diff --git a/atmosphere/CNTLALL b/atmosphere/CNTLALL
deleted file mode 100644
index b409eee..0000000
--- a/atmosphere/CNTLALL
+++ /dev/null
@@ -1,126 +0,0 @@
- &NLSTCALL
- EXPT_ID='aiih',
- JOB_ID='c',
- EXPT_ID_IN='    ',
- JOB_ID_IN=' ',
- EXPT_ALIAS='ALIAS   ',
- RUN_RESUBMIT_INC=  0 , 0 , 1 , 0 , 0 , 0 ,
- MODEL_STATUS='NonOperational',
- MODEL_BASIS_TIME=  0101 , 01 , 01 , 0 , 0 , 0 ,
- ANCIL_REFTIME=  0101 , 01 , 01 , 0 , 0 , 0 ,
- RUN_TARGET_END=  0 , 0 , 1 , 0 , 0 , 0 , 
- LCLIMREALYR=.FALSE.,
- LCAL360=.FALSE., 
- LTIMER=.TRUE., 
- L_IO_TIMER=.TRUE.,
- TIME_CONVENTION='Absolute_standard',                            
- MODEL_ANALYSIS_MINS=0,
- MODEL_ASSIM_MODE='None      ',
- RUN_ASSIM_MODE='None      ',
- CONTROL_RESUBMIT='Y',
- MODEL_HRS_PER_GROUP=0,
- FT_PLOTSEL= 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,  
- FT_WSSEND='N','N','N','N','N','N','N','N','N','N',
- PP_PACK_CODE= 1 , 1 , 1 , 1 , 1 , 1 , 1 , 0 , 1 , 1 , 1 , 1 ,
-  1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 ,
-  1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 0 , 1 , 1 , 1 , 1 ,
-  1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 ,
-  1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 ,
-  1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 ,
-  1 , 1 , 1 , 1 , 0 , 1 , 
- PP_LEN2_LOOK= 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 100000 , 100000 , 100000 , 100000 ,
-  100000 , 100000 , 100000 , 100000 , 100000 , 100000 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
- LRLE=.FALSE.,
- TYPE_LETTER_1='p','p','p','p','p','p','p','p','p','p','p','p',
- 'p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p',
- 'p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p',
- 'p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p',
- 'p','b','p','p','p','p','p','p','p','p','p','b','b','b','b','p','p','p','p',
- 'p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p',
- 'p','p','p','p','p','p','p','p','p','p','p','p','p','b','b','b','b','b','b',
- 'b','b','p','p','c','p' , 
- TYPE_LETTER_3=' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ','a','b','c','d','e','f','g','h','i','j',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ','a','b','c','d',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ','a','b','c','d','e','f',
- 'g','h',' ',' ','a','k' , 
-  
- FT_INPUT='N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N' , 
- FT_STEPS= 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,  -1 , 0 , -3 , 0 , -1, 1440 ,
-  -1 , 0 , -1 , -1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0  ,  
- FT_SELECT='N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N' , 
- FT_ARCHSEL='N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N' ,  
- FT_FIRSTSTEP= 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0  ,  
- FT_LASTSTEP= 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , -1 , 0 , -1 , 0 , -1 , -48 , -1 , 0 ,
-  -1 , -1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0  , 
- TYPE_LETTER_2=' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ','a',' ','a',' ','a','a','a',' ',' ','a',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ' , 
- Num_ALBCs=,
- / 
-
- &NLSTWRITEDATA
- L_WRIT_INIT=.FALSE.,
- T_WRITD1_START=0,
- T_WRITD1_END=0,
- T_WRITD1_INT=0,
- PEER_VN=1,
- L_PEER=.FALSE.,
- /
-
- !!! END OF FILE !!!
