Notebook

In [1]:

import netCDF4 as nc
import datetime as dt
import subprocess
import requests
import matplotlib.pyplot as plt
import cmocean
import numpy as np
import os
import glob
import dateutil as dutil
from salishsea_tools import viz_tools
%matplotlib inline

In [2]:

with nc.Dataset('/ocean/eolson/MEOPAR/NEMO-forcing/grid/mesh_mask201702_noLPE.nc') as fm:
    tmask=np.copy(fm.variables['tmask'])
    umask=np.copy(fm.variables['umask'])
    vmask=np.copy(fm.variables['vmask'])
    navlon=np.copy(fm.variables['nav_lon'])
    navlat=np.copy(fm.variables['nav_lat'])
    dept=np.copy(fm.variables['gdept_1d'])
    e3t_0=np.copy(fm.variables['e3t_0'])
    e3u_0=np.copy(fm.variables['e3u_0'])
    e3v_0=np.copy(fm.variables['e3v_0'])
    e1t=np.copy(fm.variables['e1t'])
    e2t=np.copy(fm.variables['e2t'])
    e1v=np.copy(fm.variables['e1v'])
    e2u=np.copy(fm.variables['e2u'])
    A=fm.variables['e1t'][0,:,:]*fm.variables['e2t'][0,:,:]*tmask[0,0,:,:]

In [3]:

t0=dt.datetime(2015,2,6) # 1st start date of run
#te=dt.datetime(2016,12,1)# last start date of runfnum=18
stm=np.shape(tmask)
SiN=2.0
#nlen=36*2
nlen=24
dlist=[t0+dt.timedelta(days=ii*10) for ii in range(0,nlen)]

In [4]:

#sdir0='/results/SalishSea/nowcast-green/'
#sdir1='/results/SalishSea/hindcast/'
#sdir3='/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_HCMZ/'
sdir1='/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/'

In [5]:

tmaskC=np.copy(tmask)
tmaskC[:,:,370:490,:12]=0
tmaskC[:,:,887:,30:70]=0

In [6]:

tlist=dlist
SiGlobalTot=dict()
SiTot=dict()
BSiTot=dict()
DiatTot=dict()
changeSiGlobalTot=dict()
for idir in (sdir1,):
    fformat1='%d%b%y/'
    if idir.startswith('/data/eolson/MEOPAR/SS36runs/CedarRuns/'):
        fformatT='SalishSea_1h_*_ptrc_T_%Y%m%d-*.nc'
        fformatP='SalishSea_1h_*_ptrc_T_%Y%m%d-*.nc'
    #elif idir==sdir0:
    #    fformatT='SalishSea_1h_%Y%m%d_%Y%m%d_ptrc_T.nc'
    #    fformatP='SalishSea_1h_%Y%m%d_%Y%m%d_grid_T.nc'
    elif idir==sdir1:
        fformatT='SalishSea_1h_%Y%m%d_%Y%m%d_ptrc_T.nc'
        fformatP='SalishSea_1h_%Y%m%d_%Y%m%d_carp_T.nc'
    sumSi=np.zeros((len(tlist),stm[1]))
    sumBSi=np.zeros((len(tlist),stm[1]))
    sumDiat=np.zeros((len(tlist),stm[1]))
    ind=-1
    for idt0 in tlist:
        ind=ind+1
        cdir=idt0.strftime(fformat1).lower()
        iffT=idt0.strftime(fformatT)
        iffP=idt0.strftime(fformatP)
        if idir.startswith('/data/eolson/MEOPAR/SS36runs/CedarRuns/'):
            sffT=idir+iffT
            sffP=idir+iffP
        elif idir.startswith('/results/'):
            sffT=idir+cdir+iffT
            sffP=idir+cdir+iffP
        f=nc.Dataset(glob.glob(sffT)[0])
        print(sffT)
        fP=nc.Dataset(glob.glob(sffP)[0])
        #if idir==sdir0:
        #    e3t=np.expand_dims((1+fP.variables['sossheig'][0,:,:]/np.sum(e3t_0*tmask,1)),0)*e3t_0
        if idir==sdir1:
            e3t=fP.variables['e3t'][:2,:,:,:]
        Vol=A*np.ones(np.shape(e3t))
        sumSi[ind,:]=1e-3*np.sum(np.sum(tmaskC[0,:,:,:]*Vol[0,:,:,:]*f.variables['silicon'][0,:,:,:],2),1) #mmol/m3*m3*10^-3=mol
        sumBSi[ind,:]=1e-3*np.sum(np.sum(tmaskC[0,:,:,:]*Vol[0,:,:,:]*f.variables['biogenic_silicon'][0,:,:,:],2),1) #mmol/m3*m3*10^-3=mol
        sumDiat[ind,:]=SiN*1e-3*np.sum(np.sum(tmaskC[0,:,:,:]*Vol[0,:,:,:]*f.variables['diatoms'][0,:,:,:],2),1) #mmol/m3*m3*10^-3=mol
        f.close()
        fP.close()
    SiGlobalTot[idir]=sumSi+sumBSi+sumDiat

