Uploaded scripts for calculating TOF.

systems2atoms/materials/HCOOH_decomposition_111.mkm

@@ -0,0 +1,85 @@
+#
+#Microkinetic model parameters
+#
+
+scaler = 'ThermodynamicScaler'
+
+rxn_expressions = [			   
+               '2*_s + HCOOH_g <-> HCOO-H* + *_s <-> HCOO* + H*',
+			   'HCOO* <-> H-COO* -> CO2_g + H*',
+			   'HCOO* <-> HCOO-* <-> HCOO&*',
+			   'HCOO&* <-> H-COO&* <-> CO2_g + H*',
+			   '2H* <-> H-H* + *_s <-> H2_g + 2*',
+			   '2*_s + HCOOH_g <-> H-COOH* + *_s <-> COOH* + H*',
+                           'COOH* <-> COO-H* <-> CO2_g + H*',
+			   'COOH* + *_s <-> CO-OH* + *_s <-> CO* + OH*',
+			   'CO*  -> CO_g + *',
+			   'OH*+H*  <-> H-OH* +*_s -> H2O_g + 2*',
+                   ]
+
+
+surface_names = ['Pd'] #surfaces to include in scaling (need to have descriptors defined for each)
+
+descriptor_names= ['temperature','pressure'] #descriptor names
+
+descriptor_ranges = [[300,400], [1, 100.0]]
+
+#descriptor_names= ['O_s','CO_s'] #descriptor names
+
+#descriptor_ranges = [[-1,3],[-0.5,4]]
+
+resolution = 20
+
+#temperature = 500 #Temperature of the reaction
+
+species_definitions = {}
+species_definitions['HCOOH_g'] = {'concentration':1.}
+species_definitions['H2O_g'] = {'concentration':0.}
+species_definitions['H2_g'] = {'concentration':0.}
+species_definitions['CO2_g'] = {'concentration':0.} #define the gas pressures
+species_definitions['CO_g'] = {'concentration':0.}
+
+species_definitions['s'] = {'site_names': ['111'], 'total':1} #define the sites
+
+data_file = 'HCOOH_decomposition_111.pkl'
+
+#
+#Parser parameters
+#
+
+input_file = 'energies_111.txt' #input data
+
+#
+#Scaler parameters
+#
+
+gas_thermo_mode = "shomate_gas"
+#gas_thermo_mode = "ideal_gas" #Ideal gas approximation
+#gas_thermo_mode = "zero_point_gas" #uses zero-point corrections only
+#gas_thermo_mode = "fixed_entropy_gas" #assumes entropy of 0.002 eV/K for all gasses except H2 (H2 is 0.00135 eV/K)
+#gas_thermo_mode = "frozen_gas" #neglect thermal contributions
+
+#adsorbate_thermo_mode = "frozen_adsorbate"
+adsorbate_thermo_mode = "harmonic_adsorbate"
+#adsorbate_thermo_mode = "hindered_adsorbate"
+#adsorbate_thermo_mode = "zero_point_adsorbate"
+
+scaling_constraint_dict = {
+                           'H_s':['+',0,None],
+                           'H2_s':[0,'+',None],
+                           'HCOO-H_s':'initial_state',
+                           'H-H_s':'final_state',
+                           }
+
+
+#
+#Solver parameters
+#
+
+decimal_precision = 100 #precision of numbers involved
+
+tolerance = 1e-50 #all d_theta/d_t's must be less than this at the solution
+
+max_rootfinding_iterations = 100
+
+max_bisections = 3

