v1.73

Christiaanvandertol · Jan 29, 2019 · c8a8742 · c8a8742
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diff --git a/SCOPE_v1.72/output/verificationdata/pars_and_input.dat b/SCOPE_v1.72/output/verificationdata/pars_and_input.dat
diff --git a/SCOPE_v1.72/filenames.m → SCOPE_v1.73/filenames.m b/SCOPE_v1.72/filenames.m → SCOPE_v1.73/filenames.m
diff --git a/SCOPE_v1.73/input_data.xlsx b/SCOPE_v1.73/input_data.xlsx
diff --git a/SCOPE_v1.72/input_data_default.xlsx → SCOPE_v1.73/input_data_default.xlsx b/SCOPE_v1.72/input_data_default.xlsx → SCOPE_v1.73/input_data_default.xlsx
diff --git a/SCOPE_v1.72/inputdata.txt → SCOPE_v1.73/inputdata.txt b/SCOPE_v1.72/inputdata.txt → SCOPE_v1.73/inputdata.txt
diff --git a/...xample_directional_run/BOC_irradiance.dat → ...xample_directional_run/BOC_irradiance.dat b/...xample_directional_run/BOC_irradiance.dat → ...xample_directional_run/BOC_irradiance.dat
diff --git a/...ional/Angles (SunAngle 30.00 degrees).dat → ...ional/Angles (SunAngle 30.00 degrees).dat b/...ional/Angles (SunAngle 30.00 degrees).dat → ...ional/Angles (SunAngle 30.00 degrees).dat
diff --git a/...ctional/BRDF (SunAngle 30.00 degrees).dat → ...ctional/BRDF (SunAngle 30.00 degrees).dat b/...ctional/BRDF (SunAngle 30.00 degrees).dat → ...ctional/BRDF (SunAngle 30.00 degrees).dat
diff --git a/...Fluorescence (SunAngle 30.00 degrees).dat → ...Fluorescence (SunAngle 30.00 degrees).dat b/...Fluorescence (SunAngle 30.00 degrees).dat → ...Fluorescence (SunAngle 30.00 degrees).dat
diff --git a/...Temperatures (SunAngle 30.00 degrees).dat → ...Temperatures (SunAngle 30.00 degrees).dat b/...Temperatures (SunAngle 30.00 degrees).dat → ...Temperatures (SunAngle 30.00 degrees).dat
diff --git a/...e_directional_run/Directional/read me.txt → ...e_directional_run/Directional/read me.txt b/...e_directional_run/Directional/read me.txt → ...e_directional_run/Directional/read me.txt
diff --git a/...rectional_run/Parameters/SCOPEversion.txt → ...rectional_run/Parameters/SCOPEversion.txt b/...rectional_run/Parameters/SCOPEversion.txt → ...rectional_run/Parameters/SCOPEversion.txt
diff --git a/...le_directional_run/Parameters/filenames.m → ...le_directional_run/Parameters/filenames.m b/...le_directional_run/Parameters/filenames.m → ...le_directional_run/Parameters/filenames.m
diff --git a/..._directional_run/Parameters/inputdata.txt → ..._directional_run/Parameters/inputdata.txt b/..._directional_run/Parameters/inputdata.txt → ..._directional_run/Parameters/inputdata.txt
diff --git a/...e_directional_run/Parameters/setoptions.m → ...e_directional_run/Parameters/setoptions.m b/...e_directional_run/Parameters/setoptions.m → ...e_directional_run/Parameters/setoptions.m
diff --git a/...utput/example_directional_run/aerodyn.dat → ...utput/example_directional_run/aerodyn.dat b/...utput/example_directional_run/aerodyn.dat → ...utput/example_directional_run/aerodyn.dat
diff --git a/.../example_directional_run/fluorescence.dat → .../example_directional_run/fluorescence.dat b/.../example_directional_run/fluorescence.dat → .../example_directional_run/fluorescence.dat
diff --git a/...un/fluorescence_emitted_by_all_leaves.dat → ...un/fluorescence_emitted_by_all_leaves.dat b/...un/fluorescence_emitted_by_all_leaves.dat → ...un/fluorescence_emitted_by_all_leaves.dat
diff --git a/...orescence_emitted_by_all_photosystems.dat → ...orescence_emitted_by_all_photosystems.dat b/...orescence_emitted_by_all_photosystems.dat → ...orescence_emitted_by_all_photosystems.dat
diff --git a/...le_directional_run/fluorescence_hemis.dat → ...le_directional_run/fluorescence_hemis.dat b/...le_directional_run/fluorescence_hemis.dat → ...le_directional_run/fluorescence_hemis.dat
diff --git a/...irectional_run/fluorescence_scattered.dat → ...irectional_run/fluorescence_scattered.dat b/...irectional_run/fluorescence_scattered.dat → ...irectional_run/fluorescence_scattered.dat
diff --git a/...e_directional_run/fluorescence_shaded.dat → ...e_directional_run/fluorescence_shaded.dat b/...e_directional_run/fluorescence_shaded.dat → ...e_directional_run/fluorescence_shaded.dat
diff --git a/...e_directional_run/fluorescence_sunlit.dat → ...e_directional_run/fluorescence_sunlit.dat b/...e_directional_run/fluorescence_sunlit.dat → ...e_directional_run/fluorescence_sunlit.dat
