简单量子化学问题答疑专帖

caiyan

我又把生成文件单换了一个文件夹，现在显示是这样的报错： Rotational constants (GHZ):      3.9944367      0.7804937      0.7665817
Standard basis: 6-311G(d,p) (5D, 7F)
There are   206 symmetry adapted basis functions of A   symmetry.
Integral buffers will be    262144 words long.
Raffenetti 2 integral format.
Two-electron integral symmetry is turned on.
   206 basis functions,   342 primitive gaussians,   214 cartesian basis functions
    37 alpha electrons       37 beta electrons
       nuclear repulsion energy       513.8869627342 Hartrees.
NAtoms=   17 NActive=   17 NUniq=   17 SFac= 1.00D+00 NAtFMM=   60 NAOKFM=F Big=F
One-electron integrals computed using PRISM.
NBasis=   206 RedAO= T  NBF=   206
NBsUse=   206 1.00D-06 NBFU=   206
Harris functional with IExCor=  402 diagonalized for initial guess.
ExpMin= 7.71D-02 ExpMax= 9.34D+04 ExpMxC= 3.17D+03 IAcc=2 IRadAn=         4 AccDes= 0.00D+00
HarFok:  IExCor=  402 AccDes= 0.00D+00 IRadAn=         4 IDoV= 1
ScaDFX=  1.000000  1.000000  1.000000  1.000000
FoFCou: FMM=F IPFlag=           0 FMFlag=      100000 FMFlg1=           0
         NFxFlg=           0 DoJE=T BraDBF=F KetDBF=T FulRan=T
         Omega=  0.000000  0.000000  1.000000  0.000000  0.000000 ICntrl=     500 IOpCl=  0
         NMat0=    1 NMatS0=    1 NMatT0=    0 NMatD0=    1 NMtDS0=    0 NMtDT0=    0
         I1Cent=           4 NGrid=           0.
Petite list used in FoFCou.
Initial guess orbital symmetries:
       Occupied  (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A)
       Virtual   (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A)
The electronic state of the initial guess is 1-A.
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.
Integral accuracy reduced to 1.0D-05 until final iterations.
Initial convergence to 1.0D-05 achieved.  Increase integral accuracy.
SCF Done:  E(RB3LYP) =  -798.419275331     A.U. after   14 cycles
             Convg  =    0.6536D-08             -V/T =  2.0022

LeePanda

部分信息如下：
No pseudopotential on this center.
======================================================================================================
Warning:  center   1 has no basis functions!
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Bad length for file.
FileIO: IOper= 1 IFilNo(1)=  -582 Len=           0 IPos=           0 Q=   23076802668208


dumping /fiocom/, unit = 1 NFiles =    39 SizExt =    524288 WInBlk =       512
                   defal = F LstWrd =     2829824 FType=2 FMxFil=10000

Number              0             0           501           502           503           507
Base            42379       2318454         43520        142336        250880        258994
End             42496       2829824         44520        146441        252438        261252
End1            42496       2829824         44544        146944        252438        261252
Wr Pntr         42238       2314301         43520        146441        250880        258994
Rd Pntr         42238       2314301         44520        142336        252438        258994
Length            117        511370          1000          4105          1558          2258
Int.Num             1             2             3             4             5             6

Number            511           512           521           551           552           559
Base           959696       2314301         42238         42198         41984         42377
End           1225783       2318280         42273         42236         42025         42379
End1          1225783       2318280         42273         42236         42025         42379
Wr Pntr        959696       2318280         42273         42198         41984         42379
Rd Pntr        959696       2314301         42238         42236         41984         42377
Length         266087          3979            35            38            41             2
Int.Num             7             8             9            10            11            12

Number            561           562           575           579           581           583
Base            42236       2305312        276595         42025         42305       2318280
End             42237       2313263        959696         42198         42377       2318454
End1            42237       2313263        959696         42198         42377       2318454
Wr Pntr         42236       2305312        276595         42025         42305       2318454
Rd Pntr         42236       2313263        276595         42025         42305       2318280
Length              1          7951        683101           173            72           174
Int.Num            13            14            15            16            17            18

