July 2012 - Allocations-admins - mailman3.cels.anl.gov

[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 31 Jul '12

31 Jul '12

Hello, A change in allocation has been requested: Requester: asumer (Aslihan Sumer) Project: Multicomp_Nanopart Title: Next Generation of Multicomponent Nanocatalysts: Computational Studies Description: The planned computations will explore the structural (e.g., mixed, core-shell, dumbbell-like, and other), energetic, dynamical/thermal, electronic, and chemical/catalytic properties and characteristics of multicomponent metal nanoparticles, both gas phase and deposited on supports. Among the targeted nanocatalysts are Pt-Co (the work on this system has been initiated already), Pt-Ni, Pt-Fe, CoPt3/Au, FePt/Au, Au/Fe2O3, CoPd2/Au, and others. These are the one currently investigated or planned for investigation by the experiments. The candidate supports include iron-oxide and cobalt-oxide. Among the issues that will be addressed are: 1) Use of size, structure and composition of the nanocatalysts as "knobs" for tuning their activity and selectivity, and 2) Use of functionalizing ligands such as amines of different "sizes" (different lengths of the carbon chains) as an additional means of affecting the catalytic functionality (experiments on the effects of functionalization of various multicomponent nanocatalysts by amines are currently underway). The computational studies of the structural, energetic, and electronic aspects will be performed using density functional theory. The packages that will be utilized include NWChem and Crystal (we have recently purchased the license for Crystal and installed the software on the Fusion cluster). Naturally, we will take full advantage of the parallelized versions of these packages as we intend to explore systems with an ever increasing number of atoms: 1) The properties of the nanocatalysts will be explored over the size r ange from a few tens to a few hundreds of atoms, and 2) The effects of the supports will later be incorporated as well. In addition to the DFT studies, we also plan to perform large scale molecular dynamics simulations of the dynamical and thermal behavior of the multicomponent catalytic nanosytems. The expected number of users on this project is 3 or more. Current: undetermined amount Justification: The allocation request is based on estimates made with NWChem on Fusion and on NERSC (Carver and Hopper) machines. Tests on a a relatively small Pt14 cluster with the new Stuttgart pseudopotential and a basis set of 38 contracted Gaussians per atom with a 2-butyne or 2-butene molecule on it performed with 64, 128 and 192 processors indicate a substantial increase in performance with the increase in the number of processors up to about 128. Tests with Crystal are in progress, however literature data indicates high efficiency of the parallelization of this code. 1) Scalability of NWChem on Fusion as evaluated by us for the C4H6-Pt14 system (total of 736 basis functions and with charge density fitting): Cores Average SCF cycle (s) 64 19.4 128 12.5 192 10.8 2) Scalability of MPP_Crystal on Hector (UK) as evaluated for the Ga432Sb426N6 system (19836 basis functions) [1]: Cores Average SCF cycle (s) 856 2503 1712 1308 3424 711 [1]I. J. Bush et al., Proc. Royal. Soc. 467, 2112 (2011) Requested: 200000 A specific reason has been given: One the issues that is addressed in this project is the relationship between the size of metal nanoparticles and their efficiency in selected model catalytic transformations, which includes the selective hydrogenation of unsaturated aldehydes, for example. The computational studies (within the framework of density functionals) performed to date include nanoparticles ranging from a few atoms to a few tenths of atoms. Our results provide important information on trends in catalytic activity and selectivity at this subnanometer size range. In order to provide a complete picture of the size effect, the ongoing studies have recently been expanded to include nanoparticles of a few hundreds of atoms. The increased complexity of systems at this size (i.e., the larger number of possible adsorption sites to be tested in order to reach the minimum energy adsorption configurations of the reactants on the nanoparticles), along with the computational efficiency requirements that increase in proportion with the number of atoms in the system (our scaling studies showed that maximum efficiency is obtained with 64-128 processors for the systems with approximately 300 atoms that are currently under investigation), make it necessary to request this additional allocation for the current fiscal year. 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 Request: tsvdw_nwchem
by accounts＠lcrc.anl.gov 27 Jul '12

27 Jul '12

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: Alvaro VazquezMayagoitia Applicant's institution: ANL Applicant's division: LCF Project Name: tsvdw_nwchem Project title: Implementation and validation of TS van der Waals contribution in NWCHEM Associated funding: Other Systems: Intrepid, Surveyor (1M) Science: The molecular interactions are the product of several contributions, attractive or repulsive. In weak interactions the dispersion energies are the main responsible of middle range attractions. Density Functional Theory (DFT), the most used ab initio method in material science, cannot describe appropriately multipolar energy contributions; particularly, the description of dispersion energies is one of its mayor problems. A way to take in account the dispersion energies in Generalized Gradient Approximation functionals (GGA) is by adding a correction term to the total DFT energy. This dispersion energy contribution is often evaluated by empirical methods parametrized to reproduce experimental energies or benchmark databases, nevertheless those empirical parameters may not be universal or may not be considering properly new systems. We propose to add to the ab initio code NWCHEM a parameter-free model to the dispersion energy based on atoms-in-molecules scheme. Project description: The model will use to correct dispersion energies is based on the scheme proposed by Tkatchenko-Scheffler (PRL, 102, 073005,2009), which represents the dispersion energy contribution as the sum of pairwise atoms interactions. The atoms interaction of the atoms A and B are represented by C6/R^6, where R is the distance between both atoms, and C6 is the average of the dispersion coefficients of A and B scaled by the proportion of their Hirshfeld volumes. We are implementing the TS in the quantum chemistry suite NWCHEM, and we pretend evaluate a long series of interacting molecules to validate this new model in the code. The systems to be evaluated are: the benchmark data base S66, S22, JSCH and HBC6. (see JCP, 134, 084107,2011). NWChem has been installed in Fusion and other computing facilities. NWChem was designed to execute in parallel with excellent scalability for some hundreds of processors. Project URL: Requested allocation: 150000 Q1: 90000 Q2: 20000 Q3: 20000 Q4: 20000 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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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 12 Jul '12

12 Jul '12

John Low, Does this look reasonable? If it is we might provide 120K. Ray On 7/10/12 1:43 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: > Hello, > > A change in allocation has been requested: > > Requester: hahe (Haiying He) > Project: glassforms > Title: First-principles Calculations of Mineral and Glass Dissolution > under Various pH Conditions > Description: Task I: The task of our research is to include the bulk water > effect in the process of glass and mineral dissolution. In the past year, we > have calculated hydrolysis reaction barriers of the Si-O-Si bridges and the > Si-O-Al bridges at surface sites of orthoclase feldspar (KAlSi3O8) as a model > system in different protonation states – neutral (≡SiOH), protonated (≡SiOH2+) > and deprotonated (≡SiO-) using the Nudge Elastic Band (NEB) method. In most of > the calculations, we have only considered a single H2O attack on the Si-O-Si > or Al-O-Si bridge that causes bond rupture with the simultaneous H2O > dissociation. Studies of the bulk water effect will determine the role of > proton shuttle in aqueous solution and the entropic effect of water. Both > effects contribute to the free energy reaction barriers. This task will be > accomplished by including explicit H2O molecules in a large supercell and > performing constrained molecular dynamics (MD) simulations. Hereby, the f > ree-energy profile is a thermodynamic integration over the restoring forces > along a parameterized reaction coordinate using the rare-event ensemble > technique, which is newly implemented in VASP. We will also use this > technique to determine the chemical potentials of protons in solution for the > surface site distribution model which we have developed. > > Task II: The second task for this year is to extend our study from a model > crystalline material to glasses. Using initial structures from classical > molecular dynamics, we will continue with first-principles calculations of > reaction energies and barriers. Multi-component amorphous structures are some > complexities that we need to address in the modeling of glasses. It suggests > that we need large supercells and a large number of sampling points. The > major components that we will consider in glasses are Si, Al, B (network > formers) and Na, Ca (network modifiers). We will carry out similar > investigations in terms of the surface protonation and hydrolysis reaction > barriers under various pH conditions for bridges involving these elements. The > properties that we are going to calculate in this part include structures and > energies of reactants, intermediates and products, as well as reaction > barriers (based on the NEB method). In some cases, we will validate results > using smaller clus > ters at high levels of ab initio theory such as CCSD(T) as implemented in > NWChem and Gaussian09 packages. The calculated reaction barriers together with > the surface site distributions determined from the surface model will then be > used in kinetic modeling to calculate the dissolution rates. > > This project will primarily use the density functional theory (DFT) > implemented in electronic structure code VASP. The system sizes of our > calculations ranges from 100 to 300 atoms. VASP has been tested to scale very > well in parallel processing on Fusion. The optimum number of processors used > for these systems is 16-64 processors per calculation. > > > Current: undetermined amount > Justification: The first-principles calculations will be carried out using the > electronic-structure code VASP. In Task I, ab initio MD simulations are > conducted, where each trajectory runs for 30-50 ps and it takes 16 processors > to run for 96-160 hours (average 2048 core hours per trajectory). We will > need to run 100 trajectories for five sets of calculations. That requires > 200,048 core hours. In Task II, NEB calculations are conducted to calculate > the reaction pathways for a variety of composing elements under acidic, > neutral and basic conditions. A single optimization calculation takes 48 hours > on 32 processors. We are considering 30 supercell samplings of silicate > glasses including multiple components (Si, Al, B, Na, K). The calculation for > possible reactants, intermediates, products will take about 138,240 core > hours. It takes about 48 hours on 160 processors (5 images) to calculate a > reaction barrier along the reaction pathway. The total estimated computer time > for barr > ier calculation is 460,800 core hours. In sum, the total requested allocation > for this project is 800,000 core hours. > > Requested: 150000 > > A specific reason has been given: > More allocation is needed to complete the research task. > > This needs to be approved and the final allocation amount decided upon. > > Thank You, > The LCRC Accounts System ----------------------------------------- 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

