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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 neighborLists |
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!! Implements verlet neighbor lists for force modules. |
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!! Automagically expands neighbor list if size too small |
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!! up to maxAllocations times. If after maxAllocations we try to |
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!! expand the neighbor list, we get an error message and quit. |
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!! @author Charles F. Vardeman II |
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!! @author Matthew Meineke |
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!! @author J. Daniel Gezelter |
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!! @version $Id: neighborLists.F90,v 1.6 2006-12-05 00:17:24 chuckv Exp $, |
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|
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module neighborLists |
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|
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use definitions |
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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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PRIVATE |
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|
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!--------------MODULE VARIABLES----------------------> |
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!! Default Parameter for size > # of long range particles neighbor list |
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!! should be. It is listMultiplier x nGroups for size of list |
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integer, save :: listMultiplier = 80 |
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!! Maximum number of times we should reallocate neighbor list. |
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integer, parameter :: maxAllocations = 10 |
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!! Number of times we have allocated the neighbor list. |
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integer, save :: nAllocations = 0 |
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!! Pointer array to location in list for atom i. |
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integer, dimension(:),public, pointer :: point => null() |
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!! Neighbor list for atom i. |
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integer, dimension(:),public, pointer :: list => null() |
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!! Position array of previous positions for check. Allocated first time |
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!! into saveNeighborList. |
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real( kind = dp ), dimension(:,:), allocatable, save :: q0 |
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!! Current list size |
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integer, save :: listSize |
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|
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!--------------MODULE ACCESS--------------------------> |
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public :: expandNeighborList |
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public :: checkNeighborList |
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public :: saveNeighborList |
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public :: getNeighborListSize |
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public :: setNeighbors |
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|
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contains |
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|
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|
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subroutine expandNeighborList(nGroups, error) |
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integer, intent(out) :: error |
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integer :: nGroups |
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integer :: alloc_error |
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integer :: oldSize = 0 |
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integer :: newSize = 0 |
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integer :: i |
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integer, dimension(:), pointer :: newList => null() |
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error = 0 |
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|
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!! First time through we should allocate point and list. |
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!! If one is associated and one is not, something is wrong |
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!! and return a error. |
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|
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#ifdef IS_MPI !! // MPI |
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if (.not. associated(point) .and. & |
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.not. associated(list) ) then |
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allocate(point(getNgroupsInRow(plan_group_row)+1),stat=alloc_error) |
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if (alloc_error /= 0) then |
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write(default_error,*) & |
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"ExpandNeighborLists: Error in allocating MPI point" |
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error = -1 |
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return |
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end if |
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allocate(list(listMultiplier * getNgroupsInCol(plan_group_col)),stat=alloc_error) |
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if (alloc_error /= 0) then |
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write(default_error,*) & |
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"ExpandNeighborLists: Error in allocating MPI list" |
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error = -1 |
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return |
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end if |
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listSize = size(list) |
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nAllocations = nAllocations + 1 |
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return |
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end if |
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#else !! // NONMPI |
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if (.not. associated(point) .and. & |
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.not. associated(list) ) then |
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allocate(point(nGroups),stat=alloc_error) |
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if (alloc_error /= 0) then |
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write(default_error,*) & |
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"ExpandNeighborLists: Error in allocating point" |
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error = -1 |
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return |
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end if |
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allocate(list(listMultiplier * nGroups),stat=alloc_error) |
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if (alloc_error /= 0) then |
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write(default_error,*) & |
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"ExpandNeighborLists: Error in allocating list" |
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error = -1 |
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return |
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end if |
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listSize = size(list) |
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nAllocations = nAllocations + 1 |
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return |
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end if |
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#endif !! //MPI |
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|
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! Expand the neighbor list |
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|
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! Check to see if we have exceeded the maximum number of allocations. |
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if (nAllocations > maxAllocations) then |
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write(default_error,*) & |
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"ExpandNeighborList: exceeded maximum number of re-allocations" |
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error = -1 |
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return |
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else !! Expand the list. |
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oldSize = size(list) |
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|
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|
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#ifdef IS_MPI !! MPI |
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newSize = listMultiplier * getNgroupsInCol(plan_group_col) + oldSize |
