The kmos3 software package is a vigorous attempt to make (lattice) kinetic Monte Carlo (KMC) modelling more accessible. It is designed for and by KMC model developers with the aim to facilitate and speed up KMC model development.

Code structure of the kmos3 software package.

Not sure about how and where to begin? Start with the API tutorial.

• Installation
  • Prerequisites
  • Installation
  • Dependencies
  • Test Input
  • Getting Started
• Development
  • GitLab Access
  • Issues
  • Documentation
  • Branches
  • Tags
  • Commits
  • Merges
  • CI/CD
  • Developer’s Guide
    • Introduction
    • How to Edit, Install, and Test Your Changes Locally
    • Some Nomenclature
    • The Three Backends
      • local_smart
      • lat_int
      • otf
    • The Fortran Code Files
      • local_smart
        • base.f90
        • lattice.f90
        • proclist.f90
      • lat_int
        • proclist.f90
        • proclist_constants.f90
        • nli_<lat_int_nr>.f90
        • run_proc_<lat_int_nr>.f90
      • otf
        • proclist.f90
        • proclist_constants.f90
        • proclist_pars.f90
        • run_proc_<proc_nr>.f90
    • Key Data Structures
      • Important Scalar Variables
      • Important Arrays
        • rates
        • lattice
        • nr_of_sites
        • accum_rates
        • avail_sites
        • procstat
      • otf-Specific Arrays
        • accum_rates_proc
        • rates_matrix
    • One KMC Step in kmos3
      • local_smart
      • The put and take Routines
      • Updating avail_sites
      • lat_int
      • otf
    • The Code Generation Routines
      • Source File Templates
      • write_proclist
        • Methods Called to Build local_smart Source Code
          • write_proclist_generic_part
          • write_proclist_constants
          • write_proclist_generic_subroutines
          • write_proclist_run_proc_nr_smart
          • write_proclist_put_take
          • write_proclist_touchup
          • write_proclist_multilattice
          • write_proclist_end
        • Methods Called to Build lat_int Source Code
          • write_proclist_lat_int
          • write_proclist_lat_int_run_proc_nr
          • write_proclist_lat_int_touchup
          • write_proclist_lat_int_run_proc
          • write_proclist_lat_int_nli_casetree
        • Methods Called to Build otf Source Code
          • write_proclist_pars_otf
          • write_proclist_touchup_otf
          • write_proclist_run_proc_nr_otf
          • write_proclist_run_proc_name_otf
• Tutorials
  • Introduction
  • Feature Overview
  • The Runtime View
  • A First KMC Model
    • Build the Model
    • Populate Process List and Parameter List
    • Export, Save, Compile
    • Running and Viewing the Model
    • An Alternative Way Using INI Files
    • Taking it Home
  • Running the Model From Runfiles
    • Running the Model–The API Way
    • Generate Grids of Sampled Data
    • Manipulating the Model Species at Runtime
    • Saving and Reloading the State of the Simulation
    • Running Models in Parallel
• Topic Guides
  • The Concept of Kinetic Monte Carlo
    • Why use Kinetic Monte Carlo?
