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Bugfix/use status log #38

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merged 13 commits into from
May 3, 2016
Merged

Bugfix/use status log #38

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7230e1e
Add status log to diagnostic calls
mnlevy1981 Mar 22, 2016
c3cdc12
Add status log to forcing field calls
mnlevy1981 Mar 22, 2016
026155c
Merge branch 'master' into bugfix/use_status_log
mnlevy1981 Apr 5, 2016
2703f18
Remove error_msg and status_msg from marbl_logging
mnlevy1981 Apr 5, 2016
e257a8c
First pass removing 'error code returned' messages
mnlevy1981 Apr 5, 2016
8213853
Remove 'error code returned' from diagnostics mod
mnlevy1981 Apr 5, 2016
00d1635
Add description of logging module to source code
mnlevy1981 Apr 6, 2016
3344b3c
Remove 'error code returned' from forcing field
mnlevy1981 Apr 6, 2016
2c42d81
Use proper formatting when writing to string
mnlevy1981 Apr 7, 2016
1bd3def
Standardize formatting for subname
mnlevy1981 Apr 22, 2016
844db84
Improve documentation in marbl_logging.F90
mnlevy1981 Apr 22, 2016
bcc9497
Merge branch 'master' into bugfix/use_status_log
mnlevy1981 May 2, 2016
29dc48a
Formatting clean-up
mnlevy1981 May 3, 2016
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64 changes: 33 additions & 31 deletions src/marbl_ciso_mod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,6 @@ module marbl_ciso_mod
use marbl_sizes , only : zooplankton_cnt
use marbl_sizes , only : grazer_prey_cnt

use marbl_logging , only : error_msg
use marbl_logging , only : status_msg
use marbl_logging , only : marbl_log_type

use marbl_interface_types , only : marbl_tracer_metadata_type
Expand Down Expand Up @@ -135,6 +133,7 @@ subroutine marbl_ciso_init_nml(nl_buffer, marbl_status_log)
! local variables
!-----------------------------------------------------------------------
character(*), parameter :: subname = 'marbl_ciso_mod:marbl_ciso_init_nml'
character(len=char_len) :: log_message

integer (int_kind) :: &
n, & ! index
Expand All @@ -143,8 +142,7 @@ subroutine marbl_ciso_init_nml(nl_buffer, marbl_status_log)
character(len=marbl_nl_buffer_size) :: &
tmp_nl_buffer

character(char_len) :: &
ciso_comp_surf_avg_freq_opt
character(char_len) :: ciso_comp_surf_avg_freq_opt

! ecosys_ciso_nml namelist
namelist /ecosys_ciso_nml/ &
Expand Down Expand Up @@ -227,8 +225,8 @@ subroutine marbl_ciso_init_nml(nl_buffer, marbl_status_log)
case ('nmonth')
ciso_comp_surf_avg_freq_iopt = marbl_freq_opt_nmonth
case default
write(error_msg, "(2A)") "unknown ciso_comp_surf_avg_freq_opt: ", trim(ciso_comp_surf_avg_freq_opt)
call marbl_status_log%log_error(error_msg, subname)
write(log_message, "(2A)") "unknown ciso_comp_surf_avg_freq_opt: ", trim(ciso_comp_surf_avg_freq_opt)
call marbl_status_log%log_error(log_message, subname)
return
end select

Expand All @@ -237,11 +235,11 @@ subroutine marbl_ciso_init_nml(nl_buffer, marbl_status_log)
!-----------------------------------------------------------------------

if (ciso_use_nml_surf_vals .and. ciso_comp_surf_avg_freq_iopt /= marbl_freq_opt_never) then
write(error_msg, "(4A)") "ciso_use_nml_surf_vals can only be .true. if ", &
"ciso_comp_surf_avg_freq_opt is 'never', but", &
"ciso_comp_surf_avg_freq_opt = ", &
write(log_message, "(4A)") "ciso_use_nml_surf_vals can only be .true. if ", &
"ciso_comp_surf_avg_freq_opt is 'never', but ", &
"ciso_comp_surf_avg_freq_opt = ", &
trim(ciso_comp_surf_avg_freq_opt)
call marbl_status_log%log_error(error_msg, subname)
call marbl_status_log%log_error(log_message, subname)
return
endif

