time used 00:00:11
10-Nov-2016 18:19:07