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!! |
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!! Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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!! |
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!! The University of Notre Dame grants you ("Licensee") a |
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!! non-exclusive, royalty free, license to use, modify and |
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!! redistribute this software in source and binary code form, provided |
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!! that the following conditions are met: |
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!! |
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!! 1. Acknowledgement of the program authors must be made in any |
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!! publication of scientific results based in part on use of the |
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!! program. An acceptable form of acknowledgement is citation of |
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!! the article in which the program was described (Matthew |
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!! A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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!! J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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!! Parallel Simulation Engine for Molecular Dynamics," |
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!! J. Comput. Chem. 26, pp. 252-271 (2005)) |
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!! |
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!! 2. Redistributions of source code must retain the above copyright |
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!! notice, this list of conditions and the following disclaimer. |
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!! |
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!! 3. Redistributions in binary form must reproduce the above copyright |
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!! notice, this list of conditions and the following disclaimer in the |
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!! documentation and/or other materials provided with the |
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!! distribution. |
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!! |
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!! This software is provided "AS IS," without a warranty of any |
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!! kind. All express or implied conditions, representations and |
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!! warranties, including any implied warranty of merchantability, |
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!! fitness for a particular purpose or non-infringement, are hereby |
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!! excluded. The University of Notre Dame and its licensors shall not |
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!! be liable for any damages suffered by licensee as a result of |
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!! using, modifying or distributing the software or its |
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!! derivatives. In no event will the University of Notre Dame or its |
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!! licensors be liable for any lost revenue, profit or data, or for |
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!! direct, indirect, special, consequential, incidental or punitive |
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!! damages, however caused and regardless of the theory of liability, |
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!! arising out of the use of or inability to use software, even if the |
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!! University of Notre Dame has been advised of the possibility of |
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!! such damages. |
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!! |
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|
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|
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module gayberne |
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use force_globals |
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use definitions |
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use simulation |
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use atype_module |
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use vector_class |
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use status |
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use lj |
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#ifdef IS_MPI |
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use mpiSimulation |
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#endif |
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|
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implicit none |
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|
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private |
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|
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#define __FORTRAN90 |
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#include "UseTheForce/DarkSide/fInteractionMap.h" |
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|
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public :: newGBtype |
