diff --git a/SOAP_similarity.bkr b/SOAP_similarity.bkr
index 0c0672538fe2519994b577279f98b66d4b6f0327..d3ebda931f6d32165974236df831452d200d6db2 100644
--- a/SOAP_similarity.bkr
+++ b/SOAP_similarity.bkr
@@ -243,7 +243,7 @@
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
- "height": 72
+ "height": 71
},
"evaluatorReader": true,
"lineCount": 127
@@ -568,11 +568,11 @@
"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 $(\"#\"+bt_tag).toggleClass(\"active\");\n /*if ($(\"#\"+bt_tag).attr(\"clicked\")) {\n $(\"#\"+bt_tag).css('background-color','lightgray');\n $(\"#\"+bt_tag).attr(\"clicked\", 0)\n }\n else {\n $(\"#\"+bt_tag).css('background-color','red');\n $(\"#\"+bt_tag).attr(\"clicked\", 1)\n }*/\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 \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 \"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\": $(\"#atomic_density_use_covrad:checked\").val() == \"true\"\n },\n \"kernel\": {\n \"method\": kernel_method\n },\n \"basekernel\": {\n \"kernel.type\": \"dot\",\n \"kernel.delta\": 1.0,\n \"kernel.xi\": parseFloat($(\"#basekernel_kernel_xi\").val())\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 \"descriptor\": {\n \"soap\": {\n \"spectrum.gradients\": false,\n \"spectrum.2l1_norm\": false,\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.type\": \"dot\",\n \"kernel.adaptor\": adaptor_type,\n \"kernel.delta\": 1.0,\n \"kernel.xi\": parseFloat($(\"#basekernel_kernel_xi\").val()),\n \"exclude_centers\": [],\n \"exclude_targets\": [],\n \"type_list\": [\"C\"]\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 <br> </p><hr style=\"border-width:2px\"> <p></p>\n \n \n <table class=\"glosim_control\">\n \n <!-- DATASETS -->\n <tbody><tr style=\"line-height:40px\">\n <td><b>Dataset examples</b> </td>\n <td>\n <select class=\"select_main\" id=\"dataset_example\">\n <option value=\"zcrs\" onclick=\"allow(0)\" selected=\"\"> Zincblende / Rocksalt </option>\n <option value=\"gdb\" onclick=\"allow(1)\"> GDB7 </option> \n </select>\n <!--button class=\"btn btn-xs active\" onclick='show_hide(\"in_detail_1\")' style=\"border:1;\" >\\></button-->\n <button id=\"toggle_detail_1\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_1", "toggle_detail_1")\">Configure</button>\n <!--button id=\"toggle_detail_1\"type=\"button\" onclick='show_hide(\"in_detail_1\", \"toggle_detail_1\")'>Configure</button-->\n <g id=\"in_detail_1\" hidden=\"\"> Subsample structures <input id=\"exe_batch_size\" value=\"200\" min=\"50\" max=\"1000\" step=\"50\" class=\"in3d\" type=\"number\"> </g>\n </td>\n </tr> \n \n <!-- ATOMIC DENSITY --> \n <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>\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\" value=\"true\" unchecked=\"\" type=\"checkbox\">\n Constant atomic radius (Angstrom) <input id=\"atomic_density_atomic_radius\" value=\"0.5\" min=\"0.0\" max=\"2.0\" step=\"0.1\" class=\"in11f\" type=\"number\"> </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\" value=\"9\" min=\"1\" max=\"14\" step=\"1\" class=\"in11f\" type=\"number\">\n Radial cutoff (equispaced only) <input id=\"soap_radialbasis_Rc\" value=\"3.5\" min=\"0.1\" max=\"10.0\" step=\"0.1\" class=\"in11f\" type=\"number\">\n Radial Gaussian width <input id=\"soap_radialbasis_sigma\" value=\"0.5\" min=\"0.1\" max=\"3.0\" step=\"0.1\" class=\"in11f\" type=\"number\">\n Angular functions L = <input id=\"soap_angularbasis_L\" value=\"6\" min=\"1\" max=\"14\" step=\"1\" class=\"in11f\" type=\"number\"> \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\" value=\"3.