Configuration file format

Atomic configurations are stored on disk by NNP applications in a simple ASCII file. Data sets with training structures need to be provided in the same format. The file name for input configurations is usually input.data. A configuration file may contain multiple structures, each enclosed by the begin and end keywords. The lines in between must begin with one of the following keywords:

  • atom

  • lattice

  • comment

  • energy

  • charge

Here is a sample layout:

begin
comment <comment>
lattice <ax> <ay> <az>
lattice <bx> <by> <bz>
lattice <cx> <cy> <cz>
atom <x1> <y1> <z1> <e1> <c1> <n1> <fx1> <fy1> <fz1>
atom <x2> <y2> <z2> <e2> <c2> <n2> <fx2> <fy2> <fz2>
...
atom <xn> <yn> <zn> <en> <cn> <nn> <fxn> <fyn> <fzn>
energy <energy>
charge <charge>
end
begin
...
end
...
begin
...
end

where the arguments of the keywords are:

  • <comment> : comment line

  • <ax>… <cz> : box vectors \(\vec{\mathbf{a}}, \vec{\mathbf{b}}, \vec{\mathbf{c}}\) (see nnp::Structure::calculateInverseBox()).

  • <x1>… <zn> : atom coordinates of n atoms

  • <e1>… <en> : atom element string (e.g. Cd, S)

  • <c1>… <cn> : not (yet) used, reserved for atom charge in case of long range neural network (to be implemented)

  • <n1>… <nn> : not used

  • <fx1>… <fzn> : force components of n atoms

  • <energy> : total potential energy

  • <charge> : total charge (for long range neural network only)

The lattice section must be omitted for non-periodic structures. It is possible to mix periodic and non-periodic structures. Also, configurations may contain different numbers of atoms. If atoms in a periodic structure are initially outside of the simulation box they will be automatically mapped back into the box (see nnp::Structure::remap()). Here is an example configuration file with 3 structures, 2 periodic and 1 non-periodic:

begin
comment This periodic structure contains 2 Cd and 2 S atoms.
lattice 1.0 0.0 0.0
lattice 0.0 1.0 0.0
lattice 0.0 0.0 1.0
atom 0.1 0.2 0.3 Cd -0.1 0.0 -0.1 -0.3  0.1
atom 0.2 0.4 0.8 Cd -0.1 0.0 -0.2  0.6 -0.6
atom 0.7 0.2 0.7 S   0.1 0.0 -0.8 -0.1  0.1
atom 0.1 0.1 0.4 S   0.1 0.0  1.1 -0.2  0.4
energy 123.456
charge 0.0
end
begin
comment This non-periodic structure contains 1 Cd and 2 S atoms.
atom 0.9 0.1 0.8 Cd -0.1 0.0 -0.3 -0.3  0.1
atom 0.7 0.2 0.2 S   0.1 0.0 -0.8  0.1  0.3
atom 0.6 0.9 0.4 S   0.1 0.0  1.1  0.2 -0.4
energy 1337.00
charge 0.0
end
begin
comment This periodic structure contains 3 Cd and 3 S atoms.
lattice 2.0 0.0 0.0
lattice 1.0 2.0 0.0
lattice 1.0 1.0 2.0
atom 1.9 0.2 1.7 S   0.1 0.0  0.4 -0.1 -0.2
atom 1.1 0.2 0.5 Cd -0.1 0.0 -0.1 -0.3  0.2
atom 0.2 1.4 0.8 Cd -0.1 0.0 -0.2  0.8  0.5
atom 0.9 0.2 1.7 S   0.1 0.0 -0.7 -0.3 -0.6
atom 0.8 1.2 0.1 Cd -0.1 0.0 -0.2  0.1  0.5
atom 0.1 0.1 0.4 S   0.1 0.0  0.8 -0.2 -0.4
energy 543.210
charge 0.0
end

Manual train/test set definition

Since n2p2 version 2.3.0 it is possible to manually assign structures to the training or test set already in the input.data file. Just add the string set=train or set=test right after the structure start marker begin. For example:

begin set=train
lattice 1.0 0.0 0.0
lattice 0.0 1.0 0.0
lattice 0.0 0.0 1.0
atom 0.1 0.2 0.3 Cd -0.1 0.0 -0.1 -0.3  0.1
atom 0.1 0.1 0.4 S   0.1 0.0  1.1 -0.2  0.4
energy 123.456
charge 0.0
end
begin set=test
lattice 1.0 0.0 0.0
lattice 0.0 1.0 0.0
lattice 0.0 0.0 1.0
atom 0.1 0.2 0.3 Cd -0.1 0.0 -0.1 -0.3  0.1
atom 0.1 0.1 0.4 S   0.1 0.0  1.1 -0.2  0.4
energy 123.456
charge 0.0
end

This assignment takes precedence over the usual random split performed by nnp-train. Structures which are not labelled with the set= method will still be assigned randomly to training/test sets according to the test_fraction keyword.