From eb991d865154146296147c86d1a4951706cc653f Mon Sep 17 00:00:00 2001 From: Xiaoxu Shi Date: Tue, 4 May 2021 12:26:03 +0200 Subject: [PATCH 01/71] fesom2.1 with enabled stable water isotopes --- src/cpl_driver.F90 | 32 +++++- src/gen_forcing_couple.F90 | 187 +++++++++++++++++++++++++++++++++++- src/gen_forcing_init.F90 | 17 ++++ src/gen_ic3d.F90 | 4 + src/gen_modules_config.F90 | 5 +- src/gen_modules_forcing.F90 | 4 + src/ice_oce_coupling.F90 | 46 +++++++++ src/io_blowup.F90 | 2 +- src/io_meandata.F90 | 15 +++ src/io_restart.F90 | 99 ++++++++++++++++++- src/oce_ale_tracer.F90 | 10 +- src/oce_modules.F90 | 9 ++ src/oce_setup_step.F90 | 31 +++++- 13 files changed, 445 insertions(+), 16 deletions(-) diff --git a/src/cpl_driver.F90 b/src/cpl_driver.F90 index c87a83522..8b90e03d8 100755 --- a/src/cpl_driver.F90 +++ b/src/cpl_driver.F90 @@ -13,7 +13,7 @@ module cpl_driver ! Modules used ! use mod_oasis ! oasis module - use g_config, only : dt + use g_config, only : dt, lwiso !wiso-code add lwiso use o_param, only : rad use g_PARSUP implicit none @@ -23,11 +23,11 @@ module cpl_driver ! #if defined (__oifs) - integer, parameter :: nsend = 5 - integer, parameter :: nrecv = 13 + integer, parameter :: nsend = 8 !wiso-code 5->8 + integer, parameter :: nrecv = 19 !wiso-code 13->19 #else - integer, parameter :: nsend = 4 - integer, parameter :: nrecv = 12 + integer, parameter :: nsend = 7 !wiso-code 4->7 + integer, parameter :: nrecv = 18 !wiso-code 12->18 #endif integer, dimension(nsend) :: send_id @@ -384,11 +384,19 @@ subroutine cpl_oasis3mct_define_unstr(mesh) cpl_send( 3)='snt_feom' ! 3. snow thickness [m] -> cpl_send( 4)='ist_feom' ! 4. sea ice surface temperature [K] -> cpl_send( 5)='sia_feom' ! 5. sea ice albedo [%-100] -> +!!!!!!wiso-code!!!!!!! add more coupling fields + cpl_send( 6)='o18_feom' ! -> h2o18 + cpl_send( 7)='hdo_feom' ! -> hdo16 + cpl_send( 8)='o16_feom' ! -> h2o16 #else cpl_send( 1)='sst_feom' ! 1. sea surface temperature [°C] -> cpl_send( 2)='sit_feom' ! 2. sea ice thickness [m] -> cpl_send( 3)='sie_feom' ! 3. sea ice extent [%-100] -> cpl_send( 4)='snt_feom' ! 4. snow thickness [m] -> +!!!!!!wiso-code!!!!!!! add more coupling fields + cpl_send( 5)='o18_feom' ! -> h2o18 + cpl_send( 6)='hdo_feom' ! -> hdo16 + cpl_send( 7)='o16_feom' ! -> h2o16 #endif @@ -411,6 +419,13 @@ subroutine cpl_oasis3mct_define_unstr(mesh) cpl_recv(11) = 'heat_swo' cpl_recv(12) = 'hydr_oce' cpl_recv(13) = 'enth_oce' +!!!!!!wiso-code!!!!!!! add more coupling fields + cpl_recv(14) = 'w1_oce' + cpl_recv(15) = 'w2_oce' + cpl_recv(16) = 'w3_oce' + cpl_recv(17) = 'i1_oce' + cpl_recv(18) = 'i2_oce' + cpl_recv(19) = 'i3_oce' #else cpl_recv(1) = 'taux_oce' cpl_recv(2) = 'tauy_oce' @@ -424,6 +439,13 @@ subroutine cpl_oasis3mct_define_unstr(mesh) cpl_recv(10) = 'heat_ico' cpl_recv(11) = 'heat_swo' cpl_recv(12) = 'hydr_oce' +!!!!!!wiso-code!!!!!!! add more coupling fields + cpl_recv(13) = 'w1_oce' + cpl_recv(14) = 'w2_oce' + cpl_recv(15) = 'w3_oce' + cpl_recv(16) = 'i1_oce' + cpl_recv(17) = 'i2_oce' + cpl_recv(18) = 'i3_oce' #endif if (mype .eq. 0) then diff --git a/src/gen_forcing_couple.F90 b/src/gen_forcing_couple.F90 index 2a39b34b7..f1e6e0e17 100755 --- a/src/gen_forcing_couple.F90 +++ b/src/gen_forcing_couple.F90 @@ -111,6 +111,38 @@ subroutine update_atm_forcing(istep, mesh) exchange(:) = ice_temp(:) ! ice surface temperature elseif (i.eq.5) then exchange(:) = ice_alb(:) ! ice albedo +!!!!!wiso-code!!!!!!! + !SMOWO18 = 2005.2e-6 + !SMOWHDO = 155.76e-6 + + elseif (i.eq.6) then + if (.not. lwiso) then + exchange(:) = 0.0 + end if + if (lwiso) then + where (tr_arr(1, :, 5) > 0.0) + exchange(:) = (tr_arr(1, :, 3)/tr_arr(1, :, 5)/2005.2e-6 - 1.)*1000. ! h2O18 + elsewhere + exchange(:) = 0.0 + end where + end if + + elseif (i.eq.7) then + if (.not. lwiso) then + exchange(:) = 0.0 + end if + if (lwiso) then + where (tr_arr(1, :, 5) > 0.0) + exchange(:) = (tr_arr(1, :, 4)/tr_arr(1, :, 5)/155.76e-6 - 1.)*1000. ! hDO16 + elsewhere + exchange(:) = 0.0 + end where + end if + + elseif (i.eq.8) then + exchange(:) = 0.0 ! h2O16 is set to zero permill +!!!!!wiso-code-end!!!!!!! + else print *, 'not installed yet or error in cpl_oasis3mct_send', mype #else @@ -124,6 +156,38 @@ subroutine update_atm_forcing(istep, mesh) exchange(:) = a_ice(:) ! ice concentation [%] elseif (i.eq.4) then exchange(:) = m_snow(:) ! snow thickness +!!!!!wiso-code!!!!!!! + !SMOWO18 = 2005.2e-6 + !SMOWHDO = 155.76e-6 + + elseif (i.eq.5) then + if (.not. lwiso) then + exchange(:) = 0.0 + end if + if (lwiso) then + where (tr_arr(1, :, 5) > 0.0) + exchange(:) = (tr_arr(1, :, 3)/tr_arr(1, :, 5)/2005.2e-6 - 1.)*1000. ! h2O18 + elsewhere + exchange(:) = 0.0 + end where + end if + + elseif (i.eq.6) then + if (.not. lwiso) then + exchange(:) = 0.0 + end if + if (lwiso) then + where (tr_arr(1, :, 5) > 0.0) + exchange(:) = (tr_arr(1, :, 4)/tr_arr(1, :, 5)/155.76e-6 - 1.)*1000. ! hDO16 + elsewhere + exchange(:) = 0.0 + end where + end if + + elseif (i.eq.7) then + exchange(:) = 0.0 ! h2O16 is set to zero permill +!!!!!wiso-code-end!!!!!!! + else print *, 'not installed yet or error in cpl_oasis3mct_send', mype #endif @@ -231,6 +295,126 @@ subroutine update_atm_forcing(istep, mesh) mask=1. call force_flux_consv(enthalpyoffuse, mask, i, 0,action, mesh) end if + !!!!!wiso-code!!!!! + elseif (i.eq.15) then + if (action) then + www1(:) = exchange(:) ! tot_prec_o18 over water + end if + mask=1. + if (lwiso) then + call force_flux_consv(www1, mask, i, 0,action,mesh) + end if + elseif (i.eq.16) then + if (action) then + www2(:) = exchange(:) ! tot_prec_hdo over water + end if + mask=1. + if (lwiso) then + call force_flux_consv(www2, mask, i, 0,action,mesh) + end if + elseif (i.eq.14) then + if (action) then + www3(:) = exchange(:) ! tot_prec_o16 over water + end if + mask=1. + if (lwiso) then + call force_flux_consv(www3, mask, i, 0,action,mesh) + end if + elseif (i.eq.18) then + if (action) then + iii1(:) = exchange(:) ! snowfall_o18 over seaice + tmp_iii1(:) = exchange(:) ! to reset for flux correction + end if + mask=a_ice + iii1(:) = tmp_iii1(:) + if (lwiso) then + call force_flux_consv(iii1,mask,i,1,action, mesh) ! Northern hemisphere + call force_flux_consv(iii1,mask,i,2,action, mesh) ! Southern Hemisphere + end if + elseif (i.eq.19) then + if (action) then + iii2(:) = exchange(:) ! snowfall_hdo over seaice + tmp_iii2(:) = exchange(:) ! to reset for flux correction + end if + mask=a_ice + iii2(:) = tmp_iii2(:) + if (lwiso) then + call force_flux_consv(iii2,mask,i,1,action, mesh) ! Northern hemisphere + call force_flux_consv(iii2,mask,i,2,action, mesh) ! Southern Hemisphere + end if + elseif (i.eq.17) then + if (action) then + iii3(:) = exchange(:) ! snowfall_o16 over seaice + tmp_iii3(:) = exchange(:) ! to reset for flux correction + end if + mask=a_ice + iii3(:) = tmp_iii3(:) + if (lwiso) then + call force_flux_consv(iii3,mask,i,1,action, mesh) ! Northern hemisphere + call force_flux_consv(iii3,mask,i,2,action, mesh) ! Southern Hemisphere + end if + end if +#else + !!!!!wiso-code!!!!! + elseif (i.eq.14) then + if (action) then + www1(:) = exchange(:) ! tot_prec_o18 over water + end if + mask=1. + if (lwiso) then + call force_flux_consv(www1, mask, i, 0,action,mesh) + end if + elseif (i.eq.15) then + if (action) then + www2(:) = exchange(:) ! tot_prec_hdo over water + end if + mask=1. + if (lwiso) then + call force_flux_consv(www2, mask, i, 0,action,mesh) + end if + elseif (i.eq.13) then + if (action) then + www3(:) = exchange(:) ! tot_prec_o16 over water + end if + mask=1. + if (lwiso) then + call force_flux_consv(www3, mask, i, 0,action,mesh) + end if + elseif (i.eq.17) then + if (action) then + iii1(:) = exchange(:) ! snowfall_o18 over seaice + tmp_iii1(:) = exchange(:) ! to reset for flux correction + end if + mask=a_ice + iii1(:) = tmp_iii1(:) + if (lwiso) then + call force_flux_consv(iii1,mask,i,1,action, mesh) ! Northern hemisphere + call force_flux_consv(iii1,mask,i,2,action, mesh) ! Southern Hemisphere + end if + elseif (i.eq.18) then + if (action) then + iii2(:) = exchange(:) ! snowfall_hdo over seaice + tmp_iii2(:) = exchange(:) ! to reset for flux correction + end if + mask=a_ice + iii2(:) = tmp_iii2(:) + if (lwiso) then + call force_flux_consv(iii2,mask,i,1,action, mesh) ! Northern hemisphere + call force_flux_consv(iii2,mask,i,2,action, mesh) ! Southern Hemisphere + end if + elseif (i.eq.16) then + if (action) then + iii3(:) = exchange(:) ! snowfall_o16 over seaice + tmp_iii3(:) = exchange(:) ! to reset for flux correction + end if + mask=a_ice + iii3(:) = tmp_iii3(:) + if (lwiso) then + call force_flux_consv(iii3,mask,i,1,action, mesh) ! Northern hemisphere + call force_flux_consv(iii3,mask,i,2,action, mesh) ! Southern Hemisphere + end if + !!!!!wiso-code-end!!!!! + end if #endif #ifdef VERBOSE @@ -461,7 +645,8 @@ SUBROUTINE force_flux_consv(field2d, mask, n, h, do_stats, mesh) #endif !last flux - if (n==nrecv .AND. mype==0) write(*,*) 'Fluxes have been modified.' + !if (n==nrecv .AND. mype==0) write(*,*) 'Fluxes have been modified.' + if (n==nrecv-6 .AND. mype==0) write(*,*) 'Fluxes have been modified.' !!!wiso-code END SUBROUTINE force_flux_consv ! diff --git a/src/gen_forcing_init.F90 b/src/gen_forcing_init.F90 index cb69dba6b..a3a79cd2e 100755 --- a/src/gen_forcing_init.F90 +++ b/src/gen_forcing_init.F90 @@ -60,6 +60,16 @@ subroutine forcing_array_setup(mesh) Tair=0.0_WP shum=0.0_WP allocate(runoff(n2), evaporation(n2),ice_sublimation(n2)) + !wiso-code!!! + allocate(www1(n2), www2(n2),www3(n2), iii1(n2), iii2(n2), iii3(n2)) + www1=0.0_WP + www2=0.0_WP + www3=0.0_WP + iii1=0.0_WP + iii2=0.0_WP + iii3=0.0_WP + !wiso-code!!! + runoff=0.0_WP evaporation = 0.0_WP ice_sublimation = 0.0_WP @@ -83,6 +93,13 @@ subroutine forcing_array_setup(mesh) flux_correction_total=0.0_WP evap_no_ifrac=0.0_WP sublimation=0.0_WP + !wiso-code!!! + allocate(tmp_iii1(n2), tmp_iii2(n2), tmp_iii3(n2)) + tmp_iii1=0.0_WP + tmp_iii2=0.0_WP + tmp_iii3=0.0_WP + !wiso-code!!! + #endif diff --git a/src/gen_ic3d.F90 b/src/gen_ic3d.F90 index 5bbce229d..23d46cb34 100644 --- a/src/gen_ic3d.F90 +++ b/src/gen_ic3d.F90 @@ -513,6 +513,10 @@ SUBROUTINE do_ic3d(mesh) where (tr_arr(:,:,1) > 100._WP) tr_arr(:,:,1)=tr_arr(:,:,1)-273.15_WP end where + !!!wiso-code!!! ice tracers + tr_arr_ice=0. + !!!wiso-code!!! ice tracers + !_________________________________________________________________________ ! eliminate values within cavity that result from the extrapolation of diff --git a/src/gen_modules_config.F90 b/src/gen_modules_config.F90 index df06463bb..157d7b9bb 100755 --- a/src/gen_modules_config.F90 +++ b/src/gen_modules_config.F90 @@ -99,6 +99,9 @@ module g_config ! *** configuration*** logical :: use_sw_pene=.true. logical :: use_ice=.false. +!wiso-code!!! + logical :: lwiso =.false. ! enable isotope? +!wiso-code!!! logical :: use_floatice = .false. logical :: use_cavity = .false. ! switch on/off cavity usage logical :: use_cavity_partial_cell = .false. ! switch on/off cavity usage @@ -108,7 +111,7 @@ module g_config logical :: flag_debug=.false. ! prints name of actual subroutine he is in logical :: flag_warn_cflz=.true. ! switches off cflz warning namelist /run_config/ use_ice,use_floatice, use_sw_pene, use_cavity, & - use_cavity_partial_cell, cavity_partial_cell_thresh, toy_ocean, which_toy, flag_debug, flag_warn_cflz + use_cavity_partial_cell, cavity_partial_cell_thresh, toy_ocean, which_toy, flag_debug, flag_warn_cflz, lwiso !wiso-code add lwiso !_____________________________________________________________________________ ! *** others *** diff --git a/src/gen_modules_forcing.F90 b/src/gen_modules_forcing.F90 index 2e2f67dca..a55910253 100755 --- a/src/gen_modules_forcing.F90 +++ b/src/gen_modules_forcing.F90 @@ -58,6 +58,10 @@ module g_forcing_arrays real(kind=WP), allocatable, dimension(:) :: prec_rain, prec_snow real(kind=WP), allocatable, dimension(:) :: runoff, evaporation, ice_sublimation real(kind=WP), allocatable, dimension(:) :: cloudiness, press_air + !wiso-code!!! + real(kind=WP), allocatable, dimension(:) :: www1,www2,www3,iii1,iii2,iii3 + real(kind=WP), allocatable, dimension(:) :: tmp_iii1,tmp_iii2,tmp_iii3 + !wiso-code!!! #if defined (__oasis) real(kind=WP), target, allocatable, dimension(:) :: sublimation, evap_no_ifrac diff --git a/src/ice_oce_coupling.F90 b/src/ice_oce_coupling.F90 index 2e8bd57fc..3f517787c 100755 --- a/src/ice_oce_coupling.F90 +++ b/src/ice_oce_coupling.F90 @@ -170,10 +170,26 @@ subroutine oce_fluxes(mesh) real(kind=WP) :: rsss, net real(kind=WP), allocatable :: flux(:) + !!!wiso-code + real(kind=WP) :: zwisomin, zwisosec + real(kind=WP), allocatable :: o16_atm(:), o18_atm(:), hdo_atm(:) + real(kind=WP), allocatable :: zdelta(:) + !!!wiso-code + #include "associate_mesh.h" allocate(flux(myDim_nod2D+eDim_nod2D)) flux = 0.0_WP + + !!!wiso-code + allocate(o16_atm(myDim_nod2D+eDim_nod2D)) + allocate(o18_atm(myDim_nod2D+eDim_nod2D)) + allocate(hdo_atm(myDim_nod2D+eDim_nod2D)) + allocate(zdelta(myDim_nod2D+eDim_nod2D)) + zwisomin= 1.e-6_wp + zwisosec= 1.e-8_wp + !!!wiso-code + ! ================== ! heat and freshwater @@ -309,6 +325,36 @@ subroutine oce_fluxes(mesh) ! have there original sign water_flux=water_flux+net/ocean_area + !!!wiso-code + + ! atmospheric H216O flux = total flux over open water + flux over sea ice + o16_atm = (www3+iii3)*1000. + ! H216O flux into ocean: enforce total flux to be zero + call integrate_nod(o16_atm, net, mesh) + o16_flux=o16_atm-net/ocean_area + + ! atmospheric H218O flux = total flux over open water + flux over sea ice + ! apply correction factor for different SMOW values used in ECHAM6 vs. FESOM + o18_atm = (www1+iii1)*1000/((20./18.)*100.) + ! H218O flux into ocean: assume same ratio 18O/16O as for atmospheric fluxes + ! SMOWO18 = 2005.2e-6 + zdelta=2005.2e-6 + where (abs(o16_atm).gt.zwisomin) zdelta = o18_atm/o16_atm + where (abs(1.-zdelta).lt.zwisosec) zdelta = 1. ! cut off rounding errors + o18_flux = zdelta * o16_flux + + ! atmospheric HDO flux = total flux over open water + flux over sea ice + ! apply correction factor for different SMOW values used in ECHAM6 vs. FESOM + hdo_atm = (www2+iii2)*1000/((19./18.)*2.*1000.) + ! HDO flux into ocean: assume same ratio HDO/16O as for atmospheric fluxes + ! SMOWHDO = 155.76e-6 + zdelta=155.76e-6 + where (abs(o16_atm).gt.zwisomin) zdelta = hdo_atm/o16_atm + where (abs(1.-zdelta).lt.zwisosec) zdelta = 1. ! cut off rounding errors + hdo_flux = zdelta * o16_flux + + !!!wiso-code + !___________________________________________________________________________ if (use_sw_pene) call cal_shortwave_rad(mesh) diff --git a/src/io_blowup.F90 b/src/io_blowup.F90 index 27dcf686c..c9f4667ac 100644 --- a/src/io_blowup.F90 +++ b/src/io_blowup.F90 @@ -115,7 +115,7 @@ subroutine ini_blowup_io(year, mesh) !!PS call def_variable(bid, 'pgf_y' , (/nl-1, elem2D/) , 'meridional pressure gradient force', '???', pgf_y(:,:)); !!PS call def_variable(bid, 'density_m_rho0' , (/nl-1, nod2D/) , 'density minus rho0', '???', density_m_rho0(:,:)); - do j=1,num_tracers + do j=1,2 !wiso-code! num_tracers->2 SELECT CASE (j) CASE(1) trname='temp' diff --git a/src/io_meandata.F90 b/src/io_meandata.F90 index 23a827d8b..9e1426ed0 100644 --- a/src/io_meandata.F90 +++ b/src/io_meandata.F90 @@ -99,6 +99,7 @@ subroutine ini_mean_io(mesh) use g_PARSUP use diagnostics use i_PARAM, only: whichEVP + use g_forcing_arrays !wiso-code implicit none integer :: i, j integer, save :: nm_io_unit = 103 ! unit to open namelist file, skip 100-102 for cray @@ -278,6 +279,20 @@ subroutine ini_mean_io(mesh) call def_stream((/nl-1, nod2D/), (/nl-1, myDim_nod2D/), 'temp', 'temperature', 'C', tr_arr(:,:,1), io_list(i)%freq, io_list(i)%unit, io_list(i)%precision, mesh) CASE ('salt ') call def_stream((/nl-1, nod2D/), (/nl-1, myDim_nod2D/), 'salt', 'salinity', 'psu', tr_arr(:,:,2), io_list(i)%freq, io_list(i)%unit, io_list(i)%precision, mesh) +!wiso-code! +CASE ('h2o18 ') + call def_stream((/nl-1, nod2D/), (/nl-1, myDim_nod2D/), 'h2o18', 'h2o18 concentration', 'kmol/m**3', tr_arr(:,:,3), io_list(i)%freq, io_list(i)%unit, io_list(i)%precision, mesh) +CASE ('hDo16 ') + call def_stream((/nl-1, nod2D/), (/nl-1, myDim_nod2D/), 'hDo16', 'hDo16 concentration', 'kmol/m**3', tr_arr(:,:,4), io_list(i)%freq, io_list(i)%unit, io_list(i)%precision, mesh) +CASE ('h2o16 ') + call def_stream((/nl-1, nod2D/), (/nl-1, myDim_nod2D/), 'h2o16', 'h2o16 concentration', 'kmol/m**3', tr_arr(:,:,5), io_list(i)%freq, io_list(i)%unit, io_list(i)%precision, mesh) +CASE ('h2o18_ice ') + call def_stream(nod2D, myDim_nod2D, 'h2o18_ice', 'h2o18 concentration in sea ice', 'kmol/m**3', tr_arr_ice(:,1), io_list(i)%freq, io_list(i)%unit, io_list(i)%precision, mesh) +CASE ('hDo16_ice ') + call def_stream(nod2D, myDim_nod2D, 'hDo16_ice', 'hDo16 concentration in sea ice', 'kmol/m**3', tr_arr_ice(:,2), io_list(i)%freq, io_list(i)%unit, io_list(i)%precision, mesh) +CASE ('h2o16_ice ') + call def_stream(nod2D, myDim_nod2D, 'h2o16_ice', 'h2o16 concentration in sea ice', 'kmol/m**3', tr_arr_ice(:,3), io_list(i)%freq, io_list(i)%unit, io_list(i)%precision, mesh) +!wiso-code-end! CASE ('otracers ') do j=3, num_tracers write (id_string, "(I3.3)") tracer_id(j) diff --git a/src/io_restart.F90 b/src/io_restart.F90 index 5f6d0d674..21bcb771d 100644 --- a/src/io_restart.F90 +++ b/src/io_restart.F90 @@ -53,13 +53,13 @@ MODULE io_RESTART ! !