Keywords section

Keyword

Parameters

Description

CELL

7f

Only one CELL card is allowed in INFO.INP

icentro, icsog

If  icentro.eq.1 and isym.eq.17 (-1 point group), the file CENTRO.OUT is generated containing pairs of centro-symmetrical reflections (together with some statistics on each pair). If icentro.eq.0, the CENTRO.OUT file is closed.

The content of the file CENTRO.OUT is also reported in output.txt, for those pairs whose d/s (difference/standard dev.) is greater or equal to icsog.

More than one CENT card is allowed, but the file CENTRO.OUT is always opened as a new one; however, the output.txt file will record all the relevant pairs, according to the icsog value.

When closing an analysis with "CENT/0 icsog", it is the latter icsog value entered which is used, and not that from the previous "CENT/1 icsog" card. To perform the analysis on whatever data file, the triclinic symmetry (17) must always be chosen (independently by the real symmetry).

Writes the file DIST.HKL in: DAT0i.OUT if icq=i=1,...,5; DUMMY.INP if icq=6; DATA.INP if icq=0. See also the DIST card.

Copies files: equstat processes directly the DUMMY.INP working file, whose information (reflections) are loaded as a whole in memory. Because the data collection contained in DATA.INP can be fairly large, the latter file can be splitted in several segments (up to 5) using the THET or SMIS Kwd's; these last 2 Kwd's generate the files DATA0i.OUT (i=1,5) which can be copied in DUMMY.INP by means of  the COPY card.

"COPY i1 i2 i3" copies DAT0i2.OUT in DUMMY.INP (note that for this operation only the 2nd i1 integer parameter is relevant). An i1 different from 0 will copy the file DAT0i1.END in DAT0i1.OUT (the files DAT0i.END are generated by other instructions, e.g. WEAK or ELIM); if i1=6 all files DAT0i.END will be copied in DAT0i.OUT (i=1,5). The sequence of operations is: copy END files in OUT files then OUT files in DUMMY.INP (if i2 is not 0); so, "COPY 3 3 0" will copy DAT03.END in DAT03.OUT and DAT03.OUT in DUMMY.INP; "COPY 6 1 0" will copy all the DAT0i.END files in DAT0i.OUT and DAT01.OUT in DUMMY.INP. The i3 parameter is used to copy DATA.SPC in DATA0i3.OUT (DATA.SPC is generated by the COND Kwd).

or

0 0 0

Sets special conditions for selecting particular classes of reflections.

id specifies direct (id=1) or complementary (id=2) conditions, that is, if id=1, reflections are selected and displayed if they match the conditions); if id=2 such reflections are not selected whereas, reflections NOT matching the condition are selected.

ia is the "and/or" flag: if id=1 and if more than one condition has been chosen, reflections are selected if they, at least, match one condition (ia=0) or only if they match all the conditions (ia=1). If id=2 (complementary condition) and if ia=0 ("or" flag) all the reflections which do not match at least one condition are selected, whereas if ia=1, only the reflections which do not match any condition are selected.

n specifies the number of conditions listed in the row below. See the TABLE  for a list of possible values of i1,..,in, together with the corresponding condition.

COND 0 0 0 deactivate special condition selection.

COND will affect the statistics on the number of equivalents in each star: only COND-selected reflections will be taken into account.

All reflections selected are written in the file DATA.SPC.

See also the STAT card and the NOTE on the COND card.

Calculates interplanar distances for planes with indices between those given in input (ih1,...,il2). If if1=1 the hkl list is written in the file DIST.HKL (with dummy F and sigma's); if if2=1, the list is written in output.txt. It is possible to specify a range for sin(theta)/lambda, by setting the values of the variables stl1 (minimum) and stl2 (maximum); if stl2.eq.0., all reflections will be generated. See also CEQU.

Searches and eliminates from the files DAT0i.OUT the reflections given in input. For each reflection j, only irj reflections are retained.

Resulting files: DAT0i.END  (a "COPY 6 0 0" instruction will copy all the END files, back to the OUT ones).

Only stars with at least ieq equivalents are printed in the output.txt file. However, cluster and global statistics are evaluated on all stars (whose average F or I is greater then the cut-off specified in the STAT card).

Evaluates the distribution of intensities in the data collection files. The histogram of the intensities is divided into ng groups. If ifile=0, the file DATA.INP is considered; if ifile=i (i<>0), the file DAT0i.OUT is considered.

Writes a summary of the input (info.inp file) at the end of the output.txt file. For some cards, only the card itself without its numerical parameters is written.

Activates inconsistency detection (if ainc=0. the detection is deactivated). This option works so that if the percentage difference between the ratios F/e.s.d. and F/sig. [where e.s.d. is the standard deviation (std. dev.) of the intensities of reflections derived from the counting statistic, whereas sig. is the std. dev. of the intensities of the equivalent reflections, with respect to the average intensity] is higher than the value ainc, then the inconsistency is detected. Inconsistent equivalent reflections are written in the file DATA.DBL if jincof.eq.1, and can be deleted from the data collection (see WEAK instruction).

See NOTE to the STAT card.

Prints summary statistic at the stage of the analysis at which the instruction is encountered; this is the default at the end of the analysis.

Defines a distribution of intensities for the statistical evaluation of std. dev. (sig.) of the intensities (see SIGM instruction). The integer n defines how many groups of intensities (a1,..., an) follow in the line.

This instruction must be used in conjunction with SIGM.
Only one INTS card is allowed in INFO.INP

Optimal values for all of the parameters to be supplied in INTS are determined by the smart program.

See also SIGM, SOUT

Such card is to be used in connection with SELE (it is effective only if SELE is used). It creates the file LIST.HKL containing only the hkl indices of reflections selected by means of SELE card. If ilist=1, the file LIST.HKL is created; if ilist=2, such a file is opened in append mode; if ilist=0, LIST is deactivated and LIST.HKL is closed. The iustar parameter is the number of equivalents, for each star, to be written in the LIST.HKL file (and in the  SELECT.HKL one; see SELE card); if iustar.eq.0, all the equivalents are written.

See also SELE, RANK and SORT cards.

This is a printing option; LONG (the default mode) causes all reflections to be written in the output.txt file and should be used to deactivate the SHOR instruction.

Transforms the hkl indices according to the matrix whose elements are imij. Both the input file and the output file is  DATA.INP. Cell is transformed accordingly, The MATR card should follow a CELL card.

 It is to be noted that the reflection data file (DATA.INP) is modified by the MATR card.

See also SWAP.

Merges files: if mer=0, n files DAT0i1.END, DAT0in.END are merged in DATA.END. If mer=1, n files DAT0i1.OUT, DAT0in.OUT are merged in DATA.OUT.

Sets parameters used in the calculation of rank of reflections, as performed by the SELE card, within each star of equivalents. Default values (if SELE card is active, whereas RANK is not present) are: i1=100, i2=10, i3=1. Several RANK cards are allowed to be present in a info.inp file.

See also SELE and LIST cards.

Searches for specific stars in the data collection file. if iwfh.eq.0, stars are not written on DATA.SPC; if iwsh.eq.1, DATA.SPC is opened as a new file; if iwsh.eq.2, DATA.SPC is opened in append mode; if a COND card has previously been used and a DATA.SPC file is still opened: use iwsh.eq.4 to preserve reflections in it, or iwsh.eq.3 to open it as a new file.

SEAR will load a list of n reflections from the input file INFO.INP (jhs1,...jlsn), or from the file SEARCH.INP if n.eq.-1; from the loaded reflections, SEAR calculates all the equivalent reflections according to the selected Laue group (if a non centrosymm. point group has been selected, the inversion center is added) and performs the searching. The list of all reflections (input + symmetry generated) is printed if iprs.eq.2; if iprs.eq.1 only the input reflections are printed, whereas no refl. are printed if iprs.eq.0. If n.eq.0, the searching is deactivated.

All the input intensities and standard deviations are multiplied by the factor 1/isca. isca=0 deactivates the scaling.

Selects reflections to be written in the SELECT.HKL file, according to the number of equivalents (N): if ig=0, a star is written in the file if  N equals one of the ns is(i) values; if ig=1, the star is written if N is greater than or equal to is(1). If ig=1, ns should be set to 1; if ns > 1, only the last is(i) is considered. If ns=0, no is(i) numbers have to be given, and selection is deactivated. If  iop=0, a new SELECT.HKL file is created; if iop=1 such file is opened in append mode.

A number of several SELE cards are allowed in info.inp, each new one changing the selection conditions. Set iop=1 to preserve reflections already written by previous SELE cards.

If only a limited number of equivalents is to be written on SELECT.HKL (and LIST.HKL; see LIST card, variable iustar) all the reflections in each star are previously ranked and only the first ones (iustar), in the resulting ranked list, are written in the file. The rank is calculated by the following method: being H(x) the "step function" such that

H(x)=0, if x<0; H(x)=1 if x >=0,

rank = i1*[H(|h|-|k|)+H(|h|-|l|)+H(|k|-|l|)] +
       i2*[H(h)+H(k)+H(l)] +
       i3*[H(h)*H(-k)+H(h)*H(-l)+H(k)*H(-l)].

Deafult values for i1, i2 and i3 are 100, 10 and 1 respectively, but can be changed using the RANK card. With the default values for i1, i2 and i3, higher rank is given to reflections having, in the order, |h|<|k|<|l|; h,k,l>0; h>0 and k,l<0; k>0, l<0.

File SELECT.HKL file is written with free format.

Sets to 0 all the statistical variables (to be supplied, if more than one analysis cycle is performed, before each new cycle). See also INFO.

Produces a limited output on the file output.txt: if the value of the average intensity of the reflections in a given star is less than lim, the detailed information regarding that star is not written on the file output.txt. If lim=0, only summary statistics are reported.

Statistics on the number of equivalents in each star are NOT affected by SHOR.

See also LONG.

Defines parameters for the evaluation of standard deviations on the equivalent reflections. If isig=0 the sigma evaluation is deactivated (no matter what the isi and iom values are). If isig=1 the sigma evaluation is activated.

If iom=0, the transformation of the sigma's is performed only for those stars with a number of equivalent reflections greater or equal to isi; for the stars with a smaller number of equivalents, the old sigma, based on the counting statistic (e.s.d.), is retained (averaged on all the reflections belonging to the star). If  iom=1, the transformation of the sigma's is performed as in the case of iom=0, but the stars with a number of equivalents smaller than isi are neglected (i.e., they are not written in the output file of sigma transformed reflections). If iom=2, the stars with a number of reflections greater or equal to isi are sigma transformed and the new sigma values are stored according to the averaged intensity values of the reflections: a distribution of intensities is built with the INTS card (which must be present if iom=2): up to 10 intensity groups are defined so that if the intensity of one star falls within one group (i.e., if its intensity is nearer in value to that assigned to that group, with respect to any other group), then its sigma is averaged together with those of all the reflections belonging to the same group. The sigma values, for the stars with a number of equivalents smaller than isi, are then assigned on the basis of the respective intensities, using the sigma values previously evaluated for each group of intensities.

If the sigma evaluated from the equivalents is smaller than the averaged sigma from the counting statistic, the latter is retained.

The SIGM card produces the file DATA.SIG and DATA2.SIG, containing respectively the merged and all the reflections, with the sigma's transformed according to the schemes given above.

See NOTE to the STAT card.

Divides all input reflections (from DATA.INP) in 5 files DAT0i.OUT (i=1,5) according to the im = h²+k²+l² values; the ilim variables define the limits of the 5 intervals of such values (if im.lt.ilim1 the corresponding reflection is written in DAT01.OUT...).

This instruction can be used instead of THET for distributing the reflections in the files DAT0i.OUT (i=1,5), only when cubic systems are concerned.

Finds best values of theta for the repartition of reflections in the 5 files DAT0i.OUT and makes the subdivision. No THET cards should be used when SMRT is present.

CELL card must be supplied before SMRT.

See also THET card and instructions for the smart program  (which uses the same method).

Sorts the hkl indices of the file LIST.HKL, in such a way that l "runs faster" than k, which run faster than h. To be used only in connection with LIST and SELE cards.

See also SELE, LIST and RANK cards.

Forces the evaluation of standard deviations of  independent reflections, for stars with a number of equivalents smaller than isi (see SIGM card), to be performed at the point where such card is found, no matter if the analysis over all the reflections has been completed. This card can be useful if the number of reflections whose standard deviations are to be evaluated from the reflections of comparable intensity, is so high to exceed the maximum limit allowed by the program; in such a case, one or more SOUT cards would solve the problem.

If  iom (see SIGM card) is not 2, SOUT has not effect.

See Also SIGM, INTS

Eliminates from data files DAT0i.OUT (i=1,5) all the reflections selected with the COND card; shows statistics of the eliminated reflections in form of a histogram with igr groups.

Input files DAT0i.OUT; output files DAT0i.END (i=1,5).

See also COND

This is the most important card. STAT starts the statistical analysis of the reflections contained in the file DUMMY.INP (see the COPY card). Reflections are grouped together according to the symmetry (specified by the SYMM card); average intensities and standard deviations are evaluated for each star. 

j3 can have values 0, 1, 2 or 3; if some reflection, in the star, has an intensity differing from the maximum one (in the star) (j3=0) or from the average (j3=1) of a quantity greater than perc (given in percentage), then such reflection is marked (and eventually written in the file DATA.DBL, see below). If j3=2 or 3, then the ratio F/e.s.d. of the reflections is considered: the reflection is marked if F/e.s.d. is smaller than perc and j3=2, or if F/e.s.d. is greater than perc and j3=3.

