NPT simulation of 64 water molecules

ANNA VARGHESE

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Apr 7, 2020, 6:56:26 AM4/7/20

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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

! 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 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

&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

&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

water.inp

Thomas Kühne

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Apr 7, 2020, 12:23:32 PM4/7/20

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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

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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

tdku...@mail.upb.de

+49/(0)5251/60-5726

Anna Varghese

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Apr 7, 2020, 2:42:41 PM4/7/20

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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.

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