// This file contains function that are generic Javascript for TrimSP

// This is an object that contains all GUI ids and values
var All = new Object();


function isObject(item) {
    // simple object check
    // https://stackoverflow.com/a/34749873
    return (item && typeof item === 'object' && !Array.isArray(item));
}


function mergeDeep(target, ...sources) {
    // function for deep-merging objects
    // https://stackoverflow.com/a/34749873
    
    if (!sources.length) {
        return target;
    }
    
    const source = sources.shift();

    if (isObject(target) && isObject(source)) {
        for (const key in source) {
            if (isObject(source[key])) {
                if (!target[key]) Object.assign(target, { [key]: {} });
                mergeDeep(target[key], source[key]);
            } else {
                Object.assign(target, { [key]: source[key] });
            }
        }
    }

    return mergeDeep(target, ...sources);
}


// element data
const elements = {
	"H": {
		"Z": 1,
		"A": 1.008,
		"rho": 0.08,
		"Elast": 0.1
	},
	"He": {
		"Z": 2,
		"A": 4.003,
		"rho": 0.12,
		"Elast": 0.1
	},
	"Li": {
		"Z": 3,
		"A": 6.939,
		"rho": 0.53,
		"Elast": 1.63
	},
	"Be": {
		"Z": 4,
		"A": 9.012,
		"rho": 1.85,
		"Elast": 3.32
	},
	"B": {
		"Z": 5,
		"A": 10.811,
		"rho": 2.34,
		"Elast": 5.77
	},
	"C": {
		"Z": 6,
		"A": 12.011,
		"rho": 2.26,
		"Elast": 7.37
	},
	"N": {
		"Z": 7,
		"A": 14.007,
		"rho": 1.03,
		"Elast": 4.92
	},
	"O": {
		"Z": 8,
		"A": 15.999,
		"rho": 2,
		"Elast": 2.6
	},
	"F": {
		"Z": 9,
		"A": 18.998,
		"rho": 1.11,
		"Elast": 0.84
	},
	"Ne": {
		"Z": 10,
		"A": 20.183,
		"rho": 1.5,
		"Elast": 0.02
	},
	"Na": {
		"Z": 11,
		"A": 22.99,
		"rho": 0.97,
		"Elast": 1.11
	},
	"Mg": {
		"Z": 12,
		"A": 24.312,
		"rho": 1.74,
		"Elast": 1.51
	},
	"Al": {
		"Z": 13,
		"A": 26.982,
		"rho": 2.7,
		"Elast": 3.39
	},
	"Si": {
		"Z": 14,
		"A": 28.086,
		"rho": 2.33,
		"Elast": 4.63
	},
	"P": {
		"Z": 15,
		"A": 30.974,
		"rho": 1,
		"Elast": 3.43
	},
	"S": {
		"Z": 16,
		"A": 32.064,
		"rho": 2.07,
		"Elast": 2.85
	},
	"Cl": {
		"Z": 17,
		"A": 35.453,
		"rho": 2.03,
		"Elast": 1.4
	},
	"Ar": {
		"Z": 18,
		"A": 39.948,
		"rho": 1.77,
		"Elast": 0.08
	},
	"K": {
		"Z": 19,
		"A": 39.102,
		"rho": 0.86,
		"Elast": 0.93
	},
	"Ca": {
		"Z": 20,
		"A": 40.08,
		"rho": 1.55,
		"Elast": 1.84
	},
	"Sc": {
		"Z": 21,
		"A": 44.956,
		"rho": 2.99,
		"Elast": 3.9
	},
	"Ti": {
		"Z": 22,
		"A": 47.9,
		"rho": 4.54,
		"Elast": 4.85
	},
	"V": {
		"Z": 23,
		"A": 50.942,
		"rho": 6.11,
		"Elast": 5.31
	},
	"Cr": {
		"Z": 24,
		"A": 51.996,
		"rho": 7.19,
		"Elast": 4.1
	},
	"Mn": {
		"Z": 25,
		"A": 54.938,
		"rho": 7.43,
		"Elast": 2.92
	},
	"Fe": {
		"Z": 26,
		"A": 55.847,
		"rho": 7.87,
		"Elast": 4.28
	},
	"Co": {
		"Z": 27,
		"A": 58.933,
		"rho": 8.9,
		"Elast": 4.39
	},
	"Ni": {
		"Z": 28,
		"A": 58.71,
		"rho": 8.9,
		"Elast": 4.44
	},
	"Cu": {
		"Z": 29,
		"A": 63.54,
		"rho": 8.96,
		"Elast": 3.49
	},
	"Zn": {
		"Z": 30,
		"A": 65.37,
		"rho": 7.13,
		"Elast": 1.35
	},
	"Ga": {
		"Z": 31,
		"A": 69.72,
		"rho": 5.91,
		"Elast": 2.81
	},
	"Ge": {
		"Z": 32,
		"A": 72.59,
		"rho": 5.32,
		"Elast": 3.85
	},
	"As": {
		"Z": 33,
		"A": 74.922,
		"rho": 5.72,
		"Elast": 2.96
	},
	"Se": {
		"Z": 34,
		"A": 78.96,
		"rho": 4.79,
		"Elast": 2.25
	},
	"Br": {
		"Z": 35,
		"A": 79.909,
		"rho": 3.14,
		"Elast": 1.22
	},
	"Kr": {
		"Z": 36,
		"A": 83.8,
		"rho": 3.1,
		"Elast": 0.12
	},
	"Rb": {
		"Z": 37,
		"A": 85.47,
		"rho": 1.53,
		"Elast": 0.85
	},
	"Sr": {
		"Z": 38,
		"A": 87.62,
		"rho": 2.54,
		"Elast": 1.72
	},
	"Y": {
		"Z": 39,
		"A": 88.905,
		"rho": 4.47,
		"Elast": 4.37
	},
	"Zr": {
		"Z": 40,
		"A": 91.22,
		"rho": 6.51,
		"Elast": 6.25
	},
	"Nb": {
		"Z": 41,
		"A": 92.906,
		"rho": 8.57,
		"Elast": 7.57
	},
	"Mo": {
		"Z": 42,
		"A": 95.94,
		"rho": 10.22,
		"Elast": 6.82
	},
	"Tc": {
		"Z": 43,
		"A": 98,
		"rho": 11.5,
		"Elast": 6.85
	},
	"Ru": {
		"Z": 44,
		"A": 101.07,
		"rho": 12.37,
		"Elast": 6.74
	},
	"Rh": {
		"Z": 45,
		"A": 102.905,
		"rho": 12.41,
		"Elast": 5.75
	},
	"Pd": {
		"Z": 46,
		"A": 106.4,
		"rho": 12.02,
		"Elast": 3.89
	},
	"Ag": {
		"Z": 47,
		"A": 107.87,
		"rho": 10.5,
		"Elast": 2.95
	},
	"Cd": {
		"Z": 48,
		"A": 112.4,
		"rho": 8.65,
		"Elast": 1.16
	},
	"In": {
		"Z": 49,
		"A": 114.82,
		"rho": 7.31,
		"Elast": 2.52
	},
	"Sn": {
		"Z": 50,
		"A": 118.69,
		"rho": 7.31,
		"Elast": 3.14
	},
	"Sb": {
		"Z": 51,
		"A": 121.75,
		"rho": 6.68,
		"Elast": 2.75
	},
	"Te": {
		"Z": 52,
		"A": 127.6,
		"rho": 6.24,
		"Elast": 2.23
	},
	"I": {
		"Z": 53,
		"A": 126.904,
		"rho": 4.93,
		"Elast": 1.11
	},
	"Xe": {
		"Z": 54,
		"A": 131.3,
		"rho": 3.8,
		"Elast": 0.16
	},
	"Cs": {
		"Z": 55,
		"A": 132.905,
		"rho": 1.9,
		"Elast": 0.8
	},
	"Ba": {
		"Z": 56,
		"A": 137.34,
		"rho": 3.59,
		"Elast": 1.9
	},
	"La": {
		"Z": 57,
		"A": 138.91,
		"rho": 6.15,
		"Elast": 4.47
	},
	"Ce": {
		"Z": 58,
		"A": 140.12,
		"rho": 6.77,
		"Elast": 4.32
	},
	"Pr": {
		"Z": 59,
		"A": 140.907,
		"rho": 6.77,
		"Elast": 3.7
	},
	"Nd": {
		"Z": 60,
		"A": 144.24001,
		"rho": 7.01,
		"Elast": 3.4
	},
	"Pm": {
		"Z": 61,
		"A": 147,
		"rho": 7.22,
		"Elast": 0.1
	},
	"Sm": {
		"Z": 62,
		"A": 150.35001,
		"rho": 7.52,
		"Elast": 2.14
	},
	"Eu": {
		"Z": 63,
		"A": 151.96001,
		"rho": 5.24,
		"Elast": 1.86
	},
	"Gd": {
		"Z": 64,
		"A": 157.25,
		"rho": 7.9,
		"Elast": 4.14
	},
	"Tb": {
		"Z": 65,
		"A": 158.924,
		"rho": 8.23,
		"Elast": 4.05
	},
	"Dy": {
		"Z": 66,
		"A": 162.5,
		"rho": 8.55,
		"Elast": 3.04
	},
	"Ho": {
		"Z": 67,
		"A": 164.92999,
		"rho": 8.8,
		"Elast": 3.14
	},
	"Er": {
		"Z": 68,
		"A": 167.25999,
		"rho": 9.07,
		"Elast": 3.29
	},
	"Tm": {
		"Z": 69,
		"A": 168.93401,
		"rho": 9.32,
		"Elast": 2.42
	},
	"Yb": {
		"Z": 70,
		"A": 173.03999,
		"rho": 6.9,
		"Elast": 1.6
	},
	"Lu": {
		"Z": 71,
		"A": 174.97,
		"rho": 9.84,
		"Elast": 4.43
	},
	"Hf": {
		"Z": 72,
		"A": 178.49001,
		"rho": 13.31,
		"Elast": 6.44
	},
	"Ta": {
		"Z": 73,
		"A": 180.948,
		"rho": 16.65,
		"Elast": 8.1
	},
	"W": {
		"Z": 74,
		"A": 183.85001,
		"rho": 19.35,
		"Elast": 8.9
	},
	"Re": {
		"Z": 75,
		"A": 186.2,
		"rho": 21.04,
		"Elast": 8.03
	},
	"Os": {
		"Z": 76,
		"A": 190.2,
		"rho": 22.6,
		"Elast": 8.17
	},
	"Ir": {
		"Z": 77,
		"A": 192.2,
		"rho": 22.4,
		"Elast": 6.94
	},
	"Pt": {
		"Z": 78,
		"A": 195.09,
		"rho": 21.45,
		"Elast": 5.84
	},
	"Au": {
		"Z": 79,
		"A": 196.967,
		"rho": 19.32,
		"Elast": 3.81
	},
	"Hg": {
		"Z": 80,
		"A": 200.59,
		"rho": 13.55,
		"Elast": 0.67
	},
	"Tl": {
		"Z": 81,
		"A": 204.37,
		"rho": 11.85,
		"Elast": 1.88
	},
	"Pb": {
		"Z": 82,
		"A": 207.19,
		"rho": 11.35,
		"Elast": 2.03
	},
	"Bi": {
		"Z": 83,
		"A": 208.98,
		"rho": 9.75,
		"Elast": 2.18
	},
	"Po": {
		"Z": 84,
		"A": 210,
		"rho": 9.3,
		"Elast": 1.5
	},
	"At": {
		"Z": 85,
		"A": 210,
		"rho": 0,
		"Elast": 0.1
	},
	"Rn": {
		"Z": 86,
		"A": 222,
		"rho": 0,
		"Elast": 0.2
	},
	"Fr": {
		"Z": 87,
		"A": 223,
		"rho": 0,
		"Elast": 0.1
	},
	"Ra": {
		"Z": 88,
		"A": 226,
		"rho": 0,
		"Elast": 1.66
	},
	"Ac": {
		"Z": 89,
		"A": 227,
		"rho": 0,
		"Elast": 4.25
	},
	"Th": {
		"Z": 90,
		"A": 232.03799,
		"rho": 11.72,
		"Elast": 6.2
	},
	"Pa": {
		"Z": 91,
		"A": 231,
		"rho": 15.4,
		"Elast": 0.1
	},
	"U": {
		"Z": 92,
		"A": 238.03,
		"rho": 18.95,
		"Elast": 5.55
	},
	"": {
		"Z": 0,
		"A": 0,
		"rho": 0,
		"Elast": 0
	}
}


