+------------------------------------------------------------------------------+
| |
| Atomistix ToolKit 11.2.0 [Build 3044] |
| |
+------------------------------------------------------------------------------+
.....omitted for the maximum allowed length of this message^_^
Calculating Eigenvalues : ==================================================
Calculating Density Matrix : ==================================================
+------------------------------------------------------------------------------+
| Density Matrix Report DM DD |
+------------------------------------------------------------------------------+
| 0 Si [ 15.666 , 15.465 , 0.000 ] 4.00008 0.00008 |
| 1 Si [ 16.119 , 17.398 , 1.116 ] 3.99996 -0.00004 |
| 2 Si [ 15.666 , 17.398 , 3.348 ] 4.00000 0.00000 |
| 3 Si [ 16.119 , 15.465 , 4.464 ] 4.00001 0.00001 |
| 4 Si [ 15.666 , 15.465 , 6.696 ] 4.00003 0.00003 |
| 5 Si [ 16.119 , 17.398 , 7.812 ] 3.99992 -0.00008 |
| 6 Si [ 15.666 , 17.398 , 10.044 ] 4.00006 0.00006 |
| 7 Si [ 16.119 , 15.465 , 11.160 ] 3.99997 -0.00003 |
| 8 Si [ 15.666 , 15.465 , 13.392 ] 4.00003 0.00003 |
| 9 Si [ 16.119 , 17.398 , 14.508 ] 3.99999 -0.00001 |
| 10 Si [ 15.666 , 17.398 , 16.740 ] 3.99999 -0.00001 |
| 11 Si [ 16.119 , 15.465 , 17.856 ] 3.99996 -0.00004 |
| 12 Si [ 15.666 , 15.465 , 20.088 ] 4.00008 0.00008 |
| 13 Si [ 16.119 , 17.398 , 21.204 ] 3.99994 -0.00006 |
| 14 Si [ 15.666 , 17.398 , 23.436 ] 4.00002 0.00002 |
| 15 Si [ 16.119 , 15.465 , 24.552 ] 4.00002 0.00002 |
| 16 Si [ 15.666 , 15.465 , 26.784 ] 4.00002 0.00002 |
| 17 Si [ 16.119 , 17.398 , 27.900 ] 3.99994 -0.00006 |
| 18 Si [ 15.666 , 17.398 , 30.132 ] 4.00005 0.00005 |
| 19 Si [ 16.119 , 15.465 , 31.249 ] 3.99996 -0.00004 |
| 20 Si [ 15.666 , 15.465 , 33.481 ] 4.00005 0.00005 |
| 21 Si [ 16.119 , 17.398 , 34.597 ] 3.99999 -0.00001 |
| 22 Si [ 15.666 , 17.398 , 36.829 ] 3.99998 -0.00002 |
| 23 Si [ 16.119 , 15.465 , 37.945 ] 3.99997 -0.00003 |
| 24 Si [ 15.666 , 15.465 , 40.177 ] 4.00007 0.00007 |
| 25 Si [ 16.119 , 17.398 , 41.293 ] 3.99993 -0.00007 |
| 26 Si [ 15.666 , 17.398 , 43.525 ] 4.00003 0.00003 |
| 27 Si [ 16.119 , 15.465 , 44.641 ] 4.00001 0.00001 |
| 28 Si [ 15.666 , 15.465 , 46.873 ] 4.00001 0.00001 |
| 29 Si [ 16.119 , 17.398 , 47.989 ] 3.99995 -0.00005 |
| 30 Si [ 15.666 , 17.398 , 50.221 ] 4.00004 0.00004 |
| 31 Si [ 16.119 , 15.465 , 51.337 ] 3.99995 -0.00005 |
| 32 Si [ 15.666 , 15.465 , 53.569 ] 4.00007 0.00007 |
| 33 Si [ 16.119 , 17.398 , 54.685 ] 3.99998 -0.00002 |
| 34 Si [ 15.666 , 17.398 , 56.917 ] 3.99998 -0.00002 |
| 35 Si [ 16.119 , 15.465 , 58.033 ] 3.99999 -0.00001 |
| 36 Si [ 15.666 , 15.465 , 60.265 ] 4.00006 0.00006 |
