From owner-chemistry@ccl.net Sat Aug 15 15:24:01 2015 From: "Marcel Swart marcel.swart%%icrea.cat" To: CCL Subject: CCL:G: Error in termination for a transition state of large organic molecule Message-Id: <-51586-150815150025-19767-1L5tyEvjIxRplCu0C92Fiw-x-server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary="Apple-Mail=_B8BB1543-5127-4FE4-8309-8A0A8602F4EE" Date: Sat, 15 Aug 2015 21:00:14 +0200 Mime-Version: 1.0 (Mac OS X Mail 8.2 \(2104\)) Sent to CCL by: Marcel Swart [marcel.swart^_^icrea.cat] --Apple-Mail=_B8BB1543-5127-4FE4-8309-8A0A8602F4EE Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Dear Mallika, why the heck do you specify a maximum of 4092 SCF cycles??? It should be done within 50 max, otherwise you have to try some other SCF scheme such as EDIIS. What happens if you take the last geometry, and put that in the input? Does it stop at the same point, or does it continue for some steps? This will help you understand whether this is technical or scientific. I.e., if it stops and does not go on for not even ONE step, then it means that there=E2=80=99s something with THAT geometry; if it = continues, then probably you=E2=80=99re running into some memory or disc problem. Marcel > On 2015-08-15, at 18:36, Mallika Khare mkhare__mtu.edu = wrote: >=20 > Hello Igors >=20 > As per your guidance, I tried increasing the optimization cycles,used = CalcFC and also used SCF=3DXQC. But, everytime I am getting the same = result (Error in Termination). The output is ending after the rotational = constant calculation. >=20 > I would be very thankful to you, if you could look at my input = output(attached below)and guide me what can be done. >=20 > Many Thanks and Regards > Mallika Khare >=20 > Here's my input and output: > Input: > %nprocshared=3D12 > %mem=3D30GB > %OldChk=3Dfile_name.chk > %Chk=3Dfile_name.chk > #p opt=3D(qst3,noeigentest,MaxCycle=3D2048,CalcFC) freq = oniom(b3lyp/3-21+g*:b3lyp/sto-3g*:pm3) scf=3D(xqc,IntRep,maxcycle=3D4092) > geom=3Dconnectivity >=20 > Reacrtant >=20 > -3 2 0 2 0 2 0 2 0 2 0 2 >=20 >=20 > Output >=20 > 90 1 0 5.940783 1.161302 -1.505445 > 91 1 0 4.214536 1.555958 0.749945 > 92 8 0 -7.269357 -0.588603 -0.813879 > 93 1 0 -7.352913 -1.345087 -0.172271 > --------------------------------------------------------------------- > Rotational constants (GHZ): 0.0701555 0.0201527 = 0.0192135 > Leave Link 202 at Sat Aug 15 06:39:14 2015, MaxMem=3D 4026531840 = cpu: 0.1 > (Enter /share/apps/gaussian/D01/g09/l9999.exe) >=20 >=20 > A people that values its privileges above its principles soon loses = both. > -- Dwight D. Eisenhower > Error termination request processed by link 9999. > Error termination via Lnk1e in /share/apps/gaussian/D01/g09/l9999.exe = at Sat Aug 15 06:39:14 2015. > Job cpu time: 1 days 13 hours 27 minutes 31.6 seconds. > File lengths (MBytes): RWF=3D 4865 Int=3D 0 D2E=3D 0 = Chk=3D 70 Scr=3D 2 > Error: segmentation violation > rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff > rdx 000000000001fa18, rsp 00007fffffffa118, rbp 00007fffffffa690 > rsi 000000000000000b, rdi 000000000001fa18, r8 00002aaaaaaaf620 > r9 0000000000000000, r10 00007fffffff9ea0, r11 0000000000000206 > r12 0000000000000000, r13 0000000000000000, r14 00007fffffffa6d8 > r15 00000000000003e6 >=20 >=20 > On Fri, Aug 14, 2015 at 1:16 PM, Mallika Khare mkhare.:.mtu.edu = > wrote: > Hello Igors Mihailovs >=20 > Thank you very much for your quick response. >=20 > My output didn't terminate at all as per the input I provided. The = geometry optimization does not converge as per the output I received. I = didn't attach the output because it is really long but, I can show the = last RMS Force and Displacement values. They are as follows: >=20 > Item Value = Threshold Converged? > Maximum Force 0.030490 0.000450 = NO=20 > RMS Force 0.004366 0.000300 = NO=20 > Maximum Displacement 0.372605 0.001800 = NO=20 > RMS Displacement 0.068999 0.001200 = NO=20 > Predicted change in Energy=3D-6.415468D-03 > =20 > I am really thankful to you for the information you provided and will = try to implement these techniques you told me in your previous email. >=20 > Many Thanks and Regards >=20 > Mallika Khare >=20 >=20 >=20 >=20 >=20 > On Thu, Aug 13, 2015 at 2:39 PM, Igors Mihailovs = igors.mihailovs0-$-gmail.com = > wrote: > Dear Mallika, >=20 > At which exactly part of calculation does it terminate? =46rom Your = output (which is just some last lines in file) nobody is able to = determine whether this is SCF convergence failure or Geometry = optimization failure, or something else... >=20 > If it is geometry optimization that does not converge, You can = probably increase MaxCycle of it, too, not just for SCF: = Opt=3D(QST3,NoEigenTest,MaxCyc=3D2048). Also (and better), Opt=3DCalcFC = might have helped =E2=80=93 as You are requesting frequency calculation = after the Opt, I assume You have resources for it. To use it, determine = the step where Your calculation was most close to convergence, e. g. by = using this command (stolen from "Exploring Chemistry with Electronic = Structure Methods" by Foresman and Frisch): >=20 > egrep 'out of|SCF Don|Converged| NO | YES | exceeded' your-output-file = | grep -v '\\\\' >=20 > and choosing the step with the least values; then adding to Your next = input file keyword Geom=3D(Check,Step=3DN) where N is number of the best = step. And Opt=3D(QST3,NoEigenTest,MaxCyc=3D2048,CalcFC). >=20 > It is also quite convenient to use XQC or YQC instead of QC nowadays: = XQC is using quadratic algorithm only if regular SCF does not converge, = whereas YQC is doing steepest descent following by regular SCF and only = if the last fails does QC (however, YQC does not work in all cases, see, = e. g. http://ccl.net/cgi-bin/ccl/message-new?2015+05+30+001 = ). Sometimes = SCF=3DFermi helps, too. See = http://www.ccl.net/cca/documents/dyoung/topics-orig/converge.html = for = further options. >=20 > With best wishes, > Igors Mihailovs (engineer) > Institute of Solid State Physics > University of Latvia >=20 >=20 > 2015-08-13 19:19 GMT+03:00 Mallika Khare mkhare__mtu.edu = >: >=20 > Sent to CCL by: "Mallika Khare" [mkhare- -mtu.edu ] > Hello > I am struggling hard to get my job terminated. But, at this point I > couldn't figure out the reason for this error stated below. I checked = by > increasing the maxcycle of SCF,increasing the memory and also checked = my > checkpoint file but even then it is not optimized.(Using Geom=3DAllCheck= > also makes no difference) > I would be very thankful if anyone can help me with this problem. > Thanks and Regards > Malllika Khare > mkhare[A]mtu.edu >=20 > Input > %nprocshared=3D12 > %mem=3D30GB > %OldChk=3Dfilename.chk > %Chk=3Dfilename.chk > #p opt=3D(qst3,noeigentest) freq = oniom(b3lyp/3-21+g*:b3lyp/sto-3g*:pm3) > scf=3D(qc,tight,maxcycle=3D6500) > geom=3Dconnectivity >=20 > Output > Error termination request processed by link 9999. > Error termination via Lnk1e in /share/apps/gaussian/D01/g09/l9999.exe = at > Wed Aug 12 09:49:37 2015. > Job cpu time: 3 days 5 hours 47 minutes 0.4 seconds. > File lengths (MBytes): RWF=3D 150 Int=3D 0 D2E=3D 0 = Chk=3D 70 > Scr=3D 2 > Error: segmentation violation > rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff > rdx 000000000002a8ac, rsp 00007fffffffa168, rbp 00007fffffffa6e0 > rsi 000000000000000b, rdi 000000000002a8ac, r8 00002aaaaaaaf620 > r9 0000000000000000, r10 00007fffffff9ef0, r11 0000000000000202 > r12 0000000000000000, r13 0000000000000000, r14 00007fffffffa728 > r15 00000000000003e6 > --- traceback not available >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D-=20 > E-mail to subscribers: CHEMISTRY]^[ccl.net = or use:= >=20 > E-mail to administrators: CHEMISTRY-REQUEST]^[ccl.net = or use= >=20= >=20= >=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ = >=20= >=20= >=20 >=20 >=20 >=20 >=20 _______________________________________________________ Prof. Marcel Swart ICREA Research Professor at Inst. Comput. Chem. Catal. (IQCC) Univ. Girona (Spain) Member of Young Academy of Europe www.yacadeuro.org Chair COST Action CM1305 (ECOSTBio) www.ecostbio.eu Organizer Girona Seminar 2016 www.gironaseminar.com web http://www.marcelswart.eu vCard addressbook://www.marcelswart.eu/MSwart.vcf --Apple-Mail=_B8BB1543-5127-4FE4-8309-8A0A8602F4EE Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Dear Mallika,

