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!! |
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!! Copyright (c) 2007 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 Metal-Non Metal interactions. |
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!! @author Charles F. Vardeman II |
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!! @version $Id: MetalNonMetal.F90,v 1.9 2008-03-11 21:06:54 chuckv Exp $, $Date: 2008-03-11 21:06:54 $, $Name: not supported by cvs2svn $, $Revision: 1.9 $ |
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module MetalNonMetal |
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use definitions |
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use atype_module |
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use vector_class |
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use simulation |
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use status |
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use fForceOptions |
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#ifdef IS_MPI |
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use mpiSimulation |
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#endif |
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use force_globals |
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|
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implicit none |
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PRIVATE |
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#define __FORTRAN90 |
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#include "UseTheForce/DarkSide/fInteractionMap.h" |
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#include "UseTheForce/DarkSide/fMnMInteractions.h" |
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|
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logical, save :: useGeometricDistanceMixing = .false. |
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logical, save :: haveInteractionLookup = .false. |
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|
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real(kind=DP), save :: defaultCutoff = 0.0_DP |
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|
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logical, save :: defaultShiftPot = .false. |
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logical, save :: defaultShiftFrc = .false. |
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logical, save :: haveDefaultCutoff = .false. |
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|
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type :: MnMinteraction |
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integer :: metal_atid |
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integer :: nonmetal_atid |
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integer :: interaction_type |
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real(kind=dp) :: R0 |
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real(kind=dp) :: D0 |
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real(kind=dp) :: beta0 |
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real(kind=dp) :: betaH |
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real(kind=dp) :: alpha |
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real(kind=dp) :: gamma |
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real(kind=dp) :: sigma |
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real(kind=dp) :: epsilon |
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real(kind=dp) :: rCut = 0.0_dp |
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logical :: rCutWasSet = .false. |
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logical :: shiftedPot = .false. |
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logical :: shiftedFrc = .false. |
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end type MnMinteraction |
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|
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type :: MnMinteractionMap |
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PRIVATE |
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integer :: initialCapacity = 10 |
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integer :: capacityIncrement = 0 |
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integer :: interactionCount = 0 |
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type(MnMinteraction), pointer :: interactions(:) => null() |
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end type MnMinteractionMap |
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|
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type (MnMInteractionMap), pointer :: MnM_Map |
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|
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integer, allocatable, dimension(:,:) :: MnMinteractionLookup |
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|
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public :: setMnMDefaultCutoff |
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public :: addInteraction |
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public :: deleteInteractions |
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public :: MNMtype |
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public :: do_mnm_pair |
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|
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contains |
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|
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|
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subroutine do_mnm_pair(Atom1, Atom2, D, Rij, R2, Rcut, Sw, Vpair, Fpair, & |