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\" type=\"number\">\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\" value=\"1\" min=\"1\" max=\"5\" step=\"1\" class=\"in11f\" type=\"number\">\n Base radius <input id=\"graph:r0\" value=\"1.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\" type=\"number\">\n Scale <input id=\"graph:alpha\" value=\"2.0\" min=\"0.1\" max=\"5.0\" step=\"0.1\" class=\"in11f\" type=\"number\">\n </g>\n </td>\n </tr> \n \n <!-- KERNEL DECOMPOSITION -->\n <tr style=\"line-height:40px\">\n <td><b>Embedding</b> </td>\n <td>\n <select class=\"select_main\" id=\"dimred_method\">\n <option value=\"kernelpca\" selected=\"\"> Kernel PCA </option>\n <option value=\"mds\"> Multi-dimensional scaling </option> \n </select>\n <button id=\"toggle_detail_6\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_6", "toggle_detail_6")\">Configure</button>\n <g id=\"in_detail_6\" hidden=\"\">\n Distance metric (MDS) \n <select id=\"dimred_distance\">\n <option value=\"dot\"> Hypersphere chord </option>\n </select>\n </g>\n </td>\n </tr>\n \n <!-- EXECUTION -->\n <tr style=\"line-height:40px\">\n <td><b>Parallel execution</b></td>\n <td>\n <select class=\"select_main\" id=\"threading_mode\">\n <option value=\"single_threaded\"> Single-threaded </option>\n <option value=\"multi_threaded\" selected=\"\"> Multi-threaded </option> \n </select>\n <button id=\"toggle_detail_7\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_7", "toggle_detail_7")\">Configure</button>\n <g id=\"in_detail_7\" hidden=\"\">\n Number of cores <input id=\"exe_n_procs\" value=\"2\" min=\"1\" max=\"4\" step=\"1\" class=\"in11f\" type=\"number\">\n Batch size <input id=\"exe_batch_size_parallel\" value=\"200\" min=\"50\" max=\"1000\" step=\"50\" class=\"in3d\" type=\"number\"> </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 SOAP</button> \n <button class=\"btn btn-default\" onclick=\"reset_soap()\">RESET SOAP</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\n<!-- \nGDB7:\nel-spec + cov-radii + re-match + pca\nel-agno - cov-radii + re-match + pca\n\nRS/ZB\ncore-chrg + cov-radii + re-match + pca\nel-agno - cov-radii + re-match + pca\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 $(\"#\"+bt_tag).toggleClass(\"active\");\n /*if ($(\"#\"+bt_tag).attr(\"clicked\")) {\n $(\"#\"+bt_tag).css('background-color','lightgray');\n $(\"#\"+bt_tag).attr(\"clicked\", 0)\n }\n else {\n $(\"#\"+bt_tag).css('background-color','red');\n $(\"#\"+bt_tag).attr(\"clicked\", 1)\n }*/\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 \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 \"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\": $(\"#atomic_density_use_covrad:checked\").val() == \"true\"\n },\n \"kernel\": {\n \"method\": kernel_method\n },\n \"basekernel\": {\n \"kernel.type\": \"dot\",\n \"kernel.delta\": 1.0,\n \"kernel.xi\": parseFloat($(\"#basekernel_kernel_xi\").val())\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 \"descriptor\": {\n \"soap\": {\n \"spectrum.gradients\": false,\n \"spectrum.2l1_norm\": false,\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.type\": \"dot\",\n \"kernel.adaptor\": adaptor_type,\n \"kernel.delta\": 1.0,\n \"kernel.xi\": parseFloat($(\"#basekernel_kernel_xi\").val()),\n \"exclude_centers\": [],\n \"exclude_targets\": [],\n \"type_list\": [\"C\"]\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 <br> </p><hr style=\"border-width:2px\"> <p></p>\n \n \n <table class=\"glosim_control\">\n \n <!-- DATASETS -->\n <tbody><tr style=\"line-height:40px\">\n <td><b>Dataset examples</b> </td>\n <td>\n <select class=\"select_main\" id=\"dataset_example\">\n <option value=\"zcrs\" onclick=\"allow(0)\" selected=\"\"> Zincblende / Rocksalt </option>\n <option value=\"gdb\" onclick=\"allow(1)\"> GDB7 </option> \n </select>\n <!--button class=\"btn btn-xs active\" onclick='show_hide(\"in_detail_1\")' style=\"border:1;\" >\\></button-->\n <button id=\"toggle_detail_1\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_1", "toggle_detail_1")\">Configure</button>\n <!--button id=\"toggle_detail_1\"type=\"button\" onclick='show_hide(\"in_detail_1\", \"toggle_detail_1\")'>Configure</button-->\n <g id=\"in_detail_1\" hidden=\"\"> Subsample structures <input id=\"exe_batch_size\" type=\"number\" value=\"200\" min=\"50\" max=\"1000\" step=\"50\" class=\"in3d\"> </g>\n </td>\n </tr> \n \n <!-- ATOMIC DENSITY --> \n <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>\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 <!-- KERNEL DECOMPOSITION -->\n <tr style=\"line-height:40px\">\n <td><b>Embedding</b> </td>\n <td>\n <select class=\"select_main\" id=\"dimred_method\">\n <option value=\"kernelpca\" selected=\"\"> Kernel PCA </option>\n <option value=\"mds\"> Multi-dimensional scaling </option> \n </select>\n <button id=\"toggle_detail_6\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_6", "toggle_detail_6")\">Configure</button>\n <g id=\"in_detail_6\" hidden=\"\">\n Distance metric (MDS) \n <select id=\"dimred_distance\">\n <option value=\"dot\"> Hypersphere chord </option>\n </select>\n </g>\n </td>\n </tr>\n \n <!-- EXECUTION -->\n <tr style=\"line-height:40px\">\n <td><b>Parallel execution</b></td>\n <td>\n <select class=\"select_main\" id=\"threading_mode\">\n <option value=\"single_threaded\"> Single-threaded </option>\n <option value=\"multi_threaded\" selected=\"\"> Multi-threaded </option> \n </select>\n <button id=\"toggle_detail_7\" type=\"button\" class=\"btn btn-xs\" onclick=\"show_hide("in_detail_7", "toggle_detail_7")\">Configure</button>\n <g id=\"in_detail_7\" hidden=\"\">\n Number of cores <input id=\"exe_n_procs\" type=\"number\" value=\"2\" min=\"1\" max=\"4\" step=\"1\" class=\"in11f\">\n Batch size <input id=\"exe_batch_size_parallel\" type=\"number\" value=\"200\" min=\"50\" max=\"1000\" step=\"50\" class=\"in3d\"> </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 SOAP</button> \n <button class=\"btn btn-default\" onclick=\"reset_soap()\">RESET SOAP</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\n<!-- \nGDB7:\nel-spec + cov-radii + re-match + pca\nel-agno - cov-radii + re-match + pca\n\nRS/ZB\ncore-chrg + cov-radii + re-match + pca\nel-agno - cov-radii + re-match + pca\n-->"
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
- "height": 466
+ "height": 470
},
"evaluatorReader": true,
"lineCount": 306,
@@ -649,12 +649,13 @@
" data_file_format = 'NOMAD'",
" frame_list = None",
" frame_list_idcs = [ (0,0) ]",
- " target_labels = [1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 1, 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 0, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 1, 1, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, 0, 1, 1]",
- " def get_set_target(ase_struct, nmd_struct, frame_idx, json_idx): ",
- " return target_labels[json_idx]",
+ " target_label_dict = {'Pr3FCvAQdEAhm50azZGFTika5ufc0.json': 0, 'PxHdhQW40tQ6oO-dlMLlhW06qetRo.json': 1, 'Phw2RDlr8RJrjY8nb2PfCE6Bf--N0.json': 1, 'PiL5ii9imlcqPiNaYBJ9tOcXcg56e.json': 0, 'PtpUsDnCNiVY4S9huagte8WgJsqW4.json': 1, 'PWkXOKoiw0iAE585QkElUZNCYOqYI.json': 1, 'P9sheCSX6Gol5L-IsCvDlnmT_MEGG.json': 1, 'Pl2qc7lsKm2JURV9VYH_4NvBTSSAm.json': 1, 'PkJJgsBeAbrdWgqxCqVxRPHqtzerU.json': 0, 'PMdcyic7VqZ-VnZCutL0yS32quixd.json': 1, 'PhF_jMdta8Ncok9i2JHC7G1ZM5KPP.json': 0, 'PLlJ5V_E4KaSGS-UidfeQ-jaPzqRK.json': 1, 'P7phsDEr7Yr60VY4pRQEh7JA3-BCU.json': 0, 'Pq1Tvh6kPeJ-PO77jXvOsp92PMK4P.json': 1, 'P5qW79CScZurGS9wr-JIkKCz97jD6.json': 1, 'PZuBrsUzsdX__rAeKn_JQgfX-YGoo.json': 1, 'PMzA-SS1rkEgFx1pxcPzphJxK3EAS.json': 0, 'P7JW4GQVa_xQ4YKM88F9LFzyVoXke.json': 1, 'PudM2fYFckG7O5R4BJqg04tK_l1bd.json': 1, 'PnDuMg7HQBdozot1Vju9mRHL145JQ.json': 1, 'P-4rlq5MeGBSt_WkDZ4GAlQk9K477.json': 0, 'P7kHL_6prXXdx5_MzMVmwsmStNoc0.json': 1, 'P6cnGQQxSVmVNSXGhmW0Eo3F05f0S.json': 1, 'Pst86UVhV07OfKDhwlp0PNxiMtXki.json': 0, 'Pv8lUdwjbTPis4RMoPukIK9ddyfN2.json': 0, 'PV-FWv2PmdvoxclC0V6wu19FLkmzS.json': 0, 'PvoFY-VPodUwjiYz4GC8oup1lgHE5.json': 1, 'Pp4wUDDucIEdS9euDT89Y6xQA_JPq.json': 1, 'PVFeviV3V9KpZKfv_PgHIwsJ55Cta.json': 1, 'Ppp1-jWodHR_jn9MYrya_8nTIzOYr.json': 1, 'PsJUIeSLEotoIZk6R54H-G2JWPnQG.json': 0, 'PCuUA5Okfb61uS21MtbACmRZRgg_S.json': 0, 'PvctQLLbVwTdrcOT414rRTdEee6te.json': 0, 'PguAhp1UagznD1eGM48s7Q1xhl356.json': 0, 'Pgg6lKW9mNnK_JsGGEZ3WcTE5hd8U.json': 1, 'PsK4ECtTc4sdm7Y2ItXj_PYIQ7Uxi.json': 1, 'P5I94-ZnwC4e19Q-2KL5peI-mHW-3.json': 1, 'PC0ikq0ulkygT2Co59UBAl9YcYxbG.json': 1, 'PItWNNwGWlKJ12UjZAOfNetX3xlkd.json': 1, 'Pn_JMZdRKlBskR5YNFU09ZPlI25yQ.json': 0, 'Pd23q1LJrA4DOKbForwH4cvHWRk6U.json': 0, 'PDZZd1lzu5VkgVNru0CvP5lPSFZdg.json': 1, 'PB-GqTDr-DZ-j4OKjRNJEp1hnOGvG.json': 0, 'Pz1nKnfqor_aI3wdO2eNlvwxf2XyM.json': 1, 'PHZfSFK_jwrcAKMVDKVl5zy0iG__7.json': 1, 'Pp5ld58IKi6ZKVY1FkOVHRNaxNGpM.json': 1, 'Pzu2Kvm9kVotZbNGSNJ5OkmX0Le9t.json': 0, 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+ " #target_labels = [1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 1, 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 0, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 1, 1, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, 0, 1, 1]",
+ " def get_set_target(ase_struct, nmd_struct, frame_idx, json_idx, json_file): ",
+ " return target_label_dict[os.path.basename(json_file)]",
