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General Questions and Answers / DFTB optimization freezes for large system (~1100 atoms)
« on: February 10, 2017, 23:55 »
Hi,
I'm trying to optimization the geometry of a system containing ~1100 atoms at the DFTB level (SK=3-ob-2-1(C,O,N,H)). I get the energy, within seconds using 36 CPUs (1 node), but the calculation freezes right before generating the forces for the first time:
However, the calculation remains running, it just doesn't appear to be doing anything. I ran a test on a smaller system (~200) and the calculation completes successfully (geometry optimization). The larger system is just a supercell of the smaller one. Note, ATK input file is below.
Also, can you add an empirical dispersion correction to DFTB in ATK-SE?
Thanks
ATK-SE input:
I'm trying to optimization the geometry of a system containing ~1100 atoms at the DFTB level (SK=3-ob-2-1(C,O,N,H)). I get the energy, within seconds using 36 CPUs (1 node), but the calculation freezes right before generating the forces for the first time:
Code
+------------------------------------------------------------------------------+
| 15 E = -3329.86 dE = 1.941906e-06 dM = 4.086617e-06 dH = 2.739183e-06 |
+------------------------------------------------------------------------------+
| Calculation Converged in 15 steps |
| |
| Fermi Level = -4.457349 eV |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Slater-Koster Calculation [Finished Fri Feb 10 15:32:14 2017] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Size of dense matrices = 3760 x 3760 [216 MB per matrix] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| DiagonalizationSolver parallelization report. |
+------------------------------------------------------------------------------+
| Total number of processes: 36 |
| Total number of k-points: 1 |
| Processes per k-point: 36 |
| Number of process groups: 1 |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Size of dense matrices = 3760 x 3760 [216 MB per matrix] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Slater-Koster Calculation [Started Fri Feb 10 15:32:17 2017] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| CPU Information |
| |
+------------------------------------------------------------------------------+
| Process ID 0 at ser7 |
| Process ID 1 at ser7 |
.
.
.
| Process ID 34 at ser7 |
| Process ID 35 at ser7 |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Size of dense matrices = 3760 x 3760 [216 MB per matrix] |
| |
+------------------------------------------------------------------------------+
|--------------------------------------------------|
Calculating Kinetic Matrix : ==================================================
+------------------------------------------------------------------------------+
| |
| Real space grid sampling is (68, 95, 116) in a, b, and c directions. |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Size of dense matrices = 3760 x 3760 [216 MB per matrix] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| DiagonalizationSolver parallelization report. |
+------------------------------------------------------------------------------+
| Total number of processes: 36 |
| Total number of k-points: 1 |
| Processes per k-point: 36 |
| Number of process groups: 1 |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Checkpoint Handler |
| Filename : /tmp/1634514/checkpoint72536830.nc |
| Interval : 0.5 h |
+------------------------------------------------------------------------------+
|--------------------------------------------------|
Calculating Eigenvalues : ==================================================
Calculating Density Matrix :
However, the calculation remains running, it just doesn't appear to be doing anything. I ran a test on a smaller system (~200) and the calculation completes successfully (geometry optimization). The larger system is just a supercell of the smaller one. Note, ATK input file is below.
Also, can you add an empirical dispersion correction to DFTB in ATK-SE?
Thanks
ATK-SE input:
Code
# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------
# Set up lattice
vector_a = [25.0, 0.0, 0.0]*Angstrom
vector_b = [0.0, 35.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 42.8547]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)
# Define elements
elements = [Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
.
.
.
[ 6.31005 , 23.683765 , 41.56293078],
[ 7.211625 , 24.46654 , 41.76113377],
[ 5.4128 , 23.838465 , 40.53407514]]*Angstrom
# Set up configuration
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=fractional_coordinates
)
# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = DFTBDirectory("/home/mefoste/DFTB+/DFTB_parameters/3ob-2-1")
#----------------------------------------
# Pair Potentials
#----------------------------------------
pair_potentials = DFTBDirectory("/home/mefoste/DFTB+/DFTB_parameters/3ob-2-1")
iteration_control_parameters = IterationControlParameters()
calculator = SlaterKosterCalculator(
basis_set=basis_set,
pair_potentials=pair_potentials,
iteration_control_parameters=iteration_control_parameters,
)
bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('DR-CT_trans.nc', bulk_configuration)
# -------------------------------------------------------------
# Optimize Geometry
# -------------------------------------------------------------
bulk_configuration = OptimizeGeometry(
bulk_configuration,
max_forces=0.05*eV/Ang,
max_steps=5000,
max_step_length=0.2*Ang,
trajectory_filename=None,
disable_stress=True,
optimizer_method=LBFGS(),
)
nlsave('DR-CT_trans.nc', bulk_configuration)
nlprint(bulk_configuration)
# -------------------------------------------------------------
# Electron Density
# -------------------------------------------------------------
electron_density = ElectronDensity(
configuration=bulk_configuration,
)
nlsave('DR-CT_trans.nc', electron_density)
# -------------------------------------------------------------
# Electrostatic Potential
# -------------------------------------------------------------
electrostatic_potential = ElectrostaticPotential(bulk_configuration)
nlsave('DR-CT_trans.nc', electrostatic_potential)