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Pot, A, F,t, Do_pot) |
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integer, intent(in) :: atom1, atom2 |
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integer :: atid1, atid2, ljt1, ljt2 |
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real( kind = dp ), intent(in) :: rij, r2, rcut |
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real( kind = dp ) :: pot, sw, vpair |
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real( kind = dp ), intent(inout), dimension(3,nLocal) :: f |
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real (kind=dp), intent(in), dimension(9,nLocal) :: A |
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real (kind=dp), intent(inout), dimension(3,nLocal) :: t |
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real( kind = dp ), intent(in), dimension(3) :: d |
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real( kind = dp ), intent(inout), dimension(3) :: fpair |
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logical, intent(in) :: do_pot |
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|
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integer :: interaction_id |
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integer :: interaction_type |
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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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if(.not.haveInteractionLookup) then |
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call createInteractionLookup(MnM_MAP) |
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haveInteractionLookup =.true. |
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end if |
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|
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interaction_id = MnMinteractionLookup(atid1, atid2) |
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interaction_type = MnM_Map%interactions(interaction_id)%interaction_type |
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|
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|
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|
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select case (interaction_type) |
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case (MNM_LENNARDJONES) |
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call calc_mnm_lennardjones(Atom1, Atom2, D, Rij, R2, Rcut, Sw, Vpair, & |
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Fpair, Pot, F, Do_pot, interaction_id) |
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case(MNM_REPULSIVEMORSE, MNM_SHIFTEDMORSE) |
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call calc_mnm_morse(Atom1, Atom2, D, Rij, R2, Rcut, Sw, Vpair, Fpair, & |
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Pot, F, Do_pot, interaction_id, interaction_type) |
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case(MNM_MAW) |
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call calc_mnm_maw(Atom1, Atom2, D, Rij, R2, Rcut, Sw, Vpair, Fpair, & |
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Pot,A, F,t, Do_pot, interaction_id) |
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case default |
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call handleError("MetalNonMetal","Unknown interaction type") |
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end select |
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|
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end subroutine do_mnm_pair |
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|
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subroutine calc_mnm_lennardjones(Atom1, Atom2, D, Rij, R2, Rcut, Sw, Vpair, & |
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Fpair, Pot, F, Do_pot, interaction_id) |
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|
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integer, intent(in) :: atom1, atom2 |
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real( kind = dp ), intent(in) :: rij, r2, rcut |
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real( kind = dp ) :: pot, sw, vpair |
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real( kind = dp ), intent(inout), dimension(3,nLocal) :: f |
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real( kind = dp ), intent(in), dimension(3) :: d |
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real( kind = dp ), intent(inout), dimension(3) :: fpair |
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logical, intent(in) :: do_pot |
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integer, intent(in) :: interaction_id |
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|
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! local Variables |
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real( kind = dp ) :: drdx, drdy, drdz |
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real( kind = dp ) :: fx, fy, fz |
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real( kind = dp ) :: myPot, myPotC, myDeriv, myDerivC, ros, rcos |
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real( kind = dp ) :: pot_temp, dudr |
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real( kind = dp ) :: sigmai |
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real( kind = dp ) :: epsilon |
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logical :: isSoftCore, shiftedPot, shiftedFrc |
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integer :: id1, id2, localError |
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|
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sigmai = 1.0_dp / MnM_Map%interactions(interaction_id)%sigma |
