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Table of contents
Introduction
What is pyZacros
What can be done with pyZacros
Simple example
Components overview
Species / Species List
API
Lattice
API
Cluster / Cluster Expansion
API
Elementary Reaction / Mechanism
API
LatticeState
API
Settings
API
ZacrosJob
API
ZacrosResults
API
Examples
Simple examples
Water-gas shift reaction on Pt(111).
The Ziff-Gulari-Barshad (ZGB) model.
Advanced examples
Poisoning of Pt(111) by CO: From atomistic to mesoscopic modeling
Getting the Energy Landscape
Getting the KMC Lattice
Generating the pyZacros objects
Running the pyZacros simulation
Phase Transitions in the ZGB model.
Citations
pyZacros
Documentation
/
pyZacros
/
Index
Index
A
|
C
|
E
|
F
|
G
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
Z
A
append() (ClusterExpansion method)
(Mechanism method)
C
check() (ZacrosJob method)
Cluster (class in scm.pyzacros.core.Cluster)
ClusterExpansion (class in scm.pyzacros.core.ClusterExpansion)
composition() (Species method)
coverage_fractions() (LatticeState method)
E
elementary_steps_names() (ZacrosResults method)
ElementaryReaction (class in scm.pyzacros.core.ElementaryReaction)
empty() (LatticeState method)
extend() (ClusterExpansion method)
(Mechanism method)
F
fill_all_sites() (LatticeState method)
fill_site() (LatticeState method)
fill_sites_random() (LatticeState method)
G
gas_species() (Cluster method)
(ClusterExpansion method)
(Mechanism method)
(SpeciesList method)
gas_species_names() (ZacrosResults method)
get_energetics_input() (ZacrosJob method)
get_initial_state_input() (ZacrosJob method)
get_input() (ZacrosJob method)
get_lattice_input() (ZacrosJob method)
get_mechanism_input() (ZacrosJob method)
get_process_statistics() (ZacrosResults method)
get_reaction_network() (ZacrosResults method)
get_restart_input() (ZacrosJob method)
get_runscript() (ZacrosJob method)
get_simulation_input() (ZacrosJob method)
get_TOFs() (ZacrosResults method)
get_zacros_version() (ZacrosResults method)
I
insert() (ClusterExpansion method)
(Mechanism method)
is_adsorbed() (Species method)
is_gas() (Species method)
L
label() (Cluster method)
(ElementaryReaction method)
(SpeciesList method)
last_lattice_state() (ZacrosResults method)
Lattice (class in scm.pyzacros.core.Lattice)
lattice_states() (ZacrosResults method)
LatticeState (class in scm.pyzacros.core.LatticeState)
load_external() (scm.pyzacros.core.ZacrosJob.ZacrosJob class method)
M
mass() (Cluster method)
(Species method)
(SpeciesList method)
Mechanism (class in scm.pyzacros.core.Mechanism)
N
number_of_filled_sites() (LatticeState method)
number_of_lattice_sites() (ZacrosResults method)
number_of_process_statistics() (ZacrosResults method)
number_of_sites() (Lattice method)
number_of_snapshots() (ZacrosResults method)
O
ok() (ZacrosResults method)
P
plot() (Lattice method)
(LatticeState method)
plot_lattice_states() (ZacrosResults method)
plot_molecule_numbers() (ZacrosResults method)
plot_process_statistics() (ZacrosResults method)
provided_quantities() (ZacrosResults method)
R
remove_duplicates() (SpeciesList method)
replace_site_types_names() (Cluster method)
(ClusterExpansion method)
(ElementaryReaction method)
(Lattice method)
(Mechanism method)
S
set_repeat_cell() (Lattice method)
Settings (class in scm.pyzacros.core.Settings)
site_type_names() (ZacrosResults method)
site_types_set() (Cluster method)
(ClusterExpansion method)
(ElementaryReaction method)
(Lattice method)
(Mechanism method)
Species (class in scm.pyzacros.core.Species)
species() (Mechanism method)
SpeciesList (class in scm.pyzacros.core.SpeciesList)
surface_species() (Cluster method)
(ClusterExpansion method)
(Mechanism method)
(SpeciesList method)
surface_species_names() (ZacrosResults method)
Z
ZacrosJob (class in scm.pyzacros.core.ZacrosJob)
ZacrosResults (class in scm.pyzacros.core.ZacrosResults)