AtChem · rs028 · Jan 10, 2022 · Dec 31, 2021 · Jan 4, 2022 · Jan 4, 2022
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,6 +1,6 @@
 name: CI
 
-# Controls when the action will run. 
+# Controls when the action will run.
 on:
   # Triggers the workflow on push or pull request events but only for the master branch
   pull_request:
@@ -22,7 +22,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest, macos-10.15]
         fortran: [8, 9]
 
     # Steps represent a sequence of tasks that will be executed as part of the job
@@ -35,7 +35,7 @@ jobs:
       # Install gfortran 8 since both Ubuntu and macOS don't supply it
       # macOS only
       - name: Install gfortran-8 on macOS
-        if: matrix.os == 'macos-latest' && matrix.fortran == 8
+        if: matrix.os == 'macos-10.15' && matrix.fortran == 8
         run: brew install gcc@8
 
       # ubuntu only
@@ -51,17 +51,17 @@ jobs:
 
       # macOS only
       - name: Install cvode (macOS)
-        if: matrix.os == 'macos-latest'
+        if: matrix.os == 'macos-10.15'
         run: ./tools/install/install_cvode.sh $PWD $(which gfortran-${{ matrix.fortran }})
-      
+
       # Install all dependencies
       # both OSs
       - name: Install openlibm
         run: ./tools/install/install_openlibm.sh $PWD
-      
+
       - name: Install numdiff
         run: ./tools/install/install_numdiff.sh $PWD
-      
+
       - name: Install fruit
         run: sudo ./tools/install/install_fruit.sh $PWD
 
@@ -73,13 +73,13 @@ jobs:
         run: |
           cp tools/install/Makefile.skel Makefile
           ./build/build_atchem2.sh ./mcm/mechanism_test.fac
-          if [ $RUNNER_OS != 'Linux' ] ; then 
-            install_name_tool -change libopenlibm.dylib.1 $PWD/openlibm-0.4.1/libopenlibm.dylib.1 atchem2 ; 
-            install_name_tool -change @rpath/libsundials_cvode.2.dylib $PWD/cvode/lib/libsundials_cvode.dylib atchem2 ; 
-            install_name_tool -change @rpath/libsundials_fnvecserial.2.dylib $PWD/cvode/lib/libsundials_fnvecserial.dylib atchem2 ; 
+          if [ $RUNNER_OS != 'Linux' ] ; then
+            install_name_tool -change libopenlibm.dylib.1 $PWD/openlibm-0.4.1/libopenlibm.dylib.1 atchem2 ;
+            install_name_tool -change @rpath/libsundials_cvode.2.dylib $PWD/cvode/lib/libsundials_cvode.dylib atchem2 ;
+            install_name_tool -change @rpath/libsundials_fnvecserial.2.dylib $PWD/cvode/lib/libsundials_fnvecserial.dylib atchem2 ;
             install_name_tool -change @rpath/libsundials_nvecserial.2.dylib $PWD/cvode/lib/libsundials_nvecserial.dylib atchem2 ;
           fi
-      
+
       - name: Indent and style tests
         run: |
           make indenttest
@@ -91,7 +91,7 @@ jobs:
           ./atchem2
           # Upload 'build' coverage to codecov
           if [[ "$RUNNER_OS" == "Linux" ]]; then sudo ln -f -s /usr/bin/gcov-${{ matrix.fortran }} /usr/bin/gcov ; bash <(curl -s https://codecov.io/bash) -F build ; fi
-      
+
       - name: Run tests
         # Set FORT_VERSION for use inside the Makefile
         env:

diff --git a/test/fruit_generator.rb → tests/fruit_generator.rb b/test/fruit_generator.rb → tests/fruit_generator.rb
diff --git a/...onfiguration/photolysisConstrained.config → tests/model_tests/.gitignore b/...onfiguration/photolysisConstrained.config → tests/model_tests/.gitignore
diff --git a/test/run_indent_test.sh → tests/run_indent_test.sh b/test/run_indent_test.sh → tests/run_indent_test.sh
@@ -14,7 +14,7 @@
 # that they conform to the coding guidelines, described in the manual
 # (doc/AtChem2-Manual.pdf)
 
-RESULTS_FILE=test/tests/testsuite.log
+RESULTS_FILE=tests/tests/testsuite.log
 
 echo "Running indent script on:"
 for file in src/*.f90 ; do

diff --git a/test/run_style_test.sh → tests/run_style_test.sh b/test/run_style_test.sh → tests/run_style_test.sh
@@ -14,7 +14,7 @@
 # that they conform to the coding guidelines, described in the manual
 # (doc/AtChem2-Manual.pdf)
 
-RESULTS_FILE=test/tests/testsuite.log
+RESULTS_FILE=tests/tests/testsuite.log
 
 echo "Running style script on:"
 for file in src/*.f90 ; do

diff --git a/test/run_tests.sh → tests/run_tests.sh b/test/run_tests.sh → tests/run_tests.sh
@@ -21,8 +21,8 @@ function test_output_text {
   # $3 start line number of section to compare
   # $4 end line number of section to compare
   # $5 name of test
-  file1=test/tests/$5/output/temporary_file.tmp
-  file2=test/tests/$5/output/temporary_file.tmp.cmp
+  file1=tests/tests/$5/output/temporary_file.tmp
+  file2=tests/tests/$5/output/temporary_file.tmp.cmp
   ndselect -b $3 -e $4 -o $file1 $1
   ndselect -b $3 -e $4 -o $file2 $2
   # Save output of test_output_file
@@ -62,7 +62,7 @@ function find_string {
 # $skip_test. This requires extra machinery to handle splitting the file into
 # sections between the skipped lines, and to numdiff those sections.
 
-TESTS_DIR=test/tests
+TESTS_DIR=tests/tests
 RESULTS_FILE=$TESTS_DIR/testsuite.log
 export DYLD_LIBRARY_PATH=$2
 

diff --git a/test/tests/.gitignore → tests/tests/.gitignore b/test/tests/.gitignore → tests/tests/.gitignore
diff --git a/test/tests/INFO.md → tests/tests/INFO.md b/test/tests/INFO.md → tests/tests/INFO.md
diff --git a/test/tests/firstorder/firstorder.out.cmp → tests/tests/firstorder/firstorder.out.cmp b/test/tests/firstorder/firstorder.out.cmp → tests/tests/firstorder/firstorder.out.cmp
@@ -4,15 +4,15 @@ AtChem2 v1.3-dev
  Directories
 -------------
  Model directory is: model
- Output directory is: test/tests/firstorder/output
- Reaction Rates directory is: test/tests/firstorder/output/reactionRates
- Configuration directory is: test/tests/firstorder/model/configuration
- Constraints directory is: test/tests/firstorder/model/constraints
- Environment Constraints directory is: test/tests/firstorder/model/constraints/environment
- Photolysis Constraints directory is: test/tests/firstorder/model/constraints/photolysis
- Species Constraints directory is: test/tests/firstorder/model/constraints/species
+ Output directory is: tests/tests/firstorder/output
+ Reaction Rates directory is: tests/tests/firstorder/output/reactionRates
+ Configuration directory is: tests/tests/firstorder/model/configuration
+ Constraints directory is: tests/tests/firstorder/model/constraints
+ Environment Constraints directory is: tests/tests/firstorder/model/constraints/environment
+ Photolysis Constraints directory is: tests/tests/firstorder/model/constraints/photolysis
+ Species Constraints directory is: tests/tests/firstorder/model/constraints/species
  MCM directory is: mcm
- Shared library is: test/tests/firstorder/model/configuration/mechanism.so
+ Shared library is: tests/tests/firstorder/model/configuration/mechanism.so
 
