DAMASK_EICMD/src/mesh_grid.f90

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!--------------------------------------------------------------------------------------------------
!> @author Franz Roters, Max-Planck-Institut für Eisenforschung GmbH
!> @author Philip Eisenlohr, Max-Planck-Institut für Eisenforschung GmbH
!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
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!> @brief Parse geometry file to set up discretization and geometry for nonlocal model
!--------------------------------------------------------------------------------------------------
module mesh
#include <petsc/finclude/petscsys.h>
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use PETScsys
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use prec
use system_routines
use DAMASK_interface
use IO
use debug
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use numerics
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use discretization
use geometry_plastic_nonlocal
use FEsolving
implicit none
private
real(pReal), dimension(:,:,:), allocatable, public :: &
mesh_ipCoordinates !< IP x,y,z coordinates (after deformation!)
integer, dimension(3), public, protected :: &
grid !< (global) grid
integer, public, protected :: &
grid3, & !< (local) grid in 3rd direction
grid3Offset !< (local) grid offset in 3rd direction
real(pReal), dimension(3), public, protected :: &
geomSize
real(pReal), public, protected :: &
size3, & !< (local) size in 3rd direction
size3offset !< (local) size offset in 3rd direction
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public :: &
mesh_init
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contains
!--------------------------------------------------------------------------------------------------
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!> @brief reads the geometry file to obtain information on discretization
!--------------------------------------------------------------------------------------------------
subroutine mesh_init(ip,el)
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integer, intent(in), optional :: el, ip ! for compatibility reasons
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include 'fftw3-mpi.f03'
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real(pReal), dimension(3) :: &
mySize !< domain size of this process
integer, dimension(3) :: &
myGrid !< domain grid of this process
integer, dimension(:), allocatable :: &
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microstructureAt, &
homogenizationAt
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logical :: myDebug
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integer :: j
integer(C_INTPTR_T) :: &
devNull, z, z_offset
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write(6,'(/,a)') ' <<<+- mesh init -+>>>'
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myDebug = iand(debug_level(debug_mesh),debug_levelBasic) /= 0
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call mesh_spectral_read_grid(grid,geomSize,microstructureAt,homogenizationAt)
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if(worldsize>grid(3)) call IO_error(894, ext_msg='number of processes exceeds grid(3)')
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call fftw_mpi_init
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devNull = fftw_mpi_local_size_3d(int(grid(3),C_INTPTR_T), &
int(grid(2),C_INTPTR_T), &
int(grid(1),C_INTPTR_T)/2+1, &
PETSC_COMM_WORLD, &
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z, & ! domain grid size along z
z_offset) ! domain grid offset along z
grid3 = int(z)
grid3Offset = int(z_offset)
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size3 = geomSize(3)*real(grid3,pReal) /real(grid(3),pReal)
size3Offset = geomSize(3)*real(grid3Offset,pReal)/real(grid(3),pReal)
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myGrid = [grid(1:2),grid3]
mySize = [geomSize(1:2),size3]
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microstructureAt = microstructureAt(product(grid(1:2))*grid3Offset+1: &
product(grid(1:2))*(grid3Offset+grid3)) ! reallocate/shrink in case of MPI
homogenizationAt = homogenizationAt(product(grid(1:2))*grid3Offset+1: &
product(grid(1:2))*(grid3Offset+grid3)) ! reallocate/shrink in case of MPI
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mesh_ipCoordinates = mesh_build_ipCoordinates(myGrid,mySize,grid3Offset)
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if (myDebug) write(6,'(a)') ' Built IP coordinates'; flush(6)
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call geometry_plastic_nonlocal_setIPvolume( &
reshape([(product(mySize/real(myGrid,pReal)),j=1,product(myGrid))],[1,product(myGrid)]))
call geometry_plastic_nonlocal_setIParea(mesh_build_ipAreas(mySize,myGrid))
call geometry_plastic_nonlocal_setIPareaNormal(mesh_build_ipNormals(product(myGrid)))
call geometry_plastic_nonlocal_setIPneighborhood(mesh_spectral_build_ipNeighborhood(myGrid))
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if (myDebug) write(6,'(a)') ' Built nonlocal geometry'; flush(6)
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if (debug_e < 1 .or. debug_e > product(myGrid)) &
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call IO_error(602,ext_msg='element') ! selected element does not exist
if (debug_i /= 1) &
call IO_error(602,ext_msg='IP') ! selected element does not have requested IP
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FEsolving_execElem = [1,product(myGrid)] ! parallel loop bounds set to comprise all elements
allocate(FEsolving_execIP(2,product(myGrid)),source=1) ! parallel loop bounds set to comprise the only IP
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call discretization_init(homogenizationAt,microstructureAt, &
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reshape(mesh_ipCoordinates,[3,product(myGrid)]), &
mesh_spectral_build_nodes(myGrid,mySize,grid3Offset))
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end subroutine mesh_init
!--------------------------------------------------------------------------------------------------
!> @brief Parses geometry file
!> @details important variables have an implicit "save" attribute. Therefore, this function is
! supposed to be called only once!
