#!/bin/sh

#extract only variables used for parameters.  These have dimension allpfts.

ncks -v
aereoxid,atmch4,bdnr,br_mr,capthick,cn_s1,cn_s2,cn_s3,cn_s4,cnscalefactor,compet_decomp_nh4,compet_decomp_no3,compet_denit,compet_nit,compet_plant_nh4,compet_plant_no3,crit_dayl,crit_offset_fdd,crit_offset_swi,crit_onset_fdd,crit_onset_swi,cryoturb_diffusion_k,cwd_fcel,cwd_flig,dayscrecover,decomp_depth_efolding,depth_runoff_Nloss,dnp,ef_time,f_ch4,f_sat,froz_q10,fstor2tran,gddfunc_p1,gddfunc_p2,highlatfact,k_frag,k_l1,k_l2,k_l3,k_m,k_m_o2,k_m_unsat,k_mort,k_nitr_max,k_s1,k_s2,k_s3,k_s4,lake_decomp_fact,lwtop_ann,max_altdepth_cryoturbation,max_altmultiplier_cryoturb,me_herb,me_woody,minfuel,mino2lim,minpsi_hr,ndays_off,ndays_on,nongrassporosratio,organic_max,oxinhib,pHmax,pHmin,porosmin,q10_ch4oxid,q10_hr,q10_mr,q10ch4,q10lakebase,qflxlagd,r_mort,rc_npool,redoxlag,redoxlag_vertical,rf_l1s1,rf_l2s2,rf_l3s3,rf_s1s2,rf_s2s3,rf_s3s4,rij_kro_a,rij_kro_alpha,rij_kro_beta,rij_kro_delta,rij_kro_gamma,rob,rootlitfrac,satpow,scale_factor_aere,scale_factor_gasdiff,scale_factor_liqdiff,sf_minn,sf_no3,shape_fluxprof_param1,smp_crit,soilpsi_off,soilpsi_on,som_diffus,surface_tension_water,tau_cwd,tau_l1,tau_l2_l3,tau_s1,tau_s2,tau_s3,unsat_aere_ratio,vgc_max,vmax_ch4_oxid,vmax_oxid_unsat,wcf,cn_s1_bgc,cn_s2_bgc,cn_s3_bgc,rf_cwdl2_bgc,rf_cwdl3_bgc,rf_l1s1_bgc,rf_l2s1_bgc,rf_l3s2_bgc,rf_s2s1_bgc,rf_s2s3_bgc,rf_s3s1_bgc clmParams.c130802.nc paramDataNoPft.nc

# remove coodinate attribute

ncatted -O -a coordinates,,d,f," " paramDataNoPft.nc

# remove pftname:

ncks -x -v pftname paramDataNoPft.nc paramDataNoPft2.nc

#make copy of pft-phys file:

mv pft-physiology.c130503.nc clm_params.c130815.nc

#combine files

ncks paramDataNoPft2.nc clm_params.c130815.nc

add some other vars:



ncatted -O -a long_name,compet_denit,o,c,"Relative competitiveness of denitrifiers for NO3" clm_params.c130815.nc
ncap2 -O -s compet_decomp_no3=1.0 clm_params.c130815.nc clm_params.c130815.nc
ncatted -O -a long_name,compet_decomp_no3,o,c,"Relative competitiveness of immobilizers for NO3" clm_params.c130815.nc 
ncap2 -O -s compet_plant_nh4=1.0 clm_params.c130815.nc clm_params.c130815.nc
ncatted -O -a long_name,compet_plant_nh4,o,c,"Relative compettiveness of plants for NH4" clm_params.c130815.nc 
ncap2 -O -s compet_plant_no3=1.0 clm_params.c130815.nc clm_params.c130815.nc
ncatted -O -a long_name,compet_plant_no3,o,c,"Relative compettiveness of plants for NO3" clm_params.c130815.nc