pele.storage.TransitionState#

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

Transition state object

The TransitionState class represents a saddle point in the database.

Parameters:

energyfloat
coordsnumpy array
min1Minimum object: first minimum
min2Minimum object: first minimum
eigenvalfloat, optional: lowest (single negative) eigenvalue of the saddle point
eigenvecnumpy array, optional: eigenvector which corresponds to the negative eigenvalue
fvibfloat: log product of squared frequencies for free energy calculation
pgorderinteger: point group order

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

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

Methods

id()

return the sql id of the object

Attributes

`coords`	coordinates of transition state
`eigenval`	coordinates of transition state
`eigenvec`	coordinates of transition state
`energy`	energy of transition state
`fvib`	log product of the squared normal mode frequencies
`invalid`	flag indicating if the transition state is invalid
`metadata`
`minimum1`	first minimum which connects to transition state
`minimum2`	second minimum which connects to transition state
`pgorder`	point group order
`registry`
`user_data`	this can be used to store information about the transition state