    • Basic Kinetic Carlo Algorithm
    • Justification of the Algorithm
    • Further Reading
  • Modelling Workflows
    • KMC Modeling
    • Kmos3 Workflows
  • The kmos3 Implementation
    • How the kmos3 KMC Algorithm Works
    • The kmos3 O(1) Solver
  • The kmos3 Data Model
  • The Site/Coordinate Syntax
    • Manual Generation
    • Advanced Coordinate Techniques
    • Taking it Home
  • The Process Syntax
    • Adsorption
    • Diffusion
    • Avoid Double Counting
    • Taking It Home
  • Modeling Lateral Interactions
    • Lateral Interaction Models
    • Conquering Combinatorics with itertools
    • The otf Backend
      • Usage
      • Example
      • Advanced otf Rate Expressions
      • Running otf Models
      • Known Issues
  • Temporal Acceleration
• Reference
  • Command Line Interface (CLI)
    • Positional Arguments
    • Named Arguments
    • Sub-commands
      • benchmark
        • Named Arguments
      • build
        • Named Arguments
      • export
        • Positional Arguments
        • Named Arguments
      • settings-export
        • Positional Arguments
        • Named Arguments
      • import
        • Positional Arguments
      • rebuild
        • Named Arguments
      • shell (run)
      • view
        • Named Arguments
      • xml
  • Data Types
    • kmos3.types
      • Action
      • Bystander
        • Bystander._shorthand()
        • Bystander.attributes
      • Condition
      • ConditionAction
        • ConditionAction._shorthand()
        • ConditionAction.attributes
      • Coord
        • Coord.pos
        • Coord._get_genstring()
        • Coord.attributes
        • Coord.eq_mod_offset()
        • Coord.ff()
        • Coord.radd_ff()
        • Coord.rsub_ff()
        • Coord.site_offset_unpacked()
        • Coord.sort_key()
      • FixedObject
        • FixedObject.attributes
      • LatIntProcess
        • LatIntProcess.attributes
      • Layer
        • Layer.add_site()
        • Layer.attributes
        • Layer.get_info()
        • Layer.get_site()
      • LayerList
        • LayerList.attributes
        • LayerList.generate_coord()
        • LayerList.generate_coord_set()
        • LayerList.set_representation()
      • Meta
        • Meta.add()
        • Meta.get_extra()
        • Meta.name
        • Meta.setattribute()
      • OutputItem
        • OutputItem.attributes
      • OutputList
        • OutputList.attributes
      • Parameter
        • Parameter.attributes
        • Parameter.get_info()
        • Parameter.on_adjustable__do_toggled()
        • Parameter.on_name__content_changed()
      • ParameterList
        • ParameterList.attributes
      • Process
        • Process._get_max_d()
        • Process.add_action()
        • Process.add_bystander()
        • Process.add_condition()
        • Process.attributes
        • Process.evaluate_rate_expression()
        • Process.executing_coord()
        • Process.get_info()
      • ProcessFormSite
        • ProcessFormSite.attributes
      • ProcessList
        • ProcessList.attributes
      • Project
        • Project._get_etree_xml()
        • Project._get_ini_string()
        • Project._get_xml_string()
        • Project.add_layer()
        • Project.add_parameter()
        • Project.add_process()
        • Project.add_site()
        • Project.add_species()
        • Project.clear_model()
        • Project.compile_model()
        • Project.export_xml_file()
        • Project.get_parameters()
        • Project.get_processes()
        • Project.get_speciess()
        • Project.import_file()
        • Project.import_ini_file()
        • Project.import_xml_file()
        • Project.parse_and_add_process()
        • Project.parse_process()
        • Project.print_statistics()
        • Project.save()
        • Project.save_model()
        • Project.set_meta()
        • Project.shorten_names()
        • Project.validate_model()
      • SingleLatIntProcess
        • SingleLatIntProcess.attributes
      • Site
        • Site.attributes
      • Species
        • Species.attributes
      • SpeciesList
        • SpeciesList.attributes
      • cmp_coords()
      • create_kmc_model()
      • parse_chemical_expression()
      • parse_process()
      • prettify_xml()
    • kmos3.io
      • ProcListWriter
        • ProcListWriter._db_print()
        • ProcListWriter._get_lat_int_groups()
        • ProcListWriter._get_site_params()
        • ProcListWriter._gpl_message()
        • ProcListWriter._otf_get_auxilirary_params()
        • ProcListWriter._parse_otf_rate()
