| 1 |
!! Calculates Long Range forces Lennard-Jones interactions. |
| 2 |
!! Corresponds to the force field defined in lj_FF.cpp |
| 3 |
!! @author Charles F. Vardeman II |
| 4 |
!! @author Matthew Meineke |
| 5 |
!! @version $Id: lj_FF.F90,v 1.10 2003-01-24 21:36:52 chuckv Exp $, $Date: 2003-01-24 21:36:52 $, $Name: not supported by cvs2svn $, $Revision: 1.10 $ |
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| 8 |
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| 9 |
module lj_ff |
| 10 |
use simulation |
| 11 |
use definitions |
| 12 |
#ifdef IS_MPI |
| 13 |
use mpiSimulation |
| 14 |
#endif |
| 15 |
implicit none |
| 16 |
PRIVATE |
| 17 |
|
| 18 |
!! Number of lj_atypes in lj_atype_list |
| 19 |
integer, save :: n_lj_atypes = 0 |
| 20 |
|
| 21 |
!! Starting Size for ljMixed Array |
| 22 |
integer, parameter :: ljMixed_blocksize = 10 |
| 23 |
|
| 24 |
!! Basic atom type for a Lennard-Jones Atom. |
| 25 |
type, public :: lj_atype |
| 26 |
private |
| 27 |
sequence |
| 28 |
!! Unique number for place in linked list |
| 29 |
integer :: atype_number = 0 |
| 30 |
!! Unique indentifier number (ie atomic no, etc) |
| 31 |
integer :: atype_ident = 0 |
| 32 |
!! Mass of Particle |
| 33 |
real ( kind = dp ) :: mass = 0.0_dp |
| 34 |
!! Lennard-Jones epslon |
| 35 |
real ( kind = dp ) :: epsilon = 0.0_dp |
| 36 |
!! Lennard-Jones Sigma |
| 37 |
real ( kind = dp ) :: sigma = 0.0_dp |
| 38 |
!! Lennard-Jones Sigma Squared |
| 39 |
real ( kind = dp ) :: sigma2 = 0.0_dp |
| 40 |
!! Lennard-Jones Sigma to sixth |
| 41 |
real ( kind = dp ) :: sigma6 = 0.0_dp |
| 42 |
!! Pointer for linked list creation |
| 43 |
type (lj_atype), pointer :: next => null() |
| 44 |
end type lj_atype |
| 45 |
|
| 46 |
!! 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 |
| 50 |
|
| 51 |
!! Global list of lj atypes in simulation |
| 52 |
type (lj_atype), pointer :: lj_atype_list => null() |
| 53 |
!! LJ mixing array |
| 54 |
type (lj_atype), dimension(:,:), pointer :: ljMixed => null() |
| 55 |
!! identity pointer list for force loop. |
| 56 |
type (lj_atypePtr), dimension(:), pointer :: identPtrList => null() |
| 57 |
|
| 58 |
|
| 59 |
!! Neighbor list and commom arrays |
| 60 |
!! This should eventally get moved to a neighbor list type |
| 61 |
integer, allocatable, dimension(:) :: point |
| 62 |
integer, allocatable, dimension(:) :: list |
| 63 |
integer, parameter :: listMultiplier = 80 |
| 64 |
integer :: nListAllocs = 0 |
| 65 |
integer, parameter :: maxListAllocs = 5 |
| 66 |
|
| 67 |
#ifdef IS_MPI |
| 68 |
! Universal routines: All types of force calculations will need these arrays |
| 69 |
! Arrays specific to a type of force calculation should be declared in that module. |
| 70 |
!! Row position array. |
| 71 |
real( kind = dp ), allocatable, dimension(:,:) :: qRow |
| 72 |
!! Column position array. |
| 73 |
real( kind = dp ), allocatable, dimension(:,:) :: qColumn |
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|
| 75 |
!! Row Force array. |
| 76 |
real( kind = dp ), allocatable, dimension(:,:) :: fRow |
| 77 |
!! Column Force Array. |
| 78 |
real( kind = dp ), allocatable, dimension(:,:) :: fColumn |
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|
| 80 |
!! Row potential energy array |
| 81 |
real( kind = dp ), allocatable, dimension(:) :: eRow |
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!! Column potential energy array |
| 83 |
real( kind = dp ), allocatable, dimension(:) :: eColumn |
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|
| 85 |
|
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!! Row lj_atype pointer list |
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type (lj_atypePtr), dimension(:), pointer :: identPtrListRow => null() |
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!! Column lj_atype pointer list |
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type (lj_atypePtr), dimension(:), pointer :: identPtrListColumn => null() |
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#endif |
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|
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|
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!! Logical has lj force field module been initialized? |
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logical, save :: isljFFinit = .false. |
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|
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|
