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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 gb_pair |
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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 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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|
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logical, save :: haveGayBerneLJMap = .false. |
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logical, save :: gb_pair_initialized = .false. |
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logical, save :: gb_lj_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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real(kind=dp), save :: lj_sigma |
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real(kind=dp), save :: lj_eps |
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real(kind=dp), save :: gb_sigma_l |
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real(kind=dp), save :: gb_eps_l |
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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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public :: do_gb_pair |
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public :: getGayBerneCut |
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!!$ public :: check_gb_lj_pair_FF |
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!!$ public :: set_gb_lj_pair_params |
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public :: do_gb_lj_pair |
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public :: createGayBerneLJMap |
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public :: destroyGayBerneTypes |
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public :: complete_GayBerne_FF |
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!!may not need |
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type, private :: LJtype |
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integer :: atid |
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real(kind=dp) :: sigma |
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real(kind=dp) :: epsilon |
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end type LJtype |
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!!may not need |
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type, private :: LJList |
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integer :: Nljtypes =0 |
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integer :: currentLJtype= 0 |
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type(LJtype), pointer :: LJtype(:) => null() |
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integer, pointer :: atidToLJtype(:) =>null() |
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end type LJList |
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|
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type(LJList), save :: LJMap |
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|
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type :: GayBerneLJ |
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!!$ integer :: atid |
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!!$ real(kind = dp ),pointer, dimension(:) :: epsil_GB =>null() |
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!!$ real(kind = dp ),pointer, dimension(:) :: sigma_GB =>null() |
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!!$ real(kind = dp ),pointer, dimension(:) :: epsilon_ratio =>null() |
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!!$ real(kind = dp ),pointer, dimension(:) :: sigma_ratio =>null() |
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!!$ real(kind = dp ),pointer, dimension(:) :: mu =>null() |
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|
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real(kind = dp ) :: sigma_l |
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real(kind = dp ) :: sigma_s |
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real(kind = dp ) :: sigma_ratio |
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real(kind = dp ) :: eps_s |
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real(kind = dp ) :: eps_l |
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real(kind = dp ) :: eps_ratio |
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integer :: c_ident |
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integer :: status |
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end type GayBerneLJ |
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|
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!!$ type, private :: gayberneLJlist |
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!!$ integer:: n_gaybernelj = 0 |
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!!$ integer:: currentgayberneLJ = 0 |
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!!$ type(GayBerneLJ),pointer :: GayBerneLJ(:) => null() |
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!!$ integer, pointer :: atidToGayBerneLJ(:) => null() |
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!!$ end type gayberneLJlist |
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|
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type(gayberneLJ), dimension(:), allocatable :: gayBerneLJMap |
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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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return |
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end subroutine check_gb_pair_FF |
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|
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!!$ subroutine check_gb_lj_pair_FF(status) |
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!!$ integer :: status |
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!!$ status = -1 |
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!!$ if (gb_lj_pair_initialized) status = 0 |
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!!$ return |
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!!$ end subroutine check_gb_lj_pair_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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integer :: ntypes, nljtypes |
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!! integer, intent(in) :: c_ident |
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integer, pointer :: MatchList(:) => null () |
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integer :: status |
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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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gb_sigma_l = gb_sigma*l2b_ratio |
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gb_eps_l = gb_eps*gb_eps_ratio |
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status = 0 |
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|
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|
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|
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|
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return |
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end subroutine set_gb_pair_params |
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|
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!!$ subroutine set_gb_lj_pair_params(sigma_gb, l2b_ratio, eps_gb, eps_ratio, mu, nu, sigma_lj, eps_lj, c_ident, status) |
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!!$ real( kind = dp ), intent(in) :: sigma_gb, l2b_ratio, eps_gb, eps_ratio, mu, nu |
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!!$ real( kind = dp ), intent(in) :: sigma_lj, eps_lj |
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!!$ integer, intent(in) :: c_ident |
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!!$ integer :: nLJTYPES, nGayBerneTypes, ntypes, current, status |
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!!$ |
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!!$ integer :: myATID |
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!!$ logical :: thisProperty |
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!!$ real(kind=dp):: fake |
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!!$ |
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!!$ status = 0 |
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!!$ |
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!!$ if(.not.associated(LJMap%Ljtype)) then |
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|
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!!$ call getMatchingElementList(atypes, "is_GayBerne", .true., & |
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!!$ nGayBerneTypes, 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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!!$ LJMap%nLJtypes = nLJTypes |
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!!$ |
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!!$ allocate(LJMap% LJtype(nLJTypes)) |
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!!$ |
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!!$ ntypes = getSize(atypes) |
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!!$ |
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!!$ allocate(LJMap%atidToLJtype(ntypes)) |
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!!$ |
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!!$ endif |
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!!$ |
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!!$ LJmap%currentLJtype = LJMap%currentLJtype + 1 |
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!!$ |
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!!$ current = LJMap%currentLJtype |
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!!$ LJMap%atidToLJtype(myATID) = current |
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!!$ myATID = getFirstMatchingElement(atypes, "c_ident", c_ident) |
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!!$ call getElementProperty(atypes, myATID, "is_LennardJones",thisProperty) |
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!!$ if(thisProperty) then |
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!!$ |
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!!$ LJMap%LJtype(current)%atid = myatid |
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!!$!!for testing |
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!!$ fake = getSigma(myATID) |
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!!$ LJMap%LJtype(current)%sigma = getSigma(myATID) |
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!!$ LJMap%LJtype(current)%epsilon = getEpsilon(myATID) |
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!!$ end if |
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|
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!!$ gb_sigma = sigma_gb |
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!!$ gb_l2b_ratio = l2b_ratio |
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!!$ gb_eps = eps_gb |
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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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!!$ |
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!!$ lj_sigma = sigma_lj |
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!!$ lj_eps = eps_lj |
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|
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!! gb_lj_pair_initialized = .true. |
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!!$ endsubroutine set_gb_lj_pair_params |
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|
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subroutine createGayBerneLJMap |
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integer :: ntypes, i, j |
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real(kind=dp) :: s1, s2, e1, e2 |
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real(kind=dp) :: sigma_s,sigma_l,eps_s, eps_l |
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|
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if(LJMap%currentLJtype == 0)then |
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call handleError("gayberneLJ", "no members in gayberneLJMap") |
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return |
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end if |
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|
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ntypes = getSize(atypes) |
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|
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if(.not.allocated(gayBerneLJMap))then |
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allocate(gayBerneLJMap(ntypes)) |
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endif |
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|
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do i = 1, ntypes |
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s1 = LJMap%LJtype(i)%sigma |
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e1 = LJMap%LJtype(i)%epsilon |
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|
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!!$ sigma_s = 0.5d0 *(s1+gb_sigma) |
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!!$ sigma_l = 0.5d0 *(s1+gb_sigma*gb_l2b_ratio) |
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sigma_s = gb_sigma |
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sigma_l = gb_sigma*gb_l2b_ratio |
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gayBerneLJMap(i)%sigma_s = sigma_s |
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gayBerneLJMap(i)%sigma_l = sigma_l |
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gayBerneLJMap(i)%sigma_ratio = sigma_l/sigma_s |
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eps_s = dsqrt(e1*gb_eps) |
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eps_l = dsqrt(e1*gb_eps_l) |
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gayBerneLJMap(i)%eps_s = eps_s |
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gayBerneLJMap(i)%eps_l = eps_l |
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gayBerneLJMap(i)%eps_ratio = eps_l/eps_s |
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enddo |
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haveGayBerneLJMap = .true. |
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gb_lj_pair_initialized = .true. |
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endsubroutine createGayBerneLJMap |
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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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function getGayBerneCut(atomID) result(cutValue) |
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integer, intent(in) :: atomID !! nah... we don't need to use this... |
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real(kind=dp) :: cutValue |
