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module gb_pair |
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!! |
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!! Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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!! |
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!! The University of Notre Dame grants you ("Licensee") a |
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!! non-exclusive, royalty free, license to use, modify and |
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!! redistribute this software in source and binary code form, provided |
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!! that the following conditions are met: |
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!! |
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!! 1. Acknowledgement of the program authors must be made in any |
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!! publication of scientific results based in part on use of the |
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!! program. An acceptable form of acknowledgement is citation of |
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!! the article in which the program was described (Matthew |
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!! A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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!! J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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!! Parallel Simulation Engine for Molecular Dynamics," |
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!! J. Comput. Chem. 26, pp. 252-271 (2005)) |
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!! |
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!! 2. Redistributions of source code must retain the above copyright |
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!! notice, this list of conditions and the following disclaimer. |
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!! |
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!! 3. Redistributions in binary form must reproduce the above copyright |
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!! notice, this list of conditions and the following disclaimer in the |
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!! documentation and/or other materials provided with the |
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!! distribution. |
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!! |
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!! This software is provided "AS IS," without a warranty of any |
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!! kind. All express or implied conditions, representations and |
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!! warranties, including any implied warranty of merchantability, |
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!! fitness for a particular purpose or non-infringement, are hereby |
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!! excluded. The University of Notre Dame and its licensors shall not |
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!! be liable for any damages suffered by licensee as a result of |
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!! using, modifying or distributing the software or its |
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!! derivatives. In no event will the University of Notre Dame or its |
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!! licensors be liable for any lost revenue, profit or data, or for |
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!! direct, indirect, special, consequential, incidental or punitive |
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!! damages, however caused and regardless of the theory of liability, |
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!! arising out of the use of or inability to use software, even if the |
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!! University of Notre Dame has been advised of the possibility of |
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!! such damages. |
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!! |
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|
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|
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module gayberne |
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use force_globals |
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use definitions |
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use simulation |
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use atype_module |
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use vector_class |
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use linearalgebra |
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use status |
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use lj |
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#ifdef IS_MPI |
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use mpiSimulation |
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#endif |
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|
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implicit none |
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|
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PRIVATE |
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private |
