problem in MD with constrained atoms using a Shell-model (Fist)

Gabriele Tocci gabri... at gmail.com
Fri Jul 1 11:13:16 CEST 2011


Dear All,

I am trying to run a classical MD using the shell model (NVT ensemble)
of a ZnO surface slab, while constraining the bottom layer atoms.
However, I get an error relating to the initialization of the
velocities. I believe that there is a problem with attaching the Nose`-
Hover thermostat. I have tried different ways of attaching the
thermostat, but none of them worked. If anybody has a clue on how to
fix this I would be very grateful. Thanks.
Gabriele.

Below there is my input:

&FORCE_EVAL
  METHOD FIST
 STRESS_TENSOR ANALYTICAL
  &MM
    &FORCEFIELD
   &CHARGE
    ATOM Zn
    CHARGE +2.0
   &END CHARGE
   &CHARGE
    ATOM O
    CHARGE -2.0
   &END CHARGE
      &CHARGE
        ATOM Of
        CHARGE -2.0
      &END CHARGE
      &CHARGE
        ATOM Znf
        CHARGE 2.0
      &END CHARGE
      &CHARGE
        ATOM O
        CHARGE -2.0
      &END CHARGE
      &CHARGE
        ATOM Zn
        CHARGE +2.0
      &END CHARGE


      &SHELL Zn
      CORE_CHARGE  -0.1
      SHELL_CHARGE 2.1
#    MASS_FRACTION 0.1 #Default is it correct?
      SPRING [eV*angstrom^-2] 5.77
#      K4 [eV*angstrom^-4] 0 #31506.80834
      MAX_DISTANCE 0.5
    &END SHELL
     &SHELL O
      CORE_CHARGE 0.3
      SHELL_CHARGE -2.3
      MASS_FRACTION 0.1 !what found for oxygen
      SPRING [eV*angstrom^-2]  6.3 #15.52  #80.21
#      K4 [eV*angstrom^-4] 31506.80834
      MAX_DISTANCE 0.5 #Try with this setting
     &END SHELL

     &NONBONDED
        &WILLIAMS
          ATOMS Zn  O
          A [eV] 529.70 #499.6   #529.70 #700.30
          B [angstrom^-1] 2.792516 # 2.781641168 #2.792516
#2.958579882
          C [eV*angstrom^6] 0.0
        &END WILLIAMS


        &WILLIAMS
          ATOMS O  O
          A [eV] 9547.96 #22764.3
          B [angstrom^-1] 4.562876 #6.711409 #4.562876  # 6.71141
          C [eV*angstrom^6] 32.0 # 27.88 #32.0 #33.476469
        &END WILLIAMS


        &WILLIAMS
          ATOMS Zn Zn
          A [eV] 0
          B [angstrom^-1] 0
          C [eV*angstrom^6] 0
        &END WILLIAMS

        &WILLIAMS
          ATOMS Znf  Of
          A [eV] 529.70 #499.6   #529.70 #700.30
          B [angstrom^-1] 2.792516 # 2.781641168 #2.792516
#2.958579882
          C [eV*angstrom^6] 0.0
        &END WILLIAMS

        &WILLIAMS
          ATOMS Zn  Of
          A [eV] 529.70 #499.6   #529.70 #700.30
          B [angstrom^-1] 2.792516 # 2.781641168 #2.792516
#2.958579882
          C [eV*angstrom^6] 0.0
        &END WILLIAMS

        &WILLIAMS
          ATOMS Znf  O
          A [eV] 529.70
          B [angstrom^-1] 2.792516
          C [eV*angstrom^6] 0.0
        &END WILLIAMS

        &WILLIAMS
          ATOMS Of  O
          A [eV] 9547.96 #22764.3
          B [angstrom^-1] 4.562876
          C [eV*angstrom^6] 32.0
        &END WILLIAMS



        &WILLIAMS
          ATOMS Of  Of
          A [eV] 9547.96
          B [angstrom^-1] 4.562876
          C [eV*angstrom^6] 32.0
        &END WILLIAMS


        &WILLIAMS
          ATOMS Znf Znf
          A [eV] 0
          B [angstrom^-1] 0
          C [eV*angstrom^6] 0
        &END WILLIAMS

        &WILLIAMS
          ATOMS Zn Znf
          A [eV] 0
          B [angstrom^-1] 0
          C [eV*angstrom^6] 0
        &END WILLIAMS


