<div dir="ltr">Hi<div><br></div><div>Thank you all for your replies. I found that the problem was with the actual cube files that were not same size. This issue is now resolved.</div><div><br></div><div>Nick<br><br>On Sunday, February 17, 2019 at 1:43:10 PM UTC-6, Varesh wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr"><div dir="ltr"><div dir="ltr">dear Nicholas Dimakis,<div><br></div><div>another way to subtracting cubes is the following code (shared by Tassem El-Sayed<span style="background-color:rgb(241,248,255);color:rgb(36,41,46);font-family:-apple-system,BlinkMacSystemFont,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol";font-size:12px;font-weight:600;white-space:nowrap">)</span> :</div><div>"<a href="https://github.com/funkymunkycool/Cube-Toolz" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Ffunkymunkycool%2FCube-Toolz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEyqHAgQ2ztplMqCD9T8DMJ4T325A';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Ffunkymunkycool%2FCube-Toolz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEyqHAgQ2ztplMqCD9T8DMJ4T325A';return true;">https://github.com/<wbr>funkymunkycool/Cube-Toolz</a>"<br></div><div><br></div><div>with this command:</div><div>e.g: "python2.7 cube_tools.py -s 1.cube 2.cube "</div></div></div></div><br><div class="gmail_quote"><div dir="ltr">On Sun, Feb 17, 2019 at 4:10 AM Nicholas Dimakis <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="kjQ71HgnGwAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">ndi...@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hello<div><br></div><div>I am new to this group and I am trying to obtain electron density differences using cube files (attached). I am using <font color="#000000" face="Menlo"><span style="font-size:14px">cubecruncher (on </span><span style="font-size:14px">macOS)</span><span style="font-size:14px">, where I do</span></font></div><div><span style="color:rgb(0,0,0);font-family:Menlo;font-size:14px"><br></span></div><div><p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span>$ ./cubecruncher.x -i MoS2-1water1.cube -substract MoS2-1water1-slab.cube -o 1.cube</span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> Reading from cube MoS2-1water1.cube</span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> Writing to cube 1.cube</span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span>Reading cube ... Done</span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> 23.410000000000000 5.0000000000000001E-004 0.0000000000000000 </span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> -11.704699999999999 20.268400000000000 0.0000000000000000 </span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> 0.0000000000000000 0.0000000000000000 11.005332000000001 </span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> 5221.9100357117386 </span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span>Writing cube ... Done</span></p></div><div><span><br></span></div><div><span>and </span></div><div><span><br></span></div><div><span><p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span>$ ./cubecruncher.x -i 1.cube -substract MoS2-1water1-water.cube -o 2.cube</span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> Reading from cube 1.cube</span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> Writing to cube 2.cube</span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span>Reading cube ... Done</span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> 23.410000000000000 5.0000000000000001E-004 0.0000000000000000 </span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> -11.704699999999999 20.268400000000000 0.0000000000000000 </span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> 0.0000000000000000 0.0000000000000000 11.005332000000001 </span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> 5221.9100357117386 </span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span>Writing cube ... Done</span></p><div><span><br></span></div><div><span>However, the final file 2.cube does not seem to be correct. Moreover I found that if I do</span></div><div><span><br></span></div><div><span><p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ./cubecruncher.x -i MoS2-1water1-water.cube -substract MoS2-1water1-water.cube -o test.cube</span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> Reading from cube