Calculated ELM size.
Modified options using parallel hyper-viscous diffusion for pressure;
Added options using parallel hyper-viscous diffusion for
(1) Parallel vorticity;
(2) Parallel vector potential diffusion.

Conflicts:
	examples/elm-pb/elm_pb.cxx
Added the updated IDL line-tracing code to the repository.
Added elm size calculation for single null divertor.
Added a configure file for LC Chaos 5 systems.
Adding utilities for structures and resizing grid.
Adding capability to write vertex info and write data mapped to poloidal plane.
Adding tools/idllib/README.write_polslice
Adding tools/numlib files from dev-bout-1.1 that were lost in the transition to master
Add idl routine named as "prof_write.pro"

Writes the density profile with tanh function into grid file.
The temperatures are deirved from pressure in grid file and this written density.
Add cross term in vorticity definition and gyro-viscous terms into 3-field elm_pb.cxx
The switch for gyro-viscous terms is: gyroviscous = true
The switch for cross term is: constn0 = false
n0_fake_prof is used as the swith to generate a tanh function for equilibrium density profile.

Conflicts:
	examples/elm-pb/elm_pb.cxx
	examples/elm-pb/test/BOUT.inp
modified elm_size.pro: corrected poloidal angle, added one more option to calculate 3D elm size, added a option to change the 1D intetral location yind
modified elm_pb.pro: now in out put E_loss and E_total has unit J; need Bbar as a input

Conflicts:
	tools/idllib/elm_size.pro
Added file configure.edison for compile BOUT++ on Edison.
Please swap to gnu compiler, load fftw and DONOT load netcdf.
To compile BOUT++ on Edison, execute ./configure.edison before make.
tow source boundary files 'boundary_standard.cxx' and 'boundary_standard.hxx' are implemented
to support fixed gradient for neumann boundary condition
1) neumann = zero gradient;   same as before
2) neumann(val) = fixed gradient equal to (val) at core, but equal to (-val) at edge. Be careful!
Added four functions for poloidal lowpass filtering for n=0 mode
  void slice_r_y(BoutReal *fori, BoutReal * fxy, int ystart, int ncy);
  void get_ri( dcomplex * ayn, int ncy, BoutReal * ayn_Real, BoutReal * ayn_Imag);
  void set_ri( dcomplex * ayn, int ncy, BoutReal * ayn_Real, BoutReal * ayn_Imag);
  const Field2D lowPass_poloidal(const Field2D &var,int mmax);

Conflicts:
	src/mesh/impls/bout/boutmesh.hxx
Added a memo Gradperp_op.tex to explain the zonal mode approximations.
Volume integral of Field2D variable
Usage : example of volume average
    mesh->Vol_Integral(Field2D var)/mesh->Vol_Integral(Field2D var1=1);
Added :
  BoutReal Average_XY(const Field2D &var);
  BoutReal Vol_Integral(const Field2D &

Switch Y and Z coordinate of Field3D variable for inverse Laplace of n=0 mode
Added :
  const Field3D Switch_YZ(const Field3D &var);

Conflicts:
	src/mesh/impls/bout/boutmesh.hxx
modified configure file for hopper

Conflicts:
	configure.hopper
some python post-processing scripts