简单量子化学问题答疑专帖

糖糖糖豆9988 · 发表于 Post on 2024-5-23 20:34:07

本帖最后由糖糖糖豆9988 于 2024-5-23 20:38 编辑

wzkchem5 发表于 2024-5-23 20:17
任何量化教材都会讲

嗯老师我可能表示地不清楚，我想问的是双自由基结构的16HONO明显偏离2，17LUNO明显偏离0，是不是就可以证明体系有明显双自由基特征，轨道选择的合理？

wzkchem5 · 发表于 Post on 2024-5-23 23:20:17

糖糖糖豆9988 发表于 2024-5-23 13:34
嗯老师我可能表示地不清楚，我想问的是双自由基结构的16HONO明显偏离2，17LUNO明显偏离0，是不是就可以证 ...

可以，至少定性上正确

moiumuio · 发表于 Post on 2024-5-23 23:32:59

本帖最后由 moiumuio 于 2024-5-24 00:47 编辑

Sorry for the absurd question, but am I able to claim that through oscillator strength (image below), the S2 is the first excited state in an article without any question? And for adiabatic excitation structure, should I set "opt td(nstates=5,root=2) out=wfn" (without vibration analysis)?

sobereva · 发表于 Post on 2024-5-24 04:26:04

糖糖糖豆9988 发表于 2024-5-23 20:34
嗯老师我可能表示地不清楚，我想问的是双自由基结构的16HONO明显偏离2，17LUNO明显偏离0，是不是就可以证 ...

把此文看了有益
CASSCF计算双自由基以及双自由基特征的计算
http://sobereva.com/264（http://bbs.keinsci.com/thread-322-1-1.html）

sobereva · 发表于 Post on 2024-5-24 04:27:32

moiumuio 发表于 2024-5-23 23:32
Sorry for the absurd question, but am I able to claim that through oscillator strength (image below) ...

S2 is the second excited state in common sense. However, you may refer it to as the first "bright" state, because it is the lowest excited state with notable oscillator strength.

You should set.

moiumuio · 发表于 Post on 2024-5-24 11:07:01

sobereva 发表于 2024-5-23 04:49
This depends on the state of interest. For example, if you want to characterize the lowest 10 exci ...

When I changed the functional and basis sets to b3lyp/aug-cc-vdz, the structure was a bit weird but not broken into pieces anymore. However, when I changed the functional and basis set back to wB97XD/6-311G**, it was broken again. Are there any methods to overcome this?
Thank you, Prof.

sobereva · 发表于 Post on 2024-5-24 12:13:17

moiumuio 发表于 2024-5-24 11:07
When I changed the functional and basis sets to b3lyp/aug-cc-vdz, the structure was a bit weird bu ...

Do not change two conditions at the same time, otherwise you cannot figure out the reason (functional or basis set) causing the break of molecule.

批发香菜 · 发表于 Post on 2024-5-24 12:37:22

各位老师，我想请教一下。我是优化和sp分开计算的。做完优化后，我在做sp计算，就出现了下面的问题。是系统和软件不兼容吗？希望各位老师指教一下，麻烦各位老师。
%nprocshared=12
%mem=16GB
%chk=IM1-SP.chk
#p M06/genecp

