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Chore/sof 1549 (#32)
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* feat: calculate dimensions from reciprocal lattice

* chore: add made.js to peerDependencies

* fix: import of ReciprocalLattice

* fix: undefined indices

* chore: adjust complementary indices

* chore: add isUsingJinjaVariable logic

* chore: disable preferKPPRA when using Jinja variables

* chore: adjust default dimensions

* chore: decrease default KPPRA

* chore: add ConvergenceParameter classes

* chore: add scope variable for non-uniform kgrid

* chore: generalize convergence subworkflow

* chore: use stringify for initialValue property

* refactor: move k-grid related functions to ReciprocalLattice

* chore: add reciprocal vector ratios to form

* style: adjust precision of ratios + remove array buttons

* style: adjust name and position of reciprocalVectorRatios

* fix: typo in ui schema directive

* chore: add increment units to convergence subworkflow

* chore: handle context variables of parameter step unit

* fix: increment undefined in factory

* chore: adjust order of initializing units

* fix: initial value missing in increment

* fix: typo

* chore: use initial value as string

* chore: use parameter instead of destructuring

* chore: use context property from local scope

* chore: generalize boolean logic for vector type

* chore: use lodash for rounding to precision

* chore: ensure float value for context variable

* chore: rename non-uniform N_k parameter

* chore: add names to convergence units

* feat: calculate dimension from spacing

* chore: round calculated spacing to 3 decimals

* refactor: reciprocral lattice functions + reordering

use single instance of reciprocal lattice in order to avoid creating an instance every time the function is called. Also functions setting defaults are grouped together.

* chore: use closure for uiSchema functions

* chore: initialize recLattice before calculating defaults

* fix: form description is not shown correctly

* style: adjust default classnames

* style: add custom classname for select widget

* chore: calculate spacing in 1/Ang

* chore: use default value for units

* chore: made.js++

* chore: made.js++
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@azech-hqs
azech-hqs committed Mar 8, 2023
1 parent 256f023 commit d73791a
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Showing 2 changed files with 169 additions and 78 deletions.
2 changes: 1 addition & 1 deletion package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@
"@exabyte-io/code.js": "2022.11.11-0",
"@exabyte-io/eslint-config": "^2022.11.17-0",
"@exabyte-io/ide.js": "2022.7.28-1",
"@exabyte-io/made.js": "2023.3.6-0",
"@exabyte-io/made.js": "2023.3.8-0",
"@exabyte-io/mode.js": "2022.10.11-0",
"chai": "^4.3.4",
"eslint": "7.32.0",
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245 changes: 168 additions & 77 deletions src/context/providers/PointsGridFormDataProvider.js
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
import { units as UNITS } from "@exabyte-io/code.js/dist/constants";
import { JSONSchemaFormDataProvider, MaterialContextMixin } from "@exabyte-io/code.js/dist/context";
import { math as codeJSMath } from "@exabyte-io/code.js/dist/math";
import { Made } from "@exabyte-io/made.js";
Expand All @@ -13,13 +14,22 @@ export class PointsGridFormDataProvider extends mix(JSONSchemaFormDataProvider).
constructor(config) {
super(config);
this._divisor = config.divisor || 1; // KPPRA will be divided by this number
this.reciprocalLattice = new Made.ReciprocalLattice(this.material.lattice);

this.dimensions = lodash.get(this.data, "dimensions") || this._defaultDimensions;
this.shifts = lodash.get(this.data, "shifts") || this._defaultShifts;

// init class fields from data (as constructed from context in parent)
this.KPPRA = lodash.get(this.data, "KPPRA") || this._defaultKPPRA;
this.preferKPPRA = lodash.get(this.data, "preferKPPRA", false);
this.gridMetricType = lodash.get(this.data, "gridMetricType") || "KPPRA";
this.gridMetricValue =
lodash.get(this.data, "gridMetricValue") || this._getDefaultGridMetricValue("KPPRA");
this.preferGridMetric = lodash.get(this.data, "preferGridMetric", false);

this._metricDescription = {
KPPRA: `${this.name[0].toUpperCase()}PPRA (${this.name[0]}pt per reciprocal atom)`, // KPPRA or QPPRA
spacing: "grid spacing",
};
this.defaultClassNames = "col-xs-12 col-sm-6 col-md-3 col-lg-2";
}

