Visualization of distortions of crystals containing dislocations using the differential displacement maps. Both screw and edge view are implemented, comparison of two different distortions, geometrical transforms, user-defined styles. Imports data in a variety of formats, exports to Postscript, bitmap and internal .dd formats. The change in the separations of neighboring atoms is depicted by arrows whose lengths correspond to the magnitudes of the changes of their separation relative to their distance in the ideal crystal.
The main features implemented in ddplot are:
- plotting of atomic structure
- visualization of screw and edge components around a dislocation line
- projection of relative displacements into an arbitrary direction
- scaling of arrows (for the plotting of edge components)
- automatic finding of the first to fifth nearest neighbors
- unrelaxed/relaxed configuration
- coordinate transformations
- output to Postscript, .XYZ (JMol), standard .CFG (AtomEye)
- group loading of a set of plot files
- internal .DD format containing the coordinate system, position of the dislocation, lattice parameter, etc.
- creating a .GIF animation from the uploaded blocks
- changing colors, line thickness and radii of atoms and arrows
- distinguishing atomic layers or atomic types
- user-defined settings can be stored in ~/.ddplot or loaded at the start
To compile ddplot, you first need to download the Qt library. If you are using Ubuntu/Debian, run this
sudo apt install build-essential sudo apt install qt5-default
To install ddplot, clone the latest version using git, compile and run it as follows:
git clone https://github.com/romangroger/ddplot.git ddplot cd ddplot qmake make ./ddplot
You should also copy (and edit) the settings file into your home directory:
cp .ddplot ~/
Following is a list of file formats that are readable by ddplot. If you want to use this code for plotting, you are supposed to prepare your data in one of the supported formats. The only format that ddplot uses for saving is the internal .dd format that whose complexity will evolve in future releases to accommodate all possible information required for effective plotting of the differential displacement maps. The underlined words are keywords and must appear as written below.
This is the most trivial format that does not contain any information about the orientation of the block, periodicity and the like. It is entirely up to the user of ddplot to remember these parameters.
ninit # number of atoms in the initial structure title_init el1 x(1) y(1) z(1) el2 x(2) y(2) z(2) : : : : # coordinates of atoms in the initial configuration : : : : # (usually unrelaxed ideal lattice) eln x(n) y(n) z(n) nrel title_rel el1 x(1) y(1) z(1) el2 x(2) y(2) z(2) : : : : # coordinates of atoms in the relaxed : : : : # configuration (relaxed structure) eln x(n) y(n) z(n)
BVECT bx by bz # Burgers vector of screw dislocation (if any)
This is an old format used in one of our simulation codes. Note, that the number of atoms in the relaxed configuration should be identical to that in the perfect lattice. The relaxed configuration is usually obtained by stressing a perfect crystal, where the initial positions of atoms correspond to the perfect lattice.
nrel # number of atoms in the relaxed configuration z(1) z(2) : # z-positions of atoms in the relaxed : # configuration z(nrel) x(1) y(1) zlayer(1) x(2) y(2) zlayer(2) : : : # (x,y) positions of atoms in the : : : # relaxed configuration x(nrel) y(nrel) zlayer(nrel) ninit # number of atoms in the perfect lattice z(1) z(2) : # z-positions of atoms in the perfect lattice : z(nrel) x(1) y(1) x(2) y(2) : : # (x,y) positions of atoms in the perfect : : # lattice x(ninit) y(ninit) 0 # unused, don't ask me why xperiod yperiod # periodicity in the x, y, z directions zperiod CORE xpos ypos # (x,y) position of the screw dislocation If the block does not contain any screw dislocation, simply omit the last line.
This is another format from the same simulation code that we are using. The format is a bit complicated and is not supposed to be used any more. It is left in ddplot only for the sake of quick visualization of the results of our simulations.
LEN xlen ylen zlen # x, y and z size of the block LATPAR latpar # lattice parameter ND nd # number of active atoms D x(1) y(1) z(1) elem(1) x(2) y(2) z(2) elem(2) # coordinates of active atoms in the : : : : # relaxed configuration and the name : : : : # of the element, e.g. Mo x(nd) y(nd) z(nd) elem(nd) NINERT ninert # number of inert atoms DINERT x(1) y(1) z(1) elem(1) x(2) y(2) z(2) elem(2) # coordinates of inert atoms in the : : : : # relaxed configuration and the name : : : : # of the element, e.g. Mo x(ninert) y(ninert) z(ninert) elem(ninert) UNRLD x(1) y(1) z(1) elem(1) x(2) y(2) z(2) elem(2) # coordinates of atoms in the : : : : # perfect lattice and the name : : : : # of the element, e.g. Mo x(nunrld) y(nunrld) z(nunrld) elem(nunrld) # nurld=nd+ninert
In our simulations, the block is usually divided into two parts. Outer part of the (x,y) plane contains inert atoms into which we apply anisotropic displacements corresponding to a given stress field. The inner part then contains active atoms whose position is obtained by minimization. In the relaxed configuration, the force on each atom is essentially zero.
This is the internal ddplot's format that contain all possible information about the block, including the orientation of the block, positions of dislocations, periodicity, etc. Each block starts with a header that is written below in capital letters. Comments begin with '#' and are ignored by ddplot. Number of spaces between each number in a row and between lines is arbitrary.
CSYS # orientation of the block given by three x1 y1 z1 # vectors defined in the cube coordinate system x2 y2 z2 # [100], [010], [001] x3 y3 z3 PERIOD xperiod yperiod zperiod # periodicity along x, y and z DISLO_CENTER xpos ypos # (x,y) position of the screw dislocation NUM_UNREL ninit # number of atoms in the perfect lattice COOR_UNREL x(1) y(1) z(1) elem(1) x(2) y(2) z(2) elem(2) # coordinates of atoms in the : : : : # perfect lattice and the index : : : : # of the element of this atom x(ninit) y(ninit) z(ninit) elem(ninit) # (count from 0) NUM_REL nrel # number of atoms in the relaxed configuration COOR_REL x(1) y(1) z(1) x(2) y(2) z(2) # coordinates of atoms in the relaxed : : : # configuration : : : x(nrel) y(nrel) z(nrel)
The mandatory fields are NUM_UNREL, COOR_UNREL, NUM_REL, COOR_REL, and PERIOD.
The main website of the ddplot project is http://groger.ipm.cz/download/ddplot.html.
Contact: Roman Gröger (groger@ipm.cz)
To keep you updated about new versions of ddplot, send me your e-mail and I will add you into the ddplot mailing list. I will be glad to hear about your experience with ddplot, your suggestions but also criticism. If you have some nice figures from ddplot, please, send me .JPG or .GIF to put them here as screenshots.