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Merged
Rick-Methot-NOAA merged 5 commits into from
Aug 11, 2022
Merged

320 standardize exit message #366

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e81a7b5
Added new options for messages
nschindler-noaa Aug 2, 2022
d469161
replaced all N_warn messages
nschindler-noaa Aug 5, 2022
db2031b
Merge branch 'main' into 320-standardize-exit-message
nschindler-noaa Aug 5, 2022
5c49624
Removed old code/comments
nschindler-noaa Aug 5, 2022
d1e0cf1
Update SS_global.tpl
nschindler-noaa Aug 11, 2022
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65 changes: 34 additions & 31 deletions SS_benchfore.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -134,8 +134,8 @@ FUNCTION void setup_Benchmark()
{
if (timevary_MG(y, 4) > 0)
{
N_warn++;
warning << N_warn << " mean recruitment for forecast is incompatible with timevary recr_dist in yr: " << y << "; user must adjust manually" << endl;
warnstream << "mean recruitment for forecast is incompatible with timevary recr_dist in yr: " << y << "; user must adjust manually";
write_message(WARN, 0);
}
recr_dist(y) = recr_dist_endyr;
}
Expand Down Expand Up @@ -192,8 +192,8 @@ FUNCTION void setup_Benchmark()
if (Fcast_RelF_Use(s, f) == 0. && bycatch_setup(f, 3) > 0)
{
Fcast_RelF_Use(s, f) = 1.0e-6;
N_warn++;
warning << N_warn << " setting positive forecast relF for bycatch fleet: " << f << endl;
warnstream << "setting positive forecast relF for bycatch fleet: " << f;
write_message(ADJUST, 0);
}
}
}
Expand All @@ -205,8 +205,8 @@ FUNCTION void setup_Benchmark()
if (Fcast_RelF_special(s, f) == 1 && Fcast_RelF_Use(s, f) == 0.0)
{
Fcast_RelF_Use(s, f) = 1.0e-6;
N_warn++;
warning << N_warn << " setting positive forecast relF for forecast only fleet: " << f << endl;
warnstream << "setting positive forecast relF for forecast only fleet: " << f;
write_message(ADJUST, 0);
}
}
}
Expand Down Expand Up @@ -761,13 +761,13 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
{
if (fabs(SPR_actual - SPR_target100) >= 0.1)
{
N_warn++;
warning << N_warn << " warning: poor convergence in Fspr search " << SPR_target << " " << SPR_actual / 100. << endl;
warnstream << "poor convergence in Fspr search " << SPR_target << " " << SPR_actual / 100.;
write_message(WARN, 0);
}
if (SPR_actual / SPR_target100 >= 1.01)
{
N_warn++;
warning << N_warn << " warning: Fmult = " << Fmult << " cannot get high enough to achieve low SPR target: " << SPR_target << "; SPR achieved is: " << SPR_actual / 100. << endl;
warnstream << "Fmult = " << Fmult << " cannot get high enough to achieve low SPR target: " << SPR_target << "; SPR achieved is: " << SPR_actual / 100.;
write_message(WARN, 0);
}

