diff --git a/msspecbook/_build/.doctrees/Activity05/Activity05.doctree b/msspecbook/_build/.doctrees/Activity05/Activity05.doctree index cd5da2f..061335d 100644 Binary files a/msspecbook/_build/.doctrees/Activity05/Activity05.doctree and b/msspecbook/_build/.doctrees/Activity05/Activity05.doctree differ diff --git a/msspecbook/_build/.doctrees/Activity07/Activity07.doctree b/msspecbook/_build/.doctrees/Activity07/Activity07.doctree index 2dc8629..be09c4b 100644 Binary files a/msspecbook/_build/.doctrees/Activity07/Activity07.doctree and b/msspecbook/_build/.doctrees/Activity07/Activity07.doctree differ diff --git a/msspecbook/_build/.doctrees/environment.pickle b/msspecbook/_build/.doctrees/environment.pickle index 3665b66..428499f 100644 Binary files a/msspecbook/_build/.doctrees/environment.pickle and b/msspecbook/_build/.doctrees/environment.pickle differ diff --git a/msspecbook/_build/html/.buildinfo b/msspecbook/_build/html/.buildinfo index 556b4d6..a78a743 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: d64285b76259d47aa1d35d9bc7e7829a +config: 0b896abf2c995b3493312dcbe0e8b47f tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/msspecbook/_build/html/Activity05/Activity05.html b/msspecbook/_build/html/Activity05/Activity05.html index 28cc2b8..a4bc40f 100644 --- a/msspecbook/_build/html/Activity05/Activity05.html +++ b/msspecbook/_build/html/Activity05/Activity05.html @@ -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/Activity07/Activity07.html b/msspecbook/_build/html/Activity07/Activity07.html index 7690d89..cccde8f 100644 --- a/msspecbook/_build/html/Activity07/Activity07.html +++ b/msspecbook/_build/html/Activity07/Activity07.html @@ -418,7 +418,8 @@ document.write(`

Application to a deep plane in a Si(001) sample#

-

The following script will compute contribution of all the planes of a Si(001) substrate to get the total photoelectron intensity of a Si(2s) polar scan.

+

The following script will compute the contribution of a Si(2p) atom in the 4th plane of a Si(001) cluster at scattering order 3.

+

Taking into account all scattering paths took 15 minutes to compute.

See also

based on this paper from S. Tricot et al. @@ -428,8 +429,139 @@ document.write(`

-

The script is almost completed, try to define path filtering options and compare results with and without filtering for emitter in plane n° 3 at scattering order 2.

-

Compute the contribution of plane n° 7

+

The following script is almost completed, try to define path filtering options (no backscattering, accept all paths with forward angles < 40° and reject paths longer than the diameter of the cluster).

+
 1# coding: utf8
+ 2
+ 3import numpy as np
+ 4from ase.build import bulk
+ 5
+ 6from msspec.calculator import MSSPEC, XRaySource
+ 7from msspec.iodata import Data
+ 8from msspec.utils import hemispherical_cluster, get_atom_index
+ 9
+10
+11# Create the cluster
+12a = 5.43
+13Si = bulk('Si', a=a, cubic=True)
+14cluster = hemispherical_cluster(Si,
+15                                diameter=30, planes=4,
+16                                emitter_plane=3,
+17                                shape = 'cylindrical',
+18                                )
+19for atom in cluster:
+20    atom.set('mean_square_vibration', 0.006)
+21    atom.set('mt_radius', 1.1)
+22cluster.emitter = get_atom_index(cluster, 0, 0, 0)
+23
+24# Create a calculator and set parameters
+25calc = MSSPEC(spectroscopy='PED', algorithm='expansion')
+26
+27calc.source_parameters.energy = XRaySource.AL_KALPHA
+28calc.source_parameters.theta  = -54.7
+29calc.source_parameters.phi    = 90
+30calc.spectroscopy_parameters.final_state = 1
+31
+32calc.calculation_parameters.scattering_order = 3
+33calc.tmatrix_parameters.tl_threshold = 1e-4
+34calc.calculation_parameters.vibrational_damping = 'averaged_tl'
+35calc.calculation_parameters.RA_cutoff = 2
+36 
+37# Define path filtering options such that you only
+38# accept scattering paths with a forward cone <= 40°
+39# and whose length are <= cluster diameter
+40#
+41#
+42
+43calc.set_atoms(cluster)
+44
+45# Compute and add previous data for comparison
+46data = calc.get_theta_scan(level='2p',
+47                            theta=np.arange(-30., 80., 0.5),
+48                            phi=0,
+49                            kinetic_energy=1382.28)
+50no_filters = Data.load('path_filtering.hdf5')
+51data[0].add_columns(**{'no_filters': no_filters[0].cross_section})
+52view = data[0].views[0]
+53view.select('theta', 'cross_section', index=0, legend="With path filtering")
+54view.select('theta', 'no_filters', legend="Without path filtering")
+55
+56data.view()
+
+
+
    +

