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

zuohen... at gmail.com zuohen... at gmail.com
Wed Aug 22 14:56:51 CEST 2018


Hi, Sergey,

In my opinion, your suggestions are reasonable. I will try to change my 
input file according your advice.
Thank you very much.

Best wishes,

Zuoheng

在 2018年8月21日星期二 UTC+2下午10:02:52,Sergey Chulkov写道:
>
> 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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