[CP2K-user] [CP2K:13074] NPT simulation of 64 water molecules
Anna Varghese
annav... at gmail.com
Tue Apr 7 18:41:53 UTC 2020
Dear Thomas,
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.
Thanks
Anna.
On Tue, Apr 7, 2020 at 9:53 PM Thomas Kühne <tku... at gmail.com> wrote:
> Dear Anna,
>
> looks mostly fine to me. However, is SCALE_C 0.0 intentionally and
> correct?
> If so, can you please provide a similar density plot than in the paper or
> at least
> quantify the drop in particle density?
>
> Cheers,
> Thomas
>
> Am 07.04.2020 um 12:56 schrieb ANNA VARGHESE <annav... at gmail.com>:
>
>
> Dear All,
> I am trying to run NPT simulation of 64 water molecules following
> https://aip.scitation.org/doi/am-pdf/10.1063/1.4986284 . 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?
>
> Thanks in advance,
>
>
> &GLOBAL
> ! the project name is made part of most output files... useful to keep
> order
> PROJECT WATER
> ! various runtypes (energy, geo_opt, etc.) available.
> RUN_TYPE MD
> ! reduce the amount of IO
> IOLEVEL LOW
> &END GLOBAL
>
> &FORCE_EVAL
> ! the electronic structure part of CP2K is named Quickstep
> METHOD Quickstep
> STRESS_TENSOR ANALYTICAL
> &DFT
> ! basis sets and pseudopotential files can be found in cp2k/data
> BASIS_SET_FILE_NAME GTH_BASIS_SETS
> POTENTIAL_FILE_NAME GTH_POTENTIALS
>
>
> ! Charge and multiplicity
> CHARGE 0
> MULTIPLICITY 1
>
> &MGRID
> ! PW cutoff ... depends on the element (basis) too small cutoffs
> lead to the eggbox effect.
> ! certain calculations (e.g. geometry optimization, vibrational
> frequencies,
> ! NPT and cell optimizations, need higher cutoffs)
> CUTOFF [Ry] 800
> &END
>
> &QS
> ! use the GPW method (i.e. pseudopotential based calculations with
> the Gaussian and Plane Waves scheme).
> METHOD GPW
> ! default threshold for numerics ~ roughly numerical accuracy of
> the total energy per electron,
> ! sets reasonable values for all other thresholds.
> EPS_DEFAULT 1.0E-10
> ! used for MD, the method used to generate the initial guess.
> EXTRAPOLATION ASPC
> &END
>
> &POISSON
> PERIODIC XYZ ! the default, gas phase systems should have 'NONE'
> and a wavelet solver
> &END
>
> &PRINT
> ! at the end of the SCF procedure generate cube files of the density
> &E_DENSITY_CUBE OFF
> &END E_DENSITY_CUBE
> ! compute eigenvalues and homo-lumo gap each 10nd MD step
> &MO_CUBES
> NLUMO 4
> NHOMO 4
> WRITE_CUBE .FALSE.
> &EACH
> MD 10
> &END
> &END
> &END
>
>
> ! use the OT METHOD for robust and efficient SCF, suitable for all
> non-metallic systems.
> &SCF
> SCF_GUESS ATOMIC ! can be used to RESTART an interrupted calculation
> MAX_SCF 30
> EPS_SCF 1.0E-6 ! accuracy of the SCF procedure typically 1.0E-6 -
> 1.0E-7
> &OT
> ! an accurate preconditioner suitable also for larger systems
> PRECONDITIONER FULL_SINGLE_INVERSE
> ! the most robust choice (DIIS might sometimes be faster, but not
> as stable).
