From owner-chemistry@ccl.net Thu Nov 20 02:02:00 2008 From: "Jerome Kieffer jerome.Kieffer:_:terre-adelie.org" To: CCL Subject: CCL: HOMO y LUMO Message-Id: <-38122-081119164943-24804-OUT/MN3pEjiQzPdF+i/wdA . server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Wed, 19 Nov 2008 22:18:53 +0100 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer(0)terre-adelie.org] On Wed, 19 Nov 2008 12:27:43 -0600 ""MQO. Carlos Javier N=FA=F1ez Aguero" carlosjavierna*gmail.com" wrote: > the representation of the orbital molecular HOMO normally is in two=20 > colors: eg., red and blue, ok? > What means the colors? Red =3D negative density? Blue =3D positive densit= y? It is the mathematical sign of the wavefunction at this place, either positive or negative. As only the density of probability of presence of electrons makes =ABphysically sens=BB, an this density is the square (i.e. postitive) of the wavefunction, no mater if Red/Blue is positive or negative, only the variation of sign matters for interactions. With my best regards,=20 --=20 J=E9r=F4me KIEFFER =20 http://www.terre-adelie.org From owner-chemistry@ccl.net Thu Nov 20 04:30:00 2008 From: "Christos Kefalidis kefalidi^-^chem.auth.gr" To: CCL Subject: CCL:G: Gaussian error Message-Id: <-38123-081120041712-2222-MlJUHAopw/DOkg6TREUnHQ-,-server.ccl.net> X-Original-From: Christos Kefalidis Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 20 Nov 2008 10:45:26 +0200 MIME-Version: 1.0 Sent to CCL by: Christos Kefalidis [kefalidi#%#chem.auth.gr] Dear Neha, You should try the below sequence of keywords: %chk=3Dpenta.chk %Mem=3D2GB %NProc=3D4 #p hf/6-31g(d) opt=3D(calcfc,vtight,restart,maxcyc=3D100) scf(Conver=3D8) = =20 freq nosymm test Hope this will help you. Christos ?????? ?????? ??? "Neha S Gandhi n.gandhiau[#]gmail.com" =20 : > > Sent to CCL by: "Neha S Gandhi" [n.gandhiau,,gmail.com] > Hi All, > > I am running Gaussian job as below: > > %chk=3Dpenta.chk > %Mem=3D2GB > %NProc=3D4 > > #P hf/6-31G* Opt=3D(VTight,CalcFC) Freq SCF(Conver=3D8) Test nosymm > > The walltime exceeds and I need to restart the job. How do I =20 > restart. When I restart (based on previous mailing list) I get the =20 > same errors. > > dumping /fiocom/, unit =3D 2 NFiles =3D 8 SizExt =3D 0 WInBlk= =20 > =3D 2048 > defal =3D F LstWrd =3D 5763072 FType=3D2 FMxFil=3D1= 0000 > > Number 0 508 522 536 538 =20 > 634 670 998 > Base 5762012 50048 50178 3858992 4810502 =20 > 52936 40960 50078 > End 5763072 50078 52936 4810502 5762012 =20 > 3858992 50048 50178 > End1 5763072 50078 52936 4810502 5762012 =20 > 3858992 50048 50178 > Wr Pntr 5762012 50048 50178 3858992 4810502 =20 > 52936 40960 50078 > Rd Pntr 5762012 50048 50178 3858992 4810502 =20 > 52936 40960 50078 > Length 1060 30 2758 951510 951510 =20 > 3806056 9088 100 > > > dumping /fiocom/, unit =3D 3 NFiles =3D 1 SizExt =3D 524288 WInBlk= =20 > =3D 2048 > defal =3D T LstWrd =3D 65536 FType=3D2 FMxFil=3D1= 0000 > > Number 0 > Base 40960 > End 65536 > End1 65536 > Wr Pntr 40960 > Rd Pntr 40960 > Length 24576 > Error termination in NtrErr: > NtrErr Called from FileIO. > > > I tried following keywords with no luck. > %chk=3Dpenta.chk > %Mem=3D2GB > %NProc=3D4 > #p hf/6-31g(d) opt=3D(calcfc,vtight,restart) scf(Conver=3D8) freq =20 > density=3D(current,checkpoint)nosymm geom=3Dcheck test > > Regards > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > --=20 Christos E. Kefalidis, PhD Candidate, Research Group of Prof. Tsipis, Laboratory of Applied Quantum Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, GREECE From owner-chemistry@ccl.net Thu Nov 20 16:54:01 2008 From: "Alcides Simao alsimao(~)gmail.com" To: CCL Subject: CCL:G: Gaussian error Message-Id: <-38124-081120164330-11458-IwfayYlrblGNboM+Qls+ag:+:server.ccl.net> X-Original-From: "Alcides Simao" Content-Type: multipart/alternative; boundary="----=_Part_100034_2249982.1227217394970" Date: Thu, 20 Nov 2008 21:43:14 +0000 MIME-Version: 1.0 Sent to CCL by: "Alcides Simao" [alsimao[A]gmail.com] ------=_Part_100034_2249982.1227217394970 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Neha, In addittion to Christos suggestion, I would also suggest you to increase the walltime ( I believe you're running the Gaussian Linux version under LINDA in a supercomputer/cluster)! Best, Alcides 2008/11/20 Christos Kefalidis kefalidi^-^chem.auth.gr < owner-chemistry##ccl.net> > > Sent to CCL by: Christos Kefalidis [kefalidi#%#chem.auth.gr] > Dear Neha, > You should try the below sequence of keywords: > > %chk=penta.chk > %Mem=2GB > %NProc=4 > #p hf/6-31g(d) opt=(calcfc,vtight,restart,maxcyc=100) scf(Conver=8) freq > nosymm test > > Hope this will help you. > > Christos > > > ?????? ?????? ??? "Neha S Gandhi n.gandhiau[#]gmail.com" > : > > >> Sent to CCL by: "Neha S Gandhi" [n.gandhiau,,gmail.com] >> Hi All, >> >> I am running Gaussian job as below: >> >> %chk=penta.chk >> %Mem=2GB >> %NProc=4 >> >> #P hf/6-31G* Opt=(VTight,CalcFC) Freq SCF(Conver=8) Test nosymm >> >> The walltime exceeds and I need to restart the job. How do I restart. >> When I restart (based on previous mailing list) I get the same errors. >> >> dumping /fiocom/, unit = 2 NFiles = 8 SizExt = 0 WInBlk = >> 2048 >> defal = F LstWrd = 5763072 FType=2 FMxFil=10000 >> >> Number 0 508 522 536 538 >> 634 670 998 >> Base 5762012 50048 50178 3858992 4810502 >> 52936 40960 50078 >> End 5763072 50078 52936 4810502 5762012 >> 3858992 50048 50178 >> End1 5763072 50078 52936 4810502 5762012 >> 3858992 50048 50178 >> Wr Pntr 5762012 50048 50178 3858992 4810502 >> 52936 40960 50078 >> Rd Pntr 5762012 50048 50178 3858992 4810502 >> 52936 40960 50078 >> Length 1060 30 2758 951510 951510 >> 3806056 9088 100 >> >> >> dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = >> 2048 >> defal = T LstWrd = 65536 FType=2 FMxFil=10000 >> >> Number 0 >> Base 40960 >> End 65536 >> End1 65536 >> Wr Pntr 40960 >> Rd Pntr 40960 >> Length 24576 >> Error termination in NtrErr: >> NtrErr Called from FileIO. >> >> >> I tried following keywords with no luck. >> %chk=penta.chk >> %Mem=2GB >> %NProc=4 >> #p hf/6-31g(d) opt=(calcfc,vtight,restart) scf(Conver=8) freq >> density=(current,checkpoint)nosymm geom=check test >> >> Regards> >> >> >> > > > -- > Christos E. Kefalidis, > PhD Candidate, > Research Group of Prof. Tsipis, > Laboratory of Applied Quantum Chemistry, > Department of Chemistry, > Aristotle University of Thessaloniki, > GREECE > > > > - This is automatically added to each message by the mailing script -http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > ------=_Part_100034_2249982.1227217394970 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Neha,

