pele.landscape.connect_manager

Module source

classes to organize strategies for selecting which minima in a database to choose for a double ended connect run.

class pele.landscape.connect_manager.ConnectManagerGMin

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class ConnectManagerGMin(BaseConnectManager):

return connect jobs in order to connect everything to the global minimum

class pele.landscape.connect_manager.ConnectManagerUntrap

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class ConnectManagerUntrap(BaseConnectManager):

class to select double ended connect jobs using the untrap strategy

Notes
------
the untrap strategy selects minima with the goal of eliminating artificially high
energy barriers.  Each minima is weighted by the energy barrier to get to the global
minimum divided by the energy difference with the global minimum.  This weight determines
the order with in the minima are selected for a double ended connect run.

Parameters
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database : pele Database object
list_len : int
    the class will create a list of minima pairs of length
    list_len.  When this list is empty the list will be rebuilt.
    Essentially this parameter indicates how often to rebuild the list
    of minima pairs to connect

class pele.landscape.connect_manager.ConnectManagerCombine

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class ConnectManagerCombine(BaseConnectManager):

a class to organize choosing minima in order to combine disconnected clusters of minima

Parameters:

databaseDatabase object

list_lenint

the class will create a list of minima pairs of length list_len. When this list is empty the list will be rebuilt. Essentially this parameter indicates how often to rebuild the list of minima pairs to connect

clust_minint

Clusters of minima below this size will be ignored.

class pele.landscape.connect_manager.ConnectManagerRandom

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class ConnectManagerRandom(BaseConnectManager):

manager to return random minima to connect

ConnectManagerRandom.get_connect_job()

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def get_connect_job(self):

select two minima randomly

class pele.landscape.connect_manager.ConnectManager

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class ConnectManager:

class to manage which minima to try to connect

Parameters:

databasepele Database object

strategystring

define the default strategy for the connect runs. Can be one of [“random”, “combine”, “untrap”, “gmin”]

Notes

Organize which minima pairs to submit for double ended connect jobs. This class chooses between the different selection strategies. The actual strategies are implemented in separate classes.

Selection strategies:

1. “random” : choose two minima randomly

2. “gmin” : connect all minima to the global minimum

3. “combine” : try to connect disconnected clusters of minima.

4. “untrap” : try to eliminate non-physical barriers to the global minimum

class ConnectManager.NoMoreConnectionsError

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class NoMoreConnectionsError(Exception):

raised when the connect manager can’t find any more pairs to connect

ConnectManager.untried()

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def untried(self, min1, min2):

return true if this minima pair have not been tried yet

ConnectManager.get_connect_job()

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def get_connect_job(self, strategy=None):

return the next connect job according to the chosen strategy