problem in MD with constrained atoms using a Shell-model (Fist)
Gabriele Tocci
gabri... at gmail.com
Fri Jul 1 09:23:20 UTC 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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