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|
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logical, save :: gb_pair_initialized = .false. |
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real(kind=dp), save :: gb_sigma |
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real(kind=dp), save :: gb_l2b_ratio |
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real(kind=dp), save :: gb_eps |
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real(kind=dp), save :: gb_eps_ratio |
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real(kind=dp), save :: gb_mu |
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real(kind=dp), save :: gb_nu |
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#define __FORTRAN90 |
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#include "UseTheForce/DarkSide/fInteractionMap.h" |
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|
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public :: check_gb_pair_FF |
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public :: set_gb_pair_params |
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logical, save :: haveGBMap = .false. |
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logical, save :: haveMixingMap = .false. |
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real(kind=dp), save :: mu = 2.0_dp |
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real(kind=dp), save :: nu = 1.0_dp |
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|
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|
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public :: newGBtype |
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public :: complete_GB_FF |
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public :: do_gb_pair |
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public :: getGayBerneCut |
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public :: destroyGBtypes |
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|
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type :: GBtype |
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integer :: atid |
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real(kind = dp ) :: d |
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real(kind = dp ) :: l |
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real(kind = dp ) :: eps |
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real(kind = dp ) :: eps_ratio |
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real(kind = dp ) :: dw |
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logical :: isLJ |
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end type GBtype |
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|
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type, private :: GBList |
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integer :: nGBtypes = 0 |
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integer :: currentGBtype = 0 |
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type(GBtype), pointer :: GBtypes(:) => null() |
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integer, pointer :: atidToGBtype(:) => null() |
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end type GBList |
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|
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type(GBList), save :: GBMap |
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|
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type :: GBMixParameters |
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real(kind=DP) :: sigma0 |
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real(kind=DP) :: eps0 |
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real(kind=DP) :: dw |
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real(kind=DP) :: x2 |
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real(kind=DP) :: xa2 |
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real(kind=DP) :: xai2 |
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real(kind=DP) :: xp2 |
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real(kind=DP) :: xpap2 |
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real(kind=DP) :: xpapi2 |
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end type GBMixParameters |
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|
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type(GBMixParameters), dimension(:,:), allocatable :: GBMixingMap |
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|
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contains |
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|
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subroutine check_gb_pair_FF(status) |
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integer :: status |
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status = -1 |
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if (gb_pair_initialized) status = 0 |
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|
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subroutine newGBtype(c_ident, d, l, eps, eps_ratio, dw, status) |
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|
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integer, intent(in) :: c_ident |
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real( kind = dp ), intent(in) :: d, l, eps, eps_ratio, dw |
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integer, intent(out) :: status |
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|
