[ase-users] NPTBerendsen()
Vitaly Vitalievich
vvchaban at gmail.com
Sun Oct 27 22:06:18 CET 2024
Dear Tristan -
The EMT() calculator does work.
Time[ps] Etot[eV] Epot[eV] Ekin[eV] T[K]
0.0000 225.0608 205.4279 19.6329 2373.2
0.0010 224.5121 205.4400 19.0721 2305.4
0.0020 224.5179 205.4400 19.0779 2306.1
0.0030 224.5236 205.4400 19.0836 2306.8
0.0040 224.5293 205.4400 19.0893 2307.5
0.0050 224.5351 205.4400 19.0951 2308.2
0.0060 224.5408 205.4400 19.1008 2308.9
0.0070 224.5465 205.4400 19.1065 2309.6
0.0080 224.5522 205.4400 19.1122 2310.3
0.0090 224.5579 205.4400 19.1179 2311.0
0.0100 224.5636 205.4400 19.1236 2311.7
0.0110 224.5693 205.4400 19.1293 2312.4
0.0120 224.5750 205.4400 19.1350 2313.0
0.0130 224.5807 205.4400 19.1407 2313.7
0.0140 224.5864 205.4400 19.1464 2314.4
0.0150 224.5920 205.4400 19.1520 2315.1
0.0160 224.5977 205.4400 19.1577 2315.8
0.0170 224.6034 205.4400 19.1634 2316.5
0.0180 224.6090 205.4400 19.1690 2317.2
0.0190 224.6147 205.4400 19.1747 2317.8
0.0200 224.6203 205.4400 19.1803 2318.5
0.0210 224.6260 205.4400 19.1860 2319.2
0.0220 224.6316 205.4400 19.1916 2319.9
0.0230 224.6372 205.4400 19.1972 2320.6
0.0240 224.6428 205.4400 19.2028 2321.2
0.0250 224.6484 205.4400 19.2084 2321.9
0.0260 224.6541 205.4400 19.2141 2322.6
0.0270 224.6597 205.4400 19.2197 2323.3
0.0280 224.6653 205.4400 19.2253 2324.0
The same system using the MOPAC() calculator does not work, see the
screenshot.
[image: image.png]
Thanks, Vitaly
On Sun, Oct 27, 2024 at 8:36 PM Tristan Maxson <tgmaxson at gmail.com> wrote:
> I think we would need a much more complete input to help. This could be
> an error in the calculator instead for example. I do know the NPTBerendsen
> should work more or less with your input. Please confirm an EMT run of
> metal with those parameters works.
>
> Thank you,
> Tristan Maxson
>
> On Sun, Oct 27, 2024, 11:30 AM Vitaly Vitalievich <vvchaban at gmail.com>
> wrote:
>
>> Right, regarding T. But the problem looks to be deeper. Below is what I
>> found. The simulation started correctly but after the first NPT step the
>> cell size got to (0,0,0).
>>
>> MOPAC Job: "vvc.mop" ended normally on Oct 27, 2024, at 20:23.
>> MOPAC Job: "vvc.mop" ended normally on Oct 27, 2024, at 20:23.
>> *Cell([10.0, 10.0, 10.0])*
>> Error in the loop occurred. Probably the SCF procedure did not converge.
>> Continuing to the next configuration.
>> *Cell([0.0, 0.0, 0.0])*
>> Error in the loop occurred. Probably the SCF procedure did not converge.
>> Continuing to the next configuration.
>> Cell([0.0, 0.0, 0.0])
>> Error in the loop occurred. Probably the SCF procedure did not converge.
>> Continuing to the next configuration.
>>
>>
>> Also, the logfile -
>> Time[ps] Etot[eV] Epot[eV] Ekin[eV] T[K]
>> 0.0000 15.4172 15.4048 0.0123 1.0
>> Time[ps] Etot[eV] Epot[eV] Ekin[eV] T[K]
>> 0.0000 15.4178 15.4048 0.0130 1.1
>> Time[ps] Etot[eV] Epot[eV] Ekin[eV] T[K]
>> 0.0000 15.4166 15.4048 0.0117 1.0
>> Time[ps] Etot[eV] Epot[eV] Ekin[eV] T[K]
>> 0.0000 15.4158 15.4048 0.0109 0.9
>>
>>
>>
>>
>>
>> On Sun, Oct 27, 2024 at 5:59 PM Tristan Maxson <tgmaxson at gmail.com>
>> wrote:
>>
>>> What does the log file say? I believe you should set temperature as
>>> temperature_K=400, there may be a unit mismatch.
>>>
>>> On Sun, Oct 27, 2024, 7:26 AM Vitaly Vitalievich <vvchaban at gmail.com>
>>> wrote:
>>>
>>>> MD = NPTBerendsen(SYSTEM, 1 * units.fs, 400 * units.K, pressure=1 *
>>>> units.bar, taut=100*units.fs, taup=1000*units.fs,
>>>> compressibility=5e-5/units.bar)
>>>>
>>>> The execution terminates after the first time step due to the SCF
>>>> convergence error. However, the first SCF does converge.
>>>>
>>>>
>>>>
>>>>
>>>> On Sun, Oct 27, 2024 at 4:04 PM Tristan Maxson <tgmaxson at gmail.com>
>>>> wrote:
>>>>
>>>>> Please supply a minimum failing example for us to look at for you.
>>>>>
>>>>> Thank you,
>>>>> Tristan Maxson
>>>>>
>>>>> On Sun, Oct 27, 2024, 4:37 AM Vitaly Vitalievich via ase-users <
>>>>> ase-users at listserv.fysik.dtu.dk> wrote:
>>>>>
>>>>>> I would like to reiterate my request, please.
>>>>>>
>>>>>> The NPT() function of ASE appears to exhibit the same type of
>>>>>> misbehavior.
>>>>>>
>>>>>> Thank you for your attention to this matter.
>>>>>>
>>>>>>
>>>>>> On Sun, Oct 20, 2024 at 10:09 AM Vitaly Vitalievich <
>>>>>> vvchaban at gmail.com> wrote:
>>>>>>
>>>>>>> Dear All -
>>>>>>>
>>>>>>> I would greatly appreciate getting an example of using
>>>>>>>
>>>>>>> NPTBerendsen()
>>>>>>>
>>>>>>> function, say, for a liquid water system, dt = 1fs. I have some
>>>>>>> misunderstanding with the input constants / units ending with bad geometry.
>>>>>>>
>>>>>>> Cheers, Vitaly
>>>>>>>
>>>>>>> _______________________________________________
>>>>>> ase-users mailing list
>>>>>> ase-users at listserv.fysik.dtu.dk
>>>>>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>>>>>>
>>>>>
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