From owner-nwchem-users@emsl.pnl.gov Wed Apr 16 14:13:33 2008 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.14.1/8.14.1) with ESMTP id m3GLDWei028802 for ; Wed, 16 Apr 2008 14:13:33 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.14.1/8.14.1/Submit) id m3GLDWvJ028801 for nwchem-users-outgoing-0915; Wed, 16 Apr 2008 14:13:32 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Ironport-SG: OK_Domains X-Ironport-SBRS: 4.1 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AooAAPcIBkjArjqXjWdsb2JhbACCRjKOZAEBAQEJBQkdnCoB X-IronPort-AV: E=Sophos;i="4.25,666,1199692800"; d="scan'208,217";a="51339695" X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C8A006.B6D7330D" Subject: RE: [NWCHEM] QMMM optimization restart--how are coordinates passed? Date: Wed, 16 Apr 2008 15:13:27 -0600 Message-ID: In-Reply-To: <1692FA5FE0EBFD40B2B4097DAFEA887C038912B1@EMAIL02.pnl.gov> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: [NWCHEM] QMMM optimization restart--how are coordinates passed? Thread-Index: Acif7uTbMHoQHfWaRf27ceSp98+RHAACHAOAAAPIEpA= References: <1692FA5FE0EBFD40B2B4097DAFEA887C038912B1@EMAIL02.pnl.gov> From: "Chang, Christopher" To: "DeJong, Wibe A" , X-OriginalArrivalTime: 16 Apr 2008 21:13:28.0265 (UTC) FILETIME=[B7203B90:01C8A006] Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk This is a multi-part message in MIME format. ------_=_NextPart_001_01C8A006.B6D7330D Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Hi Bert, =20 That tracks; then, shouldn't the geometries reported during the gradient calculations differ between cycles 3 and 4 (equivalently, between jobs 1c and 1e)? =20 - Chris ________________________________ From: DeJong, Wibe A [mailto:Wibe.DeJong@pnl.gov]=20 Sent: Wednesday, April 16, 2008 1:25 PM To: Chang, Christopher; nwchem-users@emsl.pnl.gov Subject: RE: [NWCHEM] QMMM optimization restart--how are coordinates passed? =09 =09 Chris, =20 In your input deck below I see you define "start" and not "restart". By specifying start the RTDB is brand new (not restarted from), and your geometry will be obtained from the restart files generated by the QM/MM (.top /.rst). Bert de Jong, Ph.D. Chief Scientist=20 Capability Steward=20 High Performance Software Development=20 Environmental Molecular Science Laboratory=20 Pacific Northwest National Laboratory=20 P.O. Box 999, Mail Stop K8-91=20 Richland, WA 99352=20 Phone: (509) 371-6476 Email: bert.dejong@pnl.gov=20 Fax: (509) 371-6445 Room: EMSL 1371=20 Web: http://mscf.emsl.pnl.gov =20 =20 ________________________________ From: owner-nwchem-developers@emsl.pnl.gov [mailto:owner-nwchem-developers@emsl.pnl.gov] On Behalf Of Chang, Christopher Sent: Wednesday, April 16, 2008 11:23 AM To: nwchem-users@emsl.pnl.gov Subject: [NWCHEM] QMMM optimization restart--how are coordinates passed? =09 =09 Hi, =20 I was comparing output from a continuation of a QMMM geometry optimization with a preceding calculation. Calculation "...1c.log" got through several DFT optimization steps, while "...1d.log" failed to converge the SCF. "...1e.log" was a restart from the vectors from ...1d. In each case, I simply restarted the QMMM calculation from the scratch files present in the directory. =20 grep -A10 'DFT ENERGY GRADIENTS' QMMM_opt1[ce].log =20 QMMM_opt1c.log: DFT ENERGY GRADIENTS QMMM_opt1c.log- QMMM_opt1c.log- atom coordinates gradient QMMM_opt1c.log- x y z x y z QMMM_opt1c.log- 1 N 21.941608 172.227737 137.785591 -0.028706 -0.006824 0.056941 QMMM_opt1c.log- 2 H 20.637698 171.623024 136.564828 0.029059 0.012163 -0.011127 QMMM_opt1c.log- 3 C 24.133691 173.414485 136.632858 -0.003433 -0.010364 -0.001724 QMMM_opt1c.log- 4 H 25.632243 173.433382 138.029366 -0.015064 0.003432 -0.005131 QMMM_opt1c.log- 5 C 24.897140 171.983962 134.221568 0.003058 0.029756 -0.010798 QMMM_opt1c.log- 6 H 23.179379 171.452949 133.133086 -0.005151 -0.004147 0.001271 QMMM_opt1c.log- 7 H 25.785311 170.173605 134.824390 0.004683 -0.003498 0.002594 -- QMMM_opt1c.log: DFT ENERGY GRADIENTS QMMM_opt1c.log- QMMM_opt1c.log- atom coordinates gradient QMMM_opt1c.log- x y z x y z QMMM_opt1c.log- 1 N 21.981641 172.252596 137.571753 -0.026111 0.008512 -0.096356 QMMM_opt1c.log- 2 H 20.610111 171.612507 136.577712 0.056892 0.024329 0.019713 QMMM_opt1c.log- 3 C 24.138714 173.421682 136.632897 -0.017938 -0.022434 0.020339 QMMM_opt1c.log- 4 H 25.645188 173.420094 138.026422 -0.011550 0.004714 -0.005757 QMMM_opt1c.log- 5 C 24.894390 171.959011 134.230293 -0.002757 0.015700 -0.001076 QMMM_opt1c.log- 6 H 23.183993 171.455957 133.132630 -0.004067 -0.002887 0.002269 QMMM_opt1c.log- 7 H 25.781281 170.176592 134.822180 0.002162 0.003270 -0.000195 -- QMMM_opt1c.log: DFT ENERGY GRADIENTS QMMM_opt1c.log- QMMM_opt1c.log- atom coordinates gradient QMMM_opt1c.log- x y z x y z QMMM_opt1c.log- 1 N 21.988372 172.246947 137.630522 -0.003368 0.015256 -0.047565 QMMM_opt1c.log- 2 H 20.584923 171.602616 136.566604 0.027820 0.010573 -0.001840 QMMM_opt1c.log- 3 C 24.147306 173.430766 136.621126 -0.013934 -0.015437 0.010889 QMMM_opt1c.log- 4 H 25.650386 173.412191 138.025336 -0.011507 0.002949 -0.003788 QMMM_opt1c.log- 5 C 24.895507 171.951692 134.230687 -0.001237 0.011757 -0.001698 QMMM_opt1c.log- 6 H 23.186043 171.457039 133.131923 -0.003359 -0.002420 0.002387 QMMM_opt1c.log- 7 H 25.780211 170.175149 134.822233 0.001247 0.004818 -0.000668 -- QMMM_opt1e.log: DFT ENERGY GRADIENTS QMMM_opt1e.log- QMMM_opt1e.log- atom coordinates gradient QMMM_opt1e.log- x y z x y z QMMM_opt1e.log- 1 N 21.988372 172.246946 137.630522 -0.003377 0.015255 -0.047552 QMMM_opt1e.log- 2 H 20.584923 171.602616 136.566604 0.027822 0.010574 -0.001836 QMMM_opt1e.log- 3 C 24.147306 173.430766 136.621126 -0.013929 -0.015439 0.010896 QMMM_opt1e.log- 4 H 25.650386 173.412191 138.025336 -0.011516 0.002947 -0.003790 QMMM_opt1e.log- 5 C 24.895507 171.951692 134.230687 -0.001234 0.011755 -0.001692 QMMM_opt1e.log- 6 H 23.186043 171.457039 133.131923 -0.003353 -0.002419 0.002387 QMMM_opt1e.log- 7 H 25.780211 170.175149 134.822233 0.001242 0.004826 -0.000673 =20 I would have expected the last set of coordinates to be different from the third set, if the geometry was being passed correctly from run to run. I'm probably missing a step somewhere; is the restart geometry coming from the RTDB, the restart file, or one of the PDB files? =20 Thanks in advance, =20 Chris =20 -------- QMMM restart input deck: =20 start CpI_OOOOOO memory total 390 mw ECHO TITLE "QM/MM optimization of [H3+F'2+] H-cluster in CpI model" print medium =20 md system CpI_OOOOOO; noshake solute; msa 10000; end =20 qmmm eref 0.0; bqzone 9.0; mm_charges exclude linkbond; link_atoms hydrogen; link_ecp auto; region qmlink mm_solute all; method lbfgs lbfgs lbfgs; ncycles 10; print high; end =20 charge -3.0 =20 basis "ao basis" spherical Fe library 6-31g* S library 6-31+g* O library 6-31+g* N library 6-31+g* C library 6-31g* H library 6-31g** end =20 basis "cd basis" spherical * library "Ahlrichs Coulomb Fitting" end =20 charge -3.0 =20 dft ODFT; MULT 20; XC xpbe96 cpbe96; iterations 1000; direct; vectors input input.movecs output opt_temp.movecs; end =20 task qmmm dft optimize =09 ------_=_NextPart_001_01C8A006.B6D7330D Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable
Hi Bert,
 
