CatMAP Tutorial 2 Input Files

CO_oxidation.mkm

rxn_expressions = [
    '*_s + CO_g -> CO*',
    '2*_s + O2_g <-> O-O* + *_s -> 2O*',
    'CO* + O* <-> O-CO* + * -> CO2_g + 2*'
                  ]


surface_names = ['Pt', 'Ag', 'Cu', 'Rh', 'Pd', 'Au', 'Ru', 'Ni']

descriptor_names = ['O_s', 'CO_s']

descriptor_ranges = [[-1, 3], [-.5, 4]]

resolution = 15

temperature = 500

species_definitions = {
    'CO_g': {'presssure': 1.},
    'O2_g': {'pressure': 1./3},
    'CO2_g': {'pressure':0},
    's': {'site_names': ['111'],
          'total': 1},
}

data_file = 'CO_oxidation.pkl'

input_file = 'energies.txt'

gas_thermo_mode = 'shomate_gas'

adsorbate_thermo_mode = 'frozen_adsorbate'

scaling_constraint_dict = {
    'O_s': ['+', 0, None],
    'CO_s': [0, '+', None],
    'O_CO_s': 'initial_state',
    'O-O_s': 'final_state',
}

decimal_precision = 100

tolerance = 1e-50

max_rootfinding_iterations = 100
max_bisections = 3

energies.txt

surface_name	site_name	species_name	formation_energy	bulk_structure	frequencies	other_parameters	reference
None	gas	CO2	2.45	None	[1333,2349,667,667]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
None	gas	CO	2.74	None	[2170]	[]	"Energy	Environ.	Sci.,	3,	1311-1315	(2010)"
None	gas	O2	5.42	None	[1580]	[]	"Falsig	et	al	(2012)"
Ru	111	O	-0.07	fcc	[]	[]	"Falsig	et	al	(2012)"
Ni	111	O	0.35	fcc	[]	[]	"Falsig	et	al	(2012)"
Rh	111	O	0.55	fcc	[]	[]	"Falsig	et	al	(2012)"
Cu	111	O	1.07	fcc	[]	[]	"Falsig	et	al	(2012)"
Pd	111	O	1.55	fcc	[]	[]	"Falsig	et	al	(2012)"
Pt	111	O	1.62	fcc	[]	[]	"Falsig	et	al	(2012)"
Ag	111	O	2.05	fcc	[]	[]	"Falsig	et	al	(2012)"
Au	111	O	2.61	fcc	[]	[]	"Falsig	et	al	(2012)"
Ru	111	CO	1.3	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Rh	111	CO	1.34	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Pd	111	CO	1.55	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Ni	111	CO	1.63	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Pt	111	CO	1.7	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Cu	111	CO	2.58	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Ag	111	CO	2.99	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Au	111	CO	3.04	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Ru	111	O-CO	2.53	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Rh	111	O-CO	3.1	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Ni	111	O-CO	3.25	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Pt	111	O-CO	4.04	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Cu	111	O-CO	4.18	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Pd	111	O-CO	4.2	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Ag	111	O-CO	5.05	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Au	111	O-CO	5.74	fcc	[]	[]	"Angew.	Chem.	Int.	Ed.,	47,	4835	(2008)"
Ag	111	O-O	5.98	fcc	[]	[]	"Falsig	et	al	(2012)"
Au	111	O-O	7.22	fcc	[]	[]	"Falsig	et	al	(2012)"
Cu	111	O-O	4.74	fcc	[]	[]	"Falsig	et	al	(2012)"
Pt	111	O-O	5.35	fcc	[]	[]	"Falsig	et	al	(2012)"
Rh	111	O-O	3.79	fcc	[]	[]	"Falsig	et	al	(2012)"
Ru	111	O-O	3.34	fcc	[]	[]	"Falsig	et	al	(2012)"
Pd	111	O-O	5.34	fcc	[]	[]	"Falsig	et	al	(2012)"

mkm_job.py

#!/usr/bin/env python

from catmap import ReactionModel

mkm_file = 'CO_oxidation.mkm'
model = ReactionModel(setup_file=mkm_file)
model.run()

STDOUT_ERROR.log

mapper_iteration_0: status - 225 points do not have valid solution.
Traceback (most recent call last):
  File "./mkm_job.py", line 7, in <module>
    model.run()
  File "/Users/maxjh/Library/Python/2.7/lib/python/site-packages/catmap/model.py", line 215, in run
    self.descriptor_space_analysis()
  File "/Users/maxjh/Library/Python/2.7/lib/python/site-packages/catmap/model.py", line 272, in descriptor_space_analysis
    self.mapper.get_output_map(self.descriptor_ranges,self.resolution)
  File "/Users/maxjh/Library/Python/2.7/lib/python/site-packages/catmap/mappers/mapper_base.py", line 94, in get_output_map
    descriptor_ranges,resolution,*args,**kwargs)
  File "/Users/maxjh/Library/Python/2.7/lib/python/site-packages/catmap/mappers/min_resid_mapper.py", line 506, in get_coverage_map
    isMapped = minresid_iteration(isMapped)
  File "/Users/maxjh/Library/Python/2.7/lib/python/site-packages/catmap/mappers/min_resid_mapper.py", line 420, in minresid_iteration
    this_pt)
  File "/Users/maxjh/Library/Python/2.7/lib/python/site-packages/catmap/mappers/min_resid_mapper.py", line 60, in get_initial_coverage
    params = self.scaler.get_rxn_parameters(descriptors)
  File "/Users/maxjh/Library/Python/2.7/lib/python/site-packages/catmap/scalers/generalized_linear_scaler.py", line 328, in get_rxn_parameters
    params = self.get_formation_energy_parameters(descriptors)
  File "/Users/maxjh/Library/Python/2.7/lib/python/site-packages/catmap/scalers/generalized_linear_scaler.py", line 332, in get_formation_energy_parameters
    free_energy_dict = self.get_free_energies(descriptors)
  File "/Users/maxjh/Library/Python/2.7/lib/python/site-packages/catmap/scalers/scaler_base.py", line 137, in get_free_energies
    descriptors=descriptors,**kwargs)
  File "/Users/maxjh/Library/Python/2.7/lib/python/site-packages/catmap/scalers/scaler_base.py", line 131, in get_thermodynamic_energies
    **kwargs)
  File "/Users/maxjh/Library/Python/2.7/lib/python/site-packages/catmap/thermodynamics/enthalpy_entropy.py", line 115, in get_thermodynamic_corrections
    getattr(self,self.pressure_mode+'_pressure')()
  File "/Users/maxjh/Library/Python/2.7/lib/python/site-packages/catmap/thermodynamics/enthalpy_entropy.py", line 551, in static_pressure
    self.gas_pressures = [self.species_definitions[g]['pressure'] for g in self.gas_names]
KeyError: 'pressure'

This is an easy one - you have a typo in the word "pressure" for defining the pressure of CO_g. Nevertheless, a more verbose error would probably be helpful here.