diff --git a/...output/example_directional_run/fluxes.dat → ...output/example_directional_run/fluxes.dat b/...output/example_directional_run/fluxes.dat → ...output/example_directional_run/fluxes.dat
diff --git a/...le_directional_run/irradiance_spectra.dat → ...le_directional_run/irradiance_spectra.dat b/...le_directional_run/irradiance_spectra.dat → ...le_directional_run/irradiance_spectra.dat
diff --git a/...xample_directional_run/pars_and_input.dat → ...xample_directional_run/pars_and_input.dat b/...xample_directional_run/pars_and_input.dat → ...xample_directional_run/pars_and_input.dat
diff --git a/..._directional_run/pars_and_input_short.dat → ..._directional_run/pars_and_input_short.dat b/..._directional_run/pars_and_input_short.dat → ..._directional_run/pars_and_input_short.dat
diff --git a/...put/example_directional_run/radiation.dat → ...put/example_directional_run/radiation.dat b/...put/example_directional_run/radiation.dat → ...put/example_directional_run/radiation.dat
diff --git a/...t/example_directional_run/reflectance.dat → ...t/example_directional_run/reflectance.dat b/...t/example_directional_run/reflectance.dat → ...t/example_directional_run/reflectance.dat
diff --git a/...irectional_run/spectrum_hemis_optical.dat → ...irectional_run/spectrum_hemis_optical.dat b/...irectional_run/spectrum_hemis_optical.dat → ...irectional_run/spectrum_hemis_optical.dat
diff --git a/...irectional_run/spectrum_hemis_thermal.dat → ...irectional_run/spectrum_hemis_thermal.dat b/...irectional_run/spectrum_hemis_thermal.dat → ...irectional_run/spectrum_hemis_thermal.dat
diff --git a/...ctional_run/spectrum_obsdir_BlackBody.dat → ...ctional_run/spectrum_obsdir_BlackBody.dat b/...ctional_run/spectrum_obsdir_BlackBody.dat → ...ctional_run/spectrum_obsdir_BlackBody.dat
diff --git a/...rectional_run/spectrum_obsdir_optical.dat → ...rectional_run/spectrum_obsdir_optical.dat b/...rectional_run/spectrum_obsdir_optical.dat → ...rectional_run/spectrum_obsdir_optical.dat
diff --git a/...rectional_run/spectrum_obsdir_thermal.dat → ...rectional_run/spectrum_obsdir_thermal.dat b/...rectional_run/spectrum_obsdir_thermal.dat → ...rectional_run/spectrum_obsdir_thermal.dat
diff --git a/...tput/example_directional_run/surftemp.dat → ...tput/example_directional_run/surftemp.dat b/...tput/example_directional_run/surftemp.dat → ...tput/example_directional_run/surftemp.dat
diff --git a/....72/output/example_directional_run/wl.dat → ....73/output/example_directional_run/wl.dat b/....72/output/example_directional_run/wl.dat → ....73/output/example_directional_run/wl.dat
diff --git a/...utput/verificationdata/BOC_irradiance.dat → ...utput/verificationdata/BOC_irradiance.dat b/...utput/verificationdata/BOC_irradiance.dat → ...utput/verificationdata/BOC_irradiance.dat
diff --git a/...ificationdata/Parameters/SCOPEversion.txt → ...ificationdata/Parameters/SCOPEversion.txt b/...ificationdata/Parameters/SCOPEversion.txt → ...ificationdata/Parameters/SCOPEversion.txt
diff --git a/...t/verificationdata/Parameters/filenames.m → ...t/verificationdata/Parameters/filenames.m b/...t/verificationdata/Parameters/filenames.m → ...t/verificationdata/Parameters/filenames.m
diff --git a/...verificationdata/Parameters/inputdata.txt → ...verificationdata/Parameters/inputdata.txt b/...verificationdata/Parameters/inputdata.txt → ...verificationdata/Parameters/inputdata.txt
diff --git a/.../verificationdata/Parameters/setoptions.m → .../verificationdata/Parameters/setoptions.m b/.../verificationdata/Parameters/setoptions.m → .../verificationdata/Parameters/setoptions.m
diff --git a/...v1.72/output/verificationdata/aerodyn.dat → ...v1.73/output/verificationdata/aerodyn.dat b/...v1.72/output/verificationdata/aerodyn.dat → ...v1.73/output/verificationdata/aerodyn.dat
diff --git a/.../output/verificationdata/fluorescence.dat → .../output/verificationdata/fluorescence.dat b/.../output/verificationdata/fluorescence.dat → .../output/verificationdata/fluorescence.dat
diff --git a/...ta/fluorescence_emitted_by_all_leaves.dat → ...ta/fluorescence_emitted_by_all_leaves.dat b/...ta/fluorescence_emitted_by_all_leaves.dat → ...ta/fluorescence_emitted_by_all_leaves.dat
diff --git a/...orescence_emitted_by_all_photosystems.dat → ...orescence_emitted_by_all_photosystems.dat b/...orescence_emitted_by_all_photosystems.dat → ...orescence_emitted_by_all_photosystems.dat
