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romerogroup · Jan 12, 2025 · 41c38af · 41c38af
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diff --git a/docs/.buildinfo b/docs/.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: 2bf8b6c249800b9e5576fdf60f2d3208
+config: 047c98e64e80ccba5a217592924f64ec
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_downloads/08a8c7a6ee0fbe29036613b0ba9f7c51/plot_subsitution_pyposcar.zip b/docs/_downloads/08a8c7a6ee0fbe29036613b0ba9f7c51/plot_subsitution_pyposcar.zip
diff --git a/docs/_downloads/0b72843559a0e5323f24e00c93009819/plot_fermi3d_plain.ipynb b/docs/_downloads/0b72843559a0e5323f24e00c93009819/plot_fermi3d_plain.ipynb
@@ -100,7 +100,7 @@
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       "pygments_lexer": "ipython3",
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diff --git a/docs/_downloads/0efb556a3850f930418f858c97e197e3/plot_2d_bands.zip b/docs/_downloads/0efb556a3850f930418f858c97e197e3/plot_2d_bands.zip
diff --git a/docs/_downloads/108db922454e1f15c7e1561bfc36c9de/plot_colinear.ipynb b/docs/_downloads/108db922454e1f15c7e1561bfc36c9de/plot_colinear.ipynb
@@ -186,7 +186,7 @@
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diff --git a/docs/_downloads/118695b22cb342905260e71e7c4f819c/plot_noncolinear_dos_qe.ipynb b/docs/_downloads/118695b22cb342905260e71e7c4f819c/plot_noncolinear_dos_qe.ipynb
@@ -60,7 +60,7 @@
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diff --git a/docs/_downloads/125ddf5661961df70befabc5dc6cf39e/plot_fermi3d_cross_section.zip b/docs/_downloads/125ddf5661961df70befabc5dc6cf39e/plot_fermi3d_cross_section.zip
diff --git a/docs/_downloads/1d7bddaa2f20c6f6d31ec8edb52ba8e9/plot_kpath_generation.ipynb b/docs/_downloads/1d7bddaa2f20c6f6d31ec8edb52ba8e9/plot_kpath_generation.ipynb
@@ -71,7 +71,7 @@
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diff --git a/docs/_downloads/1dee1a739fe9f2d431f3a2a69b9efbea/plot_fermi3d_configurations.ipynb b/docs/_downloads/1dee1a739fe9f2d431f3a2a69b9efbea/plot_fermi3d_configurations.ipynb
@@ -57,7 +57,7 @@
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diff --git a/docs/_downloads/1eece99f8b23cdc98ef72380a2df4e50/plot_colinear_dos.ipynb b/docs/_downloads/1eece99f8b23cdc98ef72380a2df4e50/plot_colinear_dos.ipynb
@@ -204,7 +204,7 @@
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diff --git a/docs/_downloads/1efe8c4aa8431c5249fe9e1cacb09796/plot_bandsplot_configurations.ipynb b/docs/_downloads/1efe8c4aa8431c5249fe9e1cacb09796/plot_bandsplot_configurations.ipynb
@@ -79,7 +79,7 @@
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diff --git a/docs/_downloads/232c0bb63fb36b84099e0072c62587ff/plot_compare_bands.zip b/docs/_downloads/232c0bb63fb36b84099e0072c62587ff/plot_compare_bands.zip
diff --git a/docs/_downloads/2340e2f1bb297fb16b73c1eabca11c06/plot_bandsdosplot_configurations.zip b/docs/_downloads/2340e2f1bb297fb16b73c1eabca11c06/plot_bandsdosplot_configurations.zip
diff --git a/docs/_downloads/2361b4e1061930157c218e64a85f2d6d/plot_fermi3d_plain.zip b/docs/_downloads/2361b4e1061930157c218e64a85f2d6d/plot_fermi3d_plain.zip
diff --git a/docs/_downloads/294e564dcdaead9f260037a1f92a49cb/plot_colinear.zip b/docs/_downloads/294e564dcdaead9f260037a1f92a49cb/plot_colinear.zip
