<div dir="ltr">Matt,<div><br></div><div> Thanks for the specification. </div><div><br></div><div> But I still have several other questions.</div><div><br></div><div> 1) In the part of <a href="http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL.html" style="font-family: monospace; text-transform: uppercase;">FORCE_EVAL</a><span style="color: rgb(0, 0, 0); font-family: monospace; text-transform: uppercase;"> / </span><a href="http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS.html" style="font-family: monospace; text-transform: uppercase;">SUBSYS</a><span style="color: rgb(0, 0, 0); font-family: monospace; text-transform: uppercase;"> / </span><a href="http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/KIND.html" style="font-family: monospace; text-transform: uppercase;">KIND</a> section, should I set all the types of atoms in both QM_KINDS and MM_KINDS, or just in QM_KINDS ?</div><div><br></div><div> 2) And, The section of <a href="http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL.html" style="font-family: monospace; text-transform: uppercase;">FORCE_EVAL</a><span style="color: rgb(0, 0, 0); font-family: monospace; text-transform: uppercase;"> / </span><a href="http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/QMMM.html" style="font-family: monospace; text-transform: uppercase;">QMMM</a><span style="color: rgb(0, 0, 0); font-family: monospace; text-transform: uppercase;"> / </span><a href="http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/QMMM/FORCE_MIXING.html" style="font-family: monospace; text-transform: uppercase;">FORCE_MIXING</a>, which uses the method of <span style="color: rgb(0, 0, 0); font-family: Simsun; font-size: medium;">[</span><a href="http://manual.cp2k.org/cp2k-2_6-branch/references.html#reference_106" style="font-family: Simsun; font-size: medium;">Bernstein2012</a><span style="color: rgb(0, 0, 0); font-family: Simsun; font-size: medium;">] is the place to set the adaptive QMMM method. If I don't want to use that method,</span></div><div><font color="#000000" face="Simsun" size="3"><br></font></div><div><font color="#000000" face="Simsun" size="3"> I could just leave this section not been used. At this momenta, the numbers of atoms in QM and MM parts do not change during simulation. Am I right ?. </font></div><div><span style="color: rgb(0, 0, 0); font-family: Simsun; font-size: medium;"><br></span></div><div><span style="color: rgb(0, 0, 0); font-family: Simsun; font-size: medium;"> If I do not use the force_mixing scheme, the total energy E=E(qm)+E(mm)+E(qm-mm). The forces are the derivatives of the energy, so the energy should be </span><span style="color: rgb(0, 0, 0); font-family: Simsun; font-size: medium;"> conservative in principle rather than in the force_mixing scheme. Do I understand correctly ?</span></div><div><span style="color: rgb(0, 0, 0); font-family: Simsun; font-size: medium;"><br></span></div><div><span style="color: rgb(0, 0, 0); font-family: Simsun; font-size: medium;"> Thanks in advance</span></div><div><span style="color: rgb(0, 0, 0); font-family: Simsun; font-size: medium;"><br></span></div><div><span style="color: rgb(0, 0, 0); font-family: Simsun; font-size: medium;"> Geng Sun</span></div><div><br>在 2015年8月28日星期五 UTC+8下午8:01:46，Matt W写道：<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Hi,<div><br></div><div>the MM_index is just the number of the atom in the coordinate file (by default), so you give </div><div><br></div><div>$QM_KIND Pt</div><div> LIST 104 105 106</div><div>&END</div><div> </div><div>in your example.</div><div><br></div><div>The need for a topology depends on the classical part of the calculation. So in your case, if Al2O3 is just charges and non bonding parameters then no topology is needed. If you had a forcefield with say Al-O-Al bend parameters you would need a topology that specified those.