![]() For linear molecules we keep tabs on 3N-5 coordinates. Using internal coordinates reduces our 3N requirement set by the Cartesian space down to a 3N-6 requirement (for non-linear molecules). With Z-matrices, we keep tabs on internal coordinates: bond length (R), bond angle (A), and torsional/dihedral angle (T/D). We increased the distance between the two atoms by some length R. What did we change? We simply changed the bond length, one variable. We now have altered the molecule in such a way that the properties of that molecule has changed. However, say we increase the distance between the hydrogen atoms. An H2 molecule centered around the origin (0,0,0) is no different from the same H2 molecule being centered around (1,1,1). The translation of the molecule through space (assuming a vacuum) will have no affect on the properties of the molecule. A point located at (0,0,1) is an absolute location for a coordinate space that extends to infinity. Cartesian space is 'absolute' so to speak. When dealing with Z-matrices, we keep track of the relative positions of points in space. The general ruling is that for Cartesian space, 3N variables must be accounted for (where N is the number of points in space you wish to index). To describe the locations of two atomic nuclei, a total of 6 variables must be written down and kept track of. The point group symmetry and symmetry tolerance can be supplied.In Cartesian space, three variables (XYZ) are used to describe the position of a point in space, typically an atomic nucleus or a basis function. ![]() Note that the the symmetry used in AMS does not have to be the same as is used in ADF. There exist a System%Symmetry key in the AMS part of the input, which can be used with the System%Symmetrize key to symmetrize coordinates. Thus input atomic coordinates that are off from their correct positions, even if they are only slightly off, are not adjusted by ADF. You can use the System%Symmetrize key in the AMS part of the input, such that AMS will symmetrize the coordinates. Note that this is a specification of the Symmetry key in the Engine ADF part of the input. This is used for analysis (see orientation of the z-axis). It is possible to specify the input geometry as a Z-Matrix.ĪTOMS \). However, you must not give different fragment types names that differ only by case: at various places in the program fragment type names are compared in a case-insensitive way Z-Matrix ¶ Errors may occur if you are sloppy in this respect. Since (to be discussed below) the name of the fragment type as it is defined under atoms (explicitly with the adf.f=option, or implicitly as the name of the atom type) might also directly indicate the fragment file, the specification of fragment types is in principle case-sensitive. Exceptions are the names of files and directories. Note: Input items are generally case insensitive. ![]() (The numbering |n is then added automatically by the program, by counting the number of times that this single-atom fragment type occurs in the list of atoms). When adf.f=fragment is omitted altogether, the fragment type is taken to be the atom type that was specified earlier on the same line. The numbering suffix |n is not required if there is only one fragment of that type. The integer n, after the pipe |, counts the individual fragments of that type. The fragment name must be of the form fragtype|n, where fragtype is the name of one of the types of fragments in the molecule. Specifies that the atom belongs to a particular fragment. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |