From 435d9d4647b65bed2c61d9ae2e81e073b82ba137 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Thu, 21 Jul 2022 13:20:13 -0400
Subject: [PATCH 01/22] remove rst_dir for MERRA-2

---
 .../post/remap_restart/remap_analysis.py      |  66 +++++++++++
 .../post/remap_restart/remap_catchANDcn.py    |  26 +++++
 .../remap_lake_landice_saltwater.py           |  29 +++++
 GEOS_Util/post/remap_restart/remap_params.py  | 103 ------------------
 GEOS_Util/post/remap_restart/remap_params.tpl |   1 +
 .../post/remap_restart/remap_questions.py     |  21 ++--
 .../post/remap_restart/remap_restarts.py      |   4 -
 GEOS_Util/post/remap_restart/remap_upper.py   |  31 ++++++
 8 files changed, 161 insertions(+), 120 deletions(-)

diff --git a/GEOS_Util/post/remap_restart/remap_analysis.py b/GEOS_Util/post/remap_restart/remap_analysis.py
index 0990f497..eab791db 100755
--- a/GEOS_Util/post/remap_restart/remap_analysis.py
+++ b/GEOS_Util/post/remap_restart/remap_analysis.py
@@ -19,6 +19,8 @@
 class analysis(remap_base):
   def __init__(self, **configs):
      super().__init__(**configs)
+     if self.config['input']['shared']['MERRA-2']:
+       self.copy_merra2()
 
   def remap(self):
      config = self.config
@@ -132,6 +134,70 @@ def find_analysis(self):
      analysis_in = bkgs + sfcs + traks + anasat
      return list(dict.fromkeys(analysis_in))
 
+  def copy_merra2(self):
+    if not self.config['input']['shared']['MERRA-2']:
+      return
+    bkg = self.config['output']['shared'][['bkg']
+    if ( not bkg ): return
+
+    expid = self.config['input']['shared']['expid']
+    yyyymmddhh_ = str(self.config['input']['shared']['yyyymmddhh'])
+    yyyy_ = yyyymmddhh_[0:4]
+    mm_   = yyyymmddhh_[4:6]
+    dd_   = yyyymmddhh_[6:8]
+    hh_   = yyyymmddhh_[8:10]
+
+    merra_2_rst_dir = '/archive/users/gmao_ops/MERRA2/gmao_ops/GEOSadas-5_12_4/'+expid +'/rs/Y'+yyyy_ +'/M'+mm_+'/'
+    rst_dir = self.config['input']['shared']['rst_dir'] + '/'
+    os.makedirs(rst_dir, exist_ok = True)
+    print(' Copy MERRA-2 analysis files \n from \n    ' + merra_2_rst_dir + '\n to\n    '+ rst_dir +'\n')
+
+    rst_time = datetime(year=int(yyyy_), month=int(mm_), day=int(dd_), hour = int(hh_))
+
+    anafiles=[]
+    for h in [3,4,5,6,7,8,9]:
+       delt = timedelta(hours = h-3)
+       new_time = rst_time + delt
+       yyyy = "Y"+str(new_time.year)
+       mm   = 'M%02d'%new_time.month
+       ymd  = '%04d%02d%02d'%(new_time.year,new_time.month, new_time.day)
+       hh   = '%02d'%h
+       newhh= '%02d'%new_time.hour
+       m2_rst_dir = merra_2_rst_dir.replace('Y'+yyyy_,yyyy).replace('M'+mm_,mm)
+       # bkg files
+       for ftype in ['sfc', 'eta']:
+          fname = expid + '.bkg'+hh+'_'+ftype+'_rst.'+ymd+'_'+newhh+'z.nc4'
+          f = m2_rst_dir+'/'+fname
+          if(os.path.isfile(f)):
+             anafiles.append(f)
+          else:
+             print('Warning: Cannot find '+f)
+
+       # gaas_bkg_sfc files
+       if (h==6 or h==9):
+          fname = expid+'.gaas_bkg_sfc_rst.'+ymd+'_'+newhh+'z.nc4'
+          f = m2_rst_dir+'/'+fname
+          if (os.path.isfile(f)):
+            anafiles.append(f)
+          else:
+            print('Warning: Cannot find '+f)
+    # trak.GDA.rst file
+    delt = timedelta(hours = 3)
+    new_time = rst_time - delt
+    yyyy = "Y"+str(new_time.year)
+    mm   = 'M%02d'%new_time.month
+    ymdh = '%04d%02d%02d%02d'%(new_time.year, new_time.month, new_time.day, new_time.hour)
+    m2_rst_dir = merra_2_rst_dir.replace('Y'+yyyy_,yyyy).replace('M'+mm_,mm)
+    fname = expid+'.trak.GDA.rst.'+ymdh+'z.txt'
+    f = m2_rst_dir+'/'+fname
+    if (os.path.isfile(f)): anafiles.append(f)
+
+    for f in anafiles:
+      fname    = os.path.basename(f)
+      f_tmp = rst_dir+'/'+fname
+      print("Copy file "+f +" to " + rst_dir)
+      shutil.copy(f,f_tmp)
+
 if __name__ == '__main__' :
    ana = analysis(params_file='remap_params.yaml')
    ana.remap()
diff --git a/GEOS_Util/post/remap_restart/remap_catchANDcn.py b/GEOS_Util/post/remap_restart/remap_catchANDcn.py
index 44337f3e..1ef13cad 100755
--- a/GEOS_Util/post/remap_restart/remap_catchANDcn.py
+++ b/GEOS_Util/post/remap_restart/remap_catchANDcn.py
@@ -12,6 +12,8 @@
 class catchANDcn(remap_base):
   def __init__(self, **configs):
      super().__init__(**configs)
+     if self.config['input']['shared']['MERRA-2']:
+       self.copy_merra2()
 
   def remap(self):
      if not self.config['output']['surface']['remap_catch']:
@@ -129,6 +131,30 @@ def remap(self):
      print( "cd " + cwdir)
      os.chdir(cwdir)
 
+  def copy_merra2(self):
+    if not self.config['input']['shared']['MERRA-2']:
+      return
+
+    expid = self.config['input']['shared']['expid']
+    yyyymmddhh_ = str(self.config['input']['shared']['yyyymmddhh'])
+    yyyy_ = yyyymmddhh_[0:4]
+    mm_   = yyyymmddhh_[4:6]
+    dd_   = yyyymmddhh_[6:8]
+    hh_   = yyyymmddhh_[8:10]
+
+    suffix = yyyymmddhh_[0:8]+'_'+ hh_ + 'z.bin'
+    merra_2_rst_dir = '/archive/users/gmao_ops/MERRA2/gmao_ops/GEOSadas-5_12_4/'+expid +'/rs/Y'+yyyy_ +'/M'+mm_+'/'
+    rst_dir = self.config['input']['shared']['rst_dir'] + '/'
+    os.makedirs(rst_dir, exist_ok = True)
+    print(' Copy MERRA-2 catchment Restart \n from \n    ' + merra_2_rst_dir + '\n to\n    '+ rst_dir +'\n')
+
+    f =  merra_2_rst_dir +  expid+'.catch_internal_rst.'    + suffix
+
+    fname = os.path.basename(f)
+    dest = rst_dir + '/'+fname
+    print("Copy file "+f +" to " + rst_dir)
+    shutil.copy(f, dest)
+
 if __name__ == '__main__' :
    catch = catchANDcn(params_file='remap_params.yaml')
    catch.remap()
diff --git a/GEOS_Util/post/remap_restart/remap_lake_landice_saltwater.py b/GEOS_Util/post/remap_restart/remap_lake_landice_saltwater.py
index 4d25ae33..76cb9809 100755
--- a/GEOS_Util/post/remap_restart/remap_lake_landice_saltwater.py
+++ b/GEOS_Util/post/remap_restart/remap_lake_landice_saltwater.py
@@ -11,6 +11,8 @@
 class lake_landice_saltwater(remap_base):
   def __init__(self, **configs):
      super().__init__(**configs)
+     if self.config['input']['shared']['MERRA-2']:
+       self.copy_merra2()
 
   def remap(self):
      if not self.config['output']['surface']['remap_water']:
@@ -164,6 +166,33 @@ def find_rst(self):
 
      return restarts_in
 
+  def copy_merra2(self):
+    if not self.config['input']['shared']['MERRA-2']:
+      return
+
+    expid = self.config['input']['shared']['expid']
+    yyyymmddhh_ = str(self.config['input']['shared']['yyyymmddhh'])
+    yyyy_ = yyyymmddhh_[0:4]
+    mm_   = yyyymmddhh_[4:6]
+    dd_   = yyyymmddhh_[6:8]
+    hh_   = yyyymmddhh_[8:10]
+
+    suffix = yyyymmddhh_[0:8]+'_'+ hh_ + 'z.bin'
+    merra_2_rst_dir = '/archive/users/gmao_ops/MERRA2/gmao_ops/GEOSadas-5_12_4/'+expid +'/rs/Y'+yyyy_ +'/M'+mm_+'/'
+    rst_dir = self.config['input']['shared']['rst_dir'] + '/'
+    os.makedirs(rst_dir, exist_ok = True)
+    print(' Copy MERRA-2 surface restarts \n from \n    ' + merra_2_rst_dir + '\n to\n    '+ rst_dir +'\n')
+
+    surfin = [ merra_2_rst_dir +  expid+'.lake_internal_rst.'     + suffix,
+               merra_2_rst_dir +  expid+'.landice_internal_rst.'  + suffix,
+               merra_2_rst_dir +  expid+'.saltwater_internal_rst.'+ suffix]
+
+    for f in surfin :
+       fname = os.path.basename(f)
+       dest = rst_dir + '/'+fname
+       print("Copy file "+f +" to " + rst_dir)
+       shutil.copy(f, dest)
+
 if __name__ == '__main__' :
    lls = lake_landice_saltwater(params_file='remap_params.yaml')
    lls.remap()
diff --git a/GEOS_Util/post/remap_restart/remap_params.py b/GEOS_Util/post/remap_restart/remap_params.py
index cd5ec03c..7f1e93da 100755
--- a/GEOS_Util/post/remap_restart/remap_params.py
+++ b/GEOS_Util/post/remap_restart/remap_params.py
@@ -268,109 +268,6 @@ def init_merra2(self):
     self.common_in['bc_base']= 'discover_ops'
     self.common_in['tag']= 'Ganymed-4_0'
 
-  def copy_merra2(self):
-    if not self.common_in['MERRA-2']:
-      return
-    print("\n Copy MERRA-2 :\n")
-    expid = self.common_in['expid']
-    yyyymmddhh_ = str(self.common_in['yyyymmddhh'])
-    surfix = yyyymmddhh_[0:8]+'_'+self.hh+'z.bin'
-    merra_2_rst_dir = '/archive/users/gmao_ops/MERRA2/gmao_ops/GEOSadas-5_12_4/'+expid +'/rs/Y'+self.yyyy +'/M'+self.mm+'/'
-    rst_dir = self.common_in['rst_dir'] + '/'
-    os.makedirs(rst_dir, exist_ok = True)
-    print(' Copy MERRA-2 Restart \n from \n    ' + merra_2_rst_dir + '\n to\n    '+ rst_dir +'\n') 
-
-    upperin =[merra_2_rst_dir +  expid+'.fvcore_internal_rst.' + surfix,
-              merra_2_rst_dir +  expid+'.moist_internal_rst.'  + surfix,
-              merra_2_rst_dir +  expid+'.agcm_import_rst.'     + surfix,
-              merra_2_rst_dir +  expid+'.gocart_internal_rst.' + surfix,
-              merra_2_rst_dir +  expid+'.pchem_internal_rst.'  + surfix ]
-
-    surfin = [ merra_2_rst_dir +  expid+'.catch_internal_rst.'    + surfix, 
-               merra_2_rst_dir +  expid+'.lake_internal_rst.'     + surfix,
-               merra_2_rst_dir +  expid+'.landice_internal_rst.'  + surfix,
-               merra_2_rst_dir +  expid+'.saltwater_internal_rst.'+ surfix]
-
-    for f in upperin :
-       fname = os.path.basename(f)
-       dest = rst_dir + '/'+fname
-       print("Copy file "+f +" to " + rst_dir)
-       shutil.copy(f, dest)
-
-    for f in surfin :
-       fname = os.path.basename(f)
-       dest = rst_dir + '/'+fname
-       print("Copy file "+f +" to " + rst_dir)
-       shutil.copy(f, dest)
-
-    # prepare analysis files
-    bkg = self.ana_out['bkg']
-    if ( not bkg ): return
-    yyyy_ = yyyymmddhh_[0:4]
-    mm_   = yyyymmddhh_[4:6]
-    dd_   = yyyymmddhh_[6:8]
-    hh_   = yyyymmddhh_[8:10]
-    rst_time = datetime(year=int(yyyy_), month=int(mm_), day=int(dd_), hour = int(hh_))
-    expid_in  = self.common_in['expid']
-    expid_out = self.common_out['expid']
-    if (expid_out) :
-       expid_out = expid_out + '.'
-    else:
-       expid_out = ''
-
-    agrid_in  = self.common_in['agrid']
-    agrid_out = self.common_out['agrid']
-
-    anafiles=[]
-    for h in [3,4,5,6,7,8,9]:
-       delt = timedelta(hours = h-3)
-       new_time = rst_time + delt
-       yyyy = "Y"+str(new_time.year)
-       mm   = 'M%02d'%new_time.month
-       ymd  = '%04d%02d%02d'%(new_time.year,new_time.month, new_time.day)
-       hh   = '%02d'%h
-       newhh= '%02d'%new_time.hour
-       m2_rst_dir = merra_2_rst_dir.replace('Y'+yyyy_,yyyy).replace('M'+mm_,mm)
-       # bkg files
-       for ftype in ['sfc', 'eta']:
-          fname = expid_in+'.bkg'+hh+'_'+ftype+'_rst.'+ymd+'_'+newhh+'z.nc4'
-          f = m2_rst_dir+'/'+fname
-          if(os.path.isfile(f)):
-             anafiles.append(f)
-          else:
-             print('Warning: Cannot find '+f)
-       # cbkg file
-       fname = expid_in + '.cbkg' + hh + '_eta_rst.' + ymd + '_' + newhh + 'z.nc4'
-       f = m2_rst_dir+'/'+fname
-       if(os.path.isfile(f)):
-         anafiles.append(f)
-       else:
-         print('Warning: Cannot find '+f)
-       # gaas_bkg_sfc files
-       if (h==6 or h==9):
-          fname = expid_in+'.gaas_bkg_sfc_rst.'+ymd+'_'+newhh+'z.nc4'
-          f = m2_rst_dir+'/'+fname
-          if (os.path.isfile(f)):
-            anafiles.append(f)
-          else:
-            print('Warning: Cannot find '+f)
-     # trak.GDA.rst file
-    delt = timedelta(hours = 3)
-    new_time = rst_time - delt
-    yyyy = "Y"+str(new_time.year)
-    mm   = 'M%02d'%new_time.month
-    ymdh = '%04d%02d%02d%02d'%(new_time.year, new_time.month, new_time.day, new_time.hour)
-    m2_rst_dir = merra_2_rst_dir.replace('Y'+yyyy_,yyyy).replace('M'+mm_,mm)
-    fname = expid_in+'.trak.GDA.rst.'+ymdh+'z.txt'
-    f = m2_rst_dir+'/'+fname
-    if (os.path.isfile(f)): anafiles.append(f)
-
-    for f in anafiles:
-      fname    = os.path.basename(f)
-      f_tmp = rst_dir+'/'+fname
-      print("Copy file "+f +" to " + rst_dir)
-      shutil.copy(f,f_tmp)
-
   def get_bcbase(self, opt):
      base = ''
      model = ''
diff --git a/GEOS_Util/post/remap_restart/remap_params.tpl b/GEOS_Util/post/remap_restart/remap_params.tpl
index d08caee7..6cba4c75 100644
--- a/GEOS_Util/post/remap_restart/remap_params.tpl
+++ b/GEOS_Util/post/remap_restart/remap_params.tpl
@@ -8,6 +8,7 @@ input:
     drymass: 1
     hydrostatic: 0
   shared:
+    MERRA-2: false
     agrid: 
     bcs_dir:
     expid:
diff --git a/GEOS_Util/post/remap_restart/remap_questions.py b/GEOS_Util/post/remap_restart/remap_questions.py
index 8547bfc0..09333fb8 100755
--- a/GEOS_Util/post/remap_restart/remap_questions.py
+++ b/GEOS_Util/post/remap_restart/remap_questions.py
@@ -30,13 +30,7 @@ def fvcore_name(x):
     return False
 
 def tmp_merra2_dir(x):
-   cmd = 'whoami'
-   p = subprocess.Popen(shlex.split(cmd), stdout=subprocess.PIPE)
-   (user, err) = p.communicate()
-   p_status = p.wait()
-   print(user)
-   user = user.decode().split()
-   tmp_merra2 = '/discover/nobackup/'+user[0]+'/merra2_tmp'+x['input:shared:yyyymmddhh']+'/'
+   tmp_merra2 = x['output:shared:out_dir']+ '/merra2_tmp_'+x['input:shared:yyyymmddhh']+'/'
    return tmp_merra2
 
 def we_default(tag):
@@ -101,18 +95,19 @@ def ask_questions():
             "message": "From what restart date/time would you like to remap? (must be 10 digits: yyyymmddhh)",
             "validate": lambda text: len(text)==10 ,
         },
+
         {
             "type": "path",
-            "name": "input:shared:rst_dir",
-            "message": "Enter a directory to which the archived MERRA-2 archive files can be copied: ",
-            "default": lambda x: tmp_merra2_dir(x),
-            "when": lambda x: x['input:shared:MERRA-2'],
+            "name": "output:shared:out_dir",
+            "message": "Enter the directory for new restarts:\n"
         },
 
         {
             "type": "path",
-            "name": "output:shared:out_dir",
-            "message": "Enter the directory for new restarts:\n"
+            "name": "input:shared:rst_dir",
+            "message": "Enter a temporary directory for archived MERRA-2 files: ",
+            "default": lambda x: tmp_merra2_dir(x),
+            "when": lambda x: x['input:shared:MERRA-2'],
         },
 
         {
diff --git a/GEOS_Util/post/remap_restart/remap_restarts.py b/GEOS_Util/post/remap_restart/remap_restarts.py
index f91e4af3..c90852e2 100644
--- a/GEOS_Util/post/remap_restart/remap_restarts.py
+++ b/GEOS_Util/post/remap_restart/remap_restarts.py
@@ -70,10 +70,6 @@ def main(argv):
      print("\nYou answered not to continue, exiting.\n")
      sys.exit(0)
   
-  # copy merra2 files from archives
-  if params:
-     params.copy_merra2()
-
   # upper air
   upper = upperair(params_file=config_yaml)
   upper.remap()
diff --git a/GEOS_Util/post/remap_restart/remap_upper.py b/GEOS_Util/post/remap_restart/remap_upper.py
index 090eb7af..5938627f 100755
--- a/GEOS_Util/post/remap_restart/remap_upper.py
+++ b/GEOS_Util/post/remap_restart/remap_upper.py
@@ -11,6 +11,8 @@
 class upperair(remap_base):
   def __init__(self, **configs):
      super().__init__(**configs)
+     if self.config['input']['shared']['MERRA-2']:
+       self.copy_merra2()
 
   def remap(self):
      if not self.config['output']['air']['remap'] :
@@ -267,6 +269,35 @@ def find_rst(self):
         
      return restarts_in
 
+  def copy_merra2(self):
+    if not self.config['input']['shared']['MERRA-2']:
+      return
+
+    expid = self.config['input']['shared']['expid']
+    yyyymmddhh_ = str(self.config['input']['shared']['yyyymmddhh'])
+    yyyy_ = yyyymmddhh_[0:4]
+    mm_   = yyyymmddhh_[4:6]
+    dd_   = yyyymmddhh_[6:8]
+    hh_   = yyyymmddhh_[8:10]
+
+    suffix = yyyymmddhh_[0:8]+'_'+ hh_ + 'z.bin'
+    merra_2_rst_dir = '/archive/users/gmao_ops/MERRA2/gmao_ops/GEOSadas-5_12_4/'+expid +'/rs/Y'+yyyy_ +'/M'+mm_+'/'
+    rst_dir = self.config['input']['shared']['rst_dir'] + '/'
+    os.makedirs(rst_dir, exist_ok = True)
+    print(' Copy MERRA-2 upper air restarts \n from \n    ' + merra_2_rst_dir + '\n to\n    '+ rst_dir +'\n')
+
+    upperin =[merra_2_rst_dir +  expid+'.fvcore_internal_rst.' + suffix,
+              merra_2_rst_dir +  expid+'.moist_internal_rst.'  + suffix,
+              merra_2_rst_dir +  expid+'.agcm_import_rst.'     + suffix,
+              merra_2_rst_dir +  expid+'.gocart_internal_rst.' + suffix,
+              merra_2_rst_dir +  expid+'.pchem_internal_rst.'  + suffix ]
+
+    for f in upperin :
+       fname = os.path.basename(f)
+       dest = rst_dir + '/'+fname
+       print("Copy file "+f +" to " + rst_dir)
+       shutil.copy(f, dest)
+
 if __name__ == '__main__' :
    air = upperair(params_file='remap_params.yaml')
    air.remap()

From 0dd190806a8483fae65989425c0f71ba9b22cfa9 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Thu, 21 Jul 2022 14:17:45 -0400
Subject: [PATCH 02/22] fix typos

---
 GEOS_Util/post/remap_restart/remap_analysis.py | 2 +-
 GEOS_Util/post/remap_restart/remap_params.py   | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/GEOS_Util/post/remap_restart/remap_analysis.py b/GEOS_Util/post/remap_restart/remap_analysis.py
index eab791db..9627e030 100755
--- a/GEOS_Util/post/remap_restart/remap_analysis.py
+++ b/GEOS_Util/post/remap_restart/remap_analysis.py
@@ -137,7 +137,7 @@ def find_analysis(self):
   def copy_merra2(self):
     if not self.config['input']['shared']['MERRA-2']:
       return
-    bkg = self.config['output']['shared'][['bkg']
+    bkg = self.config['output']['analysis']['bkg']
     if ( not bkg ): return
 
     expid = self.config['input']['shared']['expid']
diff --git a/GEOS_Util/post/remap_restart/remap_params.py b/GEOS_Util/post/remap_restart/remap_params.py
index 7f1e93da..e5ade55a 100755
--- a/GEOS_Util/post/remap_restart/remap_params.py
+++ b/GEOS_Util/post/remap_restart/remap_params.py
@@ -35,6 +35,7 @@ def __init__(self, config_from_question):
      config_tpl = yaml.load(stream)
 
      # params for shared
+     config_tpl['input']['shared']['MERRA-2']  = self.common_in.get('MERRA-2')
      config_tpl['input']['shared']['agrid']    = self.common_in.get('agrid')
      config_tpl['input']['shared']['ogrid']    = self.common_in.get('ogrid')
      config_tpl['input']['shared']['rst_dir']  = self.common_in['rst_dir']+'/'
@@ -43,6 +44,7 @@ def __init__(self, config_from_question):
 
      config_tpl['output']['air']['nlevel']     = self.upper_out.get('nlevel')
      config_tpl['output']['air']['remap']      = self.upper_out.get('remap')
+     config_tpl['input']['surface']['catch_model']       = self.surf_in.get('catch_model')
      config_tpl['output']['surface']['remap_water']      = self.surf_out.get('remap')
      config_tpl['output']['surface']['remap_catch']      = self.surf_out.get('remap')
      config_tpl['output']['shared']['agrid']   = self.common_out['agrid']
@@ -267,6 +269,7 @@ def init_merra2(self):
     self.common_in['ogrid'] = '1440x720'
     self.common_in['bc_base']= 'discover_ops'
     self.common_in['tag']= 'Ganymed-4_0'
+    self.surf_in['catch_model'] = 'catch'
 
   def get_bcbase(self, opt):
      base = ''

From 08131a54065ed20cf78f6e6c724cb2ad17fd2844 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Fri, 22 Jul 2022 15:21:02 -0400
Subject: [PATCH 03/22] changelog

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1738bbad..2cf45fae 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- change the location of the temporary folder for remap_restarts MERRA-2 case 
+
 ### Fixed
 
 ### Removed

From bb5e4b008698bcf4ea00e72b1e6d79de6650c3a6 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Tue, 26 Jul 2022 13:27:36 -0400
Subject: [PATCH 04/22] add command line to run the program.

---
 .../post/remap_restart/remap_restarts.py      | 49 ++++++----
 GEOS_Util/post/remap_restart/remap_utils.py   | 89 +++++++++++++++++++
 2 files changed, 123 insertions(+), 15 deletions(-)
 create mode 100644 GEOS_Util/post/remap_restart/remap_utils.py

diff --git a/GEOS_Util/post/remap_restart/remap_restarts.py b/GEOS_Util/post/remap_restart/remap_restarts.py
index c90852e2..41be3a0a 100644
--- a/GEOS_Util/post/remap_restart/remap_restarts.py
+++ b/GEOS_Util/post/remap_restart/remap_restarts.py
@@ -9,6 +9,7 @@
 import sys, getopt
 import ruamel.yaml
 import questionary
+from remap_utils import *
 from remap_questions import get_config_from_questionary 
 from remap_params import *
 from remap_upper import *
@@ -17,11 +18,16 @@
 from remap_catchANDcn  import *
 
 def main(argv):
-  config_yaml = ''
+
+  question_flag = False
+  cmd2yaml_flag = False
+  yaml_flag     = False
+  config        = ''
+
   try:
-    opts, args = getopt.getopt(argv,"hc:", ['config_file='])
+    opts, args = getopt.getopt(argv,"hc:o", ['config_file='])
   except getopt.GetoptError:
-    print('Usage: remap_restarts.py -c remap_params.yaml or ./remap_restarts.py ')
+    print('Usage: remap_restarts.py -c remap_params.yaml or ./remap_restarts.py or ./remap_restarts.py -o key=value ....')
     sys.exit('command line error')
   for opt, arg in opts:
     if opt == '-h':
@@ -31,6 +37,8 @@ def main(argv):
               2) Use questionary to convert template remap_params.tpl to \n
                  remap_params.yaml and then remap. \n
                 ./remap_restarts.py \n
+              3) Use command line to input a flattened yaml file: \n
+                ./remap_restarts.py -o input:air:drymass=1 input:air:hydrostatic=0 ... 
               \nHelp message: \n
               1) Each individual script can be executed independently
               2) remap_questions.py generates raw_answer.yaml
@@ -42,21 +50,29 @@ def main(argv):
       sys.exit(0)
     if opt in("-c", "--config_file"):
       config_yaml = arg
+      yaml_flag = True
+      
+    if opt == '-o':
+      print("\n Use command line to input a flattened yaml config file \n")
+      cmd2yaml_flag = True
+      config_yaml = 'remap_params.yaml'
 
-  params = ''
-  if config_yaml == '':
-    config = get_config_from_questionary()
-    params = remap_params(config)
-    params.convert_to_yaml()
-    config_yaml = 'remap_params.yaml'
+  if yaml_flag :
+     config  = yaml_to_config(config_yaml)
 
-  with  open(config_yaml, 'r') as f:
-    for line in f.readlines():
-      trimmed_line = line.rstrip()
-      if trimmed_line: # Don't print blank lines
-          print(trimmed_line)
+  if cmd2yaml_flag :
+     config  = args_to_config(args)
 
+  if not ( yaml_flag or cmd2yaml_flag) :
+     raw_config = get_config_from_questionary()
+     params = remap_params(raw_config)
+     config = params.config
+     question_flag = True  
+     config_yaml = 'remap_params.yaml'
+ 
   print('\n')
+  print_config(config)
+  
   questions = [
         {
             "type": "confirm",
@@ -69,7 +85,10 @@ def main(argv):
   if not answer['Continue'] :
      print("\nYou answered not to continue, exiting.\n")
      sys.exit(0)
-  
+ 
+  if yaml_flag     or question_flag :  write_cmd(config)
+  if cmd2yaml_flag or question_flag :  config_to_yaml(config, config_yaml)
+
   # upper air
   upper = upperair(params_file=config_yaml)
   upper.remap()
diff --git a/GEOS_Util/post/remap_restart/remap_utils.py b/GEOS_Util/post/remap_restart/remap_utils.py
new file mode 100644
index 00000000..199e418c
--- /dev/null
+++ b/GEOS_Util/post/remap_restart/remap_utils.py
@@ -0,0 +1,89 @@
+import os
+import subprocess
+import ruamel.yaml
+from collections import OrderedDict
+
+def config_to_yaml(config, yaml_file):
+   yaml = ruamel.yaml.YAML()
+   with open(yaml_file, "w") as f:
+      yaml.dump(config, f)
+
+def yaml_to_config(yaml_file):
+   yaml = ruamel.yaml.YAML()
+   stream =''
+   with  open(yaml_file, 'r') as f:
+     stream = f.read()
+   config = yaml.load(stream)
+   return config
+
+def write_cmd(config) :
+   def flatten_nested(nested_dict, result=None, prefix=''):
+     if result is None:
+       result = dict()
+     for k, v in nested_dict.items():
+       new_k = ':'.join((prefix, k)) if prefix else k
+       if not (isinstance(v, dict) or isinstance(v, OrderedDict)):
+         result.update({new_k: v})
+       else:
+         flatten_nested(v, result, new_k)
+     return result
+
+   out_dir = config['output']['shared']['out_dir']
+   if not os.path.exists(out_dir) : os.makedirs(out_dir)
+   bin_path = os.path.dirname(os.path.realpath(__file__))
+
+   cmd = '#!/usr/local/bin/csh \n'
+   cmd = cmd + 'set BINPATH=' + bin_path +'\n'
+   cmd = cmd + 'source $BINPATH/g5_modules \n'
+
+   flat_dict = flatten_nested(config)
+
+   k = 1   
+   for key, value in flat_dict.items():
+     if isinstance(value, int) :   value = str(value)
+     if isinstance(value, float) : value = str(value)
+     if k == 1:
+       cmd = cmd + 'set FLATYAML="' + key+"="+ value+ '"\n'
+     else:
+       cmd = cmd + 'set FLATYAML="$FLATYAML '+ key+"="+ value+ '"\n'
+     k = k+1
+
+   cmd = cmd + '$BINPATH/remap_restarts.py -o $FLATYAML'
+
+   with open(out_dir + '/remap_restarts.CMD', 'w') as f:
+     f.write(cmd)
+   subprocess.call(['chmod', '+x',out_dir + '/remap_restarts.CMD'])
+
+def args_to_config(args):
+   config  = {}
+   config['input'] = {}
+   config['input']['air'] = {}
+   config['input']['shared'] = {}
+   config['input']['surface'] = {}
+   config['output'] = {}
+   config['output']['shared'] = {}
+   config['output']['air'] = {}
+   config['output']['surface'] = {}
+   config['output']['analysis'] = {}
+   config['slurm'] = {}
+   for values in args:
+     [keys, value] = values.split("=")
+     key = keys.split(':')
+     if value.lower() in ['false', 'null'] :
+        value = False
+     elif value.lower() in ['true'] :
+        value = True
+     if len(key) == 2:
+        config[key[0]][key[1]] = value
+     if len(key) == 3:
+        config[key[0]][key[1]][key[2]] = value
+
+   return config
+
+def print_config( config, indent = 0 ):
+   for k, v in config.items():
+     if isinstance(v, dict):
+        print("   " * indent, f"{k}:")
+        print_config(v, indent+1)
+     else:
+        print("   " * indent, f"{k}: {v}")

From 9f73755a07a42d03957554f2b1d62bb86e4dad69 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <52509753+weiyuan-jiang@users.noreply.github.com>
Date: Tue, 26 Jul 2022 14:47:20 -0400
Subject: [PATCH 05/22] Update CHANGELOG.md

---
 CHANGELOG.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2cf45fae..7c4cedb3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,7 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
-- change the location of the temporary folder for remap_restarts MERRA-2 case 
+- Generated command line to run the program
+- changed the location of the temporary folder for remap_restarts MERRA-2 case 
 
 ### Fixed
 

From 2ce38281700ed5f7a8bc85bd10df0e649fe2df63 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Tue, 26 Jul 2022 15:10:01 -0400
Subject: [PATCH 06/22] consolidate converting to yaml file

---
 GEOS_Util/post/remap_restart/remap_params.py | 19 ++-----------------
 GEOS_Util/post/remap_restart/remap_utils.py  | 12 ++++++++++++
 2 files changed, 14 insertions(+), 17 deletions(-)

diff --git a/GEOS_Util/post/remap_restart/remap_params.py b/GEOS_Util/post/remap_restart/remap_params.py
index e5ade55a..12967c2c 100755
--- a/GEOS_Util/post/remap_restart/remap_params.py
+++ b/GEOS_Util/post/remap_restart/remap_params.py
@@ -7,9 +7,9 @@
 import time
 import shlex
 import subprocess
-import questionary
 from datetime import datetime
 from datetime import timedelta
+from remap_utils import config_to_yaml
 
 class remap_params(object):
   def __init__(self, config_from_question):
@@ -66,21 +66,6 @@ def __init__(self, config_from_question):
 
      self.config = config_tpl
 
-  def convert_to_yaml(self) :
-     if os.path.exists('remap_params.yaml') :
-       overwrite = questionary.confirm("Do you want to overwrite remap_params.yaml file?", default=False).ask()
-       if not overwrite :
-         while True:
-           new_name = questionary.text("What's the backup name for existing remap_params.yaml?", default='remap_params.yaml.1').ask()
-           if os.path.exists(new_name):
-              print('\n'+ new_name + ' exists, please enter a new one. \n')
-           else:
-              shutil.move('remap_params.yaml', new_name)
-              break
-     yaml = ruamel.yaml.YAML()
-     with open("remap_params.yaml", "w") as f:
-        yaml.dump(self.config, f)
-
   def init_tags(self):
      # copy and paste from remap.pl
      # minor change. Add "D" to the number for each group
@@ -508,4 +493,4 @@ def params_for_analysis(self, config_tpl):
      stream = f.read()
   config = yaml.load(stream)
   param = remap_params(config) 
-  param.convert_to_yaml() 
+  config_to_yaml(param.config, 'remap_params.yaml') 
diff --git a/GEOS_Util/post/remap_restart/remap_utils.py b/GEOS_Util/post/remap_restart/remap_utils.py
index 199e418c..d04c4cb3 100644
--- a/GEOS_Util/post/remap_restart/remap_utils.py
+++ b/GEOS_Util/post/remap_restart/remap_utils.py
@@ -2,8 +2,20 @@
 import subprocess
 import ruamel.yaml
 from collections import OrderedDict
+import shutil
+import questionary
 
 def config_to_yaml(config, yaml_file):
+   if os.path.exists(yaml_file) :
+      overwrite = questionary.confirm("Do you want to overwrite " + yaml_file + "?" , default=False).ask()
+      if not overwrite :
+         while True:
+           new_name = questionary.text("What's the backup name?  ", default=yaml_file +'.1').ask()
+           if os.path.exists(new_name):
+              print('\n'+ new_name + ' exists, please enter a new one. \n')
+           else:
+              shutil.move(yaml_file, new_name)
+              break
    yaml = ruamel.yaml.YAML()
    with open(yaml_file, "w") as f:
       yaml.dump(config, f)

From 735979553a9305557bcdf6d16258081c7d9fb77f Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Wed, 27 Jul 2022 13:19:04 -0400
Subject: [PATCH 07/22] hide temporary folder for merra-2 from users

---
 GEOS_Util/post/remap_restart/remap_questions.py | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/GEOS_Util/post/remap_restart/remap_questions.py b/GEOS_Util/post/remap_restart/remap_questions.py
index 09333fb8..a5706612 100755
--- a/GEOS_Util/post/remap_restart/remap_questions.py
+++ b/GEOS_Util/post/remap_restart/remap_questions.py
@@ -17,13 +17,15 @@
 def fvcore_name(x):
   ymdh = x['input:shared:yyyymmddhh']
   time = ymdh[0:8] + '_'+ymdh[8:10]
-  files = glob.glob(x['input:shared:rst_dir']+'/*fvcore_*'+time+'*')
+  rst_dir = x.get('input:shared:rst_dir')
+  if not rst_dir : return False
+  files = glob.glob(rst_dir+'/*fvcore_*'+time+'*')
   if len(files) ==1 :
     fname = files[0]
     print('\nFound ' + fname) 
     return fname
   else:
-    fname = x['input:shared:rst_dir']+'/fvcore_internal_rst'
+    fname = rst_dir+'/fvcore_internal_rst'
     if os.path.exists(fname):
        print('\nFound ' + fname) 
        return fname
@@ -102,14 +104,6 @@ def ask_questions():
             "message": "Enter the directory for new restarts:\n"
         },
 
-        {
-            "type": "path",
-            "name": "input:shared:rst_dir",
-            "message": "Enter a temporary directory for archived MERRA-2 files: ",
-            "default": lambda x: tmp_merra2_dir(x),
-            "when": lambda x: x['input:shared:MERRA-2'],
-        },
-
         {
             "type": "text",
             "name": "input:shared:agrid",
@@ -328,6 +322,8 @@ def ask_questions():
    answers = questionary.prompt(questions)
    if not answers.get('input:shared:model') :
       answers['input:shared:model'] = 'data'
+   if answers['input:shared:MERRA-2']:
+     answers['input:shared:rst_dir'] = tmp_merra2_dir(answers)
    answers['input:shared:rst_dir'] = os.path.abspath(answers['input:shared:rst_dir'])
    if answers.get('output:shared:ogrid') == 'CS':
       answers['output:shared:ogrid'] = answers['output:shared:agrid']

From ee96b752afcbfdc374676b2380b880297b322451 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Wed, 27 Jul 2022 14:48:56 -0400
Subject: [PATCH 08/22] remove temporary merra2 folder

---
 GEOS_Util/post/remap_restart/remap_analysis.py               | 5 +++--
 GEOS_Util/post/remap_restart/remap_base.py                   | 5 +++++
 GEOS_Util/post/remap_restart/remap_catchANDcn.py             | 5 +++--
 GEOS_Util/post/remap_restart/remap_lake_landice_saltwater.py | 5 +++--
 GEOS_Util/post/remap_restart/remap_upper.py                  | 5 +++--
 5 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/GEOS_Util/post/remap_restart/remap_analysis.py b/GEOS_Util/post/remap_restart/remap_analysis.py
index 9627e030..f7160289 100755
--- a/GEOS_Util/post/remap_restart/remap_analysis.py
+++ b/GEOS_Util/post/remap_restart/remap_analysis.py
@@ -19,8 +19,7 @@
 class analysis(remap_base):
   def __init__(self, **configs):
      super().__init__(**configs)
-     if self.config['input']['shared']['MERRA-2']:
-       self.copy_merra2()
+     self.copy_merra2()
 
   def remap(self):
      config = self.config
@@ -107,6 +106,8 @@ def remap(self):
      print( "cd " + cwdir)
      os.chdir(cwdir)
 
+     self.remove_merra2()
+
   def get_grid_kind(this, grid):
      hgrd = {}
      hgrd['C12']   = 'a'
diff --git a/GEOS_Util/post/remap_restart/remap_base.py b/GEOS_Util/post/remap_restart/remap_base.py
index 2f5a9406..5163c91e 100755
--- a/GEOS_Util/post/remap_restart/remap_base.py
+++ b/GEOS_Util/post/remap_restart/remap_base.py
@@ -3,6 +3,7 @@
 import os
 import ruamel.yaml
 import shutil
+import subprocess
 
 class remap_base(object):
   def __init__(self, **configs):
@@ -28,3 +29,7 @@ def __init__(self, **configs):
           out_dir    = self.config['output']['shared']['out_dir']
           if not os.path.exists(out_dir) : os.makedirs(out_dir)
         break
+  def remove_merra2(self):
+    if self.config['input']['shared']['MERRA-2']:
+      print(" remove temporary folder that contains MERRA-2 archived files ... \n")
+      subprocess.call(['/bin/rm', '-rf', self.config['input']['shared']['rst_dir']])
diff --git a/GEOS_Util/post/remap_restart/remap_catchANDcn.py b/GEOS_Util/post/remap_restart/remap_catchANDcn.py
index 1ef13cad..35db3e99 100755
--- a/GEOS_Util/post/remap_restart/remap_catchANDcn.py
+++ b/GEOS_Util/post/remap_restart/remap_catchANDcn.py
@@ -12,8 +12,7 @@
 class catchANDcn(remap_base):
   def __init__(self, **configs):
      super().__init__(**configs)
-     if self.config['input']['shared']['MERRA-2']:
-       self.copy_merra2()
+     self.copy_merra2()
 
   def remap(self):
      if not self.config['output']['surface']['remap_catch']:
@@ -131,6 +130,8 @@ def remap(self):
      print( "cd " + cwdir)
      os.chdir(cwdir)
 
+     self.remove_merra2()
+
   def copy_merra2(self):
     if not self.config['input']['shared']['MERRA-2']:
       return
diff --git a/GEOS_Util/post/remap_restart/remap_lake_landice_saltwater.py b/GEOS_Util/post/remap_restart/remap_lake_landice_saltwater.py
index 76cb9809..45c1c1dd 100755
--- a/GEOS_Util/post/remap_restart/remap_lake_landice_saltwater.py
+++ b/GEOS_Util/post/remap_restart/remap_lake_landice_saltwater.py
@@ -11,8 +11,7 @@
 class lake_landice_saltwater(remap_base):
   def __init__(self, **configs):
      super().__init__(**configs)
-     if self.config['input']['shared']['MERRA-2']:
-       self.copy_merra2()
+     self.copy_merra2()
 
   def remap(self):
      if not self.config['output']['surface']['remap_water']:
@@ -140,6 +139,8 @@ def remap(self):
      print('cd ' + cwdir)
      os.chdir(cwdir)
 
+     self.remove_merra2()
+
   def find_rst(self):
      surf_restarts =[
                  "route_internal_rst"       ,
diff --git a/GEOS_Util/post/remap_restart/remap_upper.py b/GEOS_Util/post/remap_restart/remap_upper.py
index 5938627f..2fa1f0f2 100755
--- a/GEOS_Util/post/remap_restart/remap_upper.py
+++ b/GEOS_Util/post/remap_restart/remap_upper.py
@@ -11,8 +11,7 @@
 class upperair(remap_base):
   def __init__(self, **configs):
      super().__init__(**configs)
-     if self.config['input']['shared']['MERRA-2']:
-       self.copy_merra2()
+     self.copy_merra2()
 
   def remap(self):
      if not self.config['output']['air']['remap'] :
@@ -251,6 +250,8 @@ def remap(self):
      print('cd ' + cwdir)
      os.chdir(cwdir)
 
+     self.remove_merra2()
+
   def find_rst(self):
      rst_dir = self.config['input']['shared']['rst_dir']
      yyyymmddhh_ = str(self.config['input']['shared']['yyyymmddhh'])

From 4f74f97029932070d4306ac509b12dc28730b128 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Wed, 27 Jul 2022 15:03:16 -0400
Subject: [PATCH 09/22] more clean up

---
 GEOS_Util/post/remap_restart/remap_utils.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/GEOS_Util/post/remap_restart/remap_utils.py b/GEOS_Util/post/remap_restart/remap_utils.py
index d04c4cb3..e85d1e9a 100644
--- a/GEOS_Util/post/remap_restart/remap_utils.py
+++ b/GEOS_Util/post/remap_restart/remap_utils.py
@@ -52,15 +52,14 @@ def flatten_nested(nested_dict, result=None, prefix=''):
 
    k = 1   
    for key, value in flat_dict.items():
-     if isinstance(value, int) :   value = str(value)
-     if isinstance(value, float) : value = str(value)
+     if isinstance(value, int) or isinstance(value, float) :   value = str(value)
      if k == 1:
-       cmd = cmd + 'set FLATYAML="' + key+"="+ value+ '"\n'
+       cmd = cmd + 'set FLAT_YAML="' + key+"="+ value+ '"\n'
      else:
-       cmd = cmd + 'set FLATYAML="$FLATYAML '+ key+"="+ value+ '"\n'
+       cmd = cmd + 'set FLAT_YAML="$FLAT_YAML '+ key+"="+ value+ '"\n'
      k = k+1
 
