[CP2K:10271] MD melting problem
Josip Lovrić
josip7... at gmail.com
Fri May 4 07:54:20 UTC 2018
What do you exactly get when you try to reproduce paper results?
I do not have experience with this tipe of forcefield, but generally I
would try to understand physical meaning of this parameters and maybe to
find error. It could be some mistake in writing, etc.
Josip
2018-05-04 8:03 GMT+02:00 jie wu <4985... at qq.com>:
> The whole input is listed below:
> &GLOBAL ! Section with general information
> regarding which kind of simulation to perform an parameters for the whole
> PROGRAM
> PROJECT NaCl ! Name of the project. This word will
> appear as part of a name of all ouput files (except main ouput file,
> specified with -o option)
> RUN_TYPE MD ! Molecular Dynamics
> PRINT_LEVEL low
> &END GLOBAL
>
>
> &FORCE_EVAL ! This section defines method for calculating energy and
> forces
> METHOD FIST ! Using Molecular Mechanics
> STRESS_TENSOR DIAGONAL_ANALYTICAL
> &MM
> &FORCEFIELD ! This section specifies forcefield parameters
> &SPLINE ! This section specifies parameters to set up the splines
> used in the nonboned interactions (both pair body potential and many body
> potential)
> EMAX_SPLINE 5.E-1
> EPS_SPLINE 1.E-6 ! Specify the maximum value of the potential up to
> which splines will be constructed
> &END
> &NONBONDED
> &BMHFTD
> atoms Cl Cl
> A 275.10
> B 3.3958
> C 3.0742
> D 1.7217
> BD 3.2125
> &END BMHFTD
> &BMHFTD
> atoms Cl Na
> A 67.500
> B 3.2617
> C 1.0408
> D 1.1517
> BD 3.2125
> &END BMHFTD
> &BMHFTD
> atoms Na Na
> A 1.0000
> B 9.4486
> C 0.2569
> D 0.3185
> BD 3.2125
> &END BMHFTD
> &END NONBONDED
> &CHARGE
> atom Cl
> CHARGE -1.000
> &END CHARGE
> &CHARGE
> atom Na
> CHARGE 1.000
> &END CHARGE
> &DIPOLE
> atom Cl
> APOL 2.9637
> &DAMPING
> TYPE Tang-Toennies
> ATOM Na
> BIJ 3.3259
> ORDER 4
> CIJ 3.0000
> &END DAMPING
> &END DIPOLE
> &DIPOLE
> atom Na
> APOL 0.1319
> &DAMPING
> TYPE Tang-Toennies
> ATOM Cl
> BIJ 3.3259
> ORDER 4
> CIJ 0.6970
> &END DAMPING
> &END DIPOLE
> &END FORCEFIELD
> &POISSON ! This section specifies parameters for the Poisson solver
> &EWALD ! This section specifies parameters for the EWALD summation
> method (for the electrostatics)
> EWALD_TYPE none ! Standard real-space coulomb potential is
> computed together with the non-bonded contributions.
> &END EWALD
> &END POISSON
> &NEIGHBOR_LISTS
> GEO_CHECK TRUE
> NEIGHBOR_LISTS_FROM_SCRATCH TRUE
> VERLET_SKIN 1
> &END NEIGHBOR_LISTS
> &END MM
> &SUBSYS ! This section defines the system
> &CELL ! Unit cell set up
> ABC 22.56 22.56 22.56 ! Lengths of the cell vectors A, B, and C
> ALPHA_BETA_GAMMA 90.0 90.0 90.0
> PERIODIC XYZ
> &END CELL
> &TOPOLOGY
> COORD_FILE_NAME NaCl.xyz
> COORDINATE xyz ! The type of the file is XYZ
> &END TOPOLOGY
> &END SUBSYS
> &END FORCE_EVAL
>
> &MOTION ! This section defines a set of tool connected with the motion of
> the nuclei.
> &PRINT
> &TRAJECTORY
> LOG_PRINT_KEY T
> FORMAT XMOL
> &EACH
> MD 10000
> &END EACH
> ADD_LAST NUMERIC
> &END TRAJECTORY
> &END PRINT
> &MD
> ENSEMBLE NPT_I
> TEMPERATURE 2000
> &BAROSTAT
> PRESSURE 1.01325 !100000 Pa
> TEMPERATURE 2000
> &END BAROSTAT
> &THERMOSTAT
> TYPE NOSE
> REGION MASSIVE
> &NOSE
> TIMECON 100
> LENGTH 3
> MTS 2
> &END NOSE
> &END THERMOSTAT
> TIMESTEP 1.0
> STEPS 100000
> &END MD
>
> &PRINT
> &RESTART
> LOG_PRINT_KEY T
> &EACH
> MD 10000
> &END EACH
> ADD_LAST NUMERIC
> &END RESTART
> &END PRINT
> &END MOTION
> &END
> &END MOTION
>
>
> 在 2018年5月3日星期四 UTC+8下午9:46:26，Josip Lovrić写道：
>>
>> Maybe wise thing to do is to check force field first, maybe you have some
>> mistake in definition of force field.
>> Try to take just few atoms and check how energy evolves. If the potential
>> is wrong you will get strange values.
