<div dir="ltr"><div>Dear Prof. Hutter,</div><div>Thanks for your reply! I have considered your suggestion of CUTOFF, functional and GAPW and smoothened density. The result is as follows.</div><div><br></div><div>(1) If we only increase CUTOFF, or or change the functional from BLYP to PBE, the Na atoms are still fixed.</div><div>(2) With the GAPW, the Na atoms moves.</div><div>(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.</div><p style="text-align:center;clear:both"><a href="https://lh3.googleusercontent.com/-GBDAWhqMuKg/Vcr91M48-NI/AAAAAAAAAMg/X_Ge2AXtxUY/s1600/Screenshot%2Bfrom%2B2015-08-12-Cutoff_PBE_GAPW.png" style="margin-left:1em;margin-right:1em" target="_blank"><img src="https://lh3.googleusercontent.com/-GBDAWhqMuKg/Vcr91M48-NI/AAAAAAAAAMg/X_Ge2AXtxUY/s320/Screenshot%2Bfrom%2B2015-08-12-Cutoff_PBE_GAPW.png" border="0" width="320" height="247"></a></p><div><br></div><div>So the main reason is I did not use GAPW before.</div><div>PS: </div><div>--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. (<a href="http://scitation.aip.org/content/aip/journal/jcp/138/10/10.1063/1.4793260" target="_blank">http://scitation.aip.org/<wbr>content/aip/journal/jcp/138/<wbr>10/10.1063/1.4793260</a>) </div><div><br></div><div>--Now the input (restart file) is as follows.</div><div>
<p style="margin-bottom:0in">&GLOBAL</p>
<pre> 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</pre><pre><br></pre><pre><br></pre><pre><br></pre><pre><div style="font-family:Arial,Helvetica,sans-serif;white-space:normal">With best regards,</div><div style="font-family:Arial,Helvetica,sans-serif;white-space:normal">jia</div></pre></div><div><br></div><br>On Tuesday, August 11, 2015 at 9:22:59 AM UTC+2, jgh wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi
<br>
<br>there is a known issue with the BLYP functional on low cutoff grids
<br>with high density ions.
<br>You could switch functional, increase (considerably) the cutoff,
<br>use GAPW, use NLCC pseudopotentials, use smoothened density (see XC section).
<br>
<br>BTW: your definition of the D3 vdW correction has some inconsistencies:
<br>
<br>- you use PBE as reference functional (not BLYP?)
<br>- you have a small system, long range correction should not be used
<br> ( this simulates a uniform system)
<br>
<br>regards
<br>
<br>Juerg Hutter
<br>------------------------------<wbr>------------------------------<wbr>--
<br>Juerg Hutter <wbr> Phone : ++41 44 635 4491
<br>Institut für Chemie C FAX : ++41 44 635 6838
<br>Universität Zürich E-<wbr>mail: <a rel="nofollow">hut...@chem.uzh.ch</a>
<br>Winterthurerstrasse 190
<br>CH-8057 Zürich, Switzerland
<br>------------------------------<wbr>------------------------------<wbr>---
<br>
<br></blockquote></div>