ext-mcfadd_r
391c25ef93
This patch modularizes the code responsible for selecting the stopping power coefficients. Specifically, it: - moves the data in `elemPars` to seperate JSON files in the `data/` directory. This makes it easier to modify the existing data or add new data sources. Note that this refactoring does not alter the previous functionality - the contents of each file are simply read and deep-merged into an initially empty `elemPars` object. - adds the original Varelas-Biersack parameters from Anderson & Ziegler (1977). - updates the "Other Parameters" tab in the GUI for easy toggling between the different stopping power coefficient data sources.
844 lines
27 KiB
JavaScript
844 lines
27 KiB
JavaScript
// This file contains function that are generic Javascript for TrimSP
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// This is an object that contains all GUI ids and values
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var All = new Object();
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function isObject(item) {
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// simple object check
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// https://stackoverflow.com/a/34749873
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return (item && typeof item === 'object' && !Array.isArray(item));
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}
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function mergeDeep(target, ...sources) {
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// function for deep-merging objects
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// https://stackoverflow.com/a/34749873
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if (!sources.length) {
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return target;
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}
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const source = sources.shift();
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if (isObject(target) && isObject(source)) {
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for (const key in source) {
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if (isObject(source[key])) {
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if (!target[key]) Object.assign(target, { [key]: {} });
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mergeDeep(target[key], source[key]);
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} else {
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Object.assign(target, { [key]: source[key] });
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}
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}
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}
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return mergeDeep(target, ...sources);
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}
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// list of json files containing all projectile/target element data
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const dataFiles = [
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"./data/elements.json",
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"./data/projectiles.json",
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"./data/az_table.json",
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"./data/icru_table.json",
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"./data/iaea_table.json"
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];
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// empty "main" object - to be filled with *all* projectile/target data
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const elemPars = {}
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// loop over each json file
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for (const df of dataFiles) {
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// read its contents...
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const data = require(df)
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// ...and deep-merge them to the "main" object
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mergeDeep(elemPars, data);
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};
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// Extra densities (i.e., for chemical compounds)
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var rhos = require("./data/densities.json")
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function parse_formula (mf) {
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// This function takes a chemical formula and returns
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// an object that contains the atoms and their number
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// replace all types of brackets into ()
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var mf = mf.replace(/\[/g,"(").replace(/\]/g,")").replace(/\{/g,"(").replace(/\}/g,")").replace(/\s+/g,"");
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if(/^\d+/.test(mf)) throw new SyntaxError("Molecular formula should not start with a number!");
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var mol = {};
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// go into brackets and collect info
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while(mf.includes("(")){
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var x = mf.lastIndexOf("(");
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var y = mf.indexOf(")", mf.lastIndexOf("("));
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var z = mf.substr(x+1, y-x-1);
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var c = mf.substr(y+1);
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c = /^\d+/.exec(c);
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c=(c!= null)?Number(c[0]):1;
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// recursive
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var a = this.parse_formula(z);
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var b = "";
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for(var k in a){
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b+=k+""+a[k]*c;
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}
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mf = mf.substr(0, x)+ b + mf.substr(y+1+((c>1)?(c+'').length:0));
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}
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var m = "";
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// Separate element name from stoichiometry
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// while(m = /([A-Z]{1}[a-z]{0,}[0-9]{0,})/.exec(mf)){
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while(m = /([A-Z]{1}[a-z]{0,}[0-9]{0,}\.?[0-9]{0,})/.exec(mf)){
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// Element
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var m1 = /([A-Z]{1,}[a-z]{0,})/.exec(m[0]);
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// Stoichiometry
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//var m2 = /\d+/.exec(m[0]);
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var m2 = /\d+\.?\d{0,}/.exec(m[0]);
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if(typeof mol[m1[0]] == 'undefined') mol[m1[0]]=(m2!=null)?Number(m2[0]):1;
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else mol[m1[0]] += (m2!=null)?Number(m2[0]):1;
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mf = mf.replace(m[0], "");
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}
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return mol;
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}
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function StoppingCoefficients(Element, flag)
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{
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// Select which tabulation to use for the Varelas-Biersack parameterization
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// of electronic stopping cross sections for proton-like projectiles
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// implanted in elemental targets.
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// flag = 1: use coefficients from Anderson & Ziegler (1977).
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if (flag == 1) {
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return elemPars[Element].AZ;
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}
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// flag = 2: use coefficients from ICRU Report 49 (1973).
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if (flag == 2) {
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return elemPars[Element].ICRU;
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}
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// flag = 3: use coefficients from McFadden et al. (2023) and McFadden et al. (unpublished).
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//
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// NOTE: these values were derived from up-to-date stopping data found inthe
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// IAEA's database of electronic stopping cross sections
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// (https://www-nds.iaea.org/stopping/).
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// For further details on their determination, see, e.g.:
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// Appendix A in McFadden at al., Phys. Rev. Applied 19, 044018 (2023).
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// https://doi.org/10.1103/PhysRevApplied.19.044018
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if (flag == 3 && elemPars[Element].IAEA.length == 5) {
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return elemPars[Element].IAEA;
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// in the event that updated coefficients are unavailable for given element
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// fall back to using values from ICRU Report 49
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} else {
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return elemPars[Element].ICRU;
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}
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}
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function rho_fun()
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{
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var irow = this.parentNode.parentNode.rowIndex;
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var caller = this.id;
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var chem = document.getElementById(caller).value;
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var rhoLi = "L"+irow+"rho";
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var rho = 0;
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if (elemPars[chem]) {
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rho = elemPars[chem].rho;
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} else {
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// Did not find density in elements list
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if (isFinite(rhos[chem])) {
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// Found in densities list of compositions
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rho = rhos[chem];
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} else {
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// suggest a material density based on composition (when it's undefined)
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let layer_formula = parse_formula(chem);
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// determine the stoichiometry sum (for normalization)
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let stoichiometry_sum = 0;
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for (key of Object.keys(layer_formula)) {
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stoichiometry_sum = stoichiometry_sum + layer_formula[key];
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}
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// determine the density using on a weighted average of the elemental densities
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let density_estimate = 0;
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for (key of Object.keys(layer_formula)) {
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if (layer_formula[key] != null) {
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density_estimate = density_estimate + (layer_formula[key] / stoichiometry_sum) * elemPars[key].rho;
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}
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}
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rho = density_estimate;
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alert("Warning: The density for this layer is only an estimate!")
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}
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}
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// Set value in appropriate cell
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document.getElementById(rhoLi).value = rho;
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}
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function openTab(event, tabName) {
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// Declare all variables
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var i, tabcontent, tablinks;
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// Get all elements with class="tabcontent" and hide them
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tabcontent = document.getElementsByClassName("tabcontent");
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for (i = 0; i < tabcontent.length; i++) {
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tabcontent[i].style.display = "none";
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}
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// Get all elements with class="tablinks" and remove the class "active"
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tablinks = document.getElementsByClassName("tablinks");
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for (i = 0; i < tablinks.length; i++) {
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tablinks[i].className = tablinks[i].className.replace(" active", "");
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}
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// Show the current tab, and add an "active" class to the button that opened the tab
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document.getElementById(tabName).style.display = "block";
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if (event) event.currentTarget.className += " active";
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}
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function adjust_table()
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{
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var numLayer = document.getElementById("numLayer").value;
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var LTable = document.getElementById("LTable");
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var Nrows = LTable.rows.length;
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var Comps = [];
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var Rhos = [];
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var Ds = [];
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// Need to loop to get the right number of rows when reloading
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if (numLayer >= Nrows) {
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for (i = Nrows;i<=numLayer;i++) {
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var row = LTable.insertRow(i);
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var Li = row.insertCell(0);
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Li.innerHTML = i;
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var compL = row.insertCell(1);
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var compCell = document.createElement("input");
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compCell.id = "L"+i+"Comp";
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compCell.name = "L"+i+"Comp";
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compCell.size = 15;
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compCell.onchange = rho_fun;
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if (Comps[i-1]) {compCell.value = Comps[i-1];}else{compCell.value = 'SrTiO3';}
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compL.appendChild(compCell);
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var rhoL = row.insertCell(2);
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var rhoCell = document.createElement("input");
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rhoCell.id = "L"+i+"rho";
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rhoCell.name = "L"+i+"rho";
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rhoCell.size = 5;
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rhoL.appendChild(rhoCell);
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if (Rhos[i-1]) {rhoCell.value = Rhos[i-1];}else{rhoCell.value = '5.12';}
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var thickL = row.insertCell(3);
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var thickCell = document.createElement("input");
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thickCell.id = "L"+i+"d";
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thickCell.name = "L"+i+"d";
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thickCell.size = 7;
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thickL.appendChild(thickCell);
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if (Ds[i-1]) {thickCell.value = Ds[i-1];}else{thickCell.value = '10000';}
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}
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} else {
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for (i = Nrows-1;i>numLayer;i--) {
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LTable.deleteRow(i);
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}
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}
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}
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function adjust_scans()
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{
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// Deal with scans checkbox and type
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var scanSeq = document.getElementById("scanSeq").checked;
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var sender = document.getElementById("scanSeq");
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var scanType = document.getElementById("scanType").value;
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// consider only if scans checkbox is checked
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if (scanSeq) {
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// Which type of scan
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if (scanType == "scanLoop") {
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ShowHide(1,'ScansTable');
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ShowHide(0,'ScansLine');
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} else {
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ShowHide(1,'ScansLine');
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ShowHide(0,'ScansTable');
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}
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} else {
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// Hide both
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ShowHide(0,'ScansTable');
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ShowHide(0,'ScansLine');
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}
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}
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function ProjSmartDefaults()
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{
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var Proj = document.getElementById("ProjType").value;
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var sigEnergy = document.getElementById("sigEnergy");
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var sigAngle = document.getElementById("sigAngle");
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if (Proj == "muon") {
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sigEnergy.value = "450";
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sigAngle.value = "15";
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} else {
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sigEnergy.value = "0";
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sigAngle.value = "0";
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}
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}
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function ProjNumberLimit()
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{
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var numberProj = document.getElementById("numberProj").value;
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if (numberProj > 5000) {
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alert("Maximum number is 5000");
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document.getElementById("numberProj").value = 5000;
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}
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}
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function ShowHide(onoff,item) {
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// this function can switch item to visible/hidden onoff=1/0
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if(onoff){
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// document.getElementById(item).style.display = 'block';
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document.getElementById(item).style.visibility = "visible";
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} else {
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// document.getElementById(item).style.display = 'none';
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document.getElementById(item).style.visibility = "hidden";
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}
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}
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function prep_cfg(toggle) {
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// This function collects various values and returns
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// toggle=1 : returns object with all values
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// toggle!=1 : returns string containing cfg file
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let TrimSPcfg = "";
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let strtmp = "";
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let valtmp = "";
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All['trimPath']=document.getElementById("trimPath").value;
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// Prepare Layers section
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let LayersSec = "[Layers]\n";
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let numLayer = document.getElementById("numLayer").value;
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All['numLayer']=numLayer;
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LayersSec = LayersSec + "numLayer="+numLayer+"\n";
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for (i = 1;i<=numLayer;i++) {
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strtmp = "L"+i+"Comp";
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valtmp = document.getElementById(strtmp).value;
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All[strtmp]=valtmp;
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LayersSec = LayersSec + strtmp +"="+ valtmp+"\n";
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strtmp = "L"+i+"rho";
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valtmp = document.getElementById(strtmp).value;
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All[strtmp]=valtmp;
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LayersSec = LayersSec + strtmp +"="+ valtmp+"\n";
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strtmp = "L"+i+"d";
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valtmp = document.getElementById(strtmp).value;
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All[strtmp]=valtmp;
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LayersSec = LayersSec + strtmp +"="+ valtmp+"\n";
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}
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// Prepare projectile parameters section
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let parProj = ["workPath","fileNamePrefix","ProjType","numberProj","z0","dz","valEnergy","sigEnergy","valAngle","sigAngle","ranSeed"];
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let ProjSec = "[ProjectileParameters]\n";
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for (key of parProj) {
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All[key]= document.getElementById(key).value;
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ProjSec = ProjSec + key + "=" + All[key] + "\n";
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}
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// Prepare Files section
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let FilesSec = "[Files]\n";
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FilesSec = FilesSec + "fileNamePrefix="+All["fileNamePrefix"]+"\nworkPath="+All["workPath"]+"\n";
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// Prepare ScanSequence section
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let ScanSec = "[ScanSequence]\n";
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strtmp = "scanSeq";
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valtmp = 1*(document.getElementById(strtmp).checked);
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All[strtmp]=valtmp;
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ScanSec = ScanSec + strtmp +"="+ valtmp+"\n";
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let parScan = ["comboScan","scanType","scanFrom","scanStep","scanTo","scanList","scanListdz"];
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for (key of parScan) {
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All[key]= document.getElementById(key).value;
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ScanSec = ScanSec + key + "=" + All[key] + "\n";
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}
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// Collect other parameters
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let parOther = ["parEF", "parESB", "parSHEATH", "parERC", "parRD", "parCA", "parKK0", "parKK0R", "parKDEE1", "parKDEE2", "parIPOT", "parIPOTR", "parIRL"];
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for (key of parOther) {
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All[key]= document.getElementById(key).value;
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}
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// Get the stopping power coefficient (SPC) flag
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All["flagSPC"] = document.getElementById("flagSPC").value;
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// Construct full content of cfg file
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TrimSPcfg = FilesSec + LayersSec + ProjSec + ScanSec;
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if (toggle) {
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return All;
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} else {
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return TrimSPcfg;
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}
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}
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function setValues(content) {
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// This function takes cfg file content and substitutes values in the GUI
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// Split file content into lines
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var event = new Event('change');
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var lines = content.toString().split('\n');
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// Remove comment lines, empty lines and those starting with "["
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var PATTERN= /^(?!\[)(?!\#)(\S)/,
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flines = lines.filter(function (str) {return PATTERN.test(str);});
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for (var i=0; i<flines.length; i++) {
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// Loop over parameters, set appropriate values and trigger associated onChange
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var param=flines[i].replace(/\s+/,'').split('=');
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if (param[0] == 'scanSeq') {
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// This is a checkbox
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var seqChecked = true;
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if (param[1] == 0) {seqChecked = false;}
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document.getElementById(param[0]).checked = seqChecked;
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document.getElementById(param[0]).dispatchEvent(event);
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} else {
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document.getElementById(param[0]).value = param[1];
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document.getElementById(param[0]).dispatchEvent(event);
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}
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}
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}
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function CreateInpFile() {
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// Create and return input file for the Trim.SP simulation binary
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// Takes object All as input for all relevant parameters
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// This is the form of the begining of the input file:
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var TemplateFile = "ProjZ ProjAM valEnergy sigEnergy valAngle sigAngle parEF parESB parSHEATH parERC\n"
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TemplateFile += "numberProj ranSeed ranSeed ranSeed z0 parRD dz parCA parKK0 parKK0R parKDEE1 parKDEE2 parIPOT parIPOTR parIRL";
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// Then comes the number of layers (new format) for example 4 layers:
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// N_Layers=4
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TemplateFile=TemplateFile+"\n"+"N_Layers=numLayer";
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// Then loop over the layers and for each give the following structure
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// chemical formula, thickness, density, correction factor, number of elements
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var TemplateLayer = "L1Comp L1d L1rho L1CK L1Elem\n";
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// Z number of elements
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TemplateLayer += "L1ELZ1 L1ELZ2 L1ELZ3 L1ELZ4 L1ELZ5\n";
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// A number of elements
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TemplateLayer += "L1ELW1 L1ELW2 L1ELW3 L1ELW4 L1ELW5\n";
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// Weigth of element in composition
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TemplateLayer += "L1ELC1 L1ELC2 L1ELC3 L1ELC4 L1ELC5\n";
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// Surface binding energy of elements
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TemplateLayer += "L1ELE1 L1ELE2 L1ELE3 L1ELE4 L1ELE5\n";
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// Displacement energy of elements, always 30 eV??
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TemplateLayer += "L10301 L10302 L10303 L10304 L10305\n";
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// Bulk binding energy of elements, usually zero
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TemplateLayer += "0 0 0 0 0\n";
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// value A-1 of the ziegler tables
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TemplateLayer += "L1ELST11 L1ELST21 L1ELST31 L1ELST41 L1ELST51\n";
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// value A-2 of the ziegler tables
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TemplateLayer += "L1ELST12 L1ELST22 L1ELST32 L1ELST42 L1ELST52\n";
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// value A-3 of the ziegler tables
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TemplateLayer += "L1ELST13 L1ELST23 L1ELST33 L1ELST43 L1ELST53\n";
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// value A-4 of the ziegler tables
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TemplateLayer += "L1ELST14 L1ELST24 L1ELST34 L1ELST44 L1ELST54\n";
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// value A-5 of the ziegler tables
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TemplateLayer += "L1ELST15 L1ELST25 L1ELST35 L1ELST45 L1ELST55";
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let projectile = All['ProjType'];
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All['ProjZ'] = elemPars[projectile].Z;
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All['ProjAM'] = elemPars[projectile].A;
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// This is the flag for checking layers
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let Check=0;
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let Layer='';
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// Loop over layers an create appropriate values
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for (var i=1; i<=All['numLayer'];i++){
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// Arry containing 12 lines for each layer
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let newLayer = ["","","","","","","","","","","",""];
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Check=0;
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// Composition of layers
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let LComp="L"+i+"Comp";
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let Comp = All[LComp];
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if (Comp == "" || typeof Comp == 'undefined') {Check++;}
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let LElComp=parse_formula(Comp);
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for (key of Object.keys(LElComp)) {
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// Check if composition is understood
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if (key=="" || elemPars[key].Z =="") {
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Check++;
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}
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}
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// 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;
|
|
}
|
|
}
|
|
|