1) M3C.analysis now shows only one-way reactions to simplify the reac…

…tions network

2) M3C.viewXYZ new uses by default converted to generate the .eps files. It is neccesary to check if the convert's bug is already fixed in all ubuntu platforms
3) molecule.ZPE now returns the ZPE value even for transition states by ignoring negative frequencies

src/M3C.analysis

@@ -1686,6 +1686,8 @@ function averReactionsDiagram()
 	local eDistfile=`getValueFromIFIle ${iFile%.*}.m3c FIT_BRANCHING_RATIOS:eDistfile`
 
 	echo "strict digraph G {" > .dataReac-$$.dot
+# 	echo "overlap=scalexy; //false, compress, ..." >> .dataReac-$$.dot
+# 	echo "sep=\"+1\"; // 0.1, +1" >> .dataReac-$$.dot
 	echo "	rankdir=LR" >> .dataReac-$$.dot
 	echo "	node [shape=box,style=filled,fillcolor=yellow,color=black]" >> .dataReac-$$.dot
 
@@ -1695,7 +1697,7 @@ function averReactionsDiagram()
 		weight=`n1df.evaluate $eDistfile $E`
 
 		grep ".*(.*\-\->" $f \
-			| awk '{$1=$1*$weight; print $0}' \
+			| awk '{$1=$1*'"$weight"'; print $0}' \
 			| sed -E 's/\([[:alnum:]]+\)//g' \
 			| awk '{r=$2;split($2,arr,"-->"); if( arr[1]!=arr[2] ) print $0}'
 	done ) | \
@@ -1707,7 +1709,29 @@ function averReactionsDiagram()
 		for(k in map)
 			if( map[k]/sum > '$maxP' )
 				printf "%10.5f  %s\n", map[k]/sum, k
-	}' | sed 's/-->/"->"/g' \
+	}' \
+	| gawk '
+	{
+		r=$2
+		split($2,arr,"-->")
+		line[arr[1]"-->"arr[2]]=$1
+		
+		if( arr[2]"-->"arr[1] in line ){
+			if( $1 > line[arr[2]"-->"arr[1]] ){
+				delete line[arr[2]"-->"arr[1]]
+			}else{
+				delete line[arr[1]"-->"arr[2]]
+			}
+		}
+	}
+	END{
+		for( k in line ){
+			print line[k], k
+			print line[k], k > "/dev/stderr"
+		}
+	}
+	' \
+	| sed 's/-->/"->"/g' \
 	| gawk '
 		{
 			print "\""$2"\"", "[label="$1",fontcolor=blue]"
@@ -2062,8 +2086,8 @@ EOF
 		smoothStrength=4e3
 # 		smoothThr="1e-9"
 		smoothThr="1e-4"
-		errFact=0.1 # << SSeq
-# 		errFact=1.0 # << Srand
+# 		errFact=0.1 # << SSeq
+		errFact=1.0 # << Srand
 
 # 		if [ "`echo "${keys[$(($i-1))]}" | sed 's/\// /g' | wc -w`" -eq 3 ]
 # 		then
@@ -2590,6 +2614,7 @@ function channelBRDiagram()
 	'"`cat $M3C_HOME/utils/M3CUtils.gawk`"'   # Debería ser la anterior linea, pero solo está disponible para gawk >= 2011
 	($1!~/^#/){
 		print reduceM3CLabel($1), $2, $3, $4
+# 		print reduceM3CLabel($1), $2, 0.0, 0.0
 	}' tmp-$$ > $BRFile
 	rm tmp-$$
 
@@ -2600,6 +2625,7 @@ function channelBRDiagram()
 	sed -i -r '{s/([[:alpha:]]+)p/\1^{+}/g}' $BRFile  # Escribir bien los superindices, caso Cp(??)
 	sed -i -r '{s/([[:alpha:]]+)([[:digit:]]+)/\1_{\2}/g}' $BRFile  # Escribir bien los superindices, caso C_2(??)
 