Marked reflections are written in the file DATA.DBL (but see also j5)  if j1=1; using  j2=1 causes the file DATA.DBL to be opened in append mode so that successive STAT cards cumulate all the marked reflections in the same file; if j2=0, DATA.DBL is opened as a new file.

The marked reflections are written in DATA.DBL only if, in a given star, the ratio not_marked/marked reflections (normal/anomal) is greater than j5; because the reflections written in DATA.DBL can be eliminated from the data collection with the WEAK card (since they are classified as anomalous according to the criteria, codified in the j3 and perc values), if the ratio normal/anomal is too low, it is hard to say which  reflections are normal and which are not; in this case it is preferable to retain such reflections, since the large value of the corresponding evaluated standard deviation will give them a low weight in the structural refinement; with this idea in mind, an elimination criterion based on j5 has been conceived.

If j4=1, all the reflections in a stars are written in order of intensity; if j4=2, they are ordered according to a ranking calculated as in the case of SELE and LIST cards (to be used in the analysis of the indices generated by DIST). If j4=0, no ranking is performed and the reflections appear in the order they have in the input file.

Analysis is performed only for  those stars whose average intensity is higher than ctf.

NOTE: some of the functions performed using the cards previously discussed (COND, INCO, SIGM...) become effective only when STAT is executed.

Performs the swap of the indices hkl according to the values of  j1, j2 and j3: e.g., if  the values 2, 1 and 3 are assigned to j1, j2 and j3 , respectively, then the indices will be transformed from hkl to khl, etc...

The operation will be active on the indices in the file DAT0i.OUT if ifile = i < 6; if ifile=6, the indices in all of the 5 files DAT0i.OUT will be transformed.

The same operation could be performed by MATR.

Specifies the symmetry according to which the reflections are to be grouped. See the TABLE for the correspondence isim - symmetry.

Selects reflections from DATA.INP which have  correspondent theta values in the interval th1 - th2, and copies them in DATOi.OUT (i = ifile). This is the card to be used, at the beginning of the analysis, to split the DATA.INP file in up to 5 files DAT0i.OUT.

NOTE: the CELL card must be provided before the THET one.

See also SMRT card.

Allows the introduction of titles or comments in output.txt. More TITL cards can be used and they can be placed everywhere in info.inp.

Transforms data from F to I (itr1=1) or from I to F (itr1=2); if itr1 has any other value, the transformation is deactivated. If itr2=0 also the standard deviations are transformed; if itr2=1, the standard deviations are evaluated as square root of the resulting F or I.

if (ns.ne.0) then
 i(1), ni(1)
iv(1),...iv(ni(1)) 
.
.
i(ns), ni(ns) 
iv(1)...iv(ni(ns)) 
end if 

This card allows the selection of reflections according to rules specified by the user. Three groups of rules can be defined: (1)  linear combination of indices; (2) restrained  values; (3) special relations between the indices or special conditions on the indices.

If more than one rule is specified, every star is selected if at least one reflection, in it, satisfies all the given rules. In case of the type (1) rules, the user can specify the three coefficients of the linear combination (l1, l2 and l3); the result of the combination:

is compared to the lc value: if lc=1, the star is selected if isum is odd (for at least one reflection in the star); il lc=2, the star is selected if isum is even; if lc.gt.2, the star is selected if isum is a multiple of lc.

If l1=l2=l3=0 and lc=2, the rule is deactivated (that is, every reflection is selected, since isum is always even).

If ns.ne.0, ns restraints on indices are used: for each restraint j, if i(j)=1, the h index is considered; if i(j)=2 or i(j)=3, the k and l indices are respectively considered. Stars are selected if their indices equal one of those specified by the iv(j) values (ni(j) is the number of such values, for each i(j) index).

If nr.ne.0, a number (nr) of special relations are considered; see the TABLE for the list of relations available. 

All the selected stars are written in the file DATA.SPC; the file is opened as a new one if ifile=0; if ifile=1, it is opened in append mode.

that is: reflections (stars) are selected if h+k is even, k=l and l=0, 2, 4 or 6.

that is: reflections with h=k and l even are selected.

Eliminates from the files DAT0i.OUT (i=1,5) all the reflections contained in the file DATA.DBL. A statistic of the eliminated reflections is shown in the form of a histogram with igr groups.

Output files are DAT0i.END (i=1,5). Such files can be merged in a unique DATA.HKL file, with the me command of the integrated system.