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

[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 07 Jul '17

07 Jul '17

Hello, A change in allocation has been requested: Requester: botana (Antia Sanchez Botana) Project: Materials_Genome_SCs Title: Materials Genome Approach for Discovery of HTS Description: We intend to create a framework for designing novel superconductors combining first principles electronic-structure tools, materials databases, and evolutionary algorithms, capable of exploring large configurational spaces. We will continue applying this framework to transition metal nitrochlorides (TNCl (T= Ti, Zr, Hf)) and layered nickelates. We will use different doping mechanisms and atomic substitutions to design novel compositions. We will intensively use DFT codes such as VASP, WIEN2k and Quantum Espresso as well as crystal structure prediction methods that merge ab initio total energy calculations and a specific evolutionary algorithm like USPEX. Jobs requesting up to 10 nodes will be launched for a typical DFT-based calculation. Current: undetermined amount Justification: Requested: 100000 A specific reason has been given: I am currently running high priority calculations that need to be performed in the biggpu nodes given the scratch storage on the rest of the nodes of 15gb that is not enough for these (large files output of 50gb are produced). As a consequence, I am being charged twice and hence already consumed half of my allocation for the current quarter in only one week. 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: eic
by Roberts, John E. 30 Jun '17

30 Jun '17

This project has been created. -- John Roberts Argonne National Laboratory CELS Systems jeroberts(a)anl.gov On 6/27/17, 7:28 PM, "allocations-admins on behalf of Bair, Raymond A." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of rbair(a)anl.gov> wrote: This looks fine. Recommend we approve 50K for Q3 and 100K for Q4. ----------------------------------------- Ray Bair Argonne National Laboratory and the University of Chicago On 6/27/17, 5:34 PM, "allocations-admins on behalf of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov on behalf of accounts(a)lcrc.anl.gov> wrote: Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: Whitney Armstrong Applicant's institution: ANL Applicant's division: PHY Project Name: eic Project title: EIC Simulations Associated funding: ANL LDRD Other Systems: Science: We will be running detector simulations for the EIC. This will include running Monte Carlo event generators, running full detector (Geant4) simulations, and reconstructing the simulated data. The goal is to help guild the design and construction of the Electron Ion Collider and develop a new Argonne-led detector concept. Project description: We will run a variety of event generators. The main detector simulation will be Geant4 based. The reconstruction chain will have many interchangeable pieces and will be under active development. We will be using the blues and bebop systems. We will build and run ROOT (root.cern.ch), Geant4 (geant4.cern.ch), and many other interconnected libraries. The current code base is not currently tuned for HPC, mostly because the limitations of the Blue Gene to running the software needed. With the intel based machines, we can run the full software stack, however, we will need to work on maximizing the efficiency. This will be the primary focus of our initial work. Initially most of the jobs will be single core jobs but we plan on exploiting the parallelism and concurrency available in the hardware and software. Industry partnership: Project URL: Requested allocation: 150000 Q1: 0 Q2: 0 Q3: 50000 Q4: 100000 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 _______________________________________________ allocations-admins mailing list allocations-admins(a)lcrc.anl.gov https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins _______________________________________________ allocations-admins mailing list allocations-admins(a)lcrc.anl.gov https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Request: ibr2
by Roberts, John E. 30 Jun '17

