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标题: 用ADF做能量分解(EDA)出错，求指教 [打印本页]

作者
Author: xzxueren 时间: 2016-3-3 11:05
标题: 用ADF做能量分解(EDA)出错，求指教
用ADF2014做一个过渡态结构的能量分解(EDA),两个片段正常结束，但在计算复合物时出错，不知什么问题？刚接触adf，请教大家我用的是微机，win7+32位。

错误提示：

<Mar02-2016> <21:47:16>  ADF 2014  RunTime: Mar02-2016 21:47:16  Nodes: 1  Procs: 2
<Mar02-2016> <21:47:17>  BrDou1acetone
<Mar02-2016> <21:47:17>  RunType : SINGLE POINT
<Mar02-2016> <21:47:17>  D:\ADF2014\SCMTEMP\kid_0.a18300/f
<Mar02-2016> <21:47:17>  ERROR DETECTED: not (one or all) processes have the file
<Mar02-2016> <21:47:17>  END
unable to read the cmd header on the pmi context, Error = -1
.
Error posting readv, 远程主机强迫关闭了一个现有的连接。(10054)
unable to read the cmd header on the pmi context, Error = -1
.
Error posting readv, 远程主机强迫关闭了一个现有的连接。(10054)

job aborted:
rank: node: exit code[: error message]
0: localhost: 666: process 0 exited without calling finalize
1: localhost: 123

--------------------------------------------------------------------------------
输入文件：

#! /bin/sh

"$ADFBIN/adf" <<eor
title BrDou1acetone_A

atoms
C                -5.80156600 2.72771500 1.57543500
C                -5.93104400 2.50942000 2.96917100
C                -5.11819000 1.60543400 3.60227100
C                -4.13746600 0.88169200 2.87265100
C                -4.00223300 1.09917300 1.47247800
C                -4.86708000 2.03921800 0.84453400
C                -3.30385900 -0.07196800 3.50503000
C                -2.34960800 -0.74682300 2.79246800
C                -2.17879400 -0.50834000 1.40187200
C                -3.01202600 0.37811300 0.72985300
C                -3.00702500 0.52862000 -0.75745600
C                -2.25106100 1.49299800 -1.40520900
C                -2.28470200 1.58310000 -2.83028900
C                -3.09395800 0.77109300 -3.56830400
C                -3.94971700 -0.17417500 -2.93454800
C                -3.91820800 -0.28222700 -1.51594200
C                -4.82952300 -0.99434200 -3.68420000
C                -5.67689200 -1.87721700 -3.05837500
C                -5.66968500 -1.96903500 -1.64872800
C                -4.81017200 -1.20081900 -0.89800500
P                -0.73895200 -1.24504500 0.55856600
H                -6.44931500 3.44733300 1.08410800
H                -6.67854900 3.06061900 3.53164400
H                -5.20839400 1.42514700 4.67019300
H                -4.77274800 2.21457300 -0.22220900
H                -3.43384800 -0.26575200 4.56623500
H                -1.73667800 -1.48265000 3.29820600
H                -1.64385900 2.32740900 -3.29355400
H                -3.10862100 0.84558900 -4.65292300
H                -4.82466500 -0.90184100 -4.76777800
H                -6.35245400 -2.49690300 -3.64009500
H                -6.34544400 -2.65976800 -1.15230500
H                -4.81196800 -1.29812100 0.18371200
C                0.05276700 -2.50829800 1.60032700
C                0.24323800 -3.80001900 1.09498800
C                0.56582300 -2.18274300 2.86610900
C                0.91980900 -4.75437700 1.85037400
H                -0.12368100 -4.06988300 0.11101200
C                1.23889500 -3.14276100 3.61370400
H                0.44387800 -1.18524900 3.27364900
C                1.41533900 -4.42973900 3.10921400
H                1.05942200 -5.75191500 1.44618800
H                1.62806500 -2.87928200 4.59202900
H                1.94256200 -5.17612500 3.69558100
C                -1.21941300 -2.04103000 -0.98978200
C                -2.20839000 -3.03173600 -0.97646200
C                -0.59801800 -1.67980100 -2.18924000
C                -2.56835300 -3.66278000 -2.16260800
H                -2.69813300 -3.30573900 -0.04428800
C                -0.97142200 -2.31102900 -3.37340500
H                0.16383800 -0.90610300 -2.21225700
C                -1.95222000 -3.30068000 -3.36008300
H                -3.33936100 -4.42730200 -2.15286200
H                -0.49479600 -2.02535600 -4.30592500
H                -2.24110400 -3.78961700 -4.28572400
O                -1.45738800 2.38687800 -0.80771600
H                -1.31173300 2.26251400 0.18463800
C                0.95527200 0.76737400 1.47534300
C                0.49770600 0.06073700 0.23683400
C                0.18157000 1.74411700 2.12567700
O                -0.82348300 2.35591700 1.69222300
H                1.65943300 0.23078500 2.10375300
H                1.35065100 -0.44447200 -0.23851100
H                0.05893100 0.75390300 -0.49028200
H                0.56525600 2.05140300 3.11681000
end

