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小木虫论坛-学术科研互动平台 » 计算模拟区 » 量子化学 » 量化图形可视化软件 » G09在Linux下的ntrex1错误
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vincentmomo

新虫 (初入文坛)

[求助] G09在Linux下的ntrex1错误已有2人参与

本人接触Gaussian09时间不长，
之前一直在windows上使用，
今天尝试在Linux上使用时出现了如下错误，
Gaussian版本：G09 E01
虚拟机：VMware
Linux版本：ubuntu 14.04 LTS

输入文件：
# opt freq b3lyp/6-31g(d) geom=connectivity

1119-3

1 1
C                 -3.01323902   -1.27056041   -0.11278525
H                 -4.07766210   -1.22925058   -0.01180503
C                 -2.35627505   -0.12026210   -0.30727261
H                 -2.86097177    0.82158153   -0.36305616
N                 -0.99758355   -0.39457409   -0.41124538
N                 -2.31987063   -2.56449511   -0.03614803
C                 -0.74520212   -2.02077300   -0.25336995
H                 -0.40943366   -1.87513395   -1.12092938
C                 -034343591    0.65791955    0.37948088
H                  0.71691701    0.51706020    0.35282911
H                 -0.58644599    1.61562822   -0.03117738
H                 -0.68463070    0.60717070    1.39235337
C                 -2.90322345   -3.36963526    1.04660256
H                 -2.36534311   -4.29028063    1.13602757
H                 -2.83962463   -2.82850179    1.96748787
C                 -4.38003498   -3.66690162    0.72682076
H                 -4.99319944   -2.87615245    1.10582617
H                 -4.50765804   -3.74052082   -0.33298704
C                 -4.79066573   -4.99629885    1.38688546
H                 -5.83718181   -5.16088384    1.23649969
H                 -4.23654204   -5.79902546    0.94702535
H                 -4.58358159   -4.95265894    2.43574756

1 2 1.0 3 2.0 6 1.0
2
3 4 1.0 5 1.0
4
5 7 1.0 9 1.0
6 7 2.0 13 1.0
7 8 1.0
8
9 10 1.0 11 1.0 12 1.0
10
11
12
13 14 1.0 15 1.0 16 1.0
14
15
16 17 1.0 18 1.0 19 1.0
17
18
19 20 1.0 21 1.0 22 1.0
20
21
22

输出文件：
Entering Gaussian System, Link 0=g09
Input=1119-Pmim+_1.gjf
Output=1119-Pmim+_1.log
Initial command:
/home/vincent/user/g09/l1.exe "/mnt/hgfs/Share/Gau-5413.inp" -scrdir="/mnt/hgfs/Share/"
Entering Link 1 = /home/vincent/user/g09/l1.exe PID=      5415.
  
Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2015,
            Gaussian, Inc.  All Rights Reserved.
  
This is part of the Gaussian(R) 09 program.  It is based on
the Gaussian(R) 03 system (copyright 2003, Gaussian, Inc.),
the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.),
the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.),
the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.),
the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.),
the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.),
the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon
University), and the Gaussian 82(TM) system (copyright 1983,
Carnegie Mellon University). Gaussian is a federally registered
trademark of Gaussian, Inc.
  
This software contains proprietary and confidential information,
including trade secrets, belonging to Gaussian, Inc.
  
This software is provided under written license and may be
used, copied, transmitted, or stored only in accord with that
written license.
  
The following legend is applicable only to US Government
contracts under FAR:
  
                    RESTRICTED RIGHTS LEGEND
  
Use, reproduction and disclosure by the US Government is
subject to restrictions as set forth in subparagraphs (a)
and (c) of the Commercial Computer Software - Restricted
Rights clause in FAR 52.227-19.
  