Title Card Required

0 2
Ru             -1.13278400 0.36399600 -0.46246200
C                -3.32276900 0.54866700 -0.31601800
C                -2.82553600 1.79266900 -0.81616600
C                -1.88839300 2.55699100 -0.07489900
C                -1.40074000 1.97356600 1.13071100
C                -1.92889800 0.75351100 1.64866000
C                -2.93938800 0.03282900 0.95862200
H                -4.01198100 -0.02283800 -0.93033600
H                -3.15876400 2.14291200 -1.78859900
H                -0.60387600 2.47284100 1.67383500
H                -1.52155700 0.36312100 2.57582300
C                -3.58180500 -1.22838300 1.51311200
H                -4.17374100 -1.66327500 0.69710900
C                -4.55276900 -0.87341100 2.65786400
H                -4.01378700 -0.44501200 3.51200700
H                -5.30279200 -0.14214000 2.33548100
H                -5.07926100 -1.76930800 3.00840000
C                -2.56087600 -2.29346600 1.94441900
H                -3.08078700 -3.18880100 2.30697600
H                -1.93023600 -2.56887100 1.09412800
H                -1.92341500 -1.93281900 2.76236900
C                -1.42476300 3.91050200 -0.54414000
H                -1.48583700 3.99396400 -1.63444800
H                -2.05260200 4.70426000 -0.11522600
H                -0.39134300 4.10557400 -0.24342800
C                -0.75750500 -2.62559000 -3.59167400
H                -1.24503100 -3.60445500 -3.60472500
H                0.31589300 -2.78608600 -3.75206200
H                -1.13753400 -2.00052300 -4.40335900
C                -0.95405900 -1.96186100 -2.23121600
O                -1.08500100 -0.67903200 -2.27392500
O                -0.95531100 -2.66130400 -1.20046300
C                3.53744700 3.50357800 1.15360900
C                3.19610000 2.15111900 1.18698800
C                2.42026400 1.58902500 0.16238200
C                1.99290600 2.40062700 -0.89870900
C                2.35558400 3.74698100 -0.94185500
C                3.12447500 4.30235500 0.08486800
H                4.12653100 3.93263600 1.95978400
H                3.51434100 1.53097500 2.02038800
H                1.38953900 1.96280900 -1.68797700
H                2.03917100 4.36325000 -1.77908800
H                3.40027600 5.35300600 0.05187100
C                2.07256900 0.13142900 0.13913000
O                0.94746900 -0.26200700 -0.27908300
C                3.07085300 -0.76679500 0.57412500
H                4.09998700 -0.46128300 0.71876800
S                2.89401600 -2.44836700 0.38590500
O                3.26074800 -3.10621100 -0.89358900
C                3.96817800 -3.11697700 1.68339400
H                3.62112400 -2.79012600 2.66513900
H                3.94758100 -4.20528800 1.59171900
H                4.97888400 -2.75031300 1.48963500
C                1.24329600 -2.95714900 0.89189100
H                1.30065100 -4.03577300 1.06205600
H                0.96560500 -2.41972500 1.80000300
H                0.54293600 -2.73352800 0.07351700

