[CP2K:5389] CUTTOFF and REL_CUTTOFF for large molecular system

Tobias Kraemer 161brun... at gmail.com
Thu Jun 12 07:31:49 UTC 2014


Dear Jürg,


thank you for your detailed answer. This was very useful information,
in particular how to get an estimate of the total cutoff value,
this is very good to know. A number of things to try out now.


Cheers


Tobias



On Wednesday, June 11, 2014 1:46:55 PM UTC+1, jgh wrote:
>
> Hi 
>
> some info on cutoffs: 
>
> - The relative cutoff is the minimal cutoff that is used to 
>   integrate a Gaussian with exponent 1. This scales linearly. 
>   Exponent a -> a*RelCutoff. 
>   40 Rydberg usually gives reasonable results. 
>   60 Rydberg should be close to 'convergence'. 
>   80 Rydberg should always be converged. 
>   !!! Remember, convergence tests always also depend on other 
>   factors, like the Max. Cutoff, number of grids, how subgrids are 
>   calculated. 
>
> - Estimate of total cutoff: Max. exponent in your basis set=a 
>   Cutoff = 2*a*Rel_cutoff 
>   This is usually way too high but can be used to work your way down 
>   to smaller cutoffs. 
>
> - For larger systems (many atoms and electrons) and dense systems, 
>   CPU time is not dominated by the cutoff 
>
> - For some GGA functionals convergence with Cutoff can be slow. 
>   Dirty trick: use one of the smoothing options (XC_GRID) 
>   Better: use higher cutoff for XC calculation only(testing needed) 
>
> - Sometimes slow convergence with cutoff points to a problem with 
>   the GTH pseudopotentials and GGA functionals. 
>   There are NLCC pseudos available that solve this issue. 
>   -> more testing needed 
>
> regards 
>
> Juerg 
> -------------------------------------------------------------- 
> Juerg Hutter                         Phone : ++41 44 635 4491 
> Institut für Chemie C                FAX   : ++41 44 635 6838 
> Universität Zürich                   E-mail: hut... at chem.uzh.ch 
> <javascript:> 
> Winterthurerstrasse 190 
> CH-8057 Zürich, Switzerland 
> --------------------------------------------------------------- 
>
> -----cp... at googlegroups.com <javascript:> wrote: ----- 
> To: cp... at googlegroups.com <javascript:> 
> From: Tobias Kraemer <161br... at gmail.com <javascript:>> 
> Sent by: cp... at googlegroups.com <javascript:> 
> Date: 06/10/2014 07:06PM 
> Subject: [CP2K:5389] CUTTOFF and REL_CUTTOFF for large molecular system 
>
> Dear CP2K group, 
>
>
> being a relatively new cp2k user, I was wondering if this group could give 
> me some advice on the choice of (REL) CUTOFF values. 
> The system I am considering is a somewhat extended molecular crystal 
>  structure, containing organometallic fragments (basically a rhodium 
>  phosphine complex with additional ligand plus large borate counteranions 
> (BArF4-).The full system contains about 600+ atoms in the unit cell, 
> basically 4 cation/anion pairs 
> (asymmetric units). I think the system cannot be reduced in size, and the 
> full unit cell has to be taken into account.I have attached a cif file 
> which gives you 
> an idea about the kind of system (not exactly the one used in the 
> calculation below, but very much related) 
>   
> The basic idea behind determining the CUTOFF is clear to me and I have 
> done the tutorial on bulk Si. I have used the same protocol for my system 
> (running a series of calculations with varying CUTOFF and REL_CUTOFF 
> values). In contrast to the suggested method in the tutorial, I have 
> fully converged the SCF cycle) Below are the (first) results of this 
> series. The energy appears to be converging towards higher CUTOFF values 
> (some more calculations are currently running) 
>
> (1) I wonder if choosing such a large value for the cutoff is reasonable? 
> It should also increase the accuracy of the calculations, but also the 
> cost. 
> Also, with respect to the number of Gaussian being mapped onto the finest 
> grid, what would one need to look for?  