/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150206-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150216-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150226-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150308-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150318-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150328-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150407-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150417-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150427-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150507-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150517-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150527-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150606-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150616-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150626-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150706-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150716-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150726-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150805-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150815-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150825-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150904-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150914-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150924-*.nc

In [7]:

sffT

Out[7]:

'/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150924-*.nc'

In [8]:

siplot=SiGlobalTot[idir]-SiGlobalTot[idir][0,:]

In [9]:

cm1=cmocean.cm.balance
#plt.pcolormesh([t0+dt.timedelta(10*ii) for ii in range(0,30)],dept[0,:],np.transpose(siplot[:30,:]),cmap=cm1,vmin=-1e9,vmax=1e9)
plt.pcolormesh([t0+dt.timedelta(10*ii) for ii in range(0,nlen)],dept[0,:],np.transpose(siplot),cmap=cm1,vmin=-1e8,vmax=1e8)
plt.ylim(400,0)
plt.colorbar()

Out[9]:

<matplotlib.colorbar.Colorbar at 0x7fea75d06208>

repeat for N¶

In [10]:

tlist=dlist
NGlobalTot=dict()
VolTot=dict()
NO3Tot=dict()
NH4Tot=dict()
PONTot=dict()
DONTot=dict()
DiatTot=dict()
MyriTot=dict()
NanoTot=dict()
MiZoTot=dict()
changeNGlobalTot=dict()
for idir in (sdir1,):
    fformat1='%d%b%y/'
    if idir.startswith('/data/eolson/MEOPAR/SS36runs/CedarRuns/'):
        fformatT='SalishSea_1h_*_ptrc_T_%Y%m%d-*.nc'
        fformatP='SalishSea_1h_*_ptrc_T_%Y%m%d-*.nc'
    #elif idir==sdir0:
    #    fformatT='SalishSea_1h_%Y%m%d_%Y%m%d_ptrc_T.nc'
    #    fformatP='SalishSea_1h_%Y%m%d_%Y%m%d_grid_T.nc'
    elif idir==sdir1:
        fformatT='SalishSea_1h_%Y%m%d_%Y%m%d_ptrc_T.nc'
        fformatP='SalishSea_1h_%Y%m%d_%Y%m%d_carp_T.nc'
    sumNO3=np.zeros((len(tlist),stm[1]))
    sumVol=np.zeros((len(tlist),stm[1]))
    sumNH4=np.zeros((len(tlist),stm[1]))
    sumPON=np.zeros((len(tlist),stm[1]))
    sumDON=np.zeros((len(tlist),stm[1]))
    sumDiat=np.zeros((len(tlist),stm[1]))
    sumMyri=np.zeros((len(tlist),stm[1]))
    sumNano=np.zeros((len(tlist),stm[1]))
    sumMiZo=np.zeros((len(tlist),stm[1]))
    ind=-1
    for idt0 in tlist:
        ind=ind+1
        cdir=idt0.strftime(fformat1).lower()
        iffT=idt0.strftime(fformatT)
        iffP=idt0.strftime(fformatP)
        if idir.startswith('/data/eolson/MEOPAR/SS36runs/CedarRuns/'):
            sffT=idir+iffT
            sffP=idir+iffP
        elif idir.startswith('/results/'):
            sffT=idir+cdir+iffT
