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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -9,9 +9,9 @@ | |
| (GCH) analysis (see `Anelli et al., Phys. Rev. Materials | ||
| (2018) <https://doi.org/10.1103/PhysRevMaterials.2.103804>`__). | ||
| It uses features computed with `rascaline <https://github.com/lab-cosmo/rascaline>`__ | ||
| and uses the directional convex hull function from | ||
| `scikit-matter <https://github.com/lab-cosmo/scikit-matter>`__ | ||
| to make the figure. | ||
| and uses the directional convex hull function from | ||
| `scikit-matter <https://github.com/lab-cosmo/scikit-matter>`__ | ||
| to make the figure. | ||
| """ | ||
|
|
||
| import chemiscope | ||
|
|
@@ -93,27 +93,33 @@ | |
| # requires having the ``chemiscope`` package installed. | ||
| # | ||
|
|
||
| if chemiscope.jupyter._is_running_in_notebook(): | ||
| chemiscope.show( | ||
| structures, | ||
| dict( | ||
| energy=energy, | ||
| density=density, | ||
| hull_energy=dch_dist, | ||
| structure_type=structype, | ||
| ), | ||
| settings={ | ||
| "map": { | ||
| "x": {"property": "density"}, | ||
| "y": {"property": "energy"}, | ||
| "color": {"property": "hull_energy"}, | ||
| "symbol": "structure_type", | ||
| "size": {"factor": 35}, | ||
| }, | ||
| "structure": [{"unitCell": True, "supercell": {"0": 2, "1": 2, "2": 2}}], | ||
| cs = chemiscope.show( | ||
| structures, | ||
| dict( | ||
| energy=energy, | ||
| density=density, | ||
| hull_energy=dch_dist, | ||
| structure_type=structype, | ||
| ), | ||
| settings={ | ||
| "map": { | ||
| "x": {"property": "density"}, | ||
| "y": {"property": "energy"}, | ||
| "color": {"property": "hull_energy"}, | ||
| "symbol": "structure_type", | ||
| "size": {"factor": 35}, | ||
| }, | ||
| ) | ||
| "structure": [{"unitCell": True, "supercell": {"0": 2, "1": 2, "2": 2}}], | ||
| }, | ||
| ) | ||
|
|
||
|
|
||
| if chemiscope.jupyter._is_running_in_notebook(): | ||
| from IPython.display import display | ||
|
|
||
| display(cs) | ||
| else: | ||
| cs.save("roy_ch.json.gz") | ||
|
|
||
| # %% | ||
| # Generalized Convex Hull | ||
|
|
@@ -232,46 +238,55 @@ | |
| # shows chemiscope if not run in terminal | ||
|
|
||
| cs = chemiscope.show( | ||
| frames=structures, | ||
| properties=structure_properties, | ||
| meta={"name" : "GCH for ROY polymorphs", | ||
| "description": | ||
| """ | ||
| Demonstration of the Generalized Convex Hull construction for polymorphs of the ROY molecule. | ||
| Molecules that are closest to the hull built on PCA-based structural descriptors and having the | ||
| internal energy predicted by electronic-structure calculations as the z axis are the most | ||
| thermodynamically stable. Indeed most of the known polymorphs of ROY are on (or very close) to | ||
| this hull. | ||
| frames=structures, | ||
| properties=structure_properties, | ||
| meta={ | ||
| "name": "GCH for ROY polymorphs", | ||
| "description": """ | ||
| Demonstration of the Generalized Convex Hull construction for | ||
| polymorphs of the ROY molecule. Molecules that are closest to | ||
| the hull built on PCA-based structural descriptors and having the | ||
| internal energy predicted by electronic-structure calculations as | ||
| the z axis are the most thermodynamically stable. Indeed most of the | ||
| known polymorphs of ROY are on (or very close) to this hull. | ||
| """, | ||
| "authors": "Michele Ceriotti <[email protected]>", | ||
| "references": ['A. Anelli, E. A. Engel, C. J. Pickard, and M. Ceriotti, "Generalized convex hull construction for materials discovery," Physical Review Materials 2(10), 103804 (2018).', | ||
| '1. G. J. O. Beran, I. J. Sugden, C. Greenwell, D. H. Bowskill, C. C. Pantelides, and C. S. Adjiman, "How many more polymorphs of ROY remain undiscovered," Chem. Sci. 13(5), 1288–1297 (2022).' | ||
| ]}, | ||
| settings={ | ||
| "map": { | ||
| "x": {"property": "pca_1"}, | ||
| "y": {"property": "pca_2"}, | ||
| "z": {"property": "energy"}, | ||
| "symbol": "type", | ||
| "color": {"property": "hull_energy"}, | ||
| "size": { | ||
| "factor": 35, | ||
| "mode": "linear", | ||
| "property": "", | ||
| "reverse": True, | ||
| }, | ||
| "authors": ["Michele Ceriotti <[email protected]>"], | ||
| "references": [ | ||
| 'A. Anelli, E. A. Engel, C. J. Pickard, and M. Ceriotti, \ | ||
| "Generalized convex hull construction for materials discovery," \ | ||
| Physical Review Materials 2(10), 103804 (2018).', | ||
| 'G. J. O. Beran, I. J. Sugden, C. Greenwell, D. H. Bowskill, \ | ||
| C. C. Pantelides, and C. S. Adjiman, "How many more polymorphs of \ | ||
| ROY remain undiscovered," Chem. Sci. 13(5), 1288–1297 (2022).', | ||
| ], | ||
| }, | ||
| settings={ | ||
| "map": { | ||
| "x": {"property": "pca_1"}, | ||
| "y": {"property": "pca_2"}, | ||
| "z": {"property": "energy"}, | ||
| "symbol": "type", | ||
| "color": {"property": "hull_energy"}, | ||
| "size": { | ||
| "factor": 35, | ||
| "mode": "linear", | ||
| "property": "", | ||
| "reverse": True, | ||
| }, | ||
| "structure": [ | ||
| { | ||
| "bonds": True, | ||
| "unitCell": True, | ||
| "keepOrientation": True, | ||
| } | ||
| ], | ||
| }, | ||
| ) | ||
| "structure": [ | ||
| { | ||
| "bonds": True, | ||
| "unitCell": True, | ||
| "keepOrientation": True, | ||
| } | ||
| ], | ||
| }, | ||
| ) | ||
|
|
||
| if chemiscope.jupyter._is_running_in_notebook(): | ||
| from IPython.display import display | ||
|
|
||
| display(cs) | ||
| else: | ||
| cs.save("roy_gch.json.gz") | ||