-   cmd = cmd + '$BINPATH/remap_restarts.py -o $FLATYAML'
+   cmd = cmd + '$BINPATH/remap_restarts.py -o $FLAT_YAML'
 
    with open(out_dir + '/remap_restarts.CMD', 'w') as f:
      f.write(cmd)
@@ -81,7 +80,7 @@ def args_to_config(args):
    for values in args:
      [keys, value] = values.split("=")
      key = keys.split(':')
-     if value.lower() in ['false', 'null'] :
+     if value.lower() in ['false', 'null', 'none'] :
         value = False
      elif value.lower() in ['true'] :
         value = True

From e1d6234f35a6bbe500eea98a12c94a6b5ce68468 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Thu, 28 Jul 2022 09:22:23 -0400
Subject: [PATCH 10/22] add catch_tilefile entry. Catch can be in local domain

---
 GEOS_Util/post/remap_restart/remap_params.tpl |  5 ++++-
 GEOS_Util/post/remap_restart/remap_utils.py   | 15 ++++-----------
 2 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/GEOS_Util/post/remap_restart/remap_params.tpl b/GEOS_Util/post/remap_restart/remap_params.tpl
index 6cba4c75..94cedbfd 100644
--- a/GEOS_Util/post/remap_restart/remap_params.tpl
+++ b/GEOS_Util/post/remap_restart/remap_params.tpl
@@ -20,7 +20,8 @@ input:
     wemin:
     # it supports three models: catch, catchcnclm40, catchcnclm45
     catch_model: null
-
+    # if catch_tilefile is null, it searches bcs_dir     
+    catch_tilefile: null
 output:
   shared:
     agrid:
@@ -40,6 +41,8 @@ output:
     remap_water: true
     # remap catch(cn)
     remap_catch: true
+    # if catch_tilefile is null, it searches bcs_dir     
+    catch_tilefile: null
   analysis:
     bkg: true
     aqua: False
diff --git a/GEOS_Util/post/remap_restart/remap_utils.py b/GEOS_Util/post/remap_restart/remap_utils.py
index e85d1e9a..582a7a15 100644
--- a/GEOS_Util/post/remap_restart/remap_utils.py
+++ b/GEOS_Util/post/remap_restart/remap_utils.py
@@ -66,17 +66,10 @@ def flatten_nested(nested_dict, result=None, prefix=''):
    subprocess.call(['chmod', '+x',out_dir + '/remap_restarts.CMD'])
 
 def args_to_config(args):
-   config  = {}
-   config['input'] = {}
-   config['input']['air'] = {}
-   config['input']['shared'] = {}
-   config['input']['surface'] = {}
-   config['output'] = {}
-   config['output']['shared'] = {}
-   config['output']['air'] = {}
-   config['output']['surface'] = {}
-   config['output']['analysis'] = {}
-   config['slurm'] = {}
+   # template file should be with this util file
+   remap_tpl = os.path.dirname(os.path.realpath(__file__)) + '/remap_params.tpl'
+   config = yaml_to_config(remap_tpl)
+   # fill in the config with args
    for values in args:
      [keys, value] = values.split("=")
      key = keys.split(':')

From d08e6332d87b6a9286aa5cc9b9f5447cba2b465c Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Thu, 28 Jul 2022 09:33:15 -0400
Subject: [PATCH 11/22] get catch tile file from catc_tilefile entry first

---
 GEOS_Util/post/remap_restart/remap_catchANDcn.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/GEOS_Util/post/remap_restart/remap_catchANDcn.py b/GEOS_Util/post/remap_restart/remap_catchANDcn.py
index 35db3e99..3aa1d7f0 100755
--- a/GEOS_Util/post/remap_restart/remap_catchANDcn.py
+++ b/GEOS_Util/post/remap_restart/remap_catchANDcn.py
@@ -43,8 +43,12 @@ def remap(self):
      in_wemin   = config['input']['surface']['wemin']
      out_wemin  = config['output']['surface']['wemin']
      surflay    = config['output']['surface']['surflay']
-     in_tilefile  = glob.glob(in_bcsdir+ '/*-Pfafstetter.til')[0]
-     out_tilefile = glob.glob(out_bcsdir+ '/*-Pfafstetter.til')[0]
+     in_tilefile = config['input']['surface']['catch_tilefile']
+     if not in_tilefile :
+        in_tilefile  = glob.glob(in_bcsdir+ '/*-Pfafstetter.til')[0]
+     out_tilefile = config['output']['surface']['catch_tilefile']
+     if not out_tilefile :
+        out_tilefile = glob.glob(out_bcsdir+ '/*-Pfafstetter.til')[0]
      account    = config['slurm']['account']
      # even the input is binary, the output si nc4
      suffix     = time+'z.nc4'

From a92be4660070890b62ced0bd8ef6886b93f3cc0c Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Mon, 1 Aug 2022 13:14:43 -0400
Subject: [PATCH 12/22] add more test cases

---
 GEOS_Util/post/remap_restart/remap_params.py | 15 +-----
 GEOS_Util/post/remap_restart/remap_utils.py  | 20 ++++++++
 GEOS_Util/post/tests/amip_c180Toc90.yaml     | 52 ++++++++++++++++++++
 GEOS_Util/post/tests/c180Toc360.yaml         | 52 ++++++++++++++++++++
 GEOS_Util/post/tests/c360Toc24.yaml          | 52 ++++++++++++++++++++
 GEOS_Util/post/tests/test_remap_cases.yaml   | 11 ++++-
 6 files changed, 188 insertions(+), 14 deletions(-)
 create mode 100644 GEOS_Util/post/tests/amip_c180Toc90.yaml
 create mode 100644 GEOS_Util/post/tests/c180Toc360.yaml
 create mode 100644 GEOS_Util/post/tests/c360Toc24.yaml

diff --git a/GEOS_Util/post/remap_restart/remap_params.py b/GEOS_Util/post/remap_restart/remap_params.py
index 12967c2c..b112aab3 100755
--- a/GEOS_Util/post/remap_restart/remap_params.py
+++ b/GEOS_Util/post/remap_restart/remap_params.py
@@ -9,7 +9,7 @@
 import subprocess
 from datetime import datetime
 from datetime import timedelta
-from remap_utils import config_to_yaml
+from remap_utils import config_to_yaml, merra2_expid
 
 class remap_params(object):
   def __init__(self, config_from_question):
@@ -237,18 +237,7 @@ def init_time(self):
   def init_merra2(self):
     if not self.common_in['MERRA-2']:
       return
-    print("\n MERRA-2 sources:\n")
-    yyyymm = int(self.yyyymm)
-    if yyyymm < 197901 :
-      exit("Error. MERRA-2 data < 1979 not available\n")
-    elif (yyyymm < 199201):
-      self.common_in['expid'] = "d5124_m2_jan79"     
-    elif (yyyymm < 200106):
-      self.common_in['expid'] = "d5124_m2_jan91"
-    elif (yyyymm < 201101):
-      self.common_in['expid'] = "d5124_m2_jan00"
-    else:
-      self.common_in['expid'] = "d5124_m2_jan10"
+    self.common_in = merra2_expid(self.common_in)
 
