[CP2K-user] [CP2K:13306] COF cell optimize exploded
shixun sun
suns... at gmail.com
Fri May 15 07:11:17 UTC 2020
Dear Gan
That helps a lot. Thank you!
Best
Linfeng Gan <linfe... at gmail.com> 于2020年5月15日周五 上午8:29写道：
> Hi, Sun
>
> I would like to share some of my experience with you.
>
>
>
> (1) CUTOFF
>
> As you can see from the cutoff test, you must increase cutoff at least up
> to 1000 Ry. I had test cutoff ranged from 600 to 2500, the highest the
> best. At 1200 Ry, the cell optimization result is very close to the
> experimental data.
>
>
> # Grid cutoff vs total energy
>
> # Date: Tue Apr 7 10:28:38 2020
>
> # rel_cutoff = 60
>
> # Cutoff (Ry) | Total Energy (Ha) | Energy per Atom (eV) | NG on grid 1 |
> NG on grid 2 | NG on grid 3 | NG on grid 4 | NG on grid 5
>
> 50 -511.8311527382 -145.0795204885 1191545
> 55218 480 0 0
>
> 100 -498.0188507854 -141.1643970471 1191545
> 55218 480 0 0
>
> 150 -498.1333770910 -141.1968597477 1084277
> 152208 10758 0 0
>
> 200 -498.0596390179 -141.1759585497 1011045
> 180500 55218 480 0
>
> 250 -498.0576533189 -141.1753956995 894935
> 264998 86030 1280 0
>
> 300 -498.0561376050 -141.1749660675 839389
> 277782 127992 2080 0
>
> 350 -498.0556031621 -141.1748145786 784888
> 299389 152208 10758 0
>
> 400 -498.0546430297 -141.1745424273 743542
> 307599 172215 23887 0
>
> 450 -498.0543833523 -141.1744688212 715246
> 305115 187987 38415 480
>
> 500 -498.0547962093 -141.1745858463 664938
> 346107 180500 55218 480
>
> 550 -498.0548813984 -141.1746099933 648732
> 310339 223070 63822 1280
>
> 600 -498.0548597218 -141.1746038491 597516
> 325211 250210 73026 1280
>
> 650 -498.0549993006 -141.1746434129 558534
> 336401 264998 86030 1280
>
> 700 -498.0548179649 -141.1745920130 513592
> 356057 290284 85230 2080
>
> 750 -498.0547555671 -141.1745743262 499950
> 340239 294170 110804 2080
>
> 800 -498.0547613057 -141.1745759528 452398
> 386991 277782 127992 2080
>
> 850 -498.0547622822 -141.1745762296 415918
> 410299 267688 147908 5430
>
> 900 -498.0547014016 -141.1745589729 403034
> 388334 292909 157536 5430
>
> 950 -498.0547014005 -141.1745589726 390150
> 394738 299389 152208 10758
>
> 1000 -498.0546629837 -141.1745480833 374096
> 381572 318409 162408 10758
>
> 1050 -498.0546627095 -141.1745480056 372626
> 379024 308511 172231 14851
>
> 1100 -498.0546627489 -141.1745480167 333972
> 409570 307599 172215 23887
>
> 1150 -498.0546599853 -141.1745472334 291540
> 452002 287140 192674 23887
>
> 1200 -498.0546599398 -141.1745472205 283078
> 459664 282659 188911 32931
>
> 1250 -498.0546664857 -141.1745490759 265352
> 449894 305115 187987 38895
>
> 1300 -498.0546695315 -141.1745499393 257340
> 430648 331573 180200 47482
>
> 1350 -498.0546694852 -141.1745499261 249304
> 433344 336433 172464 55698
>
> 1400 -498.0546619268 -141.1745477837 249304
> 415634 346107 180500 55698
>
> 1450 -498.0546657092 -141.1745488558 237064
> 427874 330835 195772 55698
>
> 1500 -498.0546657265 -141.1745488607 237064
> 419238 322207 203632 65102
>
> 1550 -498.0546649445 -141.1745486391 232240
> 416492 310339 223070 65102
>