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public :: do_gb_pair |
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public :: do_gb_lj_pair |
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public :: getGayBerneCut |
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public :: destroyGBtypes |
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|
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type :: GBtype |
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integer :: atid |
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real(kind = dp ) :: sigma |
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real(kind = dp ) :: l2b_ratio |
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real(kind = dp ) :: eps |
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real(kind = dp ) :: eps_ratio |
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real(kind = dp ) :: mu |
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real(kind = dp ) :: nu |
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real(kind = dp ) :: sigma_l |
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real(kind = dp ) :: eps_l |
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end type GBtype |
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|
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type, private :: GBList |
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integer :: nGBtypes = 0 |
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integer :: currentGBtype = 0 |
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type(GBtype), pointer :: GBtypes(:) => null() |
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integer, pointer :: atidToGBtype(:) => null() |
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end type GBList |
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|
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type(GBList), save :: GBMap |
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|
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contains |
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|
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subroutine newGBtype(c_ident, sigma, l2b_ratio, eps, eps_ratio, mu, nu, & |
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status) |
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|
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integer, intent(in) :: c_ident |
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real( kind = dp ), intent(in) :: sigma, l2b_ratio, eps, eps_ratio |
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real( kind = dp ), intent(in) :: mu, nu |
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integer, intent(out) :: status |
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|
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integer :: nGBTypes, ntypes, myATID |
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integer, pointer :: MatchList(:) => null() |
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integer :: current, i |
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status = 0 |
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|
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if (.not.associated(GBMap%GBtypes)) then |
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|
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call getMatchingElementList(atypes, "is_GayBerne", .true., & |
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nGBtypes, MatchList) |
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|
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GBMap%nGBtypes = nGBtypes |
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|
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allocate(GBMap%GBtypes(nGBtypes)) |
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|
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ntypes = getSize(atypes) |
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|
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allocate(GBMap%atidToGBtype(ntypes)) |
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|
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!! initialize atidToGBtype to -1 so that we can use this |
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!! array to figure out which atom comes first in the GBLJ |
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!! routine |
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|
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do i = 1, ntypes |
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GBMap%atidToGBtype(i) = -1 |
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enddo |
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|
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endif |
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|
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GBMap%currentGBtype = GBMap%currentGBtype + 1 |
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current = GBMap%currentGBtype |
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|
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myATID = getFirstMatchingElement(atypes, "c_ident", c_ident) |
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GBMap%atidToGBtype(myATID) = current |
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GBMap%GBtypes(current)%atid = myATID |
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GBMap%GBtypes(current)%sigma = sigma |
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GBMap%GBtypes(current)%l2b_ratio = l2b_ratio |
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GBMap%GBtypes(current)%eps = eps |