     self.common_in['agrid'] = 'C180'
     self.common_in['ogrid'] = '1440x720'
diff --git a/GEOS_Util/post/remap_restart/remap_utils.py b/GEOS_Util/post/remap_restart/remap_utils.py
index 582a7a15..acde6274 100644
--- a/GEOS_Util/post/remap_restart/remap_utils.py
+++ b/GEOS_Util/post/remap_restart/remap_utils.py
@@ -91,3 +91,23 @@ def print_config( config, indent = 0 ):
         print_config(v, indent+1)
      else:
         print("   " * indent, f"{k}: {v}")
+
+def merra2_expid(config):
+   if not config['MERRA-2']:
+      return config
+   yyyymm = int(config.get('yyyymmddhh')[0:6])
+   if yyyymm < 197901 :
+      exit("Error. MERRA-2 data < 1979 not available\n")
+   elif (yyyymm < 199201):
+      expid = "d5124_m2_jan79"
+   elif (yyyymm < 200106):
+      expid = "d5124_m2_jan91"
+   elif (yyyymm < 201101):
+      expid = "d5124_m2_jan00"
+   else:
+      expid = "d5124_m2_jan10"
+   config['expid'] = expid
+
+   return config
+ 
+
diff --git a/GEOS_Util/post/tests/amip_c180Toc90.yaml b/GEOS_Util/post/tests/amip_c180Toc90.yaml
new file mode 100644
index 00000000..103c38fd
--- /dev/null
+++ b/GEOS_Util/post/tests/amip_c180Toc90.yaml
@@ -0,0 +1,52 @@
+#
+# This template file can be filled with questionary or manually
+# 
+# 
+
+input:
+  air:
+    drymass: 1
+    hydrostatic: 0
+  shared:
+    MERRA-2: false
+    agrid: C180
+    bcs_dir: /discover/nobackup/ltakacs/bcs/Icarus-NLv3/Icarus-NLv3_MERRA-2//CF0180x6C_DE1440xPE0720/
+    expid: JM_v10.22.2_L072_C180_AMIP
+    ogrid: 1440X720
+    rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/amip_c180Toc90/inputs/ 
+    yyyymmddhh: '1990062621'
+  surface:
+    zoom: '2'
+    wemin: '13'
+    # it supports three models: catch, catchcnclm40, catchcnclm45
+    catch_model: catch
+    catch_tilefile: null
+output:
+  shared:
+    agrid: C90
+    bcs_dir: /discover/nobackup/ltakacs/bcs/Icarus-NLv3/Icarus-NLv3_Ostia//CF0090x6C_CF0090x6C/
+    expid: C90CS_JM_v10.22.2_L072_C180_AMIP
+    ogrid: C90
+    out_dir: $NOBACKUP/REMAP_TESTS/amip_c180Toc90/ 
+  air:
+    # remap upper air or not
+    remap: true
+    nlevel: '72'
+  surface:
+    split_saltwater: true
+    surflay: 50.0
+    wemin: '13'
+    # remap lake, saltwater, landicet
+    remap_water: true
+    # remap catch(cn)
+    remap_catch: true
+    catch_tilefile: null
+  analysis:
+    bkg: false
+    aqua: true
+    lcv: false
+
+slurm:
+  account: g0620
+  qos: debug
+  constraint: sky
diff --git a/GEOS_Util/post/tests/c180Toc360.yaml b/GEOS_Util/post/tests/c180Toc360.yaml
new file mode 100644
index 00000000..58b9e253
--- /dev/null
+++ b/GEOS_Util/post/tests/c180Toc360.yaml
@@ -0,0 +1,52 @@
+#
+# This template file can be filled with questionary or manually
+# 
+# 
+
+input:
+  air:
+    drymass: 1
+    hydrostatic: 0
+  shared:
+    MERRA-2: false
+    agrid: C180
+    bcs_dir: /discover/nobackup/ltakacs/bcs/Icarus-NLv3/Icarus-NLv3_MERRA-2//CF0180x6C_DE1440xPE0720/
+    expid: Jason-3_4_NL_REAMIP_MERRA2_C180
+    ogrid: 1440X720
+    rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/c180Toc360/inputs/ 
+    yyyymmddhh: '1985050921'
+  surface:
+    zoom: '2'
+    wemin: '13'
+    # it supports three models: catch, catchcnclm40, catchcnclm45
+    catch_model: catch
+    catch_tilefile: null
+output:
+  shared:
+    agrid: C360
+    bcs_dir: /discover/nobackup/ltakacs/bcs/Icarus-NLv3/Icarus-NLv3_Ostia//CF0360x6C_CF0360x6C/
+    expid: C360CS_Jason-3_4_NL_REAMIP_MERRA2_C180
+    ogrid: C360
+    out_dir: $NOBACKUP/REMAP_TESTS/c360Toc24/
+  air:
+    # remap upper air or not
+    remap: true
+    nlevel: '91'
+  surface:
+    split_saltwater: true
+    surflay: 50.0
+    wemin: '13'
+    # remap lake, saltwater, landicet
+    remap_water: true
+    # remap catch(cn)
+    remap_catch: true
+    catch_tilefile: null
+  analysis:
+    bkg: false
+    aqua: true
+    lcv: false
+
+slurm:
+  account: g0620
+  qos: debug
+  constraint: sky
diff --git a/GEOS_Util/post/tests/c360Toc24.yaml b/GEOS_Util/post/tests/c360Toc24.yaml
new file mode 100644
index 00000000..62c38681
--- /dev/null
+++ b/GEOS_Util/post/tests/c360Toc24.yaml
@@ -0,0 +1,52 @@
+#
+# This template file can be filled with questionary or manually
+# 
+# 
+
+input:
+  air:
+    drymass: 1
+    hydrostatic: 0
+  shared:
+    MERRA-2: false
+    agrid: C360
+    bcs_dir: /discover/nobackup/projects/gmao/share/gmao_ops/fvInput/g5gcm/bcs/Icarus-NLv3/Icarus-NLv3_Ostia//CF0360x6C_CF0360x6C/
+    expid: x0046a
+    ogrid: C360
+    rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/c360Toc24/inputs 
+    yyyymmddhh: '2022010121'
+  surface:
+    zoom: '4'
+    wemin: '13'
+    # it supports three models: catch, catchcnclm40, catchcnclm45
+    catch_model: catch
+    catch_tilefile: null
+output:
+  shared:
+    agrid: C24
+    bcs_dir: /discover/nobackup/ltakacs/bcs/Icarus-NLv3/Icarus-NLv3_Reynolds//CF0024x6C_DE0360xPE0180/
+    expid: C24c_x0046a
+    ogrid: 360X180
+    out_dir: $NOBACKUP/REMAP_TESTS/c360Toc24/ 
+  air:
+    # remap upper air or not
+    remap: true
+    nlevel: '181'
+  surface:
+    split_saltwater: true
+    surflay: 50.0
+    wemin: '13'
+    # remap lake, saltwater, landicet
+    remap_water: true
+    # remap catch(cn)
+    remap_catch: true
+    catch_tilefile: null
+  analysis:
+    bkg: false
+    aqua: true
+    lcv: false
+
+slurm:
+  account: g0620
+  qos: debug
+  constraint: sky
diff --git a/GEOS_Util/post/tests/test_remap_cases.yaml b/GEOS_Util/post/tests/test_remap_cases.yaml
index 30640090..0c59af44 100644
--- a/GEOS_Util/post/tests/test_remap_cases.yaml
+++ b/GEOS_Util/post/tests/test_remap_cases.yaml
@@ -4,4 +4,13 @@ c24Toc12:
 f522Toc360:
   base_line: '/discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/f522Toc360/baseline/'
   config: 'f522Toc360.yaml'
-  
+amip_c180Toc90:
+  base_line: '/discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/amip_c180Toc90/baseline/'
+  config: 'amip_c180Toc90.yaml' 
+c180Toc360:
+  base_line: '/discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/c180Toc360/baseline/'
+  config: 'c180Toc360.yaml'
+c360Toc24:
+  base_line: '/discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/c360Toc24/baseline/'
+  config: 'c360Toc24.yaml'
+

From 5372815eff01620e63bd4fe4cc05ec00c8a8c2e6 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Mon, 8 Aug 2022 09:14:44 -0400
Subject: [PATCH 13/22] add main for self testing in remap_utils

---
 GEOS_Util/post/remap_restart/remap_utils.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/GEOS_Util/post/remap_restart/remap_utils.py b/GEOS_Util/post/remap_restart/remap_utils.py
index acde6274..d3c6a7d2 100644
--- a/GEOS_Util/post/remap_restart/remap_utils.py
+++ b/GEOS_Util/post/remap_restart/remap_utils.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+#
 import os
 import subprocess
 import ruamel.yaml
@@ -110,4 +112,6 @@ def merra2_expid(config):
 
    return config
  
-
+if __name__ == '__main__' :
+   config = yaml_to_config('c24Toc12.yaml')
+   print_config(config)

From e77c56fe935ef051374b807ba05941ca6c6c25c7 Mon Sep 17 00:00:00 2001
From: Matthew Thompson <matthew.thompson@nasa.gov>
Date: Mon, 15 Aug 2022 13:42:00 -0400
Subject: [PATCH 14/22] Add S2S Test. Add YAML validator

---
 .github/workflows/changelog-enforcer.yml   |  2 +-
 .github/workflows/validate_yaml_files.yml  | 31 ++++++++++++++
 .yamllint.yml                              | 29 +++++++++++++
 CHANGELOG.md                               |  7 +++
 GEOS_Util/post/tests/amip_c180Toc90.yaml   |  8 ++--
 GEOS_Util/post/tests/c180Toc360.yaml       |  6 +--
 GEOS_Util/post/tests/c24Toc12.yaml         |  4 +-
 GEOS_Util/post/tests/c360Toc24.yaml        |  8 ++--
 GEOS_Util/post/tests/f522Toc360.yaml       |  6 +--
 GEOS_Util/post/tests/s2sToc12MOM6.yaml     | 50 ++++++++++++++++++++++
 GEOS_Util/post/tests/test_remap_cases.yaml |  6 ++-
 11 files changed, 138 insertions(+), 19 deletions(-)
 create mode 100644 .github/workflows/validate_yaml_files.yml
 create mode 100644 .yamllint.yml
 create mode 100644 GEOS_Util/post/tests/s2sToc12MOM6.yaml

diff --git a/.github/workflows/changelog-enforcer.yml b/.github/workflows/changelog-enforcer.yml
index 6e46cfc2..b709e98b 100644
--- a/.github/workflows/changelog-enforcer.yml
+++ b/.github/workflows/changelog-enforcer.yml
@@ -4,7 +4,7 @@ on:
       types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
 
 jobs:
-  # Enforces the update of a changelog file on every pull request 
+  # Enforces the update of a changelog file on every pull request
   changelog:
     runs-on: ubuntu-latest
     steps:
diff --git a/.github/workflows/validate_yaml_files.yml b/.github/workflows/validate_yaml_files.yml
new file mode 100644
index 00000000..36ecf876
--- /dev/null
+++ b/.github/workflows/validate_yaml_files.yml
@@ -0,0 +1,31 @@
+---
+
+# Based on code from https://github.com/marketplace/actions/yaml-lint
+
+name: Yaml Lint
+
+on:
+  pull_request:
+      types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+# This validation is equivalent to running on the command line:
+#   yamllint -d relaxed --no-warnings
+# and is controlled by the .yamllint.yml file
+jobs:
+  validate-YAML:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - id: yaml-lint
+        name: yaml-lint
+        uses: ibiqlik/action-yamllint@v3
+        with:
+          no_warnings: true
+          format: colored
+          config_file: .yamllint.yml
+
+      - uses: actions/upload-artifact@v3
+        if: always()
+        with:
+          name: yamllint-logfile
+          path: ${{ steps.yaml-lint.outputs.logfile }}
diff --git a/.yamllint.yml b/.yamllint.yml
new file mode 100644
index 00000000..83f5340c
--- /dev/null
+++ b/.yamllint.yml
@@ -0,0 +1,29 @@
+---
+
+extends: default
+
+rules:
+  braces:
+    level: warning
+    max-spaces-inside: 1
+  brackets:
+    level: warning
+    max-spaces-inside: 1
+  colons:
+    level: warning
+  commas:
+    level: warning
+  comments: disable
+  comments-indentation: disable
+  document-start: disable
+  empty-lines:
+    level: warning
+  hyphens:
+    level: warning
+  indentation:
+    level: warning
+    indent-sequences: consistent
+  line-length:
+    level: warning
+    allow-non-breakable-inline-mappings: true
+  truthy: disable
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7c4cedb3..408cfb98 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,10 +9,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- Add YAML validator
+
 ### Changed
 
 - Generated command line to run the program
 - changed the location of the temporary folder for remap_restarts MERRA-2 case 
+- Added new remap tests
+  - amip_c180Toc90
+  - c180Toc360
+  - c360Toc24
+  - s2sToc12MOM6
 
 ### Fixed
 
diff --git a/GEOS_Util/post/tests/amip_c180Toc90.yaml b/GEOS_Util/post/tests/amip_c180Toc90.yaml
index 103c38fd..2c04fbd6 100644
--- a/GEOS_Util/post/tests/amip_c180Toc90.yaml
+++ b/GEOS_Util/post/tests/amip_c180Toc90.yaml
@@ -1,7 +1,7 @@
 #
 # This template file can be filled with questionary or manually
-# 
-# 
+#
+#
 
 input:
   air:
@@ -13,7 +13,7 @@ input:
     bcs_dir: /discover/nobackup/ltakacs/bcs/Icarus-NLv3/Icarus-NLv3_MERRA-2//CF0180x6C_DE1440xPE0720/
     expid: JM_v10.22.2_L072_C180_AMIP
     ogrid: 1440X720
-    rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/amip_c180Toc90/inputs/ 
+    rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/amip_c180Toc90/inputs/
     yyyymmddhh: '1990062621'
   surface:
     zoom: '2'
@@ -27,7 +27,7 @@ output:
     bcs_dir: /discover/nobackup/ltakacs/bcs/Icarus-NLv3/Icarus-NLv3_Ostia//CF0090x6C_CF0090x6C/
     expid: C90CS_JM_v10.22.2_L072_C180_AMIP
     ogrid: C90
-    out_dir: $NOBACKUP/REMAP_TESTS/amip_c180Toc90/ 
+    out_dir: $NOBACKUP/REMAP_TESTS/amip_c180Toc90/
   air:
     # remap upper air or not
     remap: true
diff --git a/GEOS_Util/post/tests/c180Toc360.yaml b/GEOS_Util/post/tests/c180Toc360.yaml
index 58b9e253..7a5bc65b 100644
--- a/GEOS_Util/post/tests/c180Toc360.yaml
+++ b/GEOS_Util/post/tests/c180Toc360.yaml
@@ -1,7 +1,7 @@
 #
 # This template file can be filled with questionary or manually
-# 
-# 
+#
+#
 
