From owner-chemistry@ccl.net Sun Aug 23 11:27:01 2015 From: "Francesco Pietra chiendarret=-=gmail.com" To: CCL Subject: CCL:G: QM geometry optimization at MP2 level with Gaussian Message-Id: <-51611-150823040623-32716-MQ8vBICDUxb679QdFnncjw ~~ server.ccl.net> X-Original-From: "Francesco Pietra" Date: Sun, 23 Aug 2015 04:06:21 -0400 Sent to CCL by: "Francesco Pietra" [chiendarret^_^gmail.com] Hello: I am trying to get geometry optimization at MP2/6-31G* level for 52-atom molecule with latest Gaussian on a single node, 12 cores 120GB maxdisk=900GB. Restarting from previous chk successful geometry optimization at SCF/6-31G* level, with Stable=Opt keyword as the program misinterpreted the singlet as triplet. The process crashes with end-log message ===================== NBsUse= 509 1.00D-06 EigRej= -1.00D+00 NBFU= 509 Initial guess from the checkpoint file: "fmnh-opt_HF_20min.chk" B after Tr= 0.000000 0.000000 0.000000 Rot= 1.000000 0.000000 0.000000 0.000000 Ang= 0.00 deg. Initial guess = 0.0000 = 0.0000 = 0.0000 = 0.9707 S= 0.6048 Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. Restarting incremental Fock formation. SCF Done: E(UHF) = -1887.07583456 A.U. after 24 cycles NFock= 24 Conv=0.36D-08 -V/T= 1.9987 = 0.0000 = 0.0000 = 0.0000 = 0.4958 S= 0.3636 = 0.000000000000E+00 Annihilation of the first spin contaminant: S**2 before annihilation 0.4958, after 0.3885 ExpMin= 9.98D-02 ExpMax= 1.94D+04 ExpMxC= 2.91D+03 IAcc=3 IRadAn= 5 AccDes= 0.00D+00 HarFok: IExCor= 205 AccDes= 0.00D+00 IRadAn= 5 IDoV=-2 UseB2=F ITyADJ=14 ICtDFT= 12500011 ScaDFX= 1.000000 1.000000 1.000000 1.000000 Range of M.O.s used for correlation: 36 509 NBasis= 509 NAE= 120 NBE= 120 NFC= 35 NFV= 0 NROrb= 474 NOA= 85 NOB= 85 NVA= 389 NVB= 389 Semi-Direct transformation. ModeAB= 4 MOrb= 85 LenV= 16100299751 LASXX= 3982407420 LTotXX= 3982407420 LenRXX= 8116161420 LTotAB= 4133754000 MaxLAS= 3186173490 LenRXY= 0 NonZer= 12098568840 LenScr= 24197464064 LnRSAI= 3186173490 LnScr1= 6372720640 LExtra= 27090350 Total= 41899609964 MaxDsk=120795955200 SrtSym= T ITran= 4 JobTyp=1 Pass 1: I= 1 to 85. (rs|ai) integrals will be sorted in core. ModeAB= 4 MOrb= 85 LenV= 16100299751 LASXX= 3982407420 LTotXX= 3982407420 LenRXX= 6767803020 LTotAB= 2785395600 MaxLAS= 3186173490 LenRXY= 0 NonZer= 10750210440 LenScr= 21500526592 LnRSAI= 3186173490 LnScr1= 6372720640 LExtra= 8143506427 Total= 45970730169 MaxDsk=120795955200 SrtSym= T ITran= 4 JobTyp=2 Pass 1: I= 1 to 85. (rs|ai) integrals will be sorted in core. SymMOI: orbitals are not symmetric. Spin components of T(2) and E(2): alpha-alpha T2 = 0.1952657779D+00 E2= -0.6186401423D+00 alpha-beta T2 = 0.9897063485D+00 E2= -0.3241890891D+01 beta-beta T2 = 0.1941391244D+00 E2= -0.6171858226D+00 ANorm= 0.1542436790D+01 E2 = -0.4477716856D+01 EUMP2 = -0.18915535514164D+04 (S**2,0)= 0.49577D+00 (S**2,1)= 0.39665D+00 E(PUHF)= -0.18871168171D+04 E(PMP2)= -0.18915915926D+04 Would need an additional 807073191 words for in-memory AO integral storage. DD1Dir will call FoFJK 6 times, MxPair= 3600 NAB= 7225 NAA= 3570 NBB= 3570 NumPrc= 16. FoFJK: IHMeth= 1 ICntrl= 200 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F IRaf= 990000000 NMat=3600 IRICut= 1297 DoRegI=F DoRafI=T ISym2E= 