<div dir="ltr">Hi Matt,<div><br><div>Thanks very much for your reply. Maybe I should try hybrid functional for my system in CP2K. </div><div><br></div><div>Please forgive <span style="font-family:tahoma,verdana,arial,helvetica,sans-serif">my ignorance, but what's the meaning of </span><span style="font-size:13px;font-family:arial,sans-serif"><font color="#0000ff">> grep '</font></span><span style="font-size:13px;font-family:arial,sans-serif"><font color="#0000ff"> 5 C 1' </font><font color="#000000">?</font></span><br>
</div><div><br></div><div>The reason I choose PBE functional is that I first optimized the geometry in Gaussian09 with different functionals, and the PBE functional gave a reasonable structure and spectrum compared to experimental spectrum, while BLYP, B3LYP, PW91 etc. could not get the same structure. However, In CP2K, my system run too slow with PBE functional, so I just try to use BLYP functional to check if it also low speed with different functionals. That comes to this question.</div>
<div><br></div><div>It's really a big challenge that a proton shared with two water molecules and have two pi-hydrogen bonds in one system. Anyway, thanks very much for discussion. </div><div><br></div><div>Best wishes,</div>
<div>Huan</div><div><br><span style="font-size:13px;font-family:arial,sans-serif"><font color="#000000"></font></span></div><div><span style="font-size:13px;font-family:arial,sans-serif"><font color="#000000"><br></font></span></div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Dec 11, 2013 at 9:31 PM, Matt W <span dir="ltr"><<a href="mailto:MattWa...@gmail.com" target="_blank">MattWa...@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>I can't comment on exactly what is happening, but you are having problems with SCF convergence. This is not the same as one functional running much slower than another, as such - i.e. it is a more or less physical problem not that the code doesn't / can't run the two funcitonals with a similar speed.</div>
<div><br></div><div>It appears that you get huge charge oscillations between the two centres in your system - try</div><div><br></div><div>> grep ' 5 C 1'</div><div><br></div><div>PBE must place HOMO/SOMO, or similar, of both systems at very similar energies. The slow down occurs when your system spin polarizes and you get a fluctuating biradical solution.</div>
<div><br></div><div>At this point you need to wonder why this is happening. Maybe hybrid functionals are needed?, maybe it is true that charge transfer between the two things can occur, but this is a difficult problem for DFT.</div>
<div><br></div><div><div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div><br></div>
<div>I don't know what happened when calculation comes to the step 27. Last time you mentioned that there are some usual keywords in my input file. What are they? Would you please help me to fix this problem? Thank you very much.</div>
<div><br></div></div></div></blockquote></div><div>I seem to remember (this is going back some time so likely I am wrong) that you were using self interaction corrections - I have no experience with them. Perhaps what works for BLYP doesn't do good things to PBE.</div>
<div><br></div><div>Again, it is the SCF convergence and possible problems with your system/hamiltonian that gives the speed differential, not PBE being slower.</div><div><br></div><div>Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr"><div><div></div><div>Best wishes,<br>Huan</div><div><br></div><div><br></div><div><br></div><div><br><br>
<div class="gmail_quote"><div><div>On Mon, Oct 7, 2013 at 8:27 PM, Matt W <span dir="ltr"><<a>Matt...@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div><div><div dir="ltr"><div>Sorry, please don't try to post everything!!!!<br>
</div><div><br></div><div>But what happens during a couple of SCF cycles, during localization, of a single MD step.</div>
<span><font color="#888888"><div><br></div><div>Matt</div></font></span><div><div><br>On Monday, October 7, 2013 1:56:34 PM UTC+1, <a>hua...@mail.huji.ac.il</a> wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">Dear All,<br><br>I am now using CP2K to run MD simulations on the benzen-Zundel cation with BLYP and PBE functional, respectively. I use the same number of CPU, but for PBE functional, the speed is 3 times slower than BLYP. In addition, the calculation with PBE functional takes nearly whole the memory, shown below.<br>
