diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..453955a --- /dev/null +++ b/.travis.yml @@ -0,0 +1,56 @@ +# This will run on Travis' 'new' container-based infrastructure +sudo: false + +before_install: + - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh + - chmod +x miniconda.sh + - "./miniconda.sh -b" + - export PATH=/home/travis/miniconda2/bin:$PATH + - conda update --yes conda + +install: + - conda install --yes sphinx + - pip install sphinx_rtd_theme + +# Blacklist +branches: + only: + - ufs_public_release + - release/public-v1 + +# Environment variables +env: + global: + - GH_REPO_NAME: stochastic_physics + - DOXYFILE: $TRAVIS_BUILD_DIR/ + - GH_REPO_REF: github.com/noaa-psd/stochastic_physics.git + +# Install dependencies +addons: + apt: + packages: + - doxygen + - graphviz + +# Build your code e.g. by calling make +script: + - doxygen + - pushd docs +# Use Sphinx to make the html docs + - make html +# Tell GitHub not to use jekyll to compile the docs + - touch build/html/.nojekyll + - popd + +# Generate and deploy documentation +before_deploy: + - cp -r html docs/build/html/doxygen +deploy: + provider: pages + skip_cleanup: true + local_dir: docs/build/html + github_token: $GH_REPO_TOKEN + on: + branch: + - ufs_public_release + - release/public-v1 diff --git a/Doxyfile b/Doxyfile new file mode 100644 index 0000000..c3664a8 --- /dev/null +++ b/Doxyfile @@ -0,0 +1,22 @@ +PROJECT_NAME = "stochastic physics" +PROJECT_NUMBER = v1 +STRIP_FROM_PATH = +INPUT = +FILE_PATTERNS = *.md \ + *.h \ + *.doc \ + *.c \ + *.f \ + *.F90 +RECURSIVE = YES +USE_MDFILE_AS_MAINPAGE = README.md +OPTIMIZE_FOR_FORTRAN = YES +GENERATE_XML = NO +INLINE_SIMPLE_STRUCTS = YES +EXTRACT_ALL = YES +HAVE_DOT = YES +CALL_GRAPH = YES +CALLER_GRAPH = YES +PROJECT_LOGO = docs/UFS_logo.png +DISABLE_INDEX = YES +GENERATE_TREEVIEW = YES diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..fcd4df5 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,21 @@ +Copyright 2020 The Regents of the University of Colorado + +The stochastic_physics code incorporated in the Unified Forecast System (UFS) +was jointly developed by the National Oceanic and Atmospheric Administration and the +University of Colorado, Boulder. The gold standard copy of the Code +will be maintained by NOAA at https://github.com/noaa-psd/stochastic_physics. + +In cooperation with the Copyright Holder, the National Oceanic and +Atmospheric Administration is releasing this code under the +GNU Lesser General PUblic License v3.0 (the "License"); you may not use this +file except in compliance with the License. + +You may obtain a copy of the License at + + https://www.gnu.org/licenses/lgpl-3.0.en.html + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License diff --git a/cellular_automata_global.F90 b/cellular_automata_global.F90 new file mode 100644 index 0000000..be2dcb9 --- /dev/null +++ b/cellular_automata_global.F90 @@ -0,0 +1,352 @@ +subroutine cellular_automata_global(kstep,Statein,Coupling,Diag,nblks,nlev, & + nca,ncells,nlives,nfracseed,nseed,nthresh,ca_global,ca_sgs,iseed_ca, & + ca_smooth,nspinup,blocksize,nsmooth,ca_amplitude) + +use machine +use update_ca, only: update_cells_sgs, update_cells_global +#ifdef STOCHY_UNIT_TEST +use standalone_stochy_module, only: GFS_Coupling_type, GFS_diag_type, GFS_statein_type +use atmosphere_stub_mod, only: atmosphere_resolution, atmosphere_domain, & + atmosphere_scalar_field_halo, atmosphere_control_data +#else +use GFS_typedefs, only: GFS_Coupling_type, GFS_diag_type, GFS_statein_type +use atmosphere_mod, only: atmosphere_resolution, atmosphere_domain, & + atmosphere_scalar_field_halo, atmosphere_control_data +#endif +use mersenne_twister, only: random_setseed,random_gauss,random_stat,random_number +use mpp_domains_mod, only: domain2D +use block_control_mod, only: block_control_type, define_blocks_packed +use fv_mp_mod, only : mp_reduce_sum,mp_bcst,mp_reduce_max,mp_reduce_min,is_master +use mpp_mod, only : mpp_pe + + +implicit none + +!L.Bengtsson, 2017-06 + +!This program evolves a cellular automaton uniform over the globe given +!the flag ca_global + +integer,intent(in) :: kstep,ncells,nca,nlives,nseed,nspinup,nsmooth +integer,intent(in) :: iseed_ca +real,intent(in) :: nfracseed,nthresh,ca_amplitude +logical,intent(in) :: ca_global, ca_sgs, ca_smooth +integer, intent(in) :: nblks,nlev,blocksize +type(GFS_coupling_type),intent(inout) :: Coupling(nblks) +type(GFS_diag_type),intent(inout) :: Diag(nblks) +type(GFS_statein_type),intent(in) :: Statein(nblks) +type(block_control_type) :: Atm_block +type(random_stat) :: rstate +integer :: nlon, nlat, isize,jsize,nf,nn +integer :: inci, incj, nxc, nyc, nxch, nych +integer :: halo, k_in, i, j, k, iec, jec, isc, jsc +integer :: seed, ierr7,blk, ix, iix, count4,ih,jh +integer :: blocksz,levs +integer(8) :: count, count_rate, count_max, count_trunc +integer(8) :: iscale = 10000000000 +integer, allocatable :: iini_g(:,:,:),ilives_g(:,:) +real(kind=kind_phys), allocatable :: field_out(:,:,:), field_in(:,:),field_smooth(:,:) +real(kind=kind_phys), allocatable :: CA(:,:),CA1(:,:),CA2(:,:),CA3(:,:) +real(kind=kind_phys), allocatable :: noise1D(:),vertvelhigh(:,:),noise(:,:,:) +real(kind=kind_phys) :: psum,csum,CAmean,sq_diff,CAstdv +real(kind=kind_phys) :: Detmax(nca),Detmin(nca),Detmean(nca) +logical,save :: block_message=.true. + + +!nca :: switch for number of cellular automata to be used. +!ca_global :: switch for global cellular automata +!ca_sgs :: switch for cellular automata conditioned on SGS perturbed vertvel. +!nfracseed :: switch for number of random cells initially seeded +!nlives :: switch for maximum number of lives a cell can have +!nspinup :: switch for number of itterations to spin up the ca +!ncells :: switch for higher resolution grid e.g ncells=4 +! gives 4x4 times the FV3 model grid resolution. +!ca_smooth :: switch to smooth the cellular automata +!nthresh :: threshold of perturbed vertical velocity used in case of sgs + + +halo=1 +k_in=1 + +!---------------------------------------------------------------------------- +! Get information about the compute domain, allocate fields on this +! domain + +! WRITE(*,*)'Entering cellular automata calculations' + +! Some security checks for namelist combinations: + if(nca > 3)then + write(0,*)'Namelist option nca cannot be larger than 3 - exiting' + stop + endif + +! if(ca_global == .true. .and. ca_sgs == .true.)then +! write(0,*)'Namelist options ca_global and ca_sgs cannot both be true - exiting' +! stop +! endif + +! if(ca_sgs == .true. .and. ca_smooth == .true.)then +! write(0,*)'Currently ca_smooth does not work with ca_sgs - exiting' +! stop +! endif + + + call atmosphere_resolution (nlon, nlat, global=.false.) + isize=nlon+2*halo + jsize=nlat+2*halo + !nlon,nlat is the compute domain - without haloes + !mlon,mlat is the cubed-sphere tile size. + + inci=ncells + incj=ncells + + nxc=nlon*ncells + nyc=nlat*ncells + + nxch=nxc+2*halo + nych=nyc+2*halo + + + !Allocate fields: + + allocate(field_in(nlon*nlat,1)) + allocate(field_out(isize,jsize,1)) + allocate(field_smooth(nlon,nlat)) + allocate(iini_g(nxc,nyc,nca)) + allocate(ilives_g(nxc,nyc)) + allocate(vertvelhigh(nxc,nyc)) + allocate(CA(nlon,nlat)) + allocate(CA1(nlon,nlat)) + allocate(CA2(nlon,nlat)) + allocate(CA3(nlon,nlat)) + allocate(noise(nxc,nyc,nca)) + allocate(noise1D(nxc*nyc)) + + !Initialize: + + noise(:,:,:) = 0.0 + noise1D(:) = 0.0 + iini_g(:,:,:) = 0 + ilives_g(:,:) = 0 + CA1(:,:) = 0.0 + CA2(:,:) = 0.0 + CA3(:,:) = 0.0 + +!Put the blocks of model fields into a 2d array + levs=nlev + blocksz=blocksize + + call atmosphere_control_data(isc, iec, jsc, jec, levs) + call define_blocks_packed('cellular_automata', Atm_block, isc, iec, jsc, jec, levs, & + blocksz, block_message) + + isc = Atm_block%isc + iec = Atm_block%iec + jsc = Atm_block%jsc + jec = Atm_block%jec + +!Generate random number, following stochastic physics code: +if(kstep==0) then + if (iseed_ca == 0) then + ! generate a random seed from system clock and ens member number + call system_clock(count, count_rate, count_max) + ! iseed is elapsed time since unix epoch began (secs) + ! truncate to 4 byte integer + count_trunc = iscale*(count/iscale) + count4 = count - count_trunc + else if (iseed_ca > 0) then + ! don't rely on compiler to truncate integer(8) to integer(4) on + ! overflow, do wrap around explicitly. + count4 = mod(mpp_pe() + iseed_ca + 2147483648, 4294967296) - 2147483648 + endif +endif !kstep == 0 + + call random_setseed(count4,rstate) + do nf=1,nca + !Set seed (to be different) on all tasks. Save random state. + call random_number(noise1D,rstate) + !Put on 2D: + do j=1,nyc + do i=1,nxc + noise(i,j,nf)=noise1D(i+(j-1)*nxc) + enddo + enddo + enddo + +!Initiate the cellular automaton with random numbers larger than nfracseed +if(kstep ==0)then + do nf=1,nca + do j = 1,nyc + do i = 1,nxc + if (noise(i,j,nf) > nfracseed ) then + iini_g(i,j,nf)=1 + else + iini_g(i,j,nf)=0 + endif + enddo + enddo + enddo !nf +endif ! kstep==0 + +!In case we want to condition the cellular automaton on a large scale field +!we here set the "condition" variable to a different model field depending +!on nf. (this is not used if ca_global = .true.) + + + do nf=1,nca !update each ca + + do j = 1,nyc + do i = 1,nxc + ilives_g(i,j)=int(real(nlives)*1.5*noise(i,j,nf)) + enddo + enddo + + + +!Calculate neighbours and update the automata +!If ca-global is used, then nca independent CAs are called and weighted together to create one field; CA + + + CA(:,:)=0. + + call update_cells_global(kstep,nca,nxc,nyc,nxch,nych,nlon,nlat,CA,iini_g,ilives_g, & + nlives, ncells, nfracseed, nseed,nthresh, nspinup,nf) + + +if (ca_smooth) then + +do nn=1,nsmooth !number of itterations for the smoothing. + +field_in=0. + +!get halo +do j=1,nlat + do i=1,nlon + field_in(i+(j-1)*nlon,1)=CA(i,j) + enddo +enddo + +field_out=0. + +call atmosphere_scalar_field_halo(field_out,halo,isize,jsize,k_in,field_in) + +do j=1,nlat + do i=1,nlon + ih=i+halo + jh=j+halo + field_smooth(i,j)=(2.0*field_out(ih,jh,1)+2.0*field_out(ih-1,jh,1)+ & + 2.0*field_out(ih,jh-1,1)+2.0*field_out(ih+1,jh,1)+& + 2.0*field_out(ih,jh+1,1)+2.0*field_out(ih-1,jh-1,1)+& + 2.0*field_out(ih-1,jh+1,1)+2.0*field_out(ih+1,jh+1,1)+& + 2.0*field_out(ih+1,jh-1,1))/18. + enddo +enddo + +do j=1,nlat + do i=1,nlon + CA(i,j)=field_smooth(i,j) + enddo +enddo + +enddo !nn +endif !smooth + +!!!!Post processing, should be made into a separate subroutine + +Detmax(1)=maxval(CA) +call mp_reduce_max(Detmax(1)) +Detmin(1)=minval(CA) +call mp_reduce_min(Detmin(1)) + +do j=1,nlat + do i=1,nlon + CA(i,j) = ((CA(i,j) - Detmin(1))/(Detmax(1)-Detmin(1))) + enddo +enddo + +!mean: +CAmean=0. +psum=0. +csum=0. +do j=1,nlat + do i=1,nlon + psum=psum+(CA(i,j)) + csum=csum+1 + enddo +enddo + +call mp_reduce_sum(psum) +call mp_reduce_sum(csum) + +CAmean=psum/csum + +!std: +CAstdv=0. +sq_diff = 0. +do j=1,nlat + do i=1,nlon + sq_diff = sq_diff + (CA(i,j)-CAmean)**2.0 + enddo +enddo + +call mp_reduce_sum(sq_diff) + +CAstdv = sqrt(sq_diff/csum) + +!Transform to mean of 1 and ca_amplitude standard deviation + +do j=1,nlat + do i=1,nlon + CA(i,j)=1.0 + (CA(i,j)-CAmean)*(ca_amplitude/CAstdv) + enddo +enddo + +do j=1,nlat + do i=1,nlon + CA(i,j)=min(max(CA(i,j),0.),2.0) + enddo +enddo + +!Put back into blocks 1D array to be passed to physics +!or diagnostics output +if(kstep < 1)then +CA(:,:)=1. +endif + + if(nf==1)then + CA1(:,:)=CA(:,:) + elseif(nf==2)then + CA2(:,:)=CA(:,:) + else + CA3(:,:)=CA(:,:) + endif + +enddo !nf + + do blk = 1, Atm_block%nblks + do ix = 1,Atm_block%blksz(blk) + i = Atm_block%index(blk)%ii(ix) - isc + 1 + j = Atm_block%index(blk)%jj(ix) - jsc + 1 + Diag(blk)%ca1(ix)=CA1(i,j) + Diag(blk)%ca2(ix)=CA2(i,j) + Diag(blk)%ca3(ix)=CA3(i,j) + Coupling(blk)%ca1(ix)=CA1(i,j) + Coupling(blk)%ca2(ix)=CA2(i,j) + Coupling(blk)%ca3(ix)=CA3(i,j) + enddo + enddo + + + deallocate(field_in) + deallocate(field_out) + deallocate(field_smooth) + deallocate(iini_g) + deallocate(ilives_g) + deallocate(CA) + deallocate(CA1) + deallocate(CA2) + deallocate(CA3) + deallocate(noise) + deallocate(noise1D) + +end subroutine cellular_automata_global diff --git a/cellular_automata.f90 b/cellular_automata_sgs.F90 similarity index 52% rename from cellular_automata.f90 rename to cellular_automata_sgs.F90 index b8da0c2..035ca9a 100644 --- a/cellular_automata.f90 +++ b/cellular_automata_sgs.F90 @@ -1,16 +1,23 @@ -subroutine cellular_automata(kstep,Statein,Coupling,Diag,nblks,nlev, & +subroutine cellular_automata_sgs(kstep,Statein,Coupling,Diag,nblks,nlev, & nca,ncells,nlives,nfracseed,nseed,nthresh,ca_global,ca_sgs,iseed_ca, & ca_smooth,nspinup,blocksize) use machine -use update_ca, only: update_cells +use update_ca, only: update_cells_sgs, update_cells_global +#ifdef STOCHY_UNIT_TEST +use standalone_stochy_module, only: GFS_Coupling_type, GFS_diag_type, GFS_statein_type +use atmosphere_stub_mod, only: atmosphere_resolution, atmosphere_domain, & + atmosphere_scalar_field_halo, atmosphere_control_data +#else +use GFS_typedefs, only: GFS_Coupling_type, GFS_diag_type, GFS_statein_type use atmosphere_mod, only: atmosphere_resolution, atmosphere_domain, & atmosphere_scalar_field_halo, atmosphere_control_data +#endif use mersenne_twister, only: random_setseed,random_gauss,random_stat,random_number -use GFS_typedefs, only: GFS_Coupling_type, GFS_diag_type, GFS_statein_type use mpp_domains_mod, only: domain2D use block_control_mod, only: block_control_type, define_blocks_packed -use fv_mp_mod, only : mp_reduce_sum,mp_bcst,mp_reduce_max,is_master +use fv_mp_mod, only : mp_reduce_sum,mp_bcst,mp_reduce_max,mp_reduce_min,is_master +use mpp_mod, only : mpp_pe implicit none @@ -18,20 +25,18 @@ subroutine cellular_automata(kstep,Statein,Coupling,Diag,nblks,nlev, & !L.Bengtsson, 2017-06 !This program evolves a cellular automaton uniform over the globe given -!the flag ca_global, if instead ca_sgs is .true. it evolves a cellular automata conditioned on -!perturbed grid-box mean field. The perturbations to the mean field are given by a +!the flag ca_global, if instead ca_sgs is .true. it evolves a cellular automata conditioned on +!perturbed grid-box mean field. The perturbations to the mean field are given by a !stochastic gaussian skewed (SGS) distribution. !If ca_global is .true. it weighs the number of ca (nca) together to produce 1 output pattern -!If instead ca_sgs is given, it produces nca ca: -! 1 CA_DEEP = deep convection -! 2 CA_SHAL = shallow convection -! 3 CA_TURB = turbulence -! 4 CA_RAD = radiation -! 5 CA_MICRO = microphysics +!If instead ca_sgs is given, it produces nca ca: +! 1 CA_DEEP = deep convection +! 2 CA_SHAL = shallow convection +! 