Directives

Preparation of data for the DATA routine

ALPHA

It is used to start the a₂ stripping.

CELL a b c a b g

cell dimensions a, b, and c are in angstroms, a, b and g in degrees.

CONTENTS El1 n1 El2 n2 El3 n3 .........

Unit cell contents. Eli is the chemical symbol of atomic species i, ni is the corresponding number of atoms in the unit cell (to a maximum of 8 atomic species). For each chemical element up to Cf (Z=98) X-ray scattering factor constants are stored, together with information on the atomic number and weight, covalent and Van-der-Waals radii, etc. in a file (see notes on implementation). Neutron scattering factors are coded in the program for elements up to Pu (Z=94).

DOUBLE

It is used when the reading of the odd lines (or, of the even lines, if JUMP is activated) in the input pattern file must be skipped.

EQUIPORTION

If this directive is given the overall intensity of a group of overlapping reflections is equiportioned among the reflections in the group (equal E-values are obtained).

EXTEFILE string

This directive is used to supply an external file containing 'd' or '2q' values of peak positions. In the latter case the additional '2-THETA' directive has to be used.
This directive is used in place of the "peaksearch " directive.

FINDSPACE

FWHM x

This directive supplies the value of x for the overlapping calculation. Two reflections are assumed to be in overlapping if 2q₁ -2q₂ < x * FWHM₁. Default is x = 0.1.

FORMAT string

String is the run time format to read profile counts (default value per string is 10f8.0) or to read reflections (default value is 3i4,2f15.4).

HISTOGRAM n

n is the number of bars in the histogram for the a₂ stripping procedure (only if ALPHA directive is used).

ISOTOPE El sf

To modify the value of the neutron scattering factor for element El using the value sf. It must be used if NEUTRON directive is given.

JUMP

It is used to skip the reading of the first line (comment line) in the input pattern file.

MOREPEAKS

This directive is used together with the peaksearch directive in order to add more low intensity peaks to the set of peaks already detected via the peaksearch directive.

NEUTRON

This directive is used to specify that neutron radiation has been used.

NOREFINE

This directive is used to skip the cluster refinement step in the peak search procedure.

PATTERN filename

Filename is the name of the profile counts file (up to 40 characters). It is used to change the default. [Default is name.pow where name is defined using the command %STRUCTURE].

PEAKSEARCH

To enable the peak search step in the low 2q region of the pattern. A file named "ntreor.pea" containing the d values of peak positions is automatically created by the program. A graphic interface enables to change the peak search conditions. This directives can be used if the graphic interface has been request by the "windows" command.

RANGE thmin thmax thstep

thmin, thmax and thstep are the minimum 2q, the maximum 2q and the step width respectively of the powder pattern (thmin must be equal to the 2q corresponding to the first count in the pattern file and should be different from zero).

RECORD n

It specifies the number of profile counts per record, when n is different from 10 (max n value is 10).

REF2 string

This directive is used to supply an external reflection file. EXPO2004 reads directly the output provided by any profile fitting program. H, K, L, FWHM and F**2 must be supplied [default format is (3i4,2f15.4)]. If a comment line is at the beginning of the reflection file, the first character must be '>'. If this directive is used, the directives 'pattern' and 'range' must not be introduced.

SHIFT sx sy sz

Origin shift components if desired by the user. They must be integral multiples of 1/24.

SPACEGROUP string

String is the symbol of the space group, according to International Tables (1974). Blanks are necessary among the terms constituting the space group symbol (see Examples).

SYNCHROTRON

This directive is used to specify that synchrotron radiation has been used.

THCORR x

x is the Dq₀ value that is used to correct by zeropoint shift the set of 2q peak positions.
The shift value will be equal to 2(n-1)Dq₀, where n is the sequential number of the N-TREOR trial.
If this directive is not introduced the Dq₀ default value is the experimental 2q step.

2-THETA

This directive is used combined with the EXTEFILE directive to supply to the indexing program N-TREOR an external file containing 2q values of peak positions.

WAVELENGTH w

w is the wavelength (in Angstrom) used to collect the powder pattern.

