problems reading hdf5 with matlab

Hello everyone,

I started looking at the fields of different modes in a PhC slab with air holes in both square or triangular lattice configurations. I use hdf5read function in matlab, in some cases the data I receive for the field components contains NaN or Inf values.

I worte a function in matlab to read a certain component form a hdf5 file and return the field:

function F = read_mpb_field_h5(filename, component_str)

data_r_str = [component_str,'.r'];

data_i_str = [component_str,'.i'];

F = hdf5read(filename,data_r_str)+1i*hdf5read(filename,data_i_str);

If it matters, I run mpb on cygwin. I wouldn't mind that much except that I have several other problems regarding the calculations I do in matlab so I think I'm not doint int right and I'm missing something basic. This is the simplest problem I could describe at the moment and perhaps from that I would figure out the other problems... Any help with this thing would be appreciated.

here's an example of a ctl script I use. if you can run this and read the files in matlab, and see if you too have Inf and/or NaN values. If you look below you could see I use cvector-field-nonbloch for the fields, because I don't want to have the bloch-phase-exponent in the fields data. Nonetheless, I comment those lines just to see what happends and I still have Inf and NaN values

;define the cell geometry of air holes in dielectric slab

(define-param eps 10.048900000000000000000000000000000000000000000000)

(define-param r 0.179999999999999990000000000000000000000000000000000)

(define-param h 0.414899999999999990000000000000000000000000000000000)

(define-param supercell-z 5.0)

(define-param dielectricon

(make dielectric

(epsilon eps)

)

)

(set! default-material air)

(set! geometry

(list

(make block

(center 0 0 0)

(size 1 1 h)

(material dielectricon)

)

(make cylinder

(center 0 0 0)

(radius r)

(height supercell-z)

(material air)

)

)

)

;define the lattice vectors of square lattice

(set! geometry-lattice

(make lattice

(size 1 1 supercell-z)

(basis1 1 0 0)

(basis2 0 1 0)

(basis3 0 0 1)

)

)

;define the k-points

(set! k-points

(list

(cartesian->reciprocal (vector3 0.1 0.0 0.0))

(cartesian->reciprocal (vector3 0.5 0.0 0.0))

)

)

(define-param k-interp 17)

(set! k-points

(interpolate k-interp k-points)

)

;define the simulation settings

(set-param! resolution 10)

(set-param! num-bands 5)

(define-param top-bands 5) ;this can sometimes be lower than num-bands

(set-param! tolerance 0.0001)

;special calculation functions to pass to run

(define (output-nonbloch-efield which-band)

(get-efield which-band)

(cvector-field-nonbloch! cur-field)

(output-field-to-file -1 "e.")

)

(define (output-nonbloch-hfield which-band)

(get-hfield which-band)

(cvector-field-nonbloch! cur-field)

(output-field-to-file -1 "h.")

)

(define (topbands-functions)

(let topbands-loop ((n (- top-bands 1)))

(output-nonbloch-efield (- num-bands n))

(output-nonbloch-hfield (- num-bands n))

(if (> n 0) (topbands-loop (- n 1)) 0)

)

)

;run command

(run-zeven topbands-functions display-group-velocities)

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