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

 Copyright (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.