Lammps_MPC

创新 | WHAT’S NEW?

In MPCv4 (MEAM Parameter Calibration, ver.4), LAMMPS+MEAM is executed as a library inside the MATLAB workspace, not as an external process. MATLAB gateway functions (mexfunctions) execute LAMMPS library functions listed in src/library.h of the LAMMPS distribution. MATLAB functions carry out user-selected calculations for single elements, binaries, and ternaries.

In previous versions, LAMMPS+MEAM is separate process executed from a Python script to calculate energies, etc, and the Python script is invoked by MATLAB. Click here for an earlier version of MPC.

许可 | LICENSE

The MPCv4 license is File:License BSD 3 MSU.PDF

The source codes are here.

For questions, comments, and suggestions regarding MPC, send e-mail to Haitham El Kadiri or Mark F Horstemeyer. The MATLAB scripts for the LAMMPS calculations and the gateway functions were written by Christopher D Barrett. The user interface was built by Ricolindo L Carino.

出版 | PUBLICATIONS

MPC is mentioned in Chapter 6 of Applications from Engineering with MATLAB Concepts - Case Studies in Using MATLAB to Build Model Calibration Tools for Multiscale Modeling

The MEAM parameter calibration tool: an explicit methodology for hierarchical bridging between ab initio and atomistic scales

Hierarchical Bridging Between Ab Initio and Atomistic Level Computations: Calibrating the Modified Embedded Atom Method (MEAM) Potential (Part A)

Hierarchical Bridging Between Ab Initio and Atomistic Level Computations: Sensitivity and Uncertainty Analysis for the Modified Embedded-Atom Method (MEAM) Potential (Part B)

总览 | OVERVIEW

MEAM Parameter Calibration (MPC) is a graphical MATLAB application for interactive editing of MEAM library and parameter files for single elements or alloys, and for semi-automated calibration of MEAM parameters to fit DFT and/or experimental data. Intended as a teaching tool, the MPC is designed to run on personal computers (Windows 7 64-bit, MacOS X Yosemite) without MATLAB. Video tutorials for use of the MPC tool can be found here, here, and here.

特色 | FEATURES

■ LAMMPS+MEAM is executed as a library inside the MATLAB workspace, not as an external process.

■ Basic operations

1. Load MEAM library file
2. Select an element, or more if working with an alloy, from the MEAM library
3. Specify primary, secondary 1, secondary 2 structures for an element or alloy component
4. Load MEAM parameter file
5. Edit library entries, parameter file entries
   

■ Operations on single elements

1. Run one or more LAMMPS calculations for a single element
2. Primary EV curve
3. Secondary EV curve
4. Secondary 2 EV curve
5. Elastic Constants Calculation
6. Vacancy Energy Calculation
7. Interstitial Energy Calculations
8. Surface Energy Calculations
9. Generalized Stacking Fault Energy (GSFE) Calculations
10. Generalized Interfacial (Twin) Fault Energy (GTFE) Calculations
11. Plot results of single element calculations
    

■ Operations on binaries

1. Specify one or more binary structures
2. Run one or more LAMMPS calculations for one of more binaries
3. Binary EV Curves
4. Binary Elastic Constants Calculations
5. Substitution Energy
6. Interstitial Substitution Energy
7. Plot results of binary calculations
   

■ Operations on ternaries

1. Run binding energy calculation for a ternary
2. Plot results of ternary calculations
3. Parametric study - investigate the effect of a single parameter on the results of LAMMPS calculations for a selected element, binary, or ternary
   

■ Calibration

1. Specify calibration target data for each LAMMPS calculation enumerated above
2. Select library file entries associated with elements as calibration parameters
3. Select parameter file entries associated with elements, binaries and ternaries as calibration parameters
4. Attempt to automatically fit the selected calibration parameters so that the results of the LAMMPS calculations will approach the calibration targets within specified tolerances
5. Recall/redisplay results of attempted fits
   

■ Output operations

1. Write MEAM library file, MEAM parameter file, MPCv4 restart file
2. Write plot data to file
3. Write file templates of calibration target data for single element, binary, ternary
4. Write LAMMPS output log to file (log.lammps), or ‘none’
   
   

安装 | SETUP on personal computers without MATLAB

■ Windows 7, 64-bit

1. Download File: MPCv4 Win7 MATLAB R2016b Installer web.zip. Unzip to a temporary folder.
2. Run MPCv4_Win7_MATLAB_R2016b_Installer_web.exe in the temporary folder.
3. Specify C:\MPCv4 as the installation destination. As part of the installation process, the appropriate MATLAB Compiler Runtime will be downloaded automatically if it is not yet installed on the local system. Be prepared to wait for a long download time.
4. Run C:\MPCv4\application\MPCv4_Win7.exe as the administrator
   切记要以管理员身份运行, 否则由于权限不够, 无法进行数据读写。一定要安装在C:\MPCv4, 其他地方, 哪怕是电脑默认的安装位置C:\Program Files\MPCv4都不可以！这应该是编程的时候就决定了的.
5. As a first time test of MPCv4, click menu item File | Load restart file, then select the file Al-MPCv4-restart.mat. The display should be similar to the figure above.
   

■ MacOS X (Yosemite) on Intel 64

1. Download File: MPCv4 OSX Installer web.zip. Unzip to a temporary folder.
2. Run MPCv4_OSX_Installer_web in the temporary folder.
3. Specify /Users/your_home_dir/MPCv4 as the installation destination. As part of the installation process, the appropriate MATLAB Compiler Runtime will be downloaded automatically if it is not yet installed on the local system. Be prepared to wait for a long download time. Take note of the installation directory for the MATLAB Runtime (for example, /Applications/MATLAB/MATLAB_Runtime/v85/) as it will be needed two steps below.
4. Open a command line window. Change directory to /Users/your_home_dir/MPCv4/application.
5. ./run_MPCv4_OSX.sh /Applications/MATLAB/MATLAB_Runtime/v85
6. As a first time test of MPCv4, click menu item File | Load restart file, then select the file Al-MPCv4-restart.mat. The display should be similar to the figure above.