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gezelter |
246 |
!! |
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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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gezelter |
115 |
!! Calculates Long Range forces Lennard-Jones interactions. |
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!! @author Charles F. Vardeman II |
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!! @author Matthew Meineke |
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gezelter |
590 |
!! @version $Id: LJ.F90,v 1.14 2005-09-14 19:02:33 gezelter Exp $, $Date: 2005-09-14 19:02:33 $, $Name: not supported by cvs2svn $, $Revision: 1.14 $ |
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gezelter |
115 |
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gezelter |
246 |
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gezelter |
115 |
module lj |
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use atype_module |
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use vector_class |
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use simulation |
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gezelter |
135 |
use status |
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gezelter |
115 |
#ifdef IS_MPI |
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use mpiSimulation |
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#endif |
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use force_globals |
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implicit none |
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PRIVATE |
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gezelter |
507 |
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chuckv |
131 |
integer, parameter :: DP = selected_real_kind(15) |
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gezelter |
507 |
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gezelter |
572 |
logical, save :: useGeometricDistanceMixing = .false. |
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logical, save :: haveMixingMap = .false. |
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real(kind=DP), save :: defaultCutoff = 0.0_DP |
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logical, save :: defaultShift = .false. |
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logical, save :: haveDefaultCutoff = .false. |
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type, private :: LJtype |
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integer :: atid |
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gezelter |
135 |
real(kind=dp) :: sigma |
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real(kind=dp) :: epsilon |
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gezelter |
572 |
logical :: isSoftCore = .false. |
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end type LJtype |
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gezelter |
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gezelter |
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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 :: LJtypes(:) => null() |
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integer, pointer :: atidToLJtype(:) => null() |
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end type LJList |
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gezelter |
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gezelter |
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type(LJList), save :: LJMap |
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gezelter |
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gezelter |
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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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gezelter |
572 |
real(kind=dp) :: sigma6 |
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real(kind=dp) :: rCut |
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real(kind=dp) :: delta |
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logical :: rCutWasSet = .false. |
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logical :: shiftedPot |
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logical :: isSoftCore = .false. |
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gezelter |
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end type MixParameters |
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gezelter |
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gezelter |
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type(MixParameters), dimension(:,:), allocatable :: MixingMap |
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gezelter |
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gezelter |
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public :: newLJtype |
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public :: setLJDefaultCutoff |
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public :: setLJUniformCutoff |
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public :: setLJCutoffByTypes |
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public :: getSigma |
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public :: getEpsilon |
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gezelter |
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public :: useGeometricMixing |
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public :: do_lj_pair |
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gezelter |
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public :: destroyLJtypes |
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gezelter |
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gezelter |
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contains |
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gezelter |
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subroutine newLJtype(c_ident, sigma, epsilon, isSoftCore, status) |
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gezelter |
