diff --git a/beaker-notebooks/Embedding.bkr b/beaker-notebooks/Embedding.bkr
index 3c90da4022c13ca4fe54280dfcf39896effda052..508aeb2ecad1768429a864f0a6dbcacaa2460175 100644
--- a/beaker-notebooks/Embedding.bkr
+++ b/beaker-notebooks/Embedding.bkr
@@ -47,38 +47,33 @@
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- "<a target=\"_blank\" href=\"http://forum.analytics-toolkit.nomad-coe.eu/\" class=\"btn btn-primary\"> Send your feedback to the analytics-toolkit forum</a><h2> Your comments are invaluable in helping us provide a user friendly experience for all! </h2>"
- ]
+ "<label style=\"text-align: left; color: #20335d; font-weight: 900; font-size: 18pt; padding-top: 2em;\">",
+ " Visualizing material-similarity:</label><br/><label style=\"color: #20335d;font-weight: 900; font-size: 15pt;\"> Octet-binary zincblende vs. rocksalt semiconductors</label>",
+ " </p>",
+ " <p style=\"font-size: 15px;\">Angelo Ziletti, Ankit Kariryaa, Emre Ahmetcik, Fawzi Mohamed, Luca Ghiringhelli, and Matthias Scheffler <span style=\"font-size: smaller;\">[version 2017-01-23]</span></p>",
+ " ",
+ "<div style=\"padding-top: 1em;\">"
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+ "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<label style=\"text-align: left; color: #20335d; font-weight: 900; font-size: 18pt; padding-top: 2em;\">\n Visualizing material-similarity:</label><br><label style=\"color: #20335d;font-weight: 900; font-size: 15pt;\"> Octet-binary zincblende vs. rocksalt semiconductors</label>\n <p></p>\n <p style=\"font-size: 15px;\">Angelo Ziletti, Ankit Kariryaa, Emre Ahmetcik, Fawzi Mohamed, Luca Ghiringhelli, and Matthias Scheffler <span style=\"font-size: smaller;\">[version 2017-01-23]</span></p>\n \n<div style=\"padding-top: 1em;\"></div>"
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- "<p style=\"color: #20335d;;font-weight: 900; font-size: 22pt;\"> NOMAD analytics toolkit</p>",
- "<label style=\"text-align: center; color: #20335d; font-weight: 900; font-size: 18pt;\">Tutorial example on Crystal prediction II:</label> <label style=\"color: #20335d;font-weight: 900; font-size: 15pt;\"> Visualizing material-similarity for the case of octet-binary zincblende-vs.-rocksalt semiconductors</label>",
- " </p>",
- " <p style=\"font-size: 15px;\"> developed by Angelo Ziletti, Ankit Kariryaa, Fawzi Mohamed, Luca Ghiringhelli, and Matthias Scheffler. [Last update November 23, 2016]</p>"
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@@ -105,23 +100,20 @@
" <h4 class=\"modal-title\" id=\"lasso-motivation-modal-label\">Introduction and motivation</h4>",
" </div>",
" <div class=\"modal-body lasso_instructions\">",
- " ",
- " <p> The prediction of RS vs ZB structure from a simple descriptor has a notable history in materials science [1-7], where descriptors were designed by chemically/physically-inspired intuition. </p>",
- "",
" <p> In this tutorial, we present a tool that produces two-dimensional structure maps for octet binary compounds, by starting from a high-dimensional set of <i>features</i> (coordinates) that identify each data point (material), based on free-atom data of the atomic species constituting the binary material. </p>",
- "",
+ " ",
" <p> The low-dimensional embedding methods (here, two-dimensional for the sake of visualization) are <i>unsupervised</i> machine-learning algorithms; so, in our example, the algorithm processes only the spatial arrangement of the points in the high-dimensional representation that is determined by the user. </p>",
" ",
" <p> In the linear method, <b>principal component analysis (<a href=\"https://en.wikipedia.org/wiki/Feature_scaling\" target=\"_blank\">PCA</a>)</b>, the direction (linear combination of the input coordinates) with the maximum variance is identified as the first principal component (PC). The direction perpendicular to the first PC with the largest variance is the second PC.",
" The process can be iterated up to as many dimensions as the initial dimensionality of the data, but here we stop at the second dimension and give the amount of total variance recovered by the first two principal components. </p>",
- " <p> In the non-linear methods we chose, <b>multidimensional scaling (<a href=\"https://en.wikipedia.org/wiki/Multidimensional_scaling\" target=\"_blank\">MDS</a>) </b> tries to preserve the distances from the given high-dimensional to the two-dimensional representation, ",
- " whereas <b>t-Distributed Stochastic Neighbor Embedding (<a href=\"https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding\" target=\"_blank\">t-SNE</a>) </b> tries to preserve the local shape for groups of neighboring points. Both methods use a notion of distance that in our example is the Euclidean norm, even if in principle it could be any proper norm. </p>",
+ " <p> In the two popular non-linear method we chose, <b>multidimensional scaling (<a href=\"https://en.wikipedia.org/wiki/Multidimensional_scaling\" target=\"_blank\">MDS</a>) </b> tries to preserve the distances from the given high-dimensional to the two-dimensional representation, ",
+ " and the <b>t-Distributed Stochastic Neighbor Embedding (<a href=\"https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding\" target=\"_blank\">t-SNE</a>) </b> tries to preserve the local shape of groups of neighboring points. Both methods use a notion of distance that in our example is the Euclidean norm, even if in principle it could be any proper norm. </p>",
"",
" <p> In the results, we show the data points colored according to the difference in energy between the Rocksalt (RS) and Zincblende (ZB) crystal structures (both relaxed to their local minima) of the material they represent. The labeling and consequent coloring is independent of the embedding method used, therefore the labeling is an <i>a posteriori</i>",
- " check that the high-dimensional representation could contain information about the labeling itself. In practice, if the coloring identifies clearly distinct areas, then the two dimensional representation is a map for the prediction of the labels, so that a new data point of unknown labeling, that lands in the two-dimensional map in an area of points with known labeling, is expected to belong to that same labeling. </p>",
+ " check that the high-dimensional representation could contain information about the labeling itself. In practice, if the coloring identifies clearly distinct areas, then the two dimensional representation is a map for the prediction of the labels, so that a new data point of unknown labeling, that lands in the 2D map in a area of points with known labeling, is expected to belong to that same labeling. </p>",
" ",
"<p>The merit of the embedding methods is to provide relatively inexpensive tools to visually test whether a given set of features contains information about an investigated property (label). For this reason, they are widely used as preliminary tools for discovering structures in the data. </p>",
- "",
+ "<p> The prediction of RS vs ZB structure from a simple descriptor has a notable history in materials science [1-7], where descriptors were designed by chemically/physically-inspired intuition. </p>",
"",
" <p>References:</p>",
" <ol>",
@@ -149,14 +141,14 @@
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- "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<style type=\"text/css\">\n .lasso_instructions{\n font-size: 15px;\n } \n</style>\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-motivation-modal\">\n Introduction and motivation\n</button>\n\n<!-- Modal -->\n<div style=\"display: none;\" class=\"modal fade\" id=\"lasso-motivation-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-motivation-modal-label\">\n <div class=\"modal-dialog modal-lg\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-motivation-modal-label\">Introduction and motivation</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n \n <p> The prediction of RS vs ZB structure from a simple descriptor has a notable history in materials science [1-7], where descriptors were designed by chemically/physically-inspired intuition. </p>\n\n <p> In this tutorial, we present a tool that produces two-dimensional structure maps for octet binary compounds, by starting from a high-dimensional set of <i>features</i> (coordinates) that identify each data point (material), based on free-atom data of the atomic species constituting the binary material. </p>\n\n <p> The low-dimensional embedding methods (here, two-dimensional for the sake of visualization) are <i>unsupervised</i> machine-learning algorithms; so, in our example, the algorithm processes only the spatial arrangement of the points in the high-dimensional representation that is determined by the user. </p>\n \n <p> In the linear method, <b>principal component analysis (<a href=\"https://en.wikipedia.org/wiki/Feature_scaling\" target=\"_blank\">PCA</a>)</b>, the direction (linear combination of the input coordinates) with the maximum variance is identified as the first principal component (PC). The direction perpendicular to the first PC with the largest variance is the second PC.\n The process can be iterated up to as many dimensions as the initial dimensionality of the data, but here we stop at the second dimension and give the amount of total variance recovered by the first two principal components. </p>\n <p> In the non-linear methods we chose, <b>multidimensional scaling (<a href=\"https://en.wikipedia.org/wiki/Multidimensional_scaling\" target=\"_blank\">MDS</a>) </b> tries to preserve the distances from the given high-dimensional to the two-dimensional representation, \n whereas <b>t-Distributed Stochastic Neighbor Embedding (<a href=\"https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding\" target=\"_blank\">t-SNE</a>) </b> tries to preserve the local shape for groups of neighboring points. Both methods use a notion of distance that in our example is the Euclidean norm, even if in principle it could be any proper norm. </p>\n\n <p> In the results, we show the data points colored according to the difference in energy between the Rocksalt (RS) and Zincblende (ZB) crystal structures (both relaxed to their local minima) of the material they represent. The labeling and consequent coloring is independent of the embedding method used, therefore the labeling is an <i>a posteriori</i>\n check that the high-dimensional representation could contain information about the labeling itself. In practice, if the coloring identifies clearly distinct areas, then the two-dimensional representation is a map for the prediction of the labels. In other words, if a new data point of unknown labeling lands in the two-dimensional map in an area of points with known labeling, is expected to belong to that same labeling. </p>\n \n<p>The merit of the embedding methods is to provide relatively inexpensive tools to visually test whether a given set of features contains information about an investigated property (label). For this reason, they are widely used as preliminary tools for discovering structures in the data. </p>\n\n\n <p>References:</p>\n <ol>\n <li>J. A. van Vechten, Phys. Rev. 182, 891 (1969).</li>\n <li>J. C. Phillips, Rev. Mod. Phys. 42, 317 (1970).</li>\n <li>J. St. John and A.N. Bloch, Phys. Rev. Lett. 33, 1095 (1974).</li>\n <li>J. R. Chelikowsky and J. C. Phillips, Phys. Rev. B 17, 2453 (1978).</li>\n <li>A. Zunger, Phys. Rev. B 22, 5839 (1980).</li>\n <li>D. G. Pettifor, Solid State Commun. 51, 31 (1984).</li>\n <li>Y. Saad, D. Gao, T. Ngo, S. Bobbitt, J. R. Chelikowsky, and W. Andreoni, Phys. Rev. B 85, 104104 (2012).</li>\n </ol>\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>"
+ "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<style type=\"text/css\">\n .lasso_instructions{\n font-size: 15px;\n } \n</style>\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-motivation-modal\">\n Introduction and motivation\n</button>\n\n<!-- Modal -->\n<div class=\"modal fade\" id=\"lasso-motivation-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-motivation-modal-label\">\n <div class=\"modal-dialog modal-lg\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-motivation-modal-label\">Introduction and motivation</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n <p> In this tutorial, we present a tool that produces two-dimensional structure maps for octet binary compounds, by starting from a high-dimensional set of <i>features</i> (coordinates) that identify each data point (material), based on free-atom data of the atomic species constituting the binary material. </p>\n \n <p> The low-dimensional embedding methods (here, two-dimensional for the sake of visualization) are <i>unsupervised</i> machine-learning algorithms; so, in our example, the algorithm processes only the spatial arrangement of the points in the high-dimensional representation that is determined by the user. </p>\n \n <p> In the linear method, <b>principal component analysis (<a href=\"https://en.wikipedia.org/wiki/Feature_scaling\" target=\"_blank\">PCA</a>)</b>, the direction (linear combination of the input coordinates) with the maximum variance is identified as the first principal component (PC). The direction perpendicular to the first PC with the largest variance is the second PC.\n The process can be iterated up to as many dimensions as the initial dimensionality of the data, but here we stop at the second dimension and give the amount of total variance recovered by the first two principal components. </p>\n <p> In the two popular non-linear method we chose, <b>multidimensional scaling (<a href=\"https://en.wikipedia.org/wiki/Multidimensional_scaling\" target=\"_blank\">MDS</a>) </b> tries to preserve the distances from the given high-dimensional to the two-dimensional representation, \n and the <b>t-Distributed Stochastic Neighbor Embedding (<a href=\"https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding\" target=\"_blank\">t-SNE</a>) </b> tries to preserve the local shape of groups of neighboring points. Both methods use a notion of distance that in our example is the Euclidean norm, even if in principle it could be any proper norm. </p>\n\n <p> In the results, we show the data points colored according to the difference in energy between the Rocksalt (RS) and Zincblende (ZB) crystal structures (both relaxed to their local minima) of the material they represent. The labeling and consequent coloring is independent of the embedding method used, therefore the labeling is an <i>a posteriori</i>\n check that the high-dimensional representation could contain information about the labeling itself. In practice, if the coloring identifies clearly distinct areas, then the two dimensional representation is a map for the prediction of the labels, so that a new data point of unknown labeling, that lands in the 2D map in a area of points with known labeling, is expected to belong to that same labeling. </p>\n \n<p>The merit of the embedding methods is to provide relatively inexpensive tools to visually test whether a given set of features contains information about an investigated property (label). For this reason, they are widely used as preliminary tools for discovering structures in the data. </p>\n<p> The prediction of RS vs ZB structure from a simple descriptor has a notable history in materials science [1-7], where descriptors were designed by chemically/physically-inspired intuition. </p>\n\n <p>References:</p>\n <ol>\n <li>J. A. van Vechten, Phys. Rev. 182, 891 (1969).</li>\n <li>J. C. Phillips, Rev. Mod. Phys. 42, 317 (1970).</li>\n <li>J. St. John and A.N. Bloch, Phys. Rev. Lett. 33, 1095 (1974).</li>\n <li>J. R. Chelikowsky and J. C. Phillips, Phys. Rev. B 17, 2453 (1978).</li>\n <li>A. Zunger, Phys. Rev. B 22, 5839 (1980).</li>\n <li>D. G. Pettifor, Solid State Commun. 51, 31 (1984).</li>\n <li>Y. Saad, D. Gao, T. Ngo, S. Bobbitt, J. R. Chelikowsky, and W. Andreoni, Phys. Rev. B 85, 104104 (2012).</li>\n </ol>\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>"
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@@ -195,18 +187,18 @@
"<p> In this example, you can run the linear low-dimensional embedding method, <b>principal component analysis (<a href=\"https://en.wikipedia.org/wiki/Feature_scaling\" target=\"_blank\">PCA</a>)</b> and two selected non-linear methods, <b>multidimensional scaling (<a href=\"https://en.wikipedia.org/wiki/Multidimensional_scaling\" target=\"_blank\">MDS</a>) </b>",
" and <b>t-Distributed Stochastic Neighbor Embedding (<a href=\"https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding\" target=\"_blank\">t-SNE</a>) </b>. </p>",
" ",
- "<p> The input features, that can be selected in the checklist below (any number of features larger than two is allowed), represent chemical elements constituting (AB-type) binary octet materials, which typically crystallize into rocksalt or zincblende crystal structure. </p>",
+ "<p> The input features, that can be selected in the checklist below (any number of features larger than 2 is allowed), represent chemical elements constituting binary octet materials, that crystallize typically into rocksalt or zincblende crystal structure. </p>",
"<p> The next step is to select the embedding method (exclusive selection) and whether each feature is pre-processed by dividing it by the standard deviation of the whole population (all data points). Note that the feature are anyhow centered around their mean value as pre-processing.</p> ",
" ",
"<p> After selecting the list of features, the method, and the normalization criterion, click <b>“Run two-dimensional embedding”</b> to apply the selected method. </p>",
" ",
"<p> During and at the end of the run, a brief summary is printed out below the <b>“Run two-dimensional embedding”</b> button. After the end of the run, click on <b>“View interactive 2D scatter plot”</b> (it is unlocked at the end of the run) to open a new tab where the two-dimensional map is shown as an interactive scatter plot. </p>",
- "<p> Note1: the plot remains active even if another run is performed, so that the output of several sets of input parameters can be compared in the viewer tabs.</p>",
- " <p> Note2: with the following selection of features:<br> ",
+ "<p> Note1: the plot stays active also after another run is performed, so that the output of several sets of input parameters can be compared in the viewer tabs.</p>",
+ " <!--- <p> Note2: with the following selection of features:<br> ",