| 37 Si [ 16.119 , 17.398 , 61.381 ] 3.99992 -0.00008 |
| 38 Si [ 15.666 , 17.398 , 63.613 ] 4.00005 0.00005 |
| 39 Si [ 16.119 , 15.465 , 64.729 ] 4.00000 0.00000 |
| 40 Si [ 15.666 , 15.465 , 66.961 ] 4.00001 0.00001 |
| 41 Si [ 16.119 , 17.398 , 68.077 ] 3.99997 -0.00003 |
| 42 Si [ 15.666 , 17.398 , 70.309 ] 4.00002 0.00002 |
| 43 Si [ 16.119 , 15.465 , 71.425 ] 3.99994 -0.00006 |
| 44 Si [ 15.666 , 15.465 , 73.657 ] 4.00008 0.00008 |
| 45 Si [ 16.119 , 17.398 , 74.773 ] 3.99997 -0.00003 |
| 46 Si [ 15.666 , 17.398 , 77.005 ] 3.99999 -0.00001 |
| 47 Si [ 16.119 , 15.465 , 78.121 ] 4.00000 0.00000 |
| 48 Si [ 15.666 , 15.465 , 80.353 ] 4.00004 0.00004 |
| 49 Si [ 16.119 , 17.398 , 81.469 ] 3.99992 -0.00008 |
| 50 Si [ 15.666 , 17.398 , 83.701 ] 4.00006 0.00006 |
| 51 Si [ 16.119 , 15.465 , 84.817 ] 3.99999 -0.00001 |
| 52 Si [ 15.666 , 15.465 , 87.049 ] 4.00002 0.00002 |
| 53 Si [ 16.119 , 17.398 , 88.165 ] 3.99998 -0.00002 |
| 54 Si [ 15.666 , 17.398 , 90.397 ] 4.00001 0.00001 |
| 55 Si [ 16.119 , 15.465 , 91.514 ] 3.99995 -0.00005 |
| 56 Si [ 15.666 , 15.465 , 93.746 ] 4.00008 0.00008 |
| 57 Si [ 16.119 , 17.398 , 94.862 ] 3.99996 -0.00004 |
| 58 Si [ 15.666 , 17.398 , 97.094 ] 4.00000 0.00000 |
| 59 Si [ 16.119 , 15.465 , 98.210 ] 4.00001 0.00001 |
| 60 Si [ 15.666 , 15.465 , 100.442 ] 4.00003 0.00003 |
| 61 Si [ 16.119 , 17.398 , 101.558 ] 3.99992 -0.00008 |
| 62 Si [ 15.666 , 17.398 , 103.790 ] 4.00006 0.00006 |
| 63 Si [ 16.119 , 15.465 , 104.906 ] 3.99997 -0.00003 |
| 64 Si [ 15.666 , 15.465 , 107.138 ] 4.00003 0.00003 |
| 65 Si [ 16.119 , 17.398 , 108.254 ] 3.99999 -0.00001 |
| 66 Si [ 15.666 , 17.398 , 110.486 ] 3.99999 -0.00001 |
| 67 Si [ 16.119 , 15.465 , 111.602 ] 3.99996 -0.00004 |
| 68 Si [ 15.666 , 15.465 , 113.834 ] 4.00008 0.00008 |
| 69 Si [ 16.119 , 17.398 , 114.950 ] 3.99994 -0.00006 |
| 70 Si [ 15.666 , 17.398 , 117.182 ] 4.00002 0.00002 |
| 71 Si [ 16.119 , 15.465 , 118.298 ] 4.00002 0.00002 |
| 72 Si [ 15.666 , 15.465 , 120.530 ] 4.00002 0.00002 |
| 73 Si [ 16.119 , 17.398 , 121.646 ] 3.99994 -0.00006 |
| 74 Si [ 15.666 , 17.398 , 123.878 ] 4.00005 0.00005 |
| 75 Si [ 16.119 , 15.465 , 124.994 ] 3.99996 -0.00004 |
| 76 Si [ 15.666 , 15.465 , 127.226 ] 4.00005 0.00005 |
| 77 Si [ 16.119 , 17.398 , 128.342 ] 3.99999 -0.00001 |
| 78 Si [ 15.666 , 17.398 , 130.574 ] 3.99998 -0.00002 |
| 79 Si [ 16.119 , 15.465 , 131.690 ] 3.99997 -0.00003 |
| 80 Si [ 15.666 , 15.465 , 133.922 ] 4.00007 0.00007 |
| 81 Si [ 16.119 , 17.398 , 135.038 ] 3.99993 -0.00007 |
| 82 Si [ 15.666 , 17.398 , 137.270 ] 4.00003 0.00003 |
| 83 Si [ 16.119 , 15.465 , 138.386 ] 4.00001 0.00001 |
| 84 Si [ 15.666 , 15.465 , 140.618 ] 4.00001 0.00001 |
