Re: Value for "firsttimestep" when restarting MD

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Thu Jul 02 2009 - 04:05:23 CDT

On Tuesday 05 May 2009 18:05:49 eprates_at_iqm.unicamp.br wrote:
> > Hi all,
> >
> > I have a short question about the "firsttimestep" keyword:
> >
> > If my simulation ran for 10000 steps with a "dcdfreq" of 500, what would
> > I specify for "firsttimestep" to get a trajectory without gap when
> > restarting
> > the simulation?
> >
> > 10000 or 10500?
> >
> > ------------------------------
> > firsttimestep 0
> > restartfreq 500
> > dcdfreq 500
> > xstFreq 500
> > outputEnergies 100
> > outputPressure 100
> >
> > run 10000
> > -------------------------------
> >
>
> If the simulation of 10000 steps ended normally, you have 20 steps
> recorded in the dcd file (10000/500). You have to restart it setting 10000
> as firsttimestep.
> But if the simulation stopped due to an external reason, you have to check
> in the end of the output file if it wrote the current step in the dcd
> file. Otherwise, you have to use 9500 as firsttimestep.
>
> Bests,
> Erica
>

Mmmh, are you sure about that?

I looks wrong to me when I have two output files, one ending with:
-----------------------------------------------------------------------------------
PRESSURE: 101000 -352.132 -198.274 296.808 -198.274 -50.0892 143.841 296.808
143.841 71.0443
GPRESSURE: 101000 -253.52 -152.978 361.241 -152.776 -64.5259 210.32 99.7172
-199.479 28.0411
PRESSAVG: 101000 -46.0969 -16.9593 -56.4544 -16.9593 -78.7821 124.251 -56.4544
124.251 38.5236
GPRESSAVG: 101000 -46.096 -23.5381 -54.1682 -4.71731 -88.2117 124.158 -75.5281
119.876 44.8061
TIMING: 101000 CPU: 10151.3, 0.101193/step Wall: 12770.8, 0.126914/step, 0
hours remaining, 24176 kB of memory in use.
ETITLE: TS BOND ANGLE DIHED IMPRP
ELECT VDW BOUNDARY MISC KINETIC
TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 101000 2820.8155 8467.0260 4618.3233 42.7590
-38973.4919 -1550.6067 0.0000 0.0000 13554.6942
-11020.4806 305.9308 -10890.3705 -10904.2422 303.7045
-110.3922 -96.6684 185098.0880 -28.7851 -29.8339

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 101000
WRITING COORDINATES TO DCD FILE AT STEP 101000
WRITING COORDINATES TO RESTART FILE AT STEP 101000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 101000
FINISHED WRITING RESTART VELOCITIES
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 101000
CLOSING EXTENDED SYSTEM TRAJECTORY FILE
WRITING COORDINATES TO OUTPUT FILE AT STEP 101000
CLOSING COORDINATE DCD FILE
WRITING VELOCITIES TO OUTPUT FILE AT STEP 101000
==========================================
WallClock: 12794.715820 CPUTime: 10174.600586 Memory: 24176 kB
-----------------------------------------------------------------------------------

and the other on starting with:
-----------------------------------------------------------------------------------
[...SniP...]
TCL: Running for 500000 steps
PRESSURE: 101000 -341.103 -193.253 290.413 -193.253 -67.5269 144.635 290.413
144.635 77.1003
GPRESSURE: 101000 -255.589 -148.646 361.366 -148.447 -70.0897 209.335 99.8459
-200.464 27.8261
ETITLE: TS BOND ANGLE DIHED IMPRP
ELECT VDW BOUNDARY MISC KINETIC
TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 101000 2820.8155 8467.0260 4618.3233 42.7590
-38973.5209 -1550.5782 0.0000 0.0000 13552.7937
-11022.3816 305.8879 -10895.6962 -10895.6962 305.8879
-110.5100 -99.2840 185098.1185 -110.5100 -99.2840

ENERGY: 101000 2820.8155 8467.0260 4618.3233 42.7590
-38973.4919 -1550.6067 0.0000 0.0000 13554.6942
-11020.4806 305.9308 -10890.3705 -10904.2422 303.7045
-110.3922 -96.6684 185098.0880 -28.7851 -29.8339

OPENING EXTENDED SYSTEM TRAJECTORY FILE
Info: Initial time: 16 CPUs 0.417786 s/step 2.41774 days/ns 19640 kB memory
LDB: LOAD: AVG 5.03175 MAX 21.0031 MSGS: TOTAL 70 MAXC 7 MAXP 9 None
Info: Adjusted background load on 8 nodes.
LDB: LOAD: AVG 5.55801 MAX 6.18653 MSGS: TOTAL 70 MAXC 7 MAXP 9 Alg7
LDB: LOAD: AVG 5.55801 MAX 5.83152 MSGS: TOTAL 73 MAXC 7 MAXP 10 Alg7
PRESSURE: 101100 -1311.17 37.0522 -198.676 37.0522 -533.071 118.16 -198.676
118.16 282.8
GPRESSURE: 101100 -1211.74 148.615 -161.789 158.327 -597.089 234.329 -310.893
201.087 304.963
PRESSAVG: 101100 114.112 -58.2849 -85.1387 -58.2849 -76.7942 181.721 -85.1387
181.721 -4.79569
GPRESSAVG: 101100 104.659 -40.8439 -74.3317 -67.6216 -68.0336 177.784 -78.5232
199.381 -6.66746
Info: Initial time: 16 CPUs 0.405543 s/step 2.34689 days/ns 24640 kB memory
ENERGY: 101100 2848.1027 8415.6134 4568.7941 43.2275
-39005.4994 -1563.0732 0.0000 0.0000 13512.5405
-11180.2945 304.9794 -11054.9037 -11047.4127 304.4621
-520.4789 -501.2876 185067.3579 10.8407 9.9859
-----------------------------------------------------------------------------------

-----------------------------
restartfreq 500
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100
run 500000
-----------------------------

Shouldn't the second file from the restarted run start with either the exact
same Values for Step 101000 as for the first file or start with Steps +
"outputEnergies/outputPressure/dcdfreq"

It looks odd to me when you have the same timestep and two different sets of
values assigned to it... (as you can see above)

Any ideas? Anyone?

Thanks and kind regards
Bjoern


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