<br><span style="color:rgb(0,0,255)">For BLYP functional-- Mem: 64380M total, 16753M used, 47626M free</span><br><br style="color:rgb(0,0,255)"><span style="color:rgb(0,0,255)">For PBE functional-- Mem: 64380M total, 63976M used, 403M free</span><br>
<br>Is that common for PBE functional? <br><br>Actually, I just copied the BLYP input file, and then changed the functional into PBE and added long range correction, C9 term. The rest of options, parameters, coordinates and basis sets are the same with BLYP input file.<br>
<br>I pasted my input file below. Can anyone give me some suggestion? I appreciate it very much. <br><br>Best wishes,<br>Huan<br><br>======== INPUT FILE ===========<br><br>&GLOBAL<br> PREFERRED_FFT_LIBRARY FFTW <span style="color:rgb(61,133,198)">#FFTSG # FFTESSL</span><br style="color:rgb(61,133,198)">
<span style="color:rgb(61,133,198)"># FFT_POOL_SCRATCH_LIMIT 10</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># PROGRAM Quickstep</span><br> PROJECT nve_50K <span style="color:rgb(61,133,198)"># #</span><br>
RUN_TYPE MD <span style="color:rgb(61,133,198)"># # MD ## GEO_OPT ## ENERGY ----------</span><br> PRINT_LEVEL LOW<br><span style="color:rgb(61,133,198)"># SEED -6</span><br>&END GLOBAL<br>&FORCE_EVAL<br> &DFT<br>
CHARGE 1<br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"> # UKS # ROKS with self-interaction correction (SIC)</span><br> UKS<br> &SIC<br> SIC_METHOD MAURI_SPZ<br> SIC_SCALING_A 0.2<br>
SIC_SCALING_B 0.0<br> &END<br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"> # non-periodic Poisson (cluster boundary condition)</span><br> &POISSON<br> POISSON_SOLVER MT<br> &MT<br>
ALPHA 7.0<br> REL_CUTOFF 2.0<br> &END MT<br> PERIODIC NONE<br> &END POISSON<br> BASIS_SET_FILE_NAME GTH_BASIS_SETS<br> POTENTIAL_FILE_NAME GTH_POTENTIALS<br> &MGRID<br> CUTOFF 300<br>
&END MGRID<br> &PRINT<br> &MOMENTS ON<br> COMMON_ITERATION_LEVELS 20000<br> FILENAME ./MOMENTS<br> ADD_LAST NUMERIC<br> PERIODIC FALSE<br> REFERENCE COAC<br> &EACH 1<br>
&END<br> &END MOMENTS<br> &LOCALIZATION ON<br> &TOTAL_DIPOLE<br> COMMON_ITERATION_LEVELS 20000<br> FILENAME ./TOTAL_DIPOLE.dat<br> ADD_LAST NUMERIC<br>
PERIODIC FALSE<br> REFERENCE COAC<br> &EACH 1<br> &END<br> &END TOTAL_DIPOLE<br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># &MOLECULAR_DIPOLES</span><br style="color:rgb(61,133,198)">
<span style="color:rgb(61,133,198)"># COMMON_ITERATION_LEVELS 20000 </span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># FILENAME ./MOLECULAR_DIPOLES.dat</span><br style="color:rgb(61,133,198)">
<span style="color:rgb(61,133,198)"># ADD_LAST NUMERIC</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># PERIODIC FALSE</span><br style="color:rgb(61,133,198)">
<span style="color:rgb(61,133,198)"># REFERENCE COAC</span><br style="color:rgb(61,133,198)">
<span style="color:rgb(61,133,198)"># &EACH 1</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># &END</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># &END MOLECULAR_DIPOLES</span><br>
&END LOCALIZATION<br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># &MO_CUBES</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># NLUMO=1</span><br style="color:rgb(61,133,198)">
<span style="color:rgb(61,133,198)"># NHOMO=1</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># &END MO_CUBES</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># &MO</span><br style="color:rgb(61,133,198)">
<span style="color:rgb(61,133,198)"># EIGENVALUES T</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># OCCUPATION_NUMBERS T</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># COMMON_ITERATION_LEVELS 0</span><br style="color:rgb(61,133,198)">
<span style="color:rgb(61,133,198)"># EACH 1</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># &END MO</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># &E_DENSITY_CUBE</span><br style="color:rgb(61,133,198)">
<span style="color:rgb(61,133,198)"># &END E_DENSITY_CUBE</span><br> &MULLIKEN<br> &END MULLIKEN<br> &LOWDIN<br> &END LOWDIN<br> &END PRINT<br> &QS<br> EPS_DEFAULT 1.0E-12<br>
EXTRAPOLATION PS<br> EXTRAPOLATION_ORDER 3<br> &END QS<br> &LOCALIZE T<br> EPS_LOCALIZATION 1.0E-4<br> EPS_OCCUPATION 1.E-6<br> OPERATOR BERRY<br> METHOD JACOBI<br> MAX_ITER 2000<br>
MAX_CRAZY_ANGLE 0.05<br> &END LOCALIZE<br> &SCF<br> MAX_SCF 150<br> SCF_GUESS ATOMIC # ATOMIC # RESTART ---cont use RESTART<br> &MIXING<br> &END MIXING<br> &OT<br> MINIMIZER DIIS<br>
#ROTATION TRUE #needed for ROKS+SIC!!<br> &END OT<br> &OUTER_SCF<br> MAX_SCF 20<br> EPS_SCF 1.0E-5<br> &END OUTER_SCF<br> &END SCF<br> &XC<br> &XC_FUNCTIONAL <span style="color:rgb(255,0,0)">PBE</span> <span style="color:rgb(61,133,198)">#specified the functional</span><br>
