SpectroscopySchool/msspecbook/_build/html/searchindex.js

1 line
26 KiB
JavaScript

Search.setIndex({"alltitles": {"Activity 10: Parallelization and multi-processing in MsSpec": [[9, null]], "Activity 11: Spectral radius and convergence": [[10, null]], "Activity 1: Getting started": [[0, null]], "Activity 2: Setting up the \u201cexperiment\u201d": [[1, null]], "Activity 3: Adsorbates and the single scattering approach": [[2, null]], "Activity 4: From single scattering to multiple scattering": [[3, null]], "Activity 5: Multiple scattering in the forward scattering regime": [[4, null]], "Activity 6: Effect of the temperature": [[5, null]], "Activity 7: Large clusters and path filtering": [[6, null]], "Activity 8: Inequivalent emitters and the XPD of a substrate": [[7, null]], "Activity 9: Comparing simulation and experiment with R-factors": [[8, null]], "Application to a deep plane in a Si(001) sample": [[6, "application-to-a-deep-plane-in-a-si-001-sample"]], "Barebone script for MsSpec": [[0, "barebone-script-for-msspec"]], "Building atomic systems": [[0, "building-atomic-systems"]], "Building the cluster": [[1, "building-the-cluster"]], "Compute an azimuthal scan": [[1, "compute-an-azimuthal-scan"]], "Computing the scattering factor": [[2, "computing-the-scattering-factor"]], "Creating the TiSe2 cluster": [[4, "creating-the-tise2-cluster"]], "Effect of the scattering order": [[4, "effect-of-the-scattering-order"]], "Final word": [[11, null]], "Future developpements": [[11, "future-developpements"]], "How to install MsSpec": [[11, "how-to-install-msspec"]], "Interferences due to backscattering": [[2, "interferences-due-to-backscattering"]], "Matrix inversion parallelization": [[9, "matrix-inversion-parallelization"]], "Our work": [[11, "our-work"]], "Oxygen on Rh(001)": [[2, "oxygen-on-rh-001"]], "PED of the 1T-TiSe<sub>2</sub> surface": [[4, "ped-of-the-1t-tise2-surface"]], "PED polar scan for Cu(001)": [[0, "ped-polar-scan-for-cu-001"]], "Paths filtering in MsSpec": [[6, "paths-filtering-in-msspec"]], "Process-based parallelism": [[9, "process-based-parallelism"]], "Sb-induced smooth growth of Ag on Ag(111) example": [[1, "sb-induced-smooth-growth-of-ag-on-ag-111-example"]], "Shaping a cluster": [[0, "shaping-a-cluster"]], "Surface and bulk effects of the temperature": [[5, "surface-and-bulk-effects-of-the-temperature"]], "The Aluminium Nitride (AlN) polarity": [[7, "the-aluminium-nitride-aln-polarity"]], "The number of scattering paths": [[6, "the-number-of-scattering-paths"]], "The script": [[5, "the-script"]], "The unusual tilt of CO molecule on Fe(001)": [[8, "the-unusual-tilt-of-co-molecule-on-fe-001"]], "Welcome to this small MsSpec tour": [[12, null]]}, "docnames": ["Activity01/Activity01", "Activity02/Activity02", "Activity03/Activity03", "Activity04/Activity04", "Activity05/Activity05", "Activity06/Activity06", "Activity07/Activity07", "Activity08/Activity08", "Activity09/Activity09", "Activity10/Activity10", "Activity11/Activity11", "backmatter", "intro"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinxcontrib.bibtex": 9}, "filenames": ["Activity01/Activity01.ipynb", "Activity02/Activity02.ipynb", "Activity03/Activity03.ipynb", "Activity04/Activity04.ipynb", "Activity05/Activity05.ipynb", "Activity06/Activity06.ipynb", "Activity07/Activity07.ipynb", "Activity08/Activity08.ipynb", "Activity09/Activity09.ipynb", "Activity10/Activity10.ipynb", "Activity11/Activity11.ipynb", "backmatter.md", "intro.md"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": [1, 