Reactive Molecular Dynamics Progress Report Mar 7 th

  • Slides: 41
Download presentation
Reactive Molecular Dynamics Progress Report Mar. 7 th 2008 Andrei. Smirnov, Jaggu Nanduri, and

Reactive Molecular Dynamics Progress Report Mar. 7 th 2008 Andrei. Smirnov, Jaggu Nanduri, and R. A. Carreno-Chavez Jaggu Nanduri

Objectives • To develop the capabilities of simulating 107 molecules and more on a

Objectives • To develop the capabilities of simulating 107 molecules and more on a workstation.

Progress • Segmentation algorithm implemented. • Chemical reactions between species implemented • Surface reactions

Progress • Segmentation algorithm implemented. • Chemical reactions between species implemented • Surface reactions between species and active surface sites implemented • Simulations of several million molecules on a single workstation have been conducted.

Interaction Acceleration Space segmentation scheme Enables to achieve near linear dependence of execution time

Interaction Acceleration Space segmentation scheme Enables to achieve near linear dependence of execution time on the number of molecules.

Looped Lined Lists Enable to avoid memory allocations and deallocations. Instead.

Looped Lined Lists Enable to avoid memory allocations and deallocations. Instead.

Looped Lined Lists Enable to avoid memory allocations and deallocations. Instead.

Looped Lined Lists Enable to avoid memory allocations and deallocations. Instead.

Looped Lined Lists Enable to avoid memory allocations and deallocations. Instead new links are

Looped Lined Lists Enable to avoid memory allocations and deallocations. Instead new links are created.

Looped Lined Lists Enable to avoid memory allocations and deallocations. Instead new links are

Looped Lined Lists Enable to avoid memory allocations and deallocations. Instead new links are created and old links are reassigned.

Looped Lined Lists Enable to avoid memory allocations and deallocations. Instead new links are

Looped Lined Lists Enable to avoid memory allocations and deallocations. Instead new links are created and old links are reassigned.

Looped Lined Lists Enables more efficient nested looping over neighboring particles.

Looped Lined Lists Enables more efficient nested looping over neighboring particles.

Looped Lined Lists Enables more efficient nested looping over neighboring particles.

Looped Lined Lists Enables more efficient nested looping over neighboring particles.

Looped Lined Lists Enables more efficient nested looping over neighboring particles.

Looped Lined Lists Enables more efficient nested looping over neighboring particles.

O 2 + H(s) Time: 2. 00 e-01 ns, Molecules: 117946, Temperature: 300 K

O 2 + H(s) Time: 2. 00 e-01 ns, Molecules: 117946, Temperature: 300 K Species: O 2: 100. 00%

O 2 + H(s) Time: 3. 00 e-01 ns, Molecules: 176550, Temperature: 300 K

O 2 + H(s) Time: 3. 00 e-01 ns, Molecules: 176550, Temperature: 300 K Species: O 2: 100. 00%

O 2 + H(s) Time: 4. 00 e-01 ns, Molecules: 235058, Temperature: 300 K

O 2 + H(s) Time: 4. 00 e-01 ns, Molecules: 235058, Temperature: 300 K Species: O 2: 100. 00%

O 2 + H(s) Time: 5. 00 e-01 ns, Molecules: 293696, Temperature: 300 K

O 2 + H(s) Time: 5. 00 e-01 ns, Molecules: 293696, Temperature: 300 K Species: O 2: 100. 00%

O 2 + H(s) Time: 6. 00 e-01 ns, Molecules: 352297, Temperature: 300 K

O 2 + H(s) Time: 6. 00 e-01 ns, Molecules: 352297, Temperature: 300 K Species: O 2: 100. 00%

O 2 + H(s) Time: 7. 00 e-01 ns, Molecules: 410841, Temperature: 300 K

O 2 + H(s) Time: 7. 00 e-01 ns, Molecules: 410841, Temperature: 300 K Species: O 2: 100. 00%

O 2 + H(s) Time: 8. 00 e-01 ns, Molecules: 469132, Temperature: 300 K

O 2 + H(s) Time: 8. 00 e-01 ns, Molecules: 469132, Temperature: 300 K Species: O 2: 100. 00%

O 2 + H(s) Time: 9. 00 e-01 ns, Molecules: 527563, Temperature: 301 K

O 2 + H(s) Time: 9. 00 e-01 ns, Molecules: 527563, Temperature: 301 K Species: O 2: 100. 00%

O 2 + H(s) Time: 1. 00 e-00 ns, Molecules: 585979, Temperature: 301 K

O 2 + H(s) Time: 1. 00 e-00 ns, Molecules: 585979, Temperature: 301 K Species: O 2: 100. 00%

