From 9ae79c8e98dcb1ebdf2ceeba08caa23c818c168b Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sat, 9 Feb 2019 21:23:43 -0700
Subject: [PATCH 01/57] First part about implementing transition states

---
 src/Fragment.f90    |  7 -------
 src/FragmentsDB.f90 | 29 ++++++++++++++++++-----------
 src/Reactor.f90     | 15 +++++++++++++++
 3 files changed, 33 insertions(+), 18 deletions(-)

diff --git a/src/Fragment.f90 b/src/Fragment.f90
index 513e4a4..f39cf10 100644
--- a/src/Fragment.f90
+++ b/src/Fragment.f90
@@ -389,15 +389,8 @@ end subroutine destroyFragment
 	subroutine updateFormula( this )
 		class(Fragment) :: this 
 		
-		integer :: isLineal
 		character(100), allocatable :: tokens(:)
 		
-		if( this.isLineal() ) then
-			isLineal = 1
-		else
-			isLineal = 0
-		end if
-		
 		this.dlabel_ = this.name
 		
 		call FString_split( this.name, tokens, "(" )
diff --git a/src/FragmentsDB.f90 b/src/FragmentsDB.f90
index a62abaa..ee1834d 100644
--- a/src/FragmentsDB.f90
+++ b/src/FragmentsDB.f90
@@ -62,6 +62,7 @@ module FragmentsDB_
 	use StringIntegerMap_
 	
 	use Fragment_
+	use FragmentsList_
 	use ModelPotential_
 	use GOptionsM3C_
 	
@@ -79,11 +80,11 @@ module FragmentsDB_
 		type(StringIntegerMap) :: forbiddenReactions
 		logical :: useForbiddenReactionsDetails
 		
-! 		"C2(d1)+C(t1)-->C3(s1)" --> 5 --> transitionState(5)
+! 		"C2(d1)+C(t1)-->C3(s1)" --> 5 . It means transitionState(5)
 ! 		|----------str2id_TS----------|
 		type(Fragment), allocatable :: transitionState(:)
 		type(StringIntegerMap) :: str2id_TS
-		logical, allocatable :: involvedInTS(:) ! One for each group. For speed purposes only.
+		logical, allocatable :: involvedInTS(:) ! One for each cluster. For speed purposes only.
 		
 		real(8), private :: energyReference_
 		logical, private :: useAtomicPotentials
@@ -360,6 +361,10 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 		character(100), allocatable :: tokens(:), tokens2(:), tokens3(:)
 		real(8) :: rBuffer
 		
+		! Only for transition states. They are neccessary to calculate the right label (mass sorted)
+		type(FragmentsList) :: reactives
+		type(FragmentsList) :: products
+		
 		if( allocated(this.transitionState) ) deallocate( this.transitionState )
 		allocate( this.transitionState(size(transitionStatesTable)) )
 		
@@ -395,28 +400,28 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 			! Choosing the reactives and products
 			!------------------------------------------
 			if( size(tokens) >= 9 .and. this.transitionState(i).nAtoms() /= 1 ) then
-				call FString_split( trim(adjustl(tokens(9))), tokens2, "-->" )
+				call FString_split( trim(adjustl(tokens(9))), tokens2, "<-->" )
 				
-				write(*,*) "Reactivos"
 				call FString_split( trim(adjustl(tokens2(1))), tokens3, "+" )
+				call reactives.init( size(tokens3) )
+				
 				do j=1,size(tokens3)
-					write(*,*) "token = ", trim(tokens3(j))
 					do k=1,size(this.clusters)
 						if( trim(tokens3(j)) == this.clusters(k).label() ) then
-							write(IO_STDOUT,*) k, this.clusters(k).id
+							reactives.clusters(j) = this.clusters(k)
 							this.involvedInTS(k) = .true.
 						end if
 					end do
 				end do
 				deallocate( tokens3 )
 				
-				write(*,*) "Productos"
 				call FString_split( trim(adjustl(tokens2(2))), tokens3, "+" )
+				call products.init( size(tokens3) )
+				
 				do j=1,size(tokens3)
-					write(*,*) "token = ", trim(tokens3(j))
 					do k=1,size(this.clusters)
 						if( trim(tokens3(j)) == this.clusters(k).label() ) then
-							write(IO_STDOUT,*) k, this.clusters(k).id
+							products.clusters(j) = this.clusters(k)
 							this.involvedInTS(k) = .true.
 						end if
 					end do
@@ -425,8 +430,10 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 				
 				deallocate( tokens2 )
 				
-				write(*,*) "Agregado: ", FString_toString(trim(adjustl(tokens(9)))//"-->"//trim(adjustl(tokens(10)))), ">>", i
-				call this.str2id_TS.insert( FString_toString(trim(adjustl(tokens(9)))//"-->"//trim(adjustl(tokens(10)))), i )
+				write(*,"(4X,A22,A)")  "Path = ", trim(reactives.label())//"<-->"//trim(products.label())
+				call this.str2id_TS.insert( FString_toString(trim(reactives.label())//"<-->"//trim(products.label())), i )
+				call this.str2id_TS.insert( FString_toString(trim(products.label())//"<-->"//trim(reactives.label())), i )
+				
 			else
 				call GOptions_error( &
 						"Bad number of atoms in transition state (N=0)", &
diff --git a/src/Reactor.f90 b/src/Reactor.f90
index fe839c1..600948a 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -112,6 +112,7 @@ module Reactor_
 			procedure, private, NOPASS :: isSpinForbidden
 			procedure, private, NOPASS :: reactorConstraint
 			procedure, private, NOPASS :: reactionString
+			procedure, private, NOPASS :: reduceToTransitionStates
 			
 			procedure :: execute
 			procedure :: executeMinFragmentationEnergy
@@ -315,6 +316,11 @@ subroutine changeComposition( this, dNfrag )
 				maxIterForbidden = maxIterForbidden + 1
 				cycle
 			else
+				
+				if( allocated(FragmentsDB_instance.transitionState) ) then
+					call reduceToTransitionStates( this.reactives, this.products )
+				end if
+				
 				exit
 			end if
 			
@@ -464,6 +470,15 @@ function reactionString( reactives, products, details ) result( output )
 		output = trim(reactives.label( details=effDetails ))//"-->"//trim(products.label( details=effDetails ))
 	end function reactionString
 	
+	!>
+	!! @brief Replaces products for the corresponding transition states. Only composition is changed
+	!!
+	subroutine reduceToTransitionStates( reactives, products )
+		type(FragmentsList), intent(in) :: reactives
+		type(FragmentsList), intent(inout) :: products
+		
+	end subroutine reduceToTransitionStates
+	
 	!>
 	!! @brief Change the composition of the system
 	!!

From 127e60378709a0e232752c0c2833893c029aea19 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 16:31:15 -0700
Subject: [PATCH 02/57] Second trial for TS. There is a bug when all products
 fit with one TS

---
 src/Reactor.f90 | 162 +++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 159 insertions(+), 3 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 600948a..910d369 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -57,13 +57,13 @@ module Reactor_
 	use IOStream_
 	use Timer_
 	use UnitsConverter_
-	use IVector_
 	use RandomUtils_
 	use StringList_
 	use AtomicElementsDB_
 	use BlocksIFileParser_
 	use RealHistogram_
 	use RealList_
+	use IntegerVector_
 	use StringIntegerMap_
 	use StringRealMap_
 	use StringRealPair_
@@ -92,6 +92,9 @@ module Reactor_
 		type(FragmentsList) :: products
 		logical :: state
 		
+		type(FragmentsList) :: productsTS
+		logical :: replaceTS
+		
 		character(3), private :: name
 		integer, private :: type
 		integer, allocatable :: dNFrag(:)
@@ -318,7 +321,9 @@ subroutine changeComposition( this, dNfrag )
 			else
 				
 				if( allocated(FragmentsDB_instance.transitionState) ) then
-					call reduceToTransitionStates( this.reactives, this.products )
+					call reduceToTransitionStates( this.reactives, this.products, this.productsTS )
+					
+					if( this.productsTS.nMolecules() > 0 ) this.replaceTS = .true.
 				end if
 				
 				exit
@@ -473,10 +478,157 @@ end function reactionString
 	!>
 	!! @brief Replaces products for the corresponding transition states. Only composition is changed
 	!!
-	subroutine reduceToTransitionStates( reactives, products )
+	subroutine reduceToTransitionStates( reactives, products, productsTS )
 		type(FragmentsList), intent(in) :: reactives
 		type(FragmentsList), intent(inout) :: products
+		type(FragmentsList), intent(out) :: productsTS
+		
+		integer :: i, j, id
+		integer :: ir, jr, kr
+		integer :: ip, jp, kp
+		type(IntegerVector) :: reactiveInTS
+		type(IntegerVector) :: productInTS
+		integer, allocatable :: reactiveInTScomb(:,:)
+		integer, allocatable :: productInTScomb(:,:)
+		integer :: nAtomsR, nAtomsP
+		integer :: massNumberR, massNumberP
+		type(FragmentsList) :: lReactives, lProducts
+		type(String) :: labelTS, label
+		logical :: locatedTS
+		
+		call reactiveInTS.init( resizeIncrement=reactives.nMolecules() )
+		call productInTS.init( resizeIncrement=products.nMolecules() )
+		
+		do i=1,reactives.nMolecules()
+			id = FragmentsDB_instance.getIdFromName( reactives.clusters(i).label() )
+			if( FragmentsDB_instance.involvedInTS( id ) ) then
+					call reactiveInTS.append( i )
+			end if
+		end do
 		
+		do i=1,products.nMolecules()
+			id = FragmentsDB_instance.getIdFromName( products.clusters(i).label() )
+			if( FragmentsDB_instance.involvedInTS( id ) ) then
+					call productInTS.append( i )
+			end if
+		end do
+		
+		if( .not. reactiveInTS.isEmpty() .and. .not. productInTS.isEmpty() ) then
+! 			write(*,"(A)",advance="no") "Reactives "
+! 			do i=1,reactives.nMolecules()
+! 				write(*,"(A)",advance="no") trim(reactives.clusters(i).label())//"+"
+! 			end do
+! 			write(*,*) ""
+! 			write(*,*) "reactiveInTS = ", reactiveInTS.data(1:reactiveInTS.size())
+! 			write(*,"(A)",advance="no") "Products "
+! 			do i=1,products.nMolecules()
+! 				write(*,"(A)",advance="no") trim(products.clusters(i).label())//"+"
+! 			end do
+! 			write(*,*) ""
+! 			write(*,*) "productInTS = ", productInTS.data(1:productInTS.size())
+			
+			locatedTS = .false.
+			
+			do ir=1,reactiveInTS.size()
+				call Math_combinations( reactiveInTS.size(), ir, reactiveInTScomb )
+				
+				do jr=1,size(reactiveInTScomb,dim=1)
+					
+					nAtomsR = 0
+					massNumberR = 0
+					do kr=1,size(reactiveInTScomb,dim=2)
+						massNumberR = massNumberR + reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) ).massNumber()
+						nAtomsR = nAtomsR + reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) ).nAtoms()
+					end do
+					
+					do ip=1,productInTS.size()
+						call Math_combinations( productInTS.size(), ip, productInTScomb )
+						
+						do jp=1,size(productInTScomb,dim=1)
+							
+							nAtomsP = 0
+							massNumberP = 0
+							do kp=1,size(productInTScomb,dim=2)
+								massNumberP = massNumberP + products.clusters( productInTS.at(productInTScomb(jp,kp)) ).massNumber()
+								nAtomsP = nAtomsP + products.clusters( productInTS.at(productInTScomb(jp,kp)) ).nAtoms()
+							end do
+							
+							if( massNumberR == massNumberP .and. nAtomsR > 1 .and. nAtomsP > 1 ) then
+								
+								call lReactives.init( size(reactiveInTScomb,dim=2) )
+								call lProducts.init( size(productInTScomb,dim=2) )
+								
+								do kr=1,size(reactiveInTScomb,dim=2)
+									lReactives.clusters(kr) = reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) )
+								end do
+							
+								do kp=1,size(productInTScomb,dim=2)
+									lProducts.clusters(kp) = products.clusters( productInTS.at(productInTScomb(jp,kp)) )
+								end do
+								
+								if( trim(lReactives.label()) /= trim(lProducts.label()) ) then
+									
+									labelTS = trim(lReactives.label())//"<-->"//trim(lProducts.label())
+									
+									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "      reactives = ", trim(reactives.label())
+										write(*,*) "       products = ", trim(products.label())
+										write(*,*) "     TS located = ", trim(labelTS.fstr)
+									end if
+									
+									call productsTS.init( products.nMolecules() - lProducts.nMolecules() + 1 )
+									
+									! @TODO Aca el problema aparece cuando todos los productos estan en un TS como C(t1)+C(t1)+C(t1)
+									!       En este caso nunca se entra en el if
+									j=1
+									do i=1,products.nMolecules()
+										do kp=1,size(productInTScomb,dim=2)
+											label = trim(products.clusters( productInTS.at(productInTScomb(jp,kp)) ).label())
+											if( label /= trim(products.clusters(i).label()) &
+												.and. j<=lProducts.nMolecules() ) then
+												call productsTS.set( j, products.clusters(i) )
+												j = j+1
+												exit
+											end if
+										end do
+									end do
+									
+									call productsTS.set( j, &
+													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									
+									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
+									end if
+									
+									locatedTS = .true.
+									exit ! Only one TS is accepted. The one with minimum size
+									
+								end if
+								
+							end if
+							
+						end do
+						
+						if( locatedTS ) exit
+						
+					end do
+					
+					if( locatedTS ) exit
+					
+				end do
+				
+				if( locatedTS ) exit
+				
+			end do
+			
+		end if
+		
+		if( GOptions_debugLevel >= 2 ) then
+			write(*,*) ""
+		end if
+		
+		if( allocated(reactiveInTScomb) ) deallocate( reactiveInTScomb )
+		if( allocated(productInTScomb) ) deallocate( productInTScomb )
 	end subroutine reduceToTransitionStates
 	
 	!>
@@ -867,6 +1019,8 @@ subroutine run( this )
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				
@@ -947,6 +1101,8 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
+		if( this.replaceTS ) this.replaceTS = .false.
+		
 	end subroutine run
 	
 	!>

From a9a625b1728d12d261608eadb2087a4e5dfde6ea Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 17:05:57 -0700
Subject: [PATCH 03/57] Bug replacing products by TS fixed

---
 src/Reactor.f90 | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 910d369..e3dd10b 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -578,14 +578,17 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 									
 									call productsTS.init( products.nMolecules() - lProducts.nMolecules() + 1 )
 									
+									call productsTS.set( 1, &
+													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									
 									! @TODO Aca el problema aparece cuando todos los productos estan en un TS como C(t1)+C(t1)+C(t1)
 									!       En este caso nunca se entra en el if
-									j=1
+									j=2
 									do i=1,products.nMolecules()
 										do kp=1,size(productInTScomb,dim=2)
 											label = trim(products.clusters( productInTS.at(productInTScomb(jp,kp)) ).label())
 											if( label /= trim(products.clusters(i).label()) &
-												.and. j<=lProducts.nMolecules() ) then
+												.and. j<=productsTS.nMolecules() ) then
 												call productsTS.set( j, products.clusters(i) )
 												j = j+1
 												exit
@@ -593,8 +596,14 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 										end do
 									end do
 									
-									call productsTS.set( j, &
-													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									if( j==2 ) then
+										do i=1,products.nMolecules()
+											if( j<=productsTS.nMolecules() ) then
+												call productsTS.set( j, products.clusters(i) )
+												j = j+1
+											end if
+										end do
+									end if
 									
 									if( GOptions_debugLevel >= 2 ) then
 										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
@@ -1016,11 +1025,11 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				

From 0664677f31e7427dd90e80500f2d165895bbb132 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Wed, 13 Feb 2019 22:09:08 -0700
Subject: [PATCH 04/57] First version working with TS

---
 src/FragmentsDB.f90 |  1 +
 src/MarkovChain.f90 | 11 ++++++++---
 src/Reactor.f90     | 35 ++++++++++++++++++++++++++++-------
 3 files changed, 37 insertions(+), 10 deletions(-)

diff --git a/src/FragmentsDB.f90 b/src/FragmentsDB.f90
index ee1834d..3baaa84 100644
--- a/src/FragmentsDB.f90
+++ b/src/FragmentsDB.f90
@@ -377,6 +377,7 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 		
 		do i=1,size(transitionStatesTable)
 			call this.transitionState(i).fromMassTableRow( transitionStatesTable(i).fstr, id=i, store=store.fstr )
+			this.transitionState(i).isTransitionState = .true.
 			
 			call FString_split( transitionStatesTable(i).fstr, tokens, " " )
 			
diff --git a/src/MarkovChain.f90 b/src/MarkovChain.f90
index a34d07c..2c8e433 100644
--- a/src/MarkovChain.f90
+++ b/src/MarkovChain.f90
@@ -442,7 +442,7 @@ subroutine run( this, reactives )
 	! 							sBuffer = react.reactives.weightHistoryLine( origin )
 	! 						end if
 	! 					end if
-
+	
 						call react.run()
 						
 						! Si la energía cinetica es negativa
@@ -483,7 +483,12 @@ subroutine run( this, reactives )
 						
 							nTimesBlocked = 0  ! El bloqueo debe ser consecutivo, así que si no pasa por negative energy se cuenta nuevamente
 							
-							Pi = react.products.LnW()-react.reactives.LnW()
+							if( react.replaceTS ) then
+								react.replaceTS = .false.
+								Pi = react.productsTS.LnW()-react.reactives.LnW()
+							else
+								Pi = react.products.LnW()-react.reactives.LnW()
+							end if
 							
 							if( Pi > 0.0_8 ) then
 								if( trim(react.reactives.label( details=.false. )) /= trim(react.products.label( details=.false. )) ) then
@@ -518,7 +523,7 @@ subroutine run( this, reactives )
 										sBuffer = trim(react.reactives.label( details=.true. ))//"-->"//trim(react.products.label( details=.true. ))
 										call this.transitionDetHistogram.add( sBuffer )
 									end if
-
+									
 									react.reactives = react.products
 									
 									call GOptions_info( &
diff --git a/src/Reactor.f90 b/src/Reactor.f90
index e3dd10b..4a74d46 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -606,6 +606,7 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 									end if
 									
 									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "       products = ", trim(products.label())
 										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
 									end if
 									
@@ -1011,11 +1012,12 @@ subroutine run( this )
 		
 		real(8) :: min_dLnW
 		
-		integer :: n, nMin
+		integer :: nMin
 		real(8) :: rBuffer
 		type(String) :: sBuffer
 		
 		this.state = .true.
+		this.replaceTS = .false.
 		
 		call this.showReactorHeader()
 		
@@ -1025,8 +1027,6 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
@@ -1039,16 +1039,37 @@ subroutine run( this )
 ! 				call this.products.changeVibrationalEnergy()
 ! 				call this.products.changeGeometry()
 ! 				call this.products.changeOrientations()
+
+				if( this.replaceTS ) then
+					! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
+					call this.productsTS.setReactorEnergy( this.reactives.reactorEnergy() )
+					
+					! Para que fuerce los centros aleatorios en la siguiente iteración
+					this.productsTS.forceRandomCenters = .true.
+					
+					! Los productos utilizan parte de la energía
+					call this.productsTS.initialGuessFragmentsList()
+					
+! 					write(*,*) "reactive ", trim(this.reactives.label())
+! 					write(*,*) "products ", trim(this.products.label())
+! 					write(*,*) "TS located ", trim(this.productsTS.label())
+! 					sBuffer = this.products.energyHistoryLine()
+! 					write(*,"(A)") trim(sBuffer.fstr)
+! 					sBuffer = this.productsTS.energyHistoryLine()
+! 					write(*,"(A)") trim(sBuffer.fstr)
+					
+				end if
 				
 			case( VIBRATIONAL_REACTOR )
-				
+			
 				! La composición es igual antes y después
 				this.products = this.reactives
 				
 				! Los productos utilizan parte de la energía cinética en vibracional
 				call this.products.changeVibrationalEnergy()
-			
+				
 			case( TRANSLATIONAL_REACTOR )
+			
 				! La composición es igual antes y después
 				this.products = this.reactives
 				
@@ -1056,11 +1077,13 @@ subroutine run( this )
 				call this.products.changeGeometry()
 				
 			case( ROTATIONAL_REACTOR )
+			
 				! La composición es igual antes y después
 				this.products = this.reactives
 				
 				! Los productos utilizan parte de la energía
 				call this.products.changeOrientations()
+				
 		end select
 		
 		if( GOptions_printLevel >= 2 ) then
@@ -1110,8 +1133,6 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
-		if( this.replaceTS ) this.replaceTS = .false.
-		
 	end subroutine run
 	
 	!>

From 8d1b53a0cfb2b65a781b341c11761e81b38ed3ac Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Wed, 13 Feb 2019 22:10:35 -0700
Subject: [PATCH 05/57] Version updated

---
 VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/VERSION b/VERSION
index cd5ac03..2789166 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2.0
+2.1a

From e7ea48b5b1d933daacbbf85e74a306ef3fdead59 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Thu, 28 Feb 2019 23:22:23 -0700
Subject: [PATCH 06/57] Gaussian template freqs updated to improve symmetry
 detection

---
 templates/b3lyp.freqs-GAUSSIAN.inp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/b3lyp.freqs-GAUSSIAN.inp b/templates/b3lyp.freqs-GAUSSIAN.inp
index e8e1d55..0d144fa 100644
--- a/templates/b3lyp.freqs-GAUSSIAN.inp
+++ b/templates/b3lyp.freqs-GAUSSIAN.inp
@@ -1,4 +1,4 @@
-#p b3lyp/6-311++G(3df,2p) freq
+#p b3lyp/6-311++G(3df,2p) freq IOp(2/17=3) IOp(2/18=3)
 
  b3lyp opt
 

From 9755ba4201baf154da4e105158714155cdd043f5 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 3 Mar 2019 01:48:59 -0700
Subject: [PATCH 07/57] M3C.check now checks the right value of the
 multiplicity based on the stoichiometry and charge

---
 src/M3C.check | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/src/M3C.check b/src/M3C.check
index 37c2f37..28fd605 100755
--- a/src/M3C.check
+++ b/src/M3C.check
@@ -146,8 +146,19 @@ function checkConsistence()
 			kill $$
 		fi
 		
-		if [[ ! "$multID" =~ ^m[1-9]+$ ]]
+		if [[ "$multID" =~ ^m[1-9]+$ ]]
 		then
+			minMult=`molecule.minMult $ifile ${chargeID#q}`
+			
+			if [ ! "$multID" = "m$(($minMult+0))" -a  ! "$multID" = "m$(($minMult+2))" \
+					-a  ! "$multID" = "m$(($minMult+4))" -a  ! "$multID" = "m$(($minMult+6))" ]
+			then
+				echo ""
+				echo -n "### ERROR ### Inconsistency in multiplicity ( $multID --> "
+				echo "m$(($minMult+0)), m$(($minMult+2)), m$(($minMult+4)), or m$(($minMult+6)) ) )"
+				kill $$
+			fi
+		else
 			echo ""
 			echo "### ERROR ### Inconsistency in multID ( $multID --> m[1-9]+ )"
 			kill $$

From 655336c80e694ecf7c977809fe148645a42e8c34 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Tue, 5 Mar 2019 20:46:53 -0700
Subject: [PATCH 08/57] oGaussian2rxyz bug fixed

---
 utils/oGaussian2rxyz.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/utils/oGaussian2rxyz.sh b/utils/oGaussian2rxyz.sh
index 62be55e..b28e1a3 100755
--- a/utils/oGaussian2rxyz.sh
+++ b/utils/oGaussian2rxyz.sh
@@ -114,7 +114,7 @@ then
 		echo "ELECTRONIC_STATE ??"
 	else
 		#group=`grep "Full point group" $iFile | tail -n1 | gawk '{print $4}'`
-		group=`grep "Framework group" $iFile | sed 's/\[/ /g' | gawk '{print $3}'`
+		group=`grep "Framework group" $iFile | sed 's/\[/ /g' | gawk '{print $3}' | tail -n1`
 		if [ "$group" = "Nop" -o "$group" = "NOp" ]
 		then
 			echo "SYMMETRY ??"

From d2c7d410931f87774c0ccbf6af30e775a809b3f9 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sat, 9 Feb 2019 21:23:43 -0700
Subject: [PATCH 09/57] First part about implementing transition states

---
 src/Fragment.f90    |  7 -------
 src/FragmentsDB.f90 | 29 ++++++++++++++++++-----------
 src/Reactor.f90     | 15 +++++++++++++++
 3 files changed, 33 insertions(+), 18 deletions(-)

diff --git a/src/Fragment.f90 b/src/Fragment.f90
index 513e4a4..f39cf10 100644
--- a/src/Fragment.f90
+++ b/src/Fragment.f90
@@ -389,15 +389,8 @@ end subroutine destroyFragment
 	subroutine updateFormula( this )
 		class(Fragment) :: this 
 		
-		integer :: isLineal
 		character(100), allocatable :: tokens(:)
 		
-		if( this.isLineal() ) then
-			isLineal = 1
-		else
-			isLineal = 0
-		end if
-		
 		this.dlabel_ = this.name
 		
 		call FString_split( this.name, tokens, "(" )
diff --git a/src/FragmentsDB.f90 b/src/FragmentsDB.f90
index a62abaa..ee1834d 100644
--- a/src/FragmentsDB.f90
+++ b/src/FragmentsDB.f90
@@ -62,6 +62,7 @@ module FragmentsDB_
 	use StringIntegerMap_
 	
 	use Fragment_
+	use FragmentsList_
 	use ModelPotential_
 	use GOptionsM3C_
 	
@@ -79,11 +80,11 @@ module FragmentsDB_
 		type(StringIntegerMap) :: forbiddenReactions
 		logical :: useForbiddenReactionsDetails
 		
-! 		"C2(d1)+C(t1)-->C3(s1)" --> 5 --> transitionState(5)
+! 		"C2(d1)+C(t1)-->C3(s1)" --> 5 . It means transitionState(5)
 ! 		|----------str2id_TS----------|
 		type(Fragment), allocatable :: transitionState(:)
 		type(StringIntegerMap) :: str2id_TS
-		logical, allocatable :: involvedInTS(:) ! One for each group. For speed purposes only.
+		logical, allocatable :: involvedInTS(:) ! One for each cluster. For speed purposes only.
 		
 		real(8), private :: energyReference_
 		logical, private :: useAtomicPotentials
@@ -360,6 +361,10 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 		character(100), allocatable :: tokens(:), tokens2(:), tokens3(:)
 		real(8) :: rBuffer
 		
+		! Only for transition states. They are neccessary to calculate the right label (mass sorted)
+		type(FragmentsList) :: reactives
+		type(FragmentsList) :: products
+		
 		if( allocated(this.transitionState) ) deallocate( this.transitionState )
 		allocate( this.transitionState(size(transitionStatesTable)) )
 		
@@ -395,28 +400,28 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 			! Choosing the reactives and products
 			!------------------------------------------
 			if( size(tokens) >= 9 .and. this.transitionState(i).nAtoms() /= 1 ) then
-				call FString_split( trim(adjustl(tokens(9))), tokens2, "-->" )
+				call FString_split( trim(adjustl(tokens(9))), tokens2, "<-->" )
 				
-				write(*,*) "Reactivos"
 				call FString_split( trim(adjustl(tokens2(1))), tokens3, "+" )
+				call reactives.init( size(tokens3) )
+				
 				do j=1,size(tokens3)
-					write(*,*) "token = ", trim(tokens3(j))
 					do k=1,size(this.clusters)
 						if( trim(tokens3(j)) == this.clusters(k).label() ) then
-							write(IO_STDOUT,*) k, this.clusters(k).id
+							reactives.clusters(j) = this.clusters(k)
 							this.involvedInTS(k) = .true.
 						end if
 					end do
 				end do
 				deallocate( tokens3 )
 				
-				write(*,*) "Productos"
 				call FString_split( trim(adjustl(tokens2(2))), tokens3, "+" )
+				call products.init( size(tokens3) )
+				
 				do j=1,size(tokens3)
-					write(*,*) "token = ", trim(tokens3(j))
 					do k=1,size(this.clusters)
 						if( trim(tokens3(j)) == this.clusters(k).label() ) then
-							write(IO_STDOUT,*) k, this.clusters(k).id
+							products.clusters(j) = this.clusters(k)
 							this.involvedInTS(k) = .true.
 						end if
 					end do
@@ -425,8 +430,10 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 				
 				deallocate( tokens2 )
 				
-				write(*,*) "Agregado: ", FString_toString(trim(adjustl(tokens(9)))//"-->"//trim(adjustl(tokens(10)))), ">>", i
-				call this.str2id_TS.insert( FString_toString(trim(adjustl(tokens(9)))//"-->"//trim(adjustl(tokens(10)))), i )
+				write(*,"(4X,A22,A)")  "Path = ", trim(reactives.label())//"<-->"//trim(products.label())
+				call this.str2id_TS.insert( FString_toString(trim(reactives.label())//"<-->"//trim(products.label())), i )
+				call this.str2id_TS.insert( FString_toString(trim(products.label())//"<-->"//trim(reactives.label())), i )
+				
 			else
 				call GOptions_error( &
 						"Bad number of atoms in transition state (N=0)", &
diff --git a/src/Reactor.f90 b/src/Reactor.f90
index fe839c1..600948a 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -112,6 +112,7 @@ module Reactor_
 			procedure, private, NOPASS :: isSpinForbidden
 			procedure, private, NOPASS :: reactorConstraint
 			procedure, private, NOPASS :: reactionString
+			procedure, private, NOPASS :: reduceToTransitionStates
 			
 			procedure :: execute
 			procedure :: executeMinFragmentationEnergy
@@ -315,6 +316,11 @@ subroutine changeComposition( this, dNfrag )
 				maxIterForbidden = maxIterForbidden + 1
 				cycle
 			else
+				
+				if( allocated(FragmentsDB_instance.transitionState) ) then
+					call reduceToTransitionStates( this.reactives, this.products )
+				end if
+				
 				exit
 			end if
 			
@@ -464,6 +470,15 @@ function reactionString( reactives, products, details ) result( output )
 		output = trim(reactives.label( details=effDetails ))//"-->"//trim(products.label( details=effDetails ))
 	end function reactionString
 	
+	!>
+	!! @brief Replaces products for the corresponding transition states. Only composition is changed
+	!!
+	subroutine reduceToTransitionStates( reactives, products )
+		type(FragmentsList), intent(in) :: reactives
+		type(FragmentsList), intent(inout) :: products
+		
+	end subroutine reduceToTransitionStates
+	
 	!>
 	!! @brief Change the composition of the system
 	!!

