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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) / sqrt(2.0_dp) |
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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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|
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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 = 1, 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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! Cleaver paper uses sqrt of squares to get sigma0 for |
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! mixed interactions. |
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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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enddo |
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enddo |
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haveMixingMap = .true. |
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mu = getGayBerneMu() |
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nu = getGayBerneNu() |
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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) |
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integer, intent(in) :: atomID |
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integer :: gbt1 |
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real(kind=dp) :: cutValue, l, d |
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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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gbt1 = GBMap%atidToGBtype(atomID) |
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l = GBMap%GBtypes(gbt1)%l |
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d = GBMap%GBtypes(gbt1)%d |
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|
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! sigma is actually sqrt(2)*l for prolate ellipsoids |
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|
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cutValue = 2.5_dp*sqrt(2.0_dp)*max(l,d) |
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|
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end function getGayBerneCut |
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|
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subroutine do_gb_pair(atom1, atom2, d, r, r2, sw, vpair, fpair, & |
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pot, Amat, f, t, do_pot) |
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|
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integer, intent(in) :: atom1, atom2 |
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integer :: atid1, atid2, gbt1, gbt2, id1, id2 |
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real (kind=dp), intent(inout) :: r, r2 |
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real (kind=dp), dimension(3), intent(in) :: d |
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real (kind=dp), dimension(3), intent(inout) :: fpair |
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real (kind=dp) :: pot, sw, vpair |
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real (kind=dp), dimension(9,nLocal) :: Amat |
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real (kind=dp), dimension(3,nLocal) :: f |
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real (kind=dp), dimension(3,nLocal) :: t |
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logical, intent(in) :: do_pot |
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real (kind = dp), dimension(3) :: ul1, ul2, rxu1, rxu2, uxu, rhat |
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|
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real (kind = dp) :: sigma0, dw, eps0, x2, xa2, xai2, xp2, xpap2, xpapi2 |
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real (kind = dp) :: e1, e2, eps, sigma, s3, s03, au2, bu2, au, bu, a, b, g, g2 |
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real (kind = dp) :: U, BigR, R3, R6, R7, R12, R13, H, Hp, fx, fy, fz |
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real (kind = dp) :: dUdr, dUda, dUdb, dUdg, pref1, pref2 |
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logical :: i_is_lj, j_is_lj |
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|
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if (.not.haveMixingMap) then |
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call createGBMixingMap() |
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endif |
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|
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#ifdef IS_MPI |
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atid1 = atid_Row(atom1) |
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atid2 = atid_Col(atom2) |
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#else |
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atid1 = atid(atom1) |