2. E(PMP3)= -0.18916618537D+04 MP4(D)= -0.93363445D-01 MP4(S)= -0.58146163D-01 MP4(R+Q)= 0.84912525D-01 ========================== Then crashed before expected "discarding MO integrals" without error messages, without carrying out "Population analysis" MY QUESTION: 807073191=ca 6GB at 64bit? correct? does this means that 6GB memory lack from the shared available and the scratch disk can not be used to this purpose? maxdisk (currently 900GB)? thanks for advice francesco pietra From owner-chemistry@ccl.net Sun Aug 23 17:13:00 2015 From: "Alavi, Saman Saman.Alavi-#-nrc-cnrc.gc.ca" To: CCL Subject: CCL: NPT vs. NVT, considerations for crystal simulations and nucleation Message-Id: <-51612-150823170121-4931-jA64+WXLB4eY9uordtNmwg!A!server.ccl.net> X-Original-From: "Alavi, Saman" Content-Language: en-CA Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 23 Aug 2015 16:58:51 -0400 MIME-Version: 1.0 Sent to CCL by: "Alavi, Saman" [Saman.Alavi . nrc-cnrc.gc.ca] Hi Conor, You can read the following paper: M. Matsumoto et al. Nature, 416, 409-416 (2002) for a simulation work on ice formation. The conditions for the MD are given there and you can compare them with your simulation set-up. Saman ________________________________________ > From: owner-chemistry+saman.alavi==nrc.ca===ccl.net [owner-chemistry+saman.alavi==nrc.ca===ccl.net] On Behalf Of conor d parks coparks2012-$-gmail.com [owner-chemistry===ccl.net] Sent: August 21, 2015 5:11 PM To: Alavi, Saman Subject: CCL: NPT vs. NVT, considerations for crystal simulations and nucleation Sent to CCL by: "conor d parks" [coparks2012{}gmail.com] Hello everyone, I was wondering if someone could potentially help me work through a very conceptual problem. I recently was trying to run nucleation simulations of water at 1.00 g/cm^3 217 K in the NVT ensemble. However, I wasn't seeing the types of cluster size fluctuations (I.E. any) I was expecting, and started to wonder if it was due to my use of the NVT ensemble. Now firstly, this isn't due to finite size effects I believe, because the simulation was ran with 2000 water molecules. My issue with water above made me start to think about how I wanted to handle my glycine simulations as well. I am interested in running glycine in water nucleation simulations. For instance, I know glycine's solubility is .338 g/ml at 324 K. So I was going to make my initial box size based off the 0.338 g/ml, equilibrate a fluid at 354 K, and then crash to 270 K. Now I can't seem to figure out if I should run this simulation in NPT or NVT. The solubility data is gathered experimentally at 1 atm, obviously. So if I run NVT, my pressure average will almost assuredly not be 1 atm. However, if I run NPT and fix the pressure at 1 atm, I don't see why I should be guaranteed to fluctuate around the correct solubility. If I think to my undergrad thermo, in the NPT ensemble with a constant number of glycine and water molecules (hence mol fraction is determined), there should be only one equilibrium concentration. I don't see why this equilibrium concentration hopefully generated from an NPT equilibration would correspond to my solubility point. Sorry if that didn't make sense. Conorhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt