Statistical Thermostats

Mitglied der Helmholtz-Gemeinschaft
Efcient Communication Schemes for Stochastic Thermostats in parallel MD Simulations

September 25, 2012 Felix Uhl
Parallel Stochastic Thermostats

Outline
A Short Introduction to Molecular Dynamics Thermostats

Why Thermostats? The Andersen Thermostat The Lowe-Andersen Thermostat
Implementation of the Lowe-Andersen Thermostat

The IBIsCO code The Current Lowe-Andersen Implementation The New Implementation of the Lowe-Andersen Thermostat More Ways to Parallelize the Lowe-Andersen Thermostat
September 25, 2012
Felix Uhl
Slide 2

Part I: A Short Introduction to Molecular Dynamics

A Short Introduction to Molecular Dynamics

Basic Theory
System of point like particles Coordinates: {r (t )}, momenta: p(t ) Newtons equations of motion: m d 2r i = dt 2 Ekin,i = i V (r )
i
Etot = Ekin + V ,
pi2 1 = mi vi2 , 2mi 2
V = V (r )
September 25, 2012
Felix Uhl
Slide 4
A Short Introduction to Molecular Dynamics

Numerical Solution of Hamiltons Equations of Motion
Solving equations of motion numerically via discretization Starting positions and velocities are given at time t = 0
1 2 3
r (t + t ) = r (t ) + v (t )t + v (t + t ) = v (t ) +
1 2m
1 2 2m F (t )t
F (t + t ) = V (r (t + t )) [F (t ) + F (t + t )] t If t < tmax then repeat
September 25, 2012
Felix Uhl
Slide 5

Part II: Thermostats
September 25, 2012
Felix Uhl
Thermostats
Why Thermostats?
TD: Ekin = CM: Ekin =
3 KB T 2 1 N
N i =1
1 mi v 2 i 2
3 1 KB T = 2 N
N i =1
1 mi v 2 i 2
Boltzmann distribution He at 298.15 K 0.00025 Probability density
Boltzmann Distribution
0.0002 0.00015 0.0001 5e-05 0 0 300 600 900 1200 1500 1800 Speed / (m/s)
A Boltzmann distribution corresponds to a specic temperature

September 25, 2012
Felix Uhl
Slide 7
Thermostats
Why Thermostats? NVE-Simulation
Give particles velocities according to Boltzmann distribution Guess starting positions
September 25, 2012
Felix Uhl
Slide 8
Thermostats

Evolution of Temperature
6 Temperature
2
100
200 Timesteps
300
400
September 25, 2012
Felix Uhl
Slide 8
Thermostats

Evolution of Temperature
6 Temperature
2
100
200 Timesteps
300
400
1 2
Optimize geometry with respect to the energy Add/subtract kinetic energy from the system
Felix Uhl Slide 8
September 25, 2012
Thermostats
The Andersen Thermostat
Simulation Cell with a Real and a Bath System y
Real system (grey) Bath system(red) Bath has xed temperature Collisions between real particles and bath particles adjust temperature in real system
0 0 x
Implementation
Randomly select particles up to a certain frequency. The velocity is replaced by a random velocity according to the Boltzmann distribution.
September 25, 2012 Felix Uhl Slide 9
Thermostats
The Lowe-Andersen Thermostat
v1 v2 1 2
September 25, 2012
Felix Uhl
Slide 10
Thermostats
v1 v2 1 v12,proj 2
Project v 1 v 2 on the connecting unit vector
September 25, 2012
Felix Uhl
Slide 10
Thermostats
v1 v2 1 v12,proj vnew 2
Project v 1 v 2 on the connecting unit vector Pick random new velocity from Boltzmann distribution
September 25, 2012
Felix Uhl
Slide 10
Thermostats
v1,new 1 v12,proj vnew v12,proj vnew v12,proj

