# sdr_periodic_module.f90 Source File

## Source Code

! Copyright (c) 2012-2013, 2019 Kannan Masilamani <kannan.masilamani@uni-siegen.de>
! Copyright (c) 2013, 2022 Harald Klimach <harald.klimach@dlr.de>
! Copyright (c) 2013 Simon Zimny <s.zimny@grs-sim.de>
! Copyright (c) 2016 Tobias Girresser <tobias.girresser@student.uni-siegen.de>
!
! Redistribution and use in source and binary forms, with or without
! modification, are permitted provided that the following conditions are met:
!
! 1. Redistributions of source code must retain the above copyright notice, this
! list of conditions and the following disclaimer.
!
! 2. Redistributions in binary form must reproduce the above copyright notice,
! this list of conditions and the following disclaimer in the documentation
! and/or other materials provided with the distribution.
!
! THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
! AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
! IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
! DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
! FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
! DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
! SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
! CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
! OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
! OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
! Copyright (c) 2012-2013 Simon Zimny <s.zimny@grs-sim.de>
! Copyright (c) 2012 Manuel Hasert <m.hasert@grs-sim.de>
! Copyright (c) 2012-2016 Harald Klimach <harald.klimach@uni-siegen.de>
! Copyright (c) 2012, 2015-2016 Kannan Masilamani <kannan.masilamani@uni-siegen.de>
! Copyright (c) 2013 Daniel Harlacher <d.harlacher@grs-sim.de>
! Copyright (c) 2014 Kartik Jain <kartik.jain@uni-siegen.de>
! Copyright (c) 2014 Verena Krupp <verena.krupp@uni-siegen.de>
! Copyright (c) 2015-2017 Jiaxing Qi <jiaxing.qi@uni-siegen.de>
! Copyright (c) 2015-2016 Peter Vitt <peter.vitt2@uni-siegen.de>
! Copyright (c) 2016 Daniel Fleischer <daniel.fleischer@student.uni-siegen.de>
! Copyright (c) 2016 Tobias Schneider <tobias1.schneider@student.uni-siegen.de>
! Copyright (c) 2017 Daniel Petró <daniel.petro@student.uni-siegen.de>
!
! Parts of this file were written by Harald Klimach, Simon Zimny and Manuel
! Hasert for German Research School for Simulation Sciences GmbH.
!
! Parts of this file were written by Harald Klimach, Kannan Masilamani,
! Daniel Harlacher, Kartik Jain, Verena Krupp, Jiaxing Qi, Peter Vitt,
! Daniel Fleischer, Tobias Girresser and Daniel Petró for University Siegen.
!
! Redistribution and use in source and binary forms, with or without
! modification, are permitted provided that the following conditions are met:
!
! 1. Redistributions of source code must retain the above copyright notice, this
! list of conditions and the following disclaimer.
!
! 2. Redistributions in binary form must reproduce the above copyright notice,
! this list of conditions and the following disclaimer in the documentation
! and/or other materials provided with the distribution.
!
! THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
! AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
! IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
! DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
! FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
! DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
! SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
! CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
! OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
! OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

! This file contains the source code for growing and dynamic arrays.
! This is used for arrays of primitives (int, long_int, real, ...) as well as
! for arrays of derived datatypes (tem_variable_type,...).
!
! To use these macros include the following to your source file.
!
! Smart growing array (GA) for ?tstring?
! Growing Arrays:
!
! declaration
!
!
! implementation
!

! -----------------------------------------------------------------
! 2d Array, which can grow in second dimension only (GA2d)
! tname ... indicates type of dynamic array (long, int, real, ...)

!
!------------------------------------------------------------------------------
!
! dynamic Arrays:
!
! declaration
!
!
! implementation
!
! ******************************************************************************
!> author: Kannan Masilamani
!! This module contains periodic boundary definition and routines
! ******************************************************************************
module sdr_periodic_module
use env_module,                only: rk, minLength, zeroLength
use tem_logging_module,        only: tem_log, tem_toStr
use tem_canonicalND_module,    only: tem_canonicalND_type,                   &
use tem_triangle_module,       only: tem_triangle_type, &
&                                  tem_triangleCubeOverlap
use tem_plane_module,          only: tem_plane_type
use tem_cube_module,           only: tem_cube_type
use tem_transformation_module, only: tem_transformation_type

