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标题: 自定义基组+引用外部文件+cosmo文件 [打印本页]

作者
Author: whtu 时间: 2016-6-14 14:36
标题: 自定义基组+引用外部文件+cosmo文件
想学习自定义基组的使用，以H2O为例生成cosmo文件，输入文件如下：
%chk=water.chk
%nprocshared=8
%mem=5GB
# opt freq b3lyp/gen

Title Card Required

0 1
O                -0.85039369 -0.71653542 0.00000000
H                0.10960631 -0.71653542 0.00000000
H                -1.17084828 0.18840041 0.00000000

@/home/whtu/cation/def_TZVP/def-TZVP_gaussian.gbs

--Link1--
%chk=water.chk
#p opt b3lyp/gen int=ultrafine geom=allcheck guess=read scrf=cosmo test

@/home/whtu/cation/def_TZVP/def-TZVP_gaussian.gbs

--Link1--
%chk=water.chk
#p b3lyp/gen geom=allcheck guess=read int=ultrafine scrf=cosmors test

@/home/whtu/cation/def_TZVP/def-TZVP_gaussian.gbs

water.cosmo

自定义的基组文件为def-TZVP_gaussian.gbs，内容如下：
! def-TZVP Basis set for H, B, C, N, O, F, Al, P, S, Cl, Ca, Fe, In and Sb in Gaussian-format
-H 0
S  3  1.00
34.061341    .60251978E-02
5.1235746    .45021094E-01
1.1646626    .20189726
S  1  1.00
.32723041    1.0000000
S  1  1.00
.10307241    1.0000000
P  1  1.00
.80 1.00
****
! unpublished
-B 0
S  6  1.00
  8564.8660687    .22837198155E-03
  1284.1516263    .17682576447E-02
  292.27871604    .91407080516E-02
  82.775469176    .36342638989E-01
  27.017939269    .11063458441
  9.8149619660    .23367344321
S  2  1.00
  3.9318559059    .41818777978
  1.6595599712    .22325473798
S  1  1.00
  .35762965239    1.0000000000
S  1  1.00
  .14246277496    1.0000000000
S  1  1.00
  .60560594768E-01  1.0000000000
P  4  1.00
  22.453875803    .50265575179E-02
  5.1045058330    .32801738965E-01
  1.4986081344    .13151230768
  .50927831315    .33197167769
P  1  1.00
  .18147077798    .47314319570
P  1  1.00
  .64621893904E-01  .25802783943
D  1  1.00
  .50  1.00
****
! A. Sch?fer, C. Huber, R. Ahlrichs; J. Chem. Phys. 100, 5829 (1994).
-C 0
S  6  1.00
  13575.349682    .22245814352E-03
  2035.2333680    .17232738252E-02
  463.22562359    .89255715314E-02
  131.20019598    .35727984502E-01
  42.853015891    .11076259931
  15.584185766    .24295627626
S  2  1.00
  6.2067138508    .41440263448
  2.5764896527    .23744968655
S  1  1.00
  .57696339419    1.0000000000
S  1  1.00
  .22972831358    1.0000000000
S  1  1.00
  .95164440028E-01  1.0000000000
P  4  1.00
  34.697232244    .53333657805E-02
  7.9582622826    .35864109092E-01
  2.3780826883    .14215873329
  .81433208183    .34270471845
P  1  1.00
  .28887547253    .46445822433
P  1  1.00
  .10056823671    .24955789874
D  1  1.00
  .80 1.00
****
! A. Sch?fer, C. Huber, R. Ahlrichs; J. Chem. Phys. 100, 5829 (1994).
-N 0
S  6  1.00
  19730.800647    .21887984991E-03
  2957.8958745    .16960708803E-02
  673.22133595    .87954603538E-02
  190.68249494    .35359382605E-01
  62.295441898    .11095789217
  22.654161182    .24982972552
S  2  1.00
  8.9791477428    .40623896148
  3.6863002370    .24338217176
S  1  1.00
  .84660076805    1.0000000000
S  1  1.00
  .33647133771    1.0000000000
S  1  1.00
  .13647653675    1.0000000000
P  4  1.00
  49.200380510    .55552416751E-02
  11.346790537    .38052379723E-01
  3.4273972411    .14953671029
  1.1785525134    .34949305230
P  1  1.00
  .41642204972    .45843153697
P  1  1.00
  .14260826011    .24428771672
D  1  1.00
  1.00 1.00
****
! A. Sch?fer, C. Huber, R. Ahlrichs; J. Chem. Phys. 100, 5829 (1994).
-O 0
S  6  1.00
  27032.382631    .21726302465E-03
  4052.3871392    .16838662199E-02
  922.32722710    .87395616265E-02
  261.24070989    .35239968808E-01
  85.354641351    .11153519115
  31.035035245    .25588953961
S  2  1.00
  12.260860728    .39768730901
  4.9987076005    .24627849430
S  1  1.00
  1.1703108158    1.0000000000
S  1  1.00
  .46474740994    1.0000000000
S  1  1.00
  .18504536357    1.0000000000
P  4  1.00
  63.274954801    .60685103418E-02
  14.627049379    .41912575824E-01
  4.4501223456    .16153841088
  1.5275799647    .35706951311
P  1  1.00
  .52935117943    .44794207502
P  1  1.00
  .17478421270    .24446069663
D  1  1.00
  1.20 1.00
****
! A. Sch?fer, C. Huber, R. Ahlrichs; J. Chem. Phys. 100, 5829 (1994).