MoS2-1water1-water.cube</span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> Writing to cube test.cube</span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span>Reading cube ... Done</span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> 23.410000000000000 5.0000000000000001E-004 0.0000000000000000 </span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> -11.704699999999999 20.268400000000000 0.0000000000000000 </span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> 0.0000000000000000 0.0000000000000000 1.3843440000000000 </span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> 656.85613359754439 </span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span>Writing cube ... Done</span></p><div><span><br></span></div><div><span>the output cube (i.e., </span><span style="color:rgb(0,0,0);font-family:Menlo;font-size:14px">test.cube) is not a zero density file as expected by it seems similar to the original.</span></div><div><span style="color:rgb(0,0,0);font-family:Menlo;font-size:14px"><br></span></div><div><span style="color:rgb(0,0,0);font-family:Menlo;font-size:14px">Thank you,</span></div><div><span style="color:rgb(0,0,0);font-family:Menlo;font-size:14px"><br></span></div><div><br></div><div><span style="color:rgb(0,0,0);font-family:Menlo;font-size:14px">Nick</span></div><div><span style="color:rgb(0,0,0);font-family:Menlo;font-size:14px"><br></span></div><div><span style="color:rgb(0,0,0);font-family:Menlo;font-size:14px">cube files can be found here </span></div><div><span style="color:rgb(0,0,0);font-family:Menlo;font-size:14px"><br></span></div><div><a href="https://drive.google.com/file/d/1pikUv9RQKYc3w0E0W4iA4H5RLaaODYVn/view?usp=sharing" target="_blank" rel="nofollow" onmousedown="this.href='https://drive.google.com/file/d/1pikUv9RQKYc3w0E0W4iA4H5RLaaODYVn/view?usp\x3dsharing';return true;" onclick="this.href='https://drive.google.com/file/d/1pikUv9RQKYc3w0E0W4iA4H5RLaaODYVn/view?usp\x3dsharing';return true;">https://drive.google.com/file/<wbr>d/<wbr>1pikUv9RQKYc3w0E0W4iA4H5RLaaOD<wbr>YVn/view?usp=sharing</a><span style="color:rgb(0,0,0);font-family:Menlo;font-size:14px"><br></span></div><div><a href="https://drive.google.com/file/d/11XzpX7ISZdZWtvCi1d1i8I1D0LtrW81l/view?usp=sharing" target="_blank" rel="nofollow" onmousedown="this.href='https://drive.google.com/file/d/11XzpX7ISZdZWtvCi1d1i8I1D0LtrW81l/view?usp\x3dsharing';return true;" onclick="this.href='https://drive.google.com/file/d/11XzpX7ISZdZWtvCi1d1i8I1D0LtrW81l/view?usp\x3dsharing';return true;">https://drive.google.com/file/<wbr>d/<wbr>11XzpX7ISZdZWtvCi1d1i8I1D0LtrW<wbr>81l/view?usp=sharing</a><br></div><div><a href="https://drive.google.com/file/d/1LjfoZreh6-stIi6Mk0YSUSKbKLa3v4ri/view?usp=sharing" target="_blank" rel="nofollow" onmousedown="this.href='https://drive.google.com/file/d/1LjfoZreh6-stIi6Mk0YSUSKbKLa3v4ri/view?usp\x3dsharing';return true;" onclick="this.href='https://drive.google.com/file/d/1LjfoZreh6-stIi6Mk0YSUSKbKLa3v4ri/view?usp\x3dsharing';return true;">https://drive.google.com/file/<wbr>d/1LjfoZreh6-<wbr>stIi6Mk0YSUSKbKLa3v4ri/view?<wbr>usp=sharing</a><br></div><div><a href="https://drive.google.com/file/d/1euo52DFENdtQhuMco2jlLUAphSPJB5Jz/view?usp=sharing" target="_blank" rel="nofollow" onmousedown="this.href='https://drive.google.com/file/d/1euo52DFENdtQhuMco2jlLUAphSPJB5Jz/view?usp\x3dsharing';return true;" onclick="this.href='https://drive.google.com/file/d/1euo52DFENdtQhuMco2jlLUAphSPJB5Jz/view?usp\x3dsharing';return true;">https://drive.google.com/file/<wbr>d/<wbr>1euo52DFENdtQhuMco2jlLUAphSPJB<wbr>5Jz/view?usp=sharing</a><br></div><div><a href="https://drive.google.com/file/d/1UtaUJnyZZBmuAq_2FydezchX7h_FNtEt/view?usp=sharing" target="_blank" rel="nofollow" onmousedown="this.href='https://drive.google.com/file/d/1UtaUJnyZZBmuAq_2FydezchX7h_FNtEt/view?usp\x3dsharing';return true;" onclick="this.href='https://drive.google.com/file/d/1UtaUJnyZZBmuAq_2FydezchX7h_FNtEt/view?usp\x3dsharing';return true;">https://drive.google.com/file/<wbr>d/1UtaUJnyZZBmuAq_2FydezchX7h_<wbr>FNtEt/view?usp=sharing</a><br></div><div><br></div><div><br></div><div><br></div></span></div></span></div></div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr">Best Regards,<br>Fatemeh Khalili<br>PhD candidate <br>Department of Physics <br>Shahid Beheshti University</div></div>
</blockquote></div></div>