Help Required For Simulating Simple H20 Molecule Using Quickstep.

[Satchith PS]

Hey all!

I'm a student starting to learn CP2K software. I don't have much background in molecular dynamics simulation, have just started. From what I understood so far, I created an input file "water_AIMD.inp" and a separate coordinate file "water.xyz" as follows. They run but end abruptly.  Can anyone please find any mistakes in these files and help me?

Input file:

@SET PROJECT water_AIMD
@SET STEPS 20000
@SET TIMESTEP 0.5
@SET TEMP 300

&GLOBAL
  PROJECT ${PROJECT}
  RUN_TYPE MD
  PRINT_LEVEL LOW
&END GLOBAL


&FORCE_EVAL
  METHOD QS

  &DFT
    BASIS_SET_FILE_NAME/BASIS_MOLOPT
    POTENTIAL_FILE_NAME/GTH_POTENTIALS

    &MGRID
      CUTOFF 400
      REL_CUTOFF 50
    &END MGRID

    &SCF
      SCF_GUESS ATOMIC
      EPS_SCF 1.0E-6
      MAX_SCF 50
      &OT
        MINIMIZER DIIS
        PRECONDITIONER FULL_SINGLE_INVERSE
      &END OT
    &END SCF

    &XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
    &END XC
  &END DFT


  &SUBSYS
    &CELL
      ABC 9.86 9.86 9.86
      PERIODIC XYZ
    &END CELL

    &COORD
      @INCLUDE water.xyz
    &END COORD

    &KIND O
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE
    &END KIND

    &KIND H
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE
    &END KIND
  &END SUBSYS
&END FORCE_EVAL


&MOTION
  &MD
    ENSEMBLE NVT
    STEPS ${STEPS}
    TIMESTEP ${TIMESTEP}
    TEMPERATURE ${TEMP}

    &THERMOSTAT
      TYPE NOSE
      &NOSE
        LENGTH 3
        TIMECON 1000
      &END NOSE
    &END THERMOSTAT
  &END MD

  &PRINT
    &TRAJECTORY
      FORMAT XYZ
      &EACH
        MD 10
      &END EACH
    &END TRAJECTORY

    &VELOCITIES
      &EACH
        MD 10
      &END EACH
    &END VELOCITIES

    &RESTART
      FILENAME ${PROJECT}
      ADD_LAST NUMERIC
      &EACH
        MD 200
      &END EACH
    &END RESTART
  &END PRINT
&END MOTION

Coordinate file :

96
32 water molecules, cubic box ~9.86 A

O   1.000000   1.000000   1.000000
H   1.957200   1.000000   1.000000
H   0.760000   1.926627   1.000000

O   3.000000   1.000000   1.000000
H   3.957200   1.000000   1.000000
H   2.760000   1.926627   1.000000

O   5.000000   1.000000   1.000000
H   5.957200   1.000000   1.000000
H   4.760000   1.926627   1.000000

O   7.000000   1.000000   1.000000
H   7.957200   1.000000   1.000000
H   6.760000   1.926627   1.000000

O   1.000000   3.000000   1.000000
H   1.957200   3.000000   1.000000
H   0.760000   3.926627   1.000000

O   3.000000   3.000000   1.000000
H   3.957200   3.000000   1.000000
H   2.760000   3.926627   1.000000

O   5.000000   3.000000   1.000000
H   5.957200   3.000000   1.000000
H   4.760000   3.926627   1.000000

O   7.000000   3.000000   1.000000
H   7.957200   3.000000   1.000000
H   6.760000   3.926627   1.000000

O   1.000000   5.000000   1.000000
H   1.957200   5.000000   1.000000
H   0.760000   5.926627   1.000000

O   3.000000   5.000000   1.000000
H   3.957200   5.000000   1.000000
H   2.760000   5.926627   1.000000

O   5.000000   5.000000   1.000000
H   5.957200   5.000000   1.000000
H   4.760000   5.926627   1.000000

O   7.000000   5.000000   1.000000
H   7.957200   5.000000   1.000000
H   6.760000   5.926627   1.000000

O   1.000000   7.000000   1.000000
H   1.957200   7.000000   1.000000
H   0.760000   7.926627   1.000000

O   3.000000   7.000000   1.000000
H   3.957200   7.000000   1.000000
H   2.760000   7.926627   1.000000

O   5.000000   7.000000   1.000000
H   5.957200   7.000000   1.000000
H   4.760000   7.926627   1.000000

O   7.000000   7.000000   1.000000
H   7.957200   7.000000   1.000000
H   6.760000   7.926627   1.000000


O   1.000000   1.000000   5.000000
H   1.957200   1.000000   5.000000
H   0.760000   1.926627   5.000000

O   3.000000   1.000000   5.000000
H   3.957200   1.000000   5.000000
H   2.760000   1.926627   5.000000

O   5.000000   1.000000   5.000000
H   5.957200   1.000000   5.000000
H   4.760000   1.926627   5.000000

O   7.000000   1.000000   5.000000
H   7.957200   1.000000   5.000000
H   6.760000   1.926627   5.000000

O   1.000000   3.000000   5.000000
H   1.957200   3.000000   5.000000
H   0.760000   3.926627   5.000000

O   3.000000   3.000000   5.000000
H   3.957200   3.000000   5.000000
H   2.760000   3.926627   5.000000

O   5.000000   3.000000   5.000000
H   5.957200   3.000000   5.000000
H   4.760000   3.926627   5.000000

O   7.000000   3.000000   5.000000
H   7.957200   3.000000   5.000000
H   6.760000   3.926627   5.000000

O   1.000000   5.000000   5.000000
H   1.957200   5.000000   5.000000
H   0.760000   5.926627   5.000000

O   3.000000   5.000000   5.000000
H   3.957200   5.000000   5.000000
H   2.760000   5.926627   5.000000

O   5.000000   5.000000   5.000000
H   5.957200   5.000000   5.000000
H   4.760000   5.926627   5.000000

O   7.000000   5.000000   5.000000
H   7.957200   5.000000   5.000000
H   6.760000   5.926627   5.000000

O   1.000000   7.000000   5.000000
H   1.957200   7.000000   5.000000
H   0.760000   7.926627   5.000000

O   3.000000   7.000000   5.000000
H   3.957200   7.000000   5.000000
H   2.760000   7.926627   5.000000

O   5.000000   7.000000   5.000000
H   5.957200   7.000000   5.000000
H   4.760000   7.926627   5.000000

O   7.000000   7.000000   5.000000
H   7.957200   7.000000   5.000000
H   6.760000   7.926627   5.000000

[Frederick Stein]

Dear Satchith,

I guess the culprit is  the COORD-section. Remove it and use

&TOPOLOGY

  COORD_FILE_NAME water.xyz

&END

instead. The parser expects the coordinates directly without the header of the XYZ-file here.

Otherwise, please always include the actual output file or error message.

Best,

Frederick