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|
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cutValue = gb_l2b_ratio*gb_sigma*2.5_dp |
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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, A, f, t, do_pot) |
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|
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integer, intent(in) :: atom1, atom2 |
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integer :: 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) :: A |
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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 |
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real (kind = dp), dimension(3) :: ul2 |
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|
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real(kind=dp) :: chi, chiprime, emu, s2 |
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real(kind=dp) :: r4, rdotu1, rdotu2, u1dotu2, g, gp, gpi, gmu, gmum |
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real(kind=dp) :: curlyE, enu, enum, eps, dotsum, dotdiff, ds2, dd2 |
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real(kind=dp) :: opXdot, omXdot, opXpdot, omXpdot, pref, gfact |
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real(kind=dp) :: BigR, Ri, Ri2, Ri6, Ri7, Ri12, Ri13, R126, R137 |
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real(kind=dp) :: dru1dx, dru1dy, dru1dz |
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real(kind=dp) :: dru2dx, dru2dy, dru2dz |
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real(kind=dp) :: dBigRdx, dBigRdy, dBigRdz |
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real(kind=dp) :: dBigRdu1x, dBigRdu1y, dBigRdu1z |
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real(kind=dp) :: dBigRdu2x, dBigRdu2y, dBigRdu2z |
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real(kind=dp) :: dUdx, dUdy, dUdz |
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real(kind=dp) :: dUdu1x, dUdu1y, dUdu1z, dUdu2x, dUdu2y, dUdu2z |
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real(kind=dp) :: dcE, dcEdu1x, dcEdu1y, dcEdu1z, dcEdu2x, dcEdu2y, dcEdu2z |
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real(kind=dp) :: depsdu1x, depsdu1y, depsdu1z, depsdu2x, depsdu2y, depsdu2z |
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real(kind=dp) :: drdx, drdy, drdz |
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real(kind=dp) :: dgdx, dgdy, dgdz |
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real(kind=dp) :: dgdu1x, dgdu1y, dgdu1z, dgdu2x, dgdu2y, dgdu2z |
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real(kind=dp) :: dgpdx, dgpdy, dgpdz |
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real(kind=dp) :: dgpdu1x, dgpdu1y, dgpdu1z, dgpdu2x, dgpdu2y, dgpdu2z |
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real(kind=dp) :: line1a, line1bx, line1by, line1bz |
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real(kind=dp) :: line2a, line2bx, line2by, line2bz |
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real(kind=dp) :: line3a, line3b, line3, line3x, line3y, line3z |
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real(kind=dp) :: term1x, term1y, term1z, term1u1x, term1u1y, term1u1z |
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real(kind=dp) :: term1u2x, term1u2y, term1u2z |
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real(kind=dp) :: term2a, term2b, term2u1x, term2u1y, term2u1z |
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real(kind=dp) :: term2u2x, term2u2y, term2u2z |
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real(kind=dp) :: yick1, yick2, mess1, mess2 |
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|
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s2 = (gb_l2b_ratio)**2 |
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emu = (gb_eps_ratio)**(1.0d0/gb_mu) |
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|
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chi = (s2 - 1.0d0)/(s2 + 1.0d0) |
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chiprime = (1.0d0 - emu)/(1.0d0 + emu) |
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|
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r4 = r2*r2 |
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|
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#ifdef IS_MPI |
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ul1(1) = A_Row(3,atom1) |
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ul1(2) = A_Row(6,atom1) |
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ul1(3) = A_Row(9,atom1) |
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|
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ul2(1) = A_Col(3,atom2) |
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ul2(2) = A_Col(6,atom2) |
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ul2(3) = A_Col(9,atom2) |
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#else |