30 Jun '17

This project has been created. -- John Roberts Argonne National Laboratory CELS Systems jeroberts(a)anl.gov From: allocations-admins <allocations-admins-bounces(a)lcrc.anl.gov> on behalf of "Aithal, Shashikant M." <aithal(a)cels.anl.gov> Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Date: Wednesday, June 28, 2017 at 10:51 AM To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Subject: Re: [allocations-admins] [LCRC Accounts] Project Request: ibr2 Please grant 150K core-hours for Q4 for this project. Thanks, Shashi ________________________________ From: allocations-admins <allocations-admins-bounces(a)lcrc.anl.gov> on behalf of accounts(a)lcrc.anl.gov <accounts(a)lcrc.anl.gov> Sent: Tuesday, June 27, 2017 4:47 PM To: allocations-admins(a)lcrc.anl.gov Subject: [allocations-admins] [LCRC Accounts] Project Request: ibr2 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: alberto talamo Applicant's institution: ANL Applicant's division: NE Project Name: ibr2 Project title: IBR-2M Transient Associated funding: NNSA M3 Other Systems: eddy cluster of NE Science: The transient of the IBR-2M research reactor of Russia will be simulated using the Serpent and OpenFOAM software and the simulations results will be compared with the experimental data. At present, no neutronics software can model the IBR-2M transient because the reactor is moderated by two reflectors rotating, in opposite directions, very rapidly and this invalidates the point kinetics equations that are inside the computer programs used in nuclear engineering. The precursor-based delayed neutron emission model, unique of the Serpent software, does not rely on the point kinetics equations and can successfully model the IBR-2M transient. Serpent is developed at VTT Technical Research Center of Finland. During the transient, the reactor changes from subcritical to supercritical and delivers a peak power of 1,850 MW. Serpent simulations will model the rotation of the two movable reflectors and the thermal feedback from the power excursion of the IBR-2M reactor will be modeled using the OpenFOAM CFD software developed at Argonne National Laboratory. The IBR-2M reactor uses high enriched plutonium fuel, has a fast neutron spectrum, and is cooled by sodium. Argonne National Laboratory has an outstanding record in the design and modeling of sodium cooled nuclear reactors. Project description: The IBR-2M research reactor is located in Dubna (Russia) and has been in operation since the end of 2011. The facility mainly consists of a sodium-cooled pulsed nuclear reactor loading high-enriched plutonium fuel. Two reflectors, that rotate in opposite directions generate, for about 200 ms, a neutron pulse and change the reactor configuration from deep subcritical to supercritical. Supercriticality is reached when both nickel reflectors are aligned with the fuel zone. The blades of the two rotating reflectors are made of nickel alloy; the main rotating reflector blade has two rounded rectangle holes, whereas the auxiliary rotating reflector blade has just one rounded rectangular hole. The nickel blades are attached to steel blade-holders. In the fuel rods zone, the fuel assembly has hexagonal shape and contains 7 fuel rods and 6 steel displacers. The average thermal power during the pulse repetition period is 2 MWth; the peak thermal power is 1830 MWth. The previous number reduces to 0.16 MWth when the reflectors are not aligned with the fuel. The IBR-2M reactor includes: the core (containing the fuel rods and the fuel assemblies), the vessel, the stationary and rotating reflectors, the control rods in the stationary reflector, the cooling system of the stationary and rotating reflectors, and the shielding. The facility is used for experiments in many branches of physics, including: condensed matter, biology, chemistry, and material science. The IBR-2M reactor has been modeled using the Serpent software (written in C laguage and developed at VTT Finland) at Argonne National Laboratory using stereolithography (STL) geometry with unstructured meshes. In the STL geometry representation, volumes are defined by the union of triangular surfaces (facets). When SERPENT uses the STL geometry, it defines a regular lattice of cells superimposed to the STL geometry and starts a ray-tracing procedure from the triangular surfaces. This ray-tracing procedure defines the volume that a neutron enters after crossing a triangular facet and is referred to as adaptive search mesh. The adaptive search mesh algorithm of SERPENT attaches to each STL facet a list of the intersected regular lattice cells. The latter define a rectangular bounding box containing the minimum and maximum values of the three vertices of the triangular facets. The adaptive search mesh algorithm for the STL geometry has been introduced in the Serpent software to reduce the computing time. The rotating reflector blades move so fast that point kinetics equations fail to accurately model the power transient. The Serpent software does not use point kinetics equations, it relies on the precursor-based delayed neutrons emission model, and can accurately describe the power transient. The objective of this project is modeling the IBR-2M transient by the Serpent software and including the thermal-hydraulic feedback by the OpenFOAM software. The milestones of the project are the following: 1. perform the IBR-2M Serpent simulation of the power transient without any thermahydraulics feedback; 2. achieving a strong scalability for the simulations at point 1; 3. repeating the IBR-2M analyses with the inclusion of the thermalhydraulics feedback from OpenFOAM simulations. The simulation of the IBR-2M research reactor transient will be accomplished by the following team: â€¢ Dr. Alberto Talamo (ANL USA) will be responsible for the project coordination, the geometry modeling of the IBR-2M research reactor, and the Serpent simulations. â€¢ Dr. Jaakko LeppÃ¤nen (VTT Finland) is the head of the Serpent development team, he will provide the support to efficiently run the Serpent software program and act as consultant for the Serpent simulations. â€¢ Dr. Ville Valtavirta (VTT Finland) has written the moving geometry and thermal feedback subroutines of the Serpent software, he will provide the support to efficiently run the Serpent software program and act as consultant for the Serpent simulations. â€¢ Dr. Yousry Gohar (ANL USA) is Argonne National Laboratory fellow, he has more than 40 years experience in nuclear engineering and will act as advisor for accomplishing high fidelity simulations. The only member of the team who will access the Blues cluster is Dr. Alberto Talamo. Industry partnership: Project URL: http://flnph.jinr.ru/en/facilities/ibr-2 IBR-2<http://flnph.jinr.ru/en/facilities/ibr-2> flnph.jinr.ru The IBR-2 reactor hall. Virtual excursion on the complex of spectrometers of the IBR-2 pulsed reactor. The IBR-2 reactor with its unique technical approach produces ... Requested allocation: 980000 Q1: 0 Q2: 0 Q3: 490000 Q4: 490000 Justification: A static simulation (no transient) of the IBR-2M reactor takes 2 days using 32 cores of the eddy cluster of the NE division. 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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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by qiaob 28 Jun '17

