#! /usr/bin/env python
import os, sys, glob, shutil, fileinput, re, time, stat

from datetime import datetime

from os import path

import nmmbUsh

import produtil.setup, produtil.run, produtil.fileop, produtil.cd, produtil.batchsystem, produtil.numerics, produtil.config

from produtil.fileop import remove_file, make_symlink, chdir, fortlink, deliver_file, makedirs

from produtil.run import run, exe, runstr

from produtil.numerics import to_datetime, to_datetime_rel

import logging

from nmmbUsh import logger
					
produtil.setup.setup()

logger.info("relocate started")

workdir=os.environ.get('WORKhmon')
parmdir=os.environ.get('PARMhmon')
ushdir=os.environ.get('USHhmon')

conf=produtil.config.from_file(parmdir + "/hmon.conf")
conf.cycle=os.environ.get('CYCLE')
USE_MESSAGE=conf.get('config','use_message')
STORMLABEL=conf.get('config','stormlabel')
LABEL=STORMLABEL[5]
msgdir=conf.get('dir','COMmsg')
comdir=conf.get('dir','COM')
HISTDATA=conf.get('dir','HISTDATA')
fixdir=conf.get('dir','FIXhmon')
exedir=conf.get('dir','EXEChmon')
INPUT=conf.get('dir','COMgfs')

chdir(workdir, logger=logger)

############ GET THE INPUT VARIABLES AND EXPORT ENVIRONMENTAL VARIABLES ##############
with open(workdir + "/get_storm_info/storm_info", 'r') as f:
    for line in f:
        if "STORM_LAT=" in line:
            STORM_LAT = line.replace("STORM_LAT=", "")
            STORM_LAT = float(STORM_LAT)
        if "STORM_LON=" in line:
            STORM_LON = line.replace("STORM_LON=", "")
            STORM_LON = float(STORM_LON)
        if "CEN_LAT=" in line:
            CEN_LAT = line.replace("CEN_LAT=", "")
            CEN_LAT = float(CEN_LAT)
        if "CEN_LON=" in line:
            CEN_LON = line.replace("CEN_LON=", "")
            CEN_LON = float(CEN_LON)
        if "START_DATE=" in line:
           cycle = line.replace("START_DATE=", "")
           cycle = cycle.strip('\n')
        if "STORM_NAME=" in line:
           STORM_NAME = line.replace("STORM_NAME=", "")
           STORM_NAME = STORM_NAME.strip('\n')
        if "STORM_ID=" in line:
           storm_id = line.replace("STORM_ID=","")
           storm_id = storm_id.strip('\n')
        if "START_DATE06=" in line:
           cycle_m06= line.replace("START_DATE06=","")
           cycle_m06= cycle_m06.strip('\n')

astr = STORM_NAME
storm_name = astr.lower()
astr = storm_id
STORM_ID = astr.lower()

n_st=1
cdate=produtil.numerics.to_datetime(cycle)

logger.info("n_st = " + str(n_st))
logger.info("cdate = " + str(cdate))

yyyy=cdate.strftime("%Y")
cc=cdate.strftime("%C")
yy=cdate.strftime("%y")
mm=cdate.strftime("%m")
dd=cdate.strftime("%d")
hh=cdate.strftime("%H")
yymmdd=cdate.strftime("%y%m%d")
yyyymmdd=cdate.strftime("%Y%m%d")
yymmddhh=cdate.strftime("%y%m%d%H")
yyyymmddhh=cdate.strftime("%Y%m%d%H")

YEAR=yyyy
MONTH=mm
DATE=dd
CYCLE=hh

FHR=0

logger.info('YEAR = ' + str(YEAR))
logger.info('MONTH = ' + str(MONTH))
logger.info('DATE = ' + str(DATE))
logger.info('CYCLE = ' + str(CYCLE))
logger.info('storm_id = ' +  str(storm_id))

# export environent: #
MODEL='NMMB'
PARAFLAG='YES'
INIT='YES'
GSI='NO'
GSID01='NO'
GSID02='NO'
GSID03='NO'
innercoremerge='NO'
IO_FORM=1
FIND_GFS_VORTEX='NO'
FGATSTR=-3
FGATEND=3
FGATINV=3
MODIN='GFS'
CASE_ROOT='HISTORY'
DATA= workdir +"/reloc/" + yyyymmddhh + "/" + storm_id
ATMOS_INPUT = conf.get('dir','COMgfso')
atmos_d=comdir 

gfstrack="trak.gfso.atcfunix."+yyyymmddhh

if USE_MESSAGE=='YES':
    SYNDAT_CORRECTED= msgdir + "/message" + LABEL
else:
    SYNDAT_CORRECTED= conf.get('dir','syndat') + "/syndat_tcvitals." + yyyy

logger.info('SYNDAT_CORRECTED='+str(SYNDAT_CORRECTED))

############### Run Tracker for GFS data ################################################################
gfstrackdir = workdir + "/gfstrack"
nmmbUsh.removeall(gfstrackdir)
makedirs(gfstrackdir)
chdir(gfstrackdir)

stormHour =  yy + mm + dd + " " +  hh

lines_seen = set()
with open("vitals.gfso","w") as f:
    with open(SYNDAT_CORRECTED,"r") as myfile:
        for line in myfile.readlines():
            if re.search(stormHour, line) and re.search(storm_id, line) and re.search("NHC", line) and re.search(STORM_NAME, line):
                if line not in lines_seen:
                    lines_seen.add(line)
                    f.write(line)

if USE_MESSAGE == 'YES':
    for line in fileinput.FileInput("vitals.gfso",inplace=1):
        line = line.replace(yymmdd,yyyymmdd)
        print(line, end=' ')

produtil.fileop.deliver_file(parmdir + "/namelist.gfs.in", "namelist.gfs",logger=logger)

for line in fileinput.FileInput("namelist.gfs",inplace=1):
    line = line.replace("_BCC_",cc)
    line = line.replace("_BYY_",yy)
    line = line.replace("_BMM_",mm)
    line = line.replace("_BDD_",dd)
    line = line.replace("_BHH_",hh)
    line = line.replace("_YMDH_",cycle)
    print(line, end=' ')

FHR = 0
FHR3 = "%03d" %(FHR)

gfsfile = "gfs.t" + hh + "z.pgrb2.0p25.f" + FHR3
FileName= "../nps_ic/GRIBFILE.AAA"
make_symlink(FileName, gfsfile, True)
wgrib_s=runstr(exe(os.environ["WGRIB2"])['-s', gfsfile])
keep=''
for line in wgrib_s.splitlines():
    if re.search('(:HGT:850 mb:|:HGT:700 mb:|:UGRD:850 mb:|:UGRD:700 mb:|:UGRD:500 mb:|:VGRD:850 mb:|:VGRD:700 mb:|:VGRD:500 mb:|:ABSV:850 mb:|:ABSV:700 mb:|:MSLET:mean sea level:|:UGRD:10 m above ground:|:VGRD:10 m above ground:)',line):
        keep+=line+'\n'

gfile="gfsgribfile." + yyyy + mm + dd + hh
ixfile="gfsixfile." + yyyy + mm + dd + hh

produtil.run.checkrun(exe(os.environ["WGRIB2"])['-i', gfsfile, '-grib', gfile] << keep)

gbi=os.environ.get("GRB2INDEX")
cmd=exe(gbi)[gfile,ixfile]
produtil.run.run(cmd, logger=logger)

