********>Bugfix 31:
Prepared by: Bob Duke
Date: 2/6/2010

Programs: pmemd

Description:  Some systems, such as from the extra points versions of GLYCAM,
              have more "extra points" than was allowed for in the original
              code.

Usage: Apply the following patch in $AMBERHOME/src/pmemd/src/

----------------------------------------------------------------------------
--- extra_pnts_nb14.fpp	2010-03-08 09:45:53.000000000 -0500
+++ extra_pnts_nb14.fpp	2010-03-08 09:50:56.000000000 -0500
@@ -125,6 +125,9 @@
 
   integer,              allocatable, save       :: cit_nb14(:,:)
 
+  ! Nonbonded 1-4 interactions possibly increase by:
+  integer, parameter                            :: nb14_mult_fac = 9
+
   ! Extra Points Frame datatype:
 
   type ep_frame_rec
@@ -505,7 +508,7 @@
   gbl_nb14_cnt = 0
   gbl_frame_cnt = 0
 
-  call alloc_extra_pnts_nb14_mem(numextra, 3 * (nphih + nphia), &
+  call alloc_extra_pnts_nb14_mem(numextra, nb14_mult_fac * (nphih + nphia), &
                                  num_ints, num_reals)
    
   numextra_test = 0
@@ -523,7 +526,7 @@
   max11 = natom + numextra
   max12 = 3 * (nbonh + nbona)
   max13 = 3 * (ntheth + ntheta)
-  max14 = 3 * (nphih + nphia)
+  max14 = nb14_mult_fac * (nphih + nphia)
   maxa = max(max11, max12, max13, max14)
 
   allocate(epbtyp(5, natom), &
@@ -537,7 +540,7 @@
            i11(2, (natom + numextra)), &
            i12(2, 3 * (nbonh + nbona)), &
            i13(2, 3 * (ntheth + ntheta)), &
-           i14(2, 3 * (nphih + nphia)), &
+           i14(2, nb14_mult_fac * (nphih + nphia)), &
            nb_14_list(3,nphih + nphia), &
            s3(maxa), &
            stat = alloc_failed)

--- nb_exclusions.fpp	2008-04-09 16:40:54.000000000 -0400
+++ nb_exclusions.fpp	2010-02-05 16:50:33.000000000 -0500
@@ -31,6 +31,7 @@
 subroutine alloc_nb_exclusions_mem(atm_cnt, ext_cnt, num_ints, num_reals)
 
   use pmemd_lib_mod
+  use prmtop_dat_mod
 
   implicit none
 
@@ -47,9 +48,9 @@
 
   integer               :: alloc_failed
 
-  allocate(gbl_nb_adjust_pairlst(atm_cnt + ext_cnt + ext_cnt), &
+  allocate(gbl_nb_adjust_pairlst(atm_cnt + ext_cnt * next_mult_fac), &
            atm_nb_maskdata(atm_cnt), &
-           atm_nb_mask(ext_cnt + ext_cnt), &
+           atm_nb_mask(ext_cnt * next_mult_fac), &
            stat = alloc_failed)
 
   if (alloc_failed .ne. 0) call setup_alloc_error
@@ -128,22 +129,24 @@
 !              
 !*******************************************************************************
 
-subroutine make_atm_excl_mask_list(atm_cnt, numex, next, natex)
+subroutine make_atm_excl_mask_list(atm_cnt, numex, natex)
 
   use gbl_constants_mod
   use file_io_dat_mod, only : mdout
   use constraints_mod, only : atm_igroup
   use mdin_ctrl_dat_mod, only : ibelly
   use pmemd_lib_mod
+  use prmtop_dat_mod
 
   implicit none
 
 ! Formal arguments:
 
   integer               :: atm_cnt
-  integer               :: numex(atm_cnt) ! Excluded atom count for each atom.
-  integer               :: next           ! natex() size, from prmtop.
-  integer               :: natex(next)    ! Excluded atom concatenated list.
+  ! Excluded atom count for each atom.
+  integer               :: numex(atm_cnt)
+  ! Excluded atom concatenated list:
+  integer               :: natex(next * next_mult_fac)
 
 ! Local variables:
 
@@ -179,7 +182,7 @@
     total_excl = total_excl + atm_nb_maskdata(atm_i)%cnt
   end do
 
-  if (total_excl .gt. 2 * next) then
+  if (total_excl .gt. next * next_mult_fac) then
     write(mdout, '(a,a)') error_hdr, &
       'Variable next has inconsistent value in prmtop!'
     call mexit(6, 1)

--- pme_alltasks_setup.fpp	2008-02-27 15:41:37.000000000 -0500
+++ pme_alltasks_setup.fpp	2010-02-03 18:07:03.000000000 -0500
@@ -98,7 +98,7 @@
   ! to keep nonbonded calcs from being done on excluded atoms.  The lists are
   ! static (atom-based).
 
-  call make_atm_excl_mask_list(natom, atm_numex, next, gbl_natex)
+  call make_atm_excl_mask_list(natom, atm_numex, gbl_natex)
 
   if (ntb .ne. 0) then
     call bcast_pbc
@@ -184,7 +184,7 @@
   ! to keep nonbonded calcs from being done on excluded atoms.  The lists are
   ! static (atom-based).
 
-  call make_atm_excl_mask_list(natom, atm_numex, next, gbl_natex)
+  call make_atm_excl_mask_list(natom, atm_numex, gbl_natex)
 
   ! Need new molecule list structures to support no_intermolecular_bonds option.
 

--- prmtop_dat.fpp	2010-03-08 09:45:53.000000000 -0500
+++ prmtop_dat.fpp	2010-03-08 10:00:42.000000000 -0500
@@ -26,14 +26,14 @@
   ! Starting with nttyp, the integer values are derived rather than read.
   ! nttyp is the number of 6-12 vdw parameters.
 
-  integer, parameter    :: prmtop_int_cnt = 35
+  integer, parameter    :: prmtop_int_cnt = 36
 
   integer               natom, ntypes, nbonh, ntheth, nphih, next, nres, &    !7
                         nbona, ntheta, nphia, numbnd, numang, nptra, nphb, &  !14
                         ifbox, ifcap, nspm, numextra, ncopy, nttyp, &         !20
                         bonda_idx, anglea_idx, diheda_idx, &                  !23
                         gbl_bond_allocsize, gbl_angle_allocsize, &            !25
-                        gbl_dihed_allocsize, &                                !26
+                        gbl_dihed_allocsize, next_mult_fac, &                 !26
                         nub, nubtypes, &                                      !28
                         nimphi, nimprtyp, &                                   !30
                         gbl_angle_ub_allocsize, gbl_dihed_imp_allocsize,&     !32
@@ -54,6 +54,12 @@
 
   save  :: / prmtop_int /
 
+! next_mult_fac is a multiplier that is set to handle differences in gbl_natex,
+! etc. storage requirements due to extra points nb14 redefinition.  It is set
+! to 2 for non-ep code (handles list doubling), but bumped up to 9 for ep
+! code; so far only glycam-associated ep really seem to need this...  This
+! is a hack...
+
 ! Cap data not currently supported...
 
 ! integer, parameter    :: prmtop_dbl_cnt = 4
@@ -62,6 +68,7 @@
 
 ! common / prmtop_dbl / cutcap, xcap, ycap, zcap
 
+
   ! atm_qterm = the atom partial charge array for amber pme.
   ! atm_mass = the atom mass array.
   ! atm_iac = TBS
@@ -310,6 +317,17 @@
       'You must use no_intermolecular_bonds = 1 (the default) for this prmtop.'
   end if
 
+  ! BUGBUG:
+  ! This is a heuristic for possible nb exclusions list growth, a total
+  ! hack that may fail in some circumstances.  Need to reengineer a bunch
+  ! of code to avoid this in the future...
+
+  if (numextra .eq. 0) then
+    next_mult_fac = 2
+  else
+    next_mult_fac = 8
+  end if
+
   nttyp = ntypes * (ntypes + 1) / 2
 
   !    --- Read the force field information from the prmtop if available
@@ -1384,7 +1402,7 @@
   call mpi_bcast(atm_numex, natom, mpi_integer, 0, &
                  mpi_comm_world, err_code_mpi)
 
-  call mpi_bcast(gbl_natex, next, mpi_integer, 0, &
+  call mpi_bcast(gbl_natex, next * next_mult_fac, mpi_integer, 0, &
                  mpi_comm_world, err_code_mpi)
 
   call mpi_bcast(atm_nsp, nspm, mpi_integer, 0, &
@@ -1576,13 +1594,15 @@
   ! elements are read and subsequently broadcast.
 
   allocate(atm_numex(natom), &
-           gbl_natex(next * 2), &
+           gbl_natex(next * next_mult_fac), &
            stat = alloc_failed)
 
   if (alloc_failed .ne. 0) call setup_alloc_error
 
   num_ints = num_ints + size(atm_numex) + size(gbl_natex)
 
+  gbl_natex(:) = 0
+
   ! Allocation of stuff that will later be deallocated that is only used in
   ! the master:
 

--- f90depends	2008-04-16 12:19:26.000000000 -0400
+++ f90depends	2010-02-05 16:51:14.000000000 -0500
@@ -207,6 +207,7 @@
 mol_list.o: copyright.i
 nb_exclusions.o: gbl_datatypes.o
 nb_exclusions.o: pmemd_lib.o
+nb_exclusions.o: prmtop_dat.o
 nb_exclusions.o: parallel_dat.o
 nb_exclusions.o: gbl_constants.o
 nb_exclusions.o: file_io_dat.o
----------------------------------------------------------------------------
Workaround: none