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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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public :: init_ljFF |
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|
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|
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contains |
| 107 |
|
| 108 |
subroutine new_lj_atype(ident,mass,epsilon,sigma,status) |
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real( kind = dp ), intent(in) :: mass |
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real( kind = dp ), intent(in) :: epsilon |
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real( kind = dp ), intent(in) :: sigma |
| 112 |
integer, intent(in) :: ident |
| 113 |
integer, intent(out) :: status |
| 114 |
|
| 115 |
type (lj_atype), pointer :: this_lj_atype |
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type (lj_atype), pointer :: lj_atype_ptr |
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|
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type (lj_atype), dimension(:,:), pointer :: thisMix |
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type (lj_atype), dimension(:,:), pointer :: oldMix |
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integer :: alloc_error |
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integer :: atype_counter = 0 |
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integer :: alloc_size |
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|
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status = 0 |
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|
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|
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|
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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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|
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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%epsilon = epsilon |
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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%atype_number = n_lj_atypes + 1 |
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|
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|
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! First time through allocate a array of size ljMixed_blocksize |
| 148 |
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(ljMixed) |
| 159 |
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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|
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|
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|
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|
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|
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! Find bottom of atype master list |
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! if lj_atype_list is null then we are at the top of the list. |
| 180 |
if (.not. associated(lj_atype_list)) then |
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|
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write(*,*) "Associating lists for first time" |
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|
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|
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this_lj_atype%atype_number = 1 |
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|
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ljMixed(n_lj_atypes,n_lj_atypes)%sigma = this_lj_atype%sigma |
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|
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ljMixed(n_lj_atypes,n_lj_atypes)%sigma2 = ljMixed(n_lj_atypes,n_lj_atypes)%sigma & |
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* ljMixed(n_lj_atypes,n_lj_atypes)%sigma |
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|
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ljMixed(n_lj_atypes,n_lj_atypes)%sigma6 = ljMixed(n_lj_atypes,n_lj_atypes)%sigma2 & |
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* ljMixed(n_lj_atypes,n_lj_atypes)%sigma2 & |
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* ljMixed(n_lj_atypes,n_lj_atypes)%sigma2 |
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|
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ljMixed(n_lj_atypes,n_lj_atypes)%epsilon = this_lj_atype%epsilon |
