UPD: update Test Case model output and reports

Casal2 · Oct 6, 2021 · 70b2b4f · 70b2b4f
1 parent dc0d435
commit 70b2b4f
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Showing 48 changed files with 36,376 additions and 470,655 deletions.
diff --git a/CASAL2/source/Reports/Age/AgeLength.cpp b/CASAL2/source/Reports/Age/AgeLength.cpp
@@ -19,7 +19,7 @@ namespace age {
 
 AgeLength::AgeLength() {
   run_mode_    = (RunMode::Type)(RunMode::kBasic | RunMode::kProjection | RunMode::kSimulation | RunMode::kEstimation | RunMode::kProfiling);
-  model_state_ = State::kExecute;
+  model_state_ = State::kIterationComplete;
 
   parameters_.Bind<string>(PARAM_TIME_STEP, &time_step_, "The time step label", "", "");
   parameters_.Bind<unsigned>(PARAM_YEARS, &years_, "The years for the report", "", true);

diff --git a/CASAL2/source/Version.h b/CASAL2/source/Version.h
@@ -3,10 +3,10 @@
 #define VERSION_H_
 #define VERSION "21.10 (2021-10-06)"
 #define VERSION_NUMBER "21.10"
-#define SOURCE_CONTROL_REVISION 31dad4ec5fde045bc6153ed54ca140b80d8ebb35
+#define SOURCE_CONTROL_REVISION dc0d435166d511e3e64d585a898a7a3f443e4197
 #define SOURCE_CONTROL_DATE "2021-10-06"
 #define SOURCE_CONTROL_YEAR "2021"
 #define SOURCE_CONTROL_MONTH "October"
-#define SOURCE_CONTROL_TIME "22:14:26"
-#define SOURCE_CONTROL_VERSION "2021-10-06 22:14:26 UTC (rev. 31dad4ec)"
+#define SOURCE_CONTROL_TIME "22:23:02"
+#define SOURCE_CONTROL_VERSION "2021-10-06 22:23:02 UTC (rev. dc0d4351)"
 #endif
diff --git a/Documentation/UserManual/CASAL2.pdf b/Documentation/UserManual/CASAL2.pdf
diff --git a/Documentation/UserManual/Version.tex b/Documentation/UserManual/Version.tex
@@ -1,9 +1,9 @@
 % WARNING: THIS FILE IS AUTOMATICALLY GENERATED BY doBuild version. DO NOT EDIT THIS FILE
 \newcommand{\Version}{21.10 (2021-10-06)}
 \newcommand{\VersionNumber}{21.10}
-\newcommand{\SourceControlRevision}{31dad4ec5fde045bc6153ed54ca140b80d8ebb35}
+\newcommand{\SourceControlRevision}{dc0d435166d511e3e64d585a898a7a3f443e4197}
 \newcommand{\SourceControlDateDoc}{2021-10-06}
 \newcommand{\SourceControlYearDoc}{2021}
 \newcommand{\SourceControlMonthDoc}{October}
-\newcommand{\SourceControlTimeDoc}{22:14:26}
-\newcommand{\SourceControlVersion}{2021-10-06 22:14:26 UTC (rev. 31dad4ec)}
+\newcommand{\SourceControlTimeDoc}{22:23:02}
+\newcommand{\SourceControlVersion}{2021-10-06 22:23:02 UTC (rev. dc0d4351)}
diff --git a/R-libraries/Version.R b/R-libraries/Version.R
@@ -1,9 +1,9 @@
 # WARNING: THIS FILE IS AUTOMATICALLY GENERATED BY doBuild version. DO NOT EDIT THIS FILE
 Version<-"21.10 (2021-10-06)"
 VersionNumber<-"21.10"
-SourceControlRevision<-"31dad4ec5fde045bc6153ed54ca140b80d8ebb35"
+SourceControlRevision<-"dc0d435166d511e3e64d585a898a7a3f443e4197"
 SourceControlDateDoc<-"2021-10-06"
 SourceControlYearDoc<-"2021"
 SourceControlMonthDoc<-"October"
-SourceControlTimeDoc<-"22:14:26"
-SourceControlVersion<-"2021-10-06 22:14:26 UTC (rev. 31dad4ec)"
+SourceControlTimeDoc<-"22:23:02"
+SourceControlVersion<-"2021-10-06 22:23:02 UTC (rev. dc0d4351)"
diff --git a/TestCases/R-functions/report_read_in_Casal2_MPD_files.R b/TestCases/R-functions/report_read_in_Casal2_MPD_files.R
@@ -1,8 +1,6 @@
 C2_subdir <- c('betadiff_casal_flags_on',
                'betadiff_casal_flags_off',
                'betadiff_casal_flags_on_low_tol',
-#                'cppad_casal_flags_on',
-#                'cppad_casal_flags_off',
                'adolc_casal_flags_on',
                'adolc_casal_flags_off',
                'adolc_casal_flags_on_low_tol')
@@ -29,22 +27,9 @@ for (c in 1:num_C2_models)
 {
     cas2_mpd_filename <- file.path(base_dir, 'Casal2', C2_subdir[c], mpd_run)
 