 -----------------------
  Species and reactions

diff --git a/...configuration/environmentVariables.config → ...configuration/environmentVariables.config b/...configuration/environmentVariables.config → ...configuration/environmentVariables.config
diff --git a/...torder/model/configuration/firstorder.fac → ...torder/model/configuration/firstorder.fac b/...torder/model/configuration/firstorder.fac → ...torder/model/configuration/firstorder.fac
diff --git a/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config b/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config
diff --git a/...er/model/configuration/mechanism.prod.cmp → ...er/model/configuration/mechanism.prod.cmp b/...er/model/configuration/mechanism.prod.cmp → ...er/model/configuration/mechanism.prod.cmp
diff --git a/...er/model/configuration/mechanism.reac.cmp → ...er/model/configuration/mechanism.reac.cmp b/...er/model/configuration/mechanism.reac.cmp → ...er/model/configuration/mechanism.reac.cmp
diff --git a/...der/model/configuration/mechanism.ro2.cmp → ...der/model/configuration/mechanism.ro2.cmp b/...der/model/configuration/mechanism.ro2.cmp → ...der/model/configuration/mechanism.ro2.cmp
diff --git a/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp b/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp
diff --git a/...rder/model/configuration/model.parameters → ...rder/model/configuration/model.parameters b/...rder/model/configuration/model.parameters → ...rder/model/configuration/model.parameters
diff --git a/...er/model/configuration/outputRates.config → ...er/model/configuration/outputRates.config b/...er/model/configuration/outputRates.config → ...er/model/configuration/outputRates.config
diff --git a/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config b/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config
diff --git a/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config b/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config
diff --git a/...der/model/configuration/solver.parameters → ...der/model/configuration/solver.parameters b/...der/model/configuration/solver.parameters → ...der/model/configuration/solver.parameters
diff --git a/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config b/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config
diff --git a/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config b/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config
diff --git a/...er/output/environmentVariables.output.cmp → ...er/output/environmentVariables.output.cmp b/...er/output/environmentVariables.output.cmp → ...er/output/environmentVariables.output.cmp
diff --git a/...tests/firstorder/output/errors.output.cmp → ...tests/firstorder/output/errors.output.cmp b/...tests/firstorder/output/errors.output.cmp → ...tests/firstorder/output/errors.output.cmp
diff --git a/...storder/output/finalModelState.output.cmp → ...storder/output/finalModelState.output.cmp b/...storder/output/finalModelState.output.cmp → ...storder/output/finalModelState.output.cmp
diff --git a/...sts/firstorder/output/jacobian.output.cmp → ...sts/firstorder/output/jacobian.output.cmp b/...sts/firstorder/output/jacobian.output.cmp → ...sts/firstorder/output/jacobian.output.cmp
diff --git a/...ts/firstorder/output/lossRates.output.cmp → ...ts/firstorder/output/lossRates.output.cmp b/...ts/firstorder/output/lossRates.output.cmp → ...ts/firstorder/output/lossRates.output.cmp
diff --git a/...er/output/mainSolverParameters.output.cmp → ...er/output/mainSolverParameters.output.cmp b/...er/output/mainSolverParameters.output.cmp → ...er/output/mainSolverParameters.output.cmp
diff --git a/...storder/output/photolysisRates.output.cmp → ...storder/output/photolysisRates.output.cmp b/...storder/output/photolysisRates.output.cmp → ...storder/output/photolysisRates.output.cmp
diff --git a/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp b/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp
diff --git a/...storder/output/productionRates.output.cmp → ...storder/output/productionRates.output.cmp b/...storder/output/productionRates.output.cmp → ...storder/output/productionRates.output.cmp
diff --git a/...s/firstorder/output/reactionRates/100.cmp → ...s/firstorder/output/reactionRates/100.cmp b/...s/firstorder/output/reactionRates/100.cmp → ...s/firstorder/output/reactionRates/100.cmp
diff --git a/.../firstorder/output/reactionRates/1000.cmp → .../firstorder/output/reactionRates/1000.cmp b/.../firstorder/output/reactionRates/1000.cmp → .../firstorder/output/reactionRates/1000.cmp
diff --git a/.../firstorder/output/reactionRates/1100.cmp → .../firstorder/output/reactionRates/1100.cmp b/.../firstorder/output/reactionRates/1100.cmp → .../firstorder/output/reactionRates/1100.cmp
diff --git a/.../firstorder/output/reactionRates/1200.cmp → .../firstorder/output/reactionRates/1200.cmp b/.../firstorder/output/reactionRates/1200.cmp → .../firstorder/output/reactionRates/1200.cmp
diff --git a/.../firstorder/output/reactionRates/1300.cmp → .../firstorder/output/reactionRates/1300.cmp b/.../firstorder/output/reactionRates/1300.cmp → .../firstorder/output/reactionRates/1300.cmp
diff --git a/.../firstorder/output/reactionRates/1400.cmp → .../firstorder/output/reactionRates/1400.cmp b/.../firstorder/output/reactionRates/1400.cmp → .../firstorder/output/reactionRates/1400.cmp
diff --git a/.../firstorder/output/reactionRates/1500.cmp → .../firstorder/output/reactionRates/1500.cmp b/.../firstorder/output/reactionRates/1500.cmp → .../firstorder/output/reactionRates/1500.cmp
diff --git a/...s/firstorder/output/reactionRates/200.cmp → ...s/firstorder/output/reactionRates/200.cmp b/...s/firstorder/output/reactionRates/200.cmp → ...s/firstorder/output/reactionRates/200.cmp
diff --git a/...s/firstorder/output/reactionRates/300.cmp → ...s/firstorder/output/reactionRates/300.cmp b/...s/firstorder/output/reactionRates/300.cmp → ...s/firstorder/output/reactionRates/300.cmp
diff --git a/...s/firstorder/output/reactionRates/400.cmp → ...s/firstorder/output/reactionRates/400.cmp b/...s/firstorder/output/reactionRates/400.cmp → ...s/firstorder/output/reactionRates/400.cmp
diff --git a/...s/firstorder/output/reactionRates/500.cmp → ...s/firstorder/output/reactionRates/500.cmp b/...s/firstorder/output/reactionRates/500.cmp → ...s/firstorder/output/reactionRates/500.cmp
diff --git a/...s/firstorder/output/reactionRates/600.cmp → ...s/firstorder/output/reactionRates/600.cmp b/...s/firstorder/output/reactionRates/600.cmp → ...s/firstorder/output/reactionRates/600.cmp
diff --git a/...s/firstorder/output/reactionRates/700.cmp → ...s/firstorder/output/reactionRates/700.cmp b/...s/firstorder/output/reactionRates/700.cmp → ...s/firstorder/output/reactionRates/700.cmp
diff --git a/...s/firstorder/output/reactionRates/800.cmp → ...s/firstorder/output/reactionRates/800.cmp b/...s/firstorder/output/reactionRates/800.cmp → ...s/firstorder/output/reactionRates/800.cmp
diff --git a/...s/firstorder/output/reactionRates/900.cmp → ...s/firstorder/output/reactionRates/900.cmp b/...s/firstorder/output/reactionRates/900.cmp → ...s/firstorder/output/reactionRates/900.cmp
diff --git a/...r/output/speciesConcentrations.output.cmp → ...r/output/speciesConcentrations.output.cmp b/...r/output/speciesConcentrations.output.cmp → ...r/output/speciesConcentrations.output.cmp
diff --git a/...configuration/environmentVariables.config → ...configuration/environmentVariables.config b/...configuration/environmentVariables.config → ...configuration/environmentVariables.config
diff --git a/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config b/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config
diff --git a/...er/model/configuration/mechanism.prod.cmp → ...er/model/configuration/mechanism.prod.cmp b/...er/model/configuration/mechanism.prod.cmp → ...er/model/configuration/mechanism.prod.cmp
diff --git a/...er/model/configuration/mechanism.reac.cmp → ...er/model/configuration/mechanism.reac.cmp b/...er/model/configuration/mechanism.reac.cmp → ...er/model/configuration/mechanism.reac.cmp
diff --git a/...der/model/configuration/mechanism.ro2.cmp → ...der/model/configuration/mechanism.ro2.cmp b/...der/model/configuration/mechanism.ro2.cmp → ...der/model/configuration/mechanism.ro2.cmp
diff --git a/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp b/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp
diff --git a/...rder/model/configuration/model.parameters → ...rder/model/configuration/model.parameters b/...rder/model/configuration/model.parameters → ...rder/model/configuration/model.parameters
diff --git a/...er/model/configuration/outputRates.config → ...er/model/configuration/outputRates.config b/...er/model/configuration/outputRates.config → ...er/model/configuration/outputRates.config
diff --git a/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config b/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config
diff --git a/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config b/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config
diff --git a/...order/model/configuration/secondorder.fac → ...order/model/configuration/secondorder.fac b/...order/model/configuration/secondorder.fac → ...order/model/configuration/secondorder.fac
diff --git a/...der/model/configuration/solver.parameters → ...der/model/configuration/solver.parameters b/...der/model/configuration/solver.parameters → ...der/model/configuration/solver.parameters
diff --git a/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config b/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config
diff --git a/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config b/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config
diff --git a/...er/output/environmentVariables.output.cmp → ...er/output/environmentVariables.output.cmp b/...er/output/environmentVariables.output.cmp → ...er/output/environmentVariables.output.cmp
diff --git a/...ests/secondorder/output/errors.output.cmp → ...ests/secondorder/output/errors.output.cmp b/...ests/secondorder/output/errors.output.cmp → ...ests/secondorder/output/errors.output.cmp
diff --git a/...ndorder/output/finalModelState.output.cmp → ...ndorder/output/finalModelState.output.cmp b/...ndorder/output/finalModelState.output.cmp → ...ndorder/output/finalModelState.output.cmp
diff --git a/...ts/secondorder/output/jacobian.output.cmp → ...ts/secondorder/output/jacobian.output.cmp b/...ts/secondorder/output/jacobian.output.cmp → ...ts/secondorder/output/jacobian.output.cmp
diff --git a/...s/secondorder/output/lossRates.output.cmp → ...s/secondorder/output/lossRates.output.cmp b/...s/secondorder/output/lossRates.output.cmp → ...s/secondorder/output/lossRates.output.cmp
diff --git a/...er/output/mainSolverParameters.output.cmp → ...er/output/mainSolverParameters.output.cmp b/...er/output/mainSolverParameters.output.cmp → ...er/output/mainSolverParameters.output.cmp
diff --git a/...ndorder/output/photolysisRates.output.cmp → ...ndorder/output/photolysisRates.output.cmp b/...ndorder/output/photolysisRates.output.cmp → ...ndorder/output/photolysisRates.output.cmp
diff --git a/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp b/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp
diff --git a/...ndorder/output/productionRates.output.cmp → ...ndorder/output/productionRates.output.cmp b/...ndorder/output/productionRates.output.cmp → ...ndorder/output/productionRates.output.cmp
diff --git a/.../secondorder/output/reactionRates/100.cmp → .../secondorder/output/reactionRates/100.cmp b/.../secondorder/output/reactionRates/100.cmp → .../secondorder/output/reactionRates/100.cmp
diff --git a/...secondorder/output/reactionRates/1000.cmp → ...secondorder/output/reactionRates/1000.cmp b/...secondorder/output/reactionRates/1000.cmp → ...secondorder/output/reactionRates/1000.cmp
diff --git a/...secondorder/output/reactionRates/1100.cmp → ...secondorder/output/reactionRates/1100.cmp b/...secondorder/output/reactionRates/1100.cmp → ...secondorder/output/reactionRates/1100.cmp
diff --git a/...secondorder/output/reactionRates/1200.cmp → ...secondorder/output/reactionRates/1200.cmp b/...secondorder/output/reactionRates/1200.cmp → ...secondorder/output/reactionRates/1200.cmp
diff --git a/...secondorder/output/reactionRates/1300.cmp → ...secondorder/output/reactionRates/1300.cmp b/...secondorder/output/reactionRates/1300.cmp → ...secondorder/output/reactionRates/1300.cmp
diff --git a/...secondorder/output/reactionRates/1400.cmp → ...secondorder/output/reactionRates/1400.cmp b/...secondorder/output/reactionRates/1400.cmp → ...secondorder/output/reactionRates/1400.cmp
diff --git a/...secondorder/output/reactionRates/1500.cmp → ...secondorder/output/reactionRates/1500.cmp b/...secondorder/output/reactionRates/1500.cmp → ...secondorder/output/reactionRates/1500.cmp
diff --git a/.../secondorder/output/reactionRates/200.cmp → .../secondorder/output/reactionRates/200.cmp b/.../secondorder/output/reactionRates/200.cmp → .../secondorder/output/reactionRates/200.cmp
diff --git a/.../secondorder/output/reactionRates/300.cmp → .../secondorder/output/reactionRates/300.cmp b/.../secondorder/output/reactionRates/300.cmp → .../secondorder/output/reactionRates/300.cmp
diff --git a/.../secondorder/output/reactionRates/400.cmp → .../secondorder/output/reactionRates/400.cmp b/.../secondorder/output/reactionRates/400.cmp → .../secondorder/output/reactionRates/400.cmp
diff --git a/.../secondorder/output/reactionRates/500.cmp → .../secondorder/output/reactionRates/500.cmp b/.../secondorder/output/reactionRates/500.cmp → .../secondorder/output/reactionRates/500.cmp
diff --git a/.../secondorder/output/reactionRates/600.cmp → .../secondorder/output/reactionRates/600.cmp b/.../secondorder/output/reactionRates/600.cmp → .../secondorder/output/reactionRates/600.cmp
diff --git a/.../secondorder/output/reactionRates/700.cmp → .../secondorder/output/reactionRates/700.cmp b/.../secondorder/output/reactionRates/700.cmp → .../secondorder/output/reactionRates/700.cmp
diff --git a/.../secondorder/output/reactionRates/800.cmp → .../secondorder/output/reactionRates/800.cmp b/.../secondorder/output/reactionRates/800.cmp → .../secondorder/output/reactionRates/800.cmp
diff --git a/.../secondorder/output/reactionRates/900.cmp → .../secondorder/output/reactionRates/900.cmp b/.../secondorder/output/reactionRates/900.cmp → .../secondorder/output/reactionRates/900.cmp
diff --git a/...r/output/speciesConcentrations.output.cmp → ...r/output/speciesConcentrations.output.cmp b/...r/output/speciesConcentrations.output.cmp → ...r/output/speciesConcentrations.output.cmp
diff --git a/test/tests/secondorder/secondorder.out.cmp → tests/tests/secondorder/secondorder.out.cmp b/test/tests/secondorder/secondorder.out.cmp → tests/tests/secondorder/secondorder.out.cmp
@@ -4,15 +4,15 @@ AtChem2 v1.3-dev
  Directories
 -------------
  Model directory is: model
- Output directory is: test/tests/secondorder/output
- Reaction Rates directory is: test/tests/secondorder/output/reactionRates
- Configuration directory is: test/tests/secondorder/model/configuration
- Constraints directory is: test/tests/secondorder/model/constraints
- Environment Constraints directory is: test/tests/secondorder/model/constraints/environment
- Photolysis Constraints directory is: test/tests/secondorder/model/constraints/photolysis
- Species Constraints directory is: test/tests/secondorder/model/constraints/species
+ Output directory is: tests/tests/secondorder/output
+ Reaction Rates directory is: tests/tests/secondorder/output/reactionRates
+ Configuration directory is: tests/tests/secondorder/model/configuration
+ Constraints directory is: tests/tests/secondorder/model/constraints
+ Environment Constraints directory is: tests/tests/secondorder/model/constraints/environment
+ Photolysis Constraints directory is: tests/tests/secondorder/model/constraints/photolysis
+ Species Constraints directory is: tests/tests/secondorder/model/constraints/species
  MCM directory is: mcm
- Shared library is: test/tests/secondorder/model/configuration/mechanism.so
+ Shared library is: tests/tests/secondorder/model/configuration/mechanism.so
 
