[CP2K:4024] Energy conservation NVT/NVE simulation
garold
g.murd... at gmail.com
Wed Sep 12 10:38:09 UTC 2012
Hi Alberto,
May I suggest use of smoothing, i.e., including a section:
&XC_GRID
XC_SMOOTH_RHO NN10 ! (or NN50)
XC_DERIV SPLINE2_SMOOTH
&END XC_GRID
You can also see the previous discussion on this forum:
https://groups.google.com/forum/?hl=it&fromgroups=#!topic/cp2k/dc4kzNqNw-8
where a similar discussion occurred.
Best,
Garold
On Tuesday, September 11, 2012 12:35:42 PM UTC+3, albe... at virgilio.it
wrote:
>
> Hi,
>
> for the restart I used the last restart file of the previous run,
> modifying the parameters in $QS or $SCF to test the new ones.
> I observed a drift also for NVE even if most of the tests have been done
> for NVT.
> I will carry out more tests for NVE to reduce the number of variables and
> avoid also the problem of thermostat setting.
>
> About the drift, after few ps it is about 10^-3 au, depending on the
> simulations.
> Changing the parameters to increase the accuracy, in some cases I observed
> no drift but sudden jumps in the total energy.
>
> I will keep you updated about further NVE tests.
> Thanks
>
> alberto
>
> Il giorno martedì 11 settembre 2012 11:04:00 UTC+2, jgh ha scritto:
>>
>> Hi
>>
>> it is difficult to give good advice without more information.
>>
>> Possible problems might be:
>>
>> - Restarts: do you correctly restart all variables
>> - Thermostat: I don't know if the setting you have is reasonable
>> and adequate for this timestep.
>> Do you see a drift also for NVE?
>> - How big is the drift and how long is your trajectory?
>>
>> regards
>>
>> Juerg
>>
>> --------------------------------------------------------------
>> Juerg Hutter Phone : ++41 44 635 4491
>> Physical Chemistry Institute FAX : ++41 44 635 6838
>> University of Zurich E-mail: hut... at pci.uzh.ch
>> Winterthurerstrasse 190
>> CH-8057 Zurich, Switzerland
>> ---------------------------------------------------------------
>>
>> -----cp... at googlegroups.com wrote: -----
>> To: cp... at googlegroups.com
>> From: "albe... at virgilio.it"
>> Sent by: cp... at googlegroups.com
>> Date: 09/11/2012 10:06AM
>> Subject: Re: [CP2K:4024] Energy conservation NVT/NVE simulation
>>
>> Dear Juerg,
>>
>> thank you very much.
>>
>> I changed the functional to BLYP and I used ASPC interpolator.
>> I carried out different tests where I tried different values of the
>> EXTRAPOLATION_ORDER (up to 6), I increased the EPS_SCF and used defaults
>> for most of the other parameters.
>> Unfortunately, I still observe either drifts or jumps in the total
>> energy.
>>
>> I think that there is still a problem in the input, reported below.
>>
>> Many thanks for your help.
