[CP2K:6898] Why the trajecoty of na atom is fixed ?
jia
huangji... at gmail.com
Mon Aug 17 07:36:03 UTC 2015
Dear Professor Hutte,
Thanks a lot. I have test for different Cutoff. Indeed when I use GAPW, I
find that 300 Ry is quite enough.
Best regards,
jia
On Wednesday, August 12, 2015 at 10:30:08 AM UTC+2, jgh wrote:
>
> Hi
>
> if you are using GAPW you most likely can keep the Cutoff rather
> low (about 200-300), but in any case I would set the REL_CUTOFF
> to a value of 50-60.
> If possible I would also not use the smoothing with GAPW.
>
> regards
>
> Juerg
> --------------------------------------------------------------
> Juerg Hutter Phone : ++41 44 635 4491
> Institut für Chemie C FAX : ++41 44 635 6838
> Universität Zürich E-mail: hut... at chem.uzh.ch
> <javascript:>
> Winterthurerstrasse 190
> CH-8057 Zürich, Switzerland
> ---------------------------------------------------------------
>
> -----cp... at googlegroups.com <javascript:> wrote: -----To: cp2k <
> cp... at googlegroups.com <javascript:>>
> From: jia
> Sent by: cp... at googlegroups.com <javascript:>
> Date: 08/12/2015 10:17AM
> Subject: Re: [CP2K:6898] Why the trajecoty of na atom is fixed ?
>
> Prof. Hutter,Thanks for your reply! I have considered your suggestion of
> CUTOFF, functional and GAPW and smoothen.
> Now the reatart file is like this:
>
>
>
> The result is as follows.
> (1) If we only increase CUTOFF, or or change the functional from BLYP to
> PBE, the Na atoms are still fixed.(2) With the GAPW, the Na atoms moves.(3)
> And for the test we increase CUTOFF, change the functional to PBE, use
> GAPW and XC_SMOOTH_RHO, the Na atoms moves. The trajectory for 0.36 ps is
> shown here.
> So the main reason is I did not use GAPW before.PS: --Because this is a
> test model, I still kept the long range correction. For the NLCC
> pseudopotentials, after reading Alex Willand et al 's paper (2013),
> Norm-conserving pseudopotentials with chemical accuracy compared to
> all-electron calculations. I also did not use the NLCC pseudopotentials. (
> http://scitation.aip.org/content/aip/journal/jcp/138/10/10.1063/1.4793260)
>
> --Now the input (restart file) is as follows.
>
>
>
>
>
> &GLOBAL
> PRINT_LEVEL MEDIUM
> PROJECT_NAME 2w_2Na
> RUN_TYPE MD
> &END GLOBAL
> &MOTION
> &GEO_OPT
> TYPE MINIMIZATION
> OPTIMIZER BFGS
> MAX_ITER 20
> &END GEO_OPT
> &MD
> ENSEMBLE NVT
> STEPS 1000
> TIMESTEP 4.9999999999999989E-01
> STEP_START_VAL 1584
> TIME_START_VAL 7.9200000000000932E+02
> ECONS_START_VAL -2.2970419127064038E+03
> TEMPERATURE 3.3000000000000006E+02
> TEMP_TOL 8.0000000000000000E+01
> &THERMOSTAT
> &NOSE
> LENGTH 3
> YOSHIDA 3
> TIMECON 9.9999999999999955E+02
> MTS 2
> &COORD
> 4.6804334715900502E-02 6.4063067951588215E-01
> -1.7671728013981677E-01
> &END COORD
> &VELOCITY
> 1.0848945164897635E-06 4.3154851784712554E-05
> 1.1317451952244691E-06
> &END VELOCITY
> &MASS
> 1.5271179928232741E+09 1.7861029155827765E+06
> 1.7861029155827765E+06
> &END MASS
> &FORCE
> -1.1179502436284231E-12 4.2123153718162141E-10
> 1.2772410940594576E-09
> &END FORCE