diff --git a/...t/verificationdata/fluorescence_hemis.dat → ...t/verificationdata/fluorescence_hemis.dat b/...t/verificationdata/fluorescence_hemis.dat → ...t/verificationdata/fluorescence_hemis.dat
diff --git a/...rificationdata/fluorescence_scattered.dat → ...rificationdata/fluorescence_scattered.dat b/...rificationdata/fluorescence_scattered.dat → ...rificationdata/fluorescence_scattered.dat
diff --git a/.../verificationdata/fluorescence_shaded.dat → .../verificationdata/fluorescence_shaded.dat b/.../verificationdata/fluorescence_shaded.dat → .../verificationdata/fluorescence_shaded.dat
diff --git a/.../verificationdata/fluorescence_sunlit.dat → .../verificationdata/fluorescence_sunlit.dat b/.../verificationdata/fluorescence_sunlit.dat → .../verificationdata/fluorescence_sunlit.dat
diff --git a/..._v1.72/output/verificationdata/fluxes.dat → ..._v1.73/output/verificationdata/fluxes.dat b/..._v1.72/output/verificationdata/fluxes.dat → ..._v1.73/output/verificationdata/fluxes.dat
diff --git a/...t/verificationdata/irradiance_spectra.dat → ...t/verificationdata/irradiance_spectra.dat b/...t/verificationdata/irradiance_spectra.dat → ...t/verificationdata/irradiance_spectra.dat
diff --git a/SCOPE_v1.73/output/verificationdata/pars_and_input.dat b/SCOPE_v1.73/output/verificationdata/pars_and_input.dat
diff --git a/...verificationdata/pars_and_input_short.dat → ...verificationdata/pars_and_input_short.dat b/...verificationdata/pars_and_input_short.dat → ...verificationdata/pars_and_input_short.dat
diff --git a/....72/output/verificationdata/radiation.dat → ....73/output/verificationdata/radiation.dat b/....72/output/verificationdata/radiation.dat → ....73/output/verificationdata/radiation.dat
diff --git a/...2/output/verificationdata/reflectance.dat → ...3/output/verificationdata/reflectance.dat b/...2/output/verificationdata/reflectance.dat → ...3/output/verificationdata/reflectance.dat
diff --git a/...rificationdata/spectrum_hemis_optical.dat → ...rificationdata/spectrum_hemis_optical.dat b/...rificationdata/spectrum_hemis_optical.dat → ...rificationdata/spectrum_hemis_optical.dat
diff --git a/...icationdata/spectrum_obsdir_BlackBody.dat → ...icationdata/spectrum_obsdir_BlackBody.dat b/...icationdata/spectrum_obsdir_BlackBody.dat → ...icationdata/spectrum_obsdir_BlackBody.dat
diff --git a/...ificationdata/spectrum_obsdir_optical.dat → ...ificationdata/spectrum_obsdir_optical.dat b/...ificationdata/spectrum_obsdir_optical.dat → ...ificationdata/spectrum_obsdir_optical.dat
diff --git a/...1.72/output/verificationdata/surftemp.dat → ...1.73/output/verificationdata/surftemp.dat b/...1.72/output/verificationdata/surftemp.dat → ...1.73/output/verificationdata/surftemp.dat
diff --git a/SCOPE_v1.72/output/verificationdata/wl.dat → SCOPE_v1.73/output/verificationdata/wl.dat b/SCOPE_v1.72/output/verificationdata/wl.dat → SCOPE_v1.73/output/verificationdata/wl.dat
diff --git a/SCOPE_v1.72/set_parameter_filenames.m → SCOPE_v1.73/set_parameter_filenames.m b/SCOPE_v1.72/set_parameter_filenames.m → SCOPE_v1.73/set_parameter_filenames.m
diff --git a/SCOPE_v1.72/setoptions.m → SCOPE_v1.73/setoptions.m b/SCOPE_v1.72/setoptions.m → SCOPE_v1.73/setoptions.m
diff --git a/SCOPE_v1.72/src/+equations/Planck.m → SCOPE_v1.73/src/+equations/Planck.m b/SCOPE_v1.72/src/+equations/Planck.m → SCOPE_v1.73/src/+equations/Planck.m
diff --git a/SCOPE_v1.72/src/+equations/Soil_Inertia0.m → SCOPE_v1.73/src/+equations/Soil_Inertia0.m b/SCOPE_v1.72/src/+equations/Soil_Inertia0.m → SCOPE_v1.73/src/+equations/Soil_Inertia0.m
diff --git a/SCOPE_v1.72/src/+equations/Soil_Inertia1.m → SCOPE_v1.73/src/+equations/Soil_Inertia1.m b/SCOPE_v1.72/src/+equations/Soil_Inertia1.m → SCOPE_v1.73/src/+equations/Soil_Inertia1.m
diff --git a/SCOPE_v1.72/src/+equations/calc_rssrbs.m → SCOPE_v1.73/src/+equations/calc_rssrbs.m b/SCOPE_v1.72/src/+equations/calc_rssrbs.m → SCOPE_v1.73/src/+equations/calc_rssrbs.m
diff --git a/SCOPE_v1.72/src/+equations/calczenithangle.m → SCOPE_v1.73/src/+equations/calczenithangle.m b/SCOPE_v1.72/src/+equations/calczenithangle.m → SCOPE_v1.73/src/+equations/calczenithangle.m
diff --git a/...E_v1.72/src/+equations/fixedp_brent_ari.m → ...E_v1.73/src/+equations/fixedp_brent_ari.m b/...E_v1.72/src/+equations/fixedp_brent_ari.m → ...E_v1.73/src/+equations/fixedp_brent_ari.m
diff --git a/SCOPE_v1.72/src/+equations/leafangles.m → SCOPE_v1.73/src/+equations/leafangles.m b/SCOPE_v1.72/src/+equations/leafangles.m → SCOPE_v1.73/src/+equations/leafangles.m
