From d172ee785a076fefedee5fff8679cf1abc11d7f9 Mon Sep 17 00:00:00 2001
From: Aaron James Ridley <ridley@umich.edu>
Date: Thu, 8 May 2025 08:32:29 -0400
Subject: [PATCH 01/12] BUG: should sort file list to process oldest files
 first

---
 srcPython/pGITM.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/srcPython/pGITM.py b/srcPython/pGITM.py
index d90e8c05..48e0e592 100755
--- a/srcPython/pGITM.py
+++ b/srcPython/pGITM.py
@@ -381,7 +381,7 @@ def post_process_gitm(dir, doRemove, isVerbose = False):
     os.chdir(processDir)
 
     # Get list of header files to process:
-    headers = glob('*.header')
+    headers = sorted(glob('*.header'))
     if (isVerbose):
         print('Found %i files to process' % len(headers))
     

From e5ad5e2fafe0c8246b65bf4ee418e3846fa5ecc1 Mon Sep 17 00:00:00 2001
From: Aaron James Ridley <ridley@umich.edu>
Date: Thu, 8 May 2025 16:29:17 -0400
Subject: [PATCH 02/12] FEAT: work from UA and UA/data directories too!

---
 srcPython/post_process.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/srcPython/post_process.py b/srcPython/post_process.py
index be56f573..1247c8df 100755
--- a/srcPython/post_process.py
+++ b/srcPython/post_process.py
@@ -426,7 +426,14 @@ def do_loop(doTarZip, user, server, dir, IsRemote):
     if (doTarZip):
         DidWork = tar_and_zip_gitm()
     else:
+        # Default should be UA/data
         processDir = 'UA/data' 
+        if (not os.path.exists(processDir)):
+            # Maybe we are in the UA directory?
+            processDir = 'data'
+            if (not os.path.exists(processDir)):
+                # Maybe we are already in the data directory???
+                processDir = '.'
         DidWork = post_process_gitm(processDir, DoRm, isVerbose = IsVerbose)
         #DidWork = post_process_gitm()
         

From fdf1f5ef82337ee4a9cf03fe93a30c38fdf71c16 Mon Sep 17 00:00:00 2001
From: Aaron Bukowski <abukowski21@gmail.com>
Date: Tue, 13 May 2025 13:34:58 +0000
Subject: [PATCH 03/12] STY: Different exit messages when not looping (in
 post_process.py)

---
 srcPython/post_process.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/srcPython/post_process.py b/srcPython/post_process.py
index 1247c8df..4297baa3 100755
--- a/srcPython/post_process.py
+++ b/srcPython/post_process.py
@@ -515,7 +515,11 @@ def load_remote_file(args):
                 currentTime = datetime.now()
                 dt = ((currentTime - startTime).total_seconds())/3600.0
                 if (dt > args.totaltime):
-                    print("  --> Stopping due to totaltime exceeded!")
+                    if args.totaltime == 0:
+                        # Different exit message for non-continuous runs 
+                        print("  --> All done!")
+                    else:
+                        print("  --> Stopping due to totaltime exceeded!")
                     # want to break out of loop, so set loop breaking condition:
                     DidWork = False
 

From 0828753c32a5a0cbc22caf4e4fba71ff48802866 Mon Sep 17 00:00:00 2001
From: Aaron Bukowski <abukowski21@gmail.com>
Date: Wed, 14 May 2025 15:38:48 +0000
Subject: [PATCH 04/12] MAINT: Don't build legacy postprocessors by default
 (can still be made with `make POST`)

---
 Makefile     | 1 -
 src/Makefile | 2 --
 2 files changed, 3 deletions(-)

diff --git a/Makefile b/Makefile
index 8b66be20..de673704 100644
--- a/Makefile
+++ b/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
diff --git a/src/Makefile b/src/Makefile
index 1922f6f1..b79819d6 100644
--- a/src/Makefile
+++ b/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}

From 224013caf30725c4dd2c47ff4b11c96b06ddfedd Mon Sep 17 00:00:00 2001
From: Aaron Bukowski <abukowski21@gmail.com>
Date: Wed, 14 May 2025 15:43:12 +0000
Subject: [PATCH 05/12] FEAT: Change default postprocessor! details:

- do not copy postprocess.exe (pGITM)
- do not copy pGITM.py
- yes copy post_process.py
- update README with new postprocess info
---
 Makefile  |  4 +---
 README.md | 21 ++++++++++-----------
 2 files changed, 11 insertions(+), 14 deletions(-)

diff --git a/Makefile b/Makefile
index de673704..6ae6b49f 100644
--- a/Makefile
+++ b/Makefile
@@ -108,12 +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} ;                                   \
diff --git a/README.md b/README.md
index be572f4b..c5106b60 100644
--- a/README.md
+++ b/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>

From ec4f24ae0448c157efec4eefa1437086097a191b Mon Sep 17 00:00:00 2001
From: Aaron Bukowski <abukowski21@gmail.com>
Date: Wed, 14 May 2025 15:43:55 +0000
Subject: [PATCH 06/12] doc: edit comments in pGITM.py - it doesn't use
 postGITM.exe

---
 srcPython/pGITM.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/srcPython/pGITM.py b/srcPython/pGITM.py
index 48e0e592..236d1f84 100755
--- a/srcPython/pGITM.py
+++ b/srcPython/pGITM.py
@@ -1,10 +1,10 @@
 #!/usr/bin/env python3
 '''
-A wrapper for PostGITM.exe to handle all unconcatenated output fragments 
+Handle all unconcatenated output fragments 
 produced during a GITM simulation.
 