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GBMap%GBtypes(current)%eps_ratio = eps_ratio |
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GBMap%GBtypes(current)%mu = mu |
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GBMap%GBtypes(current)%nu = nu |
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GBMap%GBtypes(current)%sigma_l = sigma*l2b_ratio |
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GBMap%GBtypes(current)%eps_l = eps*eps_ratio |
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|
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return |
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end subroutine newGBtype |
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|
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|
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!! gay berne cutoff should be a parameter in globals, this is a temporary |
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!! work around - this should be fixed when gay berne is up and running |
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|
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function getGayBerneCut(atomID) result(cutValue) |
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integer, intent(in) :: atomID |
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integer :: gbt1 |
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real(kind=dp) :: cutValue, sigma, l2b_ratio |
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|
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if (GBMap%currentGBtype == 0) then |
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call handleError("GB", "No members in GBMap") |
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return |
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end if |
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|
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gbt1 = GBMap%atidToGBtype(atomID) |
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sigma = GBMap%GBtypes(gbt1)%sigma |
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l2b_ratio = GBMap%GBtypes(gbt1)%l2b_ratio |
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|
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cutValue = l2b_ratio*sigma*2.5_dp |
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end function getGayBerneCut |
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|
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subroutine do_gb_pair(atom1, atom2, d, r, r2, sw, vpair, fpair, & |
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pot, A, f, t, do_pot) |
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|
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integer, intent(in) :: atom1, atom2 |
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integer :: atid1, atid2, gbt1, gbt2, id1, id2 |
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real (kind=dp), intent(inout) :: r, r2 |
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real (kind=dp), dimension(3), intent(in) :: d |
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real (kind=dp), dimension(3), intent(inout) :: fpair |
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real (kind=dp) :: pot, sw, vpair |
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real (kind=dp), dimension(9,nLocal) :: A |
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real (kind=dp), dimension(3,nLocal) :: f |
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real (kind=dp), dimension(3,nLocal) :: t |
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logical, intent(in) :: do_pot |
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real (kind = dp), dimension(3) :: ul1 |
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real (kind = dp), dimension(3) :: ul2 |
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|
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real(kind=dp) :: sigma, l2b_ratio, epsilon, eps_ratio, mu, nu, sigma_l, eps_l |
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real(kind=dp) :: chi, chiprime, emu, s2 |
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real(kind=dp) :: r4, rdotu1, rdotu2, u1dotu2, g, gp, gpi, gmu, gmum |
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real(kind=dp) :: curlyE, enu, enum, eps, dotsum, dotdiff, ds2, dd2 |
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real(kind=dp) :: opXdot, omXdot, opXpdot, omXpdot, pref, gfact |
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real(kind=dp) :: BigR, Ri, Ri2, Ri6, Ri7, Ri12, Ri13, R126, R137 |
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real(kind=dp) :: dru1dx, dru1dy, dru1dz |
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real(kind=dp) :: dru2dx, dru2dy, dru2dz |
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real(kind=dp) :: dBigRdx, dBigRdy, dBigRdz |
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real(kind=dp) :: dBigRdu1x, dBigRdu1y, dBigRdu1z |
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real(kind=dp) :: dBigRdu2x, dBigRdu2y, dBigRdu2z |
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real(kind=dp) :: dUdx, dUdy, dUdz |
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real(kind=dp) :: dUdu1x, dUdu1y, dUdu1z, dUdu2x, dUdu2y, dUdu2z |
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real(kind=dp) :: dcE, dcEdu1x, dcEdu1y, dcEdu1z, dcEdu2x, dcEdu2y, dcEdu2z |
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real(kind=dp) :: depsdu1x, depsdu1y, depsdu1z, depsdu2x, depsdu2y, depsdu2z |
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real(kind=dp) :: drdx, drdy, drdz |