28 Jun '17

Dear John, Thanks a lot for the prompt assistance! best regards, Baofu On 06/28/2017 11:54 AM, Roberts, John E. wrote: > Hi, > > This time has been added and is active starting right now. > > Thanks. > -- > John Roberts > Argonne National Laboratory > CELS Systems > jeroberts(a)anl.gov > > On 6/28/17, 11:21 AM, "allocations-admins on behalf of qiaob" <allocations-admins-bounces(a)lcrc.anl.gov on behalf of qiaob(a)anl.gov> wrote: > > Dear Ray, > > Yes. I need another 150,000 core hours for Q4. Thanks a lot! > > PS: I just submitted a very short simulation. The system complained that > my allocation is negative now. > > regards, > > Baofu > > > On 06/28/2017 11:09 AM, Bair, Raymond A. wrote: > > Dear Baofu, > > > > There are only 3 days left in the current quarter, and a new DMDOHEMA_1 allocation will start July 1. That will add 50,000 core hours on July 1. Is what you need another 150,000 hours for Q4? > > > > Regards, > > > > Ray > > > > ----------------------------------------- > > Ray Bair > > > > Argonne National Laboratory > > > > and the University of Chicago > > > > > > > > On 6/28/17, 11:00 AM, "allocations-admins on behalf of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov on behalf of accounts(a)lcrc.anl.gov> wrote: > > > > Hello, > > > > A change in allocation has been requested: > > > > Requester: qiaobf (Baofu Qiao) > > Project: DMDOHEMA_1 > > Title: Metal Ion Transport through Nano-Structured Lipophilic Systems: Atomistic MD Simulations > > Description: In the last one year, large-scale atomistic molecular dynamics (MD) simulations were performed using the LCRC cluster. In the simulations, we were aiming to couple computer simulations with synchrotron X-ray scattering technique to understand the aggregation behaviors of lanthanide metal-bearing systems. These systems root their significant role in the refinery of lanthanide metals using the solvent extraction technique. We have shown the large-scale MD simulations are able to reproduce the X-ray scattering data (e.g., SAXS). Consequently, the experimental structural feature could be inferred from the simulation structures. Moreover, the energetics which drive the metal transport from aqueous phase to organic phase have been explained. We have published two papers, and submitted one paper. We are currently preparing some manuscripts, which will be submitted soon. Detailed discussion have been provided in the progress report. > > In the coming facial year, we are aiming to study two projects. In the first project, we are planning to study the interfacial behavior of alcohol at water-organic interface. The role of water-organic interface for the metal separations in the solvent extraction process is still unknown to us. In the present project, we are studying a simple model system of alcohol/water/organic biphasic solution. We are aiming to study the surface activity of alcohol molecules at water-organic interface. Alcohol molecular was sometimes used as co-extractant to enhance the transport kinetics of metal from aqueous phase to organic phase. In our preliminary simulations using the classical pairwise CGenFF force field, the aggregation of alcohol was observed to form a monolayer at the water-dodecane biphasic solution. More interestingly, a second layer of alcohol is also observed in some systems, even though it is relatively very weak. This suggests that the alcohols are preorganized into > an asy > > mmetric bilayer at the water-organic interface, which might explain the elevated extraction kinetics of metal transport across the interface. Such an asymmetric bilayer has never been reported to the best of our knowledge. In the coming facial year, we are aiming to run MD simulations using polarizable force field. These polarizable force field simulations will be used to double check the influences of the simulations force field. > > In these project, polarizable molecular dynamics (MD) simulations will be performed using the Drude force field. Drude force field has been well developed for simple systems as in the present project. We will run the simulations using the NAMD simulation package. The NAMD package supports Drude force field, and scales well up to thousands of CPUs. > > High impact publications are expected based on the novel finding, and its significance in both the fundamental research and technical application. > > In the second project, we are aiming to continue our existing project to study the surface feature of metallate (platinum group metal). In collaboration with the SFG experiments led by Dr. Ahmet Uysal (Assistant Chemist at CSE), we are aiming to study the surface aggregation feature of different metallate (i.e, PtCl62- and PdCl42-), and understand their roles of in metallate separation. We have obtained some results. And Some more simulations are planned to complete the project. Some papers are expected when appropriate. > > Current: undetermined amount > > Justification: Note that this account (DMDOHEMA_1) was very recently granted 200,000 CPU hours. Therefore, I am not asking for the allocation for the first two quarters. > > > > Requested: 200000 > > > > A specific reason has been given: > > Dear Sir/Madam, > > > > Could you please provide some amount of allocation time for my account? Thanks. > > > > My simulations have not been converged yet. For instance, in the simulation where I am aiming to study the aggregation of surfactant in the presence of trivalent metal ions. After 200ns simulation, the surfactants are forming one large aggregate and some small aggregates. I am extending the simulations to carefully check the convergence of the aggregations. Thanks a lot! > > regards, > > Baofu > > > > > > > > This needs to be approved and the final allocation amount decided upon. > > > > Thank You, > > The LCRC Accounts System > > _______________________________________________ > > allocations-admins mailing list > > allocations-admins(a)lcrc.anl.gov > > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > > > > > > > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > >

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Roberts, John E. 28 Jun '17

28 Jun '17

Hi, This time has been added and is active starting right now. Thanks. -- John Roberts Argonne National Laboratory CELS Systems jeroberts(a)anl.gov On 6/28/17, 11:21 AM, "allocations-admins on behalf of qiaob" <allocations-admins-bounces(a)lcrc.anl.gov on behalf of qiaob(a)anl.gov> wrote: Dear Ray, Yes. I need another 150,000 core hours for Q4. Thanks a lot! PS: I just submitted a very short simulation. The system complained that my allocation is negative now. regards, Baofu On 06/28/2017 11:09 AM, Bair, Raymond A. wrote: > Dear Baofu, > > There are only 3 days left in the current quarter, and a new DMDOHEMA_1 allocation will start July 1. That will add 50,000 core hours on July 1. Is what you need another 150,000 hours for Q4? > > Regards, > > Ray > > ----------------------------------------- > Ray Bair > > Argonne National Laboratory > > and the University of Chicago > > > > On 6/28/17, 11:00 AM, "allocations-admins on behalf of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov on behalf of accounts(a)lcrc.anl.gov> wrote: > > Hello, > > A change in allocation has been requested: > > Requester: qiaobf (Baofu Qiao) > Project: DMDOHEMA_1 > Title: Metal Ion Transport through Nano-Structured Lipophilic Systems: Atomistic MD Simulations > Description: In the last one year, large-scale atomistic molecular dynamics (MD) simulations were performed using the LCRC cluster. In the simulations, we were aiming to couple computer simulations with synchrotron X-ray scattering technique to understand the aggregation behaviors of lanthanide metal-bearing systems. These systems root their significant role in the refinery of lanthanide metals using the solvent extraction technique. We have shown the large-scale MD simulations are able to reproduce the X-ray scattering data (e.g., SAXS). Consequently, the experimental structural feature could be inferred from the simulation structures. Moreover, the energetics which drive the metal transport from aqueous phase to organic phase have been explained. We have published two papers, and submitted one paper. We are currently preparing some manuscripts, which will be submitted soon. Detailed discussion have been provided in the progress report. > In the coming facial year, we are aiming to study two projects. In the first project, we are planning to study the interfacial behavior of alcohol at water-organic interface. The role of water-organic interface for the metal separations in the solvent extraction process is still unknown to us. In the present project, we are studying a simple model system of alcohol/water/organic biphasic solution. We are aiming to study the surface activity of alcohol molecules at water-organic interface. Alcohol molecular was sometimes used as co-extractant to enhance the transport kinetics of metal from aqueous phase to organic phase. In our preliminary simulations using the classical pairwise CGenFF force field, the aggregation of alcohol was observed to form a monolayer at the water-dodecane biphasic solution. More interestingly, a second layer of alcohol is also observed in some systems, even though it is relatively very weak. This suggests that the alcohols are preorganized into an asy > mmetric bilayer at the water-organic interface, which might explain the elevated extraction kinetics of metal transport across the interface. Such an asymmetric bilayer has never been reported to the best of our knowledge. In the coming facial year, we are aiming to run MD simulations using polarizable force field. These polarizable force field simulations will be used to double check the influences of the simulations force field. > In these project, polarizable molecular dynamics (MD) simulations will be performed using the Drude force field. Drude force field has been well developed for simple systems as in the present project. We will run the simulations using the NAMD simulation package. The NAMD package supports Drude force field, and scales well up to thousands of CPUs. > High impact publications are expected based on the novel finding, and its significance in both the fundamental research and technical application. > In the second project, we are aiming to continue our existing project to study the surface feature of metallate (platinum group metal). In collaboration with the SFG experiments led by Dr. Ahmet Uysal (Assistant Chemist at CSE), we are aiming to study the surface aggregation feature of different metallate (i.e, PtCl62- and PdCl42-), and understand their roles of in metallate separation. We have obtained some results. And Some more simulations are planned to complete the project. Some papers are expected when appropriate. > Current: undetermined amount > Justification: Note that this account (DMDOHEMA_1) was very recently granted 200,000 CPU hours. Therefore, I am not asking for the allocation for the first two quarters. > > Requested: 200000 > > A specific reason has been given: > Dear Sir/Madam, > > Could you please provide some amount of allocation time for my account? Thanks. > > My simulations have not been converged yet. For instance, in the simulation where I am aiming to study the aggregation of surfactant in the presence of trivalent metal ions. After 200ns simulation, the surfactants are forming one large aggregate and some small aggregates. I am extending the simulations to carefully check the convergence of the aggregations. Thanks a lot! > regards, > Baofu > > > > This needs to be approved and the final allocation amount decided upon. > > Thank You, > The LCRC Accounts System > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > > _______________________________________________ allocations-admins mailing list allocations-admins(a)lcrc.anl.gov https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 28 Jun '17