report5 << "seas fleet Hrate encB deadB retB encN deadN retN: " << endl;
Expand Down Expand Up @@ -877,8 +877,8 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
{
if (sfabs(F01_origin * 0.1 - F01_actual) >= 0.001)
{
N_warn++;
warning << N_warn << " warning: poor convergence in F0.1 search target= " << F01_origin * 0.1 << " actual= " << F01_actual << endl;
warnstream << "poor convergence in F0.1 search target= " << F01_origin * 0.1 << " actual= " << F01_actual;
write_message(WARN, 0);
}
report5 << "seas fleet Hrate encB deadB retB encN deadN retN): " << endl;
for (s = 1; s <= nseas; s++)
Expand Down Expand Up @@ -1041,8 +1041,8 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
{
if (fabs(log(Btgt / Btgttgt)) >= 0.001)
{
N_warn++;
warning << N_warn << " warning: poor convergence in Btarget search " << Btgttgt << " " << Btgt << endl;
warnstream << "poor convergence in Btarget search " << Btgttgt << " " << Btgt;
write_message (WARN, 0);
}
report5 << "seas fleet Hrate encB deadB retB encN deadN retN): " << endl;
for (s = 1; s <= nseas; s++)
Expand Down Expand Up @@ -1387,8 +1387,8 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
{
if (fabs(dyld / dyldp) >= 0.001)
{
N_warn++;
warning << N_warn << " warning: poor convergence in Fmsy, final dy/dy2= " << dyld / dyldp << endl;
warnstream << "poor convergence in Fmsy, final dy/dy2= " << dyld / dyldp;
write_message (WARN, 0);
}
report5 << "seas fleet Hrate encB deadB retB encN deadN retN): " << endl;
for (s = 1; s <= nseas; s++)
Expand Down Expand Up @@ -1496,18 +1496,18 @@ FUNCTION void Get_Benchmarks(const int show_MSY)

if (Fmult * 3.0 <= SPR_Fmult)
{
N_warn++;
warning << N_warn << " Fmsy/mey is <1/3 of Fspr are you sure? check for convergence " << endl;
warnstream << "Fmsy/mey is <1/3 of Fspr are you sure? check for convergence ";
write_message (WARN, 0);
}
if (Fmult / 3.0 >= SPR_Fmult)
{
N_warn++;
warning << N_warn << " Fmsy/mey is >3x of Fspr are you sure? check for convergence " << endl;
warnstream << "Fmsy/mey is >3x of Fspr are you sure? check for convergence ";
write_message (WARN, 0);
}
if (Fmult / 0.98 >= Fmax)
{
N_warn++;
warning << N_warn << " Fmsy.mey is close to max allowed; check for convergence " << endl;
warnstream << "Fmsy.mey is close to max allowed; check for convergence ";
write_message (WARN, 0);
}
report5 << "end Seach for MSY" << endl;
} // end Do_MSY = 2
Expand Down Expand Up @@ -1645,8 +1645,8 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
{
if (fabs(log(Btgt2 / Btgttgt2)) >= 0.001)
{
N_warn++;
warning << N_warn << " warning: poor convergence in Blimit search " << Btgttgt2 << " " << Btgt2 << endl;
warnstream << "poor convergence in Blimit search " << Btgttgt2 << " " << Btgt2 ;
write_message (WARN, 0);
}
report5 << "seas fleet Hrate encB deadB retB encN deadN retN): " << endl;
for (s = 1; s <= nseas; s++)
Expand Down Expand Up @@ -1880,9 +1880,9 @@ FUNCTION void Get_Forecast()
Fcast_Fmult = join1 * Fcast_Fmult + (1. - join1) * max_harvest_rate; // new F value for this fleet, constrained by max_harvest_rate
if (join1 < 0.999)
{
report5 << "Forecast F capped by max possible F from control file" << max_harvest_rate << endl;
N_warn++;
warning << N_warn << " Forecast F capped by max possible F from control file: " << max_harvest_rate << endl;
warnstream << "Forecast F capped by max possible F from control file" << max_harvest_rate;
report5 << warnstream.str() << endl;
write_message (WARN, 0);
}
}
else
Expand Down Expand Up @@ -2005,13 +2005,17 @@ FUNCTION void Get_Forecast()
report5 << endl;
}
}

if (H4010_top_rd < 0.0)
{
H4010_top = Bmsy / SSB_unf;
if (H4010_bot > 0.25) {N_warn++; warning<<N_warn<<" Beware: control rule cutoff is large ("<<H4010_bot<<"); so may not be < calculated Bmsy/SSB_unf ("<<H4010_top<<")"<<endl;}
if (H4010_bot > 0.25)
{
warnstream << "control rule cutoff is large (" << H4010_bot << "); so may not be < calculated Bmsy/SSB_unf (" << H4010_top << ")";
write_message (WARN, 0);
}
}
else
else
{
H4010_top = H4010_top_rd;
}
Expand Down Expand Up @@ -3506,4 +3510,3 @@ FUNCTION void Get_Forecast()
} // end Fcast_Loop1 for the different stages of the forecast
}
// end forecast function