Preparation of data for N-TREOR routine

TREORCELL num1 num2

This directive enables to select for refinement at the N-TREOR run "num2" (among all the N-TREOR runs carried out by EXPO2004) the cell numbered "num1" [among the possible cell ranked in function of the M'₂₀ figure of merit (Altomare, Giacovazzo, Guagliardi, Moliterni, Rizzi & Werner, 2000)]. The selected cell will be automatically refined via the program PIRUM (Eriksson & Werner, 1995).

All the directives of the indexing program TREOR90 (Werner, Eriksson & Westdahl, 1985) are still valid for the N-TREOR command and have to be used with the same sintax (see the N-TREOR manual for the details)

Preparation of data for EXTRACTION routine

ALL

To activate the procedure of selection of the profile function type (among Pearson VII, Gaussian, Lorentzian, Pseudo-Voigt) from the best fit of each interval.

DAMPING x

x is the damping factor used in the least squares routine (default value 0.1). It is convenient to use a small x value.

FAST

This directive is used if the graphic interface has been requested by the "window" command. In this case, the user graphic interaction in a default run is avoided.

FIRST

To activate the procedure of selection of the profile function type (among Pearson VII, Gaussian, Lorentzian, Pseudo-Voigt) from the best fit of the first interval .

FORMAT string

String is the run time format to read F-squared file if the directive FRECYCLE is used and if the default value for string is different by (3i4,15x,f15.4).

FRECYCLE filename

If the "filename" file is available from a previous run of EXPO2004 (or EXTRA), or from any source containing h, k, l and the corresponding F-squared values, Le Bail algorithm is started again for obtaining new estimates.

GAUSSIAN

To use only if the gaussian function is preferred.

INTERVAL n

n is the number of intervals in which the powder pattern is divided (max 8). n is only given if the user wants to change the automatic division of the pattern.

LORENTZIAN

To use only if the lorentzian function is preferred.

LOWBACK

To reduce the bakground by a constant factor equal to the minimum value observed count.

NCYCLE n

n is the number of cycles for each interval (default value is 60).

NOBACK

To not refined the background.

NOCELL

To skip the cell refinement.

NOSINGLE

This directive is used if the preliminary fitting of the standard peak (automatically selected by the program) is omitted. In this case a preliminary fitting of the first interval is carried out.

OPTIMIZE

To continue the refinement procedure for each interval.

POLYNOMIAL k

k is the background polynomial degree (max 10). k is given if the user wants to use a fixed degree in each interval and not the degree automatically selected by the program.

PVOIGT

To use only if the Pseudo-Voigt function is preferred.

RANDOM p

To activate the random procedure in the integrated intensity extraction step. p is the coefficient for the reflection overlapping definition. Default value = 0.5 (0<p</=1).

SMOOTHING

To actived the procedure for calculating the background by following Bruckner (2000). In this case the background is not refined.

STANDARD

To activate the procedure of selection of the profile function type (among Pearson VII, Gaussian, Lorentzian, Pseudo-Voigt) from the best fit of the standard peak.

SLOW

This directive can be used if the graphic interface has been requested by the "window" command. In this case the program stands by after some relevant calculations and waits for the user graphic interaction to go on.

VERBOSE

This directive is used to have a more detailed print in the output file. In this case, the R_p and R_pw values and the values of the refined variables are printed interval by interval.

WIDTH x

x is the factor which, multiplied by the FWHM of each peak, gives the total peak width. In this case the automatic calculation of x is not taken into account.

ZEROPROFILE x

x is the 2q shift value supplied by the user (to be substracted from the 2q observed positions). In this case the automatic calculation of the 2q shift using the preliminary fitting of the standard peak is skipped by the program.

Preparation of data for NORMAL routine


BFACTOR x

Temperature factor if the user wants to supply it. The scale factor is assumed equal to 1.

NOPREFERRED

If this directive is given the program does not apply the correction for preferred orientation.

NOPSEUDO

If this directive is given the program does not recycle the PSEUDOTRANSLATION information in a new extraction process.

