Fixed bug when handling a wrong chemical formula (issue MUSR-303).

trimsp/src/Chem.pm

@@ -83,19 +83,19 @@ sub internal_formula_parser {
 sub add_formula_strings {
     my ($formula, $coef, %elements) = @_;
 
-#  print "Getting Formula of $formula\n";
+    if ($formula =~ /^(?:([A-Z][a-z]*)(\d+\.?\d*)?)+$/o) {
-    $formula =~ /^(?:([A-Z][a-z]*)(\d+\.?\d*)?)+$/o # XXX new
+#        or die "Invalid Portion of Formula $formula";
-        or die "Invalid Portion of Formula $formula";
+	while ($formula =~ m/([A-Z][a-z]*)(\d+\.?\d*)?/go) { # XXX new
-    while ($formula =~ m/([A-Z][a-z]*)(\d+\.?\d*)?/go) { # XXX new
+	    my ($elm, $count) = ($1, $2);
-        my ($elm, $count) = ($1, $2);
+	    $count = 1 unless defined $count;
-        $count = 1 unless defined $count;
+	    if (defined $elements{$elm}) {
-        if (defined $elements{$elm}) {
+		$elements{$elm} += $count * $coef;
-            $elements{$elm} += $count * $coef;
+	    } else {
-        } else {
+		$elements{$elm} = $count * $coef;
-            $elements{$elm} = $count * $coef;
+	    }
-        }
+	}
+	return %elements;
     }
-    return %elements;
 }
 
 sub ParensBalanced {

trimsp/src/TrimSPGUI4/TrimSPGUI4.pm

@@ -31,7 +31,6 @@ use QtCore4::slots
     SaveFileAs => [];
 use Ui_TrimSPGUI4;
 
-
 sub NEW {
     my ( $class, $parent ) = @_;
     $class->SUPER::NEW($parent);
@@ -52,7 +51,7 @@ sub child {
 sub CollectValues
 {
     my %All=();
-    $All{"numLayer"}=this->{ui}->numLayer->value();
+    $All{"numLayer"}= this->{ui}->numLayer->value();
 # Collect layers parameters
     for (my $i=1;$i<=$All{"numLayer"};$i++) {
 	my $LComp = "L".$i."Comp";
@@ -353,7 +352,9 @@ 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 "") {$Check++;}}
 	if ($Comp eq "") {$Check++;}
+# Write composition to results file header
 	
 # Densities of layers
 	my $Lrho="L".$i."rho";
@@ -369,7 +370,7 @@ sub CreateInpFile
 	
 # Sanity check, is the layer supposed to have value? are they all there?
 	if ($Check!=0) {
-	    my $ErrMsg="Error: Layer $i is empty. Expecting it to be defined!\n";
+	    my $ErrMsg="Error: Layer $i is empty or bad chemical formula.\nPleach check!\n";
 	    print STDERR $ErrMsg;
 	    my $HelpWindow = Qt::MessageBox::information( this, "Error!",$ErrMsg);
 	    return("ERROR");
@@ -417,10 +418,9 @@ sub CreateInpFile
     }
     
     foreach my $key (keys %All) {
-#	print $key,$All{$key},"\n";
 	if ($All{$key} ne ""){
 	    $TemplateFile =~ s/$key/$All{$key}/;
-# Seed repeats three times
+	    # Seed repeats three times
 	    if ($key eq "ranSeed") { $TemplateFile =~ s/$key/$All{$key}/g;}
 	}
     }
@@ -477,6 +477,8 @@ sub StartSequenceOne
     my @SdzValues=();
     my $cmd="";
     
