Merge pull request #67 from rsdefever/fix/ring-frags

Fix/ring fragments

Documentation/Tex/howto.tex

@@ -82,7 +82,13 @@ \subsection{Fragment Library Generation}
 bonded to the ring atoms. For each fragment identified, Cassandra runs
 a pre\textendash simulation in the gas phase to sample the intramolecular degrees
 of freedom. A library of a large number of these conformations are
-stored for use in an actual simulation. \\ \\
+stored for use in an actual simulation. \emph{Note that intramolecular
+degrees of freedom may not be properly sampled in fused-ring systems. We
+highly encourage anyone simulating such systems to compare the internal
+angle and dihedral distributions in the fragment library with a 
+constrained bond length molecular dynamics simulation of the relevant fragment
+in vacuum.}\\ \\
+
 %
 %
 The gas phase library generation has been automated with the script \texttt{library\_setup.py} located in the \texttt{Scripts/Frag\_Library\_Setup}

Documentation/Tex/introduction.tex

@@ -6,7 +6,8 @@ \chapter{Introduction}
 I''-type force field having fixed bond lengths, harmonic bond angles
 and improper angles, a CHARMM or OPLS-style dihedral potential, a
 Lennard-Jones 12-6 potential and fixed partial charges. It does {\em
-  not} treat flexible bond lengths. Cassandra uses OpenMP parallelization and comes
+  not} treat flexible bond lengths. Fused ring systems should
+  be simulated with caution. Cassandra uses OpenMP parallelization and comes
 with a number of scripts, utilities and examples to help with
 simulation setup. \\ \\ 
 %

Src/move_ring_flip.f90

@@ -85,12 +85,18 @@ SUBROUTINE Flip_Move
 
   ! save the orignal coordinates
   Call Save_Old_Cartesian_Coordinates(im,is)
-
-  ! Choose a ring atom to flip
-  atom_num = INT ( rranf() * nring_atoms(is)) + 1
 
-  ! obtain id 
-  this_atom = ring_atom_ids(atom_num,is)
+  ! This do loop is safe b/c ring_fragment_driver
+  ! confirms that not all ring_atoms are multiring_atoms
+  DO WHILE (.TRUE.)
+    ! Choose a ring atom to flip
+    atom_num = INT ( rranf() * nring_atoms(is)) + 1
+    ! obtain id
+    this_atom = ring_atom_ids(atom_num,is)
+    IF (nonbond_list(this_atom, is)%multiring_atom .EQV. .FALSE.) THEN
+       EXIT
+    ENDIF
+  END DO
 
   ! Figure out the bond angle that contains this_atom at the apex
   DO i = 1, angle_part_list(this_atom,is)%nangles

Src/participation.f90

@@ -527,9 +527,9 @@ SUBROUTINE Participation
                    ! and all other do not need to be scaled by kboltz. Valid for LJ and Mie.
                    ! Other (and future) potentials perhaps not.
                    IF (j == 1) THEN
-                     WRITE(201,'(F11.7,2X)',ADVANCE='NO') nonbond_list(ia,is)%vdw_param(j)/kboltz
+                     WRITE(201,'(F11.7,2X)',ADVANCE='NO') nonbond_list(this_atom,is)%vdw_param(j)/kboltz
                    ELSE
-                     WRITE(201,'(F11.7,2X)',ADVANCE='NO') nonbond_list(ia,is)%vdw_param(j)
+                     WRITE(201,'(F11.7,2X)',ADVANCE='NO') nonbond_list(this_atom,is)%vdw_param(j)
                    END IF
                  END DO
                  IF (nonbond_list(this_atom,is)%ring_atom) THEN

Src/ring_fragment_driver.f90

@@ -51,7 +51,7 @@ SUBROUTINE Ring_Fragment_Driver
   !        main
   !
   ! CALLS
-  !
+  !        ID_Multiring_Atoms
   !        Flip_Move
   !        Atom_Displacement
   !
@@ -63,18 +63,21 @@ SUBROUTINE Ring_Fragment_Driver
 
   IMPLICIT NONE
 
-  INTEGER :: is, im, ibox, i, ia, nring_success, nexoring_success
+  INTEGER :: is, im, ibox, ia, nring_success, nexoring_success
   INTEGER :: nexoring_trials, nring_trials
 
   REAL(DP) :: rand_no 
 
-  LOGICAL :: overlap
-
   ! Fragment routine is only called with 1 box, species, and molecule
   is = 1
   im = 1
   ibox = 1
 
+  ! ID atoms that belong to more than 1 ring
+  IF (cut_ring >= 0.0) THEN
+     CALL ID_Multiring_Atoms(is)
+  ENDIF
+
   nring_success = 0
   nexoring_success = 0
   nring_trials = 0
@@ -133,4 +136,63 @@ SUBROUTINE Ring_Fragment_Driver
   WRITE(*,'(X,A,T40,I8)') 'Number of successful exoring trials', nexoring_success
 
 END SUBROUTINE Ring_Fragment_Driver
+
+SUBROUTINE ID_Multiring_Atoms(is)
+  !*****************************************************************************
+  !
+  ! CALLED BY
+  !
+  !        Ring_Fragment_Driver
+  !
+  ! CALLS
+  !
+  !*****************************************************************************
+
+  USE Global_Variables
+
+  IMPLICIT NONE
+
+  INTEGER, INTENT(IN) :: is
+  INTEGER :: i, j, atom1, atom2, this_atom, angle_id
+  INTEGER :: nmultiring_atoms, atom_ring_count
+
+  ! If trying ring flip moves, identify the ring atoms that
+  ! belong to multiple rings. They cannot be used for flip
+  ! moves. Also ensure >0 atoms can be used for the flip move.
+  nmultiring_atoms = 0
+  DO i = 1, nring_atoms(is)
+     this_atom = ring_atom_ids(i, is)
+     ! Count the number of rings this_atom belongs to
+     atom_ring_count = 0
+     ! Loop over all angles
+     DO j = 1, angle_part_list(this_atom, is)%nangles
+        IF (angle_part_list(this_atom, is)%position(j) == 2 ) THEN
+           ! this_atom is at the apex
+           angle_id = angle_part_list(this_atom, is)%which_angle(j)
+           ! check if other atoms in the angle are ring atoms
+           atom1 = angle_list(angle_id, is)%atom1
+           atom2 = angle_list(angle_id, is)%atom3
+           IF (nonbond_list(atom1, is)%ring_atom .AND. nonbond_list(atom2, is)%ring_atom) THEN
+              ! If yes, increment counter
+              atom_ring_count = atom_ring_count + 1
+           ENDIF
+        ENDIF
+     ENDDO
+     IF (atom_ring_count > 1) THEN
+        nonbond_list(this_atom, is)%multiring_atom = .TRUE.
+        nmultiring_atoms = nmultiring_atoms + 1
+     ENDIF
+  ENDDO
+  ! Check that at least 1 atom can be used for a flip move
+  IF (nmultiring_atoms > 0) THEN
+     WRITE(*,*) "Found", nmultiring_atoms, "multiring atoms"
+  ENDIF
+  IF (nmultiring_atoms == nring_atoms(is)) THEN
+     err_msg = ''
+     err_msg(1) = 'All ring atoms belong to multiple rings.'
+     err_msg(2) = 'No flip moves can be performed'
+     CALL Clean_Abort(err_msg,'ID_Multiring_Atoms')
+  ENDIF
+
+END SUBROUTINE ID_Multiring_Atoms
 !*******************************************************************************

Src/type_definitions.f90

@@ -228,7 +228,7 @@ MODULE Type_Definitions
      REAL(DP) :: mass, charge
      INTEGER :: atom_type_number
 
-     LOGICAL :: ring_atom
+     LOGICAL :: ring_atom, multiring_atom
 
   END TYPE Nonbond_Class
   !****************************************************************************