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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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!! @author Charles F. Vardeman II |
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!! @author Matthew Meineke |
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!! @version $Id: LJ.F90,v 1.3 2004-10-21 20:15:25 gezelter Exp $, $Date: 2004-10-21 20:15:25 $, $Name: not supported by cvs2svn $, $Revision: 1.3 $ |
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!! @version $Id: LJ.F90,v 1.12 2005-05-19 15:49:53 tim Exp $, $Date: 2005-05-19 15:49:53 $, $Name: not supported by cvs2svn $, $Revision: 1.12 $ |
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module lj |
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use atype_module |
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use switcheroo |
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|
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implicit none |
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PRIVATE |
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|
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|
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integer, parameter :: DP = selected_real_kind(15) |
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|
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|
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type, private :: LjType |
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integer :: ident |
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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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logical :: soft_pot |
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end type LjType |
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|
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|
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type(LjType), dimension(:), allocatable :: ParameterMap |
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|
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|
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logical, save :: haveMixingMap = .false. |
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|
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|
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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) :: tp6 |
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real(kind=dp) :: tp12 |
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real(kind=dp) :: delta |
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logical :: soft_pot |
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end type MixParameters |
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|
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|
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type(MixParameters), dimension(:,:), allocatable :: MixingMap |
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|
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|
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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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|
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!! Public methods and data |
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|
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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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|
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public :: getSigma |
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public :: getEpsilon |
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public :: destroyLJTypes |
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|
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contains |
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|
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subroutine newLJtype(ident, sigma, epsilon, status) |
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integer,intent(in) :: ident |
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subroutine newLJtype(c_ident, sigma, epsilon, soft_pot, 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(in) :: soft_pot |
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integer,intent(out) :: status |
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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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!! Be simple-minded and assume that we need a ParameterMap that |
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!! is the same size as the total number of atom types |
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|
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myATID = getFirstMatchingElement(atypes, "c_ident", c_ident) |
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|
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if (.not.allocated(ParameterMap)) then |
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|