CHARGE 0

BASIS
type DZ
core None
END

eprint
sfo eigval
end

XC
Hybrid B3LYP
END

endinput
eor

mv TAPE21 BrDou1acetone_A.t21

"$ADFBIN/adf" <<eor
title BrDou1acetone_B

atoms
C                -3.13925365 4.07918361 2.00083419
N                -2.39347465 3.15245161 1.40513519
S                -1.50519265 2.21251761 2.40596919
O                -2.10254365 0.86969761 2.44687419
O                -1.22709965 2.85945861 3.69747719
H                -2.86788965 4.45101361 2.99022719
C                -3.88433265 5.01310461 1.13002219
C                -5.20607265 6.84606061 -0.51604581
C                -4.47856165 6.15505561 1.67695019
C                -3.97168165 4.78949961 -0.24995481
C                -4.62621665 5.70387661 -1.06727081
C                -5.13194265 7.06933761 0.85679119
H                -4.41295365 6.33039261 2.74776019
H                -3.49807065 3.90811461 -0.67247681
H                -4.67673365 5.53071261 -2.13875181
H                -5.58041965 7.95846061 1.29033919
H                -5.71293065 7.56227561 -1.15678981
C                0.02867635 2.08324861 1.51630019
C                0.10110935 1.24155161 0.40714519
C                1.12599235 2.83215261 1.92390219
C                1.29126535 1.16390461 -0.30387181
H                -0.76170365 0.65063261 0.11461719
C                2.31346535 2.74029261 1.20106719
H                1.05082835 3.47087261 2.79827619
C                2.41133235 1.91437861 0.07885919
H                1.35749035 0.50907861 -1.16912181
H                3.17771435 3.31994661 1.51437319
C                3.68537535 1.83785661 -0.71976081
H                3.56832235 2.34758361 -1.68284481
H                4.51596835 2.30953961 -0.18862981
H                3.95508435 0.79899961 -0.93379081
end