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real(kind=dp) :: dgdx, dgdy, dgdz |
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real(kind=dp) :: dgdu1x, dgdu1y, dgdu1z, dgdu2x, dgdu2y, dgdu2z |
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real(kind=dp) :: dgpdx, dgpdy, dgpdz |
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real(kind=dp) :: dgpdu1x, dgpdu1y, dgpdu1z, dgpdu2x, dgpdu2y, dgpdu2z |
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real(kind=dp) :: line1a, line1bx, line1by, line1bz |
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real(kind=dp) :: line2a, line2bx, line2by, line2bz |
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real(kind=dp) :: line3a, line3b, line3, line3x, line3y, line3z |
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real(kind=dp) :: term1x, term1y, term1z, term1u1x, term1u1y, term1u1z |
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real(kind=dp) :: term1u2x, term1u2y, term1u2z |
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real(kind=dp) :: term2a, term2b, term2u1x, term2u1y, term2u1z |
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real(kind=dp) :: term2u2x, term2u2y, term2u2z |
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real(kind=dp) :: yick1, yick2, mess1, mess2 |
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|
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#ifdef IS_MPI |
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atid1 = atid_Row(atom1) |
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atid2 = atid_Col(atom2) |
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#else |
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atid1 = atid(atom1) |
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atid2 = atid(atom2) |
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#endif |
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|
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gbt1 = GBMap%atidToGBtype(atid1) |
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gbt2 = GBMap%atidToGBtype(atid2) |
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|
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if (gbt1 .eq. gbt2) then |
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sigma = GBMap%GBtypes(gbt1)%sigma |
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l2b_ratio = GBMap%GBtypes(gbt1)%l2b_ratio |
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epsilon = GBMap%GBtypes(gbt1)%eps |
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eps_ratio = GBMap%GBtypes(gbt1)%eps_ratio |
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mu = GBMap%GBtypes(gbt1)%mu |
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nu = GBMap%GBtypes(gbt1)%nu |
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sigma_l = GBMap%GBtypes(gbt1)%sigma_l |
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eps_l = GBMap%GBtypes(gbt1)%eps_l |
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else |
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call handleError("GB", "GB-pair was called with two different GB types! OOPSE can only handle interactions for one GB type at a time.") |
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endif |
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|
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s2 = (l2b_ratio)**2 |
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emu = (eps_ratio)**(1.0d0/mu) |
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|
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chi = (s2 - 1.0d0)/(s2 + 1.0d0) |
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chiprime = (1.0d0 - emu)/(1.0d0 + emu) |
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|
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r4 = r2*r2 |
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|
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#ifdef IS_MPI |
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ul1(1) = A_Row(3,atom1) |
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ul1(2) = A_Row(6,atom1) |
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ul1(3) = A_Row(9,atom1) |
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|
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ul2(1) = A_Col(3,atom2) |
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ul2(2) = A_Col(6,atom2) |
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ul2(3) = A_Col(9,atom2) |
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#else |
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ul1(1) = A(3,atom1) |
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ul1(2) = A(6,atom1) |
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ul1(3) = A(9,atom1) |
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|
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ul2(1) = A(3,atom2) |
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ul2(2) = A(6,atom2) |
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ul2(3) = A(9,atom2) |
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#endif |
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|
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dru1dx = ul1(1) |
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dru2dx = ul2(1) |
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dru1dy = ul1(2) |
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dru2dy = ul2(2) |
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dru1dz = ul1(3) |
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dru2dz = ul2(3) |
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|