diff --git a/atmosphere/CONTCNTL b/atmosphere/CONTCNTL
deleted file mode 100644
index a3589e2..0000000
--- a/atmosphere/CONTCNTL
+++ /dev/null
@@ -1,312 +0,0 @@
- &NLSTCALL
- EXPT_ID='aiih',
- JOB_ID='c',
- EXPT_ID_IN='    ',
- JOB_ID_IN=' ',
- EXPT_ALIAS='ALIAS   ',
- RUN_RESUBMIT_INC= REPLACE_RESUBMIT_INC
- MODEL_STATUS='NonOperational',
- MODEL_BASIS_TIME= REPLACE_BASIS_TIME
- ANCIL_REFTIME= REPLACE_BASIS_TIME
- RUN_TARGET_END= REPLACE_RUNLENGTH
- LCLIMREALYR=.FALSE.,
- LCAL360=.FALSE., 
- LTIMER=.TRUE., 
- L_IO_TIMER=.TRUE.,
- TIME_CONVENTION='Absolute_standard',                            
- MODEL_ANALYSIS_MINS=0,
- MODEL_ASSIM_MODE='None      ',
- RUN_ASSIM_MODE='None      ',
- CONTROL_RESUBMIT='Y',
- MODEL_HRS_PER_GROUP=0,
- FT_PLOTSEL= 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,  
- FT_WSSEND='N','N','N','N','N','N','N','N','N','N',
- PP_PACK_CODE= 1 , 1 , 1 , 1 , 1 , 1 , 1 , 0 , 1 , 1 , 1 , 1 ,
-  1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 ,
-  1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 0 , 1 , 1 , 1 , 1 ,
-  1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 ,
-  1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 ,
-  1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 ,
-  1 , 1 , 1 , 1 , 0 , 1 , 
- PP_LEN2_LOOK= 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 
- LRLE=.FALSE.,
- TYPE_LETTER_1='p','p','p','p','p','p','p','p','p','p','p','p',
- 'p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p',
- 'p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p',
- 'p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p',
- 'p','b','p','p','p','p','p','p','p','p','p','b','b','b','b','p','p','p','p',
- 'p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p','p',
- 'p','p','p','p','p','p','p','p','p','p','p','p','p','b','b','b','b','b','b',
- 'b','b','p','p','c','p' , 
- TYPE_LETTER_3=' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ','a','b','c','d','e','f','g','h','i','j',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ','a','b','c','d',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ','a','b','c','d','e','f',
- 'g','h',' ',' ','a','k' , 
-  
- FT_INPUT='N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N' , 
- FT_STEPS= 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1440 , 0 , 1440 , 0 , 1440 , 1440 ,
-  1440 , 0 , 0 , 480 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0  ,  
- FT_SELECT='N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N' , 
- FT_ARCHSEL='N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N' ,  
- FT_FIRSTSTEP= 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  108000 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0  ,  
- FT_LASTSTEP= 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , -48 , 0 , -48 , 0 , -48 , -48 , -48 , 0 ,
-  0 , 195840 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ,
-  0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0  , 
