From 6cc2ccf3534ed4560e41a5ad3b53edb532abd184 Mon Sep 17 00:00:00 2001
From: salman <zaher.salman@psi.ch>
Date: Wed, 25 Jan 2023 10:37:14 +0100
Subject: [PATCH] Fix bug in plotting multiple rge files.

---
 TrimSPlib.js | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/TrimSPlib.js b/TrimSPlib.js
index f9e2800..098ff96 100644
--- a/TrimSPlib.js
+++ b/TrimSPlib.js
@@ -1222,7 +1222,6 @@ function CreateInpFile() {
 	// Number of elements
 	let LElem = "L"+i+"Elem";
 	All[LElem] = Object.keys(LElComp).length;
-	console.log(LElem,All[LElem]);
 	
 	// Densities of layers
 	let Lrho="layer"+i+"rho";
@@ -1405,22 +1404,22 @@ function startSequence() {
 	// Single run: Start 
 	let eingabe1=CreateInpFile();
 	if (eingabe1=="ERROR") {return(0);}
-	let FILENAME=All["workPath"]+"/"+All["fileNamePrefix"]+"_"+ScanName+SValue;
-	writeAsciiFile(FILENAME+".inp",eingabe1);
+	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;
-	    cmd += "; mv -f ausgabe1.rge " + FILENAME + ".rge";
-	    cmd += "; mv -f ausgabe1.out " + FILENAME + ".out";
-	    cmd += "; mv -f ausgabe1.err " + FILENAME + ".err";
+	    //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(FILENAME+".rge");
+	let [cols,data]= readDatFile(All["workPath"]+"/"+FILENAME+".rge");
 	// convert depth to nm and normalize stopping profile
 	let depth=data[0];
 	let nmuons=data[1];
@@ -1457,7 +1456,8 @@ function startSequence() {
 
     // 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"] + ";rm -f eingabe1.inp; mv -f fort.33 " + seq_file;
+	cmd="cd " + All["workPath"] + "; mv -f fort.33 " + seq_file;
 	execute(cmd);
     }
     Progress=100;
@@ -1504,16 +1504,16 @@ function plotProfiles(filenames) {
     var plotDiv=win.document.getElementById("newPlot");
 
     // Extract energies from run files if available
-    var files= new Object();
+    //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];
+	//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]]);
+	let [cols,data]= readDatFile(filenames[i]);
 	// convert depth to nm and normalize profile
 	let depth=data[0];
 	let nmuons=data[1];