mech2d is a python package that used to calculate the mechanics properties of two dimenional materials, including elstaic constant tensor, stress-strain curve and other relavant properties. mech2d is user friendly to generate deformed structures, submit DFT calculation tasks and process results.
For more information, check the document or paper
You may clone the source code from gitee
git clone git@gitee.com:haidi-hfut/mech2d.git or from
git clone git@github.com:haidi-ustc/mech2d.gitBefore you install the mech2d. It is better to create a virtual python enviroment via conda
conda create -n mech2d python=3.10After creating the virtual enviroment, activate it and install the mech2d
conda activate mech2d
cd mech2d
pip install .
or directly download the source code zip package and then install it
wget https://gitee.com/haidi-hfut/mech2d/repository/archive/master.zip
unzip mech2d.zip
cd mech2d
pip install .Please refer to mech2d The polar plot of Young's modulus and Poisson's ratio is obtained by following equation:
The calculation of mechanical properties can be divided into three stages:
init , run and post
all of operation in mech2d software is carried out by command line arguments, to get the help information by
m2d -h
it shows
usage: m2d [-h] [-v] {init,run,post} ...
Desctiption:
------------
mech2d is a convenient script that use to calculate the mechanical properties of
2D materials, including EOS, Stress-Strain Curve, elastic constants and revalant
properties. The script works based on several sub-commands with their own options.
To see the options for the sub-commands, type "m2d sub-command -h".
positional arguments:
{init,run,post}
init Generating initial data for elastic systems.
run Run the DFT calculation for deformed structures.
post Post processing for elastic calculation.
optional arguments:
-h, --help show this help message and exit
-v, --version Display version
- the init stage used to generate the deformed structures.
use subcomand to show the help information
m2d init -h
it shows
usage: m2d init [-h] [-c CONFIG] [-a {stress,energy}] [-m MAXS] [-n NUMBER] [-d {xx,yy,bi,xy} [{xx,yy,bi,xy} ...]] [-r RANGES [RANGES ...]]
[-p {elc,ssc}] [-v] [-b]
optional arguments:
-h, --help show this help message and exit
-c CONFIG, --config CONFIG
The structure filename. Supported format: ['.vasp','POSCAR','.cif','.xsf']
-a {stress,energy}, --approach {stress,energy}
Support 'Energy' or 'Stress' approach.
-m MAXS, --maxs MAXS For elastic constant calculation, it stands for the maximum Lagrangian strain, suggested value is [0.030, 0.150] for
Energy approach, [0.0010, 0.0050] for Stress approach; for stress strain cuver calcuation, this value has no above
limitation
-n NUMBER, --number NUMBER
The number of the deformed structures [odd number > 4].
-d {xx,yy,bi,xy} [{xx,yy,bi,xy} ...], --direction {xx,yy,bi,xy} [{xx,yy,bi,xy} ...]
The direction used for stress strain curve, default value: 'xx'. 'xx' for 'x' direction; 'yy' for 'y' direction; 'bi'
for bi-axis strain and 'xy' for shear strain.
-r RANGES [RANGES ...], --ranges RANGES [RANGES ...]
The Lagrangian strain range used for stress-strain curve calculation. e.g. 0.0 0.2
-p {elc,ssc}, --properties {elc,ssc}
What do you want to calcuation? elastic constant or stress strain curve? default value: 'elc'.
-v, --verbose print verbose information or not.
-b, --back Whether back the old folder? default value: False.
To obtain the deformed structures according to different symmetry, a relaxed structure if needed. Suppose you have a POSCAR file in current folder, using the following command to generate the deformed structures by stress fitting approach:
m2d init -c POSCAR -n 9 -m 0.02 -a stressAfter running this command, it will build a elc_stess folder with subfolders.
elc_stress/
├── Def_1
│ ├── Def_1_001
│ ├── Def_1_002
│ ├── Def_1_003
│ ├── Def_1_004
│ ├── Def_1_005
│ ├── Def_1_006
│ ├── Def_1_007
│ ├── Def_1_008
│ └── Def_1_009
└── Def_2
├── Def_2_001
├── Def_2_002
├── Def_2_003
├── Def_2_004
├── Def_2_005
├── Def_2_006
├── Def_2_007
├── Def_2_008
└── Def_2_009
likewise, the deformed structures based on energy fitting approach can be obtained by:
m2d init -c POSCAR -n 9 -m 0.02 -a stressthe deformed structures used for stress strain curve calculation can be obtained by:
m2d init -c POSCAR -n 21 -r 0.0 0.2 -a stress -d 'xx' 'yy' -p ssc if the -r parameter exist, it means that Lagrangian stress will be set by a range, e.g. 0 0.2
if the -m parameter exist, it means the Lagrangian stress equals [-max,+max]
tips: .vasp .xsf .cif format files are all supported
- the run stage used to conduct the DFT calculation.