- TYPE_LETTER_2=' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ','a',' ','a',' ','a','a','a',' ',' ','a',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
- ' ',' ',' ',' ',' ',' ' , 
- Num_ALBCs=,
- / 
- &NLSTCGEN
- STEPS_PER_PERIODim=48,0,0,0,
- SECS_PER_PERIODim=86400,0,0,0,
- EXITFREQim=48,0,0,0,
- DUMPFREQim=0,0,0,0,
- ARCHDUMP_OFFSETim=0,0,0,0,
- ARCHDUMP_FREQim=0,0,0,0,
- DUMPTIMESim=REPLACE_DUMPTIMES,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- PPSELECTim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- PLOTSELim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- MEANWSim='N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N',
- ARCHPPSELim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- MEANARCHim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- MEANFREQim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- PRINTFREQim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- MEAN_REFTIMEim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- JOBREL_STEPim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- DUMP_PACKim=3,0,0,0,
- PP_LEN2_MEANim=4096,4096,4096,4096,4096,4096,4096,4096,4096,4096,4096,4096,
- 4096,4096,4096,4096,
- FT_MEANim=27,27,27,27,
- LLBOUTim=.FALSE.,
- /
- &NLST_MPP
- extended_halo_size_EW=4,
- extended_halo_size_NS=5,
- gcom_coll_limit=64,
- /
- &NLSTCATM
- MODEL_DOMAIN=1 ,
- L_SNOW_ALBEDO=.FALSE.,
- L_SSICE_ALBEDO=.TRUE.,
- L_SICE_MELTPONDS=.TRUE.,
- L_SICE_SCATTERING=.TRUE., 
- L_SICE_HADGEM1A=.TRUE.,
- A_SW_RADSTEP=6,
- A_LW_RADSTEP=6,
- L_RAD_DEG=.FALSE.,
- L_MOD_BARKER_ALBEDO=.TRUE.,
- L_USE_SPEC_SEA=.TRUE.,
- L_SICE_HEATFLUX=.TRUE.,
- L_MURK=.FALSE.,
- L_MURK_SOURCE=.FALSE.,
- L_MURK_ADVECT=.FALSE.,
- L_MURK_BDRY=.FALSE.,
- L_MURK_RAD=.FALSE.,
- L_BL_TRACER_MIX=.FALSE.,
- L_MICROPHY=.TRUE.,
- L_SULPC_SO2=.TRUE.,
- L_SOOT=.TRUE.,
- CALL_CHEM_FREQ=1,
- L_SO2_SURFEM=.TRUE.,
- L_SO2_HILEM=.TRUE.,
- L_SO2_NATEM=.TRUE.,
- L_SULPC_DMS=.TRUE.,
- L_DMS_EM=.TRUE.,
- L_DMS_EM_INTER=.TRUE.,
- L_DMS_OINTER=.FALSE.,
- L_DMS_Liss_Merlivat=.FALSE.,
- L_DMS_Wanninkhof=.TRUE.,
- L_DMS_Nightingale=.FALSE.,
- L_SULPC_OZONE=.TRUE.,
- L_SULPC_ONLINE_OXIDANTS=.FALSE.,
- L_SULPC_NH3=.TRUE.,
- L_USE_SULPC_DIRECT=.TRUE.,
- L_NH3_EM=.FALSE.,
- L_SULPC_SO2_O3_NONBUFFERED=.TRUE.,
- L_USE_SULPC_INDIRECT_SW=.TRUE.,
- L_USE_SULPC_INDIRECT_LW=.TRUE.,
- L_USE_SULPHATE_AUTOCONV=.TRUE.,
- L_USE_SULPHATE_SULPC=.TRUE.,
- L_USE_SEASALT_INDIRECT=.TRUE.,
- L_USE_SEASALT_AUTOCONV=.TRUE.,
- L_USE_SEASALT_SULPC=.TRUE.,
- L_USE_SEASALT_DIRECT=.TRUE.,
- L_SOOT_SUREM=.FALSE.,
- L_SOOT_HILEM=.TRUE.,
- L_USE_SOOT_DIRECT=.TRUE.,
- L_USE_SOOT_INDIRECT=.FALSE.,
- L_USE_SOOT_AUTOCONV=.FALSE.,
- L_USE_SOOT_SULPC=.FALSE.,
- L_BIOMASS=.TRUE.,
- L_BMASS_SUREM=.TRUE.,
- L_BMASS_HILEM=.TRUE.,
- L_USE_BMASS_DIRECT=.TRUE.,
- L_USE_BMASS_INDIRECT=.TRUE.,
- L_USE_BMASS_AUTOCONV=.TRUE.,
- L_USE_BMASS_SULPC=.TRUE.,
- L_USE_BIOGENIC=.TRUE.,
- L_USE_ARCLBIOM=.FALSE.,
- L_USE_ARCLBLCK=.FALSE.,
- L_USE_ARCLSSLT=.FALSE.,
- L_USE_ARCLSULP=.FALSE.,
- L_USE_ARCLDUST=.FALSE.,
- L_USE_ARCLOCFF=.FALSE.,
- L_USE_ARCLDLTA=.FALSE.,
- L_OCFF=.FALSE.,
- L_OCFF_SUREM=.FALSE.,
- L_OCFF_HILEM=.FALSE.,  
- L_USE_OCFF_DIRECT=.FALSE.,  
- L_USE_OCFF_INDIRECT=.FALSE.,  
- L_USE_OCFF_AUTOCONV=.FALSE.,
- L_USE_OCFF_SULPC=.FALSE., 
- L_DUST=.TRUE.,
- L_USE_DUST=.TRUE.,
- L_CAM_DUST=.FALSE.,
- L_USE_STOCHEM_CH4=.FALSE.,
- L_USE_STOCHEM_O3=.FALSE.,
- H_SWBANDS= 6,
- H_LWBANDS= 9,
- L_CLD_AREA=.TRUE.,
- L_ACF_CUSACK=.FALSE.,
- L_ACF_BROOKS=.TRUE., 
- L_PC2=.TRUE., 
- L_PC2_RESET=.FALSE.,
- l_pc2_diag_sh=.FALSE.,
- L_VINT_TP=.FALSE.,
- NPMSL_HEIGHT=500.00,
- L_EMCORR=.TRUE.,
- LMASS_CORR=.TRUE.,
- LQT_CORR=.FALSE.,
- LEMQ_PRINT=.TRUE.,
- A_ENERGYSTEPS=48,
- L_RHCPT=.TRUE.,
- L_AUTO_DEBIAS=.TRUE.,
- L_3D_CCA=.TRUE.,
- L_PHASE_LIM=.TRUE.,
- L_CO2_INTERACTIVE=.FALSE.,
- L_CO2_EMITS= .FALSE.,
- L_Q10= .TRUE.,
- L_VEG_FRACS=.TRUE.,
- L_TRIFFID=.FALSE.,
- L_PHENOL=.FALSE.,
- L_TRIF_EQ=.FALSE.,
- L_NRUN_MID_TRIF=.FALSE.,
- PHENOL_PERIOD=0,
- TRIFFID_PERIOD=0,
- L_DISTURB=.FALSE.,
- CAN_MODEL=3,
- L_CTILE=.TRUE.,
- A_ASSIM_MODE='AC',
- L_NEG_TSTAR=.FALSE.,
- problem_number=0,
- L_USE_METHOX=.FALSE.,
- L_UPPER_STRATQ=.FALSE.,
- L_GWD=.TRUE.,
- L_USE_USSP=.FALSE.,
- L_RIVERS=.TRUE.,
- L_INLAND=.TRUE., 
- RIVER_STEP=#REPL_RIVER_STEP,
- L_MCR_QCF2=.FALSE.,	
- L_MCR_QRAIN=.FALSE.,
- L_MCR_QGRAUP=.FALSE.,
- L_MCR_QCF2_LBC=.FALSE.,
- L_MCR_QRAIN_LBC=.FALSE.,
- L_MCR_QGRAUP_LBC=.FALSE., 
- L_PC2_LBC=.FALSE.,
- L_MURK_LBC=.FALSE., 
- L_int_uvw_lbc=.FALSE.,
- L_TOP= .FALSE.,
- L_PDM= .FALSE.,
- L_USE_TPPS_OZONE= .FALSE.,
- I_OZONE_INT= 5,
- L_RADIATION=.TRUE.,
- L_RAIN=.TRUE.,
- L_MR_PHYSICS1=.FALSE.,
- L_BL=.TRUE.,
- L_HYDROLOGY=.TRUE.,
- L_SOIL_SAT_DOWN=.TRUE.,
- l_anthrop_heat_src=.FALSE.,
- L_ICOUNT=.FALSE.,
- L_UKCA=.FALSE.,
- L_RADIANCE=.FALSE.,
- L_INHOM_CLOUD=.TRUE.,
- L_USE_OROG_CORR= .FALSE.,
- L_USE_GRAD_CORR= .FALSE.,
- L_USE_AOD= .TRUE.,
- L_USE_CLEARRH= .TRUE.,
- L_MOD_K_FLUX=.TRUE.,
- L_CTILE_FIX=.TRUE.,
- L_Wenyi=.TRUE.,
- L_CCRad= .FALSE.,
- L_3d_ccw=.FALSE.,
- L_USE_CARIOLLE=.FALSE.,
- L_USE_OZONEINRAD=.FALSE.,
- L_QUAD_SRC_FIX=.TRUE.,
- L_OASIS=.TRUE.,
- L_COUPLE_MASTER=REPLACE_L_CPL_M, 
- OASIS_COUPLE_FREQ=REPLACE_DT_CPL_AI,
- /
- ###END OF FILE###
diff --git a/atmosphere/INITHIS b/atmosphere/INITHIS
deleted file mode 100644
index f936f6a..0000000
--- a/atmosphere/INITHIS
+++ /dev/null
@@ -1,120 +0,0 @@
- &NLIHISTO 
- /
-
- &NLCHISTO
- RUN_RESUBMIT='Y', 
- RUN_RESUBMIT_Q='other',
- RUN_RESUBMIT_TIME='',
- RUN_RESUBMIT_CPU='400000',
- RUN_JOB_NAME='aiihc000',
- /
-
- &NLIHISTG 
- /
-
- &NLCHISTG 
- /
- 
- &NLCFILES
- BIOMASS= 'BIOMASS : $CMIP5ANCIL_AEROSOL/Bio_1850_ESM1.anc',
- SURGEOUT='SURGEOUT: $DATAW/$PREFIXW$RUNID.surgeout',
- PPSMC='PPSMC   : $DATAW/$PREFIXW$RUNID.ppsmc',
- WFOUT='WFOUT   : $DATAW/$PREFIXW$RUNID.wfout',
- HFLUXOUT='HFLUXOUT: $DATAW/$PREFIXW$RUNID.hfluxout',
- PMEOUT='PMEOUT  : $DATAW/$PREFIXW$RUNID.pmeout',
- ICEFOUT='ICEFOUT : $DATAW/$PREFIXW$RUNID.icefout',
- MOSOUT='MOSOUT  : $DATAW/$PREFIXW$RUNID.mosout',
- PPSCREEN='PPSCREEN: $DATAW/$PREFIXW$RUNID.ppscreen',
- SSTOUT='SSTOUT  : $DATAW/$PREFIXW$RUNID.sstout',
- SICEOUT='SICEOUT : $DATAW/$PREFIXW$RUNID.siceout',
- CURNTOUT='CURNTOUT: $DATAW/$PREFIXW$RUNID.curntout',
- FLXCROUT='FLXCROUT: $DATAW/$PREFIXW$RUNID.flxcrout',
- ATMANL='ATMANL  : $DATAW/$PREFIXW$RUNID.atmanl',
- OCNANL='OCNANL  : $DATAW/$PREFIXW$RUNID.ocnanl',
- ALABCOU1='ALABCOU1: $DATAW/$PREFIXW$RUNID.alabcou1',
- ALABCOU2='ALABCOU2: $DATAW/$PREFIXW$RUNID.alabcou2',
- ALABCOU3='ALABCOU3: $DATAW/$PREFIXW$RUNID.alabcou3',
- ALABCOU4='ALABCOU4: $DATAW/$PREFIXW$RUNID.alabcou4',
- ALABCOU5='ALABCOU5: $DATAW/$PREFIXW$RUNID.alabcou5',
- ALABCOU6='ALABCOU6: $DATAW/$PREFIXW$RUNID.alabcou6',
- ALABCOU7='ALABCOU7: $DATAW/$PREFIXW$RUNID.alabcou7',
- ALABCOU8='ALABCOU8: $DATAW/$PREFIXW$RUNID.alabcou8',
- OLABCOU1='OLABCOU1: $DATAW/$PREFIXW$RUNID.olabcou1',
- OLABCOU2='OLABCOU2: $DATAW/$PREFIXW$RUNID.olabcou2',
- OLABCOU3='OLABCOU3: $DATAW/$PREFIXW$RUNID.olabcou3',
- OLABCOU4='OLABCOU4: $DATAW/$PREFIXW$RUNID.olabcou4',
- WAVEOUT='WAVEOUT : $DATAW/$PREFIXW$RUNID.waveout',
- PPVAR='PPVAR   : $DATAW/$PREFIXW$RUNID.ppvar',
- PP0='PP0     : $DATAW/$PREFIXW$RUNID.pp0',
- PP1='PP1     : $DATAW/$PREFIXW$RUNID.pp1',
- PP2='PP2     : $DATAW/$PREFIXW$RUNID.pp2',
- PP3='PP3     : $DATAW/$PREFIXW$RUNID.pp3',
- PP4='PP4     : $DATAW/$PREFIXW$RUNID.pp4',
- PP5='PP5     : $DATAW/$PREFIXW$RUNID.pp5',
- PP6='PP6     : $DATAW/$PREFIXW$RUNID.pp6',
- PP7='PP7     : $DATAW/$PREFIXW$RUNID.pp7',
- PP8='PP8     : $DATAW/$PREFIXW$RUNID.pp8',
- PP9='PP9     : $DATAW/$PREFIXW$RUNID.pp9',
- PP10='PP10    : $DATAW/$PREFIXW$RUNID.pp10',
- WLABCOU1='WLABCOU1: $DATAW/$PREFIXW$RUNID.wlabcou1',
- WLABCOU2='WLABCOU2: $DATAW/$PREFIXW$RUNID.wlabcou2',
- WLABCOU3='WLABCOU3: $DATAW/$PREFIXW$RUNID.wlabcou3',
- WLABCOU4='WLABCOU4: $DATAW/$PREFIXW$RUNID.wlabcou4',
- AINITIAL='AINITIAL:                                 ', 
- ASTART=  'ASTART  : $DATAW/$RUNID.astart',
- VERT_LEV='VERT_LEV: $UMDIR/vn7.3/ctldata/vert/vertlevs_G3',
- ALABCIN1= 'ALABCIN1: $DATAW/alabcin',
- ALABCIN2='ALABCIN2:                                 ',
- TRANSP=  'TRANSP  : ',
- PERTURB= 'PERTURB : ',
- SWSPECTD='SWSPECTD: $ANCIL_ATMOS/spec3a_sw_hadgem1_6on',
- LWSPECTD='LWSPECTD: $ANCIL_ATMOS/spec3a_lw_hadgem1_6on',
- RPSEED='RPSEED:                                  ',
- OZONE= 'OZONE : $CMIP5ANCIL_AEROSOL/ozone_1850_ESM1.anc',
- SMCSNOWD= 'SMCSNOWD : $ANCIL_LAND/qrclim.smow',
- DSOILTMP= 'DSOILTMP : $ANCIL_LAND/qrclim.slt',
- SOILTYPE= 'SOILTYPE : $ANCIL_LAND/qrparm.soil_igbp_vg',
- VEGTYPE= 'VEGTYPE : ',
- SSTIN= 'SSTIN : $ANCIL_ATMOS/sst_amip2_7803_n96_v6.0',
- SICEIN= 'SICEIN : $ANCIL_ATMOS/sice_amip2_7803_n96_v6.0',
- CURNTIN= 'CURNTIN : ',
- MASK= 'MASK : $ANCIL_LAND/qrparm.mask',
- OROG= 'OROG : $ANCIL_LAND/qrparm.orog',
- SULPEMIS= 'SULPEMIS : $CMIP5ANCIL_AEROSOL/scycl_1850_ESM1_v4.anc',
- MURKFILE= 'MURKFILE : ',
- USRANCIL= 'USRANCIL : ',
- USRMULTI= 'USRMULTI : ',
- SO2NATEM= 'SO2NATEM : $ANCIL_ATMOS/VOLC_ND_N96_L38',
