4 Output¶

4.1 Output of PREPARE module¶

All the outputs of PREPARE module are in the dec directory, and the following is the directory tree:

dec
├── 1prepare.out
├── dasp.in
├── madelung
│   │   └── INCAR
│   │   └── KPOINTS
│   │   └── ...
├── AEXX
│   ├── 0.25
│   │   └── static
│   │       ├── INCAR
│   │       ├── KPOINTS
│   │       ├── ...
│   ├── 0.3
│   │   └── static
│   │       ├── ...
├── relax
│   ├── ...

4.1.1 INCAR¶

It is the input file for VASP calculation. This module will output two kinds of INCAR files including INCAR-relax (INCAR for structure relaxation) and INCAR-static (INCAR for static calculation).

4.1.2 POSCAR¶

It is the input file for VASP calculation. This module will output files including POSCAR (provided by the user), POSCAR_refined (POSCAR for the refined cell), POSCAR_nearlycube (POSCAR of nearly cubic supercell), and POSCAR_final (POSCAR of the relaxed supercell).

4.1.3 KPOINTS¶

It is the input file for VASP calculation. This module will output files as KPOINTS . Note: KPOINTS generated by DASP is always Gamma only. Do not replace KPOINTS with multiple k points.

4.1.4 POTCAR¶

It is the input file for VASP calculation. This module will output files including POTCAR (POTCAR for intrinsic defect calculation) and POTCAR_X (POTCAR for X dopant).

4.1.5 Submission script¶

It is the script used to submit job for DFT calculation.

4.1.6 Directory of Madelung constant calculation¶

The madelung directory would be created in the dec directory by PREPARE to calculate Madelung constant, and output it to the parameter madelung in dasp.in .

4.1.7 Directory of HSE exchange parameter calculation¶

If the level=2 or 3 and Eg_real is set, the AEXX directory will be created in the dec directory to calculate exchange proportion and output to the corresponding setting in INCAR.

4.1.8 Directory of Supercell optimization¶

No matter how level is set, the supercell optimization is always carried out under the relax directory.

4.1.9 1prepare.out¶

All details of running, and results and errors on this module are written into the file 1prepare.out . The user can query the execution status in this file.

4.2 Output of TSC module¶

All the outputs of TSC module are in the tsc directory, and the following is the directory tree of TSC:

tsc
├── 2tsc.out
├── dasp.in
├── materials_info.yaml
├── materials_info_recalc.yaml
├── pure_phase_energy.yaml
├── key_phases_info_recalc.yaml
├── host compound
│   ├── relaxation1
│   │   └── INCAR ...
│   ├── relaxation2
│   │   └── INCAR ...
│   ├── static
│   │   └── INCAR ...
│   ├── static_recalc
│   │   └── INCAR ...
├── secondary compound 1
│   ├── static_recalc
│   │   └── INCAR ...
├── secondary compound 2
│   ├── static_recalc
│   │   └── INCAR ...

4.2.1 materials_info.yaml¶

materials_info.yaml is the output file when TSC performs the first calculation and analysis. The file contains the thermodynamic stability results of the host compound, including the following information:

FE : the formation energy of the host compound (eV/per atom).

TE : the total energy of the host compound (eV/per atom).

TS : the thermodynamic stability of the host compound (True or False).

chemical_potentials : the chemical potential range of each element of the host compound.
- < element name>
- < the maximum value of the chemical potential of the element (eV) >
- < the minimum value of the chemical potential of the element (eV) >
decomp : the most probable path of decomposition of the host compound.
- < name of each decomposition >

direct : the band gap of the host compound is direct or indirect.

e_above_hull : the energy difference between the host compound and the equilibrium phase with the same composition, namely Energy above hull (eV/per atom). It is positive when the material is unstable, otherwise, it is negative.

gap : the band gap of the host compound (eV).

hull_points : the chemical potential of the elements at the boundary of the stable region of the host compound.
- < element name >
- < the chemical potential of each element at p1 (eV) >
- < the chemical potential of each element at p2 (eV) >
- …

key_phases : the critical competing compounds that limit the stability.
- < the name of the critical competing compounds >
XX_doped_key_phases : the critical competing compounds used to calculate the chemical potential of dopants X.
- < the name of the critical competing compounds >

key_phases_2d : the critical competing compounds that affect the stability of the host compounds in the two-dimensional stable region phase diagram.
- < the name of the critical competing compounds >

secondary_phases : all the considered competing secondary compounds in the analysis of the stability of the host compound.
- < the name of the secondary compounds >
- < the total energy of the secondary compounds (eV/ per atom) >
- < the formation energy of the secondary compounds (eV/ per atom) >

4.2.2 materials_info_recalc.yaml¶

materials_info_recalc.yaml is the output file when TSC performs the second calculation and analysis. The file structure is similar to that of materials_info.yaml .

4.2.3 pure_phase_energy.yaml¶

pure_phase_energy.yaml is the intermediate output file when TSC performs the first calculation and analysis. It recorded the information about the pure phases extracted from the MP database or provided by this module during the first calculation and analysis.

< the name of the pure phase>
- TE : total energy of the pure phase (eV/per atom).
- cif : the structure of the pure phase.
- id : the id of the pure phase in the MP database.
- space group : the space group information of the pure phase.

For the pure phases H2, O2, N2, F2, Cl2 and Br2, the id = 0 , space group = null , and cif = null , due to the structure and energy provided by this module adopted.

4.2.4 key_phases_info_recalc.yaml¶

key_phases_info_recalc.yaml is the intermediate output file when TSC performs the second calculation and analysis. It recorded the information about the key hetero-phases involved in the second calculation and analysis.

< the name of the key hetero-phases>
- TE : total energy of the key hetero-phases (eV/ per atom).
- direct : total energy of the key hetero-phases (eV/ per atom).
- gap : the band gap of the key hetero-phases (eV).

4.2.5 stable_2d.out¶

stable_2d.out is the output file when TSC performs the first stage analysis, which is located in the directory tsc/2d-figures/. It recorded the chemical potentials of the elements at the boundary of the two dimensional stable region. Meanwhile, for ternary or multinary compounds, the stable region picture with png format will output, corresponding to the analysis of the first stage. The specific content can be seen in the case description, and the format is as follows.

<element>            <element>            <element>
-------------------  -------------------  -------------------
<chemical potential> <chemical potential> <chemical potential>
<chemical potential> <chemical potential> <chemical potential>
<chemical potential> <chemical potential> <chemical potential>
<chemical potential> <chemical potential> <chemical potential>

4.2.6 stable_recalc_2d.out¶

stable_recalc_2d.out is the output file when TSC performs the second stage analysis, which is located in the directory tsc/2d-figures/. It recorded the chemical potentials of the elements at the boundary of the two dimensional stable region. The specific content can be seen in the case description, the format is the same as stable_2d.out . Meanwhile, for ternary or multinary compounds, the stable region picture with png format will be output, corresponding to the analysis of the second stage.

4.2.7 stable.out¶

stable.out is the output file when TSC performs the first stage analysis, which is located in the directory tsc/3d-figures/. It recorded the chemical potentials of the elements at the boundary of the three dimensional stable region. The specific content can be seen in the case description, and the format is as follows.

<element>            <element>            <element>
-------------------  -------------------  -------------------
<chemical potential> <chemical potential> <chemical potential>
<chemical potential> <chemical potential> <chemical potential>
<chemical potential> <chemical potential> <chemical potential>
<chemical potential> <chemical potential> <chemical potential>

4.2.8 stable_recalc.out¶

stable_recalc_2d.out is the output file when TSC performs the second stage analysis, which is located in the directory tsc/3d-figures/. It recorded the chemical potentials of the elements at the boundary of the three dimensional stable region. The specific content can be seen in the case description, the format is the same as stable.out .

4.2.9 ori_data_MP¶

The detailed output files of the first stage analysis of TSC module are retained in the directory ori_data_MP , including the subdirectory all_cif\ which retained all hetero-phase structure files, and the data DataRecord_XX.pkl extracted from the MP database and corresponding subdirectory XX\ . Generally, The name of the subdirectory XX\ consists of the name of the host compound ( and the doped element), which retains the hetero-phases structure and data for the corresponding case.

