Core-shell model and QM/MM ECOUPL GAUSS are not compatible?

Sergey Chulkov sergeya... at gmail.com
Tue Aug 21 22:02:51 CEST 2018


Hi Zuoheng,

Thank you again for the report. You input file triggers two bugs. The first 
one can be easily fixed with the attached patch and it is due to wrong 
indices when accessing the 'pbc' array. The second bug is a little tricky 
one. When you define shell charge for an atomic kind, all atoms of this 
kind are taken into account, even if some of them are assigned to the QM 
region. For such atoms from the QM region the corresponding entries within 
the list qmmm_env%qm%added_shells remain uninitialised that leads to the 
segmentation fault. If I understand correctly, such atoms should not appear 
in this list at all. As a temporary workaround you can use a distinct 
atomic kind for atoms from the QM region, for example, O_QM for oxygen 
atoms (see the input file attached).

Best wishes,
Sergey

On Tuesday, August 21, 2018 at 4:42:39 PM UTC+1, zuoh... at gmail.com wrote:
>
> Thank you for your response.
> I am using the EWALD_TYPE SPME for MM. It is OK for MM force field. 
> However, I want to combine QM and MM and I have to specifies the type of 
> the QM - MM electrostatic coupling (ECOUPL). This is different from 
> EWALD_TYPE.
>
> Best wishes,
> Zuoheng
>
>
> 在 2018年8月21日星期二 UTC+2下午4:21:35,Sergey Chulkov写道:
>>
>> Thank you for sharing your experience.
>>
>> Core shell model is currently not implemented for the ewald sums. Try to 
>> use a different EWALD_TYPE, for example, SPME.
>>
>> Best wishes,
>>
>> Sergey
>>
>> On Tuesday, August 21, 2018 at 1:39:19 PM UTC+1, zuoh... at gmail.com 
>> wrote:
>>>
>>> Dear CP2Kers,
>>>
>>> I am using core-shell model in MM. I found a Segmentation fault during 
>>> QM/MM simulation with ECOUPL GAUSS. 
>>> I am not sure if it is a bug? or do I have to use ECOUPL NONE? (I am 
>>> using the CP2K of 6.1 version)
>>> The attached file is the input file I used to test this fault. This is 
>>> changed from the test file of CP2K.
>>>
>>> The fault is following:
>>>
>>> Program received signal SIGSEGV: Segmentation fault - invalid memory 
>>> reference.
>>>
>>> Backtrace for this error:
>>> #0  0x7FDD41DCCE08
>>> #1  0x7FDD41DCBF90
>>> #2  0x7FDD412C44AF
>>> #3  0x13180AF in __qmmm_gpw_energy_MOD_qmmm_elec_with_gaussian_lr at 
>>> qmmm_gpw_energy.F:800
>>> #4  0x131A147 in __qmmm_gpw_energy_MOD_qmmm_elec_with_gaussian_low at 
>>> qmmm_gpw_energy.F:503
>>> #5  0x131A645 in __qmmm_gpw_energy_MOD_qmmm_elec_with_gaussian at 
>>> qmmm_gpw_energy.F:310
>>> #6  0x131B643 in __qmmm_gpw_energy_MOD_qmmm_el_coupling at 
>>> qmmm_gpw_energy.F:197
>>> #7  0x9E3635 in __qmmm_force_MOD_qmmm_calc_energy_force at 
>>> qmmm_force.F:160
>>> #8  0x8015AF in __force_env_methods_MOD_force_env_calc_energy_force at 
>>> force_env_methods.F:251
>>> #9  0x5CF918 in __md_run_MOD_qs_mol_dyn_low at md_run.F:371
>>> #10  0x5D095E in __md_run_MOD_qs_mol_dyn at md_run.F:152
>>> #11  0x4EF51E in __cp2k_runs_MOD_cp2k_run at cp2k_runs.F:356
>>> #12  0x4F1D6B in __cp2k_runs_MOD_run_input at cp2k_runs.F:1103
>>> #13  0x4DBB21 in MAIN__ at cp2k.F:281
>>>
>>>
>>> ===================================================================================
>>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>> =   PID 13646 RUNNING AT ubuntu
>>> =   EXIT CODE: 139
>>> =   CLEANING UP REMAINING PROCESSES
>>> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>
>>> ===================================================================================
>>> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault 
>>> (signal 11)
>>> This typically refers to a problem with your application.
>>> Please see the FAQ page for debugging suggestions
>>>
>>>
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