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Revert "Revert "Merge branch 'singhbalwinder/atm/add-bc-pom-coarse-mo…
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…de' (PR #416)""

This reverts commit 21ecb5b.

This re-implements the merge of PR #416.
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@susburrows
susburrows committed Dec 23, 2015
1 parent 2504aa1 commit 23419bd
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Showing 24 changed files with 8,495 additions and 686 deletions.
173 changes: 122 additions & 51 deletions components/cam/bld/build-namelist
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Original file line number Diff line number Diff line change
Expand Up @@ -685,6 +685,10 @@ add_default($nl, 'atm_cpl_dt', 'val'=>$nl->get_value('dtime'));
# Change default to using a single file.
add_default($nl, 'profile_single_file', 'val'=>'.true.');

#BSINGH - Get the value of RAIN_EVAP_TO_COARSE_AERO variable
my $rain_evap_to_coarse_aero = $cfg->get('rain_evap_to_coarse_aero'); #BSINGH - See if rain_evap_to_coarse_aero option is selected
if ($print>=1) { print "Running model with rain_evap_to_coarse_aero (1-YES, 0-NO)?: $rain_evap_to_coarse_aero $eol"; }

#-----------------------------------------------------------------------------------------------
# Add defaults for the CAM component

Expand Down Expand Up @@ -1068,37 +1072,73 @@ if ($aer_model eq 'mam' ) {
@mode_types = qw(accum aitken coarse);
@mode_num = qw(num_a1 num_a2 num_a3);
@mode_num_cw = qw(num_c1 num_c2 num_c3);
@mode_spec = (
[qw(so4_a1 pom_a1 soa_a1 bc_a1 dst_a1 ncl_a1)],
[qw(so4_a2 soa_a2 ncl_a2)],
[qw(dst_a3 ncl_a3 so4_a3)],
);
@mode_spec_type = (
[qw(sulfate p-organic s-organic black-c dust seasalt)],
[qw(sulfate s-organic seasalt)],
[qw(dust seasalt sulfate)],
);
@mode_spec_cw = (
[qw(so4_c1 pom_c1 soa_c1 bc_c1 dst_c1 ncl_c1)],
[qw(so4_c2 soa_c2 ncl_c2)],
[qw(dst_c3 ncl_c3 so4_c3)],
);

if ($rain_evap_to_coarse_aero == 0) { #default
@mode_spec = (
[qw(so4_a1 pom_a1 soa_a1 bc_a1 dst_a1 ncl_a1)],
[qw(so4_a2 soa_a2 ncl_a2)],
[qw(dst_a3 ncl_a3 so4_a3)],
);
@mode_spec_type = (
[qw(sulfate p-organic s-organic black-c dust seasalt)],
[qw(sulfate s-organic seasalt)],
[qw(dust seasalt sulfate)],
);
@mode_spec_cw = (
[qw(so4_c1 pom_c1 soa_c1 bc_c1 dst_c1 ncl_c1)],
[qw(so4_c2 soa_c2 ncl_c2)],
[qw(dst_c3 ncl_c3 so4_c3)],
);
}
else{
@mode_spec = (
[qw(so4_a1 pom_a1 soa_a1 bc_a1 dst_a1 ncl_a1)],
[qw(so4_a2 soa_a2 ncl_a2)],
[qw(dst_a3 ncl_a3 so4_a3 bc_a3 pom_a3 soa_a3)],
);
@mode_spec_type = (
[qw(sulfate p-organic s-organic black-c dust seasalt)],
[qw(sulfate s-organic seasalt)],
[qw(dust seasalt sulfate black-c p-organic s-organic)],
);
@mode_spec_cw = (
[qw(so4_c1 pom_c1 soa_c1 bc_c1 dst_c1 ncl_c1)],
[qw(so4_c2 soa_c2 ncl_c2)],
[qw(dst_c3 ncl_c3 so4_c3 bc_c3 pom_c3 soa_c3)],
);
}
if ($chem =~ /_mam3/) {
@mode_num_src = qw(A A A);
@mode_spec_src = (
[qw(A A A A A A)],
[qw(A A A)],
[qw(A A A)],
);
if ($rain_evap_to_coarse_aero == 0) { #default
@mode_spec_src = (
[qw(A A A A A A)],
[qw(A A A)],
[qw(A A A)],
);
}
else{
@mode_spec_src = (
[qw(A A A A A A)],
[qw(A A A)],
[qw(A A A A A A)],
);
}
}
else {
@mode_num_src = qw(N N N);
@mode_spec_src = (
[qw(N N N N N N)],
[qw(N N N)],
[qw(N N N)],
);
if ($rain_evap_to_coarse_aero == 0) { #default
@mode_spec_src = (
[qw(N N N N N N)],
[qw(N N N)],
[qw(N N N)],
);
}
else{
@mode_spec_src = (
[qw(N N N N N N)],
[qw(N N N)],
[qw(N N N N N N)],
);
}
}
} elsif($aero_modes eq '4mode') {
# For 4 modes
Expand All @@ -1113,32 +1153,62 @@ if ($aer_model eq 'mam' ) {
@mode_types = qw(accum aitken coarse primary_carbon);
@mode_num = qw(num_a1 num_a2 num_a3 num_a4);
@mode_num_cw = qw(num_c1 num_c2 num_c3 num_c4);
@mode_spec = (
[qw(so4_a1 pom_a1 soa_a1 bc_a1 dst_a1 ncl_a1)],
[qw(so4_a2 soa_a2 ncl_a2)],
[qw(dst_a3 ncl_a3 so4_a3)],
[qw(pom_a4 bc_a4)],
);
@mode_spec_type = (
[qw(sulfate p-organic s-organic black-c dust seasalt)],
[qw(sulfate s-organic seasalt)],
[qw(dust seasalt sulfate)],
[qw(p-organic black-c)],
);
@mode_spec_cw = (
[qw(so4_c1 pom_c1 soa_c1 bc_c1 dst_c1 ncl_c1)],
[qw(so4_c2 soa_c2 ncl_c2)],
[qw(dst_c3 ncl_c3 so4_c3)],
[qw(pom_c4 bc_c4)],
);
if ($rain_evap_to_coarse_aero == 0) { #default
@mode_spec = (
[qw(so4_a1 pom_a1 soa_a1 bc_a1 dst_a1 ncl_a1)],
[qw(so4_a2 soa_a2 ncl_a2)],
[qw(dst_a3 ncl_a3 so4_a3)],
[qw(pom_a4 bc_a4)],
);
@mode_spec_type = (
[qw(sulfate p-organic s-organic black-c dust seasalt)],
[qw(sulfate s-organic seasalt)],
[qw(dust seasalt sulfate)],
[qw(p-organic black-c)],
);
@mode_spec_cw = (
[qw(so4_c1 pom_c1 soa_c1 bc_c1 dst_c1 ncl_c1)],
[qw(so4_c2 soa_c2 ncl_c2)],
[qw(dst_c3 ncl_c3 so4_c3)],
[qw(pom_c4 bc_c4)],
);

