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chuckv |
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!! Calculates Long Range forces Lennard-Jones interactions. |
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!! Corresponds to the force field defined in lj_FF.cpp |
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!! @author Charles F. Vardeman II |
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!! @author Matthew Meineke |
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chuckv |
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!! @version $Id: lj_FF.F90,v 1.9 2003-01-22 21:45:20 chuckv Exp $, $Date: 2003-01-22 21:45:20 $, $Name: not supported by cvs2svn $, $Revision: 1.9 $ |
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chuckv |
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chuckv |
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module lj_ff |
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use simulation |
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use definitions, ONLY : dp, ndim |
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#ifdef IS_MPI |
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use mpiSimulation |
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#endif |
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chuckv |
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implicit none |
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PRIVATE |
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!! Number of lj_atypes in lj_atype_list |
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integer, save :: n_lj_atypes = 0 |
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!! Starting Size for ljMixed Array |
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integer, parameter :: ljMixed_blocksize = 10 |
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chuckv |
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!! Basic atom type for a Lennard-Jones Atom. |
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type, public :: lj_atype |
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private |
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sequence |
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!! Unique number for place in linked list |
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integer :: atype_number = 0 |
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!! Unique indentifier number (ie atomic no, etc) |
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integer :: atype_ident = 0 |
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!! Mass of Particle |
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real ( kind = dp ) :: mass = 0.0_dp |
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!! Lennard-Jones epslon |
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real ( kind = dp ) :: epslon = 0.0_dp |
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!! Lennard-Jones Sigma |
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real ( kind = dp ) :: sigma = 0.0_dp |
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!! Lennard-Jones Sigma Squared |
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real ( kind = dp ) :: sigma2 = 0.0_dp |
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!! Lennard-Jones Sigma to sixth |
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real ( kind = dp ) :: sigma6 = 0.0_dp |
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!! Pointer for linked list creation |
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type (lj_atype), pointer :: next => null() |
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end type lj_atype |
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!! Pointer type for atype ident array |
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type, public :: lj_atypePtr |
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type (lj_atype), pointer :: this => null() |
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end type lj_atypePtr |
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!! Global list of lj atypes in simulation |
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type (lj_atype), pointer :: lj_atype_list => null() |
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!! LJ mixing array |
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type (lj_atype), dimension(:,:), allocatable, pointer :: ljMixed =>null() |
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!! identity pointer list for force loop. |
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type (lj_atypePtr), dimension(:), allocatable :: identPtrList |
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!! Neighbor list and commom arrays |
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!! This should eventally get moved to a neighbor list type |
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integer, allocatable, dimension(:) :: point |
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integer, allocatable, dimension(:) :: list |
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integer, parameter :: listMultiplier = 80 |
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integer :: nListAllocs = 0 |
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integer, parameter :: maxListAllocs = 5 |
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#ifdef IS_MPI |
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! Universal routines: All types of force calculations will need these arrays |
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! Arrays specific to a type of force calculation should be declared in that module. |
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real( kind = dp ), allocatable, dimension(:,:) :: qRow |
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real( kind = dp ), allocatable, dimension(:,:) :: qColumn |
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real( kind = dp ), allocatable, dimension(:,:) :: fRow |
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real( kind = dp ), allocatable, dimension(:,:) :: fColumn |
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type (lj_atypePtr), dimension(:), allocatable :: identPtrListRow |
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type (lj_atypePtr), dimension(:), allocatable :: identPtrListColumn |
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#endif |
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logical :: isljFFinit = .false. |
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!! Public methods and data |
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public :: new_lj_atype |
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public :: do_lj_ff |
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public :: getLjPot |
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contains |
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subroutine new_lj_atype(ident,mass,epslon,sigma,status) |
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real( kind = dp ), intent(in) :: mass |
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real( kind = dp ), intent(in) :: epslon |
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real( kind = dp ), intent(in) :: sigma |
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integer, intent(in) :: ident |
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integer, intent(out) :: status |
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type (lj_atype), pointer :: this_lj_atype |
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type (lj_atype), pointer :: lj_atype_ptr |
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type (lj_atype), allocatable, dimension(:,:), pointer :: thisMix |
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type (lj_atype), allocatable, dimension(:,:), pointer :: oldMix |
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chuckv |
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integer :: alloc_error |
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integer :: atype_counter = 0 |
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chuckv |
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integer :: alloc_size |
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chuckv |
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chuckv |
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status = 0 |
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chuckv |
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! allocate a new atype |
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allocate(this_lj_atype,stat=alloc_error) |
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if (alloc_error /= 0 ) then |
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status = -1 |
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return |
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end if |
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! assign our new lj_atype information |
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this_lj_atype%mass = mass |
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this_lj_atype%epslon = epslon |
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this_lj_atype%sigma = sigma |
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this_lj_atype%sigma2 = sigma * sigma |
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this_lj_atype%sigma6 = this_lj_atype%sigma2 * this_lj_atype%sigma2 & |
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* this_lj_atype%sigma2 |
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! assume that this atype will be successfully added |
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this_lj_atype%atype_ident = ident |
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this_lj_atype%number = n_lj_atypes + 1 |
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chuckv |
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chuckv |
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! First time through allocate a array of size ljMixed_blocksize |
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if(.not. associated(ljMixed)) then |
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allocate(thisMix(ljMixed_blocksize,ljMixed_blocksize)) |
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if (alloc_error /= 0 ) then |
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status = -1 |
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return |
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end if |
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ljMixed => thisMix |
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! If we have outgrown ljMixed_blocksize, allocate a new matrix twice the size and |
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! point ljMix at the new matrix. |
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else if( (n_lj_atypes + 1) > size(ljMixed)) then |
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alloc_size = 2*size(ljMix) |
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allocate(thisMix(alloc_size,alloc_size)) |
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if (alloc_error /= 0 ) then |
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status = -1 |
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return |
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end if |
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! point oldMix at old ljMixed array |
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oldMix => ljMixed |
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! Copy oldMix into new Mixed array |
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thisMix = oldMix |
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! Point ljMixed at new array |
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ljMixed => thisMix |
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! Free old array so we don't have a memory leak |
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deallocate(oldMix) |
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endif |
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! Find bottom of atype master list |
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chuckv |
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! if lj_atype_list is null then we are at the top of the list. |
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if (.not. associated(lj_atype_list)) then |
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lj_atype_ptr => this_lj_atype |
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atype_counter = 1 |
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chuckv |
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else ! we need to find the bottom of the list to insert new atype |
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chuckv |
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lj_atype_ptr => lj_atype_list%next |
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atype_counter = 1 |
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chuckv |
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find_end: do |
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if (.not. associated(lj_atype_ptr%next)) then |
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exit find_end |
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end if |
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chuckv |
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! Set up mixing for new atype and current atype in list |
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ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma = & |
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calcLJMix("sigma",this_lj_atype%sigma, & |
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lj_atype_prt%sigma) |
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ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 = & |
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ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma & |
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* ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma |
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ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma6 = & |
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ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 & |
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* ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 & |
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* ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 |
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ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%epslon = & |
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calcLJMix("epslon",this_lj_atype%epslon, & |
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lj_atype_prt%epslon) |
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! Advance to next pointer |
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lj_atype_ptr => lj_atype_ptr%next |
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atype_counter = atype_counter + 1 |
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chuckv |
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end do find_end |
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end if |
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chuckv |
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chuckv |
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chuckv |
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! Insert new atype at end of list |
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lj_atype_ptr => this_lj_atype |
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chuckv |
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! Increment number of atypes |
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n_lj_atypes = n_lj_atypes + 1 |
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! Set up self mixing |
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ljMix(n_lj_atypes,n_lj_atypes)%sigma = this_lj_atype%sigma |
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ljMix(n_lj_atypes,n_lj_atypes)%sigma2 = ljMix(n_lj_atypes,n_lj_atypes)%sigma & |
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* ljMix(n_lj_atypes,n_lj_atypes)%sigma |
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ljMix(n_lj_atypes,n_lj_atypes)%sigma6 = ljMix(n_lj_atypes,n_lj_atypes)%sigma2 & |
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* ljMix(n_lj_atypes,n_lj_atypes)%sigma2 & |
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* ljMix(n_lj_atypes,n_lj_atypes)%sigma2 |
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ljMix(n_lj_atypes,n_lj_atypes)%epslon = this_lj_atype%epslon |
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chuckv |
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end subroutine new_lj_atype |
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chuckv |
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subroutine init_ljFF(nComponents,ident, status) |
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!! Number of components in ident array |
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integer, intent(inout) :: nComponents |
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!! Array of identities nComponents long corresponding to |
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!! ljatype ident. |
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integer, dimension(nComponents),intent(inout) :: ident |
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!! Result status, success = 0, error = -1 |
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integer, intent(out) :: Status |
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chuckv |
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chuckv |
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integer :: thisStat |
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chuckv |
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#ifdef IS_MPI |
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chuckv |
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integer, allocatable, dimension(:) :: identRow |
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integer, allocatable, dimension(:) :: identCol |
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integer :: nrow |
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integer :: ncol |
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integer :: alloc_stat |
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#endif |
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status = 0 |
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chuckv |
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chuckv |
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!! if were're not in MPI, we just update ljatypePtrList |
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#ifndef IS_MPI |
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call new_ljatypePtrList(nComponents,ident,identPtrList,thisStat) |
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if ( thisStat /= 0 ) then |
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status = -1 |
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return |
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endif |
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!! Allocate pointer lists |
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allocate(point(nComponents),stat=alloc_stat) |
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if (alloc_stat /=0) then |
259 |
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status = -1 |
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return |
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endif |
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allocate(list(nComponents*listMultiplier),stat=alloc_stat) |
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if (alloc_stat /=0) then |
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status = -1 |
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return |
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endif |
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chuckv |
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chuckv |
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! if were're in MPI, we also have to worry about row and col lists |
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#else |
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! We can only set up forces if mpiSimulation has been setup. |
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if (.not. isMPISimSet()) then |
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status = -1 |
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return |
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endif |
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nrow = getNrow() |
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ncol = getNcol() |
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!! Allocate temperary arrays to hold gather information |
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allocate(identRow(nrow),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
281 |
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status = -1 |
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return |
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endif |
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chuckv |
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chuckv |
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allocate(identCol(ncol),stat=alloc_stat) |
286 |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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!! Gather idents into row and column idents |
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call gather(ident,identRow,plan_row) |
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call gather(ident,identCol,plan_col) |
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!! Create row and col pointer lists |
295 |
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call new_ljatypePtrList(nrow,identRow,identPtrListRow,thisStat) |
296 |
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if (thisStat /= 0 ) then |
297 |
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status = -1 |
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return |
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endif |
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call new_ljatypePtrList(ncol,identCol,identPtrListCol,thisStat) |
302 |
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if (thisStat /= 0 ) then |
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status = -1 |
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return |
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endif |
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!! free temporary ident arrays |
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deallocate(identCol) |
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deallocate(identRow) |
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!! Allocate Simulation arrays |
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!! NOTE: This bit of code should be fixed, it can cause large |
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!! memory fragmentation if call repeatedly |
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if (.not.allocated(qRow)) then |
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allocate(qRow(3,nrow),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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else |
322 |
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deallocate(qrow) |
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allocate(qRow(3,nrow),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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endif |
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if (.not.allocated(3,qCol)) then |
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allocate(qCol(ncol),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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else |
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deallocate(qCol) |
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allocate(qCol(3,ncol),stat=alloc_stat) |
339 |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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endif |
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if (.not.allocated(fRow)) then |
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allocate(fRow(3,nrow),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
351 |
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else |
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deallocate(fRow) |
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allocate(fRow(3,nrow),stat=alloc_stat) |
354 |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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endif |
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if (.not.allocated(fCol)) then |
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allocate(fCol(3,ncol),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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else |
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deallocate(fCol) |
368 |
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allocate(fCol(3,ncol),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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endif |
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!! Allocate neighbor lists for mpi simulations. |
375 |
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if (.not. allocated(point)) then |
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allocate(point(nrow),stat=alloc_stat) |
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|
|
if (alloc_stat /=0) then |
378 |
|
|
status = -1 |
379 |
|
|
return |
380 |
|
|
endif |
381 |
|
|
|
382 |
|
|
allocate(list(ncol*listMultiplier),stat=alloc_stat) |
383 |
|
|
if (alloc_stat /=0) then |
384 |
|
|
status = -1 |
385 |
|
|
return |
386 |
|
|
endif |
387 |
|
|
else |
388 |
|
|
deallocate(list) |
389 |
|
|
deallocate(point) |
390 |
|
|
allocate(point(nrow),stat=alloc_stat) |
391 |
|
|
if (alloc_stat /=0) then |
392 |
|
|
status = -1 |
393 |
|
|
return |
394 |
|
|
endif |
395 |
|
|
|
396 |
|
|
allocate(list(ncol*listMultiplier),stat=alloc_stat) |
397 |
|
|
if (alloc_stat /=0) then |
398 |
|
|
status = -1 |
399 |
|
|
return |
400 |
|
|
endif |
401 |
|
|
endif |
402 |
|
|
|
403 |
chuckv |
230 |
#endif |
404 |
chuckv |
239 |
|
405 |
chuckv |
230 |
|
406 |
chuckv |
239 |
isljFFinit = .true. |
407 |
|
|
|
408 |
|
|
|
409 |
chuckv |
230 |
end subroutine init_ljFF |
410 |
|
|
|
411 |
chuckv |
239 |
|
412 |
|
|
|
413 |
|
|
|
414 |
|
|
|
415 |
chuckv |
230 |
!! Takes an ident array and creates an atype pointer list |
416 |
|
|
!! based on those identities |
417 |
|
|
subroutine new_ljatypePtrList(mysize,ident,PtrList,status) |
418 |
|
|
integer, intent(in) :: mysize |
419 |
|
|
integer, intent(in) :: ident |
420 |
|
|
integer, optional :: status |
421 |
|
|
type(lj_atypePtr), dimension(:) :: PtrList |
422 |
|
|
|
423 |
|
|
integer :: thisIdent |
424 |
|
|
integer :: i |
425 |
|
|
integer :: alloc_error |
426 |
|
|
type (lj_atype), pointer :: tmpPtr |
427 |
|
|
|
428 |
|
|
if (present(status)) status = 0 |
429 |
|
|
|
430 |
|
|
! First time through, allocate list |
431 |
|
|
if (.not.(allocated)) then |
432 |
|
|
allocate(PtrList(mysize)) |
433 |
|
|
else |
434 |
|
|
! We want to creat a new ident list so free old list |
435 |
|
|
deallocate(PrtList) |
436 |
|
|
allocate(PtrList(mysize)) |
437 |
|
|
endif |
438 |
|
|
|
439 |
|
|
! Match pointer list |
440 |
|
|
do i = 1, mysize |
441 |
|
|
thisIdent = ident(i) |
442 |
|
|
call getLJatype(thisIdent,tmpPtr) |
443 |
|
|
|
444 |
|
|
if (.not. associated(tmpPtr)) then |
445 |
|
|
status = -1 |
446 |
|
|
return |
447 |
|
|
endif |
448 |
|
|
|
449 |
|
|
PtrList(i)%this => tmpPtr |
450 |
|
|
end do |
451 |
|
|
|
452 |
|
|
end subroutine new_ljatypePtrList |
453 |
|
|
|
454 |
|
|
!! Finds a lj_atype based upon numerical ident |
455 |
|
|
!! returns a null pointer if error |
456 |
|
|
subroutine getLJatype(ident,ljAtypePtr) |
457 |
|
|
integer, intent(in) :: ident |
458 |
|
|
type (lj_atype), intent(out),pointer :: ljAtypePtr => null() |
459 |
|
|
|
460 |
|
|
type (lj_atype), pointer :: tmplj_atype_ptr => null() |
461 |
|
|
|
462 |
|
|
if(.not. associated(lj_atype_list)) return |
463 |
|
|
|
464 |
|
|
! Point at head of list. |
465 |
|
|
tmplj_atype_ptr => lj_atype_list |
466 |
|
|
find_ident: do |
467 |
|
|
if (.not.associated(tmplj_atype_ptr)) then |
468 |
|
|
exit find_ident |
469 |
|
|
else if( lj_atype_ptr%atype_ident == ident) |
470 |
|
|
ljAtypePtr => tmplj_atype_ptr |
471 |
|
|
exit find_ident |
472 |
|
|
endif |
473 |
|
|
tmplj_atype_ptr => tmplj_atype_ptr%next |
474 |
|
|
end do find_ident |
475 |
|
|
|
476 |
|
|
end subroutine getLJatype |
477 |
|
|
|
478 |
|
|
|
479 |
chuckv |
239 |
!! FORCE routine Calculates Lennard Jones forces. |
480 |
chuckv |
230 |
!-------------------------------------------------------------> |
481 |
|
|
subroutine do_lj_ff(q,f,potE,do_pot) |
482 |
chuckv |
222 |
real ( kind = dp ), dimension(ndim,) :: q |
483 |
|
|
real ( kind = dp ), dimension(ndim,nLRparticles) :: f |
484 |
|
|
real ( kind = dp ) :: potE |
485 |
mmeineke |
235 |
logical ( kind = 2) :: do_pot |
486 |
chuckv |
239 |
|
487 |
|
|
type(lj_atype), pointer :: ljAtype_i |
488 |
|
|
type(lj_atype), pointer :: ljAtype_j |
489 |
|
|
|
490 |
chuckv |
230 |
#ifdef MPI |
491 |
|
|
real( kind = DP ), dimension(3,ncol) :: efr |
492 |
|
|
real( kind = DP ) :: pot_local |
493 |
|
|
#else |
494 |
|
|
! real( kind = DP ), dimension(3,natoms) :: efr |
495 |
|
|
#endif |
496 |
|
|
|
497 |
|
|
real( kind = DP ) :: pe |
498 |
|
|
logical, :: update_nlist |
499 |
chuckv |
216 |
|
500 |
chuckv |
232 |
|
501 |
chuckv |
230 |
integer :: i, j, jbeg, jend, jnab, idim, jdim, idim2, jdim2, dim, dim2 |
502 |
|
|
integer :: nlist |
503 |
|
|
integer :: j_start |
504 |
|
|
integer :: tag_i,tag_j |
505 |
|
|
real( kind = DP ) :: r, pot, ftmp, dudr, d2, drdx1, kt1, kt2, kt3, ktmp |
506 |
|
|
real( kind = DP ) :: rxi, ryi, rzi, rxij, ryij, rzij, rijsq |
507 |
chuckv |
240 |
real( kind = DP ) :: rlistsq, rcutsq |
508 |
chuckv |
222 |
|
509 |
chuckv |
230 |
integer :: nrow |
510 |
|
|
integer :: ncol |
511 |
chuckv |
222 |
|
512 |
chuckv |
239 |
if (.not. isljFFInit) then |
513 |
|
|
write(default_error,*) "ERROR: lj_FF has not been properly initialized" |
514 |
|
|
return |
515 |
|
|
endif |
516 |
chuckv |
222 |
|
517 |
chuckv |
230 |
#ifndef IS_MPI |
518 |
|
|
nrow = natoms - 1 |
519 |
|
|
ncol = natoms |
520 |
|
|
#else |
521 |
chuckv |
239 |
nrow = getNrow(plan_row) |
522 |
|
|
ncol = getNcol(plan_col) |
523 |
chuckv |
230 |
j_start = 1 |
524 |
|
|
#endif |
525 |
chuckv |
222 |
|
526 |
chuckv |
239 |
|
527 |
|
|
|
528 |
chuckv |
230 |
call check(update_nlist) |
529 |
|
|
|
530 |
chuckv |
239 |
!--------------WARNING........................... |
531 |
|
|
! Zero variables, NOTE:::: Forces are zeroed in C |
532 |
|
|
! Zeroing them here could delete previously computed |
533 |
|
|
! Forces. |
534 |
|
|
!------------------------------------------------ |
535 |
chuckv |
230 |
#ifndef IS_MPI |
536 |
|
|
nloops = nloops + 1 |
537 |
|
|
pot = 0.0E0_DP |
538 |
|
|
e = 0.0E0_DP |
539 |
|
|
#else |
540 |
|
|
f_row = 0.0E0_DP |
541 |
|
|
f_col = 0.0E0_DP |
542 |
|
|
|
543 |
|
|
pot_local = 0.0E0_DP |
544 |
|
|
|
545 |
|
|
e_row = 0.0E0_DP |
546 |
|
|
e_col = 0.0E0_DP |
547 |
|
|
e_tmp = 0.0E0_DP |
548 |
|
|
#endif |
549 |
|
|
efr = 0.0E0_DP |
550 |
|
|
|
551 |
|
|
! communicate MPI positions |
552 |
|
|
#ifdef MPI |
553 |
chuckv |
239 |
call gather(q,qRow,plan_row3) |
554 |
|
|
call gather(q,qCol,plan_col3) |
555 |
chuckv |
230 |
#endif |
556 |
|
|
|
557 |
|
|
#ifndef MPI |
558 |
|
|
|
559 |
|
|
#endif |
560 |
|
|
|
561 |
|
|
if (update_nlist) then |
562 |
|
|
|
563 |
|
|
! save current configuration, contruct neighbor list, |
564 |
|
|
! and calculate forces |
565 |
|
|
call save_nlist() |
566 |
|
|
|
567 |
|
|
nlist = 0 |
568 |
|
|
|
569 |
|
|
|
570 |
|
|
|
571 |
|
|
do i = 1, nrow |
572 |
|
|
point(i) = nlist + 1 |
573 |
|
|
#ifdef MPI |
574 |
chuckv |
239 |
ljAtype_i => identPtrListRow(i)%this |
575 |
|
|
tag_i = tagRow(i) |
576 |
|
|
rxi = qRow(1,i) |
577 |
|
|
ryi = qRow(2,i) |
578 |
|
|
rzi = qRow(3,i) |
579 |
chuckv |
230 |
#else |
580 |
chuckv |
239 |
ljAtype_i => identPtrList(i)%this |
581 |
chuckv |
230 |
j_start = i + 1 |
582 |
|
|
rxi = q(1,i) |
583 |
|
|
ryi = q(2,i) |
584 |
|
|
rzi = q(3,i) |
585 |
|
|
#endif |
586 |
|
|
|
587 |
|
|
inner: do j = j_start, ncol |
588 |
|
|
#ifdef MPI |
589 |
chuckv |
239 |
! Assign identity pointers and tags |
590 |
|
|
ljAtype_j => identPtrListColumn(j)%this |
591 |
|
|
tag_j = tagCol(j) |
592 |
chuckv |
230 |
if (newtons_thrd) then |
593 |
|
|
if (tag_i <= tag_j) then |
594 |
|
|
if (mod(tag_i + tag_j,2) == 0) cycle inner |
595 |
|
|
else |
596 |
|
|
if (mod(tag_i + tag_j,2) == 1) cycle inner |
597 |
|
|
endif |
598 |
|
|
endif |
599 |
|
|
|
600 |
chuckv |
239 |
rxij = wrap(rxi - qCol(1,j), 1) |
601 |
|
|
ryij = wrap(ryi - qCol(2,j), 2) |
602 |
|
|
rzij = wrap(rzi - qCol(3,j), 3) |
603 |
chuckv |
230 |
#else |
604 |
chuckv |
239 |
ljAtype_j => identPtrList(j)%this |
605 |
chuckv |
230 |
rxij = wrap(rxi - q(1,j), 1) |
606 |
|
|
ryij = wrap(ryi - q(2,j), 2) |
607 |
|
|
rzij = wrap(rzi - q(3,j), 3) |
608 |
|
|
|
609 |
|
|
#endif |
610 |
|
|
rijsq = rxij*rxij + ryij*ryij + rzij*rzij |
611 |
|
|
|
612 |
|
|
#ifdef MPI |
613 |
|
|
if (rijsq <= rlstsq .AND. & |
614 |
|
|
tag_j /= tag_i) then |
615 |
|
|
#else |
616 |
|
|
if (rijsq < rlstsq) then |
617 |
|
|
#endif |
618 |
|
|
|
619 |
|
|
nlist = nlist + 1 |
620 |
|
|
if (nlist > size(list)) then |
621 |
chuckv |
239 |
#warning "Change how nlist size is done" |
622 |
|
|
write(DEFAULT_ERROR,*) "ERROR: nlist > list size" |
623 |
chuckv |
230 |
endif |
624 |
|
|
list(nlist) = j |
625 |
|
|
|
626 |
|
|
|
627 |
|
|
if (rijsq < rcutsq) then |
628 |
|
|
|
629 |
|
|
r = dsqrt(rijsq) |
630 |
|
|
|
631 |
chuckv |
239 |
call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j) |
632 |
chuckv |
230 |
|
633 |
|
|
#ifdef MPI |
634 |
|
|
e_row(i) = e_row(i) + pot*0.5 |
635 |
|
|
e_col(i) = e_col(i) + pot*0.5 |
636 |
|
|
#else |
637 |
|
|
pe = pe + pot |
638 |
|
|
#endif |
639 |
|
|
|
640 |
|
|
efr(1,j) = -rxij |
641 |
|
|
efr(2,j) = -ryij |
642 |
|
|
efr(3,j) = -rzij |
643 |
|
|
|
644 |
|
|
do dim = 1, 3 |
645 |
|
|
|
646 |
|
|
|
647 |
|
|
drdx1 = efr(dim,j) / r |
648 |
|
|
ftmp = dudr * drdx1 |
649 |
|
|
|
650 |
|
|
|
651 |
|
|
#ifdef MPI |
652 |
chuckv |
239 |
fCol(dim,j) = fCol(dim,j) - ftmp |
653 |
|
|
fRow(dim,i) = fRow(dim,i) + ftmp |
654 |
chuckv |
230 |
#else |
655 |
|
|
|
656 |
|
|
f(dim,j) = f(dim,j) - ftmp |
657 |
|
|
f(dim,i) = f(dim,i) + ftmp |
658 |
|
|
|
659 |
|
|
#endif |
660 |
|
|
enddo |
661 |
|
|
endif |
662 |
|
|
endif |
663 |
|
|
enddo inner |
664 |
|
|
enddo |
665 |
|
|
|
666 |
|
|
#ifdef MPI |
667 |
|
|
point(nrow + 1) = nlist + 1 |
668 |
|
|
#else |
669 |
|
|
point(natoms) = nlist + 1 |
670 |
|
|
#endif |
671 |
|
|
|
672 |
|
|
else |
673 |
|
|
|
674 |
|
|
! use the list to find the neighbors |
675 |
|
|
do i = 1, nrow |
676 |
|
|
JBEG = POINT(i) |
677 |
|
|
JEND = POINT(i+1) - 1 |
678 |
|
|
! check thiat molecule i has neighbors |
679 |
|
|
if (jbeg .le. jend) then |
680 |
|
|
#ifdef MPI |
681 |
chuckv |
239 |
ljAtype_i => identPtrListRow(i)%this |
682 |
|
|
rxi = qRow(1,i) |
683 |
|
|
ryi = qRow(2,i) |
684 |
|
|
rzi = qRow(3,i) |
685 |
chuckv |
230 |
#else |
686 |
chuckv |
239 |
ljAtype_i => identPtrList(i)%this |
687 |
chuckv |
230 |
rxi = q(1,i) |
688 |
|
|
ryi = q(2,i) |
689 |
|
|
rzi = q(3,i) |
690 |
|
|
#endif |
691 |
|
|
do jnab = jbeg, jend |
692 |
|
|
j = list(jnab) |
693 |
|
|
#ifdef MPI |
694 |
chuckv |
239 |
ljAtype_j = identPtrListColumn(j)%this |
695 |
|
|
rxij = wrap(rxi - q_col(1,j), 1) |
696 |
|
|
ryij = wrap(ryi - q_col(2,j), 2) |
697 |
|
|
rzij = wrap(rzi - q_col(3,j), 3) |
698 |
chuckv |
230 |
#else |
699 |
chuckv |
239 |
ljAtype_j = identPtrList(j)%this |
700 |
|
|
rxij = wrap(rxi - q(1,j), 1) |
701 |
|
|
ryij = wrap(ryi - q(2,j), 2) |
702 |
|
|
rzij = wrap(rzi - q(3,j), 3) |
703 |
chuckv |
230 |
#endif |
704 |
|
|
rijsq = rxij*rxij + ryij*ryij + rzij*rzij |
705 |
|
|
|
706 |
|
|
if (rijsq < rcutsq) then |
707 |
|
|
|
708 |
|
|
r = dsqrt(rijsq) |
709 |
|
|
|
710 |
chuckv |
239 |
call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j) |
711 |
chuckv |
230 |
#ifdef MPI |
712 |
|
|
e_row(i) = e_row(i) + pot*0.5 |
713 |
|
|
e_col(i) = e_col(i) + pot*0.5 |
714 |
|
|
#else |
715 |
|
|
if (do_pot) pe = pe + pot |
716 |
|
|
#endif |
717 |
|
|
|
718 |
|
|
|
719 |
|
|
efr(1,j) = -rxij |
720 |
|
|
efr(2,j) = -ryij |
721 |
|
|
efr(3,j) = -rzij |
722 |
|
|
|
723 |
|
|
do dim = 1, 3 |
724 |
|
|
|
725 |
|
|
drdx1 = efr(dim,j) / r |
726 |
|
|
ftmp = dudr * drdx1 |
727 |
|
|
#ifdef MPI |
728 |
chuckv |
239 |
fCol(dim,j) = fCol(dim,j) - ftmp |
729 |
|
|
fRow(dim,i) = fRow(dim,i) + ftmp |
730 |
chuckv |
230 |
#else |
731 |
|
|
f(dim,j) = f(dim,j) - ftmp |
732 |