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drdx = d(1) / r |
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drdy = d(2) / r |
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drdz = d(3) / r |
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|
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! do some dot products: |
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! NB the r in these dot products is the actual intermolecular vector, |
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! and is not the unit vector in that direction. |
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|
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rdotu1 = d(1)*ul1(1) + d(2)*ul1(2) + d(3)*ul1(3) |
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rdotu2 = d(1)*ul2(1) + d(2)*ul2(2) + d(3)*ul2(3) |
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u1dotu2 = ul1(1)*ul2(1) + ul1(2)*ul2(2) + ul1(3)*ul2(3) |
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|
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! This stuff is all for the calculation of g(Chi) and dgdx |
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! Line numbers roughly follow the lines in equation A25 of Luckhurst |
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! et al. Liquid Crystals 8, 451-464 (1990). |
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! We note however, that there are some major typos in that Appendix |
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! of the Luckhurst paper, particularly in equations A23, A29 and A31 |
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! We have attempted to correct them below. |
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|
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dotsum = rdotu1+rdotu2 |
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dotdiff = rdotu1-rdotu2 |
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ds2 = dotsum*dotsum |
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dd2 = dotdiff*dotdiff |
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|
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opXdot = 1.0d0 + Chi*u1dotu2 |
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omXdot = 1.0d0 - Chi*u1dotu2 |
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opXpdot = 1.0d0 + ChiPrime*u1dotu2 |
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omXpdot = 1.0d0 - ChiPrime*u1dotu2 |
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|
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line1a = dotsum/opXdot |
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line1bx = dru1dx + dru2dx |
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line1by = dru1dy + dru2dy |
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line1bz = dru1dz + dru2dz |
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|
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line2a = dotdiff/omXdot |
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line2bx = dru1dx - dru2dx |
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line2by = dru1dy - dru2dy |
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line2bz = dru1dz - dru2dz |
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|
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term1x = -Chi*(line1a*line1bx + line2a*line2bx)/r2 |
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term1y = -Chi*(line1a*line1by + line2a*line2by)/r2 |
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term1z = -Chi*(line1a*line1bz + line2a*line2bz)/r2 |
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|
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line3a = ds2/opXdot |
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line3b = dd2/omXdot |
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line3 = Chi*(line3a + line3b)/r4 |
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line3x = d(1)*line3 |
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line3y = d(2)*line3 |
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line3z = d(3)*line3 |
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|
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dgdx = term1x + line3x |
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dgdy = term1y + line3y |
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dgdz = term1z + line3z |
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|
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term1u1x = 2.0d0*(line1a+line2a)*d(1) |
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term1u1y = 2.0d0*(line1a+line2a)*d(2) |
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term1u1z = 2.0d0*(line1a+line2a)*d(3) |
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term1u2x = 2.0d0*(line1a-line2a)*d(1) |
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term1u2y = 2.0d0*(line1a-line2a)*d(2) |
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term1u2z = 2.0d0*(line1a-line2a)*d(3) |
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|
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term2a = -line3a/opXdot |
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term2b = line3b/omXdot |
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|
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term2u1x = Chi*ul2(1)*(term2a + term2b) |
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term2u1y = Chi*ul2(2)*(term2a + term2b) |
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term2u1z = Chi*ul2(3)*(term2a + term2b) |
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term2u2x = Chi*ul1(1)*(term2a + term2b) |
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term2u2y = Chi*ul1(2)*(term2a + term2b) |
