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GitFlow: Merge develop into main #141

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GitFlow: Merge develop into main #141

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8cee206
Merge pull request #86 from GEOS-ESM/develop
mathomp4 Dec 7, 2021
bb4eb2c
Merge pull request #100 from GEOS-ESM/develop
mathomp4 Feb 14, 2022
150f6b8
Merge pull request #107 from GEOS-ESM/develop
amdasilva Feb 18, 2022
4d4f27c
Merge pull request #121 from GEOS-ESM/develop
amdasilva Mar 14, 2022
8ca2da2
Fixes #130. Initialize allocatable variables in Process Library
mathomp4 Mar 24, 2022
e54dc86
Changes for consistency
mathomp4 Mar 24, 2022
783fed1
Update changelog
mathomp4 Apr 28, 2022
9077e85
Merge pull request #131 from GEOS-ESM/hotfix/mathomp4/#130-fix-klid-i…
mathomp4 Apr 28, 2022
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8 changes: 7 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -7,12 +7,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## [Unreleased]

## [2.0.6] - 2021-04-28

### Fixed

- Initialize allocatable variables in Process Library. Fixes #130

## [2.0.5] - 2021-03-14

### Added

- Added AMIP.20C ExtData configs to allow AMIP GOCART runs to work before Y2000 (during the transition from HFED to QFED)
- Note 1: This is not a *new* scenario but rather a stopgap until Extdata is updated to allow time ranges to be specified.
- Note 1: This is not a *new* scenario but rather a stopgap until Extdata is updated to allow time ranges to be specified.
- Note 2: Temporarily, this will allow runs before Y2000 using magic-data scripting in `gcm_run.j` (a la MERRA2 in GOCART1).

### Fixed
Expand Down
2 changes: 1 addition & 1 deletion CMakeLists.txt
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Expand Up @@ -4,7 +4,7 @@ cmake_policy (SET CMP0054 NEW)

project (
GOCART
VERSION 2.0.5
VERSION 2.0.6
LANGUAGES Fortran CXX C) # Note - CXX is required for ESMF

if ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}")
Expand Down
89 changes: 54 additions & 35 deletions Process_Library/GOCART2G_Process.F90
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Expand Up @@ -661,8 +661,8 @@ subroutine DustEmissionK14( km, t_soil, w_top, rho_air, &
i2 = ubound(t_soil,1)
j2 = ubound(t_soil,2)

allocate(w_g(i2,j2), w_gt(i2,j2), f_veg(i2,j2), clay(i2,j2), silt(i2,j2), k_gamma(i2,j2))
allocate(z0s(i2,j2), Dp_size(i2,j2))
allocate(w_g(i2,j2), w_gt(i2,j2), f_veg(i2,j2), clay(i2,j2), silt(i2,j2), k_gamma(i2,j2), source=0.0)
allocate(z0s(i2,j2), Dp_size(i2,j2), source=0.0)

! typical size of soil particles for optimal saltation is about 75e-6m
Dp_size = 75e-6
Expand Down Expand Up @@ -1183,10 +1183,8 @@ subroutine Chem_SettlingSimple ( km, klid, flag, cdt, grav, &

hsurf => hghte(i1:i2,j1:j2,km)

allocate(dz(i2,j2,km), radius(i2,j2,km), rhop(i2,j2,km), vsettle(i2,j2,km), qa(i2,j2,km))
allocate(cmass_before(i2,j2), cmass_after(i2,j2))
cmass_before = 0.d0
cmass_after = 0.d0
allocate(dz(i2,j2,km), radius(i2,j2,km), rhop(i2,j2,km), vsettle(i2,j2,km), qa(i2,j2,km), source=0.0)
allocate(cmass_before(i2,j2), cmass_after(i2,j2), source=0.0_DP)

qa = int_qa

Expand Down Expand Up @@ -1359,10 +1357,8 @@ subroutine Chem_Settling ( km, klid, bin, flag, cdt, grav, &

hsurf => hghte(i1:i2,j1:j2,km)

allocate(dz(i2,j2,km), radius(i2,j2,km), rhop(i2,j2,km), vsettle(i2,j2,km), qa(i2,j2,km))
allocate(cmass_before(i2,j2), cmass_after(i2,j2))
cmass_before = 0.d0
cmass_after = 0.d0
allocate(dz(i2,j2,km), radius(i2,j2,km), rhop(i2,j2,km), vsettle(i2,j2,km), qa(i2,j2,km), source=0.0)
allocate(cmass_before(i2,j2), cmass_after(i2,j2), source=0.0_DP)

qa = int_qa

Expand Down Expand Up @@ -1967,7 +1963,7 @@ subroutine Chem_Settling2Gorig (km, klid, flag, bin, int_qa, grav, delp, &
real, dimension(:,:,:), allocatable :: vsettle ! fall speed [m s-1]
real(kind=DP), dimension(:,:,:), allocatable :: dzd, vsd, qa, qa_temp
real(kind=DP), dimension(:,:), allocatable :: cmass_before, cmass_after
real(kind=DP) :: qdel, qsrc, d_p, dpm1
real(kind=DP) :: qdel, qsrc, d_p, d_pm1

integer :: status

Expand All @@ -1986,9 +1982,10 @@ subroutine Chem_Settling2Gorig (km, klid, flag, bin, int_qa, grav, delp, &

! Allocate arrays
! ---------------
allocate(dz, mold=rhoa);
allocate(dzd(i2,j2,km), vsd(i2,j2,km), qa(i2,j2,km), vsettle(i2,j2,km), qa_temp(i2,j2,km))
allocate(cmass_before(i2,j2), cmass_after(i2,j2))
allocate(dz, mold=rhoa)
allocate(vsettle(i2,j2,km), source=0.0)
allocate(dzd(i2,j2,km), vsd(i2,j2,km), qa(i2,j2,km), qa_temp(i2,j2,km), source=0.0_DP)
allocate(cmass_before(i2,j2), cmass_after(i2,j2), source=0.0_DP)

! Handle the fact that hghte may be in the range [1,km+1] or [0,km]
! -----------------------------------------------------------------
Expand Down Expand Up @@ -2119,8 +2116,8 @@ subroutine Chem_Settling2Gorig (km, klid, flag, bin, int_qa, grav, delp, &
! do k = 2, km
do k = klid+1, km
d_p = delp(i,j,k)
dpm1 = delp(i,j,k-1)
qsrc = qdel * dpm1 / d_p
d_pm1 = delp(i,j,k-1)
qsrc = qdel * d_pm1 / d_p
qdel = qa(i,j,k)*dt_settle*vsd(i,j,k)/dzd(i,j,k)
qa(i,j,k) = qa(i,j,k) - qdel + qsrc
end do
Expand Down Expand Up @@ -2313,7 +2310,7 @@ subroutine Chem_SettlingSimpleOrig ( km, klid, flag, grav, cdt, radiusInp, rhopI
real, dimension(:,:,:), allocatable :: vsettle ! fall speed [m s-1]
real(kind=DP), dimension(:,:,:), allocatable :: dzd, vsd, qa, qa_temp
real(kind=DP), dimension(:,:), allocatable :: cmass_before, cmass_after, qdel, &
dp, dpm1, qsrc
d_p, d_pm1, qsrc

!EOP
!-------------------------------------------------------------------------
Expand All @@ -2328,10 +2325,11 @@ subroutine Chem_SettlingSimpleOrig ( km, klid, flag, grav, cdt, radiusInp, rhopI

! Allocate arrays
! ---------------
allocate(dz, mold=rhoa);
allocate(dzd(i2,j2,km), vsd(i2,j2,km), qa(i2,j2,km), vsettle(i2,j2,km), qa_temp(i2,j2,km))
allocate(cmass_before(i2,j2), cmass_after(i2,j2), qdel(i2,j2), dp(i2,j2), &
dpm1(i2,j2), qsrc(i2,j2))
allocate(dz, mold=rhoa)
allocate(vsettle(i2,j2,km), source=0.0)
allocate(dzd(i2,j2,km), vsd(i2,j2,km), qa(i2,j2,km), qa_temp(i2,j2,km), source=0.0_DP)
allocate(cmass_before(i2,j2), cmass_after(i2,j2), qdel(i2,j2), d_p(i2,j2), &
d_pm1(i2,j2), qsrc(i2,j2), source=0.0_DP)