4, 5, 6, 7, 8, 9], "0": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9], "00": 7, "0001": 7, "001": [5, 9], "004": 4, "005": [], "006": 6, "01": 6, "010": 8, "02": 2, "05": 2, "0f": 5, "1": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12], "10": [0, 1, 2, 7, 8, 12], "100": [5, 8], "1000": [3, 5], "1000k": 5, "1010": [], "1030": 4, "1083": 7, "11": [7, 8], "110": 8, "111": 2, "114": 6, "11h": [], "12": [8, 9], "1202": 8, "121": 1, "1382": 6, "14": 5, "1407": 7, "147176": 6, "15": [1, 4, 6, 8], "1525": 6, "157": [8, 9], "170\u00b5": [], "171": [], "18": [], "19": 7, "1986": 5, "1989": [3, 8], "1998": 2, "1999": 7, "1e": 6, "1e12": 4, "2": [0, 2, 3, 5, 6, 7, 8, 9, 12], "20": [1, 6, 7], "2012": [4, 5], "2022": 6, "207": 7, "22": 1, "23": 7, "240": 1, "25": [4, 8], "256": 6, "27": 5, "28": 6, "298k": 5, "2d": 4, "2f": 2, "2p": [0, 4, 5, 6, 7], "2p3": 0, "3": [0, 3, 4, 5, 6, 7, 8, 9, 12], "30": [1, 6, 7, 8], "300": 5, "31557600": [], "31902333327338293": [], "32": 7, "337": [], "34": 5, "343": 5, "35": [7, 8], "3600": [], "39": 3, "3f": 4, "3rd": 0, "4": [0, 1, 2, 4, 5, 6, 7, 8, 9, 12], "40": [1, 6], "400": 5, "43": 6, "45": [1, 3, 5, 6, 8, 9], "450": 4, "499": 3, "4d": 1, "5": [1, 3, 5, 6, 7, 8, 12], "50": 9, "500": 7, "51": 5, "535": 4, "54": 6, "55": [1, 8], "554": 4, "560": 5, "564": [], "58": 7, "59": 7, "5th": 3, "6": [1, 4, 6, 7, 8, 9, 12], "60": [4, 8, 9], "600px": [], "606": 4, "63": [8, 9], "64": 4, "65": 2, "67": 9, "685": 4, "6a_0": 6, "7": [5, 7, 12], "70": [4, 7], "72": 7, "723": 2, "739": 6, "76": 9, "77": 9, "8": [1, 2, 3, 4, 12], "80": [3, 6, 7], "81": 2, "83": 5, "85": [], "86": [], "86400": [], "9": [5, 9, 12], "90": 6, "900": 4, "945": 6, "975": 7, "98": 5, "A": [2, 3, 5, 8, 9], "AED": 0, "ASE": [0, 1, 2, 4], "As": [0, 2, 4, 6, 7, 9], "But": 4, "By": 2, "For": [1, 4, 5, 6, 9], "If": 6, "In": [0, 1, 2, 4, 5, 6, 7, 8, 9], "It": [1, 4, 7, 8, 9], "Not": 0, "On": 2, "One": 6, "Or": 0, "The": [0, 1, 2, 3, 4, 9], "There": 0, "These": 7, "To": [0, 1, 2, 4, 5, 6, 9], "With": [5, 6, 9], "_": 7, "_4": [], "__main__": 5, "__name__": 5, "_plotopt": 5, "a_0": [4, 6], "aa": [], "abl": 6, "about": [2, 4], "abov": [0, 2, 4, 5, 6], "abscissa": 8, "absolut": 3, "absorb": [3, 5, 7], "accept": [6, 8, 9], "accepth": [], "access": 7, "accord": 8, "accordingli": 3, "account": [0, 4, 6], "accur": [2, 4, 8], "accuraci": 2, "act": 1, "activ": 12, "actual": [3, 5, 6], "ad": [2, 7], "add": [1, 2, 5, 6, 7, 9], "add_adsorb": [2, 8], "add_column": [1, 5, 6, 7], "add_dset": [5, 7], "add_view": [5, 7], "adjust": 8, "adsorb": [8, 12], "adsorpt": [2, 7, 8, 9], "advantag": 2, "after": [4, 8], "agit": 5, "agre": 8, "agreement": [1, 8], "al": [1, 2, 3, 4, 6, 7, 8], "al_al": 7, "al_kalpha": [5, 6, 7], "al_n": 7, "al_plan": 7, "al_sid": 7, "alber": [4, 6, 7], "algorithm": [0, 2, 4, 5, 6, 7], "align": [1, 4, 8], "all": [0, 2, 3, 5, 6, 7, 9, 12], "all_data": 3, "all_t": 5, "all_theta": 5, "all_z": 2, "allow": [0, 6, 9], "almost": [4, 6, 7], "along": [3, 8], "alreadi": 4, "also": [4, 5, 8, 9], "altern": 6, "although": [1, 9], "altitud": 2, "aluminum": 7, "amplitud": 7, "an": [0, 2, 3, 4, 5, 6, 7, 9], "analysi": [5, 7, 8], "analyz": 0, "angl": [1, 5, 6, 7, 8, 