-------------------------------------------------------------------------------------------- ! id will keep the IDs of all required dimentions and variables - type(nc_file), save :: oid, iid + type(nc_file), save :: oid, iid, wid !wiso-code! add wid integer, save :: globalstep=0 type(nc_file), save :: ip_id real(kind=WP) :: ctime !current time in seconds from the beginning of the year PRIVATE - PUBLIC :: restart, oid, iid + PUBLIC :: restart, oid, iid, wid !wiso-code! add wid PUBLIC :: ip_id, def_dim, def_variable_1d, def_variable_2d ! !-------------------------------------------------------------------------------------------- @@ -130,7 +130,7 @@ subroutine ini_ocean_io(year, mesh) call def_variable(oid, 'uke_rhs', (/nl-1, elem2D/), 'unresolved kinetic energy rhs', 'm2/s2', uke_rhs(:,:)); endif - do j=1,num_tracers + do j=1,2 !wiso-code! num_tracers->2 SELECT CASE (j) CASE(1) trname='temp' @@ -153,6 +153,80 @@ subroutine ini_ocean_io(year, mesh) call def_variable(oid, 'w_expl', (/nl, nod2D/), 'vertical velocity', 'm/s', Wvel_e); call def_variable(oid, 'w_impl', (/nl, nod2D/), 'vertical velocity', 'm/s', Wvel_i); end subroutine ini_ocean_io + +!!!!wiso-code!!! +subroutine ini_wiso_io(year,mesh) + implicit none + + integer, intent(in) :: year + integer :: ncid, j + integer :: varid + character(500) :: longname + character(500) :: filename + character(500) :: trname, units + character(4) :: cyear + type(t_mesh), intent(in) , target :: mesh + +#include "associate_mesh.h" + + write(cyear,'(i4)') year + ! create a wiso restart file; serial output implemented so far + wid%filename=trim(ResultPath)//trim(runid)//'.'//cyear//'.wiso.restart.nc' + if (wid%is_in_use) return + wid%is_in_use=.true. + call def_dim(wid, 'node', nod2d) + call def_dim(wid, 'elem', elem2d) + call def_dim(wid, 'nz_1', nl-1) + call def_dim(wid, 'nz', nl) + do j=3,num_tracers + SELECT CASE (j) + CASE(3) + trname='h2o18' + longname='h2o18 concentration' + units='kmol/m**3' + CASE(4) + trname='hDo16' + longname='hDo16 concentration' + units='kmol/m**3' + CASE(5) + trname='h2o16' + longname='h2o16 concentration' + units='kmol/m**3' + CASE DEFAULT + write(trname,'(A3,i1)') 'tra_', j + write(longname,'(A15,i1)') 'passive tracer ', j + units='none' + END SELECT + call def_variable(wid, trim(trname), (/nl-1, nod2D/),trim(longname),trim(units), tr_arr(:,:,j)); + longname=trim(longname)//', Adams–Bashforth' + call def_variable(wid, trim(trname)//'_AB',(/nl-1, nod2D/),trim(longname),trim(units), tr_arr_old(:,:,j)); + end do + do j=1,num_tracers_ice + SELECT CASE (j) + CASE(1) + trname='h2o18_ice' + longname='h2o18 concentration in sea ice' + units='kmol/m**3' + CASE(2) + trname='hDo16_ice' + longname='hDo16 concentration in sea ice' + units='kmol/m**3' + CASE(3) + trname='h2o16_ice' + longname='h2o16 concentration in sea ice' + units='kmol/m**3' + CASE DEFAULT + write(trname,'(A3,i1)') 'tra_', j + write(longname,'(A15,i1)') 'passive tracer ', j + units='none' + END SELECT + call def_variable(wid, trim(trname), (/nod2D/),trim(longname),trim(units), tr_arr_ice(:,j)); + end do + +end subroutine ini_wiso_io +!!!!wiso-code!!! + + ! !-------------------------------------------------------------------------------------------- ! ini_ice_io initializes iid datatype which contains information of all variables need to be written into @@ -216,12 +290,18 @@ subroutine restart(istep, l_write, l_read, mesh) ctime=timeold+(dayold-1.)*86400 if (.not. l_read) then call ini_ocean_io(yearnew, mesh) +!!wiso-code!!! + if (lwiso) call ini_wiso_io(yearnew, mesh) +!!wiso-code!!! if (use_ice) call ini_ice_io (yearnew, mesh) #if defined(__icepack) if (use_ice) call init_restart_icepack(yearnew, mesh) #endif else call ini_ocean_io(yearold, mesh) +!!wiso-code!!! + if (lwiso) call ini_wiso_io(yearold, mesh) +!!wiso-code!!! if (use_ice) call ini_ice_io (yearold, mesh) #if defined(__icepack) if (use_ice) call init_restart_icepack(yearold, mesh) @@ -239,6 +319,12 @@ subroutine restart(istep, l_write, l_read, mesh) call read_restart(ip_id, mesh); call was_error(ip_id) #endif end if +!!wiso-code!!! + if (lwiso) then + call assoc_ids(wid); call was_error(wid) + call read_restart(wid, mesh); call was_error(wid) + end if +!!wiso-code!!! end if if (istep==0) return @@ -279,6 +365,13 @@ subroutine restart(istep, l_write, l_read, mesh) call write_restart(ip_id, istep, mesh); call was_error(ip_id) #endif end if +!!!wiso-code!!!! + if (lwiso) then + call assoc_ids(wid); call was_error(wid) + call write_restart(wid, istep, mesh); call was_error(wid) + end if +!!!wiso-code!!!! + ! actualize clock file to latest restart point if (mype==0) then diff --git a/src/oce_ale_tracer.F90 b/src/oce_ale_tracer.F90 index dd8d8411f..6f1587563 100644 --- a/src/oce_ale_tracer.F90 +++ b/src/oce_ale_tracer.F90 @@ -1025,8 +1025,14 @@ FUNCTION bc_surface(n, id, mesh) ! by forming/melting of sea ice bc_surface= dt*(virtual_salt(n) & !--> is zeros for zlevel/zstar + relax_salt(n) - real_salt_flux(n)*is_nonlinfs) - CASE (101) ! apply boundary conditions to tracer ID=101 - bc_surface= dt*(prec_rain(n))! - real_salt_flux(n)*is_nonlinfs) +!!!wiso-code!!! + CASE (101) ! apply boundary conditions to tracer ID=101 (H218O) + bc_surface = dt*o18_flux(n) + CASE (102) ! apply boundary conditions to tracer ID=102 (HDO) + bc_surface = dt*hdo_flux(n) + CASE (103) ! apply boundary conditions to tracer ID=103 (H216O) + bc_surface = dt*o16_flux(n) +!!!wiso-code-end!!! CASE (301) bc_surface=0.0_WP CASE (302) diff --git a/src/oce_modules.F90 b/src/oce_modules.F90 index 6ac8506bc..5dd91102e 100755 --- a/src/oce_modules.F90 +++ b/src/oce_modules.F90 @@ -97,6 +97,13 @@ MODULE o_PARAM END TYPE tracer_source3d_type integer :: num_tracers=2 +!!!wiso-code!!! add ice tracers +integer :: num_tracers_ice=3 +integer :: ih2o18_ice=1 +integer :: ihDo16_ice=2 +integer :: ih2o16_ice=3 +!!!wiso-code!!! add ice tracers + integer, dimension(100) :: tracer_ID = RESHAPE((/0, 1/), (/100/), (/0/)) ! ID for each tracer for treating the initialization and surface boundary condition ! 0=temp, 1=salt etc. type(tracer_source3d_type), & @@ -235,11 +242,13 @@ MODULE o_ARRAYS real(kind=WP), allocatable :: heat_flux_in(:) !to keep the unmodified (by SW penetration etc.) heat flux real(kind=WP), allocatable :: S_rhs(:,:) real(kind=WP), allocatable :: tr_arr(:,:,:),tr_arr_old(:,:,:) +real(kind=WP), allocatable :: tr_arr_ice(:,:) !!!wiso-code!!! add ice tracers real(kind=WP), allocatable :: del_ttf(:,:) real(kind=WP), allocatable :: del_ttf_advhoriz(:,:),del_ttf_advvert(:,:) !!PS ,del_ttf_diff(:,:) real(kind=WP), allocatable :: water_flux(:), Ssurf(:) real(kind=WP), allocatable :: virtual_salt(:), relax_salt(:) +real(kind=WP), allocatable :: o16_flux(:), o18_flux(:), hdo_flux(:) !!!wiso-code!!! add isotope fluxes real(kind=WP), allocatable :: Tclim(:,:), Sclim(:,:) real(kind=WP), allocatable :: Visc(:,:) real(kind=WP), allocatable :: Tsurf_t(:,:), Ssurf_t(:,:) diff --git a/src/oce_setup_step.F90 b/src/oce_setup_step.F90 index 0d9dc083b..77507f09a 100755 --- a/src/oce_setup_step.F90 +++ b/src/oce_setup_step.F90 @@ -229,6 +229,7 @@ SUBROUTINE array_setup(mesh) allocate(T_rhs(nl-1, node_size)) allocate(S_rhs(nl-1, node_size)) allocate(tr_arr(nl-1,node_size,num_tracers),tr_arr_old(nl-1,node_size,num_tracers)) +allocate(tr_arr_ice(node_size,num_tracers_ice)) !!!wiso-code!!! add ice tracers allocate(del_ttf(nl-1,node_size)) allocate(del_ttf_advhoriz(nl-1,node_size),del_ttf_advvert(nl-1,node_size)) del_ttf = 0.0_WP @@ -253,7 +254,8 @@ SUBROUTINE array_setup(mesh) allocate(water_flux(node_size), Ssurf(node_size)) allocate(relax_salt(node_size)) allocate(virtual_salt(node_size)) - +!!!wiso-code!!! allocate isotope fluxes +allocate(o16_flux(node_size), o18_flux(node_size), hdo_flux(node_size)) allocate(heat_flux_in(node_size)) allocate(real_salt_flux(node_size)) !PS ! ================= @@ -390,6 +392,12 @@ SUBROUTINE array_setup(mesh) relax_salt=0.0_WP virtual_salt=0.0_WP +!!!wiso-code!!! + o16_flux=0.0_WP + o18_flux=0.0_WP + hdo_flux=0.0_WP +!!!wiso-code!!! + Ssurf=0.0_WP real_salt_flux=0.0_WP @@ -497,13 +505,30 @@ SUBROUTINE oce_initial_state(mesh) DO i=3, num_tracers id=tracer_ID(i) SELECT CASE (id) - CASE (101) ! initialize tracer ID=101 - tr_arr(:,:,i)=0.0_WP + !wiso-code for tracers 101, 102, 103 + CASE (101) ! initialize tracer ID=101 h2o18 ysun + if (mype==0) then + write (i_string, "(I3)") i + write (id_string, "(I3)") id + write(*,*) 'initializing '//trim(i_string)//'th tracer with ID='//trim(id_string) + write (*,*) tr_arr(1,1,i) + end if + CASE (102) ! initialize tracer ID=102 hDo16 ysun if (mype==0) then write (i_string, "(I3)") i write (id_string, "(I3)") id write(*,*) 'initializing '//trim(i_string)//'th tracer with ID='//trim(id_string) + write (*,*) tr_arr(1,1,i) end if + CASE (103) ! initialize tracer ID=103 h2o16 ysun + if (mype==0) then + write (i_string, "(I3)") i + write (id_string, "(I3)") id + write(*,*) 'initializing '//trim(i_string)//'th tracer with ID='//trim(id_string) + write (*,*) tr_arr(1,1,i) + end if + !wiso-code for tracers 101, 102, 103 + CASE (301) !Fram Strait 3d restored passive tracer tr_arr(:,:,i)=0.0_WP rcounter3 =rcounter3+1 From fb6eab8aa3bbdf1c0201359bbc841fdafd8507ee Mon Sep 17 00:00:00 2001 From: Xiaoxu Shi Date: Wed, 5 May 2021 13:41:28 +0200 Subject: [PATCH 02/71] update --- CMakeLists.txt | 7 +- COPYING.LESSER.txt | 165 - HOWTO.run | 45 + LICENSE.txt | 867 +- Makefile.in_dkrz | 54 + ...in_gnu_impi => Makefile.in_hlrn3_crayintel | 40 +- Makefile.in_intel => Makefile.in_ollie | 21 +- README.md | 28 +- cmake/FindOASIS.cmake | 2 +- cmake/FindOASIS_oifs.cmake | 11 + config/namelist.config | 70 +- config/namelist.config.dkrz | 85 + config/namelist.config.hlrn | 97 + config/namelist.config.orig | 94 + config/namelist.config.toy_soufflet | 62 - config/namelist.cvmix | 72 - config/namelist.forcing | 66 +- config/namelist.forcing.era5 | 58 - config/namelist.forcing.ncep 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view_pscholz/main_plot_line.ipynb create mode 100644 view_pscholz/sub_fesom_data.py delete mode 100644 view_pscholz/sub_fesom_data_netcdf4.py delete mode 100644 view_pscholz/sub_fesom_paperplot.py delete mode 100755 work/job_bsc delete mode 100755 work/job_ollie_chain delete mode 100755 work/job_ubuntu create mode 100644 work/namelist.oce diff --git a/CMakeLists.txt b/CMakeLists.txt index 95b7e7b78..176faa3aa 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -8,10 +8,9 @@ endif() project(FESOM2.0) set(TOPLEVEL_DIR ${CMAKE_CURRENT_LIST_DIR}) -set(FESOM_COUPLED OFF CACHE BOOL "compile fesom standalone or with oasis support (i.e. coupled)") -set(OIFS_COUPLED OFF CACHE BOOL "compile fesom coupled to OpenIFS. (Also needs FESOM_COUPLED to work)") -set(CRAY OFF CACHE BOOL "compile with cray ftn") -set(USE_ICEPACK OFF CACHE BOOL "compile fesom with the Iceapck modules for sea ice column physics.") +set(FESOM_COUPLED ON CACHE BOOL "compile fesom standalone or with oasis support (i.e. coupled)") +#set(FESOM_COUPLED ON CACHE BOOL "compile fesom standalone or with oasis support (i.e. coupled)") +#set(OIFS_COUPLED ON CACHE BOOL "compile fesom coupled to OpenIFS. Also needs FESOM_COUPLED to work)") #set(VERBOSE OFF CACHE BOOL "toggle debug output") #add_subdirectory(oasis3-mct/lib/psmile) add_subdirectory(src) diff --git a/COPYING.LESSER.txt b/COPYING.LESSER.txt deleted file mode 100644 index 0a041280b..000000000 --- a/COPYING.LESSER.txt +++ /dev/null @@ -1,165 +0,0 @@ - GNU LESSER GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - - This version of the GNU Lesser General Public License incorporates -the terms and conditions of version 3 of the GNU General Public -License, supplemented by the additional permissions listed below. - - 0. Additional Definitions. - - As used herein, "this License" refers to version 3 of the GNU Lesser -General Public License, and the "GNU GPL" refers to version 3 of the GNU -General Public License. - - "The Library" refers to a covered work governed by this License, -other than an Application or a Combined Work as defined below. - - An "Application" is any work that makes use of an interface provided -by the Library, but which is not otherwise based on the Library. -Defining a subclass of a class defined by the Library is deemed a mode -of using an interface provided by the Library. - - A "Combined Work" is a work produced by combining or linking an -Application with the Library. The particular version of the Library -with which the Combined Work was made is also called the "Linked -Version". - - The "Minimal Corresponding Source" for a Combined Work means the -Corresponding Source for the Combined Work, excluding any source code -for portions of the Combined Work that, considered in isolation, are -based on the Application, and not on the Linked Version. - - The "Corresponding Application Code" for a Combined Work means the -object code and/or source code for the Application, including any data -and utility programs needed for reproducing the Combined Work from the -Application, but excluding the System Libraries of the Combined Work. - - 1. Exception to Section 3 of the GNU GPL. - - You may convey a covered work under sections 3 and 4 of this License -without being bound by section 3 of the GNU GPL. - - 2. Conveying Modified Versions. - - If you modify a copy of the Library, and, in your modifications, a -facility refers to a function or data to be supplied by an Application -that uses the facility (other than as an argument passed when the -facility is invoked), then you may convey a copy of the modified -version: - - a) under this License, provided that you make a good faith effort to - ensure that, in the event an Application does not supply the - function or data, the facility still operates, and performs - whatever part of its purpose remains meaningful, or - - b) under the GNU GPL, with none of the additional permissions of - this License applicable to that copy. - - 3. Object Code Incorporating Material from Library Header Files. - - The object code form of an Application may incorporate material from -a header file that is part of the Library. You may convey such object -code under terms of your choice, provided that, if the incorporated -material is not limited to numerical parameters, data structure -layouts and accessors, or small macros, inline functions and templates -(ten or fewer lines in length), you do both of the following: - - a) Give prominent notice with each copy of the object code that the - Library is used in it and that the Library and its use are - covered by this License. - - b) Accompany the object code with a copy of the GNU GPL and this license - document. - - 4. Combined Works. - - You may convey a Combined Work under terms of your choice that, -taken together, effectively do not restrict modification of the -portions of the Library contained in the Combined Work and reverse -engineering for debugging such modifications, if you also do each of -the following: - - a) Give prominent notice with each copy of the Combined Work that - the Library is used in it and that the Library and its use are - covered by this License. - - b) Accompany the Combined Work with a copy of the GNU GPL and this license - document. - - c) For a Combined Work that displays copyright notices during - execution, include the copyright notice for the Library among - these notices, as well as a reference directing the user to the - copies of the GNU GPL and this license document. - - d) Do one of the following: - - 0) Convey the Minimal Corresponding Source under the terms of this - License, and the Corresponding Application Code in a form - suitable for, and under terms that permit, the user to - recombine or relink the Application with a modified version of - the Linked Version to produce a modified Combined Work, in the - manner specified by section 6 of the GNU GPL for conveying - Corresponding Source. - - 1) Use a suitable shared library mechanism for linking with the - Library. 