improved regridding, especially interfacing to python (also for nearest neighbor search)
This commit is contained in:
Krishna Komerla
parent
e33c34d86b
commit
83e89fba3c
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@ -1,7 +1,7 @@
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! $Id$
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! -*- f90 -*-
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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! Note: the context of this file is case sensitive.
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! Note: the syntax of this file is case sensitive.
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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! This file was auto-generated with f2py (version:2_5972).
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! See http://cens.ioc.ee/projects/f2py2e/
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@ -160,27 +160,22 @@ python module core ! in
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real*8, dimension(res[0],res[1],res[2]),intent(out),depend(res[0],res[1],res[2]) :: vm
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end subroutine math_equivStrain33_field
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subroutine math_nearestNeighborSearch(res_new,Npoints_old,defgrad_av,geomdim,spatial_dim,deformed_set,result_indices) ! in :math:math.f90
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subroutine math_nearestNeighborSearch(res_new,res_old,defgrad_av,geomdim,deformed_set,result_indices) ! in :math:math.f90
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! input variables
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integer, dimension(3), intent(in) :: res_new
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integer, intent(in) :: Npoints_old
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integer, intent(in) :: spatial_dim
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real, dimension(3), intent(in) :: geomdim
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real, dimension(3,3), intent(in) :: defgrad_av
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real, dimension(spatial_dim,Npoints_old), intent(in),depend(spatial_dim,Npoints_old) :: deformed_set
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integer, dimension(3), intent(in) :: res_new
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integer, dimension(3), intent(in) :: res_old
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real, dimension(3,3), intent(in) :: defgrad_av
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real, dimension(3), intent(in) :: geomdim
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real, dimension(res_old[0],res_old[1],res_old[2],3), intent(in), depend(res_old[0],res_old[1],res_old[2]) :: deformed_set
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! output variables
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integer, dimension(res_new[0]*res_new[1]*res_new[2]), intent(out),depend(res_new[0],res_new[1],res_new[2]) :: result_indices
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integer, dimension(res_new[0]*res_new[1]*res_new[2]), intent(out), depend(res_new[0],res_new[1],res_new[2]):: result_indices
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end subroutine math_nearestNeighborSearch
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end module math
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module mesh ! in :mesh:mesh.f90
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subroutine mesh_regrid(res,resNew) ! in :mesh:mesh.f90
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integer, dimension(3), intent(in) :: res
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integer, dimension(3), intent(in,out) :: resNew
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real*8, dimension(res[0],res[1],res[2],3,3), depend(res[0],res[1],res[2]) :: F
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subroutine mesh_regrid(resNew) ! in :mesh:mesh.f90
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integer, dimension(3), intent(in,out), optional :: resNew
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end subroutine mesh_regrid
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end module mesh
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@ -3817,49 +3817,64 @@ subroutine calculate_cauchy(res,defgrad,p_stress,c_stress)
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end subroutine calculate_cauchy
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!############################################################################
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! subroutine to find nearest_neighbor.
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!############################################################################
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subroutine math_nearestNeighborSearch(res_new, Npoints_old, defgrad_av, geomdim, &
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spatial_dim, deformed_set, result_indices)
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!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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subroutine math_nearestNeighborSearch(res_old, res_new, defgrad_av, geomdim, &
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deformed_set, result_indices)
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!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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!Obtain the nearest neighbour
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!
