Feature/sof 6598 clean up parsers implementation (DRAFT)

.github/workflows/cicd.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        node-version: [10.x, 12.x, 14.x, 16.x]
+        node-version: [12.x, 14.x, 16.x]
 
     steps:
       - name: Checkout this repository

src/parsers/enums.js

@@ -0,0 +1,14 @@
+export const STRUCTURAL_INFORMATION_FORMATS = {
+    JSON: "json",
+    POSCAR: "poscar",
+    CIF: "cif",
+    QE: "qe",
+    XYZ: "xyz",
+    UNKNOWN: "unknown",
+};
+
+export const APPLICATIONS = {
+    ESPRESSO: "espresso",
+    VASP: "vasp",
+    UNKNOWN: "unknown",
+};

src/parsers/espresso/parser.js

@@ -0,0 +1,271 @@
+import { ATOMIC_COORD_UNITS, coefficients } from "@exabyte-io/code.js/dist/constants";
+import { mix } from "mixwith";
+
+import { primitiveCell } from "../../cell/primitive_cell";
+import { Lattice } from "../../lattice/lattice";
+import math from "../../math";
+import { MaterialParser } from "../structure";
+import { FortranParserMixin } from "../utils/fortran";
+import { IBRAV_TO_LATTICE_TYPE_MAP, regex } from "./settings";
+
+export class ESPRESSOMaterialParser extends mix(MaterialParser).with(FortranParserMixin) {
+    parse(content) {
+        this.data = this.parseNamelists(content);
+        return this.parseMaterial();
+    }
+
+    /**
+     * @summary Return unit cell parameters from CELL_PARAMETERS card
+     * @returns {{cell: Number[][], units: String}}
+     */
+    getCell() {
+        return this.getCellConfig(this.data.cards);
+    }
+
+    /**
+     * @summary Return elements from ATOMIC_SPECIES card
+     * @returns {{id: Number, value: String}[]}
+     */
+    getElements() {
+        const text = this.data.cards;
+        const atomicPositionsMatches = Array.from(text.matchAll(regex.atomicPositions));
+        const elements = atomicPositionsMatches.map((match, index) => ({
+            id: index,
+            value: match[1],
+        }));
+        return elements;
+    }
+
+    /**
+     * @summary Return atomic positions from ATOMIC_POSITIONS card
+     * @returns {{id: Number, value: Number[]}[]}
+     */
+    getCoordinates() {
+        const text = this.data.cards;
+        const atomicPositionsMatches = Array.from(text.matchAll(regex.atomicPositions));
+        const units = text.match(regex.atomicPositionsUnits)[1];
+        const { scalingFactor } = this.getCoordinatesUnitsScalingFactor(units);
+        const coordinates = atomicPositionsMatches.map((match, index) => ({
+            id: index,
+            value: [
+                parseFloat(match[2]) * scalingFactor,
+                parseFloat(match[3]) * scalingFactor,
+                parseFloat(match[4]) * scalingFactor,
+            ],
+        }));
+        return coordinates;
+    }
+
+    /**
+     * @summary Return atomic constraints from ATOMIC_POSITIONS card
+     * @returns {{id: Number, value: Boolean[]}[]}
+     */
+    getConstraints() {
+        const text = this.data.cards;
+        const atomicPositionsMatches = Array.from(text.matchAll(regex.atomicPositions));
+        const constraints = atomicPositionsMatches.map((match, index) => {
+            const value = [];
+
+            if (match[5] && match[6] && match[7]) {
+                value.push(match[5] === "1", match[6] === "1", match[7] === "1");
+            }
+
+            return {
+                id: index,
+                value,
+            };
+        });
+
+        return constraints;
+    }
+
+    /**
+     * @summary Return atomic coordinates units from ATOMIC_POSITIONS card
+     * @returns {String}
+     */
+    getUnits() {
+        const text = this.data.cards;
+        const units = text.match(regex.atomicPositionsUnits)[1];
+        return this.getCoordinatesUnitsScalingFactor(units).units;
+    }
+
+    /**
+     * @summary Return material name from CONTROL card
+     * If not present, later will be generated from the formula in materialConfig object
+     * @returns {String}
+     */
+    getName() {
+        return this.data.control.title;
+    }
+
+    /**
+     * @summary Return unit cell parameters from CELL_PARAMETERS card
+     * @param {String} text - cards data
+     * @return {{cell: Number[][], units: String}}
+     */
+    getCellConfig(text) {
+        let cell = {};
+        if (this.data.system === undefined)
+            throw new Error("No &SYSTEM section found in input this.data.");
+        if (this.data.system.ibrav === undefined) throw new Error("ibrav is required in &SYSTEM.");
+
+        if (this.data.system.ibrav === 0) {
+            const match = regex.cellParameters.exec(text);
+            if (match) {
+                const units = match[1];
+                const values = match.slice(2, 11);
+                // creating matrix 3 by 3 of numbers from 9 strings
+                const vectors = Array.from({ length: 3 }, (_, i) =>
+                    values.slice(i * 3, i * 3 + 3).map(Number),
+                );
+                cell = { cell: vectors, units };
+                cell.type = "TRI"; // TODO: implement type detection, now defaults to TRI
+                return cell;
+            }
+        } else {
+            cell = this.ibravToCellConfig(this.data.system);
+            return cell;
+        }
+        throw new Error("Couldn't read cell parameters");
+    }
+
+    /**
+     * @summary Returns cell config from ibrav and celldm(i) parameters
+     *
+     * QE docs: https://www.quantum-espresso.org/Doc/INPUT_PW.html#ibrav
+     * "If ibrav /= 0, specify EITHER [ celldm(1)-celldm(6) ]
+     *   OR [ A, B, C, cosAB, cosAC, cosBC ]
