! Copyright (c) 2019 Kannan Masilamani <kannan.masilamani@uni-siegen.de> ! Copyright (c) 2019 Harald Klimach <harald.klimach@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. ! ****************************************************************************** !> author: Kannan Masilamani !! This module contains sphere definition and routines related to spheres ! 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 PetrĂ³ <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 PetrĂ³ 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 ! module tem_sphere_module use env_module, only: rk, minLength, labelLen, zeroLength use tem_aux_module, only: tem_abort use tem_logging_module, only: logunit use tem_cube_module, only: tem_cube_type use tem_transformation_module, only: tem_transformation_type ! include aotus modules use aotus_module, only: aot_get_val, aoterr_Fatal, aoterr_WrongType, & & flu_State, aoterr_NonExistent use aot_table_module, only: aot_table_open, aot_table_close, aot_table_length use aot_out_module, only: aot_out_type, aot_out_val, & & aot_out_open_table, aot_out_close_table implicit none private public :: grw_sphereArray_type public :: init, append, truncate, destroy, empty, placeAt public :: tem_sphere_type public :: tem_sphereCubeOverlap public :: tem_sphere_out public :: tem_load_sphere !> type contains sphere information type tem_sphere_type real(kind=rk) :: origin(3) !< origin of the sphere real(kind=rk) :: radius !< radius of the sphere !> To choose what to do with intersection of this object !! if only_surface = true than the only the surface of the object !! is intersected !! if only_surface = false then the whole object is intersected !! default is set to false logical :: only_surface end type tem_sphere_type !> growing array type for type(tem_sphere_type) type grw_spherearray_type integer :: nvals = 0 integer :: containersize = 0 type(tem_sphere_type), allocatable :: val(:) end type !> initialize the dynamic array interface init module procedure init_ga_sphere end interface !> truncate the array, meaning !! cut off the trailing empty entries interface truncate module procedure truncate_ga_sphere end interface !> empty the entries without changing arrays interface empty module procedure empty_ga_sphere end interface !> destroy the dynamic array interface destroy module procedure destroy_ga_sphere end interface !> insert an element at a given position interface placeat module procedure placeat_ga_sphere module procedure placeat_ga_sphere_vec end interface !> append a value to the dynamic array !! and return its position. interface append module procedure append_ga_sphere module procedure append_ga_sphere_vec end interface !> increase the size of the container !! for the array. interface expand module procedure expand_ga_sphere end interface !> interface to write out spheres in lua format to a file interface tem_sphere_out module procedure tem_sphere_out_scal module procedure tem_sphere_out_vec end interface tem_sphere_out !> interface to load spheres interface tem_load_sphere module procedure tem_load_sphere module procedure tem_load_sphere_single end interface tem_load_sphere contains ! **************************************************************************** !> Load sphere information from config file. subroutine tem_load_sphere(me, transform, conf, thandle ) ! -------------------------------------------------------------------------! !inferface variables !> Array of spheres type(tem_sphere_type), allocatable, intent(out) :: me(:) !> transformation for spatial object type(tem_transformation_type), intent(in) :: transform !> lua state type(flu_state) :: conf integer, intent(in) :: thandle !< handle for canonical objects ! -------------------------------------------------------------------------! ! local varaibles integer :: sph_handle, sph_subHandle integer :: iObj, nObjects ! -------------------------------------------------------------------------! write(logunit(1),*) 'Loading sphere: ' call aot_table_open(L = conf, parent = thandle, thandle = sph_handle, & & key = 'object') call aot_table_open(L=conf, parent = sph_handle, thandle = sph_subHandle, & & pos = 1 ) if ( sph_subHandle .eq. 0) then !object is a single table allocate(me(1)) call aot_table_close(L=conf, thandle=sph_subHandle) call tem_load_sphere_single( me(1), transform, conf, sph_handle ) else !object is a multiple table call aot_table_close(L=conf, thandle=sph_subHandle) nObjects = aot_table_length(L=conf, thandle=sph_handle) allocate(me(nObjects)) do iObj=1,nObjects call aot_table_open(L=conf, parent=sph_handle, thandle=sph_suBHandle,& & pos=iObj) call tem_load_sphere_single( me(iObj), transform, conf, sph_Subhandle ) call aot_table_close(L=conf, thandle=sph_subHandle) end do end if call aot_table_close(L=conf, thandle=sph_Handle) end subroutine tem_load_sphere ! **************************************************************************** ! **************************************************************************** !> This routine single sphere from object table subroutine tem_load_sphere_single(me, transform, conf, thandle ) ! -------------------------------------------------------------------------! !inferface variables !> single sphere type(tem_sphere_type), intent(out) :: me !> transformation for spatial object type(tem_transformation_type), intent(in) :: transform !