diff --git a/SCOPE_v1.72/src/+equations/meanleaf.m → SCOPE_v1.73/src/+equations/meanleaf.m b/SCOPE_v1.72/src/+equations/meanleaf.m → SCOPE_v1.73/src/+equations/meanleaf.m
diff --git a/SCOPE_v1.72/src/+equations/satvap.m → SCOPE_v1.73/src/+equations/satvap.m b/SCOPE_v1.72/src/+equations/satvap.m → SCOPE_v1.73/src/+equations/satvap.m
diff --git a/...E_v1.72/src/+equations/soil_respiration.m → ...E_v1.73/src/+equations/soil_respiration.m b/...E_v1.72/src/+equations/soil_respiration.m → ...E_v1.73/src/+equations/soil_respiration.m
diff --git a/SCOPE_v1.72/src/+equations/tav.m → SCOPE_v1.73/src/+equations/tav.m b/SCOPE_v1.72/src/+equations/tav.m → SCOPE_v1.73/src/+equations/tav.m
diff --git a/SCOPE_v1.72/src/+equations/zo_and_d.m → SCOPE_v1.73/src/+equations/zo_and_d.m b/SCOPE_v1.72/src/+equations/zo_and_d.m → SCOPE_v1.73/src/+equations/zo_and_d.m
diff --git a/SCOPE_v1.72/src/+helpers/Sint.m → SCOPE_v1.73/src/+helpers/Sint.m b/SCOPE_v1.72/src/+helpers/Sint.m → SCOPE_v1.73/src/+helpers/Sint.m
diff --git a/SCOPE_v1.72/src/+helpers/aggreg.m → SCOPE_v1.73/src/+helpers/aggreg.m b/SCOPE_v1.72/src/+helpers/aggreg.m → SCOPE_v1.73/src/+helpers/aggreg.m
diff --git a/SCOPE_v1.72/src/+helpers/count.m → SCOPE_v1.73/src/+helpers/count.m b/SCOPE_v1.72/src/+helpers/count.m → SCOPE_v1.73/src/+helpers/count.m
diff --git a/SCOPE_v1.72/src/+io/assignvarnames.m → SCOPE_v1.73/src/+io/assignvarnames.m b/SCOPE_v1.72/src/+io/assignvarnames.m → SCOPE_v1.73/src/+io/assignvarnames.m
diff --git a/SCOPE_v1.72/src/+io/create_output_files.m → SCOPE_v1.73/src/+io/create_output_files.m b/SCOPE_v1.72/src/+io/create_output_files.m → SCOPE_v1.73/src/+io/create_output_files.m
diff --git a/SCOPE_v1.72/src/+io/define_bands.m → SCOPE_v1.73/src/+io/define_bands.m b/SCOPE_v1.72/src/+io/define_bands.m → SCOPE_v1.73/src/+io/define_bands.m
diff --git a/SCOPE_v1.72/src/+io/define_constants.m → SCOPE_v1.73/src/+io/define_constants.m b/SCOPE_v1.72/src/+io/define_constants.m → SCOPE_v1.73/src/+io/define_constants.m
diff --git a/...72/src/+io/initialize_output_structures.m → ...73/src/+io/initialize_output_structures.m b/...72/src/+io/initialize_output_structures.m → ...73/src/+io/initialize_output_structures.m
diff --git a/SCOPE_v1.72/src/+io/load_timeseries.m → SCOPE_v1.73/src/+io/load_timeseries.m b/SCOPE_v1.72/src/+io/load_timeseries.m → SCOPE_v1.73/src/+io/load_timeseries.m
diff --git a/SCOPE_v1.72/src/+io/output_data.m → SCOPE_v1.73/src/+io/output_data.m b/SCOPE_v1.72/src/+io/output_data.m → SCOPE_v1.73/src/+io/output_data.m
diff --git a/SCOPE_v1.72/src/+io/output_verification.m → SCOPE_v1.73/src/+io/output_verification.m b/SCOPE_v1.72/src/+io/output_verification.m → SCOPE_v1.73/src/+io/output_verification.m
diff --git a/SCOPE_v1.72/src/+io/readStructFromExcel.m → SCOPE_v1.73/src/+io/readStructFromExcel.m b/SCOPE_v1.72/src/+io/readStructFromExcel.m → SCOPE_v1.73/src/+io/readStructFromExcel.m
diff --git a/SCOPE_v1.72/src/+io/select_input.m → SCOPE_v1.73/src/+io/select_input.m b/SCOPE_v1.72/src/+io/select_input.m → SCOPE_v1.73/src/+io/select_input.m
diff --git a/SCOPE_v1.72/src/+plot/plots.m → SCOPE_v1.73/src/+plot/plots.m b/SCOPE_v1.72/src/+plot/plots.m → SCOPE_v1.73/src/+plot/plots.m
diff --git a/SCOPE_v1.72/src/+plot/vis.m → SCOPE_v1.73/src/+plot/vis.m b/SCOPE_v1.72/src/+plot/vis.m → SCOPE_v1.73/src/+plot/vis.m
diff --git a/SCOPE_v1.72/src/BSM.m → SCOPE_v1.73/src/BSM.m b/SCOPE_v1.72/src/BSM.m → SCOPE_v1.73/src/BSM.m
diff --git a/SCOPE_v1.72/src/RTMf.m → SCOPE_v1.73/src/RTMf.m b/SCOPE_v1.72/src/RTMf.m → SCOPE_v1.73/src/RTMf.m
diff --git a/SCOPE_v1.72/src/RTMo.m → SCOPE_v1.73/src/RTMo.m b/SCOPE_v1.72/src/RTMo.m → SCOPE_v1.73/src/RTMo.m
diff --git a/SCOPE_v1.72/src/RTMt_planck.m → SCOPE_v1.73/src/RTMt_planck.m b/SCOPE_v1.72/src/RTMt_planck.m → SCOPE_v1.73/src/RTMt_planck.m
diff --git a/SCOPE_v1.72/src/RTMt_sb.m → SCOPE_v1.73/src/RTMt_sb.m b/SCOPE_v1.72/src/RTMt_sb.m → SCOPE_v1.73/src/RTMt_sb.m
diff --git a/SCOPE_v1.72/src/RTMz.m → SCOPE_v1.73/src/RTMz.m b/SCOPE_v1.72/src/RTMz.m → SCOPE_v1.73/src/RTMz.m
diff --git a/SCOPE_v1.72/src/SCOPE.exe → SCOPE_v1.73/src/SCOPE.exe b/SCOPE_v1.72/src/SCOPE.exe → SCOPE_v1.73/src/SCOPE.exe
diff --git a/SCOPE_v1.72/src/SCOPE.m → SCOPE_v1.73/src/SCOPE.m b/SCOPE_v1.72/src/SCOPE.m → SCOPE_v1.73/src/SCOPE.m
@@ -17,8 +17,8 @@
 %     along with this program.  If not, see <http://www.gnu.org/licenses/>.
