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

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 Zof(Element)
{
    var ElementsZ = {
	"muon":1,
	"Li-8":3,
	"B-12":5,
	"Mg-31":12,
	"H":1,
	"He":2,
	"Li":3,
	"Be":4,
	"B":5,
	"C":6,
	"N":7,
	"O":8,
	"F":9,
	"Ne":10,
	"Na":11,
	"Mg":12,
	"Al":13,
	"Si":14,
	"P":15,
	"S":16,
	"Cl":17,
	"Ar":18,
	"K":19,
	"Ca":20,
	"Sc":21,
	"Ti":22,
	"V":23,
	"Cr":24,
	"Mn":25,
	"Fe":26,
	"Co":27,
	"Ni":28,
	"Cu":29,
	"Zn":30,
	"Ga":31,
	"Ge":32,
	"As":33,
	"Se":34,
	"Br":35,
	"Kr":36,
	"Rb":37,
	"Sr":38,
	"Y":39,
	"Zr":40,
	"Nb":41,
	"Mo":42,
	"Tc":43,
	"Ru":44,
	"Rh":45,
	"Pd":46,
	"Ag":47,
	"Cd":48,
	"In":49,
	"Sn":50,
	"Sb":51,
	"Te":52,
	"I":53,
	"Xe":54,
	"Cs":55,
	"Ba":56,
	"La":57,
	"Ce":58,
	"Pr":59,
	"Nd":60,
	"Pm":61,
	"Sm":62,
	"Eu":63,
	"Gd":64,
	"Tb":65,
	"Dy":66,
	"Ho":67,
	"Er":68,
	"Tm":69,
	"Yb":70,
	"Lu":71,
	"Hf":72,
	"Ta":73,
	"W":74,
	"Re":75,
	"Os":76,
	"Ir":77,
	"Pt":78,
	"Au":79,
	"Hg":80,
	"Tl":81,
	"Pb":82,
	"Bi":83,
	"Po":84,
	"At":85,
	"Rn":86,
	"Fr":87,
	"Ra":88,
	"Ac":89,
	"Th":90,
	"Pa":91,
	"U":92,
	"":0.0000
    }
    return ElementsZ[Element];
}

function Massof(Element)
{
    var ElementsA = {
	"muon":0.1134289259,
	"Li-8":8.02248624,
	"B-12":12.0143526,
	"Mg-31":30.996648,
	"H":1.00800,
	"He":4.00300,
	"Li":6.93900,
	"Be":9.01200,
	"B":10.81100,
	"C":12.01100,
	"N":14.00700,
	"O":15.99900,
	"F":18.99800,
	"Ne":20.18300,
	"Na":22.99000,
	"Mg":24.31200,
	"Al":26.98200,
	"Si":28.08600,
	"P":30.97400,
	"S":32.06400,
	"Cl":35.45300,
	"Ar":39.94800,
	"K":39.10200,
	"Ca":40.08000,
	"Sc":44.95600,
	"Ti":47.90000,
	"V":50.94200,
	"Cr":51.99600,
	"Mn":54.93800,
	"Fe":55.84700,
	"Co":58.93300,
	"Ni":58.71000,
	"Cu":63.54000,
	"Zn":65.37000,
	"Ga":69.72000,
	"Ge":72.59000,
	"As":74.92200,
	"Se":78.96000,
	"Br":79.90900,
	"Kr":83.80000,
	"Rb":85.47000,
	"Sr":87.62000,
	"Y":88.90500,
	"Zr":91.22000,
	"Nb":92.90600,
	"Mo":95.94000,
	"Tc":98.00000,
	"Ru":101.07000,
	"Rh":102.90500,
	"Pd":106.40000,
	"Ag":107.87000,
	"Cd":112.40000,
	"In":114.82000,
	"Sn":118.69000,
	"Sb":121.75000,
	"Te":127.60000,
	"I":126.90400,
	"Xe":131.30000,
	"Cs":132.90500,
	"Ba":137.34000,
	"La":138.91000,
	"Ce":140.12000,
	"Pr":140.90700,
	"Nd":144.24001,
	"Pm":147.00000,
	"Sm":150.35001,
	"Eu":151.96001,
	"Gd":157.25000,
	"Tb":158.92400,
	"Dy":162.50000,
	"Ho":164.92999,
	"Er":167.25999,
	"Tm":168.93401,
	"Yb":173.03999,
	"Lu":174.97000,
	"Hf":178.49001,
	"Ta":180.94800,
	"W":183.85001,
	"Re":186.20000,
	"Os":190.20000,
	"Ir":192.20000,
	"Pt":195.09000,
	"Au":196.96700,
	"Hg":200.59000,
	"Tl":204.37000,
	"Pb":207.19000,
	"Bi":208.98000,
	"Po":210.00000,
	"At":210.00000,
	"Rn":222.00000,
	"Fr":223.00000,
	"Ra":226.00000,
	"Ac":227.00000,
	"Th":232.03799,
	"Pa":231.00000,
	"U":238.03000,
	"":0.0000     
    }
    return ElementsA[Element];
}

function Elastof(Element) {
    var Elast ={
	"H":0.10000,
	"He":0.10000,
	"Li":1.63000,
	"Be":3.32000,
	"B":5.77000,
	"C":7.37000,
	"N":4.92000,
	"O":2.60000,
	"F":0.84000,
	"Ne":0.02000,
	"Na":1.11000,
	"Mg":1.51000,
	"Al":3.39000,
	"Si":4.63000,
	"P":3.43000,
	"S":2.85000,
	"Cl":1.40000,
	"Ar":0.08000,
	"K":0.93000,
	"Ca":1.84000,
	"Sc":3.90000,
	"Ti":4.85000,
	"V":5.31000,
	"Cr":4.10000,
	"Mn":2.92000,
	"Fe":4.28000,
	"Co":4.39000,
	"Ni":4.44000,
	"Cu":3.49000,
	"Zn":1.35000,
	"Ga":2.81000,
	"Ge":3.85000,
	"As":2.96000,
	"Se":2.25000,
	"Br":1.22000,
	"Kr":0.12000,
	"Rb":0.85000,
	"Sr":1.72000,
	"Y":4.37000,
	"Zr":6.25000,
	"Nb":7.57000,
	"Mo":6.82000,
	"Tc":6.85000,
	"Ru":6.74000,
	"Rh":5.75000,
	"Pd":3.89000,
	"Ag":2.95000,
	"Cd":1.16000,
	"In":2.52000,
	"Sn":3.14000,
	"Sb":2.75000,
	"Te":2.23000,
	"I":1.11000,
	"Xe":0.16000,
	"Cs":0.80000,
	"Ba":1.90000,
	"La":4.47000,
	"Ce":4.32000,
	"Pr":3.70000,
	"Nd":3.40000,
	"Pm":0.10000,
	"Sm":2.14000,
	"Eu":1.86000,
	"Gd":4.14000,
	"Tb":4.05000,
	"Dy":3.04000,
	"Ho":3.14000,
	"Er":3.29000,
	"Tm":2.42000,
	"Yb":1.60000,
	"Lu":4.43000,
	"Hf":6.44000,
	"Ta":8.10000,
	"W":8.90000,
	"Re":8.03000,
	"Os":8.17000,
	"Ir":6.94000,
	"Pt":5.84000,
	"Au":3.81000,
	"Hg":0.67000,
	"Tl":1.88000,
	"Pb":2.03000,
	"Bi":2.18000,
	"Po":1.50000,
	"At":0.10000,
	"Rn":0.20000,
	"Fr":0.10000,
	"Ra":1.66000,
	"Ac":4.25000,
	"Th":6.20000,
	"Pa":0.10000,
	"U":5.55000,
	"":0.00000
    };
    return Elast[Element];
}

function StoppingCoefficients(Element,flag)
{
    // flag = 1 prefer ICRU
    // otherwise prefer IAEA
    var StoppingCoefficientsICRU = {
	"H":"1.25400,1.44000,242.60001,12000.00000,0.11590",
	"He":"1.22900,1.39700,484.50000,5873.00000,0.05225",
	"Li":"1.41100,1.60000,725.59998,3013.00000,0.04578",
	"Be":"2.24800,2.59000,966.00000,153.80000,0.03475",
	"B":"2.47400,2.81500,1206.00000,1060.00000,0.02855",
	"C":"2.60100,2.60100,1701.00000,1279.00000,0.01638",
	"N":"2.95400,3.35000,1683.00000,1900.00000,0.02513",
	"O":"2.65200,3.00000,1920.00000,2000.00000,0.02230",
	"F":"2.08500,2.35200,2157.00000,2634.00000,0.01816",
	"Ne":"1.95100,2.19900,2393.00000,2699.00000,0.01568",
	"Na":"2.54200,2.86900,2628.00000,1854.00000,0.01472",
	"Mg":"3.79100,4.29300,2862.00000,1009.00000,0.01397",
	"Al":"4.15400,4.73900,2766.00000,164.50000,0.02023",
	"Si":"4.91400,5.59800,3193.00000,232.70000,0.01419",
	"P":"3.23200,3.64700,3561.00000,1560.00000,0.01267",
	"S":"3.44700,3.89100,3792.00000,1219.00000,0.01211",
	"Cl":"5.30100,6.00800,3969.00000,645.09998,0.01183",
	"Ar":"5.73100,6.50000,4253.00000,530.00000,0.01123",
	"K":"5.15200,5.83300,4482.00000,545.70001,0.01129",
	"Ca":"5.52100,6.25200,4710.00000,553.29999,0.01120",
	"Sc":"5.20100,5.88400,4938.00000,560.90002,0.01000",
	"Ti":"4.85800,5.48900,5260.00000,651.09998,0.00893",
	"V":"4.47900,5.05500,5391.00000,952.29999,0.00912",
	"Cr":"3.98300,4.48900,5616.00000,1336.00000,0.00841",
	"Mn":"3.46900,3.90700,5725.00000,1461.00000,0.00883",
	"Fe":"3.51900,3.96300,6065.00000,1243.00000,0.00778",
	"Co":"3.14000,3.53500,6288.00000,1372.00000,0.00736",
	"Ni":"3.55300,4.00400,6205.00000,555.09998,0.00876",
	"Cu":"3.69600,4.19400,4649.00000,81.13000,0.02242",
	"Zn":"4.21000,4.75000,6953.00000,295.20001,0.00681",
	"Ga":"5.04100,5.69700,7137.00000,202.60001,0.00673",
	"Ge":"5.55400,6.30000,6496.00000,110.00000,0.00969",
	"As":"5.32300,6.01200,7611.00000,292.50000,0.00645",
	"Se":"5.87400,6.65600,7395.00000,117.50000,0.00768",
	"Br":"6.65800,7.53600,7694.00000,222.30000,0.00651",
	"Kr":"6.41300,7.24000,11850.00000,153.70000,0.00288",
	"Rb":"5.69400,6.42900,8478.00000,292.89999,0.00609",
	"Sr":"6.33900,7.15900,8693.00000,330.29999,0.00600",
	"Y":"6.40700,7.23400,8907.00000,367.79999,0.00589",
	"Zr":"6.73400,7.60300,9120.00000,405.20001,0.00576",
	"Nb":"6.90100,7.79100,9333.00000,442.70001,0.00559",
	"Mo":"6.42400,7.24800,9545.00000,480.20001,0.00538",
	"Tc":"6.79900,7.67100,9756.00000,517.59998,0.00532",
	"Ru":"6.10900,6.88700,9966.00000,555.09998,0.00515",
	"Rh":"5.92400,6.67700,10180.00000,592.50000,0.00492",
	"Pd":"5.23800,5.90000,10380.00000,630.00000,0.00476",
	"Ag":"5.34500,6.03800,6790.00000,397.79999,0.01676",
	"Cd":"5.81400,6.55400,10800.00000,355.50000,0.00463",
	"In":"6.22900,7.02400,11010.00000,370.89999,0.00454",
	"Sn":"6.40900,7.22700,11210.00000,386.39999,0.00447",
	"Sb":"7.50000,8.48000,8608.00000,348.00000,0.00907",
	"Te":"6.97900,7.87100,11620.00000,392.39999,0.00440",
	"I":"7.72500,8.71600,11830.00000,394.79999,0.00438",
	"Xe":"8.33700,9.42500,10510.00000,269.60001,0.00621",
	"Cs":"7.28700,8.21800,12230.00000,399.70001,0.00445",
	"Ba":"7.89900,8.91100,12430.00000,402.10001,0.00451",
	"La":"8.04100,9.07100,12630.00000,404.50000,0.00454",
	"Ce":"7.48800,8.44400,12830.00000,406.89999,0.00442",
	"Pr":"7.29100,8.21900,13030.00000,409.29999,0.00430",
	"Nd":"7.09800,8.00000,13230.00000,411.79999,0.00418",
	"Pm":"6.90900,7.78600,13430.00000,414.20001,0.00406",
	"Sm":"6.72800,7.58000,13620.00000,416.60001,0.00398",
	"Eu":"6.55100,7.38000,13820.00000,419.00000,0.00388",
	"Gd":"6.73900,7.59200,14020.00000,421.39999,0.00386",
	"Tb":"6.21200,6.99600,14210.00000,423.89999,0.00372",
	"Dy":"5.51700,6.21000,14400.00000,426.29999,0.00363",
	"Ho":"5.22000,5.87400,14600.00000,428.70001,0.00350",
	"Er":"5.07100,5.70600,14790.00000,433.00000,0.00341",
	"Tm":"4.92600,5.54200,14980.00000,433.50000,0.00334",
	"Yb":"4.78800,5.38600,15170.00000,435.89999,0.00329",
	"Lu":"4.89300,5.50500,15360.00000,438.29999,0.00324",
	"Hf":"5.02800,5.65700,15550.00000,440.79999,0.00320",
	"Ta":"4.73800,5.32900,15740.00000,443.20001,0.00319",
	"W":"4.58700,5.16000,15410.00000,415.29999,0.00341",
	"Re":"5.20100,5.85100,16120.00000,441.60001,0.00312",
	"Os":"5.07100,5.70400,16300.00000,440.89999,0.00308",
	"Ir":"4.94600,5.56300,16490.00000,440.10001,0.00296",
	"Pt":"4.47700,5.03400,16670.00000,439.29999,0.00287",
	"Au":"4.84400,5.45800,7852.00000,975.79999,0.02077",
	"Hg":"4.30700,4.84300,17040.00000,487.79999,0.00288",
	"Tl":"4.72300,5.31100,17220.00000,537.00000,0.00291",
	"Pb":"5.31900,5.98200,17400.00000,586.29999,0.00287",
	"Bi":"5.95600,6.70000,17800.00000,677.00000,0.00266",
	"Po":"6.15800,6.92800,17770.00000,586.29999,0.00281",
	"At":"6.20300,6.97900,17950.00000,586.29999,0.00278",
	"Rn":"6.18100,6.95400,18120.00000,586.29999,0.00275",
	"Fr":"6.94900,7.82000,18300.00000,586.29999,0.00274",
	"Ra":"7.50600,8.44800,18480.00000,586.29999,0.00273",
	"Ac":"7.64800,8.60900,18660.00000,586.29999,0.00270",
	"Th":"7.71100,8.67900,18830.00000,586.29999,0.00264",
	"Pa":"7.40700,8.33600,19010.00000,586.29999,0.00260",
	"U":"7.29000,8.20400,19180.00000,586.29999,0.00267",
	"":"0.00000,0.00000,0.00000,0.00000,0.00000"
    };

    // Updated Anderson-Ziegler table values for hydrogen projectiles using
    // up-to-date stopping data from the IAEA database (https://www-nds.iaea.org/stopping/).
    // For further details on their determination, see e.g.:
    // R. M. L. McFadden at al., arXiv:2212.11081 [cond-mat.supr-con]
    // https://doi.org/10.48550/arXiv.2212.11081
    var StoppingCoefficientsIAEA = {
        "H": "1.21941306,1.39705253,316.72610292,3622.08960714,0.03609996",
        "Li": "2.55867734,2.98398784,672.22623329,223.63937274,0.05756479",
        "Be": "2.13846776,2.43024550,1353.80005691,500.78353377,0.01143076",
        "B": "2.92598306,3.33271910,1523.83401267,574.31712932,0.01671298",
        "C": "2.51057212,2.84874359,1325.63086028,2111.57332043,0.03815981",
        "N": "3.03231463,3.44621744,1287.27189959,3445.25706665,0.06909550",
        "O": "2.58218404,2.91913321,2066.69556610,1937.28839450,0.01708201",
        "Mg": "4.32219620,4.95332934,2711.05757349,99.32422512,0.01692829",
        "Al": "4.16266645,4.73942640,3007.21967155,192.15430476,0.01478852",
        "Si": "4.56277193,5.17964542,3812.93366288,249.45105835,0.00951865",
        "Cl": "5.18954121,5.87010049,5726.20198003,338.90592713,0.00527894",
        "Ca": "7.38419020,8.41800474,4257.94547049,311.84732092,0.01482602",
        "Sc": "6.27366940,7.11486087,5202.32117316,349.64931132,0.00808596",
        "Ti": "4.89215322,5.52996090,4733.05002706,821.54929980,0.01141794",
        "V": "4.39418898,4.95984106,5216.28902299,873.00768319,0.00982301",
        "Cr": "4.22355616,4.76724205,4805.40719904,1062.25237873,0.01508696",
        "Mn": "3.45870888,3.89580224,5452.18588822,1778.16054656,0.01057380",
        "Fe": "3.69846643,4.16916938,5392.90710239,1040.38447053,0.01152298",
        "Co": "3.55890909,4.00775461,6796.04145497,933.86447935,0.00558368",
        "Ni": "3.42262695,3.86234880,4759.65515188,520.18934465,0.02026669",
        "Cu": "3.54912421,4.02142201,4344.22605325,128.32905834,0.02886218",
        "Zn": "4.31895518,4.91763977,5346.03925560,46.16548699,0.01518164",
        "Ga": "4.11015447,4.63998531,7681.41419449,149.38563152,0.00628772",
        "Ge": "5.80984815,6.60667983,6039.04808738,87.19744473,0.01158192",
        "Se": "5.58734301,6.31119973,8423.01872583,221.61559131,0.00530434",
        "Br": "6.28480648,7.09489448,11732.76411988,150.96205589,0.00281298",
        "Kr": "6.47378266,7.31581518,9199.06183849,216.98680923,0.00437111",
        "Rb": "8.48759187,9.62951209,7271.11124671,272.67996745,0.00818815",
        "Sr": "8.66447838,9.84912713,5979.31960977,334.15705556,0.01184544",
        "Y": "7.54854264,8.54789357,6885.34110669,429.53252110,0.00930644",
        "Zr": "6.24168401,7.04236496,10674.06252597,269.66181445,0.00339805",
        "Nb": "5.96194954,6.72632300,10250.57513827,275.25886405,0.00386599",
        "Mo": "5.58867862,6.29983727,9573.16605660,523.57577519,0.00473082",
        "Pd": "4.74762031,5.34871025,8086.17802763,942.05721488,0.00842671",
        "Ag": "5.42052240,6.17824432,4642.18214950,90.75350922,0.06061521",
        "Cd": "4.89128643,5.50754704,11831.77188508,396.06905848,0.00412049",
        "In": "5.98978289,6.77050040,6343.54720062,564.65410792,0.02270520",
        "Sn": "6.73191335,7.61854414,6946.18830598,347.19391310,0.01677246",
        "Sb": "7.92400389,8.99628409,5736.29881090,403.11722206,0.02973016",
        "Xe": "8.96826400,10.16224223,8543.27304860,283.90067433,0.01019984",
        "La": "8.16949326,9.21144395,13933.96869212,429.99442382,0.00347440",
        "Nd": "8.60801371,10.26060598,6798.65217629,7.06731816,0.02713704",
        "Gd": "8.38379061,9.50012183,10804.38767518,110.71066098,0.00761735",
        "Tb": "8.69907359,10.36476708,5985.09307671,7.76175759,0.04237031",
        "Dy": "6.69350026,7.81543484,5289.65107666,12.11560717,0.05746489",
        "Er": "4.31497049,4.85346547,12995.54504003,691.00380321,0.00499022",
        "Yb": "6.38304258,7.21491284,12327.74719685,82.30064162,0.00516845",
        "Lu": "7.00205766,8.09268611,4589.67801229,31.06321362,0.11142124",
        "Hf": "5.32763157,6.00140558,13853.49562768,206.93150053,0.00411522",
        "Ta": "5.15280708,5.80545310,12417.25115167,231.48549646,0.00530723",
        "W": "4.81261962,5.41579909,15245.84079976,286.09077182,0.00344862",
        "Re": "4.26021967,4.80273372,3191.05524918,76051.48730893,0.00003161",
        "Ir": "4.16543126,4.68849191,6887.94139926,4263.90641919,0.00000004",
        "Pt": "4.62228847,5.20033612,16308.49878855,266.02263275,0.00309560",
        "Au": "4.84253074,5.44769072,15602.21662947,412.25485588,0.00331383",
        "Pb": "9.42473604,17.46235676,11946.86905435,0.00000001,0.00652912",
        "Bi": "10.25823796,12.26670424,7765.05387481,7.37274504,0.02310050"
    };

    if (flag) {
	// Using stopping coefficients derived from ICRU Report 49
	return StoppingCoefficientsICRU[Element];
    } else {
	// Using stopping coefficients derived from data in the IAEA database;
	// however, if they are unavailable, return those from ICRU Report 49
	return (Element in StoppingCoefficientsIAEA) ? StoppingCoefficientsIAEA[Element] : StoppingCoefficientsICRU[Element];
    }
}


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 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":3.60,
        "NdGaO3":7.57,
        "YAlO3":4.88,
        "Y3Al5O12":4.55,
        "LiF":2.60,
        "CaF2":3.18,
        "BaFe":4.83,
        "MgF2":3.18,
        "SiO2":2.65,
        "TiO2":4.26,
        "KTaO3":6.967,
        "LaAlO3":6.70,
        "Al2O3":3.98,
        "SrTiO3":5.12,
        "SrLaGaO4":6.389,
        "SrLaAlO4":5.924,
        "NbSe2":6.30,
        "MgO":3.58,
        "YBa2Cu3O7":6.54,
        "GaAs":5.32,
        "C60":1.65,
        "H":0.08,
        "He":0.12,
        "Li":0.53,
        "Be":1.85,
        "B":2.34,
        "C":2.26,
        "N":1.03,
        "O":2.00,
        "F":1.11,
        "Ne":1.50,
        "Na":0.97,
        "Mg":1.74,
        "Al":2.7,
        "Si":2.33,
        "P":1.00,
        "S":2.07,
        "Cl":2.03,
        "Ar":1.77,
        "K":0.86,
        "Ca":1.55,
        "Sc":2.99,
        "Ti":4.54,
        "V":6.11,
        "Cr":7.19,
        "Mn":7.43,
        "Fe":7.87,
        "Co":8.9,
        "Ni":8.9,
        "Cu":8.96,
        "Zn":7.13,
        "Ga":5.91,
        "Ge":5.32,
        "As":5.72,
        "Se":4.79,
        "Br":3.14,
        "Kr":3.10,
        "Rb":1.53,
        "Sr":2.54,
        "Y":4.47,
        "Zr":6.51,
        "Nb":8.57,
        "Mo":10.22,
        "Tc":11.5,
        "Ru":12.37,
        "Rh":12.41,
        "Pd":12.02,
        "Ag":10.5,
        "Cd":8.65,
        "In":7.31,
        "Sn":7.31,
        "Sb":6.68,
        "Te":6.24,
        "I":4.93,
        "Xe":3.80,
        "Cs":1.90,
        "Ba":3.59,
        "La":6.15,
        "Ce":6.77,
        "Pr":6.77,
        "Nd":7.01,
        "Pm":7.22,
        "Sm":7.52,
        "Eu":5.24,
        "Gd":7.9,
        "Tb":8.23,
        "Dy":8.55,
        "Ho":8.8,
        "Er":9.07,
        "Tm":9.32,
        "Yb":6.9,
        "Lu":9.84,
        "Hf":13.31,
        "Ta":16.65,
        "W":19.35,
        "Re":21.04,
        "Os":22.6,
        "Ir":22.4,
        "Pt":21.45,
        "Au":19.32,
        "Hg":13.55,
        "Tl":11.85,
        "Pb":11.35,
        "Bi":9.75,
        "Po":9.3,
        "Th":11.72,
        "Pa":15.4,
        "U":18.95,
        "":""
    }
    document.getElementById(rhoLi).value = rhos[chem];

    // suggest a material density based on composition (when it's undefined)
    if (!isFinite(document.getElementById(rhoLi).value)) {
        let layer_formula = parse_formula(chem);

        // determine the stoichiometry sum (for normalization)
        let stoichiometry_sum = 0;
	    for (key of Object.keys(layer_formula)) {
	        stoichiometry_sum = stoichiometry_sum + layer_formula[key];
	    }

	    // determine the density using on a weighted average of the elemental densities
	    let density_estimate = 0;
	    for (key of Object.keys(layer_formula)) {
	        if (layer_formula[key] != null) {
	            density_estimate = density_estimate + (layer_formula[key] / stoichiometry_sum) * rhos[key];
	        }
	    }

        document.getElementById(rhoLi).value = density_estimate;
	alert("Warning: The density for this layer is only an estimate!")
    }
}

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 = "";

    let All = new Object();
    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;
    }

    // Check ICRU flag, if checked use it
    All["flagICRU"] = document.getElementById("flagICRU").checked;
    
    // 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(All) {
    // 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 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
       var TemplateLayer= "L1d L1rho L1CK\n L1ELZ1 L1ELZ2 L1ELZ3 L1ELZ4 L1ELZ5\n L1ELW1 L1ELW2 L1ELW3 L1ELW4 L1ELW5\n L1ELC1 L1ELC2 L1ELC3 L1ELC4 L1ELC5\n L1ELE1 L1ELE2 L1ELE3 L1ELE4 L1ELE5\n L10301 L10302 L10303 L10304 L10305\n 0.0000   0.0000   0.0000   0.0000   0.0000\n L1ELST11 L1ELST21 L1ELST31 L1ELST41 L1ELST51\n L1ELST12 L1ELST22 L1ELST32 L1ELST42 L1ELST52\n L1ELST13 L1ELST23 L1ELST33 L1ELST43 L1ELST53\n L1ELST14 L1ELST24 L1ELST34 L1ELST44 L1ELST54\n L1ELST15 L1ELST25 L1ELST35 L1ELST45 L1ELST55";

    let projectile = All['ProjType'];
    All['ProjZ']=Zof(projectile);
    All['ProjAM']=Massof(projectile);

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

    // This containes mapped object pairs of original:replace
    let repAll = new Object();
    // Loop over layers an create appropriate values
    for (var i=1; i<=All['numLayer'];i++){
	Li = 'L'+i;
	Layer = TemplateLayer;
	Layer = Layer.replace(/L1/g,Li);
	TemplateFile = TemplateFile+"\n"+Layer;
	Check=0;
	// Composition of layers	
	let LComp="L"+i+"Comp";
	let Comp = document.getElementById(LComp).value;
	All[LComp] = Comp;
	let LElComp=parse_formula(Comp);
	for (key of Object.keys(LElComp)) {
	    // Check if composition is understood
	    if (key=="" || Zof(key)=="") {
		Check++;
	    }  
	}
	if (Comp == "" || typeof Comp == 'undefined') {Check++;}
	// Write composition to results file header

	// Densities of layers
	let Lrho="layer"+i+"rho";
	let rho = 1*All[Lrho];
	
	// How to do this? All[Lrho]=sprintf("%6.2f",rho);
	if (rho=="") {Check++;}
	
	// Thickness of layers
	let Ld ="L"+i+"d";
	let d = All[Ld];
	// How to do this? All[Ld]=sprintf("%8.2f",d);
	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 tmp = "L"+i+"CK";
	All[tmp]=1.0; // sprintf("%6.2f",1.0);
	
	let Sum = 0;
	for (key of Object.keys(LElComp)) {
	    Sum=Sum+LElComp[key];
	}
	if (Sum==0) {Sum=1;}
	
	let Els = Object.keys(LElComp);
	
	for (let NEl=1;NEl<=5;NEl++) {
	    let El = "";
	    if (NEl <= Els.length) {
		El = Els[NEl-1];
	    }
	    let LEkey = "L"+i+"EL";
	    let ElZ = Zof(El);
	    let ElW = Massof(El);
	    let ElC = 0;
	    if (LElComp[El] != null){ElC=LElComp[El]/Sum;}
	    let ElE = Elastof(El);
	    let El030 = 30;
	    if (El=="") { El030 = 0.0;}

	    All[LEkey+"Z"+NEl]=ElZ; // sprintf("%8.4f",$ElZ);
	    All[LEkey+"W"+NEl]=ElW; // sprintf("%8.4f",$ElW);
	    All[LEkey+"C"+NEl]=ElC; // sprintf("%8.4f",$ElC);
	    All[LEkey+"E"+NEl]=ElE; // sprintf("%8.4f",$ElE);
	    All["L"+i+"030"+NEl]=El030; // sprintf("%8.4f",$El030);
	    
	    let ElST = StoppingCoefficients(El,All["flagICRU"]);
	    let ElSTs = ElST.split(',');
	    let j=1;
	    for (let iElST of ElSTs) {
		LEkey = "L"+i+"ELST"+NEl+j;
		j++;
		All[LEkey]=iElST; // sprintf("%11.6f",$_);
	    }
	}
    }

    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 replaceAll(str,mapObj){
    // Takes string str and replaces all mapped objects in it
    // The mapped object are pairs of original:replace
    var re = new RegExp(Object.keys(mapObj).join("|"),"gi");

    return str.replace(re, function(matched){
        return mapObj[matched.toLowerCase()];
    });
}

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(All) {
    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)) {
	    // 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(All);
	if (eingabe1=="ERROR") {return(0);}
	let FILENAME=All["workPath"]+"/"+All["fileNamePrefix"]+"_"+ScanName+SValue;
	writeAsciiFile(FILENAME+".inp",eingabe1);
	if (!webOrApp) {
	    // Prepare command and execute
	    cmd = "cd " + All["workPath"];
	    cmd += ";cp " + FILENAME + ".inp eingabe1.inp";
	    cmd += ";" + trimBin;
	    cmd += "; mv -f ausgabe1.rge " + FILENAME + ".reg";
	    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(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++;
    }
    //},1000);
    // An easy way to keep track of chemical formula is to replace impL_i by the corresponding chemical formula of layer i
    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 the fort.33 and other redundant files
    if (!webOrApp) {
	cmd="cd " + All["workPath"] + ";rm -f eingabe1.inp; rm -f fort.33";
	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 files= new Object();
    var Es = [];
    for (let i=0;i<filenames.length;i++) {
	Es[i]=Number(filenames[i].substring(filenames[i].indexOf('_')+2,filenames[i].indexOf('.')));
	files[Es[i]] = filenames[i];
    }

    // loop on sorted values and plot
    for (let i=0;i<Es.length;i++) {
	let [cols,data]= readDatFile(files[Es[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
    var 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(All)
    //CreateInpFile(All);
    //  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;
    }
}