Merge branch 'energy_by_species' of github.com:Pheosics/RAM-SCB into energy_by_species

Author: Miles A. Engel

Dockerfile.RoR

@@ -10,8 +10,8 @@ ENV PERL5LIB=.
 ENV DEBIAN_FRONTEND=noninteractive 
 
 RUN apt-get update && apt-get install -y ssh make gcc git g++ gfortran libopenmpi-dev openmpi-bin libgsl-dev libgsl23 gsl-bin libgsl-dbg libnetcdf-dev libnetcdff-dev nco netcdf-bin python3 python3-pip python-is-python3
-
-RUN pip install numpy==1.21 && pip install spacepy==0.4.1 && pip install netCDF4
+RUN pip install --upgrade pip
+RUN pip install numpy==1.21 && pip install spacepy==0.6.0 && pip install netCDF4
 
 COPY flux-model /SHIELDS/flux-model
 WORKDIR /SHIELDS/flux-model

Makefile

@@ -4,11 +4,13 @@ default : RAM_SCB
 include Makefile.def
 
 srcDir = src
+GlowDir= srcGlow
+
 INSTALLFILES = ${srcDir}/Makefile.DEPEND \
 	       ${srcDir}/Makefile.RULES  \
 	       srcInterface/Makefile.DEPEND \
-	       srcExternal/Makefile.DEPEND
-
+	       srcExternal/Makefile.DEPEND \
+		${GlowDir}/Makefile.DEPEND
 help:
 	@echo ' '
 	@echo ' You can "make" the following:'
@@ -30,6 +32,7 @@ PDF:
 RAM_SCB:
 	@cd ${SHAREDIR}; make LIB
 	@cd srcExternal; make LIB
+	@cd ${GlowDir}; make LIB
 	@cd ${srcDir};   make LIB
 	@cd ${srcDir};   make RAM_SCB
 
@@ -41,12 +44,14 @@ LIB:
 	cd ${srcDir};    make LIB
 	cd srcInterface; make LIB
 	cd srcExternal;  make LIB
+	cd ${GlowDir}; make LIB
 
 clean:
 	@touch ${INSTALLFILES}
 	@cd ${srcDir};          make clean
 	@cd srcInterface; make clean
 	@cd srcExternal; make clean
+	@cd ${GlowDir}; make clean
 	@(if [ -d util ];  then cd util;  make clean; fi);
 	@(if [ -d share ]; then cd share; make clean; fi);
 
@@ -59,6 +64,7 @@ allclean:
 	@(if [ -d srcPspline ]; then rm -rf srcPspline; fi);
 	@cd ${srcDir}; make distclean
 	@cd srcInterface; make distclean
+	@cd ${GlowDir}; make distclean
 	rm -f *~
 
 rundir: 
@@ -75,9 +81,9 @@ rundir:
 	cd ${RUNDIR}; \
 	ln -s ../input/bav_diffcoef_chorus_rpa_Kp*.PAonly.dat .
 	cd ${RUNDIR}/IM/output; \
-		mkdir -p ram/Dsbnd scb/Day00
+		mkdir -p ram/Dsbnd scb/Day00 sce/
 	cd ${RUNDIR}/IM; \
-		mkdir input_ram input_scb output_swmf;    \
+		mkdir input_ram input_scb input_sce output_swmf;    \
 		mkdir restartIN restartOUT;               \
 		tar xzf ${IMDIR}/input/ramscb_inputs.tgz; \
 		mv Input_git/EMIC_model input_ram/; \
@@ -89,7 +95,8 @@ rundir:
 		mv Input_git/*geomlt*.txt input_ram/; \
                 mv initialization.nc input_ram/;            \
 		mv QinDenton_20130317_1min.txt input_scb/;  \
-		mv NitrogenCrossSections.dat input_ram/;
+		mv NitrogenCrossSections.dat input_ram/; \
+		cp -r ${IMDIR}/input/glow_data input_sce/;	
 	@(if [ "$(STANDALONE)" != "NO" ]; then \
 		cd ${RUNDIR} ; \
 		cp ${IMDIR}/Param/PARAM.in.default ./PARAM.in; \
@@ -98,6 +105,7 @@ rundir:
 		rm -f output; \
 		ln -s IM/output/ram output_ram; \
 		ln -s IM/output/scb output_scb; \
+		ln -s IM/output/sce output_sce;\
 	fi)
 
 
@@ -438,7 +446,6 @@ testEMIC_check:
 	        >> testEMIC.diff
 	@echo "Test Successful!"
 
