Manual

Required data files

NanoMAD requires 3 files (in text format) to run:

• cell.dat

- this file lists the 6 unit cell parameters and the spacegroup name or number -in practice you can put P1 as the spacegroup is ignored:

5.4309 5.4309 5.4309 90 90 90 Fd-3m

• FpFs.dat

-this files lists the number of energies and the atom element on the first line, energy values (eV) on the second line, f' values on the third line, and the f" values on the fourth line:

Ge 12
11003 11053 11093 11199 11101 11102 11103 11104 11105 11108 11113 11203
-4.49 -5.15 -6.73 -4.20 -8.39 -8.77 -8.88 -8.79 -8.52 -7.63 -5.78 -4.07
 0.38  0.69  0.82  0.97  1.36  1.94  2.64  3.24  3.84  4.67  4.75  3.88

• HKLMAD.dat

- this file has the number of points (nb) in reciprocal space on the first line, and the following nb lines list nbnrj+3 values, corresponding to H K L and the recorded intensities at this point for all the energies:

21120
 1.01031 -0.02100 4.15338       0.00239       0.00208       0.00321       0.00296       0.00323       0.00325       0.00307       0.00286       0.00281       0.00252       0.00413       0.00264 
 1.01093 -0.02066 4.15175       0.00177       0.00375       0.00316       0.00234       0.00220       0.00232       0.00292       0.00234       0.00281       0.00278       0.00272       0.00331 

... 

Running NanoMAD

The help is given using 'nanomad --help':

NanoMAD, command-line arguments:
  --unitcell cell.dat : read unit cell parameters from file 'cell.dat'
  --fpfs FpFs.dat     : read unit f' and f" from file 'FpFs.dat'
  --HKLMAD obs.dat    : read HKL MAD data from file 'obs.dat'
  --out FTFAFNDPHI.dat: Saving FT, FA, FN & DPhi in file 'FTFAFNDPHI.dat'
  --fixDeltaPhi 0.0 : use fixed PhiT-PhiA (use with caution, for 2 or 3-wavelength experiments)'
  --importDeltaPhi dphi.dat : use PhiT-PhiA values from file:'dphi.dat'
  --corrfluo_points 0 4 0.85: correct fluorescence with fluo= average value over 4 points, starting at point #0, multiplied by 0.85
  --corrfluo_fsecond 0.01 : correct fluo, with fluo=0.01*f"
  --algo-pt  100000  : (OBSOLETED) optimize using Parallel Tempering, with 100000 trial/point
  --algo-lsq 30  : optimize using a Least-Squares algorithm, with 10 cycles/point
  --corr-factor corr.dat 1.0 : use correction factor (1 per energy) from file: corr.dat
                               The corrextion factors are elevated to the power given 
                               as a second argument (here 1.0), so that it can easily be changed.
  --silent            : try not to write anything !

Recommended usage (assuming you have the standard FpFs.dat, cell.dat and HKLMAD.dat files):
NanoMAD --algo-lsq 30

Results

The results are listed in the __

FTFAFNDPHI.dat.calc

file, with the first line giving the number of reciprocal space points, and the following lines giving the data for each point, with 13 values per line:

H  K  L  F_T  sigma(F_T)  F_A  sigma(F_A)  F_N  sigma(F_N)  Phi_T-Phi_A  sigma(Phi_T-Phi_A)  Phi_N-Phi_A  sigma(Phi_N-Phi_A)