28 Jun '17

Let’s add 150K to DMDOHEMA_1 for Q4, but also let him start using the time now. Ray ----------------------------------------- Ray Bair Argonne National Laboratory and the University of Chicago On 6/28/17, 11:21 AM, "qiaob" <qiaob(a)anl.gov> wrote: Dear Ray, Yes. I need another 150,000 core hours for Q4. Thanks a lot! PS: I just submitted a very short simulation. The system complained that my allocation is negative now. regards, Baofu On 06/28/2017 11:09 AM, Bair, Raymond A. wrote: > Dear Baofu, > > There are only 3 days left in the current quarter, and a new DMDOHEMA_1 allocation will start July 1. That will add 50,000 core hours on July 1. Is what you need another 150,000 hours for Q4? > > Regards, > > Ray > > ----------------------------------------- > Ray Bair > > Argonne National Laboratory > > and the University of Chicago > > > > On 6/28/17, 11:00 AM, "allocations-admins on behalf of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov on behalf of accounts(a)lcrc.anl.gov> wrote: > > Hello, > > A change in allocation has been requested: > > Requester: qiaobf (Baofu Qiao) > Project: DMDOHEMA_1 > Title: Metal Ion Transport through Nano-Structured Lipophilic Systems: Atomistic MD Simulations > Description: In the last one year, large-scale atomistic molecular dynamics (MD) simulations were performed using the LCRC cluster. In the simulations, we were aiming to couple computer simulations with synchrotron X-ray scattering technique to understand the aggregation behaviors of lanthanide metal-bearing systems. These systems root their significant role in the refinery of lanthanide metals using the solvent extraction technique. We have shown the large-scale MD simulations are able to reproduce the X-ray scattering data (e.g., SAXS). Consequently, the experimental structural feature could be inferred from the simulation structures. Moreover, the energetics which drive the metal transport from aqueous phase to organic phase have been explained. We have published two papers, and submitted one paper. We are currently preparing some manuscripts, which will be submitted soon. Detailed discussion have been provided in the progress report. > In the coming facial year, we are aiming to study two projects. In the first project, we are planning to study the interfacial behavior of alcohol at water-organic interface. The role of water-organic interface for the metal separations in the solvent extraction process is still unknown to us. In the present project, we are studying a simple model system of alcohol/water/organic biphasic solution. We are aiming to study the surface activity of alcohol molecules at water-organic interface. Alcohol molecular was sometimes used as co-extractant to enhance the transport kinetics of metal from aqueous phase to organic phase. In our preliminary simulations using the classical pairwise CGenFF force field, the aggregation of alcohol was observed to form a monolayer at the water-dodecane biphasic solution. More interestingly, a second layer of alcohol is also observed in some systems, even though it is relatively very weak. This suggests that the alcohols are preorganized into an asy > mmetric bilayer at the water-organic interface, which might explain the elevated extraction kinetics of metal transport across the interface. Such an asymmetric bilayer has never been reported to the best of our knowledge. In the coming facial year, we are aiming to run MD simulations using polarizable force field. These polarizable force field simulations will be used to double check the influences of the simulations force field. > In these project, polarizable molecular dynamics (MD) simulations will be performed using the Drude force field. Drude force field has been well developed for simple systems as in the present project. We will run the simulations using the NAMD simulation package. The NAMD package supports Drude force field, and scales well up to thousands of CPUs. > High impact publications are expected based on the novel finding, and its significance in both the fundamental research and technical application. > In the second project, we are aiming to continue our existing project to study the surface feature of metallate (platinum group metal). In collaboration with the SFG experiments led by Dr. Ahmet Uysal (Assistant Chemist at CSE), we are aiming to study the surface aggregation feature of different metallate (i.e, PtCl62- and PdCl42-), and understand their roles of in metallate separation. We have obtained some results. And Some more simulations are planned to complete the project. Some papers are expected when appropriate. > Current: undetermined amount > Justification: Note that this account (DMDOHEMA_1) was very recently granted 200,000 CPU hours. Therefore, I am not asking for the allocation for the first two quarters. > > Requested: 200000 > > A specific reason has been given: > Dear Sir/Madam, > > Could you please provide some amount of allocation time for my account? Thanks. > > My simulations have not been converged yet. For instance, in the simulation where I am aiming to study the aggregation of surfactant in the presence of trivalent metal ions. After 200ns simulation, the surfactants are forming one large aggregate and some small aggregates. I am extending the simulations to carefully check the convergence of the aggregations. Thanks a lot! > regards, > Baofu > > > > 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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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by qiaob 28 Jun '17