// projectile data
const projectiles = {
	"muon": {
		"Z": 1,
		"A": 0.1134289259,
		"rho": 0,
		"Elast": 0,
		"ICRU": [],
		"IAEA": []
	},
	"Li-8": {
		"Z": 3,
		"A": 8.02248624,
		"rho": 0,
		"Elast": 0,
		"ICRU": [],
		"IAEA": []
	},
	"B-12": {
		"Z": 5,
		"A": 12.0143526,
		"rho": 0,
		"Elast": 0,
		"ICRU": [],
		"IAEA": []
	},
	"Mg-31": {
		"Z": 12,
		"A": 30.996648,
		"rho": 0,
		"Elast": 0,
		"ICRU": [],
		"IAEA": []
	}
}


// electronic stopping coefficients from Anderson & Zeigler (1977).
const az_table = {
	"H": {
		"AZ": [
			1.262,
			1.44,
			242.6,
			12000.0,
			0.1159
		]
	},
	"He": {
		"AZ": [
			1.229,
			1.397,
			484.5,
			5873.0,
			0.05225
		]
	},
	"Li": {
		"AZ": [
			1.411,
			1.6,
			725.6,
			3013.0,
			0.04578
		]
	},
	"Be": {
		"AZ": [
			2.248,
			2.59,
			966.0,
			153.8,
			0.03475
		]
	},
	"B": {
		"AZ": [
			2.474,
			2.815,
			1206.0,
			1060.0,
			0.02855
		]
	},
	"C": {
		"AZ": [
			2.631,
			2.989,
			1445.0,
			957.2,
			0.02819
		]
	},
	"N": {
		"AZ": [
			2.954,
			3.35,
			1683.0,
			1900.0,
			0.02513
		]
	},
	"O": {
		"AZ": [
			2.652,
			3.0,
			1920.0,
			2000.0,
			0.0223
		]
	},
	"F": {
		"AZ": [
			2.085,
			2.352,
			2157.0,
			2634.0,
			0.01816
		]
	},
	"Ne": {
		"AZ": [
			1.951,
			2.199,
			2393.0,
			2699.0,
			0.01568
		]
	},
	"Na": {
		"AZ": [
			2.542,
			2.869,
			2628.0,
			1854.0,
			0.01472
		]
	},
	"Mg": {
		"AZ": [
			3.792,
			4.293,
			2862.0,
			1009.0,
			0.01397
		]
	},
	"Al": {
		"AZ": [
			4.154,
			4.739,
			2766.0,
			164.5,
			0.01397
		]
	},
	"Si": {
		"AZ": [
			4.15,
			4.7,
			3329.0,
			550.0,
			0.01321
		]
	},
	"P": {
		"AZ": [
			3.232,
			3.647,
			3561.0,
			1560.0,
			0.01267
		]
	},
	"S": {
		"AZ": [
			3.447,
			3.891,
			3792.0,
			1219.0,
			0.01211
		]
	},
	"Cl": {
		"AZ": [
			5.047,
			5.714,
			4023.0,
			878.6,
			0.01178
		]
	},
	"Ar": {
		"AZ": [
			5.731,
			6.5,
			4253.0,
			530.0,
			0.01123
		]
	},
	"K": {
		"AZ": [
			5.151,
			5.833,
			4482.0,
			545.7,
			0.01129
		]
	},
	"Ca": {
		"AZ": [
			5.521,
			6.252,
			4710.0,
			553.3,
			0.01112
		]
	},
	"Sc": {
		"AZ": [
			5.201,
			5.884,
			4938.0,
			560.9,
			0.009995
		]
	},
	"Ti": {
		"AZ": [
			4.862,
			5.496,
			5165.0,
			568.5,
			0.009474
		]
	},
	"V": {
		"AZ": [
			4.48,
			5.055,
			5391.0,
			952.3,
			0.009117
		]
	},
	"Cr": {
		"AZ": [
			3.983,
			4.489,
			5616.0,
			1336.0,
			0.008413
		]
	},
	"Mn": {
		"AZ": [
			3.469,
			3.907,
			5725.0,
			1461.0,
			0.008829
		]
	},
	"Fe": {
		"AZ": [
			3.519,
			3.963,
			6065.0,
			1243.0,
			0.007782
		]
	},
	"Co": {
		"AZ": [
			3.14,
			3.535,
			6288.0,
			1372.0,
			0.007361
		]
	},
	"Ni": {
		"AZ": [
			3.553,
			4.004,
			6205.0,
			555.1,
			0.008763
		]
	},
	"Cu": {
		"AZ": [
			3.696,
			4.175,
			4673.0,
			387.8,
			0.02188
		]
	},
	"Zn": {
		"AZ": [
			4.21,
			4.75,
			6953.0,
			295.2,
			0.006809
		]
	},
	"Ga": {
		"AZ": [
			5.041,
			5.697,
			7173.0,
			202.6,
			0.006725
		]
	},
	"Ge": {
		"AZ": [
			5.554,
			6.3,
			6496.0,
			110.0,
			0.009689
		]
	},
	"As": {
		"AZ": [
			5.323,
			6.012,
			7611.0,
			292.5,
			0.006447
		]
	},
	"Se": {
		"AZ": [
			5.874,
			6.656,
			7395.0,
			117.5,
			0.007684
		]
	},
	"Br": {
		"AZ": [
			5.611,
			6.335,
			8046.0,
			365.2,
			0.006244
		]
	},
	"Kr": {
		"AZ": [
			6.411,
			7.25,
			8262.0,
			220.0,
			0.006087
		]
	},
	"Rb": {
		"AZ": [
			5.694,
			6.429,
			8478.0,
			292.9,
			0.006087
		]
	},
	"Sr": {
		"AZ": [
			6.339,
			7.159,
			8693.0,
			330.3,
			0.006003
		]
	},
	"Y": {
		"AZ": [
			6.407,
			7.234,
			8907.0,
			367.8,
			0.005889
		]
	},
	"Zr": {
		"AZ": [
			6.734,
			7.603,
			9120.0,
			405.2,
			0.005765
		]
	},
	"Nb": {
		"AZ": [
			6.902,
			7.791,
			9333.0,
			442.7,
			0.005587
		]
	},
	"Mo": {
		"AZ": [
			6.425,
			7.248,
			9545.0,
			480.2,
			0.005367
		]
	},
	"Tc": {
		"AZ": [
			6.799,
			7.671,
			9756.0,
			517.6,
			0.005315
		]
	},
	"Ru": {
		"AZ": [
			6.108,
			6.887,
			9966.0,
			555.1,
			0.005151
		]
	},
	"Rh": {
		"AZ": [
			5.924,
			6.677,
			10180.0,
			592.5,
			0.004919
		]
	},
	"Pd": {
		"AZ": [
			5.238,
			5.9,
			10380.0,
			630.0,
			0.004758
		]
	},
	"Ag": {
		"AZ": [
			5.623,
			6.354,
			7160.0,
			337.6,
			0.01394
		]
	},
	"Cd": {
		"AZ": [
			5.814,
			6.554,
			10800.0,
			355.5,
			0.004626
		]
	},
	"In": {
		"AZ": [
			6.23,
			7.024,
			11010.0,
			370.9,
			0.00454
		]
	},
	"Sn": {
		"AZ": [
			6.41,
			7.227,
			11210.0,
			386.4,
			0.004474
		]
	},
	"Sb": {
		"AZ": [
			7.5,
			8.48,
			8608.0,
			348.0,
			0.009074
		]
	},
	"Te": {
		"AZ": [
			6.979,
			7.871,
			11620.0,
			392.4,
			0.004402
		]
	},
	"I": {
		"AZ": [
			7.725,
			8.716,
			11830.0,
			394.8,
			0.004376
		]
	},
	"Xe": {
		"AZ": [
			8.231,
			9.289,
			12030.0,
			397.3,
			0.004384
		]
	},
	"Cs": {
		"AZ": [
			7.287,
			8.218,
			12230.0,
			399.7,
			0.004447
		]
	},
	"Ba": {
		"AZ": [
			7.899,
			8.911,
			12430.0,
			402.1,
			0.004511
		]
	},
	"La": {
		"AZ": [
			8.041,
			9.071,
			12630.0,
			404.5,
			0.00454
		]
	},
	"Ce": {
		"AZ": [
			7.489,
			8.444,
			12830.0,
			406.9,
			0.00442
		]
	},
	"Pr": {
		"AZ": [
			7.291,
			8.219,
			13030.0,
			409.3,
			0.004298
		]
	},
	"Nd": {
		"AZ": [
			7.098,
			8.0,
			13230.0,
			411.8,
			0.004182
		]
	},
	"Pm": {
		"AZ": [
			6.91,
			7.786,
			13430.0,
			414.2,
			0.004058
		]
	},
	"Sm": {
		"AZ": [
			6.728,
			7.58,
			13620.0,
			416.6,
			0.003976
		]
	},
	"Eu": {
		"AZ": [
			6.551,
			7.38,
			13820.0,
			419.0,
			0.003877
		]
	},
	"Gd": {
		"AZ": [
			6.739,
			7.592,
			14020.0,
			421.4,
			0.003863
		]
	},
	"Tb": {
		"AZ": [
			6.212,
			6.996,
			14210.0,
			423.9,
			0.003725
		]
	},
	"Dy": {
		"AZ": [
			5.517,
			6.21,
			14400.0,
			426.3,
			0.003632
		]
	},
	"Ho": {
		"AZ": [
			5.219,
			5.874,
			14600.0,
			428.7,
			0.003498
		]
	},
	"Er": {
		"AZ": [
			5.071,
			5.706,
			14790.0,
			433.0,
			0.003405
		]
	},
	"Tm": {
		"AZ": [
			4.926,
			5.542,
			14980.0,
			433.5,
			0.003342
		]
	},
	"Yb": {
		"AZ": [
			4.787,
			5.386,
			15170.0,
			435.9,
			0.003292
		]
	},
	"Lu": {
		"AZ": [
			4.893,
			5.505,
			15360.0,
			438.4,
			0.003243
		]
	},
	"Hf": {
		"AZ": [
			5.028,
			5.657,
			15550.0,
			440.8,
			0.003195
		]
	},
	"Ta": {
		"AZ": [
			4.738,
			5.329,
			15740.0,
			443.2,
			0.003186
		]
	},
	"W": {
		"AZ": [
			4.574,
			5.144,
			15930.0,
			442.4,
			0.003144
		]
	},
	"Re": {
		"AZ": [
			5.2,
			5.851,
			16120.0,
			441.6,
			0.003122
		]
	},
	"Os": {
		"AZ": [
			5.07,
			5.704,
			16300.0,
			440.9,
			0.003082
		]
	},
	"Ir": {
		"AZ": [
			4.945,
			5.563,
			16490.0,
			440.1,
			0.002965
		]
	},
	"Pt": {
		"AZ": [
			4.476,
			5.034,
			16670.0,
			439.3,
			0.002871
		]
	},
	"Au": {
		"AZ": [
			4.856,
			5.46,
			18320.0,
			438.5,
			0.002542
		]
	},
	"Hg": {
		"AZ": [
			4.308,
			4.843,
			17040.0,
			487.8,
			0.002882
		]
	},
	"Tl": {
		"AZ": [
			4.723,
			5.311,
			17220.0,
			537.0,
			0.002913
		]
	},
	"Pb": {
		"AZ": [
			5.319,
			5.982,
			17400.0,
			586.3,
			0.002871
		]
	},
	"Bi": {
		"AZ": [
			5.956,
			6.7,
			17800.0,
			677.0,
			0.00266
		]
	},
	"Po": {
		"AZ": [
			6.158,
			6.928,
			17770.0,
			586.3,
			0.002812
		]
	},
	"At": {
		"AZ": [
			6.204,
			6.979,
			17950.0,
			586.3,
			0.002776
		]
	},
	"Rn": {
		"AZ": [
			6.181,
			6.954,
			18120.0,
			586.3,
			0.002748
		]
	},
	"Fr": {
		"AZ": [
			6.949,
			7.82,
			18300.0,
			586.3,
			0.002737
		]
	},
	"Ra": {
		"AZ": [
			7.506,
			8.448,
			18480.0,
			586.3,
			0.002727
		]
	},
	"Ac": {
		"AZ": [
			7.649,
			8.609,
			18660.0,
			586.3,
			0.002697
		]
	},
	"Th": {
		"AZ": [
			7.71,
			8.679,
			18830.0,
			586.3,
			0.002641
		]
	},
	"Pa": {
		"AZ": [
			7.407,
			8.336,
			19010.0,
			586.3,
			0.002603
		]
	},
	"U": {
		"AZ": [
			7.29,
			8.204,
			19180.0,
			586.3,
			0.002573
		]
	}
}