  1. How long was your calculation ?

    2. +

  2. How does it compare to the calculation with all scattering paths up to order 3 ?

    3. +

  3. What is the proportion of scattering paths of order 3 that were actually taken into account ?

    4. +
+
+
+
+

The calculation took few seconds and the result is very close to the calculation with all scattering paths.

+

Only 0.01% of 3rd order paths were actually taken into account

+
+Si polar scan + +
+

Fig. 18 Si(2p) polar scan (contribution of an emitter in the 4th plane with all 7 114 945 scattering paths taken into account (orange curve), and for only 1525 filtered paths (blue curve).#

+
+
+
 1# coding: utf8
+ 2
+ 3import numpy as np
+ 4from ase.build import bulk
+ 5
+ 6from msspec.calculator import MSSPEC, XRaySource
+ 7from msspec.iodata import Data
+ 8from msspec.utils import hemispherical_cluster, get_atom_index
+ 9
+10
+11# Create the cluster
+12a = 5.43
+13Si = bulk('Si', a=a, cubic=True)
+14cluster = hemispherical_cluster(Si,
+15                                diameter=30, planes=4,
+16                                emitter_plane=3,
+17                                shape = 'cylindrical',
+18                                )
+19for atom in cluster:
+20    atom.set('mean_square_vibration', 0.006)
+21    atom.set('mt_radius', 1.1)
+22cluster.emitter = get_atom_index(cluster, 0, 0, 0)
+23
+24# Create a calculator and set parameters
+25calc = MSSPEC(spectroscopy='PED', algorithm='expansion')
+26
+27calc.source_parameters.energy = XRaySource.AL_KALPHA
+28calc.source_parameters.theta  = -54.7
+29calc.source_parameters.phi    = 90
+30calc.spectroscopy_parameters.final_state = 1
+31
+32calc.calculation_parameters.scattering_order = 3
+33calc.tmatrix_parameters.tl_threshold = 1e-4
+34calc.calculation_parameters.vibrational_damping = 'averaged_tl'
+35calc.calculation_parameters.RA_cutoff = 2
+36
+37my_filters = ('forward_scattering', 'distance_cutoff')
+38calc.calculation_parameters.path_filtering = my_filters
+39calc.calculation_parameters.distance = 30
+40calc.calculation_parameters.off_cone_events = 0
+41[a.set('forward_angle', 40) for a in cluster]
+42
+43calc.set_atoms(cluster)
+44
+45# Compute and add previous data for comparison
+46data = calc.get_theta_scan(level='2p',
+47                            theta=np.arange(-30., 80., 0.5),
+48                            phi=0,
+49                            kinetic_energy=1382.28)
+50no_filters = Data.load('path_filtering.hdf5')
+51data[0].add_columns(**{'no_filters': no_filters[0].cross_section})
+52view = data[0].views[0]
+53view.select('theta', 'cross_section', index=0, legend="With path filtering")
+54view.select('theta', 'no_filters', legend="Without path filtering")
+55
+56data.view()
+
diff --git a/msspecbook/_build/html/_images/results.png b/msspecbook/_build/html/_images/results.png new file mode 100644 index 0000000..2dbf754 Binary files /dev/null and b/msspecbook/_build/html/_images/results.png differ diff --git a/msspecbook/_build/html/_sources/Activity05/Activity05.ipynb b/msspecbook/_build/html/_sources/Activity05/Activity05.ipynb index ca3f110..a7fe237 100644 --- a/msspecbook/_build/html/_sources/Activity05/Activity05.ipynb +++ b/msspecbook/_build/html/_sources/Activity05/Activity05.ipynb @@ -878,7 +878,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" + "version": "3.11.13" } }, "nbformat": 4, diff --git a/msspecbook/_build/html/_sources/Activity06/Activity06.ipynb b/msspecbook/_build/html/_sources/Activity06/Activity06.ipynb index f114ebd..a95699d 100644 --- a/msspecbook/_build/html/_sources/Activity06/Activity06.ipynb +++ b/msspecbook/_build/html/_sources/Activity06/Activity06.ipynb @@ -133,7 +133,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" + "version": "3.11.13" } }, "nbformat": 4, diff --git a/msspecbook/_build/html/_sources/Activity07/Activity07.ipynb b/msspecbook/_build/html/_sources/Activity07/Activity07.ipynb index 9f612ce..1e99041 100644 --- a/msspecbook/_build/html/_sources/Activity07/Activity07.ipynb +++ b/msspecbook/_build/html/_sources/Activity07/Activity07.ipynb @@ -103,7 +103,8 @@ ":::{figure-md} filters-fig\n", "\"path\n", "\n", - "Some examples of scattering paths with `forward_scattering`, `backward_scattering` and `distance` filters selected. The accepted forward angle is 45°, the accepted backscattering angle is 20° and the threshold distance is $6a_0$ where $a_0$ is the lattice parameter. Note that the yellow path is rejected but if the `off_cone_events` option is set to a value > 1, then it could have been accepted." + "Some examples of scattering paths with `forward_scattering`, `backward_scattering` and `distance` filters selected. The accepted forward angle is 45°, the accepted backscattering angle is 20° and the threshold distance is $6a_0$ where $a_0$ is the lattice parameter. Note that the yellow path is rejected but if the `off_cone_events` option is set to a value > 1, then it could have been accepted.\n", + ":::" ] }, { @@ -113,7 +114,9 @@ "source": [ "## Application to a deep plane in a Si(001) sample\n", "\n", - "The following script will compute contribution of all the planes of a Si(001) substrate to get the total photoelectron intensity of a Si(2s) polar scan. \n", + "The following script will compute the contribution of a Si(2p) atom in the 4{sup}`th` plane of a Si(001) cluster at scattering order 3.\n", + "\n", + "Taking into account all scattering paths took 15 minutes to compute.\n", "\n", "(msd-paper)=\n", ":::{seealso}\n", @@ -126,14 +129,46 @@ "\n", ":::{tab-item} Quiz\n", "\n", - "The script is almost completed, try to define path filtering options and compare results with and without filtering for emitter in plane n° 3 at scattering order 2.\n", + "The following script is almost completed, try to define path filtering options (no backscattering, accept all paths with forward angles < 40° and reject paths longer than the diameter of the cluster).\n", "\n", - "Compute the contribution of plane n° 7\n", + "```{literalinclude} Si001.py\n", + ":lineno-match:\n", + ":emphasize-lines: 37-41\n", + "```\n", + "\n", + "1. How long was your calculation ?\n", + "2. How does it compare to the calculation with **all** scattering paths up to order 3 ?\n", + "3. What is the proportion of scattering paths of order 3 that were actually taken into account ?\n", "\n", ":::\n", "\n", "::::" ] + }, + { + "cell_type": "markdown", + "id": "19fbd486-b0c1-450c-a00d-79984945aefd", + "metadata": {}, + "source": [ + "```{toggle}\n", + "The calculation took few seconds and the result is very close to the calculation with all scattering paths.\n", + "\n", + "Only 0.01% of 3{sup}`rd` order paths were actually taken into account\n", + "\n", + ":::{figure-md} si-fig\n", + "\"Si\n", + "\n", + "Si(2p) polar scan (contribution of an emitter in the 4{sup}`th` plane with all 7 114 945 scattering paths taken into account (orange curve), and for only 1525 filtered paths (blue curve).\n", + "\n", + ":::\n", + "\n", + ":::{literalinclude} Si001_completed.py\n", + ":lineno-match:\n", + ":emphasize-lines: 37-41\n", + ":::\n", + "\n", + "``` " + ] } ], "metadata": { @@ -152,7 +187,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" + "version": "3.11.13" } }, "nbformat": 4, diff --git a/msspecbook/_build/html/objects.inv b/msspecbook/_build/html/objects.inv index fce4965..a1f28f0 100644 Binary files a/msspecbook/_build/html/objects.inv and b/msspecbook/_build/html/objects.inv differ diff --git a/msspecbook/_build/html/searchindex.js b/msspecbook/_build/html/searchindex.js index 655704c..90862c4 100644 --- a/msspecbook/_build/html/searchindex.js +++ b/msspecbook/_build/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"Activity 10: Auger Electron Diffraction": [[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: 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4, "valu": [2, 4, 5, 6], "van": 4, "vari": [2, 5], "variabl": [1, 3], "variat": [2, 5], "variou": [2, 12], "veri": [2, 6], "version": 0, "versu": 5, "vibrat": 5, "vibration_sc": 5, "vibrational_damp": [5, 6], "view": [0, 1, 2, 3, 4, 5, 6], "visual": [0, 1, 2, 4], "volum": 4, "wa": 6, "waal": 4, "wai": 5, "waller": 5, "want": [3, 5], "water": 0, "wave": [0, 2, 4], "we": [0, 1, 2, 3, 4, 5, 6, 12], "well": [0, 3, 4, 5], "were": 6, "what": [0, 2, 4, 6], "when": [1, 5, 6], "where": [2, 3, 4, 5, 6], "which": [2, 6], "while": 3, "whose": 6, "why": 6, "wide": 2, "window": 3, "within": 6, "without": [0, 6], "word": 12, "work": [0, 5], "would": [1, 4, 6], "written": 0, "x": [1, 3, 5], "x_alpha_r": 5, "xlabel": 5, "xpd": [4, 12], "xraysourc": [5, 6], "xu": 3, "y": [1, 3], "year": [], "yellow": 6, "ylabel": 5, "ylim": 3, "you": [0, 1, 2, 3, 4, 5, 6, 12], "your": [1, 2, 3, 5, 6], "z": [1, 2, 3, 4], "z0": 2, "z_0": 2, "zi": 2, "zip": [], "\u00b5": 6, "\u00e5": [2, 4, 6]}, "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: Auger Electron Diffraction", "Activity 11: Spectral radius and convergence", "Final word", "Welcome to this small MsSpec tour"], "titleterms": {"001": [0, 2, 6], "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], "activ": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10], "adsorb": 2, "ag": 1, "an": 1, "applic": 6, "approach": 2, "atom": 0, "auger": 9, "azimuth": 1, "backscatt": 2, "barebon": 0, "build": [0, 1], "bulk": 5, "cluster": [0, 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a/msspecbook/_build/jupyter_execute/Activity05/Activity05.ipynb b/msspecbook/_build/jupyter_execute/Activity05/Activity05.ipynb index 8459e16..73d41ea 100644 --- a/msspecbook/_build/jupyter_execute/Activity05/Activity05.ipynb +++ b/msspecbook/_build/jupyter_execute/Activity05/Activity05.ipynb @@ -266,7 +266,7 @@ "\n", "\n", "\n", - " \n", + " \n", " \n", " \n", " \n", @@ -634,7 +634,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -642,7 +642,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -698,7 +698,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -706,7 +706,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -754,7 +754,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -878,7 +878,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" + "version": "3.11.13" } }, "nbformat": 4, diff --git a/msspecbook/_build/jupyter_execute/Activity06/Activity06.ipynb b/msspecbook/_build/jupyter_execute/Activity06/Activity06.ipynb index 4ab9cb6..afa19b3 100644 --- a/msspecbook/_build/jupyter_execute/Activity06/Activity06.ipynb +++ b/msspecbook/_build/jupyter_execute/Activity06/Activity06.ipynb @@ -133,7 +133,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" + "version": "3.11.13" } }, "nbformat": 4, diff --git a/msspecbook/_build/jupyter_execute/Activity07/Activity07.ipynb b/msspecbook/_build/jupyter_execute/Activity07/Activity07.ipynb index c80e6c1..db8f15b 100644 --- a/msspecbook/_build/jupyter_execute/Activity07/Activity07.ipynb +++ b/msspecbook/_build/jupyter_execute/Activity07/Activity07.ipynb @@ -103,7 +103,8 @@ ":::{figure-md} filters-fig\n", "\"path\n", "\n", - "Some examples of scattering paths with `forward_scattering`, `backward_scattering` and `distance` filters selected. The accepted forward angle is 45°, the accepted backscattering angle is 20° and the threshold distance is $6a_0$ where $a_0$ is the lattice parameter. Note that the yellow path is rejected but if the `off_cone_events` option is set to a value > 1, then it could have been accepted." + "Some examples of scattering paths with `forward_scattering`, `backward_scattering` and `distance` filters selected. The accepted forward angle is 45°, the accepted backscattering angle is 20° and the threshold distance is $6a_0$ where $a_0$ is the lattice parameter. Note that the yellow path is rejected but if the `off_cone_events` option is set to a value > 1, then it could have been accepted.\n", + ":::" ] }, { @@ -113,7 +114,9 @@ "source": [ "## Application to a deep plane in a Si(001) sample\n", "\n", - "The following script will compute contribution of all the planes of a Si(001) substrate to get the total photoelectron intensity of a Si(2s) polar scan. \n", + "The following script will compute the contribution of a Si(2p) atom in the 4{sup}`th` plane of a Si(001) cluster at scattering order 3.\n", + "\n", + "Taking into account all scattering paths took 15 minutes to compute.\n", "\n", "(msd-paper)=\n", ":::{seealso}\n", @@ -126,14 +129,46 @@ "\n", ":::{tab-item} Quiz\n", "\n", - "The script is almost completed, try to define path filtering options and compare results with and without filtering for emitter in plane n° 3 at scattering order 2.\n", + "The following script is almost completed, try to define path filtering options (no backscattering, accept all paths with forward angles < 40° and reject paths longer than the diameter of the cluster).\n", "\n", - "Compute the contribution of plane n° 7\n", + "```{literalinclude} Si001.py\n", + ":lineno-match:\n", + ":emphasize-lines: 37-41\n", + "```\n", + "\n", + "1. How long was your calculation ?\n", + "2. How does it compare to the calculation with **all** scattering paths up to order 3 ?\n", + "3. What is the proportion of scattering paths of order 3 that were actually taken into account ?\n", "\n", ":::\n", "\n", "::::" ] + }, + { + "cell_type": "markdown", + "id": "19fbd486-b0c1-450c-a00d-79984945aefd", + "metadata": {}, + "source": [ + "```{toggle}\n", + "The calculation took few seconds and the result is very close to the calculation with all scattering paths.\n", + "\n", + "Only 0.01% of 3{sup}`rd` order paths were actually taken into account\n", + "\n", + ":::{figure-md} si-fig\n", + "\"Si\n", + "\n", + "Si(2p) polar scan (contribution of an emitter in the 4{sup}`th` plane with all 7 114 945 scattering paths taken into account (orange curve), and for only 1525 filtered paths (blue curve).\n", + "\n", + ":::\n", + "\n", + ":::{literalinclude} Si001_completed.py\n", + ":lineno-match:\n", + ":emphasize-lines: 37-41\n", + ":::\n", + "\n", + "``` " + ] } ], "metadata": { @@ -152,7 +187,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" + "version": "3.11.13" } }, "nbformat": 4,