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If the Library as you -received it does not specify a version number of the GNU Lesser -General Public License, you may choose any version of the GNU Lesser -General Public License ever published by the Free Software Foundation. - - If the Library as you received it specifies that a proxy can decide -whether future versions of the GNU Lesser General Public License shall -apply, that proxy's public statement of acceptance of any version is -permanent authorization for you to choose that version for the -Library. diff --git a/HOWTO.run b/HOWTO.run new file mode 100644 index 000000000..805f5d9c7 --- /dev/null +++ b/HOWTO.run @@ -0,0 +1,45 @@ +# Tutorial in 6 steps: how to run FESOM 2.0 ocean only +# Cray CS400 (ollie) platform with intel enviroment was used! + +cd $HOME + +1. get the code (DKRZ account aXXXXXX must be provided!): + git clone https://aXXXXXX@gitlab.dkrz.de/FESOM/fesom2.git fesom2.0 + +2.ollie: prepare the mesh: + mkdir /work/ollie/$USER/mesh_F2GLO04 + cp /work/ollie/dsidoren/input/fesom2.0/meshes/mesh_F2GLO04/* /work/ollie/$USER/mesh_F2GLO04/. + mkdir /work/ollie/$USER/mesh_F2GLO04/dist_1440 + +3. path for the results: + mkdir /work/ollie/$USER/results + cd fesom2.0_ALE/ + ln -s /work/ollie/dsidoren/results/ results + cp /home/ollie/dsidoren/fesom2.0_ALE/results/fesom.clock results/. + +4. FESOM 2.0 basic settings: + edit config/namelist.config: + &paths: meshpath + & run_config !from Vadym + +5. compile the code +5.1 Simple way (use Cmake, Recomended): + cd fesom2.0 + bash -l configure.sh +5.2 Less simple way (use make, not recomended, you should have proper Makefile.in for your platform) + cd lib/parms/; make cleanall; make; cd ../../ # Solver for solving linear systems of equations + cd src/; make clean; make run; cd ../ # FESOM2.0 +5.3 Compile executable that is needed for mesh partitioning + cd lib/metis-5.1.0/; make clean; make; cd ../../ # Metis 5 will be used to partition the mesh + cd src/; make clean; make run_ini; cd ../ # mesh partitioner + +6. run the model: +cd work/ + +edit: + job_ini_ollie # to run the mesh partitioning + job_ollie # to run FESOM2.0 model + +and run! + sbatch job_ini_ollie # for partitioning + sbatch job_ollie # for model run diff --git a/LICENSE.txt b/LICENSE.txt index 0a2daba84..2f095a5ad 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,622 +1,301 @@ GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 + Version 2, June 1991 - Copyright (C) 2007 Free Software Foundation, Inc. + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. 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END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + FESOM 2 (Finite-volumE Sea ice-Ocean Model) - multi-resolution ocean general circulation model + Copyright (C) 2018 FESOM team + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + diff --git a/Makefile.in_dkrz b/Makefile.in_dkrz new file mode 100644 index 000000000..121a84748 --- /dev/null +++ b/Makefile.in_dkrz @@ -0,0 +1,54 @@ + +# Compiler and Linker +CC = icc +MPICC = mpiicc +MPIFC = mpiifort +LD = $(MPIFC) + +# Optimization specs for compiler - used for FESOM an parms. +# Metis falls back to conservative and non-compiler specific -O2, as +# it is only used in the less runtime-critical setup phase. +OPT = -O3 -r8 -fp-model precise -xHost -ip -implicitnone +COPT = -O3 -xHost -DLINUX -DUNDER_ -DMPI2 -Iinclude + +# NetCDF library and include definitions +NCFDIR = /sw/rhel6-x64/netcdf/netcdf_fortran-4.4.3-intel14 +NC_LIB = -L$(NCFDIR)/lib -lnetcdff +NC_INC = -I$(NCFDIR)/include + +# Definitions for MPI, if not set by compiler wrappers +MPIROOT = /sw/rhel6-x64/intel/impi/5.1.3.223/compilers_and_libraries/linux/mpi/intel64 +MPI_LIB = -L$(MPIROOT)/lib +MPI_INC = -I$(MPIROOT)/include + +# Definition of BLAS and LAPACK include and library +LIB_LAP = -mkl=sequential -static-intel + + +## For partitioning, the FESOM initialization offers an interface to Metis 5. +## The option -DPART_WEIGHTED distributes 2D _and_ 3D-nodes equally, but the +## partitioning might be quite irregular. +## Without DPART_WEIGHTED, only the number of 2D nodes is considered for load balancing. +## You can start Metis 5 with different random seeds -> different partitions. + +METIS_DEFS = -DMETIS_VERSION=5 -DPART_WEIGHTED -DMETISRANDOMSEED=35243 +# METISRANDDOMSEED: any integer + +# Used to compile the fesom wrapper to parms +PARMS_DEFS = -DUSE_MPI -DREAL=double -DDBL -DVOID_POINTER_SIZE_8 + +###################################################### +# +# Preprocessor +CPP = /usr/bin/cpp -P -C + +###################################################### +# Preprocessor definition + +CPP_DEFS= + +####################################################### +# for pARMS and metis Library, archive and options + +AR = ar qv +RANLIB = ranlib diff --git a/Makefile.in_gnu_impi b/Makefile.in_hlrn3_crayintel similarity index 65% rename from Makefile.in_gnu_impi rename to Makefile.in_hlrn3_crayintel index cdf9a6792..e73c5080c 100644 --- a/Makefile.in_gnu_impi +++ b/Makefile.in_hlrn3_crayintel @@ -1,30 +1,28 @@ # Compiler and Linker -CC = gcc -MPICC = mpicc -MPIFC = mpif90 +CC = cc +MPICC = cc +MPIFC = ftn LD = $(MPIFC) # Optimization specs for compiler - used for FESOM an parms. # Metis falls back to conservative and non-compiler specific -O2, as # it is only used in the less runtime-critical setup phase. -OPT = -O3 -march=native -funroll-loops -ffree-line-length-none -COPT = -O3 -march=native -funroll-loops -DLINUX -DUNDER_ -DMPI2 -Iinclude -## Options for debugging: -# OPT = -g -fbounds-check -fbacktrace - -# Preprocessor flags for FESOM2 -CPP_DEFS = -DDISABLE_MULTITHREADING +OPT = -O3 -r8 -fp-model precise -xHost -ip -implicitnone +COPT = -O3 -xHost -DLINUX -DMPI2 -Iinclude # NetCDF library and include definitions -NCFDIR = /global/AWIsoft/netcdf/4.6.1_gnu -NC_LIB = -L$(NCFDIR)/lib -Wl,-rpath,$(NCFDIR)/lib -lnetcdff -NC_INC = -I$(NCFDIR)/include +NCDIR = /opt/cray/netcdf/4.4.1/INTEL/15.0 +NC_LIB = -L$(NCDIR)/lib -Wl,-rpath,$(NCDIR)/lib -lnetcdff -lnetcdf +NC_INC = -I$(NCDIR)/include # Definitions for MPI, if not set by compiler wrappers -MPIROOT = -MPI_LIB = -MPI_INC = +MPI_LIB = +MPI_INC = + +# Definition of BLAS, LAPACK include and library +LIB_LAP = -mkl + ## For partitioning, the FESOM initialization offers an interface to Metis 5. ## The option -DPART_WEIGHTED distributes 2D _and_ 3D-nodes equally, but the @@ -38,6 +36,16 @@ METIS_DEFS = -DMETIS_VERSION=5 -DPART_WEIGHTED -DMETISRANDOMSEED=35243 # Used to compile the fesom wrapper to parms PARMS_DEFS = -DUSE_MPI -DREAL=double -DDBL -DVOID_POINTER_SIZE_8 +###################################################### +# +# Preprocessor +CPP = /usr/bin/cpp -P -C + +###################################################### +# Preprocessor definition + +CPP_DEFS= + ####################################################### # for pARMS and metis Library, archive and options diff --git a/Makefile.in_intel b/Makefile.in_ollie similarity index 79% rename from Makefile.in_intel rename to Makefile.in_ollie index 1bb5c4800..2a582f0d3 100644 --- a/Makefile.in_intel +++ b/Makefile.in_ollie @@ -8,13 +8,8 @@ LD = $(MPIFC) # Optimization specs for compiler - used for FESOM an parms. # Metis falls back to conservative and non-compiler specific -O2, as # it is only used in the less runtime-critical setup phase. -OPT = -O3 -r8 -fp-model precise -xHost -ip -implicitnone -static-intel +OPT = -O3 -r8 -fp-model precise -xHost -ip -implicitnone COPT = -O3 -xHost -DLINUX -DUNDER_ -DMPI2 -Iinclude -## Options for debugging: -# OPT = -g -xHost -traceback -fpe:0 -check all -static-intel - -# Preprocessor flags for FESOM2 -CPP_DEFS = -DDISABLE_MULTITHREADING # NetCDF library and include definitions NCFDIR = /global/AWIsoft/netcdf/4.6.1_intel_18.0.3 @@ -26,6 +21,10 @@ MPIROOT = MPI_LIB = MPI_INC = +# Definition of BLAS and LAPACK include and library +LIB_LAP = -mkl=sequential -static-intel + + ## For partitioning, the FESOM initialization offers an interface to Metis 5. ## The option -DPART_WEIGHTED distributes 2D _and_ 3D-nodes equally, but the ## partitioning might be quite irregular. @@ -38,6 +37,16 @@ METIS_DEFS = -DMETIS_VERSION=5 -DPART_WEIGHTED -DMETISRANDOMSEED=35243 # Used to compile the fesom wrapper to parms PARMS_DEFS = -DUSE_MPI -DREAL=double -DDBL -DVOID_POINTER_SIZE_8 +###################################################### +# +# Preprocessor +CPP = /usr/bin/cpp -P -C + +###################################################### +# Preprocessor definition + +CPP_DEFS= + ####################################################### # for pARMS and metis Library, archive and options diff --git a/README.md b/README.md index de34d9620..5c31ef790 100644 --- a/README.md +++ b/README.md @@ -1,29 +1,19 @@ The Finite Element Sea Ice-Ocean Model (FESOM2) ====== -[![Build Status](https://github.com/FESOM/fesom2/workflows/FESOM2%20main%20test/badge.svg)](https://github.com/FESOM/fesom2/actions) Multi-resolution ocean general circulation model that solves the equations of motion describing the ocean and sea ice using finite-element and finite-volume methods on unstructured computational grids. The model is developed and supported by researchers at the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), in Bremerhaven, Germany. -**Website:** [fesom.de](https://fesom.de/) +Documentation +============= -**Documentation:** [fesom2.readthedocs.io](https://fesom2.readthedocs.io/en/latest/index.html) +[Quick Start (HOWTO.run)](HOWTO.run) -**Basic tutorial:** [Getting started](https://fesom2.readthedocs.io/en/latest/getting_started/getting_started.html) +[Basic tutorial](/docs/README.md) +[Convert grid to netCDF that CDO understands](/docs/convert_grid_to_nc.md) References ----------- - -[Complete list of references on fesom.de](https://fesom.de/publications/) - -* **[Ocean model formulation]** Danilov, S., Sidorenko, D., Wang, Q., and Jung, T.: The Finite-volumE Sea ice–Ocean Model (FESOM2), Geosci. Model Dev., 10, 765–789, https://doi.org/10.5194/gmd-10-765-2017, 2017. - -* **[Sea ice model formulation]** Danilov, S., Q. Wang, R. Timmermann, N. Iakovlev, D. Sidorenko, M. Kimmritz, T. Jung, and Schröter, J. (2015), Finite-Element Sea Ice Model (FESIM), version 2, Geosci. Model Dev., 8, 1747–1761, http://www.geosci-model-dev.net/8/1747/2015/ - -* **[Evaluation of standard sumulations]** Scholz, P., Sidorenko, D., Gurses, O., Danilov, S., Koldunov, N., Wang, Q., Sein, D., Smolentseva, M., Rakowsky, N., and Jung, T.: Assessment of the Finite-volumE Sea ice-Ocean Model (FESOM2.0) – Part 1: Description of selected key model elements and comparison to its predecessor version, Geosci. Model Dev., 12, 4875–4899, https://doi.org/10.5194/gmd-12-4875-2019, 2019. - -* **[Evaluation of computational performance]** Koldunov, N. V., Aizinger, V., Rakowsky, N., Scholz, P., Sidorenko, D., Danilov, S., and Jung, T.: Scalability and some optimization of the Finite-volumE Sea ice–Ocean Model, Version 2.0 (FESOM2), Geosci. Model Dev., 12, 3991–4012, https://doi.org/10.5194/gmd-12-3991-2019, 2019. - -* **[Version coupled with ECHAM6 atmosphere]** Sidorenko, D., Goessling, H. F., Koldunov, N. V., Scholz, P., Danilov, S., Barbi, D., et al ( 2019). Evaluation of FESOM2.0 coupled to ECHAM6.3: Pre‐industrial and HighResMIP simulations. Journal of Advances in Modeling Earth Systems, 11. https://doi.org/10.1029/2019MS001696 - -* **[Version with ICEPACK sea ice thermodynamics]** Zampieri, Lorenzo, Frank Kauker, Jörg Fröhle, Hiroshi Sumata, Elizabeth C. Hunke, and Helge Goessling. Impact of Sea-Ice Model Complexity on the Performance of an Unstructured-Mesh Sea-ice/ocean Model Under Different Atmospheric Forcings. Washington: American Geophysical Union, 2020. https://dx.doi.org/10.1002/essoar.10505308.1. +========== +* Danilov, S., Q. Wang, R. Timmermann, N. Iakovlev, D. Sidorenko, M. Kimmritz, T. Jung, and Schröter, J. (2015), Finite-Element Sea Ice Model (FESIM), version 2, Geosci. Model Dev., 8, 1747–1761, http://www.geosci-model-dev.net/8/1747/2015/ +* Wang, Q., Danilov, S., Sidorenko, D., Timmermann, R., Wekerle, C., Wang, X., Jung, T., and Schröter, J. (2014), The Finite Element Sea Ice-Ocean Model (FESOM) v.1.4: formulation of an ocean general circulation model, Geosci. Model Dev., 7, 663–693, doi:10.5194/gmd-7-663-2014, http://www.geosci-model-dev.net/7/663/2014/ +* Sidorenko, D., Rackow, T., Jung, T., Semmler, T., Barbi, D., Danilov, S., Dethloff, K., Dorn, W., Fieg, K., Goessling, H. F., Handorf, D., Harig, S., Hiller, W., Juricke, S., Losch, M., Schröter, J., Sein, D. V., & Wang, Q. (2014), Towards multi-resolution global climate modeling with ECHAM6-FESOM. Part I: model formulation and mean climate. Clim. Dyn., 44, 757–780, doi:10.1007/s00382-014-2290-6 \ No newline at end of file diff --git a/cmake/FindOASIS.cmake b/cmake/FindOASIS.cmake index cb669ea1a..acac55f21 100644 --- a/cmake/FindOASIS.cmake +++ b/cmake/FindOASIS.cmake @@ -7,5 +7,5 @@ find_library(MCT_Fortran_LIBRARIES mct HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/ find_path(MPEU_Fortran_INCLUDE_DIRECTORIES m_mpout.mod HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/mct/mpeu) find_library(MPEU_Fortran_LIBRARIES mpeu HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/mct/mpeu) -find_path(SCRIP_Fortran_INCLUDE_DIRECTORIES remap_bicubic_reduced.mod HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/scrip) +find_path(SCRIP_Fortran_INCLUDE_DIRECTORIES remap_bicubic.mod HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/scrip) find_library(SCRIP_Fortran_LIBRARIES scrip HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/scrip) diff --git a/cmake/FindOASIS_oifs.cmake b/cmake/FindOASIS_oifs.cmake new file mode 100644 index 000000000..ac3b749e7 --- /dev/null +++ b/cmake/FindOASIS_oifs.cmake @@ -0,0 +1,11 @@ +find_path(OASIS_Fortran_INCLUDE_DIRECTORIES mod_oasis.mod HINTS ${TOPLEVEL_DIR}/../oasis3-mct/ecconf/build/lib/psmile.MPI1) +find_library(OASIS_Fortran_LIBRARIES psmile HINTS ${TOPLEVEL_DIR}/../oasis3-mct/ecconf/lib) + +find_path(MCT_Fortran_INCLUDE_DIRECTORIES mct_mod.mod HINTS ${TOPLEVEL_DIR}/../oasis3-mct/ecconf/build/lib/mct) +find_library(MCT_Fortran_LIBRARIES mct HINTS ${TOPLEVEL_DIR}/../oasis3-mct/ecconf/build/lib/mctdir/mct) + +find_path(MPEU_Fortran_INCLUDE_DIRECTORIES m_mpout.mod HINTS ${TOPLEVEL_DIR}/../oasis3-mct//ecconf/build/lib/mct) +find_library(MPEU_Fortran_LIBRARIES mpeu HINTS ${TOPLEVEL_DIR}/../oasis3-mct/ecconf/build/lib/mctdir/mpeu) + +find_path(SCRIP_Fortran_INCLUDE_DIRECTORIES remap_bicubic.mod HINTS ${TOPLEVEL_DIR}/../oasis3-mct/ecconf/build/lib/scrip) +find_library(SCRIP_Fortran_LIBRARIES scrip HINTS ${TOPLEVEL_DIR}/../oasis3-mct/ecconf/lib) diff --git a/config/namelist.config b/config/namelist.config old mode 100644 new mode 100755 index b283fdd8d..ee26f087f --- a/config/namelist.config +++ b/config/namelist.config @@ -10,53 +10,77 @@ run_length= 62 !62 !62 !62 !28 run_length_unit='y' ! y, m, d, s / -&clockinit ! the model starts at +&clockinit ! the model starts at timenew=0.0 daynew=1 -yearnew=1958 +yearnew=1948 / &paths -MeshPath='/work/ollie/projects/clidyn/FESOM2/meshes/core2/' -ClimateDataPath='/work/ollie/projects/clidyn/FESOM2/hydrography/phc3.0/' -ResultPath='../result_tmp/' +MeshPath='/work/ollie/pscholz/mesh_fesom2.0/mesh_CORE2_finaltopo_mean/' +OpbndPath='' +ClimateDataPath='/work/ollie/dsidoren/input/hydrography/phc3.0/' +ForcingDataPath='/work/ollie/dsein/input/forcing/' +TideForcingPath='/work/ollie/dsein/input/tide_forcing/' +ResultPath='../results/linfs/zmeanval/3/' / -&restart_log -restart_length=1 !only required for d,h,s cases, y, m take 1 -restart_length_unit='y' !output period: y, d, h, s -logfile_outfreq=960 !in logfile info. output frequency, # steps +&initialization +OceClimaDataName='Winter_PHC3_ts.out' !which T/S data to initial. ocean + !'Winter_PHC3_ts.out' + !'Annual_PHC3_ts.out' +use_prepared_init_ice=.false. !how to init. ice; runid.initial_ice.nc / -&ale_def -which_ALE='zstar' ! 'linfs','zlevel', 'zstar' -use_partial_cell=.true. +&inout +restartflag='last' !restart from which saved record,'last','#' +restart_length=1 !only required for d,h,s cases, y, m take 1 +restart_length_unit='y' !output period: y, d, h, s +restart_offset=64 +logfile_outfreq=960 !in logfile info. output frequency, # steps +use_means=.false. !average output, if false prints out snapshots +/ + +&mesh_def +grid_type=1 !1 z-level, 2 sigma, 3 z+sigma +use_ALE=.true. ! switch on/off ALE +which_ALE='linfs' ! 