Some file formats support multiple frames. A file containing more than one frame is considered an animation. This menu item brings up the animation dialog box which allows you to control the animation playback.
If the molecular model contains frequency information, the vibrational modes can be animated and controlled with the vibrate dialog box.
Note that Display->Vectors should be checked in order to render vibrational vectors.
Good examples are samples/phenylnitrene.g92.out and samples/ammonia.adf.out
This opens a window in which a energy versus frames plot is viewed. This option currently only works when reading a CML animation with energies given for each frame.
An example file is supplied: conformeren.cml.
Opens the crystal properties dialog box.
The three primitive vectors of the crystal can be defined in two different ways: by using either a "cartesian" or a "crystallographic" representation. The choice of the representation is only a question of convenience and one can always switch from one representation to the other by using the "Representation" combo box. However, the "cartesian" representation allows to orient the crystal freely in space whereas the crystallographic representation restricts the "a" edge to be parallel to the x axis and the "b" edge to be in the xy-plane.
There is three lines containing two fields each. Each line corresponds to a primitive vector. The first field contains the x, y, and z components of the vector separated with a coma. The second field is a multiplication factor for the first field and is barely a matter of convenience. The unit of the resulting vector is the Angstrom. When the values are settled, clicking on the Apply button will update the data in the crystallographic representation and will update the Display Panel.
The a, b and c fields contain the three edge lengths (in angstrom) of the crystal. As soon as the apply button is clicked, the a edge will be set parallel to x and the b edge will lie in plane (x,y). The alpha, beta and gamma fields contain the angles (in degrees) between the a and b, b and c, and b and a edges, respectively.
Note that the atomic positions are always assumed in reduced coordinates of the primitive vectors. So, for instance, when the primitive vectors are scaled, the atoms remains in the same relative position. However, when a file containing no crystal information (and therefore no primitive vector) is loaded into jmol, reduced coordinates doesn't exist yet. In this case the Crystal dialog is only available via the Make Crystal item in the Edit menu. The primitive vectors must be entered in a way to correspond to the atomic position defined in the input file.
For example, the file bulk_Si.xyz in the samples directory contains the atomic positions of the crystalline silicon, i.e. one atom at (0, 0, 0) and another one at (1.347, 1.347, 1.347). A valid set of primitive vector is (0.0 0.5 0.5), (0.5 0.0 0.5) and (0.5 0.5 0.0) with a multiplication factor of 5.387. In this case, the crystallographic representation cannot be used to create the crystal because a set of 3 primitive vectors whose one is parallel to x cannot lead to the Silicon crystal with the given particular atomic positions.
This is the place to define the visualization range of the crystal. Three subpanels are present: the Atom Box, the Bond Box and the Unit Cell Box. In each subpanel, two fields are present: the minimum and the maximum coordinates in term of the unit vectors. They define a parallelepipede where the visualization take place.
For instance, minimum = (0,0,0) and maximum = (1,1,2) leads to 2 unit cells aligned in the direction of the third primitive vector. Non integer values are also accepted.
One can define a visualization range for three different aspects, the atoms, the bonds and the unit cell frame:
Only the atoms of the crystal lying in the Atom Box will be displayed. If an atom exactly lie on a face, edge or corner of the unit cell, it will be displayed respectively 2, 4 or 8 times in the unit cell, one for each equivalent face, edge or corner. This is due to a limitation of Jmol that cannot display a partial atom. It results that the total number of displayed atoms can be larger than the expected (in a crystallographic point of view) number of atoms. Another nasty effect can be shown with the sample file slab_7Si_3Vac_2x_relax_2x1.out. If you create an animation with frame interpolation, the interpolation results in erroneous frames due to the different number of atoms in two successive frames.
If the "Original atoms only" check box is checked, only the original atoms, i.e. the atoms as specified in the input file, will be displayed.
A bond between two atoms will be drawn if these are lying in the Bond Box. Of course, if the distance is bigger than the bond fudge, no bond will be drawn.
In this panel, you will find the atomic position and the type of the base atoms in either cartesian (angstrom) or lattice (=reduced) coordinates depending on what is selected in the combo box.
This panel allows you to generate band plots used to represent the electronic band structure or the phonon dispersion curves of crystals. So far, data can only be loaded from ABINIT output files and only electronic bands are supported. An example, Si_eband.out, can be found in the samples directory. This file contains 2 datasets. Only dataset 2 contains information for a band plot.
A band plot or band diagram, represents the electronic energy (the phonon frequency) of a state (mode) versus its wave vector along particular lines. Each line of the table on the top of the panel represents such particular line. The first field is an index that is used to refer to the line (it will be referred below as the "line index"). The second ("Origin") and forth ("End") fields are the position of the first end last point of the line given in reduced coordinates of the primitive reciprocal vectors. The third ("Origin Label") and fith ("End Label") are the labels of the origin and end point of the line respectively. These two fields are editable. Typically it will consist of a single letter ("X" for instance). Greek letters are also supported by putting a "\S" in front of the letter (for instance "\S G" gives the Greekletter Gamma). A complete description of the syntax is given below in the section called “Text Formatting”. The last field is the total number of points n in that line. The first point of the line has index 0 and the last point has index n-1. Below the table, are a number of fields used to tune the aspect of the plot:
Resolution: the horizontal resolution of the plot in pixels.
Ratio: the y/x ratio of the plot.
Fontsize 1: fontsize of the abscisse values.
Fontsize 2: fontsize of the ordinate values.
Fontsize 3: fontsize of the ordinate label.
Energy Units: the units of the ordinate axis. As you may have noticed, the dimensions are either an energy or an inverse wavelength (corresponding to the wavelength that would have light of that energy).
Minimum Energy: the minimum energy of the ordinate axis.
Maximum Energy: the maximum energy of the ordinate axis.
Fermi Level: an horizontal line will be ploted at that position.
The Fix Fraction Digits/Exp Fraction Digits combo box: indicates the number format of the ordinate values - fixed or exponential. The number on the right of the combo box is the number of decimal figures.
Vertical Tics: the number of tics on the ordinate axis.
Horizontal Tics: the number of tics on the abscisse axis.
Separator size: the size of the separation between two subplot (see below ";").
The Y label: The label of the ordinate axis.
Define Plot: defines the structure of the plot.
The structure is basically defined by a string which is a coma separated list of the line numbers in the table in the top of the panel. For example "0,1,2" with the sample file Si_eband.out/dataset2 will draw a continuous band plot along the path (0.5, 0.0, 0.0) - (0.0, 0.0, 0.0) - (0.0, 0.5, 0.5) - (1.0, 1.0, 1.0) or X - G - M - G.
A coma in the list can be replaced by a ";". In that case, the plot is no more continuous but a separation is drawn (see "Separator Size" hier above). For example "0,1;2" will draw the band diagram along the path X - G | M - G with a separation between the first G and M.
A partial line can also be drawn by specifying the range in square brackets. For example "0,1[0-7];2" will only draw line 1 between points 0 and 7. The user has to know the position of the points as there are defined in the input file. Notice that the maximum range is [0,Number Of Points - 1] and is assumed by default.
A line can also be drawn in the reverse direction. For this, a minus has to be prepended in front of the line number. For example "0,1;-2" will draw band diagram along the path X - G | G - M.
A very basic text formatting alows to combine greek and latin characters. Greek characters are obtained by preceding the text with \S, latin characters by \N. If nothing is specified, latin characters are assumed. Superscript characters are obtained with a ^.
For example : \S l \N \ ( \S m \N m^-1 ).