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integer,intent(in) :: c_ident |
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gezelter |
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real(kind=dp),intent(in) :: sigma |
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real(kind=dp),intent(in) :: epsilon |
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gezelter |
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integer, intent(in) :: isSoftCore |
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chuckv |
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integer,intent(out) :: status |
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gezelter |
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integer :: nLJTypes, ntypes, myATID |
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gezelter |
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integer, pointer :: MatchList(:) => null() |
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gezelter |
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integer :: current |
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gezelter |
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chuckv |
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status = 0 |
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gezelter |
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! check to see if this is the first time into this routine... |
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if (.not.associated(LJMap%LJtypes)) then |
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gezelter |
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gezelter |
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call getMatchingElementList(atypes, "is_LennardJones", .true., & |
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nLJTypes, MatchList) |
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LJMap%nLJtypes = nLJTypes |
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allocate(LJMap%LJtypes(nLJTypes)) |
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ntypes = getSize(atypes) |
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allocate(LJMap%atidToLJtype(ntypes)) |
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end if |
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LJMap%currentLJtype = LJMap%currentLJtype + 1 |
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current = LJMap%currentLJtype |
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gezelter |
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myATID = getFirstMatchingElement(atypes, "c_ident", c_ident) |
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gezelter |
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LJMap%atidToLJtype(myATID) = current |
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LJMap%LJtypes(current)%atid = myATID |
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LJMap%LJtypes(current)%sigma = sigma |
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LJMap%LJtypes(current)%epsilon = epsilon |
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if (isSoftCore .eq. 1) then |
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LJMap%LJtypes(current)%isSoftCore = .true. |
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else |
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LJMap%LJtypes(current)%isSoftCore = .false. |
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endif |
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end subroutine newLJtype |
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chuckv |
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gezelter |
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subroutine setLJDefaultCutoff(thisRcut, shiftedPot) |
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real(kind=dp), intent(in) :: thisRcut |
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logical, intent(in) :: shiftedPot |
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defaultCutoff = thisRcut |
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defaultShift = shiftedPot |
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haveDefaultCutoff = .true. |
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end subroutine setLJDefaultCutoff |
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gezelter |
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gezelter |
572 |
subroutine setLJUniformCutoff(thisRcut, shiftedPot) |
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real(kind=dp), intent(in) :: thisRcut |
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logical, intent(in) :: shiftedPot |
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integer :: nLJtypes, i, j |
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gezelter |
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gezelter |
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if (LJMap%currentLJtype == 0) then |
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call handleError("LJ", "No members in LJMap") |
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return |
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chuckv |
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end if |
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gezelter |
572 |
nLJtypes = LJMap%nLJtypes |
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if (.not. allocated(MixingMap)) then |
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allocate(MixingMap(nLJtypes, nLJtypes)) |
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gezelter |
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endif |
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gezelter |
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gezelter |
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do i = 1, nLJtypes |
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do j = 1, nLJtypes |
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MixingMap(i,j)%rCut = thisRcut |
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MixingMap(i,j)%shiftedPot = shiftedPot |
