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suosuosky

鐵桿木蟲 (著名寫手)

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[求助] 關(guān)于勢能面掃描��！

我想問一下，我用relaxed-PES來掃描勢能面，為什么結(jié)果是這樣的呢？
能量值下面沒有數(shù)值，全是些星號，我做其他分子的時候沒出現(xiàn)過這種情況的，不知道為什么？誰能解釋一下？

謝謝大家

這是輸出文件：

Summary of Optimized Potential Surface Scan
                        1       2       3       4       5
   Eigenvalues --  **************************************************
         R1          1.08425 1.08424 1.08422 1.08422 1.08420
         R2          1.34553 1.34547 1.34537 1.34515 1.34493
         R3          1.48828 1.48845 1.48838 1.48825 1.48825
         R4          1.41335 1.41343 1.41338 1.41335 1.41335
         R5          1.76829 1.76802 1.76797 1.76789 1.76776
         R6          1.21079 1.21074 1.21054 1.21031 1.20999
         R7          1.79741 1.79717 1.79748 1.79771 1.79807
         R8          1.20510 1.20507 1.20502 1.20492 1.20482
         R9          2.26968 2.27242 2.28563 2.30743 2.33576
         R10       1.06395 1.06394 1.06391 1.06388 1.06385
         R11       1.34767 1.34770 1.34758 1.34749 1.34750
         A1       116.97301 117.02162 117.09989 117.21394 117.35981
         A2       109.99372 110.04340 110.16586 110.33963 110.57102
         A3       133.03327 132.93334 132.72023 132.40650 131.98870
         A4       130.35332 130.27880 130.16903 129.99489 129.78161
         A5       117.45686 117.48329 117.51747 117.58099 117.66017
         A6       112.18982 112.23427 112.30637 112.41392 112.54495
         A7       118.32883 118.34824 118.42456 118.53879 118.69386
         A8       124.33387 124.23952 124.10194 123.91963 123.66381
         A9       117.33727 117.41181 117.46955 117.53002 117.61889
         A10       98.52797  98.44052  98.42802  98.46347  98.45801
         A11       179.21920 179.16255 179.12131 179.09615 179.07491
         A12       180.02397 179.83030 179.75692 179.72048 179.69416
         A13       175.34857 175.33571 175.41435 175.56093 175.74886
         A14       179.99985 180.21665 180.35880 180.46750 180.59279
         D1       -179.99704-178.92816-178.22319-177.61342-177.07420
         D2          0.00255 0.31791 0.72058 1.12513 1.48950
         D3          0.00511 0.55238 0.25832  -0.16996  -0.69073
         D4       -179.99530 179.79845 179.20210 178.56859 177.87297
         D5          0.00000 5.00000  10.00000  15.00000  20.00000
         D6          0.00467 1.32599 1.14706 0.81918 0.45451
         D7       -180.05600-178.43271-178.11641-177.92283-177.75796
                        6       7       8       9       10
   Eigenvalues --  **************************************************
         R1          1.08417 1.08414 1.08412 1.08411 1.08410
         R2          1.34462 1.34421 1.34374 1.34321 1.34260
         R3          1.48838 1.48873 1.48915 1.48987 1.49077
         R4          1.41333 1.41331 1.41336 1.41346 1.41360
         R5          1.76755 1.76753 1.76737 1.76720 1.76708
         R6          1.20954 1.20896 1.20835 1.20771 1.20701
         R7          1.79853 1.79916 1.79968 1.80023 1.80062
         R8          1.20469 1.20457 1.20443 1.20430 1.20418
         R9          2.37048 2.41254 2.46162 2.51680 2.57834
         R10       1.06380 1.06376 1.06371 1.06366 1.06361
         R11       1.34753 1.34751 1.34749 1.34759 1.34767
         A1       117.53780 117.74022 117.97338 118.21213 118.46783
         A2       110.84858 111.16729 111.52815 111.88612 112.26016
         A3       131.47889 130.89408 130.22410 129.53965 128.81634
         A4       129.52588 129.24497 128.91797 128.58234 128.22708
         A5       117.75441 117.86445 118.00188 118.14537 118.30489
         A6       112.70398 112.87326 113.06205 113.25562 113.45391
         A7       118.86433 119.07924 119.32024 119.56163 119.81356
         A8       123.33617 122.93332 122.47366 121.99672 121.48388
         A9       117.75939 117.92694 118.12281 118.33072 118.56182
         A10       98.43507  98.36107  98.26918  98.15113  97.98968
         A11       179.04798 179.03958 179.03458 179.04491 179.07315
         A12       179.68314 179.69413 179.71550 179.74191 179.76354
         A13       175.93175 176.17727 176.45185 176.74041 177.05968
         A14       180.70979 180.79432 180.85595 180.85561 180.79765
         D1       -176.59594-176.16787-175.80309-175.57950-175.44734
         D2          1.84324 2.19802 2.53054 2.82464 3.08774
         D3       -1.25650  -1.79774  -2.38940  -3.10734  -3.84753
         D4       177.18268 176.56815 175.94423 175.29680 174.68755
         D5       25.00000  29.99999  34.99999  39.99999  44.99998