        • ProcListWriter._parse_otf_rate_line()
        • ProcListWriter._write_optimal_iftree()
        • ProcListWriter._write_optimal_iftree_otf()
        • ProcListWriter.write_proclist()
        • ProcListWriter.write_proclist_acf()
        • ProcListWriter.write_proclist_acf_end()
        • ProcListWriter.write_proclist_constants()
        • ProcListWriter.write_proclist_end()
        • ProcListWriter.write_proclist_generic_part()
        • ProcListWriter.write_proclist_generic_subroutines()
        • ProcListWriter.write_proclist_generic_subroutines_acf()
        • ProcListWriter.write_proclist_get_diff_sites_acf_otf()
        • ProcListWriter.write_proclist_get_diff_sites_acf_smart()
        • ProcListWriter.write_proclist_get_diff_sites_displacement_otf()
        • ProcListWriter.write_proclist_get_diff_sites_displacement_smart()
        • ProcListWriter.write_proclist_lat_int()
        • ProcListWriter.write_proclist_lat_int_nli_caselist()
        • ProcListWriter.write_proclist_lat_int_nli_casetree()
        • ProcListWriter.write_proclist_lat_int_run_proc()
        • ProcListWriter.write_proclist_lat_int_run_proc_nr()
        • ProcListWriter.write_proclist_lat_int_touchup()
        • ProcListWriter.write_proclist_multilattice()
        • ProcListWriter.write_proclist_otf()
        • ProcListWriter.write_proclist_pars_otf()
        • ProcListWriter.write_proclist_put_take()
        • ProcListWriter.write_proclist_run_proc_name_otf()
        • ProcListWriter.write_proclist_run_proc_nr_otf()
        • ProcListWriter.write_proclist_run_proc_nr_smart()
        • ProcListWriter.write_proclist_touchup()
        • ProcListWriter.write_proclist_touchup_otf()
        • ProcListWriter.write_settings()
        • ProcListWriter.write_template()
      • _casetree_dict()
      • _chop_line()
      • _flatten()
      • _most_common()
      • _print_dict()
      • clear_model()
      • export_source()
      • export_xml()
      • import_xml()
      • import_xml_file()
  • Runtime Frontend
    • kmos3.run
      • KMC_Model
        • KMC_Model._adjust_database()
        • KMC_Model._get_configuration()
        • KMC_Model._put()
        • KMC_Model._set_configuration()
        • KMC_Model.create_configuration_plot()
        • KMC_Model.deallocate()
        • KMC_Model.do_acc_steps()
        • KMC_Model.do_steps()
        • KMC_Model.do_steps_time()
        • KMC_Model.double()
        • KMC_Model.dump_config()
        • KMC_Model.export_movie()
        • KMC_Model.export_picture()
        • KMC_Model.get_atoms()
        • KMC_Model.get_avail()
        • KMC_Model.get_backend()
        • KMC_Model.get_buffer_parameter()
        • KMC_Model.get_executed_rates()
        • KMC_Model.get_executed_rates_limit()
        • KMC_Model.get_execution_steps()
        • KMC_Model.get_global_configuration()
        • KMC_Model.get_local_configurations()
        • KMC_Model.get_next_kmc_step()
        • KMC_Model.get_occupation_header()
        • KMC_Model.get_param_header()
        • KMC_Model.get_param_value()
        • KMC_Model.get_sampling_steps()
        • KMC_Model.get_save_limit()
        • KMC_Model.get_saved_executions()
        • KMC_Model.get_scaling_stats()
        • KMC_Model.get_species_coordinates()
        • KMC_Model.get_std_header()
        • KMC_Model.get_std_sampled_data()
        • KMC_Model.get_threshold_parameter()
        • KMC_Model.get_tof_header()
        • KMC_Model.halve()
        • KMC_Model.inverse()
        • KMC_Model.load_config()
        • KMC_Model.nr2site()
        • KMC_Model.peek()
        • KMC_Model.pickle_export_atoms()
        • KMC_Model.play_ascii_movie()
        • KMC_Model.plot_configuration()
        • KMC_Model.post_mortem()
        • KMC_Model.print_accum_rate_summation()
        • KMC_Model.print_adjustable_parameters()
        • KMC_Model.print_coverages()
        • KMC_Model.print_kmc_state()
        • KMC_Model.print_proc_pair_eq()
        • KMC_Model.print_procstat()
        • KMC_Model.print_scaling_factors()
        • KMC_Model.print_scaling_stats()
        • KMC_Model.print_state_summary()
        • KMC_Model.procstat_normalized()
        • KMC_Model.procstat_pprint()
        • KMC_Model.put()
        • KMC_Model.rate_ratios()
        • KMC_Model.reset()
        • KMC_Model.run()
        • KMC_Model.run_proc_nr()
        • KMC_Model.set_buffer_parameter()
        • KMC_Model.set_debug_level()
        • KMC_Model.set_executed_rates_limit()
        • KMC_Model.set_execution_steps()
        • KMC_Model.set_sampling_steps()
        • KMC_Model.set_save_limit()
