From fed5ccd6671ebe6650fc749c9e00476d64eafa21 Mon Sep 17 00:00:00 2001
From: Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>
Date: Fri, 11 Jul 2025 16:59:50 +0200
Subject: [PATCH] Update Activity 7

---
 msspecbook/Activity07/Activity07.ipynb        |   7 +++++++
 .../.doctrees/Activity07/Activity07.doctree   | Bin 20613 -> 22125 bytes
 .../_build/.doctrees/environment.pickle       | Bin 57595 -> 57595 bytes
 .../_build/html/Activity07/Activity07.html    |   5 +++++
 .../html/_sources/Activity07/Activity07.ipynb |   7 +++++++
 msspecbook/_build/html/objects.inv            | Bin 1725 -> 1726 bytes
 msspecbook/_build/html/searchindex.js         |   2 +-
 .../Activity07/Activity07.ipynb               |   7 +++++++
 8 files changed, 27 insertions(+), 1 deletion(-)

diff --git a/msspecbook/Activity07/Activity07.ipynb b/msspecbook/Activity07/Activity07.ipynb
index ee11a68..9f612ce 100644
--- a/msspecbook/Activity07/Activity07.ipynb
+++ b/msspecbook/Activity07/Activity07.ipynb
@@ -115,6 +115,13 @@
     "\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",
     "\n",
+    "(msd-paper)=\n",
+    ":::{seealso}\n",
+    "based on this paper from S. Tricot *et al.*\n",
+    "[J. Electron. Spectrosc. Relat. Phenom. **256** 147176 (2022)](https://doi.org/10.1016/j.elspec.2022.147176)\n",
+    ":::\n",
+    "\n",
+    "\n",
     "::::{tab-set}\n",
     "\n",
     ":::{tab-item} <i class=\"fa-solid fa-circle-question\"></i> Quiz\n",
diff --git a/msspecbook/_build/.doctrees/Activity07/Activity07.doctree b/msspecbook/_build/.doctrees/Activity07/Activity07.doctree
index 82cb32dcdf5a8faf7f7855b7fe6b7076e12d663b..2dc8629c335cab76647654c19581de2a32d3ccde 100644
GIT binary patch
delta 1697
zcmcIlO>7fK6!vVg8=M4`7(-Ja$;44h?569rl^+C69m0Q{IEGXe2wCbTSu&nFUTb&F
zUlqAjMG9yINV7;efqE?Df{eIv0(#+sgxX4QK#GI}LL7QSocd;$#CB7)>7ke1**EjP
z`R4oHo4xoGdb@<g@5Sp=U*8d54{d1*UvTD~9wOTQIdkUof?CiFhp8c4s`@UH4$??E
zM^CpRAHk%Hgy=W*J|F2Ob;T*-vl~oJQ*);7FlQBRaY{9{8La2AMY1M#f$=FrpTm<f
z{>sQs>lTh^7FKg|r19jaj1T0rY0J>_GM+5JsATBow2Y5wIn|PJnrL}_PR5Z)yni4P
z!Lh!<*x&%}i7WAVIMYKct6=VqMrZV_tQ)h@m?FoN*g%xZTFwMCnXi+*q_9I8G7kCT
zUzo!F>!td?FfGCPJgPlJvAfryrgPEpybRH6AKW20MLJX9(ZSWzN}lGP2#US(S;<}W
za#<qL&7KU^mkxmOXDh~YXaH1f)c8*u`fb0Voze^~Kdn`l#jdqZ|E+vrvuAQ?#buW<
z*J9^7A*$#t{Z$XYEt$O7W~;f?!KN#^xMMC#1MiLyy~kQddI#xU4pgHDhj#VYR9lqQ
zyR(~#b~YSqPTLZQQZ%xT-TPlk)`143x7KWZt)5-&=qiytwTx_+kxE)P^FYR-mmr{$
zAQb)9j8om`Drtk@wv3B^nd9^3?i@YC?XL7V{aNt&<{kPBR?reWOnTdkaAe5~u{T3c
z(Q8mC%wB!Dz3GAn@e&p=Wm8z7?^dQlRa35TB0gHop0CpDCFnJXmdn2<7LX7WnYvfm
z_(P=vTSazbuOWoIi63hwCPq?dncWyUiC(bxBa>*poZ9yt5>ANa$NSF;Xra9S&~n|!
z@xE1?`(f<WJ{<TLmPihuhwOB+13hBblOgmQMB3PsB!=i8$^QBWBAlm`+=6~(!(*|C
zD=jF@MNx}(LtdTJvNI;XQRxX-O4{jhc+p9bT^akVH^s+E{&1z_>J@E2PqNMxv`X3n
zWU=RCJKA`{C3o>ckp#G(?c`IA<{$5Cae??f?6RPCdEfXV5<ZgHaB?eC#O4iq;7CCU
z2zLoPSaZ6S^-W-Z00PA+x>;gJgWK4diE$xbn-Q&K1cY9R;q>;}q)&+C-k^#dJq)ys
pTsHqLwp3#lZkEvMPlVl1bqHg%&_~ul2b<iV3a{^g#D>y`{{(}p2IT+%

delta 474
zcmaF6hOu=aBWnZe)T)4utS@aRUvRp>*g1KjvkOO+AR|MDQdaBax6ZngB^<OSpK_K~
zf(f!PFq9@`81%3z1eRu2O=+FdIHh)q23UEci#cP{=AAAbjEq}=25C;dV9UW<4Khq2
zLlLNABg^Clw<5+vaJgC(IYW0p#-_;)?$M0(lkd0(GnQ>O@Tg{F`pL3+t!D)jqsC@6
zpGVA+h6YnI*kh*vUBGM#WJBx+8lE;;F~E#5WpYG-9AoO_@&F~qGN6dW<V^tzK+($q
zrYy;<3=ESK14J21Co2US%9i%9=OyN*W~LN_JdpJh=&=mhtRFxs>od#b+Cc4qcOdp_
zkcWFXK}t(13sMn^JHTo?v$&WU7&@~)GBGf8WW@p%cV>kG$&M_L?#|K-AyDYZW~hM-
z<p?ri1DThVu-PYQ1|#D(pbNz(8?f?lSOa~q8RR}iCYi}PA%>hAft=E$tWB(w14X1J
fH-z{yUPMuR4xw0(IqNj*WX(`%rj4wVRl__0$e@^R

diff --git a/msspecbook/_build/.doctrees/environment.pickle b/msspecbook/_build/.doctrees/environment.pickle
index 8e47235732f38f96a0b77009d5892bf70ee55e01..3665b6681e4b0b297d6c91f54f119f2ff12cae8d 100644
GIT binary patch
delta 1123
zcmY+?OH30{6adgp3zilvh=SIFK$VEb7AisU6BT1LNW@Su23kUfe+OD?KPnrEQ7J-^
zk~{uU(L`Np7>FMdp=vau2&CXID8vL^VAO?)3tV{b6dPUiyuN$idw1sDnf1$N{jxhh
z3nG=}Y(<@wb-Ah>aND>7Rux4-tZ_NKFsZ<4R70a_vD_POvAG-vfX!Be$*6=ZjL#TT
z!C$-tVhYpZPlib(-UxAx-df3XUYcv*SaF;}Z?QMn%6YC0>I=0@6SSkv&|Rp7Uxm@|
z{6Q3KyAc65i&U_(Z+>WX3uub8j0d)$r-4OV;RNb~Tj(hmEYdVmQI0359CwCjBhC^{
z#5tmwI8U?_7l;nxBGE!zB0NMVahkYHv=UbcA90m9MRbJ;mHWEFl(eZu{=0kX2&hUr
zVWLC>YfQ_)U$O`yO(_s-S{QE7bM_kOFG-ABlvCld9J06?GBVSRwR_8))p~mal$)+E
zhzVs3=@o8@O3gahZdNNQYFUd713cuJ)hRyi9Tsfo)4cJa9a-s)DyO^N<rM2onG@lW
zIT<`=t-{B>53YvP(j<`MZ%64?13faGurPGO`t)i`jrf@SKj%`k9={5w&{LW>pYe3p
z<ucMJsgPIyMUJiMuxp{ZdlUFv9~qBuz}>tVgKSq8d_TGY6UT8@a8xbGgtZLj*Y&j1
z@U*v!hMKzyDGmqkJLloD>HfoL=|Clh9u4S}IQcQS58e4<9772&15!{8r|lLSv|1&R
