Nonperiodic Poisson solvers

[Jadzia]

Hi Matt, 

thank you very much for answering a part of my questions (despite your 12 
hour flight), really appreciate it. 

Best wishes,
Jadzia




On Saturday, September 30, 2017 at 10:26:49 PM UTC+2, Matt W wrote:
>
> Hi,
>
> I'm a zombie after 12 hours on a plane, so may contain mistakes:
>
> On Wednesday, September 27, 2017 at 5:29:47 PM UTC+4, Jadzia wrote:
>>
>> Hi everyone, 
>>
>> I am trying to simulate a system with an isolated molecule, therefore I 
>> need a non-periodic setup. I have read the previous posts about the topic, 
>> but there are a number of questions open. They are both for the wavelet and 
>> the MT Poisson solver. 
>>
>> *1) System size*
>> My simulations will be quite long (both MM and QM) and due to the 
>> movement of the molecule, to my understanding it needs to be avoided that 
>> the molecule leaves the box. Will it be fine if I set the box size to 1000 
>> Angstrom for security reasons or is this not recommended? 
>>
>> Definitely not fine for QM, because you will run out of memory - we store 
> densities etc on grids that grow with the volume of the system. MM you 
> could be OK if totally non-periodic.
>  
>
>> *2) Periodic cells*
>> This question is closely related to question 1). If I set the Poisson 
>> solver to non-periodic, could one set the CELL to periodic, and thus solve 
>> the problem that the molecule leaves the box?
>>
>> This would work for MM, I think. I suspect that MT doesn't care where the 
> molecule is in the box, but haven't every tried it.
>  
>
>> *3) Ewald methods*
>> Also closely related to question 1). If I set the box size to 1000, even 
>> with Ewald as Poisson solver the system should be effectively non-periodic 
>> due to the large distance, right? Would this be a plausible alternative to 
>> the MT or wavelet solvers?
>>
>> Yes, at least for neutral systems, but it would be extremely expensive.
>  
>
>> *4) Mixed force evaluations*
>> In the case that I have a mixed force evaluation setup and use the 
>> Wavelet solver (see the config file below), do I need to include the 
>> &CENTER_COORDINATES section also in the mixed force eval section, or only 
>> in the real force evaluation section?
>>
>> No idea. Test _very_ carefully.
>  
>
>> *5) MT solver for periodic systems*
>> Is the MT solver only for nonperiodic systems in CP2K, or does it also 
>> work for periodic systems? In the publication it is at least written it 
>> works for periodic systems and even with ewald/spme. 
>>
>> Don't know, try it. 
>  
> Matt
>
> Looking forward to hearing from you.
>>
>> Best wishes,
>> Jadzia
>>
>>
>> &GLOBAL
>>   PROJECT system
>>   RUN_TYPE md
>>   PRINT_LEVEL medium
>> &END global
>>
>> &MOTION
>>   &MD
>>     ENSEMBLE langevin
>>     &LANGEVIN 
>>       GAMMA [fs^-1] 1.0E-3                        # "Langevin" gamma 
>> (adapt for your system) 
>>     &END LANGEVIN
>>     STEPS 5000000
>>     TIMESTEP 0.5
>>     TEMPERATURE 300.0
>>   &END MD  
>> &END MOTION
>>
>> &MULTIPLE_FORCE_EVALS
>>    FORCE_EVAL_ORDER 2 3
>>    MULTIPLE_SUBSYS true
>> &END
>>
>> &FORCE_EVAL
>>   STRESS_TENSOR analytical
>>   METHOD mixed
>>   &MIXED
>>     MIXING_TYPE genmix
>>     &GENERIC
>>       VARIABLES a b
>>       MIXING_FUNCTION a+b
>>     &END
>>     @include cp2k.in.mapping
>>   &END
>>   &SUBSYS
>>     &TOPOLOGY
>>       &CENTER_COORDINATES 
>>       &END 
>>       CONNECTIVITY off
>>       COORDINATE pdb
>>       COORD_FILE_NAME system.pdb
>>     &END TOPOLOGY
>>     &CELL
>>       PERIODIC NONE
>>       ABC 20 20 20 
>>     &END CELL
>>   &END SUBSYS
>> &END FORCE_EVAL
>>
>> &FORCE_EVAL
>>   STRESS_TENSOR analytical
>>   METHOD fist
>>   &MM
>>     &FORCEFIELD
>>       PARM_FILE_NAME system1.prm
>>       PARMTYPE chm
>>       &SPLINE
>>         EMAX_SPLINE 100000
>>         RCUT_NB 12.
>>       &END
>>     &END FORCEFIELD    
>>     &POISSON
>>       POISSON_SOLVER WAVELET
>>       PERIODIC NONE
>>       &EWALD 
>>         EWALD_TYPE NONE 
>>       &END EWALD 
>>     &END POISSON
>>   &END MM
>>   &SUBSYS
>>     &CELL
>>       PERIODIC NONE
>>       ABC 20 20 20
>>     &END CELL
>>     &TOPOLOGY
>>       &CENTER_COORDINATES 
>>       &END 
>>       COORDINATE pdb
>>       COORD_FILE_NAME system1.pdb
>>       CONN_FILE_FORMAT psf
>>       CONN_FILE_NAME system1.psf
>>     &END TOPOLOGY
>>   &END SUBSYS
>> &END FORCE_EVAL
>>
>> &FORCE_EVAL
>>   STRESS_TENSOR analytical
>>   METHOD fist
>>   &MM
>>     &FORCEFIELD
>>       PARM_FILE_NAME system2.prm
>>       PARMTYPE chm
>>       &SPLINE
>>         EMAX_SPLINE 100000
>>         RCUT_NB 12.
>>       &END
>>     &END FORCEFIELD    
>>     &POISSON
>>       POISSON_SOLVER WAVELET
>>       PERIODIC NONE
>>       &EWALD 
>>         EWALD_TYPE NONE 
>>       &END EWALD 
>>     &END POISSON
>>   &END MM
>>   &SUBSYS
>>     &CELL
>>       PERIODIC NONE
>>       ABC 20 20 20
>>     &END CELL
>>     &TOPOLOGY
>>       &CENTER_COORDINATES 
>>       &END 
>>       COORDINATE pdb
>>       COORD_FILE_NAME system2.pdb
>>       CONN_FILE_FORMAT psf
>>       CONN_FILE_NAME system2.psf
>>     &END TOPOLOGY
>>   &END SUBSYS
>> &END FORCE_EVAL
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20171001/36f70fa4/attachment.htm>