Messages

1

General Questions and Answers / Quanlist

« on: August 10, 2012, 12:37 »

i have just finished calculating my IV curve and i want to calculate MPSH but first i need to know how to calculate the Quanlist [      ] and how to determine which is the quantum number so as to set up my script can some one show me an example  i have read the whole manual but i cannot get it.

thanks in advance
  

2

General Questions and Answers / the script to calculate both -VE and +VE bias for unsymmetrical central region

« on: March 29, 2012, 04:11 »

i have been trying to calculate  the above problem using the below script but when i try it only gives me positive bias but no negative how should i set my script to bet the negative bias

#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
    basis_set=basis_set,
    electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
    )

nlsave('liliB-IV.nc', device_configuration)

for bias in numpy.linspace(0.,3.,16)*Volt:
   
    device_configuration.setCalculator(
        calculator(electrode_voltages=(0.5*bias,-0.5*bias)),
        initial_state=device_configuration
    )
    device_configuration.update()

# -------------------------------------------------------------
# Transmission spectrum
# -------------------------------------------------------------
    transmission_spectrum = TransmissionSpectrum(
        configuration=device_configuration,
        energies=numpy.linspace(-3,3,100)*eV,
        kpoints=MonkhorstPackGrid(1,1),
        energy_zero_parameter=AverageFermiLevel,
        infinitesimal=1e-06*eV,
        self_energy_calculator=KrylovSelfEnergy(),
        )
    nlsave('liliB-IV.nc', transmission_spectrum, object_id="transmission %s" % bias)
    nlprint(transmission_spectrum)

3

General Questions and Answers / bulk optmoziation

« on: March 12, 2012, 05:15 »

does optimizing a device in bulk mode then using the optimized bulk  and switch it to device mode have any effect on transmission or IV curve

4

General Questions and Answers / optimization and transmission

« on: February 28, 2012, 11:20 »

1) I have a two probe system molecular device which is made or 56 atoms in central scattering region and i want to calculate it's transmission  spectrum but i have limited computer resource so am asking does optimization have effects on transmission spectrum and I-V curve.

2) when calculating the I-V of a two probe molecular device does the length of the electrode have any effect for i have calculated one with a long and the same with a short electrode but the the IV curve is the same.  what might be the problem?

 help urgently needed
 
 thank you in advance   

5

General Questions and Answers / logfile

« on: February 15, 2012, 04:05 »

someone please assit me!!!!!
whenever i start my job in my cluster it does not start but insted it gives me this logfile and the job stops
 
mpiexec_node9.local: cannot connect to local mpd (/tmp/mpd2.console_hassan); possible causes:
  1. no mpd is running on this host
  2. an mpd is running but was started without a "console" (-n option)

 what can be the possiable reaso for this? 

6

General Questions and Answers / optimization

« on: January 18, 2012, 06:08 »

does applying constrain in the first two layer of an electrode during optmization affect tranport behavior of a system when we calculate the tranmission properties o0f the same system

7

General Questions and Answers / optimaization

« on: December 27, 2011, 07:02 »

does second order interaction affect optimaization  for whenever i try to optmize my device when i have expanded the electrode to avoid second ordr intraction the optmization does not finish it stops in the middle.

8

General Questions and Answers / conductance

« on: June 26, 2011, 14:28 »

question 1
what does the id values in conductance curve stand for?

2) i calculated an IV curve and out of it i analyzed the conductance but the conductance curve does not start from 0 on the id values it starts some where around 1 is it correct?

3) what are the best boundary conditions to use when optimizing bulk devices is it ok to use the Iteration Control Settings?

looking forward for positive response
thanks in advance

9

General Questions and Answers / optimization pbs output file what does it mean

« on: May 4, 2011, 06:00 »