zH1V7chhWF_!GIwYSStp+3ahhHXJ_qI4qjaNZ$My&M`cUD1}}me!O`c9qK@D_WZ*S|
zE}&5cF9d7Nz`;Ng^9?!z8{u;x7Cr<N8ztf5C30`Xy%D%CQ*XD`@VHzymwGFvBJ(YD
zs^M>T9wd(?GvSakmdHdv*;o#vgll8k#^||S^pZX=9T=(~^Is}*t}E1SEa%2nauf9O
z_lPINJK`DPCq{@NVvv|70z@CtOT3OIKM|9}L!n^&9uxP9!T%$~Ffl}o3d`PD71*7e
i$)qI-xy5Y$9<SWtwz(|UDt_0tnAL-A`|a>}D*F$Rpm{(5

delta 1145
zcmZA0ZAep57yw|eQ@3eO`<S|BDzm^8=NFb)lt%P{P&nrgb<3vv=-xJ++qDo%k+Rfo
zIel;6R_jMW|H5l!3Z)eler3!utt^TNqOc!9KZ5GKcf-m*&)GTe`<`>pdD+h)$<HCl
zjqk;j5|Z>v8PA2%HLR-^GIYt%uTy~|FA{F(!eOLB0ef_+i0~>?^*)D*Wi2i^RH5o3
zX`^M4;4O=Tce*%;E=h^uLV|)gnYfMCVdj~mI9Ee+nNqH$oeecrJktjD5)E|{I*7-h
zr$htS^a^;=9|;9lWnmrug2aKp1;;_H*HA66k=P0*;t4pS*T9bw1@!8bR67jo)lGOZ
z!y|Yma|&rgP9rCgGsrRIEaE}VA$TZr9yyL&Kw6M)q!qb{oIoxioycXR9r1<;=2CA+
zI2N@_n`>W{f}*^8$+E&~mflaZ4VgI^y1lz9-By?_SA|t+ZM2n#>*ewAp*%NFy&$W)
z*5R~USc_TfY~Z=r1yL()%hEDV8}AVx{a{5a#2V5-Vps~B4Jx@9cGlQ<C?YctGflpz
zgHM4OL-H~%W`3{S441`SZ)e?b%diT(1~o~Y38bzxCV|wL09%Zkq<A4L_Zn4;xux^v
zYcud1q1RXxNwxIs+d&2YqJ$#*Cn;%Dr&9ygp7r2iXQ>vUw!U=(Su}ZbVXko<2^=P~
z;zpGq5wa-~U(?%x!=syC9BjAc!DOhr;|?QfAMYI?8VAi}>Hc7PIGKDKE+uXqc}|w%
zM}5I7IJv`ZPIsD|78ftx;NJ!KI-Z&)HZoNa6m*nl(#hcOtk%DfHNTKeehH?h&m>Un
zi&>p1J~647^FIJHK}HX^2)j7n0TTWKb-qOEGj#g$sb4VaTb}<rP%tGH$VhUI7W+Yx
zgG0r~WL}D)h@G^5t3Xr+Ns~!b7!*#fphBT?vXF{^E0db0=s*?T!^7c*{{E8<qy7s;
zSZO=?Yq|rUUQhbQJjDCGM&2VIkqKl7nMPh9H<1D4E;5D;BYjcmTf~Pv7K)$uQOai&
y`8|e=BNNC|Az{iPC+#VGn-~|r{ZV6A9Vd0w*RZt1!fz{xPTl<`G!q`Y%liZVOoNR8

diff --git a/msspecbook/_build/html/Activity07/Activity07.html b/msspecbook/_build/html/Activity07/Activity07.html
index d0a5d0f..7690d89 100644
--- a/msspecbook/_build/html/Activity07/Activity07.html
+++ b/msspecbook/_build/html/Activity07/Activity07.html
@@ -419,6 +419,11 @@ document.write(`
 <section id="application-to-a-deep-plane-in-a-si-001-sample">
 <h2>Application to a deep plane in a Si(001) sample<a class="headerlink" href="#application-to-a-deep-plane-in-a-si-001-sample" title="Link to this heading">#</a></h2>
 <p>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.</p>
+<div class="admonition seealso" id="msd-paper">
+<p class="admonition-title">See also</p>
+<p>based on this paper from S. Tricot <em>et al.</em>
+<a class="reference external" href="https://doi.org/10.1016/j.elspec.2022.147176">J. Electron. Spectrosc. Relat. Phenom. <strong>256</strong> 147176 (2022)</a></p>
+</div>
 <div class="sd-tab-set docutils">
 <input checked="checked" id="sd-tab-item-1" name="sd-tab-set-1" type="radio">
 <label class="sd-tab-label" for="sd-tab-item-1">
diff --git a/msspecbook/_build/html/_sources/Activity07/Activity07.ipynb b/msspecbook/_build/html/_sources/Activity07/Activity07.ipynb
index ee11a68..9f612ce 100644
--- a/msspecbook/_build/html/_sources/Activity07/Activity07.ipynb
+++ b/msspecbook/_build/html/_sources/Activity07/Activity07.ipynb
@@ -115,6 +115,13 @@
     "\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",
     "\n",
+    "(msd-paper)=\n",
+    ":::{seealso}\n",
+    "based on this paper from S. Tricot *et al.*\n",
+    "[J. Electron. Spectrosc. Relat. Phenom. **256** 147176 (2022)](https://doi.org/10.1016/j.elspec.2022.147176)\n",
+    ":::\n",
+    "\n",
+    "\n",
     "::::{tab-set}\n",
     "\n",
     ":::{tab-item} <i class=\"fa-solid fa-circle-question\"></i> Quiz\n",
diff --git a/msspecbook/_build/html/objects.inv b/msspecbook/_build/html/objects.inv
index 07acfaf25427ffe8097c6f6376e066372563b0d7..fce4965c1443740d23014cc2e3db32f69ebd0765 100644
GIT binary patch
delta 671
zcmV;Q0$}~U4ZaPqECheAl!i{aG9`0h3F@Lyh(vYOBrnZqr~TI{Mk66ozu?T=drJUP
zytj1Rk_V|`XP^hfjE-^EE|_XQnVb?+St4B;yi9qW>`clsL9XM(3M|87UpG-K=u=1}
zk3Rh&kDOF!3%xIxxHsCt#OsE`OzVFk$d8yXzsAFvy^OK0n)-jVF-fUnlg)$K_WDOH
z3tdNFdsvSz2YCFjv8a`zf04V_8x<joc2XGBgsPN79oQIz^H4(f)%P1zuVTYDc_eBF
z-U!nfz*ydBG9vz(-inli*NCT>1vX#kccCaG_^A*v+vwbgd8lbAE|c`g7+%Rq4t5J#
zf`wQ|wWLdznDu|D07?2;0rPSrtXXf3MI8ytes#A(9=Y3OLX|CR?v-v6&ZW)IdXEO7
zeg$}1^9&Qk){p;t?;m+D${z6C-Ww2}d!9l~i0+AYDhUs~p!9Vc+?ZQ+`Z71Kmo3Ve
z9e}eijbh7WrL==VZF*(3>&O*bKSVow?`2)*@9_*kXODkrpflj8nW7e}!8ADPhFE1e
z*`Og!&esFa^Gu#hXZu;w+-UqCxzQs_?nxPjXv|_KQ-qGDR6+?BFLMk$ss5rflz=<7
ztph#U=j}75bRaSwyE8{}Rv>S8EVXNv`WANonytAb!vk~8wuge}s0ZAv?%$@Ink=(#
zHb*B4KQw=x7v|8qVDP%H(^-#ofH5=g%Yi42>!ma=Mn#vH7|-ZrJkf5h_#nIAto7W6
zUgbbahsHFs(D%`{l%5Om;&>HR-3(f8F^pvTorbYYl>zGL{c_|eA^G?~9$ToQ^v%Qq
z5btJqBNlv20}QrjEBsB|*<?nafBF3p`S^M4jz$+#`!m4abT+a-F3u3jnb|pV{sb-$
FpB(i5P1pbc

delta 670
zcmV;P0%85W4ZRJpEChcKdg!DpQ!)pZpe_o9NK{u%^3sfU+JBv5G!i293(m~Fw*(-?