O 2 + H(s) Time: 1. 10 e-00 ns, Molecules: 644366, Temperature: 301 K

O 2 + H(s) Time: 1. 10 e-00 ns, Molecules: 644366, Temperature: 301 K Species: O 2: 100. 00%

O 2 + H(s) Time: 1. 20 e-00 ns, Molecules: 702483, Temperature: 301 K

O 2 + H(s) Time: 1. 20 e-00 ns, Molecules: 702483, Temperature: 301 K Species: O 2: 100. 00%

O 2 + H(s) Time: 1. 30 e-00 ns, Molecules: 760778, Temperature: 301 K

O 2 + H(s) Time: 1. 30 e-00 ns, Molecules: 760778, Temperature: 301 K Species: O 2: 100. 00%

O 2 + H(s) Time: 1. 40 e-00 ns, Molecules: 819017, Temperature: 301 K

O 2 + H(s) Time: 1. 40 e-00 ns, Molecules: 819017, Temperature: 301 K Species: O 2: 100. 00%

O 2 + H(s) Time: 1. 50 e-00 ns, Molecules: 877058, Temperature: 301 K

O 2 + H(s) Time: 1. 50 e-00 ns, Molecules: 877058, Temperature: 301 K Species: O 2: 100. 00%

O 2 + H(s) Time: 1. 60 e-00 ns, Molecules: 935192, Temperature: 301 K

O 2 + H(s) Time: 1. 60 e-00 ns, Molecules: 935192, Temperature: 301 K Species: O 2: 100. 00%

O 2 + H(s) Time: 1. 70 e-00 ns, Molecules: 993331, Temperature: 301 K

O 2 + H(s) Time: 1. 70 e-00 ns, Molecules: 993331, Temperature: 301 K Species: O 2: 100. 00% HO 2: 0. 0001%

O 2 + H(s) Time: 1. 80 e-00 ns, Molecules: 1051165, Temperature: 301 K

O 2 + H(s) Time: 1. 80 e-00 ns, Molecules: 1051165, Temperature: 301 K Species: O: 0. 0001% O 2: 99. 9996% OH: 0. 0001% HO 2: 0. 0005%

O 2 + H(s) Time: 1. 90 e-00 ns, Molecules: 1109255, Temperature: 301 K

O 2 + H(s) Time: 1. 90 e-00 ns, Molecules: 1109255, Temperature: 301 K Species: O: 0. 0012% O 2: 99. 9971% OH: 0. 0011% HO 2: 0. 0009%

O 2 + H(s) Time: 2. 00 e-00 ns, Molecules: 1167072, Temperature: 301 K

O 2 + H(s) Time: 2. 00 e-00 ns, Molecules: 1167072, Temperature: 301 K Species: O: 0. 0021% O 2: 99. 9938% OH: 0. 0021% HO 2: 0. 0023%

O 2 + H(s) Time: 2. 10 e-00 ns, Molecules: 1224971, Temperature: 301 K

O 2 + H(s) Time: 2. 10 e-00 ns, Molecules: 1224971, Temperature: 301 K Species: O: 0. 0040% O 2: 99. 9888% OH: 0. 0040% HO 2: 0. 0035%

O 2 + H(s) Time: 2. 20 e-00 ns, Molecules: 1282836, Temperature: 301 K

O 2 + H(s) Time: 2. 20 e-00 ns, Molecules: 1282836, Temperature: 301 K Species: O: 0. 0067% O 2: 99. 9812% OH: 0. 0067% HO 2: 0. 0057%

O 2 + H(s) Time: 2. 30 e-00 ns, Molecules: 1340490, Temperature: 301 K

O 2 + H(s) Time: 2. 30 e-00 ns, Molecules: 1340490, Temperature: 301 K Species: O: 0. 0093% O 2: 99. 9729% OH: 0. 0093% HO 2: 0. 0087%

O 2 + H(s) Time: 2. 40 e-00 ns, Molecules: 1398206, Temperature: 301 K

O 2 + H(s) Time: 2. 40 e-00 ns, Molecules: 1398206, Temperature: 301 K Species: O: 0. 0147% O 2: 99. 9569% OH: 0. 0147% HO 2: 0. 0136%

O 2 + H(s) Time: 2. 50 e-00 ns, Molecules: 1513973, Temperature: 301 K

O 2 + H(s) Time: 2. 50 e-00 ns, Molecules: 1513973, Temperature: 301 K Species: O: 0. 0482% O 2: 99. 8585% OH: 0. 0482% HO 2: 0. 0453%

