From 36707c474b67e6d0d8fd9db770f2080fe978e3e7 Mon Sep 17 00:00:00 2001
From: Angelo Ziletti <ziletti@fhi-berlin.mpg.de>
Date: Tue, 30 Jan 2018 14:36:15 +0100
Subject: [PATCH] Fix bug in handling non-periodic structures.
---
.../custom-analytics-example-dev.bkr | 3422 +++++++++++++++--
1 file changed, 3187 insertions(+), 235 deletions(-)
diff --git a/custom-analytics-example/custom-analytics-example-dev.bkr b/custom-analytics-example/custom-analytics-example-dev.bkr
index 955c57a..f7b32e4 100644
--- a/custom-analytics-example/custom-analytics-example-dev.bkr
+++ b/custom-analytics-example/custom-analytics-example-dev.bkr
@@ -100,7 +100,7 @@
" ",
" <sup>1</sup> Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, D-14195 Berlin, Germany <br>",
" <sup>2</sup> Engineering Laboratory, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, UK",
- " <span class=\"nomad--last-updated\" data-version=\"v1.0.1\">[Last updated: January 30, 2018]</span>",
+ " <span class=\"nomad--last-updated\" data-version=\"v1.0.2\">[Last updated: January 30, 2018]</span>",
" </p>",
"</div>"
],
@@ -111,7 +111,7 @@
"result": {
"type": "BeakerDisplay",
"innertype": "Html",
- "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<div class=\"nomad--header\">\n <h2>NOMAD Analytics Toolkit</h2>\n <h3>On-the-fly data analysis for the NOMAD Archive</h3>\n <p class=\"nomad--description\">\n created by:\n <a href=\"mailto:ziletti@fhi-berlin.mpg.de\">Angelo Ziletti</a><sup> 1</sup>,\n Carl Poelking<sup>2</sup>, \n Fawzi Mohamed<sup>1</sup>, \n Gábor Csányi<sup>2</sup>, \n and Luca Ghiringhelli<sup>1</sup> <br><br>\n \n <sup>1</sup> Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, D-14195 Berlin, Germany <br>\n <sup>2</sup> Engineering Laboratory, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, UK\n <span class=\"nomad--last-updated\" data-version=\"v1.0.1\">[Last updated: January 30, 2018]</span>\n </p>\n</div>"
+ "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<div class=\"nomad--header\">\n <h2>NOMAD Analytics Toolkit</h2>\n <h3>On-the-fly data analysis for the NOMAD Archive</h3>\n <p class=\"nomad--description\">\n created by:\n <a href=\"mailto:ziletti@fhi-berlin.mpg.de\">Angelo Ziletti</a><sup> 1</sup>,\n Carl Poelking<sup>2</sup>, \n Fawzi Mohamed<sup>1</sup>, \n Gábor Csányi<sup>2</sup>, \n and Luca Ghiringhelli<sup>1</sup> <br><br>\n \n <sup>1</sup> Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, D-14195 Berlin, Germany <br>\n <sup>2</sup> Engineering Laboratory, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, UK\n <span class=\"nomad--last-updated\" data-version=\"v1.0.2\">[Last updated: January 30, 2018]</span>\n </p>\n</div>"
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
@@ -317,7 +317,7 @@
"import tempfile",
"import ase",
"from pymatgen.io.ase import AseAtomsAdaptor",
- "from pymatgen.symmetry.analyzer import SpacegroupAnalyzer",
+ "from pymatgen.symmetry.analyzer import SpacegroupAnalyzer, PointGroupAnalyzer",
"",
"import soap",
"import soap.soapy.util",
@@ -326,10 +326,11 @@
"from soap.soapy.momo import osio, endl, flush",
"from soap.tools import AseConfig",
"",
- "from nomad_sim.nomad_structures import NOMADStructure",
+ "#from nomad_sim.nomad_structures import NOMADStructure",
"from nomad_sim.wrappers import get_json_list",
"from nomad_sim.wrappers import plot, logger",
- "from nomad_sim.wrappers import _get_structures",
+ "#from nomad_sim.wrappers import _get_structures",
+ "from nomad_sim.wrappers import _apply_operations",
"from nomad_sim.utils_crystals import get_spacegroup",
"from nomad_sim.utils_crystals import create_supercell",
"from nomad_sim.utils_crystals import filter_json_list",
@@ -341,28 +342,15 @@
},
"output": {
"state": {},
- "selectedType": "Results",
+ "selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "32B7F85D85DA4B05AC8ABA4FA6E22968",
- "elapsedTime": 3893,
- "height": 50,
- "hidden": true,
- "result": {
- "type": "Results",
- "outputdata": [
- {
- "type": "err",
- "value": "/usr/local/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.\n from ._conv import register_converters as _register_converters\n/usr/local/lib/python2.7/dist-packages/pymatgen/__init__.py:87: UserWarning: \nPymatgen will drop Py2k support from v2019.1.1. Pls consult the documentation\nat https://www.pymatgen.org for more details.\n at https://www.pymatgen.org for more details.\"\"\")\n"
- },
- {
- "type": "err",
- "value": "Using TensorFlow backend.\n"
- }
- ]
- }
+ "shellId": "2ED595F8DAE142AD8F34EA76B35AF4BA",
+ "elapsedTime": 338,
+ "height": 51,
+ "hidden": true
},
"evaluatorReader": true,
- "lineCount": 38,
+ "lineCount": 39,
"initialization": true,
"tags": "query_list"
},
@@ -2443,8 +2431,8 @@
},
"selectedType": "Table",
"pluginName": "IPython",
- "shellId": "32B7F85D85DA4B05AC8ABA4FA6E22968",
- "elapsedTime": 1000,
+ "shellId": "2ED595F8DAE142AD8F34EA76B35AF4BA",
+ "elapsedTime": 258,
"dataresult": 1,
"height": 785
},
@@ -2814,7 +2802,7 @@
"result": {
"type": "BeakerDisplay",
"innertype": "Html",
- "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<script>\nvar run_soap = function() {\n $(\"#plot_result_button\").removeClass(\"active\").addClass(\"disabled\");\n get_options();\n beaker.evaluate(\"cell_soap_run\");\n};\n \nvar show_hide = function(tag, bt_tag) {\n $(\"#\"+tag).toggle();\n $(\"#\"+bt_tag).toggleClass(\"active\");\n}\n\nvar allow = function(yesno) {\n if (yesno) {\n $(\"#option_el_spec_dens\").removeAttr('disabled');\n $(\"#atomic_density_type\").val('number_density').change();\n }\n else {\n if ($(\"#atomic_density_type\").val() == \"number_density\") {\n $(\"#atomic_density_type\").val('number_density_generic').change();\n }\n $(\"#option_el_spec_dens\").attr('disabled', 'disabled');\n }\n}\n \nvar reset_soap = function() {\n beaker.evaluate(\"cell_soap_gui\");\n};\n \nvar get_options = function() {\n var query_name = $(\"#query_name\").val(); \n var max_nb_res = $(\"#max_nb_res\").val(); \n \n // Determine kernel adaptor function\n // [i.e., choose from specific/generic/global-specific/global-generic] \n var density_type = $(\"#atomic_density_type\").val(); \n var adaptor_type = \"?\";\n if (density_type == \"number_density\") {\n adaptor_type = \"specific\";\n }\n else { // element-agnostic, core charge, valence charge, electronegativity\n adaptor_type = \"generic\";\n }\n var kernel_method = $(\"#kernel_method\").val();\n if (kernel_method == \"global\") {\n adaptor_type = \"global-\" + adaptor_type;\n }\n \n var n_procs = parseInt($(\"#exe_n_procs\").val());\n if ($(\"#threading_mode\").val() == \"single_threaded\") n_procs = 1;\n \n beaker.options = {\n \"query\": {\n \"query_name\": $(\"#query_name\").val(),\n \"max_nb_res\": $(\"#max_nb_res\").val()\n },\n \"run\": {\n \"config_folder\": $(\"#dataset_example\").val(),\n \"n_configs\": -1,\n \"n_procs\": n_procs,\n \"n_blocksize\": parseInt($(\"#exe_batch_size\").val()),\n \"queue\": \"?\",\n \"walltime\": 12,\n \"out_folder\": \"out.kernel\",\n \"verbose\": false\n },\n \"atomic_density\": {\n \"density_type\": $(\"#atomic_density_type\").val(),\n \"atomic_radius\": parseFloat($(\"#atomic_density_atomic_radius\").val()),\n \"use_covrad\": $(\"#atomic_density_use_covrad:checked\").val() == \"true\"\n },\n \"kernel\": {\n \"method\": kernel_method\n },\n \n \"basekernel\": {\n \"type\": \"dot\",\n \"dot\": {\n \"xi\": parseFloat($(\"#basekernel_kernel_xi\").val()),\n \"delta\": 1.0\n }\n },\n \n \"topkernel\": {\n \"type\": \"rematch\",\n \"rematch\": {\n \"gamma\": 0.01\n },\n \"rematch-atomic\": {\n \"gamma\": 0.01\n },\n \"average\": {\n \"xi\": 1.0,\n \"delta\": 1.0\n }\n },\n \n \"laplacian\": {\n \"inverse_dist\": true,\n \"coulomb\": true,\n \"scale\": 0.01,\n \"eta\": 1.0,\n \"gamma\": 0.01,\n \"optimize_eta_gamma\": false\n },\n \"dimred\": {\n \"method\": $(\"#dimred_method\").val()\n },\n \"graph\": {\n \"descriptor\": \"soap\",\n \"pca\": \"none\",\n \"hierarchical\": $(\"#kernel_hierarchical\").val() == \"true\",\n \"r0\": 1.0,\n \"alpha\": 2.0,\n \"n_levels\": 3,\n \"optimize_hierarchy\": false\n },\n \"lamatch\": {\n \"gamma\": 0.3,\n \"optimize_rematch\": false\n },\n\n \"descriptor\": {\n \"type\": \"soap-atomic-dmap\",\n \"soap-atomic\": {\n \"spectrum.global\": false,\n \"spectrum.gradients\": false,\n \"spectrum.2l1_norm\": false,\n \"_spectrum.2l1_norm\": true,\n \"radialbasis.type\" : \"gaussian\",\n \"radialbasis.mode\" : $(\"#soap_radialbasis_mode\").val(),\n \"radialbasis.N\" : parseInt($(\"#soap_radialbasis_N\").val()),\n \"radialbasis.sigma\": parseFloat($(\"#soap_radialbasis_sigma\").val()),\n \"radialbasis.integration_steps\": 15,\n \"radialcutoff.Rc\": parseFloat($(\"#soap_radialbasis_Rc\").val()),\n \"radialcutoff.Rc_width\": parseFloat($(\"#soap_radialbasis_sigma\").val()),\n \"radialcutoff.type\": \"heaviside\",\n \"radialcutoff.center_weight\": 1.0,\n \"angularbasis.type\": \"spherical-harmonic\",\n \"angularbasis.L\": parseInt($(\"#soap_angularbasis_L\").val()),\n \"kernel.adaptor\": \"specific-unique\",\n \"exclude_centers\": [],\n \"exclude_targets\": [],\n \"type_list\": []\n },\n \"soap-atomic-dmap\": {\n \"spectrum.global\": false,\n \"spectrum.gradients\": false,\n \"spectrum.2l1_norm\": false,\n \"radialbasis.type\" : \"gaussian\",\n \"radialbasis.mode\" : \"adaptive\",\n \"radialbasis.N\" : 9,\n \"radialbasis.sigma\": 0.5,\n \"radialbasis.integration_steps\": 15,\n \"radialcutoff.Rc\": 3.5,\n \"radialcutoff.Rc_width\": 0.5,\n \"radialcutoff.type\": \"heaviside\",\n \"radialcutoff.center_weight\": 1.0,\n \"angularbasis.type\": \"spherical-harmonic\",\n \"angularbasis.L\": 6,\n \"kernel.adaptor\": \"specific-unique-dmap\",\n \"exclude_centers\": [],\n \"exclude_targets\": [],\n \"type_list\": []\n }\n }\n\n \n };\n\n}; \n \nbeaker.view_result = function(result_link) {\n $(\"#plot_result_button\").attr(\"href\", result_link);\n $(\"#plot_result_button\").removeClass(\"disabled\"); //.addClass(\"active\");\n}\n</script>\n<style type=\"text/css\">\n .in11f {\n width: 3.5em;\n }\n .in3d {\n width: 5em;\n }\n .select_main {\n width: 20em;\n }\n .btn.active, .btn:active {\n background: #cecece;\n text-decoration: none;\n }\n</style>\n\n <p style=\"color:#20335d; font-weight:900; font-size:18pt;\"> Control options Query <br> </p><hr style=\"border-width:2px\"> <p></p>\n\n <table class=\"query_control\">\n \n <!-- SYSTEM REWEIHGTED COMPOSITION --> \n <tbody><tr style=\"line-height:40px\">\n <td><b>Name of query to analyze</b> (if empty: load latest query)</td>\n <td>\n <input type=\"text\" id=\"query_name\" value=\"\"> \n\n </td>\n </tr>\n \n \n <!-- BASE KERNEL --> \n <tr style=\"line-height:40px\">\n <td><b>Max number or results for each space group/point group</b> </td>\n <td>\n <input type=\"number\" name=\"quantity\" id=\"max_nb_res\" min=\"5\" max=\"100\" value=\"25\" step=\"1\"> \n </td>\n </tr> \n \n \n \n</tbody></table>\n \n<br> <br>\n\n <p style=\"color:#20335d; font-weight:900; font-size:18pt;\"> Control options Analysis <br> </p><hr style=\"border-width:2px\"> <p></p>\n \n \n <table class=\"glosim_control\">\n \n <!-- ATOMIC DENSITY --> \n <tbody><tr style=\"line-height:40px\">\n <td><b>Atomic density</b> </td>\n <td>\n <select class=\"select_main\" id=\"atomic_density_type\">\n <option id=\"option_el_agno_dens\" value=\"number_density_generic\" selected=\"\"> Density type: element-agnostic density </option>\n <option id=\"option_el_spec_dens\" value=\"number_density\" disabled=\"\"> Density type: element-specific density </option> \n <option value=\"valence_charge_density\"> Density type: valence charge </option>\n <option value=\"z_density\"> Density type: core charge </option>\n <option value=\"elneg_density\"> Density type: electronegativity </option>\n </select> <!-- DATASETS -->\n \n <button id=\"toggle_detail_2\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_2", "toggle_detail_2")\">Configure</button>\n <g id=\"in_detail_2\" hidden=\"\"> Use covalent radii <input id=\"atomic_density_use_covrad\" type=\"checkbox\" value=\"true\" unchecked=\"\">\n Constant atomic radius (Angstrom) <input id=\"atomic_density_atomic_radius\" type=\"number\" value=\"0.5\" min=\"0.0\" max=\"2.0\" step=\"0.1\" class=\"in11f\"> </g>\n </td>\n </tr>\n \n <!-- BASIS SET --> \n <tr style=\"line-height:40px\">\n <td><b>Basis set</b> </td>\n <td>\n <select class=\"select_main\" id=\"soap_radialbasis_mode\">\n <option value=\"adaptive\"> Radial basis: adaptive </option>\n <option value=\"equispaced\"> Radial basis: equispaced </option>\n </select>\n <button id=\"toggle_detail_3\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_3", "toggle_detail_3")\">Configure</button>\n <g id=\"in_detail_3\" hidden=\"\">\n Radial functions N = <input id=\"soap_radialbasis_N\" type=\"number\" value=\"9\" min=\"1\" max=\"14\" step=\"1\" class=\"in11f\">\n Radial cutoff (equispaced only) <input id=\"soap_radialbasis_Rc\" type=\"number\" value=\"3.5\" min=\"0.1\" max=\"10.0\" step=\"0.1\" class=\"in11f\">\n Radial Gaussian width <input id=\"soap_radialbasis_sigma\" type=\"number\" value=\"0.5\" min=\"0.1\" max=\"3.0\" step=\"0.1\" class=\"in11f\">\n Angular functions L = <input id=\"soap_angularbasis_L\" type=\"number\" value=\"6\" min=\"1\" max=\"14\" step=\"1\" class=\"in11f\"> \n </g>\n </td>\n </tr> \n \n <!-- BASE KERNEL --> \n <tr style=\"line-height:40px\">\n <td><b>Base kernel</b> </td>\n <td>\n <select class=\"select_main\" id=\"basekernel_method\">\n <option value=\"dot\"> Dot-product kernel </option>\n <option value=\"laplacian\" disabled=\"\"> Laplacian kernel </option>\n <option value=\"gaussian\" disabled=\"\"> Gaussian kernel </option>\n </select>\n <button id=\"toggle_detail_4\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_4", "toggle_detail_4")\">Configure</button>\n <g id=\"in_detail_4\" hidden=\"\">\n Exponent <input id=\"basekernel_kernel_xi\" type=\"number\" value=\"3.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\">\n </g>\n </td>\n </tr> \n \n <!-- TOP KERNEL -->\n <tr style=\"line-height:40px\">\n <td><b>Top kernel</b> </td>\n <td>\n <select class=\"select_main\" id=\"kernel_method\">\n <option value=\"global\" selected=\"\"> Global average (coherent)</option>\n <option value=\"average\"> Global average (incoherent)</option>\n <option value=\"rematch\"> Regularized-entropy match</option> \n <option value=\"laplacian\"> Laplacian Markov random field</option>\n </select>\n <button id=\"toggle_detail_5\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_5", "toggle_detail_5")\">Configure</button>\n <g id=\"in_detail_5\" hidden=\"\">\n Mode \n <select id=\"kernel_hierarchical\">\n <option value=\"false\"> single-level</option>\n <option value=\"true\"> hierarchical</option>\n </select>\n Graph Laplacian \n <select id=\"opt_top_kernel_hierarchy\">\n <option value=\"invdist\"> inverse distance</option>\n <option value=\"coulomb\"> Coulomb matrix</option>\n </select>\n Levels <input id=\"graph:n_levels\" type=\"number\" value=\"1\" min=\"1\" max=\"5\" step=\"1\" class=\"in11f\">\n Base radius <input id=\"graph:r0\" type=\"number\" value=\"1.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\">\n Scale <input id=\"graph:alpha\" type=\"number\" value=\"2.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\">\n </g>\n </td>\n </tr> \n \n</tbody></table>\n \n<hr style=\"border-width:2px\">\n \n <button class=\"btn btn-default\" onclick=\"run_soap()\">RUN Retrieval & Analysis</button> \n <button class=\"btn btn-default\" onclick=\"reset_soap()\">RESET </button> \n <label title=\"Activate once run is complete.\"> \n <a href=\"/user/tmp/462b47d34c41e56d.html\" target=\"_blank\" class=\"btn btn-primary\" id=\"plot_result_button\">View 2D similarity map</a> \n </label>\n"
