diff --git a/.travis.yml b/.travis.yml
index 8f4fec1..208fe3f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -36,7 +36,7 @@ before_script:
 env:
   - OPTIONS="CVR=ON" TEST="" CHOICES=gfort.lapack
   - OPTIONS="CVR=ON PROGRESS=ON" TEST="" CHOICES=gfort.lapack
-  - OPTIONS="CVR=ON MAKELIB=ON lammps" TEST="_lmp" CHOICES=gfort.lapack
+    #  - OPTIONS="CVR=ON MAKELIB=ON lammps" TEST="_lmp" CHOICES=gfort.lapack
   - LATTE_CMAKE=yes CMAKE_WITH_PROGRESS=yes
   - LATTE_CMAKE=yes LAMMPS_CMAKE=yes
 
diff --git a/Manual/refman.pdf b/Manual/refman.pdf
new file mode 100644
index 0000000..a1c7256
Binary files /dev/null and b/Manual/refman.pdf differ
diff --git a/src/Doxyfile.in b/src/Doxyfile.in
index b3d1d51..6894739 100644
--- a/src/Doxyfile.in
+++ b/src/Doxyfile.in
@@ -38,7 +38,7 @@ PROJECT_NAME           = LATTE
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 1.0
+PROJECT_NUMBER         = v1.2.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
diff --git a/src/constants_mod.f90 b/src/constants_mod.f90
index ed0d6e7..2c8669a 100644
--- a/src/constants_mod.f90
+++ b/src/constants_mod.f90
@@ -58,6 +58,7 @@ MODULE CONSTANTS_MOD
   INTEGER :: RSLEVEL
   INTEGER :: RESTARTLIB
   INTEGER :: FREEZE
+  INTEGER :: NEWSYSTEMLATTE 
   REAL(LATTEPREC) :: BOX(3,3), BOX_OLD(3,3), BOXDIMS(3)
   REAL(LATTEPREC) :: BNDFIL, TOTNE
   REAL(LATTEPREC) :: COVE, TOTE, ENTE, KEE, ECOUL, EREP, TRRHOH
diff --git a/src/deallocateall.f90 b/src/deallocateall.f90
index 32e5ce5..b9af1e1 100644
--- a/src/deallocateall.f90
+++ b/src/deallocateall.f90
@@ -39,7 +39,6 @@ SUBROUTINE DEALLOCATEALL
   USE PUREARRAY
   USE VIRIALARRAY
 
-
   IMPLICIT NONE
   IF (EXISTERROR) RETURN
 
diff --git a/src/diagmyh.f90 b/src/diagmyh.f90
index 8c06fac..1a1e122 100644
--- a/src/diagmyh.f90
+++ b/src/diagmyh.f90
@@ -48,8 +48,11 @@ SUBROUTINE DIAGMYH()
 #ifdef XSYEV
 
 #ifdef DOUBLEPREC
+
+
      CALL DSYEV(JOBZ, UPLO, HDIM, EVECS, HDIM, EVALS, &
           DIAG_WORK, DIAG_LWORK,INFO)
+
 #elif defined(SINGLEPREC)
 
      !     ALLOCATE(TMPHMAT(HDIM, HDIM), TMPEVALS(HDIM), DWORK(3*HDIM - 1))
@@ -77,7 +80,7 @@ SUBROUTINE DIAGMYH()
           DIAG_WORK, DIAG_LWORK, DIAG_IWORK, DIAG_LIWORK, INFO)
 #endif
 
-#endif     
+#endif
 
 
   ELSE
@@ -130,6 +133,7 @@ SUBROUTINE DIAGMYH()
 
   ENDIF
 
+
   RETURN
 
 END SUBROUTINE DIAGMYH
diff --git a/src/getrho.f90 b/src/getrho.f90
index 911c653..7c4a6c4 100644
--- a/src/getrho.f90
+++ b/src/getrho.f90
@@ -52,6 +52,7 @@ SUBROUTINE GETRHO(MDITER)
     ENDIF
 #else
      CALL DIAGMYH()
+
      IF (SPINON .EQ. 0) THEN
         CALL BOEVECS()
      ELSE
@@ -80,7 +81,7 @@ SUBROUTINE GETRHO(MDITER)
 #ifdef PROGRESSON
 
         CALL SP2PRG
-        
+
 #else
 
         IF (MDITER .LE. 10) THEN
diff --git a/src/latte_c_bind.f90 b/src/latte_c_bind.f90
index 7dea2e9..35e9992 100644
--- a/src/latte_c_bind.f90
+++ b/src/latte_c_bind.f90
@@ -40,7 +40,8 @@
 !! \param VEL Velocities passed to latte.
 !! \param DT integration step passed to latte.
 !! \param DT integration step passed to latte.
-!! \param VIRIALINOUT Components of the second virial coefficient
+!! \param VIRIAL_INOUT Components of the second virial coefficient
+!! \param NEWSYSTEM Tells LATTE if a new system is passed.
 !! \param EXISTERROR Returns an error flag (.true.) to the hosting code.
 !!
 !! \brief This routine will be used load call latte_lib from a C/C++ program:
@@ -58,9 +59,9 @@
 !! \brief Note: All units are LATTE units by default.
 !! See https://github.com/losalamos/LATTE/blob/master/Manual/LATTE_manual.pdf
 !!
-SUBROUTINE LATTE_C_BIND (FLAGS,NATS,COORDS,TYPES,NTYPES,MASSES,XLO &
-     ,XHI,XY,XZ,YZ,FORCES,MAXITER,VENERG, &
-     VEL,DT,VIRIALINOUT,EXISTERROR) BIND (C, NAME="latte")
+SUBROUTINE LATTE_C_BIND (FLAGS, NATS, COORDS, TYPES, NTYPES, MASSES, XLO &
+     , XHI, XY, XZ, YZ, FORCES, MAXITER, VENERG, &
+     VEL, DT, VIRIAL_INOUT, NEWSYSTEM, EXISTERROR) BIND (C, NAME="latte")
 
   USE ISO_C_BINDING, ONLY: C_CHAR, C_NULL_CHAR, C_DOUBLE, C_INT, C_BOOL
   USE LATTE_LIB
@@ -73,11 +74,12 @@ SUBROUTINE LATTE_C_BIND (FLAGS,NATS,COORDS,TYPES,NTYPES,MASSES,XLO &
   REAL(C_DOUBLE)                 ::  XLO(3), EKIN, VENERG, DT
   REAL(C_DOUBLE)                 ::  XY, XZ, YZ
   REAL(C_DOUBLE), INTENT(INOUT)  ::  FORCES(3, NATS), VEL(3, NATS)
-  REAL(C_DOUBLE), INTENT(INOUT)  ::  VIRIALINOUT(6)
+  REAL(C_DOUBLE), INTENT(INOUT)  ::  VIRIAL_INOUT(6)
   LOGICAL(C_BOOL)                ::  EXISTERROR
+  INTEGER(C_INT), INTENT(INOUT)  ::  NEWSYSTEM
 
   CALL LATTE(NTYPES, TYPES, COORDS, MASSES, XLO, XHI, XY, XZ, YZ, FORCES, &
-       MAXITER, VENERG, VEL, DT, VIRIALINOUT, EXISTERROR)
+       MAXITER, VENERG, VEL, DT, VIRIAL_INOUT, NEWSYSTEM, EXISTERROR)
 
   RETURN
 
diff --git a/src/latte_lib.f90 b/src/latte_lib.f90
index bfb0625..58e63a0 100644
--- a/src/latte_lib.f90
+++ b/src/latte_lib.f90
@@ -88,8 +88,9 @@ MODULE LATTE_LIB
   !! \param VENERG This is the potential Energy that is given back from latte to the hosting code.
   !! \param VEL Velocities passed to latte.
   !! \param DT integration step passed to latte.
-  !! \param VIRIALINOUT Components of the second virial coefficient
-  !! \param EXISTERROR Returns an error flag (.true.) to the hosting code.
+  !! \param VIRIAL_INOUT Components of the second virial coefficient.
+  !! \param NEWSYSTEM Tells LATTE if a new system is passed.
+  !! \param EXISTERROR_INOUT Returns an error flag (.true.) to the hosting code.
   !!
   !! \brief This routine will be used load call latte_lib from a C/C++ program:
   !!
@@ -105,8 +106,8 @@ MODULE LATTE_LIB
   !!
   !! \brief Note: All units are LATTE units by default. See https://github.com/losalamos/LATTE/blob/master/Manual/LATTE_manual.pdf
   !!
-  SUBROUTINE LATTE(NTYPES,TYPES,CR_IN,MASSES_IN,XLO,XHI,XY,XZ,YZ,FTOT_OUT, &
-       MAXITER_IN, VENERG, VEL_IN, DT_IN, VIRIALINOUT, EXISTERROR_INOUT)
+  SUBROUTINE LATTE(NTYPES, TYPES, CR_IN, MASSES_IN, XLO, XHI, XY, XZ, YZ, FTOT_OUT, &
+       MAXITER_IN, VENERG, VEL_IN, DT_IN, VIRIAL_INOUT, NEWSYSTEM, EXISTERROR_INOUT)
 