9], "angstrom": [2, 3], "angstr\u00f6m": [4, 8, 9], "angular_accept": [1, 5, 7], "ani": 2, "anisotropi": [5, 9], "anisotropy_dset": 5, "anisotropy_view": 5, "anneal": 7, "annular": 2, "anoth": [4, 9], "answer": 3, "apart": 2, "apec": 0, "apertur": 6, "append": [5, 7, 8], "approach": [0, 4, 12], "approxim": [2, 4], "ar": [0, 1, 2, 4, 5, 6, 7, 8, 9], "arang": [2, 3, 5, 6, 7, 8], "arbitrarili": 5, "argument": [8, 9], "aris": 7, "around": [4, 7], "arrai": 5, "arrang": 6, "articl": 5, "ase": [0, 1, 2, 3, 4, 5, 6, 7, 8], "assum": [1, 6, 7, 8], "atom": [1, 2, 3, 4, 5, 6, 7, 8], "atomist": 0, "attach": 2, "attempt": 5, "attribut": [1, 9], "auger": [], "author": 7, "autoscal": [5, 7], "avail": [0, 4, 9], "averag": 5, "average_sampl": [1, 5, 7], "averaged_tl": [5, 6], "axi": [3, 4], "azimth": 8, "azimut": 5, "azimuth": [5, 7, 8, 9], "b": [1, 3, 5], "b_0": 4, "backascatt": [], "backscatt": 6, "backward_scatt": 6, "bar": 7, "base": [0, 1, 2, 3, 4, 5, 6, 7, 8], "basi": 0, "beamlin": 1, "becaus": 6, "becom": [2, 6], "been": 6, "begin": 2, "being": [2, 5], "belong": 8, "below": [2, 3, 4, 5, 6, 7, 8], "best": 8, "better": 1, "between": [0, 1, 2, 3, 4, 5, 7, 8, 9], "bewteen": 3, "big": [], "bin": [], "bit": 4, "black": 9, "blue": [1, 6], "bodi": 8, "boltzmann": 5, "bond": [2, 8], "bond_length": [8, 9], "both": [2, 5, 7], "bright": 2, "bring": 12, "build": [2, 3, 4, 5, 6, 7, 8], "built": 8, "bulk": [0, 1, 6, 7, 8], "c": [4, 5, 7, 8], "c1": 8, "c_0": 4, "calc": [0, 1, 2, 3, 4, 5, 6, 7], "calc_": 9, "calcul": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9], "calculation_paramet": [1, 2, 3, 4, 5, 6, 7], "calculationparamet": 5, "calcult": 8, "call": 8, "can": [0, 2, 3, 5, 6, 7, 8, 9], "cannot": 4, "carbon": 8, "carri": 2, "case": [2, 7], "categori": 1, "cell": [1, 4, 7], "center": [2, 4], "chain": [2, 3], "chain_length": 3, "chang": [1, 2, 3, 5, 9], "check": 7, "chosen": 5, "cif": 0, "circl": 2, "cite": 5, "class": 2, "clear": 5, "close": 6, "cluster": [2, 5, 7, 8, 9, 12], "cnr": 0, "co": 9, "code": [0, 2, 3, 4, 6, 8, 9], "cofe_mp": [], "cofe_mp_complet": [], "col_nam": 5, "col_valu": 5, "column": [4, 7], "com": 2, "combin": 9, "come": [2, 5], "comment": [2, 7, 9], "common": [5, 6], "commonli": 8, "compar": [1, 6, 9, 12], "comparison": [0, 1, 6], "complet": [2, 4, 5, 6, 8, 9], "complex": 4, "compon": 0, "comput": [0, 3, 4, 5, 6, 7, 8], "computation": 2, "compute_polar_scan": [8, 9], "concept": [0, 12], "conclud": [0, 4], "cone": 6, "configur": [1, 6], "consid": 2, "constant": [3, 4, 5], "construct": 2, "consum": 9, "consumpt": 2, "contain": [0, 1, 4, 5, 8], "content": 9, "contrast": 7, "contribut": [0, 6], "control": [5, 7, 8], "converg": [1, 4], "convers": [], "convert": 9, "copi": [7, 8], "copper": [0, 4, 5], "core": [7, 9], "correctli": 1, "correspond": [4, 6, 7, 8], "could": 6, "cover": 0, "cp": 8, "creat": [0, 1, 2, 6, 8, 9], "create_clust": [5, 7, 8, 9], "cristal": 7, "cross_sect": [1, 3, 5, 6, 7, 8, 9], "cruguel": 1, "cryst": 7, "crystal": 7, "crystallin": 2, "crystallograph": [7, 8], "crystallograpph": 7, "crystalstructur": 7, "cu": 5, "cubic": [0, 1, 5, 6, 8], "curv": [6, 8], "custom": 3, "cut_plan": 1, "cylindr": [5, 6], "d": [0, 2, 3, 4, 5, 7, 9], "dai": [], "damp": 5, "dark": 2, "data": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9], "datafram": 9, "dataset": [1, 3, 5], "datetim": [], "deby": 5, "debye_temperatur": 