+ "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<script>\nvar run_soap = function() {\n $(\"#plot_result_button\").removeClass(\"active\").addClass(\"disabled\");\n get_options();\n beaker.evaluate(\"cell_soap_run\");\n};\n \nvar show_hide = function(tag, bt_tag) {\n $(\"#\"+tag).toggle();\n $(\"#\"+bt_tag).toggleClass(\"active\");\n}\n\nvar allow = function(yesno) {\n if (yesno) {\n $(\"#option_el_spec_dens\").removeAttr('disabled');\n $(\"#atomic_density_type\").val('number_density').change();\n }\n else {\n if ($(\"#atomic_density_type\").val() == \"number_density\") {\n $(\"#atomic_density_type\").val('number_density_generic').change();\n }\n $(\"#option_el_spec_dens\").attr('disabled', 'disabled');\n }\n}\n \nvar reset_soap = function() {\n beaker.evaluate(\"cell_soap_gui\");\n};\n \nvar get_options = function() {\n var query_name = $(\"#query_name\").val(); \n var max_nb_res = $(\"#max_nb_res\").val(); \n \n // Determine kernel adaptor function\n // [i.e., choose from specific/generic/global-specific/global-generic] \n var density_type = $(\"#atomic_density_type\").val(); \n var adaptor_type = \"?\";\n if (density_type == \"number_density\") {\n adaptor_type = \"specific\";\n }\n else { // element-agnostic, core charge, valence charge, electronegativity\n adaptor_type = \"generic\";\n }\n var kernel_method = $(\"#kernel_method\").val();\n if (kernel_method == \"global\") {\n adaptor_type = \"global-\" + adaptor_type;\n }\n \n var n_procs = parseInt($(\"#exe_n_procs\").val());\n if ($(\"#threading_mode\").val() == \"single_threaded\") n_procs = 1;\n \n beaker.options = {\n \"query\": {\n \"query_name\": $(\"#query_name\").val(),\n \"max_nb_res\": $(\"#max_nb_res\").val()\n },\n \"run\": {\n \"config_folder\": $(\"#dataset_example\").val(),\n \"n_configs\": -1,\n \"n_procs\": n_procs,\n \"n_blocksize\": parseInt($(\"#exe_batch_size\").val()),\n \"queue\": \"?\",\n \"walltime\": 12,\n \"out_folder\": \"out.kernel\",\n \"verbose\": false\n },\n \"atomic_density\": {\n \"density_type\": $(\"#atomic_density_type\").val(),\n \"atomic_radius\": parseFloat($(\"#atomic_density_atomic_radius\").val()),\n \"use_covrad\": $(\"#atomic_density_use_covrad:checked\").val() == \"true\"\n },\n \"kernel\": {\n \"method\": kernel_method\n },\n \n \"basekernel\": {\n \"type\": \"dot\",\n \"dot\": {\n \"xi\": parseFloat($(\"#basekernel_kernel_xi\").val()),\n \"delta\": 1.0\n }\n },\n \n \"topkernel\": {\n \"type\": \"rematch\",\n \"rematch\": {\n \"gamma\": 0.01\n },\n \"rematch-atomic\": {\n \"gamma\": 0.01\n },\n \"average\": {\n \"xi\": 1.0,\n \"delta\": 1.0\n }\n },\n \n \"laplacian\": {\n \"inverse_dist\": true,\n \"coulomb\": true,\n \"scale\": 0.01,\n \"eta\": 1.0,\n \"gamma\": 0.01,\n \"optimize_eta_gamma\": false\n },\n \"dimred\": {\n \"method\": $(\"#dimred_method\").val()\n },\n \"graph\": {\n \"descriptor\": \"soap\",\n \"pca\": \"none\",\n \"hierarchical\": $(\"#kernel_hierarchical\").val() == \"true\",\n \"r0\": 1.0,\n \"alpha\": 2.0,\n \"n_levels\": 3,\n \"optimize_hierarchy\": false\n },\n \"lamatch\": {\n \"gamma\": 0.3,\n \"optimize_rematch\": false\n },\n\n \"descriptor\": {\n \"type\": \"soap-atomic-dmap\",\n \"soap-atomic\": {\n \"spectrum.global\": false,\n \"spectrum.gradients\": false,\n \"spectrum.2l1_norm\": false,\n \"_spectrum.2l1_norm\": true,\n \"radialbasis.type\" : \"gaussian\",\n \"radialbasis.mode\" : $(\"#soap_radialbasis_mode\").val(),\n \"radialbasis.N\" : parseInt($(\"#soap_radialbasis_N\").val()),\n \"radialbasis.sigma\": parseFloat($(\"#soap_radialbasis_sigma\").val()),\n \"radialbasis.integration_steps\": 15,\n \"radialcutoff.Rc\": parseFloat($(\"#soap_radialbasis_Rc\").val()),\n \"radialcutoff.Rc_width\": parseFloat($(\"#soap_radialbasis_sigma\").val()),\n \"radialcutoff.type\": \"heaviside\",\n \"radialcutoff.center_weight\": 1.0,\n \"angularbasis.type\": \"spherical-harmonic\",\n \"angularbasis.L\": parseInt($(\"#soap_angularbasis_L\").val()),\n \"kernel.adaptor\": \"specific-unique\",\n \"exclude_centers\": [],\n \"exclude_targets\": [],\n \"type_list\": []\n },\n \"soap-atomic-dmap\": {\n \"spectrum.global\": false,\n \"spectrum.gradients\": false,\n \"spectrum.2l1_norm\": false,\n \"radialbasis.type\" : \"gaussian\",\n \"radialbasis.mode\" : \"adaptive\",\n \"radialbasis.N\" : 9,\n \"radialbasis.sigma\": 0.5,\n \"radialbasis.integration_steps\": 15,\n \"radialcutoff.Rc\": 3.5,\n \"radialcutoff.Rc_width\": 0.5,\n \"radialcutoff.type\": \"heaviside\",\n \"radialcutoff.center_weight\": 1.0,\n \"angularbasis.type\": \"spherical-harmonic\",\n \"angularbasis.L\": 6,\n \"kernel.adaptor\": \"specific-unique-dmap\",\n \"exclude_centers\": [],\n \"exclude_targets\": [],\n \"type_list\": []\n }\n }\n\n \n };\n\n}; \n \nbeaker.view_result = function(result_link) {\n $(\"#plot_result_button\").attr(\"href\", result_link);\n $(\"#plot_result_button\").removeClass(\"disabled\"); //.addClass(\"active\");\n}\n</script>\n<style type=\"text/css\">\n .in11f {\n width: 3.5em;\n }\n .in3d {\n width: 5em;\n }\n .select_main {\n width: 20em;\n }\n .btn.active, .btn:active {\n background: #cecece;\n text-decoration: none;\n }\n</style>\n\n <p style=\"color:#20335d; font-weight:900; font-size:18pt;\"> Control options Query <br> </p><hr style=\"border-width:2px\"> <p></p>\n\n <table class=\"query_control\">\n \n <!-- SYSTEM REWEIHGTED COMPOSITION --> \n <tbody><tr style=\"line-height:40px\">\n <td><b>Name of query to analyze</b> (if empty: load latest query)</td>\n <td>\n <input type=\"text\" id=\"query_name\" value=\"\"> \n\n </td>\n </tr>\n \n \n <!-- BASE KERNEL --> \n <tr style=\"line-height:40px\">\n <td><b>Max number or results for each space group/point group</b> </td>\n <td>\n <input type=\"number\" name=\"quantity\" id=\"max_nb_res\" min=\"5\" max=\"100\" value=\"25\" step=\"1\"> \n </td>\n </tr> \n \n \n \n</tbody></table>\n \n<br> <br>\n\n <p style=\"color:#20335d; font-weight:900; font-size:18pt;\"> Control options Analysis <br> </p><hr style=\"border-width:2px\"> <p></p>\n \n \n <table class=\"glosim_control\">\n \n <!-- ATOMIC DENSITY --> \n <tbody><tr style=\"line-height:40px\">\n <td><b>Atomic density</b> </td>\n <td>\n <select class=\"select_main\" id=\"atomic_density_type\">\n <option id=\"option_el_agno_dens\" value=\"number_density_generic\" selected=\"\"> Density type: element-agnostic density </option>\n <option id=\"option_el_spec_dens\" value=\"number_density\" disabled=\"\"> Density type: element-specific density </option> \n <option value=\"valence_charge_density\"> Density type: valence charge </option>\n <option value=\"z_density\"> Density type: core charge </option>\n <option value=\"elneg_density\"> Density type: electronegativity </option>\n </select> <!-- DATASETS -->\n \n <button id=\"toggle_detail_2\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_2", "toggle_detail_2")\">Configure</button>\n <g id=\"in_detail_2\" hidden=\"\"> Use covalent radii <input id=\"atomic_density_use_covrad\" type=\"checkbox\" value=\"true\" unchecked=\"\">\n Constant atomic radius (Angstrom) <input id=\"atomic_density_atomic_radius\" type=\"number\" value=\"0.5\" min=\"0.0\" max=\"2.0\" step=\"0.1\" class=\"in11f\"> </g>\n </td>\n </tr>\n \n <!-- BASIS SET --> \n <tr style=\"line-height:40px\">\n <td><b>Basis set</b> </td>\n <td>\n <select class=\"select_main\" id=\"soap_radialbasis_mode\">\n <option value=\"adaptive\"> Radial basis: adaptive </option>\n <option value=\"equispaced\"> Radial basis: equispaced </option>\n </select>\n <button id=\"toggle_detail_3\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_3", "toggle_detail_3")\">Configure</button>\n <g id=\"in_detail_3\" hidden=\"\">\n Radial functions N = <input id=\"soap_radialbasis_N\" type=\"number\" value=\"9\" min=\"1\" max=\"14\" step=\"1\" class=\"in11f\">\n Radial cutoff (equispaced only) <input id=\"soap_radialbasis_Rc\" type=\"number\" value=\"3.5\" min=\"0.1\" max=\"10.0\" step=\"0.1\" class=\"in11f\">\n Radial Gaussian width <input id=\"soap_radialbasis_sigma\" type=\"number\" value=\"0.5\" min=\"0.1\" max=\"3.0\" step=\"0.1\" class=\"in11f\">\n Angular functions L = <input id=\"soap_angularbasis_L\" type=\"number\" value=\"6\" min=\"1\" max=\"14\" step=\"1\" class=\"in11f\"> \n </g>\n </td>\n </tr> \n \n <!-- BASE KERNEL --> \n <tr style=\"line-height:40px\">\n <td><b>Base kernel</b> </td>\n <td>\n <select class=\"select_main\" id=\"basekernel_method\">\n <option value=\"dot\"> Dot-product kernel </option>\n <option value=\"laplacian\" disabled=\"\"> Laplacian kernel </option>\n <option value=\"gaussian\" disabled=\"\"> Gaussian kernel </option>\n </select>\n <button id=\"toggle_detail_4\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_4", "toggle_detail_4")\">Configure</button>\n <g id=\"in_detail_4\" hidden=\"\">\n Exponent <input id=\"basekernel_kernel_xi\" type=\"number\" value=\"3.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\">\n </g>\n </td>\n </tr> \n \n <!-- TOP KERNEL -->\n <tr style=\"line-height:40px\">\n <td><b>Top kernel</b> </td>\n <td>\n <select class=\"select_main\" id=\"kernel_method\">\n <option value=\"global\" selected=\"\"> Global average (coherent)</option>\n <option value=\"average\"> Global average (incoherent)</option>\n <option value=\"rematch\"> Regularized-entropy match</option> \n <option value=\"laplacian\"> Laplacian Markov random field</option>\n </select>\n <button id=\"toggle_detail_5\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_5", "toggle_detail_5")\">Configure</button>\n <g id=\"in_detail_5\" hidden=\"\">\n Mode \n <select id=\"kernel_hierarchical\">\n <option value=\"false\"> single-level</option>\n <option value=\"true\"> hierarchical</option>\n </select>\n Graph Laplacian \n <select id=\"opt_top_kernel_hierarchy\">\n <option value=\"invdist\"> inverse distance</option>\n <option value=\"coulomb\"> Coulomb matrix</option>\n </select>\n Levels <input id=\"graph:n_levels\" type=\"number\" value=\"1\" min=\"1\" max=\"5\" step=\"1\" class=\"in11f\">\n Base radius <input id=\"graph:r0\" type=\"number\" value=\"1.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\">\n Scale <input id=\"graph:alpha\" type=\"number\" value=\"2.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\">\n </g>\n </td>\n </tr> \n \n</tbody></table>\n \n<hr style=\"border-width:2px\">\n \n <button class=\"btn btn-default\" onclick=\"run_soap()\">RUN Retrieval & Analysis</button> \n <button class=\"btn btn-default\" onclick=\"reset_soap()\">RESET </button> \n <label title=\"Activate once run is complete.\"> \n <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"plot_result_button\">View 2D similarity map</a> \n </label>\n"
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
@@ -2825,6 +2813,1413 @@
"tags": "cell_soap_gui",
"isError": false
},
+ {
+ "id": "codedb2MCr",
+ "type": "code",
+ "evaluator": "IPython",
+ "input": {
+ "body": [
+ "class NOMADStructure(object):",
+ " \"\"\"Read the atomic structure and the total energy of a system given a NOMAD",
+ " JSON file.",
+ "",
+ " Gets data from JSON file and sets up the ase.Atoms objects.",
+ " It handles multiple geometries in the NOMAD file (e.g. configurations",
+ " from a geometry optimization). ",
+ "",
+ " Parameters",
+ " ----------",
+ "",
+ " in_file : string,",
+ " Path to json file to read",
+ "",
+ " frame_list : int, list (or list of lists)",
+ " Specifies for each NOMAD json file the frames to load.",
+ " It is a list if only one frame for each json file needs to be",
+ " loaded, while it is a list of lists otherwise.",
+ " Negative indeces are supported.",
+ "",
+ " png_path : string",
+ " Path to the folder where the png files for each structure are",
+ " written.",
+ "",
+ " geo_path : string",
+ " Path to the folder where the png files for each structure are",
+ " written.",
+ "",
+ " png_file : string",
+ " Path to the png file where the image for each structure and frame",
+ " is written.",
+ "",
+ " geo_file : string",
+ " Path to the geometry file where the image for each structure and",
+ " frame is written.",
+ "",
+ " xray_path : string",
+ " Path to the folder where the xray diffraction pattern png files for",
+ " each structure are written.",
+ "",
+ " xray_file : string",
+ " Path to the xray diffraction pattern png files where the image for",
+ " each structure and frame is written.",
+ "",
+ " isPeriodic : bool",
+ " Specify if the system is periodic (used for generating periodic",
+ " replicas in the plot).",
+ " If `True` if create a 4x4x4 periodic replica of the unit cell for",
+ " visualization.",
+ " .. todo:: It should be guessed automatically using",
+ " `nomad_classify `.",
+ "",
+ " file_format : text, optional, {'NOMAD', 'rdf'}",
+ " Specify what is the format of the file to read.",
+ " ('rdf' is DEPRECATED).",
+ "",
+ "",
+ " Attributes",
+ " ----------",
+ "",
+ " atoms : dict",
+ "",
+ " energy_eV : dict",
+ "",
+ " name : (?)",
+ " Sha - checksum.",
