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Constraints.md

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Constraints

The constraints directive allows the user to specify which constraints should be imposed on the system during the analysis of potential energy surface. Currently such constraints are limited to fixed atom positions and harmonic restraints (springs) on the distance between the two atoms. The general form of constraints block is presented below:

CONSTRAINTS [string name ] \  
          [clear] \  
          [enable||disable] \  
          [fix atom <integer list>] \  
          [spring bond `<integer atom1> <integer atom2> <real k> <real r0> ]  
          [spring bondings <real K0> <real gamma0> [<real ca> <integer atom1a> <integer atom2a> 
                                             <real cb> <integer atom1b> <integer atom2b>
                                             ...]]
          [penalty pbondings <real K0> <real gcut0> <real gamma0> [<real ca> <integer atom1a> <integer atom2a> 
                                                           <real cb> <integer atom1b> <integer atom2b>
                                                           ...]]
 END

The keywords are described below

  • name - optional keyword that associates a name with a given set of constraints. Any unnamed set of constraints will be given a name default and will be automatically loaded prior to a calculation. Any constraints with the name other than default will have to be loaded manually using SET directive. For example,
 CONSTRAINTS one  
   spring bond 1 3 5.0 1.3
   fix atom 1  
 END 
  
 #the above constraints can be loaded using the set directive`  
 set constraints one  
 ....  
 task ....
  • clear - destroys any prior constraint information. This may be useful when the same constraints have to be redefined or completely removed from the runtime database.
  • enable||disable - enables or disables particular set of constraints without actually removing the information from the runtime database.
  • fix atom - fixes atom positions during geometry optimization. This directive requires an integer list that specifies which atoms are to be fixed. This directive can be repeated within a given constraints block. To illustrate the use "fix atom" directive let us consider a situation where we would like to fix atoms 1, 3, 4, 5, 6 while performing an optimization on some hypothetical system. There are actually several ways to enter this particular constraint.
  • There is a straightforward option which requires the most typing:
       constraints  
         fix atom 1 3 4 5 6 
       end
  • Second method uses list input:
       constraints  
         fix atom 1 3:6  
       end
  • Third approach illustrates the use of multiple fix atom directives:
       constraints 
         fix atom 1 
         fix atom 3:6 
       end
  • spring bond $<i j k r_0>$ - places a spring with a spring constant k and equilibrium length $r_0$ between atoms i and j (all in atomic units). Please note that this type of constraint adds an additional term to the total energy expression

$E=E_{total}+ \,\!\frac{1}{2} k(r_{ij}-r_0)^2$

This additional term forces the distance between atoms i and j to be in the vicinity of $r_0$ but never exactly that. In general the spring energy term will always have some nonzero residual value, and this has to be accounted for when comparing total energies. The "spring bond" directive can be repeated within a given constraints block. If the spring between the same pair of atoms is defined more than once, it will be replaced by the latest specification in the order it appears in the input block.