3 CA_TURB = turbulence -!PLEASE NOTE: This is considered to be version 0 of the cellular automata code for FV3GFS, some functionally -!is missing/limited. +!PLEASE NOTE: This is considered to be version 0 of the cellular automata code for FV3GFS, some functionally +!is missing/limited. integer,intent(in) :: kstep,ncells,nca,nlives,nseed,iseed_ca,nspinup real,intent(in) :: nfracseed,nthresh @@ -42,93 +47,85 @@ subroutine cellular_automata(kstep,Statein,Coupling,Diag,nblks,nlev, & type(GFS_statein_type),intent(in) :: Statein(nblks) type(block_control_type) :: Atm_block type(random_stat) :: rstate -integer :: nlon, nlat, isize,jsize,nf,k350,k850 +integer :: nlon, nlat, isize,jsize,nf,nn integer :: inci, incj, nxc, nyc, nxch, nych integer :: halo, k_in, i, j, k, iec, jec, isc, jsc integer :: seed, ierr7,blk, ix, iix, count4,ih,jh -integer :: blocksz,levs,ra,rb,rc +integer :: blocksz,levs,k350,k850 integer(8) :: count, count_rate, count_max, count_trunc integer(8) :: iscale = 10000000000 -integer, allocatable :: iini(:,:,:),ilives(:,:),ca_plumes(:,:) +integer, allocatable :: iini(:,:,:),ilives(:,:,:),iini_g(:,:,:),ilives_g(:,:),ca_plumes(:,:) real(kind=kind_phys), allocatable :: field_out(:,:,:), field_in(:,:),field_smooth(:,:),Detfield(:,:,:) -real(kind=kind_phys), allocatable :: omega(:,:,:),pressure(:,:,:),cloud(:,:),humidity(:,:) -real(kind=kind_phys), allocatable :: vertvelsum(:,:),vertvelmean(:,:),dp(:,:,:),surfp(:,:) -real(kind=kind_phys), allocatable :: CA(:,:),CAstore(:,:),CAavg(:,:),condition(:,:),rho(:,:),cape(:,:) -real(kind=kind_phys), allocatable :: CA_DEEP(:,:),CA_TURB(:,:),CA_RAD(:,:),CA_MICRO(:,:),CA_SHAL(:,:) +real(kind=kind_phys), allocatable :: omega(:,:,:),pressure(:,:,:),cloud(:,:),humidity(:,:),uwind(:,:) +real(kind=kind_phys), allocatable :: vertvelsum(:,:),vertvelmean(:,:),dp(:,:,:),surfp(:,:),shalp(:,:),gamt(:,:) +real(kind=kind_phys), allocatable :: CA(:,:),condition(:,:),rho(:,:),conditiongrid(:,:) +real(kind=kind_phys), allocatable :: CA_DEEP(:,:),CA_TURB(:,:),CA_SHAL(:,:) real(kind=kind_phys), allocatable :: noise1D(:),vertvelhigh(:,:),noise(:,:,:) -real(kind=kind_phys) :: psum,csum,CAmean,sq_diff,CAstdv,count1,alpha -real(kind=kind_phys) :: Detmax(nca),Detmean(nca),phi,stdev,delt +real(kind=kind_phys) :: psum,csum,CAmean,sq_diff,CAstdv,count1,lambda +real(kind=kind_phys) :: Detmax(nca),Detmin(nca),Detmean(nca),phi,stdev,delt,condmax logical,save :: block_message=.true. logical :: nca_plumes !nca :: switch for number of cellular automata to be used. !ca_global :: switch for global cellular automata -!ca_sgs :: switch for cellular automata conditioned on SGS perturbed vertvel. +!ca_sgs :: switch for cellular automata conditioned on SGS perturbed vertvel. !nfracseed :: switch for number of random cells initially seeded !nlives :: switch for maximum number of lives a cell can have !nspinup :: switch for number of itterations to spin up the ca -!ncells :: switch for higher resolution grid e.g ncells=4 -! gives 4x4 times the FV3 model grid resolution. +!ncells :: switch for higher resolution grid e.g ncells=4 +! gives 4x4 times the FV3 model grid resolution. !ca_smooth :: switch to smooth the cellular automata !nthresh :: threshold of perturbed vertical velocity used in case of sgs !nca_plumes :: compute number of CA-cells ("plumes") within a NWP gridbox. -k350 = 29 -k850 = 13 -alpha = 1.5 -ra = 201 -rb = 2147483648 -rc = 4294967296 - halo=1 k_in=1 -nca_plumes = .false. +if (nlev .EQ. 64) then + k350=29 + k850=13 +elseif (nlev .EQ. 127) then + k350=61 + k850=28 +else ! make a guess + k350=int(nlev/2) + k850=int(nlev/5) + print*,'this level selection is not supported, making an approximation for k350 and k850' +endif + +nca_plumes = .true. !---------------------------------------------------------------------------- ! Get information about the compute domain, allocate fields on this ! domain -! WRITE(*,*)'Entering cellular automata calculations' - ! Some security checks for namelist combinations: if(nca > 5)then write(0,*)'Namelist option nca cannot be larger than 5 - exiting' stop endif - if(ca_global .and. ca_sgs)then - write(0,*)'Namelist options ca_global and ca_sgs cannot both be true - exiting' - stop - endif - - if(ca_sgs .and. ca_smooth)then - write(0,*)'Currently ca_smooth does not work with ca_sgs - exiting' - stop - endif - call atmosphere_resolution (nlon, nlat, global=.false.) isize=nlon+2*halo jsize=nlat+2*halo - !nlon,nlat is the compute domain - without haloes - !mlon,mlat is the cubed-sphere tile size. inci=ncells incj=ncells - + nxc=nlon*ncells nyc=nlat*ncells - + nxch=nxc+2*halo nych=nyc+2*halo - !Allocate fields: + levs=nlev allocate(cloud(nlon,nlat)) - allocate(omega(nlon,nlat,k350)) - allocate(pressure(nlon,nlat,k350)) + allocate(omega(nlon,nlat,levs)) + allocate(pressure(nlon,nlat,levs)) allocate(humidity(nlon,nlat)) - allocate(dp(nlon,nlat,k350)) + allocate(uwind(nlon,nlat)) + allocate(dp(nlon,nlat,levs)) allocate(rho(nlon,nlat)) allocate(surfp(nlon,nlat)) allocate(vertvelmean(nlon,nlat)) @@ -137,44 +134,42 @@ subroutine cellular_automata(kstep,Statein,Coupling,Diag,nblks,nlev, & allocate(field_out(isize,jsize,1)) allocate(field_smooth(nlon,nlat)) allocate(iini(nxc,nyc,nca)) - allocate(ilives(nxc,nyc)) + allocate(ilives(nxc,nyc,nca)) + allocate(iini_g(nxc,nyc,nca)) + allocate(ilives_g(nxc,nyc)) allocate(vertvelhigh(nxc,nyc)) allocate(condition(nxc,nyc)) - allocate(cape(nlon,nlat)) + allocate(conditiongrid(nlon,nlat)) + allocate(shalp(nlon,nlat)) + allocate(gamt(nlon,nlat)) allocate(Detfield(nlon,nlat,nca)) allocate(CA(nlon,nlat)) allocate(ca_plumes(nlon,nlat)) - allocate(CAstore(nlon,nlat)) - allocate(CAavg(nlon,nlat)) allocate(CA_TURB(nlon,nlat)) - allocate(CA_RAD(nlon,nlat)) - allocate(CA_DEEP(nlon,nlat)) - allocate(CA_MICRO(nlon,nlat)) + allocate(CA_DEEP(nlon,nlat)) allocate(CA_SHAL(nlon,nlat)) allocate(noise(nxc,nyc,nca)) allocate(noise1D(nxc*nyc)) - + !Initialize: Detfield(:,:,:)=0. vertvelmean(:,:) =0. vertvelsum(:,:)=0. - cloud(:,:)=0. + cloud(:,:)=0. humidity(:,:)=0. + uwind(:,:) = 0. condition(:,:)=0. - cape(:,:)=0. + conditiongrid(:,:)=0. vertvelhigh(:,:)=0. + ca_plumes(:,:) = 0 noise(:,:,:) = 0.0 noise1D(:) = 0.0 iini(:,:,:) = 0 - ilives(:,:) = 0 - CA(:,:) = 0.0 - CAavg(:,:) = 0.0 - ca_plumes(:,:) = 0 - CA_TURB(:,:) = 0.0 - CA_RAD(:,:) = 0.0 - CA_DEEP(:,:) = 0.0 - CA_MICRO(:,:) = 0.0 - CA_SHAL(:,:) = 0.0 + ilives(:,:,:) = 0 + iini_g(:,:,:) = 0 + ilives_g(:,:) = 0 + Detmax(:)=0. + Detmin(:)=0. !Put the blocks of model fields into a 2d array levs=nlev @@ -187,22 +182,29 @@ subroutine cellular_automata(kstep,Statein,Coupling,Diag,nblks,nlev, & isc = Atm_block%isc iec = Atm_block%iec jsc = Atm_block%jsc - jec = Atm_block%jec + jec = Atm_block%jec do blk = 1,Atm_block%nblks do ix = 1, Atm_block%blksz(blk) i = Atm_block%index(blk)%ii(ix) - isc + 1 j = Atm_block%index(blk)%jj(ix) - jsc + 1 - cape(i,j) = Coupling(blk)%cape(ix) + uwind(i,j) = Statein(blk)%ugrs(ix,k350) + conditiongrid(i,j) = Coupling(blk)%condition(ix) + shalp(i,j) = Coupling(blk)%ca_shal(ix) + gamt(i,j) = Coupling(blk)%ca_turb(ix) surfp(i,j) = Statein(blk)%pgr(ix) humidity(i,j)=Statein(blk)%qgrs(ix,k850,1) !about 850 hpa - do k = 1,k350 !Lower troposphere: level k350 is about 350hPa + do k = 1,k350 !Lower troposphere omega(i,j,k) = Statein(blk)%vvl(ix,k) ! layer mean vertical velocity in pa/sec pressure(i,j,k) = Statein(blk)%prsl(ix,k) ! layer mean pressure in Pa enddo enddo enddo + CA_TURB(:,:) = 0.0 + CA_DEEP(:,:) = 0.0 + CA_SHAL(:,:) = 0.0 + !Compute layer averaged vertical velocity (Pa/s) vertvelsum=0. vertvelmean=0. @@ -227,62 +229,62 @@ subroutine cellular_automata(kstep,Statein,Coupling,Diag,nblks,nlev, & enddo !Generate random number, following stochastic physics code: -do nf=1,nca +if(kstep==2) then if (iseed_ca == 0) then ! generate a random seed from system clock and ens member number call system_clock(count, count_rate, count_max) ! iseed is elapsed time since unix epoch began (secs) ! truncate to 4 byte integer count_trunc = iscale*(count/iscale) - count4 = count - count_trunc + nf*ra + count4 = count - count_trunc else ! don't rely on compiler to truncate integer(8) to integer(4) on ! overflow, do wrap around explicitly. - count4 = mod(iseed_ca + rb, rc) - rb + nf*ra + count4 = mod(mpp_pe() + iseed_ca + 2147483648, 4294967296) - 2147483648 endif - !Set seed (to be the same) on all tasks. Save random state. - call random_setseed(count4,rstate) - call random_number(noise1D,rstate) - !Put on 2D: - do j=1,nyc - do i=1,nxc - noise(i,j,nf)=noise1D(i+(j-1)*nxc) - enddo - enddo - + call random_setseed(count4) -!Initiate the cellular automaton with random numbers larger than nfracseed - - do j = 1,nyc - do i = 1,nxc - if (noise(i,j,nf) > nfracseed ) then - iini(i,j,nf)=1 - else - iini(i,j,nf)=0 - endif + do nf=1,nca + call random_number(noise1D) + !Put on 2D: + do j=1,nyc + do i=1,nxc + noise(i,j,nf)=noise1D(i+(j-1)*nxc) + enddo enddo - enddo - enddo !nf +!Initiate the cellular automaton with random numbers larger than nfracseed + + do j = 1,nyc + do i = 1,nxc + if (noise(i,j,nf) > nfracseed ) then + iini(i,j,nf)=1 + else + iini(i,j,nf)=0 + endif + enddo + enddo + + enddo !nf +endif ! kstep=0 + !In case we want to condition the cellular automaton on a large scale field !we here set the "condition" variable to a different model field depending !on nf. (this is not used if ca_global = .true.) -CAstore = 0. do nf=1,nca !update each ca - - if(ca_sgs)then - - if(nf==1)then + + + if(nf==1)then inci=ncells incj=ncells do j=1,nyc do i=1,nxc - condition(i,j)=cape(inci/ncells,incj/ncells) + condition(i,j)=conditiongrid(inci/ncells,incj/ncells) if(i.eq.inci)then inci=inci+ncells endif @@ -293,9 +295,12 @@ subroutine cellular_automata(kstep,Statein,Coupling,Diag,nblks,nlev, & endif enddo + condmax=maxval(condition) + call mp_reduce_max(condmax) + do j = 1,nyc - do i = 1,nxc - ilives(i,j)=int(real(nlives)*alpha*noise(i,j,nf)) + do i = 1,nxc + ilives(i,j,nf)=real(nlives)*(condition(i,j)/condmax) enddo enddo @@ -304,7 +309,7 @@ subroutine cellular_automata(kstep,Statein,Coupling,Diag,nblks,nlev, & incj=ncells do j=1,nyc do i=1,nxc - condition(i,j)=humidity(inci/ncells,incj/ncells) + condition(i,j)=conditiongrid(inci/ncells,incj/ncells) if(i.eq.inci)then inci=inci+ncells endif @@ -315,40 +320,22 @@ subroutine cellular_automata(kstep,Statein,Coupling,Diag,nblks,nlev, & endif enddo + condmax=maxval(condition) + call mp_reduce_max(condmax) + do j = 1,nyc do i = 1,nxc - ilives(i,j)=int(real(nlives)*alpha*noise(i,j,nf)) + ilives(i,j,nf)=real(nlives)*(condition(i,j)/condmax) enddo enddo - elseif(nf==3)then - inci=ncells - incj=ncells - do j=1,nyc - do i=1,nxc - condition(i,j)=cape(inci/ncells,incj/ncells) - if(i.eq.inci)then - inci=inci+ncells - endif - enddo - inci=ncells - if(j.eq.incj)then - incj=incj+ncells - endif - enddo + else - do j = 1,nyc - do i = 1,nxc - ilives(i,j)=int(real(nlives)*alpha*noise(i,j,nf)) - enddo - enddo - - elseif(nf==4)then inci=ncells incj=ncells do j=1,nyc do i=1,nxc - condition(i,j)=cape(inci/ncells,incj/ncells) + condition(i,j)=conditiongrid(inci/ncells,incj/ncells) if(i.eq.inci)then inci=inci+ncells endif @@ -359,38 +346,18 @@ subroutine cellular_automata(kstep,Statein,Coupling,Diag,nblks,nlev, & endif enddo - do j = 1,nyc - do i = 1,nxc - ilives(i,j)=int(real(nlives)*alpha*noise(i,j,nf)) - enddo - enddo - - else - inci=ncells - incj=ncells - do j=1,nyc - do i=1,nxc - condition(i,j)=cape(inci/ncells,incj/ncells) - if(i.eq.inci)then - inci=inci+ncells - endif - enddo - inci=ncells - if(j.eq.incj)then - incj=incj+ncells - endif - enddo + condmax=maxval(condition) + call mp_reduce_max(condmax) do j = 1,nyc do i = 1,nxc - ilives(i,j)=int(real(nlives)*alpha*noise(i,j,nf)) + ilives(i,j,nf)=real(nlives)*(condition(i,j)/condmax) enddo enddo - endif !nf - + !Vertical velocity has its own variable in order to condition on combination !of "condition" and vertical velocity. @@ -409,144 +376,139 @@ subroutine cellular_automata(kstep,Statein,Coupling,Diag,nblks,nlev, & endif enddo +!Calculate neighbours and update the automata +!If ca-global is used, then nca independent CAs are called and weighted together to create one field; CA + + call update_cells_sgs(kstep,nca,nxc,nyc,nxch,nych,nlon,nlat,CA,ca_plumes,iini,ilives, & + nlives, ncells, nfracseed, nseed,nthresh,nspinup,nf,nca_plumes) - else !ca_global - - do j = 1,nyc - do i = 1,nxc - ilives(i,j)=int(real(nlives)*alpha*noise(i,j,nf)) - enddo - enddo - - endif !sgs/global - -!Calculate neighbours and update the automata -!If ca-global is used, then nca independent CAs are called and weighted together to create one field; CA - - call update_cells(kstep,nca,nxc,nyc,nxch,nych,nlon,nlat,CA,ca_plumes,iini,ilives, & - nlives, ncells, nfracseed, nseed,nthresh, ca_global, & - ca_sgs,nspinup, condition, vertvelhigh,nf,nca_plumes) - - if(ca_global)then - CAstore(:,:) = CAstore(:,:) + CA(:,:) - elseif(ca_sgs)then if(nf==1)then - CA_DEEP(:,:)=CA(:,:) + CA_DEEP(:,:)=CA(:,:) elseif(nf==2)then - CA_TURB(:,:)=CA(:,:) - elseif(nf==3)then - CA_SHAL(:,:)=CA(:,:) - elseif(nf==4)then - CA_RAD(:,:)=CA(:,:) + CA_SHAL(:,:)=CA(:,:) else - CA_MICRO(:,:)=CA(:,:) + CA_TURB(:,:)=CA(:,:) endif - else - write(*,*)'Either sgs or global needs to be selected' - endif - enddo !nf (nca) - if(ca_global)then - CAavg = CAstore / real(nca) - endif + enddo !nf (nca) -!smooth CA field +!!Post-processesing - could be made into a separate sub-routine -if (ca_smooth .and. ca_global) then -field_in=0. +!Deep convection ==================================== -!get halo -do j=1,nlat - do i=1,nlon - field_in(i+(j-1)*nlon,1)=CAavg(i,j) - enddo -enddo +if(kstep > 1)then -field_out=0. +!Use min-max method to normalize range +Detmax(1)=maxval(CA_DEEP,CA_DEEP.NE.0.) +call mp_reduce_max(Detmax(1)) +Detmin(1)=minval(CA_DEEP,CA_DEEP.NE.0.) +call mp_reduce_min(Detmin(1)) -call atmosphere_scalar_field_halo(field_out,halo,isize,jsize,k_in,field_in) do j=1,nlat do i=1,nlon - ih=i+halo - jh=j+halo - field_smooth(i,j)=(4.0*field_out(ih,jh,1)+2.0*field_out(ih-1,jh,1)+ & - 2.0*field_out(ih,jh-1,1)+2.0*field_out(ih+1,jh,1)+& - 2.0*field_out(ih,jh+1,1)+2.0*field_out(ih-1,jh-1,1)+& - 2.0*field_out(ih-1,jh+1,1)+2.0*field_out(ih+1,jh+1,1)+& - 2.0*field_out(ih+1,jh-1,1))/20. + if(CA_DEEP(i,j).NE.0.)then + CA_DEEP(i,j) =(CA_DEEP(i,j) - Detmin(1))/(Detmax(1)-Detmin(1)) + endif enddo enddo +!Compute the mean of the new range and subtract +CAmean=0. +psum=0. +csum=0. do j=1,nlat do i=1,nlon - CAavg(i,j)=field_smooth(i,j) + if(CA_DEEP(i,j).NE.0.)then + psum=psum+(CA_DEEP(i,j)) + csum=csum+1 + endif enddo enddo -endif !smooth +call mp_reduce_sum(psum) +call mp_reduce_sum(csum) -!In case of ca_global give data zero mean and unit standard deviation +CAmean=psum/csum -!if(ca_global == .true.)then +do j=1,nlat + do i=1,nlon + if(CA_DEEP(i,j).NE.0.)then + CA_DEEP(i,j)=(CA_DEEP(i,j)-CAmean) + endif + enddo +enddo -!CAmean=0. -!psum=0. -!csum=0. -!do j=1,nlat -! do i=1,nlon -! psum=psum+CAavg(i,j) -! csum=csum+1 -! enddo -!enddo +Detmin(1) = minval(CA_DEEP,CA_DEEP.NE.0) +call mp_reduce_min(Detmin(1)) -!call mp_reduce_sum(psum) -!call mp_reduce_sum(csum) +!Shallow convection ============================================================ -!CAmean=psum/csum +!Use min-max method to normalize range +Detmax(2)=maxval(CA_SHAL,CA_SHAL.NE.0) +call mp_reduce_max(Detmax(2)) +Detmin(2)=minval(CA_SHAL,CA_SHAL.NE.0) +call mp_reduce_min(Detmin(2)) -!CAstdv=0. -!sq_diff = 0. -!do j=1,nlat -! do i=1,nlon -! sq_diff = sq_diff + (CAavg(i,j)-CAmean)**2.0 -! enddo -!enddo +do j=1,nlat + do i=1,nlon + if(CA_SHAL(i,j).NE.0.)then + CA_SHAL(i,j)=(CA_SHAL(i,j) - Detmin(2))/(Detmax(2)-Detmin(2)) + endif + enddo +enddo -!call mp_reduce_sum(sq_diff) +!Compute the mean of the new range and subtract +CAmean=0. +psum=0. +csum=0. +do j=1,nlat + do i=1,nlon + if(CA_SHAL(i,j).NE.0.)then + psum=psum+(CA_SHAL(i,j)) + csum=csum+1 + endif + enddo +enddo -!CAstdv = sqrt( sq_diff / (csum-1.0) ) +call mp_reduce_sum(psum) +call mp_reduce_sum(csum) -!do j=1,nlat -! do i=1,nlon -! CAavg(i,j)=(CAavg(i,j)-CAmean)/CAstdv -! enddo -!enddo +CAmean=psum/csum -!endif +do j=1,nlat + do i=1,nlon + if(CA_SHAL(i,j).NE.0.)then + CA_SHAL(i,j)=(CA_SHAL(i,j)-CAmean) + endif + enddo +enddo -!Set the range for the nca individual ca_sgs patterns: -if(ca_sgs)then +!Turbulence ============================================================================= -Detmax(1)=maxval(CA_DEEP(:,:)) -call mp_reduce_max(Detmax(1)) +!Use min-max method to normalize range +Detmax(3)=maxval(CA_TURB,CA_TURB.NE.0) +call mp_reduce_max(Detmax(3)) +Detmin(3)=minval(CA_TURB,CA_TURB.NE.0) +call mp_reduce_min(Detmin(3)) do j=1,nlat do i=1,nlon - if(CA_DEEP(i,j)>0.)then - CA_DEEP(i,j)=CA_DEEP(i,j)/Detmax(1) !Now the range goes from 0-1 - endif + if(CA_TURB(i,j).NE.0.)then + CA_TURB(i,j)=(CA_TURB(i,j) - Detmin(3))/(Detmax(3)-Detmin(3)) + endif enddo enddo +!Compute the mean of the new range and subtract CAmean=0. psum=0. csum=0. do j=1,nlat do i=1,nlon - if(CA_DEEP(i,j)>0.)then - psum=psum+(CA_DEEP(i,j)) + if(CA_TURB(i,j).NE.0.)then + psum=psum+(CA_TURB(i,j)) csum=csum+1 endif enddo @@ -559,54 +521,55 @@ subroutine cellular_automata(kstep,Statein,Coupling,Diag,nblks,nlev, & do j=1,nlat do i=1,nlon - if(CA_DEEP(i,j)>0.)then - CA_DEEP(i,j)=(CA_DEEP(i,j)-CAmean) !Can we compute the median? + if(CA_TURB(i,j).NE.0.)then + CA_TURB(i,j)=(CA_TURB(i,j)-CAmean) endif enddo enddo -!!! +endif !kstep >1 - -!This is used for coupling with the Chikira-Sugiyama deep -!cumulus scheme. do j=1,nlat do i=1,nlon - if(ca_plumes(i,j)==0)then - ca_plumes(i,j)=20 - endif + if(conditiongrid(i,j) == 0)then + CA_DEEP(i,j)=0. + ca_plumes(i,j)=0. + endif enddo enddo +if(kstep == 1)then +do j=1,nlat + do i=1,nlon + ca_plumes(i,j)=0. + enddo +enddo endif !Put back into blocks 1D array to be passed to physics !or diagnostics output - + do blk = 1, Atm_block%nblks do ix = 1,Atm_block%blksz(blk) i = Atm_block%index(blk)%ii(ix) - isc + 1 j = Atm_block%index(blk)%jj(ix) - jsc + 1 - Diag(blk)%ca_out(ix)=CAavg(i,j) - Diag(blk)%ca_deep(ix)=CA_DEEP(i,j) - Diag(blk)%ca_turb(ix)=CA_TURB(i,j) + Diag(blk)%ca_deep(ix)=ca_plumes(i,j) + Diag(blk)%ca_turb(ix)=conditiongrid(i,j) Diag(blk)%ca_shal(ix)=CA_SHAL(i,j) - Diag(blk)%ca_rad(ix)=CA_RAD(i,j) - Diag(blk)%ca_micro(ix)=CA_MICRO(i,j) - Coupling(blk)%ca_out(ix)=CAavg(i,j) !Cellular Automata - Coupling(blk)%ca_deep(ix)=CA_DEEP(i,j) + Coupling(blk)%ca_deep(ix)=ca_plumes(i,j) Coupling(blk)%ca_turb(ix)=CA_TURB(i,j) Coupling(blk)%ca_shal(ix)=CA_SHAL(i,j) - Coupling(blk)%ca_rad(ix)=CA_RAD(i,j) - Coupling(blk)%ca_micro(ix)=CA_MICRO(i,j) enddo enddo + deallocate(omega) deallocate(pressure) deallocate(humidity) deallocate(dp) - deallocate(cape) + deallocate(conditiongrid) + deallocate(shalp) + deallocate(gamt) deallocate(rho) deallocate(surfp) deallocate(vertvelmean) @@ -620,14 +583,10 @@ subroutine cellular_automata(kstep,Statein,Coupling,Diag,nblks,nlev, & deallocate(Detfield) deallocate(CA) deallocate(ca_plumes) - deallocate(CAstore) - deallocate(CAavg) deallocate(CA_TURB) deallocate(CA_DEEP) - deallocate(CA_MICRO) deallocate(CA_SHAL) - deallocate(CA_RAD) deallocate(noise) deallocate(noise1D) -end subroutine cellular_automata +end subroutine cellular_automata_sgs diff --git a/compile_standalone b/compile_standalone index 11daf3e..981a280 100755 --- a/compile_standalone +++ b/compile_standalone @@ -1,5 +1,5 @@ #!