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integer :: nGBTypes, nLJTypes, ntypes, myATID |
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integer, pointer :: MatchList(:) => null() |
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integer :: current, i |
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status = 0 |
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|
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if (.not.associated(GBMap%GBtypes)) then |
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|
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call getMatchingElementList(atypes, "is_GayBerne", .true., & |
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nGBtypes, MatchList) |
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|
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call getMatchingElementList(atypes, "is_LennardJones", .true., & |
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nLJTypes, MatchList) |
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|
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GBMap%nGBtypes = nGBtypes + nLJTypes |
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|
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allocate(GBMap%GBtypes(nGBtypes + nLJTypes)) |
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|
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ntypes = getSize(atypes) |
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|
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allocate(GBMap%atidToGBtype(ntypes)) |
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endif |
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|
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GBMap%currentGBtype = GBMap%currentGBtype + 1 |
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current = GBMap%currentGBtype |
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|
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myATID = getFirstMatchingElement(atypes, "c_ident", c_ident) |
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|
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GBMap%atidToGBtype(myATID) = current |
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GBMap%GBtypes(current)%atid = myATID |
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GBMap%GBtypes(current)%d = d |
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GBMap%GBtypes(current)%l = l |
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GBMap%GBtypes(current)%eps = eps |
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GBMap%GBtypes(current)%eps_ratio = eps_ratio |
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GBMap%GBtypes(current)%dw = dw |
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GBMap%GBtypes(current)%isLJ = .false. |
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|
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return |
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end subroutine check_gb_pair_FF |
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> |
end subroutine newGBtype |
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|
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subroutine complete_GB_FF(status) |
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integer :: status |
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integer :: i, j, l, m, lm, function_type |
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real(kind=dp) :: thisDP, sigma |
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> |
integer :: alloc_stat, iTheta, iPhi, nSteps, nAtypes, myATID, current |
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logical :: thisProperty |
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|
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status = 0 |
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if (GBMap%currentGBtype == 0) then |
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call handleError("complete_GB_FF", "No members in GBMap") |
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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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nAtypes = getSize(atypes) |
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|
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if (nAtypes == 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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! atypes comes from c side |
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do i = 1, nAtypes |
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|
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myATID = getFirstMatchingElement(atypes, 'c_ident', i) |
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call getElementProperty(atypes, myATID, "is_LennardJones", thisProperty) |
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|
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if (thisProperty) then |
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GBMap%currentGBtype = GBMap%currentGBtype + 1 |
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current = GBMap%currentGBtype |
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|
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GBMap%atidToGBtype(myATID) = current |
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GBMap%GBtypes(current)%atid = myATID |
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GBMap%GBtypes(current)%isLJ = .true. |
