restarting NPT MD
Luca
luca.d... at gmail.com
Thu Oct 19 06:48:26 UTC 2017
HI Matt
Thank you for your efforts. I am going to follow your advice.
Best Regards
Luca
Il giorno martedì 17 ottobre 2017 17:01:04 UTC+2, Matt W ha scritto:
>
> Hi,
>
> it seems to be a problem with the &VELOCITY and &MASS of &BAROSTAT section.
>
> For NPT_I they are single valued. For NPT_F they should be a 3x3 tensor,
> and CP2K dies when it doesn't find the extra elements.
>
> As a hack you could try putting in a diagonal tensor with the isotropic
> element in the correct positions (I guess elements 1,5,9 with fortran
> indices).
>
> This seems to work for me with a fairly up-to-date src.
>
> Matt
>
> On Tuesday, October 17, 2017 at 10:44:50 AM UTC+1, Luca wrote:
>>
>> Hi Matt
>>
>> please find attached the restart file I obtain from i1.inp.
>>
>> Luca
>>
>> Il giorno martedì 17 ottobre 2017 11:37:50 UTC+2, Matt W ha scritto:
>>>
>>> Could you attach the actual restart (feel free to delete coords and
>>> velocities if confidential).
>>>
>>> Can you run an NPT_F (one or two steps fine), restart NPT_I, then
>>> restart NPT_F?
>>>
>>> I guess that some default settings needed for NPT_F must not be properly
>>> set during an NPT_I run, then cause the problem when you restart.
>>>
>>> Matt
>>>
>>> On Tuesday, October 17, 2017 at 10:32:15 AM UTC+1, Luca wrote:
>>>>
>>>> Dear Matt and Marcella
>>>>
>>>> I tried almost every kind of combination of the keywords in the
>>>> external restart section. However, cp2k always complains if I try to
>>>> restart an NPT_F from a NPT_I.
>>>> I have attached 2 inputs which give similar errors. i1.inp is the
>>>> initial NPT_I run and i2.inp is the restart.
>>>> If you find my mistake please let me know...
>>>>
>>>> Luca
>>>> Best Wishes.
>>>> Luca
>>>>
>>>>
>>>> Il giorno martedì 17 ottobre 2017 09:38:17 UTC+2, Marcella Iannuzzi ha
>>>> scritto:
>>>>>
>>>>> Dear Luca,
>>>>>
>>>>> you can leave RESTART DEFAULTS F, and select what exactly has to be
>>>>> restarted with the specific keywords.
>>>>> In a NPT run, for sure the CELL.
>>>>> If the problem you have now is related to some constraints that need
>>>>> to be released, you can try with RESTART_CONSTRAINTS F
>>>>> Hope this help.
>>>>> Kind regards
>>>>> Marcella
>>>>>
>>>>>
>>>>> On Monday, October 16, 2017 at 10:08:57 PM UTC+2, Luca wrote:
>>>>>>
>>>>>> Dear Marcella
>>>>>>
>>>>>> thank you for your answer. Putting RESTART DEFAULTS T fixes the
>>>>>> oscillation in the average pressure.
>>>>>> However, I am still not able to restart an NPT_F from the NPT_I. I
>>>>>> also added the key RESTART_CELL T,
>>>>>> but just after the first scf -loop I get the error
>>>>>>
>>>>>> MD_ENERGIES| Initialization proceeding
>>>>>>
>>>>>> ******************************** GO CP2K GO!
>>>>>> **********************************
>>>>>> INITIAL POTENTIAL ENERGY[hartree] =
>>>>>> -0.220770726164E+04
>>>>>> INITIAL KINETIC ENERGY[hartree] =
>>>>>> 0.403768735935E+00
>>>>>> INITIAL TEMPERATURE[K] =
>>>>>> 284.281
>>>>>> INITIAL BAROSTAT TEMP[K] =
>>>>>> 0.482402310612E+02
>>>>>> INITIAL PRESSURE[bar] =
>>>>>> -0.416980916246E+04
>>>>>> INITIAL VOLUME[bohr^3] =
>>>>>> 0.223680134131E+05
>>>>>> INITIAL CELL LNTHS[bohr] = 0.2817577E+02 0.2817577E+02
>>>>>> 0.2817577E+02
>>>>>> INITIAL CELL ANGLS[deg] = 0.9000000E+02 0.9000000E+02
>>>>>> 0.9000000E+02
>>>>>> ******************************** GO CP2K GO!
>>>>>> **********************************
>>>>>>
>>>>>>
>>>>>> *******************************************************************************
>>>>>> * ___
>>>>>> *
>>>>>> * / \
>>>>>> *
>>>>>> * [ABORT]
>>>>>> *
>>>>>> * \___/ Error in diagonalisation
>>>>>> *
>>>>>> * |
>>>>>> *
>>>>>> * O/|
>>>>>> *
>>>>>> * /| |
>>>>>> *
>>>>>> * / \
>>>>>> common/eigenvalueproblems.F:88 *
>>>>>>
>>>>>> *******************************************************************************
>>>>>>
>>>>>> which is a bit odd considering that I use the OT algorithm.
>>>>>> I also tried the restart by reducing the time step from 0.5 to 0.1 fs
>>>>>> but I always get the same error.
>>>>>> If I leave the keyword NPT_I in my input everything goes fine.
>>>>>> Any ideas...?
>>>>>>
>>>>>> Best Regards
>>>>>> Luca
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ===== Routine Calling Stack =====
>>>>>>
>>>>>> 3 velocity_verlet
>>>>>> 2 qs_mol_dyn_low
>>>>>> 1 CP2K
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Il giorno lunedì 16 ottobre 2017 09:49:41 UTC+2, Marcella Iannuzzi ha
>>>>>> scritto:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Hi Luca,
>>>>>>>
>>>>>>> you have set RESTART DEFAULTS as False, hence it is probably not
>>>>>>> restarting the CELL.
>>>>>>> I may want to restart it as well.
>>>>>>>
>>>>>>> Kind regards,
>>>>>>> Marcella
>>>>>>>
>>>>>>>
>>>>>>> On Sunday, October 15, 2017 at 7:58:17 PM UTC+2, Luca wrote:
>>>>>>>>
>>>>>>>> Dear all
>>>>>>>> I tried to restart an NPT simulation by putting in my input file
>>>>>>>> the following section:
>>>>>>>>
>>>>>>>> &EXT_RESTART ON
>>>>>>>> RESTART_DEFAULT F
>>>>>>>> RESTART_FILE_NAME myjob-1.restart
>>>>>>>> RESTART_POS T
>>>>>>>> RESTART_COUNTERS T
>>>>>>>> RESTART_VEL T
>>>>>>>> RESTART_THERMOSTAT T
>>>>>>>> RESTART_BAROSTAT T
>>>>>>>> RESTART_BAROSTAT_THERMOSTAT T
>>>>>>>> &END EXT_RESTART
>>>>>>>>
>>>>>>>> Notwithstanding the restart section, I get strong oscillation in
>>>>>>>> the average pressure at the beginning of the restarted simulation (please
>>>>>>>> see the attached).
>>>>>>>> On the contrary, the temperature and the potential energy do not
>>>>>>>> show (as expected) jumps. Could someone point out whether I am missing
>>>>>>>> something in the restart section?
>>>>>>>> The simulation is an NPT_I simulation. I have also found the
>>>>>>>> calculation crashes at the first iteration if I try a restart by changing
>>>>>>>> NPT_I with NPT_F. Is this normal?
>>>>>>>> Do I have to add something else in the restart section?
>>>>>>>>
>>>>>>>> Luca
>>>>>>>>
>>>>>>>
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