July 2014 - Allocations-admins - mailman3.cels.anl.gov

[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 14 Jul '14

14 Jul '14

Hello, A change in allocation has been requested: Requester: chasman (Richard Chasman) Project: NuclearStructure Title: Optimization of many-body wavefunctions Description: We are studying medium mass nuclei using an interaction that includes n-p pairing together with deformation. At present, we are investigating several interactions that give rise to deformation in order to determine which ones provide a good description of nuclei having almost equal numbers of protons and neutrons. We are generalizing the treatment to rotationally invariant interactions. Current: undetermined amount Justification: Requested: 5000 A specific reason has been given: need more time This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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FW: [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 11 Jul '14

11 Jul '14

On 7/11/14, 10:00 AM, "Liu, Cong" <congliu(a)anl.gov> wrote: >Dear Ray, > >In that case, 80,000 hrs would be enough till Sept 30th. > >Thanks! >Cong >Cong Liu >Director's Postdoctoral Fellow >Materials Science Division >Argonne National Laboratory >Email: congliu(a)anl.gov >Phone: +1(630)252-7020 >________________________________________ >From: Bair, Raymond A. >Sent: Thursday, July 10, 2014 5:52 PM >To: Liu, Cong >Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >Request > >Dear Cong Liu, > >At this time of year people can request additional computer time to be >used between now and September 30th. How many core-hours would that be for >the Bio_catalysis project? In August you will be able to request time for >FY2015. > >Best regards, > >Ray Bair > > > >----------------------------------------- >Ray Bair >LCRC Direct >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 7/10/14, 5:42 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> >wrote: > >>Hello, >> >>A change in allocation has been requested: >> >> Requester: coliu (Cong Liu) >> Project: Bio_catalysis >> Title: Biomass Catalysis for Energy >> Description: Both methodological and chemical investigations will be >>carried out. Methodological studies will be focused on identifying >>suitable computational methods for calculating thermochemical properties, >>which include reaction energies and barriers. For chemical reaction >>investigations, initial studies on transformations from C5-C6 to C8-C21 >>will be to map out the reaction pathways. Based on the thermodynamics, >>dominant reaction pathways will be chosen to explore catalytic reactions. >>A series of metal nanoparticle catalysts will be screened to determine >>their catalytic properties. The factors that will be analyzed for the >>catalytic properties include particle sizes and surface structures. These >>potential catalysts will be initially chosen from available catalysts for >>C-C coupling reaction and hydrogenation. This work will be in >>collaboration with the experimental groups at the National Renewable >>Energy Laboratory (NREL) and Argonne National Lab (ANL). >> Current: undetermined amount >>Justification: >> >> Requested: 240000 >> >>A specific reason has been given: >>More allocation is needed to complete this project. VASP calculations of >>systems that have about 300 atoms are necessary for investigating >>catalytic C-C coupling reactions by zeolite catalysts. >> >>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 >

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 10 Jul '14

10 Jul '14

Hello, A change in allocation has been requested: Requester: coliu (Cong Liu) Project: Bio_catalysis Title: Biomass Catalysis for Energy Description: Both methodological and chemical investigations will be carried out. Methodological studies will be focused on identifying suitable computational methods for calculating thermochemical properties, which include reaction energies and barriers. For chemical reaction investigations, initial studies on transformations from C5-C6 to C8-C21 will be to map out the reaction pathways. Based on the thermodynamics, dominant reaction pathways will be chosen to explore catalytic reactions. A series of metal nanoparticle catalysts will be screened to determine their catalytic properties. The factors that will be analyzed for the catalytic properties include particle sizes and surface structures. These potential catalysts will be initially chosen from available catalysts for C-C coupling reaction and hydrogenation. This work will be in collaboration with the experimental groups at the National Renewable Energy Laboratory (NREL) and Argonne National Lab (ANL). Current: undetermined amount Justification: Requested: 240000 A specific reason has been given: More allocation is needed to complete this project. VASP calculations of systems that have about 300 atoms are necessary for investigating catalytic C-C coupling reactions by zeolite catalysts. 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 Request: entropy
by Low, John J. 10 Jul '14