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|
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lj_atype_list => this_lj_atype |
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|
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write(*,*) "lj_atype_list first time through -- ident", lj_atype_list%atype_ident |
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else ! we need to find the bottom of the list to insert new atype |
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write(*,*) "Second time through" |
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lj_atype_ptr => lj_atype_list |
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write(*,*) "lj_atype_ptr to next" |
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atype_counter = 1 |
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find_end: do |
| 207 |
if (.not. associated(lj_atype_ptr)) exit find_end |
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|
| 209 |
write(*,*) "Inside find_end-this ident", lj_atype_ptr%atype_ident |
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! Set up mixing for new atype and current atype in list |
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ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma = & |
| 212 |
calcLJMix("sigma",this_lj_atype%sigma, & |
| 213 |
lj_atype_ptr%sigma) |
| 214 |
|
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ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 = & |
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ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma & |
| 217 |
* ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma |
| 218 |
|
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ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma6 = & |
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ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 & |
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* ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 & |
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* ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 |
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|
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ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%epsilon = & |
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calcLJMix("epsilon",this_lj_atype%epsilon, & |
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lj_atype_ptr%epsilon) |
| 227 |
|
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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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end do find_end |
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|
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lj_atype_ptr => this_lj_atype |
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write(*,*) "just added: ", lj_atype_ptr%atype_ident |
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end if |
| 236 |
|
| 237 |
write(*,*) "lj_atype_list now contains.." |
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|
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lj_atype_ptr => lj_atype_list |
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do while (associated(lj_atype_ptr)) |
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write(*,*) "lj_atype_list contains ident", lj_atype_ptr%atype_ident |
| 242 |
lj_atype_ptr => lj_atype_ptr%next |
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end do |
| 244 |
|
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! Insert new atype at end of list |
| 246 |
|
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! Increment number of atypes |
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|
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n_lj_atypes = n_lj_atypes + 1 |
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|
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! Set up self mixing |
| 252 |
|
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end subroutine new_lj_atype |
| 254 |
|
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|
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subroutine init_ljFF(nComponents,ident, status) |
| 257 |
!! Number of components in ident array |
| 258 |
integer, intent(inout) :: nComponents |
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!! Array of identities nComponents long corresponding to |
| 260 |
!! ljatype ident. |
| 261 |
