Ticket #8587 (closed: fixed)

Opened 7 years ago

Last modified 5 years ago

[Indirect] Port DOS script to Mantid

Reported by: Samuel Jackson Owned by: Samuel Jackson
Priority: major Milestone: Release 3.1
Component: Indirect Inelastic Keywords:
Cc: Blocked By:
Blocking: Tester: Roman Tolchenov

Description

Request from Sanghamitra. She has a perl script that reads .phonon and .castep files and calculates the density of states, ir and raman intensities and does some plotting. The aim of this ticket is to bring this loading functionality within Mantid.

Attachments

dos.pl​ (25.5 KB) - added by Samuel Jackson 7 years ago.
Original Perl script
squaricn.castep​ (76.3 KB) - added by Samuel Jackson 7 years ago.
Data file for testing
squaricn.phonon​ (276.4 KB) - added by Samuel Jackson 7 years ago.
Data file for testing
ref.py​ (705 bytes) - added by Samuel Jackson 7 years ago.
python script for testing

Change History

Changed 7 years ago by Samuel Jackson

Original Perl script

Changed 7 years ago by Samuel Jackson

Data file for testing

Changed 7 years ago by Samuel Jackson

Data file for testing

comment:1 Changed 7 years ago by Samuel Jackson

  • Status changed from new to inprogress

Refs #8587 Adding existing work on algorithm.

Changeset: feca0cb55f7e0b4f50940d90ccd780e7f22844da

comment:2 Changed 7 years ago by Samuel Jackson

  • Milestone changed from Backlog to Release 3.1

comment:3 Changed 7 years ago by Samuel Jackson

Refs #8587 Refactored loading functions to be faster with large files.

Changeset: 1ae5eaf7006ac71a0bdbf3eee6fe82677e31e3ba

comment:4 Changed 7 years ago by Samuel Jackson

Refs #8587 Missed numpy array conversion.

Changeset: ab8f4ed3fef4f711257d3276788171729e948aae

comment:5 Changed 7 years ago by Samuel Jackson

Refs #8587 Fixing issues found developing system tests

Changeset: 108febedaca7d9e204ca3b04d827824d52250de9

comment:6 Changed 7 years ago by Samuel Jackson

Refs #8587 Add units tests for DensityOfStates algorithm.

Changeset: ea0612d90b5605542fcb36b9317958c9ff35f488

comment:7 Changed 7 years ago by Samuel Jackson

Refs #8587 Updating reference result.

Changeset: 71e79a0ca7c5b47505a76113e0d2ad1c5b98274b

comment:8 Changed 7 years ago by Samuel Jackson

Refs #8587 Fixing issues with system tests.

Changeset: 45f3c344bc28c4bed885a4f0777e666dd333168b

comment:9 Changed 7 years ago by Samuel Jackson

Refs #8587 Relax tolerance on system test.

Changeset: 5c8ae66a1990bdf4f969b57c9eae7cb2d7afb252

comment:10 Changed 7 years ago by Samuel Jackson

Refs #8587 Refactoring and code tidy.

Changeset: 52636de9b1d6c7242d650e0270a40bd4bc23da5c

comment:11 Changed 7 years ago by Samuel Jackson

Refs #8587 Fix broken bin width option.

Changeset: f0fcc15fb54fb9a10f54a01dcc61d50b3f5a7483

comment:12 Changed 7 years ago by Samuel Jackson

Refs #8587 Wiki adjustment.

Changeset: d3cc730473a8350ac07453984874ac64391fb469

comment:13 Changed 7 years ago by Samuel Jackson

To Tester:

Check that the algorithm (DensityOfStates) runs and produces sensible output. The two examples of input files are provided with this ticket.

I've provided the original pearl script so you can compare output with the existing program. I'm also attaching a python script (ref.py) that can be used to run the perl script and load the output into mantid. You should see that the output of both is comparable.

Finally, check that the system tests are passing and merge both the system tests and main repo into master.

Changed 7 years ago by Samuel Jackson

python script for testing

comment:14 Changed 7 years ago by Samuel Jackson

  • Status changed from inprogress to verify
  • Resolution set to fixed

comment:15 Changed 7 years ago by Samuel Jackson

  • Status changed from verify to reopened
  • Resolution fixed deleted

comment:16 Changed 7 years ago by Samuel Jackson

  • Status changed from reopened to inprogress

Refs #8587 Fix bad logic causing an exception to be incorrectly thrown

Changeset: 5df917e8a975d4a79035d3840a96512fcfaef8c3

comment:17 Changed 7 years ago by Samuel Jackson

Refs #8587 Remove unnecessary exception.

Changeset: 3dffb9e7016c8d8d62041485d3315a11e0a98957

comment:18 Changed 7 years ago by Samuel Jackson

  • Status changed from inprogress to verify
  • Resolution set to fixed

comment:19 Changed 7 years ago by Samuel Jackson

  • Status changed from verify to reopened
  • Resolution fixed deleted

comment:20 Changed 7 years ago by Samuel Jackson

  • Status changed from reopened to inprogress

Refs #8587 Fix support for platform independent new lines.

Changeset: bc37fff1355aa775520dab0cbdc07bc9246ee967

comment:21 Changed 7 years ago by Samuel Jackson

  • Status changed from inprogress to verify
  • Resolution set to fixed

To Tester:

See comment 13. Also check that running a file with both windows and unix line endings works regardless of platform.

comment:22 Changed 7 years ago by Roman Tolchenov

  • Status changed from verify to verifying
  • Tester set to Roman Tolchenov

comment:23 Changed 7 years ago by Roman Tolchenov

  • Status changed from verifying to closed

Merge remote-tracking branch 'origin/feature/8587_DOS_port'

Full changeset: ​87b3a12bcf6e223c9755b18442cbe8f72ecd3471

comment:24 Changed 7 years ago by Roman Tolchenov

Merge remote-tracking branch 'origin/feature/8587_DOS_port'

Full changeset: ​fc679082ee62d3b347f4aaa4cb6abee83a76549d

comment:25 Changed 5 years ago by Stuart Campbell

This ticket has been transferred to github issue ​9431

Note: See TracTickets for help on using tickets.