IFHR = 1
MINUTES = FHR * 60
LINE= "%4d %5d" % (IFHR, MINUTES)
LINE = LINE + "\n"
with open("fcst_minutes",'a') as f: f.write(LINE)

with open(gfstrack,"at"):pass

make_symlink(gfile, "fort.11", True)
make_symlink(ixfile, "fort.31", True)
make_symlink("vitals.gfso", "fort.12", True)
with open("fort.14","at"):pass
make_symlink("fcst_minutes", "fort.15", True)
make_symlink(gfstrack, "fort.64", True)


produtil.run.run(exe(exedir + "/hmon_unified_tracker")<"namelist.gfs", logger=logger)

if os.stat(gfstrack).st_size==0:
    logger.info("NO GFS storms")
    produtil.fileop.deliver_file(atmos_d+"/" + storm_name + STORM_ID + "." + cycle + "." + "input_domain_01_nemsio_nps",atmos_d+"/" + storm_name + STORM_ID + "." + cycle + "." + "input_domain_01_nemsio",logger=logger)
    produtil.fileop.deliver_file(atmos_d+"/" + storm_name + STORM_ID + "." + cycle + "." + "input_domain_02_nemsio_nps",atmos_d+"/" + storm_name + STORM_ID + "." + cycle + "." + "input_domain_02_nemsio",logger=logger)
    produtil.fileop.deliver_file(atmos_d+"/" + storm_name + STORM_ID + "." + cycle + "." + "input_domain_03_nemsio_nps",atmos_d+"/" + storm_name + STORM_ID + "." + cycle + "." + "input_domain_03_nemsio",logger=logger)
    sys.exit(0)

#########################################################################################################

data_tmp = comdir
datadir = DATA 

nmmbUsh.removeall(DATA)
makedirs(DATA)
chdir(DATA)

##############################################################################

now=datetime.utcnow()
logger.info(now.strftime("%Y-%m-%d %H:%M"))

INIT='YES'
if INIT == 'NO':
    sys.exit("Initialization not requested.  INIT = NO This script need not be run")
 
logger.info("VORTEX RELOCATION BEGINS")

storm_n=str(storm_id)[0:2]
basin=str(storm_id)[2:3] 

if basin == 'L' or basin == 'l': 
    basin='AL'
elif basin == 'E' or basin == 'e' :
    basin='EP'
else:
    logger.info("add basin parameters")

logger.info('basin=' + str(basin))

n_st2 = n_st * 2
n_st3 = n_st2 + 1

logger.info("n_st2 = " + str(n_st2))
logger.info("n_st3 = " + str(n_st3))

logger.info("Runs the hmon_diffwrf_3dvar program to update the output  domains.")

stormHour =  yy + mm + dd + " " +  hh

with open("tmpvit","w") as f:
    with open(SYNDAT_CORRECTED,"r") as myfile:
        for line in myfile.readlines():
            if re.search(stormHour, line) and re.search(storm_id, line) and re.search("NHC", line) and re.search(STORM_NAME, line):
                f.write(line)

if USE_MESSAGE == 'YES':
    for line in fileinput.FileInput("tmpvit",inplace=1):
        line = line.replace(yymmdd,yyyymmdd)
        print(line, end=' ')


numvit = sum(1 for line in open(path.join(DATA,"tmpvit")))

if numvit == 0:
    logger.info("!!! ERROR: No vitals for storm_id  = ---> $storm_id  <---\n !!! and yymmddhh = ---> ${PDY}${cyc} <---\n            was found in the tcvitals archive....")
    sys.exit(98)
else:
    logger.info("Vitals record for requested run follows....")
    with open(DATA+"/tmpvit", 'r') as fin:
        logger.info(fin.read())
    logger.info(DATA)
	
    deliver_file(path.join(DATA,"tmpvit"), path.join(datadir,"message1"),logger=logger)	
	
    with open(datadir + "/nestnum",'w+') as f: f.write("3")
    with open(datadir + "/nstorms",'w+') as f: f.write("1")
    with open(datadir + "/stormdate",'w+') as f: f.write(yymmddhh)

logger.info(os.getcwd())
deliver_file(path.join(DATA,"tmpvit"), "./tcvitals.as",logger=logger)
with open("tmpvit", 'r') as fin:
    logger.info(fin.read())
 
with open("tcvitals.as", 'r') as f:
    name = f.readline().split()
    STORM_NAME = name[2]

with open("./tcvitals.as", 'r') as fin:
    STORM_INT = str(fin.read())[67:69]
 
with open("./tcvitals.as", 'r') as fin:
    STORM_DEPTH = str(fin.read())[94:95]

logger.info('STORM_NAME='+str(STORM_NAME))
logger.info('STORM_INT='+str(STORM_INT))
logger.info('STORM_DEPTH='+str(STORM_DEPTH))

stormid=storm_id

storm_name=STORM_NAME.lower()
STORM_ID=storm_id.lower()

# CENLA and CENLO are the parent domain center lat/lon (in degrees)

CENLA=CEN_LAT
CENLO=CEN_LON


with open(datadir+"/domain.center","w+") as f: 
    f.write(str(CENLA)+"\n"+str(CENLO))

deliver_file(datadir+"/domain.center", path.join(DATA, storm_id+"." + yyyy + mm + dd + CYCLE+".domain.center"),logger=logger)
storm=STORM_NAME
CLAT=CENLA
CLON=CENLO

############### vortex initialization options ##################
initopt=0
############### vortex initialization options ##################

##################### cold start TC vortex #####################
if MODIN == "GFS":
    coldvortex="GFS"
else:
    if GSID02 == "YES" or GSID03 == "YES":
        coldvortex="GDAS"
    else:
        coldvortex="HDAS"
   
##################### cold start TC vortex #####################

################## relocation success flags ####################

# The script must set these before exiting to indicate a warm or cold
# start, or to veto cycling.

# $warm_cold_flag: set to "warm" for a warm start or "cold" for a cold
# start.  All other values are invalid.

warm_cold_flag="unknown"

# $cold_ok: set to "yes" to intentionally veto cycling (such as for a
# weak storm).  Set to "no" if this is a cold start due to missing or
# erroneous data (such as a missing wrfout file or an incomplete
# track).
cold_ok="no"

################## relocation success flags ####################
# Control settings

if FHR > 0:
    FGATH = FHR - 6
    gesfhr_fgat = FHR
else:
    FGATH = 0	
    gesfhr_fgat = 6

gdate=produtil.numerics.to_datetime_rel(6*-3600, yyyymmddhh)
gm=gdate.strftime("%m")
gd=gdate.strftime("%d")
gh=gdate.strftime("%H")

fdate=produtil.numerics.to_datetime_rel(FGATH*3600, yyyymmddhh)

yyyy=fdate.strftime("%Y")
yy=fdate.strftime("%y")
im=fdate.strftime("%m")
id=fdate.strftime("%d")
ih=fdate.strftime("%H")

edate=produtil.numerics.to_datetime_rel(FGATEND*3600, yyyymmddhh)
ime=edate.strftime("%m")
ide=edate.strftime("%d")
ihe=edate.strftime("%H")

domdir=datadir

VIT=path.join(DATA,"tmpvit")
logger.info(DATA)
logger.info(VIT)

logger.info("yyyy = " + str(yyyy))
logger.info("yy   = " + str(yy))
logger.info("im   = " + str(im))
logger.info("ih   = " + str(ih))

# Set paths for runtime and save directories
if FHR > 0:
    tmpdir = path.join(DATA, "3DVAR/nmmb_rel", storm+ "." + fdate)
    savdir = path.join(DATA, storm + "."+ yyyymmddhh, "gdas1.f"+fdate)
else:
    tmpdir = path.join(DATA, "hwrf_rel", storm + "." + yyyymmddhh)
    savdir = path.join(DATA, storm + "." + yyyymmddhh, "ATMOS")

vitdir=ATMOS_INPUT

if not(path.isdir(savdir)):
    makedirs(savdir)

# Set up directories
nmmbUsh.removeall(tmpdir)
makedirs(tmpdir)
chdir(tmpdir)

#find corresponding stormid from previous cycle:
prev_date=produtil.numerics.to_datetime_rel(6*-3600, yyyymmddhh)
prev_stormid=stormid

if PARAFLAG == "YES":
    k = HISTDATA.rfind(".")
    HISTDATA_base = HISTDATA[:k]
	 
