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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