         D6       -0.00259  -0.49184  -0.94207  -1.64722  -2.37334
         D7       -177.66915-177.63377-177.59778-177.79892-178.05152
                        11       12       13       14       15
   Eigenvalues --  **************************************************
         R1          1.08411 1.08414 1.08416 1.08418 1.08425
         R2          1.34198 1.34128 1.34052 1.33974 1.33892
         R3          1.49186 1.49310 1.49450 1.49608 1.49758
         R4          1.41379 1.41401 1.41422 1.41440 1.41463
         R5          1.76704 1.76696 1.76692 1.76710 1.76704
         R6          1.20630 1.20553 1.20477 1.20398 1.20321
         R7          1.80114 1.80164 1.80213 1.80247 1.80324
         R8          1.20406 1.20397 1.20389 1.20381 1.20376
         R9          2.64952 2.72762 2.81341 2.91222 3.02592
         R10       1.06356 1.06352 1.06348 1.06344 1.06340
         R11       1.34782 1.34795 1.34809 1.34819 1.34834
         A1       118.73039 119.00478 119.29057 119.59211 119.88363
         A2       112.63190 113.00879 113.37744 113.77550 114.15011
         A3       128.10168 127.38443 126.68605 125.99122 125.38734
         A4       127.87540 127.50776 127.13861 126.79464 126.44925
         A5       118.46641 118.63815 118.81064 118.97373 119.12993
         A6       113.64680 113.84565 114.04521 114.22802 114.41789
         A7       120.07189 120.35671 120.64844 120.97172 121.34118
         A8       120.97152 120.43223 119.90161 119.35821 118.79751
         A9       118.78515 119.00998 119.22113 119.42610 119.61535
         A10       97.84363  97.67957  97.50260  97.31690  97.13583
         A11       179.10314 179.14927 179.21037 179.27312 179.34590
         A12       179.78277 179.79256 179.80916 179.82101 179.82010
         A13       177.37328 177.68947 178.02169 178.34569 178.66774
         A14       180.72460 180.60211 180.49239 180.42629 180.39988
         D1       -175.40952-175.46419-175.61674-175.83947-176.11238
         D2          3.27806 3.40902 3.47245 3.42766 3.22763
         D3       -4.47439  -5.02331  -5.47301  -5.61500  -5.36594
         D4       174.21319 173.84989 173.61618 173.65212 173.97408
         D5       49.99998  54.99999  59.99998  64.99997  69.99997
         D6       -3.19864  -4.03570  -4.89220  -5.47980  -5.78197
         D7       -178.44278-178.90157-179.43290-179.86188 179.83782
                        16       17       18       19       20
   Eigenvalues --  **************************************************
         R1          1.08428 1.08433 1.08434 1.08435 1.08430
         R2          1.33816 1.33749 1.33698 1.33673 1.33679
         R3          1.49909 1.50037 1.50138 1.50173 1.50136
         R4          1.41476 1.41489 1.41484 1.41480 1.41458
         R5          1.76727 1.76730 1.76760 1.76754 1.76772
         R6          1.20247 1.20179 1.20118 1.20063 1.20025
         R7          1.80372 1.80463 1.80524 1.80679 1.80776
         R8          1.20371 1.20367 1.20363 1.20360 1.20354
         R9          3.14796 3.27955 3.41692 3.56076 3.70420
         R10       1.06337 1.06335 1.06334 1.06332 1.06330
         R11       1.34840 1.34855 1.34869 1.34882 1.34886
         A1       120.17752 120.42819 120.63773 120.75703 120.77743
         A2       114.54969 114.91605 115.31031 115.66499 116.04677
         A3       124.79306 124.29763 123.83970 123.48427 123.15562
         A4       126.15041 125.89586 125.71354 125.60399 125.59625
         A5       119.26640 119.37442 119.44813 119.47672 119.46072
         A6       114.58122 114.72836 114.83773 114.91912 114.94295
         A7       121.74578 122.16462 122.66150 123.18196 123.69607
         A8       118.27356 117.76051 117.24367 116.73404 116.28775
         A9       119.74912 119.87079 119.93563 119.97488 119.95655
         A10       97.00150  96.87642  96.79271  96.73828  96.73539
         A11       179.41755 179.48029 179.53110 179.56524 179.56588
         A12       179.81710 179.80086 179.77445 179.71501 179.65979
         A13       178.95776 179.21617 179.42293 179.54866 179.56749
         A14       180.37822 180.27596 180.20180 180.06084 179.92621
         D1       -176.58418-177.17443-178.00006-178.92761 179.96755
         D2          2.87562 2.37754 1.70139 0.91769 0.07971
         D3       -4.97624  -4.40230  -3.54658  -2.60247  -1.73237
         D4       174.48356 175.14967 176.15487 177.24283 178.37980
         D5       74.99998  79.99998  85.00001  90.00002  95.00002
         D6       -5.96103  -5.91132  -5.78501  -5.38201  -4.88418
         D7       179.46984 179.16672 178.67884 178.29545 177.82083