</div><div><br></div><div>Matt</div><div><br></div><div><br><br>On Friday, August 28, 2015 at 9:40:36 AM UTC+1, Geng Sun wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello CP2K users,<div><br></div><div> I am trying to study the Pt6 clusters adsorption on the Al2O3 surface, using the QMMM method in CP2K. </div><div> In this study, I want to simulate the Al2O3 surface by classical forcefield assuming that the Al2O3 interacts with Pt clusters only by electrostatic interaction and Van der Waals' source. </div><div> The Pt cluster is studied by GPW method. In the structure optimization, all the Al and O atoms are fixed. </div><div> </div><div> And assuming that, Al are all the atoms whose ID from 1 to 40</div><div> O are all the atoms whose ID from 41 to 100</div><div> Pt are all the atoms whose ID from 101 to 106</div><div><br></div><div> So, there is something which is not clear for me:</div><div> </div><div> 1) How to appoint the QM atoms and MM atoms? There are two subsections, QM_KIND and MM_KIND, in the <a href="http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL.html" style="font-family:monospace;text-transform:uppercase" rel="nofollow" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fmanual.cp2k.org%2Fcp2k-2_6-branch%2FCP2K_INPUT%2FFORCE_EVAL.html\46sa\75D\46sntz\0751\46usg\75AFQjCNGUeUhHGFZ_eHShXGlQ-u0awzJVbg';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fmanual.cp2k.org%2Fcp2k-2_6-branch%2FCP2K_INPUT%2FFORCE_EVAL.html\46sa\75D\46sntz\0751\46usg\75AFQjCNGUeUhHGFZ_eHShXGlQ-u0awzJVbg';return true;">FORCE_EVAL</a><span style="color:rgb(0,0,0);font-family:monospace;text-transform:uppercase"> / </span><a href="http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/QMMM.html" style="font-family:monospace;text-transform:uppercase" rel="nofollow" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fmanual.cp2k.org%2Fcp2k-2_6-branch%2FCP2K_INPUT%2FFORCE_EVAL%2FQMMM.html\46sa\75D\46sntz\0751\46usg\75AFQjCNGv9bAO8w-shHSuDQIWfbJA_duJSw';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fmanual.cp2k.org%2Fcp2k-2_6-branch%2FCP2K_INPUT%2FFORCE_EVAL%2FQMMM.html\46sa\75D\46sntz\0751\46usg\75AFQjCNGv9bAO8w-shHSuDQIWfbJA_duJSw';return true;">QMMM</a> section. But I don't know what are the MM_indexs in QM_KIND section ?</div><div> Are they the atoms ID in the <span style="color:rgb(0,0,0);font-family:monospace;text-transform:uppercase"> </span><a href="http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL.html" style="font-family:monospace;text-transform:uppercase" rel="nofollow" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fmanual.cp2k.org%2Fcp2k-2_6-branch%2FCP2K_INPUT%2FFORCE_EVAL.html\46sa\75D\46sntz\0751\46usg\75AFQjCNGUeUhHGFZ_eHShXGlQ-u0awzJVbg';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fmanual.cp2k.org%2Fcp2k-2_6-branch%2FCP2K_INPUT%2FFORCE_EVAL.html\46sa\75D\46sntz\0751\46usg\75AFQjCNGUeUhHGFZ_eHShXGlQ-u0awzJVbg';return true;">FORCE_EVAL</a><span style="color:rgb(0,0,0);font-family:monospace;text-transform:uppercase"> / </span><a href="http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS.html" style="font-family:monospace;text-transform:uppercase" rel="nofollow" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fmanual.cp2k.org%2Fcp2k-2_6-branch%2FCP2K_INPUT%2FFORCE_EVAL%2FSUBSYS.html\46sa\75D\46sntz\0751\46usg\75AFQjCNFxrKfRaDC7A0ZQ0Iihb5GHsIaWyw';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fmanual.cp2k.org%2Fcp2k-2_6-branch%2FCP2K_INPUT%2FFORCE_EVAL%2FSUBSYS.html\46sa\75D\46sntz\0751\46usg\75AFQjCNFxrKfRaDC7A0ZQ0Iihb5GHsIaWyw';return true;">SUBSYS</a><span style="color:rgb(0,0,0);font-family:monospace;text-transform:uppercase"> / </span><a href="http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/COORD.html" style="font-family:monospace;text-transform:uppercase" rel="nofollow" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fmanual.cp2k.org%2Fcp2k-2_6-branch%2FCP2K_INPUT%2FFORCE_EVAL%2FSUBSYS%2FCOORD.html\46sa\75D\46sntz\0751\46usg\75AFQjCNFKJe5wH6cZaNYaIMYl-cNV6ePlJw';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fmanual.cp2k.org%2Fcp2k-2_6-branch%2FCP2K_INPUT%2FFORCE_EVAL%2FSUBSYS%2FCOORD.html\46sa\75D\46sntz\0751\46usg\75AFQjCNFKJe5wH6cZaNYaIMYl-cNV6ePlJw';return true;">COO<wbr>RD</a> section ? And why there are no keyword for assign the Index for MM_KIND ?