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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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|
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if (nAtypes == 0) then |
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status = -1 |
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return |
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end if |
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|
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|
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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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|
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end if |
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|
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if (ident .gt. size(ParameterMap)) then |
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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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|
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|
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! set the values for ParameterMap for this atom type: |
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|
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ParameterMap(ident)%ident = ident |
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ParameterMap(ident)%epsilon = epsilon |
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ParameterMap(ident)%sigma = sigma |
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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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if (soft_pot == 1) then |
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ParameterMap(myATID)%soft_pot = .true. |
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else |
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ParameterMap(myATID)%soft_pot = .false. |
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endif |
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end subroutine newLJtype |
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|
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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 |
157 |
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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 getSigma!") |
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return |
161 |
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end if |
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|
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s = ParameterMap(atid)%sigma |
164 |
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end function getSigma |
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|
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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 |
170 |
> |
|
171 |
> |
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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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_do_shift = do_shift |
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call set_switch(LJ_SWITCH, rcut, rcut) |
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have_rcut = .true. |
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|
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|
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return |
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end subroutine setCutoffLJ |
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|
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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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|
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subroutine createMixingMap(status) |
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integer :: nAtypes |
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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 ) :: 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_is_LJ, j_is_LJ |
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|
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status = 0 |
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nAtypes = size(ParameterMap) |
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|
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if (nAtypes == 0) then |
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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 call of createMixingMap!") |
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status = -1 |
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return |
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endif |
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|
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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. allocated(MixingMap)) then |
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allocate(MixingMap(nATIDs, nATIDs)) |
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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(nAtypes, nAtypes)) |