" #return nmd_struct.energy_eV[(0,0)]/1e5",
- " def get_set_label(ase_struct, nmd_struct, frame_idx, json_idx):",
- " return 'Rocksalt' if target_labels[json_idx] == 1 else 'Zincblende'",
+ " def get_set_label(ase_struct, nmd_struct, frame_idx, json_idx, json_file):",
+ " return 'Rocksalt' if target_label_dict[os.path.basename(json_file)] == 1 else 'Zincblende'",
" label_name = 'Structure'",
" target_name = 'Structure type'",
" target_type = str",
@@ -666,11 +667,11 @@
" data_file_format = 'xyz'",
" frame_list = [ i for i in range(options['run']['n_blocksize']) ]",
" frame_list_idcs = [ (0,i) for i in frame_list ]",
- " def get_set_target(ase_struct, nmd_struct, frame_idx, json_idx):",
+ " def get_set_target(ase_struct, nmd_struct, frame_idx, json_idx, json_file):",
" target = float(ase_struct.info['ae_pbe0'])",
" nmd_struct.energy_eV[frame_idx] = target",
" return target/23.045108 # convert from kcal/mol to eV",
- " def get_set_label(ase_struct, nmd_struct, frame_idx, json_idx):",
+ " def get_set_label(ase_struct, nmd_struct, frame_idx, json_idx, json_file):",
" return None",
" label_name = None",
" target_name = 'Atomization energy'",
@@ -699,8 +700,8 @@
" datastring='') ",
" ase_config_list.append(ase_config)",
" frame_list_idx_list[-1].append(idx[1])",
- " target_list.append(get_set_target(ase_atoms, nmd_struct, idx, json_idx))",
- " label_list.append(get_set_label(ase_atoms, nmd_struct, idx, json_idx))",
+ " target_list.append(get_set_target(ase_atoms, nmd_struct, idx, json_idx, json_file))",
+ " label_list.append(get_set_label(ase_atoms, nmd_struct, idx, json_idx, json_file))",
" for z, n_z in ase_config.z_count.items():",
" if not z in z_count_global or z_count_global[z] < n_z:",
" z_count_global[z] = n_z",
@@ -755,7 +756,7 @@
"selectedType": "Results",
"state": {},
"pluginName": "IPython",
- "shellId": "F5EFFC19397E4F4C8C0D9695BB0785FB",
+ "shellId": "DA4EB0C12CEE4B07AE48B0E9A9F278A6",
"height": 222,
"dataresult": [
"HARTREE_TO_EV",
@@ -847,7 +848,7 @@
]
},
"evaluatorReader": true,
- "lineCount": 164,
+ "lineCount": 165,
"tags": "cell_soap_run"
},
{
@@ -2055,7 +2056,7 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "F5EFFC19397E4F4C8C0D9695BB0785FB"
+ "shellId": "DA4EB0C12CEE4B07AE48B0E9A9F278A6"
},
"evaluatorReader": true,
"lineCount": 1192,
@@ -2177,7 +2178,7 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "F5EFFC19397E4F4C8C0D9695BB0785FB",
+ "shellId": "DA4EB0C12CEE4B07AE48B0E9A9F278A6",
"height": 78
},
"evaluatorReader": true,
@@ -2262,7 +2263,7 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "F5EFFC19397E4F4C8C0D9695BB0785FB",
+ "shellId": "DA4EB0C12CEE4B07AE48B0E9A9F278A6",
"height": 1462
},
"evaluatorReader": true,
@@ -2329,7 +2330,7 @@
"config_folder": "zcrs",
"n_configs": -1,
"n_procs": 2,
- "n_blocksize": 50,
+ "n_blocksize": 200,
"queue": "?",
"walltime": 12,
"out_folder": "out.kernel",
@@ -2341,7 +2342,7 @@
"use_covrad": false
},
"kernel": {
- "method": "global"
+ "method": "rematch"
},
"basekernel": {
"kernel.type": "dot",
@@ -2388,7 +2389,7 @@
"angularbasis.type": "spherical-harmonic",
"angularbasis.L": 6,
"kernel.type": "dot",
- "kernel.adaptor": "global-generic",
+ "kernel.adaptor": "generic",
"kernel.delta": 1,
"kernel.xi": 3,
"exclude_centers": [],