v1 v2 2 v2,new
Project v 1 v 2 on the connecting unit vector Pick random new velocity from Boltzmann distribution Add/subtract difference of projected and chosen velocity to obtain new velocities
September 25, 2012
Felix Uhl
Slide 10
Thermostats
v1,new 1 v12,proj vnew v12,proj vnew v12,proj

v1 v2 2 v2,new
Project v 1 v 2 on the connecting unit vector Pick random new velocity from Boltzmann distribution Add/subtract difference of projected and chosen velocity to obtain new velocities
Advantage
Conserves linear and angular momentum due to pairwise correction
Thermostats
How to Correct the Velocities?
Usually one particle has more than one neighbour
Lowe-Andersen-1
Take already corrected velocity
Evolution of Temperature using LA1 10 8 Temperature
Lowe-Andersen-2
Take original velocity and add up changes
Evolution of Temperature using LA2 10 Temperature Freq = 0.1 Freq = 5.0 Freq = 50.0 Freq = 100.0
6 4 2 5000
Freq = 0.1 Freq = 5.0 Freq = 50.0 Freq = 100.0
8 6 4 2
6000 7000 Timesteps
8000
5000
6000 7000 Timesteps
8000
September 25, 2012
Felix Uhl
Slide 11

Part III: Implementation of the Lowe-Andersen Thermostat


The IBIsCO-Code It is Boltzmann Inversion Software for COarse Graining Simulations
IBIsCO
Code for coarse graining simulations Time propagation with Leap-Frog-Algorithm (Verlet-Family)
Boltzmann inversion is used to calculate the forces


The Current Lowe-Andersen Implementation
Prepare data for sending(velocities, coordinates, neighbourlist)
September 25, 2012
Felix Uhl
Slide 14

Prepare data for sending(velocities, coordinates, neighbourlist) Send data to master processor
September 25, 2012
Felix Uhl
Slide 14

Prepare data for sending(velocities, coordinates, neighbourlist) Send data to master processor Correct velocities on master processor
3
September 25, 2012
Felix Uhl
Slide 14

Prepare data for sending(velocities, coordinates, neighbourlist) Send data to master processor Correct velocities on master processor Send back velocities
3
September 25, 2012
Felix Uhl
Slide 14

Temperature / K
Prepare data for sending(velocities, coordinates, neighbourlist) Send data to master processor Correct velocities on master processor Send back velocities
Evolution of Temperature using the old Implementation 500 490 480 470 460 450 440 0 250 500 Timesteps 750 1000
3
September 25, 2012
Felix Uhl
Slide 14

The New Implementation of the Lowe-Andersen Thermostat
September 25, 2012
Felix Uhl
Slide 15

Correct velocity of pairs resident on processor
September 25, 2012
Felix Uhl
Slide 15

Correct velocity of pairs resident on processor Send remaining pairs to master processor
September 25, 2012
Felix Uhl
Slide 15

Correct velocity of pairs resident on processor Send remaining pairs to master processor Correct velocities over boundaries on master processor
September 25, 2012
Felix Uhl
Slide 15

Correct velocity of pairs resident on processor Send remaining pairs to master processor Correct velocities over boundaries on master processor Send back velocities
September 25, 2012
Felix Uhl
Slide 15

Correct velocity of pairs resident on processor Send remaining pairs to master processor Correct velocities over boundaries on master processor Send back velocities
Temperature / K
Evolution of Temperature using the new Implementation(red) 500 490 480 470 460 450 440 0 250 500 Timesteps 750 1000
September 25, 2012
Felix Uhl
Slide 15

Scaling of the two methods
160000 particles, 1000 timesteps

Scaling of the old Lowe-Andersen Implementation 1650 Time / s Time / s 8 27 # Processors 64 Scaling of the new Lowe-Andersen Implementation 250
1600
200
1550
150
1500
100 8 27 # Processors 64
#proc . 8 27 64
September 25, 2012
time(old)/s
time(new)/s
1588.771 1572.881 1550.005