/bin/sh -x -compile_all=1 +compile_all=0 FC=mpif90 INCS="-I. -I../FV3/gfsphysics/ -I../FMS/include -I../FV3/atmos_cubed_sphere -I../FMS/fv3gfs" FLAGS64=" -traceback -real-size 64 -DSTOCHY_UNIT_TEST -c "$INCS @@ -18,7 +18,6 @@ if [ $compile_all -eq 1 ];then $FC ${FLAGS64} setlats_lag_stochy.f $FC ${FLAGS64} glats_stochy.f $FC ${FLAGS64} gozrineo_stochy.f - $FC ${FLAGS64} num_parthds_stochy.f $FC ${FLAGS64} dezouv_stochy.f $FC ${FLAGS64} dozeuv_stochy.f $FC ${FLAGS64} epslon_stochy.f diff --git a/compns_stochy.F90 b/compns_stochy.F90 index a30afa5..40d51f4 100644 --- a/compns_stochy.F90 +++ b/compns_stochy.F90 @@ -1,3 +1,4 @@ +!>@brief The module 'compns_stochy_mod' contains the subroutine compns_stochy module compns_stochy_mod implicit none @@ -5,6 +6,9 @@ module compns_stochy_mod contains !----------------------------------------------------------------------- +!>@brief The module 'compns_stochy_mod' set the default namelist options reads in the stochastic physics namelist +!! and sets logicals and other parameters based on the namelist +!>@details Namelist can be either a file, or an internal namelist subroutine compns_stochy (me,sz_nml,input_nml_file,fn_nml,nlunit,deltim,iret) !$$$ Subprogram Documentation Block ! @@ -79,6 +83,7 @@ subroutine compns_stochy (me,sz_nml,input_nml_file,fn_nml,nlunit,deltim,iret) new_lscale = .false. do_shum = .false. do_skeb = .false. +! C. Draper July 2020. ! input land pert variables: ! LNDP_TYPE = 0 ! no explicit land perturbations @@ -86,7 +91,11 @@ subroutine compns_stochy (me,sz_nml,input_nml_file,fn_nml,nlunit,deltim,iret) ! this is the initial land sfc pert scheme, introduced and tested for impact on GEFS forecasts. ! see https://journals.ametsoc.org/doi/full/10.1175/MWR-D-18-0057.1 ! perturbations are assigned once at the start of the forecast - lndp_type = 0 ! 0 -none, 1 - lndp_fcst, 2 - lndp_edas +! LNDP_TYPE = 2 +! this is the newer land pert scheme, introduced and tested for impact on UFS/GDAS cycling stsyem +! perturbations are assigned at each time step (for state variables), or each time parameters are updated +! and the perturbations evolve over time. + lndp_type = 0 ! lndp_lscale = -999. ! length scales lndp_tau = -999. ! time scales iseed_lndp = 0 ! random seeds (if 0 use system clock) @@ -248,7 +257,13 @@ subroutine compns_stochy (me,sz_nml,input_nml_file,fn_nml,nlunit,deltim,iret) cycle else n_var_lndp=n_var_lndp+1 - lndp_var_list( n_var_lndp) = lndp_var_list(k) + lndp_var_list( n_var_lndp) = lndp_var_list(k) ! for lndp_type==2: + ! for state variables, unit is pert per hour + ! for parmaters, no time dimension in unit + ! since perturbations do not accumulate + ! (i.e., global_cycle overwrites the paramaters + ! each time it's called, so any previous perturbations + ! are lost). lndp_prt_list( n_var_lndp) = lndp_prt_list(k) endif enddo @@ -264,12 +279,22 @@ subroutine compns_stochy (me,sz_nml,input_nml_file,fn_nml,nlunit,deltim,iret) case default print*, 'ERROR: land perturbation requested for unknown parameter', lndp_var_list(k) iret = 10 - stop + return end select enddo elseif(lndp_type==2) then if (me==0) print*, & 'land perturbations will be applied to selected paramaters, using newer scheme designed for DA ens spread' + do k =1,n_var_lndp + select case (lndp_var_list(k)) + case('vgf','smc','stc') + if (me==0) print*, 'land perturbation will be applied to ', lndp_var_list(k) + case default + print*, 'ERROR: land perturbation requested for new parameter - will need to be coded in GFS_land_pert', lndp_var_list(k) + iret = 10 + return + end select + enddo endif case default diff --git a/dezouv_stochy.f b/dezouv_stochy.f index 32f4e7d..9707a00 100644 --- a/dezouv_stochy.f +++ b/dezouv_stochy.f @@ -1,9 +1,14 @@ +!>@brief The module 'dezouv_stochy_mod' contains the subroutine dezouv_stochy +! of divergence and odd harmonics of vorticty module dezouv_stochy_mod implicit none contains +!>@brief The subroutine 'dezouv_stochy' caculates even u and odd v winds harmonics from the even harmonics +! of divergence and odd harmonics of vorticty +!>@details This code is taken from the legacy spectral GFS subroutine dezouv_stochy(dev,zod,uev,vod,epsedn,epsodn, & snnp1ev,snnp1od,ls_node) cc diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d0c3cbf --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/UFS_logo.png b/docs/UFS_logo.png new file mode 100644 index 0000000..0e46c12 Binary files /dev/null and b/docs/UFS_logo.png differ diff --git a/docs/environment.yml b/docs/environment.yml new file mode 100644 index 0000000..5c23c82 --- /dev/null +++ b/docs/environment.yml @@ -0,0 +1,7 @@ +name: stochast_physics-docs + +channels: + - conda-forge + +dependencies: + - breathe diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..6247f7e --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build + +if "%1" == "" goto help + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.http://sphinx-doc.org/ + exit /b 1 +) + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..b33583b --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,70 @@ +# Configuration file for the Sphinx documentation builder. +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# http://www.sphinx-doc.org/en/master/config + +# -- Path setup -------------------------------------------------------------- + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# +#import os +#import sys +#sys.path.append( "/Users/ppegion/.local/bin" ) +#sys.path.insert(0, os.path.abspath('.')) + + +# -- Project information ----------------------------------------------------- + +project = 'UFS stochastic physics' +copyright = '2020, The Regents of the University of Colorado' +author = 'Philip Pegion' + +# The full version, including alpha/beta/rc tags +release = 'public' + +# assign master document + +master_doc = 'index' + + +# -- General configuration --------------------------------------------------- + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. + +# create doxygen documentation +#import subprocess +#read_the_docs_build = os.environ.get('READTHEDOCS', None) == 'True' +#print('read_the_docs_build',read_the_docs_build) +#if read_the_docs_build: +# subprocess.call('cd ../../ ; doxygen', shell=True) +#extensions = ['sphinx.ext.autodoc', 'breathe'] +##extensions = ['breathe'] +#breathe_projects = { "stochastic_physics": "../../xml/" } +#breathe_default_project = "stochastic_physics" + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = [] + + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = 'sphinx_rtd_theme' + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + diff --git a/docs/source/developers_guide.rst b/docs/source/developers_guide.rst new file mode 100644 index 0000000..b70bf7d --- /dev/null +++ b/docs/source/developers_guide.rst @@ -0,0 +1,14 @@ +Developer's guide +================= + +Code is housed on github at https://github.com/noaa-psd/stochastic_physics. Please read more about the Development process at https://github.com/ufs-community/ufs/wiki/Development-Processes#Developing-with-Gitflow. + +Please make a fork and checkout the entire ufs-community weather model at https://github.com/ufs-community/ufs-weather-model and point to your fork of the stochastic_physics submodule. + +Standalone testing +"""""""""""""""""" +If you intend to make modifications to the stochastic physics source code, there is a simplified program that exercises the random pattern generator without needing to run the entire model. Please see README.standalone in the stochastic_physics directory. + +Full model tests +"""""""""""""""" +The code updates are not expected to change existing results, so the full model regression tests need to be run. All of the tests must pass, although only a sub-set of tests are needed to consider adding changes to the stochastic_physics repository: fv3_control, fv3_stochy, fv3_ccpp_control, and fv3_ccpp_stochy. If the results are expected to change, then there needs to be scientific evidience that the change in results are what is expected. diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst new file mode 100644 index 0000000..13764b7 --- /dev/null +++ b/docs/source/getting_started.rst @@ -0,0 +1,10 @@ +Getting Started +================================================== +The stochastic physics currently only works with the UFS-atmosphere model + +You should get the full system at https://github.com/ufs-community/ufs-weather-model, which will include the stochastic physics code. + +In order to enable stochastic physics in a model run, you will need to turn it on via `namelist options `_ + +If using the CIME workflow decribed at https://ufs-mrweather-app.readthedocs.io/en/latest/, please add do_sppt=T, etc. to user_nl_ufsatm in the case directory. + diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..65a44df --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,18 @@ +Welcome to UFS stochastic physics's documentation! +================================================== + +.. toctree:: + :maxdepth: 2 + + getting_started + users_guide + namelist_options + developers_guide + references + + +Source Code Documentation +========================== + +Doxygen generated `content `_ + diff --git a/docs/source/namelist_options.rst b/docs/source/namelist_options.rst new file mode 100644 index 0000000..f243739 --- /dev/null +++ b/docs/source/namelist_options.rst @@ -0,0 +1,72 @@ +Stochastic Physics Namelist +=========================== + +General options +""""""""""""""" + +.. csv-table:: + :header: "Option", "Description" + :widths: 30, 50 + + "NTRUNC", "Optional, Spectral resolution (e.g. T126) of random patterns, default is for model to determine proper truncation" + "LAT_S", "Optional, number of latitude points for the gaussian grid (must be even), default is for model to determine gaussian grid" + "LON_S", "Optional, number of longitude points for the gaussian grid (recommend 2xLAT_S, default is for model to determine gaussian grid" + "FHSTOCH", "Optional, forecast hour to write out random pattern in order to restart the pattern for a different forecast (used in DA), file is stoch_out.F" + "STOCHINI", "Optional, set to true if wanting to read in a previous random pattern (input file needs to be named stoch_ini)." + +SPPT options +"""""""""""" + +.. csv-table:: + :header: "Option", "Description" + :widths: 30, 50 + + "DO_SPPT", "logical to tell parent atmospheric model to use SPPT" + "SPPT", "Amplitudes of random patterns (0.8,0.4,0.2,0.08,0.04) *" + "SPPT_TAU", "Decorrelation timescales in seconds (21600,1.728E5,6.912E5,7.776E6,3.1536E7) *" + "SPPT_LSCALE", "Decorrelation spatial scales in meters (250.E3,1000.E3,2000.E3,2000.E3,2000.E3) *" + "SPPT_LOGIT", "Should be true to limit the SPPT perturbations between 0 and 2. Otherwise model will crash." + "ISEED_SPPT", "Seeds for setting the random number sequence (ignored if stochini is true)" + "SPPT_SIGTOP1", "lower sigma level to taper perturbations to zero (default is 0.1)" + "SPPT_SIGTOP2", "upper sigma level to taper perturbations to zero (0.025)" + "SPPT_SFCLIMIT", ".T.=tapers the SPPT perturbations to zero at model’s lowest level (helps reduce model crashes)" + "SPPTINT", "Optional, interval in seconds to update random pattern. Perturbations still get applied every time-step" + "USE_ZMTNBLCK", ".T.=do not apply perturbations below the dividing streamline that is diagnosed by the gravity wave drag, mountain blocking scheme" + +``*`` **SPPT** uses 5 different patterns of varying time/length scales that are added together before being passed to physics + +SHUM options +"""""""""""" + +.. csv-table:: + :header: "Option", "Description" + :widths: 20, 50 + + "DO_SHUM", "logical to tell parent atmospheric model to use SHUM" + "SHUM", "Amplitudes of random patterns (0.004)" + "SHUM_TAU", "Decorrelation timescales in seconds (21600)" + "SHUM_LSCALE", "ecorrelation spatial scales in meters (250000)" + "SHUM_SIGEFOLD", "e-folding lengthscale (in units of sigma) of specific humidity perturbations, default is 0.2)" + "SHUMINT", "Optional, interval in seconds to update random pattern. Perturbations still get applied every time-step" + "ISEED_SHUM", "Seeds for setting the random number sequence (ignored if stochini is true)." + +SKEB options +"""""""""""" + +.. csv-table:: + :header: "Option", "Description" + :widths: 30, 50 + + "DO_SKEB", "logical to tell parent atmospheric model to use SKEB" + "SKEB", "Amplitudes of random patterns (0.5)" + "SKEB_TAU", "Decorrelation timescales in seconds (21600)" + "SKEB_LSCALE", "Decorrelation spatial scales in meters (250)" + "ISEED_SKEB", "Seeds for setting the random number sequence (ignored if stochini is true)." + "SKEBNORM", "0-random pattern is stream function, 1-pattern is K.E. norm, 2-pattern is vorticity (default is 0)" + "SKEB_VARSPECT_OPT", "0-gaussian (default), 1-power law (not tested)" + "SKEB_NPASS", "number of passes of the del2 smoothing for the dissipation estimate (default is 11, minimum is 3)" + "SKEB_VDOF", "the number of degrees of freedom in the vertical for the SKEB random pattern (default is 5)" + "SKEB_SIGTOP1", "lower sigma level to taper perturbations to zero (default is 0.1)" + "SKEB_SIGTOP2", "upper sigma level to taper perturbations to zero (0.025)" + "SKEBINT", "Optional, interval in seconds to update random pattern. Perturbations still get applied every time-step" + diff --git a/docs/source/references.rst b/docs/source/references.rst new file mode 100644 index 0000000..ac2a261 --- /dev/null +++ b/docs/source/references.rst @@ -0,0 +1,12 @@ +References +========== + +Berner, J., G. Shutts, M. Leutbecher, and T. Palmer, 2009: A spectral stochastic kinetic energy backscatter scheme and its impact on flow- dependent predictability in the ECMWF ensemble prediction system. J. Atmos. Sci., 66, 603–626, `doi:10.1175/2008JAS2677.1 `_ + +Gehne, M., T. Hamill, G. Bates, P. Pegion, W. Kolczynski 