[CP2K:6890] Why the trajecoty of na atom is fixed ?
jia
huangji... at gmail.com
Wed Aug 12 08:20:48 UTC 2015
Dear Prof. Hutter,
Thanks for your reply! I have considered your suggestion of CUTOFF,
functional and GAPW and smoothened density. 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.
<https://lh3.googleusercontent.com/-GBDAWhqMuKg/Vcr91M48-NI/AAAAAAAAAMg/X_Ge2AXtxUY/s1600/Screenshot%2Bfrom%2B2015-08-12-Cutoff_PBE_GAPW.png>
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). 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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