In addittion to Christos suggestion, I would also suggest you to increase the walltime ( I believe you're running the Gaussian Linux version under LINDA in a supercomputer/cluster)!

Best,

Alcides

2008/11/20 Christos Kefalidis kefalidi^-^chem.auth.gr <owner-chemistry##ccl.net>

Sent to CCL by: Christos Kefalidis [kefalidi#%#chem.auth.gr]
Dear Neha,
You should try the below sequence of keywords:

%chk=penta.chk
%Mem=2GB
%NProc=4
#p hf/6-31g(d) opt=(calcfc,vtight,restart,maxcyc=100) scf(Conver=8) freq nosymm test

Hope this will help you.

Christos


?????? ?????? ??? "Neha S Gandhi n.gandhiau[#]gmail.com" <owner-chemistry+/-ccl.net>:


Sent to CCL by: "Neha S Gandhi" [n.gandhiau,,gmail.com]
Hi All,

I am running Gaussian job as below:

%chk=penta.chk
%Mem=2GB
%NProc=4

#P hf/6-31G* Opt=(VTight,CalcFC) Freq SCF(Conver=8) Test nosymm

The walltime exceeds and I need to restart the job. How do I  restart. When I restart (based on previous mailing list) I get the  same errors.

 dumping /fiocom/, unit = 2 NFiles =     8 SizExt =         0 WInBlk  =      2048
                  defal = F LstWrd =     5763072 FType=2 FMxFil=10000

 Number           0        508        522        536        538         634        670        998
 Base       5762012      50048      50178    3858992    4810502       52936      40960      50078
 End        5763072      50078      52936    4810502    5762012     3858992      50048      50178
 End1       5763072      50078      52936    4810502    5762012     3858992      50048      50178
 Wr Pntr    5762012      50048      50178    3858992    4810502       52936      40960      50078
 Rd Pntr    5762012      50048      50178    3858992    4810502       52936      40960      50078
 Length        1060         30       2758     951510     951510     3806056       9088        100


 dumping /fiocom/, unit = 3 NFiles =     1 SizExt =    524288 WInBlk  =      2048
                  defal = T LstWrd =       65536 FType=2 FMxFil=10000

 Number           0
 Base         40960
 End          65536
 End1         65536
 Wr Pntr      40960
 Rd Pntr      40960
 Length       24576
 Error termination in NtrErr:
 NtrErr Called from FileIO.


 I tried following keywords with no luck.
%chk=penta.chk
%Mem=2GB
%NProc=4
#p hf/6-31g(d) opt=(calcfc,vtight,restart) scf(Conver=8) freq  density=(current,checkpoint)nosymm geom=check test

Regards







--
Christos E. Kefalidis,
PhD Candidate,
Research Group of Prof. Tsipis,
Laboratory of Applied Quantum Chemistry,
Department of Chemistry,
Aristotle University of Thessaloniki,
GREECE