Numbers of Processors:  16
---------------------------
started mpd Number: 4
---------------------------
Traceback (most recent call last):
  File "./zipdir/NL/Calculators/DeviceCalculatorInterface.py", line 279, in _update
  File "./zipdir/NL/Calculators/LCAOCalculator/DeviceLCAOCalculator.py", line 1581, in scfLoopDevice
  File "./zipdir/NL/Calculators/LCAOCalculator/DeviceLCAOCalculator.py", line 823, in scfLoopDeviceHamiltonian
  File "./zipdir/NL/Calculators/GenericParameters/CheckpointHandler.py", line 129, in _storeIfNecessary
  File "./zipdir/NL/IO/NetCDFFile.py", line 194, in flush
  File "./zipdir/NL/IO/NetCDFFile.py", line 207, in _write
  File "./zipdir/NL/IO/NetCDFFile.py", line 267, in _write_var_array
  File "./zipdir/NL/IO/NetCDFFile.py", line 315, in _write_var_data
IOError: [Errno 28] No space left on device
Fatal error in PMPI_Barrier: Other MPI error, error stack:
PMPI_Barrier(476).................: MPI_Barrier(MPI_COMM_WORLD) failed
MPIR_Barrier(82)..................:
MPIC_Sendrecv(164)................:
MPIC_Wait(513)....................:
MPIDI_CH3I_Progress(150)..........:
MPID_nem_mpich2_blocking_recv(948):
MPID_nem_tcp_connpoll(1720).......:
state_commrdy_handler(1556).......:
MPID_nem_tcp_recv_handler(1446)...: socket closed
Fatal error in PMPI_Barrier: Other MPI error, error stack:
PMPI_Barrier(476).................: MPI_Barrier(MPI_COMM_WORLD) failed
MPIR_Bcast(1031)..................:
MPIR_Bcast_binomial(157)..........:
MPIC_Recv(83).....................:
MPIC_Wait(513)....................:
MPIDI_CH3I_Progress(150)..........:
MPID_nem_mpich2_blocking_recv(948):
MPID_nem_tcp_connpoll(1720).......:
state_commrdy_handler(1556).......:
MPID_nem_tcp_recv_handler(1446)...: socket closed
Fatal error in PMPI_Barrier: Other MPI error, error stack:
PMPI_Barrier(476).................: MPI_Barrier(MPI_COMM_WORLD) failed
MPIR_Bcast(1031)..................:
MPIR_Bcast_binomial(157)..........:
MPIC_Recv(83).....................:
MPIC_Wait(513)....................:
MPIDI_CH3I_Progress(150)..........:
MPID_nem_mpich2_blocking_recv(948):
MPID_nem_tcp_connpoll(1720).......:
state_commrdy_handler(1556).......:
MPID_nem_tcp_recv_handler(1446)...: socket closed
Fatal error in PMPI_Barrier: Other MPI error, error stack:
PMPI_Barrier(476).................: MPI_Barrier(MPI_COMM_WORLD) failed
MPIR_Bcast(1031)..................:
MPIR_Bcast_binomial(157)..........:
MPIC_Recv(83).....................:
MPIC_Wait(513)....................:
MPIDI_CH3I_Progress(150)..........:
MPID_nem_mpich2_blocking_recv(948):
MPID_nem_tcp_connpoll(1720).......:
state_commrdy_handler(1556).......:
MPID_nem_tcp_recv_handler(1446)...: socket closed
Fatal error in PMPI_Barrier: Other MPI error, error stack:
PMPI_Barrier(476).................: MPI_Barrier(MPI_COMM_WORLD) failed
MPIR_Bcast(1031)..................:
MPIR_Bcast_binomial(157)..........:
MPIC_Recv(83).....................:
MPIC_Wait(513)....................:
MPIDI_CH3I_Progress(150)..........:
MPID_nem_mpich2_blocking_recv(948):
MPID_nem_tcp_connpoll(1720).......:
state_commrdy_handler(1556).......:
MPID_nem_tcp_recv_handler(1446)...: socket closed
Fatal error in PMPI_Barrier: Other MPI error, error stack:
PMPI_Barrier(476).................: MPI_Barrier(MPI_COMM_WORLD) failed
MPIR_Bcast(1031)..................:
MPIR_Bcast_binomial(157)..........:
MPIC_Recv(83).....................:
MPIC_Wait(513)....................:
MPIDI_CH3I_Progress(150)..........:
MPID_nem_mpich2_blocking_recv(948):
MPID_nem_tcp_connpoll(1720).......:
state_commrdy_handler(1556).......:
MPID_nem_tcp_recv_handler(1446)...: socket closed
Fatal error in PMPI_Barrier: Other MPI error, error stack:
PMPI_Barrier(476).................: MPI_Barrier(MPI_COMM_WORLD) failed
MPIR_Bcast(1031)..................:
MPIR_Bcast_binomial(157)..........:
MPIC_Recv(83).....................:
MPIC_Wait(513)....................:
MPIDI_CH3I_Progress(150)..........:
MPID_nem_mpich2_blocking_recv(948):
MPID_nem_tcp_connpoll(1720).......:
state_commrdy_handler(1556).......:
MPID_nem_tcp_