" ['rs(A)', 'rs(B)', 'rp(A)', 'rp(B)', 'Es(A)/sqrt(Zval(A))', 'Es(B)/sqrt(Zval(B))', 'Ep(A)/sqrt(Zval(A))', 'Ep(B)/sqrt(Zval(B))']<br>",
" and PCA method, one obtains a result similar to Fig. 4 in Y. Saad, D. Gao, T. Ngo, S. Bobbitt, J. R. Chelikowsky, and W. Andreoni, Phys. Rev. B 85, 104104 (2012).",
- " The plot may appear mirrored because the sign of the principal component is immaterial. Besides, the input data are slightly different (here, everything is calculated at the converged local-density approximation level).",
- " </p>",
+ " The plot may appear mirrored because the sign of the principal component is immaterial. Besides, the input data are slightly different (here, everything is calculated at the converged LDA level).",
+ " </p> -->",
" </div>",
" <div class=\"modal-footer\">",
" <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>",
@@ -223,7 +215,7 @@
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"innertype": "Html",
- "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<style type=\"text/css\">\n .lasso_instructions{\n font-size: 15px;\n } \n</style>\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-instructions-modal\">\n Instructions\n</button>\n\n<!-- Modal -->\n<div style=\"display: none;\" class=\"modal fade\" id=\"lasso-instructions-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-instructions-modal-label\">\n <div class=\"modal-dialog\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-instructions-modal-label\">Instructions</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n<p> In this example, you can run the linear low-dimensional embedding method, <b>principal component analysis (<a href=\"https://en.wikipedia.org/wiki/Feature_scaling\" target=\"_blank\">PCA</a>)</b> and two selected non-linear methods, <b>multidimensional scaling (<a href=\"https://en.wikipedia.org/wiki/Multidimensional_scaling\" target=\"_blank\">MDS</a>) </b>\n and <b>t-Distributed Stochastic Neighbor Embedding (<a href=\"https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding\" target=\"_blank\">t-SNE</a>) </b>. </p>\n \n<p> The input features, that can be selected in the checklist below (any number of features larger than two is allowed), represent chemical elements constituting (AB-type) binary octet materials, which typically crystallize into rocksalt or zincblende crystal structure. </p>\n<p> The next step is to select the embedding method (exclusive selection) and whether each feature is pre-processed by dividing it by the standard deviation of the whole population (all data points). Note that the feature are anyhow centered around their mean value as pre-processing.</p> \n \n<p> After selecting the list of features, the method, and the normalization criterion, click <b>“Run two-dimensional embedding”</b> to apply the selected method. </p>\n \n<p> During and at the end of the run, a brief summary is printed out below the <b>“Run two-dimensional embedding”</b> button. After the end of the run, click on <b>“View interactive 2D scatter plot”</b> (it is unlocked at the end of the run) to open a new tab where the two-dimensional map is shown as an interactive scatter plot. </p>\n<p> Note1: the plot remains active even if another run is performed, so that the output of several sets of input parameters can be compared in the viewer tabs.</p>\n <p> Note2: with the following selection of features:<br> \n ['rs(A)', 'rs(B)', 'rp(A)', 'rp(B)', 'Es(A)/sqrt(Zval(A))', 'Es(B)/sqrt(Zval(B))', 'Ep(A)/sqrt(Zval(A))', 'Ep(B)/sqrt(Zval(B))']<br>\n and PCA method, one obtains a result similar to Fig. 4 in Y. Saad, D. Gao, T. Ngo, S. Bobbitt, J. R. Chelikowsky, and W. Andreoni, Phys. Rev. B 85, 104104 (2012).\n The plot may appear mirrored because the sign of the principal component is immaterial. Besides, the input data are slightly different (here, everything is calculated at the converged local-density approximation level).\n </p>\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>"
+ "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<style type=\"text/css\">\n .lasso_instructions{\n font-size: 15px;\n } \n</style>\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-instructions-modal\">\n Instructions\n</button>\n\n<!-- Modal -->\n<div style=\"display: none;\" class=\"modal fade\" id=\"lasso-instructions-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-instructions-modal-label\">\n <div class=\"modal-dialog\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-instructions-modal-label\">Instructions</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n<p> In this example, you can run the linear low-dimensional embedding method, <b>principal component analysis (<a href=\"https://en.wikipedia.org/wiki/Feature_scaling\" target=\"_blank\">PCA</a>)</b> and two selected non-linear methods, <b>multidimensional scaling (<a href=\"https://en.wikipedia.org/wiki/Multidimensional_scaling\" target=\"_blank\">MDS</a>) </b>\n and <b>t-Distributed Stochastic Neighbor Embedding (<a href=\"https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding\" target=\"_blank\">t-SNE</a>) </b>. </p>\n \n<p> The input features, that can be selected in the checklist below (any number of features larger than 2 is allowed), represent chemical elements constituting binary octet materials, that crystallize typically into rocksalt or zincblende crystal structure. </p>\n<p> The next step is to select the embedding method (exclusive selection) and whether each feature is pre-processed by dividing it by the standard deviation of the whole population (all data points). Note that the feature are anyhow centered around their mean value as pre-processing.</p> \n \n<p> After selecting the list of features, the method, and the normalization criterion, click <b>“Run two-dimensional embedding”</b> to apply the selected method. </p>\n \n<p> During and at the end of the run, a brief summary is printed out below the <b>“Run two-dimensional embedding”</b> button. After the end of the run, click on <b>“View interactive 2D scatter plot”</b> (it is unlocked at the end of the run) to open a new tab where the two-dimensional map is shown as an interactive scatter plot. </p>\n<p> Note1: the plot stays active also after another run is performed, so that the output of several sets of input parameters can be compared in the viewer tabs.</p>\n <!--- <p> Note2: with the following selection of features:<br> \n ['rs(A)', 'rs(B)', 'rp(A)', 'rp(B)', 'Es(A)/sqrt(Zval(A))', 'Es(B)/sqrt(Zval(B))', 'Ep(A)/sqrt(Zval(A))', 'Ep(B)/sqrt(Zval(B))']<br>\n and PCA method, one obtains a result similar to Fig. 4 in Y. Saad, D. Gao, T. Ngo, S. Bobbitt, J. R. Chelikowsky, and W. Andreoni, Phys. Rev. B 85, 104104 (2012).\n The plot may appear mirrored because the sign of the principal component is immaterial. Besides, the input data are slightly different (here, everything is calculated at the converged LDA level).\n </p> -->\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>"
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
@@ -244,6 +236,7 @@
" getFeatures();",
" getEmbedMethod();",
" getStandardize();",
+ " getUnits();",
" beaker.evaluate(\"lasso_cell\"); // evaluate cells with tag \"lasso_cell\"",
" // view_result()",
"};",
@@ -257,7 +250,10 @@
" beaker.selected_feature_list.push(this.value);",
" });",
"};",
- "",
+ " ",
+ "var getUnits = function() {",
+ " beaker.units = $(\"#units_select\").val();",
+ "};",
" ",
"var getEmbedMethod = function() {",
" beaker.embed_method = \"pca\";",
@@ -305,54 +301,43 @@
"<div class=\"lasso_control\">",
" <div class=\"row\">",
" <p class=\"lasso_selection_description\"><b>Primary features </b>",
- " (all energies are in eV and all distances in Å; hover the mouse pointer over the feature names to see their full description):</p>",
+ " (hover the mouse pointer over the feature names to see a full description):</p>",
" <form id=\"lasso_features_select\">",
" <div class=\"lasso_form_group\">",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\" title=\"Ionization potential of atom A\"> <input type=\"checkbox\" value=\"IP(A)\" > <i>IP</i> <sup>A</sup></label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"IP(B)\" > <span title=\"Ionization potential of atom B\"><i>IP</i> <sup>B</sup></span></label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"EA(A)\" > <span title=\"Electron affinity of atom A\"> <i>EA</i> <sup>A</sup></span></label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"EA(B)\" > <span title=\"Electron affinity of atom B\"> <i>EA</i> <sup>B</sup></span></label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"HOMO(A)\" > <span title=\"Energy of highest occupied molecular orbital for atom A\"><i>E</i> <sup>A</sup><sub>HOMO</sub></span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"HOMO(B)\" > <span title=\"Energy of highest occupied molecular orbital for atom B\"> <i>E</i> <sup>B</sup><sub>HOMO</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"LUMO(A)\" > <span title=\"Energy of lowest unoccupied molecular orbital for atom A\"> <i>E</i> <sup>A</sup><sub>LUMO</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"LUMO(B)\" > <span title=\"Energy of lowest unoccupied molecular orbital for atom B\"> <i>E</i> <sup>B</sup><sub>LUMO</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"rs(A)\" CHECKED > <span title=\"Radius at which the radial probability density of the valence s orbital is maximum for atom A\"> <i>r</i><sub>s</sub><sup>A</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"rs(B)\" CHECKED > <span title=\"Radius at which the radial probability density of the valence s orbital is maximum for atom B\"> <i>r</i><sub>s</sub><sup>B</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"rp(A)\" CHECKED > <span title=\"Radius at which the radial probability density of the valence p orbital is maximum for atom A\"> <i>r</i><sub>p</sub><sup>A</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"rp(B)\" CHECKED > <span title=\"Radius at which the radial probability density of the valence p orbital is maximum for atom B\"> <i>r</i><sub>p</sub><sup>B</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"rd(A)\" CHECKED > <span title=\"Radius at which the radial probability density of the valence d orbital is maximum for atom A\"> <i>r</i><sub>d</sub><sup>A</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"rd(B)\" CHECKED > <span title=\"Radius at which the radial probability density of the valence d orbital is maximum for atom B\"> <i>r</i><sub>d</sub><sup>B</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"Es(A)/sqrt(Zval(A))\" > ",
- " <span title=\"Energy of the valence s orbital(s) divided by the square root of the number of valence electrons of atom A. [Phys. Rev. B 85, 104104 (2012)]\"> <i>E</i><sub>s</sub><sup>A</sup>/sqrt(<i>Z</i> <sup>A</sup><sub>val</sub>) </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"Es(B)/sqrt(Zval(B))\" > ",
- " <span title=\"Energy of the valence s orbital(s) divided by the square root of the number of valence electrons of atom B. [Phys. Rev. B 85, 104104 (2012)]\"> <i>E</i><sub>s</sub><sup>B</sup>/sqrt(<i>Z</i> <sup>B</sup><sub>val</sub>) </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"Ep(A)/sqrt(Zval(A))\" > ",
- " <span title=\"Energy of the valence p orbital(s) divided by the square root of the number of valence electrons of atom A. [Phys. Rev. B 85, 104104 (2012)]\"> <i>E</i><sub>p</sub><sup>A</sup>/sqrt(<i>Z</i> <sup>A</sup><sub>val</sub>) </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"Ep(B)/sqrt(Zval(B))\" > ",
- " <span title=\"Energy of the valence p orbital(s) divided by the square root of the number of valence electrons of atom B. [Phys. Rev. B 85, 104104 (2012)]\"> <i>E</i><sub>p</sub><sup>B</sup>/sqrt(<i>Z</i> <sup>B</sup><sub>val</sub>) </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_ionization_potential\" CHECKED > <span title=\"Atomic ionization potential\"><i>IP</i> </span></label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_electron_affinity\" CHECKED > <span title=\"Atomic electron affinity\"> <i>EA</i></span></label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_homo\" > <span title=\"Energy of highest occupied molecular orbital\"><i>E</i> <sub>HOMO</sub></span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"atomic_lumo\" > <span title=\"Energy of lowest unoccupied molecular orbital\"> <i>E</i> <sub>LUMO</sub> </span> </label>",
" ",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"d_AA\" > <span title=\"Bond length of atomA-atomA dimer\"> <i>d</i><sup>AA</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"d_BB\"> <span title=\"Bond length of atomB-atomB dimer\"> <i>d</i><sup>BB</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"HL_gap_AA\" > <span title=\"HOMO-LUMO gap of atomA-atomA dimer\"> Δ<i>E</i> <sup>AA</sup><sub>HL</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"HL_gap_BB\" > <span title=\"HOMO-LUMO gap of atomB-atomB dimer\"> Δ<i>E</i> <sup>BB</sup><sub>HL</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"Ebinding_AA\" > <span title=\"Binding energy of atomA-atomA dimer\"> <i>E</i> <sup>AA</sup><sub>b</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"Ebinding_BB\" > <span title=\"Binding energy of atomB-atomB dimer\"> <i>E</i> <sup>BB</sup><sub>b</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"Z(A)\" > <span title=\"Atomic number of atom A\"> <i>Z</i> <sup>A</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"Z(B)\" > <span title=\"Atomic number of atom B\"> <i>Z</i> <sup>B</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"val(A)\" > <span title=\"Number of valence electrons of atom A\"> <i>Z</i> <sup>A</sup><sub>val</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"val(B)\" > <span title=\"Number of valence electrons of atom B\"> <i>Z</i> <sup>B</sup><sub>val</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"period(A)\" > <span title=\"Period (in the periodic table) of atom A\"> <i>n</i> <sup>A</sup><sub>period</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"period(B)\" > <span title=\"Period (in the periodic table) of atom B\"> <i>n</i> <sup>B</sup><sub>period</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"r_sigma\" > <span title=\"John-Bloch's indicator1: |rp(A) + rs(A) - rp(B) -rs(B)| ",
- " [Phys. Rev. Lett. 33. 1095 (1974)]\"> r<sub>σ</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"r_pi\" > <span title=\"John-Bloch's indicator2: |rp(A) - rs(A)| +| rp(B) -rs(B)| ",
- " [Phys. Rev. Lett. 33. 1095 (1974)]\"> r<sub>π</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"d_AB\" > <span title=\"Bond length of atomA-atomB dimer\"> <i>d</i><sup>AB</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"HL_gap_AB\" > <span title=\"HOMO-LUMO gap of atomA-atomB dimer\"> Δ<i>E</i> <sup>AB</sup><sub>HL</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-2\"> <input type=\"checkbox\" value=\"Ebinding_AB\" > <span title=\"Binding energy of atomA-atomB dimer\"> <i>E</i> <sup>AB</sup><sub>b</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_rs_max\" CHECKED > <span title=\"Radius at which the radial probability density of the valence s orbital is maximum\"> <i>r</i><sub>s</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_rp_max\" CHECKED > <span title=\"Radius at which the radial probability density of the valence p orbital is maximum\"> <i>r</i><sub>p</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_rd_max\" CHECKED > <span title=\"Radius at which the radial probability density of the valence d orbital is maximum\"> <i>r</i><sub>d</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_number\" > <span title=\"Atomic number\"> <i>Z</i> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_number_valence_electrons\" > <span title=\"Number of valence electrons\"> <i>Z</i><sub>val</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"period\" > <span title=\"Period (in the periodic table)\"> <i>n</i> <sub>period</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_r_by_2_dimer\" > <span title=\"Bond length of the dimer\"> <i>d</i> <sub>dimer</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_electronic_binding_energy_dimer\" > <span title=\"Binding energy of the dimer\"> <i>E</i> <sub>b</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_homo_lumo_diff\" > <span title=\"HOMO-LUMO gap of the dimer\"> Δ<i>E</i><sub>HL</sub> </span> </label>",
+ " ",
+ "<!--- <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"Es/sqrt(Zval)\" > ",
+ " <span title=\"Energy of the valence s orbital(s) divided by the square root of the number of valence electrons. [Phys. Rev. B 85, 104104 (2012)]\"> <i>E</i><sub>s</sub>/sqrt(<i>Z</i> <sub>val</sub>) </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"Ep/sqrt(Zval)\" > ",
+ " <span title=\"Energy of the valence p orbital(s) divided by the square root of the number of valence electrons. [Phys. Rev. B 85, 104104 (2012)]\"> <i>E</i><sub>p</sub>/sqrt(<i>Z</i> <sub>val</sub>) </span> </label>",
+ "--> ",
" </div>",
" </form>",
" </div> <!-- End of row-->",
+ " ",
+ " <br>",
+ " <div class=\"row\"> <!-- Start of row-->",
+ " <p class=\"lasso_selection_description\"><b>Unit of measures: </b> ",
+ " <select id='units_select'>",
+ " <option value=\"eV_angstrom\" > [energy]=eV; [length]=angstrom</option>",
+ " <option value=\"J_m\" > [energy]=J; [length]=m</option>",
+ " <option value=\"kcal/mol_angstrom\" > [energy]=kcal/mol; [length]=angstrom</option>",
+ " </select> </p>",
+ " </div><!-- End of row-->",
+ " ",
" <br>",
" <div class=\"row\"> <!-- Start of second row-->",
" <div class=\"lasso_form_group\">",
@@ -393,12 +378,12 @@
"result": {
"type": "BeakerDisplay",
"innertype": "Html",