NREFLECTIONS n

Number of active reflections with largest E-values subject to a minimum value of E(obs) = 1.0.
Default = 4 * number of independent atoms + 50 if centrosymmetric + 50 if triclinic + 150 to a maximum of 499. If PSEUDOTRANSLATION directive is on, the program tries to use all the E's down to 1.0.

NPLA n

n is the number of candidate planes for preferred orientation analysis (default 10; maximum 30).
The number includes the equivalent planes which will not be considered.

NZRO n

Number of smallest E-values (maximum E-value 0.3) to calculate psi-zero triplets. The default (and the maximum) is 1/3 of the strong reflections. The directive allows to decrease that number.

PLANE h k l G

Preferred orientation direction supplied by the user; G is the correction factor.

PSEUDOTRANSLATION n(1,1) n(2,1) n(3,1) n(4,1) n(1,2) . . . n(4,3)

If parameters are equal to zero, or omitted, the normalization routine performs statistics for the pseudotraslation effects and renormalizes the reflections on assuming the most probable pseudotranslation as prior information.
If user wants to supply a specific pseudotranslational symmetry, and this corresponds to a class given in Table 1, the n(1,1) can be set to the class number and the other values must be omitted.
If the pseudotranslation is more complex, it should be specified by up to 3 sets of 4 values n(i,j) so that

( n(1,j)*h + n(2,j)*k +n(3,j)*l = n(4,j)*m ) j=1,..,3

where m is an integer number.

THRP x

Threshold value of the mean fractionary scattering power (M.F.S.P.) to recycle the pseudotranslational symmetry information in a new extraction process.

Preparation of data for INVARIANTS routine

COCHRAN

To use the P3 formula. By default P10 formula is used.

CORRECTION x

If a PSEUDOTRANSLATION procedure is on, a correction factor depending on x is applied to the probabilistic argument of weak-weak-weak triplets when they are present. The default value is calculated by program.

x = -1 eliminates weak-weak-weak triplets,

x = 1 corresponds to the largest confidence in them.

EMAX x

x is the maximum value of E for the weak reflections for the psi-zero search (up to a maximum of NRPSIZERO reflections). x > 0.3 not accepted.

EMIN x

x is the minimum value for the normalized structure factors in the sigma2 search. x < 1.0 not accepted.

Default = minimum value of E for the strongest reflections selected by normalization routine.

ESTIMATION

To run the procedure which estimates the |E|'s for all the reflections and use them as a prior information in a new extraction process.

The procedure will not be applied if PSEUDOTRANSLATIONAL information has been recycled.

GMIN x

Positive triplets with G < x are not actively used.

Default value x=0.6 (in any case 0.2 < x < / = 1.0 is accepted range of value).

NLARGE n

To supply the number of largest reflections for the psi-zero search ( default = number of strongest reflections used for sigma2 search).

nlarge > nrtriplets is not accepted.

NPSI0

To not calculate PSI-0 triplets (default uses them).

NQUARTETS

To not calculate negative quartets (default uses them).

NRPSIZERO n

The number of weakest reflections for the psi-zero search.

Default = number computed by normalization routine.

The value will substitute the default one in the direct access file.

NRTRIPLETS n

The number of strongest reflections for the sigma2 search (up to Emin = 1.0).

Default = number computed by normalization routine (nstrong).

The value will substitute the default one in the direct access file.

Value less than nstrong/2 is not accepted.

NUMK n

The number of free-vectors used by P10 formula.

Default value is provided by EXPO according to the structural complexity:

n = min ( natom / msym + 30, 70 )

where natom is the number of atoms in the cell and msym is the number of symmetry operators of the space group.

YPSIE

To calculate PSI-E triplets (default doesn't use them).

Preparation of data for PHASE routine


ENANTIOMORPH n

Code of the reflection chosen by the user to fix the enantiomorph (by default the enantiomorph is chosen by the program ).

LIST n

n is the number of reflections at the top of the divergence map for which a list of the map is obtained. Default = no printout of the map.

MAXTRIALS n

n is the maximum number of trials when random approach is used (default 100). Only if RANDOM directive is on.

MINFOM x n

If this directive is used the program automatically stops when a solution is found with CFOM > x . Default value of x is 1.00.

n is the maximum number of phase sets (with the largest combined figure of merit - CFOM) to retain (default value = 10).