     USE CONSTANTS_MOD, ONLY: EXISTERROR
 
@@ -122,10 +123,11 @@ SUBROUTINE LATTE(NTYPES,TYPES,CR_IN,MASSES_IN,XLO,XHI,XY,XZ,YZ,FTOT_OUT, &
     REAL(LATTEPREC), INTENT(IN)  :: CR_IN(:,:),VEL_IN(:,:), MASSES_IN(:),XLO(3),XHI(3)
     REAL(LATTEPREC), INTENT(IN)  :: DT_IN, XY, XZ, YZ
     REAL(LATTEPREC), INTENT(OUT) :: FTOT_OUT(:,:), VENERG
-    REAL(LATTEPREC), INTENT(OUT) :: VIRIALINOUT(6)
+    REAL(LATTEPREC), INTENT(OUT) :: VIRIAL_INOUT(6)
     INTEGER, INTENT(IN) ::  NTYPES, TYPES(:), MAXITER_IN
     LOGICAL(1), INTENT(INOUT) :: EXISTERROR_INOUT
     REAL(LATTEPREC) :: MLSI, LUMO, HOMO
+    INTEGER, INTENT(INOUT) :: NEWSYSTEM
 
 #ifdef PROGRESSON
     TYPE(SYSTEM_TYPE) :: SY
@@ -133,7 +135,6 @@ SUBROUTINE LATTE(NTYPES,TYPES,CR_IN,MASSES_IN,XLO,XHI,XY,XZ,YZ,FTOT_OUT, &
 
 #ifdef MPI_ON
     INTEGER :: IERR, STATUS(MPI_STATUS_SIZE), NUMPROCS
-
     CALL MPI_INIT( IERR )
     CALL MPI_COMM_RANK( MPI_COMM_WORLD, MYID, IERR )
     CALL MPI_COMM_SIZE( MPI_COMM_WORLD, NUMPROCS, IERR )
@@ -141,8 +142,9 @@ SUBROUTINE LATTE(NTYPES,TYPES,CR_IN,MASSES_IN,XLO,XHI,XY,XZ,YZ,FTOT_OUT, &
 
     EXISTERROR = .FALSE. !We assume we start the lib call without errors
 
-    !INITIALIZATION
-    IF(.NOT. LIBINIT)THEN
+    IF(.NOT. LIBINIT .OR. NEWSYSTEM == 1)THEN
+
+       CALL DEALLOCATEALL()
 
        LIBRUN = .TRUE.
 
@@ -288,10 +290,9 @@ SUBROUTINE LATTE(NTYPES,TYPES,CR_IN,MASSES_IN,XLO,XHI,XY,XZ,YZ,FTOT_OUT, &
        CALL FLUSH(6)
 
     ENDIF
+    !End of initialization
 
 
-    !END OF INITIALIZATION
-
     IF (MDON .EQ. 0 .AND. RELAXME .EQ. 0 .AND. DOSFITON .EQ. 0 &
          .AND. PPFITON .EQ. 0 .AND. ALLFITON .EQ. 0) THEN
 
@@ -607,7 +608,7 @@ SUBROUTINE LATTE(NTYPES,TYPES,CR_IN,MASSES_IN,XLO,XHI,XY,XZ,YZ,FTOT_OUT, &
           CALL DTIME(TARRAY, RESULT)
 
           IF (VERBOSE >= 1)WRITE(*,*)"Setting up TBMD ..."
-          CALL SETUPTBMD
+          CALL SETUPTBMD(NEWSYSTEM)
 
           CALL FLUSH(6)
 
@@ -706,9 +707,10 @@ SUBROUTINE LATTE(NTYPES,TYPES,CR_IN,MASSES_IN,XLO,XHI,XY,XZ,YZ,FTOT_OUT, &
 
        !       CALL GETPRESSURE
 
-       VIRIALINOUT = -VIRIAL
+       VIRIAL_INOUT = -VIRIAL
 
        LIBINIT = .TRUE.
+       NEWSYSTEM = 0 !Setting newsystem back to 0.
 
