problem about featurizer.featurize（）

Matminer
1

Dear teacher, I am a graduate student at Xidian University in China. I want to use matminer to do structural analysis in my research. When I use this function: ‘featurizer.featurize(structure)’ I will get an array of size 273. I want to know what this data is for the structure. What does it mean? Can you help me?
The best wishes to you!
The code I am running is as follows:

from matminer.featurizers.base import MultipleFeaturizer

featurizer = MultipleFeaturizer([

SiteStatsFingerprint.from_preset("CoordinationNumber_ward-prb-2017"),

StructuralHeterogeneity(),

ChemicalOrdering(),

MaximumPackingEfficiency(),

SiteStatsFingerprint.from_preset("LocalPropertyDifference_ward-prb-2017"),

StructureComposition(Stoichiometry()),

StructureComposition(ElementProperty.from_preset("magpie")),

StructureComposition(ValenceOrbital(props=['frac'])),

StructureComposition(IonProperty(fast=True))

])

featurizer.featurize(structure)

array([5.203013181604477, 6.817652290080106, 1.6146391084756297,

   5.592184425025464, 0.34723505116817455, 0.013361439725905543,

   1.0647221702796115, 0.9809909605147994, 0.13076956124515735,

   0.24748673989195105, 0.1167171786467937, 0.16768996529115587,

   0.019795973332121672, 0.03397421075711816, 0, 0, 0,

   0.30915395949320784, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1, 1.0, 1.0, 1.0,

   1.0, 1.0, 6.0, 6.0, 0.0, 6.0, 0.0, 6.0, 77.0, 77.0, 0.0, 77.0, 0.0,

   77.0, 12.0107, 12.0107, 0.0, 12.0107, 0.0, 12.0107, 3823.0, 3823.0,

   0.0, 3823.0, 0.0, 3823.0, 14.0, 14.0, 0.0, 14.0, 0.0, 14.0, 2.0,

   2.0, 0.0, 2.0, 0.0, 2.0, 76.0, 76.0, 0.0, 76.0, 0.0, 76.0, 2.55,

   2.55, 0.0, 2.55, 0.0, 2.55, 2.0, 2.0, 0.0, 2.0, 0.0, 2.0, 2.0, 2.0,

   0.0, 2.0, 0.0, 2.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 4.0, 4.0, 0.0, 4.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 4.0, 4.0, 0.0, 4.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 4.0, 4.0, 0.0, 4.0, 0.0, 4.0,

   5.64, 5.64, 0.0, 5.64, 0.0, 5.64, 4.496, 4.496, 0.0, 4.496, 0.0,

   4.496, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 194.0, 194.0, 0.0, 194.0, 0.0,

   194.0, 0.5, 0.5, 0.0, 0.0, True, 0, 0], dtype=object)

What does this array stand for? What operation did it get?

structure：

Structure Summary

Lattice

abc : 2.51821 5.130159874304601 5.130159874304601

angles : 114.5539198217954 90.0 90.0

volume : 60.28234828537518

B : -4.459734178828981e-16 -2.773255 -4.31597

C : -4.459734178828981e-16 -2.773255 4.31597

PeriodicSite: C (-1.2591, -1.2957, 1.3323) [0.5000, 0.0793, 0.3880]

PeriodicSite: C (-0.0000, -2.0083, 1.8897) [0.0000, 0.1432, 0.5810]

PeriodicSite: C (-1.2591, -0.8159, -0.1612) [0.5000, 0.1658, 0.1284]

PeriodicSite: C (-1.2591, -4.7306, -0.1612) [0.5000, 0.8716, 0.8342]

PeriodicSite: C (-1.2591, -2.7733, -2.1947) [0.5000, 0.7542, 0.2458]

PeriodicSite: C (-0.0000, -3.5382, 1.8897) [0.0000, 0.4190, 0.8568]

PeriodicSite: C (-0.0000, -2.7733, -1.3267) [0.0000, 0.6537, 0.3463]

PeriodicSite: C (-1.2591, -4.2508, 1.3323) [0.5000, 0.6120, 0.9207]

PeriodicSite: C (-0.0000, -1.2961, -0.8897) [0.0000, 0.3367, 0.1306]

PeriodicSite: C (-2.5182, -4.2504, -0.8897) [1.0000, 0.8694, 0.6632]

···

A : -2.51821 0.0 -1.541958908040428e-16

2

Hello,

This particular featurizer you are running is based on work from my colleagues and I in 2017: https://journals.aps.org/prb/abstract/10.1103/PhysRevB.96.024104

Each of the different types of features are based on descriptions of the local environments of atoms within a crystal, as defined using a Voronoi tessellation. For example, the first featurizer in the list, “SiteStatsFingerprint.from_preset(“CoordinationNumber_ward-prb-2017”)”, describes the number of average and variance in the number of 1st nearest neighbors for each atom in the crystal. The 273-member array you returned in the results of feature of the different featurizers in the list for “MultipleFeaturizer”

To get a more detailed knowledge of each feature, I have two recommendations:

  1. Run the “featurizer.feature_labels()” operation to get the names for each feature
  2. Look up the description for each featurizer in our Table of Featurizers. The documentation for each of the featurizers should have a short description for each of the types of features it generates.

Feel free to email me off list if you have any specific questions. I’d be happy to help.

Best,

Logan

···

From: [email protected]
Sent: Friday, September 28, 2018 3:28 AM
To: matminer
Subject: problem about featurizer.featurize（）

Dear teacher, I am a graduate student at Xidian University in China. I want to use matminer to do structural analysis in my research. When I use this function: ‘featurizer.featurize(structure)’ I will get an array of size 273. I want to know what this data is for the structure. What does it mean? Can you help me?

The best wishes to you!

The code I am running is as follows:

from matminer.featurizers.base import MultipleFeaturizer

featurizer = MultipleFeaturizer([

SiteStatsFingerprint.from_preset("CoordinationNumber_ward-prb-2017"),

StructuralHeterogeneity(),

ChemicalOrdering(),

MaximumPackingEfficiency(),

SiteStatsFingerprint.from_preset("LocalPropertyDifference_ward-prb-2017"),

StructureComposition(Stoichiometry()),

StructureComposition(ElementProperty.from_preset("magpie")),

StructureComposition(ValenceOrbital(props=['frac'])),

StructureComposition(IonProperty(fast=True))

])

featurizer.featurize(structure)

array([5.203013181604477, 6.817652290080106, 1.6146391084756297,

   5.592184425025464, 0.34723505116817455, 0.013361439725905543,

   1.0647221702796115, 0.9809909605147994, 0.13076956124515735,

   0.24748673989195105, 0.1167171786467937, 0.16768996529115587,

   0.019795973332121672, 0.03397421075711816, 0, 0, 0,

   0.30915395949320784, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1, 1.0, 1.0, 1.0,

   1.0, 1.0, 6.0, 6.0, 0.0, 6.0, 0.0, 6.0, 77.0, 77.0, 0.0, 77.0, 0.0,

   77.0, 12.0107, 12.0107, 0.0, 12.0107, 0.0, 12.0107, 3823.0, 3823.0,

   0.0, 3823.0, 0.0, 3823.0, 14.0, 14.0, 0.0, 14.0, 0.0, 14.0, 2.0,

   2.0, 0.0, 2.0, 0.0, 2.0, 76.0, 76.0, 0.0, 76.0, 0.0, 76.0, 2.55,

   2.55, 0.0, 2.55, 0.0, 2.55, 2.0, 2.0, 0.0, 2.0, 0.0, 2.0, 2.0, 2.0,

   0.0, 2.0, 0.0, 2.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 4.0, 4.0, 0.0, 4.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 4.0, 4.0, 0.0, 4.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0, 0.0,

   0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 4.0, 4.0, 0.0, 4.0, 0.0, 4.0,

   5.64, 5.64, 0.0, 5.64, 0.0, 5.64, 4.496, 4.496, 0.0, 4.496, 0.0,

   4.496, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 194.0, 194.0, 0.0, 194.0, 0.0,

   194.0, 0.5, 0.5, 0.0, 0.0, True, 0, 0], dtype=object)

What does this array stand for? What operation did it get?

structure**：**

Structure Summary

Lattice

abc : 2.51821 5.130159874304601 5.130159874304601

angles : 114.5539198217954 90.0 90.0

volume : 60.28234828537518

A : -2.51821 0.0 -1.541958908040428e-16

B : -4.459734178828981e-16 -2.773255 -4.31597

C : -4.459734178828981e-16 -2.773255 4.31597

PeriodicSite: C (-1.2591, -1.2957, 1.3323) [0.5000, 0.0793, 0.3880]

PeriodicSite: C (-0.0000, -2.0083, 1.8897) [0.0000, 0.1432, 0.5810]

PeriodicSite: C (-1.2591, -0.8159, -0.1612) [0.5000, 0.1658, 0.1284]

PeriodicSite: C (-1.2591, -4.7306, -0.1612) [0.5000, 0.8716, 0.8342]

PeriodicSite: C (-1.2591, -2.7733, -2.1947) [0.5000, 0.7542, 0.2458]

PeriodicSite: C (-0.0000, -3.5382, 1.8897) [0.0000, 0.4190, 0.8568]

PeriodicSite: C (-0.0000, -2.7733, -1.3267) [0.0000, 0.6537, 0.3463]

PeriodicSite: C (-1.2591, -4.2508, 1.3323) [0.5000, 0.6120, 0.9207]

PeriodicSite: C (-0.0000, -1.2961, -0.8897) [0.0000, 0.3367, 0.1306]

PeriodicSite: C (-2.5182, -4.2504, -0.8897) [1.0000, 0.8694, 0.6632]

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