// electronic stopping coefficients from Berger et al. (1991)
const icru_table = {
	"H": {
		"ICRU": [
			1.254,
			1.44,
			242.6,
			12000.0,
			0.1159
		]
	},
	"He": {
		"ICRU": [
			1.229,
			1.397,
			484.5,
			5873.0,
			0.05225
		]
	},
	"Li": {
		"ICRU": [
			1.411,
			1.6,
			725.6,
			3013.0,
			0.04578
		]
	},
	"Be": {
		"ICRU": [
			2.248,
			2.59,
			966.0,
			153.8,
			0.03475
		]
	},
	"B": {
		"ICRU": [
			2.474,
			2.815,
			1206.0,
			1060.0,
			0.02855
		]
	},
	"C": {
		"ICRU": [
			2.2977695717982596,
			2.601,
			1701.0,
			1279.0,
			0.01638
		]
	},
	"N": {
		"ICRU": [
			2.954,
			3.35,
			1683.0,
			1900.0,
			0.02513
		]
	},
	"O": {
		"ICRU": [
			2.652,
			3.0,
			1920.0,
			2000.0,
			0.0223
		]
	},
	"F": {
		"ICRU": [
			2.085,
			2.352,
			2157.0,
			2634.0,
			0.01816
		]
	},
	"Ne": {
		"ICRU": [
			1.951,
			2.199,
			2393.0,
			2699.0,
			0.01568
		]
	},
	"Na": {
		"ICRU": [
			2.542,
			2.869,
			2628.0,
			1854.0,
			0.01472
		]
	},
	"Mg": {
		"ICRU": [
			3.791,
			4.293,
			2862.0,
			1009.0,
			0.01397
		]
	},
	"Al": {
		"ICRU": [
			4.154,
			4.739,
			2766.0,
			164.5,
			0.02023
		]
	},
	"Si": {
		"ICRU": [
			4.914,
			5.598,
			3193.0,
			232.7,
			0.01419
		]
	},
	"P": {
		"ICRU": [
			3.232,
			3.647,
			3561.0,
			1560.0,
			0.01267
		]
	},
	"S": {
		"ICRU": [
			3.447,
			3.891,
			3792.0,
			1219.0,
			0.01211
		]
	},
	"Cl": {
		"ICRU": [
			5.301,
			6.008,
			3969.0,
			645.1,
			0.01183
		]
	},
	"Ar": {
		"ICRU": [
			5.731,
			6.5,
			4253.0,
			530.0,
			0.01123
		]
	},
	"K": {
		"ICRU": [
			5.152,
			5.833,
			4482.0,
			545.7,
			0.01129
		]
	},
	"Ca": {
		"ICRU": [
			5.521,
			6.252,
			4710.0,
			553.3,
			0.01112
		]
	},
	"Sc": {
		"ICRU": [
			5.201,
			5.884,
			4938.0,
			560.9,
			0.009995
		]
	},
	"Ti": {
		"ICRU": [
			4.858,
			5.489,
			5260.0,
			651.1,
			0.00893
		]
	},
	"V": {
		"ICRU": [
			4.479,
			5.055,
			5391.0,
			952.3,
			0.009117
		]
	},
	"Cr": {
		"ICRU": [
			3.983,
			4.489,
			5616.0,
			1336.0,
			0.008413
		]
	},
	"Mn": {
		"ICRU": [
			3.469,
			3.907,
			5725.0,
			1461.0,
			0.008829
		]
	},
	"Fe": {
		"ICRU": [
			3.519,
			3.963,
			6065.0,
			1243.0,
			0.007782
		]
	},
	"Co": {
		"ICRU": [
			3.14,
			3.535,
			6288.0,
			1372.0,
			0.007361
		]
	},
	"Ni": {
		"ICRU": [
			3.553,
			4.004,
			6205.0,
			555.1,
			0.008763
		]
	},
	"Cu": {
		"ICRU": [
			3.696,
			4.194,
			4649.0,
			81.13,
			0.02242
		]
	},
	"Zn": {
		"ICRU": [
			4.21,
			4.75,
			6953.0,
			295.2,
			0.006809
		]
	},
	"Ga": {
		"ICRU": [
			5.041,
			5.697,
			7173.0,
			202.6,
			0.006725
		]
	},
	"Ge": {
		"ICRU": [
			5.554,
			6.3,
			6496.0,
			110.0,
			0.009689
		]
	},
	"As": {
		"ICRU": [
			5.323,
			6.012,
			7611.0,
			292.5,
			0.006447
		]
	},
	"Se": {
		"ICRU": [
			5.874,
			6.656,
			7395.0,
			117.5,
			0.007684
		]
	},
	"Br": {
		"ICRU": [
			6.658,
			7.536,
			7694.0,
			222.3,
			0.006509
		]
	},
	"Kr": {
		"ICRU": [
			6.413,
			7.24,
			11850.0,
			153.7,
			0.00288
		]
	},
	"Rb": {
		"ICRU": [
			5.694,
			6.429,
			8478.0,
			292.9,
			0.006087
		]
	},
	"Sr": {
		"ICRU": [
			6.339,
			7.159,
			8693.0,
			330.3,
			0.006003
		]
	},
	"Y": {
		"ICRU": [
			6.407,
			7.234,
			8907.0,
			367.8,
			0.005889
		]
	},
	"Zr": {
		"ICRU": [
			6.734,
			7.603,
			9120.0,
			405.2,
			0.005765
		]
	},
	"Nb": {
		"ICRU": [
			6.901,
			7.791,
			9333.0,
			442.7,
			0.005587
		]
	},
	"Mo": {
		"ICRU": [
			6.424,
			7.248,
			9545.0,
			480.2,
			0.005376
		]
	},
	"Tc": {
		"ICRU": [
			6.799,
			7.671,
			9756.0,
			517.6,
			0.005315
		]
	},
	"Ru": {
		"ICRU": [
			6.109,
			6.887,
			9966.0,
			555.1,
			0.005151
		]
	},
	"Rh": {
		"ICRU": [
			5.924,
			6.677,
			10180.0,
			592.5,
			0.004919
		]
	},
	"Pd": {
		"ICRU": [
			5.238,
			5.9,
			10380.0,
			630.0,
			0.004758
		]
	},
	"Ag": {
		"ICRU": [
			5.345,
			6.038,
			6790.0,
			397.8,
			0.01676
		]
	},
	"Cd": {
		"ICRU": [
			5.814,
			6.554,
			10800.0,
			355.5,
			0.004626
		]
	},
	"In": {
		"ICRU": [
			6.229,
			7.024,
			11010.0,
			370.9,
			0.00454
		]
	},
	"Sn": {
		"ICRU": [
			6.409,
			7.227,
			11210.0,
			386.4,
			0.004474
		]
	},
	"Sb": {
		"ICRU": [
			7.5,
			8.48,
			8608.0,
			348.0,
			0.009074
		]
	},
	"Te": {
		"ICRU": [
			6.979,
			7.871,
			11620.0,
			392.4,
			0.004402
		]
	},
	"I": {
		"ICRU": [
			7.725,
			8.716,
			11830.0,
			394.8,
			0.004376
		]
	},
	"Xe": {
		"ICRU": [
			8.337,
			9.425,
			10510.0,
			269.6,
			0.006206
		]
	},
	"Cs": {
		"ICRU": [
			7.287,
			8.218,
			12230.0,
			399.7,
			0.004447
		]
	},
	"Ba": {
		"ICRU": [
			7.899,
			8.911,
			12430.0,
			402.1,
			0.004511
		]
	},
	"La": {
		"ICRU": [
			8.041,
			9.071,
			12630.0,
			404.5,
			0.00454
		]
	},
	"Ce": {
		"ICRU": [
			7.488,
			8.444,
			12830.0,
			406.9,
			0.00442
		]
	},
	"Pr": {
		"ICRU": [
			7.291,
			8.219,
			13030.0,
			409.3,
			0.004298
		]
	},
	"Nd": {
		"ICRU": [
			7.098,
			8.0,
			13230.0,
			411.8,
			0.004182
		]
	},
	"Pm": {
		"ICRU": [
			6.909,
			7.786,
			13430.0,
			414.2,
			0.004058
		]
	},
	"Sm": {
		"ICRU": [
			6.728,
			7.58,
			13620.0,
			416.6,
			0.003976
		]
	},
	"Eu": {
		"ICRU": [
			6.551,
			7.38,
			13820.0,
			419.0,
			0.003877
		]
	},
	"Gd": {
		"ICRU": [
			6.739,
			7.592,
			14020.0,
			421.4,
			0.003863
		]
	},
	"Tb": {
		"ICRU": [
			6.212,
			6.996,
			14210.0,
			423.9,
			0.003725
		]
	},
	"Dy": {
		"ICRU": [
			5.517,
			6.21,
			14400.0,
			426.3,
			0.003632
		]
	},
	"Ho": {
		"ICRU": [
			5.22,
			5.874,
			14600.0,
			428.7,
			0.003498
		]
	},
	"Er": {
		"ICRU": [
			5.071,
			5.706,
			14790.0,
			433.0,
			0.003405
		]
	},
	"Tm": {
		"ICRU": [
			4.926,
			5.542,
			14980.0,
			433.5,
			0.003342
		]
	},
	"Yb": {
		"ICRU": [
			4.788,
			5.386,
			15170.0,
			435.9,
			0.003292
		]
	},
	"Lu": {
		"ICRU": [
			4.893,
			5.505,
			15360.0,
			438.4,
			0.003243
		]
	},
	"Hf": {
		"ICRU": [
			5.028,
			5.657,
			15550.0,
			440.8,
			0.003195
		]
	},
	"Ta": {
		"ICRU": [
			4.738,
			5.329,
			15740.0,
			443.2,
			0.003186
		]
	},
	"W": {
		"ICRU": [
			4.587,
			5.16,
			15410.0,
			415.3,
			0.003406
		]
	},
	"Re": {
		"ICRU": [
			5.201,
			5.851,
			16120.0,
			441.6,
			0.003122
		]
	},
	"Os": {
		"ICRU": [
			5.071,
			5.704,
			16300.0,
			440.9,
			0.003082
		]
	},
	"Ir": {
		"ICRU": [
			4.946,
			5.563,
			16490.0,
			440.1,
			0.002965
		]
	},
	"Pt": {
		"ICRU": [
			4.477,
			5.034,
			16670.0,
			439.3,
			0.002871
		]
	},
	"Au": {
		"ICRU": [
			4.844,
			5.458,
			7852.0,
			975.8,
			0.02077
		]
	},
	"Hg": {
		"ICRU": [
			4.307,
			4.843,
			17040.0,
			487.8,
			0.002882
		]
	},
	"Tl": {
		"ICRU": [
			4.723,
			5.311,
			17220.0,
			537.0,
			0.002913
		]
	},
	"Pb": {
		"ICRU": [
			5.319,
			5.982,
			17400.0,
			586.3,
			0.002871
		]
	},
	"Bi": {
		"ICRU": [
			5.956,
			6.7,
			17800.0,
			677.0,
			0.00266
		]
	},
	"Po": {
		"ICRU": [
			6.158,
			6.928,
			17770.0,
			586.3,
			0.002812
		]
	},
	"At": {
		"ICRU": [
			6.203,
			6.979,
			17950.0,
			586.3,
			0.002776
		]
	},
	"Rn": {
		"ICRU": [
			6.181,
			6.954,
			18120.0,
			586.3,
			0.002748
		]
	},
	"Fr": {
		"ICRU": [
			6.949,
			7.82,
			18300.0,
			586.3,
			0.002737
		]
	},
	"Ra": {
		"ICRU": [
			7.506,
			8.448,
			18480.0,
			586.3,
			0.002727
		]
	},
	"Ac": {
		"ICRU": [
			7.648,
			8.609,
			18660.0,
			586.3,
			0.002697
		]
	},
	"Th": {
		"ICRU": [
			7.711,
			8.679,
			18830.0,
			586.3,
			0.002641
		]
	},
	"Pa": {
		"ICRU": [
			7.407,
			8.336,
			19010.0,
			586.3,
			0.002603
		]
	},
	"U": {
		"ICRU": [
			7.29,
			8.204,
			19180.0,
			586.3,
			0.002673
		]
	}
}


// Electronic stopping coefficients derived from analyzing the IAEA database
// https://www-nds.iaea.org/stopping/
// <ost of the values here are derived from version 2021-12, with the exception
// of O, Si, and Nb, where version 2024-03 was used.
// Details of the analysis can be found in:
// R. M. L. McFadden et al., Phys. Rev. Appl. 19, 044018 (2023).
// R. M. L. McFadden et al., unpublished (2025).
const iaea_table = {
	"H": {
		"IAEA": [
			1.21941306,
			1.39705253,
			316.72610292,
			3622.08960714,
			0.03609996
		]
	},
	"He": {
		"IAEA": []
	},
	"Li": {
		"IAEA": [
			2.55867734,
			2.98398784,
			672.22623329,
			223.63937274,
			0.05756479
		]
	},
	"Be": {
		"IAEA": [
			2.13846776,
			2.4302455,
			1353.80005691,
			500.78353377,
			0.01143076
		]
	},
	"B": {
		"IAEA": [
			2.92598306,
			3.3327191,
			1523.83401267,
			574.31712932,
			0.01671298
		]
	},
	"C": {
		"IAEA": [
			2.51057212,
			2.84874359,
			1325.63086028,
			2111.57332043,
			0.03815981
		]
	},
	"N": {
		"IAEA": [
			3.03231463,
			3.44621744,
			1287.27189959,
			3445.25706665,
			0.0690955
		]
	},
	"O": {
		"IAEA": [
			2.64525591541112,
			2.99207340296791,
			1983.59086293942,
			1899.40582231425,
			0.0194714278702055
		]
	},
	"F": {
		"IAEA": []
	},
	"Ne": {
		"IAEA": []
	},
	"Na": {
		"IAEA": []
	},
	"Mg": {
		"IAEA": [
			4.3221962,
			4.95332934,
			2711.05757349,
			99.32422512,
			0.01692829
		]
	},
	"Al": {
		"IAEA": [
			4.16266645,
			4.7394264,
			3007.21967155,
			192.15430476,
			0.01478852
		]
	},
	"Si": {
		"IAEA": [
			4.92174725194867,
			5.61439738985486,
			2614.54841139624,
			369.526489722846,
			0.0253413402253883
		]
	},
	"P": {
		"IAEA": []
	},
	"S": {
		"IAEA": []
	},
	"Cl": {
		"IAEA": [
			5.18954121,
			5.87010049,
			5726.20198003,
			338.90592713,
			0.00527894
		]
	},
	"Ar": {
		"IAEA": []
	},
	"K": {
		"IAEA": []
	},
	"Ca": {
		"IAEA": [
			7.3841902,
			8.41800474,
			4257.94547049,
			311.84732092,
			0.01482602
		]
	},
	"Sc": {
		"IAEA": [
			6.2736694,
			7.11486087,
			5202.32117316,
			349.64931132,
			0.00808596
		]
	},
	"Ti": {
		"IAEA": [
			4.89215322,
			5.5299609,
			4733.05002706,
			821.5492998,
			0.01141794
		]
	},
	"V": {
		"IAEA": [
			4.39418898,
			4.95984106,
			5216.28902299,
			873.00768319,
			0.00982301
		]
	},
	"Cr": {
		"IAEA": [
			4.22355616,
			4.76724205,
			4805.40719904,
			1062.25237873,
			0.01508696
		]
	},
	"Mn": {
		"IAEA": [
			3.45870888,
			3.89580224,
			5452.18588822,
			1778.16054656,
			0.0105738
		]
	},
	"Fe": {
		"IAEA": [
			3.69846643,
			4.16916938,
			5392.90710239,
			1040.38447053,
			0.01152298
		]
	},
	"Co": {
		"IAEA": [
			3.55890909,
			4.00775461,
			6796.04145497,
			933.86447935,
			0.00558368
		]
	},
	"Ni": {
		"IAEA": [
			3.42262695,
			3.8623488,
			4759.65515188,
			520.18934465,
			0.02026669
		]
	},
	"Cu": {
		"IAEA": [
			3.54912421,
			4.02142201,
			4344.22605325,
			128.32905834,
			0.02886218
		]
	},
	"Zn": {
		"IAEA": [
			4.31895518,
			4.91763977,
			5346.0392556,
			46.16548699,
			0.01518164
		]
	},
	"Ga": {
		"IAEA": [
			4.11015447,
			4.63998531,
			7681.41419449,
			149.38563152,
			0.00628772
		]
	},
	"Ge": {
		"IAEA": [
			5.80984815,
			6.60667983,
			6039.04808738,
			87.19744473,
			0.01158192
		]
	},
	"As": {
		"IAEA": []
	},
	"Se": {
		"IAEA": [
			5.58734301,
			6.31119973,
			8423.01872583,
			221.61559131,
			0.00530434
		]
	},
	"Br": {
		"IAEA": [
			6.28480648,
			7.09489448,
			11732.76411988,
			150.96205589,
			0.00281298
		]
	},
	"Kr": {
		"IAEA": [
			6.47378266,
			7.31581518,
			9199.06183849,
			216.98680923,
			0.00437111
		]
	},
	"Rb": {
		"IAEA": [
			8.48759187,
			9.62951209,
			7271.11124671,
			272.67996745,
			0.00818815
		]
	},
	"Sr": {
		"IAEA": [
			8.66447838,
			9.84912713,
			5979.31960977,
			334.15705556,
			0.01184544
		]
	},
	"Y": {
		"IAEA": [
			7.54854264,
			8.54789357,
			6885.34110669,
			429.5325211,
			0.00930644
		]
	},
	"Zr": {
		"IAEA": [
			6.24168401,
			7.04236496,
			10674.06252597,
			269.66181445,
			0.00339805
		]
	},
	"Nb": {
		"IAEA": [
			5.83800567770461,
			6.58179495443619,
			12601.224783492,
			206.20626866439,
			0.00270151372920993
		]
	},
	"Mo": {
		"IAEA": [
			5.58867862,
			6.29983727,
			9573.1660566,
			523.57577519,
			0.00473082
		]
	},
	"Tc": {
		"IAEA": []
	},
	"Ru": {
		"IAEA": []
	},
	"Rh": {
		"IAEA": []
	},
	"Pd": {
		"IAEA": [
			4.74762031,
			5.34871025,
			8086.17802763,
			942.05721488,
			0.00842671
		]
	},
	"Ag": {
		"IAEA": [
			5.4205224,
			6.17824432,
			4642.1821495,
			90.75350922,
			0.06061521
		]
	},
	"Cd": {
		"IAEA": [
			4.89128643,
			5.50754704,
			11831.77188508,
			396.06905848,
			0.00412049
		]
	},
	"In": {
		"IAEA": [
			5.98978289,
			6.7705004,
			6343.54720062,
			564.65410792,
			0.0227052
		]
	},
	"Sn": {
		"IAEA": [
			6.73191335,
			7.61854414,
			6946.18830598,
			347.1939131,
			0.01677246
		]
	},
	"Sb": {
		"IAEA": [
			7.92400389,
			8.99628409,
			5736.2988109,
			403.11722206,
			0.02973016
		]
	},
	"Te": {
		"IAEA": []
	},
	"I": {
		"IAEA": []
	},
	"Xe": {
		"IAEA": [
			8.968264,
			10.16224223,
			8543.2730486,
			283.90067433,
			0.01019984
		]
	},
	"Cs": {
		"IAEA": []
	},
	"Ba": {
		"IAEA": []
	},
	"La": {
		"IAEA": [
			8.16949326,
			9.21144395,
			13933.96869212,
			429.99442382,
			0.0034744
		]
	},
	"Ce": {
		"IAEA": []
	},
	"Pr": {
		"IAEA": []
	},
	"Nd": {
		"IAEA": [
			8.60801371,
			10.26060598,
			6798.65217629,
			7.06731816,
			0.02713704
		]
	},
	"Pm": {
		"IAEA": []
	},
	"Sm": {
		"IAEA": []
	},
	"Eu": {
		"IAEA": []
	},
	"Gd": {
		"IAEA": [
			8.38379061,
			9.50012183,
			10804.38767518,
			110.71066098,
			0.00761735
		]
	},
	"Tb": {
		"IAEA": [
			8.69907359,
			10.36476708,
			5985.09307671,
			7.76175759,
			0.04237031
		]
	},
	"Dy": {
		"IAEA": [
			6.69350026,
			7.81543484,
			5289.65107666,
			12.11560717,
			0.05746489
		]
	},
	"Ho": {
		"IAEA": []
	},
	"Er": {
		"IAEA": [
			4.31497049,
			4.85346547,
			12995.54504003,
			691.00380321,
			0.00499022
		]
	},
	"Tm": {
		"IAEA": []
	},
	"Yb": {
		"IAEA": [
			6.38304258,
			7.21491284,
			12327.74719685,
			82.30064162,
			0.00516845
		]
	},
	"Lu": {
		"IAEA": [
			7.00205766,
			8.09268611,
			4589.67801229,
			31.06321362,
			0.11142124
		]
	},
	"Hf": {
		"IAEA": [
			5.32763157,
			6.00140558,
			13853.49562768,
			206.93150053,
			0.00411522
		]
	},
	"Ta": {
		"IAEA": [
			5.15280708,
			5.8054531,
			12417.25115167,
			231.48549646,
			0.00530723
		]
	},
	"W": {
		"IAEA": [
			4.81261962,
			5.41579909,
			15245.84079976,
			286.09077182,
			0.00344862
		]
	},
	"Re": {
		"IAEA": [
			4.26021967,
			4.80273372,
			3191.05524918,
			76051.48730893,
			3.161e-05
		]
	},
	"Os": {
		"IAEA": []
	},
	"Ir": {
		"IAEA": [
			4.16543126,
			4.68849191,
			6887.94139926,
			4263.90641919,
			4e-08
		]
	},
	"Pt": {
		"IAEA": [
			4.62228847,
			5.20033612,
			16308.49878855,
			266.02263275,
			0.0030956
		]
	},
	"Au": {
		"IAEA": [
			4.84253074,
			5.44769072,
			15602.21662947,
			412.25485588,
			0.00331383
		]
	},
	"Hg": {
		"IAEA": []
	},
	"Tl": {
		"IAEA": []
	},
	"Pb": {
		"IAEA": [
			9.42473604,
			17.46235676,
			11946.86905435,
			1e-08,
			0.00652912
		]
	},
	"Bi": {
		"IAEA": [
			10.25823796,
			12.26670424,
			7765.05387481,
			7.37274504,
			0.0231005
		]
	},
	"Po": {
		"IAEA": []
	},
	"At": {
		"IAEA": []
	},
	"Rn": {
		"IAEA": []
	},
	"Fr": {
		"IAEA": []
	},
	"Ra": {
		"IAEA": []
	},
	"Ac": {
		"IAEA": []
	},
	"Th": {
		"IAEA": []
	},
	"Pa": {
		"IAEA": []
	},
	"U": {
		"IAEA": []
	},
	"": {
		"IAEA": []
	}
}


// list of JS objects containing all projectile/target element data
const dataObjects = [
    elements,
    projectiles,
    az_table,
    icru_table,
    iaea_table
];

// empty "main" object - to be filled with *all* projectile/target data
const elemPars = {}

// loop over each JS object...
for (const d of dataObjects) {
    // ...and deep-merge them to the "main" object
    mergeDeep(elemPars, d);
};

// Extra densities (i.e., for chemical compounds)
const rhos = {
	"NbN": 8.47,
	"Bi2Se3": 7.51,
	"La2CuO4": 7.08,
	"La1.84Sr0.16CuO4": 6.94,
	"N2": 1.145,
	"ZnO": 5.61,
	"ZnSe": 5.26,
	"ZnS": 4.09,
	"ZrO": 6.0,
	"Gd3Ga5O12": 7.08,
	"MgAl2O4": 3.6,
	"NdGaO3": 7.57,
	"YAlO3": 4.88,
	"Y3Al5O12": 4.55,
	"LiF": 2.6,
	"CaF2": 3.18,
	"BaFe": 4.83,
	"MgF2": 3.18,
	"SiO2": 2.65,
	"TiO2": 4.26,
	"KTaO3": 6.967,
	"LaAlO3": 6.7,
	"Al2O3": 3.98,
	"SrTiO3": 5.12,
	"SrLaGaO4": 6.389,
	"SrLaAlO4": 5.924,
	"NbSe2": 6.3,
	"MgO": 3.58,
	"YBa2Cu3O7": 6.54,
	"GaAs": 5.32,
	"C60": 1.65
}


function parse_formula (mf) {
    // This function takes a chemical formula and returns
    // an object that contains the atoms and their number

    // replace all types of brackets into ()
    var mf = mf.replace(/\[/g,"(").replace(/\]/g,")").replace(/\{/g,"(").replace(/\}/g,")").replace(/\s+/g,"");
    if(/^\d+/.test(mf)) throw new SyntaxError("Molecular formula should not start with a number!");
    var mol = {};
    // go into brackets and collect info
    while(mf.includes("(")){
	var x = mf.lastIndexOf("(");
	var y = mf.indexOf(")", mf.lastIndexOf("("));
	
	var z = mf.substr(x+1, y-x-1);
	var c = mf.substr(y+1);
	c = /^\d+/.exec(c);
	c=(c!= null)?Number(c[0]):1;
	// recursive
	var a = this.parse_formula(z);
	var b = "";
	for(var k in a){
	    b+=k+""+a[k]*c;
	} 
	mf = mf.substr(0, x)+ b + mf.substr(y+1+((c>1)?(c+'').length:0));		
    }
		
    var m = "";
    // Separate element name from stoichiometry
    //    while(m = /([A-Z]{1}[a-z]{0,}[0-9]{0,})/.exec(mf)){
    while(m = /([A-Z]{1}[a-z]{0,}[0-9]{0,}\.?[0-9]{0,})/.exec(mf)){
	// Element
	var m1 = /([A-Z]{1,}[a-z]{0,})/.exec(m[0]);
	// Stoichiometry
	//var m2 = /\d+/.exec(m[0]);
	var m2 = /\d+\.?\d{0,}/.exec(m[0]);
	if(typeof mol[m1[0]] == 'undefined') mol[m1[0]]=(m2!=null)?Number(m2[0]):1;
	else mol[m1[0]] += (m2!=null)?Number(m2[0]):1;
	mf = mf.replace(m[0], "");
    }
    return mol;
}

function StoppingCoefficients(Element, flag)
{
    // Select which tabulation to use for the Varelas-Biersack parameterization
    // of electronic stopping cross sections for proton-like projectiles
    // implanted in elemental targets.

    // flag = 1: use coefficients from Anderson & Ziegler (1977).
    if (flag == 1) {
        return elemPars[Element].AZ;
    }

    // flag = 2: use coefficients from ICRU Report 49 (1973).
    if (flag == 2) {
        return elemPars[Element].ICRU;
    }

    // flag = 3: use coefficients from McFadden et al. (2023) and McFadden et al. (unpublished).
    //
    // NOTE: these values were derived from up-to-date stopping data found inthe
    // IAEA's database of electronic stopping cross sections
    // (https://www-nds.iaea.org/stopping/).
    // For further details on their determination, see, e.g.:
    // Appendix A in McFadden at al., Phys. Rev. Applied 19, 044018 (2023).
    // https://doi.org/10.1103/PhysRevApplied.19.044018
    if (flag == 3 && elemPars[Element].IAEA.length == 5) {
        return elemPars[Element].IAEA;
    // in the event that updated coefficients are unavailable for given element
    // fall back to using values from ICRU Report 49
    } else {
        return elemPars[Element].ICRU;
    }
}

let transientWarningTimeout = null;
function showTransientWarning(message, targetElement, duration = 4000) {
    let warning = document.getElementById('transientWarning');
    if (!warning) {
	warning = document.createElement('div');
	warning.id = 'transientWarning';
	warning.className = 'transient-warning';
	document.body.appendChild(warning);
    }

    warning.textContent = message;
    if (targetElement) {
	const rect = targetElement.getBoundingClientRect();
	warning.style.left = `${Math.max(12, rect.left + window.scrollX)}px`;
	warning.style.top = `${rect.bottom + window.scrollY + 8}px`;
    }
    warning.classList.add('visible');

    if (transientWarningTimeout) {
	clearTimeout(transientWarningTimeout);
    }

    transientWarningTimeout = setTimeout(() => {
	warning.classList.remove('visible');
    }, duration);
}


function rho_fun()
{
    var irow = this.parentNode.parentNode.rowIndex;
    var caller = this.id;
    var chem = document.getElementById(caller).value;
    var rhoLi = "L"+irow+"rho";

    var rho = 0;
    
    if (elemPars[chem]) {
	rho = elemPars[chem].rho;
    } else {
	// Did not find density in elements list
	if (isFinite(rhos[chem])) {
	    // Found in densities list of compositions
	    rho = rhos[chem];
		} else {
		    // suggest a material density based on composition (when it's undefined)
	            let layer_formula = parse_formula(chem);

	            // determine the stoichiometry sum (for normalization)
	            let stoichiometry_sum = 0;
		    for (const key of Object.keys(layer_formula)) {
		        const amount = Number(layer_formula[key]);
		        if (isFinite(amount) && amount > 0) {
			    stoichiometry_sum += amount;
			}
		    }

		    // estimate the density from additive elemental molar volumes:
		    // rho ~= total molar mass / total molar volume
		    let total_molar_mass = 0;
		    let total_molar_volume = 0;
		    for (const key of Object.keys(layer_formula)) {
		        const amount = Number(layer_formula[key]);
		        if (!isFinite(amount) || amount <= 0) {
			    continue;
			}
			if (!elemPars[key] || !isFinite(elemPars[key].rho) || !isFinite(elemPars[key].A) || elemPars[key].rho <= 0) {
			    continue;
			}
			total_molar_mass += amount * elemPars[key].A;
			total_molar_volume += amount * (elemPars[key].A / elemPars[key].rho);
		    }

	            rho = 0;
		    if (total_molar_volume > 0) {
			rho = total_molar_mass / total_molar_volume;
		    }
		    if (rho > 0) {
			showTransientWarning("Warning: Estimated density from additive elemental molar volumes; please verify manually.", document.getElementById(rhoLi));
		    }
		}
	    }
    // Set value in appropriate cell
    document.getElementById(rhoLi).value = rho;    
}

function openTab(event, tabName) {
    // Declare all variables
    var i, tabcontent, tablinks;
    // Get all elements with class="tabcontent" and hide them
    tabcontent = document.getElementsByClassName("tabcontent");
    for (i = 0; i < tabcontent.length; i++) {
	tabcontent[i].style.display = "none";
    }

    // Get all elements with class="tablinks" and remove the class "active"
    tablinks = document.getElementsByClassName("tablinks");
    for (i = 0; i < tablinks.length; i++) {
	tablinks[i].className = tablinks[i].className.replace(" active", "");
    }

    // Show the current tab, and add an "active" class to the button that opened the tab
    document.getElementById(tabName).style.display = "block";
    if (event) event.currentTarget.className += " active";
}

function adjust_table()
{
   var numLayer = document.getElementById("numLayer").value;
   var LTable = document.getElementById("LTable");
   var Nrows = LTable.rows.length;

   var Comps = [];
   var Rhos = [];
   var Ds = [];

// Need to loop to get the right number of rows when reloading
   if (numLayer >= Nrows) {
      for (i = Nrows;i<=numLayer;i++) {
          var row = LTable.insertRow(i);
          var Li = row.insertCell(0);
          Li.innerHTML = i;
          var compL = row.insertCell(1);
          var compCell = document.createElement("input");
          compCell.id = "L"+i+"Comp";
          compCell.name = "L"+i+"Comp";
          compCell.size = 15;
	  compCell.onchange = rho_fun;
	  if (Comps[i-1]) {compCell.value = Comps[i-1];}else{compCell.value = 'SrTiO3';}
          compL.appendChild(compCell);
          var rhoL = row.insertCell(2);
          var rhoCell = document.createElement("input");
          rhoCell.id = "L"+i+"rho";
          rhoCell.name = "L"+i+"rho";
	  rhoCell.size = 5;
          rhoL.appendChild(rhoCell);
	  if (Rhos[i-1]) {rhoCell.value = Rhos[i-1];}else{rhoCell.value = '5.12';}
          var thickL = row.insertCell(3);
          var thickCell = document.createElement("input");
          thickCell.id = "L"+i+"d";
          thickCell.name = "L"+i+"d";
	  thickCell.size = 7;
          thickL.appendChild(thickCell);
	  if (Ds[i-1]) {thickCell.value = Ds[i-1];}else{thickCell.value = '10000';}
       }
    } else {
      for (i = Nrows-1;i>numLayer;i--) {
          LTable.deleteRow(i);
      }
    }
}

function adjust_scans()
{
    // Deal with scans checkbox and type
    var scanSeq = document.getElementById("scanSeq").checked;
    var sender = document.getElementById("scanSeq");
    var scanType = document.getElementById("scanType").value;
    // consider only if scans checkbox is checked
    if (scanSeq) {
	// Which type of scan
	if (scanType == "scanLoop") {
	    ShowHide(1,'ScansTable');
	    ShowHide(0,'ScansLine');
	} else {
	    ShowHide(1,'ScansLine');
	    ShowHide(0,'ScansTable');
	}
    } else {
	// Hide both
	    ShowHide(0,'ScansTable');
	    ShowHide(0,'ScansLine');
    }
}

function ProjSmartDefaults()
{
   var Proj = document.getElementById("ProjType").value;
   var sigEnergy = document.getElementById("sigEnergy");
   var sigAngle = document.getElementById("sigAngle");

   if (Proj == "muon") {
      sigEnergy.value = "450";
      sigAngle.value = "15";
   } else {
      sigEnergy.value = "0";
      sigAngle.value = "0";
   }      
}

function ProjNumberLimit()
{
   var numberProj = document.getElementById("numberProj").value;

   if (numberProj > 5000) {
       alert("Maximum number is 5000");
       document.getElementById("numberProj").value = 5000;
   }      
}


function ShowHide(onoff,item) {
// this function can switch item to visible/hidden onoff=1/0
    if(onoff){
//       document.getElementById(item).style.display = 'block';
       document.getElementById(item).style.visibility = "visible";
    } else {
//       document.getElementById(item).style.display = 'none';
       document.getElementById(item).style.visibility = "hidden";
    }
}

function prep_cfg(toggle) {
    // This function collects various values and returns
    // toggle=1  : returns object with all values
    // toggle!=1 : returns string containing cfg file
    let TrimSPcfg = "";
    let strtmp = "";
    let valtmp = "";

    All['trimPath']=document.getElementById("trimPath").value;
    
    // Prepare Layers section
    let LayersSec = "[Layers]\n";
    let numLayer = document.getElementById("numLayer").value;
    All['numLayer']=numLayer;
    LayersSec = LayersSec + "numLayer="+numLayer+"\n";
    for (i = 1;i<=numLayer;i++) {
	strtmp = "L"+i+"Comp";
	valtmp = document.getElementById(strtmp).value;
	All[strtmp]=valtmp;
	LayersSec = LayersSec + strtmp +"="+ valtmp+"\n";
	strtmp = "L"+i+"rho";
	valtmp = document.getElementById(strtmp).value;
	All[strtmp]=valtmp;
	LayersSec = LayersSec + strtmp +"="+ valtmp+"\n";
	strtmp = "L"+i+"d";
	valtmp = document.getElementById(strtmp).value;
	All[strtmp]=valtmp;
	LayersSec = LayersSec + strtmp +"="+ valtmp+"\n";
    }

    // Prepare projectile parameters section
    let parProj = ["workPath","fileNamePrefix","ProjType","numberProj","z0","dz","valEnergy","sigEnergy","valAngle","sigAngle","ranSeed"];
    let ProjSec = "[ProjectileParameters]\n";
    for (key of parProj) {
	All[key]= document.getElementById(key).value;
	ProjSec = ProjSec + key + "=" + All[key] + "\n";
    }
    
    // Prepare Files section
    let FilesSec = "[Files]\n";
    FilesSec = FilesSec + "fileNamePrefix="+All["fileNamePrefix"]+"\nworkPath="+All["workPath"]+"\n";

    // Prepare ScanSequence section
    let ScanSec = "[ScanSequence]\n";
    strtmp = "scanSeq";
    valtmp = 1*(document.getElementById(strtmp).checked);
    All[strtmp]=valtmp;
    ScanSec = ScanSec + strtmp +"="+ valtmp+"\n";
    let parScan = ["comboScan","scanType","scanFrom","scanStep","scanTo","scanList","scanListdz"];
    for (key of parScan) {
	All[key]= document.getElementById(key).value;
	ScanSec = ScanSec + key + "=" + All[key] + "\n";
    }

    // Collect other parameters
    let parOther = ["parEF", "parESB", "parSHEATH", "parERC", "parRD", "parCA", "parKK0", "parKK0R", "parKDEE1", "parKDEE2", "parIPOT", "parIPOTR", "parIRL"];
    for (key of parOther) {
	All[key]= document.getElementById(key).value;
    }

    // Get the stopping power coefficient (SPC) flag
    All["flagSPC"] = document.getElementById("flagSPC").value;
    
    // Construct full content of cfg file
    TrimSPcfg = FilesSec + LayersSec + ProjSec + ScanSec;
    if (toggle) {
	return All;
    } else {
	return TrimSPcfg;
    }
}

function setValues(content) {
    // This function takes cfg file content and substitutes values in the GUI
    // Split file content into lines
    var event = new Event('change');
    var lines = content.toString().split('\n');
    // Remove comment lines, empty lines and those starting with "["
    var PATTERN= /^(?!\[)(?!\#)(\S)/,
	flines = lines.filter(function (str) {return PATTERN.test(str);});
    for (var i=0; i<flines.length; i++) {
	// Loop over parameters, set appropriate values and trigger associated onChange
	var param=flines[i].replace(/\s+/,'').split('=');
	if (param[0] == 'scanSeq') {
	    // This is a checkbox
	    var seqChecked = true;
	    if (param[1] == 0) {seqChecked = false;}
	    document.getElementById(param[0]).checked = seqChecked;
	    document.getElementById(param[0]).dispatchEvent(event);
	} else {
	    document.getElementById(param[0]).value = param[1];
	    document.getElementById(param[0]).dispatchEvent(event);
	}
    }
}


function CreateInpFile() {
    // Create and return input file for the Trim.SP simulation binary
    // Takes object All as input for all relevant parameters 

    // This is the form of the begining of the input file:
    var TemplateFile = "ProjZ ProjAM valEnergy sigEnergy valAngle sigAngle parEF parESB parSHEATH parERC\n"
    TemplateFile += "numberProj ranSeed ranSeed ranSeed z0 parRD dz parCA parKK0 parKK0R parKDEE1 parKDEE2 parIPOT parIPOTR parIRL";

    // Then comes the number of layers (new format) for example 4 layers:
    // N_Layers=4
    TemplateFile=TemplateFile+"\n"+"N_Layers=numLayer";

    // Then loop over the layers and for each give the following structure
    // chemical formula, thickness, density, correction factor, number of elements
    var TemplateLayer = "L1Comp L1d L1rho L1CK L1Elem\n";
    // Z number of elements
    TemplateLayer += "L1ELZ1 L1ELZ2 L1ELZ3 L1ELZ4 L1ELZ5\n";
    // A number of elements
    TemplateLayer += "L1ELW1 L1ELW2 L1ELW3 L1ELW4 L1ELW5\n";
    // Weigth of element in composition
    TemplateLayer += "L1ELC1 L1ELC2 L1ELC3 L1ELC4 L1ELC5\n";
    // Surface binding energy of elements
    TemplateLayer += "L1ELE1 L1ELE2 L1ELE3 L1ELE4 L1ELE5\n";
    // Displacement energy of elements, always 30 eV??
    TemplateLayer += "L10301 L10302 L10303 L10304 L10305\n";
    // Bulk binding energy of elements, usually zero
    TemplateLayer += "0 0 0 0 0\n";
    // value A-1 of the ziegler tables
    TemplateLayer += "L1ELST11 L1ELST21 L1ELST31 L1ELST41 L1ELST51\n";
    // value A-2 of the ziegler tables
    TemplateLayer += "L1ELST12 L1ELST22 L1ELST32 L1ELST42 L1ELST52\n";
    // value A-3 of the ziegler tables
    TemplateLayer += "L1ELST13 L1ELST23 L1ELST33 L1ELST43 L1ELST53\n";
    // value A-4 of the ziegler tables
    TemplateLayer += "L1ELST14 L1ELST24 L1ELST34 L1ELST44 L1ELST54\n";
    // value A-5 of the ziegler tables
    TemplateLayer += "L1ELST15 L1ELST25 L1ELST35 L1ELST45 L1ELST55";

    let projectile = All['ProjType'];
    All['ProjZ'] = elemPars[projectile].Z;
    All['ProjAM'] = elemPars[projectile].A;

    // This is the flag for checking layers    
    let Check=0;
    let Layer='';

    // Loop over layers an create appropriate values
    for (var i=1; i<=All['numLayer'];i++){
	// Arry containing 12 lines for each layer
	let newLayer = ["","","","","","","","","","","",""];
    
	Check=0;
	// Composition of layers	
	let LComp="L"+i+"Comp";
	let Comp = All[LComp];
	if (Comp == "" || typeof Comp == 'undefined') {Check++;}
	let LElComp=parse_formula(Comp);
	for (key of Object.keys(LElComp)) {
	    // Check if composition is understood
	    if (key=="" || elemPars[key].Z =="") {
		Check++;
	    }  
	}

	// Number of elements
	let LElem = "L"+i+"Elem";
	All[LElem] = Object.keys(LElComp).length;
	let nEl = All[LElem];
	
	// Densities of layers
	let Lrho="L"+i+"rho";
	let rho = 1*All[Lrho];
	
	if (rho==0) {Check++;}
	
	// Thickness of layers
	let Ld ="L"+i+"d";
	let d = All[Ld];
	if (d=="") {Check++;}

	// Sanity check, is the layer supposed to have value? are they all there?
	if (Check!=0) {
	    ErrMsg="Error: Bad chemical formula in Layer $i.\nPlease check!\n";
	    console.log($ErrMsg);
	    return ErrMsg;
	}
	
	let Sum = 0;
	for (key of Object.keys(LElComp)) {
	    Sum=Sum+LElComp[key];
	}
	if (Sum==0) {Sum=1;}
	
	let Els = Object.keys(LElComp);
	
	// first line: chemical formula, thickness, density, correction factor, number of elements
	newLayer[0] += Comp + " " + d + " " + rho + " 1 " + nEl;
	for (var j=0;j<Els.length;j++) {
	    let El = Els[j];
	    let ElSTs = StoppingCoefficients(El, All["flagSPC"]);
	   
	    // Next 11 lines depend on number of elements
	    newLayer[1]  +=  elemPars[El].Z + " " ;
	    newLayer[2]  +=  elemPars[El].A + " " ;
	    newLayer[3]  +=  LElComp[El]/Sum + " " ;
	    newLayer[4]  +=  elemPars[El].Elast + " " ;
	    newLayer[5]  +=  "30 " ;
	    newLayer[6]  +=  "0  " ;
	    newLayer[7]  +=  ElSTs[0] + " " ;
	    newLayer[8]  +=  ElSTs[1] + " " ;
	    newLayer[9]  +=  ElSTs[2] + " " ;
	    newLayer[10] +=  ElSTs[3] + " " ;
	    newLayer[11] +=  ElSTs[4] + " " ;
	}
	TemplateFile += "\n" + newLayer.join("\n");
    }

    for (let key of Object.keys(All)) {
	if (All[key]!=null){
	    if (key=="ranSeed") {
		// Seed repeats three times
		TemplateFile = TemplateFile.replace(/ranSeed/g,All[key]);
	    } else {
		TemplateFile = TemplateFile.replace(key,All[key]);
	    }
	}
    }
    return TemplateFile;
}

function sum(array){
    // Takes and array and returns the sum of its elements
    let sum_array = array.reduce(function(a, b){
        return a + b;
    }, 0);
    return sum_array;
}

function startSequence() {
    let cmd = '';
    let trimBin = All['trimPath']+"/trimspNL";
    let randStr = '';
    let webOrApp = amIWeb();
    // Only for Node.js 
    if (!webOrApp) {
	// Check if the trimspNL binary is found
	if (!fileExists(trimBin)) {
	    // check if it is in rpm
	    trimBin = "/usr/lib/TrimSP/resources/app/trimspNL";
	    if (!fileExists(trimBin)) {
		// if not found, try in PATH and hope for the best
		trimBin = "trimspNL";
	    }
	}
	// Check if workPath exists otherwise create it
	checkDir(All['workPath']); // from TrimSPelec.js, Electron/Node specific
    } else {
	// Add random string (5 char) to file names
	randStr = (Math.random() + 1).toString(36).substring(7);
	All["fileNamePrefix"] = randStr;
	All["workPath"] = "/tmp/" + randStr;
    }
    
    let Progress =0;
    document.getElementById("pBar").style.width = Progress + "%";
    document.getElementById("pBar").innerHTML = Progress + "%";

    // This is a flag to indicate whether the lists of values and inclements are the same size
    All["SdzFlag"]=0;
    var SValues = [];
    let ScanName = "E";
    let ScanAttrib = "valEnergy";
    // Generate an arry of scanned values (one element for a single run)
    if (All["scanSeq"]) {
	// For multiple runs or a scan
	if (All["scanType"]=="scanVals") {
	    var SValues=All["scanList"].split(/,/);
	    var SdzValues=All["scanListdz"].split(/,/);
	    if (SValues.length == SdzValues.length) {All["SdzFlag"]=1;}
	} else {
	    for (let Val=parseInt(All["scanFrom"]);Val<=parseInt(All["scanTo"]);Val=Val+parseInt(All["scanStep"])) {
		SValues.push(Val);
	    }
	}

	if (All["comboScan"]==1) {
	    ScanName = "SigE";
	    ScanAttrib = "sigEnergy";
	} else if (All["comboScan"]==2) {
	    ScanName = "Angle";
	    ScanAttrib = "valAngle";
	} else if (All["comboScan"]==3) {
	    ScanName = "SigAngle";
	    ScanAttrib = "sigAngle";
	} else if (All["comboScan"]==4) {
	    ScanName = "N";
	    ScanAttrib = "numberProj";
	} else if (All["comboScan"]==5) { 
	    ScanName = "Ld"+All["scandL"];
	    ScanAttrib = "L"+All["scandL"]+"d";
	}
    } else {
	// For single run, array with single value of valEnergy
	SValues.push(parseInt(All["valEnergy"]));
    }

    // Now start the actual simulation
    //setInterval(() => {
    let iScan=0;
    for (var SValue of SValues) {
	// Update value in GUI
	document.getElementById(ScanAttrib).value = SValue;
	All[ScanAttrib]=SValue;
	if ( All["SdzFlag"] == 1) {
	    if (All["comboScan"]=="Energy") {
		document.getElementById(ScanAttrib).value = SdzValues[iScan];
	    } else if (All["comboScan"]=="") {
		document.getElementById(ScanAttrib).value = SdzValues[iScan];
	    }
	}
	// Update GUI progress bar
	Progress=Math.round(Progress+90/SValues.length);
	document.getElementById("pBar").style.width = Progress + "%";
	document.getElementById("pBar").innerHTML = Progress + "%";
	
	// Single run: Start 
	let eingabe1=CreateInpFile();
	if (eingabe1=="ERROR") {return(0);}
	let FILENAME=All["fileNamePrefix"]+"_"+ScanName+SValue;
	writeAsciiFile(All["workPath"]+"/"+FILENAME+".inp",eingabe1);
	if (!webOrApp) {
	    // Prepare command and execute
	    cmd = "cd " + All["workPath"];
	    //cmd += ";cp " + FILENAME + ".inp eingabe1.inp";
	    cmd += ";" + trimBin + ' ' + FILENAME;
	    //cmd += "; mv -f ausgabe1.rge " + FILENAME + ".rge";
	    //cmd += "; mv -f ausgabe1.out " + FILENAME + ".out";
	    //cmd += "; mv -f ausgabe1.err " + FILENAME + ".err";
	    execute(cmd);
	}
	// Single run: End

	// Read stopping profiels
	let [cols,data]= readDatFile(All["workPath"]+"/"+FILENAME+".rge");
	// convert depth to nm and normalize stopping profile
	let depth=data[0];
	let nmuons=data[1];
	let dz = (depth[1]-depth[0])/10;
	let norm = dz*sum(nmuons)/100;
	for (let i=0; i<depth.length; i++) {
	    depth[i]=depth[i]/10;
	    nmuons[i]=nmuons[i]/norm;
	}
	Plot_xy("plotRge",depth,nmuons,['Depth (nm)','Stopped muons (%/nm)',ScanName+'='+Number(SValue)/1000+'keV']);		
	// Read the sequence data
	let [cfort,cdata]= readDatFile(All["workPath"]+"/fort.33");
	let lyrs = [6]; // back scattered muons
	for (let ilayer=18;ilayer<cdata.length;ilayer++){lyrs.push(ilayer);} // the rest of the layers
	// Now loop over all
	Plotly.purge("plotFrac")
	for (let ilayer of lyrs) {
	    // Normalize
	    let idata = cdata[ilayer];
	    for (let i=0; i<idata.length; i++) {
		idata[i]=100*idata[i]/cdata[4][i];
	    }
	    let chem = cfort[ilayer];
	    if (ilayer != 6) {
		let LComp = "L"+(ilayer-17)+"Comp";
		chem = All[LComp];
	    }
	    Plot_xy("plotFrac",cdata[0],cdata[ilayer],['E (keV)','Fraction of muons (%)',chem]);
	}
	iScan++;
    }
    
    let data = readAsciiFile(All["workPath"]+"/"+"fort.33");
    let LComp = "";
    let chem_formula = "";
    let place_holder = "";
    let re = new RegExp(place_holder,"g");
    for (let i=1;i<=All["numLayer"];i++) {
	LComp = "L"+i+"Comp";
	chem_formula = All[LComp];
	place_holder = "impL"+i;
	re = new RegExp(place_holder,"g");
	data = data.replace(re, chem_formula);
    }
    let seq_file = All["workPath"]+"/"+All["fileNamePrefix"]+"_Seq_Results.dat";
    writeAsciiFile(seq_file, data);
    
    // Remove redundant files and change the name fort.33
    if (!webOrApp) {
	//	cmd="cd " + All["workPath"] + ";rm -f eingabe1.inp; mv -f fort.33 " + seq_file;
	cmd="cd " + All["workPath"] + "; mv -f fort.33 " + seq_file;
	execute(cmd);
    }
    Progress=100;
    document.getElementById("pBar").style.width = Progress + "%";
    document.getElementById("pBar").innerHTML = Progress + "%";
    return(0);
}

function readDatFile(filename) {
    // Read column data file and return
    // cols - labels of columns
    // data - 2D array with the columns
    let lines = "";
    lines = readAsciiFile(filename);
    
    let data = [];
    let i=0; // line counter
    for (let line of lines.trim().split('\n')) {
	// take labels from the first row
	if (i==0) {
	    var cols = line.trim().split(/[#\s]+/g);
	} else {
	    let words = line.trim().split(/[#\s]+/g);
	    for (let j=0; j<cols.length;j++) {
		if (data[j] == null) {data[j]=[];}
		data[j].push(parseFloat(words[j]));
	    }
	}
	i++;
    }
    return [cols,data];
}

function plotProfiles(filenames) {
    // Plot rge files filenames

    var win = window.open("", "_blank", "toolbar=no, menubar=no");
    win.document.open();
    win.document.write('<html><head><link rel="stylesheet" href="plotly.css"></head><body>');
    win.document.write('<table style="width: 100%"><tr><td><div id="newPlot"><!-- Plotly chart will be drawn inside this DIV --></div></td></tr></table>');
    win.document.write('</body></html>');
    win.addEventListener('resize', sizePlot);
    win.document.close();
    var plotDiv=win.document.getElementById("newPlot");

    // Extract energies from run files if available
    var Es = [];
    for (let i=0;i<filenames.length;i++) {
	Es[i]=Number(filenames[i].substring(filenames[i].indexOf('_')+2,filenames[i].indexOf('.')));
    }

    // loop on sorted values and plot
    for (let i=0;i<Es.length;i++) {
	let [cols,data]= readDatFile(filenames[i]);
	// convert depth to nm and normalize profile
	let depth=data[0];
	let nmuons=data[1];
	let dz = (depth[1]-depth[0])/10;
	let norm = dz*sum(nmuons)/100;
	for (let i=0; i<depth.length; i++) {
	    depth[i]=depth[i]/10;
	    nmuons[i]=nmuons[i]/norm;
	}
	Plot_xy(plotDiv,depth,nmuons,['Depth (nm)','Stopped muons (%/nm)','E='+(Es[i]/1000)+'keV']);		
    }
    
}

function plotFractions(filename) {
    // Plot fractions stopped in layers from sequence file

    var win = window.open("", "_blank", "toolbar=no, menubar=no");
    win.document.open();
    win.document.write('<html><head><link rel="stylesheet" href="plotly.css"></head><body>');
    win.document.write('<table style="width: 100%"><tr><td><div id="newPlot"><!-- Plotly chart will be drawn inside this DIV --></div></td></tr></table>');
    win.document.write('</body></html>');
    win.addEventListener('resize', sizePlot);
    win.document.close();
    var plotDiv=win.document.getElementById("newPlot");

    var [cfort,cdata]= readDatFile(filename);
    let lyrs = [6]; // back scattered muons
    for (let ilayer=18;ilayer<cdata.length;ilayer++){lyrs.push(ilayer);} // the rest of the layers
    // Now loop over all
    for (let ilayer of lyrs) {
	// Normalize
	let idata = cdata[ilayer];
	for (let i=0; i<idata.length; i++) {
	    idata[i]=100*idata[i]/cdata[4][i];
	}
	Plot_xy(plotDiv,cdata[0],cdata[ilayer],['E (keV)','Fraction of muons (%)',cfort[ilayer]]);
    }
    plotDiv=win.document.getElementById("newPlot");
}

function plotMean(filename) {
    // Plot mean and straggeling from sequence file

    var win = window.open("", "_blank", "toolbar=no, menubar=no");
    win.document.open();
    win.document.write('<html><head><link rel="stylesheet" href="plotly.css"></head><body>');
    win.document.write('<table style="width: 100%"><tr><td><div id="newPlot" style="width: 500px; height: 400px;"><!-- Plotly chart will be drawn inside this DIV --></div></td></tr></table>');
    win.document.write('</body></html>');
    win.addEventListener('resize', sizePlot);
    win.document.close();
    var plotDiv=win.document.getElementById("newPlot");
    
    let [cfort,cdata]= readDatFile(filename);
    let mean = cdata[10];
    let strag = cdata[11];
    for (let i=0; i<mean.length; i++) {
	mean[i]=mean[i]/10;
	strag[i]=strag[i]/10;
    }
    Plot_xy(plotDiv,cdata[0],mean,['E (keV)','Mean Depth/Stragg. (nm)',cfort[10]]);
    Plot_xy(plotDiv,cdata[0],strag,['E (keV)','Mean Depth/Stragg. (nm)',cfort[11]]);
}

function startSim() {
    // Collect data from GUI
    All=prep_cfg(1);
    // Switch to plots tab
    document.getElementById("btnPlots").click();
    // Clear plots first
    Plotly.purge("plotFrac");
    Plotly.purge("plotRge");

    // start simulation sequence
    startSequence();
    //CreateInpFile();
    //  document.location =
    //
    //  "http://musruser.psi.ch/cgi-bin/TrimSP.cgi?TrimSPcfg="+TrimSPcfg+'go=start';
}

function amIWeb() {
    if (typeof module !== 'undefined' && module.exports) {
	// Run as standalone app
	return 0;
    } else {
	// Run as a web app
	return 1;
    }
}

async function getDensity(formula) {
    function normalizeCodFormula(codFormula) {
	return codFormula.replace(/-/g, ' ').replace(/\s+/g, '').trim();
    }

    function sameFormula(formulaA, formulaB) {
	const a = parse_formula(formulaA);
	const b = parse_formula(formulaB);
	const aKeys = Object.keys(a).sort();
	const bKeys = Object.keys(b).sort();
	if (aKeys.length !== bKeys.length) {
	    return false;
	}
	for (let i = 0; i < aKeys.length; i++) {
	    const key = aKeys[i];
	    if (key !== bKeys[i] || Math.abs(a[key] - b[key]) > 1e-8) {
		return false;
	    }
	}
	return true;
    }

    function scaleFormula(formulaObj, factor) {
	const scaled = {};
	for (const key of Object.keys(formulaObj)) {
	    scaled[key] = formulaObj[key] * factor;
	}
	return scaled;
    }

    function sameFormulaObject(formulaA, formulaB) {
	const aKeys = Object.keys(formulaA).sort();
	const bKeys = Object.keys(formulaB).sort();
	if (aKeys.length !== bKeys.length) {
	    return false;
	}
	for (let i = 0; i < aKeys.length; i++) {
	    const key = aKeys[i];
	    if (key !== bKeys[i] || Math.abs(formulaA[key] - formulaB[key]) > 1e-8) {
		return false;
	    }
	}
	return true;
    }

    function molarMass(formulaObj) {
	let mass = 0;
	for (const key of Object.keys(formulaObj)) {
	    if (!elemPars[key] || !elemPars[key].A) {
		return null;
	    }
	    mass += formulaObj[key] * elemPars[key].A;
	}
	return mass;
    }

    try {
	const parsedFormula = parse_formula(formula);
	const formulaMass = molarMass(parsedFormula);
	if (formulaMass == null) {
	    return null;
	}

	const encodedFormula = encodeURIComponent(formula);
	const codRes = await fetch(`https://www.crystallography.net/cod/result?formula=${encodedFormula}&format=json`);
	if (!codRes.ok) {
	    throw new Error(`COD lookup failed with status ${codRes.status}`);
	}

	let records = await codRes.json();
	if ((!Array.isArray(records) || records.length === 0) && Object.keys(parsedFormula).length > 0) {
	    const params = new URLSearchParams();
	    const elements = Object.keys(parsedFormula).sort();
	    elements.forEach((element, index) => {
		params.append(`el${index + 1}`, element);
	    });
	    params.append('strictmin', elements.length);
	    params.append('strictmax', elements.length);
	    params.append('format', 'json');

	    const fallbackRes = await fetch(`https://www.crystallography.net/cod/result?${params.toString()}`);
	    if (!fallbackRes.ok) {
		throw new Error(`COD fallback lookup failed with status ${fallbackRes.status}`);
	    }
	    records = await fallbackRes.json();
	}
	if (!Array.isArray(records) || records.length === 0) {
	    return null;
	}

	for (const record of records) {
	    const z = parseFloat(record.Z);
	    const vol = parseFloat(record.vol);
	    if (!isFinite(z) || !isFinite(vol) || z <= 0 || vol <= 0) {
		continue;
	    }

	    const recordFormula = normalizeCodFormula(record.formula || '');
	    if (!sameFormula(formula, recordFormula)) {
		continue;
	    }

	    const cellFormula = normalizeCodFormula(record.cellformula || '');
	    if (cellFormula !== '') {
		const parsedCellFormula = parse_formula(cellFormula);
		const expectedCellFormula = scaleFormula(parsedFormula, z);
		if (!sameFormulaObject(parsedCellFormula, expectedCellFormula)) {
		    continue;
		}
	    }

	    // Convert unit-cell data (A^3, Z) into density in g/cm^3.
	    return 1.66053906660 * z * formulaMass / vol;
	}
    } catch (error) {
	console.error("Error fetching data from COD:", error);
    }

    return null;
}