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term2u2z = Chi*ul1(3)*(term2a + term2b) |
| 338 |
|
| 339 |
pref = -Chi*0.5d0/r2 |
| 340 |
|
| 341 |
dgdu1x = pref*(term1u1x+term2u1x) |
| 342 |
dgdu1y = pref*(term1u1y+term2u1y) |
| 343 |
dgdu1z = pref*(term1u1z+term2u1z) |
| 344 |
dgdu2x = pref*(term1u2x+term2u2x) |
| 345 |
dgdu2y = pref*(term1u2y+term2u2y) |
| 346 |
dgdu2z = pref*(term1u2z+term2u2z) |
| 347 |
|
| 348 |
g = 1.0d0 - Chi*(line3a + line3b)/(2.0d0*r2) |
| 349 |
|
| 350 |
BigR = (r - sigma*(g**(-0.5d0)) + sigma)/sigma |
| 351 |
Ri = 1.0d0/BigR |
| 352 |
Ri2 = Ri*Ri |
| 353 |
Ri6 = Ri2*Ri2*Ri2 |
| 354 |
Ri7 = Ri6*Ri |
| 355 |
Ri12 = Ri6*Ri6 |
| 356 |
Ri13 = Ri6*Ri7 |
| 357 |
|
| 358 |
gfact = (g**(-1.5d0))*0.5d0 |
| 359 |
|
| 360 |
dBigRdx = drdx/sigma + dgdx*gfact |
| 361 |
dBigRdy = drdy/sigma + dgdy*gfact |
| 362 |
dBigRdz = drdz/sigma + dgdz*gfact |
| 363 |
|
| 364 |
dBigRdu1x = dgdu1x*gfact |
| 365 |
dBigRdu1y = dgdu1y*gfact |
| 366 |
dBigRdu1z = dgdu1z*gfact |
| 367 |
dBigRdu2x = dgdu2x*gfact |
| 368 |
dBigRdu2y = dgdu2y*gfact |
| 369 |
dBigRdu2z = dgdu2z*gfact |
| 370 |
|
| 371 |
! Now, we must do it again for g(ChiPrime) and dgpdx |
| 372 |
|
| 373 |
line1a = dotsum/opXpdot |
| 374 |
line2a = dotdiff/omXpdot |
| 375 |
term1x = -ChiPrime*(line1a*line1bx + line2a*line2bx)/r2 |
| 376 |
term1y = -ChiPrime*(line1a*line1by + line2a*line2by)/r2 |
| 377 |
term1z = -ChiPrime*(line1a*line1bz + line2a*line2bz)/r2 |
| 378 |
line3a = ds2/opXpdot |
| 379 |
line3b = dd2/omXpdot |
| 380 |
line3 = ChiPrime*(line3a + line3b)/r4 |
| 381 |
line3x = d(1)*line3 |
| 382 |
line3y = d(2)*line3 |
| 383 |
line3z = d(3)*line3 |
| 384 |
|
| 385 |
dgpdx = term1x + line3x |
| 386 |
dgpdy = term1y + line3y |
| 387 |
dgpdz = term1z + line3z |
| 388 |
|
| 389 |
term1u1x = 2.00d0*(line1a+line2a)*d(1) |
| 390 |
term1u1y = 2.00d0*(line1a+line2a)*d(2) |
| 391 |
term1u1z = 2.00d0*(line1a+line2a)*d(3) |
| 392 |
term1u2x = 2.0d0*(line1a-line2a)*d(1) |
| 393 |
term1u2y = 2.0d0*(line1a-line2a)*d(2) |
| 394 |
term1u2z = 2.0d0*(line1a-line2a)*d(3) |
| 395 |
|
| 396 |
term2a = -line3a/opXpdot |
| 397 |
term2b = line3b/omXpdot |
| 398 |
|
| 399 |
term2u1x = ChiPrime*ul2(1)*(term2a + term2b) |
| 400 |
term2u1y = ChiPrime*ul2(2)*(term2a + term2b) |
| 401 |
term2u1z = ChiPrime*ul2(3)*(term2a + term2b) |
| 402 |
term2u2x = ChiPrime*ul1(1)*(term2a + term2b) |
| 403 |
term2u2y = ChiPrime*ul1(2)*(term2a + term2b) |
| 404 |
term2u2z = ChiPrime*ul1(3)*(term2a + term2b) |
| 405 |
|
| 406 |
pref = -ChiPrime*0.5d0/r2 |
| 407 |
|
| 408 |
dgpdu1x = pref*(term1u1x+term2u1x) |
| 409 |
dgpdu1y = pref*(term1u1y+term2u1y) |
| 410 |
dgpdu1z = pref*(term1u1z+term2u1z) |
| 411 |
dgpdu2x = pref*(term1u2x+term2u2x) |
| 412 |
dgpdu2y = pref*(term1u2y+term2u2y) |
| 413 |
dgpdu2z = pref*(term1u2z+term2u2z) |
| 414 |
|
| 415 |
gp = 1.0d0 - ChiPrime*(line3a + line3b)/(2.0d0*r2) |
| 416 |
gmu = gp**mu |
| 417 |
gpi = 1.0d0 / gp |
| 418 |
gmum = gmu*gpi |
| 419 |
|
| 420 |
curlyE = 1.0d0/dsqrt(1.0d0 - Chi*Chi*u1dotu2*u1dotu2) |
| 421 |
!!$ |
| 422 |
!!$ dcE = -(curlyE**3)*Chi*Chi*u1dotu2 |
| 423 |
dcE = (curlyE**3)*Chi*Chi*u1dotu2 |
| 424 |
|
| 425 |
dcEdu1x = dcE*ul2(1) |
| 426 |
dcEdu1y = dcE*ul2(2) |
| 427 |
dcEdu1z = dcE*ul2(3) |
| 428 |
dcEdu2x = dcE*ul1(1) |
| 429 |
dcEdu2y = dcE*ul1(2) |
| 430 |
dcEdu2z = dcE*ul1(3) |
| 431 |
|
| 432 |
enu = curlyE**nu |
| 433 |
enum = enu/curlyE |
| 434 |
|
| 435 |
eps = epsilon*enu*gmu |
| 436 |
|
| 437 |
yick1 = epsilon*enu*mu*gmum |
| 438 |
yick2 = epsilon*gmu*nu*enum |
| 439 |
|
| 440 |
depsdu1x = yick1*dgpdu1x + yick2*dcEdu1x |
| 441 |
depsdu1y = yick1*dgpdu1y + yick2*dcEdu1y |
| 442 |
depsdu1z = yick1*dgpdu1z + yick2*dcEdu1z |
| 443 |
depsdu2x = yick1*dgpdu2x + yick2*dcEdu2x |
| 444 |
depsdu2y = yick1*dgpdu2y + yick2*dcEdu2y |
| 445 |
depsdu2z = yick1*dgpdu2z + yick2*dcEdu2z |
| 446 |
|
| 447 |
R126 = Ri12 - Ri6 |
| 448 |
R137 = 6.0d0*Ri7 - 12.0d0*Ri13 |
| 449 |
|
| 450 |
mess1 = gmu*R137 |
| 451 |
mess2 = R126*mu*gmum |
| 452 |
|
| 453 |
dUdx = 4.0d0*epsilon*enu*(mess1*dBigRdx + mess2*dgpdx)*sw |
| 454 |
dUdy = 4.0d0*epsilon*enu*(mess1*dBigRdy + mess2*dgpdy)*sw |
| 455 |
dUdz = 4.0d0*epsilon*enu*(mess1*dBigRdz + mess2*dgpdz)*sw |
| 456 |
|
| 457 |
dUdu1x = 4.0d0*(R126*depsdu1x + eps*R137*dBigRdu1x)*sw |
| 458 |
dUdu1y = 4.0d0*(R126*depsdu1y + eps*R137*dBigRdu1y)*sw |
| 459 |
dUdu1z = 4.0d0*(R126*depsdu1z + eps*R137*dBigRdu1z)*sw |
| 460 |
dUdu2x = 4.0d0*(R126*depsdu2x + eps*R137*dBigRdu2x)*sw |
| 461 |
dUdu2y = 4.0d0*(R126*depsdu2y + eps*R137*dBigRdu2y)*sw |
| 462 |
dUdu2z = 4.0d0*(R126*depsdu2z + eps*R137*dBigRdu2z)*sw |
| 463 |
|
| 464 |
#ifdef IS_MPI |
| 465 |
f_Row(1,atom1) = f_Row(1,atom1) + dUdx |
| 466 |
f_Row(2,atom1) = f_Row(2,atom1) + dUdy |
| 467 |
f_Row(3,atom1) = f_Row(3,atom1) + dUdz |
| 468 |
|
| 469 |
f_Col(1,atom2) = f_Col(1,atom2) - dUdx |
| 470 |
f_Col(2,atom2) = f_Col(2,atom2) - dUdy |
| 471 |
f_Col(3,atom2) = f_Col(3,atom2) - dUdz |
| 472 |
|
| 473 |
t_Row(1,atom1) = t_Row(1,atom1)- ul1(3)*dUdu1y + ul1(2)*dUdu1z |
| 474 |
t_Row(2,atom1) = t_Row(2,atom1)- ul1(1)*dUdu1z + ul1(3)*dUdu1x |
| 475 |
t_Row(3,atom1) = t_Row(3,atom1)- ul1(2)*dUdu1x + ul1(1)*dUdu1y |
| 476 |
|
| 477 |
t_Col(1,atom2) = t_Col(1,atom2) - ul2(3)*dUdu2y + ul2(2)*dUdu2z |
| 478 |
t_Col(2,atom2) = t_Col(2,atom2) - ul2(1)*dUdu2z + ul2(3)*dUdu2x |
| 479 |
t_Col(3,atom2) = t_Col(3,atom2) - ul2(2)*dUdu2x + ul2(1)*dUdu2y |
| 480 |
#else |
| 481 |
f(1,atom1) = f(1,atom1) + dUdx |
| 482 |
f(2,atom1) = f(2,atom1) + dUdy |
| 483 |
f(3,atom1) = f(3,atom1) + dUdz |
| 484 |
|
| 485 |
f(1,atom2) = f(1,atom2) - dUdx |
| 486 |
f(2,atom2) = f(2,atom2) - dUdy |