diff --git a/docs/_downloads/2ccce647e0ac59b9f555853f69095794/plot_unfolding.ipynb b/docs/_downloads/2ccce647e0ac59b9f555853f69095794/plot_unfolding.ipynb
@@ -78,7 +78,7 @@
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diff --git a/docs/_downloads/3199d9cf1b4a404903cfdfdd5d748571/plot_atomic_levels.ipynb b/docs/_downloads/3199d9cf1b4a404903cfdfdd5d748571/plot_atomic_levels.ipynb
@@ -60,7 +60,7 @@
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       "pygments_lexer": "ipython3",
-      "version": "3.8.0"
+      "version": "3.9.20"
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diff --git a/docs/_downloads/33c7196b83349016135848f270f44935/plot_bandsplot_configurations.zip b/docs/_downloads/33c7196b83349016135848f270f44935/plot_bandsplot_configurations.zip
diff --git a/docs/_downloads/36ac06b70334644e00a88e872a435e53/plot_fermi3d_spin-polarized.ipynb b/docs/_downloads/36ac06b70334644e00a88e872a435e53/plot_fermi3d_spin-polarized.ipynb
@@ -100,7 +100,7 @@
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       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.0"
+      "version": "3.9.20"
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diff --git a/docs/_downloads/3a34777fc720c39085494138831a04fa/plot_spin_polarized_dos.ipynb b/docs/_downloads/3a34777fc720c39085494138831a04fa/plot_spin_polarized_dos.ipynb
@@ -222,7 +222,7 @@
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       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.0"
+      "version": "3.9.20"
     }
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diff --git a/docs/_downloads/3a75f21d33e21871a892b51e09bfa892/plot_atomic_levels.zip b/docs/_downloads/3a75f21d33e21871a892b51e09bfa892/plot_atomic_levels.zip
diff --git a/docs/_downloads/3b7521f82ed503140f6ba66d69ec9d0a/plot_autobands.ipynb b/docs/_downloads/3b7521f82ed503140f6ba66d69ec9d0a/plot_autobands.ipynb
@@ -60,7 +60,7 @@
       "name": "python",
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       "pygments_lexer": "ipython3",
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+      "version": "3.9.20"
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diff --git a/docs/_downloads/3e9c7fa427fc36cf83eaeaed4dd526ef/plot_rdf_cutoff_pyposcar.zip b/docs/_downloads/3e9c7fa427fc36cf83eaeaed4dd526ef/plot_rdf_cutoff_pyposcar.zip
diff --git a/docs/_downloads/458d1f0647d99fcac120ceb3cbf2dacc/plot_bandgap.ipynb b/docs/_downloads/458d1f0647d99fcac120ceb3cbf2dacc/plot_bandgap.ipynb
@@ -53,7 +53,7 @@
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-      "version": "3.8.0"
+      "version": "3.9.20"
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diff --git a/docs/_downloads/498b7e12b5246f70935a30cb0236fa20/plot_rashba_spin_spliting.ipynb b/docs/_downloads/498b7e12b5246f70935a30cb0236fa20/plot_rashba_spin_spliting.ipynb
@@ -186,7 +186,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.0"
+      "version": "3.9.20"
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diff --git a/docs/_downloads/4c08dffeb77ab9b4e56b218d9d90e26b/plot_colinear_dos.zip b/docs/_downloads/4c08dffeb77ab9b4e56b218d9d90e26b/plot_colinear_dos.zip
diff --git a/docs/_downloads/4df4aea1a6f82010ff5f16d9d88e8610/plot_compare_bands.ipynb b/docs/_downloads/4df4aea1a6f82010ff5f16d9d88e8610/plot_compare_bands.ipynb
@@ -60,7 +60,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.0"