systems2atoms/materials/HCOOH_decomposition_211.mkm

@@ -0,0 +1,85 @@
+#
+#Microkinetic model parameters
+#
+
+scaler = 'ThermodynamicScaler'
+
+rxn_expressions = [			   
+               '2*_s + HCOOH_g <-> HCOO-H* + *_s -> HCOO* + H*',
+			   'HCOO* <-> CO2_g + H*',
+			   'HCOO* <-> HCOO-* <-> HCOO&*',
+			   'HCOO&* <-> H-COO&* <-> CO2_g + H*',
+			   '2H* <-> H-H*+*_s <-> H2_g + 2*_s',
+			   '2*_s + HCOOH_g <-> H-COOH* + *_s -> COOH* + H*',
+                           'COOH* <-> COO-H* <-> CO2_g + H*',
+			   'COOH* + *_s <-> CO-OH* + *_s -> CO* + OH*',
+			   'CO*  <-> CO_g + *_s',
+			   'OH*+H*  <-> H-OH* +*_s <-> H2O_g + 2*_s',
+                   ]
+
+
+surface_names = ['Pd'] #surfaces to include in scaling (need to have descriptors defined for each)
+
+descriptor_names= ['temperature','pressure'] #descriptor names
+
+descriptor_ranges = [[300,400], [1, 100.0]]
+
+#descriptor_names= ['O_s','CO_s'] #descriptor names
+
+#descriptor_ranges = [[-1,3],[-0.5,4]]
+
+resolution = 20
+
+#temperature = 500 #Temperature of the reaction
+
+species_definitions = {}
+species_definitions['HCOOH_g'] = {'concentration':1.}
+species_definitions['H2O_g'] = {'concentration':0.}
+species_definitions['H2_g'] = {'concentration':0.}
+species_definitions['CO2_g'] = {'concentration':0.} #define the gas pressures
+species_definitions['CO_g'] = {'concentration':0.}
+
+species_definitions['s'] = {'site_names': ['211'], 'total':1} #define the sites
+
+data_file = 'HCOOH_decomposition_211.pkl'
+
+#
+#Parser parameters
+#
+
+input_file = 'energies_211.txt' #input data
+
+#
+#Scaler parameters
+#
+
+gas_thermo_mode = "shomate_gas"
+#gas_thermo_mode = "ideal_gas" #Ideal gas approximation
+#gas_thermo_mode = "zero_point_gas" #uses zero-point corrections only
+#gas_thermo_mode = "fixed_entropy_gas" #assumes entropy of 0.002 eV/K for all gasses except H2 (H2 is 0.00135 eV/K)
+#gas_thermo_mode = "frozen_gas" #neglect thermal contributions
+
+#adsorbate_thermo_mode = "frozen_adsorbate"
+adsorbate_thermo_mode = "harmonic_adsorbate"
+#adsorbate_thermo_mode = "hindered_adsorbate"
+#adsorbate_thermo_mode = "zero_point_adsorbate"
+
+scaling_constraint_dict = {
+                           'H_s':['+',0,None],
+                           'H2_s':[0,'+',None],
+                           'HCOO-H_s':'initial_state',
+                           'H-H_s':'final_state',
+                           }
+
+
+#
+#Solver parameters
+#
+
+decimal_precision = 100 #precision of numbers involved
+
+tolerance = 1e-50 #all d_theta/d_t's must be less than this at the solution
+
+max_rootfinding_iterations = 100
+
+max_bisections = 3

systems2atoms/materials/NN_list_fn.py

@@ -0,0 +1,51 @@
+#Depends on ASAP3 - check out https://wiki.fysik.dtu.dk/asap/Neighbor%20lists
+#By Joakim Halldin Stenlid SUNCAT center, SLAC/Stanford Uni 2020
+# syntax python2 structure-file
+# make sure to set equillibrium distance for metal in your system!
+from ase import Atoms
+from ase import geometry
+from ase.build import bulk, make_supercell
+from ase.io import read, write
+import numpy as np
+import sys, math
+from ase import neighborlist
+from asap3 import *
+
+
+# loop over all atoms
+def NN_list_fn(infile):
+    #INPUT
+    #infile=sys.argv[1]          # Name of structure input file
+    eq_dist=2.772               # Metal equilibrium distance in favored coordination environment, 2.772 for Pt
+    tol=0.1                     # Max tolerated bond strain. Note: strain model not tested beyond 8%
+    eq_dist_tol=eq_dist*(1+tol) # Max bond distance to be considered a bond
+    #read structure and basic analysis
+    atoms=read(infile)
+    N = atoms.get_number_of_atoms()
+    nblist = FullNeighborList(eq_dist_tol, atoms, driftfactor=0.05)
+    pos=atoms.get_positions()
+    cell=atoms.get_cell()
+    elements=atoms.get_chemical_symbols()
+    cn_site_record=[]
+    for i in range(len(atoms)):
+        nb, dvec, d2 = nblist.get_neighbors(i) #neigborlist, pairwise distance vector, and squared norm of distance vectors
+    #    print("\n", nb,"for atom",i)
+        #print(dvec,"for atom",i)
+        cn_site = len(nb)
+    # print(cn_site)
+        cn_nb = []
+        alpha = np.zeros(12,dtype='int') #change to 12
+        alpha[np.arange(cn_site)] = alpha[np.arange(cn_site)] + 1
+        for ii in range(cn_site):
+            neighbor = nb[ii]
+            cn_neighbor = len(nblist.get_neighbors(neighbor)[0])
+            cn_nb.append(cn_neighbor)
+            alpha[cn_neighbor-1] = alpha[cn_neighbor-1] + 1
+        alpha = np.delete(alpha,[1,2])
+        # print(i, cn_site, alpha)
+        cn_site_record.append(cn_site)
+    #print(cn_site_record)
+    unique, counts = np.unique(cn_site_record, return_counts=True)
+
+    # print("\n", dict(zip(unique, counts)))
+    return dict(zip(unique, counts))