In this case, the atom-position-parameters are the labels or line numbers for previously-specified atoms which will be used to define the current atom’s position we will designate them here as atom1, atom2 and atom3. Z-matrix molecule specifications are also accepted. ![]() The available items are documented in the other tabs. Here is a simple molecule specification section for ethane which uses element labels for the carbon atoms and element types for the hydrogen atoms:Īdditional information can be specified for each atom with a parenthecized keyword list following the element specification/label. The remaining items on each line are Cartesian coordinates specifying the position of that nucleus. The maximum length of the element label is 4 characters. A common practice is to follow the element name with a secondary identifying integer: C1, C2, C3, and so on this technique is useful in following conventional chemical numbering. If the elemental symbol is used, it may be optionally followed by other alphanumeric characters to create an identifying label for that atom. freeze-code is an optional parameter related to freezing atoms during optimizations.Įlement-label is a character string consisting of either the chemical symbol for the atom or its atomic number. The position of the atom is specified in Cartesian coordinates. Here is the basic format for specifying atoms within the molecule specification (omitting all of the optional items): Element-label x y zĪlthough these examples use spaces to separate items within a line, any valid separator may be used. ![]() We'll begin by considering the initial and final items, and then go on to discuss the remaining items. The remainder of the line contains information about the atom's location, either as Cartesian coordinates or as a Z-matrix definition. Nuclear parameters for this atom are specified in the parenthesized list. The most general format for the line within it is the following: Element-label])] Atom-position-parametersĮach line contains the element type, and possibly an optional molecular mechanics atom type and partial charge. ![]() The remainder of the molecule specification gives the element type and nuclear position for each atom in the molecular system. The entire molecule specification (and title section) may be omitted by including Geom=AllCheck in the route section. The charge and spin line is the only molecule specification input required if Geom=Checkpoint is used. Multiple charge/spin pairs may/must be included for some calculation types. ![]() Thus, for a neutral molecule in a singlet state, the entry 0 1 is appropriate. The first line of the molecule specification section specifies the net electric charge (a signed integer) and the spin multiplicity (usually a positive integer). There are several ways in which the nuclear configuration can be specified: as a Z-matrix, as Cartesian coordinates, or as a mixture of the two (note that Cartesian coordinates are just a special case of the Z-matrix). This input section specifies the nuclear positions and the number of electrons of α- and β-spin.
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