From 1dff2798a12004f361ec68603f780e266c1c8b81 Mon Sep 17 00:00:00 2001
From: Zaher Salman <zaher.salman@psi.ch>
Date: Thu, 27 Aug 2015 15:50:33 +0200
Subject: [PATCH] Fixed some bugs and cleaned up the code.

---
 trimsp/src/TrimSPGUI4/TrimSPGUI4.pm | 23 +++++++++++++++--------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/trimsp/src/TrimSPGUI4/TrimSPGUI4.pm b/trimsp/src/TrimSPGUI4/TrimSPGUI4.pm
index 1f5cb35..8f93810 100644
--- a/trimsp/src/TrimSPGUI4/TrimSPGUI4.pm
+++ b/trimsp/src/TrimSPGUI4/TrimSPGUI4.pm
@@ -359,7 +359,11 @@ sub CreateInpFile
 	my $Comp = this->{ui}->layerTable->item($i-1,0)->text();
 	$All{$LComp} = $Comp;
 	my %LElComp=Chem::parse_formula($Comp);
-	foreach my $key (keys %LElComp) {if ($key eq "") {$Check++;}}
+	foreach my $key (keys %LElComp) {
+	    if ($key eq "") {
+		$Check++;
+	    }
+	}
 	if ($Comp eq "") {$Check++;}
 # Write composition to results file header
 	
@@ -393,19 +397,23 @@ sub CreateInpFile
 	if ($Sum==0) {$Sum=1;}
 		
 	my @Els = keys %LElComp;
-	#print join("--",@Els)."\n";
-	my $El="";
+
 	for (my $NEl=1;$NEl<=5;$NEl++) {
-	    if ($NEl <= $#Els) {
+	    my $El = "";
+	    if ($#Els >= $NEl-1) {
 		$El = $Els[$NEl-1];
 	    }
 	    my $LEkey = "L".$i."EL";
 	    my $ElZ = Chem::Zof($El);
 	    my $ElW = Chem::Massof($El);
-	    my $ElC = $LElComp{$El}/$Sum;
 	    my $ElE = Chem::Elastof($El);
+	    my $ElC = 0;
 	    my $El030 = 30;
-	    if ($El eq "") { $El030 = 0.0;}
+	    if ($El) {
+		$ElC = $LElComp{$El}/$Sum;
+	    } else {
+		$El030 = 0.0;
+	    }
 	    
 	    $All{$LEkey."Z".$NEl}=sprintf("%8.4f",$ElZ);
 	    $All{$LEkey."W".$NEl}=sprintf("%8.4f",$ElW);
@@ -571,7 +579,6 @@ sub StartSequenceOne
 	    }
 	    $iScan++;
 	    print "iScan=".$iScan."\n";
-
 	}
     } else {
 # For a single run
@@ -695,7 +702,7 @@ sub OpenFile
 	my $Attrib="";
 	foreach my $line (@lines) {
 # Remove white spaces
-#	    $line =~ s/\s+//g;	    
+	    $line =~ s/\s+//g;	    
 	    my @InitPar = split (/=/,$line);
 # Check it is not empty or title line
 	    if ($InitPar[0] || $InitPar[1]) {