- "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<script>\nvar run_lasso = function() {\n $(\"#lasso_result_button\").removeClass(\"active\").addClass(\"disabled\");\n getFeatures();\n getEmbedMethod();\n getStandardize();\n beaker.evaluate(\"lasso_cell\"); // evaluate cells with tag \"lasso_cell\"\n // view_result()\n};\nvar reset_lasso = function(){\n beaker.evaluate(\"lasso_gui\");\n};\nvar getFeatures = function() {\n beaker.selected_feature_list = [];\n $('#lasso_features_select input:checkbox').each(function () {\n if(this.checked )\n beaker.selected_feature_list.push(this.value);\n });\n};\n\n \nvar getEmbedMethod = function() {\n beaker.embed_method = \"pca\";\n $('#embed_method_selector input:radio').each(function () {\n if(this.checked )\n beaker.embed_method = this.value;\n });\n};\n \nvar getStandardize = function() {\n beaker.standardize = \"yes\";\n $('#standardize input:radio').each(function () {\n if(this.checked )\n beaker.standardize = this.value;\n });\n};\n \nbeaker.view_result = function(result_link) {\n// beaker.evaluate(\"lasso_viewer_result\").then(function(x) {\n $(\"#lasso_result_button\").attr(\"href\", result_link);\n// }); \n $(\"#lasso_result_button\").removeClass(\"disabled\").addClass(\"active\");\n}\n</script>\n<style type=\"text/css\">\n label {\n font-size: 18px;\n }\n .lasso_control{\n font-size: 18px;\n } \n.lasso_form_group input {\n width: 15px;\n height: 15px;\n padding: 0;\n margin:0;\n padding-right:5px; \n vertical-align: bottom;\n top: -1px;\n} \n .lasso_selection_description{\n padding: 10px 15px;\n }\n</style>\n<div class=\"lasso_control\">\n <div class=\"row\">\n <p class=\"lasso_selection_description\"><b>Primary features </b>\n (all energies are in eV and all distances in Å; hover the mouse pointer over the feature names to see their full description):</p>\n <form id=\"lasso_features_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-2\" title=\"Ionization potential of atom A\"> <input value=\"IP(A)\" type=\"checkbox\"> <i>IP</i> <sup>A</sup></label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"IP(B)\" type=\"checkbox\"> <span title=\"Ionization potential of atom B\"><i>IP</i> <sup>B</sup></span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"EA(A)\" type=\"checkbox\"> <span title=\"Electron affinity of atom A\"> <i>EA</i> <sup>A</sup></span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"EA(B)\" type=\"checkbox\"> <span title=\"Electron affinity of atom B\"> <i>EA</i> <sup>B</sup></span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"HOMO(A)\" type=\"checkbox\"> <span title=\"Energy of highest occupied molecular orbital for atom A\"><i>E</i> <sup>A</sup><sub>HOMO</sub></span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"HOMO(B)\" type=\"checkbox\"> <span title=\"Energy of highest occupied molecular orbital for atom B\"> <i>E</i> <sup>B</sup><sub>HOMO</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"LUMO(A)\" type=\"checkbox\"> <span title=\"Energy of lowest unoccupied molecular orbital for atom A\"> <i>E</i> <sup>A</sup><sub>LUMO</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"LUMO(B)\" type=\"checkbox\"> <span title=\"Energy of lowest unoccupied molecular orbital for atom B\"> <i>E</i> <sup>B</sup><sub>LUMO</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"rs(A)\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence s orbital is maximum for atom A\"> <i>r</i><sub>s</sub><sup>A</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"rs(B)\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence s orbital is maximum for atom B\"> <i>r</i><sub>s</sub><sup>B</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"rp(A)\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence p orbital is maximum for atom A\"> <i>r</i><sub>p</sub><sup>A</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"rp(B)\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence p orbital is maximum for atom B\"> <i>r</i><sub>p</sub><sup>B</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"rd(A)\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence d orbital is maximum for atom A\"> <i>r</i><sub>d</sub><sup>A</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"rd(B)\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence d orbital is maximum for atom B\"> <i>r</i><sub>d</sub><sup>B</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"Es(A)/sqrt(Zval(A))\" type=\"checkbox\"> \n <span title=\"Energy of the valence s orbital(s) divided by the square root of the number of valence electrons of atom A. [Phys. Rev. B 85, 104104 (2012)]\"> <i>E</i><sub>s</sub><sup>A</sup>/sqrt(<i>Z</i> <sup>A</sup><sub>val</sub>) </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"Es(B)/sqrt(Zval(B))\" type=\"checkbox\"> \n <span title=\"Energy of the valence s orbital(s) divided by the square root of the number of valence electrons of atom B. [Phys. Rev. B 85, 104104 (2012)]\"> <i>E</i><sub>s</sub><sup>B</sup>/sqrt(<i>Z</i> <sup>B</sup><sub>val</sub>) </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"Ep(A)/sqrt(Zval(A))\" type=\"checkbox\"> \n <span title=\"Energy of the valence p orbital(s) divided by the square root of the number of valence electrons of atom A. [Phys. Rev. B 85, 104104 (2012)]\"> <i>E</i><sub>p</sub><sup>A</sup>/sqrt(<i>Z</i> <sup>A</sup><sub>val</sub>) </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"Ep(B)/sqrt(Zval(B))\" type=\"checkbox\"> \n <span title=\"Energy of the valence p orbital(s) divided by the square root of the number of valence electrons of atom B. [Phys. Rev. B 85, 104104 (2012)]\"> <i>E</i><sub>p</sub><sup>B</sup>/sqrt(<i>Z</i> <sup>B</sup><sub>val</sub>) </span> </label>\n \n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"d_AA\" type=\"checkbox\"> <span title=\"Bond length of atomA-atomA dimer\"> <i>d</i><sup>AA</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"d_BB\" type=\"checkbox\"> <span title=\"Bond length of atomB-atomB dimer\"> <i>d</i><sup>BB</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"HL_gap_AA\" type=\"checkbox\"> <span title=\"HOMO-LUMO gap of atomA-atomA dimer\"> Δ<i>E</i> <sup>AA</sup><sub>HL</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"HL_gap_BB\" type=\"checkbox\"> <span title=\"HOMO-LUMO gap of atomB-atomB dimer\"> Δ<i>E</i> <sup>BB</sup><sub>HL</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"Ebinding_AA\" type=\"checkbox\"> <span title=\"Binding energy of atomA-atomA dimer\"> <i>E</i> <sup>AA</sup><sub>b</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"Ebinding_BB\" type=\"checkbox\"> <span title=\"Binding energy of atomB-atomB dimer\"> <i>E</i> <sup>BB</sup><sub>b</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"Z(A)\" type=\"checkbox\"> <span title=\"Atomic number of atom A\"> <i>Z</i> <sup>A</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"Z(B)\" type=\"checkbox\"> <span title=\"Atomic number of atom B\"> <i>Z</i> <sup>B</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"val(A)\" type=\"checkbox\"> <span title=\"Number of valence electrons of atom A\"> <i>Z</i> <sup>A</sup><sub>val</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"val(B)\" type=\"checkbox\"> <span title=\"Number of valence electrons of atom B\"> <i>Z</i> <sup>B</sup><sub>val</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"period(A)\" type=\"checkbox\"> <span title=\"Period (in the periodic table) of atom A\"> <i>n</i> <sup>A</sup><sub>period</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"period(B)\" type=\"checkbox\"> <span title=\"Period (in the periodic table) of atom B\"> <i>n</i> <sup>B</sup><sub>period</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"r_sigma\" type=\"checkbox\"> <span title=\"John-Bloch's indicator1: |rp(A) + rs(A) - rp(B) -rs(B)| \n [Phys. Rev. Lett. 33. 1095 (1974)]\"> r<sub>σ</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"r_pi\" type=\"checkbox\"> <span title=\"John-Bloch's indicator2: |rp(A) - rs(A)| +| rp(B) -rs(B)| \n [Phys. Rev. Lett. 33. 1095 (1974)]\"> r<sub>π</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"d_AB\" type=\"checkbox\"> <span title=\"Bond length of atomA-atomB dimer\"> <i>d</i><sup>AB</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"HL_gap_AB\" type=\"checkbox\"> <span title=\"HOMO-LUMO gap of atomA-atomB dimer\"> Δ<i>E</i> <sup>AB</sup><sub>HL</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"Ebinding_AB\" type=\"checkbox\"> <span title=\"Binding energy of atomA-atomB dimer\"> <i>E</i> <sup>AB</sup><sub>b</sub> </span> </label>\n </div>\n </form>\n </div> <!-- End of row-->\n <br>\n <div class=\"row\"> <!-- Start of second row-->\n <div class=\"lasso_form_group\">\n <p class=\"lasso_selection_description\"><b>Embedding methods:</b> </p>\n <div id=\"embed_method_selector\">\n <label class=\"col-xs-4 col-md-4 col-lg-4\"><input name=\"inlineRadioOptions\" id=\"inlineRadio1\" value=\"pca\" checked=\"\" type=\"radio\"> Principal Compenent Analysis (PCA) [<a href=\"https://en.wikipedia.org/wiki/Principal_component_analysis\" target=\"_blank\">more info</a>]</label>\n <label class=\"col-xs-4 col-md-4 col-lg-4\"><input name=\"inlineRadioOptions\" id=\"inlineRadio2\" value=\"mds\" type=\"radio\"> Multidimensional scaling (MDS) [<a href=\"https://en.wikipedia.org/wiki/Multidimensional_scaling\" target=\"_blank\">more info</a>]</label>\n <label class=\"col-xs-4 col-md-4 col-lg-4\"><input name=\"inlineRadioOptions\" id=\"inlineRadio3\" value=\"tsne_pca\" type=\"radio\"> t-Distributed Stochastic Neighbor Embedding (t-SNE) [<a href=\"https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding\" target=\"_blank\">more info</a>]</label>\n </div> \n </div>\n </div><!-- End of row--> \n <div class=\"row\"> <!-- Start of second row-->\n <div class=\"lasso_form_group\">\n <p class=\"lasso_selection_description\"><b>Scale data to unit-variance:</b>\n (data are centered around the mean in any case) [<a href=\"https://en.wikipedia.org/wiki/Feature_scaling\" target=\"_blank\">more info</a>]</p>\n <div id=\"standardize\">\n <label class=\"col-xs-4 col-md-4 col-lg-4\"><input name=\"inlineRadioOptionsStandardize\" id=\"inlineRadio4\" value=\"True\" checked=\"\" type=\"radio\"> yes </label>\n <label class=\"col-xs-4 col-md-4 col-lg-4\"><input name=\"inlineRadioOptionsStandardize\" id=\"inlineRadio5\" value=\"False\" type=\"radio\"> no </label>\n </div> \n </div>\n </div><!-- End of row--> \n <br>\n\n<!-- <span title=''> <img src=\"http://images.clipartpanda.com/question-purzen_Icon_with_question_mark_Vector_Clipart.png\" style=\"height: 30px; width: 30px;\"> </span> -->\n <button class=\"btn btn-default\" onclick=\"run_lasso()\">RUN TWO-DIMENSIONAL EMBEDDING</button>\n <button class=\"btn btn-default\" onclick=\"reset_lasso()\">RESET</button>\n <label title=\"This button becomes active when the run is finished. By clicking it, an interactive structural-similarity plot will be opened\"> <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\">View interactive 2D scatter plot</a> </label>\n</div> <!-- End of lasso_control -->\n"
+ "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<script>\nvar run_lasso = function() {\n $(\"#lasso_result_button\").removeClass(\"active\").addClass(\"disabled\");\n getFeatures();\n getEmbedMethod();\n getStandardize();\n getUnits();\n beaker.evaluate(\"lasso_cell\"); // evaluate cells with tag \"lasso_cell\"\n // view_result()\n};\nvar reset_lasso = function(){\n beaker.evaluate(\"lasso_gui\");\n};\nvar getFeatures = function() {\n beaker.selected_feature_list = [];\n $('#lasso_features_select input:checkbox').each(function () {\n if(this.checked )\n beaker.selected_feature_list.push(this.value);\n });\n};\n \nvar getUnits = function() {\n beaker.units = $(\"#units_select\").val();\n};\n \nvar getEmbedMethod = function() {\n beaker.embed_method = \"pca\";\n $('#embed_method_selector input:radio').each(function () {\n if(this.checked )\n beaker.embed_method = this.value;\n });\n};\n \nvar getStandardize = function() {\n beaker.standardize = \"yes\";\n $('#standardize input:radio').each(function () {\n if(this.checked )\n beaker.standardize = this.value;\n });\n};\n \nbeaker.view_result = function(result_link) {\n// beaker.evaluate(\"lasso_viewer_result\").then(function(x) {\n $(\"#lasso_result_button\").attr(\"href\", result_link);\n// }); \n $(\"#lasso_result_button\").removeClass(\"disabled\").addClass(\"active\");\n}\n</script>\n<style type=\"text/css\">\n label {\n font-size: 18px;\n }\n .lasso_control{\n font-size: 18px;\n } \n.lasso_form_group input {\n width: 15px;\n height: 15px;\n padding: 0;\n margin:0;\n padding-right:5px; \n vertical-align: bottom;\n top: -1px;\n} \n .lasso_selection_description{\n padding: 10px 15px;\n }\n</style>\n<div class=\"lasso_control\">\n <div class=\"row\">\n <p class=\"lasso_selection_description\"><b>Primary features </b>\n (hover the mouse pointer over the feature names to see a full description):</p>\n <form id=\"lasso_features_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_ionization_potential\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic ionization potential\"><i>IP</i> </span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_electron_affinity\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic electron affinity\"> <i>EA</i></span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_homo\" type=\"checkbox\"> <span title=\"Energy of highest occupied molecular orbital\"><i>E</i> <sub>HOMO</sub></span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-2\"> <input value=\"atomic_lumo\" type=\"checkbox\"> <span title=\"Energy of lowest unoccupied molecular orbital\"> <i>E</i> <sub>LUMO</sub> </span> </label>\n \n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_rs_max\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence s orbital is maximum\"> <i>r</i><sub>s</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_rp_max\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence p orbital is maximum\"> <i>r</i><sub>p</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_rd_max\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence d orbital is maximum\"> <i>r</i><sub>d</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_number\" type=\"checkbox\"> <span title=\"Atomic number\"> <i>Z</i> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_number_valence_electrons\" type=\"checkbox\"> <span title=\"Number of valence electrons\"> <i>Z</i><sub>val</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"period\" type=\"checkbox\"> <span title=\"Period (in the periodic table)\"> <i>n</i> <sub>period</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_r_by_2_dimer\" type=\"checkbox\"> <span title=\"Bond length of the dimer\"> <i>d</i> <sub>dimer</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_electronic_binding_energy_dimer\" type=\"checkbox\"> <span title=\"Binding energy of the dimer\"> <i>E</i> <sub>b</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_homo_lumo_diff\" type=\"checkbox\"> <span title=\"HOMO-LUMO gap of the dimer\"> Δ<i>E</i><sub>HL</sub> </span> </label>\n \n<!--- <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"Es/sqrt(Zval)\" > \n <span title=\"Energy of the valence s orbital(s) divided by the square root of the number of valence electrons. [Phys. Rev. B 85, 104104 (2012)]\"> <i>E</i><sub>s</sub>/sqrt(<i>Z</i> <sub>val</sub>) </span> </label>\n <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"Ep/sqrt(Zval)\" > \n <span title=\"Energy of the valence p orbital(s) divided by the square root of the number of valence electrons. [Phys. Rev. B 85, 104104 (2012)]\"> <i>E</i><sub>p</sub>/sqrt(<i>Z</i> <sub>val</sub>) </span> </label>\n--> \n </div>\n </form>\n </div> <!-- End of row-->\n \n <br>\n <div class=\"row\"> <!-- Start of row-->\n <p class=\"lasso_selection_description\"><b>Unit of measures: </b> \n <select id=\"units_select\">\n <option value=\"eV_angstrom\"> [energy]=eV; [length]=angstrom</option>\n <option value=\"J_m\"> [energy]=J; [length]=m</option>\n <option value=\"kcal/mol_angstrom\"> [energy]=kcal/mol; [length]=angstrom</option>\n </select> </p>\n </div><!-- End of row-->\n \n <br>\n <div class=\"row\"> <!-- Start of second row-->\n <div class=\"lasso_form_group\">\n <p class=\"lasso_selection_description\"><b>Embedding methods:</b> </p>\n <div id=\"embed_method_selector\">\n <label class=\"col-xs-4 col-md-4 col-lg-4\"><input name=\"inlineRadioOptions\" id=\"inlineRadio1\" value=\"pca\" checked=\"\" type=\"radio\"> Principal Compenent Analysis (PCA) [<a href=\"https://en.wikipedia.org/wiki/Principal_component_analysis\" target=\"_blank\">more info</a>]</label>\n <label class=\"col-xs-4 col-md-4 col-lg-4\"><input name=\"inlineRadioOptions\" id=\"inlineRadio2\" value=\"mds\" type=\"radio\"> Multidimensional scaling (MDS) [<a href=\"https://en.wikipedia.org/wiki/Multidimensional_scaling\" target=\"_blank\">more info</a>]</label>\n <label class=\"col-xs-4 col-md-4 col-lg-4\"><input name=\"inlineRadioOptions\" id=\"inlineRadio3\" value=\"tsne_pca\" type=\"radio\"> t-Distributed Stochastic Neighbor Embedding (t-SNE) [<a href=\"https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding\" target=\"_blank\">more info</a>]</label>\n </div> \n </div>\n </div><!-- End of row--> \n <div class=\"row\"> <!-- Start of second row-->\n <div class=\"lasso_form_group\">\n <p class=\"lasso_selection_description\"><b>Scale data to unit-variance:</b>\n (data are centered around the mean in any case) [<a href=\"https://en.wikipedia.org/wiki/Feature_scaling\" target=\"_blank\">more info</a>]</p>\n <div id=\"standardize\">\n <label class=\"col-xs-4 col-md-4 col-lg-4\"><input name=\"inlineRadioOptionsStandardize\" id=\"inlineRadio4\" value=\"True\" checked=\"\" type=\"radio\"> yes </label>\n <label class=\"col-xs-4 col-md-4 col-lg-4\"><input name=\"inlineRadioOptionsStandardize\" id=\"inlineRadio5\" value=\"False\" type=\"radio\"> no </label>\n </div> \n </div>\n </div><!-- End of row--> \n <br>\n\n<!-- <span title=''> <img src=\"http://images.clipartpanda.com/question-purzen_Icon_with_question_mark_Vector_Clipart.png\" style=\"height: 30px; width: 30px;\"> </span> -->\n <button class=\"btn btn-default\" onclick=\"run_lasso()\">RUN TWO-DIMENSIONAL EMBEDDING</button>\n <button class=\"btn btn-default\" onclick=\"reset_lasso()\">RESET</button>\n <label title=\"This button becomes active when the run is finished. By clicking it, an interactive structural-similarity plot will be opened\"> <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\">View interactive 2D scatter plot</a> </label>\n</div> <!-- End of lasso_control -->\n"
},
- "height": 473
+ "height": 570
},
"evaluatorReader": true,
- "lineCount": 144
+ "lineCount": 137
},
{
"id": "code2uVtKX",
@@ -407,51 +392,331 @@
"input": {
"body": [
"from IPython.core.display import HTML ",
- "",
- "# load packages",
- "from nomad_sim.wrappers_desc_class import get_json_list, calc_descriptor ",
- "from nomad_sim.wrappers_desc_class import calc_model, calc_embedding, plot",
+ "from nomad_sim.wrappers import get_json_list, calc_descriptor ",
+ "from nomad_sim.wrappers import calc_model, calc_embedding, plot",
+ "from nomad_sim.parsing_utils import read_gdb_7k",
