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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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!! Calculates Long Range forces Lennard-Jones interactions. |
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!! Corresponds to the force field defined in lj_FF.cpp |
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!! @author Charles F. Vardeman II |
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!! @author Matthew Meineke |
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< |
!! @version $Id: LJ.F90,v 1.2 2004-10-21 15:25:30 chuckv Exp $, $Date: 2004-10-21 15:25:30 $, $Name: not supported by cvs2svn $, $Revision: 1.2 $ |
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!! @version $Id: LJ.F90,v 1.7 2005-01-14 20:31:16 gezelter Exp $, $Date: 2005-01-14 20:31:16 $, $Name: not supported by cvs2svn $, $Revision: 1.7 $ |
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module lj |
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use atype_module |
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use switcheroo |
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use vector_class |
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use simulation |
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use status |
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#ifdef IS_MPI |
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use mpiSimulation |
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#endif |
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PRIVATE |
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integer, parameter :: DP = selected_real_kind(15) |
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|
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#define __FORTRAN90 |
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#include "UseTheForce/fForceField.h" |
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– |
|
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integer, save :: LJ_Mixing_Policy |
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real(kind=DP), save :: LJ_rcut |
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logical, save :: havePolicy = .false. |
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logical, save :: haveCut = .false. |
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logical, save :: LJ_do_shift = .false. |
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|
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< |
!! Logical has lj force field module been initialized? |
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> |
type, private :: LjType |
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> |
integer :: c_ident |
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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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|
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logical, save :: LJ_FF_initialized = .false. |
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> |
type(LjType), dimension(:), allocatable :: ParameterMap |
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|
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!! Public methods and data |
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public :: init_LJ_FF |
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public :: setCutoffLJ |
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public :: do_lj_pair |
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public :: newLJtype |
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> |
logical, save :: haveMixingMap = .false. |
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|
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!! structure for lj type parameters |
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type, private :: ljType |
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integer :: lj_ident |
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real(kind=dp) :: lj_sigma |
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real(kind=dp) :: lj_epsilon |
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end type ljType |
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> |
type :: MixParameters |
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real(kind=DP) :: sigma |
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real(kind=DP) :: epsilon |
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real(kind=dp) :: sigma6 |
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real(kind=dp) :: tp6 |
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real(kind=dp) :: tp12 |
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real(kind=dp) :: delta |
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end type MixParameters |
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|
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!! List of lj type parameters |
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type, private :: ljTypeList |
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integer :: n_lj_types = 0 |
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integer :: currentAddition = 0 |
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type(ljType), pointer :: ljParams(:) => null() |
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end type ljTypeList |
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type(MixParameters), dimension(:,:), allocatable :: MixingMap |
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|
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!! The list of lj Parameters |
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type (ljTypeList), save :: ljParameterList |
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> |
real(kind=DP), save :: LJ_rcut |
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logical, save :: have_rcut = .false. |
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logical, save :: LJ_do_shift = .false. |