            sffP=idir+cdir+iffP
        f=nc.Dataset(glob.glob(sffT)[0])
        print(sffT)
        fP=nc.Dataset(glob.glob(sffP)[0])
        #if idir==sdir0:
        #    e3t=np.expand_dims((1+fP.variables['sossheig'][0,:,:]/np.sum(e3t_0*tmask,1)),0)*e3t_0
        if idir==sdir1:
            e3t=fP.variables['e3t'][:2,:,:,:]
        Vol=A*np.ones(np.shape(e3t))
        sumVol[ind,:]=1e-3*np.sum(np.sum(tmaskC[0,:,:,:]*Vol[0,:,:,:],2),1) #mmol/m3*m3*10^-3=mol
        sumNO3[ind,:]=1e-3*np.sum(np.sum(tmaskC[0,:,:,:]*Vol[0,:,:,:]*f.variables['nitrate'][0,:,:,:],2),1) #mmol/m3*m3*10^-3=mol
        sumNH4[ind,:]=1e-3*np.sum(np.sum(tmaskC[0,:,:,:]*Vol[0,:,:,:]*f.variables['ammonium'][0,:,:,:],2),1) #mmol/m3*m3*10^-3=mol
        sumPON[ind,:]=1e-3*np.sum(np.sum(tmaskC[0,:,:,:]*Vol[0,:,:,:]*f.variables['particulate_organic_nitrogen'][0,:,:,:],2),1) #mmol/m3*m3*10^-3=mol
        sumDON[ind,:]=1e-3*np.sum(np.sum(tmaskC[0,:,:,:]*Vol[0,:,:,:]*f.variables['dissolved_organic_nitrogen'][0,:,:,:],2),1) #mmol/m3*m3*10^-3=mol
        sumDiat[ind,:]=1e-3*np.sum(np.sum(tmaskC[0,:,:,:]*Vol[0,:,:,:]*f.variables['diatoms'][0,:,:,:],2),1) #mmol/m3*m3*10^-3=mol
        sumMyri[ind,:]=1e-3*np.sum(np.sum(tmaskC[0,:,:,:]*Vol[0,:,:,:]*f.variables['ciliates'][0,:,:,:],2),1) #mmol/m3*m3*10^-3=mol
        sumMiZo[ind,:]=1e-3*np.sum(np.sum(tmaskC[0,:,:,:]*Vol[0,:,:,:]*f.variables['microzooplankton'][0,:,:,:],2),1) #mmol/m3*m3*10^-3=mol
        f.close()
        fP.close()
    NGlobalTot[idir]=sumNO3+sumNH4+sumPON+sumDON+sumDiat+sumMyri+sumNano+sumMiZo

/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150206-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150216-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150226-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150308-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150318-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150328-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150407-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150417-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150427-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150507-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150517-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150527-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150606-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150616-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150626-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150706-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150716-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150726-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150805-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150815-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150825-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150904-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150914-*.nc
/data/eolson/MEOPAR/SS36runs/CedarRuns/spring2015_NoMZME/SalishSea_1h_*_ptrc_T_20150924-*.nc

In [11]:

Nplot=NGlobalTot[idir]-NGlobalTot[idir][0,:]

In [12]:

#plt.pcolormesh([t0+dt.timedelta(10*ii) for ii in range(0,30)],dept[0,:],np.transpose(siplot[:30,:]),cmap=cm1,vmin=-1e9,vmax=1e9)
plt.pcolormesh([t0+dt.timedelta(10*ii) for ii in range(0,nlen)],dept[0,:],np.transpose(Nplot),cmap=cm1,vmin=-1e8,vmax=1e8)
plt.ylim(400,0)
plt.colorbar()

Out[12]:

<matplotlib.colorbar.Colorbar at 0x7fea5e056f98>

In [ ]: