November 2015 - Allocations-admins - mailman3.cels.anl.gov

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Blaas 25 Nov '15

25 Nov '15

Granted 90k - JB On Wed, Nov 25, 2015 at 11:37 AM, accounts(a)lcrc.anl.gov <accounts(a)lcrc.anl.gov> wrote: > Hello, > > A change in allocation has been requested: > > Requester: verdicm (Marco Verdicchio) > Project: LowF_VRC-TST > Title: Low frequencies modes coupling in Variable Reaction Coordinate TST > Description: - Computational methods: > > We intend to use VRC-TST theory to study the effect of coupled low frequencies motions on EJ-resolved, microcanonical and canonical kinetic constants for several radical-radical association reactions. The central focus of VRC-TST is the evaluation of the reactive flux through an arbitrary dividing surface for several temperatures. In particular a multifaceted dividing surface approach, which allow for the incorporation of multiple dividing surfaces for each binding site, will be adopted. This scheme allows high flexibility on the dividing surface shape and the possibility to take into account additional reaction pathways (i.e. H atom abstraction). Unfortunately the computational cost of each kinetic calculation increases with the number of considered dividing surfaces. A variational minimization of the reactive flux is then performed with respect to both the location of the pivot points and the distances between them. > > > The previous allocation let us to investigate the low-frequencies effect on the rate constants for several systems: > > - CH3 + H > - CH3 + CH3 > - CH2CH3 + H > - CH2CH3 + CH3 > - H +C2H3 > > with excellent results. > > The Blues machine has been found to be of great help for this type of studies allowing us to use a large number of processors (128 cpu for an average of 24h per job) and speed up considerably our calculations. > > In this third stage of the project, we would like to move our attention to different systems like: > - CH3 + CH2OH > - H + CH2OH > These systems, in fact, have been already investigated within the previous allocation, but the complexity of their potential energy surface require additional work in order to work out an accurate rate constant (the low-freq effect has a strong dependence on the potential energy surface). > Moreover the extension of this method to oxygenated systems: > - O2 + CH3 > - O2 + CH2CH3 > requires the use of high level ab initio calculations (because of the presence of the O2 molecule) which are highly computationally demanding. > > - Technical details: > > Kinetic calculations will be performed using the VRC-TST method as implemented in the computer code VaReCoF (Y. Georgievskii, S.J. Klippenstein, VaReCoF, Sandia National Laboratories and Argonne National Laboratory, 2006). > The code makes use of the MOLPRO or GAUSSIAN quantum chemistry software for on-the-fly evaluation of the potential energy. > A Python interface to the code has been implemented for the management of the input files (reference energy evaluation, pivot points positions, etc.), for the generation of the input different structures ([Phi,Chi] grid of points) and for results post processing. > > The code does not require large amount of memory (less than 1GB) and works very efficiently on parallel architectures. The code makes use of MPI and shows a speed-up efficiency of about 60% for up to 96 CPUâ€™s (test performed on a 8 cpu/cores AMD Operton 2354 machine). Improvement is expected with better CPUs and fastest internode connections. > > > - Expected number of project members:1 > > Current: undetermined amount > Justification: > > Requested: 90000 > > A specific reason has been given: > Development of analytical potential energy surfaces for the investigated systems. > > The code for the calculation of the abinitio points has been already developed and tested, with great results, within previous allocation. > > This needs to be approved and the final allocation amount decided upon. > > Thank You, > The LCRC Accounts System

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 25 Nov '15

25 Nov '15

Hello, A change in allocation has been requested: Requester: verdicm (Marco Verdicchio) Project: LowF_VRC-TST Title: Low frequencies modes coupling in Variable Reaction Coordinate TST Description: - Computational methods: We intend to use VRC-TST theory to study the effect of coupled low frequencies motions on EJ-resolved, microcanonical and canonical kinetic constants for several radical-radical association reactions. The central focus of VRC-TST is the evaluation of the reactive flux through an arbitrary dividing surface for several temperatures. In particular a multifaceted dividing surface approach, which allow for the incorporation of multiple dividing surfaces for each binding site, will be adopted. This scheme allows high flexibility on the dividing surface shape and the possibility to take into account additional reaction pathways (i.e. H atom abstraction). Unfortunately the computational cost of each kinetic calculation increases with the number of considered dividing surfaces. A variational minimization of the reactive flux is then performed with respect to both the location of the pivot points and the distances between them. The previous allocation let us to investigate the low-frequencies effect on the rate constants for several systems: - CH3 + H - CH3 + CH3 - CH2CH3 + H - CH2CH3 + CH3 - H +C2H3 with excellent results. The Blues machine has been found to be of great help for this type of studies allowing us to use a large number of processors (128 cpu for an average of 24h per job) and speed up considerably our calculations. In this third stage of the project, we would like to move our attention to different systems like: - CH3 + CH2OH - H + CH2OH These systems, in fact, have been already investigated within the previous allocation, but the complexity of their potential energy surface require additional work in order to work out an accurate rate constant (the low-freq effect has a strong dependence on the potential energy surface). Moreover the extension of this method to oxygenated systems: - O2 + CH3 - O2 + CH2CH3 requires the use of high level ab initio calculations (because of the presence of the O2 molecule) which are highly computationally demanding. - Technical details: Kinetic calculations will be performed using the VRC-TST method as implemented in the computer code VaReCoF (Y. Georgievskii, S.J. Klippenstein, VaReCoF, Sandia National Laboratories and Argonne National Laboratory, 2006). The code makes use of the MOLPRO or GAUSSIAN quantum chemistry software for on-the-fly evaluation of the potential energy. A Python interface to the code has been implemented for the management of the input files (reference energy evaluation, pivot points positions, etc.), for the generation of the input different structures ([Phi,Chi] grid of points) and for results post processing. The code does not require large amount of memory (less than 1GB) and works very efficiently on parallel architectures. The code makes use of MPI and shows a speed-up efficiency of about 60% for up to 96 CPU’s (test performed on a 8 cpu/cores AMD Operton 2354 machine). Improvement is expected with better CPUs and fastest internode connections. - Expected number of project members:1 Current: undetermined amount Justification: Requested: 90000 A specific reason has been given: Development of analytical potential energy surfaces for the investigated systems. The code for the calculation of the abinitio points has been already developed and tested, with great results, within previous allocation. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Blaas 24 Nov '15