-This script is an alternative to pGITM (written in cshell) that works robustly
-and securely on a range of unix-like environments with Python available
+This script works robustly and securely on a range of
+unix-like environments with Python available
 (i.e., any modern computer.)
 '''
 
@@ -28,7 +28,7 @@
 
 def get_args_pgitm():
     parser = argparse.ArgumentParser(
-        description = 'Plot Aether / GITM model results')
+        description = 'Post-process GITM model results')
     parser.add_argument('-v',  \
                         action='store_true', default = False, \
                         help = 'set verbose to true')
@@ -374,7 +374,7 @@ def post_process_gitm(dir, doRemove, isVerbose = False):
         print('Processing directory doesnt exist: ', processDir)
         print('Make sure to put in a valid -dir= ')
         exit()
-    # Move into the UA/data directory (required by PostGITM.exe)
+    # Move into the UA/data directory
     if (isVerbose):
         print('Moving into processing directory : ', processDir)
     cwd = os.getcwd()

From 1bb9854ea48d28715fe1c9cfbe5e9b8b6871e360 Mon Sep 17 00:00:00 2001
From: Aaron Bukowski <abukowski21@gmail.com>
Date: Wed, 14 May 2025 15:44:20 +0000
Subject: [PATCH 07/12] doc: update docstrings & help messages in
 post_process.py

---
 srcPython/post_process.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/srcPython/post_process.py b/srcPython/post_process.py
index 4297baa3..1a0deb72 100755
--- a/srcPython/post_process.py
+++ b/srcPython/post_process.py
@@ -16,8 +16,11 @@
 
 def parse_args_post():
 
-    parser = argparse.ArgumentParser(description =
-                                     'Post process and move model results')
+    parser = argparse.ArgumentParser(
+        description = "Post process and (optionally) move model results.\n"+
+        "- This functions similar to pGITM.py, but can copy files to\n"+
+        "  a remote location, or postprocess files as they are created.",
+        formatter_class=argparse.RawTextHelpFormatter)
     parser.add_argument('-remotefile',
                         help = 'File that contains info. about remote system',
                         default = 'remote')
@@ -31,15 +34,15 @@ def parse_args_post():
                         default = 'none')
     
     parser.add_argument('-dir',
-                        help = 'remote directory to use',
+                        help = 'remote directory to use (default none)',
                         default = 'none')
     
     parser.add_argument('-sleep',
-                        help = 'how long to sleep between loops',
+                        help = 'how long to sleep between loops in seconds, (default 300)',
                         default = 300, type = int)
 
     parser.add_argument('-totaltime',
-                        help = 'specify how long to run in total (in hours)',
+                        help = 'specify how long to run in total in hours, (default 0 - only run once)',
                         default = 0, type = int)
 
     parser.add_argument('-q',

From eadcc7f2c48aa042d992751aa0be474479a0c91c Mon Sep 17 00:00:00 2001
From: Aaron Bukowski <abukowski21@gmail.com>
Date: Wed, 14 May 2025 15:57:22 +0000
Subject: [PATCH 08/12] sty: prettifying

---
 src/ModInputs.f90              |   2 +-
 src/init_altitude.f90          |   4 +-
 src/init_msis.Earth.f90        | 137 ++++++++++++++++-----------------
 src/set_inputs.f90             |   4 +-
 src/set_vertical_bcs.Earth.f90 |  16 ++--
 5 files changed, 81 insertions(+), 82 deletions(-)

diff --git a/src/ModInputs.f90 b/src/ModInputs.f90
index 17a586f4..44b40c71 100644
--- a/src/ModInputs.f90
+++ b/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
diff --git a/src/init_altitude.f90 b/src/init_altitude.f90
index cf372382..96b1abc5 100644
--- a/src/init_altitude.f90
+++ b/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
 
diff --git a/src/init_msis.Earth.f90 b/src/init_msis.Earth.f90
index 5fed7104..c650cf13 100644
--- a/src/init_msis.Earth.f90
+++ b/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)
@@ -201,7 +201,7 @@ 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)
@@ -209,11 +209,11 @@ subroutine initialize_msis_routines
 
   ! 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)
diff --git a/src/set_inputs.f90 b/src/set_inputs.f90
index 45d3e1a6..4bcc49db 100644
--- a/src/set_inputs.f90
+++ b/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
diff --git a/src/set_vertical_bcs.Earth.f90 b/src/set_vertical_bcs.Earth.f90
index 6990e9f7..539dbe6d 100644
--- a/src/set_vertical_bcs.Earth.f90
+++ b/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

