From 77adea5b1bf1a309001b2709afd3e7b3fc751fb8 Mon Sep 17 00:00:00 2001 From: Sylvain Tricot Date: Fri, 18 Jul 2025 17:22:25 +0200 Subject: [PATCH] Update html --- msspecbook/_build/html/.buildinfo | 2 +- .../_build/html/Activity01/Activity01.html | 2 +- .../_build/html/Activity02/Activity02.html | 178 ++++++------ .../_build/html/Activity03/Activity03.html | 2 +- .../_build/html/Activity04/Activity04.html | 2 +- .../_build/html/Activity05/Activity05.html | 14 +- .../_build/html/Activity06/Activity06.html | 2 +- .../_build/html/Activity07/Activity07.html | 2 +- .../_build/html/Activity08/Activity08.html | 263 +++++++++--------- .../_build/html/Activity09/Activity09.html | 41 ++- .../_build/html/Activity10/Activity10.html | 10 +- .../_build/html/Activity11/Activity11.html | 6 +- .../0e4320262cbcdc4d473d0b9d43e0f7e9/AlN.py | 4 - .../html/_sources/Activity07/Activity07.ipynb | 2 +- .../html/_sources/Activity08/Activity08.ipynb | 4 +- .../html/_sources/Activity09/Activity09.ipynb | 17 +- .../html/_sources/Activity10/Activity10.ipynb | 4 +- msspecbook/_build/html/backmatter.html | 2 +- msspecbook/_build/html/genindex.html | 2 +- msspecbook/_build/html/intro.html | 4 +- msspecbook/_build/html/objects.inv | Bin 2161 -> 2167 bytes msspecbook/_build/html/search.html | 2 +- msspecbook/_build/html/searchindex.js | 2 +- 23 files changed, 296 insertions(+), 271 deletions(-) diff --git a/msspecbook/_build/html/.buildinfo b/msspecbook/_build/html/.buildinfo index a78a743..556b4d6 100644 --- a/msspecbook/_build/html/.buildinfo +++ b/msspecbook/_build/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 0b896abf2c995b3493312dcbe0e8b47f +config: d64285b76259d47aa1d35d9bc7e7829a tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/msspecbook/_build/html/Activity01/Activity01.html b/msspecbook/_build/html/Activity01/Activity01.html index 97c5361..91e753d 100644 --- a/msspecbook/_build/html/Activity01/Activity01.html +++ b/msspecbook/_build/html/Activity01/Activity01.html @@ -189,7 +189,7 @@
  • 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: Auger Electron Diffraction
    • +
  • Activity 10: Parallelization and multi-processing in MsSpec
  • Activity 11: Spectral radius and convergence
  • Final word
    • diff --git a/msspecbook/_build/html/Activity02/Activity02.html b/msspecbook/_build/html/Activity02/Activity02.html index c03f46a..90a4077 100644 --- a/msspecbook/_build/html/Activity02/Activity02.html +++ b/msspecbook/_build/html/Activity02/Activity02.html @@ -191,7 +191,7 @@
  • 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: Auger Electron Diffraction
    • +
  • Activity 10: Parallelization and multi-processing in MsSpec
  • Activity 11: Spectral radius and convergence
  • Final word
    • @@ -467,7 +467,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -491,7 +491,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -499,7 +499,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -515,7 +515,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -523,7 +523,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -531,7 +531,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -539,7 +539,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -547,7 +547,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -555,7 +555,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -563,7 +563,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -571,7 +571,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -579,7 +579,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -587,7 +587,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -595,7 +595,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -603,7 +603,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -611,7 +611,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -619,7 +619,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -627,7 +627,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -683,7 +683,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -707,7 +707,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -715,7 +715,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -723,7 +723,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -731,7 +731,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -771,7 +771,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -779,7 +779,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -787,7 +787,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -795,7 +795,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -803,7 +803,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -811,7 +811,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -819,7 +819,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -827,7 +827,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -835,7 +835,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -843,7 +843,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -851,7 +851,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -859,7 +859,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -867,7 +867,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -875,7 +875,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -883,7 +883,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -891,7 +891,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -899,7 +899,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -907,7 +907,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -915,7 +915,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -923,7 +923,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -931,7 +931,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -939,7 +939,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -947,7 +947,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -955,7 +955,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -963,7 +963,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -971,7 +971,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -979,7 +979,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -987,7 +987,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1027,7 +1027,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1035,7 +1035,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1043,7 +1043,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1051,7 +1051,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1059,7 +1059,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1075,7 +1075,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1083,7 +1083,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1091,7 +1091,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1099,7 +1099,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1107,7 +1107,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1115,7 +1115,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1123,7 +1123,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1131,7 +1131,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1139,7 +1139,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1147,7 +1147,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1155,7 +1155,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1163,7 +1163,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1171,7 +1171,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1179,7 +1179,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1187,7 +1187,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1195,7 +1195,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1203,7 +1203,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1211,7 +1211,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1219,7 +1219,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1227,7 +1227,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1235,7 +1235,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1243,7 +1243,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1251,7 +1251,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1259,7 +1259,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1267,7 +1267,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1283,7 +1283,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1291,7 +1291,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1299,7 +1299,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1307,7 +1307,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1315,7 +1315,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1323,7 +1323,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + @@ -1331,7 +1331,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution - + diff --git a/msspecbook/_build/html/Activity03/Activity03.html b/msspecbook/_build/html/Activity03/Activity03.html index 4fc9033..9f700d0 100644 --- a/msspecbook/_build/html/Activity03/Activity03.html +++ b/msspecbook/_build/html/Activity03/Activity03.html @@ -191,7 +191,7 @@
  • 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: Auger Electron Diffraction
    • +
  • Activity 10: Parallelization and multi-processing in MsSpec
  • Activity 11: Spectral radius and convergence
  • Final word
    • diff --git a/msspecbook/_build/html/Activity04/Activity04.html b/msspecbook/_build/html/Activity04/Activity04.html index 78824fe..89270d0 100644 --- a/msspecbook/_build/html/Activity04/Activity04.html +++ b/msspecbook/_build/html/Activity04/Activity04.html @@ -189,7 +189,7 @@
  • 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: Auger Electron Diffraction
    • +
  • Activity 10: Parallelization and multi-processing in MsSpec
  • Activity 11: Spectral radius and convergence
  • Final word
    • diff --git a/msspecbook/_build/html/Activity05/Activity05.html b/msspecbook/_build/html/Activity05/Activity05.html index a4bc40f..e36092d 100644 --- a/msspecbook/_build/html/Activity05/Activity05.html +++ b/msspecbook/_build/html/Activity05/Activity05.html @@ -191,7 +191,7 @@
  • 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: Auger Electron Diffraction
    • +
  • Activity 10: Parallelization and multi-processing in MsSpec
  • Activity 11: Spectral radius and convergence
  • Final word
    • @@ -516,7 +516,7 @@ document.write(` - + @@ -884,7 +884,7 @@ document.write(`     - + @@ -892,7 +892,7 @@ document.write(` - + @@ -948,7 +948,7 @@ document.write(` - + @@ -956,7 +956,7 @@ document.write(` - + @@ -1004,7 +1004,7 @@ document.write(` - + diff --git a/msspecbook/_build/html/Activity06/Activity06.html b/msspecbook/_build/html/Activity06/Activity06.html index 7e2ae0f..30e2f80 100644 --- a/msspecbook/_build/html/Activity06/Activity06.html +++ b/msspecbook/_build/html/Activity06/Activity06.html @@ -191,7 +191,7 @@
  • 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: Auger Electron Diffraction
    • +
  • Activity 10: Parallelization and multi-processing in MsSpec
  • Activity 11: Spectral radius and convergence
  • Final word
    • diff --git a/msspecbook/_build/html/Activity07/Activity07.html b/msspecbook/_build/html/Activity07/Activity07.html index cccde8f..6b82b45 100644 --- a/msspecbook/_build/html/Activity07/Activity07.html +++ b/msspecbook/_build/html/Activity07/Activity07.html @@ -191,7 +191,7 @@
  • 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: Auger Electron Diffraction
    • +
  • Activity 10: Parallelization and multi-processing in MsSpec
  • Activity 11: Spectral radius and convergence
  • Final word
    • diff --git a/msspecbook/_build/html/Activity08/Activity08.html b/msspecbook/_build/html/Activity08/Activity08.html index 27e6f63..88c0608 100644 --- a/msspecbook/_build/html/Activity08/Activity08.html +++ b/msspecbook/_build/html/Activity08/Activity08.html @@ -191,7 +191,7 @@
  • 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: Auger Electron Diffraction
    • +
  • Activity 10: Parallelization and multi-processing in MsSpec
  • Activity 11: Spectral radius and convergence
  • Final word
    • @@ -428,141 +428,138 @@ This is the key to computing the total photodiffraction signal of a substrat

