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313588908

木虫 (正式写手)

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虫号: 577296
注册: 2008-06-22
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专业: 有机合成

[交流] 【求助】金属配位，为什么结构总是跑掉

S配位Ag，为什么最后优化到Ag-S很短很短了，是不是初始结构有误？
下面是输入和部分输出文件。
%mem=60MW
# opt b3lyp/gen pseudo=read

Title Card Required

1 1
C                2.06002300 -0.16901900 0.51928100
C                1.77675900 1.28586500 0.23651600
H                1.76551800 -0.51969000 1.50377400
H                2.51092900 1.83474000 -0.34043500
H                1.34165200 1.87799500 1.03222900
S                0.73027200 0.13991400 -0.62333200
H                2.97407438 -0.60996682 0.18020124
Ag             -1.50483170 -0.09283415 0.06415600
O                -3.59400592 -0.33021625 0.80705628
H                -4.36051528 -0.86372240 0.58471738
H                -3.78874008 0.20378078 1.58070075

C H  0
3-21G
************
S  0
6-31G+(d)
************
Ag 0
Lanl2dz
***********
输出
  Pseudopotential Parameters
=============================================
  Center    Atomic    Valence    Angular    Power                                                    Coordinates
  Number    Number    Electrons    Momentum    of R    Exponent       Coefficient             X          Y          Z
===============================================
1       6                                                                                  5.036939  0.824875  1.550419
                                 No pseudopotential on this center.
2       6                                                                                  4.977538  1.224997 -1.272216
                                 No pseudopotential on this center.
3       1                                                                                  4.211615  2.330812  2.673375
                                 No pseudopotential on this center.
4       1                                                                                  6.603558  0.602463 -2.348262
                                 No pseudopotential on this center.
5       1                                                                                  4.194591  2.983575 -1.967628
                                 No pseudopotential on this center.
6       16                                                                                  2.858965 -1.109961 -0.131962
                                 No pseudopotential on this center.
7       1                                                                                  6.671309  0.010061  2.418420
                                 No pseudopotential on this center.
8       47                                                                                  -1.487095 -0.202091 -0.038455
                                 No pseudopotential on this center.
9       8                                                                                  -5.573152  0.812261  0.145325
                                 No pseudopotential on this center.
10       1                                                                                  -7.110844  0.020828  0.693259
                                 No pseudopotential on this center.
11       1                                                                                  -5.921848  2.512611 -0.382229
                                 No pseudopotential on this center.
=======================================
There are 74 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.
74 basis functions, 159 primitive gaussians, 76 cartesian basis functions
44 alpha electrons    44 beta electrons
   nuclear repulsion energy    528.2177437134 Hartrees.

Warning!  S  atom 6 may be hypervalent but has no d functions.
Warning!  Ag atom 8 has 47 valence electrons but only  22 basis functions.
This is less than a minimal basis set!

NAtoms= 11 NActive= 11 NUniq= 11 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=F Big=F
One-electron integrals computed using PRISM.
1 Symmetry operations used in ECPInt.
ECPInt:  NShTT=    561 NPrTT= 2552 LenC2=    527 LenP2D= 2014.
LDataN:  DoStor=F MaxTD1= 4 Len= 56
LDataN:  DoStor=T MaxTD1= 4 Len= 56
NBasis= 74 RedAO= T  NBF= 74
NBsUse= 74 1.00D-06 NBFU= 74
Defaulting to unpruned grid for atomic number  47.
Harris functional with IExCor=  402 diagonalized for initial guess.
ExpMin= 2.52D-02 ExpMax= 2.19D+04 ExpMxC= 3.30D+03 IAcc=3 IRadAn=       5 AccDes= 0.00D+00
HarFok:  IExCor= 402 AccDes= 0.00D+00 IRadAn=       5 IDoV=1
ScaDFX=  1.000000  1.000000  1.000000  1.000000
Defaulting to unpruned grid for atomic number  47.
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) (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)
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.
Keep R1 integrals in memory in canonical form, NReq=    6135976.
Defaulting to unpruned grid for atomic number  47.
EnCoef did    7 forward-backward iterations
EnCoef did 100 forward-backward iterations
EnCoef did    2 forward-backward iterations
EnCoef did    8 forward-backward iterations
EnCoef did 100 forward-backward iterations
EnCoef did    2 forward-backward iterations
EnCoef did 20 forward-backward iterations
Rare condition: small coef for last iteration:  0.555D-15
EnCoef did 19 forward-backward iterations
Restarting incremental Fock formation.
SCF Done:  E(RB+HF-LYP) =  -1418.89008804    A.U. after 27 cycles
         Convg  = 0.5583D-08          -V/T =  3.2077
         S**2 = 0.0000

1 Symmetry operations used in ECPInt.
ECPInt:  NShTT=    561 NPrTT= 2552 LenC2=    527 LenP2D= 2014.
LDataN:  DoStor=F MaxTD1= 5 Len=  102
LDataN:  DoStor=T MaxTD1= 5 Len=  102
Defaulting to unpruned grid for atomic number  47.