10

General Questions and Answers / logfile meaning

« on: April 4, 2011, 06:23 »

Numbers of Processors:  10
---------------------------
started mpd Number: 5
---------------------------
/share/apps/ATK/atkpython/bin/atkpython: line 3:  7097 Killed                  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 $*


rank 8 in job 1  node9_42312   caused collective abort of all ranks
  exit status of rank 8: return code 137

 what does the above message mean

11

General Questions and Answers / Transmission spectrum

« on: April 4, 2011, 06:22 »

# 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]
    )

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = [
    LDABasis.Gold_SingleZetaPolarized,
    LDABasis.Carbon_DoubleZetaPolarized,
    ]

#----------------------------------------
# Numerical Accuracy Settings
#----------------------------------------
left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=(10, 10, 100),
    )

right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=(10, 10, 100),
    )

device_numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=(10, 10, 100),
    )

#----------------------------------------
# Poisson Solver Settings
#----------------------------------------
device_poisson_solver = MultigridSolver(
    boundary_conditions=[[PeriodicBoundaryCondition,PeriodicBoundaryCondition],
                         [PeriodicBoundaryCondition,PeriodicBoundaryCondition],
                         [DirichletBoundaryCondition,DirichletBoundaryCondition]]
    )

#----------------------------------------
# Electrode Calculators
#----------------------------------------
left_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    numerical_accuracy_parameters=left_electrode_numerical_accuracy_parameters,
    )

right_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    numerical_accuracy_parameters=right_electrode_numerical_accuracy_parameters,
    )

#----------------------------------------
# Device Calculator
#----------------------------------------
voltagelist=[0.2*i for i in range(26)]
for myvolt in voltagelist:     
    calculator = DeviceLCAOCalculator(
    basis_set=basis_set,
    numerical_accuracy_parameters=device_numerical_accuracy_parameters,
    electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
    electrode_voltages=( 0.0*Volt, myvolt*Volt)
    )

    device_configuration.setCalculator(calculator)
    nlprint(device_configuration)
    device_configuration.update()
    if(myvolt<0.3):
        nlsave('/home/hassan/C80/C80mr61.nc', device_configuration)

# -------------------------------------------------------------
# Transmission spectrum
# -------------------------------------------------------------
    transmission_spectrum = TransmissionSpectrum(
    configuration=device_configuration,
    energies=numpy.linspace(-5,5,100)*eV,
    kpoints=MonkhorstPackGrid(1,1),
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    self_energy_calculator=KrylovSelfEnergy(),
    )
    nlsave('/home/hassan/C80/C80mr61.nc', transmission_spectrum)
    nlprint(transmission_spectrum)




what is wrom with the above script for it does not generate the specified number of transmission curves

12

General Questions and Answers / transmissionspectrum

« on: March 22, 2011, 06:55 »

look at this script and tell me why i can not obtain the 25 spectrum am looking for  so that i can have the I-V curve
what is wrong in the script
can i submit to jobs in the same maste

Code: python

voltagelist=[0.2*i for i in range(26)]
for myvolt in voltagelist:      
    calculator = DeviceLCAOCalculator(
    basis_set=basis_set,
    numerical_accuracy_parameters=device_numerical_accuracy_parameters,
    electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
    electrode_voltages=( 0.0*Volt, myvolt*Volt)
    )

    device_configuration.setCalculator(calculator)
    nlprint(device_configuration)
    device_configuration.update()
    if(myvolt<0.3)
        nlsave('C80sixmr.nc', device_configuration)

# -------------------------------------------------------------
# Transmission spectrum
# -------------------------------------------------------------
    transmission_spectrum = TransmissionSpectrum(
    configuration=device_configuration,
    energies=numpy.linspace(-5,5,100)*eV,
    kpoints=MonkhorstPackGrid(1,1),
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    self_energy_calculator=KrylovSelfEnergy(),
    )
    nlsave('C80sixmr.nc', transmission_spectrum)
    nlprint(transmission_spectrum)