4.2.10 2tsc.out¶

2tsc.out is the log file during the execution of TSC module, including the progress of calculation and analysis and possible error messages. The specific content can be seen in the case description.

4.3 Output of DEC module¶

All the outputs of DEC module are in the dec directory, and the following is the directory tree of DEC:

dec
├── 3dec.out
├── dasp.in
├── Formation_Energy_Intrinsic_Defect
│   ├── p1.dat
│   ├── p2.dat
│   ├── p1.png
│   ├── p2.png
├── Transition_Level_Intrinsic_Defect
│   ├── tl.dat
│   ├── tl.png
├── defect 1
├── defect 2
├── defect 3
...

4.3.1 Formation_Energy_(Intrinsic_Defect)¶

This directory contains the pictures of the formation energy of intrinsic or dopants (subject to the folder name) as a function of Fermi level, including raw data with .dat format, as p1.dat, p2.dat, ... , and pictures with png format, as p1.png, p2.png, ... , The user can open and compile the .dat file using origin, and draw by self.

4.3.2 Transition_Level_(Intrinsic_Defect)¶

This directory contains the pictures of the transition energy level of intrinsic or dopants (subject to the folder name), including raw data with .dat format like tl.dat , and pictures with png format like tl.png . The user can open and compile the .dat file using origin, and draw by self.

4.3.3 3dec.out¶

All details of running, and results and errors on this module are written into the file 3dec.out . The user can query the execution status in this file. The specific content can be seen in the case description.

4.4 Output of DDC module¶

All the outputs of DDC module are in the ddc directory, and the following is the directory tree of DDC:

ddc
├── 4ddc.out
├── DefectParams.txt
├── Fermi.dat
├── Carrier.dat
├── Defect_charge.dat

4.4.1 DefectParams.txt¶

DefectParams.txt contains the required input parameters for DDC calculation, including defect name, Nsites, degeneracy factor, transition energy level, and formation energy of neutral defect. Taking ZnGeP2 as example, after run this module DefectParams.txt ：

1000 300
0.360000 0.190000
2.067143
P_Zn1 1.245078e+22 2 1.0959 1 0.7854 2 0.602 1 0.3478 2 1.3758 1 1.8193 2 1.8431 1 2.0373 2 3.993075 2.591475
Zn_P1 2.490156e+22 2 0.9803 1 0.4186 2 0.1979 1 x x 1.3004 1 1.6611 2 1.8974 1 2.0551 2 2.013776 3.415376
Ge_P1 2.490156e+22 2 0.017 1 x x x x x x 0.6089 1 1.4605 2 1.7595 1 x x 1.214661 1.681861
P_Ge1 1.245078e+22 2 1.5928 1 0.6776 2 0.3533 1 x x 1.8788 1 2.0787 2 x x x x 2.242467 1.775267
...
...

The script, dissected

# The growth temperature is 1000 K and the working (measuring) temperature is 300 K, as read from file dasp.in.
1000 300

# The electron effective mass is 0.36m_0 and that of hole is 0.19m_0, as read from file dasp.in.
0.360000 0.190000

# Tha band gap of supercell as read from dec/Intrinsic_Defect/host/EIGENVAL or dec/Doping_XX/host/EIGENVAL.
2.067143

# From left to right: defect name, Nsites, degeneracy factor for q=0, transition energy level (0/+), degeneracy factor for q=+1, transition energy level (0/2+), degeneracy factor for q=+2, transition energy level (0/3+), degeneracy factor for q=+3, transition energy level (0/4+), degeneracy factor for q=+4, transition energy level (0/-), degeneracy factor for q=-1, transition energy level (0/2-), degeneracy factor for q=-2, transition energy level (0/3-), degeneracy factor for q=-3, transition energy level (0/4-), degeneracy factor for q=-4, formation energy 1, formation energy 2.
# Formation energy 1 and formation energy 2 correspond to the neutral defect formation energy when the chemical potential (in dasp.in) at p1 and p2, respectively.
# From the fourth row, there are 21 strings in every row, all the data is from the output of defect calculation in dec directory.
P_Zn1 1.245078e+22 2 1.0959 1 0.7854 2 0.602 1 0.3478 2 1.3758 1 1.8193 2 1.8431 1 2.0373 2 3.993075 2.591475

