Data Entry and Data Input are all encompassing terms for any task that requires information to be entered into a computer. This manual page describes data input which is provided mainly through configuration files (.pamocrc, pamoc.rc, pamoc.cf), auxiliary input files (keyword inp) and files redirected to the standard input. PAMoC data input consists of a series of lines in an ASCII text file. The basic structure of a PAMoC input file may include several different sections, in any order:
An input section may consist of either a single line or a block of lines.
In general, PAMoC input is free-format and case-insensitive.
The contents of an external file may be included within a PAMoC input file using the following syntax: @filename. This causes the entire file to be placed at the current location in the input stream. Appending /N to such commands will prevent the included file´s contents from being echoed at the start of the output file.
Comments begin with an exclamation point (!), which may appear anywhere on a line, or with the number sign (#), which must be the first character of the line. Separate comment lines may appear anywhere within the input file.
A single line input section has the following form:
keyword <option1 option2 .... >
A block input section starts with a line that specifies the section-name and possibly a number of options and terminates with an end-of-section line according to the general form:
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[begin] section-name <option1 option2 .... > .................... .................... .................... end [section-name] |
The lines that are embedded between the begin-of-section and the end-of-section lines are subject to syntax rules that depend on the specific section.
Most of data-input sections override proviously entered data, when they are repeated (atom coordinates, lattice specification, space group, dma). A few data-input sections can be repeated as many times as needed to add required data, symmetry operations, rotation matrix, comments).
The input of atom coordinates consists of a series of lines of the form:
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[begin] coord [<units>] .................... element-label atomic-number x-coordinate y-coordinate z-coordinate atomic-number element-label x-coordinate y-coordinate z-coordinate .................... element-label x-coordinate y-coordinate z-coordinate atomic-number x-coordinate y-coordinate z-coordinate .................... end [coord] |
Any coordinate line must have either 4 or 5 fields, as indicated above.
The keyword coord, which specifies the section name, is followed by the option units, which specifies the units of the atomic coordinates. The allowed values are angstrom, bohr and au for cartesian coordinates, and fract[ional] otherwise. The latter is the default.
Element-label is a character string consisting of the chemical symbol for the atom. The elemental symbol may be optionally followed by other alphanumeric characters to create an identifying label for that atom. A common practice is to follow the element name with a secondary identifying integer: C1, C2, C3, and so on; this technique is useful in following conventional chemical numbering. The maximum length of the element label is 4 characters.
Both the element-label and the atomic number can be specified on the same line, but only one of them is usually given.
The remaining items on each line are Cartesian/Fractional coordinates specifying the position of that nucleus.
Cell parameters are entered on a single line input section, which has the following form:
cell <a b c alpha beta gamma>
The arguments are cell parameters (a, b, c), with lengths in angstrom or 1/angstrom, and angles (alpha, beta, gamma) in degrees or cosines of angles.
Lattice specifications are entered on a single line input section, which has the following form:
latt <centric-specification lattice-type>
The argument centric-specification is either A or C, for Acentric or Centrosymmetric crystal respectively, and lattice-type is P, I, R, F, A, B, C.
Symmetry operations are entered on a single line input section, which has the following form:
sym|symm|symtry <symmetry-operation-elements>
symmetry operation elements are given exactly as in the International Tables, the three general position coordinates being separated either by commas or spaces. If desired, more positions can be entered on a single sym line, by placing a semicolon between each of them. Alternatively, the symmetry operation is written in a purely numerical way by giving a translation vector and a 3 by 3 rotation matrix, i.e.: tx r11 r12 r13 ty r21 r22 r23 tz r31 r32 r33.
Single-line symmetry sections are repeated until the full number of symmetry operations is covered. Alternatively, symmetry operations can be entered as a block-of-lines input section:
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[begin] sym|symm|symtry symmetry-operation-elements end [sym|symm|symtry] |
The space group can be specified either by its International Tables number (1 through 230) or by its symbol. Explicit definition of the space group is an alternative to specify the lattice type and symmetry operations separately. It is entered by a single line input section of the form:
spac[e group] <number|symbol>
The first line of a DMA (Distributed Multipole Analysis) section contains the keyword DMA followed by the specification of the DMA-type:
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[BEGIN] DMA <DMA-type> .................... END [DMA] |
The DMA section is terminated either by the end-of-file or by an END line.
Types of DMA accepted by PAMoC are described in a separate page, that describes the External DMA Data Input File (.ext) addressed by keyword ext.
A rotation matrix can be provided to rotate, for example, the external multipole moments to the same orientation of the IDF moments:
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[begin] rotate [invert] R11 R12 R13 R21 R22 R23 R31 R32 R33 end [rotate] |
or
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[begin] rotate [invert] R11 R12 R13 R21 R22 R23 R31 R32 R33 end [rotate] |
Matrix elements can be distributed on 1 to 9 lines, provided that they are in row order.
The option invert requires that the inverse of the input matrix (instead of the input matrix itself)
is used to rotated the moments. If a second rotation matrix is given (in a separate section), the two
rotations are applied in sequence.
Control of a PAMoC run is realized through keywords and options which are entered in the form of single-line data-input sections:
keyword <option1 option2 .... >
Keywords and options can be entered also as environment variables or on the command line. In the latter case the keyword must be prepended by the minus sign (-). A complete list of keywords is given in a specific page of the manual.
Comments are entered as a block of lines which contains strings of ascii characters:
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[begin] comment[s] .................... .................... .................... end [comment[s]] |
Comment lines are printed on the standard output as they are read. Comment sections differ from the comments identified by an exclamation point (!) or by a number sign (#), which usually are not echoed on the standard output.