From 8fdcc6045f8b94fb1dc104a30ed1064c7bbe7c23 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 16:31:15 -0700
Subject: [PATCH 10/57] Second trial for TS. There is a bug when all products
 fit with one TS

---
 src/Reactor.f90 | 162 +++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 159 insertions(+), 3 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 600948a..910d369 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -57,13 +57,13 @@ module Reactor_
 	use IOStream_
 	use Timer_
 	use UnitsConverter_
-	use IVector_
 	use RandomUtils_
 	use StringList_
 	use AtomicElementsDB_
 	use BlocksIFileParser_
 	use RealHistogram_
 	use RealList_
+	use IntegerVector_
 	use StringIntegerMap_
 	use StringRealMap_
 	use StringRealPair_
@@ -92,6 +92,9 @@ module Reactor_
 		type(FragmentsList) :: products
 		logical :: state
 		
+		type(FragmentsList) :: productsTS
+		logical :: replaceTS
+		
 		character(3), private :: name
 		integer, private :: type
 		integer, allocatable :: dNFrag(:)
@@ -318,7 +321,9 @@ subroutine changeComposition( this, dNfrag )
 			else
 				
 				if( allocated(FragmentsDB_instance.transitionState) ) then
-					call reduceToTransitionStates( this.reactives, this.products )
+					call reduceToTransitionStates( this.reactives, this.products, this.productsTS )
+					
+					if( this.productsTS.nMolecules() > 0 ) this.replaceTS = .true.
 				end if
 				
 				exit
@@ -473,10 +478,157 @@ end function reactionString
 	!>
 	!! @brief Replaces products for the corresponding transition states. Only composition is changed
 	!!
-	subroutine reduceToTransitionStates( reactives, products )
+	subroutine reduceToTransitionStates( reactives, products, productsTS )
 		type(FragmentsList), intent(in) :: reactives
 		type(FragmentsList), intent(inout) :: products
+		type(FragmentsList), intent(out) :: productsTS
+		
+		integer :: i, j, id
+		integer :: ir, jr, kr
+		integer :: ip, jp, kp
+		type(IntegerVector) :: reactiveInTS
+		type(IntegerVector) :: productInTS
+		integer, allocatable :: reactiveInTScomb(:,:)
+		integer, allocatable :: productInTScomb(:,:)
+		integer :: nAtomsR, nAtomsP
+		integer :: massNumberR, massNumberP
+		type(FragmentsList) :: lReactives, lProducts
+		type(String) :: labelTS, label
+		logical :: locatedTS
+		
+		call reactiveInTS.init( resizeIncrement=reactives.nMolecules() )
+		call productInTS.init( resizeIncrement=products.nMolecules() )
+		
+		do i=1,reactives.nMolecules()
+			id = FragmentsDB_instance.getIdFromName( reactives.clusters(i).label() )
+			if( FragmentsDB_instance.involvedInTS( id ) ) then
+					call reactiveInTS.append( i )
+			end if
+		end do
 		
+		do i=1,products.nMolecules()
+			id = FragmentsDB_instance.getIdFromName( products.clusters(i).label() )
+			if( FragmentsDB_instance.involvedInTS( id ) ) then
+					call productInTS.append( i )
+			end if
+		end do
+		
+		if( .not. reactiveInTS.isEmpty() .and. .not. productInTS.isEmpty() ) then
+! 			write(*,"(A)",advance="no") "Reactives "
+! 			do i=1,reactives.nMolecules()
+! 				write(*,"(A)",advance="no") trim(reactives.clusters(i).label())//"+"
+! 			end do
+! 			write(*,*) ""
+! 			write(*,*) "reactiveInTS = ", reactiveInTS.data(1:reactiveInTS.size())
+! 			write(*,"(A)",advance="no") "Products "
+! 			do i=1,products.nMolecules()
+! 				write(*,"(A)",advance="no") trim(products.clusters(i).label())//"+"
+! 			end do
+! 			write(*,*) ""
+! 			write(*,*) "productInTS = ", productInTS.data(1:productInTS.size())
+			
+			locatedTS = .false.
+			
+			do ir=1,reactiveInTS.size()
+				call Math_combinations( reactiveInTS.size(), ir, reactiveInTScomb )
+				
+				do jr=1,size(reactiveInTScomb,dim=1)
+					
+					nAtomsR = 0
+					massNumberR = 0
+					do kr=1,size(reactiveInTScomb,dim=2)
+						massNumberR = massNumberR + reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) ).massNumber()
+						nAtomsR = nAtomsR + reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) ).nAtoms()
+					end do
+					
+					do ip=1,productInTS.size()
+						call Math_combinations( productInTS.size(), ip, productInTScomb )
+						
+						do jp=1,size(productInTScomb,dim=1)
+							
+							nAtomsP = 0
+							massNumberP = 0
+							do kp=1,size(productInTScomb,dim=2)
+								massNumberP = massNumberP + products.clusters( productInTS.at(productInTScomb(jp,kp)) ).massNumber()
+								nAtomsP = nAtomsP + products.clusters( productInTS.at(productInTScomb(jp,kp)) ).nAtoms()
+							end do
+							
+							if( massNumberR == massNumberP .and. nAtomsR > 1 .and. nAtomsP > 1 ) then
+								
+								call lReactives.init( size(reactiveInTScomb,dim=2) )
+								call lProducts.init( size(productInTScomb,dim=2) )
+								
+								do kr=1,size(reactiveInTScomb,dim=2)
+									lReactives.clusters(kr) = reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) )
+								end do
+							
+								do kp=1,size(productInTScomb,dim=2)
+									lProducts.clusters(kp) = products.clusters( productInTS.at(productInTScomb(jp,kp)) )
+								end do
+								
+								if( trim(lReactives.label()) /= trim(lProducts.label()) ) then
+									
+									labelTS = trim(lReactives.label())//"<-->"//trim(lProducts.label())
+									
+									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "      reactives = ", trim(reactives.label())
+										write(*,*) "       products = ", trim(products.label())
+										write(*,*) "     TS located = ", trim(labelTS.fstr)
+									end if
+									
+									call productsTS.init( products.nMolecules() - lProducts.nMolecules() + 1 )
+									
+									! @TODO Aca el problema aparece cuando todos los productos estan en un TS como C(t1)+C(t1)+C(t1)
+									!       En este caso nunca se entra en el if
+									j=1
+									do i=1,products.nMolecules()
+										do kp=1,size(productInTScomb,dim=2)
+											label = trim(products.clusters( productInTS.at(productInTScomb(jp,kp)) ).label())
+											if( label /= trim(products.clusters(i).label()) &
+												.and. j<=lProducts.nMolecules() ) then
+												call productsTS.set( j, products.clusters(i) )
+												j = j+1
+												exit
+											end if
+										end do
+									end do
+									
+									call productsTS.set( j, &
+													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									
+									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
+									end if
+									
+									locatedTS = .true.
+									exit ! Only one TS is accepted. The one with minimum size
+									
+								end if
+								
+							end if
+							
+						end do
+						
+						if( locatedTS ) exit
+						
+					end do
+					
+					if( locatedTS ) exit
+					
+				end do
+				
+				if( locatedTS ) exit
+				
+			end do
+			
+		end if
+		
+		if( GOptions_debugLevel >= 2 ) then
+			write(*,*) ""
+		end if
+		
+		if( allocated(reactiveInTScomb) ) deallocate( reactiveInTScomb )
+		if( allocated(productInTScomb) ) deallocate( productInTScomb )
 	end subroutine reduceToTransitionStates
 	
 	!>
@@ -867,6 +1019,8 @@ subroutine run( this )
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				
@@ -947,6 +1101,8 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
+		if( this.replaceTS ) this.replaceTS = .false.
+		
 	end subroutine run
 	
 	!>

From ec3184353112fec3becc848576b1a2202a5ba8c5 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 17:05:57 -0700
Subject: [PATCH 11/57] Bug replacing products by TS fixed

---
 src/Reactor.f90 | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 910d369..e3dd10b 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -578,14 +578,17 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 									
 									call productsTS.init( products.nMolecules() - lProducts.nMolecules() + 1 )
 									
+									call productsTS.set( 1, &
+													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									
 									! @TODO Aca el problema aparece cuando todos los productos estan en un TS como C(t1)+C(t1)+C(t1)
 									!       En este caso nunca se entra en el if
-									j=1
+									j=2
 									do i=1,products.nMolecules()
 										do kp=1,size(productInTScomb,dim=2)
 											label = trim(products.clusters( productInTS.at(productInTScomb(jp,kp)) ).label())
 											if( label /= trim(products.clusters(i).label()) &
-												.and. j<=lProducts.nMolecules() ) then
+												.and. j<=productsTS.nMolecules() ) then
 												call productsTS.set( j, products.clusters(i) )
 												j = j+1
 												exit
@@ -593,8 +596,14 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 										end do
 									end do
 									
-									call productsTS.set( j, &
-													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									if( j==2 ) then
+										do i=1,products.nMolecules()
+											if( j<=productsTS.nMolecules() ) then
+												call productsTS.set( j, products.clusters(i) )
+												j = j+1
+											end if
+										end do
+									end if
 									
 									if( GOptions_debugLevel >= 2 ) then
 										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
@@ -1016,11 +1025,11 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				

From 5d1b6e75810b2fbe3e43d50979ab15558cdc1e35 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Wed, 13 Feb 2019 22:09:08 -0700
Subject: [PATCH 12/57] First version working with TS

---
 src/FragmentsDB.f90 |  1 +
 src/MarkovChain.f90 | 11 ++++++++---
 src/Reactor.f90     | 35 ++++++++++++++++++++++++++++-------
 3 files changed, 37 insertions(+), 10 deletions(-)

diff --git a/src/FragmentsDB.f90 b/src/FragmentsDB.f90
index ee1834d..3baaa84 100644
--- a/src/FragmentsDB.f90
+++ b/src/FragmentsDB.f90
@@ -377,6 +377,7 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 		
 		do i=1,size(transitionStatesTable)
 			call this.transitionState(i).fromMassTableRow( transitionStatesTable(i).fstr, id=i, store=store.fstr )
+			this.transitionState(i).isTransitionState = .true.
 			
 			call FString_split( transitionStatesTable(i).fstr, tokens, " " )
 			
diff --git a/src/MarkovChain.f90 b/src/MarkovChain.f90
index a34d07c..2c8e433 100644
--- a/src/MarkovChain.f90
+++ b/src/MarkovChain.f90
@@ -442,7 +442,7 @@ subroutine run( this, reactives )
 	! 							sBuffer = react.reactives.weightHistoryLine( origin )
 	! 						end if
 	! 					end if
-
+	
 						call react.run()
 						
 						! Si la energía cinetica es negativa
@@ -483,7 +483,12 @@ subroutine run( this, reactives )
 						
 							nTimesBlocked = 0  ! El bloqueo debe ser consecutivo, así que si no pasa por negative energy se cuenta nuevamente
 							
-							Pi = react.products.LnW()-react.reactives.LnW()
+							if( react.replaceTS ) then
+								react.replaceTS = .false.
+								Pi = react.productsTS.LnW()-react.reactives.LnW()
+							else
+								Pi = react.products.LnW()-react.reactives.LnW()
+							end if
 							
 							if( Pi > 0.0_8 ) then
 								if( trim(react.reactives.label( details=.false. )) /= trim(react.products.label( details=.false. )) ) then
@@ -518,7 +523,7 @@ subroutine run( this, reactives )
 										sBuffer = trim(react.reactives.label( details=.true. ))//"-->"//trim(react.products.label( details=.true. ))
 										call this.transitionDetHistogram.add( sBuffer )
 									end if
-
+									
 									react.reactives = react.products
 									
 									call GOptions_info( &
diff --git a/src/Reactor.f90 b/src/Reactor.f90
index e3dd10b..4a74d46 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -606,6 +606,7 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 									end if
 									
 									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "       products = ", trim(products.label())
 										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
 									end if
 									
@@ -1011,11 +1012,12 @@ subroutine run( this )
 		
 		real(8) :: min_dLnW
 		
-		integer :: n, nMin
+		integer :: nMin
 		real(8) :: rBuffer
 		type(String) :: sBuffer
 		
 		this.state = .true.
+		this.replaceTS = .false.
 		
 		call this.showReactorHeader()
 		
@@ -1025,8 +1027,6 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
@@ -1039,16 +1039,37 @@ subroutine run( this )
 ! 				call this.products.changeVibrationalEnergy()
 ! 				call this.products.changeGeometry()
 ! 				call this.products.changeOrientations()
+
+				if( this.replaceTS ) then
+					! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
+					call this.productsTS.setReactorEnergy( this.reactives.reactorEnergy() )
+					
+					! Para que fuerce los centros aleatorios en la siguiente iteración
+					this.productsTS.forceRandomCenters = .true.
+					
+					! Los productos utilizan parte de la energía
+					call this.productsTS.initialGuessFragmentsList()
+					
+! 					write(*,*) "reactive ", trim(this.reactives.label())
+! 					write(*,*) "products ", trim(this.products.label())
+! 					write(*,*) "TS located ", trim(this.productsTS.label())
+! 					sBuffer = this.products.energyHistoryLine()
+! 					write(*,"(A)") trim(sBuffer.fstr)
+! 					sBuffer = this.productsTS.energyHistoryLine()
+! 					write(*,"(A)") trim(sBuffer.fstr)
+					
+				end if
 				
 			case( VIBRATIONAL_REACTOR )
-				
+			
 				! La composición es igual antes y después
 				this.products = this.reactives
 				
 				! Los productos utilizan parte de la energía cinética en vibracional
 				call this.products.changeVibrationalEnergy()
-			
+				
 			case( TRANSLATIONAL_REACTOR )
+			
 				! La composición es igual antes y después
 				this.products = this.reactives
 				
@@ -1056,11 +1077,13 @@ subroutine run( this )
 				call this.products.changeGeometry()
 				
 			case( ROTATIONAL_REACTOR )
+			
 				! La composición es igual antes y después
 				this.products = this.reactives
 				
 				! Los productos utilizan parte de la energía
 				call this.products.changeOrientations()
+				
 		end select
 		
 		if( GOptions_printLevel >= 2 ) then
@@ -1110,8 +1133,6 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
-		if( this.replaceTS ) this.replaceTS = .false.
-		
 	end subroutine run
 	
 	!>

From af1095bf022b20cef1585850be866b83647eaee6 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Wed, 13 Feb 2019 22:10:35 -0700
Subject: [PATCH 13/57] Version updated

---
 VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/VERSION b/VERSION
index cd5ac03..2789166 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2.0
+2.1a

From f302f27460790cc1ff722eae11e3397d647c8f0d Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Thu, 28 Feb 2019 23:22:23 -0700
Subject: [PATCH 14/57] Gaussian template freqs updated to improve symmetry
 detection

---
 templates/b3lyp.freqs-GAUSSIAN.inp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/b3lyp.freqs-GAUSSIAN.inp b/templates/b3lyp.freqs-GAUSSIAN.inp
index e8e1d55..0d144fa 100644
--- a/templates/b3lyp.freqs-GAUSSIAN.inp
+++ b/templates/b3lyp.freqs-GAUSSIAN.inp
@@ -1,4 +1,4 @@
-#p b3lyp/6-311++G(3df,2p) freq
+#p b3lyp/6-311++G(3df,2p) freq IOp(2/17=3) IOp(2/18=3)
 
  b3lyp opt
 

From 85071b367b0dc14425d7dac08e132aacb274385a Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 3 Mar 2019 01:48:59 -0700
Subject: [PATCH 15/57] M3C.check now checks the right value of the
 multiplicity based on the stoichiometry and charge

---
 src/M3C.check | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/src/M3C.check b/src/M3C.check
index d55c056..31afbaf 100755
--- a/src/M3C.check
+++ b/src/M3C.check
@@ -165,20 +165,22 @@ function checkConsistence()
 			
 		fi
 		
-		if [[ ! "$multID" =~ ^m[1-9]+$ ]]
+		if [[ "$multID" =~ ^m[1-9]+$ ]]
 		then
-		
-			if [ "$REMOVE_WRONGFORMAT" = "TRUE" ]
+			minMult=`molecule.minMult $ifile ${chargeID#q}`
+			
+			if [ ! "$multID" = "m$(($minMult+0))" -a  ! "$multID" = "m$(($minMult+2))" \
+					-a  ! "$multID" = "m$(($minMult+4))" -a  ! "$multID" = "m$(($minMult+6))" ]
 			then
-				echo "--> Removed ($ifile) Inconsistency in multID ( $multID --> m[1-9]+ )"
-				rm $ifile
-				continue
-			else
 				echo ""
-				echo "### ERROR ### Inconsistency in multID ( $multID --> m[1-9]+ )"
+				echo -n "### ERROR ### Inconsistency in multiplicity ( $multID --> "
+				echo "m$(($minMult+0)), m$(($minMult+2)), m$(($minMult+4)), or m$(($minMult+6)) ) )"
 				kill $$
 			fi
-			
+		else
+			echo ""
+			echo "### ERROR ### Inconsistency in multID ( $multID --> m[1-9]+ )"
+			kill $$
 		fi
 		
 		if [[ ! "$isomerID" =~ ^[0-9]+$ ]]

From 06bf8ff34a6e6b031ccffe5f193e1886764bf3a1 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Tue, 5 Mar 2019 20:46:53 -0700
Subject: [PATCH 16/57] oGaussian2rxyz bug fixed

---
 utils/oGaussian2rxyz.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/utils/oGaussian2rxyz.sh b/utils/oGaussian2rxyz.sh
index 62be55e..b28e1a3 100755
--- a/utils/oGaussian2rxyz.sh
+++ b/utils/oGaussian2rxyz.sh
@@ -114,7 +114,7 @@ then
 		echo "ELECTRONIC_STATE ??"
 	else
 		#group=`grep "Full point group" $iFile | tail -n1 | gawk '{print $4}'`
-		group=`grep "Framework group" $iFile | sed 's/\[/ /g' | gawk '{print $3}'`
+		group=`grep "Framework group" $iFile | sed 's/\[/ /g' | gawk '{print $3}' | tail -n1`
 		if [ "$group" = "Nop" -o "$group" = "NOp" ]
 		then
 			echo "SYMMETRY ??"

From d1d82778ed027af39aba95e04e02fff395b0ad72 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sat, 9 Feb 2019 21:23:43 -0700
Subject: [PATCH 17/57] First part about implementing transition states

---
 src/Fragment.f90    |  7 -------
 src/FragmentsDB.f90 | 29 ++++++++++++++++++-----------
 src/Reactor.f90     | 15 +++++++++++++++
 3 files changed, 33 insertions(+), 18 deletions(-)

diff --git a/src/Fragment.f90 b/src/Fragment.f90
index 513e4a4..f39cf10 100644
--- a/src/Fragment.f90
+++ b/src/Fragment.f90
@@ -389,15 +389,8 @@ end subroutine destroyFragment
 	subroutine updateFormula( this )
 		class(Fragment) :: this 
 		
-		integer :: isLineal
 		character(100), allocatable :: tokens(:)
 		
-		if( this.isLineal() ) then
-			isLineal = 1
-		else
-			isLineal = 0
-		end if
-		
 		this.dlabel_ = this.name
 		
 		call FString_split( this.name, tokens, "(" )
diff --git a/src/FragmentsDB.f90 b/src/FragmentsDB.f90
index a62abaa..ee1834d 100644
--- a/src/FragmentsDB.f90
+++ b/src/FragmentsDB.f90
@@ -62,6 +62,7 @@ module FragmentsDB_
 	use StringIntegerMap_
 	
 	use Fragment_
+	use FragmentsList_
 	use ModelPotential_
 	use GOptionsM3C_
 	
@@ -79,11 +80,11 @@ module FragmentsDB_
 		type(StringIntegerMap) :: forbiddenReactions
 		logical :: useForbiddenReactionsDetails
 		
-! 		"C2(d1)+C(t1)-->C3(s1)" --> 5 --> transitionState(5)
+! 		"C2(d1)+C(t1)-->C3(s1)" --> 5 . It means transitionState(5)
 ! 		|----------str2id_TS----------|
 		type(Fragment), allocatable :: transitionState(:)
 		type(StringIntegerMap) :: str2id_TS
-		logical, allocatable :: involvedInTS(:) ! One for each group. For speed purposes only.
+		logical, allocatable :: involvedInTS(:) ! One for each cluster. For speed purposes only.
 		
 		real(8), private :: energyReference_
 		logical, private :: useAtomicPotentials
@@ -360,6 +361,10 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 		character(100), allocatable :: tokens(:), tokens2(:), tokens3(:)
 		real(8) :: rBuffer
 		
+		! Only for transition states. They are neccessary to calculate the right label (mass sorted)
+		type(FragmentsList) :: reactives
+		type(FragmentsList) :: products
+		
 		if( allocated(this.transitionState) ) deallocate( this.transitionState )
 		allocate( this.transitionState(size(transitionStatesTable)) )
 		
@@ -395,28 +400,28 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 			! Choosing the reactives and products
 			!------------------------------------------
 			if( size(tokens) >= 9 .and. this.transitionState(i).nAtoms() /= 1 ) then
-				call FString_split( trim(adjustl(tokens(9))), tokens2, "-->" )
+				call FString_split( trim(adjustl(tokens(9))), tokens2, "<-->" )
 				
-				write(*,*) "Reactivos"
 				call FString_split( trim(adjustl(tokens2(1))), tokens3, "+" )
+				call reactives.init( size(tokens3) )
+				
 				do j=1,size(tokens3)
-					write(*,*) "token = ", trim(tokens3(j))
 					do k=1,size(this.clusters)
 						if( trim(tokens3(j)) == this.clusters(k).label() ) then
-							write(IO_STDOUT,*) k, this.clusters(k).id
+							reactives.clusters(j) = this.clusters(k)
 							this.involvedInTS(k) = .true.
 						end if
 					end do
 				end do
 				deallocate( tokens3 )
 				
-				write(*,*) "Productos"
 				call FString_split( trim(adjustl(tokens2(2))), tokens3, "+" )
+				call products.init( size(tokens3) )
+				
 				do j=1,size(tokens3)
-					write(*,*) "token = ", trim(tokens3(j))
 					do k=1,size(this.clusters)
 						if( trim(tokens3(j)) == this.clusters(k).label() ) then
-							write(IO_STDOUT,*) k, this.clusters(k).id
+							products.clusters(j) = this.clusters(k)
 							this.involvedInTS(k) = .true.
 						end if
 					end do
@@ -425,8 +430,10 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 				
 				deallocate( tokens2 )
 				
-				write(*,*) "Agregado: ", FString_toString(trim(adjustl(tokens(9)))//"-->"//trim(adjustl(tokens(10)))), ">>", i
-				call this.str2id_TS.insert( FString_toString(trim(adjustl(tokens(9)))//"-->"//trim(adjustl(tokens(10)))), i )
+				write(*,"(4X,A22,A)")  "Path = ", trim(reactives.label())//"<-->"//trim(products.label())
+				call this.str2id_TS.insert( FString_toString(trim(reactives.label())//"<-->"//trim(products.label())), i )
+				call this.str2id_TS.insert( FString_toString(trim(products.label())//"<-->"//trim(reactives.label())), i )
+				
 			else
 				call GOptions_error( &
 						"Bad number of atoms in transition state (N=0)", &
diff --git a/src/Reactor.f90 b/src/Reactor.f90
index fe839c1..600948a 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -112,6 +112,7 @@ module Reactor_
 			procedure, private, NOPASS :: isSpinForbidden
 			procedure, private, NOPASS :: reactorConstraint
 			procedure, private, NOPASS :: reactionString
+			procedure, private, NOPASS :: reduceToTransitionStates
 			
 			procedure :: execute
 			procedure :: executeMinFragmentationEnergy
@@ -315,6 +316,11 @@ subroutine changeComposition( this, dNfrag )
 				maxIterForbidden = maxIterForbidden + 1
 				cycle
 			else
+				
+				if( allocated(FragmentsDB_instance.transitionState) ) then
+					call reduceToTransitionStates( this.reactives, this.products )
+				end if
+				
 				exit
 			end if
 			
@@ -464,6 +470,15 @@ function reactionString( reactives, products, details ) result( output )
 		output = trim(reactives.label( details=effDetails ))//"-->"//trim(products.label( details=effDetails ))
 	end function reactionString
 	
+	!>
+	!! @brief Replaces products for the corresponding transition states. Only composition is changed
+	!!
+	subroutine reduceToTransitionStates( reactives, products )
+		type(FragmentsList), intent(in) :: reactives
+		type(FragmentsList), intent(inout) :: products
+		
+	end subroutine reduceToTransitionStates
+	
 	!>
 	!! @brief Change the composition of the system
 	!!

From 13555e234e5c3be631c48d2b3749496bbee17cd8 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 16:31:15 -0700
Subject: [PATCH 18/57] Second trial for TS. There is a bug when all products
 fit with one TS

---
 src/Reactor.f90 | 162 +++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 159 insertions(+), 3 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 600948a..910d369 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -57,13 +57,13 @@ module Reactor_
 	use IOStream_
 	use Timer_
 	use UnitsConverter_
-	use IVector_
 	use RandomUtils_
 	use StringList_
 	use AtomicElementsDB_
 	use BlocksIFileParser_
 	use RealHistogram_
 	use RealList_
+	use IntegerVector_
 	use StringIntegerMap_
 	use StringRealMap_
 	use StringRealPair_
@@ -92,6 +92,9 @@ module Reactor_
 		type(FragmentsList) :: products
 		logical :: state
 		
+		type(FragmentsList) :: productsTS
+		logical :: replaceTS
+		
 		character(3), private :: name
 		integer, private :: type
 		integer, allocatable :: dNFrag(:)
@@ -318,7 +321,9 @@ subroutine changeComposition( this, dNfrag )
 			else
 				
 				if( allocated(FragmentsDB_instance.transitionState) ) then
-					call reduceToTransitionStates( this.reactives, this.products )
+					call reduceToTransitionStates( this.reactives, this.products, this.productsTS )
+					
+					if( this.productsTS.nMolecules() > 0 ) this.replaceTS = .true.
 				end if
 				
 				exit
@@ -473,10 +478,157 @@ end function reactionString
 	!>
 	!! @brief Replaces products for the corresponding transition states. Only composition is changed
 	!!
-	subroutine reduceToTransitionStates( reactives, products )
+	subroutine reduceToTransitionStates( reactives, products, productsTS )
 		type(FragmentsList), intent(in) :: reactives
 		type(FragmentsList), intent(inout) :: products
+		type(FragmentsList), intent(out) :: productsTS
+		
+		integer :: i, j, id
+		integer :: ir, jr, kr
+		integer :: ip, jp, kp
+		type(IntegerVector) :: reactiveInTS
+		type(IntegerVector) :: productInTS
+		integer, allocatable :: reactiveInTScomb(:,:)
+		integer, allocatable :: productInTScomb(:,:)
+		integer :: nAtomsR, nAtomsP
+		integer :: massNumberR, massNumberP
+		type(FragmentsList) :: lReactives, lProducts
+		type(String) :: labelTS, label
+		logical :: locatedTS
+		
+		call reactiveInTS.init( resizeIncrement=reactives.nMolecules() )
+		call productInTS.init( resizeIncrement=products.nMolecules() )
+		
+		do i=1,reactives.nMolecules()
+			id = FragmentsDB_instance.getIdFromName( reactives.clusters(i).label() )
+			if( FragmentsDB_instance.involvedInTS( id ) ) then
+					call reactiveInTS.append( i )
+			end if
+		end do
 		
+		do i=1,products.nMolecules()
+			id = FragmentsDB_instance.getIdFromName( products.clusters(i).label() )
+			if( FragmentsDB_instance.involvedInTS( id ) ) then
+					call productInTS.append( i )
+			end if
+		end do
+		
+		if( .not. reactiveInTS.isEmpty() .and. .not. productInTS.isEmpty() ) then
+! 			write(*,"(A)",advance="no") "Reactives "
+! 			do i=1,reactives.nMolecules()
+! 				write(*,"(A)",advance="no") trim(reactives.clusters(i).label())//"+"
+! 			end do
+! 			write(*,*) ""
+! 			write(*,*) "reactiveInTS = ", reactiveInTS.data(1:reactiveInTS.size())
+! 			write(*,"(A)",advance="no") "Products "
+! 			do i=1,products.nMolecules()
+! 				write(*,"(A)",advance="no") trim(products.clusters(i).label())//"+"
+! 			end do
+! 			write(*,*) ""
+! 			write(*,*) "productInTS = ", productInTS.data(1:productInTS.size())
+			
+			locatedTS = .false.
+			
+			do ir=1,reactiveInTS.size()
+				call Math_combinations( reactiveInTS.size(), ir, reactiveInTScomb )
+				
+				do jr=1,size(reactiveInTScomb,dim=1)
+					
+					nAtomsR = 0
+					massNumberR = 0
+					do kr=1,size(reactiveInTScomb,dim=2)
+						massNumberR = massNumberR + reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) ).massNumber()
+						nAtomsR = nAtomsR + reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) ).nAtoms()
+					end do
+					
+					do ip=1,productInTS.size()
+						call Math_combinations( productInTS.size(), ip, productInTScomb )
+						
+						do jp=1,size(productInTScomb,dim=1)
+							
+							nAtomsP = 0
+							massNumberP = 0
+							do kp=1,size(productInTScomb,dim=2)
+								massNumberP = massNumberP + products.clusters( productInTS.at(productInTScomb(jp,kp)) ).massNumber()
+								nAtomsP = nAtomsP + products.clusters( productInTS.at(productInTScomb(jp,kp)) ).nAtoms()
+							end do
+							
+							if( massNumberR == massNumberP .and. nAtomsR > 1 .and. nAtomsP > 1 ) then
+								
+								call lReactives.init( size(reactiveInTScomb,dim=2) )
+								call lProducts.init( size(productInTScomb,dim=2) )
+								
+								do kr=1,size(reactiveInTScomb,dim=2)
+									lReactives.clusters(kr) = reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) )
+								end do
+							
+								do kp=1,size(productInTScomb,dim=2)
+									lProducts.clusters(kp) = products.clusters( productInTS.at(productInTScomb(jp,kp)) )
+								end do
+								
+								if( trim(lReactives.label()) /= trim(lProducts.label()) ) then
+									
+									labelTS = trim(lReactives.label())//"<-->"//trim(lProducts.label())
+									
+									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "      reactives = ", trim(reactives.label())
+										write(*,*) "       products = ", trim(products.label())
+										write(*,*) "     TS located = ", trim(labelTS.fstr)
+									end if
+									
+									call productsTS.init( products.nMolecules() - lProducts.nMolecules() + 1 )
+									
+									! @TODO Aca el problema aparece cuando todos los productos estan en un TS como C(t1)+C(t1)+C(t1)
+									!       En este caso nunca se entra en el if
+									j=1
+									do i=1,products.nMolecules()
+										do kp=1,size(productInTScomb,dim=2)
+											label = trim(products.clusters( productInTS.at(productInTScomb(jp,kp)) ).label())
+											if( label /= trim(products.clusters(i).label()) &
+												.and. j<=lProducts.nMolecules() ) then
+												call productsTS.set( j, products.clusters(i) )
+												j = j+1
+												exit
+											end if
+										end do
+									end do
+									
+									call productsTS.set( j, &
+													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									
+									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
+									end if
+									
+									locatedTS = .true.
+									exit ! Only one TS is accepted. The one with minimum size
+									
+								end if
+								
+							end if
+							
+						end do
+						
+						if( locatedTS ) exit
+						
+					end do
+					
+					if( locatedTS ) exit
+					
+				end do
+				
+				if( locatedTS ) exit
+				
+			end do
+			
+		end if
+		
+		if( GOptions_debugLevel >= 2 ) then
+			write(*,*) ""
+		end if
+		
+		if( allocated(reactiveInTScomb) ) deallocate( reactiveInTScomb )
+		if( allocated(productInTScomb) ) deallocate( productInTScomb )
 	end subroutine reduceToTransitionStates
 	
 	!>
@@ -867,6 +1019,8 @@ subroutine run( this )
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				
@@ -947,6 +1101,8 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
+		if( this.replaceTS ) this.replaceTS = .false.
+		
 	end subroutine run
 	
 	!>

From 40b34ebb40242c3c9d8e5a46ddfd2638c07574e5 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 17:05:57 -0700
Subject: [PATCH 19/57] Bug replacing products by TS fixed

---
 src/Reactor.f90 | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 910d369..e3dd10b 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -578,14 +578,17 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 									
 									call productsTS.init( products.nMolecules() - lProducts.nMolecules() + 1 )
 									
+									call productsTS.set( 1, &
+													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									
 									! @TODO Aca el problema aparece cuando todos los productos estan en un TS como C(t1)+C(t1)+C(t1)
 									!       En este caso nunca se entra en el if
-									j=1
+									j=2
 									do i=1,products.nMolecules()
 										do kp=1,size(productInTScomb,dim=2)
 											label = trim(products.clusters( productInTS.at(productInTScomb(jp,kp)) ).label())
 											if( label /= trim(products.clusters(i).label()) &
-												.and. j<=lProducts.nMolecules() ) then
+												.and. j<=productsTS.nMolecules() ) then
 												call productsTS.set( j, products.clusters(i) )
 												j = j+1
 												exit
@@ -593,8 +596,14 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 										end do
 									end do
 									
-									call productsTS.set( j, &
-													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									if( j==2 ) then
+										do i=1,products.nMolecules()
+											if( j<=productsTS.nMolecules() ) then
+												call productsTS.set( j, products.clusters(i) )
+												j = j+1
+											end if
+										end do
+									end if
 									
 									if( GOptions_debugLevel >= 2 ) then
 										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
@@ -1016,11 +1025,11 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				

From d4c9617d8655656fccd50ec853e9f72f00bb0eae Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Wed, 13 Feb 2019 22:09:08 -0700
Subject: [PATCH 20/57] First version working with TS

---
 src/FragmentsDB.f90 |  1 +
 src/MarkovChain.f90 | 11 ++++++++---
 src/Reactor.f90     | 35 ++++++++++++++++++++++++++++-------
 3 files changed, 37 insertions(+), 10 deletions(-)

diff --git a/src/FragmentsDB.f90 b/src/FragmentsDB.f90
index ee1834d..3baaa84 100644
--- a/src/FragmentsDB.f90
+++ b/src/FragmentsDB.f90
@@ -377,6 +377,7 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 		
 		do i=1,size(transitionStatesTable)
 			call this.transitionState(i).fromMassTableRow( transitionStatesTable(i).fstr, id=i, store=store.fstr )
+			this.transitionState(i).isTransitionState = .true.
 			
 			call FString_split( transitionStatesTable(i).fstr, tokens, " " )
 			
diff --git a/src/MarkovChain.f90 b/src/MarkovChain.f90
index a34d07c..2c8e433 100644
--- a/src/MarkovChain.f90
+++ b/src/MarkovChain.f90
@@ -442,7 +442,7 @@ subroutine run( this, reactives )
 	! 							sBuffer = react.reactives.weightHistoryLine( origin )
 	! 						end if
 	! 					end if
-
+	
 						call react.run()
 						
 						! Si la energía cinetica es negativa
@@ -483,7 +483,12 @@ subroutine run( this, reactives )
 						
 							nTimesBlocked = 0  ! El bloqueo debe ser consecutivo, así que si no pasa por negative energy se cuenta nuevamente
 							
-							Pi = react.products.LnW()-react.reactives.LnW()
+							if( react.replaceTS ) then
+								react.replaceTS = .false.
+								Pi = react.productsTS.LnW()-react.reactives.LnW()
+							else
+								Pi = react.products.LnW()-react.reactives.LnW()
+							end if
 							
 							if( Pi > 0.0_8 ) then
 								if( trim(react.reactives.label( details=.false. )) /= trim(react.products.label( details=.false. )) ) then
@@ -518,7 +523,7 @@ subroutine run( this, reactives )
 										sBuffer = trim(react.reactives.label( details=.true. ))//"-->"//trim(react.products.label( details=.true. ))
 										call this.transitionDetHistogram.add( sBuffer )
 									end if
-
+									
 									react.reactives = react.products
 									
 									call GOptions_info( &
diff --git a/src/Reactor.f90 b/src/Reactor.f90
index e3dd10b..4a74d46 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -606,6 +606,7 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 									end if
 									
 									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "       products = ", trim(products.label())
 										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
 									end if
 									
@@ -1011,11 +1012,12 @@ subroutine run( this )
 		
 		real(8) :: min_dLnW
 		
-		integer :: n, nMin
+		integer :: nMin
 		real(8) :: rBuffer
 		type(String) :: sBuffer
 		
 		this.state = .true.
+		this.replaceTS = .false.
 		
 		call this.showReactorHeader()
 		
@@ -1025,8 +1027,6 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
@@ -1039,16 +1039,37 @@ subroutine run( this )
 ! 				call this.products.changeVibrationalEnergy()
 ! 				call this.products.changeGeometry()
 ! 				call this.products.changeOrientations()
+
+				if( this.replaceTS ) then
+					! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
+					call this.productsTS.setReactorEnergy( this.reactives.reactorEnergy() )
+					
+					! Para que fuerce los centros aleatorios en la siguiente iteración
+					this.productsTS.forceRandomCenters = .true.
+					
+					! Los productos utilizan parte de la energía
+					call this.productsTS.initialGuessFragmentsList()
+					
+! 					write(*,*) "reactive ", trim(this.reactives.label())
+! 					write(*,*) "products ", trim(this.products.label())
+! 					write(*,*) "TS located ", trim(this.productsTS.label())
+! 					sBuffer = this.products.energyHistoryLine()
+! 					write(*,"(A)") trim(sBuffer.fstr)
+! 					sBuffer = this.productsTS.energyHistoryLine()
+! 					write(*,"(A)") trim(sBuffer.fstr)
+					
+				end if
 				
 			case( VIBRATIONAL_REACTOR )
-				
+			
 				! La composición es igual antes y después
 				this.products = this.reactives
 				
 				! Los productos utilizan parte de la energía cinética en vibracional
 				call this.products.changeVibrationalEnergy()
-			
+				
 			case( TRANSLATIONAL_REACTOR )
+			
 				! La composición es igual antes y después
 				this.products = this.reactives
 				
@@ -1056,11 +1077,13 @@ subroutine run( this )
 				call this.products.changeGeometry()
 				
 			case( ROTATIONAL_REACTOR )
+			
 				! La composición es igual antes y después
 				this.products = this.reactives
 				
 				! Los productos utilizan parte de la energía
 				call this.products.changeOrientations()
+				
 		end select
 		
 		if( GOptions_printLevel >= 2 ) then
@@ -1110,8 +1133,6 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
-		if( this.replaceTS ) this.replaceTS = .false.
-		
 	end subroutine run
 	
 	!>

From eed0c50440a6970e1330546bdda4aeb9f51cf979 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Wed, 13 Feb 2019 22:10:35 -0700
Subject: [PATCH 21/57] Version updated

---
 VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/VERSION b/VERSION
index cd5ac03..2789166 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2.0
+2.1a

From 57c930b41c41f9aeb7a1a593787eabffe7c270c9 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Thu, 28 Feb 2019 23:22:23 -0700
Subject: [PATCH 22/57] Gaussian template freqs updated to improve symmetry
 detection

---
 templates/b3lyp.freqs-GAUSSIAN.inp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/b3lyp.freqs-GAUSSIAN.inp b/templates/b3lyp.freqs-GAUSSIAN.inp
index e8e1d55..0d144fa 100644
--- a/templates/b3lyp.freqs-GAUSSIAN.inp
+++ b/templates/b3lyp.freqs-GAUSSIAN.inp
@@ -1,4 +1,4 @@
-#p b3lyp/6-311++G(3df,2p) freq
+#p b3lyp/6-311++G(3df,2p) freq IOp(2/17=3) IOp(2/18=3)
 
  b3lyp opt
 

From dd5fb4f8ae2d5a6cef8b62da4f442686ceca117f Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 3 Mar 2019 01:48:59 -0700
Subject: [PATCH 23/57] M3C.check now checks the right value of the
 multiplicity based on the stoichiometry and charge

---
 src/M3C.check | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/src/M3C.check b/src/M3C.check
index d55c056..31afbaf 100755
--- a/src/M3C.check
+++ b/src/M3C.check
@@ -165,20 +165,22 @@ function checkConsistence()
 			
 		fi
 		
-		if [[ ! "$multID" =~ ^m[1-9]+$ ]]
+		if [[ "$multID" =~ ^m[1-9]+$ ]]
 		then
-		
-			if [ "$REMOVE_WRONGFORMAT" = "TRUE" ]
+			minMult=`molecule.minMult $ifile ${chargeID#q}`
+			
+			if [ ! "$multID" = "m$(($minMult+0))" -a  ! "$multID" = "m$(($minMult+2))" \
+					-a  ! "$multID" = "m$(($minMult+4))" -a  ! "$multID" = "m$(($minMult+6))" ]
 			then
-				echo "--> Removed ($ifile) Inconsistency in multID ( $multID --> m[1-9]+ )"
-				rm $ifile
-				continue
-			else
 				echo ""
-				echo "### ERROR ### Inconsistency in multID ( $multID --> m[1-9]+ )"
+				echo -n "### ERROR ### Inconsistency in multiplicity ( $multID --> "
+				echo "m$(($minMult+0)), m$(($minMult+2)), m$(($minMult+4)), or m$(($minMult+6)) ) )"
 				kill $$
 			fi
-			
+		else
+			echo ""
+			echo "### ERROR ### Inconsistency in multID ( $multID --> m[1-9]+ )"
+			kill $$
 		fi
 		
 		if [[ ! "$isomerID" =~ ^[0-9]+$ ]]

From 20804508c84bab0879b93f48a611c809d3acd61e Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sat, 9 Feb 2019 21:23:43 -0700
Subject: [PATCH 24/57] First part about implementing transition states

---
 src/Reactor.f90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 4a74d46..1a0960b 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -639,6 +639,7 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 		
 		if( allocated(reactiveInTScomb) ) deallocate( reactiveInTScomb )
 		if( allocated(productInTScomb) ) deallocate( productInTScomb )
+		
 	end subroutine reduceToTransitionStates
 	
 	!>

From 3301641a04a7c6e1c1399f02c0556ff8139d6035 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 16:31:15 -0700
Subject: [PATCH 25/57] Second trial for TS. There is a bug when all products
 fit with one TS

---
 src/Reactor.f90 | 127 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 127 insertions(+)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 1a0960b..3ee5cea 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -640,6 +640,129 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 		if( allocated(reactiveInTScomb) ) deallocate( reactiveInTScomb )
 		if( allocated(productInTScomb) ) deallocate( productInTScomb )
 		
+		do i=1,products.nMolecules()
+			id = FragmentsDB_instance.getIdFromName( products.clusters(i).label() )
+			if( FragmentsDB_instance.involvedInTS( id ) ) then
+					call productInTS.append( i )
+			end if
+		end do
+		
+		if( .not. reactiveInTS.isEmpty() .and. .not. productInTS.isEmpty() ) then
+! 			write(*,"(A)",advance="no") "Reactives "
+! 			do i=1,reactives.nMolecules()
+! 				write(*,"(A)",advance="no") trim(reactives.clusters(i).label())//"+"
+! 			end do
+! 			write(*,*) ""
+! 			write(*,*) "reactiveInTS = ", reactiveInTS.data(1:reactiveInTS.size())
+! 			write(*,"(A)",advance="no") "Products "
+! 			do i=1,products.nMolecules()
+! 				write(*,"(A)",advance="no") trim(products.clusters(i).label())//"+"
+! 			end do
+! 			write(*,*) ""
+! 			write(*,*) "productInTS = ", productInTS.data(1:productInTS.size())
+			
+			locatedTS = .false.
+			
+			do ir=1,reactiveInTS.size()
+				call Math_combinations( reactiveInTS.size(), ir, reactiveInTScomb )
+				
+				do jr=1,size(reactiveInTScomb,dim=1)
+					
+					nAtomsR = 0
+					massNumberR = 0
+					do kr=1,size(reactiveInTScomb,dim=2)
+						massNumberR = massNumberR + reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) ).massNumber()
+						nAtomsR = nAtomsR + reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) ).nAtoms()
+					end do
+					
+					do ip=1,productInTS.size()
+						call Math_combinations( productInTS.size(), ip, productInTScomb )
+						
+						do jp=1,size(productInTScomb,dim=1)
+							
+							nAtomsP = 0
+							massNumberP = 0
+							do kp=1,size(productInTScomb,dim=2)
+								massNumberP = massNumberP + products.clusters( productInTS.at(productInTScomb(jp,kp)) ).massNumber()
+								nAtomsP = nAtomsP + products.clusters( productInTS.at(productInTScomb(jp,kp)) ).nAtoms()
+							end do
+							
+							if( massNumberR == massNumberP .and. nAtomsR > 1 .and. nAtomsP > 1 ) then
+								
+								call lReactives.init( size(reactiveInTScomb,dim=2) )
+								call lProducts.init( size(productInTScomb,dim=2) )
+								
+								do kr=1,size(reactiveInTScomb,dim=2)
+									lReactives.clusters(kr) = reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) )
+								end do
+							
+								do kp=1,size(productInTScomb,dim=2)
+									lProducts.clusters(kp) = products.clusters( productInTS.at(productInTScomb(jp,kp)) )
+								end do
+								
+								if( trim(lReactives.label()) /= trim(lProducts.label()) ) then
+									
+									labelTS = trim(lReactives.label())//"<-->"//trim(lProducts.label())
+									
+									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "      reactives = ", trim(reactives.label())
+										write(*,*) "       products = ", trim(products.label())
+										write(*,*) "     TS located = ", trim(labelTS.fstr)
+									end if
+									
+									call productsTS.init( products.nMolecules() - lProducts.nMolecules() + 1 )
+									
+									! @TODO Aca el problema aparece cuando todos los productos estan en un TS como C(t1)+C(t1)+C(t1)
+									!       En este caso nunca se entra en el if
+									j=1
+									do i=1,products.nMolecules()
+										do kp=1,size(productInTScomb,dim=2)
+											label = trim(products.clusters( productInTS.at(productInTScomb(jp,kp)) ).label())
+											if( label /= trim(products.clusters(i).label()) &
+												.and. j<=lProducts.nMolecules() ) then
+												call productsTS.set( j, products.clusters(i) )
+												j = j+1
+												exit
+											end if
+										end do
+									end do
+									
+									call productsTS.set( j, &
+													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									
+									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
+									end if
+									
+									locatedTS = .true.
+									exit ! Only one TS is accepted. The one with minimum size
+									
+								end if
+								
+							end if
+							
+						end do
+						
+						if( locatedTS ) exit
+						
+					end do
+					
+					if( locatedTS ) exit
+					
+				end do
+				
+				if( locatedTS ) exit
+				
+			end do
+			
+		end if
+		
+		if( GOptions_debugLevel >= 2 ) then
+			write(*,*) ""
+		end if
+		
+		if( allocated(reactiveInTScomb) ) deallocate( reactiveInTScomb )
+		if( allocated(productInTScomb) ) deallocate( productInTScomb )
 	end subroutine reduceToTransitionStates
 	
 	!>
@@ -1031,6 +1154,8 @@ subroutine run( this )
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				
@@ -1134,6 +1259,8 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
+		if( this.replaceTS ) this.replaceTS = .false.
+		
 	end subroutine run
 	
 	!>

From d0fba4a6d10a76b667652f20882c9839f43571bc Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 17:05:57 -0700
Subject: [PATCH 26/57] Bug replacing products by TS fixed

---
 src/Reactor.f90 | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 3ee5cea..07bfba6 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -712,14 +712,17 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 									
 									call productsTS.init( products.nMolecules() - lProducts.nMolecules() + 1 )
 									
+									call productsTS.set( 1, &
+													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									
 									! @TODO Aca el problema aparece cuando todos los productos estan en un TS como C(t1)+C(t1)+C(t1)
 									!       En este caso nunca se entra en el if
-									j=1
+									j=2
 									do i=1,products.nMolecules()
 										do kp=1,size(productInTScomb,dim=2)
 											label = trim(products.clusters( productInTS.at(productInTScomb(jp,kp)) ).label())
 											if( label /= trim(products.clusters(i).label()) &
-												.and. j<=lProducts.nMolecules() ) then
+												.and. j<=productsTS.nMolecules() ) then
 												call productsTS.set( j, products.clusters(i) )
 												j = j+1
 												exit
@@ -727,8 +730,14 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 										end do
 									end do
 									
-									call productsTS.set( j, &
-													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									if( j==2 ) then
+										do i=1,products.nMolecules()
+											if( j<=productsTS.nMolecules() ) then
+												call productsTS.set( j, products.clusters(i) )
+												j = j+1
+											end if
+										end do
+									end if
 									
 									if( GOptions_debugLevel >= 2 ) then
 										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
@@ -1151,11 +1160,11 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				

From 5a65369d0226b6aa765c0deb03748b822c941ff2 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Wed, 13 Feb 2019 22:09:08 -0700
Subject: [PATCH 27/57] First version working with TS

---
 src/Reactor.f90 | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 07bfba6..311f983 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -1160,8 +1160,6 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
@@ -1268,8 +1266,6 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
-		if( this.replaceTS ) this.replaceTS = .false.
-		
 	end subroutine run
 	
 	!>

From 3c76f16ee615468ad71c8fef2af8703025459ab7 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Tue, 5 Mar 2019 20:46:53 -0700
Subject: [PATCH 28/57] oGaussian2rxyz bug fixed

---
 utils/oGaussian2rxyz.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/utils/oGaussian2rxyz.sh b/utils/oGaussian2rxyz.sh
index deff9e1..b226483 100755
--- a/utils/oGaussian2rxyz.sh
+++ b/utils/oGaussian2rxyz.sh
@@ -113,7 +113,8 @@ then
 		echo "SYMMETRY R3"
 		echo "ELECTRONIC_STATE ??"
 	else
-		group=`grep "Full point group" $iFile | tail -n1 | gawk '{print $4}'`
+		#group=`grep "Full point group" $iFile | tail -n1 | gawk '{print $4}'`
+		group=`grep "Framework group" $iFile | sed 's/\[/ /g' | gawk '{print $3}' | tail -n1`
 		if [ "$group" = "Nop" -o "$group" = "NOp" ]
 		then
 			echo "SYMMETRY ??"

From 8dff71b9015a8ee51f7fc833f0a9ee5dcc15bf50 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 8 Mar 2020 10:02:22 +0100
Subject: [PATCH 29/57] Files needed to compile

---
 utils/libmsym/CMakeCache.txt      |  89 ++++++++++++++++++++--
 utils/libmsym/Makefile            | 119 ++++++++++++++++--------------
 utils/libmsym/cmake_install.cmake |  20 ++++-
 3 files changed, 162 insertions(+), 66 deletions(-)

diff --git a/utils/libmsym/CMakeCache.txt b/utils/libmsym/CMakeCache.txt
index 87baf04..e51f32a 100644
--- a/utils/libmsym/CMakeCache.txt
+++ b/utils/libmsym/CMakeCache.txt
@@ -1,5 +1,5 @@
 # This is the CMakeCache file.
-# For build in directory: /home/nestor/Develop/M3C/utils/libmsym
+# For build in directory: /home/natalia/Develop/M3C/utils/libmsym
 # It was generated by CMake: /usr/bin/cmake
 # You can edit this file to change values found and used by cmake.
 # If you do not want to change any of the values, simply exit the editor.
@@ -14,6 +14,9 @@
 # EXTERNAL cache entries
 ########################
 
+//Path to a program.
+CMAKE_AR:FILEPATH=/usr/bin/ar
+
 //Choose the type of build, options are: None(CMAKE_CXX_FLAGS or
 // CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel.
 CMAKE_BUILD_TYPE:STRING=
@@ -21,6 +24,17 @@ CMAKE_BUILD_TYPE:STRING=
 //Enable/Disable color output during build.
 CMAKE_COLOR_MAKEFILE:BOOL=ON
 
+//CXX compiler
+CMAKE_CXX_COMPILER:FILEPATH=/usr/bin/c++
+
+//A wrapper around 'ar' adding the appropriate '--plugin' option
+// for the GCC compiler
+CMAKE_CXX_COMPILER_AR:FILEPATH=/usr/bin/gcc-ar-7
+
+//A wrapper around 'ranlib' adding the appropriate '--plugin' option
+// for the GCC compiler
+CMAKE_CXX_COMPILER_RANLIB:FILEPATH=/usr/bin/gcc-ranlib-7
+
 //Flags used by the compiler during all build types.
 CMAKE_CXX_FLAGS:STRING=
 
@@ -37,6 +51,17 @@ CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG
 //Flags used by the compiler during release builds with debug info.
 CMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG
 
+//C compiler
+CMAKE_C_COMPILER:FILEPATH=/usr/bin/cc
+
+//A wrapper around 'ar' adding the appropriate '--plugin' option
+// for the GCC compiler
+CMAKE_C_COMPILER_AR:FILEPATH=/usr/bin/gcc-ar-7
+
+//A wrapper around 'ranlib' adding the appropriate '--plugin' option
+// for the GCC compiler
+CMAKE_C_COMPILER_RANLIB:FILEPATH=/usr/bin/gcc-ranlib-7
+
 //Flags used by the compiler during all build types.
 CMAKE_C_FLAGS:STRING=
 
@@ -74,6 +99,9 @@ CMAKE_EXPORT_COMPILE_COMMANDS:BOOL=OFF
 //Install path prefix, prepended onto install directories.
 CMAKE_INSTALL_PREFIX:PATH=/usr/local
 
+//Path to a program.
+CMAKE_LINKER:FILEPATH=/usr/bin/ld
+
 //Path to a program.
 CMAKE_MAKE_PROGRAM:FILEPATH=/usr/bin/make
 
@@ -92,9 +120,21 @@ CMAKE_MODULE_LINKER_FLAGS_RELEASE:STRING=
 //Flags used by the linker during Release with Debug Info builds.
 CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO:STRING=
 
+//Path to a program.
+CMAKE_NM:FILEPATH=/usr/bin/nm
+
+//Path to a program.
+CMAKE_OBJCOPY:FILEPATH=/usr/bin/objcopy
+
+//Path to a program.
+CMAKE_OBJDUMP:FILEPATH=/usr/bin/objdump
+
 //Value Computed by CMake
 CMAKE_PROJECT_NAME:STATIC=msym
 
+//Path to a program.
+CMAKE_RANLIB:FILEPATH=/usr/bin/ranlib
+
 //Flags used by the linker during the creation of dll's.
 CMAKE_SHARED_LINKER_FLAGS:STRING=
 
@@ -132,6 +172,9 @@ CMAKE_STATIC_LINKER_FLAGS_RELEASE:STRING=
 //Flags used by the linker during Release with Debug Info builds.
 CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO:STRING=
 
+//Path to a program.
+CMAKE_STRIP:FILEPATH=/usr/bin/strip
+
 //If this value is on, makefiles will be generated without the
 // .SILENT directive, and all commands will be echoed to the console
 // during the make.  This is useful for debugging only. With Visual
@@ -139,25 +182,27 @@ CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO:STRING=
 CMAKE_VERBOSE_MAKEFILE:BOOL=FALSE
 
 //Value Computed by CMake
-msym_BINARY_DIR:STATIC=/home/nestor/Develop/M3C/utils/libmsym
+msym_BINARY_DIR:STATIC=/home/natalia/Develop/M3C/utils/libmsym
 
 //Dependencies for target
 msym_LIB_DEPENDS:STATIC=
 
 //Value Computed by CMake
-msym_SOURCE_DIR:STATIC=/home/nestor/Develop/M3C/utils/libmsym
+msym_SOURCE_DIR:STATIC=/home/natalia/Develop/M3C/utils/libmsym
 
 
 ########################
 # INTERNAL cache entries
 ########################
 
+//ADVANCED property for variable: CMAKE_AR
+CMAKE_AR-ADVANCED:INTERNAL=1
 //This is the directory where this CMakeCache.txt was created
-CMAKE_CACHEFILE_DIR:INTERNAL=/home/nestor/Develop/M3C/utils/libmsym
+CMAKE_CACHEFILE_DIR:INTERNAL=/home/natalia/Develop/M3C/utils/libmsym
 //Major version of cmake used to create the current loaded cache
 CMAKE_CACHE_MAJOR_VERSION:INTERNAL=3
 //Minor version of cmake used to create the current loaded cache
-CMAKE_CACHE_MINOR_VERSION:INTERNAL=5
+CMAKE_CACHE_MINOR_VERSION:INTERNAL=9
 //Patch version of cmake used to create the current loaded cache
 CMAKE_CACHE_PATCH_VERSION:INTERNAL=1
 //ADVANCED property for variable: CMAKE_COLOR_MAKEFILE
@@ -168,6 +213,12 @@ CMAKE_COMMAND:INTERNAL=/usr/bin/cmake
 CMAKE_CPACK_COMMAND:INTERNAL=/usr/bin/cpack
 //Path to ctest program executable.
 CMAKE_CTEST_COMMAND:INTERNAL=/usr/bin/ctest
+//ADVANCED property for variable: CMAKE_CXX_COMPILER
+CMAKE_CXX_COMPILER-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_CXX_COMPILER_AR
+CMAKE_CXX_COMPILER_AR-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_CXX_COMPILER_RANLIB
+CMAKE_CXX_COMPILER_RANLIB-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_CXX_FLAGS
 CMAKE_CXX_FLAGS-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_CXX_FLAGS_DEBUG
@@ -178,6 +229,12 @@ CMAKE_CXX_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
 CMAKE_CXX_FLAGS_RELEASE-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_CXX_FLAGS_RELWITHDEBINFO
 CMAKE_CXX_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_C_COMPILER
+CMAKE_C_COMPILER-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_C_COMPILER_AR
+CMAKE_C_COMPILER_AR-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_C_COMPILER_RANLIB
+CMAKE_C_COMPILER_RANLIB-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_C_FLAGS
 CMAKE_C_FLAGS-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_C_FLAGS_DEBUG
@@ -188,6 +245,8 @@ CMAKE_C_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
 CMAKE_C_FLAGS_RELEASE-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_C_FLAGS_RELWITHDEBINFO
 CMAKE_C_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
+//Executable file format
+CMAKE_EXECUTABLE_FORMAT:INTERNAL=ELF
 //ADVANCED property for variable: CMAKE_EXE_LINKER_FLAGS
 CMAKE_EXE_LINKER_FLAGS-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_EXE_LINKER_FLAGS_DEBUG
@@ -210,9 +269,11 @@ CMAKE_GENERATOR_PLATFORM:INTERNAL=
 CMAKE_GENERATOR_TOOLSET:INTERNAL=
 //Source directory with the top level CMakeLists.txt file for this
 // project
-CMAKE_HOME_DIRECTORY:INTERNAL=/home/nestor/Develop/M3C/utils/libmsym
+CMAKE_HOME_DIRECTORY:INTERNAL=/home/natalia/Develop/M3C/utils/libmsym
 //Install .so files without execute permission.
 CMAKE_INSTALL_SO_NO_EXE:INTERNAL=1
+//ADVANCED property for variable: CMAKE_LINKER
+CMAKE_LINKER-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_MAKE_PROGRAM
 CMAKE_MAKE_PROGRAM-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_MODULE_LINKER_FLAGS
@@ -225,10 +286,20 @@ CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
 CMAKE_MODULE_LINKER_FLAGS_RELEASE-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO
 CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_NM
+CMAKE_NM-ADVANCED:INTERNAL=1
 //number of local generators
 CMAKE_NUMBER_OF_MAKEFILES:INTERNAL=1
+//ADVANCED property for variable: CMAKE_OBJCOPY
+CMAKE_OBJCOPY-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_OBJDUMP
+CMAKE_OBJDUMP-ADVANCED:INTERNAL=1
+//Platform information initialized
+CMAKE_PLATFORM_INFO_INITIALIZED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_RANLIB
+CMAKE_RANLIB-ADVANCED:INTERNAL=1
 //Path to CMake installation.
-CMAKE_ROOT:INTERNAL=/usr/share/cmake-3.5
+CMAKE_ROOT:INTERNAL=/usr/share/cmake-3.9
 //ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS
 CMAKE_SHARED_LINKER_FLAGS-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS_DEBUG
@@ -253,6 +324,10 @@ CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
 CMAKE_STATIC_LINKER_FLAGS_RELEASE-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO
 CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_STRIP
+CMAKE_STRIP-ADVANCED:INTERNAL=1
+//uname command
+CMAKE_UNAME:INTERNAL=/bin/uname
 //ADVANCED property for variable: CMAKE_VERBOSE_MAKEFILE
 CMAKE_VERBOSE_MAKEFILE-ADVANCED:INTERNAL=1
 
diff --git a/utils/libmsym/Makefile b/utils/libmsym/Makefile
index 15632a7..1e9a3f5 100644
--- a/utils/libmsym/Makefile
+++ b/utils/libmsym/Makefile
@@ -1,5 +1,5 @@
 # CMAKE generated file: DO NOT EDIT!
-# Generated by "Unix Makefiles" Generator, CMake Version 3.5
+# Generated by "Unix Makefiles" Generator, CMake Version 3.9
 
 # Default target executed when no arguments are given to make.
 default_target: all
@@ -48,35 +48,37 @@ RM = /usr/bin/cmake -E remove -f
 EQUALS = =
 
 # The top-level source directory on which CMake was run.
-CMAKE_SOURCE_DIR = /home/nestor/Develop/M3C/utils/libmsym
+CMAKE_SOURCE_DIR = /home/natalia/Develop/M3C/utils/libmsym
 
 # The top-level build directory on which CMake was run.
-CMAKE_BINARY_DIR = /home/nestor/Develop/M3C/utils/libmsym
+CMAKE_BINARY_DIR = /home/natalia/Develop/M3C/utils/libmsym
 
 #=============================================================================
 # Targets provided globally by CMake.
 