-F 0
S  6  1.00
  35479.100441    .21545014888E-03
  5318.4728983    .16700686527E-02
  1210.4810975    .86733211476E-02
  342.85518140    .35049933175E-01
  112.01943181    .11165320133
  40.714740248    .25988506647
S  2  1.00
  16.039678111    .39422966880
  6.5038186740    .24998238551
S  1  1.00
  1.5440477509    1.0000000000
S  1  1.00
  .61223452862    1.0000000000
S  1  1.00
  .24027979698    1.0000000000
P  4  1.00
  80.233900483    .63685999134E-02
  18.594010743    .44303143530E-01
  5.6867902653    .16867248708
  1.9511006294    .36166346255
P  1  1.00
  .66970211298    .44202901491
P  1  1.00
  .21651300410    .24319875730
D  1  1.00
  1.40 1.00
****
! A. Sch?fer, C. Huber, R. Ahlrichs; J. Chem. Phys. 100, 5829 (1994).
-Al 0
S  7  1.00
  37792.550772    .57047888709E-03
  5668.0682165    .44093016538E-02
  1289.8582841    .22630967411E-01
  364.86596028    .88025644295E-01
  118.57631515    .25223701612
  42.024867605    .45960547169
  15.499501629    .33277886014
S  3  1.00
  75.208026598    .19250560190E-01
  23.031408972    .87906743952E-01
  3.6348797649    -.34246704535
S  2  1.00
  1.6065049957    1.5106266058
  .76103394581    .58071016470
S  1  1.00
  .16556708849    1.0000000000
S  1  1.00
  .60041577113E-01  1.0000000000
P  6  1.00
  452.52303192    .23110812466E-02
  107.08195049    .18568641823E-01
  34.131021255    .87216237035E-01
  12.587037428    .26902101523
  4.9811919704    .52128324272
  2.0070350900    .60271687494
P  1  1.00
  .80083714374    1.0000000000
P  1  1.00
  .20178927472    1.0000000000
P  1  1.00
  .57895550392E-01  1.0000000000
D  1  1.00
  .30 1.00
****
! A. Sch?fer, C. Huber, R. Ahlrichs; J. Chem. Phys. 100, 5829 (1994).
-P 0
S  7  1.00
  52426.999233    .55207164100E-03
  7863.2660552    .42678595308E-02
  1789.5227333    .21931529186E-01
  506.27300165    .85667168373E-01
  164.60698546    .24840686605
  58.391918722    .46336753971
  21.643663201    .35350558156
S  3  1.00
  99.013837620    .21895679958E-01
  30.550439817    .95650470295E-01
  5.4537087661    -.29454270186
S  2  1.00
  2.6503362563    1.3294381200
  1.2726688867    .66109396473
S  1  1.00
  .31645005203    1.0000000000
S  1  1.00
  .11417466938    1.0000000000
P  6  1.00
  472.27219248    .25710623052E-02
  111.58882756    .20250297999E-01
  35.445936418    .91580716787E-01
  12.990776875    .25749454014
  5.0486221658    .42862899758
  1.9934049566    .34359817849
P  1  1.00
  .66527284430    1.0000000000
P  1  1.00
  .25516832128    1.0000000000
P  1  1.00
  .90357762251E-01  1.0000000000
D  1  1.00
  .45 1.00
****
! A. Sch?fer, C. Huber, R. Ahlrichs; J. Chem. Phys. 100, 5829 (1994).
-S 0
S  7  1.00
  60700.928104    .54695944225E-03
  9102.6106854    .42297224557E-02
  2071.4166009    .21747824159E-01
  586.02476821    .85100053589E-01
  190.55395021    .24799128459
  67.630384260    .46703640406
  25.127306905    .36434587550
S  3  1.00
  112.57463010    .21670040240E-01
  34.795554217    .93602301760E-01
  6.5115556215    -.26068001422
S  2  1.00
  3.2399032261    1.2842089435
  1.5477160881    .66036416584
S  1  1.00
  .40541030112    1.0000000000
S  1  1.00
  .14550651059    1.0000000000
P  6  1.00
  564.36716027    .24796796317E-02
  133.42624379    .19677930250E-01
  42.468271189    .89980008258E-01
  15.616527580    .25705880575
  6.1093988469    .43515167292
  2.4404160198    .34883240595
P  1  1.00
  .83882201296    1.0000000000
P  1  1.00
  .31288746900    1.0000000000
P  1  1.00
  .10770109004    1.0000000000
D  1  1.00
  .55  1.00
****
! A. Sch?fer, C. Huber, R. Ahlrichs; J. Chem. Phys. 100, 5829 (1994).
-Cl 0
S  7  1.00
  69507.990945    .54314897497E-03
  10426.156880    .41990463961E-02
  2373.2334061    .21592141679E-01
  671.56420071    .84598850094E-01
  218.41999790    .24757249724
  77.572249714    .47016930228
  28.888815277    .37436370716
S  3  1.00
  127.10527185    .25182166603E-01
  39.339582961    .10786112456
  7.6740679989    -.27408821574
S  2  1.00
  3.8745627630    1.3213875014
  1.8385832573    .68636955368