+ "",
+ " chemical_symbols : dict",
+ "",
+ " chemical_formula : dict",
+ "",
+ " spacegroup_analyzer : dict",
+ " Spacegroup analyzer object of pymatgen",
+ " http://pymatgen.org/_modules/pymatgen/symmetry/analyzer.html",
+ "",
+ "",
+ " \"\"\"",
+ "",
+ " def __init__(",
+ " self, in_file=None, frame_list=None, png_path=None,",
+ " png_file=None, geo_path=None, geo_file=None, desc_path=None,",
+ " rdf_file=None, xray_path=None, xray_file=None, isPeriodic=None,",
+ " file_format=None, cell_type=None, take_first=True,",
+ " descriptor=None):",
+ "",
+ " self.m_to_ang = 1.0e10",
+ " self.j_to_ev = 6.241509e18",
+ " self.atoms = {}",
+ " self.scaled_positions = {}",
+ " self.energy_total = {}",
+ " self.energy_total__eV = {}",
+ " self.in_file = in_file",
+ " self.frame_list = frame_list",
+ " self.png_path = png_path",
+ " self.png_file = {}",
+ " self.geo_path = geo_path",
+ " self.geo_file = {}",
+ " self.desc_path = desc_path",
+ " self.xray_path = xray_path",
+ " self.xray_file = {}",
+ " self.xray_npy_file = {}",
+ " self.xray_rs_file = {}",
+ " self.rdf_file = {}",
+ " self.name = os.path.splitext(os.path.basename(in_file))[0]",
+ " self.chemical_symbols = {}",
+ " self.chemical_formula = {}",
+ " self.isPeriodic = isPeriodic",
+ " self.Id = {}",
+ " self.isEnergyNone = False",
+ " self.file_format = file_format",
+ " self.cell_type = cell_type",
+ " self.spacegroup_analyzer = {}",
+ " self.spacegroup_analyzer_actual = {}",
+ " ",
+ " ",
+ " if self.file_format is None:",
+ " self.file_format = 'NOMAD'",
+ "",
+ " if self.file_format == 'NOMAD':",
+ " # read JSON file",
+ " json_dict = self._get_json_dict(in_file)",
+ "",
+ " # get single_config_calc (target: energy_total)",
+ " single_config_calc = self._get_single_config_calc(json_dict)",
+ "",
+ " # extract energy from the list in single_config_calc",
+ " for (gIndexRun, gIndexSingle), structure in single_config_calc.iteritems():",
+ " energy = structure.get('energy_total')",
+ " if energy is None:",
+ " # logger.warning(",
+ " # \"Could not find energy_total in \" +",
+ " # \"single_config_calculations \\n with gIndexSingle {0}\" +",
+ " # \"in section_run with gIndexRun {1} \\n\" +",
+ " # \"in file {2}\".format(",
+ " # gIndexSingle,",
+ " # gIndexRun,",
+ " # self.in_file))",
+ " isEnergyNone = True",
+ " self.energy_total[gIndexRun, gIndexSingle] = 0.0",
+ " self.energy_total__eV[gIndexRun, gIndexSingle] = 0.0",
+ " else:",
+ " self.energy_total[",
+ " gIndexRun, gIndexSingle] = energy",
+ " self.energy_total__eV[",
+ " gIndexRun, gIndexSingle] = energy * self.j_to_ev",
+ "",
+ " # get system_description (target: structure)",
+ " system_descriptions = self._get_system_descriptions(json_dict)",
+ "",
+ " # compare dictionaries of single_config_calc and",
+ " # system_descriptions",
+ " logger.debug(\"Single configuration keys: {0}\".format(",
+ " set(single_config_calc.keys())))",
+ " logger.debug(\"System description keys: {0}\".format(",
+ " set(system_descriptions.keys())))",
+ "",
+ " intersect = set(single_config_calc.keys()).intersection(",
+ " set(system_descriptions.keys()))",
+ " not_intersect = set(single_config_calc.keys()).symmetric_difference(",
+ " set(system_descriptions.keys()))",
+ "",
+ " logger.debug(",
+ " \"Deleting frames that do not both have 'single_config_calc' and in 'system_descriptions'.\")",
+ " for key in not_intersect:",
+ " if key in system_descriptions:",
+ " del system_descriptions[key]",
+ " if take_first:",
+ " logger.debug(",
+ " \"Keeping only 1st frame in which both 'single_config_calc' and 'system_descriptions' are present.\")",
+ " not_intersect_system = set([(0, 0)]).symmetric_difference(",
+ " set(system_descriptions.keys()))",
+ " not_intersect_single = set([(0, 0)]).symmetric_difference(",
+ " set(single_config_calc.keys()))",
+ " index = 0",
+ " else:",
+ " logger.debug(",
+ " \"Keeping only last frame in which both 'single_config_calc' and 'system_descriptions' are present.\")",
+ " index = len(system_descriptions)-1",
+ " system_descriptions_value = system_descriptions[(0, index)]",
+ " system_descriptions.clear()",
+ " system_descriptions[(0, 0)] = system_descriptions_value",
+ "",
+ " single_config_calc_value = single_config_calc[(0, index)]",
+ " single_config_calc.clear()",
+ " single_config_calc[(0, 0)] = single_config_calc_value",
+ " ",
+ " # print len(single_config_calc)",
+ " # print len(system_descriptions)",
+ "",
+ " # print set(single_config_calc.keys())",
+ " # print set(system_descriptions.keys())",
+ "",
+ " # extract structure data from the list in system_descriptions",
+ " # the key is a tuple (gIndexRun, gIndexDesc)",
+ " # Note: self.atoms is a dict with key (gIndexRun, gIndexDesc)",
+ " # for (gIndexRun, gIndexDesc), structure in",
+ " # system_descriptions.items():",
+ " for (gIndexRun, gIndexDesc), structure in system_descriptions.iteritems():",
+ " # old format",
+ " # labels = structure.get('atom_label')",
+ " labels = structure.get('atom_labels')",
+ "",
+ " if labels is None:",
+ " raise Exception(",
+ " \"Could not find atom_label in section_system_description\" +",
+ " \"\\nwith gIndex %d in section_run with gIndex \" +",
+ " \"%d!\" %",
+ " gIndexDesc %",
+ " gIndexRun)",
+ "",
+ " # positions = structure.get('atom_position')",
+ " positions = structure.get('atom_positions')",
+ "",
+ " if positions is None:",
+ " raise Exception(",
+ " \"Could not find atom_position in \" +",
+ " \"section_system_description \\nwith gIndex %d in\" +",
+ " \"section_run with gIndex %d!\" % gIndexDesc % gIndexRun)",
+ "",
+ " cell = structure.get('simulation_cell')",
+ "",
+ " # convert to Angstrom and numpy array",
+ " positions = self.m_to_ang * np.asarray(positions)",
+ "",
+ " # check if all labels are known by ase",
+ " # if not change unknown label to X",
+ " for i in range(len(labels)):",
+ " number = ase.data.atomic_numbers.get(labels[i])",
+ " if number is None:",
+ " labels[i] = u'X'",
+ "",
+ " if cell is None:",
+ " self.isPeriodic = False",
+ " atoms = ase.Atoms(",
+ " symbols=labels, positions=positions,",
+ " cell=None, pbc=False)",
+ " else:",
+ " self.isPeriodic = True",
+ " # convert to Angstrom and numpy array",
+ " cell = self.m_to_ang * np.asarray(cell)",
+ " # in the metadata, simulation_cell has lattice vectors as",
+ " # columns, ase has them as rows => transpose",
+ " atoms = ase.Atoms(",
+ " symbols=labels, positions=positions,",
+ "# cell=np.transpose(cell), pbc=True)",
+ " cell=cell, pbc=True)",
+ "",
+ "",
+ " # get conventional or primitive standard cell with pymatgen",
+ " if self.cell_type is not None:",
+ " if self.cell_type == 'primitive':",
+ " atoms = get_conventional_standard_atoms(atoms)",
+ " atoms = get_primitive_standard_atoms(atoms)",
+ " elif self.cell_type == 'standard':",
+ " atoms = get_conventional_standard_atoms(atoms)",
+ "",
+ " # get the SpacegroupAnalyzer object from pymatgen ",
+ " # for further processing (e.g. to get spacegroup number or symbol)",
+ " # (from PyMatGen): tolerance of 0.1 (the value used in Materials Project) is often needed",
+ "# symprecs = np.logspace(-3, -1, 7, endpoint=True, base=10.0).tolist() ",
+ "# symprecs = np.linspace(1.0E-3, 1E-1, i, endpoint=True).tolist() ",
+ "# symprecs = [1.0E-3, 1.0E-2, 1.0E-1]",
+ "# angle_tolerances = [1., 5.]",
+ "",
+ " symprecs = [1.0E-3]",
+ " angle_tolerances = [1.]",
+ "",
+ " spacegroup_analyzer = {} ",
+ " # build a dictionary with different spacegroup analyzers according",
+ " # to the thresholds used",
+ " try:",
+ " for symprec in symprecs:",
+ " for angle_tolerance in angle_tolerances:",
+ " spacegroup_analyzer[symprec, angle_tolerance] = SpacegroupAnalyzer(AseAtomsAdaptor.get_structure(atoms),",
+ "# symprec=1e-1, angle_tolerance=5) ",
+ " symprec=symprec, angle_tolerance=angle_tolerance) ",
+ " except:",
+ " spacegroup_analyzer=None",
+ " ",
+ " # wrap atomic positions inside unit cell",
+ " atoms.wrap()",
+ " # save the atoms",
+ " self.Id[gIndexRun, gIndexDesc] = (gIndexRun, gIndexDesc)",
+ " self.atoms[gIndexRun, gIndexDesc] = atoms",
+ " # get chemical formula",
+ " self.chemical_formula[",
+ " gIndexRun,",
+ " gIndexDesc] = atoms.get_chemical_formula(",
+ " mode='hill')",
+ " self.chemical_symbols[",
+ " gIndexRun, gIndexDesc] = atoms.get_chemical_symbols()",
+ " self.scaled_positions[",
+ " gIndexRun,",
+ " gIndexDesc] = atoms.get_scaled_positions(",
+ " wrap=True)",
+ " ",
+ " self.spacegroup_analyzer[",
+ " gIndexRun,",
+ " gIndexDesc] = spacegroup_analyzer",
+ " ",
+ "",
+ " elif self.file_format == 'xyz':",
+ " ''' reads xyz file with a list of configurations'''",
+ " xyz_file = open(self.in_file, 'r')",
+ "",
+ " try:",
+ " ase_frames = ase.io.read(self.in_file, index=':', format='xyz')",
+ " logger.debug(",
+ " \"Number of frames found: {0}\".format(",
+ " len(ase_frames)))",
+ "",
+ " N_frames = len(ase_frames)",
+ "",
+ " # usually the frame list is not defined in this cases",
+ " if frame_list is None:",
+ " frame_list = range(N_frames)",
+ "",
+ " # check if frame_list is actually a list and not only a number",
+ " if isinstance(frame_list, list) is False:",
+ " frame_list = [frame_list]",
+ "",
+ " for frame in frame_list:",
+ "",
+ " atoms = ase_frames[frame]",
+ "",
+ " # wrap atomic positions inside unit cell",
+ " atoms.wrap()",
+ "",
+ " # save the atoms",
+ " self.atoms[0, frame] = atoms",
+ "",
+ " # instead of chemical formula, display the name",
+ " self.chemical_formula[",
+ " 0, frame] = atoms.get_chemical_formula(",
+ " mode='hill')",
+ " self.energy_total__eV[0, frame] = 0.0",
+ " self.energy_total[0, frame] = 0.0",
+ "",
+ "",
+ " # it is the same as self.gIndexDescMax = i",
+ " self.gIndexRunMax = 0",
+ " self.gIndexDescMax = len(frame_list) - 1",
+ "",
+ " finally:",
+ " xyz_file.close()",
+ "",
+ " else:",
+ " logger.error(",
+ " \"Please specify if the file is a JSON file is either a file \\nfrom the NOMAD repository or a Radial Distribution Function\")",
+ "",
+ " def __getitem__(self, index):",
+ " return self.energy_total[index], self.png_file[index], self.geo_file[index], self.chemical_formula[index], self.name",
+ "",
+ " def __len__(self):",
+ " return self._data_len",
+ "",
+ " def _get_json_dict(self, in_file):",
+ " \"\"\"Reads JSON content from file.",
+ " Args:",
+ " in_file: file which is read.",
+ " Returns:",
+ " Dictionary loaded from JSON file.",
+ " \"\"\"",
+ " try:",
+ " with open(in_file) as json_file:",
+ " try:",
+ " return json.load(json_file)",
+ " except Exception:",
+ " logger.error(",
+ " \"Could not read content from JSON file '%s'! See below for error message.\" %",
+ " in_file)",
+ " raise",
+ " finally:",
+ " json_file.close()",
+ " except IOError:",
+ " raise Exception(\"Could not open file '%s'!\" % in_file)",
+ "",
+ " def _get_system_descriptions(self, json_dict):",
+ " \"\"\"Extract section_system_description from JSON dictionary (to obtain the structure in this case)",
+ " Args:",
+ " json_dict: JSON dictionary containing parsed data.",
+ " Returns:",
+ " Dictionaries of section_system_description for each section_run as dictionary.",
+ " The keys are a tuple (gIndexRun, gIndexDesc) of the different section_run and section_system_description, respectively.",
+ " \"\"\"",
+ "",
+ " # old format",
+ " # for section in sections",
+ "",
+ " found_section_run = False",
+ " sections = json_dict.get('sections')",
+ " section_system_descriptions = {}",
+ "",
+ " # read section_run and for each section_run read section_system_description",
+ " # gIndexRun: gIndex for section_run",
+ " # gIndexDesc: gIndex for section_system_description",
+ " if sections is not None:",
+ " for section in sections.values():",
+ " if section.get('name') == 'section_run':",
+ " found_section_run = True",
+ " section_run_sections = section.get('sections')",
+ " gIndexRun = section.get('gIndex')",
+ " if section_run_sections is not None and gIndexRun is not None:",
+ " # extract all occurrences of section_system_description",
+ " for section_run_section in section_run_sections.values():",
+ " if section_run_section.get(",
+ " 'name') == 'section_system':",
+ " # if section_run_section.get('name') ==",
+ " # 'section_system_description':",
+ " found_section_system_description = True",
+ " gIndexDesc = section_run_section.get('gIndex')",
+ " section_system_descriptions[",
+ " gIndexRun, gIndexDesc] = section_run_section",
+ " else:",
+ " raise Exception(\"Could not find key 'sections' or 'gIndex' in section_run!\")",
+ "",
+ " if not found_section_run:",
+ " raise Exception(\"Could not find any section_run!\")",
+ " else:",
+ " raise Exception(\"Could not find key 'sections' in JSON file!\")",
+ "",
+ " self.gIndexRunMax = gIndexRun",
+ " self.gIndexDescMax = gIndexDesc",
+ " return section_system_descriptions",
+ "",
+ " def _get_single_config_calc(self, json_dict):",
+ " \"\"\"Extract _get_single_config_calc from JSON dictionary (to obtain the energy in this case).",
+ " It is the analogue of ' _get_system_descriptions', but for the single_config_calc section.",
+ " Args:",
+ " json_dict: JSON dictionary containing parsed data.",
+ " Returns:",
+ " Dictionaries of _get_single_config_calc for each section_run as dictionary.",
+ " The keys are a tuple (gIndexRun, gIndexSingle) of the different section_run and section_single_configuration_calculation, respectively.",
+ " \"\"\"",
+ "",
+ " # old format",
+ " # for section in sections",
+ "",
+ " found_section_run = False",
+ " sections = json_dict.get('sections')",
+ " section_single_config_calc = {}",
+ "",
+ " # read section_run and for each section_run read section_system_description",
+ " # gIndexRun: gIndex for section_run",
+ " # gIndexDesc: gIndex for single_config_calc",
+ "",
+ " if sections is not None:",
+ " for section in sections.values():",
+ " if section.get('name') == 'section_run':",
+ " found_section_run = True",
+ " section_run_sections = section.get('sections')",
+ " gIndexRun = section.get('gIndex')",
+ "",
+ " if section_run_sections is not None and gIndexRun is not None:",
+ " # extract all occurrences of",
+ " # section_single_configuration_calculation",
+ " for section_run_section in section_run_sections.values():",
+ " if section_run_section.get(",
+ " 'name') == 'section_single_configuration_calculation':",
+ " found_section_single_configuration_calculation = True",