10 Jul '14

Yet another big NAMD user. 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/ On 7/10/14, 9:46 AM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: >Hello, > >A new project on the LCRC cluster has been requested. Please forward >the information on to the LCRC Allocation sub-committee. > > Applicant's name: Sunhwan Jo >Applicant's institution: ANL > Applicant's division: LCF > Project Name: entropy > Project title: Quantifying protein-protein binding with >greatly scalable multiple copy algorithms of NAMD > Associated funding: None > Other Systems: 0 (previously had 10M core hours in BG/Q, but >is expired and submitted extension) > Science: Protein-protein interactions (PPIs) represent a >critical aspect of a wide range of biological processes, as most proteins >need to associate to various binding partners to carry out their >functions. While the basic principles of PPIs are generally understood, >it is a grand challenge to accurately predict the binding affinity >quantitatively for any given complex. Recently, this potential of mean >force (PMF)-based methodology was extended to a much larger >protein-peptide system, and we accurately determined the absolute binding >free energy between the receptor protein and the ligand peptide. We plan >to use our PMF-based methodology to probe effects of mutations in >thermodynamics of protein-protein interaction, i.e., thermodynamic >decomposition of barstar-barnase protein complex association. > Project description: In PMF-based framework, a set of geometric and >conformational restraints is applied to the proteins to reduce sampling >noise and accelerate the convergence of the resulting free energy >profile. These biases are rigorously accounted for to produce the >absolute binding free energy. To enhance the PMF convergence, we will >combine the umbrella sampling with Hamiltonian and temperature (ℋ and T) >replica-exchange molecular dynamics (REM) algorithm. In the US/(ℋ,T)-REMD >simulation approach, multiple copies of the molecular  systems are >simulated concurrently, but  all with different  conditions, e.g., >umbrella potential (Hamiltonians) or temperature. Attempts are >periodically made to exchange configurations between different systems >using a Metropolis-type Monte Carlo acceptance criterion, insuring >Boltzmann-weighted statistics. Such REMD  methodology is extremely >scalable, yet also very effective to sample a rugged free energy surface. > >We anticipate the simulation systems will be comprised of ~50,000 atoms >and using at least 255 replicas concurrently. Because of its large size, >we plan to use primarily Mira for production and Fusion will be used for >initial system preparation and development of enhanced methodology in >PMF-based framework. All planned simulations will be carried out by the >open-source NAMD molecular dynamics software. The software engine used >for the planned simulations is NAMD 2.10 with Charm++ 6.4.0. We have >tested t he performance on BG/Q Mira. The scaling of parallel performance >was linear up to 512 cores for our test system comprised of 100,000 atoms >without using restraint potential and achieved the speed of about 0.025 >s/step. Using restraint potential reduces the parallel performance >significantly (~0.2 s/step). > >The expected number of project member is 3. I, Sunhwan Jo, recently >joined LCF as a postdoctoral appointee and will be the main person >performing code improvement and algorithm development under the >supervision of Wei Jiang (LCF) and Benoit Roux (UChicago). > > > > Project URL: > Requested allocation: 400000 > Q1: 100000 > Q2: 100000 > Q3: 100000 > Q4: 100000 > Justification: > > >The requester has used undetermined amount hours of their initial startup >project. > >In addition to approving an initial amount, please specify a Category >and Subcategory for this project. For a list of the current selection >of approved categories, please see: > > https://wiki.lcrc.anl.gov/wiki/Processes/Categories > >Once the Allocation committee has approved the project, please go to >the Project Management page to create it: > >https://accounts.lcrc.anl.gov/projects.php > >Thank You, >The LCRC Accounts System

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[LCRC Accounts] Project Request: entropy
by accounts＠lcrc.anl.gov 10 Jul '14

10 Jul '14

Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: Sunhwan Jo Applicant's institution: ANL Applicant's division: LCF Project Name: entropy Project title: Quantifying protein-protein binding with greatly scalable multiple copy algorithms of NAMD Associated funding: None Other Systems: 0 (previously had 10M core hours in BG/Q, but is expired and submitted extension) Science: Protein-protein interactions (PPIs) represent a critical aspect of a wide range of biological processes, as most proteins need to associate to various binding partners to carry out their functions. While the basic principles of PPIs are generally understood, it is a grand challenge to accurately predict the binding affinity quantitatively for any given complex. Recently, this potential of mean force (PMF)-based methodology was extended to a much larger protein-peptide system, and we accurately determined the absolute binding free energy between the receptor protein and the ligand peptide. We plan to use our PMF-based methodology to probe effects of mutations in thermodynamics of protein-protein interaction, i.e., thermodynamic decomposition of barstar-barnase protein complex association. Project description: In PMF-based framework, a set of geometric and conformational restraints is applied to the proteins to reduce sampling noise and accelerate the convergence of the resulting free energy profile. These biases are rigorously accounted for to produce the absolute binding free energy. To enhance the PMF convergence, we will combine the umbrella sampling with Hamiltonian and temperature (ℋ and T) replica-exchange molecular dynamics (REM) algorithm. In the US/(ℋ,T)-REMD simulation approach, multiple copies of the molecular  systems are simulated concurrently, but  all with different  conditions, e.g., umbrella potential (Hamiltonians) or temperature. Attempts are periodically made to exchange configurations between different systems using a Metropolis-type Monte Carlo acceptance criterion, insuring Boltzmann-weighted statistics. Such REMD  methodology is extremely scalable, yet also very effective to sample a rugged free energy surface. We anticipate the simulation systems will be comprised of ~50,000 atoms and using at least 255 replicas concurrently. Because of its large size, we plan to use primarily Mira for production and Fusion will be used for initial system preparation and development of enhanced methodology in PMF-based framework. All planned simulations will be carried out by the open-source NAMD molecular dynamics software. The software engine used for the planned simulations is NAMD 2.10 with Charm++ 6.4.0. We have tested t he performance on BG/Q Mira. The scaling of parallel performance was linear up to 512 cores for our test system comprised of 100,000 atoms without using restraint potential and achieved the speed of about 0.025 s/step. Using restraint potential reduces the parallel performance significantly (~0.2 s/step). The expected number of project member is 3. I, Sunhwan Jo, recently joined LCF as a postdoctoral appointee and will be the main person performing code improvement and algorithm development under the supervision of Wei Jiang (LCF) and Benoit Roux (UChicago). Project URL: Requested allocation: 400000 Q1: 100000 Q2: 100000 Q3: 100000 Q4: 100000 Justification: The requester has used undetermined amount hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System

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FW: [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 09 Jul '14

