Ticket #9200 (closed: fixed)

Opened 7 years ago

Last modified 5 years ago

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

S327T100K_transfomred_to_Orthorhombic_C.integrate​ (1.7 MB) - added by Vickie Lynch 7 years ago.

Change History

comment:1 Changed 7 years ago by Martyn Gigg

  • Status changed from new to assigned

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

Last edited 7 years ago by Vickie Lynch (previous) (diff)

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

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

Last edited 7 years ago by Vickie Lynch (previous) (diff)

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

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