43 changes: 22 additions & 21 deletions SS_biofxn.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -28,9 +28,11 @@ FUNCTION void get_MGsetup(const int yz)
{
if (mgp_adj(f) < MGparm_1(f, 1) || mgp_adj(f) > MGparm_1(f, 2))
{
N_warn++;
warning << N_warn << " "
<< " adjusted MGparm out of base parm bounds. Phase: " << current_phase() << "; Inter: " << niter << "; parm#: " << f << "; y: " << yz << "; min: " << MGparm_1(f, 1) << "; max: " << MGparm_1(f, 2) << "; base: " << MGparm(f) << " timevary_val: " << mgp_adj(f) << " " << ParmLabel(f) << endl;
warnstream << "adjusted MGparm out of base parm bounds. Phase: " << current_phase()
<< "; Inter: " << niter << "; parm#: " << f << "; y: " << yz << "; min: "
<< MGparm_1(f, 1) << "; max: " << MGparm_1(f, 2) << "; base: " << MGparm(f)
<< " timevary_val: " << mgp_adj(f) << " " << ParmLabel(f);
write_message (WARN, 0);
}
}
}
Expand Down Expand Up @@ -1229,45 +1231,45 @@ FUNCTION void get_natmort()
for (s = nseas ; s >= 1; s--)
{
int Loren_t = styr + (yz - styr) * nseas + s - 1;
dvariable loren_scale_extra = 0; //start with no extra scaler. This will be used if the maximum reference age is greater than nages.
dvariable loren_scale_extra = 0; //start with no extra scaler. This will be used if the maximum reference age is greater than nages.
int ref_age = int(natM_amax); //start with reference age equal to the input maximum age. This will be adjusted below to equal nages if the maximum age is greater than nages.
if (ref_age > nages)//if reference age is greater than accumulator age need math to approximate the unknown size/age bins
{
int extra_years = ref_age - nages;//determine how many extra ages will be included between accumulator age and reference age

//The following code is a simple difference approach to approximate the first and second rate of change in relative M to estimate approximate M for ages older than nages
//calculate proportional change in lorenzen M between second to last and last age group
dvariable d1 = 1 + (log((Ave_Size(Loren_t, mid_subseas, g)(nages)) / (Ave_Size(Loren_t, mid_subseas, g)(nages) + Loren_temp2)) -
//calculate proportional change in lorenzen M between second to last and last age group
dvariable d1 = 1 + (log((Ave_Size(Loren_t, mid_subseas, g)(nages)) / (Ave_Size(Loren_t, mid_subseas, g)(nages) + Loren_temp2)) -
log((Ave_Size(Loren_t, mid_subseas, g)(nages - 1)) / (Ave_Size(Loren_t, mid_subseas, g)(nages-1) + Loren_temp2))) /
log((Ave_Size(Loren_t, mid_subseas, g)(nages)) / (Ave_Size(Loren_t, mid_subseas, g)(nages) + Loren_temp2));
//calculate proportional change in lorenzen M between third to last and second to last age group
dvariable d2 = 1 + (log((Ave_Size(Loren_t, mid_subseas, g)(nages - 1))/(Ave_Size(Loren_t, mid_subseas, g)(nages - 1) + Loren_temp2)) -

//calculate proportional change in lorenzen M between third to last and second to last age group
dvariable d2 = 1 + (log((Ave_Size(Loren_t, mid_subseas, g)(nages - 1))/(Ave_Size(Loren_t, mid_subseas, g)(nages - 1) + Loren_temp2)) -
log((Ave_Size(Loren_t, mid_subseas, g)(nages - 2)) / (Ave_Size(Loren_t, mid_subseas, g)(nages - 2) + Loren_temp2))) /
log((Ave_Size(Loren_t, mid_subseas, g)(nages - 1)) / (Ave_Size(Loren_t, mid_subseas, g)(nages - 1) + Loren_temp2));
//calculate the second order proportional change in proportional changes during the last two age pairs

