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* ReaxFF Force Field Parameter Parser
* Parses ReaxFF parameter files and extracts atom definitions and properties
* @module simulation/forceFieldParser
*/
import logger from '../utils/logger';
/**
* @typedef {Object} AtomParameters
* @property {string} symbol - Atomic symbol (e.g., 'C', 'H', 'O')
* @property {string} name - Full element name
* @property {number} mass - Atomic mass in amu
* @property {number} roSigma - Sigma bond radius
* @property {number} valency - Number of valence electrons
* @property {number} rvdw - Van der Waals radius
* @property {number} evdw - Van der Waals well depth
* @property {number} gammaEEM - EEM gamma parameter
* @property {number} roPi - Pi bond radius
* @property {number} alfa - Alpha parameter
* @property {number} gammavdW - Van der Waals gamma
* @property {number} chiEEM - EEM electronegativity
* @property {number} etaEEM - EEM hardness
* @property {number} roPiPi - Double pi bond radius
*/
/**
* @typedef {Object} ParsedForceField
* @property {string} name - Force field name/description
* @property {number} generalParamsCount - Number of general parameters
* @property {number[]} generalParams - Array of general parameters
* @property {AtomParameters[]} atoms - Array of atom definitions
* @property {Object[]} bonds - Array of bond parameters
*/
/**
* Element name lookup from symbol
* @type {Object<string, string>}
*/
const ELEMENT_NAMES = {
'C': 'Carbon',
'H': 'Hydrogen',
'O': 'Oxygen',
'N': 'Nitrogen',
'S': 'Sulfur',
'P': 'Phosphorus',
'Si': 'Silicon',
'Au': 'Gold',
'Pt': 'Platinum',
'Zn': 'Zinc',
'Zr': 'Zirconium',
'Ni': 'Nickel',
'Cu': 'Copper',
'Ti': 'Titanium',
'V': 'Vanadium',
'Bi': 'Bismuth',
'Mg': 'Magnesium',
'Na': 'Sodium',
'Fe': 'Iron',
'Al': 'Aluminum',
'B': 'Boron',
'Cl': 'Chlorine',
'F': 'Fluorine',
'X': 'Placeholder',
};
/**
* CPK color scheme for elements
* @type {Object<string, Object>}
*/
const CPK_COLORS = {
'C': { color: '#222222', highlightColor: '#555555' },
'H': { color: '#FFFFFF', highlightColor: '#E8E8E8' },
'O': { color: '#FF0D0D', highlightColor: '#FF6666' },
'N': { color: '#3050F8', highlightColor: '#7090FF' },
'S': { color: '#FFFF30', highlightColor: '#FFFF80' },
'P': { color: '#FF8000', highlightColor: '#FFAA55' },
'Si': { color: '#F0C8A0', highlightColor: '#F5DCC8' },
'Au': { color: '#FFD123', highlightColor: '#FFE066' },
'Pt': { color: '#D0D0E0', highlightColor: '#E8E8F0' },
'Zn': { color: '#7D80B0', highlightColor: '#A0A3C8' },
'Zr': { color: '#94E0E0', highlightColor: '#B8F0F0' },
'Ni': { color: '#50D050', highlightColor: '#80E080' },
'Cu': { color: '#C88033', highlightColor: '#D9A066' },
'Ti': { color: '#BFC2C7', highlightColor: '#D5D8DD' },
'V': { color: '#A6A6AB', highlightColor: '#C0C0C5' },
'Bi': { color: '#9E4FB5', highlightColor: '#B878C8' },
'Mg': { color: '#8AFF00', highlightColor: '#B5FF55' },
'Na': { color: '#AB5CF2', highlightColor: '#C88FF8' },
'Fe': { color: '#E06633', highlightColor: '#F09966' },
'Al': { color: '#BFA6A6', highlightColor: '#D5C8C8' },
'B': { color: '#FFB5B5', highlightColor: '#FFD5D5' },
'Cl': { color: '#1FF01F', highlightColor: '#66F066' },
'F': { color: '#90E050', highlightColor: '#B5F080' },
'X': { color: '#808080', highlightColor: '#A0A0A0' },
};
/**
* Parse a line of atom parameters from ReaxFF file
* @param {string[]} lines - Array of 4 consecutive lines for one atom
* @returns {AtomParameters|null} Parsed atom parameters or null if invalid
*/
const parseAtomBlock = (lines) => {
Iif (lines.length < 4) {
return null;
}
try {
// First line: symbol and first row of parameters
const line1Parts = lines[0].trim().split(/\s+/);
const symbol = line1Parts[0];
Iif (!symbol || symbol.length > 2 || /^\d/.test(symbol)) {
return null;
}
const roSigma = parseFloat(line1Parts[1]) || 0;
const valency = parseFloat(line1Parts[2]) || 0;
const mass = parseFloat(line1Parts[3]) || 0;
const rvdw = parseFloat(line1Parts[4]) || 0;
const evdw = parseFloat(line1Parts[5]) || 0;
const gammaEEM = parseFloat(line1Parts[6]) || 0;
const roPi = parseFloat(line1Parts[7]) || 0;
// Second line: more parameters
const line2Parts = lines[1].trim().split(/\s+/);
const alfa = parseFloat(line2Parts[0]) || 0;
const gammavdW = parseFloat(line2Parts[1]) || 0;
const chiEEM = parseFloat(line2Parts[5]) || 0;
const etaEEM = parseFloat(line2Parts[6]) || 0;
// Third line: more parameters including roPiPi
const line3Parts = lines[2].trim().split(/\s+/);
const roPiPi = parseFloat(line3Parts[0]) || 0;
const colors = CPK_COLORS[symbol] || { color: '#808080', highlightColor: '#A0A0A0' };
return {
symbol,
