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PCM计算单点能结果文件分析

2017-10-12 20:30阅读：

http://blog.sina.cn/dpool/blog/u/5855462563

PCM计算单点能结果文件分析

作者：shims
输出文件如下，将一次分析结果模块:
Link 0这个模块主要是输入输出相关文件的配置，如这里的输入文件，输出文件，初始化的命令和gaussian所使用的临时文件夹。
L0初始化程序，控制分层
Entering Gaussian System, Link 0=g09
Input=ligandOptimized.com
Output=ligandOptimized.log
Initial command:
/home/shims/install/g09/l1.exe /newdisk-1T/scratch/Gau-220823.inp -scrdir=/newdisk-1T/scratch/
L1处理执行路径，创建执行连接的列表，并初始化可擦写文件
Link 1开始输出gaussian软件相关的基本信息和输入文件的内容
Entering Link 1 = /home/shims/install/g09/l1.exe PID= 220824.
版权信息
Copyrigh
t (c) 1988,1990,1992,1993,1995,1998,2003,2009, Gaussian, Inc.
All Rights Reserved.
******************************************************

引用形式
Cite this work as:
Gaussian 09, Revision A.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, 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, 2009.
版本
******************************************
Gaussian 09: EM64L-G09RevA.01 8-May-2009
22-Mar-2017
******************************************
输入文件内容
%nproc=16
Will use up to 16 processors via shared memory.
%chk=ligand
%mem=8GB
----------------------------------------------
#p b3lyp/6-31g scrf=(pcm,solvent=water) NoSymm
----------------------------------------------
将输入文件的字符形式的参数数字化。
1/38=1/1;
2/12=2,15=1,17=6,18=5,40=1/2;
3/5=1,6=6,11=2,16=1,25=1,30=1,70=2201,72=1,74=-5/1,2,3;
4//1;
5/5=2,38=5,53=1/2;
6/7=2,8=2,9=2,10=2,28=1/1;
99/5=1,9=1/99;
Leave Link 1 at Wed Mar 22 22:50:41 2017, MaxMem= 1073741824 cpu: 0.8
L101 读取坐标和分子说明部分
完成初始化，退出Link 1，进入l101.exe读取分子说明部分
(Enter /home/shims/install/g09/l101.exe)
---------------------
remark line goes here
---------------------
Symbolic Z-matrix:
Charge = 0 Multiplicity = 1
C 27.174 24.217 30.57
******************************************************
H 15.494 18.972 24.49

NAtoms= 77 NQM= 77 NQMF= 0 NMic= 0 NMicF= 0 NTot= 77.
Isotopes and Nuclear Properties:
(Nuclear quadrupole moments (NQMom) in fm**2, nuclear magnetic moments (NMagM)
in nuclear magnetons)