+ "from nomad_sim.utils_crystals import create_supercell",
+ "from nomad_sim.utils_crystals import create_vacancies",
+ "from nomad_sim.utils_crystals import random_displace_atoms",
+ "from nomad_sim.utils_crystals import substitute_atoms",
+ "from nomad_sim.descriptors import XrayDiffraction",
"from nomad_sim.utils_crystals import create_supercell",
"",
+ "# hack to change to local/Beaker mode in all files in the packages",
+ "# DEPRECATED",
+ "import __builtin__",
+ "__builtin__.isBeaker = True",
+ "",
"import hashlib",
"",
+ "import sys, os",
+ "import pandas as pd",
+ "import numpy as np",
+ "import json",
+ "",
+ "",
"# define paths",
"tmp_folder = '/home/beaker/.beaker/v1/web/tmp/'",
"control_file = '/home/beaker/.beaker/v1/web/tmp/control.json'",
- "data_folder='/home/beaker/test/nomad_sim/data_zcrs'",
+ "data_folder='/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/'",
"lookup_file = '/home/beaker/.beaker/v1/web/tmp/lookup.dat'",
- "atomic_data_file = '/home/beaker/test/nomad_sim/lasso_example/atom_info.csv'",
- "binary_data_file = '/home/beaker/test/nomad_sim/lasso_example/dimer_info.csv'",
+ "collection_path = '/home/beaker/test/nomad_sim/data_zcrs/ExtendedBinaries_Dimers_Atoms_new.json'",
+ "path_to_collection = '/home/beaker/test/nomad_sim/data_zcrs/ExtendedBinaries_Dimers_Atoms_new.json'",
"",
+ "# define units",
+ "if beaker.units == 'eV_angstrom':",
+ " energy_unit = 'eV'",
+ " length_unit = 'angstrom'",
+ "elif beaker.units == 'J_m':",
+ " energy_unit = 'J'",
+ " length_unit = 'm'",
+ "elif beaker.units == 'kcal/mol_angstrom':",
+ " energy_unit = 'kcal/mol'",
+ " length_unit = 'angstrom'"
+ ],
+ "hidden": true
+ },
+ "output": {
+ "selectedType": "BeakerDisplay",
+ "state": {},
+ "pluginName": "IPython",
+ "shellId": "D7DE8A033E0A49EB8A87DC9597DD4326",
+ "height": 103,
+ "elapsedTime": 1101
+ },
+ "evaluatorReader": true,
+ "lineCount": 42,
+ "tags": "lasso_cell"
+ },
+ {
+ "id": "codelrvhSB",
+ "type": "code",
+ "evaluator": "IPython",
+ "input": {
+ "body": [
"# get the json_list",
- "json_list = get_json_list(method='folder', drop_duplicates=False, ",
- " data_folder=data_folder, tmp_folder=tmp_folder)",
+ "#json_list = get_json_list(method='folder', drop_duplicates=False, ",
+ "# data_folder=data_folder, tmp_folder=tmp_folder)",
"",
- "# 3x3 supercell for visualization purposes",
+ "# pass only lowest energy structures to save time for demonstation purposes",
+ "json_list = [",
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+ ""
+ ],
+ "hidden": true
+ },
+ "output": {
+ "state": {},
+ "selectedType": "Hidden",
+ "pluginName": "IPython",
+ "shellId": "D7DE8A033E0A49EB8A87DC9597DD4326",
+ "elapsedTime": 457
+ },
+ "evaluatorReader": true,
+ "lineCount": 89,
+ "tags": "lasso_cell"
+ },
+ {
+ "id": "codeVePPlk",
+ "type": "code",
+ "evaluator": "IPython",
+ "input": {
+ "body": [
"operations_on_structure = [(create_supercell, {'replicas': [3, 3, 3]})]",
"op_list = np.zeros(len(json_list))",
"",
- "calc_descriptor(desc_type='atomic_features', ",
+ "kwargs = {'path_to_collection': path_to_collection,",
+ " 'feature_order_by': 'atomic_mulliken_electronegativity',",
+ " 'energy_unit': energy_unit,",
+ " 'length_unit': length_unit}",
+ "",
+ "dict_delta_e = {'SeZn': 4.2159179660687287e-20, 'InSb': 1.2506570609555687e-20, 'AgCl': -6.8568799955090609e-21, 'SZn': 4.4190167090138643e-20, 'BN': 2.7430550221687302e-19, 'GaSb': 2.4773702178144287e-20, 'BrRb': -2.6246943074069208e-20, 'BaTe': -6.0143598233041078e-20, 'BeSe': 7.9298202208796193e-20, 'MgS': -1.3890792272791661e-20, 'AsB': 1.4018696180162358e-19, 'AlAs': 3.416831556361176e-20, 'BP': 1.632978757533666e-19, 'TeZn': 3.9253535511316122e-20, 'MgSe': -8.8603255975880209e-21, 'ClLi': -6.149391549293258e-21, 'FK': -2.3456843288794608e-20, 'BrLi': -5.2465217764284492e-21, 'BSb': 9.3062289002001379e-20, 'ClRb': -2.5715504707788539e-20, 'GeSn': 1.3083912918128912e-20, 'CsI': -2.6017342042091155e-20, 'CaTe': -5.6149286826500206e-20, 'ClK': -2.6349506219210773e-20, 'Sn2': 2.7179163244033424e-21, 'BrCs': -2.4972695386489382e-20, 'CsF': -1.734569615637085e-20, 'BrCu': 2.442400384019518e-20, 'CaSe': -5.7806170659176063e-20, 'AgF': -2.4634695420313482e-20, 'MgTe': -7.3560522736479063e-22, 'FLi': -9.5310792412059186e-21, 'CuF': -2.7272687327072279e-21, 'FNa': -2.3357835066436331e-20, 'C2': 4.2114873809101575e-19, 'BaO': -1.4900011177054134e-20, 'AgBr': -4.8118839046830307e-21, 'MgO': -3.721451404088126e-20, 'FRb': -2.1724838814450727e-20, 'AlN': 1.1687730189874494e-20, 'Si2': 4.4727296163305501e-20, 'SiSn': 2.1646816357014748e-20, 'OSr': -3.5297012817210187e-20, 'ClNa': -2.1307665354820141e-20, 'AsIn': 2.14767895373523e-20, 'OZn': 1.633710321777262e-20, 'CGe': 1.3000748379902827e-19, 'CdO': -1.348413629348854e-20, 'InP': 2.8709930119109753e-20, 'SSr': -5.9029656118592692e-20, 'InN': 2.4628706405675984e-20, 'BaSe': -5.5025977545738119e-20, 'BrK': -2.6624325013472597e-20, 'BeTe': 7.5075740576200973e-20, 'CdS': 1.1643465692630618e-20, 'CdTe': 1.8351256432814928e-20, 'GeSi': 4.217091895225337e-20, 'GaP': 5.5876198809236085e-20, 'CdSe': 1.3389702567051265e-20, 'INa': -1.8399111846593045e-20, 'AlP': 3.5080994271602511e-20, 'BeO': 1.1084460139894976e-19, 'AsGa': 4.3944144343852047e-20, 'Ge2': 3.218012279776111e-20, 'SeSr': -6.0003270319365202e-20, 'CSi': 1.071894196156348e-19, 'BaS': -5.1231589897332471e-20, 'AgI': 5.9161045280535275e-21, 'GaN': 6.9445584247860156e-20, 'CaS': -5.9141658617526103e-20, 'AlSb': 2.5133142314028706e-20, 'IK': -2.6762621853286689e-20, 'ILi': -3.4704646494924847e-21, 'ClCs': -2.4088110334584613e-20, 'CaO': -4.2492775596486839e-20, 'CuI': 3.2792483878850995e-20, 'CSn': 7.2664795347721018e-20, 'BeS': 8.1122637897805144e-20, 'IRb': -2.6788624696652254e-20, 'BrNa': -2.0256115610545176e-20, 'SrTe': -6.0769715445352658e-20, 'ClCu': 2.5035406212316063e-20}",
+ "",
+ "#derived_features = []",
+ "#selected_feature_list = beaker.selected_feature_list",
+ "",
+ "#if 'Es/sqrt(Zval)' in selected_feature_list:",
+ "# derived_features.append('Es/sqrt(Zval)')",
+ "# selected_feature_list.remove('Es/sqrt(Zval)')",
+ "# selected_feature_list.append('atomic_valence_s_orbital')",
+ "# selected_feature_list.append('atomic_number_valence_electrons')",
+ " ",
+ "#if 'Ep/sqrt(Zval)' in selected_feature_list:",
+ "# derived_features.append('Ep/sqrt(Zval)')",
+ "# selected_feature_list.remove('Ep/sqrt(Zval)')",
+ "# selected_feature_list.append('atomic_valence_p_orbital')",
+ "# selected_feature_list.append('atomic_number_valence_electrons')",
+ " ",
+ "descriptor = calc_descriptor(",
+ " desc_type='atomic_features',",
" selected_feature_list=beaker.selected_feature_list,",
- " atomic_data_file=atomic_data_file,",
- " binary_data_file=binary_data_file,",
- " op_list=op_list, operations_on_structure=operations_on_structure,",
- " json_list=json_list, tmp_folder=tmp_folder)"
+ " dict_delta_e=dict_delta_e,",
+ " op_list=op_list,",
+ " operations_on_structure=operations_on_structure,",
+ " json_list=json_list, tmp_folder=tmp_folder,",
+ " **kwargs)"
],
"hidden": true
},
"output": {
- "selectedType": "Results",
"state": {},
+ "selectedType": "Results",
"pluginName": "IPython",
- "shellId": "5FCF2F4B5D1447E9B2FEBE19E7207F37",
- "height": 103,
- "elapsedTime": 16833
+ "shellId": "D7DE8A033E0A49EB8A87DC9597DD4326",
+ "elapsedTime": 7947,
+ "height": 166
},
"evaluatorReader": true,
- "lineCount": 31,
+ "lineCount": 33,
"tags": "lasso_cell"
},
+ {
+ "id": "codeZFE5kr",
+ "type": "code",
+ "evaluator": "IPython",
+ "input": {
+ "body": [
+ "# pass only lowest energy structures to save time for demonstation purposes",
+ "json_list = [",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pm0_fbKdKA2iyued6niH-AARk8hhM.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PzZe8HJ1RoiT6LBluiHmTN9IDP6vE.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P6N-eaR5japcqjIGylr67mAGo9L-S.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PMbzdub7JONozp5LPWlPqLbGuLt3F.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PyBnwEdQ98isxcx9_miHJ2Tr82JrN.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PECMSMMNgxQUVLxlv5IWYEvWOatMh.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PK5EwBMnyyGjm5_lykmBBaMU7FzFl.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PezFp7D_Pzi-KwwYE9WlnFWtpTP_2.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PlQ7NfvecVk8-o2I_Fbz0hNtkAJAw.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PWBxopsGbXEANMPDUxcMi-PzKvqxH.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PUC2t35p9KOEdmaAyB7I91DoUyae7.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P1RXpIJmIprXumBAD3Lk20-RwmC19.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PoXHWtsIc1BlQ7N2bsUiZ0PJnFa6O.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PVvk2rLGsl4Gd6Q3l0Cbnyi1bM4XO.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pb4Ku0TY7IkW9pjHBECQguVhvtd6Q.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pqky2IgyYljS01KXKFanIV11nbcCT.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PeXUCf_QcDwfIhLJTg61D3lsjvJQu.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PVH2AkTXt2QDVEfJdFkGPAMk1_dQO.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PLoQIJtvhgUQcXFhb0k_6mWOPV9NI.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pp-9DTkK5y5w7fFZOf-5JJc9SCPD1.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PN0pxdAiZpbbUV2jORc4LSy5MaYWe.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PGex81N1PxLHkRkSGopRqqLQ4tSkp.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PWNJV2eK0tIrw_AEg-EpXTggLH88h.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PbkJ-LOXCmwltwIWDXwnHWXpySRVi.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PB-GqTDr-DZ-j4OKjRNJEp1hnOGvG.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pb4jnAWzhAL1kkV-J0QHJTsWUtBCj.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PwXFVrN5zPsZq5W93S0r3XPR3O7kq.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PhF_jMdta8Ncok9i2JHC7G1ZM5KPP.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pt5thhX-pEWdlL6-DGsQe2r6Gr-lu.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PSvyfO0p4QEfhh7dUujLdUg8lCNs0.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PHQG6-EPlnROo0wmc11YFOLefErCO.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P_Lx9ePtVOK5MyoQBlUWA_kePKF_J.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P-WFXv4pg5JXNw8v86SVKW9_gFrbO.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PkP9vxbD_d5in7JZZd-W-Rv7yvYzJ.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pi1rNqBwWwWQBy5RoGVMcJaix-ISM.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pz-zWbbn5PNd-5CJdBVD60npmzSwn.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PTijdgDWu11E79tuyylukptiyCtv2.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pr3fuw6xCJS5vZiUf9B5tW2KT_LQW.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PGsPQn1h36VyBTthr3CnA6yAtlzs3.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Ph-6A75k6v-qJ-tgzcs-BoIWFGqQb.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P4dSQn4GKPhaTawz0JtVOyotDaGom.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PbV7iF5sNHb5Y7MIF4vaxwqWLsHdh.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PVQgfnLx6_iwg7AoMC0GB0VQmBJ6g.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Ppn_-f3QxBgeCwkICEO4BL62GIBx6.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PJYTR_x-6ANZ-cAsi75D5h9Gvb1e-.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PJz4SOdD_cp-YPSfaJ0QWYOzYiZB7.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PcpD0axNY3fEO1jmggSHMCtnWuX2q.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pb0-IKoZYu3Pmbu323yUsGR8jQe_e.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P-1SH_T1kd13-U3MEB7Xz-_eToBHT.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PUcFCGgEnxeFQIWTg8qeByla9jJJg.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pd23q1LJrA4DOKbForwH4cvHWRk6U.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PB8zc5-R1ZXaxutxBRsD247NMyR2N.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Phb63KR9BOj86coXGS0bKGD2xq5O2.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PZo5v3_KRI2CARrYsoiYNun-FaJCd.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PLlOCjkEQ61Se5wdc_H7h4MP65gOC.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PSFiXUNv75SzlqJDfVZ0BFKrSsAax.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PWoElPtI5U48PFUHK-yXJfn4JaasP.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P0Zgt21TvKKb18vKKFKXYNI-bDofb.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pv4l5-nI7xyQQgnAULtpVXTuXvZo9.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PtPzGOtC64C9WwpqoUjnlET1liwRP.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PC4jwHwSTdNEilYtIDuuNIRBUH_Df.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PkUwSxY7ro62M6SUfGJGZJTa1z1G0.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/POHjGTnYd8JGgqzKrI5tTc_o8GPAy.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pg4Lo5RY8cWWojQUOg9ikurdCqPnb.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PC0ikq0ulkygT2Co59UBAl9YcYxbG.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pw3ao50E0u9EV1Kb8W3-o-fSnuyxs.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PF8Zb1nzPb5YMugWmjUm0gAS0JySC.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PKCyiUMeNTeE2Qp-8ElDtGu3iDVh0.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PokNGy5MbvPoNIi4g95YgX_oF4AI6.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P0KVR6NK-7BxgOXt-9FWllzZwD66-.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PleD1AL4HSm48SHMVamKaMdll77TE.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PKUz1_qykpLy_iKM-at6yErVDGuXD.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PCgNXVu7zVP-rO_jZl4Vc-Z0K_WPH.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PavCzBt15bIH5NeKUXulmwe7uQyAM.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PRakENtX-ME-LrbIo19w0RDyRE6Bi.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pbb6tWhL8Cn4P0j4XcwS8O6oopygF.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PwTh1t979bFWSWD2gFWLF_rVtJKv8.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P1cjW50CGsQC-wkw0ZfTGzpzrdXCQ.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pq0gpi99XHDz4L10rfZOe1YlMTo5R.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PFvJLQd4N-p0O9ytP6TRzvEqM94gJ.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PUzjQT0patVJ9CyvEnKl_xQwoO7iX.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pj4jIPerqprBjHAT6ZKsbXGPsSmze.json']",
+ ""
+ ],
+ "hidden": true
+ },
+ "output": {
+ "state": {},
+ "selectedType": "Hidden",
+ "pluginName": "IPython",
+ "shellId": "D7DE8A033E0A49EB8A87DC9597DD4326",
+ "elapsedTime": 383,
+ "height": 78
+ },
+ "evaluatorReader": true,
+ "tags": "lasso_cell",
+ "lineCount": 85
+ },
{
"id": "codeeWTtU4",
"type": "code",
@@ -462,6 +727,8 @@
"",
"calc_embedding(embed_method=beaker.embed_method, embed_params=embed_params,",
" desc_type='atomic_features',",
+ " energy_unit=energy_unit,",
+ " length_unit=length_unit,",
" lookup_file=lookup_file, tmp_folder=tmp_folder,",
" standardize=beaker.standardize)",
""
@@ -472,12 +739,12 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "5FCF2F4B5D1447E9B2FEBE19E7207F37",
- "height": 215,
- "elapsedTime": 397
+ "shellId": "D7DE8A033E0A49EB8A87DC9597DD4326",
+ "height": 78,
+ "elapsedTime": 384
},
"evaluatorReader": true,
- "lineCount": 7,
+ "lineCount": 9,
"tags": "lasso_cell"
},
{
@@ -495,13 +762,12 @@
" path_to_file=lookup_file, drop_duplicates=True, displace_duplicates=True, predicted_value=False)",
"beaker.viewer_result = name_html_page",
"",
- "",
"plot_result = plot(name=name_html_page, json_list=json_list, frames='list', frame_list=frame_list, ",
" file_format='NOMAD', clustering_x_list=x_list, clustering_y_list=y_list, target_list=target_list,",
- " target_unit='eV', legend_title='Reference E(RS)-E(ZB)', target_name='E(RS)-E(ZB)', ",
- " plot_title = 'Two-dimensional embedding',",
- " op_list=op_list, operations_on_structure=operations_on_structure,",
- " clustering_point_size=12, tmp_folder=tmp_folder, control_file=control_file)",
+ " target_unit=energy_unit, energy_unit=energy_unit, legend_title='Reference E(RS)-E(ZB)', target_name='E(RS)-E(ZB)',",
+ " plot_title='Two-dimensional embedding',",
+ " clustering_point_size=12, tmp_folder=tmp_folder, control_file=control_file,",
+ " op_list=op_list, operations_on_structure=operations_on_structure)",
""
],
"hidden": true
@@ -510,12 +776,12 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "5FCF2F4B5D1447E9B2FEBE19E7207F37",
- "height": 103,
- "elapsedTime": 5506
+ "shellId": "D7DE8A033E0A49EB8A87DC9597DD4326",
+ "height": 78,
+ "elapsedTime": 6634
},
"evaluatorReader": true,
- "lineCount": 17,
+ "lineCount": 16,
"tags": "lasso_cell"
},
{
@@ -546,7 +812,8 @@
"pluginName": "JavaScript",
"state": {},
"hidden": true,
- "elapsedTime": 46
+ "elapsedTime": 50,
+ "height": 51
},
"evaluatorReader": true,
"lineCount": 2,
@@ -555,12 +822,8 @@
],
"namespace": {
"selected_feature_list": [
- "rs(A)",
- "rs(B)",
- "rp(A)",
- "rp(B)",
- "rd(A)",
- "rd(B)"
+ "atomic_ionization_potential",
+ "atomic_rs_max"
],
"allowed_operations": [
"|-|",
@@ -575,9 +838,10 @@
11
],
"runInfo": "running Lasso",
- "viewer_result": "a07a590d6030cf73",
+ "viewer_result": "68013492a0f6f33e",
"embed_method": "pca",
- "standardize": "True"
+ "standardize": "False",
+ "units": "eV_angstrom"
},
"locked": true
}
diff --git a/beaker-notebooks/LASSO_L0.bkr b/beaker-notebooks/LASSO_L0.bkr
index c533be458d50eb31bb0f064e74bc7266983ed64b..05e55b5b671064bd503b9202e1677655af345c28 100644
--- a/beaker-notebooks/LASSO_L0.bkr
+++ b/beaker-notebooks/LASSO_L0.bkr
@@ -11,66 +11,69 @@
}
},
{
- "name": "TeX",
- "plugin": "TeX",
+ "name": "JavaScript",
+ "plugin": "JavaScript",
"view": {
"cm": {
- "mode": "stex"
+ "mode": "javascript",
+ "background": "#FFE0F0"
}
- }
+ },
+ "languageVersion": "ES2015"
},
{
"name": "IPython",
"plugin": "IPython",
- "imports": "",
- "supplementalClassPath": "",
+ "setup": "%matplotlib inline\nimport numpy\nimport matplotlib\nfrom matplotlib import pylab, mlab, pyplot\nnp = numpy\nplt = pyplot\nfrom IPython.display import display\nfrom IPython.core.pylabtools import figsize, getfigs\nfrom pylab import *\nfrom numpy import *\n",
"view": {
"cm": {
"mode": "python"
}
- },
- "setup": "%matplotlib inline\nimport numpy\nimport matplotlib\nfrom matplotlib import pylab, mlab, pyplot\nnp = numpy\nplt = pyplot\nfrom IPython.display import display\nfrom IPython.core.pylabtools import figsize, getfigs\nfrom pylab import *\nfrom numpy import *\n"
