From cea734908d1de27e9f16bd87a8f86936698b06de Mon Sep 17 00:00:00 2001 From: Mauro Rovezzi Date: Mon, 25 Sep 2023 09:48:35 +0200 Subject: [PATCH] fix experimental data --- examples/Jupyter/struct2xas_examples.ipynb | 924 ++++++++------------- examples/fdmnes/ZnO_SSHADE.data.txt | 870 +++++-------------- 2 files changed, 559 insertions(+), 1235 deletions(-) mode change 100755 => 100644 examples/fdmnes/ZnO_SSHADE.data.txt diff --git a/examples/Jupyter/struct2xas_examples.ipynb b/examples/Jupyter/struct2xas_examples.ipynb index 30dd770c8..9e47613f9 100755 --- a/examples/Jupyter/struct2xas_examples.ipynb +++ b/examples/Jupyter/struct2xas_examples.ipynb @@ -83,33 +83,33 @@ "text/html": [ "\n", - "\n", + "
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idx_absspeciefrac_coordswyckoff_sitecart_coordsoccupancyidx_in_structidx_absspeciefrac_coordswyckoff_sitecart_coordsoccupancyidx_in_struct
0Zn[0.3333, 0.6667, 0.4995]2b[-1.6446 0.9495 -2.6505]100Zn[0.3333, 0.6667, 0.4995]2b[-1.6446 0.9495 -2.6505]10
\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 3, @@ -285,25 +285,25 @@ "text/plain": [ "[['Coord. Env. for Site 0',\n", " [{'ce_symbol': 'T:4',\n", - " 'ce_fraction': 0.859684856109345,\n", - " 'csm': 0.005691442451729411,\n", + " 'ce_fraction': 0.8596848561093448,\n", + " 'csm': 0.005691442451729833,\n", " 'permutation': [0, 1, 2, 3]},\n", " {'ce_symbol': 'T:5',\n", - " 'ce_fraction': 0.14031514389065505,\n", - " 'csm': 4.062381866591052,\n", - " 'permutation': [1, 2, 3, 0, 4]}],\n", - " [{'site': PeriodicSite: O (-0.0000, 1.8990, -3.2915) [-0.3333, 0.3333, 0.6202],\n", - " 'index': 3,\n", - " 'image_cell': array([-1, 0, 0])},\n", - " {'site': PeriodicSite: O (-3.2891, 1.8990, -3.2915) [0.6667, 1.3333, 0.6202],\n", + " 'ce_fraction': 0.14031514389065516,\n", + " 'csm': 4.062381866591051,\n", + " 'permutation': [0, 2, 4, 1, 3]}],\n", + " [{'site': PeriodicSite: O (-3.2891, 1.8990, -3.2915) [0.6667, 1.3333, 0.6202],\n", " 'index': 3,\n", " 'image_cell': array([0, 1, 0])},\n", - " {'site': PeriodicSite: O (-1.6446, -0.9495, -3.2915) [0.6667, 0.3333, 0.6202],\n", + " {'site': PeriodicSite: O (-0.0000, 1.8990, -3.2915) [-0.3333, 0.3333, 0.6202],\n", " 'index': 3,\n", - " 'image_cell': array([0, 0, 0])},\n", + " 'image_cell': array([-1, 0, 0])},\n", " {'site': PeriodicSite: O (-1.6446, 0.9495, -0.6381) [0.3333, 0.6667, 0.1202],\n", " 'index': 2,\n", " 'image_cell': array([0, 0, 0])},\n", + " {'site': PeriodicSite: O (-1.6446, -0.9495, -3.2915) [0.6667, 0.3333, 0.6202],\n", + " 'index': 3,\n", + " 'image_cell': array([0, 0, 0])},\n", " {'site': PeriodicSite: O (-1.6446, 0.9495, -5.9449) [0.3333, 0.6667, 1.1202],\n", " 'index': 2,\n", " 'image_cell': array([0, 0, 1])}]]]" @@ -333,10 +333,10 @@ "outputs": [ { "data": { - "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", "text/html": [ - "
\n", - "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + "

\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", " jupyter labextension install jupyterlab_3dmol

\n", "
