Test format w Postprocess PR

.fprettify.rc

@@ -9,7 +9,7 @@ i: 2
 recursive
 # Excluded files:
 # Anything compiled, src/venus.f90 (it's incomplete), old fortran files, makefiles, template files
-exclude: ["*.exe","*.o","Venus.f90","*.f","Makef*","*emplate.f90"]
+exclude: ["*.exe","*.o","Venus.f90","*.f","Makef*","*emplate.f90","*Msis21.F90"]
 
 # Whitespace option 2 (check fprettify -h for info):
 whitespace: 2

.github/workflows/Format-Doc-Test.yml

@@ -26,7 +26,8 @@ jobs:
           pip install .
       - name: Clone GITM
         uses: actions/checkout@v4
-        with: 
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
           path:
             GITM
       - name: Format check entire GITM repository

Makefile

@@ -61,7 +61,6 @@ LIB:
 	cd $(GLDIR)     ; make LIBPREV=${LIBDIR}/libSphere.a   LIBADD
 	cd $(MAINDIR)   ; make LIBPREV=${GITM}/${GLDIR}/libUPTOGL.a   LIB
 	cd srcInterface ; make LIBPREV=${GITM}/${MAINDIR}/libUA.a     LIB
-	make POST
 
 nompirun:
 	make GITM
@@ -109,12 +108,10 @@ rundir:
 		if [ ! -e "EIE/README" ]; then \
 			ln -s ${EMPIRICALIEDIR}/data EIE;\
 		fi;
-	cd ${RUNDIR}; rm -f ./PostGITM.exe ; ln -s ${UADIR}/src/PostProcess.exe ./PostGITM.exe
 	cd ${RUNDIR}/UA; \
 		mkdir restartOUT data DataIn; \
 		ln -s restartOUT restartIN; \
-		ln -s ${UADIR}/src/pGITM .; \
-		ln -s ${UADIR}/srcPython/pGITM.py .; \
+		ln -s ${UADIR}/srcPython/post_process.py .; \
 		ln -s ${UADIR}/srcData/* DataIn; rm -f DataIn/CVS; \
 		ln -s ${UADIR}/data/* DataIn;    rm -f DataIn/CVS
 	cd ${RUNDIR} ;                                   \

README.md

@@ -115,25 +115,24 @@ blocks with 9 x 9 cells each, so the default resolution is 180 (deg
 lat) / (2 \* 9) = 10 deg lat, by 360 (deg lon) / (2 \* 9) = 20 deg
 lon. See below for how to set the resolution.
 
-8\. Go into the directory which contains many of the outputs:
+8\. Post process the output files by running:
 
 ```shell
-cd UA
+./post_process.py
 ```
 
-9\. Post process the output files by running:
+> This can be called from `run/` and will postprocess the files in UA/output.
+> It also has functionality to copy files to a remote location, monitor the
+> output folder throughout a run, and more. Run `./post_process.py --help` to
+> see available options.
 
-```shell
-./pGITM
-```
-
-10\. Go into the output directory:
+9\. Go into the output directory:
 
 ```shell
 cd data
 ```
 
-11\. Make some plots with an old plotter:
+10\. Make some plots with an old plotter:
 
 ```shell
 ../../../srcPython/plot_model_results.py -var=3 -alt=120 3DALL_t021221_000500.bin
@@ -142,7 +141,7 @@ cd data
 Then look at the png file that is created.  You can use a `-h` to see
 how to run this code.
 
-11b\. A more advanced plotter is available through aetherpy. This is a bit more
+10b\. A more advanced plotter is available through aetherpy. This is a bit more
 complicated, since you need to install aetherpy. If you don't use python
 much, this is harder. Here is how to do this:
 
@@ -165,7 +164,7 @@ git checkout develop
 python setup.py develop --user
 ```
 