| 85 Si [ 16.119 , 17.398 , 141.734 ] 3.99995 -0.00005 |
| 86 Si [ 15.666 , 17.398 , 143.966 ] 4.00004 0.00004 |
| 87 Si [ 16.119 , 15.465 , 145.082 ] 3.99995 -0.00005 |
| 88 Si [ 15.666 , 15.465 , 147.314 ] 4.00007 0.00007 |
| 89 Si [ 16.119 , 17.398 , 148.430 ] 3.99998 -0.00002 |
| 90 Si [ 15.666 , 17.398 , 150.662 ] 3.99998 -0.00002 |
| 91 Si [ 16.119 , 15.465 , 151.779 ] 3.99999 -0.00001 |
| 92 Si [ 15.666 , 15.465 , 154.011 ] 4.00006 0.00006 |
| 93 Si [ 16.119 , 17.398 , 155.127 ] 3.99992 -0.00008 |
| 94 Si [ 15.666 , 17.398 , 157.359 ] 4.00005 0.00005 |
| 95 Si [ 16.119 , 15.465 , 158.475 ] 4.00000 0.00000 |
| 96 Si [ 15.666 , 15.465 , 160.707 ] 4.00001 0.00001 |
| 97 Si [ 16.119 , 17.398 , 161.823 ] 3.99997 -0.00003 |
| 98 Si [ 15.666 , 17.398 , 164.055 ] 4.00002 0.00002 |
| 99 Si [ 16.119 , 15.465 , 165.171 ] 3.99994 -0.00006 |
| 100 Si [ 15.666 , 15.465 , 167.403 ] 4.00008 0.00008 |
| 101 Si [ 16.119 , 17.398 , 168.519 ] 3.99997 -0.00003 |
| 102 Si [ 15.666 , 17.398 , 170.751 ] 3.99999 -0.00001 |
| 103 Si [ 16.119 , 15.465 , 171.867 ] 4.00000 0.00000 |
| 104 Si [ 15.666 , 15.465 , 174.099 ] 4.00004 0.00004 |
| 105 Si [ 16.119 , 17.398 , 175.215 ] 3.99992 -0.00008 |
| 106 Si [ 15.666 , 17.398 , 177.447 ] 4.00006 0.00006 |
| 107 Si [ 16.119 , 15.465 , 178.563 ] 3.99999 -0.00001 |
| 108 Si [ 15.666 , 15.465 , 180.795 ] 4.00002 0.00002 |
| 109 Si [ 16.119 , 17.398 , 181.911 ] 3.99998 -0.00002 |
| 110 Si [ 15.666 , 17.398 , 184.143 ] 4.00001 0.00001 |
| 111 Si [ 16.119 , 15.465 , 185.259 ] 3.99995 -0.00005 |
+------------------------------------------------------------------------------+
| 2 E = -144.593 dE = 3.562179e-03 dH = 1.152072e-03 |
+------------------------------------------------------------------------------+
| Calculation Converged in 2 steps |
| |
| Fermi Level = -3.679114 eV |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Equivalent Bulk [Finished Mon Apr 11 23:23:39 2011] |
| |
+------------------------------------------------------------------------------+
/home/zxgao/QuantumWise/atk-11.2.0/atkpython/bin/atkpython: line 3: 18596 Segmentation fault PSEUDOPOTENTIALS_PATH=$EXEC_DIR/../share/pseudopotentials GPAW_SETUP_PATH=$EXEC_DIR/../share/gpaw-setups/ PYTHONHOME=$EXEC_DIR/.. PYTHONPATH= LD_LIBRARY_PATH=$EXEC_DIR/../lib $EXEC_DIR/atkpython_exec $*
In some sense it seems pretty clear that you are out of memory, if the smaller system works and the bigger not. On the other hand, it's rather unusual that the device calculation would use more memory than the equivalent bulk. But it's hard to say much more without seeing the exact geometry. Are there any metallic/dielectric regions in the system?
