CompChem Library

From Henkelman Group

This is for the design of a common library for our group computational chemistry purposes.

Be sure to use the discussion page for any changes you make.

[edit] Numerical

1. Vector
   1. Members
      1. elements: an array of the Vector elements
      2. dimension: the dimension of the Vector (same as the number of elements)
   2. Methods
      1. magnitude: returns the length of the Vector
      2. unit: returns a unit Vector in the direction of the Vector
      3. plus: returns a new Vector which is the sum of the Vector and another Vector
      4. minus: returns a new Vector which is the Vector minus another Vector
      5. dot: returns the dot product of the Vector and another Vector
      6. random: returns a new Vector of random direction and unit length
2. Point
   1. Members
      1. coordinates: an array of the coordinates of the point
      2. dimension: the dimension of the Point (same as the number of coordinates)
   2. Methods
      1. random: returns a random Point
      2. vectorTo: returns a Vector to another Point
      3. distanceTo: returns the distance to another Point
      4. plus: returns a new Point with a Vector added to it
      5. minus returns a new Point with a Vector subtracted from it
3. Path
   1. Members
      1. images: an array of Points that defines the Path
   2. Methods
      1. length: returns the length of the Path
   3. EnergyPath
      1. Members
         1. potential: a Potential associated with the Path
         2. forceCalls: records the number of force calls made
      2. Methods
         1. imageForce: returns the force Vector due to the Potential on an image in the Path
         2. totalForce: returns the magnitude of the total force being exerted on all the images of the Path
         3. resetForceCalls: resets the number of recorded force calls to zero (redundant if we go with an public member framework)
      3. MinimumEnergyPath
         1. ElasticBand
            1. Members
               1. k: the spring force constant
            2. Methods
               1. springForce: returns the spring force Vector on a single image
               2. step: calculates and implements the next step
            3. NEB
               1. Methods
                  1. tangentForce: returns the spring force tangent to the Path
                  2. step: calculates and implements the next step (override)
               2. NEBSwitching
                  1. Methods
                     1. switchingForce: returns the spring force Vector perpendicular to the Path, taking the switching function into account
         2. String
            1. Methods
               1. redistribute: redistributes the images along the Path
         3. GrowingString
            1. note: Not a type of "String", so it is not a subclass.
4. Function
   1. Methods
      1. value: returns the value at a Point
      2. derivative: returns the derivative at a Point (1D functions only)
      3. partialDerivative: returns the partial derivative at a point, given one independent variable.
      4. gradient: returns a Vector which is the gradient at a point.
   2. Potential
      1. Methods
         1. force: returns a Vector representing the force at a Point
      2. Morse
      3. LEPS

[edit] I/O

1. Visualizer
   1. I propose we do this entirely in 3D, with any required 2D graphics done on a plane in 3D space. (Rye Terrell 08:04, 2 May 2007 (CDT))
2. Camera
   1. Defines a camera in 3D space.
3. TextIO
   1. Opens a window with a text field for textual output and a field for textual input.