'linfs','zlevel', 'zstar','zstar-weight', 'ztilde' +use_partial_cell=.false. +min_hnode=0.5 +lzstar_lev=4 / &geometry cartesian=.false. fplane=.false. -cyclic_length=360 ![degree] -rotated_grid=.true. !option only valid for coupled model case now -force_rotation=.true. -alphaEuler=50. ![degree] Euler angles, convention: -betaEuler=15. ![degree] first around z, then around new x, -gammaEuler=-90. ![degree] then around new z. +betaplane=.false. +f_fplane=-1.4e-4 ![1/s] +beta_betaplane=2.0e-11 ![1/s/m] +cyclic_length=360. ![degree] +rotated_grid=.true. !option only valid for coupled model case now +alphaEuler=50. ![degree] Euler angles, convention: +betaEuler=15. ![degree] first around z, then around new x, +gammaEuler=-90. ![degree] then around new z. +force_rotation=.false. / &calendar -include_fleapyear=.true. +include_fleapyear=.false. / &run_config use_ice=.true. ! ocean+ice -use_cavity=.false. ! -use_cavity_partial_cell=.false. use_floatice = .false. use_sw_pene=.true. +toy_ocean=.false. ! use toy forcing/initialization / &machine -n_levels=2 -n_part= 12, 36 ! 432 number of partitions on each hierarchy level +! system_arch=1 +n_levels=3 +!n_part= 2, 4, 36 ! number of partitions on each hierarchy level +n_part= 2, 12, 36 ! 864 number of partitions on each hierarchy level +!n_part= 2, 6, 36 ! 432 number of partitions on each hierarchy level +!n_part= 2, 4, 36 ! 288 number of partitions on each hierarchy level + / diff --git a/config/namelist.config.dkrz b/config/namelist.config.dkrz new file mode 100755 index 000000000..a488c5604 --- /dev/null +++ b/config/namelist.config.dkrz @@ -0,0 +1,85 @@ +! This is the namelist file for model general configuration + +&modelname +runid='fesom' +/ + +×tep +step_per_day=1440 +run_length=1 +run_length_unit='m' ! y, m, d, s +/ + +&clockinit ! the model starts at +timenew=0.0 +daynew=1 +yearnew=1948 +/ + +&paths +MeshPath='/mnt/lustre02/work/ab0995/a270029/fesom2.0/meshes/fron_l1/' +OpbndPath='' +ClimateDataPath='/mnt/lustre01/work/ba1035/a270092/input/fesom2/hydrography/' +ForcingDataPath='/mnt/lustre01/work/ba1035/a270092/input/fesom2/forcing/' +TideForcingPath='/mnt/lustre01/work/ba1035/a270092/input/fesom2/tide_forcing/' +ResultPath='/work/ab0995/a270029/fesom2output/' +/ + +&initialization +OceClimaDataName='Winter_PHC3_ts.out' !which T/S data to initial. ocean + !'Winter_PHC3_ts.out' + !'Annual_PHC3_ts.out' +use_prepared_init_ice=.false. !how to init. ice; runid.initial_ice.nc +/ + +&inout +restartflag='last' !restart from which saved record,'last','#' +output_length=1 !only required for d,h,s cases, y, m take 1 +output_length_unit='y' !output period: y, d, h, s +output_offset=64 +restart_length=1 !only required for d,h,s cases, y, m take 1 +restart_length_unit='m' !output period: y, d, h, s +restart_offset=64 +logfile_outfreq=10 !in logfile info. output frequency, # steps +use_means=.false. !average output, if false prints out snapshots +/ + +&mesh_def +grid_type=1 !1 z-level, 2 sigma, 3 z+sigma +use_ALE=.true. ! switch on/off ALE +which_ALE='linfs' ! 'linfs','zlevel', 'zstar','zstar-weight', 'ztilde' +use_partial_cell=.false. +min_hnode=0.25 +lzstar_lev=3 +/ + +&geometry +cartesian=.false. +fplane=.false. +betaplane=.false. +f_fplane=-1.4e-4 ![1/s] +beta_betaplane=2.0e-11 ![1/s/m] +cyclic_length=360. ![degree] +rotated_grid=.true. !option only valid for coupled model case now +alphaEuler=50. ![degree] Euler angles, convention: +betaEuler=15. ![degree] first around z, then around new x, +gammaEuler=-90. ![degree] then around new z. +force_rotation=.true. +/ + +&calendar +include_fleapyear=.false. +/ + +&run_config +use_ice=.true. ! ocean+ice +use_floatice = .false. +use_sw_pene=.true. +toy_ocean=.false. ! use toy forcing/initialization +/ + +&machine +! system_arch=1 +n_levels=3 +n_part= 2, 4, 36 ! number of partitions on each hierarchy level +/ diff --git a/config/namelist.config.hlrn b/config/namelist.config.hlrn new file mode 100755 index 000000000..707e5d079 --- /dev/null +++ b/config/namelist.config.hlrn @@ -0,0 +1,97 @@ +! This is the namelist file for model general configuration + +&modelname +runid='fesom' +/ + +×tep +! 96 100 108 120 128 135 144 150 160 180 240 +! 288 360 480 720 1440 +step_per_day=120 !288 !96 + +run_length=20 !24 +run_length_unit='y' ! y, m, d, s +/ + +&clockinit ! the model starts at +timenew=0.0 +daynew=1 +yearnew=1948 +/ + +&paths +!MeshPath='/work/ollie/dsidoren/input/fesom2.0/meshes/mesh_CORE2_final/' +MeshPath='/work/ollie/pscholz/mesh_fesom2.0/mesh_CORE2_final/' +!MeshPath='/work/ollie/dsidoren/input/fesom2.0/meshes/mesh_CORE2_topo_smooth_77/' +!MeshPath='/work/ollie/pscholz/mesh_fesom2.0/mesh_CORE2_topo_smooth_77/' + +OpbndPath='' +ClimateDataPath='/work/ollie/dsidoren/input/hydrography/' +ForcingDataPath='/work/ollie/dsein/input/forcing/' +TideForcingPath='/work/ollie/dsein/input/tide_forcing/' +ResultPath='../results/git/' +/ + +&initialization +OceClimaDataName='Winter_PHC3_ts.out' !which T/S data to initial. ocean + !'Winter_PHC3_ts.out' + !'Annual_PHC3_ts.out' +use_prepared_init_ice=.false. !how to init. ice; runid.initial_ice.nc +/ + +&inout +restartflag='last' !restart from which saved record,'last','#' +output_length=1 !only required for d,h,s cases, y, m take 1 +output_length_unit='d' !output period: y, d, h, s +output_offset=64 +restart_length=1 !only required for d,h,s cases, y, m take 1 +restart_length_unit='m' !output period: y, d, h, s +restart_offset=64 +logfile_outfreq=600 !in logfile info. output frequency, # steps +use_means=.true. !average output, if false prints out snapshots +/ + +&mesh_def +grid_type=1 !1 z-level, 2 sigma, 3 z+sigma +use_ALE=.true. ! switch on/off ALE +which_ALE='zlevel' ! 'linfs','zlevel', 'zstar','zstar-weight', 'ztilde' +use_partial_cell=.true. +min_hnode=0.5 +lzstar_lev=20 +max_ice_loading=4.0 +/ + +&geometry +cartesian=.false. +fplane=.false. +betaplane=.false. +f_fplane=-1.4e-4 ![1/s] +beta_betaplane=2.0e-11 ![1/s/m] +cyclic_length=360. ![degree] +rotated_grid=.true. !option only valid for coupled model case now +alphaEuler=50. ![degree] Euler angles, convention: +betaEuler=15. ![degree] first around z, then around new x, +gammaEuler=-90. ![degree] then around new z. +force_rotation=.false. +/ + +&calendar +include_fleapyear=.false. +/ + +&run_config +use_ice=.true. ! ocean+ice +use_floatice = .true. +use_sw_pene=.false. +toy_ocean=.false. ! use toy forcing/initialization +/ + +&machine +! system_arch=1 +n_levels=3 +!n_part= 18, 2, 10 ! number of partitions on each hierarchy level +n_part= 18, 2, 12 ! 432 number of partitions on each hierarchy level +! n_part= 15, 2, 12 ! 360 number of partitions on each hierarchy level +!n_part= 12, 2, 12 ! 288 number of partitions on each hierarchy level + +/ diff --git a/config/namelist.config.orig b/config/namelist.config.orig new file mode 100755 index 000000000..342ca287e --- /dev/null +++ b/config/namelist.config.orig @@ -0,0 +1,94 @@ +! This is the namelist file for model general configuration + +&modelname +runid='fesom' +/ + +×tep +! 96 100 108 120 128 135 144 150 160 180 240 +! 288 360 480 720 1440 +step_per_day=120 !288 !96 + +run_length=20 !24 +run_length_unit='y' ! y, m, d, s +/ + +&clockinit ! the model starts at +timenew=0.0 +daynew=1 +yearnew=1948 +/ + +&paths +!MeshPath='/work/ollie/dsidoren/input/fesom2.0/meshes/mesh_CORE2_final/' +MeshPath='/work/ollie/pscholz/mesh_fesom2.0/mesh_CORE2_final/' +!MeshPath='/work/ollie/dsidoren/input/fesom2.0/meshes/mesh_CORE2_topo_smooth_77/' +!MeshPath='/work/ollie/pscholz/mesh_fesom2.0/mesh_CORE2_topo_smooth_77/' + +OpbndPath='' +ClimateDataPath='/work/ollie/dsidoren/input/hydrography/' +ForcingDataPath='/work/ollie/dsein/input/forcing/' +TideForcingPath='/work/ollie/dsein/input/tide_forcing/' +ResultPath='../results/git/' +/ + +&initialization +OceClimaDataName='Winter_PHC3_ts.out' !which T/S data to initial. ocean + !'Winter_PHC3_ts.out' + !'Annual_PHC3_ts.out' +use_prepared_init_ice=.false. !how to init. ice; runid.initial_ice.nc +/ + +&inout +restartflag='last' !restart from which saved record,'last','#' +restart_length=1 !only required for d,h,s cases, y, m take 1 +restart_length_unit='m' !output period: y, d, h, s +restart_offset=64 +logfile_outfreq=600 !in logfile info. output frequency, # steps +use_means=.true. !average output, if false prints out snapshots +/ + +&mesh_def +grid_type=1 !1 z-level, 2 sigma, 3 z+sigma +use_ALE=.true. ! switch on/off ALE +which_ALE='zlevel' ! 'linfs','zlevel', 'zstar','zstar-weight', 'ztilde' +use_partial_cell=.true. +min_hnode=0.5 +lzstar_lev=20 +max_ice_loading=4.0 +/ + +&geometry +cartesian=.false. +fplane=.false. +betaplane=.false. +f_fplane=-1.4e-4 ![1/s] +beta_betaplane=2.0e-11 ![1/s/m] +cyclic_length=360. ![degree] +rotated_grid=.true. !option only valid for coupled model case now +alphaEuler=50. ![degree] Euler angles, convention: +betaEuler=15. ![degree] first around z, then around new x, +gammaEuler=-90. ![degree] then around new z. +force_rotation=.false. +/ + +&calendar +include_fleapyear=.false. +/ + +&run_config +use_ice=.true. ! ocean+ice +use_floatice = .true. +use_sw_pene=.false. +toy_ocean=.false. ! use toy forcing/initialization +/ + +&machine +! system_arch=1 +n_levels=3 +!n_part= 18, 2, 10 ! number of partitions on each hierarchy level +n_part= 18, 2, 12 ! 432 number of partitions on each hierarchy level +! n_part= 15, 2, 12 ! 360 number of partitions on each hierarchy level +!n_part= 12, 2, 12 ! 288 number of partitions on each hierarchy level + +/ diff --git a/config/namelist.config.toy_soufflet b/config/namelist.config.toy_soufflet deleted file mode 100644 index b074865ba..000000000 --- a/config/namelist.config.toy_soufflet +++ /dev/null @@ -1,62 +0,0 @@ -! This is the namelist file for model general configuration - -&modelname -runid='fesom' -/ - -×tep -step_per_day=72 !96 !96 !72 !72 !45 !72 !96 -run_length= 10 !62 !62 !62 !28 -run_length_unit='y' ! y, m, d, s -/ - -&clockinit ! the model starts at -timenew=0.0 -daynew=1 -yearnew=1948 -/ - -&paths -MeshPath='/work/ollie/sjuricke/Soufflet_20/' -ClimateDataPath='/work/ollie/dsidoren/input/hydrography/phc3.0/' -ResultPath='/home/ollie/dsidoren/test_visc/' -/ - -&restart_log -restart_length=1 !only required for d,h,s cases, y, m take 1 -restart_length_unit='y' !output period: y, d, h, s -logfile_outfreq=960 !in logfile info. output frequency, # steps -/ - -&ale_def -which_ALE='linfs' ! 'linfs','zlevel', 'zstar' -use_partial_cell=.false. -/ - -&geometry -cartesian=.false. -fplane=.false. -cyclic_length=4.5 ![degree] -rotated_grid=.false. !option only valid for coupled model case now -force_rotation=.false. -alphaEuler=50. ![degree] Euler angles, convention: -betaEuler=15. ![degree] first around z, then around new x, -gammaEuler=-90. ![degree] then around new z. -/ - -&calendar -include_fleapyear=.false. -/ - -&run_config -use_ice=.false. ! ocean+ice -use_floatice = .false. -use_sw_pene=.false. -toy_ocean=.true. -which_toy="soufflet" -/ - -&machine -n_levels=2 -n_part= 12, 36 ! 432 number of partitions on each hierarchy level -/ diff --git a/config/namelist.cvmix b/config/namelist.cvmix deleted file mode 100644 index 00754cca1..000000000 --- a/config/namelist.cvmix +++ /dev/null @@ -1,72 +0,0 @@ -! namelist for Turbulent Kinetic Energy (TKE) -¶m_tke -tke_c_k = 0.1 -tke_c_eps = 0.7 -tke_alpha = 30.0 -tke_mxl_min = 1.0e-8 -tke_kappaM_min = 0.0 -tke_kappaM_max = 100.0 -tke_cd = 3.75 ! for Dirichlet boundary conditions -!tke_cd = 1.0 ! for Neumann boundary conditions -tke_surf_min = 1.0e-4 -tke_min = 1.0e-6 -! tke_mxl_choice ... Can only be 1 or 2, choice of calculation of mixing -! length; currently only Blanke, B., P. Delecluse option is implemented -tke_mxl_choice = 2 -/ - -! namelist for IDEMIX -¶m_idemix -idemix_tau_v = 86400.0 ! time scale for vertical symmetrisation (sec) -idemix_tau_h = 1296000.0 ! time scale for horizontal symmetrisation -idemix_gamma = 1.570 ! constant of order one derived from the shape of the spectrum in m space (dimensionless) -idemix_jstar = 10.0 ! spectral bandwidth in modes (dimensionless) -idemix_mu0 = 1.33333333 ! dissipation parameter (dimensionless) -idemix_sforcusage = 0.2 -idemix_n_hor_iwe_prop_iter = 5 ! iterations for contribution from horiz. wave propagation -idemix_surforc_file = '/work/ollie/clidyn/forcing/IDEMIX/fourier_smooth_2005_cfsr_inert_rgrid.nc' -idemix_botforc_file = '/work/ollie/clidyn/forcing/IDEMIX/tidal_energy_gx1v6_20090205_rgrid.nc' -/ - -! namelist for PP -¶m_pp -pp_use_fesompp = .true. ! if true use fesom flavor off PP if false use original PP of Pacanowski & Philander -pp_Av0 = 0.01 ! mixing coeff. for PP -pp_alpha = 5.0 ! alpha param eq. (1) in Pacanowski and Philander 1981 -pp_exp = 2.0 ! n param eq. (1) in Pacanowski and Philander 1981 -pp_Avbckg = 1.0e-4 ! const. pp background viscosity -pp_Kvbckg = 1.0e-5 ! const. pp background diffusivity -pp_use_nonconstKvb = .true. ! use lat and depth dependent background diffusivity -/ - -! namelist for KPP -¶m_kpp -kpp_use_fesomkpp = .false. ! if true use cvmix MOM5 like kpp if false use cvmix MOM6 like kpp -kpp_use_enhanceKv = .true. ! If true, add enhanced diffusivity at base of boundary layer -kpp_use_compEkman = .true. ! If true, compute Ekman depth limit for OBLdepth -kpp_use_monob = .true. ! If true, compute Monin-Obukhov limit for OBLdepth -kpp_interptype_ri = "linear" ! Type of interpolation in determining OBL depth: linear,quadratic,cubic -kpp_interptype_atobl= "LMD94" ! Type of interpolation of visc and diff at obl depth: linear,quadratic,cubic,LMD94 -kpp_matchtechc = "ParabolicNonLocal" ! Setting diffusivity and NLT profile functions:SimpleShapes, MatchGradient, MatchBoth, ParabolicNonLocal -kpp_internalmix = "KPP" ! Ri-number dependet mixing scheme below the OBL: 'PP' or 'KPP' -kpp_reduce_tauuice = .false. ! If True, reduce the wind stress (ustar) under sea ice. -kpp_Av0 = 5.0e-3 ! leading coefficient of shear mixing formula, units: m^2/s: default= 5e-3 -kpp_Kv0 = 5.0e-3 -kpp_Ri0 = 0.7 ! critical Richardson number value, units: unitless (0.7 in LMD94) -kpp_pp_Av0 = 0.01 ! Parameter in case of PP mixing below the OBL -kpp_use_nonconstKvb= .true. ! If True use non constant background diffusivity of Qiang from FESOM1.4 -kpp_Avbckg = 1.0e-4 ! Values for const. background viscosity and diffusivity -kpp_Kvbckg = 1.0e-5 -/ - -! namelist for TIDAL -¶m_tidal -tidal_mixscheme = "Simmons" -tidal_efficiency = 0.2 ! units: unitless (fraction); (Gamma in Simmons et al.) -tidal_vert_decayscale= 500.0 ! units: m; zeta in Simmons et al. (used to compute the vertical deposition function) -tidal_max_coeff = 50e-4 ! units: m^2/s; largest acceptable value for diffusivity -tidal_lcl_mixfrac = 0.33 !tidal dissipation efficiency (q in Simmons et al.), i.e. fraction of energy that dissipates locally -tidal_depth_cutoff = 0.0 !depth of the shallowest column where tidal mixing is computed (positive below surface) -tidal_botforc_file = '/work/ollie/pscholz/FORCING/IDEMIX/tidal_energy_gx1v6_20090205_rgrid.nc' -/ - diff --git a/config/namelist.forcing b/config/namelist.forcing old mode 100644 new mode 100755 index 79eb1374f..bc36172c3 --- a/config/namelist.forcing +++ b/config/namelist.forcing @@ -1,22 +1,17 @@ ! This is the namelist file for forcing &forcing_exchange_coeff -Ce_atm_oce=0.00175 ! exchange coeff. of latent heat over open water -Ch_atm_oce=0.00175 ! exchange coeff. of sensible heat over open water -Cd_atm_oce=0.001 ! drag coefficient between atmosphere and water -Ce_atm_ice=0.00175 ! exchange coeff. of latent heat over ice -Ch_atm_ice=0.00175 ! exchange coeff. of sensible heat over ice -Cd_atm_ice=0.0012 ! drag coefficient between atmosphere and ice -Swind =0.0 ! parameterization for coupled current feedback +Ce_atm_oce=1.75e-3 ! exchange coeff. of latent heat over open water +Ch_atm_oce=1.75e-3 ! exchange coeff. of sensible heat over open water +Cd_atm_oce=1.0e-3 ! drag coefficient between atmosphere and water +Ce_atm_ice=1.75e-3 ! exchange coeff. of latent heat over ice +Ch_atm_ice=1.75e-3 ! exchange coeff. of sensible heat over ice +Cd_atm_ice=1.2e-3 ! drag coefficient between atmosphere and ice / &forcing_bulk AOMIP_drag_coeff=.false. ncar_bulk_formulae=.true. -ncar_bulk_z_wind=10.0 ! height at which wind forcing is located (CORE, JRA-do: 10m, JRA, NCEP:2m) -ncar_bulk_z_tair=10.0 ! height at which temp forcing is located (CORE, JRA-do: 10m, JRA, NCEP:2m) -ncar_bulk_z_shum=10.0 ! height at which humi forcing is located (CORE, JRA-do: 10m, JRA, NCEP:2m) - / &land_ice @@ -26,35 +21,32 @@ landice_end_mon=10 / &nam_sbc - nm_xwind_file = '/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/uas.' ! name of file with winds, if nm_sbc=2 - nm_ywind_file = '/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/vas.' ! name of file with winds, if nm_sbc=2 - nm_humi_file = '/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/huss.' ! name of file with humidity - nm_qsr_file = '/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/rsds.' ! name of file with solar heat - nm_qlw_file = '/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/rlds.' ! name of file with Long wave - nm_tair_file = '/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/tas.' ! name of file with 2m air temperature - nm_prec_file = '/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/prra.' ! name of file with total precipitation - nm_snow_file = '/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/prsn.' ! name of file with snow precipitation - nm_mslp_file = '/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/psl.' ! air_pressure_at_sea_level - nm_xwind_var = 'uas' ! name of variable in file with wind - nm_ywind_var = 'vas' ! name of variable in file with wind - nm_humi_var = 'huss' ! name of variable in file with humidity - nm_qsr_var = 'rsds' ! name of variable in file with solar heat - nm_qlw_var = 'rlds' ! name of variable in file with Long wave - nm_tair_var = 'tas' ! name of variable in file with 2m air temperature - nm_prec_var = 'prra' ! name of variable in file with total precipitation - nm_snow_var = 'prsn' ! name of variable in file with total precipitation - nm_mslp_var = 'psl' ! name of variable in file with air_pressure_at_sea_level - nm_nc_iyear = 1900 + nm_xwind_file = '/work/ollie/dsein/input/forcing/CORE2/u_10.' ! name of file with winds, if nm_sbc=2 + nm_ywind_file = '/work/ollie/dsein/input/forcing/CORE2/v_10.' ! name of file with winds, if nm_sbc=2 + nm_humi_file = '/work/ollie/dsein/input/forcing/CORE2/q_10.' ! name of file with humidity + nm_qsr_file = '/work/ollie/dsein/input/forcing/CORE2/ncar_rad.' ! name of file with solar heat + nm_qlw_file = '/work/ollie/dsein/input/forcing/CORE2/ncar_rad.' ! name of file with Long wave + nm_tair_file = '/work/ollie/dsein/input/forcing/CORE2/t_10.' ! name of file with 2m air temperature + nm_prec_file = '/work/ollie/dsein/input/forcing/CORE2/ncar_precip.' ! name of file with total precipitation + nm_snow_file = '/work/ollie/dsein/input/forcing/CORE2/ncar_precip.' ! name of file with snow precipitation + nm_mslp_file = '/work/ollie/dsein/input/forcing/CORE2/slp.' ! air_pressure_at_sea_level + nm_xwind_var = 'U_10_MOD' ! name of variable in file with wind + nm_ywind_var = 'V_10_MOD' ! name of variable in file with wind + nm_humi_var = 'Q_10_MOD' ! name of variable in file with humidity + nm_qsr_var = 'SWDN_MOD' ! name of variable in file with solar heat + nm_qlw_var = 'LWDN_MOD' ! name of variable in file with Long wave + nm_tair_var = 'T_10_MOD' ! name of variable in file with 2m air temperature + nm_prec_var = 'RAIN' ! name of variable in file with total precipitation + nm_snow_var = 'SNOW' ! name of variable in file with total precipitation + nm_mslp_var = 'SLP' ! name of variable in file with air_pressure_at_sea_level + nm_nc_iyear = 1948 nm_nc_imm = 1 ! initial month of time axis in netCDF nm_nc_idd = 1 ! initial day of time axis in netCDF nm_nc_freq = 1 ! data points per day (i.e. 86400 if the time axis is in seconds) - nm_nc_tmid = 0 ! 1 if the time stamps are given at the mid points of the netcdf file, 0 otherwise (i.e. 1 in CORE1, CORE2; 0 in JRA55) - l_xwind=.true. l_ywind=.true. l_humi=.true. l_qsr=.true. l_qlw=.true. l_tair=.true. l_prec=.true. l_mslp=.false. l_cloud=.false. l_snow=.true. - nm_runoff_file ='/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/CORE2_runoff.nc' + nm_nc_tmid = 1 ! 1 if the time stamps are given at the mid points of the netcdf file, 0 otherwise (i.e. 1 in CORE1, CORE2; 0 in JRA55) + l_xwind=.true., l_ywind=.true., l_humi=.true., l_qsr=.true., l_qlw=.true., l_tair=.true., l_prec=.true., l_mslp=.false., l_cloud=.false., l_snow=.true. + nm_runoff_file ='/work/ollie/dsein/input/forcing/CORE2/runoff.nc' runoff_data_source ='CORE2' !Dai09, CORE2 - !nm_runoff_file ='/work/ollie/qwang/FESOM2_input/mesh/CORE2_finaltopo_mean/forcing_data_on_grid/runoff_clim.nc' - !runoff_data_source ='Dai09' !Dai09, CORE2, JRA55 - !runoff_climatology =.true. - nm_sss_data_file ='/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/PHC2_salx.nc' + nm_sss_data_file ='/work/ollie/dsein/input/forcing/CORE2/PHC2_salx.nc' sss_data_source ='CORE2' / diff --git a/config/namelist.forcing.era5 b/config/namelist.forcing.era5 deleted file mode 100644 index c01ed1981..000000000 --- a/config/namelist.forcing.era5 +++ /dev/null @@ -1,58 +0,0 @@ -! This is the namelist file for forcing - -&forcing_exchange_coeff -Ce_atm_oce=1.75e-3 ! exchange coeff. of latent heat over open water -Ch_atm_oce=1.75e-3 ! exchange coeff. of sensible heat over open water -Cd_atm_oce=1.0e-3 ! drag coefficient between atmosphere and water -Ce_atm_ice=1.75e-3 ! exchange coeff. of latent heat over ice -Ch_atm_ice=1.75e-3 ! exchange coeff. of sensible heat over ice -Cd_atm_ice=1.2e-3 ! drag coefficient between atmosphere and ice -Swind =0.0 ! parameterization for coupled current feedback -/ - -&forcing_bulk -AOMIP_drag_coeff=.false. -ncar_bulk_formulae=.true. -ncar_bulk_z_wind=10.0 ! height at which wind forcing is located (CORE:10m, JRA:2m) -ncar_bulk_z_tair=2.0 ! height at which temp forcing is located (CORE:10m, JRA:2m) -ncar_bulk_z_shum=2.0 ! height at which humi forcing is located (CORE:10m, JRA:2m) - -/ - -&land_ice -use_landice_water=.false. -landice_start_mon=5 -landice_end_mon=10 -/ - -&nam_sbc - nm_xwind_file = '/mnt/lustre01/work/ba1138/a270099/era5/forcing/inverted/u.' ! name of file with winds, if nm_sbc=2 - nm_ywind_file = '/mnt/lustre01/work/ba1138/a270099/era5/forcing/inverted/v.' ! name of file with winds, if nm_sbc=2 - nm_humi_file = '/mnt/lustre01/work/ba1138/a270099/era5/forcing/inverted/q.' ! name of file with humidity - nm_qsr_file = '/mnt/lustre01/work/ba1138/a270099/era5/forcing/inverted/ssrd.' ! name of file with solar heat - nm_qlw_file = '/mnt/lustre01/work/ba1138/a270099/era5/forcing/inverted/strd.' ! name of file with Long wave - nm_tair_file = '/mnt/lustre01/work/ba1138/a270099/era5/forcing/inverted/t2m.' ! name of file with 2m air temperature - nm_prec_file = '/mnt/lustre01/work/ba1138/a270099/era5/forcing/inverted/rf.' ! name of file with total precipitation - nm_snow_file = '/mnt/lustre01/work/ba1138/a270099/era5/forcing/inverted/sf.' ! name of file with snow precipitation - nm_mslp_file = '/mnt/lustre01/work/ba1138/a270099/era5/forcing/inverted/sp.' ! air_pressure_at_sea_level - nm_xwind_var = 'u' ! name of variable in file with wind - nm_ywind_var = 'v' ! name of variable in file with wind - nm_humi_var = 'q' ! name of variable in file with humidity - nm_qsr_var = 'ssrd' ! name of variable in file with solar heat - nm_qlw_var = 'strd' ! name of variable in file with Long wave - nm_tair_var = 't2m' ! name of variable in file with 2m air temperature - nm_prec_var = 'rf' ! name of variable in file with total precipitation - nm_snow_var = 'sf' ! name of variable in file with total precipitation - nm_mslp_var = 'sp' ! name of variable in file with air_pressure_at_sea_level - nm_nc_iyear = 1900 - nm_nc_imm = 1 ! initial month of time axis in netCDF - nm_nc_idd = 1 ! initial day of time axis in netCDF - nm_nc_freq = 1 ! data points per day (i.e. 86400 if the time axis is in seconds) - nm_nc_tmid = 0 ! 1 if the time stamps are given at the mid points of the netcdf file, 0 otherwise (i.e. 1 in CORE1, CORE2; 0 in JRA55) - l_xwind=.true., l_ywind=.true., l_humi=.true., l_qsr=.true., l_qlw=.true., l_tair=.true., l_prec=.true., l_mslp=.false., l_cloud=.false., l_snow=.true. - nm_runoff_file ='/pool/data/AWICM/FESOM2/FORCING/CORE2/runoff.nc' - runoff_data_source ='CORE2' !Dai09, CORE2, JRA55 - !runoff_climatology =.true. ???? - nm_sss_data_file ='/pool/data/AWICM/FESOM2/FORCING/CORE2/PHC2_salx.nc' - sss_data_source ='CORE2' -/ diff --git a/config/namelist.forcing.ncep b/config/namelist.forcing.ncep deleted file mode 100644 index 7e7ee68ac..000000000 --- a/config/namelist.forcing.ncep +++ /dev/null @@ -1,55 +0,0 @@ -/bin/bash: This: cng_exchange_coeff -Ce_atm_oce=1.75e-3 ! exchange coeff. of latent heat over open water -Ch_atm_oce=1.75e-3 ! exchange coeff. of sensible heat over open water -Cd_atm_oce=1.0e-3 ! drag coefficient between atmosphere and water -Ce_atm_ice=1.75e-3 ! exchange coeff. of latent heat over ice -Ch_atm_ice=1.75e-3 ! exchange coeff. of sensible heat over ice -Cd_atm_ice=1.2e-3 ! drag coefficient between atmosphere and ice -Swind =0.0 ! parameterization for coupled current feedback -/ - -&forcing_bulk -AOMIP_drag_coeff=.false. -ncar_bulk_formulae=.true. -ncar_bulk_z_wind=2.0 ! height at which wind forcing is located (CORE, JRA-do: 10m, JRA, NCEP:2m) -ncar_bulk_z_tair=2.0 ! height at which temp forcing is located (CORE, JRA-do: 10m, JRA, NCEP:2m) -ncar_bulk_z_shum=2.0 ! height at which humi forcing is located (CORE, JRA-do: 10m, JRA, NCEP:2m) - -/ - -&land_ice -use_landice_water=.false. -landice_start_mon=5 -landice_end_mon=10 -/ - -&nam_sbc - nm_xwind_file = '/mnt/lustre01/work/ba1138/a270099/ncep/forcing/UGRD_10maboveground.flxf06.gdas.' ! name of file with winds, if nm_sbc=2 - nm_ywind_file = '/mnt/lustre01/work/ba1138/a270099/ncep/forcing/VGRD_10maboveground.flxf06.gdas.' ! name of file with winds, if nm_sbc=2 - nm_humi_file = '/mnt/lustre01/work/ba1138/a270099/ncep/forcing/SPFH_2maboveground.flxf06.gdas.' ! name of file with 2m specific humidity - nm_qsr_file = '/mnt/lustre01/work/ba1138/a270099/ncep/forcing/DSWRF_surface.flxf06.gdas.' ! name of file with solar heat - nm_qlw_file = '/mnt/lustre01/work/ba1138/a270099/ncep/forcing/DLWRF_surface.flxf06.gdas.' ! name of file with Long wave - nm_tair_file = '/mnt/lustre01/work/ba1138/a270099/ncep/forcing/TMP_2maboveground.flxf06.gdas.' ! name of file with 2m air temperature - nm_prec_file = '/mnt/lustre01/work/ba1138/a270099/ncep/forcing/RRATE_surface.flxf06.gdas.' ! name of file with rain fall - nm_snow_file = '/mnt/lustre01/work/ba1138/a270099/ncep/forcing/SRATE_surface.flxf06.gdas.' ! name of file with snow fall - nm_mslp_file = '/work/ollie/fkauker/fesom2/cfsr/' ! air_pressure_at_sea_level - nm_xwind_var = 'UGRD_10maboveground' ! name of variable in file with wind - nm_ywind_var = 'VGRD_10maboveground' ! name of variable in file with wind - nm_humi_var = 'SPFH_2maboveground' ! name of variable in file with humidity - nm_qsr_var = 'DSWRF_surface' ! name of variable in file with solar heat - nm_qlw_var = 'DLWRF_surface' ! name of variable in file with Long wave - nm_tair_var = 'TMP_2maboveground' ! name of variable in file with 2m air temperature - nm_prec_var = 'RRATE_surface' ! name of variable in file with total precipitation - nm_snow_var = 'SRATE_surface' ! name of variable in file with total precipitation - nm_mslp_var = '' ! name of variable in file with air_pressure_at_sea_level - nm_nc_iyear = 1970 - nm_nc_imm = 1 ! initial month of time axis in netCDF - nm_nc_idd = 1 ! initial day of time axis in netCDF - nm_nc_freq = 86400 ! data points per day (i.e. 86400 if the time axis is in seconds) - nm_nc_tmid = 0 ! 1 if the time stamps are given at the mid points of the netcdf file, 0 otherwise (i.e. 1 in CORE1, CORE2; 0 in JRA55) - l_xwind=.true., l_ywind=.true., l_humi=.true., l_qsr=.true., l_qlw=.true., l_tair=.true., l_prec=.true., l_mslp=.false., l_cloud=.false., l_snow=.true. - nm_runoff_file ='/pool/data/AWICM/FESOM2/FORCING/CORE2/runoff.nc' - runoff_data_source ='CORE2' !Dai09, CORE2, JRA55 - nm_sss_data_file ='/pool/data/AWICM/FESOM2/FORCING/CORE2/PHC2_salx.nc' - sss_data_source ='CORE2' -/ diff --git a/config/namelist.forcing_COREI b/config/namelist.forcing_COREI deleted file mode 100644 index 0e24bb196..000000000 --- a/config/namelist.forcing_COREI +++ /dev/null @@ -1,57 +0,0 @@ -! This is the namelist file for forcing - -&forcing_exchange_coeff -Ce_atm_oce=1.75e-3 ! exchange coeff. of latent heat over open water -Ch_atm_oce=1.75e-3 ! exchange coeff. of sensible heat over open water -Cd_atm_oce=1.0e-3 ! drag coefficient between atmosphere and water -Ce_atm_ice=1.75e-3 ! exchange coeff. of latent heat over ice -Ch_atm_ice=1.75e-3 ! exchange coeff. of sensible heat over ice -Cd_atm_ice=1.2e-3 ! drag coefficient between atmosphere and ice -/ - -&forcing_bulk -AOMIP_drag_coeff=.false. -ncar_bulk_formulae=.true. -ncar_bulk_z_wind=10.0 ! height at which wind forcing is located (CORE:10m, JRA:2m) -ncar_bulk_z_tair=10.0 ! height at which temp forcing is located (CORE:10m, JRA:2m) -ncar_bulk_z_shum=10.0 ! height at which humi forcing is located (CORE:10m, JRA:2m) - -/ - -&land_ice -use_landice_water=.false. -landice_start_mon=5 -landice_end_mon=10 -/ - -&nam_sbc - nm_xwind_file = '/work/ollie/clidyn/forcing/CORE1/u_10' ! name of file with winds, if nm_sbc=2 - nm_ywind_file = '/work/ollie/clidyn/forcing/CORE1/v_10' ! name of file with winds, if nm_sbc=2 - nm_humi_file = '/work/ollie/clidyn/forcing/CORE1/q_10' ! name of file with humidity - nm_qsr_file = '/work/ollie/clidyn/forcing/CORE1/ncar_rad' ! name of file with solar heat - nm_qlw_file = '/work/ollie/clidyn/forcing/CORE1/ncar_rad' ! name of file with Long wave - nm_tair_file = '/work/ollie/clidyn/forcing/CORE1/t_10' ! name of file with 2m air temperature - nm_prec_file = '/work/ollie/clidyn/forcing/CORE1/ncar_precip' ! name of file with total precipitation - nm_snow_file = '/work/ollie/clidyn/forcing/CORE1/ncar_precip' ! name of file with snow precipitation - nm_mslp_file = '/work/ollie/clidyn/forcing/CORE1/slp.' ! air_pressure_at_sea_level - nm_xwind_var = 'U_10_MOD' ! name of variable in file with wind - nm_ywind_var = 'V_10_MOD' ! name of variable in file with wind - nm_humi_var = 'Q_10_MOD' ! name of variable in file with humidity - nm_qsr_var = 'SWDN_MOD' ! name of variable in file with solar heat - nm_qlw_var = 'LWDN_MOD' ! name of variable in file with Long wave - nm_tair_var = 'T_10_MOD' ! name of variable in file with 2m air temperature - nm_prec_var = 'RAIN' ! name of variable in file with total precipitation - nm_snow_var = 'SNOW' ! name of variable in file with total precipitation - nm_mslp_var = 'SLP' ! name of variable in file with air_pressure_at_sea_level - nm_nc_iyear = 1948 - nm_nc_imm = 1 ! initial month of time axis in netCDF - nm_nc_idd = 1 ! initial day of time axis in netCDF - nm_nc_freq = 1 ! data points per day (i.e. 86400 if the time axis is in seconds) - nm_nc_tmid = 1 ! 1 if the time stamps are given at the mid points of the netcdf file, 0 otherwise (i.e. 1 in CORE1, CORE2; 0 in JRA55) - y_perpetual = .true. - l_xwind=.true., l_ywind=.true., l_humi=.true., l_qsr=.true., l_qlw=.true., l_tair=.true., l_prec=.true., l_mslp=.false., l_cloud=.false., l_snow=.true. - nm_runoff_file ='/work/ollie/dsein/input/forcing/CORE2/runoff.nc' - runoff_data_source ='CORE2' !Dai09, CORE2 - nm_sss_data_file ='/work/ollie/dsein/input/forcing/CORE2/PHC2_salx.nc' - sss_data_source ='CORE2' -/ diff --git a/config/namelist.ice b/config/namelist.ice old mode 100644 new mode 100755 index bcd86f145..4f5d512e5 --- a/config/namelist.ice +++ b/config/namelist.ice @@ -1,31 +1,24 @@ ! Ice namelist &ice_dyn -whichEVP=0 ! 0=standart; 1=mEVP; 2=aEVP -Pstar=30000.0 ! [N/m^2] -ellipse=2.0 -c_pressure=20.0 ! ice concentration parameter used in ice strength computation -delta_min=1.0e-11 ! [s^(-1)] -evp_rheol_steps=120 ! number of EVP subcycles -alpha_evp=250 ! constant that control numerical stability of mEVP. Adjust with resolution. -beta_evp=250 ! constant that control numerical stability of mEVP. Adjust with resolution. -c_aevp=0.15 ! a tuning constant in aEVP. Adjust with resolution. -Cd_oce_ice=0.0055 ! drag coef. oce - ice -ice_gamma_fct=0.5 ! smoothing parameter -ice_diff=0.0 ! diffusion to stabilize -theta_io=0.0 ! rotation angle -ice_ave_steps=1 ! ice step=ice_ave_steps*oce_step +whichEVP=0 +Pstar=30000.0 +delta_min=1.0e-11 +evp_rheol_steps=150 +Cd_oce_ice=0.0055 +ice_gamma_fct=0.5 +ice_diff=0.0 +theta_io=0.0 !0.436 +ice_ave_steps=1 !ice step=ice_ave_steps*oce_step / &ice_therm -Sice=4.0 ! Ice salinity 3.2--5.0 ppt. -h0=.5 ! Lead closing parameter [m] -emiss_ice=0.97 ! Emissivity of Snow/Ice, -emiss_wat=0.97 ! Emissivity of open water -albsn=0.81 ! Albedo: frozen snow -albsnm=0.77 ! melting snow -albi=0.7 ! frozen ice -albim=0.68 ! melting ice -albw=0.1 ! open water -con=2.1656 ! Thermal conductivities: ice; W/m/K -consn=0.31 ! snow +Sice=4.0 +h0=.5 +emiss_ice=0.97 +emiss_wat=0.97 +albsn=0.81 +albsnm=0.77 +albi=0.7 +albim=0.68 +albw=0.1 / diff --git a/config/namelist.icepack b/config/namelist.icepack deleted file mode 100644 index ed0dd4d4c..000000000 --- a/config/namelist.icepack +++ /dev/null @@ -1,146 +0,0 @@ -&env_nml ! In the original release these variables are defined in the icepack.settings - nicecat = 5 ! number of ice thickness categories - nfsdcat = 1 ! number of floe size categories - nicelyr = 4 ! number of vertical layers in the ice - nsnwlyr = 4 ! number of vertical layers in the snow - ntraero = 0 ! number of aerosol tracers (up to max_aero in ice_domain_size.F90) - trzaero = 0 ! number of z aerosol tracers (up to max_aero = 6) - tralg = 0 ! number of algal tracers (up to max_algae = 3) - trdoc = 0 ! number of dissolve organic carbon (up to max_doc = 3) - trdic = 0 ! number of dissolve inorganic carbon (up to max_dic = 1) - trdon = 0 ! number of dissolve organic nitrogen (up to max_don = 1) - trfed = 0 ! number of dissolved iron tracers (up to max_fe = 2) - trfep = 0 ! number of particulate iron tracers (up to max_fe = 2) - nbgclyr = 0 ! number of zbgc layers - trbgcz = 0 ! set to 1 for zbgc tracers (needs TRBGCS = 0 and TRBRI = 1) - trzs = 0 ! set to 1 for zsalinity tracer (needs TRBRI = 1) - trbri = 0 ! set to 1 for brine height tracer - trage = 0 ! set to 1 for ice age tracer - trfy = 0 ! set to 1 for first-year ice area tracer - trlvl = 0 ! set to 1 for level and deformed ice tracers - trpnd = 0 ! set to 1 for melt pond tracers - trbgcs = 0 ! set to 1 for skeletal layer tracers (needs TRBGCZ = 0) - ndtd = 1 ! dynamic time steps per thermodynamic time step -/ - -&grid_nml - kcatbound = 1 -/ - -&tracer_nml - tr_iage = .false. - tr_FY = .false. - tr_lvl = .false. - tr_pond_cesm = .false. - tr_pond_topo = .false. - tr_pond_lvl = .false. - tr_aero = .false. - tr_fsd = .false. -/ - -&thermo_nml - kitd = 1 - ktherm = 1 - conduct = 'bubbly' - a_rapid_mode = 0.5e-3 - Rac_rapid_mode = 10.0 - aspect_rapid_mode = 1.0 - dSdt_slow_mode = -5.0e-8 - phi_c_slow_mode = 0.05 - phi_i_mushy = 0.85 - ksno = 0.3 -/ - -&shortwave_nml - shortwave = 'ccsm3' - albedo_type = 'ccsm3' - albicev = 0.78 - albicei = 0.36 - albsnowv = 0.98 - albsnowi = 0.70 - albocn = 0.1 - ahmax = 0.3 - R_ice = 0. - R_pnd = 0. - R_snw = 1.5 - dT_mlt = 1.5 - rsnw_mlt = 1500. - kalg = 0.6 -/ - -&ponds_nml - hp1 = 0.01 - hs0 = 0. - hs1 = 0.03 - dpscale = 1.e-3 - frzpnd = 'hlid' - rfracmin = 0.15 - rfracmax = 1. - pndaspect = 0.8 -/ - -&forcing_nml - formdrag = .false. - atmbndy = 'default' - calc_strair = .true. - calc_Tsfc = .true. - highfreq = .false. - natmiter = 5 - ustar_min = 0.0005 - emissivity = 0.95 - fbot_xfer_type = 'constant' - update_ocn_f = .false. - l_mpond_fresh = .false. - tfrz_option = 'linear_salt' - oceanmixed_ice = .true. - wave_spec_type = 'none' -/ - -&dynamics_nml - kstrength = 1 - krdg_partic = 1 - krdg_redist = 1 - mu_rdg = 3 - Cf = 17. - P_star = 27000. - C_star = 20. -/ - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!! Icepack output namelist !!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -&nml_list_icepack -io_list_icepack = 'aicen ',1, 'm', 4, ! Sea ice concentration - 'vicen ',1, 'm', 4, ! Volume per unit area of ice - 'vsnon ',1, 'm', 4, ! Volume per unit area of snow - !'Tsfcn ',1, 'm', 4, ! Sea ice surf. temperature - !'iagen ',1, 'm', 4, ! Sea ice age - !'FYn ',1, 'm', 4, ! First year ice - !'lvln ',1, 'm', 4, ! Ridged sea ice area and volume - !'pond_cesmn',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness - !'pond_topon',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness - !'pond_lvln ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness - !'brinen ',1, 'm', 4, ! Volume fraction of ice with dynamic salt - !'qicen ',1, 'm', 4, ! Sea ice enthalpy - !'sicen ',1, 'm', 4, ! Sea ice salinity - !'qsnon ',1, 'm', 4, ! Snow enthalpy - ! Average over thicknes classes - !'aice ',1, 'm', 4, ! Sea ice concentration - !'vice ',1, 'm', 4, ! Volume per unit area of ice - !'vsno ',1, 'm', 4, ! Volume per unit area of snow - !'Tsfc ',1, 'm', 4, ! Sea ice surf. temperature - !'iage ',1, 'm', 4, ! Sea ice age - !'FY ',1, 'm', 4, ! First year ice - !'lvl ',1, 'm', 4, ! Ridged sea ice area and volume - !'pond_cesm ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness - !'pond_topo ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness - !'pond_lvl ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness - !'brine ',1, 'm', 4, ! Volume fraction of ice with dynamic salt - !'qice ',1, 'm', 4, ! Sea ice enthalpy - !'sice ',1, 'm', 4, ! Sea ice salinity - !'qsno ',1, 'm', 4, ! Snow enthalpy - ! Other variables - !'uvel ',1, 'm', 4, ! x-component of sea ice velocity - !'vvel ',1, 'm', 4, ! y-component of sea ice velocity -/ diff --git a/config/namelist.icepack.cesm.ponds b/config/namelist.icepack.cesm.ponds deleted file mode 100644 index 51aa33191..000000000 --- a/config/namelist.icepack.cesm.ponds +++ /dev/null @@ -1,144 +0,0 @@ -&env_nml ! In the original release these variables are defined in the icepack.settings - nicecat = 5 ! number of ice thickness categories - nfsdcat = 1 ! number of floe size categories - nicelyr = 4 ! number of vertical layers in the ice - nsnwlyr = 4 ! number of vertical layers in the snow - ntraero = 0 ! number of aerosol tracers (up to max_aero in ice_domain_size.F90) - trzaero = 0 ! number of z aerosol tracers (up to max_aero = 6) - tralg = 0 ! number of algal tracers (up to max_algae = 3) - trdoc = 0 ! number of dissolve organic carbon (up to max_doc = 3) - trdic = 0 ! number of dissolve inorganic carbon (up to max_dic = 1) - trdon = 0 ! number of dissolve organic nitrogen (up to max_don = 1) - trfed = 0 ! number of dissolved iron tracers (up to max_fe = 2) - trfep = 0 ! number of particulate iron tracers (up to max_fe = 2) - nbgclyr = 0 ! number of zbgc layers - trbgcz = 0 ! set to 1 for zbgc tracers (needs TRBGCS = 0 and TRBRI = 1) - trzs = 0 ! set to 1 for zsalinity tracer (needs TRBRI = 1) - trbri = 0 ! set to 1 for brine height tracer - trage = 0 ! set to 1 for ice age tracer - trfy = 0 ! set to 1 for first-year ice area tracer - trlvl = 0 ! set to 1 for level and deformed ice tracers - trpnd = 1 ! set to 1 for melt pond tracers - trbgcs = 0 ! set to 1 for skeletal layer tracers (needs TRBGCZ = 0) - ndtd = 1 ! dynamic time steps per thermodynamic time step -/ - -&grid_nml - kcatbound = 1 -/ - -&tracer_nml - tr_iage = .false. - tr_FY = .false. - tr_lvl = .false. - tr_pond_cesm = .true. - tr_pond_topo = .false. - tr_pond_lvl = .false. - tr_aero = .false. - tr_fsd = .false. -/ - -&thermo_nml - kitd = 1 - ktherm = 1 - conduct = 'bubbly' - a_rapid_mode = 0.5e-3 - Rac_rapid_mode = 10.0 - aspect_rapid_mode = 1.0 - dSdt_slow_mode = -5.0e-8 - phi_c_slow_mode = 0.05 - phi_i_mushy = 0.85 -/ - -&shortwave_nml - shortwave = 'dEdd' - albedo_type = 'ccsm3' - albicev = 0.78 - albicei = 0.36 - albsnowv = 0.98 - albsnowi = 0.70 - ahmax = 0.3 - R_ice = 0. - R_pnd = 0. - R_snw = 1.5 - dT_mlt = 1.5 - rsnw_mlt = 1500. - kalg = 0.6 -/ - -&ponds_nml - hp1 = 0.01 - hs0 = 0. - hs1 = 0.03 - dpscale = 1.e-3 - frzpnd = 'hlid' - rfracmin = 0.15 - rfracmax = 1. - pndaspect = 0.8 -/ - -&forcing_nml - formdrag = .false. - atmbndy = 'default' - calc_strair = .true. - calc_Tsfc = .true. - highfreq = .false. - natmiter = 5 - ustar_min = 0.0005 - emissivity = 0.95 - fbot_xfer_type = 'constant' - update_ocn_f = .false. - l_mpond_fresh = .false. - tfrz_option = 'linear_salt' - oceanmixed_ice = .true. - wave_spec_type = 'none' -/ - -&dynamics_nml - kstrength = 1 - krdg_partic = 1 - krdg_redist = 1 - mu_rdg = 3 - Cf = 17. - P_star = 27000. - C_star = 20. -/ - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!! Icepack output namelist !!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -&nml_list_icepack -io_list_icepack = 'aicen ',1, 'm', 4, ! Sea ice concentration - 'vicen ',1, 'm', 4, ! Volume per unit area of ice - 'vsnon ',1, 'm', 4, ! Volume per unit area of snow - !'Tsfcn ',1, 'm', 4, ! Sea ice surf. temperature - !'iagen ',1, 'm', 4, ! Sea ice age - !'FYn ',1, 'm', 4, ! First year ice - !'lvln ',1, 'm', 4, ! Ridged sea ice area and volume - !'pond_cesmn',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness - !'pond_topon',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness - !'pond_lvln ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness - !'brinen ',1, 'm', 4, ! Volume fraction of ice with dynamic salt - !'qicen ',1, 'm', 4, ! Sea ice enthalpy - !'sicen ',1, 'm', 4, ! Sea ice salinity - !'qsnon ',1, 'm', 4, ! Snow enthalpy - ! Average over thicknes classes - !'aice ',1, 'm', 4, ! Sea ice concentration - !'vice ',1, 'm', 4, ! Volume per unit area of ice - !'vsno ',1, 'm', 4, ! Volume per unit area of snow - !'Tsfc ',1, 'm', 4, ! Sea ice surf. temperature - !'iage ',1, 'm', 4, ! Sea ice age - !'FY ',1, 'm', 4, ! First year ice - !'lvl ',1, 'm', 4, ! Ridged sea ice area and volume - !'pond_cesm ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness - !'pond_topo ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness - !'pond_lvl ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness - !'brine ',1, 'm', 4, ! Volume fraction of ice with dynamic salt - !'qice ',1, 'm', 4, ! Sea ice enthalpy - !'sice ',1, 'm', 4, ! Sea ice salinity - !'qsno ',1, 'm', 4, ! Snow enthalpy - ! Other variables - !'uvel ',1, 'm', 4, ! x-component of sea ice velocity - !'vvel ',1, 'm', 4, ! y-component of sea ice velocity -/ diff --git a/config/namelist.io b/config/namelist.io deleted file mode 100644 index 0a3270c4a..000000000 --- a/config/namelist.io +++ /dev/null @@ -1,45 +0,0 @@ -&diag_list -ldiag_solver =.false. -lcurt_stress_surf=.false. -ldiag_curl_vel3 =.false. -ldiag_energy =.false. -ldiag_salt3D =.false. -ldiag_dMOC =.false. -ldiag_DVD =.false. -ldiag_forc =.false. -/ - -&nml_listsize -io_listsize=100 !number of streams to allocate. shallbe large or equal to the number of streams in &nml_list -/ - -! for sea ice related variables use_ice should be true, otherewise there will be no output -! for 'curl_surf' to work lcurt_stress_surf must be .true. otherwise no output -! for 'fer_C', 'bolus_u', 'bolus_v', 'bolus_w', 'fer_K' to work Fer_GM must be .true. otherwise no output -! 'otracers' - all other tracers if applicable -! for 'dMOC' to work ldiag_dMOC must be .true. otherwise no output -&nml_list -io_list = 'sst ',1, 'm', 4, - 'sss ',1, 'm', 4, - 'ssh ',1, 'm', 4, - 'uice ',1, 'm', 4, - 'vice ',1, 'm', 4, - 'a_ice ',1, 'm', 4, - 'm_ice ',1, 'm', 4, - 'm_snow ',1, 'm', 4, - 'MLD1 ',1, 'm', 4, - 'MLD2 ',1, 'm', 4, - 'tx_sur ',1, 'm', 4, - 'ty_sur ',1, 'm', 4, - 'temp ',1, 'y', 4, - 'salt ',1, 'y', 8, - 'N2 ',1, 'y', 4, - 'Kv ',1, 'y', 4, - 'u ',1, 'y', 4, - 'v ',1, 'y', 4, - 'w ',1, 'y', 4, - 'Av ',1, 'y', 4, - 'bolus_u ',1, 'y', 4, - 'bolus_v ',1, 'y', 4, - 'bolus_w ',1, 'y', 4, -/ diff --git a/config/namelist.oce b/config/namelist.oce index af71c7741..6c89715f4 100644 --- a/config/namelist.oce +++ b/config/namelist.oce @@ -2,40 +2,29 @@ &oce_dyn C_d=0.0025 ! Bottom drag, nondimensional -gamma0=0.003 ! [m/s], backgroung viscosity= gamma0*len, it should be as small as possible (keep it < 0.01 m/s). -gamma1=0.1 ! [nodim], for computation of the flow aware viscosity -gamma2=0.285 ! [s/m], is only used in easy backscatter option -Div_c=.5 ! the strength of the modified Leith viscosity, nondimensional, 0.3 -- 1.0 -Leith_c=.05 ! the strength of the Leith viscosity -visc_option=5 ! 1=Harmonic Leith parameterization; - ! 2=Laplacian+Leith+biharmonic background - ! 3=Biharmonic Leith parameterization - ! 4=Biharmonic flow aware - ! 5=Kinematic (easy) Backscatter - ! 6=Biharmonic flow aware (viscosity depends on velocity Laplacian) - ! 7=Biharmonic flow aware (viscosity depends on velocity differences) - ! 8=Dynamic Backscatter -easy_bs_return= 1.5 ! coefficient for returned sub-gridscale energy, to be used with visc_option=5 (easy backscatter) A_ver= 1.e-4 ! Vertical viscosity, m^2/s +laplacian=.false. ! Use Laplacian viscosity +A_hor=0. ! 500. ! Background horizontal viscosity +A_hor_max=0. ! 8000. ! Maximum viscosity allowed (to limit Smag and Leith contributions when they are too large +Div_c=.5 ! 0.35 ! Modified Leith viscosity, nondimensional, 0.3 -- 1.0 +Leith_c=.05 ! The strength of the Leith viscosity +tau_c= 0. ! 1.5 !0.2 !1.5 ! Controls the strength of filters (1.5 and 0.2 for dt=1min and 15min, respectively) +Smag_c=0. ! 0.2 Smagorinsky viscosity, nondimensional, 0.1 --0.2 +biharmonic=.false. ! Use biharmonic viscosity +Abh0=0. ! 1.e12 ! Biharmonic viscosity, m^4/s scale_area=5.8e9 ! Visc. and diffus. are for an element with scale_area mom_adv=2 ! 1=vector CV, p1 vel, 2=sca. CV, 3=vector inv. free_slip=.false. ! Switch on free slip i_vert_visc=.true. w_split=.false. -w_max_cfl=1.0 ! maximum allowed CFL criteria in vertical (0.5 < w_max_cfl < 1.) ! in older FESOM it used to be w_exp_max=1.e-3 -SPP=.false. ! Salt Plume Parameterization +w_exp_max=1.e-3 +SPP=.false. ! Salt Plume Parameterization Fer_GM=.true. ! to swith on/off GM after Ferrari et al. 2010 -K_GM_max = 2000.0 ! max. GM thickness diffusivity (m2/s) -K_GM_min = 2.0 ! max. GM thickness diffusivity (m2/s) -K_GM_bvref = 2 ! def of bvref in ferreira scaling 0=srf,1=bot mld,2=mean over mld,3=weighted mean over mld -K_GM_rampmax = -1.0 ! Resol >K_GM_rampmax[km] GM on -K_GM_rampmin = -1.0 ! Resol TB04 mixing -momix_lat = -50.0 ! latitidinal treshhold for TB04, =90 --> global -momix_kv = 0.01 ! PP/KPP, mixing coefficient within MO length -use_instabmix = .true. ! enhance convection in case of instable stratification -instabmix_kv = 0.1 -use_windmix = .false. ! enhance mixing trough wind only for PP mixing (for stability) -windmix_kv = 1.e-3 -windmix_nl = 2 - -smooth_bh_tra =.false. ! use biharmonic diffusion (filter implementation) for tracers -gamma0_tra = 0.0005 ! gammaX_tra are analogous to those in the dynamical part -gamma1_tra = 0.0125 -gamma2_tra = 0. - -diff_sh_limit=5.0e-3 ! for KPP, max diff due to shear instability -Kv0_const=.true. +diff_sh_limit=0.05 !5.0e-3 ! for KPP, max diff due to shear instability +Kv0_const=.false. double_diffusion=.false. ! for KPP,dd switch K_ver=1.0e-5 K_hor=3000. @@ -70,16 +45,8 @@ balance_salt_water =.true. ! balance virtual-salt or freshwater flux or not clim_relax=0.0 ! 1/s, geometrical information has to be supplied ref_sss_local=.true. ref_sss=34. -i_vert_diff =.true. ! true -tra_adv_hor ='MFCT' !'MUSCL', 'UPW1' -tra_adv_ver ='QR4C' !'QR4C', 'CDIFF', 'UPW1' -tra_adv_lim ='FCT' !'FCT', 'NONE' (default) -tra_adv_ph = 1. ! a parameter to be used in horizontal advection (for MUSCL it is the fraction of fourth-order contribution in the solution) -tra_adv_pv = 1. ! a parameter to be used in horizontal advection (for QR4C it is the fraction of fourth-order contribution in the solution) -! Implemented trassers (3d restoring): -! 301 - Fram strait. -! 302 - Bering Strait -! 303 - BSO +i_vert_diff=.true. ! true +tracer_adv =2 ! 1=MUSCL, 2=MUSCL+FCT num_tracers=2 !number of all tracers tracer_ID =0,1 !their IDs (0 and 1 are reserved for temperature and salinity) / diff --git a/config/namelist.oce.toy_soufflet b/config/namelist.oce.toy_soufflet deleted file mode 100644 index f367c9f0c..000000000 --- a/config/namelist.oce.toy_soufflet +++ /dev/null @@ -1,83 +0,0 @@ -! The namelist file for the finite-volume ocean model - -&oce_dyn -state_equation=0 ! 1 - full equation of state, 0 - linear equation of state -C_d=0.0025 ! Bottom drag, nondimensional -gamma0=0.00 ! [m/s], backgroung viscosity= gamma0*len, it should be as small as possible (keep it < 0.01 m/s). -gamma1=0.002 ! [nodim], for computation of the flow aware viscosity -gamma2=0.02 ! [s/m], is only used in easy backscatter option -Div_c=.5 ! the strength of the modified Leith viscosity, nondimensional, 0.3 -- 1.0 -Leith_c=.5 ! the strength of the Leith viscosity -visc_option=5 ! 1=Harmonic Leith parameterization; - ! 2=Laplacian+Leith+biharmonic background - ! 3=Biharmonic Leith parameterization - ! 4=Biharmonic flow aware - ! 5=Easy Backscatter - ! 6=Biharmonic flow aware (viscosity depends on velocity Laplacian) - ! 7=Biharmonic flow aware (viscosity depends on velocity differences) -easy_bs_return= 1.5 ! coefficient for returned sub-gridscale energy, to be used with visc_option=5 (easy backscatter) -A_ver= 1.e-4 ! Vertical viscosity, m^2/s -scale_area=5.8e9 ! Visc. and diffus. are for an element with scale_area -mom_adv=2 ! 