Atom 1 2 3 4 5 6 7 8 9 10
IAtWgt= 12 1 1 1 12 12 1 1 1 1
AtmWgt= 12.0000000 1.0078250 1.0078250 1.0078250 12.0000000 12.0000000 1.0078250 1.0078250 1.0078250 1.0078250
NucSpn= 0 1 1 1 0 0 1 1 1 1
AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NMagM= 0.0000000 2.7928460 2.7928460 2.7928460 0.0000000 0.0000000 2.7928460 2.7928460 2.7928460 2.7928460
******************************************************
Leave Link 101 at Wed Mar 22 22:50:42 2017, MaxMem= 1073741824 cpu: 1.6
L202重新定位坐标，计算对称性，检查变量
(Enter /home/shims/install/g09/l202.exe)
在输入文件中明确写明了没有对称性控制（NoSymm ）
Symmetry turned off by external request.
化学式
Stoichiometry C28H48O
骨架构型
Framework group C1[X(C28H48O)]
自由度
Deg. of freedom 225
点群
Full point group C1 NOp 1
Z矩阵
Z-Matrix orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 6 0 27.174000 24.217000 30.570000
******************************************************
77 1 0 15.494000 18.972000 24.490000
---------------------------------------------------------------------
旋转常数
Rotational constants (GHZ): 0.5825729 0.0476191 0.0460439
Leave Link 202 at Wed Mar 22 22:50:42 2017, MaxMem= 1073741824 cpu: 0.2
L301产生基组信息
(Enter /home/shims/install/g09/l301.exe)
基组
Standard basis: 6-31G (6D, 7F)
Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F.
积分缓冲大小
Integral buffers will be 131072 words long.
Raffenetti 2 integral format.
不进行双电子对称积分
Two-electron integral symmetry is turned off.
基函数信息：357个基函数，830个简单高斯基，357笛卡尔基函数，112个alpha电子，112个beta电子，原子排斥能2912.0102557185 Hartrees
357 basis functions, 830 primitive gaussians, 357 cartesian basis functions
112 alpha electrons 112 beta electrons
nuclear repulsion energy 2912.0102557185 Hartrees.
IExCor= 402 DFT=T Ex Corr=B3LYP ExCW=0 ScaHFX= 0.200000
ScaDFX= 0.800000 0.720000 1.000000 0.810000 ScalE2= 1.000000 1.000000
IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0
NAtoms= 77 NActive= 77 NUniq= 77 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=F Big=T
PCM溶剂化模型信息
------------------------------------------------------------------------------
Polarizable Continuum Model (PCM)
=================================
Model : PCM.
Atomic radii : UFF (Universal Force Field).
Polarization charges : Total charges.
Charge compensation : None.
Solution method : Matrix inversion.
Cavity type : Scaled VdW (van der Waals Surface) (Alpha=1.100).
Cavity algorithm : GePol (No added spheres)
Default sphere list used, NSphG= 77.
Lebedev-Laikov grids with approx. 5.0 points / Ang**2.
Smoothing algorithm: Karplus/York (Gamma=1.0000).
Polarization charges: spherical gaussians, with
point-specific exponents (IZeta= 3).
Self-potential: point-specific (ISelfS= 7).
Self-field : sphere-specific E.n sum rule (ISelfD= 2).
Solvent : Water, Eps= 78.355300 Eps(inf)= 1.777849
------------------------------------------------------------------------------
GePol: Number of generator spheres = 77
GePol: Total number of spheres = 77
GePol: Number of exposed spheres = 76 ( 98.70%)
GePol: Number of points = 4087
GePol: Average weight of points = 0.13
GePol: Minimum weight of points = 0.31D-09
GePol: Maximum weight of points = 0.20577
GePol: Number of points with low weight = 330
GePol: Fraction of low-weight points (<1% of avg) = 8.07%
GePol: Cavity surface area = 540.146 Ang**2
GePol: Cavity volume = 644.362 Ang**3
Leave Link 301 at Wed Mar 22 22:50:42 2017, MaxMem= 1073741824 cpu: 2.4
L302计算重叠，动能和势能积分
(Enter /home/shims/install/g09/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.
NBasis= 357 RedAO= T NBF= 357
NBsUse= 357 1.00D-06 NBFU= 357
Precomputing XC quadrature grid using
IXCGrd= 2 IRadAn= 0 IRanWt= -1 IRanGd= 0 AccXCQ= 1.00D-10.
NRdTot= 4993 NPtTot= 638246 NUsed= 674211 NTot= 674243
NSgBfM= 328 328 329 330 332 NAtAll= 77 77.
Leave Link 302 at Wed Mar 22 22:50:43 2017, MaxMem= 1073741824 cpu: 15.8
L303计算多级积分
(Enter /home/shims/install/g09/l303.exe)
DipDrv: MaxL=1.
Leave Link 303 at Wed Mar 22 22:50:44 2017, MaxMem= 1073741824 cpu: 2.5
L401形成初始MO猜测
(Enter /home/shims/install/g09/l401.exe)
Harris functional with IExCor= 402 diagonalized for initial guess.
ExpMin= 1.61D-01 ExpMax= 5.48D 03 ExpMxC= 8.25D 02 IAcc=1 IRadAn= 1 AccDes= 0.00D 00
HarFok: IExCor= 402 AccDes= 0.00D 00 IRadAn= 1 IDoV= 1
ScaDFX= 1.000000 1.000000 1.000000 1.000000
FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 1
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.
Symmetry not used in FoFCou.
Harris En= -1171.00040939413
Leave Link 401 at Wed Mar 22 22:50:45 2017, MaxMem= 1073741824 cpu: 22.3
L502迭代求解SCF方程，用于常规的UHF和ROHF
(Enter /home/shims/install/g09/l502.exe)
Closed shell SCF:
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.
Using DIIS extrapolation, IDIIS= 1040.
Two-electron integral symmetry not used.
673505 words used for storage of precomputed grid.
IEnd= 1082006 IEndB= 1082006 NGot= 1073741824 MDV= 1072804265
LenX= 1072804265 LenY= 1072676375
Fock matrices will be formed incrementally for 20 cycles.

Cycle 1 Pass 1 IDiag 1:
FoFCou: FMM=T IPFlag= 0 FMFlag= 100000 FMFlg1= 1
NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T
Omega= 0.000000 0.000000 1.000000 0.000000 0.000000 ICntrl= 0 IOpCl= 0
NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0
I1Cent= 0 NGrid= 0.
Symmetry not used in FoFCou.
FMM levels: 10 Number of levels for PrismC: 9
E= -1169.92565428443
DIIS: error= 2.25D-02 at cycle 1 NSaved= 1.
NSaved= 1 IEnMin= 1 EnMin= -1169.92565428443 IErMin= 1 ErrMin= 2.25D-02
ErrMax= 2.25D-02 EMaxC= 1.00D-01 BMatC= 8.00D-01 BMatP= 8.00D-01
IDIUse=3 WtCom= 7.75D-01 WtEn= 2.25D-01
Coeff-Com: 0.100D 01
Coeff-En: 0.100D 01
Coeff: 0.100D 01
Gap= 0.258 Goal= None Shift= 0.000
GapD= 0.258 DampG=1.000 DampE=0.500 DampFc=0.5000 IDamp=-1.
Damping current iteration by 5.00D-01
RMSDP=6.28D-03 MaxDP=1.43D-01 OVMax= 1.62D-01

******************************************************

Cycle 12 Pass 1 IDiag 1:
RMSU= 5.16D-09 CP: 9.76D-01 8.59D-01 8.15D-01 6.02D-01 8.03D-01
CP: 5.97D-01 7.51D-01 6.51D-01 7.81D-01 7.66D-01
CP: 7.96D-01
E= -1170.83358469440 Delta-E= 0.000000000019 Rises=F Damp=F
DIIS: error= 2.47D-08 at cycle 12 NSaved= 12.
NSaved=12 IEnMin=11 EnMin= -1170.83358469442 IErMin=12 ErrMin= 2.47D-08
ErrMax= 2.47D-08 EMaxC= 1.00D-01 BMatC= 7.20D-13 BMatP= 5.31D-12
IDIUse=1 WtCom= 1.00D 00 WtEn= 0.00D 00
Coeff-Com: -0.160D-06 0.116D-05-0.133D-04-0.269D-04-0.230D-03-0.321D-03
Coeff-Com: -0.129D-02 0.243D-03 0.135D-01 0.596D-01 0.302D 00 0.626D 00
Coeff: -0.160D-06 0.116D-05-0.133D-04-0.269D-04-0.230D-03-0.321D-03
Coeff: -0.129D-02 0.243D-03 0.135D-01 0.596D-01 0.302D 00 0.626D 00
Gap= 0.256 Goal= None Shift= 0.000
RMSDP=3.68D-09 MaxDP=1.68D-07 DE= 1.86D-11 OVMax= 1.09D-07

Error on total polarization charges = 0.01490
SCF Done: E(RB3LYP) = -1170.83358469 A.U. after 12 cycles
Convg = 0.3684D-08 -V/T = 2.0058
KE= 1.164111313490D 03 PE=-8.538415041080D 03 EE= 3.291459887177D 03
Leave Link 502 at Wed Mar 22 22:52:27 2017, MaxMem= 1073741824 cpu: 1535.4
L601布居分布相关的分析包括多极矩的分析
(Enter /home/shims/install/g09/l601.exe)
Copying SCF densities to generalized density rwf, IOpCl= 0 IROHF=0.

**********************************************************************

Population analysis using the SCF density.