|
|
f(dim,i) = f(dim,i) + ftmp |
733 |
|
|
#endif |
734 |
|
|
enddo |
735 |
|
|
endif |
736 |
|
|
enddo |
737 |
|
|
endif |
738 |
|
|
enddo |
739 |
|
|
endif |
740 |
|
|
|
741 |
|
|
|
742 |
|
|
|
743 |
|
|
#ifdef MPI |
744 |
|
|
!!distribute forces |
745 |
chuckv |
239 |
call scatter(fRow,f,plan_row3) |
746 |
chuckv |
230 |
|
747 |
chuckv |
239 |
call scatter(fCol,f_tmp,plan_col3) |
748 |
chuckv |
230 |
do i = 1,nlocal |
749 |
|
|
do dim = 1,3 |
750 |
|
|
f(dim,i) = f(dim,i) + f_tmp(dim,i) |
751 |
|
|
end do |
752 |
|
|
end do |
753 |
|
|
|
754 |
|
|
|
755 |
|
|
|
756 |
|
|
if (do_pot) then |
757 |
|
|
! scatter/gather pot_row into the members of my column |
758 |
chuckv |
232 |
call scatter(e_row,e_tmp,plan_row) |
759 |
chuckv |
230 |
|
760 |
|
|
! scatter/gather pot_local into all other procs |
761 |
|
|
! add resultant to get total pot |
762 |
|
|
do i = 1, nlocal |
763 |
|
|
pot_local = pot_local + e_tmp(i) |
764 |
|
|
enddo |
765 |
|
|
if (newtons_thrd) then |
766 |
|
|
e_tmp = 0.0E0_DP |
767 |
|
|
call scatter(e_col,e_tmp,plan_col) |
768 |
|
|
do i = 1, nlocal |
769 |
|
|
pot_local = pot_local + e_tmp(i) |
770 |
|
|
enddo |
771 |
|
|
endif |
772 |
|
|
endif |
773 |
|
|
#endif |
774 |
|
|
|
775 |
|
|
|
776 |
|
|
|
777 |
|
|
|
778 |
chuckv |
222 |
end subroutine do_lj_ff |
779 |
|
|
|
780 |
chuckv |
239 |
!! Calculates the potential between two lj particles based on two lj_atype pointers, optionally returns second |
781 |
chuckv |
230 |
!! derivatives. |
782 |
|
|
subroutine getLjPot(r,pot,dudr,atype1,atype2,d2,status) |
783 |
|
|
! arguments |
784 |
|
|
!! Length of vector between particles |
785 |
|
|
real( kind = dp ), intent(in) :: r |
786 |
|
|
!! Potential Energy |
787 |
|
|
real( kind = dp ), intent(out) :: pot |
788 |
|
|
!! Derivatve wrt postion |
789 |
|
|
real( kind = dp ), intent(out) :: dudr |
790 |
|
|
!! Second Derivative, optional, used mainly for normal mode calculations. |
791 |
|
|
real( kind = dp ), intent(out), optional :: d2 |
792 |
|
|
|
793 |
chuckv |
239 |
type (lj_atype), intent(in), pointer :: atype1 |
794 |
|
|
type (lj_atype), intent(in), pointer :: atype2 |
795 |
chuckv |
222 |
|
796 |
chuckv |
230 |
integer, intent(out), optional :: status |
797 |
chuckv |
222 |
|
798 |
chuckv |
230 |
! local Variables |
799 |
|
|
real( kind = dp ) :: sigma |
800 |
|
|
real( kind = dp ) :: sigma2 |
801 |
|
|
real( kind = dp ) :: sigma6 |
802 |
|
|
real( kind = dp ) :: epslon |
803 |
|
|
|
804 |
|
|
real( kind = dp ) :: rcut |
805 |
|
|
real( kind = dp ) :: rcut2 |
806 |
|
|
real( kind = dp ) :: rcut6 |
807 |
|
|
real( kind = dp ) :: r2 |
808 |
|
|
real( kind = dp ) :: r6 |
809 |
|
|
|
810 |
|
|
real( kind = dp ) :: t6 |
811 |
|
|
real( kind = dp ) :: t12 |
812 |
|
|
real( kind = dp ) :: tp6 |
813 |
|
|
real( kind = dp ) :: tp12 |
814 |
|
|
real( kind = dp ) :: delta |
815 |
|
|
|
816 |
|
|
logical :: doSec = .false. |
817 |
|
|
|
818 |
|
|
integer :: errorStat |
819 |
|
|
|
820 |
|
|
!! Optional Argument Checking |
821 |
|
|
! Check to see if we need to do second derivatives |
822 |
|
|
|
823 |
|
|
if (present(d2)) doSec = .true. |
824 |
|
|
if (present(status)) status = 0 |
825 |
|
|
|
826 |
|
|
! Look up the correct parameters in the mixing matrix |
827 |
|
|
sigma = ljMixed(atype1%atype_ident,atype2_atype_ident)%sigma |
828 |
|
|
sigma2 = ljMixed(atype1%atype_ident,atype2_atype_ident)%sigma2 |
829 |
|
|
sigma6 = ljMixed(atype1%atype_ident,atype2_atype_ident)%sigma6 |
830 |
|
|
epslon = ljMixed(atype1%atype_ident,atype2_atype_ident)%epslon |
831 |
|
|
|
832 |
|
|
|
833 |
|
|
|
834 |
|
|
call getRcut(rcut,rcut2=rcut2,rcut6=rcut6,status=errorStat) |
835 |
|
|
|
836 |
|
|
r2 = r * r |
837 |
|
|
r6 = r2 * r2 * r2 |
838 |
|
|
|
839 |
|
|
t6 = sigma6/ r6 |
840 |
|
|
t12 = t6 * t6 |
841 |
|
|
|
842 |
|
|
|
843 |
|
|
|
844 |
|
|
tp6 = sigma6 / rcut6 |
845 |
|
|
tp12 = tp6*tp6 |
846 |
|
|
|
847 |
|
|
delta = -4.0E0_DP*epsilon * (tp12 - tp6) |
848 |
|
|
|
849 |
|
|
if (r.le.rcut) then |
850 |
|
|
u = 4.0E0_DP * epsilon * (t12 - t6) + delta |
851 |
|
|
dudr = 24.0E0_DP * epsilon * (t6 - 2.0E0_DP*t12) / r |
852 |
|
|
if(doSec) d2 = 24.0E0_DP * epsilon * (26.0E0_DP*t12 - 7.0E0_DP*t6)/r/r |
853 |
|
|
else |
854 |
|
|
u = 0.0E0_DP |
855 |
|
|
dudr = 0.0E0_DP |
856 |
|
|
if(doSec) d2 = 0.0E0_DP |
857 |
|
|
endif |
858 |
|
|
|
859 |
|
|
return |
860 |
|
|
|
861 |
|
|
|
862 |
|
|
|
863 |
|
|
end subroutine getLjPot |
864 |
|
|
|
865 |
|
|
|
866 |
chuckv |
239 |
!! Calculates the mixing for sigma or epslon based on character string for initialzition of mixing array. |
867 |
chuckv |
230 |
function calcLJMix(thisParam,param1,param2,status) result(myMixParam) |
868 |
|
|
character(len=*) :: thisParam |
869 |
|
|
real(kind = dp) :: param1 |
870 |
|
|
real(kind = dp) :: param2 |
871 |
|
|
real(kind = dp ) :: myMixParam |
872 |
|
|
integer, optional :: status |
873 |
|
|
|
874 |
|
|
|
875 |
|
|
myMixParam = 0.0_dp |
876 |
|
|
|
877 |
|
|
if (present(status)) status = 0 |
878 |
|
|
|
879 |
|
|
select case (thisParam) |
880 |
|
|
|
881 |
|
|
case ("sigma") |
882 |
|
|
myMixParam = 0.5_dp * (param1 + param2) |
883 |
|
|
case ("epslon") |
884 |
|
|
myMixParam = sqrt(param1 * param2) |
885 |
|
|
case default |
886 |
|
|
status = -1 |
887 |
|
|
end select |
888 |
|
|
|
889 |
|
|
end function calcLJMix |
890 |
|
|
|
891 |
|
|
|
892 |
|
|
|
893 |
chuckv |
215 |
end module lj_ff |