zdrQYHd5|i026{lu=on}1f~n?{$tf|FCDNtA%aqs2&ZI08<T_5Qz%nfMbrZ#cK7~Z`
z=+hta$Vr8^(EEakd!rppylyzmwEh=@{D=wjYdoCU%NXmbsZW0!lawkp**utSuYc6C
z&~@~+hxPb!fX5FTi&`oA7rA@AQ4z9eCxt;xs7g81fsH{p4<&S8eZN8VDmHwRN1}G%
zjWC@7jOC3cBjT^=tw=d|jd+S#VDp837m7lHp9&GPjn0jjhnkk+GD(k&;gy`^V7H(p
zScr90OS*K4S)YFjkffg#FfTX4n)TLL)RD04S9dGqk-JSMRN1oTUg<XBT-yAs_h=C6
zSAeHA&oEJJ{rJE4{*m{h>;cd1y#e95=PA^L=$>e&lJLL_N?*6Zjk#5)FLU#H*`kcu
z0XPfOD7H*iN;??TrdL+Gj$E<zL$tH^Ue<N~9?t-D_LzSLIs=ZHDQdAAOoO9th*g%8
z4I0wqd_C|y&*aH;wx1=<jmH0x8$Gh*o|IvT#w>O+Md)ZsC6r+CGRMG^>MuG&3Akh1
zI?$ti-acbW2O{IKJ98vw1@d;sQoClUZ(;YZ*_t~tJTTX6dnkC0dce)<{%y*s$uj$9
zb9AEcL(_kGVGgYe2Cw@%o%L7;7&G&}9C*^WUP|*~RCI}n@r+K!6Yb`T53>8sTF-6h
zRSu+dXiPH;eIIR0>A4Uuj#p9D&7kEL!$_vzX&B2?8K92dFGr3Nl8+DMv4tv1-%Kn3
z@ot7UV!_8Wz+ii}!r#Q5O=k4@m){?ekDtfxXfzhJKLhMdXCwRL;tZjjnVlo&PaKq=
E8h1QbGXMYp

diff --git a/msspecbook/_build/html/searchindex.js b/msspecbook/_build/html/searchindex.js
index f3b3c28..655704c 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: 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"]], "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"]], "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 number of scattering paths": [[6, "the-number-of-scattering-paths"]], "The script": [[5, "the-script"]], "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], "0": [0, 1, 2, 3, 4, 5, 6], "001": 5, "004": 4, "02": 2, "05": 2, "0f": 5, "1": [1, 2, 3, 4, 5, 6, 12], "10": [0, 1, 2, 12], "100": 5, "1000": [3, 5], "1000k": 5, "1010": [], "1030": 4, "11": 12, "111": 2, "11h": [], "121": 1, "14": 5, "15": [1, 4], "170\u00b5": [], "171": [], "1986": 5, "1989": 3, "1998": 2, "1e": [], "1e12": 4, "2": [0, 2, 3, 5, 6, 12], "20": [1, 6], "2012": [4, 5], "22": 1, "240": 1, "25": 4, "27": 5, "298k": 5, "2d": 4, "2f": 2, "2p": [0, 4, 5], "2p3": 0, "3": [0, 3, 4, 5, 6, 12], "30": 1, "300": 5, "31557600": [], "31902333327338293": [], "337": [], "34": 5, "343": 5, "3600": [], "39": 3, "3f": 4, "3rd": 0, "4": [0, 1, 2, 4, 5, 12], "40": [1, 6], "400": 5, "45": [1, 3, 5, 6], "450": 4, "499": 3, "4d": 1, "5": [1, 3, 5, 6, 12], "51": 5, "535": 4, "55": 1, "554": 4, "560": 5, "564": [], "5th": 3, "6": [1, 4, 6, 12], "60": 4, "606": 4, "64": 4, "65": 2, "685": 4, "6a_0": 6, "7": [5, 12], "70": 4, "723": 2, "739": 6, "8": [1, 2, 3, 4, 12], "80": 3, "81": 2, "83": 5, "86400": [], "9": [5, 12], "900": 4, "98": 5, "A": [2, 3, 5], "AED": 0, "ASE": [0, 1, 2, 4], "As": [0, 2, 4, 6], "But": 4, "By": 2, "For": [1, 4, 5, 6], "If": 6, "In": [0, 1, 2, 4, 5, 6], "It": [1, 4], "Not": 0, "On": 2, "One": 6, "Or": 0, "The": [0, 1, 2, 3, 4], "There": 0, "To": [0, 1, 2, 4, 5, 6], "With": 5, "_": [], "__main__": 5, "__name__": 5, "_plotopt": 5, "a_0": [4, 6], "abl": 6, "about": [2, 4], "abov": [0, 2, 4, 5, 6], "absolut": 3, "absorb": [3, 5], "accept": 6, "accordingli": 3, "account": [0, 4, 6], "accur": [2, 4], "accuraci": 2, "act": 1, "activ": 12, "actual": [3, 5], "ad": 2, "add": [1, 2, 5], "add_adsorb": 2, "add_column": [1, 5], "add_dset": 5, "add_view": 5, "adsorb": 12, "adsorpt": 2, "advantag": 2, "after": 4, "agit": 5, "agreement": 1, "al": [1, 2, 3, 4], "al_kalpha": 5, "alber": [4, 6], "algorithm": [0, 2, 4, 5, 6], "align": [1, 4], "all": [0, 2, 3, 5, 6, 12], "all_data": 3, "all_t": 5, "all_theta": 5, "all_z": 2, "allow": [0, 6], "almost": [4, 6], "along": 3, "alreadi": 4, "also": [4, 5], "altern": 6, "although": 1, "altitud": 2, "an": [0, 2, 3, 4, 5, 6], "analysi": 5, "analyz": 0, "angl": [1, 5, 6], "angstrom": [2, 3], "angstr\u00f6m": 4, "angular_accept": [1, 5], "ani": 2, "anisotropi": 5, "anisotropy_dset": 5, "anisotropy_view": 5, "annular": 2, "anoth": 4, "answer": 3, "apart": 2, "apec": 0, "apertur": 6, "append": 5, "approach": [0, 4, 12], "approxim": [2, 4], "ar": [0, 1, 2, 4, 5, 6], "arang": [2, 3, 5], "arbitrarili": 5, "around": 4, "arrai": 5, "arrang": 6, "articl": 5, "ase": [0, 1, 2, 3, 4, 5], "assum": [1, 6], "atom": [1, 2, 3, 4, 5, 6], "atomist": 0, "attach": 2, "attempt": 5, "attribut": 1, "auger": 12, "autoscal": 5, "avail": [0, 4], "averag": 5, "average_sampl": [1, 5], "averaged_tl": 5, "axi": [3, 4], "azimut": 5, "azimuth": 5, "b": [1, 3, 5], "b_0": 4, "backascatt": [], "backscatt": 6, "backward_scatt": 6, "base": [0, 1, 2, 3, 4, 5], "basi": 0, "beamlin": 1, "becaus": 6, "becom": [2, 6], "been": 6, "begin": 2, "being": [2, 5], "below": [2, 3, 4, 5, 6], "better": 1, "between": [0, 1, 2, 3, 4, 5], "bewteen": 3, "big": [], "bit": 4, "blue": 1, "boltzmann": 5, "bond": 2, "both": [2, 5], "bright": 2, "bring": 12, "build": [2, 3, 4, 5], "bulk": [0, 1, 6], "c": [4, 5], "c_0": 4, "calc": [0, 1, 2, 3, 4, 5], "calcul": [0, 1, 2, 3, 4, 5, 6], "calculation_paramet": [1, 2, 3, 4, 5], "calculationparamet": 5, "can": [0, 2, 3, 5, 6], "cannot": 4, "carri": 2, "case": 2, "categori": 1, "cell": [1, 4], "center": [2, 4], "chain": [2, 3], "chain_length": 3, "chang": [1, 2, 3, 5], "chosen": 5, "cif": 0, "circl": 2, "cite": 5, "class": 2, "clear": 5, "cluster": [2, 5, 12], "cnr": 0, "code": [0, 2, 3, 4], "col_nam": 5, "col_valu": 5, "column": 4, "com": 2, "come": [2, 5], "comment": 2, "common": [5, 6], "compar": [1, 6, 12], "comparison": [0, 1], "complet": [2, 4, 5, 6], "complex": 4, "compon": 0, "comput": [0, 3, 4, 5, 6], "computation": 2, "concept": [0, 12], "conclud": [0, 4], "cone": 6, "configur": [1, 6], "consid": 2, "constant": [3, 4, 