 input:
   air:
@@ -13,7 +13,7 @@ input:
     bcs_dir: /discover/nobackup/ltakacs/bcs/Icarus-NLv3/Icarus-NLv3_MERRA-2//CF0180x6C_DE1440xPE0720/
     expid: Jason-3_4_NL_REAMIP_MERRA2_C180
     ogrid: 1440X720
-    rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/c180Toc360/inputs/ 
+    rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/c180Toc360/inputs/
     yyyymmddhh: '1985050921'
   surface:
     zoom: '2'
diff --git a/GEOS_Util/post/tests/c24Toc12.yaml b/GEOS_Util/post/tests/c24Toc12.yaml
index 3bd204a4..367a6974 100644
--- a/GEOS_Util/post/tests/c24Toc12.yaml
+++ b/GEOS_Util/post/tests/c24Toc12.yaml
@@ -1,7 +1,7 @@
 #
 # This template file can be filled with questionary or manually
-# 
-# 
+#
+#
 
 input:
   air:
diff --git a/GEOS_Util/post/tests/c360Toc24.yaml b/GEOS_Util/post/tests/c360Toc24.yaml
index 62c38681..e23dd4d3 100644
--- a/GEOS_Util/post/tests/c360Toc24.yaml
+++ b/GEOS_Util/post/tests/c360Toc24.yaml
@@ -1,7 +1,7 @@
 #
 # This template file can be filled with questionary or manually
-# 
-# 
+#
+#
 
 input:
   air:
@@ -13,7 +13,7 @@ input:
     bcs_dir: /discover/nobackup/projects/gmao/share/gmao_ops/fvInput/g5gcm/bcs/Icarus-NLv3/Icarus-NLv3_Ostia//CF0360x6C_CF0360x6C/
     expid: x0046a
     ogrid: C360
-    rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/c360Toc24/inputs 
+    rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/c360Toc24/inputs
     yyyymmddhh: '2022010121'
   surface:
     zoom: '4'
@@ -27,7 +27,7 @@ output:
     bcs_dir: /discover/nobackup/ltakacs/bcs/Icarus-NLv3/Icarus-NLv3_Reynolds//CF0024x6C_DE0360xPE0180/
     expid: C24c_x0046a
     ogrid: 360X180
-    out_dir: $NOBACKUP/REMAP_TESTS/c360Toc24/ 
+    out_dir: $NOBACKUP/REMAP_TESTS/c360Toc24/
   air:
     # remap upper air or not
     remap: true
diff --git a/GEOS_Util/post/tests/f522Toc360.yaml b/GEOS_Util/post/tests/f522Toc360.yaml
index f4450582..48048b38 100644
--- a/GEOS_Util/post/tests/f522Toc360.yaml
+++ b/GEOS_Util/post/tests/f522Toc360.yaml
@@ -1,7 +1,7 @@
 #
 # This template file can be filled with questionary or manually
-# 
-# 
+#
+#
 
 input:
   air:
@@ -13,7 +13,7 @@ input:
     bcs_dir: /discover/nobackup/projects/gmao/share/gmao_ops/fvInput/g5gcm/bcs/Icarus_Updated/Icarus_Ostia//CF0720x6C_CF0720x6C/
     expid: f522_fp
     ogrid: C720
-    rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/f522Toc360/inputs/ 
+    rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/f522Toc360/inputs/
     yyyymmddhh: '2019061421'
   surface:
     zoom: '8'
diff --git a/GEOS_Util/post/tests/s2sToc12MOM6.yaml b/GEOS_Util/post/tests/s2sToc12MOM6.yaml
new file mode 100644
index 00000000..ef66f2b9
--- /dev/null
+++ b/GEOS_Util/post/tests/s2sToc12MOM6.yaml
@@ -0,0 +1,50 @@
+#
+# This template file can be filled with questionary or manually
+#
+#
+
+input:
+  air:
+    drymass: 1
+    hydrostatic: 0
+  shared:
+    agrid: C180
+    bcs_dir: /discover/nobackup/projects/gmao/ssd/aogcm/atmosphere_bcs/Ganymed/MOM5//CF0180x6C_TM0720xTM0410/
+    expid: S2S-2_1_ANA_001
+    ogrid: 720X410
+    rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/s2sToc12MOM6/inputs
+    yyyymmddhh: '2021041600'
+  surface:
+    zoom: '2'
+    wemin: '26'
+    # it supports three models: catch, catchcnclm40, catchcnclm45
+    catch_model: catch
+
+output:
+  shared:
+    agrid: C12
+    bcs_dir: /discover/nobackup/projects/gmao/ssd/aogcm/atmosphere_bcs/Icarus-NLv3/MOM6//CF0012x6C_TM0072xTM0036/
+    expid: c12-MOM6
+    ogrid: 72X36
+    out_dir: $NOBACKUP/REMAP_TESTS/s2sToc12MOM6/
+  air:
+    # remap upper air or not
+    remap: true
+    nlevel: '72'
+  surface:
+    split_saltwater: true
+    surflay: 50.0
+    wemin: '13'
+    # remap lake, saltwater, landicet
+    remap_water: true
+    # remap catch(cn)
+    remap_catch: true
+  analysis:
+    bkg: false
+    aqua: true
+    lcv: false
+
+slurm:
+  account: g0620
+  qos: debug
+  constraint: cas
diff --git a/GEOS_Util/post/tests/test_remap_cases.yaml b/GEOS_Util/post/tests/test_remap_cases.yaml
index 0c59af44..4fdebfc7 100644
--- a/GEOS_Util/post/tests/test_remap_cases.yaml
+++ b/GEOS_Util/post/tests/test_remap_cases.yaml
@@ -6,11 +6,13 @@ f522Toc360:
   config: 'f522Toc360.yaml'
 amip_c180Toc90:
   base_line: '/discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/amip_c180Toc90/baseline/'
-  config: 'amip_c180Toc90.yaml' 
+  config: 'amip_c180Toc90.yaml'
 c180Toc360:
   base_line: '/discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/c180Toc360/baseline/'
   config: 'c180Toc360.yaml'
 c360Toc24:
   base_line: '/discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/c360Toc24/baseline/'
   config: 'c360Toc24.yaml'
-
+s2sToc12MOM6:
+  base_line: '/discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/s2sToc12MOM6/baseline/'
+  config: 's2sToc12MOM6.yaml'

From c188423736c0438b8b9769592831c721844d7a44 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Mon, 15 Aug 2022 14:53:38 -0400
Subject: [PATCH 15/22] add item catch_tilefile

---
 GEOS_Util/post/tests/c24Toc12.yaml   | 3 ++-
 GEOS_Util/post/tests/f522Toc360.yaml | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/GEOS_Util/post/tests/c24Toc12.yaml b/GEOS_Util/post/tests/c24Toc12.yaml
index 3bd204a4..3167a096 100644
--- a/GEOS_Util/post/tests/c24Toc12.yaml
+++ b/GEOS_Util/post/tests/c24Toc12.yaml
@@ -20,7 +20,7 @@ input:
     wemin: '13'
     # it supports three models: catch, catchcnclm40, catchcnclm45
     catch_model: catch
-
+    catch_tilefile: null
 output:
   shared:
     agrid: C12
@@ -37,6 +37,7 @@ output:
     wemin: '13'
     remap_water: true
     remap_catch: true
+    catch_tilefile: null
   analysis:
     bkg: false
     aqua: true
diff --git a/GEOS_Util/post/tests/f522Toc360.yaml b/GEOS_Util/post/tests/f522Toc360.yaml
index f4450582..3a013ae1 100644
--- a/GEOS_Util/post/tests/f522Toc360.yaml
+++ b/GEOS_Util/post/tests/f522Toc360.yaml
@@ -19,7 +19,7 @@ input:
     zoom: '8'
     wemin: '26'
     catch_model: catch
-
+    catch_tilefile: null
 output:
   shared:
     agrid: C360
@@ -36,6 +36,7 @@ output:
     wemin: '13'
     remap_catch: true
     remap_water: true
+    catch_tilefile: null
   analysis:
     bkg: true
     aqua: true

From 252afbf85709fb2d2d94e30c3898e5df27288b9e Mon Sep 17 00:00:00 2001
From: Matthew Thompson <matthew.thompson@nasa.gov>
Date: Mon, 15 Aug 2022 15:01:53 -0400
Subject: [PATCH 16/22] Add catch_tilefile: null

---
 GEOS_Util/post/tests/c24Toc12.yaml     | 6 +++++-
 GEOS_Util/post/tests/f522Toc360.yaml   | 3 ++-
 GEOS_Util/post/tests/s2sToc12MOM6.yaml | 3 ++-
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/GEOS_Util/post/tests/c24Toc12.yaml b/GEOS_Util/post/tests/c24Toc12.yaml
index 367a6974..0b96e65e 100644
--- a/GEOS_Util/post/tests/c24Toc12.yaml
+++ b/GEOS_Util/post/tests/c24Toc12.yaml
@@ -20,7 +20,7 @@ input:
     wemin: '13'
     # it supports three models: catch, catchcnclm40, catchcnclm45
     catch_model: catch
-
+    catch_tilefile: null
 output:
   shared:
     agrid: C12
@@ -29,14 +29,18 @@ output:
     ogrid: 360X180
     out_dir: $NOBACKUP/REMAP_TESTS/c24Toc12/
   air:
+    # remap upper air or not
     remap: true
     nlevel: '72'
   surface:
     split_saltwater: true
     surflay: 50.0
     wemin: '13'
+    # remap lake, saltwater, landicet
     remap_water: true
+    # remap catch(cn)
     remap_catch: true
+    catch_tilefile: null
   analysis:
     bkg: false
     aqua: true
diff --git a/GEOS_Util/post/tests/f522Toc360.yaml b/GEOS_Util/post/tests/f522Toc360.yaml
index 48048b38..5d3dfd0f 100644
--- a/GEOS_Util/post/tests/f522Toc360.yaml
+++ b/GEOS_Util/post/tests/f522Toc360.yaml
@@ -19,7 +19,7 @@ input:
     zoom: '8'
     wemin: '26'
     catch_model: catch
-
+    catch_tilefile: null
 output:
   shared:
     agrid: C360
@@ -35,6 +35,7 @@ output:
     surflay: 50.0
     wemin: '13'
     remap_catch: true
+    catch_tilefile: null
     remap_water: true
   analysis:
     bkg: true
diff --git a/GEOS_Util/post/tests/s2sToc12MOM6.yaml b/GEOS_Util/post/tests/s2sToc12MOM6.yaml
index ef66f2b9..57634b8e 100644
--- a/GEOS_Util/post/tests/s2sToc12MOM6.yaml
+++ b/GEOS_Util/post/tests/s2sToc12MOM6.yaml
@@ -19,7 +19,7 @@ input:
     wemin: '26'
     # it supports three models: catch, catchcnclm40, catchcnclm45
     catch_model: catch
-
+    catch_tilefile: null
 output:
   shared:
     agrid: C12
@@ -39,6 +39,7 @@ output:
     remap_water: true
     # remap catch(cn)
     remap_catch: true
+    catch_tilefile: null
   analysis:
     bkg: false
     aqua: true

From a2483335db8bedb3ba0683666d0277eecb969261 Mon Sep 17 00:00:00 2001
From: Matthew Thompson <matthew.thompson@nasa.gov>
Date: Mon, 15 Aug 2022 15:56:12 -0400
Subject: [PATCH 17/22] Add false merra-2

