/doc/ase/gui/basics.rst
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1.. module:: basics 2 3======================================= 4ase-gui basics and command line options 5======================================= 6 7General use 8----------- 9 10Visualizing a system with ase-gui is straight-forward using a regular 11mouse. The scroll function allows to change the magnification, the 12left mouse button selects atoms, the right mouse button allows to 13rotate, and the middle button allows to translate the system on the 14screen. 15 16Depending on the number of selected atoms, ase-gui automatically measures 17different quantities: 18 19================================= ====================================== 20Selection measurement 21================================= ====================================== 22single atom xyz position and atomic symbol 23two atoms interatomic distance and symbols 24three atoms all three internal angles and 25 symbols 26four atoms, selected sequentially Measures the dihedral angle, 27 e.g. the angle between bonds 12 and 34 28more than four atoms chemical composition of selection. 29================================= ====================================== 30 31ase-gui can save the following file formats: 32 33=========== ================================= 34File format Comment 35=========== ================================= 36xyz XYZ file 37traj ASE trajectory 38pdb PDB file 39cube Gaussian cube file 40py Python script 41vnl VNL file 42png Portable Network Graphics 43pov Persistance of Vision 44eps Encapsulated PostScript 45in FHI-aims geometry input 46POSCAR VASP geometry input 47bundle ASE bundle trajectory 48cif Crystallographic Information File 49=========== ================================= 50 51Files 52----- 53 54The :ref:`ase-gui` program can read all the file formats the ASE's 55:func:`~ase.io.read` function can understand. 56 57:: 58 59 $ ase-gui N2Fe110-path.traj 60 61 62Selecting part of a trajectory 63------------------------------ 64 65A Python-like syntax for selecting a subset of configurations can be 66used. Instead of the Python syntax ``list[start:stop:step]``, you use 67:file:`filaname@start:stop:step`:: 68 69 $ ase-gui x.traj@0:10:1 # first 10 images 70 $ ase-gui x.traj@0:10 # first 10 images 71 $ ase-gui x.traj@:10 # first 10 images 72 $ ase-gui x.traj@-10: # last 10 images 73 $ ase-gui x.traj@0 # first image 74 $ ase-gui x.traj@-1 # last image 75 $ ase-gui x.traj@::2 # every second image 76 77If you want to select the same range from many files, the you can use 78the :option:`-n` or :option:`--image-number` option:: 79 80 $ ase-gui -n -1 *.traj # last image from all files 81 $ ase-gui -n 0 *.traj # first image from all files 82 83.. tip:: 84 85 Type :command:`ase-gui -h` for a description of all command line options. 86 87 88Writing files 89------------- 90 91:: 92 93 $ ase-gui -n -1 a*.traj -o new.traj 94 95Possible formats are: ``traj``, ``xyz``, ``cube``, ``pdb``, ``eps``, 96``png``, and ``pov``. For details, see the :mod:`~ase.io` module 97documentation. 98 99Interactive use 100--------------- 101 102The :ref:`ase-gui` program can also be launched directly from a Python 103script or interactive session: 104 105>>> from ase import * 106>>> atoms = ... 107>>> view(atoms) 108 109or 110 111>>> view(atoms, repeat=(3, 3, 2)) 112 113or, to keep changes to your atoms: 114 115>>> atoms.edit() 116 117 118NEB calculations 119---------------- 120 121Use :menuselection:`Tools --> NEB` to plot energy barrier. 122 123:: 124 125 $ ase-gui --interpolate 3 initial.xyz final.xyz -o interpolated_path.traj 126 127 128Plotting data from the command line 129----------------------------------- 130Plot the energy relative to the energy of the first image as a 131function of the distance between atom 0 and 5:: 132 133 $ ase-gui -g "d(0,5),e-E[0]" x.traj 134 $ ase-gui -t -g "d(0,5),e-E[0]" x.traj > x.dat # No GUI, write data to stdout 135 136The symbols are the same as used in the plotting data function. 137 138 139Defaults for ase-gui 140-------------------- 141 142Using a file ``~/.ase/gui.py``, certain defaults can be set. If it exists, 143this file is executed after initializing the variables and colours 144normally used in ase-gui. One can change the default graphs that are 145plotted, and the default radii for displaying specific atoms. This 146example will display the energy evolution and the maximal force in a 147graph and also display Cu atoms (Z=29) with a radius of 1.6 Angstrom. 148 149:: 150 151 gui_default_settings['gui_graphs_string'] = "i, e - min(E), fmax" 152 gui_default_settings['covalent_radii'] = [[29,1.6]] 153 154 155.. _high contrast: 156 157High contrast settings for ase-gui 158---------------------------------- 159 160In revision 2600 or later, it is possible to change the foreground and 161background colors used to draw the atoms, for instance to draw white 162graphics on a black background. This can be done in ``~/.ase/gui.py``. 163 164:: 165 166 gui_default_settings['gui_foreground_color'] = '#ffffff' #white 167 gui_default_settings['gui_background_color'] = '#000000' #black 168 169To change the color scheme of graphs it is necessary to change the 170default behaviour of Matplotlib in a similar way by using a file 171``~/.matplotlib/matplotlibrc``. 172 173:: 174 175 patch.edgecolor : white 176 text.color : white 177 axes.facecolor : black 178 axes.edgecolor : white 179 axes.labelcolor : white 180 axes.color_cycle : b, g, r, c, m, y, w 181 xtick.color : white 182 ytick.color : white 183 grid.color : white 184 figure.facecolor : 0.1 185 figure.edgecolor : black 186 187Finally, the color scheme of the windows themselves (i.e. menus, buttons 188and text etc.) can be changed by choosing a different desktop theme. In 189Ubuntu it is possible to get white on a dark background by selecting the 190theme HighContrastInverse under Appearances in the system settings dialog.