 -----------------------
  Species and reactions

diff --git a/...configuration/environmentVariables.config → ...configuration/environmentVariables.config b/...configuration/environmentVariables.config → ...configuration/environmentVariables.config
diff --git a/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config b/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config
diff --git a/...rt/model/configuration/mechanism.prod.cmp → ...rt/model/configuration/mechanism.prod.cmp b/...rt/model/configuration/mechanism.prod.cmp → ...rt/model/configuration/mechanism.prod.cmp
diff --git a/...rt/model/configuration/mechanism.reac.cmp → ...rt/model/configuration/mechanism.reac.cmp b/...rt/model/configuration/mechanism.reac.cmp → ...rt/model/configuration/mechanism.reac.cmp
diff --git a/...ort/model/configuration/mechanism.ro2.cmp → ...ort/model/configuration/mechanism.ro2.cmp b/...ort/model/configuration/mechanism.ro2.cmp → ...ort/model/configuration/mechanism.ro2.cmp
diff --git a/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp b/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp
diff --git a/...hort/model/configuration/model.parameters → ...hort/model/configuration/model.parameters b/...hort/model/configuration/model.parameters → ...hort/model/configuration/model.parameters
diff --git a/...rt/model/configuration/outputRates.config → ...rt/model/configuration/outputRates.config b/...rt/model/configuration/outputRates.config → ...rt/model/configuration/outputRates.config
diff --git a/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config b/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config
diff --git a/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config b/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config
diff --git a/...tests/short/model/configuration/short.fac → ...tests/short/model/configuration/short.fac b/...tests/short/model/configuration/short.fac → ...tests/short/model/configuration/short.fac
diff --git a/...ort/model/configuration/solver.parameters → ...ort/model/configuration/solver.parameters b/...ort/model/configuration/solver.parameters → ...ort/model/configuration/solver.parameters
diff --git a/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config b/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config
diff --git a/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config b/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config
diff --git a/...rt/output/environmentVariables.output.cmp → ...rt/output/environmentVariables.output.cmp b/...rt/output/environmentVariables.output.cmp → ...rt/output/environmentVariables.output.cmp
diff --git a/test/tests/short/output/errors.output.cmp → tests/tests/short/output/errors.output.cmp b/test/tests/short/output/errors.output.cmp → tests/tests/short/output/errors.output.cmp
diff --git a/...s/short/output/finalModelState.output.cmp → ...s/short/output/finalModelState.output.cmp b/...s/short/output/finalModelState.output.cmp → ...s/short/output/finalModelState.output.cmp
diff --git a/test/tests/short/output/jacobian.output.cmp → tests/tests/short/output/jacobian.output.cmp b/test/tests/short/output/jacobian.output.cmp → tests/tests/short/output/jacobian.output.cmp
diff --git a/test/tests/short/output/lossRates.output.cmp → ...s/tests/short/output/lossRates.output.cmp b/test/tests/short/output/lossRates.output.cmp → ...s/tests/short/output/lossRates.output.cmp
diff --git a/...rt/output/mainSolverParameters.output.cmp → ...rt/output/mainSolverParameters.output.cmp b/...rt/output/mainSolverParameters.output.cmp → ...rt/output/mainSolverParameters.output.cmp
diff --git a/...s/short/output/photolysisRates.output.cmp → ...s/short/output/photolysisRates.output.cmp b/...s/short/output/photolysisRates.output.cmp → ...s/short/output/photolysisRates.output.cmp
diff --git a/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp b/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp
diff --git a/...s/short/output/productionRates.output.cmp → ...s/short/output/productionRates.output.cmp b/...s/short/output/productionRates.output.cmp → ...s/short/output/productionRates.output.cmp
diff --git a/...ests/short/output/reactionRates/43500.cmp → ...ests/short/output/reactionRates/43500.cmp b/...ests/short/output/reactionRates/43500.cmp → ...ests/short/output/reactionRates/43500.cmp
diff --git a/...ests/short/output/reactionRates/43800.cmp → ...ests/short/output/reactionRates/43800.cmp b/...ests/short/output/reactionRates/43800.cmp → ...ests/short/output/reactionRates/43800.cmp
diff --git a/...ests/short/output/reactionRates/44100.cmp → ...ests/short/output/reactionRates/44100.cmp b/...ests/short/output/reactionRates/44100.cmp → ...ests/short/output/reactionRates/44100.cmp
diff --git a/...t/output/speciesConcentrations.output.cmp → ...t/output/speciesConcentrations.output.cmp b/...t/output/speciesConcentrations.output.cmp → ...t/output/speciesConcentrations.output.cmp
diff --git a/test/tests/short/short.out.cmp → tests/tests/short/short.out.cmp b/test/tests/short/short.out.cmp → tests/tests/short/short.out.cmp
@@ -4,15 +4,15 @@ AtChem2 v1.3-dev
  Directories
 -------------
  Model directory is: model
- Output directory is: test/tests/short/output
- Reaction Rates directory is: test/tests/short/output/reactionRates
- Configuration directory is: test/tests/short/model/configuration
- Constraints directory is: test/tests/short/model/constraints
- Environment Constraints directory is: test/tests/short/model/constraints/environment
- Photolysis Constraints directory is: test/tests/short/model/constraints/photolysis
- Species Constraints directory is: test/tests/short/model/constraints/species
+ Output directory is: tests/tests/short/output
+ Reaction Rates directory is: tests/tests/short/output/reactionRates
+ Configuration directory is: tests/tests/short/model/configuration
+ Constraints directory is: tests/tests/short/model/constraints
+ Environment Constraints directory is: tests/tests/short/model/constraints/environment
+ Photolysis Constraints directory is: tests/tests/short/model/constraints/photolysis
+ Species Constraints directory is: tests/tests/short/model/constraints/species
  MCM directory is: mcm
- Shared library is: test/tests/short/model/configuration/mechanism.so
+ Shared library is: tests/tests/short/model/configuration/mechanism.so
 