>>
>> Alberto
>>
>> ************
>>
>> &FORCE_EVAL
>> METHOD QS
>> &DFT
>> BASIS_SET_FILE_NAME GTH_BASIS_SETS
>> POTENTIAL_FILE_NAME GTH_POTENTIALS
>> &MGRID
>> CUTOFF 300
>> REL_CUTOFF 40
>> &END MGRID
>> &QS
>> EPS_DEFAULT 1.0E-12
>> WF_INTERPOLATION ASPC
>> EXTRAPOLATION_ORDER 3
>> &END QS
>> &SCF
>> SCF_GUESS ATOMIC
>> EPS_SCF 1.0E-6
>> &OT T
>> &END OT
>> &PRINT
>> &RESTART OFF
>> &END
>> &END
>> &END SCF
>> &XC
>> &XC_FUNCTIONAL BLYP
>> &END XC_FUNCTIONAL
>> &END XC
>> &PRINT
>> &MOMENTS MEDIUM
>> &END
>> &END PRINT
>> &END DFT
>> &SUBSYS
>> &CELL
>> ABC 9.8528 9.8528 9.8528
>> &END CELL
>> # 32 H2O (TIP5P,1bar,300K) a = 9.8528
>> &COORD
>> O 2.280398 9.146539 5.088696
>> O 1.251703 2.406261 7.769908
>> O 1.596302 6.920128 0.656695
>> O 2.957518 3.771868 1.877387
>> O 0.228972 5.884026 6.532308
>> O 9.023431 6.119654 0.092451
>> O 7.256289 8.493641 5.772041
>> O 5.090422 9.467016 0.743177
>> O 6.330888 7.363471 3.747750
>> O 7.763819 8.349367 9.279457
>> O 8.280798 3.837153 5.799282
>> O 8.878250 2.025797 1.664102
>> O 9.160372 0.285100 6.871004
>> O 4.962043 4.134437 0.173376
>> O 2.802896 8.690383 2.435952
>> O 9.123223 3.549232 8.876721
>> O 1.453702 1.402538 2.358278
>> O 6.536550 1.146790 7.609732
>> O 2.766709 0.881503 9.544263
>> O 0.856426 2.075964 5.010625
>> O 6.386036 1.918950 0.242690
>> O 2.733023 4.452756 5.850203
>> O 4.600039 9.254314 6.575944
>> O 3.665373 6.210561 3.158420
>> O 3.371648 6.925594 7.476036
>> O 5.287920 3.270653 6.155080
>> O 5.225237 6.959594 9.582991
>> O 0.846293 5.595877 3.820630
>> O 9.785620 8.164617 3.657879
>> O 8.509982 4.430362 2.679946
>> O 1.337625 8.580920 8.272484
>> O 8.054437 9.221335 1.991376
>> H 1.762019 9.820429 5.528454
>> H 3.095987 9.107088 5.588186
>> H 0.554129 2.982634 8.082024
>> H 1.771257 2.954779 7.182181
>> H 2.112148 6.126321 0.798136
>> H 1.776389 7.463264 1.424030
>> H 3.754249 3.824017 1.349436
>> H 3.010580 4.524142 2.466878
>> H 0.939475 5.243834 6.571945
>> H 0.515723 6.520548 5.877445
>> H 9.852960 6.490366 0.393593
>> H 8.556008 6.860063 -0.294256
>> H 7.886607 7.941321 6.234506
>> H 7.793855 9.141028 5.315813
>> H 4.467366 9.971162 0.219851
>> H 5.758685 10.102795 0.998994
>> H 6.652693 7.917443 3.036562
>> H 6.711966 7.743594 4.539279
>> H 7.751955 8.745180 10.150905
>> H 7.829208 9.092212 8.679343
>> H 8.312540 3.218330 6.528858
>> H 8.508855 4.680699 6.189990
>> H 9.742249 1.704975 1.922581
>> H 8.799060 2.876412 2.095861
>> H 9.505360 1.161677 6.701213
>> H 9.920117 -0.219794 7.161006
>> H 4.749903 4.186003 -0.758595
>> H 5.248010 5.018415 0.403676
>> H 3.576065 9.078451 2.026264
>> H 2.720238 9.146974 3.273164
>> H 9.085561 4.493058 9.031660
>> H 9.215391 3.166305 9.749133
>> H 1.999705 2.060411 1.927796
>> H 1.824184 0.564565 2.081195
>> H 7.430334 0.849764 7.438978
>> H 6.576029 1.537017 8.482885
>> H 2.415851 1.576460 8.987338
>> H 2.276957 0.099537 9.289499
>> H 1.160987 1.818023 4.140602
>> H 0.350256 2.874437 4.860741
>> H 5.768804 2.638450 0.375264
>> H 7.221823 2.257514 0.563730
>> H 3.260797 5.243390 5.962382
>> H 3.347848 3.732214 5.988196
>> H 5.328688 9.073059 5.982269
>> H 5.007063 9.672150 7.334875
>> H 4.566850 6.413356 3.408312
>> H 3.273115 7.061666 2.963521
>> H 3.878372 7.435003 6.843607
>> H 3.884673 6.966316 8.283117
>> H 5.918240 3.116802 5.451335
>> H 5.355924 2.495093 6.711958
>> H 5.071858 7.687254 10.185667
>> H 6.106394 7.112302 9.241707
>> H 1.637363 5.184910 4.169264
