# %% SurfacePhaseDiagrma def surface_phase_diagrma(): # Defined variables. temperature = 100.0 * Kelvin p0 = 1.013 * bar mass_species1 = 18.015 * atomicMassUnit mu_species1_max = 0.5 * eV mu_species1_min = -2.5 * eV mass_species2 = 32.0 * atomicMassUnit mu_species2_max = 0.0 * eV mu_species2_min = -2.5 * eV # Script. # Surface Phase Diagram Generator # ============================================================================= # SURFACE PHASE DIAGRAM GENERATION SCRIPT # ============================================================================= # # STEP-BY-STEP GUIDE TO RUN THIS SCRIPT: # # STEP 1: GENERATE SURFACE ADSORBED CONFIGURATIONS # ------------------------------------------------ # Use QuantumATK's Adsorption Tool to create surface configurations: # a. Start with a clean surface structure # b. Use the Adsorption Tool (Builder > Surface Tools > Add Adsorbates) # c. Generate different adsorption configurations: # - Molecular, dissociated, and various coverages of adsorption on surface sites # - Clean surface (without adsorbates) # d. Save each configuration as separate structure files # # STEP 2: COMPUTE THERMOCHEMISTRY PROPERTIES # ------------------------------------------ # Calculate thermochemistry data for all species/configurations: # # FOR GAS SPECIES (species1, species2): # - Use IdealGasThermoChemistry workflow template # # FOR BULK AND SURFACE CONFIGURATIONS: # - Use CrystalThermoChemistry workflow template # # STEP 3: UPLOAD THERMOCHEMISTRY DATA TO DATABASE # ----------------------------------------------- # Store all computed thermochemistry data in the thermochemistry database: # a. Open the Thermochemistry Database window through Thermochemistry Analyzer # - This should be uploaded in : C:\Users\user_name\.quantumatk\databases\thermochemistry/.. # b. Create a new entry for each configuration # - Enter a unique name (this name will be used in STEP 5) # # STEP 4: DEFINE USER PARAMETERS THROUGH WIDGET # ------------------------------ # Set the following parameters at the top of this script: # - temperature: Temperature for phase diagram (e.g., 100.0*Kelvin) # - p0: Reference pressure (e.g., 1.013*bar for 1 atm) # - mu_species2_min, mu_species2_max: Range for species2 chemical potential (eV) # - mu_species1_min, mu_species1_max: Range for species1 chemical potential (eV) # - mass_species2, mass_species1: Molecular masses for flux calculations # # STEP 5: EDIT SCRIPT TO INCORPORATE YOUR DATA # -------------------------------------------- # Update the following sections in this script: # A. SYSTEM_ENTRIES dictionary: # - 'bulk_config': Name you used when uploading bulk configuration # - 'bulk_stoichiometry': Number of formula units in bulk structure # - 'gas_species2': Name you used for gas_species2 gas thermochemistry # - 'gas_species1': Name you used for gas_species2 gas thermochemistry # - 'clean_surface': Name you used for clean surface # - 'surface_stoichiometry': Number of bulk units in surface slab # - 'clean_surface_label': Label for clean surface in plot # # C. 