+     *   but NOT both. The lattice parameter "alat" is set to
+     *   alat = celldm(1) (in a.u.) or alat = A (in Angstrom);"
+     *
+     * @param {Object} system - The system parameters from &SYSTEM namelist
+     * @param {Number} system.ibrav - ibrav parameter
+     * @param {Number[]} [system.celldm] - celldm parameters
+     * @param {Number} [system.a] - A parameter in angstroms
+     * @param {Number} [system.b] - B parameter in angstroms
+     * @param {Number} [system.c] - C parameter in angstroms
+     * @param {Number} [system.cosab] - cosAB parameter
+     * @param {Number} [system.cosac] - cosAC parameter
+     * @param {Number} [system.cosbc] - cosBC parameter
+     * @returns {{cell: Number[][], type: String}}
+     */
+    ibravToCellConfig(system) {
+        const { ibrav, celldm, cosab, cosac, cosbc } = system;
+        let { a, b, c } = system;
+        if (celldm && a) {
+            throw new Error("Both celldm and A are given");
+        } else if (!celldm && !a) {
+            throw new Error("Missing celldm(1)");
+        }
+
+        const type = this.ibravToCellType(ibrav);
+        [a, b, c] = celldm ? this.getLatticeConstants(celldm) : [a, b, c];
+        const [alpha, beta, gamma] = this.getLatticeAngles(celldm, cosbc, cosac, cosab);
+
+        const lattice = new Lattice({
+            a,
+            b,
+            c,
+            alpha,
+            beta,
+            gamma,
+            type,
+        });
+        const cell = primitiveCell(lattice);
+        return { cell, type };
+    }
+
+    /**
+     * @summary Converts ibrav value to cell type according to Quantum ESPRESSO docs
+     * https://www.quantum-espresso.org/Doc/INPUT_PW.html#ibrav
+     * @param {Number} ibrav - ibrav parameter
+     * @returns {String}
+     */
+    ibravToCellType(ibrav) {
+        const type = IBRAV_TO_LATTICE_TYPE_MAP[ibrav];
+        if (type === undefined) {
+            throw new Error(`Invalid ibrav value: ${ibrav}`);
+        }
+        return type;
+    }
+
+    /**
+     * @summary Calculates cell parameters from celldm(i) or A, B, C parameters depending on which are present. Specific to Quantum ESPRESSO.
+     * @param {Number[]} celldm - celldm(i) parameters
+     * @returns {Number[]}
+     * */
+    getLatticeConstants(celldm) {
+        // celldm indices shifted -1 from fortran list representation. In QE input file celldm(1) list starts with 1, but parsed starting with 0.
+        const a = celldm[0] * coefficients.BOHR_TO_ANGSTROM; // celldm(1) is a in bohr
+        const b = celldm[1] * celldm[0] * coefficients.BOHR_TO_ANGSTROM; // celldm(2) is b/a
+        const c = celldm[2] * celldm[0] * coefficients.BOHR_TO_ANGSTROM; // celldm(3) is c/a
+        return [a, b, c];
+    }
+
+    /**
+     * @summary Calculates cell angles from celldm(i) or cosAB, cosAC, cosBC parameters. Specific to Quantum ESPRESSO.
+     * @param {Number[]} [celldm] - celldm(i) parameters
+     * @param {Number} [cosbc] - cosBC parameter
+     * @param {Number} [cosac] - cosAC parameter
+     * @param {Number} [cosab]   - cosAB parameter
+     * @returns {Array<Number | undefined>}
+     * */
+    getLatticeAngles(celldm, cosbc, cosac, cosab) {
+        let alpha, beta, gamma;
+        if (cosbc) alpha = math.acos(cosbc);
+        if (cosac) beta = math.acos(cosac);
+        if (cosab) gamma = math.acos(cosab);
+
+        // Case for some of the cell types in QE docs
+        // celldm indices shifted -1 from fortran list representation. In QE input file celdm(1) array starts with 1, but parsed starting with 0.
+        if (celldm && celldm[3]) {
+            gamma = math.acos(celldm[3]);
+        }
+
+        // Specific case for hexagonal cell in QE docs
+        // celldm indices shifted -1 from fortran list representation. In QE input file celdm(1) array starts with 1, but parsed starting with 0.
+        if (celldm && celldm[3] && celldm[4] && celldm[5]) {
+            alpha = math.acos(celldm[3]);
+            beta = math.acos(celldm[4]);
+            gamma = math.acos(celldm[5]);
+        }
+
+        // Convert radians to degrees which are used in lattice definitions
+        [alpha, beta, gamma] = [alpha, beta, gamma].map((x) =>
+            x === undefined ? x : (x * 180) / math.PI,
+        );
+        return [alpha, beta, gamma];
+    }
+
+    /**
+     * @summary Return units and scaling factor according to Quantum ESPRESSO 7.2 docs
+     * @param {String} units - units from ATOMIC_POSITIONS card
+     * @returns {{units: String, scalingFactor: Number}}
+     */
+    getCoordinatesUnitsScalingFactor(units) {
+        let _units, scalingFactor;
+        switch (units) {
+            case "alat":
+                scalingFactor = 1.0;
+                _units = ATOMIC_COORD_UNITS.crystal;
+                break;
+            case "bohr":
+                scalingFactor = coefficients.BOHR_TO_ANGSTROM;
+                _units = ATOMIC_COORD_UNITS.cartesian;
+                break;
+            case "angstrom":
+                scalingFactor = 1.0;
+                _units = ATOMIC_COORD_UNITS.cartesian;
+                break;
+            case "crystal":
+                scalingFactor = 1.0;
+                _units = ATOMIC_COORD_UNITS.crystal;
+                break;
+            case "crystal_sg":
+                throw new Error("crystal_sg not supported yet");
+            default:
+                throw new Error(`Units ${units} not supported`);
+        }
+        return { units: _units, scalingFactor };
+    }
+}