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endif |
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|
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|
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rcut6 = LJ_rcut**6 |
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|
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|
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! This loops through all atypes, even those that don't support LJ forces. |
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do i = 1, nAtypes |
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|
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Epsilon_i = ParameterMap(i)%epsilon |
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Sigma_i = ParameterMap(i)%sigma |
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|
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! do self mixing rule |
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MixingMap(i,i)%sigma = Sigma_i |
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MixingMap(i,i)%sigma6 = Sigma_i ** 6 |
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MixingMap(i,i)%tp6 = (MixingMap(i,i)%sigma6)/rcut6 |
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MixingMap(i,i)%tp12 = (MixingMap(i,i)%tp6) ** 2 |
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MixingMap(i,i)%epsilon = Epsilon_i |
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MixingMap(i,i)%delta = -4.0_DP * MixingMap(i,i)%epsilon * & |
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(MixingMap(i,i)%tp12 - MixingMap(i,i)%tp6) |
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< |
|
255 |
< |
do j = i + 1, nAtypes |
256 |
< |
|
257 |
< |
Epsilon_j = ParameterMap(j)%epsilon |
258 |
< |
Sigma_j = ParameterMap(j)%sigma |
259 |
< |
|
260 |
< |
! only the distance parameter uses different mixing policies |
261 |
< |
if (useGeometricDistanceMixing) then |
262 |
< |
! only for OPLS as far as we can tell |
263 |
< |
MixingMap(i,j)%sigma = dsqrt(Sigma_i * Sigma_j) |
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else |
265 |
< |
! everyone else |
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< |
MixingMap(i,j)%sigma = 0.5_dp * (Sigma_i + Sigma_j) |
267 |
< |
endif |
268 |
< |
|
269 |
< |
! energy parameter is always geometric mean: |
270 |
< |
MixingMap(i,j)%epsilon = dsqrt(Epsilon_i * Epsilon_j) |
271 |
< |
|
272 |
< |
MixingMap(i,j)%sigma6 = (MixingMap(i,j)%sigma)**6 |
273 |
< |
MixingMap(i,j)%tp6 = MixingMap(i,j)%sigma6/rcut6 |
274 |
< |
MixingMap(i,j)%tp12 = (MixingMap(i,j)%tp6) ** 2 |
275 |
< |
|
276 |
< |
MixingMap(i,j)%delta = -4.0_DP * MixingMap(i,j)%epsilon * & |
277 |
< |
(MixingMap(i,j)%tp12 - MixingMap(i,j)%tp6) |
278 |
< |
|
279 |
< |
MixingMap(j,i)%sigma = MixingMap(i,j)%sigma |
280 |
< |
MixingMap(j,i)%sigma6 = MixingMap(i,j)%sigma6 |
281 |
< |
MixingMap(j,i)%tp6 = MixingMap(i,j)%tp6 |
282 |
< |
MixingMap(j,i)%tp12 = MixingMap(i,j)%tp12 |
283 |
< |
MixingMap(j,i)%epsilon = MixingMap(i,j)%epsilon |
284 |
< |
MixingMap(j,i)%delta = MixingMap(i,j)%delta |
285 |
< |
|
286 |
< |
end do |
241 |
> |
do i = 1, nATIDs |
242 |
> |
call getElementProperty(atypes, i, "is_LennardJones", i_is_LJ) |
243 |
> |
if (i_is_LJ) then |
244 |
> |
Epsilon_i = ParameterMap(i)%epsilon |
245 |
> |
Sigma_i = ParameterMap(i)%sigma |
246 |
> |
|
247 |
> |
! do self mixing rule |
248 |
> |
MixingMap(i,i)%sigma = Sigma_i |
249 |
> |
MixingMap(i,i)%sigma6 = Sigma_i ** 6 |
250 |
> |
MixingMap(i,i)%tp6 = (MixingMap(i,i)%sigma6)/rcut6 |
251 |
> |
MixingMap(i,i)%tp12 = (MixingMap(i,i)%tp6) ** 2 |
252 |
> |
MixingMap(i,i)%epsilon = Epsilon_i |
253 |
> |
MixingMap(i,i)%delta = -4.0_DP * MixingMap(i,i)%epsilon * & |
254 |
> |
(MixingMap(i,i)%tp12 - MixingMap(i,i)%tp6) |
255 |
> |
MixingMap(i,i)%soft_pot = ParameterMap(i)%soft_pot |
256 |
> |
|
257 |
> |
do j = i + 1, nATIDs |
258 |
> |
call getElementProperty(atypes, j, "is_LennardJones", j_is_LJ) |
259 |
> |
|
260 |
> |
if (j_is_LJ) then |
261 |
> |
Epsilon_j = ParameterMap(j)%epsilon |
262 |
> |
Sigma_j = ParameterMap(j)%sigma |
263 |
> |
|
264 |
> |
! only the distance parameter uses different mixing policies |
265 |
> |
if (useGeometricDistanceMixing) then |
266 |
> |
! only for OPLS as far as we can tell |
267 |
> |
MixingMap(i,j)%sigma = dsqrt(Sigma_i * Sigma_j) |
268 |
> |
else |
269 |
> |
! everyone else |
270 |
> |
MixingMap(i,j)%sigma = 0.5_dp * (Sigma_i + Sigma_j) |
271 |
> |
endif |
272 |
> |
|
273 |
> |
! energy parameter is always geometric mean: |
274 |
> |
MixingMap(i,j)%epsilon = dsqrt(Epsilon_i * Epsilon_j) |
275 |
> |
|
276 |
> |
MixingMap(i,j)%sigma6 = (MixingMap(i,j)%sigma)**6 |
277 |
> |
MixingMap(i,j)%tp6 = MixingMap(i,j)%sigma6/rcut6 |
278 |
> |
MixingMap(i,j)%tp12 = (MixingMap(i,j)%tp6) ** 2 |
279 |
> |
|
280 |
> |
MixingMap(i,j)%delta = -4.0_DP * MixingMap(i,j)%epsilon * & |
281 |
> |
(MixingMap(i,j)%tp12 - MixingMap(i,j)%tp6) |
282 |
> |
|
283 |
> |
MixingMap(i,j)%soft_pot = ParameterMap(i)%soft_pot .or. ParameterMap(j)%soft_pot |
284 |
> |
|
285 |
> |
|
286 |
> |
MixingMap(j,i)%sigma = MixingMap(i,j)%sigma |
287 |
> |
MixingMap(j,i)%sigma6 = MixingMap(i,j)%sigma6 |
