Advanced Photon Source

A U.S. Department of Energy, Office of Science,
Office of Basic Energy Sciences national synchrotron x-ray research facility

 

Visualizing Magnetic Spin Directions GSAS with VRSTPLOT

To visualize the contents of magnetic unit cell, the following input can be supplied to program VRSTPLOT in the GSAS suite to generate a VRML file that can then be viewed with an external program. In this example, the experiment PMMMFMMM has been selected and the VRSTPLOT program will create file PMMMFMMM.wrl. Note that the VRML files generated by VRSTPLOT are VRML version 1.0, which is somewhat out of date; not all VRML viewers can process these files. Also, the exact mechanism for viewing the file will depend on the viewer that is in use and how it is installed. Typically the file is viewed by opening it in a web viewer that after the VRML application has been installed.

Program VRSTPLOT is run in EXPGUI by selecting the appropriate menu item from the Graphs menu item. A sample run of VRSTPLOT is shown below. User-typed input is emphasized by display in this font: Input. Note that results from versions of this program prior to ?????? of 2005 should not be trusted.

---

                   |-----------------------------------------|
                   |     Program VRSTPLOT Version MacOSX     |
                   | VRML crystal structure plotting program |
                   | Distributed on Thu Sep 30 14:58:40 2004 |
                   |-----------------------------------------|

        |---------------------------------------------------------------|
        |            Allen C. Larson and Robert B. Von Dreele           |
        |      Manuel Lujan, Jr. Neutron Scattering Center, MS-H805     |
        |      Los Alamos National Laboratory, Los Alamos, NM  87545    |
        |                                                               |
        | Copyright, 2000, The Regents of the University of California. |
        |---------------------------------------------------------------|

 Enter  to continue >
  Enter phase number >2
 New phase selected

 All of the following data refer to the current space group symbol
 Phase name: from /Users/toby/proj/ybafe/FeOnly_Fmmm.cif                       
 Lattice parameters:
 a,b,c            =     7.8530    7.8169   23.5813
 alpha,beta,gamma =     90.000    90.000    90.000

 Space group   F m m m           
 The lattice is centric  F-centered orthorhombic  Laue symmetry mmm   
  Multiplicity of a general site is  32
  The symmetry of the point 0,0,0 contains 1bar

 The equivalent positions are:

 ( 1)     X      Y      Z  ( 2)    -X      Y      Z 
 ( 3)     X     -Y      Z  ( 4)    -X     -Y      Z 
 
 Spin flip operators:  1. -1. -1.  1.  1.  1.
 Enter  to continue >
 Atomic coordinates (Uij*100):
 ser.   x       y       z     name      U11    U22    U33    U12    U13    U23
        Mx      My      Mz
   1  0.0000  0.0000  0.0000 Fe1a       0.58   0.00   0.00   0.00   0.00   0.00
       3.479   0.000   0.000
   2  0.0000  0.0000  0.5000 Fe1b       0.58   0.00   0.00   0.00   0.00   0.00
      -3.479   0.000   0.000
   3  0.0000  0.0000  0.1700 Fe2a       0.58   0.00   0.00   0.00   0.00   0.00
      -3.479   0.000   0.000
   4  0.0000  0.0000  0.3300 Fe2b       0.58   0.00   0.00   0.00   0.00   0.00
       3.479   0.000   0.000
 Space filling atoms will not be plotted
 Thermal ellipsoids will be plotted
 The ellipsoid probability is    0.500
 Unit cell edges will not be plotted
 Enter VRSTPLOT command (<?>,A,B,C,E,F,H,L,M,N,P,U,W,Q) >
 VRSTPLOT commands:
  <?>   - Type this help listing
  A     - Select atoms for drawing
  B     - Select bonds for drawing
  C     - Modify atom colors
  E     - Toggle plot of space filling atoms or ellipsoids
  F     - Setup plot of Fourier contours
  H     - Toggle of hkl plane plot
  L     - List structure data
  M     - Change ellipsoid probability or atom radius multiplier
  N n   - Select a new phase n
  P     - Select polyhedra for drawing
  U     - Toggle plot of unit cell edges
  W     - Write VRML plot file
  Q     - Quit VRSTPLOT
 Enter VRSTPLOT command (<?>,A,B,C,E,F,H,L,M,N,P,U,W,Q) >A
 List of atoms to be plotted
 No atoms in drawing array
 Atom names:
    1 Fe1a        2 Fe1b        3 Fe2a        4 Fe2b    
 Enter atom selection control (<?>,A,L,U,X) >U
 Enter atom seq. or type to be included >1:4
 Enter minimum and maximum along X axis >0 1
 Enter minimum and maximum along Y axis >0 1
 Enter minimum and maximum along Z axis >0 1
 List of atoms to be plotted
  At.No.  Designator    At.No.  Designator    At.No.  Designator  
      1    1(   1 0 0 0)      2    1(   1 0 0 1)      3    1(   1 0 1 0)
      4    1(   1 0 1 1)      5    1(   1 1 0 0)      6    1(   1 1 0 1)
      7    1(   1 1 1 0)      8    1(   1 1 1 1)      9    1( 101 0 0 0)
     10    1( 101 1 0 0)     11    1( 201 0 0 0)     12    1( 201 0 1 0)
     13    1( 301 0 0 0)     14    1( 301 0 0 1)     15    2(   1 0 0 0)
     16    2(   1 0 1 0)     17    2(   1 1 0 0)     18    2(   1 1 1 0)
     19    2( 101 0 0-1)     20    2( 101 0 0 0)     21    2( 101 1 0-1)
     22    2( 101 1 0 0)     23    2( 201 0 0-1)     24    2( 201 0 0 0)
     25    2( 201 0 1-1)     26    2( 201 0 1 0)     27    2( 301 0 0 0)
     28    3(   1 0 0 0)     29    3(   1 0 1 0)     30    3(   1 1 0 0)
     31    3(   1 1 1 0)     32    3(  -1 0 0 1)     33    3(  -1 0 1 1)
     34    3(  -1 1 0 1)     35    3(  -1 1 1 1)     36    3( 101 0 0 0)
     37    3( 101 1 0 0)     38    3(-101 0 0 0)     39    3(-101 1 0 0)
     40    3( 201 0 0 0)     41    3( 201 0 1 0)     42    3(-201 0 0 0)
     43    3(-201 0 1 0)     44    3( 301 0 0 0)     45    3(-301 0 0 1)
     46    4(   1 0 0 0)     47    4(   1 0 1 0)     48    4(   1 1 0 0)
     49    4(   1 1 1 0)     50    4(  -1 0 0 1)     51    4(  -1 0 1 1)
     52    4(  -1 1 0 1)     53    4(  -1 1 1 1)     54    4( 101 0 0 0)
     55    4( 101 1 0 0)     56    4(-101 0 0 0)     57    4(-101 1 0 0)
     58    4( 201 0 0 0)     59    4( 201 0 1 0)     60    4(-201 0 0 0)
 Enter  to continue >
  At.No.  Designator    At.No.  Designator    At.No.  Designator  
     61    4(-201 0 1 0)     62    4( 301 0 0 0)     63    4(-301 0 0 1)
 Atom names:
    1 Fe1a        2 Fe1b        3 Fe2a        4 Fe2b    
 Enter atom selection control (<?>,A,B,D,L,R,U,X) >x
 Enter VRSTPLOT command (<?>,A,B,C,E,F,H,L,M,N,P,U,W,Q) >U
 Unit cell edges will be plotted
 Enter VRSTPLOT command (<?>,A,B,C,E,F,H,L,M,N,P,U,W,Q) >w
 The color number for the background is  54 (Gray85            )
 Enter new color number (1-120, 0 for list) >/
 The VRML .wrl file has been written, you may
 now view it with your favorite viewer.
 Enter VRSTPLOT command (<?>,A,B,C,E,F,H,L,M,N,P,U,W,Q) >Q
STOP VRSTPLOT has finished statement executed
Press Enter to continue