+      "version": "3.9.20"
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diff --git a/docs/_downloads/57075226b5867cf0b886d23565a447ab/plot_fermi2d_configurations.zip b/docs/_downloads/57075226b5867cf0b886d23565a447ab/plot_fermi2d_configurations.zip
diff --git a/docs/_downloads/57e6799781d7f427ad1cc2a8e9087bdf/plot_fermi3d_spin_texture.zip b/docs/_downloads/57e6799781d7f427ad1cc2a8e9087bdf/plot_fermi3d_spin_texture.zip
diff --git a/docs/_downloads/596210a8656d0349621199ea5ab59d0e/plot_dosplot_configurations.ipynb b/docs/_downloads/596210a8656d0349621199ea5ab59d0e/plot_dosplot_configurations.ipynb
@@ -68,7 +68,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.0"
+      "version": "3.9.20"
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diff --git a/docs/_downloads/5db0ea33b40512b7b9dc4be5f07909d8/plot_finding_defects_pyposcar.zip b/docs/_downloads/5db0ea33b40512b7b9dc4be5f07909d8/plot_finding_defects_pyposcar.zip
diff --git a/docs/_downloads/5f26677de6f34020da8d425b0fc9f564/plot_unfolding.zip b/docs/_downloads/5f26677de6f34020da8d425b0fc9f564/plot_unfolding.zip
diff --git a/docs/_downloads/623c13043defbaebb32ed4a792b7cde2/plot_noncolinear_vasp.zip b/docs/_downloads/623c13043defbaebb32ed4a792b7cde2/plot_noncolinear_vasp.zip
diff --git a/docs/_downloads/632225c37dff473638cb222867ee9a93/plot_finding_defects_pyposcar.ipynb b/docs/_downloads/632225c37dff473638cb222867ee9a93/plot_finding_defects_pyposcar.ipynb
@@ -71,7 +71,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.0"
+      "version": "3.9.20"
     }
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diff --git a/docs/_downloads/6f007bae86be3db34e6881409cd42249/plot_fermi3d_spin_texture.ipynb b/docs/_downloads/6f007bae86be3db34e6881409cd42249/plot_fermi3d_spin_texture.ipynb
@@ -82,7 +82,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.0"
+      "version": "3.9.20"
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diff --git a/docs/_downloads/74de0d0d5c3ecce985974c96c391ad6a/plot_noncolinear_qe.ipynb b/docs/_downloads/74de0d0d5c3ecce985974c96c391ad6a/plot_noncolinear_qe.ipynb
@@ -89,7 +89,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.0"
+      "version": "3.9.20"
     }
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diff --git a/docs/_downloads/7d5fac8f167a447dfe3776fb7e26563a/plot_dosplot_configurations.zip b/docs/_downloads/7d5fac8f167a447dfe3776fb7e26563a/plot_dosplot_configurations.zip
diff --git a/docs/_downloads/8495fda3a3e9038d76ed721a29deae61/plot_utils_pyposcar.ipynb b/docs/_downloads/8495fda3a3e9038d76ed721a29deae61/plot_utils_pyposcar.ipynb
@@ -107,7 +107,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.0"
+      "version": "3.9.20"
     }
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diff --git a/docs/_downloads/8a9ce445958edf3c9905338271c656f8/plot_spin_polarized.zip b/docs/_downloads/8a9ce445958edf3c9905338271c656f8/plot_spin_polarized.zip
diff --git a/docs/_downloads/9158268fd95e17740417379b77c121fa/plot_de_hass_van_alphen.ipynb b/docs/_downloads/9158268fd95e17740417379b77c121fa/plot_de_hass_van_alphen.ipynb
@@ -139,7 +139,7 @@
       "name": "python",
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       "pygments_lexer": "ipython3",
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+      "version": "3.9.20"
