function ok = compare_all(outdir, refdir)

% the absolute and relative tolerance account for slight IEEE-754 based differences,

% including non-associativity of floating-point arithmetic.

% these parameters are a bit arbitrary.

% per MZ Oct 17, 2018:

% Ti,Te=1 K

% ne=1e6 m-3

% vi,v2,v3=1 m/s

% J1,J2,J3 = 1e-9

% MZ wants to change what we consider signficant...

% Ti,Te=5 K

% ne=1e7 m-3

% vi,v2,v3=2 m/s

% J1,J2,J3 = 1e-9

narginchk(2,2)

cwd = fileparts(mfilename('fullpath'));

addpath([cwd,filesep,'..',filesep,'script_utils'])

addpath([cwd, filesep, '..', filesep, 'vis'])

tol.rtol = 1e-5;

tol.rtolN = 1e-5;

tol.rtolT = 1e-5;

tol.rtolJ = 1e-5;

tol.rtolV = 1e-5;

tol.atol=1e-8;

tol.atolN=1e9;

tol.atolT=100;

tol.atolJ=1e-7;

tol.atolV=50;

exist_or_skip(outdir, 'dir')

exist_or_skip(refdir, 'dir')

%% check that paths not the same

% this is not a very good check. Matlab has no native way to resolve absolute paths

% and GetFullPath.m can arbitrarily change working directory, breaking the script.

if strcmp(outdir, refdir), error([outdir, ' and ', refdir, ' directories are the same']), end

%% READ IN THE SIMULATION INFORMATION

params = read_config([outdir, filesep, 'inputs']);

lxs = simsize(outdir);

disp(['sim grid dimensions: ',num2str(lxs)])

%% TIMES OF INTEREST

times = params.UTsec0:params.dtout:params.UTsec0 + params.tdur;

Nt = length(times);

assert(Nt > 1, [outdir, ' simulation did not run long enough'])

ymd=params.ymd;

UTsec=params.UTsec0;

ok = false;

for it=1:Nt

st = ['UTsec ', num2str(times(it))];

[neA,~,~,~,v1A,TiA,TeA,J1A,v2A,v3A,J2A,J3A] = loadframe(outdir,ymd,UTsec);

[neB,~,~,~,v1B,TiB,TeB,J1B,v2B,v3B,J2B,J3B] = loadframe(refdir,ymd,UTsec);

ok = ok + ~assert_allclose(neA,neB,tol.rtolN,tol.atolN,['Ne ',st], true);

if false

ok = ok + ~assert_allclose(v1A,v1B,tol.rtolV,tol.atolV,['V1 ', st], true);

end

ok = ok + ~assert_allclose(v2A,v2B,tol.rtolV,tol.atolV,['V2 ', st], true);

ok = ok + ~assert_allclose(v3A,v3B,tol.rtolV,tol.atolV,['V3 ', st], true);

if false

ok = ok + ~assert_allclose(TiA,TiB,tol.rtolT,tol.atolT,['Ti ', st], true);

end

ok = ok + ~assert_allclose(TeA,TeB,tol.rtolT,tol.atolT,['Te ', st], true);

ok = ok + ~assert_allclose(J1A,J1B,tol.rtolJ,tol.atolJ,['J1 ', st], true);

ok = ok + ~assert_allclose(J2A,J2B,tol.rtolJ,tol.atolJ,['J2 ', st], true);

ok = ok + ~assert_allclose(J3A,J3B,tol.rtolJ,tol.atolJ,['J3 ', st], true);

%% assert time steps have unique output (earth always rotating...)

if it>1

ok = ok + ~assert_allclose(Ne,neA,tol.rtol,tol.atol,['Ne ', st,' too similar to prior step'],true, true);

%ok = ok + ~assert_allclose(v1,v1A,tol.rtol,tol.atol,['V1 ', st,' too similar to prior step'],true, true);

ok = ok + ~assert_allclose(v2,v2A,tol.rtol,tol.atol,['V2 ', st,' too similar to prior step'],true, true);

ok = ok + ~assert_allclose(v3,v3A,tol.rtol,tol.atol,['V3 ', st,' too similar to prior step'],true, true);

end

if it==3

%ok = ok + ~assert_allclose(Ti,TiA,tol.rtol,tol.atol,['Ti ', st,' too similar to prior step'],true, true);

ok = ok + ~assert_allclose(Te,TeA,tol.rtol,tol.atol,['Te ', st,' too similar to prior step'],true, true);

end

if it==2

ok = ok + ~assert_allclose(J1,J1A,tol.rtol,tol.atol,['J1 ', st,' too similar to prior step'],true,true, true);

ok = ok + ~assert_allclose(J2,J2A,tol.rtol,tol.atol,['J2 ', st,' too similar to prior step'],true,true, true);

ok = ok + ~assert_allclose(J3,J3A,tol.rtol,tol.atol,['J3 ', st,' too similar to prior step'],true,true, true);

end

Ne = neA; v1=v1A; v2=v2A; v3=v3A; Ti=TiA; Te=TeA; J1=J1A; J2=J2A; J3=J3A;

[ymd,UTsec] = dateinc(params.dtout,ymd,UTsec);

end

if ok ~= 0

error([int2str(ok), ' compare errors'])

else

disp(['OK: Gemini output comparison of ',int2str(Nt),' time steps.'])

end

if nargout==0, clear('ok'), end

end % function