[CP2K-user] [CP2K:13301] COF cell optimize exploded
Linfeng Gan
linfe... at gmail.com
Fri May 15 00:29:28 UTC 2020
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 <javascript:>> 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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