>>
>> Josip
>>
>> 2018-05-03 14:12 GMT+02:00 <498... at qq.com>:
>>
>>> Hello, Josip, thanks very much for the answer. The system is bulk. 10s
>>> is too long to simulate, maybe build the initial configuration based on the
>>> experimental density in random way is a good choice. However, I also
>>> encountered a problem in that way, the pre-equilibriumed system is a little
>>> larger than the experimental density evaluated volume. So in avoid to the
>>> error of 'GEOMETRY wrong or EMAX_SPLINE too small!', I set the cell abc
>>> accoording to the pre-equilibriumed volume. With the time accumulating, I
>>> found the volume expanded in NVT ensemble which is ridiculous and holes
>>> began to form in the bulk. I don't know what caused this.
>>>
>>> 在 2018年5月3日星期四 UTC+8下午3:33:29，Josip Lovrić写道：
>>>>
>>>> Normaly, phase transitions are hard to reproduce. You are not first one
>>>> to be frustrated. Secondly 100 ps is way to short, you need to go at least
>>>> to 10s of ns and maybe if you are lucky you will see some melting. Also, do
>>>> you have slab or bulk?
>>>>
>>>> Josip
>>>> Greetings from Gothenburg
>>>>
>>>> 2018-05-03 2:37 GMT+02:00 <498... at qq.com>:
>>>>
>>>>> Hello, everyone, I recently want simulated the melting structure of
>>>>> molten salts. The simulation begin with the crystal structure and intend to
>>>>> be melt at 3000 K in NPT ensemble， but the result is frustrating. After 100
>>>>> ps runs, the ions still in crystal structure. The parameters in the force
>>>>> field is in published paper and widely used, so I wonder maybe I write
>>>>> something of the input wrong. The input file is listed below, pls help out
>>>>> the dilemma, thanks very much.
>>>>>
>>>>>
>>>>> &GLOBAL ! Section with general information
>>>>> regarding which kind of simulation to perform an parameters for the whole
>>>>> PROGRAM
>>>>> PROJECT C6 ! Name of the project. This word will
>>>>> appear as part of a name of all ouput files (except main ouput file,
>>>>> specified with -o option)
>>>>> RUN_TYPE MD ! Molecular Dynamics
>>>>> PRINT_LEVEL low
>>>>> &END GLOBAL
>>>>>
>>>>>
>>>>> &FORCE_EVAL ! This section defines method for calculating energy and
>>>>> forces
>>>>> METHOD FIST ! Using Molecular Mechanics
>>>>> STRESS_TENSOR NUMERICAL
>>>>> &MM
>>>>> &FORCEFIELD ! This section specifies forcefield parameters
>>>>> ..........
>>>>> &END FORCEFIELD
>>>>> &POISSON ! This section specifies parameters for the Poisson
>>>>> solver
>>>>> &EWALD ! This section specifies parameters for the EWALD
>>>>> summation method (for the electrostatics)
>>>>> EWALD_TYPE none ! Standard real-space coulomb potential is
>>>>> computed together with the non-bonded contributions.
>>>>> &END EWALD
>>>>> &END POISSON
>>>>> &NEIGHBOR_LISTS
>>>>> GEO_CHECK TRUE
>>>>> NEIGHBOR_LISTS_FROM_SCRATCH TRUE
>>>>> VERLET_SKIN 1
>>>>> &END NEIGHBOR_LISTS
>>>>> &END MM
>>>>> &SUBSYS ! This section defines the system
>>>>> &CELL ! Unit cell set up
>>>>> ABC 22.56 22.56 22.56 ! Lengths of the cell vectors A, B, and C
>>>>> ALPHA_BETA_GAMMA 90.0 90.0 90.0
>>>>> PERIODIC XYZ
>>>>> &END CELL
>>>>> &TOPOLOGY
>>>>> COORD_FILE_NAME NaCl.xyz
>>>>> COORDINATE xyz ! The type of the file is XYZ
>>>>> &END TOPOLOGY
>>>>> &END SUBSYS
>>>>> &END FORCE_EVAL
>>>>>
>>>>> &MOTION ! This section defines a set of tool connected with the
>>>>> motion of the nuclei.
>>>>> &PRINT
>>>>> &TRAJECTORY
>>>>> LOG_PRINT_KEY T
>>>>> FORMAT XMOL
>>>>> &EACH
>>>>> MD 10000
>>>>> &END EACH
>>>>> ADD_LAST NUMERIC
>>>>> &END TRAJECTORY
>>>>> &END PRINT
>>>>> &MD
>>>>> ENSEMBLE NPT_I
>>>>> TEMPERATURE 3000
>>>>> &BAROSTAT
>>>>> PRESSURE 0
>>>>> TEMPERATURE 3000
>>>>> &END BAROSTAT
>>>>> &THERMOSTAT
>>>>> TYPE NOSE
>>>>> REGION GLOBAL
>>>>> &NOSE
>>>>> TIMECON 100
>>>>> LENGTH 3
>>>>> MTS 2
>>>>> &END NOSE
>>>>> &END THERMOSTAT
>>>>> TIMESTEP 1.0
>>>>> STEPS 100000
>>>>> &END MD
>>>>>
>>>>> &PRINT
>>>>> &RESTART
>>>>> LOG_PRINT_KEY T
>>>>> &EACH
>>>>> MD 10000
>>>>> &END EACH
>>>>> ADD_LAST NUMERIC
>>>>> &END RESTART
>>>>> &END PRINT
>>>>> &END MOTION
>>>>> &END
>>>>> &END MOTION
>>>>>
>>>>> --
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>>>>
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