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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 1.4 2004-10-22 20:22:47 gezelter Exp $, $Date: 2004-10-22 20:22:47 $, $Name: not supported by cvs2svn $, $Revision: 1.4 $ |
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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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implicit none |
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PRIVATE |
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integer, parameter :: DP = selected_real_kind(15) |
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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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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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!! Public methods and data |
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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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public :: destroyLJTypes |
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|
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contains |
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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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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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!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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end if |
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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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! 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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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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> |
|
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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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> |
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s = ParameterMap(atid)%sigma |
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end function getSigma |
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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("dipole-dipole", "no ParameterMap was present before first call of getEpsilon!") |
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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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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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return |
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end subroutine setCutoffLJ |
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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 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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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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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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! 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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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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< |
|
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< |
do j = i + 1, nAtypes |
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< |
|
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Epsilon_j = ParameterMap(j)%epsilon |
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< |
Sigma_j = ParameterMap(j)%sigma |
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< |
|
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< |
! only the distance parameter uses different mixing policies |
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< |
if (useGeometricDistanceMixing) then |
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< |
! only for OPLS as far as we can tell |
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< |
MixingMap(i,j)%sigma = dsqrt(Sigma_i * Sigma_j) |
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< |
else |
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< |
! everyone else |
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< |
MixingMap(i,j)%sigma = 0.5_dp * (Sigma_i + Sigma_j) |
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< |
endif |
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< |
|
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< |
! energy parameter is always geometric mean: |
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< |
MixingMap(i,j)%epsilon = dsqrt(Epsilon_i * Epsilon_j) |
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< |
|
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< |
MixingMap(i,j)%sigma6 = (MixingMap(i,j)%sigma)**6 |
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< |
MixingMap(i,j)%tp6 = MixingMap(i,j)%sigma6/rcut6 |
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< |
MixingMap(i,j)%tp12 = (MixingMap(i,j)%tp6) ** 2 |
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< |
|
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< |
MixingMap(i,j)%delta = -4.0_DP * MixingMap(i,j)%epsilon * & |
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< |
(MixingMap(i,j)%tp12 - MixingMap(i,j)%tp6) |
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< |
|
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< |
MixingMap(j,i)%sigma = MixingMap(i,j)%sigma |
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< |
MixingMap(j,i)%sigma6 = MixingMap(i,j)%sigma6 |
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< |
MixingMap(j,i)%tp6 = MixingMap(i,j)%tp6 |
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< |
MixingMap(j,i)%tp12 = MixingMap(i,j)%tp12 |
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< |
MixingMap(j,i)%epsilon = MixingMap(i,j)%epsilon |
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< |
MixingMap(j,i)%delta = MixingMap(i,j)%delta |
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< |
|
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< |
end do |
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> |
do i = 1, nATIDs |
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> |
call getElementProperty(atypes, i, "is_LennardJones", i_is_LJ) |
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> |
if (i_is_LJ) then |
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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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> |
MixingMap(i,i)%soft_pot = ParameterMap(i)%soft_pot |
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> |
|
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> |
do j = i + 1, nATIDs |
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> |
call getElementProperty(atypes, j, "is_LennardJones", j_is_LJ) |
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> |
|
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> |
if (j_is_LJ) then |
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> |
Epsilon_j = ParameterMap(j)%epsilon |
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> |
Sigma_j = ParameterMap(j)%sigma |
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> |
|
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> |
! only the distance parameter uses different mixing policies |
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> |
if (useGeometricDistanceMixing) then |
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> |
! only for OPLS as far as we can tell |
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> |
MixingMap(i,j)%sigma = dsqrt(Sigma_i * Sigma_j) |
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> |
else |
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> |
! everyone else |
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> |
MixingMap(i,j)%sigma = 0.5_dp * (Sigma_i + Sigma_j) |
| 271 |
> |
endif |
| 272 |
> |
|
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> |
! energy parameter is always geometric mean: |
| 274 |
> |
MixingMap(i,j)%epsilon = dsqrt(Epsilon_i * Epsilon_j) |
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> |
|
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> |
MixingMap(i,j)%sigma6 = (MixingMap(i,j)%sigma)**6 |
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> |
MixingMap(i,j)%tp6 = MixingMap(i,j)%sigma6/rcut6 |
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> |
MixingMap(i,j)%tp12 = (MixingMap(i,j)%tp6) ** 2 |
| 279 |
> |
|
| 280 |
> |
MixingMap(i,j)%delta = -4.0_DP * MixingMap(i,j)%epsilon * & |
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> |
(MixingMap(i,j)%tp12 - MixingMap(i,j)%tp6) |
| 282 |
> |
|
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> |
MixingMap(i,j)%soft_pot = ParameterMap(i)%soft_pot .or. ParameterMap(j)%soft_pot |
| 284 |
> |
|
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> |
|
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> |
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 |
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end do |
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< |
|
| 297 |
> |
|
| 298 |
> |
haveMixingMap = .true. |
| 299 |
> |
|
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|
end subroutine createMixingMap |
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< |
|
| 301 |
> |
|
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|
subroutine do_lj_pair(atom1, atom2, d, rij, r2, sw, vpair, fpair, & |
| 303 |
|
pot, f, do_pot) |
| 304 |
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|
| 320 |
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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 |
|
|
| 283 |
– |
vpair = vpair + pot_temp |
| 284 |
– |
|
| 285 |
– |
dudr = sw * 24.0E0_DP * epsilon * (t6 - 2.0E0_DP*t12) / rij |
| 286 |
– |
|
| 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 |
| 341 |
– |
|
| 342 |
– |
|
| 343 |
– |
!! Calculates the mixing for sigma or epslon |
| 344 |
– |
|
| 345 |
– |
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 |
| 352 |
< |
real(kind=dp),intent(inout) :: epsilon |
| 353 |
< |
integer,intent(inout) :: status |
| 354 |
< |
|
| 355 |
< |
call module_newLJtype(ident, sigma, epsilon, status) |
| 356 |
< |
|
| 357 |
< |
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 |
| 361 |
< |
|
| 362 |
< |
call module_useGeometricMixing() |
| 363 |
< |
return |
| 364 |
< |
end subroutine useGeometricMixing |
| 436 |
> |
|
| 437 |
> |
end module lj |