why the heck do you specify a maximum of 4092 SCF = cycles???
It should be done within 50 max, = otherwise you have to try some
other SCF scheme = such as EDIIS.

What happens if you take the last geometry, and put that in = the
input? Does it stop at the same point, or does = it continue for some
steps?
This= will help you understand whether this is technical or = scientific.
I.e., if it stops and does not go on = for not even ONE step, then it
means that there=E2=80= =99s something with THAT geometry; if it continues,
then probably you=E2=80=99re running into some memory or disc = problem.

Marcel

On 2015-08-15, at 18:36, = Mallika Khare mkhare__mtu.edu <owner-chemistry*o*ccl.net> wrote:

Hello Igors

As per your guidance, I tried increasing the optimization = cycles,used CalcFC and also used SCF=3DXQC. But, everytime I am getting = the same result (Error in Termination). The output is ending after the = rotational constant calculation.

I would be very thankful to you, if you = could look at my input output(attached below)and guide me what can be = done.

Many = Thanks and Regards
Mallika Khare

Here's my input and = output:
Input:
%nprocshared=3D12
%mem=3D30GB
%OldChk=3Dfile_name.chk
%Chk=3Dfile_name.chk
#p = opt=3D(qst3,noeigentest,MaxCycle=3D2048,CalcFC) freq = oniom(b3lyp/3-21+g*:b3lyp/sto-3g*:pm3) = scf=3D(xqc,IntRep,maxcycle=3D4092)
geom=3Dconnectivity

Reacrtant

-3 2 0 2 0 2 0 2 0 2 0 2


Output

 90          1 =           0        5.940783 =    1.161302   -1.505445
  =    91          1       =     0        4.214536   =  1.555958    0.749945
    =  92          8         =   0       -7.269357   -0.588603   = -0.813879
     93     =      1           0     =   -7.352913   -1.345087   -0.172271
 ---------------------------------------------------------= ------------
 Rotational constants (GHZ): =      0.0701555      0.0201527   =    0.0192135
 Leave Link  202 = at Sat Aug 15 06:39:14 2015, MaxMem=3D  4026531840 cpu:   =       0.1
 (Enter = /share/apps/gaussian/D01/g09/l9999.exe)


 A people that values its privileges above its = principles soon loses both.
 -- Dwight D. = Eisenhower
 Error termination request = processed by link 9999.
 Error termination via = Lnk1e in /share/apps/gaussian/D01/g09/l9999.exe at Sat Aug 15 06:39:14 = 2015.
 Job cpu time:       1 = days 13 hours 27 minutes 31.6 seconds.
 File = lengths (MBytes):  RWF=3D   4865 Int=3D      0 = D2E=3D      0 Chk=3D     70 Scr=3D   =    2
Error: segmentation = violation
   rax 0000000000000000, rbx = ffffffffffffffff, rcx ffffffffffffffff
  =  rdx 000000000001fa18, rsp 00007fffffffa118, rbp = 00007fffffffa690
   rsi 000000000000000b, = rdi 000000000001fa18, r8  00002aaaaaaaf620
   r9  0000000000000000, r10 00007fffffff9ea0, = r11 0000000000000206
   r12 = 0000000000000000, r13 0000000000000000, r14 00007fffffffa6d8
   r15 00000000000003e6


On Fri, Aug 14, 2015 at 1:16 PM, = Mallika Khare mkhare.:.mtu.edu = <owner-chemistry!=3D!ccl.net> wrote:
Hello Igors Mihailovs

Thank you very much for = your quick response.

My output didn't terminate at all as per the input I = provided. The geometry optimization does not converge as per the output = I received. I didn't attach the output because it is really long but, I = can show the last RMS Force and Displacement values. They are as = follows:

Item                 =                 Value   =                     =  Threshold                 =          Converged?
 Maximum Force           =  0.030490                 =   0.000450                 =                     =       NO 
 RMS   =   Force               =  0.004366                 =      0.000300             =                     =               NO 
 Maximum Displacement     0.372605   =           0.001800         =                     =          NO 
 RMS =     Displacement     0.068999       =            0.001200       =                     =               NO 
 Predicted change in Energy=3D-6.415468D-03
 
I am really thankful to you for = the information you provided and will try to implement these techniques = you told me in your previous email.