#Specify fixed field and data directories.
testf_d1=path.join(HISTDATA,storm_id + "." + cycle_m06 + "." + "nmmb_hst_01_nio_0006h_00m_00.00s")   # 6h earlier forecast
testf_d2=path.join(HISTDATA,storm_id + "." + cycle_m06 + "." + "nmmb_hst_0" + str(n_st2) + "_nio_0006h_00m_00.00s")   # 6h earlier forecast
testf_d3=path.join(HISTDATA,storm_id + "." + cycle_m06 + "." + "nmmb_hst_0" + str(n_st3) + "_nio_0006h_00m_00.00s")  # 6h earlier forecast

if PARAFLAG == "YES":
    wait_time=5400 # wait 1.5 hours due to queue wait times
elif not(path.isfile(testf_d1)):
# cold start waitting time
    wait_time=2400
else:
# warm start waitting time
    wait_time=1200

# check if the HWRF forecast at the end of the FGAT window is available
tmp1 = FGATSTR + 6
tmp2 = FGATEND + 6
gesstr_fgat = FGATSTR + 6
gesend_fgat = FGATEND + 6

#teste_d1=testf_d1

if IO_FORM != 2 and GSID02 == "YES": 
    deliver_file(path.join(savdir,"/log-anl/namelist.input"), "./namelist_analysis0.input",logger=logger)
    deliver_file("./namelist_analysis0.input", "./namelist.input",logger=logger)

iflag_cold=0

if not ((path.isfile(testf_d1) and path.getsize(testf_d1)>0)) :
    iflag_cold=1
    logger.info("Previous " + str(gesfhr_fgat) + " hour forecast is not located at " + str(testf_d1))
    logger.info("This is a cold start. " + str(coldvortex) + " vortex will be used as first guess")
    logger.info("This script will contnue from step 2 onwards")
    warm_cold_flag="cold"
elif FGATEND > FGATSTR and not(path.isfile(testf_d1) and path.getsize(testf_d1)>0) :
    iflag_cold=1
    logger.info("Previous " + str(gesend_fgat) + " hour forecast is not located at " + str(teste_d1))
    logger.info("Previous " + str(gesstr_fgat) + " to " + str(gesend_fgat) + " hours forecast")
    logger.info("with " + str(FGATINV) + " hourly output are needed for FGAT")
    logger.info("This is a cold start due to HWRF forecast storm being weak")
    logger.info("This is a cold start. " + str(coldvortex) + " vortex will be used as first guess")
    logger.info("This script will contnue from step 2 onwards")
    warm_cold_flag="cold"
    cold_ok="yes"
else:
# script will run to end of script 
    st_int = STORM_INT
    st_depth = STORM_DEPTH
    logger.info("relocate line 469")
    logger.info("st_int=" + str(st_int))
    logger.info("st_depth=" + str(st_depth))
	
    if st_depth == 'S' and int(st_int) < 14:
        iflag_cold=1
        logger.info("Previous " + str(gesfhr_fgat) + " hour forecast is located at " + testf_d1)
        logger.info("storm is a shallow and weak storm")
        logger.info(str(st_int))
        logger.info(str(st_depth))
        logger.info("This is a cold start. " + str(coldvortex) + " vortex will be used as first guess")
        logger.info("This script will contnue from step 2 onwards")
        warm_cold_flag="cold"
        cold_ok="yes"
    elif int(st_int) < 14:
        iflag_cold=1
        logger.info( "Previous " + str(gesfhr_fgat) + " hour forecast is located at " + testf_d1)
        logger.info("storm is a weak storm, max wind speed < 14 m/s")
        logger.info(str(st_int))
        logger.info(str(st_depth))
        logger.info("This is a cold start" + str(coldvortex) + " vortex will be used as first guess")
        logger.info("This script will contnue from step 2 onwards")
        warm_cold_flag="cold"
        cold_ok="yes"
    else:
        logger.info( "Previous " + str(gesfhr_fgat) + " hour forecast is located at " + testf_d1)
        logger.info("This is not a cold start")
        logger.info("The script nmmb_relocate.sh will continue")
        warm_cold_flag="warm"
        
# Copy executables to $tmpdir
        deliver_file(path.join(exedir,"hmon_diffwrf_3dvar"),          "./hmon_diffwrf_3dvar.exe",logger=logger)
        deliver_file(path.join(exedir,"hmon_nemsio"),         "./nems_bin_io.exe",logger=logger)
        deliver_file(path.join(exedir,"hmon_merge_nest_4x_step12_3n"),"./merge_nest_4x_step12_3n.x",logger=logger)
        deliver_file(path.join(exedir,"hmon_split1"),                 "./wrf_split.x",logger=logger)
        deliver_file(path.join(exedir,"hmon_create_trak_guess"),      "./create_trak_guess.x",logger=logger)
        deliver_file(path.join(exedir,"hmon_pert_ct1"),               "./hmon_pert_ct.x",logger=logger)

        deliver_file(VIT, "./tmpvit",logger=logger)
        

        with open ("./tmpvit", "r") as myfile:
            for line in myfile.readlines():
                if re.search(storm_id, line, re.IGNORECASE):
                    f = open("./tcvitals.as", 'w')
                    f.write(line)
                    f.close()

        if not (path.isfile("tcvitals.as") and path.getsize("tcvitals.as")>0) :
            logger.info("tcvitals file is missing - check the path names and the status of GFS forecast run")
    
        st_int=STORM_INT
        logger.info("relocate line 521")
        logger.info("st_int=" + str(st_int))

        deliver_file(testf_d1, "./wrfout_d01",logger=logger)
        deliver_file(testf_d2, "./wrfout_d02",logger=logger)

        if path.isfile(testf_d3):	
            deliver_file(testf_d3,"./wrfout_d03",logger=logger)
        
        if IO_FORM == 2:
            nmmbUsh.relocate_storm(logger, 1)
        else:
            nmmbUsh.nems_relocate(logger, 4, "wrfout", "old_hwrf", 1)

        if IO_FORM == 2:
            nmmbUsh.relocate_storm(logger, 2)
            if path.isfile(testf_d3):
                nmmbUsh.relocate_storm(logger, 3)
        else:
            nmmbUsh.nems_relocate(logger, 5, "wrfout", "old_hwrf", 2)
            if path.isfile(testf_d3):
                nmmbUsh.nems_relocate(logger, 6,"wrfout", "old_hwrf", 3)
				
# correct data, regenerate inner nest data,test only
        remove_file(path.join(tmpdir,"roughness"))
        remove_file(path.join(tmpdir,"roughness1"))
        remove_file(path.join(tmpdir,"storm_pert_new"))

        nmmbUsh.delete_file("fort.*")

        produtil.fileop.fortlink({11: path.join(tmpdir, "tcvitals.as"),
                                  26: path.join(tmpdir, "old_hwrf_d01"),
                                  36: path.join(tmpdir, "old_hwrf_d02"),
                                  46: path.join(tmpdir, "old_hwrf_d03"),
                                  56: path.join(tmpdir, "data_4x_hwrf"),
                                  66: path.join(tmpdir, "roughness1"),
                                  61: path.join(tmpdir, "30_degree_data")},logger=logger,force=True)

        gesfhr=6
        ibgs=0
        nmmbUsh.hmon_pgm(logger, path.join(tmpdir,"merge_nest_4x_step12_3n.x"), 6, st_int, ibgs, CLAT, CLON, MODEL)
        nmmbUsh.delete_file("fort.*")
	
        if int(st_int) > 10:	
            deliver_file(HISTDATA + "/" + storm_id + "." + yyyy + gm + gd + gh +".trak.hmon.atcfunix" ,  path.join(tmpdir, "hdas_atcfunix"),logger=logger) 
        else:
            deliver_file(HISTDATA + "/" + storm_id + "." + yyyy + gm + gd + gh  +".trak.hmon.atcfunix" ,  path.join(tmpdir, "hdas_atcfunix"),logger=logger) 
	