- CHEMOXID= 'CHEMOXID : $ANCIL_ATMOS/sulpc_oxidants_N96_L38',
- FRACINIT= 'FRACINIT : $ANCIL_LAND/qrparm.veg.frac_1860',
- VEGINIT= 'VEGINIT : $ANCIL_LAND/cable_vegfunc_N96.anc',
- DISTURB= 'DISTURB : ',
- SOOTEMIS= 'SOOTEMIS : $CMIP5ANCIL_AEROSOL/BC_hi_1850_ESM1.anc',
- CO2EMITS= 'CO2EMITS : ',
- TPPSOZON= 'TPPSOZON : $PRE_ANCIL_51/qrparm.lfrac',
- LANDFRAC= 'LANDFRAC : $ANCIL_LAND/qrparm.fracmask_n96_sn',
- DUSTSOIL= 'DUSTSOIL : $ANCIL_LAND/qrparm.soil.dust_igbp',
- DMSCONC= 'DMSCONC : $ANCIL_ATMOS/DMS_conc.N96',
- RIVSTOR= 'RIVSTOR : $ANCIL_ATMOS/riv_store_ancil.new2-c',
- RIVCHAN= 'RIVCHAN : $ANCIL_ATMOS/riv_seqdir_ancil.new2-c',
- RIVER2A= 'RIVER2A : ',
- SURFEMIS= 'SURFEMIS : /blankdir/surf_emiss/blankfile',
- AIRCREMS= 'AIRCREMS : /blankdir/air_emiss/blankfile',
- STRATEMS= 'STRATEMS : ',
- EXTRAEMS= 'EXTRAEMS : ',
- RADONEMS= 'RADONEMS : ',
- ARCLBIOG= 'ARCLBIOG : $ANCIL_ATMOS/biogenic_351sm.N96L38',
- ARCLBIOM= 'ARCLBIOM : ',
- ARCLBLCK= 'ARCLBLCK : ',
- ARCLSSLT= 'ARCLSSLT : ',
- ARCLSULP= 'ARCLSULP : ',
- ARCLDUST= 'ARCLDUST : ',
- ARCLOCFF= 'ARCLOCFF : ',
- ARCLDLTA= 'ARCLDLTA : ',
- CARIOLO3= 'CARIOLO3 : ',
- OCFFEMIS= 'OCFFEMIS : $CMIP5ANCIL_AEROSOL/OCFF_1850_ESM1.anc',
-NDEPFIL= 'NDEPFIL  : /g/data1a/p66/txz599/data/ancil/CMIP6/Ndep_1850_ESM1.anc',
- IDEALISE='IDEALISE: ',
- ICFILE=  'ICFILE  : ',
- /
- ### END OF FILE ###
diff --git a/atmosphere/PPCNTL b/atmosphere/PPCNTL
deleted file mode 100644
index e69de29..0000000
diff --git a/atmosphere/SIZES b/atmosphere/SIZES
deleted file mode 100644
index 3186370..0000000
--- a/atmosphere/SIZES
+++ /dev/null
@@ -1,81 +0,0 @@
-
- &NSUBMODL
- N_INTERNAL_MODEL=1,
- INTERNAL_MODEL_LIST= 1 ,
- SUBMODEL_FOR_IM= 1 ,
- /
-
- &NLSIZES
- PP_LEN_INTHD=46, PP_LEN_REALHD=38,
- CLOUD_LEVELS=38,
- LAND_FIELD=10865,
- MODEL_LEVELS=38, WET_LEVELS=38,
- global_ROW_LENGTH=192, global_ROWS=145,
- RIMWIDTHA=1, NRIM_TIMESA=1,
- TR_LEVELS=38,
- TR_VARS=2,
- N_INTF_A=0,
- ST_LEVELS=6,
- SM_LEVELS=6,
- BL_LEVELS=12,
- OZONE_LEVELS=38, 
- A_LEN_INTHD=46,
- A_LEN_REALHD=38,
- A_LEN2_LEVDEPC=8,
- A_LEN2_ROWDEPC=0,
- A_LEN2_COLDEPC=0,
- A_LEN2_FLDDEPC=0,
- A_LEN_EXTCNST=0, 
- NANCIL_LOOKUPSA=100000,
- THETA_PV_P_LEVS=18,
- NTILES=17,
- N_AOBS=0,
- A_LEN_CFI1=0,
- A_LEN_CFI2=0,
- A_LEN_CFI3=0,
- TR_UKCA=0,
- RIVER_ROW_LENGTH=360,
- RIVER_ROWS=180, 
- NICE=5,
- /
- &STSHCOMP
- RUN_TARGET_END=  0 , 0 , 1 , 0 , 0 , 0 ,
- OCAAA=1,
- INDEP_SR='1A','  ','  ','  ','  ','  ','  ','  ','  ',
- '  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','0A','  ','  ','  ','  ',
- '  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ',
- '  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ',
- '  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ',
- '  ','1A','1A','0A','  ','  ','  ','  ','  ','  ','  ','1A','  ','1A','  ',
- '1A','  ','  ','1A','  ','  ','  ','0A','2A','0A','1A','2A','1C','3A','  ',
- '0A',
- SWBND=6, LWBND=9,
- SWINC=8, LWINC=8,
- OROGR='Y',
- SWMCR='Y',
- ATMOS_SR='  ','3A','3A','8C','3D','4A','4A','  ','7A',
- '2A','2A','2A','2A','2A','1B','1A','1A','2B','0A','1A','1A','1A','1A','1A',
- '1A','0A','1A','  ','  ','  ','1A','0A','1A','1A','0A','0A','0A','0A','0A',
- '  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ',
- '  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ',
- '  ','1B','1A','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ','  ',
- '  ','  ','  ','0A',
- ZonAvOzone=.TRUE.,
- OCALB=1, 
- FLOOR='N', 
- TOTAE='N', TOTEM='N',
- TCA=2,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,
- TC_UKCA=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,
- SSTAnom='N',
- AOBINC= 0 ,
- AOBGRP= 0 ,
- /
-  ## End of file ##
diff --git a/atmosphere/exstat b/atmosphere/exstat
deleted file mode 100644
index e39f653..0000000
--- a/atmosphere/exstat
+++ /dev/null
@@ -1 +0,0 @@
-Failed in model executable
diff --git a/atmosphere/ftxx b/atmosphere/ftxx
deleted file mode 100644
index 8b13789..0000000
--- a/atmosphere/ftxx
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/atmosphere/ftxx.new b/atmosphere/ftxx.new
deleted file mode 100755
index 8b13789..0000000
--- a/atmosphere/ftxx.new
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/atmosphere/ftxx.vars b/atmosphere/ftxx.vars
deleted file mode 100755
index 8b13789..0000000
--- a/atmosphere/ftxx.vars
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/atmosphere/parexe b/atmosphere/parexe
deleted file mode 100644
index e69de29..0000000
diff --git a/atmosphere/prefix.CNTLATM b/atmosphere/prefix.CNTLATM
deleted file mode 100644
index 8b13789..0000000
--- a/atmosphere/prefix.CNTLATM
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/atmosphere/prefix.CNTLGEN b/atmosphere/prefix.CNTLGEN
deleted file mode 100644
index 219f2f5..0000000
--- a/atmosphere/prefix.CNTLGEN
+++ /dev/null
@@ -1,40 +0,0 @@
- &NLSTCGEN
- STEPS_PER_PERIODim=48,0,0,0,
- SECS_PER_PERIODim=86400,0,0,0,
- EXITFREQim=48,0,0,0,
- DUMPFREQim=-9999,0,0,0,
- ARCHDUMP_OFFSETim=0,0,0,0,
- ARCHDUMP_FREQim=0,0,0,0,
- DUMPTIMESim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- PPSELECTim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- PLOTSELim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- MEANWSim='N','N','N','N','N','N','N','N','N','N','N','N',
- 'N','N','N','N',
- ARCHPPSELim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- MEANARCHim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- MEANFREQim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- PRINTFREQim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- MEAN_REFTIMEim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- JOBREL_STEPim=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- DUMP_PACKim=3,0,0,0,
- PP_LEN2_MEANim=500000,500000,500000,500000,500000,500000,500000,500000,500000,500000,500000,500000,500000,500000,500000,500000,
- FT_MEANim=27,27,27,27,
- LLBOUTim=.FALSE.,
- /
- &NLST_MPP
- extended_halo_size_EW=4,
- extended_halo_size_NS=5,
- gcom_coll_limit=64,
- /
-
- &BOUNCNST
- BOUND_FIELDCODE=0,0,0,0,
- /
-
-
- !!! END OF FILE !!!