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epsilon = MnM_Map%interactions(interaction_id)%epsilon |
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shiftedPot = MnM_Map%interactions(interaction_id)%shiftedPot |
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shiftedFrc = MnM_Map%interactions(interaction_id)%shiftedFrc |
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|
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ros = rij * sigmai |
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|
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call getLJfunc(ros, myPot, myDeriv) |
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|
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if (shiftedPot) then |
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rcos = rcut * sigmai |
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call getLJfunc(rcos, myPotC, myDerivC) |
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myDerivC = 0.0_dp |
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elseif (shiftedFrc) then |
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rcos = rcut * sigmai |
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call getLJfunc(rcos, myPotC, myDerivC) |
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myPotC = myPotC + myDerivC * (rij - rcut) * sigmai |
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else |
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myPotC = 0.0_dp |
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myDerivC = 0.0_dp |
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endif |
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|
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pot_temp = epsilon * (myPot - myPotC) |
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vpair = vpair + pot_temp |
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dudr = sw * epsilon * (myDeriv - myDerivC) * sigmai |
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|
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drdx = d(1) / rij |
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drdy = d(2) / rij |
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drdz = d(3) / rij |
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|
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fx = dudr * drdx |
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fy = dudr * drdy |
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fz = dudr * drdz |
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|
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#ifdef IS_MPI |
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if (do_pot) then |
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pot_Row(VDW_POT,atom1) = pot_Row(VDW_POT,atom1) + sw*pot_temp*0.5 |
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pot_Col(VDW_POT,atom2) = pot_Col(VDW_POT,atom2) + sw*pot_temp*0.5 |
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endif |
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|
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f_Row(1,atom1) = f_Row(1,atom1) + fx |
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f_Row(2,atom1) = f_Row(2,atom1) + fy |
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f_Row(3,atom1) = f_Row(3,atom1) + fz |
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|
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f_Col(1,atom2) = f_Col(1,atom2) - fx |
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f_Col(2,atom2) = f_Col(2,atom2) - fy |
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f_Col(3,atom2) = f_Col(3,atom2) - fz |
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|
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#else |
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if (do_pot) pot = pot + sw*pot_temp |
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|
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f(1,atom1) = f(1,atom1) + fx |
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f(2,atom1) = f(2,atom1) + fy |
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f(3,atom1) = f(3,atom1) + fz |
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|
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f(1,atom2) = f(1,atom2) - fx |
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f(2,atom2) = f(2,atom2) - fy |
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f(3,atom2) = f(3,atom2) - fz |
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#endif |
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|
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#ifdef IS_MPI |
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id1 = AtomRowToGlobal(atom1) |
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id2 = AtomColToGlobal(atom2) |
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#else |
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id1 = atom1 |
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id2 = atom2 |
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#endif |
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|
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if (molMembershipList(id1) .ne. molMembershipList(id2)) then |
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|
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fpair(1) = fpair(1) + fx |
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fpair(2) = fpair(2) + fy |
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fpair(3) = fpair(3) + fz |
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|
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endif |
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return |
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end subroutine calc_mnm_lennardjones |