</div><div> 2 ) I think I don't need to specify the topology structure for my systems, so could I just leave this section empty ?</div><div><br></div><div><br></div><div> A trial input is shown below which is written according to my understanding and the examples in test folders. </div><div> </div><div> I know my questions are quite silly for my poor understanding of the philosophy in QMMM settings in CP2K. So any suggestions and advices would be much appreciated.</div><div><br></div><div> Geng Sun</div><div><br></div><div><div>&FORCE_EVAL</div><div> METHOD QMMM</div><div> &DFT</div><div> BASIS_SET_FILE_NAME BASIS_SET</div><div> POTENTIAL_FILE_NAME GTH_POTENTIALS</div><div> &MGRID</div><div> COMMENSURATE</div><div> CUTOFF 20</div><div> &END MGRID</div><div> &QS</div><div> &END QS</div><div> &SCF</div><div> SCF_GUESS atomic</div><div> &END SCF</div><div> &XC</div><div> &XC_FUNCTIONAL PADE</div><div> &END XC_FUNCTIONAL</div><div> &END XC</div><div> &END DFT</div><div> &MM</div><div> &FORCEFIELD</div><div> IGNORE_MISSING_CRITICAL_PARAMS T</div><div> &CHARGE</div><div> ATOM Al</div><div> CHARGE 1.4175</div><div> &END CHARGE</div><div> &CHARGE</div><div> ATOM O</div><div> CHARGE -0.9450</div><div> &END CHARGE</div><div> &END FORCEFIELD</div><div> &POISSON</div><div> &EWALD</div></div><div><div> EWALD_TYPE ewald</div><div> ALPHA .44 </div><div> GMAX 21</div><div> &END EWALD</div><div> &END POISSON</div><div> &END MM</div><div> &QMMM</div><div> USE_GEEP_LIB 10</div><div> CENTER NEVER</div><div> &CELL</div><div> ABC 16.8260 16.1360 25.0003</div><div> &END CELL</div><div> ECOUPL GAUSS</div><div> NOCOMPATIBILITY</div><div> &INTERPOLATOR</div><div> EPS_R 1.0e-14</div><div> EPS_X 1.0e-14</div><div> MAXITER 100 </div><div> &END INTERPOLATOR</div><div> &QM_KIND Pt</div><div> MM_INDEX 101..106</div><div> &END QM_KIND</div><div> &MM_KIND Al</div><div> &END MM_KIND</div><div> &MM_KIND O</div><div> &END MM_KIND </div><div> &END QMMM</div><div> &SUBSYS</div><div> &CELL</div><div> ABC 16.8260 16.1360 25.0003</div><div> &END CELL</div><div> &COORD</div></div><div>.................many O and Al positions, not shown here.</div><div><div>O 16.24701734 14.39169840 5.63706764 </div><div>O 16.24701734 14.31456832 2.94428533</div><div>O 16.24701734 14.25696280 8.53085237</div><div>Al 12.04034908 13.30606832 2.94428533</div><div>Al 12.04034908 13.24846280 8.53085237</div><div>O 12.04034908 12.14588992 4.36330236</div><div>O 12.04034908 12.08828440 9.94986940</div><div>O 12.04034908 12.28046416 1.46926763</div><div>O 12.04034908 12.22285864 7.05608467</div><div>Pt 8.14041880 4.95391336 12.72190266</div><div>Pt 10.22314108 4.88420584 12.97940575</div><div>Pt 6.98161218 7.10855344 12.92565511</div><div>Pt 8.98171880 7.10855344 12.92565511</div><div>Pt 11.31195154 7.17826096 12.66815202</div><div>Pt 5.81018606 4.88420584 12.97940575</div><div> &END COORD</div><div> &KIND Pt</div><div> BASIS_SET DZV-GTH-PADE</div><div> POTENTIAL GTH-PADE-q10</div><div> &END KIND</div><div> &TOPOLOGY</div><div> &END TOPOLOGY</div><div> &END SUBSYS</div><div>&END FORCE_EVAL</div><div>&GLOBAL</div><div> PROJECT qmmm_test</div><div> PRINT_LEVEL MEDIUM</div><div> RUN_TYPE ENERGY</div><div>&END GLOBAL</div></div><div><br></div><div> </div><div><br></div></div></blockquote></div></div></blockquote></div></div>