!--------------------------------------------------------------------------------------------------
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subroutine mesh_spectral_read_grid(grid,geomSize,microstructure,homogenization)
integer, dimension(3), intent(out) :: grid ! grid (for all processes!)
real(pReal), dimension(3), intent(out) :: geomSize ! size (for all processes!)
integer, dimension(:), intent(out), allocatable :: &
microstructure, &
homogenization
character(len=:), allocatable :: rawData
character(len=65536) :: line
integer(pInt), allocatable, dimension(:) :: chunkPos
integer(pInt) :: h =- 1_pInt
integer(pInt) :: &
headerLength = -1_pInt, & !< length of header (in lines)
fileLength, & !< length of the geom file (in characters)
fileUnit, &
startPos, endPos, &
myStat, &
l, & !< line counter
c, & !< counter for # microstructures in line
o, & !< order of "to" packing
e, & !< "element", i.e. spectral collocation point
i, j
grid = -1_pInt
geomSize = -1.0_pReal
!--------------------------------------------------------------------------------------------------
! read data as stream
inquire(file = trim(geometryFile), size=fileLength)
open(newunit=fileUnit, file=trim(geometryFile), access='stream',&
status='old', position='rewind', action='read',iostat=myStat)
if(myStat /= 0_pInt) call IO_error(100_pInt,ext_msg=trim(geometryFile))
allocate(character(len=fileLength)::rawData)
read(fileUnit) rawData
close(fileUnit)
!--------------------------------------------------------------------------------------------------
! get header length
endPos = index(rawData,new_line(''))
if(endPos <= index(rawData,'head')) then
startPos = len(rawData)
call IO_error(error_ID=841_pInt, ext_msg='mesh_spectral_read_grid')
else
chunkPos = IO_stringPos(rawData(1:endPos))
if (chunkPos(1) < 2_pInt) call IO_error(error_ID=841_pInt, ext_msg='mesh_spectral_read_grid')
headerLength = IO_intValue(rawData(1:endPos),chunkPos,1_pInt)
startPos = endPos + 1_pInt
endif
!--------------------------------------------------------------------------------------------------
! read and interprete header
l = 0
do while (l < headerLength .and. startPos < len(rawData))
endPos = startPos + index(rawData(startPos:),new_line('')) - 1_pInt
if (endPos < startPos) endPos = len(rawData) ! end of file without new line
line = rawData(startPos:endPos)
startPos = endPos + 1_pInt
l = l + 1_pInt
chunkPos = IO_stringPos(trim(line))
if (chunkPos(1) < 2) cycle ! need at least one keyword value pair
select case ( IO_lc(IO_StringValue(trim(line),chunkPos,1_pInt,.true.)) )
case ('grid')
if (chunkPos(1) > 6) then
do j = 2_pInt,6_pInt,2_pInt
select case (IO_lc(IO_stringValue(line,chunkPos,j)))
case('a')
grid(1) = IO_intValue(line,chunkPos,j+1_pInt)
case('b')
grid(2) = IO_intValue(line,chunkPos,j+1_pInt)
case('c')
grid(3) = IO_intValue(line,chunkPos,j+1_pInt)
end select
enddo
endif
case ('size')
if (chunkPos(1) > 6) then
do j = 2_pInt,6_pInt,2_pInt
select case (IO_lc(IO_stringValue(line,chunkPos,j)))
case('x')
geomSize(1) = IO_floatValue(line,chunkPos,j+1_pInt)
case('y')
geomSize(2) = IO_floatValue(line,chunkPos,j+1_pInt)
case('z')
geomSize(3) = IO_floatValue(line,chunkPos,j+1_pInt)
end select
enddo
endif
case ('homogenization')
if (chunkPos(1) > 1) h = IO_intValue(line,chunkPos,2_pInt)
end select
enddo
!--------------------------------------------------------------------------------------------------
! sanity checks
if(h < 1_pInt) &
call IO_error(error_ID = 842_pInt, ext_msg='homogenization (mesh_spectral_read_grid)')
if(any(grid < 1_pInt)) &
call IO_error(error_ID = 842_pInt, ext_msg='grid (mesh_spectral_read_grid)')
if(any(geomSize < 0.0_pReal)) &
call IO_error(error_ID = 842_pInt, ext_msg='size (mesh_spectral_read_grid)')