      Item             Value    Threshold  Converged?
Maximum Force          ********    0.000450    NO
RMS    Force          2.079823    0.000300    NO
Maximum Displacement    0.273738    0.001800    NO
RMS    Displacement    0.097829    0.001200    NO
Predicted change in Energy=-3.939808D+00
GradGradGradGdGradGradGradGradGradGradGrad

  Stoichiometry C2H6AgOS(1+)
Framework group  C1[X(C2H6AgOS)]
Deg. of freedom 27
Full point group                C1
Largest Abelian subgroup       C1    NOp 1
Largest concise Abelian subgroup C1    NOp 1
                     Standard orientation:
---------------------------------------------------------------------
Center    Atomic    Atomic             Coordinates (Angstroms)
Number    Number    Type             X          Y          Z
---------------------------------------------------------------------
1       6          0       2.542763 0.434575 0.826849
2       6          0       2.512174 0.647129 -0.677042
3       1          0       2.098956 1.229995 1.417046
4       1          0       3.374254 0.324785 -1.247773
5       1          0       2.091405 1.574893 -1.043792
6       16          0       1.414621 -0.583145 -0.068172
7       1          0       3.408249 0.010250 1.291217
8       47          0    -0.730848 -0.107985 -0.022210
9       8          0    -2.859416 0.428209 0.080814
10       1          0    -3.677271 0.016126 0.371936
11       1          0    -3.033979 1.333662 -0.199356
---------------------------------------------------------------------
Rotational constants (GHZ):    10.3927024    1.0536788    1.0372554
Basis read from rwf:  (5D, 7F)
Pseudo-potential data read from rwf file.
There are 74 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.
74 basis functions, 159 primitive gaussians, 76 cartesian basis functions
44 alpha electrons    44 beta electrons
   nuclear repulsion energy    548.4177370444 Hartrees.

Warning!  S  atom 6 may be hypervalent but has no d functions.
Warning!  Ag atom 8 has 47 valence electrons but only  22 basis functions.
This is less than a minimal basis set!

NAtoms= 11 NActive= 11 NUniq= 11 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=F Big=F
One-electron integrals computed using PRISM.
1 Symmetry operations used in ECPInt.
ECPInt:  NShTT=    561 NPrTT= 2552 LenC2=    530 LenP2D= 2039.
LDataN:  DoStor=F MaxTD1= 4 Len= 56
LDataN:  DoStor=T MaxTD1= 4 Len= 56
NBasis= 74 RedAO= T  NBF= 74
NBsUse= 74 1.00D-06 NBFU= 74
Defaulting to unpruned grid for atomic number  47.
Initial guess read from the read-write file:
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) (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)
Harris functional with IExCor=  402 diagonalized for initial guess.
ExpMin= 2.52D-02 ExpMax= 2.19D+04 ExpMxC= 3.30D+03 IAcc=3 IRadAn=       5 AccDes= 0.00D+00
HarFok:  IExCor= 402 AccDes= 0.00D+00 IRadAn=       5 IDoV=1
ScaDFX=  1.000000  1.000000  1.000000  1.000000
Defaulting to unpruned grid for atomic number  47.
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.
Keep R1 integrals in memory in canonical form, NReq=    6135976.
Defaulting to unpruned grid for atomic number  47.
Restarting incremental Fock formation.
SCF Done:  E(RB+HF-LYP) =  -1423.97794199    A.U. after 20 cycles
         Convg  = 0.3758D-08          -V/T =  3.2074
         S**2 = 0.0000
1 Symmetry operations used in ECPInt.
ECPInt:  NShTT=    561 NPrTT= 2552 LenC2=    530 LenP2D= 2039.
LDataN:  DoStor=F MaxTD1= 5 Len=  102
LDataN:  DoStor=T MaxTD1= 5 Len=  102
Defaulting to unpruned grid for atomic number  47.
***** Axes restored to original set *****
-------------------------------------------------------------------
Center    Atomic                Forces (Hartrees/Bohr)
Number    Number             X             Y             Z
-------------------------------------------------------------------
1       6       -1.875684836 -1.427670063 -1.067220384
2       6       -2.124501680 0.192549494 -1.232917970
3       1          0.096289570 0.115270667 -0.046079021
4       1          0.094173163 -0.027478282 0.131404112
5       1          0.104251899 -0.063478803 -0.016390417
6       16       -16.111498451 -1.151456308 7.527507379
7       1          0.116096133 0.165574898 0.139544117
8       47       16.154554015 2.004242491 -3.706122435
9       8          3.204146632 -0.205825695 -1.971308278
10       1       -0.055018314 0.035493422 0.029130750
11       1          0.397191869 0.362778179 0.212452147
-------------------------------------------------------------------
Cartesian Forces:  Max 16.154554015 RMS    4.347480409

