Electron Properties Calculations

Electron properties allow you to produce band structures, charge densities, density of states, and more. To run an electronic properties calculation, you will need the wavefunction file (extension .f9) generated from a single-point calculation—for a graphene example, see the end of this page—and an input file (extension .d3). The input file depends on the property you are calculating. A good tutorial to follow is provided here: http://tutorials.crystalsolutions.eu/tutorial.html?td=properties&tf=properties_tut.

If you wonder how to choose the optimal directions for the k-points, you can use:

http://www.cryst.ehu.es/cryst/get_kvec.html

or

https://www.materialscloud.org/work/tools/seekpath

Alternatively, you can use the pathways already provided in the d3_input directory.

Band Structure Input File

A band structure is designated by the .d3 extension and BAND in the first line. The general form of the file will have the following format:

BAND

<file name>

<1. n number of paths in reciprocal space> <2. shrinking factor of segments> <3. total number of k points along the path> <4. first band to be saved> <5. last band to be saved> <6. plotting option> <7. activated printing option>

k-point 1    k-point 2

.

.

.

k-point n-1  k-point n

END

Example: graphene

BAND

graphene

3 6 1000 1 36 1 0

 0  0  0   3  0  0    GAMMA -> M 

 3  0  0   2  2  0    M  -> K 

 2  2  0   0  0  0    K  -> GAMMA

END

Example: MgO

Here is another example file, called MgO.d3:

BAND

MgO

4 8 60 1 18 1 0

0 0 0   0 4 0  # Gamma to X

4 0 4   4 2 6  # X to W

4 2 6   4 4 4  # W to L

4 4 4   0 0 0  # L to Gamma

END

Note that the path is continuous running from Gamma back to Gamma, however, you may set paths to be discontinuous.

An alternative way to set the path is with the labels of the high points of symmetry. This requires setting the second part of the third line to 0. Here's the same example above with the label notation:

BAND

MgO

4 8 60 1 18 1 0

G   X  # Gamma to X

X   W  # X to W

W   L  # W to L

L   G  # L to Gamma

END

This notation in general works, but some symmetry groups do not have their labels included. In particular, P1 is not included.

DOS Input File

A DOS calculation is designated by the .d3 extension, NEWK in the first line, and DOSS after the NEWK input parameters. The general form of the file will have the following format:

NEWK

<shrinking factor for reciprocal space Park-Monkhorst net> <shrinking factor for reciprocal space Gilat net>

<evaluation of Fermi surface with same or new net> <print option>

DOSS

< n number of projections> <number of points along the energy axis in which the DOSS is calculated> <first band> <last band> <plot option> <degree of polynomial used for DOS expansion> <printing option>

total number of shells in projection 1    number of each shell in projection 1

total number of shells in projection 2    number of each shell in projection 2

.

.

.

total number of shells in projection n    number of each shell in projection n

END

Here is an example for graphene.

NEWK

30 60

1 0

DOSS

4 250000 1 36 1 14 0

8  1  2  3  4  19  20  21  22  #C S

18  5  6  7  8  9  10  11  12  13  23  24  25  26  27  28  29  30  31  #C P

10  14  15  16  17  18  32  33  34  35  36  #C D

36    1  2  3  4  19  20  21  22   5  6  7  8  9  10  11  12  13  23  24  25  26  27  28  29  30  31   14  15  16  17  18  32  33  34  35  36  #C all

END

Here is another example for a file Be.d3 which separates the shells for s orbitals and p orbitals containing just Be atoms:

NEWK

20 20 

1 0 #new net different from SCF output and no printing option

DOSS

3 100 3 6 1 14 0

4   1 3 5 7 #s shells

4   4 5 8 9 # px and py shells

2   6 10    #pz shells

END

Many structures contain many atoms with s-, p-, sp-, d-, and f- shells. Such structures will make it very complicated to copy shell information which makes it best to use a script to parse the shell and atom information. The alldos.py script in our group's GitHub can be used to generate a DOS input file automatically. To run this script, copy the .d12, .out, and .f9 files from a single-point or geometry optimization calculation in a new folder, and run the command: python alldos.py

Submission script

Here is an example submission script (graphene_sp_BAND.sh) for a band structure calculation of graphene. The same script can be used for DOS by changing the name accordingly (e.g. graphene_sp_DOSS).  

