[CP2K-user] Convergence problem- MD calculation for metal surface
Kevin
amin.ja... at gmail.com
Mon May 13 11:04:22 UTC 2019
Dear Matt,
Thank you very much for the time that you put in to my question.
Actually I want to know why it doesn't work when I use smearing instead of
OT method. I tried to look it up 'what is the "Bad condition number
R_COND = 0.000E+00" error?' but couldn't find any useful information. I
think if I can manage to get the system running with smearing (while using
DFTB or PM6) I can get the results that I seek. Any idea about PM6?
Kind regards,
Kevin
On Monday, May 13, 2019 at 12:07:02 PM UTC+2, Matt W wrote:
>
> Hard identify the real problem.
>
> You system runs sort of 'OK' with OT, i.e. it converges electronically,
> but the MD explodes after a few steps.
>
> I guess the initial guess it too poor for mixing to cope. It converges if
> you start from the converged OT WFN. There seem to be further problems with
> mixing and DFTB when moving atoms, doubt it has ever been tested.
>
> I no very little about DFTB setups, so have no idea if the explosion is
> due to bad parameters etc.
>
> Matt
>
> On Sunday, May 12, 2019 at 12:41:59 AM UTC+1, Kevin wrote:
>>
>> Dear Matt,
>>
>> Enclosed please find the necessary files for testing. Thank you in
>> advance.
>>
>> Kind regards,
>>
>> Kevin
>>
>> On Friday, May 10, 2019 at 8:37:55 PM UTC+2, Matt W wrote:
>>>
>>> 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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