2019: Land-surface parameter and state perturbations in the Global Ensemble Forecast System. Mon. Wea. Rev. 147, 1319–1340 `doi:10.1175/MWR-D-18-0057.1 `_ + +Palmer, T. N., R. Buizza, F. Doblas-Reyes, T. Jung, M. Leutbecher, G. J. Shutts,M. Steinheimer, and A.Weisheimer, 2009: Stochastic parametrization and model uncertainty. ECMWF Tech. Memo. 598, 42 pp `doi:10.21957/ps8gbwbdv `_ + + +Tompkins, A. M., and J. Berner, 2008: A stochastic convective approach to account for model uncertainty due to unresolved humidity variability. J. Geophys. Res., 113, D18101, `doi:10.1029/2007JD009284 `_ + diff --git a/docs/source/users_guide.rst b/docs/source/users_guide.rst new file mode 100644 index 0000000..0d25818 --- /dev/null +++ b/docs/source/users_guide.rst @@ -0,0 +1,19 @@ +Users Guide +================================================== +The stochastic physics currently only works with the UFS-atmosphere model + +Currently, 3 stochastic schemes are used operationally at NCEP/EMC: Stochastic Kinetic Energy Backscatter (SKEB; Berner et al., 2009), Stochastically Perturbed Physics Tendencies (SPPT; Palmer et al., 2009), and Specific Humidity perturbations (SHUM), which is inspired by Tompkins and Berner, 2008. In addition there is the ability to perturb certain land model/surface parameters (Gehne et al, 2019), and a cellular automata scheme (Bengtsson et al. 2019) which interacts directly with the convective parameterization. + +SKEB adds wind perturbations to model state. Perturbations are random in space/time, but amplitude is determined by a smoothed dissipation estimate provided by the dynamical core. +Addresses errors in the dynamics - more active in the mid-latitudes + +SPPT multiplies the physics tendencies by a random number O [0,2] before updating the model state. Addresses error in the physics parameterizations (either missing physics or unresolved subgrid processes). It is most active in boundary layer and convective regions + +SHUM multiply the low-level specific humidity by a small random number each time-step. It attempts to address missing physics (cold pools, gust fronts), most active in convective regions + +Land surface perturbations allow for land surface parameters such as Albedo, Soil Hydraulic Conductivity, LAI, and roughness lengths to vary in space. Addresses error in the land model and land-atmosphere interactions. + +Due to the model’s numerics, any stochastic perturbation needs to be correlated in space and time in order to have the desired effect of upscale growth of the perturbations. This is achieved by creating a random pattern that has a specified decorrelation length-scale and is a first order auto-regressive process AR(1) in time with a specified decorrelation time-scale. (The CA random pattern generator also satisfies this condition) + +Currently the Land surface perturbations and cellular automata are not supported at the workflow level. + diff --git a/dozeuv_stochy.f b/dozeuv_stochy.f index 4ff5ad8..03e27ce 100644 --- a/dozeuv_stochy.f +++ b/dozeuv_stochy.f @@ -1,9 +1,14 @@ +!>@brief The module 'dodeuv_stochy_mod' contains the subroutine dezouv_stochy +! module dozeuv_stochy_mod implicit none contains +!>@brief The subroutine 'dezouv_stochy' caculates odd u and even v winds harmonics from the odd harmonics +! of divergence and even harmonics of vorticty +!>@details This code is taken from the legacy spectral GFS subroutine dozeuv_stochy(dod,zev,uod,vev,epsedn,epsodn, & snnp1ev,snnp1od,ls_node) cc diff --git a/epslon_stochy.f b/epslon_stochy.f index c7aace5..06acfea 100644 --- a/epslon_stochy.f +++ b/epslon_stochy.f @@ -1,9 +1,12 @@ +!>@brief The module 'epslon_stochy_mod' contains the subroute epslon_stochy module epslon_stochy_mod implicit none contains +!>@brief The subroutine 'epslon_stochy' calculate coeffients for use in spectral space +!>@details This code is taken from the legacy spectral GFS subroutine epslon_stochy(epse,epso,epsedn,epsodn, & ls_node) cc diff --git a/get_lats_node_a_stochy.f b/get_lats_node_a_stochy.f index 86e85ec..34c78a0 100644 --- a/get_lats_node_a_stochy.f +++ b/get_lats_node_a_stochy.f @@ -1,9 +1,11 @@ +!>@brief The module 'get_lats_node_a_stochy_mod' contains the subroutine get_lats_node_a_stochy module get_lats_node_a_stochy_mod implicit none contains - +!>@brief The subroutine 'get_lats_node_a_stochy' calculates the decomposition of the gaussian grid based on the processor layout +!>@details This code is taken from the legacy spectral GFS subroutine get_lats_node_a_stochy(me_fake,global_lats_a, & lats_nodes_a_fake,gl_lats_index, & global_time_sort_index,iprint) diff --git a/get_ls_node_stochy.f b/get_ls_node_stochy.f index 51d9f85..fad01e2 100644 --- a/get_ls_node_stochy.f +++ b/get_ls_node_stochy.f @@ -1,10 +1,13 @@ +!>@brief The module 'get_ls_node_stochy_mod' contains the subroutine get_ls_node_stochy module get_ls_node_stochy_mod implicit none contains +!>@brief The subroutine 'get_ls_node_stochy' calculates the decomposition of the spherical harmonics based on the processor layout subroutine get_ls_node_stochy(me_fake,ls_node,ls_max_node_fake, +!>@details This code is taken from the legacy spectral GFS c iprint) ! use stochy_resol_def diff --git a/get_stochy_pattern.F90 b/get_stochy_pattern.F90 index f489970..97e8e59 100644 --- a/get_stochy_pattern.F90 +++ b/get_stochy_pattern.F90 @@ -1,4 +1,6 @@ +!>@brief The module 'get_stochy_pattern_mod' contains the subroutines to retrieve the random pattern in the cubed-sphere grid module get_stochy_pattern_mod +!! the stochastic physics random pattern generators use machine, only : kind_dbl_prec, kind_evod use stochy_resol_def, only : latg, latg2, levs, lonf, skeblevs use spectral_layout_mod, only : ipt_lats_node_a, lat1s_a, lats_dim_a, & @@ -33,8 +35,11 @@ module get_stochy_pattern_mod logical :: first_call=.true. contains +!>@brief The subroutine 'get_random_pattern_fv3' converts spherical harmonics to the gaussian grid then interpolates to the cubed-sphere grid +!>@details This subroutine is for a 2-D (lat-lon) scalar field subroutine get_random_pattern_fv3(rpattern,npatterns,& gis_stochy,Model,Grid,nblks,maxlen,pattern_2d) +!\callgraph ! generate a random pattern for stochastic physics implicit none @@ -101,8 +106,11 @@ subroutine get_random_pattern_fv3(rpattern,npatterns,& end subroutine get_random_pattern_fv3 +!>@brief The subroutine 'get_random_pattern_fv3_sfc' converts spherical harmonics to the gaussian grid then interpolates to the cubed-sphere grid once +!>@details This subroutine is for a 2-D (lat-lon) scalar field subroutine get_random_pattern_fv3_sfc(rpattern,npatterns,& gis_stochy,Model,Grid,nblks,maxlen,do_advance_pattern,pattern_3d) +!\callgraph ! generate a random pattern for stochastic physics implicit none @@ -176,8 +184,11 @@ subroutine get_random_pattern_fv3_sfc(rpattern,npatterns,& end subroutine get_random_pattern_fv3_sfc +!>@brief The subroutine 'get_random_pattern_fv3_vect' converts spherical harmonics to a vector on gaussian grid then interpolates to the cubed-sphere grid +!>@details This subroutine is for a 2-D (lat-lon) vector field subroutine get_random_pattern_fv3_vect(rpattern,npatterns,& gis_stochy,Model,Grid,nblks,maxlen,upattern_3d,vpattern_3d) +!\callgraph ! generate a random pattern for stochastic physics implicit none @@ -325,11 +336,14 @@ subroutine get_random_pattern_fv3_vect(rpattern,npatterns,& end subroutine get_random_pattern_fv3_vect +!>@brief The subroutine 'scalarspect_to_gaugrid' converts scalar spherical harmonics to a scalar on a gaussian grid +!>@details This subroutine is for a 2-D (lat-lon) scalar field subroutine scalarspect_to_gaugrid(& trie_ls,trio_ls,datag,& ls_node,ls_nodes,max_ls_nodes,& lats_nodes_a,global_lats_a,lonsperlat,& plnev_a,plnod_a,nlevs) +!\callgraph implicit none @@ -378,7 +392,10 @@ subroutine scalarspect_to_gaugrid(& return end subroutine scalarspect_to_gaugrid +!>@brief The subroutine 'dump_patterns' writes out the speherical harmonics to a file, controlled by FHSTOCH +!>@details Only the active patterns are written out subroutine dump_patterns(sfile) +!\callgraph implicit none character*120 :: sfile integer :: stochlun,k,n @@ -415,7 +432,10 @@ subroutine dump_patterns(sfile) endif close(stochlun) end subroutine dump_patterns +!>@brief The subroutine 'write_patterns' writes out a single pattern and the seed associated with the random number sequence +!>@details Spherical harminoncs are stored with trianglular truncation subroutine write_pattern(rpattern,lev,lunptn) +!\callgraph implicit none type(random_pattern), intent(inout) :: rpattern integer, intent(in) :: lunptn,lev @@ -456,12 +476,16 @@ subroutine write_pattern(rpattern,lev,lunptn) endif deallocate(pattern2d) end subroutine write_pattern +!>@brief The subroutine 'vrtdivspect_to_uvgrid' converts vorticty and divergence spherical harmonics to +! zonal and meridional winds on the gaussian grid +!>@details This subroutine is for a 2-D (lat-lon) vector field subroutine vrtdivspect_to_uvgrid(& trie_di,trio_di,trie_ze,trio_ze,& uug,vvg,& ls_node,ls_nodes,max_ls_nodes,& lats_nodes_a,global_lats_a,lonsperlar,& epsedn,epsodn,snnp1ev,snnp1od,plnev_a,plnod_a,nlevs) +!\callgraph implicit none real(kind=kind_dbl_prec), intent(in) :: trie_di(len_trie_ls,2,nlevs) diff --git a/getcon_lag_stochy.f b/getcon_lag_stochy.f index c92ed0d..7fe23e4 100644 --- a/getcon_lag_stochy.f +++ b/getcon_lag_stochy.f @@ -1,9 +1,12 @@ +!>@brief The module 'getcon_lag_stochy_mod' contains the subroute getcon_lag_stochy module getcon_lag_stochy_mod implicit none contains +!>@brief The subroutine 'getcon_lag' calculates grid properties and domain decompostion for the gaussian grid +!>@details This code is taken from the legacy spectral GFS subroutine getcon_lag_stochy(lats_nodes_a,global_lats_a, & lats_nodes_h,global_lats_h_sn, & lonsperlat,xhalo,yhalo) diff --git a/getcon_spectral.F90 b/getcon_spectral.F90 index 387fc11..a9e8b21 100644 --- a/getcon_spectral.F90 +++ b/getcon_spectral.F90 @@ -1,9 +1,13 @@ +!>@brief The module 'getcon_spectral_mod' contains the subroutine getcon_spectral module getcon_spectral_mod implicit none contains +!>@brief The subroutine 'getcon_spectral' gets various constants for the spectral and related gaussian grid +!! and caluated the assoicate legendre polynomials +!>@details This code is taken from the legacy spectral GFS subroutine getcon_spectral ( ls_node,ls_nodes,max_ls_nodes, & lats_nodes_a,global_lats_a, & lonsperlat,latsmax, & @@ -81,6 +85,7 @@ subroutine getcon_spectral ( ls_node,ls_nodes,max_ls_nodes, & do lat = 1, latg2 lonsperlat(latg+1-lat) = lonsperlat(lat) end do +! decompostion of gaussian grid across nodes do node=1,nodes call get_lats_node_a_stochy( node-1, global_lats_a,lats_nodes_a(node),& gl_lats_index,global_time_sort_index_a, iprint) diff --git a/glats_stochy.f b/glats_stochy.f index 4ed9d38..b4abbdd 100644 --- a/glats_stochy.f +++ b/glats_stochy.f @@ -1,9 +1,13 @@ +!>@brief The module 'glats_stochy_mod' contains the subroute glats_stochy module glats_stochy_mod + implicit none contains +!>@brief The subroutine 'glats_stochy' calculate the latitudes for the gaussian grid +!>@details This code is taken from the legacy spectral GFS subroutine glats_stochy(lgghaf,colrad,wgt,wgtcs,rcs2,iprint) ! ! Jan 2013 Henry Juang increase precision by kind_qdt_prec=16 @@ -80,6 +84,8 @@ subroutine glats_stochy(lgghaf,colrad,wgt,wgtcs,rcs2,iprint) return end +!>@brief The subroutine 'poly' does something with latitudes +!>@details This code is taken from the legacy spectral GFS subroutine poly(n,rad,p) use machine ! diff --git a/gozrineo_stochy.f b/gozrineo_stochy.f index 01210ff..30c6d66 100644 --- a/gozrineo_stochy.f +++ b/gozrineo_stochy.f @@ -1,9 +1,11 @@ +!>@brief The module 'gozrineo_a_stochy_mod' contains the subroutine 'gozrineo_a_stochy' module gozrineo_a_stochy_mod implicit none contains - +!>@brief The subroutine 'gozrineo_a_stochy' calculates the deriviates of assoicate legendre polynomials +!>@details This code is taken from the legacy spectral GFS subroutine gozrineo_a_stochy(plnev_a,plnod_a, & pddev_a,pddod_a, & plnew_a,plnow_a, diff --git a/initialize_spectral_mod.F90 b/initialize_spectral_mod.F90 index 78cff2f..bc82299 100644 --- a/initialize_spectral_mod.F90 +++ b/initialize_spectral_mod.F90 @@ -1,3 +1,5 @@ +!>@brief The module 'initialize_spectral_mod' cotains the subroutine initialize_spectral +! generato ! !module: stochy_initialize_spectral ! --- initialize module of the ! gridded component of the stochastic physics patteern @@ -37,6 +39,9 @@ module initialize_spectral_mod contains +!>@brief The subroutine 'initialize_spectral' initializes the +!gridded component of the stochastic physics pattern +!>@details This code is taken from the legacy spectral GFS subroutine initialize_spectral(gis_stochy, rc) ! this subroutine set up the internal state variables, diff --git a/main.doc b/main.doc new file mode 100644 index 0000000..eeedbef --- /dev/null +++ b/main.doc @@ -0,0 +1,34 @@ +/*! \mainpage My Personal Index Page + * + * \section intro_sec Introduction + * + * + * + *The stochastic physics currently only works with the UFS-atmosphere model + * + *Currently, 3 stochastic schemes are used operationally at NCEP/EMC: Stochastic Kinetic Energy Backscatter (SKEB; Berner et al., 2009), Stochastically Perturbed Physics Tendencies (SPPT; Palmer et al., 2009), and Specific Humidity perturbations (SHUM), which is inspired by Tompkins and Berner, 2008. In addition there is the ability to perturb certain land model/surface parameters (Gehne et al, 2019), and a cellular automata scheme (Bengtsson et al. 20XX) which interacts directly with the convective parameterization. + * + *SKEB adds wind perturbations to model state. Perturbations are random in space/time, but amplitude is determined by a smoothed dissipation estimate provided by the dynamical core. + *Addresses errors in the dynamics - more active in the mid-latitudes + * + *SPPT multiplies the physics tendencies by a random number O [0,2] before updating the model state. Addresses error in the physics parameterizations (either missing physics or unresolved subgrid processes). It is most active in boundary layer and convective regions + * + *SHUM multiply the low-level specific humidity by a small random number each time-step. It attempts to address missing physics (cold pools, gust fronts), most active in convective regions + *Land surface perturbations allow for land surface parameters such as Albedo, Soil Hydraulic Conductivity, LAI, and roughness lengths to vary in space. Addresses error in the land model and land-atmosphere interactions + * + *Due to the model’s numerics, any stochastic perturbation needs to be correlated in space and time in order to have the desired effect of upscale growth of the perturbations. This is achieved by creating a random pattern that has a specified decorrelation length-scale and is a first order auto-regressive process AR(1) in time with a specified decorrelation time-scale. (The CA random pattern generator also satisfies this condition). + * + * \section install_sec Installation + * + * \subsection step1 1: clone the entire github repo: + * >git clone https://github.com/ufs-community/ufs-weather-model + * + * >cd ufs-weather-model + * + * >git submodule update --init --recursive + * + * \subsection step2 2: build the ufs-weather-model + * >build the system + * + * follow the CMAKE build instructions + */ diff --git a/makefile b/makefile index 6a7575c..89eb477 100644 --- a/makefile +++ b/makefile @@ -17,13 +17,11 @@ endif LIBRARY = libstochastic_physics.a -FFLAGS += -I../FV3/gfsphysics/ -I../FV3/atmos_cubed_sphere -I$(FMS_DIR) -I../FV3/namphysics +FFLAGS += -I../FV3/gfsphysics/ -I../FV3/atmos_cubed_sphere -I$(FMS_DIR) SRCS_F = SRCS_f90 = \ - ./cellular_automata.f90 \ - ./update_ca.f90 \ ./plumes.f90 SRCS_f = \ @@ -34,7 +32,6 @@ SRCS_f = \ ./glats_stochy.f \ ./sumfln_stochy.f \ ./gozrineo_stochy.f \ - ./num_parthds_stochy.f \ ./get_ls_node_stochy.f \ ./get_lats_node_a_stochy.f \ ./setlats_a_stochy.f \ @@ -55,7 +52,10 @@ SRCS_F90 = \ ./stochy_patterngenerator.F90 \ ./stochy_data_mod.F90 \ ./get_stochy_pattern.F90 \ - ./initialize_spectral_mod.F90 + ./initialize_spectral_mod.F90 \ + ./cellular_automata_global.F90 \ + ./cellular_automata_sgs.F90 \ + ./update_ca.F90 SRCS_c = diff --git a/num_parthds_stochy.f b/num_parthds_stochy.f index 2a71d45..58b7ccb 100644 --- a/num_parthds_stochy.f +++ b/num_parthds_stochy.f @@ -1,3 +1,4 @@ +! this function is no longer used, and will be removed soon function num_parthds_stochy() integer:: number_of_openMP_threads character(2) :: omp_threads diff --git a/pln2eo_stochy.f b/pln2eo_stochy.f index 4c6576b..c66a2a4 100644 --- a/pln2eo_stochy.f +++ b/pln2eo_stochy.f @@ -1,9 +1,12 @@ +!