+	cat $BRFile
 	yMax=`gawk '($0!~/#/){printf "%s\n%s\n",$2,$3}' $BRFile | sort -k 1 -n | tail -n1`
 	yErrorMax=`gawk '($0!~/#/){printf "%s\n",$4}' $BRFile | sort -k 1 -n | tail -n1`
 	yMax=`echo "$yMax+$yErrorMax" | bc -l` 

src/M3C.viewXYZ

@@ -78,13 +78,13 @@ function convertImage()
   local iFile=$1
   local oFile=$2
 
-  if [ "$CONVERTER" = "convert" ]
-  then
+#  if [ "$CONVERTER" = "convert" ]
+#  then
     convert $iFile $oFile > /dev/null 2>&1
-  elif [ "$CONVERTER" = "inkscape" ]
-  then
-    inkscape -z -f $iFile -E $oFile > /dev/null 2>&1
-  fi
+#  elif [ "$CONVERTER" = "inkscape" ]
+#  then
+#    inkscape -z -f $iFile -E $oFile > /dev/null 2>&1
+#  fi
 }
 
 ##

src/Makefile

@@ -4,7 +4,7 @@ FCFLAGS = -static -static-intel -static-libgcc -traceback -w -I. -g -fpp -mkl -I
 LDFLAGS = -L${HOME}/Develop/scift/src -lscift
 TLIB = 
 
-all: AzizSlamanPotential.o Fragment.o FragmentsDB.o FragmentsListBase.o FragmentsList.o GOptionsM3C.o MarkovChain.o ModelPotential.o NNLS.o Reactor.o  $(TLIB) M3CBR M3C M3CfitBR 
+all: AzizSlamanPotential.o Fragment.o FragmentsDB.o FragmentsListBase.o FragmentsList.o GOptionsM3C.o MarkovChain.o ModelPotential.o NNLS.o Reactor.o  $(TLIB) M3CBR M3C M3CfitBR molecule.ZPE 
 
 AzizSlamanPotential.o azizslamanpotential_.mod: AzizSlamanPotential.f90 
 	fmake
@@ -61,6 +61,11 @@ ModelPotential.o modelpotential_.mod: ModelPotential.f90 goptionsm3c_.mod azizsl
 	echo -n 'Building ModelPotential.f90 '
 	time -f "(%E)" $(FC) $(FCFLAGS) -c ModelPotential.f90
 
+molecule.ZPE: molecule.ZPE.f90 Fragment.o GOptionsM3C.o fragment_.mod goptionsm3c_.mod
+	fmake
+	echo -n 'Building molecule.ZPE.f90 '
+	time -f "(%E)" $(FC) $(FCFLAGS) molecule.ZPE.f90 Fragment.o GOptionsM3C.o -o molecule.ZPE $(LDFLAGS)
+
 NNLS.o nnls_.mod: NNLS.f90 
 	fmake
 	echo -n 'Building NNLS.f90 '
@@ -72,10 +77,10 @@ Reactor.o reactor_.mod: Reactor.f90 fragment_.mod azizslamanpotential_.mod gopti
 	time -f "(%E)" $(FC) $(FCFLAGS) -c Reactor.f90
 
 clean:
-	rm -f *.o *.mod *~ .deps M3CBR M3C M3CfitBR  2> /dev/null
+	rm -f *.o *.mod *~ .deps M3CBR M3C M3CfitBR molecule.ZPE  2> /dev/null
 
 distclean:
-	rm -f *.o *.mod *~ .deps Makefile M3CBR M3C M3CfitBR  2> /dev/null
+	rm -f *.o *.mod *~ .deps Makefile M3CBR M3C M3CfitBR molecule.ZPE  2> /dev/null
 
 Makefile: .deps
 	fmake

src/molecule.ZPE.f90

@@ -50,6 +50,7 @@ program main
 	character(1000) :: sBuffer
 	type(String) :: iFileName
 	type(Fragment) :: mol
+	real(8) :: ZPE
 
 	if( command_argument_count() < 1 ) then
 		write(*,*) "## ERROR ## Number of Parameter == 1"
@@ -62,5 +63,11 @@ program main
 	call mol.init()
 	call mol.loadRXYZ( iFileName.fstr )
 
-	write(*,"(F20.5,A)") mol.ZPE/eV, " eV"
+	ZPE = 0.0_8
+	if( mol.nAtoms() > 1 ) then
+		ZPE = sum( merge(mol.vibFrequencies, 0.0_8,mol.vibFrequencies>0.0_8) )/2.0_8
+	end if
+
+! 	write(*,"(F20.5,A)") mol.ZPE/eV, " eV"
+	write(*,"(F20.5,A)") ZPE/eV, " eV"
 end program main