<div dir="ltr"><p dir="ltr">I do not think there are any options in the job_control.txt file to write the reconstructed cube files in DDEC6 program. I do not know if you want to tweak the program to make it write these reconstructed files. If you have a CP2K valence electron density file with you, some relevant files may be module_format_valence_cube_density.f08 or module_add_missing_core_density.f08 (not sure)?</p><p>I believe there will a paper soon by Prof. Manz, which will provide you with the core densities that you can use to generate your own reconstructed cube files. </p><p>On a different note for interested users, when CP2K files are generated with large cutoff values and if you end up getting Fortran runtime error/End of file error, the default variable value of read_buffer_size in module_global_parameters may need to be increased from its default value. </p><p>HTH.</p><p dir="ltr">On Jul 10, 2016 5:26 AM, "David T" <<a href="mailto:amazing...@gmail.com" target="_blank">amazing...@gmail.com</a>> wrote:</p><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi<br>I downloaded the code but the documentation is a bit encrypted.<br>I can use the code for calculating the charges but I can't write any reconstructed cube file.<br><br>Do you know how to do it? Can you please explain it to me?<br><br>Cheers<br>Davide<br><br><br>On Sunday, 12 June 2016 00:44:19 UTC+2, S Ling wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi<div><br></div><div>You may try this tool, see: </div><div><br></div><div><a href="https://sourceforge.net/projects/ddec/" rel="nofollow" target="_blank">https://sourceforge.net/projects/ddec/</a> </div><div><br></div><div>Although the tool was originally developed to perform partial charge analysis using another method (see <a href="http://pubs.acs.org/doi/abs/10.1021/ct100125x" rel="nofollow" target="_blank">http://pubs.acs.org/doi/abs/10.1021/ct100125x</a>), the tool can produce a cube file which contains the core electron density based on some reference densities (included in the DDEC program). You can then perform Bader charge analysis on this new cube file using the tool developed by Henkelman. Please have a look at the manual included in the DDEC program. You may need to change some of the parameters (number of core electrons) in the DDEC program, as the GTH pseudopotentials used by CP2K may correspond to different numbers of core electrons.</div><div><br></div><div>SL</div><div><br></div></div><div><br><div class="gmail_quote">On 10 June 2016 at 23:21, Satish Kumar <span dir="ltr"><<a rel="nofollow">sati...@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div style="color:rgb(0,0,0);font-family:Tahoma;font-size:13.3333px">Hello CP2K users</div><div style="color:rgb(0,0,0);font-family:Tahoma;font-size:13.3333px"><br></div><div style="color:rgb(0,0,0);font-family:Tahoma;font-size:13.3333px">I was trying to obtain "proper?" Bader charges (Using Henkelman's program) for a CO2 molecule. Right now, I am getting the charge associated with C atom to be zero. In VASP, we can add the LAECHG=TRUE tag that will print the core charges too (<a href="http://theory.cm.utexas.edu/henkelman/code/bader/" rel="nofollow" target="_blank">http://theory.cm.utexas.edu/henkelman/code/bader/</a>). Doing so in VASP gives a reasonable (around 2 electrons) charge associated with C atom. After looking up the CP2K Google group I tried a couple of other options in an attempt to get the total (valence + core) charge density. <span style="font-size:13px">I tried the following print sections:</span></div><div style="color:rgb(0,0,0);font-family:Tahoma;font-size:13.3333px"><span style="font-size:13px"><br></span></div><div style="color:rgb(0,0,0);font-family:Tahoma;font-size:13.3333px"><font size="1"><span style="font-size:13px"><div>1)</div><div>
<p><br></p><p>&PRINT</p>
<p> &E_DENSITY_CUBE</p>
<p> STRIDE 1</p>
<p> &END E_DENSITY_CUBE<br></p>
