In INTERNAL module internal coordinates (DISTANCES, ANGLES and DIHEDRAL ANGLES) and internal coordinates connectivity table (ZTABLE) can be edited. Directly by defining values explicitly or indirectly by defining variables and their values. Each internal coordinate may have its own variable name as well as a single variable name may be shared by a group of internal coordinates. ZTABLE, however, consist only of atomic number references.
SET INTERNAL VARIABLE DISTANCE
CONSTANT ANGLE DIHEDRAL (ALL) DISTANCE real ANGLE real DIHEDRAL real (ALL) 3*real
VARIABLE STRING real AUTO DISTANCE ANGLE DIHEDRAL (ALL)
ZTABLE ATOM-NUM DISTANCE atom-num ANGLE atom-num DIHEDRAL atom-num [(0), 1 or -1] (ALL) 3 x atom-num [(0), 1 or -1]
SHOW INTERNAL VARIABLE DISTANCE
CONSTANT ANGLE DIHEDRAL (ALL) DISTANCE ANGLE DIHEDRAL (ALL)
VARIABLE string LIST
ZTABLE atom-num DISTANCE ANGLE DIHEDRAL (ALL)
EXIT exits the INT_COOR modul and returns to MAIN.
SELECT ... END
A command will allways act on the last defined SELECTION. By default all atoms are SELECTED.
Sets the distance, angle, dihedral or all internal coordinates a real value. Using VARIABLE command word the variable flag for the selected internal coordinates of atoms is set. The CONSTANT unsets the variable flags. The CONSTANCE or VARIABLE ought to be used first otherwise a real value for specified internal coordinate specification is required.
Connects the selected internal coordinates with a variable name. If a variable name exists (differs from 4 blanks(' ')), a real value can be seted to all the internal coordinates connected with that variable name. If AUTO is specified then the string is a root for automatic assigning of varible name. Each time a variable name is assigned to specified internal coordinate, a number is increased for 1 and added.
The connections in the table can be overriden by typing in the new connections. When changing the second angle specification into the dihedral angle specification two numbers are required.
Shows the data fields than can be set. VARIABLE shows only the first value of chosen variable. When the user wants to see the list of all the values, that can be different than the command word LIST should be used. While showing the ztable the output can be changed from numbers to atom symbol and vice versa by using the SYMBOL or NUMBER command word.
SYMBOL and NUMBER commands are used to set the symbol flag (fsymb) that changes from atom-number to atom symbol and vice versa in input and output. By default the numbers are required to identify the atoms. When symbol flag is set then the user shoul type in the atom symbol. The atom with this symbol will be found in the selected range if it is uniquely defined. When '-' stnands before the atom symbol then the first atom with that identifier, counting from the first atom in the selection down, will be found. When '+' stnands before the atom symbol then the first atom with that identifier, counting from the last atom in the selection up, will be found.
VARIABLE and CONSTANT commands are used to set the variable_display flag (fvari). When fvari flag is set then variable names are displayed if they exist on the place of internal coordinate value, if SHOW INTERNAL command sentence is used.
set var a auto angle generates variables for angles a1, a2, ... a56, untill the end of selection.