Number            598           665           670           672           674           698
Base           146944        252438         42273        276077        265668       2313263
End            146946        258994         42305        276595        267257       2314301
End1           147456        258994         42305        276595        267257       2314301
Wr Pntr        146944        252438         42305        276077        265668       2313263
Rd Pntr        146944        252438         42273        276077        265668       2313263
Length              2          6556            32           518          1589          1038
Int.Num            19            20            21            22            23            24

Number            701           761           800           801           988           989
Base          1225783         42237        261252        250368         65024         44544
End           2305312         42238        265668        250374        135028         64544
End1          2305312         42238        265668        250880        135168         65024
Wr Pntr       1225783         42237        261252        250368         65024         44544
Rd Pntr       1225783         42237        261252        250368        135028         44544
Length        1079529             1          4416             6         70004         20000
Int.Num            25            26            27            28            29            30

Number            991           992           993           994           995           996
Base           135680        135168         43008         40448         42496         41472
End            142242        135178         43208         40478         42516         41672
End1           142336        135680         43520         40960         43008         41984
Wr Pntr        135680        135168         43008         40448         42496         41472
Rd Pntr        142242        135178         43208         40478         42516         41672
Length           6562            10           200            30            20           200
Int.Num            31            32            33            34            35            36

Number            997           998           999
Base           267257         40960        147456
End            276077         41160        249960
End1           276077         41472        250368
Wr Pntr        267257         41160        147456
Rd Pntr        276077         41160        149960
Length           8820           200        102504
Int.Num            37            38            39


dumping /fiocom/, unit = 2 NFiles =     1 SizExt =         0 WInBlk =       512
                   defal = F LstWrd =       65536 FType=2 FMxFil=10000

Number              0
Base            40448
End             65536
End1            65536
Wr Pntr         40448
Rd Pntr         40448
Length          25088
Int.Num             1


dumping /fiocom/, unit = 3 NFiles =     1 SizExt =    524288 WInBlk =       512
                   defal = F LstWrd =       65536 FType=2 FMxFil=10000

Number              0
Base            40448
End             65536
End1            65536
Wr Pntr         40448
Rd Pntr         40448
Length          25088
Int.Num             1
Bad length for file.
FileIO: IOper= 1 IFilNo(1)=  -582 Len=           0 IPos=           0 Q=   23076802668208
Error termination in NtrErr:
NtrErr Called from FileIO.



请问，该怎么调整啊？ Cu11.gjf (10.74 KB, 下载次数 Times of downloads: 2)

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Cu11.log (115.18 KB, 下载次数 Times of downloads: 1)

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北大-陶豫

你输出文件里显示的关键词（第86行）是“opt b3lyp/genecp”，跟你提供的输入文件不符，你再检查一下

wzkchem5

caiyan 发表于 2025-12-25 10:11
我又把生成文件单换了一个文件夹，现在显示是这样的报错： Rotational constants (GHZ):      3.9944367    ...

自行检查输出文件的最后几十行。不要只看高斯窗口的内容

sobereva

caiyan 发表于 2025-12-25 10:11
我又把生成文件单换了一个文件夹，现在显示是这样的报错： Rotational constants (GHZ):      3.9944367    ...

直接上传完整输出文件，超过5MB就先压缩

sobereva

LeePanda 发表于 2025-12-25 11:00
部分信息如下：
No pseudopotential on this center.
=============================================== ...

认真看下文，别用“按照教程”这种糊涂方式描述问题
在网上求助计算化学问题的时候必须把问题描述得详细、具体、准确、清楚、完整
http://sobereva.com/620（http://bbs.keinsci.com/thread-25787-1-1.html）

Warning:  center xxx has no basis functions!纯粹是自定义基组没写对，相应原子没定义基组。认真看
详解Gaussian中混合基组、自定义基组和赝势基组的输入
http://sobereva.com/60