        produtil.fileop.fortlink({11: path.join(tmpdir, "tcvitals.as")}, logger=logger, force=True)
        if stormid == prev_stormid:
            produtil.fileop.fortlink({12: path.join(tmpdir, "hdas_atcfunix")}, logger=logger, force=True)
        else:
            storm_idnum=str(stormid)[0:2]
            prev_storm_idnum=str(prev_stormid)[0:2]
            deliver_file(path.join(tmpdir, "hdas_atcfunix"), "fort.12",logger=logger)
            for line in fileinput.FileInput(f, inplace=1):
                line = line.replace(basin+", "+prev_storm_idnum, basin+", "+storm_idnum)
                print(line, end=' ')


        make_symlink(path.join(tmpdir,"trak.fnl.all"), "fort.30", True)
        produtil.fileop.fortlink({30: path.join(tmpdir,"trak.fnl.all")}, logger=logger, force=True)

        if FGATEND > FGATSTR:
            fhr=3
            while fhr < gesend_fgat:
                fhr00="%03d" % (fhr)
                with open (path.join(tmpdir, "hdas_atcfunix"), "r") as myfile:
                    gesfhrx = 0
                    for line in myfile.readlines():
                        if re.search("HMON, " + fhr00, line):        	                	
                            gesfhrx = gesfhrx +1
                if gesfhrx < 1:
                    fhr=999
                else:
                    fhr=fhr + FGATINV
        else:
            fhr00="%03d" % (gesfhr_fgat)
            with open (path.join(tmpdir , "hdas_atcfunix"), "r") as myfile:
                gesfhrx = 0
                for line in myfile.readlines():
                    if re.search("HMON, " + fhr00, line):        	                	
                        gesfhrx = gesfhrx +1
        if gesfhrx < 1:
            logger.info("There is no " + str(fhr00) + " Forecast Position from previous cycle")
            logger.info("create_trak_guess.x can not continue with relocation")
            logger.info("This is a cold start")
            warm_cold_flag="cold"
            cold_ok="yes"
        else:
            nmmbUsh.hmon_pgm(logger, path.join(tmpdir,"create_trak_guess.x"), storm_id, str(hh))

            nmmbUsh.delete_file("fort.*")
            produtil.fileop.fortlink({11: path.join(tmpdir,"tcvitals.as"),
                                      26: path.join(tmpdir,"data_4x_hwrf"),
                                      30: path.join(tmpdir, "trak.fnl.all"),
                                      46: path.join(tmpdir,"old_hwrf_d01"),
                                      56: path.join(tmpdir,"wrf_env"),
                                      52: path.join(tmpdir,"rel_inform." + yyyymmddhh),
                                      55: path.join(tmpdir,"vital_syn." + yyyymmddhh),
                                      71: path.join(tmpdir,"storm_pert"),
                                      85: path.join(tmpdir,"storm_radius")}, logger=logger, force=True)

            nmmbUsh.hmon_pgm(logger, path.join(tmpdir, "wrf_split.x"), str(gesfhr_fgat), str(ibgs), str(st_int), str(iflag_cold))
			
            nmmbUsh.delete_file("fort.*")

            produtil.fileop.fortlink({11: path.join(tmpdir,"tcvitals.as"),
                                      26: path.join(tmpdir,"wrf_env"),
                                      46: path.join(tmpdir,"roughness1"),
                                      71: path.join(tmpdir,"storm_pert"),
                                      58: path.join(tmpdir,"storm_pert_new"),
                                      14: path.join(tmpdir,"storm_size_p"),
                                      23: path.join(tmpdir,"storm_sym"),
                                      65: path.join(tmpdir,"storm_radius"),
                                      35: path.join(tmpdir,"storm_pert_step1_1")}, logger=logger, force=True)
        
            nmmbUsh.hmon_pgm(logger, path.join(tmpdir, 'hmon_pert_ct.x'), gesfhr)

            nmmbUsh.delete_file("fort.*")

            logger.info("continue bogussing the storm in step2. This is not a cold start")
#step2
if CASE_ROOT == "FORECAST":
# check dependencies
    if GSID01 == "YES"  and GSID02 == "NO" and GSID03 == "NO":
        WAIT_INFILE=DATA+ "/3DVAR/outreg/nmm_netcdf/gsi_cvs1." + storm + "." + yyyymmddhh + "/wrfanl." + yyyymmddhh 
        minsize=100000000
    else:
        WAIT_INFILE=savdir + "/ghost_d03_0000-00-00_00:00:00"
        minsize=1000000000

    if produtil.fileop.wait_for_files([WAIT_INFILE],logger,maxwait=wait_time):
        sys.exit("timed out waiting for " + WAIT_INFILE)
        sys.exit("2")

if not (path.isdir(tmpdir)):
    makedirs(tmpdir)

chdir(tmpdir)

# Copy the fixed file to $tmpdir 
deliver_file(path.join(exedir,"hmon_pert_ct1"), "./hmon_pert_ct.x",logger=logger)
# Copy executable files to $tmpdir
deliver_file(path.join(exedir,"hmon_diffwrf_3dvar"), "./hmon_diffwrf_3dvar.exe",logger=logger)
deliver_file(path.join(exedir,"hmon_nemsio"), "./nems_bin_io.exe",logger=logger)
deliver_file(path.join(exedir,"hmon_split1"), "./wrf_split.x",logger=logger)
deliver_file(path.join(exedir,"hmon_merge_nest_4x_step12_3n"), "./merge_nest_4x_step12_3n.x",logger=logger)
deliver_file(path.join(exedir,"hmon_anl_bogus_10m"), "./hmon_anl_bogus_10m.x",logger=logger)
deliver_file(path.join(exedir,"hmon_anl_cs_10m"), "./hmon_anl_cs_10m.x",logger=logger)
deliver_file(path.join(exedir,"hmon_anl_4x_step2"), "./hmon_anl_4x_step2.x",logger=logger)
deliver_file(path.join(exedir,"hmon_inter_2to2"), "./hmon_inter_2to2.x",logger=logger)
deliver_file(path.join(exedir,"hmon_inter_4to6"), "./hmon_inter_4to6.x",logger=logger)
deliver_file(path.join(exedir,"hmon_create_trak_fnl"), "./create_trak_fnl.x",logger=logger)

if MODEL == "HWRF":
# Copy wrfnmm restart files
    if GSID01 == "YES" and GSID02 == "NO" and GSID03 == "NO":
        infile_d01=DATA + "/3DVAR/outreg/nmm_netcdf/gsi_cvs1." + storm + "." + yyyymmddhh + "/wrfanl." + yyyymmddhh
    else:
        infile_d01=savdir + "/wrfinput_d01"

    for waitfile in [infile_d01, savdir+"/wrfanl_d02_" + yyyy + "-" + im + "-" + id + "_" + ih + ":00:00", savdir + "/wrfanl_d03_" + yyyy + "-" + im + "-" + id + "_" + ih + ":00:00"]  :
        if produtil.fileop.wait_for_files([waitfile],logger,maxwait=wait_time): 
            logger.info("timed out waiting for " + str(waitfile))
            sys.exit(2)

    if GSID02 == "YES":
        waitfile=savdir+"/ghost_d02_0000-00-00_00:00:00"
        if produtil.fileop.wait_for_files([waitfile],logger,maxwait=wait_time):
            logger.info("timed out waiting for " + str(waitfile))
            sys.exit(2)

    if GSID03 == "YES":
        waitfile=savdir+"/ghost_d03_0000-00-00_00:00:00"
        if produtil.fileop.wait_for_files([waitfile],logger,maxwait=wait_time):
            logger.info("timed out waiting for " + str(waitfile))
            sys.exit(2)
    deliver_file(infile_d01, "./wrfinput_d01",logger=logger)
    deliver_file(savdir+"/wrfanl_d02_" + yyyy + "-" + im + "-" + id + "_" + ih + ":00:00", "./wrfinput_d02",logger=logger)
    deliver_file(savdir+"/wrfanl_d03_" + yyyy + "-" + im + "-" + id + "_" + ih + ":00:00", "./wrfinput_d03",logger=logger)

