Multiple trajectories¶
-
class
Replicates.Replicates[source]¶ Performs statistical data analysis for muliple kMC trajectories with the same input, but different random seeds and possibly different initial states
-
BuildJobFiles(init_states=None)[source]¶ Builds folders with Zacros input files. Each trajectory is assigned a different random seed. :param init_states: List of intial states for each trajectory.
-
Compute_batch_data(n_batches_total=1000)[source]¶ Compute varaibles needed for the analysis, based on the input
-
Compute_rate(include_ACF_CI=True)[source]¶ Use batch means to compute the reaction rate (and confidence interval) Also compute the autocorrelation function (ACF) (and confidence interval)
Params include_ACF_CI: Whether to use statistical bootstrapping to compute confidence intervals. This takes some CPU time. Returns: The rate
-
PerformSA(delta_t=None, ergodic=True, dp_per_bin=10)[source]¶ Perform likelihood ratio sensitivity analysis with a combination of time and trajectory averaging
Parameters: - delta_t – Size of the time window used for likelihood ratio sensitivity analysis. By default, it is the size of a batch.
- ergodic –
- True - average the rate over the entire time interval (centered ergodic likelihood ratio)
- False - use the rate at the end of the time interval (centered likelihood ratio)
Data between sample points is estimated with linear interpolation
-
PlotSensitivities(NSC_cut=0.05)[source]¶ Plot the results of sensitivity analysis
NSC_cut : Reactions with normalized sensitivity coefficients (NSC) below this limit will not be plotted
-
RunAllTrajectories_JobArray(max_cores=100, server='Squidward', job_name='zacros_JA')[source]¶ Runs a job array on Squidward or Farber Writes the .qs file with certain parameters changed Then, it submits it to the gridengine and waits for them to finish :param max_cores: Maximum number of cores to use :param server: Name of the server. Squidward and Farber are supported. :param job_name: Name of the job to put in the submit file.
-