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logical, save :: useGeometricDistanceMixing = .false. |
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|
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!! Public methods and data |
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|
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public :: setCutoffLJ |
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public :: useGeometricMixing |
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public :: do_lj_pair |
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public :: newLJtype |
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public :: getSigma |
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public :: getEpsilon |
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|
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type :: lj_mixed_params |
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!! Lennard-Jones epsilon |
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real ( kind = dp ) :: epsilon = 0.0_dp |
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!! Lennard-Jones Sigma |
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real ( kind = dp ) :: sigma = 0.0_dp |
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!! Lennard-Jones Sigma to sixth |
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real ( kind = dp ) :: sigma6 = 0.0_dp |
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!! |
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real ( kind = dp ) :: tp6 |
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real ( kind = dp ) :: tp12 |
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real ( kind = dp ) :: delta = 0.0_dp |
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end type lj_mixed_params |
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|
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type (lj_mixed_params), dimension(:,:), pointer :: ljMixed |
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|
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|
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|
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contains |
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subroutine newLJtype(ident,lj_sigma,lj_epsilon,status) |
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integer,intent(in) :: ident |
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real(kind=dp),intent(in) :: lj_sigma |
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real(kind=dp),intent(in) :: lj_epsilon |
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subroutine newLJtype(c_ident, sigma, epsilon, status) |
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integer,intent(in) :: c_ident |
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real(kind=dp),intent(in) :: sigma |
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real(kind=dp),intent(in) :: epsilon |
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integer,intent(out) :: status |
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|
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integer,pointer :: Matchlist(:) => null() |
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integer :: current |
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integer :: nAtypes |
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integer :: nATypes, myATID |
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integer, pointer :: MatchList(:) => null() |
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|
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status = 0 |
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|
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!! Assume that atypes has already been set and get the total number of types in atypes |
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|
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|
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myATID = getFirstMatchingElement(atypes, "c_ident", c_ident) |
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|
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! check to see if this is the first time into |
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if (.not.associated(ljParameterList%ljParams)) then |
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call getMatchingElementList(atypes, "is_lj", .true., nAtypes, MatchList) |
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ljParameterList%n_lj_types = nAtypes |
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if (.not.allocated(ParameterMap)) then |
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|
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!call getMatchingElementList(atypes, "is_LennardJones", .true., & |
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! nLJTypes, MatchList) |
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nAtypes = getSize(atypes) |
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if (nAtypes == 0) then |
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status = -1 |
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return |
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status = -1 |
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return |
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end if |
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< |
allocate(ljParameterList%ljParams(nAtypes)) |
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|
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if (.not. allocated(ParameterMap)) then |
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allocate(ParameterMap(nAtypes)) |
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endif |
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|
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end if |
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|
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ljParameterList%currentAddition = ljParameterList%currentAddition + 1 |
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current = ljParameterList%currentAddition |
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if (myATID .gt. size(ParameterMap)) then |
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status = -1 |
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return |
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endif |
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! set the values for ljParameterList |
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ljParameterList%ljParams(current)%lj_ident = ident |
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ljParameterList%ljParams(current)%lj_epsilon = lj_epsilon |
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ljParameterList%ljParams(current)%lj_sigma = lj_sigma |
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! set the values for ParameterMap for this atom type: |
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|
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ParameterMap(myATID)%c_ident = c_ident |
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ParameterMap(myATID)%atid = myATID |
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ParameterMap(myATID)%epsilon = epsilon |
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ParameterMap(myATID)%sigma = sigma |
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end subroutine newLJtype |
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|
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subroutine init_LJ_FF(mix_Policy, status) |
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integer, intent(in) :: mix_Policy |
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integer, intent(out) :: status |
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integer :: myStatus |
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|
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function getSigma(atid) result (s) |
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integer, intent(in) :: atid |
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integer :: localError |
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real(kind=dp) :: s |
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|
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< |
if (mix_Policy == LB_MIXING_RULE) then |
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LJ_Mixing_Policy = LB_MIXING_RULE |
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else |
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if (mix_Policy == EXPLICIT_MIXING_RULE) then |
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LJ_Mixing_Policy = EXPLICIT_MIXING_RULE |
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else |
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write(*,*) 'Unknown Mixing Policy!' |
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status = -1 |
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return |
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endif |
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endif |
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if (.not.allocated(ParameterMap)) then |
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call handleError("LJ", "no ParameterMap was present before first call of getSigma!") |
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return |
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end if |
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|
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s = ParameterMap(atid)%sigma |
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end function getSigma |
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< |
havePolicy = .true. |
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|
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< |
if (haveCut) then |
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status = 0 |
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< |
call createMixingList(myStatus) |
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if (myStatus /= 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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< |
LJ_FF_initialized = .true. |
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> |
function getEpsilon(atid) result (e) |
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integer, intent(in) :: atid |
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> |
integer :: localError |
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> |
real(kind=dp) :: e |
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> |
|
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> |
if (.not.allocated(ParameterMap)) then |
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> |
call handleError("LJ", "no ParameterMap was present before first call of getEpsilon!") |
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return |
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end if |
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< |
|
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< |
end subroutine init_LJ_FF |
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|
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> |
|
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e = ParameterMap(atid)%epsilon |
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> |
end function getEpsilon |
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> |
|
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|
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subroutine setCutoffLJ(rcut, do_shift, status) |
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logical, intent(in):: do_shift |
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integer :: status, myStatus |
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LJ_rcut = rcut |
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LJ_do_shift = do_shift |
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call set_switch(LJ_SWITCH, rcut, rcut) |
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< |
haveCut = .true. |
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< |
|
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< |
if (havePolicy) then |
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< |
status = 0 |
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< |
call createMixingList(myStatus) |
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< |
if (myStatus /= 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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< |
LJ_FF_initialized = .true. |
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< |
end if |
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> |
have_rcut = .true. |
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|
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return |
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end subroutine setCutoffLJ |
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+ |
|
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subroutine useGeometricMixing() |
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useGeometricDistanceMixing = .true. |
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+ |
haveMixingMap = .false. |
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+ |
return |
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+ |
end subroutine useGeometricMixing |
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|
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< |
subroutine createMixingList(status) |
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< |
integer :: nAtypes |
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> |
subroutine createMixingMap(status) |
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> |
integer :: nATIDs |
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|
integer :: status |
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|
integer :: i |
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|
integer :: j |
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< |
real ( kind = dp ) :: mySigma_i,mySigma_j |
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< |
real ( kind = dp ) :: myEpsilon_i,myEpsilon_j |
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> |
real ( kind = dp ) :: Sigma_i, Sigma_j |
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> |
real ( kind = dp ) :: Epsilon_i, Epsilon_j |
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|
real ( kind = dp ) :: rcut6 |
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< |
logical :: I_isLJ, J_isLJ |
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> |
|
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|
status = 0 |
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|
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< |
! we only allocate this array to the number of lj_atypes |
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< |
nAtypes = size(ljParameterList%ljParams) |
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< |
if (nAtypes == 0) then |
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> |
nATIDs = size(ParameterMap) |
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> |
|
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> |
if (nATIDs == 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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– |
if (.not. associated(ljMixed)) then |
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– |
allocate(ljMixed(nAtypes, nAtypes)) |
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– |
endif |
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|
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+ |
if (.not.have_rcut) then |
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+ |
status = -1 |
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+ |
return |
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+ |
endif |
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+ |
|
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+ |
if (.not. allocated(MixingMap)) then |
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+ |
allocate(MixingMap(nATIDs, nATIDs)) |
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+ |
endif |
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+ |
|
| 223 |
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rcut6 = LJ_rcut**6 |
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< |
|
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< |
! This loops through all atypes, even those that don't support LJ forces. |
| 226 |
< |
do i = 1, nAtypes |
| 227 |
< |
|
| 228 |
< |
myEpsilon_i = ljParameterList%ljParams(i)%lj_epsilon |
| 229 |
< |
mySigma_i = ljParameterList%ljParams(i)%lj_sigma |
| 224 |
> |
|
| 225 |
> |
! This loops through all atypes, even those that don't support LJ forces. |
| 226 |
> |
do i = 1, nATIDs |
| 227 |
> |
|
| 228 |
> |
Epsilon_i = ParameterMap(i)%epsilon |
| 229 |
> |
Sigma_i = ParameterMap(i)%sigma |
| 230 |
> |
|
| 231 |
> |
! do self mixing rule |
| 232 |
> |
MixingMap(i,i)%sigma = Sigma_i |
| 233 |
> |
MixingMap(i,i)%sigma6 = Sigma_i ** 6 |
| 234 |
> |
MixingMap(i,i)%tp6 = (MixingMap(i,i)%sigma6)/rcut6 |
| 235 |
> |
MixingMap(i,i)%tp12 = (MixingMap(i,i)%tp6) ** 2 |
| 236 |
> |
MixingMap(i,i)%epsilon = Epsilon_i |
| 237 |
> |
MixingMap(i,i)%delta = -4.0_DP * MixingMap(i,i)%epsilon * & |
| 238 |
> |
(MixingMap(i,i)%tp12 - MixingMap(i,i)%tp6) |
| 239 |
> |
|
| 240 |
> |
do j = i + 1, nATIDs |
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|
|
| 242 |
< |
! do self mixing rule |
| 243 |
< |
ljMixed(i,i)%sigma = mySigma_i |
| 242 |
> |
Epsilon_j = ParameterMap(j)%epsilon |
| 243 |
> |
Sigma_j = ParameterMap(j)%sigma |
| 244 |
|
|
| 245 |
< |
ljMixed(i,i)%sigma6 = (ljMixed(i,i)%sigma) ** 6 |
| 245 |
> |
! only the distance parameter uses different mixing policies |
| 246 |
> |
if (useGeometricDistanceMixing) then |
| 247 |
> |
