This program collects algorithms for determining lattice oscillations. The frequencies of lattice oscillations are important quantuties in several areas of solid state physics. Different approaches can be used to describe lattice oscillations, as the dynamic structure factor (DSF), velocity autocorrelation function (VACF), and projected velocity autocorrelations in q-space. Or the dynamic structure factor can be projected onto a set of eigenvectors. The projected velocity autocorrelation (PVACF) is a projection of the VACF onto a set of eigenvectors. The eigenvectors can for example be taken from harmonic PhonoPy calculations.

To install the DSLEAP in UNIX unpack the tarball tar -xvzf DSLEAP.tar.gz. Then go to the main. folder cd DSLEAP. Then export the desired gnu compiler export FC=gfortran. Type cmake -DCMAKE_BUILD_TYPE=Release CMakeLists.txt. Then type make and the executable will be found in ./bin/DSLEAP

There is a set of general settings for the phonon computation. These flags will specify the conditions of the molecular dynamics (MD) simulation which is analyzed. The flags shown in table are specified in the Phonon.in file

Specifing one of the methods with DSTC, DYNSTRUC, PVACF, PVACK or PROJFAC requires different input files. The different methods and their usage will be described in the following sections. The code also supports openmp parallelization. If you do not want the program to use all your cores do export OMP_NUM_THREADS=# of cores before execution.

To compute the DSF switch on the flag DYNSTRUC=True. And set the other remaining parameters defined in the Phonon.in file. To compute the DSF you have to specify a q-grid. This can be done by supplying a q-points file called QVectors.in containing on the first line an integer with the number of q-points. Then the q-points are listed in a 3 column format. If no QVectors.in file is supplied the default q-points of the commensurate q-grid are used. As output you will obtain a file called DynamicStructureFactor.out containing the DSF. The first column is the frequency axis. The frequency is inverse time units of the time step you supplied. In the following columns the signals for the different q-points are listed. The file StructureFactor.out contains the static structure factor. The first column is the Qpath then. And last the file StructureFactor_vs_t.out contains the structure factor in the time domain. The first column of the file is the time axis then the signals for different q-vectors follow.

To compute the q space projection of the velocity autocorrelation function set the flag PVACK=True. This method needs a masses.in file described in section masses.in File. The masses are needed for weighing the velocities properly. For this method the atoms have to be assigned to the unitcells in which they are located. This can be done with the BoxList.in file described in section BoxList.in File. As output you are going to obtain numbered PVACF_KO.out{II} files where {II} is an index from 1 up to the number of atoms per unit cell. The first column of this file contains the frequency grid and the following columns contain the signals for the used q-vectors. The frequency grid is given in inverse time units as defined in the Phonon.in file. In the files PVACF_KO_vs_t.out{II} you will find the time signals. These have the time axis on the first column and then the signals for the different q-values follow.

To compute the projected velocity autocorrelation function set the flag PVACF=True. This computes a PVACF projected onto a set of basis vectors and onto a set of q-vectors. The routine needs the input files BoxList.in, masses.in and BasisVector.in files. If no BasisVector.in file is supplied the code will try to find a QVectors.in file. If this file is found the q-vectors from this file are used and a diagonal basis. If no QVectors.in file is supplied the default q-vectors will be used in combination with the diagonal basis. The masses.in file is needed to weigh the velocities with their atomic masses and the BoxList.in is needed for the spatial fourier transforms. As output you will obtain PVACF.out{II} files. These files will contain the frequency axis on the first column and the signals for every q-vector on the following columns. Such a file will be written for every phonon branch denoted by the counter {II}. The files PVACF_vs_t.out{II} will contain the corresponding time signals with the time axis on the first column. Then the signals for the used q-points are listed.

To compute the projected dynamic structure factor set the flag PROJFAC=True. This computes a DSF projected onto a set of basis vectors and onto a set of q-vectors. The routine needs the input files BoxList.in and BasisVector.in. If no BasisVector.in file is supplied the code will try to find a QVectors.in file. If this file is found the q-vectors from this file are used and a diagonal basis. If no QVectors.in file is supplied the default q-vectors will be used in combination with the diagonal basis. As output you will obtain ProjectedDSF.out{II} files. These files will contain the frequency axis on the first column and the signals for every q-vector on the following columns. Such a file will be written for every phonon branch numbered by {II}. The files StructureFactorProj_vs_t.out{II} will contain the corresponding time signals with the time axis on the first column. Then the signals for the used q-points are listed.

The BoxList.in file contains a connection table assigning every atom to one of the unit cells building up the super cell. The file contains a table where the number of lines are the number of unitcells building up the supercell. Every line contains N integer numbers, where N defines the number of atoms per unitcell. The numbers represent the atom number in the XDATCAR file. This file is needed for PVACF and PVACK.

The masses.in contains the number of atoms in the unit cell on the first line. The following lines contain a single number describing the mass of the atoms in the unit cell. The order has to be the same as in the XDATCAR file. This file is needed for PVACF and PVACK.

This file is needed when computing PVACF or PROJFAC. The projected velocity autocorrelation function in q-space and onto a set of basis vectors. The PROJFAC is a projection of the dynamic structure factor onto the same set of eigenvectors. The file contains 4 integer numbers on the first line. The first number is the number of different q-points. The second number is the number of branches per q-point. The third number defines the number of atoms in the unit cell. And the last number defines the dimensionality of the underlying space, which is always 3. The file is then structured as follows. The next line contains the first q-vector. Then without an empty line in-between the first phonon branch of q-vector one follows. Then an empty line and the next phonon branch follows. The number of lines per branch is the number of atoms per unit cell. Like this all branches for the first q-point are listed. Then 2 empty lines follow and the next q-vector is defined. Followed by the first phonon branch of the second q-point. In the folder toolsPy/BasisVector/ you can find a script to extract eigenvectors from a phonopy band.yaml file. The folder contains a routine ExtractPhonoPyEigenVectors.py with which you can process the band.yaml file.

The folder Example shows representatives for all the input files needed to do a full analysis. The example treats a cubic 16x16x16 'Morse-crystal' at 100K with a single atom in the unitcell. Since a trajectory file would be too large to supply, the output files from the various methods are put there to take a look at. There is also a py script MakeBoxList.py that generates the BoxList.in file for this specific example. And there is another py script MakeEigenVectors.py generating the BasisVector.in file for this example. The output files can already be found in the Example folder. The original trajectory files would be too large to put there.