28 Jun '17

Dear Ray, Yes. I need another 150,000 core hours for Q4. Thanks a lot! PS: I just submitted a very short simulation. The system complained that my allocation is negative now. regards, Baofu On 06/28/2017 11:09 AM, Bair, Raymond A. wrote: > Dear Baofu, > > There are only 3 days left in the current quarter, and a new DMDOHEMA_1 allocation will start July 1. That will add 50,000 core hours on July 1. Is what you need another 150,000 hours for Q4? > > Regards, > > Ray > > ----------------------------------------- > Ray Bair > > Argonne National Laboratory > > and the University of Chicago > > > > On 6/28/17, 11:00 AM, "allocations-admins on behalf of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov on behalf of accounts(a)lcrc.anl.gov> wrote: > > Hello, > > A change in allocation has been requested: > > Requester: qiaobf (Baofu Qiao) > Project: DMDOHEMA_1 > Title: Metal Ion Transport through Nano-Structured Lipophilic Systems: Atomistic MD Simulations > Description: In the last one year, large-scale atomistic molecular dynamics (MD) simulations were performed using the LCRC cluster. In the simulations, we were aiming to couple computer simulations with synchrotron X-ray scattering technique to understand the aggregation behaviors of lanthanide metal-bearing systems. These systems root their significant role in the refinery of lanthanide metals using the solvent extraction technique. We have shown the large-scale MD simulations are able to reproduce the X-ray scattering data (e.g., SAXS). Consequently, the experimental structural feature could be inferred from the simulation structures. Moreover, the energetics which drive the metal transport from aqueous phase to organic phase have been explained. We have published two papers, and submitted one paper. We are currently preparing some manuscripts, which will be submitted soon. Detailed discussion have been provided in the progress report. > In the coming facial year, we are aiming to study two projects. In the first project, we are planning to study the interfacial behavior of alcohol at water-organic interface. The role of water-organic interface for the metal separations in the solvent extraction process is still unknown to us. In the present project, we are studying a simple model system of alcohol/water/organic biphasic solution. We are aiming to study the surface activity of alcohol molecules at water-organic interface. Alcohol molecular was sometimes used as co-extractant to enhance the transport kinetics of metal from aqueous phase to organic phase. In our preliminary simulations using the classical pairwise CGenFF force field, the aggregation of alcohol was observed to form a monolayer at the water-dodecane biphasic solution. More interestingly, a second layer of alcohol is also observed in some systems, even though it is relatively very weak. This suggests that the alcohols are preorganized into an asy > mmetric bilayer at the water-organic interface, which might explain the elevated extraction kinetics of metal transport across the interface. Such an asymmetric bilayer has never been reported to the best of our knowledge. In the coming facial year, we are aiming to run MD simulations using polarizable force field. These polarizable force field simulations will be used to double check the influences of the simulations force field. > In these project, polarizable molecular dynamics (MD) simulations will be performed using the Drude force field. Drude force field has been well developed for simple systems as in the present project. We will run the simulations using the NAMD simulation package. The NAMD package supports Drude force field, and scales well up to thousands of CPUs. > High impact publications are expected based on the novel finding, and its significance in both the fundamental research and technical application. > In the second project, we are aiming to continue our existing project to study the surface feature of metallate (platinum group metal). In collaboration with the SFG experiments led by Dr. Ahmet Uysal (Assistant Chemist at CSE), we are aiming to study the surface aggregation feature of different metallate (i.e, PtCl62- and PdCl42-), and understand their roles of in metallate separation. We have obtained some results. And Some more simulations are planned to complete the project. Some papers are expected when appropriate. > Current: undetermined amount > Justification: Note that this account (DMDOHEMA_1) was very recently granted 200,000 CPU hours. Therefore, I am not asking for the allocation for the first two quarters. > > Requested: 200000 > > A specific reason has been given: > Dear Sir/Madam, > > Could you please provide some amount of allocation time for my account? Thanks. > > My simulations have not been converged yet. For instance, in the simulation where I am aiming to study the aggregation of surfactant in the presence of trivalent metal ions. After 200ns simulation, the surfactants are forming one large aggregate and some small aggregates. I am extending the simulations to carefully check the convergence of the aggregations. Thanks a lot! > regards, > Baofu > > > > 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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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 28 Jun '17

28 Jun '17

Dear Baofu, There are only 3 days left in the current quarter, and a new DMDOHEMA_1 allocation will start July 1. That will add 50,000 core hours on July 1. Is what you need another 150,000 hours for Q4? Regards, Ray ----------------------------------------- Ray Bair Argonne National Laboratory and the University of Chicago On 6/28/17, 11:00 AM, "allocations-admins on behalf of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov on behalf of accounts(a)lcrc.anl.gov> wrote: Hello, A change in allocation has been requested: Requester: qiaobf (Baofu Qiao) Project: DMDOHEMA_1 Title: Metal Ion Transport through Nano-Structured Lipophilic Systems: Atomistic MD Simulations Description: In the last one year, large-scale atomistic molecular dynamics (MD) simulations were performed using the LCRC cluster. In the simulations, we were aiming to couple computer simulations with synchrotron X-ray scattering technique to understand the aggregation behaviors of lanthanide metal-bearing systems. These systems root their significant role in the refinery of lanthanide metals using the solvent extraction technique. We have shown the large-scale MD simulations are able to reproduce the X-ray scattering data (e.g., SAXS). Consequently, the experimental structural feature could be inferred from the simulation structures. Moreover, the energetics which drive the metal transport from aqueous phase to organic phase have been explained. We have published two papers, and submitted one paper. We are currently preparing some manuscripts, which will be submitted soon. Detailed discussion have been provided in the progress report. In the coming facial year, we are aiming to study two projects. In the first project, we are planning to study the interfacial behavior of alcohol at water-organic interface. The role of water-organic interface for the metal separations in the solvent extraction process is still unknown to us. In the present project, we are studying a simple model system of alcohol/water/organic biphasic solution. We are aiming to study the surface activity of alcohol molecules at water-organic interface. Alcohol molecular was sometimes used as co-extractant to enhance the transport kinetics of metal from aqueous phase to organic phase. In our preliminary simulations using the classical pairwise CGenFF force field, the aggregation of alcohol was observed to form a monolayer at the water-dodecane biphasic solution. More interestingly, a second layer of alcohol is also observed in some systems, even though it is relatively very weak. This suggests that the alcohols are preorganized into an asy mmetric bilayer at the water-organic interface, which might explain the elevated extraction kinetics of metal transport across the interface. Such an asymmetric bilayer has never been reported to the best of our knowledge. In the coming facial year, we are aiming to run MD simulations using polarizable force field. These polarizable force field simulations will be used to double check the influences of the simulations force field. In these project, polarizable molecular dynamics (MD) simulations will be performed using the Drude force field. Drude force field has been well developed for simple systems as in the present project. We will run the simulations using the NAMD simulation package. The NAMD package supports Drude force field, and scales well up to thousands of CPUs. High impact publications are expected based on the novel finding, and its significance in both the fundamental research and technical application. In the second project, we are aiming to continue our existing project to study the surface feature of metallate (platinum group metal). In collaboration with the SFG experiments led by Dr. Ahmet Uysal (Assistant Chemist at CSE), we are aiming to study the surface aggregation feature of different metallate (i.e, PtCl62- and PdCl42-), and understand their roles of in metallate separation. We have obtained some results. And Some more simulations are planned to complete the project. Some papers are expected when appropriate. Current: undetermined amount Justification: Note that this account (DMDOHEMA_1) was very recently granted 200,000 CPU hours. Therefore, I am not asking for the allocation for the first two quarters. Requested: 200000 A specific reason has been given: Dear Sir/Madam, Could you please provide some amount of allocation time for my account? Thanks. My simulations have not been converged yet. For instance, in the simulation where I am aiming to study the aggregation of surfactant in the presence of trivalent metal ions. After 200ns simulation, the surfactants are forming one large aggregate and some small aggregates. I am extending the simulations to carefully check the convergence of the aggregations. Thanks a lot! regards, Baofu 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 28 Jun '17

