本文是南开大学孙宏伟老师《量子化学与分子力学/分子模拟》课程
Gaussian 实操部分的笔记，孙老师这部分的授课内容主要基于《Exploring
Chemistry with Electronic Structure
Methods》第二版和第三版中的实例，这本书也被称为“高斯圣经”，非常具有代表性。我在孙老师的授课基础上，同时也参考了此书和其它的一些资料，尽可能从解决实际问题的角度出发，整理整篇笔记。
1 Gaussian 文件
1.1 Gaussian 输入文件结构
Gaussian 的输入文件后缀名为“.gjf”，下面以示例的“e2_01.gjf”为例：
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%chk=e2_01 # RHF/6-31G(d) sp
Formaldehyde Single Point Energy
0 1 C 0. 0. 0. O 0. 1.22 0. H .94 -.54 0. H -.94 -.54 0.
输入文件解析：
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%chk=e2_01 ## 生成 chk 文件 # RHF/6-31G(d) sp ## Route Section，理论方法/基组 计算内容 ## 必须空一行 Formaldehyde Single Point Energy ## Job 名，不能为空 ## 必须空一行 0 1 ## 分子的 charge 和 spin，中间以空格隔开 C 0. 0. 0. ## 分子结构，可以是内坐标，也可以是直角坐标系 O 0. 1.22 0. H .94 -.54 0. H -.94 -.54 0. ## 结尾必须空一行
注：chk
文件可以理解为日志文件，包含了比输出文件更多的信息，考虑到过去计算机的磁盘占用，《Exploring
Chemistry with Electronic Structure Methods》第二版示例默认不生成 chk
文件，今天的计算机已经不需要再担心这个问题。
1.2 Gaussian 输出文件结构
Gaussian 的输出文件后缀名是“.out”，下面以示例的“e2_01.out”为例：
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Default is to use a total of 4 processors: ## 硬件调用信息 4 via shared-memory 1 via Linda Entering Link 1 = E:\G09W\l1.exe PID= 9760.
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Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2013, ## 版权声明 Gaussian, Inc. All Rights Reserved. ...
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Cite this work as: ## 引文格式 Gaussian 09, Revision D.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2013.
Input orientation: ## 输入的分子坐标 --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 0.000000 0.000000 0.000000 2 8 0 0.000000 1.220000 0.000000 3 1 0 0.940000 -0.540000 0.000000 4 1 0 -0.940000 -0.540000 0.000000 ---------------------------------------------------------------------
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Framework group C2V[C2(CO),SGV(H2)] ## 分子所属的点群 Deg. of freedom 3 Full point group C2V NOp 4 Largest Abelian subgroup C2V NOp 4 Largest concise Abelian subgroup C2 NOp 2 Standard orientation: ## 转换成的标准坐标 --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 0.000000 0.000000 -0.542500 2 8 0 0.000000 0.000000 0.677500 3 1 0 0.000000 0.940000 -1.082500 4 1 0 0.000000 -0.940000 -1.082500 ---------------------------------------------------------------------
REPARTEE - WHAT YOU THINK OF AFTER YOU BECOME A DEPARTEE. ## Gaussian 结果中会随机输出一句名人名言 Job cpu time: 0 days 0 hours 0 minutes 2.0 seconds. ## Job 耗时 File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1 Normal termination of Gaussian 09 at Wed Feb 10 09:35:46 2021. ## Job 正常结束会输出“Normal termination”
Pop=X X=NONE no orbital information displayed X=REG HOMO-5 up to
LUMO+5 orbital information displayed X=FULL all orbitals information
displayed X=NBO Mulliken analysis is replaced by Natural Bond-Order
analysis X=MK, CHELP, OR CHELPG produce charges fit to electrostatic
potential (ESP)
在需要分析分子轨道时推荐使用
pop=full，输出完整分子轨道：
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%chk=e2_01 # RHF/6-31G(d) pop=full
Formaldehyde Single Point Energy
0 1 C 0. 0. 0. O 0. 1.22 0. H .94 -.54 0. H -.94 -.54 0.
Item Value Threshold Converged? Maximum Force 0.014805 0.000450 NO RMS Force 0.010422 0.000300 NO Maximum Displacement 0.040615 0.001800 NO RMS Displacement 0.025747 0.001200 NO
...
