[CP2K:4045] Re: Energy conservation NVT/NVE simulation

Matt W MattWa... at gmail.com
Mon Sep 24 15:00:18 UTC 2012


Hi,

Taking the H2O-32_SPME.inp file and reducing the timestep to 2 fs I get no 
drift with NVT.

In NVE there is still a little drift, but decreasing the SHAKE tolerance to 
1.0E-07 this seems to be removed (see attached, changed the SHAKE tolerance 
at ~2.1 ns.

In all cases the drift seems to be smaller than being reported, I think. 
Which version did you use? Mine is serial compiled under cygwin with 
internal FFTSG.

 "CP2K| version string: CP2K version 2.2.356 (Development Version)
CP2K| is freely available from http://cp2k.berlios.de/
CP2K| Program compiled at Tue Sep 27 14:10:08 GMTDT 2011
CP2K| Program compiled on palliata
 CP2K| Program compiled for Cygwin-i686-gfortran"

Matt

On Monday, September 24, 2012 9:36:07 AM UTC+1, jgh wrote:
>
> Hi 
>
> my guess is that you can get better results by tuning the Ewald 
> parameters. 
> I see the following sources of errors that can lead to drifts. 
> 1) the cutoff for the LJ potential (there is no smoothing at the cutoff 
> used) 
> 2) An inadequate combination of length cutoff (real space), alpha 
>    and grid cutoff 
> 3) timestep 
>
> In CP2K the two cutoff in 1) and 2) are the same. A rule of thumb 
> says alpha*rc should be at least 7 (0.5*11.4=5.7 in your case). 
>
> To get better conservation of energy I would: 
>
> - shorten the timestep (2fs probably) 
> - increase the LJ cutoff (14) 
> - increase alpha (1.) and the grid cutoff (more points) 
>   Warning: the grid cutoff is given as number of points, if you 
>   go to bigger systems you have to scale the number of points with 
>   the box size. 
>
> I don't do long time simulations with classical force fields, 
> so the values above are only guesses. 
>
> 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<javascript:> 
> Winterthurerstrasse 190 
> CH-8057 Zurich, Switzerland 
> --------------------------------------------------------------- 
>
> -----cp... at googlegroups.com <javascript:> wrote: ----- 
> To: cp... at googlegroups.com <javascript:> 
> From: paolo nicolini 
> Sent by: cp... at googlegroups.com <javascript:> 
> Date: 09/21/2012 05:45PM 
> Subject: Re: [CP2K:4045] Re: Energy conservation NVT/NVE simulation 
>
> Hi 
>
> I tried to use the H2O-32_SPME.inp in the tests/Fist directory by changing 
> only the length of the simulation (1 ns) and I got also a significant 
> energy drift (see attachment). Then I tried to reduce the integration time 
> step to 1.0 fs. The drift become lower but it do not vanish. I did also 1ns 
> of NVE dynamics (starting from the last restart of the previous 
> simulations) and here the drift become even more clear. 
> The inputs that I used are below. 
> Best regards 
> Paolo 
>
> NVT input: 
> &FORCE_EVAL 
>   METHOD FIST 
>   &MM 
>     &FORCEFIELD 
>       &BEND 
>         ATOMS H O H 
>         K 0. 
>         THETA0 1.8 
>       &END BEND 
>       &BOND 
>         ATOMS O H 
>         K 0. 
>         R0 1.8 
>       &END BOND 
>       &CHARGE 
>         ATOM O 
>         CHARGE -0.8476 
>       &END CHARGE 
>       &CHARGE 
>         ATOM H 
>         CHARGE 0.4238 
>       &END CHARGE 
>       &NONBONDED 
>         &LENNARD-JONES 
>           atoms O O 
>           EPSILON 78.198 
>           SIGMA 3.166 
>           RCUT 11.4 
>         &END LENNARD-JONES 
>         &LENNARD-JONES 
>           atoms O H 
>           EPSILON 0.0 
>           SIGMA 3.6705 
>           RCUT 11.4 
>         &END LENNARD-JONES 
>         &LENNARD-JONES 
>           atoms H H 
>           EPSILON 0.0 
>           SIGMA 3.30523 
>           RCUT 11.4 
>         &END LENNARD-JONES 
>       &END NONBONDED 
>     &END FORCEFIELD 
>     &POISSON 
>       &EWALD 
>         EWALD_TYPE spme 
>         ALPHA .5 
>         GMAX 21 
>         O_SPLINE 6 
>       &END EWALD 
>     &END POISSON 
>   &END MM 
>   &SUBSYS 
>     &CELL 
>       ABC 9.865 9.865 9.865 
>     &END CELL 
>     &COORD 
>     O                  -4.583   5.333   1.560   H2O 
>     H                  -3.777   5.331   0.943   H2O 
