pele.storage.TransitionState

class pele.storage.TransitionState(energy, coords, min1, min2, eigenval=None, eigenvec=None)

Transition state object

The TransitionState class represents a saddle point in the database.

Parameters :

energy : float

coords : numpy array

min1 : Minimum object

first minimum

min2 : Minimum object

first minimum

eigenval : float, optional

lowest (single negative) eigenvalue of the saddle point

eigenvec : numpy array, optional

eigenvector which corresponds to the negative eigenvalue

fvib : float

log product of squared frequencies for free energy calculation

pgorder : integer

point group order

See also

Database, Minimum

Notes

To avoid any double entries and be able to compare them, only use Database.addTransitionState to create a TransitionStateobject.

programming note: The functions in the database require that ts.minimum1._id < ts.minimum2._id. This will be handled automatically by the database, but we must remember not to screw it up

Attributes

energy :	The energy of the transition state
coords :	The coordinates of the transition state. This is stored as a pickled numpy array which SQL interprets as a BLOB.
fvib :	The log product of the squared normal mode frequencies. This is used in the free energy calcualations
pgorder :	The point group order
invalid :	A flag that is used to indicate a problem with the transition state. E.g. if the Hessian has more than one negaive eigenvalue then it is a higher order saddle.
user_data :	Space to store anything that the user wants. This is stored in SQL as a BLOB, so you can put anything here you want as long as it’s serializable. Usually a dictionary works best.
minimum1, minimum2 :	These returns the minima on either side of the transition state
eigenvec :	The vector which points along the direction crossing the transition state. This is the eigenvector of the lowest non-zero eigenvalue.
eigenval :	The eigenvalue corresponding to eigenvec. A.k.a. the curvature along the direction given by eigenvec

Methods

id()	return the sql id of the object