      &END NONBONDED


   &SPLINE
    EMAX_ACCURACY [hartree] 0.02
    EMAX_SPLINE [hartree] 1.0E4
    EPS_SPLINE [hartree] 1.0E-7
    R0_NB [angstrom] 0.1
   &END SPLINE


    &END FORCEFIELD
    &POISSON
      &EWALD
        EWALD_TYPE spme
        ALPHA [angstrom^-1] 0.35
        GMAX 10 16 60
        EWALD_ACCURACY 1.00000000E-06
    &RS_GRID
     DISTRIBUTION_TYPE replicated
    &END RS_GRID
#        O_SPLINE 6
      &END EWALD
    &END POISSON
  &END MM
 &PRINT
  &GRID_INFORMATION OFF
  &END GRID_INFORMATION
  &PROGRAM_RUN_INFO
   &EACH
    MD 1
   &END EACH
  &END PROGRAM_RUN_INFO
  &STRESS_TENSOR
   &EACH
    MD 1
   &END EACH
  &END STRESS_TENSOR
 &END PRINT

  &SUBSYS
   &TOPOLOGY

   CONNECTIVITY user
   PARA_RES off

   &END TOPOLOGY
    &PRINT
       &TOPOLOGY_INFO
          GENERATE_INFO
       &END
    &END
    &CELL


ABC   9.903   15.795285  59.612
      ALPHA_BETA_GAMMA   90         120          90
&END CELL
&COORD

Znf     0.0000000000        0.0000000000        0.0000000000   ZnOf
1
Znf     1.6505000000        2.6325480000        0.9529170000   ZnOf
1
Of      0.0000000000        2.0107400000        0.0000000000  ZnOf   1
Of      1.6505000000        4.6432870000        0.9529170000  ZnOf   1
Znf     3.3010000000        0.0000000000        0.0000000000   ZnOf
2
Znf     4.9515000000        2.6325480000        0.9529170000   ZnOf
2
Of      3.3010000000        2.0107400000        0.0000000000  ZnOf   2
Of      4.9515000000        4.6432870000        0.9529170000  ZnOf   2
Znf     6.6020000000        0.0000000000        0.0000000000   ZnOf
3
Znf     8.2525000000        2.6325480000        0.9529170000   ZnOf
3
Of      6.6020000000        2.0107400000        0.0000000000  ZnOf   3
Of      8.2525000000        4.6432870000        0.9529170000  ZnOf   3
Znf     0.0000000000        5.2650950000        0.0000000000   ZnOf
4
Znf     1.6505000000        7.8976430000        0.9529170000   ZnOf
4
Of      0.0000000000        7.2758350000        0.0000000000  ZnOf   4
Of      1.6505000000        9.9083820000        0.9529170000  ZnOf   4
Znf     3.3010000000        5.2650950000        0.0000000000   ZnOf
5
Znf     4.9515000000        7.8976430000        0.9529170000   ZnOf
5
Of      3.3010000000        7.2758350000        0.0000000000  ZnOf   5
Of      4.9515000000        9.9083820000        0.9529170000  ZnOf   5
Znf     6.6020000000        5.2650950000        0.0000000000   ZnOf
6
Znf     8.2525000000        7.8976430000        0.9529170000   ZnOf
6
Of      6.6020000000        7.2758350000        0.0000000000  ZnOf   6
Of      8.2525000000        9.9083820000        0.9529170000  ZnOf   6
Znf     0.0000000000       10.5301900000        0.0000000000    ZnOf
7
Znf     1.6505000000       13.1627380000        0.9529170000    ZnOf
7
Of      0.0000000000       12.5409300000        0.0000000000   ZnOf
7
Of      1.6505000000       15.1734770000        0.9529170000   ZnOf
7
Znf     3.3010000000       10.5301900000        0.0000000000    ZnOf
8
Znf     4.9515000000       13.1627380000        0.9529170000    ZnOf
8
Of      3.3010000000       12.5409300000        0.0000000000   ZnOf
8
Of      4.9515000000       15.1734770000        0.9529170000   ZnOf
8
Znf     6.6020000000       10.5301900000        0.0000000000    ZnOf
9
Znf     8.2525000000       13.1627380000        0.9529170000    ZnOf
9
Of      6.6020000000       12.5409300000        0.0000000000   ZnOf
9
Of      8.2525000000       15.1734770000        0.9529170000   ZnOf
9
Zn     -1.6504981250       -0.0191332517        2.8533367648
ZnO   10
Zn      0.0000382528        2.6129908722        3.7405132992
ZnO   10
O      -1.6504780137        1.9994595922        2.8470216876
ZnO   10
O       0.0000203518        4.6300805730        3.7494308529
ZnO   10
Zn      1.6505018750       -0.0191332517        2.8533367648
ZnO   11
Zn      3.3010382528        2.6129908722        3.7405132992
ZnO   11
O       1.6505219863        1.9994595922        2.8470216876
ZnO   11
O       3.3010203518        4.6300805730        3.7494308529
ZnO   11
Zn      4.9515018750       -0.0191332517        2.8533367648
ZnO   12
Zn      6.6020382528        2.6129908722        3.7405132992
ZnO   12
O       4.9515219863        1.9994595922        2.8470216876
ZnO   12
O       6.6020203518        4.6300805730        3.7494308529
ZnO   12
Zn     -1.6504981989        5.2460538324        2.8534253501
ZnO   13
Zn      0.0000381830        7.8783556946        3.7406928745
ZnO   13
O      -1.6504781033        7.2647801513        2.8471516174
ZnO   13
O       0.0000203143        9.8952726952        3.7495928418
ZnO   13
Zn      1.6505018011        5.2460538324        2.8534253501
ZnO   14
Zn      3.3010381830        7.8783556946        3.7406928745
ZnO   14
O       1.6505218967        7.2647801513        2.8471516174
ZnO   14
O       3.3010203143        9.8952726952        3.7495928418
ZnO   14
Zn      4.9515018011        5.2460538324        2.8534253501
ZnO   15
Zn      6.6020381830        7.8783556946        3.7406928745
ZnO   15
O       4.9515218967        7.2647801513        2.8471516174
ZnO   15
O       6.6020203143        9.8952726952        3.7495928418
ZnO   15
Zn     -1.6504982128       10.5107397626        2.8534515725
ZnO   16
Zn      0.0000382545       13.1434323539        3.7405152787
ZnO   16
O      -1.6504780501       12.5294402942        2.8471043570
ZnO   16
O       0.0000203905       15.1605446993        3.7494105778
ZnO   16
Zn      1.6505017872       10.5107397626        2.8534515725
ZnO   17
Zn      3.3010382545       13.1434323539        3.7405152787
ZnO   17
O       1.6505219499       12.5294402942        2.8471043570
ZnO   17
O       3.3010203905       15.1605446993        3.7494105778
ZnO   17
Zn      4.9515017872       10.5107397626        2.8534515725
ZnO   18
Zn      6.6020382545       13.1434323539        3.7405152787
ZnO   18
O       4.9515219499       12.5294402942        2.8471043570
ZnO   18
O       6.6020203905       15.1605446993        3.7494105778
ZnO   18