> 1600 -498.0546621702 -141.1745478527 232240
> 400820 312383 236698 65102
>
> 1650 -498.0546580786 -141.1745466929 224234
> 392132 329077 228294 73506
>
> 1700 -498.0546579920 -141.1745466684 224234
> 373282 325211 250210 74306
>
> 1750 -498.0546626389 -141.1745479855 224234
> 368338 318615 255886 80170
>
> 1800 -498.0546626425 -141.1745479866 216222
> 347172 339757 263922 80170
>
> 1850 -498.0546624400 -141.1745479292 216222
> 342312 336401 264998 87310
>
> 1900 -498.0546624669 -141.1745479368 196998
> 345386 332173 285376 87310
>
> 1950 -498.0546619107 -141.1745477791 153670
> 372770 343209 290284 87310
>
> 2000 -498.0546645404 -141.1745485245 127866
> 385726 356057 290284 87310
>
> 2050 -498.0546619783 -141.1745477983 107134
> 406458 356057 285100 92494
>
> 2100 -498.0546619823 -141.1745477994 82148
> 431444 339841 296252 97558
>
> 2150 -498.0546619947 -141.1745478029 77348
> 422602 340239 294170 112884
>
> 2200 -498.0546617280 -141.1745477273 69312
> 400926 369951 294170 112884
>
> 2250 -498.0546617309 -141.1745477282 64488
> 392818 382883 285546 121508
>
> 2300 -498.0546623124 -141.1745478930 64488
> 387910 386991 277782 130072
>
> 2350 -498.0546623561 -141.1745479054 53548
> 378466 399339 285818 130072
>
> 2400 -498.0546621789 -141.1745478552 53548
> 370382 407423 270648 145242
>
> 2450 -498.0546621769 -141.1745478546 43948
> 371970 410299 267688 153338
>
> 2500 -498.0546611280 -141.1745475573 35936
> 379982 402203 274984 154138
>
>
>
>
>
>
>
> (2) CELL_REF
>
> I had tested the CELL_REF vectors A, B, and C from 1 to 3 times of origin
> CELL corresponding vectors with 0.2 interval. I think 1.2 time of the CELL
> vectors ABC is enough which has a good balancing the computational time and
> accuracy.
>
>
> On Thursday, May 14, 2020 at 6:54:53 PM UTC+8, shixun sun wrote:
>>
>> Hi, Gan
>> I had the same problem with you now, and could you tell me how much you
>> increase your cutoff. and did you change your c axis, like you want 6, so
>> you increase it to 10 in your input
>> Millions of thanks for your help
>> best
>>
>> Linfeng Gan <li... at gmail.com> 于2020年5月14日周四 下午6:48写道：
>>
>>> I had carefully tested the CUTOFF and the CELL_REF. The test results
>>> showed that increased the CUTOFF had most helpful.
>>>
>>>
>>> So, the problem solved
>>>
>>> On Tuesday, April 7, 2020 at 4:11:46 PM UTC+8, Linfeng Gan wrote:
>>>>
>>>> Thanks Juerg. I will try as you suggest and update a few days later.
>>>>
>>>>
>>>> On Monday, April 6, 2020 at 3:32:56 PM UTC+8, jgh wrote:
>>>>>
>>>>> Hi
>>>>>
>>>>> I assume your system is weakly bound in z-direction. Small force
>>>>> changes in that direction can cause large changes.
>>>>> The only obvious problem I could spot is the definition of the
>>>>> reference cell. In order to minimize the effect of a change in
>>>>> volume, the reference cell should be larger than the initial
>>>>> and final cell. I would set c=10 or 12 and I would also increase
>>>>> the cutoff.
>>>>> You could test this by just scan the energy as function of c and
>>>>> correctly adapt the geometry of course.