   That tracks; then, shouldn't the = geometries=20 reported during the gradient calculations differ between cycles 3 and 4=20 (equivalently, between jobs 1c and 1e)?
 
- Chris

From: DeJong, Wibe A=20 [mailto:Wibe.DeJong@pnl.gov]
Sent: Wednesday, April 16, = 2008 1:25=20 PM
To: Chang, Christopher;=20 nwchem-users@emsl.pnl.gov
Subject: RE: [NWCHEM] QMMM = optimization=20 restart--how are coordinates passed?

Chris,
 
In your input deck below I see you define = "start" and not=20 "restart". By specifying start the RTDB is brand new (not restarted = from), and=20 your geometry will be obtained from the restart files generated by the = QM/MM=20 (.top /.rst).

Bert de Jong, = Ph.D.  Chief Scientist=20
Capability = Steward=20
High Performance = Software=20 Development
Environmental Molecular Science Laboratory =
Pacific Northwest National=20 Laboratory
P.O. Box=20 999, Mail Stop K8-91
Richland, WA 99352

Phone: (509) = 371-6476 Email:=20 bert.dejong@pnl.gov
Fax: (509) 371-6445     Room: EMSL=20 1371
Web: http://mscf.emsl.pnl.gov=20

 

From: = owner-nwchem-developers@emsl.pnl.gov=20 [mailto:owner-nwchem-developers@emsl.pnl.gov] On Behalf Of = Chang,=20 Christopher
Sent: Wednesday, April 16, 2008 11:23 = AM
To:=20 nwchem-users@emsl.pnl.gov
Subject: [NWCHEM] QMMM = optimization=20 restart--how are coordinates passed?

Hi,
 
   I was=20 comparing output from a continuation of a QMMM geometry optimization = with a=20 preceding calculation. Calculation "...1c.log" got through several DFT = optimization steps, while "...1d.log" failed to converge the SCF. = "...1e.log"=20 was a restart from the vectors from ...1d. In each case, I simply = restarted=20 the QMMM calculation from the scratch files present in the=20 directory.
 