Item Value Threshold Converged? Maximum Force 0.000157 0.000450 YES RMS Force 0.000094 0.000300 YES Maximum Displacement 0.000709 0.001800 YES RMS Displacement 0.000509 0.001200 YES
0 1 C 0.94120000 1.44630000 -0.38240000 C 1.47590000 0.20170000 -0.04990000 C 0.62750000 -0.86850000 0.23390000 C -0.75550000 -0.69400000 0.18530000 C -1.29020000 0.55060000 -0.14710000 C -0.44180000 1.62080000 -0.43100000 N -1.52550000 -1.66540000 0.44290000 H 1.61020000 2.29020000 -0.60630000 H 2.56660000 0.06410000 -0.01150000 H 1.04910000 -1.85010000 0.49610000 H -2.38090000 0.68820000 -0.18530000 H -0.86340000 2.60230000 -0.69320000 H -2.56660000 -1.53410000 0.40640000 H -1.12300000 -2.60230000 0.69320000
Sum of electronic and zero-point Energies= -287.484373 Sum of electronic and thermal Energies= -287.478589 Sum of electronic and thermal Enthalpies= -287.477645 Sum of electronic and thermal Free Energies= -287.513525
可以看到，默认条件是 298.150 K，1 个标准大气压。如果计算不同温度下的
Thermochemistry 值，需要在输入文件中指定，单位分别是 K 和 1
atmosphere。
p-(dimethylamino)-benzonitrile ground state gas-phase optimization
0 1 N -0.04101341 2.28408831 0.00000000 C -0.02177167 0.91831518 0.00000000 C 0.02336490 3.01083873 1.24505177 C 0.02336490 3.01083873 -1.24505177 C -0.01240990 0.18624041 1.20656105 C -0.01240990 0.18624041 -1.20656105 H -0.01204696 4.07826791 1.03677119 H -0.82469723 2.76995589 1.89489375 H 0.94871081 2.80294502 1.79639727 H -0.01204696 4.07826791 -1.03677119 H 0.94871081 2.80294502 -1.79639727 H -0.82469723 2.76995589 -1.89489375 C -0.00416976 -1.19229071 1.20143517 C -0.00416976 -1.19229071 -1.20143517 H -0.01086478 0.69917093 2.15922890 H -0.01086478 0.69917093 -2.15922890 C -0.00122206 -1.90542362 0.00000000 H 0.00200625 -1.73299624 2.14146609 H 0.00200625 -1.73299624 -2.14146609 C 0.00836716 -3.32900547 0.00000000 N 0.01597995 -4.48349542 0.00000000
Counterpoise corrected energy = -114.205331718236 BSSE energy = 0.000770265286 sum of monomers = -114.200971733922 complexation energy = -3.22 kcal/mole (raw) complexation energy = -2.74 kcal/mole (corrected)
The following calculation defaults are different in Gaussian 16:
Integral accuracy is 10-12 rather than 10-10 in Gaussian 09.
The default DFT grid for general use is UltraFine rather than
FineGrid in G09; the default grid for CPHF is SG1 rather than
CoarseGrid. See the discussion of the Integral keyword for
details.
SCRF defaults to the symmetric form of IEFPCM [Lipparini10] (not
present in Gaussian 09) rather than the non-symmetric version.
Physical constants use the 2010 values rather than the 2006 values
in Gaussian 09.
The first two items were changed to ensure accuracy in several new
calculation types (e.g., TD-DFT frequencies, anharmonic ROA). For these
reasons, Integral=(UltraFine,Acc2E=12) was made the default. Using these
settings generally improve the reliability of calculations involving
numerical integration, e.g., DFT optimizations in solution. There is a
modest increase in the CPU requirements for these options compared to
the Gaussian 09 defaults of Integral=(FineGrid,Acc2E=10).
The G09Defaults keyword sets
all four of these defaults back to the Gaussian 09 values. It is
provided for compatibility with previous calculations, but the new
defaults are strongly recommended for new studies.
Default Memory Use
Gaussian 16 defaults memory usage to %Mem=100MW (800MB).
TD-DFT Frequencies
TDDFT frequency calculations compute second derivatives analytically
by default, since these are much faster than the numerical derivatives
(the only choice in Gaussian 09).
