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Geometry.md

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The GEOMETRY directive is a compound directive that allows the user to define the geometry to be used for a given calculation. The directive allows the user to specify the geometry with a relatively small amount of input, but there are a large number of optional keywords and additional subordinate directives that the user can specify, if needed. The directive therefore appears to be rather long and complicated when presented in its general form, as follows:

 GEOMETRY [<string name default geometry>] \  
          [units <string units default angstroms>] \  
          [(angstrom_to_au || ang2au) \  
                 <real angstrom_to_au default 1.8897265>] \  
          [print [xyz] || noprint] \  
          [center || nocenter] \  
          [bqbq] \  
          [autosym [real tol default 1d-2] || noautosym] \  
          [autoz || noautoz] \  
          [adjust] \  
          [(nuc || nucl || nucleus) <string nucmodel>]  
   [SYMMETRY [group] <string group_name> [print] \  
          [tol <real tol default 1d-2>]]  
   [ [LOAD] [format xyz||pdb]  [frame <int frame>] \  
          [select [not] \  
               [name <string atomname>] \  
               [rname <string residue-name>]  
               [id  <int atom-id>|<int range atom-id1:atom-id2> ... ]  
               [resi <int residue-id>|<int range residue-id1:residue-id2> ... ]  
         ]  
   <string filename> ]  
    
   <string tag> <real x y z> [vx vy vz] [charge <real charge>] \  
          [mass <real mass>] \  
          [(nuc || nucl || nucleus) <string nucmodel>]  
   ... ]  
   [ZMATRIX || ZMT || ZMAT  
        <string tagn> <list_of_zmatrix_variables>  
        ...   
        [VARIABLES  
             <string symbol> <real value>  
             ... ]  
        [CONSTANTS  
             <string symbol> <real value>  
             ... ]  
    (END || ZEND)]  
    [ZCOORD  
         CVR_SCALING <real value>  
         BOND    <integer i> <integer j> \  
                 [<real value>] [<string name>] [constant]  
         ANGLE   <integer i> <integer j> \  
                     [<real value>] [<string name>] [constant]  
         TORSION <integer i> <integer j> <integer k> <integer l> \  
                 [<real value>] [<string name>] [constant]  
     END]  
           
     [SYSTEM surface  <molecule polymer surface crystal default molecule>  
          lat_a <real lat_a> lat_b <real lat_b> lat_c <real lat_c>  
          alpha <real alpha> beta <real beta> gamma <real gamma>  
     END]  
  END

The three main parts of the GEOMETRY directive are:

  • keywords on the first line of the directive (to specify such optional input as the geometry name, input units, and print level for the output)
  • symmetry information
  • Cartesian coordinates or Z-matrix input to specify the locations of the atoms and centers
  • lattice parameters (needed only for periodic systems)

The following sections present the input for this compound directive in detail, describing the options available and the usages of the various keywords in each of the three main parts.