Water-gas shift reaction on Pt(111).¶
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 Mapping DFT Energies to Zacros Input as an example. All physical/chemical description of the system is described in detail there. This example shows how to include gas species, transition states, as well as stable surface species, and the lateral interactions between them. All information about the energetics is obtained via density functional theory (DFT) calculations. Importantly, lateral interactions are also discussed and included in the example’s script. 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 WaterGasShiftOnPt111.py
.
If everything is working well, you should get the following information in the standard output and the figure shown at the end.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 | $ amspython WaterGasShiftOnPt111.py
PLAMS working folder: /home/user/pyzacros/examples/WaterGasShiftOnPt111/plams_workdir
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simulation_input.dat
---------------------------------------------------------------------
random_seed 123278
temperature 500.0
pressure 10.0
snapshots on time 0.0005
process_statistics on time 0.0005
species_numbers on time 0.0005
event_report off
max_steps infinity
max_time 0.25
n_gas_species 4
gas_specs_names CO H2 H2O CO2
gas_energies 0.00000e+00 0.00000e+00 0.00000e+00 -6.15000e-01
gas_molec_weights 2.79949e+01 2.01560e+00 1.80105e+01 4.39898e+01
gas_molar_fracs 1.00000e-05 0.00000e+00 9.50000e-01 0.00000e+00
n_surf_species 6
surf_specs_names CO* H* H2O* OH* O* COOH*
surf_specs_dent 1 1 1 1 1 1
finish
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lattice_input.dat
---------------------------------------------------------------------
lattice default_choice
hexagonal_periodic 1.0 8 10
end_lattice
---------------------------------------------------------------------
energetics_input.dat
---------------------------------------------------------------------
energetics
cluster CO_point
sites 1
lattice_state
1 CO* 1
site_types 1
graph_multiplicity 1
cluster_eng -2.07700e+00
end_cluster
cluster H2O_point
sites 1
lattice_state
1 H2O* 1
site_types 1
graph_multiplicity 1
cluster_eng -3.62000e-01
end_cluster
cluster OH_point
sites 1
lattice_state
1 OH* 1
site_types 1
graph_multiplicity 1
cluster_eng 8.30000e-01
end_cluster
cluster O_point
sites 1
lattice_state
1 O* 1
site_types 1
graph_multiplicity 1
cluster_eng 1.29800e+00
end_cluster
cluster H_point
sites 1
lattice_state
1 H* 1
site_types 1
graph_multiplicity 1
cluster_eng -6.19000e-01
end_cluster
cluster COOH_point
sites 1
lattice_state
1 COOH* 1
site_types 1
graph_multiplicity 1
cluster_eng -1.48700e+00
end_cluster
cluster CO_pair_1NN
sites 2
neighboring 1-2
lattice_state
1 CO* 1
2 CO* 1
site_types 1 1
graph_multiplicity 1
cluster_eng 5.60000e-01
end_cluster
cluster OH_H_1NN
sites 2
neighboring 1-2
lattice_state
1 OH* 1
2 H* 1
site_types 1 1
graph_multiplicity 1
cluster_eng 2.10000e-02
end_cluster
cluster O_H_1NN
sites 2
neighboring 1-2
lattice_state
1 O* 1
2 H* 1
site_types 1 1
graph_multiplicity 1
cluster_eng 1.98000e-01
end_cluster
cluster CO_OH_1NN
sites 2
neighboring 1-2
lattice_state
1 CO* 1
2 OH* 1
site_types 1 1
graph_multiplicity 1
cluster_eng 6.60000e-02
end_cluster
cluster CO_O_1NN
sites 2
neighboring 1-2
lattice_state
1 CO* 1
2 O* 1
site_types 1 1
graph_multiplicity 1
cluster_eng 4.23000e-01
end_cluster
end_energetics
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mechanism_input.dat
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mechanism
reversible_step CO_adsorption
gas_reacs_prods CO -1
sites 1
initial
1 * 1
final
1 CO* 1
site_types 1
pre_expon 2.22600e+07
pe_ratio 2.13700e-06
activ_eng 0.00000e+00
end_reversible_step
reversible_step H2_dissoc_adsorp
gas_reacs_prods H2 -1
sites 2
neighboring 1-2
initial
1 * 1
2 * 1
final
1 H* 1
2 H* 1
site_types 1 1
pre_expon 8.29900e+07
pe_ratio 7.96600e-06
activ_eng 0.00000e+00
end_reversible_step
reversible_step H2O_adsorption
gas_reacs_prods H2O -1
sites 1
initial
1 * 1
final
1 H2O* 1
site_types 1
pre_expon 2.77600e+02
pe_ratio 2.66500e-06
activ_eng 0.00000e+00
end_reversible_step
reversible_step H2O_dissoc_adsorp
sites 2
neighboring 1-2
initial
1 H2O* 1
2 * 1
final
1 OH* 1
2 H* 1
site_types 1 1
pre_expon 1.04200e+13
pe_ratio 1.00000e+00
activ_eng 7.77000e-01
end_reversible_step
reversible_step OH_decomposition
sites 2
neighboring 1-2
initial
1 * 1
2 OH* 1
final
1 O* 1
2 H* 1
site_types 1 1
pre_expon 1.04200e+13
pe_ratio 1.00000e+00
activ_eng 9.40000e-01
end_reversible_step
reversible_step COOH_formation
sites 2
neighboring 1-2
initial
1 CO* 1
2 OH* 1
final
1 * 1
2 COOH* 1
site_types 1 1
pre_expon 1.04200e+13
pe_ratio 1.00000e+00
activ_eng 4.05000e-01
end_reversible_step
step COOH_decomposition
gas_reacs_prods CO2 1
sites 2
neighboring 1-2
initial
1 COOH* 1
2 * 1
final
1 * 1
2 H* 1
site_types 1 1
pre_expon 1.04200e+13
activ_eng 8.52000e-01
end_step
step CO_oxidation
gas_reacs_prods CO2 1
sites 2
neighboring 1-2
initial
1 CO* 1
2 O* 1
final
1 * 1
2 * 1
site_types 1 1
pre_expon 1.04200e+13
activ_eng 9.88000e-01
end_step
end_mechanism
[08.02|15:34:32] JOB plamsjob STARTED
[08.02|15:34:32] JOB plamsjob RUNNING
[08.02|15:34:57] JOB plamsjob FINISHED
[08.02|15:34:57] JOB plamsjob SUCCESSFUL
[08.02|15:35:10] PLAMS run finished. Goodbye
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