[ase-users] Parallelization of GPAW MD simulation

[Jens Jørgen Mortensen]

On Thu, 2011-04-28 at 09:00 +0200, Aleksander Dawid wrote:
> Hi ASE users
> 
> I am about to simulate simple 13-atoms argon cluster
> I have run the GPAW software over MPI library
> 
> mpiexec -n 32 gpaw-python Ar13MD.py
> 
> The Ar13MD.py script is shown at the end of this letter

Let's continue the discussion of this on the gpaw-users mailing list:

https://wiki.fysik.dtu.dk/gpaw/mailinglists.html

One comment about setting up clusters with ASE.  ASE's GUI now has a
very nice tool for that:  Start ag, choose Setup -> Nanoparticle and
experiment until you get a 13 atom cluster.  When you are satisfied, you
can click the Python button to get something like this:

import ase
from ase.cluster.cubic import FaceCenteredCubic

surfaces = [(1, 0, 0), (1, 1, 1)]
layers = [1, 1]
lc = 3.00000
atoms = FaceCenteredCubic('Ar', surfaces, layers, latticeconstant=lc)

# OPTIONAL: Cast to ase.Atoms object, discarding extra information:
# atoms = ase.Atoms(atoms)

Jens Jørgen

> 
> I wonder if I can speed up more my calculations.
> I have a box of 12 angstroms as the simulation cell.
> But i don't want periodic boundary conditions.
> 
> I am not an Expert, but the output below sugest me some solutions;
> 
> Total number of cores used: 32
> Domain Decomposition: 4 x 4 x 2
> Diagonalizer layout: Serial LAPACK
> Orthonormalizer layout: Serial LAPACK
> 
> 1 k-point in the Irreducible Part of the Brillouin Zone (total: 1)
> Linear Mixing Parameter:           0.25
> Pulay Mixing with 3 Old Densities
> No Damping of Long Wave Oscillations
> 
> 1. Serial LAPACK (could it be parallel version)
> 2. k-points (is this possible to set the k-points for cluster,  
> especially if i want to simulate liquid state)
> 3. Damping of Long Wave Oscillations (how to set cut-off energy ?)
> 
> I will be very appriciated for any sugestions
> 
> With the best regards
> Aleksander Dawid
> 
> ======================================================
> Aleksander Dawid
> University of Silesia, Devision Of Computational Physics And Electronics
> email: aleksander.dawid at us.edu.pl
> ======================================================
> 
> #!/usr/bin/env python
> from ase import *
> import gpaw.mpi as mpi
> from gpaw import GPAW, setup_paths
> from ase.lattice.surface import *
> from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
> from ase.md.verlet import VelocityVerlet
> from ase.md.langevin import Langevin
> from ase import units
> from ase.parallel import rank, barrier
> from gpaw.vdw import FFTVDWFunctional
> from gpaw.atom.generator import Generator, parameters
> 
> 
> gO = Generator('Ar', 'revPBE', scalarrel=True, nofiles=True)
> gO.run(**parameters['Ar'])
> 
> barrier()
> setup_paths.insert(0, '.')
> 
> a = 12.  # Size of unit cell (Angstrom)
> ayz= 12.
> c = ayz / 2
> s = a / 2
> 
> 
> d = 3.42  # Bond length
> 
> 
> fname="PAR500.txt"
> vname="Velocities500.txt"
> 
> cluster = Atoms([Atom('Ar', (s - d, c, c)),
>                            Atom('Ar', (s + d, c, c)),
>                            Atom('Ar', (s + d, c + d, c)),
>                            Atom('Ar', (s - d, c + d, c)),
>                            Atom('Ar', (s, c + d, c)),
>                            Atom('Ar', (s + d, c - d, c)),
>                            Atom('Ar', (s - d, c - d, c)),
>                            Atom('Ar', (s, c - d, c)),
>                            Atom('Ar', (s + d, c, c + d)),
>                            Atom('Ar', (s - d, c, c + d)),
>                            Atom('Ar', (s, c, c + d)),
>                            Atom('Ar', (s, c, c - d)),
>                            Atom('Ar', (s, c, c))],
>                             cell=(a, ayz, ayz), pbc=False)
> 
> 
> vdw = FFTVDWFunctional(nspins=1,verbose=0)
> calc=GPAW(width=0.1,eigensolver='cg',xc=vdw,txt=fname)
> 
> 
> cluster.set_calculator(calc)
> # Set the momenta corresponding to T=300K
> #MaxwellBoltzmannDistribution(cluster, 20*units.kB)
> 
> # We want to run MD with constant energy using the VelocityVerlet algorithm.
> dyn = Langevin(cluster, 5*units.fs, 2*units.kB, 0.02)
> #dyn = VelocityVerlet(cluster, dt=5.0*units.fs)  # 5 fs time step.
> 
> def printenergy(a=cluster):    #store a reference to atoms in the definition.
>      epot = a.get_potential_energy() / len(a)
>      ekin = a.get_kinetic_energy() / len(a)
>      if mpi.rank==0:
> 	#count+=1
> 	FILE = open("EnergyArCluster500.txt","a")
> 	FILE.write("Energy per atom: Epot = %.3feV  Ekin = %.3feV (T=%3.0fK)   
> Etot = %.3feV" % (epot, ekin, ekin/(1.5*units.kB), epot+ekin))
>      	#print ("Energy per atom: Epot = %.3feV  Ekin = %.3feV  
> (T=%3.0fK)  Etot = %.3feV" % (epot, ekin, ekin/(1.5*units.kB),  
> epot+ekin))
> 	FILE.close()
> 
> 
> 
> dyn.attach(printenergy, interval=1)
> #We also want to save the positions of all atoms after every 100th time step.
> traj = PickleTrajectory("Ar13dyn500.traj", 'w', cluster)
> dyn.attach(traj.write, interval=1)
> 
> 
> # Now run the dynamics
> if mpi.rank==0:
> 	print ("START MOLECULAR QUANTUM DYNAMICS")
> ############################
> #MD main loops
> ###########################
> dyn.run(steps=1) # Make dyn.run(steps) MD simulations
> 
> 
> if mpi.rank==0:
> 	v=cluster.get_velocities()
> 	FILE = open(vname,"w")
> 	FILE.write(str(len(v))+"\n")
> 	for i in range(0,len(v)):
>         		s=cluster[i].symbol
> 		x=v[i][0]
>     		y=v[i][1]
>          	z=v[i][2]
> 		FILE.write(str(s)+" "+str(x)+" "+str(y)+" "+str(z)+"\n")
> 	FILE.close()
> 
> 	write('Ar13po500.xyz', cluster)
> 
> ----------------------------------------------------
> Uniwersytet Śląski w Katowicach http://www.us.edu.pl
> 
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