>> H 0.427645 4.908936 3.301903
>> H 9.971698 7.227076 3.709104
>> H 10.647901 8.579244 3.629806
>> H 8.046808 5.126383 2.213838
>> H 7.995317 4.290074 3.474723
>> H 1.872601 7.864672 7.930401
>> H 0.837635 8.186808 8.987268
>> H 8.314696 10.115534 2.212519
>> H 8.687134 8.667252 2.448452
>> &END COORD
>> &KIND H
>> BASIS_SET TZV2P-GTH
>> POTENTIAL GTH-BLYP-q1
>> &END KIND
>> &KIND O
>> BASIS_SET TZV2P-GTH
>> POTENTIAL GTH-BLYP-q6
>> &END KIND
>> &END SUBSYS
>> &END FORCE_EVAL
>> &GLOBAL
>> PROJECT H2O-32
>> RUN_TYPE MD
>> PRINT_LEVEL MEDIUM
>> &TIMINGS
>> THRESHOLD 0.000001
>> &END
>> &END GLOBAL
>> &MOTION
>> &MD
>> ENSEMBLE NVT
>> STEPS 30000
>> TIMESTEP 0.5
>> TEMPERATURE 300.0
>> &THERMOSTAT
>> TYPE CSVR
>> &CSVR
>> TIMECON 100.0
>> &END CSVR
>> &END THERMOSTAT
>> &END MD
>> &PRINT
>> &VELOCITIES LOW
>> &END
>> &END PRINT
>> &END MOTION
>>
>> **************
>>
>>
>> Il giorno mercoledì 5 settembre 2012 09:56:16 UTC+2, jgh ha scritto:Hi
>>
>> the main problem is
>>
>> &QS
>> EPS_DEFAULT 1.0E-12
>> WF_INTERPOLATION PS
>> EXTRAPOLATION_ORDER 3
>> &END QS
>>
>> change to WF_INTERPOLATION ASPC (the default) and maybe
>> increase the EXTRAPOLATION_ORDER slightly.
>> See
>> J. Hutter, Car-Parrinello molecular dynamics
>> Wiley Interdisciplinary Reviews: Computational Molecular Science 2 (4) ,
>> pp. 604-612
>> for an explanation.
>>
>> You should also change to a more reasonable DFT functional.
>> LDA (PADE) will lead to an extremly overstructured system.
>> See
>> J. Schmidt et al.,
>> Isobaric-isothermal molecular dynamics simulations utilizing density
>> functional theory: An assessment of the structure and density of water at
>> near-ambient conditions
>> Journal of Physical Chemistry B Volume 113, Issue 35, 3 September 2009,
>> Pages 11959-11964
>>
>> regards
>>
>> Juerg
>>
>> --------------------------------------------------------------
>> Juerg Hutter Phone : ++41 44 635 4491
>> Physical Chemistry Institute FAX : ++41 44 635 6838
>> University of Zurich E-mail: hut... at pci.uzh.ch
>> Winterthurerstrasse 190
>> CH-8057 Zurich, Switzerland
>> ---------------------------------------------------------------
>>
>> -----cp... at googlegroups.com wrote: -----
>> To: cp... at googlegroups.com
>> From: "albe... at virgilio.it"
>> Sent by: cp... at googlegroups.com
>> Date: 09/05/2012 09:44AM
>> Subject: [CP2K:4010] Energy conservation NVT/NVE simulation
>>
>> Dear all,
>>
>> I'm carrying out some tests to reproduce the VDOS of water and I used as
>> starting points the input files 'H2O-32.inp' and 'H2O-64.inp' in
>> tests/QS/benchmark directory.
>>
>> In both cases I ran a NVT simulation at 300K for 15 ps followed by an NVE
>> simulation on the equilibrated system.
>>
>> I'm puzzled about the results in the energies: in both NVT and NVE the
>> plot of
>> "Cons Qty" show a constant and linear drift while temperature, kinetic
>> and
>> potential energy are equilibrated and stable.
>>
>> Since "Cons Qty" should be conserved and this is not the case I think
>> that
>> there are some problems in the setup of the simulation.
>> I did not modify the parameters of the benchmark inputs but I just added
>> the
>> thermostat section in NVT and I modified only the printing option.
>>
>> Thank you very much for your help and suggestions,
>>
>> Alberto
>>
>>
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>
>
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