    As can be seen in Fig. 23, the peaks at 32° and 58.5° are well reproduced by the calculation for an Al polarity. Some discreapancies arise between the experimental work and this simulation especially for large polar angles. This may be due to a too small cluster in diameter for the deeper emitters.

    -
      1#!/usr/bin/env python
-  2# coding: utf8
-  3
-  4from ase.build import bulk
-  5import numpy as np
-  6from msspec.calculator import MSSPEC, XRaySource
-  7from msspec.utils import hemispherical_cluster, get_atom_index
-  8
-  9def create_clusters(nplanes=6):
- 10    def get_AlN_tags_planes(side, emitter):
- 11        AlN = bulk('AlN', crystalstructure='wurtzite', a=3.11, c=4.975)
- 12        [atom.set('tag', i) for i, atom in enumerate(AlN)]
- 13        if side == 'Al':
- 14            AlN.rotate([0,0,1],[0,0,-1])
- 15            Al_planes = range(0, nplanes, 2)
- 16            N_planes  = range(1, nplanes, 2)
- 17        else:
- 18            N_planes  = range(0, nplanes, 2)
- 19            Al_planes = range(1, nplanes, 2)
- 20        if emitter == 'Al':
- 21            tags = [0, 2]
- 22            planes = Al_planes
- 23        else:
- 24           tags = [1, 3]
- 25           planes = N_planes
- 26        return AlN, tags, planes
- 27
- 28    clusters = []
- 29    for side in ('Al', 'N'):
- 30        for emitter in ('Al', 'N'):
- 31            AlN, tags, planes = get_AlN_tags_planes(side, emitter)
- 32            for emitter_tag in tags:
- 33                for emitter_plane in planes:
- 34                    cluster = hemispherical_cluster(AlN,
- 35                                                    emitter_tag=emitter_tag,
- 36                                                    emitter_plane=emitter_plane,
- 37                                                    planes=emitter_plane+2)
- 38                    cluster.absorber = get_atom_index(cluster, 0, 0, 0)
- 39                    cluster.info.update({
- 40                        'emitter_plane': emitter_plane,
- 41                        'emitter_tag'  : emitter_tag,
- 42                        'emitter'      : emitter,
- 43                        'side'         : side,
- 44                    })
- 45                    clusters.append(cluster)
- 46                    print("Added cluster {}-side, emitter {}(tag {:d}) in "
- 47                          "plane #{:d}".format(side, emitter, emitter_tag,
- 48                                               emitter_plane))
- 49    return clusters
- 50
- 51
- 52def compute(clusters, theta=np.arange(-20., 80., 1.), phi=0.):
- 53    data = None
- 54    for ic, cluster in enumerate(clusters):
- 55        # Retrieve info from cluster object
- 56        side    = cluster.info['side']
- 57        emitter = cluster.info['emitter']
- 58        plane   = cluster.info['emitter_plane']
- 59        tag     = cluster.info['emitter_tag']
- 60
- 61        # Set the level and the kinetic energy
- 62        if emitter == 'Al':
- 63            level = '2p'
- 64            ke    = 1407.
- 65        elif emitter == 'N':
- 66            level = '1s'
- 67            ke    = 1083.
- 68
- 69        calc = MSSPEC(spectroscopy='PED', algorithm='expansion')
- 70
- 71        calc.source_parameters.energy = XRaySource.AL_KALPHA
- 72        calc.source_parameters.theta  = -35
+
      1from ase.build import bulk
+  2import numpy as np
+  3from msspec.calculator import MSSPEC, XRaySource
+  4from msspec.utils import hemispherical_cluster, get_atom_index
+  5
+  6def create_clusters(nplanes=6):
+  7    def get_AlN_tags_planes(side, emitter):
+  8        AlN = bulk('AlN', crystalstructure='wurtzite', a=3.11, c=4.975)
+  9        [atom.set('tag', i) for i, atom in enumerate(AlN)]
+ 10        if side == 'Al':
+ 11            AlN.rotate([0,0,1],[0,0,-1])
+ 12            Al_planes = range(0, nplanes, 2)
+ 13            N_planes  = range(1, nplanes, 2)
+ 14        else:
+ 15            N_planes  = range(0, nplanes, 2)
+ 16            Al_planes = range(1, nplanes, 2)
+ 17        if emitter == 'Al':
+ 18            tags = [0, 2]
+ 19            planes = Al_planes
+ 20        else:
+ 21           tags = [1, 3]
+ 22           planes = N_planes
+ 23        return AlN, tags, planes
+ 24
+ 25    clusters = []
+ 26    for side in ('Al', 'N'):
+ 27        for emitter in ('Al', 'N'):
+ 28            AlN, tags, planes = get_AlN_tags_planes(side, emitter)
+ 29            for emitter_tag in tags:
+ 30                for emitter_plane in planes:
+ 31                    cluster = hemispherical_cluster(AlN,
+ 32                                                    emitter_tag=emitter_tag,
+ 33                                                    emitter_plane=emitter_plane,
+ 34                                                    planes=emitter_plane+2)
+ 35                    cluster.absorber = get_atom_index(cluster, 0, 0, 0)
+ 36                    cluster.info.update({
+ 37                        'emitter_plane': emitter_plane,
+ 38                        'emitter_tag'  : emitter_tag,
+ 39                        'emitter'      : emitter,
+ 40                        'side'         : side,
+ 41                    })
+ 42                    clusters.append(cluster)
+ 43                    print("Added cluster {}-side, emitter {}(tag {:d}) in "
+ 44                          "plane #{:d}".format(side, emitter, emitter_tag,
+ 45                                               emitter_plane))
+ 46    return clusters
+ 47
+ 48
+ 49def compute(clusters, theta=np.arange(-20., 80., 1.), phi=0.):
+ 50    data = None
+ 51    for ic, cluster in enumerate(clusters):
+ 52        # Retrieve info from cluster object
+ 53        side    = cluster.info['side']
+ 54        emitter = cluster.info['emitter']
+ 55        plane   = cluster.info['emitter_plane']
+ 56        tag     = cluster.info['emitter_tag']
+ 57
+ 58        # Set the level and the kinetic energy
+ 59        if emitter == 'Al':
+ 60            level = '2p'
+ 61            ke    = 1407.
+ 62        elif emitter == 'N':
+ 63            level = '1s'
+ 64            ke    = 1083.
+ 65
+ 66        calc = MSSPEC(spectroscopy='PED', algorithm='expansion')
+ 67
+ 68        calc.source_parameters.energy = XRaySource.AL_KALPHA
+ 69        calc.source_parameters.theta  = -35
+ 70
+ 71        calc.detector_parameters.angular_acceptance = 4.
+ 72        calc.detector_parameters.average_sampling   = 'medium'
  73
- 74        calc.detector_parameters.angular_acceptance = 4.
- 75        calc.detector_parameters.average_sampling   = 'medium'
- 76
- 77        calc.calculation_parameters.scattering_order = max(1, min(4, plane))
- 78        calc.calculation_parameters.path_filtering  = 'forward_scattering'
- 79        calc.calculation_parameters.off_cone_events = 1
- 80        [a.set('forward_angle', 30.) for a in cluster]
- 81
- 82        calc.set_atoms(cluster)
- 83
- 84        data = calc.get_theta_scan(level=level, theta=theta, phi=phi,
- 85                                   kinetic_energy=ke, data=data)
- 86        dset = data[-1]
- 87        dset.title = "\'{}\' side - {}({}) tag #{:d}, plane #{:d}".format(
- 88            side, emitter, level, tag, plane)
+ 74        calc.calculation_parameters.scattering_order = max(1, min(4, plane))
+ 75        calc.calculation_parameters.path_filtering  = 'forward_scattering'
+ 76        calc.calculation_parameters.off_cone_events = 1
+ 77        [a.set('forward_angle', 30.) for a in cluster]
+ 78
+ 79        calc.set_atoms(cluster)
+ 80
+ 81        data = calc.get_theta_scan(level=level, theta=theta, phi=phi,
+ 82                                   kinetic_energy=ke, data=data)
+ 83        dset = data[-1]
+ 84        dset.title = "\'{}\' side - {}({}) tag #{:d}, plane #{:d}".format(
+ 85            side, emitter, level, tag, plane)
+ 86
+ 87    return data
+ 88
  89
- 90    return data
- 91
- 92
- 93def analysis(data):
- 94    tmp_data = {}
- 95    for dset in data:
- 96        info = dset.get_cluster().info
- 97        side = info['side']
- 98        emitter = info['emitter']
- 99        try:
-100            key = '{}_{}'.format(side, emitter)
-101            tmp_data[key] += dset.cross_section
-102        except KeyError:
-103            tmp_data[key] = dset.cross_section.copy()
-104
-105    tmp_data['theta']   = dset.theta.copy()
-106    tmp_data['Al_side'] = tmp_data['Al_Al'] / tmp_data['Al_N']
-107    tmp_data['N_side']  = tmp_data['N_Al']  / tmp_data['N_N']
-108