 -----------------------
  Species and reactions

diff --git a/...configuration/environmentVariables.config → ...configuration/environmentVariables.config b/...configuration/environmentVariables.config → ...configuration/environmentVariables.config
diff --git a/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config b/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config
diff --git a/...se/model/configuration/mechanism.prod.cmp → ...se/model/configuration/mechanism.prod.cmp b/...se/model/configuration/mechanism.prod.cmp → ...se/model/configuration/mechanism.prod.cmp
diff --git a/...se/model/configuration/mechanism.reac.cmp → ...se/model/configuration/mechanism.reac.cmp b/...se/model/configuration/mechanism.reac.cmp → ...se/model/configuration/mechanism.reac.cmp
diff --git a/...nse/model/configuration/mechanism.ro2.cmp → ...nse/model/configuration/mechanism.ro2.cmp b/...nse/model/configuration/mechanism.ro2.cmp → ...nse/model/configuration/mechanism.ro2.cmp
diff --git a/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp b/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp
diff --git a/...ense/model/configuration/model.parameters → ...ense/model/configuration/model.parameters b/...ense/model/configuration/model.parameters → ...ense/model/configuration/model.parameters
diff --git a/...se/model/configuration/outputRates.config → ...se/model/configuration/outputRates.config b/...se/model/configuration/outputRates.config → ...se/model/configuration/outputRates.config
diff --git a/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config b/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config
diff --git a/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config b/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config
diff --git a/...dense/model/configuration/short_dense.fac → ...dense/model/configuration/short_dense.fac b/...dense/model/configuration/short_dense.fac → ...dense/model/configuration/short_dense.fac
diff --git a/...nse/model/configuration/solver.parameters → ...nse/model/configuration/solver.parameters b/...nse/model/configuration/solver.parameters → ...nse/model/configuration/solver.parameters
diff --git a/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config b/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config
diff --git a/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config b/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config
diff --git a/...se/output/environmentVariables.output.cmp → ...se/output/environmentVariables.output.cmp b/...se/output/environmentVariables.output.cmp → ...se/output/environmentVariables.output.cmp
diff --git a/...ests/short_dense/output/errors.output.cmp → ...ests/short_dense/output/errors.output.cmp b/...ests/short_dense/output/errors.output.cmp → ...ests/short_dense/output/errors.output.cmp
diff --git a/...t_dense/output/finalModelState.output.cmp → ...t_dense/output/finalModelState.output.cmp b/...t_dense/output/finalModelState.output.cmp → ...t_dense/output/finalModelState.output.cmp
diff --git a/...ts/short_dense/output/jacobian.output.cmp → ...ts/short_dense/output/jacobian.output.cmp b/...ts/short_dense/output/jacobian.output.cmp → ...ts/short_dense/output/jacobian.output.cmp
diff --git a/...s/short_dense/output/lossRates.output.cmp → ...s/short_dense/output/lossRates.output.cmp b/...s/short_dense/output/lossRates.output.cmp → ...s/short_dense/output/lossRates.output.cmp
diff --git a/...se/output/mainSolverParameters.output.cmp → ...se/output/mainSolverParameters.output.cmp b/...se/output/mainSolverParameters.output.cmp → ...se/output/mainSolverParameters.output.cmp
diff --git a/...t_dense/output/photolysisRates.output.cmp → ...t_dense/output/photolysisRates.output.cmp b/...t_dense/output/photolysisRates.output.cmp → ...t_dense/output/photolysisRates.output.cmp
diff --git a/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp b/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp
diff --git a/...t_dense/output/productionRates.output.cmp → ...t_dense/output/productionRates.output.cmp b/...t_dense/output/productionRates.output.cmp → ...t_dense/output/productionRates.output.cmp
diff --git a/...hort_dense/output/reactionRates/43500.cmp → ...hort_dense/output/reactionRates/43500.cmp b/...hort_dense/output/reactionRates/43500.cmp → ...hort_dense/output/reactionRates/43500.cmp
diff --git a/...hort_dense/output/reactionRates/43800.cmp → ...hort_dense/output/reactionRates/43800.cmp b/...hort_dense/output/reactionRates/43800.cmp → ...hort_dense/output/reactionRates/43800.cmp
diff --git a/...hort_dense/output/reactionRates/44100.cmp → ...hort_dense/output/reactionRates/44100.cmp b/...hort_dense/output/reactionRates/44100.cmp → ...hort_dense/output/reactionRates/44100.cmp
diff --git a/...e/output/speciesConcentrations.output.cmp → ...e/output/speciesConcentrations.output.cmp b/...e/output/speciesConcentrations.output.cmp → ...e/output/speciesConcentrations.output.cmp
diff --git a/test/tests/short_dense/short_dense.out.cmp → tests/tests/short_dense/short_dense.out.cmp b/test/tests/short_dense/short_dense.out.cmp → tests/tests/short_dense/short_dense.out.cmp
@@ -4,15 +4,15 @@ AtChem2 v1.3-dev
  Directories
 -------------
  Model directory is: model
- Output directory is: test/tests/short_dense/output
- Reaction Rates directory is: test/tests/short_dense/output/reactionRates
- Configuration directory is: test/tests/short_dense/model/configuration
- Constraints directory is: test/tests/short_dense/model/constraints
- Environment Constraints directory is: test/tests/short_dense/model/constraints/environment
- Photolysis Constraints directory is: test/tests/short_dense/model/constraints/photolysis
- Species Constraints directory is: test/tests/short_dense/model/constraints/species
+ Output directory is: tests/tests/short_dense/output
+ Reaction Rates directory is: tests/tests/short_dense/output/reactionRates
+ Configuration directory is: tests/tests/short_dense/model/configuration
+ Constraints directory is: tests/tests/short_dense/model/constraints
+ Environment Constraints directory is: tests/tests/short_dense/model/constraints/environment
+ Photolysis Constraints directory is: tests/tests/short_dense/model/constraints/photolysis
+ Species Constraints directory is: tests/tests/short_dense/model/constraints/species
  MCM directory is: mcm
- Shared library is: test/tests/short_dense/model/configuration/mechanism.so
+ Shared library is: tests/tests/short_dense/model/configuration/mechanism.so
 
