Use VMD to rotate the coordinate structure according to a certain coordinate axis

关注 M r . m a t e r i a l   , \color{Violet} \rm Mr.material\ , Mr.material ,  more\color{red}{more}More \color{blue}{more}Much fine\color{orange}{fine}Wonderful \color{green}{color}Colorful !


The main column contents include:
  † "LAMMPS Tips": ‾ \textbf{ \underline{\dag "LAMMPS Tips": }} " LAMMPS Tips" :Mainly introduces the use of molecular dynamics ( L ammps LammpsL amm p s ) simulation related installation tutorials, principles and simulation tips (difficulty:★ \bigstar )
  "LAMMPS Example Tutorial—Detailed Explanation of In File": ‾ \textbf{ \underline{\dag\dag"LAMMPS Example Tutorial—Detailed Explanation of In File":}}  " LAMMPS Example Tutorial —In File Detailed Explanation" :Mainly introduces the use of molecular dynamics ( L ammps LammpsL amm p s ) simulation related physical process simulation. (Including: calculation of thermal conductivity, calculation of specific heat capacity at constant pressure, difficulty:★ \bigstar ★ \bigstar ★ \bigstar )
  《Lammps Programming Techniques and Post-processing Programming Techniques》: ‾ \textbf{ \underline{\dag\dag\dag《Lammps Programming Techniques and Post-processing Programming Techniques》:}}  " Lammps Programming Techniques and Post-Processing Programming Techniques" :Mainly introduces the post-related processing and analysis of the dynamic process (trajectory file) of molecular simulation (requires certain programming ability. Difficulty: ★ \bigstar ★ \bigstar ★ \bigstar ★ \bigstar ★ \bigstar ).
  《Molecular dynamics post-processing integrated function—Matlab》: ‾ \textbf{ \underline{\dag\dag\dag\dag《Molecular dynamics post-processing integrated function—Matlab》:}}  "Molecular Dynamics Post-processing Integrated Function —Matlab " :It mainly introduces the packaging of specified functions in the post-processing process to facilitate users to call them directly (requires certain programming ability, difficulty: ★ \bigstar ★ \bigstar ★ \bigstar ★ \bigstar ).
  ‾ \textbf{ \underline{\dag\dag\dag\dag\dag"SCI Paper Drawing—Commonly used templates and techniques for Python drawing": }}  " SCI Paper Drawing Commonly Used Templates and Techniques for Python Drawing" :It mainly introduces the visualization of processed data and provides corresponding drawing templates (requires certain programming ability, difficulty: ★ \bigstar ★ \bigstar ★ \bigstar ★ \bigstar ).
  ‾ \textbf{ \underline{\dag\dag\dag\dag\dag\dag "Molecular Simulation—Ovito Rendering Case Tutorial": }}  "Molecular Simulation —Ovito Rendering Case Tutorial" :Mainly using O vito \rm OvitoOvito software, forL ammps \rm LammpsRendering of trajectory files generated by Lammps (difficulty: ★ \bigstar ★ \bigstar)。

  Column description (you can browse all blog posts of the corresponding column after subscribing): ‾ \color{red}{\textbf{ \underline{Column description (you can browse all blog posts of the corresponding column after subscribing): }}} Column description (you can browse all blog posts of the corresponding column after subscribing) :
Note: \color{red} Note:Note: If you only want to subscribe to a single blog post, please contact the blogger’s email address for consultation. lammps _ materials @ 163. com \rm lammps\[email protected][email protected]

♠ \spadesuit † \day Open source post-processing integration program: Please pay attention to the column"LAMMPS post-processing - MATLAB sub-function collection"
♠ \spadesuit † \day † \day If you need to pay to customize the post-processing program, please contact us by email:lammps _ materials @ 163. com \rm lammps\[email protected][email protected]


Select all atoms and record them as all allall

 set all [atomselect top all]


Rotate 90 degrees around the z-axis

 $all move [transaxis z -90]

1. Before rotation

insert image description here

2. Rotate 30° around the Y axis. After rotation

insert image description here

3. Adjust the box size

measure minmax $all

$all moveby {
    
    1.5506435602219426e-6 1.8080943391396431e-6 8.952644634518947e-7}

measure minmax $all

pbc set {
    
    123.67752075195313 142.7479705810547 71.4052505493164}

insert image description here

Guess you like

Origin blog.csdn.net/qq_43689832/article/details/131548942