- },
- {
- "name": "JavaScript",
- "plugin": "JavaScript",
- "jsSetting2": "",
- "jsSetting1": "",
- "view": {
- "cm": {
- "mode": "javascript",
- "background": "#FFE0F0"
- }
- },
- "languageVersion": "ES2015"
+ }
}
],
"cells": [
{
- "id": "markdownpEW8aT",
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- "<label style=\"text-align: left; color: #20335d; font-weight: 900; font-size: 18pt; padding-top: 2em;\">",
- " Predicting energy differences between crystal structures:</label><br/><label style=\"color: #20335d;font-weight: 900; font-size: 15pt;\"> Octet-binary zincblende vs. rocksalt semiconductors</label>",
- " </p>",
- " <p style=\"font-size: 15px;\">Angelo Ziletti, Ankit Kariryaa, Emre Ahmetcik, Fawzi Mohamed, Luca Ghiringhelli, Matthias Scheffler <span style=\"font-size: smaller;\">[version 2017-01-02]</span></p>",
- " ",
- "<div style=\"padding-top: 1em;\">",
- "This tutorial shows how to find descriptive parameters (short formulas) that predict crystal structure, using the example of octet binary compounds that have either rocksalt (RS) or zincblende (ZB) structure. It is based on</div>",
- "<div style=\"padding: 1ex; margin-top: 1ex; margin-bottom: 1ex; border-style: dotted; border-width: 1pt; border-color: blue; border-radius: 3px;\">",
- "L. M. Ghiringhelli, J. Vybiral, S. V. Levchenko, C. Draxl, M. Scheffler: <span style=\"font-style: italic;\">Big Data of Materials Science: Critical Role of the Descriptor</span>, Phys. Rev. Lett. 114, 105503 (2015) <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\">[PDF]</a>",
- "</div>",
- "<div>",
- "Click on \"Run\" below to reproduce results from this publication; click \"Background\" for an explanation of the approach; or, modify \"Settings\" to produce your own results.",
- "</div>",
- "<div style=\"padding-top: 2ex;\">",
- "<span style=\"font-weight: bold;\">Idea: </span> Starting from simple physical quantities (\"building blocks\", here properties of the constituent free atoms such as orbital radii), thousands of candidate formulas are generated by applying arithmetic operations combining building blocks, for example forming sums and products of them. Then, a sparse regression method is used to select only a few of these formulas that explain the data.",
- "</div>"
- ],
- "evaluatorReader": false
+ "id": "code61yhp1",
+ "type": "code",
+ "evaluator": "HTML",
+ "input": {
+ "body": [
+ "<label style=\"text-align: left; color: #20335d; font-weight: 900; font-size: 18pt; padding-top: 2em;\">",
+ " Predicting energy differences between crystal structures I (large feature space):</label><br/><label style=\"color: #20335d;font-weight: 900; font-size: 15pt;\"> Octet-binary zincblende vs. rocksalt semiconductors</label>",
+ " </p>",
+ " <p style=\"font-size: 15px;\">Angelo Ziletti, Ankit Kariryaa, Emre Ahmetcik, Fawzi Mohamed, Luca Ghiringhelli, and Matthias Scheffler <span style=\"font-size: smaller;\">[version 2017-01-26]</span></p>",
+ " ",
+ "<div style=\"padding-top: 1em;\">",
+ "This tutorial shows how to find descriptive parameters (short formulas) that predict crystal structure, using the example of octet binary compounds that have either rocksalt (RS) or zincblende (ZB) structure. It is based on</div>",
+ "<div style=\"padding: 1ex; margin-top: 1ex; margin-bottom: 1ex; border-style: dotted; border-width: 1pt; border-color: blue; border-radius: 3px;\">",
+ "L. M. Ghiringhelli, J. Vybiral, S. V. Levchenko, C. Draxl, M. Scheffler: <span style=\"font-style: italic;\">Big Data of Materials Science: Critical Role of the Descriptor</span>, Phys. Rev. Lett. 114, 105503 (2015) <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\">[PDF]</a>",
+ "</div>",
+ "<div>",
+ "Click on \"Run\" below to reproduce results from this publication; click \"Background\" for an explanation of the approach; or, modify \"Settings\" to produce your own results.",
+ "</div>",
+ "<div style=\"padding-top: 2ex;\">",
+ "<span style=\"font-weight: bold;\">Idea: </span> Starting from simple physical quantities (\"building blocks\", here properties of the constituent free atoms such as orbital radii), thousands of candidate formulas are generated by applying arithmetic operations combining building blocks, for example forming sums and products of them. Then, a sparse regression method is used to select only a few of these formulas that explain the data.",
+ "</div>"
+ ],
+ "hidden": true
+ },
+ "output": {
+ "state": {},
+ "result": {
+ "type": "BeakerDisplay",
+ "innertype": "Html",
+ "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<label style=\"text-align: left; color: #20335d; font-weight: 900; font-size: 18pt; padding-top: 2em;\">\n Predicting energy differences between crystal structures I (large feature space):</label><br><label style=\"color: #20335d;font-weight: 900; font-size: 15pt;\"> Octet-binary zincblende vs. rocksalt semiconductors</label>\n <p></p>\n <p style=\"font-size: 15px;\">Angelo Ziletti, Ankit Kariryaa, Emre Ahmetcik, Fawzi Mohamed, Luca Ghiringhelli, and Matthias Scheffler <span style=\"font-size: smaller;\">[version 2017-01-26]</span></p>\n \n<div style=\"padding-top: 1em;\">\nThis tutorial shows how to find descriptive parameters (short formulas) that predict crystal structure, using the example of octet binary compounds that have either rocksalt (RS) or zincblende (ZB) structure. It is based on</div>\n<div style=\"padding: 1ex; margin-top: 1ex; margin-bottom: 1ex; border-style: dotted; border-width: 1pt; border-color: blue; border-radius: 3px;\">\nL. M. Ghiringhelli, J. Vybiral, S. V. Levchenko, C. Draxl, M. Scheffler: <span style=\"font-style: italic;\">Big Data of Materials Science: Critical Role of the Descriptor</span>, Phys. Rev. Lett. 114, 105503 (2015) <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\">[PDF]</a>\n</div>\n<div>\nClick on \"Run\" below to reproduce results from this publication; click \"Background\" for an explanation of the approach; or, modify \"Settings\" to produce your own results.\n</div>\n<div style=\"padding-top: 2ex;\">\n<span style=\"font-weight: bold;\">Idea: </span> Starting from simple physical quantities (\"building blocks\", here properties of the constituent free atoms such as orbital radii), thousands of candidate formulas are generated by applying arithmetic operations combining building blocks, for example forming sums and products of them. Then, a sparse regression method is used to select only a few of these formulas that explain the data.\n</div>"
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- "id": "code43f7kq",
+ "id": "code83Tpsb",
"type": "code",
"evaluator": "HTML",
"input": {
@@ -81,7 +84,8 @@
" getFeatures();",
" getOperators();",
" getMaxDim();",
- " beaker.evaluate(\"lasso_cell\"); // evaluate cells with tag \"lasso_cell\"",
+ " getUnits();",
+ " beaker.evaluate(\"calc_cell\"); // evaluate cells with tag \"calc_cell\"",
" // view_result()",
"};",
"var reset_lasso = function(){",
@@ -108,6 +112,10 @@
"var getMaxDim = function() {",
" beaker.max_dim = $(\"#lasso_max_dim_selector\").val();",
"};",
+ " ",
+ "var getUnits = function() {",
+ " beaker.units = $(\"#units_select\").val();",
+ "};",
"var toggle_settings = function(){",
" var e = document.getElementById('lasso-hidden-settings-div');",
" var b = document.getElementById('lasso-hidden-settings-button');",
@@ -161,7 +169,7 @@
" <img style=\"width:67%;height:67%\" src=\"https://gitlab.mpcdf.mpg.de/nomad-lab/public-wiki/uploads/eb33f1415db1b6d489cbbc3e6a899942/2016-08-02_ZB_RS3-2.png\">",
" <br/>",
" <br/>",
- " <p> In this map the octet binaries are located via the descriptor found by our LASSO+L0 approach. The descriptor is based purely on free-atom data, namely radii of the s and p valence orbitals (rs and rp) of the atomic species and their Ionizaiton Potential and Electron Affinity (IP and EA). Materials in the red (bue) region crystallize preferably in the zincblende (rocksalt) structure. The distance to the green line is proportional to the difference in energy between the two structures. In the interactive plot accessible at the end of the learning performed by the present tool, one can obtain information on the materials by hovering and clicking on the data points. </p>",
+ " <p> In this map the octet binaries are located via the descriptor found by our LASSO+L0 approach. The descriptor is based purely on free-atom data, namely radii of the s and p valence orbitals (rs and rp) of the atomic species and their Ionizaiton Potential and Electron Affinity (IP and EA). Materials in the red (blue) region crystallize preferably in the zincblende (rocksalt) structure. The distance to the green line is proportional to the difference in energy between the two structures. In the interactive plot accessible at the end of the learning performed by the present tool, one can obtain information on the materials by hovering and clicking on the data points. </p>",
" <p>References:</p>",
" <ol>",
" <li>J. A. van Vechten, Phys. Rev. 182, 891 (1969).</li>",
@@ -195,14 +203,14 @@
" <h4 class=\"modal-title\" id=\"lasso-instructions-modal-label\">Instructions</h4>",
" </div>",
" <div class=\"modal-body lasso_instructions\">",
- "<p>In this example, you can run a compressed-sensing based algorithm for finding the optimal descriptor and model that predicts the difference in energy between crystal structures (here, rocksalt vs. zincblende). </p>",
+ "<p>In this example, you can run a compressed-sensing based algorithm for finding the optimal descriptor (and model) that predicts the difference in energy between crystal structures (here, rocksalt vs. zincblende). </p>",
"",
"<p>The descriptor is selected out of a large number of candidates constructed as functions of basic input features, the primary features. </p>",
"",
"<p>You can select the primary features as well as which kind of unary and binary operations are allowed from the checklist below. You can also select the maximum dimensionality of the descriptor. </p>",
- "<p> After the wished features have been selected, click <b>RUN!</b> for performing the calculations (loading the values of the primary features, creation of the feature space, and optimization via LASSO+L0). </p>",
+ "<p> After the wished features have been selected, click <b>RUN</b> to perform the calculations (loading the values of the primary features, creation of the feature space, and optimization via LASSO+L0). </p>",
"",
- "During the run, a brief summary is printed out below the <b>RUN!</b> button. At the end of the run: ",
+ "During the run, a brief summary is printed out below the <b>RUN</b> button. At the end of the run: ",
" <ul>",
" <li> the solution (machine-learned descriptor, model, and its performance in terms of training error) is printed out underneath starting from the one-dimensional solution to the selected maximum dimensionality and</li>",
"<li> the “View interactive 2D scatter plot” button unlocks; by clicking, the scatter plot with the two-dimensional descriptor appears in a separate tab. In case a dimensionality higher than 2 was selected for the descriptor, the plot displays the first two dimensions.</li>",
@@ -232,14 +240,14 @@
"result": {
"type": "BeakerDisplay",
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- "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<script>\nvar run_lasso = function() {\n $(\"#lasso_result_button\").removeClass(\"active\").addClass(\"disabled\");\n getFeatures();\n getOperators();\n getMaxDim();\n beaker.evaluate(\"lasso_cell\"); // evaluate cells with tag \"lasso_cell\"\n // view_result()\n};\nvar reset_lasso = function(){\n beaker.evaluate(\"lasso-settings-cell\");\n var e = document.getElementById('lasso-hidden-settings-div');\n var b = document.getElementById('lasso-hidden-settings-button');\n e.style.display = 'block';\n b.style.display = 'inline';\n};\nvar getFeatures = function() {\n beaker.selected_feature_list = [];\n $('#lasso_features_select input:checkbox').each(function () {\n if(this.checked )\n beaker.selected_feature_list.push(this.value);\n });\n};\nvar getOperators = function() {\n beaker.allowed_operations = [];\n $('#lasso_operators_select input:checkbox').each(function () {\n if(this.checked )\n beaker.allowed_operations.push(this.value);\n });\n}; \nvar getMaxDim = function() {\n beaker.max_dim = $(\"#lasso_max_dim_selector\").val();\n};\nvar toggle_settings = function(){\n var e = document.getElementById('lasso-hidden-settings-div');\n var b = document.getElementById('lasso-hidden-settings-button');\n if(e.style.display == 'block'){\n e.style.display = 'none';\n b.style.display = 'none';\n }\n else{\n e.style.display = 'block';\n b.style.display = 'inline';\n }\n};\nbeaker.view_result = function(result_link) {\n// beaker.evaluate(\"lasso_viewer_result\").then(function(x) {\n $(\"#lasso_result_button\").attr(\"href\", result_link);\n// }); \n $(\"#lasso_result_button\").removeClass(\"disabled\").addClass(\"active\");\n}\n</script>\n<style type=\"text/css\">\n .lasso_instructions{\n font-size: 15px;\n } \n</style>\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-motivation-modal\">\n Background\n</button> \n\n<!-- Modal -->\n<div class=\"modal fade\" id=\"lasso-motivation-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-motivation-modal-label\">\n <div class=\"modal-dialog modal-lg\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-motivation-modal-label\">Background</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n <p> In this tutorial we present a tool for predicting the crystal structure of octet binary compounds, by using a set of descriptive parameters (a descriptor) based on free-atom data of the atomic species constituting the binary material.</p>\n\n <p>In this example, we address only Rocksalt (RS) and Zincblende (ZB) crystal structures, that are the most common for the material class of octet binaries. Specifically, the tool predicts the difference in total energy between RS and ZB equilibrated structures (i.e., each structure is relaxed to its local minimum).</p>\n\n <p>The prediction of RS vs ZB structure from a simple descriptor has a notable history in materials science [1-7], where descriptors were designed by chemically/physically-inspired intuition. The tool presented here allows for the machine-learning-aided automatic discovery of a descriptor and a model for the prediction of the difference in energy between RS and ZB for 82 octet binary materials.</p>\n\n <p>The tool is based on Compressed-sensing (LASSO performed on a tailor-made feature space, followed by L0-regularized minimization, click <a href=\"https://gitlab.rzg.mpg.de/nomad-lab/public-wiki/wikis/analytics/LASSO_L0\" target=\"_blank\">here</a> for more info on the LASSO+L0 method), as introduced in: </p>\n\n <p> \"Big Data of Materials Science: Critical Role of the Descriptor\". L. M. Ghiringhelli, J. Vybiral, S. V. Levchenko, C. Draxl, and M. Scheffler Phys. Rev. Lett. 114, 105503 (2015) <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\"> (Click here for the free access pdf) </a></p>\n\n <p> By running the tutorial with the default setting, the results of the <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\">PRL 2015</a> can be recovered. In particular, by clicking on “View interactive 2D plot”, an interactive structure-map (a chart where different structures are located in different regions of a low-dimensional representation, here two dimensional) will be opened in a new tab, similar to the following (an extended version of Fig. 2 in <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\">PRL 2015</a>): </p>\n \n <img style=\"width:67%;height:67%\" src=\"https://gitlab.mpcdf.mpg.de/nomad-lab/public-wiki/uploads/eb33f1415db1b6d489cbbc3e6a899942/2016-08-02_ZB_RS3-2.png\">\n <br>\n <br>\n <p> In this map the octet binaries are located via the descriptor found by our LASSO+L0 approach. The descriptor is based purely on free-atom data, namely radii of the s and p valence orbitals (rs and rp) of the atomic species and their Ionizaiton Potential and Electron Affinity (IP and EA). Materials in the red (bue) region crystallize preferably in the zincblende (rocksalt) structure. The distance to the green line is proportional to the difference in energy between the two structures. In the interactive plot accessible at the end of the learning performed by the present tool, one can obtain information on the materials by hovering and clicking on the data points. </p>\n <p>References:</p>\n <ol>\n <li>J. A. van Vechten, Phys. Rev. 182, 891 (1969).</li>\n <li>J. C. Phillips, Rev. Mod. Phys. 42, 317 (1970).</li>\n <li>J. St. John and A.N. Bloch, Phys. Rev. Lett. 33, 1095 (1974).</li>\n <li>J. R. Chelikowsky and J. C. Phillips, Phys. Rev. B 17, 2453 (1978).</li>\n <li>A. Zunger, Phys. Rev. B 22, 5839 (1980).</li>\n <li>D. G. Pettifor, Solid State Commun. 51, 31 (1984).</li>\n <li>Y. Saad, D. Gao, T. Ngo, S. Bobbitt, J. R. Chelikowsky, and W. Andreoni, Phys. Rev. B 85, 104104 (2012).</li>\n </ol>\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>\n\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-instructions-modal\">\n Instructions\n</button> \n\n<!-- Modal -->\n<div class=\"modal fade\" id=\"lasso-instructions-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-instructions-modal-label\">\n <div class=\"modal-dialog\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-instructions-modal-label\">Instructions</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n<p>In this example, you can run a compressed-sensing based algorithm for finding the optimal descriptor and model that predicts the difference in energy between crystal structures (here, rocksalt vs. zincblende). </p>\n\n<p>The descriptor is selected out of a large number of candidates constructed as functions of basic input features, the primary features. </p>\n\n<p>You can select the primary features as well as which kind of unary and binary operations are allowed from the checklist below. You can also select the maximum dimensionality of the descriptor. </p>\n<p> After the wished features have been selected, click <b>RUN!</b> for performing the calculations (loading the values of the primary features, creation of the feature space, and optimization via LASSO+L0). </p>\n\nDuring the run, a brief summary is printed out below the <b>RUN!</b> button. At the end of the run: \n <ul>\n <li> the solution (machine-learned descriptor, model, and its performance in terms of training error) is printed out underneath starting from the one-dimensional solution to the selected maximum dimensionality and</li>\n<li> the “View interactive 2D scatter plot” button unlocks; by clicking, the scatter plot with the two-dimensional descriptor appears in a separate tab. In case a dimensionality higher than 2 was selected for the descriptor, the plot displays the first two dimensions.</li>\n</ul>\n<p>Note: the plot stays active also after another run is performed, so that the output of several sets of input parameters can be compared in the viewer tabs.</p>\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>\n\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" onclick=\"toggle_settings()\">\n Settings\n</button> \n\n\n<a target=\"_blank\" href=\"http://forum.analytics-toolkit.nomad-coe.eu/\" class=\"btn btn-primary\"> Tell us what you think</a>"