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allocate(microstructure(product(grid)), source = -1) ! too large in case of MPI (shrink later, not very elegant)
allocate(homogenization(product(grid)), source = h) ! too large in case of MPI (shrink later, not very elegant)
!--------------------------------------------------------------------------------------------------
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! read and interpret content
e = 1_pInt
do while (startPos < len(rawData))
endPos = startPos + index(rawData(startPos:),new_line('')) - 1_pInt
if (endPos < startPos) endPos = len(rawData) ! end of file without new line
line = rawData(startPos:endPos)
startPos = endPos + 1_pInt
l = l + 1_pInt
chunkPos = IO_stringPos(trim(line))
noCompression: if (chunkPos(1) /= 3) then
c = chunkPos(1)
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microstructure(e:e+c-1_pInt) = [(IO_intValue(line,chunkPos,i+1_pInt), i=0_pInt, c-1_pInt)]
else noCompression
compression: if (IO_lc(IO_stringValue(line,chunkPos,2)) == 'of') then
c = IO_intValue(line,chunkPos,1)
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microstructure(e:e+c-1_pInt) = [(IO_intValue(line,chunkPos,3),i = 1_pInt,IO_intValue(line,chunkPos,1))]
else if (IO_lc(IO_stringValue(line,chunkPos,2)) == 'to') then compression
c = abs(IO_intValue(line,chunkPos,3) - IO_intValue(line,chunkPos,1)) + 1_pInt
o = merge(+1_pInt, -1_pInt, IO_intValue(line,chunkPos,3) > IO_intValue(line,chunkPos,1))
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microstructure(e:e+c-1_pInt) = [(i, i = IO_intValue(line,chunkPos,1),IO_intValue(line,chunkPos,3),o)]
else compression
c = chunkPos(1)
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microstructure(e:e+c-1_pInt) = [(IO_intValue(line,chunkPos,i+1_pInt), i=0_pInt, c-1_pInt)]
endif compression
endif noCompression
e = e+c
end do
if (e-1 /= product(grid)) call IO_error(error_ID = 843_pInt, el=e)
end subroutine mesh_spectral_read_grid
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!---------------------------------------------------------------------------------------------------
!> @brief Calculates position of nodes (pretend to be an element)
!---------------------------------------------------------------------------------------------------
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pure function mesh_spectral_build_nodes(grid,geomSize,grid3Offset) result(nodes)
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integer, dimension(3), intent(in) :: grid ! grid (for this process!)
real(pReal), dimension(3), intent(in) :: geomSize ! size (for this process!)
integer, intent(in) :: grid3Offset ! grid(3) offset
real(pReal), dimension(3,product(grid+1)) :: nodes
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integer :: n,a,b,c
n = 0
do c = 0, grid3
do b = 0, grid(2)
do a = 0, grid(1)
n = n + 1
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nodes(1:3,n) = geomSize/real(grid,pReal) * real([a,b,grid3Offset+c],pReal)
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enddo
enddo
enddo
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end function mesh_spectral_build_nodes
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!---------------------------------------------------------------------------------------------------
!> @brief Calculates position of IPs/cell centres (pretend to be an element)
!---------------------------------------------------------------------------------------------------
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function mesh_build_ipCoordinates(grid,geomSize,grid3Offset) result(ipCoordinates)
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integer, dimension(3), intent(in) :: grid ! grid (for this process!)
