Ticket #5146 (closed: fixed)

Opened 8 years ago

Last modified 5 years ago

Algorithm to read Sassena output

Reported by: Jose Borreguero Owned by: Jose Borreguero
Priority: major Milestone: Release 2.4
Component: Mantid Keywords:
Cc: Blocked By: #5401
Blocking: Tester: Andrei Savici

Description

Sassena (​http://www.sassena.org/) calculates neutron and xray scattering intensities from all-atomic molecular dynamics simulations. Output files HDF5 format

Attachments

fqt_Q44_T90.h5​ (1.3 MB) - added by Jose Borreguero 8 years ago.
Incoherent intermediate structure factor for an MD simulation of concentrated LiCl in water

Change History

comment:1 Changed 8 years ago by Jose Borreguero

  • Status changed from new to accepted

comment:2 Changed 8 years ago by Jose Borreguero

Refs #5146 Initial header file

LoadSassena class derived from IDataFileChecker

Changeset: b615ccaef5decb6a756994d2d91a2d7db596d2e7

comment:3 Changed 8 years ago by Jose Borreguero

Refs #5146 Initial header file

LoadSassena class derived from IDataFileChecker

Changeset: b615ccaef5decb6a756994d2d91a2d7db596d2e7

comment:4 Changed 8 years ago by Jose Borreguero

Refs #5146 initial source file

Changeset: 9ddb15feb9c17291fba84f0c082b677c3a1208ab

comment:5 Changed 8 years ago by Jose Borreguero

Refs #5146 started exec() method

Changeset: da93be58cffd9896b01845d70302c3b62024d4b7

comment:6 Changed 8 years ago by Jose Borreguero

Refs #5146 Writing filechecks

Changeset: 542a4de059b0f0f98cd46ec1fc76fcca6411c917

comment:7 Changed 8 years ago by Jose Borreguero

Refs #5146 Wrote fileCheck method

Changeset: bfbf58da5c00fb45d08f7b27514655003c2c7e4a

comment:8 Changed 8 years ago by Jose Borreguero

Refs #5146 Begin test unit file

modified: LoadSassena.h modified: LoadSassena.cpp new file: LoadSassenaTest.h new file: AutoTestData/outputSassena_1.4.1.h5 Changeset: 08dcae6038886b66689c072999fc029b16accf59

comment:9 Changed 8 years ago by Jose Borreguero

Refs #5146 Remove private field GWS

modified: LoadSassena.h modified: LoadSassena.cpp Changeset: 95162cb51155d3dd7e24c8a8b62e2f87043dffea

comment:10 Changed 8 years ago by Jose Borreguero

Refs #5146 first version of exec method

modified: CMakeLists.txt modified: inc/MantidDataHandling/LoadSassena.h modified: src/LoadSassena.cpp

Changeset: 1a95cbe9ed366067453ea0ea2fb37d9793fc863f

comment:11 Changed 8 years ago by Jose Borreguero

Refs #5146 comment lines in CMakeList.txt

lines commented until HDF5 libraries properly installed modified: CMakeLists.txt

Changeset: 18b751471e6524ca13f7359cf47b290cc4d6fe24

comment:12 Changed 8 years ago by Jose Borreguero

Refs #5146 registerWorkspace method

modified: ../Mantid/Framework/DataHandling/src/LoadSassena.cpp

Changeset: 572c6b95e2b7e78c16e3233a34c62f68c075f47f

comment:13 Changed 8 years ago by Jose Borreguero

Refs #5146 Refactor code into a few new methods

modified: ../Framework/DataHandling/inc/MantidDataHandling/LoadSassena.h modified: ../Framework/DataHandling/src/LoadSassena.cpp

Changeset: 639561c662ad5acddef411ea3e88e40d442f4693

comment:14 Changed 8 years ago by Jose Borreguero

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

comment:15 Changed 8 years ago by Stuart Campbell

Ticket #5401 will deal with the CMake / HDF5 config that is needed to compile this algorithm

comment:16 Changed 8 years ago by Jose Borreguero

Refs #5146 registerWorkspace method

modified: ../Mantid/Framework/DataHandling/src/LoadSassena.cpp

Changeset: 572c6b95e2b7e78c16e3233a34c62f68c075f47f

comment:17 Changed 8 years ago by Jose Borreguero

Refs #5146 Refactor code into a few new methods

modified: ../Framework/DataHandling/inc/MantidDataHandling/LoadSassena.h modified: ../Framework/DataHandling/src/LoadSassena.cpp

Changeset: 639561c662ad5acddef411ea3e88e40d442f4693

comment:18 Changed 8 years ago by Jose Borreguero

Refs #5146 registerWorkspace method

modified: ../Mantid/Framework/DataHandling/src/LoadSassena.cpp

Changeset: 572c6b95e2b7e78c16e3233a34c62f68c075f47f

comment:19 Changed 8 years ago by Jose Borreguero

Refs #5146 Refactor code into a few new methods

modified: ../Framework/DataHandling/inc/MantidDataHandling/LoadSassena.h modified: ../Framework/DataHandling/src/LoadSassena.cpp