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diff --git a/docs/_downloads/943aee90e9972c44ed770bfe4b44f761/plot_clusters_pyposcar.zip b/docs/_downloads/943aee90e9972c44ed770bfe4b44f761/plot_clusters_pyposcar.zip
diff --git a/docs/_downloads/944a0173409f4bb08246c2e0702fcaa4/plot_bandsdosplot.ipynb b/docs/_downloads/944a0173409f4bb08246c2e0702fcaa4/plot_bandsdosplot.ipynb
@@ -60,7 +60,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.0"
+      "version": "3.9.20"
     }
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diff --git a/docs/_downloads/95b1f2ce8020c06eab35a8dbfe66fd57/plot_noncolinear_qe.zip b/docs/_downloads/95b1f2ce8020c06eab35a8dbfe66fd57/plot_noncolinear_qe.zip
diff --git a/docs/_downloads/96c6fcc7313d05faabb1380bd9d8e0fe/plot_rashba_spin_spliting.zip b/docs/_downloads/96c6fcc7313d05faabb1380bd9d8e0fe/plot_rashba_spin_spliting.zip
diff --git a/docs/_downloads/9ba1da3ed9db5c2b7d81064dd83ac4d3/plot_noncolinear_dos_vasp.zip b/docs/_downloads/9ba1da3ed9db5c2b7d81064dd83ac4d3/plot_noncolinear_dos_vasp.zip
diff --git a/docs/_downloads/a0e60cef7183ead80a62a9c9f749b50d/plot_fermi3d_spin-polarized.zip b/docs/_downloads/a0e60cef7183ead80a62a9c9f749b50d/plot_fermi3d_spin-polarized.zip
diff --git a/docs/_downloads/a2d394839c76c3532ba989d6c8da8679/plot_ipr.zip b/docs/_downloads/a2d394839c76c3532ba989d6c8da8679/plot_ipr.zip
diff --git a/docs/_downloads/a465cd27f60a408dabcb3eeea9d2c399/plot_fermi3d_isoslider.zip b/docs/_downloads/a465cd27f60a408dabcb3eeea9d2c399/plot_fermi3d_isoslider.zip
diff --git a/docs/_downloads/a4d58aea2e817c98a59198535b1f1cda/plot_utils_pyposcar.zip b/docs/_downloads/a4d58aea2e817c98a59198535b1f1cda/plot_utils_pyposcar.zip
diff --git a/docs/_downloads/a5890fb88d040bf16c474641f98c10b9/plot_ipr.ipynb b/docs/_downloads/a5890fb88d040bf16c474641f98c10b9/plot_ipr.ipynb
@@ -22,14 +22,14 @@
       },
       "outputs": [],
       "source": [
-        "import os\nimport pyprocar\n\n# Define the directory containing the example data\nbi2se3_data_dir = f\"{pyprocar.utils.ROOT}{os.sep}data{os.sep}examples{os.sep}Bi2Se3-spinorbit-surface\"\n\n\nC_data_dir = f\"{pyprocar.utils.ROOT}{os.sep}data{os.sep}examples{os.sep}NV-center\""
+        "import os\n\nimport pyprocar\n\n# Define the directory containing the example data\nbi2se3_data_dir = (\n    f\"{pyprocar.utils.ROOT}{os.sep}data{os.sep}examples{os.sep}Bi2Se3-spinorbit-surface\"\n)\n\n\nC_data_dir = f\"{pyprocar.utils.ROOT}{os.sep}data{os.sep}examples{os.sep}NV-center\""
       ]
     },
     {
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Topologically-protected surface states in $Bi_2Se_3$\n\nThe first example is the detection of topologically-protected surface states in $Bi_2Se_3$, [zhang2009]. \nThe whole slab has six van der Waals layers (quintuple layers), each is five atom thick. The surface states localize on the outer quintuple layers, \nin contrast a extended state cover the six quintuple layers. \nThe ratio between the localization of both types of states is 1 to 3, and the $IPR$ has enough resolution to provide a clear visual identification. \nThe PyProcar code is:\n\n"