NOREJECT

Used to retain equivalent sets of phases.

ORIGIN n(i) phi(i)

Codes and phases of the reflections chosen by the user to fix the origin. The total number of reflections (max 3) needed to fix the origin must be given (by default the origin is chosen by the program).

PERMUTE n(i)

Codes of the permuted reflections chosen by the user (i.e. included in the number of required symbols, max 12).

PHASE n(i) phi(i) wt(i)

Codes, phases and weights of reflections with known phase (max 200).

If one card is not sufficient, the directive PHASE must be repeated in the other card(s).

RANDOM n

To use random phases starting sets.

n is the number of random phases. If n is omitted, it is equal to one half of the strong reflections (nstrong).

Maximum value allowed for n = nstrong - 4.

Minimum value allowed for n = nstrong / 4.

Default value for random generation seed is 67543.

This directive is not consistent with SYMBOLS directive.

SEED n

Random generation seed. n must be an integer large value and must be odd.

SPECIALS n

The number of reflections with restricted phase to be permuted (i.e. included in the number of required symbols, max 12).

SYMBOLS n

The number of permuted phases (max 12). Default = 5.

This directive is not consistent with RANDOM directive.

TABLE

To print the table of alpha values (at the beginning of PHASE procedure).

TEST

To restart the random number generator using the default seed. Only if RANDOM directive is on.

TRIAL n

To print the final phases for the specified trial n .

YNEG

To actively use negative triplets in the phasing process (default does not use them).

YNGQ

To actively use negative quartets in the phasing process (default does not use them).

Preparation of data for FOURIER/LEAST SQUARES routine

COORDINATION El dmin dmax n

The minimum and maximum value of the bond distance are assigned to element El. n is the coordination type.

Allowed values for bond angles are:

EDMO

This directive is used to enable a direct space procedure consisting of an Electron Density Modification (EDM) process followed by successive Fourier maps using (2Fobs -Fcalc) coefficients. Except for the Fourier directive 'set', all the rest of Fourier recycling directives are not valid for EDM procedure.

2EOEC

This directive enables to use (2Eobs-Ecalc) as Fourier coefficients in the Fourier step (if EDM procedure is applied).

EOBS

This directive enables to use the observed normalised structure factors (Eobs) as Fourier coefficients in the Fourier step (if EDM procedure is applied).

FRAGMENT string

Used to supply a known fragment to be completed. String is the name of the file in which, for each atom, are stored: Element X, Y, Z, isotropic thermal factor. If no isotropic thermal factor is supplied the program uses the Wilson-plot thermal factor for each atom.

FWHM D

This directive is used in order to change the value of D that is the parameter for the overlap condition 2q₁ - 2q₂ < D*FWHM₁.
Default value is approximately 0.9 depending on the ratio between the number of observations and the number of parameters to refine.

GRID x

The grid on which the Fourier-map is evaluated will have a spacing of approximately x angstroms. The default spacing is computed by the program (1/3 Å).

INTEGRATION x n

x is the radius of integration in the peak search routine (default value 0.5). n may be 1 to use the gaussian fitting of the fourier peak in the map or 2 to use the peak average density (default value 2).

LAYX

This directive can be used only if MAP directive is given. The Fourier-map will be printed in section of constant x.

LAYY

This directive can be used only if MAP directive is given. The Fourier-map will be printed in section of constant y.

LAYZ

This directive can be used only if MAP directive is given. The Fourier-map will be printed in section of constant z.

LEVEL n

All numerical values in the E-map greater than n will be underlined with **** in the lineprinter output to facilitate contouring.

The default is 100. The map is automatically scaled between ± 999 (approximately) at the grid points at which it is calculated.

Note, however, that it is printed between ± 99. This directive can be used only if associated to MAP directive.

LIMITS x1 x2 x3

The E-map will be printed from 0 to x1 along x, from 0 to x2 along y, from 0 to x3 along z. This directive can be used only if associated to MAP directive.

MAP

If MAP is specified, the E-map will be printed on the lineprinter. The printing of the E-map is rarely used.

The output is in sections of constant y with x across the page and z running down it on a grid of about three points per angstrom.