use sdr_attribute_module,      only: sdr_attribute_type
use sdr_spatialObj_module,     only: grw_spatialObjArray_type,               &
&                                  sdr_spatialObj_type, append,            &
&                                  PeriodicPlane

use aotus_module,              only: flu_State, aot_get_val, &
&                                  aoterr_Fatal, aoterr_NonExistent,       &
&                                  aoterr_WrongType
use aot_table_module,          only: aot_table_open, aot_table_close,        &
&                                  aot_table_length

implicit none

private

public :: grw_periPlaneArray_type
public :: sdr_periodicPlane_type
public :: init, append, truncate, destroy, empty, placeAt
public :: sdr_periodicPlaneCubeOverlap

!> type contains Periodic plane information
type sdr_PeriodicPlane_type
!> intrinsic seeder plane
type(tem_plane_type) :: plane
!> Position of opposite periodic plane in the spatial object list
integer :: oppPlane_pos
end type sdr_PeriodicPlane_type

!> growing array type for type(sdr_periodicplane_type)
type grw_periplanearray_type
integer :: nvals = 0
integer :: containersize = 0
type(sdr_periodicplane_type), allocatable :: val(:)
end type

!> initialize the dynamic array
interface init
module procedure init_ga_periplane
end interface

!> truncate the array, meaning
!! cut off the trailing empty entries
interface truncate
module procedure truncate_ga_periplane
end interface

!> empty the entries  without changing arrays
interface empty
module procedure empty_ga_periplane
end interface

!> destroy the dynamic array
interface destroy
module procedure destroy_ga_periplane
end interface

!> insert an element at a given position
interface placeat
module procedure placeat_ga_periplane
module procedure placeat_ga_periplane_vec
end interface

!> append a value to the dynamic array
!! and return its position.
interface append
module procedure append_ga_periplane
module procedure append_ga_periplane_vec
end interface

!> increase the size of the container
!! for the array.
interface expand
module procedure expand_ga_periplane
end interface

contains

subroutine init_ga_periplane(me, length)
type(grw_periplanearray_type), intent(out) :: me !< dynamic array to init
integer, intent(in), optional :: length !< initial length of the container

if (present(length)) then
me%containersize = length
else
me%containersize = zerolength
end if
! deallocate ...
if( allocated( me%val ))     &
deallocate(me%val)
! ... and reallocate
allocate(me%val(me%containersize))
me%nvals = 0

end subroutine init_ga_periplane

subroutine destroy_ga_periplane(me)
type(grw_periplanearray_type), intent(inout) :: me !< dynamic array to destroy

me%containersize = 0
me%nvals = 0
if( allocated( me%val ) ) deallocate(me%val)

end subroutine destroy_ga_periplane

subroutine truncate_ga_periplane(me)
!------------------------------------------------------------------------
type(grw_periplanearray_type) :: me !< array to truncate
!------------------------------------------------------------------------
type(sdr_periodicplane_type), allocatable :: tarray(:)
!------------------------------------------------------------------------
integer :: ii
!------------------------------------------------------------------------

! nothing to do if container size is not larger than the number of values
! in the array.
if (me%containersize > me%nvals) then
allocate(tarray(me%nvals))
do ii = 1, me%nvals
tarray(ii) = me%val(ii)
end do
call move_alloc(tarray, me%val)
me%containersize = me%nvals
end if

end subroutine truncate_ga_periplane

subroutine empty_ga_periplane(me)
!------------------------------------------------------------------------
type(grw_periplanearray_type) :: me !< array to sorttruncate
!------------------------------------------------------------------------

me%nvals = 0

end subroutine empty_ga_periplane

!> adds the value to a given position inside the growing array.
!!
!! if the requested position is outside the current array bounds, the array
!! will be resized accordingly. if it is inside the current array bounds, the
!! element at the requested position will be replaced.
subroutine placeat_ga_periplane(me, val, pos, length)
type(grw_periplanearray_type) :: me !< array to place the value into
type(sdr_periodicplane_type), intent(in) :: val !< value to place at the given position
integer, intent(in) :: pos !< predefined position
!> optional length to expand the array
integer, intent(in), optional :: length