C H O S 0
6-311+G(d,P)
****
Ru 0
SDD
****

Ru 0
SDD

Ernie: Thresh=  0.10000D-02 Tol=  0.10000D-05 Strict=F.
There are 842 symmetry adapted cartesian basis functions of A symmetry.
There are 812 symmetry adapted basis functions of A symmetry.
812 basis functions,  1283 primitive gaussians, 842 cartesian basis functions
113 alpha electrons    112 beta electrons
   nuclear repulsion energy    3225.6933252197 Hartrees.
IExCor= 4235 DFT=T Ex+Corr=M06 ExCW=0 ScaHFX=  0.270000
ScaDFX=  1.000000  1.000000  1.000000  1.000000 ScalE2=  1.000000  1.000000
IRadAn=    5 IRanWt=    -1 IRanGd=          0 ICorTp=0 IEmpDi=  4
NAtoms= 57 NActive= 57 NUniq= 57 SFac= 1.00D+00 NAtFMM= 60 NAOKFM=F Big=F
Integral buffers will be 131072 words long.
Raffenetti 2 integral format.
Two-electron integral symmetry is turned on.
Leave Link  301 at Wed Jun 24 07:38:53 2020, MaxMem=  2147483648 cpu:             0.8 elap:             0.1
(Enter /opt/app/g16a03/g16/l302.exe)
NPDir=0 NMtPBC=    1 NCelOv=    1 NCel=    1 NClECP=    1 NCelD=    1
      NCelK=    1 NCelE2=    1 NClLst=    1 CellRange=    0.0.
One-electron integrals computed using PRISM.
One-electron integral symmetry used in STVInt
1 Symmetry operations used in ECPInt.
ECPInt:  NShTT= 44850 NPrTT=  155994 LenC2= 37966 LenP2D= 86079.
LDataN:  DoStor=T MaxTD1= 6 Len=  172
NBasis= 812 RedAO= T EigKep=  1.15D-06  NBF= 812
NBsUse= 809 1.00D-06 EigRej=  8.74D-07 NBFU= 809
Precomputing XC quadrature grid using
IXCGrd= 4 IRadAn=          5 IRanWt=       -1 IRanGd=          0 AccXCQ= 0.00D+00.
Defaulting to unpruned grid for atomic number  44.
Generated NRdTot=    0 NPtTot=          0 NUsed=          0 NTot=       32
NSgBfM= 830 830 830 830 830 MxSgAt= 57 MxSgA2= 57.
Leave Link  302 at Wed Jun 24 07:38:55 2020, MaxMem=  2147483648 cpu:             20.6 elap:             1.7
(Enter /opt/app/g16a03/g16/l303.exe)
DipDrv:  MaxL=1.
Leave Link  303 at Wed Jun 24 07:38:55 2020, MaxMem=  2147483648 cpu:             1.6 elap:             0.2
(Enter /opt/app/g16a03/g16/l401.exe)
ExpMin= 1.60D-02 ExpMax= 9.34D+04 ExpMxC= 3.17D+03 IAcc=3 IRadAn=       5 AccDes= 0.00D+00
Harris functional with IExCor= 1009 and IRadAn=    5 diagonalized for initial guess.
HarFok:  IExCor= 1009 AccDes= 0.00D+00 IRadAn=       5 IDoV= 1 UseB2=F ITyADJ=14
ICtDFT=  3500011 ScaDFX=  1.000000  1.000000  1.000000  1.000000
Defaulting to unpruned grid for atomic number  44.
FoFCou: FMM=F IPFlag=          0 FMFlag=    100000 FMFlg1=          0
      NFxFlg=          0 DoJE=T BraDBF=F KetDBF=T FulRan=T
      wScrn=  0.000000 ICntrl=    500 IOpCl=  0 I1Cent= 200000004 NGrid=          0
      NMat0= 1 NMatS0=    1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0
Petite list used in FoFCou.
Harris En= -1649.15500340717
JPrj=0 DoOrth=F DoCkMO=F.
Initial guess <Sx>= 0.0000 <Sy>= 0.0000 <Sz>= 0.5000 <S**2>= 0.7500 S= 0.5000
Leave Link  401 at Wed Jun 24 07:39:00 2020, MaxMem=  2147483648 cpu:             59.8 elap:             5.0
(Enter /opt/app/g16a03/g16/l502.exe)
Integral symmetry usage will be decided dynamically.
UHF open shell SCF:
Using DIIS extrapolation, IDIIS=  1040.
NGot=  2147483648 LenX=  2146047058 LenY=  2145337252
Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
Requested convergence on MAX density matrix=1.00D-06.
Requested convergence on          energy=1.00D-06.
No special actions if energy rises.
Fock matrices will be formed incrementally for  20 cycles.

Cycle 1  Pass 1  IDiag  1:
FoFJK:  IHMeth= 1 ICntrl=    0 DoSepK=F KAlg= 0 I1Cent=          0 FoldK=F
IRaf= 770000000 NMat=    1 IRICut=    1 DoRegI=T DoRafI=F ISym2E= 0 IDoP0=0 IntGTp=1.
FoFCou: FMM=F IPFlag=          0 FMFlag=    100000 FMFlg1=          0
      NFxFlg=          0 DoJE=F BraDBF=F KetDBF=F FulRan=T
      wScrn=  0.000000 ICntrl=       0 IOpCl=  1 I1Cent=          0 NGrid=          0
      NMat0= 1 NMatS0=    1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0
Symmetry not used in FoFCou.

sobereva · 发表于 Post on 2024-5-24 12:59:12

批发香菜发表于 2024-5-24 12:37
各位老师，我想请教一下。我是优化和sp分开计算的。做完优化后，我在做sp计算，就出现了下面的问题。是系统 ...