# In the same order as the previous row, there are 21 strings.
# If one charge state does not exist, its transition energy level and degeneracy factor will be denoted by x. For example, there has no q=+4 state, so the (0/4+) level and degeneracy factor for q=+4 is x.
Zn_P1 2.490156e+22 2 0.9803 1 0.4186 2 0.1979 1 x x 1.3004 1 1.6611 2 1.8974 1 2.0551 2 2.013776 3.415376

# Similarly, there has no q=+2, +3, +4, and -4 state, so their levels and degeneracy factors are x.
Ge_P1 2.490156e+22 2 0.017 1 x x x x x x 0.6089 1 1.4605 2 1.7595 1 x x 1.214661 1.681861

# Similarly, there has no q=+4, -3, and -4 state, so their levels and degeneracy factors are x.
P_Ge1 1.245078e+22 2 1.5928 1 0.6776 2 0.3533 1 x x 1.8788 1 2.0787 2 x x x x 2.242467 1.775267

备注

The DDC module can be used independently of DASP-TSC and DASP-DEC, namely, the user only needs to prepare DefectParams.txt as the format described in this section, and DASP can treat it as an input and perform calculations. The degeneracy factor of the defect does not affect the order of magnitude of the concentration, so it can be set to 1 if uncertain.

4.4.2 Fermi.dat¶

The output of Fermi.dat has two columns. The first column shows the linear change of chemical potential from p1 to p2 (chemical potential in dasp. in). And the second column is the Fermi level corresponding to the chemical potential. EF=0 indicates that the Fermi level is located in VBM.

4.4.3 Carrier.dat¶

The output of Carrier.dat has three columns. The first column shows the linear change of chemical potential from p1 to p2 (chemical potential in dasp. in). The second and third columns are the electron and hole (free) carrier densities corresponding to the chemical potential respectively.

4.4.4 Defect_charge.dat¶

The output of Defect_charge.dat has multiple columns. The first column shows the linear change of chemical potential from p1 to p2 (chemical potential in dasp. in). From the second column, every column is the concentration of defects on different charge states at the corresponding chemical potential.

4.4.5 4ddc.out¶

All details of running, and results and errors on DDC module are written into the file 4ddc.out . The user can query the execution status in this file. The specific content can be seen in the case description.

4.5 Output of CDC module¶

All the outputs of CDC module are in the cdc directory, and the following is the directory tree of CDC:

cdc
├── 5cdc.out
├── dasp.in
├── pl_calc.list
├── POSCAR
├── specify defect
│   │   └── Radiate_calc
│   │   │   └── specify the initial and final state
│   │   │   │   ├── final_state
│   │   │   │   ├── initial_state
│   │   │   │   ├── intermediate_state
│   │   │   │   ├── pl.out
│   │   │   │   ├── rad_rate.out
│   │   │   │   ├── lineshape.dat
│   │   │   │   ├── lineshape.png
│   │   │   │   └── ccdiagram.png
│   │   └── ...

4.5.1 5cdc.out¶

All details of running, and results and errors on CDC module are written into the file 5cdc.out . The user can query the execution status in this file. The specific content can be seen in the case description.

4.5.2 lineshape.dat & lineshape.png¶

The file lineshape.dat is the raw data of the output after PL spectrum calculation, while lineshape.png is the image of PL spectrum on the basis of lineshape.dat . The specific content can be seen in the case description.

4.5.3 ccdiagram.png¶

The image ccdiagram.png is the configuration coordinate diagram when the defects are in initial and final states. The specific content can be seen in the case description.

4.5.4 pl.out¶

The file pl.out is a backup of 5cdc.out after the PL spectrum calculation is completed.

4.5.5 rad_rate.out¶

The file rad_rate.out is a backup of 5cdc.out after the radiative capture coefficient calculation is completed.