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|
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subroutine calc_mnm_morse(Atom1, Atom2, D, Rij, R2, Rcut, Sw, Vpair, Fpair, & |
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Pot, f, Do_pot, interaction_id, interaction_type) |
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integer, intent(in) :: atom1, atom2 |
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real( kind = dp ), intent(in) :: rij, r2, rcut |
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real( kind = dp ) :: pot, sw, vpair |
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real( kind = dp ), intent(inout), dimension(3,nLocal) :: f |
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real( kind = dp ), intent(in), dimension(3) :: d |
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real( kind = dp ), intent(inout), dimension(3) :: fpair |
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logical, intent(in) :: do_pot |
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integer, intent(in) :: interaction_id, interaction_type |
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logical :: shiftedPot, shiftedFrc |
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|
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! Local Variables |
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real(kind=dp) :: Beta0 |
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real(kind=dp) :: R0 |
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real(kind=dp) :: D0 |
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real(kind=dp) :: expt |
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real(kind=dp) :: expt2 |
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real(kind=dp) :: expfnc |
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real(kind=dp) :: expfnc2 |
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real(kind=dp) :: D_expt |
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real(kind=dp) :: D_expt2 |
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real(kind=dp) :: rcos |
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real(kind=dp) :: exptC |
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real(kind=dp) :: expt2C |
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real(kind=dp) :: expfncC |
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real(kind=dp) :: expfnc2C |
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real(kind=dp) :: D_expt2C |
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real(kind=dp) :: D_exptC |
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|
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real(kind=dp) :: myPot |
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real(kind=dp) :: myPotC |
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real(kind=dp) :: myDeriv |
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real(kind=dp) :: myDerivC |
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real(kind=dp) :: pot_temp |
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real(kind=dp) :: fx,fy,fz |
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real(kind=dp) :: drdx,drdy,drdz |
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real(kind=dp) :: dudr |
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integer :: id1,id2 |
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|
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|
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D0 = MnM_Map%interactions(interaction_id)%D0 |
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R0 = MnM_Map%interactions(interaction_id)%r0 |
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Beta0 = MnM_Map%interactions(interaction_id)%Beta0 |
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shiftedPot = MnM_Map%interactions(interaction_id)%shiftedPot |
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shiftedFrc = MnM_Map%interactions(interaction_id)%shiftedFrc |
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|
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! V(r) = D_e exp(-a(r-re)(exp(-a(r-re))-2) |
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|
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expt = -beta0*(rij - R0) |
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expfnc = exp(expt) |
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expfnc2 = expfnc*expfnc |
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|
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if (shiftedPot .or. shiftedFrc) then |
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exptC = -beta0*(rcut - R0) |
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expfncC = exp(exptC) |
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expfnc2C = expfncC*expfncC |
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endif |
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|
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select case (interaction_type) |
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case (MNM_SHIFTEDMORSE) |
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|
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myPot = D0 * (expfnc2 - 2.0_dp * expfnc) |
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myDeriv = 2.0*D0*beta0*(expfnc - expfnc2) |
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|
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if (shiftedPot) then |
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myPotC = D0 * (expfnc2C - 2.0_dp * expfncC) |
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myDerivC = 0.0_dp |
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elseif (shiftedFrc) then |
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myPotC = D0 * (expfnc2C - 2.0_dp * expfncC) |