// eslint-disable-next-line class-methods-use-this
Expand All @@ -28,26 +38,61 @@ export class PointsGridFormDataProvider extends mix(JSONSchemaFormDataProvider).
}

get _defaultDimensions() {
return this._getGridFromKPPRA(this._defaultKPPRA).dimensions;
return this.calculateDimensions({
gridMetricType: "KPPRA",
gridMetricValue: this._getDefaultGridMetricValue("KPPRA"),
});
}

get _defaultShifts() {
return Array(3).fill(this.getDefaultShift());
}

get _defaultKPPRA() {
return Math.floor(5 / this._divisor);
_getDefaultGridMetricValue(metric) {
switch (metric) {
case "KPPRA":
return Math.floor(5 / this._divisor);
case "spacing":
return 0.3;
default:
console.error("Metric type not recognized!");
return 1;
}
}

get _defaultData() {
return {
dimensions: this._defaultDimensions,
shifts: this._defaultShifts,
gridMetricType: "KPPRA",
gridMetricValue: this._getDefaultGridMetricValue("KPPRA"),
preferGridMetric: false,
reciprocalVectorRatios: this.reciprocalVectorRatios,
};
}

get _defaultDataWithMaterial() {
const { gridMetricType, gridMetricValue } = this;
// if `data` is present and material is updated, prioritize `data` when `preferGridMetric` is not set
return this.preferGridMetric
? {
dimensions: this.calculateDimensions({ gridMetricType, gridMetricValue }),
shifts: this._defaultShifts,
}
: this.data || this._defaultData;
}

get defaultData() {
return this.material ? this._defaultDataWithMaterial : this._defaultData;
}

get reciprocalVectorRatios() {
const lattice = new Made.ReciprocalLattice(this.material.lattice);
return lattice.reciprocalVectorRatios.map((r) =>
return this.reciprocalLattice.reciprocalVectorRatios.map((r) =>
Number(codeJSMath.numberToPrecision(r, 3)),
);
}

get jsonSchema() {
const kOrQ = this.name[0];
const vector = {
type: "array",
items: {
Expand All @@ -71,55 +116,103 @@ export class PointsGridFormDataProvider extends mix(JSONSchemaFormDataProvider).

return {
$schema: "http://json-schema.org/draft-04/schema#",
description: `3D grid with shifts. Default min value for ${kOrQ.toUpperCase()}PPRA (${kOrQ}pt per reciprocal atom) is ${
this._defaultKPPRA
}.`,
description: `3D grid with shifts. Default min value for ${
this._metricDescription[this.gridMetricType]
} is ${this._getDefaultGridMetricValue(this.gridMetricType)}.`,
type: "object",
properties: {
dimensions: vector_(this._defaultDimensions, this.isUsingJinjaVariables),
shifts: vector_(this.getDefaultShift()),
reciprocalVectorRatios: vector_(this.reciprocalVectorRatios),
KPPRA: {
type: "integer",
minimum: 1,
default: this.KPPRA,
gridMetricType: {
type: "string",
enum: ["KPPRA", "spacing"],
default: "KPPRA",
},
gridMetricValue: {
type: "number",
},
preferKPPRA: {
preferGridMetric: {
type: "boolean",
default: this.preferKPPRA,
},
},
dependencies: {
gridMetricType: {
oneOf: [
{
properties: {
gridMetricType: {
enum: ["KPPRA"],
},
gridMetricValue: {
type: "integer",
minimum: 1,
title: "Value",
default: this.gridMetricValue,
},
preferGridMetric: {
type: "boolean",
title: "prefer KPPRA",
default: this.preferGridMetric,
},
},
},
{
properties: {
gridMetricType: {
enum: ["spacing"],
},
gridMetricValue: {
type: "number",
minimum: 0,
title: "Value [1/Å]",
default: this.gridMetricValue,
},
preferGridMetric: {
type: "boolean",
title: "prefer spacing",
default: this.preferGridMetric,
},
},
},
],
},
},
required: ["dimensions", "shifts"],
};
}