>>>>>
>>>>> regards
>>>>>
>>>>> Juerg Hutter
>>>>> --------------------------------------------------------------
>>>>> Juerg Hutter Phone : ++41 44 635 4491
>>>>> Institut für Chemie C FAX : ++41 44 635 6838
>>>>> Universität Zürich E-mail: h... at chem.uzh.ch
>>>>> Winterthurerstrasse 190
>>>>> CH-8057 Zürich, Switzerland
>>>>> ---------------------------------------------------------------
>>>>>
>>>>> -----c... at googlegroups.com wrote: -----
>>>>> To: "cp2k" <c... at googlegroups.com>
>>>>> From: "Linfeng Gan"
>>>>> Sent by: c... at googlegroups.com
>>>>> Date: 04/05/2020 04:27AM
>>>>> Subject: [CP2K:13056] COF cell optimize exploded
>>>>>
>>>>>
>>>>> Hello all,
>>>>> I need some help about the covalent-organic frameworks (COF) 2D
>>>>> sheet cell optimize. After I optimized the COF with a 2X2X2 supercell, the
>>>>> cell size was totally exploded. I had kept the cell vectors and symmetry
>>>>> constant, changed different basis sets and different XC functions but the
>>>>> cell exploded anyway.
>>>>> I had tried basis sets DZVP-MOLOPT-GTH and DZVP-MOLOPT-SR-GTH with
>>>>> PADE, PBE and BLYP. And the DFTD3 correction was also add to each
>>>>> calculation. The GAPW method I also had tried, but none of them worked.
>>>>>
>>>>> Any suggestion is welcome, thanks!
>>>>> Linfeng
>>>>>
>>>>> The COF-5-2X2X2 supercell vectors should be:
>>>>> CELL_TOP| Volume [angstrom^3]:
>>>>> 21253.270
>>>>> CELL_TOP| Vector a [angstrom 60.040 0.000 0.000 |a| =
>>>>> 60.040
>>>>> CELL_TOP| Vector b [angstrom -30.020 51.996 0.000 |b| =
>>>>> 60.040
>>>>> CELL_TOP| Vector c [angstrom 0.000 0.000 6.808 |c| =
>>>>> 6.808
>>>>> CELL_TOP| Angle (b,c), alpha [degree]:
>>>>> 90.000
>>>>> CELL_TOP| Angle (a,c), beta [degree]:
>>>>> 90.000
>>>>> CELL_TOP| Angle (a,b), gamma [degree]:
>>>>> 120.000
>>>>>
>>>>> But after cell optimized calculation the output cell vectors are:
>>>>>
>>>>> *******************************************************************************
>>>>>
>>>>> *** GEOMETRY OPTIMIZATION COMPLETED
>>>>> ***
>>>>>
>>>>> *******************************************************************************
>>>>>
>>>>>
>>>>> Reevaluating energy at the minimum
>>>>>
>>>>> CELL| Volume [angstrom^3]:
>>>>> 25653.623
>>>>> CELL| Vector a [angstrom]: 60.345 0.000 0.000 |a| =
>>>>> 60.345
>>>>> CELL| Vector b [angstrom]: -30.173 52.260 0.000 |b| =
>>>>> 60.345
>>>>> CELL| Vector c [angstrom]: 0.000 -0.000 8.135 |c| =
>>>>> 8.135
>>>>> CELL| Angle (b,c), alpha [degree]:
>>>>> 90.000
>>>>> CELL| Angle (a,c), beta [degree]:
>>>>> 90.000
>>>>> CELL| Angle (a,b), gamma [degree]:
>>>>> 120.000
>>>>>
>>>>> --
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>>>>>
>>>>>
>>>>>
>>>>> [attachment "COF-5-2X2X2.xyz" removed by Jürg Hutter/at/UZH]
>>>>> [attachment "opt_cell.inp" removed by Jürg Hutter/at/UZH]
>>>>>
>>>> --
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>>> .
>>>
>> --
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