-# Special rule for the target install
-install: preinstall
-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
-	/usr/bin/cmake -P cmake_install.cmake
-.PHONY : install
+# Special rule for the target install/strip
+install/strip: preinstall
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing the project stripped..."
+	/usr/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake
+.PHONY : install/strip
 
-# Special rule for the target install
-install/fast: preinstall/fast
-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
-	/usr/bin/cmake -P cmake_install.cmake
-.PHONY : install/fast
+# Special rule for the target install/strip
+install/strip/fast: preinstall/fast
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing the project stripped..."
+	/usr/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake
+.PHONY : install/strip/fast
 
-# Special rule for the target list_install_components
-list_install_components:
-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Available install components are: \"Unspecified\""
-.PHONY : list_install_components
-
-# Special rule for the target list_install_components
-list_install_components/fast: list_install_components
+# Special rule for the target install/local
+install/local: preinstall
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing only the local directory..."
+	/usr/bin/cmake -DCMAKE_INSTALL_LOCAL_ONLY=1 -P cmake_install.cmake
+.PHONY : install/local
 
-.PHONY : list_install_components/fast
+# Special rule for the target install/local
+install/local/fast: preinstall/fast
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing only the local directory..."
+	/usr/bin/cmake -DCMAKE_INSTALL_LOCAL_ONLY=1 -P cmake_install.cmake
+.PHONY : install/local/fast
 
 # Special rule for the target rebuild_cache
 rebuild_cache:
@@ -89,17 +91,6 @@ rebuild_cache/fast: rebuild_cache
 
 .PHONY : rebuild_cache/fast
 
-# Special rule for the target install/local
-install/local: preinstall
-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing only the local directory..."
-	/usr/bin/cmake -DCMAKE_INSTALL_LOCAL_ONLY=1 -P cmake_install.cmake
-.PHONY : install/local
-
-# Special rule for the target install/local
-install/local/fast: install/local
-
-.PHONY : install/local/fast
-
 # Special rule for the target edit_cache
 edit_cache:
 	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "No interactive CMake dialog available..."
@@ -111,11 +102,33 @@ edit_cache/fast: edit_cache
 
 .PHONY : edit_cache/fast
 
+# Special rule for the target list_install_components
+list_install_components:
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Available install components are: \"Unspecified\""
+.PHONY : list_install_components
+
+# Special rule for the target list_install_components
+list_install_components/fast: list_install_components
+
+.PHONY : list_install_components/fast
+
+# Special rule for the target install
+install: preinstall
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+	/usr/bin/cmake -P cmake_install.cmake
+.PHONY : install
+
+# Special rule for the target install
+install/fast: preinstall/fast
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+	/usr/bin/cmake -P cmake_install.cmake
+.PHONY : install/fast
+
 # The main all target
 all: cmake_check_build_system
-	$(CMAKE_COMMAND) -E cmake_progress_start /home/nestor/Develop/M3C/utils/libmsym/CMakeFiles /home/nestor/Develop/M3C/utils/libmsym/CMakeFiles/progress.marks
+	$(CMAKE_COMMAND) -E cmake_progress_start /home/natalia/Develop/M3C/utils/libmsym/CMakeFiles /home/natalia/Develop/M3C/utils/libmsym/CMakeFiles/progress.marks
 	$(MAKE) -f CMakeFiles/Makefile2 all
-	$(CMAKE_COMMAND) -E cmake_progress_start /home/nestor/Develop/M3C/utils/libmsym/CMakeFiles 0
+	$(CMAKE_COMMAND) -E cmake_progress_start /home/natalia/Develop/M3C/utils/libmsym/CMakeFiles 0
 .PHONY : all
 
 # The main clean target
@@ -143,19 +156,6 @@ depend:
 	$(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 1
 .PHONY : depend
 
-#=============================================================================
-# Target rules for targets named msym
-
-# Build rule for target.
-msym: cmake_check_build_system
-	$(MAKE) -f CMakeFiles/Makefile2 msym
-.PHONY : msym
-
-# fast build rule for target.
-msym/fast:
-	$(MAKE) -f CMakeFiles/msym.dir/build.make CMakeFiles/msym.dir/build
-.PHONY : msym/fast
-
 #=============================================================================
 # Target rules for targets named molecule.symmetrize
 
@@ -169,10 +169,18 @@ molecule.symmetrize/fast:
 	$(MAKE) -f CMakeFiles/molecule.symmetrize.dir/build.make CMakeFiles/molecule.symmetrize.dir/build
 .PHONY : molecule.symmetrize/fast
 
-# Manual pre-install relink rule for target.
-molecule.symmetrize/preinstall:
-	$(MAKE) -f CMakeFiles/molecule.symmetrize.dir/build.make CMakeFiles/molecule.symmetrize.dir/preinstall
-.PHONY : molecule.symmetrize/preinstall
+#=============================================================================
+# Target rules for targets named msym
+
+# Build rule for target.
+msym: cmake_check_build_system
+	$(MAKE) -f CMakeFiles/Makefile2 msym
+.PHONY : msym
+
+# fast build rule for target.
+msym/fast:
+	$(MAKE) -f CMakeFiles/msym.dir/build.make CMakeFiles/msym.dir/build
+.PHONY : msym/fast
 
 basis_function.o: basis_function.c.o
 
@@ -666,13 +674,14 @@ help:
 	@echo "... all (the default if no target is provided)"
 	@echo "... clean"
 	@echo "... depend"
-	@echo "... install"
-	@echo "... list_install_components"
-	@echo "... rebuild_cache"
-	@echo "... msym"
+	@echo "... install/strip"
 	@echo "... install/local"
 	@echo "... molecule.symmetrize"
+	@echo "... rebuild_cache"
+	@echo "... msym"
 	@echo "... edit_cache"
+	@echo "... list_install_components"
+	@echo "... install"
 	@echo "... basis_function.o"
 	@echo "... basis_function.i"
 	@echo "... basis_function.s"
diff --git a/utils/libmsym/cmake_install.cmake b/utils/libmsym/cmake_install.cmake
index e5c8fb2..1e314eb 100644
--- a/utils/libmsym/cmake_install.cmake
+++ b/utils/libmsym/cmake_install.cmake
@@ -1,4 +1,4 @@
-# Install script for directory: /home/nestor/Develop/M3C/utils/libmsym
+# Install script for directory: /home/natalia/Develop/M3C/utils/libmsym
 
 # Set the install prefix
 if(NOT DEFINED CMAKE_INSTALL_PREFIX)
@@ -32,8 +32,20 @@ if(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
   set(CMAKE_INSTALL_SO_NO_EXE "1")
 endif()
 
-if(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
-  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/bin" TYPE EXECUTABLE FILES "/home/nestor/Develop/M3C/utils/libmsym/CMakeFiles/CMakeRelink.dir/molecule.symmetrize")
+if("${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified" OR NOT CMAKE_INSTALL_COMPONENT)
+  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/molecule.symmetrize" AND
+     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/molecule.symmetrize")
+    file(RPATH_CHECK
+         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/molecule.symmetrize"
+         RPATH "")
+  endif()
+  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/bin" TYPE EXECUTABLE FILES "/home/natalia/Develop/M3C/utils/molecule.symmetrize")
+  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/molecule.symmetrize" AND
+     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/molecule.symmetrize")
+    if(CMAKE_INSTALL_DO_STRIP)
+      execute_process(COMMAND "/usr/bin/strip" "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/molecule.symmetrize")
+    endif()
+  endif()
 endif()
 
 if(CMAKE_INSTALL_COMPONENT)
@@ -44,5 +56,5 @@ endif()
 
 string(REPLACE ";" "\n" CMAKE_INSTALL_MANIFEST_CONTENT
        "${CMAKE_INSTALL_MANIFEST_FILES}")
-file(WRITE "/home/nestor/Develop/M3C/utils/libmsym/${CMAKE_INSTALL_MANIFEST}"
+file(WRITE "/home/natalia/Develop/M3C/utils/libmsym/${CMAKE_INSTALL_MANIFEST}"
      "${CMAKE_INSTALL_MANIFEST_CONTENT}")

From 326d8d4b1608e5664aac58168cdcd9c674619f6a Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sat, 9 Feb 2019 21:23:43 -0700
Subject: [PATCH 30/57] First part about implementing transition states

---
 src/Fragment.f90    |  7 -------
 src/FragmentsDB.f90 | 29 ++++++++++++++++++-----------
 src/Reactor.f90     | 15 +++++++++++++++
 3 files changed, 33 insertions(+), 18 deletions(-)

diff --git a/src/Fragment.f90 b/src/Fragment.f90
index a45db2c..59ca9ad 100644
--- a/src/Fragment.f90
+++ b/src/Fragment.f90
@@ -391,15 +391,8 @@ end subroutine destroyFragment
 	subroutine updateFormula( this )
 		class(Fragment) :: this 
 		
-		integer :: isLineal
 		character(100), allocatable :: tokens(:)
 		
-		if( this.isLineal() ) then
-			isLineal = 1
-		else
-			isLineal = 0
-		end if
-		
 		this.dlabel_ = this.name
 		
 		call FString_split( this.name, tokens, "(" )
diff --git a/src/FragmentsDB.f90 b/src/FragmentsDB.f90
index a62abaa..ee1834d 100644
--- a/src/FragmentsDB.f90
+++ b/src/FragmentsDB.f90
@@ -62,6 +62,7 @@ module FragmentsDB_
 	use StringIntegerMap_
 	
 	use Fragment_
+	use FragmentsList_
 	use ModelPotential_
 	use GOptionsM3C_
 	
@@ -79,11 +80,11 @@ module FragmentsDB_
 		type(StringIntegerMap) :: forbiddenReactions
 		logical :: useForbiddenReactionsDetails
 		
-! 		"C2(d1)+C(t1)-->C3(s1)" --> 5 --> transitionState(5)
+! 		"C2(d1)+C(t1)-->C3(s1)" --> 5 . It means transitionState(5)
 ! 		|----------str2id_TS----------|
 		type(Fragment), allocatable :: transitionState(:)
 		type(StringIntegerMap) :: str2id_TS
-		logical, allocatable :: involvedInTS(:) ! One for each group. For speed purposes only.
+		logical, allocatable :: involvedInTS(:) ! One for each cluster. For speed purposes only.
 		
 		real(8), private :: energyReference_
 		logical, private :: useAtomicPotentials
@@ -360,6 +361,10 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 		character(100), allocatable :: tokens(:), tokens2(:), tokens3(:)
 		real(8) :: rBuffer
 		
+		! Only for transition states. They are neccessary to calculate the right label (mass sorted)
+		type(FragmentsList) :: reactives
+		type(FragmentsList) :: products
+		
 		if( allocated(this.transitionState) ) deallocate( this.transitionState )
 		allocate( this.transitionState(size(transitionStatesTable)) )
 		
@@ -395,28 +400,28 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 			! Choosing the reactives and products
 			!------------------------------------------
 			if( size(tokens) >= 9 .and. this.transitionState(i).nAtoms() /= 1 ) then
-				call FString_split( trim(adjustl(tokens(9))), tokens2, "-->" )
+				call FString_split( trim(adjustl(tokens(9))), tokens2, "<-->" )
 				
-				write(*,*) "Reactivos"
 				call FString_split( trim(adjustl(tokens2(1))), tokens3, "+" )
+				call reactives.init( size(tokens3) )
+				
 				do j=1,size(tokens3)
-					write(*,*) "token = ", trim(tokens3(j))
 					do k=1,size(this.clusters)
 						if( trim(tokens3(j)) == this.clusters(k).label() ) then
-							write(IO_STDOUT,*) k, this.clusters(k).id
+							reactives.clusters(j) = this.clusters(k)
 							this.involvedInTS(k) = .true.
 						end if
 					end do
 				end do
 				deallocate( tokens3 )
 				
-				write(*,*) "Productos"
 				call FString_split( trim(adjustl(tokens2(2))), tokens3, "+" )
+				call products.init( size(tokens3) )
+				
 				do j=1,size(tokens3)
-					write(*,*) "token = ", trim(tokens3(j))
 					do k=1,size(this.clusters)
 						if( trim(tokens3(j)) == this.clusters(k).label() ) then
-							write(IO_STDOUT,*) k, this.clusters(k).id
+							products.clusters(j) = this.clusters(k)
 							this.involvedInTS(k) = .true.
 						end if
 					end do
@@ -425,8 +430,10 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 				
 				deallocate( tokens2 )
 				
-				write(*,*) "Agregado: ", FString_toString(trim(adjustl(tokens(9)))//"-->"//trim(adjustl(tokens(10)))), ">>", i
-				call this.str2id_TS.insert( FString_toString(trim(adjustl(tokens(9)))//"-->"//trim(adjustl(tokens(10)))), i )
+				write(*,"(4X,A22,A)")  "Path = ", trim(reactives.label())//"<-->"//trim(products.label())
+				call this.str2id_TS.insert( FString_toString(trim(reactives.label())//"<-->"//trim(products.label())), i )
+				call this.str2id_TS.insert( FString_toString(trim(products.label())//"<-->"//trim(reactives.label())), i )
+				
 			else
 				call GOptions_error( &
 						"Bad number of atoms in transition state (N=0)", &
diff --git a/src/Reactor.f90 b/src/Reactor.f90
index fe839c1..600948a 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -112,6 +112,7 @@ module Reactor_
 			procedure, private, NOPASS :: isSpinForbidden
 			procedure, private, NOPASS :: reactorConstraint
 			procedure, private, NOPASS :: reactionString
+			procedure, private, NOPASS :: reduceToTransitionStates
 			
 			procedure :: execute
 			procedure :: executeMinFragmentationEnergy
@@ -315,6 +316,11 @@ subroutine changeComposition( this, dNfrag )
 				maxIterForbidden = maxIterForbidden + 1
 				cycle
 			else
+				
+				if( allocated(FragmentsDB_instance.transitionState) ) then
+					call reduceToTransitionStates( this.reactives, this.products )
+				end if
+				
 				exit
 			end if
 			
@@ -464,6 +470,15 @@ function reactionString( reactives, products, details ) result( output )
 		output = trim(reactives.label( details=effDetails ))//"-->"//trim(products.label( details=effDetails ))
 	end function reactionString
 	
+	!>
+	!! @brief Replaces products for the corresponding transition states. Only composition is changed
+	!!
+	subroutine reduceToTransitionStates( reactives, products )
+		type(FragmentsList), intent(in) :: reactives
+		type(FragmentsList), intent(inout) :: products
+		
+	end subroutine reduceToTransitionStates
+	
 	!>
 	!! @brief Change the composition of the system
 	!!

From 4b5ffed0dcc19edccf74c23d5e11bcf343fb402e Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 16:31:15 -0700
Subject: [PATCH 31/57] Second trial for TS. There is a bug when all products
 fit with one TS

---
 src/Reactor.f90 | 162 +++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 159 insertions(+), 3 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 600948a..910d369 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -57,13 +57,13 @@ module Reactor_
 	use IOStream_
 	use Timer_
 	use UnitsConverter_
-	use IVector_
 	use RandomUtils_
 	use StringList_
 	use AtomicElementsDB_
 	use BlocksIFileParser_
 	use RealHistogram_
 	use RealList_
+	use IntegerVector_
 	use StringIntegerMap_
 	use StringRealMap_
 	use StringRealPair_
@@ -92,6 +92,9 @@ module Reactor_
 		type(FragmentsList) :: products
 		logical :: state
 		
+		type(FragmentsList) :: productsTS
+		logical :: replaceTS
+		
 		character(3), private :: name
 		integer, private :: type
 		integer, allocatable :: dNFrag(:)
@@ -318,7 +321,9 @@ subroutine changeComposition( this, dNfrag )
 			else
 				
 				if( allocated(FragmentsDB_instance.transitionState) ) then
-					call reduceToTransitionStates( this.reactives, this.products )
+					call reduceToTransitionStates( this.reactives, this.products, this.productsTS )
+					
+					if( this.productsTS.nMolecules() > 0 ) this.replaceTS = .true.
 				end if
 				
 				exit
@@ -473,10 +478,157 @@ end function reactionString
 	!>
 	!! @brief Replaces products for the corresponding transition states. Only composition is changed
 	!!
-	subroutine reduceToTransitionStates( reactives, products )
+	subroutine reduceToTransitionStates( reactives, products, productsTS )
 		type(FragmentsList), intent(in) :: reactives
 		type(FragmentsList), intent(inout) :: products
+		type(FragmentsList), intent(out) :: productsTS
+		
+		integer :: i, j, id
+		integer :: ir, jr, kr
+		integer :: ip, jp, kp
+		type(IntegerVector) :: reactiveInTS
+		type(IntegerVector) :: productInTS
+		integer, allocatable :: reactiveInTScomb(:,:)
+		integer, allocatable :: productInTScomb(:,:)
+		integer :: nAtomsR, nAtomsP
+		integer :: massNumberR, massNumberP
+		type(FragmentsList) :: lReactives, lProducts
+		type(String) :: labelTS, label
+		logical :: locatedTS
+		
+		call reactiveInTS.init( resizeIncrement=reactives.nMolecules() )
+		call productInTS.init( resizeIncrement=products.nMolecules() )
+		
+		do i=1,reactives.nMolecules()
+			id = FragmentsDB_instance.getIdFromName( reactives.clusters(i).label() )
+			if( FragmentsDB_instance.involvedInTS( id ) ) then
+					call reactiveInTS.append( i )
+			end if
+		end do
 		
+		do i=1,products.nMolecules()
+			id = FragmentsDB_instance.getIdFromName( products.clusters(i).label() )
+			if( FragmentsDB_instance.involvedInTS( id ) ) then
+					call productInTS.append( i )
+			end if
+		end do
+		
+		if( .not. reactiveInTS.isEmpty() .and. .not. productInTS.isEmpty() ) then
+! 			write(*,"(A)",advance="no") "Reactives "
+! 			do i=1,reactives.nMolecules()
+! 				write(*,"(A)",advance="no") trim(reactives.clusters(i).label())//"+"
+! 			end do
+! 			write(*,*) ""
+! 			write(*,*) "reactiveInTS = ", reactiveInTS.data(1:reactiveInTS.size())
+! 			write(*,"(A)",advance="no") "Products "
+! 			do i=1,products.nMolecules()
+! 				write(*,"(A)",advance="no") trim(products.clusters(i).label())//"+"
+! 			end do
+! 			write(*,*) ""
+! 			write(*,*) "productInTS = ", productInTS.data(1:productInTS.size())
+			
+			locatedTS = .false.
+			
+			do ir=1,reactiveInTS.size()
+				call Math_combinations( reactiveInTS.size(), ir, reactiveInTScomb )
+				
+				do jr=1,size(reactiveInTScomb,dim=1)
+					
+					nAtomsR = 0
+					massNumberR = 0
+					do kr=1,size(reactiveInTScomb,dim=2)
+						massNumberR = massNumberR + reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) ).massNumber()
+						nAtomsR = nAtomsR + reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) ).nAtoms()
+					end do
+					
+					do ip=1,productInTS.size()
+						call Math_combinations( productInTS.size(), ip, productInTScomb )
+						
+						do jp=1,size(productInTScomb,dim=1)
+							
+							nAtomsP = 0
+							massNumberP = 0
+							do kp=1,size(productInTScomb,dim=2)
+								massNumberP = massNumberP + products.clusters( productInTS.at(productInTScomb(jp,kp)) ).massNumber()
+								nAtomsP = nAtomsP + products.clusters( productInTS.at(productInTScomb(jp,kp)) ).nAtoms()
+							end do
+							
+							if( massNumberR == massNumberP .and. nAtomsR > 1 .and. nAtomsP > 1 ) then
+								
+								call lReactives.init( size(reactiveInTScomb,dim=2) )
+								call lProducts.init( size(productInTScomb,dim=2) )
+								
+								do kr=1,size(reactiveInTScomb,dim=2)
+									lReactives.clusters(kr) = reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) )
+								end do
+							
+								do kp=1,size(productInTScomb,dim=2)
+									lProducts.clusters(kp) = products.clusters( productInTS.at(productInTScomb(jp,kp)) )
+								end do
+								
+								if( trim(lReactives.label()) /= trim(lProducts.label()) ) then
+									
+									labelTS = trim(lReactives.label())//"<-->"//trim(lProducts.label())
+									
+									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "      reactives = ", trim(reactives.label())
+										write(*,*) "       products = ", trim(products.label())
+										write(*,*) "     TS located = ", trim(labelTS.fstr)
+									end if
+									
+									call productsTS.init( products.nMolecules() - lProducts.nMolecules() + 1 )
+									
+									! @TODO Aca el problema aparece cuando todos los productos estan en un TS como C(t1)+C(t1)+C(t1)
+									!       En este caso nunca se entra en el if
+									j=1
+									do i=1,products.nMolecules()
+										do kp=1,size(productInTScomb,dim=2)
+											label = trim(products.clusters( productInTS.at(productInTScomb(jp,kp)) ).label())
+											if( label /= trim(products.clusters(i).label()) &
+												.and. j<=lProducts.nMolecules() ) then
+												call productsTS.set( j, products.clusters(i) )
+												j = j+1
+												exit
+											end if
+										end do
+									end do
+									
+									call productsTS.set( j, &
+													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									
+									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
+									end if
+									
+									locatedTS = .true.
+									exit ! Only one TS is accepted. The one with minimum size
+									
+								end if
+								
+							end if
+							
+						end do
+						
+						if( locatedTS ) exit
+						
+					end do
+					
+					if( locatedTS ) exit
+					
+				end do
+				
+				if( locatedTS ) exit
+				
+			end do
+			
+		end if
+		
+		if( GOptions_debugLevel >= 2 ) then
+			write(*,*) ""
+		end if
+		
+		if( allocated(reactiveInTScomb) ) deallocate( reactiveInTScomb )
+		if( allocated(productInTScomb) ) deallocate( productInTScomb )
 	end subroutine reduceToTransitionStates
 	
 	!>
@@ -867,6 +1019,8 @@ subroutine run( this )
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				
@@ -947,6 +1101,8 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
+		if( this.replaceTS ) this.replaceTS = .false.
+		
 	end subroutine run
 	
 	!>

From cf595577e6436fa7f020f59f94a8f997628fae70 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 17:05:57 -0700
Subject: [PATCH 32/57] Bug replacing products by TS fixed

---
 src/Reactor.f90 | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 910d369..e3dd10b 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -578,14 +578,17 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 									
 									call productsTS.init( products.nMolecules() - lProducts.nMolecules() + 1 )
 									
+									call productsTS.set( 1, &
+													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									
 									! @TODO Aca el problema aparece cuando todos los productos estan en un TS como C(t1)+C(t1)+C(t1)
 									!       En este caso nunca se entra en el if
-									j=1
+									j=2
 									do i=1,products.nMolecules()
 										do kp=1,size(productInTScomb,dim=2)
 											label = trim(products.clusters( productInTS.at(productInTScomb(jp,kp)) ).label())
 											if( label /= trim(products.clusters(i).label()) &
-												.and. j<=lProducts.nMolecules() ) then
+												.and. j<=productsTS.nMolecules() ) then
 												call productsTS.set( j, products.clusters(i) )
 												j = j+1
 												exit
@@ -593,8 +596,14 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 										end do
 									end do
 									
-									call productsTS.set( j, &
-													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									if( j==2 ) then
+										do i=1,products.nMolecules()
+											if( j<=productsTS.nMolecules() ) then
+												call productsTS.set( j, products.clusters(i) )
+												j = j+1
+											end if
+										end do
+									end if
 									
 									if( GOptions_debugLevel >= 2 ) then
 										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
@@ -1016,11 +1025,11 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				

From 17395aa1305c56879663ccc3a6da69dbd3e04a69 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Wed, 13 Feb 2019 22:09:08 -0700
Subject: [PATCH 33/57] First version working with TS

---
 src/FragmentsDB.f90 |  1 +
 src/MarkovChain.f90 | 11 ++++++++---
 src/Reactor.f90     | 35 ++++++++++++++++++++++++++++-------
 3 files changed, 37 insertions(+), 10 deletions(-)

diff --git a/src/FragmentsDB.f90 b/src/FragmentsDB.f90
index ee1834d..3baaa84 100644
--- a/src/FragmentsDB.f90
+++ b/src/FragmentsDB.f90
@@ -377,6 +377,7 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 		
 		do i=1,size(transitionStatesTable)
 			call this.transitionState(i).fromMassTableRow( transitionStatesTable(i).fstr, id=i, store=store.fstr )
+			this.transitionState(i).isTransitionState = .true.
 			
 			call FString_split( transitionStatesTable(i).fstr, tokens, " " )
 			
diff --git a/src/MarkovChain.f90 b/src/MarkovChain.f90
index a34d07c..2c8e433 100644
--- a/src/MarkovChain.f90
+++ b/src/MarkovChain.f90
@@ -442,7 +442,7 @@ subroutine run( this, reactives )
 	! 							sBuffer = react.reactives.weightHistoryLine( origin )
 	! 						end if
 	! 					end if
-
+	
 						call react.run()
 						
 						! Si la energía cinetica es negativa
@@ -483,7 +483,12 @@ subroutine run( this, reactives )
 						
 							nTimesBlocked = 0  ! El bloqueo debe ser consecutivo, así que si no pasa por negative energy se cuenta nuevamente
 							
-							Pi = react.products.LnW()-react.reactives.LnW()
+							if( react.replaceTS ) then
+								react.replaceTS = .false.
+								Pi = react.productsTS.LnW()-react.reactives.LnW()
+							else
+								Pi = react.products.LnW()-react.reactives.LnW()
+							end if
 							
 							if( Pi > 0.0_8 ) then
 								if( trim(react.reactives.label( details=.false. )) /= trim(react.products.label( details=.false. )) ) then
@@ -518,7 +523,7 @@ subroutine run( this, reactives )
 										sBuffer = trim(react.reactives.label( details=.true. ))//"-->"//trim(react.products.label( details=.true. ))
 										call this.transitionDetHistogram.add( sBuffer )
 									end if
-
+									
 									react.reactives = react.products
 									
 									call GOptions_info( &
diff --git a/src/Reactor.f90 b/src/Reactor.f90
index e3dd10b..4a74d46 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -606,6 +606,7 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 									end if
 									
 									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "       products = ", trim(products.label())
 										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
 									end if
 									
@@ -1011,11 +1012,12 @@ subroutine run( this )
 		
 		real(8) :: min_dLnW
 		
-		integer :: n, nMin
+		integer :: nMin
 		real(8) :: rBuffer
 		type(String) :: sBuffer
 		
 		this.state = .true.
+		this.replaceTS = .false.
 		
 		call this.showReactorHeader()
 		
@@ -1025,8 +1027,6 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
@@ -1039,16 +1039,37 @@ subroutine run( this )
 ! 				call this.products.changeVibrationalEnergy()
 ! 				call this.products.changeGeometry()
 ! 				call this.products.changeOrientations()
+
+				if( this.replaceTS ) then
+					! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
+					call this.productsTS.setReactorEnergy( this.reactives.reactorEnergy() )
+					
+					! Para que fuerce los centros aleatorios en la siguiente iteración
+					this.productsTS.forceRandomCenters = .true.
+					
+					! Los productos utilizan parte de la energía
+					call this.productsTS.initialGuessFragmentsList()
+					
+! 					write(*,*) "reactive ", trim(this.reactives.label())
+! 					write(*,*) "products ", trim(this.products.label())
+! 					write(*,*) "TS located ", trim(this.productsTS.label())
+! 					sBuffer = this.products.energyHistoryLine()
+! 					write(*,"(A)") trim(sBuffer.fstr)
+! 					sBuffer = this.productsTS.energyHistoryLine()
+! 					write(*,"(A)") trim(sBuffer.fstr)
+					
+				end if
 				
 			case( VIBRATIONAL_REACTOR )
-				
+			
 				! La composición es igual antes y después
 				this.products = this.reactives
 				
 				! Los productos utilizan parte de la energía cinética en vibracional
 				call this.products.changeVibrationalEnergy()
-			
+				
 			case( TRANSLATIONAL_REACTOR )
+			
 				! La composición es igual antes y después
 				this.products = this.reactives
 				
@@ -1056,11 +1077,13 @@ subroutine run( this )
 				call this.products.changeGeometry()
 				
 			case( ROTATIONAL_REACTOR )
+			
 				! La composición es igual antes y después
 				this.products = this.reactives
 				
 				! Los productos utilizan parte de la energía
 				call this.products.changeOrientations()
+				
 		end select
 		
 		if( GOptions_printLevel >= 2 ) then
@@ -1110,8 +1133,6 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
-		if( this.replaceTS ) this.replaceTS = .false.
-		
 	end subroutine run
 	
 	!>

From d4563a833fc1c36195daa7816501c92565051d84 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Wed, 13 Feb 2019 22:10:35 -0700
Subject: [PATCH 34/57] Version updated

---
 VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/VERSION b/VERSION
index cd5ac03..2789166 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2.0
+2.1a

From 20f7cc367014654936320752e81166ed9af8a376 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Thu, 28 Feb 2019 23:22:23 -0700
Subject: [PATCH 35/57] Gaussian template freqs updated to improve symmetry
 detection

---
 templates/b3lyp.freqs-GAUSSIAN.inp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/b3lyp.freqs-GAUSSIAN.inp b/templates/b3lyp.freqs-GAUSSIAN.inp
index e8e1d55..0d144fa 100644
--- a/templates/b3lyp.freqs-GAUSSIAN.inp
+++ b/templates/b3lyp.freqs-GAUSSIAN.inp
@@ -1,4 +1,4 @@
-#p b3lyp/6-311++G(3df,2p) freq
+#p b3lyp/6-311++G(3df,2p) freq IOp(2/17=3) IOp(2/18=3)
 
  b3lyp opt
 

From 0ae740c2dc8eb4be29db4632693b866fe6255a3e Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 3 Mar 2019 01:48:59 -0700
Subject: [PATCH 36/57] M3C.check now checks the right value of the
 multiplicity based on the stoichiometry and charge

---
 src/M3C.check | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/src/M3C.check b/src/M3C.check
index d55c056..31afbaf 100755
--- a/src/M3C.check
+++ b/src/M3C.check
@@ -165,20 +165,22 @@ function checkConsistence()
 			
 		fi
 		
-		if [[ ! "$multID" =~ ^m[1-9]+$ ]]
+		if [[ "$multID" =~ ^m[1-9]+$ ]]
 		then
-		
-			if [ "$REMOVE_WRONGFORMAT" = "TRUE" ]
+			minMult=`molecule.minMult $ifile ${chargeID#q}`
+			
+			if [ ! "$multID" = "m$(($minMult+0))" -a  ! "$multID" = "m$(($minMult+2))" \
+					-a  ! "$multID" = "m$(($minMult+4))" -a  ! "$multID" = "m$(($minMult+6))" ]
 			then
-				echo "--> Removed ($ifile) Inconsistency in multID ( $multID --> m[1-9]+ )"
-				rm $ifile
-				continue
-			else
 				echo ""
-				echo "### ERROR ### Inconsistency in multID ( $multID --> m[1-9]+ )"
+				echo -n "### ERROR ### Inconsistency in multiplicity ( $multID --> "
+				echo "m$(($minMult+0)), m$(($minMult+2)), m$(($minMult+4)), or m$(($minMult+6)) ) )"
 				kill $$
 			fi
-			
+		else
+			echo ""
+			echo "### ERROR ### Inconsistency in multID ( $multID --> m[1-9]+ )"
+			kill $$
 		fi
 		
 		if [[ ! "$isomerID" =~ ^[0-9]+$ ]]

From 8e157b2bec6c2bbd35ea987682f5960bd870724e Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Tue, 5 Mar 2019 20:46:53 -0700
Subject: [PATCH 37/57] oGaussian2rxyz bug fixed

---
 utils/oGaussian2rxyz.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/utils/oGaussian2rxyz.sh b/utils/oGaussian2rxyz.sh
index deff9e1..b226483 100755
--- a/utils/oGaussian2rxyz.sh
+++ b/utils/oGaussian2rxyz.sh
@@ -113,7 +113,8 @@ then
 		echo "SYMMETRY R3"
 		echo "ELECTRONIC_STATE ??"
 	else
-		group=`grep "Full point group" $iFile | tail -n1 | gawk '{print $4}'`
+		#group=`grep "Full point group" $iFile | tail -n1 | gawk '{print $4}'`
+		group=`grep "Framework group" $iFile | sed 's/\[/ /g' | gawk '{print $3}' | tail -n1`
 		if [ "$group" = "Nop" -o "$group" = "NOp" ]
 		then
 			echo "SYMMETRY ??"

From c15a6a9f2c5195caa6108bfba80d28017b6afca4 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 16:31:15 -0700
Subject: [PATCH 38/57] Second trial for TS. There is a bug when all products
 fit with one TS

---
 src/Reactor.f90 | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 4a74d46..49f5ee3 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -1030,6 +1030,8 @@ subroutine run( this )
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				
@@ -1133,6 +1135,8 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
+		if( this.replaceTS ) this.replaceTS = .false.
+		
 	end subroutine run
 	
 	!>

From 145fc8a250009a21e4df9c9c3a8ef92855d6edb1 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 17:05:57 -0700
Subject: [PATCH 39/57] Bug replacing products by TS fixed

---
 src/Reactor.f90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 49f5ee3..7b6b5a2 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -1027,11 +1027,11 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				

From ee566cafb2b10b635b854ce08012d169d45465cd Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Wed, 13 Feb 2019 22:09:08 -0700
Subject: [PATCH 40/57] First version working with TS

---
 src/Reactor.f90 | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 7b6b5a2..4a74d46 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -1027,8 +1027,6 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
@@ -1135,8 +1133,6 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
-		if( this.replaceTS ) this.replaceTS = .false.
-		
 	end subroutine run
 	
 	!>

From cca1ebe202c9eac3ca68009dd2adb1eb0d3306a7 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 16:31:15 -0700
Subject: [PATCH 41/57] Second trial for TS. There is a bug when all products
 fit with one TS

---
 src/Reactor.f90 | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 4a74d46..49f5ee3 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -1030,6 +1030,8 @@ subroutine run( this )
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				
@@ -1133,6 +1135,8 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
+		if( this.replaceTS ) this.replaceTS = .false.
+		
 	end subroutine run
 	
 	!>

From f4b394be1f8f6abcdafa4e0552a263f5f0c379da Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 17:05:57 -0700
Subject: [PATCH 42/57] Bug replacing products by TS fixed

---
 src/Reactor.f90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 49f5ee3..7b6b5a2 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -1027,11 +1027,11 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				

From 0d400f53ec324447ca2a78d805b415ef255608f7 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Wed, 13 Feb 2019 22:09:08 -0700
Subject: [PATCH 43/57] First version working with TS

---
 src/Reactor.f90 | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 7b6b5a2..4a74d46 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -1027,8 +1027,6 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
@@ -1135,8 +1133,6 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
-		if( this.replaceTS ) this.replaceTS = .false.
-		
 	end subroutine run
 	
 	!>

From ecb1761dbf9115c31b7ab8fc521222acc6865f72 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sat, 9 Feb 2019 21:23:43 -0700
Subject: [PATCH 44/57] First part about implementing transition states

---
 src/Reactor.f90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 4a74d46..1a0960b 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -639,6 +639,7 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 		
 		if( allocated(reactiveInTScomb) ) deallocate( reactiveInTScomb )
 		if( allocated(productInTScomb) ) deallocate( productInTScomb )
+		
 	end subroutine reduceToTransitionStates
 	
 	!>

From 65737b1c34b8a8bb308d7cb5caa431ac9e6d9c92 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 16:31:15 -0700
Subject: [PATCH 45/57] Second trial for TS. There is a bug when all products
 fit with one TS

---
 src/Reactor.f90 | 127 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 127 insertions(+)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 1a0960b..3ee5cea 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -640,6 +640,129 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 		if( allocated(reactiveInTScomb) ) deallocate( reactiveInTScomb )
 		if( allocated(productInTScomb) ) deallocate( productInTScomb )
 		
+		do i=1,products.nMolecules()
+			id = FragmentsDB_instance.getIdFromName( products.clusters(i).label() )
+			if( FragmentsDB_instance.involvedInTS( id ) ) then
+					call productInTS.append( i )
+			end if
+		end do
+		
+		if( .not. reactiveInTS.isEmpty() .and. .not. productInTS.isEmpty() ) then
+! 			write(*,"(A)",advance="no") "Reactives "
+! 			do i=1,reactives.nMolecules()
+! 				write(*,"(A)",advance="no") trim(reactives.clusters(i).label())//"+"
+! 			end do
+! 			write(*,*) ""
+! 			write(*,*) "reactiveInTS = ", reactiveInTS.data(1:reactiveInTS.size())
+! 			write(*,"(A)",advance="no") "Products "
+! 			do i=1,products.nMolecules()
+! 				write(*,"(A)",advance="no") trim(products.clusters(i).label())//"+"
+! 			end do
+! 			write(*,*) ""
+! 			write(*,*) "productInTS = ", productInTS.data(1:productInTS.size())
+			
+			locatedTS = .false.
+			
+			do ir=1,reactiveInTS.size()
+				call Math_combinations( reactiveInTS.size(), ir, reactiveInTScomb )
+				
+				do jr=1,size(reactiveInTScomb,dim=1)
+					
+					nAtomsR = 0
+					massNumberR = 0
+					do kr=1,size(reactiveInTScomb,dim=2)
+						massNumberR = massNumberR + reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) ).massNumber()
+						nAtomsR = nAtomsR + reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) ).nAtoms()
+					end do
+					
+					do ip=1,productInTS.size()
+						call Math_combinations( productInTS.size(), ip, productInTScomb )
+						
+						do jp=1,size(productInTScomb,dim=1)
+							
+							nAtomsP = 0
+							massNumberP = 0
+							do kp=1,size(productInTScomb,dim=2)
+								massNumberP = massNumberP + products.clusters( productInTS.at(productInTScomb(jp,kp)) ).massNumber()
+								nAtomsP = nAtomsP + products.clusters( productInTS.at(productInTScomb(jp,kp)) ).nAtoms()
+							end do
+							
+							if( massNumberR == massNumberP .and. nAtomsR > 1 .and. nAtomsP > 1 ) then
+								
+								call lReactives.init( size(reactiveInTScomb,dim=2) )
+								call lProducts.init( size(productInTScomb,dim=2) )
+								
+								do kr=1,size(reactiveInTScomb,dim=2)
+									lReactives.clusters(kr) = reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) )
+								end do
+							
+								do kp=1,size(productInTScomb,dim=2)
+									lProducts.clusters(kp) = products.clusters( productInTS.at(productInTScomb(jp,kp)) )
+								end do
+								
+								if( trim(lReactives.label()) /= trim(lProducts.label()) ) then
+									
+									labelTS = trim(lReactives.label())//"<-->"//trim(lProducts.label())
+									
+									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "      reactives = ", trim(reactives.label())
+										write(*,*) "       products = ", trim(products.label())
+										write(*,*) "     TS located = ", trim(labelTS.fstr)
+									end if
+									
+									call productsTS.init( products.nMolecules() - lProducts.nMolecules() + 1 )
+									
+									! @TODO Aca el problema aparece cuando todos los productos estan en un TS como C(t1)+C(t1)+C(t1)
+									!       En este caso nunca se entra en el if
+									j=1
+									do i=1,products.nMolecules()
+										do kp=1,size(productInTScomb,dim=2)
+											label = trim(products.clusters( productInTS.at(productInTScomb(jp,kp)) ).label())
+											if( label /= trim(products.clusters(i).label()) &
+												.and. j<=lProducts.nMolecules() ) then
+												call productsTS.set( j, products.clusters(i) )
+												j = j+1
+												exit
+											end if
+										end do
+									end do
+									
+									call productsTS.set( j, &
+													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									
+									if( GOptions_debugLevel >= 2 ) then
+										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
+									end if
+									
+									locatedTS = .true.
+									exit ! Only one TS is accepted. The one with minimum size
+									
+								end if
+								
+							end if
+							
+						end do
+						
+						if( locatedTS ) exit
+						
+					end do
+					
+					if( locatedTS ) exit
+					
+				end do
+				
+				if( locatedTS ) exit
+				
+			end do
+			
+		end if
+		
+		if( GOptions_debugLevel >= 2 ) then
+			write(*,*) ""
+		end if
+		
+		if( allocated(reactiveInTScomb) ) deallocate( reactiveInTScomb )
+		if( allocated(productInTScomb) ) deallocate( productInTScomb )
 	end subroutine reduceToTransitionStates
 	
 	!>
@@ -1031,6 +1154,8 @@ subroutine run( this )
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				
@@ -1134,6 +1259,8 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
+		if( this.replaceTS ) this.replaceTS = .false.
+		
 	end subroutine run
 	
 	!>

From f11d9eca69d937357b8fe06f7a6b1383dda7e2e4 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 10 Feb 2019 17:05:57 -0700
Subject: [PATCH 46/57] Bug replacing products by TS fixed

---
 src/Reactor.f90 | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 3ee5cea..07bfba6 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -712,14 +712,17 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 									
 									call productsTS.init( products.nMolecules() - lProducts.nMolecules() + 1 )
 									
+									call productsTS.set( 1, &
+													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									
 									! @TODO Aca el problema aparece cuando todos los productos estan en un TS como C(t1)+C(t1)+C(t1)
 									!       En este caso nunca se entra en el if
-									j=1
+									j=2
 									do i=1,products.nMolecules()
 										do kp=1,size(productInTScomb,dim=2)
 											label = trim(products.clusters( productInTS.at(productInTScomb(jp,kp)) ).label())
 											if( label /= trim(products.clusters(i).label()) &
-												.and. j<=lProducts.nMolecules() ) then
+												.and. j<=productsTS.nMolecules() ) then
 												call productsTS.set( j, products.clusters(i) )
 												j = j+1
 												exit
@@ -727,8 +730,14 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 										end do
 									end do
 									
-									call productsTS.set( j, &
-													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									if( j==2 ) then
+										do i=1,products.nMolecules()
+											if( j<=productsTS.nMolecules() ) then
+												call productsTS.set( j, products.clusters(i) )
+												j = j+1
+											end if
+										end do
+									end if
 									
 									if( GOptions_debugLevel >= 2 ) then
 										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
@@ -1151,11 +1160,11 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
+				if( this.replaceTS ) this.products = this.productsTS
+				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Para que fuerce los centros aleatorios en la siguiente iteración
 				this.products.forceRandomCenters = .true.
 				

From 32c3bbabd77e3185748ce101753a22ed7bfe91e5 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Wed, 13 Feb 2019 22:09:08 -0700
Subject: [PATCH 47/57] First version working with TS

---
 src/Reactor.f90 | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 07bfba6..311f983 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -1160,8 +1160,6 @@ subroutine run( this )
 				! Se actualiza la composición
 				call this.changeComposition( this.dNFrag )
 				
-				if( this.replaceTS ) this.products = this.productsTS
-				
 				! Se le asocia la energía del reactor para asegurar que calcula un peso Wt es adecuado para los productos
 				call this.products.setReactorEnergy( this.reactives.reactorEnergy() )
 				
@@ -1268,8 +1266,6 @@ subroutine run( this )
 			this.state = .false.
 		end if
 		
-		if( this.replaceTS ) this.replaceTS = .false.
-		
 	end subroutine run
 	
 	!>

From 4eda88e5ae7c4f9b5e4f4fc5386755e8cf4bc1f3 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 8 Mar 2020 10:02:22 +0100
Subject: [PATCH 48/57] Files needed to compile

---
 utils/libmsym/CMakeCache.txt      |  89 ++++++++++++++++++++--
 utils/libmsym/Makefile            | 119 ++++++++++++++++--------------
 utils/libmsym/cmake_install.cmake |  20 ++++-
 3 files changed, 162 insertions(+), 66 deletions(-)

diff --git a/utils/libmsym/CMakeCache.txt b/utils/libmsym/CMakeCache.txt
index 87baf04..e51f32a 100644
--- a/utils/libmsym/CMakeCache.txt
+++ b/utils/libmsym/CMakeCache.txt
@@ -1,5 +1,5 @@
 # This is the CMakeCache file.
-# For build in directory: /home/nestor/Develop/M3C/utils/libmsym
+# For build in directory: /home/natalia/Develop/M3C/utils/libmsym
 # It was generated by CMake: /usr/bin/cmake
 # You can edit this file to change values found and used by cmake.
 # If you do not want to change any of the values, simply exit the editor.
@@ -14,6 +14,9 @@
 # EXTERNAL cache entries
 ########################
 
+//Path to a program.
+CMAKE_AR:FILEPATH=/usr/bin/ar
+
 //Choose the type of build, options are: None(CMAKE_CXX_FLAGS or
 // CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel.
 CMAKE_BUILD_TYPE:STRING=
@@ -21,6 +24,17 @@ CMAKE_BUILD_TYPE:STRING=
 //Enable/Disable color output during build.
 CMAKE_COLOR_MAKEFILE:BOOL=ON
 
+//CXX compiler
+CMAKE_CXX_COMPILER:FILEPATH=/usr/bin/c++
+
+//A wrapper around 'ar' adding the appropriate '--plugin' option
+// for the GCC compiler
+CMAKE_CXX_COMPILER_AR:FILEPATH=/usr/bin/gcc-ar-7
+
+//A wrapper around 'ranlib' adding the appropriate '--plugin' option
+// for the GCC compiler
+CMAKE_CXX_COMPILER_RANLIB:FILEPATH=/usr/bin/gcc-ranlib-7
+
 //Flags used by the compiler during all build types.
 CMAKE_CXX_FLAGS:STRING=
 
@@ -37,6 +51,17 @@ CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG
 //Flags used by the compiler during release builds with debug info.
 CMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG
 
+//C compiler
+CMAKE_C_COMPILER:FILEPATH=/usr/bin/cc
+
+//A wrapper around 'ar' adding the appropriate '--plugin' option
+// for the GCC compiler
+CMAKE_C_COMPILER_AR:FILEPATH=/usr/bin/gcc-ar-7
+
+//A wrapper around 'ranlib' adding the appropriate '--plugin' option
+// for the GCC compiler
+CMAKE_C_COMPILER_RANLIB:FILEPATH=/usr/bin/gcc-ranlib-7
+
 //Flags used by the compiler during all build types.
 CMAKE_C_FLAGS:STRING=
 
@@ -74,6 +99,9 @@ CMAKE_EXPORT_COMPILE_COMMANDS:BOOL=OFF
 //Install path prefix, prepended onto install directories.
 CMAKE_INSTALL_PREFIX:PATH=/usr/local
 
+//Path to a program.
+CMAKE_LINKER:FILEPATH=/usr/bin/ld
+
 //Path to a program.
 CMAKE_MAKE_PROGRAM:FILEPATH=/usr/bin/make
 
@@ -92,9 +120,21 @@ CMAKE_MODULE_LINKER_FLAGS_RELEASE:STRING=
 //Flags used by the linker during Release with Debug Info builds.
 CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO:STRING=
 
+//Path to a program.
+CMAKE_NM:FILEPATH=/usr/bin/nm
+
+//Path to a program.
+CMAKE_OBJCOPY:FILEPATH=/usr/bin/objcopy
+
+//Path to a program.
+CMAKE_OBJDUMP:FILEPATH=/usr/bin/objdump
+
 //Value Computed by CMake
 CMAKE_PROJECT_NAME:STATIC=msym
 
+//Path to a program.
+CMAKE_RANLIB:FILEPATH=/usr/bin/ranlib
+
 //Flags used by the linker during the creation of dll's.
 CMAKE_SHARED_LINKER_FLAGS:STRING=
 
@@ -132,6 +172,9 @@ CMAKE_STATIC_LINKER_FLAGS_RELEASE:STRING=
 //Flags used by the linker during Release with Debug Info builds.
 CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO:STRING=
 
+//Path to a program.
+CMAKE_STRIP:FILEPATH=/usr/bin/strip
+
 //If this value is on, makefiles will be generated without the
 // .SILENT directive, and all commands will be echoed to the console
 // during the make.  This is useful for debugging only. With Visual
@@ -139,25 +182,27 @@ CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO:STRING=
 CMAKE_VERBOSE_MAKEFILE:BOOL=FALSE
 
 //Value Computed by CMake
-msym_BINARY_DIR:STATIC=/home/nestor/Develop/M3C/utils/libmsym
+msym_BINARY_DIR:STATIC=/home/natalia/Develop/M3C/utils/libmsym
 
 //Dependencies for target
 msym_LIB_DEPENDS:STATIC=
 
 //Value Computed by CMake
-msym_SOURCE_DIR:STATIC=/home/nestor/Develop/M3C/utils/libmsym
+msym_SOURCE_DIR:STATIC=/home/natalia/Develop/M3C/utils/libmsym
 
 
 ########################
 # INTERNAL cache entries
 ########################
 
+//ADVANCED property for variable: CMAKE_AR
+CMAKE_AR-ADVANCED:INTERNAL=1
 //This is the directory where this CMakeCache.txt was created
-CMAKE_CACHEFILE_DIR:INTERNAL=/home/nestor/Develop/M3C/utils/libmsym
+CMAKE_CACHEFILE_DIR:INTERNAL=/home/natalia/Develop/M3C/utils/libmsym
 //Major version of cmake used to create the current loaded cache
 CMAKE_CACHE_MAJOR_VERSION:INTERNAL=3
 //Minor version of cmake used to create the current loaded cache
-CMAKE_CACHE_MINOR_VERSION:INTERNAL=5
+CMAKE_CACHE_MINOR_VERSION:INTERNAL=9
 //Patch version of cmake used to create the current loaded cache
 CMAKE_CACHE_PATCH_VERSION:INTERNAL=1
 //ADVANCED property for variable: CMAKE_COLOR_MAKEFILE
@@ -168,6 +213,12 @@ CMAKE_COMMAND:INTERNAL=/usr/bin/cmake
 CMAKE_CPACK_COMMAND:INTERNAL=/usr/bin/cpack
 //Path to ctest program executable.
 CMAKE_CTEST_COMMAND:INTERNAL=/usr/bin/ctest
+//ADVANCED property for variable: CMAKE_CXX_COMPILER
+CMAKE_CXX_COMPILER-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_CXX_COMPILER_AR
+CMAKE_CXX_COMPILER_AR-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_CXX_COMPILER_RANLIB
+CMAKE_CXX_COMPILER_RANLIB-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_CXX_FLAGS
 CMAKE_CXX_FLAGS-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_CXX_FLAGS_DEBUG
@@ -178,6 +229,12 @@ CMAKE_CXX_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
 CMAKE_CXX_FLAGS_RELEASE-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_CXX_FLAGS_RELWITHDEBINFO
 CMAKE_CXX_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_C_COMPILER
+CMAKE_C_COMPILER-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_C_COMPILER_AR
+CMAKE_C_COMPILER_AR-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_C_COMPILER_RANLIB
+CMAKE_C_COMPILER_RANLIB-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_C_FLAGS
 CMAKE_C_FLAGS-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_C_FLAGS_DEBUG
@@ -188,6 +245,8 @@ CMAKE_C_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
 CMAKE_C_FLAGS_RELEASE-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_C_FLAGS_RELWITHDEBINFO
 CMAKE_C_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
+//Executable file format
+CMAKE_EXECUTABLE_FORMAT:INTERNAL=ELF
 //ADVANCED property for variable: CMAKE_EXE_LINKER_FLAGS
 CMAKE_EXE_LINKER_FLAGS-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_EXE_LINKER_FLAGS_DEBUG
@@ -210,9 +269,11 @@ CMAKE_GENERATOR_PLATFORM:INTERNAL=
 CMAKE_GENERATOR_TOOLSET:INTERNAL=
 //Source directory with the top level CMakeLists.txt file for this
 // project
-CMAKE_HOME_DIRECTORY:INTERNAL=/home/nestor/Develop/M3C/utils/libmsym
+CMAKE_HOME_DIRECTORY:INTERNAL=/home/natalia/Develop/M3C/utils/libmsym
 //Install .so files without execute permission.
 CMAKE_INSTALL_SO_NO_EXE:INTERNAL=1
+//ADVANCED property for variable: CMAKE_LINKER
+CMAKE_LINKER-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_MAKE_PROGRAM
 CMAKE_MAKE_PROGRAM-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_MODULE_LINKER_FLAGS
@@ -225,10 +286,20 @@ CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
 CMAKE_MODULE_LINKER_FLAGS_RELEASE-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO
 CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_NM
+CMAKE_NM-ADVANCED:INTERNAL=1
 //number of local generators
 CMAKE_NUMBER_OF_MAKEFILES:INTERNAL=1
+//ADVANCED property for variable: CMAKE_OBJCOPY
+CMAKE_OBJCOPY-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_OBJDUMP
+CMAKE_OBJDUMP-ADVANCED:INTERNAL=1
+//Platform information initialized
+CMAKE_PLATFORM_INFO_INITIALIZED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_RANLIB
+CMAKE_RANLIB-ADVANCED:INTERNAL=1
 //Path to CMake installation.
-CMAKE_ROOT:INTERNAL=/usr/share/cmake-3.5
+CMAKE_ROOT:INTERNAL=/usr/share/cmake-3.9
 //ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS
 CMAKE_SHARED_LINKER_FLAGS-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS_DEBUG
@@ -253,6 +324,10 @@ CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
 CMAKE_STATIC_LINKER_FLAGS_RELEASE-ADVANCED:INTERNAL=1
 //ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO
 CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_STRIP
+CMAKE_STRIP-ADVANCED:INTERNAL=1
+//uname command
+CMAKE_UNAME:INTERNAL=/bin/uname
 //ADVANCED property for variable: CMAKE_VERBOSE_MAKEFILE
 CMAKE_VERBOSE_MAKEFILE-ADVANCED:INTERNAL=1
 
diff --git a/utils/libmsym/Makefile b/utils/libmsym/Makefile
index 15632a7..1e9a3f5 100644
--- a/utils/libmsym/Makefile
+++ b/utils/libmsym/Makefile
@@ -1,5 +1,5 @@
 # CMAKE generated file: DO NOT EDIT!
-# Generated by "Unix Makefiles" Generator, CMake Version 3.5
+# Generated by "Unix Makefiles" Generator, CMake Version 3.9
 
 # Default target executed when no arguments are given to make.
 default_target: all
@@ -48,35 +48,37 @@ RM = /usr/bin/cmake -E remove -f
 EQUALS = =
 
 # The top-level source directory on which CMake was run.
-CMAKE_SOURCE_DIR = /home/nestor/Develop/M3C/utils/libmsym
+CMAKE_SOURCE_DIR = /home/natalia/Develop/M3C/utils/libmsym
 
 # The top-level build directory on which CMake was run.
-CMAKE_BINARY_DIR = /home/nestor/Develop/M3C/utils/libmsym
+CMAKE_BINARY_DIR = /home/natalia/Develop/M3C/utils/libmsym
 
 #=============================================================================
 # Targets provided globally by CMake.
 
-# Special rule for the target install
-install: preinstall
-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
-	/usr/bin/cmake -P cmake_install.cmake
-.PHONY : install
+# Special rule for the target install/strip
+install/strip: preinstall
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing the project stripped..."
+	/usr/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake
+.PHONY : install/strip
 
-# Special rule for the target install
-install/fast: preinstall/fast
-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
-	/usr/bin/cmake -P cmake_install.cmake
-.PHONY : install/fast
+# Special rule for the target install/strip
+install/strip/fast: preinstall/fast
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing the project stripped..."
+	/usr/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake
+.PHONY : install/strip/fast
 
-# Special rule for the target list_install_components
-list_install_components:
-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Available install components are: \"Unspecified\""
-.PHONY : list_install_components
-
-# Special rule for the target list_install_components
-list_install_components/fast: list_install_components
+# Special rule for the target install/local
+install/local: preinstall
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing only the local directory..."
+	/usr/bin/cmake -DCMAKE_INSTALL_LOCAL_ONLY=1 -P cmake_install.cmake
+.PHONY : install/local
 
-.PHONY : list_install_components/fast
+# Special rule for the target install/local
+install/local/fast: preinstall/fast
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing only the local directory..."
+	/usr/bin/cmake -DCMAKE_INSTALL_LOCAL_ONLY=1 -P cmake_install.cmake
+.PHONY : install/local/fast
 
 # Special rule for the target rebuild_cache
 rebuild_cache:
@@ -89,17 +91,6 @@ rebuild_cache/fast: rebuild_cache
 
 .PHONY : rebuild_cache/fast
 
-# Special rule for the target install/local
-install/local: preinstall
-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing only the local directory..."
-	/usr/bin/cmake -DCMAKE_INSTALL_LOCAL_ONLY=1 -P cmake_install.cmake
-.PHONY : install/local
-
-# Special rule for the target install/local
-install/local/fast: install/local
-
-.PHONY : install/local/fast
-
 # Special rule for the target edit_cache
 edit_cache:
 	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "No interactive CMake dialog available..."
@@ -111,11 +102,33 @@ edit_cache/fast: edit_cache
 
 .PHONY : edit_cache/fast
 
+# Special rule for the target list_install_components
+list_install_components:
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Available install components are: \"Unspecified\""
+.PHONY : list_install_components
+
+# Special rule for the target list_install_components
+list_install_components/fast: list_install_components
+
+.PHONY : list_install_components/fast
+
+# Special rule for the target install
+install: preinstall
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+	/usr/bin/cmake -P cmake_install.cmake
+.PHONY : install
+
+# Special rule for the target install
+install/fast: preinstall/fast
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+	/usr/bin/cmake -P cmake_install.cmake
+.PHONY : install/fast
+
 # The main all target
 all: cmake_check_build_system
-	$(CMAKE_COMMAND) -E cmake_progress_start /home/nestor/Develop/M3C/utils/libmsym/CMakeFiles /home/nestor/Develop/M3C/utils/libmsym/CMakeFiles/progress.marks
+	$(CMAKE_COMMAND) -E cmake_progress_start /home/natalia/Develop/M3C/utils/libmsym/CMakeFiles /home/natalia/Develop/M3C/utils/libmsym/CMakeFiles/progress.marks
 	$(MAKE) -f CMakeFiles/Makefile2 all
-	$(CMAKE_COMMAND) -E cmake_progress_start /home/nestor/Develop/M3C/utils/libmsym/CMakeFiles 0
+	$(CMAKE_COMMAND) -E cmake_progress_start /home/natalia/Develop/M3C/utils/libmsym/CMakeFiles 0
 .PHONY : all
 
 # The main clean target
@@ -143,19 +156,6 @@ depend:
 	$(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 1
 .PHONY : depend
 
-#=============================================================================
-# Target rules for targets named msym
-
-# Build rule for target.
-msym: cmake_check_build_system
-	$(MAKE) -f CMakeFiles/Makefile2 msym
-.PHONY : msym
-
-# fast build rule for target.
-msym/fast:
-	$(MAKE) -f CMakeFiles/msym.dir/build.make CMakeFiles/msym.dir/build
-.PHONY : msym/fast
-
 #=============================================================================
 # Target rules for targets named molecule.symmetrize
 
@@ -169,10 +169,18 @@ molecule.symmetrize/fast:
 	$(MAKE) -f CMakeFiles/molecule.symmetrize.dir/build.make CMakeFiles/molecule.symmetrize.dir/build
 .PHONY : molecule.symmetrize/fast
 
-# Manual pre-install relink rule for target.
-molecule.symmetrize/preinstall:
-	$(MAKE) -f CMakeFiles/molecule.symmetrize.dir/build.make CMakeFiles/molecule.symmetrize.dir/preinstall
-.PHONY : molecule.symmetrize/preinstall
+#=============================================================================
+# Target rules for targets named msym
+
+# Build rule for target.
+msym: cmake_check_build_system
+	$(MAKE) -f CMakeFiles/Makefile2 msym
+.PHONY : msym
+
+# fast build rule for target.
+msym/fast:
+	$(MAKE) -f CMakeFiles/msym.dir/build.make CMakeFiles/msym.dir/build
+.PHONY : msym/fast
 
 basis_function.o: basis_function.c.o
 
@@ -666,13 +674,14 @@ help:
 	@echo "... all (the default if no target is provided)"
 	@echo "... clean"
 	@echo "... depend"
-	@echo "... install"
-	@echo "... list_install_components"
-	@echo "... rebuild_cache"
-	@echo "... msym"
+	@echo "... install/strip"
 	@echo "... install/local"
 	@echo "... molecule.symmetrize"
+	@echo "... rebuild_cache"
+	@echo "... msym"
 	@echo "... edit_cache"
+	@echo "... list_install_components"
+	@echo "... install"
 	@echo "... basis_function.o"
 	@echo "... basis_function.i"
 	@echo "... basis_function.s"
diff --git a/utils/libmsym/cmake_install.cmake b/utils/libmsym/cmake_install.cmake
index e5c8fb2..1e314eb 100644
--- a/utils/libmsym/cmake_install.cmake
+++ b/utils/libmsym/cmake_install.cmake
@@ -1,4 +1,4 @@
-# Install script for directory: /home/nestor/Develop/M3C/utils/libmsym
+# Install script for directory: /home/natalia/Develop/M3C/utils/libmsym
 
 # Set the install prefix
 if(NOT DEFINED CMAKE_INSTALL_PREFIX)
@@ -32,8 +32,20 @@ if(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
   set(CMAKE_INSTALL_SO_NO_EXE "1")
 endif()
 
-if(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
-  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/bin" TYPE EXECUTABLE FILES "/home/nestor/Develop/M3C/utils/libmsym/CMakeFiles/CMakeRelink.dir/molecule.symmetrize")
+if("${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified" OR NOT CMAKE_INSTALL_COMPONENT)
+  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/molecule.symmetrize" AND
+     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/molecule.symmetrize")
+    file(RPATH_CHECK
+         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/molecule.symmetrize"
+         RPATH "")
+  endif()
+  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/bin" TYPE EXECUTABLE FILES "/home/natalia/Develop/M3C/utils/molecule.symmetrize")
+  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/molecule.symmetrize" AND
+     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/molecule.symmetrize")
+    if(CMAKE_INSTALL_DO_STRIP)
+      execute_process(COMMAND "/usr/bin/strip" "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/molecule.symmetrize")
+    endif()
+  endif()
 endif()
 
 if(CMAKE_INSTALL_COMPONENT)
@@ -44,5 +56,5 @@ endif()
 
 string(REPLACE ";" "\n" CMAKE_INSTALL_MANIFEST_CONTENT
        "${CMAKE_INSTALL_MANIFEST_FILES}")
-file(WRITE "/home/nestor/Develop/M3C/utils/libmsym/${CMAKE_INSTALL_MANIFEST}"
+file(WRITE "/home/natalia/Develop/M3C/utils/libmsym/${CMAKE_INSTALL_MANIFEST}"
      "${CMAKE_INSTALL_MANIFEST_CONTENT}")

From 269c08ba85029d3268c1393fc8073b403b22ad48 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 8 Mar 2020 11:37:28 +0100
Subject: [PATCH 49/57] Examples directory included

---
 examples/ts/TS-examples/C2.m3c            | 69 ++++++++++++++++++++++
 examples/ts/TS-examples/C2ts.q0.m1-1.rxyz | 10 ++++
 examples/ts/TS-examples/C3.m3c            | 71 +++++++++++++++++++++++
 3 files changed, 150 insertions(+)
 create mode 100644 examples/ts/TS-examples/C2.m3c
 create mode 100644 examples/ts/TS-examples/C2ts.q0.m1-1.rxyz
 create mode 100644 examples/ts/TS-examples/C3.m3c

diff --git a/examples/ts/TS-examples/C2.m3c b/examples/ts/TS-examples/C2.m3c
new file mode 100644
index 0000000..22b92af
--- /dev/null
+++ b/examples/ts/TS-examples/C2.m3c
@@ -0,0 +1,69 @@
+BEGIN EXCITATION_ENERGY_SCAN
+	excitationEnergy  =  0:12:13  # dE = 1.0 eV
+END EXCITATION_ENERGY_SCAN
+
+BEGIN GOPTIONS
+        systemRadius = 10.0
+        overlappingRadius = 0.2
+        
+        useRandomWalkers = FALSE
+        randomWalkStepRadius = 1.0
+        
+        useZPECorrection = FALSE
+        useSpinConservationRules = FALSE
+        
+        angularMomentumCouplingScheme = JJL
+	#debugLevel = 3
+END GOPTIONS
+
+BEGIN MARKOV_CHAIN
+	task = 5*V,T,R,S:0,5*V,T,R,S:-1:1
+        burnInFraction = 0.0
+        
+	reactives = C2(s1)
+        excitationEnergy = 7.0
+        
+        tracking = weight
+        
+#         numberOfExperiments = 6
+#         numberOfEvents = 100000
+        numberOfExperiments = 3
+#         numberOfEvents = 50000
+        numberOfEvents = 20000
+#        historyFileFrequency = 100
+        historyFileFrequency = 1
+
+#        geometryHistoryFilePrefix = geom
+        energyHistoryFile = energy.dat
+        weightHistoryFile = weight.dat
+#        JHistoryFile = J.dat
+#        LHistoryFile = L.dat
+        histogramFile = histogram.dat
+END MARKOV_CHAIN
+
+BEGIN FRAGMENTS_DATABASE
+
+	store = /home/nestor/Develop/M3C-store/master/6-311++G.3df.2p/ccsdt
+	reference = C2(s1)
+
+	#--------------------------------------------------------------------------------------
+	#  Label    Z  M WL  SYM          geomFile         Eelec     maxVib
+	#--------------------------------------------------------------------------------------
+           C(s1)    0  1  5    1    C.q0.m1-1.rxyz  -1026.574168                      #           ¹D (2s²2p²) 
+           C(t1)    0  3  3    1    C.q0.m3-1.rxyz  -1028.024016                      #           ³P (2s²2p²)
+           
+          C2(s1)    0  1  1    2   C2.q0.m1-1.rxyz  -2062.151541     C(t1)+C(t1)      # 6.10351   ^1\Sigma_g^+
+          #C2(t1)    0  3  2    2   C2.q0.m3-1.rxyz  -2062.058719     C(t1)+C(t1)      # 6.01069   ^3\Pi_u 
+	#--------------------------------------------------------------------------------------
+END FRAGMENTS_DATABASE
+
+BEGIN TRANSITION_STATES_DATABASE
+
+ 	store = .
+	
+	#--------------------------------------------------------------------------------------
+	#  Label    Z  M WL  SYM          geomFile         Eelec     maxVib     TS
+	#--------------------------------------------------------------------------------------
+          C2(ts1)   0  1  1    2 C2ts.q0.m1-1.rxyz  -2054.048032        4.0     C2(s1)<-->C(t1)+C(t1)
+	#--------------------------------------------------------------------------------------
+END TRANSITION_STATES_DATABASE
diff --git a/examples/ts/TS-examples/C2ts.q0.m1-1.rxyz b/examples/ts/TS-examples/C2ts.q0.m1-1.rxyz
new file mode 100644
index 0000000..1668844
--- /dev/null
+++ b/examples/ts/TS-examples/C2ts.q0.m1-1.rxyz
@@ -0,0 +1,10 @@
+2
+Energy =   -75.8561424407255
+    C    0.823543    0.000000    0.000000
+    C   -0.823543    0.000000    0.000000
+
+FREQUENCIES 1
+1872.9045
+
+SYMMETRY D*H
+ELECTRONIC_STATE 1-SGG
diff --git a/examples/ts/TS-examples/C3.m3c b/examples/ts/TS-examples/C3.m3c
new file mode 100644
index 0000000..78bbf8b
--- /dev/null
+++ b/examples/ts/TS-examples/C3.m3c
@@ -0,0 +1,71 @@
+BEGIN EXCITATION_ENERGY_SCAN
+	excitationEnergy  =  0:20:21  # dE = 1.0 eV
+END EXCITATION_ENERGY_SCAN
+
+BEGIN GOPTIONS
+        systemRadius = 10.0
+        overlappingRadius = 0.2
+        
+        useRandomWalkers = FALSE
+        randomWalkStepRadius = 1.0
+        
+        useZPECorrection = FALSE
+        useSpinConservationRules = FALSE
+        
+        angularMomentumCouplingScheme = JJL
+	debugLevel = 2
+END GOPTIONS
+
+BEGIN MARKOV_CHAIN
+	task = 5*V,T,R,S:0,5*V,T,R,S:-1:1
+        burnInFraction = 0.0
+        
+# 	reactives = C3(s1)
+	reactives = C(t1)+C2(s1)
+        excitationEnergy = 20.0
+        
+        tracking = energy
+        
+#         numberOfExperiments = 6
+#         numberOfEvents = 100000
+        numberOfExperiments = 3
+#         numberOfEvents = 50000
+        numberOfEvents = 30000
+        historyFileFrequency = 100
+
+#        geometryHistoryFilePrefix = geom
+        energyHistoryFile = energy.dat
+        weightHistoryFile = weight.dat
+#        JHistoryFile = J.dat
+#        LHistoryFile = L.dat
+        histogramFile = histogram.dat
+END MARKOV_CHAIN
+
+BEGIN FRAGMENTS_DATABASE
+
+	store = /home/nestor/Develop/M3C-store/master/6-311++G.3df.2p/ccsdt
+	reference = C3(s1)
+
+	#--------------------------------------------------------------------------------------
+	#  Label    Z  M WL  SYM          geomFile         Eelec     maxVib
+	#--------------------------------------------------------------------------------------
+           C(s1)    0  1  5    1    C.q0.m1-1.rxyz  -1026.574168                      #           ¹D (2s²2p²) 
+           C(t1)    0  3  3    1    C.q0.m3-1.rxyz  -1028.024016                      #           ³P (2s²2p²)
+           
+          C2(s1)    0  1  1    2   C2.q0.m1-1.rxyz  -2062.151541     C(t1)+C(t1)      # 6.10351   ^1\Sigma_g^+
+          C2(t1)    0  3  2    2   C2.q0.m3-1.rxyz  -2062.058719     C(t1)+C(t1)      # 6.01069   ^3\Pi_u     
+          
+          C3(s1)    0  1  1    2   C3.q0.m1-1.rxyz  -3097.545476     C(t1)+C2(s1)     # 7.36992   D*H, 1-SGG
+	#--------------------------------------------------------------------------------------
+END FRAGMENTS_DATABASE
+
+BEGIN TRANSITION_STATES_DATABASE
+
+	store = .
+	
+	#--------------------------------------------------------------------------------------
+	#  Label    Z  M WL  SYM          geomFile         Eelec     maxVib     TS
+	#--------------------------------------------------------------------------------------
+          C2(ts1)   0  1  1    2 C2ts.q0.m1-1.rxyz  -2064.151541        4.0     C2(s1)<-->C(t1)+C(t1)
+	#--------------------------------------------------------------------------------------
+END TRANSITION_STATES_DATABASE

From 0f27436815d02225519572af8673d4e1427dc8fd Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 8 Mar 2020 21:30:33 +0100
Subject: [PATCH 50/57] First trial of fixing the cyclic dependency.

---
 src/FragmentsDB.f90 | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/FragmentsDB.f90 b/src/FragmentsDB.f90
index 3baaa84..5e5f462 100644
--- a/src/FragmentsDB.f90
+++ b/src/FragmentsDB.f90
@@ -364,6 +364,8 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 		! Only for transition states. They are neccessary to calculate the right label (mass sorted)
 		type(FragmentsList) :: reactives
 		type(FragmentsList) :: products
+! 		type(Fragment), allocatable :: reactives(:)
+! 		type(Fragment), allocatable :: products(:)
 		
 		if( allocated(this.transitionState) ) deallocate( this.transitionState )
 		allocate( this.transitionState(size(transitionStatesTable)) )
@@ -405,11 +407,13 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 				
 				call FString_split( trim(adjustl(tokens2(1))), tokens3, "+" )
 				call reactives.init( size(tokens3) )
+! 				allocate( reactives(size(tokens3)) )
 				
 				do j=1,size(tokens3)
 					do k=1,size(this.clusters)
 						if( trim(tokens3(j)) == this.clusters(k).label() ) then
 							reactives.clusters(j) = this.clusters(k)
+! 							reactives(j) = this.clusters(k)
 							this.involvedInTS(k) = .true.
 						end if
 					end do
@@ -418,11 +422,13 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 				
 				call FString_split( trim(adjustl(tokens2(2))), tokens3, "+" )
 				call products.init( size(tokens3) )
+! 				allocate( products(size(tokens3)) )
 				
 				do j=1,size(tokens3)
 					do k=1,size(this.clusters)
 						if( trim(tokens3(j)) == this.clusters(k).label() ) then
 							products.clusters(j) = this.clusters(k)
+! 							products(j) = this.clusters(k)
 							this.involvedInTS(k) = .true.
 						end if
 					end do
@@ -450,6 +456,9 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 		
 		call GOptions_section( "END TRANSITION_STATES DATABASE INITIALIZATION", indent=1 )
 		
+! 		deallocate(reactives)
+! 		deallocate(products)
+		
 	end subroutine setTransitionStatesTable
 	
 	!>

From 14256adef41551280fcd02dd6ef9ffcd6dd8948c Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sun, 8 Mar 2020 21:45:34 +0100
Subject: [PATCH 51/57] Improvement of examples

---
 examples/ts/TS-examples/C.q0.m1-1.rxyz  |  8 ++++++++
 examples/ts/TS-examples/C.q0.m3-1.rxyz  |  8 ++++++++
 examples/ts/TS-examples/C2.m3c          |  7 ++++---
 examples/ts/TS-examples/C2.q0.m1-1.rxyz | 10 ++++++++++
 examples/ts/TS-examples/C2.q0.m3-1.rxyz | 10 ++++++++++
 examples/ts/TS-examples/C3.m3c          |  4 ++--
 examples/ts/TS-examples/C3.q0.m1-1.rxyz | 14 ++++++++++++++
 7 files changed, 56 insertions(+), 5 deletions(-)
 create mode 100644 examples/ts/TS-examples/C.q0.m1-1.rxyz
 create mode 100644 examples/ts/TS-examples/C.q0.m3-1.rxyz
 create mode 100644 examples/ts/TS-examples/C2.q0.m1-1.rxyz
 create mode 100644 examples/ts/TS-examples/C2.q0.m3-1.rxyz
 create mode 100644 examples/ts/TS-examples/C3.q0.m1-1.rxyz

diff --git a/examples/ts/TS-examples/C.q0.m1-1.rxyz b/examples/ts/TS-examples/C.q0.m1-1.rxyz
new file mode 100644
index 0000000..87d71e5
--- /dev/null
+++ b/examples/ts/TS-examples/C.q0.m1-1.rxyz
@@ -0,0 +1,8 @@
+1
+Energy =   -37.7258911420
+  C            0.00000000          0.00000000          0.00000000
+
+FREQUENCIES 0
+
+SYMMETRY R3
+ELECTRONIC_STATE 1-D
diff --git a/examples/ts/TS-examples/C.q0.m3-1.rxyz b/examples/ts/TS-examples/C.q0.m3-1.rxyz
new file mode 100644
index 0000000..c64a6bd
--- /dev/null
+++ b/examples/ts/TS-examples/C.q0.m3-1.rxyz
@@ -0,0 +1,8 @@
+1
+Energy =   -37.7791720550
+  C            0.00000000          0.00000000          0.00000000
+
+FREQUENCIES 0
+
+SYMMETRY R3
+ELECTRONIC_STATE 3-P
diff --git a/examples/ts/TS-examples/C2.m3c b/examples/ts/TS-examples/C2.m3c
index 22b92af..0c5b563 100644
--- a/examples/ts/TS-examples/C2.m3c
+++ b/examples/ts/TS-examples/C2.m3c
@@ -21,7 +21,7 @@ BEGIN MARKOV_CHAIN
         burnInFraction = 0.0
         
 	reactives = C2(s1)
-        excitationEnergy = 7.0
+        excitationEnergy = 10.0
         
         tracking = weight
         
@@ -39,11 +39,12 @@ BEGIN MARKOV_CHAIN
 #        JHistoryFile = J.dat
 #        LHistoryFile = L.dat
         histogramFile = histogram.dat
+	debugLevel = 4
 END MARKOV_CHAIN
 
 BEGIN FRAGMENTS_DATABASE
 
-	store = /home/nestor/Develop/M3C-store/master/6-311++G.3df.2p/ccsdt
+	store = .
 	reference = C2(s1)
 
 	#--------------------------------------------------------------------------------------
@@ -64,6 +65,6 @@ BEGIN TRANSITION_STATES_DATABASE
 	#--------------------------------------------------------------------------------------
 	#  Label    Z  M WL  SYM          geomFile         Eelec     maxVib     TS
 	#--------------------------------------------------------------------------------------
-          C2(ts1)   0  1  1    2 C2ts.q0.m1-1.rxyz  -2054.048032        4.0     C2(s1)<-->C(t1)+C(t1)
+          C2(ts1)   0  1  1    2 C2ts.q0.m1-1.rxyz  -2054.048032        4.0     C2(s1)<-->C(s1)+C(t1)
 	#--------------------------------------------------------------------------------------
 END TRANSITION_STATES_DATABASE
diff --git a/examples/ts/TS-examples/C2.q0.m1-1.rxyz b/examples/ts/TS-examples/C2.q0.m1-1.rxyz
new file mode 100644
index 0000000..bb05d1e
--- /dev/null
+++ b/examples/ts/TS-examples/C2.q0.m1-1.rxyz
@@ -0,0 +1,10 @@
+2
+Energy =   -75.7826438160
+    C    0.623543    0.000000    0.000000
+    C   -0.623543    0.000000    0.000000
+
+FREQUENCIES 1
+1872.9045
+
+SYMMETRY D*H
+ELECTRONIC_STATE 1-SGG
diff --git a/examples/ts/TS-examples/C2.q0.m3-1.rxyz b/examples/ts/TS-examples/C2.q0.m3-1.rxyz
new file mode 100644
index 0000000..440aa4d
--- /dev/null
+++ b/examples/ts/TS-examples/C2.q0.m3-1.rxyz
@@ -0,0 +1,10 @@
+2
+Energy =   -75.7792326870
+    C    0.650535    0.000000    0.000000
+    C   -0.650535    0.000000    0.000000
+
+FREQUENCIES 1
+1693.6178
+
+SYMMETRY D*H
+ELECTRONIC_STATE 3-PIU
diff --git a/examples/ts/TS-examples/C3.m3c b/examples/ts/TS-examples/C3.m3c
index 78bbf8b..15be2c3 100644
--- a/examples/ts/TS-examples/C3.m3c
+++ b/examples/ts/TS-examples/C3.m3c
@@ -13,7 +13,7 @@ BEGIN GOPTIONS
         useSpinConservationRules = FALSE
         
         angularMomentumCouplingScheme = JJL
-	debugLevel = 2
+# 	debugLevel = 2
 END GOPTIONS
 
 BEGIN MARKOV_CHAIN
@@ -43,7 +43,7 @@ END MARKOV_CHAIN
 
 BEGIN FRAGMENTS_DATABASE
 
-	store = /home/nestor/Develop/M3C-store/master/6-311++G.3df.2p/ccsdt
+	store = .
 	reference = C3(s1)
 
 	#--------------------------------------------------------------------------------------
diff --git a/examples/ts/TS-examples/C3.q0.m1-1.rxyz b/examples/ts/TS-examples/C3.q0.m1-1.rxyz
new file mode 100644
index 0000000..6f24579
--- /dev/null
+++ b/examples/ts/TS-examples/C3.q0.m1-1.rxyz
@@ -0,0 +1,14 @@
+3
+Energy =   -113.8326552900
+    C    1.290898    0.000000   -0.000000
+    C   -0.000000   -0.000000    0.000000
+    C   -1.290898    0.000000   -0.000000
+
+FREQUENCIES 4
+154.6817
+154.6817
+1226.0212
+2119.4308
+
+SYMMETRY D*H
+ELECTRONIC_STATE 1-SGG

From 0d12ffcf3b051ef18ebea85bdc64fee7300d5011 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Tue, 10 Mar 2020 00:39:50 +0100
Subject: [PATCH 52/57] 1) Bug fixed: Cyclic dependence between FragmentsList
 and FragmentsListDB 2) Some refactoring of the code

---
 .../{ts/TS-examples => TS}/C.q0.m1-1.rxyz     |   0
 .../{ts/TS-examples => TS}/C.q0.m3-1.rxyz     |   0
 examples/{ts/TS-examples => TS}/C2.m3c        |  14 +-
 .../{ts/TS-examples => TS}/C2.q0.m1-1.rxyz    |   0
 .../{ts/TS-examples => TS}/C2.q0.m3-1.rxyz    |   0
 .../{ts/TS-examples => TS}/C2ts.q0.m1-1.rxyz  |   0
 examples/{ts/TS-examples => TS}/C3.m3c        |   0
 .../{ts/TS-examples => TS}/C3.q0.m1-1.rxyz    |   0
 src/Fragment.f90                              |  65 +++++-
 src/FragmentsDB.f90                           |  91 ++++++---
 src/FragmentsList.f90                         |   2 +-
 src/FragmentsListBase.f90                     |  57 +-----
 src/MarkovChain.f90                           |  14 +-
 src/Reactor.f90                               | 185 +++---------------
 14 files changed, 176 insertions(+), 252 deletions(-)
 rename examples/{ts/TS-examples => TS}/C.q0.m1-1.rxyz (100%)
 rename examples/{ts/TS-examples => TS}/C.q0.m3-1.rxyz (100%)
 rename examples/{ts/TS-examples => TS}/C2.m3c (74%)
 rename examples/{ts/TS-examples => TS}/C2.q0.m1-1.rxyz (100%)
 rename examples/{ts/TS-examples => TS}/C2.q0.m3-1.rxyz (100%)
 rename examples/{ts/TS-examples => TS}/C2ts.q0.m1-1.rxyz (100%)
 rename examples/{ts/TS-examples => TS}/C3.m3c (100%)
 rename examples/{ts/TS-examples => TS}/C3.q0.m1-1.rxyz (100%)

diff --git a/examples/ts/TS-examples/C.q0.m1-1.rxyz b/examples/TS/C.q0.m1-1.rxyz
similarity index 100%
rename from examples/ts/TS-examples/C.q0.m1-1.rxyz
rename to examples/TS/C.q0.m1-1.rxyz
diff --git a/examples/ts/TS-examples/C.q0.m3-1.rxyz b/examples/TS/C.q0.m3-1.rxyz
similarity index 100%
rename from examples/ts/TS-examples/C.q0.m3-1.rxyz
rename to examples/TS/C.q0.m3-1.rxyz
diff --git a/examples/ts/TS-examples/C2.m3c b/examples/TS/C2.m3c
similarity index 74%
rename from examples/ts/TS-examples/C2.m3c
rename to examples/TS/C2.m3c
index 0c5b563..576b381 100644
--- a/examples/ts/TS-examples/C2.m3c
+++ b/examples/TS/C2.m3c
@@ -13,7 +13,7 @@ BEGIN GOPTIONS
         useSpinConservationRules = FALSE
         
         angularMomentumCouplingScheme = JJL
-	#debugLevel = 3
+# 	debugLevel = 3
 END GOPTIONS
 
 BEGIN MARKOV_CHAIN
@@ -29,7 +29,7 @@ BEGIN MARKOV_CHAIN
 #         numberOfEvents = 100000
         numberOfExperiments = 3
 #         numberOfEvents = 50000
-        numberOfEvents = 20000
+        numberOfEvents = 2000
 #        historyFileFrequency = 100
         historyFileFrequency = 1
 
@@ -39,7 +39,6 @@ BEGIN MARKOV_CHAIN
 #        JHistoryFile = J.dat
 #        LHistoryFile = L.dat
         histogramFile = histogram.dat
-	debugLevel = 4
 END MARKOV_CHAIN
 
 BEGIN FRAGMENTS_DATABASE
@@ -50,11 +49,8 @@ BEGIN FRAGMENTS_DATABASE
 	#--------------------------------------------------------------------------------------
 	#  Label    Z  M WL  SYM          geomFile         Eelec     maxVib
 	#--------------------------------------------------------------------------------------
-           C(s1)    0  1  5    1    C.q0.m1-1.rxyz  -1026.574168                      #           ¹D (2s²2p²) 
-           C(t1)    0  3  3    1    C.q0.m3-1.rxyz  -1028.024016                      #           ³P (2s²2p²)
-           
-          C2(s1)    0  1  1    2   C2.q0.m1-1.rxyz  -2062.151541     C(t1)+C(t1)      # 6.10351   ^1\Sigma_g^+
-          #C2(t1)    0  3  2    2   C2.q0.m3-1.rxyz  -2062.058719     C(t1)+C(t1)      # 6.01069   ^3\Pi_u 
+           C(t1)    0  3  3    1    C.q0.m3-1.rxyz            3.0                      #       ³P (2s²2p²)
+          C2(s1)    0  1  1    2   C2.q0.m1-1.rxyz            0.0     C(t1)+C(t1)      # 6.0   ^1\Sigma_g^+
 	#--------------------------------------------------------------------------------------
 END FRAGMENTS_DATABASE
 
@@ -65,6 +61,6 @@ BEGIN TRANSITION_STATES_DATABASE
 	#--------------------------------------------------------------------------------------
 	#  Label    Z  M WL  SYM          geomFile         Eelec     maxVib     TS
 	#--------------------------------------------------------------------------------------
-          C2(ts1)   0  1  1    2 C2ts.q0.m1-1.rxyz  -2054.048032        4.0     C2(s1)<-->C(s1)+C(t1)
+          C2(ts1)   0  1  1    2 C2ts.q0.m1-1.rxyz           8.0        4.0     C2(s1)<-->C(t1)+C(t1)
 	#--------------------------------------------------------------------------------------
 END TRANSITION_STATES_DATABASE
diff --git a/examples/ts/TS-examples/C2.q0.m1-1.rxyz b/examples/TS/C2.q0.m1-1.rxyz
similarity index 100%
rename from examples/ts/TS-examples/C2.q0.m1-1.rxyz
rename to examples/TS/C2.q0.m1-1.rxyz
diff --git a/examples/ts/TS-examples/C2.q0.m3-1.rxyz b/examples/TS/C2.q0.m3-1.rxyz
similarity index 100%
rename from examples/ts/TS-examples/C2.q0.m3-1.rxyz
rename to examples/TS/C2.q0.m3-1.rxyz
diff --git a/examples/ts/TS-examples/C2ts.q0.m1-1.rxyz b/examples/TS/C2ts.q0.m1-1.rxyz
similarity index 100%
rename from examples/ts/TS-examples/C2ts.q0.m1-1.rxyz
rename to examples/TS/C2ts.q0.m1-1.rxyz
diff --git a/examples/ts/TS-examples/C3.m3c b/examples/TS/C3.m3c
similarity index 100%
rename from examples/ts/TS-examples/C3.m3c
rename to examples/TS/C3.m3c
diff --git a/examples/ts/TS-examples/C3.q0.m1-1.rxyz b/examples/TS/C3.q0.m1-1.rxyz
similarity index 100%
rename from examples/ts/TS-examples/C3.q0.m1-1.rxyz
rename to examples/TS/C3.q0.m1-1.rxyz
diff --git a/src/Fragment.f90 b/src/Fragment.f90
index 59ca9ad..d868191 100644
--- a/src/Fragment.f90
+++ b/src/Fragment.f90
@@ -69,6 +69,7 @@ module Fragment_
 	private
 	
 	public :: &
+		Fragment_getLabelFragments, &
 		Fragment_test
 	
 	type, public, extends( Molecule ):: Fragment
@@ -110,7 +111,7 @@ module Fragment_
 			procedure :: copyFragment
 			final :: destroyFragment
 			
-			procedure, private :: updateFormula
+			procedure, private :: updateLabel
 			procedure :: label
 			
 ! 			procedure, private :: loadRXYZ
@@ -291,6 +292,7 @@ subroutine fromMassTableRow( this, strRow, id, store )
 		
 ! 		if( GOptions_printLevel >= 4 ) then
 			write(IO_STDOUT,"(A)") ""
+! 			write(IO_STDOUT,"(4X,A22,I15)") "id = ", this.id
 			write(IO_STDOUT,"(4X,A22,A)") "file name = ", this.fileName
 			write(IO_STDOUT,"(4X,A22,A)") "name = ", this.name
 			write(IO_STDOUT,"(4X,A22,A)") "formula = ", trim(this.chemicalFormula())
@@ -388,7 +390,7 @@ end subroutine destroyFragment
 	!>
 	!! @brief
 	!!
-	subroutine updateFormula( this )
+	subroutine updateLabel( this )
 		class(Fragment) :: this 
 		
 		character(100), allocatable :: tokens(:)
@@ -400,7 +402,7 @@ subroutine updateFormula( this )
 		this.label_ = trim(tokens(1))
 		
 		deallocate( tokens )
-	end subroutine updateFormula
+	end subroutine updateLabel
 	
 	!>
 	!! @brief
@@ -416,7 +418,7 @@ function label( this, details ) result( output )
 		if( present(details) ) effDetails = details
 		
 		if( .not. this.testLabel_ ) then
-			call this.updateFormula()
+			call this.updateLabel()
 			this.testLabel_ = .true.
 		end if
 		
@@ -1297,6 +1299,61 @@ end function spinAvailable
 !       endIf
 !       Return
 !       End
+
+	!>
+	!! @brief
+	!!
+	subroutine Fragment_getLabelFragments( clusters, label, dlabel, idSorted )
+		type(Fragment), allocatable, intent(in) :: clusters(:)
+		character(200), intent(out) :: label
+		character(200), intent(out) :: dlabel
+		integer, allocatable, intent(out), optional :: idSorted(:)
+		
+		integer :: i
+		real(8), allocatable :: massVec(:) ! @todo Hay que hacer el Math_sort para enteros
+		integer, allocatable :: effIdSorted(:)
+		
+		allocate( massVec(size(clusters)) )
+		allocate( effIdSorted(size(clusters)) )
+		
+		do i=1,size(clusters)
+		
+			massVec(i) = clusters(i).mass()/amu &
+					+ clusters(i).charge/10.0 &
+						+ clusters(i).multiplicity/100.0_8 
+
+! 			massVec(i) = 10000000*clusters(i).mass()/amu + 1000000*clusters(i).nAtoms() + 100*clusters(i).charge &
+! 					+ clusters(i).multiplicity
+
+		end do
+			
+		call Math_sort( massVec, effIdSorted )
+		
+		label = ""
+		dlabel = ""
+		do i=1,size(clusters)
+			if( i /= size(clusters) ) then
+				label = trim(label)//trim(clusters( effIdSorted(i) ).label( details=.false. ))//"+"
+				dlabel = trim(dlabel)//trim(clusters( effIdSorted(i) ).label( details=.true. ))//"+"
+			else
+				label = trim(label)//trim(clusters( effIdSorted(i) ).label( details=.false. ))
+				dlabel = trim(dlabel)//trim(clusters( effIdSorted(i) ).label( details=.true. ))
+			end if
+		end do
+		
+		if( present(idSorted) ) then
+			if( allocated(idSorted) .and. size(idSorted) == size(effIdSorted) ) then
+				idSorted = effIdSorted
+			else
+				if( allocated(idSorted) ) deallocate(idSorted)
+				allocate( idSorted(size(clusters)) )
+				idSorted = effIdSorted
+			end if
+		end if
+		
+		deallocate( massVec )
+		deallocate( effIdSorted )
+	end subroutine Fragment_getLabelFragments
 	
 	!>
 	!! @brief Test method
diff --git a/src/FragmentsDB.f90 b/src/FragmentsDB.f90
index 5e5f462..2e8af74 100644
--- a/src/FragmentsDB.f90
+++ b/src/FragmentsDB.f90
@@ -62,7 +62,6 @@ module FragmentsDB_
 	use StringIntegerMap_
 	
 	use Fragment_
-	use FragmentsList_
 	use ModelPotential_
 	use GOptionsM3C_
 	
@@ -102,7 +101,8 @@ module FragmentsDB_
 			procedure, private :: checkPotentials
 			final :: destroyFragmentsDB
 			procedure :: nMolecules
-			procedure :: getIdFromName
+			procedure :: getIdClusterFromLabel
+			procedure :: getIdTransitionStateFromLabel
 			procedure :: getEelecFromName
 			procedure :: extendFragmentsListName
 			procedure :: potential
@@ -359,13 +359,19 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 		
 		integer :: i, j, k, n
 		character(100), allocatable :: tokens(:), tokens2(:), tokens3(:)
+		type(String) :: path
 		real(8) :: rBuffer
 		
 		! Only for transition states. They are neccessary to calculate the right label (mass sorted)
-		type(FragmentsList) :: reactives
-		type(FragmentsList) :: products
-! 		type(Fragment), allocatable :: reactives(:)
-! 		type(Fragment), allocatable :: products(:)
+! 		type(FragmentsList) :: reactives
+! 		type(FragmentsList) :: products
+		logical :: useDetailsInLabel
+		type(Fragment), allocatable :: reactives(:)
+		type(Fragment), allocatable :: products(:)
+		character(200) :: reactivesLabel, reactivesdLabel
+		character(200) :: productsLabel, productsdLabel
+		
+		useDetailsInLabel = .true.
 		
 		if( allocated(this.transitionState) ) deallocate( this.transitionState )
 		allocate( this.transitionState(size(transitionStatesTable)) )
@@ -403,17 +409,18 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 			! Choosing the reactives and products
 			!------------------------------------------
 			if( size(tokens) >= 9 .and. this.transitionState(i).nAtoms() /= 1 ) then
-				call FString_split( trim(adjustl(tokens(9))), tokens2, "<-->" )
+				path = trim(adjustl(tokens(9)))
+				call path.split( tokens2, "<-->" )
 				
 				call FString_split( trim(adjustl(tokens2(1))), tokens3, "+" )
-				call reactives.init( size(tokens3) )
-! 				allocate( reactives(size(tokens3)) )
+! 				call reactives.init( size(tokens3) )
+				allocate( reactives(size(tokens3)) )
 				
 				do j=1,size(tokens3)
 					do k=1,size(this.clusters)
-						if( trim(tokens3(j)) == this.clusters(k).label() ) then
-							reactives.clusters(j) = this.clusters(k)
-! 							reactives(j) = this.clusters(k)
+						if( trim(tokens3(j)) == this.clusters(k).label( details=useDetailsInLabel ) ) then
+! 							reactives.clusters(j) = this.clusters(k)
+							reactives(j) = this.clusters(k)
 							this.involvedInTS(k) = .true.
 						end if
 					end do
@@ -421,14 +428,14 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 				deallocate( tokens3 )
 				
 				call FString_split( trim(adjustl(tokens2(2))), tokens3, "+" )
-				call products.init( size(tokens3) )
-! 				allocate( products(size(tokens3)) )
+! 				call products.init( size(tokens3) )
+				allocate( products(size(tokens3)) )
 				
 				do j=1,size(tokens3)
 					do k=1,size(this.clusters)
-						if( trim(tokens3(j)) == this.clusters(k).label() ) then
-							products.clusters(j) = this.clusters(k)
-! 							products(j) = this.clusters(k)
+						if( trim(tokens3(j)) == this.clusters(k).label( details=useDetailsInLabel ) ) then
+! 							products.clusters(j) = this.clusters(k)
+							products(j) = this.clusters(k)
 							this.involvedInTS(k) = .true.
 						end if
 					end do
@@ -437,9 +444,16 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 				
 				deallocate( tokens2 )
 				
-				write(*,"(4X,A22,A)")  "Path = ", trim(reactives.label())//"<-->"//trim(products.label())
-				call this.str2id_TS.insert( FString_toString(trim(reactives.label())//"<-->"//trim(products.label())), i )
-				call this.str2id_TS.insert( FString_toString(trim(products.label())//"<-->"//trim(reactives.label())), i )
+				call Fragment_getLabelFragments( reactives, reactivesLabel, reactivesdLabel )
+				call Fragment_getLabelFragments( products, productsLabel, productsdLabel )
+				
+				write(*,"(4X,A22,A)")  "Path = ", trim(path.fstr)
+! 				call this.str2id_TS.insert( FString_toString(trim(reactivesLabel)//"<-->"//trim(productsLabel)), i )
+! 				call this.str2id_TS.insert( FString_toString(trim(productsLabel)//"<-->"//trim(reactivesLabel)), i )
+! 				write(*,"(4X,A22,A)")  "Interpreted Path = ", trim(reactivesLabel)//"<-->"//trim(productsLabel)
+				call this.str2id_TS.insert( FString_toString(trim(reactivesdLabel)//"<-->"//trim(productsdLabel)), i )
+				call this.str2id_TS.insert( FString_toString(trim(productsdLabel)//"<-->"//trim(reactivesdLabel)), i )
+				write(*,"(4X,A22,A)")  "Interpreted Path = ", trim(reactivesdLabel)//"<-->"//trim(productsdLabel)
 				
 			else
 				call GOptions_error( &
@@ -679,8 +693,8 @@ subroutine setPotentialTable( this, potentialTable, coulombContribution )
 			if( size(cols) >= 2 ) then
 				call FString_split( cols(1), tokens, "+" )
 				