#!/bin/bash

#SBATCH -J graphene_sp_BAND

#SBATCH -o graphene_sp_BAND-%J.o

#SBATCH --cpus-per-task=1

#SBATCH --ntasks=16

#SBATCH -A general

#SBATCH -N 1

#SBATCH -t 0-04:00:00

#SBATCH --mem-per-cpu=3G

export JOB=graphene_sp_BAND

export DIR=$SLURM_SUBMIT_DIR

export scratch=$SCRATCH/crys17

echo "submit directory: "

echo $SLURM_SUBMIT_DIR

ml -* CRYSTAL/17

mkdir  -p $scratch/$JOB

cp $DIR/$JOB.d3  $scratch/$JOB/INPUT

cp $DIR/$JOB.f9  $scratch/$JOB/fort.9

cd $scratch/$JOB

srun Pproperties 2>&1 >& $DIR/${JOB}.out

cp BAND.DAT  ${DIR}/${JOB}.BAND.dat

cp DOSS.DAT  ${DIR}/${JOB}.DOSS.dat

cp POTC.DAT  ${DIR}/${JOB}.POTC.dat

Note: The parameters that can/should be changed are highlighted in bold.

Jobs are submitted with the sbatch command: sbatch graphene_sp_BAND.sh 

Plotting

Plotting can be done using the ipBANDS.py and ipDOS.py scripts in the Mendoza group GitHub. It is necessary to have the .dat, .d3, and .out files (generated from a property calculation) in the same folder as the python script.

To plot the electronic band structure, run the command python ipBANDS.py <E1> <E2>, where <E1> and <E2> denote an energy range (in eV) around the Fermi level. For example, python ipBANDS.py -5 5.

To plot the electronic density of states, run the command python ipDOS.py <E1> <E2>, where <E1> and <E2> denote an energy range (in eV) around the Fermi level. For example, python ipDOS.py -5 5. Once this command is executed, the program will show you a list of projections. First, you will have to tell the program the number of projections you would like to plot, and then specify the projections. For example, if we wanted to plot the carbon s and p orbital contributions for graphene, we would do the following:

python ipDOS.py -5 5

graphene

Available projections:

['C_s', 'C_p', 'C_d', 'C_all']

Enter how many projections you want to plot: 2

Enter string for projection:

Projection 1: C_s

Projection 2: C_p

Note: The above arguments in bold are the only user inputs; everything else is generated by the script.

Graphene single-point calculation

This is an example single-point calculation for graphene (extension .d12). This will generate the .f9 (density matrix file) required for obtaining properties.

graphene

SLAB

1

2.444016   2.444015  120.0000

2

6   0.333333  0.666667  9.999960   Biso    1.000000    C

6   0.000000  0.000000  10.000040  Biso    1.000000    C

END

6 8

0 0 6 2.0 1.0

 13575.349682 0.00022245814352

 2035.2333680 0.00172327382520

 463.22562359 0.00892557153140

 131.20019598 0.03572798450200

 42.853015891 0.11076259931000

 15.584185766 0.24295627626000

0 0 2 2.0 1.0

 6.2067138508 0.41440263448000

 2.5764896527 0.23744968655000

0 0 1 0.0 1.0

 0.4941102000 1.00000000000000

0 0 1 0.0 1.0

 0.1644071000 1.00000000000000

0 2 4 2.0 1.0

 34.697232244 0.00533336578050

 7.9582622826 0.03586410909200

 2.3780826883 0.14215873329000

 0.8143320818 0.34270471845000

0 2 1 0.0 1.0

 0.5662417100 1.00000000000000

0 2 1 0.0 1.0

 0.2673545000 1.00000000000000

0 3 1 0.0 1.0

 0.8791584200 1.00000000000000

99 0

END

DFT

SPIN

HSE06-D3

XLGRID

END

TOLINTEG

9 9 9 9 18

TOLDEE

7

SHRINK

0 60

 30 30 1

SCFDIR

BIPOSIZE

110000000

EXCHSIZE

110000000

MAXCYCLE

800

FMIXING

30

DIIS

PPAN

END

Complementary Files/Scripts

Band Input Pathway and Input Files