CHARGE 0

BASIS
type DZ
core None
END

XC
Hybrid B3LYP
END

eprint
sfo eigval
end

endinput
eor

mv TAPE21 BrDou1acetone_B.t21

"$ADFBIN/adf" <<eor
title BrDou1acetone

eprint
frag rot sfo eig
subend
end

xc
Hybrid B3LYP
end

BASIS
type DZ
core None
END

charge 0

atoms
6          0    -5.801566 2.727715 1.575435    f=BrDou1acetone_A
6          0    -5.931044 2.509420 2.969171    f=BrDou1acetone_A
6          0    -5.118190 1.605434 3.602271    f=BrDou1acetone_A
6          0    -4.137466 0.881692 2.872651    f=BrDou1acetone_A
6          0    -4.002233 1.099173 1.472478    f=BrDou1acetone_A
6          0    -4.867080 2.039218 0.844534    f=BrDou1acetone_A
6          0    -3.303859 -0.071968 3.505030    f=BrDou1acetone_A
6          0    -2.349608 -0.746823 2.792468    f=BrDou1acetone_A
6          0    -2.178794 -0.508340 1.401872    f=BrDou1acetone_A
6          0    -3.012026 0.378113 0.729853    f=BrDou1acetone_A
6          0    -3.007025 0.528620 -0.757456    f=BrDou1acetone_A
6          0    -2.251061 1.492998 -1.405209    f=BrDou1acetone_A
6          0    -2.284702 1.583100 -2.830289    f=BrDou1acetone_A
6          0    -3.093958 0.771093 -3.568304    f=BrDou1acetone_A
6          0    -3.949717 -0.174175 -2.934548    f=BrDou1acetone_A
6          0    -3.918208 -0.282227 -1.515942    f=BrDou1acetone_A
6          0    -4.829523 -0.994342 -3.684200    f=BrDou1acetone_A
6          0    -5.676892 -1.877217 -3.058375    f=BrDou1acetone_A
6          0    -5.669685 -1.969035 -1.648728    f=BrDou1acetone_A
6          0    -4.810172 -1.200819 -0.898005    f=BrDou1acetone_A
  15          0    -0.738952 -1.245045 0.558566    f=BrDou1acetone_A
1          0    -6.449315 3.447333 1.084108    f=BrDou1acetone_A
1          0    -6.678549 3.060619 3.531644       f=BrDou1acetone_A
1          0    -5.208394 1.425147 4.670193       f=BrDou1acetone_A
1          0    -4.772748 2.214573 -0.222209       f=BrDou1acetone_A
1          0    -3.433848 -0.265752 4.566235       f=BrDou1acetone_A
1          0    -1.736678 -1.482650 3.298206       f=BrDou1acetone_A
1          0    -1.643859 2.327409 -3.293554       f=BrDou1acetone_A
1          0    -3.108621 0.845589 -4.652923       f=BrDou1acetone_A
1          0    -4.824665 -0.901841 -4.767778       f=BrDou1acetone_A
1          0    -6.352454 -2.496903 -3.640095       f=BrDou1acetone_A
1          0    -6.345444 -2.659768 -1.152305       f=BrDou1acetone_A
1          0    -4.811968 -1.298121 0.183712       f=BrDou1acetone_A
6          0       0.052767 -2.508298 1.600327       f=BrDou1acetone_A
6          0       0.243238 -3.800019 1.094988       f=BrDou1acetone_A
6          0       0.565823 -2.182743 2.866109       f=BrDou1acetone_A
6          0       0.919809 -4.754377 1.850374       f=BrDou1acetone_A
1          0    -0.123681 -4.069883 0.111012       f=BrDou1acetone_A
6          0       1.238895 -3.142761 3.613704       f=BrDou1acetone_A
1          0       0.443878 -1.185249 3.273649       f=BrDou1acetone_A
6          0       1.415339 -4.429739 3.109214       f=BrDou1acetone_A
1          0       1.059422 -5.751915 1.446188       f=BrDou1acetone_A
1          0       1.628065 -2.879282 4.592029       f=BrDou1acetone_A
1          0       1.942562 -5.176125 3.695581       f=BrDou1acetone_A
6          0    -1.219413 -2.041030 -0.989782       f=BrDou1acetone_A
6          0    -2.208390 -3.031736 -0.976462 f=BrDou1acetone_A
6          0    -0.598018 -1.679801 -2.189240 f=BrDou1acetone_A
6          0    -2.568353 -3.662780 -2.162608 f=BrDou1acetone_A
1          0    -2.698133 -3.305739 -0.044288 f=BrDou1acetone_A
6          0    -0.971422 -2.311029 -3.373405 f=BrDou1acetone_A
1          0       0.163838 -0.906103 -2.212257 f=BrDou1acetone_A
6          0    -1.952220 -3.300680 -3.360083 f=BrDou1acetone_A
1          0    -3.339361 -4.427302 -2.152862 f=BrDou1acetone_A
1          0    -0.494796 -2.025356 -4.305925 f=BrDou1acetone_A
1          0    -2.241104 -3.789617 -4.285724 f=BrDou1acetone_A
8          0    -1.457388 2.386878 -0.807716 f=BrDou1acetone_A
1          0    -1.311733 2.262514 0.184638 f=BrDou1acetone_A
6          0       0.955272 0.767374 1.475343 f=BrDou1acetone_A
6          0       0.497706 0.060737 0.236834       f=BrDou1acetone_A
6          0       0.181570 1.744117 2.125677 f=BrDou1acetone_A
8          0    -0.823483 2.355917 1.692223 f=BrDou1acetone_A
1          0       1.659433 0.230785 2.103753 f=BrDou1acetone_A
1          0       1.350651 -0.444472 -0.238511 f=BrDou1acetone_A
1          0       0.058931 0.753903 -0.490282 f=BrDou1acetone_A
1          0       0.565256 2.051403 3.116810    f=BrDou1acetone_A
6          0       2.611634 1.923313 0.568650  f=BrDou1acetone_B
7          0       3.357413 0.996581 -0.027049  f=BrDou1acetone_B
  16          0       4.245695 0.056647 0.973785  f=BrDou1acetone_B
8          0       3.648344 -1.286173 1.014690  f=BrDou1acetone_B
8          0       4.523788 0.703588 2.265293  f=BrDou1acetone_B
1          0       2.882998 2.295143 1.558043  f=BrDou1acetone_B
6          0       1.866555 2.857234 -0.302162  f=BrDou1acetone_B
6          0       0.544815 4.690190 -1.948230  f=BrDou1acetone_B
6          0       1.272326 3.999185 0.244766  f=BrDou1acetone_B
6          0       1.779206 2.633629 -1.682139  f=BrDou1acetone_B
6          0       1.124671 3.548006 -2.499455  f=BrDou1acetone_B
6          0       0.618945 4.913467 -0.575393  f=BrDou1acetone_B
1          0       1.337934 4.174522 1.315576  f=BrDou1acetone_B
1          0       2.252817 1.752244 -2.104661  f=BrDou1acetone_B
1          0       1.074154 3.374842 -3.570936  f=BrDou1acetone_B
1          0       0.170468 5.802590 -0.141845  f=BrDou1acetone_B
1          0       0.037957 5.406405 -2.588974  f=BrDou1acetone_B
6          0       5.779564 -0.072622 0.084116  f=BrDou1acetone_B
6          0       5.851997 -0.914319 -1.025039  f=BrDou1acetone_B
6          0       6.876880 0.676282 0.491718  f=BrDou1acetone_B
6          0       7.042153 -0.991966 -1.736056  f=BrDou1acetone_B
1          0       4.989184 -1.505238 -1.317567  f=BrDou1acetone_B
6          0       8.064353 0.584422 -0.231117  f=BrDou1acetone_B
1          0       6.801716 1.315002 1.366092  f=BrDou1acetone_B
6          0       8.162220 -0.241492 -1.353325  f=BrDou1acetone_B
1          0       7.108378 -1.646792 -2.601306  f=BrDou1acetone_B
1          0       8.928602 1.164076 0.082189  f=BrDou1acetone_B
6          0       9.436263 -0.318014 -2.151945  f=BrDou1acetone_B
1          0       9.319210 0.191713 -3.115029  f=BrDou1acetone_B
1          0    10.266856 0.153669 -1.620814  f=BrDou1acetone_B
1          0       9.705972 -1.356871 -2.365975  f=BrDou1acetone_B
END