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GBMap%GBtypes(current)%d = getSigma(myATID) |
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GBMap%GBtypes(current)%l = GBMap%GBtypes(current)%d |
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GBMap%GBtypes(current)%eps = getEpsilon(myATID) |
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GBMap%GBtypes(current)%eps_ratio = 1.0_dp |
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GBMap%GBtypes(current)%dw = 1.0_dp |
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|
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endif |
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|
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end do |
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|
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haveGBMap = .true. |
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|
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end subroutine complete_GB_FF |
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|
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subroutine set_gb_pair_params(sigma, l2b_ratio, eps, eps_ratio, mu, nu) |
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real( kind = dp ), intent(in) :: sigma, l2b_ratio, eps, eps_ratio |
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real( kind = dp ), intent(in) :: mu, nu |
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|
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gb_sigma = sigma |
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gb_l2b_ratio = l2b_ratio |
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gb_eps = eps |
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gb_eps_ratio = eps_ratio |
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gb_mu = mu |
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gb_nu = nu |
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subroutine createGBMixingMap() |
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integer :: nGBtypes, i, j |
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real (kind = dp) :: d1, l1, e1, er1, dw1 |
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real (kind = dp) :: d2, l2, e2, er2, dw2 |
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real (kind = dp) :: er, ermu, xp, ap2 |
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|
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gb_pair_initialized = .true. |
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return |
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end subroutine set_gb_pair_params |
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if (GBMap%currentGBtype == 0) then |
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call handleError("GB", "No members in GBMap") |
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return |
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end if |
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|
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nGBtypes = GBMap%nGBtypes |
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|
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if (.not. allocated(GBMixingMap)) then |
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allocate(GBMixingMap(nGBtypes, nGBtypes)) |
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endif |
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|
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do i = 1, nGBtypes |
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|
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d1 = GBMap%GBtypes(i)%d |
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l1 = GBMap%GBtypes(i)%l |
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e1 = GBMap%GBtypes(i)%eps |
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+ |
er1 = GBMap%GBtypes(i)%eps_ratio |
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dw1 = GBMap%GBtypes(i)%dw |
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|
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do j = i, nGBtypes |
229 |
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|
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d2 = GBMap%GBtypes(j)%d |
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l2 = GBMap%GBtypes(j)%l |
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e2 = GBMap%GBtypes(j)%eps |
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+ |
er2 = GBMap%GBtypes(j)%eps_ratio |
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+ |
dw2 = GBMap%GBtypes(j)%dw |
235 |
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|
236 |
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GBMixingMap(i,j)%sigma0 = sqrt(d1*d1 + d2*d2) |
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+ |
GBMixingMap(i,j)%xa2 = (l1*l1 - d1*d1)/(l1*l1 + d2*d2) |
238 |
+ |
GBMixingMap(i,j)%xai2 = (l2*l2 - d2*d2)/(l2*l2 + d1*d1) |
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+ |
GBMixingMap(i,j)%x2 = (l1*l1 - d1*d1) * (l2*l2 - d2*d2) / & |
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+ |
((l2*l2 + d1*d1) * (l1*l1 + d2*d2)) |
241 |
+ |
|
242 |
+ |
! assumed LB mixing rules for now: |
243 |
+ |
|
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+ |
GBMixingMap(i,j)%dw = 0.5_dp * (dw1 + dw2) |
245 |
+ |
GBMixingMap(i,j)%eps0 = sqrt(e1 * e2) |
246 |
+ |
|
247 |
+ |
er = sqrt(er1 * er2) |
248 |
+ |
ermu = er**(1.0_dp / mu) |
249 |
+ |
xp = (1.0_dp - ermu) / (1.0_dp + ermu) |
250 |
+ |
ap2 = 1.0_dp / (1.0_dp + ermu) |
