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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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use fForceOptions |
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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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|
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#define __FORTRAN90 |
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#include "UseTheForce/DarkSide/fInteractionMap.h" |
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|
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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 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 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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mu = getGayBerneMu() |
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nu = getGayBerneNu() |
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|
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|
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end subroutine complete_GB_FF |
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|
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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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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 |
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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 |
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|
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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) |
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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)) |
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|
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! assumed LB mixing rules for now: |
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|
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GBMixingMap(i,j)%dw = 0.5_dp * (dw1 + dw2) |
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GBMixingMap(i,j)%eps0 = sqrt(e1 * e2) |
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|
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er = sqrt(er1 * er2) |
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ermu = er**(1.0_dp / mu) |
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xp = (1.0_dp - ermu) / (1.0_dp + ermu) |
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ap2 = 1.0_dp / (1.0_dp + ermu) |
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|
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GBMixingMap(i,j)%xp2 = xp*xp |
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GBMixingMap(i,j)%xpap2 = xp*ap2 |
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GBMixingMap(i,j)%xpapi2 = xp/ap2 |
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|
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if (i.ne.j) then |
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GBMixingMap(j,i)%sigma0 = GBMixingMap(i,j)%sigma0 |
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GBMixingMap(j,i)%dw = GBMixingMap(i,j)%dw |