testf1_d1=data_tmp + "/" + storm_name + STORM_ID + "." + cycle + "." + "input_domain_01_nemsio_nps"   # GFS analysis
testf1_d2=data_tmp + "/" + storm_name + STORM_ID + "." + cycle + "." + "input_domain_02_nemsio_nps"   # GFS analysis
testf1_d3=data_tmp + "/" + storm_name + STORM_ID + "." + cycle + "." + "input_domain_03_nemsio_nps"   # GFS analysis

deliver_file(testf1_d1, "./wrfinput_d01",logger=logger)
deliver_file(testf1_d2, "./wrfinput_d02",logger=logger)
deliver_file(testf1_d3, "./wrfinput_d03",logger=logger)

if GSID02 == "YES":
    deliver_file(path.join(savdir,"/ghost_d02_0000-00-00_00:00:00"), "./wrfghost_d02",logger=logger)

if GSID03 == "YES":
    deliver_file(path.join(savdir,"/ghost_d03_0000-00-00_00:00:00"), "./wrfghost_d03",logger=logger)


deliver_file(VIT, "./tmpvit",logger=logger)
with open ("./tmpvit", "r") as myfile:
    for line in myfile.readlines():
        if re.search(storm_id, line, re.IGNORECASE):
            deliver_file("./tmpvit", "./tcvitals.as",logger=logger)			
	

#with open ("tcvitals.as", "r") as myfile:
#    for line in myfile.readlines():
#        st_int = str(line)[67:69]

with open("tcvitals.as", 'r') as myfile:
    st_int = str(myfile.read())[67:69]
    logger.info("relocate line 731")
    logger.info("st_int=" + str(st_int))


domain_test=domdir+"/domain.center"

if path.isfile(domain_test):
    deliver_file(domdir+"/domain.center" , tmpdir + "/domain.center",logger=logger)
else:
    logger.info("Domain Center at " + str(domain_test) + " does not exist")
    logger.info("Check the directory " + str(domdir)+ " =  provide domain.center")
    looger.info("And run this script again.  Now exiting")       
    err=911
    sys.exit("Domain Center at " + domain + "_test does not exist")


if IO_FORM == 2:
    nmmbUsh.relocate_storm(logger,1)
else:
    nmmbUsh.nems_relocate(logger, 1,"wrfinput", "new_gfs", 1)
   

if IO_FORM == 2:
    nmmbUsh.relocate_storm(logger, 2)
    nmmbUsh.relocate_storm(logger, 3)
else:
    nmmbUsh.nems_relocate(logger, 2,"wrfinput", "new_gfs", 2)
    nmmbUsh.nems_relocate(logger, 3,"wrfinput", "new_gfs", 3)



if IO_FORM != 2 and GSID02 == 'YES':
    nmmbUsh.deliver_file(savdir+"/log-ghost/namelist.input", "./namelist_ghost.input",logger=logger)

if GSID02 == "YES":
    if IO_FORM == 2:
        nmmbUsh.relocate_storm(logger, 2) #run ./hmon_diffwrf_3dvar.exe" for d02
    else:
        deliver_file("./namelist_ghost.input", "./namelist.input",logger=logger)
        with open("itag3",'w'):
            f.write(tmpdir="\n")
            f.write("wrfghost_d02\n")
            f.write("relocate\n")
            f.write(path.join(tmpdir,"new_ght_d02\n"))
            f.write(path.join(tmpdir,"domain.center\n"))

    nmmbUsh.nems_relocate(logger, 3, "wrfghost", "relocate", 2)  
	
if GSID03 == "YES":
    if IO_FORM == 2:
        nmmbUsh.relocate_storm(logger, 3) #run ./hmon_diffwrf_3dvar.exe" for d03
    else:
        deliver_file("./namelist_ghost.input", "./namelist.input",logger=logger)
        with open("itag3",'w'):
            f.write(tmpdir="\n")
            f.write("wrfghost_d03\n")
            f.write("relocate\n")
            f.write(path.join(tmpdir,"new_ght_d03\n"))
            f.write(path.join(tmpdir,"domain.center\n"))
        nmmbUsh.nems_relocate(logger, 3, "wrfghost", "relocate", 3)

# correct data, regenerate inner nest data

nmmbUsh.delete_file("fort.*")

if FIND_GFS_VORTEX != "NO":
# Use HWRF scripts to find the GFS track, done in hwrf_gfs_track0 job:
    track0file=savdir = "/gfs-anl.atcfunix"

# Wait for the file to exist.  In NCO mode, the file already should exist
# since the job is run in parallel with the dummy job, but takes less
# time.  Just in case, we wait up to 5 minutes here in NCO mode.
# In non-NCO mode, we wait a half hour to allow jobs to run out of order.
    naptime=1800
	
    if not produtil.fileop.wait_for_files([track0file],logger,maxwait=naptime):
# The file did not exist.
        if PARAFLAG == "YES":
            sys.exit("timed out waiting for ", track0file)
        else:
            logger.info("Time out waiting for" + str(track0file) + ":will use tcvitals for the vortex relocation instead.")
            cmd=exe("./atcfunix") # create an empty track file
            produtil.run.checkrun(cmd, logger=logger)
    else:
        if not (path.isfile("tcvitals.as") and path.getsize("tcvitals.as")>0) :
            logger.info("Track file is empty; will use tcvitals instead: " + str(track0file))        
            deliver_file(track0file, "./atcfunix",logger=logger)
else:
# Use GFS track file 
    #nmmbUsh.grep_file(yyyymmddhh, ATMOS_INPUT+"/gfso.t"+CYCLE+"z.cyclone.trackatcfunix", "./tmp11", re.IGNORECASE)
    nmmbUsh.grep_file(yyyymmddhh, gfstrackdir+"/trak.gfso.atcfunix."+yyyymmddhh, "./tmp11", re.IGNORECASE)
    nmmbUsh.grep_file(basin, "./tmp11", "./tmp12", re.IGNORECASE)
    nmmbUsh.grep_file("GFSO|PRE1|PRD1", "./tmp12", "./atcfunix", re.IGNORECASE)

produtil.fileop.fortlink({11: path.join(tmpdir,"tcvitals.as"),
                          12: path.join(tmpdir,"atcfunix"),
                          30: path.join(tmpdir,"trak.fnl.all_gfs")}, logger=logger, force=True)

# run the executable create_trak_fnl.x
nmmbUsh.hmon_pgm(logger, path.join(tmpdir, "create_trak_fnl.x"), storm_id, yyyy, basin)

remove_file(path.join(tmpdir,"roughness"))
remove_file(path.join(tmpdir,"roughness2"))

nmmbUsh.delete_file("fort*")

produtil.fileop.fortlink({11: path.join(tmpdir,"tcvitals.as"),
                          26: path.join(tmpdir,"new_gfs_d01"),
                          36: path.join(tmpdir,"new_gfs_d02"),
                          46: path.join(tmpdir,"new_gfs_d03"),
                          56: path.join(tmpdir,"data_4x_gfs"),
                          66: path.join(tmpdir,"roughness2")}, logger=logger, force=True)

gesfhr=6
ibgs=1
vobs=0

nmmbUsh.hmon_pgm(logger, path.join(tmpdir,"merge_nest_4x_step12_3n.x"), gesfhr,  vobs, ibgs , CLAT , CLON ,  MODEL )

nmmbUsh.delete_file("fort.*")

produtil.fileop.fortlink({11: path.join(tmpdir,"tcvitals.as"),
                          26: path.join(tmpdir,"data_4x_gfs"),
                          30: path.join(tmpdir,"trak.fnl.all_gfs"),
                          46: path.join(tmpdir,"new_gfs_d01"),
                          56: path.join(tmpdir,"gfs_env"),
                          52: path.join(tmpdir,"rel_inform_gfs." + yyyymmddhh),
                          55: path.join(tmpdir,"vital_syn_gfs." + yyyymmddhh),
                          71: path.join(tmpdir,"storm_pert_gfs"),
                          65: path.join(tmpdir,"storm_radius"),
                          85: path.join(tmpdir,"storm_radius_gfs")}, logger=logger, force=True)