251 |
+ |
|
252 |
+ |
GBMixingMap(i,j)%xp2 = xp*xp |
253 |
+ |
GBMixingMap(i,j)%xpap2 = xp*ap2 |
254 |
+ |
GBMixingMap(i,j)%xpapi2 = xp/ap2 |
255 |
+ |
|
256 |
+ |
if (i.ne.j) then |
257 |
+ |
GBMixingMap(j,i)%sigma0 = GBMixingMap(i,j)%sigma0 |
258 |
+ |
GBMixingMap(j,i)%dw = GBMixingMap(i,j)%dw |
259 |
+ |
GBMixingMap(j,i)%eps0 = GBMixingMap(i,j)%eps0 |
260 |
+ |
GBMixingMap(j,i)%x2 = GBMixingMap(i,j)%x2 |
261 |
+ |
GBMixingMap(j,i)%xa2 = GBMixingMap(i,j)%xa2 |
262 |
+ |
GBMixingMap(j,i)%xai2 = GBMixingMap(i,j)%xai2 |
263 |
+ |
GBMixingMap(j,i)%xp2 = GBMixingMap(i,j)%xp2 |
264 |
+ |
GBMixingMap(j,i)%xpap2 = GBMixingMap(i,j)%xpap2 |
265 |
+ |
GBMixingMap(j,i)%xpapi2 = GBMixingMap(i,j)%xpapi2 |
266 |
+ |
endif |
267 |
+ |
enddo |
268 |
+ |
enddo |
269 |
+ |
haveMixingMap = .true. |
270 |
+ |
|
271 |
+ |
end subroutine createGBMixingMap |
272 |
+ |
|
273 |
+ |
|
274 |
+ |
!! gay berne cutoff should be a parameter in globals, this is a temporary |
275 |
+ |
!! work around - this should be fixed when gay berne is up and running |
276 |
+ |
|
277 |
+ |
function getGayBerneCut(atomID) result(cutValue) |
278 |
+ |
integer, intent(in) :: atomID |
279 |
+ |
integer :: gbt1 |
280 |
+ |
real(kind=dp) :: cutValue, l, d |
281 |
+ |
|
282 |
+ |
if (GBMap%currentGBtype == 0) then |
283 |
+ |
call handleError("GB", "No members in GBMap") |
284 |
+ |
return |
285 |
+ |
end if |
286 |
+ |
|
287 |
+ |
gbt1 = GBMap%atidToGBtype(atomID) |
288 |
+ |
l = GBMap%GBtypes(gbt1)%l |
289 |
+ |
d = GBMap%GBtypes(gbt1)%d |
290 |
+ |
cutValue = 2.5_dp*max(l,d) |
291 |
+ |
|
292 |
+ |
end function getGayBerneCut |
293 |
+ |
|
294 |
|
subroutine do_gb_pair(atom1, atom2, d, r, r2, sw, vpair, fpair, & |
295 |
< |
pot, u_l, f, t, do_pot) |
295 |
> |
pot, Amat, f, t, do_pot) |
296 |
|
|
297 |
|
integer, intent(in) :: atom1, atom2 |
298 |
< |
integer :: id1, id2 |
298 |
> |
integer :: atid1, atid2, gbt1, gbt2, id1, id2 |
299 |
|
real (kind=dp), intent(inout) :: r, r2 |
300 |
|
real (kind=dp), dimension(3), intent(in) :: d |
301 |
|
real (kind=dp), dimension(3), intent(inout) :: fpair |
302 |
|
real (kind=dp) :: pot, sw, vpair |
303 |
< |
real (kind=dp), dimension(3,nLocal) :: u_l |
303 |
> |
real (kind=dp), dimension(9,nLocal) :: Amat |
304 |
|
real (kind=dp), dimension(3,nLocal) :: f |
305 |
|
real (kind=dp), dimension(3,nLocal) :: t |
306 |
|
logical, intent(in) :: do_pot |
307 |
< |
real (kind = dp), dimension(3) :: ul1 |
64 |
< |
real (kind = dp), dimension(3) :: ul2 |
307 |
> |
real (kind = dp), dimension(3) :: ul1, ul2, rxu1, rxu2, uxu, rhat |
308 |
|
|
309 |
< |
real(kind=dp) :: chi, chiprime, emu, s2 |
310 |
< |
real(kind=dp) :: r4, rdotu1, rdotu2, u1dotu2, g, gp, gpi, gmu, gmum |
311 |
< |
real(kind=dp) :: curlyE, enu, enum, eps, dotsum, dotdiff, ds2, dd2 |
312 |
< |
real(kind=dp) :: opXdot, omXdot, opXpdot, omXpdot, pref, gfact |
313 |
< |
real(kind=dp) :: BigR, Ri, Ri2, Ri6, Ri7, Ri12, Ri13, R126, R137 |
71 |
< |
real(kind=dp) :: dru1dx, dru1dy, dru1dz |
72 |
< |
real(kind=dp) :: dru2dx, dru2dy, dru2dz |
73 |
< |
real(kind=dp) :: dBigRdx, dBigRdy, dBigRdz |
74 |
< |
real(kind=dp) :: dBigRdu1x, dBigRdu1y, dBigRdu1z |
75 |
< |
real(kind=dp) :: dBigRdu2x, dBigRdu2y, dBigRdu2z |
76 |
< |
real(kind=dp) :: dUdx, dUdy, dUdz |
77 |
< |
real(kind=dp) :: dUdu1x, dUdu1y, dUdu1z, dUdu2x, dUdu2y, dUdu2z |
78 |
< |
real(kind=dp) :: dcE, dcEdu1x, dcEdu1y, dcEdu1z, dcEdu2x, dcEdu2y, dcEdu2z |
79 |
< |
real(kind=dp) :: depsdu1x, depsdu1y, depsdu1z, depsdu2x, depsdu2y, depsdu2z |
80 |
< |
real(kind=dp) :: drdx, drdy, drdz |
81 |
< |
real(kind=dp) :: dgdx, dgdy, dgdz |
82 |
< |
real(kind=dp) :: dgdu1x, dgdu1y, dgdu1z, dgdu2x, dgdu2y, dgdu2z |
83 |
< |
real(kind=dp) :: dgpdx, dgpdy, dgpdz |
84 |
< |
real(kind=dp) :: dgpdu1x, dgpdu1y, dgpdu1z, dgpdu2x, dgpdu2y, dgpdu2z |
85 |
< |
real(kind=dp) :: line1a, line1bx, line1by, line1bz |
86 |
< |
real(kind=dp) :: line2a, line2bx, line2by, line2bz |
87 |
< |
real(kind=dp) :: line3a, line3b, line3, line3x, line3y, line3z |
88 |
< |
real(kind=dp) :: term1x, term1y, term1z, term1u1x, term1u1y, term1u1z |
89 |
< |
real(kind=dp) :: term1u2x, term1u2y, term1u2z |
90 |
< |
real(kind=dp) :: term2a, term2b, term2u1x, term2u1y, term2u1z |
91 |
< |
real(kind=dp) :: term2u2x, term2u2y, term2u2z |
92 |
< |
real(kind=dp) :: yick1, yick2, mess1, mess2 |
93 |
< |
|
94 |
< |
s2 = (gb_l2b_ratio)**2 |
95 |
< |
emu = (gb_eps_ratio)**(1.0d0/gb_mu) |
309 |
> |
real (kind = dp) :: sigma0, dw, eps0, x2, xa2, xai2, xp2, xpap2, xpapi2 |
310 |
> |
real (kind = dp) :: e1, e2, eps, sigma, s3, s03, au, bu, a, b, g, g2 |
311 |
> |
real (kind = dp) :: U, BigR, R3, R6, R7, R12, R13, H, Hp, fx, fy, fz |
312 |
> |
real (kind = dp) :: dUdr, dUda, dUdb, dUdg, pref1, pref2 |
313 |
> |
logical :: i_is_lj, j_is_lj |
314 |
|
|
315 |
< |
chi = (s2 - 1.0d0)/(s2 + 1.0d0) |
316 |
< |
chiprime = (1.0d0 - emu)/(1.0d0 + emu) |
315 |
> |
if (.not.haveMixingMap) then |
316 |
> |
call createGBMixingMap() |
317 |
> |
endif |
318 |
|
|
319 |
< |
r4 = r2*r2 |
319 |
> |
#ifdef IS_MPI |
320 |
> |
atid1 = atid_Row(atom1) |
321 |
> |
atid2 = atid_Col(atom2) |
322 |
> |
#else |
323 |
> |
atid1 = atid(atom1) |
324 |
> |
atid2 = atid(atom2) |
325 |
> |
#endif |
326 |
|
|
327 |
+ |
gbt1 = GBMap%atidToGBtype(atid1) |
328 |
+ |
gbt2 = GBMap%atidToGBtype(atid2) |
329 |
+ |
|
330 |
+ |
i_is_LJ = GBMap%GBTypes(gbt1)%isLJ |
331 |
+ |
j_is_LJ = GBMap%GBTypes(gbt2)%isLJ |
332 |
+ |
|
333 |
+ |
sigma0 = GBMixingMap(gbt1, gbt2)%sigma0 |
334 |
+ |
dw = GBMixingMap(gbt1, gbt2)%dw |
335 |
+ |