5], "construct": 2, "consumpt": 2, "contain": [0, 1, 4, 5], "contribut": [0, 6], "control": 5, "converg": [1, 4, 12], "convers": [], "copper": [0, 4, 5], "correctli": 1, "correspond": [4, 6], "could": 6, "cover": 0, "creat": [0, 1, 2, 6], "create_clust": 5, "cross_sect": [1, 3, 5], "cruguel": 1, "crystallin": 2, "cu": 5, "cubic": [0, 1, 5], "custom": 3, "cut_plan": 1, "cylindr": 5, "d": [0, 2, 3, 4, 5], "dai": [], "damp": 5, "dark": 2, "data": [0, 1, 2, 3, 4, 5], "dataset": [1, 3, 5], "datetim": [], "deby": 5, "debye_temperatur": 5, "decreas": 5, "deep": [], "deeper": 4, "deepest": [0, 5], "def": 5, "default": 3, "defin": [1, 2, 3, 4, 5, 6], "degre": [2, 3, 5], "delta": 5, "demonstr": 2, "dens": 4, "depth": 5, "der": 4, "describ": 4, "detail": 5, "detector_paramet": [1, 5], "deviat": 4, "diamet": [1, 5, 6], "dichalcogenid": 4, "dict": 5, "differ": [0, 1, 2, 5, 6], "differnt": 3, "difficulti": 12, "diffract": [0, 1, 2, 4, 5, 12], "diffus": 3, "direct": [1, 2, 4, 6], "directli": 0, "disord": 5, "displac": 5, "displai": [0, 3], "distanc": [2, 3, 6], "distinguish": 5, "do": [0, 4, 5], "document": [2, 5], "doubl": 4, "drastic": 6, "dset": [1, 2, 3, 5], "due": 5, "e": 1, "e_0": 2, "each": [1, 3, 4, 5, 6], "eas": 1, "edit": 0, "effect": [1, 2, 6, 12], "either": 5, "eject": 2, "electron": [0, 2, 4, 12], "element": 4, "els": 5, "emiss": [2, 5], "emit": 2, "emitt": [0, 1, 2, 4, 5, 6, 12], "emitter_plan": [0, 1, 4, 5], "emitter_tag": 4, "empti": 3, "end": 3, "energi": [1, 2, 4, 5, 6], "enlarg": 3, "enumer": 2, "environ": 0, "equal": 0, "equat": 5, "escap": 1, "estim": 5, "et": [1, 2, 3, 4], "ev": [1, 2, 4, 5], "evalu": [4, 6], "event": 4, "exact": 2, "exaf": 0, "exampl": [5, 6], "exchange_correl": 5, "exp": 1, "expand": 4, "expans": [2, 4, 5, 6], "expect": [5, 6], "experi": 12, "experiment": [1, 2], "explain": 5, "explor": [4, 5, 6, 12], "extra": 5, "extrem": 2, "f": [4, 5], "factor": [4, 12], "fadlei": 5, "far": 6, "fast": 2, "fcc": [2, 4], "fcc111": 2, "featur": [0, 1, 12], "fewer": 0, "figur": [2, 3, 4, 5, 6], "file": [0, 1], "fill": 2, "filter": [5, 12], "final": [1, 12], "find": 3, "first": [2, 3, 4, 6], "fix": 6, "flexibl": 0, "float": 5, "focu": [0, 12], "folder": 3, "follow": [0, 1, 5, 6], "format": [2, 3, 5], "former": 1, "formula": [4, 6], "forthcom": 0, "fortran": 0, "forward": [6, 12], "forward_scatt": 6, "fr": 0, "frac": 5, "free": [4, 5], "fring": 2, "from": [0, 1, 2, 4, 5, 6, 12], "fromkei": 5, "fulli": 0, "function": [3, 4, 5], "fundament": 0, "g": 1, "gap": 4, "gener": [1, 4, 6], "geometri": 1, "gerber": 2, "get": [3, 5, 6, 12], "get_atom_index": [0, 1, 4, 5], "get_paramet": 5, "get_phi_scan": [1, 5], "get_scattering_factor": 2, "get_theta_phi_scan": [2, 4], "get_theta_scan": [0, 3], "give": 2, "given": [1, 5], "graphic": 3, "graze": 5, "great": 2, "greater": 4, "greatli": 0, "greber": 2, "group": 1, "grow": [4, 12], "gui": [0, 1], "h": 1, "h2o": 0, "ha": [4, 6], "half": 5, "hand": 2, "harmon": [0, 4], "have": [2, 6], "hbar": 5, "height": 2, "help": [4, 5], "hemispher": [0, 4], "hemispherical_clust": [0, 1, 4, 5], "here": [2, 3], "high": [2, 4, 6], "hilight": 5, "how": [1, 2, 3, 4, 5, 6, 12], "howev": 0, "http": 0, "i": [0, 1, 2, 3, 4, 5, 6], "i_": 5, "idea": [1, 5, 6], "identifi": 1, "ignor": 6, "illustr": [2, 6], "imax": 5, "imin": 5, "impact": 0, "import": [0, 1, 2, 3, 4, 5], "imposs": 6, "improv": 3, "incid": 5, "includ": [0, 2], "incom": 1, "increas": [2, 4, 5, 6], "incres": 5, "index": 0, "indic": 2, "inequival": [4, 12], "info": 5, "inform": [2, 5], "inner": 1, "inner_potenti": 1, "insid": 1, "int": 4, "intens": [0, 1, 2, 4, 5, 6], "intentis": 4, "interact": 0, "interfac": 0, "intern": 1, "interplai": 0, "interstitial_potenti": [1, 5], "introduc": 5, "invers": [0, 2, 4, 6], "io": 0, "iter": 3, "its": [2, 3], "itself": 4, "join": [], "k": 5, "k_b": 5, "keep": 3, "kind": [3, 4, 5], "kinet": [1, 2, 4, 6], "kinetic_energi": [1, 2, 3, 4, 5], "known": 4, "kuznetsov": 4, "l": 3, "l_": 4, "lambda_": 5, "larg": [1, 2, 4, 5, 12], "larger": 4, "last": [2, 3], "later": 2, "latter": 5, "lattic": [4, 6], "layer": [1, 5], "lead": [2, 6], "learn": 12, "least": 6, "leed": 0, "left": 4, "legend": [1, 5], "len": [2, 5], "length": [2, 3], "let": [1, 2, 4], "lett": 2, "level": [0, 1, 2, 3, 4, 5], "light": 1, "like": [0, 4], "line": [1, 2, 3, 4, 5], "linspac": [1, 5], "list": 2, "littl": 6, "ll": 2, "lmax": 4, "loadtxt": 1, "locat": 0, "long": 6, "longer": 6, "look": [1, 5], "loop": [2, 3], "loss": 5, "low": [1, 5], "lower": 5, "lure": 1, "m": [3, 4, 5, 6], "magnitud": 5, "mai": [1, 6], "mani": 6, "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], "max_c": 3, "maxima": 2, "maximum": 3, "mean": [4, 5], "mean_free_path": 5, "measur": 4, "memori": [0, 1, 2, 4, 6], "metal": 4, "method": 2, "metrial": 1, "mfp": 4, "middl": 0, "min": [1, 3, 5], "min_c": 3, "minim": 0, "minimum": 3, "miss": 1, "model": [1, 4, 5, 12], "modul": [0, 5], "molecul": [0, 2], "moment": 0, "more": [0, 4, 5], "most": [0, 1, 2, 6], "msd": 5, "msspec": [1, 2, 3, 4, 5], "mt_radiu": 3, "much": [0, 1, 4, 5], "muffin": 3, "muffintin_paramet": [1, 5], "multi": 4, "multipl": [0, 2, 5, 6, 12], "mutlipl": 3, "mx2": 4, "n": [3, 4, 6], "natoli": 0, "nd": [4, 6], "ndif": 4, "need": [1, 3, 4, 5, 6, 12], "nest": 3, "new": [0, 3], "ni": 3, "none": [2, 3, 4, 5], "normal": 1, "note": 6, "now": 