<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Anna, <div class=""><br class=""></div><div class="">looks mostly fine to me. However, is SCALE_C 0.0 intentionally and correct? </div><div class="">If so, can you please provide a similar density plot than in the paper or at least </div><div class="">quantify the drop in particle density?</div><div class=""><br class=""></div><div class="">Cheers, </div><div class="">Thomas<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">Am 07.04.2020 um 12:56 schrieb ANNA VARGHESE <<a href="mailto:annav...@gmail.com" class="">annav...@gmail.com</a>>:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><br class=""></div><div class="">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" class="">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 class=""><br class=""></div><div class="">Thanks in advance,</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><div class="">&GLOBAL</div><div class=""> ! the project name is made part of most output files... useful to keep order</div><div class=""> PROJECT WATER</div><div class=""> ! various runtypes (energy, geo_opt, etc.) available.</div><div class=""> RUN_TYPE MD</div><div class=""> ! reduce the amount of IO</div><div class=""> IOLEVEL LOW</div><div class="">&END GLOBAL</div><div class=""><br class=""></div><div class="">&FORCE_EVAL</div><div class=""> ! the electronic structure part of CP2K is named Quickstep</div><div class=""> METHOD Quickstep</div><div class="">STRESS_TENSOR ANALYTICAL</div><div class=""> &DFT</div><div class=""> ! basis sets and pseudopotential files can be found in cp2k/data</div><div class=""> BASIS_SET_FILE_NAME GTH_BASIS_SETS</div><div class=""> POTENTIAL_FILE_NAME GTH_POTENTIALS </div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""> ! Charge and multiplicity</div><div class=""> CHARGE 0</div><div class=""> MULTIPLICITY 1</div><div class=""><br class=""></div><div class=""> &MGRID</div><div class=""> ! PW cutoff ... depends on the element (basis) too small cutoffs lead to the eggbox effect.</div><div class=""> ! certain calculations (e.g. geometry optimization, vibrational frequencies,</div><div class=""> ! NPT and cell optimizations, need higher cutoffs)</div><div class=""> CUTOFF [Ry] 800 </div><div class=""> &END</div><div class=""><br class=""></div><div class=""> &QS</div><div class=""> ! use the GPW method (i.e. pseudopotential based calculations with the Gaussian and Plane Waves scheme).</div><div class=""> METHOD GPW </div><div class=""> ! default threshold for numerics ~ roughly numerical accuracy of the total energy per electron,</div><div class=""> ! sets reasonable values for all other thresholds.</div><div class=""> EPS_DEFAULT 1.0E-10 </div><div class=""> ! used for MD, the method used to generate the initial guess.</div><div class=""> EXTRAPOLATION ASPC </div><div class=""> &END</div><div class=""><br class=""></div><div class=""> &POISSON</div><div class=""> PERIODIC XYZ ! the default, gas phase systems should have 'NONE' and a wavelet solver</div><div class=""> &END</div><div class=""><br class=""></div><div class=""> &PRINT</div><div class=""> ! at the end of the SCF procedure generate cube files of the density</div><div class=""> &E_DENSITY_CUBE OFF</div><div class=""> &END E_DENSITY_CUBE</div><div class=""> ! compute eigenvalues and homo-lumo gap each 10nd MD step</div><div class=""> &MO_CUBES</div><div class=""> NLUMO 4</div><div class=""> NHOMO 4</div><div class=""> WRITE_CUBE .FALSE.</div><div class=""> &EACH</div><div class=""> MD 10</div><div class=""> &END</div><div class=""> &END</div><div class=""> &END</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""> ! use the OT METHOD for robust and efficient SCF, suitable for all non-metallic systems.</div><div class=""> &SCF </div><div class=""> SCF_GUESS ATOMIC ! can be used to RESTART an interrupted calculation</div><div class=""> MAX_SCF 30</div><div class=""> EPS_SCF 1.0E-6 ! accuracy of the SCF procedure typically 1.0E-6 - 1.0E-7</div><div class=""> &OT</div><div class=""> ! an accurate preconditioner suitable also for larger systems</div><div class=""> PRECONDITIONER FULL_SINGLE_INVERSE</div><div class=""> ! the most robust choice (DIIS might sometimes be faster, but not as stable).</div><div class=""> MINIMIZER DIIS</div><div class=""> &END OT</div><div class=""> &OUTER_SCF ! repeat the inner SCF cycle 10 times</div><div class=""> MAX_SCF 10</div><div class=""> EPS_SCF 1.0E-6 ! must match the above</div><div class=""> &END</div><div class=""> ! do not store the wfn during MD</div><div class=""> &PRINT</div><div class=""> &RESTART OFF</div><div class=""> &END</div><div class=""> &END</div><div class=""> &END SCF</div><div class=""><br class=""></div><div class=""> ! specify the exchange and correlation treatment</div><div class=""> &XC</div><div class=""> ! use a PBE functional </div><div class=""> &XC_FUNCTIONAL </div><div class=""> &PBE</div><div class=""> PARAMETRIZATION revPBE</div><div class=""> SCALE_C 0.0</div><div class=""> &END</div><div class=""> &END XC_FUNCTIONAL</div><div class=""> ! adding Grimme's