> MINIMIZER DIIS
> &END OT
> &OUTER_SCF ! repeat the inner SCF cycle 10 times
> MAX_SCF 10
> EPS_SCF 1.0E-6 ! must match the above
> &END
> ! do not store the wfn during MD
> &PRINT
> &RESTART OFF
> &END
> &END
> &END SCF
>
> ! specify the exchange and correlation treatment
> &XC
> ! use a PBE functional
> &XC_FUNCTIONAL
> &PBE
> PARAMETRIZATION revPBE
> SCALE_C 0.0
> &END
> &END XC_FUNCTIONAL
> ! adding Grimme's D3 correction (by default without C9 terms)
> &VDW_POTENTIAL
> POTENTIAL_TYPE PAIR_POTENTIAL
> &PAIR_POTENTIAL
> PARAMETER_FILE_NAME dftd3.dat
> TYPE DFTD3
> REFERENCE_FUNCTIONAL PBE
> R_CUTOFF [angstrom] 16
> &END
> &END VDW_POTENTIAL
> &END XC
> &END DFT
>
> ! description of the system
> &SUBSYS
> &CELL
> ! unit cells that are orthorhombic are more efficient with CP2K
> ABC [angstrom] 14.77 14.77 14.77
> &END CELL
>
> ! atom coordinates can be in the &COORD section,
> ! or provided as an external file.
> &TOPOLOGY
> COORD_FILE_NAME water.xyz
> COORD_FILE_FORMAT XYZ
> &END
>
> &KIND H
> BASIS_SET TZV2P-GTH
> POTENTIAL GTH-PBE-q1
> &END KIND
> &KIND O
> BASIS_SET TZV2P-GTH
> POTENTIAL GTH-PBE-q6
> &END KIND
>
> &END SUBSYS
> &END FORCE_EVAL
>
> ! how to propagate the system, selection via RUN_TYPE in the &GLOBAL
> section
> &MOTION
> &GEO_OPT
> OPTIMIZER BFGS ! Good choice for 'small' systems (use LBFGS for large
> systems)
> MAX_ITER 100
> MAX_DR [bohr] 0.003 ! adjust target as needed
> &BFGS
> &END
> &END
> &MD
> ENSEMBLE NPT_I ! sampling the canonical ensemble, accurate properties
> might need NVE
> TEMPERATURE [K] 300
> TIMESTEP [fs] 0.5
> STEPS 10000
> &BAROSTAT
> PRESSURE 1.03 # PRESSURE, unit[bar]
> TIMECON 300
> &END BAROSTAT
>
> &THERMOSTAT
> REGION MASSIVE
> &NOSE #Uses the Nose-Hoover thermostat
> TIMECON 11.12 #timeconstant of the thermostat chain, how
> often does thermostat adjust your system
> &END NOSE
> &END
>
> &END
> &PRINT
> &TRAJECTORY
> &EACH
> MD 1
> &END EACH
> &END TRAJECTORY
> &VELOCITIES OFF
> &END VELOCITIES
> &FORCES OFF
> &END FORCES
> &RESTART_HISTORY
> &EACH
> MD 500
> &END EACH
> &END RESTART_HISTORY
> &RESTART
> BACKUP_COPIES 3
> &EACH
> MD 1
> &END EACH
> &END RESTART
> &END PRINT
> &END
>
>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp... at googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/9b4f65fa-f7a3-46e0-9b78-5d72d3be1c84%40googlegroups.com
> <https://groups.google.com/d/msgid/cp2k/9b4f65fa-f7a3-46e0-9b78-5d72d3be1c84%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
> <water.inp>
>
>
>
>
> ==============================
> Thomas D. Kühne
> Dynamics of Condensed Matter
> Chair of Theoretical Chemistry
> University of Paderborn
> Warburger Str. 100
> D-33098 Paderborn
> Germany
> tdku... at mail.upb.de
> +49/(0)5251/60-5726
>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp... at googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/86CAD953-54B8-4FE5-AED5-5D1E6AE0490C%40gmail.com
> <https://groups.google.com/d/msgid/cp2k/86CAD953-54B8-4FE5-AED5-5D1E6AE0490C%40gmail.com?utm_medium=email&utm_source=footer>
> .
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20200408/5a657ca1/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: density.svg
Type: image/svg+xml
Size: 393824 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20200408/5a657ca1/attachment.svg>
More information about the CP2K-user
mailing list