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COMMANDS Block Fullprof

Particular keywords can be included in the COMMANDS/END_COMMANDS section of a PCR file, after the line given the name of the current phase. The number of these commands is limited to 20 per phase. There are two type of COMMAND block

Local
Placed after the line given the name of the current phase. The commands ( limited to 20) modifies only the current phase

Global
Two lines starting with VARY and FIX   for controlling the refinement of global parameters of each pattern should be in the PCR file just after  following items: Lambda1, Lambda2, ... (CW) or Bkpos, Wdt, Iabscor (TOF).Moreover using this method one can refine the ratio of the intensity of the two wavelength    components in a constant wavelength (CW) pattern.
 The first line should be the VARY line and the second one the FIX line. After this two  master keywords, other keywords may be give for refining or fixing different parameters.   The presently available keywords are the following (notice that they are case sensitive)

     Global keywords:
         backgd   : all linear interpolation background parameters outside excluded regions
         add_back : all additional parameters of the linear combinations of external profiles
         back_nn  : Background parameters from 1 to nn are varied or fixed
         Microabs : Microabsorption parameters (P0, Cp, Tau -> only with FIX)
          Scale_Factors   -> Produces the refinement of all scale factors
          Cells           -> Produces the refinement of all cell parameters (only for automatic mode)
          Boveralls       -> Produces the refinement of all overall temperature factors Bov
          Ysize           -> Produces the refinement of Y (isotropic Lorentzian size) for all phases
          Gsize           -> Produces the refinement of G (isotropic Gaussian size) for all phases
          Xstrain         -> Produces the refinement of X (isotropic Lorentzian strain) for all phases
          Ustrain         -> Produces the refinement of U (isotropic Gaussian strain) for all phases

     CW:
         zero, sycos, sysin, P0, Cp, Tau
         ratio -> Ratio of the intensity of the two wavelength components

     TOF:
         zero, dtt1, dtt2, Zt, dtt1t, dtt2t, xcross, width

     All this can be combined with the traditional method of putting manually the codes
     (or just a 1.0) for refining parameters.

  Example:
................
!
! Lambda1  Lambda2    Ratio    Bkpos    Wdt    Cthm     muR   AsyLim   Rpolarz ->Patt# 1
 1.540560 1.544330  0.45002   25.000 15.0000  0.9100  0.0000   30.00    0.0000
!
 VARY ratio  back_4
 FIX    Tau
!
!NCY  Eps  R_at  R_an  R_pr  R_gl     Thmin       Step       Thmax    PSD    Sent0
  6  0.10  1.00  1.00  1.00  1.00     25.0000   0.025000   143.0000   0.000   0.000


VARY/FIX

Within an instruction VARY of an instruction FIX individual parameters of selected atoms are allowed.
The available structural parameters are:

The names of the AtmLabel must be identical to those given in the list of the asymmetric unit (The instructions are case sensitive). As usual the instructions are applied as they appear. For instance a FIX instruction after a VARY may suppress a refinement code.

In case of multiple patterns the instruction VARY keyword affect to all the pattern sections of the particular phase, in which the COMMANDS block is defined, providing  independent codewords.
For varying or fixing parameters for an individual pattern,  the suffix "_n" is appended to the keyword with "n" being the number of the pattern. This last option has also been implemented for the profile parameters of CW case.

!-------------------------------------------------------------------------------
!  Data for PHASE number:   1  ==> Current R_Bragg for Pattern#  1:     0.23
!-------------------------------------------------------------------------------
My Phase name
COMMANDS
     VARY  xyz_Fe  xyz_O1
     VARY  x_Mn1  z_O27  y_Ho1 b_Al
     FIX   b_Mn1 x_C23
     VARY cell yy
     VARY occ_Fe2
   END COMMANDS

tells to the program that it should refine all positional parameters of atoms Fe and O1, the "x" coordinate of Mn1, the "z" coordinate of O27, the "y" coordinate of Ho1 and the temperature factor(s) of atom Al. If Al is anisotropic all beta-parameters compatible with the site symmetry are refined.The instruction FIX avoid the refinement of the thermal parameters of Mn1 and the "x" coordinate of atom C23.

EQUAL/MVARY/MFIX

The keyword EQUAL appearing within a COMMANDS block allows to make constraints between parameters belonging to different phases or patterns. The format of the instruction EQUAL/MVARY/MFIX  is the following:
EQUAL  name_parent_parameter   name1  mult1   name2 mult2  .... nameN multN
The name of the parent parameter informs the program that this parameter will be refined (implicit VARY) and the other parameters are simultaneously refined using the same code but with other multipliers.
An example is given below:
EQUAL  occ_Fe2_ph1  occ_Mg2_ph1 -1.0  occ_Fe3_ph1 -1.0  occ_Mg3_ph1 1.0
This means that we are refining the distribution of Fe and Mg between two sites
maintaining full occupation of both sites and fixing the composition. Remember that the EQUAL instruction means that the variations of the initial parameters are constrained and not the values themselves. For structural parameters it is not needed to explicit the number of the pattern, however for some parameters it is needed to explicit this.
Is is possible to make constraints between parameters of different phase or different patterns. In principle the name of the parameters are those appearing in the output files below the title: SYMBOLIC NAMES AND INITIAL VALUES OF PARAMETERS TO BE VARIED.