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myDerivC = 2.0*D0*beta0*(expfnc2C - expfnc2C) |
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myPotC = myPotC + myDerivC * (rij - rcut) |
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else |
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myPotC = 0.0_dp |
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myDerivC = 0.0_dp |
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endif |
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|
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case (MNM_REPULSIVEMORSE) |
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|
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myPot = D0 * expfnc2 |
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myDeriv = -2.0_dp * D0 * beta0 * expfnc2 |
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|
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if (shiftedPot) then |
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myPotC = D0 * expfnc2C |
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myDerivC = 0.0_dp |
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elseif (shiftedFrc) then |
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myPotC = D0 * expfnc2C |
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myDerivC = -2.0_dp * D0* beta0 * expfnc2C |
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myPotC = myPotC + myDerivC * (rij - rcut) |
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else |
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myPotC = 0.0_dp |
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myDerivC = 0.0_dp |
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endif |
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end select |
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|
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pot_temp = (myPot - myPotC) |
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vpair = vpair + pot_temp |
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dudr = sw * (myDeriv - myDerivC) |
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|
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drdx = d(1) / rij |
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drdy = d(2) / rij |
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drdz = d(3) / rij |
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|
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fx = dudr * drdx |
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fy = dudr * drdy |
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fz = dudr * drdz |
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|
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#ifdef IS_MPI |
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if (do_pot) then |
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pot_Row(VDW_POT,atom1) = pot_Row(VDW_POT,atom1) + sw*pot_temp*0.5 |
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pot_Col(VDW_POT,atom2) = pot_Col(VDW_POT,atom2) + sw*pot_temp*0.5 |
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endif |
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|
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f_Row(1,atom1) = f_Row(1,atom1) + fx |
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f_Row(2,atom1) = f_Row(2,atom1) + fy |
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f_Row(3,atom1) = f_Row(3,atom1) + fz |
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|
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f_Col(1,atom2) = f_Col(1,atom2) - fx |
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f_Col(2,atom2) = f_Col(2,atom2) - fy |
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f_Col(3,atom2) = f_Col(3,atom2) - fz |
| 384 |
|
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#else |
| 386 |
if (do_pot) pot = pot + sw*pot_temp |
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|
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f(1,atom1) = f(1,atom1) + fx |
| 389 |
f(2,atom1) = f(2,atom1) + fy |
| 390 |
f(3,atom1) = f(3,atom1) + fz |
| 391 |
|
| 392 |
f(1,atom2) = f(1,atom2) - fx |
| 393 |
f(2,atom2) = f(2,atom2) - fy |
| 394 |
f(3,atom2) = f(3,atom2) - fz |
| 395 |
#endif |
| 396 |
|
| 397 |
#ifdef IS_MPI |
| 398 |
id1 = AtomRowToGlobal(atom1) |
| 399 |
id2 = AtomColToGlobal(atom2) |
| 400 |
#else |
| 401 |
id1 = atom1 |
| 402 |
id2 = atom2 |
| 403 |
#endif |
| 404 |
|
| 405 |
if (molMembershipList(id1) .ne. molMembershipList(id2)) then |
| 406 |
|
| 407 |
fpair(1) = fpair(1) + fx |
| 408 |
fpair(2) = fpair(2) + fy |
| 409 |
fpair(3) = fpair(3) + fz |
| 410 |
|
| 411 |
endif |
| 412 |
|
| 413 |
return |
| 414 |
end subroutine calc_mnm_morse |
| 415 |
|
| 416 |
subroutine calc_mnm_maw(Atom1, Atom2, D, Rij, R2, Rcut, Sw, Vpair, Fpair, & |
| 417 |
Pot, A, F,t, Do_pot, interaction_id) |
| 418 |
integer, intent(in) :: atom1, atom2 |
| 419 |
real( kind = dp ), intent(in) :: rij, r2, rcut |
| 420 |
real( kind = dp ) :: pot, sw, vpair |
| 421 |
real( kind = dp ), intent(inout), dimension(3,nLocal) :: f |
| 422 |
real (kind=dp),intent(in), dimension(9,nLocal) :: A |
| 423 |
real (kind=dp),intent(inout), dimension(3,nLocal) :: t |
| 424 |
|
| 425 |
real( kind = dp ), intent(in), dimension(3) :: d |
| 426 |
real( kind = dp ), intent(inout), dimension(3) :: fpair |
| 427 |
logical, intent(in) :: do_pot |
| 428 |
|
| 429 |
integer, intent(in) :: interaction_id |
| 430 |
|
| 431 |
real(kind = dp) :: D0, R0, beta0, alpha, pot_temp |
| 432 |
real(kind = dp) :: expt0, expfnc0, expfnc02 |
| 433 |
real(kind = dp) :: exptH, expfncH, expfncH2 |
| 434 |
real(kind = dp) :: x, y, z, x2, y2, z2, r3, r4 |
| 435 |
real(kind = dp) :: drdx, drdy, drdz |