---
 GEOS_Util/post/tests/s2sToc12MOM6.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/GEOS_Util/post/tests/s2sToc12MOM6.yaml b/GEOS_Util/post/tests/s2sToc12MOM6.yaml
index 57634b8e..58cada6c 100644
--- a/GEOS_Util/post/tests/s2sToc12MOM6.yaml
+++ b/GEOS_Util/post/tests/s2sToc12MOM6.yaml
@@ -8,6 +8,7 @@ input:
     drymass: 1
     hydrostatic: 0
   shared:
+    MERRA-2: false
     agrid: C180
     bcs_dir: /discover/nobackup/projects/gmao/ssd/aogcm/atmosphere_bcs/Ganymed/MOM5//CF0180x6C_TM0720xTM0410/
     expid: S2S-2_1_ANA_001

From c5e82ecc949e1eb9c4ce4a81f678ca40436e2ca0 Mon Sep 17 00:00:00 2001
From: Matthew Thompson <matthew.thompson@nasa.gov>
Date: Tue, 16 Aug 2022 11:14:36 -0400
Subject: [PATCH 18/22] Clean up after merge

---
 GEOS_Util/post/tests/f522Toc360.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/GEOS_Util/post/tests/f522Toc360.yaml b/GEOS_Util/post/tests/f522Toc360.yaml
index ce0e5c81..17deaa62 100644
--- a/GEOS_Util/post/tests/f522Toc360.yaml
+++ b/GEOS_Util/post/tests/f522Toc360.yaml
@@ -35,7 +35,6 @@ output:
     surflay: 50.0
     wemin: '13'
     remap_catch: true
-    catch_tilefile: null
     remap_water: true
     catch_tilefile: null
   analysis:

From 838d14377e556c51d50543f3a676a39cc1615624 Mon Sep 17 00:00:00 2001
From: Matthew Thompson <matthew.thompson@nasa.gov>
Date: Tue, 16 Aug 2022 13:02:40 -0400
Subject: [PATCH 19/22] Add extra isinstance per Weiyuan

---
 GEOS_Util/post/remap_restart/remap_utils.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/GEOS_Util/post/remap_restart/remap_utils.py b/GEOS_Util/post/remap_restart/remap_utils.py
index d3c6a7d2..3c39cc47 100644
--- a/GEOS_Util/post/remap_restart/remap_utils.py
+++ b/GEOS_Util/post/remap_restart/remap_utils.py
@@ -52,9 +52,9 @@ def flatten_nested(nested_dict, result=None, prefix=''):
 
    flat_dict = flatten_nested(config)
 
-   k = 1   
+   k = 1
    for key, value in flat_dict.items():
-     if isinstance(value, int) or isinstance(value, float) :   value = str(value)
+     if isinstance(value, int) or isinstance(value, float) or isinstance(value, bool) or isinstance(value, type(None)): value = str(value)
      if k == 1:
        cmd = cmd + 'set FLAT_YAML="' + key+"="+ value+ '"\n'
      else:
@@ -111,7 +111,7 @@ def merra2_expid(config):
    config['expid'] = expid
 
    return config
- 
+
 if __name__ == '__main__' :
    config = yaml_to_config('c24Toc12.yaml')
    print_config(config)

From 9e5defb4ceca55c9827e4ee9dc8f649edab81821 Mon Sep 17 00:00:00 2001
From: Matthew Thompson <matthew.thompson@nasa.gov>
Date: Wed, 17 Aug 2022 10:36:51 -0400
Subject: [PATCH 20/22] Move to use S2Sv3 inputs

---
 CHANGELOG.md                                  |  6 +++---
 ...{s2sToc12MOM6.yaml => s2sv3Toc12MOM6.yaml} | 20 ++++++++++---------
 GEOS_Util/post/tests/test_remap_cases.yaml    |  6 +++---
 3 files changed, 17 insertions(+), 15 deletions(-)
 rename GEOS_Util/post/tests/{s2sToc12MOM6.yaml => s2sv3Toc12MOM6.yaml} (71%)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 408cfb98..18417aa7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,12 +14,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - Generated command line to run the program
-- changed the location of the temporary folder for remap_restarts MERRA-2 case 
+- changed the location of the temporary folder for remap_restarts MERRA-2 case
 - Added new remap tests
   - amip_c180Toc90
   - c180Toc360
   - c360Toc24
-  - s2sToc12MOM6
+  - s2sv3Toc12MOM6
 
 ### Fixed
 
@@ -54,7 +54,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-- Added statsNx.rc for screen level variable fstats 
+- Added statsNx.rc for screen level variable fstats
 
 ### Changed
 
diff --git a/GEOS_Util/post/tests/s2sToc12MOM6.yaml b/GEOS_Util/post/tests/s2sv3Toc12MOM6.yaml
similarity index 71%
rename from GEOS_Util/post/tests/s2sToc12MOM6.yaml
rename to GEOS_Util/post/tests/s2sv3Toc12MOM6.yaml
index 58cada6c..d280414f 100644
--- a/GEOS_Util/post/tests/s2sToc12MOM6.yaml
+++ b/GEOS_Util/post/tests/s2sv3Toc12MOM6.yaml
@@ -10,24 +10,25 @@ input:
   shared:
     MERRA-2: false
     agrid: C180
-    bcs_dir: /discover/nobackup/projects/gmao/ssd/aogcm/atmosphere_bcs/Ganymed/MOM5//CF0180x6C_TM0720xTM0410/
-    expid: S2S-2_1_ANA_001
-    ogrid: 720X410
-    rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/s2sToc12MOM6/inputs
-    yyyymmddhh: '2021041600'
+    bcs_dir: /discover/nobackup/projects/gmao/ssd/aogcm/atmosphere_bcs/Icarus/MOM5//CF0180x6C_TM1440xTM1080/
+    expid: M2OCEAN_S2SV3
+    ogrid: 1440X1080
+    rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/s2sv3Toc12MOM6/inputs
+    yyyymmddhh: '1982010100'
   surface:
     zoom: '2'
     wemin: '26'
     # it supports three models: catch, catchcnclm40, catchcnclm45
     catch_model: catch
-    catch_tilefile: null
+    # if catch_tilefile is null, it searches bcs_dir
+    catch_tilefile:
 output:
   shared:
     agrid: C12
     bcs_dir: /discover/nobackup/projects/gmao/ssd/aogcm/atmosphere_bcs/Icarus-NLv3/MOM6//CF0012x6C_TM0072xTM0036/
-    expid: c12-MOM6
+    expid: C12-MOM6-from-S2Sv3
     ogrid: 72X36
-    out_dir: $NOBACKUP/REMAP_TESTS/s2sToc12MOM6/
+    out_dir: $NOBACKUP/REMAP_TESTS/s2sv3Toc12MOM6/
   air:
     # remap upper air or not
     remap: true
@@ -40,7 +41,8 @@ output:
     remap_water: true
     # remap catch(cn)
     remap_catch: true
-    catch_tilefile: null
+    # if catch_tilefile is null, it searches bcs_dir
+    catch_tilefile:
   analysis:
     bkg: false
     aqua: true
diff --git a/GEOS_Util/post/tests/test_remap_cases.yaml b/GEOS_Util/post/tests/test_remap_cases.yaml
index 4fdebfc7..166d091a 100644
--- a/GEOS_Util/post/tests/test_remap_cases.yaml
+++ b/GEOS_Util/post/tests/test_remap_cases.yaml
@@ -13,6 +13,6 @@ c180Toc360:
 c360Toc24:
   base_line: '/discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/c360Toc24/baseline/'
   config: 'c360Toc24.yaml'
-s2sToc12MOM6:
-  base_line: '/discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/s2sToc12MOM6/baseline/'
-  config: 's2sToc12MOM6.yaml'
+s2sv3Toc12MOM6:
+  base_line: '/discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/s2sv3Toc12MOM6/baseline/'
+  config: 's2sv3Toc12MOM6.yaml'

From 9176e53ce0aa115fea3709cd5cb617850ebfcc54 Mon Sep 17 00:00:00 2001
From: Matthew Thompson <matthew.thompson@nasa.gov>
Date: Wed, 17 Aug 2022 10:37:09 -0400
Subject: [PATCH 21/22] Clean up template to remove trailing spaces

---
 GEOS_Util/post/remap_restart/remap_params.tpl | 22 +++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/GEOS_Util/post/remap_restart/remap_params.tpl b/GEOS_Util/post/remap_restart/remap_params.tpl
index 94cedbfd..a8ca9ac9 100644
--- a/GEOS_Util/post/remap_restart/remap_params.tpl
+++ b/GEOS_Util/post/remap_restart/remap_params.tpl
@@ -1,7 +1,7 @@
 #
 # This template file can be filled with questionary or manually
-# 
-# 
+#
+#
 
 input:
   air:
@@ -9,7 +9,7 @@ input:
     hydrostatic: 0
   shared:
     MERRA-2: false
-    agrid: 
+    agrid:
     bcs_dir:
     expid:
     ogrid:
@@ -20,14 +20,14 @@ input:
     wemin:
     # it supports three models: catch, catchcnclm40, catchcnclm45
     catch_model: null
-    # if catch_tilefile is null, it searches bcs_dir     
+    # if catch_tilefile is null, it searches bcs_dir
     catch_tilefile: null
 output:
   shared:
     agrid:
-    bcs_dir: 
-    expid: 
-    ogrid: 
+    bcs_dir:
+    expid:
+    ogrid:
     out_dir:
   air:
     # remap upper air or not
@@ -41,7 +41,7 @@ output:
     remap_water: true
     # remap catch(cn)
     remap_catch: true
-    # if catch_tilefile is null, it searches bcs_dir     
+    # if catch_tilefile is null, it searches bcs_dir
     catch_tilefile: null
   analysis:
     bkg: true
@@ -49,6 +49,6 @@ output:
     lcv: false
 
 slurm:
-  account: 
-  qos: 
-  constraint: 
+  account:
+  qos:
+  constraint:

From 9125540412e621b6c949602e645d10c538756ee9 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Thu, 18 Aug 2022 10:35:29 -0400
Subject: [PATCH 22/22] add final report

---
 GEOS_Util/post/tests/test_remap_restarts.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/GEOS_Util/post/tests/test_remap_restarts.py b/GEOS_Util/post/tests/test_remap_restarts.py
index f699ba7c..69c6707c 100755
--- a/GEOS_Util/post/tests/test_remap_restarts.py
+++ b/GEOS_Util/post/tests/test_remap_restarts.py
@@ -69,7 +69,8 @@ def test_remap(config):
   (user, err) = p.communicate()
   p_status = p.wait()
   user = user.decode().split()[0]  
-
+  
+  report ={}
   for case, values in cases.items():
      base_line        = values['base_line']
      config_yaml_file = values['config']
@@ -87,6 +88,11 @@ def test_remap(config):
      rc = compare(base_line, out_dir)
      if (not rc) :
        print ("failed in " + case)
+       report[case] = "Failed"
      else :
+       report[case] = "Succeeded"
        print (case +" test is successful")
  
+  print("\n\n")
+  for case, result in report.items():
+     print(case + ":   " + result)