 -----------------------
  Species and reactions

diff --git a/...configuration/environmentVariables.config → ...configuration/environmentVariables.config b/...configuration/environmentVariables.config → ...configuration/environmentVariables.config
diff --git a/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config b/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config
diff --git a/...ay/model/configuration/mechanism.prod.cmp → ...ay/model/configuration/mechanism.prod.cmp b/...ay/model/configuration/mechanism.prod.cmp → ...ay/model/configuration/mechanism.prod.cmp
diff --git a/...ay/model/configuration/mechanism.reac.cmp → ...ay/model/configuration/mechanism.reac.cmp b/...ay/model/configuration/mechanism.reac.cmp → ...ay/model/configuration/mechanism.reac.cmp
diff --git a/...day/model/configuration/mechanism.ro2.cmp → ...day/model/configuration/mechanism.ro2.cmp b/...day/model/configuration/mechanism.ro2.cmp → ...day/model/configuration/mechanism.ro2.cmp
diff --git a/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp b/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp
diff --git a/..._day/model/configuration/model.parameters → ..._day/model/configuration/model.parameters b/..._day/model/configuration/model.parameters → ..._day/model/configuration/model.parameters
diff --git a/...ay/model/configuration/outputRates.config → ...ay/model/configuration/outputRates.config b/...ay/model/configuration/outputRates.config → ...ay/model/configuration/outputRates.config
diff --git a/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config b/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config
diff --git a/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config b/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config
diff --git a/.../model/configuration/short_end_of_day.fac → .../model/configuration/short_end_of_day.fac b/.../model/configuration/short_end_of_day.fac → .../model/configuration/short_end_of_day.fac
diff --git a/...day/model/configuration/solver.parameters → ...day/model/configuration/solver.parameters b/...day/model/configuration/solver.parameters → ...day/model/configuration/solver.parameters
diff --git a/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config b/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config
diff --git a/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config b/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config
diff --git a/...ay/output/environmentVariables.output.cmp → ...ay/output/environmentVariables.output.cmp b/...ay/output/environmentVariables.output.cmp → ...ay/output/environmentVariables.output.cmp
diff --git a/...short_end_of_day/output/errors.output.cmp → ...short_end_of_day/output/errors.output.cmp b/...short_end_of_day/output/errors.output.cmp → ...short_end_of_day/output/errors.output.cmp
diff --git a/..._of_day/output/finalModelState.output.cmp → ..._of_day/output/finalModelState.output.cmp b/..._of_day/output/finalModelState.output.cmp → ..._of_day/output/finalModelState.output.cmp
diff --git a/...ort_end_of_day/output/jacobian.output.cmp → ...ort_end_of_day/output/jacobian.output.cmp b/...ort_end_of_day/output/jacobian.output.cmp → ...ort_end_of_day/output/jacobian.output.cmp
diff --git a/...rt_end_of_day/output/lossRates.output.cmp → ...rt_end_of_day/output/lossRates.output.cmp b/...rt_end_of_day/output/lossRates.output.cmp → ...rt_end_of_day/output/lossRates.output.cmp
diff --git a/...ay/output/mainSolverParameters.output.cmp → ...ay/output/mainSolverParameters.output.cmp b/...ay/output/mainSolverParameters.output.cmp → ...ay/output/mainSolverParameters.output.cmp
diff --git a/..._of_day/output/photolysisRates.output.cmp → ..._of_day/output/photolysisRates.output.cmp b/..._of_day/output/photolysisRates.output.cmp → ..._of_day/output/photolysisRates.output.cmp
diff --git a/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp b/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp
diff --git a/..._of_day/output/productionRates.output.cmp → ..._of_day/output/productionRates.output.cmp b/..._of_day/output/productionRates.output.cmp → ..._of_day/output/productionRates.output.cmp
diff --git a/...end_of_day/output/reactionRates/84900.cmp → ...end_of_day/output/reactionRates/84900.cmp b/...end_of_day/output/reactionRates/84900.cmp → ...end_of_day/output/reactionRates/84900.cmp
diff --git a/...end_of_day/output/reactionRates/85200.cmp → ...end_of_day/output/reactionRates/85200.cmp b/...end_of_day/output/reactionRates/85200.cmp → ...end_of_day/output/reactionRates/85200.cmp
diff --git a/...end_of_day/output/reactionRates/85500.cmp → ...end_of_day/output/reactionRates/85500.cmp b/...end_of_day/output/reactionRates/85500.cmp → ...end_of_day/output/reactionRates/85500.cmp
diff --git a/...end_of_day/output/reactionRates/85800.cmp → ...end_of_day/output/reactionRates/85800.cmp b/...end_of_day/output/reactionRates/85800.cmp → ...end_of_day/output/reactionRates/85800.cmp
diff --git a/...end_of_day/output/reactionRates/86100.cmp → ...end_of_day/output/reactionRates/86100.cmp b/...end_of_day/output/reactionRates/86100.cmp → ...end_of_day/output/reactionRates/86100.cmp
diff --git a/...end_of_day/output/reactionRates/86400.cmp → ...end_of_day/output/reactionRates/86400.cmp b/...end_of_day/output/reactionRates/86400.cmp → ...end_of_day/output/reactionRates/86400.cmp
diff --git a/...end_of_day/output/reactionRates/86700.cmp → ...end_of_day/output/reactionRates/86700.cmp b/...end_of_day/output/reactionRates/86700.cmp → ...end_of_day/output/reactionRates/86700.cmp
diff --git a/...end_of_day/output/reactionRates/87000.cmp → ...end_of_day/output/reactionRates/87000.cmp b/...end_of_day/output/reactionRates/87000.cmp → ...end_of_day/output/reactionRates/87000.cmp
diff --git a/...end_of_day/output/reactionRates/87300.cmp → ...end_of_day/output/reactionRates/87300.cmp b/...end_of_day/output/reactionRates/87300.cmp → ...end_of_day/output/reactionRates/87300.cmp
diff --git a/...end_of_day/output/reactionRates/87600.cmp → ...end_of_day/output/reactionRates/87600.cmp b/...end_of_day/output/reactionRates/87600.cmp → ...end_of_day/output/reactionRates/87600.cmp
diff --git a/...y/output/speciesConcentrations.output.cmp → ...y/output/speciesConcentrations.output.cmp b/...y/output/speciesConcentrations.output.cmp → ...y/output/speciesConcentrations.output.cmp
diff --git a/...short_end_of_day/short_end_of_day.out.cmp → ...short_end_of_day/short_end_of_day.out.cmp b/...short_end_of_day/short_end_of_day.out.cmp → ...short_end_of_day/short_end_of_day.out.cmp
@@ -4,15 +4,15 @@ AtChem2 v1.3-dev
  Directories
 -------------
  Model directory is: model
- Output directory is: test/tests/short_end_of_day/output
- Reaction Rates directory is: test/tests/short_end_of_day/output/reactionRates
- Configuration directory is: test/tests/short_end_of_day/model/configuration
- Constraints directory is: test/tests/short_end_of_day/model/constraints
- Environment Constraints directory is: test/tests/short_end_of_day/model/constraints/environment
- Photolysis Constraints directory is: test/tests/short_end_of_day/model/constraints/photolysis
- Species Constraints directory is: test/tests/short_end_of_day/model/constraints/species
+ Output directory is: tests/tests/short_end_of_day/output
+ Reaction Rates directory is: tests/tests/short_end_of_day/output/reactionRates
+ Configuration directory is: tests/tests/short_end_of_day/model/configuration
+ Constraints directory is: tests/tests/short_end_of_day/model/constraints
+ Environment Constraints directory is: tests/tests/short_end_of_day/model/constraints/environment
+ Photolysis Constraints directory is: tests/tests/short_end_of_day/model/constraints/photolysis
+ Species Constraints directory is: tests/tests/short_end_of_day/model/constraints/species
  MCM directory is: mcm
- Shared library is: test/tests/short_end_of_day/model/configuration/mechanism.so
+ Shared library is: tests/tests/short_end_of_day/model/configuration/mechanism.so
 
