<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Thank you so much! I'll try that.<br><br><br></div><div><br>On Dec 22, 2014, at 11:52, xiaochuan Ge <<a href="mailto:ustc.scgyer@gmail.com">ustc.scgyer@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div><div dir="ltr"><div class="gmail_default" style="font-family:trebuchet ms,sans-serif">Dear Jing, <br></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif">If you are able to compile a simple Fortran code, I believe the piece of code in the attachment can be helpful. This is a small piece of code used by myself to do some simple calculation with the .cube file. After compiling and running the code, you should have the wavefunction or potential stored in wfcv, you can add your own code afterwards to do the analysis you wish to. Hope this helps. <br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr">===================<br>Dr. Xiaochuan Ge (Giovanni)<div>Center for Functional Nanomaterials<br><div>Brookhaven national laboratory </div><div>===================</div></div></div></div></div>
<br><div class="gmail_quote">On 20 December 2014 at 11:43, Jing Wang <span dir="ltr"><<a href="mailto:ffyuyuzaoa@gmail.com" target="_blank">ffyuyuzaoa@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto"><div>Thanks. Okay, let me make sure I understand that, so all the data shown in the file are potentials at nth position and I have to calculate the corresponding real space coordinate myself. Right?</div><div>And I've actually got another relevant question for my situation: is it possible to convert fildv files made during ph.x calculation into human readable files like pw2casino does to the wavefunction in pw.x pw2casino <input> output precess?</div><div><br></div><div>Thanks.</div><div><div class="h5"><div><br><br><br></div><div><br>On Dec 20, 2014, at 6:36, xiaochuan Ge <<a href="mailto:ustc.scgyer@gmail.com" target="_blank">ustc.scgyer@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div>Nop, the first three columns are not coordinates. The coordinates are implicitly given. you have the size of the cell, and the number of grids at the first few lines, then you should be able to have a formula to calculate the coordinate of the n-th data.<div><span></span><br><br>On Saturday, December 20, 2014, Jing Wang <<a href="mailto:ffyuyuzaoa@gmail.com" target="_blank">ffyuyuzaoa@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thanks for the very detailed explanation of the output file. I read the format explanation in the link you gave again and again and I still can't figure out what the five columns are. For example in the main part of the data file (shown as below), if the first three columns are the coordinates in the real r space with the unit in alat, then what are the left two columns recording? Which column is the potential? How does the datafile represent the Vscf(r) function in real space? <div>.....</div><div>.....</div><div>3.248268856E+00 3.159870688E+00 2.515974539E+00 6.186557012E-01 -2.154636042E+00<br> -3.866568628E+00 -3.274420891E+00 -2.365272143E+00 -2.086628582E+00 -1.945051309E+00<br> -1.918992011E+00 -1.927145835E+00 -1.943940931E+00 -1.943940931E+00 -1.927145835E+00<br></div><div><span style="font-size:14px">.....</span></div><div><span style="font-size:14px">.....</span></div><div><span style="font-size:14px"><br></span></div><div><span style="font-size:14px">Thank you.</span></div><div><span style="font-size:14px"><br></span></div><div><span style="font-size:14px">Jing Wang</span></div><div><span style="font-size:14px">Dept. of Physics,</span></div><div><span style="font-size:14px">Georgia Tech, GA</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">2014-12-19 11:42 GMT-05:00 Paolo Giannozzi <span dir="ltr"><<a>paolo.giannozzi@uniud.it</a>></span>:<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span>On Wed, 2014-12-17 at 10:59 -0500, Jing Wang wrote:<br>
<br>
> I'm really confused about how can I read the local potential out<br>
