[CP2K-user] [CP2K:13074] NPT simulation of 64 water molecules
Travis
polla... at gmail.com
Tue Apr 7 18:58:53 UTC 2020
Hi,
SCALE_C set to zero ignores the correlation part of the potential, hence
the much smaller than expected density. Delete this line or set it to 1
(default is 1).
-T
On Tuesday, April 7, 2020 at 2:42:41 PM UTC-4, Anna Varghese wrote:
>
> 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 <t... at gmail.com
> <javascript:>> 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 <an... at gmail.com
>> <javascript:>>:
>>
>>
>> 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
>>
>>
>> --
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>> .
>> <water.inp>
>>
>>
>>
>>
>> ==============================
>> Thomas D. Kühne
>> Dynamics of Condensed Matter
>> Chair of Theoretical Chemistry
>> University of Paderborn
>> Warburger Str. 100
>> D-33098 Paderborn
>> Germany
>> td... at mail.upb.de <javascript:>
>> +49/(0)5251/60-5726
>>
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>> .
>>
>
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