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  Output-file-format

 

 

 
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Output-file-format

There are several options for 1D, 2D and 3D. You can specify the desired output file format to suit your favorite visualization software package.
We recommend to first try it with our in-house visualization software nextnanomat.

All nextnano output is with respect to a rectilinear grid.

 

1D

2D

 

3D

 

!------------------------------------------------------!
$output-file-format                           optional !
 simulation-dimension          integer        required ! CHOICE[1,2,3]
 VTK-XML                       character      optional ! CHOICE[yes,no]
 VTK-legacy                    character      optional ! CHOICE[no,yes]
 AVS-Express                   character      optional ! CHOICE[no,yes]
 number-of-AVS-files           integer        optional ! CHOICE[1,2,3]
 file-format                   character      optional ! CHOICE[Origin,ASCII,AVS-ASCII,AVS-binary,AVS-binary-single,AVS-binary-double]
 resolution                    character      optional ! CHOICE[default,average,all]
only 2D/3D
$end_output-file-format
                       optional !
!------------------------------------------------------!
 

Syntax

!------------------------------------------------------!
$output-file-format                                    !
                                                       !
 simulation-dimension = 1                              !
1D
 file-format          = Origin                         ! (ASCII format + *.plt Origin files)
!file-format          = ASCII                          ! (ASCII format)


 simulation-dimension = 2                              !
2D
                                                       !
 VTK-XML              = yes                            !
VTK XML ASCII format (.vtr, r = rectilinear grid)
 VTK-legacy           = no                             !
legacy VTK binary format (.vtk)
                                                       !
 AVS-Express          = yes                            !
AVS/Express format (.fld) (default)
                                                       !
 file-format          = AVS-ASCII                      !
AVS/Express (ASCII format)
!file-format          = AVS-binary                     !
AVS/Express (Fortran's binary format, i.e. 'unformatted' in single  precision), same as AVS-binary-single
!file-format          = AVS-binary-single              !
AVS/Express (Fortran's binary format, i.e. 'unformatted' in single  precision)
!file-format          = AVS-binary-double              !
AVS/Express (Fortran's binary format, i.e. 'unformatted' in double precision)
                                                       !
 resolution           = default                        ! default / all / average


 simulation-dimension = 3                              !
3D
 ...
same as simulation-dimension = 2
                                                       !
$end_output-file-format                                !
!------------------------------------------------------!

The file size of AVS-binary-single *.dat files is only half the size of AVS-binary-double.
This is relevant for simulations where the number of grid points is very large.
The output of AVS-binary-single/AVS-binary-double is much faster than AVS-ASCII, especially for large arrays of data.

 

VTK format for rectilinear grid

 VTK-XML              = yes                            ! VTK XML ASCII format (.vtr, r = rectilinear grid)
                      = no                             !
(default)
 VTK-legacy           = yes                            !
legacy VTK binary format (.vtk)
                      = no                             !
(default)

==> VTK - The Visualization Toolkit

The .vtr format can be read by the following software:

 

AVS/Express format for rectilinear grid

 AVS-Express          = yes                            ! AVS/Express ASCII format (.fld) (default)
                      = no                             !
==>
AVS/Express

 number-of-AVS-files  = 1                              ! .fld file                 - Everything is written into the .fld file. (default)
                      = 2                              ! .fld,          .dat
files - The .coord information is put into the .fld file.
                      = 3                              ! .fld, .coord., .dat
files
                      = 4                              ! .fld, .coord., .dat
files. Additionally, a .v file is written out. It is related to the AVS/Express software.
 

 

Resolution

In 2D/3D you can additionally specify, how many points you want to plot (resolution) in order to make large amounts of visualization data to be handled more efficiently.
In 2D, for each point on material grid, 4 octants are created each containing one point (only relevant for grid lines at interfaces).
In 3D, for each point on material grid, 8 octants are created each containing one point (only relevant for grid lines at interfaces).

 resolution           = default                        !   
plot multiple points at material interfaces where useful (default)
                      = all                            !   
plot multiple points at material interfaces
                      = average                        !
average multiple points at material interfaces
                                                       ! ==>
The average value of the 8 (3D) / 4 (2D) points lying in these 8 (3D) / 4 (2D) octants will be taken.
The option default will plot multiple points at material interfaces where useful, e.g. for conduction band edges or valence band edges where there are abrupt steps at interfaces.
In cases where this is not necessary (e.g. for electrostatic potential, wave functions, ...), no multiple points are written out unless all is chosen..

 

1D

x, f(x)

That's plane ASCII, suitable for everything.

  • Origin

 

2D

x, y, f(x,y)

  1. Output files that will be produced are:
  2. The output files can be read in with the AVS/Express software that can be obtained by Advanced Visual Systems.
    AVS output files
    described in the next three paragraphs:
    - material_grid.fld
    - material_grid.coord
    - material_grid.dat
  3. - material_grid.fld
    This is an AVS field file specifying the input files and data format needed for processing the 2D/3D visualization.

    # AVS field file        !
    #                       !
    ndim   =  2             !
    dimension of data
    dim1   = 46             !
    no. of grid points in x direction
    dim2   = 112            !
    no. of grid points in y direction
    nspace =  2             !
    dimension of data
    veclen =  1             !
    length of data vector (1 means scalar quantity)
    data   = float          !
    data type   integer / float / double  (integer precision / single-precision real number / double-precision real number)
    field  = rectilinear    !
    rectilinear coordinate system
    label  = material_grid  !
    name of data files to be proceeded

    variable 1 file=material_grid.dat   filetype=ascii       skip = 0     offset = 0   stride=1  !
    if file-format = AVS-ASCII
    variable 1 file=material_grid.dat   filetype=unformatted skip = 0     offset = 0   stride=1  !
    if file-format = AVS-binary

    coord 1    file=material_grid.coord filetype=ascii       skip = 0     offset = 0   stride=1
    coord 2    file=material_grid.coord filetype=ascii       skip = 112   offset = 0   stride=1  !
    As an empty line separates the coordinate axes, we have 112 + 1 = 113.