        • KMC_Model.set_threshold_parameter()
        • KMC_Model.show()
        • KMC_Model.show_ascii_picture()
        • KMC_Model.switch_surface_processes_off()
        • KMC_Model.switch_surface_processes_on()
        • KMC_Model.view()
        • KMC_Model.xml()
      • Model_Rate_Constants
        • Model_Rate_Constants.__call__()
        • Model_Rate_Constants.by_name()
        • Model_Rate_Constants.inverse()
        • Model_Rate_Constants.names()
        • Model_Rate_Constants.set()
      • Model_Parameters
        • Model_Parameters.__call__()
        • Model_Parameters.names()
      • ModelRunner
        • ModelRunner.__product()
        • ModelRunner.__run_sublist()
        • ModelRunner.__split_seq()
        • ModelRunner.__touch()
        • ModelRunner.parameters
        • ModelRunner.plot()
        • ModelRunner.run()
        • ModelRunner.runner_name
      • ModelParameter
        • ModelParameter.get_grid()
      • PressureParameter
        • PressureParameter.get_grid()
      • TemperatureParameter
        • TemperatureParameter.get_grid()
      • LinearParameter
        • LinearParameter.get_grid()
      • LogParameter
        • LogParameter.get_grid()
    • kmos3.view
      • AutoScrollbar
        • AutoScrollbar.set()
      • KMC_PlotBox
        • KMC_PlotBox.on_resize()
        • KMC_PlotBox.update_plots()
      • KMC_Viewer
        • KMC_Viewer.exit()
        • KMC_Viewer.parameter_callback()
      • ParamSlider
        • ParamSlider.linlog_scale_format()
        • ParamSlider.value_changed()
      • main()
    • kmos3.cli
      • _benchmark()
      • _build()
      • _export()
      • _import()
      • _parser()
      • _rebuild()
      • _settings_export()
      • _shell()
      • _view()
      • _xml()
      • get_options()
      • main()
      • shell()
    • kmos3.utils
      • CorrectlyNamed
        • CorrectlyNamed.on_name__validate()
      • T_grid()
      • build()
      • col_str2tuple()
      • col_tuple2str()
      • evaluate_kind_values()
      • evaluate_template()
      • get_ase_constructor()
      • jmolcolor_in_hex()
      • p_grid()
      • product()
      • split_sequence()
      • timeit()
      • write_py()
  • Connected Variables
  • kmos3 KMC Project DTD
  • Backends
    • local_smart
      • kmos3/base
        • base/accum_rates
        • base/add_proc
        • base/allocate_system
        • base/assertion_fail
        • base/avail_sites
        • base/can_do
        • base/deallocate_system
        • base/del_proc
        • base/determine_procsite
        • base/get_accum_rate
        • base/get_avail_site
        • base/get_integ_rate
        • base/get_kmc_step
        • base/get_kmc_time
        • base/get_kmc_time_step
        • base/get_kmc_volume
        • base/get_nrofsites
        • base/get_procstat
        • base/get_rate
        • base/get_species
        • base/get_system_name
        • base/get_walltime
        • base/increment_procstat
        • base/integ_rates
        • base/interval_search_real
        • base/kmc_step
        • base/kmc_time
        • base/kmc_time_step
        • base/lattice
        • base/nr_of_proc
        • base/nr_of_sites
        • base/procstat
        • base/rates
        • base/reload_system
        • base/replace_species
        • base/reset_site
        • base/save_system
        • base/set_kmc_step
        • base/set_kmc_time
        • base/set_rate_const
        • base/set_system_name
        • base/start_time
        • base/system_name
        • base/update_accum_rate
        • base/update_clocks
        • base/update_integ_rate
        • base/volume
        • base/walltime
      • kmos3/lattice
        • lattice/allocate_system
        • lattice/calculate_lattice2nr
        • lattice/calculate_nr2lattice
        • lattice/deallocate_system
        • lattice/default_layer
        • lattice/lattice2nr
        • lattice/model_dimension
        • lattice/nr2lattice
        • lattice/nr_of_layers
        • lattice/site_positions
        • lattice/spuck
        • lattice/system_size
        • lattice/unit_cell_size
      • kmos3/proclist
        • proclist/do_kmc_step
        • proclist/do_kmc_steps
        • proclist/do_kmc_steps_time
        • proclist/get_next_kmc_step
        • proclist/get_occupation
        • proclist/get_seed
        • proclist/init
        • proclist/initialize_state
        • proclist/put_seed
        • proclist/run_proc_nr
        • proclist/seed_gen
      • kmos3/kind_values
    • lat_int
      • kmos3/base
        • base/accum_rates
        • base/add_proc