28 Jun '17

Hello, A change in allocation has been requested: Requester: qiaobf (Baofu Qiao) Project: DMDOHEMA_1 Title: Metal Ion Transport through Nano-Structured Lipophilic Systems: Atomistic MD Simulations Description: In the last one year, large-scale atomistic molecular dynamics (MD) simulations were performed using the LCRC cluster. In the simulations, we were aiming to couple computer simulations with synchrotron X-ray scattering technique to understand the aggregation behaviors of lanthanide metal-bearing systems. These systems root their significant role in the refinery of lanthanide metals using the solvent extraction technique. We have shown the large-scale MD simulations are able to reproduce the X-ray scattering data (e.g., SAXS). Consequently, the experimental structural feature could be inferred from the simulation structures. Moreover, the energetics which drive the metal transport from aqueous phase to organic phase have been explained. We have published two papers, and submitted one paper. We are currently preparing some manuscripts, which will be submitted soon. Detailed discussion have been provided in the progress report. In the coming facial year, we are aiming to study two projects. In the first project, we are planning to study the interfacial behavior of alcohol at water-organic interface. The role of water-organic interface for the metal separations in the solvent extraction process is still unknown to us. In the present project, we are studying a simple model system of alcohol/water/organic biphasic solution. We are aiming to study the surface activity of alcohol molecules at water-organic interface. Alcohol molecular was sometimes used as co-extractant to enhance the transport kinetics of metal from aqueous phase to organic phase. In our preliminary simulations using the classical pairwise CGenFF force field, the aggregation of alcohol was observed to form a monolayer at the water-dodecane biphasic solution. More interestingly, a second layer of alcohol is also observed in some systems, even though it is relatively very weak. This suggests that the alcohols are preorganized into an asy mmetric bilayer at the water-organic interface, which might explain the elevated extraction kinetics of metal transport across the interface. Such an asymmetric bilayer has never been reported to the best of our knowledge. In the coming facial year, we are aiming to run MD simulations using polarizable force field. These polarizable force field simulations will be used to double check the influences of the simulations force field. In these project, polarizable molecular dynamics (MD) simulations will be performed using the Drude force field. Drude force field has been well developed for simple systems as in the present project. We will run the simulations using the NAMD simulation package. The NAMD package supports Drude force field, and scales well up to thousands of CPUs. High impact publications are expected based on the novel finding, and its significance in both the fundamental research and technical application. In the second project, we are aiming to continue our existing project to study the surface feature of metallate (platinum group metal). In collaboration with the SFG experiments led by Dr. Ahmet Uysal (Assistant Chemist at CSE), we are aiming to study the surface aggregation feature of different metallate (i.e, PtCl62- and PdCl42-), and understand their roles of in metallate separation. We have obtained some results. And Some more simulations are planned to complete the project. Some papers are expected when appropriate. Current: undetermined amount Justification: Note that this account (DMDOHEMA_1) was very recently granted 200,000 CPU hours. Therefore, I am not asking for the allocation for the first two quarters. Requested: 200000 A specific reason has been given: Dear Sir/Madam, Could you please provide some amount of allocation time for my account? Thanks. My simulations have not been converged yet. For instance, in the simulation where I am aiming to study the aggregation of surfactant in the presence of trivalent metal ions. After 200ns simulation, the surfactants are forming one large aggregate and some small aggregates. I am extending the simulations to carefully check the convergence of the aggregations. Thanks a lot! regards, Baofu 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: ibr2
by Aithal, Shashikant M. 28 Jun '17

