Running
NEIGHBOURS
NEIGHBOURS 3.01 may be run in the following 3 ways.
1. Running
interactively without default values - useful for initial setups
for geometry
2. Running with default values
3. Running non-interactively - useful for repeated
setups
The input file can
be either an FDAT format file (Cambridge Crystallographic Database), or
a SHELX format file. The interactive input is exactly the same in both
cases, except that SHELX files must be run interactively (there is no
option 2.). NEIGHBOURS reads the first character of the first record,
if it is # it is assumed to be an FDAT file, anything else is assumed
to be SHELX. If the file is in FDAT format, then characters 2-9 are the
refcod. Some of the input and output files from neighbours can use this
refcod as part of the filename. The FDAT filename must not be the same
as the refcod to run interactively. The cutoff filename should be cutoff
or file_1.cutoff, otherwise its name will be asked for.
Below is
a typical interactive run. > indicates output from NEIGHBOURS
> TYPE I FOR INTERACTIVE MODE
i
> File name containing basis set ?
filename.fdat
> Filename differs from csd refcod, interactive mode
> Used
> cutoff
> as file with standard bond lengths
> Maximum required inter-molecular contact?
4.0
> nbonds= 4
> Do you want to standardise bond lengths to hydrogen?
y
> Do you wish to insert any bond centre sites (Y/N) ?
n
> CVECTOR
> 14.861000000000
> Input zero for no symmetry subgroup or n to remove representation n
0
> Do you have a punch file yet (y/n)
y
> File name for punch file
filename.punch
> Labelled basis to be written to
> filename.dmain
> This file will be overwritten
> Do you have an axis definition file?
y
> Enter filename for axis definition file.
filename.axis
> Do you want to paste coordinates?
n
> Do you have a potential input file?
y
> Enter filename for potential input file.
pote.dat
> Labelled nearest neighbour list to be written to filename.nnl
> This file will be overwritten
> Labelled close contact list to be written to filename.ccl
> This file will be overwritten
> MACROMODEL file to be written to filename.mac
> This file will be overwritten
> NEMESIS file to be written to filename.nem
> This
file will be overwritten
Notes on responses
to questions
> TYPE I FOR INTERACTIVE MODE
i
I or i will run interactively, if response is N or n it will run according to option 3.
> File name containing basis set ?
filename.fdat
> Filename differs from csd refcod, interactive mode
If the filename is refcod.fdat, then it would proceed to run as option 2 for running with default values. This message is not printed if the file is in SHELX format
> Used
> cutoff
> as file with standard bond lengths
The file name with the bond cutoff should be cutoff or file_1.cutoff. This will then be used with message. If this file does not exist NEIGHBOURS will prompt for a name. (> File name with standard bond lengths ?)
> Maximum required inter-molecular contact?
4.0
This prints the intermolecular atom-atom contacts less than 4 Å in the output. Usually 4.0 is large enough.
> nbonds= 4
Number of records read from cutoff file, i.e. number of types of covalent bond.
> Do you want to standardise bond lengths to hydrogen?
y or n
This is necessary when X-ray hydrogen positions are used to correct fof the appointment of shortening of bonds. A few defaults are C...H - 1.08 Å, N...H -1.01 Å and O...H - 1.02 Å. See options for more details.
> Do you wish to insert any bond centre sites (Y/N) ?
n
Normally n, but for high accuracy work on small polyatomics, e.g. N2, then an additional multipole site at the centre of bond will provide a more accurate description of the close contact list.
> CVECTOR
> 14.861000000000
> Input zero for no symmetry subgroup or n to remove representation n
0
Normally 0 to use crystallographic symmetry. When DMAREL shows that the minimum has a lower symmetry, then a number of the representatio with negative values is given.
See options for more information.
> Do you have a punch file yet (y/n)
y or n
n only used for runs to establish molecular geometry in local axis system.
> File name for punch file
filename.punch
If n is typed, dmain file is set up with LEVEL 0 multipoles. Note that charges of free ions are not read from the punch file, the dmain file will need to be changed. If more than one type of molecule in crystal, then the punch file will need to be constructed from punch files from individual ab initio calculation. Free ions, e.g. Cl- needs to be added manually.
See input files for punch file format.
> Labelled basis to be written to
> filename.dmain
> This file will be overwritten if file exists
> Do you have an axis definition file?
y
n is only useful to print out the atomic numbering and intramolecular connectively table if you do not have a chemical diagram from which to choose your axis definition.
> Enter filename for axis definition file.
This must correspond to the axis definition used for calculating DMAs.
See input files for axis file format.
> Do you want to paste coordinates?
n
Normally n. This option can be used to paste another molecular structure into the crystal, so that the centre of mass matches and the molecular local axes are parallel. It is particularly useful for comparing the minimum structure with an ab initio optimised version of the experimental structure. Type y if you want to paste coordinates over an experimental structure.
See options for more information.
> Do you have a potential input file?
y
> Enter filename for potential input file.
pote.dat
NEIGHBOURS 3.01 can insert Buckingham potentials from a file into the dmain dataset. pote.dat should contain any number of buckingham potentials in the same format as used in the dmain file, beginning with BUCK and ending with ENDS. Only Buckingham potentials needed for the structure are copied to the dmain file. Missing potentials are set to zero.
See input files for potential format.
> Labelled nearest neighbour list to be written to filename.nnl
> This file will be overwritten
> Labelled close contact list to be written to filename.ccl
> This file will be overwritten
> MACROMODEL file to be written to filename.mac
> This file will be overwritten
> NEMESIS file to be written to filename.nem
> This file will be overwritten
These files can be used to find atoms to define the axis system if a graphics program is not available.
Again responses
to the terminal from NEIGHBOURS are indicated by >
2
a. Redirecting
the input from a file
Start the program by typing the following at the unix prompt
neigh.out < BAWNIW01.fdat
>TYPE I FOR INTERACTIVE MODE
Ignore this message.
Neighbours will run
only if fort.22 file exits, and it will
not be expecting any more user input assuming the default values and file
names described below.
2
b. Using
an FDAT filename which is the same as the refcod
Start the program by typing the following at the unix prompt
neigh.out
>TYPE I FOR INTERACTIVE MODE
I or i
>File name containing basis set ?
BAWNIW01.fdat
Neighbours will run without expecting any more user input assuming the default values and file names described below.
Start the program by typing the following at the unix prompt
neigh.out
>TYPE I FOR INTERACTIVE MODE
I or i
>File name containing basis set ?
BAWNIW01.fdat
Neighbours will run
without expecting any more user input assuming the default values and
file names described below.
If no punch file is present, multipoles are written as LEVEL 0. If no axes file is present, no axes are written to dmain. If no pote.dat file is present, BUCK potentials are written as zero.
DEFAULT VALUES OF
CONSTANTS AND ANSWERS TO QUESTIONS
which are input interactively using option 1.
>Maximum
required inter-molecular contact?
4.0
>Do you want to standardise bond lengths to hydrogen?
y
>Do you wish to insert any bond centre sites (Y/N) ?
n
>Input zero for no symmetry subgroup or n to remove representation
n
0
>Do you want to paste coordinates?
n
> TYPE I FOR INTERACTIVE MODE
n
NEIGHBOURS will read fort.22 and interpret this as the user input.
Here is a typical fort.22 file
file_1.fdat
4.0000000000000
y
n
0
y
file_1.punch
y
file_1.axis
n
y
pote.dat
fort.22 may be edited to
a) change the input fdat file
b) change the options that NEIGHBOURS uses
This way of running
NEIGHBOURS is useful for running a series of cells where the default options
are not used.