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ul1(1) = A(3,atom1) |
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ul1(2) = A(6,atom1) |
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ul1(3) = A(9,atom1) |
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|
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ul2(1) = A(3,atom2) |
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ul2(2) = A(6,atom2) |
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ul2(3) = A(9,atom2) |
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|
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#endif |
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|
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dru1dx = ul1(1) |
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dru2dx = ul2(1) |
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dru1dy = ul1(2) |
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dru2dy = ul2(2) |
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dru1dz = ul1(3) |
344 |
dru2dz = ul2(3) |
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|
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|
347 |
|
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drdx = d(1) / r |
349 |
drdy = d(2) / r |
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drdz = d(3) / r |
351 |
|
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! do some dot products: |
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! NB the r in these dot products is the actual intermolecular vector, |
354 |
! and is not the unit vector in that direction. |
355 |
|
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rdotu1 = d(1)*ul1(1) + d(2)*ul1(2) + d(3)*ul1(3) |
357 |
rdotu2 = d(1)*ul2(1) + d(2)*ul2(2) + d(3)*ul2(3) |
358 |
u1dotu2 = ul1(1)*ul2(1) + ul1(2)*ul2(2) + ul1(3)*ul2(3) |
359 |
|
360 |
! This stuff is all for the calculation of g(Chi) and dgdx |
361 |
! Line numbers roughly follow the lines in equation A25 of Luckhurst |
362 |
! et al. Liquid Crystals 8, 451-464 (1990). |
363 |
! We note however, that there are some major typos in that Appendix |
364 |
! of the Luckhurst paper, particularly in equations A23, A29 and A31 |
365 |
! We have attempted to correct them below. |
366 |
|
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dotsum = rdotu1+rdotu2 |
368 |
dotdiff = rdotu1-rdotu2 |
369 |
ds2 = dotsum*dotsum |
370 |
dd2 = dotdiff*dotdiff |
371 |
|
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opXdot = 1.0d0 + Chi*u1dotu2 |
373 |
omXdot = 1.0d0 - Chi*u1dotu2 |
374 |
opXpdot = 1.0d0 + ChiPrime*u1dotu2 |
375 |
omXpdot = 1.0d0 - ChiPrime*u1dotu2 |
376 |
|
377 |
line1a = dotsum/opXdot |
378 |
line1bx = dru1dx + dru2dx |
379 |
line1by = dru1dy + dru2dy |
380 |
line1bz = dru1dz + dru2dz |
381 |
|
382 |
line2a = dotdiff/omXdot |
383 |
line2bx = dru1dx - dru2dx |
384 |
line2by = dru1dy - dru2dy |
385 |
line2bz = dru1dz - dru2dz |
386 |
|
387 |
term1x = -Chi*(line1a*line1bx + line2a*line2bx)/r2 |
388 |
term1y = -Chi*(line1a*line1by + line2a*line2by)/r2 |
389 |
term1z = -Chi*(line1a*line1bz + line2a*line2bz)/r2 |
390 |
|
391 |
line3a = ds2/opXdot |
392 |
line3b = dd2/omXdot |
393 |
line3 = Chi*(line3a + line3b)/r4 |
394 |
line3x = d(1)*line3 |
395 |
line3y = d(2)*line3 |
396 |
line3z = d(3)*line3 |
397 |
|
398 |
dgdx = term1x + line3x |
399 |
dgdy = term1y + line3y |
400 |
dgdz = term1z + line3z |
401 |
|
402 |
term1u1x = 2.0d0*(line1a+line2a)*d(1) |
403 |
term1u1y = 2.0d0*(line1a+line2a)*d(2) |
404 |
term1u1z = 2.0d0*(line1a+line2a)*d(3) |
405 |
term1u2x = 2.0d0*(line1a-line2a)*d(1) |
406 |
term1u2y = 2.0d0*(line1a-line2a)*d(2) |
407 |
term1u2z = 2.0d0*(line1a-line2a)*d(3) |
408 |
|
409 |
term2a = -line3a/opXdot |
410 |
term2b = line3b/omXdot |
411 |
|
412 |
term2u1x = Chi*ul2(1)*(term2a + term2b) |
413 |
term2u1y = Chi*ul2(2)*(term2a + term2b) |
414 |
term2u1z = Chi*ul2(3)*(term2a + term2b) |
415 |
term2u2x = Chi*ul1(1)*(term2a + term2b) |
416 |
term2u2y = Chi*ul1(2)*(term2a + term2b) |
417 |
term2u2z = Chi*ul1(3)*(term2a + term2b) |
418 |
|
419 |
pref = -Chi*0.5d0/r2 |
420 |
|
421 |
dgdu1x = pref*(term1u1x+term2u1x) |
422 |
dgdu1y = pref*(term1u1y+term2u1y) |
423 |
dgdu1z = pref*(term1u1z+term2u1z) |
424 |
dgdu2x = pref*(term1u2x+term2u2x) |
425 |
dgdu2y = pref*(term1u2y+term2u2y) |
426 |
dgdu2z = pref*(term1u2z+term2u2z) |
427 |
|
428 |
g = 1.0d0 - Chi*(line3a + line3b)/(2.0d0*r2) |
429 |
|
430 |
BigR = (r - gb_sigma*(g**(-0.5d0)) + gb_sigma)/gb_sigma |
431 |
Ri = 1.0d0/BigR |
432 |
Ri2 = Ri*Ri |
433 |
Ri6 = Ri2*Ri2*Ri2 |
434 |
Ri7 = Ri6*Ri |
435 |
Ri12 = Ri6*Ri6 |
436 |
Ri13 = Ri6*Ri7 |
437 |
|
438 |
gfact = (g**(-1.5d0))*0.5d0 |
439 |
|
440 |
dBigRdx = drdx/gb_sigma + dgdx*gfact |
441 |
dBigRdy = drdy/gb_sigma + dgdy*gfact |
442 |
dBigRdz = drdz/gb_sigma + dgdz*gfact |
443 |
|
444 |
dBigRdu1x = dgdu1x*gfact |
445 |
dBigRdu1y = dgdu1y*gfact |
446 |
dBigRdu1z = dgdu1z*gfact |
447 |
dBigRdu2x = dgdu2x*gfact |
448 |
dBigRdu2y = dgdu2y*gfact |
449 |
dBigRdu2z = dgdu2z*gfact |
450 |
|
451 |
! Now, we must do it again for g(ChiPrime) and dgpdx |
452 |
|
453 |
line1a = dotsum/opXpdot |
454 |
line2a = dotdiff/omXpdot |
455 |
term1x = -ChiPrime*(line1a*line1bx + line2a*line2bx)/r2 |
456 |
term1y = -ChiPrime*(line1a*line1by + line2a*line2by)/r2 |
457 |
term1z = -ChiPrime*(line1a*line1bz + line2a*line2bz)/r2 |
458 |
line3a = ds2/opXpdot |
459 |
line3b = dd2/omXpdot |
460 |
line3 = ChiPrime*(line3a + line3b)/r4 |
461 |
line3x = d(1)*line3 |
462 |
line3y = d(2)*line3 |
463 |
line3z = d(3)*line3 |
464 |
|
465 |
dgpdx = term1x + line3x |
466 |
dgpdy = term1y + line3y |
467 |
dgpdz = term1z + line3z |
468 |
|
469 |
term1u1x = 2.00d0*(line1a+line2a)*d(1) |
470 |
term1u1y = 2.00d0*(line1a+line2a)*d(2) |
471 |
term1u1z = 2.00d0*(line1a+line2a)*d(3) |
472 |
term1u2x = 2.0d0*(line1a-line2a)*d(1) |
473 |
term1u2y = 2.0d0*(line1a-line2a)*d(2) |
474 |
term1u2z = 2.0d0*(line1a-line2a)*d(3) |
475 |
|
476 |
term2a = -line3a/opXpdot |
477 |
term2b = line3b/omXpdot |
478 |
|
479 |
term2u1x = ChiPrime*ul2(1)*(term2a + term2b) |
480 |
term2u1y = ChiPrime*ul2(2)*(term2a + term2b) |
481 |
term2u1z = ChiPrime*ul2(3)*(term2a + term2b) |
482 |
term2u2x = ChiPrime*ul1(1)*(term2a + term2b) |
483 |
term2u2y = ChiPrime*ul1(2)*(term2a + term2b) |
484 |
term2u2z = ChiPrime*ul1(3)*(term2a + term2b) |
485 |
|
486 |
pref = -ChiPrime*0.5d0/r2 |
487 |
|
488 |
dgpdu1x = pref*(term1u1x+term2u1x) |
489 |
dgpdu1y = pref*(term1u1y+term2u1y) |
490 |
dgpdu1z = pref*(term1u1z+term2u1z) |
491 |
dgpdu2x = pref*(term1u2x+term2u2x) |
492 |
dgpdu2y = pref*(term1u2y+term2u2y) |
493 |
dgpdu2z = pref*(term1u2z+term2u2z) |
494 |
|
495 |
gp = 1.0d0 - ChiPrime*(line3a + line3b)/(2.0d0*r2) |
496 |
gmu = gp**gb_mu |
497 |
gpi = 1.0d0 / gp |
498 |
gmum = gmu*gpi |
499 |
|
500 |
curlyE = 1.0d0/dsqrt(1.0d0 - Chi*Chi*u1dotu2*u1dotu2) |
501 |
!!$ |
502 |
!!$ dcE = -(curlyE**3)*Chi*Chi*u1dotu2 |
503 |
dcE = (curlyE**3)*Chi*Chi*u1dotu2 |
504 |
|
505 |
dcEdu1x = dcE*ul2(1) |
506 |
dcEdu1y = dcE*ul2(2) |
507 |
dcEdu1z = dcE*ul2(3) |
508 |
dcEdu2x = dcE*ul1(1) |
509 |
dcEdu2y = dcE*ul1(2) |
510 |
dcEdu2z = dcE*ul1(3) |
511 |
|
512 |
enu = curlyE**gb_nu |
513 |
enum = enu/curlyE |
514 |
|
515 |
eps = gb_eps*enu*gmu |
516 |
|
517 |
yick1 = gb_eps*enu*gb_mu*gmum |
518 |
yick2 = gb_eps*gmu*gb_nu*enum |
519 |
|
520 |
depsdu1x = yick1*dgpdu1x + yick2*dcEdu1x |
521 |
depsdu1y = yick1*dgpdu1y + yick2*dcEdu1y |
522 |
depsdu1z = yick1*dgpdu1z + yick2*dcEdu1z |
523 |
depsdu2x = yick1*dgpdu2x + yick2*dcEdu2x |
524 |
depsdu2y = yick1*dgpdu2y + yick2*dcEdu2y |
525 |
depsdu2z = yick1*dgpdu2z + yick2*dcEdu2z |
526 |
|
527 |
R126 = Ri12 - Ri6 |
528 |
R137 = 6.0d0*Ri7 - 12.0d0*Ri13 |
529 |
|
530 |
mess1 = gmu*R137 |
531 |
mess2 = R126*gb_mu*gmum |
532 |
|
533 |
dUdx = 4.0d0*gb_eps*enu*(mess1*dBigRdx + mess2*dgpdx)*sw |
534 |
dUdy = 4.0d0*gb_eps*enu*(mess1*dBigRdy + mess2*dgpdy)*sw |
535 |
dUdz = 4.0d0*gb_eps*enu*(mess1*dBigRdz + mess2*dgpdz)*sw |
536 |
|
537 |
dUdu1x = 4.0d0*(R126*depsdu1x + eps*R137*dBigRdu1x)*sw |
538 |
dUdu1y = 4.0d0*(R126*depsdu1y + eps*R137*dBigRdu1y)*sw |
539 |
dUdu1z = 4.0d0*(R126*depsdu1z + eps*R137*dBigRdu1z)*sw |
540 |
dUdu2x = 4.0d0*(R126*depsdu2x + eps*R137*dBigRdu2x)*sw |
541 |
dUdu2y = 4.0d0*(R126*depsdu2y + eps*R137*dBigRdu2y)*sw |
542 |
dUdu2z = 4.0d0*(R126*depsdu2z + eps*R137*dBigRdu2z)*sw |
543 |
|
544 |
#ifdef IS_MPI |
545 |
f_Row(1,atom1) = f_Row(1,atom1) + dUdx |
546 |
f_Row(2,atom1) = f_Row(2,atom1) + dUdy |
547 |
f_Row(3,atom1) = f_Row(3,atom1) + dUdz |
548 |
|
549 |
f_Col(1,atom2) = f_Col(1,atom2) - dUdx |
550 |
f_Col(2,atom2) = f_Col(2,atom2) - dUdy |
551 |
f_Col(3,atom2) = f_Col(3,atom2) - dUdz |
552 |
|
553 |
t_Row(1,atom1) = t_Row(1,atom1)- ul1(3)*dUdu1y + ul1(2)*dUdu1z |
554 |
t_Row(2,atom1) = t_Row(2,atom1)- ul1(1)*dUdu1z + ul1(3)*dUdu1x |
555 |
t_Row(3,atom1) = t_Row(3,atom1)- ul1(2)*dUdu1x + ul1(1)*dUdu1y |
556 |
|
557 |
t_Col(1,atom2) = t_Col(1,atom2) - ul2(3)*dUdu2y + ul2(2)*dUdu2z |
558 |
t_Col(2,atom2) = t_Col(2,atom2) - ul2(1)*dUdu2z + ul2(3)*dUdu2x |
559 |
t_Col(3,atom2) = t_Col(3,atom2) - ul2(2)*dUdu2x + ul2(1)*dUdu2y |
560 |
#else |
561 |
f(1,atom1) = f(1,atom1) + dUdx |
562 |
f(2,atom1) = f(2,atom1) + dUdy |
563 |
f(3,atom1) = f(3,atom1) + dUdz |
564 |
|
565 |
f(1,atom2) = f(1,atom2) - dUdx |
566 |
f(2,atom2) = f(2,atom2) - dUdy |
567 |
f(3,atom2) = f(3,atom2) - dUdz |
568 |
|
569 |
t(1,atom1) = t(1,atom1)- ul1(3)*dUdu1y + ul1(2)*dUdu1z |
570 |
t(2,atom1) = t(2,atom1)- ul1(1)*dUdu1z + ul1(3)*dUdu1x |
571 |
t(3,atom1) = t(3,atom1)- ul1(2)*dUdu1x + ul1(1)*dUdu1y |
572 |
|
573 |
t(1,atom2) = t(1,atom2)- ul2(3)*dUdu2y + ul2(2)*dUdu2z |
574 |
t(2,atom2) = t(2,atom2)- ul2(1)*dUdu2z + ul2(3)*dUdu2x |
575 |
t(3,atom2) = t(3,atom2)- ul2(2)*dUdu2x + ul2(1)*dUdu2y |
576 |
#endif |
577 |
|
578 |
if (do_pot) then |
579 |
#ifdef IS_MPI |
580 |
pot_row(atom1) = pot_row(atom1) + 2.0d0*eps*R126*sw |
581 |
pot_col(atom2) = pot_col(atom2) + 2.0d0*eps*R126*sw |
582 |
#else |
583 |
pot = pot + 4.0*eps*R126*sw |
584 |