Expand Down Expand Up @@ -271,6 +269,7 @@ subroutine marbl_ciso_init_tracer_metadata(marbl_tracer_metadata, marbl_status_l
! local variables
!-----------------------------------------------------------------------
character(*), parameter :: subname = 'marbl_ciso_mod:marbl_ciso_init_tracer_metadata'
character(len=char_len) :: log_message

integer (int_kind) :: n ! tracer index
integer (int_kind) :: auto_ind ! autotroph functional group index
Expand Down Expand Up @@ -327,9 +326,10 @@ subroutine marbl_ciso_init_tracer_metadata(marbl_tracer_metadata, marbl_status_l
end do

if (ecosys_ciso_tracer_cnt /= n) then
write(error_msg, "(4A)") "ecosys_ciso_tracer_cnt = ", ecosys_ciso_tracer_cnt, &
"but computed ecosys_ciso_tracer_cnt = ", n
call marbl_status_log%log_error(error_msg, subname)
write(log_message, "(A,I0,A,I0)") "ecosys_ciso_tracer_cnt = ", &
ecosys_ciso_tracer_cnt, &
"but computed tracer count is ", n
call marbl_status_log%log_error(log_message, subname)
return
endif

Expand Down Expand Up @@ -378,22 +378,22 @@ subroutine marbl_ciso_init_tracer_metadata(marbl_tracer_metadata, marbl_status_l
endif
end do

write (status_msg,"(A)") '----- autotroph tracer indices -----'
call marbl_status_log%log_noerror(status_msg, subname)
write (log_message,"(A)") '----- autotroph tracer indices -----'
call marbl_status_log%log_noerror(log_message, subname)
do auto_ind = 1, autotroph_cnt
write (status_msg, "(3A,I0)") 'C13_ind(' , trim(autotrophs(auto_ind)%sname), ') = ', autotrophs(auto_ind)%C13_ind
call marbl_status_log%log_noerror(status_msg, subname)
write (status_msg, "(3A,I0)") 'C14_ind(' , trim(autotrophs(auto_ind)%sname), ') = ', autotrophs(auto_ind)%C14_ind
call marbl_status_log%log_noerror(status_msg, subname)
write (status_msg, "(3A,I0)") 'Ca13CO3_ind(' , trim(autotrophs(auto_ind)%sname), ') = ', autotrophs(auto_ind)%Ca13CO3_ind
call marbl_status_log%log_noerror(status_msg, subname)
write (status_msg, "(3A,I0)") 'Ca14CO3_ind(' , trim(autotrophs(auto_ind)%sname), ') = ', autotrophs(auto_ind)%Ca14CO3_ind
call marbl_status_log%log_noerror(status_msg, subname)
write (log_message, "(3A,I0)") 'C13_ind(' , trim(autotrophs(auto_ind)%sname), ') = ', autotrophs(auto_ind)%C13_ind
call marbl_status_log%log_noerror(log_message, subname)
write (log_message, "(3A,I0)") 'C14_ind(' , trim(autotrophs(auto_ind)%sname), ') = ', autotrophs(auto_ind)%C14_ind
call marbl_status_log%log_noerror(log_message, subname)
write (log_message, "(3A,I0)") 'Ca13CO3_ind(' , trim(autotrophs(auto_ind)%sname), ') = ', autotrophs(auto_ind)%Ca13CO3_ind
call marbl_status_log%log_noerror(log_message, subname)
write (log_message, "(3A,I0)") 'Ca14CO3_ind(' , trim(autotrophs(auto_ind)%sname), ') = ', autotrophs(auto_ind)%Ca14CO3_ind
call marbl_status_log%log_noerror(log_message, subname)
end do
write (status_msg, "(A,I0)") 'autotroph_cnt = ', autotroph_cnt
call marbl_status_log%log_noerror(status_msg, subname)
write (status_msg,"(A)") '------------------------------------'
call marbl_status_log%log_noerror(status_msg, subname)
write (log_message, "(A,I0)") 'autotroph_cnt = ', autotroph_cnt
call marbl_status_log%log_noerror(log_message, subname)
write (log_message,"(A)") '------------------------------------'
call marbl_status_log%log_noerror(log_message, subname)

