33 ppstm simple to functions #36
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| title = "Default configuration" | ||
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| [scan] | ||
| scan_type = 'v-scan' # 'didv'='dIdV''='didv-single' -- only dIdV for one voltage = V ; 'v-scan'='V-scan'='Voltage-scan' -- both STM & dIdV scan - V .. Vmax; 'STM'='STM-single' -- STM for one Voltage = V, use V-scan rather; "states"="STATES" -- dIdV scancs at the eigenenergies, beware it still uses all other states for calculations # | ||
| tip_type = 'fixed' # 'fixed'='f' -- for stiff/metal tip apexes ; 'relaxed'='r' -- for flexible tip apexes (precalculated by PP-AFM) . For this option you have to have "installed" PPAFM in your PPSTM directory # | ||
| scan_window = [[0, 0, 10], [15.9, 15.9, 11.9]] # [[x0, y0, z0], [x1, y1, z1]] -- scan window in Angstroms, used for fixed scan # | ||
| scan_dim = [128, 128, 20] # [Nx, Ny, Nz] -- number of points in [x, y, z] used for fixed scan # | ||
| V = -0.5 # !!!! V = Vmin for SCAN !!!! # | ||
| V_max = +0.5 # V = V_min >= -2.0 V ; V_max <= 2.0 V (othervise changes in the later code needed) # | ||
| dV = 0.1 # # voltage step , dV <= 0.1 V # | ||
| eta = 0.1 # Lorentzian width of states in energy scale: typically 0.1; can be in range of 0.3-0.05 eV in some cases (low amount of layers ...) even up to 1.0 eV # | ||
| tip_orb = 's' # 's' ; 'pxy' -- px & py ; 'spxy' -- 50% s & 50% pxy ; '5spxy' -- 5% s & 95% pxy ; '10spxy' -- 10% s & 90% pxy ; 'CO' -- 13% s & 87% pxy (PRL 119, 166001 (2017)) ; 'pz' ; For sample_orbs = 'sp' , possible 'dz2' and 'dxzyz' -- dxz & dyz # | ||
| sample_orbs = 'sp' # orbitals of the sample 'sp' (light atoms only, faster) or 'spd' (all atoms) # | ||
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| [input] | ||
| path = './' # where are files fron DFT code # | ||
| dft_code = 'aims' # 'fireball'='Fireball'='FIREBALL' ; 'aims'='AIMS'='FHI-AIMS' ; 'cp2k'='CP2K' ; 'gpaw'='GPAW' # | ||
| geometry_file = 'geometry.in' # E.G. 'input.xyz' , 'input.bas' , 'geometry.in'; None for GPAW # | ||
| pbc = [0,0] # (0,0) = None = False -- only original geometry ; (0.5,0.5) -- 2x2 cell ; (1,1) -- 3x3 cell (around original) ; (2,2) -- 5x5 cell (around original) ... # | ||
| lvs = [[1,0,0],[0,1,0],[0,0,1]] # None ; [[ax,ay,0],[bx,by,0]],[0,0,cz]] or [[ax,ay],[bx,by]] ; 'input.lvs' -- files with specified cell ; in FHI-AIMS & GPAW allready specified with geometry # | ||
| spin = false # None=False ; for FHI-AIMS & CP2K: None -- spin-unpolarized/spin-restricted calc. ; 'both' , 'up'='alpha' or 'down" (last 3 are for spin-polarizes or spin-unrestricted calculations) # | ||
| cp2k_name = 'crazy_mol' # Name used in CP2K calculations or GPAW calc # | ||
| Q = 0.0 # charge (PP-AFM) ; Ocharge PP-AFM complex_tip autumn 2018) ; [e] (monopole), [e*A] (dipole), [e*A^2] (quadrupole) # | ||
| K = 0.24 # x stiffness (PP-AFM master autumn 2018); klat (PP-AFM dev/OpenCl autumn 2018); Oklat (PP-AFM complex_tip autumn 2018) ; [N/m] # | ||
| data_format = 'npy' # 'xsf'='XSF' ; 'npy'='NPY' ; -- format in which PPpos are stored from PP-AFM run # | ||
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| [advanced] | ||
| cut_atoms = -1 # None = -1 -- All atoms of the sample contributes to tunelling ; 1 -- only 1st atom of the sample contributes to the tunelling ; 57 -- first 57 atoms of the sample contributes to the tunelling ; ... # | ||
| lower_atoms = [] # [] = None -- No atoms has lowered hopping ; be aware python numbering occurs here: [0] - means lowering of the 1st atom; [0,1,2,3] -- lowering of 1st 4 atoms ... # | ||
| lower_coefs = [] # [] = None -- No lowering of the hoppings ; [0.5] -- lowering of the 1st atom hopping to 0.5 ; [0.5,0.5,0.5,0.5] -- lowering of 1st 4 atoms to 0.5 ... # | ||
| work_function = 5.0 # 5.0 eV is standart # | ||
| work_function_decay = 0.5 # 0.0 <= WF_decay <= 1.0 ; How fast WorkFunction tunnelling barrier is changing with Voltage : (WF = WF_0 + V*WF_decay) -- 0.0 no change ; 1.0 - the same change as voltage # | ||
| fermi = 0.0 # None=0.0 -- no change to the Fermi Level ; -0.1 -- shifts the Fermi Level by 0.1 eV lower ... # | ||
| cut_min = -3 # cut out all orbitals lower than -2.5 eV bellow Rermi (should be: cut_min <= Vmin-2*eta) . taken to the Fermi Level # | ||
| cut_max = 3 # cut out all orbitals higher than -2.5 eV above Fermi (should be: cut_max >= Vmax+2*eta) . taken to the Fermi Level # | ||
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| [output] | ||
| plot_atoms = false # True / False -- plot "png" images (2D constant height) # | ||