+    my @called = caller;
+    print "pck=".$called[0]." fln=".$called[1]." line=".$called[2];
     if (!$ENV{'TRIMBIN'}) {
 # If trim.sp binary is not defined give warning and return
 	my $Warning = Qt::MessageBox::information( this, "Warning!",
@@ -492,7 +494,9 @@ sub StartSequenceOne
     }
     
     my $Progress=0;
+    $All{"SdzFlag"}=0;
     if ($All{"scanSeq"}) {
+# For multiple runs or a scan
 	if ($All{"radioList"}) {
 	    @SValues=split(/,/,$All{"scanList"});
 	    @SdzValues=split(/,/,$All{"scanListdz"});
@@ -522,7 +526,7 @@ sub StartSequenceOne
 	    $ScanAttrib = child("Qt::LineEdit","numberProj");
 	} elsif ($All{"comboScan"}==5) { 
 	    $ScanName = "Ld".$All{"scandL"};
-	    $ScanAttrib = this->{ui}->layerTable->item($All{"ScandL"}-1,2);
+	    $ScanAttrib = this->{ui}->layerTable->item($All{"scandL"}-1,2);
 	}
 	
 	my $iScan=0;
@@ -541,17 +545,26 @@ sub StartSequenceOne
 	    open (INPF,q{>}, "$FILENAME.inp" );
 	    print INPF $eingabe1;
 	    close(INPF);
-# Use Linux version	    
+	    # Use Linux version	    
 	    $Progress=$Progress+90/$#SValues;
 	    this->{ui}->progress->setValue($Progress);
 	    this->{ui}->progress->update();
 	    $cmd = "cp $FILENAME.inp eingabe1.inp; ".$ENV{'TRIMBIN'};
-	    system($cmd);
+	    my $pid = fork();
+	    die "Unable to fork: $!" unless defined($pid);
+	    if (!$pid) {  # child
+	     	exec($cmd);
+	     	die "Unable to exec: $!";
+	    }	
+	    while (wait () != -1){}
+	    #system($cmd);
 	    
 	    foreach ("err","out","rge") {
 		system("mv -f ausgabe1.$_ $FILENAME.$_");
 	    }
 	    $iScan++;
+	    print "iScan=".$iScan."\n";
+
 	}
     } else {
 # For a single run
@@ -563,25 +576,38 @@ sub StartSequenceOne
 	close(INPF);
 	$Progress=20;
 	this->{ui}->progress->setValue($Progress);
+	this->{ui}->progress->update();
 	
 # Use Linux version
 	$cmd = "cp $FILENAME.inp eingabe1.inp; ".$ENV{'TRIMBIN'};
-	system($cmd);
+	my $pid = fork();
+	die "Unable to fork: $!" unless defined($pid);
+	if (!$pid) {  # child
+	    exec($cmd);
+	    die "Unable to exec: $!";
+	}	
+	while (wait () != -1){}
+        #system($cmd);
 	foreach ("err","out","rge") {
 	    system("mv -f ausgabe1.$_ $FILENAME.$_");
 	}
 	$Progress=90;
 	this->{ui}->progress->setValue($Progress);
+	this->{ui}->progress->update();
+	sleep(10);
     }
+
 # Move the fort.33 file into the subdirectory and change its name
     $cmd="rm -f eingabe1.inp; mv -f fort.33 ".$All{"workPath"}."/".$All{"fileNamePrefix"}."_Seq_Results.dat";
     system($cmd);
     $Progress=100;
     this->{ui}->progress->setValue($Progress);
+    this->{ui}->progress->update();
     undef %All;
     undef $cmd;
     print "at end\n";
-    return(1);
+    sleep(10);
+    return(0);
 }
 
 
@@ -790,7 +816,13 @@ sub PlotProfiles
 	my $TrimPath = $ENV{'PERLLIB'};	
 # Now that we have the file list send it to root macro for plotting.
 	my $cmd='root -n -l "'.$TrimPath.'/../plotRge.C(\"'.$filenames.'\")"&';
-	my $pid=system($cmd);	
+	my $pid = fork();
+	die "Unable to fork: $!" unless defined($pid);
+	if (!$pid) {  # child
+	    exec($cmd);
+	    die "Unable to exec: $!";
+	}	
+	# my $pid=system($cmd);	
     }
 }
 