Indeed you have a lot of RAM, but perhaps you are running in parallel, with several MPI processes on the same node?
import numpy
# Constant for adjustment
delta=-0.000006922-0.00001
layer_thickness=1.118640452-0.666359548
y_offset=-7.731953546-0.00001
# Cell repetition
repeat_cell=10
repeat_cell_electrode=2
buffer_cell=2
# Layey_distance including buckling,attention!
layer_distance=30
# Gate Geometry
gate_distance1=gate_distance2=10.
gate_thickness1=gate_thickness2=1.
# Dielectric region: Approximately SiO2 :float
di_constant1=di_constant2=3.9
di_thickness1=di_thickness2=gate_distance1-3.
gate_di_seg1=gate_di_seg2=0.
##di_layer_seg=gate_distance-gate_di_seg-di_thickness
# Electrode Voltage
e_volt_list=[0.1]
# Gate Voltage
e_gate_list=[-0.2,1.]
# Electric Field Voltage
e_field_list=[1.,2.]
# Numerical and Iteration Parameters
device_numerical=NumericalAccuracyParameters(
grid_mesh_cutoff= 75 *Hartree, #Default: HuckelCalculator=10*Hartree, LCAOCalculator=75*Hartree
k_point_sampling=(1,300,1), #default (1,1,1)
radial_step_size=0.01*Angstrom, #length > 0.0*Angstrom
density_cutoff=1.0e-6, #float>0., default:1.0e-6
interaction_max_range=10.*Angstrom, #The maximum allowed interaction distance between two orbitals.
number_of_reciprocal_points=1024, #The number of reciprocal points used for evaluating two-center integrals.
reciprocal_energy_cutoff=1250.*Hartree, #The energy cutoff in reciprocal space used for evaluating of the two-center integrals.
electron_temperature=300*Kelvin #default:100K??
)
device_iteration=IterationControlParameters(
tolerance=4.0e-5, #default 4.e-5
max_steps=500, #default 100
algorithm=PulayMixer, #NoMixer | LinearMixer | PulayMixer | AndersonMixer ,for histroy mixing
damping_factor=0.1, #float in (0.,1.]
number_of_history_steps=10, #int>0, for history mixing
start_mixing_after_step=0, #The total number of steps to wait before the mixing algorithm is used.
mixing_variable=HamiltonianVariable #HamiltonianVariable | DensityMatrixVariable
)
# filename.nc
filename='silicene_DZP_c'+str(repeat_cell)
cell = [[ 0.666359548+layer_distance/2, 7.731953546-y_offset, -0.000006922-delta],
[ 1.118640452+layer_distance/2, 9.665046454-y_offset, 1.116024993-delta],
[ 0.666359548+layer_distance/2, 9.664953546-y_offset, 3.348047289-delta],
[ 1.118640452+layer_distance/2, 7.732046454-y_offset, 4.464079204-delta]]
temp=cell
i=1
while i<repeat_cell+buffer_cell*2+repeat_cell_electrode*2:
temp=temp+numpy.add(cell,[0,0,i*6.69611]).tolist()
i=i+1
###############################################################
# Left electrode
###############################################################
# Set up lattice
vector_a = [layer_distance, 0.0, 0.0]*Angstrom
vector_b = [0.0, 3.866, 0.0]*Angstrom
vector_c = [0.0, 0.0, 6.69611*repeat_cell_electrode]*Angstrom
left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)
# Define elements
left_electrode_elements = [Silicon]*4*repeat_cell_electrode
# Define coordinates
left_electrode_coordinates = temp[0:4*repeat_cell_electrode]*Angstrom
# Set up configuration
left_electrode = BulkConfiguration(
bravais_lattice=left_electrode_lattice,
elements=left_electrode_elements,
cartesian_coordinates=left_electrode_coordinates
)
###############################################################
# Right electrode
###############################################################
# Set up lattice
vector_a = [layer_distance, 0.0, 0.0]*Angstrom
vector_b = [0.0, 3.866, 0.0]*Angstrom
vector_c = [0.0, 0.0, 6.69611*repeat_cell_electrode]*Angstrom
right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)
# Define elements
right_electrode_elements = [Silicon]*4*repeat_cell_electrode
# Define coordinates
right_electrode_coordinates = temp[0:4*repeat_cell_electrode]*Angstrom
# Set up configuration
right_electrode = BulkConfiguration(
bravais_lattice=right_electrode_lattice,
elements=right_electrode_elements,
cartesian_coordinates=right_electrode_coordinates
)
###############################################################
# Central region
###############################################################
# Set up lattice
vector_a = [layer_distance, 0.0, 0.0]*Angstrom
vector_b = [0.0, 3.866, 0.0]*Angstrom
vector_c = [0.0, 0.0, 6.69611*(repeat_cell+buffer_cell*2+repeat_cell_electrode*2)]*Angstrom
central_region_lattice = UnitCell(vector_a, vector_b, vector_c)
# Define elements
central_region_elements = [Silicon]*4*(repeat_cell+buffer_cell*2+repeat_cell_electrode*2)
# Define coordinates
central_region_coordinates = temp*Angstrom
# Set up configuration
central_region = BulkConfiguration(
bravais_lattice=central_region_lattice,
elements=central_region_elements,
cartesian_coordinates=central_region_coordinates
)
device_configuration = DeviceConfiguration(
central_region,
[left_electrode, right_electrode]
)
###############################################################
# Define gates
###############################################################
gate1=BoxRegion(
value=1*Volt,
xmin=(0.666359548+layer_distance/2-gate_distance1-gate_thickness1)*Angstrom,xmax=(0.666359548+layer_distance/2-gate_distance1)*Angstrom,
ymin=0*Angstrom,ymax=3.866*Angstrom,
zmin=(buffer_cell+repeat_cell_electrode)*6.69611*Angstrom,zmax=6.69611*(repeat_cell+buffer_cell+repeat_cell_electrode)*Angstrom
)
gate2=gate1(
value=-1*Volt,
xmin=(1.118640452+layer_distance/2+gate_distance2)*Angstrom,xmax=(1.118640452+layer_distance/2+gate_distance2+gate_thickness2)*Angstrom
)
e_field=e_field_list[0]
e_gate=e_gate_list[0]
gate_bottom=gate1(value= (e_field*di_thickness1/di_constant1+e_gate/2.)*Volt)
gate_top=gate2(value= (-e_field*di_thickness1/di_constant1+e_gate/2.)*Volt)
device_configuration.setMetallicRegions([gate_bottom,gate_top])
##############################################################
# Define dielectrics
##############################################################
di1=BoxRegion(
value=di_constant1,
xmin=(0.666359548+layer_distance/2-gate_distance1+gate_di_seg1)*Angstrom,xmax=(0.666359548+layer_distance/2-gate_distance1+gate_di_seg1+di_thickness1)*Angstrom,
ymin=0*Angstrom,ymax=3.866*Angstrom,
zmin=(buffer_cell+repeat_cell_electrode)*6.69611*Angstrom,zmax=6.69611*(repeat_cell+buffer_cell+repeat_cell_electrode)*Angstrom
)
di2=di1(
value=di_constant2,
xmin=(1.118640452+layer_distance/2+gate_distance2-gate_di_seg2-di_thickness2)*Angstrom,xmax=(1.118640452+layer_distance/2+gate_distance2-gate_di_seg2)*Angstrom
)
device_configuration.setDielectricRegions([di1,di2])
###############################################################
# Calculator
###############################################################
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = GGABasis.SingleZeta
#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = GGA.PBE
#----------------------------------------
# Numerical Accuracy Settings
#----------------------------------------
left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
k_point_sampling=(1, 300, 300),
)
right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
k_point_sampling=(1, 300, 300),
)
#----------------------------------------
# Electrode Calculators
#----------------------------------------
