Dear ATK,
Sorry for a really dumb question, but I could use some help. OK, I made a simple graphite NC file test
job with VNL. It runs fine when I run it from VNL. Now I want to run the job on a cluster with multiple nodes.
I tried to submit the job to the cluster like this:
$IMPI_HOME/bin/mpiexec.hydra \
-machinefile $PBS_NODEFILE \
-np $(wc -l < $PBS_NODEFILE) \
atkpython graphite.nc > graphite.out
This crashes and I don't really understand why. I tried to run it interactively using atkpython from the
command line, and it didn't like the grahite.nc job file. But I know the job is ok because it ran fine in
VNL on the login node.
What do I need to do to make a .nc file run with atkpython?
For my project, I just want to be able to optimize a large structure with multiple processors (MPI on
cluster) using DFTB, with an output of a XYZ file, lattice vectors, and a total energy of the optimized structure.
I will do a bigger structure when I can get the test job to run on multiple nodes.
Thanks for the help! Again sorry if this is obvious but its not clear to me.
John
# -------------------------------------------------------------
# Bulk configuration
# -------------------------------------------------------------
# Define A,B directions of lattice
vector_a = [ 2.461599, 0.000000, 0.000000]*Angstrom
vector_b = [-1.230800, 2.131808, 0.000000]*Angstrom
vector_c = [0.0, 0.0, 100.0]*Angstrom
# Define elements
elements = [Carbon, Carbon]
# Define coordinates
cartesian_coordinates= [[-0.615400, -0.355301, 0.000000],
[ 0.615400, 0.355301, 0.000000]]*Angstrom
# Set up configuration
bulk_configuration = BulkConfiguration(
bravais_lattice=UnitCell(vector_a,vector_b,vector_c),
elements=elements,
cartesian_coordinates=cartesian_coordinates
)
# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = DFTBDirectory("cp2k/scc/")
#----------------------------------------
# Pair Potentials
#----------------------------------------
pair_potentials = DFTBDirectory("cp2k/scc/")
numerical_accuracy_parameters = NumericalAccuracyParameters(
interaction_max_range=10.0*Ang,
electron_temperature=300.0*Kelvin,
reciprocal_energy_cutoff=1250.0*Hartree,
number_of_reciprocal_points=1024,
grid_mesh_cutoff=10.0*Hartree,
radial_step_size=0.01*Ang,
density_cutoff=1e-06,
k_point_sampling=(1, 1, 1),
)
iteration_control_parameters = IterationControlParameters(
damping_factor=0.1,
linear_dependence_threshold=0.0,
algorithm=PulayMixer(),
preconditioner=Preconditioner.Off,
start_mixing_after_step=0,
number_of_history_steps=20,
max_steps=100,
tolerance=0.0001,
mixing_variable=HamiltonianVariable,
)
poisson_solver = FastFourierSolver()
calculator = SlaterKosterCalculator(
basis_set=basis_set,
pair_potentials=pair_potentials,
numerical_accuracy_parameters=numerical_accuracy_parameters,
iteration_control_parameters=iteration_control_parameters,
poisson_solver=poisson_solver,
charge=0.0,
spin_polarization=False,
)
bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('bulk.nc', bulk_configuration)
bulk_configuration = OptimizeGeometry(
bulk_configuration,
max_forces=0.05*eV/Ang,
max_steps=200,
max_step_length=0.5*Ang,
trajectory_filename=None,
disable_stress=True,
optimizer_method=QuasiNewton(),
)
nlsave('opt.nc', bulk_configuration)
nlprint(bulk_configuration)
printXYZFile('dump.xyz',bulk_configuration)
# -------------------------------------------------------------
# Total energy
# -------------------------------------------------------------
total_energy = TotalEnergy(bulk_configuration)
nlsave('energy.nc', total_energy)
nlprint(total_energy)