+ "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<script>\nvar run_lasso = function() {\n $(\"#lasso_result_button\").removeClass(\"active\").addClass(\"disabled\");\n getFeatures();\n getOperators();\n getMaxDim();\n getUnits();\n beaker.evaluate(\"calc_cell\"); // evaluate cells with tag \"calc_cell\"\n // view_result()\n};\nvar reset_lasso = function(){\n beaker.evaluate(\"lasso-settings-cell\");\n var e = document.getElementById('lasso-hidden-settings-div');\n var b = document.getElementById('lasso-hidden-settings-button');\n e.style.display = 'block';\n b.style.display = 'inline';\n};\nvar getFeatures = function() {\n beaker.selected_feature_list = [];\n $('#lasso_features_select input:checkbox').each(function () {\n if(this.checked )\n beaker.selected_feature_list.push(this.value);\n });\n};\nvar getOperators = function() {\n beaker.allowed_operations = [];\n $('#lasso_operators_select input:checkbox').each(function () {\n if(this.checked )\n beaker.allowed_operations.push(this.value);\n });\n}; \nvar getMaxDim = function() {\n beaker.max_dim = $(\"#lasso_max_dim_selector\").val();\n};\n \nvar getUnits = function() {\n beaker.units = $(\"#units_select\").val();\n};\nvar toggle_settings = function(){\n var e = document.getElementById('lasso-hidden-settings-div');\n var b = document.getElementById('lasso-hidden-settings-button');\n if(e.style.display == 'block'){\n e.style.display = 'none';\n b.style.display = 'none';\n }\n else{\n e.style.display = 'block';\n b.style.display = 'inline';\n }\n};\nbeaker.view_result = function(result_link) {\n// beaker.evaluate(\"lasso_viewer_result\").then(function(x) {\n $(\"#lasso_result_button\").attr(\"href\", result_link);\n// }); \n $(\"#lasso_result_button\").removeClass(\"disabled\").addClass(\"active\");\n}\n</script>\n<style type=\"text/css\">\n .lasso_instructions{\n font-size: 15px;\n } \n</style>\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-motivation-modal\">\n Background\n</button> \n\n<!-- Modal -->\n<div class=\"modal fade\" id=\"lasso-motivation-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-motivation-modal-label\">\n <div class=\"modal-dialog modal-lg\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-motivation-modal-label\">Background</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n <p> In this tutorial we present a tool for predicting the crystal structure of octet binary compounds, by using a set of descriptive parameters (a descriptor) based on free-atom data of the atomic species constituting the binary material.</p>\n\n <p>In this example, we address only Rocksalt (RS) and Zincblende (ZB) crystal structures, that are the most common for the material class of octet binaries. Specifically, the tool predicts the difference in total energy between RS and ZB equilibrated structures (i.e., each structure is relaxed to its local minimum).</p>\n\n <p>The prediction of RS vs ZB structure from a simple descriptor has a notable history in materials science [1-7], where descriptors were designed by chemically/physically-inspired intuition. The tool presented here allows for the machine-learning-aided automatic discovery of a descriptor and a model for the prediction of the difference in energy between RS and ZB for 82 octet binary materials.</p>\n\n <p>The tool is based on Compressed-sensing (LASSO performed on a tailor-made feature space, followed by L0-regularized minimization, click <a href=\"https://gitlab.rzg.mpg.de/nomad-lab/public-wiki/wikis/analytics/LASSO_L0\" target=\"_blank\">here</a> for more info on the LASSO+L0 method), as introduced in: </p>\n\n <p> \"Big Data of Materials Science: Critical Role of the Descriptor\". L. M. Ghiringhelli, J. Vybiral, S. V. Levchenko, C. Draxl, and M. Scheffler Phys. Rev. Lett. 114, 105503 (2015) <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\"> (Click here for the free access pdf) </a></p>\n\n <p> By running the tutorial with the default setting, the results of the <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\">PRL 2015</a> can be recovered. In particular, by clicking on “View interactive 2D plot”, an interactive structure-map (a chart where different structures are located in different regions of a low-dimensional representation, here two dimensional) will be opened in a new tab, similar to the following (an extended version of Fig. 2 in <a href=\"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503\" target=\"_blank\">PRL 2015</a>): </p>\n \n <img style=\"width:67%;height:67%\" src=\"https://gitlab.mpcdf.mpg.de/nomad-lab/public-wiki/uploads/eb33f1415db1b6d489cbbc3e6a899942/2016-08-02_ZB_RS3-2.png\">\n <br>\n <br>\n <p> In this map the octet binaries are located via the descriptor found by our LASSO+L0 approach. The descriptor is based purely on free-atom data, namely radii of the s and p valence orbitals (rs and rp) of the atomic species and their Ionizaiton Potential and Electron Affinity (IP and EA). Materials in the red (blue) region crystallize preferably in the zincblende (rocksalt) structure. The distance to the green line is proportional to the difference in energy between the two structures. In the interactive plot accessible at the end of the learning performed by the present tool, one can obtain information on the materials by hovering and clicking on the data points. </p>\n <p>References:</p>\n <ol>\n <li>J. A. van Vechten, Phys. Rev. 182, 891 (1969).</li>\n <li>J. C. Phillips, Rev. Mod. Phys. 42, 317 (1970).</li>\n <li>J. St. John and A.N. Bloch, Phys. Rev. Lett. 33, 1095 (1974).</li>\n <li>J. R. Chelikowsky and J. C. Phillips, Phys. Rev. B 17, 2453 (1978).</li>\n <li>A. Zunger, Phys. Rev. B 22, 5839 (1980).</li>\n <li>D. G. Pettifor, Solid State Commun. 51, 31 (1984).</li>\n <li>Y. Saad, D. Gao, T. Ngo, S. Bobbitt, J. R. Chelikowsky, and W. Andreoni, Phys. Rev. B 85, 104104 (2012).</li>\n </ol>\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>\n\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" data-toggle=\"modal\" data-target=\"#lasso-instructions-modal\">\n Instructions\n</button> \n\n<!-- Modal -->\n<div class=\"modal fade\" id=\"lasso-instructions-modal\" tabindex=\"-1\" role=\"dialog\" aria-labelledby=\"lasso-instructions-modal-label\">\n <div class=\"modal-dialog\" role=\"document\">\n <div class=\"modal-content\">\n <div class=\"modal-header\">\n <button type=\"button\" class=\"close\" data-dismiss=\"modal\" aria-label=\"Close\"><span aria-hidden=\"true\">×</span></button>\n <h4 class=\"modal-title\" id=\"lasso-instructions-modal-label\">Instructions</h4>\n </div>\n <div class=\"modal-body lasso_instructions\">\n<p>In this example, you can run a compressed-sensing based algorithm for finding the optimal descriptor (and model) that predicts the difference in energy between crystal structures (here, rocksalt vs. zincblende). </p>\n\n<p>The descriptor is selected out of a large number of candidates constructed as functions of basic input features, the primary features. </p>\n\n<p>You can select the primary features as well as which kind of unary and binary operations are allowed from the checklist below. You can also select the maximum dimensionality of the descriptor. </p>\n<p> After the wished features have been selected, click <b>RUN</b> to perform the calculations (loading the values of the primary features, creation of the feature space, and optimization via LASSO+L0). </p>\n\nDuring the run, a brief summary is printed out below the <b>RUN</b> button. At the end of the run: \n <ul>\n <li> the solution (machine-learned descriptor, model, and its performance in terms of training error) is printed out underneath starting from the one-dimensional solution to the selected maximum dimensionality and</li>\n<li> the “View interactive 2D scatter plot” button unlocks; by clicking, the scatter plot with the two-dimensional descriptor appears in a separate tab. In case a dimensionality higher than 2 was selected for the descriptor, the plot displays the first two dimensions.</li>\n</ul>\n<p>Note: the plot stays active also after another run is performed, so that the output of several sets of input parameters can be compared in the viewer tabs.</p>\n </div>\n <div class=\"modal-footer\">\n <button type=\"button\" class=\"btn btn-default\" data-dismiss=\"modal\">Close</button>\n<!-- <button type=\"button\" class=\"btn btn-primary\">Save changes</button> -->\n </div>\n </div>\n </div>\n</div>\n\n<!-- Button trigger modal -->\n<button type=\"button\" class=\"btn btn-default\" onclick=\"toggle_settings()\">\n Settings\n</button> \n\n\n<a target=\"_blank\" href=\"http://forum.analytics-toolkit.nomad-coe.eu/\" class=\"btn btn-primary\"> Tell us what you think</a>"
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
- "height": 52
+ "height": 72
},
"evaluatorReader": true,
- "lineCount": 149
+ "lineCount": 154
},
{
"id": "lasso-settings-cell",
@@ -262,39 +270,24 @@
"pointer over the feature names to see a full description):</p>",
" <form id=\"lasso_features_select\">",
" <div class=\"lasso_form_group\">",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\" title=\"Ionization potential of atom A\"> <input type=\"checkbox\" value=\"IP(A)\" CHECKED > <i>IP</i> <sup>A</sup></label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"IP(B)\" CHECKED > <span title=\"Ionization potential of atom B\"><i>IP</i> <sup>B</sup></span></label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"EA(A)\" CHECKED > <span title=\"Electron affinity of atom A\"> <i>EA</i> <sup>A</sup></span></label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"EA(B)\" CHECKED > <span title=\"Electron affinity of atom B\"> <i>EA</i> <sup>B</sup></span></label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"HOMO(A)\" CHECKED > <span title=\"Energy of highest occupied molecular orbital for atom A\"><i>E</i> <sup>A</sup><sub>HOMO</sub></span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"HOMO(B)\" CHECKED > <span title=\"Energy of highest occupied molecular orbital for atom B\"> <i>E</i> <sup>B</sup><sub>HOMO</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"LUMO(A)\" CHECKED > <span title=\"Energy of lowest unoccupied molecular orbital for atom A\"> <i>E</i> <sup>A</sup><sub>LUMO</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"LUMO(B)\" CHECKED > <span title=\"Energy of lowest unoccupied molecular orbital for atom B\"> <i>E</i> <sup>B</sup><sub>LUMO</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"rs(A)\" CHECKED > <span title=\"Radius at which the radial probability density of the valence s orbital is maximum for atom A\"> <i>r</i><sub>s</sub><sup>A</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"rs(B)\" CHECKED > <span title=\"Radius at which the radial probability density of the valence s orbital is maximum for atom B\"> <i>r</i><sub>s</sub><sup>B</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"rp(A)\" CHECKED > <span title=\"Radius at which the radial probability density of the valence p orbital is maximum for atom A\"> <i>r</i><sub>p</sub><sup>A</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"rp(B)\" CHECKED > <span title=\"Radius at which the radial probability density of the valence p orbital is maximum for atom B\"> <i>r</i><sub>p</sub><sup>B</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"rd(A)\" CHECKED > <span title=\"Radius at which the radial probability density of the valence d orbital is maximum for atom A\"> <i>r</i><sub>d</sub><sup>A</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"rd(B)\" CHECKED > <span title=\"Radius at which the radial probability density of the valence d orbital is maximum for atom B\"> <i>r</i><sub>d</sub><sup>B</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"d_AA\" > <span title=\"Bond length of atomA-atomA dimer\"> <i>d</i><sup>AA</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"d_BB\"> <span title=\"Bond length of atomB-atomB dimer\"> <i>d</i><sup>BB</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"HL_gap_AA\" > <span title=\"HOMO-LUMO gap of atomA-atomA dimer\"> Δ<i>E</i> <sup>AA</sup><sub>HL</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"HL_gap_BB\" > <span title=\"HOMO-LUMO gap of atomB-atomB dimer\"> Δ<i>E</i> <sup>BB</sup><sub>HL</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"Ebinding_AA\" > <span title=\"Binding energy of atomA-atomA dimer\"> <i>E</i> <sup>AA</sup><sub>b</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"Ebinding_BB\" > <span title=\"Binding energy of atomB-atomB dimer\"> <i>E</i> <sup>BB</sup><sub>b</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"Z(A)\" > <span title=\"Atomic number of atom A\"> <i>Z</i> <sup>A</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"Z(B)\" > <span title=\"Atomic number of atom B\"> <i>Z</i> <sup>B</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"val(A)\" > <span title=\"Number of valence electron of atom A\"> <i>Z</i> <sup>A</sup><sub>val</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"val(B)\" > <span title=\"Number of valence electron of atom B\"> <i>Z</i> <sup>B</sup><sub>val</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"period(A)\" > <span title=\"Period (in the periodic table) of atom A\"> <i>n</i> <sup>A</sup><sub>period</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"period(B)\" > <span title=\"Period (in the periodic table) of atom B\"> <i>n</i> <sup>B</sup><sub>period</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_ionization_potential\" CHECKED > <span title=\"Atomic ionization potential\"><i>IP</i> </span></label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_electron_affinity\" CHECKED > <span title=\"Atomic electron affinity\"> <i>EA</i></span></label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_homo\" > <span title=\"Energy of highest occupied molecular orbital\"><i>E</i> <sub>HOMO</sub></span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_lumo\" > <span title=\"Energy of lowest unoccupied molecular orbital\"> <i>E</i> <sub>LUMO</sub> </span> </label>",
+ " ",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_rs_max\" CHECKED > <span title=\"Radius at which the radial probability density of the valence s orbital is maximum\"> <i>r</i><sub>s</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_rp_max\" CHECKED > <span title=\"Radius at which the radial probability density of the valence p orbital is maximum\"> <i>r</i><sub>p</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_rd_max\" CHECKED > <span title=\"Radius at which the radial probability density of the valence d orbital is maximum\"> <i>r</i><sub>d</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_number\" > <span title=\"Atomic number\"> <i>Z</i> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_number_valence_electrons\" > <span title=\"Number of valence electrons\"> <i>Z</i><sub>val</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"period\" > <span title=\"Period (in the periodic table)\"> <i>n</i> <sub>period</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_r_by_2_dimer\" > <span title=\"Bond length of the dimer\"> <i>d</i> <sub>dimer</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_electronic_binding_energy_dimer\" > <span title=\"Binding energy of the dimer\"> <i>E</i> <sub>b</sub> </span> </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"atomic_homo_lumo_diff\" > <span title=\"HOMO-LUMO gap of the dimer\"> Δ<i>E</i><sub>HL</sub> </span> </label>",
" <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"r_sigma\" > <span title=\"John-Bloch's indicator1: |rp(A) + rs(A) - rp(B) -rs(B)| ",
" [Phys. Rev. Lett. 33. 1095 (1974)]\"> r<sub>σ</sub> </span> </label>",
" <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"r_pi\" > <span title=\"John-Bloch's indicator2: |rp(A) - rs(A)| +| rp(B) -rs(B)| ",
" [Phys. Rev. Lett. 33. 1095 (1974)]\"> r<sub>π</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"d_AB\" > <span title=\"Bond length of atomA-atomB dimer\"> <i>d</i><sup>AB</sup> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"HL_gap_AB\" > <span title=\"HOMO-LUMO gap of atomA-atomB dimer\"> Δ<i>E</i> <sup>AB</sup><sub>HL</sub> </span> </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"Ebinding_AB\" > <span title=\"Binding energy of atomA-atomB dimer\"> <i>E</i> <sup>AB</sup><sub>b</sub> </span> </label>",
" </div>",
" </form>",
" </div> <!-- End of row-->",
@@ -303,19 +296,19 @@
" Given features x and y, apply these operations:</p>",
" <form id=\"lasso_operators_select\">",
" <div class=\"lasso_form_group\">",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"|+|\" CHECKED > |x+y| </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"+\" > x+y </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"|-|\" CHECKED > |x-y| </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"-\" > x-y </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"/\" CHECKED > x/y </label>",
- " <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"^2\" CHECKED > x^2 </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"+\" CHECKED > x+y </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"-\" > x-y </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"|-|\" CHECKED > |x-y| </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"*\" > x · y </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"/\" CHECKED > x/y </label>",
+ " <label class =\"col-xs-4 col-md-4 col-lg-1\"> <input type=\"checkbox\" value=\"^2\" CHECKED > x^2 </label>",
" <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"^3\" > x^3 </label>",
" <label class =\"col-xs-4 col-md-4 col-lg-3\"> <input type=\"checkbox\" value=\"exp\" CHECKED > exp(x) </label>",
" </div>",
" </form>",
" </div> <!-- End of row-->",
" <div class=\"row\"> <!-- Start of third row-->",
- " <p class=\"lasso_selection_description\"><b>Optimal descriptor maximum dimension: </b> ",
+ " <p class=\"lasso_selection_description\"><b>Optimal descriptor maximum dimension: </b> ",
" <select id='lasso_max_dim_selector'>",
" <option value=\"2\" > 2D</option>",
" <option value=\"3\" > 3D</option>",
@@ -323,6 +316,14 @@
" <option value=\"5\" > 5D</option>",
" </select> </p>",
" </div><!-- End of row-->",
+ " <div class=\"row\"> <!-- Start of forth row-->",
+ " <p class=\"lasso_selection_description\"><b>Unit of measures: </b> ",
+ " <select id='units_select'>",
+ " <option value=\"eV_angstrom\" > [energy]=eV; [length]=angstrom</option>",
+ " <option value=\"J_m\" > [energy]=J; [length]=m</option>",
+ " <option value=\"kcal/mol_angstrom\" > [energy]=kcal/mol; [length]=angstrom</option>",
+ " </select> </p>",
+ " </div><!-- End of row-->",
"<!-- <span title=''> <img src=\"http://images.clipartpanda.com/question-purzen_Icon_with_question_mark_Vector_Clipart.png\" style=\"height: 30px; width: 30px;\"> </span> -->",
"<!-- <button class=\"btn btn-default\" onclick='run_lasso()'>RUN LASSO+L0</button> -->",
"<!-- <button class=\"btn btn-default\" onclick='reset_lasso()'>RESET</button> -->",
@@ -339,18 +340,18 @@
"result": {
"type": "BeakerDisplay",
"innertype": "Html",
- "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<style type=\"text/css\">\n #lasso-hidden-settings-div{\n display:none;\n } \n #lasso-hidden-settings-button{\n display:none;\n } \n</style>\n<div class=\"lasso_control\" id=\"lasso-hidden-settings-div\">\n <div class=\"row\">\n <p class=\"lasso_selection_description\"><b>Primary features </b>\n (hover the mouse\npointer over the feature names to see a full description):</p>\n <form id=\"lasso_features_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-3\" title=\"Ionization potential of atom A\"> <input value=\"IP(A)\" checked=\"\" type=\"checkbox\"> <i>IP</i> <sup>A</sup></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"IP(B)\" checked=\"\" type=\"checkbox\"> <span title=\"Ionization potential of atom B\"><i>IP</i> <sup>B</sup></span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"EA(A)\" checked=\"\" type=\"checkbox\"> <span title=\"Electron affinity of atom A\"> <i>EA</i> <sup>A</sup></span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"EA(B)\" checked=\"\" type=\"checkbox\"> <span title=\"Electron affinity of atom B\"> <i>EA</i> <sup>B</sup></span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"HOMO(A)\" checked=\"\" type=\"checkbox\"> <span title=\"Energy of highest occupied molecular orbital for atom A\"><i>E</i> <sup>A</sup><sub>HOMO</sub></span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"HOMO(B)\" checked=\"\" type=\"checkbox\"> <span title=\"Energy of highest occupied molecular orbital for atom B\"> <i>E</i> <sup>B</sup><sub>HOMO</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"LUMO(A)\" checked=\"\" type=\"checkbox\"> <span title=\"Energy of lowest unoccupied molecular orbital for atom A\"> <i>E</i> <sup>A</sup><sub>LUMO</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"LUMO(B)\" checked=\"\" type=\"checkbox\"> <span title=\"Energy of lowest unoccupied molecular orbital for atom B\"> <i>E</i> <sup>B</sup><sub>LUMO</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"rs(A)\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence s orbital is maximum for atom A\"> <i>r</i><sub>s</sub><sup>A</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"rs(B)\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence s orbital is maximum for atom B\"> <i>r</i><sub>s</sub><sup>B</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"rp(A)\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence p orbital is maximum for atom A\"> <i>r</i><sub>p</sub><sup>A</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"rp(B)\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence p orbital is maximum for atom B\"> <i>r</i><sub>p</sub><sup>B</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"rd(A)\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence d orbital is maximum for atom A\"> <i>r</i><sub>d</sub><sup>A</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"rd(B)\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence d orbital is maximum for atom B\"> <i>r</i><sub>d</sub><sup>B</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"d_AA\" type=\"checkbox\"> <span title=\"Bond length of atomA-atomA dimer\"> <i>d</i><sup>AA</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"d_BB\" type=\"checkbox\"> <span title=\"Bond length of atomB-atomB dimer\"> <i>d</i><sup>BB</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"HL_gap_AA\" type=\"checkbox\"> <span title=\"HOMO-LUMO gap of atomA-atomA dimer\"> Δ<i>E</i> <sup>AA</sup><sub>HL</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"HL_gap_BB\" type=\"checkbox\"> <span title=\"HOMO-LUMO gap of atomB-atomB dimer\"> Δ<i>E</i> <sup>BB</sup><sub>HL</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"Ebinding_AA\" type=\"checkbox\"> <span title=\"Binding energy of atomA-atomA dimer\"> <i>E</i> <sup>AA</sup><sub>b</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"Ebinding_BB\" type=\"checkbox\"> <span title=\"Binding energy of atomB-atomB dimer\"> <i>E</i> <sup>BB</sup><sub>b</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"Z(A)\" type=\"checkbox\"> <span title=\"Atomic number of atom A\"> <i>Z</i> <sup>A</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"Z(B)\" type=\"checkbox\"> <span title=\"Atomic number of atom B\"> <i>Z</i> <sup>B</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"val(A)\" type=\"checkbox\"> <span title=\"Number of valence electron of atom A\"> <i>Z</i> <sup>A</sup><sub>val</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"val(B)\" type=\"checkbox\"> <span title=\"Number of valence electron of atom B\"> <i>Z</i> <sup>B</sup><sub>val</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"period(A)\" type=\"checkbox\"> <span title=\"Period (in the periodic table) of atom A\"> <i>n</i> <sup>A</sup><sub>period</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"period(B)\" type=\"checkbox\"> <span title=\"Period (in the periodic table) of atom B\"> <i>n</i> <sup>B</sup><sub>period</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"r_sigma\" type=\"checkbox\"> <span title=\"John-Bloch's indicator1: |rp(A) + rs(A) - rp(B) -rs(B)| \n [Phys. Rev. Lett. 33. 1095 (1974)]\"> r<sub>σ</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"r_pi\" type=\"checkbox\"> <span title=\"John-Bloch's indicator2: |rp(A) - rs(A)| +| rp(B) -rs(B)| \n [Phys. Rev. Lett. 33. 1095 (1974)]\"> r<sub>π</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"d_AB\" type=\"checkbox\"> <span title=\"Bond length of atomA-atomB dimer\"> <i>d</i><sup>AB</sup> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"HL_gap_AB\" type=\"checkbox\"> <span title=\"HOMO-LUMO gap of atomA-atomB dimer\"> Δ<i>E</i> <sup>AB</sup><sub>HL</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"Ebinding_AB\" type=\"checkbox\"> <span title=\"Binding energy of atomA-atomB dimer\"> <i>E</i> <sup>AB</sup><sub>b</sub> </span> </label>\n </div>\n </form>\n </div> <!-- End of row-->\n <div class=\"row\"> <!-- Start of second row-->\n <p class=\"lasso_selection_description\"><b>Allowed operations:</b> <br>\n Given features x and y, apply these operations:</p>\n <form id=\"lasso_operators_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"|+|\" checked=\"\" type=\"checkbox\"> |x+y| </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"+\" type=\"checkbox\"> x+y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"|-|\" checked=\"\" type=\"checkbox\"> |x-y| </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"-\" type=\"checkbox\"> x-y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"/\" checked=\"\" type=\"checkbox\"> x/y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"^2\" checked=\"\" type=\"checkbox\"> x^2 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"^3\" type=\"checkbox\"> x^3 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"exp\" checked=\"\" type=\"checkbox\"> exp(x) </label>\n </div>\n </form>\n </div> <!-- End of row-->\n <div class=\"row\"> <!-- Start of third row-->\n <p class=\"lasso_selection_description\"><b>Optimal descriptor maximum dimension: </b> \n <select id=\"lasso_max_dim_selector\">\n <option value=\"2\"> 2D</option>\n <option value=\"3\"> 3D</option>\n <option value=\"4\"> 4D</option>\n <option value=\"5\"> 5D</option>\n </select> </p>\n </div><!-- End of row-->\n<!-- <span title=''> <img src=\"http://images.clipartpanda.com/question-purzen_Icon_with_question_mark_Vector_Clipart.png\" style=\"height: 30px; width: 30px;\"> </span> -->\n<!-- <button class=\"btn btn-default\" onclick='run_lasso()'>RUN LASSO+L0</button> -->\n<!-- <button class=\"btn btn-default\" onclick='reset_lasso()'>RESET</button> -->\n<!-- <label title=\"This button becomes active when the\nrun is finished. By clicking it, an interactive plot of the first 2\ndimensions of the optimized descriptor will be opened\"> \n <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\" >View interactive 2D scatter plot</a> </label> -->\n</div>"
+ "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<style type=\"text/css\">\n #lasso-hidden-settings-div{\n display:none;\n } \n #lasso-hidden-settings-button{\n display:none;\n } \n</style>\n<div style=\"display: none;\" class=\"lasso_control\" id=\"lasso-hidden-settings-div\">\n <div class=\"row\">\n <p class=\"lasso_selection_description\"><b>Primary features </b>\n (hover the mouse\npointer over the feature names to see a full description):</p>\n <form id=\"lasso_features_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_ionization_potential\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic ionization potential\"><i>IP</i> </span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_electron_affinity\" checked=\"\" type=\"checkbox\"> <span title=\"Atomic electron affinity\"> <i>EA</i></span></label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_homo\" type=\"checkbox\"> <span title=\"Energy of highest occupied molecular orbital\"><i>E</i> <sub>HOMO</sub></span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_lumo\" type=\"checkbox\"> <span title=\"Energy of lowest unoccupied molecular orbital\"> <i>E</i> <sub>LUMO</sub> </span> </label>\n \n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_rs_max\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence s orbital is maximum\"> <i>r</i><sub>s</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_rp_max\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence p orbital is maximum\"> <i>r</i><sub>p</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_rd_max\" checked=\"\" type=\"checkbox\"> <span title=\"Radius at which the radial probability density of the valence d orbital is maximum\"> <i>r</i><sub>d</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_number\" type=\"checkbox\"> <span title=\"Atomic number\"> <i>Z</i> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_number_valence_electrons\" type=\"checkbox\"> <span title=\"Number of valence electrons\"> <i>Z</i><sub>val</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"period\" type=\"checkbox\"> <span title=\"Period (in the periodic table)\"> <i>n</i> <sub>period</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_r_by_2_dimer\" type=\"checkbox\"> <span title=\"Bond length of the dimer\"> <i>d</i> <sub>dimer</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_electronic_binding_energy_dimer\" type=\"checkbox\"> <span title=\"Binding energy of the dimer\"> <i>E</i> <sub>b</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"atomic_homo_lumo_diff\" type=\"checkbox\"> <span title=\"HOMO-LUMO gap of the dimer\"> Δ<i>E</i><sub>HL</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"r_sigma\" type=\"checkbox\"> <span title=\"John-Bloch's indicator1: |rp(A) + rs(A) - rp(B) -rs(B)| \n [Phys. Rev. Lett. 33. 1095 (1974)]\"> r<sub>σ</sub> </span> </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"r_pi\" type=\"checkbox\"> <span title=\"John-Bloch's indicator2: |rp(A) - rs(A)| +| rp(B) -rs(B)| \n [Phys. Rev. Lett. 33. 1095 (1974)]\"> r<sub>π</sub> </span> </label>\n </div>\n </form>\n </div> <!-- End of row-->\n <div class=\"row\"> <!-- Start of second row-->\n <p class=\"lasso_selection_description\"><b>Allowed operations:</b> <br>\n Given features x and y, apply these operations:</p>\n <form id=\"lasso_operators_select\">\n <div class=\"lasso_form_group\">\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"+\" checked=\"\" type=\"checkbox\"> x+y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"-\" type=\"checkbox\"> x-y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"|-|\" checked=\"\" type=\"checkbox\"> |x-y| </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"*\" type=\"checkbox\"> x · y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"/\" checked=\"\" type=\"checkbox\"> x/y </label>\n <label class=\"col-xs-4 col-md-4 col-lg-1\"> <input value=\"^2\" checked=\"\" type=\"checkbox\"> x^2 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"^3\" type=\"checkbox\"> x^3 </label>\n <label class=\"col-xs-4 col-md-4 col-lg-3\"> <input value=\"exp\" checked=\"\" type=\"checkbox\"> exp(x) </label>\n </div>\n </form>\n </div> <!-- End of row-->\n <div class=\"row\"> <!-- Start of third row-->\n <p class=\"lasso_selection_description\"><b>Optimal descriptor maximum dimension: </b> \n <select id=\"lasso_max_dim_selector\">\n <option value=\"2\"> 2D</option>\n <option value=\"3\"> 3D</option>\n <option value=\"4\"> 4D</option>\n <option value=\"5\"> 5D</option>\n </select> </p>\n </div><!-- End of row-->\n <div class=\"row\"> <!-- Start of forth row-->\n <p class=\"lasso_selection_description\"><b>Unit of measures: </b> \n <select id=\"units_select\">\n <option value=\"eV_angstrom\"> [energy]=eV; [length]=angstrom</option>\n <option value=\"J_m\"> [energy]=J; [length]=m</option>\n <option value=\"kcal/mol_angstrom\"> [energy]=kcal/mol; [length]=angstrom</option>\n </select> </p>\n </div><!-- End of row-->\n<!-- <span title=''> <img src=\"http://images.clipartpanda.com/question-purzen_Icon_with_question_mark_Vector_Clipart.png\" style=\"height: 30px; width: 30px;\"> </span> -->\n<!-- <button class=\"btn btn-default\" onclick='run_lasso()'>RUN LASSO+L0</button> -->\n<!-- <button class=\"btn btn-default\" onclick='reset_lasso()'>RESET</button> -->\n<!-- <label title=\"This button becomes active when the\nrun is finished. By clicking it, an interactive plot of the first 2\ndimensions of the optimized descriptor will be opened\"> \n <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\" >View interactive 2D scatter plot</a> </label> -->\n</div>"
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
- "height": 33
+ "height": 50
},
"evaluatorReader": true,
- "lineCount": 84,
- "tags": "lasso-setting"
+ "lineCount": 77,
+ "tags": "lasso-settings"
},
{
- "id": "codevOZFSW",
+ "id": "codezrTu93",
"type": "code",
"evaluator": "HTML",
"input": {
@@ -364,8 +365,7 @@
"run is finished. By clicking it, an interactive plot of the first 2",
"dimensions of the optimized descriptor will be opened\"> ",
" <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\" >View interactive 2D scatter plot</a> </label>",
- "</div>",
- ""
+ "</div>"
],
"hidden": true
},
@@ -374,69 +374,245 @@
"result": {
"type": "BeakerDisplay",
"innertype": "Html",
- "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<div class=\"lasso_control\">\n\n <p style=\"margin-top: 1ex;\"></p>\n <button class=\"btn btn-default\" onclick=\"run_lasso()\" style=\"font-weight: bold;\">RUN</button> \n <div id=\"lasso-hidden-settings-button\"><button class=\"btn btn-default\" onclick=\"reset_lasso()\">RESET</button> </div>\n <label title=\"This button becomes active when the\nrun is finished. By clicking it, an interactive plot of the first 2\ndimensions of the optimized descriptor will be opened\"> \n <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\">View interactive 2D scatter plot</a> </label>\n</div>\n"
+ "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<div class=\"lasso_control\">\n\n <p style=\"margin-top: 1ex;\"></p>\n <button class=\"btn btn-default\" onclick=\"run_lasso()\" style=\"font-weight: bold;\">RUN</button> \n <div id=\"lasso-hidden-settings-button\"><button class=\"btn btn-default\" onclick=\"reset_lasso()\">RESET</button> </div>\n <label title=\"This button becomes active when the\nrun is finished. By clicking it, an interactive plot of the first 2\ndimensions of the optimized descriptor will be opened\"> \n <a href=\"#\" target=\"_blank\" class=\"btn btn-primary disabled\" id=\"lasso_result_button\">View interactive 2D scatter plot</a> </label>\n</div>"
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
- "height": 66
+ "height": 86
},
"evaluatorReader": true,
- "lineCount": 11
+ "lineCount": 10
},
{
- "id": "code2uVtKX",
+ "id": "codeGcV7G3",
"type": "code",
"evaluator": "IPython",
"input": {
"body": [
- "from IPython.core.display import HTML ",
- "",
- "# load packages",
- "from nomad_sim.wrappers_desc_class import get_json_list, calc_descriptor ",
- "from nomad_sim.wrappers_desc_class import calc_model, calc_embedding, plot",
+ "from nomad_sim.wrappers import get_json_list, calc_descriptor ",
+ "from nomad_sim.wrappers import calc_model, calc_embedding, plot",
+ "from nomad_sim.parsing_utils import read_gdb_7k",
"from nomad_sim.utils_crystals import create_supercell",
+ "from nomad_sim.utils_crystals import create_vacancies",
+ "from nomad_sim.utils_crystals import random_displace_atoms",
+ "from nomad_sim.utils_crystals import substitute_atoms",
+ "from nomad_sim.descriptors import XrayDiffraction",
+ "from nomad_sim.utils_crystals import create_supercell",
+ "",
+ "# hack to change to local/Beaker mode in all files in the packages",
+ "# DEPRECATED",
+ "import __builtin__",
+ "__builtin__.isBeaker = True",
"",
"import hashlib",
"",
+ "import sys, os",
+ "import pandas as pd",
+ "import numpy as np",
+ "import json",
+ "",
+ "",
"# define paths",
"tmp_folder = '/home/beaker/.beaker/v1/web/tmp/'",
"control_file = '/home/beaker/.beaker/v1/web/tmp/control.json'",
- "data_folder='/home/beaker/test/nomad_sim/data_zcrs'",