left_electrode_calculator = LCAOCalculator(
basis_set=basis_set,
exchange_correlation=exchange_correlation,
numerical_accuracy_parameters=left_electrode_numerical_accuracy_parameters,
)
right_electrode_calculator = LCAOCalculator(
basis_set=basis_set,
exchange_correlation=exchange_correlation,
numerical_accuracy_parameters=right_electrode_numerical_accuracy_parameters,
)
for e_field in e_field_list:
for e_gate in e_gate_list:
e_field_volt=e_field*(di_thickness1/di_constant1+di_thickness2/di_constant2+layer_thickness+gate_distance1+gate_distance2-di_thickness1-di_thickness2)
gate_bottom=gate1(value= (e_field_volt/2+e_gate/2.)*Volt)
gate_top=gate2(value= (-e_field_volt/2+e_gate/2.)*Volt)
device_configuration.setMetallicRegions([gate_bottom,gate_top])
for e_volt in e_volt_list:
electrode_volt=(e_volt/2.,-e_volt/2.)*Volt
#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
basis_set=basis_set,
exchange_correlation=exchange_correlation,
electrode_calculators=
[left_electrode_calculator, right_electrode_calculator],
electrode_voltages=electrode_volt,
numerical_accuracy_parameters=device_numerical
)
device_configuration.setCalculator(calculator)
nlprint(device_configuration)
device_configuration.update()
nlsave(filename+'_ef'+str(e_field)+'_vg'+str(e_gate)+'_vb'+str(e_volt)+'.nc', device_configuration)
#device_configuration = OptimizeGeometry(
# device_configuration,
# maximum_forces=0.05*eV/Ang,
# constraints=[],
# trajectory_filename=None,
# )
#nlsave('silicene_opt.nc', device_configuration)
#nlprint(device_configuration)
#
#total_energy = TotalEnergy(device_configuration)
#nlsave(filename+'_ef'+str(e_field)+'_vg'+str(e_gate)+'_vb'+str(e_volt)+'.nc', total_energy)
#nlprint(total_energy)
transmission_spectrum = TransmissionSpectrum(
configuration=device_configuration,
energies=numpy.linspace(-0.5,0.5,500)*eV,
kpoints=MonkhorstPackGrid(1,1000,1),
energy_zero_parameter=AverageFermiLevel,
infinitesimal=1e-06*eV,
self_energy_calculator=KrylovSelfEnergy(),
)
nlsave(filename+'_ef'+str(e_field)+'_vg'+str(e_gate)+'_vb'+str(e_volt)+'.nc', transmission_spectrum)
nlprint(transmission_spectrum)
#device_density_of_states = DeviceDensityOfStates(
# configuration=device_configuration,
# energies=numpy.linspace(-0.5,0.5,500)*eV,
# kpoints=MonkhorstPackGrid(1,1000),
# contributions=All,
# energy_zero_parameter=AverageFermiLevel,
# infinitesimal=1e-06*eV,
# self_energy_calculator=KrylovSelfEnergy(),
# )
#nlsave(filename+'DOS_ef'+str(e_field)+'_vg'+str(e_gate)+'_vb'+str(e_volt)+'.nc', device_density_of_states)
#nlprint(device_density_of_states)
nlprint('#Parameters!')
print 'vt'
print gate_top.value()
print 'vb'
print gate_bottom.value()
print 'current'
nlprint(transmission_spectrum.current())
print filename+'_ef'+str(e_field)+'_vg'+str(e_gate)+'_vb'+str(e_volt)+'.nc'
print '#done'
There is a k-point sampling of (1,300,300). Are you sure that you want this k-point sampling?
First of all it does appear the default temperature is not stated correctly in the manual. Indeed it's 300 K. Sorry for the inconvenience, although for all practical purposes the difference is probably completely negligible, since the temperature only serves to smear the Fermi level a bit.
It does seem we have some problem with metallic and dielectric regions in DFT, and we are now implementing a new multigrid solver for 11.8 which should improve on this situation.
I'm not 100% sure it's a matter of running out of RAM, although it would be helpful for us if you could estimate how much RAM is needed with and without the regions for one of the jobs that did run through.