1, "np": [1, 2, 3, 4, 5], "npath": [], "nplane": 5, "number": [0, 2, 4, 5], "numer": 2, "numpi": [1, 2, 3, 4, 5], "o": [2, 5], "object": [1, 5], "observ": 4, "off_cone_ev": 6, "offer": [6, 12], "one": [3, 5, 6], "ones": 5, "onli": [0, 2, 3, 6], "option": [3, 5, 6], "orang": 1, "order": [2, 3, 5, 6], "orient": [1, 2], "other": [0, 2], "our": [2, 5], "out": 6, "over": [2, 3, 5], "p": 6, "p1654": 2, "p1760": 4, "p6784": 5, "p6785": 5, "p6791": 5, "p8275": 3, "packag": 2, "paper": [1, 2, 3, 4, 5], "paragraph": 5, "paramet": [1, 4, 5, 6], "path": [2, 4, 5, 12], "pattern": 4, "peak": 4, "ped": [2, 3, 5], "perform": [5, 12], "phagen": 0, "phase": [0, 5], "phi": [1, 2, 4, 5], "photodiffract": 2, "photoelectron": [0, 1, 2, 4, 5, 6, 12], "phy": [1, 2, 3, 5], "physic": 5, "pi": 4, "planck": 5, "plane": [0, 1, 4, 5], "plot": [0, 3, 5], "plt": [0, 1], "pm": 2, "point": 1, "polar": [1, 2, 3, 5, 6], "pop": [2, 3], "popup": [1, 2], "posit": [2, 3], "possibl": [2, 6], "potenti": [1, 5], "practic": 5, "precis": 4, "preiou": 4, "pretti": 0, "previou": [0, 6], "previous": 2, "print": 4, "probe": 2, "problem": 2, "process": [0, 6], "produc": 2, "program": 0, "project": 2, "pronounc": 5, "propag": 0, "propos": [2, 5], "provid": 4, "publish": [2, 5], "put": 2, "pyplot": [0, 1], "python": [0, 5], "qualit": 5, "quantit": 2, "question": [3, 6], "quit": 2, "quiz": [0, 1, 2, 3, 4, 5, 6], "r": [0, 4, 5, 12], "r16061": 1, "radian": 3, "radiu": [3, 4, 12], "rai": [1, 5], "rang": [3, 4, 5], "rather": 2, "rd": 0, "read": 0, "real": 5, "realli": 0, "recent": 0, "red": 2, "reduc": [5, 6], "ref": 1, "refer": 1, "refract": 1, "regardless": 5, "regim": [6, 12], "rehr": [4, 6], "reject": 6, "rel": 5, "relat": 1, "rememb": 6, "remov": [0, 1, 3], "repres": [2, 5], "represent": 2, "reproduc": 5, "requir": 6, "respect": [1, 2, 3], "result": [0, 1, 2, 3, 5, 6], "retriev": 5, "return": 5, "rev": [1, 2, 3, 5], "rhodium": 2, "right": 4, "rotat": [1, 3, 4], "rotate_cel": [1, 4], "roughli": 5, "row": 4, "run": [0, 3], "sa73": 1, "same": [0, 3, 6], "sampl": [1, 4, 5], "satisfactori": [1, 2], "save": 0, "scale": 3, "scan": [2, 3, 4, 5, 6], "scatter": [0, 5, 12], "scattering_ord": [2, 3, 4, 5], "sci": 4, "script": [2, 3, 6], "se": 4, "second": [4, 5], "section": 5, "see": [1, 2, 5, 6], "seen": 6, "select": [1, 5, 6], "sensit": 2, "sequenti": 6, "seri": [4, 6], "serial": 6, "set": [0, 3, 5, 6, 12], "set_atom": [0, 2, 3, 4, 5], "set_plot_opt": [3, 5], "sever": 6, "shape": [1, 2, 5], "shift": [0, 5], "should": [1, 4], "show": 0, "shutdown": [1, 3, 5], "si": [], "signal": [0, 2, 5, 6], "signific": 1, "significantli": 6, "silver": 1, "sim": 5, "similar": 6, "simpl": [3, 5], "simplist": 2, "simul": [0, 2, 12], "sin": 5, "sinc": [0, 4, 5, 6, 12], "singl": [4, 5, 6, 12], "sinl": 2, "site": 2, "size": [1, 2, 4, 6], "small": [1, 2, 4, 5], "smaller": 1, "snipet": 4, "so": [2, 6], "softwar": 12, "some": [0, 1, 2, 3, 4, 5, 6], "soon": 2, "sourc": 1, "source_paramet": [1, 5], "spec": 0, "speci": 2, "specif": 1, "spectral": 12, "spectroscopi": [0, 1, 2, 3, 4, 5, 12], "spheric": [0, 4], "sqrt": 3, "squar": 5, "stack": 3, "start": [1, 2, 3, 4, 12], "step": [0, 1], "stereograph": 2, "store": [3, 4, 5], "straightforward": 0, "strongli": 4, "structur": [0, 4, 5], "studi": 2, "substitut": 1, "substrat": [5, 6, 12], "subsurfac": 6, "suit": 0, "sum": 5, "sum_": 6, "surf": 4, "surfac": [1, 2], "symbol": [1, 3], "synchrotron": 1, "s\u00e9billeau": 0, "t": [1, 2, 3, 5], "tag": 4, "take": [0, 1, 4, 6], "tb": 4, "td": [], "techniqu": [0, 12], "temp": 1, "temperatur": 12, "temporari": 3, "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], "theta_d": 5, "thi": [0, 1, 2, 3, 4, 5, 6], "thick": 4, "those": [0, 1], "threshold": 6, "through": 12, "ti": 4, "ti2p": 4, "time": [0, 4, 6], "timedelta": [], "tin": 3, "titl": [2, 3, 5], "tmatrix_paramet": 5, "togeth": 12, "too": [1, 2, 4, 6], "tool": 0, "top": [1, 2], "total": [0, 5, 6], "toward": 2, "transit": 4, "treat": 6, "trehan": 5, "trilay": 4, "true": [0, 1, 4, 5], "try": [1, 2, 4, 6], "tweak": 3, "two": [0, 1, 2, 5, 6], "txt": 1, "type": 4, "typic": [0, 4, 5], "u": 4, "u0000212b": [], "u_j": 5, "underli": 2, "unit": 4, "up": [0, 3, 6, 12], "updat": 5, "us": [0, 1, 2, 3, 4, 5, 6, 12], "use_debye_model": 5, "useful": 4, "usual": 4, "utf": 3, "util": [0, 1, 4, 5], "v": [3, 4], "vacuum": 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, "view": [0, 1, 2, 3, 4, 5], "visual": [0, 1, 2, 4], "volum": 4, "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], "when": [1, 5, 6], "where": [2, 3, 4, 5, 6], "which": [2, 6], "while": 3, "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, "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], "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, 1, 4, 6], "compar": 8, "comput": [1, 2], "converg": 10, "creat": 4, "cu": 0, "deep": 6, "developp": 11, "diffract": 9, "due": 2, "effect": [4, 5], "electron": 9, "emitt": 7, "exampl": 1, "experi": [1, 8], "factor": [2, 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, "larg": 6, "msspec": [0, 6, 11, 12], "multipl": [3, 4], "number": 6, "order": 4, "our": 11, "oxygen": 2, "path": 6, "ped": [0, 4], "plane": 6, "polar": 0, "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, "tise": 4, "tise2": 4, "tour": 12, "up": 1, "welcom": 12, "word": 11, "work": 11, "xpd": 7}})