name: ELEMENT_NAMES[symbol] || symbol,
mass,
roSigma,
valency: Math.round(valency),
radius: rvdw,
rvdw,
evdw,
gammaEEM,
roPi,
alfa,
gammavdW,
chiEEM,
etaEEM,
roPiPi,
charge: 0,
...colors,
};
} catch (error) {
logger.warn('Failed to parse atom block:', error.message);
return null;
}
};
/**
* Parse a ReaxFF force field file content
* @param {string} content - Raw file content
* @returns {ParsedForceField} Parsed force field data
*/
export const parseForceField = (content) => {
const lines = content.split('\n');
const result = {
name: '',
generalParamsCount: 0,
generalParams: [],
atoms: [],
bonds: [],
};
Iif (lines.length === 0) {
logger.warn('Empty force field file');
return result;
}
// First line is the force field name/description
result.name = lines[0].trim();
// Find the number of general parameters
let lineIndex = 1;
while (lineIndex < lines.length) {
const line = lines[lineIndex].trim();
const match = line.match(/^\s*(\d+)\s*!\s*Number of general parameters/i);
Eif (match) {
result.generalParamsCount = parseInt(match[1], 10);
lineIndex++;
break;
}
// Also try simpler format
const simpleMatch = line.match(/^\s*(\d+)\s+/);
if (simpleMatch && line.includes('!')) {
result.generalParamsCount = parseInt(simpleMatch[1], 10);
lineIndex++;
break;
}
lineIndex++;
}
// Skip general parameters
lineIndex += result.generalParamsCount;
// Find atom section
while (lineIndex < lines.length) {
const line = lines[lineIndex].trim();
const atomCountMatch = line.match(/^\s*(\d+)\s*!\s*Nr of atoms/i);
Eif (atomCountMatch) {
const atomCount = parseInt(atomCountMatch[1], 10);
lineIndex += 4; // Skip header lines (4 header comment lines after count)
// Parse each atom (4 lines per atom)
for (let i = 0; i < atomCount && lineIndex + 3 < lines.length; i++) {
const atomLines = [
lines[lineIndex],
lines[lineIndex + 1],
lines[lineIndex + 2],
lines[lineIndex + 3],
];
const atom = parseAtomBlock(atomLines);
Eif (atom) {
result.atoms.push(atom);
}
lineIndex += 4;
}
break;
}
lineIndex++;
}
logger.info(`Parsed force field "${result.name}" with ${result.atoms.length} atom types`);
return result;
};
/**
* Convert parsed force field atoms to ATOM_TYPES format
* @param {AtomParameters[]} atoms - Parsed atoms from force field
* @param {number} startingId - Starting ID for atom types
* @returns {Object} ATOM_TYPES compatible object
*/
export const toAtomTypes = (atoms, startingId = 1) => {
const atomTypes = {};
atoms.forEach((atom, index) => {
atomTypes[startingId + index] = {
name: atom.name,
symbol: atom.symbol,
mass: atom.mass,
radius: atom.radius || atom.rvdw || 1.5,
valency: atom.valency,
color: atom.color,
highlightColor: atom.highlightColor,
charge: atom.charge || 0,
roSigma: atom.roSigma,
roPi: atom.roPi,
roPiPi: atom.roPiPi,
};
});
return atomTypes;
};
/**
* Get available force field file names
* @returns {string[]} Array of force field file names
*/
export const getAvailableForceFields = () => [
'ffield.reax.cho',
'BaeAiken2013.ff',
'van_duin_zno.ff',
'reaxff_glycine_force_field1.txt',
'reaxff_biomolecules_param1.txt',
'reaxff_aluminum_oxygen_carbon.txt',
'reaxff_boron_carbide0.txt',
];
/**
* Get force field description
* @param {string} filename - Force field filename
* @returns {Object} Description object
*/
export const getForceFieldInfo = (filename) => {
const info = {
'ffield.reax.cho': {
name: 'CHO Combustion',
description: 'Carbon-Hydrogen-Oxygen combustion chemistry',
elements: ['C', 'H', 'O'],
},
'BaeAiken2013.ff': {
name: 'Gold-Sulfur-Carbon',
description: 'Gold nanoparticle with thiol ligands',
elements: ['C', 'H', 'S', 'Au'],
},
'van_duin_zno.ff': {
name: 'Water/ZnO System',
description: 'Zinc oxide surfaces with water',
elements: ['C', 'H', 'O', 'N', 'S', 'Si', 'Pt', 'Zr', 'Ni', 'Au', 'V', 'Bi', 'Ti', 'Zn'],
},
'reaxff_glycine_force_field1.txt': {
name: 'Glycine',
description: 'Amino acid glycine simulation',
elements: ['C', 'H', 'O', 'N'],
},
'reaxff_biomolecules_param1.txt': {
name: 'Biomolecules',
description: 'Protein and biomolecule simulations',
elements: ['C', 'H', 'O', 'N', 'S', 'Mg', 'P', 'Na', 'Cu'],
},
'reaxff_aluminum_oxygen_carbon.txt': {
name: 'Aluminum Oxide',
description: 'Aluminum and aluminum oxide systems',
elements: ['Al', 'O', 'C', 'H'],
},
'reaxff_boron_carbide0.txt': {
name: 'Boron Carbide',
description: 'Boron carbide ceramic systems',
elements: ['B', 'C', 'H'],
},
};
return info[filename] || { name: filename, description: 'Unknown force field', elements: [] };
};
export default {
parseForceField,
toAtomTypes,
getAvailableForceFields,
getForceFieldInfo,
ELEMENT_NAMES,
CPK_COLORS,
};
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