D_Atomview users guide

To use D_Atomview you can either use three different options:

The starting gui program
          ./D_Atomview

A command line program that starts atomview and the navigation gui
         ./forker data_file color_file[optional]

A command line program that starts only atomview
         ./atomstarter data_file color_file[optional]

Most users will prefer to use the starting gui (./D_Atomview) but if you are setting the program up for automated demos you may be interested in using the the command line equivalents.

The starting gui:



This is the graphical front end to atomview, this gui has three main uses:
         
  • Starting D_Atomview with predefined configuration files
    •          
  • Entering configuration information by hand
    •          
  • Saving configuration data to files

    • Predefined configurations are broken up into two parts:
              The first part is the data format that holds the file information to load, the number of polygons per atom and an offset from the global origin.
              The second part holds color information about atom types.

    Data file format is as follows: 
    FILE DATA
frame 101 113
NUM POLYGONS
100
X Y Z H P R Info
0 0 0 0 0 0

    Color file format is as follows: 
    Au red
Pd white

    Data file explanation:
    frame 101 113 stands for load file frame.101, frame.102 ... frame.113, etc..
    The number of polygons line defines how many polygons to use in making each atom. The fewer number of polygons the more box like of a structure you get, and along with this you get higher performance.
    X Y Z H P R Info holds the data for starting at a position off of the global origin, say at a crack tip

    Color file explanation:
    This basically allows you to make an atom appear in a certain color. The colors D_Atomview understands are blue, red, green, yellow, orange, white, and purple. Their is a separate class that handles defining colors so it is easy to add more colors if you would like to.
    To associate the atoms with a specif color simply use this format:

    AtomName AtomColor

    You can also enter the file information and color information into the gui interface. If you do this you can start the program by pressing Start, or you can save your data to a specific file by typing the information in the space next to save and then clicking Save. When you click Save the configuration files are saved to the name you specify and then _data holds the file data and then _color holds the color data. So if you entered mydata as the name and then clicked save you would have mydata_data and mydata_color saved into your current working directory.


    Navigating and changing the atoms
    This program allows for interaction in D_Atomview. You can make the atoms larger and smaller by moving the slider below Scale Atoms. You can make the whole model smaller and larger by moving the slider below Scale World. You can either scale based on the global origin or based on your current position. You can either manually move to a specific time step in the dataset by moving the slider below Atoms at time or by press the play button. While playing you can press the stop button to stop the animation at the current position, or you can press the loop button which will cause the animation to go to the beginning of the data set when it reaches the end, instead of stopping.

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