-#TEST EMIC----------------------------------
 testSpecies:
 	@echo "starting..." > testSpecies.diff
 	@echo "testSpecies_compile..." >> testSpecies.diff
@@ -471,4 +478,39 @@ testSpecies_check:
 	        ${TESTDIRC}/output_ram/pressure_d20130317_t001500.dat   \
 	        ${IMDIR}/output/testSpecies/pressure.ref                      \
 	        >> testSpecies.diff
+
+#TEST SCE----------------------------------
+testSCE:
+	@echo "starting..." > testSCE.diff
+	@echo "testSCE_compile..." >> testSCE.diff
+	make testSCE_compile
+	@echo "testSCE_rundir..." >> testSCE.diff
+	make testSCE_rundir PARAMFILE=PARAM.in.testSCE
+	@echo "testSCE_run..." >> testSCE.diff
+	make testSCE_run MPIRUN=
+	@echo "testSCE_check..." >> testSCE.diff
+	make testSCE_check
+
+testSCE_compile:
+	make
+
+testSCE_rundir:
+	rm -rf ${TESTDIRC}
+	make rundir RUNDIR=${TESTDIRC} STANDALONE="YES"
+	cp Param/${PARAMFILE} ${TESTDIRC}/PARAM.in
+	cp -r input/glow_data ${TESTDIRC}/=
+
+testSCE_run:
+	cd ${TESTDIRC}; ${MPIRUN} ./ram_scb.exe | tee runlog;
+
+testSCE_check:
+	${SCRIPTDIR}/DiffNum.pl -b -a=1e-9                              \
+	        ${TESTDIRC}/output_ram/log_d20130317_t000000.log        \
+	        ${IMDIR}/output/testSCE/log.ref                           \
+	        > testSCE.diff
+	${SCRIPTDIR}/DiffNum.pl -b -a=1e-9                              \
+	        ${TESTDIRC}/output_ram/pressure_d20130317_t001000.dat   \
+	        ${IMDIR}/output/testSCE/pressure.ref                      \
+	        >> testSCE.diff
+
 	@echo "Test Successful!"

PARAM.XML

@@ -137,13 +137,15 @@ If using nitrogen in the species this command will convert a percent of the oxyg
 	<parameter name="DoUseBASdiff" type="logical" default="F"/>
 	<parameter name="DoUseKpdiff" type="logical" default="F"/>
 	<parameter name="DoUseEMIC" type="logical" default="F"/>
+	<parameter name="DoSaveLwgr" type="logical" default="F"/>
 #USEWPI
 F	DoUseWPI
 F	DoUseBASdiff
 F	DoUseKpdiff
 F	DoUseEMIC
+F	DoSaveLwgr
 
-Flag to turn on pitch angle diffusion. The default setting for the Kp-based version uses Kp=0 coefficients. Turning this flag on interpolates Kp-dependent diffusion coefficents for Kp in the range (0-4). Different options are available if selecting DoUseBASDiff. EMIC wave pitch angle diffusion is used for ions wave-particle interaction.
+Flag to turn on pitch angle diffusion. The default setting for the Kp-based version uses Kp=0 coefficients. Turning this flag on interpolates Kp-dependent diffusion coefficents for Kp in the range (0-4). Different options are available if selecting DoUseBASDiff. EMIC wave pitch angle diffusion is used for ions wave-particle interaction. DoSaveLwgr is used to save hourly output for linear wave growth calculations.
 </command>
 