Felix Uhl
263.700 115.830 108.446

Slide 16

More Ways to Implement the Lowe-Andersen Thermostat Efciently
One processor has 26 neighbours
September 25, 2012
Felix Uhl
Slide 17

One processor has 26 neighbours Send data to 13 neighbour cells Receive data from other 13 neighbour cells
September 25, 2012
Felix Uhl
Slide 17

One processor has 26 neighbours Send data to 13 neighbour cells Receive data from other 13 neighbour cells Partially LA2 method
4
September 25, 2012
Felix Uhl
Slide 17

One processor has 26 neighbours Send data to 13 neighbour cells Receive data from other 13 neighbour cells Partially LA2 method Equivalent to LA1, if sending and receiving to the 13 neighbours is performed step by step
Felix Uhl Slide 17
4
September 25, 2012
Thank you for your attention.
September 25, 2012
Felix Uhl
Slide 18

Statistical Thermostats

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Statistical Thermostats

Cargado por

Copyright:

Formatos disponibles

Mitglied der Helmholtz-Gemeinschaft

Efcient Communication Schemes for Stochastic Thermostats in parallel MD Simulations

Parallel Stochastic Thermostats

A Short Introduction to Molecular Dynamics Thermostats

Implementation of the Lowe-Andersen Thermostat

Mitglied der Helmholtz-Gemeinschaft

September 25, 2012

Parallel Stochastic Thermostats

Part I: A Short Introduction to Molecular Dynamics

A Short Introduction to Molecular Dynamics

Mitglied der Helmholtz-Gemeinschaft

pi2 1 = mi vi2 , 2mi 2

September 25, 2012

A Short Introduction to Molecular Dynamics

F (t + t ) = V (r (t + t )) [F (t ) + F (t + t )] t If t < tmax then repeat

September 25, 2012

Parallel Stochastic Thermostats

September 25, 2012

TD: Ekin = CM: Ekin =

Boltzmann distribution He at 298.15 K 0.00025 Probability density

A Boltzmann distribution corresponds to a specic temperature

Give particles velocities according to Boltzmann distribution Guess starting positions

Mitglied der Helmholtz-Gemeinschaft

September 25, 2012

Give particles velocities according to Boltzmann distribution Guess starting positions

September 25, 2012

Give particles velocities according to Boltzmann distribution Guess starting positions

September 25, 2012

Mitglied der Helmholtz-Gemeinschaft

Mitglied der Helmholtz-Gemeinschaft

September 25, 2012

Project v 1 v 2 on the connecting unit vector

Mitglied der Helmholtz-Gemeinschaft

September 25, 2012

Mitglied der Helmholtz-Gemeinschaft

September 25, 2012

v1,new 1 v12,proj vnew v12,proj vnew v12,proj

September 25, 2012

v1,new 1 v12,proj vnew v12,proj vnew v12,proj

Usually one particle has more than one neighbour

Freq = 0.1 Freq = 5.0 Freq = 50.0 Freq = 100.0

6000 7000 Timesteps

6000 7000 Timesteps

September 25, 2012

Parallel Stochastic Thermostats

Part III: Implementation of the Lowe-Andersen Thermostat

Implementation of the Lowe-Andersen Thermostat

Boltzmann inversion is used to calculate the forces

Implementation of the Lowe-Andersen Thermostat

Prepare data for sending(velocities, coordinates, neighbourlist)

Mitglied der Helmholtz-Gemeinschaft

September 25, 2012

Implementation of the Lowe-Andersen Thermostat

Mitglied der Helmholtz-Gemeinschaft

September 25, 2012

Implementation of the Lowe-Andersen Thermostat

September 25, 2012

Implementation of the Lowe-Andersen Thermostat

September 25, 2012

Implementation of the Lowe-Andersen Thermostat

September 25, 2012

Implementation of the Lowe-Andersen Thermostat

Mitglied der Helmholtz-Gemeinschaft