[CPMD-list] How to rerun the same job for statistical purpose?
Archilles
archilles02 at gmail.com
Thu Dec 9 17:13:54 CET 2004
Thank you all for your help.
After reading all the replies, I think I have the following options to
do what I want:
1) Run a certain LONG time, I will get good enough statistical
simulation results
2) Change the default random number generator DURAND to a different
one, then recompile the CPMD code.
3) Use RANDOMIZE COORDINATES combined with QUENCH BO keywords to
randomize the optimized initial position
Since I am interested in selectivity of epoxide ring openning (two
possible positions), once the ring openned, I cannot afford to run it
until the reaction reverse and happen again: it take about 80 hours to
see the ring openning, and even after 200 hours running the system
remained as product. Here I would like to try RANDOMIZE COORDINATES
with QUENCH BO method.
Here is the input file I am using. With "# New Line", it means I just
added these lines.
Thanks again for all of you.
Best regards,
Peng
&CPMD
MOLECULAR DYNAMICS CP
RESTART WAVEFUNCTION COORDINATES LATEST
RANDOMIZE COORDINATES #New Line
0.03 #New Line
QUENCH BO #New Line
TEMPERATURE
401.0
NOSE IONS MASSIVE
300.0 2500.0
NOSE ELECTRONS
0.02 10000.0
TRAJECTORY SAMPLE
10
TIMESTEP
4.0
EMASS
600.0
STORE
1000
&END
&SYSTEM
ANGSTROM
SYMMETRY
0
CHARGE
0.0
CELL
15.0 1.0 1.0 0.0 0.0 0.0
CUTOFF
70.0
&END
&DFT
NEWCODE
FUNCTIONAL BLYP
GC-CUTOFF
5.0E-06
&END
&ATOMS
*C_SG_BLYP
LMAX=P
22
-6.9130 1.3380 -1.9970
-5.7840 2.2900 -1.5960
-6.9190 3.7400 0.0690
-7.3940 5.1700 0.3920
-8.4160 5.5820 -0.6650
-6.2570 6.2120 0.5080
-6.7610 7.5060 1.1690
-5.6270 8.5220 1.3030
-5.0740 8.8240 -0.0890
-7.6830 1.9180 -3.1830
-8.2440 3.2810 -2.7830
-7.1100 4.2350 -2.3700
-7.6660 5.6270 -1.9930
-6.5990 6.7350 -1.9070
-4.5670 7.5340 -0.7380
-3.9110 5.5590 -4.9450
-2.1500 4.7170 -3.5660
-1.3830 6.0130 -3.3180
-0.6140 5.7760 -1.8780
-1.0240 4.3720 -1.4430
-1.5720 4.3780 -0.0050
2.3010 5.2530 -4.7730
*O_SG_BLYP
LMAX=P
4
-3.5560 4.9740 -3.6850
-1.6790 6.5400 -2.1270
-2.0690 3.9290 -2.3520
1.2320 5.0660 -3.9860
*N_SG_BLYP
LMAX=P
3
-6.2870 3.6510 -1.2740
-5.6240 6.4910 -0.8120
-2.6290 3.3550 0.1640
*Li_SG_BLYP
LMAX=P
1
-4.0840 4.6790 -1.3450
*H_SG_BLYP
LMAX=S
40
-5.2530 1.8710 -0.7400
-5.0860 2.3580 -2.4320
-6.2030 3.4310 0.8320
-7.7790 3.0730 0.1250
-7.9050 5.1240 1.3560
-8.8470 6.5570 -0.4430
-9.2360 4.8660 -0.6940
-5.4970 5.7960 1.1700
-7.1450 7.2790 2.1650
-7.5590 7.9680 0.5910
-6.0100 9.4400 1.7510
-4.8380 8.1180 1.9390
-5.8470 9.2870 -0.7030
-4.2450 9.5270 0.0040
-6.4860 0.3770 -2.2880
-7.5920 1.1710 -1.1600
-7.0190 2.0260 -4.0420
-8.5020 1.2490 -3.4490
-8.7790 3.7010 -3.6360
-8.9550 3.1290 -1.9730
-6.4720 4.3620 -3.2450
-8.3720 5.9270 -2.7700
-7.1080 7.6870 -1.7520
-6.0730 6.7870 -2.8610
-4.1900 7.7630 -1.7360
-3.7380 7.1600 -0.1370
-3.4340 6.5330 -5.0640
-4.9920 5.6920 -4.9880
-3.6080 4.9060 -5.7650
-1.7440 4.1560 -4.4180
-0.9720 6.5860 -4.1590
0.3790 6.1700 -1.6240
-0.1740 3.6820 -1.5260
-1.9880 5.3560 0.2410
-0.7480 4.1770 0.6830
-2.7600 3.2050 1.1620
-2.2520 2.4810 -0.1980
3.3160 5.1330 -4.2670
2.3840 6.2830 -5.2580
2.3850 4.5490 -5.6690
&END
On Thu, 9 Dec 2004 10:53:32 +0100, Alessandro Curioni
<cur at zurich.ibm.com> wrote:
>
>
> Some clarifications:
>
> -the first time you start an MD after a wfn optimization you have
> positions assigned but not velocities - the velocity are assigned
> randomly using a Maxwell distribution for the ions for a temperature T -
> the seed for this depends on timec() so you will get different velocity
> distributions for different runs - Of course this is not true if you
> start your dynamics with T=0 - all the initial velocities will be zero -
> and you will have identical dynamics (divergences only on very long
> runs)- small changes of the temperature (1K) (this dipends however on
> the temperature control chosen) could remain hidden for many steps since
> the coupled electrons-ions system has a finite relaxation time.