use subcomand to show the help information
m2d run -h
it shows
usage: m2d run [-h] [-a {stress,energy}] [-p {elc,ssc}] [--manual] [-v] input
positional arguments:
input input file for supplying information about DFT
calculation, json/yaml format. The 'machine', 'tasks',
'code', 'resources' should be supplied.
optional arguments:
-h, --help show this help message and exit
-a {stress,energy}, --approach {stress,energy}
Support 'Energy' or 'Stress' approach.
-p {elc,ssc}, --properties {elc,ssc}
What do you want to calcuation? elastic constant or
stress strain curve? default value: 'elc'.
--manual manual model, only for generating the input files
without runing
-v, --verbose print verbose information or not.
For this stage, the running command is :
m2d run -a stress input.yaml
the input.yaml use to set the configure file, it includes machine , resources , tasks and code.
- machine dict set the machine information, local or remote ? what kind of queue system will use ? what is the working directory
- resources dict set the queue task infomation, how many cores will use? which queue to use? and set the enviroment variables
- task dict set the task related infomation, the excutable command , the input files (forward_files) and necessary result files that need to be copied back (back_files)
- code dict set the DFT engine information. including code name, input file location
An example for input.yaml is shown below:
---
machine:
batch_type: Slurm
context_type: LocalContext
local_root: "./work"
remote_root: "./work"
remote_profile:
hostname: localhost
username: wang
port: 22
timeout: 10
resources:
number_node: 1
cpu_per_node: 48
gpu_per_node: 0
queue_name: batch
task_max: 10
group_size: 1
custom_flags:
- "ulimit -s unlimited"
module_list:
- "vasp/5.4.1"
#source_list:
# - "/opt/intel/parallel_studio_xe_2020.2.108/psxevars.sh intel64"
#envs:
# PATH: "/opt/soft/vasp541:$PATH"
tasks:
command: "mpirun -np 48 vasp_std"
task_work_path:
forward_files:
- INCAR
- KPOINTS
- POTCAR
- POSCAR
backward_files:
- runlog
- errlog
- OUTCAR
- OSZICAR
- vasprun.xml
- CONTCAR
outlog: runlog
errlog: errlog
code:
name: vasp
input:
INCAR: "./INCAR"
#KPOINTS: "./KPOINTS"
KPOINTS:
kspacing: 5000
kgamma: false
POTCAR: "./POTCAR"
#vdw_kernel: vdw_kernel.bindat
The input.yaml can also be setted by JSON format, however it seems that Yaml format is much easier to read.
If you dont want to use the dpdispatcher to automatically submit the jobs, you can run the command:
m2d run --manual input.yaml. In this way, only the input files of vasp tasks will be generated.
- the post stage used analysis the result and plot the result.
use subcomand to show the help information
m2d post -h
it shows
usage: m2d post [-h] [-a {stress,energy}] [-i INPUTFILE] [-p {elc,ssc}]
[--skip] [-o ORDER] [-f FMT] [-d DPI] [--plot] [-v]
optional arguments:
-h, --help show this help message and exit
-a {stress,energy}, --approach {stress,energy}
Support 'Energy' or 'Stress' approach.
-i INPUTFILE, --inputfile INPUTFILE
Parsing elastic constant tensor from input file
-p {elc,ssc}, --properties {elc,ssc}
What do you want to calcuation? elastic constant or
stress strain curve? default value: 'elc'.
--skip Whether skip the data parsing ? if true, it means the
Def_*_Energy.dat should be exists in corresponding
folder. default value: False.
-o ORDER, --order ORDER
The order of polynomial for fitting. Default value: 4
for strain-stress approach and 3 for stress-strain
method
-f FMT, --fmt FMT The format of output figure. Default value: .jpg
-d DPI, --dpi DPI The resolution of output figure. Default value: 100
--plot plot the figures
-v, --verbose print verbose information or not.
For this stage, the running command is :
m2d post -a stress --plot
A figure named stress-EV.jpg will be generated.
or for stress-strain calculation
m2d post -a stress -p ssc --plot
Wang, H.; Li, T.; Liu, X.; Zhu, W.; Chen, Z.; Li, Z.; Yang, J. mech2d: An Efficient Tool for High-Throughput Calculation of Mechanical Properties for Two-Dimensional Materials. Link