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MixingMap(i,j)%rCutWasSet = .true. |
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enddo |
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enddo |
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call createMixingMap() |
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end subroutine setLJUniformCutoff |
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gezelter |
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gezelter |
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subroutine setLJCutoffByTypes(atid1, atid2, thisRcut, shiftedPot) |
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integer, intent(in) :: atid1, atid2 |
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real(kind=dp), intent(in) :: thisRcut |
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logical, intent(in) :: shiftedPot |
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integer :: nLJtypes, ljt1, ljt2 |
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if (LJMap%currentLJtype == 0) then |
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call handleError("LJ", "No members in LJMap") |
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return |
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end if |
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nLJtypes = LJMap%nLJtypes |
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if (.not. allocated(MixingMap)) then |
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allocate(MixingMap(nLJtypes, nLJtypes)) |
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tim |
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endif |
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gezelter |
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gezelter |
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ljt1 = LJMap%atidToLJtype(atid1) |
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ljt2 = LJMap%atidToLJtype(atid2) |
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MixingMap(ljt1,ljt2)%rCut = thisRcut |
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MixingMap(ljt1,ljt2)%shiftedPot = shiftedPot |
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MixingMap(ljt1,ljt2)%rCutWasSet = .true. |
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MixingMap(ljt2,ljt1)%rCut = thisRcut |
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MixingMap(ljt2,ljt1)%shiftedPot = shiftedPot |
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MixingMap(ljt2,ljt1)%rCutWasSet = .true. |
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call createMixingMap() |
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end subroutine setLJCutoffByTypes |
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gezelter |
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function getSigma(atid) result (s) |
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integer, intent(in) :: atid |
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gezelter |
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integer :: ljt1 |
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gezelter |
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real(kind=dp) :: s |
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gezelter |
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gezelter |
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if (LJMap%currentLJtype == 0) then |
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call handleError("LJ", "No members in LJMap") |
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gezelter |
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return |
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end if |
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gezelter |
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gezelter |
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ljt1 = LJMap%atidToLJtype(atid) |
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s = LJMap%LJtypes(ljt1)%sigma |
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gezelter |
140 |
end function getSigma |
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function getEpsilon(atid) result (e) |
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integer, intent(in) :: atid |
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gezelter |
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integer :: ljt1 |
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gezelter |
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real(kind=dp) :: e |
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gezelter |
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gezelter |
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if (LJMap%currentLJtype == 0) then |
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call handleError("LJ", "No members in LJMap") |
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gezelter |
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return |
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end if |
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gezelter |
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gezelter |
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ljt1 = LJMap%atidToLJtype(atid) |
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e = LJMap%LJtypes(ljt1)%epsilon |
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gezelter |
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end function getEpsilon |
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gezelter |
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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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gezelter |
507 |
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gezelter |
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subroutine createMixingMap() |
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integer :: nLJtypes, i, j |
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real ( kind = dp ) :: s1, s2, e1, e2 |
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real ( kind = dp ) :: rcut6, tp6, tp12 |