> &END NOSE
> &END THERMOSTAT
> &AVERAGES T
> &RESTART_AVERAGES
> ITIMES_START 1
> AVECPU 8.3660323358309768E+01
> AVEHUGONIOT 0.0000000000000000E+00
> AVETEMP_BARO 0.0000000000000000E+00
> AVEPOT -1.2952630029344064E+03
> AVEKIN 2.7106480019472567E-01
> AVETEMP 3.5561567432356406E+02
> AVEKIN_QM 0.0000000000000000E+00
> AVETEMP_QM 0.0000000000000000E+00
> AVEVOL 5.1174547637613250E+04
> AVECELL_A 5.8581510119454805E+01
> AVECELL_B 2.9556072608784607E+01
> AVECELL_C 2.9556072608784607E+01
> AVEALPHA 9.0000000000000043E+01
> AVEBETA 9.0000000000000043E+01
> AVEGAMMA 9.0000000000000043E+01
> AVE_ECONS 3.9657707679004423E+07
> AVE_PRESS 0.0000000000000000E+00
> AVE_PXX 0.0000000000000000E+00
> &END RESTART_AVERAGES
> &END AVERAGES
> &END MD
> &PRINT
> &TRAJECTORY SILENT
> &EACH
> MD 1
> &END EACH
> &END TRAJECTORY
> &VELOCITIES ON
> &EACH
> MD 1
> &END EACH
> &END VELOCITIES
> &FORCES ON
> &EACH
> MD 1
> &END EACH
> &END FORCES
> &RESTART SILENT
> BACKUP_COPIES 1
> &EACH
> MD 1
> &END EACH
> &END RESTART
> &RESTART_HISTORY SILENT
> &EACH
> MD 1000
> &END EACH
> &END RESTART_HISTORY
> &END PRINT
> &END MOTION
> &FORCE_EVAL
> METHOD QS
> &DFT
> BASIS_SET_FILE_NAME ../BASIS_MOLOPT
> POTENTIAL_FILE_NAME ../GTH_POTENTIALS
> &SCF
> MAX_SCF 300
> EPS_SCF 4.9999999999999998E-07
> SCF_GUESS RESTART
> &OT T
> &END OT
> &END SCF
> &QS
> EPS_DEFAULT 9.9999999999999998E-13
> EXTRAPOLATION PS
> EXTRAPOLATION_ORDER 3
> METHOD GAPW
> &END QS
> &MGRID
> CUTOFF 9.0000000000000000E+02
> &END MGRID
> &XC
> DENSITY_CUTOFF 1.0000000000000000E-10
> GRADIENT_CUTOFF 1.0000000000000000E-10
> TAU_CUTOFF 1.0000000000000000E-10
> &XC_GRID
> XC_SMOOTH_RHO SPLINE3
> &END XC_GRID
> &XC_FUNCTIONAL NO_SHORTCUT
> &BECKE88 T
> &END BECKE88
> &LYP T
> &END LYP
> &END XC_FUNCTIONAL
> &VDW_POTENTIAL
> POTENTIAL_TYPE PAIR_POTENTIAL
> &PAIR_POTENTIAL
> R_CUTOFF 8.0000000000000000E+00
> TYPE DFTD3
> PARAMETER_FILE_NAME ../dftd3.dat
> REFERENCE_FUNCTIONAL PBE
> EPS_CN 1.0000000000000000E-02
> CALCULATE_C9_TERM T
> REFERENCE_C9_TERM T
> LONG_RANGE_CORRECTION T
> &END PAIR_POTENTIAL
> &END VDW_POTENTIAL
> &END XC
> &END DFT
> &SUBSYS
> &CELL
> A 3.1000000000000011E+01 0.0000000000000000E+00
> 0.0000000000000000E+00
> B 0.0000000000000000E+00 1.5640400000000005E+01
> 0.0000000000000000E+00
> C 0.0000000000000000E+00 0.0000000000000000E+00
> 1.5640400000000005E+01
> MULTIPLE_UNIT_CELL 1 1 1
> &END CELL
> &COORD
> Na 1.3286318921035836E+01 1.3614063967463656E+01
> 1.1728050930092907E+01
> Na 1.2523358969849829E+01 -7.3462122629921822E-01
> 9.7120169705560766E+00
> O 2.0870269874930649E+00 4.0865703183420337E+00
> 5.8562334048014435E+00
> H 2.0316447793438357E+00 5.0584745221132268E+00
> 5.9610023039145279E+00
> H 1.3184285000575218E+00 3.8776053202627789E+00
> 5.3040976629339323E+00
> O 3.1555919884652632E+00 9.2452722166802115E+00
> 1.4471916934492752E+01
> H 3.7928078117053126E+00 9.9774533993926227E+00
> 1.4468959613505644E+01
> H 3.4123636142611913E+00 8.6672215399732266E+00
> 1.3736009577898940E+01
> &END COORD
> &VELOCITY
> -4.4606192041125074E-05 2.2910283712135158E-04