> from the scf calculation. I used pp.x, plot_num=1 to extract the scf<br>
> potential of the the system, however I can't really understand the<br>
> output?<br>
<br>
</span>the "output" is not meant to be read by humans but by other codes.<br>
<span><br>
> Should it show the potential in cofficients of G-vectors?<br>
<br>
</span>no, it is in real space, in the format explained here:<br>
<a href="http://www.quantum-espresso.org/wp-content/uploads/Doc//developer_man/developer_man.html#SECTION00080000000000000000" target="_blank">http://www.quantum-espresso.org/wp-content/uploads/Doc//developer_man/developer_man.html#SECTION00080000000000000000</a><br>
<span><br>
> Head of the output is like this:<br>
<br>
> 25 25 100 25 25 100 2 1<br>
<br>
</span>FFT maximum dimensions and grids (nr1x nr2x nr3x nr1 nr2 nr3),<br>
number of atoms, number of species<br>
<span><br>
> 4 4.64900000 0.00000000 4.00000000<br>
> 0.00000000 0.00000000 0.00000000<br>
<br>
</span>ibrav, celldm(1-3) as given in scf input<br>
<br>
> 153.2912575334 4.0000000000 70.0000000000 1<br>
<br>
Gmax in (2pi/a)^2 units, dual (ecutrho=dual*ecutwfc), cutoff (Ry)<br>
<span><br>
> 1 C 4.00<br>
> 1 0.000000000 0.000000000 0.000000000 1<br>
> 2 0.500000000 -0.288675135 0.000000000 1<br>
<br>
</span>atomic species and atomic positions. The plotted quantity in real space<br>
(array length nr1x*nr2x*nr3) follows<br>
<br>
Paolo<br>
<div><div><br>
> 3.248268856E+00 3.159870688E+00 2.515974539E+00 6.186557012E-01<br>
> -2.154636042E+00<br>
> -3.866568628E+00 -3.274420891E+00 -2.365272143E+00 -2.086628582E+00<br>
> -1.945051309E+00<br>
> -1.918992011E+00 -1.927145835E+00 -1.943940931E+00 -1.943940931E+00<br>
> -1.927145835E+00<br>
> -1.918992010E+00 -1.945051309E+00 -2.086628581E+00 -2.365272143E+00<br>
> -3.274420890E+00<br>
> -3.866568627E+00 -2.154636041E+00 6.186557014E-01 2.515974539E+00<br>
> 3.159870688E+00<br>
> 3.159870688E+00 3.159870688E+00 2.802339131E+00 1.452305376E+00<br>
> -1.033031298E+00<br>
> -3.409639826E+00 -3.654745566E+00 -2.575759384E+00 -2.021392120E+00<br>
> -1.762140769E+00<br>
> -1.637123367E+00 -1.599819700E+00 -1.588050229E+00 -1.591678304E+00<br>
> -1.588050228E+00<br>
> -1.599819700E+00 -1.637123366E+00 -1.762140768E+00 -2.021392119E+00<br>
> -2.575759383E+00<br>
> -3.654745566E+00 -3.409639826E+00 -1.033031298E+00 1.452305376E+00<br>
> 2.802339131E+00<br>
> 2.515974539E+00 2.794920980E+00 2.515974539E+00 1.452305376E+00<br>
> -6.088327143E-01<br>
> -2.976954364E+00 -3.787496708E+00 -2.827784418E+00 -2.048224903E+00<br>
> -1.714196738E+00<br>
> -1.488710208E+00 -1.380390580E+00 -1.313398615E+00 -1.296957599E+00<br>
> -1.296957599E+00<br>
> -1.313398615E+00 -1.380390580E+00 -1.488710208E+00 -1.714196738E+00<br>
> -2.048224903E+00<br>
> -2.827784418E+00 -3.787496708E+00 -2.976954363E+00 -6.088327142E-01<br>
> 1.452305376E+00<br>
> 6.186557014E-01 1.426203806E+00 1.426203806E+00 6.186557014E-01<br>
> -1.033031298E+00<br>
> -2.976954363E+00 -3.792558359E+00 -2.995197487E+00 -2.094921250E+00<br>
> -1.698073457<br>
><br>
><br>
><br>
> Thanks.<br>
><br>
><br>
> Jing Wang<br>
><br>
> Dept. of Physics<br>
><br>
> Georgia Tech, GA, U.S.A<br>
><br>
</div></div>> _______________________________________________<br>
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<span><font color="#888888"><br>
--<br>
Paolo Giannozzi, Dept. Chemistry&Physics&Environment,<br>
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
Phone <a href="tel:%2B39-0432-558216" value="+390432558216" target="_blank">+39-0432-558216</a>, fax <a href="tel:%2B39-0432-558222" value="+390432558222" target="_blank">+39-0432-558222</a><br>
<br>
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</font></span></blockquote></div></div>
</blockquote></div><br><br>-- <br><div dir="ltr">===================<br>Dr. Xiaochuan Ge (Giovanni)<div>Center for Functional Nanomaterials<br><div>Brookhaven national laboratory </div><div>===================</div></div></div><br>
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