gesfhr=6
ibgs=2

#check HWRF vortex
testf_d1=tmpdir+"/storm_pert_new"

if path.isfile(testf_d1):
    ibgs=1

# run the executable wrf_split.x

logger.info("gesfhr_fgat=" + str(gesfhr_fgat))
logger.info("ibgs=" + str(ibgs))
logger.info("st_int=" + str(st_int))
logger.info("iflag_cold=" + str(iflag_cold))
nmmbUsh.hmon_pgm(logger, path.join(tmpdir, "wrf_split.x"), str(gesfhr_fgat), str(ibgs), str(st_int), str(iflag_cold))

gfs_flag=6
if path.isfile(testf_d1):
    logger.info(" This is not a cold start.  The " + str(gesfhr_fgat) + "-h HWRF vortex will be used")
    gfs_flag=6
    warm_cold_flag="warm"
    hwrf_vortex="yes"
else:
    logger.info(" This is cold start.  The " + str(gesfhr_fgat) + "-h HWRF vortex is absent")
    warm_cold_flag="cold"
    hwrf_vortex="no"
    if int(st_int) < 20:
        logger.info(" This is a cold start.  The " + str(coldvortex) + " vortex will be used")
        gfs_flag=0

        nmmbUsh.delete_file("fort.*")

# correct data, regenerate inner nest data,test only
        deliver_file(path.join(tmpdir,"storm_pert_gfs"),  path.join(tmpdir,"storm_pert"),logger=logger)
        deliver_file(path.join(tmpdir,"storm_radius_gfs"), path.join(tmpdir,"storm_radius"),logger=logger)
        deliver_file(path.join(tmpdir,"atcfunix"),path.join(tmpdir,"hdas_atcfunix"),logger=logger)
        deliver_file(path.join(tmpdir,"roughness2"), path.join(tmpdir,"roughness1"),logger=logger)

        produtil.fileop.fortlink({12: path.join(tmpdir,"atcfunix"),
                                  11: path.join(tmpdir,"tcvitals.as"),
                                  26: path.join(tmpdir,"gfs_env"),
                                  71: path.join(tmpdir,"storm_pert"),
                                  58: path.join(tmpdir,"storm_pert_new"),
                                  14: path.join(tmpdir,"storm_size_p"),
                                  23: path.join(tmpdir,"storm_sym"),
                                  46: path.join(tmpdir,"roughness1"),
                                  65: path.join(tmpdir,"storm_radius"),
                                  35: path.join(tmpdir,"storm_pert_step1_1")}, logger=logger, force=True)

# run executable hmon_pert_ct.x
##    sh ${utilscript}/setup.sh
        nmmbUsh.hmon_pgm(logger,path.join(tmpdir, 'hmon_pert_ct.x'), 6)
        nmmbUsh.delete_file("fort.*")	

        if FIND_GFS_VORTEX != 'NO':
# Use HWRF scripts to find the GFS track, done in hwrf_gfs_track0 job:
            track0file="$savdir/gfs-anl.atcfunix"

# Wait for the file to exist.  In NCO mode, the file already should exist
# since the job is run in parallel with the dummy job, but takes less
# time.  Just in case, we wait up to 5 minutes here in NCO mode.
# In non-NCO mode, we wait a half hour to allow jobs to run out of order.
            naptime=3000
            waitfile=path.join(savdir,"gfs-anl.atcfunix")
            if not produtil.fileop.wait_for_files([waitfile],logger,maxwait=naptime):
# The file did not exist.
                if PARAFLAG == "YES":
                    sys.exit("timed out waiting for " + track0file)
                else:
                    logger.info("Timed out waiting for " + str(track0file) + ": will use tcvitals for the vortex relocation instead.")
                    open("./atcfunix",'w')
            else:
                if not( path.isfile(track0file) and path.size(track0file)>0):
# The track file exists but is empty.  That means we could not
# find the GFS vortex.
                    logger.info("Track file is empty; will use tcvitals instead: " + str(track0file))
                    deliver_file(track0file,  "./atcfunix",logger=logger)
		      
        else:
# Use GFS track file
            #nmmbUsh.grep_file(yyyymmddhh, ATMOS_INPUT+"/gfso.t"+CYCLE+"z.cyclone.trackatcfunix", "./tmp11", re.IGNORECASE)
            nmmbUsh.grep_file(yyyymmddhh, gfstrackdir + "/trak.gfso.atcfunix."+yyyymmddhh, "./tmp11", re.IGNORECASE)
            nmmbUsh.grep_file(basin, "./tmp11", "./tmp12", re.IGNORECASE)
            nmmbUsh.grep_file("GFSO|PRE1|PRD1", "./tmp12", "./atcfunix", re.IGNORECASE)

        produtil.fileop.fortlink({11: path.join(tmpdir,"tcvitals.as"),
                                  12: path.join(tmpdir,"atcfunix"),
                                  30: path.join(tmpdir,"trak.fnl.all_gfs_06")}, logger=logger, force=True)

# run the executable create_trak_fnl.x
        nmmbUsh.hmon_pgm(logger, path.join(tmpdir,"create_trak_fnl.x"), storm_id, yyyy, basin)

testf_d1 = path.join(tmpdir, "storm_pert_new")

if path.isfile(testf_d1):
    if hwrf_vortex == 'yes':
        logger.info("Previous HWRF " + str(gesfhr_fgat) + "-h forecast vortex (warm start) is located at " + str(testf_d1))
    else:
        logger.info(str(coldvortex) + " vortex (cold start) is located at " + str(testf_d1))
    

    nmmbUsh.delete_file("fort.*")

    remove_file(path.join(tmpdir,"flag_file"))
    remove_file(path.join(tmpdir,"flag_file2"))

    produtil.fileop.fortlink({14: path.join(tmpdir,"storm_size_p"),
                              11: path.join(tmpdir,"tcvitals.as"),
                              12: path.join(tmpdir,"hdas_atcfunix"),
                              26: path.join(tmpdir, "gfs_env"),
                              36: path.join(tmpdir, "wrf_env_new"),
                              71: path.join(tmpdir, "storm_pert_new"),
                              46: path.join(tmpdir, "roughness1"),
                              56: path.join(tmpdir, "new_data_4x"),
                              23: path.join(tmpdir, "storm_sym")}, logger=logger, force=True)

    if path.isfile(path.join(tmpdir, "trak.fnl.all") ) and  path.getsize(path.join(tmpdir,  "trak.fnl.all"))>0:
        produtil.fileop.fortlink({30: path.join(tmpdir, "trak.fnl.all")}, logger=logger, force=True)
    else:
        produtil.fileop.fortlink({30: path.join(tmpdir, "trak.fnl.all_gfs_06")}, logger=logger, force=True)

	
    nmmbUsh.hmon_pgm(logger, path.join(tmpdir,"hmon_anl_4x_step2.x"), str(gesfhr_fgat), str(gfs_flag), str(initopt))
    deliver_file(path.join(tmpdir, "storm_radius"), path.join(tmpdir, "storm_radius_1"),logger=logger)