S  1  1.00
  .50229057542    1.0000000000
S  1  1.00
  .17962723420    1.0000000000
P  6  1.00
  666.50423284    .23632663836E-02
  157.64241690    .18879300374E-01
  50.262520978    .87206341273E-01
  18.536078105    .25285612970
  7.2940532777    .43507154820
  2.9433248995    .35026513165
P  1  1.00
  1.0404970818    1.0000000000
P  1  1.00
  .38456415080    1.0000000000
P  1  1.00
  .13069642732    1.0000000000
D  1  1.00
  .65 1.00
****
! A. Sch?fer, C. Huber, R. Ahlrichs; J. Chem. Phys. 100, 5829 (1994).
-Ca 0
S  8  1.00
  172517.32685    .23317502546E-03
  25861.519275    .18076521980E-02
  5885.6618668    .93943844255E-02
  1665.9730031    .38108409009E-01
  542.36718148    .12331203853
  194.57803492    .29004470954
  75.303597636    .40587151157
  29.574062589    .20398410743
S  4  1.00
  191.20074660    -.24419759759E-01
  58.840299883    -.11547027448
  8.9642540845    .56356636717
  3.6856960541    .56709682704
S  2  1.00
  5.2464289726    -.22825334325
  .84862621528    .72625219172
S  1  1.00
  .36743300538    1.0000000000
S  1  1.00
  .66821582613E-01  1.0000000000
S  1  1.00
  .26759730445E-01  1.0000000000
P  6  1.00
  836.97262058    .25258346092E-02
  197.93040142    .20076506686E-01
  63.135558054    .91302987366E-01
  23.282687170    .25247029915
  9.1176444932    .39426326344
  3.6336120139    .23011559492
P  3  1.00
  13.494163120    -.26495021951E-01
  1.8139259790    .55088108210
  .71981826006    1.0280616620
P  1  1.00
  .27629576992    1.0000000000
P  1  1.00
  .074979 1.000000
D  3  1.00
  5.4979093879    0.73770011433E-01
  1.3177128032    0.26052853169
0.32188682649    0.45233836380
D  1  1.00
0.70528614919E-01 1.0000000000
****
! A. Sch?fer, C. Huber, R. Ahlrichs; J. Chem. Phys. 100, 5829 (1994).
-Fe 0
S  8  1.00
  300784.84637    .22806273096E-03
  45088.970557    .17681788761E-02
  10262.516317    .91927083490E-02
  2905.2897293    .37355495807E-01
  946.11487137    .12151108426
  339.87832894    .28818881468
  131.94425588    .41126612677
  52.111494077    .21518583573
S  4  1.00
  329.48839267    -.24745216477E-01
  101.92332739    -.11683089050
  16.240462745    .55293621136
  6.8840675801    .53601640182
S  2  1.00
  10.470693782    -.22912708577
  1.7360039648    .71159319984
S  1  1.00
  .72577288979    1.0000000000
S  1  1.00
  .11595528203    1.0000000000
S  1  1.00
  .41968227746E-01  1.0000000000
P  6  1.00
  1585.3959970    .23793960179E-02
  375.38006499    .19253154755E-01
  120.31816501    .90021836536E-01
  44.788749031    .25798172356
  17.829278584    .41492649744
  7.2247153786    .24207474784
P  3  1.00
  28.143219756    -.29041755152E-01
  3.8743241412    .55312260343
  1.5410752281    .96771136842
P  1  1.00
  .58285615250    1.0000000000
D  4  1.00
  61.996675034    .11971972255E-01
  17.873732552    .73210135410E-01
  6.2744782934    .23103094314
  2.3552337175    .39910706494
D  1  1.00
  .85432239901    .41391589765
D  1  1.00
  .27869254413    .21909269782
P  1  1.00
.134915 1.000000
****
! A. Sch?fer, C. Huber, R. Ahlrichs; J. Chem. Phys. 100, 5829 (1994).
-In 0
S  3  1.00
  1.5325620000    .26928901457517
  .95607154373    -.6264188666183
  .16950454967    .68519003450820
S  1  1.00
  .61810098073E-01  1.0000000000
P  3  1.00
  .59575805846    -.28453860489547
  .37619975148    .31165827132835
  .11204325838    .53298765184379
P  1  1.00
  .43317823898E-01  1.0000000000
P  1  1.00
  .15345553962E-01  1.0000000000
D  1  1.00
  .160             1.000
****
! K. Eichkorn, F. Weigend, O. Treutler, R. Ahlrichs; Theor. Chem. Acc. 97, 119 (1997).
-Sb 0
S  3  1.00
  2.2207990000    -.28359577785279
  1.3267299347    .67243405240451
  .23092426451    -.74735362100535
S  1  1.00
  .89371099439E-01  1.0000000000
P  3  1.00
  2.1493490000    -.09074673957374
  1.3484119943    .24517102301965
  .29142485251    -.38487489687832
P  1  1.00
  .12692192582    1.0000000000
P  1  1.00
  .52990353280E-01  1.0000000000
D  1  1.00
  .211             1.000
****
! K. Eichkorn, F. Weigend, O. Treutler, R. Ahlrichs; Theor. Chem. Acc. 97, 119 (1997).