根本没报错
如果自动停了，看

Q：Gaussian任务没有报错，但是却停了怎么办？
A：有以下可能原因
1 巧合。尝试重算，或者尝试其它也能达到类似目的的关键词再试
2 Gaussian的bug。尝试其它版本或其它平台的Gaussian
3 当前Gaussian版本和软件环境有兼容性问题。尝试其它版本或其它平台的Gaussian。对于Linux尝试装其它版本或其它发行版Linux再试，对于Windows把各种安全防护程序都关掉再试
4 任务被bad people杀了。重算，并找管理员告状
5 内存分配得不够。增大%mem或配置文件里的默认的内存设置。也可能虽然内存分配得够，但实际空余物理内存不够，或者一开始空余物理内存够但运行中途有其它程序占了过多内存
6 计算机硬件不稳定，检修或换成其它机子

批发香菜 · 发表于 Post on 2024-5-24 13:34:20

sobereva 发表于 2024-5-24 12:59
根本没报错
如果自动停了，看

了解了，非常感谢老师。

cokie · 发表于 Post on 2024-5-25 13:52:01

本帖最后由 cokie 于 2024-5-25 13:53 编辑

各位老师好，在使用xTB或者使用gentor/genmer+mopac配合molclus做单体/二聚体构象筛选的时候，筛选出用DFT做OPT的构象，应该取什么范围比较合适呢？
我看到有帖子说选择【和能量最低的构象做差，选delta_E < 3 kcal/mol的全部构象】，也有的说【选取能量最低的10-20个构象】就足矣。但并没有提供Ref.。
请问各位老师，这个用作后续高精度计算（如DFT，CCSD(T)）的构象的选择范围，在量化领域有没有一个比较通行的标准呢？是否有较权威的文献可以参考和引用呢？

望指教，先谢过各位老师！

wzkchem5 · 发表于 Post on 2024-5-25 16:54:53

cokie 发表于 2024-5-25 06:52
各位老师好，在使用xTB或者使用gentor/genmer+mopac配合molclus做单体/二聚体构象筛选的时候，筛选出用DFT ...

首先容易看出，不能抛开分子大小说选能量最低的N个构象。考虑一个大分子，有M个基团，每个基团都有k个能量很低的构象，那么显然至少要取k^M个构象才能算得完全。所以需要取的构象数是随体系大小指数增长的。如果一个人一辈子都只研究比如说100个原子以内的体系，那“只取最低的10~20个构象”可能对这个人做过的所有体系都成立，但是另一个人算200个原子的体系，可能就不能用这个标准了。
所以一定要用单独的一个数作为筛选标准的话，基本只能是能量或自由能。这个能量或者自由能的阈值选3kcal/mol还是其他数字可能文献没有定论，但是可以大概从Boltzmann分布估算出，选不同阈值大概会漏掉总Boltzmann分布的多大比例的构象，这个级别的遗漏对你需要的精度而言是否可以接受。
这个能量或者自由能的阈值，如果是你所用的构象搜索软件默认给定的，而且你用的构象搜索软件比较主流，那么可以认为默认值是经过充分考虑确定的，是可靠的，需要引文献就引构象搜索软件的原始文献。如果必须手动指定，那么取值可以参考Grimme组发表的文章，或者Neese组算List的手性催化体系的文章

dengg · 发表于 Post on 2024-5-25 17:32:55

采用高斯16 m062X def2tzvp 优化的，优化后结构发生了变化，该怎么解决？

dengg · 发表于 Post on 2024-5-25 17:34:04

这个是优化前的

liang666 · 发表于 Post on 2024-5-25 18:59:33

http://sobereva.com/414

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