288 |
> |
MixingMap(j,i)%tp6 = MixingMap(i,j)%tp6 |
289 |
> |
MixingMap(j,i)%tp12 = MixingMap(i,j)%tp12 |
290 |
> |
MixingMap(j,i)%epsilon = MixingMap(i,j)%epsilon |
291 |
> |
MixingMap(j,i)%delta = MixingMap(i,j)%delta |
292 |
> |
MixingMap(j,i)%soft_pot = MixingMap(i,j)%soft_pot |
293 |
> |
endif |
294 |
> |
end do |
295 |
> |
endif |
296 |
|
end do |
297 |
< |
|
297 |
> |
|
298 |
> |
haveMixingMap = .true. |
299 |
> |
|
300 |
|
end subroutine createMixingMap |
301 |
< |
|
301 |
> |
|
302 |
|
subroutine do_lj_pair(atom1, atom2, d, rij, r2, sw, vpair, fpair, & |
303 |
|
pot, f, do_pot) |
304 |
|
|
320 |
|
real( kind = dp ) :: t6 |
321 |
|
real( kind = dp ) :: t12 |
322 |
|
real( kind = dp ) :: delta |
323 |
+ |
logical :: soft_pot |
324 |
|
integer :: id1, id2, localError |
325 |
|
|
326 |
|
if (.not.haveMixingMap) then |
337 |
|
sigma6 = MixingMap(atid_Row(atom1),atid_Col(atom2))%sigma6 |
338 |
|
epsilon = MixingMap(atid_Row(atom1),atid_Col(atom2))%epsilon |
339 |
|
delta = MixingMap(atid_Row(atom1),atid_Col(atom2))%delta |
340 |
+ |
soft_pot = MixingMap(atid_Row(atom1),atid_Col(atom2))%soft_pot |
341 |
|
#else |
342 |
|
sigma6 = MixingMap(atid(atom1),atid(atom2))%sigma6 |
343 |
|
epsilon = MixingMap(atid(atom1),atid(atom2))%epsilon |
344 |
|
delta = MixingMap(atid(atom1),atid(atom2))%delta |
345 |
+ |
soft_pot = MixingMap(atid(atom1),atid(atom2))%soft_pot |
346 |
|
#endif |
347 |
|
|
348 |
|
r6 = r2 * r2 * r2 |
349 |
< |
|
349 |
> |
|
350 |
|
t6 = sigma6/ r6 |
351 |
|
t12 = t6 * t6 |
352 |
< |
|
353 |
< |
pot_temp = 4.0E0_DP * epsilon * (t12 - t6) |
354 |
< |
if (LJ_do_shift) then |
355 |
< |
pot_temp = pot_temp + delta |
352 |
> |
|
353 |
> |
if (soft_pot) then |
354 |
> |
|
355 |
> |
pot_temp = 4.0E0_DP * epsilon * t6 |
356 |
> |
if (LJ_do_shift) then |
357 |
> |
pot_temp = pot_temp + delta |
358 |
> |
endif |
359 |
> |
|
360 |
> |
vpair = vpair + pot_temp |
361 |
> |
|
362 |
> |
dudr = -sw * 24.0E0_DP * epsilon * t6 / rij |
363 |
> |
|
364 |
> |
else |
365 |
> |
pot_temp = 4.0E0_DP * epsilon * (t12 - t6) |
366 |
> |
if (LJ_do_shift) then |
367 |
> |
pot_temp = pot_temp + delta |
368 |
> |
endif |
369 |
> |
|
370 |
> |
vpair = vpair + pot_temp |
371 |
> |
|
372 |
> |
dudr = sw * 24.0E0_DP * epsilon * (t6 - 2.0E0_DP*t12) / rij |
373 |
|
endif |
374 |
|
|
254 |
– |
vpair = vpair + pot_temp |
255 |
– |
|
256 |
– |
dudr = sw * 24.0E0_DP * epsilon * (t6 - 2.0E0_DP*t12) / rij |
257 |
– |
|
375 |
|
drdx = d(1) / rij |
376 |
|
drdy = d(2) / rij |
377 |
|
drdz = d(3) / rij |
378 |
< |
|
378 |
> |
|
379 |
|
fx = dudr * drdx |
380 |
|
fy = dudr * drdy |
381 |
|
fz = dudr * drdz |
382 |
< |
|
383 |
< |
|
382 |
> |
|
383 |
> |
|
384 |
|
#ifdef IS_MPI |
385 |
|
if (do_pot) then |
386 |
|
pot_Row(atom1) = pot_Row(atom1) + sw*pot_temp*0.5 |
387 |
|
pot_Col(atom2) = pot_Col(atom2) + sw*pot_temp*0.5 |
388 |
|
endif |
389 |
< |
|
389 |
> |
|
390 |
|
f_Row(1,atom1) = f_Row(1,atom1) + fx |
391 |
|
f_Row(2,atom1) = f_Row(2,atom1) + fy |
392 |
|
f_Row(3,atom1) = f_Row(3,atom1) + fz |
393 |
< |
|
393 |
> |
|
394 |
|
f_Col(1,atom2) = f_Col(1,atom2) - fx |
395 |
|
f_Col(2,atom2) = f_Col(2,atom2) - fy |
396 |
|
f_Col(3,atom2) = f_Col(3,atom2) - fz |
397 |
< |
|
397 |
> |
|
398 |
|
#else |
399 |
|
if (do_pot) pot = pot + sw*pot_temp |
400 |
|
|
401 |
|
f(1,atom1) = f(1,atom1) + fx |
402 |
|
f(2,atom1) = f(2,atom1) + fy |
403 |
|
f(3,atom1) = f(3,atom1) + fz |
404 |
< |
|
404 |
> |
|
405 |
|
f(1,atom2) = f(1,atom2) - fx |
406 |
|
f(2,atom2) = f(2,atom2) - fy |
407 |
|
f(3,atom2) = f(3,atom2) - fz |
408 |
|
#endif |
409 |
< |
|
409 |
> |
|
410 |
|
#ifdef IS_MPI |
411 |
|
id1 = AtomRowToGlobal(atom1) |
412 |
|
id2 = AtomColToGlobal(atom2) |
416 |
|
#endif |
417 |
|
|
418 |
|
if (molMembershipList(id1) .ne. molMembershipList(id2)) then |
419 |
< |
|
419 |
> |
|
420 |
|
fpair(1) = fpair(1) + fx |
421 |
|
fpair(2) = fpair(2) + fy |
422 |
|
fpair(3) = fpair(3) + fz |
424 |
|
endif |
425 |
|
|
426 |
|
return |
427 |
< |
|
427 |
> |
|
428 |
|
end subroutine do_lj_pair |
312 |
– |
|
313 |
– |
|
314 |
– |
!! Calculates the mixing for sigma or epslon |
315 |
– |
|
316 |
– |
end module lj |
429 |
|
|
430 |
< |
subroutine newLJtype(ident, sigma, epsilon, status) |
431 |
< |
use lj, ONLY : module_newLJtype => newLJtype |
432 |
< |
integer, parameter :: DP = selected_real_kind(15) |
433 |
< |
integer,intent(inout) :: ident |
434 |
< |
real(kind=dp),intent(inout) :: sigma |
323 |
< |
real(kind=dp),intent(inout) :: epsilon |
324 |
< |
integer,intent(inout) :: status |
325 |
< |
|
326 |
< |
call module_newLJtype(ident, sigma, epsilon, status) |
327 |
< |
|
328 |
< |
end subroutine newLJtype |
430 |
> |
subroutine destroyLJTypes() |
431 |
> |
if(allocated(ParameterMap)) deallocate(ParameterMap) |
432 |
> |
if(allocated(MixingMap)) deallocate(MixingMap) |
433 |
> |
haveMixingMap = .false. |
434 |
> |
end subroutine destroyLJTypes |
435 |
|
|
436 |
< |
subroutine useGeometricMixing() |
437 |
< |
use lj, ONLY: module_useGeometricMixing => useGeometricMixing |
332 |
< |
|
333 |
< |
call module_useGeometricMixing() |
334 |
< |
return |
335 |
< |
end subroutine useGeometricMixing |
436 |
> |
|
437 |
> |
end module lj |