Changeset: 639561c662ad5acddef411ea3e88e40d442f4693

comment:20 Changed 8 years ago by Wenduo Zhou

  • Status changed from verify to verifying
  • Tester set to Wenduo Zhou

comment:21 Changed 8 years ago by Wenduo Zhou

  • Status changed from verifying to verify
  • Tester Wenduo Zhou deleted

comment:22 Changed 8 years ago by Jose Borreguero

  • Milestone changed from Release 2.2 to Release 2.3

comment:23 Changed 8 years ago by Jose Borreguero

  • Status changed from verify to reopened
  • Resolution fixed deleted

comment:24 Changed 8 years ago by Jose Borreguero

  • Milestone changed from Release 2.3 to Release 2.4

comment:25 Changed 8 years ago by Jose Borreguero

Refs #5146 Added time and Q units

modified: SassenaFFT.cpp modified: CurveFitting/CMakeLists.txt modified: LoadSassena.cpp

Changeset: 7c8b8307b077c6b10ce6c1227434e2142ce5ecbf

comment:26 Changed 8 years ago by Jose Borreguero

Refs #5146 Added time and Q units

modified: SassenaFFT.cpp modified: CurveFitting/CMakeLists.txt modified: LoadSassena.cpp

Changeset: 7c8b8307b077c6b10ce6c1227434e2142ce5ecbf

comment:27 Changed 8 years ago by Stuart Campbell

  • Blocked By 5401 added

comment:28 Changed 8 years ago by Stuart Campbell

refs #5401 & #5146. Added LoadSassena to build

Enable LoadSassena and unit test on all platforms.

Changeset: b48c1c458cbc13199ba1b09162da1ba7a1c1751a

comment:29 Changed 8 years ago by Stuart Campbell

refs #5146. Fix bug in fileCheck()

fileCheck() was always returning 99 so it was being for all hdf5 files.

Changeset: f0d7022bd48c716b29a87ebd05cbd23f9cca796f

comment:30 Changed 8 years ago by Russell Taylor

Re #5146. Be sure to close the file at the end of fileCheck().

Not doing so broke ADARA event nexus file loading (which also have a .h5 extension. Also downgraded a log message to debug.

Changeset: 791e3f29f4db774b5526b145ffa6f84f3bc01c1d

comment:31 Changed 8 years ago by Jose Borreguero

Refs #5146 Close HDF5 file at end of exec method

modified: DataHandling/src/LoadSassena.cpp

Changeset: 0788eae489054069c71424a1b041c3e1a9c7b9ff

comment:32 Changed 8 years ago by Stuart Campbell

refs #5401 & #5146. Added LoadSassena to build

Enable LoadSassena and unit test on all platforms.

Changeset: 1c85837192eace78f2fb0923a0319224ba2439f8

comment:33 Changed 8 years ago by Stuart Campbell

refs #5146. Fix bug in fileCheck()

fileCheck() was always returning 99 so it was being for all hdf5 files.

Changeset: 7db05f174efa16d6482092a1e8db54ef55a84d3e

comment:34 Changed 8 years ago by Russell Taylor

Re #5146. Be sure to close the file at the end of fileCheck().

Not doing so broke ADARA event nexus file loading (which also have a .h5 extension. Also downgraded a log message to debug.

Changeset: fc5956eab7256b0fbb9ade6de44985b9af9c6d6f

comment:35 Changed 8 years ago by Jose Borreguero

Refs #5146 Close HDF5 file at end of exec method

modified: DataHandling/src/LoadSassena.cpp

Changeset: a7de18c9d7f912c746faf50895486d7465d844df

comment:36 Changed 8 years ago by Jose Borreguero

Refs #5146 Throwing exception if Sassena version not found

modified: LoadSassena.cpp

Changeset: aacd025babf561f139922f1943f4da2017cba82b

comment:37 Changed 8 years ago by Jose Borreguero

Refs #5146 Change message to error

modified: LoadSassena.cpp

Changeset: 95d6f6264546b63147c2597f2762f9ac5ae45fd2

Changed 8 years ago by Jose Borreguero

Incoherent intermediate structure factor for an MD simulation of concentrated LiCl in water

comment:38 Changed 8 years ago by Jose Borreguero

  • Status changed from reopened to accepted

comment:39 Changed 8 years ago by Jose Borreguero

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

For the tester: See if you can load the attached file (fqt_Q44_T90.h5). It should produce a group workspace with the following workspace members: _qvectors _fq _fq0 _fq2 _fqt.Re (the real part of the dynamic intermediate structure factor) _fqt.Im (the imaginary part of the dynamic intermediate structure factor)

comment:40 Changed 8 years ago by Jose Borreguero

Refs #5146 Throwing exception if Sassena version not found

modified: LoadSassena.cpp

Changeset: df8d1c0a97fc17c1c1b6723f1b6b41ed2d967433

comment:41 Changed 8 years ago by Jose Borreguero

Refs #5146 Change message to error

modified: LoadSassena.cpp

Changeset: 2f539f969eec17a2eb84c6edf84f4976014593f1

comment:42 Changed 8 years ago by Andrei Savici

  • Status changed from verify to verifying
  • Tester set to Andrei Savici

comment:43 Changed 8 years ago by Andrei Savici

  • Status changed from verifying to closed

Kind of works. Load Sassena is OK. When trying to run just Load, it loads all the workspaces, it does not create a group and complains 

Error storing output workspace in AnalysisDataService
Error in execution of algorithm Load:
WorkspaceProperty doesn't point to a workspace

The ticket for this defect is #6466

comment:44 Changed 5 years ago by Stuart Campbell

This ticket has been transferred to github issue ​5992

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