integer, dimension(nComponents),intent(inout) :: ident |
| 262 |
!! Result status, success = 0, error = -1 |
| 263 |
integer, intent(out) :: Status |
| 264 |
|
| 265 |
integer :: alloc_stat |
| 266 |
|
| 267 |
integer :: thisStat |
| 268 |
integer :: i |
| 269 |
#ifdef IS_MPI |
| 270 |
integer, allocatable, dimension(:) :: identRow |
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integer, allocatable, dimension(:) :: identCol |
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integer :: nrow |
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integer :: ncol |
| 274 |
integer :: alloc_stat |
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#endif |
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status = 0 |
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|
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write(*,*) "Initializing ljFF" |
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!! if were're not in MPI, we just update ljatypePtrList |
| 280 |
#ifndef IS_MPI |
| 281 |
call new_ljatypePtrList(nComponents,ident,identPtrList,thisStat) |
| 282 |
if ( thisStat /= 0 ) then |
| 283 |
status = -1 |
| 284 |
return |
| 285 |
endif |
| 286 |
write(*,*) "component pointer list initialized" |
| 287 |
!! Allocate pointer lists |
| 288 |
allocate(point(nComponents),stat=alloc_stat) |
| 289 |
if (alloc_stat /=0) then |
| 290 |
status = -1 |
| 291 |
return |
| 292 |
endif |
| 293 |
|
| 294 |
allocate(list(nComponents*listMultiplier),stat=alloc_stat) |
| 295 |
if (alloc_stat /=0) then |
| 296 |
status = -1 |
| 297 |
return |
| 298 |
endif |
| 299 |
|
| 300 |
! if were're in MPI, we also have to worry about row and col lists |
| 301 |
#else |
| 302 |
! We can only set up forces if mpiSimulation has been setup. |
| 303 |
if (.not. isMPISimSet()) then |
| 304 |
status = -1 |
| 305 |
return |
| 306 |
endif |
| 307 |
nrow = getNrow() |
| 308 |
ncol = getNcol() |
| 309 |
!! Allocate temperary arrays to hold gather information |
| 310 |
allocate(identRow(nrow),stat=alloc_stat) |
| 311 |
if (alloc_stat /= 0 ) then |
| 312 |
status = -1 |
| 313 |
return |
| 314 |
endif |
| 315 |
|
| 316 |
allocate(identCol(ncol),stat=alloc_stat) |
| 317 |
if (alloc_stat /= 0 ) then |
| 318 |
status = -1 |
| 319 |
return |
| 320 |
endif |
| 321 |
!! Gather idents into row and column idents |
| 322 |
call gather(ident,identRow,plan_row) |
| 323 |
call gather(ident,identCol,plan_col) |
| 324 |
|
| 325 |
!! Create row and col pointer lists |
| 326 |
call new_ljatypePtrList(nrow,identRow,identPtrListRow,thisStat) |
| 327 |
if (thisStat /= 0 ) then |
| 328 |
status = -1 |
| 329 |
return |
| 330 |
endif |
| 331 |
|
| 332 |
call new_ljatypePtrList(ncol,identCol,identPtrListCol,thisStat) |
| 333 |
if (thisStat /= 0 ) then |
| 334 |
status = -1 |
| 335 |
return |
| 336 |
endif |
| 337 |
|
| 338 |
!! free temporary ident arrays |
| 339 |
deallocate(identCol) |
| 340 |
deallocate(identRow) |
| 341 |
|
| 342 |
!! Allocate Simulation arrays |
| 343 |
!! NOTE: This bit of code should be fixed, it can cause large |
| 344 |
!! memory fragmentation if call repeatedly |
| 345 |
|
| 346 |
if (.not.allocated(qRow)) then |
| 347 |
allocate(qRow(3,nrow),stat=alloc_stat) |
| 348 |
if (alloc_stat /= 0 ) then |
| 349 |
status = -1 |
| 350 |
return |
| 351 |
endif |
| 352 |
else |
| 353 |
deallocate(qrow) |
| 354 |
allocate(qRow(3,nrow),stat=alloc_stat) |
| 355 |
if (alloc_stat /= 0 ) then |
| 356 |
status = -1 |
| 357 |
return |
| 358 |
endif |
| 359 |
endif |
| 360 |
|
| 361 |
if (.not.allocated(3,qCol)) then |
| 362 |
allocate(qCol(ncol),stat=alloc_stat) |
| 363 |
if (alloc_stat /= 0 ) then |
| 364 |
status = -1 |
| 365 |
return |
| 366 |
endif |
| 367 |
else |
| 368 |
deallocate(qCol) |
| 369 |
allocate(qCol(3,ncol),stat=alloc_stat) |
| 370 |
if (alloc_stat /= 0 ) then |
| 371 |
status = -1 |
| 372 |
return |
| 373 |
endif |
| 374 |
endif |
| 375 |
|
| 376 |
if (.not.allocated(fRow)) then |
| 377 |
allocate(fRow(3,nrow),stat=alloc_stat) |
| 378 |
if (alloc_stat /= 0 ) then |
| 379 |
status = -1 |
| 380 |
return |
| 381 |
endif |
| 382 |
else |
| 383 |
deallocate(fRow) |
| 384 |
allocate(fRow(3,nrow),stat=alloc_stat) |
| 385 |
if (alloc_stat /= 0 ) then |
| 386 |
status = -1 |
| 387 |
return |
| 388 |
endif |
| 389 |
endif |
| 390 |
|
| 391 |
if (.not.allocated(fCol)) then |
| 392 |
allocate(fCol(3,ncol),stat=alloc_stat) |
| 393 |
if (alloc_stat /= 0 ) then |
| 394 |
status = -1 |
| 395 |
return |
| 396 |
endif |