The maximum number of grid points across the page is 36 ( i.e. about 12 angstroms in length). If more are needed, a new page is started.

PEAKS n

The number of peaks to be searched for in the map. The default is the number of peaks for which

å(occ(i)*m) = 1.3 * n

where occ is the crystallographic site occupancy factor, m is the number of symmetry operators, n is the number of non-hydrogen atoms in the unit cell.

PSE

To actively use PSI-E triplets in these procedures (default doesn't use them). This directive can be used only if associated to YPSIE directive of INVARIANTS routine.

RADIUS El x

The value x of the radius used to compute the connectivity is assigned to element El.

RECYCLE n

Used to stop the recycling procedure after cycle number n. If n is equal to zero only the E-map will be calculated.

SET n

The serial number of the set from which to calculate the E-map. If 'SET n' is not specified, the set with the highest combined figure of merit will be used, and then if FOURIER routine is re-run, the set with the next highest combined FOM will be used.

SOGF x

The percentage of the largest |F| value reflections actively used in the Fourier recycling routine.

The reflections with the smallest |F| values corresponding to the rejected percentage have a zero weight value in the refinement process (default value 100.0).

SOGI x

The percentage of the most intense groups of overlapping reflections actively used in the Fourier recycling routine (default value 91.0).

STOPF x

This directive enables to stop the Fourier step at the cycle number x (if EDM procedure is applied). The default value of x is 10 (the maximum allowed value).

THRE x

x is the threshold for the E value of the reflections actively used in the Electron Density Modification step. The default value is 0.8.

THRM x

x is the fraction of the Fourier map points actively used in the Electron Density Modification step. The default value is 0.025.

THRW x

x is the threshold of the Sim-like weight of the reflections actively used in the Fourier step (if EDM procedure is applied). The default value is 0.5.

Preparation of data for LABEL routine

DLIGHT d tol

d is the expected heavy atom to light atom distance;

tol is the tolerance around the ideal distances. Default value = 0.5.

The program uses only one value of 'd' for all types of light atoms.

DWEIGHT d tol

d is the expected heavy atom to heavy atom distance;

tol defines the tolerance around the ideal distances. Default value = 0.5.

The program uses only one value of 'd' for all types of heavy atoms.

LABEL n1 El1 n2 El2

n is the number of peaks to relabel using El element;

El is the atomic species to assign to the peaks.

Only two combination (n, El) can be used.

COORD x_i

x_i specifies the expected number of heavy atoms surrounding each i-th heavy atom (the coordination type) (i = 1,2).

Preparation of data for POLYHEDRA routine

MISSING n1 n2 El tetrahedron (octahedron) d tol1 tol2

n1 and n2 are the two order numbers (taken from an external file or from a Fourier map) of the cations between which the missing cation must be located;
El is the missing cation label;
tetrahedron (octahedron) is the type of coordination of the missing cation (the procedure can only handle octahedron and tetrahedron);
d is the expected cation-anion distance;
tol1, tol2 are the tolerance about the distance and the tetrahedron (octahedron) angle, respectively. Default values are 0.3.

OCTAHEDRON El d tol1 tol2

d is the expected octahedral coordination distance around the El element;
tol1 and tol2 are the tolerance parameters for distances and angles, respectively.

TETRAHEDRON El d tol1 tol2

d is the expected tetrahedral coordination distance around the El element;
tol1 and tol2 are the tolerance parameters for the distances and angles, respectively.

Preparation of data for PATTERSON routine

E**2 (or E*E)

Coefficients to be used in the Patterson synthesis. This is the default.

E*F (or F*E)

Coefficients to be used in the Patterson synthesis.

F**2 (or F*F)

Coefficients to be used in the Patterson synthesis.

INVERSE

To activate the procedure of calculating the |F| values from an inverted suitably modified Patterson map to use as starting point for the Le Bail algorithm in the extraction routine.

MAP, LAYX, LAYY, LAYZ, PEAKS, LIMIT, GRID: See FOURIER directives.

NPAT n

The number of cycles of successive inversions of the Patterson map (default values: 6 for X-ray data, 5 for neutron data).