+        "## Topologically-protected surface states in $Bi_2Se_3$\n\nThe first example is the detection of topologically-protected surface states in $Bi_2Se_3$, [zhang2009].\nThe whole slab has six van der Waals layers (quintuple layers), each is five atom thick. The surface states localize on the outer quintuple layers,\nin contrast a extended state cover the six quintuple layers.\nThe ratio between the localization of both types of states is 1 to 3, and the $IPR$ has enough resolution to provide a clear visual identification.\nThe PyProcar code is:\n\n"
       ]
     },
     {
@@ -40,14 +40,14 @@
       },
       "outputs": [],
       "source": [
-        "pyprocar.bandsplot(dirname=bi2se3_data_dir,\n                   elimit=[-1.0,1.0],\n                   mode='ipr',\n                   code='vasp',\n                   spins=[0],\n                   clim=[0,0.2])"
+        "pyprocar.bandsplot(\n    dirname=bi2se3_data_dir,\n    elimit=[-1.0, 1.0],\n    mode=\"ipr\",\n    code=\"vasp\",\n    spins=[0],\n    fermi=2.0446,\n    clim=[0, 0.2],\n)"
       ]
     },
     {
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## $NV^-$ defect in diamond\n\nThe second example is the $NV^-$ defect in diamond, it is a negatively charged N substitution plus an adjacent vacancy. \nThis defect if of interest as a source of single photons. Its ground state is a triplet, allowing the control of the spin by microwave radiation.[DOHERTY2013] \nThe supercell has 215 atoms, hence $IPR\\to0$ for bulk states (blue lines). \nSeveral defect levels lie within the fundamental band gap of diamond (dark red lines). The closest levels to the Fermi energy are double degenerate (**i.e.** triplet), \nbut only occupied for the spin majority. Hence, according to the optical transition takes place between the bands with index $430\\to431$ or $430\\to432$\nof the spin channel labelled `spin-1`. The calculation of the main emission line involves a calculation of the excited state, \nwhich can be simulated by fixing the occupations of the mentioned levels, **i.e.** the $\\Delta$ SCFmethod.[Jin2021]\nThe pyprocar code is:\n\n"
+        "## $NV^-$ defect in diamond\n\nThe second example is the $NV^-$ defect in diamond, it is a negatively charged N substitution plus an adjacent vacancy.\nThis defect if of interest as a source of single photons. Its ground state is a triplet, allowing the control of the spin by microwave radiation.[DOHERTY2013]\nThe supercell has 215 atoms, hence $IPR\\to0$ for bulk states (blue lines).\nSeveral defect levels lie within the fundamental band gap of diamond (dark red lines). The closest levels to the Fermi energy are double degenerate (**i.e.** triplet),\nbut only occupied for the spin majority. Hence, according to the optical transition takes place between the bands with index $430\\to431$ or $430\\to432$\nof the spin channel labelled `spin-1`. The calculation of the main emission line involves a calculation of the excited state,\nwhich can be simulated by fixing the occupations of the mentioned levels, **i.e.** the $\\Delta$ SCFmethod.[Jin2021]\nThe pyprocar code is:\n\n"
       ]
     },
     {
@@ -58,7 +58,7 @@
       },
       "outputs": [],
       "source": [
-        "pyprocar.bandsplot(dirname=C_data_dir, \n                   elimit=[-3.0,2.5], \n                   mode='ipr',\n                   code='vasp', \n                   spins=[0,1], \n                   clim=[0,0.1])"
+        "pyprocar.bandsplot(\n    dirname=C_data_dir,\n    elimit=[-3.0, 2.5],\n    mode=\"ipr\",\n    code=\"vasp\",\n    fermi=12.4563,\n    spins=[0, 1],\n    clim=[0, 0.1],\n)"