| 487 |
f(3,atom2) = f(3,atom2) - dUdz |
| 488 |
|
| 489 |
t(1,atom1) = t(1,atom1)- ul1(3)*dUdu1y + ul1(2)*dUdu1z |
| 490 |
t(2,atom1) = t(2,atom1)- ul1(1)*dUdu1z + ul1(3)*dUdu1x |
| 491 |
t(3,atom1) = t(3,atom1)- ul1(2)*dUdu1x + ul1(1)*dUdu1y |
| 492 |
|
| 493 |
t(1,atom2) = t(1,atom2)- ul2(3)*dUdu2y + ul2(2)*dUdu2z |
| 494 |
t(2,atom2) = t(2,atom2)- ul2(1)*dUdu2z + ul2(3)*dUdu2x |
| 495 |
t(3,atom2) = t(3,atom2)- ul2(2)*dUdu2x + ul2(1)*dUdu2y |
| 496 |
#endif |
| 497 |
|
| 498 |
if (do_pot) then |
| 499 |
#ifdef IS_MPI |
| 500 |
pot_row(VDW_POT,atom1) = pot_row(VDW_POT,atom1) + 2.0d0*eps*R126*sw |
| 501 |
pot_col(VDW_POT,atom2) = pot_col(VDW_POT,atom2) + 2.0d0*eps*R126*sw |
| 502 |
#else |
| 503 |
pot = pot + 4.0*eps*R126*sw |
| 504 |
#endif |
| 505 |
endif |
| 506 |
|
| 507 |
vpair = vpair + 4.0*eps*R126 |
| 508 |
#ifdef IS_MPI |
| 509 |
id1 = AtomRowToGlobal(atom1) |
| 510 |
id2 = AtomColToGlobal(atom2) |
| 511 |
#else |
| 512 |
id1 = atom1 |
| 513 |
id2 = atom2 |
| 514 |
#endif |
| 515 |
|
| 516 |
if (molMembershipList(id1) .ne. molMembershipList(id2)) then |
| 517 |
|
| 518 |
fpair(1) = fpair(1) + dUdx |
| 519 |
fpair(2) = fpair(2) + dUdy |
| 520 |
fpair(3) = fpair(3) + dUdz |
| 521 |
|
| 522 |
endif |
| 523 |
|
| 524 |
return |
| 525 |
end subroutine do_gb_pair |
| 526 |
|
| 527 |
subroutine do_gb_lj_pair(atom1, atom2, d, r, r2, sw, vpair, fpair, & |
| 528 |
pot, A, f, t, do_pot) |
| 529 |
|
| 530 |
integer, intent(in) :: atom1, atom2 |
| 531 |
integer :: id1, id2 |
| 532 |
real (kind=dp), intent(inout) :: r, r2 |
| 533 |
real (kind=dp), dimension(3), intent(in) :: d |
| 534 |
real (kind=dp), dimension(3), intent(inout) :: fpair |
| 535 |
real (kind=dp) :: pot, sw, vpair |
| 536 |
real (kind=dp), dimension(9,nLocal) :: A |
| 537 |
real (kind=dp), dimension(3,nLocal) :: f |
| 538 |
real (kind=dp), dimension(3,nLocal) :: t |
| 539 |
logical, intent(in) :: do_pot |
| 540 |
real (kind = dp), dimension(3) :: ul |
| 541 |
|
| 542 |
real(kind=dp) :: gb_sigma, gb_eps, gb_eps_ratio, gb_mu, gb_sigma_l |
| 543 |
real(kind=dp) :: spar, sperp, slj, par2, perp2, sc, slj2 |
| 544 |
real(kind=dp) :: s_par2mperp2, s_lj2ppar2 |
| 545 |
real(kind=dp) :: enot, eperp, epar, eab, eabf,moom, mum1 |
| 546 |
real(kind=dp) :: dx, dy, dz, drdx,drdy,drdz, rdotu |
| 547 |
real(kind=dp) :: mess, sab, dsabdct, eprime, deprimedct, depmudct |
| 548 |
real(kind=dp) :: epmu, depmudx, depmudy, depmudz |
| 549 |
real(kind=dp) :: depmudux, depmuduy, depmuduz |
| 550 |
real(kind=dp) :: BigR, dBigRdx, dBigRdy, dBigRdz |
| 551 |
real(kind=dp) :: dBigRdux, dBigRduy, dBigRduz |
| 552 |
real(kind=dp) :: dUdx, dUdy, dUdz, dUdux, dUduy, dUduz, e0 |
| 553 |
real(kind=dp) :: Ri, Ri3, Ri6, Ri7, Ri12, Ri13, R126, R137, prefactor |
| 554 |
real(kind=dp) :: chipoalphap2, chioalpha2, ec, epsnot |
| 555 |
real(kind=dp) :: drdotudx, drdotudy, drdotudz |
| 556 |
real(kind=dp) :: drdotudux, drdotuduy, drdotuduz |
| 557 |
real(kind=dp) :: ljeps, ljsigma, sigmaratio, sigmaratioi |
| 558 |
integer :: ljt1, ljt2, atid1, atid2, gbt1, gbt2 |
| 559 |
logical :: gb_first |
| 560 |
|
| 561 |
#ifdef IS_MPI |
| 562 |
atid1 = atid_Row(atom1) |
| 563 |
atid2 = atid_Col(atom2) |
| 564 |
#else |
| 565 |
atid1 = atid(atom1) |
| 566 |
atid2 = atid(atom2) |
| 567 |
#endif |
| 568 |
|
| 569 |
gbt1 = GBMap%atidToGBtype(atid1) |
| 570 |
gbt2 = GBMap%atidToGBtype(atid2) |
| 571 |
|
| 572 |
if (gbt1 .eq. -1) then |
| 573 |
gb_first = .false. |
| 574 |
if (gbt2 .eq. -1) then |
| 575 |
call handleError("GB", "GBLJ was called without a GB type.") |
| 576 |
endif |
| 577 |
else |
| 578 |
gb_first = .true. |
| 579 |
if (gbt2 .ne. -1) then |
| 580 |
call handleError("GB", "GBLJ was called with two GB types (instead of one).") |
| 581 |
endif |
| 582 |
endif |
| 583 |
|
| 584 |
ri =1/r |
| 585 |
|
| 586 |
dx = d(1) |
| 587 |
dy = d(2) |
| 588 |
dz = d(3) |
| 589 |
|
| 590 |
drdx = dx *ri |
| 591 |
drdy = dy *ri |
| 592 |
drdz = dz *ri |
| 593 |
|
| 594 |
if(gb_first)then |
| 595 |
#ifdef IS_MPI |
| 596 |
ul(1) = A_Row(3,atom1) |
| 597 |
ul(2) = A_Row(6,atom1) |
| 598 |
ul(3) = A_Row(9,atom1) |
| 599 |
#else |
| 600 |
ul(1) = A(3,atom1) |
| 601 |
ul(2) = A(6,atom1) |
| 602 |
ul(3) = A(9,atom1) |
| 603 |
#endif |
| 604 |
gb_sigma = GBMap%GBtypes(gbt1)%sigma |
| 605 |
gb_eps = GBMap%GBtypes(gbt1)%eps |
| 606 |
gb_eps_ratio = GBMap%GBtypes(gbt1)%eps_ratio |
| 607 |
gb_mu = GBMap%GBtypes(gbt1)%mu |
| 608 |
gb_sigma_l = GBMap%GBtypes(gbt1)%sigma_l |
| 609 |
|
| 610 |
ljsigma = getSigma(atid2) |
| 611 |
ljeps = getEpsilon(atid2) |
| 612 |
else |
| 613 |
#ifdef IS_MPI |
| 614 |
ul(1) = A_Col(3,atom2) |
| 615 |
ul(2) = A_Col(6,atom2) |
| 616 |
ul(3) = A_Col(9,atom2) |
| 617 |
#else |
| 618 |
ul(1) = A(3,atom2) |
| 619 |
ul(2) = A(6,atom2) |
| 620 |
ul(3) = A(9,atom2) |
| 621 |
#endif |
| 622 |
gb_sigma = GBMap%GBtypes(gbt2)%sigma |
| 623 |
gb_eps = GBMap%GBtypes(gbt2)%eps |
| 624 |
gb_eps_ratio = GBMap%GBtypes(gbt2)%eps_ratio |
| 625 |
gb_mu = GBMap%GBtypes(gbt2)%mu |
| 626 |
gb_sigma_l = GBMap%GBtypes(gbt2)%sigma_l |
| 627 |
|
| 628 |
ljsigma = getSigma(atid1) |
| 629 |
ljeps = getEpsilon(atid1) |
| 630 |
endif |
| 631 |
|
| 632 |
write(*,*) 'd u', dx, dy, dz, ul(1), ul(2), ul(3) |
| 633 |
|
| 634 |
rdotu = (dx*ul(1)+dy*ul(2)+dz*ul(3))*ri |
| 635 |
|
| 636 |
drdotudx = ul(1)*ri-rdotu*dx*ri*ri |
| 637 |
drdotudy = ul(2)*ri-rdotu*dy*ri*ri |
| 638 |
drdotudz = ul(3)*ri-rdotu*dz*ri*ri |
| 639 |
drdotudux = drdx |
| 640 |
drdotuduy = drdy |
| 641 |
drdotuduz = drdz |
| 642 |
|
| 643 |
|
| 644 |
moom = 1.0d0 / gb_mu |
| 645 |
mum1 = gb_mu-1 |
| 646 |
|
| 647 |
sperp = gb_sigma |
| 648 |
spar = gb_sigma_l |
| 649 |
slj = ljsigma |
| 650 |
slj2 = slj*slj |