> In the tutorial the decision was  based on the fact that "the distribution 
> of Gaussian functions on the grids are reasonable". Could  somebody 
> elaborate on this 
> and give me some guidance how to decide  this? 
> (2) How does the size of the CUTOFF value correlate with the system size, 
> if there is any correlation?  
> (3) Are there some rule of thumbs as how to choose the REL_CUTOFF with 
> respect to the CUTOFF? For now I have tried 30, 60 and 100 Ry. 
> But I may need to go to higher numbers in this particular case. 
>
>
>
> # Grid cutoff vs total energy 
> # Date: Tue Jun 10 17:26:55 BST 2014 
> # REL_CUTOFF = 60 
> # Cutoff (Ry) | Total Energy (Ha) | Charge | SCF | | NG on grid 1 | NG on 
> grid 2 | NG on grid 3 | NG on grid 4 
>      50.00  -4583.1402739393   -8.4046446120  200  1623260  248362    
> 2112       0 
>     100.00  -4477.8479306771   -0.0745436930  128  1264867  519816   
> 89051       0 
>     150.00  -4479.5978060995   -0.0191170935  128  1150415  472845  
> 248362    2112 
>     200.00  -4478.5030451759    0.0008175249  128  905641  531280  
> 432781    4032 
>     250.00  -4478.4529157377   -0.0000917804  128  838757  500556  
> 523109   11312 
>     300.00  -4478.4141842105   -0.0000534995  128  796882  467985  
> 519816   89051 
>     350.00  -4478.3827319182   -0.0000170792  128  748308  474790  454036  
> 196600 
>     400.00  -4478.3597765363    0.0000003328  128  679828  499675  489931  
> 204300 
>     450.00  -4478.3498795935    0.0000000149  128  621687  528728  472845  
> 250474 
>     500.00  -4478.3399690553    0.0000000147  128  567997  416013  600098  
> 289626 
>     550.00  -4478.3338555119   -0.0000000007  128  485909  446314  559882  
> 381629 
>     600.00  -4478.3312330111    0.0000000007  128  442629  463012  531280  
> 436813 
>     650.00  -4478.3291405214    0.0000000006  128  399089  473084  554024  
> 447537 
>     700.00  -4478.3308119206    0.0000000008  128  375655  473218  509402  
> 515459 
>     750.00  -4478.3298871109    0.0000000008  128  365399  473358  500556  
> 534421 
>     800.00  -4478.3266993684    0.0000000007  128  353459  468098  461722  
> 590455 
>     850.00  -4478.3266987930    0.0000000007  128  348184  458373  472494  
> 594683 
>     900.00  -4478.3273848891    0.0000000007  128  336984  459898  467985  
> 608867 
>     950.00  -4478.3277135782    0.0000000007  128  309758  476872  469877  
> 617227 
>    1000.00  -4478.3277705414    0.0000000008  128  291089  482269  455857  
> 644519 
>    1050.00  -4478.3278605666    0.0000000007  128  229036  519272  474790  
> 650636 
>
> Some further questions; 
>
> (4) Could you recommend some literature (books) which explains the theory 
> of solid state calculations, k-sampling, planewaves? 
>
> (5) As a next step I would like to manipulate the structure, i.e. 
> rotate/move ligands around? Is there a good visualizer that can do such 
> things for periodic systems? The problem I am facing is that I would like 
> to do these things simultaneously for all 4 asymmetric units. 
> I think it becomes impracticable to do this for each unit separately. I 
> have started using GDIS but I am a little bit uncertain about its 
> abilities (great program though!!). Has anyone experience with VESTA? I am 
> particularly looking for free software. 
>
>
> Thank you very much for your help, this is very much appreciated. There 
> are a lot of questions right a the beginning, and it is not always easy to 
> find some answers.   
>
> Best 
>
>
> Tobias 
>
>
>   Dr. Tobias Kraemer 
>   Research Associate 
>   Institute of Chemical Sciences 
>   School of Engineering & Physical Sciences 
>   Heriot-Watt University 
>   Edinburgh EH14 4AS 
>   United Kingdom 
>   
>   
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>
> [attachment "input_test.inp" removed by Jürg Hutter/at/UZH] 
> [attachment "PCCPiBu_NBA.cif" removed by Jürg Hutter/at/UZH] 
>
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