O 2 + H(s) Time: 2. 60 e-00 ns, Molecules: 1632640, Temperature: 300 K

O 2 + H(s) Time: 2. 60 e-00 ns, Molecules: 1632640, Temperature: 300 K Species: O: 0. 2868% O 2: 99. 1400% OH: 0. 2867% HO 2: 0. 2866%

O 2 + H(s) Time: 2. 60 e-00 ns, Molecules: 1671433, Temperature: 300 K

O 2 + H(s) Time: 2. 60 e-00 ns, Molecules: 1671433, Temperature: 300 K Species: O: 0. 3428% O 2: 98. 4403% OH: 0. 3568% HO 2: 0. 3668%

O 2 + H(s) Time: 2. 70 e-00 ns, Molecules: 1693223, Temperature: 300 K

O 2 + H(s) Time: 2. 70 e-00 ns, Molecules: 1693223, Temperature: 300 K Species: H 2: 0. 0001% O: 0. 4824% O 2: 98. 549% H 2 O: 0. 0001% OH: 0. 4821% HO 2: 0. 4864%

Chemical Reactions Bulk reactions Surface reactions

Chemical Reactions Bulk reactions Surface reactions

Conclusions • The efficiency bursting measures are working. • Tens of millions of particles

Conclusions • The efficiency bursting measures are working. • Tens of millions of particles can be accommodated on a single workstation. • Time of execution becomes one day for 10 M particles and 1000 time-steps. • Effect of interaction cutoff should be investigated.

Reactive Molecular Dynamics Progress Report Hassan Metin AktulgaReactive Molecular Dynamics Progress Report Hassan Metin Aktulga
Reactive Molecular Dynamics Progress Report Nov 2 ndReactive Molecular Dynamics Progress Report Nov 2 nd
Reactive Molecular Dynamics Progress Report Nov 9 2007Reactive Molecular Dynamics Progress Report Nov 9 2007
Molecular Dynamics Molecular dynamics MD is a formMolecular Dynamics Molecular dynamics MD is a form
Molecular Biophysics III dynamics Molecular Dynamics Simulations 011305Molecular Biophysics III dynamics Molecular Dynamics Simulations 011305
Molecular Dynamics Molecular dynamics Some random notes onMolecular Dynamics Molecular dynamics Some random notes on
Limitations of Molecular Dynamics What can Molecular DynamicsLimitations of Molecular Dynamics What can Molecular Dynamics
Molecular Dynamics Sauro Succi History Molecular Dynamics MDMolecular Dynamics Sauro Succi History Molecular Dynamics MD
Pu Re MD Purdue Reactive Molecular Dynamics SoftwarePu Re MD Purdue Reactive Molecular Dynamics Software
Pu Re MD Purdue Reactive Molecular Dynamics SoftwarePu Re MD Purdue Reactive Molecular Dynamics Software
Pu Re MD Purdue Reactive Molecular Dynamics ProgramPu Re MD Purdue Reactive Molecular Dynamics Program
Pu Re MD Purdue Reactive Molecular Dynamics PackagePu Re MD Purdue Reactive Molecular Dynamics Package
Reactive Molecular Dynamics Forcefield Optimization Reax Forcefield OptimizationReactive Molecular Dynamics Forcefield Optimization Reax Forcefield Optimization
Where do we stand Progress Progress Progress ProgressWhere do we stand Progress Progress Progress Progress
MAR BARII 1 MAR BARII VE KAPSAMI marMAR BARII 1 MAR BARII VE KAPSAMI mar
Recursos Martimos Mar Mar sonoro mar sem fundoRecursos Martimos Mar Mar sonoro mar sem fundo
Producciones El mar La mar El mar SloProducciones El mar La mar El mar Slo
MAR BARII MAR BARII NEDR mar mevzuatna veMAR BARII MAR BARII NEDR mar mevzuatna ve
MAR KANUNU mar Uygulama Yntemleri mar Uygulama YntemleriMAR KANUNU mar Uygulama Yntemleri mar Uygulama Yntemleri
REACTIVE ARTHRITIS Definition Reactive arthritis Re A refersREACTIVE ARTHRITIS Definition Reactive arthritis Re A refers
Reactive Powder Concrete Presented By Seminartopics info ReactiveReactive Powder Concrete Presented By Seminartopics info Reactive
Reactive Ion Etching Outline Reactive Ion Etching RIEReactive Ion Etching Outline Reactive Ion Etching RIE
Reactive and Explosive Materials An Introduction Reactive andReactive and Explosive Materials An Introduction Reactive and
RMW Workshop on Reactive Metal Processing Reactive MetalRMW Workshop on Reactive Metal Processing Reactive Metal