5, "declar": 9, "decreas": 5, "deep": [], "deeper": [4, 7], "deepest": [0, 5], "def": [5, 7, 8, 9], "default": 3, "defin": [1, 2, 3, 4, 5, 6, 9], "definit": 9, "degre": [2, 3, 5, 7, 8, 9], "delta": 5, "demonstr": [2, 7, 8, 9], "dens": 4, "depth": 5, "der": 4, "describ": 4, "detail": 5, "detector_paramet": [1, 5, 7], "determin": 7, "deviat": 4, "df": 9, "diagram": 7, "diamet": [1, 5, 6, 7, 8], "dichalcogenid": 4, "dict": [5, 9], "dictionari": 8, "differ": [0, 1, 2, 5, 6, 7, 8, 9], "differnt": 3, "difficulti": 12, "diffract": [0, 1, 2, 4, 5, 7, 12], "diffus": 3, "direct": [1, 2, 4, 6, 7, 8], "directli": 0, "discreap": 7, "discuss": 9, "disord": 5, "displac": 5, "displai": [0, 3, 8], "distanc": [2, 3, 6, 7, 8], "distance_cutoff": 6, "distinguish": 5, "distribut": 9, "dk": [], "do": [0, 4, 5, 7, 8], "document": [2, 5], "doe": [6, 9], "done": [7, 8], "doubl": 4, "download": [7, 8], "downward": 7, "drastic": 6, "dset": [1, 2, 3, 5, 7, 9], "dtu": [], "due": [5, 7], "dure": [7, 9], "e": 1, "e_0": 2, "each": [1, 3, 4, 5, 6, 8], "eas": 1, "easier": 9, "edit": [0, 7], "effect": [1, 2, 6, 12], "either": [5, 8], "eject": 2, "electron": [0, 2, 4, 6, 8, 12], "element": [4, 7], "elif": 7, "els": [5, 7], "emiss": [2, 5], "emit": [2, 7], "emitt": [0, 1, 2, 4, 5, 6, 12], "emitter_plan": [0, 1, 4, 5, 6, 7, 8], "emitter_tag": [4, 7], "emphas": [], "empti": 3, "end": [3, 8], "energi": [1, 2, 4, 5, 6, 7], "enlarg": 3, "enumer": [2, 7], "env": [], "environ": [0, 9], "equal": 0, "equat": 5, "escap": 1, "especi": 7, "estim": [5, 8], "et": [1, 2, 3, 4, 6, 7, 8], "ev": [1, 2, 4, 5, 7, 8], "evalu": [4, 6], "event": 4, "exact": 2, "exaf": 0, "exampl": [5, 6, 7, 8, 9], "except": 7, "exchang": 7, "exchange_correl": 5, "execut": 9, "exhibit": 7, "exit": 7, "exp": 1, "exp_data": [], "expand": 4, "expans": [2, 4, 5, 6, 7], "expect": [5, 6, 7], "experi": [9, 12], "experiment": [1, 2, 7, 8, 9], "experimental_data": [], "explain": 5, "explor": [4, 5, 6, 9, 12], "extra": 5, "extract": 8, "extrem": 2, "f": [4, 5, 9], "face": 7, "factor": [4, 9, 12], "fadlei": 5, "far": 6, "fast": 2, "fcc": [2, 4], "fcc111": 2, "fe": 9, "featur": [0, 1, 7, 9, 12], "few": 6, "fewer": 0, "fig": [7, 8], "fig1": [], "fig2": [], "figur": [2, 3, 4, 5, 6, 7, 8], "file": [0, 1], "fill": [2, 7, 8], "filter": [5, 7, 12], "final": [1, 8], "final_st": 6, "find": [3, 8], "first": [2, 3, 4, 6], "fix": 6, "flexibl": 0, "float": 5, "focu": [0, 12], "folder": [3, 9], "follow": [0, 1, 5, 6, 7, 8], "format": [2, 3, 5, 7], "former": 1, "formula": [4, 6, 8], "forthcom": 0, "fortran": 0, "forward": [6, 12], "forward_angl": [6, 7], "forward_scatt": [6, 7], "found": 7, "fr": 0, "frac": 5, "free": [4, 5], "fring": 2, "from": [0, 1, 2, 4, 5, 6, 7, 8, 9, 12], "fromkei": 5, "fulli": [0, 9], "function": [3, 4, 5, 8, 9], "fundament": 0, "futur": 9, "fysik": [], "g": 1, "gap": 4, "gener": [1, 4, 6], "geometr": 7, "geometri": [1, 8, 9], "gerber": 2, "get": [3, 5, 6, 7, 9, 12], "get_aln_tags_plan": 7, "get_atom_index": [0, 1, 4, 5, 6, 7], "get_chemical_symbol": [], "get_clust": 7, "get_paramet": 5, "get_phi_scan": [1, 5], "get_scattering_factor": 2, "get_theta_phi_scan": [2, 4], "get_theta_scan": [0, 3, 6, 7], "give": [2, 7, 8], "given": [1, 5, 8], "graphic": 3, "graze": 5, "great": 2, "greater": 4, "greatli": 0, "greber": 2, "group": 1, "grow": [4, 12], "growth": 7, "gtrsim": 7, "gui": [0, 1], "h": 1, "h2o": 0, "ha": [4, 6], "half": 5, "hand": [2, 8], "hardwar": 9, "harmon": [0, 4], "have": [2, 6, 7], "hbar": 5, "hdf5": 6, "height": [2, 8, 9], "help": [4, 5], "hemispher": [0, 4], "hemispherical_clust": [0, 1, 4, 5, 6, 7, 8], "here": [2, 3, 7, 8, 9], "hexagon": 7, "high": [2, 4, 6], "highli": 7, "hilight": 5, "hollow": 8, "how": [1, 2, 3, 4, 5, 6, 7, 8, 12], "howev": 0, "html": [], "http": 0, "i": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9], "i_": 5, "ic": 7, "idea": [1, 5, 6], "identifi": 1, "ie": 8, "ignor": 6, "illustr": [2, 6], "imax": 5, "imin": 5, "impact": 0, "import": [0, 1, 2, 3, 4, 5, 6, 7, 9], "imposs": 6, "improv": 3, "incid": 5, "includ": [0, 2], "incoher": 7, "incom": 1, "increas": [2, 4, 5, 6], "incres": 5, "independ": 9, "index": [0, 6], "indic": [2, 7], "individu": 9, "inequival": [4, 12], "info": [5, 7, 8], "inform": [2, 5, 8], "inner": 1, "inner_potenti": 1, "inset": 7, "insid": [1, 9], "instal": 9, "instanc": 9, "int": 4, "intenisti": 7, "intens": [0, 1, 2, 4, 5, 6, 7, 9], "intentis": 4, "interact": 0, "interfac": 0, "intern": 1, "interplai": 0, "interstitial_potenti": [1, 5], "introduc": 5, "invalid": [], "invas": 7, "invers": [0, 2, 4, 6], "invert": 9, "involv": 7, "io": 0, "iodata": 6, "iron": 8, "iter": 3, "its": [2, 3, 9], "itself": [4, 8], "j": [6, 7], "join": [], "just": 9, "k": 5, "k_b": 5, "ke": 7, "keep": [3, 8], "kei": [7, 9], "keyerror": 7, "keyword": 8, "kind": [3, 4, 5, 9], "kinet": [1, 2, 4, 6, 7], "kinetic_energi": [1, 2, 3, 4, 5, 6, 7], "known": 4, "kuznetsov": 4, "kwarg": 9, "l": 3, "l_": 4, "label": [], "lambda_": 5, "lapack": 9, "larg": [1, 2, 4, 5, 7, 12], "larger": 4, "last": [2, 3], "later": 2, "latter": 5, "lattic": [4, 6, 7], "layer": [1, 5], "lead": [2, 6], "learn": 12, "least": 6, "lebedev": 7, "leed": 0, "left": [4, 7, 8], "legend": [1, 5, 6, 7], "len": [2, 5], "length": [2, 3, 6, 8], "let": [1, 2, 4, 7, 9], "lett": [2, 8], "level": [0, 1, 2, 3, 4, 5, 6, 7], "librari": 9, "light": 1, "like": [0, 4, 8], "line": [1, 2, 3, 4, 5, 7, 8, 9], "lineno": [], "link": 9, "linspac": [1, 5], "list": [2, 8, 9], "literalinclud": [], "littl": 6, "ll": 2, "lmax": 4, "load": 6, "loadtxt": 1, "local": 7, "locat": [0, 7], "long": 6, "longer": 6, "look": [1, 5, 7, 8], "loop": [2, 3, 8, 9], "looper": 9, "loss": 5, "low": [1, 5], "lower": 5, "lure": 1, "m": [3, 4, 5, 6], "magic": 9, "magnitud": 5, "mai": [1, 6, 7, 9], "main": [7, 8], "major": 8, "make": 9, "mani": [6, 7, 8, 9], "manipul": 0, "manual": 5, "marker": 5, "mass": 5, "match": 1, "materi": [1, 4], "mathr": 2, "matplotlib": [0, 1], "matrix": [2, 4, 6], "matter": 0, "max": [1, 3, 4, 5, 7], "max_c": 3, "maxima": 2, "maximum": 3, "mean": [4, 5], "mean_free_path": 5, "mean_square_vibr": 6, "measur": 4, "mediawiki": [], "medium": 7, "memori": [0, 1, 2, 4, 6, 9], "metal": 4, "method": 2, "metrial": 1, "mfp": 4, "middl": 0, "min": [1, 3, 5, 7], "min_c": 3, "minim": 0, "minimum": 3, "minut": 6, "miss": 1, "model": [1, 4, 5, 7, 8, 12], "modifi": 9, "modul": [0, 5], "molecul": [0, 2, 7, 9], "moment": 0, "monoxid": 8, "more": [0, 4, 5], "most": [0, 1, 2, 6, 9], "msd": 5, "msspec": [1, 2, 3, 4, 5, 7, 8], "mt_radiu": [3, 6], "much": [0, 1, 4, 5], "muffin": 3, "muffintin_paramet": [1, 5], "multi": [4, 12], "multipl": [0, 2, 5, 6, 9, 12], "multiprocess": 9, "must": 9, "mutlipl": 3, "mx2": 4, "my_filt": 6, "my_script": 