grep = -A10 'DFT=20 ENERGY GRADIENTS' QMMM_opt1[ce].log
 
QMMM_opt1c.log:        &= nbsp;           &n= bsp;   =20 DFT ENERGY = GRADIENTS
QMMM_opt1c.log-
QMMM_opt1c.log-   =20 = atom           &nb= sp;  =20 = coordinates          &n= bsp;           &nb= sp;=20 = gradient
QMMM_opt1c.log-       &nbs= p;        =20 x         =20 y         =20 z          =20 x         =20 y         =20 z
QMMM_opt1c.log-   1 N      = 21.941608=20 172.227737 137.785591   -0.028706  = -0.006824  =20 0.056941
QMMM_opt1c.log-   2 = H     =20 20.637698 171.623024 136.564828    0.029059   = 0.012163  -0.011127
QMMM_opt1c.log-   3=20 C      24.133691 173.414485 = 136.632858  =20 -0.003433  -0.010364  = -0.001724
QMMM_opt1c.log-   4=20 H      25.632243 173.433382 = 138.029366  =20 -0.015064   0.003432  = -0.005131
QMMM_opt1c.log-  =20 5 C      24.897140 171.983962=20 134.221568    0.003058   0.029756 =20 -0.010798
QMMM_opt1c.log-   6 = H     =20 23.179379 171.452949 133.133086   -0.005151 =20 -0.004147   0.001271
QMMM_opt1c.log-   7=20 H      25.785311 170.173605=20 134.824390    0.004683  -0.003498  =20 = 0.002594
--
QMMM_opt1c.log:      &nbs= p;            = ;     =20 DFT ENERGY = GRADIENTS
QMMM_opt1c.log-
QMMM_opt1c.log-   =20 = atom           &nb= sp;  =20 = coordinates          &n= bsp;           &nb= sp;=20 = gradient
QMMM_opt1c.log-       &nbs= p;        =20 x         =20 y         =20 z          =20 x         =20 y         =20 z
QMMM_opt1c.log-   1 N      = 21.981641=20 172.252596 137.571753   -0.026111   0.008512  = -0.096356
QMMM_opt1c.log-   2 = H     =20 20.610111 171.612507 136.577712    0.056892   = 0.024329   0.019713
QMMM_opt1c.log-   3=20 C      24.138714 173.421682 = 136.632897  =20 -0.017938  -0.022434   = 0.020339
QMMM_opt1c.log-  =20 4 H      25.645188 173.420094 = 138.026422  =20 -0.011550   0.004714  = -0.005757
QMMM_opt1c.log-  =20 5 C      24.894390 171.959011 = 134.230293  =20 -0.002757   0.015700  = -0.001076
QMMM_opt1c.log-  =20 6 H      23.183993 171.455957 = 133.132630  =20 -0.004067  -0.002887   = 0.002269
QMMM_opt1c.log-  =20 7 H      25.781281 170.176592=20 134.822180    0.002162   0.003270 =20 = -0.000195
--
QMMM_opt1c.log:      &nb= sp;           &nbs= p;     =20 DFT ENERGY = GRADIENTS
QMMM_opt1c.log-
QMMM_opt1c.log-   =20 = atom           &nb= sp;  =20 = coordinates          &n= bsp;           &nb= sp;=20 = gradient
QMMM_opt1c.log-       &nbs= p;        =20 x         =20 y         =20 z          =20 x         =20 y         =20 z
QMMM_opt1c.log-   1 N      = 21.988372=20 172.246947 137.630522   -0.003368   0.015256  = -0.047565
QMMM_opt1c.log-   2 = H     =20 20.584923 171.602616 136.566604    0.027820   = 0.010573  -0.001840
QMMM_opt1c.log-   3=20 C      24.147306 173.430766 = 136.621126  =20 -0.013934  -0.015437   = 0.010889
QMMM_opt1c.log-  =20 4 H      25.650386 173.412191 = 138.025336  =20 -0.011507   0.002949  = -0.003788
QMMM_opt1c.log-  =20 5 C      24.895507 171.951692 = 134.230687  =20 -0.001237   0.011757  = -0.001698
QMMM_opt1c.log-  =20 6 H      23.186043 171.457039 = 133.131923  =20 -0.003359  -0.002420   = 0.002387
QMMM_opt1c.log-  =20 7 H      25.780211 170.175149=20 134.822233    0.001247   0.004818 =20 = -0.000668
--
QMMM_opt1e.log:      &nb= sp;           &nbs= p;     =20 DFT ENERGY = GRADIENTS
QMMM_opt1e.log-
QMMM_opt1e.log-   =20 = atom           &nb= sp;  =20 = coordinates          &n= bsp;           &nb= sp;=20 = gradient
QMMM_opt1e.log-       &nbs= p;        =20 x         =20 y         =20 z          =20 x         =20 y         =20 z
QMMM_opt1e.log-   1 N      = 21.988372=20 172.246946 137.630522   -0.003377   0.015255  = -0.047552
QMMM_opt1e.log-   2 = H     =20 20.584923 171.602616 136.566604    0.027822   = 0.010574  -0.001836
QMMM_opt1e.log-   3=20 C      24.147306 173.430766 = 136.621126  =20 -0.013929  -0.015439   = 0.010896
QMMM_opt1e.log-  =20 4 H      25.650386 173.412191 = 138.025336  =20 -0.011516   0.002947  = -0.003790
QMMM_opt1e.log-  =20 5 C      24.895507 171.951692 = 134.230687  =20 -0.001234   0.011755  = -0.001692
QMMM_opt1e.log-  =20 6 H      23.186043 171.457039 = 133.131923  =20 -0.003353  -0.002419   = 0.002387
QMMM_opt1e.log-  =20 7 H      25.780211 170.175149=20 134.822233    0.001242   0.004826 =20 -0.000673
 
I = would have=20 expected the last set of coordinates to be different from the third = set, if=20 the geometry was being passed correctly from run to run. I'm probably = missing=20 a step somewhere; is the restart geometry coming from the RTDB, the = restart=20 file, or one of the PDB files?
 
Thanks in=20 advance,
 
Chris
 
--------
QMMM = restart input=20 deck:
 
start=20 CpI_OOOOOO
memory total 390 mw
ECHO
TITLE "QM/MM optimization = of=20 [H3+F'2+] H-cluster in CpI model"
print medium
 
md
system=20 CpI_OOOOOO;
noshake solute;
msa = 10000;
end
 
qmmm
   eref 0.0;
   bqzone=20 9.0;
   mm_charges exclude linkbond;
   = link_atoms=20 hydrogen;
   link_ecp auto;
   region qmlink = mm_solute all;
   method lbfgs lbfgs = lbfgs;
  =20 ncycles 10;
   print high;
end
 
charge=20 -3.0
 
basis "ao basis"=20 spherical
  Fe library 6-31g*
   S library=20 6-31+g*
   O library 6-31+g*
   N library=20 6-31+g*
   C library 6-31g*
   H library=20 6-31g**
end
 
basis "cd basis"=20 spherical
   * library "Ahlrichs Coulomb=20 Fitting"
end
 
charge=20 -3.0
 
dft
ODFT; MULT=20 20; XC xpbe96 cpbe96;
   iterations 1000;
   = direct;
   vectors input input.movecs output=20 opt_temp.movecs;
end
 
task = qmmm dft=20 optimize
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