CM234

各位老师好，我的计算内容为：乳酸、氯化胆碱、氯化铁三种分子间的弱相互作用，b3lyp/def2svp、对Fe使用SDD，向之前已经计算完成的体系中多加入了一个乳酸分子，目前还在结构优化，有以下几个问题：
1、结构优化过程中，为了解决SCF不收敛，参考 http://sobereva.com/61 同时使用了小基组3-21G逐步提升、降低收敛限至6、guess=huckel和能级移动法四种方法结合解决，如果完成优化，是优先换大基组还是先恢复gaussian默认的收敛限？还是说两者没有绝对的先后顺序，需要根据情况来看
2、如果SCF依旧不收敛，是优先考虑更改自旋多重度还是先用闭壳层计算再读取波函数进行开壳层计算？
3、换用闭壳层计算，该体系的离子态的电荷应该设置为多少？（体系为乳酸/氯化胆碱/氯化铁=2：1：1）还是说直接在方法前面加R就好？
4、http://sobereva.com/164 提到，在GDIIS下即使加了cartesian，也是使用默认冗余内坐标进行优化。但是笛卡尔坐标比较适合对多分子簇的优化。我的体系中含有过渡金属和比较多的分子，如果结构优化中只使用GDIIS方法结果依旧震荡的话，是否可以尝试换用笛卡尔坐标？

sobereva

CM234 发表于 2025-12-28 20:36
各位老师好，我的计算内容为：乳酸、氯化胆碱、氯化铁三种分子间的弱相互作用，b3lyp/def2svp、对Fe使用SDD ...

1 同时。
2 这两种都不是最值得优先考虑的方法。博文里有的是其它方法
4 先尝试用下文的其它做法，诸如减小步长上限、用更好的Hessian
量子化学计算中帮助几何优化收敛的常用方法
http://sobereva.com/164

CM234

sobereva 发表于 2025-12-30 14:43
1 同时。
2 这两种都不是最值得优先考虑的方法。博文里有的是其它方法
4 先尝试用下文的其它做法，诸如 ...

好的，谢谢老师

2429783189

我使用Gaussian计算团簇对Cd2+的吸附，在团簇中一个脱质子的羧基（提供两个配体）和三个不带电的O提供配体，也就是说吸附后的结构中Cd2+与团簇能形成五根配位键，已经考虑了水溶液中脱去Cd2+的水配体的能量（只考虑了与溶剂配位的一层共6个水分子），也就是说吸附能是当成配体交换吸附来计算的，使用的计算基组为def2-TZVP，结果算出来有点大，吸附能大小为-125.5 kcal/mol，也就是-5.44 eV，想请问一下各位老师这个数值是否合理？

sobereva

2429783189 发表于 2026-1-8 01:15
我使用Gaussian计算团簇对Cd2+的吸附，在团簇中一个脱质子的羧基（提供两个配体）和三个不带电的O提供配体 ...

没法说必然有什么问题。如果怀疑的话，建议设计热力学循环，把脱溶剂、气相结合分开考察，更容易判断合理性

化小白

老师您好，看了您《透彻认识氢键本质、简单可靠地估计氢键强度：一篇2019年JCC上的重要研究文章介绍》这篇博文，想问一下您E_HB = -223.08*ρ(BCP)+0.7423这个公式是不是不能计算N-H这个实打实成键的键能呢？那如果想比较N-H键断裂需要的能量比断裂N-CH3的能量更低，那可以用AIM寻找临界点后得出的Density of all electrons能量直接比较吗？能垒已经算出来了，就是想再辅助证明一下

wzkchem5

化小白 发表于 2026-1-8 12:36
老师您好，看了您《透彻认识氢键本质、简单可靠地估计氢键强度：一篇2019年JCC上的重要研究文章介绍》这篇 ...

不能，因为这个公式是拟合出来的经验公式，训练集里没有共价键
不能这么比较，即使N-H键键能和ρ(BCP)有线性关系，N-C键键能和ρ(BCP)的相关系数也肯定和N-H完全不同。再者，Density of all electrons不是能量

化小白

老师，想问一下对比不同路径通过的难易程度，是只看能垒吗？如果路径A与C的能垒相差0.2kcal/mol，但是路径A中的反应物和过渡态的相对能量（13→TS9 相对能量 -13.4 → -1.9 能垒 11.5 kcal/mol）都比路径C中的反应物和过渡态低（11 → TS14 相对能量 0.4 → 11.3 能垒10.9 kcal/mol），但是能垒高出0.6kcal/mol，这不能排除路径C吗

wzkchem5

化小白 发表于 2026-1-15 12:24
老师，想问一下对比不同路径通过的难易程度，是只看能垒吗？如果路径A与C的能垒相差0.2kcal/mol，但是路径A ...

看自由能垒
具体参见http://sobereva.com/506