 %%
 % try   % for Compiler .exe
-%clc
-%clear all
+% clc
+% clear all
 
 %% 0. globals
 global constants

diff --git a/SCOPE_v1.72/src/biochemical.m → SCOPE_v1.73/src/biochemical.m b/SCOPE_v1.72/src/biochemical.m → SCOPE_v1.73/src/biochemical.m
diff --git a/SCOPE_v1.72/src/biochemical_MD12.m → SCOPE_v1.73/src/biochemical_MD12.m b/SCOPE_v1.72/src/biochemical_MD12.m → SCOPE_v1.73/src/biochemical_MD12.m
diff --git a/SCOPE_v1.72/src/calc_brdf.m → SCOPE_v1.73/src/calc_brdf.m b/SCOPE_v1.72/src/calc_brdf.m → SCOPE_v1.73/src/calc_brdf.m
diff --git a/SCOPE_v1.72/src/ebal.m → SCOPE_v1.73/src/ebal.m b/SCOPE_v1.72/src/ebal.m → SCOPE_v1.73/src/ebal.m
diff --git a/SCOPE_v1.72/src/fluspect_B_CX.m → SCOPE_v1.73/src/fluspect_B_CX.m b/SCOPE_v1.72/src/fluspect_B_CX.m → SCOPE_v1.73/src/fluspect_B_CX.m
diff --git a/....72/src/fluspect_B_CX_PSI_PSII_combined.m → ....73/src/fluspect_B_CX_PSI_PSII_combined.m b/....72/src/fluspect_B_CX_PSI_PSII_combined.m → ....73/src/fluspect_B_CX_PSI_PSII_combined.m
diff --git a/SCOPE_v1.72/src/heatfluxes.m → SCOPE_v1.73/src/heatfluxes.m b/SCOPE_v1.72/src/heatfluxes.m → SCOPE_v1.73/src/heatfluxes.m
diff --git a/SCOPE_v1.72/src/not_used/Brightness_T.m → SCOPE_v1.73/src/not_used/Brightness_T.m b/SCOPE_v1.72/src/not_used/Brightness_T.m → SCOPE_v1.73/src/not_used/Brightness_T.m
diff --git a/...72/src/not_used/calculate_vert_profiles.m → ...73/src/not_used/calculate_vert_profiles.m b/...72/src/not_used/calculate_vert_profiles.m → ...73/src/not_used/calculate_vert_profiles.m
diff --git a/SCOPE_v1.72/src/not_used/e2phot.m → SCOPE_v1.73/src/not_used/e2phot.m b/SCOPE_v1.72/src/not_used/e2phot.m → SCOPE_v1.73/src/not_used/e2phot.m
diff --git a/SCOPE_v1.72/src/not_used/ephoton.m → SCOPE_v1.73/src/not_used/ephoton.m b/SCOPE_v1.72/src/not_used/ephoton.m → SCOPE_v1.73/src/not_used/ephoton.m
diff --git a/..._used/plot_directional_figure4_function.m → ..._used/plot_directional_figure4_function.m b/..._used/plot_directional_figure4_function.m → ..._used/plot_directional_figure4_function.m
diff --git a/SCOPE_v1.72/src/not_used/progressbar.m → SCOPE_v1.73/src/not_used/progressbar.m b/SCOPE_v1.72/src/not_used/progressbar.m → SCOPE_v1.73/src/not_used/progressbar.m
diff --git a/SCOPE_v1.72/src/not_used/resizefigure.m → SCOPE_v1.73/src/not_used/resizefigure.m b/SCOPE_v1.72/src/not_used/resizefigure.m → SCOPE_v1.73/src/not_used/resizefigure.m
diff --git a/SCOPE_v1.72/src/not_used/vangenuchten.m → SCOPE_v1.73/src/not_used/vangenuchten.m b/SCOPE_v1.72/src/not_used/vangenuchten.m → SCOPE_v1.73/src/not_used/vangenuchten.m
diff --git a/SCOPE_v1.72/src/resistances.m → SCOPE_v1.73/src/resistances.m b/SCOPE_v1.72/src/resistances.m → SCOPE_v1.73/src/resistances.m
diff --git a/docs/_build/doctrees/acknowledgements.doctree b/docs/_build/doctrees/acknowledgements.doctree
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diff --git a/docs/_build/doctrees/api/equations.doctree b/docs/_build/doctrees/api/equations.doctree
diff --git a/docs/_build/doctrees/api/helpers.doctree b/docs/_build/doctrees/api/helpers.doctree
diff --git a/docs/_build/doctrees/api/io.doctree b/docs/_build/doctrees/api/io.doctree
diff --git a/docs/_build/doctrees/api/not_used.doctree b/docs/_build/doctrees/api/not_used.doctree
diff --git a/docs/_build/doctrees/api/plot.doctree b/docs/_build/doctrees/api/plot.doctree
diff --git a/docs/_build/doctrees/directories.doctree b/docs/_build/doctrees/directories.doctree
diff --git a/docs/_build/doctrees/directories/data.doctree b/docs/_build/doctrees/directories/data.doctree
diff --git a/docs/_build/doctrees/directories/scope.doctree b/docs/_build/doctrees/directories/scope.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/from_readme/architecture.doctree b/docs/_build/doctrees/from_readme/architecture.doctree
diff --git a/docs/_build/doctrees/from_readme/improvements.doctree b/docs/_build/doctrees/from_readme/improvements.doctree
diff --git a/docs/_build/doctrees/getting_started.doctree b/docs/_build/doctrees/getting_started.doctree
diff --git a/docs/_build/doctrees/history.doctree b/docs/_build/doctrees/history.doctree
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/model_capabilities.doctree b/docs/_build/doctrees/model_capabilities.doctree
diff --git a/docs/_build/doctrees/my_proposal/brdf.doctree b/docs/_build/doctrees/my_proposal/brdf.doctree
diff --git a/docs/_build/doctrees/my_proposal/energy_balance.doctree b/docs/_build/doctrees/my_proposal/energy_balance.doctree
diff --git a/docs/_build/doctrees/my_proposal/fluorescence.doctree b/docs/_build/doctrees/my_proposal/fluorescence.doctree