28 Jun '17

Please grant 150K core-hours for Q4 for this project. Thanks, Shashi ________________________________ From: allocations-admins <allocations-admins-bounces(a)lcrc.anl.gov> on behalf of accounts(a)lcrc.anl.gov <accounts(a)lcrc.anl.gov> Sent: Tuesday, June 27, 2017 4:47 PM To: allocations-admins(a)lcrc.anl.gov Subject: [allocations-admins] [LCRC Accounts] Project Request: ibr2 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: alberto talamo Applicant's institution: ANL Applicant's division: NE Project Name: ibr2 Project title: IBR-2M Transient Associated funding: NNSA M3 Other Systems: eddy cluster of NE Science: The transient of the IBR-2M research reactor of Russia will be simulated using the Serpent and OpenFOAM software and the simulations results will be compared with the experimental data. At present, no neutronics software can model the IBR-2M transient because the reactor is moderated by two reflectors rotating, in opposite directions, very rapidly and this invalidates the point kinetics equations that are inside the computer programs used in nuclear engineering. The precursor-based delayed neutron emission model, unique of the Serpent software, does not rely on the point kinetics equations and can successfully model the IBR-2M transient. Serpent is developed at VTT Technical Research Center of Finland. During the transient, the reactor changes from subcritical to supercritical and delivers a peak power of 1,850 MW. Serpent simulations will model the rotation of the two movable reflectors and the thermal feedback from the power excursion of the IBR-2M reactor will be modeled using the OpenFOAM CFD software developed at Argonne National Laboratory. The IBR-2M reactor uses high enriched plutonium fuel, has a fast neutron spectrum, and is cooled by sodium. Argonne National Laboratory has an outstanding record in the design and modeling of sodium cooled nuclear reactors. Project description: The IBR-2M research reactor is located in Dubna (Russia) and has been in operation since the end of 2011. The facility mainly consists of a sodium-cooled pulsed nuclear reactor loading high-enriched plutonium fuel. Two reflectors, that rotate in opposite directions generate, for about 200 ms, a neutron pulse and change the reactor configuration from deep subcritical to supercritical. Supercriticality is reached when both nickel reflectors are aligned with the fuel zone. The blades of the two rotating reflectors are made of nickel alloy; the main rotating reflector blade has two rounded rectangle holes, whereas the auxiliary rotating reflector blade has just one rounded rectangular hole. The nickel blades are attached to steel blade-holders. In the fuel rods zone, the fuel assembly has hexagonal shape and contains 7 fuel rods and 6 steel displacers. The average thermal power during the pulse repetition period is 2 MWth; the peak thermal power is 1830 MWth. The previous number reduces to 0.16 MWth when the reflectors are not aligned with the fuel. The IBR-2M reactor includes: the core (containing the fuel rods and the fuel assemblies), the vessel, the stationary and rotating reflectors, the control rods in the stationary reflector, the cooling system of the stationary and rotating reflectors, and the shielding. The facility is used for experiments in many branches of physics, including: condensed matter, biology, chemistry, and material science. The IBR-2M reactor has been modeled using the Serpent software (written in C laguage and developed at VTT Finland) at Argonne National Laboratory using stereolithography (STL) geometry with unstructured meshes. In the STL geometry representation, volumes are defined by the union of triangular surfaces (facets). When SERPENT uses the STL geometry, it defines a regular lattice of cells superimposed to the STL geometry and starts a ray-tracing procedure from the triangular surfaces. This ray-tracing procedure defines the volume that a neutron enters after crossing a triangular facet and is referred to as adaptive search mesh. The adaptive search mesh algorithm of SERPENT attaches to each STL facet a list of the intersected regular lattice cells. The latter define a rectangular bounding box containing the minimum and maximum values of the three vertices of the triangular facets. The adaptive search mesh algorithm for the STL geometry has been introduced in the Serpent software to reduce the computing time. The rotating reflector blades move so fast that point kinetics equations fail to accurately model the power transient. The Serpent software does not use point kinetics equations, it relies on the precursor-based delayed neutrons emission model, and can accurately describe the power transient. The objective of this project is modeling the IBR-2M transient by the Serpent software and including the thermal-hydraulic feedback by the OpenFOAM software. The milestones of the project are the following: 1. perform the IBR-2M Serpent simulation of the power transient without any thermahydraulics feedback; 2. achieving a strong scalability for the simulations at point 1; 3. repeating the IBR-2M analyses with the inclusion of the thermalhydraulics feedback from OpenFOAM simulations. The simulation of the IBR-2M research reactor transient will be accomplished by the following team: â€¢ Dr. Alberto Talamo (ANL USA) will be responsible for the project coordination, the geometry modeling of the IBR-2M research reactor, and the Serpent simulations. â€¢ Dr. Jaakko LeppÃ¤nen (VTT Finland) is the head of the Serpent development team, he will provide the support to efficiently run the Serpent software program and act as consultant for the Serpent simulations. â€¢ Dr. Ville Valtavirta (VTT Finland) has written the moving geometry and thermal feedback subroutines of the Serpent software, he will provide the support to efficiently run the Serpent software program and act as consultant for the Serpent simulations. â€¢ Dr. Yousry Gohar (ANL USA) is Argonne National Laboratory fellow, he has more than 40 years experience in nuclear engineering and will act as advisor for accomplishing high fidelity simulations. The only member of the team who will access the Blues cluster is Dr. Alberto Talamo. Industry partnership: Project URL: http://flnph.jinr.ru/en/facilities/ibr-2 IBR-2<http://flnph.jinr.ru/en/facilities/ibr-2> flnph.jinr.ru The IBR-2 reactor hall. Virtual excursion on the complex of spectrometers of the IBR-2 pulsed reactor. The IBR-2 reactor with its unique technical approach produces ... Requested allocation: 980000 Q1: 0 Q2: 0 Q3: 490000 Q4: 490000 Justification: A static simulation (no transient) of the IBR-2M reactor takes 2 days using 32 cores of the eddy cluster of the NE division. 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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