09 Jul '14

Stand by . . . On 7/9/14, 5:45 PM, "Benoit Roux" <roux.uchicago(a)gmail.com> wrote: >Lei can tell exactly how many SUs he needs > >Sent from my iPhone > >> On Jul 9, 2014, at 4:44 PM, "Bair, Raymond A." <rbair(a)anl.gov> wrote: >> >> Dear Benoit, >> >> At this time of year people can request additional computer time to be >>used between now and September 30th. How many core-hours would that be >>for the Drude project? In August you will be able to request time for >>FY2015. >> >> Best regards, >> >> Ray Bair >> >> Sent from my iPhone >> >>> On Jul 9, 2014, at 3:06 PM, "accounts(a)lcrc.anl.gov" >>><accounts(a)lcrc.anl.gov> wrote: >>> >>> Hello, >>> >>> A change in allocation has been requested: >>> >>> Requester: roux (Benoit Roux) >>> Project: Drude >>> Title: Development and validation of new polarizable force field >>>for molecular dynamics >>> Description: We are mainly interested in ions binding to proteins at >>>this point. In biomolecular simulations, the challenge is to construct >>>functional forms that are amenable to computationally efficient >>>simulations while remaining able to accurately capture the microscopic >>>interactions between molecules. Our efforts, done in collaboration with >>>Alex MacKerell, have been to develop a polarizable force field for >>>proteins, membranes, and nucleic acids based on classical Drude >>>oscillators. The Drude polarizable force field has been implemented in >>>the program NAMD. It runs efficiently, at a computational cost >>>comparable to that of non-polarizable force fields (slower only by a >>>factor of about 1.4).By now, the parameterization for water, ions, >>>phospholipids, and proteins has been done and we are entering an >>>exciting phase where we will start to apply the new force field to real >>>systems and investigate a wide range of processes (ion selectivity, >>>ligand binding, pKa, membranes, etc >>> ). As an example, we have recently started to directly tackle the >>>conditions under which selectivity has been quantitatively measured for >>>KcsA, namely from the Ba2+ block experiments of Piasta and Miller.66 >>>Now we have an accurate polarizable force field, including divalent >>>ions,67 proteins and lipids,68 and we are in a position to carry out >>>these calculations on the KcsA channel with its activation gate open. >>>Comparison of the Drude model with density functional theory (DFT) >>>calculations at the B3PW91/lanl2dz level shows that one Ba2+ >>>coordinated by two N-methylacetamides have an energy of -133.0 kcal/mol >>>compared to -131.4 kcal/mol with the Drude model. Preliminary MD >>>simulations of KcsA blocked by >>> Ba2+ with the Drude force field for the protein, lipids, water, and >>>ions show that the system remains close to the X-ray configuration. >>> >>> We want to optimize ion parameters for the KcsA potassium channel and >>>then simulate the blockade by barium ions. For this we will have to run >>>classical MD simulations (with a force field), extract snapshots of the >>>ion with its surrounding atoms, and then use compute energies and >>>forces from ab initio methods as target data to optimize the force >>>field parameters. Most of the classical simulations will be executed >>>elsewhere, but the ab initio calculations will be carried out with >>>Gaussian on fusion. We also want to run QM/MM simulations of the same >>>set of atoms using CPMD to compare the atomic forces from force field >>>and QM. We expect that about 200 snapshots for each ion type should do >>>the job. We have to consider K+, Na+ and Ba2+. There are about 250 >>>atoms to consider in the QM region. >>> Current: undetermined amount >>> Justification: Gaussian and CPMD are established programs that runs >>>efficiently on fusion. These calculations are fairly standard. >>> >>> Requested: 875000 >>> >>> A specific reason has been given: >>> These SUs are urgently needed to complete the LDRD project on force >>>field optimization before the end of FY1. >>> >>> 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

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 09 Jul '14

09 Jul '14

Hello, A change in allocation has been requested: Requester: roux (Benoit Roux) Project: Drude Title: Development and validation of new polarizable force field for molecular dynamics Description: We are mainly interested in ions binding to proteins at this point. In biomolecular simulations, the challenge is to construct functional forms that are amenable to computationally efficient simulations while remaining able to accurately capture the microscopic interactions between molecules. Our efforts, done in collaboration with Alex MacKerell, have been to develop a polarizable force field for proteins, membranes, and nucleic acids based on classical Drude oscillators. The Drude polarizable force field has been implemented in the program NAMD. It runs efficiently, at a computational cost comparable to that of non-polarizable force fields (slower only by a factor of about 1.4).By now, the parameterization for water, ions, phospholipids, and proteins has been done and we are entering an exciting phase where we will start to apply the new force field to real systems and investigate a wide range of processes (ion selectivity, ligand binding, pKa, membranes, etc ). As an example, we have recently started to directly tackle the conditions under which selectivity has been quantitatively measured for KcsA, namely from the Ba2+ block experiments of Piasta and Miller.66 Now we have an accurate polarizable force field, including divalent ions,67 proteins and lipids,68 and we are in a position to carry out these calculations on the KcsA channel with its activation gate open. Comparison of the Drude model with density functional theory (DFT) calculations at the B3PW91/lanl2dz level shows that one Ba2+ coordinated by two N-methylacetamides have an energy of -133.0 kcal/mol compared to -131.4 kcal/mol with the Drude model. Preliminary MD simulations of KcsA blocked by Ba2+ with the Drude force field for the protein, lipids, water, and ions show that the system remains close to the X-ray configuration. We want to optimize ion parameters for the KcsA potassium channel and then simulate the blockade by barium ions. For this we will have to run classical MD simulations (with a force field), extract snapshots of the ion with its surrounding atoms, and then use compute energies and forces from ab initio methods as target data to optimize the force field parameters. Most of the classical simulations will be executed elsewhere, but the ab initio calculations will be carried out with Gaussian on fusion. We also want to run QM/MM simulations of the same set of atoms using CPMD to compare the atomic forces from force field and QM. We expect that about 200 snapshots for each ion type should do the job. We have to consider K+, Na+ and Ba2+. There are about 250 atoms to consider in the QM region. Current: undetermined amount Justification: Gaussian and CPMD are established programs that runs efficiently on fusion. These calculations are fairly standard. Requested: 875000 A specific reason has been given: These SUs are urgently needed to complete the LDRD project on force field optimization before the end of FY1. 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 Valdes 08 Jul '14

08 Jul '14

Granting 55K. John On Tue, Jul 08, 2014 at 03:34:10PM +0000, Bair, Raymond A. wrote: > Sounds fine to me. > > Ray > > > On 7/7/14, 4:43 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: > > >A change in allocation has been requested: > > > > Requester: jlow (John J. Low) > > Project: Raney_Nickel [...] > > Requested: 55000 > > > >A specific reason has been given: > >In order to complete the ongoing Molecular Dynamics study on Raney > >Nickel, we need an additional allocation. We are currently writing a > >manuscript and need to run some more expensive calculations for studying > >the dependence of the pore size on the unit cell size of our molecular > >models of Raney Nickel. For getting our final results, we will require to > >launch about 20 calculations using the LAMMPS code. Each job is estimated > >to take about 20 hours using up to 8 nodes on Fusion. This will require > >and additional 3,200 core-hours.

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 08 Jul '14

08 Jul '14

Sounds fine to me. Ray On 7/7/14, 4:43 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: >Hello, > >A change in allocation has been requested: > > Requester: jlow (John J. Low) > Project: Raney_Nickel > Title: A Molecular Model of Raney Ni > Description: During the first phase of the project, molecular dynamics >(MD) simulations have been performed on fusion using the LAMMPS software >package in order to analyze the influence of the initial composition of >the alloy on the structural properties of the precursor. Model structures >for four different compositions (40/50/60/70 wt% Ni) have been created >using Scienomics MAPS platform by randomly replacing Ni and Al in the >corresponding fractions in a NiAl3 supercell. In order to ensure a >statistically relevant sampling, five initial starting configurations >have been generated for each of these model structures. The structures >were equilibrated at 2000 K and then cooled down to room temperature over >1 ns as described by Noya, et al. [J. Non-Crystal. Solids 298, 6066 >(2002)]. > >The MD simulations performed so far provided insight to what extent the >initial configuration and compositions affects the structure of the >precursor. The analysis density and cell parameters of the final >structures indicates that the composition has a significant influence, >while the configuration has only a very minor impact. In general, the >density, cell parameters, total energy and volume over the simulation >time show a consistent behavior. > >The final structures as obtained from the quenching simulations will >serve as basis for additional MD simulations and equilibrated for 1 ns at >room temperature to ensure convergence. The trajectories will be analyzed >with respect to the formation of nanostructured clusters based on a next >neighbour search, for which MAPS scripting facilities will be used. The >trajectories will be analyzed with respect to the formation of >nanostructured clusters. In addition we plan to ues the open source >program RINGS (http://rings-code.sourceforge.net] will be used to >analyze local structural environments and voids. From each model, Al will >be removed and only 5-10 % Al will be left which corresponds to the >experimentally observed final catalyst composition. These porous models >will be minimized, which will only require a few hundred core-hours, and >afterwards analyzed with regard to pore size, pore distribution, and >accessibility from surface for the various compositions and initial config > urations to explore trends that can be linked to the catalytic >performance. > >In this way, we can gain a fundamental understanding about the formation >of nanostructures in the precursor alloy in dependence of the initial >composition. In the laboratory, the precursor is activated though >treatment with sodium hydroxide leaching out the majority of the Al and >leading to structural re-arrangements of the Ni bulk. This process will >not be simulated as it is beyond the scope of the present project. >Instead, we will focus on modeling the structure of the final catalyst. >To provide a reliable description of the nanoporous structure, large >system sizes will be required which will also allow to capture effects of >grain boundaries that a supposed to be important for the chemistry of the >final catalyst. > >The computational time needed for performing MD simulations and analyzing >the trajectories of all 20 models will be considerable. Each model >structure contains more than 65,000 atoms. According to the LAMMPS Cu >benchmarks[ http://lammps.sandia.gov/bench.html#eam] 100 steps for a >system size of 32,000 atoms would take 0.3 s (fixed CPU time) on 512 >cores. A 1 ns trajectory (1,000,000 steps) for 32,000 atoms would take >500 core-hours and a 65,000 atom system about 1250 core-hours. 25,000 >core-hours will be needed for the simulations of the 20 alloy model >structures. > >Characterization studies of Raney Nickel by Anderson¹s group and others >which yield a qualitative picture of Raney Nickel. [J. Cat. 16, 281291 >(1970)] The void volume of these particles ranges from 0.05 to 0.15 >cc/g. X-ray diffraction and X-ray Absorption Spectra show that local >structure of Raney Ni¹s is similar to FCC Ni. Fouilloux gives a >qualitative description of Raney Nickel as a spongy material composed of >100 nm agglomerates of smaller 2.5 to 15 nm nanocrystals. Our model of >Raney Nickel starts with 500 randomly packed 12.5 Å spherical >nanocrystallites of Nickel in a 100 nm sphere. The procedure of >Lubachevsky, et al. will be used to generate random packing of the >spheres.