-11c\. Test out the new plotter:
+10c\. Test out the new plotter:
 
 ```shell
 cd <directory where you started from>

src/Makefile

@@ -145,7 +145,6 @@ SAMIEXE = ${BINDIR}/GITMSAMI.exe
 
 GITM:	DEPEND
 	@make ${EXE}
-	@make POST
 	@echo
 	@echo "${EXE} has been created"
 	@echo
@@ -158,7 +157,6 @@ ${EXE}:	${OBJECTS_EXE}
 
 SAMI:	DEPENDSAMI
 	@make ${SAMIEXE}
-	@make POST
 	@echo "${SAMIEXE} has been created"
 
 ${SAMIEXE}:	${OBJECTS_SAMI}

src/ModInputs.f90

@@ -285,7 +285,7 @@ module ModInputs
   real    :: CO2ppm = 225.0
 
   logical :: DoN4SHack = .false.
-  
+
   ! Allow the user to change the planet's characteristics:
   real :: RotationPeriodInput = Rotation_Period
   real :: OmegaBodyInput = 2.0*pi/Rotation_Period

src/init_altitude.f90

@@ -16,8 +16,8 @@ subroutine get_temperature(lon, lat, alt, t, h)
   !---------------------------------------------------------------------------
   if (UseMsis) then
 
-     call initialize_msis_routines
-     call get_msis_temperature(lon, lat, alt, t, h)
+    call initialize_msis_routines
+    call get_msis_temperature(lon, lat, alt, t, h)
 
   else
 

src/init_msis.Earth.f90

@@ -29,7 +29,7 @@ subroutine call_msis(lonDeg, latDeg, altKm, f107, f107a, densities10, temp)
   use ModConstants, only: Boltzmanns_Constant, AMU
 
   implicit none
-  
+
   real, intent(in) :: lonDeg, latDeg, altKm, f107, f107a
   real, intent(out) :: densities10(10)
   real, intent(out) :: temp
@@ -58,52 +58,52 @@ subroutine call_msis(lonDeg, latDeg, altKm, f107, f107a, densities10, temp)
   AP = 10
 
   if (useMsis21) then
-     iyd = iJulianDay
-     sec = utime
-     alt = altKm
-     glat = latDeg
-     glong = lonDeg
-     stl = LST
-     f107a_4 = f107a
-     f107_4 = f107
-     ap_4 = AP
-     ! mass is not used, but passed anyways
-     mass = -1     
-     call gtd8d(iyd,sec,alt,glat,glong,stl,f107a_4,f107_4,ap_4,mass,d,t)
-     temp = t(2)
-     ! Convert to /m3
-     ! 10th density is NO now!
-     densities10 = d * 1e6
+    iyd = iJulianDay
+    sec = utime
+    alt = altKm
+    glat = latDeg
+    glong = lonDeg
+    stl = LST
+    f107a_4 = f107a
+    f107_4 = f107
+    ap_4 = AP
+    ! mass is not used, but passed anyways
+    mass = -1
+    call gtd8d(iyd, sec, alt, glat, glong, stl, f107a_4, f107_4, ap_4, mass, d, t)
+    temp = t(2)
+    ! Convert to /m3
+    ! 10th density is NO now!
+    densities10 = d*1e6
   else
-     CALL GTD7(iJulianDay, utime, AltKm, LatDeg, LonDeg, LST, &
-          f107a, f107, AP, 48, msis_dens9, msis_temp)
-     temp = msis_temp(2)
-     densities10(1:9) = msis_dens9
-
-     ! Very old code:
-     !  ! The initial profile of [NO] is refered to:
-     !  !  [Charles A. Barth, AGU, 1995]
-     !
-     !  if (geo_alt < 120.) then
-     !     NDensityS(iLon,iLat,iAlt,iNO_,iBlock)=  &
-     !          max(1e14-1e10*abs((geo_alt-110.0))**3.5, 100.0)
-     !          !10**(-0.003*(geo_alt-105.)**2 +14+LOG10(3.))
-     !  else
-     !     m = (1e10-3.9e13)/(200)
-     !     k = 1e10+(-m*300.)
-     !     NDensityS(iLon,iLat,iAlt,iNO_,iBlock)=  &
-     !          MAX(k+(m*geo_alt)-(geo_alt - 120.0)**2,100.0)
