<div dir="ltr">Dear Thomas, <div><br></div><div>Thank you, for the reply. I am not sure about SCALE, I saw it on one website. Please find the attached density plot. Please let me know the corrections.<br></div><div><br></div><div>Thanks</div><div>Anna.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Apr 7, 2020 at 9:53 PM Thomas Kühne <<a href="mailto:tku...@gmail.com" target="_blank">tku...@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>Dear Anna, <div><br></div><div>looks mostly fine to me. However, is SCALE_C 0.0 intentionally and correct? </div><div>If so, can you please provide a similar density plot than in the paper or at least </div><div>quantify the drop in particle density?</div><div><br></div><div>Cheers, </div><div>Thomas<br><div><br><blockquote type="cite"><div>Am 07.04.2020 um 12:56 schrieb ANNA VARGHESE <<a href="mailto:annav...@gmail.com" target="_blank">annav...@gmail.com</a>>:</div><br><div><div dir="ltr"><div><br></div><div>Dear All,</div>I am trying to run NPT simulation of 64 water molecules following <a href="https://aip.scitation.org/doi/am-pdf/10.1063/1.4986284" target="_blank">https://aip.scitation.org/doi/am-pdf/10.1063/1.4986284</a> . I observe a drop in density at the end of density. Can anyone look at this input file and tell me where am I going wrong? <div><br></div><div>Thanks in advance,</div><div><br><div><br></div><div><div>&GLOBAL</div><div> ! the project name is made part of most output files... useful to keep order</div><div> PROJECT WATER</div><div> ! various runtypes (energy, geo_opt, etc.) available.</div><div> RUN_TYPE MD</div><div> ! reduce the amount of IO</div><div> IOLEVEL LOW</div><div>&END GLOBAL</div><div><br></div><div>&FORCE_EVAL</div><div> ! the electronic structure part of CP2K is named Quickstep</div><div> METHOD Quickstep</div><div>STRESS_TENSOR ANALYTICAL</div><div> &DFT</div><div> ! basis sets and pseudopotential files can be found in cp2k/data</div><div> BASIS_SET_FILE_NAME GTH_BASIS_SETS</div><div> POTENTIAL_FILE_NAME GTH_POTENTIALS </div><div><br></div><div><br></div><div> ! Charge and multiplicity</div><div> CHARGE 0</div><div> MULTIPLICITY 1</div><div><br></div><div> &MGRID</div><div> ! PW cutoff ... depends on the element (basis) too small cutoffs lead to the eggbox effect.</div><div> ! certain calculations (e.g. geometry optimization, vibrational frequencies,</div><div> ! NPT and cell optimizations, need higher cutoffs)</div><div> CUTOFF [Ry] 800 </div><div> &END</div><div><br></div><div> &QS</div><div> ! use the GPW method (i.e. pseudopotential based calculations with the Gaussian and Plane Waves scheme).</div><div> METHOD GPW </div><div> ! default threshold for numerics ~ roughly numerical accuracy of the total energy per electron,</div><div> ! sets reasonable values for all other thresholds.</div><div> EPS_DEFAULT 1.0E-10 </div><div> ! used for MD, the method used to generate the initial guess.</div><div> EXTRAPOLATION ASPC </div><div> &END</div><div><br></div><div> &POISSON</div><div> PERIODIC XYZ ! the default, gas phase systems should have 'NONE' and a wavelet solver</div><div> &END</div><div><br></div><div> &PRINT</div><div> ! at the end of the SCF procedure generate cube files of the density</div><div> &E_DENSITY_CUBE OFF</div><div> &END E_DENSITY_CUBE</div><div> ! compute eigenvalues and homo-lumo gap each 10nd MD step</div><div> &MO_CUBES</div><div> NLUMO 4</div><div> NHOMO 4</div><div> WRITE_CUBE .FALSE.</div><div> &EACH</div><div> MD 10</div><div> &END</div><div> &END</div><div> &END</div><div><br></div><div><br></div><div> ! use the OT METHOD for robust and efficient SCF, suitable for all non-metallic systems.