| 397 |
else |
| 398 |
deallocate(fCol) |
| 399 |
allocate(fCol(3,ncol),stat=alloc_stat) |
| 400 |
if (alloc_stat /= 0 ) then |
| 401 |
status = -1 |
| 402 |
return |
| 403 |
endif |
| 404 |
endif |
| 405 |
|
| 406 |
if (.not.allocated(eRow)) then |
| 407 |
allocate(eRow(nrow),stat=alloc_stat) |
| 408 |
if (alloc_stat /= 0 ) then |
| 409 |
status = -1 |
| 410 |
return |
| 411 |
endif |
| 412 |
else |
| 413 |
deallocate(eRow) |
| 414 |
allocate(eRow(nrow),stat=alloc_stat) |
| 415 |
if (alloc_stat /= 0 ) then |
| 416 |
status = -1 |
| 417 |
return |
| 418 |
endif |
| 419 |
endif |
| 420 |
|
| 421 |
if (.not.allocated(eCol)) then |
| 422 |
allocate(eCol(ncol),stat=alloc_stat) |
| 423 |
if (alloc_stat /= 0 ) then |
| 424 |
status = -1 |
| 425 |
return |
| 426 |
endif |
| 427 |
else |
| 428 |
deallocate(eCol) |
| 429 |
allocate(eCol(ncol),stat=alloc_stat) |
| 430 |
if (alloc_stat /= 0 ) then |
| 431 |
status = -1 |
| 432 |
return |
| 433 |
endif |
| 434 |
endif |
| 435 |
|
| 436 |
if (.not.allocated(eTemp)) then |
| 437 |
allocate(eTemp(nComponents),stat=alloc_stat) |
| 438 |
if (alloc_stat /= 0 ) then |
| 439 |
status = -1 |
| 440 |
return |
| 441 |
endif |
| 442 |
else |
| 443 |
deallocate(eTemp) |
| 444 |
allocate(eTemp(nComponets),stat=alloc_stat) |
| 445 |
if (alloc_stat /= 0 ) then |
| 446 |
status = -1 |
| 447 |
return |
| 448 |
endif |
| 449 |
endif |
| 450 |
|
| 451 |
|
| 452 |
!! Allocate neighbor lists for mpi simulations. |
| 453 |
if (.not. allocated(point)) then |
| 454 |
allocate(point(nrow),stat=alloc_stat) |
| 455 |
if (alloc_stat /=0) then |
| 456 |
status = -1 |
| 457 |
return |
| 458 |
endif |
| 459 |
|
| 460 |
allocate(list(ncol*listMultiplier),stat=alloc_stat) |
| 461 |
if (alloc_stat /=0) then |
| 462 |
status = -1 |
| 463 |
return |
| 464 |
endif |
| 465 |
else |
| 466 |
deallocate(list) |
| 467 |
deallocate(point) |
| 468 |
allocate(point(nrow),stat=alloc_stat) |
| 469 |
if (alloc_stat /=0) then |
| 470 |
status = -1 |
| 471 |
return |
| 472 |
endif |
| 473 |
|
| 474 |
allocate(list(ncol*listMultiplier),stat=alloc_stat) |
| 475 |
if (alloc_stat /=0) then |
| 476 |
status = -1 |
| 477 |
return |
| 478 |
endif |
| 479 |
endif |
| 480 |
|
| 481 |
#endif |
| 482 |
|
| 483 |
|
| 484 |
do i = 1, nComponents |
| 485 |
write(*,*) "Ident pointer list ident: ", identPtrList(i)%this%atype_ident |
| 486 |
end do |
| 487 |
|
| 488 |
isljFFinit = .true. |
| 489 |
|
| 490 |
end subroutine init_ljFF |
| 491 |
|
| 492 |
|
| 493 |
|
| 494 |
|
| 495 |
|
| 496 |
!! Takes an ident array and creates an atype pointer list |
| 497 |
!! based on those identities |
| 498 |
subroutine new_ljatypePtrList(mysize,ident,PtrList,status) |
| 499 |
integer, intent(in) :: mysize |
| 500 |
integer,dimension(:), intent(in) :: ident |
| 501 |
integer, optional :: status |
| 502 |
type(lj_atypePtr), dimension(:), pointer :: PtrList |
| 503 |
|
| 504 |
integer :: thisIdent |
| 505 |
integer :: i |
| 506 |
integer :: alloc_error |
| 507 |
type (lj_atype), pointer :: tmpPtr |
| 508 |
|
| 509 |
if (present(status)) status = 0 |
| 510 |
|
| 511 |
write(*,*) "Creating new ljatypePtrList...." |
| 512 |
! First time through, allocate list |
| 513 |
if (.not.associated(PtrList)) then |
| 514 |
write(*,*) "allocating pointer list...." |
| 515 |
allocate(PtrList(mysize)) |
| 516 |
else |
| 517 |
! We want to creat a new ident list so free old list |
| 518 |
deallocate(PtrList) |
| 519 |
allocate(PtrList(mysize)) |
| 520 |
endif |
| 521 |
|
| 522 |
! Match pointer list |
| 523 |
write(*,*) "Doing ident search" |
| 524 |
do i = 1, mysize |
| 525 |
thisIdent = ident(i) |
| 526 |
write(*,*) "Calling getLJatype for ident ", thisIdent |
| 527 |
call getLJatype(thisIdent,tmpPtr) |
| 528 |
|
| 529 |
if (.not. associated(tmpPtr)) then |
| 530 |
write(*,*) "tmpptr was not associated" |
| 531 |
status = -1 |
| 532 |
return |
| 533 |
endif |
| 534 |
|
| 535 |
PtrList(i)%this => tmpPtr |
| 536 |
end do |
| 537 |
|
| 538 |
end subroutine new_ljatypePtrList |
| 539 |
|
| 540 |
!! Finds a lj_atype based upon numerical ident |
| 541 |
!! returns a null pointer if error |
| 542 |
subroutine getLJatype(ident,ljAtypePtr) |
| 543 |
integer, intent(in) :: ident |
| 544 |
type (lj_atype), pointer :: ljAtypePtr |
| 545 |
type (lj_atype), pointer :: tmplj_atype_ptr => null() |
| 546 |
|
| 547 |
write(*,*) "Finding ljAtype for ident ", ident |
| 548 |
ljAtypePtr => null() |
| 549 |
|
| 550 |
if(.not. associated(lj_atype_list)) return |