# cold start: using GFS vortex

    testf2=path.join(tmpdir,"flag_file2")
    if path.isfile(testf2) and gfs_flag> 2 and MODIN == "GFS":       
        gfs_flag=0

        nmmbUsh.delete_file("fort.*")

        remove_file(path.join(tmpdir,"flag_file"))
        remove_file(path.join(tmpdir,"flag_file2"))
        remove_file(path.join(tmpdir,"storm_pert_new"))


        deliver_file(path.join(tmpdir, "storm_pert_gfs"), path.join(tmpdir, "storm_pert"),logger=logger)
        deliver_file(path.join(tmpdir, "storm_radius_gfs"), path.join(tmpdir, "storm_radius"),logger=logger)
        deliver_file(path.join(tmpdir, "atcfunix"),  path.join(tmpdir, "hdas_atcfunix"),logger=logger)
        deliver_file(path.join(tmpdir, "roughness2"), path.join(tmpdir, "roughness1"),logger=logger)

        produtil.fileop.fortlink({12: path.join(tmpdir,"atcfunix"),
                                  11: path.join(tmpdir,"tcvitals.as"),
                                  26: path.join(tmpdir,"gfs_env"),
                                  71: path.join(tmpdir,"storm_pert"),
                                  58: path.join(tmpdir,"storm_pert_new"),
                                  14: path.join(tmpdir,"storm_size_p"),
                                  23: path.join(tmpdir,"storm_sym"),
                                  46: path.join(tmpdir,"roughness1"),
                                  65: path.join(tmpdir,"storm_radius"),
                                  35: path.join(tmpdir,"storm_pert_step1_1")}, logger=logger, force=True)

        gesfhr=6

# run executable hmon_pert_ct.x
        nmmbUsh.hmon_pgm(logger, path.join(tmpdir,"hmon_pert_ct.x"), gesfhr)

        nmmbUsh.delete_file("fort.*")

        produtil.fileop.fortlink({14: path.join(tmpdir, "storm_size_p"),
                                  11: path.join(tmpdir, "tcvitals.as"),
                                  12: path.join(tmpdir, "atcfunix"),
                                  26: path.join(tmpdir, "gfs_env"),
                                  36: path.join(tmpdir, "wrf_env_new"),
                                  71: path.join(tmpdir, "storm_pert_new"),
                                  46: path.join(tmpdir, "roughness2"),
                                  56: path.join(tmpdir, "new_data_4x"),
                                  23: path.join(tmpdir,"storm_sym")}, logger=logger, force=True)

        gesfhr=6

# run the executable hmon_anl_4x_step2.x 
        nmmbUsh.hmon_pgm(logger, path.join(tmpdir,"hmon_anl_4x_step2.x"), gesfhr_fgat, gfs_flag, initopt)

        deliver_file(path.join(tmpdir,"storm_radius"),path.join(tmpdir,"storm_radius_1"),logger=logger)

    testf1 = path.join(tmpdir, "flag_file")
    if path.isfile(testf1):
        with open(path.join(tmpdir,testf1), 'r') as f:
            print(f.readline())

        nmmbUsh.delete_file("fort.*")

        remove_file(path.join(tmpdir,"new_data_4x"))
        produtil.fileop.fortlink({11: path.join(tmpdir,"tcvitals.as"),
                                  26: path.join(tmpdir,"wrf_env_new")}, logger=logger, force=True)

        produtil.fileop.fortcopy({71: path.join(fixdir,"hmon_storm_cyn_axisy_47"),
                                  72: path.join(fixdir,"hmon_storm_cyn_axisy_47"),
                                  73: path.join(fixdir,"hmon_storm_cyn_axisy_47"),
                                  74: path.join(fixdir,"hmon_storm_cyn_axisy_47"),
                                  75: path.join(fixdir,"hmon_storm_20"),
                                  76: path.join(fixdir,"hmon_storm_20"),
                                  77: path.join(fixdir,"hmon_storm_20"),
                                  78: path.join(fixdir,"hmon_storm_cyn_axisy_47")}, logger=logger)
		
        for f in glob.glob("fort.7*"):
            os.chmod(f, stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH)

        produtil.fileop.fortlink({85: path.join(tmpdir,"storm_radius"),
                                  56: path.join(tmpdir,"new_data_4x"),
                                  46: path.join(tmpdir,"roughness1"),
                                  25: path.join(tmpdir,"test_data"),
                                  23: path.join(tmpdir,"storm_sym")}, logger=logger, force=True)

# run the executable hmon_anl_cs_10m.x
        nmmbUsh.hmon_pgm(logger, path.join(tmpdir,"hmon_anl_cs_10m.x"), str(gesfhr), str(iflag_cold))

    testf2 = path.join(tmpdir,"flag_file2")
    if path.isfile(testf2):
        with open(path.join(tmpdir,"flag_file2"), 'r') as fin:
            logger.info(fin.read())	
        nmmbUsh.delete_file("fort.*")

        remove_file(path.join(tmpdir,"new_data_4x"))
        produtil.fileop.fortlink({11: path.join(tmpdir,"tcvitals.as"),
                                  26: path.join(tmpdir,"gfs_env"),
                                  36: path.join(tmpdir,"data_4x_gfs"),
                                  61: path.join(tmpdir,"storm_pert_gfs")}, logger=logger, force=True)

        produtil.fileop.fortcopy({71: path.join(fixdir,"hmon_storm_cyn_axisy_47"),
                                  72: path.join(fixdir,"hmon_storm_cyn_axisy_47"),
                                  73: path.join(fixdir,"hmon_storm_cyn_axisy_47"),
                                  74: path.join(fixdir,"hmon_storm_cyn_axisy_47"),
                                  75: path.join(fixdir,"hmon_storm_cyn_axisy_47"),
                                  76: path.join(fixdir,"hmon_storm_20"),
                                  77: path.join(fixdir,"hmon_storm_20"),
                                  78: path.join(fixdir,"hmon_storm_cyn_axisy_47")}, logger=logger)

        os.chmod("fort.7*", stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH)

        produtil.fileop.fortlink({85: path.join(tmpdir,"storm_radius_gfs"),
                                  46: path.join(tmpdir,"roughness2"),
                                  56: path.join(tmpdir,"new_data_4x"),
                                  25: path.join(tmpdir,"test_data")}, logger=logger, force=True)

       	
# run executable hmon_anl_bogus_10m.x
        nmmbUsh.hmon_pgm(logger, path.join(tmpdir,"hmon_anl_bogus_10m.x"), gesfhr)
        deliver_file(path.join(tmpdir,"hmon_anl_bogus_10m.x"), path.join(tmpdir,"storm_radius_1"),logger=logger)

    if path.isfile(testf_d3):
        iflag_ghost=0
    else:
        iflag_ghost=1

else:
    logger.info("This is a cold start, " + str(gesfhr_fgat) + "-h HWRF or " + str(coldvortex) + " vortex is absent")
    logger.info("Using bogus vortex")
    warm_cold_flag="cold"

    nmmbUsh.delete_file("fort.*")

    produtil.fileop.fortlink({11: path.join(tmpdir,"tcvitals.as"),
                                  26: path.join(tmpdir, "gfs_env"),
                                  36: path.join(tmpdir, "data_4x_gfs"),
                                  61: path.join(tmpdir, "storm_pert_gfs")}, logger=logger, force=True)

    produtil.fileop.fortcopy({71: path.join(fixdir, "hmon_storm_cyn_axisy_47"),
                              72: path.join(fixdir, "hmon_storm_cyn_axisy_47"),
                              73: path.join(fixdir, "hmon_storm_cyn_axisy_47"),
                              74: path.join(fixdir, "hmon_storm_cyn_axisy_47"),
                              75: path.join(fixdir, "hmon_storm_cyn_axisy_47"),
                              76: path.join(fixdir, "hmon_storm_20"),
                              77: path.join(fixdir, "hmon_storm_20"),
                              78: path.join(fixdir, "hmon_storm_cyn_axisy_47")}, logger=logger) 

    for f in glob.glob("fort.7*"):
        os.chmod(f, stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH)
	
    produtil.fileop.fortlink({85: path.join(tmpdir,"storm_radius_gfs"),
                              46: path.join(tmpdir,"roughness2"),
                              56: path.join(tmpdir,"new_data_4x"),
                              25: path.join(tmpdir,"test_data")}, logger=logger, force=True)

    gesfhr=6
   	   	
# run executable hmon_anl_bogus_10m.x 
    nmmbUsh.hmon_pgm(logger, path.join(tmpdir, "hmon_anl_bogus_10m.x"),gesfhr)	

logger.info("#######################################")
logger.info(str(GSID02) + " " + str(GSID03))


if GSID02 == "NO"  and GSID03 == "NO":
# interpoplate to d02
    nmmbUsh.delete_file("fort*")
    produtil.fileop.fortlink({11: path.join(tmpdir,"tcvitals.as"),
                              26: path.join(tmpdir,"new_data_4x"),
                              36: path.join(tmpdir,"new_gfs_d02"),
                              46: path.join(tmpdir,"new_gfs_d01"),
                              56: path.join(tmpdir,"data_merge_d02")}, logger=logger, force=True)
	