D3 correction (by default without C9 terms) </div><div class=""> &VDW_POTENTIAL</div><div class=""> POTENTIAL_TYPE PAIR_POTENTIAL </div><div class=""> &PAIR_POTENTIAL</div><div class=""> PARAMETER_FILE_NAME dftd3.dat</div><div class=""> TYPE DFTD3</div><div class=""> REFERENCE_FUNCTIONAL PBE</div><div class=""> R_CUTOFF [angstrom] 16</div><div class=""> &END</div><div class=""> &END VDW_POTENTIAL</div><div class=""> &END XC</div><div class=""> &END DFT</div><div class=""> </div><div class=""> ! description of the system</div><div class=""> &SUBSYS</div><div class=""> &CELL </div><div class=""> ! unit cells that are orthorhombic are more efficient with CP2K</div><div class=""> ABC [angstrom] 14.77 14.77 14.77</div><div class=""> &END CELL</div><div class=""><br class=""></div><div class=""> ! atom coordinates can be in the &COORD section,</div><div class=""> ! or provided as an external file.</div><div class=""> &TOPOLOGY</div><div class=""> COORD_FILE_NAME <a href="http://water.xyz" class="">water.xyz</a></div><div class=""> COORD_FILE_FORMAT XYZ</div><div class=""> &END</div><div class=""><br class=""></div><div class=""> &KIND H</div><div class=""> BASIS_SET TZV2P-GTH</div><div class=""> POTENTIAL GTH-PBE-q1</div><div class=""> &END KIND</div><div class=""> &KIND O</div><div class=""> BASIS_SET TZV2P-GTH</div><div class=""> POTENTIAL GTH-PBE-q6</div><div class=""> &END KIND</div><div class=""><br class=""></div><div class=""> &END SUBSYS</div><div class="">&END FORCE_EVAL</div><div class=""><br class=""></div><div class="">! how to propagate the system, selection via RUN_TYPE in the &GLOBAL section</div><div class="">&MOTION</div><div class=""> &GEO_OPT</div><div class=""> OPTIMIZER BFGS ! Good choice for 'small' systems (use LBFGS for large systems)</div><div class=""> MAX_ITER 100</div><div class=""> MAX_DR [bohr] 0.003 ! adjust target as needed</div><div class=""> &BFGS</div><div class=""> &END</div><div class=""> &END</div><div class=""> &MD</div><div class=""> ENSEMBLE NPT_I ! sampling the canonical ensemble, accurate properties might need NVE</div><div class=""> TEMPERATURE [K] 300</div><div class=""> TIMESTEP [fs] 0.5</div><div class=""> STEPS 10000</div><div class=""> &BAROSTAT</div><div class=""> PRESSURE 1.03 # PRESSURE, unit[bar]</div><div class=""> TIMECON 300</div><div class=""> &END BAROSTAT</div><div class=""><br class=""></div><div class="">&THERMOSTAT</div><div class=""> REGION MASSIVE</div><div class=""> &NOSE #Uses the Nose-Hoover thermostat</div><div class=""> TIMECON 11.12 #timeconstant of the thermostat chain, how often does thermostat adjust your system</div><div class=""> &END NOSE</div><div class=""> &END</div><div class=""><br class=""></div><div class=""> &END</div><div class=""> &PRINT</div><div class=""> &TRAJECTORY</div><div class=""> &EACH</div><div class=""> MD 1</div><div class=""> &END EACH</div><div class=""> &END TRAJECTORY</div><div class=""> &VELOCITIES OFF</div><div class=""> &END VELOCITIES</div><div class=""> &FORCES OFF</div><div class=""> &END FORCES</div><div class=""> &RESTART_HISTORY</div><div class=""> &EACH</div><div class=""> MD 500</div><div class=""> &END EACH</div><div class=""> &END RESTART_HISTORY</div><div class=""> &RESTART</div><div class=""> BACKUP_COPIES 3</div><div class=""> &EACH</div><div class=""> MD 1</div><div class=""> &END EACH</div><div class=""> &END RESTART</div><div class=""> &END PRINT</div><div class="">&END</div></div><div class=""><br class=""></div></div></div><div class=""><br class="webkit-block-placeholder"></div> -- <br class=""> You received this message because you are subscribed to the Google Groups "cp2k" group.<br class=""> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp...@googlegroups.com" class="">cp...@googlegroups.com</a>.<br class=""> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/9b4f65fa-f7a3-46e0-9b78-5d72d3be1c84%40googlegroups.com?utm_medium=email&utm_source=footer" class="">https://groups.google.com/d/msgid/cp2k/9b4f65fa-f7a3-46e0-9b78-5d72d3be1c84%40googlegroups.com</a>.<br class=""> <span id="cid:4b6b9de6-df95-40c9-bafb-b345d765b95f"><water.inp></span></div></blockquote></div><br class=""></div><br class=""><br class=""><div class=""> <div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">==============================</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">Thomas D. Kühne</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">Dynamics of Condensed Matter</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">Chair of Theoretical Chemistry</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">University of Paderborn</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">Warburger Str. 100</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">D-33098 Paderborn</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">Germany</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class=""><a href="mailto:tdku...@mail.upb.de" class="">tdku...@mail.upb.de</a></div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">+49/(0)5251/60-5726</div></div></div></div> </div> <br class=""></body></html>