24 Nov '15

Granted 100k to project Redoxshuttles. - JB On Mon, Nov 23, 2015 at 2:31 PM, Bair, Raymond A. <rbair(a)anl.gov> wrote: > Yes, it is a 2-node job, and that seems fine for a Gaussian user. > > It is hard to know whether Paul's work could be run on more nodes > efficiently. It does not seem to be a high priority for a 100K request. > > Ray > > > > On 11/23/15, 1:21 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf > of Low, John J." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of > jlow(a)mcs.anl.gov> wrote: > >>Ray, >> >>It would be good to look at the input, output, logs and scripts, as >>opposed to just some PBS parameters and command and a few Gaussian >>keywords. >> >>This looks like a command for two node job. Not a single node job. >> >>I would recommend that he used 60GB of memory rather than 30GB. >> >>If gaussian really does not scale past one or two nodes for his cases, >>then he should consider some other program, we have MOLPRO, Orca, GAMMES >>and NWCHEM. By the way, what is the status of Qchem? >> >>John J. Low >>Principal Computational Science Specialist >>Computing, Environment and Life Sciences >>Building 240, 2143 >>9700 South Cass Avenue >>Argonne National Laboratory >>Argonne, IL 60439. >>630-252-0045 >>www.linkedin.com/pub/john-low/15/8b0/5aa/ >> >> >> >> >> >> >>-----Original Message----- >>From: <allocations-admins-bounces(a)lcrc.anl.gov> on behalf of "Bair, >>Raymond A." <rbair(a)anl.gov> >>Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >>Date: Monday, November 23, 2015 at 1:12 PM >>To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>Request >> >>>I queried Paul ... >>> >>> >>>Ray, >>>My pbs file was set up as follows on Blues: >>>#PBS -l nodes=2:ppn=16 >>> >>>My Gaussian jobs request memory and shared processors as follows on >>>Blues: >>>%mem=30GB >>>%Nprocshared=16 >>> >>>Thanks, >>>Paul >>> >>> >>>Overall it seems to be a reasonable request for 100K hours. >>> >>>Ray >>> >>> >>> >>>----------------------------------------- >>>Ray Bair >>>Computing, Environment, and Life Sciences >>>Argonne National Laboratory >>> and the University of Chicago >>>TCS Building 240, Room 4122 >>>9700 South Cass Avenue >>>Argonne, IL 60439 >>>email: rbair(at)anl.gov >>>Phone: (630)252-5751 >>> >>> >>> >>> >>> >>>On 11/20/15, 5:59 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf >>>of Low, John J." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of >>>jlow(a)mcs.anl.gov> wrote: >>> >>>>It does not sound correct that high level ab initio methods only scale >>>>to >>>>16 processors. Unless he means 16 16-core processors. >>>> >>>> >>>>John J. Low >>>>Principal Computational Science Specialist >>>>Computing, Environment and Life Sciences >>>>Building 240, 2143 >>>>9700 South Cass Avenue >>>>Argonne National Laboratory >>>>Argonne, IL 60439. >>>>630-252-0045 >>>>www.linkedin.com/pub/john-low/15/8b0/5aa/ >>>> >>>> >>>>________________________________________ >>>>From: allocations-admins-bounces(a)lcrc.anl.gov >>>>[allocations-admins-bounces(a)lcrc.anl.gov] on behalf of Aithal, >>>>Shashikant >>>>M. [aithal(a)cels.anl.gov] >>>>Sent: Friday, November 20, 2015 4:06 PM >>>>To: LCRC Allocations Admins >>>>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>>>Request >>>> >>>>I think he should also submit a list of anticipated runs to be made >>>>along >>>>with the approximate time for each of those runs to justify the 100K >>>>request. It is not clear from the request how he plans to use the 100K >>>>between now and Dec 31st (first quarter) and the second quarter. >>>>His proposal also says that "...the high-level ab initio methods scale >>>>only up to 16 processors. Therefore these calculations do require a >>>>longer execution time." which means he will be running a lot of >>>>single-node jobs for a long time - which won't be good for the queue. >>>>Since he will be using only 384 core-hours/day (16x24) he would have to >>>>submit some 150 such day-long node jobs to use up 50K (half the request) >>>>between now and Dec 31st (40 days or so). He can do that if he has >>>>about >>>>4 nodes reserved for himself till the end of Dec. >>>>________________________________________ >>>>From: allocations-admins-bounces(a)lcrc.anl.gov >>>>[allocations-admins-bounces(a)lcrc.anl.gov] on behalf of John Blaas >>>>[wilshire(a)mcs.anl.gov] >>>>Sent: Friday, November 20, 2015 3:44 PM >>>>To: LCRC Allocations Admins >>>>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>>>Request >>>> >>>>From Paul. >>>> >>>>John, >>>>A lot more Gaussian 09 calculations of oxidation and reduction >>>>potentials as well as transition states for decomposition and >>>>polymerization of redoxshuttles were required than we originally >>>>anticipated. >>>> >>>>Paul >>>> >>>> >>>>On Fri, Nov 20, 2015 at 1:51 PM, John Blaas <wilshire(a)mcs.anl.gov> >>>>wrote: >>>>> What you don't call this a justification? >>>>> >>>>>>A specific reason has been given: >>>>>>ran out of time >>>>> >>>>> I'll ping Paul. >>>>> >>>>> - JB >>>>> >>>>> On Fri, Nov 20, 2015 at 1:39 PM, Bair, Raymond A. <rbair(a)anl.gov> >>>>>wrote: >>>>>> I do not see any justification for the additional time. >>>>>> >>>>>> Ray >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 11/19/15, 11:14 AM, "allocations-admins-bounces(a)lcrc.anl.gov on >>>>>>behalf >>>>>> of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov on >>>>>> behalf of accounts(a)lcrc.anl.gov> wrote: >>>>>> >>>>>>>Hello, >>>>>>> >>>>>>>A change in allocation has been requested: >>>>>>> >>>>>>> Requester: redfern (Paul Redfern) >>>>>>> Project: Redoxshuttles >>>>>>> Title: Redox Shuttles and Additives for Lithium-Ion Batteries >>>>>>> Description: Over the past year we have calculated solvation free >>>>>>>energies of molecular LiO2 and Li2O2 in various solvents were >>>>>>>calculated >>>>>>>using various explicit and implicit solvent models, as well as ab >>>>>>>initio >>>>>>>molecular dynamics (AIMD) methods. Best estimates for the solvation >>>>>>>energies from these calculations along with calculated lattice >>>>>>>energies >>>>>>>of Li2O2 and LiO2 were used to determine the solubility of bulk LiO2 >>>>>>>and >>>>>>>Li2O2. The solubility of LiO2 was found to be about 17 orders higher >>>>>>>than >>>>>>>that of Li2O2. The effect of finite crystal size of LiO2 and Li2O2 on >>>>>>>the >>>>>>>solubility was also considered and was found to increase the >>>>>>>solubility, >>>>>>>although LiO2 is still much more soluble. The difference in >>>>>>>solubilities >>>>>>>between LiO2 and Li2O2 will likely affect the growth mechanism and >>>>>>>resulting morphologies of the products formed during battery >>>>>>>discharge, >>>>>>>affecting the performance of the battery cell. We also examined >>>>>>>production of a lithium superoxide discharge product on the cathod >>>>>>> e in a Li-O2 battery. DFT was used to obtain values of material >>>>>>>properties not available experimentally such as LiO2 solubility in >>>>>>>DME >>>>>>>and elastic properties of the particles. The mesoscale model predicts >>>>>>>that coarsening, in which large particles grow and small ones >>>>>>>disappear, >>>>>>>has a substantial effect on the size distribution of the LiO2 >>>>>>>particles >>>>>>>during the discharge process. The size evolution during discharge is >>>>>>>the >>>>>>>result of an interplay between this coarsening process as well as >>>>>>>growth. >>>>>>>The growth through continued deposition of LiO2 has the effect of >>>>>>>causing >>>>>>>large particles to grow faster and delays the dissolution of small >>>>>>>particles. The predicted size evolution is consistent with >>>>>>>experimental >>>>>>>results for a previously reported cathode material based on activated >>>>>>>carbon during discharge and when it is at rest. The model, even >>>>>>>without >>>>>>>complex microstructure, can capture size and number of LiO2 >>>>>>>particles, >>>>>>>but not the shape, e.g. toroid formation. Best estimates for the L >>>>>>> iO2 solvation energy from these calculations along with a calculated >>>>>>>lattice energy of LiO2 were used to determine the solubility of bulk >>>>>>>LiO2. The best estimate for the solubility of LiO2 is about 1 mM, >>>>>>>although this has very large uncertainties because small differences >>>>>>>in >>>>>>>the calculated solvation energy leads to large differences in the >>>>>>>solubility due to the exponential. For example, a difference of 2 >>>>>>>kcal/mol in solvation energy translates to more than 2 orders of >>>>>>>magnitude difference in solubility. The solvation energies are >>>>>>>difficult >>>>>>>to calculate even to 2 kcal/mol in accuracy. This value from density >>>>>>>functional calculations is used initially in the model and >>>>>>>subsequently a >>>>>>>value for solubility is derived from fits to reproduce experimental >>>>>>>data. >>>>>>> The solubility from these fits is similar to that predicted from the >>>>>>>DFT >>>>>>>calculations. >>>>>>> >>>>>>>We intend to evaluate at least 200 electrolytes for Lithium-O2 >>>>>>>batteries. >>>>>>>The most important challenge in Lithium-Air battery research is >>>>>>>finding >>>>>>>stable non-aqueous electrolytes which permit reversible cycling of >>>>>>>the >>>>>>>cell. A solvent should have a high dielectric constant in order to >>>>>>>dissolve Li+, low viscosity for fast Li+ transport, high stability, >>>>>>>low >>>>>>>vapor pressure, high oxygen solubility, high O2 and superoxide >>>>>>>transport >>>>>>>properties, and low toxicity. Solvents should partially dissolve >>>>>>>lithium >>>>>>>oxide species in order to reduce clogging and increase charge current >>>>>>>rate. Quantum chemical calculations can help identify reaction >>>>>>>pathways >>>>>>>which affect reversibility. So far organic solvents such as ethers, >>>>>>>amides, lactams, oxazolidinones, phosphorus compounds and nitriles >>>>>>>have >>>>>>>been screened for Lithium-Air batteries based on susceptibility to >>>>>>>attack >>>>>>>by superoxide anion and pKa. No correlation between simple molecular >>>>>>>descriptors and activation free energies was found. Low electro >>>>>>> philicity has also been used to identify potential candidates, since >>>>>>>they would be less susceptible to attack by superoxide or other >>>>>>>anion. >>>>>>>Other solvents such as sulfones, sulfoxides and ionic liquids have >>>>>>>been >>>>>>>examined. Lithium salts like LiTFSI can decompose at the lithium >>>>>>>electrode and the resulting CF3 radicals can abstract hydrogens from >>>>>>>solvents like ethers. Hydrogens on carbons adjacent to heteroatoms >>>>>>>(e.g. >>>>>>>O, N, F) are more labile due to the anomeric effect. Superoxide anion >>>>>>>can >>>>>>>abstract protons from proton source impurities (e.g. water) leading >>>>>>>to >>>>>>>formation of the strong base HOO- via disproportionation which can >>>>>>>then >>>>>>>react as a nucleophile with the solvent. Superoxide was found not to >>>>>>>react with TEGDME ether (Nazar). We will use hydrogen and proton >>>>>>>abstraction from and nucleophilic attack by a strong base on the >>>>>>>electrolyte along with advanced descriptors (e.g. Fukui functions, >>>>>>>hardness and chemical potential) to screen for stable solvents. >>>>>>> >>>>>>>Oxygen reduction in the aprotic Li-O2 battery takes place at the >>>>>>>boundary >>>>>>>between the electrolyte and the cathode so oxygen must dissolve and >>>>>>>diffuse in the electrolyte. Unfortunately, aprotic solvents are >>>>>>>inadequate in this regard so oxygen enriching materials must be >>>>>>>developed. Oxygen enriching materials that have been examined include >>>>>>>cobalt porphyrin, iron phthalocyanine, artificial hemoglobin, >>>>>>>membranes >>>>>>>and perfluorochemicals (PFCs). PFCs have high oxygen solubility, low >>>>>>>surface tension and viscosity to enhance O2 diffusivity and Li+ >>>>>>>transference number as well as wettability of the cathode surface, >>>>>>>high >>>>>>>chemical and thermal stability, hydrophobicity and low flammability. >>>>>>>In >>>>>>>the Li-O2 battery the PFC must be miscible with the polar organic >>>>>>>solvent >>>>>>>and resistant to nucleophilic attack by superoxide anion radical or >>>>>>>HOO-. >>>>>>>Miscibility of PFCs with polar organic solvents is increased if >>>>>>>LiPFOS >>>>>>>is >>>>>>>used instead of LiTFSI. Increasing O2 pressure increases O2 >>>>>>>diffusivity >>>>>>>as well >>>>>>> as solubility. We will examine many PFCs for susceptibility to >>>>>>>nucleophilic attack by superoxide anion radical and HOO- using DFT >>>>>>>calculations. Ab initio calculations will also be done to improve our >>>>>>>understanding of interactions between PFCs and O2. Other oxygen >>>>>>>enriching >>>>>>>materials include reversible oxygen carriers like perfluoro cryptands >>>>>>>and >>>>>>>crown ethers which are known to have high oxygen carrying capacities, >>>>>>>while acyclic perfluoro ethers do not bind O2. DFT calculations will >>>>>>>be >>>>>>>used to examine perfluoro cryptands and crown ethers. Hybrid ionic >>>>>>>liquid >>>>>>>fluoro-organic solvent mixtures are also promising as they combine >>>>>>>the >>>>>>>stability to anion attack of ionic liquids with the high oxygen >>>>>>>transport >>>>>>>and safety of nonflammable fluoro-organics. >>>>>>>We intend to use Gaussian 09 for quantum chemical calculations. In >>>>>>>Gaussian 09 the DFT calculations scale well up to 64 processors, >>>>>>>however >>>>>>>the high-level ab initio methods scale only up to 16 processors. >>>>>>>Therefore these calculations do require a longer execution time. >>>>>>> >>>>>>> Current: undetermined amount >>>>>>>Justification: >>>>>>> >>>>>>> Requested: 100000 >>>>>>> >>>>>>>A specific reason has been given: >>>>>>>ran out of time >>>>>>> >>>>>>>This needs to be approved and the final allocation amount decided >>>>>>>upon. >>>>>>> >>>>>>>Thank You, >>>>>>>The LCRC Accounts System >>>>>>>_______________________________________________ >>>>>>>allocations-admins mailing list >>>>>>>allocations-admins(a)lcrc.anl.gov >>>>>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>>>> >>>>>> _______________________________________________ >>>>>> allocations-admins mailing list >>>>>> allocations-admins(a)lcrc.anl.gov >>>>>> https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>>_______________________________________________ >>>>allocations-admins mailing list >>>>allocations-admins(a)lcrc.anl.gov >>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>>_______________________________________________ >>>>allocations-admins mailing list >>>>allocations-admins(a)lcrc.anl.gov >>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>>_______________________________________________ >>>>allocations-admins mailing list >>>>allocations-admins(a)lcrc.anl.gov >>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>> >>>_______________________________________________ >>>allocations-admins mailing list >>>allocations-admins(a)lcrc.anl.gov >>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >> >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 24 Nov '15

