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SOF-7870: made #199

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Merged
timurbazhirov merged 4 commits into from
May 28, 2026
Merged

SOF-7870: made #199

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e729e50
chore: new made
k0stik Apr 25, 2026
dacf3e1
fix: use Math.abs for non-periodic boundary atom coordinates
k0stik May 22, 2026
c7a682e
chore: mathjs from utils
k0stik May 28, 2026
fee0498
chore: mathjs from utils
k0stik May 28, 2026
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7 changes: 3 additions & 4 deletions dist/mixins/bonds.js
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
import { math } from "@mat3ra/code/dist/js/math";
import { Made } from "@mat3ra/made";
import { filterBondsDataByElementsAndOrder, getElementsBondsData } from "@mat3ra/periodic-table";
import { sharedUtils } from "@mat3ra/utils";
import createKDTree from "static-kdtree";
import * as THREE from "three";
/*
Expand Down Expand Up @@ -38,7 +37,7 @@ export const BondsMixin = (superclass) => class extends superclass {
*/
// TODO: move to made basis bonded
areElementsBonded(element1, coordinate1, element2, coordinate2, bondsData) {
const distance = Made.math.vDist(coordinate1, coordinate2);
const distance = sharedUtils.math.vDist(coordinate1, coordinate2);
const connectivityFactor = this.settings.chemicalConnectivityFactor;
return Boolean(filterBondsDataByElementsAndOrder(bondsData, element1, element2).find((b) => {
return (b.length.value &&
Expand Down Expand Up @@ -73,7 +72,7 @@ export const BondsMixin = (superclass) => class extends superclass {
getMaxBondLength(bondsData) {
const connectivityFactor = this.settings.chemicalConnectivityFactor;
return (connectivityFactor *
math.max(bondsData.map((b) => b.length.value || 0)));
sharedUtils.math.max(bondsData.map((b) => b.length.value || 0)));
}
/**
* Returns an array of [element, coordinate] for all elements and their neighbors.
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3 changes: 1 addition & 2 deletions dist/mixins/boundary.js
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Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
import { Made } from "@mat3ra/made";
import * as THREE from "three";
import { BOUNDARY_CONDITIONS } from "../enums";
export const BoundaryMixin = (superclass) => class extends superclass {
Expand Down Expand Up @@ -88,7 +87,7 @@ export const BoundaryMixin = (superclass) => class extends superclass {
coordinate: [
coord[0],
coord[1],
Made.math.abs(coord[2]) <= 0.5 ? coord[2] : coord[2] - 1,
Math.abs(coord[2]) <= 0.5 ? coord[2] : coord[2] - 1,
],
});
});
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