9, "n": [3, 4, 6, 7, 8], "n_al": 7, "n_n": 7, "n_plane": 7, "n_side": 7, "name": 9, "natoli": 0, "ncpu": 9, "nd": [4, 6], "ndif": 4, "nearest": 7, "need": [1, 3, 4, 5, 6, 7, 8, 9, 12], "neighbor": 7, "neighbordist": [], "neighbour": 7, "nest": [3, 8, 9], "new": [0, 3], "next": 8, "ni": 3, "nitrid": [], "nitrogen": 7, "no_filt": 6, "non": 7, "none": [2, 3, 4, 5, 7], "normal": [1, 8], "note": 6, "now": [1, 7, 8, 9], "np": [1, 2, 3, 4, 5, 6, 7, 8, 9], "npath": [], "nplane": [5, 7], "num": 9, "number": [0, 2, 4, 5, 7, 8, 9], "numer": 2, "numpi": [1, 2, 3, 4, 5, 6, 7], "o": [2, 5, 8, 9], "object": [1, 5, 7, 8, 9], "observ": 4, "obvious": 8, "off_cone_ev": [6, 7], "offer": [6, 9, 12], "often": 9, "omp_num_thread": 9, "one": [3, 5, 6, 7, 9], "ones": 5, "onli": [0, 2, 3, 6, 7], "onto": 8, "optim": 9, "optimis": [], "option": [3, 5, 6, 9], "orang": [1, 6], "order": [2, 3, 5, 6, 8], "orient": [1, 2, 8], "origin": 7, "other": [0, 2], "our": [2, 5], "out": [6, 8], "output": 9, "over": [2, 3, 5, 9], "p": [6, 8], "p1654": 2, "p1760": 4, "p266": 7, "p283": 8, "p6784": 5, "p6785": 5, "p6791": 5, "p8275": 3, "packag": [2, 9], "panda": 9, "paper": [1, 2, 3, 4, 5, 6, 7, 8, 9], "paragraph": 5, "parallel": 12, "paramet": [1, 4, 5, 6, 8, 9], "part": [8, 9], "path": [2, 4, 5, 7, 12], "path_filt": [6, 7], "pattern": [4, 7], "peak": [4, 7], "ped": [2, 3, 5, 6, 7], "pendri": 8, "perform": [5, 12], "phagen": 0, "phase": [0, 5], "phenom": 6, "phi": [1, 2, 4, 5, 6, 7, 8, 9], "photodiffract": [2, 7], "photoelectron": [0, 1, 2, 4, 5, 7, 12], "photoemiss": 7, "phy": [1, 2, 3, 5, 8], "physic": 5, "pi": 4, "pipelin": 9, "planck": 5, "plane": [0, 1, 4, 5, 7, 8], "plot": [0, 3, 5], "plt": [0, 1], "pm": [2, 8], "point": [1, 7], "polar": [1, 2, 3, 5, 6, 8], "polar_angl": [], "pop": [2, 3, 9], "popup": [1, 2], "posit": [2, 3, 8], "possibl": [2, 6, 8, 9], "potenti": [1, 5], "practic": 5, "precis": [4, 8], "preiou": 4, "pretti": 0, "previou": [0, 6, 7, 9], "previous": 2, "print": [4, 7], "probe": [2, 7], "problem": 2, "process": [0, 6, 12], "processor": 9, "produc": 2, "program": 0, "project": 2, "pronounc": 5, "propag": 0, "proport": 6, "propos": [2, 5], "provid": [4, 8, 9], "publish": [2, 5, 7], "put": 2, "py": 9, "pyplot": [0, 1], "python": [0, 5, 9], "qualit": 5, "quantit": 2, "question": [3, 6], "quick": 7, "quit": [2, 9], "quiz": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9], "r": [0, 4, 5, 7, 9, 12], "r16061": 1, "ra_cutoff": 6, "radian": [3, 8], "radiu": [3, 4], "rai": [1, 5], "rang": [3, 4, 5, 7], "rather": 2, "ratio": 7, "rd": [0, 6], "read": 0, "real": 5, "realli": 0, "reason": 9, "recent": 0, "red": 2, "reduc": [5, 6], "ref": 1, "refer": 1, "refract": 1, "regardless": 5, "regim": [6, 12], "rehr": [4, 6, 7], "reject": 6, "rel": [5, 7], "relat": [1, 6], "reliabl": 8, "rememb": [6, 8], "remov": [0, 1, 3], "replac": 9, "repres": [2, 5], "represent": 2, "reproduc": [5, 7, 8], "requir": [6, 9], "reshap": 9, "resourc": 9, "respect": [1, 2, 3, 7], "rest": 8, "resulst": 9, "result": [0, 1, 2, 3, 5, 6, 8, 9], "retriev": [5, 7], "return": [5, 7, 8, 9], "rev": [1, 2, 3, 5, 8], "rfactor": [], "rfc": [], "rhodium": 2, "right": [4, 7, 8], "rotat": [1, 3, 4, 7], "rotate_cel": [1, 4], "roughli": 5, "row": 4, "run": [0, 3, 7, 8, 9], "rune": 8, "sa73": 1, "saiki": 8, "same": [0, 3, 6, 7], "sampl": [1, 4, 5], "satisfactori": [1, 2], "save": 