Single trajectory

KMC_Run.append_trajectories(run1, run2)

Take two trajectories and append them together.

Parameters:

• run1 – First trajectory - a kmc_traj object
• run2 – Second trajectory - a kmc_traj object which continues the simulation where the first one terminated

Returns:

A kmc_traj object that has the trajectories appended

class KMC_Run.kmc_traj(path=None)

Handles a single Zacros trajectory.

AdjustPreExponentials(delta_sdf)

Adjust the pre-exponential ratios of all elementary reactions

Parameters:delta_sdf – list or vector of ratios to apply. Must have length equal to the number of reactions.

CheckComplete()

Check to see if a Zacros run has completed successfully

LatticeMovie(include_neighbor_lines=False, spec_color_list=['b', 'g', 'r', 'c', 'm', 'y', 'k'])

Create a subfolder called lattice_frames Create a .png file with a picture of a lattice for every snapshot in history_output.txt

include_neighbor_lines : If true, will draw lines between neighboring lattice sites (takes more time) spec_color_list : List of colors to use for different species, will cycle through if there are more species than colors

PlotElemStepFreqs(window=[0.0, 1.0], time_norm=False, site_norm=1)

Plot a bar graph of elementary step frequencies versus time - output in elem_step_freqs.png in the directory with the Zacros run

Parameters:

• window – Beginning and ending fraction of the trajectory over which to count steps.
• time_norm – True - normalizes event frequencies by time. False - Plots total event firings.
• site_norm – Normalization factor for event frequencies.

PlotGasSpecVsTime()

Plot gas phase species profiles versus time - output in gas_spec_vs_time.png in the directory with the Zacros run

PlotLattice()

Plot the lattice - output in lattice.png in the run directory

PlotSurfSpecVsTime(site_norm=1)

Plot surface species profiles versus time - output in surf_spec_vs_time.png in the directory with the Zacros run

Parameters:site_norm – Normalizing factor for the coverages (e.g. nubmer of top sites). Default value if 1.

ReadAllInput()

Read all Zacros input files

ReadAllOutput(build_lattice=False)

Read all Zacros output files

:param build_lattice : True - builds a Lattice object

False - reads lattice_output.txt as text only

Run_sim()

Call the Zacros executable and run the simulation. self.exe_file must have been initialized with the full file path of the Zacros executable.

WriteAllInput()

Write all Zacros input files

time_avg_covs(t1=0, t2=None)

Time average surface species counts

Parameters:

• t1 – Start time for time averaging interval
• t2 – End time for time averaging interval, if left as None it will be set as the final time

time_search(t)

Given a time, look up the index of the smallest time greater than or equal to that time

Parameters:t – time to search for

time_search_interp(t)

Get the information necessary to linearly interpolate data between time points

Parameters:t – Time at which you want to compute interpolated data Returns:A 2-item list of 2-items each in the order: Index of time point less than or equal to t, index of time point greater than or equal to t weighting factor for lower point weighting factor for higher point