%Start defining model parameters here

%Geometry and observation
x         = transpose(ncread('../Data/Pig.nc','x'));
y         = transpose(ncread('../Data/Pig.nc','y'));
vx_obs    = transpose(ncread('../Data/Pig.nc','vx_obs'));
vy_obs    = transpose(ncread('../Data/Pig.nc','vy_obs'));
index     = transpose(ncread('../Data/Pig.nc','index'));
surface   = transpose(ncread('../Data/Pig.nc','surface'));
thickness = transpose(ncread('../Data/Pig.nc','thickness'));
md.inversion.vx_obs   =InterpFromMeshToMesh2d(index,x,y,vx_obs,md.mesh.x,md.mesh.y);
md.inversion.vy_obs   =InterpFromMeshToMesh2d(index,x,y,vy_obs,md.mesh.x,md.mesh.y);
md.geometry.surface  =InterpFromMeshToMesh2d(index,x,y,surface,md.mesh.x,md.mesh.y);
md.geometry.thickness=InterpFromMeshToMesh2d(index,x,y,thickness,md.mesh.x,md.mesh.y);
md.geometry.bed=md.geometry.surface-md.geometry.thickness;
clear surface thickness vx_obs vy_obs x y index;
md.initialization.vx=md.inversion.vx_obs;
md.initialization.vy=md.inversion.vy_obs;
md.initialization.vz=zeros(md.mesh.numberofvertices,1);
md.initialization.pressure=zeros(md.mesh.numberofvertices,1);

%Materials
md.initialization.temperature=(273-20)*ones(md.mesh.numberofvertices,1);
md.materials.rheology_B=paterson(md.initialization.temperature);
md.materials.rheology_n=3*ones(md.mesh.numberofelements,1);
md.initialization.temperature=md.initialization.temperature;

%Friction
pos=find(md.mask.elementonfloatingice);
md.friction.coefficient=50*ones(md.mesh.numberofvertices,1);
md.friction.coefficient(md.mesh.elements(pos,:))=0;
md.friction.p=ones(md.mesh.numberofelements,1);
md.friction.q=ones(md.mesh.numberofelements,1);

%Numerical parameters
md.diagnostic.viscosity_overshoot=0.3;
md.prognostic.stabilization=1;
md.verbose=verbose(0);
md.settings.waitonlock=30;
md.timestepping.time_step=1;
md.timestepping.final_time=2;
md.diagnostic.restol=0.05;
md.diagnostic.reltol=1;
md.steadystate.reltol=1;
md.diagnostic.abstol=NaN;

%Boundary conditions:
md=SetMarineIceSheetBC(md);

%Change name so that no test have the same name
A=dbstack;
if (length(A)>2), md.miscellaneous.name=A(3).file(1:end-2); end