@mode_num_src = qw(A A A A);
@mode_spec_src = (
[qw(A A A A A A)],
[qw(A A A)],
[qw(A A A)],
[qw(A A)],
);
@mode_num_src = qw(A A A A);
@mode_spec_src = (
[qw(A A A A A A)],
[qw(A A A)],
[qw(A A A)],
[qw(A A)],
);
}
else{
@mode_spec = (
[qw(so4_a1 pom_a1 soa_a1 bc_a1 dst_a1 ncl_a1)],
[qw(so4_a2 soa_a2 ncl_a2)],
[qw(dst_a3 ncl_a3 so4_a3 bc_a3 pom_a3 soa_a3)],
[qw(pom_a4 bc_a4)],
);
@mode_spec_type = (
[qw(sulfate p-organic s-organic black-c dust seasalt)],
[qw(sulfate s-organic seasalt)],
[qw(dust seasalt sulfate black-c p-organic s-organic)],
[qw(p-organic black-c)],
);
@mode_spec_cw = (
[qw(so4_c1 pom_c1 soa_c1 bc_c1 dst_c1 ncl_c1)],
[qw(so4_c2 soa_c2 ncl_c2)],
[qw(dst_c3 ncl_c3 so4_c3 bc_c3 pom_c3 soa_c3)],
[qw(pom_c4 bc_c4)],
);

@mode_num_src = qw(A A A A);
@mode_spec_src = (
[qw(A A A A A A)],
[qw(A A A)],
[qw(A A A A A A)],
[qw(A A)],
);
}

} elsif($aero_modes eq '7mode') {

Expand Down Expand Up @@ -2608,6 +2678,7 @@ add_default($nl, 'convproc_do_gas');
add_default($nl, 'demott_ice_nuc');
#BSINGH - ENDS

add_default($nl, 'mam_amicphys_optaa'); #for enabling amicphys code in cam

# Microphysics scheme
add_default($nl, 'use_subcol_microp');
Expand Down
3 changes: 3 additions & 0 deletions components/cam/bld/config_files/definition.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -208,6 +208,9 @@ User specified Fortran compiler overrides Makefile default.
Type of Fortran compiler. Used when -fc specifies a generic wrapper script
such as mpif90 or ftn.
</entry>
<entry id="rain_evap_to_coarse_aero" valid_values="0,1" value="0">
Switch to enable extra species (BC, POM and SOA) in coarse mode for MAM3 and MAM4 simulations: 0=off, 1=on.
</entry>
<entry id="debug" valid_values="0,1" value="0">
Switch to enable debugging options for Fortran compiler: 0=off, 1=on.
</entry>
Expand Down
14 changes: 14 additions & 0 deletions components/cam/bld/configure
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Original file line number Diff line number Diff line change
Expand Up @@ -219,6 +219,7 @@ OPTIONS
Makefile defaults.
-cosp Enable the COSP simulator.
-debug Switch to turn on building CAM with debugging compiler options.
-rain_evap_to_coarse_aero Switch to turn on BC, POM and SOA in the MAM3 and MAM4 coarse mode (mam mode 3)
-defaults <file> Specify a configuration file which will be used to supply defaults instead of
one of the config_files/defaults_*.xml files. This file is used to specify model
configuration parameters only. Parameters relating to the build which
Expand Down Expand Up @@ -318,6 +319,7 @@ GetOptions(
"cosp" => \$opts{'cosp'},
"cppdefs=s" => \$opts{'cppdefs'},
"debug" => \$opts{'debug'},
"rain_evap_to_coarse_aero" => \$opts{'rain_evap_to_coarse_aero'},
"defaults=s" => \$opts{'defaults'},
"dyn=s" => \$opts{'dyn'},
"edit_chem_mech" => \$opts{'edit_chem_mech'},
Expand Down Expand Up @@ -825,6 +827,14 @@ if (defined $opts{'waccmx'}) {
}
my $waccmx = $cfg_ref->get('waccmx');