1=vector CV, p1 vel, 2=sca. CV, 3=vector inv. -free_slip=.false. ! Switch on free slip -i_vert_visc=.true. -w_split=.false. -w_exp_max=1.e-3 -SPP=.false. ! Salt Plume Parameterization -Fer_GM=.false. ! to swith on/off GM after Ferrari et al. 2010 -K_GM_max = 3000.0 ! max. GM thickness diffusivity (m2/s) -K_GM_min = 2.0 ! max. GM thickness diffusivity (m2/s) -K_GM_bvref = 2 ! def of bvref in ferreira scaling 0=srf,1=bot mld,2=mean over mld,3=weighted mean over mld -K_GM_rampmax = 40.0 ! Resol >K_GM_rampmax[km] GM on -K_GM_rampmin = 30.0 ! Resol TB04 mixing -momix_lat = -50.0 ! latitidinal treshhold for TB04, =90 --> global -momix_kv = 0.01 ! PP/KPP, mixing coefficient within MO length -use_instabmix = .true. ! enhance convection in case of instable stratification -instabmix_kv = 0.1 -use_windmix = .false. ! enhance mixing trough wind only for PP mixing (for stability) -windmix_kv = 1.e-3 -windmix_nl = 2 - -diff_sh_limit=5.0e-3 ! for KPP, max diff due to shear instability -Kv0_const=.false. -double_diffusion=.false. ! for KPP,dd switch -K_ver=1.0e-5 -K_hor=10. -surf_relax_T=0.0 -surf_relax_S=0.0 ! 50m/300days 6.43e-07! m/s 10./(180.*86400.) -balance_salt_water =.false. ! balance virtual-salt or freshwater flux or not -clim_relax=0.0 ! 1/s, geometrical information has to be supplied -ref_sss_local=.true. -ref_sss=34. -i_vert_diff=.true. ! true -tracer_adv =2 ! 1=MUSCL, 2=MUSCL+FCT -! Implemented trassers (3d restoring): -! 301 - Fram strait. -! 302 - Bering Strait -! 303 - BSO -num_tracers=2 !number of all tracers -tracer_ID =0,1 !their IDs (0 and 1 are reserved for temperature and salinity) -/ - -&oce_init3d ! initial conditions for tracers -n_ic3d = 2 ! number of tracers to initialize -idlist = 1, 0 ! their IDs (0 is temperature, 1 is salinity, etc.). The reading order is defined here! -filelist = 'phc3.0_winter.nc', 'phc3.0_winter.nc' ! list of files in ClimateDataPath to read (one file per tracer), same order as idlist -varlist = 'salt', 'temp' ! variables to read from specified files -t_insitu = .true. ! if T is insitu it will be converted to potential after reading it -/ diff --git a/docs/.gitkeep b/docs/.gitkeep new file mode 100644 index 000000000..e69de29bb diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 000000000..9e23d16d4 --- /dev/null +++ b/docs/README.md @@ -0,0 +1,227 @@ +FESOM2 tutorial +============== + +Very fast version +---------------- +```bash +git clone https://gitlab.dkrz.de/FESOM/fesom2.git fesom2 +cd fesom2 +bash -l configure.sh +``` + +create file fesom.clock in the output directory with the following content: + +```bash + 0 1 1948 + 0 1 1948 +``` + +```bash +cd ../bin +sbatch job_ollie +``` + +Longer version +------------- + +First thing is to checkout FESOM 2 code from the repository. Now it is located at DKRZ gitlab (https://gitlab.dkrz.de/). You have to have an active DKRZ account (more information on how to register [here](https://www.dkrz.de/up/my-dkrz/getting-started/account/DKRZ-user-account)). Before your account can be added to the members of the project you have to at least once log in to https://gitlab.dkrz.de/ with your DKRZ account so that it appears in the GitLab data base. To be added as a member of the FESOM project on GitLab you have to send an email to Dmitry Sidorenko (dmitry.sidorenko@awi.de) with the request. Please make sure that you are able to login to https://gitlab.dkrz.de/ before sending the request. + +The project with FESOM2 is located here: +https://gitlab.dkrz.de/FESOM/fesom2/ + +Clone the repository with git command: + +```bash +git clone https://gitlab.dkrz.de/FESOM/fesom2.git +``` +The repository contains model code and two additional libraries (`Metis` and `Parms`) necessary for running FESOM2. To build FESOM2 executable one have to compile `Parms` library and the code of the model (`src` folder). In order to build executable that is used for model domain partitioning (distribution of the model mesh between CPUs) one have to compile `Metis` library and also some code located in the `src` directory. The first step of building model executable is usually done automatically with the use of CMake, but it will work only on supported platforms (ollie, DKRZ, HLRN, and HAZELHEN). To build executable for partitioning and model executable on other, unsupported, platforms you can still use good old Makefiles for now, but it might change in the future in favor of complete CMake based build process. Both ways will be explained below. + +#### Build model executable with Cmake (default and recommended) + +Go to the `fesom2` folder and execute: + +```bash +bash -l configure.sh +``` +In the best case scenario, your platform will be recognized and the `Parms` library and model executable will be built and copied to the `bin` directory. If it does not work - try to use `make` (see below). + +#### Build partitioner executable with make (the only way for now) + +First, build `Metis` library. In the ideal case, the only things you have to do is: + +```bash +cd lib/metis-5.1.0 +make clean +make install +``` + +However, you might need modification of the build options in your `Makefile`. The `Makefile` consist of the two parts - generic one contained in the `Makefile` itself and the `Makefile.in` that have all platform/compiler specific options and is "imported" during the `make` command execution. There are several `Makefile.in_*` files present, and you have to copy the one that is suitable for your platform into the `Makefile.in`. + +After successful compilation of `Metis` you can build partitioner executable: +```bash +cd ../src/ +make run_ini +``` +The `Makefiles` have the same structure, and you might need to replace default `Makefile.ini` with the one that is suitable for your platform. + +#### Build model executable with make (not recommended, but sometimes the only way) + +If Cmake fails, your platform is not supported, or you would like to do something crazy, you still can use make. +First, we have to build `Parms` library: + +```bash +cd ../parms/ +make cleanall +make +``` +note the `cleanall` instead of usual `clean`. + +To build model executable: +```bash +cd ../../src/ +make clean +make +``` + +Please see note related to the Makefiles in the previous section. + +Preparing the run +---------------- + +You have to do several basic things in order to prepare the run. First, create a directory where results will be stored. Usually, it is created in the model root directory: + +```bash +mkdir results +``` + +you might make a link to some other directory located on the part of the system where you have a lot of storage. In the `results` directory, you have to create `runid.clock` file, where `runid` is usually `fesom`, so the file is most often named `fesom.clock`. Inside the file you have to put two identical lines: +``` +0 1 1948 +0 1 1948 +``` +the meaning of this lines will be explained later. + +The next step is to make some changes in the model configuration. All runtime options can be set in the namelists that are located in the `config` directory: +```bash +cd ../config/ +``` + +There are four configuration files, but we are only interested in the `namelist.config` for now. The options that you might want to change for your first FESOM2 run are: + +* `run_length` length of the model run in `run_length_unit` (see below) +* `run_length_unit` units of the `run_length`. Can be `y`(year), `m`(month), `d`(days), `s`(model steps) +* `MeshPath` - path to the mesh you would like to use +* `ClimateDataPath` - path to the file with model temperature and salinity initial conditions +* `ForcingDataPath` - path to the forcing data + +Running mesh partitioner +----------------------- +You have to do this step only if your mesh does not have partitioning for the desired amount of CPU yet. You can understand if the partitioning exists by the presence of the `dist_XXXX` folder in the folder with your mesh, where `XXX` is the number of CPUs. If the folder contains files with partitioning, you can just skip to the next step, otherwise see instructions in this section. + +Partitioning is going to split your mesh into pieces that correspond to the number of CPUs you going to request. Now FESOM2 scales until 300 nodes per CPU, further increase in the amount of CPU will probably have relatively small effect. + +In order to tell the partitioner how many CPUs you need the partitioning for, one has to edit `&machine` section in the `namelist.config` file. There are two options: `n_levels` and `n_part`. FESOM mesh can be partitioned with use of several hierarchy levels and `n_levels` define the number of levels while `n_part` the number of partitions on each hierarchy level. The simplest case is to use one level and `n_part` just equal to the number of CPUs: +```bash +n_levels=1 +n_part= 288 +``` +If you would like to use more level, note that the product of levels should be equal to the number of CPUs, so for three levels and 288 CPUs: +```bash +n_levels=3 +n_part= 2, 4, 36 +``` + +Then change to the `work` directory. You should find several batch scripts that are used to submit model jobs to HPC machines. The scripts also link `fvom_ini.x` executable to the `work` directory and copy namelists with configurations from `config` folder. **NOTE, model executable, configuration namelists and job script have to be located in the same directory (usually `work`)**. + +If you are working on AWI's `ollie` supercomputer, you have to use `job_ini_ollie`, in other case use the job script for your specific HPC platform, or try to modify one of the existing ones. + +On `ollie` the submission of your partitioning job is done by executing the following command: +```bash +sbatch job_ini_ollie +``` +The job is then submitted to the supercomputer. In order to check the status of your job on `ollie` you can execute: +```bash +squeue -u yourusername +``` + + +Running the model +---------------- +Change to the `work` directory. You should find several batch scripts that are used to submit model jobs to HPC machines. The scripts also link `fesom.x` executable to the `work` directory and copy namelists with configurations from `config` folder. **NOTE, model executable, configuration namelists and job script have to be located in the same directory (usually `work`)**. If you are working on AWI's `ollie` supercomputer, you have to use `job_ollie`, in other case use the job script for your specific HPC platform, or try to modify one of the existing ones. + +On `ollie` the submission of your job is done by executing the following command: +```bash +sbatch job_ollie +``` +The job is then submitted to the supercomputer. In order to check the status of your job on `ollie` you can execute: +```bash +squeue -u yourusername +``` + +Results of the model run should appear in the `results` directory that you have specified in the `namelist.config`. After the run is finished the `fesom.clock`file (or if you change your `runid`, `runid.clock`) will be updated with information about the time of your run's end, that allows running the next time portion of the model experiment by just resubmitting the job with `sbatch job_ollie`. + + +The clock file +---------------- + +The clock file is usually located in your output directory (e.g. `results`) and controls the time. +At the start of a new experiment that we want to be initialized from climatology (a so-called cold start), +the `fesom.clock` file would usually look like this +``` +0 1 1948 +0 1 1948 +``` +In this example, 1948 is the first available year of the atmospheric `CORE2` forcing. The two identical +lines tell the model that this is the start of the experiment and that there is no restart file to be read. + +Let's assume that we run the model with a timestep of 30 minutes (= 1800 seconds) for a full year (1948). +After the run is successfully finished, the clock file will then automatically be updated and look like this: +``` +84600.0 365 1948 +0.0 1 1949 +``` +where the first row is the second last time step of the model, and the second row gives the time where the simulation +is to be continued. The first row indicates that the model ran for 365 days (in 1948) and 84600 seconds, which is `1 day - 1 FESOM timestep` +in seconds. In the next job, FESOM2 will look for restart files for the year 1948 and continue the simulation at the 1st of January in 1949. + +Since 1948 is a leap year (366 days), this is an exceptional case and the `fesom.clock` file after two full years +(1948--1949) would look like this: +``` +84600.0 364 1949 +0.0 1 1950 +``` +Note that dependent on the forcing data set (using a different calendar), a year could only have 360 days. + +Tricking FESOM2 into accepting existing restart files +---------------- + +The simple time management of FESOM allows to easily trick FESOM to accept existing restart files. Let's assume that you have performed a full `CORE2` cycle until the year 2009 and you want +to perform a second cycle, restarting from the last year of the first cycle. This can be done by (copying and) +renaming the last year into: +```bash +mv fesom.2009.ice.nc fesom.1947.ice.nc +mv fesom.2009.oce.nc fesom.1947.oce.nc +``` +By changing the clock file into +``` +84600.0 364 1947 +0.0 1 1948 +``` +the model will then restart from the last year of the first cycle, but using CORE2 forcing from 1948 onwards. + +Model spinup / Cold start at higher resolutions +---------------- + +Cold starting the model at high mesh resolutions with standard values for timestep and viscosity will lead to instabilities that cause the model to crash. If no restart files are available and a spinup has to be performed, the following changes should be made for the first month long simulation and then taken back gradually over the next 6-8 months: +In config.namelist set: +``` +step_per_day=720 +``` +In namelist.oce set: +``` +Div_c=5 +Leith_c=.5 +``` +After one month change one of the parameters to more standard values. Increase the timestep gradually. Very highly resolved meshes may require an inital timestep of one instead of two minutes. + + diff --git a/docs/convert_grid_to_nc.md b/docs/convert_grid_to_nc.md new file mode 100644 index 000000000..f1223163a --- /dev/null +++ b/docs/convert_grid_to_nc.md @@ -0,0 +1,65 @@ +Convert grid to netCDF that CDO understands +=========================================== + +We are going to use spheRlab for conversion. You have to have R already installed. + +Clone spheRlab + +```bash +git clone https://github.com/FESOM/spheRlab.git spheRlab +``` +Build package: +```bash +cd spheRlab/ +R CMD build spheRlab +``` +Make sure you have cdo installed (`cdo -V`) and launch R (type `R`). +Install the package: +```R +R>install.packages("spheRlab_1.1.0.tar.gz",repos=NULL) +``` +If you don;t have netCDF library installed, you also have to do: + +```R +R>install.packages("ncdf4") +``` + +Load libraries: +```R +R>library(spheRlab) +R>ibrary(ncdf4) +``` +You can get help (for any function) by typing, e.g.: +```R +R>?sl.grid.writeCDO +``` + +Define path to the mesh +```R +R>meshpath="/work/ollie/dsidoren/input/fesom2.0/meshes/mesh_CORE2_final/" +``` +Read the grid in to R structure (the arguments `rot` etc. might be different for different meshes, but this is the standard): +For rotated meshes: +```R +R>grid = sl.grid.readFESOM(griddir=meshpath,rot=TRUE,rot.invert=TRUE,rot.abg=c(50,15,-90)) +``` +For unrotated meshes: +```R +R>grid = sl.grid.readFESOM(griddir=meshpath,rot=FALSE,rot.invert=FALSE,rot.abg=c(0,0,0), threeD=FALSE) +``` +Define path to the output file: +```R +R>ofile = paste0(meshpath, "sl.grid.CDO", , sep = "") +``` +Directrly write netCDF file with mesh description: +```R +R>sl.grid.writeCDO(grid, ofile=ofile, netcdf=TRUE, depth=FALSE) +``` + +Conservative remapping with cdo (interpolate topography to mesh) +--------------------------------------------------------------- +```bash +$bash> export MESHPATH=/work/ollie/dsidoren/input/fesom2.0/meshes/mesh_CORE2_final/ +$bash> export DATAPATH=/work/ollie/dsidoren/ETOPO5/etopo5_lonlat.nc +$bash> cdo remapycon,$MESHPATH/sl.grid.CDO.nc -selname,topo $DATAPATH $MESHPATH/topo.nc +``` \ No newline at end of file diff --git a/docs/initial_conditions.md b/docs/initial_conditions.md new file mode 100644 index 000000000..6c82b87e9 --- /dev/null +++ b/docs/initial_conditions.md @@ -0,0 +1,66 @@ +## Initial conditions in FESOM2 + +Initial conditions are loaded from netCDF file (or files) that contain values on regular grid. + +### In the namelist.oce + +One