      Item             Value    Threshold  Converged?
Maximum Force          ********    0.000450    NO
RMS    Force          3.370126    0.000300    NO
Maximum Displacement    0.365043    0.001800    NO
RMS    Displacement    0.132480    0.001200    NO
Predicted change in Energy=-1.149627D+01
GradGradGradGradGradGradGradGradGradGradGradGradGradGrad

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1楼 2009-12-26 12:33:55

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

yjcmwgk

禁虫 (文坛精英)

密度泛函·小卒

QC强帖: 38
应助: 165 (高中生)
贵宾: 16.999
金币: 553.8
散金: 39880
红花: 395
沙发: 2
帖子: 10406
在线: 1528.1小时
虫号: 448368
注册: 2007-11-01
专业: 理论和计算化学
管辖: 科研工具资源

★ ★ ★ ★
小木虫(金币+0.5):给个红包，谢谢回帖交流
erylingjet(金币+3,VIP+0):感谢交流 12-27 10:48

谁教你这么写的？
重写输入文件
==文件开始==
%mem=60MW
# opt b3lyp/genecp

Title Card Required

1 1
C                2.06002300 -0.16901900 0.51928100
C                1.77675900 1.28586500 0.23651600
H                1.76551800 -0.51969000 1.50377400
H                2.51092900 1.83474000 -0.34043500
H                1.34165200 1.87799500 1.03222900
S                0.73027200 0.13991400 -0.62333200
H                2.97407438 -0.60996682 0.18020124
Ag             -1.50483170 -0.09283415 0.06415600
O                -3.59400592 -0.33021625 0.80705628
H                -4.36051528 -0.86372240 0.58471738
H                -3.78874008 0.20378078 1.58070075

C H  0
3-21G
****
S  0
6-31+G(d)
****
Ag 0
Lanl2dz
****

Ag 0
Lanl2dz

==文件结束==
(注意不要丢掉最后一个空行)
请看http://muchong.com/bbs/viewthread.php?tid=1566146这个帖子的第二章第六节
谁教你这么写的，你可以把他拖出去打死。高斯输入文件的格式是严格的。

*这个符号不是你随便写的
空行也不是随便空的

[ Last edited by yjcmwgk on 2009-12-26 at 12:58 ]

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2楼2009-12-26 12:52:04

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

yjcmwgk

禁虫 (文坛精英)

密度泛函·小卒

QC强帖: 38
应助: 165 (高中生)
贵宾: 16.999
金币: 553.8
散金: 39880
红花: 395
沙发: 2
帖子: 10406
在线: 1528.1小时
虫号: 448368
注册: 2007-11-01
专业: 理论和计算化学
管辖: 科研工具资源

★ ★ ★ ★
小木虫(金币+0.5):给个红包，谢谢回帖交流
erylingjet(金币+3,VIP+0):感谢交流 12-27 10:48

你的8号原子是Ag，但是输出文件中写着你的八号原子的提示是No pseudopotential on this center。况且，输出文件中已经给你警告了：
Warning! Ag atom 8 has 47 valence electrons but only 22 basis functions.
This is less than a minimal basis set!（这一句很重要，说明你没有把赝势电子输入进高斯中）
再看看这个警告Warning! S atom 6 may be hypervalent but has no d functions.谁教给你6-31g+(d)？改成6-31+g(d).
还有，你确定这个体系是带电荷的吗？

[ Last edited by yjcmwgk on 2009-12-26 at 12:58 ]

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3楼2009-12-26 12:57:31

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