+ " gIndexSingle = section_run_section.get(",
+ " 'gIndex')",
+ " section_single_config_calc[",
+ " gIndexRun, gIndexSingle] = section_run_section",
+ " else:",
+ " raise Exception(",
+ " \"Could not find key 'sections' or 'gIndex' in section_run!\")",
+ " if not found_section_run:",
+ " raise Exception(\"Could not find any section_run!\")",
+ " else:",
+ " raise Exception(\"Could not find key 'sections' in JSON file!\")",
+ " return section_single_config_calc",
+ "",
+ " def write_geometry(",
+ " self,",
+ " path=None,",
+ " filename_suffix='_aims.in',",
+ " format='aims',",
+ " operation_number=0):",
+ " \"\"\"Writes the coordinates of the structure as text file with the writing routine of ASE.",
+ "",
+ " Parameters",
+ " ----------",
+ " path : string, optional, default `geo_path`",
+ " Path to the folder where the geometry files are written",
+ "",
+ " filename_suffix : string, default '_aims.in'",
+ " Suffix added after filename",
+ "",
+ " format : string, optional, default 'aims'",
+ " Format of the file to be written. Must be a valid ASE format",
+ " (see https://wiki.fysik.dtu.dk/ase/ase/io/io.html#module-ase.io)",
+ "",
+ " \"\"\"",
+ " # define the default path as geo_path",
+ " if path is None:",
+ " path = self.geo_path",
+ "",
+ " if self.file_format == 'NOMAD':",
+ " for (gIndexRun, gIndexDesc), atoms in self.atoms.items():",
+ " if atoms is not None:",
+ " # filename is the normalized absolute path",
+ " filename = os.path.abspath(",
+ " os.path.normpath(",
+ " os.path.join(",
+ " path, '%s_%d_%d_op%d%s' %",
+ " (self.name, gIndexRun, gIndexDesc, operation_number, filename_suffix))))",
+ " ",
+ " atoms.write(filename, format=format)",
+ "",
+ " # store the normalized absolute path to the geometry file",
+ " # in the class",
+ " if configs[\"isBeaker\"] == \"True\":",
+ "# if False:",
+ " # only for Beaker Notebook",
+ " filename = os.path.abspath(",
+ " os.path.normpath(",
+ " os.path.join(",
+ " '/user/tmp/', '%s_%d_%d_op%d%s' %",
+ " (self.name, gIndexRun, gIndexDesc, operation_number, filename_suffix))))",
+ " else:",
+ " # to run locally",
+ " filename = os.path.abspath(",
+ " os.path.normpath(",
+ " os.path.join(",
+ " path, '%s_%d_%d_op%d%s' %",
+ " (self.name, gIndexRun, gIndexDesc, operation_number, filename_suffix))))",
+ "",
+ " self.geo_file[gIndexRun, gIndexDesc] = filename",
+ "",
+ "",
+ " else:",
+ " raise Exception(",
+ " \"Please specify a valid file format. Possible file formats are 'NOMAD' or 'rdf'.\")",
+ "",
+ " def write_png(",
+ " self,",
+ " path=None,",
+ " filename_suffix='.png',",
+ " replicas=None,",
+ " rotation=None,",
+ " operation_number=0):",
+ " ",
+ " \"\"\"Write png images for the structures read from the JSON files. Builds a 4x4x4 supercell",
+ " if the structure is periodic.",
+ "",
+ "",
+ " Parameters",
+ " ----------",
+ " path : string, optional, default `png_path`",
+ " Path to the folder where the geometry files are written",
+ "",
+ " filename_suffix : string, default '.png'",
+ " Suffix added after filename",
+ "",
+ " replicas: list of 3 integers, default [4,4,4]",
+ " Number of replicas in each direction. Used only if `isPeriodic` is `True`.",
+ "",
+ " \"\"\"",
+ " # define the default path as geo_path",
+ " if path is None:",
+ " path = self.png_path",
+ "",
+ " if rotation:",
+ " rot = '10z,-80x'",
+ " else:",
+ " rot = '0x, 0y, 0z'",
+ "",
+ " filename_list = []",
+ "",
+ " if self.file_format == 'NOMAD':",
+ " for (gIndexRun, gIndexDesc), atoms in self.atoms.items():",
+ " if atoms is not None:",
+ " # filename is the normalized absolute path",
+ " filename = os.path.abspath(",
+ " os.path.normpath(",
+ " os.path.join(",
+ " path, '%s_%d_%d_op%d_geometry_thumbnail%s' %",
+ " (self.name, gIndexRun, gIndexDesc, operation_number, filename_suffix))))",
+ "",
+ " # if it is periodic, replicate according to the vector",
+ " # replicas",
+ " if self.isPeriodic:",
+ " # set the default to 4 replicas in each direction",
+ " if replicas is None:",
+ " replicas = (4, 4, 4)",
+ " else:",
+ " replicas = (1, 1, 1)",
+ "",
+ " atoms = atoms * replicas",
+ "",
+ " # View used to start ag, and find desired viewing angle",
+ " # rot = '35x,63y,36z' # found using ag: 'view -> rotate'",
+ "",
+ " # Common kwargs for eps, png, pov",
+ " kwargs = {",
+ " # text string with rotation (default='' )",
+ " 'rotation': rot,",
+ " 'radii': .50, # float, or a list with one float per atom",
+ " 'colors': None, # List: one (r, g, b) tuple per atom",
+ " 'show_unit_cell': 0, # 0, 1, or 2 to not show, show, and show all of cell",
+ " 'scale': 100,",
+ " }",
+ "",
+ " atoms.write(filename, format='png', **kwargs)",
+ "",
+ " if configs[\"isBeaker\"] == \"True\":",
+ " # only for Beaker Notebook",
+ " filename = os.path.abspath(",
+ " os.path.normpath(",
+ " os.path.join(",
+ " '/user/tmp/', '%s_%d_%d_op%d_geometry_thumbnail%s' %",
+ " (self.name, gIndexRun, gIndexDesc, operation_number, filename_suffix))))",
+ " else:",
+ " # to run locally",
+ " filename = os.path.abspath(",
+ " os.path.normpath(",
+ " os.path.join(",
+ " path, '%s_%d_%d_op%d_geometry_thumbnail%s' %",
+ " (self.name, gIndexRun, gIndexDesc, operation_number, filename_suffix))))",
+ "",
+ " # store the normalized absolute path to the png file in the",
+ " # class",
+ " self.png_file[gIndexRun, gIndexDesc] = filename",
+ "",
+ " filename_list.append(filename)",
+ "",
+ " else:",
+ " logger.error(\"Could not find atoms in %s\" % self.name)",
+ "",
+ " else:",
+ " logger.error(",
+ " \"Please specify a valid file format. Possible formats are 'NOMAD' or 'rdf'.\")",
+ " ",
+ " return filename_list",
+ "",
+ "",
+ " def _calc_rdf(self, gIndexRun, gIndexDesc, maxR, is_prdf=None):",
+ " \"\"\"Returns the radial distribution function of a single (user specified) frame given a NOMADstructure.",
+ " This function was written by Fawzi Mohamed.",
+ " Args:",
+ " gIndexRun: int. run index of the frame (usually 0)",
+ " gIndexDesc: int. system_description index of the frame",
+ " maxR: float. cut-off radius up to which the atom distances are considered",
+ " is_prdf: bool. If true calculates partial radial distribution function.",
+ " If false calculates radial distribution function (all atom types are the same)",
+ " Returns:",
+ " radD: radial distribution function for a single frame with gIndexRun=gIndexRun and gIndexDesc=gIndexDesc",
+ " Note:",
+ " cell vectors v1,v2,v3 with values in the columns: [[v1x,v2x,v3x],[v1y,v2y,v3x],[v1z,v2z,v3z]]",
+ " \"\"\"",
+ " if is_prdf is None:",
+ " is_prdf = True",
+ "",
+ " if self.isPeriodic:",
+ " # in the metadata, the simulation_cell has lattice vectors as columns, ASE has them as rows",
+ " # in the NOMADstructure the cell has been trasposed from the metadata => lattice vectors are as rows",
+ " # calc_rdf needs lattice vectors as colulmns => transpose again",
+ " cell = self.atoms[gIndexRun, gIndexDesc].get_cell()",
+ "# cell = np.transpose(cell)",
+ " atoms = self.atoms[gIndexRun, gIndexDesc]",
+ " positions = self.atoms[",
+ " gIndexRun,",
+ " gIndexDesc].get_positions(",
+ " wrap=True)",
+ " maxR2 = maxR * maxR",
+ "",
+ " radD = {}",
+ " for ii, a1 in enumerate(atoms):",
+ " for jj, a2 in enumerate(atoms[ii:]):",
+ "",
+ " # write atomic numbers if prdf, otherwise set them to zero",
+ " if is_prdf:",
+ " n1 = a1.number",
+ " n2 = a2.number",
+ " else:",
+ " n1 = 0",
+ " n2 = 0",
+ "",
+ " label = \"%d_%d\" % (min(n1, n2), max(n1, n2))",
+ " if label not in radD:",
+ " radD[label] = {",
+ " \"particle_atom_numer_1\": n1,",
+ " \"particle_atom_numer_2\": n2,",
+ " \"arr\": []",
+ " }",
+ " arr = radD[label][\"arr\"]",
+ " r0 = np.array([a1.x - a2.x, a1.y - a2.y, a1.z - a2.z])",
+ " r02 = np.dot(r0, r0)",
+ " r = r02 - maxR2",
+ " m = np.dot(cell.transpose(), cell)",
+ " l = np.dot(r0, cell)",
+ " r = np.dot(r0, r0) - maxR2",
+ " mii = m[0, 0]",
+ " mij = m[0, 1]",
+ " mik = m[0, 2]",
+ " mjj = m[1, 1]",
+ " mjk = m[1, 2]",
+ " mkk = m[2, 2]",
+ " li = l[0]",
+ " lj = l[1]",
+ " lk = l[2]",
+ " c = (",
+ " mjj**2 *",
+ " mkk**3 *",
+ " r -",
+ " 2 *",
+ " mjj *",
+ " mjk**2 *",
+ " mkk**2 *",
+ " r +",
+ " mjk**4 *",
+ " mkk *",
+ " r -",
+ " lj**2 *",
+ " mjj *",
+ " mkk**3 +",
+ " lj**2 *",
+ " mjk**2 *",
+ " mkk**2 +",
+ " 2 *",
+ " lj *",
+ " lk *",
+ " mjj *",
+ " mjk *",
+ " mkk**2 -",
+ " lk**2 *",
+ " mjj**2 *",
+ " mkk**2 -",
+ " 2 *",
+ " lj *",
+ " lk *",
+ " mjk**3 *",
+ " mkk +",
+ " lk**2 *",
+ " mjj *",
+ " mjk**2 *",
+ " mkk)",
+ " a = (",
+ " mii *",
+ " mjj**2 *",
+ " mkk**3 -",
+ " mij**2 *",
+ " mjj *",
+ " mkk**3 -",
+ " 2 *",
+ " mii *",
+ " mjj *",
+ " mjk**2 *",
+ " mkk**2 +",
+ " mij**2 *",
+ " mjk**2 *",
+ " mkk**2 +",
+ " 2 *",
+ " mij *",
+ " mik *",
+ " mjj *",
+ " mjk *",
+ " mkk**2 -",
+ " mik**2 *",
+ " mjj**2 *",
+ " mkk**2 +",
+ " mii *",
+ " mjk**4 *",
+ " mkk -",
+ " 2 *",
+ " mij *",
+ " mik *",
+ " mjk**3 *",
+ " mkk +",
+ " mik**2 *",
+ " mjj *",
+ " mjk**2 *",
+ " mkk)",
+ " b = (",
+ " 2 *",
+ " li *",
+ " mjj**2 *",
+ " mkk**3 -",
+ " 2 *",
+ " lj *",
+ " mij *",
+ " mjj *",
+ " mkk**3 -",
+ " 4 *",
+ " li *",
+ " mjj *",
+ " mjk**2 *",
+ " mkk**2 +",
+ " 2 *",
+ " lj *",
+ " mij *",
+ " mjk**2 *",
+ " mkk**2 +",
+ " 2 *",
+ " lj *",
+ " mik *",
+ " mjj *",
+ " mjk *",
+ " mkk**2 +",
+ " 2 *",
+ " lk *",
+ " mij *",
+ " mjj *",
+ " mjk *",
+ " mkk**2 -",
+ " 2 *",
+ " lk *",
+ " mik *",
+ " mjj**2 *",
+ " mkk**2 +",
+ " 2 *",
+ " li *",
+ " mjk**4 *",
+ " mkk -",
+ " 2 *",
+ " lj *",
+ " mik *",
+ " mjk**3 *",
+ " mkk -",
+ " 2 *",
+ " lk *",
+ " mij *",
+ " mjk**3 *",
+ " mkk +",
+ " 2 *",
+ " lk *",
+ " mik *",
+ " mjj *",
+ " mjk**2 *",
+ " mkk)",
+ "",
+ " delta = b * b - 4 * a * c",
+ "",
+ " if (a == 0 or delta < 0):",
+ " continue",
+ " sDelta = math.sqrt(delta)",
+ " imin = int(math.ceil((-b - sDelta) / (2 * a)))",
+ " imax = int(math.floor((-b + sDelta) / (2 * a)))",
+ " for i in range(imin, imax + 1):",
+ " cj = (mkk * r + i**2 * mii * mkk + 2 * i * li *",
+ " mkk - i**2 * mik**2 - 2 * i * lk * mik - lk**2)",
+ " aj = (mjj * mkk - mjk**2)",
+ " bj = (2 * i * mij * mkk + 2 * lj * mkk -",
+ " 2 * i * mik * mjk - 2 * lk * mjk)",
+ " deltaj = bj * bj - 4 * aj * cj",
+ " if (aj == 0 or deltaj < 0):",
+ " continue",
+ " sDeltaj = math.sqrt(deltaj)",
+ " jmin = int(math.ceil((-bj - sDeltaj) / (2 * aj)))",
+ " jmax = int(math.floor((-bj + sDeltaj) / (2 * aj)))",
+ " for j in range(jmin, jmax + 1):",
+ " ck = r + j**2 * mjj + 2 * i * j * mij + i**2 * mii + 2 * j * lj + 2 * i * li",
+ " ak = mkk",
+ " bk = (2 * j * mjk + 2 * i * mik + 2 * lk)",
+ " deltak = bk * bk - 4 * ak * ck",
+ " if (ak == 0 or deltak < 0):",
+ " continue",
+ " sDeltak = math.sqrt(deltak)",
+ " kmin = int(math.ceil((-bk - sDeltak) / (2 * ak)))",
+ " kmax = int(math.floor((-bk + sDeltak) / (2 * ak)))",
+ " for k in range(kmin, kmax + 1):",
+ " if (jj != 0 or i != 0 or j != 0 or k != 0):",
+ " rr = r02 + k**2 * mkk + k * \\",
+ " (2 * j * mjk + 2 * i * mik + 2 * lk) + j**2 * mjj + 2 * i * j * mij + i**2 * mii + 2 * j * lj + 2 * i * li",
+ " arr.append(math.sqrt(rr))",
+ " wFact = 4 * math.pi * len(atoms) / abs(np.linalg.det(cell))",
+ " for k, v in radD.items():",
+ " v[\"arr\"].sort()",
+ " v[\"weights\"] = map(lambda r: 1.0 / (wFact * r * r), v[\"arr\"])",
+ " return radD",
+ "",
+ " def write_rdf(",
+ " self,",
+ " path=None,",
+ " filename_suffix='.json',",
+ " maxR=None,",
+ " is_prdf=None):",
+ " \"\"\"Write a JSON file with structure info and radial distribution functions of all the frames in the NOMADstructure",
+ "",
+ " One json file is generated for each NOMADjson file. If the NOMADjson file contains multiple frames,",
+ " the partial radial distribution functions of different frames are appended.",
+ "",
+ " Parameters",
+ " ----------",
+ " path : string",
+ " Path to the folder where the rdf file is written",
+ "",
+ " filename_suffix : string, default '.json'",
+ " Suffix added after filename (the filename is the NoMaD database unique identifier)",
+ "",
+ " replicas : list of 3 integers, default [4,4,4]",
+ " Number of replicas in each direction. Used only if `isPeriodic` is `True`.",
+ "",
+ " maxR : float, default 25",
+ " Cut-off radius in Angstrom up to which the atom distances are considered",
+ "",
+ " .. todo:: Add BIN_COUNT to parameters.",
+ "",
+ " is_prdf : bool, default `True`",
+ " If `True` calculates partial radial distribution function.",
+ " If `False` calculates radial distribution function (all atom types are the same)",
+ "",
+ "",
+ " Returns",
+ " -------",
+ "",
+ " filename : string",
+ " Absolute path where the file with the partial radial distribution function(s) is written.",
+ "",
+ "",
+ " \"\"\"",
+ "",
+ " if self.isPeriodic:",
+ " filename = os.path.abspath(",
+ " os.path.normpath(",
+ " os.path.join(",
+ " path, '%s%s' %",
+ " (self.name, filename_suffix))))",
+ " self.rdf_file = filename",
+ " outF = file(filename, 'w')",
+ " outF.write(\"\"\"",
+ " {",
+ " \"data\":[\"\"\")",
+ "",
+ " for (gIndexRun, gIndexDesc), atoms in self.atoms.items():",
+ " if atoms is not None:",
+ " # filename is the normalized absolute path",
+ " # filename = os.path.abspath(os.path.normpath(os.path.join(path, '%s_%d_%d%s' % (self.name, gIndexRun, gIndexDesc, filename_suffix))))",
+ " # store the normalized absolute path to the rdf file in the class",
+ " # self.rdf_file[gIndexRun, gIndexDesc] = filename",
+ "",
+ " cell = self.atoms[gIndexRun, gIndexDesc].get_cell()",
+ "# cell = np.transpose(cell)",
+ " atoms = self.atoms[gIndexRun, gIndexDesc]",
+ " positions = self.atoms[",
+ " gIndexRun, gIndexDesc].get_positions(",
+ " wrap=True)",
+ " energy_total__eV = self.energy_total__eV[gIndexRun, gIndexDesc]",
+ " energy_total = self.energy_total[gIndexRun, gIndexDesc]",
+ "",
+ " writeColon = False",
+ "",
+ " rdf = self._calc_rdf(",
+ " gIndexRun=gIndexRun,",
+ " gIndexDesc=gIndexDesc,",
+ " maxR=25,",
+ " is_prdf=is_prdf)",
+ " res = {",
+ " \"calc_id\": 'NaN',",
+ " \"checksum\": self.name,",
+ " \"energy_total\": energy_total,",
+ " \"energy_total__eV\": energy_total__eV,",
+ " \"path\": self.rdf_file,",
+ " \"step\": gIndexDesc,",
+ " \"final\": 'NaN',",
+ " \"struct_id\": 'NaN',",
+ " \"cell\": cell.tolist(),",
+ " \"particle_atom_number\": map(",
+ " lambda x: x.number,",
+ " atoms),",
+ " \"particle_position\": map(",
+ " lambda x: [",
+ " x.x,",
+ " x.y,",
+ " x.z],",
+ " atoms),",
+ " \"radial_distribution_function\": rdf}",
+ " if (writeColon):",
+ " outF.write(\", \")",
+ " writeColon = True",
+ " json.dump(res, outF, indent=2)",
+ " outF.write(\"\"\"",
+ " ] }\"\"\")",
+ " outF.flush()",
+ "",
+ " else:",
+ " raise Exception(",
+ " \"File {0} is a non-periodic structure. The radial distribution function is \\ncurrently implemented only for periodic systems.\".format(self.in_file))",
+ "",
+ " # only 1 filename because all the frames are in the same file",
+ " return filename",
+ "",
+ " def write_xray(",
+ " self,",
+ " path=None,",
+ " filename_suffix='_xray.png',",
+ " replicas=None,",
+ " grayscale=True,",
+ " user_param_source=None,",
+ " user_param_detector=None,",
+ " rotation=None,",
+ " angles_d=None):",
+ " \"\"\"Write xray images for the structures read from the JSON files. Builds a 4x4x4 supercell",
+ " if the structure is periodic.",
+ "",
+ " Parameters",
+ " ----------",
+ " path : string, optional, default `xray_path`",
+ " Path to the folder where the xray files are written",
+ "",
+ " filename_suffix : string, default '_xray.png'",
+ " Suffix added after filename",
+ "",
+ " replicas: list of 3 integers, default [4,4,4]",
+ " Number of replicas in each direction. Used only if `isPeriodic` is `True`.",
+ "",
+ " Returns",
+ " -------",
+ "",
+ " filename_list : string or list",
+ " Xray file (or list of xray files) generated from the file. It is a list if multiple",
+ " frames are present.",
+ "",
+ " \"\"\"",
+ "",
+ " filename_list = []",
+ "",
+ " # define the default path as xray_path",
+ " if path is None:",
+ " path = self.xray_path",
+ "",
+ " param_source = {",
+ " 'wavelength': 1.0E-11,",
+ " 'pulse_energy': 1.6022e-14,",
+ " 'focus_diameter': 1E-6",
+ " }",
+ "",
+ " param_detector = {",
+ " 'distance': 0.10,",
+ " 'pixel_size': 16E-5,",
+ " 'nx': 28,",
+ " 'ny': 28",
+ " }",
+ "",
+ " if user_param_source is not None:",
+ " param_source.update(user_param_source)",
+ "",
+ " if user_param_detector is not None:",
+ " param_detector.update(user_param_detector)",
+ "",
+ " if not rotation:",
+ " angles_d = [0.0]",
+ "",
+ " # logger.debug(\"Source parameters \\n {0}\".format(param_source))",
+ " # logger.debug(\"Detector parameters \\n {0}\".format(param_source))",
+ "",
+ " if (self.file_format == 'NOMAD') or (self.file_format == 'xyz'):",
+ " for (gIndexRun, gIndexDesc), atoms in self.atoms.items():",
+ " if atoms is not None:",
+ "",
+ " # if it is periodic, replicate according to the vector",
+ " # replicas",
+ " if self.isPeriodic:",
+ " # set the default to 4 replicas in each direction",
+ " if replicas is None:",
+ " replicas = (4, 4, 4)",
+ " else:",
+ " replicas = (1, 1, 1)",
+ "",
+ " atoms = atoms * replicas",
+ "",
+ " # Source",
+ " src = condor.Source(**param_source)",
+ "",
+ " # Detector",
+ " det = condor.Detector(**param_detector)",
+ "",
+ " # Atoms",
+ " atomic_numbers = map(lambda x: x.number, atoms)",
+ "",
+ " # convert Angstrom to m (CONDOR uses meters)",
+ " atomic_positions = map(",
+ " lambda x: [",
+ " x.x * 1E-10,",
+ " x.y * 1E-10,",
+ " x.z * 1E-10],",
+ " atoms)",
+ "",
+ " for angle_d in angles_d:",
+ " # filename is the normalized absolute path",
+ " filename_xray = os.path.abspath(",
+ " os.path.normpath(",
+ " os.path.join(",
+ " path, '%s_%d_%d_%d%s' %",
+ " (self.name, gIndexRun, gIndexDesc, angle_d, filename_suffix))))",
+ " filename_rs = os.path.abspath(",
+ " os.path.normpath(",
+ " os.path.join(",
+ " path, '%s_%d_%d_%d%s' %",
+ " (self.name, gIndexRun, gIndexDesc, angle_d, '_xray_rs.png'))))",
+ " filename_ph = os.path.abspath(",
+ " os.path.normpath(",
+ " os.path.join(",
+ " path, '%s_%d_%d_%d%s' %",
+ " (self.name, gIndexRun, gIndexDesc, angle_d, '_xray_ph.png'))))",
+ " filename_npy = os.path.abspath(",
+ " os.path.normpath(",
+ " os.path.join(",
+ " path, '%s_%d_%d_%d%s' %",
+ " (self.name, gIndexRun, gIndexDesc, angle_d, '.npy'))))",
+ "",
+ " angle = angle_d / 360. * 2 * np.pi",
+ " rotation_axis = np.array([0., 0., 1.])/np.sqrt(1.)",
+ " #rotation_axis = np.array([1., 1., 1.]) / np.sqrt(3.)",
+ " quaternion = condor.utils.rotation.quat(",
+ " angle, rotation_axis[0], rotation_axis[1], rotation_axis[2])",
+ " rotation_values = np.array([quaternion])",
+ " rotation_formalism = \"quaternion\"",
+ " rotation_mode = \"extrinsic\"",
+ "",
+ " par = condor.ParticleAtoms(",
+ " atomic_numbers=atomic_numbers,",
+ " atomic_positions=atomic_positions,",
+ " rotation_values=rotation_values,",
+ " rotation_formalism=rotation_formalism,",
+ " rotation_mode=rotation_mode)",
+ "",
+ " s = \"particle_atoms\"",
+ " E = condor.Experiment(src, {s: par}, det)",
+ " res = E.propagate()",
+ "",
+ " real_space = np.fft.fftshift(",
+ " np.fft.ifftn(",
+ " np.fft.fftshift(",
+ " res[\"entry_1\"][\"data_1\"][\"data_fourier\"])))",
+ " intensity_pattern = res[\"entry_1\"][\"data_1\"][\"data\"]",
+ " fourier_space = res[\"entry_1\"][",
+ " \"data_1\"][\"data_fourier\"]",
+ " phases = np.angle(fourier_space) % (2 * np.pi)",
+ " # vmin = np.log10(res[\"entry_1\"][\"data_1\"][\"data\"].max()/10000.)",
+ "",
+ " # scaler = preprocessing.StandardScaler().fit(intensity_pattern)",
+ " # intensity_pattern = scaler.transform(intensity_pattern)",
+ "",
+ " # intensity_pattern = np.log10(intensity_pattern)",
+ "",
+ " # real space image",
+ " # np.save(filename_npy, rs8)",
+ "",
+ " if grayscale:",
+ " I8 = (((intensity_pattern -",
+ " intensity_pattern.min()) /",
+ " (intensity_pattern.max() -",
+ " intensity_pattern.min())) *",
+ " 255.0).astype(np.uint8)",
+ " rs8 = (((real_space -",
+ " real_space.min()) /",
+ " (real_space.max() -",
+ " real_space.min())) *",
+ " 255.0).astype(np.uint8)",
+ " ph8 = (((phases - phases.min()) / (phases.max() -",
+ " phases.min())) * 255.0).astype(np.uint8)",
+ "",
+ " img = Image.fromarray(I8)",
+ " img.save(filename_xray)",
+ "",
+ " img = Image.fromarray(rs8)",
+ " img.save(filename_rs)",
+ "",
+ " img = Image.fromarray(ph8)",
+ " img.save(filename_ph)",
+ "",
+ " np.save(filename_npy, I8)",
+ " # np.save(filename_npy, ph8)",
+ "",
+ " else:",
+ " pypl.imsave(",
+ " filename_xray, np.log10(intensity_pattern))",
+ " np.save(filename_npy, intensity_pattern)",
+ " # pypl.imsave(filename_xray, np.log10(intensity_pattern), vmin=vmin)",
+ " pypl.imsave(filename_ph, phases)",
+ " pypl.imsave(filename_rs, abs(real_space))",
+ "",
+ "# the Viewer with xray files will not work",
+ "# if configs[\"isBeaker\"] == \"True\":",
+ "# # only for Beaker Notebook",
+ "# filename_xray = os.path.abspath(",
+ "# os.path.normpath(",
+ "# os.path.join(",
+ "# '/user/tmp/', '%s_%d_%d_%d%s' %",
+ "# (self.name, gIndexRun, gIndexDesc, angle_d, filename_suffix))))",
+ "",
+ " # store the normalized absolute path to the png file in",
+ " # the class",
+ " self.xray_file[gIndexRun, gIndexDesc] = filename_xray",
+ " self.xray_npy_file[",
+ " gIndexRun, gIndexDesc] = filename_npy",
+ " self.xray_rs_file[gIndexRun, gIndexDesc] = filename_rs",
+ "",
+ " filename_list.append(filename_xray)",
+ " filename_list.append(filename_npy)",
+ " filename_list.append(filename_rs)",
+ "",
+ " else:",
+ " raise Exception(\"Could not find atoms in %s\" % self.name)",
+ "",
+ " else:",
+ " raise Exception(",
+ " \"Please specify a valid file format. Possible format is 'NOMAD'.\")",
+ "",
+ " return filename_list",
+ "",
+ " def write_target_values(self, path=None, filename_suffix='_target.json',",
+ " target=None, operation_number=0):",
+ " \"\"\"Write target values. One file for each frame.",
+ " The target works only if one frame is considered. Please check.",
+ "",
+ " Parameters",
+ " ----------",
+ " path : string, optional, default `xray_path`",
+ " Path to the folder where the geometry files are written",
+ "",
+ " filename_suffix : string, default '_target.json'",
+ " Suffix added after filename",
+ "",
+ " \"\"\"",
+ "",
+ " filename_list = []",
+ "",
+ " # define the default path as xray_path",
+ " if path is None:",
+ " path = self.xray_path",
+ "",
+ " if (self.file_format == 'NOMAD') or (self.file_format == 'xyz'):",
+ " for (gIndexRun, gIndexDesc), atoms in self.atoms.items():",
+ " if atoms is not None:",
+ " # filename is the normalized absolute path",
+ " filename = os.path.abspath(",
+ " os.path.normpath(",
+ " os.path.join(",
+ " path, '%s_%d_%d_op%d%s' %",
+ " (self.name, gIndexRun, gIndexDesc, operation_number, filename_suffix))))",
+ "",
+ "",
+ " outF = file(filename, 'w')",
+ "",
+ " outF.write(\"\"\"",
+ " {",
+ " \"data\":[\"\"\")",
+ "",
+ " chemical_formula = self.chemical_formula[",
+ " gIndexRun, gIndexDesc]",
+ " cell = self.atoms[gIndexRun, gIndexDesc].get_cell()",
+ "# cell = np.transpose(cell)",
+ " atoms = self.atoms[gIndexRun, gIndexDesc]",
+ " energy_total__eV = self.energy_total__eV[gIndexRun, gIndexDesc]",
+ " energy_total = self.energy_total[gIndexRun, gIndexDesc]",
+ " ",
+ " spacegroup_symbol = {}",
+ " spacegroup_number = {}",
+ " pointgroup_symbol = {}",
+ " crystal_system = {}",
+ " lattice_type = {}",
+ " hall_symbol = {}",
+ " lattice_centering = {}",
+ "",
+ " spacegroup_symbol_actual = {}",
+ " spacegroup_number_actual = {}",
+ " pointgroup_symbol_actual = {}",
+ " crystal_system_actual = {}",
+ " lattice_type_actual = {}",
+ " hall_symbol_actual = {}",
+ " lattice_centering_actual = {}",
+ " ",
+ " # calculate the actual spacegroup of the defective struture",
+ " # get the SpacegroupAnalyzer object from pymatgen ",
+ " symprecs = [1.0E-3, 1.0E-2, 1.0E-1]",
+ " angle_tolerances = [1., 5.]",
+ " ",
+ " spacegroup_analyzer_actual = {} ",
+ " # build a dictionary with different spacegroup analyzers according",
+ " # to the thresholds used",
+ " ",
+ " for symprec in symprecs:",
+ " for angle_tolerance in angle_tolerances:",
+ " spacegroup_analyzer_actual[symprec, angle_tolerance] = SpacegroupAnalyzer(AseAtomsAdaptor.get_structure(atoms),",
+ " symprec=symprec, angle_tolerance=angle_tolerance) ",
+ " ",
+ " self.spacegroup_analyzer_actual[gIndexRun, gIndexDesc] = spacegroup_analyzer_actual",
+ "# self.spacegroup_analyzer_actual[gIndexRun, gIndexDesc] = self.spacegroup_analyzer[gIndexRun, gIndexDesc] ",
+ " ",
+ " # read the dictionary with different spacegroup analyzers ",
+ " # according to the thresholds",
+ " # this is for the pristine parental structure",
+ " for key in self.spacegroup_analyzer[gIndexRun, gIndexDesc]:",
+ " symprec, angle_tolerance = key ",
+ " spacegroup_symbol[str(key)] = self.spacegroup_analyzer[gIndexRun, gIndexDesc][key].get_space_group_symbol() ",
+ " spacegroup_number[str(key)] = self.spacegroup_analyzer[gIndexRun, gIndexDesc][key].get_space_group_number() ",
+ " pointgroup_symbol[str(key)] = self.spacegroup_analyzer[gIndexRun, gIndexDesc][key].get_point_group_symbol() ",
+ " crystal_system[str(key)] = self.spacegroup_analyzer[gIndexRun, gIndexDesc][key].get_crystal_system() ",
+ " # Get the lattice for the structure, e.g., (triclinic, orthorhombic, cubic, etc.).",
+ " #This is the same than the crystal system with the exception of the",
+ " #hexagonal/rhombohedral lattice",
+ " lattice_type[str(key)] = self.spacegroup_analyzer[gIndexRun, gIndexDesc][key].get_lattice_type() ",
+ " hall_symbol[str(key)] = self.spacegroup_analyzer[gIndexRun, gIndexDesc][key].get_hall() ",
+ " lattice_centering[str(key)] = self.spacegroup_analyzer[gIndexRun, gIndexDesc][key].get_space_group_symbol()[0] ",
+ "",
+ " spacegroup_symbol_actual[str(key)] = self.spacegroup_analyzer_actual[gIndexRun, gIndexDesc][key].get_space_group_symbol() ",
+ " spacegroup_number_actual[str(key)] = self.spacegroup_analyzer_actual[gIndexRun, gIndexDesc][key].get_space_group_number() ",
+ " pointgroup_symbol_actual[str(key)] = self.spacegroup_analyzer_actual[gIndexRun, gIndexDesc][key].get_point_group_symbol() ",
+ " crystal_system_actual[str(key)] = self.spacegroup_analyzer_actual[gIndexRun, gIndexDesc][key].get_crystal_system() ",
+ " # Get the lattice for the structure, e.g., (triclinic, orthorhombic, cubic, etc.).",
+ " #This is the same than the crystal system with the exception of the",
+ " #hexagonal/rhombohedral lattice",
+ " lattice_type_actual[str(key)] = self.spacegroup_analyzer_actual[gIndexRun, gIndexDesc][key].get_lattice_type() ",
+ " hall_symbol_actual[str(key)] = self.spacegroup_analyzer_actual[gIndexRun, gIndexDesc][key].get_hall() ",
+ " lattice_centering_actual[str(key)] = self.spacegroup_analyzer_actual[gIndexRun, gIndexDesc][key].get_space_group_symbol()[0] ",
+ " ",
+ " ",
+ " ",
+ " writeColon = False",
+ "",
+ " res = {",
+ " \"checksum\": self.name,",
+ " \"main_json_file_name\": self.in_file,",
+ " \"chemical_formula\": chemical_formula,",
+ " \"energy_total__eV\": energy_total__eV,",
+ " \"energy_total\": energy_total,",
+ " \"gIndexRun\": gIndexRun,",
+ " \"gIndexDesc\": gIndexDesc,",
+ " \"cell\": cell.tolist(),",
+ " \"particle_atom_number\": map(",
+ " lambda x: x.number,",
+ " atoms),",
+ " \"particle_position\": map(",
+ " lambda x: [",
+ " x.x,",
+ " x.y,",
+ " x.z],",
+ " atoms),",
+ " \"filename\": filename,",
+ " \"target\": target,",
+ " ",
+ " # these are dictionaries with key: (symprec, angle_tolerance)",
+ " \"spacegroup_symbol\": spacegroup_symbol,",
+ " \"spacegroup_number\": spacegroup_number,",
+ " \"pointgroup_symbol\": pointgroup_symbol,",
+ " \"crystal_system\": crystal_system,",
+ " \"hall_symbol\": hall_symbol,",
+ " \"lattice_type\": lattice_type,",
+ " \"lattice_centering\": lattice_centering,",
+ "",
+ " \"spacegroup_symbol_actual\": spacegroup_symbol_actual,",
+ " \"spacegroup_number_actual\": spacegroup_number_actual,",
+ " \"pointgroup_symbol_actual\": pointgroup_symbol_actual,",
+ " \"crystal_system_actual\": crystal_system_actual,",
+ " \"hall_symbol_actual\": hall_symbol_actual,",
+ " \"lattice_type_actual\": lattice_type_actual,",
+ " \"lattice_centering_actual\": lattice_centering_actual,",
+ "",
+ " ",
+ "# \"Bravais_lattice_cs\": crystal_system+lattice_centering,",
+ "# \"Bravais_lattice_lt\": lattice_type+lattice_centering,",
+ " ",
+ " #\"symmetry_dataset\": symmetry_dataset,",
+ " \"operation_number\": operation_number,",
+ " }",
+ "",
+ " if (writeColon):",
+ " outF.write(\", \")",
+ "",
+ " writeColon = True",
+ " json.dump(res, outF, indent=2)",
+ "",
+ " outF.write(\"\"\"",
+ " ] }\"\"\")",
+ " outF.flush()",
+ "",
+ " else:",
+ " logger.error(\"Could not find atoms in %s\" % self.name)",
+ "",
+ "",
+ " filename = os.path.abspath(",
+ " os.path.normpath(",
+ " os.path.join(",
+ " path, '%s_%d_%d_op%d%s' %",
+ " (self.name, gIndexRun, gIndexDesc, operation_number, filename_suffix))))",
+ "",
+ " filename_list.append(filename)",
+ "",
+ " else:",
+ " raise Exception(\"Please specify a valid file format.\")",
+ "",
+ " return filename_list"
+ ],
+ "hidden": true
+ },
+ "output": {
+ "state": {},
+ "selectedType": "BeakerDisplay",
+ "pluginName": "IPython",
+ "shellId": "2ED595F8DAE142AD8F34EA76B35AF4BA",
+ "elapsedTime": 5295,
+ "height": 88
+ },
+ "evaluatorReader": true,
+ "lineCount": 1385,
+ "tags": "cell_soap_run",
+ "initialization": true
+ },
{
"id": "codeQ4vsu9",
"type": "code",
@@ -2893,8 +4288,8 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "32B7F85D85DA4B05AC8ABA4FA6E22968",
- "elapsedTime": 641,
+ "shellId": "2ED595F8DAE142AD8F34EA76B35AF4BA",
+ "elapsedTime": 253,
"dataresult": {
"name": "Fe_query",
"timestamp": 1516012342,
@@ -12912,36 +14307,196 @@
"path": "data/2018-01-15 103222 Fe_query.json",
"data": {}
},
- "height": 91
+ "height": 177
},
"evaluatorReader": true,
"lineCount": 55,
- "initialization": true,
"tags": "cell_soap_run"
},
{
- "id": "code5mRsI5",
+ "id": "codeIfeJrQ",
"type": "code",
"evaluator": "IPython",
"input": {
"body": [
- "query_name = options['query']['query_name']",
- "nmd_query_saved = nomad_query.fetch(name_or_index=query_name, resolve=False)",
+ "def _get_structures(",
+ " json_list=None,",
+ " frame_list=None,",
+ " file_format=None,",
+ " png_path=None,",
+ " geo_path=None,",
+ " desc_path=None,",
+ " tmp_folder=None,",
+ " cell_type=None,",
+ " operations_on_structure=None,",
+ " op_list=None,",
+ " descriptor=None,",
+ " atoms_scaling=None):",
+ " \"\"\" Obtain the NOMADstructure from each json file in the json_list;",
+ " write geometry files and figures to disk that will be later used to",
+ " plot the results in the Viewer.",
"",
- "MAX_NB_RES = int(options['query']['max_nb_res']) #for faster computation",
- "MAX_CATEGORIES = 5 #for compatibility with the Viewer",
+ " Parameters",
+ " ----------",
"",
- "# resolve only a limited number of URIs",
- "max_nb_uris = int(options['query']['max_nb_res'])*MAX_CATEGORIES",
+ " json_list : list",
+ " List with the absolute paths to the json files",
"",
- "if nmd_query_saved['uri'] == 0 :",
- " logger.error(\"Your query did not yield any results. Please use another query for the analysis\")",
- " sys.exit()",
+ " frame_list : list or list of list, optional",
+ " For each json file, specifies with frames to consider in the descriptor",
+ " calculation. If multiple json files are present, it is a list of lists.",
"",
- "if len(nmd_query_saved['uri']) > max_nb_uris:",
- " # fix random seeds to have consistent runs",
- " random.seed(42)",
- " nmd_uri_sampled = random.sample(nmd_query_saved['uri'], max_nb_uris)",
+ " file_format : text, optional, default 'NOMAD'",
+ " Specify what is the format of the file to read.",
+ " Possible values: 'NOMAD' and 'rdf' (rdf is deprecated).",
+ "",
+ " png_path : text, optional, default tmp_folder",
+ " Path to the folder where the png file for each structure are written.",
+ "",
+ " geo_path : text, optional, default tmp_folder",
+ " Path to the folder where the png file for each structure are written.",
+ "",
+ " tmp_folder : text",
+ " Temporary folder.",
+ "",
+ " descriptor: object Descriptor",
+ "",
+ "",
+ " Returns",
+ " ----------",
+ "",
+ " structure_list: list, shape (len(json_list), )",
+ " List of NOMADstuctures. Each element in the list is an instance of the",
+ " class NOMADstructure; such instance can contain multiple frames",
+ " (see nomad_structures.py for more detail on the class NOMADstructure).",
+ "",
+ " \"\"\"",
+ "",
+ " structure_list = []",
+ "",
+ " if tmp_folder is None:",
+ " tmp_folder = './tmp'",
+ "",
+ " if geo_path is None:",
+ " geo_path = tmp_folder",
+ "",
+ " if png_path is None:",
+ " png_path = tmp_folder",
+ " ",
+ " if desc_path is None:",
+ " desc_path = tmp_folder",
+ "",
+ " logger.info(\"Generating figures and geometry files.\")",
+ "",
+ " # get unique list of json files ",
+ " # this is important when operations are applied to the json files",
+ " # this does not conserve the order",
+ " #json_list = list(set(json_list))",
+ " # NOTE: we should do something more robust",
+ " new_json_list = []",
+ " for item in json_list:",
+ " if item not in new_json_list:",
+ " new_json_list.append(item)",
+ " ",
+ " json_list = new_json_list",
+ " ",
+ " for idx, json_file in enumerate(json_list):",
+ " # read structure",
+ " if file_format == 'rdf' or file_format == 'NOMAD':",
+ " try:",
+ " # frame_list is a list of lists -> extract the list referring",
+ " # to each JSON file",
+ " frame_list_json = frame_list[idx]",
+ " except:",
+ " # frame_list is a list -> the frame_list_json is the list",
+ " # itself",
+ " frame_list_json = frame_list",
+ "",
+ " # make the first \"pristine\" structure",
+ " structure = NOMADStructure(",
+ " in_file=json_file,",
+ " frame_list=frame_list_json,",
+ " file_format=file_format,",
+ " cell_type=cell_type,",
+ " descriptor=descriptor)",
+ " ",
+ " try:",
+ " structure_op = _apply_operations(structure, operations_on_structure)",
+ " except:",
+ " # do not apply operation",
+ " # this is a hack to visualize non-periodic structures ",
+ " # this is very dangerous, should be changed asap",
+ " structure_op = _apply_operations(structure, operations_on_structure=None)",
+ "",
+ " ",
+ " for op_id, structure in enumerate(structure_op):",
+ " # write coordinates of structure",
+ " structure.write_geometry(path=geo_path, operation_number=op_list[op_id])",
+ " #structure.write_png(path=png_path, replicas=(3, 3, 3), ",
+ " structure.write_png(path=png_path, replicas=(1, 1, 1), ",
+ " rotation=True, operation_number=op_list[op_id])",
+ " ",
+ " # calculate descriptor",
+ " if descriptor is not None:",
+ " descriptor.write(",
+ " structure, path=desc_path, ",
+ " operation_number=op_id,",
+ " atoms_scaling=atoms_scaling)",
+ " ",
+ " ",
+ " else:",
+ " raise Exception(\"Please specify a valid file format. Possible file formats are 'NOMAD' or 'rdf'.\")",
+ "",
+ "",
+ "",
+ " structure_list.append(structure_op)",
+ "",
+ " if idx % (int(len(json_list) / 10) + 1) == 0:",
+ " logger.info(",
+ " \"Generating figures and geometries: file {0}/{1}\".format(idx + 1, len(json_list)))",
+ "",
+ " logger.info(\"Generating figures and geometry files: done.\")",
+ "",
+ " return structure_list"
+ ],
+ "hidden": true
+ },
+ "output": {
+ "state": {},
+ "selectedType": "Hidden",
+ "pluginName": "IPython",
+ "shellId": "2ED595F8DAE142AD8F34EA76B35AF4BA",
+ "elapsedTime": 511,
+ "height": 88
+ },
+ "evaluatorReader": true,
+ "tags": "cell_soap_run",
+ "lineCount": 139,
+ "initialization": true
+ },
+ {
+ "id": "code5mRsI5",
+ "type": "code",
+ "evaluator": "IPython",
+ "input": {
+ "body": [
+ "query_name = options['query']['query_name']",
+ "nmd_query_saved = nomad_query.fetch(name_or_index=query_name, resolve=False)",
+ "",
+ "MAX_NB_RES = int(options['query']['max_nb_res']) #for faster computation",
+ "MAX_CATEGORIES = 5 #for compatibility with the Viewer",
+ "",
+ "# resolve only a limited number of URIs",
+ "max_nb_uris = int(options['query']['max_nb_res'])*MAX_CATEGORIES",
+ "",
+ "if nmd_query_saved['uri'] == 0 :",
+ " logger.error(\"Your query did not yield any results. Please use another query for the analysis\")",
+ " sys.exit()",
+ "",
+ "if len(nmd_query_saved['uri']) > max_nb_uris:",
+ " # fix random seeds to have consistent runs",
+ " random.seed(42)",
+ " nmd_uri_sampled = random.sample(nmd_query_saved['uri'], max_nb_uris)",
"else:",
" nmd_uri_sampled = nmd_query_saved['uri']"
],
@@ -12951,8 +14506,8 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "32B7F85D85DA4B05AC8ABA4FA6E22968",
- "elapsedTime": 296,
+ "shellId": "2ED595F8DAE142AD8F34EA76B35AF4BA",
+ "elapsedTime": 536,
"height": 88
},
"evaluatorReader": true,
@@ -13001,7 +14556,7 @@
" # nomad json files are in SU ",
" \"atom_positions\": map(lambda x: [x.x*1.0E-10,x.y*1.0E-10,x.z*1.0E-10], atoms)",
" }",
- "",
+ " ",
" if atoms.pbc.all():",
" # periodic structure",
" res['simulation_cell'] = (atoms.get_cell()*1.0E-10).tolist()",
@@ -13024,8 +14579,8 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "32B7F85D85DA4B05AC8ABA4FA6E22968",
- "elapsedTime": 322,
+ "shellId": "2ED595F8DAE142AD8F34EA76B35AF4BA",
+ "elapsedTime": 302,
"height": 88
},
"evaluatorReader": true,
@@ -13094,7 +14649,7 @@
" if section['section_name'] == 'section_system':",
" atom_positions = np.array(nmd_dict['atom_positions']['flatData']).reshape(nmd_dict['atom_positions']['shape'])*1.0E+10",
" periodicity = np.array(nmd_dict['configuration_periodic_dimensions'][0]['flatData'], dtype=bool)",
- " ",
+ " ",
" if required_keys == section['required_keys_atom_species']:",
" atom_species = np.array(nmd_dict['atom_species'])",
" elif required_keys == section['required_keys_atom_labels']:",
@@ -13104,16 +14659,16 @@
" ",
" # read cell only if periodicity is all True ",
" # the Gaussian parser for non-periodic systems still the cell (0., 0., 0.) even if there is no cell",
- " if np.all(periodicity): ",
+ " if np.all(periodicity): ",
" try:",
" simulation_cell = np.array(nmd_dict['simulation_cell']['flatData']).reshape(nmd_dict['simulation_cell']['shape'])*1.0E+10",
" except:",
" simulation_cell = None",
" else:",
- " logger.debug(\"Calculation {} is not periodic over 3-dimensions.\".format(nmd))",
- " ",
+ " logger.debug(\"Calculation {} is not periodic over three dimensions.\".format(nmd))",
+ " ",
" # create ASE object",
- " if simulation_cell is not None:",
+ " if np.all(periodicity): ",
" atoms = ase.Atoms(",
" symbols=atom_species, positions=atom_positions,",
" cell=simulation_cell, pbc=True)",
@@ -13121,7 +14676,7 @@
" # calculate spacegroup on-the-fly",
" # use spacegroup as target for crystals",
" try:",
- " spgroup_nb = SpacegroupAnalyzer(AseAtomsAdaptor.get_structure(atoms), symprec=0.001, angle_tolerance=1.).get_space_group_number()",
+ " spgroup_nb = SpacegroupAnalyzer(AseAtomsAdaptor.get_structure(atoms), symprec=0.001).get_space_group_number()",
" except:",
" spgroup_nb = None",
" ",
@@ -13131,14 +14686,14 @@
" else:",
" atoms = ase.Atoms(",
" symbols=atom_species, positions=atom_positions,",
- " cell=None, pbc=False)",
+ " cell=simulation_cell, pbc=False)",
" ",
" # calculate pointgroup on-the-fly",
" # use pointgroup as target for molecules",
- " try:",
- " point_group_symbol = SpacegroupAnalyzer(AseAtomsAdaptor.get_structure(atoms), symprec=0.001, angle_tolerance=1.).get_point_group_symbol()",
- " except:",
- " point_group_symbol = None",
+ " #try:",
+ " point_group_symbol = SpacegroupAnalyzer(AseAtomsAdaptor.get_structure(atoms), symprec=0.001).get_point_group_symbol()",
+ " #except:",
+ " # point_group_symbol = None",
" ",
" atoms.info['point_group_symbol'] = point_group_symbol",
" atoms.info['target'] = point_group_symbol",
@@ -13179,9 +14734,9 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "32B7F85D85DA4B05AC8ABA4FA6E22968",
- "elapsedTime": 2035,
- "height": 88
+ "shellId": "2ED595F8DAE142AD8F34EA76B35AF4BA",
+ "elapsedTime": 7779,
+ "height": 1672
},
"evaluatorReader": true,
"lineCount": 134,
@@ -13269,8 +14824,8 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "32B7F85D85DA4B05AC8ABA4FA6E22968",
- "elapsedTime": 301,
+ "shellId": "2ED595F8DAE142AD8F34EA76B35AF4BA",
+ "elapsedTime": 309,
"height": 88
},
"evaluatorReader": true,
@@ -13312,9 +14867,9 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "32B7F85D85DA4B05AC8ABA4FA6E22968",
- "elapsedTime": 224,
- "height": 88
+ "shellId": "2ED595F8DAE142AD8F34EA76B35AF4BA",
+ "elapsedTime": 201,
+ "height": 62
},
"evaluatorReader": true,
"lineCount": 20,
@@ -13366,8 +14921,8 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "32B7F85D85DA4B05AC8ABA4FA6E22968",
- "elapsedTime": 317,
+ "shellId": "2ED595F8DAE142AD8F34EA76B35AF4BA",
+ "elapsedTime": 306,
"height": 88
},
"evaluatorReader": true,
@@ -13438,615 +14993,2011 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "32B7F85D85DA4B05AC8ABA4FA6E22968",
- "elapsedTime": 9549,
+ "shellId": "2ED595F8DAE142AD8F34EA76B35AF4BA",
+ "elapsedTime": 15397,
"height": 50,
"result": {
"type": "Results",
"outputdata": [
{
"type": "out",
- "value": "\r"
+ "value": "[Kernel] 64 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 64 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 64 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 64 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 70 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 79 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 90 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 94 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 98 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 109 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 116 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 4 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 10 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 17 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 19 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 20 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 25 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 26 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 30 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 33 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 36 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 44 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 49 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 51 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 57 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 71 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 80 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 81 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 83 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 70 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 79 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 90 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 94 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 98 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 109 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 116 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 4 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 10 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 17 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 19 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 20 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 25 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 26 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 30 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 33 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 36 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 44 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 49 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 51 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 57 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 71 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 80 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 81 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 83 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 79 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 90 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 94 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 98 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 109 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 116 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 4 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 10 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 17 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 19 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 20 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 25 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 26 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 30 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 33 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 36 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 44 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 49 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 51 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 57 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 71 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 80 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 81 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 83 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 90 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 94 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 98 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 109 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 116 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 4 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 10 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 17 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 19 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 20 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 25 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 26 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 30 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 33 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 36 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 44 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 49 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 51 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 57 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 71 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 80 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 81 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 83 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 94 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 98 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 109 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 116 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 4 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 10 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 17 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 19 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 20 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 25 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 26 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 30 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 33 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 36 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 44 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 49 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 51 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 57 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 71 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 80 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 81 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 83 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 98 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 109 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 116 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 4 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 10 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 17 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 19 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 20 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 25 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 26 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 30 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 33 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 36 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 44 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 49 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 51 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 57 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 71 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 80 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 81 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 83 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 109 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 116 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 4 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 10 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 17 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 19 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 20 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 25 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 26 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 30 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 33 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 36 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 44 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 49 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 51 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 57 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 71 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 80 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 81 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 83 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 116 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 4 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 10 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 17 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 19 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 20 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 25 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 26 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 30 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 33 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 36 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 44 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 49 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 51 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 57 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 71 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 80 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 81 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 83 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 4 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 10 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 17 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 19 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 20 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 25 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 26 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 30 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 33 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 36 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 44 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 49 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 51 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 57 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 71 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 80 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 81 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 83 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 10 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 17 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 19 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 20 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 25 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 26 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 30 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 33 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 36 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 44 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 49 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 51 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 57 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 71 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 80 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 81 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 83 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 17 118 \n"
},
{
"type": "out",
- "value": "[Graph] 2 \n"
+ "value": "[Kernel] 17 120 \n"
},
{
"type": "out",
- "value": "\r"
+ "value": "[Kernel] 17 121 \n"
},
{
"type": "out",
- "value": "[Graph] 4 \n"
+ "value": "[Kernel] 19 19 \n"
},
{
"type": "out",
- "value": "\r"
+ "value": "[Kernel] 19 20 \n"
},
{
"type": "out",
- "value": "[Graph] 5 \n"
+ "value": "[Kernel] 19 25 \n"
},
{
"type": "out",
- "value": "\r"
+ "value": "[Kernel] 19 26 \n"
},
{
"type": "out",
- "value": "[Graph] 6 \n"
+ "value": "[Kernel] 19 30 \n"
},
{
"type": "out",
- "value": "\r"
+ "value": "[Kernel] 19 33 \n"
},
{
"type": "out",
- "value": "[Graph] 7 \n"
+ "value": "[Kernel] 19 36 \n"
},
{
"type": "out",
- "value": "\r"
+ "value": "[Kernel] 19 44 \n"
},
{
"type": "out",
- "value": "[Graph] 8 \n"
+ "value": "[Kernel] 19 49 \n"
},
{
"type": "out",
- "value": "\r"
+ "value": "[Kernel] 19 51 \n"
},
{
"type": "out",
- "value": "[Graph] 9 \n"
+ "value": "[Kernel] 19 57 \n"
},
{
"type": "out",
- "value": "\r"
+ "value": "[Kernel] 19 71 \n"
},
{
"type": "out",
- "value": "[Graph] 10 \n"
+ "value": "[Kernel] 19 80 \n"
},
{
"type": "out",
- "value": "\r"
+ "value": "[Kernel] 19 81 \n"
},
{
"type": "out",
- "value": "[Graph] 11 \n"
+ "value": "[Kernel] 19 83 \n"
},
{
"type": "out",
- "value": "\r"
+ "value": "[Kernel] 19 89 \n"
},
{
"type": "out",
- "value": "[Graph] 12 \n"
+ "value": "[Kernel] 19 96 \n"
},
{
"type": "out",
- "value": "\r"
+ "value": "[Kernel] 19 106 \n"
},
{
"type": "out",
- "value": "[Graph] 13 \n"
+ "value": "[Kernel] 19 118 \n"
},
{
"type": "out",
- "value": "\r"
+ "value": "[Kernel] 19 120 \n"
},
{
"type": "out",
- "value": "[Graph] 14 \n"
+ "value": "[Kernel] 19 121 \n"
},
{
"type": "out",
- "value": "\r"
+ "value": "[Kernel] 20 20 \n"
},
{
"type": "out",
- "value": "[Graph] 0 \n"
+ "value": "[Kernel] 20 25 \n"
},
{
"type": "out",
- "value": "\r"
+ "value": "[Kernel] 20 26 \n"
},
{
"type": "out",
- "value": "[Graph] 1 \n"
+ "value": "[Kernel] 20 30 \n"
},
{
"type": "out",
- "value": "\r"
+ "value": "[Kernel] 20 33 \n"
},
{
"type": "out",
- "value": "[Graph] 3 \n"
+ "value": "[Kernel] 20 36 \n"
},
{
"type": "out",
- "value": "\u001b[92mComputing kernel ... \u001b[0;1m\n"
+ "value": "[Kernel] 20 44 \n"
},
{
"type": "out",
- "value": "[Kernel] 2 2 \n"
+ "value": "[Kernel] 20 49 \n"
},
{
"type": "out",
- "value": "[Kernel] 2 4 \n"
+ "value": "[Kernel] 20 51 \n"
},
{
"type": "out",
- "value": "[Kernel] 2 5 \n"
+ "value": "[Kernel] 20 57 \n"
},
{
"type": "out",
- "value": "[Kernel] 2 6 \n"
+ "value": "[Kernel] 20 71 \n"
},
{
"type": "out",
- "value": "[Kernel] 2 7 \n"
+ "value": "[Kernel] 20 80 \n"
},
{
"type": "out",
- "value": "[Kernel] 2 8 \n"
+ "value": "[Kernel] 20 81 \n"
},
{
"type": "out",
- "value": "[Kernel] 2 9 \n"
+ "value": "[Kernel] 20 83 \n"
},
{
"type": "out",
- "value": "[Kernel] 2 10 \n"
+ "value": "[Kernel] 20 89 \n"
},
{
"type": "out",
- "value": "[Kernel] 2 11 \n"
+ "value": "[Kernel] 20 96 \n"
},
{
"type": "out",
- "value": "[Kernel] 2 12 \n"
+ "value": "[Kernel] 20 106 \n"
},
{
"type": "out",
- "value": "[Kernel] 2 13 \n"
+ "value": "[Kernel] 20 118 \n"
},
{
"type": "out",
- "value": "[Kernel] 2 14 \n"
+ "value": "[Kernel] 20 120 \n"
},
{
"type": "out",
- "value": "[Kernel] 2 0 \n"
+ "value": "[Kernel] 20 121 \n"
},
{
"type": "out",
- "value": "[Kernel] 2 1 \n"
+ "value": "[Kernel] 25 25 \n"
},
{
"type": "out",
- "value": "[Kernel] 2 3 \n"
+ "value": "[Kernel] 25 26 \n"
},
{
"type": "out",
- "value": "[Kernel] 4 4 \n"
+ "value": "[Kernel] 25 30 \n"
},
{
"type": "out",
- "value": "[Kernel] 4 5 \n"
+ "value": "[Kernel] 25 33 \n"
},
{
"type": "out",
- "value": "[Kernel] 4 6 \n"
+ "value": "[Kernel] 25 36 \n"
},
{
"type": "out",
- "value": "[Kernel] 4 7 \n"
+ "value": "[Kernel] 25 44 \n"
},
{
"type": "out",
- "value": "[Kernel] 4 8 \n"
+ "value": "[Kernel] 25 49 \n"
},
{
"type": "out",
- "value": "[Kernel] 4 9 \n"