>@brief The module 'pln2eo_a_stochy_mod' contains the subroutine pln2eo_a_stochy module pln2eo_a_stochy_mod implicit none contains +!>@brief The subroutine 'pln2eo_a_stochy' calculates the assoicate legendre polynomials +!>@details This code is taken from the legacy spectral GFS subroutine pln2eo_a_stochy(plnev_a,plnod_a,epse,epso,colrad_a, & ls_node,num_lat) ! diff --git a/plumes.f90 b/plumes.f90 index 410cc47..80b301f 100644 --- a/plumes.f90 +++ b/plumes.f90 @@ -1,31 +1,24 @@ -subroutine plumes(V,L,a,row,col,kend) +subroutine plumes(V,L,AG,a,row,col,kend) implicit none -!!January 2018 adapted from Mathworkds "ISLANDS" - -!! plumes finds all islands of four-connected elements in a matrix. -!! plumes returns a matrix the same size as the input matrix, with all of -!! the four-connected elements assigned an arbitrary island number. A second -!! return argument is an nx3 matrix. Each row of this matrix has -!! information about a particular island: the first column is the island -!! number which corresponds to the numbers in the first return argument, the -!! second column is the number of elements in the island, the third column -!! is the value of the elements in that island (the elements of the input -!! matrix). plumes will also return a binary matrix with ones in the -!! positions of the elements of the largest four-connected island. The -!! largest four-connected island is determined first by value; for example -!! if there are 2 islands each with 5 elements, one of which is made up of -!! 6's and the other of which is made up of 4's, the island with the 6's -!! will be returned. In the case where there are 2 islands with the same -!! number of elements and the same value, an arbitrary choice will be -!! returned. +!!January 2018 + +! The routine identifies all four-connected elements in a matrix. +! The returns are: +! V - arbitrary island number +! L - nx3 matrix where earch row has information about a particular cluster. +! the first column is the cluster number which corresponds to V. The second +! column is the number of elements in the cluster, and the third column is +! the value of the elements in that cluster (the elements of the input field). +! AG - Binary matrix with ones in the positions of the elements of the largers +! four-connected clusters. integer, intent(in) :: row,col,kend integer, intent(in), dimension(row,col) :: a -integer, intent(out), dimension(kend) :: V,L +integer, intent(out), dimension(kend) :: L,V integer :: cnt,pp,mm,kk integer :: i,j,cntr,gg,hh,ii,jj,idxx,IDX -integer, dimension(row,col) :: AG +integer, intent(out), dimension(row,col) :: AG diff --git a/setlats_a_stochy.f b/setlats_a_stochy.f index c58dc56..49f0f46 100644 --- a/setlats_a_stochy.f +++ b/setlats_a_stochy.f @@ -1,9 +1,11 @@ +!>@brief The module 'setlats_a_stochy_mod' contains the subroutine setlats_a_stochy module setlats_a_stochy_mod implicit none contains - +!>@brief The subroutine 'setlats_a_stochy' selects the latitude points on this task +!>@details This code is taken from the legacy spectral GFS subroutine setlats_a_stochy(lats_nodes_a,global_lats_a, & iprint,lonsperlat) ! diff --git a/setlats_lag_stochy.f b/setlats_lag_stochy.f index ff4e4f0..539c96e 100644 --- a/setlats_lag_stochy.f +++ b/setlats_lag_stochy.f @@ -1,9 +1,13 @@ +!>@brief The module 'setlats_lag_stochy_mod' contains the subroutine setlats_lag_stochy module setlats_lag_stochy_mod implicit none contains +!>@brief The subroutine 'setlats_a_stochy' selects the latitude points on this task +! and halos +!>@details This code is taken from the legacy spectral GFS subroutine setlats_lag_stochy(lats_nodes_a, global_lats_a, & lats_nodes_h, global_lats_h, yhalo) ! diff --git a/spectral_layout.F90 b/spectral_layout.F90 index 247b69f..d55ca2b 100644 --- a/spectral_layout.F90 +++ b/spectral_layout.F90 @@ -1,3 +1,5 @@ +!>@brief The module 'spectral_layout_mod' contains the gaussian grid domain decompostion +! and the subroutine to interpolate from the gaussian grid to cubed-sphere (or any lat-lon pair) module spectral_layout_mod implicit none @@ -35,6 +37,9 @@ module spectral_layout_mod ! ! interpolation from lat/lon or gaussian grid to other lat/lon grid ! +!>@brief The subroutine 'stochy_la2ga' intepolates from the global gaussian grid +!! to the cubed sphere points +!>@details This code is taken from the legacy spectral GFS subroutine stochy_la2ga(regin,imxin,jmxin,rinlon,rinlat,rlon,rlat, & gauout,len,rslmsk, outlat, outlon) use machine , only : kind_io8, kind_io4 diff --git a/standalone_stochy.F90 b/standalone_stochy.F90 index ca28143..e6a1ea9 100644 --- a/standalone_stochy.F90 +++ b/standalone_stochy.F90 @@ -20,8 +20,8 @@ program standalone_stochy integer, parameter :: nlevs=64 integer :: ntasks,fid integer :: nthreads,omp_get_num_threads -integer :: ncid,xt_dim_id,yt_dim_id,time_dim_id,xt_var_id,yt_var_id,time_var_id -integer :: varid1,varid2,varid3,varid4 +integer :: ncid,xt_dim_id,yt_dim_id,time_dim_id,xt_var_id,yt_var_id,time_var_id,var_id_lat,var_id_lon,var_id_tile +integer :: varid1,varid2,varid3,varid4,varid_lon,varid_lat,varid_tile integer :: zt_dim_id,zt_var_id character*1 :: strid type(GFS_grid_type),allocatable :: Grid(:) @@ -73,8 +73,9 @@ program standalone_stochy integer :: nargs,ntile_out,nlunit,pe,npes,stackmax=4000000 character*80 :: fname character*1 :: ntile_out_str +integer :: iret -real(kind=4),allocatable,dimension(:,:) :: workg +real(kind=4),allocatable,dimension(:,:) :: workg,tile_number real(kind=4),allocatable,dimension(:,:,:) :: workg3d real(kind=4),allocatable,dimension(:) :: grid_xt,grid_yt real(kind=8),pointer ,dimension(:,:) :: area @@ -139,6 +140,7 @@ program standalone_stochy nx=Atm(1)%npx-1 ny=Atm(1)%npy-1 allocate(workg(nx,ny)) +allocate(tile_number(nx,ny)) allocate(workg3d(nx,ny,nlevs)) nblks=ny blksz=nx @@ -188,7 +190,8 @@ program standalone_stochy enddo !setup GFS_coupling allocate(Coupling(nblks)) -call init_stochastic_physics(Model, Init_parm, ntasks, nthreads) +call init_stochastic_physics(Model, Init_parm, ntasks, nthreads, iret) +if (iret .ne. 0) print *, 'ERROR init_stochastic_physics call' ! Draper - need proper error trapping here call get_outfile(fname) write(strid,'(I1.1)') my_id+1 if (ntile_out.EQ.0) write_this_tile=.true. @@ -211,6 +214,20 @@ program standalone_stochy ierr=NF90_PUT_ATT(ncid,yt_var_id,"long_name","T-cell latitude") ierr=NF90_PUT_ATT(ncid,yt_var_id,"cartesian_axis","Y") ierr=NF90_PUT_ATT(ncid,yt_var_id,"units","degrees_N") +ierr=NF90_DEF_VAR(ncid,"grid_lat",NF90_FLOAT,(/ xt_dim_id, yt_dim_id, time_dim_id /), var_id_lat) +ierr=NF90_PUT_ATT(ncid,var_id_lat,"long_name","T-cell latitudes") +ierr=NF90_PUT_ATT(ncid,var_id_lat,"units","degrees_N") +ierr=NF90_PUT_ATT(ncid,var_id_lat,"missing_value",undef) +ierr=NF90_PUT_ATT(ncid,var_id_lat,"_FillValue",undef) +ierr=NF90_DEF_VAR(ncid,"grid_lon",NF90_FLOAT,(/ xt_dim_id, yt_dim_id, time_dim_id /), var_id_lon) +ierr=NF90_PUT_ATT(ncid,var_id_lon,"long_name","T-cell longitudes") +ierr=NF90_PUT_ATT(ncid,var_id_lon,"units","degrees_N") +ierr=NF90_PUT_ATT(ncid,var_id_lon,"missing_value",undef) +ierr=NF90_PUT_ATT(ncid,var_id_lon,"_FillValue",undef) +ierr=NF90_DEF_VAR(ncid,"tile_num",NF90_FLOAT,(/ xt_dim_id, yt_dim_id, time_dim_id /), var_id_tile) +ierr=NF90_PUT_ATT(ncid,var_id_tile,"long_name","tile number") +ierr=NF90_PUT_ATT(ncid,var_id_tile,"missing_value",undef) +ierr=NF90_PUT_ATT(ncid,var_id_tile,"_FillValue",undef) if (Model%do_skeb)then ierr=NF90_DEF_VAR(ncid,"p_ref",NF90_FLOAT,(/ zt_dim_id /), zt_var_id) ierr=NF90_PUT_ATT(ncid,zt_var_id,"long_name","reference pressure") @@ -261,7 +278,11 @@ program standalone_stochy ierr=NF90_PUT_VAR(ncid,zt_var_id,pressl) endif endif - +! put lat lon and tile number +ierr=NF90_PUT_VAR(ncid,var_id_lon,Init_parm%xlon,(/1,1,1/)) +ierr=NF90_PUT_VAR(ncid,var_id_lat,Init_parm%xlat,(/1,1,1/)) +tile_number=my_id+1 +ierr=NF90_PUT_VAR(ncid,var_id_tile,tile_number,(/1,1,1/)) do i=1,nblks if (Model%do_sppt)allocate(Coupling(i)%sppt_wts(blksz,nlevs)) if (Model%do_shum)allocate(Coupling(i)%shum_wts(blksz,nlevs)) diff --git a/stochastic_physics.F90 b/stochastic_physics.F90 index 611dc6a..b47d3e7 100644 --- a/stochastic_physics.F90 +++ b/stochastic_physics.F90 @@ -15,7 +15,9 @@ module stochastic_physics !!pattern genertors !>@details It reads the stochastic physics namelist (nam_stoch and nam_sfcperts) !allocates and polulates the necessary arrays -subroutine init_stochastic_physics(Model, Init_parm, ntasks, nthreads) + +subroutine init_stochastic_physics(Model, Init_parm, ntasks, nthreads, iret) +!\callgraph use fv_mp_mod, only : is_master use stochy_internal_state_mod use stochy_data_mod, only : nshum,rpattern_shum,init_stochdata,rpattern_sppt,nsppt,rpattern_skeb,nskeb,gg_lats,gg_lons,& @@ -37,9 +39,9 @@ subroutine init_stochastic_physics(Model, Init_parm, ntasks, nthreads) type(GFS_init_type), intent(in) :: Init_parm integer, intent(in) :: ntasks integer, intent(in) :: nthreads +integer, intent(out) :: iret integer :: nblks -integer :: iret real*8 :: PRSI(Model%levs),PRSL(Model%levs),dx real, allocatable :: skeb_vloc(:) integer :: k,kflip,latghf,blk,k2 @@ -48,6 +50,9 @@ subroutine init_stochastic_physics(Model, Init_parm, ntasks, nthreads) ! Set/update shared variables in spectral_layout_mod ompthreads = nthreads +iret = 0 ! Draper, abnormal returns were not being error trapped + ! I fixed those I noticed, by there may be more + ! ------------------------------------------ nblks = size(Model%blksz) @@ -60,6 +65,7 @@ subroutine init_stochastic_physics(Model, Init_parm, ntasks, nthreads) gis_stochy%me=me gis_stochy%nodes=nodes call init_stochdata(Model%levs,Model%dtp,Model%input_nml_file,Model%fn_nml,Init_parm%nlunit,iret) +if (iret .ne. 0) return ! check to see decomposition !if(Model%isppt_deep == .true.)then !do_sppt = .true. @@ -68,24 +74,28 @@ subroutine init_stochastic_physics(Model, Init_parm, ntasks, nthreads) if (Model%do_sppt.neqv.do_sppt) then write(0,'(*(a))') 'Logic error in stochastic_physics_init: incompatible', & & ' namelist settings do_sppt and sppt' - stop + iret = 20 + return else if (Model%do_shum.neqv.do_shum) then write(0,'(*(a))') 'Logic error in stochastic_physics_init: incompatible', & & ' namelist settings do_shum and shum' - stop + iret = 20 + return else if (Model%do_skeb.neqv.do_skeb) then write(0,'(*(a))') 'Logic error in stochastic_physics_init: incompatible', & & ' namelist settings do_skeb and skeb' - stop + iret = 20 + return else if (Model%lndp_type.neqv.lndp_type) then write(0,'(*(a))') 'Logic error in stochastic_physics_init: incompatible', & & ' namelist settings lndp_type in physics and nam_sfcperts' - stop + iret = 20 + return else if (Model%n_var_lndp .ne. n_var_lndp) then write(0,'(*(a))') 'Logic error in stochastic_physics_init: incompatible', & & ' namelist settings n_var_lndp in physics nml, and lndp_* in nam_sfcperts' - stop ! return is not being error-trapped. Need to either kill the execution here, - ! or set iret non-zero, then trap it from the calling routine (also, in many other places) + iret = 20 + return end if ! update remaining model configuration parameters from namelist Model%use_zmtnblck=use_zmtnblck @@ -198,9 +208,14 @@ subroutine init_stochastic_physics(Model, Init_parm, ntasks, nthreads) end subroutine init_stochastic_physics + !>@brief The subroutine 'run_stochastic_physics' updates the random patterns if -!!necessary +!!necessary +!>@details It updates the AR(1) in spectral space +!allocates and polulates the necessary arrays + subroutine run_stochastic_physics(Model, Grid, Coupling, nthreads) +!\callgraph use fv_mp_mod, only : is_master use stochy_internal_state_mod use stochy_data_mod, only : nshum,rpattern_shum,rpattern_sppt,nsppt,rpattern_skeb,nskeb,& diff --git a/stochy_data_mod.F90 b/stochy_data_mod.F90 index 1cdc2b9..12ab8ef 100644 --- a/stochy_data_mod.F90 +++ b/stochy_data_mod.F90 @@ -1,3 +1,5 @@ +!>@brief The module 'stochy_data_mod' contains the initilization routine that read the stochastic phyiscs +!! namelist and determins the number of random patterns. module stochy_data_mod ! set up and initialize stochastic random patterns. @@ -37,7 +39,11 @@ module stochy_data_mod type(stochy_internal_state),public :: gis_stochy contains +!>@brief The subroutine 'init_stochdata' determins which stochastic physics +!!pattern genertors are needed. +!>@details it reads the nam_stochy namelist and allocates necessary arrays subroutine init_stochdata(nlevs,delt,input_nml_file,fn_nml,nlunit,iret) +!\callgraph ! initialize random patterns. A spinup period of spinup_efolds times the ! temporal time scale is run for each pattern. @@ -59,16 +65,19 @@ subroutine init_stochdata(nlevs,delt,input_nml_file,fn_nml,nlunit,iret) levs=nlevs iret=0 +! read in namelist call compns_stochy (me,size(input_nml_file,1),input_nml_file(:),fn_nml,nlunit,delt,iret) - if (iret/=0) stop ! CSD - error trapping is not currently set-up properly. + if (iret/=0) return ! need to make sure that non-zero irets are being trapped. if(is_master()) print*,'in init stochdata',nodes,lat_s if ( (.NOT. do_sppt) .AND. (.NOT. do_shum) .AND. (.NOT. do_skeb) .AND. (lndp_type==0) ) return +! initialize the specratl pattern generatore (including gaussian grid decomposition) ! if (nodes.GE.lat_s/2) then ! lat_s=(int(nodes/12)+1)*24 ! lon_s=lat_s*2 ! ntrunc=lat_s-2 ! if (is_master()) print*,'WARNING: spectral resolution is too low for number of mpi_tasks, resetting lon_s,lat_s,and ntrunc to',lon_s,lat_s,ntrunc ! endif + call initialize_spectral(gis_stochy, iret) if (iret/=0) return allocate(noise_e(len_trie_ls,2),noise_o(len_trio_ls,2)) @@ -97,7 +106,7 @@ subroutine init_stochdata(nlevs,delt,input_nml_file,fn_nml,nlunit,iret) endif enddo if (is_master()) print *,'nskeb = ',nskeb - ! CSD - nlndp>1 was not properly coded. Hardcode to 1 for now + ! Draper: nlndp>1 was not properly coded. Hardcode to 1 for now !do n=1,size(lndp_z0) ! if (lndp_z0(n) > 0 .or. lndp_zt(n)>0 .or. lndp_hc(n)>0 .or. & ! lndp_vf(n)>0 .or. lndp_la(n)>0 .or. lndp_al(n)>0) then @@ -198,7 +207,6 @@ subroutine init_stochdata(nlevs,delt,input_nml_file,fn_nml,nlunit,iret) ! determine number of skeb levels to deal with temperoal/vertical correlations skeblevs=nint(skeb_tau(1)/skebint*skeb_vdof) ! backscatter noise. - if (is_master()) print *, 'CSDCSDInitialize random pattern for SKEB',skeblevs call patterngenerator_init(skeb_lscale(1:nskeb),skebint,skeb_tau(1:nskeb),skeb(1:nskeb),iseed_skeb,rpattern_skeb, & lonf,latg,jcap,gis_stochy%ls_node,nskeb,skeblevs,skeb_varspect_opt,new_lscale) do n=1,nskeb @@ -327,11 +335,13 @@ subroutine init_stochdata(nlevs,delt,input_nml_file,fn_nml,nlunit,iret) enddo ! n, nlndp endif ! nlndp > 0 if (is_master() .and. stochini) CLOSE(stochlun) - if (is_master() ) print *, 'CSD - leaving init_stochdata' deallocate(noise_e,noise_o) end subroutine init_stochdata - +!>@brief This subroutine 'read_pattern' will read in the spectral coeffients from a previous run (stored in stoch_ini, +!!turned on by setting STOCHINI=.true.) +!>@details Data read in are flat binary, so the number of stochastic physics patterns running must match previous run subroutine read_pattern(rpattern,k,lunptn) +!