<div dir="ltr">This is not a CP2K related problem. <div><br></div><div>According to my understanding, you should first perform calculations for each single He atom placed at positions in the dimer, and you print out electron density cube files of each He atom, and then you sum them up, let's say you have cube file 1. Then you perform a calculation for the He dimer, and you print out the electron density cube file 2 (you named it rut_density). Finally, you take the difference of the two cube files by subtracting one from the other.<div><br></div><div>To manipulate the cube files, e.g. summation or subtraction, you can use the cubecruncher tool supplied with CP2K, see $CP2K/cp2k/tools/cubecruncher (where $CP2K is the main directory of your CP2K source code). Alternatively, you can use the cubman utility of Gaussian 09 to perform the cube file manipulations.</div><div><br></div><div>SL<br><br>On Monday, March 9, 2015 at 7:07:52 PM UTC, Xun Wang wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Hello,<div><br></div><div>I am a new user to cp2k and I would like to know how I can plot the atomic density difference from the cube file.</div><div>In my calculation of He dimer, I added the following lines to my input file to get the cube file. </div><div>
                
        
        
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                                        <p><span style="font-size:11.000000pt;font-family:'CourierNewPSMT'"> &E_DENSITY_CUBE
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                                        <p><span style="font-size:11.000000pt;font-family:'CourierNewPSMT'"> FILENAME ./rut_density
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                                        <p><span style="font-size:11.000000pt;font-family:'CourierNewPSMT'"> &END E_DENSITY_CUBE</span><span style="font-family:CourierNewPSMT;font-size:11pt"> </span></p><p>I would like to get a plot as figure 2 in the following literature: <a href="http://scitation.aip.org/content/aip/journal/jcp/117/24/10.1063/1.1522715" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fscitation.aip.org%2Fcontent%2Faip%2Fjournal%2Fjcp%2F117%2F24%2F10.1063%2F1.1522715\46sa\75D\46sntz\0751\46usg\75AFQjCNFq1BVySxzpCJR3Qd3erG1R5bhsdQ';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fscitation.aip.org%2Fcontent%2Faip%2Fjournal%2Fjcp%2F117%2F24%2F10.1063%2F1.1522715\46sa\75D\46sntz\0751\46usg\75AFQjCNFq1BVySxzpCJR3Qd3erG1R5bhsdQ';return true;">http://scitation.<wbr>aip.org/content/aip/journal/<wbr>jcp/117/24/10.1063/1.1522715</a></p><p>I appreciate your help me with this!</p><p><br></p><p>Xun</p>
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