diff --git a/docs/_build/doctrees/my_proposal/spectra.doctree b/docs/_build/doctrees/my_proposal/spectra.doctree
diff --git a/docs/_build/doctrees/my_proposal/vertical_profiles.doctree b/docs/_build/doctrees/my_proposal/vertical_profiles.doctree
diff --git a/docs/_build/doctrees/options.doctree b/docs/_build/doctrees/options.doctree
diff --git a/docs/_build/doctrees/outfiles.doctree b/docs/_build/doctrees/outfiles.doctree
diff --git a/...ild/doctrees/outfiles/Directional.doctree → ...ild/doctrees/outfiles/directional.doctree b/...ild/doctrees/outfiles/Directional.doctree → ...ild/doctrees/outfiles/directional.doctree
diff --git a/docs/_build/doctrees/outfiles/each.doctree b/docs/_build/doctrees/outfiles/each.doctree
diff --git a/docs/_build/doctrees/outfiles/fluorescence.doctree b/docs/_build/doctrees/outfiles/fluorescence.doctree
diff --git a/docs/_build/doctrees/outfiles/planck.doctree b/docs/_build/doctrees/outfiles/planck.doctree
diff --git a/docs/_build/doctrees/outfiles/profiles.doctree b/docs/_build/doctrees/outfiles/profiles.doctree
diff --git a/docs/_build/doctrees/roadmap.doctree b/docs/_build/doctrees/roadmap.doctree
diff --git a/docs/_build/doctrees/structs.doctree b/docs/_build/doctrees/structs.doctree
diff --git a/docs/_build/doctrees/structs/constants/constants.doctree b/docs/_build/doctrees/structs/constants/constants.doctree
diff --git a/docs/_build/doctrees/structs/constants/constants_index.doctree b/docs/_build/doctrees/structs/constants/constants_index.doctree
diff --git a/docs/_build/doctrees/structs/constants/optipar.doctree b/docs/_build/doctrees/structs/constants/optipar.doctree
diff --git a/docs/_build/doctrees/structs/constants/soilemp.doctree b/docs/_build/doctrees/structs/constants/soilemp.doctree
diff --git a/docs/_build/doctrees/structs/constants/spectral.doctree b/docs/_build/doctrees/structs/constants/spectral.doctree
diff --git a/docs/_build/doctrees/structs/input/F.doctree b/docs/_build/doctrees/structs/input/F.doctree
diff --git a/docs/_build/doctrees/structs/input/angles.doctree b/docs/_build/doctrees/structs/input/angles.doctree
diff --git a/docs/_build/doctrees/structs/input/atmo.doctree b/docs/_build/doctrees/structs/input/atmo.doctree
diff --git a/docs/_build/doctrees/structs/input/canopy.doctree b/docs/_build/doctrees/structs/input/canopy.doctree
diff --git a/docs/_build/doctrees/structs/input/input_index.doctree b/docs/_build/doctrees/structs/input/input_index.doctree
diff --git a/docs/_build/doctrees/structs/input/iter.doctree b/docs/_build/doctrees/structs/input/iter.doctree
diff --git a/docs/_build/doctrees/structs/input/leafbio.doctree b/docs/_build/doctrees/structs/input/leafbio.doctree
diff --git a/docs/_build/doctrees/structs/input/meteo.doctree b/docs/_build/doctrees/structs/input/meteo.doctree
diff --git a/docs/_build/doctrees/structs/input/soil.doctree b/docs/_build/doctrees/structs/input/soil.doctree
diff --git a/docs/_build/doctrees/structs/input/xyt.doctree b/docs/_build/doctrees/structs/input/xyt.doctree
diff --git a/docs/_build/doctrees/structs/internal/V.doctree b/docs/_build/doctrees/structs/internal/V.doctree
diff --git a/docs/_build/doctrees/structs/internal/biochem_in.doctree b/docs/_build/doctrees/structs/internal/biochem_in.doctree
diff --git a/docs/_build/doctrees/structs/internal/biochem_out.doctree b/docs/_build/doctrees/structs/internal/biochem_out.doctree
diff --git a/docs/_build/doctrees/structs/internal/internal_index.doctree b/docs/_build/doctrees/structs/internal/internal_index.doctree
diff --git a/docs/_build/doctrees/structs/internal/resist_in.doctree b/docs/_build/doctrees/structs/internal/resist_in.doctree
diff --git a/docs/_build/doctrees/structs/internal/resist_out.doctree b/docs/_build/doctrees/structs/internal/resist_out.doctree
diff --git a/docs/_build/doctrees/structs/output/directional.doctree b/docs/_build/doctrees/structs/output/directional.doctree
diff --git a/docs/_build/doctrees/structs/output/fluxes.doctree b/docs/_build/doctrees/structs/output/fluxes.doctree
diff --git a/docs/_build/doctrees/structs/output/gap.doctree b/docs/_build/doctrees/structs/output/gap.doctree
diff --git a/docs/_build/doctrees/structs/output/leafopt.doctree b/docs/_build/doctrees/structs/output/leafopt.doctree
diff --git a/docs/_build/doctrees/structs/output/output_index.doctree b/docs/_build/doctrees/structs/output/output_index.doctree
diff --git a/docs/_build/doctrees/structs/output/profiles.doctree b/docs/_build/doctrees/structs/output/profiles.doctree
diff --git a/docs/_build/doctrees/structs/output/rad.doctree b/docs/_build/doctrees/structs/output/rad.doctree