@@ -809,7 +841,13 @@ sub PlotFraction
 	my $TrimPath = $ENV{'PERLLIB'};	
 # Now that we have the file name send it to root macro for plotting.
 	my $cmd='root -n -l "'.$TrimPath.'/../plotFrc.C(\"'.$file.'\")"&';
-	my $pid=system($cmd);	
+	my $pid = fork();
+	die "Unable to fork: $!" unless defined($pid);
+	if (!$pid) {  # child
+	    exec($cmd);
+	    die "Unable to exec: $!";
+	}	
+	# my $pid=system($cmd);	
     }
 }
 
@@ -827,7 +865,13 @@ sub PlotMean
 	my $TrimPath = $ENV{'PERLLIB'};	
 # Now that we have the file name send it to root macro for plotting.
 	my $cmd='root -n -l "'.$TrimPath.'/../plotMean.C(\"'.$file.'\")"&';
-	my $pid=system($cmd);	
+	my $pid = fork();
+	die "Unable to fork: $!" unless defined($pid);
+	if (!$pid) {  # child
+	    exec($cmd);
+	    die "Unable to exec: $!";
+	}	
+	# my $pid=system($cmd);	
     }
 }
 

trimsp/src/plotFrc.C

@@ -154,6 +154,7 @@ void plotFrc(char *FileName)
     gr1->SetMarkerStyle(20);
     gr1->SetMarkerColor(TColor::kRed);
     gr1->SetLineColor(TColor::kRed);
+    // Preferably get the chemical formula from header
     legend->AddEntry(gr1,"Layer 1");
     mg->Add(gr1);
   }
@@ -164,6 +165,7 @@ void plotFrc(char *FileName)
     gr2->SetMarkerColor(TColor::kGreen);
     gr2->SetLineColor(TColor::kGreen);
     //  gr2->Draw("PC");
+    // Preferably get the chemical formula from header
     legend->AddEntry(gr2,"Layer 2");
     mg->Add(gr2);
   }
@@ -174,6 +176,7 @@ void plotFrc(char *FileName)
     gr3->SetMarkerColor(TColor::kBlue);
     gr3->SetLineColor(TColor::kBlue);
     //  gr3->Draw("PC");
+    // Preferably get the chemical formula from header
     legend->AddEntry(gr3,"Layer 3");
     mg->Add(gr3);
   }
@@ -184,6 +187,7 @@ void plotFrc(char *FileName)
     gr4->SetMarkerColor(TColor::kMagenta);
     gr4->SetLineColor(TColor::kMagenta);
     //  gr4->Draw("PC");
+    // Preferably get the chemical formula from header
     legend->AddEntry(gr4,"Layer 4");
     mg->Add(gr4);
   }
@@ -194,6 +198,7 @@ void plotFrc(char *FileName)
     gr5->SetMarkerColor(TColor::kOrange);
     gr5->SetLineColor(TColor::kOrange);
     //  gr5->Draw("PC");
+    // Preferably get the chemical formula from header
     legend->AddEntry(gr5,"Layer 5");
     mg->Add(gr5);
   }
@@ -204,6 +209,7 @@ void plotFrc(char *FileName)
     gr6->SetMarkerColor(TColor::kViolet);
     gr6->SetLineColor(TColor::kViolet);
     //  gr6->Draw("PC");
+    // Preferably get the chemical formula from header
     legend->AddEntry(gr6,"Layer 6");
     mg->Add(gr6);
   }
@@ -214,6 +220,7 @@ void plotFrc(char *FileName)
     gr7->SetMarkerColor(TColor::kAzure+7);
     gr7->SetLineColor(TColor::kAzure+7);
     //  gr7->Draw("PC");
+    // Preferably get the chemical formula from header
     legend->AddEntry(gr7,"Layer 7");
     mg->Add(gr7);
   }