eps0 = GBMixingMap(gbt1, gbt2)%eps0 |
336 |
+ |
x2 = GBMixingMap(gbt1, gbt2)%x2 |
337 |
+ |
xa2 = GBMixingMap(gbt1, gbt2)%xa2 |
338 |
+ |
xai2 = GBMixingMap(gbt1, gbt2)%xai2 |
339 |
+ |
xp2 = GBMixingMap(gbt1, gbt2)%xp2 |
340 |
+ |
xpap2 = GBMixingMap(gbt1, gbt2)%xpap2 |
341 |
+ |
xpapi2 = GBMixingMap(gbt1, gbt2)%xpapi2 |
342 |
+ |
|
343 |
|
#ifdef IS_MPI |
344 |
< |
ul1(1) = u_l_Row(1,atom1) |
345 |
< |
ul1(2) = u_l_Row(2,atom1) |
346 |
< |
ul1(3) = u_l_Row(3,atom1) |
344 |
> |
ul1(1) = A_Row(7,atom1) |
345 |
> |
ul1(2) = A_Row(8,atom1) |
346 |
> |
ul1(3) = A_Row(9,atom1) |
347 |
|
|
348 |
< |
ul2(1) = u_l_Col(1,atom2) |
349 |
< |
ul2(2) = u_l_Col(2,atom2) |
350 |
< |
ul2(3) = u_l_Col(3,atom2) |
348 |
> |
ul2(1) = A_Col(7,atom2) |
349 |
> |
ul2(2) = A_Col(8,atom2) |
350 |
> |
ul2(3) = A_Col(9,atom2) |
351 |
|
#else |
352 |
< |
ul1(1) = u_l(1,atom1) |
353 |
< |
ul1(2) = u_l(2,atom1) |
354 |
< |
ul1(3) = u_l(3,atom1) |
355 |
< |
|
356 |
< |
ul2(1) = u_l(1,atom2) |
357 |
< |
ul2(2) = u_l(2,atom2) |
358 |
< |
ul2(3) = u_l(3,atom2) |
352 |
> |
ul1(1) = Amat(7,atom1) |
353 |
> |
ul1(2) = Amat(8,atom1) |
354 |
> |
ul1(3) = Amat(9,atom1) |
355 |
> |
|
356 |
> |
ul2(1) = Amat(7,atom2) |
357 |
> |
ul2(2) = Amat(8,atom2) |
358 |
> |
ul2(3) = Amat(9,atom2) |
359 |
|
#endif |
360 |
|
|
361 |
< |
dru1dx = ul1(1) |
362 |
< |
dru2dx = ul2(1) |
363 |
< |
dru1dy = ul1(2) |
364 |
< |
dru2dy = ul2(2) |
365 |
< |
dru1dz = ul1(3) |
366 |
< |
dru2dz = ul2(3) |
126 |
< |
|
127 |
< |
drdx = d(1) / r |
128 |
< |
drdy = d(2) / r |
129 |
< |
drdz = d(3) / r |
130 |
< |
|
131 |
< |
! do some dot products: |
132 |
< |
! NB the r in these dot products is the actual intermolecular vector, |
133 |
< |
! and is not the unit vector in that direction. |
134 |
< |
|
135 |
< |
rdotu1 = d(1)*ul1(1) + d(2)*ul1(2) + d(3)*ul1(3) |
136 |
< |
rdotu2 = d(1)*ul2(1) + d(2)*ul2(2) + d(3)*ul2(3) |
137 |
< |
u1dotu2 = ul1(1)*ul2(1) + ul1(2)*ul2(2) + ul1(3)*ul2(3) |
361 |
> |
if (i_is_LJ) then |
362 |
> |
a = 0.0_dp |
363 |
> |
ul1 = 0.0_dp |
364 |
> |
else |
365 |
> |
a = d(1)*ul1(1) + d(2)*ul1(2) + d(3)*ul1(3) |
366 |
> |
endif |
367 |
|
|
368 |
< |
! This stuff is all for the calculation of g(Chi) and dgdx |
369 |
< |
! Line numbers roughly follow the lines in equation A25 of Luckhurst |
370 |
< |
! et al. Liquid Crystals 8, 451-464 (1990). |
371 |
< |
! We note however, that there are some major typos in that Appendix |
372 |
< |
! of the Luckhurst paper, particularly in equations A23, A29 and A31 |
373 |
< |
! We have attempted to correct them below. |
145 |
< |
|
146 |
< |
dotsum = rdotu1+rdotu2 |
147 |
< |
dotdiff = rdotu1-rdotu2 |
148 |
< |
ds2 = dotsum*dotsum |
149 |
< |
dd2 = dotdiff*dotdiff |
150 |
< |
|
151 |
< |
opXdot = 1.0d0 + Chi*u1dotu2 |
152 |
< |
omXdot = 1.0d0 - Chi*u1dotu2 |
153 |
< |
opXpdot = 1.0d0 + ChiPrime*u1dotu2 |
154 |
< |
omXpdot = 1.0d0 - ChiPrime*u1dotu2 |
155 |
< |
|
156 |
< |
line1a = dotsum/opXdot |
157 |
< |
line1bx = dru1dx + dru2dx |
158 |
< |
line1by = dru1dy + dru2dy |
159 |
< |
line1bz = dru1dz + dru2dz |
160 |
< |
|
161 |
< |
line2a = dotdiff/omXdot |
162 |
< |
line2bx = dru1dx - dru2dx |
163 |
< |
line2by = dru1dy - dru2dy |
164 |
< |
line2bz = dru1dz - dru2dz |
165 |
< |
|
166 |
< |
term1x = -Chi*(line1a*line1bx + line2a*line2bx)/r2 |
167 |
< |
term1y = -Chi*(line1a*line1by + line2a*line2by)/r2 |
168 |
< |
term1z = -Chi*(line1a*line1bz + line2a*line2bz)/r2 |
169 |
< |
|
170 |
< |
line3a = ds2/opXdot |
171 |
< |
line3b = dd2/omXdot |
172 |
< |
line3 = Chi*(line3a + line3b)/r4 |
173 |
< |
line3x = d(1)*line3 |
174 |
< |
line3y = d(2)*line3 |
175 |
< |
line3z = d(3)*line3 |
176 |
< |
|
177 |
< |
dgdx = term1x + line3x |
178 |
< |
dgdy = term1y + line3y |
179 |
< |
dgdz = term1z + line3z |
368 |
> |
if (j_is_LJ) then |
369 |
> |
b = 0.0_dp |
370 |
> |
ul2 = 0.0_dp |
371 |
> |
else |
372 |
> |
b = d(1)*ul2(1) + d(2)*ul2(2) + d(3)*ul2(3) |
373 |
> |
endif |
374 |
|
|
375 |
< |
term1u1x = 2.0d0*(line1a+line2a)*d(1) |
376 |
< |
term1u1y = 2.0d0*(line1a+line2a)*d(2) |
377 |
< |
term1u1z = 2.0d0*(line1a+line2a)*d(3) |
378 |
< |
term1u2x = 2.0d0*(line1a-line2a)*d(1) |
379 |
< |
term1u2y = 2.0d0*(line1a-line2a)*d(2) |
186 |
< |
term1u2z = 2.0d0*(line1a-line2a)*d(3) |
187 |
< |
|
188 |
< |
term2a = -line3a/opXdot |
189 |
< |
term2b = line3b/omXdot |
190 |
< |
|
191 |
< |
term2u1x = Chi*ul2(1)*(term2a + term2b) |
192 |
< |
term2u1y = Chi*ul2(2)*(term2a + term2b) |
193 |
< |
term2u1z = Chi*ul2(3)*(term2a + term2b) |
194 |
< |
term2u2x = Chi*ul1(1)*(term2a + term2b) |
195 |
< |
term2u2y = Chi*ul1(2)*(term2a + term2b) |
196 |
< |
term2u2z = Chi*ul1(3)*(term2a + term2b) |
197 |
< |
|
198 |
< |
pref = -Chi*0.5d0/r2 |
375 |
> |
if (i_is_LJ.or.j_is_LJ) then |
376 |
> |
g = 0.0_dp |
377 |
> |
else |
378 |
> |
g = ul1(1)*ul2(1) + ul1(2)*ul2(2) + ul1(3)*ul2(3) |
379 |
> |
endif |
380 |
|
|
381 |
< |
dgdu1x = pref*(term1u1x+term2u1x) |
382 |
< |
dgdu1y = pref*(term1u1y+term2u1y) |
383 |
< |
dgdu1z = pref*(term1u1z+term2u1z) |
203 |
< |
dgdu2x = pref*(term1u2x+term2u2x) |
204 |
< |
dgdu2y = pref*(term1u2y+term2u2y) |
205 |
< |
dgdu2z = pref*(term1u2z+term2u2z) |
381 |
> |
au = a / r |
382 |
> |
bu = b / r |
383 |
> |
g2 = g*g |
384 |
|
|
385 |
< |
g = 1.0d0 - Chi*(line3a + line3b)/(2.0d0*r2) |
386 |
< |
|
387 |
< |
BigR = (r - gb_sigma*(g**(-0.5d0)) + gb_sigma)/gb_sigma |
388 |
< |
Ri = 1.0d0/BigR |
389 |
< |
Ri2 = Ri*Ri |
390 |
< |
Ri6 = Ri2*Ri2*Ri2 |
391 |
< |
Ri7 = Ri6*Ri |
392 |
< |
Ri12 = Ri6*Ri6 |
393 |
< |
Ri13 = Ri6*Ri7 |
385 |
> |