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use kdtree2_module
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implicit none
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integer(pInt), dimension(3), intent(in) :: res_new
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integer(pInt), intent(in):: spatial_dim, Npoints_old
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! input variables
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integer(pInt), dimension(3), intent(in) :: res_new, res_old
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real(pReal), dimension(3), intent(in) :: geomdim
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real(pReal), dimension(3,3), intent(in) :: defgrad_av
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real(pReal), dimension(spatial_dim,Npoints_old), intent(in) :: deformed_set
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real(pReal), dimension( res_old(1), res_old(2),res_old(3),3), intent(in) :: deformed_set
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! other variables
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integer(pInt), dimension(res_new(1)*res_new(2)*res_new(3)), intent(out) :: result_indices
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! other variables
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real(pReal), dimension(:,:), allocatable :: deformed_set_large
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integer(pInt) :: i,j,k, l,m,n, ielem_large, spatial_dim
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real(pReal), dimension(3) :: shift, query_point
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type(kdtree2), pointer :: tree
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type(kdtree2_result), dimension(1) :: Results
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integer(pInt), dimension(res_new(1)*res_new(2)*res_new(3)), intent(out) :: result_indices
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real(pReal), dimension(spatial_dim,Npoints_old*3_pInt**spatial_dim) :: deformed_set_large
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integer(pInt):: i, j, k, ielem_small, ielem_large
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real(pReal), dimension(3) :: shift, query_point
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type(kdtree2), pointer :: tree
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type(kdtree2_result), dimension(1) :: Results
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shift = math_mul33x3(defgrad_av,geomdim)
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ielem_large = 0_pInt
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do ielem_small=1_pInt, Npoints_old ! making copies (27 for 3D, 9 for 2D)
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do k = -1, 1
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do j = -1, 1
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do i = -1, 1
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ielem_large = ielem_large + 1_pInt
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deformed_set_large(1:spatial_dim,ielem_large) = &
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deformed_set(1:spatial_dim,ielem_small) + real([i,j,k],pReal)* shift
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enddo; enddo; enddo; enddo
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ielem_large = 0_pInt
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if(res_old(3)==1_pInt) then
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spatial_dim = 2_pInt
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allocate(deformed_set_large(2,(res_new(1)*res_new(2))*9_pInt))
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do j=1_pInt, res_old(2); do i=1_pInt, res_old(1)
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do l = -1, 1; do m = -1, 1
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ielem_large = ielem_large + 1_pInt
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deformed_set_large(1:2,ielem_large) = deformed_set(i,j,1,1:2) + real([l,m],pReal)* shift(1:2)
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enddo; enddo;
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enddo; enddo
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else
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allocate(deformed_set_large(3,(res_new(1)*res_new(2)*res_new(3))*27))
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spatial_dim = 3_pInt
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do k=1_pInt,res_old(3); do j=1_pInt, res_old(2); do i=1_pInt, res_old(1)
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do l = -1, 1; do m = -1, 1; do n = -1, 1
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ielem_large = ielem_large + 1_pInt
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deformed_set_large(1:3,ielem_large) = deformed_set(i,j,k,1:3) + real([l,m,n],pReal)* shift
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enddo; enddo; enddo;
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enddo; enddo; enddo
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endif
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tree => kdtree2_create(deformed_set_large,sort=.true.,rearrange=.true.)
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do k=1_pInt,res_new(3); do j=1_pInt, res_new(2); do i=1_pInt, res_new(1)
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query_point = math_mul33x3(defgrad_av,(real([i,j,k],pReal)-0.5_pReal)/geomdim*real(res_new,pReal))
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call kdtree2_n_nearest(tp=tree, qv=query_point(1_pInt:spatial_dim),nn=1_pInt, results = Results)
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result_indices(i) = Results(1)%idx
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enddo; enddo; enddo
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ielem_large = 0_pInt
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do k=1_pInt,res_new(3); do j=1_pInt, res_new(2); do i=1_pInt, res_new(1)
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ielem_large = ielem_large + 1_pInt
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query_point = math_mul33x3(defgrad_av, &
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geomdim/real(res_new,pReal)*real([i,j,k],pReal) - geomdim/real(2_pInt*res_new,pReal))
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call kdtree2_n_nearest(tp=tree, qv=query_point(1:spatial_dim),nn=1_pInt, results = Results)
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result_indices(ielem_large) = Results(1)%idx /3_pInt**spatial_dim +1_pInt
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enddo; enddo; enddo
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deallocate(deformed_set_large)
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end subroutine math_nearestNeighborSearch
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end module math
