Ticket #9200 (closed: fixed)
Problem with ShowPossibleCells and SelectCellOfType
Reported by: | Vickie Lynch | Owned by: | Vickie Lynch |
---|---|---|---|
Priority: | major | Milestone: | Release 3.2 |
Component: | Framework | Keywords: | |
Cc: | saviciat@…, petersonpf@… | Blocked By: | |
Blocking: | Tester: | Peter Peterson |
Description
There is a problem with unit cell transform from Niggli to Orthorhombic C centered cell.
The Orthorhombic cells obtained ShowPossibleCells and SelectCellOfType are not correct for the user data in TOPAZ IPTS-10509. The niggli cell was transformed incorrectly to a 5 x 5 x 20 “Orthorhombic C centered cell” when use SelectCellOfType or using Form number 36 and 40.
The correct transformation matrix from Niggli to Orthorhombic C should be '0,1,0,0,1,2,1,0,0'. Attached please find the python script used for testing. It gives the C-centered Orthorhombic cell 5 x 20 x 5.
The data can be found in /SNS/TOPAZ/IPTS-10509/shared/T100K/20140317/
Attachments
Change History
comment:2 Changed 7 years ago by Vickie Lynch
- Status changed from assigned to inprogress
Refs #9200 check if system tests break without this call
Changeset: d5fa5a256bc35bbd0f8b76c444633c0236d5804c
comment:3 Changed 7 years ago by Vickie Lynch
Refs #9200 use exact transformations for each cell form number
Changeset: 09a772edcb23f264c9f62f5bfe7200a7b96ef290
comment:4 Changed 7 years ago by Vickie Lynch
To test make sure lattice parameters for TransformHKL match Form 40 only:
# Transform Niggli to Orthorhombic C LoadIsawPeaks(Filename='S327T100K_Niggli.integrate',OutputWorkspace='T100K.peaks') FindUBUsingIndexedPeaks(PeaksWorkspace='T100K.peaks',Tolerance='0.12') TransformHKL(PeaksWorkspace='T100K.peaks',Tolerance='0.12',HKLTransform='0,-1,0,0,1,2,-1,0,0') LoadIsawPeaks(Filename='/home/vel/workspace/S327T100K_Niggli.integrate',OutputWorkspace='T100K.peaks2') FindUBUsingIndexedPeaks(PeaksWorkspace='T100K.peaks2',Tolerance='0.12') ShowPossibleCells(PeaksWorkspace='T100K.peaks2',MaxScalarError=10)
Changed 7 years ago by Vickie Lynch
- Attachment S327T100K_transfomred_to_Orthorhombic_C.integrate added
comment:5 Changed 7 years ago by Vickie Lynch
Refs #9200 fix ScalarUtils test
Changeset: cb381c377dc12cd9f00be65cd4bfe4463729bf5f
comment:6 Changed 7 years ago by Vickie Lynch
- Cc saviciat@…, petersonpf@… added
- Status changed from inprogress to verify
- Resolution set to fixed
Prefer that Pete Peterson or Andrei Savici test since they know crystallography and will know if these requested changes are needed.
comment:7 Changed 7 years ago by Vickie Lynch
- Status changed from verify to reopened
- Resolution fixed deleted
Maybe both options should be available with default of exact transformation
comment:8 Changed 7 years ago by Vickie Lynch
- Status changed from reopened to inprogress
Refs #9200 option for permutations of conventional cells
Changeset: 9216c8b09fa23bf259edacdf58913c48a70858c3
comment:9 Changed 7 years ago by Vickie Lynch
- Status changed from inprogress to verify
- Resolution set to fixed
comment:10 Changed 7 years ago by Martyn Gigg
- Status changed from verify to reopened
- Resolution fixed deleted
It looks like there is a compiler warning on RHEL6 in ScalarUtils about an unused parameter.
comment:11 Changed 7 years ago by Vickie Lynch
Refs #9200 fix compiler warning Changeset inserted manually: 4e762357ec0dbefb8334efa012bb8a6ff4b70c77
comment:12 Changed 7 years ago by Vickie Lynch
- Status changed from reopened to verify
- Resolution set to fixed
comment:13 Changed 7 years ago by Martyn Gigg
- Status changed from verify to reopened
- Resolution fixed deleted
Sorry to be the bearer of bad news again but there are some cppcheck warnings in ScalarUtils.
comment:14 Changed 7 years ago by Vickie Lynch
- Status changed from reopened to inprogress
Refs #9200 remove cppcheck warnings
Changeset: aceffe80596c82d9243d9645182aa3a79e81dc4a
comment:15 Changed 7 years ago by Vickie Lynch
- Status changed from inprogress to verify
- Resolution set to fixed
comment:16 Changed 7 years ago by Peter Peterson
- Status changed from verify to verifying
- Tester set to Peter Peterson
comment:17 Changed 7 years ago by Peter Peterson
- Status changed from verifying to closed
Merge remote branch 'origin/feature/9200_cell_type_wrong'
Full changeset: 83bc4d5c3ee90cde118018712460d0a0383881de
comment:18 Changed 5 years ago by Stuart Campbell
This ticket has been transferred to github issue 10043