have to specify several parameters in the `namelist.oce`. The section of the `namelist.oce` might look like this: + +```bash +&oce_init3d ! initial conditions for tracers +n_ic3d = 2 ! number of tracers to initialize +idlist = 1, 0 ! their IDs (0 is temperature, 1 is salinity, etc.). The reading order is defined here! +filelist = 'phc3.0_winter.nc', 'phc3.0_winter.nc' ! list of files in ClimateDataPath to read (one file per tracer), same order as idlist +varlist = 'salt', 'temp' ! variables to read from specified files +t_insitu = .true. ! if T is insitu it will be converted to potential after reading it +``` + +* **n_ic3d** - how many tracers you want to initialise. As a minimum you have to initialise temperature and salinity. They have reserved id's 0 and 1 respectivelly (see `idlist` below). In this example only two tracers (temperature and salinity) are initialised. +* **idlist** - IDs of tracers. In this variable you define the reading order. Here we on purpose change the order of temperature and salinity to demonstrate that the order can be arbitrary. Once again remember that ID 0 and 1 are reserved for temperature and salinity respectively. +* **filelist** - coma separated list of files (each in qoutation marks) that contain initial conditions (see the section below about requirements to the file format). The path to the folder with this files is defined in `namelist.config` (`ClimateDataPath` variable). In this case the file `phc3.0_winter.nc` is the same for temperature and salinity since it contains both variables. +* **varlist** - names of the variables in the netCDF files specified above. Note again the order of the variables in the example, it can be arbitrary and in this case temperature comes after salinity. +* **t_insitu** - most of climatologies are distributed with *in situ* temperature, while model needs potential temperature. This flag allows to do the conversion (UNESCO equation) on the fly. + +### netCDF files for initial conditions + +The netCDF files have to satisfy the following criteria: + +* shoudl have dimentions named lon/longitude/LON , lat/latitude/LAT and depth +* should have variables named lon/longitude/LON , lat/latitude/LAT and depth +* lon/lat dimentions should be one dimentional (e.g `lon(lon)`) +* each variable with initial conditions should have only three dimentions (e.g. `temp(depth, lat, lon)`) +* The fields should start from 0th meridian and longitudes should have values from 0 to 360 +* the missing values should have values larger than 1e11 + +The file that would be read potentially without problems can be created with the following python code (variables `lat`,`lon_reshaped`, `depth`, `salt_reshaped`, `temp_reshaped` should be prepeared from the original file): + +```python +from netCDF4 import Dataset + +fw = Dataset('woa18_netcdf.nc', 'w', ) + +fw.createDimension('time', 366) +fw.createDimension('lat', lat.shape[0]) +fw.createDimension('lon', lon_reshaped.shape[0]) +fw.createDimension('depth', depth.shape[0]) + +latitude = fw.createVariable('lat', 'd', ('lat',)) +latitude[:] = lat[:] + +longitude = fw.createVariable('lon', 'd', ('lon',)) +longitude[:] = lon_reshaped[:] + +ddepth = fw.createVariable('depth', 'd', ('depth',)) +ddepth[:] = depth[:] + +salinity = fw.createVariable('salt','d', ('depth', 'lat', 'lon'), fill_value= 1e+20) +salinity[:] = salt_reshaped[:] +salinity.missing_value = 1e+20 + +temperature = fw.createVariable('temp','d', ('depth', 'lat', 'lon'), fill_value= 1e+20) +temperature[:] = temp_reshaped[:] +temperature.missing_value = 1e+20 +``` + +We will try to provide convertion instructions in the form of jupyter notebooks to all files with initial conditions. + diff --git a/env.sh b/env.sh index f568651e3..57ffd1874 100755 --- a/env.sh +++ b/env.sh @@ -37,16 +37,8 @@ elif [[ $LOGINHOST =~ \.hww\.de$ ]] || [[ $LOGINHOST =~ ^nid[0-9]{5}$ ]]; then STRATEGY="hazelhen.hww.de" elif [[ $LOGINHOST =~ \.jureca$ ]]; then STRATEGY="jureca" -elif [[ $LOGINHOST = ubuntu ]]; then - STRATEGY="ubuntu" -elif [[ $LOGINHOST = bsc ]]; then - STRATEGY="bsc" -elif [[ $LOGINHOST =~ ^juwels[0-9][0-9].ib.juwels.fzj.de$ ]]; then +elif [[ $LOGINHOST =~ ^juwels[0-9]+\.fz\-juelich\.de$ ]]; then STRATEGY="juwels" -elif [[ $LOGINHOST =~ ^jwlogin[0-9][0-9].juwels$ ]]; then - STRATEGY="juwels" -elif [[ $LOGINHOST =~ ^cc[a-b]+-login[0-9]+\.ecmwf\.int$ ]]; then - STRATEGY="ecaccess.ecmwf.int" else echo "can not determine environment for host: "$LOGINHOST [ $BEING_EXECUTED = true ] && exit 1 diff --git a/env/bsc/shell b/env/bsc/shell deleted file mode 100644 index a5ccfb77a..000000000 --- a/env/bsc/shell +++ /dev/null @@ -1,7 +0,0 @@ - -module load intel/2017.4 impi/2017.4 mkl/2017.4 bsc/1.0 netcdf/4.2 - -export FC=mpiifort CC=mpiicc CXX=mpiicpc - - - diff --git a/env/ecaccess.ecmwf.int/shell b/env/ecaccess.ecmwf.int/shell deleted file mode 100644 index 743116a12..000000000 --- a/env/ecaccess.ecmwf.int/shell +++ /dev/null @@ -1,11 +0,0 @@ -export PATH=/home/rd/natr/cmake-3.11.2-Linux-x86_64/bin:$PATH - -module unload cray-hdf5 -module load cray-netcdf -module load cray-hdf5 - -#export CRAYPE_LINK_TYPE=dynamic - -# enable full MPI thread support level (MPI_THREAD_MULTIPLE) -export MPICH_MAX_THREAD_SAFETY=multiple # to also switch to an alternative (probably with faster locking) multi threading implementation of the cray-mpich library, use the compiler flag -craympich-mt -export FC=ftn CC=cc CXX=CC diff --git a/env/juwels/shell b/env/juwels/shell index 0b5451c82..833976b88 100644 --- a/env/juwels/shell +++ b/env/juwels/shell @@ -1,22 +1,10 @@ -########## -module --force purge -module use /gpfs/software/juwels/otherstages -module load Stages/2019a -module load StdEnv -# For intel MPI -#module load Intel/2019.3.199-GCC-8.3.0 IntelMPI/2018.5.288 imkl/2019.3.199 -#export FC=mpiifort CC=mpiicc CXX=mpiicpc +# make the contents as shell agnostic as possible so we can include them with bash, zsh and others -# For ParaStation MPI -module load Intel/2019.3.199-GCC-8.3.0 ParaStationMPI/5.4 imkl/2019.5.281 -export FC=mpifort CC=mpicc CXX=mpicxx +module load CMake Intel IntelMPI imkl netCDF netCDF-Fortran #intel.compiler intel.mpi netcdf/4.4.0_intel +# the netcdf c++ path given by the netcdf module is broken, we have to workaround this +export FC=mpiifort CC=mpiicc CXX=mpiicpc +export NETCDF_Fortran_INCLUDE_DIRECTORIES=/gpfs/software/juwels/stages/2018a/software/netCDF-Fortran/4.4.4-iimpi-2018a/include/ +export NETCDF_C_INCLUDE_DIRECTORIES=/gpfs/software/juwels/stages/2018a/software/netCDF/4.6.1-iimpi-2018a/include/ +export NETCDF_CXX_INCLUDE_DIRECTORIES=/gpfs/software/juwels/stages/2018a/software/netCDF/4.6.1-iimpi-2018a/include/ -module load netCDF/4.6.3 -module load netCDF-Fortran/4.4.5 -module load CMake -export NETCDF_DIR=$EBROOTNETCDF -export NETCDFF_DIR=$EBROOTNETCDFMINFORTRAN -export NETCDF_Fortran_INCLUDE_DIRECTORIES=${NETCDFF_DIR}/include/ -export NETCDF_C_INCLUDE_DIRECTORIES=${NETCDF_DIR}/include/ -export NETCDF_CXX_INCLUDE_DIRECTORIES=${NETCDFCXX_DIR}/include/ diff --git a/env/ollie/shell b/env/ollie/shell index 3b9efbf52..27eabcd3c 100644 --- a/env/ollie/shell +++ b/env/ollie/shell @@ -1,11 +1,9 @@ # make the contents as shell agnostic as possible so we can include them with bash, zsh and others module load intel.compiler intel.mpi netcdf/4.4.0_intel -module load centoslibs # required on compute nodes - # the netcdf c++ path given by the netcdf module is broken, we have to workaround this export NETCDF_CXX_INCLUDE_DIRECTORIES=/global/AWIsoft/tkleiner/netcdf/4.4.0_intel_impi/include -export PATH=/home/ollie/dsidoren/cmake-3.13.2-Linux-x86_64/bin:$PATH +export PATH=/work/ollie/jhegewal/sw/cmake/bin:$PATH export FC="mpiifort -mkl" CC=mpiicc CXX=mpiicpc diff --git a/env/ollie/shell_cray b/env/ollie/shell_cray deleted file mode 100644 index 4c7d399f8..000000000 --- a/env/ollie/shell_cray +++ /dev/null @@ -1,6 +0,0 @@ -# make the contents as shell agnostic as possible so we can include them with bash, zsh and others - -module load cmake -module load PrgEnv-cray - -export FC=ftn CC=cc CXX=CC diff --git a/env/ubuntu/shell b/env/ubuntu/shell deleted file mode 100644 index 29fc59dbc..000000000 --- a/env/ubuntu/shell +++ /dev/null @@ -1,5 +0,0 @@ -export FC=mpifort CC=mpicc CXX=mpicxx -export BLAS_LIBRARIES=/usr/lib/x86_64-linux-gnu/blas/ -export UBUNTU_BLAS_LIBRARY="libblas.a" - - diff --git a/fpost2/do_work.F90 b/fpost2/do_work.F90 index d550acc0e..ebf0f1ba2 100644 --- a/fpost2/do_work.F90 +++ b/fpost2/do_work.F90 @@ -16,7 +16,7 @@ PROGRAM MAIN INTEGER :: year, io, ncid real, allocatable, dimension(:) :: temp, salt, ssh -character(len=MAX_PATH) :: nmlfile +character(len=100) :: nmlfile nmlfile ='namelist.interp' ! name of general configuration namelist file open (20,file=nmlfile) diff --git a/fpost2/g_oce_2_reg.F90 b/fpost2/g_oce_2_reg.F90 index cb936d716..bdbb38c87 100644 --- a/fpost2/g_oce_2_reg.F90 +++ b/fpost2/g_oce_2_reg.F90 @@ -16,7 +16,7 @@ module g_oce_2_reg real(kind=8) :: RegDx=.25, RegDy=.25 real(kind=8), allocatable :: reg_lon(:), reg_lat(:) type(sparse_matrix) :: oce_2_reg, oce_2_reg_el - character(MAX_PATH) :: o2r_filename='oce_2_reg.bin_25' + character*100 :: o2r_filename='oce_2_reg.bin_25' logical :: do_mesh=.false. namelist /regular_mesh/ LonMin, LonMax, LatMin, LatMax, RegDx, RegDy, o2r_filename, do_mesh diff --git a/fpost2/gen_modules_config.F90 b/fpost2/gen_modules_config.F90 index f5e1c56ca..196ce7855 100644 --- a/fpost2/gen_modules_config.F90 +++ b/fpost2/gen_modules_config.F90 @@ -6,12 +6,12 @@ module g_config ! *** Modelname *** character(5) :: runid='fesom' ! a model/setup name integer :: year_start=1948, year_end=1953, snap_per_year=12 - CHARACTER(MAX_PATH) :: datapath ='/home/h/hbkdsido/fvom/results/core2_sw_chl0.1/' - CHARACTER(MAX_PATH) :: outpath ='/home/h/hbkdsido/fvom/results/' + CHARACTER*100 :: datapath ='/home/h/hbkdsido/fvom/results/core2_sw_chl0.1/' + CHARACTER*100 :: outpath ='/home/h/hbkdsido/fvom/results/' namelist /config/ runid, datapath, outpath, year_start, year_end, snap_per_year logical :: use_mask=.false. - character(MAX_PATH) :: mask_file='/uv/user/dsidoren/mask_NA.dat' + character(500) :: mask_file='/uv/user/dsidoren/mask_NA.dat' real(kind=8), dimension(:), allocatable :: mask_n2 namelist /mask/ use_mask, mask_file @@ -31,6 +31,6 @@ module g_config real(kind=8) :: alphaEuler=50. ![grad] Euler angles, convention: real(kind=8) :: betaEuler=15. ![grad] first around z, then around new x, real(kind=8) :: gammaEuler=-90. ![grad] then around new z. - CHARACTER(MAX_PATH) :: meshpath ='/gfs2/work/hbkdsido/input/mesh/mesh_CORE2_final/' + CHARACTER*100 :: meshpath ='/gfs2/work/hbkdsido/input/mesh/mesh_CORE2_final/' namelist /fesom_mesh/ meshpath, rotated_grid, rotated_rslt, alphaEuler, betaEuler, gammaEuler end module g_config diff --git a/lib/metis-4.0/CHANGES b/lib/metis-4.0/CHANGES new file mode 100755 index 000000000..b15cacc2c --- /dev/null +++ b/lib/metis-4.0/CHANGES @@ -0,0 +1,149 @@ + +METIS 4.0.1, 11/29/98 +------------------------------------------------------------------------------ +This is mostly a bug-fix release + + - Fixed some bugs in the multi-constraint partitioning routines + - Fixed some bugs in the volume-minimization routines + + + +METIS 4.0.0, 9/20/98 +------------------------------------------------------------------------------ +METIS 4.0 contains a number of changes over the previous major release (ver +3.0.x). Most of these changes are concentrated on the graph and mesh +partitioning routines and they do not affect the sparse matrix re-ordering +routines. Here is a list of the major changes: + + Multi-Constraint Partitioning + ----------------------------- + METIS now includes partitioning routines that can be used to a partition + a graph in the presence of multiple balancing constraints. + + Minimizing the Total Communication Volume + ----------------------------------------- + METIS now includes partitioning routines whose objective is to minimize + the total communication volume (as opposed to minimizing the edge-cut). + + Minimizing the Maximum Connectivity of the Subdomains + ----------------------------------------------------- + The k-way partitioning routines in METIS can now directly minimize the number + of adjacent subdomains. For most graphs corresponding to finite element + meshes, METIS is able to significantly reduce the maximum (and total) number of + adjacent subdomains. + + + + +METIS 3.0.6, 1/28/98 +------------------------------------------------------------------------------- + - Fixed some problems when too many partitions were asked, and each partition + end up having 0 vertices + - Fixed some bugs in the I/O routines + - Added support for the g77 compiler under Linux + + +METIS 3.0.5, 12/22/97 +------------------------------------------------------------------------------- + - Fixed problems on 64-bit architectures (eg., -64 option on SGIs). + - Added some options in Makefile.in + + +METIS 3.0.4, 12/1/97 +------------------------------------------------------------------------------- + Fixed a memory leak in the ordering code. + + +METIS 3.0.3, 11/5/97 +------------------------------------------------------------------------------- + This is mostly a bug-fix release with just a few additions + + Added functionality + - Added support for quadrilateral elements. + - Added a routine METIS_EstimateMemory that estimates the amount of + memory that will be allocated by METIS. This is useful in determining + if a problem can run on your system. + - Added hooks to allow PARMETIS to use the orderings produced by METIS. + This is hidden from the user but it will be used in the next release + of PARMETIS. + + Bug-fixes + - Fixed a bug related to memory allocation. This should somewhat reduce the + overall memory used by METIS. + - Fixed some bugs in the 'graphchk' program in the case of weighted graphs. + - Removed some code corresponding to unused options. + - Fixed some minor bugs in the node-refinement code + + + +------------------------------------------------------------------------------- +METIS 3.0 contains a number of changes over METIS 2.0. +The major changes are the following: + + General Changes + --------------- + 1. Added code to directly partition finite element meshes. + + 2. Added code to convert finite element meshes into graphs so they + can be used by METIS. + + 1. The names, calling sequences, and options of the routines in + METISlib have been changed. + + 2. Better support has been added for Fortran programs. + + 3. Eliminated the 'metis' program. The only way to tune METIS's + behavior is to use METISlib. + + 4. Improved memory management. METIS should now only abort if truly + there is no more memory left in the system. + + + Graph Partitioning + ------------------ + 1. Added partitioning routines that can be used to compute a partition + with prescribed partition weights. For example, they can be used to + compute a 3-way partition such that partition 1 has 50% of the weight, + partition 2 has 20% of the way, and partition 3 has 30% of the weight. + + 2. Improved the speed of the k-way partitioning algorithm (kmetis). The + new code has better cache locality which dramatically improves the + speed for large graphs. A factor of 4 speedup can be obtained for + certain graphs. METIS can now partition a 4 million node graph + in well under a minute on a MIPS R10000. + + 3. Eliminated some of the options that were seldom used. + + + Fill-Reducing Orderings + ---------------------- + 1. Added a node based ordering code `onmetis' that greatly improves + ordering quality. + + 2. Improved the quality of the orderings produced by the original + edge-based ordering code (it is now called 'oemetis'). + + 3. METIS can now analyze the graph and try to compress together + nodes with identical sparsity pattern. For some problems, this + significantly reduces ordering time + + 4. METIS can now prune dense columns prior to ordering. This can be + helpful for LP matrices. + + + Mesh Partitioning + ----------------- + 1. METIS can now directly partition the element node array of finite + element meshes. It produces two partitioning vectors. One for the + elements and one for the nodes. METIS supports the following + elements: triangles, tetrahedra, hexahedra + + + Mesh-To-Graph Conversion Routines + --------------------------------- + 1. METIS now includes a number of mesh conversion functions that can + be used to create the dual and nodal graphs directly from the + element connectivity arrays. 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