 -----------------------
  Species and reactions

diff --git a/...configuration/environmentVariables.config → ...configuration/environmentVariables.config b/...configuration/environmentVariables.config → ...configuration/environmentVariables.config
diff --git a/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config b/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config
diff --git a/...t1/model/configuration/mechanism.prod.cmp → ...t1/model/configuration/mechanism.prod.cmp b/...t1/model/configuration/mechanism.prod.cmp → ...t1/model/configuration/mechanism.prod.cmp
diff --git a/...t1/model/configuration/mechanism.reac.cmp → ...t1/model/configuration/mechanism.reac.cmp b/...t1/model/configuration/mechanism.reac.cmp → ...t1/model/configuration/mechanism.reac.cmp
diff --git a/...xt1/model/configuration/mechanism.ro2.cmp → ...xt1/model/configuration/mechanism.ro2.cmp b/...xt1/model/configuration/mechanism.ro2.cmp → ...xt1/model/configuration/mechanism.ro2.cmp
diff --git a/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp b/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp
diff --git a/...ext1/model/configuration/model.parameters → ...ext1/model/configuration/model.parameters b/...ext1/model/configuration/model.parameters → ...ext1/model/configuration/model.parameters
diff --git a/...t1/model/configuration/outputRates.config → ...t1/model/configuration/outputRates.config b/...t1/model/configuration/outputRates.config → ...t1/model/configuration/outputRates.config
diff --git a/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config b/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config
diff --git a/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config b/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config
diff --git a/...t_ext1/model/configuration/short_ext1.fac → ...t_ext1/model/configuration/short_ext1.fac b/...t_ext1/model/configuration/short_ext1.fac → ...t_ext1/model/configuration/short_ext1.fac
diff --git a/...xt1/model/configuration/solver.parameters → ...xt1/model/configuration/solver.parameters b/...xt1/model/configuration/solver.parameters → ...xt1/model/configuration/solver.parameters
diff --git a/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config b/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config
diff --git a/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config b/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config
diff --git a/...t1/output/environmentVariables.output.cmp → ...t1/output/environmentVariables.output.cmp b/...t1/output/environmentVariables.output.cmp → ...t1/output/environmentVariables.output.cmp
diff --git a/...tests/short_ext1/output/errors.output.cmp → ...tests/short_ext1/output/errors.output.cmp b/...tests/short_ext1/output/errors.output.cmp → ...tests/short_ext1/output/errors.output.cmp
diff --git a/...rt_ext1/output/finalModelState.output.cmp → ...rt_ext1/output/finalModelState.output.cmp b/...rt_ext1/output/finalModelState.output.cmp → ...rt_ext1/output/finalModelState.output.cmp
diff --git a/...sts/short_ext1/output/jacobian.output.cmp → ...sts/short_ext1/output/jacobian.output.cmp b/...sts/short_ext1/output/jacobian.output.cmp → ...sts/short_ext1/output/jacobian.output.cmp
diff --git a/...ts/short_ext1/output/lossRates.output.cmp → ...ts/short_ext1/output/lossRates.output.cmp b/...ts/short_ext1/output/lossRates.output.cmp → ...ts/short_ext1/output/lossRates.output.cmp
diff --git a/...t1/output/mainSolverParameters.output.cmp → ...t1/output/mainSolverParameters.output.cmp b/...t1/output/mainSolverParameters.output.cmp → ...t1/output/mainSolverParameters.output.cmp
diff --git a/...rt_ext1/output/photolysisRates.output.cmp → ...rt_ext1/output/photolysisRates.output.cmp b/...rt_ext1/output/photolysisRates.output.cmp → ...rt_ext1/output/photolysisRates.output.cmp
diff --git a/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp b/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp
diff --git a/...rt_ext1/output/productionRates.output.cmp → ...rt_ext1/output/productionRates.output.cmp b/...rt_ext1/output/productionRates.output.cmp → ...rt_ext1/output/productionRates.output.cmp
diff --git a/...short_ext1/output/reactionRates/43500.cmp → ...short_ext1/output/reactionRates/43500.cmp b/...short_ext1/output/reactionRates/43500.cmp → ...short_ext1/output/reactionRates/43500.cmp
diff --git a/...short_ext1/output/reactionRates/43800.cmp → ...short_ext1/output/reactionRates/43800.cmp b/...short_ext1/output/reactionRates/43800.cmp → ...short_ext1/output/reactionRates/43800.cmp
diff --git a/...short_ext1/output/reactionRates/44100.cmp → ...short_ext1/output/reactionRates/44100.cmp b/...short_ext1/output/reactionRates/44100.cmp → ...short_ext1/output/reactionRates/44100.cmp
diff --git a/...1/output/speciesConcentrations.output.cmp → ...1/output/speciesConcentrations.output.cmp b/...1/output/speciesConcentrations.output.cmp → ...1/output/speciesConcentrations.output.cmp
diff --git a/test/tests/short_ext1/short_ext1.out.cmp → tests/tests/short_ext1/short_ext1.out.cmp b/test/tests/short_ext1/short_ext1.out.cmp → tests/tests/short_ext1/short_ext1.out.cmp
@@ -4,15 +4,15 @@ AtChem2 v1.3-dev
  Directories
 -------------
  Model directory is: model
- Output directory is: test/tests/short_ext1/output
- Reaction Rates directory is: test/tests/short_ext1/output/reactionRates
- Configuration directory is: test/tests/short_ext1/model/configuration
- Constraints directory is: test/tests/short_ext1/model/constraints
- Environment Constraints directory is: test/tests/short_ext1/model/constraints/environment
- Photolysis Constraints directory is: test/tests/short_ext1/model/constraints/photolysis
- Species Constraints directory is: test/tests/short_ext1/model/constraints/species
+ Output directory is: tests/tests/short_ext1/output
+ Reaction Rates directory is: tests/tests/short_ext1/output/reactionRates
+ Configuration directory is: tests/tests/short_ext1/model/configuration
+ Constraints directory is: tests/tests/short_ext1/model/constraints
+ Environment Constraints directory is: tests/tests/short_ext1/model/constraints/environment
+ Photolysis Constraints directory is: tests/tests/short_ext1/model/constraints/photolysis
+ Species Constraints directory is: tests/tests/short_ext1/model/constraints/species
  MCM directory is: mcm
- Shared library is: test/tests/short_ext1/model/configuration/mechanism.so
+ Shared library is: tests/tests/short_ext1/model/configuration/mechanism.so
 
 -----------------------
  Species and reactions

diff --git a/...configuration/environmentVariables.config → ...configuration/environmentVariables.config b/...configuration/environmentVariables.config → ...configuration/environmentVariables.config
diff --git a/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config b/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config
diff --git a/...t2/model/configuration/mechanism.prod.cmp → ...t2/model/configuration/mechanism.prod.cmp b/...t2/model/configuration/mechanism.prod.cmp → ...t2/model/configuration/mechanism.prod.cmp
diff --git a/...t2/model/configuration/mechanism.reac.cmp → ...t2/model/configuration/mechanism.reac.cmp b/...t2/model/configuration/mechanism.reac.cmp → ...t2/model/configuration/mechanism.reac.cmp
diff --git a/...xt2/model/configuration/mechanism.ro2.cmp → ...xt2/model/configuration/mechanism.ro2.cmp b/...xt2/model/configuration/mechanism.ro2.cmp → ...xt2/model/configuration/mechanism.ro2.cmp
diff --git a/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp b/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp
diff --git a/...ext2/model/configuration/model.parameters → ...ext2/model/configuration/model.parameters b/...ext2/model/configuration/model.parameters → ...ext2/model/configuration/model.parameters
diff --git a/...t2/model/configuration/outputRates.config → ...t2/model/configuration/outputRates.config b/...t2/model/configuration/outputRates.config → ...t2/model/configuration/outputRates.config
diff --git a/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config b/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config
diff --git a/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config b/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config
diff --git a/...t_ext2/model/configuration/short_ext2.fac → ...t_ext2/model/configuration/short_ext2.fac b/...t_ext2/model/configuration/short_ext2.fac → ...t_ext2/model/configuration/short_ext2.fac
diff --git a/...xt2/model/configuration/solver.parameters → ...xt2/model/configuration/solver.parameters b/...xt2/model/configuration/solver.parameters → ...xt2/model/configuration/solver.parameters
diff --git a/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config b/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config
diff --git a/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config b/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config
diff --git a/...t2/output/environmentVariables.output.cmp → ...t2/output/environmentVariables.output.cmp b/...t2/output/environmentVariables.output.cmp → ...t2/output/environmentVariables.output.cmp
diff --git a/...tests/short_ext2/output/errors.output.cmp → ...tests/short_ext2/output/errors.output.cmp b/...tests/short_ext2/output/errors.output.cmp → ...tests/short_ext2/output/errors.output.cmp
diff --git a/...rt_ext2/output/finalModelState.output.cmp → ...rt_ext2/output/finalModelState.output.cmp b/...rt_ext2/output/finalModelState.output.cmp → ...rt_ext2/output/finalModelState.output.cmp
diff --git a/...sts/short_ext2/output/jacobian.output.cmp → ...sts/short_ext2/output/jacobian.output.cmp b/...sts/short_ext2/output/jacobian.output.cmp → ...sts/short_ext2/output/jacobian.output.cmp
diff --git a/...ts/short_ext2/output/lossRates.output.cmp → ...ts/short_ext2/output/lossRates.output.cmp b/...ts/short_ext2/output/lossRates.output.cmp → ...ts/short_ext2/output/lossRates.output.cmp
diff --git a/...t2/output/mainSolverParameters.output.cmp → ...t2/output/mainSolverParameters.output.cmp b/...t2/output/mainSolverParameters.output.cmp → ...t2/output/mainSolverParameters.output.cmp
diff --git a/...rt_ext2/output/photolysisRates.output.cmp → ...rt_ext2/output/photolysisRates.output.cmp b/...rt_ext2/output/photolysisRates.output.cmp → ...rt_ext2/output/photolysisRates.output.cmp
diff --git a/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp b/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp
diff --git a/...rt_ext2/output/productionRates.output.cmp → ...rt_ext2/output/productionRates.output.cmp b/...rt_ext2/output/productionRates.output.cmp → ...rt_ext2/output/productionRates.output.cmp
diff --git a/...short_ext2/output/reactionRates/43500.cmp → ...short_ext2/output/reactionRates/43500.cmp b/...short_ext2/output/reactionRates/43500.cmp → ...short_ext2/output/reactionRates/43500.cmp
diff --git a/...short_ext2/output/reactionRates/43800.cmp → ...short_ext2/output/reactionRates/43800.cmp b/...short_ext2/output/reactionRates/43800.cmp → ...short_ext2/output/reactionRates/43800.cmp
diff --git a/...short_ext2/output/reactionRates/44100.cmp → ...short_ext2/output/reactionRates/44100.cmp b/...short_ext2/output/reactionRates/44100.cmp → ...short_ext2/output/reactionRates/44100.cmp
diff --git a/...2/output/speciesConcentrations.output.cmp → ...2/output/speciesConcentrations.output.cmp b/...2/output/speciesConcentrations.output.cmp → ...2/output/speciesConcentrations.output.cmp
diff --git a/test/tests/short_ext2/short_ext2.out.cmp → tests/tests/short_ext2/short_ext2.out.cmp b/test/tests/short_ext2/short_ext2.out.cmp → tests/tests/short_ext2/short_ext2.out.cmp
@@ -4,15 +4,15 @@ AtChem2 v1.3-dev
  Directories
 -------------
  Model directory is: model
- Output directory is: test/tests/short_ext2/output
- Reaction Rates directory is: test/tests/short_ext2/output/reactionRates
- Configuration directory is: test/tests/short_ext2/model/configuration
- Constraints directory is: test/tests/short_ext2/model/constraints
- Environment Constraints directory is: test/tests/short_ext2/model/constraints/environment
- Photolysis Constraints directory is: test/tests/short_ext2/model/constraints/photolysis
- Species Constraints directory is: test/tests/short_ext2/model/constraints/species
+ Output directory is: tests/tests/short_ext2/output
+ Reaction Rates directory is: tests/tests/short_ext2/output/reactionRates
+ Configuration directory is: tests/tests/short_ext2/model/configuration
+ Constraints directory is: tests/tests/short_ext2/model/constraints
+ Environment Constraints directory is: tests/tests/short_ext2/model/constraints/environment
+ Photolysis Constraints directory is: tests/tests/short_ext2/model/constraints/photolysis
+ Species Constraints directory is: tests/tests/short_ext2/model/constraints/species
  MCM directory is: mcm
- Shared library is: test/tests/short_ext2/model/configuration/mechanism.so
+ Shared library is: tests/tests/short_ext2/model/configuration/mechanism.so
 
