[ase-users] NPTBerendsen()
Vitaly Vitalievich
vvchaban at gmail.com
Sun Oct 27 22:49:27 CET 2024
No, the temperature is as I've set it. I guess the Mopac calculator simply
does not have its "get_stress()" function.
On Sun, Oct 27, 2024 at 11:20 PM Tristan Maxson <tgmaxson at gmail.com> wrote:
> See the temperature column, it is being set wrong.
>
> Thank you,
> Tristan Maxson
>
> On Sun, Oct 27, 2024, 2:06 PM Vitaly Vitalievich <vvchaban at gmail.com>
> wrote:
>
>> 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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