-IN    0
IN-ECP    3    46
f POTENTIAL
  1
2    0.88436900          -6.01909200
s-f POTENTIAL
  3
2    1.43509100          29.16521900
2    0.69580500          -4.19080600
2    0.88436900          6.01909200
p-f POTENTIAL
  3
2    1.44083200          36.99054200
2    0.70139200          -3.36582000
2    0.88436900          6.01909200
d-f POTENTIAL
  2
2    0.96123600          20.00053100
2    0.88436900          6.01909200
! A. Bergner, M. Dolg, W. Kuechle, H. Stoll, H. Preuss; Mol. Phys. 80, 1431 (1993).
-SB    0
SB-ECP    3    46
f POTENTIAL
  1
2    1.60925100       -14.51768700
s-f POTENTIAL
  3
2    2.49109100          68.42793800
2    1.34157500          -4.39863100
2    1.60925100          14.51768700
p-f POTENTIAL
  3
2    2.14386400          63.96546900
2    0.58550300          -0.57872600
2    1.60925100          14.51768700
d-f POTENTIAL
  2
2    0.79540100          7.80366100
2    1.60925100          14.51768700
! A. Bergner, M. Dolg, W. Kuechle, H. Stoll, H. Preuss; Mol. Phys. 80, 1431 (1993).