-109    # now add all columns
-110    substrate_dset = data.add_dset('Total substrate signal')
-111    substrate_dset.add_columns(**tmp_data)
-112
-113    view = substrate_dset.add_view('Ratios',
-114                                   title=r'Al(2p)/N(1s) ratios on both polar '
-115                                         r'sides of AlN in the (10$\bar{1}$0) '
-116                                         r'azimuthal plane',
-117                                   xlabel=r'$\Theta (\degree$)',
-118                                   ylabel='Intenisty ratio')
-119    view.select('theta', 'Al_side', legend='Al side',
-120                where="theta >= 0 and theta <=70")
-121    view.select('theta', 'N_side', legend='N side',
-122                where="theta >= 0 and theta <=70")
-123    view.set_plot_options(autoscale=True)
+ 90def analysis(data):
+ 91    tmp_data = {}
+ 92    for dset in data:
+ 93        info = dset.get_cluster().info
+ 94        side = info['side']
+ 95        emitter = info['emitter']
+ 96        try:
+ 97            key = '{}_{}'.format(side, emitter)
+ 98            tmp_data[key] += dset.cross_section
+ 99        except KeyError:
+100            tmp_data[key] = dset.cross_section.copy()
+101
+102    tmp_data['theta']   = dset.theta.copy()
+103    tmp_data['Al_side'] = tmp_data['Al_Al'] / tmp_data['Al_N']
+104    tmp_data['N_side']  = tmp_data['N_Al']  / tmp_data['N_N']
+105
+106    # now add all columns
+107    substrate_dset = data.add_dset('Total substrate signal')
+108    substrate_dset.add_columns(**tmp_data)
+109
+110    view = substrate_dset.add_view('Ratios',
+111                                   title=r'Al(2p)/N(1s) ratios on both polar '
+112                                         r'sides of AlN in the (10$\bar{1}$0) '
+113                                         r'azimuthal plane',
+114                                   xlabel=r'$\Theta (\degree$)',
+115                                   ylabel='Intenisty ratio')
+116    view.select('theta', 'Al_side', legend='Al side',
+117                where="theta >= 0 and theta <=70")
+118    view.select('theta', 'N_side', legend='N side',
+119                where="theta >= 0 and theta <=70")
+120    view.set_plot_options(autoscale=True)
+121
+122    return data
+123
 124
-125    return data
-126
-127
-128clusters = create_clusters()
-129for cluster in clusters:
-130    cluster.edit()
-131exit()
-132data     = compute(clusters)
-133data     = analysis(data)
-134data.view()
-135
+125clusters = create_clusters()
+126for cluster in clusters:
+127    cluster.edit()
+128exit()
+129data     = compute(clusters)
+130data     = analysis(data)
+131data.view()
+132
    diff --git a/msspecbook/_build/html/Activity09/Activity09.html b/msspecbook/_build/html/Activity09/Activity09.html index 6604e3b..216f07d 100644 --- a/msspecbook/_build/html/Activity09/Activity09.html +++ b/msspecbook/_build/html/Activity09/Activity09.html @@ -57,10 +57,12 @@ + + - + @@ -189,7 +191,7 @@
  • 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: Auger Electron Diffraction
    • +
  • Activity 10: Parallelization and multi-processing in MsSpec
  • Activity 11: Spectral radius and convergence
  • Final word
    • @@ -317,7 +319,9 @@ document.write(` `); - +
    @@ -333,6 +337,14 @@ document.write(`
    @@ -344,6 +356,12 @@ document.write(`

    Activity 9: Comparing simulation and experiment with R-factors#

    +

    In order to extract precise crystallographic information from electronic spectroscopy, we need to compare MsSpec calculations with experimental results and adjust the modelling parameters to simulate the experiment as accurately as possible.

    +

    R-factors (reliability factors) are commonly used for this task. In the following example, we will see how MsSpec can extract the adsorption geometry of molecule.

    +
    +

    The unusual tilt of CO molecule on Fe(001)#

    +

    The carbon monoxide molecule can be adsorbed onto a Fe(001) surface in the hollow site. It was experimentally demonstrated that the CO molecule is tilted by 55\(\pm\)2° in <100> azimuthal directions. The molecule is bonded to the Fe surface by the carbon atom and the adsorption height was estimated to be \(\sim\) 0.6 Å.

    +