[J. Stat. Phys. 64 501524 (1991)] Since random close packing >has a density of approximately 0.63, this model will have a void volume >(0.06 cc/g) similar to Raney Ni. The initial positions of the atoms in >the Ni nanospheres will be created from a randomly oriented and shifted >FCC latt > ice. The final structure will be determined through simulated annealing >and the EAM potentials as implemented in LAMMPS. Our model should be >qualitatively similar to experimental structure of Raney Nickel. These >structures will be tested by comparing calculated properties from the >predicted structure to the experimentally determined pore size >distribution, heterogeneities from small angle X-ray scattering and line >broadening in X-ray diffraction. > >Several modeling studies of grain boundaries use molecular dynamics to >generate structures. Van Swygenhoven and Caro used a stochastic >procedure that starts with randomly placed seed particles with the rest >of the space filled with a Voroni construction.[Phys. Rev. B 58, >1124611251 (1998)] Keblinski randomly placed seed particles in a liquid >metal and then quenched the melt to generate a model crystal with grain >boundaries. [Scr. Mater. 41, 631636 (1999)] These procedures yield a >model of a solid composed of nanocrystalline grains. > >We will follow the spirit of these modeling approaches by randomly >placing seeds of Ni crystallites in a gas (or liquid) of Ni atoms and use >simulated annealing to generate a low energy structure. Raney Nickel, >which has a void volume of 0.1 cc/g, is essentially half void by volume. >A simple model would be to seed a gas with a density half that of Ni >metal. The gas will condense on the seed crystallites and create an >agglomerate with the appropriate void volume. Since the condensation is >exothermic, a Nose or Andersen thermostat will keep the temperature below >the melting temperature (1728K) of Ni during the simulation. Starting at >1500 K and scaling the temperature to 0K over 100 picoseconds will quench >to a low energy structure through simulated annealing. Since the low >energy structure will create particles which have the density of Ni >metal, the voids between the particles should have half the volume of the >initial volume. The number of crystallites should control > the size of the nanocrystals formed during simulated annealing. A >careful choice of initial conditions should lead to the desired size of >nanocrystals and void volumes. The RINGS program will allow a systematic >and analytical analysis of these structures. > >A 100 nm droplet of Ni with half the density of bulk Ni is a model of >Fouilloux¹s description of Raney Nickel.[J. Cat. 25, 212 (1972)] The >scale of this calculation would be significant. The model would be >initiated by randomly placing 500 seed crystallites (Ni55 clusters) in a >hundred nanometer sphere and then randomly inserting 25 million atoms >into the space between the seeds. The embedded atom method as >implemented in LAMMPS can handle simulated annealing of models of this >size. The Cu EAM benchmark on the LAMMPS website shows that 100 steps of >molecular dynamics for 16 million atoms could be done on 512 cores of a >Xeon/Myrinet cluster in 21 seconds. >[http://lammps.sandia.gov/bench.html#eam] A 100 picosecond trajectory >(100,000 steps) would take 60 hours (30,000 core-hours). Fusion or Blues >have faster processors and an InfiniBand interconnect that will yield >better performance. The estimated CPU requirements derived from timings >for the Xeon/Myrinet cluster is an > upper bound. We anticipate repeating this calculation a few times with >three different compositions requiring 100,000 core-hours. > >Our initial calculations will use a periodic model containing a million >atoms and 20 seeds to verify this approach will give morphology similar >to Raney Nickel. The test will involve comparing calculated properties >from the predicted structure to the experimentally determined pore size >distribution, heterogeneities from small angle X-ray scattering and line >broadening in X-ray diffraction. [J. Cat. 23, 286 (1971), Cat. Today 163, >1319 (2011)] If this model does not yield a satisfactory result we will >implement and test a stochastic Voroni procedure. [Phys. Rev. B 58, >1124611251 (1998)] These calculations will require a few thousand core >hours and will not exhaust our allocation before developing a working >model. Once we have established a procedure that generates a model of a >porous solid composed of nanocrystalline grains, we will carry out >calculations on a more realistic 50 million atom droplet model of Raney >Ni. 50,000 core hours will be needed for these experimen > ts with smaller periodic models. > >We will use EAM to model hydrogen adsorption on our model of Raney >Nickel. The model will have monolayer coverage (one hydrogen atom per >surface Ni atom). The surface will be defined by Ni atoms with >coordination less than twelve. Simulated annealing will be use to find a >low energy distribution of hydrogen on the surface of Raney Ni. The >predicted binding energies, vibrational frequencies and geometries will >be used to classify the chemisorption sites to a smaller number of >representative sites. 50,000 core-hours will be required for the >chemisorption models. > >The pore size, pore distribution, and the accessibility of the droplet >model and chemisorbed model will be compared with the results obtained >for the precursor models. This strategy will allow to explore to what >extent the nanostructural agglomerations in the precursor are reflected >in the porous active form. > >The generalized chemisorption sites will form the basis of smaller >periodic models. We will use the smaller models to model hydrogenation of >benzene on Raney Nickel with an electronic structure program like abinit, >bigdft, cp2k or qbox. These calculations will be done in a future >project. > >Overall, 200,000 core-hours will be needed over a period of five months >for performing the in silico experiments for the project. > > >About Scienomics > >Scienomics was established in 2004 and with selected partnerships with >the best-of-the-breed (e.g.: Sandia National Labs, Max Planck Institute, >Fraunhofer Institute, University of Illinois, Demokritos, University of >Shanghai), Scienomics¹s MAPS platform offers a unique and powerful blend >of multiscale and multiparadigm modeling and simulation modules. > >With high quality science and industrial solution oriented applied >research, Scienomics has garnered collaborative projects with companies >in the areas of energy and green chemistry, alternate fuels, catalysis, >polymers, biodefense, auto exhaust, etc. > >Biography of Relevant Members > >John J. Low, Principal Computational Science Specialist at Argonne >National Laboratory has a Ph.D. in Chemistry from the California >Institute of Technology. After graduation John worked at UOP LLC, a >Honeywell Company. His work at UOP focused on modeling and >characterization of catalysts and adsorbents used in the petrochemical >industry, hydrogen storage and carbon sequestration. John supports the >computational chemistry applications at high performance computers and >performing research on Li-Ion batteries, converting biomass to fuels, and >nuclear materials at Argonne. He is expert in quantum chemistry, >molecular dynamics and Monte Carlo methods on high performance computers. >Dr. Sabine Schweizer, Senior Scientist at Scienomics has a Ph. D. in >Theoretical Chemistry from University of Tuebingen, Germany. Her work >experience is in the area of applying quantum chemical methods to large >and small molecules. Her experience is particularly useful in the areas >of homogenous and heterogenous catalysis, where energetics and dynamics >play an important role in the reactions. She has experience working with >multiscale hybrid methods combining quantum chemical and classical >methods which makes her particularly versatile in applying Scienomics¹ >multiscale, multiparadigm MAPS platform to study hard materials such as >surfaces, coatings, semiconductors, solar cells, etc. >Dr. Lalitha Subramanian, Chief Scientific Officer and VP of Services has >18 years of experience providing insight into chemical systems and >processes that are of critical interest to industry. Following her Ph. >D. in Chemistry, her post-doctoral work was with Prof. Roald Hoffmann >(Nobel Laureate) at Cornell University. She has been a leading architect >of solutions in the areas of alternate energy, catalysis, materials >design, and process optimization. She has worked on numerous proprietary >projects for diverse companies and in this pursuit; she has delivered >product enhancements, process optimization and cost savings to her >customers. Lalitha maintains a broad range of partnerships in oil and >gas, chemical, personal care, materials, semiconductors, automotive, >aerospace, and pharmaceutical industries. She has co-authored a book on >software techniques used in Materials Science published by CRC Press, >2005. She continues to present invited lectures and has numerous scienti > fic publications. > >Recent References: > >Kimberly-Clark Corporation use Scienomics software and services for >predicting properties of new polymer systems (2012). > >US Army Research Lab use Scienomics software and services for proprietary >research on polymeric systems (2012). > >Materials Engineering Research group at Purdue University used Scienomics >software suite for studying the crosslinking process of thermosetting >polymers (2010). > > > Current: undetermined amount >Justification: > > Requested: 55000 > >A specific reason has been given: >In order to complete the ongoing Molecular Dynamics study on Raney >Nickel, we need an additional allocation. We are currently writing a >manuscript and need to run some more expensive calculations for studying >the dependence of the pore size on the unit cell size of our molecular >models of Raney Nickel. For getting our final results, we will require to >launch about 20 calculations using the LAMMPS code. Each job is estimated >to take about 20 hours using up to 8 nodes on Fusion. This will require >and additional 3,200 core-hours. > >An Adaptive Kinetic Monte Carlo (akmc) simulation will also be carried >out using the Eon Software Package >(http://theory.cm.utexas.edu/eon/index.html) This method will allow us >to simulate the dealloying reaction to from Raney Nickel from Nickel >Aluminide over longer time scales and check equilibration. >The AKMC study will require an additional 50,000 core-hours. > >Our total request of 55,000 core hours will also cover our current >project deficit for 1,500 core hours. > >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 07 Jul '14

07 Jul '14

Hello, A change in allocation has been requested: Requester: jlow (John J. Low) Project: Raney_Nickel Title: A Molecular Model of Raney Ni Description: During the first phase of the project, molecular dynamics (MD) simulations have been performed on fusion using the LAMMPS software package in order to analyze the influence of the initial composition of the alloy on the structural properties of the precursor. Model structures for four different compositions (40/50/60/70 wt% Ni) have been created using Scienomics MAPS platform by randomly replacing Ni and Al in the corresponding fractions in a NiAl3 supercell. In order to ensure a statistically relevant sampling, five initial starting configurations have been generated for each of these model structures. The structures were equilibrated at 2000 K and then cooled down to room temperature over 1 ns as described by Noya, et al. [J. Non-Crystal. Solids 298, 60–66 (2002)]. The MD simulations performed so far provided insight to what extent the initial configuration and compositions affects the structure of the precursor. The analysis density and cell parameters of the final structures indicates that the composition has a significant influence, while the configuration has only a very minor impact. In general, the density, cell parameters, total energy and volume over the simulation time show a consistent behavior. The final structures as obtained from the quenching simulations will serve as basis for additional MD simulations and equilibrated for 1 ns at room temperature to ensure convergence. The trajectories will be analyzed with respect to the formation of nanostructured clusters based on a next neighbour search, for which MAPS scripting facilities will be used. The trajectories will be analyzed with respect to the formation of nanostructured clusters. In addition we plan to ues the open source program RINGS (http://rings-code.sourceforge.net] will be used to analyze local structural environments and voids. From each model, Al will be removed and only 5-10 % Al will be left which corresponds to the experimentally observed final catalyst composition. These porous models will be minimized, which will only require a few hundred core-hours, and afterwards analyzed with regard to pore size, pore distribution, and accessibility from surface for the various compositions and initial config urations to explore trends that can be linked to the catalytic performance. In this way, we can gain a fundamental understanding about the formation of nanostructures in the precursor alloy in dependence of the initial composition. In the laboratory, the precursor is activated though treatment with sodium hydroxide leaching out the majority of the Al and leading to structural re-arrangements of the Ni bulk. This process will not be simulated as it is beyond the scope of the present project. Instead, we will focus on modeling the structure of the final catalyst. To provide a reliable description of the nanoporous structure, large system sizes will be required which will also allow to capture effects of grain boundaries that a supposed to be important for the chemistry of the final catalyst. The computational time needed for performing MD simulations and analyzing the trajectories of all 20 models will be considerable. Each model structure contains more than 65,000 atoms. According to the LAMMPS Cu benchmarks[ http://lammps.sandia.gov/bench.html#eam] 100 steps for a system size of 32,000 atoms would take 0.3 s (fixed CPU time) on 512 cores. A 1 ns trajectory (1,000,000 steps) for 32,000 atoms would take 500 core-hours and a 65,000 atom system about 1250 core-hours. 25,000 core-hours will be needed for the simulations of the 20 alloy model structures. Characterization studies of Raney Nickel by Anderson’s group and others which yield a qualitative picture of Raney Nickel. [J. Cat. 16, 281–291 (1970)] The void volume of these particles ranges from 0.05 to 0.15 cc/g. X-ray diffraction and X-ray Absorption Spectra show that local structure of Raney Ni’s is similar to FCC Ni. Fouilloux gives a qualitative description of Raney Nickel as a spongy material composed of 100 nm agglomerates of smaller 2.5 to 15 nm nanocrystals. Our model of Raney Nickel starts with 500 randomly packed 12.5 Å spherical nanocrystallites of Nickel in a 100 nm sphere. The procedure of Lubachevsky, et al. will be used to generate random packing of the spheres.[J. Stat. Phys. 64 501–524 (1991)] Since random close packing has a density of approximately 0.63, this model will have a void volume (0.06 cc/g) similar to Raney Ni. The initial positions of the atoms in the Ni nanospheres will be created from a randomly oriented and shifted FCC latt ice. The final structure will be determined through simulated annealing and the EAM potentials as implemented in LAMMPS. Our model should be qualitatively similar to experimental structure of Raney Nickel. These structures will be tested by comparing calculated properties from the predicted structure to the experimentally determined pore size distribution, heterogeneities from small angle X-ray scattering and line broadening in X-ray diffraction. Several modeling studies of grain boundaries use molecular dynamics to generate structures. Van Swygenhoven and Caro used a stochastic procedure that starts with randomly placed seed particles with the rest of the space filled with a Voroni construction.[Phys. Rev. B 58, 11246–11251 (1998)] Keblinski randomly placed seed particles in a liquid metal and then quenched the melt to generate a model crystal with grain boundaries. [Scr. Mater. 41, 631–636 (1999)] These procedures yield a model of a solid composed of nanocrystalline grains. We will follow the spirit of these modeling approaches by randomly placing seeds of Ni crystallites in a gas (or liquid) of Ni atoms and use simulated annealing to generate a low energy structure. Raney Nickel, which has a void volume of 0.1 cc/g, is essentially half void by volume. A simple model would be to seed a gas with a density half that of Ni metal. The gas will condense on the seed crystallites and create an agglomerate with the appropriate void volume. Since the condensation is exothermic, a Nose or Andersen thermostat will keep the temperature below the melting temperature (1728K) of Ni during the simulation. Starting at 1500 K and scaling the temperature to 0K over 100 picoseconds will quench to a low energy structure through simulated annealing. Since the low energy structure will create particles which have the density of Ni metal, the voids between the particles should have half the volume of the initial volume. The number of crystallites should control the size of the nanocrystals formed during simulated annealing. A careful choice of initial conditions should lead to the desired size of nanocrystals and void volumes. The RINGS program will allow a systematic and analytical analysis of these structures. A 100 nm droplet of Ni with half the density of bulk Ni is a model of Fouilloux’s description of Raney Nickel.[J. Cat. 25, 212 (1972)] The scale of this calculation would be significant. The model would be initiated by randomly placing 500 seed crystallites (Ni55 clusters) in a hundred nanometer sphere and then randomly inserting 25 million atoms into the space between the seeds. The embedded atom method as implemented in LAMMPS can handle simulated annealing of models of this size. The Cu EAM benchmark on the LAMMPS website shows that 100 steps of molecular dynamics for 16 million atoms could be done on 512 cores of a Xeon/Myrinet cluster in 21 seconds. [http://lammps.sandia.gov/bench.html#eam] A 100 picosecond trajectory (100,000 steps) would take 60 hours (30,000 core-hours). Fusion or Blues have faster processors and an InfiniBand interconnect that will yield better performance. The estimated CPU requirements derived from timings for the Xeon/Myrinet cluster is an upper bound. We anticipate repeating this calculation a few times with three different compositions requiring 100,000 core-hours. Our initial calculations will use a periodic model containing a million atoms and 20 seeds to verify this approach will give morphology similar to Raney Nickel. The test will involve comparing calculated properties from the predicted structure to the experimentally determined pore size distribution, heterogeneities from small angle X-ray scattering and line broadening in X-ray diffraction. [J. Cat. 23, 286 (1971), Cat. Today 163, 13–19 (2011)] If this model does not yield a satisfactory result we will implement and test a stochastic Voroni procedure. [Phys. Rev. B 58, 11246–11251 (1998)] These calculations will require a few thousand core hours and will not exhaust our allocation before developing a working model. Once we have established a procedure that generates a model of a porous solid composed of nanocrystalline grains, we will carry out calculations on a more realistic 50 million atom droplet model of Raney Ni. 50,000 core hours will be needed for these experimen ts with smaller periodic models. We will use EAM to model hydrogen adsorption on our model of Raney Nickel. The model will have monolayer coverage (one hydrogen atom per surface Ni atom). The surface will be defined by Ni atoms with coordination less than twelve. Simulated annealing will be use to find a low energy distribution of hydrogen on the surface of Raney Ni. The predicted binding energies, vibrational frequencies and geometries will be used to classify the chemisorption sites to a smaller number of representative sites. 50,000 core-hours will be required for the chemisorption models. The pore size, pore distribution, and the accessibility of the droplet model and chemisorbed model will be compared with the results obtained for the precursor models. This strategy will allow to explore to what extent the nanostructural agglomerations in the precursor are reflected in the porous active form. The generalized chemisorption sites will form the basis of smaller periodic models. We will use the smaller models to model hydrogenation of benzene on Raney Nickel with an electronic structure program like abinit, bigdft, cp2k or qbox. These calculations will be done in a future project. Overall, 200,000 core-hours will be needed over a period of five months for performing the in silico experiments for the project. About Scienomics Scienomics was established in 2004 and with selected partnerships with the best-of-the-breed (e.g.: Sandia National Labs, Max Planck Institute, Fraunhofer Institute, University of Illinois, Demokritos, University of Shanghai), Scienomics’s MAPS platform offers a unique and powerful blend of multiscale and multiparadigm modeling and simulation modules. With high quality science and industrial solution oriented applied research, Scienomics has garnered collaborative projects with companies in the areas of energy and green chemistry, alternate fuels, catalysis, polymers, biodefense, auto exhaust, etc. Biography of Relevant Members John J. Low, Principal Computational Science Specialist at Argonne National Laboratory has a Ph.D. in Chemistry from the California Institute of Technology. After graduation John worked at UOP LLC, a Honeywell Company. His work at UOP focused on modeling and characterization of catalysts and adsorbents used in the petrochemical industry, hydrogen storage and carbon sequestration. John supports the computational chemistry applications at high performance computers and performing research on Li-Ion batteries, converting biomass to fuels, and nuclear materials at Argonne. He is expert in quantum chemistry, molecular dynamics and Monte Carlo methods on high performance computers. Dr. Sabine Schweizer, Senior Scientist at Scienomics has a Ph. D. in Theoretical Chemistry from University of Tuebingen, Germany. Her work experience is in the area of applying quantum chemical methods to large and small molecules. Her experience is particularly useful in the areas of homogenous and heterogenous catalysis, where energetics and dynamics play an important role in the reactions. She has experience working with multiscale hybrid methods combining quantum chemical and classical methods which makes her particularly versatile in applying Scienomics’ multiscale, multiparadigm MAPS platform to study hard materials such as surfaces, coatings, semiconductors, solar cells, etc. Dr. Lalitha Subramanian, Chief Scientific Officer and VP of Services has 18 years of experience providing insight into chemical systems and processes that are of critical interest to industry. Following her Ph. D. in Chemistry, her post-doctoral work was with Prof. Roald Hoffmann (Nobel Laureate) at Cornell University. She has been a leading architect of solutions in the areas of alternate energy, catalysis, materials design, and process optimization. She has worked on numerous proprietary projects for diverse companies and in this pursuit; she has delivered product enhancements, process optimization and cost savings to her customers. Lalitha maintains a broad range of partnerships in oil and gas, chemical, personal care, materials, semiconductors, automotive, aerospace, and pharmaceutical industries. She has co-authored a book on software techniques used in Materials Science published by CRC Press, 2005. She continues to present invited lectures and has numerous scienti fic publications. Recent References: Kimberly-Clark Corporation use Scienomics software and services for predicting properties of new polymer systems (2012). US Army Research Lab use Scienomics software and services for proprietary research on polymeric systems (2012). Materials Engineering Research group at Purdue University used Scienomics software suite for studying the crosslinking process of thermosetting polymers (2010). Current: undetermined amount Justification: Requested: 55000 A specific reason has been given: In order to complete the ongoing Molecular Dynamics study on Raney Nickel, we need an additional allocation. We are currently writing a manuscript and need to run some more expensive calculations for studying the dependence of the pore size on the unit cell size of our molecular models of Raney Nickel. For getting our final results, we will require to launch about 20 calculations using the LAMMPS code. Each job is estimated to take about 20 hours using up to 8 nodes on Fusion. This will require and additional 3,200 core-hours. An Adaptive Kinetic Monte Carlo (akmc) simulation will also be carried out using the Eon Software Package (http://theory.cm.utexas.edu/eon/index.html) This method will allow us to simulate the dealloying reaction to from Raney Nickel from Nickel Aluminide over longer time scales and check equilibration. The AKMC study will require an additional 50,000 core-hours. Our total request of 55,000 core hours will also cover our current project deficit for 1,500 core hours. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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