    These three lines specify where the data is located in each file:
    The x coordinates are located at position 0 to 112 in the file material_grid.coord, y coordinates are located in the same file at position 112 to 158.
    The variable data is stored in the .dat file and is related to the coordinates in a systematic order.

    Note: Fortran 'unformatted' data is binary data with additional words (of length 4 bytes) written at the beginning and end of each data block stating the number of bytes or words in the data block.

    More information on the .fld type can be found here.
     
  4. AVS input files: material_grid.coord, material_grid.dat
  5. - material_grid.coord
        Coordinates of the grid, i.e. 112+46 real numbers that specify the grid points on each axis.
  6. - material_grid.dat
        Contains information about the regions.
        Each grid point is specified by a region number as defined in the input file (see table at top of this page).
  7. All other folders contain the same structure for AVS field files:
    - *.fld
    - *.coord
    - *.dat

 

3D

x, y, z, f(x,y,z)

  1. The output files can be read in with the AVS/Express software that can be obtained by Advanced Visual Systems.
    AVS output files
    described in the next three paragraphs:
    - material_grid.fld
    - material_grid.coord
    - material_grid.dat
  2. - material_grid.fld
    This is an AVS field file specifying the input files and data format needed for processing the 3D visualization.

    # AVS field file        !
    #                       !
    ndim   =  3             !
    dimension of data
    dim1   = 53             !
    no. of grid points in x direction
    dim2   = 53             !
    no. of grid points in y direction
    dim3   = 70             !
    no. of grid points in z direction
    nspace =  3             !
    dimension of data
    veclen =  1             !
    length of data vector (1 means scalar quantity)
    data   = float          !
    data type   integer / float / double  (integer precision / single-precision real number / double-precision real number)
    field  = rectilinear    !
    rectilinear coordinate system
    label  = material_grid  !
    name of data files to be proceeded

    variable 1 file=material_grid.dat   filetype=ascii       skip = 0    offset = 0  stride=1  !
    if file-format = AVS-ASCII
    variable 1 file=material_grid.dat   filetype=unformatted skip = 0    offset = 0  stride=1  !
    if file-format = AVS-binary

    coord 1    file=material_grid.coord filetype=ascii       skip = 0    offset = 0  stride=1
    coord 2    file=material_grid.coord filetype=ascii       skip = 70   offset = 0  stride=1  !
    As an empty line separates the coordinate axes, we have 70 + 1 = 71.
    coord 3    file=material_grid.coord filetype=ascii       skip = 123  offset = 0  stride=1  !
    As an empty line separates the coordinate axes, we have 123 + 2 = 70 + 1 + 53 + 1 = 125.

    These four lines specify where the data is located in each file:
    The x coordinates are located at position 0 to 70 in the file material_grid.coord, y coordinates are located in the same file at position 71 to 123, ...
    The variable data is stored in the .dat file and is related to the coordinates in a systematic order.

    Note: Fortran 'unformatted' data is binary data with additional words (of length 4 bytes) written at the beginning and end of each data block stating the number of bytes or words in the data block.
     
  3. AVS input files: material_grid.coord, material_grid.dat
  4. - material_grid.coord
        Coordinates of the grid, i.e. 53+53+70 real numbers that specify the grid points on each axis.
  5. - material_grid.dat
        Contains information about the different materials used in the simulation.
        Each grid point is associated with a certain material number as defined in the input file.
  6. All other folders contain the same structure for AVS field files:
    - *.fld
    - *.coord
    - *.dat

 

The data values are written to the .dat file in the following order:

   DO   k=1,dim3
    DO  j=1,dim2
     DO i=1,dim1
        WRITE(*,*) matrixM(1:DimVector,i,j,k) ! DimVector = 1 for scalar quantity
     END DO
    END DO
   END DO
 

 

How to plot 2D AVS/Express output data with Origin?

  • You must have three files in your directory:
       your_filename.fld
    , your_filename.coord, your_filename.dat
  • Use this perl script:  avs2xyz.pl (avs2xyz_pl.zip)
    Usage: avs2xyz.pl your_filename
  • Output that will be created (containing three columns: x, y, f(x,y)):
       your_filename.xyz
    On the screen there will be some output about the number of x and y coordinates (you will need it later!).
  • Open Origin.
  • Import your_filename.xyz to an Origin worksheet.
  • Mark the third column as Z.
    - Mark third column.
    -
    Column -> Set as Z
  • Worksheet -> Convert to Matrix -> Random XYZ ->
                     No. of columns  = no. of x grid coordinates
                     No. of rows     = no. of y grid coordinates
                     Gridding method = Weighted average or
                                       Correlation
  • Plot3D -> 3D Colormap Surface (for instance)
  • If the Origin plot doesn't satisfy you, there are some ways around to improve it. We are not experts in that but maybe you could contribute to improve this documentation with your know-how. Many thanks!

    Some hints:
    -
    Right mouse button
       -> Layer Contents...
          -> Layer Properties
             -> Size/Speed ->
    untick "Skip Points" (to show all/more points)
             -> Axis -> Length -> type in x and y real scale values (to scale properly)
  • Example (2D wave function):


     

 

AVS/Express Hints

  • => Turn the (default) black background color into a white background color:

    -> Editors -> View -> General -> Background Color Editor -> Set Value to 1.0.

     
  • => Change line thickness (of e.g. orthoslice):
    -> Select: Editors -> Object -> Properties -> Type -> Point/Line -> Line Thickness -> ...