24 Nov '15

Perhaps there will be an opportunity to bring it up casually. Ray On 11/23/15, 2:37 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf of Low, John J." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of jlow(a)mcs.anl.gov> wrote: >Ray, > >I have noticed another gaussian user running hundreds of single node jobs >because they did not how to use Linda. Although Paul has been around for >a while and I expect that he knows how to run Gaussian in parallel, it >would be good to check. > > >John J. Low >Principal Computational Science Specialist >Computing, Environment and Life Sciences >Building 240, 2143 >9700 South Cass Avenue >Argonne National Laboratory >Argonne, IL 60439. >630-252-0045 >www.linkedin.com/pub/john-low/15/8b0/5aa/ > > > > > > >-----Original Message----- >From: <allocations-admins-bounces(a)lcrc.anl.gov> on behalf of "Bair, >Raymond A." <rbair(a)anl.gov> >Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >Date: Monday, November 23, 2015 at 2:31 PM >To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >Request > >>Yes, it is a 2-node job, and that seems fine for a Gaussian user. >> >>It is hard to know whether Paul's work could be run on more nodes >>efficiently. It does not seem to be a high priority for a 100K request. >> >>Ray >> >> >> >>On 11/23/15, 1:21 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf >>of Low, John J." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of >>jlow(a)mcs.anl.gov> wrote: >> >>>Ray, >>> >>>It would be good to look at the input, output, logs and scripts, as >>>opposed to just some PBS parameters and command and a few Gaussian >>>keywords. >>> >>>This looks like a command for two node job. Not a single node job. >>> >>>I would recommend that he used 60GB of memory rather than 30GB. >>> >>>If gaussian really does not scale past one or two nodes for his cases, >>>then he should consider some other program, we have MOLPRO, Orca, GAMMES >>>and NWCHEM. By the way, what is the status of Qchem? >>> >>>John J. Low >>>Principal Computational Science Specialist >>>Computing, Environment and Life Sciences >>>Building 240, 2143 >>>9700 South Cass Avenue >>>Argonne National Laboratory >>>Argonne, IL 60439. >>>630-252-0045 >>>www.linkedin.com/pub/john-low/15/8b0/5aa/ >>> >>> >>> >>> >>> >>> >>>-----Original Message----- >>>From: <allocations-admins-bounces(a)lcrc.anl.gov> on behalf of "Bair, >>>Raymond A." <rbair(a)anl.gov> >>>Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >>>Date: Monday, November 23, 2015 at 1:12 PM >>>To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >>>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>>Request >>> >>>>I queried Paul ... >>>> >>>> >>>>Ray, >>>>My pbs file was set up as follows on Blues: >>>>#PBS -l nodes=2:ppn=16 >>>> >>>>My Gaussian jobs request memory and shared processors as follows on >>>>Blues: >>>>%mem=30GB >>>>%Nprocshared=16 >>>> >>>>Thanks, >>>>Paul >>>> >>>> >>>>Overall it seems to be a reasonable request for 100K hours. >>>> >>>>Ray >>>> >>>> >>>> >>>>----------------------------------------- >>>>Ray Bair >>>>Computing, Environment, and Life Sciences >>>>Argonne National Laboratory >>>> and the University of Chicago >>>>TCS Building 240, Room 4122 >>>>9700 South Cass Avenue >>>>Argonne, IL 60439 >>>>email: rbair(at)anl.gov >>>>Phone: (630)252-5751 >>>> >>>> >>>> >>>> >>>> >>>>On 11/20/15, 5:59 PM, "allocations-admins-bounces(a)lcrc.anl.gov on >>>>behalf >>>>of Low, John J." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of >>>>jlow(a)mcs.anl.gov> wrote: >>>> >>>>>It does not sound correct that high level ab initio methods only scale >>>>>to >>>>>16 processors. Unless he means 16 16-core processors. >>>>> >>>>> >>>>>John J. Low >>>>>Principal Computational Science Specialist >>>>>Computing, Environment and Life Sciences >>>>>Building 240, 2143 >>>>>9700 South Cass Avenue >>>>>Argonne National Laboratory >>>>>Argonne, IL 60439. >>>>>630-252-0045 >>>>>www.linkedin.com/pub/john-low/15/8b0/5aa/ >>>>> >>>>> >>>>>________________________________________ >>>>>From: allocations-admins-bounces(a)lcrc.anl.gov >>>>>[allocations-admins-bounces(a)lcrc.anl.gov] on behalf of Aithal, >>>>>Shashikant >>>>>M. [aithal(a)cels.anl.gov] >>>>>Sent: Friday, November 20, 2015 4:06 PM >>>>>To: LCRC Allocations Admins >>>>>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>>>>Request >>>>> >>>>>I think he should also submit a list of anticipated runs to be made >>>>>along >>>>>with the approximate time for each of those runs to justify the 100K >>>>>request. It is not clear from the request how he plans to use the >>>>>100K >>>>>between now and Dec 31st (first quarter) and the second quarter. >>>>>His proposal also says that "...the high-level ab initio methods scale >>>>>only up to 16 processors. Therefore these calculations do require a >>>>>longer execution time." which means he will be running a lot of >>>>>single-node jobs for a long time - which won't be good for the queue. >>>>>Since he will be using only 384 core-hours/day (16x24) he would have >>>>>to >>>>>submit some 150 such day-long node jobs to use up 50K (half the >>>>>request) >>>>>between now and Dec 31st (40 days or so). He can do that if he has >>>>>about >>>>>4 nodes reserved for himself till the end of Dec. >>>>>________________________________________ >>>>>From: allocations-admins-bounces(a)lcrc.anl.gov >>>>>[allocations-admins-bounces(a)lcrc.anl.gov] on behalf of John Blaas >>>>>[wilshire(a)mcs.anl.gov] >>>>>Sent: Friday, November 20, 2015 3:44 PM >>>>>To: LCRC Allocations Admins >>>>>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>>>>Request >>>>> >>>>>From Paul. >>>>> >>>>>John, >>>>>A lot more Gaussian 09 calculations of oxidation and reduction >>>>>potentials as well as transition states for decomposition and >>>>>polymerization of redoxshuttles were required than we originally >>>>>anticipated. >>>>> >>>>>Paul >>>>> >>>>> >>>>>On Fri, Nov 20, 2015 at 1:51 PM, John Blaas <wilshire(a)mcs.anl.gov> >>>>>wrote: >>>>>> What you don't call this a justification? >>>>>> >>>>>>>A specific reason has been given: >>>>>>>ran out of time >>>>>> >>>>>> I'll ping Paul. >>>>>> >>>>>> - JB >>>>>> >>>>>> On Fri, Nov 20, 2015 at 1:39 PM, Bair, Raymond A. <rbair(a)anl.gov> >>>>>>wrote: >>>>>>> I do not see any justification for the additional time. >>>>>>> >>>>>>> Ray >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 11/19/15, 11:14 AM, "allocations-admins-bounces(a)lcrc.anl.gov on >>>>>>>behalf >>>>>>> of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov >>>>>>>on >>>>>>> behalf of accounts(a)lcrc.anl.gov> wrote: >>>>>>> >>>>>>>>Hello, >>>>>>>> >>>>>>>>A change in allocation has been requested: >>>>>>>> >>>>>>>> Requester: redfern (Paul Redfern) >>>>>>>> Project: Redoxshuttles >>>>>>>> Title: Redox Shuttles and Additives for Lithium-Ion >>>>>>>>Batteries >>>>>>>> Description: Over the past year we have calculated solvation free >>>>>>>>energies of molecular LiO2 and Li2O2 in various solvents were >>>>>>>>calculated >>>>>>>>using various explicit and implicit solvent models, as well as ab >>>>>>>>initio >>>>>>>>molecular dynamics (AIMD) methods. Best estimates for the solvation >>>>>>>>energies from these calculations along with calculated lattice >>>>>>>>energies >>>>>>>>of Li2O2 and LiO2 were used to determine the solubility of bulk >>>>>>>>LiO2 >>>>>>>>and >>>>>>>>Li2O2. The solubility of LiO2 was found to be about 17 orders >>>>>>>>higher >>>>>>>>than >>>>>>>>that of Li2O2. The effect of finite crystal size of LiO2 and Li2O2 >>>>>>>>on >>>>>>>>the >>>>>>>>solubility was also considered and was found to increase the >>>>>>>>solubility, >>>>>>>>although LiO2 is still much more soluble. The difference in >>>>>>>>solubilities >>>>>>>>between LiO2 and Li2O2 will likely affect the growth mechanism and >>>>>>>>resulting morphologies of the products formed during battery >>>>>>>>discharge, >>>>>>>>affecting the performance of the battery cell. We also examined >>>>>>>>production of a lithium superoxide discharge product on the cathod >>>>>>>> e in a Li-O2 battery. DFT was used to obtain values of material >>>>>>>>properties not available experimentally such as LiO2 solubility in >>>>>>>>DME >>>>>>>>and elastic properties of the particles. The mesoscale model >>>>>>>>predicts >>>>>>>>that coarsening, in which large particles grow and small ones >>>>>>>>disappear, >>>>>>>>has a substantial effect on the size distribution of the LiO2 >>>>>>>>particles >>>>>>>>during the discharge process. The size evolution during discharge >>>>>>>>is >>>>>>>>the >>>>>>>>result of an interplay between this coarsening process as well as >>>>>>>>growth. >>>>>>>>The growth through continued deposition of LiO2 has the effect of >>>>>>>>causing >>>>>>>>large particles to grow faster and delays the dissolution of small >>>>>>>>particles. The predicted size evolution is consistent with >>>>>>>>experimental >>>>>>>>results for a previously reported cathode material based on >>>>>>>>activated >>>>>>>>carbon during discharge and when it is at rest. The model, even >>>>>>>>without >>>>>>>>complex microstructure, can capture size and number of LiO2 >>>>>>>>particles, >>>>>>>>but not the shape, e.g. toroid formation. Best estimates for the L >>>>>>>> iO2 solvation energy from these calculations along with a >>>>>>>>calculated >>>>>>>>lattice energy of LiO2 were used to determine the solubility of >>>>>>>>bulk >>>>>>>>LiO2. The best estimate for the solubility of LiO2 is about 1 mM, >>>>>>>>although this has very large uncertainties because small >>>>>>>>differences >>>>>>>>in >>>>>>>>the calculated solvation energy leads to large differences in the >>>>>>>>solubility due to the exponential. For example, a difference of 2 >>>>>>>>kcal/mol in solvation energy translates to more than 2 orders of >>>>>>>>magnitude difference in solubility. The solvation energies are >>>>>>>>difficult >>>>>>>>to calculate even to 2 kcal/mol in accuracy. This value from >>>>>>>>density >>>>>>>>functional calculations is used initially in the model and >>>>>>>>subsequently a >>>>>>>>value for solubility is derived from fits to reproduce experimental >>>>>>>>data. >>>>>>>> The solubility from these fits is similar to that predicted from >>>>>>>>the >>>>>>>>DFT >>>>>>>>calculations. >>>>>>>> >>>>>>>>We intend to evaluate at least 200 electrolytes for Lithium-O2 >>>>>>>>batteries. >>>>>>>>The most important challenge in Lithium-Air battery research is >>>>>>>>finding >>>>>>>>stable non-aqueous electrolytes which permit reversible cycling of >>>>>>>>the >>>>>>>>cell. A solvent should have a high dielectric constant in order to >>>>>>>>dissolve Li+, low viscosity for fast Li+ transport, high stability, >>>>>>>>low >>>>>>>>vapor pressure, high oxygen solubility, high O2 and superoxide >>>>>>>>transport >>>>>>>>properties, and low toxicity. Solvents should partially dissolve >>>>>>>>lithium >>>>>>>>oxide species in order to reduce clogging and increase charge >>>>>>>>current >>>>>>>>rate. Quantum chemical calculations can help identify reaction >>>>>>>>pathways >>>>>>>>which affect reversibility. So far organic solvents such as ethers, >>>>>>>>amides, lactams, oxazolidinones, phosphorus compounds and nitriles >>>>>>>>have >>>>>>>>been screened for Lithium-Air batteries based on susceptibility to >>>>>>>>attack >>>>>>>>by superoxide anion and pKa. No correlation between simple >>>>>>>>molecular >>>>>>>>descriptors and activation free energies was found. Low electro >>>>>>>> philicity has also been used to identify potential candidates, >>>>>>>>since >>>>>>>>they would be less susceptible to attack by superoxide or other >>>>>>>>anion. >>>>>>>>Other solvents such as sulfones, sulfoxides and ionic liquids have >>>>>>>>been >>>>>>>>examined. Lithium salts like LiTFSI can decompose at the lithium >>>>>>>>electrode and the resulting CF3 radicals can abstract hydrogens >>>>>>>>from >>>>>>>>solvents like ethers. Hydrogens on carbons adjacent to heteroatoms >>>>>>>>(e.g. >>>>>>>>O, N, F) are more labile due to the anomeric effect. Superoxide >>>>>>>>anion >>>>>>>>can >>>>>>>>abstract protons from proton source impurities (e.g. water) leading >>>>>>>>to >>>>>>>>formation of the strong base HOO- via disproportionation which can >>>>>>>>then >>>>>>>>react as a nucleophile with the solvent. Superoxide was found not >>>>>>>>to >>>>>>>>react with TEGDME ether (Nazar). We will use hydrogen and proton >>>>>>>>abstraction from and nucleophilic attack by a strong base on the >>>>>>>>electrolyte along with advanced descriptors (e.g. Fukui functions, >>>>>>>>hardness and chemical potential) to screen for stable solvents. >>>>>>>> >>>>>>>>Oxygen reduction in the aprotic Li-O2 battery takes place at the >>>>>>>>boundary >>>>>>>>between the electrolyte and the cathode so oxygen must dissolve and >>>>>>>>diffuse in the electrolyte. Unfortunately, aprotic solvents are >>>>>>>>inadequate in this regard so oxygen enriching materials must be >>>>>>>>developed. Oxygen enriching materials that have been examined >>>>>>>>include >>>>>>>>cobalt porphyrin, iron phthalocyanine, artificial hemoglobin, >>>>>>>>membranes >>>>>>>>and perfluorochemicals (PFCs). PFCs have high oxygen solubility, >>>>>>>>low >>>>>>>>surface tension and viscosity to enhance O2 diffusivity and Li+ >>>>>>>>transference number as well as wettability of the cathode surface, >>>>>>>>high >>>>>>>>chemical and thermal stability, hydrophobicity and low >>>>>>>>flammability. >>>>>>>>In >>>>>>>>the Li-O2 battery the PFC must be miscible with the polar organic >>>>>>>>solvent >>>>>>>>and resistant to nucleophilic attack by superoxide anion radical or >>>>>>>>HOO-. >>>>>>>>Miscibility of PFCs with polar organic solvents is increased if >>>>>>>>LiPFOS >>>>>>>>is >>>>>>>>used instead of LiTFSI. Increasing O2 pressure increases O2 >>>>>>>>diffusivity >>>>>>>>as well >>>>>>>> as solubility. We will examine many PFCs for susceptibility to >>>>>>>>nucleophilic attack by superoxide anion radical and HOO- using DFT >>>>>>>>calculations. Ab initio calculations will also be done to improve >>>>>>>>our >>>>>>>>understanding of interactions between PFCs and O2. Other oxygen >>>>>>>>enriching >>>>>>>>materials include reversible oxygen carriers like perfluoro >>>>>>>>cryptands >>>>>>>>and >>>>>>>>crown ethers which are known to have high oxygen carrying >>>>>>>>capacities, >>>>>>>>while acyclic perfluoro ethers do not bind O2. DFT calculations >>>>>>>>will >>>>>>>>be >>>>>>>>used to examine perfluoro cryptands and crown ethers. Hybrid ionic >>>>>>>>liquid >>>>>>>>fluoro-organic solvent mixtures are also promising as they combine >>>>>>>>the >>>>>>>>stability to anion attack of ionic liquids with the high oxygen >>>>>>>>transport >>>>>>>>and safety of nonflammable fluoro-organics. >>>>>>>>We intend to use Gaussian 09 for quantum chemical calculations. In >>>>>>>>Gaussian 09 the DFT calculations scale well up to 64 processors, >>>>>>>>however >>>>>>>>the high-level ab initio methods scale only up to 16 processors. >>>>>>>>Therefore these calculations do require a longer execution time. >>>>>>>> >>>>>>>> Current: undetermined amount >>>>>>>>Justification: >>>>>>>> >>>>>>>> Requested: 100000 >>>>>>>> >>>>>>>>A specific reason has been given: >>>>>>>>ran out of time >>>>>>>> >>>>>>>>This needs to be approved and the final allocation amount decided >>>>>>>>upon. >>>>>>>> >>>>>>>>Thank You, >>>>>>>>The LCRC Accounts System >>>>>>>>_______________________________________________ >>>>>>>>allocations-admins mailing list >>>>>>>>allocations-admins(a)lcrc.anl.gov >>>>>>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>>>>> >>>>>>> _______________________________________________ >>>>>>> allocations-admins mailing list >>>>>>> allocations-admins(a)lcrc.anl.gov >>>>>>> https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>>>_______________________________________________ >>>>>allocations-admins mailing list >>>>>allocations-admins(a)lcrc.anl.gov >>>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>>>_______________________________________________ >>>>>allocations-admins mailing list >>>>>allocations-admins(a)lcrc.anl.gov >>>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>>>_______________________________________________ >>>>>allocations-admins mailing list >>>>>allocations-admins(a)lcrc.anl.gov >>>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>> >>>>_______________________________________________ >>>>allocations-admins mailing list >>>>allocations-admins(a)lcrc.anl.gov >>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>> >>>_______________________________________________ >>>allocations-admins mailing list >>>allocations-admins(a)lcrc.anl.gov >>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >> >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Low, John J. 23 Nov '15