    &END COORD
    &KIND Znf
     ELEMENT Zn
    &END KIND
    &KIND Of
     ELEMENT O
    &END KIND

  &END SUBSYS
&END FORCE_EVAL
&GLOBAL
  PRINT_LEVEL  MEDIUM
  FLUSH_SHOULD_FLUSH
  PROJECT ZnO_try_mine_new
  RUN_TYPE MD #GEO_OPT #MD
&END GLOBAL
&MOTION
  &CONSTRAINT
   #CONSTRAINT_INIT
   &FIXED_ATOMS
 LIST 1..36
#MOLNAME ZnOf
COMPONENTS_TO_FIX XYZ
   &END FIXED_ATOMS
  &END CONSTRAINT

  &MD
    ENSEMBLE NVT
    STEPS  20
    TIMESTEP 0.5
    TEMPERATURE 300.0
    &SHELL
      TEMPERATURE 25
      TEMP_TOL 25
    &END
    COMVEL_TOL  2.0E-7
    &THERMOSTAT
      REGION DEFINED
      &DEFINE_REGION
       MOLNAME ZnO
      &END
      &NOSE
        LENGTH 6
        YOSHIDA 3
        TIMECON 1000
        MTS 2
      &END NOSE
    &END
    &END PRINT
  &END MD

  &SHELL_OPT
    OPTIMIZER CG
    MAX_DR 0.02
    RMS_DR 0.01
    MAX_FORCE 0.0002
    RMS_FORCE 0.0001
    &CG
      &LINE_SEARCH
        TYPE 2PNT
        &2PNT
        &END
      &END
    &END
  &END

&END MOTION




More information about the CP2K-user mailing list