problem in MD with constrained atoms using a Shell-model (Fist)
Gabriele Tocci
gabri... at gmail.com
Fri Jul 1 09:13:16 UTC 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