#endif |
585 |
endif |
586 |
|
587 |
vpair = vpair + 4.0*eps*R126 |
588 |
#ifdef IS_MPI |
589 |
id1 = AtomRowToGlobal(atom1) |
590 |
id2 = AtomColToGlobal(atom2) |
591 |
#else |
592 |
id1 = atom1 |
593 |
id2 = atom2 |
594 |
#endif |
595 |
|
596 |
if (molMembershipList(id1) .ne. molMembershipList(id2)) then |
597 |
|
598 |
fpair(1) = fpair(1) + dUdx |
599 |
fpair(2) = fpair(2) + dUdy |
600 |
fpair(3) = fpair(3) + dUdz |
601 |
|
602 |
endif |
603 |
|
604 |
return |
605 |
end subroutine do_gb_pair |
606 |
|
607 |
subroutine do_gb_lj_pair(atom1, atom2, d, r, r2, sw, vpair, fpair, & |
608 |
pot, A, f, t, do_pot) |
609 |
|
610 |
integer, intent(in) :: atom1, atom2 |
611 |
integer :: id1, id2 |
612 |
real (kind=dp), intent(inout) :: r, r2 |
613 |
real (kind=dp), dimension(3), intent(in) :: d |
614 |
real (kind=dp), dimension(3), intent(inout) :: fpair |
615 |
real (kind=dp) :: pot, sw, vpair |
616 |
real (kind=dp), dimension(9,nLocal) :: A |
617 |
real (kind=dp), dimension(3,nLocal) :: f |
618 |
real (kind=dp), dimension(3,nLocal) :: t |
619 |
logical, intent(in) :: do_pot |
620 |
real (kind = dp), dimension(3) :: ul |
621 |
|
622 |
!! real(kind=dp) :: lj2, s_lj2pperp2,s_perpppar2,eabnu, epspar |
623 |
real(kind=dp) :: spar, sperp, slj, par2, perp2, sc, slj2 |
624 |
real(kind=dp) :: s_par2mperp2, s_lj2ppar2 |
625 |
real(kind=dp) :: enot, eperp, epar, eab, eabf,moom, mum1 |
626 |
!! real(kind=dp) :: e_ljpperp, e_perpmpar, e_ljppar |
627 |
real(kind=dp) :: dx, dy, dz, drdx,drdy,drdz, rdotu |
628 |
!! real(kind=dp) :: ct, dctdx, dctdy, dctdz, dctdux, dctduy, dctduz |
629 |
real(kind=dp) :: mess, sab, dsabdct, eprime, deprimedct, depmudct |
630 |
real(kind=dp) :: epmu, depmudx, depmudy, depmudz |
631 |
real(kind=dp) :: depmudux, depmuduy, depmuduz |
632 |
real(kind=dp) :: BigR, dBigRdx, dBigRdy, dBigRdz |
633 |
real(kind=dp) :: dBigRdux, dBigRduy, dBigRduz |
634 |
real(kind=dp) :: dUdx, dUdy, dUdz, dUdux, dUduy, dUduz, e0 |
635 |
real(kind=dp) :: Ri, Ri3, Ri6, Ri7, Ril2, Ri13, Rl26, R137, prefactor |
636 |
real(kind=dp) :: chipoalphap2, chioalpha2, ec, epsnot |
637 |
real(kind=dp) :: drdotudx, drdotudy, drdotudz |
638 |
real(kind=dp) :: ljeps, ljsigma, sigmaratio, sigmaratioi |
639 |
integer :: ljt1, ljt2, atid1, atid2 |
640 |
logical :: thisProperty |
641 |
#ifdef IS_MPI |
642 |
atid1 = atid_Row(atom1) |
643 |
atid2 = atid_Col(atom2) |
644 |
#else |
645 |
atid1 = atid(atom1) |
646 |
atid2 = atid(atom2) |
647 |
#endif |
648 |
ri =1/r |
649 |
|
650 |
dx = d(1) |
651 |
dy = d(2) |
652 |
dz = d(3) |
653 |
|
654 |
drdx = dx *ri |
655 |
drdy = dy *ri |
656 |
drdz = dz *ri |
657 |
|
658 |
|
659 |
|
660 |
if(.not.haveGayBerneLJMap) then |
661 |
call createGayBerneLJMap() |
662 |
endif |
663 |
!!$ write(*,*) "in gbljpair" |
664 |
call getElementProperty(atypes, atid1, "is_LennardJones",thisProperty) |
665 |
!!$ write(*,*) thisProperty |
666 |
if(thisProperty.eqv..true.)then |
667 |
#ifdef IS_MPI |
668 |
ul(1) = A_Row(3,atom2) |
669 |
ul(2) = A_Row(6,atom2) |
670 |
ul(3) = A_Row(9,atom2) |
671 |
|
672 |
#else |
673 |
ul(1) = A(3,atom2) |
674 |
ul(2) = A(6,atom2) |
675 |
ul(3) = A(9,atom2) |
676 |
#endif |
677 |
|
678 |
rdotu = (dx*ul(1)+dy*ul(2)+dz*ul(3))*ri |
679 |
|
680 |
ljt1 = LJMap%atidtoLJtype(atid1) |
681 |
ljt2 = LJMap%atidtoLJtype(atid2) |
682 |
|
683 |
ljeps = LJMap%LJtype(ljt1)%epsilon |
684 |
!!$ write(*,*) "ljeps" |
685 |
!!$ write(*,*) ljeps |
686 |
drdotudx = ul(1)*ri-rdotu*dx*ri*ri |
687 |
drdotudy = ul(2)*ri-rdotu*dy*ri*ri |
688 |
drdotudz = ul(3)*ri-rdotu*dz*ri*ri |
689 |
|
690 |
|
691 |
moom = 1.0d0 / gb_mu |
692 |
mum1 = gb_mu-1 |
693 |
|
694 |
sperp = GayBerneLJMap(ljt1)%sigma_s |
695 |
spar = GayBerneLJMap(ljt1)%sigma_l |
696 |
slj = LJMap%LJtype(ljt1)%sigma |
697 |
slj2 = slj*slj |
698 |
!!$ write(*,*) "spar" |
699 |
!!$ write(*,*) sperp |
700 |
!!$ write(*,*) spar |
701 |
!! chioalpha2 = s_par2mperp2/s_lj2ppar2 |
702 |
chioalpha2 =1-((sperp+slj)*(sperp+slj))/((spar+slj)*(spar+slj)) |
703 |
sc = (sperp+slj)/2.0d0 |
704 |
|
705 |
par2 = spar*spar |
706 |
perp2 = sperp*sperp |
707 |
s_par2mperp2 = par2 - perp2 |
708 |
s_lj2ppar2 = slj2 + par2 |
709 |
|
710 |
|
711 |
!! check these ! left from old code |
712 |
!! kdaily e0 may need to be (gb_eps + lj_eps)/2 |
713 |
|
714 |
eperp = dsqrt(gb_eps*ljeps) |
715 |
epar = eperp*gb_eps_ratio |
716 |
enot = dsqrt(ljeps*eperp) |
717 |
chipoalphap2 = 1+(dsqrt(epar*ljeps)/enot)**moom |
718 |
!! to so mess matchs cleaver (eq 20) |
719 |
|
720 |
mess = 1-rdotu*rdotu*chioalpha2 |
721 |
sab = 1.0d0/dsqrt(mess) |
722 |
dsabdct = sc*sab*sab*sab*rdotu*chioalpha2 |
723 |
|
724 |
eab = 1-chipoalphap2*rdotu*rdotu |
725 |
eabf = enot*eab**gb_mu |
726 |
depmudct = -2*enot*chipoalphap2*gb_mu*rdotu*eab**mum1 |
727 |
|
728 |
|
729 |
BigR = (r - sab*sc + sc)/sc |
730 |
dBigRdx = (drdx -dsabdct*drdotudx)/sc |
731 |
dBigRdy = (drdy -dsabdct*drdotudy)/sc |
732 |
dBigRdz = (drdz -dsabdct*drdotudz)/sc |
733 |
dBigRdux = (-dsabdct*drdx)/sc |
734 |
dBigRduy = (-dsabdct*drdy)/sc |
735 |
dBigRduz = (-dsabdct*drdz)/sc |