//calculate the second order proportional change in proportional changes during the last two age pairs
dvariable d3 = 1 + (d1 - d2) / d1;

//project total proportion of last years M that will occur in all ages older than nages
for (int ey = 1; ey <= extra_years; ey++)
{
d1 = d1 * d3;//each year adjust the first order proportion by the second order proportion
loren_scale_extra += d1;//add that proportion to a scaler that will be multiplied by the nages M value
loren_scale_extra += d1;//add that proportion to a scaler that will be multiplied by the nages M value
}
ref_age = nages; //set reference age to nages to use all available Ave_Size values
ref_age = nages; //set reference age to nages to use all available Ave_Size values
}
//Calculate loren_temp multiplier that achieves target average M

//Calculate loren_temp multiplier that achieves target average M
Loren_temp = (Loren_M1 * (natM_amax - natM_amin + 1)) / (sum(log(
elem_div(Ave_Size(Loren_t, mid_subseas, g)(natM_amin, ref_age), (Ave_Size(Loren_t, mid_subseas, g)(natM_amin, ref_age) + Loren_temp2))
)) + loren_scale_extra * log((Ave_Size(Loren_t, mid_subseas, g)(ref_age)) / (Ave_Size(Loren_t, mid_subseas, g)(ref_age) + Loren_temp2)));

natM(t_base + s, 0, gpi)(0, nages) = log(
elem_div(Ave_Size(Loren_t, mid_subseas, g)(0, nages),
(Ave_Size(Loren_t, mid_subseas, g)(0, nages) + Loren_temp2)))
elem_div(Ave_Size(Loren_t, mid_subseas, g)(0, nages),
(Ave_Size(Loren_t, mid_subseas, g)(0, nages) + Loren_temp2)))
* Loren_temp;
if (s < Bseas(g))
if (s < Bseas(g))
{
natM(t_base + s, 0, gpi, 0) = natM(t_base + s + 1, 0, gpi, 0);
}
Expand Down Expand Up @@ -2118,4 +2120,3 @@ FUNCTION void Make_Fecundity()
}
}
}

46 changes: 16 additions & 30 deletions SS_expval.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -239,8 +239,10 @@ FUNCTION void Get_expected_values(const int y, const int t);
{
if (do_once == 1)
{
N_warn++;
warning << N_warn << " " << current_phase() << " " << niter << "warn in first call: Nil selected fish for year, seas, fleet " << y << " " << s << " " << f << "; SS may recover; suggest check initial parm. values for selectivity and growth" << endl;
warnstream << current_phase() << " " << niter
<< "warn in first call: Nil selected fish for year, seas, fleet " << y << " " << s << " " << f
<< "; SS may recover; suggest check initial parm. values for selectivity and growth";
write_message (WARN, 0);
}
exp_l_temp += 1.0e-09;
}
Expand Down Expand Up @@ -530,8 +532,8 @@ FUNCTION void Get_expected_values(const int y, const int t);
}
if (exp_disc(f, j) < 0.0)
{
N_warn++;
warning << N_warn << " " << f << " " << j << " " << exp_disc(f, j) << " catches " << catch_fleet(t, f) << endl;
warnstream << f << " " << j << " " << exp_disc(f, j) << " catches " << catch_fleet(t, f);
write_message (WARN, 0);
}
}
else
Expand Down Expand Up @@ -752,20 +754,14 @@ FUNCTION void Get_expected_values(const int y, const int t);
} // ignore tiny fish
if (z1 + 1 >= z2)
{
N_warn++;
cout << " EXIT - see warning " << endl;
warning << N_warn << " "
<< " error: max population size " << wt_len_low(s, 1, z1) << " is less than first data bin " << SzFreq_bins(SzFreqMethod, 1) << " for SzFreqMethod " << SzFreqMethod << endl;
exit(1);
warnstream << "max population size " << wt_len_low(s, 1, z1) << " is less than first data bin " << SzFreq_bins(SzFreqMethod, 1) << " for SzFreqMethod " << SzFreqMethod;
write_message (FATAL, 0); // EXIT!
}