| 436 |
real(kind = dp) :: dvdx, dvdy, dvdz |
| 437 |
real(kind = dp) :: Vang, dVangdx, dVangdy, dVangdz, dVangdux, dVangduy, dVangduz |
| 438 |
real(kind = dp) :: dVmorsedr |
| 439 |
real(kind = dp) :: Vmorse, dVmorsedx, dVmorsedy, dVmorsedz |
| 440 |
real(kind = dp) :: fx, fy, fz, tx, ty, tz, fxl, fyl, fzl |
| 441 |
real(kind = dp), parameter :: tf = 3.0_dp/4.0_dp |
| 442 |
real(kind = dp), parameter :: th = 3.0_dp/2.0_dp |
| 443 |
real(kind = dp), parameter :: t8 = 3.0_dp/8.0_dp |
| 444 |
real(kind = dp), parameter :: stf = sqrt(3.0_dp)/4.0_dp |
| 445 |
integer :: atid1, atid2, id1, id2 |
| 446 |
logical :: shiftedPot, shiftedFrc |
| 447 |
|
| 448 |
#ifdef IS_MPI |
| 449 |
atid1 = atid_Row(atom1) |
| 450 |
atid2 = atid_Col(atom2) |
| 451 |
|
| 452 |
if (atid2.eq.MnM_Map%interactions(interaction_id)%metal_atid) then |
| 453 |
! rotate the inter-particle separation into the two different |
| 454 |
! body-fixed coordinate systems: |
| 455 |
|
| 456 |
x = A_row(1,atom1)*d(1) + A_row(2,atom1)*d(2) + A_row(3,atom1)*d(3) |
| 457 |
y = A_row(4,atom1)*d(1) + A_row(5,atom1)*d(2) + A_row(6,atom1)*d(3) |
| 458 |
z = A_row(7,atom1)*d(1) + A_row(8,atom1)*d(2) + A_row(9,atom1)*d(3) |
| 459 |
else |
| 460 |
! negative sign because this is the vector from j to i: |
| 461 |
|
| 462 |
x = -(A_Col(1,atom2)*d(1) + A_Col(2,atom2)*d(2) + A_Col(3,atom2)*d(3)) |
| 463 |
y = -(A_Col(4,atom2)*d(1) + A_Col(5,atom2)*d(2) + A_Col(6,atom2)*d(3)) |
| 464 |
z = -(A_Col(7,atom2)*d(1) + A_Col(8,atom2)*d(2) + A_Col(9,atom2)*d(3)) |
| 465 |
endif |
| 466 |
|
| 467 |
#else |
| 468 |
atid1 = atid(atom1) |
| 469 |
atid2 = atid(atom2) |
| 470 |
|
| 471 |
if (atid2.eq.MnM_Map%interactions(interaction_id)%metal_atid) then |
| 472 |
! rotate the inter-particle separation into the two different |
| 473 |
! body-fixed coordinate systems: |
| 474 |
|
| 475 |
x = a(1,atom1)*d(1) + a(2,atom1)*d(2) + a(3,atom1)*d(3) |
| 476 |
y = a(4,atom1)*d(1) + a(5,atom1)*d(2) + a(6,atom1)*d(3) |
| 477 |
z = a(7,atom1)*d(1) + a(8,atom1)*d(2) + a(9,atom1)*d(3) |
| 478 |
else |
| 479 |
! negative sign because this is the vector from j to i: |
| 480 |
|
| 481 |
x = -(a(1,atom2)*d(1) + a(2,atom2)*d(2) + a(3,atom2)*d(3)) |
| 482 |
y = -(a(4,atom2)*d(1) + a(5,atom2)*d(2) + a(6,atom2)*d(3)) |
| 483 |
z = -(a(7,atom2)*d(1) + a(8,atom2)*d(2) + a(9,atom2)*d(3)) |
| 484 |
endif |
| 485 |
|
| 486 |
#endif |
| 487 |
|
| 488 |
D0 = MnM_Map%interactions(interaction_id)%D0 |
| 489 |
R0 = MnM_Map%interactions(interaction_id)%r0 |
| 490 |
beta0 = MnM_Map%interactions(interaction_id)%beta0 |
| 491 |
alpha = MnM_Map%interactions(interaction_id)%alpha |
| 492 |
|
| 493 |
shiftedPot = MnM_Map%interactions(interaction_id)%shiftedPot |
| 494 |
shiftedFrc = MnM_Map%interactions(interaction_id)%shiftedFrc |
| 495 |
|
| 496 |
expt0 = -beta0*(rij - R0) |
| 497 |
expfnc0 = exp(expt0) |
| 498 |
expfnc02 = expfnc0*expfnc0 |
| 499 |
|
| 500 |
!!$ if (shiftedPot .or. shiftedFrc) then |
| 501 |
!!$ exptC0 = -beta0*(rcut - R0) |
| 502 |
!!$ expfncC0 = exp(exptC0) |
| 503 |
!!$ expfncC02 = expfncC0*expfncC0 |
| 504 |
!!$ exptCH = -betaH*(rcut - R0) |
| 505 |
!!$ expfncCH = exp(exptCH) |
| 506 |
!!$ expfncCH2 = expfncCH*expfncCH |
| 507 |
!!$ endif |
| 508 |
|
| 509 |
drdx = x / rij |
| 510 |
drdy = y / rij |
| 511 |
drdz = z / rij |
| 512 |
|
| 513 |
x2 = x*x |
| 514 |
y2 = y*y |
| 515 |
z2 = z*z |
| 516 |
r3 = r2*rij |
| 517 |
r4 = r2*r2 |
| 518 |
|
| 519 |
Vmorse = D0 * (expfnc02 - 2.0_dp * expfnc0) |
| 520 |
|
| 521 |
! angular modulation of morse part of potential to approximate a sp3 orbital |
| 522 |
! Vang = 1 - alpha*(1/2 + sqrt(3.0)*cos(theta)/4.0 - 3.0*cos(2.0*phi)*sin^2(theta)/8.0) |
| 523 |
|
| 524 |
Vang = 1.0_dp - alpha*(0.5_dp + stf*z/rij - t8*(x2-y2)/r2) |
| 525 |
|
| 526 |
pot_temp = Vmorse*Vang |
| 527 |
|
| 528 |
vpair = vpair + pot_temp |
| 529 |
|
| 530 |
if (do_pot) then |
| 531 |
#ifdef IS_MPI |
| 532 |
pot_row(VDW_POT,atom1) = pot_row(VDW_POT,atom1) + 0.5_dp*pot_temp*sw |
| 533 |
pot_col(VDW_POT,atom2) = pot_col(VDW_POT,atom2) + 0.5_dp*pot_temp*sw |
| 534 |
#else |
| 535 |
pot = pot + pot_temp*sw |
| 536 |
#endif |
| 537 |
endif |
| 538 |
|
| 539 |
dVmorsedr = 2.0_dp*D0*beta0*(expfnc0 - expfnc02) |
| 540 |
|
| 541 |
dVmorsedx = dVmorsedr * drdx |
| 542 |
dVmorsedy = dVmorsedr * drdy |
| 543 |
dVmorsedz = dVmorsedr * drdz |
| 544 |
|
| 545 |
dVangdx = -alpha*(-tf*x/r2 + tf*(x2-y2)*x/r4 - stf*z*x/r3) |
| 546 |
dVangdy = -alpha*( tf*y/r2 + tf*(x2-y2)*y/r4 - stf*z*y/r3) |
| 547 |
dVangdz = -alpha*(stf/rij + tf*(x2-y2)*z/r4 - stf*z2/r3) |
| 548 |
|
| 549 |
! chain rule to put these back on x, y, z |
| 550 |
dvdx = Vang * dVmorsedx + Vmorse * dVangdx |
| 551 |
dvdy = Vang * dVmorsedy + Vmorse * dVangdy |
| 552 |
dvdz = Vang * dVmorsedz + Vmorse * dVangdz |
| 553 |
|
| 554 |
! Torques for Vang using method of Price: |
| 555 |
! S. L. Price, A. J. Stone, and M. Alderton, Mol. Phys. 52, 987 (1984). |
| 556 |
dVangdux = alpha * (tf * y * z / r2 - stf * y / rij ) |
| 557 |
dVangduy = alpha * (tf * x * z / r2 + stf * x / rij ) |
| 558 |
dVangduz = -th * alpha * x * y / r2 |
| 559 |
|
| 560 |
! do the torques first since they are easy: |
| 561 |
! remember that these are still in the body fixed axes |
| 562 |
|
| 563 |
tx = Vmorse * dVangdux * sw |
| 564 |
ty = Vmorse * dVangduy * sw |
| 565 |
tz = Vmorse * dVangduz * sw |
| 566 |
|
| 567 |
! go back to lab frame using transpose of rotation matrix: |
| 568 |
|
| 569 |
#ifdef IS_MPI |
| 570 |
if (atid2.eq.MnM_Map%interactions(interaction_id)%metal_atid) then |
| 571 |
t_Row(1,atom1) = t_Row(1,atom1) + a_Row(1,atom1)*tx + & |
| 572 |
a_Row(4,atom1)*ty + a_Row(7,atom1)*tz |
| 573 |
t_Row(2,atom1) = t_Row(2,atom1) + a_Row(2,atom1)*tx + & |
| 574 |
a_Row(5,atom1)*ty + a_Row(8,atom1)*tz |
| 575 |