!-----------------------------------------------------------------------
! set lfull_depth_tavg flag for short-lived ecosystem tracers
Expand Down Expand Up @@ -645,8 +645,7 @@ subroutine marbl_ciso_set_interior_forcing( &
cell_radius, cell_permea, cell_eps_fix, marbl_status_log)

if (marbl_status_log%labort_marbl) then
error_msg = "error code returned from setup_cell_attributes"
call marbl_status_log%log_error(error_msg, subname)
call marbl_status_log%log_error_trace("setup_cell_attributes", subname)
return
end if

Expand Down Expand Up @@ -1160,6 +1159,7 @@ subroutine setup_cell_attributes(ciso_fract_factors, &
! local variables
!-----------------------------------------------------------------------
character(*), parameter :: subname = 'marbl_ciso_mod:setup_cell_attributes'
character(len=char_len) :: log_message
integer (int_kind) :: &
n, & ! index for looping over column_tracer
auto_ind ! autotroph functional group index
Expand Down Expand Up @@ -1215,8 +1215,8 @@ subroutine setup_cell_attributes(ciso_fract_factors, &
! cell_eps_fix(auto_ind) = 23.0_r8 ! fractionation effect of carbon fixation

else if (autotrophs(auto_ind)%Nfixer .and. autotrophs(auto_ind)%kSiO3 > c0) then
error_msg = "ciso: Currently Keller and Morel fractionation does not work for Diatoms-Diazotrophs"
call marbl_status_log%log_error(error_msg, subname)
log_message = "ciso: Currently Keller and Morel fractionation does not work for Diatoms-Diazotrophs"
call marbl_status_log%log_error(log_message, subname)
return

else
Expand Down Expand Up @@ -1600,6 +1600,7 @@ subroutine compute_particulate_terms(k, column_km, column_kmt, column_delta_z, c
! local variables
!-----------------------------------------------------------------------
character(*), parameter :: subname = 'marbl_ciso_mod:ciso_compute_particulate_terms'
character(len=char_len) :: log_message

real (r8) :: &
dz_loc, & ! dz at a particular i,j location
Expand Down Expand Up @@ -1952,6 +1953,7 @@ subroutine marbl_ciso_set_surface_forcing( &
! local variables
!-----------------------------------------------------------------------
character(*), parameter :: subname = 'marbl_ciso_mod:marbl_ciso_set_surface_forcing'
character(len=char_len) :: log_message

logical (log_kind), save :: &
first = .true. ! Logical for first iteration test
Expand Down
32 changes: 15 additions & 17 deletions src/marbl_co2calc_mod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,8 @@ module marbl_co2calc_mod
! based upon OCMIP2 co2calc
!-----------------------------------------------------------------------------

use marbl_kinds_mod , only : int_kind, r8, log_kind
use marbl_kinds_mod , only : int_kind, r8, log_kind, char_len
use marbl_logging , only : marbl_log_type
use marbl_logging , only : error_msg
use marbl_logging , only : status_msg
use marbl_parms , only : p001,c3, c10
use marbl_constants_mod , only : c0, p5, c1, c2, c1000, T0_Kelvin, rho_sw

Expand Down Expand Up @@ -202,8 +200,7 @@ subroutine marbl_co2calc_surf( &

if (present (marbl_status_log)) then
if (marbl_status_log%labort_marbl) then
error_msg = "error code returned from comp_htotal"
call marbl_status_log%log_error(error_msg, subname)
call marbl_status_log%log_error_trace("comp_htotal()", subname)
return
end if
end if
Expand Down Expand Up @@ -306,6 +303,7 @@ subroutine marbl_comp_CO3terms(&
!---------------------------------------------------------------------------
! local variable declarations
!---------------------------------------------------------------------------
character(*), parameter :: subname = 'marbl_co2calc:marbl_comp_CO3terms'
integer(kind=int_kind) :: c
real(kind=r8) :: mass_to_vol ! (mol/kg) -> (mmol/m^3)
real(kind=r8) :: vol_to_mass ! (mmol/m^3) -> (mol/kg)
Expand Down Expand Up @@ -371,8 +369,7 @@ subroutine marbl_comp_CO3terms(&
phlo, phhi, htotal, marbl_status_log)