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 10 Jul '12

10 Jul '12

Hello, A change in allocation has been requested: Requester: hahe (Haiying He) Project: glassforms Title: First-principles Calculations of Mineral and Glass Dissolution under Various pH Conditions Description: Task I: The task of our research is to include the bulk water effect in the process of glass and mineral dissolution. In the past year, we have calculated hydrolysis reaction barriers of the Si-O-Si bridges and the Si-O-Al bridges at surface sites of orthoclase feldspar (KAlSi3O8) as a model system in different protonation states – neutral (≡SiOH), protonated (≡SiOH2+) and deprotonated (≡SiO-) using the Nudge Elastic Band (NEB) method. In most of the calculations, we have only considered a single H2O attack on the Si-O-Si or Al-O-Si bridge that causes bond rupture with the simultaneous H2O dissociation. Studies of the bulk water effect will determine the role of proton shuttle in aqueous solution and the entropic effect of water. Both effects contribute to the free energy reaction barriers. This task will be accomplished by including explicit H2O molecules in a large supercell and performing constrained molecular dynamics (MD) simulations. Hereby, the f ree-energy profile is a thermodynamic integration over the restoring forces along a parameterized reaction coordinate using the rare-event ensemble technique, which is newly implemented in VASP. We will also use this technique to determine the chemical potentials of protons in solution for the surface site distribution model which we have developed. Task II: The second task for this year is to extend our study from a model crystalline material to glasses. Using initial structures from classical molecular dynamics, we will continue with first-principles calculations of reaction energies and barriers. Multi-component amorphous structures are some complexities that we need to address in the modeling of glasses. It suggests that we need large supercells and a large number of sampling points. The major components that we will consider in glasses are Si, Al, B (network formers) and Na, Ca (network modifiers). We will carry out similar investigations in terms of the surface protonation and hydrolysis reaction barriers under various pH conditions for bridges involving these elements. The properties that we are going to calculate in this part include structures and energies of reactants, intermediates and products, as well as reaction barriers (based on the NEB method). In some cases, we will validate results using smaller clus ters at high levels of ab initio theory such as CCSD(T) as implemented in NWChem and Gaussian09 packages. The calculated reaction barriers together with the surface site distributions determined from the surface model will then be used in kinetic modeling to calculate the dissolution rates. This project will primarily use the density functional theory (DFT) implemented in electronic structure code VASP. The system sizes of our calculations ranges from 100 to 300 atoms. VASP has been tested to scale very well in parallel processing on Fusion. The optimum number of processors used for these systems is 16-64 processors per calculation. Current: undetermined amount Justification: The first-principles calculations will be carried out using the electronic-structure code VASP. In Task I, ab initio MD simulations are conducted, where each trajectory runs for 30-50 ps and it takes 16 processors to run for 96-160 hours (average 2048 core hours per trajectory). We will need to run 100 trajectories for five sets of calculations. That requires 200,048 core hours. In Task II, NEB calculations are conducted to calculate the reaction pathways for a variety of composing elements under acidic, neutral and basic conditions. A single optimization calculation takes 48 hours on 32 processors. We are considering 30 supercell samplings of silicate glasses including multiple components (Si, Al, B, Na, K). The calculation for possible reactants, intermediates, products will take about 138,240 core hours. It takes about 48 hours on 160 processors (5 images) to calculate a reaction barrier along the reaction pathway. The total estimated computer time for barr ier calculation is 460,800 core hours. In sum, the total requested allocation for this project is 800,000 core hours. Requested: 150000 A specific reason has been given: More allocation is needed to complete the research task. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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