! value to append is larger than all existing ones,
! just put it to the end of the list, this captures
! also the case of empty lists.
! in this case foundpos = me%nvals + 1 holds.
if (pos > me%containersize) then
! expand the array, if its boundary is reached
call expand(me = me, pos = pos, length = length)
end if

me%nvals = max( pos, me%nvals )
me%val(pos) = val

end subroutine placeat_ga_periplane

!> adds the values starting from a given position inside the growing array.
!!
!! if the requested position is outside the current array bounds, the array
!! will be resized accordingly. if it is inside the current array bounds, the
!! elements starting from the requested position will be replaced up to
!! the element at position pos + size(val) - 1.
subroutine placeat_ga_periplane_vec(me, val, pos, length)
type(grw_periplanearray_type) :: me !< array to append the value to
type(sdr_periodicplane_type), intent(in) :: val(:) !< values to append
integer, intent(in) :: pos !< predefined position
!> optional length to expand the array
integer, intent(in), optional :: length

integer :: ub, ii

if (me%nvals == huge(me%nvals)) then
write(*,*) "reached end of integer range for growing array!"
write(*,*) "aborting!!"
stop
end if

ub = pos + size(val) - 1

if (ub > me%containersize) then
! expand the array, if its boundary is reached
call expand(me = me, pos = ub, length = length)
end if

me%nvals = max( ub, me%nvals )
do ii = pos, ub
me%val(ii) = val(1+ii-pos)
end do

end subroutine placeat_ga_periplane_vec

subroutine append_ga_periplane(me, val, length)
type(grw_periplanearray_type) :: me !< array to append the value to
type(sdr_periodicplane_type), intent(in) :: val !< value to append
!> optional length to expand the array
integer, intent(in), optional :: length

! value to append is larger than all existing ones,
! just put it to the end of the list, this captures
! also the case of empty lists.
! in this case foundpos = me%nvals + 1 holds.
if (me%nvals+1 > me%containersize) then
! expand the array, if its boundary is reached
call expand(me = me, length = length)
end if

me%nvals = me%nvals+1
me%val(me%nvals) = val

end subroutine append_ga_periplane

subroutine append_ga_periplane_vec(me, val, length)
type(grw_periplanearray_type) :: me !< array to append the value to
type(sdr_periodicplane_type), intent(in) :: val(:) !< values to append
!> optional length to expand the array
integer, intent(in), optional :: length

integer :: lb, ub, ii

if (me%nvals == huge(me%nvals)) then
write(*,*) "reached end of integer range for growing array!"
write(*,*) "aborting!!"
stop
end if

lb = me%nvals + 1
ub = lb + size(val) - 1

if (ub > me%containersize) then
! expand the array, if its boundary is reached
call expand(me = me, pos = ub, length = length)
end if

me%nvals = max( ub, me%nvals )
do ii = lb, ub
me%val(ii) = val(1+ii-lb)
end do

end subroutine append_ga_periplane_vec

subroutine expand_ga_periplane(me, pos, length)
type(grw_periplanearray_type) :: me !< array to resize
integer, intent(in), optional :: pos !< optional predefined position
!> optional length to expand the array
integer, intent(in), optional :: length

type(sdr_periodicplane_type), allocatable :: swpval(:)
integer :: explen, ii

explen = 0
! increase the container by the requested length of double it
if( present(length) ) then
explen = max( length, minlength )
else
! set the global minimum length, if doubling would be smaller than that
explen = max(me%containersize, minlength)
end if

! if a position is given, increase the container to at least the size to
! fit the position.
if( present(pos) ) explen = max(explen, pos-me%containersize)

! if the current size plus explen exceeds the max container size,
! reduce the size to the max container size.
if( (huge(me%containersize) - explen) <= me%containersize) then
! set max container size
me%containersize = huge(me%containersize)
else
! set the new container size
me%containersize = me%containersize + explen
end if

if ( me%nvals > 0 ) then
allocate(swpval(me%containersize))
do ii = 1, me%nvals
swpval(ii) = me%val(ii)
end do
call move_alloc( swpval, me%val )
else ! me%nvals == 0
if ( allocated(me%val) ) deallocate( me%val )
allocate( me%val(me%containersize) )
end if