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------=_Part_100034_2249982.1227217394970-- From owner-chemistry@ccl.net Thu Nov 20 18:32:01 2008 From: "Neha Gandhi n.gandhiau]|[gmail.com" To: CCL Subject: CCL:G: Gaussian error Message-Id: <-38125-081120175442-25083-bvNxekP5mXUoFpr+u4/7vQ-,-server.ccl.net> X-Original-From: "Neha Gandhi" Content-Type: multipart/alternative; boundary="----=_Part_106576_413396.1227217175191" Date: Fri, 21 Nov 2008 06:39:35 +0900 MIME-Version: 1.0 Sent to CCL by: "Neha Gandhi" [n.gandhiau * gmail.com] ------=_Part_106576_413396.1227217175191 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Christos, It didnot work. Here is my restart file and log file.. %RWF=/short/j93/,-1 %NoSave %chk=molecule.chk %Mem=2GB %NProc=4 #P hf/6-31G* Opt=(VTight,CalcFC,restart,maxcyc=100) scf(Conver=8) Freq Test nosymm The o/p log file is Leave Link 1 at Fri Nov 21 08:37:48 2008, MaxMem= 268435456 cpu: 0.7 (Enter /opt/gaussian/g03e01/g03/l103.exe) GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Restoring state from the checkpoint file "molecule.chk". FileIO operation on non-existent file. FileIO: IOper= 2 IFilNo(1)= -997 Len= 380012 IPos= 0 Q=***************** dumping /fiocom/, unit = 1 NFiles = 19 SizExt = 524288 WInBlk = 2048 defal = T LstWrd = 9854976 FType=2 FMxFil=10000 Number 0 0 0 0 0 508 522 536 Base 464896 434176 430080 47104 9330688 432128 460800 600064 End 493568 438272 432128 428032 9854976 432158 464210 2054429 End1 493568 438272 432128 428032 9854976 434176 464896 2056192 Wr Pntr 448512 434176 430080 47104 600064 432158 464210 2054429 Rd Pntr 448512 434176 430280 427116 600064 432128 460800 600064 dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 2048 defal = T LstWrd = 65536 FType=2 FMxFil=10000 Number 0 Base 40960 End 65536 End1 65536 Wr Pntr 40960 Rd Pntr 40960 Length 24576 Error termination in NtrErr: NtrErr Called from FileIO. Any further help? Regards, Neha 2008/11/20 Christos Kefalidis kefalidi^-^chem.auth.gr < owner-chemistry+*+ccl.net> > > Sent to CCL by: Christos Kefalidis [kefalidi#%#chem.auth.gr] > Dear Neha, > You should try the below sequence of keywords: > > %chk=penta.chk > %Mem=2GB > %NProc=4 > #p hf/6-31g(d) opt=(calcfc,vtight,restart,maxcyc=100) scf(Conver=8) freq > nosymm test > > Hope this will help you. > > Christos > > > ?????? ?????? ??? "Neha S Gandhi n.gandhiau[#]gmail.com" > : > > >> Sent to CCL by: "Neha S Gandhi" [n.gandhiau,,gmail.com] >> Hi All, >> >> I am running Gaussian job as below: >> >> %chk=penta.chk >> %Mem=2GB >> %NProc=4 >> >> #P hf/6-31G* Opt=(VTight,CalcFC) Freq SCF(Conver=8) Test nosymm >> >> The walltime exceeds and I need to restart the job. How do I restart. >> When I restart (based on previous mailing list) I get the same errors. >> >> dumping /fiocom/, unit = 2 NFiles = 8 SizExt = 0 WInBlk = >> 2048 >> defal = F LstWrd = 5763072 FType=2 FMxFil=10000 >> >> Number 0 508 522 536 538 >> 634 670 998 >> Base 5762012 50048 50178 3858992 4810502 >> 52936 40960 50078 >> End 5763072 50078 52936 4810502 5762012 >> 3858992 50048 50178 >> End1 5763072 50078 52936 4810502 5762012 >> 3858992 50048 50178 >> Wr Pntr 5762012 50048 50178 3858992 4810502 >> 52936 40960 50078 >> Rd Pntr 5762012 50048 50178 3858992 4810502 >> 52936 40960 50078 >> Length 1060 30 2758 951510 951510 >> 3806056 9088 100 >> >> >> dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = >> 2048 >> defal = T LstWrd = 65536 FType=2 FMxFil=10000 >> >> Number 0 >> Base 40960 >> End 65536 >> End1 65536 >> Wr Pntr 40960 >> Rd Pntr 40960 >> Length 24576 >> Error termination in NtrErr: >> NtrErr Called from FileIO. >> >> >> I tried following keywords with no luck. >> %chk=penta.chk >> %Mem=2GB >> %NProc=4 >> #p hf/6-31g(d) opt=(calcfc,vtight,restart) scf(Conver=8) freq >> density=(current,checkpoint)nosymm geom=check test >> >> Regards> >> >> >> > > > -- > Christos E. Kefalidis, > PhD Candidate, > Research Group of Prof. Tsipis, > Laboratory of Applied Quantum Chemistry, > Department of Chemistry, > Aristotle University of Thessaloniki, > GREECE > > > > - This is automatically added to each message by the mailing script -http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Regards, Neha Gandhi, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845 ------=_Part_106576_413396.1227217175191 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Christos,

It didnot work. Here is my restart file and log file..