\ No newline at end of file
+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: 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"]], "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"]], "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 number of scattering paths": [[6, "the-number-of-scattering-paths"]], "The script": [[5, "the-script"]], "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], "0": [0, 1, 2, 3, 4, 5, 6], "001": 5, "004": 4, "02": 2, "05": 2, "0f": 5, "1": [1, 2, 3, 4, 5, 6, 12], "10": [0, 1, 2, 12], "100": 5, "1000": [3, 5], "1000k": 5, "1010": [], "1030": 4, "11": 12, "111": 2, "11h": [], "121": 1, "14": 5, "147176": 6, "15": [1, 4], "170\u00b5": [], "171": [], "1986": 5, "1989": 3, "1998": 2, "1e": [], "1e12": 4, "2": [0, 2, 3, 5, 6, 12], "20": [1, 6], "2012": [4, 5], "2022": 6, "22": 1, "240": 1, "25": 4, "256": 6, "27": 5, "298k": 5, "2d": 4, "2f": 2, "2p": [0, 4, 5], "2p3": 0, "3": [0, 3, 4, 5, 6, 12], "30": 1, "300": 5, "31557600": [], "31902333327338293": [], "337": [], "34": 5, "343": 5, "3600": [], "39": 3, "3f": 4, "3rd": 0, "4": [0, 1, 2, 4, 5, 12], "40": [1, 6], "400": 5, "45": [1, 3, 5, 6], "450": 4, "499": 3, "4d": 1, "5": [1, 3, 5, 6, 12], "51": 5, "535": 4, "55": 1, "554": 4, "560": 5, "564": [], "5th": 3, "6": [1, 4, 6, 12], "60": 4, "606": 4, "64": 4, "65": 2, "685": 4, "6a_0": 6, "7": [5, 12], "70": 4, "723": 2, "739": 6, "8": [1, 2, 3, 4, 12], "80": 3, "81": 2, "83": 5, "86400": [], "9": [5, 12], "900": 4, "98": 5, "A": [2, 3, 5], "AED": 0, "ASE": [0, 1, 2, 4], "As": [0, 2, 4, 6], "But": 4, "By": 2, "For": [1, 4, 5, 6], "If": 6, "In": [0, 1, 2, 4, 5, 6], "It": [1, 4], "Not": 0, "On": 2, "One": 6, "Or": 0, "The": [0, 1, 2, 3, 4], "There": 0, "To": [0, 1, 2, 4, 5, 6], "With": 5, "_": [], "__main__": 5, "__name__": 5, "_plotopt": 5, "a_0": [4, 6], "abl": 6, "about": [2, 4], "abov": [0, 2, 4, 5, 6], "absolut": 3, "absorb": [3, 5], "accept": 6, "accordingli": 3, "account": [0, 4, 6], "accur": [2, 4], "accuraci": 2, "act": 1, "activ": 12, "actual": [3, 5], "ad": 2, "add": [1, 2, 5], "add_adsorb": 2, "add_column": [1, 5], "add_dset": 5, "add_view": 5, "adsorb": 12, "adsorpt": 2, "advantag": 2, "after": 4, "agit": 5, "agreement": 1, "al": [1, 2, 3, 4, 6], "al_kalpha": 5, "alber": [4, 6], "algorithm": [0, 2, 4, 5, 6], "align": [1, 4], "all": [0, 2, 3, 5, 6, 12], "all_data": 3, "all_t": 5, "all_theta": 5, "all_z": 2, "allow": [0, 6], "almost": [4, 6], "along": 3, "alreadi": 4, "also": [4, 5], "altern": 6, "although": 1, "altitud": 2, "an": [0, 2, 3, 4, 5, 6], "analysi": 5, "analyz": 0, "angl": [1, 5, 6], "angstrom": [2, 3], "angstr\u00f6m": 4, "angular_accept": [1, 5], "ani": 2, "anisotropi": 5, "anisotropy_dset": 5, "anisotropy_view": 5, "annular": 2, "anoth": 4, "answer": 3, "apart": 2, "apec": 0, "apertur": 6, "append": 5, "approach": [0, 4, 12], "approxim": [2, 4], "ar": [0, 1, 2, 4, 5, 6], "arang": [2, 3, 5], "arbitrarili": 5, "around": 4, "arrai": 5, "arrang": 6, "articl": 5, "ase": [0, 1, 2, 3, 4, 5], "assum": [1, 6], "atom": [1, 2, 3, 4, 5, 6], "atomist": 0, "attach": 2, "attempt": 5, "attribut": 1, "auger": 12, "autoscal": 5, "avail": [0, 4], "averag": 5, "average_sampl": [1, 5], "averaged_tl": 5, "axi": [3, 4], "azimut": 5, "azimuth": 5, "b": [1, 3, 5], "b_0": 4, "backascatt": [], "backscatt": 6, "backward_scatt": 6, "base": [0, 1, 2, 3, 4, 5, 6], "basi": 0, "beamlin": 1, "becaus": 6, "becom": [2, 6], "been": 6, "begin": 2, "being": [2, 5], "below": [2, 3, 4, 5, 6], "better": 1, "between": [0, 1, 2, 3, 4, 5], "bewteen": 3, "big": [], "bit": 4, "blue": 1, "boltzmann": 5, "bond": 2, "both": [2, 5], "bright": 2, "bring": 12, "build": [2, 3, 4, 5], "bulk": [0, 1, 6], "c": [4, 5], "c_0": 4, "calc": [0, 1, 2, 3, 4, 5], "calcul": [0, 1, 2, 3, 4, 5, 6], "calculation_paramet": [1, 2, 3, 4, 5], "calculationparamet": 5, "can": [0, 2, 3, 5, 6], "cannot": 4, "carri": 2, "case": 2, "categori": 1, "cell": [1, 4], "center": [2, 4], "chain": [2, 3], "chain_length": 3, "chang": [1, 2, 3, 5], "chosen": 5, "cif": 0, "circl": 2, "cite": 5, "class": 2, "clear": 5, "cluster": [2, 5, 12], "cnr": 0, "code": [0, 2, 3, 4], "col_nam": 5, "col_valu": 5, "column": 4, "com": 2, "come": [2, 5], "comment": 2, "common": [5, 6], "compar": [1, 6, 12], "comparison": [0, 1], "complet": [2, 4, 5, 6], "complex": 4, "compon": 0, "comput": [0, 3, 4, 5, 6], "computation": 2, "concept": [0, 12], "conclud": [0, 4], "cone": 6, "configur": [1, 6], "consid": 2, "constant": [3, 4, 5], "construct": 2, "consumpt": 2, "contain": [0, 1, 4, 5], "contribut": [0, 6], "control": 5, "converg": [1, 4, 12], "convers": [], "copper": [0, 4, 5], "correctli": 1, "correspond": [4, 6], "could": 6, "cover": 0, "creat": [0, 1, 2, 6], "create_clust": 5, "cross_sect": [1, 3, 5], "cruguel": 1, "crystallin": 2, "cu": 5, "cubic": [0, 1, 5], "custom": 3, "cut_plan": 1, "cylindr": 5, "d": [0, 2, 3, 4, 5], "dai": [], "damp": 5, "dark": 2, "data": [0, 1, 2, 3, 4, 5], "dataset": [1, 3, 5], "datetim": [], "deby": 5, "debye_temperatur": 5, "decreas": 5, "deep": [], "deeper": 4, "deepest": [0, 5], "def": 5, "default": 3, "defin": [1, 2, 3, 4, 5, 6], "degre": [2, 3, 5], "delta": 5, "demonstr": 2, "dens": 4, "depth": 5, "der": 4, "describ": 4, "detail": 5, "detector_paramet": [1, 5], "deviat": 4, "diamet": [1, 5, 6], "dichalcogenid": 4, "dict": 5, "differ": [0, 