<div dir="ltr">Hi Davide,<div><br></div><div>I looked at this a long time ago when it was still version 3. As suggested by Satish, it looks like you will need to hack the DDEC code in order to produce a new cube file with re-inserted core density. Maybe the best way is to get in touch with Thomas Manz who may already have a solution for that.</div><div><br></div><div>Alternatively, if you are working with porous materials (e.g. MOFs), you may try the REPEAT scheme by Campana et al (DOI: 10.1021/ct9003405) which we recently implemented into CP2K. To use the method, just insert the following section into the &FORCE_EVAL section of your input:</div><div><br></div><div><div> &PROPERTIES</div><div> &RESP</div><div> USE_REPEAT_METHOD T</div><div> &SPHERE_SAMPLING</div><div> AUTO_VDW_RADII_TABLE UFF</div><div> AUTO_RMIN_SCALE 1.0</div><div> &END SPHERE_SAMPLING</div><div> &PRINT</div><div> &PROGRAM_RUN_INFO SILENT</div><div> &END PROGRAM_RUN_INFO</div><div> &END PRINT</div><div> &END RESP</div><div> &END PROPERTIES</div></div><div><br></div><div>See <a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/PROPERTIES/RESP.html#USE_REPEAT_METHOD">https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/PROPERTIES/RESP.html#USE_REPEAT_METHOD</a> for more information.</div><div><br></div><div>SL</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 10 July 2016 at 10:26, David T <span dir="ltr"><<a href="mailto:amazing...@gmail.com" target="_blank">amazing...@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="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<span class=""><br><br><br>On Sunday, 12 June 2016 00:44:19 UTC+2, S Ling wrote:</span><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><span class=""><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></span><div><br><div class="gmail_quote"><div><div class="h5">On 10 June 2016 at 23:21, Satish Kumar <span dir="ltr"><<a rel="nofollow">sati...@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><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></div></div><span><font color="#888888"><div><div class="h5">
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