%RWF=/short/j93/,-1
%NoSave
%chk=molecule.chk
%Mem=2GB
%NProc=4
#P hf/6-31G* Opt=(VTight,CalcFC,restart,maxcyc=100) scf(Conver=8) Freq Test nosymm

The o/p log file is

 Leave Link    1 at Fri Nov 21 08:37:48 2008, MaxMem=  268435456 cpu:       0.7
 (Enter /opt/gaussian/g03e01/g03/l103.exe)

 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
 Berny optimization.
 Restoring state from the checkpoint file "molecule.chk".
 FileIO operation on non-existent file.
FileIO: IOper= 2 IFilNo(1)=  -997 Len=      380012 IPos=           0 Q=*****************


 dumping /fiocom/, unit = 1 NFiles =    19 SizExt =    524288 WInBlk =      2048
                   defal = T LstWrd =     9854976 FType=2 FMxFil=10000

 Number           0          0          0          0          0        508        522        536
 Base        464896     434176     430080      47104    9330688     432128     460800     600064
 End         493568     438272     432128     428032    9854976     432158     464210    2054429
 End1        493568     438272     432128     428032    9854976     434176     464896    2056192
 Wr Pntr     448512     434176     430080      47104     600064     432158     464210    2054429
 Rd Pntr     448512     434176     430280     427116     600064     432128     460800     600064


 dumping /fiocom/, unit = 3 NFiles =     1 SizExt =    524288 WInBlk =      2048
                   defal = T LstWrd =       65536 FType=2 FMxFil=10000

 Number           0
 Base         40960
 End          65536
 End1         65536
 Wr Pntr      40960
 Rd Pntr      40960
 Length       24576
 Error termination in NtrErr:
 NtrErr Called from FileIO.


Any further help?
Regards,
Neha

2008/11/20 Christos Kefalidis kefalidi^-^chem.auth.gr <owner-chemistry+*+ccl.net>

Sent to CCL by: Christos Kefalidis [kefalidi#%#chem.auth.gr]
Dear Neha,
You should try the below sequence of keywords:

%chk=penta.chk
%Mem=2GB
%NProc=4
#p hf/6-31g(d) opt=(calcfc,vtight,restart,maxcyc=100) scf(Conver=8) freq nosymm test

Hope this will help you.

Christos


?????? ?????? ??? "Neha S Gandhi n.gandhiau[#]gmail.com" <owner-chemistry+/-ccl.net>:


Sent to CCL by: "Neha S Gandhi" [n.gandhiau,,gmail.com]
Hi All,

I am running Gaussian job as below:

%chk=penta.chk
%Mem=2GB
%NProc=4

#P hf/6-31G* Opt=(VTight,CalcFC) Freq SCF(Conver=8) Test nosymm

The walltime exceeds and I need to restart the job. How do I  restart. When I restart (based on previous mailing list) I get the  same errors.

 dumping /fiocom/, unit = 2 NFiles =     8 SizExt =         0 WInBlk  =      2048
                  defal = F LstWrd =     5763072 FType=2 FMxFil=10000

 Number           0        508        522        536        538         634        670        998
 Base       5762012      50048      50178    3858992    4810502       52936      40960      50078
 End        5763072      50078      52936    4810502    5762012     3858992      50048      50178
 End1       5763072      50078      52936    4810502    5762012     3858992      50048      50178
 Wr Pntr    5762012      50048      50178    3858992    4810502       52936      40960      50078
 Rd Pntr    5762012      50048      50178    3858992    4810502       52936      40960      50078
 Length        1060         30       2758     951510     951510     3806056       9088        100


 dumping /fiocom/, unit = 3 NFiles =     1 SizExt =    524288 WInBlk  =      2048
                  defal = T LstWrd =       65536 FType=2 FMxFil=10000

 Number           0
 Base         40960
 End          65536
 End1         65536
 Wr Pntr      40960
 Rd Pntr      40960
 Length       24576
 Error termination in NtrErr:
 NtrErr Called from FileIO.


 I tried following keywords with no luck.
%chk=penta.chk
%Mem=2GB
%NProc=4
#p hf/6-31g(d) opt=(calcfc,vtight,restart) scf(Conver=8) freq  density=(current,checkpoint)nosymm geom=check test

Regards







--
Christos E. Kefalidis,
PhD Candidate,
Research Group of Prof. Tsipis,
Laboratory of Applied Quantum Chemistry,
Department of Chemistry,
Aristotle University of Thessaloniki,
GREECE



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--
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
------=_Part_106576_413396.1227217175191--