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GBMixingMap(j,i)%eps0 = GBMixingMap(i,j)%eps0 |
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GBMixingMap(j,i)%x2 = GBMixingMap(i,j)%x2 |
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GBMixingMap(j,i)%xa2 = GBMixingMap(i,j)%xa2 |
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GBMixingMap(j,i)%xai2 = GBMixingMap(i,j)%xai2 |
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GBMixingMap(j,i)%xp2 = GBMixingMap(i,j)%xp2 |
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GBMixingMap(j,i)%xpap2 = GBMixingMap(i,j)%xpap2 |
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GBMixingMap(j,i)%xpapi2 = GBMixingMap(i,j)%xpapi2 |
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endif |
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enddo |
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enddo |
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haveMixingMap = .true. |
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|
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end subroutine createGBMixingMap |
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|
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|
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!! gay berne cutoff should be a parameter in globals, this is a temporary |
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!! work around - this should be fixed when gay berne is up and running |
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|
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function getGayBerneCut(atomID) result(cutValue) |
283 |
integer, intent(in) :: atomID |
284 |
integer :: gbt1 |
285 |
real(kind=dp) :: cutValue, l, d |
286 |
|
287 |
if (GBMap%currentGBtype == 0) then |
288 |
call handleError("GB", "No members in GBMap") |
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return |
290 |
end if |
291 |
|
292 |
gbt1 = GBMap%atidToGBtype(atomID) |
293 |
l = GBMap%GBtypes(gbt1)%l |
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d = GBMap%GBtypes(gbt1)%d |
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cutValue = 2.5_dp*max(l,d) |
296 |
|
297 |
end function getGayBerneCut |
298 |
|
299 |
subroutine do_gb_pair(atom1, atom2, d, r, r2, sw, vpair, fpair, & |
300 |
pot, Amat, f, t, do_pot) |
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|
302 |
integer, intent(in) :: atom1, atom2 |
303 |
integer :: atid1, atid2, gbt1, gbt2, id1, id2 |
304 |
real (kind=dp), intent(inout) :: r, r2 |
305 |
real (kind=dp), dimension(3), intent(in) :: d |
306 |
real (kind=dp), dimension(3), intent(inout) :: fpair |
307 |
real (kind=dp) :: pot, sw, vpair |
308 |
real (kind=dp), dimension(9,nLocal) :: Amat |
309 |
real (kind=dp), dimension(3,nLocal) :: f |
310 |
real (kind=dp), dimension(3,nLocal) :: t |
311 |
logical, intent(in) :: do_pot |
312 |
real (kind = dp), dimension(3) :: ul1, ul2, rxu1, rxu2, uxu, rhat |
313 |
|
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real (kind = dp) :: sigma0, dw, eps0, x2, xa2, xai2, xp2, xpap2, xpapi2 |
315 |
real (kind = dp) :: e1, e2, eps, sigma, s3, s03, au, bu, a, b, g, g2 |
316 |