src/parsers/espresso/settings.js

@@ -0,0 +1,55 @@
+import { LATTICE_TYPE } from "../../lattice/types";
+import { regex as commonRegex } from "../utils/settings";
+
+const { double } = commonRegex.general;
+export const regex = {
+    espressoFingerprint: /&CONTROL|&SYSTEM|ATOMIC_SPECIES/i,
+    atomicSpecies: new RegExp(
+        "([A-Z][a-z]?)\\s+" + // element symbol Aa
+            `(${double})\\s` + // mass
+            "(\\S*)\\s*" + // potential source file name
+            "(?=\\n)", // end of line
+        "gm",
+    ),
+    atomicPositionsUnits: new RegExp(
+        "ATOMIC_POSITIONS\\s+" + // start of card
+            "\\(?" + // optional parentheses
+            "(\\w+)" + // units
+            "\\)?", // end of optional parentheses
+    ),
+    atomicPositions: new RegExp(
+        `^\\s*([A-Z][a-z]*)\\s+` + // atomic element symbol
+            `(${double})\\s+(${double})\\s+(${double})` + // atomic coordinates
+            `(?:\\s+(0|1)\\s+(0|1)\\s+(0|1))?(?=\\s*\\n)`, // atomic constraints
+        "gm",
+    ),
+    cellParameters: new RegExp(
+        `CELL_PARAMETERS\\s*(?:\\(?(\\w+)\\)?)?\\n` +
+            `^\\s*(${double})\\s+(${double})\\s+(${double})\\s*\\n` +
+            `^\\s*(${double})\\s+(${double})\\s+(${double})\\s*\\n` +
+            `^\\s*(${double})\\s+(${double})\\s+(${double})\\s*\\n`,
+        "gm",
+    ),
+};
+
+export const IBRAV_TO_LATTICE_TYPE_MAP = {
+    1: LATTICE_TYPE.CUB,
+    2: LATTICE_TYPE.FCC,
+    3: LATTICE_TYPE.BCC,
+    "-3": LATTICE_TYPE.BCC,
+    4: LATTICE_TYPE.HEX,
+    5: LATTICE_TYPE.RHL,
+    "-5": LATTICE_TYPE.RHL,
+    6: LATTICE_TYPE.TET,
+    7: LATTICE_TYPE.BCT,
+    8: LATTICE_TYPE.ORC,
+    9: LATTICE_TYPE.ORCC,
+    "-9": LATTICE_TYPE.ORCC,
+    10: LATTICE_TYPE.ORCF,
+    11: LATTICE_TYPE.ORCI,
+    12: LATTICE_TYPE.MCL,
+    "-12": LATTICE_TYPE.MCL,
+    13: LATTICE_TYPE.MCLC,
+    "-13": LATTICE_TYPE.MCLC,
+    14: LATTICE_TYPE.TRI,
+};

src/parsers/init.js

@@ -0,0 +1,10 @@
+export class BaseParser {
+    constructor(options) {
+        this.options = options;
+    }
+
+    // eslint-disable-next-line class-methods-use-this
+    parse() {
+        throw new Error("parse() is implemented in children");
+    }
+}