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gezelter |
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logical :: isSoftCore1, isSoftCore2, doShift |
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gezelter |
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gezelter |
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if (LJMap%currentLJtype == 0) then |
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call handleError("LJ", "No members in LJMap") |
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gezelter |
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return |
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gezelter |
572 |
end if |
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gezelter |
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gezelter |
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nLJtypes = LJMap%nLJtypes |
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gezelter |
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gezelter |
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if (.not. allocated(MixingMap)) then |
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gezelter |
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allocate(MixingMap(nLJtypes, nLJtypes)) |
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gezelter |
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endif |
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gezelter |
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do i = 1, nLJtypes |
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gezelter |
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gezelter |
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s1 = LJMap%LJtypes(i)%sigma |
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e1 = LJMap%LJtypes(i)%epsilon |
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isSoftCore1 = LJMap%LJtypes(i)%isSoftCore |
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gezelter |
507 |
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gezelter |
572 |
do j = i, nLJtypes |
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s2 = LJMap%LJtypes(j)%sigma |
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e2 = LJMap%LJtypes(j)%epsilon |
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isSoftCore2 = LJMap%LJtypes(j)%isSoftCore |
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MixingMap(i,j)%isSoftCore = isSoftCore1 .or. isSoftCore2 |
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gezelter |
507 |
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gezelter |
572 |
! only the distance parameter uses different mixing policies |
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if (useGeometricDistanceMixing) then |
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MixingMap(i,j)%sigma = dsqrt(s1 * s2) |
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else |
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MixingMap(i,j)%sigma = 0.5_dp * (s1 + s2) |
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endif |
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MixingMap(i,j)%epsilon = dsqrt(e1 * e2) |
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gezelter |
507 |
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gezelter |
572 |
MixingMap(i,j)%sigma6 = (MixingMap(i,j)%sigma)**6 |
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gezelter |
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gezelter |
572 |
if (MixingMap(i,j)%rCutWasSet) then |
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rcut6 = (MixingMap(i,j)%rcut)**6 |
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else |
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if (haveDefaultCutoff) then |
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rcut6 = defaultCutoff**6 |
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gezelter |
590 |
doShift = defaultShift |
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gezelter |
572 |
else |
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call handleError("LJ", "No specified or default cutoff value!") |
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gezelter |
402 |
endif |
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gezelter |
572 |
endif |
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tp6 = MixingMap(i,j)%sigma6/rcut6 |
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tp12 = tp6**2 |
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gezelter |
590 |
MixingMap(i,j)%delta =-4.0_DP*MixingMap(i,j)%epsilon*(tp12 - tp6) |
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MixingMap(i,j)%shiftedPot = doShift |
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gezelter |
507 |
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gezelter |
590 |
if (i.ne.j) then |
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MixingMap(j,i)%sigma = MixingMap(i,j)%sigma |
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MixingMap(j,i)%epsilon = MixingMap(i,j)%epsilon |
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MixingMap(j,i)%sigma6 = MixingMap(i,j)%sigma6 |
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MixingMap(j,i)%rCut = MixingMap(i,j)%rCut |
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MixingMap(j,i)%delta = MixingMap(i,j)%delta |
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MixingMap(j,i)%rCutWasSet = MixingMap(i,j)%rCutWasSet |
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MixingMap(j,i)%shiftedPot = MixingMap(i,j)%shiftedPot |
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MixingMap(j,i)%isSoftCore = MixingMap(i,j)%isSoftCore |
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endif |
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gezelter |
572 |
enddo |
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enddo |
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chrisfen |
217 |
haveMixingMap = .true. |
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gezelter |
572 |
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gezelter |
135 |
end subroutine createMixingMap |
