4. Creating Input Files for Automated Pressure Dependent Network Exploration

4.1. Syntax

Network exploration starts from a pressure dependent calculation job so naturally it requires an input file containing everything required for a pressure-dependent calculation input file. In addition all species blocks must have a structure input and there must be a database block in the job. At the end of the pressure-dependent calculation input file you append an explorer block. For example

explorer(
    source=['methoxy'],
    explore_tol=0.01,
    energy_tol=1e4,
    flux_tol=1e-6,
)

The source is a list containing either the label for a single isomer or the labels corresponding to a bimolecular source channel. The network is expanded starting from this starting isomer/channel.

4.2. Network Exploration

The explore_tol is a fraction of the flux from all net reactions from the source to the other channels in the network. Network expansion is done starting from just the network source using values from the rest of the Arkane job when available, otherwise from RMG. It cycles through all of the temperature and pressure points specified for fitting in the pressure dependence job and checks the total network leak rate at each one. Whenever this rate is greater than explore_tol*kchar, where kchar is the total flux from all net reactions away from the source, the outside isomer with the most leak is added to the network and reacted and the loop is flagged to cycle through all of the temperatures and pressures again. Once this loop is finished a network_full.py file is generated in the pdep directory that has the full explored network.

4.3. Network Reduction

energy_tol and flux_tol control reduction of the full network. This is highly recommended as the full model will often contain many unimportant reactions. How strict you decide to set these parameters should be related to how much you trust the thermo and rate information being used in the job.

energy_tol is related to the maximum difference in E0 allowed between a reaction TS and the source channel/isomer. A given reaction is deemed filterable at a given condition if energy_tol * RT < E0_TS - E0_source. For example, if T = 1000 K and energy_tol is set to 100 and the source energy is 100 (kJ mol^-1), all reactions with a transition state energy more than 100 * 8.314 (J K^-1 mol^-1) * 1000 K + 100 (kJ mol^-1) = 931.4 (kJ mol^-1) will not be considered in the final network.

flux_tol is related to the solution of a steady state problem. In this problem a constant flux of 1.0 (choice of units irrelevant) is applied to the source channel/isomer while all A => B + C reactions are assumed to be irreversible. Under these conditions steady state concentrations of each isomer and the rates of every unimolecular reaction can be calculated. Since the input flux to the system is 1.0 to some degree these rates represent the fraction of the input flux passing through that reaction. When the flux through a reaction is less than flux_tol it is deemed filterable at that condition.

Overall a reaction is removed from the network if it is deemed filterable by both methods (if both specified) at every temperature and pressure combination. After reduction a network_reduced.py file is generated in the pdep directory containing the reduced network.