VMD-L Mailing List

From: Him Bandhu Upadhyay (him.upadhyay_at_my.ndsu.edu)
Date: Mon Oct 01 2012 - 12:40:44 CDT

Hello Chris,
While writing Gaussian Input file for hessian calculation in FFTK, two files (one is *-hess.chk and other is *-hess.gau) are generated. I kept both file in same folder during gaussian calculation but got the following error message:
-------------------
Entering Gaussian System, Link 0=g09
 Initial command:
 /usr/local/g09/l1.exe /scratch/g09.12349.cluster3-0.chpc.ndsu.nodak.edu/Gau-3738.inp -scrdir=/scratch/g09.12349.cluster3-0.chpc.ndsu.nodak.edu/
 Entering Link 1 = /usr/local/g09/l1.exe PID= 3739.

 Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2011,
            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 C.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, 2010.

 ******************************************
 Gaussian 09: EM64L-G09RevC.01 23-Sep-2011
                 1-Oct-2012
 ******************************************
 %chk=3HOP-hess.chk
 %nproc=4
 Will use up to 4 processors via shared memory.
 %mem=4GB
 ----------------------------------------------------------------------
 # MP2/6-31G* Geom=(AllCheck,ModRedundant) Freq NoSymm IOp(7/33=1) SCF=
 Tight
 ----------------------------------------------------------------------
 1/10=4,18=120,29=7,30=1,38=1/1,3;
 2/12=2,15=1,40=1/2;
 3/5=1,6=6,7=1,11=9,14=-4,16=1,25=1,30=1,71=2/1,2,3;
 4//1;
 5/5=2,32=2,38=5,98=1/2;
 8/6=3,8=1,10=2,19=11,30=-1/1;
 9/15=3,16=-3/6;
 11/6=1,8=1,15=11,17=12,24=-1,27=1,28=-2,29=300,31=1,32=6,42=3/1,2,10;
 10/6=2,21=1,31=1/2;
 8/6=4,8=1,10=2,19=11,30=-1/11,4;
 10/5=1,20=4,31=1/2;
 11/12=2,14=11,16=1,17=2,28=-2,31=1,42=3/2,10,12;
 6/7=2,8=2,9=2,10=2/1;
 7/8=1,10=1,12=2,25=1,30=1,33=1,44=2/1,2,3,16;
 1/10=4,30=1/3;
 99//99;
 Structure from the checkpoint file: 3HOP-hess.chk
 --------------------------------------------------
 <qmtool> simtype="Geometry optimization" </qmtool>
 --------------------------------------------------
 Charge = 0 Multiplicity = 1
 Redundant internal coordinates found in file.
 H,0,-1.0781450497,1.4872860176,0.0830204428
 O,0,1.5073822474,1.3656556547,0.1426360868
 C,0,1.1840110077,-1.0358565619,-0.0863587339
 N,0,0.3932389472,-2.1136429956,-0.2065423693
 C,0,-0.9345888361,-1.9045425422,-0.2243547896
 C,0,-1.5104724801,-0.6359496908,-0.1237499036
 C,0,-0.6852283529,0.477831554,0.0012181018
 C,0,0.6949170962,0.2708186115,0.0201019697
 H,0,2.4343314847,1.065953046,0.1411751885
 H,0,-2.5908946106,-0.5224277216,-0.1429669898
 H,0,-1.5548719097,-2.7926181455,-0.32289963
 H,0,2.2593205929,-1.2245075308,-0.0742793809
 Recover connectivity data from disk.
 The following ModRedundant input section has been read:
 B * * R
 A * * * R
 L * * * * R
 D * * * * R
 Unrecognized coordinate type "O"
 Error termination via Lnk1e in /usr/local/g09/l101.exe at Mon Oct 1 12:02:39 2012.
 Job cpu time: 0 days 0 hours 0 minutes 0.4 seconds.
 File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 3 Scr= 1
---------------------------------------------------------------------------------------------------------------------------------

Also I used only one gaussian input file (*-hess.gau) during gaussian calculation and again I got the following different error message then previous :

Entering Gaussian System, Link 0=g09
 Initial command:
 /usr/local/g09/l1.exe /scratch/g09.12350.cluster3-0.chpc.ndsu.nodak.edu/Gau-3902.inp -scrdir=/scratch/g09.12350.cluster3-0.chpc.ndsu.nodak.edu/
 Entering Link 1 = /usr/local/g09/l1.exe PID= 3904.

 Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2011,
            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 C.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, 2010.

 ******************************************
 Gaussian 09: EM64L-G09RevC.01 23-Sep-2011
                 1-Oct-2012
 ******************************************
 %chk=3HOP-hess.chk
 %nproc=4
 Will use up to 4 processors via shared memory.
 %mem=4GB
 ----------------------------------------------------------------------
 # MP2/6-31G* Geom=(AllCheck,ModRedundant) Freq NoSymm IOp(7/33=1) SCF=
 Tight
 ----------------------------------------------------------------------
 1/10=4,18=120,29=7,30=1,38=1/1,3;
 2/12=2,15=1,40=1/2;
 3/5=1,6=6,7=1,11=9,14=-4,16=1,25=1,30=1,71=2/1,2,3;
 4//1;
 5/5=2,32=2,38=5,98=1/2;
 8/6=3,8=1,10=2,19=11,30=-1/1;
 9/15=3,16=-3/6;
 11/6=1,8=1,15=11,17=12,24=-1,27=1,28=-2,29=300,31=1,32=6,42=3/1,2,10;
 10/6=2,21=1,31=1/2;
 8/6=4,8=1,10=2,19=11,30=-1/11,4;
 10/5=1,20=4,31=1/2;
 11/12=2,14=11,16=1,17=2,28=-2,31=1,42=3/2,10,12;
 6/7=2,8=2,9=2,10=2/1;
 7/8=1,10=1,12=2,25=1,30=1,33=1,44=2/1,2,3,16;
 1/10=4,30=1/3;
 99//99;
 Structure from the checkpoint file: 3HOP-hess.chk
 FileIO operation on non-existent file.
FileIO: IOper= 2 IFilNo(1)=-20502 Len= 100 IPos= 4 Q= 97586560

 dumping /fiocom/, unit = 1 NFiles = 14 SizExt = 524288 WInBlk = 512
                   defal = T LstWrd = 596480 FType=2 FMxFil=10000

 Number 0 501 502 598 989 991 992 993
 Base 180224 43520 72192 76800 44544 65536 65024 43008
 End 596480 44520 76297 76802 64544 72098 65033 43208
 End1 596480 44544 76800 77312 65024 72192 65536 43520
 Wr Pntr 180224 43520 72192 76800 44544 65536 65024 43008
 Rd Pntr 180224 43520 72192 76800 44544 72098 65033 43208
 Length 416256 1000 4105 2 20000 6562 9 200

 Number 994 995 996 997 998 999
 Base 40448 42496 41472 41984 40960 77312
 End 40478 42516 41672 42058 41160 179816
 End1 40960 43008 41984 42496 41472 180224
 Wr Pntr 40448 42496 41472 41984 40960 77312
 Rd Pntr 40478 42516 41672 42055 41160 79816
 Length 30 20 200 74 200 102504

 dumping /fiocom/, unit = 2 NFiles = 1 SizExt = 0 WInBlk = 131072
                   defal = F LstWrd = 262144 FType=2 FMxFil=10000

 Number 0
 Base 131072
 End 262144
 End1 262144
 Wr Pntr 131072
 Rd Pntr 131072
 Length 131072

 dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 512
                   defal = T LstWrd = 65536 FType=2 FMxFil=10000

 Number 0
 Base 40448
 End 65536
 End1 65536
 Wr Pntr 40448
 Rd Pntr 40448
 Length 25088
 Error termination in NtrErr:
 NtrErr Called from FileIO.
---------------------------------------------

Also I got confused whether one or both files should use during calculation. Could you please help me to solve this problem. I can provide you gaussian input files if needed.

Thanks

Regards
________________________________
Him Upadhyay