736 |
|
737 |
depmudx = depmudct*drdotudx |
738 |
depmudy = depmudct*drdotudy |
739 |
depmudz = depmudct*drdotudz |
740 |
depmudux = depmudct*drdx |
741 |
depmuduy = depmudct*drdy |
742 |
depmuduz = depmudct*drdz |
743 |
|
744 |
Ri = 1.0d0/BigR |
745 |
Ri3 = Ri*Ri*Ri |
746 |
Ri6 = Ri3*Ri3 |
747 |
Ri7 = Ri6*Ri |
748 |
Ril2 = Ri6*Ri6 |
749 |
Ri13 = Ri6*Ri7 |
750 |
Rl26 = Ril2 - Ri6 |
751 |
R137 = 6.0d0*Ri7 - 12.0d0*Ri13 |
752 |
|
753 |
prefactor = 4.0d0 |
754 |
|
755 |
dUdx = prefactor*(eabf*R137*dBigRdx + Rl26*depmudx) |
756 |
dUdy = prefactor*(eabf*R137*dBigRdy + Rl26*depmudy) |
757 |
dUdz = prefactor*(eabf*R137*dBigRdz + Rl26*depmudz) |
758 |
dUdux = prefactor*(eabf*R137*dBigRdux + Rl26*depmudux) |
759 |
dUduy = prefactor*(eabf*R137*dBigRduy + Rl26*depmuduy) |
760 |
dUduz = prefactor*(eabf*R137*dBigRduz + Rl26*depmuduz) |
761 |
|
762 |
#ifdef IS_MPI |
763 |
f_Row(1,atom1) = f_Row(1,atom1) - dUdx |
764 |
f_Row(2,atom1) = f_Row(2,atom1) - dUdy |
765 |
f_Row(3,atom1) = f_Row(3,atom1) - dUdz |
766 |
|
767 |
f_Col(1,atom2) = f_Col(1,atom2) + dUdx |
768 |
f_Col(2,atom2) = f_Col(2,atom2) + dUdy |
769 |
f_Col(3,atom2) = f_Col(3,atom2) + dUdz |
770 |
|
771 |
t_Row(1,atom2) = t_Row(1,atom1) + ul(2)*dUdu1z - ul(3)*dUdu1y |
772 |
t_Row(2,atom2) = t_Row(2,atom1) + ul(3)*dUdu1x - ul(1)*dUdu1z |
773 |
t_Row(3,atom2) = t_Row(3,atom1) + ul(1)*dUdu1y - ul(2)*dUdu1x |
774 |
|
775 |
#else |
776 |
|
777 |
!!kdaily changed flx(gbatom) to f(1,atom1) |
778 |
f(1,atom1) = f(1,atom1) + dUdx |
779 |
f(2,atom1) = f(2,atom1) + dUdy |
780 |
f(3,atom1) = f(3,atom1) + dUdz |
781 |
|
782 |
!!kdaily changed flx(ljatom) to f(2,atom2) |
783 |
f(1,atom2) = f(1,atom2) - dUdx |
784 |
f(2,atom2) = f(2,atom2) - dUdy |
785 |
f(3,atom2) = f(3,atom2) - dUdz |
786 |
|
787 |
! torques are cross products: |
788 |
!!kdaily tlx(gbatom) to t(1, atom1)and ulx(gbatom) to u11(atom1)need mpi |
789 |
t(1,atom2) = t(1,atom2) + ul(2)*dUduz - ul(3)*dUduy |
790 |
t(2,atom2) = t(2,atom2) + ul(3)*dUdux - ul(1)*dUduz |
791 |
t(3,atom2) = t(3,atom2) + ul(1)*dUduy - ul(2)*dUdux |
792 |
|
793 |
#endif |
794 |
|
795 |
if (do_pot) then |
796 |
#ifdef IS_MPI |
797 |
pot_row(atom1) = pot_row(atom1) + 2.0d0*eps*Rl26*sw |
798 |
pot_col(atom2) = pot_col(atom2) + 2.0d0*eps*Rl26*sw |
799 |
#else |
800 |
pot = pot + prefactor*eabf*Rl26*sw |
801 |
#endif |
802 |
endif |
803 |
|
804 |
vpair = vpair + 4.0*epmu*Rl26 |
805 |
#ifdef IS_MPI |
806 |
id1 = AtomRowToGlobal(atom1) |
807 |
id2 = AtomColToGlobal(atom2) |
808 |
#else |
809 |
id1 = atom1 |
810 |
id2 = atom2 |
811 |
#endif |
812 |
|
813 |
If (Molmembershiplist(Id1) .Ne. Molmembershiplist(Id2)) Then |
814 |
|
815 |
Fpair(1) = Fpair(1) + Dudx |
816 |
Fpair(2) = Fpair(2) + Dudy |
817 |
Fpair(3) = Fpair(3) + Dudz |
818 |
|
819 |
Endif |
820 |
|
821 |
else |
822 |
!!need to do this all over but switch the gb and lj |
823 |
endif |
824 |
return |
825 |
|
826 |
end subroutine do_gb_lj_pair |
827 |
|
828 |
subroutine complete_GayBerne_FF(status) |
829 |
integer :: nLJTYPES, nGayBerneTypes, ntypes, current, status, natypes |
830 |
integer, pointer :: MatchList(:) => null () |
831 |
integer :: i |
832 |
integer :: myATID |
833 |
logical :: thisProperty |
834 |
|
835 |
if(.not.associated(LJMap%Ljtype)) then |
836 |
|
837 |
natypes = getSize(atypes) |
838 |
|
839 |
if(nAtypes == 0) then |
840 |
status = -1 |
841 |
return |
842 |
end if |
843 |
|
844 |
call getMatchingElementList(atypes, "is_LennardJones", .true., & |
845 |
nLJTypes, MatchList) |
846 |
|
847 |
LJMap%nLJtypes = nLJTypes |
848 |
|
849 |
if(nLJTypes ==0) then |
850 |
write(*,*)" you broke this thing kyle" |
851 |
return |
852 |
endif |
853 |
allocate(LJMap%LJtype(nLJTypes)) |
854 |
|
855 |
ntypes = getSize(atypes) |
856 |
|
857 |
allocate(LJMap%atidToLJtype(ntypes)) |
858 |
end if |
859 |
|
860 |
do i =1, ntypes |
861 |
|
862 |
myATID = getFirstMatchingElement(atypes, 'c_ident', i) |
863 |
call getElementProperty(atypes, myATID, "is_LennardJones",thisProperty) |
864 |
|
865 |
if(thisProperty) then |
866 |
current = LJMap%currentLJtype+1 |
867 |
LJMap%currentLJtype = current |
868 |
|
869 |
LJMap%atidToLJtype(myATID) = current |
870 |
LJMap%LJtype(current)%atid = myATid |
871 |
|
872 |
LJMap%LJtype(current)%sigma = getSigma(myATID) |
873 |
LJMap%LJtype(current)%epsilon = getEpsilon(myATID) |
874 |
endif |
875 |
|
876 |
enddo |
877 |
gb_pair_initialized = .true. |
878 |
|
879 |
end subroutine complete_GayBerne_FF |
880 |
|
881 |
subroutine destroyGayBerneTypes() |
882 |
|
883 |
LJMap%Nljtypes =0 |
884 |
LJMap%currentLJtype=0 |
885 |
if(associated(LJMap%LJtype))then |
886 |
deallocate(LJMap%LJtype) |
887 |
LJMap%LJtype => null() |
888 |
end if |
889 |
|
890 |
if(associated(LJMap%atidToLJType))then |
891 |
deallocate(LJMap%atidToLJType) |
892 |
LJMap%atidToLJType => null() |
893 |
end if |
894 |
|
895 |
!! deallocate(gayBerneLJMap) |
896 |
|
897 |
haveGayBerneLJMap = .false. |
898 |
end subroutine destroyGayBerneTypes |
899 |
|
900 |
|
901 |
|
902 |
end module gb_pair |
903 |
|