[ Last edited by suosuosky on 2011-5-19 at 15:58 ]

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follow_my_dream

1樓 2011-05-19 15:56:36

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exabyss916

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【答案】應(yīng)助回帖

suosuosky(金幣+2): 2011-05-20 07:56:34
suosuosky(金幣+8): 2011-05-24 08:45:11

Possibly due to the formatted output of fortran. For example you energy has a very large absolute value.

Anyway you can 'grep' the optimized energy of each step from your output file.

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2樓2011-05-19 18:55:05

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suosuosky

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引用回帖:

Originally posted by exabyss916 at 2011-05-19 18:55:05:
Possibly due to the formatted output of fortran. For example you energy has a very large absolute value.

Anyway you can 'grep' the optimized energy of each step from your output file.

謝謝，確實(shí)是如你所說的那樣。果然高手啊，呵呵

從GV的scan菜單看，能量確實(shí)是比較大，-1000Hartree以上，那沒有辦法解決這個問題嗎？能在輸入文件中設(shè)定一下嗎？我這個有50個點(diǎn)，要是每次都單獨(dú)讀取的話有點(diǎn)麻煩呢

謝謝

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follow_my_dream

3樓2011-05-20 07:59:13

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exabyss916

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I don't know. But you can easily get the result by "grep".

for example, the SCF energy:

grep -B 9999 Optimized | grep "SCF Done" | tail -1

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4樓2011-05-20 20:37:15

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exabyss916

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Something missing in the command.

Add the output file name after "Optimized"

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5樓2011-05-20 20:38:56

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exabyss916

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Still not correct. Just use this:

grep -B n Optimized filename | grep "SCF Done"

where n should be a proper number so that you only cover one energy

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6樓2011-05-20 20:41:58

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suosuosky

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引用回帖:

Originally posted by exabyss916 at 2011-05-20 20:41:58:
Still not correct. Just use this:

grep -B n Optimized filename | grep "SCF Done"

where n should be a proper number so that you only cover one energy

非常感謝！

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follow_my_dream

7樓2011-05-24 08:45:39

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suosuosky

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引用回帖:

我還想問一下：

1.這個可以變成shell腳本將能量值提取出來，保存到一個txt文件中嗎？

2.輸出文件中的SCF DONE對應(yīng)的能量值與文件的最后（如下所示）的HF對應(yīng)的能量有什么不同嗎？是不是前者對應(yīng)相關(guān)能校正后的能量，而后者只是對應(yīng)Hartree-fock能量？

HF=-1125.9827809,-1125.9827443,-1125.9826278,-1125.9824257,-1125.982
1337,-1125.9817509,-1125.9812798,-1125.9807239,-1125.9800863,-1125.979
3713,-1125.9785878,-1125.9777522,-1125.9768915,-1125.9760442,-1125.975
2575,-1125.9745789,-1125.9740601,-1125.9737547,-1125.9736867,-1125.973
857,-1125.9742273,-1125.9747467,-1125.9753639,-1125.9760196,-1125.9766

謝謝！！
713,-1125.9772887,-1125.977841,-1125.9783025,-1125.9786619,-1125.97891
81,-1125.9790739,-1125.979132

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follow_my_dream

8樓2011-05-24 09:03:51

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exabyss916

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Sorry. My suggestion make things more difficult since you can directly read the results from the tail of the output file. They have no difference.

贊一下

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9樓2011-05-24 20:05:33

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suosuosky

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Originally posted by exabyss916 at 2011-05-24 20:05:33:
Sorry. My suggestion make things more difficult since you can directly read the results from the tail of the output file. They have no difference.

不是的，你的建議是對的

我看了一下，兩者數(shù)值是不同的，好像tail部分只是HF能量，沒有經(jīng)過相關(guān)能的校正，所以可能還是要從文件中間獲得我想要的能量，但是你之前說的那個用法不太會用呢==

贊一下

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follow_my_dream

10樓2011-05-24 20:23:58

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