> Moreover - if you want to have independent trajectories to calculate
> ensemble averages - you can create them using the randomize coordinates
> keyword (see manual) followed by a quench bo (see manual) - without having
> to randomize the initial coordinates by hand.
>
> Ciao.
>
> Alessandro CURIONI, PhD
> Research Staff Member
> Computational Biochemistry and Material Science group
> IBM Research Division - Zurich Research Laboratory
> Saumerstrasse 4
> 8003 Rueschlikon - Switzerland
> e-mail: cur at zurich.ibm.com
> www: www.zurich.ibm.com
> Tel: +41-1-7248633
> Fax: +41-1-7248958
>
> Axel Kohlmeyer
> <axel.kohlmeyer at t
> heochem.ruhr-uni- To
> bochum.de> Archilles <archilles02 at gmail.com>,
> Sent by: <cpmd-list at cpmd.org>
> cpmd-list-bounces cc
> @cpmd.org
> Subject
> Re: [CPMD-list] How to rerun the
> 12/08/2004 06:36 same job for statistical purpose?
> PM
>
>
>
>
> On Wed, 8 Dec 2004, Archilles wrote:
>
> dear peng,
>
> AP> Dear all,
> AP>
> AP>
> AP> I tried to rerun the same CPMD simulation job several times to obtain
> AP> statistical sense of multiple simulations. By "the same CPMD
> AP> simulation job ", I mean the identical input file. But what I got is
> AP> the identical output files.
>
> well, if you start every time from the same coordinates and
> electron structure (i.e. the same RESTART file), you should get
> the same trajectory for quite a while until some numerical
> noise kicks in and the trajectories will gradually diverge.
>
> if you use the restart written at the end of each simulation
> to start the next run, there should be differences.
>
> AP> After changing the temperature by 1 K, each step KS energy remains the
> AP> same with two different runs.
>
> that depends on what kind of thermostatting you use.
> with TEMPCONTROL IONS for example, the change by 1K will
> only affect the simulation, if the instantaneous temperature
> with be outside of the given bounds.
>
> it may be helpful, if you'd post your input (or at least the
> part up to the coordinates section, if you have a large system).
>
> AP> The trajectory also remains the same for two runs.
> AP>
> AP> What I expected is that each run are simillar, but quite different
> AP> from each other. Maybe each run the program use the same random seed
> AP> to start the simulation, which leads to the same results. Is there any
>
> why a random seed? you are doing molecular dynamics, in which the
> new positions are determined from the old positions of the atoms
> and the forces on them.
>
> AP> way to change it each time? Therefore, I can run the same job more
> AP> than once, and get different results to inspect the statistical
> AP> properties of the system.
>
> due to ergodicity hypothesis, you only have to run the MD long
> enough to sample phase space, povided you are in equilibrium,
> and the average over them. of course you could also use different
> starting coordinates and thus have independent trajectories, but
> those you'd have to create yourself.
>
> regards,
> axel kohlmeyer.
>
> AP>
> AP> Thank you very much.
> AP>
> AP> Peng
> AP> _______________________________________________
> AP> CPMD-list mailing list
> AP> CPMD-list at cpmd.org
> AP> http://cpmd.org/mailman/listinfo/cpmd-list
> AP>
> AP>
>
> --
>
> =======================================================================
> Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de
> Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
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