 -----------------------
  Species and reactions

diff --git a/...configuration/environmentVariables.config → ...configuration/environmentVariables.config b/...configuration/environmentVariables.config → ...configuration/environmentVariables.config
diff --git a/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config b/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config
diff --git a/...t3/model/configuration/mechanism.prod.cmp → ...t3/model/configuration/mechanism.prod.cmp b/...t3/model/configuration/mechanism.prod.cmp → ...t3/model/configuration/mechanism.prod.cmp
diff --git a/...t3/model/configuration/mechanism.reac.cmp → ...t3/model/configuration/mechanism.reac.cmp b/...t3/model/configuration/mechanism.reac.cmp → ...t3/model/configuration/mechanism.reac.cmp
diff --git a/...xt3/model/configuration/mechanism.ro2.cmp → ...xt3/model/configuration/mechanism.ro2.cmp b/...xt3/model/configuration/mechanism.ro2.cmp → ...xt3/model/configuration/mechanism.ro2.cmp
diff --git a/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp b/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp
diff --git a/...ext3/model/configuration/model.parameters → ...ext3/model/configuration/model.parameters b/...ext3/model/configuration/model.parameters → ...ext3/model/configuration/model.parameters
diff --git a/...t3/model/configuration/outputRates.config → ...t3/model/configuration/outputRates.config b/...t3/model/configuration/outputRates.config → ...t3/model/configuration/outputRates.config
diff --git a/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config b/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config
diff --git a/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config b/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config
diff --git a/...t_ext3/model/configuration/short_ext3.fac → ...t_ext3/model/configuration/short_ext3.fac b/...t_ext3/model/configuration/short_ext3.fac → ...t_ext3/model/configuration/short_ext3.fac
diff --git a/...xt3/model/configuration/solver.parameters → ...xt3/model/configuration/solver.parameters b/...xt3/model/configuration/solver.parameters → ...xt3/model/configuration/solver.parameters
diff --git a/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config b/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config
diff --git a/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config b/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config
diff --git a/...t3/output/environmentVariables.output.cmp → ...t3/output/environmentVariables.output.cmp b/...t3/output/environmentVariables.output.cmp → ...t3/output/environmentVariables.output.cmp
diff --git a/...tests/short_ext3/output/errors.output.cmp → ...tests/short_ext3/output/errors.output.cmp b/...tests/short_ext3/output/errors.output.cmp → ...tests/short_ext3/output/errors.output.cmp
diff --git a/...rt_ext3/output/finalModelState.output.cmp → ...rt_ext3/output/finalModelState.output.cmp b/...rt_ext3/output/finalModelState.output.cmp → ...rt_ext3/output/finalModelState.output.cmp
diff --git a/...sts/short_ext3/output/jacobian.output.cmp → ...sts/short_ext3/output/jacobian.output.cmp b/...sts/short_ext3/output/jacobian.output.cmp → ...sts/short_ext3/output/jacobian.output.cmp
diff --git a/...ts/short_ext3/output/lossRates.output.cmp → ...ts/short_ext3/output/lossRates.output.cmp b/...ts/short_ext3/output/lossRates.output.cmp → ...ts/short_ext3/output/lossRates.output.cmp
diff --git a/...t3/output/mainSolverParameters.output.cmp → ...t3/output/mainSolverParameters.output.cmp b/...t3/output/mainSolverParameters.output.cmp → ...t3/output/mainSolverParameters.output.cmp
diff --git a/...rt_ext3/output/photolysisRates.output.cmp → ...rt_ext3/output/photolysisRates.output.cmp b/...rt_ext3/output/photolysisRates.output.cmp → ...rt_ext3/output/photolysisRates.output.cmp
diff --git a/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp b/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp
diff --git a/...rt_ext3/output/productionRates.output.cmp → ...rt_ext3/output/productionRates.output.cmp b/...rt_ext3/output/productionRates.output.cmp → ...rt_ext3/output/productionRates.output.cmp
diff --git a/...short_ext3/output/reactionRates/43500.cmp → ...short_ext3/output/reactionRates/43500.cmp b/...short_ext3/output/reactionRates/43500.cmp → ...short_ext3/output/reactionRates/43500.cmp
diff --git a/...short_ext3/output/reactionRates/43800.cmp → ...short_ext3/output/reactionRates/43800.cmp b/...short_ext3/output/reactionRates/43800.cmp → ...short_ext3/output/reactionRates/43800.cmp
diff --git a/...short_ext3/output/reactionRates/44100.cmp → ...short_ext3/output/reactionRates/44100.cmp b/...short_ext3/output/reactionRates/44100.cmp → ...short_ext3/output/reactionRates/44100.cmp
diff --git a/...3/output/speciesConcentrations.output.cmp → ...3/output/speciesConcentrations.output.cmp b/...3/output/speciesConcentrations.output.cmp → ...3/output/speciesConcentrations.output.cmp
diff --git a/test/tests/short_ext3/short_ext3.out.cmp → tests/tests/short_ext3/short_ext3.out.cmp b/test/tests/short_ext3/short_ext3.out.cmp → tests/tests/short_ext3/short_ext3.out.cmp
@@ -4,15 +4,15 @@ AtChem2 v1.3-dev
  Directories
 -------------
  Model directory is: model
- Output directory is: test/tests/short_ext3/output
- Reaction Rates directory is: test/tests/short_ext3/output/reactionRates
- Configuration directory is: test/tests/short_ext3/model/configuration
- Constraints directory is: test/tests/short_ext3/model/constraints
- Environment Constraints directory is: test/tests/short_ext3/model/constraints/environment
- Photolysis Constraints directory is: test/tests/short_ext3/model/constraints/photolysis
- Species Constraints directory is: test/tests/short_ext3/model/constraints/species
+ Output directory is: tests/tests/short_ext3/output
+ Reaction Rates directory is: tests/tests/short_ext3/output/reactionRates
+ Configuration directory is: tests/tests/short_ext3/model/configuration
+ Constraints directory is: tests/tests/short_ext3/model/constraints
+ Environment Constraints directory is: tests/tests/short_ext3/model/constraints/environment
+ Photolysis Constraints directory is: tests/tests/short_ext3/model/constraints/photolysis
+ Species Constraints directory is: tests/tests/short_ext3/model/constraints/species
  MCM directory is: mcm
- Shared library is: test/tests/short_ext3/model/configuration/mechanism.so
+ Shared library is: tests/tests/short_ext3/model/configuration/mechanism.so
 