diff --git a/atmosphere/um_env.py b/atmosphere/um_env.py
deleted file mode 100644
index 86ca250..0000000
--- a/atmosphere/um_env.py
+++ /dev/null
@@ -1,52 +0,0 @@
-vars = {
-'AINITIAL': '',
-'ASTART': 'INPUT/pre-industrial.astart', 
-'AUSCOM_CPL': 'true',
-'DATAW': '{work_path}',
-'FASTRUN': 'true',
-'IDEALISE': '',
-'PAREXE': 'parexe',
-'PRINT_STATUS': 'PrStatus_Diag',
-'RPSEED': '',
-'RUNID': 'PI-01',
-'TYPE': 'NRUN',
-'UM_ATM_NPROCX': '16',
-'UM_ATM_NPROCY': '12',
-'UM_NAM_MAX_SECONDS': '300',
-'UM_NPES': '192',
-'UM_SECTOR_SIZE': '2048',
-'UM_STDOUT_FILE': 'atm.fort6.pe',
-'VN' : '7.3',
-
-# Config input paths
-'UNIT01': '',
-'UNIT02': 'prefix',
-'UNIT04': 'STASHC', 
-'UNIT05': 'namelists',
-'UNIT07': 'PI-01.out2',
-'UNIT08': '/dev/null',
-'UNIT09': 'CONTCNTL',
-'UNIT10': 'xhist',
-'UNIT11': 'ihist', 
-'UNIT12': 'thist',
-'UNIT14': 'errflag',
-'UNIT15': '',
-'UNIT58': '',
-'UNIT22': 'INPUT/STASHmaster',
-'UNIT57': 'INPUT/spec3a_sw_hadgem1_6on',
-'UNIT80': 'INPUT/spec3a_lw_hadgem1_6on',
-'STASETS_DIR': 'INPUT/stasets',
-'VERT_LEV': 'INPUT/vertlevs_G3',
-
-# Ancillary files
-'ARCLBIOG': 'INPUT/biogenic_351sm.N96L38',
-'BIOMASS': 'INPUT/Bio_1850_ESM1.anc',
-'CHEMOXID': 'INPUT/sulpc_oxidants_N96_L38',
-'DMSCONC': 'INPUT/DMS_conc.N96',
-'NDEPFIL': 'INPUT/Ndep_1850_ESM1.anc',
-'OCFFEMIS': 'INPUT/OCFF_1850_ESM1.anc',
-'OZONE': 'INPUT/ozone_1850_ESM1.anc',
-'SOOTEMIS': 'INPUT/BC_hi_1850_ESM1.anc',
-'SULPEMIS': 'INPUT/scycl_1850_ESM1_v4.anc',
-'VEGINIT': 'INPUT/cable_vegfunc_N96.anc',
-}
diff --git a/config.yaml b/config.yaml
index b7d02dc..e068ca0 100644
--- a/config.yaml
+++ b/config.yaml
@@ -1,16 +1,33 @@
+# A tutorial for running ACCESS ESM1.5 can be found at
+# https://access-hive.org.au/models/run-a-model/run-access-esm
+# Full details about the payu configuration settings are available at
+# https://payu.readthedocs.io/en/latest/config.html
+
+
+# PBS configuration
+
+# If submitting to a different project to your default, uncomment line below
+# and replace PROJECT_CODE with appropriate code. This may require setting shortpath
+# project: PROJECT_CODE
+
+# Force payu to always find, and save, files in this scratch project directory
+# shortpath: /scratch/PROJECT_CODE
+
+# Note: if laboratory is relative path, it is relative to shortpath/$USER
+laboratory: access-esm
+
 jobname: pre-industrial
 queue: normal
-walltime: 2:00:00
+walltime: 2:30:00
 
 # Modules for loading model executables
 modules:
   use:
-      - /g/data/vk83/modules/access-models/
+      - /g/data/vk83/modules/
   load:
       - access-esm1p5/2024.05.0
 
-# note: if laboratory is relative path, it is relative to /scratch/$PROJECT/$USER
-laboratory: access-esm
+# Model configuration
 model: access
 
 submodels:
@@ -94,6 +111,7 @@ submodels:
         - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/coupler/remapping_weights/global.oi_1deg.a_N96/2020.05.19/rmp_um1t_to_cice_CONSERV_FRACNNEI.nc
         - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/coupler/remapping_weights/global.oi_1deg.a_N96/2020.05.19/rmp_cice_to_um1v_CONSERV_FRACNNEI.nc
 
+# Collation
 collate:
     exe: mppnccombine.spack
     restart: true
@@ -102,6 +120,7 @@ collate:
 
 restart: /g/data/vk83/configurations/inputs/access-esm1p5/modern/pre-industrial/restart/
 
+# Timing controls
 calendar:
     start:
         year: 101
@@ -115,6 +134,29 @@ calendar:
 
 runspersub: 1
 
-stacksize: unlimited
+# Misc
+restart_freq: 10YS
+
+runlog: true
+manifest:
+  reproduce:
+    exe: True
+    
 
+stacksize: unlimited
 qsub_flags: -W umask=027
+
+
+# Sync options for automatically copying data from ephemeral scratch space to 
+# longer term storage
+sync:
+    enable: False # set path below and change to true
+    path: null # Set to location on /g/data or a remote server and path (rsync syntax)
+
+# If a postscript included (such as the automated netcdf conversion), the latest output and restart files will not 
+# be automatically synced at the end of a run. To sync the latest output after a postscript has completed,
+#  manually run `payu sync` from the command line.
+
+# userscripts:
+
+# postscript:
\ No newline at end of file