H = (xa2 * au + xai2 * bu - 2.0_dp*x2*au*bu*g) / (1.0_dp - x2*g2) |
386 |
> |
Hp = (xpap2*au + xpapi2*bu - 2.0_dp*xp2*au*bu*g) / (1.0_dp - xp2*g2) |
387 |
> |
sigma = sigma0 / sqrt(1.0_dp - H) |
388 |
> |
e1 = 1.0_dp / sqrt(1.0_dp - x2*g2) |
389 |
> |
e2 = 1.0_dp - Hp |
390 |
> |
eps = eps0 * (e1**nu) * (e2**mu) |
391 |
> |
BigR = dw*sigma0 / (r - sigma + dw*sigma0) |
392 |
> |
|
393 |
> |
R3 = BigR*BigR*BigR |
394 |
> |
R6 = R3*R3 |
395 |
> |
R7 = R6 * BigR |
396 |
> |
R12 = R6*R6 |
397 |
> |
R13 = R6*R7 |
398 |
|
|
399 |
< |
gfact = (g**(-1.5d0))*0.5d0 |
399 |
> |
U = 4.0_dp * eps * (R12 - R6) |
400 |
|
|
401 |
< |
dBigRdx = drdx/gb_sigma + dgdx*gfact |
402 |
< |
dBigRdy = drdy/gb_sigma + dgdy*gfact |
221 |
< |
dBigRdz = drdz/gb_sigma + dgdz*gfact |
222 |
< |
dBigRdu1x = dgdu1x*gfact |
223 |
< |
dBigRdu1y = dgdu1y*gfact |
224 |
< |
dBigRdu1z = dgdu1z*gfact |
225 |
< |
dBigRdu2x = dgdu2x*gfact |
226 |
< |
dBigRdu2y = dgdu2y*gfact |
227 |
< |
dBigRdu2z = dgdu2z*gfact |
228 |
< |
|
229 |
< |
! Now, we must do it again for g(ChiPrime) and dgpdx |
401 |
> |
s3 = sigma*sigma*sigma |
402 |
> |
s03 = sigma0*sigma0*sigma0 |
403 |
|
|
404 |
< |
line1a = dotsum/opXpdot |
405 |
< |
line2a = dotdiff/omXpdot |
406 |
< |
term1x = -ChiPrime*(line1a*line1bx + line2a*line2bx)/r2 |
407 |
< |
term1y = -ChiPrime*(line1a*line1by + line2a*line2by)/r2 |
235 |
< |
term1z = -ChiPrime*(line1a*line1bz + line2a*line2bz)/r2 |
236 |
< |
line3a = ds2/opXpdot |
237 |
< |
line3b = dd2/omXpdot |
238 |
< |
line3 = ChiPrime*(line3a + line3b)/r4 |
239 |
< |
line3x = d(1)*line3 |
240 |
< |
line3y = d(2)*line3 |
241 |
< |
line3z = d(3)*line3 |
404 |
> |
pref1 = - 8.0_dp * eps * mu * (R12 - R6) / (e2 * r) |
405 |
> |
pref2 = 8.0_dp * eps * s3 * (6.0_dp*R13 - 3.0_dp*R7) / (dw*r*s03) |
406 |
> |
|
407 |
> |
dUdr = - (pref1 * Hp + pref2 * (sigma0*sigma0*r/s3 - H)) |
408 |
|
|
409 |
< |
dgpdx = term1x + line3x |
410 |
< |
dgpdy = term1y + line3y |
245 |
< |
dgpdz = term1z + line3z |
409 |
> |
dUda = pref1 * (xpap2*au - xp2*bu*g) / (1.0_dp - xp2 * g2) & |
410 |
> |
+ pref2 * (xa2 * au - x2 *bu*g) / (1.0_dp - x2 * g2) |
411 |
|
|
412 |
< |
term1u1x = 2.0d0*(line1a+line2a)*d(1) |
413 |
< |
term1u1y = 2.0d0*(line1a+line2a)*d(2) |
249 |
< |
term1u1z = 2.0d0*(line1a+line2a)*d(3) |
250 |
< |
term1u2x = 2.0d0*(line1a-line2a)*d(1) |
251 |
< |
term1u2y = 2.0d0*(line1a-line2a)*d(2) |
252 |
< |
term1u2z = 2.0d0*(line1a-line2a)*d(3) |
253 |
< |
|
254 |
< |
term2a = -line3a/opXpdot |
255 |
< |
term2b = line3b/omXpdot |
256 |
< |
|
257 |
< |
term2u1x = ChiPrime*ul2(1)*(term2a + term2b) |
258 |
< |
term2u1y = ChiPrime*ul2(2)*(term2a + term2b) |
259 |
< |
term2u1z = ChiPrime*ul2(3)*(term2a + term2b) |
260 |
< |
term2u2x = ChiPrime*ul1(1)*(term2a + term2b) |
261 |
< |
term2u2y = ChiPrime*ul1(2)*(term2a + term2b) |
262 |
< |
term2u2z = ChiPrime*ul1(3)*(term2a + term2b) |
263 |
< |
|
264 |
< |
pref = -ChiPrime*0.5d0/r2 |
265 |
< |
|
266 |
< |
dgpdu1x = pref*(term1u1x+term2u1x) |
267 |
< |
dgpdu1y = pref*(term1u1y+term2u1y) |
268 |
< |
dgpdu1z = pref*(term1u1z+term2u1z) |
269 |
< |
dgpdu2x = pref*(term1u2x+term2u2x) |
270 |
< |
dgpdu2y = pref*(term1u2y+term2u2y) |
271 |
< |
dgpdu2z = pref*(term1u2z+term2u2z) |
272 |
< |
|
273 |
< |
gp = 1.0d0 - ChiPrime*(line3a + line3b)/(2.0d0*r2) |
274 |
< |
gmu = gp**gb_mu |
275 |
< |
gpi = 1.0d0 / gp |
276 |
< |
gmum = gmu*gpi |
277 |
< |
|
278 |
< |
! write(*,*) atom1, atom2, Chi, u1dotu2 |
279 |
< |
curlyE = 1.0d0/dsqrt(1.0d0 - Chi*Chi*u1dotu2*u1dotu2) |
412 |
> |
dUdb = pref1 * (xpapi2*bu - xp2*au*g) / (1.0_dp - xp2 * g2) & |
413 |
> |
+ pref2 * (xai2 * bu - x2 *au*g) / (1.0_dp - x2 * g2) |
414 |
|
|
415 |
< |
dcE = (curlyE**3)*Chi*Chi*u1dotu2 |
416 |
< |
|
417 |
< |
dcEdu1x = dcE*ul2(1) |
418 |
< |
dcEdu1y = dcE*ul2(2) |
419 |
< |
dcEdu1z = dcE*ul2(3) |
420 |
< |
dcEdu2x = dcE*ul1(1) |
421 |
< |
dcEdu2y = dcE*ul1(2) |
288 |
< |
dcEdu2z = dcE*ul1(3) |
289 |
< |
|
290 |
< |
enu = curlyE**gb_nu |
291 |
< |
enum = enu/curlyE |
292 |
< |
|
293 |
< |
eps = gb_eps*enu*gmu |
415 |
> |
dUdg = 4.0_dp * eps * nu * (R12 - R6) * x2 * g / (1.0_dp - x2*g2) & |
416 |
> |
+ 8.0_dp * eps * mu * (R12 - R6) * (xp2*au*bu - Hp*xp2*g) / & |
417 |
> |
(1.0_dp - xp2 * g2) / e2 & |
418 |
> |
+ 8.0_dp * eps * s3 * (3.0_dp * R7 - 6.0_dp * R13) * & |
419 |
> |
(x2 * au * bu - H * x2 * g) / (1.0_dp - x2 * g2) / (dw * s03) |
420 |
> |
|
421 |
> |
rhat = d / r |
422 |
|
|
423 |
< |
yick1 = gb_eps*enu*gb_mu*gmum |
424 |
< |
yick2 = gb_eps*gmu*gb_nu*enum |
423 |
> |
fx = -dUdr * rhat(1) - dUda * ul1(1) - dUdb * ul2(1) |
424 |
> |
fy = -dUdr * rhat(2) - dUda * ul1(2) - dUdb * ul2(2) |
425 |
> |
fx = -dUdr * rhat(3) - dUda * ul1(3) - dUdb * ul2(3) |
426 |
|
|
427 |
< |
depsdu1x = yick1*dgpdu1x + yick2*dcEdu1x |
428 |
< |
depsdu1y = yick1*dgpdu1y + yick2*dcEdu1y |
429 |
< |
depsdu1z = yick1*dgpdu1z + yick2*dcEdu1z |
430 |
< |
depsdu2x = yick1*dgpdu2x + yick2*dcEdu2x |
302 |
< |
depsdu2y = yick1*dgpdu2y + yick2*dcEdu2y |
303 |
< |
depsdu2z = yick1*dgpdu2z + yick2*dcEdu2z |
304 |
< |
|
305 |
< |
R126 = Ri12 - Ri6 |
306 |
< |
R137 = 6.0d0*Ri7 - 12.0d0*Ri13 |
307 |
< |
|
308 |
< |
mess1 = gmu*R137 |
309 |
< |
mess2 = R126*gb_mu*gmum |
310 |
< |
|
311 |
< |
dUdx = 4.0d0*gb_eps*enu*(mess1*dBigRdx + mess2*dgpdx)*sw |
312 |
< |
dUdy = 4.0d0*gb_eps*enu*(mess1*dBigRdy + mess2*dgpdy)*sw |
313 |
< |
dUdz = 4.0d0*gb_eps*enu*(mess1*dBigRdz + mess2*dgpdz)*sw |
314 |
< |
|
315 |
< |
dUdu1x = 4.0d0*(R126*depsdu1x + eps*R137*dBigRdu1x)*sw |
316 |
< |
dUdu1y = 4.0d0*(R126*depsdu1y + eps*R137*dBigRdu1y)*sw |
317 |
< |
dUdu1z = 4.0d0*(R126*depsdu1z + eps*R137*dBigRdu1z)*sw |
318 |
< |
dUdu2x = 4.0d0*(R126*depsdu2x + eps*R137*dBigRdu2x)*sw |
319 |
< |
dUdu2y = 4.0d0*(R126*depsdu2y + eps*R137*dBigRdu2y)*sw |
320 |
< |
dUdu2z = 4.0d0*(R126*depsdu2z + eps*R137*dBigRdu2z)*sw |
321 |
< |
|
427 |
> |
rxu1 = cross_product(d, ul1) |
428 |
> |
rxu2 = cross_product(d, ul2) |
429 |
> |
uxu = cross_product(ul1, ul2) |
430 |
> |
|
431 |
|
#ifdef IS_MPI |
432 |
< |
f_Row(1,atom1) = f_Row(1,atom1) + dUdx |
433 |
< |
f_Row(2,atom1) = f_Row(2,atom1) + dUdy |
434 |
< |
f_Row(3,atom1) = f_Row(3,atom1) + dUdz |
432 |
> |
f_Row(1,atom1) = f_Row(1,atom1) + fx |
433 |
> |
f_Row(2,atom1) = f_Row(2,atom1) + fy |
434 |
> |
f_Row(3,atom1) = f_Row(3,atom1) + fz |
435 |
|
|
436 |
< |
f_Col(1,atom2) = f_Col(1,atom2) - dUdx |
437 |
< |
f_Col(2,atom2) = f_Col(2,atom2) - dUdy |
438 |
< |
f_Col(3,atom2) = f_Col(3,atom2) - dUdz |
436 |
> |
f_Col(1,atom2) = f_Col(1,atom2) - fx |
437 |
> |
f_Col(2,atom2) = f_Col(2,atom2) - fy |
438 |
> |
f_Col(3,atom2) = f_Col(3,atom2) - fz |
439 |
|
|
440 |
< |
t_Row(1,atom1) = t_Row(1,atom1) - ul1(2)*dUdu1z + ul1(3)*dUdu1y |
441 |
< |
t_Row(2,atom1) = t_Row(2,atom1) - ul1(3)*dUdu1x + ul1(1)*dUdu1z |
442 |
< |
t_Row(3,atom1) = t_Row(3,atom1) - ul1(1)*dUdu1y + ul1(2)*dUdu1x |
443 |
< |
|
444 |
< |
t_Col(1,atom2) = t_Col(1,atom2) - ul2(2)*dUdu2z + ul2(3)*dUdu2y |
445 |
< |
t_Col(2,atom2) = t_Col(2,atom2) - ul2(3)*dUdu2x + ul2(1)*dUdu2z |
446 |
< |
t_Col(3,atom2) = t_Col(3,atom2) - ul2(1)*dUdu2y + ul2(2)*dUdu2x |
440 |
> |
t_Row(1,atom1) = t_Row(1,atom1) + dUda*rxu1(1) - dUdg*uxu(1) |
441 |
> |
t_Row(2,atom1) = t_Row(2,atom1) + dUda*rxu1(2) - dUdg*uxu(2) |
442 |
> |
t_Row(3,atom1) = t_Row(3,atom1) + dUda*rxu1(3) - dUdg*uxu(3) |
443 |
> |
|
444 |
> |
t_Col(1,atom2) = t_Col(1,atom2) + dUdb*rxu2(1) + dUdg*uxu(1) |
445 |
> |
t_Col(2,atom2) = t_Col(2,atom2) + dUdb*rxu2(2) + dUdg*uxu(2) |
446 |
> |
t_Col(3,atom2) = t_Col(3,atom2) + dUdb*rxu2(3) + dUdg*uxu(3) |
447 |
|
#else |
448 |
< |
f(1,atom1) = f(1,atom1) + dUdx |
449 |
< |
f(2,atom1) = f(2,atom1) + dUdy |
450 |
< |
f(3,atom1) = f(3,atom1) + dUdz |
448 |
> |
f(1,atom1) = f(1,atom1) + fx |
449 |
> |
f(2,atom1) = f(2,atom1) + fy |
450 |
> |
f(3,atom1) = f(3,atom1) + fz |
451 |
|
|
452 |
< |
f(1,atom2) = f(1,atom2) - dUdx |
453 |
< |
f(2,atom2) = f(2,atom2) - dUdy |
454 |
< |
f(3,atom2) = f(3,atom2) - dUdz |
452 |
> |
f(1,atom2) = f(1,atom2) - fx |
453 |
> |
f(2,atom2) = f(2,atom2) - fy |
454 |
> |
f(3,atom2) = f(3,atom2) - fz |
455 |
|
|
456 |
< |
t(1,atom1) = t(1,atom1) - ul1(2)*dUdu1z + ul1(3)*dUdu1y |
457 |
< |
t(2,atom1) = t(2,atom1) - ul1(3)*dUdu1x + ul1(1)*dUdu1z |
458 |
< |
t(3,atom1) = t(3,atom1) - ul1(1)*dUdu1y + ul1(2)*dUdu1x |
459 |
< |
|
460 |
< |
t(1,atom2) = t(1,atom2) - ul2(2)*dUdu2z + ul2(3)*dUdu2y |
461 |
< |
t(2,atom2) = t(2,atom2) - ul2(3)*dUdu2x + ul2(1)*dUdu2z |
462 |
< |
t(3,atom2) = t(3,atom2) - ul2(1)*dUdu2y + ul2(2)*dUdu2x |
456 |
> |
t(1,atom1) = t(1,atom1) + dUda*rxu1(1) - dUdg*uxu(1) |
457 |
> |
t(2,atom1) = t(2,atom1) + dUda*rxu1(2) - dUdg*uxu(2) |
458 |
> |
t(3,atom1) = t(3,atom1) + dUda*rxu1(3) - dUdg*uxu(3) |
459 |
> |
|
460 |
> |
t(1,atom2) = t(1,atom2) + dUdb*rxu2(1) + dUdg*uxu(1) |
461 |
> |
t(2,atom2) = t(2,atom2) + dUdb*rxu2(2) + dUdg*uxu(2) |
462 |
> |
t(3,atom2) = t(3,atom2) + dUdb*rxu2(3) + dUdg*uxu(3) |
463 |
|
#endif |
464 |
< |
|
464 |
> |
|
465 |
|
if (do_pot) then |
466 |
|
#ifdef IS_MPI |
467 |
< |
pot_row(atom1) = pot_row(atom1) + 2.0d0*eps*R126*sw |
468 |
< |
pot_col(atom2) = pot_col(atom2) + 2.0d0*eps*R126*sw |
467 |
> |
pot_row(VDW_POT,atom1) = pot_row(VDW_POT,atom1) + 0.5d0*U*sw |
468 |
> |
pot_col(VDW_POT,atom2) = pot_col(VDW_POT,atom2) + 0.5d0*U*sw |
469 |
|
#else |
470 |
< |
pot = pot + 4.0*eps*R126*sw |
470 |
> |
pot = pot + U*sw |
471 |
|
#endif |
472 |
|
endif |
473 |
< |
|
474 |
< |
vpair = vpair + 4.0*eps*R126 |
473 |
> |
|
474 |
> |
vpair = vpair + U*sw |
475 |
|
#ifdef IS_MPI |
476 |
|
id1 = AtomRowToGlobal(atom1) |
477 |
|
id2 = AtomColToGlobal(atom2) |
482 |
|
|
483 |
|
if (molMembershipList(id1) .ne. molMembershipList(id2)) then |
484 |
|
|
485 |
< |
fpair(1) = fpair(1) + dUdx |
486 |
< |
fpair(2) = fpair(2) + dUdy |
487 |
< |
fpair(3) = fpair(3) + dUdz |
485 |
> |
fpair(1) = fpair(1) + fx |
486 |
> |
fpair(2) = fpair(2) + fy |
487 |
> |
fpair(3) = fpair(3) + fz |
488 |
|
|
489 |
|
endif |
490 |
|
|
491 |
|
return |
492 |
|
end subroutine do_gb_pair |
493 |
+ |
|
494 |
+ |
subroutine destroyGBTypes() |
495 |
|
|
496 |
< |
end module gb_pair |
496 |
> |
GBMap%nGBtypes = 0 |
497 |
> |
GBMap%currentGBtype = 0 |
498 |
> |
|
499 |
> |
if (associated(GBMap%GBtypes)) then |
500 |
> |
deallocate(GBMap%GBtypes) |
501 |
> |
GBMap%GBtypes => null() |
502 |
> |
end if |
503 |
> |
|
504 |
> |
if (associated(GBMap%atidToGBtype)) then |
505 |
> |
deallocate(GBMap%atidToGBtype) |
506 |
> |
GBMap%atidToGBtype => null() |
507 |
> |
end if |
508 |
> |
|
509 |
> |
haveMixingMap = .false. |
510 |
> |
|
511 |
> |
end subroutine destroyGBTypes |
512 |
|
|
513 |
< |
|
514 |
< |
subroutine set_gb_pair_params(sigma, l2b_ratio, eps, eps_ratio, mu, nu) |
389 |
< |
use definitions, ONLY : dp |
390 |
< |
use gb_pair, ONLY : module_set_gb_pair_params => set_gb_pair_params |
391 |
< |
real( kind = dp ), intent(inout) :: sigma, l2b_ratio, eps, eps_ratio |
392 |
< |
real( kind = dp ), intent(inout) :: mu, nu |
393 |
< |
call module_set_gb_pair_params(sigma, l2b_ratio, eps, eps_ratio, mu, nu) |
394 |
< |
end subroutine set_gb_pair_params |
513 |
> |
end module gayberne |
514 |
> |
|