23 Nov '15

Ray, I have noticed another gaussian user running hundreds of single node jobs because they did not how to use Linda. Although Paul has been around for a while and I expect that he knows how to run Gaussian in parallel, it would be good to check. John J. Low Principal Computational Science Specialist Computing, Environment and Life Sciences Building 240, 2143 9700 South Cass Avenue Argonne National Laboratory Argonne, IL 60439. 630-252-0045 www.linkedin.com/pub/john-low/15/8b0/5aa/ -----Original Message----- From: <allocations-admins-bounces(a)lcrc.anl.gov> on behalf of "Bair, Raymond A." <rbair(a)anl.gov> Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Date: Monday, November 23, 2015 at 2:31 PM To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request >Yes, it is a 2-node job, and that seems fine for a Gaussian user. > >It is hard to know whether Paul's work could be run on more nodes >efficiently. It does not seem to be a high priority for a 100K request. > >Ray > > > >On 11/23/15, 1:21 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf >of Low, John J." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of >jlow(a)mcs.anl.gov> wrote: > >>Ray, >> >>It would be good to look at the input, output, logs and scripts, as >>opposed to just some PBS parameters and command and a few Gaussian >>keywords. >> >>This looks like a command for two node job. Not a single node job. >> >>I would recommend that he used 60GB of memory rather than 30GB. >> >>If gaussian really does not scale past one or two nodes for his cases, >>then he should consider some other program, we have MOLPRO, Orca, GAMMES >>and NWCHEM. By the way, what is the status of Qchem? >> >>John J. Low >>Principal Computational Science Specialist >>Computing, Environment and Life Sciences >>Building 240, 2143 >>9700 South Cass Avenue >>Argonne National Laboratory >>Argonne, IL 60439. >>630-252-0045 >>www.linkedin.com/pub/john-low/15/8b0/5aa/ >> >> >> >> >> >> >>-----Original Message----- >>From: <allocations-admins-bounces(a)lcrc.anl.gov> on behalf of "Bair, >>Raymond A." <rbair(a)anl.gov> >>Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >>Date: Monday, November 23, 2015 at 1:12 PM >>To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>Request >> >>>I queried Paul ... >>> >>> >>>Ray, >>>My pbs file was set up as follows on Blues: >>>#PBS -l nodes=2:ppn=16 >>> >>>My Gaussian jobs request memory and shared processors as follows on >>>Blues: >>>%mem=30GB >>>%Nprocshared=16 >>> >>>Thanks, >>>Paul >>> >>> >>>Overall it seems to be a reasonable request for 100K hours. >>> >>>Ray >>> >>> >>> >>>----------------------------------------- >>>Ray Bair >>>Computing, Environment, and Life Sciences >>>Argonne National Laboratory >>> and the University of Chicago >>>TCS Building 240, Room 4122 >>>9700 South Cass Avenue >>>Argonne, IL 60439 >>>email: rbair(at)anl.gov >>>Phone: (630)252-5751 >>> >>> >>> >>> >>> >>>On 11/20/15, 5:59 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf >>>of Low, John J." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of >>>jlow(a)mcs.anl.gov> wrote: >>> >>>>It does not sound correct that high level ab initio methods only scale >>>>to >>>>16 processors. Unless he means 16 16-core processors. >>>> >>>> >>>>John J. Low >>>>Principal Computational Science Specialist >>>>Computing, Environment and Life Sciences >>>>Building 240, 2143 >>>>9700 South Cass Avenue >>>>Argonne National Laboratory >>>>Argonne, IL 60439. >>>>630-252-0045 >>>>www.linkedin.com/pub/john-low/15/8b0/5aa/ >>>> >>>> >>>>________________________________________ >>>>From: allocations-admins-bounces(a)lcrc.anl.gov >>>>[allocations-admins-bounces(a)lcrc.anl.gov] on behalf of Aithal, >>>>Shashikant >>>>M. [aithal(a)cels.anl.gov] >>>>Sent: Friday, November 20, 2015 4:06 PM >>>>To: LCRC Allocations Admins >>>>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>>>Request >>>> >>>>I think he should also submit a list of anticipated runs to be made >>>>along >>>>with the approximate time for each of those runs to justify the 100K >>>>request. It is not clear from the request how he plans to use the 100K >>>>between now and Dec 31st (first quarter) and the second quarter. >>>>His proposal also says that "...the high-level ab initio methods scale >>>>only up to 16 processors. Therefore these calculations do require a >>>>longer execution time." which means he will be running a lot of >>>>single-node jobs for a long time - which won't be good for the queue. >>>>Since he will be using only 384 core-hours/day (16x24) he would have to >>>>submit some 150 such day-long node jobs to use up 50K (half the >>>>request) >>>>between now and Dec 31st (40 days or so). He can do that if he has >>>>about >>>>4 nodes reserved for himself till the end of Dec. >>>>________________________________________ >>>>From: allocations-admins-bounces(a)lcrc.anl.gov >>>>[allocations-admins-bounces(a)lcrc.anl.gov] on behalf of John Blaas >>>>[wilshire(a)mcs.anl.gov] >>>>Sent: Friday, November 20, 2015 3:44 PM >>>>To: LCRC Allocations Admins >>>>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>>>Request >>>> >>>>From Paul. >>>> >>>>John, >>>>A lot more Gaussian 09 calculations of oxidation and reduction >>>>potentials as well as transition states for decomposition and >>>>polymerization of redoxshuttles were required than we originally >>>>anticipated. >>>> >>>>Paul >>>> >>>> >>>>On Fri, Nov 20, 2015 at 1:51 PM, John Blaas <wilshire(a)mcs.anl.gov> >>>>wrote: >>>>> What you don't call this a justification? >>>>> >>>>>>A specific reason has been given: >>>>>>ran out of time >>>>> >>>>> I'll ping Paul. >>>>> >>>>> - JB >>>>> >>>>> On Fri, Nov 20, 2015 at 1:39 PM, Bair, Raymond A. <rbair(a)anl.gov> >>>>>wrote: >>>>>> I do not see any justification for the additional time. >>>>>> >>>>>> Ray >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 11/19/15, 11:14 AM, "allocations-admins-bounces(a)lcrc.anl.gov on >>>>>>behalf >>>>>> of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov >>>>>>on >>>>>> behalf of accounts(a)lcrc.anl.gov> wrote: >>>>>> >>>>>>>Hello, >>>>>>> >>>>>>>A change in allocation has been requested: >>>>>>> >>>>>>> Requester: redfern (Paul Redfern) >>>>>>> Project: Redoxshuttles >>>>>>> Title: Redox Shuttles and Additives for Lithium-Ion >>>>>>>Batteries >>>>>>> Description: Over the past year we have calculated solvation free >>>>>>>energies of molecular LiO2 and Li2O2 in various solvents were >>>>>>>calculated >>>>>>>using various explicit and implicit solvent models, as well as ab >>>>>>>initio >>>>>>>molecular dynamics (AIMD) methods. Best estimates for the solvation >>>>>>>energies from these calculations along with calculated lattice >>>>>>>energies >>>>>>>of Li2O2 and LiO2 were used to determine the solubility of bulk LiO2 >>>>>>>and >>>>>>>Li2O2. The solubility of LiO2 was found to be about 17 orders higher >>>>>>>than >>>>>>>that of Li2O2. The effect of finite crystal size of LiO2 and Li2O2 >>>>>>>on >>>>>>>the >>>>>>>solubility was also considered and was found to increase the >>>>>>>solubility, >>>>>>>although LiO2 is still much more soluble. The difference in >>>>>>>solubilities >>>>>>>between LiO2 and Li2O2 will likely affect the growth mechanism and >>>>>>>resulting morphologies of the products formed during battery >>>>>>>discharge, >>>>>>>affecting the performance of the battery cell. We also examined >>>>>>>production of a lithium superoxide discharge product on the cathod >>>>>>> e in a Li-O2 battery. DFT was used to obtain values of material >>>>>>>properties not available experimentally such as LiO2 solubility in >>>>>>>DME >>>>>>>and elastic properties of the particles. The mesoscale model >>>>>>>predicts >>>>>>>that coarsening, in which large particles grow and small ones >>>>>>>disappear, >>>>>>>has a substantial effect on the size distribution of the LiO2 >>>>>>>particles >>>>>>>during the discharge process. The size evolution during discharge is >>>>>>>the >>>>>>>result of an interplay between this coarsening process as well as >>>>>>>growth. >>>>>>>The growth through continued deposition of LiO2 has the effect of >>>>>>>causing >>>>>>>large particles to grow faster and delays the dissolution of small >>>>>>>particles. The predicted size evolution is consistent with >>>>>>>experimental >>>>>>>results for a previously reported cathode material based on >>>>>>>activated >>>>>>>carbon during discharge and when it is at rest. The model, even >>>>>>>without >>>>>>>complex microstructure, can capture size and number of LiO2 >>>>>>>particles, >>>>>>>but not the shape, e.g. toroid formation. Best estimates for the L >>>>>>> iO2 solvation energy from these calculations along with a >>>>>>>calculated >>>>>>>lattice energy of LiO2 were used to determine the solubility of bulk >>>>>>>LiO2. The best estimate for the solubility of LiO2 is about 1 mM, >>>>>>>although this has very large uncertainties because small differences >>>>>>>in >>>>>>>the calculated solvation energy leads to large differences in the >>>>>>>solubility due to the exponential. For example, a difference of 2 >>>>>>>kcal/mol in solvation energy translates to more than 2 orders of >>>>>>>magnitude difference in solubility. The solvation energies are >>>>>>>difficult >>>>>>>to calculate even to 2 kcal/mol in accuracy. This value from density >>>>>>>functional calculations is used initially in the model and >>>>>>>subsequently a >>>>>>>value for solubility is derived from fits to reproduce experimental >>>>>>>data. >>>>>>> The solubility from these fits is similar to that predicted from >>>>>>>the >>>>>>>DFT >>>>>>>calculations. >>>>>>> >>>>>>>We intend to evaluate at least 200 electrolytes for Lithium-O2 >>>>>>>batteries. >>>>>>>The most important challenge in Lithium-Air battery research is >>>>>>>finding >>>>>>>stable non-aqueous electrolytes which permit reversible cycling of >>>>>>>the >>>>>>>cell. A solvent should have a high dielectric constant in order to >>>>>>>dissolve Li+, low viscosity for fast Li+ transport, high stability, >>>>>>>low >>>>>>>vapor pressure, high oxygen solubility, high O2 and superoxide >>>>>>>transport >>>>>>>properties, and low toxicity. Solvents should partially dissolve >>>>>>>lithium >>>>>>>oxide species in order to reduce clogging and increase charge >>>>>>>current >>>>>>>rate. Quantum chemical calculations can help identify reaction >>>>>>>pathways >>>>>>>which affect reversibility. So far organic solvents such as ethers, >>>>>>>amides, lactams, oxazolidinones, phosphorus compounds and nitriles >>>>>>>have >>>>>>>been screened for Lithium-Air batteries based on susceptibility to >>>>>>>attack >>>>>>>by superoxide anion and pKa. No correlation between simple molecular >>>>>>>descriptors and activation free energies was found. Low electro >>>>>>> philicity has also been used to identify potential candidates, >>>>>>>since >>>>>>>they would be less susceptible to attack by superoxide or other >>>>>>>anion. >>>>>>>Other solvents such as sulfones, sulfoxides and ionic liquids have >>>>>>>been >>>>>>>examined. Lithium salts like LiTFSI can decompose at the lithium >>>>>>>electrode and the resulting CF3 radicals can abstract hydrogens from >>>>>>>solvents like ethers. Hydrogens on carbons adjacent to heteroatoms >>>>>>>(e.g. >>>>>>>O, N, F) are more labile due to the anomeric effect. Superoxide >>>>>>>anion >>>>>>>can >>>>>>>abstract protons from proton source impurities (e.g. water) leading >>>>>>>to >>>>>>>formation of the strong base HOO- via disproportionation which can >>>>>>>then >>>>>>>react as a nucleophile with the solvent. Superoxide was found not to >>>>>>>react with TEGDME ether (Nazar). We will use hydrogen and proton >>>>>>>abstraction from and nucleophilic attack by a strong base on the >>>>>>>electrolyte along with advanced descriptors (e.g. Fukui functions, >>>>>>>hardness and chemical potential) to screen for stable solvents. >>>>>>> >>>>>>>Oxygen reduction in the aprotic Li-O2 battery takes place at the >>>>>>>boundary >>>>>>>between the electrolyte and the cathode so oxygen must dissolve and >>>>>>>diffuse in the electrolyte. Unfortunately, aprotic solvents are >>>>>>>inadequate in this regard so oxygen enriching materials must be >>>>>>>developed. Oxygen enriching materials that have been examined >>>>>>>include >>>>>>>cobalt porphyrin, iron phthalocyanine, artificial hemoglobin, >>>>>>>membranes >>>>>>>and perfluorochemicals (PFCs). PFCs have high oxygen solubility, low >>>>>>>surface tension and viscosity to enhance O2 diffusivity and Li+ >>>>>>>transference number as well as wettability of the cathode surface, >>>>>>>high >>>>>>>chemical and thermal stability, hydrophobicity and low flammability. >>>>>>>In >>>>>>>the Li-O2 battery the PFC must be miscible with the polar organic >>>>>>>solvent >>>>>>>and resistant to nucleophilic attack by superoxide anion radical or >>>>>>>HOO-. >>>>>>>Miscibility of PFCs with polar organic solvents is increased if >>>>>>>LiPFOS >>>>>>>is >>>>>>>used instead of LiTFSI. Increasing O2 pressure increases O2 >>>>>>>diffusivity >>>>>>>as well >>>>>>> as solubility. We will examine many PFCs for susceptibility to >>>>>>>nucleophilic attack by superoxide anion radical and HOO- using DFT >>>>>>>calculations. Ab initio calculations will also be done to improve >>>>>>>our >>>>>>>understanding of interactions between PFCs and O2. Other oxygen >>>>>>>enriching >>>>>>>materials include reversible oxygen carriers like perfluoro >>>>>>>cryptands >>>>>>>and >>>>>>>crown ethers which are known to have high oxygen carrying >>>>>>>capacities, >>>>>>>while acyclic perfluoro ethers do not bind O2. DFT calculations will >>>>>>>be >>>>>>>used to examine perfluoro cryptands and crown ethers. Hybrid ionic >>>>>>>liquid >>>>>>>fluoro-organic solvent mixtures are also promising as they combine >>>>>>>the >>>>>>>stability to anion attack of ionic liquids with the high oxygen >>>>>>>transport >>>>>>>and safety of nonflammable fluoro-organics. >>>>>>>We intend to use Gaussian 09 for quantum chemical calculations. In >>>>>>>Gaussian 09 the DFT calculations scale well up to 64 processors, >>>>>>>however >>>>>>>the high-level ab initio methods scale only up to 16 processors. >>>>>>>Therefore these calculations do require a longer execution time. >>>>>>> >>>>>>> Current: undetermined amount >>>>>>>Justification: >>>>>>> >>>>>>> Requested: 100000 >>>>>>> >>>>>>>A specific reason has been given: >>>>>>>ran out of time >>>>>>> >>>>>>>This needs to be approved and the final allocation amount decided >>>>>>>upon. >>>>>>> >>>>>>>Thank You, >>>>>>>The LCRC Accounts System >>>>>>>_______________________________________________ >>>>>>>allocations-admins mailing list >>>>>>>allocations-admins(a)lcrc.anl.gov >>>>>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>>>> >>>>>> _______________________________________________ >>>>>> allocations-admins mailing list >>>>>> allocations-admins(a)lcrc.anl.gov >>>>>> https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>>_______________________________________________ >>>>allocations-admins mailing list >>>>allocations-admins(a)lcrc.anl.gov >>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>>_______________________________________________ >>>>allocations-admins mailing list >>>>allocations-admins(a)lcrc.anl.gov >>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>>_______________________________________________ >>>>allocations-admins mailing list >>>>allocations-admins(a)lcrc.anl.gov >>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>> >>>_______________________________________________ >>>allocations-admins mailing list >>>allocations-admins(a)lcrc.anl.gov >>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >> >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