\n", "" ] @@ -418,7 +418,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "[struct2xas] INFO : written FDMNES input -> /tmp/struct2xas-0q_sltgn/fdmnes/ZnO_mp-2133/Zn/frame0/site0/job_inp.txt\n" + "[struct2xas] INFO : written FDMNES input -> /tmp/struct2xas-aqrdji6p/fdmnes/ZnO_mp-2133/Zn/frame0/site0/job_inp.txt\n" ] } ], @@ -451,7 +451,7 @@ "\n", "comment\n", "cif file name: ZnO_mp-2133\n", - "creation date:2023-09-25_0711\n", + "creation date:2023-09-25_0944\n", "\n", "filout\n", "\n", @@ -543,7 +543,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "[struct2xas] INFO : written FEFF input -> /tmp/struct2xas-0q_sltgn/feff/ZnO_mp-2133/Zn/frame0/site0/feff.inp\n" + "[struct2xas] INFO : written FEFF input -> /tmp/struct2xas-aqrdji6p/feff/ZnO_mp-2133/Zn/frame0/site0/feff.inp\n" ] } ], @@ -573,7 +573,7 @@ "* FEFF8* input file generated by Struct2XAS\n", "\n", "TITLE ZnO_mp-2133\n", - "TITLE 2023-09-25_0711\n", + "TITLE 2023-09-25_0944\n", "TITLE site 0\n", "\n", "* edge energy = eV\n", @@ -766,14 +766,20 @@ " : ======== running Feff module feff8l_rdinp ========\n", " : Feff8L (EXAFS) release 0.1\n", " : ZnO_mp-2133\n", - " : 2023-09-25_0711\n", + " : 2023-09-25_0944\n", " : site 0\n", " : ======== running Feff module feff8l_pot ========\n", " : Calculating potentials ...\n", " : free atom potential and density for atom type 0\n", " : free atom potential and density for atom type 1\n", " : free atom potential and density for atom type 2\n", - " : initial state energy\n", + " : initial state energy\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ " : overlapped potential and density for unique potential 0\n", " : overlapped potential and density for unique potential 1\n", " : overlapped potential and density for unique potential 2\n", @@ -1080,7 +1086,7 @@ }, "name": "FEFF simulation", "type": "scatter", - "uid": "071e2a92-0c5f-441e-94ff-86bfcd7aab06", + "uid": "e7bc6afe-5d27-481d-b524-8635e5b9a6ef", "x": [ 0.35, 0.4, @@ -1893,7 +1899,7 @@ }, "name": "EXP data", "type": "scatter", - "uid": "0b95f165-b7d4-473a-88c9-457a64acf938", + "uid": "7f480543-a721-4fb9-8b5f-a58a3bdf27e1", "x": [ 0, 0.05, @@ -2053,408 +2059,168 @@ 7.75, 7.800000000000001, 7.8500000000000005, - 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You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", "text/html": [ - "
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You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + "

\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", " jupyter labextension install jupyterlab_3dmol

\n", "
\n", "" ] @@ -3584,16 +3350,16 @@ "name": "stdout", "output_type": "stream", "text": [ - "[struct2xas] INFO : written FDMNES input -> /tmp/struct2xas-zik6wzf8/fdmnes/ZnO_mp-997630/Zn/frame0/site0/job_inp.txt\n", - "[struct2xas] INFO : written FDMNES input -> /tmp/struct2xas-zik6wzf8/fdmnes/ZnO_mp-997630/Zn/frame0/site1/job_inp.txt\n", - "[struct2xas] INFO : written FDMNES input -> /tmp/struct2xas-zik6wzf8/fdmnes/ZnO_mp-997630/Zn/frame0/site2/job_inp.txt\n" + "[struct2xas] INFO : written FDMNES input -> /tmp/struct2xas-oamuaaql/fdmnes/ZnO_mp-997630/Zn/frame0/site0/job_inp.txt\n", + "[struct2xas] INFO : written FDMNES input -> /tmp/struct2xas-oamuaaql/fdmnes/ZnO_mp-997630/Zn/frame0/site1/job_inp.txt\n", + "[struct2xas] INFO : written FDMNES input -> /tmp/struct2xas-oamuaaql/fdmnes/ZnO_mp-997630/Zn/frame0/site2/job_inp.txt\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "[struct2xas] INFO : written FDMNES input -> /tmp/struct2xas-zik6wzf8/fdmnes/ZnO_mp-997630/Zn/frame0/site3/job_inp.txt\n" + "[struct2xas] INFO : written FDMNES input -> /tmp/struct2xas-oamuaaql/fdmnes/ZnO_mp-997630/Zn/frame0/site3/job_inp.txt\n" ] } ], @@ -3621,16 +3387,16 @@ "name": "stdout", "output_type": "stream", "text": [ - "[struct2xas] INFO : written FEFF input -> /tmp/struct2xas-zik6wzf8/feff/ZnO_mp-997630/Zn/frame0/site0/feff.inp\n", - "[struct2xas] INFO : written FEFF input -> /tmp/struct2xas-zik6wzf8/feff/ZnO_mp-997630/Zn/frame0/site1/feff.inp\n" + "[struct2xas] INFO : written FEFF input -> /tmp/struct2xas-oamuaaql/feff/ZnO_mp-997630/Zn/frame0/site0/feff.inp\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "[struct2xas] INFO : written FEFF input -> /tmp/struct2xas-zik6wzf8/feff/ZnO_mp-997630/Zn/frame0/site2/feff.inp\n", - "[struct2xas] INFO : written FEFF input -> /tmp/struct2xas-zik6wzf8/feff/ZnO_mp-997630/Zn/frame0/site3/feff.inp\n" + "[struct2xas] INFO : written FEFF input -> /tmp/struct2xas-oamuaaql/feff/ZnO_mp-997630/Zn/frame0/site1/feff.inp\n", + "[struct2xas] INFO : written FEFF input -> /tmp/struct2xas-oamuaaql/feff/ZnO_mp-997630/Zn/frame0/site2/feff.inp\n", + "[struct2xas] INFO : written FEFF input -> /tmp/struct2xas-oamuaaql/feff/ZnO_mp-997630/Zn/frame0/site3/feff.inp\n" ] } ], @@ -3848,7 +3614,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 22, "metadata": {}, "outputs": [ { @@ -3873,15 +3639,15 @@ }, { "cell_type": "code", - "execution_count": 84, + "execution_count": 23, "metadata": {}, "outputs": [ { "data": { - "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", "text/html": [ - "
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You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + "

\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", " jupyter labextension install jupyterlab_3dmol

\n", "
\n", "" ] @@ -3950,7 +3716,7 @@ }, { "cell_type": "code", - "execution_count": 85, + "execution_count": 24, "metadata": {}, "outputs": [ { @@ -3958,23 +3724,56 @@ "output_type": "stream", "text": [ "Coord. Env. from absorber atom: Ga at site 0\n", - "(For more details use get_coord_envs() method) \n" + "Elements Dict = {'H': 2}\n" ] }, { "data": { + "text/html": [ + "
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"[struct2xas] INFO : written FEFF input -> /tmp/gabr-io7plr_g/feff/GaBr_multi-frame/Ga/frame4/site0/feff.inp\n" + "[struct2xas] INFO : written FEFF input -> /tmp/gabr-8akk2mjz/feff/GaBr_multi-frame/Ga/frame0/site0/feff.inp\n", + "[struct2xas] INFO : written FEFF input -> /tmp/gabr-8akk2mjz/feff/GaBr_multi-frame/Ga/frame1/site0/feff.inp\n", + "[struct2xas] INFO : written FEFF input -> /tmp/gabr-8akk2mjz/feff/GaBr_multi-frame/Ga/frame2/site0/feff.inp\n", + "[struct2xas] INFO : written FEFF input -> /tmp/gabr-8akk2mjz/feff/GaBr_multi-frame/Ga/frame3/site0/feff.inp\n", + "[struct2xas] INFO : written FEFF input -> /tmp/gabr-8akk2mjz/feff/GaBr_multi-frame/Ga/frame4/site0/feff.inp\n" ] } ], @@ -4025,7 +3824,7 @@ }, { "cell_type": "code", - "execution_count": 74, + "execution_count": 26, "metadata": {}, "outputs": [ { @@ -4034,8 +3833,14 @@ "text": [ " : ======== running Feff module feff8l_rdinp ========\n", " : Feff8L (EXAFS) release 0.1\n", - " : GaBr_multi-frame\n", - " : 2023-08-03_1703\n", + " : GaBr_multi-frame\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " : 2023-09-25_0945\n", " : site 0\n", " : ======== running Feff module feff8l_pot ========\n", " : Calculating potentials ...\n", @@ -4128,7 +3933,7 @@ " : ======== running Feff module feff8l_rdinp ========\n", " : Feff8L (EXAFS) release 0.1\n", " : GaBr_multi-frame\n", - " : 2023-08-03_1703\n", + " : 2023-09-25_0945\n", " : site 0\n", " : ======== running Feff module feff8l_pot ========\n", " : Calculating potentials ...\n", @@ -4224,7 +4029,7 @@ " : ======== running Feff module feff8l_rdinp ========\n", " : Feff8L (EXAFS) release 0.1\n", " : GaBr_multi-frame\n", - " : 2023-08-03_1703\n", + " : 2023-09-25_0945\n", " : site 0\n", " : ======== running Feff module feff8l_pot ========\n", " : Calculating potentials ...\n", @@ -4322,7 +4127,7 @@ " : ======== running Feff module feff8l_rdinp ========\n", " : Feff8L (EXAFS) release 0.1\n", " : GaBr_multi-frame\n", - " : 2023-08-03_1703\n", + " : 2023-09-25_0945\n", " : site 0\n", " : ======== running Feff module feff8l_pot ========\n", " : Calculating potentials ...\n", @@ -4418,7 +4223,7 @@ " : ======== running Feff module feff8l_rdinp ========\n", " : Feff8L (EXAFS) release 0.1\n", " : GaBr_multi-frame\n", - " : 2023-08-03_1703\n", + " : 2023-09-25_0945\n", " : site 0\n", " : ======== running Feff module feff8l_pot ========\n", " : Calculating potentials ...\n", @@ -4536,14 +4341,14 @@ }, { "cell_type": "code", - "execution_count": 62, + "execution_count": 27, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "xmu data exported to HDF5: /tmp/gabr-faqmx65_/hdf5/gabr_exafs.h5\n" + "xmu data exported to HDF5: /tmp/gabr-8akk2mjz/hdf5/gabr_exafs.h5\n" ] } ], @@ -4583,7 +4388,7 @@ }, { "cell_type": "code", - "execution_count": 75, + "execution_count": 29, "metadata": {}, "outputs": [ { @@ -4600,7 +4405,7 @@ }, "name": "GaBr_multi-frame/frame4", "type": "scatter", - "uid": "8f9919a6-d749-4cc9-8460-dea0246b58bc", + "uid": "692ca5b6-41ec-499d-90c0-c75f6f8f7045", "x": [ 0.05, 0.1, @@ -5413,7 +5218,7 @@ }, "name": "GaBr_multi-frame/frame2", "type": "scatter", - "uid": "dbc84dff-5a57-40f5-bac4-b134c96eb57b", + "uid": "7193e0c1-7c14-4b63-bcb0-1d6370aae0a3", "x": [ 0.05, 0.1, @@ -6226,7 +6031,7 @@ }, "name": "GaBr_multi-frame/frame0", "type": "scatter", - "uid": "7f1f71a7-57cb-4b4d-ad1b-96bdb9dbaa0d", + "uid": "4f9000ea-4cd7-4779-ab08-f4cca7db54a3", "x": [ 0.05, 0.1, @@ -7039,7 +6844,7 @@ }, "name": "GaBr_multi-frame/frame3", "type": "scatter", - "uid": "8d4c9051-a24d-4f3b-8d71-33ecfe7392e2", + "uid": "e2ffa7c5-51d5-46ae-bbfa-fb18b0716e04", "x": [ 0.05, 0.1, @@ -7852,7 +7657,7 @@ }, "name": "GaBr_multi-frame/frame1", "type": "scatter", - "uid": "4138fed4-0681-4413-81b1-b93134048e72", + "uid": "bcd61859-39ee-4a60-a881-62237ab41e42", "x": [ 0, 0.05, @@ -8667,7 +8472,7 @@ }, "name": "exp data", "type": "scatter", - "uid": "fffeaa45-770a-4bdc-9ebd-79ed05c985e3", + "uid": "4fc4baa9-401a-456e-a80d-fc7489baddfb", "x": [ 0, 0.05, @@ -10164,9 +9969,9 @@ } }, "text/html": [ - "