diff --git a/docs/_build/doctrees/structs/output/thermal.doctree b/docs/_build/doctrees/structs/output/thermal.doctree
diff --git a/docs/_build/doctrees/support.doctree b/docs/_build/doctrees/support.doctree
diff --git a/docs/_build/doctrees/versions.doctree b/docs/_build/doctrees/versions.doctree
diff --git a/docs/_build/doctrees/zreferences.doctree b/docs/_build/doctrees/zreferences.doctree
diff --git a/docs/_build/html/_images/scheme.png b/docs/_build/html/_images/scheme.png
diff --git a/docs/_build/html/_images/simulation.bmp b/docs/_build/html/_images/simulation.bmp
diff --git a/docs/_build/html/_sources/directories.rst.txt b/docs/_build/html/_sources/directories.rst.txt
@@ -12,7 +12,7 @@ Directories
 ::
 
     SCOPE-master.zip
-    ├── SCOPE_v1.72
+    ├── SCOPE_v1.73
     │   ├── output
     │   │   ├── example_directional_run
     │   │   │    ├── Directional

diff --git a/docs/_build/html/_sources/directories/scope.rst.txt b/docs/_build/html/_sources/directories/scope.rst.txt
@@ -1,4 +1,4 @@
-SCOPE_v1.72
+SCOPE_v1.73
 ==============
 
 .. contents::

diff --git a/docs/_build/html/_sources/getting_started.rst.txt b/docs/_build/html/_sources/getting_started.rst.txt
@@ -6,7 +6,7 @@ Getting started
 0. Software requirements
 --------------------------
 
-The model SCOPE_v1.72 is written in Matlab R2015b running on a Windows operating system. We took care not to use functions that are available in all recent Matlab versions, but we cannot give any warranty that it works under other operating systems and other Matlab versions.
+The model SCOPE_v1.73 is written in Matlab R2015b running on a Windows operating system. We took care not to use functions that are available in all recent Matlab versions, but we cannot give any warranty that it works under other operating systems and other Matlab versions.
 
 .. warning::
     If you do **not** have Matlab on your computer you can use ``SCOPE.exe`` with `Matlab Runtime`_ **only R2017b (version 9.3)**
@@ -37,7 +37,7 @@ Unpack the model, and **leave the directory structure intact**.
 Run the model once, before modifying the parameters and input. It will check whether the software works under your system. The model runs with an example data set (``options.verify``), and the output is automatically compared to output that it should produce. If there is any difference in the results, messages will show up.
 
 * Navigate to the directory where the matlab code is
-    ./SCOPE_v1.72/:ref:`directories/scope:src`
+    ./SCOPE_v1.73/:ref:`directories/scope:src`
 * Open ``SCOPE.m`` in Matlab
 * in Matlab command window type:
     .. code-block:: matlab
@@ -51,7 +51,7 @@ Running the model may take a while because almost all options are switched on. I
 3.	Set the input in ``input_data.xlsx``
 ---------------------------------------------
 
-Main input file i``input_data.xlsx`` with 4 sheets is located in ./SCOPE_v1.72. In the documentation we refer to this file, although text alternatives are also possible.
+Main input file i``input_data.xlsx`` with 4 sheets is located in ./SCOPE_v1.73. In the documentation we refer to this file, although text alternatives are also possible.
 
 .. Note::
     If Excel is not available, it is possible to use input from text files (.m and .txt). See **alternative**.

diff --git a/docs/_build/html/_sources/outfiles.rst.txt b/docs/_build/html/_sources/outfiles.rst.txt
@@ -0,0 +1,11 @@
+Output files
+==============
+
+.. toctree::
+    :maxdepth: 2
+
+    /outfiles/each
+    /outfiles/planck
+    /outfiles/profiles
+    /outfiles/fluorescence
+    /outfiles/directional
diff --git a/...tml/_sources/outfiles/Directional.rst.txt → ...tml/_sources/outfiles/directional.rst.txt b/...tml/_sources/outfiles/Directional.rst.txt → ...tml/_sources/outfiles/directional.rst.txt
diff --git a/docs/_build/html/_sources/outfiles/each.rst.txt b/docs/_build/html/_sources/outfiles/each.rst.txt
@@ -0,0 +1,321 @@
+In each simulation
+===================
+
+.. contents::
+
+aerodyn.dat
+---------------
+
+rows - time (simulation number)
+
+columns - variables
+
+.. list-table::
+    :widths: 20 20 60
+
+    * - variable
+      - units
+      - description
+    * - **raa**
+      - s m-1
+      - total aerodynamic resistance above canopy
+    * - **rawc**
+      - s m-1
+      - canopy total aerodynamic resistance below canopy
+    * - **raws**
+      - s m-1
+      - soil total aerodynamic resistance below canopy
+    * - **ustar**
+      - m s-1
+      - friction velocity
+
+
+BOC_irradiance.dat
+---------------------
+
+BOC - bottom of canopy (61st layer)
+
+rows - timestep
+
+First 2162 columns: shaded fraction.
+
+Last 2162 columns: average BOC irradiance.