> -4.0036861008258982E-04
> 7.3058239091108217E-05 -2.0125235933338208E-04
> 3.6332784105453752E-04
> 3.8266565551863624E-05 -3.5874524380332236E-05
> -1.0679085397068891E-04
> -6.3236824320307033E-04 4.0174318998758783E-05
> 1.3824215141977153E-04
> -1.4467395239910316E-04 2.0218266649262508E-04
> 7.9202921271559446E-04
> -2.2171434510392410E-05 -6.2950590932101455E-05
> 8.8168050258192519E-05
> 5.2982772704762990E-05 1.3930419146095219E-04
> -1.8036331754184572E-04
> -1.7331312353883934E-04 5.3845779124284576E-04
> 3.9591238206890749E-04
> &END VELOCITY
> &KIND H
> BASIS_SET DZVP-MOLOPT-SR-GTH
> POTENTIAL GTH-PBE-q1
> &BASIS
> 1
> 2 0 1 5 2 1
> 0.1006846822853300E+02 -0.3391744490000000E-01 0.5919377550000000E-01
> 0.9905134400000000E-02
> 0.2680222868089000E+01 -0.1222022121000000E+00 0.8433183289000000E+00
> 0.1224495665000000E+00
> 0.7915015391220001E+00 -0.4438188612000000E+00 -0.1155707115500000E+01
> 0.4771832409000000E+00
> 0.2391161504870000E+00 -0.4531821866000000E+00 0.4947962120000000E-01
> 0.5479196782000000E+00
> 0.8219318444100000E-01 -0.1316128615000000E+00 0.5227087380000000E+00
> 0.8690318540000000E+00
> &END BASIS
> &POTENTIAL
> 1
> 0.2000000000000000E+00 2 -0.4195961470000000E+01 0.7304982100000000E+00
> 0
> &END POTENTIAL
> &END KIND
> &KIND O
> BASIS_SET DZVP-MOLOPT-SR-GTH
> POTENTIAL GTH-PBE-q6
> &BASIS
> 1
> 2 0 2 5 2 2 1
> 0.1038922801831700E+02 0.1262407229000000E+00 0.6921579790000000E-01
> -0.6130203720000000E-01 -0.2686270110000000E-01 0.2984522750000000E-01
> 0.3849621072005000E+01 0.1399337043000000E+00 0.1156345389000000E+00
> -0.1900875117000000E+00 -0.6283021000000000E-02 0.6093973390000000E-01
> 0.1388401188741000E+01 -0.4343482317000000E+00 -0.3228397194000000E+00
> -0.3777269828000000E+00 -0.2248391878000000E+00 0.7323215801000000E+00
> 0.4969550436550000E+00 -0.8527917909000000E+00 -0.9594401660000000E-01
> -0.4542660860000000E+00 0.3803246586000000E+00 0.8935649184000000E+00
> 0.1624916150400000E+00 -0.2423515378000000E+00 0.1102830348700000E+01
> -0.2573889830000000E+00 0.1054102919900000E+01 0.1529541887000000E+00
> &END BASIS
> &POTENTIAL
> 2 4
> 0.2434202600000000E+00 2 -0.1699189235000000E+02 0.2566142060000000E+01
> 2
> 0.2208314000000000E+00 1 0.1838885102000000E+02
> 0.2172007000000000E+00 0
> &END POTENTIAL
> &END KIND
> &KIND I
> BASIS_SET DZVP-MOLOPT-SR-GTH
> POTENTIAL GTH-PBE-q7
> &BASIS
> 1
> 2 0 2 5 2 2 1
> 0.9661726937760000E+00 -0.4724631893510000E+00 0.1555822203873000E+01
> -0.4312534730020000E+00 0.4374991361440000E+00 0.7909099814790000E+00
> 0.8288855705270000E+00 -0.4617483861400000E-01 -0.4052453983040000E+00
> 0.4054481330980000E+00 -0.3608369749790000E+00 -0.7067391303230000E+00
> 0.3671593108060000E+00 0.6748660286690000E+00 0.8373462810420000E+00
> 0.1544082880420000E+00 -0.4269558193280000E+00 -0.1146102256372000E+01
> 0.2013691068320000E+00 0.4418461904320000E+00 -0.2170714561688000E+01
> 0.3071310887970000E+00 -0.1428790897200000E+00 -0.1473453298743000E+01
> 0.8301507112600000E-01 0.1477007514960000E+00 0.2099200395478000E+01