 -----------------------
  Species and reactions

diff --git a/...configuration/environmentVariables.config → ...configuration/environmentVariables.config b/...configuration/environmentVariables.config → ...configuration/environmentVariables.config
diff --git a/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config b/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config
diff --git a/...t4/model/configuration/mechanism.prod.cmp → ...t4/model/configuration/mechanism.prod.cmp b/...t4/model/configuration/mechanism.prod.cmp → ...t4/model/configuration/mechanism.prod.cmp
diff --git a/...t4/model/configuration/mechanism.reac.cmp → ...t4/model/configuration/mechanism.reac.cmp b/...t4/model/configuration/mechanism.reac.cmp → ...t4/model/configuration/mechanism.reac.cmp
diff --git a/...xt4/model/configuration/mechanism.ro2.cmp → ...xt4/model/configuration/mechanism.ro2.cmp b/...xt4/model/configuration/mechanism.ro2.cmp → ...xt4/model/configuration/mechanism.ro2.cmp
diff --git a/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp b/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp
diff --git a/...ext4/model/configuration/model.parameters → ...ext4/model/configuration/model.parameters b/...ext4/model/configuration/model.parameters → ...ext4/model/configuration/model.parameters
diff --git a/...t4/model/configuration/outputRates.config → ...t4/model/configuration/outputRates.config b/...t4/model/configuration/outputRates.config → ...t4/model/configuration/outputRates.config
diff --git a/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config b/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config
diff --git a/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config b/...onfiguration/photolysisConstrained.config → ...onfiguration/photolysisConstrained.config
diff --git a/...t_ext4/model/configuration/short_ext4.fac → ...t_ext4/model/configuration/short_ext4.fac b/...t_ext4/model/configuration/short_ext4.fac → ...t_ext4/model/configuration/short_ext4.fac
diff --git a/...xt4/model/configuration/solver.parameters → ...xt4/model/configuration/solver.parameters b/...xt4/model/configuration/solver.parameters → ...xt4/model/configuration/solver.parameters
diff --git a/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config b/...odel/configuration/speciesConstant.config → ...odel/configuration/speciesConstant.config
diff --git a/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config b/...l/configuration/speciesConstrained.config → ...l/configuration/speciesConstrained.config
diff --git a/...t4/output/environmentVariables.output.cmp → ...t4/output/environmentVariables.output.cmp b/...t4/output/environmentVariables.output.cmp → ...t4/output/environmentVariables.output.cmp
diff --git a/...tests/short_ext4/output/errors.output.cmp → ...tests/short_ext4/output/errors.output.cmp b/...tests/short_ext4/output/errors.output.cmp → ...tests/short_ext4/output/errors.output.cmp
diff --git a/...rt_ext4/output/finalModelState.output.cmp → ...rt_ext4/output/finalModelState.output.cmp b/...rt_ext4/output/finalModelState.output.cmp → ...rt_ext4/output/finalModelState.output.cmp
diff --git a/...sts/short_ext4/output/jacobian.output.cmp → ...sts/short_ext4/output/jacobian.output.cmp b/...sts/short_ext4/output/jacobian.output.cmp → ...sts/short_ext4/output/jacobian.output.cmp
diff --git a/...ts/short_ext4/output/lossRates.output.cmp → ...ts/short_ext4/output/lossRates.output.cmp b/...ts/short_ext4/output/lossRates.output.cmp → ...ts/short_ext4/output/lossRates.output.cmp
diff --git a/...t4/output/mainSolverParameters.output.cmp → ...t4/output/mainSolverParameters.output.cmp b/...t4/output/mainSolverParameters.output.cmp → ...t4/output/mainSolverParameters.output.cmp
diff --git a/...rt_ext4/output/photolysisRates.output.cmp → ...rt_ext4/output/photolysisRates.output.cmp b/...rt_ext4/output/photolysisRates.output.cmp → ...rt_ext4/output/photolysisRates.output.cmp
diff --git a/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp b/...tput/photolysisRatesParameters.output.cmp → ...tput/photolysisRatesParameters.output.cmp
diff --git a/...rt_ext4/output/productionRates.output.cmp → ...rt_ext4/output/productionRates.output.cmp b/...rt_ext4/output/productionRates.output.cmp → ...rt_ext4/output/productionRates.output.cmp
diff --git a/...short_ext4/output/reactionRates/43500.cmp → ...short_ext4/output/reactionRates/43500.cmp b/...short_ext4/output/reactionRates/43500.cmp → ...short_ext4/output/reactionRates/43500.cmp
diff --git a/...short_ext4/output/reactionRates/43800.cmp → ...short_ext4/output/reactionRates/43800.cmp b/...short_ext4/output/reactionRates/43800.cmp → ...short_ext4/output/reactionRates/43800.cmp
diff --git a/...short_ext4/output/reactionRates/44100.cmp → ...short_ext4/output/reactionRates/44100.cmp b/...short_ext4/output/reactionRates/44100.cmp → ...short_ext4/output/reactionRates/44100.cmp
diff --git a/...4/output/speciesConcentrations.output.cmp → ...4/output/speciesConcentrations.output.cmp b/...4/output/speciesConcentrations.output.cmp → ...4/output/speciesConcentrations.output.cmp
diff --git a/test/tests/short_ext4/short_ext4.out.cmp → tests/tests/short_ext4/short_ext4.out.cmp b/test/tests/short_ext4/short_ext4.out.cmp → tests/tests/short_ext4/short_ext4.out.cmp
@@ -4,15 +4,15 @@ AtChem2 v1.3-dev
  Directories
 -------------
  Model directory is: model
- Output directory is: test/tests/short_ext4/output
- Reaction Rates directory is: test/tests/short_ext4/output/reactionRates
- Configuration directory is: test/tests/short_ext4/model/configuration
- Constraints directory is: test/tests/short_ext4/model/constraints
- Environment Constraints directory is: test/tests/short_ext4/model/constraints/environment
- Photolysis Constraints directory is: test/tests/short_ext4/model/constraints/photolysis
- Species Constraints directory is: test/tests/short_ext4/model/constraints/species
+ Output directory is: tests/tests/short_ext4/output
+ Reaction Rates directory is: tests/tests/short_ext4/output/reactionRates
+ Configuration directory is: tests/tests/short_ext4/model/configuration
+ Constraints directory is: tests/tests/short_ext4/model/constraints
+ Environment Constraints directory is: tests/tests/short_ext4/model/constraints/environment
+ Photolysis Constraints directory is: tests/tests/short_ext4/model/constraints/photolysis
+ Species Constraints directory is: tests/tests/short_ext4/model/constraints/species
  MCM directory is: mcm
- Shared library is: test/tests/short_ext4/model/configuration/mechanism.so
+ Shared library is: tests/tests/short_ext4/model/configuration/mechanism.so
 
 -----------------------
  Species and reactions

diff --git a/...configuration/environmentVariables.config → ...configuration/environmentVariables.config b/...configuration/environmentVariables.config → ...configuration/environmentVariables.config
diff --git a/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config b/...onfiguration/initialConcentrations.config → ...onfiguration/initialConcentrations.config
diff --git a/...re/model/configuration/mechanism.prod.cmp → ...re/model/configuration/mechanism.prod.cmp b/...re/model/configuration/mechanism.prod.cmp → ...re/model/configuration/mechanism.prod.cmp
diff --git a/...re/model/configuration/mechanism.reac.cmp → ...re/model/configuration/mechanism.reac.cmp b/...re/model/configuration/mechanism.reac.cmp → ...re/model/configuration/mechanism.reac.cmp
diff --git a/...pre/model/configuration/mechanism.ro2.cmp → ...pre/model/configuration/mechanism.ro2.cmp b/...pre/model/configuration/mechanism.ro2.cmp → ...pre/model/configuration/mechanism.ro2.cmp
diff --git a/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp b/...model/configuration/mechanism.species.cmp → ...model/configuration/mechanism.species.cmp
diff --git a/..._pre/model/configuration/model.parameters → ..._pre/model/configuration/model.parameters b/..._pre/model/configuration/model.parameters → ..._pre/model/configuration/model.parameters
diff --git a/...re/model/configuration/outputRates.config → ...re/model/configuration/outputRates.config b/...re/model/configuration/outputRates.config → ...re/model/configuration/outputRates.config
diff --git a/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config b/.../model/configuration/outputSpecies.config → .../model/configuration/outputSpecies.config