t_Row(3,atom1) = t_Row(3,atom1) + a_Row(3,atom1)*tx + & |
| 576 |
a_Row(6,atom1)*ty + a_Row(9,atom1)*tz |
| 577 |
else |
| 578 |
t_Col(1,atom2) = t_Col(1,atom2) + a_Col(1,atom2)*tx + & |
| 579 |
a_Col(4,atom2)*ty + a_Col(7,atom2)*tz |
| 580 |
t_Col(2,atom2) = t_Col(2,atom2) + a_Col(2,atom2)*tx + & |
| 581 |
a_Col(5,atom2)*ty + a_Col(8,atom2)*tz |
| 582 |
t_Col(3,atom2) = t_Col(3,atom2) + a_Col(3,atom2)*tx + & |
| 583 |
a_Col(6,atom2)*ty + a_Col(9,atom2)*tz |
| 584 |
endif |
| 585 |
#else |
| 586 |
if (atid2.eq.MnM_Map%interactions(interaction_id)%metal_atid) then |
| 587 |
t(1,atom1) = t(1,atom1) + a(1,atom1)*tx + a(4,atom1)*ty + & |
| 588 |
a(7,atom1)*tz |
| 589 |
t(2,atom1) = t(2,atom1) + a(2,atom1)*tx + a(5,atom1)*ty + & |
| 590 |
a(8,atom1)*tz |
| 591 |
t(3,atom1) = t(3,atom1) + a(3,atom1)*tx + a(6,atom1)*ty + & |
| 592 |
a(9,atom1)*tz |
| 593 |
else |
| 594 |
t(1,atom2) = t(1,atom2) + a(1,atom2)*tx + a(4,atom2)*ty + & |
| 595 |
a(7,atom2)*tz |
| 596 |
t(2,atom2) = t(2,atom2) + a(2,atom2)*tx + a(5,atom2)*ty + & |
| 597 |
a(8,atom2)*tz |
| 598 |
t(3,atom2) = t(3,atom2) + a(3,atom2)*tx + a(6,atom2)*ty + & |
| 599 |
a(9,atom2)*tz |
| 600 |
endif |
| 601 |
#endif |
| 602 |
! Now, on to the forces (still in body frame of water) |
| 603 |
|
| 604 |
fx = dvdx * sw |
| 605 |
fy = dvdy * sw |
| 606 |
fz = dvdz * sw |
| 607 |
|
| 608 |
! rotate the terms back into the lab frame: |
| 609 |
|
| 610 |
#ifdef IS_MPI |
| 611 |
if (atid2.eq.MnM_Map%interactions(interaction_id)%metal_atid) then |
| 612 |
fxl = a_Row(1,atom1)*fx + a_Row(4,atom1)*fy + a_Row(7,atom1)*fz |
| 613 |
fyl = a_Row(2,atom1)*fx + a_Row(5,atom1)*fy + a_Row(8,atom1)*fz |
| 614 |
fzl = a_Row(3,atom1)*fx + a_Row(6,atom1)*fy + a_Row(9,atom1)*fz |
| 615 |
else |
| 616 |
fxl = a_Col(1,atom2)*fx + a_Col(4,atom2)*fy + a_Col(7,atom2)*fz |
| 617 |
fyl = a_Col(2,atom2)*fx + a_Col(5,atom2)*fy + a_Col(8,atom2)*fz |
| 618 |
fzl = a_Col(3,atom2)*fx + a_Col(6,atom2)*fy + a_Col(9,atom2)*fz |
| 619 |
endif |
| 620 |
f_Row(1,atom1) = f_Row(1,atom1) + fxl |
| 621 |
f_Row(2,atom1) = f_Row(2,atom1) + fyl |
| 622 |
f_Row(3,atom1) = f_Row(3,atom1) + fzl |
| 623 |
|
| 624 |
f_Col(1,atom2) = f_Col(1,atom2) - fxl |
| 625 |
f_Col(2,atom2) = f_Col(2,atom2) - fyl |
| 626 |
f_Col(3,atom2) = f_Col(3,atom2) - fzl |
| 627 |
#else |
| 628 |
if (atid2.eq.MnM_Map%interactions(interaction_id)%metal_atid) then |
| 629 |
fxl = a(1,atom1)*fx + a(4,atom1)*fy + a(7,atom1)*fz |
| 630 |
fyl = a(2,atom1)*fx + a(5,atom1)*fy + a(8,atom1)*fz |
| 631 |
fzl = a(3,atom1)*fx + a(6,atom1)*fy + a(9,atom1)*fz |
| 632 |
else |
| 633 |
fxl = a(1,atom2)*fx + a(4,atom2)*fy + a(7,atom2)*fz |
| 634 |
fyl = a(2,atom2)*fx + a(5,atom2)*fy + a(8,atom2)*fz |
| 635 |
fzl = a(3,atom2)*fx + a(6,atom2)*fy + a(9,atom2)*fz |
| 636 |
endif |
| 637 |
f(1,atom1) = f(1,atom1) + fxl |
| 638 |
f(2,atom1) = f(2,atom1) + fyl |
| 639 |
f(3,atom1) = f(3,atom1) + fzl |
| 640 |
|
| 641 |
f(1,atom2) = f(1,atom2) - fxl |
| 642 |
f(2,atom2) = f(2,atom2) - fyl |
| 643 |
f(3,atom2) = f(3,atom2) - fzl |
| 644 |
#endif |
| 645 |
|
| 646 |
#ifdef IS_MPI |
| 647 |
id1 = AtomRowToGlobal(atom1) |
| 648 |
id2 = AtomColToGlobal(atom2) |
| 649 |
#else |
| 650 |
id1 = atom1 |
| 651 |
id2 = atom2 |
| 652 |
#endif |
| 653 |
|
| 654 |
if (molMembershipList(id1) .ne. molMembershipList(id2)) then |
| 655 |
|
| 656 |
fpair(1) = fpair(1) + fxl |
| 657 |
fpair(2) = fpair(2) + fyl |
| 658 |
fpair(3) = fpair(3) + fzl |
| 659 |
|
| 660 |
endif |
| 661 |
|
| 662 |
return |
| 663 |
end subroutine calc_mnm_maw |
| 664 |
|
| 665 |
|
| 666 |
subroutine setMnMDefaultCutoff(thisRcut, shiftedPot, shiftedFrc) |
| 667 |
real(kind=dp), intent(in) :: thisRcut |
| 668 |
logical, intent(in) :: shiftedPot |
| 669 |
logical, intent(in) :: shiftedFrc |
| 670 |
integer i, nInteractions |
| 671 |
defaultCutoff = thisRcut |
| 672 |
defaultShiftPot = shiftedPot |
| 673 |
defaultShiftFrc = shiftedFrc |
| 674 |
|
| 675 |
if (associated(MnM_Map)) then |
| 676 |
if(MnM_Map%interactionCount /= 0) then |
| 677 |
nInteractions = MnM_Map%interactionCount |
| 678 |
|
| 679 |
do i = 1, nInteractions |
| 680 |
MnM_Map%interactions(i)%shiftedPot = shiftedPot |
| 681 |
MnM_Map%interactions(i)%shiftedFrc = shiftedFrc |
| 682 |
MnM_Map%interactions(i)%rCut = thisRcut |
| 683 |
MnM_Map%interactions(i)%rCutWasSet = .true. |
| 684 |
enddo |
| 685 |
end if |
| 686 |
end if |
| 687 |
|
| 688 |
end subroutine setMnMDefaultCutoff |
| 689 |
|
| 690 |
subroutine copyAllData(v1, v2) |
| 691 |
type(MnMinteractionMap), pointer :: v1 |
| 692 |
type(MnMinteractionMap), pointer :: v2 |
| 693 |
integer :: i, j |
| 694 |
|
| 695 |
do i = 1, v1%interactionCount |
| 696 |
v2%interactions(i) = v1%interactions(i) |
| 697 |
enddo |
| 698 |
|
| 699 |
v2%interactionCount = v1%interactionCount |
| 700 |
return |
| 701 |
end subroutine copyAllData |
| 702 |
|
| 703 |
subroutine addInteraction(myInteraction) |
| 704 |
type(MNMtype) :: myInteraction |
| 705 |
type(MnMinteraction) :: nt |
| 706 |
integer :: id |
| 707 |
|
| 708 |
|
| 709 |
|
| 710 |
|
| 711 |
|
| 712 |
nt%interaction_type = myInteraction%MNMInteractionType |
| 713 |
nt%metal_atid = & |
| 714 |
getFirstMatchingElement(atypes, "c_ident", myInteraction%metal_atid) |
| 715 |
nt%nonmetal_atid = & |
| 716 |
getFirstMatchingElement(atypes, "c_ident", myInteraction%nonmetal_atid) |
| 717 |
|
| 718 |
|
| 719 |
select case (nt%interaction_type) |
| 720 |
case (MNM_LENNARDJONES) |
| 721 |
nt%sigma = myInteraction%sigma |
| 722 |
nt%epsilon = myInteraction%epsilon |
| 723 |
case(MNM_REPULSIVEMORSE, MNM_SHIFTEDMORSE) |
| 724 |
nt%R0 = myInteraction%R0 |
| 725 |
nt%D0 = myInteraction%D0 |
| 726 |
nt%beta0 = myInteraction%beta0 |
| 727 |
case(MNM_MAW) |
| 728 |
nt%R0 = myInteraction%R0 |
| 729 |
nt%D0 = myInteraction%D0 |
| 730 |
nt%beta0 = myInteraction%beta0 |
| 731 |
nt%alpha = myInteraction%alpha |
| 732 |
case default |
| 733 |
call handleError("MNM", "Unknown Interaction type") |
| 734 |
end select |
| 735 |
|
| 736 |
if (.not. associated(MnM_Map)) then |
| 737 |
call ensureCapacityHelper(MnM_Map, 1) |
| 738 |
else |
| 739 |
call ensureCapacityHelper(MnM_Map, MnM_Map%interactionCount + 1) |
| 740 |
end if |
| 741 |
|
| 742 |
MnM_Map%interactionCount = MnM_Map%interactionCount + 1 |
| 743 |
id = MnM_Map%interactionCount |
| 744 |
MnM_Map%interactions(id) = nt |
| 745 |
end subroutine addInteraction |
| 746 |
|
| 747 |
subroutine ensureCapacityHelper(this, minCapacity) |
| 748 |
type(MnMinteractionMap), pointer :: this, that |
| 749 |
integer, intent(in) :: minCapacity |
| 750 |
integer :: oldCapacity |
| 751 |
integer :: newCapacity |
| 752 |
logical :: resizeFlag |
| 753 |
|
| 754 |
resizeFlag = .false. |
| 755 |
|
| 756 |
! first time: allocate a new vector with default size |
| 757 |
|
| 758 |
if (.not. associated(this)) then |
| 759 |
this => MnMinitialize(minCapacity, 0) |
| 760 |
endif |
| 761 |
|
| 762 |
oldCapacity = size(this%interactions) |
| 763 |
|
| 764 |
if (minCapacity > oldCapacity) then |
| 765 |
if (this%capacityIncrement .gt. 0) then |
| 766 |
newCapacity = oldCapacity + this%capacityIncrement |
| 767 |
else |
| 768 |
newCapacity = oldCapacity * 2 |
| 769 |
endif |
| 770 |
if (newCapacity .lt. minCapacity) then |
| 771 |
newCapacity = minCapacity |
| 772 |
endif |
| 773 |
resizeFlag = .true. |
| 774 |
else |
| 775 |
newCapacity = oldCapacity |
| 776 |
endif |
| 777 |
|
| 778 |
if (resizeFlag) then |
| 779 |
that => MnMinitialize(newCapacity, this%capacityIncrement) |
| 780 |
call copyAllData(this, that) |
| 781 |
this => MnMdestroy(this) |
| 782 |
this => that |
| 783 |
endif |
| 784 |
end subroutine ensureCapacityHelper |
| 785 |
|
| 786 |
function MnMinitialize(cap, capinc) result(this) |
| 787 |
integer, intent(in) :: cap, capinc |
| 788 |
integer :: error |
| 789 |
type(MnMinteractionMap), pointer :: this |
| 790 |
|
| 791 |
nullify(this) |
| 792 |
|
| 793 |
if (cap < 0) then |
| 794 |
write(*,*) 'Bogus Capacity:', cap |
| 795 |
return |
| 796 |
endif |
| 797 |
allocate(this,stat=error) |
| 798 |
if ( error /= 0 ) then |
| 799 |
write(*,*) 'Could not allocate MnMinteractionMap!' |
| 800 |
return |
| 801 |
end if |
| 802 |
|
| 803 |
this%initialCapacity = cap |
| 804 |
this%capacityIncrement = capinc |
| 805 |
|
| 806 |
allocate(this%interactions(this%initialCapacity), stat=error) |
| 807 |
if(error /= 0) write(*,*) 'Could not allocate MnMinteraction!' |
| 808 |
|
| 809 |
end function MnMinitialize |
| 810 |
|
| 811 |
subroutine createInteractionLookup(this) |
| 812 |
type (MnMInteractionMap),pointer :: this |
| 813 |
integer :: biggestAtid, i, metal_atid, nonmetal_atid, error |
| 814 |
|
| 815 |
biggestAtid=-1 |
| 816 |
do i = 1, this%interactionCount |
| 817 |
metal_atid = this%interactions(i)%metal_atid |
| 818 |
nonmetal_atid = this%interactions(i)%nonmetal_atid |
| 819 |
|
| 820 |
if (metal_atid .gt. biggestAtid) biggestAtid = metal_atid |
| 821 |
if (nonmetal_atid .gt. biggestAtid) biggestAtid = nonmetal_atid |
| 822 |
enddo |
| 823 |
|
| 824 |
allocate(MnMinteractionLookup(biggestAtid,biggestAtid), stat=error) |
| 825 |
if (error /= 0) write(*,*) 'Could not allocate MnMinteractionLookup' |
| 826 |
|
| 827 |
do i = 1, this%interactionCount |
| 828 |
metal_atid = this%interactions(i)%metal_atid |
| 829 |
nonmetal_atid = this%interactions(i)%nonmetal_atid |
| 830 |
|
| 831 |
MnMinteractionLookup(metal_atid, nonmetal_atid) = i |
| 832 |
MnMinteractionLookup(nonmetal_atid, metal_atid) = i |
| 833 |
enddo |
| 834 |
end subroutine createInteractionLookup |
| 835 |
|
| 836 |
|
| 837 |
function MnMdestroy(this) result(null_this) |
| 838 |
logical :: done |
| 839 |
type(MnMinteractionMap), pointer :: this |
| 840 |
type(MnMinteractionMap), pointer :: null_this |
| 841 |
|
| 842 |
if (.not. associated(this)) then |
| 843 |
null_this => null() |
| 844 |
return |
| 845 |
end if |
| 846 |
|
| 847 |
!! Walk down the list and deallocate each of the map's components |
| 848 |
if(associated(this%interactions)) then |
| 849 |
deallocate(this%interactions) |
| 850 |
this%interactions=>null() |
| 851 |
endif |
| 852 |
deallocate(this) |
| 853 |
this => null() |
| 854 |
null_this => null() |
| 855 |
end function MnMdestroy |
| 856 |
|
| 857 |
|
| 858 |
subroutine deleteInteractions() |
| 859 |
MnM_Map => MnMdestroy(MnM_Map) |
| 860 |
return |
| 861 |
end subroutine deleteInteractions |
| 862 |
|
| 863 |
|
| 864 |
subroutine getLJfunc(r, myPot, myDeriv) |
| 865 |
|
| 866 |
real(kind=dp), intent(in) :: r |
| 867 |
real(kind=dp), intent(inout) :: myPot, myDeriv |
| 868 |
real(kind=dp) :: ri, ri2, ri6, ri7, ri12, ri13 |
| 869 |
real(kind=dp) :: a, b, c, d, dx |
| 870 |
integer :: j |
| 871 |
|
| 872 |
ri = 1.0_DP / r |
| 873 |
ri2 = ri*ri |
| 874 |
ri6 = ri2*ri2*ri2 |
| 875 |
ri7 = ri6*ri |
| 876 |
ri12 = ri6*ri6 |
| 877 |
ri13 = ri12*ri |
| 878 |
|
| 879 |
myPot = 4.0_DP * (ri12 - ri6) |
| 880 |
myDeriv = 24.0_DP * (ri7 - 2.0_DP * ri13) |
| 881 |
|
| 882 |
return |
| 883 |
end subroutine getLJfunc |
| 884 |
|
| 885 |
subroutine getSoftFunc(r, myPot, myDeriv) |
| 886 |
|
| 887 |
real(kind=dp), intent(in) :: r |
| 888 |
real(kind=dp), intent(inout) :: myPot, myDeriv |
| 889 |
real(kind=dp) :: ri, ri2, ri6, ri7 |
| 890 |
real(kind=dp) :: a, b, c, d, dx |
| 891 |
integer :: j |
| 892 |
|
| 893 |
ri = 1.0_DP / r |
| 894 |
ri2 = ri*ri |
| 895 |
ri6 = ri2*ri2*ri2 |
| 896 |
ri7 = ri6*ri |
| 897 |
myPot = 4.0_DP * (ri6) |
| 898 |
myDeriv = - 24.0_DP * ri7 |
| 899 |
|
| 900 |
return |
| 901 |
end subroutine getSoftFunc |
| 902 |
|
| 903 |
|
| 904 |
|
| 905 |
|
| 906 |
|
| 907 |
|
| 908 |
end module MetalNonMetal |