-				idR1 = this.getIdFromName( tokens(1) )
-				idR2 = this.getIdFromName( tokens(2) )
+				idR1 = this.getIdClusterFromLabel( tokens(1) )
+				idR2 = this.getIdClusterFromLabel( tokens(2) )
 				
 				write(*,"(<GOptions_indentLength*1>X,A10,A10,5X,2I3)", advance="no") &
 						this.clusters(idR1).name, this.clusters(idR2).name, idR1, idR2
@@ -908,7 +922,7 @@ end function nMolecules
 	!>
 	!! @brief
 	!!
-	function getIdFromName( this, name ) result( output )
+	function getIdClusterFromLabel( this, name ) result( output )
 		class(FragmentsDB), intent(in) :: this
 		character(*), intent(in) :: name
 		integer :: output
@@ -925,9 +939,28 @@ function getIdFromName( this, name ) result( output )
 		
 		call GOptions_error( &
 				"The cluster --"//trim(adjustl(name))//"-- doesn't exist in the database", &
-				"FragmentsDB.getIdFromName()" &
+				"FragmentsDB.getIdClusterFromLabel()" &
 			)
-	end function getIdFromName
+	end function getIdClusterFromLabel
+	
+	!>
+	!! @brief
+	!!
+	function getIdTransitionStateFromLabel( this, name ) result( output )
+		class(FragmentsDB), intent(in) :: this
+		character(*), intent(in) :: name
+		integer :: output
+		
+		if( this.str2id_TS.contains( FString_toString(name) ) ) then
+			output = this.str2id_TS.at( FString_toString(name) )
+		else
+! 			call GOptions_error( &
+! 					"The transition state --"//trim(adjustl(name))//"-- doesn't exist in the database", &
+! 					"FragmentsDB.getIdTransitionStateFromLabel()" &
+! 				)
+			output = -1
+		end if
+	end function getIdTransitionStateFromLabel
 	
 	!>
 	!! @brief
@@ -949,10 +982,10 @@ function getEelecFromName( this, name ) result( output )
 			
 			
 			if( size(subTokens) < 2 ) then
-				id = this.getIdFromName( subTokens(1) )
+				id = this.getIdClusterFromLabel( subTokens(1) )
 				factor = 1
 			else
-				id = this.getIdFromName( subTokens(2) )
+				id = this.getIdClusterFromLabel( subTokens(2) )
 				factor = FString_toInteger( subTokens(1) )
 			end if
 			
@@ -1193,7 +1226,7 @@ subroutine FragmentsDB_test()
 ! 			call FString_split( tokens(i), items, "," )
 ! 			
 ! 			do j=1,size(items)
-! 				write(*,*) i, trim(adjustl(items(j))), db.getIdFromName( items(j) )
+! 				write(*,*) i, trim(adjustl(items(j))), db.getIdClusterFromLabel( items(j) )
 ! 			end do
 ! 			write(*,*) ""
 ! 		end do
@@ -1219,7 +1252,7 @@ subroutine FragmentsDB_test()
 
 ! 		r = 0.0_8
 ! 		do while( r <= 10.0_8 )
-! 			write(*,*) r, db.potential( db.getIdFromName( "tC1" ), db.getIdFromName( "tC1" ), r*angs )/eV
+! 			write(*,*) r, db.potential( db.getIdClusterFromLabel( "tC1" ), db.getIdClusterFromLabel( "tC1" ), r*angs )/eV
 ! 			r = r + 0.2
 ! 		end do
 		
diff --git a/src/FragmentsList.f90 b/src/FragmentsList.f90
index 0bfbd6c..c145292 100644
--- a/src/FragmentsList.f90
+++ b/src/FragmentsList.f90
@@ -1324,7 +1324,7 @@ subroutine FragmentsList_test()
 ! 			call FString_split( tokens(i), items, "," )
 ! 			
 ! 			do j=1,size(items)
-! 				write(*,*) i, trim(adjustl(items(j))), RigidMoleculeDatabase_instance.getIdFromName( items(j) )
+! 				write(*,*) i, trim(adjustl(items(j))), RigidMoleculeDatabase_instance.getIdClusterFromLabel( items(j) )
 ! 			end do
 ! 			write(*,*) ""
 ! 		end do
diff --git a/src/FragmentsListBase.f90 b/src/FragmentsListBase.f90
index 9c8b159..0e3c551 100644
--- a/src/FragmentsListBase.f90
+++ b/src/FragmentsListBase.f90
@@ -77,7 +77,7 @@ module FragmentsListBase_
 	
 	type, abstract, public :: FragmentsListBase
 		type(Fragment), allocatable :: clusters(:)    !< Fragment list
-		integer, allocatable :: idSorted(:)            !< Position of the molecule sorted by mass. It is calculated in updateFormula procedure
+		integer, allocatable :: idSorted(:)            !< Position of the molecule sorted by mass. It is calculated in updateLabel procedure
 													   !<            this.clusters(i) ----> this.clusters( this.idSorted(i) )
 		
 		real(8) :: diagInertiaTensor(3)    !< Main inertia tensor components [ Ixx, Iyy, Izz ]. It is calculated into updateInertiaTensor procedure
@@ -109,8 +109,6 @@ module FragmentsListBase_
 		logical :: forceRandomCenters    !< Fuerza a utilizar randomCenters en el siguiente llamado a changeGeometryFragmentsListBase
 		logical :: forceInitializing     !< Fuerza a utilizar initialGuessFragmentsListBase
 		
-		integer :: totalComposition( AtomicElementsDB_nElems ) !< [ n1, n2, ..., nN ] n=numberOfAtomsWithZ, pos = atomicNumber 
-		
 		real(8) :: L_(3)          ! Orbital angular momentum
 		
 		integer, allocatable :: currentProducts(:,:) !< This allows to get the current potential energy surface @see updateIntermolecularPotential
@@ -130,7 +128,7 @@ module FragmentsListBase_
 			procedure, NON_OVERRIDABLE :: nAtoms
 			procedure, NON_OVERRIDABLE :: charge
 			procedure, NON_OVERRIDABLE :: mass
-			procedure, private :: updateFormula
+			procedure, private :: updateLabel
 			procedure, NON_OVERRIDABLE :: label
 			generic :: set => setFromFragment
 			procedure, NON_OVERRIDABLE :: setFromFragment
@@ -238,8 +236,6 @@ subroutine initFragmentsListBase( this, nMolecules )
 		this.forceRandomCenters = .true.
 		this.forceInitializing = .true.
 		
-		this.totalComposition = -1
-		
 		this.L_ = 0.0_8
 		
 		if( allocated(this.currentProducts) ) deallocate(this.currentProducts)
@@ -295,8 +291,6 @@ subroutine copyFragmentsListBase( this, other )
 		this.forceRandomCenters = other.forceRandomCenters
 		this.forceInitializing = other.forceInitializing
 		
-		this.totalComposition = other.totalComposition
-		
 		this.L_ = other.L_
 		
 		if( allocated(this.currentProducts) ) deallocate(this.currentProducts)
@@ -451,7 +445,7 @@ subroutine loadXYZ( this, fileName )
 			y = FString_toReal( tokens(3) )*angs
 			z = FString_toReal( tokens(4) )*angs
 			
-			idClus = FragmentsDB_instance.getIdFromName( name.fstr )
+			idClus = FragmentsDB_instance.getIdClusterFromLabel( name.fstr )
 			
 			call this.setFromFragment( i, FragmentsDB_instance.clusters( idClus ) )
 			call this.clusters(i).setCenter( [ x, y, z ] )
@@ -527,45 +521,12 @@ end function mass
 	!>
 	!! @brief
 	!!
-	subroutine updateFormula( this )
+	subroutine updateLabel( this )
 		class(FragmentsListBase) :: this
 		
-		integer :: i
-		real(8), allocatable :: massVec(:) ! @todo Hay que hacer el Math_sort para enteros
-		
-		allocate( massVec(size(this.clusters)) )
-		
-		this.totalComposition = 0
-		do i=1,size(this.clusters)
-		
-			massVec(i) = this.clusters(i).mass()/amu &
-					+ this.clusters(i).charge/10.0 &
-						+ this.clusters(i).multiplicity/100.0_8 
-
-! 			massVec(i) = 10000000*this.clusters(i).mass()/amu + 1000000*this.clusters(i).nAtoms() + 100*this.clusters(i).charge &
-! 					+ this.clusters(i).multiplicity
-
-			this.totalComposition = this.totalComposition + this.clusters( i ).composition
-		end do
-			
-		call Math_sort( massVec, this.idSorted )
-		
-		this.label_ = ""
-		this.dlabel_ = ""
-		do i=1,size(this.clusters)
-			if( i /= size(this.clusters) ) then
-				this.label_ = trim(this.label_)//trim(this.clusters( this.idSorted(i) ).label( details=.false. ))//"+"
-				this.dlabel_ = trim(this.dlabel_)//trim(this.clusters( this.idSorted(i) ).label( details=.true. ))//"+"
-			else
-				this.label_ = trim(this.label_)//trim(this.clusters( this.idSorted(i) ).label( details=.false. ))
-				this.dlabel_ = trim(this.dlabel_)//trim(this.clusters( this.idSorted(i) ).label( details=.true. ))
-			end if
-		end do
-		
+		call Fragment_getLabelFragments( this.clusters, this.label_, this.dlabel_, this.idSorted )
 		this.testLabel_ = .true.
-		
-		deallocate( massVec )
-	end subroutine updateFormula
+	end subroutine updateLabel
 	
 	!>
 	!! @brief
@@ -581,7 +542,7 @@ function label( this, details ) result( output )
 		if( present(details) ) effDetails = details
 		
 		if( .not. this.testLabel_ ) then
-			call this.updateFormula()
+			call this.updateLabel()
 		end if
 		
 		if( effDetails ) then
@@ -705,7 +666,7 @@ subroutine initialGuessFragmentsListBase( this )
 		
 		call this.orient()
 		
-		call this.updateFormula()
+		call this.updateLabel()
 		
 		call this.updateLogGFactor()
 		
@@ -2372,7 +2333,7 @@ subroutine executeRadiusOptimization( this, iParser )
 			
 			call this.init( size(reactiveTokens) )
 			do i=1,size(reactiveTokens)
-				iBuffer = FragmentsDB_instance.getIdFromName( reactiveTokens(i) )
+				iBuffer = FragmentsDB_instance.getIdClusterFromLabel( reactiveTokens(i) )
 				call this.set( i, FragmentsDB_instance.clusters(iBuffer) )
 			end do
 		end if
diff --git a/src/MarkovChain.f90 b/src/MarkovChain.f90
index 2c8e433..655ebb1 100644
--- a/src/MarkovChain.f90
+++ b/src/MarkovChain.f90
@@ -384,7 +384,7 @@ subroutine run( this, reactives )
 			write(6,"(A)") "#------------------------------------"
 			write(6,"(A)") "# ENERGY HISTORY"
 			write(6,"(A)") "#------------------------------------"
-			write(6,"(A1,3X,5A15,5X,A)") "#", "trans", "intermol", "vib", "rot", "tot", "formula"
+			write(6,"(A1,3X,5A15,5X,A)") "#", "trans", "intermol", "vib", "rot", "tot", "label"
 			write(6,"(A1,3X,5A15,5X,A)") "#", "eV", "eV", "eV", "eV", ""
 			write(6,"(A1,3X,5A15,5X,A)") "#", "-------", "--------", "-------", "-----", "-------"
 
@@ -393,7 +393,7 @@ subroutine run( this, reactives )
 			write(6,"(A)") "#------------------------------------"
 			write(6,"(A)") "# WEIGHT HISTORY"
 			write(6,"(A)") "#------------------------------------"
-			write(6,"(A1,3X,6A15,5X,A)") "#", "LnWe", "LnWv", "LnWn", "LnWr", "LnWt", "LnW", "formula"
+			write(6,"(A1,3X,6A15,5X,A)") "#", "LnWe", "LnWv", "LnWn", "LnWr", "LnWt", "LnW", "label"
 			write(6,"(A1,3X,6A15,5X,A)") "#", "arb.", "arb.", "arb.", "arb.", "arb.", "arb.", ""
 			write(6,"(A1,3X,6A15,5X,A)") "#", "-------", "-------", "--------", "--------", "--------", "-------", "-------"
 			
@@ -821,7 +821,7 @@ end subroutine showAverHistogram
 ! 		write(unit,"(A)") "#------------------------------------"
 ! 		write(unit,"(A)") "# ENERGY HISTORY"
 ! 		write(unit,"(A)") "#------------------------------------"
-! 		write(unit,"(A1,3X,5A15,5X,A)") "#", "trans", "intermol", "vib", "rot", "tot", "formula"
+! 		write(unit,"(A1,3X,5A15,5X,A)") "#", "trans", "intermol", "vib", "rot", "tot", "label"
 ! 		write(unit,"(A1,3X,5A15,5X,A)") "#", "eV", "eV", "eV", "eV", ""
 ! 		write(unit,"(A1,3X,5A15,5X,A)") "#", "-------", "--------", "-------", "-----", "-------"
 ! 		
@@ -870,7 +870,7 @@ end subroutine showAverHistogram
 ! 		write(unit,"(A)") "#------------------------------------"
 ! 		write(unit,"(A)") "# WEIGHT HISTORY"
 ! 		write(unit,"(A)") "#------------------------------------"
-! 		write(unit,"(A1,3X,6A15,5X,A)") "#", "LnWe", "LnWv", "LnWn", "LnWr", "LnWt", "LnW", "formula"
+! 		write(unit,"(A1,3X,6A15,5X,A)") "#", "LnWe", "LnWv", "LnWn", "LnWr", "LnWt", "LnW", "label"
 ! 		write(unit,"(A1,3X,6A15,5X,A)") "#", "arb.", "arb.", "arb.", "arb.", "arb.", "arb.", ""
 ! 		write(unit,"(A1,3X,6A15,5X,A)") "#", "-------", "-------", "--------", "--------", "--------", "-------", "-------"
 ! 		
@@ -1382,7 +1382,7 @@ subroutine execute( this, iParser )
 			
 			call reactives.init( size(reactiveTokens) )
 			do i=1,size(reactiveTokens)
-				iBuffer = FragmentsDB_instance.getIdFromName( reactiveTokens(i) )
+				iBuffer = FragmentsDB_instance.getIdClusterFromLabel( reactiveTokens(i) )
 				call reactives.set( i, FragmentsDB_instance.clusters(iBuffer) )
 			end do
 		end if
@@ -1420,7 +1420,7 @@ subroutine execute( this, iParser )
 			write(this.energyHistoryFile.unit,"(A)") "#------------------------------------"
 			write(this.energyHistoryFile.unit,"(A)") "# ENERGY HISTORY"
 			write(this.energyHistoryFile.unit,"(A)") "#------------------------------------"
-			write(this.energyHistoryFile.unit,"(A1,3X,5A15,5X,A)") "#", "trans", "intermol", "vib", "rot", "tot", "formula"
+			write(this.energyHistoryFile.unit,"(A1,3X,5A15,5X,A)") "#", "trans", "intermol", "vib", "rot", "tot", "label"
 			write(this.energyHistoryFile.unit,"(A1,3X,5A15,5X,A)") "#", "eV", "eV", "eV", "eV", ""
 			write(this.energyHistoryFile.unit,"(A1,3X,5A15,5X,A)") "#", "-------", "--------", "-------", "-----", "-------"
 			
@@ -1434,7 +1434,7 @@ subroutine execute( this, iParser )
 			write(this.weightHistoryFile.unit,"(A)") "#------------------------------------"
 			write(this.weightHistoryFile.unit,"(A)") "# WEIGHT HISTORY"
 			write(this.weightHistoryFile.unit,"(A)") "#------------------------------------"
-			write(this.weightHistoryFile.unit,"(A1,3X,6A15,5X,A)") "#", "LnWe", "LnWv", "LnWn", "LnWr", "LnWt", "LnW", "formula"
+			write(this.weightHistoryFile.unit,"(A1,3X,6A15,5X,A)") "#", "LnWe", "LnWv", "LnWn", "LnWr", "LnWt", "LnW", "label"
 			write(this.weightHistoryFile.unit,"(A1,3X,6A15,5X,A)") "#", "arb.", "arb.", "arb.", "arb.", "arb.", "arb.", ""
 			write(this.weightHistoryFile.unit,"(A1,3X,6A15,5X,A)") "#", "-------", "-------", "--------", "--------", "--------", "-------", "-------"
 			
diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 311f983..3ea3f41 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -495,37 +495,41 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 		type(FragmentsList) :: lReactives, lProducts
 		type(String) :: labelTS, label
 		logical :: locatedTS
+		logical :: useDetailsInLabel
+		integer :: transitionStateId
+		
+		useDetailsInLabel = .true.
 		
 		call reactiveInTS.init( resizeIncrement=reactives.nMolecules() )
 		call productInTS.init( resizeIncrement=products.nMolecules() )
 		
 		do i=1,reactives.nMolecules()
-			id = FragmentsDB_instance.getIdFromName( reactives.clusters(i).label() )
+			id = FragmentsDB_instance.getIdClusterFromLabel( reactives.clusters(i).label( details=useDetailsInLabel ) )
 			if( FragmentsDB_instance.involvedInTS( id ) ) then
-					call reactiveInTS.append( i )
+				call reactiveInTS.append( i )
 			end if
 		end do
 		
 		do i=1,products.nMolecules()
-			id = FragmentsDB_instance.getIdFromName( products.clusters(i).label() )
+			id = FragmentsDB_instance.getIdClusterFromLabel( products.clusters(i).label( details=useDetailsInLabel ) )
 			if( FragmentsDB_instance.involvedInTS( id ) ) then
 					call productInTS.append( i )
 			end if
 		end do
 		
 		if( .not. reactiveInTS.isEmpty() .and. .not. productInTS.isEmpty() ) then
-! 			write(*,"(A)",advance="no") "Reactives "
-! 			do i=1,reactives.nMolecules()
-! 				write(*,"(A)",advance="no") trim(reactives.clusters(i).label())//"+"
+! 			write(*,"(A,A)") "Reactives = ", trim(reactives.label( details=useDetailsInLabel ))
+! 			write(*,"(A)",advance="no") "reactiveInTS = "
+! 			do i=1,reactiveInTS.size()
+! 				write(*,"(A)",advance="no") trim(reactives.clusters(reactiveInTS.data(i)).label( details=useDetailsInLabel ))//"+"
 ! 			end do
 ! 			write(*,*) ""
-! 			write(*,*) "reactiveInTS = ", reactiveInTS.data(1:reactiveInTS.size())
-! 			write(*,"(A)",advance="no") "Products "
-! 			do i=1,products.nMolecules()
-! 				write(*,"(A)",advance="no") trim(products.clusters(i).label())//"+"
+! 			write(*,"(A,A)") "Products = ", trim(products.label( details=useDetailsInLabel ))
+! 			write(*,"(A)",advance="no") "productInTS = "
+! 			do i=1,productInTS.size()
+! 				write(*,"(A)",advance="no") trim(products.clusters(productInTS.data(i)).label( details=useDetailsInLabel ))//"+"
 ! 			end do
 ! 			write(*,*) ""
-! 			write(*,*) "productInTS = ", productInTS.data(1:productInTS.size())
 			
 			locatedTS = .false.
 			
@@ -566,162 +570,34 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 									lProducts.clusters(kp) = products.clusters( productInTS.at(productInTScomb(jp,kp)) )
 								end do
 								
-								if( trim(lReactives.label()) /= trim(lProducts.label()) ) then
+								if( trim(lReactives.label( details=useDetailsInLabel )) /= trim(lProducts.label( details=useDetailsInLabel )) ) then
 									
-									labelTS = trim(lReactives.label())//"<-->"//trim(lProducts.label())
+									labelTS = trim(lReactives.label( details=useDetailsInLabel ))//"<-->"//trim(lProducts.label( details=useDetailsInLabel ))
 									
 									if( GOptions_debugLevel >= 2 ) then
-										write(*,*) "      reactives = ", trim(reactives.label())
-										write(*,*) "       products = ", trim(products.label())
+										write(*,*) "      reactives = ", trim(reactives.label( details=useDetailsInLabel ))
+										write(*,*) "       products = ", trim(products.label( details=useDetailsInLabel ))
 										write(*,*) "     TS located = ", trim(labelTS.fstr)
 									end if
 									
-									call productsTS.init( products.nMolecules() - lProducts.nMolecules() + 1 )
-									
-									call productsTS.set( 1, &
-													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
-									
-									! @TODO Aca el problema aparece cuando todos los productos estan en un TS como C(t1)+C(t1)+C(t1)
-									!       En este caso nunca se entra en el if
-									j=2
-									do i=1,products.nMolecules()
-										do kp=1,size(productInTScomb,dim=2)
-											label = trim(products.clusters( productInTS.at(productInTScomb(jp,kp)) ).label())
-											if( label /= trim(products.clusters(i).label()) &
-												.and. j<=productsTS.nMolecules() ) then
-												call productsTS.set( j, products.clusters(i) )
-												j = j+1
-												exit
-											end if
-										end do
-									end do
-									
-									if( j==2 ) then
-										do i=1,products.nMolecules()
-											if( j<=productsTS.nMolecules() ) then
-												call productsTS.set( j, products.clusters(i) )
-												j = j+1
-											end if
-										end do
-									end if
+									transitionStateId = FragmentsDB_instance.getIdTransitionStateFromLabel( trim(labelTS.fstr) )
 									
 									if( GOptions_debugLevel >= 2 ) then
-										write(*,*) "       products = ", trim(products.label())
-										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
+										write(*,*) "          TS id = ", transitionStateId
 									end if
 									
-									locatedTS = .true.
-									exit ! Only one TS is accepted. The one with minimum size
-									
-								end if
-								
-							end if
-							
-						end do
-						
-						if( locatedTS ) exit
-						
-					end do
-					
-					if( locatedTS ) exit
-					
-				end do
-				
-				if( locatedTS ) exit
-				
-			end do
-			
-		end if
-		
-		if( GOptions_debugLevel >= 2 ) then
-			write(*,*) ""
-		end if
-		
-		if( allocated(reactiveInTScomb) ) deallocate( reactiveInTScomb )
-		if( allocated(productInTScomb) ) deallocate( productInTScomb )
-		
-		do i=1,products.nMolecules()
-			id = FragmentsDB_instance.getIdFromName( products.clusters(i).label() )
-			if( FragmentsDB_instance.involvedInTS( id ) ) then
-					call productInTS.append( i )
-			end if
-		end do
-		
-		if( .not. reactiveInTS.isEmpty() .and. .not. productInTS.isEmpty() ) then
-! 			write(*,"(A)",advance="no") "Reactives "
-! 			do i=1,reactives.nMolecules()
-! 				write(*,"(A)",advance="no") trim(reactives.clusters(i).label())//"+"
-! 			end do
-! 			write(*,*) ""
-! 			write(*,*) "reactiveInTS = ", reactiveInTS.data(1:reactiveInTS.size())
-! 			write(*,"(A)",advance="no") "Products "
-! 			do i=1,products.nMolecules()
-! 				write(*,"(A)",advance="no") trim(products.clusters(i).label())//"+"
-! 			end do
-! 			write(*,*) ""
-! 			write(*,*) "productInTS = ", productInTS.data(1:productInTS.size())
-			
-			locatedTS = .false.
-			
-			do ir=1,reactiveInTS.size()
-				call Math_combinations( reactiveInTS.size(), ir, reactiveInTScomb )
-				
-				do jr=1,size(reactiveInTScomb,dim=1)
-					
-					nAtomsR = 0
-					massNumberR = 0
-					do kr=1,size(reactiveInTScomb,dim=2)
-						massNumberR = massNumberR + reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) ).massNumber()
-						nAtomsR = nAtomsR + reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) ).nAtoms()
-					end do
-					
-					do ip=1,productInTS.size()
-						call Math_combinations( productInTS.size(), ip, productInTScomb )
-						
-						do jp=1,size(productInTScomb,dim=1)
-							
-							nAtomsP = 0
-							massNumberP = 0
-							do kp=1,size(productInTScomb,dim=2)
-								massNumberP = massNumberP + products.clusters( productInTS.at(productInTScomb(jp,kp)) ).massNumber()
-								nAtomsP = nAtomsP + products.clusters( productInTS.at(productInTScomb(jp,kp)) ).nAtoms()
-							end do
-							
-							if( massNumberR == massNumberP .and. nAtomsR > 1 .and. nAtomsP > 1 ) then
-								
-								call lReactives.init( size(reactiveInTScomb,dim=2) )
-								call lProducts.init( size(productInTScomb,dim=2) )
-								
-								do kr=1,size(reactiveInTScomb,dim=2)
-									lReactives.clusters(kr) = reactives.clusters( reactiveInTS.at(reactiveInTScomb(jr,kr)) )
-								end do
-							
-								do kp=1,size(productInTScomb,dim=2)
-									lProducts.clusters(kp) = products.clusters( productInTS.at(productInTScomb(jp,kp)) )
-								end do
-								
-								if( trim(lReactives.label()) /= trim(lProducts.label()) ) then
-									
-									labelTS = trim(lReactives.label())//"<-->"//trim(lProducts.label())
-									
-									if( GOptions_debugLevel >= 2 ) then
-										write(*,*) "      reactives = ", trim(reactives.label())
-										write(*,*) "       products = ", trim(products.label())
-										write(*,*) "     TS located = ", trim(labelTS.fstr)
-									end if
+									if( transitionStateId == -1 ) cycle
 									
 									call productsTS.init( products.nMolecules() - lProducts.nMolecules() + 1 )
-									
-									call productsTS.set( 1, &
-													FragmentsDB_instance.transitionState( FragmentsDB_instance.str2id_TS.at( labelTS ) ) )
+									call productsTS.set( 1, FragmentsDB_instance.transitionState( transitionStateId ) )
 									
 									! @TODO Aca el problema aparece cuando todos los productos estan en un TS como C(t1)+C(t1)+C(t1)
 									!       En este caso nunca se entra en el if
 									j=2
 									do i=1,products.nMolecules()
 										do kp=1,size(productInTScomb,dim=2)
-											label = trim(products.clusters( productInTS.at(productInTScomb(jp,kp)) ).label())
-											if( label /= trim(products.clusters(i).label()) &
+											label = trim(products.clusters( productInTS.at(productInTScomb(jp,kp)) ).label( details=useDetailsInLabel ))
+											if( label /= trim(products.clusters(i).label( details=useDetailsInLabel )) &
 												.and. j<=productsTS.nMolecules() ) then
 												call productsTS.set( j, products.clusters(i) )
 												j = j+1
@@ -740,7 +616,8 @@ subroutine reduceToTransitionStates( reactives, products, productsTS )
 									end if
 									
 									if( GOptions_debugLevel >= 2 ) then
-										write(*,*) "    Eff channel = ", trim(reactives.label())//"-->"//trim(productsTS.label())
+										write(*,*) "       products = ", trim(products.label( details=useDetailsInLabel ))
+										write(*,*) "    Eff channel = ", trim(reactives.label( details=useDetailsInLabel ))//"-->"//trim(productsTS.label( details=useDetailsInLabel ))
 									end if
 									
 									locatedTS = .true.
@@ -1221,7 +1098,7 @@ subroutine run( this )
 		
 		if( GOptions_printLevel >= 2 ) then
 			write(*,"(A)") "#--------------------------------------------------------------------------------------------------------------"
-			write(*,"(A1,3X,6A15,5X,A)") "#", "LnWe", "LnWv", "LnWn", "LnWr", "LnWt", "LnW", "formula"
+			write(*,"(A1,3X,6A15,5X,A)") "#", "LnWe", "LnWv", "LnWn", "LnWr", "LnWt", "LnW", "label"
 			write(*,"(A1,3X,6A15,5X,A)") "#", "arb.", "arb.", "arb.", "arb.", "arb.", "arb.", ""
 			write(*,"(A)") "#--------------------------------------------------------------------------------------------------------------"
 			
@@ -1236,7 +1113,7 @@ subroutine run( this )
 
 			write(*,"(A)") ""
 			write(*,"(A)") "#--------------------------------------------------------------------------------------------------------------"
-			write(*,"(A1,3X,5A15,5X,A)") "#", "trans", "intermol", "vib", "rot", "tot", "formula"
+			write(*,"(A1,3X,5A15,5X,A)") "#", "trans", "intermol", "vib", "rot", "tot", "label"
 			write(*,"(A1,3X,5A15,5X,A)") "#", "eV", "eV", "eV", "eV", ""
 			write(*,"(A)") "#--------------------------------------------------------------------------------------------------------------"
 
@@ -1311,7 +1188,7 @@ subroutine execute( this, iParser )
 			
 			call reactives.init( size(reactiveTokens) )
 			do i=1,size(reactiveTokens)
-				iBuffer = FragmentsDB_instance.getIdFromName( reactiveTokens(i) )
+				iBuffer = FragmentsDB_instance.getIdClusterFromLabel( reactiveTokens(i) )
 				call reactives.set( i, FragmentsDB_instance.clusters(iBuffer) )
 			end do
 			
@@ -1529,7 +1406,7 @@ subroutine executeReactionsAnalysis( this, iParser )
 		
 		sBuffer = iParser.getString( "FRAGMENTS_DATABASE:reference", def="@@NONE@@" )
 		if( sBuffer /= "@@NONE@@" ) then
-			id = FragmentsDB_instance.getIdFromName( trim(sBuffer.fstr) )
+			id = FragmentsDB_instance.getIdClusterFromLabel( trim(sBuffer.fstr) )
 		else
 			id = size(FragmentsDB_instance.clusters)
 		end if

From 2428b856130005d899eeb2617e7d95f199f12010 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Tue, 10 Mar 2020 01:14:59 +0100
Subject: [PATCH 53/57] 1) Bug fixed in TS detection 2) Improved example

---
 examples/TS/C2.m3c  | 13 ++++++++-----
 src/FragmentsDB.f90 |  6 +++---
 2 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/examples/TS/C2.m3c b/examples/TS/C2.m3c
index 576b381..7c4d3a8 100644
--- a/examples/TS/C2.m3c
+++ b/examples/TS/C2.m3c
@@ -1,5 +1,5 @@
 BEGIN EXCITATION_ENERGY_SCAN
-	excitationEnergy  =  0:12:13  # dE = 1.0 eV
+	excitationEnergy  =  0:12:25  # dE = 0.5 eV
 END EXCITATION_ENERGY_SCAN
 
 BEGIN GOPTIONS
@@ -13,7 +13,7 @@ BEGIN GOPTIONS
         useSpinConservationRules = FALSE
         
         angularMomentumCouplingScheme = JJL
-# 	debugLevel = 3
+	debugLevel = 3
 END GOPTIONS
 