<p>&END PRINT</p></div><div><br></div><div>2)<br></div><div> &PRINT<br></div><div><div style="margin-top:14pt;margin-bottom:14pt"> &E_DENSITY_CUBE</div><div style="margin-top:14pt;margin-bottom:14pt"> STRIDE 1</div><div style="margin-top:14pt;margin-bottom:14pt"> TOTAL_DENSITY .TRUE.</div><div style="margin-top:14pt;margin-bottom:14pt"> &END E_DENSITY_CUBE</div><div style="margin-top:14pt;margin-bottom:14pt"> &END PRINT</div><div style="margin-top:14pt;margin-bottom:14pt"><br></div></div><div>3) This one gave wrong results I think (number of electrons estimated from Bader was 0). </div><div> &PRINT<br></div><div><div style="margin-top:14pt;margin-bottom:14pt"> &TOT_DENSITY_CUBE</div><div style="margin-top:14pt;margin-bottom:14pt"> STRIDE 1</div><div style="margin-top:14pt;margin-bottom:14pt"> &END TOT_DENSITY_CUBE</div><div style="margin-top:14pt;margin-bottom:14pt"> &END PRINT</div></div><div style="margin-top:14pt;margin-bottom:14pt">Input file:<br></div><div style="margin-top:14pt;margin-bottom:14pt">
<p>&FORCE_EVAL</p>
<p> METHOD Quickstep</p>
<p> &DFT</p>
<p> UKS</p>
<p> BASIS_SET_FILE_NAME /home/siyemperumal/GTH_BASIS_SETS_5-12-10</p>
<p> POTENTIAL_FILE_NAME /home/siyemperumal/GTH_POTENTIALS_5-12-10</p>
<p> WFN_RESTART_FILE_NAME co2-RESTART.wfn</p>
<p> &MGRID</p>
<p> CUTOFF 1600</p>
<p> &END MGRID</p>
<p> &QS</p>
<p> WF_INTERPOLATION ASPC</p>
<p> EXTRAPOLATION_ORDER 3</p>
<p> &END QS</p>
<p> &SCF</p>
<p> EPS_SCF 1.E-6</p>
<p> SCF_GUESS RESTART</p>
<p> MAX_SCF 500</p>
<p> &OT T</p>
<p> PRECONDITIONER FULL_SINGLE_INVERSE</p>
<p> MINIMIZER DIIS</p>
<p> LINESEARCH 3PNT</p>
<p> &END OT</p>
<p> &END SCF</p>
<p> &XC</p>
<p> &XC_FUNCTIONAL PBE</p>
<p> &END XC_FUNCTIONAL</p>
<p> &VDW_POTENTIAL</p>
<p> DISPERSION_FUNCTIONAL PAIR_POTENTIAL</p>
<p> &PAIR_POTENTIAL</p>
<p> TYPE DFTD3(BJ)</p>
<p> PARAMETER_FILE_NAME /home/siyemperumal/Research/cp2k/package/cp2k/data/dftd3.dat </p>
<p> REFERENCE_FUNCTIONAL PBE</p>
<p> &PRINT_DFTD MEDIUM</p>
<p><span> </span> &END PRINT_DFTD</p>
<p> &END PAIR_POTENTIAL</p>
<p> &END VDW_POTENTIAL</p>
<p> &END XC</p>
<p> &PRINT</p>
<p>#Tried the above three combinations</p><p> &END PRINT<br></p>
<p> &END DFT</p>
<p> &SUBSYS</p>
<p> &CELL</p>
<p> ABC 12.00 13.00 14.00 </p>
<p> &END CELL<br></p>
<p> &TOPOLOGY</p>
<p> &END TOPOLOGY<br></p>
<p> &COORD</p>
<p>C 0.0000153980 0.0000010425 0.0006891492</p>
<p>O 1.1762907217 0.0000004039 0.0006107401</p>
<p>O -1.1763057650 -0.0000013603 0.0006092107</p>
<p> &END COORD</p>
<p> &KIND O<br></p>
<p> BASIS_SET DZVP-MOLOPT-GTH </p>
<p> POTENTIAL GTH-PBE-q6</p>
<p> &END KIND</p>
<p> &KIND C</p>
<p> BASIS_SET DZVP-MOLOPT-GTH </p>
<p> POTENTIAL GTH-PBE-q4</p>
<p> &END KIND</p>
<p> &END SUBSYS<br></p>
<p>&END FORCE_EVAL</p>
<p>&GLOBAL</p>
<p> PROJECT co2</p>
<p> RUN_TYPE ENERGY </p>
<p> #RUN_TYPE GEO_OPT </p>
<p> PRINT_LEVEL LOW</p>
<p>&END GLOBAL</p>
<p> &MOTION</p>
<p> &GEO_OPT</p>
<p> MAX_ITER 200 </p>
<p> MAX_FORCE 0.0009725 #0.05 eV/A</p>
<p> OPTIMIZER BFGS </p>
<p> &END GEO_OPT</p>
<p> &END MOTION</p><p><br></p><p>Related Output that is printed:</p><p><br></p><p> Electronic density on regular grids: -15.9999999999 0.0000000001</p><p> Core density on regular grids: 15.9999999994 -0.0000000006</p><p> Total charge density on r-space grids: -0.0000000005</p><p>
</p><p> Total charge density g-space grids: -0.0000000005</p><p><br></p><p>Thank you for any ideas. </p></div></span></font></div></div><span><font color="#888888">
<p></p>
-- <br>
You received this message because you are subscribed to the Google Groups "cp2k" group.<br>
To unsubscribe from this group and stop receiving emails from it, send an email to <a rel="nofollow">cp2k+...@googlegroups.com</a>.<br>
To post to this group, send email to <a rel="nofollow">cp...@googlegroups.com</a>.<br>
Visit this group at <a href="https://groups.google.com/group/cp2k" rel="nofollow" target="_blank">https://groups.google.com/group/cp2k</a>.<br>
For more options, visit <a href="https://groups.google.com/d/optout" rel="nofollow" target="_blank">https://groups.google.com/d/optout</a>.<br>
</font></span></blockquote></div><br></div>
</blockquote></div>
<p></p>
-- <br>
You received this message because you are subscribed to a topic in the Google Groups "cp2k" group.<br>
To unsubscribe from this topic, visit <a href="https://groups.google.com/d/topic/cp2k/q75YaO3Z4ro/unsubscribe" target="_blank">https://groups.google.com/d/topic/cp2k/q75YaO3Z4ro/unsubscribe</a>.<br>
To unsubscribe from this group and all its topics, send an email to <a href="mailto:cp2k+uns...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a>.<br>
To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br>
Visit this group at <a href="https://groups.google.com/group/cp2k" target="_blank">https://groups.google.com/group/cp2k</a>.<br>
For more options, visit <a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/optout</a>.<br>
</blockquote></div>
</div>