| 651 |
|
| 652 |
chioalpha2 =1-((sperp+slj)*(sperp+slj))/((spar+slj)*(spar+slj)) |
| 653 |
sc = (sperp+slj)/2.0d0 |
| 654 |
|
| 655 |
par2 = spar*spar |
| 656 |
perp2 = sperp*sperp |
| 657 |
s_par2mperp2 = par2 - perp2 |
| 658 |
s_lj2ppar2 = slj2 + par2 |
| 659 |
|
| 660 |
!! check these ! left from old code |
| 661 |
!! kdaily e0 may need to be (gb_eps + lj_eps)/2 |
| 662 |
|
| 663 |
eperp = dsqrt(gb_eps*ljeps) |
| 664 |
epar = eperp*gb_eps_ratio |
| 665 |
enot = dsqrt(ljeps*eperp) |
| 666 |
chipoalphap2 = 1+(dsqrt(epar*ljeps)/enot)**moom |
| 667 |
|
| 668 |
!! mess matches cleaver (eq 20) |
| 669 |
|
| 670 |
mess = 1-rdotu*rdotu*chioalpha2 |
| 671 |
sab = 1.0d0/dsqrt(mess) |
| 672 |
|
| 673 |
write(*,*) 's', sc, sab, rdotu, chioalpha2 |
| 674 |
dsabdct = sc*sab*sab*sab*rdotu*chioalpha2 |
| 675 |
|
| 676 |
eab = 1-chipoalphap2*rdotu*rdotu |
| 677 |
eabf = enot*eab**gb_mu |
| 678 |
|
| 679 |
write(*,*) 'e', enot, chipoalphap2, gb_mu, rdotu, eab, mum1 |
| 680 |
|
| 681 |
depmudct = -2*enot*chipoalphap2*gb_mu*rdotu*eab**mum1 |
| 682 |
|
| 683 |
BigR = (r - sab*sc + sc)/sc |
| 684 |
dBigRdx = (drdx -dsabdct*drdotudx)/sc |
| 685 |
dBigRdy = (drdy -dsabdct*drdotudy)/sc |
| 686 |
dBigRdz = (drdz -dsabdct*drdotudz)/sc |
| 687 |
dBigRdux = (-dsabdct*drdotudux)/sc |
| 688 |
dBigRduy = (-dsabdct*drdotuduy)/sc |
| 689 |
dBigRduz = (-dsabdct*drdotuduz)/sc |
| 690 |
|
| 691 |
write(*,*) 'ds dep', dsabdct, depmudct |
| 692 |
write(*,*) 'drdotudu', drdotudux, drdotuduy, drdotuduz |
| 693 |
depmudx = depmudct*drdotudx |
| 694 |
depmudy = depmudct*drdotudy |
| 695 |
depmudz = depmudct*drdotudz |
| 696 |
depmudux = depmudct*drdotudux |
| 697 |
depmuduy = depmudct*drdotuduy |
| 698 |
depmuduz = depmudct*drdotuduz |
| 699 |
|
| 700 |
Ri = 1.0d0/BigR |
| 701 |
Ri3 = Ri*Ri*Ri |
| 702 |
Ri6 = Ri3*Ri3 |
| 703 |
Ri7 = Ri6*Ri |
| 704 |
Ri12 = Ri6*Ri6 |
| 705 |
Ri13 = Ri6*Ri7 |
| 706 |
R126 = Ri12 - Ri6 |
| 707 |
R137 = 6.0d0*Ri7 - 12.0d0*Ri13 |
| 708 |
|
| 709 |
prefactor = 4.0d0 |
| 710 |
|
| 711 |
dUdx = prefactor*(eabf*R137*dBigRdx + R126*depmudx) |
| 712 |
dUdy = prefactor*(eabf*R137*dBigRdy + R126*depmudy) |
| 713 |
dUdz = prefactor*(eabf*R137*dBigRdz + R126*depmudz) |
| 714 |
write(*,*) 'dRdu', dbigrdux, dbigrduy, dbigrduz |
| 715 |
write(*,*) 'dEdu', depmudux, depmuduy, depmuduz |
| 716 |
dUdux = prefactor*(eabf*R137*dBigRdux + R126*depmudux) |
| 717 |
dUduy = prefactor*(eabf*R137*dBigRduy + R126*depmuduy) |
| 718 |
dUduz = prefactor*(eabf*R137*dBigRduz + R126*depmuduz) |
| 719 |
|
| 720 |
#ifdef IS_MPI |
| 721 |
f_Row(1,atom1) = f_Row(1,atom1) - dUdx |
| 722 |
f_Row(2,atom1) = f_Row(2,atom1) - dUdy |
| 723 |
f_Row(3,atom1) = f_Row(3,atom1) - dUdz |
| 724 |
|
| 725 |
f_Col(1,atom2) = f_Col(1,atom2) + dUdx |
| 726 |
f_Col(2,atom2) = f_Col(2,atom2) + dUdy |
| 727 |
f_Col(3,atom2) = f_Col(3,atom2) + dUdz |
| 728 |
|
| 729 |
if (gb_first) then |
| 730 |
t_Row(1,atom1) = t_Row(1,atom1) + ul(2)*dUduz - ul(3)*dUduy |
| 731 |
t_Row(2,atom1) = t_Row(2,atom1) + ul(3)*dUdux - ul(1)*dUduz |
| 732 |
t_Row(3,atom1) = t_Row(3,atom1) + ul(1)*dUduy - ul(2)*dUdux |
| 733 |
else |
| 734 |
t_Col(1,atom2) = t_Col(1,atom2) + ul(2)*dUduz - ul(3)*dUduy |
| 735 |
t_Col(2,atom2) = t_Col(2,atom2) + ul(3)*dUdux - ul(1)*dUduz |
| 736 |
t_Col(3,atom2) = t_Col(3,atom2) + ul(1)*dUduy - ul(2)*dUdux |
| 737 |
endif |
| 738 |
#else |
| 739 |
f(1,atom1) = f(1,atom1) + dUdx |
| 740 |
f(2,atom1) = f(2,atom1) + dUdy |
| 741 |
f(3,atom1) = f(3,atom1) + dUdz |
| 742 |
|
| 743 |
f(1,atom2) = f(1,atom2) - dUdx |
| 744 |
f(2,atom2) = f(2,atom2) - dUdy |
| 745 |
f(3,atom2) = f(3,atom2) - dUdz |
| 746 |
|
| 747 |
! torques are cross products: |
| 748 |
|
| 749 |
write(*,*) 'dU', dUdux, duduy, duduz |
| 750 |
|
| 751 |
if (gb_first) then |
| 752 |
t(1,atom1) = t(1,atom1) + ul(2)*dUduz - ul(3)*dUduy |
| 753 |
t(2,atom1) = t(2,atom1) + ul(3)*dUdux - ul(1)*dUduz |
| 754 |
t(3,atom1) = t(3,atom1) + ul(1)*dUduy - ul(2)*dUdux |
| 755 |
write(*,*) 'T1', t(1,atom1), t(2,atom1), t(3,atom1) |
| 756 |
else |
| 757 |
t(1,atom2) = t(1,atom2) + ul(2)*dUduz - ul(3)*dUduy |
| 758 |
t(2,atom2) = t(2,atom2) + ul(3)*dUdux - ul(1)*dUduz |
| 759 |
t(3,atom2) = t(3,atom2) + ul(1)*dUduy - ul(2)*dUdux |
| 760 |
|
| 761 |
write(*,*) 'T2', t(1,atom2), t(2,atom2), t(3,atom2) |
| 762 |
endif |
| 763 |
|
| 764 |
#endif |
| 765 |
|
| 766 |
if (do_pot) then |
| 767 |
#ifdef IS_MPI |
| 768 |
pot_row(VDW_POT,atom1) = pot_row(VDW_POT,atom1) + 2.0d0*eps*R126*sw |
| 769 |
pot_col(VDW_POT,atom2) = pot_col(VDW_POT,atom2) + 2.0d0*eps*R126*sw |
| 770 |
#else |
| 771 |
pot = pot + prefactor*eabf*R126*sw |
| 772 |
#endif |
| 773 |
endif |
| 774 |
|
| 775 |
vpair = vpair + 4.0*epmu*R126 |
| 776 |
#ifdef IS_MPI |
| 777 |
id1 = AtomRowToGlobal(atom1) |
| 778 |
id2 = AtomColToGlobal(atom2) |
| 779 |
#else |
| 780 |
id1 = atom1 |
| 781 |
id2 = atom2 |
| 782 |
#endif |
| 783 |
|
| 784 |
If (Molmembershiplist(Id1) .Ne. Molmembershiplist(Id2)) Then |
| 785 |
|
| 786 |
Fpair(1) = Fpair(1) + Dudx |
| 787 |
Fpair(2) = Fpair(2) + Dudy |
| 788 |
Fpair(3) = Fpair(3) + Dudz |
| 789 |
|
| 790 |
Endif |
| 791 |
|
| 792 |
return |
| 793 |
|
| 794 |
end subroutine do_gb_lj_pair |
| 795 |
|
| 796 |
subroutine destroyGBTypes() |
| 797 |
|
| 798 |
GBMap%nGBtypes = 0 |
| 799 |
GBMap%currentGBtype = 0 |
| 800 |
|
| 801 |
if (associated(GBMap%GBtypes)) then |
| 802 |
deallocate(GBMap%GBtypes) |
| 803 |
GBMap%GBtypes => null() |
| 804 |
end if |
| 805 |
|
| 806 |
if (associated(GBMap%atidToGBtype)) then |
| 807 |
deallocate(GBMap%atidToGBtype) |
| 808 |
GBMap%atidToGBtype => null() |
| 809 |
end if |
| 810 |
|
| 811 |
end subroutine destroyGBTypes |
| 812 |
|
| 813 |
end module gayberne |
| 814 |
|