# Use "rain_evap_to_coarse_aero" in MAM3 or MAM4? [BSINGH - For extra coarse mode species for BC, POM and SOA]
my $rain_evap_to_coarse_aero_opt = (defined $opts{'rain_evap_to_coarse_aero'}) ? 1 : 0;
$cfg_ref->set('rain_evap_to_coarse_aero', $rain_evap_to_coarse_aero_opt);
my $rain_evap_to_coarse_aero = $rain_evap_to_coarse_aero_opt ? 1:0;

if ($print>=2) { print "Is rain_evap_to_coarse_aero active (0-NO; 1-YES)?: $rain_evap_to_coarse_aero$eol"; }


#-----------------------------------------------------------------------------------------------

# Prognostic species package(s)
Expand Down Expand Up @@ -1347,6 +1357,10 @@ if ($chem_pkg =~ '_mam3') {
$chem_cppdefs = ' -DMODAL_AERO -DMODAL_AERO_7MODE ';
}

if ($rain_evap_to_coarse_aero == 1 && ($chem_pkg =~ '_mam3' || $chem_pkg =~ '_mam4')) {
$chem_cppdefs = "$chem_cppdefs -DRAIN_EVAP_TO_COARSE_AERO "
}

my $carma_nadv = 0;
my $carma_cppdefs = '';

Expand Down
1 change: 1 addition & 0 deletions components/cam/bld/namelist_files/master_aer_drydep_list.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
so4_a3
pom_a3
bc_a3
soa_a3
num_a3
ncl_a4
so4_a4
Expand Down
1 change: 1 addition & 0 deletions components/cam/bld/namelist_files/master_aer_wetdep_list.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@
so4_a3
pom_a3
bc_a3
soa_a3
num_a3
ncl_a4
so4_a4
Expand Down
3 changes: 3 additions & 0 deletions components/cam/bld/namelist_files/namelist_defaults_cam.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -859,6 +859,9 @@
<convproc_method_activate>2</convproc_method_activate>
<convproc_do_gas >.false.</convproc_do_gas>

<!-- To turn on amicphys codes in cam-->
<mam_amicphys_optaa >0</mam_amicphys_optaa>

<!-- wet deposition option by PNNL -->
<resus_fix>.false.</resus_fix>

Expand Down
7 changes: 7 additions & 0 deletions components/cam/bld/namelist_files/namelist_definition.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -3472,6 +3472,13 @@ Default: .false.
</entry>


<!-- Flag to turn on/off amicphys codes -->
<entry id="mam_amicphys_optaa" type="integer" category="scavenging"
group="phys_ctl_nl" valid_values="" >
invokes new microphysics code (single call to amicphys routine) if > 0
Default: 0
</entry>


<!-- Diagnostics -->

Expand Down
9 changes: 8 additions & 1 deletion components/cam/chem_proc/src/cam_chempp/eqrep.f
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Original file line number Diff line number Diff line change
Expand Up @@ -162,7 +162,11 @@ subroutine EQUATION_REP( &
end if
production = .true.
rxno = rxmap(j,1,i)
if( coeff_ind(rxno) /= 0 .and. coeffs(k-(i+1),coeff_ind(rxno)) /= 1.e0 ) then
!BSINGH(12/20/2013): Original line: if( coeff_ind(rxno) /= 0 .and. coeffs(k-(i+1),coeff_ind(rxno)) /= 1.e0 ) then
!BSINGH(12/20/2013): Mods start (first check if coeff_ind(rxno) is non zero before using it as an index of coeffs array)
if( coeff_ind(rxno) /= 0) then
if( coeffs(k-(i+1),coeff_ind(rxno)) /= 1.e0 ) then
!BSINGH -ENDS
call NUMCON( eq_piece(buf_pos:), coeffs(k-(i+1),coeff_ind(rxno)), 'l' )
buf_pos = LEN_TRIM( eq_piece ) + 1
if( rxno > phtcnt ) then
Expand All @@ -179,6 +183,9 @@ subroutine EQUATION_REP( &
end if
buf_pos = buf_pos + 1
end if
!BSINGH(12/20/2013): Mods start
endif
!BSINGH -ENDS
if( rxno > phtcnt ) then
call NUMCON( eq_piece(buf_pos:), REAL(rxno-phtcnt), 'l' )
else
Expand Down
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