! Handle the fact that hghte may be in the range [1,km+1] or [0,km]
! -----------------------------------------------------------------
Expand Down Expand Up @@ -2459,9 +2457,9 @@ subroutine Chem_SettlingSimpleOrig ( km, klid, flag, grav, cdt, radiusInp, rhopI
qa(i1:i2,j1:j2,klid) = qa(i1:i2,j1:j2,klid) - qdel

do k = klid+1, km
dp = delp(i1:i2,j1:j2,k)
dpm1 = delp(i1:i2,j1:j2,k-1)
qsrc = qdel * dpm1 / dp
d_p = delp(i1:i2,j1:j2,k)
d_pm1 = delp(i1:i2,j1:j2,k-1)
qsrc = qdel * d_pm1 / d_p
qdel = qa(i1:i2,j1:j2,k)*dt_settle*vsd(i1:i2,j1:j2,k)/dzd(i1:i2,j1:j2,k)
qa(i1:i2,j1:j2,k) = qa(i1:i2,j1:j2,k) - qdel + qsrc
enddo
Expand Down Expand Up @@ -2569,7 +2567,7 @@ subroutine DryDeposition ( km, tmpu, rhoa, hghte, oro, ustar, pblh, shflux, &
i2 = dims(1); j2 = dims(2)

allocate(dz(i2,j2),rmu(i2,j2),Ra(i2,j2),Rs(i2,j2),vdep(i2,j2), &
obk(i2,j2))
obk(i2,j2), source=0.0)

! Calculate the viscosity and thickness of the surface level
dz = hghte(:,:,km-1) - hghte(:,:,km)
Expand Down Expand Up @@ -2818,7 +2816,7 @@ subroutine WetRemovalGOCART2G ( km, klid, n1, n2, bin_ind, cdt, aero_type, kin,

! Allocate arrays
allocate(c_h2o(i2,j2,km), cldliq(i2,j2,km), cldice(i2,j2,km), pdog(i2,j2,km), &
delz(i2,j2,km), dpfli(i2,j2,km))
delz(i2,j2,km), dpfli(i2,j2,km), source=0.0)

! Initialize local variables
! --------------------------
Expand All @@ -2836,8 +2834,8 @@ subroutine WetRemovalGOCART2G ( km, klid, n1, n2, bin_ind, cdt, aero_type, kin,
Td_ls = cdt
nbins = n2-n1+1

allocate(fd(km,nbins),stat=ios)
allocate(dc(nbins),stat=ios)
allocate(fd(km,nbins),source=0.0,stat=ios)
allocate(dc(nbins),source=0.0,stat=ios)

if( associated(fluxout) ) fluxout(i1:i2,j1:j2,bin_ind) = 0.0

Expand Down Expand Up @@ -3350,8 +3348,8 @@ subroutine Aero_Compute_Diags (mie_table, km, klid, nbegin, nbins, rlow, rup, ch
nch = size(channels)
i2 = size(rhoa,1)
j2 = size(rhoa,2)
allocate(fPMfm(nbins))
allocate(fPM25(nbins))
allocate(fPMfm(nbins),source=0.0)
allocate(fPM25(nbins),source=0.0)

! Get the wavelength indices
! --------------------------
Expand Down Expand Up @@ -3416,7 +3414,7 @@ subroutine Aero_Compute_Diags (mie_table, km, klid, nbegin, nbins, rlow, rup, ch
ilam470 .ne. ilam870) do_angstrom = .true.

if( present(angstrom) .and. do_angstrom ) then
allocate(tau470(i1:i2,j1:j2), tau870(i1:i2,j1:j2))
allocate(tau470(i1:i2,j1:j2), tau870(i1:i2,j1:j2), source=0.0)
end if

! Compute the fine mode (sub-micron) and PM2.5 bin-wise fractions
Expand Down Expand Up @@ -4240,6 +4238,7 @@ subroutine hoppelCorrection (radius, rhop, rh, dz, ustar, rhFlag, &
rc = __SUCCESS__
fhoppel = 1.0
allocate(vsettle, mold=rh)
vsettle=0.0

do j = 1, ubound(rh,2)
do i = 1, ubound(rh,1)
Expand Down Expand Up @@ -4376,7 +4375,7 @@ subroutine CAEmission (mie_table, km, nbins, cdt, grav, prefix, ratPOM, eAircraf
ijl = ( i2 - i1 + 1 ) * ( j2 - j1 + 1 )

allocate(factor(i2,j2), srcHydrophobic(i2,j2), srcHydrophilic(i2,j2), srcBiofuel(i2,j2), &
srcBiomass(i2,j2), srcAnthro(i2,j2), srcBiogenic(i2,j2), f_bb_(i2,j2), exttau_bb_(i2,j2))
srcBiomass(i2,j2), srcAnthro(i2,j2), srcBiogenic(i2,j2), f_bb_(i2,j2), exttau_bb_(i2,j2), source=0.0)

! Emission factors scaling from source files to desired mass quantity
eBiomass = ratPOM
Expand Down Expand Up @@ -4427,6 +4426,11 @@ subroutine CAEmission (mie_table, km, nbins, cdt, grav, prefix, ratPOM, eAircraf
allocate(p500, mold=pblh)
allocate(pPBL, mold=pblh)
ps = 0.0
p0 = 0.0
z0 = 0.0
p100 = 0.0
p500 = 0.0
pPBL = 0.0
do k = 1, km
ps(i1:i2,j1:j2) = ps(i1:i2,j1:j2) + delp(i1:i2,j1:j2,k)
end do
Expand Down Expand Up @@ -5454,7 +5458,7 @@ subroutine SulfateDistributeEmissions ( km, nbins, cdt, grav, nymd, nhms, &
hsurf = hghte(i1:i2,j1:j2,km)

allocate(srcSO2(i2,j2), srcSO4(i2,j2), srcDMS(i2,j2), srcSO4anthro(i2,j2), &
srcSO2anthro(i2,j2), srcSO2bioburn(i2,j2))
srcSO2anthro(i2,j2), srcSO2bioburn(i2,j2), source=0.0)

! Initialize local variables
! --------------------------
Expand Down Expand Up @@ -5505,6 +5509,11 @@ subroutine SulfateDistributeEmissions ( km, nbins, cdt, grav, nymd, nhms, &
allocate(pPblh, mold=pblh)

ps = 0.0
p0 = 0.0
z0 = 0.0
p100 = 0.0
p500 = 0.0
pPblh = 0.0
do k = 1, km
ps(i1:i2,j1:j2) = ps(i1:i2,j1:j2) + delp(i1:i2,j1:j2,k)
end do
Expand Down Expand Up @@ -5942,7 +5951,7 @@ subroutine SulfateUpdateOxidants (nymd_current, nhms_current, lonRad, latRad, &
j2 = size(rhoa,2)

allocate(cossza(i1:i2,j1:j2), sza(i1:i2,j1:j2), tcosz(i1:i2,j1:j2), &
tday(i1:i2,j1:j2), tnight(i1:i2,j1:j2))
tday(i1:i2,j1:j2), tnight(i1:i2,j1:j2), source=0.0)

! Update emissions/production if necessary (daily)
! -----------------------------------------------
Expand Down Expand Up @@ -6845,7 +6854,7 @@ subroutine SU_Compute_Diags ( km, klid, rmed, sigma, rhop, grav, pi, nSO4, mie_t
j2 = ubound(tmpu, 2)
i2 = ubound(tmpu, 1)

allocate(tau470(i1:i2,j1:j2), tau870(i1:i2,j1:j2))
allocate(tau470(i1:i2,j1:j2), tau870(i1:i2,j1:j2), source=0.0)

! Get the wavelength indices
! --------------------------
Expand Down Expand Up @@ -7263,6 +7272,10 @@ subroutine SulfateChemDriver (km, klid, cdt, PI, radToDeg, von_karman, &
allocate(cossza, mold=oro)
allocate(sza, mold=oro)

drydepositionfrequency = 0.0
cossza = 0.0
sza = 0.0

! Reset the production terms
allocate(pSO2_DMS, mold=tmpu)
allocate(pMSA_DMS, mold=tmpu)
Expand Down Expand Up @@ -7464,6 +7477,8 @@ subroutine SulfateChemDriver_DMS (km, klid, cdt, airMolWght, nAvogadro, cpd, &

allocate(pSO2_DMS, mold=tmpu)
allocate(pMSA_DMS, mold=tmpu)
pSO2_DMS = 0.0
pMSA_DMS = 0.0

! spatial loop
do k = klid, km
Expand Down Expand Up @@ -7629,6 +7644,9 @@ subroutine SulfateChemDriver_SO2 (km, klid, cdt, airMolWght, nAvogadro, cpd, gra
allocate(pSO4g_SO2, mold=tmpu)
allocate(pSO4aq_SO2, mold=tmpu)
allocate(fout(i2,j2))
pSO4g_SO2 = 0.0
pSO4aq_SO2 = 0.0
fout = 0.0

! Conversion of SO2 mmr to SO2 vmr
fMR = airMolWght / fMassSO2
Expand Down Expand Up @@ -7895,6 +7913,7 @@ subroutine SulfateChemDriver_MSA (km, klid, cdt, grav, qa, nMSA, delp, drydepf,
i2 = ubound(qa, 1)

allocate(fout(i2,j2))
fout = 0.0

! spatial loop
do k = klid, km
Expand Down