</div><div> &SCF </div><div> SCF_GUESS ATOMIC ! can be used to RESTART an interrupted calculation</div><div> MAX_SCF 30</div><div> EPS_SCF 1.0E-6 ! accuracy of the SCF procedure typically 1.0E-6 - 1.0E-7</div><div> &OT</div><div> ! an accurate preconditioner suitable also for larger systems</div><div> PRECONDITIONER FULL_SINGLE_INVERSE</div><div> ! the most robust choice (DIIS might sometimes be faster, but not as stable).</div><div> MINIMIZER DIIS</div><div> &END OT</div><div> &OUTER_SCF ! repeat the inner SCF cycle 10 times</div><div> MAX_SCF 10</div><div> EPS_SCF 1.0E-6 ! must match the above</div><div> &END</div><div> ! do not store the wfn during MD</div><div> &PRINT</div><div> &RESTART OFF</div><div> &END</div><div> &END</div><div> &END SCF</div><div><br></div><div> ! specify the exchange and correlation treatment</div><div> &XC</div><div> ! use a PBE functional </div><div> &XC_FUNCTIONAL </div><div> &PBE</div><div> PARAMETRIZATION revPBE</div><div> SCALE_C 0.0</div><div> &END</div><div> &END XC_FUNCTIONAL</div><div> ! adding Grimme's D3 correction (by default without C9 terms) </div><div> &VDW_POTENTIAL</div><div> POTENTIAL_TYPE PAIR_POTENTIAL </div><div> &PAIR_POTENTIAL</div><div> PARAMETER_FILE_NAME dftd3.dat</div><div> TYPE DFTD3</div><div> REFERENCE_FUNCTIONAL PBE</div><div> R_CUTOFF [angstrom] 16</div><div> &END</div><div> &END VDW_POTENTIAL</div><div> &END XC</div><div> &END DFT</div><div> </div><div> ! description of the system</div><div> &SUBSYS</div><div> &CELL </div><div> ! unit cells that are orthorhombic are more efficient with CP2K</div><div> ABC [angstrom] 14.77 14.77 14.77</div><div> &END CELL</div><div><br></div><div> ! atom coordinates can be in the &COORD section,</div><div> ! or provided as an external file.</div><div> &TOPOLOGY</div><div> COORD_FILE_NAME <a href="http://water.xyz" target="_blank">water.xyz</a></div><div> COORD_FILE_FORMAT XYZ</div><div> &END</div><div><br></div><div> &KIND H</div><div> BASIS_SET TZV2P-GTH</div><div> POTENTIAL GTH-PBE-q1</div><div> &END KIND</div><div> &KIND O</div><div> BASIS_SET TZV2P-GTH</div><div> POTENTIAL GTH-PBE-q6</div><div> &END KIND</div><div><br></div><div> &END SUBSYS</div><div>&END FORCE_EVAL</div><div><br></div><div>! how to propagate the system, selection via RUN_TYPE in the &GLOBAL section</div><div>&MOTION</div><div> &GEO_OPT</div><div> OPTIMIZER BFGS ! Good choice for 'small' systems (use LBFGS for large systems)</div><div> MAX_ITER 100</div><div> MAX_DR [bohr] 0.003 ! adjust target as needed</div><div> &BFGS</div><div> &END</div><div> &END</div><div> &MD</div><div> ENSEMBLE NPT_I ! sampling the canonical ensemble, accurate properties might need NVE</div><div> TEMPERATURE [K] 300</div><div> TIMESTEP [fs] 0.5</div><div> STEPS 10000</div><div> &BAROSTAT</div><div> PRESSURE 1.03 # PRESSURE, unit[bar]</div><div> TIMECON 300</div><div> &END BAROSTAT</div><div><br></div><div>&THERMOSTAT</div><div> REGION MASSIVE</div><div> &NOSE #Uses the Nose-Hoover thermostat</div><div> TIMECON 11.12 #timeconstant of the thermostat chain, how often does thermostat adjust your system</div><div> &END NOSE</div><div> &END</div><div><br></div><div> &END</div><div> &PRINT</div><div> &TRAJECTORY</div><div> &EACH</div><div> MD 1</div><div> &END EACH</div><div> &END TRAJECTORY</div><div> &VELOCITIES OFF</div><div> &END VELOCITIES</div><div> &FORCES OFF</div><div> &END FORCES</div><div> &RESTART_HISTORY</div><div> &EACH</div><div> MD 500</div><div> &END EACH</div><div> &END RESTART_HISTORY</div><div> &RESTART</div><div> BACKUP_COPIES 3</div><div> &EACH</div><div> MD 1</div><div> &END EACH</div><div> &END RESTART</div><div> &END PRINT</div><div>&END</div></div><div><br></div></div></div><div><br></div>
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