1, 2, 5, 6], "differnt": 3, "difficulti": 12, "diffract": [0, 1, 2, 4, 5, 12], "diffus": 3, "direct": [1, 2, 4, 6], "directli": 0, "disord": 5, "displac": 5, "displai": [0, 3], "distanc": [2, 3, 6], "distinguish": 5, "do": [0, 4, 5], "document": [2, 5], "doubl": 4, "drastic": 6, "dset": [1, 2, 3, 5], "due": 5, "e": 1, "e_0": 2, "each": [1, 3, 4, 5, 6], "eas": 1, "edit": 0, "effect": [1, 2, 6, 12], "either": 5, "eject": 2, "electron": [0, 2, 4, 6, 12], "element": 4, "els": 5, "emiss": [2, 5], "emit": 2, "emitt": [0, 1, 2, 4, 5, 6, 12], "emitter_plan": [0, 1, 4, 5], "emitter_tag": 4, "empti": 3, "end": 3, "energi": [1, 2, 4, 5, 6], "enlarg": 3, "enumer": 2, "environ": 0, "equal": 0, "equat": 5, "escap": 1, "estim": 5, "et": [1, 2, 3, 4, 6], "ev": [1, 2, 4, 5], "evalu": [4, 6], "event": 4, "exact": 2, "exaf": 0, "exampl": [5, 6], "exchange_correl": 5, "exp": 1, "expand": 4, "expans": [2, 4, 5, 6], "expect": [5, 6], "experi": 12, "experiment": [1, 2], "explain": 5, "explor": [4, 5, 6, 12], "extra": 5, "extrem": 2, "f": [4, 5], "factor": [4, 12], "fadlei": 5, "far": 6, "fast": 2, "fcc": [2, 4], "fcc111": 2, "featur": [0, 1, 12], "fewer": 0, "figur": [2, 3, 4, 5, 6], "file": [0, 1], "fill": 2, "filter": [5, 12], "final": [1, 12], "find": 3, "first": [2, 3, 4, 6], "fix": 6, "flexibl": 0, "float": 5, "focu": [0, 12], "folder": 3, "follow": [0, 1, 5, 6], "format": [2, 3, 5], "former": 1, "formula": [4, 6], "forthcom": 0, "fortran": 0, "forward": [6, 12], "forward_scatt": 6, "fr": 0, "frac": 5, "free": [4, 5], "fring": 2, "from": [0, 1, 2, 4, 5, 6, 12], "fromkei": 5, "fulli": 0, "function": [3, 4, 5], "fundament": 0, "g": 1, "gap": 4, "gener": [1, 4, 6], "geometri": 1, "gerber": 2, "get": [3, 5, 6, 12], "get_atom_index": [0, 1, 4, 5], "get_paramet": 5, "get_phi_scan": [1, 5], "get_scattering_factor": 2, "get_theta_phi_scan": [2, 4], "get_theta_scan": [0, 3], "give": 2, "given": [1, 5], "graphic": 3, "graze": 5, "great": 2, "greater": 4, "greatli": 0, "greber": 2, "group": 1, "grow": [4, 12], "gui": [0, 1], "h": 1, "h2o": 0, "ha": [4, 6], "half": 5, "hand": 2, "harmon": [0, 4], "have": [2, 6], "hbar": 5, "height": 2, "help": [4, 5], "hemispher": [0, 4], "hemispherical_clust": [0, 1, 4, 5], "here": [2, 3], "high": [2, 4, 6], "hilight": 5, "how": [1, 2, 3, 4, 5, 6, 12], "howev": 0, "http": 0, "i": [0, 1, 2, 3, 4, 5, 6], "i_": 5, "idea": [1, 5, 6], "identifi": 1, "ignor": 6, "illustr": [2, 6], "imax": 5, "imin": 5, "impact": 0, "import": [0, 1, 2, 3, 4, 5], "imposs": 6, "improv": 3, "incid": 5, "includ": [0, 2], "incom": 1, "increas": [2, 4, 5, 6], "incres": 5, "index": 0, "indic": 2, "inequival": [4, 12], "info": 5, "inform": [2, 5], "inner": 1, "inner_potenti": 1, "insid": 1, "int": 4, "intens": [0, 1, 2, 4, 5, 6], "intentis": 4, "interact": 0, "interfac": 0, "intern": 1, "interplai": 0, "interstitial_potenti": [1, 5], "introduc": 5, "invers": [0, 2, 4, 6], "io": 0, "iter": 3, "its": [2, 3], "itself": 4, "j": 6, "join": [], "k": 5, "k_b": 5, "keep": 3, "kind": [3, 4, 5], "kinet": [1, 2, 4, 6], "kinetic_energi": [1, 2, 3, 4, 5], "known": 4, "kuznetsov": 4, "l": 3, "l_": 4, "lambda_": 5, "larg": [1, 2, 4, 5, 12], "larger": 4, "last": [2, 3], "later": 2, "latter": 5, "lattic": [4, 6], "layer": [1, 5], "lead": [2, 6], "learn": 12, "least": 6, "leed": 0, "left": 4, "legend": [1, 5], "len": [2, 5], "length": [2, 3], "let": [1, 2, 4], "lett": 2, "level": [0, 1, 2, 3, 4, 5], "light": 1, "like": [0, 4], "line": [1, 2, 3, 4, 5], "linspac": [1, 5], "list": 2, "littl": 6, "ll": 2, "lmax": 4, "loadtxt": 1, "locat": 0, "long": 6, "longer": 6, "look": [1, 5], "loop": [2, 3], "loss": 5, "low": [1, 5], "lower": 5, "lure": 1, "m": [3, 4, 5, 6], "magnitud": 5, "mai": [1, 6], "mani": 6, "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], "max_c": 3, "maxima": 2, "maximum": 3, "mean": [4, 5], "mean_free_path": 5, "measur": 4, "memori": [0, 1, 2, 4, 6], "metal": 4, "method": 2, "metrial": 1, "mfp": 4, "middl": 0, "min": [1, 3, 5], "min_c": 3, "minim": 0, "minimum": 3, "miss": 1, "model": [1, 4, 5, 12], "modul": [0, 5], "molecul": [0, 2], "moment": 0, "more": [0, 4, 5], "most": [0, 1, 2, 6], "msd": 5, "msspec": [1, 2, 3, 4, 5], "mt_radiu": 3, "much": [0, 1, 4, 5], "muffin": 3, "muffintin_paramet": [1, 5], "multi": 4, "multipl": [0, 2, 5, 6, 12], "mutlipl": 3, "mx2": 4, "n": [3, 4, 6], "natoli": 0, "nd": [4, 6], "ndif": 4, "need": [1, 3, 4, 5, 6, 12], "nest": 3, "new": [0, 3], "ni": 3, "none": [2, 3, 4, 5], "normal": 1, "note": 6, "now": 1, "np": [1, 2, 3, 4, 5], "npath": [], "nplane": 5, "number": [0, 2, 4, 5], "numer": 2, "numpi": [1, 2, 3, 4, 5], "o": [2, 5], "object": [1, 5], "observ": 4, "off_cone_ev": 6, "offer": [6, 12], "one": [3, 5, 6], "ones": 5, "onli": [0, 2, 3, 6], "option": [3, 5, 6], "orang": 1, "order": [2, 3, 5, 6], "orient": [1, 2], "other": [0, 2], "our": [2, 5], "out": 6, "over": [2, 3, 5], "p": 6, "p1654": 2, "p1760": 4, "p6784": 5, "p6785": 5, "p6791": 5, "p8275": 3, "packag": 2, "paper": [1, 2, 3, 4, 5, 6], "paragraph": 5, "paramet": [1, 4, 5, 6], "path": [2, 4, 5, 12], "pattern": 4, "peak": 4, "ped": [2, 3, 5], "perform": [5, 12], "phagen": 0, "phase": [0, 5], "phenom": 6, "phi": [1, 2, 4, 5], "photodiffract": 2, "photoelectron": [0, 1, 2, 4, 5, 6, 12], "phy": [1, 2, 3, 5], "physic": 5, "pi": 4, "planck": 5, "plane": [0, 1, 4, 5], "plot": [0, 