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layout: post title: 新版VASP轨迹文件转换为GROMACS格式 categories:

vasp轨迹文件的格式经常变动, 这样导致和vmd的插件不兼容, 查看的时候只能显示一帧. 我最近使用的vasp 5.4.4输出的轨迹文件XDATCAR就存在这个问题. 为了解决这个问题, 我写了一个简单的脚本, 将XDATCAR转换为gromacs格式以便使用vmd查看. 简单来说, gromacs的gro格式是一种类似于xyz的格式, 但其中的坐标以nm为单位, 同时最后一行添加盒子矢量的信息.

<table class="highlighttable"><th colspan="2" style="text-align:left">x2gro.bsh</th><tr><td><div class="linenodiv" style="background-color: #f0f0f0; padding-right: 10px"><pre style="line-height: 125%"> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32</pre></div></td><td class="code"><div class="highlight" style="background: #f8f8f8"><pre style="line-height: 125%"><span></span><span style="color: #B8860B">File</span><span style="color: #666666">=</span>XDATCAR awk <span style="color: #BB4444">'</span> BEGIN <span style="color: #666666">{</span> <span style="color: #B8860B">Rad2Deg</span><span style="color: #666666">=</span>180/4*atan2<span style="color: #666666">(</span>1,1<span style="color: #666666">)</span> <span style="color: #666666">}</span> <span style="color: #666666">{</span> <span style="color: #B8860B">Tips</span><span style="color: #666666">=</span><span style="color: #B8860B">$0</span> getline; <span style="color: #B8860B">a</span><span style="color: #666666">=</span><span style="color: #B8860B">$1</span>/10; <span style="color: #B8860B">b</span><span style="color: #666666">=</span>a; <span style="color: #B8860B">c</span><span style="color: #666666">=</span>a; <span style="color: #AA22FF; font-weight: bold">if</span><span style="color: #666666">(</span>NF><span style="color: #666666">=</span>2<span style="color: #666666">)</span> <span style="color: #B8860B">b</span><span style="color: #666666">=</span><span style="color: #B8860B">$2</span>/10; <span style="color: #AA22FF; font-weight: bold">if</span><span style="color: #666666">(</span>NF><span style="color: #666666">=</span>3<span style="color: #666666">)</span> <span style="color: #B8860B">c</span><span style="color: #666666">=</span><span style="color: #B8860B">$3</span>/10 getline; <span style="color: #B8860B">ax</span><span style="color: #666666">=</span><span style="color: #B8860B">$1</span>*a; <span style="color: #B8860B">ay</span><span style="color: #666666">=</span><span style="color: #B8860B">$2</span>*b; <span style="color: #B8860B">az</span><span style="color: #666666">=</span><span style="color: #B8860B">$3</span>*c getline; <span style="color: #B8860B">bx</span><span style="color: #666666">=</span><span style="color: #B8860B">$1</span>*a; <span style="color: #B8860B">by</span><span style="color: #666666">=</span><span style="color: #B8860B">$2</span>*b; <span style="color: #B8860B">bz</span><span style="color: #666666">=</span><span style="color: #B8860B">$3</span>*c getline; <span style="color: #B8860B">cx</span><span style="color: #666666">=</span><span style="color: #B8860B">$1</span>*a; <span style="color: #B8860B">cy</span><span style="color: #666666">=</span><span style="color: #B8860B">$2</span>*b; <span style="color: #B8860B">cz</span><span style="color: #666666">=</span><span style="color: #B8860B">$3</span>*c <span style="color: #B8860B">Natm</span><span style="color: #666666">=</span>0 getline; <span style="color: #B8860B">Nelm</span><span style="color: #666666">=</span>NF; <span style="color: #AA22FF; font-weight: bold">for</span><span style="color: #666666">(</span><span style="color: #B8860B">i</span><span style="color: #666666">=</span>1; i<<span style="color: #666666">=</span>Nelm; i++<span style="color: #666666">)</span> Sym<span style="color: #666666">[</span>i<span style="color: #666666">]=</span><span style="color: #B8860B">$i</span> getline; <span style="color: #AA22FF; font-weight: bold">for</span><span style="color: #666666">(</span><span style="color: #B8860B">i</span><span style="color: #666666">=</span>1; i<<span style="color: #666666">=</span>Nelm; i++<span style="color: #666666">)</span> <span style="color: #666666">{</span> Numb<span style="color: #666666">[</span>i<span style="color: #666666">]=</span><span style="color: #B8860B">$i</span>; <span style="color: #B8860B">Natm</span><span style="color: #666666">=</span>Natm+<span style="color: #B8860B">$i</span> <span style="color: #666666">}</span> getline; <span style="color: #B8860B">step</span><span style="color: #666666">=</span><span style="color: #B8860B">$NF</span> <span style="color: #B8860B">YesCar</span><span style="color: #666666">=</span>0; <span style="color: #AA22FF; font-weight: bold">if</span><span style="color: #666666">(</span><span style="color: #B8860B">$0</span>~/^<span style="color: #666666">[</span>::space::<span style="color: #666666">]</span>*<span style="color: #666666">[</span>C|c<span style="color: #666666">]</span>/<span style="color: #666666">)</span> <span style="color: #B8860B">YesCar</span><span style="color: #666666">=</span>1 print Tips <span style="color: #BB4444">" step= "</span>step print Natm <span style="color: #B8860B">n</span><span style="color: #666666">=</span>0 <span style="color: #AA22FF; font-weight: bold">for</span><span style="color: #666666">(</span><span style="color: #B8860B">i</span><span style="color: #666666">=</span>1; i<<span style="color: #666666">=</span>Nelm; i++<span style="color: #666666">)</span> <span style="color: #666666">{</span> <span style="color: #AA22FF; font-weight: bold">for</span><span style="color: #666666">(</span><span style="color: #B8860B">j</span><span style="color: #666666">=</span>1; j<<span style="color: #666666">=</span>Numb<span style="color: #666666">[</span>i<span style="color: #666666">]</span>; j++<span style="color: #666666">)</span> <span style="color: #666666">{</span> getline; n++ <span style="color: #B8860B">x</span><span style="color: #666666">=</span><span style="color: #B8860B">$1</span>/10; <span style="color: #B8860B">y</span><span style="color: #666666">=</span><span style="color: #B8860B">$2</span>/10; <span style="color: #B8860B">z</span><span style="color: #666666">=</span><span style="color: #B8860B">$3</span>/10 <span style="color: #AA22FF; font-weight: bold">if</span><span style="color: #666666">(</span>!YesCar<span style="color: #666666">)</span> <span style="color: #666666">{</span> <span style="color: #B8860B">x</span><span style="color: #666666">=</span>ax*<span style="color: #B8860B">$1</span>+ay*<span style="color: #B8860B">$2</span>+az*<span style="color: #B8860B">$3</span> <span style="color: #B8860B">y</span><span style="color: #666666">=</span>bx*<span style="color: #B8860B">$1</span>+by*<span style="color: #B8860B">$2</span>+bz*<span style="color: #B8860B">$3</span> <span style="color: #B8860B">z</span><span style="color: #666666">=</span>cx*<span style="color: #B8860B">$1</span>+cy*<span style="color: #B8860B">$2</span>+cz*<span style="color: #B8860B">$3</span> <span style="color: #666666">}</span> printf<span style="color: #666666">(</span><span style="color: #BB4444">"%8s%7s%5d%8.3f%8.3f%8.3f\n"</span>, i<span style="color: #BB4444">"ELM"</span>, Sym<span style="color: #666666">[</span>i<span style="color: #666666">]</span>, n, x, y, z<span style="color: #666666">)</span> <span style="color: #666666">}</span> <span style="color: #666666">}</span> print ax, by, cz, ay, az, bx, bz, cx, cy <span style="color: #666666">}</span> <span style="color: #BB4444">'</span> <span style="color: #B8860B">$File</span> > <span style="color: #B8860B">$File</span>.gro </pre></div> </td></tr></table>