1 0

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 23 Nov '15

23 Nov '15

Yes, it is a 2-node job, and that seems fine for a Gaussian user. It is hard to know whether Paul's work could be run on more nodes efficiently. It does not seem to be a high priority for a 100K request. Ray On 11/23/15, 1:21 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf of Low, John J." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of jlow(a)mcs.anl.gov> wrote: >Ray, > >It would be good to look at the input, output, logs and scripts, as >opposed to just some PBS parameters and command and a few Gaussian >keywords. > >This looks like a command for two node job. Not a single node job. > >I would recommend that he used 60GB of memory rather than 30GB. > >If gaussian really does not scale past one or two nodes for his cases, >then he should consider some other program, we have MOLPRO, Orca, GAMMES >and NWCHEM. By the way, what is the status of Qchem? > >John J. Low >Principal Computational Science Specialist >Computing, Environment and Life Sciences >Building 240, 2143 >9700 South Cass Avenue >Argonne National Laboratory >Argonne, IL 60439. >630-252-0045 >www.linkedin.com/pub/john-low/15/8b0/5aa/ > > > > > > >-----Original Message----- >From: <allocations-admins-bounces(a)lcrc.anl.gov> on behalf of "Bair, >Raymond A." <rbair(a)anl.gov> >Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >Date: Monday, November 23, 2015 at 1:12 PM >To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >Request > >>I queried Paul ... >> >> >>Ray, >>My pbs file was set up as follows on Blues: >>#PBS -l nodes=2:ppn=16 >> >>My Gaussian jobs request memory and shared processors as follows on >>Blues: >>%mem=30GB >>%Nprocshared=16 >> >>Thanks, >>Paul >> >> >>Overall it seems to be a reasonable request for 100K hours. >> >>Ray >> >> >> >>----------------------------------------- >>Ray Bair >>Computing, Environment, and Life Sciences >>Argonne National Laboratory >> and the University of Chicago >>TCS Building 240, Room 4122 >>9700 South Cass Avenue >>Argonne, IL 60439 >>email: rbair(at)anl.gov >>Phone: (630)252-5751 >> >> >> >> >> >>On 11/20/15, 5:59 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf >>of Low, John J." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of >>jlow(a)mcs.anl.gov> wrote: >> >>>It does not sound correct that high level ab initio methods only scale >>>to >>>16 processors. Unless he means 16 16-core processors. >>> >>> >>>John J. Low >>>Principal Computational Science Specialist >>>Computing, Environment and Life Sciences >>>Building 240, 2143 >>>9700 South Cass Avenue >>>Argonne National Laboratory >>>Argonne, IL 60439. >>>630-252-0045 >>>www.linkedin.com/pub/john-low/15/8b0/5aa/ >>> >>> >>>________________________________________ >>>From: allocations-admins-bounces(a)lcrc.anl.gov >>>[allocations-admins-bounces(a)lcrc.anl.gov] on behalf of Aithal, >>>Shashikant >>>M. [aithal(a)cels.anl.gov] >>>Sent: Friday, November 20, 2015 4:06 PM >>>To: LCRC Allocations Admins >>>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>>Request >>> >>>I think he should also submit a list of anticipated runs to be made >>>along >>>with the approximate time for each of those runs to justify the 100K >>>request. It is not clear from the request how he plans to use the 100K >>>between now and Dec 31st (first quarter) and the second quarter. >>>His proposal also says that "...the high-level ab initio methods scale >>>only up to 16 processors. Therefore these calculations do require a >>>longer execution time." which means he will be running a lot of >>>single-node jobs for a long time - which won't be good for the queue. >>>Since he will be using only 384 core-hours/day (16x24) he would have to >>>submit some 150 such day-long node jobs to use up 50K (half the request) >>>between now and Dec 31st (40 days or so). He can do that if he has >>>about >>>4 nodes reserved for himself till the end of Dec. >>>________________________________________ >>>From: allocations-admins-bounces(a)lcrc.anl.gov >>>[allocations-admins-bounces(a)lcrc.anl.gov] on behalf of John Blaas >>>[wilshire(a)mcs.anl.gov] >>>Sent: Friday, November 20, 2015 3:44 PM >>>To: LCRC Allocations Admins >>>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>>Request >>> >>>From Paul. >>> >>>John, >>>A lot more Gaussian 09 calculations of oxidation and reduction >>>potentials as well as transition states for decomposition and >>>polymerization of redoxshuttles were required than we originally >>>anticipated. >>> >>>Paul >>> >>> >>>On Fri, Nov 20, 2015 at 1:51 PM, John Blaas <wilshire(a)mcs.anl.gov> >>>wrote: >>>> What you don't call this a justification? >>>> >>>>>A specific reason has been given: >>>>>ran out of time >>>> >>>> I'll ping Paul. >>>> >>>> - JB >>>> >>>> On Fri, Nov 20, 2015 at 1:39 PM, Bair, Raymond A. <rbair(a)anl.gov> >>>>wrote: >>>>> I do not see any justification for the additional time. >>>>> >>>>> Ray >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 11/19/15, 11:14 AM, "allocations-admins-bounces(a)lcrc.anl.gov on >>>>>behalf >>>>> of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov on >>>>> behalf of accounts(a)lcrc.anl.gov> wrote: >>>>> >>>>>>Hello, >>>>>> >>>>>>A change in allocation has been requested: >>>>>> >>>>>> Requester: redfern (Paul Redfern) >>>>>> Project: Redoxshuttles >>>>>> Title: Redox Shuttles and Additives for Lithium-Ion Batteries >>>>>> Description: Over the past year we have calculated solvation free >>>>>>energies of molecular LiO2 and Li2O2 in various solvents were >>>>>>calculated >>>>>>using various explicit and implicit solvent models, as well as ab >>>>>>initio >>>>>>molecular dynamics (AIMD) methods. Best estimates for the solvation >>>>>>energies from these calculations along with calculated lattice >>>>>>energies >>>>>>of Li2O2 and LiO2 were used to determine the solubility of bulk LiO2 >>>>>>and >>>>>>Li2O2. The solubility of LiO2 was found to be about 17 orders higher >>>>>>than >>>>>>that of Li2O2. The effect of finite crystal size of LiO2 and Li2O2 on >>>>>>the >>>>>>solubility was also considered and was found to increase the >>>>>>solubility, >>>>>>although LiO2 is still much more soluble. The difference in >>>>>>solubilities >>>>>>between LiO2 and Li2O2 will likely affect the growth mechanism and >>>>>>resulting morphologies of the products formed during battery >>>>>>discharge, >>>>>>affecting the performance of the battery cell. We also examined >>>>>>production of a lithium superoxide discharge product on the cathod >>>>>> e in a Li-O2 battery. DFT was used to obtain values of material >>>>>>properties not available experimentally such as LiO2 solubility in >>>>>>DME >>>>>>and elastic properties of the particles. The mesoscale model predicts >>>>>>that coarsening, in which large particles grow and small ones >>>>>>disappear, >>>>>>has a substantial effect on the size distribution of the LiO2 >>>>>>particles >>>>>>during the discharge process. The size evolution during discharge is >>>>>>the >>>>>>result of an interplay between this coarsening process as well as >>>>>>growth. >>>>>>The growth through continued deposition of LiO2 has the effect of >>>>>>causing >>>>>>large particles to grow faster and delays the dissolution of small >>>>>>particles. The predicted size evolution is consistent with >>>>>>experimental >>>>>>results for a previously reported cathode material based on activated >>>>>>carbon during discharge and when it is at rest. The model, even >>>>>>without >>>>>>complex microstructure, can capture size and number of LiO2 >>>>>>particles, >>>>>>but not the shape, e.g. toroid formation. Best estimates for the L >>>>>> iO2 solvation energy from these calculations along with a calculated >>>>>>lattice energy of LiO2 were used to determine the solubility of bulk >>>>>>LiO2. The best estimate for the solubility of LiO2 is about 1 mM, >>>>>>although this has very large uncertainties because small differences >>>>>>in >>>>>>the calculated solvation energy leads to large differences in the >>>>>>solubility due to the exponential. For example, a difference of 2 >>>>>>kcal/mol in solvation energy translates to more than 2 orders of >>>>>>magnitude difference in solubility. The solvation energies are >>>>>>difficult >>>>>>to calculate even to 2 kcal/mol in accuracy. This value from density >>>>>>functional calculations is used initially in the model and >>>>>>subsequently a >>>>>>value for solubility is derived from fits to reproduce experimental >>>>>>data. >>>>>> The solubility from these fits is similar to that predicted from the >>>>>>DFT >>>>>>calculations. >>>>>> >>>>>>We intend to evaluate at least 200 electrolytes for Lithium-O2 >>>>>>batteries. >>>>>>The most important challenge in Lithium-Air battery research is >>>>>>finding >>>>>>stable non-aqueous electrolytes which permit reversible cycling of >>>>>>the >>>>>>cell. A solvent should have a high dielectric constant in order to >>>>>>dissolve Li+, low viscosity for fast Li+ transport, high stability, >>>>>>low >>>>>>vapor pressure, high oxygen solubility, high O2 and superoxide >>>>>>transport >>>>>>properties, and low toxicity. Solvents should partially dissolve >>>>>>lithium >>>>>>oxide species in order to reduce clogging and increase charge current >>>>>>rate. Quantum chemical calculations can help identify reaction >>>>>>pathways >>>>>>which affect reversibility. So far organic solvents such as ethers, >>>>>>amides, lactams, oxazolidinones, phosphorus compounds and nitriles >>>>>>have >>>>>>been screened for Lithium-Air batteries based on susceptibility to >>>>>>attack >>>>>>by superoxide anion and pKa. No correlation between simple molecular >>>>>>descriptors and activation free energies was found. Low electro >>>>>> philicity has also been used to identify potential candidates, since >>>>>>they would be less susceptible to attack by superoxide or other >>>>>>anion. >>>>>>Other solvents such as sulfones, sulfoxides and ionic liquids have >>>>>>been >>>>>>examined. Lithium salts like LiTFSI can decompose at the lithium >>>>>>electrode and the resulting CF3 radicals can abstract hydrogens from >>>>>>solvents like ethers. Hydrogens on carbons adjacent to heteroatoms >>>>>>(e.g. >>>>>>O, N, F) are more labile due to the anomeric effect. Superoxide anion >>>>>>can >>>>>>abstract protons from proton source impurities (e.g. water) leading >>>>>>to >>>>>>formation of the strong base HOO- via disproportionation which can >>>>>>then >>>>>>react as a nucleophile with the solvent. Superoxide was found not to >>>>>>react with TEGDME ether (Nazar). We will use hydrogen and proton >>>>>>abstraction from and nucleophilic attack by a strong base on the >>>>>>electrolyte along with advanced descriptors (e.g. Fukui functions, >>>>>>hardness and chemical potential) to screen for stable solvents. >>>>>> >>>>>>Oxygen reduction in the aprotic Li-O2 battery takes place at the >>>>>>boundary >>>>>>between the electrolyte and the cathode so oxygen must dissolve and >>>>>>diffuse in the electrolyte. Unfortunately, aprotic solvents are >>>>>>inadequate in this regard so oxygen enriching materials must be >>>>>>developed. Oxygen enriching materials that have been examined include >>>>>>cobalt porphyrin, iron phthalocyanine, artificial hemoglobin, >>>>>>membranes >>>>>>and perfluorochemicals (PFCs). PFCs have high oxygen solubility, low >>>>>>surface tension and viscosity to enhance O2 diffusivity and Li+ >>>>>>transference number as well as wettability of the cathode surface, >>>>>>high >>>>>>chemical and thermal stability, hydrophobicity and low flammability. >>>>>>In >>>>>>the Li-O2 battery the PFC must be miscible with the polar organic >>>>>>solvent >>>>>>and resistant to nucleophilic attack by superoxide anion radical or >>>>>>HOO-. >>>>>>Miscibility of PFCs with polar organic solvents is increased if >>>>>>LiPFOS >>>>>>is >>>>>>used instead of LiTFSI. Increasing O2 pressure increases O2 >>>>>>diffusivity >>>>>>as well >>>>>> as solubility. We will examine many PFCs for susceptibility to >>>>>>nucleophilic attack by superoxide anion radical and HOO- using DFT >>>>>>calculations. Ab initio calculations will also be done to improve our >>>>>>understanding of interactions between PFCs and O2. Other oxygen >>>>>>enriching >>>>>>materials include reversible oxygen carriers like perfluoro cryptands >>>>>>and >>>>>>crown ethers which are known to have high oxygen carrying capacities, >>>>>>while acyclic perfluoro ethers do not bind O2. DFT calculations will >>>>>>be >>>>>>used to examine perfluoro cryptands and crown ethers. Hybrid ionic >>>>>>liquid >>>>>>fluoro-organic solvent mixtures are also promising as they combine >>>>>>the >>>>>>stability to anion attack of ionic liquids with the high oxygen >>>>>>transport >>>>>>and safety of nonflammable fluoro-organics. >>>>>>We intend to use Gaussian 09 for quantum chemical calculations. In >>>>>>Gaussian 09 the DFT calculations scale well up to 64 processors, >>>>>>however >>>>>>the high-level ab initio methods scale only up to 16 processors. >>>>>>Therefore these calculations do require a longer execution time. >>>>>> >>>>>> Current: undetermined amount >>>>>>Justification: >>>>>> >>>>>> Requested: 100000 >>>>>> >>>>>>A specific reason has been given: >>>>>>ran out of time >>>>>> >>>>>>This needs to be approved and the final allocation amount decided >>>>>>upon. >>>>>> >>>>>>Thank You, >>>>>>The LCRC Accounts System >>>>>>_______________________________________________ >>>>>>allocations-admins mailing list >>>>>>allocations-admins(a)lcrc.anl.gov >>>>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>>> >>>>> _______________________________________________ >>>>> allocations-admins mailing list >>>>> allocations-admins(a)lcrc.anl.gov >>>>> https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>_______________________________________________ >>>allocations-admins mailing list >>>allocations-admins(a)lcrc.anl.gov >>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>_______________________________________________ >>>allocations-admins mailing list >>>allocations-admins(a)lcrc.anl.gov >>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>_______________________________________________ >>>allocations-admins mailing list >>>allocations-admins(a)lcrc.anl.gov >>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >> >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