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atid2 = atid(atom2) |
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#endif |
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|
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gbt1 = GBMap%atidToGBtype(atid1) |
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gbt2 = GBMap%atidToGBtype(atid2) |
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|
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i_is_LJ = GBMap%GBTypes(gbt1)%isLJ |
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j_is_LJ = GBMap%GBTypes(gbt2)%isLJ |
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|
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sigma0 = GBMixingMap(gbt1, gbt2)%sigma0 |
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dw = GBMixingMap(gbt1, gbt2)%dw |
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eps0 = GBMixingMap(gbt1, gbt2)%eps0 |
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x2 = GBMixingMap(gbt1, gbt2)%x2 |
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xa2 = GBMixingMap(gbt1, gbt2)%xa2 |
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xai2 = GBMixingMap(gbt1, gbt2)%xai2 |
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xp2 = GBMixingMap(gbt1, gbt2)%xp2 |
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xpap2 = GBMixingMap(gbt1, gbt2)%xpap2 |
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xpapi2 = GBMixingMap(gbt1, gbt2)%xpapi2 |
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|
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#ifdef IS_MPI |
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ul1(1) = A_Row(7,atom1) |
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ul1(2) = A_Row(8,atom1) |
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ul1(3) = A_Row(9,atom1) |
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|
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ul2(1) = A_Col(7,atom2) |
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ul2(2) = A_Col(8,atom2) |
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ul2(3) = A_Col(9,atom2) |
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#else |
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ul1(1) = Amat(7,atom1) |
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ul1(2) = Amat(8,atom1) |
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ul1(3) = Amat(9,atom1) |
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|
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ul2(1) = Amat(7,atom2) |
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ul2(2) = Amat(8,atom2) |
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ul2(3) = Amat(9,atom2) |
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#endif |
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|
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if (i_is_LJ) then |
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a = 0.0_dp |
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ul1 = 0.0_dp |
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else |
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a = d(1)*ul1(1) + d(2)*ul1(2) + d(3)*ul1(3) |
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endif |
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|
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if (j_is_LJ) then |
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b = 0.0_dp |
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ul2 = 0.0_dp |
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else |
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b = d(1)*ul2(1) + d(2)*ul2(2) + d(3)*ul2(3) |
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endif |
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|
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if (i_is_LJ.or.j_is_LJ) then |
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g = 0.0_dp |
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else |
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g = ul1(1)*ul2(1) + ul1(2)*ul2(2) + ul1(3)*ul2(3) |
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endif |
| 377 |
|
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au = a / r |
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bu = b / r |
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|
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au2 = au * au |
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bu2 = bu * bu |
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g2 = g * g |
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|
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H = (xa2 * au2 + xai2 * bu2 - 2.0_dp*x2*au*bu*g) / (1.0_dp - x2*g2) |
| 386 |
Hp = (xpap2*au2 + xpapi2*bu2 - 2.0_dp*xp2*au*bu*g) / (1.0_dp - xp2*g2) |
| 387 |
|
| 388 |
sigma = sigma0 / sqrt(1.0_dp - H) |
| 389 |
e1 = 1.0_dp / sqrt(1.0_dp - x2*g2) |
| 390 |
e2 = 1.0_dp - Hp |
| 391 |
eps = eps0 * (e1**nu) * (e2**mu) |
| 392 |
BigR = dw*sigma0 / (r - sigma + dw*sigma0) |