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174
code/mesh.f90
174
code/mesh.f90
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@ -3526,32 +3526,178 @@ deallocate(mesh_HomogMicro)
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end subroutine mesh_tell_statistics
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subroutine mesh_regrid(res,resNew) !use new_res=0.0 for automatic determination of new grid
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subroutine mesh_regrid(resNew) !use new_res=[0.0,0.0,0.0] for automatic determination of new grid
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use prec, only: &
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pInt, &
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pReal
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use DAMASK_interface, only: &
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getSolverJobName
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use IO, only: &
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IO_read_jobBinaryFile
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IO_read_jobBinaryFile ,&
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IO_write_jobBinaryFile
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use math, only: &
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math_nearestNeighborSearch, &
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deformed_FFT
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integer(pInt), dimension(3), intent(in) :: res
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integer(pInt), dimension(3), intent(inout) :: resNew
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real(pReal), dimension(res(1),res(2),res(3),3,3) :: F
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real(pReal), dimension(:,:,:,:,:), allocatable :: crystallite_F0, &
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CPFEM_dcsdE, &
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crystallite_Fp0, &
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crystallite_Lp0
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real(pReal), dimension (:,:,:,:,:,:,:), allocatable :: crystallite_dPdF0
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real(pReal), dimension (:,:,:,:), allocatable :: crystallite_Tstar0_v, &
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convergedStateConst
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integer(pInt), dimension (:,:), allocatable :: convergedSizeConst
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integer(pInt), dimension(3), optional, intent(inout) :: resNew
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integer(pInt):: maxsize, i, j, k, m, Npoints, NpointsNew
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integer(pInt), dimension(3) :: res
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integer(pInt), dimension(:), allocatable :: indices, outputSize
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real(pReal), dimension(3) :: geomdim = 0.0_pReal
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real(pReal), dimension(3,3) :: Favg
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real(pReal), dimension(:,:,:,:,:), allocatable :: &
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F, FNew, &
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Fp, FpNew, &
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Lp, LpNew, &
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dcsdE, dcsdENew
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real(pReal), dimension (:,:,:,:,:,:,:), allocatable :: &
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dPdF, dPdFNew
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real(pReal), dimension (:,:,:,:), allocatable :: &
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coordinates, &
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Tstar, TstarNew, &
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stateConst, stateConstNew, &
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stateHomog, stateHomogNew
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res = mesh_spectral_getResolution()
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geomdim = mesh_spectral_getDimension()
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if (.not. present(resNew)) then
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resNew=res
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endif
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Npoints = res(1)*res(2)*res(3)
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NpointsNew = resNew(1)*resNew(2)*resNew(3)
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print*, 'resolution ', res
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print*, 'new resolution', resNew
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allocate(coordinates(res(1),res(2),res(3),3))
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allocate(indices(Npoints))
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allocate(F(res(1),res(2),res(3),3,3))
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call IO_read_jobBinaryFile(777,'convergedSpectralDefgrad',trim(getSolverJobName()),size(F))
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read (777,rec=1) F
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close (777)
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! ----Calculate average deformation for remesh--------
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do i= 1_pInt,3_pInt; do j = 1_pInt,3_pInt
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Favg(i,j) = sum(F(1:res(1),1:res(2),1:res(3),i,j)) / Npoints
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enddo; enddo
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call deformed_fft(res,geomdim,Favg,1.0_pReal,F,coordinates)
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!----- Nearest neighbour search -----------------------
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call math_nearestNeighborSearch(res, res, Favg, geomdim, &
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coordinates, indices)
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deallocate(F)
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! ---------------------------------------------------------------------------
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allocate(F (3,3,1,1, Npoints))
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allocate(FNew(3,3,1,1, NpointsNew))
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call IO_read_jobBinaryFile(777,'convergedF',trim(getSolverJobName()),size(F))
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read (777,rec=1) F
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close (777)
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call flush(6)
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do i = 1, NpointsNew