3, 5], "plt": [0, 1], "pm": 2, "point": 1, "polar": [1, 2, 3, 5, 6], "pop": [2, 3], "popup": [1, 2], "posit": [2, 3], "possibl": [2, 6], "potenti": [1, 5], "practic": 5, "precis": 4, "preiou": 4, "pretti": 0, "previou": [0, 6], "previous": 2, "print": 4, "probe": 2, "problem": 2, "process": [0, 6], "produc": 2, "program": 0, "project": 2, "pronounc": 5, "propag": 0, "propos": [2, 5], "provid": 4, "publish": [2, 5], "put": 2, "pyplot": [0, 1], "python": [0, 5], "qualit": 5, "quantit": 2, "question": [3, 6], "quit": 2, "quiz": [0, 1, 2, 3, 4, 5, 6], "r": [0, 4, 5, 12], "r16061": 1, "radian": 3, "radiu": [3, 4, 12], "rai": [1, 5], "rang": [3, 4, 5], "rather": 2, "rd": 0, "read": 0, "real": 5, "realli": 0, "recent": 0, "red": 2, "reduc": [5, 6], "ref": 1, "refer": 1, "refract": 1, "regardless": 5, "regim": [6, 12], "rehr": [4, 6], "reject": 6, "rel": 5, "relat": [1, 6], "rememb": 6, "remov": [0, 1, 3], "repres": [2, 5], "represent": 2, "reproduc": 5, "requir": 6, "respect": [1, 2, 3], "result": [0, 1, 2, 3, 5, 6], "retriev": 5, "return": 5, "rev": [1, 2, 3, 5], "rhodium": 2, "right": 4, "rotat": [1, 3, 4], "rotate_cel": [1, 4], "roughli": 5, "row": 4, "run": [0, 3], "sa73": 1, "same": [0, 3, 6], "sampl": [1, 4, 5], "satisfactori": [1, 2], "save": 0, "scale": 3, "scan": [2, 3, 4, 5, 6], "scatter": [0, 5, 12], "scattering_ord": [2, 3, 4, 5], "sci": 4, "script": [2, 3, 6], "se": 4, "second": [4, 5], "section": 5, "see": [1, 2, 5, 6], "seen": 6, "select": [1, 5, 6], "sensit": 2, "sequenti": 6, "seri": [4, 6], "serial": 6, "set": [0, 3, 5, 6, 12], "set_atom": [0, 2, 3, 4, 5], "set_plot_opt": [3, 5], "sever": 6, "shape": [1, 2, 5], "shift": [0, 5], "should": [1, 4], "show": 0, "shutdown": [1, 3, 5], "si": [], "signal": [0, 2, 5, 6], "signific": 1, "significantli": 6, "silver": 1, "sim": 5, "similar": 6, "simpl": [3, 5], "simplist": 2, "simul": [0, 2, 12], "sin": 5, "sinc": [0, 4, 5, 6, 12], "singl": [4, 5, 6, 12], "sinl": 2, "site": 2, "size": [1, 2, 4, 6], "small": [1, 2, 4, 5], "smaller": 1, "snipet": 4, "so": [2, 6], "softwar": 12, "some": [0, 1, 2, 3, 4, 5, 6], "soon": 2, "sourc": 1, "source_paramet": [1, 5], "spec": 0, "speci": 2, "specif": 1, "spectral": 12, "spectrosc": 6, "spectroscopi": [0, 1, 2, 3, 4, 5, 12], "spheric": [0, 4], "sqrt": 3, "squar": 5, "stack": 3, "start": [1, 2, 3, 4, 12], "step": [0, 1], "stereograph": 2, "store": [3, 4, 5], "straightforward": 0, "strongli": 4, "structur": [0, 4, 5], "studi": 2, "substitut": 1, "substrat": [5, 6, 12], "subsurfac": 6, "suit": 0, "sum": 5, "sum_": 6, "surf": 4, "surfac": [1, 2], "symbol": [1, 3], "synchrotron": 1, "s\u00e9billeau": 0, "t": [1, 2, 3, 5], "tag": 4, "take": [0, 1, 4, 6], "tb": 4, "td": [], "techniqu": [0, 12], "temp": 1, "temperatur": 12, "temporari": 3, "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], "theta_d": 5, "thi": [0, 1, 2, 3, 4, 5, 6], "thick": 4, "those": [0, 1], "threshold": 6, "through": 12, "ti": 4, "ti2p": 4, "time": [0, 4, 6], "timedelta": [], "tin": 3, "titl": [2, 3, 5], "tmatrix_paramet": 5, "togeth": 12, "too": [1, 2, 4, 6], "tool": 0, "top": [1, 2], "total": [0, 5, 6], "toward": 2, "transit": 4, "treat": 6, "trehan": 5, "tricot": 6, "trilay": 4, "true": [0, 1, 4, 5], "try": [1, 2, 4, 6], "tweak": 3, "two": [0, 1, 2, 5, 6], "txt": 1, "type": 4, "typic": [0, 4, 5], "u": 4, "u0000212b": [], "u_j": 5, "underli": 2, "unit": 4, "up": [0, 3, 6, 12], "updat": 5, "us": [0, 1, 2, 3, 4, 5, 6, 12], "use_debye_model": 5, "useful": 4, "usual": 4, "utf": 3, "util": [0, 1, 4, 5], "v": [3, 4], "vacuum": 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, "view": [0, 1, 2, 3, 4, 5], "visual": [0, 1, 2, 4], "volum": 4, "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], "when": [1, 5, 6], "where": [2, 3, 4, 5, 6], "which": [2, 6], "while": 3, "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, "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], "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, 1, 4, 6], "compar": 8, "comput": [1, 2], "converg": 10, "creat": 4, "cu": 0, "deep": 6, "developp": 11, "diffract": 9, "due": 2, "effect": [4, 5], "electron": 9, "emitt": 7, "exampl": 1, "experi": [1, 8], "factor": [2, 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, "larg": 6, "msspec": [0, 6, 11, 12], "multipl": [3, 4], "number": 6, "order": 4, "our": 11, "oxygen": 2, "path": 6, "ped": [0, 4], "plane": 6, "polar": 0, "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, "tise": 4, "tise2": 4, "tour": 12, "up": 1, "welcom": 12, "word": 11, "work": 11, "xpd": 7}})
\ No newline at end of file
diff --git a/msspecbook/_build/jupyter_execute/Activity07/Activity07.ipynb b/msspecbook/_build/jupyter_execute/Activity07/Activity07.ipynb
index 5f7137e..c80e6c1 100644
--- a/msspecbook/_build/jupyter_execute/Activity07/Activity07.ipynb
+++ b/msspecbook/_build/jupyter_execute/Activity07/Activity07.ipynb
@@ -115,6 +115,13 @@
     "\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",
     "\n",
+    "(msd-paper)=\n",
+    ":::{seealso}\n",
+    "based on this paper from S. Tricot *et al.*\n",
+    "[J. Electron. Spectrosc. Relat. Phenom. **256** 147176 (2022)](https://doi.org/10.1016/j.elspec.2022.147176)\n",
+    ":::\n",
+    "\n",
+    "\n",
     "::::{tab-set}\n",
     "\n",
     ":::{tab-item} <i class=\"fa-solid fa-circle-question\"></i> Quiz\n",