The Ziff-Gulari-Barshad (ZGB) model.

This tutorial is intended to show how to use pyZacros from a Zacros perspective. Thus, we will literally show how to translate the Zacros input files to a pyZacros script. To do that, we use the system described in the Zacros tutorial Ziff-Gulari-Barshad Model in Zacros. All physical/chemical description of the system is described in detail there. We invited you first to get familiar with the tutorial cited above to quickly appreciate the parallel between the Zacros input files and the pyZacros objects. This will allow you to follow line-by-line the example’s python script easily.

You can download the example’s python script from this link ZiffGulariBarshad.py.

If everything is working well, you should get the following information in the standard output and the figure shown at the end.

  1$ amspython ZiffGulariBarshad.py
  2[14.02|17:20:01] PLAMS working folder: /home/user/pyzacros/examples/ZiffGulariBarshad/plams_workdir
  3---------------------------------------------------------------------
  4simulation_input.dat
  5---------------------------------------------------------------------
  6random_seed         953129
  7temperature          500.0
  8pressure               1.0
  9
 10snapshots                 on time       0.5
 11process_statistics        on time       0.01
 12species_numbers           on time       0.01
 13max_time          25.0
 14
 15n_gas_species    3
 16gas_specs_names              CO           O2          CO2
 17gas_energies        0.00000e+00  0.00000e+00 -2.33700e+00
 18gas_molec_weights   2.79949e+01  3.19898e+01  4.39898e+01
 19gas_molar_fracs     4.50000e-01  5.50000e-01  0.00000e+00
 20
 21n_surf_species    2
 22surf_specs_names         CO*        O*
 23surf_specs_dent            1         1
 24
 25finish
 26---------------------------------------------------------------------
 27lattice_input.dat
 28---------------------------------------------------------------------
 29lattice default_choice
 30  rectangular_periodic 1.0 50 50
 31end_lattice
 32---------------------------------------------------------------------
 33energetics_input.dat
 34---------------------------------------------------------------------
 35energetics
 36
 37cluster CO*-0
 38  sites 1
 39  lattice_state
 40    1 CO* 1
 41  site_types 1
 42  graph_multiplicity 1
 43  cluster_eng -1.30000e+00
 44end_cluster
 45
 46cluster O*-0
 47  sites 1
 48  lattice_state
 49    1 O* 1
 50  site_types 1
 51  graph_multiplicity 1
 52  cluster_eng -2.30000e+00
 53end_cluster
 54
 55end_energetics
 56---------------------------------------------------------------------
 57mechanism_input.dat
 58---------------------------------------------------------------------
 59mechanism
 60
 61step *-0:CO-->CO*-0
 62  gas_reacs_prods CO -1
 63  sites 1
 64  initial
 65    1 * 1
 66  final
 67    1 CO* 1
 68  site_types 1
 69  pre_expon  1.00000e+01
 70  activ_eng  0.00000e+00
 71end_step
 72
 73step *_0-0,*_1-0:O2-->O*_0-0,O*_1-0;(0,1)
 74  gas_reacs_prods O2 -1
 75  sites 2
 76  neighboring 1-2
 77  initial
 78    1 * 1
 79    2 * 1
 80  final
 81    1 O* 1
 82    2 O* 1
 83  site_types 1 1
 84  pre_expon  2.50000e+00
 85  activ_eng  0.00000e+00
 86end_step
 87
 88step CO*_0-0,O*_1-0-->*_0-0,*_1-0:CO2;(0,1)
 89  gas_reacs_prods CO2 1
 90  sites 2
 91  neighboring 1-2
 92  initial
 93    1 CO* 1
 94    2 O* 1
 95  final
 96    1 * 1
 97    2 * 1
 98  site_types 1 1
 99  pre_expon  1.00000e+20
100  activ_eng  0.00000e+00
101end_step
102
103end_mechanism
104[14.02|17:29:40] JOB plamsjob STARTED
105[14.02|17:29:40] JOB plamsjob RUNNING
106[14.02|17:29:41] JOB plamsjob FINISHED
107[14.02|17:29:41] JOB plamsjob SUCCESSFUL
108[14.02|17:32:01] PLAMS run finished. Goodbye
/scm-uploads/doc/pyzacros/_images/example_ZGB.gif