0, "scale": 3, "scan": [2, 3, 4, 5, 6, 7, 8], "scatter": [0, 5, 7, 8, 9, 12], "scattering_ord": [2, 3, 4, 5, 6, 7], "sci": 4, "script": [2, 3, 6, 7, 8, 9], "se": 4, "second": [4, 5, 6], "section": [5, 8], "see": [1, 2, 5, 6, 8, 9], "seen": [6, 7], "select": [1, 5, 6, 7], "sensit": 2, "sequenti": 6, "seri": [4, 6, 7], "serial": 6, "set": [0, 3, 5, 6, 7, 8, 9, 12], "set_atom": [0, 2, 3, 4, 5, 6, 7], "set_plot_opt": [3, 5, 7], "set_refer": [], "sever": [6, 9], "shape": [1, 2, 5, 6, 9], "share": [7, 9], "shift": [0, 5], "short": 7, "should": [1, 4, 8], "show": [0, 7], "shutdown": [1, 3, 5], "si": [], "side": [7, 8], "signal": [0, 2, 5, 6, 7], "signific": 1, "significantli": 6, "silver": 1, "sim": [5, 8], "similar": 6, "simpl": [3, 5, 8, 9], "simplist": 2, "simul": [0, 2, 7, 9, 12], "sin": [5, 8], "sinc": [0, 4, 5, 6, 7, 12], "singl": [4, 5, 6, 8, 12], "sinl": 2, "site": [2, 8], "size": [1, 2, 4, 6], "sketch": 7, "small": [1, 2, 4, 5, 7, 8], "smaller": 1, "snipet": 4, "so": [2, 6], "softwar": 12, "solut": 8, "some": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9], "soon": 2, "sourc": 1, "source_paramet": [1, 5, 6, 7], "spec": 0, "speci": 2, "specif": 1, "specifi": 9, "spectral": [], "spectrosc": 6, "spectroscopi": [0, 1, 2, 3, 4, 5, 6, 7, 8, 12], "spectroscopy_paramet": 6, "spheric": [0, 4], "sqrt": 3, "squar": 5, "ssc": 8, "stack": 3, "start": [1, 2, 3, 4, 9, 12], "state": 7, "step": [0, 1, 8, 9], "stereograph": 2, "stop": 9, "store": [3, 4, 5, 8], "straightforward": [0, 7], "strongest": 7, "strongli": 4, "structur": [0, 4, 5], "studi": [2, 7], "substitut": [1, 7], "substrat": [5, 9, 12], "substrate_dset": 7, "subsurfac": 6, "suggest": 9, "suit": 0, "suitabl": 7, "sum": [5, 7], "sum_": 6, "surf": 4, "surfac": [1, 2, 7, 8], "surround": 7, "sweep": 9, "sweep_index": 9, "symbol": [1, 3], "symmetri": 7, "synchrotron": 1, "syntax": [], "syntaxerror": [], "system": 9, "s\u00e9billeau": 0, "t": [1, 2, 3, 5, 8], "tag": [4, 7], "take": [0, 1, 4, 6, 7], "taken": [6, 7], "target": [], "task": [8, 9], "tb": 4, "td": [], "technic": 9, "techniqu": [0, 12], "temp": 1, "temperatur": [7, 12], "temporari": 3, "termin": 7, "tetrahedron": 7, "text": [], "texvc": [], "th": [3, 6], "than": [1, 5, 6], "thank": 2, "thei": [2, 5], "them": 0, "theori": 12, "thermal": 5, "theses": 6, "theta": [1, 2, 3, 4, 5, 6, 7, 8, 9], "theta_d": 5, "thi": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9], "thick": 4, "those": [0, 1, 8], "threshold": 6, "through": 12, "thu": 7, "ti": 4, "ti2p": 4, "tilt": 9, "time": [0, 4, 6, 9], "timedelta": [], "tin": 3, "titl": [2, 3, 5, 7], "tl_threshold": 6, "tmatrix_paramet": [5, 6], "tmp_data": 7, "to_dict": 9, "togeth": 12, "toggl": [], "too": [1, 2, 4, 6, 7], "took": 6, "tool": [0, 7], "top": [1, 2], "total": [0, 5, 6, 7, 9], "toward": 2, "transit": 4, "treat": 6, "trehan": 5, "tricot": 6, "trilay": 4, "true": [0, 1, 4, 5, 6, 7, 8], "try": [1, 2, 4, 6, 7, 8], "tweak": 3, "two": [0, 1, 2, 5, 6, 8], "txt": 1, "type": 4, "typic": [0, 4, 5], "u": 4, "u0000212b": [], "u_j": 5, "unambigu": 7, "underli": 2, "uniqu": 9, "unit": [4, 9], "up": [0, 3, 6, 12], "updat": [5, 7, 8], "upward": 7, "us": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12], "use_debye_model": 5, "useful": 4, "user": 9, "usr": [], "usual": 4, "utf": 3, "utf8": 6, "util": [0, 1, 4, 5, 6, 7, 8], "v": [3, 4, 7], "vacuum": 4, "valu": [2, 4, 5, 