real(pReal), dimension(3), intent(in) :: geomSize ! size (for this process!)
integer, intent(in) :: grid3Offset ! grid(3) offset
real(pReal), dimension(3,1,product(grid)) :: ipCoordinates
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integer :: n,a,b,c
n = 0
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do c = 1, grid(3)
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do b = 1, grid(2)
do a = 1, grid(1)
n = n + 1
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ipCoordinates(1:3,1,n) = geomSize/real(grid,pReal) * (real([a,b,grid3Offset+c],pReal) -0.5_pReal)
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enddo
enddo
enddo
end function mesh_build_ipCoordinates
!--------------------------------------------------------------------------------------------------
!> @brief build neighborhood relations for spectral
!> @details assign globals: mesh_ipNeighborhood
!--------------------------------------------------------------------------------------------------
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pure function mesh_spectral_build_ipNeighborhood(grid) result(IPneighborhood)
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integer, dimension(3), intent(in) :: grid ! grid (for this process!)
integer, dimension(3,6,1,product(grid)) :: IPneighborhood !< 6 or less neighboring IPs as [element_num, IP_index, neighbor_index that points to me]
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integer :: &
x,y,z, &
e
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e = 0
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do z = 0,grid(3)-1
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do y = 0,grid(2)-1
do x = 0,grid(1)-1
e = e + 1
IPneighborhood(1,1,1,e) = z * grid(1) * grid(2) &
+ y * grid(1) &
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+ modulo(x+1,grid(1)) &
+ 1
IPneighborhood(1,2,1,e) = z * grid(1) * grid(2) &
+ y * grid(1) &
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+ modulo(x-1,grid(1)) &
+ 1
IPneighborhood(1,3,1,e) = z * grid(1) * grid(2) &
+ modulo(y+1,grid(2)) * grid(1) &
+ x &
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+ 1
IPneighborhood(1,4,1,e) = z * grid(1) * grid(2) &
+ modulo(y-1,grid(2)) * grid(1) &
+ x &
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+ 1
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IPneighborhood(1,5,1,e) = modulo(z+1,grid(3)) * grid(1) * grid(2) &
+ y * grid(1) &
+ x &
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+ 1
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IPneighborhood(1,6,1,e) = modulo(z-1,grid(3)) * grid(1) * grid(2) &
+ y * grid(1) &
+ x &
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+ 1
IPneighborhood(2,1:6,1,e) = 1
IPneighborhood(3,1,1,e) = 2
IPneighborhood(3,2,1,e) = 1
IPneighborhood(3,3,1,e) = 4
IPneighborhood(3,4,1,e) = 3
IPneighborhood(3,5,1,e) = 6
IPneighborhood(3,6,1,e) = 5
enddo
enddo
enddo
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end function mesh_spectral_build_ipNeighborhood
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!--------------------------------------------------------------------------------------------------
!> @brief calculation of IP interface areas
!--------------------------------------------------------------------------------------------------
pure function mesh_build_ipAreas(geomSize,grid) result(IPareas)
real(pReal), dimension(3), intent(in) :: geomSize ! size (for this process!)
integer, dimension(3), intent(in) :: grid ! grid (for this process!)
