3.5

SaveZODS v1

../_images/SaveZODS-v1_dlg.png

SaveZODS dialog.

Summary

Save a MDHistoWorkspace in HKL space to a HDF5 format for use with the ZODS analysis software.

Properties

Name Direction Type Default Description
InputWorkspace Input IMDHistoWorkspace Mandatory An input MDHistoWorkspace in HKL space.
Filename Input string Mandatory The name of the HDF5 file to write, as a full or relative path. Allowed extensions: [‘.h5’]

Description

Saves a HDF5 file to the ZODS (Zurich Oak Ridge Disorder Simulation program) format. This format consists of a slice of a MDHistoWorkspace and some information about its location.

You must be in HKL space for the output of this algorithm to make sense!

From http://www.crystal.mat.ethz.ch/research/DiffuseXrayScattering:

  • In the frame of an international cooperation between our group, the University of Zurich and Oak Ridge National Laboratories, we are further developing Monte Carlo simulation techniques for modeling disordered crystal structures. A major goal of this project is to develop the Monte Carlo simulation computer program ZODS (Zurich Oak Ridge Disorder Simulation program), which is designed to be not only user friendly, but also fast and flexible. Special focus is on the efficient use of modern super-computer architectures and of multi-core desktop computers to take full advantage of current trends in computing technologies.

Summary of data format

In general it contains collection of grids with intensities and each grid is described by specifying origin, size of grid (in each direction) and grid base vectors (a1,a2,a3) so a point at node (i,j,k) of grid has coordinates r = origin+i*a1+j*a2+k*a3.

Please contact Michal Chodkiewicz (michal.chodkiewicz@gmail.com); Vickie Lynch (lynchve@ornl.gov) for more details.

Description of data fields

  • The CoordinateSystem data object has the attribute “isLocal”.
    • If isLocal=1, then we are in HKL space:
      • The direction_1 vector (0.04,0,0) represents a step of 0.04 in the (1,0,0) direction (a*) in reciprocal space.
      • This is currently the only mode in which SaveZODS saves.
    • If isLocal=0, then we are in Q-space.
      • The direction_1 vector (0.04,0,0) represents a step of 0.04 Angstrom^(-1) in X direction of Cartesian coordinate system (with X colinear with a and Z with c*)
      • In this case CoordinateSystem has additional attribute UnitCell, which is a vector with 6 components (a,b,c,alpha,beta,gamma) a,b,c in angstroms and angles in degrees.
  • The origin field gives the origin of the center of the (0,0,0) cell; in HKL space for our case of isLocal=1.
  • The size field gives the number of bins in each direction.
  • The data field contains the actual intensity at each bin.
    • The grid of points (r = origin+i*a1+j*a2+k*a3) specifies the centers of histogram, not the corners.

Usage

This algorithm can be run on a pre-existing MDEventWorkspace or a newly created one. The example below will be done with newly created one using CreateMDWorkspace.

SaveZODS HKL MDHisto Example

ws = CreateMDHistoWorkspace(SignalInput='1,2,3,4,5,6,7,8', ErrorInput='1,1,1,1,1,1,1,1',
    Dimensionality='3', Extents='-2, 2, -2, 2, -2, 2', Names=['[H,0,0]','[0,K,0]','[0,0,L]'],
    NumberOfBins='2,2,2', Units='lattice,lattice,lattice')
import os
savefile = os.path.join(config["defaultsave.directory"], "ZODS.h5")
SaveZODS(InputWorkspace=ws, FileName=savefile)
print "File created:", os.path.exists(savefile)

Output:

File created: True

Categories: Algorithms | MDAlgorithms

Source

C++ source: SaveZODS.cpp

C++ header: SaveZODS.h