Many Thanks and Regards

Mallika Khare





On Thu, = Aug 13, 2015 at 2:39 PM, Igors Mihailovs igors.mihailovs0-$-gmail.com = <owner-chemistry:_:ccl.net> wrote:
Dear = Mallika,

At which exactly part of = calculation does it terminate? =46rom Your output (which is just some = last lines in file) nobody is able to determine whether this is SCF = convergence failure or Geometry optimization failure, or something = else...

If it is geometry = optimization that does not converge, You can probably increase MaxCycle = of it, too, not just for SCF: Opt=3D(QST3,NoEigenTest,MaxCyc=3D2048). = Also (and better), Opt=3DCalcFC might have helped =E2=80=93 as You are = requesting frequency calculation after the Opt, I assume You have = resources for it. To use it, determine the step where Your calculation = was most close to convergence, e. g. by using this command (stolen from = "Exploring Chemistry with Electronic Structure Methods" by Foresman and = Frisch):

egrep 'out = of|SCF Don|Converged| NO | YES | exceeded' your-output-file | grep -v = '\\\\'

and choosing = the step with the least values; then adding to Your next input file = keyword Geom=3D(Check,Step=3DN) where N is number of the best step. And = Opt=3D(QST3,NoEigenTest,MaxCyc=3D2048,CalcFC).

It is also quite convenient to use XQC or YQC instead of QC = nowadays: XQC is using quadratic algorithm only if regular SCF does not = converge, whereas YQC is doing steepest descent following by regular SCF = and only if the last fails does QC (however, YQC does not work in all = cases, see, e. g. http://ccl.net/cgi-bin/ccl/message-new?2015+05+30+001). = Sometimes SCF=3DFermi helps, too. See http://www.ccl.net/cca/documents/dyoung/topics-orig/converge.ht= ml for further options.

With best wishes,
Igors Mihailovs (engineer)
Institute of Solid State Physics
University of Latvia


2015-08-13 19:19 GMT+03:00 Mallika Khare mkhare__mtu.edu <owner-chemistry]^[ccl.net>:

Sent to CCL by: "Mallika  Khare" [mkhare- -mtu.edu]
Hello
I am struggling hard to get my job terminated. But, at this point I
couldn't figure out the reason for this error stated below. I checked = by
increasing the maxcycle of SCF,increasing the memory and also checked = my
checkpoint file but even then it is not optimized.(Using = Geom=3DAllCheck
also makes no difference)
I would be very thankful if anyone can help me with this problem.
Thanks and Regards
Malllika Khare
mkhare[A]mtu.edu

Input
%nprocshared=3D12
%mem=3D30GB
%OldChk=3Dfilename.chk
%Chk=3Dfilename.chk
#p opt=3D(qst3,noeigentest) freq = oniom(b3lyp/3-21+g*:b3lyp/sto-3g*:pm3)
scf=3D(qc,tight,maxcycle=3D6500)
geom=3Dconnectivity

Output
Error termination request processed by link 9999.
 Error termination via Lnk1e in = /share/apps/gaussian/D01/g09/l9999.exe at
Wed Aug 12 09:49:37 2015.
 Job cpu time:       3 days  5 hours 47 = minutes  0.4 seconds.
 File lengths (MBytes):  RWF=3D    150 Int=3D  =     0 D2E=3D      0 Chk=3D    =  70
Scr=3D      2
Error: segmentation violation
   rax 0000000000000000, rbx ffffffffffffffff, rcx = ffffffffffffffff
   rdx 000000000002a8ac, rsp 00007fffffffa168, rbp = 00007fffffffa6e0
   rsi 000000000000000b, rdi 000000000002a8ac, r8  = 00002aaaaaaaf620
   r9  0000000000000000, r10 00007fffffff9ef0, r11 = 0000000000000202
   r12 0000000000000000, r13 0000000000000000, r14 = 00007fffffffa728
   r15 00000000000003e6
  --- traceback not available



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_______________________________________________________
Prof. Marcel Swart

ICREA = Research Professor at
Inst. Comput. Chem. Catal. (IQCC)
Univ. Girona (Spain)

Member of = Young Academy of Europe
www.yacadeuro.org
Chair COST Action CM1305 = (ECOSTBio)
www.ecostbio.eu
Organizer Girona = Seminar 2016
www.gironaseminar.com

web
http://www.marcelswart.eu
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addressbook://www.marcelswart.eu/MSwart.vcf






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