> 0.1514523567510000E+00 0.1946428231727000E+01 -0.5177497012720000E+00
> &END BASIS
> &POTENTIAL
> 2 5
> 0.5600000000000001E+00 1 0.1373638610000000E+02
> 3
> 0.5893900100000000E+00 3 0.2139348900000000E+00 0.8845652600000000E+00
> -0.2067022000000000E-01
> -0.1175588960000000E+01 0.5337028000000000E-01
> -0.4236135000000000E-01
> 0.5423271700000000E+00 2 0.2872106600000000E+00 0.4693267100000000E+00
> -0.5553148500000000E+00
> 0.7704050700000000E+00 1 0.3070961500000000E+00
> &END POTENTIAL
> &END KIND
> &KIND Li
> BASIS_SET DZVP-MOLOPT-SR-GTH
> POTENTIAL GTH-PBE-q3
> &END KIND
> &KIND Na
> BASIS_SET DZVP-MOLOPT-SR-GTH
> POTENTIAL GTH-PBE-q9
> &BASIS
> 1
> 2 0 1 7 3 2
> 0.2351880076196000E+02 0.3779826805300000E-01 0.5040470618000000E-02
> 0.3777907065700000E-01 -0.4123515085400000E-01 -0.5410838671000000E-02
> 0.1113565610327500E+02 0.1804152720160000E+00 0.3121004835600000E-01
> -0.1196144293190000E+00 -0.1027040656580000E+00 -0.1760933831700000E-01
> 0.4647813820246000E+01 -0.8423548988500000E-01 -0.2121458488700000E-01
> 0.2243024957020000E+00 -0.2765071563740000E+00 -0.4380300865300000E-01
> 0.1866708259982000E+01 -0.5020072394680000E+00 -0.8800642668000000E-01
> -0.1837798132120000E+00 -0.4050879856000000E+00 -0.6784423562300000E-01
> 0.7346836971960000E+00 -0.4874547129940000E+00 -0.2415626435800000E+00
> 0.1641649867502000E+01 -0.3456697625980000E+00 -0.8505797401200001E-01
> 0.2756729958600000E+00 -0.8890985577799999E-01 0.4606950361200000E-01
> -0.2281564821968000E+01 -0.1282947247740000E+00 0.1595277707190000E+00
> 0.4989510824500000E-01 -0.2456248530000000E-03 0.1008694292400000E+01
> 0.8016609909810000E+00 -0.2074313963000000E-02 0.9821494245680000E+00
> &END BASIS
> &POTENTIAL
> 3 6
> 0.2339650200000000E+00 2 -0.2689483460000000E+01 -0.5094777000000000E+00
> 2
> 0.1497769000000000E+00 1 0.3285715860000000E+02
> 0.1231990100000000E+00 1 -0.1399900802000000E+02
> &END POTENTIAL
> &END KIND
> &TOPOLOGY
> NUMBER_OF_ATOMS 8
> MULTIPLE_UNIT_CELL 1 1 1
> &END TOPOLOGY
> &END SUBSYS
> &END FORCE_EVAL
>
>
> With best regards,jia
>
> On Tuesday, August 11, 2015 at 9:22:59 AM UTC+2, jgh wrote:Hi
>
>
>
> there is a known issue with the BLYP functional on low cutoff grids
>
> with high density ions.
>
> You could switch functional, increase (considerably) the cutoff,
>
> use GAPW, use NLCC pseudopotentials, use smoothened density (see XC
> section).
>
>
>
> BTW: your definition of the D3 vdW correction has some inconsistencies:
>
>
>
> - you use PBE as reference functional (not BLYP?)
>
> - you have a small system, long range correction should not be used
>
> ( this simulates a uniform system)
>
>
>
> regards
>
>
>
> Juerg Hutter
>
> --------------------------------------------------------------
>
> Juerg Hutter Phone : ++41 44 635 4491
>
> Institut für Chemie C FAX : ++41 44 635 6838
>
> Universität Zürich E-mail: hut... at chem.uzh.ch
>
> Winterthurerstrasse 190
>
> CH-8057 Zürich, Switzerland
>
> ---------------------------------------------------------------
>
>
>
>
>
>
>
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