1 0

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Low, John J. 23 Nov '15

23 Nov '15

Ray, It would be good to look at the input, output, logs and scripts, as opposed to just some PBS parameters and command and a few Gaussian keywords. This looks like a command for two node job. Not a single node job. I would recommend that he used 60GB of memory rather than 30GB. If gaussian really does not scale past one or two nodes for his cases, then he should consider some other program, we have MOLPRO, Orca, GAMMES and NWCHEM. By the way, what is the status of Qchem? John J. Low Principal Computational Science Specialist Computing, Environment and Life Sciences Building 240, 2143 9700 South Cass Avenue Argonne National Laboratory Argonne, IL 60439. 630-252-0045 www.linkedin.com/pub/john-low/15/8b0/5aa/ -----Original Message----- From: <allocations-admins-bounces(a)lcrc.anl.gov> on behalf of "Bair, Raymond A." <rbair(a)anl.gov> Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Date: Monday, November 23, 2015 at 1:12 PM To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request >I queried Paul ... > > >Ray, >My pbs file was set up as follows on Blues: >#PBS -l nodes=2:ppn=16 > >My Gaussian jobs request memory and shared processors as follows on Blues: >%mem=30GB >%Nprocshared=16 > >Thanks, >Paul > > >Overall it seems to be a reasonable request for 100K hours. > >Ray > > > >----------------------------------------- >Ray Bair >Computing, Environment, and Life Sciences >Argonne National Laboratory > and the University of Chicago >TCS Building 240, Room 4122 >9700 South Cass Avenue >Argonne, IL 60439 >email: rbair(at)anl.gov >Phone: (630)252-5751 > > > > > >On 11/20/15, 5:59 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf >of Low, John J." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of >jlow(a)mcs.anl.gov> wrote: > >>It does not sound correct that high level ab initio methods only scale to >>16 processors. Unless he means 16 16-core processors. >> >> >>John J. Low >>Principal Computational Science Specialist >>Computing, Environment and Life Sciences >>Building 240, 2143 >>9700 South Cass Avenue >>Argonne National Laboratory >>Argonne, IL 60439. >>630-252-0045 >>www.linkedin.com/pub/john-low/15/8b0/5aa/ >> >> >>________________________________________ >>From: allocations-admins-bounces(a)lcrc.anl.gov >>[allocations-admins-bounces(a)lcrc.anl.gov] on behalf of Aithal, Shashikant >>M. [aithal(a)cels.anl.gov] >>Sent: Friday, November 20, 2015 4:06 PM >>To: LCRC Allocations Admins >>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>Request >> >>I think he should also submit a list of anticipated runs to be made along >>with the approximate time for each of those runs to justify the 100K >>request. It is not clear from the request how he plans to use the 100K >>between now and Dec 31st (first quarter) and the second quarter. >>His proposal also says that "...the high-level ab initio methods scale >>only up to 16 processors. Therefore these calculations do require a >>longer execution time." which means he will be running a lot of >>single-node jobs for a long time - which won't be good for the queue. >>Since he will be using only 384 core-hours/day (16x24) he would have to >>submit some 150 such day-long node jobs to use up 50K (half the request) >>between now and Dec 31st (40 days or so). He can do that if he has about >>4 nodes reserved for himself till the end of Dec. >>________________________________________ >>From: allocations-admins-bounces(a)lcrc.anl.gov >>[allocations-admins-bounces(a)lcrc.anl.gov] on behalf of John Blaas >>[wilshire(a)mcs.anl.gov] >>Sent: Friday, November 20, 2015 3:44 PM >>To: LCRC Allocations Admins >>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>Request >> >>From Paul. >> >>John, >>A lot more Gaussian 09 calculations of oxidation and reduction >>potentials as well as transition states for decomposition and >>polymerization of redoxshuttles were required than we originally >>anticipated. >> >>Paul >> >> >>On Fri, Nov 20, 2015 at 1:51 PM, John Blaas <wilshire(a)mcs.anl.gov> wrote: >>> What you don't call this a justification? >>> >>>>A specific reason has been given: >>>>ran out of time >>> >>> I'll ping Paul. >>> >>> - JB >>> >>> On Fri, Nov 20, 2015 at 1:39 PM, Bair, Raymond A. <rbair(a)anl.gov> >>>wrote: >>>> I do not see any justification for the additional time. >>>> >>>> Ray >>>> >>>> >>>> >>>> >>>> >>>> On 11/19/15, 11:14 AM, "allocations-admins-bounces(a)lcrc.anl.gov on >>>>behalf >>>> of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov on >>>> behalf of accounts(a)lcrc.anl.gov> wrote: >>>> >>>>>Hello, >>>>> >>>>>A change in allocation has been requested: >>>>> >>>>> Requester: redfern (Paul Redfern) >>>>> Project: Redoxshuttles >>>>> Title: Redox Shuttles and Additives for Lithium-Ion Batteries >>>>> Description: Over the past year we have calculated solvation free >>>>>energies of molecular LiO2 and Li2O2 in various solvents were >>>>>calculated >>>>>using various explicit and implicit solvent models, as well as ab >>>>>initio >>>>>molecular dynamics (AIMD) methods. Best estimates for the solvation >>>>>energies from these calculations along with calculated lattice >>>>>energies >>>>>of Li2O2 and LiO2 were used to determine the solubility of bulk LiO2 >>>>>and >>>>>Li2O2. The solubility of LiO2 was found to be about 17 orders higher >>>>>than >>>>>that of Li2O2. The effect of finite crystal size of LiO2 and Li2O2 on >>>>>the >>>>>solubility was also considered and was found to increase the >>>>>solubility, >>>>>although LiO2 is still much more soluble. The difference in >>>>>solubilities >>>>>between LiO2 and Li2O2 will likely affect the growth mechanism and >>>>>resulting morphologies of the products formed during battery >>>>>discharge, >>>>>affecting the performance of the battery cell. We also examined >>>>>production of a lithium superoxide discharge product on the cathod >>>>> e in a Li-O2 battery. DFT was used to obtain values of material >>>>>properties not available experimentally such as LiO2 solubility in DME >>>>>and elastic properties of the particles. The mesoscale model predicts >>>>>that coarsening, in which large particles grow and small ones >>>>>disappear, >>>>>has a substantial effect on the size distribution of the LiO2 >>>>>particles >>>>>during the discharge process. The size evolution during discharge is >>>>>the >>>>>result of an interplay between this coarsening process as well as >>>>>growth. >>>>>The growth through continued deposition of LiO2 has the effect of >>>>>causing >>>>>large particles to grow faster and delays the dissolution of small >>>>>particles. The predicted size evolution is consistent with >>>>>experimental >>>>>results for a previously reported cathode material based on activated >>>>>carbon during discharge and when it is at rest. The model, even >>>>>without >>>>>complex microstructure, can capture size and number of LiO2 particles, >>>>>but not the shape, e.g. toroid formation. Best estimates for the L >>>>> iO2 solvation energy from these calculations along with a calculated >>>>>lattice energy of LiO2 were used to determine the solubility of bulk >>>>>LiO2. The best estimate for the solubility of LiO2 is about 1 mM, >>>>>although this has very large uncertainties because small differences >>>>>in >>>>>the calculated solvation energy leads to large differences in the >>>>>solubility due to the exponential. For example, a difference of 2 >>>>>kcal/mol in solvation energy translates to more than 2 orders of >>>>>magnitude difference in solubility. The solvation energies are >>>>>difficult >>>>>to calculate even to 2 kcal/mol in accuracy. This value from density >>>>>functional calculations is used initially in the model and >>>>>subsequently a >>>>>value for solubility is derived from fits to reproduce experimental >>>>>data. >>>>> The solubility from these fits is similar to that predicted from the >>>>>DFT >>>>>calculations. >>>>> >>>>>We intend to evaluate at least 200 electrolytes for Lithium-O2 >>>>>batteries. >>>>>The most important challenge in Lithium-Air battery research is >>>>>finding >>>>>stable non-aqueous electrolytes which permit reversible cycling of the >>>>>cell. A solvent should have a high dielectric constant in order to >>>>>dissolve Li+, low viscosity for fast Li+ transport, high stability, >>>>>low >>>>>vapor pressure, high oxygen solubility, high O2 and superoxide >>>>>transport >>>>>properties, and low toxicity. Solvents should partially dissolve >>>>>lithium >>>>>oxide species in order to reduce clogging and increase charge current >>>>>rate. Quantum chemical calculations can help identify reaction >>>>>pathways >>>>>which affect reversibility. So far organic solvents such as ethers, >>>>>amides, lactams, oxazolidinones, phosphorus compounds and nitriles >>>>>have >>>>>been screened for Lithium-Air batteries based on susceptibility to >>>>>attack >>>>>by superoxide anion and pKa. No correlation between simple molecular >>>>>descriptors and activation free energies was found. Low electro >>>>> philicity has also been used to identify potential candidates, since >>>>>they would be less susceptible to attack by superoxide or other anion. >>>>>Other solvents such as sulfones, sulfoxides and ionic liquids have >>>>>been >>>>>examined. Lithium salts like LiTFSI can decompose at the lithium >>>>>electrode and the resulting CF3 radicals can abstract hydrogens from >>>>>solvents like ethers. Hydrogens on carbons adjacent to heteroatoms >>>>>(e.g. >>>>>O, N, F) are more labile due to the anomeric effect. Superoxide anion >>>>>can >>>>>abstract protons from proton source impurities (e.g. water) leading to >>>>>formation of the strong base HOO- via disproportionation which can >>>>>then >>>>>react as a nucleophile with the solvent. Superoxide was found not to >>>>>react with TEGDME ether (Nazar). We will use hydrogen and proton >>>>>abstraction from and nucleophilic attack by a strong base on the >>>>>electrolyte along with advanced descriptors (e.g. Fukui functions, >>>>>hardness and chemical potential) to screen for stable solvents. >>>>> >>>>>Oxygen reduction in the aprotic Li-O2 battery takes place at the >>>>>boundary >>>>>between the electrolyte and the cathode so oxygen must dissolve and >>>>>diffuse in the electrolyte. Unfortunately, aprotic solvents are >>>>>inadequate in this regard so oxygen enriching materials must be >>>>>developed. Oxygen enriching materials that have been examined include >>>>>cobalt porphyrin, iron phthalocyanine, artificial hemoglobin, >>>>>membranes >>>>>and perfluorochemicals (PFCs). PFCs have high oxygen solubility, low >>>>>surface tension and viscosity to enhance O2 diffusivity and Li+ >>>>>transference number as well as wettability of the cathode surface, >>>>>high >>>>>chemical and thermal stability, hydrophobicity and low flammability. >>>>>In >>>>>the Li-O2 battery the PFC must be miscible with the polar organic >>>>>solvent >>>>>and resistant to nucleophilic attack by superoxide anion radical or >>>>>HOO-. >>>>>Miscibility of PFCs with polar organic solvents is increased if LiPFOS >>>>>is >>>>>used instead of LiTFSI. Increasing O2 pressure increases O2 >>>>>diffusivity >>>>>as well >>>>> as solubility. We will examine many PFCs for susceptibility to >>>>>nucleophilic attack by superoxide anion radical and HOO- using DFT >>>>>calculations. Ab initio calculations will also be done to improve our >>>>>understanding of interactions between PFCs and O2. Other oxygen >>>>>enriching >>>>>materials include reversible oxygen carriers like perfluoro cryptands >>>>>and >>>>>crown ethers which are known to have high oxygen carrying capacities, >>>>>while acyclic perfluoro ethers do not bind O2. DFT calculations will >>>>>be >>>>>used to examine perfluoro cryptands and crown ethers. Hybrid ionic >>>>>liquid >>>>>fluoro-organic solvent mixtures are also promising as they combine the >>>>>stability to anion attack of ionic liquids with the high oxygen >>>>>transport >>>>>and safety of nonflammable fluoro-organics. >>>>>We intend to use Gaussian 09 for quantum chemical calculations. In >>>>>Gaussian 09 the DFT calculations scale well up to 64 processors, >>>>>however >>>>>the high-level ab initio methods scale only up to 16 processors. >>>>>Therefore these calculations do require a longer execution time. >>>>> >>>>> Current: undetermined amount >>>>>Justification: >>>>> >>>>> Requested: 100000 >>>>> >>>>>A specific reason has been given: >>>>>ran out of time >>>>> >>>>>This needs to be approved and the final allocation amount decided >>>>>upon. >>>>> >>>>>Thank You, >>>>>The LCRC Accounts System >>>>>_______________________________________________ >>>>>allocations-admins mailing list >>>>>allocations-admins(a)lcrc.anl.gov >>>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>>> >>>> _______________________________________________ >>>> allocations-admins mailing list >>>> allocations-admins(a)lcrc.anl.gov >>>> https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

