[CP2K-user] NPT simulation of 64 water molecules
ANNA VARGHESE
annav... at gmail.com
Tue Apr 7 10:56:26 UTC 2020
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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