+ "data_folder='/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/'",
"lookup_file = '/home/beaker/.beaker/v1/web/tmp/lookup.dat'",
- "atomic_data_file = '/home/beaker/test/nomad_sim/lasso_example/atom_info.csv'",
- "binary_data_file = '/home/beaker/test/nomad_sim/lasso_example/dimer_info.csv'",
+ "collection_path = '/home/beaker/test/nomad_sim/data_zcrs/ExtendedBinaries_Dimers_Atoms_new.json'",
+ "path_to_collection = '/home/beaker/test/nomad_sim/data_zcrs/ExtendedBinaries_Dimers_Atoms_new.json'",
+ "",
"",
+ "# define units",
+ "if beaker.units == 'eV_angstrom':",
+ " energy_unit = 'eV'",
+ " length_unit = 'angstrom'",
+ "elif beaker.units == 'J_m':",
+ " energy_unit = 'J'",
+ " length_unit = 'm'",
+ "elif beaker.units == 'kcal/mol_angstrom':",
+ " energy_unit = 'kcal/mol'",
+ " length_unit = 'angstrom'"
+ ],
+ "hidden": true
+ },
+ "output": {
+ "state": {},
+ "selectedType": "BeakerDisplay",
+ "pluginName": "IPython",
+ "shellId": "46D6A50712FD447B83A3E357B7DD465D",
+ "elapsedTime": 789
+ },
+ "evaluatorReader": true,
+ "tags": "calc_cell",
+ "lineCount": 42
+ },
+ {
+ "id": "codeLARUgI",
+ "type": "code",
+ "evaluator": "IPython",
+ "input": {
+ "body": [
+ "# pass only lowest energy structures to save time for demonstation purposes",
+ "json_list = [",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pm0_fbKdKA2iyued6niH-AARk8hhM.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PzZe8HJ1RoiT6LBluiHmTN9IDP6vE.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P6N-eaR5japcqjIGylr67mAGo9L-S.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PMbzdub7JONozp5LPWlPqLbGuLt3F.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PyBnwEdQ98isxcx9_miHJ2Tr82JrN.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PECMSMMNgxQUVLxlv5IWYEvWOatMh.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PK5EwBMnyyGjm5_lykmBBaMU7FzFl.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PezFp7D_Pzi-KwwYE9WlnFWtpTP_2.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PlQ7NfvecVk8-o2I_Fbz0hNtkAJAw.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PWBxopsGbXEANMPDUxcMi-PzKvqxH.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PUC2t35p9KOEdmaAyB7I91DoUyae7.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/P1RXpIJmIprXumBAD3Lk20-RwmC19.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PoXHWtsIc1BlQ7N2bsUiZ0PJnFa6O.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PVvk2rLGsl4Gd6Q3l0Cbnyi1bM4XO.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pb4Ku0TY7IkW9pjHBECQguVhvtd6Q.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pqky2IgyYljS01KXKFanIV11nbcCT.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PeXUCf_QcDwfIhLJTg61D3lsjvJQu.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PVH2AkTXt2QDVEfJdFkGPAMk1_dQO.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PLoQIJtvhgUQcXFhb0k_6mWOPV9NI.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/Pp-9DTkK5y5w7fFZOf-5JJc9SCPD1.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PN0pxdAiZpbbUV2jORc4LSy5MaYWe.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PGex81N1PxLHkRkSGopRqqLQ4tSkp.json',",
+ "'/parsed/prod-017/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/PWNJV2eK0tIrw_AEg-EpXTggLH88h.json',",
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+ ""
+ ],
+ "hidden": true
+ },
+ "output": {
+ "state": {},
+ "selectedType": "Hidden",
+ "pluginName": "IPython",
+ "shellId": "46D6A50712FD447B83A3E357B7DD465D",
+ "elapsedTime": 407,
+ "height": 986
+ },
+ "evaluatorReader": true,
+ "lineCount": 85,
+ "tags": "calc_cell"
+ },
+ {
+ "id": "codeO2f3dY",
+ "type": "code",
+ "evaluator": "IPython",
+ "input": {
+ "body": [
"# get the json_list",
- "json_list = get_json_list(method='folder', drop_duplicates=False, ",
- " data_folder=data_folder, tmp_folder=tmp_folder)",
+ "#json_list = get_json_list(method='folder', drop_duplicates=False, ",
+ "# data_folder=data_folder, tmp_folder=tmp_folder)",
"",
- "# 3x3 supercell for visualization purposes",
"operations_on_structure = [(create_supercell, {'replicas': [3, 3, 3]})]",
"op_list = np.zeros(len(json_list))",
"",
- "calc_descriptor(desc_type='atomic_features', ",
- " selected_feature_list=beaker.selected_feature_list,",
- " atomic_data_file=atomic_data_file,",
- " binary_data_file=binary_data_file,",
- " op_list=op_list, operations_on_structure=operations_on_structure,",
- " json_list=json_list, tmp_folder=tmp_folder)"
+ "kwargs = {'path_to_collection': path_to_collection,",
+ " 'feature_order_by': 'atomic_mulliken_electronegativity',",
+ " 'energy_unit': energy_unit,",
+ " 'length_unit': length_unit}",
+ "",
+ "dict_delta_e = {'SeZn': 4.2159179660687287e-20, 'InSb': 1.2506570609555687e-20, 'AgCl': -6.8568799955090609e-21, 'SZn': 4.4190167090138643e-20, 'BN': 2.7430550221687302e-19, 'GaSb': 2.4773702178144287e-20, 'BrRb': -2.6246943074069208e-20, 'BaTe': -6.0143598233041078e-20, 'BeSe': 7.9298202208796193e-20, 'MgS': -1.3890792272791661e-20, 'AsB': 1.4018696180162358e-19, 'AlAs': 3.416831556361176e-20, 'BP': 1.632978757533666e-19, 'TeZn': 3.9253535511316122e-20, 'MgSe': -8.8603255975880209e-21, 'ClLi': -6.149391549293258e-21, 'FK': -2.3456843288794608e-20, 'BrLi': -5.2465217764284492e-21, 'BSb': 9.3062289002001379e-20, 'ClRb': -2.5715504707788539e-20, 'GeSn': 1.3083912918128912e-20, 'CsI': -2.6017342042091155e-20, 'CaTe': -5.6149286826500206e-20, 'ClK': -2.6349506219210773e-20, 'Sn2': 2.7179163244033424e-21, 'BrCs': -2.4972695386489382e-20, 'CsF': -1.734569615637085e-20, 'BrCu': 2.442400384019518e-20, 'CaSe': -5.7806170659176063e-20, 'AgF': -2.4634695420313482e-20, 'MgTe': -7.3560522736479063e-22, 'FLi': -9.5310792412059186e-21, 'CuF': -2.7272687327072279e-21, 'FNa': -2.3357835066436331e-20, 'C2': 4.2114873809101575e-19, 'BaO': -1.4900011177054134e-20, 'AgBr': -4.8118839046830307e-21, 'MgO': -3.721451404088126e-20, 'FRb': -2.1724838814450727e-20, 'AlN': 1.1687730189874494e-20, 'Si2': 4.4727296163305501e-20, 'SiSn': 2.1646816357014748e-20, 'OSr': -3.5297012817210187e-20, 'ClNa': -2.1307665354820141e-20, 'AsIn': 2.14767895373523e-20, 'OZn': 1.633710321777262e-20, 'CGe': 1.3000748379902827e-19, 'CdO': -1.348413629348854e-20, 'InP': 2.8709930119109753e-20, 'SSr': -5.9029656118592692e-20, 'InN': 2.4628706405675984e-20, 'BaSe': -5.5025977545738119e-20, 'BrK': -2.6624325013472597e-20, 'BeTe': 7.5075740576200973e-20, 'CdS': 1.1643465692630618e-20, 'CdTe': 1.8351256432814928e-20, 'GeSi': 4.217091895225337e-20, 'GaP': 5.5876198809236085e-20, 'CdSe': 1.3389702567051265e-20, 'INa': -1.8399111846593045e-20, 'AlP': 3.5080994271602511e-20, 'BeO': 1.1084460139894976e-19, 'AsGa': 4.3944144343852047e-20, 'Ge2': 3.218012279776111e-20, 'SeSr': -6.0003270319365202e-20, 'CSi': 1.071894196156348e-19, 'BaS': -5.1231589897332471e-20, 'AgI': 5.9161045280535275e-21, 'GaN': 6.9445584247860156e-20, 'CaS': -5.9141658617526103e-20, 'AlSb': 2.5133142314028706e-20, 'IK': -2.6762621853286689e-20, 'ILi': -3.4704646494924847e-21, 'ClCs': -2.4088110334584613e-20, 'CaO': -4.2492775596486839e-20, 'CuI': 3.2792483878850995e-20, 'CSn': 7.2664795347721018e-20, 'BeS': 8.1122637897805144e-20, 'IRb': -2.6788624696652254e-20, 'BrNa': -2.0256115610545176e-20, 'SrTe': -6.0769715445352658e-20, 'ClCu': 2.5035406212316063e-20}",
+ "",
+ "derived_features = []",
+ "selected_feature_list = beaker.selected_feature_list",
+ "",
+ "if 'r_sigma' in selected_feature_list:",
+ " derived_features.append('r_sigma')",
+ " selected_feature_list.remove('r_sigma')",
+ " selected_feature_list.append('atomic_rs_max')",
+ " selected_feature_list.append('atomic_rp_max')",
+ " ",
+ "if 'r_pi' in selected_feature_list:",
+ " derived_features.append('r_pi')",
+ " selected_feature_list.remove('r_pi')",
+ " selected_feature_list.append('atomic_rs_max')",
+ " selected_feature_list.append('atomic_rp_max')",
+ " ",
+ "",
+ "descriptor = calc_descriptor(",
+ " desc_type='atomic_features',",
+ " selected_feature_list=selected_feature_list,",
+ " dict_delta_e=dict_delta_e,",
+ " op_list=op_list,",
+ " operations_on_structure=operations_on_structure,",
+ " json_list=json_list, tmp_folder=tmp_folder,",
+ " **kwargs)",
+ ""
],
"hidden": true
},
"output": {
- "selectedType": "Results",
"state": {},
+ "selectedType": "Results",
"pluginName": "IPython",
- "shellId": "C0BB775254314BB0B7B145DE566B81E6",
- "height": 374,
- "elapsedTime": 10979
+ "shellId": "46D6A50712FD447B83A3E357B7DD465D",
+ "elapsedTime": 12265,
+ "height": 100
},
"evaluatorReader": true,
- "lineCount": 31,
- "tags": "lasso_cell"
+ "lineCount": 39,
+ "tags": "calc_cell"
},
{
- "id": "codeeWTtU4",
+ "id": "codeo2yP7p",
"type": "code",
"evaluator": "IPython",
"input": {
@@ -444,7 +620,12 @@
"calc_model(method='ext_lasso', desc_type='atomic_features',",
" max_dim=int(beaker.max_dim),",
" allowed_operations=beaker.allowed_operations,",
- " tmp_folder=tmp_folder, lookup_file=lookup_file, control_file=control_file)"
+ " derived_features=derived_features,",
+ " tmp_folder=tmp_folder, ",
+ " lookup_file=lookup_file, ",
+ " control_file=control_file,",
+ " energy_unit=energy_unit, length_unit=length_unit)",
+ ""
],
"hidden": true
},
@@ -452,16 +633,16 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "C0BB775254314BB0B7B145DE566B81E6",
- "height": 566,
- "elapsedTime": 9011
+ "shellId": "46D6A50712FD447B83A3E357B7DD465D",
+ "elapsedTime": 6962,
+ "height": 78
},
"evaluatorReader": true,
- "lineCount": 4,
- "tags": "lasso_cell"
+ "lineCount": 9,
+ "tags": "calc_cell"
},
{
- "id": "lasso_viewer_result",
+ "id": "code7NKF5Q",
"type": "code",
"evaluator": "IPython",
"input": {
@@ -475,31 +656,32 @@
" path_to_file=lookup_file, drop_duplicates=False, displace_duplicates=True, predicted_value=True)",
"beaker.viewer_result = name_html_page",
"",
+ "",
"plot_result = plot(name=name_html_page, json_list=json_list, frames='list', frame_list=frame_list, ",
" file_format='NOMAD', clustering_x_list=x_list, clustering_y_list=y_list, target_list=target_list,",
- " target_unit='eV', legend_title='Reference E(RS)-E(ZB)', target_name='E(RS)-E(ZB)',",
+ " target_unit=energy_unit, energy_unit=energy_unit,",
+ " legend_title='Reference E(RS)-E(ZB)', target_name='E(RS)-E(ZB)',",
" target_pred_list=target_pred_list,",
" plot_title='LASSO+L0 structure map',",
- " op_list=op_list, operations_on_structure=operations_on_structure,",
- " clustering_point_size=12, tmp_folder=tmp_folder, control_file=control_file)",
- ""
+ " clustering_point_size=12, tmp_folder=tmp_folder, control_file=control_file,",
+ " op_list=op_list, operations_on_structure=operations_on_structure)"
],
"hidden": true
},
"output": {
"state": {},
"selectedType": "Results",
+ "height": 78,
"pluginName": "IPython",
- "shellId": "C0BB775254314BB0B7B145DE566B81E6",
- "height": 278,
- "elapsedTime": 3691
+ "shellId": "46D6A50712FD447B83A3E357B7DD465D",
+ "elapsedTime": 7385
},
"evaluatorReader": true,
- "lineCount": 17,
- "tags": "lasso_cell"
+ "lineCount": 18,
+ "tags": "calc_cell"
},
{
- "id": "codeVFrr3c",
+ "id": "codeoorGVf",
"type": "code",
"evaluator": "JavaScript",
"input": {
@@ -510,49 +692,38 @@
"hidden": true
},
"output": {
+ "state": {},
"selectedType": "BeakerDisplay",
+ "height": 78,
"pluginName": "JavaScript",
- "state": {},
- "hidden": true,
- "elapsedTime": 70
+ "elapsedTime": 57
},
"evaluatorReader": true,
"lineCount": 2,
- "tags": "lasso_cell"
+ "tags": "calc_cell"
}
],
"namespace": {
"selected_feature_list": [
- "IP(A)",
- "IP(B)",
- "EA(A)",
- "EA(B)",
- "HOMO(A)",
- "HOMO(B)",
- "LUMO(A)",
- "LUMO(B)",
- "rs(A)",
- "rs(B)",
- "rp(A)",
- "rp(B)",
- "rd(A)",
- "rd(B)"
+ "atomic_ionization_potential",
+ "atomic_electron_affinity",
+ "atomic_rs_max",
+ "atomic_rp_max",
+ "atomic_rd_max"
],
"allowed_operations": [
- "|+|",
+ "+",
"|-|",
"/",
"^2",
"exp"
],
- "maxDim": null,
"max_dim": "2",
- "max_dim2": 18,
- "max_dim3": [
- 11
- ],
- "runInfo": "running Lasso",
- "viewer_result": "1c69e728b7767096"
+ "ncomb": "1",
+ "n_sis": "50",
+ "n_comb": "1",
+ "viewer_result": "6edb65b9776deeb2",
+ "units": "eV_angstrom"
},
"locked": true
}
diff --git a/beaker-notebooks/SOAP_similarity.bkr b/beaker-notebooks/SOAP_similarity.bkr
index 5803cd6bfdad2668bbe469aee23dec8b09ea098d..0eff5ee1cb04f90b82a4bac8ae61d5e20994d4cd 100644
--- a/beaker-notebooks/SOAP_similarity.bkr
+++ b/beaker-notebooks/SOAP_similarity.bkr
@@ -81,29 +81,6 @@
}
],
"cells": [
- {
- "id": "code7ULgzJ",
- "type": "code",
- "evaluator": "HTML",
- "input": {
- "body": [
- "<a target=\"_blank\" href=\"http://forum.analytics-toolkit.nomad-coe.eu/\" class=\"btn btn-primary\"> Send your feedback to the analytics-toolkit forum</a><h2> Your comments are invaluable in helping us provide a user friendly experience for all! </h2>"
- ]
- },
- "output": {
- "state": {},
- "result": {
- "type": "BeakerDisplay",
- "innertype": "Html",
- "object": "<script>\nvar beaker = bkHelper.getBeakerObject().beakerObj;\n</script>\n<a target=\"_blank\" href=\"http://forum.analytics-toolkit.nomad-coe.eu/\" class=\"btn btn-primary\"> Send your feedback to the analytics-toolkit forum</a><h2> Your comments are invaluable in helping us provide a user friendly experience for all! </h2>"
- },
- "selectedType": "BeakerDisplay",
- "elapsedTime": 0,
- "height": 119
- },
- "evaluatorReader": true,
- "lineCount": 1
- },
{
"id": "markdownRBGLQA",
"type": "markdown",
@@ -113,7 +90,7 @@
"<!--label style=\"color: #20335d;font-weight: 900; font-size: 15pt;\"> Visualizing global similarity</label-->",
" </p>",
" <hr style=\"border-width:2px\">",
- " <p style=\"font-size: 15px;\"> developed by Carl Poelking, Angelo Ziletti, Luca Ghiringhelli and Gábor Csányi</p>",
+ " <p style=\"font-size: 15px;\"> developed by Carl Poelking, Angelo Ziletti, Luca Ghiringhelli and Gábor Csányi [version 2017-01-23]</p>",
" ",
" <p style=\"font-size: 15px;\"> <b> Machine learning method: </b> Nonlinear dimensionality reduction based on SOAP similarity kernel<br>",
" ",
@@ -595,7 +572,7 @@
},
"selectedType": "BeakerDisplay",
"elapsedTime": 0,
- "height": 466
+ "height": 465
},
"evaluatorReader": true,
"lineCount": 306,
@@ -625,8 +602,8 @@
"from soap.soapy.momo import osio, endl, flush",
"from soap.tools import AseConfig",
"from nomad_sim.nomad_structures import NOMADStructure",
- "from nomad_sim.wrappers_desc_class import get_json_list",
- "from nomad_sim.wrappers_desc_class import plot, logger",
+ "from nomad_sim.wrappers import get_json_list",
+ "from nomad_sim.wrappers import plot, logger",
"",
"verbose = False",
"logger.setLevel(logging.INFO)",
@@ -779,8 +756,8 @@
"selectedType": "Results",
"state": {},
"pluginName": "IPython",
- "shellId": "233A1B36B390425780D216B6AF523EB8",
- "height": 321,
+ "shellId": "D45DBD5D447246C6841321D07DDCA859",
+ "height": 222,
"dataresult": [
"HARTREE_TO_EV",
"HARTREE_TO_KCALMOL",
@@ -869,7 +846,7 @@
"update_node",
"util"
],
- "elapsedTime": 32072
+ "elapsedTime": 20822
},
"evaluatorReader": true,
"lineCount": 165,
@@ -1206,8 +1183,6 @@
" label = label_list",
" name = list(itertools.chain(*name_list))",
"",
- "",
- "",
" chemical_formula = rename_material(chemical_formula)",
"",
"",
@@ -1588,7 +1563,7 @@
" for (var i = 0; i < whichJSmol.length; i++){ ",
" whichJSmol[i] = 1;",
" }",
- " writeInfoApplet0(chemical_formula, energy, geo_file);",
+ " writeInfoApplet0(chemical_formula, 'NaN', geo_file);",
" } ",
" else if (whichJSmol[inds] == 1) {",
" //var file= \\\"javascript:Jmol.script(jmolApplet1,\" + \"'load \"+ geo_file + \" {3 3 3}; rotate x 10; rotate y 12; rotate z 6; set bondTolerance 0.45; ')\" ; ",
@@ -1597,16 +1572,16 @@
" for (var i = 0; i < whichJSmol.length; i++){",
" whichJSmol[i] = 0;",
" } ",
- " writeInfoApplet1(chemical_formula, energy, geo_file);",
+ " writeInfoApplet1(chemical_formula, 'NaN', geo_file);",
" }",
" \"\"\"",
" ",
" if target_pred_list:",
" js_loadJmol_4 = \"\"\"writeSummary(chemical_formula, target, target_pred);\"\"\"",
" elif label_name == None:",
- " js_loadJmol_4 = \"\"\"writeSummary(chemical_formula, energy, target);\"\"\"",
+ " js_loadJmol_4 = \"\"\"writeSummary(chemical_formula, 'NaN', target);\"\"\"",
" else:",
- " js_loadJmol_4 = \"\"\"writeSummary(chemical_formula, energy, label);\"\"\"",
+ " js_loadJmol_4 = \"\"\"writeSummary(chemical_formula, 'NaN', label);\"\"\"",
"",
" js_loadJmol_5 = \"\"\"",
" // save the modification in the ColumnDataSource to keep the information for the next user click",
@@ -2080,12 +2055,11 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "233A1B36B390425780D216B6AF523EB8",
- "height": 78,
- "elapsedTime": 1897
+ "shellId": "D45DBD5D447246C6841321D07DDCA859",
+ "elapsedTime": 1812
},
"evaluatorReader": true,
- "lineCount": 1192,
+ "lineCount": 1190,
"tags": "cell_soap_run"
},
{
@@ -2095,7 +2069,7 @@
"input": {
"body": [
"#from nomad_sim.viewer import Viewer",
- "from nomad_sim.wrappers_desc_class import view",
+ "from nomad_sim.wrappers import view",
"",
"def _get_structures_local(",
" json_list=None, ",
@@ -2204,9 +2178,9 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
- "shellId": "233A1B36B390425780D216B6AF523EB8",
+ "shellId": "D45DBD5D447246C6841321D07DDCA859",
"height": 78,
- "elapsedTime": 399
+ "elapsedTime": 583
},
"evaluatorReader": true,
"lineCount": 103,
@@ -2269,7 +2243,7 @@
" clustering_y_list=clust_y_list, ",
" target_list=targ_list,",
" target_name=target_name,",
- " target_unit=target_unit,",
+ " target_unit='',",
" target_type=target_type,",
" label_list = label_list,",
" label_name = label_name,",
@@ -2290,9 +2264,9 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
- "shellId": "233A1B36B390425780D216B6AF523EB8",
- "height": 78,
- "elapsedTime": 2564
+ "shellId": "D45DBD5D447246C6841321D07DDCA859",
+ "height": 1462,
+ "elapsedTime": 7510
},
"evaluatorReader": true,
"lineCount": 65,
@@ -2314,7 +2288,7 @@
"selectedType": "BeakerDisplay",
"pluginName": "JavaScript",
"height": 78,
- "elapsedTime": 79
+ "elapsedTime": 54
},
"evaluatorReader": true,
"lineCount": 2,
@@ -2356,7 +2330,7 @@
"viewer_result": "similarity-map",
"options": {
"run": {
- "config_folder": "gdb",
+ "config_folder": "zcrs",
"n_configs": -1,
"n_procs": 2,
"n_blocksize": 200,
@@ -2366,7 +2340,7 @@
"verbose": false
},
"atomic_density": {
- "density_type": "number_density",
+ "density_type": "number_density_generic",
"atomic_radius": 0.5,
"use_covrad": false
},
@@ -2418,7 +2392,7 @@
"angularbasis.type": "spherical-harmonic",
"angularbasis.L": 6,
"kernel.type": "dot",
- "kernel.adaptor": "global-specific",
+ "kernel.adaptor": "global-generic",
"kernel.delta": 1,
"kernel.xi": 3,
"exclude_centers": [],