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FNew(1:3,1:3,1,1,i) = F(1:3,1:3,1,1,indices(i))
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enddo
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call flush(6)
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call IO_write_jobBinaryFile(777,'convergedF',size(FNew))
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write (777,rec=1) FNew
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close (777)
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deallocate(F)
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deallocate(FNew)
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!---------------------------------------------------------------------
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allocate(Fp (3,3,1,1,Npoints))
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allocate(FpNew(3,3,1,1,NpointsNew))
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call IO_read_jobBinaryFile(777,'convergedFp',trim(getSolverJobName()),size(Fp))
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read (777,rec=1) Fp
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close (777)
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do i = 1, NpointsNew
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FpNew(1:3,1:3,1,1,i) = Fp(1:3,1:3,1,1,indices(i))
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enddo
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call IO_write_jobBinaryFile(777,'convergedFp',size(FpNew))
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write (777,rec=1) FpNew
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close (777)
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deallocate(Fp)
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deallocate(FpNew)
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!------------------------------------------------------------------------
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allocate(Lp (3,3,1,1,Npoints))
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allocate(LpNew(3,3,1,1,NpointsNew))
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call IO_read_jobBinaryFile(777,'convergedLp',trim(getSolverJobName()),size(Lp))
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read (777,rec=1) Lp
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close (777)
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do i = 1, NpointsNew
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LpNew(1:3,1:3,1,1,i) = Lp(1:3,1:3,1,1,indices(i))
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enddo
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call IO_write_jobBinaryFile(777,'convergedLp',size(LpNew))
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write (777,rec=1) LpNew
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close (777)
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deallocate(Lp)
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deallocate(LpNew)
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!----------------------------------------------------------------------------
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allocate(dcsdE (6,6,1,1,Npoints))
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allocate(dcsdENew(6,6,1,1,NpointsNew))
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call IO_read_jobBinaryFile(777,'convergeddcsdE',trim(getSolverJobName()),size(dcsdE))
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read (777,rec=1) dcsdE
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close (777)
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do i = 1, NpointsNew
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dcsdENew(1:6,1:6,1,1,i) = dcsdE(1:6,1:6,1,1,indices(i))
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enddo
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call IO_write_jobBinaryFile(777,'convergeddcsdE',size(dcsdENew))
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write (777,rec=1) dcsdENew
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close (777)
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deallocate(dcsdE)
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deallocate(dcsdENew)
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! ---------------------------------------------------------------------------
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allocate(dPdF (3,3,3,3,1,1,Npoints))
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allocate(dPdFNew(3,3,3,3,1,1,NpointsNew))
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call IO_read_jobBinaryFile(777,'convergeddPdF',trim(getSolverJobName()),size(dPdF))
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read (777,rec=1) dPdF
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close (777)
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do i = 1, NpointsNew
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dPdFNew(1:3,1:3,1:3,1:3,1,1,i) = dPdF(1:3,1:3,1:3,1:3,1,1,indices(i))
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enddo
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call IO_write_jobBinaryFile(777,'convergeddPdF',size(dPdFNew))
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write (777,rec=1) dPdFNew
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close (777)
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deallocate(dPdF)
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deallocate(dPdFNew)
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!---------------------------------------------------------------------------
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allocate(Tstar (6,1,1,Npoints))
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allocate(TstarNew(6,1,1,NpointsNew))
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call IO_read_jobBinaryFile(777,'convergedTstar',trim(getSolverJobName()),size(Tstar))
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read (777,rec=1) Tstar
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close (777)
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do i = 1, NpointsNew
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TstarNew(1:6,1,1,i) = Tstar(1:6,1,1,indices(i))
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enddo
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call IO_write_jobBinaryFile(777,'convergedTstar',size(TstarNew))
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write (777,rec=1) TstarNew
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close (777)
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deallocate(Tstar)
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deallocate(TstarNew)
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end subroutine mesh_regrid
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function mesh_spectral_getDimension(fileUnit)
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