<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">https://github.com/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" class="gmail_attr">On Sun, Feb 17, 2019 at 4:10 AM Nicholas Dimakis <<a href="mailto:ndim...@gmail.com">ndim...@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 style="font-variant-ligatures:no-common-ligatures">$ ./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 style="font-variant-ligatures:no-common-ligatures"> 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 style="font-variant-ligatures:no-common-ligatures"> 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 style="font-variant-ligatures:no-common-ligatures">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 style="font-variant-ligatures:no-common-ligatures"> 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 style="font-variant-ligatures:no-common-ligatures"> -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 style="font-variant-ligatures:no-common-ligatures"> 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 style="font-variant-ligatures:no-common-ligatures"> 5221.9100357117386 </span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">Writing cube ... Done</span></p></div><div><span style="font-variant-ligatures:no-common-ligatures"><br></span></div><div><span style="font-variant-ligatures:no-common-ligatures">and </span></div><div><span style="font-variant-ligatures:no-common-ligatures"><br></span></div><div><span style="font-variant-ligatures:no-common-ligatures"><p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">$ ./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 style="font-variant-ligatures:no-common-ligatures"> 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 style="font-variant-ligatures:no-common-ligatures"> 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 style="font-variant-ligatures:no-common-ligatures">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 style="font-variant-ligatures:no-common-ligatures"> 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 style="font-variant-ligatures:no-common-ligatures"> -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 style="font-variant-ligatures:no-common-ligatures"> 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 style="font-variant-ligatures:no-common-ligatures"> 5221.9100357117386 </span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">Writing cube ... Done</span></p><div><span style="font-variant-ligatures:no-common-ligatures"><br></span></div><div><span style="font-variant-ligatures:no-common-ligatures">However, the final file 2.cube does not seem to be correct. Moreover I found that if I do</span></div><div><span style="font-variant-ligatures:no-common-ligatures"><br></span></div><div><span style="font-variant-ligatures:no-common-ligatures"><p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"> ./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 style="font-variant-ligatures:no-common-ligatures"> 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 style="font-variant-ligatures:no-common-ligatures"> 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 style="font-variant-ligatures:no-common-ligatures">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 style="font-variant-ligatures:no-common-ligatures"> 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 style="font-variant-ligatures:no-common-ligatures"> -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 style="font-variant-ligatures:no-common-ligatures"> 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 style="font-variant-ligatures:no-common-ligatures"> 656.85613359754439 </span></p>
<p style="font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">Writing cube ... Done</span></p><div><span style="font-variant-ligatures:no-common-ligatures"><br></span></div><div><span style="font-variant-ligatures:no-common-ligatures">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">https://drive.google.com/file/d/1pikUv9RQKYc3w0E0W4iA4H5RLaaODYVn/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">https://drive.google.com/file/d/11XzpX7ISZdZWtvCi1d1i8I1D0LtrW81l/view?usp=sharing</a><br></div><div><a href="https://drive.google.com/file/d/1LjfoZreh6-stIi6Mk0YSUSKbKLa3v4ri/view?usp=sharing" target="_blank">https://drive.google.com/file/d/1LjfoZreh6-stIi6Mk0YSUSKbKLa3v4ri/view?usp=sharing</a><br></div><div><a href="https://drive.google.com/file/d/1euo52DFENdtQhuMco2jlLUAphSPJB5Jz/view?usp=sharing" target="_blank">https://drive.google.com/file/d/1euo52DFENdtQhuMco2jlLUAphSPJB5Jz/view?usp=sharing</a><br></div><div><a href="https://drive.google.com/file/d/1UtaUJnyZZBmuAq_2FydezchX7h_FNtEt/view?usp=sharing" target="_blank">https://drive.google.com/file/d/1UtaUJnyZZBmuAq_2FydezchX7h_FNtEt/view?usp=sharing</a><br></div><div><br></div><div><br></div><div><br></div></span></div></span></div></div>
<p></p>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr">Best Regards,<br>Fatemeh Khalili<br>PhD candidate <br>Department of Physics <br>Shahid Beheshti University</div></div>