       ]
     }
   ],
@@ -78,7 +78,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.0"
+      "version": "3.9.20"
     }
   },
   "nbformat": 4,

diff --git a/docs/_downloads/a6114776ebbf436fd6358daa96928b97/plot_fermi2d_configurations.ipynb b/docs/_downloads/a6114776ebbf436fd6358daa96928b97/plot_fermi2d_configurations.ipynb
@@ -68,7 +68,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.0"
+      "version": "3.9.20"
     }
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diff --git a/docs/_downloads/acd59b108b19e5a25cade83b65959b58/plot_noncolinear_dos_vasp.ipynb b/docs/_downloads/acd59b108b19e5a25cade83b65959b58/plot_noncolinear_dos_vasp.ipynb
@@ -60,7 +60,7 @@
       "name": "python",
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diff --git a/docs/_downloads/adae088a2c2046b932916d81c5c2e5bf/plot_fermi3d_isovalue_gif.zip b/docs/_downloads/adae088a2c2046b932916d81c5c2e5bf/plot_fermi3d_isovalue_gif.zip
diff --git a/docs/_downloads/b110f643ba1910417f890e1aace81279/plot_noncolinear_vasp.ipynb b/docs/_downloads/b110f643ba1910417f890e1aace81279/plot_noncolinear_vasp.ipynb
@@ -78,7 +78,7 @@
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diff --git a/docs/_downloads/b21e89a2c703b6147c8f0a51fa78788c/plot_fermi2d.ipynb b/docs/_downloads/b21e89a2c703b6147c8f0a51fa78788c/plot_fermi2d.ipynb
@@ -114,7 +114,7 @@
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diff --git a/docs/_downloads/b6c323afaddfad8e95934cc3242fdf06/plot_bandsdosplot_configurations.ipynb b/docs/_downloads/b6c323afaddfad8e95934cc3242fdf06/plot_bandsdosplot_configurations.ipynb
@@ -68,7 +68,7 @@
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diff --git a/docs/_downloads/ba402954cf541dbfbd448e582cc302fd/plot_fermi2d_spin_texture.ipynb b/docs/_downloads/ba402954cf541dbfbd448e582cc302fd/plot_fermi2d_spin_texture.ipynb
@@ -96,7 +96,7 @@
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@@ -82,7 +82,7 @@
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diff --git a/docs/_downloads/bc82bea3a5dd7bdba60b65220891d9e5/examples_python.zip b/docs/_downloads/bc82bea3a5dd7bdba60b65220891d9e5/examples_python.zip
diff --git a/docs/_downloads/bc90f4d893d47e09209d26cb846a8047/plot_spin_polarized_dos.zip b/docs/_downloads/bc90f4d893d47e09209d26cb846a8047/plot_spin_polarized_dos.zip
diff --git a/docs/_downloads/c00d40c3f5e9e83a29e33b9c9842ccb6/plot_bandgap.zip b/docs/_downloads/c00d40c3f5e9e83a29e33b9c9842ccb6/plot_bandgap.zip
diff --git a/docs/_downloads/c36ddad0d6a8eda5e730849b832d4505/plot_subsitution_pyposcar.ipynb b/docs/_downloads/c36ddad0d6a8eda5e730849b832d4505/plot_subsitution_pyposcar.ipynb
@@ -107,7 +107,7 @@
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diff --git a/docs/_downloads/c3caa44ef3b6c685adf075dede68f1ff/plot_rdf_cutoff_pyposcar.ipynb b/docs/_downloads/c3caa44ef3b6c685adf075dede68f1ff/plot_rdf_cutoff_pyposcar.ipynb
@@ -89,7 +89,7 @@
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diff --git a/docs/_downloads/c3d5a5dfe90d43051d6d911de7be638b/plot_autobands.zip b/docs/_downloads/c3d5a5dfe90d43051d6d911de7be638b/plot_autobands.zip
diff --git a/docs/_downloads/c81bf698aea723af190b4a2f4bff2bad/plot_bandsdosplot.zip b/docs/_downloads/c81bf698aea723af190b4a2f4bff2bad/plot_bandsdosplot.zip