[CP2K-user] [CP2K:17037] Simulating liquid DMSO
Thomas Kühne
tkuehne at gmail.com
Wed May 25 19:16:10 UTC 2022
Dear Henrique Junior,
if these are subsequent step separated by 0.5fs than this looks all very reasonable to me.
The atoms don’t move a hell a lot within half a femtosecond.
Best,
Thomas Kühne
> Am 27.04.2022 um 21:22 schrieb Henrique Junior <henriquecsj at gmail.com>:
>
> Hi everyone, I hope you are all doing fine.
>
> CP2K is completely new for me, and it is proving to be a challenge. I am attempting to simulate liquid DMSO (a simple molecule with 10 atoms) just as a test. So far, I have tried to build my input based on tutorials simulating liquid water and tweaking it for DMSO.
>
> The calculation is running fine and converging quite smoothly but looking at the DMSO-pos-1.xyz file that’s being generated I can see that the atoms are barely shaking. I’m attaching (and showing below) my input and the xyz file. Any help would be much appreciated.
>
> Thanks in advance.
>
> Vvvvvvvvvvvvvvvvvvvvvvvvvv INPUT vvvvvvvvvvvvvvvvvvvvvvvvvv
>
> &GLOBAL
> PROJECT DMSO
> RUN_TYPE MD
> &END GLOBAL
>
> &FORCE_EVAL
> METHOD Quickstep
> &DFT
> BASIS_SET_FILE_NAME GTH_BASIS_SETS
> POTENTIAL_FILE_NAME GTH_POTENTIALS
> CHARGE 0
> MULTIPLICITY 1
>
> &MGRID
> CUTOFF [Ry] 400
> &END
>
> &QS
> METHOD GPW
> EPS_DEFAULT 1.0E-10
> EXTRAPOLATION ASPC
> &END
>
> &POISSON
> PERIODIC XYZ ! the default, gas phase systems should have 'NONE' and a wavelet solver
> &END
>
> &PRINT
> &E_DENSITY_CUBE OFF
> &END E_DENSITY_CUBE
> &MO_CUBES
> NLUMO 4
> NHOMO 4
> WRITE_CUBE .FALSE.
> &EACH
> MD 10
> &END
> &END
> &END
>
> &SCF
> SCF_GUESS ATOMIC
> MAX_SCF 500
> EPS_SCF 1.0E-6
> &OT
> PRECONDITIONER FULL_SINGLE_INVERSE
> MINIMIZER DIIS
> &END OT
> &OUTER_SCF ! repeat the inner SCF cycle 10 times
> MAX_SCF 10
> EPS_SCF 1.0E-6
> &END
> &PRINT
> &RESTART OFF
> &END
> &END
> &END SCF
>
> &XC
> &XC_FUNCTIONAL
> &PBE
> &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
>
> &SUBSYS
> &CELL
> ABC [angstrom] 9.0 9.0 9.0
> &END CELL
>
> &TOPOLOGY
> COORD_FILE_NAME DMSOcaixa.xyz
> COORD_FILE_FORMAT XYZ
> &END
>
> &KIND H
> BASIS_SET DZVP-MOLOPT-SR-GTH
> POTENTIAL GTH-PBE-q1
> &END KIND
> &KIND C
> BASIS_SET DZVP-MOLOPT-SR-GTH
> POTENTIAL GTH-PBE-q4
> &END KIND
> &KIND O
> BASIS_SET DZVP-MOLOPT-SR-GTH
> POTENTIAL GTH-PBE-q6
> &END KIND
> &KIND S
> BASIS_SET DZVP-MOLOPT-SR-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
> &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
> &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 NVT ! sampling the canonical ensemble, accurate properties might need NVE
> TEMPERATURE [K] 300
> TIMESTEP [fs] 0.5
> STEPS 1000
> # GLE thermostat as generated at http://epfl-cosmo.github.io/gle4md
> # GLE provides an effective NVT sampling.
> &THERMOSTAT
> REGION MASSIVE
> TYPE GLE
> &GLE
> NDIM 5
> A_SCALE [ps^-1] 1.00
> A_LIST 1.859575861256e+2 2.726385349840e-1 1.152610045461e+1 -3.641457826260e+1 2.317337581602e+2
> A_LIST -2.780952471206e-1 8.595159180871e-5 7.218904801765e-1 -1.984453934386e-1 4.240925758342e-1
> A_LIST -1.482580813121e+1 -7.218904801765e-1 1.359090212128e+0 5.149889628035e+0 -9.994926845099e+0
> A_LIST -1.037218912688e+1 1.984453934386e-1 -5.149889628035e+0 2.666191089117e+1 1.150771549531e+1
> A_LIST 2.180134636042e+2 -4.240925758342e-1 9.994926845099e+0 -1.150771549531e+1 3.095839456559e+2
> &END GLE
> &END THERMOSTAT
> &END
> &END
>
>
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> <DMSO.inp><DMSO-pos-1.xyz>
==============================
Thomas D. Kühne
Dynamics of Condensed Matter
Chair of Theoretical Chemistry
University of Paderborn
Warburger Str. 100
D-33098 Paderborn
Germany
thomas.kuehne at upb.de
+49/(0)5251/60-5726
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