Gaussian, Inc.
340 Quinnipiac St., Bldg. 40, Wallingford CT 06492
  
  
---------------------------------------------------------------
Warning -- This program may not be used in any manner that
competes with the business of Gaussian, Inc. or will provide
assistance to any competitor of Gaussian, Inc.  The licensee
of this program is prohibited from giving any competitor of
Gaussian, Inc. access to this program.  By using this program,
the user acknowledges that Gaussian, Inc. is engaged in the
business of creating and licensing software in the field of
computational chemistry and represents and warrants to the
licensee that it is not a competitor of Gaussian, Inc. and that
it will not use this program in any manner prohibited above.
---------------------------------------------------------------
  

Cite this work as:
Gaussian 09, Revision E.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, T. Keith, 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, 2013.

******************************************
Gaussian 09:  ES64L-G09RevE.01 30-Nov-2015
                27-Nov-2016
******************************************
ntrex1

错误代码应该是这个ntrex1
因为是第一次在Linux上尝试，所以选择了一个比较简单的体系来算
之前在Windows上算是没问题的，所以不太清楚是安装，还是输入文件有问题
希望大家能帮我看看
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1楼2016-11-27 19:20:09
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Woodeninsect

银虫 (正式写手)

【答案】应助回帖

感谢参与，应助指数 +1
先把这个错误改了试试吧

C                 -034343591    0.65791955    0.37948088


改为 C                 -0.34343591    0.65791955    0.37948088
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2楼2016-11-28 01:09:20
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vincentmomo

新虫 (初入文坛)
引用回帖:
2楼: Originally posted by Woodeninsect at 2016-11-28 01:09:20
先把这个错误改了试试吧

C                 -034343591    0.65791955    0.37948088


改为 C                 -0.34343591    0.65791955    0.37948088

多谢回复，我电脑上的gjf文件没这个错误，可能是编辑帖子的时候出错了。
所以问题应该不是那个小数点造成的。
昨天又折腾了一下，终端里输出的变成这样了。
还麻烦帮我看一下是怎么回事。
多谢！

vincent@ubuntu:/mnt/hgfs/Share$ g09 1127-C2H2_2L.gjf &
[1] 7414
vincent@ubuntu:/mnt/hgfs/Share$ ntrex1: Input/output error
Error: segmentation violation
   rax 0000000000000000, rbx 00007ffffffdfe00, rcx ffffffffffffffff
   rdx 0000000000001cf8, rsp 00007ffffffdfd18, rbp 00007ffffffdfe10
   rsi 000000000000000b, rdi 0000000000001cf8, r8  00002aaaaaae8340
   r9  0000000000000000, r10 00007ffffffdfae0, r11 0000000000000206
   r12 0000000000000004, r13 0000000000759cd0, r14 0000000000000001
   r15 0000000000010000
  /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x2aaaaace0340]
  /lib/x86_64-linux-gnu/libc.so.6(kill+0x7) [0x2aaaab22b267]
  /home/vincent/g09/l1.exe() [0x49bfda]
  /home/vincent/g09/l1.exe() [0x4b4ade]
  /home/vincent/g09/l1.exe() [0x4b5b1f]
  /home/vincent/g09/l1.exe() [0x4adbab]
  /home/vincent/g09/l1.exe() [0x4b3343]
  /home/vincent/g09/l1.exe() [0x41de60]
  /home/vincent/g09/l1.exe() [0x4059ee]
  /home/vincent/g09/l1.exe() [0x403a3c]
  /home/vincent/g09/l1.exe() [0x40365c]
  /home/vincent/g09/l1.exe() [0x4035dd]
  /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x2aaaab215ec5]
  /home/vincent/g09/l1.exe() [0x4034d9]
Aborted (core dumped)
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3楼2016-11-28 11:43:46
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mgfudan

铁杆木虫 (著名写手)

mgfudan

【答案】应助回帖

ntrex1: Bad file descriptor
请把chk文件名称尽量简化，不包括路径信息。
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mgfudan
4楼2020-10-05 16:00:05
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