> lua state type(flu_state) :: conf integer, intent(in) :: thandle !< handle for canonical objects ! -------------------------------------------------------------------------! integer :: iError, vError(3), errFatal(3) ! -------------------------------------------------------------------------! errFatal = aoterr_fatal ! read origin of sphere call aot_get_val(L=conf, thandle=thandle, val=me%origin, & & ErrCode=vError, key='origin', pos = 1) if (any(btest(vError, errFatal))) then write(logunit(0),*) & & ' Error in configuration: origin is not given to define a sphere' call tem_abort() end if !read radius of sphere call aot_get_val(L=conf, thandle=thandle, val=me%radius, & & ErrCode=iError, key='radius', pos=2 ) if (btest(iError, aoterr_Fatal)) then write(logunit(0),*) 'FATAL Error occured, while retrieving radius' if (btest(iError, aoterr_NonExistent)) & & write(logunit(0),*) 'Variable not existent!' if (btest(iError, aoterr_WrongType)) & & write(logunit(0),*) 'Variable has wrong type!' call tem_abort() end if call aot_get_val(L=conf, thandle=thandle, val=me%only_surface, & & ErrCode=iError, key='only_surface', & & pos=3, default=.false.) if (btest(iError, aoterr_WrongType)) then write(logunit(0),*) 'Error occured, while retrieving sphere only_surface' write(logunit(0),*) 'Variable has wrong type!' write(logunit(0),*) 'Should be a LOGICAL!' call tem_abort() endif write(logunit(1),"(A,3E12.5)") ' origin: ', me%origin write(logunit(1),"(A,3E12.5)") ' radius: ', me%radius write(logunit(1),"(A,L5 )") ' only_surface: ', me%only_surface !apply transformation to sphere if(transform%active) then if(transform%deform%active) then write(logunit(1),*) 'WARNING: Sphere deformation is only applied to' write(logunit(1),*) ' its radius as a scaling factor of ' write(logunit(1),*) ' first entry in the deformation table.' me%radius = me%radius * transform%deform%matrix(1,1) me%origin = matmul(transform%deform%matrix, me%origin) endif if(transform%translate%active) then me%origin = me%origin + transform%translate%vec endif endif end subroutine tem_load_sphere_single ! **************************************************************************** ! **************************************************************************** !> This function checks intesection of solid cube and sphere function tem_sphereCubeOverlap(sphere, cube) result(overlap) ! -------------------------------------------------------------------------! !interface variables type(tem_sphere_type), intent(in) :: sphere !< spacer geometry data type(tem_cube_type), intent(in) :: cube logical :: overlap !< return value ! -------------------------------------------------------------------------! if(sphere%only_surface) then overlap = hollowSphereCubeOverlap(sphere, cube) else overlap = solidSphereCubeOverlap(sphere, cube) endif end function tem_sphereCubeOverlap ! **************************************************************************** ! **************************************************************************** !> This function checks intesection of solid cube and hollow sphere !! !! This algorithm is taken from !! http://tog.acm.org/resources/GraphicsGems/gems/BoxSphere.c !! function hollowSphereCubeOverlap(sphere, cube) result(overlap) ! -------------------------------------------------------------------------! !inferface variables type(tem_sphere_type), intent(in) :: sphere !< spacer geometry data type(tem_cube_type), intent(in) :: cube logical :: overlap !< return value ! -------------------------------------------------------------------------! ! local variables real(kind=rk) :: rsqr,a, b integer :: i real(kind=rk) :: dmin, dmax ! -------------------------------------------------------------------------! !minimum distance dmin = 0.0_rk !maximum distance dmax = 0.0_rk rsqr = sphere%radius**2 do i=1,3 a = ( sphere%origin(i) - cube%origin(i) )**2 b = ( sphere%origin(i) - cube%endPnt(i) )**2 dmax = dmax + max(a,b) if ( sphere%origin(i) < cube%origin(i) ) then dmin = dmin + a else if ( sphere%origin(i) > cube%endPnt(i) ) then dmin = dmin + b end if end do overlap = ( (dmin <= rsqr) .and. (dmax >= rsqr) ) end function hollowSphereCubeOverlap ! **************************************************************************** ! **************************************************************************** !> This function checks intesection of solid cube and solid sphere !! !! This algorithm is taken from !! http://tog.acm.org/resources/GraphicsGems/gems/BoxSphere.c !! function solidSphereCubeOverlap(sphere, cube) result(overlap) ! -------------------------------------------------------------------------! !inferface variables type(tem_sphere_type), intent(in) :: sphere !< spacer geometry data type(tem_cube_type), intent(in) :: cube logical :: overlap !< return value ! -------------------------------------------------------------------------! ! local variables real(kind=rk) :: rsqr integer :: i real(kind=rk) :: dmin ! -------------------------------------------------------------------------! !minimum distance dmin = 0.0_rk rsqr = sphere%radius**2 do i=1,3 if ( sphere%origin(i) < cube%origin(i) ) then dmin = dmin + ( sphere%origin(i) - cube%origin(i) )**2 else if ( sphere%origin(i) > cube%endPnt(i) ) then dmin = dmin + ( sphere%origin(i) - cube%endPnt(i) )**2 end if end do overlap = (dmin <= rsqr) end function solidSphereCubeOverlap ! **************************************************************************** ! ************************************************************************** ! !> Write out an array of spheres in lua format !! subroutine tem_sphere_out_vec( me, conf ) ! -------------------------------------------------------------------------- !> sphere types to write out type( tem_sphere_type ), intent(in) :: me(:) !> Aotus type handling the output to the file in lua format type(aot_out_type), intent(inout) :: conf ! -------------------------------------------------------------------------- ! counter integer :: i ! -------------------------------------------------------------------------- ! create a table with name sphere call aot_out_open_table( put_conf = conf, tname = 'object' ) do i = 1, size(me) call tem_sphere_out_scal( me(i), conf ) end do call aot_out_close_table( put_conf = conf ) end subroutine tem_sphere_out_vec ! ************************************************************************** ! ! ************************************************************************** ! !> Write out a sphere shape in lua format !! subroutine tem_sphere_out_scal( me, conf ) ! -------------------------------------------------------------------------- !> sphere types to write out type( tem_sphere_type ), intent(in) :: me !> Aotus type handling the output to the file in lua format type(aot_out_type), intent(inout) :: conf ! -------------------------------------------------------------------------- ! create a table with name sphere if not exist if( conf%level == 0 ) then call aot_out_open_table( put_conf = conf, tname = 'object' ) else call aot_out_open_table( put_conf = conf ) end if call aot_out_val( put_conf = conf, vname = 'origin', val = me%origin ) call aot_out_val( put_conf = conf, vname = 'radius', val = me%radius ) call aot_out_val( put_conf = conf, vname = 'only_surface', & & val = me%only_surface ) call aot_out_close_table( put_conf = conf ) end subroutine tem_sphere_out_scal ! ************************************************************************** ! subroutine init_ga_sphere(me, length) type(grw_spherearray_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_sphere subroutine destroy_ga_sphere(me) type(grw_spherearray_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_sphere subroutine truncate_ga_sphere(me) !------------------------------------------------------------------------ type(grw_spherearray_type) :: me !< array to truncate !------------------------------------------------------------------------ type(tem_sphere_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_sphere subroutine empty_ga_sphere(me) !------------------------------------------------------------------------ type(grw_spherearray_type) :: me !< array to sorttruncate !------------------------------------------------------------------------ me%nvals = 0 end subroutine empty_ga_sphere !> 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_sphere(me, val, pos, length) type(grw_spherearray_type) :: me !< array to place the value into type(tem_sphere_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_sphere !> 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_sphere_vec(me, val, pos, length) type(grw_spherearray_type) :: me !< array to append the value to type(tem_sphere_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_sphere_vec subroutine append_ga_sphere(me, val, length) type(grw_spherearray_type) :: me !< array to append the value to type(tem_sphere_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_sphere subroutine append_ga_sphere_vec(me, val, length) type(grw_spherearray_type) :: me !< array to append the value to type(tem_sphere_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_sphere_vec subroutine expand_ga_sphere(me, pos, length) type(grw_spherearray_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(tem_sphere_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_sphere end module tem_sphere_module !> \page sphere Sphere !! Spheres are defined by an origin and radius. !! Sphere is considered to be solid as default i.e. all the cubes inside the !! sphere are marked as intersected cubes. !! It is possible to created hollow spheres by setting only_surface = true, !! it will mark only the cubes intersect with sphere surface as intersected !! cubes !! !! Valid definition: !! \li Single sphere !! \verbatim !! geometry={ !! kind='sphere', !! object={ !! origin={0.0,0.0,0.0}, !! radius=0.25, !! only_surface = true, -- If not defined default is set to false !! } !! } !! \endverbatim !! !! \li Multiple sphere !! \verbatim !! geometry={ !! kind='sphere', !! object={ !! { !! origin={0.0,0.0,0.0}, !! radius=0.25 !! }, !! { !! origin={-2.0,0.0,0.0}, !! radius=0.25 !! } !! } !! } !! \endverbatim !! \n\n !! The following seeder file is to generate mesh with hollow sphere (hollow => only_surface=true) !! inside: !! \include testsuite/sphere/seeder.lua !! \n\n !! Mesh generated with hollow sphere by the seeder file: !! \image html sphere.png !! \image html sphere_withedges.png !! \n\n !! Cutview of mesh with hollow sphere: !! \image html sphere_hollow.png !! \n\n !! Cutview of mesh with solid sphere (solid => only_surface=false): !! \image html sphere_solid.png !! \n\n !! Example lua file is available at \link testsuite/sphere/seeder.lua !! \example testsuite/sphere/seeder.lua