1 0

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Blaas 23 Nov '15

23 Nov '15

I'll grant the 100k tomorrow unless anyone else has objections. - JB > I queried Paul ... > > > Ray, > My pbs file was set up as follows on Blues: > #PBS -l nodes=2:ppn=16 > > My Gaussian jobs request memory and shared processors as follows on Blues: > %mem=30GB > %Nprocshared=16 > > Thanks, > Paul > > > Overall it seems to be a reasonable request for 100K hours. > > Ray

1 0

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 23 Nov '15

23 Nov '15

I queried Paul ... Ray, My pbs file was set up as follows on Blues: #PBS -l nodes=2:ppn=16 My Gaussian jobs request memory and shared processors as follows on Blues: %mem=30GB %Nprocshared=16 Thanks, Paul Overall it seems to be a reasonable request for 100K hours. Ray ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago TCS Building 240, Room 4122 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751 On 11/20/15, 5:59 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf of Low, John J." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of jlow(a)mcs.anl.gov> wrote: >It does not sound correct that high level ab initio methods only scale to >16 processors. Unless he means 16 16-core processors. > > >John J. Low >Principal Computational Science Specialist >Computing, Environment and Life Sciences >Building 240, 2143 >9700 South Cass Avenue >Argonne National Laboratory >Argonne, IL 60439. >630-252-0045 >www.linkedin.com/pub/john-low/15/8b0/5aa/ > > >________________________________________ >From: allocations-admins-bounces(a)lcrc.anl.gov >[allocations-admins-bounces(a)lcrc.anl.gov] on behalf of Aithal, Shashikant >M. [aithal(a)cels.anl.gov] >Sent: Friday, November 20, 2015 4:06 PM >To: LCRC Allocations Admins >Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >Request > >I think he should also submit a list of anticipated runs to be made along >with the approximate time for each of those runs to justify the 100K >request. It is not clear from the request how he plans to use the 100K >between now and Dec 31st (first quarter) and the second quarter. >His proposal also says that "...the high-level ab initio methods scale >only up to 16 processors. Therefore these calculations do require a >longer execution time." which means he will be running a lot of >single-node jobs for a long time - which won't be good for the queue. >Since he will be using only 384 core-hours/day (16x24) he would have to >submit some 150 such day-long node jobs to use up 50K (half the request) >between now and Dec 31st (40 days or so). He can do that if he has about >4 nodes reserved for himself till the end of Dec. >________________________________________ >From: allocations-admins-bounces(a)lcrc.anl.gov >[allocations-admins-bounces(a)lcrc.anl.gov] on behalf of John Blaas >[wilshire(a)mcs.anl.gov] >Sent: Friday, November 20, 2015 3:44 PM >To: LCRC Allocations Admins >Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >Request > >From Paul. > >John, >A lot more Gaussian 09 calculations of oxidation and reduction >potentials as well as transition states for decomposition and >polymerization of redoxshuttles were required than we originally >anticipated. > >Paul > > >On Fri, Nov 20, 2015 at 1:51 PM, John Blaas <wilshire(a)mcs.anl.gov> wrote: >> What you don't call this a justification? >> >>>A specific reason has been given: >>>ran out of time >> >> I'll ping Paul. >> >> - JB >> >> On Fri, Nov 20, 2015 at 1:39 PM, Bair, Raymond A. <rbair(a)anl.gov> wrote: >>> I do not see any justification for the additional time. >>> >>> Ray >>> >>> >>> >>> >>> >>> On 11/19/15, 11:14 AM, "allocations-admins-bounces(a)lcrc.anl.gov on >>>behalf >>> of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov on >>> behalf of accounts(a)lcrc.anl.gov> wrote: >>> >>>>Hello, >>>> >>>>A change in allocation has been requested: >>>> >>>> Requester: redfern (Paul Redfern) >>>> Project: Redoxshuttles >>>> Title: Redox Shuttles and Additives for Lithium-Ion Batteries >>>> Description: Over the past year we have calculated solvation free >>>>energies of molecular LiO2 and Li2O2 in various solvents were >>>>calculated >>>>using various explicit and implicit solvent models, as well as ab >>>>initio >>>>molecular dynamics (AIMD) methods. Best estimates for the solvation >>>>energies from these calculations along with calculated lattice energies >>>>of Li2O2 and LiO2 were used to determine the solubility of bulk LiO2 >>>>and >>>>Li2O2. The solubility of LiO2 was found to be about 17 orders higher >>>>than >>>>that of Li2O2. The effect of finite crystal size of LiO2 and Li2O2 on >>>>the >>>>solubility was also considered and was found to increase the >>>>solubility, >>>>although LiO2 is still much more soluble. The difference in >>>>solubilities >>>>between LiO2 and Li2O2 will likely affect the growth mechanism and >>>>resulting morphologies of the products formed during battery discharge, >>>>affecting the performance of the battery cell. We also examined >>>>production of a lithium superoxide discharge product on the cathod >>>> e in a Li-O2 battery. DFT was used to obtain values of material >>>>properties not available experimentally such as LiO2 solubility in DME >>>>and elastic properties of the particles. The mesoscale model predicts >>>>that coarsening, in which large particles grow and small ones >>>>disappear, >>>>has a substantial effect on the size distribution of the LiO2 particles >>>>during the discharge process. The size evolution during discharge is >>>>the >>>>result of an interplay between this coarsening process as well as >>>>growth. >>>>The growth through continued deposition of LiO2 has the effect of >>>>causing >>>>large particles to grow faster and delays the dissolution of small >>>>particles. The predicted size evolution is consistent with experimental >>>>results for a previously reported cathode material based on activated >>>>carbon during discharge and when it is at rest. The model, even without >>>>complex microstructure, can capture size and number of LiO2 particles, >>>>but not the shape, e.g. toroid formation. Best estimates for the L >>>> iO2 solvation energy from these calculations along with a calculated >>>>lattice energy of LiO2 were used to determine the solubility of bulk >>>>LiO2. The best estimate for the solubility of LiO2 is about 1 mM, >>>>although this has very large uncertainties because small differences in >>>>the calculated solvation energy leads to large differences in the >>>>solubility due to the exponential. For example, a difference of 2 >>>>kcal/mol in solvation energy translates to more than 2 orders of >>>>magnitude difference in solubility. The solvation energies are >>>>difficult >>>>to calculate even to 2 kcal/mol in accuracy. This value from density >>>>functional calculations is used initially in the model and >>>>subsequently a >>>>value for solubility is derived from fits to reproduce experimental >>>>data. >>>> The solubility from these fits is similar to that predicted from the >>>>DFT >>>>calculations. >>>> >>>>We intend to evaluate at least 200 electrolytes for Lithium-O2 >>>>batteries. >>>>The most important challenge in Lithium-Air battery research is finding >>>>stable non-aqueous electrolytes which permit reversible cycling of the >>>>cell. A solvent should have a high dielectric constant in order to >>>>dissolve Li+, low viscosity for fast Li+ transport, high stability, low >>>>vapor pressure, high oxygen solubility, high O2 and superoxide >>>>transport >>>>properties, and low toxicity. Solvents should partially dissolve >>>>lithium >>>>oxide species in order to reduce clogging and increase charge current >>>>rate. Quantum chemical calculations can help identify reaction pathways >>>>which affect reversibility. So far organic solvents such as ethers, >>>>amides, lactams, oxazolidinones, phosphorus compounds and nitriles have >>>>been screened for Lithium-Air batteries based on susceptibility to >>>>attack >>>>by superoxide anion and pKa. No correlation between simple molecular >>>>descriptors and activation free energies was found. Low electro >>>> philicity has also been used to identify potential candidates, since >>>>they would be less susceptible to attack by superoxide or other anion. >>>>Other solvents such as sulfones, sulfoxides and ionic liquids have been >>>>examined. Lithium salts like LiTFSI can decompose at the lithium >>>>electrode and the resulting CF3 radicals can abstract hydrogens from >>>>solvents like ethers. Hydrogens on carbons adjacent to heteroatoms >>>>(e.g. >>>>O, N, F) are more labile due to the anomeric effect. Superoxide anion >>>>can >>>>abstract protons from proton source impurities (e.g. water) leading to >>>>formation of the strong base HOO- via disproportionation which can then >>>>react as a nucleophile with the solvent. Superoxide was found not to >>>>react with TEGDME ether (Nazar). We will use hydrogen and proton >>>>abstraction from and nucleophilic attack by a strong base on the >>>>electrolyte along with advanced descriptors (e.g. Fukui functions, >>>>hardness and chemical potential) to screen for stable solvents. >>>> >>>>Oxygen reduction in the aprotic Li-O2 battery takes place at the >>>>boundary >>>>between the electrolyte and the cathode so oxygen must dissolve and >>>>diffuse in the electrolyte. Unfortunately, aprotic solvents are >>>>inadequate in this regard so oxygen enriching materials must be >>>>developed. Oxygen enriching materials that have been examined include >>>>cobalt porphyrin, iron phthalocyanine, artificial hemoglobin, membranes >>>>and perfluorochemicals (PFCs). PFCs have high oxygen solubility, low >>>>surface tension and viscosity to enhance O2 diffusivity and Li+ >>>>transference number as well as wettability of the cathode surface, high >>>>chemical and thermal stability, hydrophobicity and low flammability. In >>>>the Li-O2 battery the PFC must be miscible with the polar organic >>>>solvent >>>>and resistant to nucleophilic attack by superoxide anion radical or >>>>HOO-. >>>>Miscibility of PFCs with polar organic solvents is increased if LiPFOS >>>>is >>>>used instead of LiTFSI. Increasing O2 pressure increases O2 diffusivity >>>>as well >>>> as solubility. We will examine many PFCs for susceptibility to >>>>nucleophilic attack by superoxide anion radical and HOO- using DFT >>>>calculations. Ab initio calculations will also be done to improve our >>>>understanding of interactions between PFCs and O2. Other oxygen >>>>enriching >>>>materials include reversible oxygen carriers like perfluoro cryptands >>>>and >>>>crown ethers which are known to have high oxygen carrying capacities, >>>>while acyclic perfluoro ethers do not bind O2. DFT calculations will be >>>>used to examine perfluoro cryptands and crown ethers. Hybrid ionic >>>>liquid >>>>fluoro-organic solvent mixtures are also promising as they combine the >>>>stability to anion attack of ionic liquids with the high oxygen >>>>transport >>>>and safety of nonflammable fluoro-organics. >>>>We intend to use Gaussian 09 for quantum chemical calculations. In >>>>Gaussian 09 the DFT calculations scale well up to 64 processors, >>>>however >>>>the high-level ab initio methods scale only up to 16 processors. >>>>Therefore these calculations do require a longer execution time. >>>> >>>> Current: undetermined amount >>>>Justification: >>>> >>>> Requested: 100000 >>>> >>>>A specific reason has been given: >>>>ran out of time >>>> >>>>This needs to be approved and the final allocation amount decided upon. >>>> >>>>Thank You, >>>>The LCRC Accounts System >>>>_______________________________________________ >>>>allocations-admins mailing list >>>>allocations-admins(a)lcrc.anl.gov >>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>> >>> _______________________________________________ >>> allocations-admins mailing list >>> allocations-admins(a)lcrc.anl.gov >>> https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Low, John J. 20 Nov '15

20 Nov '15

It does not sound correct that high level ab initio methods only scale to 16 processors. Unless he means 16 16-core processors. John J. Low Principal Computational Science Specialist Computing, Environment and Life Sciences Building 240, 2143 9700 South Cass Avenue Argonne National Laboratory Argonne, IL 60439. 630-252-0045 www.linkedin.com/pub/john-low/15/8b0/5aa/ ________________________________________ From: allocations-admins-bounces(a)lcrc.anl.gov [allocations-admins-bounces(a)lcrc.anl.gov] on behalf of Aithal, Shashikant M. [aithal(a)cels.anl.gov] Sent: Friday, November 20, 2015 4:06 PM To: LCRC Allocations Admins Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request I think he should also submit a list of anticipated runs to be made along with the approximate time for each of those runs to justify the 100K request. It is not clear from the request how he plans to use the 100K between now and Dec 31st (first quarter) and the second quarter. His proposal also says that "...the high-level ab initio methods scale only up to 16 processors. Therefore these calculations do require a longer execution time." which means he will be running a lot of single-node jobs for a long time - which won't be good for the queue. Since he will be using only 384 core-hours/day (16x24) he would have to submit some 150 such day-long node jobs to use up 50K (half the request) between now and Dec 31st (40 days or so). He can do that if he has about 4 nodes reserved for himself till the end of Dec. ________________________________________ From: allocations-admins-bounces(a)lcrc.anl.gov [allocations-admins-bounces(a)lcrc.anl.gov] on behalf of John Blaas [wilshire(a)mcs.anl.gov] Sent: Friday, November 20, 2015 3:44 PM To: LCRC Allocations Admins Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request >From Paul. John, A lot more Gaussian 09 calculations of oxidation and reduction potentials as well as transition states for decomposition and polymerization of redoxshuttles were required than we originally anticipated. Paul On Fri, Nov 20, 2015 at 1:51 PM, John Blaas <wilshire(a)mcs.anl.gov> wrote: > What you don't call this a justification? > >>A specific reason has been given: >>ran out of time > > I'll ping Paul. > > - JB > > On Fri, Nov 20, 2015 at 1:39 PM, Bair, Raymond A. <rbair(a)anl.gov> wrote: >> I do not see any justification for the additional time. >> >> Ray >> >> >> >> >> >> On 11/19/15, 11:14 AM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf >> of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov on >> behalf of accounts(a)lcrc.anl.gov> wrote: >> >>>Hello, >>> >>>A change in allocation has been requested: >>> >>> Requester: redfern (Paul Redfern) >>> Project: Redoxshuttles >>> Title: Redox Shuttles and Additives for Lithium-Ion Batteries >>> Description: Over the past year we have calculated solvation free >>>energies of molecular LiO2 and Li2O2 in various solvents were calculated >>>using various explicit and implicit solvent models, as well as ab initio >>>molecular dynamics (AIMD) methods. Best estimates for the solvation >>>energies from these calculations along with calculated lattice energies >>>of Li2O2 and LiO2 were used to determine the solubility of bulk LiO2 and >>>Li2O2. The solubility of LiO2 was found to be about 17 orders higher than >>>that of Li2O2. The effect of finite crystal size of LiO2 and Li2O2 on the >>>solubility was also considered and was found to increase the solubility, >>>although LiO2 is still much more soluble. The difference in solubilities >>>between LiO2 and Li2O2 will likely affect the growth mechanism and >>>resulting morphologies of the products formed during battery discharge, >>>affecting the performance of the battery cell. We also examined >>>production of a lithium superoxide discharge product on the cathod >>> e in a Li-O2 battery. DFT was used to obtain values of material >>>properties not available experimentally such as LiO2 solubility in DME >>>and elastic properties of the particles. The mesoscale model predicts >>>that coarsening, in which large particles grow and small ones disappear, >>>has a substantial effect on the size distribution of the LiO2 particles >>>during the discharge process. The size evolution during discharge is the >>>result of an interplay between this coarsening process as well as growth. >>>The growth through continued deposition of LiO2 has the effect of causing >>>large particles to grow faster and delays the dissolution of small >>>particles. The predicted size evolution is consistent with experimental >>>results for a previously reported cathode material based on activated >>>carbon during discharge and when it is at rest. The model, even without >>>complex microstructure, can capture size and number of LiO2 particles, >>>but not the shape, e.g. toroid formation. Best estimates for the L >>> iO2 solvation energy from these calculations along with a calculated >>>lattice energy of LiO2 were used to determine the solubility of bulk >>>LiO2. The best estimate for the solubility of LiO2 is about 1 mM, >>>although this has very large uncertainties because small differences in >>>the calculated solvation energy leads to large differences in the >>>solubility due to the exponential. For example, a difference of 2 >>>kcal/mol in solvation energy translates to more than 2 orders of >>>magnitude difference in solubility. The solvation energies are difficult >>>to calculate even to 2 kcal/mol in accuracy. This value from density >>>functional calculations is used initially in the model and subsequently a >>>value for solubility is derived from fits to reproduce experimental data. >>> The solubility from these fits is similar to that predicted from the DFT >>>calculations. >>> >>>We intend to evaluate at least 200 electrolytes for Lithium-O2 batteries. >>>The most important challenge in Lithium-Air battery research is finding >>>stable non-aqueous electrolytes which permit reversible cycling of the >>>cell. A solvent should have a high dielectric constant in order to >>>dissolve Li+, low viscosity for fast Li+ transport, high stability, low >>>vapor pressure, high oxygen solubility, high O2 and superoxide transport >>>properties, and low toxicity. Solvents should partially dissolve lithium >>>oxide species in order to reduce clogging and increase charge current >>>rate. Quantum chemical calculations can help identify reaction pathways >>>which affect reversibility. So far organic solvents such as ethers, >>>amides, lactams, oxazolidinones, phosphorus compounds and nitriles have >>>been screened for Lithium-Air batteries based on susceptibility to attack >>>by superoxide anion and pKa. No correlation between simple molecular >>>descriptors and activation free energies was found. Low electro >>> philicity has also been used to identify potential candidates, since >>>they would be less susceptible to attack by superoxide or other anion. >>>Other solvents such as sulfones, sulfoxides and ionic liquids have been >>>examined. Lithium salts like LiTFSI can decompose at the lithium >>>electrode and the resulting CF3 radicals can abstract hydrogens from >>>solvents like ethers. Hydrogens on carbons adjacent to heteroatoms (e.g. >>>O, N, F) are more labile due to the anomeric effect. Superoxide anion can >>>abstract protons from proton source impurities (e.g. water) leading to >>>formation of the strong base HOO- via disproportionation which can then >>>react as a nucleophile with the solvent. Superoxide was found not to >>>react with TEGDME ether (Nazar). We will use hydrogen and proton >>>abstraction from and nucleophilic attack by a strong base on the >>>electrolyte along with advanced descriptors (e.g. Fukui functions, >>>hardness and chemical potential) to screen for stable solvents. >>> >>>Oxygen reduction in the aprotic Li-O2 battery takes place at the boundary >>>between the electrolyte and the cathode so oxygen must dissolve and >>>diffuse in the electrolyte. Unfortunately, aprotic solvents are >>>inadequate in this regard so oxygen enriching materials must be >>>developed. Oxygen enriching materials that have been examined include >>>cobalt porphyrin, iron phthalocyanine, artificial hemoglobin, membranes >>>and perfluorochemicals (PFCs). PFCs have high oxygen solubility, low >>>surface tension and viscosity to enhance O2 diffusivity and Li+ >>>transference number as well as wettability of the cathode surface, high >>>chemical and thermal stability, hydrophobicity and low flammability. In >>>the Li-O2 battery the PFC must be miscible with the polar organic solvent >>>and resistant to nucleophilic attack by superoxide anion radical or HOO-. >>>Miscibility of PFCs with polar organic solvents is increased if LiPFOS is >>>used instead of LiTFSI. Increasing O2 pressure increases O2 diffusivity >>>as well >>> as solubility. We will examine many PFCs for susceptibility to >>>nucleophilic attack by superoxide anion radical and HOO- using DFT >>>calculations. Ab initio calculations will also be done to improve our >>>understanding of interactions between PFCs and O2. Other oxygen enriching >>>materials include reversible oxygen carriers like perfluoro cryptands and >>>crown ethers which are known to have high oxygen carrying capacities, >>>while acyclic perfluoro ethers do not bind O2. DFT calculations will be >>>used to examine perfluoro cryptands and crown ethers. Hybrid ionic liquid >>>fluoro-organic solvent mixtures are also promising as they combine the >>>stability to anion attack of ionic liquids with the high oxygen transport >>>and safety of nonflammable fluoro-organics. >>>We intend to use Gaussian 09 for quantum chemical calculations. In >>>Gaussian 09 the DFT calculations scale well up to 64 processors, however >>>the high-level ab initio methods scale only up to 16 processors. >>>Therefore these calculations do require a longer execution time. >>> >>> Current: undetermined amount >>>Justification: >>> >>> Requested: 100000 >>> >>>A specific reason has been given: >>>ran out of time >>> >>>This needs to be approved and the final allocation amount decided upon. >>> >>>Thank You, >>>The LCRC Accounts System >>>_______________________________________________ >>>allocations-admins mailing list >>>allocations-admins(a)lcrc.anl.gov >>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >> >> _______________________________________________ >> allocations-admins mailing list >> allocations-admins(a)lcrc.anl.gov >> https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins _______________________________________________ allocations-admins mailing list allocations-admins(a)lcrc.anl.gov https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins _______________________________________________ allocations-admins mailing list allocations-admins(a)lcrc.anl.gov https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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