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gezelter |
572 |
|
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gezelter |
115 |
subroutine do_lj_pair(atom1, atom2, d, rij, r2, sw, vpair, fpair, & |
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pot, f, do_pot) |
| 330 |
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| 331 |
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integer, intent(in) :: atom1, atom2 |
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gezelter |
572 |
integer :: atid1, atid2, ljt1, ljt2 |
| 333 |
gezelter |
115 |
real( kind = dp ), intent(in) :: rij, r2 |
| 334 |
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real( kind = dp ) :: pot, sw, vpair |
| 335 |
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real( kind = dp ), dimension(3,nLocal) :: f |
| 336 |
|
|
real( kind = dp ), intent(in), dimension(3) :: d |
| 337 |
|
|
real( kind = dp ), intent(inout), dimension(3) :: fpair |
| 338 |
|
|
logical, intent(in) :: do_pot |
| 339 |
|
|
|
| 340 |
|
|
! local Variables |
| 341 |
|
|
real( kind = dp ) :: drdx, drdy, drdz |
| 342 |
|
|
real( kind = dp ) :: fx, fy, fz |
| 343 |
|
|
real( kind = dp ) :: pot_temp, dudr |
| 344 |
|
|
real( kind = dp ) :: sigma6 |
| 345 |
|
|
real( kind = dp ) :: epsilon |
| 346 |
|
|
real( kind = dp ) :: r6 |
| 347 |
|
|
real( kind = dp ) :: t6 |
| 348 |
|
|
real( kind = dp ) :: t12 |
| 349 |
|
|
real( kind = dp ) :: delta |
| 350 |
gezelter |
572 |
logical :: isSoftCore, shiftedPot |
| 351 |
gezelter |
135 |
integer :: id1, id2, localError |
| 352 |
gezelter |
115 |
|
| 353 |
gezelter |
135 |
if (.not.haveMixingMap) then |
| 354 |
gezelter |
572 |
call createMixingMap() |
| 355 |
gezelter |
135 |
endif |
| 356 |
|
|
|
| 357 |
gezelter |
115 |
! Look up the correct parameters in the mixing matrix |
| 358 |
|
|
#ifdef IS_MPI |
| 359 |
gezelter |
572 |
atid1 = atid_Row(atom1) |
| 360 |
|
|
atid2 = atid_Col(atom2) |
| 361 |
gezelter |
115 |
#else |
| 362 |
gezelter |
572 |
atid1 = atid(atom1) |
| 363 |
|
|
atid2 = atid(atom2) |
| 364 |
gezelter |
115 |
#endif |
| 365 |
|
|
|
| 366 |
gezelter |
572 |
ljt1 = LJMap%atidToLJtype(atid1) |
| 367 |
|
|
ljt2 = LJMap%atidToLJtype(atid2) |
| 368 |
|
|
|
| 369 |
|
|
sigma6 = MixingMap(ljt1,ljt2)%sigma6 |
| 370 |
|
|
epsilon = MixingMap(ljt1,ljt2)%epsilon |
| 371 |
|
|
delta = MixingMap(ljt1,ljt2)%delta |
| 372 |
|
|
isSoftCore = MixingMap(ljt1,ljt2)%isSoftCore |
| 373 |
|
|
shiftedPot = MixingMap(ljt1,ljt2)%shiftedPot |
| 374 |
|
|
|
| 375 |
gezelter |
115 |
r6 = r2 * r2 * r2 |
| 376 |
gezelter |
507 |
|
| 377 |
gezelter |
115 |
t6 = sigma6/ r6 |
| 378 |
|
|
t12 = t6 * t6 |
| 379 |
tim |
378 |
|
| 380 |
gezelter |
572 |
if (isSoftCore) then |
| 381 |
|
|
|
| 382 |
|
|
pot_temp = 4.0E0_DP * epsilon * t6 |
| 383 |
|
|
if (shiftedPot) then |
| 384 |
|
|
pot_temp = pot_temp + delta |
| 385 |
|
|
endif |
| 386 |
|
|
|
| 387 |
|
|
vpair = vpair + pot_temp |
| 388 |
|
|
|
| 389 |
|
|
dudr = -sw * 24.0E0_DP * epsilon * t6 / rij |
| 390 |
|
|
|
| 391 |
tim |
378 |
else |
| 392 |
gezelter |
507 |
pot_temp = 4.0E0_DP * epsilon * (t12 - t6) |
| 393 |
gezelter |
572 |
if (shiftedPot) then |
| 394 |
gezelter |
507 |
pot_temp = pot_temp + delta |
| 395 |
|
|
endif |
| 396 |
gezelter |
572 |
|
| 397 |
gezelter |
507 |
vpair = vpair + pot_temp |
| 398 |
gezelter |
572 |
|
| 399 |
gezelter |
507 |
dudr = sw * 24.0E0_DP * epsilon * (t6 - 2.0E0_DP*t12) / rij |
| 400 |
gezelter |
115 |
endif |
| 401 |
gezelter |
507 |
|
| 402 |
gezelter |
115 |
drdx = d(1) / rij |
| 403 |
|
|
drdy = d(2) / rij |
| 404 |
|
|
drdz = d(3) / rij |
| 405 |
gezelter |
507 |
|
| 406 |
gezelter |
115 |
fx = dudr * drdx |
| 407 |
|
|
fy = dudr * drdy |
| 408 |
|
|
fz = dudr * drdz |
| 409 |
gezelter |
507 |
|
| 410 |
gezelter |
115 |
#ifdef IS_MPI |
| 411 |
|
|
if (do_pot) then |
| 412 |
|
|
pot_Row(atom1) = pot_Row(atom1) + sw*pot_temp*0.5 |
| 413 |
|
|
pot_Col(atom2) = pot_Col(atom2) + sw*pot_temp*0.5 |
| 414 |
|
|
endif |
| 415 |
gezelter |
507 |
|
| 416 |
gezelter |
115 |
f_Row(1,atom1) = f_Row(1,atom1) + fx |
| 417 |
|
|
f_Row(2,atom1) = f_Row(2,atom1) + fy |
| 418 |
|
|
f_Row(3,atom1) = f_Row(3,atom1) + fz |
| 419 |
gezelter |
507 |
|
| 420 |
gezelter |
115 |
f_Col(1,atom2) = f_Col(1,atom2) - fx |
| 421 |
|
|
f_Col(2,atom2) = f_Col(2,atom2) - fy |
| 422 |
|
|
f_Col(3,atom2) = f_Col(3,atom2) - fz |
| 423 |
gezelter |
507 |
|
| 424 |
gezelter |
115 |
#else |
| 425 |
|
|
if (do_pot) pot = pot + sw*pot_temp |
| 426 |
|
|
|
| 427 |
|
|
f(1,atom1) = f(1,atom1) + fx |
| 428 |
|
|
f(2,atom1) = f(2,atom1) + fy |
| 429 |
|
|
f(3,atom1) = f(3,atom1) + fz |
| 430 |
gezelter |
507 |
|
| 431 |
gezelter |
115 |
f(1,atom2) = f(1,atom2) - fx |
| 432 |
|
|
f(2,atom2) = f(2,atom2) - fy |
| 433 |
|
|
f(3,atom2) = f(3,atom2) - fz |
| 434 |
|
|
#endif |
| 435 |
gezelter |
507 |
|
| 436 |
gezelter |
115 |
#ifdef IS_MPI |
| 437 |
|
|
id1 = AtomRowToGlobal(atom1) |
| 438 |
|
|
id2 = AtomColToGlobal(atom2) |
| 439 |
|
|
#else |
| 440 |
|
|
id1 = atom1 |
| 441 |
|
|
id2 = atom2 |
| 442 |
|
|
#endif |
| 443 |
|
|
|
| 444 |
|
|
if (molMembershipList(id1) .ne. molMembershipList(id2)) then |
| 445 |
gezelter |
507 |
|
| 446 |
gezelter |
115 |
fpair(1) = fpair(1) + fx |
| 447 |
|
|
fpair(2) = fpair(2) + fy |
| 448 |
|
|
fpair(3) = fpair(3) + fz |
| 449 |
|
|
|
| 450 |
|
|
endif |
| 451 |
|
|
|
| 452 |
|
|
return |
| 453 |
gezelter |
507 |
|
| 454 |
gezelter |
115 |
end subroutine do_lj_pair |
| 455 |
gezelter |
507 |
|
| 456 |
chuckv |
492 |
subroutine destroyLJTypes() |
| 457 |
gezelter |
572 |
|
| 458 |
|
|
LJMap%nLJtypes = 0 |
| 459 |
|
|
LJMap%currentLJtype = 0 |
| 460 |
|
|
|
| 461 |
|
|
if (associated(LJMap%LJtypes)) then |
| 462 |
|
|
deallocate(LJMap%LJtypes) |
| 463 |
|
|
LJMap%LJtypes => null() |
| 464 |
|
|
end if |
| 465 |
|
|
|
| 466 |
|
|
if (associated(LJMap%atidToLJtype)) then |
| 467 |
|
|
deallocate(LJMap%atidToLJtype) |
| 468 |
|
|
LJMap%atidToLJtype => null() |
| 469 |
|
|
end if |
| 470 |
|
|
|
| 471 |
chuckv |
492 |
haveMixingMap = .false. |
| 472 |
|
|
end subroutine destroyLJTypes |
| 473 |
|
|
|
| 474 |
gezelter |
115 |
end module lj |
