<div dir="ltr">Dear Nick<div><br></div><div>you have a typo in your command line</div><div>it is -subtract and not <span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Menlo; font-size: 14px;">-substract</span></div><div><font color="#000000" face="Menlo"><span style="caret-color: rgb(0, 0, 0); font-size: 14px;">regards</span></font></div><div><font color="#000000" face="Menlo"><span style="caret-color: rgb(0, 0, 0); font-size: 14px;">Marcella</span></font></div><div><font color="#000000" face="Menlo"><span style="caret-color: rgb(0, 0, 0); font-size: 14px;"><br></span></font><br>On Sunday, February 17, 2019 at 1:39:59 AM UTC+1, Nicholas Dimakis 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 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></blockquote></div></div>