-     !       !   MAX(10**(13.-LOG10(3.)*(geo_alt-165.)/35.),1.0)
-     !  endif
-     !
-     ffactor = 6.36*log(f107) - 13.8
-     no = (ffactor*1.0e13 + 8.0e13)*1.24 ! 12.4 ! 12.4 is roughly exp
-     ! This is obviously an approximation:
-     h = Boltzmanns_Constant * msis_temp(2)/ &
-          (9.5 * 28.0 * AMU)/1000.0
-     densities10(10) = no * exp(-(altKm - 100.0)/h)
+    CALL GTD7(iJulianDay, utime, AltKm, LatDeg, LonDeg, LST, &
+              f107a, f107, AP, 48, msis_dens9, msis_temp)
+    temp = msis_temp(2)
+    densities10(1:9) = msis_dens9
+
+    ! Very old code:
+    !  ! The initial profile of [NO] is refered to:
+    !  !  [Charles A. Barth, AGU, 1995]
+    !
+    !  if (geo_alt < 120.) then
+    !     NDensityS(iLon,iLat,iAlt,iNO_,iBlock)=  &
+    !          max(1e14-1e10*abs((geo_alt-110.0))**3.5, 100.0)
+    !          !10**(-0.003*(geo_alt-105.)**2 +14+LOG10(3.))
+    !  else
+    !     m = (1e10-3.9e13)/(200)
+    !     k = 1e10+(-m*300.)
+    !     NDensityS(iLon,iLat,iAlt,iNO_,iBlock)=  &
+    !          MAX(k+(m*geo_alt)-(geo_alt - 120.0)**2,100.0)
+    !       !   MAX(10**(13.-LOG10(3.)*(geo_alt-165.)/35.),1.0)
+    !  endif
+    !
+    ffactor = 6.36*log(f107) - 13.8
+    no = (ffactor*1.0e13 + 8.0e13)*1.24 ! 12.4 ! 12.4 is roughly exp
+    ! This is obviously an approximation:
+    h = Boltzmanns_Constant*msis_temp(2)/ &
+        (9.5*28.0*AMU)/1000.0
+    densities10(10) = no*exp(-(altKm - 100.0)/h)
   endif
-  
+
 end subroutine call_msis
 
 subroutine get_msis_temperature(lon, lat, alt, t, h)
@@ -163,17 +163,17 @@ subroutine get_msis_temperature(lon, lat, alt, t, h)
 
   if (RCMRFlag .and. RCMROutType == "F107") then
 
-     call call_msis(lonDeg, latDeg, altKm, f107_msis, f107a_msis, msis_dens10, msis_temp1)
-     msis_dens = msis_dens10(1:9)
-     msis_temp = msis_temp1
-     !CALL GTD7(iJulianDay, utime, AltKm, LatDeg, LonDeg, LST, &
-     !         f107a_msis, f107_msis, AP, 48, msis_dens, msis_temp)
+    call call_msis(lonDeg, latDeg, altKm, f107_msis, f107a_msis, msis_dens10, msis_temp1)
+    msis_dens = msis_dens10(1:9)
+    msis_temp = msis_temp1
+    !CALL GTD7(iJulianDay, utime, AltKm, LatDeg, LonDeg, LST, &
+    !         f107a_msis, f107_msis, AP, 48, msis_dens, msis_temp)
   else
-     call call_msis(lonDeg, latDeg, altKm, f107, f107a, msis_dens10, msis_temp1)
-     msis_dens = msis_dens10(1:9)
-     msis_temp = msis_temp1
-     !call GTD7(iJulianDay, utime, AltKm, LatDeg, LonDeg, LST, &
-     !     F107A, F107, AP, 48, msis_dens, msis_temp)
+    call call_msis(lonDeg, latDeg, altKm, f107, f107a, msis_dens10, msis_temp1)
+    msis_dens = msis_dens10(1:9)
+    msis_temp = msis_temp1
+    !call GTD7(iJulianDay, utime, AltKm, LatDeg, LonDeg, LST, &
+    !     F107A, F107, AP, 48, msis_dens, msis_temp)
   endif
 
   t = msis_temp(2)
@@ -201,19 +201,19 @@ subroutine initialize_msis_routines
   use ModInputs, only: UseMsisTides, useMsis21, UseMsisOnly, sw_msis
   use EUA_ModMsis00, ONLY: meters, tselec
   use msis_init, only: msisinit
-  
+
   implicit none
 
   real*4 :: sw_msis4x25(25)
   logical, save :: isFirstTIme = .true.
 
   ! We only need to initialize MSIS once!
