restarting NPT MD
Matt W
mattwa... at gmail.com
Tue Oct 17 15:01:04 UTC 2017
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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