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Initial post processing of raw model output:

for long simulations:
ppnc.sh (will call monthlymean{T,U,V,Z3}.sh, record.sh)
SSW_compo.sh
filterUVT.ncl
proj_freq.ncl
proj_eddy.ncl
proj_wavenumber.ncl
proj_wavenumber_eddy.ncl
EPflux.ncl

for short ensembles:
ppnc_ens_budget.sh (will call vinthall.ncl)
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Checklist before running the figure-make code:

1. All_WA1Jan_EQ1M40(lon${lonL}${lonR})_${Amp}.nc
(climatology file for all variables, generated by nco command in initial post process)
2. SSW_WA1Jan_EQ1M40(lon${lonL}${lonR})_${Amp}.nc
(SSW time series, generated by nco command in initial post process)
3. yz_EP_(filter)_(${ShortPeriodLim})(${LongPeriodLim})_DJF_WA1Jan35_EQ1M40(lon${lonL}${lonR})_${Amp}(_Appendix).nc
(EP flux contributed by eddies with ${ShortPeriodLim}-${LongPeriodLim} Period. 1-7day is filtered by k<10, otherwise is k<3. Sometimes, the EP flux is not filtered in time and only in space, those have an appendix telling us the cutoff wavenumber. I append here the ncl code used to generate these files, EPflux_paper1.ncl)
4. vinth(3)_{MJOB, MJOC40, CTRL}_H2_ENS.nc are 800-ensemble mean of the instant output variables for MJOB, MJOC (both Amp=10K/day) and CTRL simulations. Interpolated to pressure coordinate. (generated )
5. vinth(3)_timeavg_{MJOB,MJOC40,CTRL}_ENSavg.nc are 800-ensemble mean of time-average output variables for MJOB, MJOC (both Amp=10K/day) and CTRL simulations. Interpolated to pressure coordinate. (generated )
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How to make the figures.

To get Fig.1, 2(ac), 4 in the main text and Fig.S1, S2 in the supporting information, just run the matlab code ``SSW_bootstrap.m'' and then ``SSW_analysis.m''.

The Fig.2 (bd) in the main text, and Fig.S4 in the supporting information, is plotted using panoply. Just open the corresponding All_WA1Jan_EQ1M40(lon${lonL}${lonR})_${Amp}.nc using panoply and adjust the colormap.

The Fig.3 in the main text and Fig. S3 in the supporting information, run ``drift_Evector_MJO_ETavg.m''.
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%% Experiment name: MJO amplitude (${Amp}K/day). MJO longitudinal range: (from ${lonL} to ${lonR}

For clarification, please contact wanyingkang@g.harvard.edu