| 551 |
|
| 552 |
! Point at head of list. |
| 553 |
write(*,*) "Searching at head of list" |
| 554 |
tmplj_atype_ptr => lj_atype_list |
| 555 |
find_ident: do |
| 556 |
if (.not.associated(tmplj_atype_ptr)) then |
| 557 |
write(*,*) "Find_ident, pointer not associated" |
| 558 |
exit find_ident |
| 559 |
else if( tmplj_atype_ptr%atype_ident == ident) then |
| 560 |
ljAtypePtr => tmplj_atype_ptr |
| 561 |
exit find_ident |
| 562 |
endif |
| 563 |
tmplj_atype_ptr => tmplj_atype_ptr%next |
| 564 |
end do find_ident |
| 565 |
|
| 566 |
|
| 567 |
|
| 568 |
|
| 569 |
end subroutine getLJatype |
| 570 |
|
| 571 |
|
| 572 |
!! FORCE routine Calculates Lennard Jones forces. |
| 573 |
!-------------------------------------------------------------> |
| 574 |
subroutine do_lj_ff(q,f,potE,do_pot) |
| 575 |
!! Position array provided by C, dimensioned by getNlocal |
| 576 |
real ( kind = dp ), dimension(3,getNlocal()) :: q |
| 577 |
!! Force array provided by C, dimensioned by getNlocal |
| 578 |
real ( kind = dp ), dimension(3,getNlocal()) :: f |
| 579 |
real ( kind = dp ) :: potE |
| 580 |
logical ( kind = 2) :: do_pot |
| 581 |
|
| 582 |
type(lj_atype), pointer :: ljAtype_i |
| 583 |
type(lj_atype), pointer :: ljAtype_j |
| 584 |
|
| 585 |
#ifdef MPI |
| 586 |
real( kind = DP ), dimension(3,getNcol()) :: efr |
| 587 |
real( kind = DP ) :: pot_local |
| 588 |
#else |
| 589 |
real( kind = DP ), dimension(3,getNlocal()) :: efr |
| 590 |
#endif |
| 591 |
|
| 592 |
real( kind = DP ) :: pe |
| 593 |
logical :: update_nlist |
| 594 |
|
| 595 |
|
| 596 |
integer :: i, j, jbeg, jend, jnab, idim, jdim, idim2, jdim2, dim, dim2 |
| 597 |
integer :: nlist |
| 598 |
integer :: j_start |
| 599 |
integer :: tag_i,tag_j |
| 600 |
real( kind = DP ) :: r, pot, ftmp, dudr, d2, drdx1, kt1, kt2, kt3, ktmp |
| 601 |
real( kind = DP ) :: rxi, ryi, rzi, rxij, ryij, rzij, rijsq |
| 602 |
real( kind = DP ) :: rlistsq, rcutsq,rlist,rcut |
| 603 |
|
| 604 |
! a rig that need to be fixed. |
| 605 |
#ifdef IS_MPI |
| 606 |
logical :: newtons_thrd = .true. |
| 607 |
real( kind = dp ) :: pe_local |
| 608 |
integer :: nlocal |
| 609 |
#endif |
| 610 |
integer :: nrow |
| 611 |
integer :: ncol |
| 612 |
integer :: natoms |
| 613 |
|
| 614 |
! Make sure we are properly initialized. |
| 615 |
if (.not. isljFFInit) then |
| 616 |
write(default_error,*) "ERROR: lj_FF has not been properly initialized" |
| 617 |
return |
| 618 |
endif |
| 619 |
#ifdef IS_MPI |
| 620 |
if (.not. isMPISimSet()) then |
| 621 |
write(default_error,*) "ERROR: mpiSimulation has not been properly initialized" |
| 622 |
return |
| 623 |
endif |
| 624 |
#endif |
| 625 |
|
| 626 |
!! initialize local variables |
| 627 |
natoms = getNlocal() |
| 628 |
call getRcut(rcut,rcut2=rcutsq) |
| 629 |
call getRlist(rlist,rlistsq) |
| 630 |
#ifndef IS_MPI |
| 631 |
nrow = natoms - 1 |
| 632 |
ncol = natoms |
| 633 |
#else |
| 634 |
nrow = getNrow(plan_row) |
| 635 |
ncol = getNcol(plan_col) |
| 636 |
nlocal = natoms |
| 637 |
j_start = 1 |
| 638 |
#endif |
| 639 |
|
| 640 |
|
| 641 |
!! See if we need to update neighbor lists |
| 642 |
call check(q,update_nlist) |
| 643 |
|
| 644 |
!--------------WARNING........................... |
| 645 |
! Zero variables, NOTE:::: Forces are zeroed in C |
| 646 |
! Zeroing them here could delete previously computed |
| 647 |
! Forces. |
| 648 |
!------------------------------------------------ |
| 649 |
#ifndef IS_MPI |
| 650 |
! nloops = nloops + 1 |
| 651 |
pe = 0.0E0_DP |
| 652 |
|
| 653 |
#else |
| 654 |
f_row = 0.0E0_DP |
| 655 |
f_col = 0.0E0_DP |
| 656 |
|
| 657 |
pe_local = 0.0E0_DP |
| 658 |
|
| 659 |
eRow = 0.0E0_DP |
| 660 |
eCol = 0.0E0_DP |
| 661 |
eTemp = 0.0E0_DP |
| 662 |
#endif |
| 663 |
efr = 0.0E0_DP |
| 664 |
|
| 665 |
! communicate MPI positions |
| 666 |
#ifdef MPI |
| 667 |
call gather(q,qRow,plan_row3) |
| 668 |
call gather(q,qCol,plan_col3) |
| 669 |
#endif |
| 670 |
|
| 671 |
|
| 672 |
if (update_nlist) then |
| 673 |
|
| 674 |
! save current configuration, contruct neighbor list, |
| 675 |
! and calculate forces |
| 676 |
call save_nlist(q) |
| 677 |
|
| 678 |
nlist = 0 |
| 679 |
|
| 680 |
|
| 681 |
|
| 682 |
do i = 1, nrow |
| 683 |
point(i) = nlist + 1 |
| 684 |
#ifdef MPI |
| 685 |
ljAtype_i => identPtrListRow(i)%this |
| 686 |
tag_i = tagRow(i) |
| 687 |
rxi = qRow(1,i) |
| 688 |
ryi = qRow(2,i) |
| 689 |
rzi = qRow(3,i) |
| 690 |
#else |
| 691 |
ljAtype_i => identPtrList(i)%this |
| 692 |
j_start = i + 1 |
| 693 |
rxi = q(1,i) |
| 694 |
ryi = q(2,i) |
| 695 |
rzi = q(3,i) |
| 696 |
#endif |
| 697 |
|
| 698 |
inner: do j = j_start, ncol |
| 699 |
#ifdef MPI |
| 700 |
! Assign identity pointers and tags |
| 701 |
ljAtype_j => identPtrListColumn(j)%this |
| 702 |
tag_j = tagCol(j) |
| 703 |
if (newtons_thrd) then |
| 704 |
if (tag_i <= tag_j) then |
| 705 |
if (mod(tag_i + tag_j,2) == 0) cycle inner |
| 706 |
else |
| 707 |
if (mod(tag_i + tag_j,2) == 1) cycle inner |
| 708 |
endif |
| 709 |
endif |
| 710 |
|
| 711 |
rxij = wrap(rxi - qCol(1,j), 1) |
| 712 |
ryij = wrap(ryi - qCol(2,j), 2) |
| 713 |
rzij = wrap(rzi - qCol(3,j), 3) |
| 714 |
#else |
| 715 |
ljAtype_j => identPtrList(j)%this |
| 716 |
rxij = wrap(rxi - q(1,j), 1) |
| 717 |
ryij = wrap(ryi - q(2,j), 2) |
| 718 |
rzij = wrap(rzi - q(3,j), 3) |
| 719 |
|
| 720 |
#endif |
| 721 |
rijsq = rxij*rxij + ryij*ryij + rzij*rzij |
| 722 |
|
| 723 |
#ifdef MPI |
| 724 |
if (rijsq <= rlistsq .AND. & |
| 725 |
tag_j /= tag_i) then |
| 726 |
#else |
| 727 |
if (rijsq < rlistsq) then |
| 728 |
#endif |
| 729 |
|
| 730 |
nlist = nlist + 1 |
| 731 |
if (nlist > size(list)) then |
| 732 |
!! "Change how nlist size is done" |
| 733 |
write(DEFAULT_ERROR,*) "ERROR: nlist > list size" |
| 734 |
endif |
| 735 |
list(nlist) = j |
| 736 |
|
| 737 |
|
| 738 |
if (rijsq < rcutsq) then |
| 739 |
|
| 740 |
r = dsqrt(rijsq) |
| 741 |
|
| 742 |
call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j) |
| 743 |
|
| 744 |
#ifdef MPI |
| 745 |
eRow(i) = eRow(i) + pot*0.5 |
| 746 |
eCol(i) = eCol(i) + pot*0.5 |
| 747 |
#else |
| 748 |
pe = pe + pot |
| 749 |
#endif |
| 750 |
|
| 751 |
efr(1,j) = -rxij |
| 752 |
efr(2,j) = -ryij |
| 753 |
efr(3,j) = -rzij |
| 754 |
|
| 755 |
do dim = 1, 3 |
| 756 |
|
| 757 |
|
| 758 |
drdx1 = efr(dim,j) / r |
| 759 |
ftmp = dudr * drdx1 |
| 760 |
|
| 761 |
|
| 762 |
#ifdef MPI |
| 763 |
fCol(dim,j) = fCol(dim,j) - ftmp |
| 764 |
fRow(dim,i) = fRow(dim,i) + ftmp |
| 765 |
#else |
| 766 |
|
| 767 |
f(dim,j) = f(dim,j) - ftmp |
| 768 |
f(dim,i) = f(dim,i) + ftmp |
| 769 |
|
| 770 |
#endif |
| 771 |
enddo |
| 772 |
endif |
| 773 |
endif |
| 774 |
enddo inner |
| 775 |
enddo |
| 776 |
|
| 777 |
#ifdef MPI |
| 778 |
point(nrow + 1) = nlist + 1 |
| 779 |
#else |
| 780 |
point(natoms) = nlist + 1 |
| 781 |
#endif |
| 782 |
|
| 783 |
else |
| 784 |
|
| 785 |
! use the list to find the neighbors |
| 786 |
do i = 1, nrow |
| 787 |
JBEG = POINT(i) |
| 788 |
JEND = POINT(i+1) - 1 |
| 789 |
! check thiat molecule i has neighbors |
| 790 |
if (jbeg .le. jend) then |
| 791 |
#ifdef MPI |
| 792 |
ljAtype_i => identPtrListRow(i)%this |
| 793 |
rxi = qRow(1,i) |
| 794 |
ryi = qRow(2,i) |
| 795 |
rzi = qRow(3,i) |
| 796 |
#else |
| 797 |
ljAtype_i => identPtrList(i)%this |
| 798 |
rxi = q(1,i) |
| 799 |
ryi = q(2,i) |
| 800 |
rzi = q(3,i) |
| 801 |
#endif |
| 802 |
do jnab = jbeg, jend |
| 803 |
j = list(jnab) |
| 804 |
#ifdef MPI |
| 805 |
ljAtype_j = identPtrListColumn(j)%this |
| 806 |
rxij = wrap(rxi - q_col(1,j), 1) |
| 807 |
ryij = wrap(ryi - q_col(2,j), 2) |
| 808 |
rzij = wrap(rzi - q_col(3,j), 3) |
| 809 |
#else |
| 810 |
ljAtype_j = identPtrList(j)%this |
| 811 |
rxij = wrap(rxi - q(1,j), 1) |
| 812 |
ryij = wrap(ryi - q(2,j), 2) |
| 813 |
rzij = wrap(rzi - q(3,j), 3) |
| 814 |
#endif |
| 815 |
rijsq = rxij*rxij + ryij*ryij + rzij*rzij |
| 816 |
|
| 817 |
if (rijsq < rcutsq) then |
| 818 |
|
| 819 |
r = dsqrt(rijsq) |
| 820 |
|
| 821 |
call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j) |
| 822 |
#ifdef MPI |
| 823 |
eRow(i) = eRow(i) + pot*0.5 |
| 824 |
eCol(i) = eCol(i) + pot*0.5 |
| 825 |
#else |
| 826 |
pe = pe + pot |
| 827 |
#endif |
| 828 |
|
| 829 |
|
| 830 |
efr(1,j) = -rxij |
| 831 |
efr(2,j) = -ryij |
| 832 |
efr(3,j) = -rzij |
| 833 |
|
| 834 |
do dim = 1, 3 |
| 835 |
|
| 836 |
drdx1 = efr(dim,j) / r |
| 837 |
ftmp = dudr * drdx1 |
| 838 |
#ifdef MPI |
| 839 |
fCol(dim,j) = fCol(dim,j) - ftmp |
| 840 |
fRow(dim,i) = fRow(dim,i) + ftmp |
| 841 |
#else |
| 842 |
f(dim,j) = f(dim,j) - ftmp |
| 843 |
f(dim,i) = f(dim,i) + ftmp |
| 844 |
#endif |
| 845 |
enddo |
| 846 |
endif |
| 847 |
enddo |
| 848 |
endif |
| 849 |
enddo |
| 850 |
endif |
| 851 |
|
| 852 |
|
| 853 |
|
| 854 |
#ifdef MPI |
| 855 |
!!distribute forces |
| 856 |
call scatter(fRow,f,plan_row3) |
| 857 |
|
| 858 |
call scatter(fCol,f_tmp,plan_col3) |
| 859 |
|
| 860 |
do i = 1,nlocal |
| 861 |
f(1:3,i) = f(1:3,i) + f_tmp(1:3,i) |
| 862 |
end do |
| 863 |
|
| 864 |
|
| 865 |
|
| 866 |
if (do_pot) then |
| 867 |
! scatter/gather pot_row into the members of my column |
| 868 |
call scatter(e_row,e_tmp,plan_row) |
| 869 |
|
| 870 |
! scatter/gather pot_local into all other procs |
| 871 |
! add resultant to get total pot |
| 872 |
do i = 1, nlocal |
| 873 |
pe_local = pe_local + e_tmp(i) |
| 874 |
enddo |
| 875 |
if (newtons_thrd) then |
| 876 |
e_tmp = 0.0E0_DP |
| 877 |
call scatter(e_col,e_tmp,plan_col) |
| 878 |
do i = 1, nlocal |
| 879 |
pe_local = pe_local + e_tmp(i) |
| 880 |
enddo |
| 881 |
endif |
| 882 |
endif |
| 883 |
potE = pe_local |
| 884 |
#endif |
| 885 |
|
| 886 |
potE = pe |
| 887 |
|
| 888 |
|
| 889 |
end subroutine do_lj_ff |
| 890 |
|
| 891 |
!! Calculates the potential between two lj particles based on two lj_atype pointers, optionally returns second |
| 892 |
!! derivatives. |
| 893 |
subroutine getLjPot(r,pot,dudr,atype1,atype2,d2,status) |
| 894 |
! arguments |
| 895 |
!! Length of vector between particles |
| 896 |
real( kind = dp ), intent(in) :: r |
| 897 |
!! Potential Energy |
| 898 |
real( kind = dp ), intent(out) :: pot |
| 899 |
!! Derivatve wrt postion |
| 900 |
real( kind = dp ), intent(out) :: dudr |
| 901 |
!! Second Derivative, optional, used mainly for normal mode calculations. |
| 902 |
real( kind = dp ), intent(out), optional :: d2 |
| 903 |
|
| 904 |
type (lj_atype), pointer :: atype1 |
| 905 |
type (lj_atype), pointer :: atype2 |
| 906 |
|
| 907 |
integer, intent(out), optional :: status |
| 908 |
|
| 909 |
! local Variables |
| 910 |
real( kind = dp ) :: sigma |
| 911 |
real( kind = dp ) :: sigma2 |
| 912 |
real( kind = dp ) :: sigma6 |
| 913 |
real( kind = dp ) :: epsilon |
| 914 |
|
| 915 |
real( kind = dp ) :: rcut |
| 916 |
real( kind = dp ) :: rcut2 |
| 917 |
real( kind = dp ) :: rcut6 |
| 918 |
real( kind = dp ) :: r2 |
| 919 |
real( kind = dp ) :: r6 |
| 920 |
|
| 921 |
real( kind = dp ) :: t6 |
| 922 |
real( kind = dp ) :: t12 |
| 923 |
real( kind = dp ) :: tp6 |
| 924 |
real( kind = dp ) :: tp12 |
| 925 |
real( kind = dp ) :: delta |
| 926 |
|
| 927 |
logical :: doSec = .false. |
| 928 |
|
| 929 |
integer :: errorStat |
| 930 |
|
| 931 |
!! Optional Argument Checking |
| 932 |
! Check to see if we need to do second derivatives |
| 933 |
|
| 934 |
if (present(d2)) doSec = .true. |
| 935 |
if (present(status)) status = 0 |
| 936 |
|
| 937 |
! Look up the correct parameters in the mixing matrix |
| 938 |
sigma = ljMixed(atype1%atype_ident,atype2%atype_ident)%sigma |
| 939 |
sigma2 = ljMixed(atype1%atype_ident,atype2%atype_ident)%sigma2 |
| 940 |
sigma6 = ljMixed(atype1%atype_ident,atype2%atype_ident)%sigma6 |
| 941 |
epsilon = ljMixed(atype1%atype_ident,atype2%atype_ident)%epsilon |
| 942 |
|
| 943 |
|
| 944 |
|
| 945 |
call getRcut(rcut,rcut2=rcut2,rcut6=rcut6,status=errorStat) |
| 946 |
|
| 947 |
r2 = r * r |
| 948 |
r6 = r2 * r2 * r2 |
| 949 |
|
| 950 |
t6 = sigma6/ r6 |
| 951 |
t12 = t6 * t6 |
| 952 |
|
| 953 |
|
| 954 |
|
| 955 |
tp6 = sigma6 / rcut6 |
| 956 |
tp12 = tp6*tp6 |
| 957 |
|
| 958 |
delta = -4.0E0_DP*epsilon * (tp12 - tp6) |
| 959 |
|
| 960 |
if (r.le.rcut) then |
| 961 |
pot = 4.0E0_DP * epsilon * (t12 - t6) + delta |
| 962 |
dudr = 24.0E0_DP * epsilon * (t6 - 2.0E0_DP*t12) / r |
| 963 |
if(doSec) d2 = 24.0E0_DP * epsilon * (26.0E0_DP*t12 - 7.0E0_DP*t6)/r/r |
| 964 |
else |
| 965 |
pot = 0.0E0_DP |
| 966 |
dudr = 0.0E0_DP |
| 967 |
if(doSec) d2 = 0.0E0_DP |
| 968 |
endif |
| 969 |
|
| 970 |
return |
| 971 |
|
| 972 |
|
| 973 |
|
| 974 |
end subroutine getLjPot |
| 975 |
|
| 976 |
|
| 977 |
!! Calculates the mixing for sigma or epslon based on character string for initialzition of mixing array. |
| 978 |
function calcLJMix(thisParam,param1,param2,status) result(myMixParam) |
| 979 |
character(len=*) :: thisParam |
| 980 |
real(kind = dp) :: param1 |
| 981 |
real(kind = dp) :: param2 |
| 982 |
real(kind = dp ) :: myMixParam |
| 983 |
integer, optional :: status |
| 984 |
|
| 985 |
|
| 986 |
myMixParam = 0.0_dp |
| 987 |
|
| 988 |
if (present(status)) status = 0 |
| 989 |
|
| 990 |
select case (thisParam) |
| 991 |
|
| 992 |
case ("sigma") |
| 993 |
myMixParam = 0.5_dp * (param1 + param2) |
| 994 |
case ("epsilon") |
| 995 |
myMixParam = sqrt(param1 * param2) |
| 996 |
case default |
| 997 |
status = -1 |
| 998 |
end select |
| 999 |
|
| 1000 |
end function calcLJMix |
| 1001 |
|
| 1002 |
|
| 1003 |
|
| 1004 |
end module lj_ff |