real(pReal), dimension(6,1,product(grid)) :: IPareas
IPareas(1:2,1,:) = geomSize(2)/real(grid(2)) * geomSize(3)/real(grid(3))
IPareas(3:4,1,:) = geomSize(3)/real(grid(3)) * geomSize(1)/real(grid(1))
IPareas(5:6,1,:) = geomSize(1)/real(grid(1)) * geomSize(2)/real(grid(2))
end function mesh_build_ipAreas
!--------------------------------------------------------------------------------------------------
!> @brief calculation of IP interface areas normals
!--------------------------------------------------------------------------------------------------
pure function mesh_build_ipNormals(nElems) result(IPnormals)
integer, intent(in) :: nElems
real, dimension(3,6,1,nElems) :: IPnormals
IPnormals(1:3,1,1,:) = spread([+1.0_pReal, 0.0_pReal, 0.0_pReal],2,nElems)
IPnormals(1:3,2,1,:) = spread([-1.0_pReal, 0.0_pReal, 0.0_pReal],2,nElems)
IPnormals(1:3,3,1,:) = spread([ 0.0_pReal,+1.0_pReal, 0.0_pReal],2,nElems)
IPnormals(1:3,4,1,:) = spread([ 0.0_pReal,-1.0_pReal, 0.0_pReal],2,nElems)
IPnormals(1:3,5,1,:) = spread([ 0.0_pReal, 0.0_pReal,+1.0_pReal],2,nElems)
IPnormals(1:3,6,1,:) = spread([ 0.0_pReal, 0.0_pReal,-1.0_pReal],2,nElems)
end function mesh_build_ipNormals
!--------------------------------------------------------------------------------------------------
!> @brief builds mesh of (distorted) cubes for given coordinates (= center of the cubes)
!--------------------------------------------------------------------------------------------------
function mesh_nodesAroundCentres(gDim,Favg,centres) result(nodes)
real(pReal), intent(in), dimension(:,:,:,:) :: &
centres
real(pReal), dimension(3,size(centres,2)+1,size(centres,3)+1,size(centres,4)+1) :: &
nodes
real(pReal), intent(in), dimension(3) :: &
gDim
real(pReal), intent(in), dimension(3,3) :: &
Favg
real(pReal), dimension(3,size(centres,2)+2,size(centres,3)+2,size(centres,4)+2) :: &
wrappedCentres
integer(pInt) :: &
i,j,k,n
integer(pInt), dimension(3), parameter :: &
diag = 1_pInt
integer(pInt), dimension(3) :: &
shift = 0_pInt, &
lookup = 0_pInt, &
me = 0_pInt, &
iRes = 0_pInt
integer(pInt), dimension(3,8) :: &
neighbor = reshape([ &
0_pInt, 0_pInt, 0_pInt, &
1_pInt, 0_pInt, 0_pInt, &
1_pInt, 1_pInt, 0_pInt, &
0_pInt, 1_pInt, 0_pInt, &
0_pInt, 0_pInt, 1_pInt, &
1_pInt, 0_pInt, 1_pInt, &
1_pInt, 1_pInt, 1_pInt, &
0_pInt, 1_pInt, 1_pInt ], [3,8])
!--------------------------------------------------------------------------------------------------
! initializing variables
iRes = [size(centres,2),size(centres,3),size(centres,4)]
nodes = 0.0_pReal
wrappedCentres = 0.0_pReal
!--------------------------------------------------------------------------------------------------
! building wrappedCentres = centroids + ghosts
wrappedCentres(1:3,2_pInt:iRes(1)+1_pInt,2_pInt:iRes(2)+1_pInt,2_pInt:iRes(3)+1_pInt) = centres
do k = 0_pInt,iRes(3)+1_pInt
do j = 0_pInt,iRes(2)+1_pInt
do i = 0_pInt,iRes(1)+1_pInt
if (k==0_pInt .or. k==iRes(3)+1_pInt .or. & ! z skin
j==0_pInt .or. j==iRes(2)+1_pInt .or. & ! y skin
i==0_pInt .or. i==iRes(1)+1_pInt ) then ! x skin
me = [i,j,k] ! me on skin
shift = sign(abs(iRes+diag-2_pInt*me)/(iRes+diag),iRes+diag-2_pInt*me)
lookup = me-diag+shift*iRes
wrappedCentres(1:3,i+1_pInt, j+1_pInt, k+1_pInt) = &
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centres(1:3,lookup(1)+1_pInt,lookup(2)+1_pInt,lookup(3)+1_pInt) &
- matmul(Favg, real(shift,pReal)*gDim)
endif
enddo; enddo; enddo
!--------------------------------------------------------------------------------------------------
! averaging
do k = 0_pInt,iRes(3); do j = 0_pInt,iRes(2); do i = 0_pInt,iRes(1)
do n = 1_pInt,8_pInt
nodes(1:3,i+1_pInt,j+1_pInt,k+1_pInt) = &
nodes(1:3,i+1_pInt,j+1_pInt,k+1_pInt) + wrappedCentres(1:3,i+1_pInt+neighbor(1,n), &
j+1_pInt+neighbor(2,n), &
k+1_pInt+neighbor(3,n) )
enddo
enddo; enddo; enddo
nodes = nodes/8.0_pReal
end function mesh_nodesAroundCentres
end module mesh