westpa.westext.wess package
Submodules
westpa.westext.wess.ProbAdjust module
- westpa.westext.wess.ProbAdjust.solve_steady_state(T, U, target_bins_index)
- westpa.westext.wess.ProbAdjust.prob_adjust(binprob, rates, uncert, oldindex, targets=[])
westpa.westext.wess.wess_driver module
- westpa.westext.wess.wess_driver.check_bool(value, action='warn')
Check that the given
valueis boolean in type. If not, either raise a warning (ifaction=='warn') or an exception (action=='raise').
- class westpa.westext.wess.wess_driver.RateAverager(bin_mapper, system=None, data_manager=None, work_manager=None)
Bases:
objectCalculate bin-to-bin kinetic properties (fluxes, rates, populations) at 1-tau resolution
- extract_data(iter_indices)
Extract data from the data_manger and place in dict mirroring the same underlying layout.
- task_generator(iter_start, iter_stop, block_size)
- calculate(iter_start=None, iter_stop=None, n_blocks=1, queue_size=1)
Read the HDF5 file and collect flux matrices and population vectors for each bin for each iteration in the range [iter_start, iter_stop). Break the calculation into n_blocks blocks. If the calculation is broken up into more than one block, queue_size specifies the maxmimum number of tasks in the work queue.
- westpa.westext.wess.wess_driver.prob_adjust(binprob, rates, uncert, oldindex, targets=[])
- westpa.westext.wess.wess_driver.bins_from_yaml_dict(bin_dict)
- westpa.westext.wess.wess_driver.reduce_array(Aij)
Remove empty rows and columns from an array Aij and return the reduced array Bij and the list of non-empty states
Module contents
- westpa.westext.wess.prob_adjust(binprob, rates, uncert, oldindex, targets=[])