fragments
BrDou1acetone_A BrDou1acetone_A.t21
BrDou1acetone_B BrDou1acetone_B.t21
end

endinput
eor

mv TAPE21 BrDou1acetone.t21

作者
Author: 啦啦黑还黑 时间: 2017-7-13 13:45
请问您这个问题解决了吗？我碰到了同样的问题

作者
Author: panxiao 时间: 2018-9-25 15:43

啦啦黑还黑发表于 2017-7-13 13:45
请问您这个问题解决了吗？我碰到了同样的问题

您好，请问一下，您有用ADF做能量分解(EDA)的手册或者资料吗？能不能分享一下，谢谢您。

作者
Author: mcyang 时间: 2018-9-26 09:28
Input file的话，你可以参考站内wwy的分享
http://bbs.keinsci.com/thread-349-1-1.html

SCM裡也有一些例子(请搜寻ETS-NOCV)
https://www.scm.com/doc/ADF/Examples/

ADF的使用手册内，也有相关资料(请搜寻ETS-NOCV)

文献的话，你可以看一些MP Mitoraj 和 G. Frenking的文章，例如
J. Chem. Theory Comput. 2009, 5, 962–975
Chem. Eur. J. 2015, 21, 12405 – 12413

不确定1F是什么问题，不过从错误讯息看来，似乎是读取片段资讯时发生的问题。
所以请确定在执行整个分子的ETS计算时，有读取到片段资讯(.t21)。

希望对你有帮助。

作者
Author: 雨夕子 时间: 2018-9-26 09:28
win版的不稳定，特别是你的版本是比较早一点了。我们以前2016的也经常出错。
建议1）：更换更新的版本，2）Linux下运行；3）非要WIn版的话，建议WIN7 64bit下安装试试。毕竟ADF这个Lic是不区分WIN和Linux的

欢迎光临计算化学公社 (http://bbs.keinsci.com/)