# How to make a DFSET file¶

## Format of DFSET¶

The displacement-force data sets obtained by first-principles (or classical force-field) calculations have to be saved to a file, say DFSET. Then, the force constants are estimated by setting DFSET = DFSET and with MODE = optimize.

The DFSET file must contain the atomic displacements and corresponding forces in Cartesian coordinate for at least NDATA structures (displacement patterns) in the following format:

# Structure number 1 (this is just a comment line) \begin{eqnarray*} u_{x}(1) & u_{y}(1) & u_{z}(1) & f_{x}(1) & f_{y}(1) & f_{z}(1) \\ u_{x}(2) & u_{y}(2) & u_{z}(2) & f_{x}(2) & f_{y}(2) & f_{z}(2) \\ & \vdots & & & \vdots & \\ u_{x}(\mathrm{NAT}) & u_{y}(\mathrm{NAT}) & u_{z}(\mathrm{NAT}) & f_{x}(\mathrm{NAT}) & f_{y}(\mathrm{NAT}) & f_{z}(\mathrm{NAT}) \end{eqnarray*} # Structure number 2 \begin{eqnarray*} u_{x}(1) & u_{y}(1) & u_{z}(1) & f_{x}(1) & f_{y}(1) & f_{z}(1) \\ & \vdots & & & \vdots & \end{eqnarray*}

Here, NAT is the number of atoms in the supercell. The unit of displacements and forces must be Bohr and Ryd/Bohr, respectively.

## Generation of DFSET by extract.py¶

The script extract.py in the tools directory of ALM is useful to generate DFSET files from output files of some popular DFT codes. Let us assume that we have calculated atomic forces for 10 different structures by VASP and saved the results as vasprun_01.xml … vasprun_10.xml. Then, a DFSET file can be generated as:

VASP

$python extract.py --VASP=SPOSCAR --offset=vasprun0.xml vasprun??.xml > DFSET  Here, SPOSCAR is the supercell structure without atomic displacements, and vasprun0.xml is the result of DFT calculation for SPOSCAR. The --offset option subtract the offset (residual) components of atomic forces from the data in vasprun??.xml. Important The --offset is optional, but we strongly recommend to use it when the fractional coordinates of atoms have degrees of freedom. The extract.py can also parse the data from the output files of QE, OpenMX, xTAPP, and LAMMPS: QE $ python extract.py --QE=supercell.pw.in --offset=supercell.pw.out disp??.pw.out > DFSET


OpenMX

$python extract.py --OpenMX=supercell.dat --offset=supercell.out disp??.out > DFSET  xTAPP $ python extract.py --xTAPP=supercell.cg --offset=supercell.str disp??.str > DFSET


LAMMPS

The LAMMPS case requires a special treatment. We first need to add the dump option in the LAMMPS input file as

dump            1 all custom 1 XFSET id xu xy xz fx fy fz
dump_modify     1 format float "%20.15f"


This option will generate the file XFSET which contains atomic coordinates and forces. After generating XFSET files for 10 structures and save them as XFSET.01XFSET.10 , we can create DFSET as:

\$ python extract.py --LAMMPS=supercell.lammps --offset=supercell.XFSET XFSET.?? > DFSET