if (marbl_status_log%labort_marbl) then
error_msg = "error code returned from comp_htotal"
call marbl_status_log%log_error(error_msg, "marbl_co2calc::marbl_comp_CO3terms")
call marbl_status_log%log_error_trace("comp_htotal()", subname)
return
end if

Expand Down Expand Up @@ -789,6 +786,7 @@ subroutine comp_htotal(num_elements, mask, temp, dic_in, ta_in, pt_in, sit_in, &
!---------------------------------------------------------------------------
! local variable declarations
!---------------------------------------------------------------------------
character(*), parameter :: subname = 'marbl_co2calc:marbl_comp_htotal'
integer(kind=int_kind) :: c
real(kind=r8) :: mass_to_vol ! (mol/kg) -> (mmol/m^3)
real(kind=r8) :: vol_to_mass ! (mmol/m^3) -> (mol/kg)
Expand Down Expand Up @@ -866,8 +864,7 @@ subroutine comp_htotal(num_elements, mask, temp, dic_in, ta_in, pt_in, sit_in, &
marbl_status_log)

if (marbl_status_log%labort_marbl) then
error_msg = "error code returned from drtsafe"
call marbl_status_log%log_error(error_msg, "marbl_co2calc::comp_htotal")
call marbl_status_log%log_error_trace("drtsafe", subname)
return
end if

Expand Down Expand Up @@ -908,6 +905,7 @@ subroutine drtsafe(num_elements, mask_in, k1, k2, co3_coeffs, x1, x2, xacc, &
! local variable declarations
!---------------------------------------------------------------------------
character(*), parameter :: subname = 'marbl_co2calc::drtsafe'
character(len=char_len) :: log_message
logical(kind=log_kind) :: leave_bracket, dx_decrease
logical(kind=log_kind), dimension(num_elements) :: mask
integer(kind=int_kind) :: c, it
Expand Down Expand Up @@ -942,24 +940,24 @@ subroutine drtsafe(num_elements, mask_in, k1, k2, co3_coeffs, x1, x2, xacc, &
! FIXME #21: make marbl_status_log required - this is currently needed
! since abio_dic_dic14_mod is calling this routine but has
! not itself been MARBLized yet
WRITE(status_msg,"(4A,I0,A,I0,A,I0)") '(', subname, ') ', &
WRITE(log_message,"(4A,I0,A,I0,A,I0)") '(', subname, ') ', &
', c = ', c, ', it = ', it
call marbl_status_log%log_noerror(status_msg, subname, c, .true.)
WRITE(status_msg,"(4A,2E15.7e3)") '(', subname, ') ', &
call marbl_status_log%log_noerror(log_message, subname, c, .true.)
WRITE(log_message,"(4A,2E15.7e3)") '(', subname, ') ', &
' x1,f = ', x1(c), flo(c)
call marbl_status_log%log_noerror(status_msg, subname, c, .true.)
WRITE(status_msg,"(4A,2E15.7e3)") '(', subname, ') ', &
call marbl_status_log%log_noerror(log_message, subname, c, .true.)
WRITE(log_message,"(4A,2E15.7e3)") '(', subname, ') ', &
' x2,f = ', x2(c), fhi(c)
call marbl_status_log%log_noerror(status_msg, subname, c, .true.)
call marbl_status_log%log_noerror(log_message, subname, c, .true.)
end if
end if
end do

if (it > max_bracket_grow_it) then
if (present(marbl_status_log)) then
! FIXME #21 (see above)
error_msg = "bounding bracket for pH solution not found"
call marbl_status_log%log_error(error_msg, subname, c)
log_message = "bounding bracket for pH solution not found"
call marbl_status_log%log_error(log_message, subname, c)
end if
return
end if
Expand Down
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