>     H                  -5.081   4.589   1.176   H2O 
> ... 
>     &END COORD 
>   &END SUBSYS 
> &END FORCE_EVAL 
> &GLOBAL 
>   PROJECT H2O 
>   RUN_TYPE MD 
> &END GLOBAL 
> &MOTION 
>   &CONSTRAINT 
>     &G3X3 
>       DISTANCES 1.8897268 1.8897268 3.0859239 
>       MOLECULE 1 
>       ATOMS 1 2 3 
>     &END G3X3 
>   &END CONSTRAINT 
>   &MD 
>     ENSEMBLE NVT 
>     STEPS 1000000 
>     TIMESTEP 1.0 
>     TEMPERATURE 300.0 
>     &THERMOSTAT 
>       REGION MOLECULE 
>       &NOSE 
>         LENGTH 3 
>         YOSHIDA 3 
>         TIMECON 1000 
>         MTS 2 
>       &END NOSE 
>     &END 
>   &END MD 
> &END MOTION 
>
> NVE input: 
> &FORCE_EVAL 
>   METHOD FIST 
>   &MM 
>     &FORCEFIELD 
>       &BEND 
>         ATOMS H O H 
>         K 0. 
>         THETA0 1.8 
>       &END BEND 
>       &BOND 
>         ATOMS O H 
>         K 0. 
>         R0 1.8 
>       &END BOND 
>       &CHARGE 
>         ATOM O 
>         CHARGE -0.8476 
>       &END CHARGE 
>       &CHARGE 
>         ATOM H 
>         CHARGE 0.4238 
>       &END CHARGE 
>       &NONBONDED 
>         &LENNARD-JONES 
>           atoms O O 
>           EPSILON 78.198 
>           SIGMA 3.166 
>           RCUT 11.4 
>         &END LENNARD-JONES 
>         &LENNARD-JONES 
>           atoms O H 
>           EPSILON 0.0 
>           SIGMA 3.6705 
>           RCUT 11.4 
>         &END LENNARD-JONES 
>         &LENNARD-JONES 
>           atoms H H 
>           EPSILON 0.0 
>           SIGMA 3.30523 
>           RCUT 11.4 
>         &END LENNARD-JONES 
>       &END NONBONDED 
>     &END FORCEFIELD 
>     &POISSON 
>       &EWALD 
>         EWALD_TYPE spme 
>         ALPHA .5 
>         GMAX 21 
>         O_SPLINE 6 
>       &END EWALD 
>     &END POISSON 
>   &END MM 
> &END FORCE_EVAL 
> &GLOBAL 
>   PROJECT H2O 
>   RUN_TYPE MD 
> &END GLOBAL 
> &MOTION 
>   &CONSTRAINT 
>     &G3X3 
>       DISTANCES 1.8897268 1.8897268 3.0859239 
>       MOLECULE 1 
>       ATOMS 1 2 3 
>     &END G3X3 
>   &END CONSTRAINT 
>   &MD 
>     ENSEMBLE NVE 
>     STEPS 1000000 
>     TIMESTEP 1.0 
>     TEMPERATURE 300.0 
>   &END MD 
> &END MOTION 
> &EXT_RESTART 
>   RESTART_FILE_NAME H2O-1_1000000.restart 
> &END EXT_RESTART 
>
>
>
> On Monday, September 17, 2012 1:09:54 PM UTC+2, jgh wrote:Hi 
>   
> I did some tests with the inputs from 
> ../tests/Fist 
> and get much better energy conservation that you show. 
> Probably your input use a not optimal setting for the 
> cutoffs and Ewald parameters (I was using SPME). 
>   
> 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: marco masia   
> Sent by: cp... at googlegroups.com 
> Date: 09/12/2012 03:39PM 
> Subject: [CP2K:4029] Re: Energy conservation NVT/NVE simulation 
>   
> Dear all, 
>   
> recently I have noticed the same problem with FIST simulations. I took the 
> H2O-32_ewald.inp input, equilibrated it for 1 ns and run a 1ns NVE 
> simulation from the thermalized configuration. I have tried to refine many 
> simulation parameters (e.g. time step, RCUT, Ewald pars) and also (thinking 
> that there was a bad implementation of constraints) I run the simulations 
> for a flexible model. I always get a non-negligible drift (see attachment); 
> the graph shows block averaged energies of 1 ns simulations performed with 
> cp2k and obeli.x (a program of mine). The values are shifted for a better 
> comparison. I have been looking into this, thinking that the problem was in 
> the input file...but since other people are experiencing it with QS, I 
> wonder if there is some bug in the velocity verlet routines. The results 
> are platform independent (I tried both on mac and linux). 
>   
> best 
>   
> marco 
>   
> On Wednesday, September 5, 2012 3:32:26 AM UTC-4, alber... at virgilio.itwrote: 
> 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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>   
>   
> [attachment "energy-conservation.pdf" removed by Jürg Hutter/at/UZH]   
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>
> [attachment "all.pdf" removed by Jürg Hutter/at/UZH]

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