\callgraph type(random_pattern), intent(inout) :: rpattern integer, intent(in) :: lunptn real(kind_dbl_prec),allocatable :: pattern2d(:),pattern2din(:) diff --git a/stochy_doc.conf b/stochy_doc.conf new file mode 100644 index 0000000..ab09709 --- /dev/null +++ b/stochy_doc.conf @@ -0,0 +1,2542 @@ +# Doxyfile 1.8.17 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed in +# front of the TAG it is preceding. +# +# All text after a single hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists, items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (\" \"). + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the configuration +# file that follow. 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Doxygen will use this +# information to generate all generated output in the proper direction. +# Possible values are: None, LTR, RTL and Context. +# The default value is: None. + +OUTPUT_TEXT_DIRECTION = None + +# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member +# descriptions after the members that are listed in the file and class +# documentation (similar to Javadoc). Set to NO to disable this. +# The default value is: YES. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief +# description of a member or function before the detailed description +# +# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. +# The default value is: YES. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator that is +# used to form the text in various listings. Each string in this list, if found +# as the leading text of the brief description, will be stripped from the text +# and the result, after processing the whole list, is used as the annotated +# text. Otherwise, the brief description is used as-is. If left blank, the +# following values are used ($name is automatically replaced with the name of +# the entity):The $name class, The $name widget, The $name file, is, provides, +# specifies, contains, represents, a, an and the. + +ABBREVIATE_BRIEF = "The $name class" \ + "The $name widget" \ + "The $name file" \ + is \ + provides \ + specifies \ + contains \ + represents \ + a \ + an \ + the + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# doxygen will generate a detailed section even if there is only a brief +# description. +# The default value is: NO. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. +# The default value is: NO. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path +# before files name in the file list and in the header files. If set to NO the +# shortest path that makes the file name unique will be used +# The default value is: YES. + +FULL_PATH_NAMES = YES + +# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. +# Stripping is only done if one of the specified strings matches the left-hand +# part of the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the path to +# strip. +# +# Note that you can specify absolute paths here, but also relative paths, which +# will be relative from the directory where doxygen is started. +# This tag requires that the tag FULL_PATH_NAMES is set to YES. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the +# path mentioned in the documentation of a class, which tells the reader which +# header file to include in order to use a class. If left blank only the name of +# the header file containing the class definition is used. Otherwise one should +# specify the list of include paths that are normally passed to the compiler +# using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but +# less readable) file names. This can be useful is your file systems doesn't +# support long names like on DOS, Mac, or CD-ROM. +# The default value is: NO. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the +# first line (until the first dot) of a Javadoc-style comment as the brief +# description. If set to NO, the Javadoc-style will behave just like regular Qt- +# style comments (thus requiring an explicit @brief command for a brief +# description.) +# The default value is: NO. + +JAVADOC_AUTOBRIEF = NO + +# If the JAVADOC_BANNER tag is set to YES then doxygen will interpret a line +# such as +# /*************** +# as being the beginning of a Javadoc-style comment "banner". If set to NO, the +# Javadoc-style will behave just like regular comments and it will not be +# interpreted by doxygen. +# The default value is: NO. + +JAVADOC_BANNER = NO + +# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first +# line (until the first dot) of a Qt-style comment as the brief description. If +# set to NO, the Qt-style will behave just like regular Qt-style comments (thus +# requiring an explicit \brief command for a brief description.) +# The default value is: NO. + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a +# multi-line C++ special comment block (i.e. a block of //! or /// comments) as +# a brief description. This used to be the default behavior. The new default is +# to treat a multi-line C++ comment block as a detailed description. Set this +# tag to YES if you prefer the old behavior instead. +# +# Note that setting this tag to YES also means that rational rose comments are +# not recognized any more. +# The default value is: NO. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the +# documentation from any documented member that it re-implements. +# The default value is: YES. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new +# page for each member. If set to NO, the documentation of a member will be part +# of the file/class/namespace that contains it. +# The default value is: NO. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen +# uses this value to replace tabs by spaces in code fragments. +# Minimum value: 1, maximum value: 16, default value: 4. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that act as commands in +# the documentation. An alias has the form: +# name=value +# For example adding +# "sideeffect=@par Side Effects:\n" +# will allow you to put the command \sideeffect (or @sideeffect) in the +# documentation, which will result in a user-defined paragraph with heading +# "Side Effects:". You can put \n's in the value part of an alias to insert +# newlines (in the resulting output). You can put ^^ in the value part of an +# alias to insert a newline as if a physical newline was in the original file. +# When you need a literal { or } or , in the value part of an alias you have to +# escape them by means of a backslash (\), this can lead to conflicts with the +# commands \{ and \} for these it is advised to use the version @{ and @} or use +# a double escape (\\{ and \\}) + +ALIASES = + +# This tag can be used to specify a number of word-keyword mappings (TCL only). +# A mapping has the form "name=value". For example adding "class=itcl::class" +# will allow you to use the command class in the itcl::class meaning. + +TCL_SUBST = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources +# only. Doxygen will then generate output that is more tailored for C. For +# instance, some of the names that are used will be different. The list of all +# members will be omitted, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or +# Python sources only. Doxygen will then generate output that is more tailored +# for that language. For instance, namespaces will be presented as packages, +# qualified scopes will look different, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources. Doxygen will then generate output that is tailored for Fortran. +# The default value is: NO. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for VHDL. +# The default value is: NO. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Set the OPTIMIZE_OUTPUT_SLICE tag to YES if your project consists of Slice +# sources only. Doxygen will then generate output that is more tailored for that +# language. For instance, namespaces will be presented as modules, types will be +# separated into more groups, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_SLICE = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given +# extension. Doxygen has a built-in mapping, but you can override or extend it +# using this tag. The format is ext=language, where ext is a file extension, and +# language is one of the parsers supported by doxygen: IDL, Java, Javascript, +# Csharp (C#), C, C++, D, PHP, md (Markdown), Objective-C, Python, Slice, +# Fortran (fixed format Fortran: FortranFixed, free formatted Fortran: +# FortranFree, unknown formatted Fortran: Fortran. In the later case the parser +# tries to guess whether the code is fixed or free formatted code, this is the +# default for Fortran type files), VHDL, tcl. For instance to make doxygen treat +# .inc files as Fortran files (default is PHP), and .f files as C (default is +# Fortran), use: inc=Fortran f=C. +# +# Note: For files without extension you can use no_extension as a placeholder. +# +# Note that for custom extensions you also need to set FILE_PATTERNS otherwise +# the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments +# according to the Markdown format, which allows for more readable +# documentation. See https://daringfireball.net/projects/markdown/ for details. +# The output of markdown processing is further processed by doxygen, so you can +# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in +# case of backward compatibilities issues. +# The default value is: YES. + +MARKDOWN_SUPPORT = YES + +# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up +# to that level are automatically included in the table of contents, even if +# they do not have an id attribute. +# Note: This feature currently applies only to Markdown headings. +# Minimum value: 0, maximum value: 99, default value: 5. +# This tag requires that the tag MARKDOWN_SUPPORT is set to YES. + +TOC_INCLUDE_HEADINGS = 5 + +# When enabled doxygen tries to link words that correspond to documented +# classes, or namespaces to their corresponding documentation. Such a link can +# be prevented in individual cases by putting a % sign in front of the word or +# globally by setting AUTOLINK_SUPPORT to NO. +# The default value is: YES. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should set this +# tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); +# versus func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. +# The default value is: NO. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. +# The default value is: NO. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip (see: +# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen +# will parse them like normal C++ but will assume all classes use public instead +# of private inheritance when no explicit protection keyword is present. +# The default value is: NO. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES will make +# doxygen to replace the get and set methods by a property in the documentation. +# This will only work if the methods are indeed getting or setting a simple +# type. If this is not the case, or you want to show the methods anyway, you +# should set this option to NO. +# The default value is: YES. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. +# The default value is: NO. + +DISTRIBUTE_GROUP_DOC = NO + +# If one adds a struct or class to a group and this option is enabled, then also +# any nested class or struct is added to the same group. By default this option +# is disabled and one has to add nested compounds explicitly via \ingroup. +# The default value is: NO. + +GROUP_NESTED_COMPOUNDS = NO + +# Set the SUBGROUPING tag to YES to allow class member groups of the same type +# (for instance a group of public functions) to be put as a subgroup of that +# type (e.g. under the Public Functions section). Set it to NO to prevent +# subgrouping. Alternatively, this can be done per class using the +# \nosubgrouping command. +# The default value is: YES. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions +# are shown inside the group in which they are included (e.g. using \ingroup) +# instead of on a separate page (for HTML and Man pages) or section (for LaTeX +# and RTF). +# +# Note that this feature does not work in combination with +# SEPARATE_MEMBER_PAGES. +# The default value is: NO. + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions +# with only public data fields or simple typedef fields will be shown inline in +# the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO, structs, classes, and unions are shown on a separate page (for HTML and +# Man pages) or section (for LaTeX and RTF). +# The default value is: NO. + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or +# enum is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically be +# useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. +# The default value is: NO. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can be +# an expensive process and often the same symbol appears multiple times in the +# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small +# doxygen will become slower. If the cache is too large, memory is wasted. The +# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range +# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 +# symbols. At the end of a run doxygen will report the cache usage and suggest +# the optimal cache size from a speed point of view. +# Minimum value: 0, maximum value: 9, default value: 0. + +LOOKUP_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in +# documentation are documented, even if no documentation was available. Private +# class members and static file members will be hidden unless the +# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. +# Note: This will also disable the warnings about undocumented members that are +# normally produced when WARNINGS is set to YES. +# The default value is: NO. + +EXTRACT_ALL = NO + +# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will +# be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIVATE = NO + +# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual +# methods of a class will be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIV_VIRTUAL = NO + +# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal +# scope will be included in the documentation. +# The default value is: NO. + +EXTRACT_PACKAGE = NO + +# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be +# included in the documentation. +# The default value is: NO. + +EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO, +# only classes defined in header files are included. Does not have any effect +# for Java sources. +# The default value is: YES. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. If set to YES, local methods, +# which are defined in the implementation section but not in the interface are +# included in the documentation. If set to NO, only methods in the interface are +# included. +# The default value is: NO. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base name of +# the file that contains the anonymous namespace. By default anonymous namespace +# are hidden. +# The default value is: NO. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all +# undocumented members inside documented classes or files. If set to NO these +# members will be included in the various overviews, but no documentation +# section is generated. This option has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. If set +# to NO, these classes will be included in the various overviews. This option +# has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend +# (class|struct|union) declarations. If set to NO, these declarations will be +# included in the documentation. +# The default value is: NO. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any +# documentation blocks found inside the body of a function. If set to NO, these +# blocks will be appended to the function's detailed documentation block. +# The default value is: NO. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation that is typed after a +# \internal command is included. If the tag is set to NO then the documentation +# will be excluded. Set it to YES to include the internal documentation. +# The default value is: NO. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file +# names in lower-case letters. If set to YES, upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# (including Cygwin) ands Mac users are advised to set this option to NO. +# The default value is: system dependent. + +CASE_SENSE_NAMES = NO + +# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with +# their full class and namespace scopes in the documentation. If set to YES, the +# scope will be hidden. +# The default value is: NO. + +HIDE_SCOPE_NAMES = NO + +# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will +# append additional text to a page's title, such as Class Reference. If set to +# YES the compound reference will be hidden. +# The default value is: NO. + +HIDE_COMPOUND_REFERENCE= NO + +# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of +# the files that are included by a file in the documentation of that file. +# The default value is: YES. + +SHOW_INCLUDE_FILES = YES + +# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each +# grouped member an include statement to the documentation, telling the reader +# which file to include in order to use the member. +# The default value is: NO. + +SHOW_GROUPED_MEMB_INC = NO + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include +# files with double quotes in the documentation rather than with sharp brackets. +# The default value is: NO. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the +# documentation for inline members. +# The default value is: YES. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the +# (detailed) documentation of file and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. +# The default value is: YES. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief +# descriptions of file, namespace and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. Note that +# this will also influence the order of the classes in the class list. +# The default value is: NO. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the +# (brief and detailed) documentation of class members so that constructors and +# destructors are listed first. If set to NO the constructors will appear in the +# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. +# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief +# member documentation. +# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting +# detailed member documentation. +# The default value is: NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy +# of group names into alphabetical order. If set to NO the group names will +# appear in their defined order. +# The default value is: NO. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by +# fully-qualified names, including namespaces. If set to NO, the class list will +# be sorted only by class name, not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the alphabetical +# list. +# The default value is: NO. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper +# type resolution of all parameters of a function it will reject a match between +# the prototype and the implementation of a member function even if there is +# only one candidate or it is obvious which candidate to choose by doing a +# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still +# accept a match between prototype and implementation in such cases. +# The default value is: NO. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo +# list. This list is created by putting \todo commands in the documentation. +# The default value is: YES. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test +# list. This list is created by putting \test commands in the documentation. +# The default value is: YES. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug +# list. This list is created by putting \bug commands in the documentation. +# The default value is: YES. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) +# the deprecated list. This list is created by putting \deprecated commands in +# the documentation. +# The default value is: YES. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional documentation +# sections, marked by \if ... \endif and \cond +# ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the +# initial value of a variable or macro / define can have for it to appear in the +# documentation. If the initializer consists of more lines than specified here +# it will be hidden. Use a value of 0 to hide initializers completely. The +# appearance of the value of individual variables and macros / defines can be +# controlled using \showinitializer or \hideinitializer command in the +# documentation regardless of this setting. +# Minimum value: 0, maximum value: 10000, default value: 30. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at +# the bottom of the documentation of classes and structs. If set to YES, the +# list will mention the files that were used to generate the documentation. +# The default value is: YES. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This +# will remove the Files entry from the Quick Index and from the Folder Tree View +# (if specified). +# The default value is: YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces +# page. This will remove the Namespaces entry from the Quick Index and from the +# Folder Tree View (if specified). +# The default value is: YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command command input-file, where command is the value of the +# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided +# by doxygen. Whatever the program writes to standard output is used as the file +# version. For an example see the documentation. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. You can +# optionally specify a file name after the option, if omitted DoxygenLayout.xml +# will be used as the name of the layout file. +# +# Note that if you run doxygen from a directory containing a file called +# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE +# tag is left empty. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files containing +# the reference definitions. This must be a list of .bib files. The .bib +# extension is automatically appended if omitted. This requires the bibtex tool +# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info. +# For LaTeX the style of the bibliography can be controlled using +# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the +# search path. See also \cite for info how to create references. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# Configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated to +# standard output by doxygen. If QUIET is set to YES this implies that the +# messages are off. +# The default value is: NO. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES +# this implies that the warnings are on. +# +# Tip: Turn warnings on while writing the documentation. +# The default value is: YES. + +WARNINGS = YES + +# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate +# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: YES. + +WARN_IF_UNDOCUMENTED = YES + +# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some parameters +# in a documented function, or documenting parameters that don't exist or using +# markup commands wrongly. +# The default value is: YES. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that +# are documented, but have no documentation for their parameters or return +# value. If set to NO, doxygen will only warn about wrong or incomplete +# parameter documentation, but not about the absence of documentation. If +# EXTRACT_ALL is set to YES then this flag will automatically be disabled. +# The default value is: NO. + +WARN_NO_PARAMDOC = NO + +# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when +# a warning is encountered. +# The default value is: NO. + +WARN_AS_ERROR = NO + +# The WARN_FORMAT tag determines the format of the warning messages that doxygen +# can produce. The string should contain the $file, $line, and $text tags, which +# will be replaced by the file and line number from which the warning originated +# and the warning text. Optionally the format may contain $version, which will +# be replaced by the version of the file (if it could be obtained via +# FILE_VERSION_FILTER) +# The default value is: $file:$line: $text. + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning and error +# messages should be written. If left blank the output is written to standard +# error (stderr). + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# Configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag is used to specify the files and/or directories that contain +# documented source files. You may enter file names like myfile.cpp or +# directories like /usr/src/myproject. Separate the files or directories with +# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING +# Note: If this tag is empty the current directory is searched. + +INPUT = + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses +# libiconv (or the iconv built into libc) for the transcoding. See the libiconv +# documentation (see: https://www.gnu.org/software/libiconv/) for the list of +# possible encodings. +# The default value is: UTF-8. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and +# *.h) to filter out the source-files in the directories. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# read by doxygen. +# +# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp, +# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, +# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, +# *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C comment), +# *.doc (to be provided as doxygen C comment), *.txt (to be provided as doxygen +# C comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f, *.for, *.tcl, *.vhd, +# *.vhdl, *.ucf, *.qsf and *.ice. + +FILE_PATTERNS = *.c \ + *.cc \ + *.cxx \ + *.cpp \ + *.c++ \ + *.java \ + *.ii \ + *.ixx \ + *.ipp \ + *.i++ \ + *.inl \ + *.idl \ + *.ddl \ + *.odl \ + *.h \ + *.hh \ + *.hxx \ + *.hpp \ + *.h++ \ + *.cs \ + *.d \ + *.php \ + *.php4 \ + *.php5 \ + *.phtml \ + *.inc \ + *.m \ + *.markdown \ + *.md \ + *.mm \ + *.dox \ + *.doc \ + *.txt \ + *.py \ + *.pyw \ + *.f90 \ + *.f95 \ + *.f03 \ + *.f08 \ + *.f \ + *.for \ + *.tcl \ + *.vhd \ + *.vhdl \ + *.ucf \ + *.qsf \ + *.ice + +# The RECURSIVE tag can be used to specify whether or not subdirectories should +# be searched for input files as well. +# The default value is: NO. + +RECURSIVE = NO + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. +# The default value is: NO. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories use the pattern */test/* + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or directories +# that contain example code fragments that are included (see the \include +# command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank all +# files are included. + +EXAMPLE_PATTERNS = * + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude commands +# irrespective of the value of the RECURSIVE tag. +# The default value is: NO. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or directories +# that contain images that are to be included in the documentation (see the +# \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command: +# +# +# +# where is the value of the INPUT_FILTER tag, and is the +# name of an input file. Doxygen will then use the output that the filter +# program writes to standard output. If FILTER_PATTERNS is specified, this tag +# will be ignored. +# +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: pattern=filter +# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how +# filters are used. If the FILTER_PATTERNS tag is empty or if none of the +# patterns match the file name, INPUT_FILTER is applied. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will also be used to filter the input files that are used for +# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). +# The default value is: NO. + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and +# it is also possible to disable source filtering for a specific pattern using +# *.ext= (so without naming a filter). +# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want to reuse the introduction page also for the doxygen output. + +USE_MDFILE_AS_MAINPAGE = + +#--------------------------------------------------------------------------- +# Configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will be +# generated. Documented entities will be cross-referenced with these sources. +# +# Note: To get rid of all source code in the generated output, make sure that +# also VERBATIM_HEADERS is set to NO. +# The default value is: NO. + +SOURCE_BROWSER = NO + +# Setting the INLINE_SOURCES tag to YES will include the body of functions, +# classes and enums directly into the documentation. +# The default value is: NO. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any +# special comment blocks from generated source code fragments. Normal C, C++ and +# Fortran comments will always remain visible. +# The default value is: YES. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES then for each documented +# entity all documented functions referencing it will be listed. +# The default value is: NO. + +REFERENCED_BY_RELATION = NO + +# If the REFERENCES_RELATION tag is set to YES then for each documented function +# all documented entities called/used by that function will be listed. +# The default value is: NO. + +REFERENCES_RELATION = NO + +# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set +# to YES then the hyperlinks from functions in REFERENCES_RELATION and +# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will +# link to the documentation. +# The default value is: YES. + +REFERENCES_LINK_SOURCE = YES + +# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the +# source code will show a tooltip with additional information such as prototype, +# brief description and links to the definition and documentation. Since this +# will make the HTML file larger and loading of large files a bit slower, you +# can opt to disable this feature. +# The default value is: YES. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +SOURCE_TOOLTIPS = YES + +# If the USE_HTAGS tag is set to YES then the references to source code will +# point to the HTML generated by the htags(1) tool instead of doxygen built-in +# source browser. The htags tool is part of GNU's global source tagging system +# (see https://www.gnu.org/software/global/global.html). You will need version +# 4.8.6 or higher. +# +# To use it do the following: +# - Install the latest version of global +# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file +# - Make sure the INPUT points to the root of the source tree +# - Run doxygen as normal +# +# Doxygen will invoke htags (and that will in turn invoke gtags), so these +# tools must be available from the command line (i.e. in the search path). +# +# The result: instead of the source browser generated by doxygen, the links to +# source code will now point to the output of htags. +# The default value is: NO. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a +# verbatim copy of the header file for each class for which an include is +# specified. Set to NO to disable this. +# See also: Section \class. +# The default value is: YES. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# Configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all +# compounds will be generated. Enable this if the project contains a lot of +# classes, structs, unions or interfaces. +# The default value is: YES. + +ALPHABETICAL_INDEX = YES + +# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in +# which the alphabetical index list will be split. +# Minimum value: 1, maximum value: 20, default value: 5. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all classes will +# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag +# can be used to specify a prefix (or a list of prefixes) that should be ignored +# while generating the index headers. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output +# The default value is: YES. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each +# generated HTML page (for example: .htm, .php, .asp). +# The default value is: .html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a user-defined HTML header file for +# each generated HTML page. If the tag is left blank doxygen will generate a +# standard header. +# +# To get valid HTML the header file that includes any scripts and style sheets +# that doxygen needs, which is dependent on the configuration options used (e.g. +# the setting GENERATE_TREEVIEW). It is highly recommended to start with a +# default header using +# doxygen -w html new_header.html new_footer.html new_stylesheet.css +# YourConfigFile +# and then modify the file new_header.html. See also section "Doxygen usage" +# for information on how to generate the default header that doxygen normally +# uses. +# Note: The header is subject to change so you typically have to regenerate the +# default header when upgrading to a newer version of doxygen. For a description +# of the possible markers and block names see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each +# generated HTML page. If the tag is left blank doxygen will generate a standard +# footer. See HTML_HEADER for more information on how to generate a default +# footer and what special commands can be used inside the footer. See also +# section "Doxygen usage" for information on how to generate the default footer +# that doxygen normally uses. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style +# sheet that is used by each HTML page. It can be used to fine-tune the look of +# the HTML output. If left blank doxygen will generate a default style sheet. +# See also section "Doxygen usage" for information on how to generate the style +# sheet that doxygen normally uses. +# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as +# it is more robust and this tag (HTML_STYLESHEET) will in the future become +# obsolete. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# cascading style sheets that are included after the standard style sheets +# created by doxygen. Using this option one can overrule certain style aspects. +# This is preferred over using HTML_STYLESHEET since it does not replace the +# standard style sheet and is therefore more robust against future updates. +# Doxygen will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). For an example see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that the +# files will be copied as-is; there are no commands or markers available. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen +# will adjust the colors in the style sheet and background images according to +# this color. Hue is specified as an angle on a colorwheel, see +# https://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 +# purple, and 360 is red again. +# Minimum value: 0, maximum value: 359, default value: 220. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors +# in the HTML output. For a value of 0 the output will use grayscales only. A +# value of 255 will produce the most vivid colors. +# Minimum value: 0, maximum value: 255, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the +# luminance component of the colors in the HTML output. Values below 100 +# gradually make the output lighter, whereas values above 100 make the output +# darker. The value divided by 100 is the actual gamma applied, so 80 represents +# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not +# change the gamma. +# Minimum value: 40, maximum value: 240, default value: 80. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting this +# to YES can help to show when doxygen was last run and thus if the +# documentation is up to date. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_TIMESTAMP = NO + +# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML +# documentation will contain a main index with vertical navigation menus that +# are dynamically created via Javascript. If disabled, the navigation index will +# consists of multiple levels of tabs that are statically embedded in every HTML +# page. Disable this option to support browsers that do not have Javascript, +# like the Qt help browser. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_MENUS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_SECTIONS = NO + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries +# shown in the various tree structured indices initially; the user can expand +# and collapse entries dynamically later on. Doxygen will expand the tree to +# such a level that at most the specified number of entries are visible (unless +# a fully collapsed tree already exceeds this amount). So setting the number of +# entries 1 will produce a full collapsed tree by default. 0 is a special value +# representing an infinite number of entries and will result in a full expanded +# tree by default. +# Minimum value: 0, maximum value: 9999, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files will be +# generated that can be used as input for Apple's Xcode 3 integrated development +# environment (see: https://developer.apple.com/xcode/), introduced with OSX +# 10.5 (Leopard). To create a documentation set, doxygen will generate a +# Makefile in the HTML output directory. Running make will produce the docset in +# that directory and running make install will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at +# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy +# genXcode/_index.html for more information. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_DOCSET = NO + +# This tag determines the name of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# The default value is: Doxygen generated docs. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# This tag specifies a string that should uniquely identify the documentation +# set bundle. This should be a reverse domain-name style string, e.g. +# com.mycompany.MyDocSet. Doxygen will append .docset to the name. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. +# The default value is: org.doxygen.Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. +# The default value is: Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three +# additional HTML index files: index.hhp, index.hhc, and index.hhk. The +# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop +# (see: https://www.microsoft.com/en-us/download/details.aspx?id=21138) on +# Windows. +# +# The HTML Help Workshop contains a compiler that can convert all HTML output +# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML +# files are now used as the Windows 98 help format, and will replace the old +# Windows help format (.hlp) on all Windows platforms in the future. Compressed +# HTML files also contain an index, a table of contents, and you can search for +# words in the documentation. The HTML workshop also contains a viewer for +# compressed HTML files. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_HTMLHELP = NO + +# The CHM_FILE tag can be used to specify the file name of the resulting .chm +# file. You can add a path in front of the file if the result should not be +# written to the html output directory. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_FILE = + +# The HHC_LOCATION tag can be used to specify the location (absolute path +# including file name) of the HTML help compiler (hhc.exe). If non-empty, +# doxygen will try to run the HTML help compiler on the generated index.hhp. +# The file has to be specified with full path. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +HHC_LOCATION = + +# The GENERATE_CHI flag controls if a separate .chi index file is generated +# (YES) or that it should be included in the master .chm file (NO). +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +GENERATE_CHI = NO + +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) +# and project file content. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_INDEX_ENCODING = + +# The BINARY_TOC flag controls whether a binary table of contents is generated +# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it +# enables the Previous and Next buttons. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members to +# the table of contents of the HTML help documentation and to the tree view. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that +# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help +# (.qch) of the generated HTML documentation. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify +# the file name of the resulting .qch file. The path specified is relative to +# the HTML output folder. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help +# Project output. For more information please see Qt Help Project / Namespace +# (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace). +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt +# Help Project output. For more information please see Qt Help Project / Virtual +# Folders (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual- +# folders). +# The default value is: doc. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_VIRTUAL_FOLDER = doc + +# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom +# filter to add. For more information please see Qt Help Project / Custom +# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see Qt Help Project / Custom +# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's filter section matches. Qt Help Project / Filter Attributes (see: +# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_SECT_FILTER_ATTRS = + +# The QHG_LOCATION tag can be used to specify the location of Qt's +# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the +# generated .qhp file. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be +# generated, together with the HTML files, they form an Eclipse help plugin. To +# install this plugin and make it available under the help contents menu in +# Eclipse, the contents of the directory containing the HTML and XML files needs +# to be copied into the plugins directory of eclipse. The name of the directory +# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. +# After copying Eclipse needs to be restarted before the help appears. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the Eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have this +# name. Each documentation set should have its own identifier. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# If you want full control over the layout of the generated HTML pages it might +# be necessary to disable the index and replace it with your own. The +# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top +# of each HTML page. A value of NO enables the index and the value YES disables +# it. Since the tabs in the index contain the same information as the navigation +# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. If the tag +# value is set to YES, a side panel will be generated containing a tree-like +# index structure (just like the one that is generated for HTML Help). For this +# to work a browser that supports JavaScript, DHTML, CSS and frames is required +# (i.e. any modern browser). Windows users are probably better off using the +# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can +# further fine-tune the look of the index. As an example, the default style +# sheet generated by doxygen has an example that shows how to put an image at +# the root of the tree instead of the PROJECT_NAME. Since the tree basically has +# the same information as the tab index, you could consider setting +# DISABLE_INDEX to YES when enabling this option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_TREEVIEW = NO + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that +# doxygen will group on one line in the generated HTML documentation. +# +# Note that a value of 0 will completely suppress the enum values from appearing +# in the overview section. +# Minimum value: 0, maximum value: 20, default value: 4. +# This tag requires that the tag GENERATE_HTML is set to YES. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used +# to set the initial width (in pixels) of the frame in which the tree is shown. +# Minimum value: 0, maximum value: 1500, default value: 250. +# This tag requires that the tag GENERATE_HTML is set to YES. + +TREEVIEW_WIDTH = 250 + +# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to +# external symbols imported via tag files in a separate window. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +EXT_LINKS_IN_WINDOW = NO + +# Use this tag to change the font size of LaTeX formulas included as images in +# the HTML documentation. When you change the font size after a successful +# doxygen run you need to manually remove any form_*.png images from the HTML +# output directory to force them to be regenerated. +# Minimum value: 8, maximum value: 50, default value: 10. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANSPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are not +# supported properly for IE 6.0, but are supported on all modern browsers. +# +# Note that when changing this option you need to delete any form_*.png files in +# the HTML output directory before the changes have effect. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see +# https://www.mathjax.org) which uses client side Javascript for the rendering +# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX +# installed or if you want to formulas look prettier in the HTML output. When +# enabled you may also need to install MathJax separately and configure the path +# to it using the MATHJAX_RELPATH option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +USE_MATHJAX = NO + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. See the MathJax site (see: +# http://docs.mathjax.org/en/latest/output.html) for more details. +# Possible values are: HTML-CSS (which is slower, but has the best +# compatibility), NativeMML (i.e. MathML) and SVG. +# The default value is: HTML-CSS. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the HTML +# output directory using the MATHJAX_RELPATH option. The destination directory +# should contain the MathJax.js script. For instance, if the mathjax directory +# is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax +# Content Delivery Network so you can quickly see the result without installing +# MathJax. However, it is strongly recommended to install a local copy of +# MathJax from https://www.mathjax.org before deployment. +# The default value is: https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_RELPATH = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/ + +# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax +# extension names that should be enabled during MathJax rendering. For example +# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces +# of code that will be used on startup of the MathJax code. See the MathJax site +# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an +# example see the documentation. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for +# the HTML output. The underlying search engine uses javascript and DHTML and +# should work on any modern browser. Note that when using HTML help +# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) +# there is already a search function so this one should typically be disabled. +# For large projects the javascript based search engine can be slow, then +# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to +# search using the keyboard; to jump to the search box use + S +# (what the is depends on the OS and browser, but it is typically +# , /