COMMANDS
VARY xyz b       <---> This is for refining all positions and thermal parameter
FIX z_Ba1        <---> This is for fixing an atom coordinate because the space group is non-centrosymmetric
PEQU_pha uu vv ww   <---> This tells to the program that the U,V,W Caglioti parameters are the same for all phases
VARY yy gsz      <---> This makes to refine the Lorentzian and Gaussian size parameters for the current phase
EQUAL occ_Si1_ph1 occ_Si2_ph1 -1.0 occ_Al1_ph1 -1.0 occ_Al2_ph1 1.0  <---> Constraints of occupation factors in phase 1
EQUAL Biso_Si1_ph1   Biso_Si_ph2 1.0   <---> Atoms Si1 and Si of phases 1 and 2 respectively have the same Biso
EQUAL Biso_Al3_ph1   Biso_Al1_ph2 1.0
EQUAL Biso_Al4_ph1   Biso_Al2_ph2 1.0
EQUAL Asym1_ph1_pat1 Asym1_ph2_pat1 1.0  <---> Asymmetry parameter 1 of phase 1 and 2 are the same for pattern 1.
EQUAL Asym2_ph1_pat1 Asym2_ph2_pat1 1.0
END_COMMANDS

FIX_SPC/SAME_Biso

FIX_SPC spc1 spc2 spc3 ... spcN
SAME_Biso spc1 val1 spc2 val2 ... spcN valN

Where spc"i" is the symbol used for the scattering power of the atom (normally the chemical   element symbol). the command FIX_SPC means that all free parameters of a particular chemical      species are fixed. For instance, if one wants to fix all hydrogen atoms of a structure the   command "FIX_SPC H" will fix all coordinates, occupation and displacement parameters of H-atoms.
The values val"i" correspond to the value of the isotropic temperature factor to be   assigned commonly to all atoms of species spc"i". This value should be initially be given  as negative. The program will change that to positive and only when the negative value  appears in the PCR file the Biso already existing in the file are replaced by those   given in the SAME_Biso instruction.
     Examples:
COMMANDS
FIX  O H
SAME_Biso  O -0.93  F -0.98
END_COMMANDS

PEQU_pat/PEQU_pha

 The Two new instructions have been introduced to make constraints between profile parameters
in mutipattern-multiphase cases. These instructions act as VARY but assigning common   codewords to a series of variables.
Example:
COMMANDS
PEQU_pat cell         The cell parameters of a particular phase are equal for all patterns
PEQU_pha uu           The U parameters for the different phases and  patterns have same codeword
END_COMMANDS

DLIM pat d_min

where pat is the number of the pattern and d_min the value of a d-spacing. Only the reflections having a d-spacing greater than the provided d_min value are used in the refinement of the data.
Example:
 !---------------------------------------------
My phase name DLIM 2 2.14 DLIM 3 1.5
 !Nat Dis ....
The reflections of pattern number 2 are limited to d-spacing greater than d=2.14 angstroms and those of pattern number 3 to d-spacing greater than 1.5 angstroms. This may be useful for magnetic structure refinement when using a diffraction pattern going far in Q (for instance in TOF case)

LAYER_A, LAYER_B, LAYER_C

the keywords LAYER_A, LAYER_B and LAYER_C are used to tell the program that the current phase will be treated as a single layer, so the reflections (H00),(0K0) or (00L), respectively, will be suppressed
and the atom coordinates will be given in angstroms along the corresponding direction.
Considering an artificial (quasi-empty) supercell cell with a very long axis in the perpendicular direction to the layer, the 3D diffraction pattern approach to that of the single layer diffraction pattern without need of integrating the rods in reciprocal space. To eliminate the ripples a long axis together with a special broadening is enough.
The method isbased in the idea developed by K. Ufer et al.(Z. Kristallogr. 219, 519 (2004)) making the method perfectly compatible with the Rietveld method.
The keywords LAYER_A, LAYER_B and LAYER_C must be followed by the order of the supercell used, as in:
  COMMANDS
    LAYER_C 15
  END COMMANDS
This means that corresponding supercell parameter (as given in the unit cell line)  is c=15*cs, being cs the c-parameter of the subcell. This is needed to conserve the (0,0,l=L/15) reflections that are treated separately.
This option is still at a testing stage. A complete account will be given as soon as possible.

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