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

Re: [allocations-admins] 15 more new projects
by John Blaas 15 Sep '15

15 Sep '15

I'll add the projects tomorrow after granting accounts, today I am busy getting the systems back up and updated from the power work. - JB On Tue, Sep 15, 2015 at 1:57 PM, Bair, Raymond A. <rbair(a)anl.gov> wrote: > We suddenly have 15 requests for new projects this week, all requesting > time in Q4. > > Earlier in the month we capped new requests at 100K. That should be less > now, perhaps 75K or 50K? > > Also, each of these 15 will need to be reminded to turn in a FY16 request > too. I suppose they need to wait until their FY15 time is approved, so > time is if the essence. > > Ray > > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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15 more new projects
by Bair, Raymond A. 15 Sep '15

15 Sep '15

We suddenly have 15 requests for new projects this week, all requesting time in Q4. Earlier in the month we capped new requests at 100K. That should be less now, perhaps 75K or 50K? Also, each of these 15 will need to be reminded to turn in a FY16 request too. I suppose they need to wait until their FY15 time is approved, so time is if the essence. Ray

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[LCRC Accounts] Yearly Allocation Request for Hydro-model
by accounts＠lcrc.anl.gov 15 Sep '15

15 Sep '15

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Eugene Yan Project Name: Hydro-model Division: EVS Project title: Hydrologic modeling Associated funding: NASA; DOE EDER Other Systems: MCS UNIX machines Science: Improve assessment of water resources, their response to extreme climate events, and their impacts on energy development Project description: The project includes two components: (1) evaluate the CLM model with remote sensing data and recent GRACE gravity measurements; (2) further improve usability and efficiency of the parallel calibration tool (SWAT-SWIFT). In addition, we are exploring potential applications for development of the integrated energy-water assessment framework. Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 70000 Q1: 10000 Q2: 20000 Q3: 20000 Q4: 20000 Justification: Storage requirements: Thank You, The LCRC Accounts System

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New LCRC report submitted for Hydro-model
by support＠lcrc.anl.gov 15 Sep '15

15 Sep '15

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2015/?project=Hydro-model

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[LCRC Accounts] Yearly Allocation Request for glassforms
by accounts＠lcrc.anl.gov 14 Sep '15

14 Sep '15

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Peter Zapol Project Name: glassforms Division: MSD Project title: First-principles Calculations of Mineral and Glass Dissolution Associated funding: DOE-NE Other Systems: Science: The dissolution of glass forms in nuclear waste disposal determines their long term stability, which is critical for evaluating disposal scenarios. The dissolution behavior of minerals and glasses has been found to strongly depend on the pH value of the aqueous environment. The delicate balance of ions at the solid-water interface in aqueous solutions is still a big challenge both for accurate computational modeling and for unambiguous experimental measurements. This project aims to develop physical models to simulate the water-borosilicate glass forms interface at the atomic level under various pH conditions and to calculate the rates of dissolution for Si, Al and other constituting elements under acidic, neutral and basic conditions. These studies are based on first-principles calculations and kinetic Monte Carlo simulations. The calculated reaction barriers by using DFT calculations can then be used as input in kinetic Monte Carlo simulations to estimate the over all dissolution rates and compare with experimental values. These investigations will be very important to better understanding of the dissolution behavior and prediction of dissolution rates. Project description: The first-principles calculations will be carried out using the electronic-structure code VASP. NEB calculations will be performed 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. Last year, we have performed calculations on glass with B, Si and Na. This year, we will add Al and K to these components. We are considering 60 supercell samplings of silicate glasses including multiple components (Si, Al, B, Na, K). The calculation for possible reactants, intermediates, products will take about 200,000 core hours. It takes about 50 hours on 160 processors (5 images) to calculate a reaction barrier along the reaction pathway. The total estimated computer time for barrier calculation is 640,000 core hours. kMC simulation will be performed to simulate the dissolution process of glass for 5 different temperatures and 4 different pH values for 72 hours (each simulation should run 50 times in order to get the statistical results). That requires 90,000 core hours. In sum, the total requested allocation for this project is 930,000 core hours. Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 930000 Q1: 200000 Q2: 250000 Q3: 250000 Q4: 230000 Justification: 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 Blues. The optimum number of processors used for these systems is 16-64 processors per calculation. The kMC simulation code is written in Fortran. Storage requirements: Thank You, The LCRC Accounts System

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New LCRC report submitted for glassforms
by support＠lcrc.anl.gov 14 Sep '15

14 Sep '15

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2015/?project=glassforms

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[LCRC Accounts] Yearly Allocation Request for Solar_EPR
by accounts＠lcrc.anl.gov 14 Sep '15

14 Sep '15

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Kristy Mardis Project Name: Solar_EPR Division: CSE Project title: Solar energy conversion in organic photovoltaics Associated funding: DOE Division of Chemical Sciences, Geosciences, and Biosciences Other Systems: Dr. Mardis has three small linux clusters (12/24/48 nodes) which are housed at her home institution. Her research group is the sole users of these systems. Orca, pqs, gabedit, and gamess all can be run on these systems. Science: This work is focused on the elucidating the electronic structures of donor-acceptor polymers which are the most promising solar conversion material for organic photovoltaic devices. A key process of the solar energy conversion in organic photovoltaics is the initial charge separation. Stronger delocalization of the positive polaron on the polymer minimizes wasteful charge recombination. The delocalization correlates with solar energy conversion efficiency and is determined by the electronic structures of the organic molecules. The first aim is to use Density Functional Theory (DFT) to evaluate the extent of polaron delocalization on these donor-acceptor polymers. The second aim is to explore the effect of solvent and conformation on the calculated magnetic resonance parameters in order to assess the feasibility of this approach for modeling the bulk polymers. These results will facilitate interpretation of our multifrequency Electron Paramagnetic Resonance (EPR) da ta of polymer fullerene bulk heterojunction (BHJ) solar cells. This study will provide a rationale for design of efficient BHJ blends. Project description: We are evaluating the effect of modifying the polymer portion of the BHJ solar cells to increase the delocalization of the positive polaron, which correlates with solar energy conversion efficiency. Prior work suggested delocalization ranged over multiple subunits; up to 60 Angstroms. However, due to our existing computational power we were not able to assess larger structures. Furthermore, test calculations indicated sensitivity to both conformation and external charges. The current work seeks to investigate a series of recently synthesized polymers and to include longer oligomers to test the limits of the delocalization. We intend to run a series of gas-phase model DFT optimizations to determine the low energy polymer conformations using standard ab initio optimization codes such as GAMESS, or NWCHEM. This will also allow us to generate a set of conformers likely to be present in the experimental samples. The resultant conformations will be used to calculate EPR parameters (g-tensors and hyperfine coupling constants) using Orca 3.0.3. Oligomers of varying length will be investigated to evaluate delocalization ranges and sensitivity of electronic structure parameters to oligomer length. The initial structure building, monomer and dimer test calculations, and analysis of spin densities will be carried out on our lab computers. The primary usage of fusion will be in the optimization, frequency calculation, and EPR parameter calculation steps of the work. The optimization subroutines of NWCHEM and GAMESS are highly parallelized. Orca 3.0.3 is a highly accurate program for calculating EPR parameters. It has recently been installed on fusion. Benchmarks on a small local workstation with Orca showed good scaling up to 16 processors for the EPR parameter subroutines. Test calculations performed on this small workstation for the largest oligomer we calculated so far took about 200 (small basis set) to 20,000 (large basis set) CPU hours (using PQS as the optimization engine) for optimization and frequency calculations. The existing allocation is being used to set-up and run optimizations using Density Functional Theory (B3LYP functional and 6-31G basis) using NWCHEM. Calculations for 3 oligomers with an average of six conformations each are in progress. Furthermore, calculations to support a paper on the role of physical deformation of the fullerenes and polymers in the thin film BHJ cells have been submitted. Test calculations on our local systems indicate that the amount of delocalization present is sensitive to the functional present (primarily related to the treatment of correlation effects). We thus anticipate the need to perform calculations with at least three additional functionals for the largest polymers. The EPR parameter calculation (g-tensor and hyperfine calculations) took 1200 CPU hours (using orca 3.0.3). Calculations for 8 new oligomers oligomers with an anticipated six potential conformations for each requiring 9,600 (CPU*oligomer*conformation=200*8*6) for the initial set of calculations, optimizations using alternate functionals and a medium basis set for the largest 3 oligomers will require 7200 cpu hours (400*3*6) and an additional 200,000 (20,000*10*1) CPU hours for the largest basis set calculation for the lowest energy conformation of each oligomer. The EPR parameter calculations will take 72,000 (1200*10*6) CPU hours. This totals to 288,000 CPU hours. Cons idering that these numbers are for a system slightly smaller in size to those proposed here, 300,000 CPU hours seems to be a reasonable estimate. We did not divide the CPU hours equally as Dr. Mardis is a teaching faculty member and has less research time between October 1-December 31st than she does in the late spring and summer months. Also, the largest optimization/frequency calculations are expected to occur in the second and third quarters. We expect 3 project members (Mardis, Niklas, Poluektov). No non-parallel jobs will be run and all visualization and analysis will be done on local machines. Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 300000 Q1: 50000 Q2: 75000 Q3: 100000 Q4: 75000 Justification: Storage requirements: 1TB Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Request: IVwire
by accounts＠lcrc.anl.gov 14 Sep '15

14 Sep '15

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: Pierre Darancet Applicant's institution: ANL Applicant's division: NST Project Name: IVwire Project title: Length dependence of the current-voltage characteristics of molecular wires Associated funding: Other Systems: CNM Carbon (200,000h) Science: Using non-equilibrium Green's functions methods (NEGF), we will compute the electronic structure and current response of polymers submitted to an external bias, and understand how such response is impacted by the length of the molecule. Using our recently-developed approach [1], our goals are (1) to achieve a quantitative description of the current-voltage characteristics of polyphenylene vinylene (PPV) measured by our collaborators at Columbia University and (2) to develop a minimal physical model predicting the lineshape and the conditions of appearance of non-linearities in such characteristics. This model will be used to design polymers with tailored electronic and transport properties. Project description: We will study the finite-bias electronic transport properties of single-molecule junctions --devices consisting in an individual molecule connected to macroscopic metallic electrodes. Experimental breakthroughs in the past 10 years allow to statiscally and reproducibly measure the current-voltage characteristics (IVs) emerging from such devices and to quantify the different energy scales impacting the way electrons flow at the sub-nanometer lengthscale. Among other things, these developments have led to the development of a quantitative description of such IVs characteristics based on first-principles calculations [1]. The ongoing theoretical and experimental challenge is to use this understanding in order to design molecular junctions with new functionalities, i.e. with non-linear (non-Ohmic) IVs. As transport at low-bias in these systems typically varies exponentially with length, we intend in this project to understand if (and how) the size of the molecule can be used to g enerate strongly non-linear IV characteristics. We have recently developed a bias-dependent parameter-free self-energy correction to density functional theory (DFT) that allows for a quantitative description of the current-voltage characteristics of molecular junctions [1]. This method is implemented on top of NEGF-DFT implemented in the freely-available Siesta package [2,3]. This software was already used on the CNM cluster to compute the low-bias current response of PPV molecules with a number of monomers ranging from 1 to 5: showing an excellent agreement between our results and experiments conducted by our collaborators at Columbia University. The next step is to compute the full IV characteristics and requires significantly more computational power. Siesta is efficiently parallelized for orbitals-based operation as well as number of points used to analytically continue the Green's functions to the real axis: All finite-bias calculations are done on a Keldysh contour (~100 points near the Fermi energy at 1V) and involve the explicit description of ~500-700 atoms/2000-3000 electrons. Siesta parallelization involves a 1-D block cyclic distribution for orbital-based operations, with an optimal number of orbitals per cpu in the 10-32 range (24 was optimal on Carbon). As we anticipate the scaling will deteriorate when the number of cores exceed the number of Keldysh contour points, we will use 96 cpus (16 nodes) per run. Based on the cpu time on Carbon, we anticipate that each run will require 200h of wall time. A minimum 4 voltages/molecule (5 molecules total) will be needed to quantify the non-linearity. Siesta 3.1.0 is already installed and supported on the LCRC clusters. Nevertheless, in order to implement our self-energy correction, we will need to recompile the code --which requires the use of standard libraries, available on blues/fusion: MPI/BLACS/Scalapack. [1] Darancet et al. Nano Letters 12, 6250-6254 (2012) [2] Soler et al., J. Phys.: Condens. Matter 14, 2745 (2002) [3] Brandbyge et al., Phys. Rev. B 65, 165401 (2002). Industry partnership: Project URL: Requested allocation: 400000 Q1: 0 Q2: 0 Q3: 0 Q4: 400000 Justification: Storage requirements: 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] Yearly Allocation Request for ElectrolyteRedoxFlow
by accounts＠lcrc.anl.gov 14 Sep '15

14 Sep '15

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Lei Cheng Project Name: ElectrolyteRedoxFlow Division: MSD Project title: discoveries of electrolyte for redox flow batteries Associated funding: JCESR Other Systems: NERSC Science: To meet global energy demand, renewable energy sources such as solar and wind energy are being developed and utilized. The increased use of wind and solar energy will challenge the grid’s ability to provide a stable electrical supply around the clock. Grid energy storage can be used to shift load from peak to off-peak hours and redox flow batteries are of particular interest to perform this load leveling. Redox flow batteries differ from classical batteries in that energy is stored in the liquid electrolyte in separate liquid reservoirs instead of in the electrode. This bypasses common electrode degradation issues observed in lithium ion batteries and makes the battery systems more durable and scalable. However, all flow batteries based on aqueous electrochemical couples are limited by the electrochemical properties of water which is only stable within a small potential window (typically 1.2-1.6 V) outside of which water electrolysis occurs. This means that redox- flow battery suffers from lower energy density. In order to increase the energy density, the current or potential must be increased. Employing non-aqueous electrolytes offers a wider window of electrochemical stability, enabling flow batteries to operate at higher cell potentials (>2 V) and eliminating this low energy density limitation. Among various fundamental science and engineering challenges in the design of more efficient redox flow batteries, discoveries of appropriate redox couples that operate at higher cell voltage will lead to greater system energy densities and higher energy efficiencies. It is also one of the important missions of the energy storage hub Joint Center for Energy Storage Research (JCESR). Project description: In this renewal work, we will continue focusing on fundamental properties of transition metal complexes as redox active molecules for non-aqueous redox flow battery application. In collaboration with experimental group (Prof. Thompson, University of Michigan), we have previously studied redox windows and solvation energies of some acetylacetonate based compounds. The study will now move onto triazole, and bipyridine based compounds. These complexes are currently being studied in the Thompson lab, and represent an interesting field of study, as many exhibit greater than four redox events. In non-aqueous solutions as the capacity of this type of battery is directly proportional to the number of electrons, multi-electron complexes are desired. Insight gained from these studies will greatly guide design and synthesis of the compounds experimentally. In previously proposed work, we have successfully determined the B3LYP/6-31+G* and BP86/6-31+G* combinations as proper computational treatments for these system. The same methods will be used to calculate standard potentials, solvation energies, and molecular orbital structures of Ni, Fe, and Cr based novel compounds. These energies will be calculated using implicit continuum models such as PCM, CPCM and SMD methods. Structure optimizations will be performed at each charge state of the complex to evaluate the feasibility of predicting the electrochemistry of multi-redox complexes. The solvation energies will then be compared with experimentally measured solubilities of the compounds to determine correlation between the two. Experimental stability results are also available, so molecular orbital structures will be visualized and used to identify traits which can be correlated to stable cycling. We will also guide our research efforts towards providing physical understandings o f the observed experimental results. All calculations will be performed using Gaussian and NWCHEM. These two code packages are both considered very efficient and reliable for quantum chemistry calculations. Gaussian is not very scalable but it provides really robust geometry optimizer and the G3/G4 methods are built-in. NWChem is very scalable especially for higher level calculations such as coupled cluster methods and perturbation theories. After interesting molecule candidates and appropriate calculation methods are identified, derivatives of these molecules will be subject to high-throughput screening. The high-throughput screening will be performed using NERSC supercomputers. The size of molecules we propose to study is very typical for the two computational software (Gaussian and NWChem) so they scale reasonably well for most DFT calculation. These new complexes will require more computational time as they also have counter ions. The higher level calculations will consume more memory as well as computational time. The NWChem code uses a globally-shared memory system, therefore one can request and utilize more memory through node parallelization. Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 800000 Q1: 200000 Q2: 200000 Q3: 200000 Q4: 200000 Justification: Gaussian and NWCHEM are standard quantum codes that run on Fusion and Blues very well. For medium to large sized job, Gaussian will be used with mostly 1-4 nodes. NWCHEM scales much better than Gaussian and will be used for larger jobs that require more than 4 nodes. Storage requirements: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request for ML4Maxwell
by accounts＠lcrc.anl.gov 14 Sep '15

14 Sep '15

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Alejandro Lopez Bezanilla Project Name: ML4Maxwell Division: MSD Project title: Machine Learning to Solve a Maxwell's Equation Associated funding: DOE Other Systems: Science: A machine learning approach will be used to demonstrate that the first Maxwell's equation can be solved by means of statistical methods. A large amount of data describing the potential created by a charge distribution in multidimensional space with boundary conditions will be computed to obtain a training and validating set. An algorithm is expected to learn from the training data and compute new configurations. The accuracy will be compared with the validating data set. We performed a similar study on charge transport last year and successfully published on Phys. Rev. B 89, 235411 Project description: The project is currently in progress and good results are being obtained. Numerous calculations with an in-home code have been obtained for different configurations of potential distribution of randomly distributed charges in a square lattice. A MPI parallelization over configurations was implemented with excellent results of performance. The computed potential distributions are used as the training set of a Machine Learning algorithm for the prediction of new configurations in a supervised approach. The current scripts based on the Python programming language are being translated into a more efficient C++ based code for production. The additional work will be distributed over the next three quarters. Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 150000 Q1: 50000 Q2: 50000 Q3: 50000 Q4: 0 Justification: Storage requirements: 1 TB Thank You, The LCRC Accounts System

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