'surf_ad_configs' list in SYSTEM_ENTRIES: # For each adsorbate configuration: # - 'name': Database entry name for this configuration # - 'label': Label to display in phase diagram # - 'color': Color for this phase region in the plot # - 'n_species1': Number of species1 molecules in this configuration # - 'n_species2': Number of additional species2 atoms (from dissociation) # # D. PHASE_DIAGRAM_CONFIG: # - Adjust chemical potential ranges if needed # - Set pressure tick spacing # - Customize plot title and output filename # # E. PLOT_CONFIG: # - Adjust figure size, DPI, font sizes # - Customize colors and labels # # STEP 6: RUN THE SCRIPT # --------------------- # a. The script will: # - Load all thermochemistry data from database # - Calculate surface energies across chemical potential space # - Determine most stable phase at each point # - Generate phase diagram with multiple axes (chemical potential, pressure, flux) # - Save the plot as PNG file # b. Check the output: # - Console output shows progress and verification # - Phase diagram image saved as 'surface_phase_diagram.png' # c. This can easily be run locally # ===================================================================================== # Following is an example of RuO2-water-oxygen system: will rerun a 2D surface phase diagram import SurfacePhaseDiagram as surface_phase_diagram setVerbosity(DATA_DEPRECATION_WARNING=False) # ============================================================================= # CONFIGURATION SECTION - EDIT THESE PARAMETERS # ============================================================================= # System entry names in the thermochemistry database SYSTEM_ENTRIES = { # Bulk reference 'bulk_config': 'RuO2_bulkDFT', # Bulk oxide reference (e.g., RuO2, TiO2, etc.) 'bulk_stoichiometry': 2.0, # Number of formula units in bulk reference # Gas phase references 'gas_species2': 'O2DFT', # Oxygen gas reference 'gas_species1': 'H2ODFT', # Water gas reference # Clean surface 'clean_surface': 'RuO2_O_brDFT', # Clean oxide surface 'surface_stoichiometry': 8.0, # Number of bulk units in surface slab 'clean_surface_label': 'Obr/-', # Various surface configurations on adsorption 'surf_ad_configs': [ { 'name': 'RuO2_OH2_cusDFT', # Molecular water adsorbed 'label': 'Obr/H2Ocus', # Phase label for plot 'color': 'yellow', # Color for phase region 'n_species1': 2.0, # Number of H2O molecules 'n_species2': 0.0, # Additional oxygen atoms }, { 'name': 'RuO2_OH_cusDFT', # Dissociated water (OH) 'label': 'Obr/OHcus', 'color': 'lightgreen', 'n_species1': 1.0, # One H2O dissociated 'n_species2': 1.0, # One additional O from dissociation }, { 'name': 'RuO2_O_cusDFT', # Fully dissociated (only O) 'label': 'Obr/Ocus', 'color': 'orange', 'n_species1': 0.0, 'n_species2': 2.0, # Two oxygen atoms }, ], } # Phase diagram parameters PHASE_DIAGRAM_CONFIG = { 'del_mu_species2_range': ( mu_species2_min.inUnitsOf(eV), mu_species2_max.inUnitsOf(eV), 0.01, ), # (min, max, step) for O2 chemical potential 'del_mu_species1_range': ( mu_species1_min.inUnitsOf(eV), mu_species1_max.inUnitsOf(eV), 0.01, ), # (min, max, step) for H2O chemical potential 'pressure_ticks_species2': ( mu_species2_min.inUnitsOf(eV), mu_species2_max.inUnitsOf(eV), 0.5, ), 'pressure_ticks_species1': ( mu_species1_min.inUnitsOf(eV), mu_species1_max.inUnitsOf(eV), 0.5, ), 'reference_pressure': p0, # Reference pressure (1 atm) 'title': 'Surface Phase Diagram', # Plot title 'output_filename': 'surface_phase_diagram.png', } # Molecular masses for flux calculations MOLECULAR_MASSES = { 'mass_species2': mass_species2, # Oxygen gas 'mass_species1': mass_species1, # Water } # Plot styling PLOT_CONFIG = { 'figure_size': (14, 12), 'dpi': 300, 'title_fontsize': 16, 'label_fontsize': 16, 'tick_fontsize': 14, 'phase_label_fontsize': 12, 'clean_surface_color': 'violet', # Color for clean surface phase } # Generate the plot fig, _, _ = surface_phase_diagram.generate_surface_phase_diagram( SYSTEM_ENTRIES, PHASE_DIAGRAM_CONFIG, PLOT_CONFIG, MOLECULAR_MASSES, temperature, p0, ) return surface_phase_diagrma()