**********************************************************************

Alpha occ. eigenvalues -- -19.13666 -10.22997 -10.19418 -10.18104 -10.18067
******************************************************
Alpha virt. eigenvalues -- 0.02783 0.07579 0.08031 0.08313 0.08481
******************************************************
Condensed to atoms (all electrons):
Mulliken atomic charges:
1
1 C -0.413128
******************************************************
77 H 0.127574
Sum of Mulliken atomic charges = 0.00000
Mulliken charges with hydrogens summed into heavy atoms:
1
1 C -0.022912
******************************************************
75 C 0.004658
Sum of Mulliken charges with hydrogens summed into heavy atoms = 0.00000
Electronic spatial extent (au): = 1247759.5415
Charge= 0.0000 electrons
Dipole moment (field-independent basis, Debye):
X= 0.4802 Y= 1.3888 Z= 1.6330 Tot= 2.1968
Quadrupole moment (field-independent basis, Debye-Ang):
XX= -167.4040 YY= -129.1516 ZZ= -111.6075
XY= 26.6672 XZ= 30.3790 YZ= 64.6626
Traceless Quadrupole moment (field-independent basis, Debye-Ang):
XX= -31.3496 YY= 6.9027 ZZ= 24.4468
XY= 26.6672 XZ= 30.3790 YZ= 64.6626
Octapole moment (field-independent basis, Debye-Ang**2):
XXX= -10469.3994 YYY= -10405.6635 ZZZ= -11959.4233 XYY= -2749.6161
XXY= -3455.5211 XXZ= -4196.9576 XZZ= -2521.8431 YZZ= -1824.3163
YYZ= -2864.8481 XYZ= 1003.7637
Hexadecapole moment (field-independent basis, Debye-Ang**3):
XXXX= -441388.1184 YYYY= -484025.7966 ZZZZ= -684233.6299 XXXY= -227477.8152
XXXZ= -277578.8049 YYYX= -214398.9725 YYYZ= -263452.0238 ZZZX= -254879.0319
ZZZY= -249238.3838 XXYY= -147028.1150 XXZZ= -183190.6912 YYZZ= -155283.6374
XXYZ= -87776.3727 YYXZ= -68089.9811 ZZXY= -48377.3395
N-N= 2.912010255718D 03 E-N=-8.538415032512D 03 KE= 1.164111313490D 03
No NMR shielding tensors so no spin-rotation constants.
Leave Link 601 at Wed Mar 22 22:52:27 2017, MaxMem= 1073741824 cpu: 5.7
L9999完成计算并输出结果
(Enter /home/shims/install/g09/l9999.exe)
1\1\GINC-COMPUTE-0-9\SP\RB3LYP\6-31G\C28H48O1\SHIMS\22-Mar-2017\0\\#p
b3lyp/6-31g scrf=(pcm,solvent=water) NoSymm\\remark line goes here\\0,
1\C,0,27.174,24.217,30.57\H,0,28.235,24.439,30.407\H,0,27.079,23.79,31
.576\H,0,26.626,25.168,30.555\C,0,26.646,23.25,29.49\C,0,27.46,21.939,
29.498\H,0,28.521,22.148,29.315\H,0,27.12,21.242,28.725\H,0,27.385,21.
434,30.468\H,0,26.808,23.736,28.514\C,0,25.103,23.029,29.609\C,0,24.70
3,22.233,30.869\H,0,25.167,22.645,31.772\H,0,25.002,21.181,30.786\H,0,
23.618,22.256,31.022\H,0,24.658,24.035,29.694\C,0,24.522,22.39,28.322\
H,0,24.923,21.374,28.216\H,0,24.886,22.962,27.454\C,0,22.98,22.355,28.
281\H,0,22.61,23.338,28.598\H,0,22.603,21.629,29.016\C,0,22.366,22.008
,26.894\C,0,22.843,20.619,26.424\H,0,23.936,20.551,26.445\H,0,22.527,2
0.399,25.401\H,0,22.446,19.83,27.076\H,0,22.736,22.759,26.177\C,0,20.8
17,22.133,26.96\C,0,20.351,23.565,27.414\C,0,18.965,23.829,26.755\H,0,
19.034,24.606,25.982\H,0,18.22,24.171,27.482\H,0,20.292,23.629,28.505\
H,0,21.083,24.318,27.095\H,0,20.47,21.406,27.713\C,0,19.956,21.868,25.
667\C,0,19.683,20.389,25.304\C,0,18.565,20.257,24.241\H,0,18.384,19.19
1,24.055\H,0,18.932,20.674,23.296\H,0,20.584,19.896,24.924\H,0,19.39,1
9.85,26.218\C,0,20.557,22.629,24.46\H,0,21.483,22.147,24.125\H,0,20.80
1,23.666,24.715\H,0,19.874,22.653,23.607\C,0,18.59,22.472,26.129\H,0,1
8.254,21.823,26.96\C,0,17.463,22.423,25.085\C,0,16.156,23.008,25.659\C
,0,14.939,22.634,24.858\H,0,14.027,23.188,25.083\H,0,16.029,22.664,26.
701\H,0,16.233,24.103,25.722\H,0,17.747,23.026,24.209\C,0,17.233,20.95
1,24.632\H,0,16.843,20.423,25.52\C,0,16.118,20.822,23.53\C,0,16.636,21
.27,22.134\H,0,15.825,21.297,21.4\H,0,17.398,20.583,21.752\H,0,17.069,
22.276,22.179\C,0,14.9,21.686,23.906\C,0,13.614,21.415,23.142\H,0,12.8
02,22.026,23.558\H,0,13.715,21.697,22.083\C,0,13.23,19.927,23.17\O,0,1
2.075,19.656,22.32\H,0,11.302,20.167,22.634\H,0,13.003,19.632,24.208\C
,0,14.38,19.076,22.643\H,0,14.53,19.319,21.583\H,0,14.101,18.017,22.68
7\C,0,15.661,19.324,23.462\H,0,16.475,18.716,23.049\H,0,15.494,18.972,
24.49\\Version=EM64L-G09RevA.01\HF=-1170.8335847\RMSD=3.684e-09\Dipole
=0.1889072,0.5463953,0.6424539\Quadrupole=-23.3076532,5.1320241,18.175
6292,19.8264247,22.5860703,48.0750898\PG=C01 [X(C28H48O1)]\\@


THE BEST WAY TO CONVINCE A FOOL THAT HE IS WRONG
IS TO LET HIM HAVE HIS OWN WAY.

JOSH BILLINGS
Job cpu time: 0 days 0 hours 26 minutes 28.2 seconds.
File lengths (MBytes): RWF= 403 Int= 0 D2E= 0 Chk= 8 Scr= 2
Normal termination of Gaussian 09 at Wed Mar 22 22:52:28 2017.

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