6, 8, 9], "van": 4, "vari": [2, 5], "variabl": [1, 3, 8, 9], "variat": [2, 5], "varii": 9, "variou": [2, 12], "veri": [2, 6], "version": [0, 9], "versu": [5, 7], "vibrat": 5, "vibration_sc": 5, "vibrational_damp": [5, 6], "view": [0, 1, 2, 3, 4, 5, 6, 7], "visual": [0, 1, 2, 4], "volum": [4, 7], "wa": [6, 8], "waal": 4, "wai": 5, "waller": 5, "want": [3, 5, 7], "water": 0, "wave": [0, 2, 4], "we": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12], "well": [0, 3, 4, 5, 7], "were": [6, 7], "what": [0, 2, 4, 6, 8], "when": [1, 5, 6, 9], "where": [2, 3, 4, 5, 6, 7], "which": [2, 6, 8, 9], "while": 3, "whose": [6, 9], "why": 6, "wide": 2, "width": [], "wiki": [], "window": 3, "withe": 8, "within": 6, "without": [0, 6], "word": [], "work": [0, 5, 7], "would": [1, 4, 6], "write": 8, "written": 0, "wurtzit": 7, "x": [1, 3, 5, 8], "x_alpha_r": 5, "xlabel": [5, 7], "xpd": [4, 12], "xraysourc": [5, 6, 7], "xu": 3, "y": [1, 3, 8], "year": [], "yellow": 6, "ylabel": [5, 7], "ylim": 3, "you": [0, 1, 2, 3, 4, 5, 6, 7, 9, 12], "your": [1, 2, 3, 5, 6, 8, 9], "z": [1, 2, 3, 4, 8], "z0": 2, "z_0": 2, "zi": 2, "zip": [], "\u00b5": 6, "\u00e5": [2, 4, 6, 8, 9]}, "titles": ["Activity 1: Getting started", "Activity 2: Setting up the \u201cexperiment\u201d", "Activity 3: Adsorbates and the single scattering approach", "Activity 4: From single scattering to multiple scattering", "Activity 5: Multiple scattering in the forward scattering regime", "Activity 6: Effect of the temperature", "Activity 7: Large clusters and path filtering", "Activity 8: Inequivalent emitters and the XPD of a substrate", "Activity 9: Comparing simulation and experiment with R-factors", "Activity 10: Parallelization and multi-processing in MsSpec", "Activity 11: Spectral radius and convergence", "Final word", "Welcome to this small MsSpec tour"], "titleterms": {"001": [0, 2, 6, 8], "1": 0, "10": 9, "11": 10, "111": 1, "1t": 4, "2": [1, 4], "3": 2, "4": 3, "5": 4, "6": 5, "7": 6, "8": 7, "9": 8, "The": [5, 6, 7, 8], "activ": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10], "adsorb": 2, "ag": 1, "aln": 7, "aluminium": 7, "an": 1, "applic": 6, "approach": 2, "atom": 0, "auger": [], "azimuth": 1, "backscatt": 2, "barebon": 0, "base": 9, "build": [0, 1], "bulk": 5, "cluster": [0, 1, 4, 6], "co": 8, "compar": 8, "comput": [1, 2], "converg": 10, "creat": 4, "cu": 0, "deep": 6, "developp": 11, "diffract": [], "due": 2, "effect": [4, 5], "electron": [], "emitt": 7, "exampl": 1, "experi": [1, 8], "factor": [2, 8], "fe": 8, "filter": 6, "final": 11, "forward": 4, "from": 3, "futur": 11, "get": 0, "growth": 1, "how": 11, "induc": 1, "inequival": 7, "instal": 11, "interfer": 2, "invers": 9, "larg": 6, "matrix": 9, "molecul": 8, "msspec": [0, 6, 9, 11, 12], "multi": 9, "multipl": [3, 4], "nitrid": 7, "number": 6, "order": 4, "our": 11, "oxygen": 2, "parallel": 9, "path": 6, "ped": [0, 4], "plane": 6, "polar": [0, 7], "process": 9, "r": 8, "radiu": 10, "regim": 4, "rh": 2, "sampl": 6, "sb": 1, "scan": [0, 1], "scatter": [2, 3, 4, 6], "script": [0, 5], "set": 1, "shape": 0, "si": 6, "simul": 8, "singl": [2, 3], "small": 12, "smooth": 1, "spectral": 10, "start": 0, "sub": 4, "substrat": 7, "surfac": [4, 5], "system": 0, "temperatur": 5, "thi": 12, "tilt": 8, "tise": 4, "tise2": 4, "tour": 12, "unusu": 8, "up": 1, "welcom": 12, "word": 11, "work": 11, "xpd": 7}})