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

Gabriele Tocci gabri... at gmail.com
Fri Jul 1 11:23:20 CEST 2011


Sorry everyone, my coordinates screwed up as I copied it, and I did
not realise it when I posted the message above. If you are trying to
reproduce my error, please replace the coordinates below with those
posted before. Cheers.
Gabriele


Znf     0.00000     0.00000     0.00000   ZnOf   1
Znf     1.65050     2.63254     0.95291   ZnOf   1
Of      0.00000     2.01074     0.00000  ZnOf   1
Of      1.65050     4.64328     0.95291  ZnOf   1
Znf     3.30100     0.00000     0.00000   ZnOf   2
Znf     4.95150     2.63254     0.95291   ZnOf   2
Of      3.30100     2.01074     0.00000  ZnOf   2
Of      4.95150     4.64328     0.95291  ZnOf   2
Znf     6.60200     0.00000     0.00000   ZnOf   3
Znf     8.25250     2.63254     0.95291   ZnOf   3
Of      6.60200     2.01074     0.00000  ZnOf   3
Of      8.25250     4.64328     0.95291  ZnOf   3
Znf     0.00000     5.26509     0.00000   ZnOf   4
Znf     1.65050     7.89764     0.95291   ZnOf   4
Of      0.00000     7.27583     0.00000  ZnOf   4
Of      1.65050     9.90838     0.95291  ZnOf   4
Znf     3.30100     5.26509     0.00000   ZnOf   5
Znf     4.95150     7.89764     0.95291   ZnOf   5
Of      3.30100     7.27583     0.00000  ZnOf   5
Of      4.95150     9.90838     0.95291  ZnOf   5
Znf     6.60200     5.26509     0.00000   ZnOf   6
Znf     8.25250     7.89764     0.95291   ZnOf   6
Of      6.60200     7.27583     0.00000  ZnOf   6
Of      8.25250     9.90838     0.95291  ZnOf   6
Znf     0.00000    10.53019     0.00000    ZnOf   7
Znf     1.65050    13.16273     0.95291    ZnOf   7
Of      0.00000    12.54093     0.00000   ZnOf   7
Of      1.65050    15.17347     0.95291   ZnOf   7
Znf     3.30100    10.53019     0.00000    ZnOf   8
Znf     4.95150    13.16273     0.95291    ZnOf   8
Of      3.30100    12.54093     0.00000   ZnOf   8
Of      4.95150    15.17347     0.95291   ZnOf   8
Znf     6.60200    10.53019     0.00000    ZnOf   9
Znf     8.25250    13.16273     0.95291    ZnOf   9
Of      6.60200    12.54093     0.00000   ZnOf    9
Of      8.25250    15.17347     0.95291   ZnOf    9
Zn     -1.65049    -0.01913     2.85333        ZnO   10
Zn      0.00003     2.61299     3.74051       ZnO   10
O      -1.65047     1.99945     2.84702       ZnO   10
O       0.00002     4.63008     3.74943      ZnO   10
Zn      1.65050    -0.01913     2.85333       ZnO   11
Zn      3.30103     2.61299     3.74051       ZnO   11
O       1.65052     1.99945     2.84702      ZnO   11
O       3.30102     4.63008     3.74943      ZnO   11
Zn      4.95150    -0.01913     2.85333       ZnO   12
Zn      6.60203     2.61299     3.74051       ZnO   12
O       4.95152     1.99945     2.84702      ZnO   12
O       6.60202     4.63008     3.74943      ZnO   12
Zn     -1.65049     5.24605     2.85342        ZnO   13
Zn      0.00003     7.87835     3.74069       ZnO   13
O      -1.65047     7.26478     2.84715       ZnO   13
O       0.00002     9.89527     3.74959      ZnO   13
Zn      1.65050     5.24605     2.85342       ZnO   14
Zn      3.30103     7.87835     3.74069       ZnO   14
O       1.65052     7.26478     2.84715      ZnO   14
O       3.30102     9.89527     3.74959      ZnO   14
Zn      4.95150     5.24605     2.85342       ZnO   15
Zn      6.60203     7.87835     3.74069       ZnO   15
O       4.95152     7.26478     2.84715      ZnO   15
O       6.60202     9.89527     3.74959      ZnO   15
Zn     -1.65049    10.51073     2.85345         ZnO   16
Zn      0.00003    13.14343     3.74051        ZnO   16
O      -1.65047    12.52944     2.84710        ZnO   16
O       0.00002    15.16054     3.74941       ZnO   16
Zn      1.65050    10.51073     2.85345        ZnO   17
Zn      3.30103    13.14343     3.74051        ZnO   17
O       1.65052    12.52944     2.84710       ZnO   17
O       3.30102    15.16054     3.74941       ZnO   17
Zn      4.95150    10.51073     2.85345        ZnO   18
Zn      6.60203    13.14343     3.74051        ZnO   18
O       4.95152    12.52944     2.84710       ZnO   18
O       6.60202    15.16054     3.74941       ZnO   18




On Jul 1, 10:13 am, Gabriele Tocci <gabri... at gmail.com> wrote:
> 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


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