然而没有成功输出cosmo文件，log文件的后面几行如下：
Variational C-PCM results
=========================
<psi(f)| H |psi(f)>                   (a.u.) =    -76.458862
<psi(f)|H+V(f)/2|psi(f)>                   (a.u.) =    -76.473336
Total free energy in solution:
- with all non electrostatic terms          (a.u.) =    -76.470188
--------------------------------------------------------------------
(Polarized solute)-Solvent             (kcal/mol) =    -9.08
--------------------------------------------------------------------
Cavitation energy                      (kcal/mol) =    5.66
Dispersion energy                      (kcal/mol) =    -4.21
Repulsion energy                      (kcal/mol) =    0.53
Total non electrostatic                (kcal/mol) =    1.98
--------------------------------------------------------------------
Partition over spheres:
Sphere  on Atom  Surface  Charge GEl    GCav GDR
1    O1    24.63 0.257 -4.77 3.06 -1.89
2    H2    9.19  -0.129 -2.16 1.30 -0.89
3    H3    9.19  -0.129 -2.16 1.30 -0.89
--------------------------------------------------------------------
- cavitation energy not included in the total energy.
- dispersion energy not included in the total energy.
- repulsion  energy not included in the total energy.
After PCM corrections, the energy is  -76.4733364192    a.u.
--------------------------------------------------------------------
Blank file name read.
Error termination via Lnk1e in /home/gaussian/g09/l502.exe at Tue Jun 14 04:00:39 2016.

这里显示是l502错误，我知道论坛里有各种方法解决，我想确认一下我的输入文件格式是否正确？因为我log文件中有提示： Blank file name read.

作者
Author: liyuanhe211 时间: 2016-6-14 15:17
本帖最后由 liyuanhe211 于 2016-6-14 15:27 编辑

高斯自带TZVP，自己写它干啥
从外部引用文件一定要注意它得“干净”，Gaussian只不过会原封不动的把它copy进去就完了，对空行之类的要求同样严格。如下图，你的基组文件里明明带着赝势，赝势之前还空了好多行。你也没有写genecp，只是gen，所以Gaussian认为到446行是基组结束了，读447行当成了一个cosmo文件的输出路径，当然是blank filename。

另外test是垃圾关键词，B3LYP用不着int=ultrafine。

(, 下载次数 Times of downloads: 46)

作者
Author: whtu 时间: 2016-6-15 11:41

liyuanhe211 发表于 2016-6-14 15:17
高斯自带TZVP，自己写它干啥
从外部引用文件一定要注意它得“干净”，Gaussian只不过会原封不动的把它copy ...

按你说的已经解决问题，非常感谢。
自己写基组主要是为了学习，另外我有一个问题是：B3LYP下为什么没必要用int=ultrafine?

作者
Author: sobereva 时间: 2016-6-15 12:23

whtu 发表于 2016-6-15 11:41
按你说的已经解决问题，非常感谢。
自己写基组主要是为了学习，另外我有一个问题是：B3LYP下为什么没必 ...