if (wt_len_low(s, 1, nlength2) < SzFreq_bins(SzFreqMethod, SzFreq_Nbins(SzFreqMethod)))
{
N_warn++;
cout << " EXIT - see warning " << endl;
warning << N_warn << " "
<< " error: max population size " << wt_len_low(s, 1, nlength2) << " is less than max data bin " << SzFreq_bins(SzFreqMethod, SzFreq_Nbins(SzFreqMethod)) << " for SzFreqMethod " << SzFreqMethod << endl;
exit(1);
warnstream << "max population size " << wt_len_low(s, 1, nlength2) << " is less than max data bin " << SzFreq_bins(SzFreqMethod, SzFreq_Nbins(SzFreqMethod)) << " for SzFreqMethod " << SzFreqMethod;
write_message (FATAL, 0); // EXIT!
}

for (z = z1; z <= z2; z++)
Expand Down Expand Up @@ -830,19 +826,13 @@ FUNCTION void Get_expected_values(const int y, const int t);
} // ignore tiny fish
if (z1 + 1 >= z2)
{
N_warn++;
cout << " EXIT - see warning " << endl;
warning << N_warn << " "
<< " error: max population size " << wt_len_low(s, 1, z1) << " is less than first data bin " << SzFreq_bins(SzFreqMethod, 1) << " for SzFreqMethod " << SzFreqMethod << endl;
exit(1);
warnstream << "max population size " << wt_len_low(s, 1, z1) << " is less than first data bin " << SzFreq_bins(SzFreqMethod, 1) << " for SzFreqMethod " << SzFreqMethod;
write_message (FATAL, 0); // EXIT!
}
if (wt_len_low(s, 1, nlength2) < SzFreq_bins(SzFreqMethod, SzFreq_Nbins(SzFreqMethod)))
{
N_warn++;
cout << " EXIT - see warning " << endl;
warning << N_warn << " "
<< " error: max population size " << wt_len_low(s, 1, nlength2) << " is less than max data bin " << SzFreq_bins(SzFreqMethod, SzFreq_Nbins(SzFreqMethod)) << " for SzFreqMethod " << SzFreqMethod << endl;
exit(1);
warnstream << "max population size " << wt_len_low(s, 1, nlength2) << " is less than max data bin " << SzFreq_bins(SzFreqMethod, SzFreq_Nbins(SzFreqMethod)) << " for SzFreqMethod " << SzFreqMethod;
write_message (FATAL, 0); // EXIT!
}

for (z = z1; z <= z2; z++)
Expand Down Expand Up @@ -897,11 +887,8 @@ FUNCTION void Get_expected_values(const int y, const int t);

if (len_bins2(nlength2) < SzFreq_bins(SzFreqMethod, SzFreq_Nbins(SzFreqMethod)))
{
N_warn++;
cout << " EXIT - see warning " << endl;
warning << N_warn << " "
<< " error: max population len bin " << len_bins2(nlength2) << " is less than max data bin " << SzFreq_bins(SzFreqMethod, SzFreq_Nbins(SzFreqMethod)) << " for SzFreqMethod " << SzFreqMethod << endl;
exit(1);
warnstream << "max population len bin " << len_bins2(nlength2) << " is less than max data bin " << SzFreq_bins(SzFreqMethod, SzFreq_Nbins(SzFreqMethod)) << " for SzFreqMethod " << SzFreqMethod;
write_message (FATAL, 0); // EXIT!
}

for (z = z1; z <= z2; z++)
Expand Down Expand Up @@ -1123,4 +1110,3 @@ FUNCTION void Get_expected_values(const int y, const int t);
} // end loop of subseasons
return;
} // end function

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