# run the executable hmon_inter_2to2.x
    gesfhr=6
    iflag=1
    nmmbUsh.hmon_pgm(logger, path.join(tmpdir,"hmon_inter_2to2.x"), gesfhr, iflag)
	
# interpolate to d03
    nmmbUsh.delete_file("fort.*") 

    produtil.fileop.fortlink({11: path.join(tmpdir,"tcvitals.as"),
                              26: path.join(tmpdir,"new_data_4x"),
                              36: path.join(tmpdir,"new_gfs_d03"),
                              46: path.join(tmpdir,"new_gfs_d01"),
                              56: path.join(tmpdir,"data_merge_d03")}, logger=logger, force=True)
	
# run the executable hmon_inter_2to2.x
    nmmbUsh.hmon_pgm(logger, path.join(tmpdir,"hmon_inter_2to2.x"), gesfhr, iflag)
else:
# interpolate new_data_4x to ghost_d02, ghost_d03
    if GSID02 == "YES":
        nmmbUsh.delete_file("fort.*")

    produtil.fileop.fortlink({11: path.join(tmpdir,"tcvitals.as"),
                              26: path.join(tmpdir,"new_data_4x"),
                              36: path.join(tmpdir,"new_ght_d02"),
                              46: path.join(tmpdir,"new_gfs_d01"),
                              56: path.join(tmpdir,"data_merge_g02")}, logger=logger, force=True)

    gesfhr=6
    iflag=1
# run the executable hmon_inter_2to2.x
     
    nmmbUsh.hmon_pgm(logger, path.join(tmpdir,"hmon_inter_2to2.x"), gesfhr, iflag)
  


nmmbUsh.delete_file("fort*")
remove_file(path.join(tmpdir,"flag_file"))

produtil.fileop.fortlink({11: path.join(tmpdir,"tcvitals.as"),
                          36: path.join(tmpdir,"new_data_4x"),
                          46: path.join(tmpdir,"new_gfs_d01"),
                          26: path.join(tmpdir,"new_gfs_d01"),
                          85: path.join(tmpdir,"storm_radius_gfs"),
                          56: path.join(tmpdir,"data_merge_d01")}, logger=logger, force=True)

gesfhr=6
# run executable hmon_inter_4to6.x
nmmbUsh.hmon_pgm(logger, path.join(tmpdir,"hmon_inter_4to6.x"), gesfhr)        

nmmbUsh.delete_file("fort*")

deliver_file(path.join(tmpdir,"storm_radius_gfs"), path.join(tmpdir,"storm_radius"),logger=logger)

# replace updated model files in wrf files
remove_file("itag1")
remove_file("itag3")

if IO_FORM != 2 and GSID02 == "YES" or GSID02 == "YES":
    deliver_file("./namelist_analysis0.input", "./namelist.input",logger=logger)

if IO_FORM == 2:
    nmmbUsh.update_3dvar(logger, 1)
else:
    nmmbUsh.nems_update(logger, 1,"wrfinput", "data_merge",1) 
                 
if GSID02 == "NO" and GSID03 == "NO":
    if IO_FORM == 2:
        cmd = exe("./hmon_diffwrf_3dvar.exe")["3dvar_update"]["wrfinput_d02"]["data_merge_d02"]
        produtil.run.checkrun(cmd, logger=logger)
        cmd = exe("./hmon_diffwrf_3dvar.exe")["3dvar_update"]["wrfinput_d03"]["data_merge_d03"]
        produtil.run.checkrun(cmd, logger=logger)
    else:
        nmmbUsh.nems_update(logger, 2,"wrfinput", "data_merge", 2)
        nmmbUsh.nems_update(logger, 3,"wrfinput", "data_merge", 3)


if GSID02 == 'YES':
    if IO_FORM == 2:
        nmmbUsh.update_3dvar(logger, 2)
    else:
        deliver_file("./namelist_ghost.input", "./namelist.input",logger=logger) 
        nmmbUsh.nems_update(logger, 3,"wrfghost", "update",2)
  
if GSID03 == 'YES':
    if IO_FORM == 2:
        nmmbUsh.update_3dvar(logger, 3)
    else:
        deliver_file("./namelist_ghost.input", "./namelist.input",logger=logger)
        logger.info("./nems_bin_io.exe itag wrfinput_d03 update data_merge_d03")
        nmmbUsh.nems_update(logger, 3,"wrfghost", "update",3)


deliver_file(path.join(tmpdir,"tcvitals.as"), savdir+"/tcvitals."+yyyymmddhh,logger=logger)

if GSID02 == "YES":
    deliver_file("./wrfghost_d02", "./wrfghost_d02_gsi",logger=logger)

if GSID03 == "YES":
    deliver_file("./wrfghost_d03", "./wrfghost_d03_gsi",logger=logger)

if GSID02 == "NO" and GSID03 == "NO":
    atmos_d=path.join(DATA,storm+"."+yyyymmddhh+"/ATMOS")
    nmmbUsh.removeall(atmos_d)
    makedirs(atmos_d)
    deliver_file("./wrfinput_d01",path.join(atmos_d,"wrfinput_d01"),logger=logger)
    deliver_file("./wrfinput_d02",path.join(atmos_d,"wrfanl_d02_"+yyyy+"-"+im+"-"+id+"_"+ih+":00:00"),logger=logger)
    deliver_file("./wrfinput_d03",path.join(atmos_d,"wrfanl_d03_"+yyyy+"-"+im+"-"+id+"_"+ih+":00:00"),logger=logger)
	
# Output the "CYCLING STATUS" line.  This line is parsed by the para
# automation scripts so it must be correct.  They must match the
# hwrf_fgat_relocate_kick.shell script.
if warm_cold_flag == "warm":
# Warm start: cycling was used
    logger.info("CYCLING STATUS: WARM START")
elif warm_cold_flag == "cold":
# This is a cold start.  Should it have been a cold start?
    if cold_ok == 'yes':
# Intentional cold start, such as for a weak vortex
        logger.info("CYCLING STATUS: CYCLING VETOED")
# There is a prior cycle and cycling was not vetoed, so this
#        # should have been a warm start.  It is a cold start, so that
#        # means there is an error.
#        echo CYCLING STATUS: UNEXPECTED COLD START
#        echo A prior cycle was present, but this is a cold start,
#        echo and the cold_ok variable is set to $cold_ok instead of yes.
#        echo This is an error, unless you intentionally started mid-storm.
    else:
# No prior cycle so cycling is impossible
        logger.info("CYCLING STATUS: NO PRIOR CYCLE")
  
else:
# Script error: the cycling status is uninitialized
    logger.info("CYCLING STATUS: UNKNOWN $warm_cold_flag" + str(cold_ok))

logger.info("relocate copy data to com directory")

atmos_d=comdir 
produtil.fileop.deliver_file("./wrfinput_d01",atmos_d + "/" + storm_name + STORM_ID + "." + cycle + "." + "input_domain_01_nemsio",logger=logger)
produtil.fileop.deliver_file("./wrfinput_d02",atmos_d + "/" + storm_name + STORM_ID + "." + cycle + "." + "input_domain_02_nemsio",logger=logger)
produtil.fileop.deliver_file("./wrfinput_d03",atmos_d + "/" + storm_name + STORM_ID + "." + cycle + "." + "input_domain_03_nemsio",logger=logger)

logger.info("relocate finished")