&END XC_FUNCTIONAL<br> &vdw_POTENTIAL<br> DISPERSION_FUNCTIONAL PAIR_POTENTIAL<br> &PAIR_POTENTIAL<br> TYPE DFTD3<br> REFERENCE_FUNCTIONAL<span style="color:rgb(255,0,0)"> PBE</span><br>
CALCULATE_<span style="color:rgb(255,0,0)">C9_TERM .TRUE</span>.<br> REFERENCE_<span style="color:rgb(255,0,0)">C9_TERM .TRUE.</span><br> <span style="color:rgb(255,0,0)">LONG_RANGE_CORRECTION .TRUE.</span><br>
PARAMETER_FILE_NAME <span style="color:rgb(255,0,0)">dftd3.dat</span><br> <span style="color:rgb(255,0,0)">R_CUTOFF 15.0</span><br> &END PAIR_POTENTIAL<br> &END vdW_POTENTIAL<br> &XC_GRID<br>
XC_DERIV SPLINE2_SMOOTH<br> XC_SMOOTH_RHO NN10<br> &END XC_GRID<br> &END XC<br> &END DFT<br> &SUBSYS<br> &CELL<br> PERIODIC NONE<br> ABC 20.000 20.000 20.000<br> &END CELL<br>
&COORD<br><span> C </span><br><span> C</span> <br><span> C</span> <br><span> C</span> <br><span> C</span> <br><span> C</span> <br>
<span> H</span> <br><span> H</span> <br><span> H</span> <br><span> H</span> <br><span> H</span> <br><span> H</span> <br>
<span> H</span> <br><span> H</span> <br><span> O </span><br><span> H </span><br><span> O </span><br>
<span> H </span><br><span> H </span><br><span> Ar </span><br>&END COORD<br> &KIND H<br> BASIS_SET aug-TZVP-GTH<br> POTENTIAL GTH-PBE-q1<br> &END KIND<br>
&KIND C<br> BASIS_SET aug-TZVP-GTH<br> POTENTIAL GTH-PBE-q4<br> &END KIND<br> &KIND O<br> BASIS_SET aug-TZVP-GTH<br> POTENTIAL GTH-PBE-q6<br> &END KIND<br> &KIND Ar<br> BASIS_SET DZVP-GTH<br>
POTENTIAL GTH-PBE-q8<br> &END KIND<br> &END SUBSYS<br>&END FORCE_EVAL<br>&MOTION<br> &MD<br> ENSEMBLE NVE<br> STEPS 50000 #10ps total<br> TIMESTEP 0.2 # 0.2fs<br> TEMPERATURE 50.0<br style="color:rgb(61,133,198)">
<span style="color:rgb(61,133,198)"> #TEMP_TOL 40.0</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># &THERMOSTAT</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># REGION MOLECULE</span><br style="color:rgb(61,133,198)">
<span style="color:rgb(61,133,198)"># &NOSE</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># LENGTH 3</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># YOSHIDA 3</span><br style="color:rgb(61,133,198)">
<span style="color:rgb(61,133,198)"># TIMECON 50.0</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># MTS 2</span><br style="color:rgb(61,133,198)"><span style="color:rgb(61,133,198)"># &END NOSE</span><br style="color:rgb(61,133,198)">
<span style="color:rgb(61,133,198)"># &END THERMOSTAT</span><br> &END MD<br> &PRINT<br> &RESTART<br> LOG_PRINT_KEY T<br> &EACH<br> MD 100 <br> &END EACH<br>
ADD_LAST NUMERIC<br> &END RESTART<br> &TRAJECTORY<br> LOG_PRINT_KEY T<br> FORMAT XYZ<br> UNIT angstrom<br> &EACH<br> MD 1 <br> &END EACH<br>
ADD_LAST NUMERIC<br> &END TRAJECTORY<br> &VELOCITIES<br> LOG_PRINT_KEY T<br> FORMAT XYZ<br> UNIT angstrom<br> &EACH<br> MD 1 <br> &END EACH<br>
ADD_LAST NUMERIC<br> &END VELOCITIES<br> &END PRINT<br>&END MOTION<br>==============================<u></u>==<br><br> </div></blockquote></div></div></div></div></div><div><div><div><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/ivi2a2ScZwY/unsubscribe" target="_blank">https://groups.google.com/d/<u></u>topic/cp2k/ivi2a2ScZwY/<u></u>unsubscribe</a>.<br></div></div>
To unsubscribe from this group and all its topics, send an email to <a>cp2k+uns...@googlegroups.<u></u>com</a>.<br>
To post to this group, send email to <a>cp...@googlegroups.com</a>.<div><br>
Visit this group at <a href="http://groups.google.com/group/cp2k" target="_blank">http://groups.google.com/<u></u>group/cp2k</a>.<br>
For more options, visit <a href="https://groups.google.com/groups/opt_out" target="_blank">https://groups.google.com/<u></u>groups/opt_out</a>.<br>
</div></div></div></blockquote></div><br></div></div></div>
</blockquote></div></div><div><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/ivi2a2ScZwY/unsubscribe" target="_blank">https://groups.google.com/d/topic/cp2k/ivi2a2ScZwY/unsubscribe</a>.<br>
To unsubscribe from this group and all its topics, send an email to <a href="mailto:cp2k%2Bun...@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="http://groups.google.com/group/cp2k" target="_blank">http://groups.google.com/group/cp2k</a>.<br>
For more options, visit <a href="https://groups.google.com/groups/opt_out" target="_blank">https://groups.google.com/groups/opt_out</a>.<br>
</div></div></blockquote></div><br></div><div class="gmail_extra"><br></div></div></div>