[gpaw-users] [ase-users] Parallelization of GPAW MD simulation
Jens Jørgen Mortensen
jensj at fysik.dtu.dk
Thu Apr 28 10:33:27 CEST 2011
On Thu, 2011-04-28 at 10:16 +0200, Jens Jørgen Mortensen wrote:
> 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)
I don't think you will gain much from parallel LAPACK if you only have
13 atoms. Could you show us the text output from your calculation?
That should have timing information showing where the time is spent.
> > 2. k-points (is this possible to set the k-points for cluster,
> > especially if i want to simulate liquid state)
I don't think k-point sampling is needed for such a large cell.
Jens Jørgen
> > 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
> >
> > _______________________________________________
> > ase-users mailing list
> > ase-users at listserv.fysik.dtu.dk
> > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>
>
> _______________________________________________
> gpaw-users mailing list
> gpaw-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
More information about the gpaw-users
mailing list