   if (.not. isFirstTime) then
-     return
+    return
   else
-     isFirstTime = .false.
+    isFirstTime = .false.
   endif
-  
+
   ! We want units of /m3 and not /cm3
 
   call meters(.true.)
@@ -238,12 +238,12 @@ subroutine initialize_msis_routines
   sw_msis(2) = 0
 
   if (useMsis21) then
-     sw_msis4x25 = sw_msis
-     call msisinit(parmpath = 'UA/DataIn/LowerBCs/', switch_legacy=sw_msis4x25)
+    sw_msis4x25 = sw_msis
+    call msisinit(parmpath='UA/DataIn/LowerBCs/', switch_legacy=sw_msis4x25)
   else
-     call tselec(sw_msis)
+    call tselec(sw_msis)
   endif
-  
+
 end subroutine initialize_msis_routines
 
 !--------------------------------------------------------------
@@ -299,7 +299,7 @@ subroutine init_msis
   endif
 
   call initialize_msis_routines
-  
+
   !--------------------------------------------------------------------------
   !
   !  From the msis90 library:
@@ -393,10 +393,10 @@ subroutine init_msis
           NDensityS(iLon, iLat, iAlt, iH_, iBlock) = &
             max(msis_dens(7), 100.0)
           NDensityS(iLon, iLat, iAlt, iN_4S_, iBlock) = &
-               max(msis_dens(8), 100.0)
-          NDensityS(iLon, iLat, iAlt, iNO_, iBlock) =  &
-               max(msis_dens10(10), 100.0)
-          
+            max(msis_dens(8), 100.0)
+          NDensityS(iLon, iLat, iAlt, iNO_, iBlock) = &
+            max(msis_dens10(10), 100.0)
+
           NDensityS(iLon, iLat, iAlt, iN_2P_, iBlock) = &
             NDensityS(iLon, iLat, iAlt, iN_4S_, iBlock)/10000.0
           NDensityS(iLon, iLat, iAlt, iN_2D_, iBlock) = &
@@ -554,7 +554,6 @@ subroutine msis_bcs(iJulianDay, UTime, Alt, LatIn, LonIn, Lst, &
   !----------------------------------------------------------------------------
   AP_I = AP
 
-
   !CALL GTD7(iJulianDay, uTime, Alt, Lat, Lon, LST, &
   !     F107A, F107, AP_I, 48, msis_dens, msis_temp)
   call call_msis(lon, lat, alt, f107, f107a, msis_dens10, msis_temp1)

src/set_inputs.f90

@@ -374,8 +374,8 @@ subroutine set_inputs
           write(*, *) '#MSISOBC'
           write(*, *) 'UseOBCExperiment        (logical)'
           write(*, *) 'MsisOblateFactor           (real)'
-       endif
-       
+        endif
+
       case ("#MSIS21")
         call read_in_logical(UseMsis21, iError)
         if (iError /= 0) then

src/set_vertical_bcs.Earth.f90

@@ -139,18 +139,18 @@ subroutine set_vertical_bcs(LogRho, LogNS, Vel_GD, Temp, LogINS, iVel, VertVel)
     Vel_GD(-1:0, iEast_) = 0.0
     Vel_GD(-1:0, iNorth_) = 0.0
     ! The rest of the BCs will just stay constant.
- endif
+  endif
 
- if (DoN4SHack) then
+  if (DoN4SHack) then
     !! Hack for iN_4S_ for lower altitudes:
     do iAlt = nAlts, 0, -1
-       if (NS(iAlt - 1, iN_4S_) < 1000.0) then
-          NS(iAlt - 1, iN_4S_) = NS(iAlt, iN_4S_)
-          logNS(iAlt - 1, iN_4S_) = log(NS(iAlt - 1, iN_4S_))
-       endif
+      if (NS(iAlt - 1, iN_4S_) < 1000.0) then
+        NS(iAlt - 1, iN_4S_) = NS(iAlt, iN_4S_)
+        logNS(iAlt - 1, iN_4S_) = log(NS(iAlt - 1, iN_4S_))
+      endif
     enddo
- endif
- 
+  endif
+
   if (.not. DuringPerturb) then
     Vel_GD(-1:0, iUp_) = 0.0
     VertVel(-1:0, :) = 0.0