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#else |
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newSize = listMultiplier * nGroups + oldSize |
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#endif !! MPI |
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|
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|
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|
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allocate(newList(newSize), stat=alloc_error) |
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if (alloc_error /= 0) then |
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write(*,*) "Error allocating new neighborlist" |
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error = -1 |
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return |
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end if |
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|
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!! Copy old list to new list |
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do i = 1, oldSize |
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newList(i) = list(i) |
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end do |
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!! Free old list |
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if(associated(list)) deallocate(list,stat=alloc_error) |
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if (alloc_error /= 0) then |
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error = -1 |
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return |
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end if |
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|
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!! Point list at new list |
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|
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list => newList |
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end if |
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|
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nAllocations = nAllocations + 1 |
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listSize = size(list) |
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end subroutine expandNeighborList |
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|
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!! checks to see if any long range particle has moved |
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!! through the neighbor list skin thickness. |
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subroutine checkNeighborList(nGroups, q, listSkin, update_nlist) |
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integer :: nGroups |
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real(kind = dp), intent(in) :: listSkin |
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real( kind = dp ), dimension(:,:) :: q |
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integer :: i |
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real( kind = DP ) :: dispmx |
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logical, intent(out) :: update_nlist |
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real( kind = DP ) :: dispmx_tmp |
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|
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dispmx = 0.0E0_DP |
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!! calculate the largest displacement of any atom in any direction |
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|
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!! If we have changed the particle idents, then we need to update |
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if (.not. allocated(q0)) then |
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update_nlist = .true. |
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return |
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end if |
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|
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if (size(q0,2) /= nGroups) then |
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update_nlist = .true. |
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return |
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end if |
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|
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|
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#ifdef MPI |
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|
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dispmx_tmp = 0.0E0_DP |
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do i = 1, nGroups |
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dispmx_tmp = max( abs ( q(1,i) - q0(1,i) ), dispmx_tmp ) |
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dispmx_tmp = max( abs ( q(2,i) - q0(2,i) ), dispmx_tmp ) |
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dispmx_tmp = max( abs ( q(3,i) - q0(3,i) ), dispmx_tmp ) |
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end do |
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#ifdef SINGLE_PRECISION |
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call mpi_allreduce(dispmx_tmp,dispmx,1,mpi_real, & |
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mpi_max,mpi_comm_world,mpi_err) |
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#else |
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call mpi_allreduce(dispmx_tmp,dispmx,1,mpi_double_precision, & |
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mpi_max,mpi_comm_world,mpi_err) |
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#endif |
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|
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#else |
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|
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dispmx = 0.0_DP |
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do i = 1, nGroups |
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dispmx = max( abs ( q(1,i) - q0(1,i) ), dispmx ) |
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dispmx = max( abs ( q(2,i) - q0(2,i) ), dispmx ) |
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dispmx = max( abs ( q(3,i) - q0(3,i) ), dispmx ) |
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end do |
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|
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#endif |
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|
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!! a conservative test of list skin crossings |
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dispmx = 2.0E0_DP * sqrt (3.0E0_DP * dispmx * dispmx) |
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|
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update_nlist = (dispmx.gt.listSkin) |
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|
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end subroutine checkNeighborList |
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|
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|
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!! Saves neighbor list for comparison in check. |
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!! Save_neighborList will work even if the number of |
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!! local atoms has changed. |
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subroutine saveNeighborList(nGroups, q) |
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|
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integer :: nGroups |
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real(kind = dp ), dimension(3,nGroups), intent(in) :: q |
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integer :: list_size |
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|
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!! get size of list |
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list_size = nGroups |
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|
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if (.not. allocated(q0)) then |
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allocate(q0(3,list_size)) |
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else if( list_size > size(q0,2)) then |
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deallocate(q0) |
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allocate(q0(3,list_size)) |
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endif |
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q0 = q |
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end subroutine saveNeighborList |
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|
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|
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function getNeighborListSize() result(returnListSize) |
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integer :: returnListSize |
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returnListSize = listSize |
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end function getNeighborListSize |
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|
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|
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subroutine setNeighbors(nNeighbors) |
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integer, intent(in) :: nNeighbors |
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listMultiplier = nNeighbors |
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end subroutine setNeighbors |
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|
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end module neighborLists |