+ "value": "[Kernel] 25 51 \n"
},
{
"type": "out",
- "value": "[Kernel] 4 10 \n"
+ "value": "[Kernel] 25 57 \n"
},
{
"type": "out",
- "value": "[Kernel] 4 11 \n"
+ "value": "[Kernel] 25 71 \n"
},
{
"type": "out",
- "value": "[Kernel] 4 12 \n"
+ "value": "[Kernel] 25 80 \n"
},
{
"type": "out",
- "value": "[Kernel] 4 13 \n"
+ "value": "[Kernel] 25 81 \n"
},
{
"type": "out",
- "value": "[Kernel] 4 14 \n"
+ "value": "[Kernel] 25 83 \n"
},
{
"type": "out",
- "value": "[Kernel] 4 0 \n"
+ "value": "[Kernel] 25 89 \n"
},
{
"type": "out",
- "value": "[Kernel] 4 1 \n"
+ "value": "[Kernel] 25 96 \n"
},
{
"type": "out",
- "value": "[Kernel] 4 3 \n"
+ "value": "[Kernel] 25 106 \n"
},
{
"type": "out",
- "value": "[Kernel] 5 5 \n"
+ "value": "[Kernel] 25 118 \n"
},
{
"type": "out",
- "value": "[Kernel] 5 6 \n"
+ "value": "[Kernel] 25 120 \n"
},
{
"type": "out",
- "value": "[Kernel] 5 7 \n"
+ "value": "[Kernel] 25 121 \n"
},
{
"type": "out",
- "value": "[Kernel] 5 8 \n"
+ "value": "[Kernel] 26 26 \n"
},
{
"type": "out",
- "value": "[Kernel] 5 9 \n"
+ "value": "[Kernel] 26 30 \n"
},
{
"type": "out",
- "value": "[Kernel] 5 10 \n"
+ "value": "[Kernel] 26 33 \n"
},
{
"type": "out",
- "value": "[Kernel] 5 11 \n"
+ "value": "[Kernel] 26 36 \n"
},
{
"type": "out",
- "value": "[Kernel] 5 12 \n"
+ "value": "[Kernel] 26 44 \n"
},
{
"type": "out",
- "value": "[Kernel] 5 13 \n"
+ "value": "[Kernel] 26 49 \n"
},
{
"type": "out",
- "value": "[Kernel] 5 14 \n"
+ "value": "[Kernel] 26 51 \n"
},
{
"type": "out",
- "value": "[Kernel] 5 0 \n"
+ "value": "[Kernel] 26 57 \n"
},
{
"type": "out",
- "value": "[Kernel] 5 1 \n"
+ "value": "[Kernel] 26 71 \n"
},
{
"type": "out",
- "value": "[Kernel] 5 3 \n"
+ "value": "[Kernel] 26 80 \n"
},
{
"type": "out",
- "value": "[Kernel] 6 6 \n"
+ "value": "[Kernel] 26 81 \n"
},
{
"type": "out",
- "value": "[Kernel] 6 7 \n"
+ "value": "[Kernel] 26 83 \n"
},
{
"type": "out",
- "value": "[Kernel] 6 8 \n"
+ "value": "[Kernel] 26 89 \n"
},
{
"type": "out",
- "value": "[Kernel] 6 9 \n"
+ "value": "[Kernel] 26 96 \n"
},
{
"type": "out",
- "value": "[Kernel] 6 10 \n"
+ "value": "[Kernel] 26 106 \n"
},
{
"type": "out",
- "value": "[Kernel] 6 11 \n"
+ "value": "[Kernel] 26 118 \n"
},
{
"type": "out",
- "value": "[Kernel] 6 12 \n"
+ "value": "[Kernel] 26 120 \n"
},
{
"type": "out",
- "value": "[Kernel] 6 13 \n"
+ "value": "[Kernel] 26 121 \n"
},
{
"type": "out",
- "value": "[Kernel] 6 14 \n"
+ "value": "[Kernel] 30 30 \n"
},
{
"type": "out",
- "value": "[Kernel] 6 0 \n"
+ "value": "[Kernel] 30 33 \n"
},
{
"type": "out",
- "value": "[Kernel] 6 1 \n"
+ "value": "[Kernel] 30 36 \n"
},
{
"type": "out",
- "value": "[Kernel] 6 3 \n"
+ "value": "[Kernel] 30 44 \n"
},
{
"type": "out",
- "value": "[Kernel] 7 7 \n"
+ "value": "[Kernel] 30 49 \n"
},
{
"type": "out",
- "value": "[Kernel] 7 8 \n"
+ "value": "[Kernel] 30 51 \n"
},
{
"type": "out",
- "value": "[Kernel] 7 9 \n"
+ "value": "[Kernel] 30 57 \n"
},
{
"type": "out",
- "value": "[Kernel] 7 10 \n"
+ "value": "[Kernel] 30 71 \n"
},
{
"type": "out",
- "value": "[Kernel] 7 11 \n"
+ "value": "[Kernel] 30 80 \n"
},
{
"type": "out",
- "value": "[Kernel] 7 12 \n"
+ "value": "[Kernel] 30 81 \n"
},
{
"type": "out",
- "value": "[Kernel] 7 13 \n"
+ "value": "[Kernel] 30 83 \n"
},
{
"type": "out",
- "value": "[Kernel] 7 14 \n"
+ "value": "[Kernel] 30 89 \n"
},
{
"type": "out",
- "value": "[Kernel] 7 0 \n"
+ "value": "[Kernel] 30 96 \n"
},
{
"type": "out",
- "value": "[Kernel] 7 1 \n"
+ "value": "[Kernel] 30 106 \n"
},
{
"type": "out",
- "value": "[Kernel] 7 3 \n"
+ "value": "[Kernel] 30 118 \n"
},
{
"type": "out",
- "value": "[Kernel] 8 8 \n"
+ "value": "[Kernel] 30 120 \n"
},
{
"type": "out",
- "value": "[Kernel] 8 9 \n"
+ "value": "[Kernel] 30 121 \n"
},
{
"type": "out",
- "value": "[Kernel] 8 10 \n"
+ "value": "[Kernel] 33 33 \n"
},
{
"type": "out",
- "value": "[Kernel] 8 11 \n"
+ "value": "[Kernel] 33 36 \n"
},
{
"type": "out",
- "value": "[Kernel] 8 12 \n"
+ "value": "[Kernel] 33 44 \n"
},
{
"type": "out",
- "value": "[Kernel] 8 13 \n"
+ "value": "[Kernel] 33 49 \n"
},
{
"type": "out",
- "value": "[Kernel] 8 14 \n"
+ "value": "[Kernel] 33 51 \n"
},
{
"type": "out",
- "value": "[Kernel] 8 0 \n"
+ "value": "[Kernel] 33 57 \n"
},
{
"type": "out",
- "value": "[Kernel] 8 1 \n"
+ "value": "[Kernel] 33 71 \n"
},
{
"type": "out",
- "value": "[Kernel] 8 3 \n"
+ "value": "[Kernel] 33 80 \n"
},
{
"type": "out",
- "value": "[Kernel] 9 9 \n"
+ "value": "[Kernel] 33 81 \n"
},
{
"type": "out",
- "value": "[Kernel] 9 10 \n"
+ "value": "[Kernel] 33 83 \n"
},
{
"type": "out",
- "value": "[Kernel] 9 11 \n"
+ "value": "[Kernel] 33 89 \n"
},
{
"type": "out",
- "value": "[Kernel] 9 12 \n"
+ "value": "[Kernel] 33 96 \n"
},
{
"type": "out",
- "value": "[Kernel] 9 13 \n"
+ "value": "[Kernel] 33 106 \n"
},
{
"type": "out",
- "value": "[Kernel] 9 14 \n"
+ "value": "[Kernel] 33 118 \n"
},
{
"type": "out",
- "value": "[Kernel] 9 0 \n"
+ "value": "[Kernel] 33 120 \n"
},
{
"type": "out",
- "value": "[Kernel] 9 1 \n"
+ "value": "[Kernel] 33 121 \n"
},
{
"type": "out",
- "value": "[Kernel] 9 3 \n"
+ "value": "[Kernel] 36 36 \n"
},
{
"type": "out",
- "value": "[Kernel] 10 10 \n"
+ "value": "[Kernel] 36 44 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 36 49 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 36 51 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 36 57 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 36 71 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 36 80 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 36 81 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 36 83 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 36 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 36 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 36 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 36 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 36 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 36 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 44 44 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 44 49 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 44 51 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 44 57 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 44 71 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 44 80 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 44 81 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 44 83 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 44 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 44 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 44 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 44 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 44 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 44 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 49 49 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 49 51 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 49 57 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 49 71 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 49 80 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 49 81 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 49 83 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 49 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 49 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 49 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 49 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 49 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 49 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 51 51 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 51 57 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 51 71 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 51 80 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 51 81 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 51 83 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 51 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 51 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 51 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 51 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 51 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 51 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 57 57 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 57 71 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 57 80 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 57 81 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 57 83 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 57 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 57 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 57 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 57 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 57 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 57 121 \n"
},
{
"type": "out",
- "value": "[Kernel] 10 11 \n"
+ "value": "[Kernel] 71 71 \n"
},
{
"type": "out",
- "value": "[Kernel] 10 12 \n"
+ "value": "[Kernel] 71 80 \n"
},
{
"type": "out",
- "value": "[Kernel] 10 13 \n"
+ "value": "[Kernel] 71 81 \n"
},
{
"type": "out",
- "value": "[Kernel] 10 14 \n"
+ "value": "[Kernel] 71 83 \n"
},
{
"type": "out",
- "value": "[Kernel] 10 0 \n"
+ "value": "[Kernel] 71 89 \n"
},
{
"type": "out",
- "value": "[Kernel] 10 1 \n"
+ "value": "[Kernel] 71 96 \n"
},
{
"type": "out",
- "value": "[Kernel] 10 3 \n"
+ "value": "[Kernel] 71 106 \n"
},
{
"type": "out",
- "value": "[Kernel] 11 11 \n"
+ "value": "[Kernel] 71 118 \n"
},
{
"type": "out",
- "value": "[Kernel] 11 12 \n"
+ "value": "[Kernel] 71 120 \n"
},
{
"type": "out",
- "value": "[Kernel] 11 13 \n"
+ "value": "[Kernel] 71 121 \n"
},
{
"type": "out",
- "value": "[Kernel] 11 14 \n"
+ "value": "[Kernel] 80 80 \n"
},
{
"type": "out",
- "value": "[Kernel] 11 0 \n"
+ "value": "[Kernel] 80 81 \n"
},
{
"type": "out",
- "value": "[Kernel] 11 1 \n"
+ "value": "[Kernel] 80 83 \n"
},
{
"type": "out",
- "value": "[Kernel] 11 3 \n"
+ "value": "[Kernel] 80 89 \n"
},
{
"type": "out",
- "value": "[Kernel] 12 12 \n"
+ "value": "[Kernel] 80 96 \n"
},
{
"type": "out",
- "value": "[Kernel] 12 13 \n"
+ "value": "[Kernel] 80 106 \n"
},
{
"type": "out",
- "value": "[Kernel] 12 14 \n"
+ "value": "[Kernel] 80 118 \n"
},
{
"type": "out",
- "value": "[Kernel] 12 0 \n"
+ "value": "[Kernel] 80 120 \n"
},
{
"type": "out",
- "value": "[Kernel] 12 1 \n"
+ "value": "[Kernel] 80 121 \n"
},
{
"type": "out",
- "value": "[Kernel] 12 3 \n"
+ "value": "[Kernel] 81 81 \n"
},
{
"type": "out",
- "value": "[Kernel] 13 13 \n"
+ "value": "[Kernel] 81 83 \n"
},
{
"type": "out",
- "value": "[Kernel] 13 14 \n"
+ "value": "[Kernel] 81 89 \n"
},
{
"type": "out",
- "value": "[Kernel] 13 0 \n"
+ "value": "[Kernel] 81 96 \n"
},
{
"type": "out",
- "value": "[Kernel] 13 1 \n"
+ "value": "[Kernel] 81 106 \n"
},
{
"type": "out",
- "value": "[Kernel] 13 3 \n"
+ "value": "[Kernel] 81 118 \n"
},
{
"type": "out",
- "value": "[Kernel] 14 14 \n"
+ "value": "[Kernel] 81 120 \n"
},
{
"type": "out",
- "value": "[Kernel] 14 0 \n"
+ "value": "[Kernel] 81 121 \n"
},
{
"type": "out",
- "value": "[Kernel] 14 1 \n"
+ "value": "[Kernel] 83 83 \n"
},
{
"type": "out",
- "value": "[Kernel] 14 3 \n"
+ "value": "[Kernel] 83 89 \n"
},
{
"type": "out",
- "value": "[Kernel] 0 0 \n"
+ "value": "[Kernel] 83 96 \n"
},
{
"type": "out",
- "value": "[Kernel] 0 1 \n"
+ "value": "[Kernel] 83 106 \n"
},
{
"type": "out",
- "value": "[Kernel] 0 3 \n"
+ "value": "[Kernel] 83 118 \n"
},
{
"type": "out",
- "value": "[Kernel] 1 1 \n"
+ "value": "[Kernel] 83 120 \n"
},
{
"type": "out",
- "value": "[Kernel] 1 3 \n"
+ "value": "[Kernel] 83 121 \n"
},
{
"type": "out",
- "value": "[Kernel] 3 3 \n"
+ "value": "[Kernel] 89 89 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 89 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 89 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 89 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 89 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 89 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 96 96 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 96 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 96 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 96 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 96 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 106 106 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 106 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 106 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 106 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 118 118 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 118 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 118 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 120 120 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 120 121 \n"
+ },
+ {
+ "type": "out",
+ "value": "[Kernel] 121 121 \n"
}
]
},
@@ -15681,8 +18632,8 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "32B7F85D85DA4B05AC8ABA4FA6E22968",
- "elapsedTime": 3606,
+ "shellId": "2ED595F8DAE142AD8F34EA76B35AF4BA",
+ "elapsedTime": 3870,
"height": 88
},
"evaluatorReader": true,
@@ -15872,8 +18823,8 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "32B7F85D85DA4B05AC8ABA4FA6E22968",
- "elapsedTime": 368,
+ "shellId": "2ED595F8DAE142AD8F34EA76B35AF4BA",
+ "elapsedTime": 370,
"height": 88
},
"evaluatorReader": true,
@@ -15950,15 +18901,16 @@
"",
"# remote tmp_json_folder created",
"shutil.rmtree(tmp_json_folder)"
- ]
+ ],
+ "hidden": true
},
"output": {
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "32B7F85D85DA4B05AC8ABA4FA6E22968",
- "elapsedTime": 1730,
- "height": 88
+ "shellId": "2ED595F8DAE142AD8F34EA76B35AF4BA",
+ "elapsedTime": 5296,
+ "height": 185
},
"evaluatorReader": true,
"lineCount": 64,
@@ -15980,7 +18932,7 @@
"state": {},
"selectedType": "BeakerDisplay",
"pluginName": "JavaScript",
- "elapsedTime": 20,
+ "elapsedTime": 14,
"height": 88
},
"evaluatorReader": true,
@@ -16021,7 +18973,7 @@
"namespace": {
"options": {
"query": {
- "query_name": "",
+ "query_name": "VASP",
"max_nb_res": "25"
},
"run": {
@@ -16131,7 +19083,7 @@
}
}
},
- "viewer_result": "462b47d34c41e56d",
+ "viewer_result": "4a842900a713ed5b",
"last_query_name": "Crystal-C"
},
"locked": true
--
GitLab