end subroutine expand_ga_periplane

! ****************************************************************************
!> \brief load periodic table from config file.\n
!!
!! Periodic boundary is defined by two planes and the normal of both planes
!! should point outwards the fluid domain.
!!Defintion:
!!\verbatim
!!spaial_object={
!!     attribute = {
!!       kind = 'periodic',
!!       label = 'per1',
!!     },
!!     geometry = {
!!       kind = 'periodic',
!!       object = {{plane1={
!!                         vec={{0.0,2.0,0.0},
!!                              {0.0,0.0,2.0}},
!!                         origin={2.0,-1.0,-1.0}},
!!                  plane2={
!!                         vec={{0.0,2.0,0.0},
!!                              {0.0,0.0,2.0}},
!!                         origin={-2.0,-1.0,-1.0}},
!!                  }}
!!\endverbatim
!! It is possible to define multiple periodic boundary
! ****************************************************************************
subroutine sdr_load_periodic(periArray, spaObjArray, attr_pos, transform,    &
&                          conf, thandle)
! ---------------------------------------------------------------------------!
!> grwoing periodic plane data type
type( grw_periPlaneArray_type ), intent(inout) :: periArray
!> growing array of geometrical objects.
type( grw_spatialObjArray_type), intent(inout) :: spaObjArray
!> Position of the attribute to connect this object to.
integer, intent(in) :: attr_pos
!> transformation for spatial object
type(tem_transformation_type), intent(in) :: transform
type( flu_state ) :: conf !< lua state
integer, intent(in) :: thandle !< lua table identification
! ---------------------------------------------------------------------------!
!local variable
integer :: obj_handle
integer :: plane_handle
type(tem_canonicalND_type) :: canoND
type(sdr_periodicPlane_type) :: periPlane
! ---------------------------------------------------------------------------!

call aot_table_open( L = conf, parent = thandle,                           &
&                  thandle = obj_handle, key='object')

call tem_log(2, ' Plane 1 :')
call aot_table_open(L=conf, parent=obj_handle, thandle=plane_handle, &
&                 key='plane1')

call tem_load_canonicalND( me        = canoND,      &
&                        transform = transform,   &
&                        conf      = conf,        &
&                        thandle   = plane_handle )

! Convert canoNDPlane to periodic plane
periPlane%plane = canoND%plane

call append_periodic( periPlane = periPlane, &
&                   periArray = periArray, &
&                   spaObjArray = spaObjArray, &
&                   attr_pos = attr_pos )

!position of opposite periodic plane in the spatial object array
!plane 1 is added first so opposite plane is at + 1 of spatialObjArray
periArray%val( periArray%nVals )%oppPlane_pos = spaObjArray%nVals + 1

call aot_table_close(L=conf,thandle=plane_handle)

call tem_log(2, '')

call tem_log(2, ' Plane 2 :')
call aot_table_open(L=conf, parent=obj_handle, thandle=plane_handle, &
&                 key='plane2')

call tem_load_canonicalND( me        = canoND,      &
&                        transform = transform,   &
&                        conf      = conf,        &
&                        thandle   = plane_handle )

! Convert canoNDPlane to periodic plane
periPlane%plane = canoND%plane
call aot_table_close(L=conf,thandle=plane_handle)

call append_periodic( periPlane = periPlane, &
&                   periArray = periArray, &
&                   spaObjArray = spaObjArray, &
&                   attr_pos = attr_pos )

!plane 2 is added second so opposite plane is at - 1 of spatialObjArray
periArray%val( periArray%nVals )%oppPlane_pos = spaObjArray%nVals - 1

! ****************************************************************************

! ****************************************************************************
!> This routine append periodic type to growing array of periodic
subroutine append_periodic(periPlane, periArray, spaObjArray, attr_pos)
! --------------------------------------------------------------------------!
!> seeder periodic type
type( sdr_periodicPlane_type ), intent(in) :: periPlane
!> grwoing periodic plane data type
type( grw_periPlaneArray_type ), intent(inout) :: periArray
!> growing array of geometrical objects.
type( grw_spatialObjArray_type), intent(inout) :: spaObjArray
!> Position of the attribute to connect this object to.
integer, intent(in) :: attr_pos
! --------------------------------------------------------------------------!
type(sdr_spatialObj_type) :: spatialObj
! --------------------------------------------------------------------------!

!Append periodicPlane
spatialObj%attribute_position = attr_pos
spatialObj%geometry_primitive = PeriodicPlane

call append( periArray, periPlane )

spatialObj%primitive_position = periArray%nVals

call append(spaObjArray, spatialObj)

end subroutine append_periodic
! ****************************************************************************

! ****************************************************************************
!> Function compute intersection of plane with cube by checking
!! intersection of two triangle of a plane with cube
function sdr_periodicPlaneCubeOverlap( periPlane, cube )  result(overlaps)
!> periodic plane to check intersection with cube
type(sdr_periodicPlane_type),intent(in) :: periPlane
type(tem_cube_type), intent(in) :: cube
logical overlaps
! --------------------------------------------------------------------------!
integer :: iTri, interTri
! --------------------------------------------------------------------------!
interTri = 0

overlaps = .false.

do iTri=1,2
if( tem_triangleCubeOverlap( &
&               periPlane%plane%triangle(iTri), cube) )   &
& interTri = interTri + 1
end do

if (interTri > 0 ) overlaps = .true.

end function sdr_periodicPlaneCubeOverlap
! ****************************************************************************

end module sdr_periodic_module

!> \page periodicplanes Periodic planes
!! The periodic boundary condition are used to represent the domain
!! with infinite length, which is used when the simulation domain is too long.
!! It can be used to reduce the simulation domain from higher dimension
!! to lower dimension for example 3D to 2D or 3D to 1D.
!! On the periodic boundary, the velocity at the outlet is copied to
!! the velocity at the inlet and vice versa. \n
!!
!! Periodic planes are used to define perodic boundary in the mesh.
!! Periodic plane table contains two planes, plane1 and plane2 i.e
!! fluid neighbor of plane1 is mapped to plane2 and vice versa. \n
!! Following conditions must be satisfied in defining periodic planes
!! \li \b normal diection of plane1 and plane2 should point outwards
!! fluid domain. \n
!! In seeder, the plane normal are
!! definited by <b> right hand rule</b>, where thump finger represents
!! the 1st vector and index finger represents the 2nd vector and middle finger
!! represents the normal direction. This right hand rule can be seen perfectly
!! in the left plane in the figure below.
!! \image html plane_per.png
!! Above image shows the normal directions for two planes pointing outwards
!! the fluid domain.\n
!! Normal direction of the plane can be changed by just swaping the vectors
!! defining planes.i.e order of vector as shown in image below.
!! \image html plane1.png
!! \li refinement level on both planes should be the same and there should not
!! be any level jump on the periodic planes as shown below.
!! \image html multilevel_periodic_incorrect.png
!! Correct plane definition should look like below
!! \image html multilevel_periodic_correct.png
!! This can be achieved by shifting the plane by half of element size of
!! maximum refinement level intersecting the periodic planes.\n
!!
!! <b> If any of the above condition is not satisfied then seeder will
!! terminate an error message. </b>\n
!!
!! In seeder, when the node intersect only with periodic planes then the
!! boundary id for that direction is set to huge number. So any node
!! with direction of boundary id greater than number of boundaries then
!! the following algorithm is used for that direction.\n
!!
!! \b Algorithm used to generate the periodic boundary
!! \li Find the barycenter of the current element with periodic neighbor
!! \li Find the intersected periodic plane id and its assosiated opposite
!! plane id in the growing array of periodic planes. (periodic
!! plane definition is needed to project coordinate point from one plane
!! to another and also the normal direction to get to the fluid domain)
!! \li Project the barycenter of current element on its neighbor periodic
!!     plane
!! \li Translate the projected point to the opposite plane
!! \li Use the current search direction to move to the fluid node.
!! \li get the treeID of that node and set negative of this treeID to boundary id
!!     for current direction.
!! \li if the fluid node is intersected by a boundary then set boundary id
!!     to minimun of intersected boundary.
!! \li if the fluid node is again intersected by periodic boundary,
!!     then move in the negative normal direction of opposite periodic plane
!!     and do step 3 and 4.
!!
!!
!! In the solver, the periodic boundaries are identified with the boundary
!! id with negative values.\n
!!
!! \ref periodicPlaneExample "How to define periodic planes in lua file?"
!!
!! Example lua file to generate Channel with one element in z-direction
!! is available at