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Input files required

In order to run NEIGHBOURS, the following files are required. (e.g. examples for formic acid)

Standard input (Unit 5)

If running in interactive mode, the program must read in the character 'I' or 'i' as the first character read in. If this is what is read, the rest of the screen input is read from standard input. The FDAT or SHELX input is read from unit 11.

If running from default values using the UNIX file redirection, the input file ,must be in FDAT format. The program detects FDAT format files using the first character which is always '#'. Standard input (unit 5) is used for the FDAT file input. fort.22 file must exists in order for this to run.

Running from default values using an FDAT filename which is the same as the refcode is treated the same as interactive mode.

If running in non-interactive mode, the program will read any other character as its first character. In this case, the rest of the normal screen input is read from fort.22 (written from a previous run). The FDAT or SHELX file input is read form standard input (unit 5).
fdat or shelx - crystallographic data file

The input file can be either an FDAT format file (Cambridge Crystallographic Database), or a SHELX format file for providing the crystal structure information. The are 32 types of atoms that can be included automatically.

example_fdat example_shelx
cutoff - covalent bonds specification
This file is used to establish the covalent bonds and assumed atoms within the specified distances are bonded. There is an entry for every type of covalent bond in molecule, set at just slightly larger than the maximum likely value. Only the first 2 character of the atoms needs to be specified. The cutoff filename should be cutoff or file.cutoff, otherwise its name will be asked for.

example_cutoff
punch - multipoles from DMA

This contains the atomic multipoles derive by DMA of an ab initio wavefunction of the isolated molecule. It is essential that the calcultation uses the same orientation of the molecule as in the defined axes file.It is essentially the same definition of atomic multipole moments, as multipole expansion of electrostatic energy programmed in DMAREL.

The atomic multipoles from the distributed multipole analysis (DMA) punch file, this can be calculated using either CADPAC or from GAUSSIAN files using GDMA. The GDMA file is converted into the correct punch format using a utility code.

example_punch1 - CADPAC

example_punch2 - GDMA

axis - local axis set up for molecule

This is set up to define the molecular axis system for running in DMAREL, and used for DMAs.

The axis input file is in free format as shown below.

MOLX 1

X LINE CLR1 CODA CAR2 CODA 1

Y PLANE CLR1 CODA CAR2 CODA 1 CAR3 CODA 2

Where the integer after MOLX gives the number of types of molecule in the cell. Enantiomers should not be given separately, although NEIGHBOURS will generate separate AXES for DMAREL. DMA and enantiomers defined by right handed axis system.

In the example above, the X axis runs from CLR1 to CAR2 which is a first earliest neighbour. The Y axis is in the plane formed by CLR1, CAR2 (first earliest neighbour) and CAR3 (second nearest neighbour). The Z axis always makes a right-handed set. NEIGHBOURS avoids this difficulty by setting them up as two different molecules. The multipole expansions from the punch file are changed so that all odd-z components on the inverted molecule have the sign changed. NEIGHBOURS3.01 processes this information to work out the local axis system of the molecules, previously it was necessary to run DMAREL to do this. The output is printed in fort.21, in both Angstroms and AU. While DMAREL can run with any of X, Y or Z forming the first (LINE) axis, this is not recommended as the fix for enantiomers only works if Z is the third axis. Enantiomers are automatically added. When a molecule is generated by inversion etc. (i.e. an enantiomer) then we need to ensure multipoles and axes are still right handed.

example_axis
potential -repulsion-dispersion potential

This is the file where the repulsion-dispersion potential is set up. The default is the Buckingham potential (BUCK). For details of the format and other types of potential formats, see DMAREL 3.02 manual. A set of recommended potentials along with references will be given in the DMAREL manual. Here below are the examples of the repulsion-dispersion in the form of a Buckingham potential, isotropic and anisotropic.

For anisotropic, follow the link for full detailed of the format. In addition to the potential, axes need to be set up for each atom. At present, the axes for the anisotropic atoms need to be inserted manually.

isotropic - example_pot1

anisotropic - example_pot2

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