| 393 |
|
| 394 |
R3 = BigR*BigR*BigR |
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R6 = R3*R3 |
| 396 |
R7 = R6 * BigR |
| 397 |
R12 = R6*R6 |
| 398 |
R13 = R6*R7 |
| 399 |
|
| 400 |
U = 4.0_dp * eps * (R12 - R6) |
| 401 |
|
| 402 |
s3 = sigma*sigma*sigma |
| 403 |
s03 = sigma0*sigma0*sigma0 |
| 404 |
|
| 405 |
pref1 = - 8.0_dp * eps * mu * (R12 - R6) / (e2 * r) |
| 406 |
|
| 407 |
pref2 = 8.0_dp * eps * s3 * (6.0_dp*R13 - 3.0_dp*R7) / (dw*r*s03) |
| 408 |
|
| 409 |
dUdr = - (pref1 * Hp + pref2 * (sigma0*sigma0*r/s3 + H)) |
| 410 |
|
| 411 |
dUda = pref1 * (xpap2*au - xp2*bu*g) / (1.0_dp - xp2 * g2) & |
| 412 |
+ pref2 * (xa2 * au - x2 *bu*g) / (1.0_dp - x2 * g2) |
| 413 |
|
| 414 |
dUdb = pref1 * (xpapi2*bu - xp2*au*g) / (1.0_dp - xp2 * g2) & |
| 415 |
+ pref2 * (xai2 * bu - x2 *au*g) / (1.0_dp - x2 * g2) |
| 416 |
|
| 417 |
dUdg = 4.0_dp * eps * nu * (R12 - R6) * x2 * g / (1.0_dp - x2*g2) & |
| 418 |
+ 8.0_dp * eps * mu * (R12 - R6) * (xp2*au*bu - Hp*xp2*g) / & |
| 419 |
(1.0_dp - xp2 * g2) / e2 & |
| 420 |
+ 8.0_dp * eps * s3 * (3.0_dp * R7 - 6.0_dp * R13) * & |
| 421 |
(x2 * au * bu - H * x2 * g) / (1.0_dp - x2 * g2) / (dw * s03) |
| 422 |
|
| 423 |
|
| 424 |
rhat = d / r |
| 425 |
|
| 426 |
fx = dUdr * rhat(1) + dUda * ul1(1) + dUdb * ul2(1) |
| 427 |
fy = dUdr * rhat(2) + dUda * ul1(2) + dUdb * ul2(2) |
| 428 |
fz = dUdr * rhat(3) + dUda * ul1(3) + dUdb * ul2(3) |
| 429 |
|
| 430 |
rxu1 = cross_product(d, ul1) |
| 431 |
rxu2 = cross_product(d, ul2) |
| 432 |
uxu = cross_product(ul1, ul2) |
| 433 |
|
| 434 |
!!$ write(*,*) 'pref = ' , pref1, pref2 |
| 435 |
!!$ write(*,*) 'rxu1 = ' , rxu1(1), rxu1(2), rxu1(3) |
| 436 |
!!$ write(*,*) 'rxu2 = ' , rxu2(1), rxu2(2), rxu2(3) |
| 437 |
!!$ write(*,*) 'uxu = ' , uxu(1), uxu(2), uxu(3) |
| 438 |
!!$ write(*,*) 'dUda = ', dUda, dudb, dudg, dudr |
| 439 |
!!$ write(*,*) 'H = ', H,hp,sigma, e1, e2, BigR |
| 440 |
!!$ write(*,*) 'chi = ', xa2, xai2, x2 |
| 441 |
!!$ write(*,*) 'chip = ', xpap2, xpapi2, xp2 |
| 442 |
!!$ write(*,*) 'eps = ', eps0, e1, e2, eps |
| 443 |
!!$ write(*,*) 'U =', U, pref1, pref2 |
| 444 |
!!$ write(*,*) 'f =', fx, fy, fz |
| 445 |
!!$ write(*,*) 'au =', au, bu, g |
| 446 |
!!$ |
| 447 |
|
| 448 |
|
| 449 |
#ifdef IS_MPI |
| 450 |
f_Row(1,atom1) = f_Row(1,atom1) + fx |
| 451 |
f_Row(2,atom1) = f_Row(2,atom1) + fy |
| 452 |
f_Row(3,atom1) = f_Row(3,atom1) + fz |
| 453 |
|
| 454 |
f_Col(1,atom2) = f_Col(1,atom2) - fx |
| 455 |
f_Col(2,atom2) = f_Col(2,atom2) - fy |
| 456 |
f_Col(3,atom2) = f_Col(3,atom2) - fz |
| 457 |
|
| 458 |
t_Row(1,atom1) = t_Row(1,atom1) + dUda*rxu1(1) - dUdg*uxu(1) |
| 459 |
t_Row(2,atom1) = t_Row(2,atom1) + dUda*rxu1(2) - dUdg*uxu(2) |
| 460 |
t_Row(3,atom1) = t_Row(3,atom1) + dUda*rxu1(3) - dUdg*uxu(3) |
| 461 |
|
| 462 |
t_Col(1,atom2) = t_Col(1,atom2) + dUdb*rxu2(1) + dUdg*uxu(1) |
| 463 |
t_Col(2,atom2) = t_Col(2,atom2) + dUdb*rxu2(2) + dUdg*uxu(2) |
| 464 |
t_Col(3,atom2) = t_Col(3,atom2) + dUdb*rxu2(3) + dUdg*uxu(3) |
| 465 |
#else |
| 466 |
f(1,atom1) = f(1,atom1) + fx |
| 467 |
f(2,atom1) = f(2,atom1) + fy |
| 468 |
f(3,atom1) = f(3,atom1) + fz |
| 469 |
|
| 470 |
f(1,atom2) = f(1,atom2) - fx |
| 471 |
f(2,atom2) = f(2,atom2) - fy |
| 472 |
f(3,atom2) = f(3,atom2) - fz |
| 473 |
|
| 474 |
t(1,atom1) = t(1,atom1) + dUda*rxu1(1) - dUdg*uxu(1) |
| 475 |
t(2,atom1) = t(2,atom1) + dUda*rxu1(2) - dUdg*uxu(2) |
| 476 |
t(3,atom1) = t(3,atom1) + dUda*rxu1(3) - dUdg*uxu(3) |
| 477 |
|
| 478 |
t(1,atom2) = t(1,atom2) + dUdb*rxu2(1) + dUdg*uxu(1) |
| 479 |
t(2,atom2) = t(2,atom2) + dUdb*rxu2(2) + dUdg*uxu(2) |
| 480 |
t(3,atom2) = t(3,atom2) + dUdb*rxu2(3) + dUdg*uxu(3) |
| 481 |
#endif |
| 482 |
|
| 483 |
if (do_pot) then |
| 484 |
#ifdef IS_MPI |
| 485 |
pot_row(VDW_POT,atom1) = pot_row(VDW_POT,atom1) + 0.5d0*U*sw |
| 486 |
pot_col(VDW_POT,atom2) = pot_col(VDW_POT,atom2) + 0.5d0*U*sw |
| 487 |
#else |
| 488 |
pot = pot + U*sw |
| 489 |
#endif |
| 490 |
endif |
| 491 |
|
| 492 |
vpair = vpair + U*sw |
| 493 |
#ifdef IS_MPI |
| 494 |
id1 = AtomRowToGlobal(atom1) |
| 495 |
id2 = AtomColToGlobal(atom2) |
| 496 |
#else |
| 497 |
id1 = atom1 |
| 498 |
id2 = atom2 |
| 499 |
#endif |
| 500 |
|
| 501 |
if (molMembershipList(id1) .ne. molMembershipList(id2)) then |
| 502 |
|
| 503 |
fpair(1) = fpair(1) + fx |
| 504 |
fpair(2) = fpair(2) + fy |
| 505 |
fpair(3) = fpair(3) + fz |
| 506 |
|
| 507 |
endif |
| 508 |
|
| 509 |
return |
| 510 |
end subroutine do_gb_pair |
| 511 |
|
| 512 |
subroutine destroyGBTypes() |
| 513 |
|
| 514 |
GBMap%nGBtypes = 0 |
| 515 |
GBMap%currentGBtype = 0 |
| 516 |
|
| 517 |
if (associated(GBMap%GBtypes)) then |
| 518 |
deallocate(GBMap%GBtypes) |
| 519 |
GBMap%GBtypes => null() |
| 520 |
end if |
| 521 |
|
| 522 |
if (associated(GBMap%atidToGBtype)) then |
| 523 |
deallocate(GBMap%atidToGBtype) |
| 524 |
GBMap%atidToGBtype => null() |
| 525 |
end if |
| 526 |
|
| 527 |
haveMixingMap = .false. |
| 528 |
|
| 529 |
end subroutine destroyGBTypes |
| 530 |
|
| 531 |
end module gayberne |
| 532 |
|
