Reading/writing Zacros input/output

class IO_data.Cluster

Cluster in energetics_input.dat

class IO_data.ClusterIn

Handles data from energetics_input.dat

FindCluster(Cluster_Num)

Method finds the Cluster and Variant index of the nth Cluster-Variant where n is specified by Cluster_Num and the indices are returned as C.index (Cluster) and V.index (Variant) such that Cluster[C_index].variant_name[V_index] represents the name of the nth Cluster-Variant

ReadIn(fldr)

Read energetics_input.dat

WriteIn(fldr)

Write energetics_input.dat

class IO_data.HistoryOut

Handles data from history_output.txt

ReadOut(fldr, nSites)

Read history_output.txt fldr: name of the folder containting the file nSites: number of lattice sites, obtained from lattice_output.txt

class IO_data.MechanismIn

Handles input from mechanism_input.dat

CalcThermo(fldr, T)

Calculate the forward activation energy, forward and reverse pre-exponential factors and the PE-ratio for each reaction described in Mechanism_input.dat using an input file with energies and vibrational frequencies for all species and transition states

Assumes that each reaction has only 1 variant (MPN)

FindReaction(Reaction_Num)

Method finds the Reaction and Variant index of the nth Reaction-Variant where n is specified by Cluster_Num and the indices are returned as R.index (Reaction) and V.index (Variant) such that Reaction[R_index].variant_name[V_index] represents the name of the nth Reaction-Variant

ReadIn(fldr)

Read mechanism_input.dat

WriteIn(fldr)

Write mechanism_input.dat

class IO_data.PerformanceOut

Handles data from general_output.txt

ReadOut(fldr, surf_spec_names, gas_spec_names)

Read general_output.txt

class IO_data.ProcstatOut

Handles data from procstat_output.txt

ReadOut(fldr)

Read procstat_output.txt

class IO_data.Reaction

Reaction in mechanism_input.dat

IO_data.Read_propensities(path, nRxn)

Read propenisty data from output files. The initial time point: At t = 0 or after 0 events is wrong because it is recorded before the first propensities are calculated. Instead, they are erroneously all zeros and should not be used for averaging. The rest are correct.

Parameters:Mode – 0 - Read Prop_output.bin, instantaneous propensities 1 - Read PropCounter_output.bin, time integrated propensities used for accurate time averages Returns:Matrix of time integrated surface species populations

IO_data.Read_time_integrated_propensities(path, nRxn)

Read propenisty data from output files. The initial time point: At t = 0 or after 0 events is wrong because it is recorded before the first propensities are calculated. Instead, they are erroneously all zeros and should not be used for averaging. The rest are correct.

Parameters:Mode – 0 - Read Prop_output.bin, instantaneous propensities 1 - Read PropCounter_output.bin, time integrated propensities used for accurate time averages Returns:Matrix of time integrated surface species populations

IO_data.Read_time_integrated_site_props(path, nSites, nRxn, nSnaps)

Read time integrated site propensities

Returns:List of [nSites x nRxn] matrices, one for each snapshot

IO_data.Read_time_integrated_species(path, n_surf_specs)

Read time integrated species counts

Returns:Matrix of time integrated surface species populations

IO_data.Read_trajectory_derivatives(path, nRxn)

Read SA_output.bin - get trajectory derivatives for use in likelihood ratio sensitivity analysis

Returns:Matrix of trajectory derivatives

class IO_data.SimIn

Handles input from simulation_input.dat

ReadIn(fldr)

Read simulation_input.dat

WriteIn(fldr)

Write simulation_input.dat

class IO_data.SpecnumOut

Handles data from specnum_output.txt

ReadOut(fldr)

Read specnum_output.txt

class IO_data.StateIn

Handles input from state_input.dat

ReadIn(fldr)

Read state_input.dat

WriteIn(fldr, surf_spec)

Write state_input.dat

class IO_data.cluster_variant

Variant of a cluster in energetics_input.dat

class IO_data.rxn_variant

Variant of a reaction in mechanism_input.dat