_arraySubStyle(emptyValue = 0) {
return {
"ui:options": {
addable: false,
orderable: false,
removable: false,
},
items: {
"ui:disabled": this.preferKPPRA,
// TODO: extract the actual current values from context
"ui:placeholder": "1",
"ui:emptyValue": emptyValue,
"ui:label": false,
},
get uiSchema() {
const _arraySubStyle = (emptyValue = 0) => {
return {
"ui:options": {
addable: false,
orderable: false,
removable: false,
},
items: {
"ui:disabled": this.preferGridMetric,
// TODO: extract the actual current values from context
"ui:placeholder": "1",
"ui:emptyValue": emptyValue,
"ui:label": false,
},
};
};
}

get uiSchema() {
return {
dimensions: this._arraySubStyle(1),
shifts: this._arraySubStyle(0),
KPPRA: {
"ui:disabled": !this.preferKPPRA,
"ui:emptyValue": this.KPPRA,
"ui:placeholder": this.KPPRA.toString(), // make string to prevent prop type error
dimensions: _arraySubStyle(1),
shifts: _arraySubStyle(0),
gridMetricType: {
...this.fieldStyles("rjsf-select"),
"ui:title": "Grid Metric",
},
preferKPPRA: {
gridMetricValue: {
"ui:disabled": !this.preferGridMetric,
"ui:emptyValue": this.gridMetricValue,
"ui:placeholder": this.gridMetricValue.toString(), // make string to prevent prop type error
},
preferGridMetric: {
...this.fieldStyles("p-t-20"), // add padding top to level with other elements
"ui:emptyValue": true,
"ui:disabled": this.isUsingJinjaVariables,
Expand All @@ -136,59 +229,57 @@ export class PointsGridFormDataProvider extends mix(JSONSchemaFormDataProvider).
};
}

get _defaultData() {
return {
dimensions: this._defaultDimensions,
shifts: this._defaultShifts,
KPPRA: this._defaultKPPRA,
preferKPPRA: false,
reciprocalVectorRatios: this.reciprocalVectorRatios,
};
}

get _defaultDataWithMaterial() {
// if `data` is present and material is updated, prioritize `data` when `preferKPPRA` is not set
return this.preferKPPRA
? this._getGridFromKPPRA(this.KPPRA)
: this.data || this._defaultData;
}

get defaultData() {
return this.material ? this._defaultDataWithMaterial : this._defaultData;
}

_getGridFromKPPRA(KPPRA) {
const reciprocalLattice = new Made.ReciprocalLattice(this.material.lattice);
_getDimensionsFromKPPRA(KPPRA) {
const nAtoms = this.material ? this.material.Basis.nAtoms : 1;
return {
dimensions: reciprocalLattice.getDimensionsFromPointsCount(KPPRA / nAtoms),
shifts: this._defaultShifts,
};
return this.reciprocalLattice.getDimensionsFromPointsCount(KPPRA / nAtoms);
}

_getKPPRAFromGrid(grid = this.defaultData) {
_getKPPRAFromDimensions(dimensions) {
const nAtoms = this.material ? this.material.Basis.nAtoms : 1;
return grid.dimensions.reduce((a, b) => a * b) * nAtoms;
return dimensions.reduce((a, b) => a * b) * nAtoms;
}

static _canTransform(data) {
return (
(data.preferKPPRA && data.KPPRA) ||
(!data.preferKPPRA && data.dimensions.every((d) => typeof d === "number"))
(data.preferGridMetric && data.gridMetricType && data.gridMetricValue) ||
(!data.preferGridMetric && data.dimensions.every((d) => typeof d === "number"))
);
}

calculateDimensions({ gridMetricType, gridMetricValue, units = UNITS.angstrom }) {
switch (gridMetricType) {
case "KPPRA":
return this._getDimensionsFromKPPRA(gridMetricValue);
case "spacing":
return this.reciprocalLattice.getDimensionsFromSpacing(gridMetricValue, units);
default:
return [1, 1, 1];
}
}

calculateGridMetric({ gridMetricType, dimensions, units = UNITS.angstrom }) {
switch (gridMetricType) {
case "KPPRA":
return this._getKPPRAFromDimensions(dimensions);
case "spacing":
return lodash.round(
this.reciprocalLattice.getSpacingFromDimensions(dimensions, units),
3,
);
default:
return 1;
}
}

transformData(data) {
if (!this.constructor._canTransform(data)) {
return data;
}
// 1. check if KPPRA is preferred
if (data.preferKPPRA) {
// 2. KPPRA is preferred => recalculate grid; NOTE: `data.KPPRA` is undefined at first
data.dimensions = this._getGridFromKPPRA(data.KPPRA).dimensions;
// dimensions are calculated from grid metric or vice versa
if (data.preferGridMetric) {
data.dimensions = this.calculateDimensions(data);
} else {
// 3. KPPRA is not preferred => grid was => recalculate KPPRA
data.KPPRA = this._getKPPRAFromGrid(data);
data.gridMetricValue = this.calculateGridMetric(data);
}
return data;
}
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