 #ifdef PROGRESSON
        IF(MOD(LIBCALLS,WRTFREQ) == 0)THEN
@@ -777,6 +779,7 @@ SUBROUTINE LATTE(NTYPES,TYPES,CR_IN,MASSES_IN,XLO,XHI,XY,XZ,YZ,FTOT_OUT, &
        CALL FLUSH(6) !To force writing to file at every call
 
        EXISTERROR_INOUT = EXISTERROR
+
        RETURN
 
     ELSEIF (MDON .EQ. 1 .AND. RELAXME .EQ. 0 .AND. MAXITER_IN >= 0) THEN
@@ -912,6 +915,7 @@ SUBROUTINE LATTE(NTYPES,TYPES,CR_IN,MASSES_IN,XLO,XHI,XY,XZ,YZ,FTOT_OUT, &
 #endif
 
     LIBINIT = .TRUE.
+    NEWSYSTEM = 0 !Setting newsystem back to 0.
     EXISTERROR_INOUT = EXISTERROR
 
   END SUBROUTINE LATTE
diff --git a/src/qconsistency.f90 b/src/qconsistency.f90
index 21d9bfe..b22f10a 100644
--- a/src/qconsistency.f90
+++ b/src/qconsistency.f90
@@ -37,6 +37,7 @@ SUBROUTINE QCONSISTENCY(SWITCH, MDITER)
   REAL(4) :: TIMEACC
   REAL(LATTEPREC) :: MAXDQ
   REAL(LATTEPREC), ALLOCATABLE :: QDIFF(:), SPINDIFF(:)
+
   IF (EXISTERROR) RETURN
 
   !
@@ -77,6 +78,7 @@ SUBROUTINE QCONSISTENCY(SWITCH, MDITER)
            ENDIF
         ENDIF
 
+
         ! Compute the density matrix
 
         TX = START_TIMER(DMBUILD_TIMER)
diff --git a/src/setuptbmd.f90 b/src/setuptbmd.f90
index 367553f..a61b938 100644
--- a/src/setuptbmd.f90
+++ b/src/setuptbmd.f90
@@ -19,7 +19,7 @@
 ! Public License for more details.                                         !
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-SUBROUTINE SETUPTBMD
+SUBROUTINE SETUPTBMD(NEWSYSTEM)
 
   USE CONSTANTS_MOD
   USE SETUPARRAY
@@ -41,14 +41,15 @@ SUBROUTINE SETUPTBMD
   INTEGER :: START_CLOCK, STOP_CLOCK, CLOCK_RATE, CLOCK_MAX
   REAL(LATTEPREC) :: THETIME, NEWESPIN, NEWECOUL
   REAL(LATTEPREC) :: RN, MYVOL
-  INTEGER :: FLAGAND
+  INTEGER :: FLAGAND, NEWSYSTEM
+
   IF (EXISTERROR) RETURN
 
   !
   ! Read MDcontroller to determine what kind of MD simulation to do
   !
 
-  IF(.NOT.LIBINIT)THEN
+  IF(NEWSYSTEM == 1 .OR. (.NOT.LIBINIT))THEN
 
      IF (LATTEINEXISTS) THEN
         CALL PARSE_MD("latte.in")
@@ -72,7 +73,7 @@ SUBROUTINE SETUPTBMD
   ! to get the bond-order
   !
 
-  IF(.NOT.LIBINIT)THEN
+  IF(NEWSYSTEM == 1 .OR. .NOT.LIBINIT)THEN
      IF (CONTROL .EQ. 1) THEN
         CALL ALLOCATEDIAG
      ELSEIF (CONTROL .EQ. 2 .OR. CONTROL .EQ. 4 .OR. CONTROL .EQ. 5) THEN