From 85fd88e6f348c42ba76e06a51b93170742af71bb Mon Sep 17 00:00:00 2001
From: Aaron Bukowski <abukowski21@gmail.com>
Date: Thu, 15 May 2025 21:16:49 +0000
Subject: [PATCH 09/12] BUG: Formatter issues w/ MSIS

---
 .fprettify.rc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.fprettify.rc b/.fprettify.rc
index 8052f7ca..9d14c90e 100644
--- a/.fprettify.rc
+++ b/.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

From 56c84b66b3bc0aeb32ebdbbfc8cc49266cacb135 Mon Sep 17 00:00:00 2001
From: Aaron Bukowski <abukowski21@gmail.com>
Date: Fri, 16 May 2025 10:11:30 -0400
Subject: [PATCH 10/12] Revert "sty: prettifying" UNprettifying, oy

This reverts commit eadcc7f2c48aa042d992751aa0be474479a0c91c.
---
 src/ModInputs.f90              |   2 +-
 src/init_altitude.f90          |   4 +-
 src/init_msis.Earth.f90        | 137 +++++++++++++++++----------------
 src/set_inputs.f90             |   4 +-
 src/set_vertical_bcs.Earth.f90 |  16 ++--
 5 files changed, 82 insertions(+), 81 deletions(-)

diff --git a/src/ModInputs.f90 b/src/ModInputs.f90
index 44b40c71..17a586f4 100644
--- a/src/ModInputs.f90
+++ b/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
diff --git a/src/init_altitude.f90 b/src/init_altitude.f90
index 96b1abc5..cf372382 100644
--- a/src/init_altitude.f90
+++ b/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
 
diff --git a/src/init_msis.Earth.f90 b/src/init_msis.Earth.f90
index c650cf13..5fed7104 100644
--- a/src/init_msis.Earth.f90
+++ b/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)
@@ -201,7 +201,7 @@ 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)
@@ -209,11 +209,11 @@ subroutine initialize_msis_routines
 
   ! 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) = &
@@ -554,6 +554,7 @@ 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)
diff --git a/src/set_inputs.f90 b/src/set_inputs.f90
index 4bcc49db..45d3e1a6 100644
--- a/src/set_inputs.f90
+++ b/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
diff --git a/src/set_vertical_bcs.Earth.f90 b/src/set_vertical_bcs.Earth.f90
index 539dbe6d..6990e9f7 100644
--- a/src/set_vertical_bcs.Earth.f90
+++ b/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

From 56c235c20f3036b98c900bdd1de9ddfa17be7c6d Mon Sep 17 00:00:00 2001
From: Aaron Bukowski <abukowski21@gmail.com>
Date: Fri, 16 May 2025 10:59:34 -0400
Subject: [PATCH 11/12] bug: force format test to use up-to-date PR

---
 .github/workflows/Format-Doc-Test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/Format-Doc-Test.yml b/.github/workflows/Format-Doc-Test.yml
index 42cfacfd..dd6938bb 100644
--- a/.github/workflows/Format-Doc-Test.yml
+++ b/.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

From 1361c33804f35aee5077f5487f117fa400e3a6b2 Mon Sep 17 00:00:00 2001
From: Aaron Bukowski <abukowski21@gmail.com>
Date: Fri, 16 May 2025 11:05:26 -0400
Subject: [PATCH 12/12] sty: RE prettifying, yo

Formatter wasn't grabbing the most code that it should have been.
---
 src/ModInputs.f90              |   2 +-
 src/init_altitude.f90          |   4 +-
 src/init_msis.Earth.f90        | 137 ++++++++++++++++-----------------
 src/set_inputs.f90             |   4 +-
 src/set_vertical_bcs.Earth.f90 |  16 ++--
 5 files changed, 81 insertions(+), 82 deletions(-)

diff --git a/src/ModInputs.f90 b/src/ModInputs.f90
index 17a586f4..44b40c71 100644
--- a/src/ModInputs.f90
+++ b/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
diff --git a/src/init_altitude.f90 b/src/init_altitude.f90
index cf372382..96b1abc5 100644
--- a/src/init_altitude.f90
+++ b/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
 
diff --git a/src/init_msis.Earth.f90 b/src/init_msis.Earth.f90
index 5fed7104..c650cf13 100644
--- a/src/init_msis.Earth.f90
+++ b/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)
@@ -201,7 +201,7 @@ 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)
@@ -209,11 +209,11 @@ subroutine initialize_msis_routines
 
   ! 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)
diff --git a/src/set_inputs.f90 b/src/set_inputs.f90
index 45d3e1a6..4bcc49db 100644
--- a/src/set_inputs.f90
+++ b/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
diff --git a/src/set_vertical_bcs.Earth.f90 b/src/set_vertical_bcs.Earth.f90
index 6990e9f7..539dbe6d 100644
--- a/src/set_vertical_bcs.Earth.f90
+++ b/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