[CP2K-user] Convergence problem- MD calculation for metal surface
Matt W
mattwa... at gmail.com
Fri May 10 18:37:55 UTC 2019
If you send me all files required to run (on here or to my email), I can
try and have a look.
On Friday, May 10, 2019 at 3:02:59 PM UTC+1, Kevin wrote:
>
> Dear Matt,
>
> I would highly appreciate that if you let me know about any updates.
>
> Best,
>
> Kevin
>
> On Tuesday, April 2, 2019 at 12:49:53 AM UTC+2, Kevin wrote:
>>
>> Dear Matt,
>>
>> Thanks for the feedback. Actually I have used the same super-cell size of
>> the optimized slab and also whenever I use AIMD it works (but it's
>> expensive!). So I think the structure is OK.
>> I even tried once with OT method and again didn't get the mentioned
>> error. I have encountered the error while using DFTB or PM6.
>>
>> On Monday, April 1, 2019 at 8:04:28 PM UTC+2, Matt W wrote:
>>>
>>> I've not looked at your files, but are you sure you don't have atoms on
>>> top of each other, maybe across periodic images?
>>>
>>> On Sunday, March 31, 2019 at 11:27:50 PM UTC+1, Kevin wrote:
>>>>
>>>>
>>>> Dear all,
>>>> I'm encountering convergence problem for the MD simulation of single
>>>> molecule adsorption on Ni surface. This is a test case to see if I can
>>>> calculate my desired system. I'm using a GLE thermostat.
>>>> I've tried using DFTB and PM6 but in both cases I receive the error
>>>> below, mentioning:
>>>> *"Bad condition number R_COND = 0.000E+00 (smaller than the machine
>>>> working precision" common/mathlib.F:709.*
>>>> As you know, DFTB or PM6 are chosen because of their inexpensiveness!
>>>>
>>>> [image: Capture.PNG]
>>>>
>>>>
>>>> Here is my input file and I've attached the coordinate file:
>>>>
>>>>
>>>> &GLOBAL
>>>> PROJECT CH4-Ni
>>>> RUN_TYPE MD
>>>> PRINT_LEVEL LOW
>>>> &END GLOBAL
>>>>
>>>> &FORCE_EVAL
>>>> METHOD Quickstep
>>>> &DFT
>>>> &QS
>>>> METHOD PM6
>>>> &SE
>>>> RC_INTERACTION [angstrom] 8.0
>>>> RC_COULOMB [angstrom] 8.0
>>>> RC_RANGE [angstrom] 0.05
>>>> &END
>>>> &END QS
>>>> ! &QS
>>>> ! METHOD DFTB
>>>> ! &DFTB
>>>> ! SELF_CONSISTENT T
>>>> ! DO_EWALD T
>>>> ! DISPERSION T
>>>> ! &PARAMETER
>>>> ! PARAM_FILE_PATH /data/scc
>>>> ! PARAM_FILE_NAME scc_parameter
>>>> ! UFF_FORCE_FIELD uff_table
>>>> ! &END PARAMETER
>>>> ! &END DFTB
>>>> ! &END QS
>>>> &SCF
>>>> MAX_SCF 30
>>>> EPS_SCF 5.0E-6
>>>> &OUTER_SCF
>>>> MAX_SCF 30
>>>> EPS_SCF 5.0E-6
>>>> &END
>>>> &DIAGONALIZATION ON
>>>> ALGORITHM STANDARD
>>>> &END DIAGONALIZATION
>>>> ADDED_MOS 300
>>>> &SMEAR ON
>>>> METHOD FERMI_DIRAC
>>>> ELECTRONIC_TEMPERATURE [K] 350
>>>> &END SMEAR
>>>> &MIXING
>>>> METHOD BROYDEN_MIXING
>>>> BETA 1.5
>>>> ALPHA 0.1
>>>> NBROYDEN 8
>>>> &END MIXING
>>>> &PRINT
>>>> &RESTART LOW
>>>> BACKUP_COPIES 1
>>>> &END RESTART
>>>> &END PRINT
>>>> SCF_GUESS ATOMIC
>>>> &END SCF
>>>> &POISSON
>>>> POISSON_SOLVER MT
>>>> PERIODIC XY
>>>> &EWALD
>>>> EWALD_TYPE SPME
>>>> GMAX 25
>>>> O_SPLINE 5
>>>> &END EWALD
>>>> &END POISSON
>>>> &END DFT
>>>>
>>>> &SUBSYS
>>>> &CELL
>>>> ABC 12.4597 12.9485 23.1387
>>>> PERIODIC XY
>>>> &END CELL
>>>> &COORD
>>>> @INCLUDE 'ch4-ni.coord'
>>>> &END COORD
>>>> &TOPOLOGY
>>>> &CENTER_COORDINATES
>>>> &END CENTER_COORDINATES
>>>> &END TOPOLOGY
>>>> &END SUBSYS
>>>> &END FORCE_EVAL
>>>>
>>>> &MOTION
>>>> &MD
>>>> ENSEMBLE NVT
>>>> STEPS 10000
>>>> TIMESTEP 0.5
>>>> TEMPERATURE 300
>>>> &THERMOSTAT
>>>> REGION MASSIVE
>>>> TYPE GLE
>>>> &GLE
>>>> NDIM 3
>>>> A_SCALE [ps^-1] 1.00
>>>> A_LIST 2.000000000000e+0
>>>> 1.365763041717e+1 0.000000000000e+0
>>>> A_LIST -1.365763041717e+1
>>>> 9.418257899376e-1 5.860040064992e+2
>>>> A_LIST 0.000000000000e+0
>>>> -5.860040064992e+2 0.000000000000e+0
>>>> C_LIST 3.071856358605e+2
>>>> 1.052252204958e+0 -3.083120039764e+2
>>>> C_LIST 1.052252204958e+0
>>>> 1.353606645969e+4 0.000000000000e+0
>>>> C_LIST -3.083120039764e+2
>>>> 0.000000000000e+0 1.352888082383e+4
>>>> &END GLE
>>>> &END THERMOSTAT
>>>> &PRINT
>>>> &ENERGY
>>>> &EACH
>>>> MD 10
>>>> &END EACH
>>>> &END ENERGY
>>>> &END PRINT
>>>> &END MD
>>>> &FREE_ENERGY
>>>> &FREE_ENERGY_INFO
>>>> &EACH
>>>> MD 1000
>>>> &END
>>>> &END
>>>> &METADYN
>>>> &PRINT
>>>> &COLVAR
>>>> COMMON_ITERATION_LEVELS 3
>>>> &EACH
>>>> MD 1
>>>> &END
>>>> &END
>>>> &HILLS
>>>> COMMON_ITERATION_LEVELS 3
>>>> &EACH
>>>> MD 1
>>>> &END
>>>> &END
>>>> &END
>>>> &END METADYN
>>>> &END FREE_ENERGY
>>>> &PRINT
>>>> &TRAJECTORY
>>>> FORMAT XYZ
>>>> &EACH
>>>> MD 20
>>>> &END EACH
>>>> &END TRAJECTORY
>>>> &RESTART_HISTORY
>>>> &EACH
>>>> MD 10000
>>>> &END EACH
>>>> &END RESTART_HISTORY
>>>> &RESTART OFF
>>>> &END RESTART
>>>> &END PRINT
>>>> &END MOTION
>>>>
>>>> I would be grateful if anyone could take a look to my input file and
>>>> let me know about the possible way to get the structure converged. I've
>>>> already relaxed the metal structure before using it for md simulation.
>>>>
>>>> Thanks in advance.
>>>>
>>>> Kevin
>>>>
>>>
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