-    # strip out "* grad_f[] ~~~" from CppAD model output
-    if (grepl('cppad', C2_subdir[c], ignore.case=TRUE)) {
-        tmpfile <- readLines(cas2_mpd_filename)
-        if (any(grepl(problem_str, tmpfile, fixed=TRUE))) {
-            if (file.rename(cas2_mpd_filename, paste(cas2_mpd_filename, '.orig', sep=''))) {
-                new_tmpfile <- gsub(problem_str, new_str, tmpfile, fixed=TRUE)
-                writeLines(new_tmpfile, cas2_mpd_filename)
-            } else {
-                print(paste('Error: could not rename and clean up file', cas2_mpd_filename))
-            }
-        }
-    }
-
     cas2_mpd[[c]]  <- Casal2::extract.mpd(cas2_mpd_filename)
 
-    cas2_corr[[c]] <- Casal2::extract.correlation.matrix(mpd_out, file.path(base_dir, 'Casal2', C2_subdir[c]))
+    cas2_corr[[c]] <- cas2_mpd[[c]]$Corr$correlation_matrix
 
     cas2_conv[[c]] <- get_convergence_information(cas2_mpd_filename)
 }

diff --git a/TestCases/primary/BCO/Casal2/adolc_casal_flags_off/run_estimation.txt b/TestCases/primary/BCO/Casal2/adolc_casal_flags_off/run_estimation.txt
diff --git a/TestCases/primary/BCO/Casal2/adolc_casal_flags_on/run_estimation.txt b/TestCases/primary/BCO/Casal2/adolc_casal_flags_on/run_estimation.txt
diff --git a/TestCases/primary/BCO/Casal2/adolc_casal_flags_on_low_tol/run_estimation.txt b/TestCases/primary/BCO/Casal2/adolc_casal_flags_on_low_tol/run_estimation.txt
diff --git a/TestCases/primary/BCO/Casal2/betadiff_casal_flags_off/run_estimation.txt b/TestCases/primary/BCO/Casal2/betadiff_casal_flags_off/run_estimation.txt
diff --git a/TestCases/primary/BCO/Casal2/betadiff_casal_flags_on/run_estimation.txt b/TestCases/primary/BCO/Casal2/betadiff_casal_flags_on/run_estimation.txt
diff --git a/TestCases/primary/BCO/Casal2/betadiff_casal_flags_on_low_tol/run_estimation.txt b/TestCases/primary/BCO/Casal2/betadiff_casal_flags_on_low_tol/run_estimation.txt
diff --git a/TestCases/primary/BCO/compare_BCO.MPD.html b/TestCases/primary/BCO/compare_BCO.MPD.html
diff --git a/TestCases/primary/HAK/Casal2/adolc_casal_flags_off/run_estimation.txt b/TestCases/primary/HAK/Casal2/adolc_casal_flags_off/run_estimation.txt
diff --git a/TestCases/primary/HAK/Casal2/adolc_casal_flags_on/run_estimation.txt b/TestCases/primary/HAK/Casal2/adolc_casal_flags_on/run_estimation.txt
diff --git a/TestCases/primary/HAK/Casal2/adolc_casal_flags_on_low_tol/run_estimation.txt b/TestCases/primary/HAK/Casal2/adolc_casal_flags_on_low_tol/run_estimation.txt
diff --git a/TestCases/primary/HAK/Casal2/betadiff_casal_flags_off/run_estimation.txt b/TestCases/primary/HAK/Casal2/betadiff_casal_flags_off/run_estimation.txt
diff --git a/TestCases/primary/HAK/Casal2/betadiff_casal_flags_on/run_estimation.txt b/TestCases/primary/HAK/Casal2/betadiff_casal_flags_on/run_estimation.txt
diff --git a/TestCases/primary/HAK/Casal2/betadiff_casal_flags_on_low_tol/run_estimation.txt b/TestCases/primary/HAK/Casal2/betadiff_casal_flags_on_low_tol/run_estimation.txt
diff --git a/TestCases/primary/HAK/compare_HAK.MPD.html b/TestCases/primary/HAK/compare_HAK.MPD.html
diff --git a/TestCases/primary/HOK/Casal2/adolc_casal_flags_off/run_estimation.txt b/TestCases/primary/HOK/Casal2/adolc_casal_flags_off/run_estimation.txt
@@ -1,11 +1,11 @@
 Environment: User=Casal2
 Call: ../../../../../BuildSystem/Casal2/casal2 -e -o params_est.out
-Date: Thu Oct  7 10:45:01 2021
+Date: Thu Oct  7 11:57:04 2021
 Version: v21.10 (2021-10-06)
 Copyright (c) 2017-2021, NIWA (www.niwa.co.nz)
 c2user
  Machine=c2computer (Linux 5.10.0-8-amd64 x86_64)
- PID=158320
+ PID=316998
 
 
 
@@ -12144,5 +12144,5 @@ estimated parameter 'selectivity[sel_Whome].v{7}' was within 0.001 of upper boun
 *end
 
 [INFO] Completed
-[INFO] Total CPU time: -3.90917e+08 hours
-[INFO] Total elapsed time: 5.067 minutes
+[INFO] Total CPU time: -3.90927e+08 hours
+[INFO] Total elapsed time: 5.35 minutes