+
+.. list-table::
+    :widths: 20 20 60
+
+    * - variable
+      - units
+      - description
+    * - **Emin_(61, :)**
+      - W m-2 um-1
+      - irradiance at the bottom of the canopy for the shaded fraction
+    * - **\Emin_(61, :) + \Esun_(61, :) * gap.Ps(61, :)**
+      - W m-2 um-1
+      - average BOC irradiance (sunlit + shaded fraction)
+
+
+fluxes.dat
+------------
+
+rows - time (simulation number)
+
+columns - variables
+
+.. list-table::
+    :widths: 20 20 60
+
+    * - variable
+      - units
+      - description
+    * - **timestep**
+      - \-
+      - time step counter
+    * - **counter**
+      - \-
+      - number of iterations in energy balance
+    * - **year**
+      - \-
+      - year
+    * - **T**
+      - \-
+      - decimal day of year (DOY)
+    * - **Rntot**
+      - W m-2
+      - total net radiation
+    * - **lEtot**
+      - W m-2
+      - total latent heat flux
+    * - **Htot**
+      - W m-2
+      - total sensible heat
+    * - **Rnctot**
+      - W m-2
+      - net radiation of canopy
+    * - **lEctot**
+      - W m-2
+      - latent heat flux of canopy
+    * - **Hctot**
+      - W m-2
+      - sensible heat of canopy
+    * - **Actot**
+      - umol m-2 s-1
+      - net photosynthesis of canopy
+    * - **Rnstot**
+      - W m-2
+      - net radiation of soil
+    * - **lEstot**
+      - W m-2
+      - latent heat flux of soil
+    * - **Hstot**
+      - W m-2
+      - sensible heat of soil
+    * - **Gtot**
+      - W m-2
+      - soil heat flux
+    * - **Resp**
+      - umol m-2 s-1
+      - soil respiration rate
+    * - **aPAR_Cab**
+      - umol m-2 s-1
+      - absorbed PAR by chlorophylls a, b
+    * - **aPAR**
+      - umol m-2 s-1
+      - absorbed PAR by leaves
+    * - **fPAR**
+      - \-
+      - fraction of absorbed PAR by canopy, excluding soil
+    * - **aPAR_energyunits**
+      - W m-2
+      - absorbed PAR
+    * - **iPAR**
+      - W m-2
+      - incident PAR
+    * - **fluortot**
+      - W m-2
+      - hemispherically and spectrally integrated chlorophyll fluorescence at the top
+    * - **fluor_yield**
+      - W W-1
+      - Fluortot / aPAR_energyunits
+
+
+irradiance_spectra.dat
+------------------------
+
+rows - time (simulation number)
+
+columns - wl
+
+.. list-table::
+    :widths: 20 20 60
+
+    * - variable
+      - units
+      - description
+    * - **Rin * (fEsuno + fEskyo)**
+      - W m-2 um-1
+      - spectrum of incoming radiation used in the simulation
+
+
+pars_and_input.dat
+----------------------
+
+rows - timestep
+
+columns - all input parameters from ``input_data.xlxs``
+
+
+pars_and_input_short.dat
+-----------------------------
+
+rows - timestep
+
+columns - ``Cab, Vcmo, LAI, hc,	zo,	d,	z,	Rin, Ta,	Rli,	p,	ea,	u,	Ca,	tts,	SMC``
+
+
+radiation.dat
+---------------
+
+rows - time (simulation number)
+
+columns - variables
+
+.. list-table::
+    :widths: 20 20 60
+
+    * - variable
+      - units
+      - description
+    * - **timestep**
+      - \-
+      - time step counter
+    * - **year**
+      - \-
+      - year
+    * - **T**
+      - \-
+      - decimal day of year (DOY)
+    * - **ShortIn (Rin)**
+      - W m-2
+      - Incoming shortwave radiation (copy from input)
+    * - **LongIn (Rli)**
+      - W m-2
+      - Incoming longwave radiation (copy from input)
+    * - **HemisOutShort (Eouto)**
+      - W m-2
+      - hemispherical outgoing shortwave radiation
+    * - **HemisOutLong (Eoutt + Eoutte)**
+      - W m-2
+      - hemispherical outgoing longwave radiation
+    * - **HemisOutTot (Eouto + Eoutt + Eoutte)**
+      - W m-2
+      - total hemispherical outgoing radiation
+    * - **Net (Rntot)**
+      - W m-2
+      - total net radiation
+
+
+reflectance.dat
+-----------------
+
+rows - time (simulation number)
+
+columns - wl
+
+.. list-table::
+    :widths: 20 20 60
+
+    * - variable
+      - units
+      - description
+    * - **\Lo_ * pi  / (\Esun_ + \Esky_)**
+      - \-
+      - fraction of radiation in observation direction \* pi / irradiance
+
+
+spectrum_hemis_optical.dat
+------------------------------
+
+rows - time (simulation number)
+
+columns - wl number (2162)
+
+.. list-table::
+    :widths: 20 20 60
+
+    * - variable
+      - units
+      - description
+    * - **Eout_**
+      - W m-2 um-1
+      - hemispherical outgoing radiation spectrum
+
+spectrum_obsdir_optical.dat
+-----------------------------
+
+rows - time (simulation number)
+
+columns - wl number (2162)
+
+.. list-table::
+    :widths: 20 20 60
+
+    * - variable
+      - units
+      - description
+    * - **Lo_**
+      - W m-2 um-1 sr-1
+      - radiance spectrum in observation direction
+
+surftemp.dat
+----------------
+
+rows - time (simulation number)
+
+columns - variables
+
+.. list-table::
+    :widths: 20 20 60
+
+    * - variable
+      - units
+      - description
+    * - **timestep**
+      - \-
+      - time step counter
+    * - **year**
+      - \-
+      - year
+    * - **T**
+      - \-
+      - decimal day of year (DOY)
+    * - **Ta**
+      - ºC
+      - Air temperature above the canopy
+    * - **Tss(1)**
+      - ºC
+      - Surface temperature of shaded soil
+    * - **Tss(2)**
+      - ºC
+      - Surface temperature of sunlit soil
+    * - **Tcave**
+      - ºC
+      - canopy weighted average temperature
+    * - **Tsave**
+      - ºC
+      - soil weighted average temperature
+
+wl.dat
+---------
+
+single row (2162)
+
+.. list-table::
+    :widths: 20 20 60
+
+    * - variable
+      - units
+      - description
+    * - **wl**
+      - nm
+      - wavelengths of the spectral output files