! only for OPLS as far as we can tell |
| 248 |
> |
MixingMap(i,j)%sigma = dsqrt(Sigma_i * Sigma_j) |
| 249 |
> |
else |
| 250 |
> |
! everyone else |
| 251 |
> |
MixingMap(i,j)%sigma = 0.5_dp * (Sigma_i + Sigma_j) |
| 252 |
> |
endif |
| 253 |
|
|
| 254 |
< |
ljMixed(i,i)%tp6 = (ljMixed(i,i)%sigma6)/rcut6 |
| 254 |
> |
! energy parameter is always geometric mean: |
| 255 |
> |
MixingMap(i,j)%epsilon = dsqrt(Epsilon_i * Epsilon_j) |
| 256 |
> |
|
| 257 |
> |
MixingMap(i,j)%sigma6 = (MixingMap(i,j)%sigma)**6 |
| 258 |
> |
MixingMap(i,j)%tp6 = MixingMap(i,j)%sigma6/rcut6 |
| 259 |
> |
MixingMap(i,j)%tp12 = (MixingMap(i,j)%tp6) ** 2 |
| 260 |
|
|
| 261 |
< |
ljMixed(i,i)%tp12 = (ljMixed(i,i)%tp6) ** 2 |
| 261 |
> |
MixingMap(i,j)%delta = -4.0_DP * MixingMap(i,j)%epsilon * & |
| 262 |
> |
(MixingMap(i,j)%tp12 - MixingMap(i,j)%tp6) |
| 263 |
|
|
| 264 |
+ |
MixingMap(j,i)%sigma = MixingMap(i,j)%sigma |
| 265 |
+ |
MixingMap(j,i)%sigma6 = MixingMap(i,j)%sigma6 |
| 266 |
+ |
MixingMap(j,i)%tp6 = MixingMap(i,j)%tp6 |
| 267 |
+ |
MixingMap(j,i)%tp12 = MixingMap(i,j)%tp12 |
| 268 |
+ |
MixingMap(j,i)%epsilon = MixingMap(i,j)%epsilon |
| 269 |
+ |
MixingMap(j,i)%delta = MixingMap(i,j)%delta |
| 270 |
|
|
| 271 |
< |
ljMixed(i,i)%epsilon = myEpsilon_i |
| 216 |
< |
|
| 217 |
< |
ljMixed(i,i)%delta = -4.0_DP * ljMixed(i,i)%epsilon * & |
| 218 |
< |
(ljMixed(i,i)%tp12 - ljMixed(i,i)%tp6) |
| 219 |
< |
|
| 220 |
< |
do j = i + 1, nAtypes |
| 221 |
< |
|
| 222 |
< |
myEpsilon_j = ljParameterList%ljParams(j)%lj_epsilon |
| 223 |
< |
mySigma_j = ljParameterList%ljParams(j)%lj_sigma |
| 224 |
< |
|
| 225 |
< |
|
| 226 |
< |
ljMixed(i,j)%sigma = & |
| 227 |
< |
calcLJMix("sigma",mySigma_i, & |
| 228 |
< |
mySigma_j) |
| 229 |
< |
|
| 230 |
< |
ljMixed(i,j)%sigma6 = & |
| 231 |
< |
(ljMixed(i,j)%sigma)**6 |
| 232 |
< |
|
| 233 |
< |
|
| 234 |
< |
ljMixed(i,j)%tp6 = ljMixed(i,j)%sigma6/rcut6 |
| 235 |
< |
|
| 236 |
< |
ljMixed(i,j)%tp12 = (ljMixed(i,j)%tp6) ** 2 |
| 237 |
< |
|
| 238 |
< |
|
| 239 |
< |
ljMixed(i,j)%epsilon = & |
| 240 |
< |
calcLJMix("epsilon",myEpsilon_i, & |
| 241 |
< |
myEpsilon_j) |
| 242 |
< |
|
| 243 |
< |
ljMixed(i,j)%delta = -4.0_DP * ljMixed(i,j)%epsilon * & |
| 244 |
< |
(ljMixed(i,j)%tp12 - ljMixed(i,j)%tp6) |
| 245 |
< |
|
| 246 |
< |
|
| 247 |
< |
ljMixed(j,i)%sigma = ljMixed(i,j)%sigma |
| 248 |
< |
ljMixed(j,i)%sigma6 = ljMixed(i,j)%sigma6 |
| 249 |
< |
ljMixed(j,i)%tp6 = ljMixed(i,j)%tp6 |
| 250 |
< |
ljMixed(j,i)%tp12 = ljMixed(i,j)%tp12 |
| 251 |
< |
ljMixed(j,i)%epsilon = ljMixed(i,j)%epsilon |
| 252 |
< |
ljMixed(j,i)%delta = ljMixed(i,j)%delta |
| 253 |
< |
|
| 254 |
< |
end do |
| 271 |
> |
end do |
| 272 |
|
end do |
| 273 |
|
|
| 274 |
< |
end subroutine createMixingList |
| 275 |
< |
|
| 274 |
> |
haveMixingMap = .true. |
| 275 |
> |
|
| 276 |
> |
end subroutine createMixingMap |
| 277 |
> |
|
| 278 |
|
subroutine do_lj_pair(atom1, atom2, d, rij, r2, sw, vpair, fpair, & |
| 279 |
|
pot, f, do_pot) |
| 280 |
|
|
| 296 |
|
real( kind = dp ) :: t6 |
| 297 |
|
real( kind = dp ) :: t12 |
| 298 |
|
real( kind = dp ) :: delta |
| 299 |
< |
integer :: id1, id2 |
| 299 |
> |
integer :: id1, id2, localError |
| 300 |
|
|
| 301 |
+ |
if (.not.haveMixingMap) then |
| 302 |
+ |
localError = 0 |
| 303 |
+ |
call createMixingMap(localError) |
| 304 |
+ |
if ( localError .ne. 0 ) then |
| 305 |
+ |
call handleError("LJ", "MixingMap creation failed!") |
| 306 |
+ |
return |
| 307 |
+ |
end if |
| 308 |
+ |
endif |
| 309 |
+ |
|
| 310 |
|
! Look up the correct parameters in the mixing matrix |
| 311 |
|
#ifdef IS_MPI |
| 312 |
< |
sigma6 = ljMixed(atid_Row(atom1),atid_Col(atom2))%sigma6 |
| 313 |
< |
epsilon = ljMixed(atid_Row(atom1),atid_Col(atom2))%epsilon |
| 314 |
< |
delta = ljMixed(atid_Row(atom1),atid_Col(atom2))%delta |
| 312 |
> |
sigma6 = MixingMap(atid_Row(atom1),atid_Col(atom2))%sigma6 |
| 313 |
> |
epsilon = MixingMap(atid_Row(atom1),atid_Col(atom2))%epsilon |
| 314 |
> |
delta = MixingMap(atid_Row(atom1),atid_Col(atom2))%delta |
| 315 |
|
#else |
| 316 |
< |
sigma6 = ljMixed(atid(atom1),atid(atom2))%sigma6 |
| 317 |
< |
epsilon = ljMixed(atid(atom1),atid(atom2))%epsilon |
| 318 |
< |
delta = ljMixed(atid(atom1),atid(atom2))%delta |
| 316 |
> |
sigma6 = MixingMap(atid(atom1),atid(atom2))%sigma6 |
| 317 |
> |
epsilon = MixingMap(atid(atom1),atid(atom2))%epsilon |
| 318 |
> |
delta = MixingMap(atid(atom1),atid(atom2))%delta |
| 319 |
|
#endif |
| 320 |
|
|
| 321 |
|
r6 = r2 * r2 * r2 |
| 389 |
|
|
| 390 |
|
|
| 391 |
|
!! Calculates the mixing for sigma or epslon |
| 364 |
– |
|
| 365 |
– |
function calcLJMix(thisParam,param1,param2,status) result(myMixParam) |
| 366 |
– |
character(len=*) :: thisParam |
| 367 |
– |
real(kind = dp) :: param1 |
| 368 |
– |
real(kind = dp) :: param2 |
| 369 |
– |
real(kind = dp ) :: myMixParam |
| 370 |
– |
|
| 371 |
– |
integer, optional :: status |
| 372 |
– |
|
| 373 |
– |
myMixParam = 0.0_dp |
| 392 |
|
|
| 375 |
– |
if (present(status)) status = 0 |
| 376 |
– |
select case (LJ_Mixing_Policy) |
| 377 |
– |
case (1) |
| 378 |
– |
select case (thisParam) |
| 379 |
– |
case ("sigma") |
| 380 |
– |
myMixParam = 0.5_dp * (param1 + param2) |
| 381 |
– |
case ("epsilon") |
| 382 |
– |
myMixParam = sqrt(param1 * param2) |
| 383 |
– |
case default |
| 384 |
– |
status = -1 |
| 385 |
– |
end select |
| 386 |
– |
case default |
| 387 |
– |
status = -1 |
| 388 |
– |
end select |
| 389 |
– |
end function calcLJMix |
| 390 |
– |
|
| 393 |
|
end module lj |
| 392 |
– |
|
| 393 |
– |
subroutine newLJtype(ident,lj_sigma,lj_epsilon,status) |
| 394 |
– |
use lj, ONLY : module_newLJtype => newLJtype |
| 395 |
– |
integer, parameter :: DP = selected_real_kind(15) |
| 396 |
– |
integer,intent(inout) :: ident |
| 397 |
– |
real(kind=dp),intent(inout) :: lj_sigma |
| 398 |
– |
real(kind=dp),intent(inout) :: lj_epsilon |
| 399 |
– |
integer,intent(inout) :: status |
| 400 |
– |
|
| 401 |
– |
call module_newLJtype(ident,lj_sigma,lj_epsilon,status) |
| 402 |
– |
|
| 403 |
– |
end subroutine newLJtype |
| 404 |
– |
|