| PNG = false # True / False -- write ".xyz" WSxM files (2D constant height) # | ||
| WSxM = false # True / False -- write ".xsf" files with 3D stucks of data . For this option you have to have "installed" PPAFM in your PPSTM directory # | ||
| NPY = true # True / False -- write ".npy" numpy binary files with 3D stucks of data . For this option you have to have "installed" PPAFM in your PPSTM directory # | ||
| XSF = false # True / False -- plot geometry (position of atoms into the PNG images and into the XSF files). You have to have your geometry, which you want to plot in input_plot.xyz. This doesn't change the name of the output files # |
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| import os | ||
| import sys | ||
| import tomli | ||
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| from pyPPSTM import basUtils as bU | ||
| from pyPPSTM import ReadSTM | ||
| from pyPPSTM import STMutils | ||
| from pyPPSTM import visualization | ||
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| def main(config: dict): | ||
| # ppafm needed for relaxed tip scans and npy+xsf output | ||
| tip_type = config['scan']['tip_type'] | ||
| npy_or_xsf_output = config['output']['NPY'] or config['output']['XSF'] | ||
| if tip_type in ['relaxed', 'r'] or npy_or_xsf_output: | ||
| try: | ||
| import ppafm.io as io | ||
| except ImportError: | ||
| raise ImportError("ppafm is required for relaxed tip scans and NPY/XSF output.") | ||
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| # Set tip coefficients | ||
| tip_orb = config['scan']['tip_orb'] | ||
| tip_coeffs = STMutils.get_tip_coefficients(tip_orb) | ||
| print(f"Set tip coefficients for {tip_orb}: {tip_coeffs}") | ||
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| # Read eigenenergies and coefficients | ||
| eigenenergies, coefs, atoms = ReadSTM.read_dft(config) | ||
| print(f"Read eigenenergies and coefficients.") | ||
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| # Set up atom plotting if enabled | ||
| if config['output']['plot_atoms']: | ||
| try: | ||
| geom_plot, _, _ = bU.loadAtoms( | ||
| os.path.join( | ||
| config['input']['path'], | ||
| 'input_plot.xyz' | ||
| ) | ||
| ) | ||
| except FileNotFoundError: | ||
| geom_plot = None | ||
| print("WARNING: Atom plotting disabled due to missing input_plot.xyz file.") | ||
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| # Get tip positions | ||
| ( | ||
| tip_r, | ||
| tip_r0, | ||
| lvec, | ||
| extent, | ||
| atomic_head_or_info | ||
| ) = STMutils.get_tip_positions(config) | ||
| print(f"Tip positions read for a {config['scan']['tip_type']} scan.") | ||
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| # Run STM scan | ||
| current, didv = STMutils.run_stm_scan( | ||
| config, | ||
| eigenenergies, | ||
| coefs, | ||
| tip_r, | ||
| atoms | ||
| ) | ||
| print(f"STM scan complete for scan type {config['scan']['scan_type']}.") | ||
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| # Get voltages and names | ||
| voltages, names = visualization.get_voltages_and_names(config, eigenenergies) | ||
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| # Output results | ||
| if config['output']['PNG']: | ||
| visualization.plot_png(config, current, didv, voltages, names, lvec, extent, geom_plot) | ||
| print(f"PNG output complete.") | ||
| if config['output']['WSxM']: | ||
| visualization.plot_wsxm(config, current, didv, voltages, names, tip_r0) | ||
| print(f"WSXM output complete.") | ||
| if config['output']['XSF']: | ||
| visualization.save_xsf(config, current, didv, voltages, names, geom_plot, lvec) | ||
| print(f"XSF output complete.") | ||
| if config['output']['NPY']: | ||
| visualization.save_npy(config, current, didv, voltages, names, lvec, atomic_head_or_info) | ||
| print(f"NPY output complete.") | ||
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| print(f"Output finished, exiting.") | ||
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| if __name__=='__main__': | ||
| # Get config file from command line | ||
| config_file = sys.argv[1] | ||
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| # Load config file | ||
| with open(config_file, 'rb') as f: | ||
| config = tomli.load(f) | ||
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| print(f"Loaded config from {config_file}") | ||
| print(f"Config: {config}") | ||
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| main(config) | ||
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Could you please add here a helper message, if there is no argv, or more than 1, thank you!