Get Started¶

Simplest way to run¶

Prepare the INPUT file and the input file for first principlec code
Enter the folder
Simply run elastic3rd run

Inputs¶

The inputs for Elastic3rd can be divided into two parts. The first one is the INPUT file, and the second is the input files for first princples code.

INPUT¶

Parameters	Default	Comments
BaseName	Si	The folder name of the result. In addition, For CASTEP, it must equals to the name of cell and param file For VASP, no above required
CrystalType	Cubic1	The symmetry of the crystal. It should be one of the followings triclinic or n, monoclinic or m, orthorhombic or o, tetragonal1 or t1 tetragonal2 or t2, rhombohedral1 or r1, rhombohedral2 or r2 hexagonal1 or h1, hexagonal2 or h2, cubic1 or c1, cubic2 or c2
Ord	3	The order of elastic constants
EnergyCode	CASTEP	The first principles code, currently support CASTEP and VASP
EnergyRun	1	The way to run the first principles code 1 is the default way. For CASTEP: RunCASTEP -np NP BaseName For VASP: mpirun -np NP vasp_std 0 means user defined. It will read the energyrun file in elastic3rd/energy folder. And it can be overwrite by elastic3rd.energy.glue.write_energyrun(RunStr) function
MaxStrain	5	The maximum strain, in unit of %. e.g. 5 means the strain range is -5% to 5%
STEPS	5	The number of points in each strain mode
NP	1	The number of cores used in the first principles codes

First principles inputs¶

CASTEP For CASTEP, two files are required for calculating, BaseName.cell and BaseName.param. For details, ref. CASTEP files .

VASP To run VASP, four files are required: INCAR, POSCAR, KPOINTS and POTCAR. For details, ref. VASP files .

Calculation¶

Using CASTEP or VASP¶

Currently, Elastic3rd support CASTEP and VASP to calculate the energy or stress. Hence, the user can call vasp or castep by setting the INPUT file.

Note: The CASTEP is tested using the CASTEP module in Materials Studio. By default, the user should provide RunCASTEP.bat (windows) or RunCASTEP.sh (linux) in current folder. Usually, this file loacted in Materials_Studio_ install_pathetcCASTEPbin

For VASP, it runs vasp by mpirun -np NP vasp_std. So, please ensure that mpirun and vasp_std can be found in yout PATH.

Using other first principles code¶

If the user want to use other first principles code to calculate the energy of stress, the user only need to prepare the following thing:

write a python file named with the code’s name(e.g. qe.py, lower required) under elastic3rd/energy/

In this file, the user need to write the following functions
- get_base_vec(BaseName): this function get the lattice vector from the code’s input file
- write_base_vec(BaseName, BaseVec): this function write out the lattice vector to the code’s input file
- run(NP, BaseName): this function return the string to run the code
- get_energy(BaseName): this function get the energy from the code’s output file
- copy_files(BaseName, Path): this function copy the required files of the code
Then in the INPUT file, the file can call the code by specify “EnergyCode QE”

Post¶

The SOECs and TOECs (only taking second and third order effect into consideration) are printed in the log file on the screen.

If the author want to taken higher-order effect into consideration, the user can run elastic3rd post command in the folder where the job submitted or use Elastic3rdPost.py script in the example folder

For elastic3rd post command, please use -h for detail help.

For test, the user can run elastic3rd post in the example/Si/CASTEP folder directly.

Outputs¶

The structure of outputs¶

All the output are stored in the folder named BaseName, of which the value is set in INPUT file. The following is the structure of the results.

FileStructure

Output files¶

This section gives an explanation for each file generated by Elastic3rd.

File name	Comments
INPUT	A backup of INPUT file
EEnergy.txt	The energy of each strain mode(each column) and each strain(each row)
Energy_Strain.txt	The energy of single strain, in which there are several values in different unit
Energy_Mode.txt	The eneargy of single strain mode. In unit of eV

Folders	Comments
Mode0	This folder contains the result of undeformed structure
ModeN	This folder contains the result of differen strain modes
StrainN	This folder contains the result of different strains