real (kind = dp) :: U, BigR, R3, R6, R7, R12, R13, H, Hp, fx, fy, fz |
317 |
real (kind = dp) :: dUdr, dUda, dUdb, dUdg, pref1, pref2 |
318 |
logical :: i_is_lj, j_is_lj |
319 |
|
320 |
if (.not.haveMixingMap) then |
321 |
call createGBMixingMap() |
322 |
endif |
323 |
|
324 |
#ifdef IS_MPI |
325 |
atid1 = atid_Row(atom1) |
326 |
atid2 = atid_Col(atom2) |
327 |
#else |
328 |
atid1 = atid(atom1) |
329 |
atid2 = atid(atom2) |
330 |
#endif |
331 |
|
332 |
gbt1 = GBMap%atidToGBtype(atid1) |
333 |
gbt2 = GBMap%atidToGBtype(atid2) |
334 |
|
335 |
i_is_LJ = GBMap%GBTypes(gbt1)%isLJ |
336 |
j_is_LJ = GBMap%GBTypes(gbt2)%isLJ |
337 |
|
338 |
sigma0 = GBMixingMap(gbt1, gbt2)%sigma0 |
339 |
dw = GBMixingMap(gbt1, gbt2)%dw |
340 |
eps0 = GBMixingMap(gbt1, gbt2)%eps0 |
341 |
x2 = GBMixingMap(gbt1, gbt2)%x2 |
342 |
xa2 = GBMixingMap(gbt1, gbt2)%xa2 |
343 |
xai2 = GBMixingMap(gbt1, gbt2)%xai2 |
344 |
xp2 = GBMixingMap(gbt1, gbt2)%xp2 |
345 |
xpap2 = GBMixingMap(gbt1, gbt2)%xpap2 |
346 |
xpapi2 = GBMixingMap(gbt1, gbt2)%xpapi2 |
347 |
|
348 |
#ifdef IS_MPI |
349 |
ul1(1) = A_Row(7,atom1) |
350 |
ul1(2) = A_Row(8,atom1) |
351 |
ul1(3) = A_Row(9,atom1) |
352 |
|
353 |
ul2(1) = A_Col(7,atom2) |
354 |
ul2(2) = A_Col(8,atom2) |
355 |
ul2(3) = A_Col(9,atom2) |
356 |
#else |
357 |
ul1(1) = Amat(7,atom1) |
358 |
ul1(2) = Amat(8,atom1) |
359 |
ul1(3) = Amat(9,atom1) |
360 |
|
361 |
ul2(1) = Amat(7,atom2) |
362 |
ul2(2) = Amat(8,atom2) |
363 |
ul2(3) = Amat(9,atom2) |
364 |
#endif |
365 |
|
366 |
if (i_is_LJ) then |
367 |
a = 0.0_dp |
368 |
ul1 = 0.0_dp |
369 |
else |
370 |
a = d(1)*ul1(1) + d(2)*ul1(2) + d(3)*ul1(3) |
371 |
endif |
372 |
|
373 |
if (j_is_LJ) then |
374 |
b = 0.0_dp |
375 |
ul2 = 0.0_dp |
376 |
else |
377 |
b = d(1)*ul2(1) + d(2)*ul2(2) + d(3)*ul2(3) |
378 |
endif |
379 |
|
380 |
if (i_is_LJ.or.j_is_LJ) then |
381 |
g = 0.0_dp |
382 |
else |
383 |
g = ul1(1)*ul2(1) + ul1(2)*ul2(2) + ul1(3)*ul2(3) |
384 |
endif |
385 |
|
386 |
au = a / r |
387 |
bu = b / r |
388 |
g2 = g*g |
389 |
|
390 |
H = (xa2 * au + xai2 * bu - 2.0_dp*x2*au*bu*g) / (1.0_dp - x2*g2) |
391 |
Hp = (xpap2*au + xpapi2*bu - 2.0_dp*xp2*au*bu*g) / (1.0_dp - xp2*g2) |
392 |
sigma = sigma0 / sqrt(1.0_dp - H) |
393 |
e1 = 1.0_dp / sqrt(1.0_dp - x2*g2) |
394 |
e2 = 1.0_dp - Hp |
395 |
eps = eps0 * (e1**nu) * (e2**mu) |
396 |
BigR = dw*sigma0 / (r - sigma + dw*sigma0) |
397 |
|
398 |
R3 = BigR*BigR*BigR |
399 |
R6 = R3*R3 |
400 |
R7 = R6 * BigR |
401 |
R12 = R6*R6 |
402 |
R13 = R6*R7 |
403 |
|
404 |
U = 4.0_dp * eps * (R12 - R6) |
405 |
|
406 |
s3 = sigma*sigma*sigma |
407 |
s03 = sigma0*sigma0*sigma0 |
408 |
|
409 |
pref1 = - 8.0_dp * eps * mu * (R12 - R6) / (e2 * r) |
410 |
pref2 = 8.0_dp * eps * s3 * (6.0_dp*R13 - 3.0_dp*R7) / (dw*r*s03) |
411 |
|
412 |
dUdr = - (pref1 * Hp + pref2 * (sigma0*sigma0*r/s3 - H)) |
413 |
|
414 |
dUda = pref1 * (xpap2*au - xp2*bu*g) / (1.0_dp - xp2 * g2) & |
415 |
+ pref2 * (xa2 * au - x2 *bu*g) / (1.0_dp - x2 * g2) |
416 |
|
417 |
dUdb = pref1 * (xpapi2*bu - xp2*au*g) / (1.0_dp - xp2 * g2) & |
418 |
+ pref2 * (xai2 * bu - x2 *au*g) / (1.0_dp - x2 * g2) |
419 |
|
420 |
dUdg = 4.0_dp * eps * nu * (R12 - R6) * x2 * g / (1.0_dp - x2*g2) & |
421 |
+ 8.0_dp * eps * mu * (R12 - R6) * (xp2*au*bu - Hp*xp2*g) / & |
422 |
(1.0_dp - xp2 * g2) / e2 & |
423 |
+ 8.0_dp * eps * s3 * (3.0_dp * R7 - 6.0_dp * R13) * & |
424 |
(x2 * au * bu - H * x2 * g) / (1.0_dp - x2 * g2) / (dw * s03) |
425 |
|
426 |
rhat = d / r |
427 |
|
428 |
fx = -dUdr * rhat(1) - dUda * ul1(1) - dUdb * ul2(1) |
429 |
fy = -dUdr * rhat(2) - dUda * ul1(2) - dUdb * ul2(2) |
430 |
fx = -dUdr * rhat(3) - dUda * ul1(3) - dUdb * ul2(3) |
431 |
|
432 |
rxu1 = cross_product(d, ul1) |
433 |
rxu2 = cross_product(d, ul2) |
434 |
uxu = cross_product(ul1, ul2) |
435 |
|
436 |
#ifdef IS_MPI |
437 |
f_Row(1,atom1) = f_Row(1,atom1) + fx |
438 |
f_Row(2,atom1) = f_Row(2,atom1) + fy |
439 |
f_Row(3,atom1) = f_Row(3,atom1) + fz |
440 |
|
441 |
f_Col(1,atom2) = f_Col(1,atom2) - fx |
442 |
f_Col(2,atom2) = f_Col(2,atom2) - fy |
443 |
f_Col(3,atom2) = f_Col(3,atom2) - fz |
444 |
|
445 |
t_Row(1,atom1) = t_Row(1,atom1) + dUda*rxu1(1) - dUdg*uxu(1) |
446 |
t_Row(2,atom1) = t_Row(2,atom1) + dUda*rxu1(2) - dUdg*uxu(2) |
447 |
t_Row(3,atom1) = t_Row(3,atom1) + dUda*rxu1(3) - dUdg*uxu(3) |
448 |
|
449 |
t_Col(1,atom2) = t_Col(1,atom2) + dUdb*rxu2(1) + dUdg*uxu(1) |
450 |
t_Col(2,atom2) = t_Col(2,atom2) + dUdb*rxu2(2) + dUdg*uxu(2) |
451 |
t_Col(3,atom2) = t_Col(3,atom2) + dUdb*rxu2(3) + dUdg*uxu(3) |
452 |
#else |
453 |
f(1,atom1) = f(1,atom1) + fx |
454 |
f(2,atom1) = f(2,atom1) + fy |
455 |
f(3,atom1) = f(3,atom1) + fz |
456 |
|
457 |
f(1,atom2) = f(1,atom2) - fx |
458 |
f(2,atom2) = f(2,atom2) - fy |
459 |
f(3,atom2) = f(3,atom2) - fz |
460 |
|
461 |
t(1,atom1) = t(1,atom1) + dUda*rxu1(1) - dUdg*uxu(1) |
462 |
t(2,atom1) = t(2,atom1) + dUda*rxu1(2) - dUdg*uxu(2) |
463 |
t(3,atom1) = t(3,atom1) + dUda*rxu1(3) - dUdg*uxu(3) |
464 |
|
465 |
t(1,atom2) = t(1,atom2) + dUdb*rxu2(1) + dUdg*uxu(1) |
466 |
t(2,atom2) = t(2,atom2) + dUdb*rxu2(2) + dUdg*uxu(2) |
467 |
t(3,atom2) = t(3,atom2) + dUdb*rxu2(3) + dUdg*uxu(3) |
468 |
#endif |
469 |
|
470 |
if (do_pot) then |
471 |
#ifdef IS_MPI |
472 |
pot_row(VDW_POT,atom1) = pot_row(VDW_POT,atom1) + 0.5d0*U*sw |
473 |
pot_col(VDW_POT,atom2) = pot_col(VDW_POT,atom2) + 0.5d0*U*sw |
474 |
#else |
475 |
pot = pot + U*sw |
476 |
#endif |
477 |
endif |
478 |
|
479 |
vpair = vpair + U*sw |
480 |
#ifdef IS_MPI |
481 |
id1 = AtomRowToGlobal(atom1) |
482 |
id2 = AtomColToGlobal(atom2) |
483 |
#else |
484 |
id1 = atom1 |
485 |
id2 = atom2 |
486 |
#endif |
487 |
|
488 |
if (molMembershipList(id1) .ne. molMembershipList(id2)) then |
489 |
|
490 |
fpair(1) = fpair(1) + fx |
491 |
fpair(2) = fpair(2) + fy |
492 |
fpair(3) = fpair(3) + fz |
493 |
|
494 |
endif |
495 |
|
496 |
return |
497 |
end subroutine do_gb_pair |
498 |
|
499 |
subroutine destroyGBTypes() |
500 |
|
501 |
GBMap%nGBtypes = 0 |
502 |
GBMap%currentGBtype = 0 |
503 |
|
504 |
if (associated(GBMap%GBtypes)) then |
505 |
deallocate(GBMap%GBtypes) |
506 |
GBMap%GBtypes => null() |
507 |
end if |
508 |
|
509 |
if (associated(GBMap%atidToGBtype)) then |
510 |
deallocate(GBMap%atidToGBtype) |
511 |
GBMap%atidToGBtype => null() |
512 |
end if |
513 |
|
514 |
haveMixingMap = .false. |
515 |
|
516 |
end subroutine destroyGBTypes |
517 |
|
518 |
end module gayberne |
519 |
|