        • base/allocate_system
        • base/assertion_fail
        • base/avail_sites
        • base/can_do
        • base/deallocate_system
        • base/del_proc
        • base/determine_procsite
        • base/get_accum_rate
        • base/get_avail_site
        • base/get_integ_rate
        • base/get_kmc_step
        • base/get_kmc_time
        • base/get_kmc_time_step
        • base/get_kmc_volume
        • base/get_nrofsites
        • base/get_procstat
        • base/get_rate
        • base/get_species
        • base/get_system_name
        • base/get_walltime
        • base/increment_procstat
        • base/integ_rates
        • base/interval_search_real
        • base/kmc_step
        • base/kmc_time
        • base/kmc_time_step
        • base/lattice
        • base/nr_of_proc
        • base/nr_of_sites
        • base/procstat
        • base/rates
        • base/reload_system
        • base/replace_species
        • base/reset_site
        • base/save_system
        • base/set_kmc_time
        • base/set_rate_const
        • base/set_system_name
        • base/start_time
        • base/system_name
        • base/update_accum_rate
        • base/update_clocks
        • base/update_integ_rate
        • base/volume
        • base/walltime
      • kmos3/lattice
        • lattice/allocate_system
        • lattice/calculate_lattice2nr
        • lattice/calculate_nr2lattice
        • lattice/deallocate_system
        • lattice/default_layer
        • lattice/lattice2nr
        • lattice/model_dimension
        • lattice/nr2lattice
        • lattice/nr_of_layers
        • lattice/site_positions
        • lattice/spuck
        • lattice/system_size
        • lattice/unit_cell_size
      • kmos3/proclist
      • proclist/do_kmc_step
        • proclist/do_kmc_steps
        • proclist/do_kmc_steps_time
        • proclist/get_next_kmc_step
        • proclist/get_occupation
        • proclist/get_seed
        • proclist/init
        • proclist/initialize_state
        • proclist/put_seed
        • proclist/seed_gen
      • kmos3/kind_values
    • otf
      • kmos3/base
        • base/accum_rates
        • base/accum_rates_proc
        • base/add_proc
        • base/allocate_system
        • base/assertion_fail
        • base/avail_sites
        • base/can_do
        • base/deallocate_system
        • base/debug
        • base/del_proc
        • base/determine_procsite
        • base/get_accum_rate
        • base/get_avail_site
        • base/get_integ_rate
        • base/get_kmc_step
        • base/get_kmc_time
        • base/get_kmc_time_step
        • base/get_kmc_volume
        • base/get_nrofsites
        • base/get_procstat
        • base/get_rate
        • base/get_rate
        • base/get_species
        • base/get_system_name
        • base/get_walltime
        • base/increment_procstat
        • base/integ_rates
        • base/interval_search_real
        • base/kmc_step
        • base/kmc_time
        • base/kmc_time_step
        • base/lattice
        • base/nr_of_proc
        • base/nr_of_sites
        • base/procstat
        • base/rates
        • base/rates
        • base/reaccumulate_rates_matrix
        • base/reaccumulate_rates_matrix_proc
        • base/reload_system
        • base/replace_species
        • base/reset_site
        • base/save_system
        • base/set_kmc_time
        • base/set_rate_const
        • base/set_system_name
        • base/start_time
        • base/system_name
        • base/update_accum_rate
        • base/update_clocks
        • base/update_integ_rate
        • base/update_rates_matrix
        • base/volume
        • base/walltime
      • kmos3/lattice
        • lattice/allocate_system
        • lattice/calculate_lattice2nr
        • lattice/calculate_nr2lattice
        • lattice/deallocate_system
        • lattice/default_layer
        • lattice/lattice2nr
        • lattice/model_dimension
        • lattice/nr2lattice
        • lattice/nr_of_layers
        • lattice/site_positions
        • lattice/spuck
        • lattice/system_size
        • lattice/unit_cell_size
      • kmos3/proclist
      • proclist/do_kmc_step
        • proclist/do_kmc_steps
        • proclist/do_kmc_steps_time
        • proclist/get_next_kmc_step
        • proclist/get_occupation
        • proclist/get_seed
        • proclist/init
        • proclist/initialize_state
        • proclist/put_seed
        • proclist/run_proc_nr
        • proclist/seed_gen
      • kmos3/kind_values
• Troubleshooting
• Frequently Asked Questions

This document was generated Sep 20, 2024.