 <command name="USEFLC">
@@ -339,6 +341,69 @@ F	PressureDetail
 
 </commandgroup>
 
+<commandgroup name="SCE">
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!SCE group!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+<command name="IONOSPHERE">
+         <parameter name="iConductanceModel" type="integer" default="7"/>
+	 <parameter name="StarLightPedConductance" type="float" default="2.5"/>
+	 <parameter name="DoUseFullSpec" type="logical" default="F"/>
+	 <parameter name="DoSaveGLOWConductivity" type="logical" default="F"/>
+#IONOSPHERE
+7              iConductanceModel
+2.5           StarLightPedConductance
+F              DoUseFullSpec
+F              DoSaveGLOWConductivity
+
+\begin{itemize}
+        \item iConductanceModel: 7 uses Robinson's statistical conductance model; 9 uses S. Solomon's GLOW model. If "9" is used, the last two commands are needed. When the GLOW model is used, parallelizing is recommended.
+	\item StarLightPedConductance: the background conductance due to star light
+	\item DoUseFullSpec: only needed when iConductanceModel=9; It uses full precipitating spectrum as input to the GLOW
+	\item DoSaveGLOWConductivity: only needed when iConductanceModel=9; It saves height-dependent conductivity from GLOW
+</command>
+
+<command name="BOUNDARY">
+         <parameter name="LatBoundary" type="float" default="50"/>
+#BOUNDARY
+50            LatBoundary
+
+Specify the low latitudinal boundary for the ionospheric potential solver. Default is set at 50 degree magnetic latitude.
+</command>
+
+<command name="SOLVER">
+         <parameter name="NameSolver" type="string" default="GMRES"/>
+#SOLVER
+GMRES         NameSolver (gmres or bicgstab)
+
+Specify the scheme for the ionospheric potential solver. 
+</command>
+
+<command name="KRYLOV">
+	<parameter name="UsePreconditioner" type="logical" default="T"/>
+	<parameter name="UseInitialGuess"   type="logical" default="T"/>
+	<parameter name="Tolerance" type="real" min="0" default="0.01"/>
+	<parameter name="MaxIteration" type="integer" min="1" default="100"/>
+
+#KRYLOV
+T			UsePreconditioner
+T			UseInitialGuess
+0.01			Tolerance
+100			MaxIteration
+
+This command controls the parameters for the Krylov solver used to
+solve the Poisson type equation for the electric potential.
+If UsePreconditioner is true the solver uses a preconditioner.
+If UseInitialGuess is true, the previous solution is used as an 
+initial guess. The Tolerance parameter sets the second norm of
+the final (preconditioned) residual. The MaxIteration parameter sets the
+maximum number of iterations before the linear solver gives up.
+In most cases the default values should work fine.
+
+The default values are shown above.
+</command>
+
 <commandgroup name="COMPONENTS">
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 !!!!!!!!Components group!!!!!!!!!
@@ -476,6 +541,7 @@ Set the source for the convective electric field in RAM-SCB.  The choice made wi
 	\item \textbf{VOLS}: $K_{P}$-based Volland-Stern empirical electric field (internal VS calculation).
 	\item \textbf{WESC}: Weimer 2001 empirical electric field mapped to the	equatorial plane via RAM-SCB field lines (internal W01 calculation).
 	\item \textbf{W5SC}: Weimer 2005 empirical electric field mapped to the	equatorial plane via RAM-SCB field lines (internal W05 calculation).
+	\item \textbf{RSCE}: self-consistently calculated electric field mapped to the equatorial plane via RAM-SCB field lines. If this option is chosen, the following commands are needed: IONOSPHERE, BOUNDARY, SOLVER, KRYLOV. The description of these commands are provided below.
 \end{enumerate}
 
 The parameter UseEfInd turns the use of induced electric field on or off. Default is no induced electric field.

Param/PARAM.in.testEMIC

@@ -36,6 +36,7 @@ F			DoUseWPI		! Whether to use wave particle interactions or not (Note, wave par
 F			DoUseBASDiff		! Whether to use BAS diffusion coefficients for wave particle interactions
 F			doUseKpDiff		! Whether to use KP based diffusion coefficients for wave particle interactions
 T           DoUseEMIC       !  Whether to turn on AE based EMIC wave pitch angle diffusion
+F           DoSaveLwgr
 
 *************************************************