 BEGIN MARKOV_CHAIN
@@ -21,7 +21,7 @@ BEGIN MARKOV_CHAIN
         burnInFraction = 0.0
         
 	reactives = C2(s1)
-        excitationEnergy = 10.0
+        excitationEnergy = 7.0
         
         tracking = weight
         
@@ -29,7 +29,7 @@ BEGIN MARKOV_CHAIN
 #         numberOfEvents = 100000
         numberOfExperiments = 3
 #         numberOfEvents = 50000
-        numberOfEvents = 2000
+        numberOfEvents = 5000
 #        historyFileFrequency = 100
         historyFileFrequency = 1
 
@@ -49,6 +49,7 @@ BEGIN FRAGMENTS_DATABASE
 	#--------------------------------------------------------------------------------------
 	#  Label    Z  M WL  SYM          geomFile         Eelec     maxVib
 	#--------------------------------------------------------------------------------------
+           C(s1)    0  1  3    1    C.q0.m3-1.rxyz            2.5                      #       ³P (2s²2p²)
            C(t1)    0  3  3    1    C.q0.m3-1.rxyz            3.0                      #       ³P (2s²2p²)
           C2(s1)    0  1  1    2   C2.q0.m1-1.rxyz            0.0     C(t1)+C(t1)      # 6.0   ^1\Sigma_g^+
 	#--------------------------------------------------------------------------------------
@@ -61,6 +62,8 @@ BEGIN TRANSITION_STATES_DATABASE
 	#--------------------------------------------------------------------------------------
 	#  Label    Z  M WL  SYM          geomFile         Eelec     maxVib     TS
 	#--------------------------------------------------------------------------------------
-          C2(ts1)   0  1  1    2 C2ts.q0.m1-1.rxyz           8.0        4.0     C2(s1)<-->C(t1)+C(t1)
+	  C2(ts1)   0  1  1    2 C2ts.q0.m1-1.rxyz           7.0        4.0     C2(s1)<-->C(s1)+C(s1)
+          C2(ts2)   0  1  1    2 C2ts.q0.m1-1.rxyz          20.0        4.0     C2(s1)<-->C(s1)+C(t1)
+          C2(ts3)   0  1  1    2 C2ts.q0.m1-1.rxyz          20.0        4.0     C2(s1)<-->C(t1)+C(t1)
 	#--------------------------------------------------------------------------------------
 END TRANSITION_STATES_DATABASE
diff --git a/src/FragmentsDB.f90 b/src/FragmentsDB.f90
index 2e8af74..210c4c7 100644
--- a/src/FragmentsDB.f90
+++ b/src/FragmentsDB.f90
@@ -455,6 +455,9 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 				call this.str2id_TS.insert( FString_toString(trim(productsdLabel)//"<-->"//trim(reactivesdLabel)), i )
 				write(*,"(4X,A22,A)")  "Interpreted Path = ", trim(reactivesdLabel)//"<-->"//trim(productsdLabel)
 				
+				deallocate(reactives)
+				deallocate(products)
+				
 			else
 				call GOptions_error( &
 						"Bad number of atoms in transition state (N=0)", &
@@ -470,9 +473,6 @@ subroutine setTransitionStatesTable( this, transitionStatesTable, store )
 		
 		call GOptions_section( "END TRANSITION_STATES DATABASE INITIALIZATION", indent=1 )
 		
-! 		deallocate(reactives)
-! 		deallocate(products)
-		
 	end subroutine setTransitionStatesTable
 	
 	!>

From 77037da9c05927efc182ee9ac0131483de62ebc4 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sat, 14 Mar 2020 21:15:37 +0100
Subject: [PATCH 54/57] Improved example C2 with transition state

---
 examples/{TS => testTS-C2}/C.q0.m1-1.rxyz    |   0
 examples/{TS => testTS-C2}/C.q0.m3-1.rxyz    |   0
 examples/{TS => testTS-C2}/C2.m3c            |  43 ++--
 examples/{TS => testTS-C2}/C2.q0.m1-1.rxyz   |   0
 examples/{TS => testTS-C2}/C2.q0.m3-1.rxyz   |   0
 examples/{TS => testTS-C2}/C2ts.q0.m1-1.rxyz |   2 +-
 examples/{TS => testTS-C2}/C3.m3c            |   0
 examples/{TS => testTS-C2}/C3.q0.m1-1.rxyz   |   0
 examples/testTS-C2/breakDownCurves.png       | Bin 0 -> 30496 bytes
 examples/testTS-C2/energyLandscape.png       | Bin 0 -> 52618 bytes
 examples/testTS-C2/energyLandscape.svg       | 247 +++++++++++++++++++
 11 files changed, 265 insertions(+), 27 deletions(-)
 rename examples/{TS => testTS-C2}/C.q0.m1-1.rxyz (100%)
 rename examples/{TS => testTS-C2}/C.q0.m3-1.rxyz (100%)
 rename examples/{TS => testTS-C2}/C2.m3c (50%)
 rename examples/{TS => testTS-C2}/C2.q0.m1-1.rxyz (100%)
 rename examples/{TS => testTS-C2}/C2.q0.m3-1.rxyz (100%)
 rename examples/{TS => testTS-C2}/C2ts.q0.m1-1.rxyz (83%)
 rename examples/{TS => testTS-C2}/C3.m3c (100%)
 rename examples/{TS => testTS-C2}/C3.q0.m1-1.rxyz (100%)
 create mode 100644 examples/testTS-C2/breakDownCurves.png
 create mode 100644 examples/testTS-C2/energyLandscape.png
 create mode 100644 examples/testTS-C2/energyLandscape.svg

diff --git a/examples/TS/C.q0.m1-1.rxyz b/examples/testTS-C2/C.q0.m1-1.rxyz
similarity index 100%
rename from examples/TS/C.q0.m1-1.rxyz
rename to examples/testTS-C2/C.q0.m1-1.rxyz
diff --git a/examples/TS/C.q0.m3-1.rxyz b/examples/testTS-C2/C.q0.m3-1.rxyz
similarity index 100%
rename from examples/TS/C.q0.m3-1.rxyz
rename to examples/testTS-C2/C.q0.m3-1.rxyz
diff --git a/examples/TS/C2.m3c b/examples/testTS-C2/C2.m3c
similarity index 50%
rename from examples/TS/C2.m3c
rename to examples/testTS-C2/C2.m3c
index 7c4d3a8..abe90a2 100644
--- a/examples/TS/C2.m3c
+++ b/examples/testTS-C2/C2.m3c
@@ -13,31 +13,22 @@ BEGIN GOPTIONS
         useSpinConservationRules = FALSE
         
         angularMomentumCouplingScheme = JJL
-	debugLevel = 3
 END GOPTIONS
 
 BEGIN MARKOV_CHAIN
 	task = 5*V,T,R,S:0,5*V,T,R,S:-1:1
-        burnInFraction = 0.0
+        burnInFraction = 0.1
         
 	reactives = C2(s1)
         excitationEnergy = 7.0
         
-        tracking = weight
-        
-#         numberOfExperiments = 6
-#         numberOfEvents = 100000
+        tracking = energy
         numberOfExperiments = 3
-#         numberOfEvents = 50000
-        numberOfEvents = 5000
-#        historyFileFrequency = 100
+        numberOfEvents = 10000
         historyFileFrequency = 1
 
-#        geometryHistoryFilePrefix = geom
         energyHistoryFile = energy.dat
         weightHistoryFile = weight.dat
-#        JHistoryFile = J.dat
-#        LHistoryFile = L.dat
         histogramFile = histogram.dat
 END MARKOV_CHAIN
 
@@ -46,24 +37,24 @@ BEGIN FRAGMENTS_DATABASE
 	store = .
 	reference = C2(s1)
 
-	#--------------------------------------------------------------------------------------
-	#  Label    Z  M WL  SYM          geomFile         Eelec     maxVib
-	#--------------------------------------------------------------------------------------
-           C(s1)    0  1  3    1    C.q0.m3-1.rxyz            2.5                      #       ³P (2s²2p²)
-           C(t1)    0  3  3    1    C.q0.m3-1.rxyz            3.0                      #       ³P (2s²2p²)
-          C2(s1)    0  1  1    2   C2.q0.m1-1.rxyz            0.0     C(t1)+C(t1)      # 6.0   ^1\Sigma_g^+
-	#--------------------------------------------------------------------------------------
+	#---------------------------------------------------------------------------
+	#  Label    Z  M WL  SYM          geomFile         Eelec           maxVib
+	#---------------------------------------------------------------------------
+           C(s1)    0  1  5    0    C.q0.m1-1.rxyz  -1026.574168                     #          R3(1-D)
+           C(t1)    0  3  3    0    C.q0.m3-1.rxyz  -1028.024016                     #          R3(3-P)
+          C2(s1)    0  1  1    2   C2.q0.m1-1.rxyz  -2062.151541      C(t1)+C(t1)    #    6.10  D*H(1-SGG)
+          C2(t1)    0  3  2    2   C2.q0.m3-1.rxyz  -2062.058719      C(t1)+C(t1)    #    6.01  D*H(3-PIU)
+	#---------------------------------------------------------------------------
 END FRAGMENTS_DATABASE
 
 BEGIN TRANSITION_STATES_DATABASE
 
  	store = .
 	
-	#--------------------------------------------------------------------------------------
-	#  Label    Z  M WL  SYM          geomFile         Eelec     maxVib     TS
-	#--------------------------------------------------------------------------------------
-	  C2(ts1)   0  1  1    2 C2ts.q0.m1-1.rxyz           7.0        4.0     C2(s1)<-->C(s1)+C(s1)
-          C2(ts2)   0  1  1    2 C2ts.q0.m1-1.rxyz          20.0        4.0     C2(s1)<-->C(s1)+C(t1)
-          C2(ts3)   0  1  1    2 C2ts.q0.m1-1.rxyz          20.0        4.0     C2(s1)<-->C(t1)+C(t1)
-	#--------------------------------------------------------------------------------------
+	#---------------------------------------------------------------------------------------------
+	#  Label    Z  M WL  SYM          geomFile         Eelec        maxVib     TS
+	#---------------------------------------------------------------------------------------------
+         C2ts(s1)   0  1  1    2 C2ts.q0.m1-1.rxyz  -2054.151541   C(s1)+C(s1)  C2(s1)<-->C(t1)+C(t1)  #    8.10  D*H(1-SGG)
+         C2ts(s2)   0  1  1    2 C2ts.q0.m1-1.rxyz  -2054.151541   C(s1)+C(s1)  C2(t1)<-->C(t1)+C(t1)  #    8.10  D*H(1-SGG)
+	#---------------------------------------------------------------------------------------------
 END TRANSITION_STATES_DATABASE
diff --git a/examples/TS/C2.q0.m1-1.rxyz b/examples/testTS-C2/C2.q0.m1-1.rxyz
similarity index 100%
rename from examples/TS/C2.q0.m1-1.rxyz
rename to examples/testTS-C2/C2.q0.m1-1.rxyz
diff --git a/examples/TS/C2.q0.m3-1.rxyz b/examples/testTS-C2/C2.q0.m3-1.rxyz
similarity index 100%
rename from examples/TS/C2.q0.m3-1.rxyz
rename to examples/testTS-C2/C2.q0.m3-1.rxyz
diff --git a/examples/TS/C2ts.q0.m1-1.rxyz b/examples/testTS-C2/C2ts.q0.m1-1.rxyz
similarity index 83%
rename from examples/TS/C2ts.q0.m1-1.rxyz
rename to examples/testTS-C2/C2ts.q0.m1-1.rxyz
index 1668844..d6b0257 100644
--- a/examples/TS/C2ts.q0.m1-1.rxyz
+++ b/examples/testTS-C2/C2ts.q0.m1-1.rxyz
@@ -1,5 +1,5 @@
 2
-Energy =   -75.8561424407255
+Energy =   -75.4886493524808
     C    0.823543    0.000000    0.000000
     C   -0.823543    0.000000    0.000000
 
diff --git a/examples/TS/C3.m3c b/examples/testTS-C2/C3.m3c
similarity index 100%
rename from examples/TS/C3.m3c
rename to examples/testTS-C2/C3.m3c
diff --git a/examples/TS/C3.q0.m1-1.rxyz b/examples/testTS-C2/C3.q0.m1-1.rxyz
similarity index 100%
rename from examples/TS/C3.q0.m1-1.rxyz
rename to examples/testTS-C2/C3.q0.m1-1.rxyz
diff --git a/examples/testTS-C2/breakDownCurves.png b/examples/testTS-C2/breakDownCurves.png
new file mode 100644
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+       d="m 206.16725,157.82917 h 31.63632 z"
+       id="path815-6-8"
+       sodipodi:nodetypes="ccc" />
+    <path
+       inkscape:connector-curvature="0"
+       style="fill:none;fill-rule:evenodd;stroke:#0000ff;stroke-width:2.36500001;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+       d="m 206.16726,104.64792 h 31.63631 z"
+       id="path815-6-9"
+       sodipodi:nodetypes="ccc" />
+    <path
+       style="fill:none;fill-rule:evenodd;stroke:#0000ff;stroke-width:0.765;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-miterlimit:4;stroke-dasharray:3.06,3.06;stroke-dashoffset:0"
+       d="M 124.82641,257.57465 135.7881,145.98301"
+       id="path1056"
+       inkscape:connector-curvature="0" />
+    <path
+       style="fill:none;fill-rule:evenodd;stroke:#0000ff;stroke-width:0.765;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-miterlimit:4;stroke-dasharray:3.06,3.06;stroke-dashoffset:0"
+       d="M 167.42441,145.98301 206.16726,198.575"
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+       d="M 80.376476,249.95622 135.7881,145.98301"
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+</svg>

From 62404d1680b2e4b4fa6a0759c42e203b8f3f5a73 Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Fri, 20 Mar 2020 01:12:41 +0100
Subject: [PATCH 55/57] Bug fixed in the determination of the spin forbidden
 reactions

---
 src/Fragment.f90          |   4 +-
 src/FragmentsListBase.f90 | 119 +++++++++++++++++++++++++++++---------
 src/Reactor.f90           |  43 +++++---------
 3 files changed, 107 insertions(+), 59 deletions(-)

diff --git a/src/Fragment.f90 b/src/Fragment.f90
index d868191..dca0eda 100644
--- a/src/Fragment.f90
+++ b/src/Fragment.f90
@@ -61,7 +61,7 @@ module Fragment_
 	use RandomUtils_
 	use Molecule_
 	use StringList_
-	use RealList_
+	use RealVector_
 	
 	use GOptionsM3C_
 	
@@ -929,7 +929,7 @@ end subroutine showLnWComponents
 	!!
 	function spinAvailable( this ) result( output )
 		class(Fragment), intent(in) :: this
-		type(RealList) :: output
+		type(RealVector) :: output
 		
 		real(8) :: S, Si, Sj
 		integer :: i, j
diff --git a/src/FragmentsListBase.f90 b/src/FragmentsListBase.f90
index 0e3c551..ad28241 100644
--- a/src/FragmentsListBase.f90
+++ b/src/FragmentsListBase.f90
@@ -1,6 +1,12 @@
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 !!                                                                                   !!
 !! This file is part of M3C project                                                  !!
+!!                                                                                   !!
+!! Copyright (c) 2019-2020 by authors                                                !!
+!! Authors:                                                                          !!
+!!                         * Néstor F. Aguirre (2019-2020)                           !!
+!!                           nfaguirrec@gmail.com                                    !!
+!!                                                                                   !!
 !! Copyright (c) 2013-2016 Departamento de Química                                   !!
 !!                         Universidad Autónoma de Madrid                            !!
 !!                         All rights reserved.                                      !!
@@ -66,7 +72,7 @@ module FragmentsListBase_
 	use Atom_
 	use Molecule_
 	use BlocksIFileParser_
-	use RealList_
+	use RealVector_
 	
 	use GOptionsM3C_
 	use Fragment_
@@ -75,6 +81,9 @@ module FragmentsListBase_
 	implicit none
 	private
 	
+	public :: &
+		spinListCoupling
+	
 	type, abstract, public :: FragmentsListBase
 		type(Fragment), allocatable :: clusters(:)    !< Fragment list
 		integer, allocatable :: idSorted(:)            !< Position of the molecule sorted by mass. It is calculated in updateLabel procedure
@@ -2257,43 +2266,97 @@ function spinRange( this ) result( output )
 	end function spinRange
 	
 	!>
-	!! @brief
+	!! @brief Internal. Used only by spinAvailable function
 	!!
-	function spinAvailable( this ) result( output )
-		class(FragmentsListBase), intent(in) :: this
-		type(RealList) :: output
+	function spinSpinCoupling( s1, s2 ) result( st )
+		real(8), intent(in) :: s1, s2
+		type(RealVector) :: st
 		
-		real(8) :: S, Si, Sj
-		integer :: i, j
+		real(8) :: s0
+		integer :: i
+		integer :: n
 		
-		call output.init()
+		n = s1+s2-abs(s1-s2)+1
+		s0 = abs(s1-s2)
 		
-		if( this.nMolecules() == 1 ) then
-			S = (this.clusters(1).multiplicity-1.0_8)/2.0_8
-			call output.append( S )
-		else
-			do i=1,this.nMolecules()-1
-				Si = (this.clusters(i).multiplicity-1.0_8)/2.0_8
+		call st.init( n )
+		do i=1,n
+			call st.set( i, s0+i-1 )
+		end do
 				
-				if( Si < 0.0_8 ) Si=0.0_8
+	end function spinSpinCoupling
+	
+	!>
+	!! @brief Internal. Used only by spinAvailable function
+	!!
+	function spinListSpinCoupling( sl1, s2 ) result( st )
+		type(RealVector), intent(in) :: sl1
+		real(8), intent(in) :: s2
+		type(RealVector) :: st
+		
+		real(8) :: s0
+		integer :: i
+		integer :: n
+
+		n = maxval(sl1.data(1:sl1.size())+s2)-minval(abs(sl1.data(1:sl1.size())-s2))+1
+		s0 = minval(abs(sl1.data(1:sl1.size())-s2))
+		
+		call st.init( n, 0.0_8 )
+		do i=1,n
+			call st.set( i, s0+i-1 )
+		end do
 				
-				do j=i+1,this.nMolecules()
-					Sj = (this.clusters(j).multiplicity-1.0_8)/2.0_8
-					
-					if( Sj < 0.0_8 ) Sj=0.0_8
-					
-					S = abs(Si-Sj)
-					do while( int(2.0*S) <= int(2.0*(Si+Sj)) )
-						call output.append( S )
-						
-						S = S + 1.0_8
-					end do
-				end do
+	end function spinListSpinCoupling
+	
+	!>
+	!! @brief Internal. Used only by spinAvailable function
+	!!
+	function spinListCoupling( sl ) result( st )
+		type(RealVector), intent(in) :: sl
+		type(RealVector) :: st
+		
+		integer :: i
+		type(RealVector) :: sij
+		
+		call st.init()
+		
+		if( sl.size() == 1 ) then
+			st = sl
+		else
+			sij = spinSpinCoupling( sl.at(1), sl.at(2) )
+			st = sij
+			
+			do i=3,sl.size()
+				sij = spinListSpinCoupling( sij, sl.at(i) )
+				st = sij
 			end do
 		end if
+
+	end function spinListCoupling
+	
+	!>
+	!! @brief
+	!!
+	function spinAvailable( this ) result( output )
+		class(FragmentsListBase), intent(in) :: this
+		type(RealVector) :: output
+		
+		integer :: i
+		real(8) :: S
+		type(RealVector) :: sl
+		
+		call sl.init( this.nMolecules(), 0.0_8 )
+		do i=1,this.nMolecules()
+			S = (this.clusters(i).multiplicity-1.0_8)/2.0_8
+			if( S < 0.0_8 ) S=0.0_8
+			
+			call sl.append( S )
+		end do
+		
+		output = spinListCoupling( sl )
 		
 		if( output.size() == 0 ) then
-			write(*,*) "### ERROR ### FragmentsListBase.spinAvailable.size() == 0", this.nMolecules(), S, Si, Sj
+			write(*,*) "### ERROR ### FragmentsListBase.spinAvailable.size() == 0", this.nMolecules(), S
 		end if
 	end function spinAvailable
 	
diff --git a/src/Reactor.f90 b/src/Reactor.f90
index 3ea3f41..fd221f0 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -63,6 +63,7 @@ module Reactor_
 	use BlocksIFileParser_
 	use RealHistogram_
 	use RealList_
+	use RealVector_
 	use IntegerVector_
 	use StringIntegerMap_
 	use StringRealMap_
@@ -71,6 +72,7 @@ module Reactor_
 	
 	use GOptionsM3C_
 	use Fragment_
+	use FragmentsListBase_
 	use FragmentsList_
 	use FragmentsDB_
 	
@@ -127,7 +129,7 @@ module Reactor_
 	integer, private :: internalCharge = 0
 	integer, private :: internalNTrials = 0
 ! 	real(8), private :: internalReactivesSpinRange(2) = 0.0_8
-	type(RealList), private :: internalReactivesSpinAvail
+	type(RealVector), private :: internalReactivesSpinAvail
 	
 	contains
 	
@@ -348,33 +350,25 @@ function isSpinForbidden( multisetPositions, current ) result( output )
 		logical :: output
 		
 		real(8) :: S, Si, Sj
-		type(RealList) :: spinAvail
+		type(RealVector) :: spinAvail
 		integer :: i, j
 		class(RealListIterator), pointer :: it1, it2
 		
-		call spinAvail.init()
+		call spinAvail.init( current, 0.0_8 )
 		
 		if( current == 1 ) then
 			S = (FragmentsDB_instance.clusters( multisetPositions(1) ).multiplicity-1.0_8)/2.0_8
-			call spinAvail.append( S )
+			call spinAvail.set( 1, S )
 		else
-			do i=1,current-1
+			do i=1,current
 				Si = (FragmentsDB_instance.clusters( multisetPositions(i) ).multiplicity-1.0_8)/2.0_8
-				
 				if( Si < 0.0_8 ) Si=0.0_8
 				
-				do j=i+1,current
-					Sj = (FragmentsDB_instance.clusters( multisetPositions(j) ).multiplicity-1.0_8)/2.0_8
-					
-					if( Sj < 0.0_8 ) Sj=0.0_8
-					
-					S = abs(Si-Sj)
-					do while( int(2.0*S) <= int(2.0*(Si+Sj)) )
-						call spinAvail.append( S )
-						S = S + 1.0_8
-					end do
-				end do
+				call spinAvail.set( i, Si )
 			end do
+			
+			spinAvail = spinListCoupling( spinAvail )
+
 		end if
 		
 		if( spinAvail.size() == 0 ) then
@@ -382,22 +376,13 @@ function isSpinForbidden( multisetPositions, current ) result( output )
 		end if
 		
 		output = .true.
-		
-		it1 => spinAvail.begin
-		do while( associated(it1) )
-			
-			it2 => internalReactivesSpinAvail.begin
-			do while( associated(it2) )
-			
-				if( abs( it1.data - it2.data ) < 0.1 ) then
+		do i=1,spinAvail.size()
+			do j=1,internalReactivesSpinAvail.size()
+				if( abs( spinAvail.at(i) - internalReactivesSpinAvail.at(j) ) < 0.1 ) then
 					output = .false.
 					return
 				end if
-				
-				it2 => it2.next
 			end do
-			
-			it1 => it1.next
 		end do
 		
 		call spinAvail.clear()

From 8859cb51e7e8da376d421ee3d99b31d2403b0e5a Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Sat, 21 Mar 2020 10:36:23 +0100
Subject: [PATCH 56/57] Simple bug fixed

---
 src/Reactor.f90 | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/Reactor.f90 b/src/Reactor.f90
index fd221f0..f25d55f 100644
--- a/src/Reactor.f90
+++ b/src/Reactor.f90
@@ -358,6 +358,8 @@ function isSpinForbidden( multisetPositions, current ) result( output )
 		
 		if( current == 1 ) then
 			S = (FragmentsDB_instance.clusters( multisetPositions(1) ).multiplicity-1.0_8)/2.0_8
+			if( Si < 0.0_8 ) Si=0.0_8
+			
 			call spinAvail.set( 1, S )
 		else
 			do i=1,current

From 39f60a000b920b41be97aaf831ef163de170bbca Mon Sep 17 00:00:00 2001
From: nfaguirrec <nfaguirrec@gmail.com>
Date: Mon, 23 Mar 2020 22:16:41 +0100
Subject: [PATCH 57/57] Now new properties of the deposited energy function are
 printed in M3CBR M3CfitBR programs

---
 src/M3CBR.f90    | 43 +++++++++++++++++++++++++++++++++++++++++-
 src/M3CfitBR.f90 | 49 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 91 insertions(+), 1 deletion(-)

diff --git a/src/M3CBR.f90 b/src/M3CBR.f90
index 00d358d..dc5bf7d 100644
--- a/src/M3CBR.f90
+++ b/src/M3CBR.f90
@@ -1,6 +1,12 @@
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 !!                                                                                   !!
 !! This file is part of M3C project                                                  !!
+!!                                                                                   !!
+!! Copyright (c) 2019-2020 by authors                                                !!
+!! Authors:                                                                          !!
+!!                         * Néstor F. Aguirre (2020-2020)                           !!
+!!                           nfaguirrec@gmail.com                                    !!
+!!                                                                                   !!
 !! Copyright (c) 2013-2016 Departamento de Química                                   !!
 !!                         Universidad Autónoma de Madrid                            !!
 !!                         All rights reserved.                                      !!
@@ -72,6 +78,7 @@ program M3CBR
 	logical :: lBuffer
 	
 	real(8) :: BR, rms, error
+	real(8) :: averE, stdevE, skewE
 	
 	type(CommandLineParser) :: programOptions
 	type(BlocksIFileParser) :: iParser
@@ -371,13 +378,47 @@ program M3CBR
 	rms = sqrt(rms/nChannels)
 	
 	close(11)
-
+	
+	! Maxima:
+	! B(E):=E**l*exp(-E/n)/(n**(l+1)*gamma(l+1));
+	! integrate(E*B(E),E,0,inf); #---> (l+1)*n
+	! integrate((E-mu)**2*B(E),E,0,inf); #---> (l+1)*(l+2)*n**2-2*(l+1)*n*mu+mu**2
+	! integrate(((E-mu)/sigma)**3*B(E),E,0,inf); #--> ( (l+1)*(l+2)*(l+3)*n**3-3*(l+1)*(l+2)*n**2*mu+3*(l+1)*n*mu**2-mu**3 )/sigma**3
+	
+	averE = 0.0_8
+	do k=1,basisSize
+		n = NL(k,1)
+		l = NL(k,2)
+		
+		averE = averE + (C.get(k,1)/100.0_8)*real((l+1)*n,8)
+	end do
+	
+	stdevE = 0.0_8
+	do k=1,basisSize
+		n = NL(k,1)
+		l = NL(k,2)
+		
+		stdevE = stdevE + (C.get(k,1)/100.0_8)*( real((l+1)*(l+2)*n**2,8) - 2.0_8*real((l+1)*n,8)*averE + averE**2 )
+	end do
+	stdevE = sqrt(stdevE)
+	
+	skewE = 0.0_8
+	do k=1,basisSize
+		n = NL(k,1)
+		l = NL(k,2)
+		
+		skewE = skewE + (C.get(k,1)/100.0_8)*( real((l+1)*(l+2)*(l+3)*n**3,8) - 3.0_8*real((l+1)*(l+2)*n**2,8)*averE + 3.0_8*real((l+1)*n,8)*averE**2-averE**3 )/stdevE**3
+	end do
+	
 	call f.fromFunction( energyGrid, energyFunction )
 	call f.save( energyDistFileName.fstr )
 	call integrator.init( f, NIntegrator_BOOLE )
 	write(*,*) ""
 	write(*,"(A15,F10.5)") "rms = ", rms
 	write(*,"(A15,F10.5)") "Integral = ", integrator.evaluate()
+	write(*,"(A15,F10.5)") "<E> = ", averE
+	write(*,"(A15,F10.5)") "stdev(E) = ", stdevE
+	write(*,"(A15,F10.5)") "skew(E) = ", skewE
 	
 	if( integrator.evaluate() < 98.0_8 ) then
 		write(*,*) ""
diff --git a/src/M3CfitBR.f90 b/src/M3CfitBR.f90
index 6fe8b39..3c93b9d 100644
--- a/src/M3CfitBR.f90
+++ b/src/M3CfitBR.f90
@@ -1,6 +1,12 @@
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 !!                                                                                   !!
 !! This file is part of M3C project                                                  !!
+!!                                                                                   !!
+!! Copyright (c) 2019-2020 by authors                                                !!
+!! Authors:                                                                          !!
+!!                         * Néstor F. Aguirre (2020-2020)                           !!
+!!                           nfaguirrec@gmail.com                                    !!
+!!                                                                                   !!
 !! Copyright (c) 2013-2016 Departamento de Química                                   !!
 !!                         Universidad Autónoma de Madrid                            !!
 !!                         All rights reserved.                                      !!
@@ -71,6 +77,8 @@ program M3CfitBR
 	type(Grid) :: bufferGrid
 	logical :: lBuffer
 	
+	real(8) :: averE, stdevE, skewE
+	
 	type(CommandLineParser) :: programOptions
 	type(BlocksIFileParser) :: iParser
 	
@@ -486,10 +494,51 @@ program M3CfitBR
 	write(*,"(A15,F10.5)") "rms = ", sqrt(ssum/nChannels)
 	close(11)
 	
+	! Maxima:
+	! B(E):=E**l*exp(-E/n)/(n**(l+1)*gamma(l+1));
+	! solve(diff(B(E),E)=0,E); #--> E=n*l
+	! integrate(E*B(E),E,0,inf); #---> (l+1)*n
+	! integrate((E-mu)**2*B(E),E,0,inf); #---> (l+1)*(l+2)*n**2-2*(l+1)*n*mu+mu**2
+	! integrate(((E-mu)/sigma)**3*B(E),E,0,inf); #--> ( (l+1)*(l+2)*(l+3)*n**3-3*(l+1)*(l+2)*n**2*mu+3*(l+1)*n*mu**2-mu**3 )/sigma**3
+	
+	averE = 0.0_8
+	k=1
+	do n=1,Nmax
+		do l=1,Lmax
+			averE = averE + (C.get(k,1)/100.0_8)*real((l+1)*n,8)
+			
+			k = k+1
+		end do
+	end do
+	
+	stdevE = 0.0_8
+	k=1
+	do n=1,Nmax
+		do l=1,Lmax
+			stdevE = stdevE + (C.get(k,1)/100.0_8)*( real((l+1)*(l+2)*n**2,8) - 2.0_8*real((l+1)*n,8)*averE + averE**2 )
+			
+			k = k+1
+		end do
+	end do
+	stdevE = sqrt(stdevE)
+	
+	skewE = 0.0_8
+	k=1
+	do n=1,Nmax
+		do l=1,Lmax
+			skewE = skewE + (C.get(k,1)/100.0_8)*( real((l+1)*(l+2)*(l+3)*n**3,8) - 3.0_8*real((l+1)*(l+2)*n**2,8)*averE + 3.0_8*real((l+1)*n,8)*averE**2-averE**3 )/stdevE**3
+			
+			k = k+1
+		end do
+	end do
+	
 	call f.fromFunction( energyGrid, energyFunction )
 	call f.save( energyDistFileName.fstr )
 	call integrator.init( f, NIntegrator_BOOLE )
 	write(*,"(A15,F10.5)") "Integral = ", integrator.evaluate()
+	write(*,"(A15,F10.5)") "<E> = ", averE
+	write(*,"(A15,F10.5)") "stdev(E) = ", stdevE
+	write(*,"(A15,F10.5)") "skew(E) = ", skewE
 	
 	if( abs(integrator.evaluate()-100.0_8) > 2.0_8 ) then
 		write(*,*) ""