B3LYP这类普通杂化泛函对积分格点精度没明尼苏达系列泛函那么高要求

作者
Author: 戴上墨镜看世界 时间: 2017-7-8 17:04
你好！按照你的方法，确实生成不了COSMO文件，不知道是怎么解决的呀！谢谢了！

作者
Author: sobereva 时间: 2017-7-8 18:01

戴上墨镜看世界发表于 2017-7-8 17:04
你好！按照你的方法，确实生成不了COSMO文件，不知道是怎么解决的呀！谢谢了！

scrf=cosmors，然后分子坐标后面空一行写上输出文件名

作者
Author: 戴上墨镜看世界 时间: 2017-7-11 10:14

sobereva 发表于 2016-6-15 12:23
B3LYP这类普通杂化泛函对积分格点精度没明尼苏达系列泛函那么高要求

不好意思！刚看到，谢谢了！我先试试哈！

作者
Author: 戴上墨镜看世界 时间: 2017-7-11 10:33

sobereva 发表于 2017-7-8 18:01
scrf=cosmors，然后分子坐标后面空一行写上输出文件名

%mem=2GB
%chk=h2o.chk
#p b3lyp/6-31g(d,p) opt=tight scf=tight

Title Card Required

0 1
O                -0.52402568 1.24465621 -0.01371607
H                0.43597429 1.24489731 -0.01371607
H                -0.84425298 2.14967249 -0.01371607

--link1--
%chk=h2o.chk
#p opt b3lyp/6-31g(d,p) int=ultrafine geom=allcheck guess=read scf=(tight,novaracc)
# scrf(cpcm,read)

radii=klamt

--link1--
%chk=h2o.chk
#p b3lyp/6-31g(d,p) scf=(tight,novaracc) geom=allcheck guess=read  scrf=cosmors

H2o.cosmo

老师，你好！这是输入文件，就是生不成cosmo文件，能不能帮我看看是哪里出错了？谢谢了！

作者
Author: sobereva 时间: 2017-7-11 10:37

戴上墨镜看世界发表于 2017-7-11 10:33
%mem=2GB
%chk=h2o.chk
#p b3lyp/6-31g(d,p) opt=tight scf=tight

把输出路径写成绝对路径，免得找不到

作者
Author: 戴上墨镜看世界 时间: 2017-7-11 17:28

sobereva 发表于 2017-7-11 10:37
把输出路径写成绝对路径，免得找不到

老师，你好!非常感谢你的回答。问题还是没有解决呀！好像是不用设置路径直接输出当前路径，但是就是没有COSMO文件。不知道是不是前面的输入文件是不是哪里弄错了呀！谢谢了！

作者
Author: sobereva 时间: 2017-7-11 21:49

戴上墨镜看世界发表于 2017-7-11 17:28
老师，你好!非常感谢你的回答。问题还是没有解决呀！好像是不用设置路径直接输出当前路径，但是就是没有C ...

输入文件和输出的COMOSRS文件都附上了，g09 D01跑的，对照检验

作者
Author: 戴上墨镜看世界 时间: 2017-7-12 08:31

sobereva 发表于 2017-7-11 21:49
输入文件和输出的COMOSRS文件都附上了，g09 D01跑的，对照检验

实在是太感谢了！

作者
Author: wobufan456 时间: 2019-5-21 10:20
实在是太感谢了！

作者
Author: wobufan456 时间: 2019-5-21 10:20
生成的文件在cosmotherm里读不了怎么办

作者
Author: new-hand 时间: 2021-11-20 09:49

wobufan456 发表于 2019-5-21 10:20
**** 作者被禁止或删除内容自动屏蔽 ****

你好，请问问题解决了吗？可以把文件让我参考一下吗？

作者
Author: Lumin 时间: 2023-11-17 16:39

sobereva 发表于 2017-7-11 21:49
输入文件和输出的COMOSRS文件都附上了，g09 D01跑的，对照检验

自己鼓捣半天还不如您的一个案例，haha...

作者
Author: blue11 时间: 2025-4-29 17:26

sobereva 发表于 2017-7-11 10:37
把输出路径写成绝对路径，免得找不到

sob老师，您好，请问在学校平台上可以使用这种方法可以生成cosmo文件吗？可以的话，怎么设置绝对路径？

作者
Author: sobereva 时间: 2025-4-29 23:13

blue11 发表于 2025-4-29 17:26
sob老师，您好，请问在学校平台上可以使用这种方法可以生成cosmo文件吗？可以的话，怎么设置绝对路径？

取决于平台的规则、运行方式，我没法回答，有不清楚的可以问管理员

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