[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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