1
General Questions and Answers / Re: Checkpoint handler and remote jobs
« on: July 19, 2018, 15:05 »
Thank you Petr, I will try that.
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2
General Questions and Answers / Re: Checkpoint handler and remote jobs
« on: July 16, 2018, 16:10 »
Of course, here is the python script
And here is the log file (edited for brevity):
As for the error message, it is as such :
(Do note that the reason for the error "The checkpoint file /W/sb255620/VNL/checkpointraw.hdf5 is not writable" is that this file is on the cluster and not on my local machine.)
Code
# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------
# Set up lattice
vector_a = [40.0, 0.0, 0.0]*Angstrom
vector_b = [0.0, 40.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 11.8619]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)
# Define elements
elements = [Bismuth, Bismuth, Bismuth, Bismuth, Bismuth, Bismuth, Bismuth,
Bismuth, Bismuth, Bismuth, Bismuth, Bismuth, Bismuth, Bismuth,
Bismuth, Bismuth, Bismuth, Bismuth, Bismuth, Bismuth, Bismuth,
[...]
Bismuth, Bismuth, Bismuth, Bismuth, Bismuth, Bismuth, Bismuth,
Bismuth, Bismuth, Bismuth, Bismuth, Bismuth, Bismuth, Bismuth,
Bismuth, Bismuth, Bismuth, Bismuth, Bismuth, Bismuth, Bismuth]
# Define coordinates
fractional_coordinates = [[ 0.5 , 0.171896319741, 0.192666573062],
[ 0.329512326692, 0.270327423819, 0.192666573062],
[ 0.443170775564, 0.270327423819, 0.192666573062],
[...]
[ 0.727316897743, 0.696862208155, -0.000000485839],
[ 0.443170775564, 0.795293312233, -0.000000485839],
[ 0.556829224436, 0.795293312233, -0.000000485839]]
# Set up configuration
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=fractional_coordinates
)
# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = SOGGA.PBE
k_point_sampling = MonkhorstPackGrid(
nc=7,
force_timereversal=False,
)
numerical_accuracy_parameters = NumericalAccuracyParameters(
k_point_sampling=k_point_sampling,
density_mesh_cutoff=220.0*Hartree,
)
checkpoint_handler = CheckpointHandler(
file_name=u'/W/sb255620/VNL/checkpointraw.hdf5',
)
calculator = LCAOCalculator(
exchange_correlation=exchange_correlation,
numerical_accuracy_parameters=numerical_accuracy_parameters,
checkpoint_handler=checkpoint_handler,
)
bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('Rawcut_k=7.hdf5', bulk_configuration)
# -------------------------------------------------------------
# Bandstructure
# -------------------------------------------------------------
bandstructure = Bandstructure(
configuration=bulk_configuration,
route=['G', 'Z'],
points_per_segment=50
)
nlsave('Rawcut_k=7.hdf5', bandstructure)
And here is the log file (edited for brevity):
Code
------------------------------------------------------
Allocation (N): -n 8 -ppn 8
------------------------------------------------------
MPI nodes (NCPU): 1
Cores (NCORES): 8
Threads per process: automatic
------------------------------------------------------
Node list
s148
Core list
s148
s148
s148
s148
s148
s148
s148
s148
------------------------------------------------------
PBS: qsub is running on summer.cluster
PBS: originating queue is standard
PBS: executing queue is standard
PBS: execution mode is PBS_BATCH
PBS: current home directory is /home/sb255620
PBS: working directory is /W/sb255620/VNL/180711-oYoHx5Wc
PBS: job name is 180711-oYoHx5Wc
PBS: job identifier is 1833694.summer.cluster
PBS: PATH = /home/sb255620/QuantumATK/QuantumATK-2018.06/bin:/home/sb255620/QuantumWise/VNL-ATK-2017.12/bin:/bin:/sbin:/usr/X11R6/bin:/usr/sbin:/usr/bin:/etc:/home/cmd:/usr/ccs/bin:/usr/openwin/bin:/usr/dt/bin:/opt/sfw/bin:/home/prog/SUNWspro/bin:/home/prog/s1studio/ee/bin:/home/systeme/SUNWspro/bin:/home/systeme/SUNWste/bin:/usr/ucb:/usr/local/bin:.
PBS: node file is /var/spool/torque/aux//1833694.summer.cluster
------------------------------------------------------
+------------------------------------------------------------------------------+
| |
| QuantumATK 2018.06[Build 1745fc0] |
| |
+------------------------------------------------------------------------------+
+----------------------------------------------------------+
| Bulk Bravais lattice |
+----------------------------------------------------------+
Type:
UnitCell
Lattice constants:
Primitive vectors:
u_1 = 40.000000 0.000000 0.000000 Ang
u_2 = 0.000000 40.000000 0.000000 Ang
u_3 = 0.000000 0.000000 11.861900 Ang
+----------------------------------------------------------+
| Bulk: Cartesian (Angstrom) / fractional |
+----------------------------------------------------------+
182
Bulk
Bi 2.000000e+01 6.875853e+00 2.285392e+00 0.50000 0.17190 0.19267
Bi 1.318049e+01 1.081310e+01 2.285392e+00 0.32951 0.27033 0.19267
Bi 1.772683e+01 1.081310e+01 2.285392e+00 0.44317 0.27033 0.19267
[...]
Bi 2.909268e+01 2.787449e+01 -5.762974e-06 0.72732 0.69686 -0.00000
Bi 1.772683e+01 3.181173e+01 -5.762974e-06 0.44317 0.79529 -0.00000
Bi 2.227317e+01 3.181173e+01 -5.762974e-06 0.55683 0.79529 -0.00000
+------------------------------------------------------------------------------+
| |
| DFT Calculation [Started Wed Jul 11 16:22:46 2018] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| CPU Information |
| |
+------------------------------------------------------------------------------+
| Process ID 0 at s148 (2 threads) |
| Process ID 1 at s148 (2 threads) |
| Process ID 2 at s148 (2 threads) |
| Process ID 3 at s148 (2 threads) |
| Process ID 4 at s148 (2 threads) |
| Process ID 5 at s148 (2 threads) |
| Process ID 6 at s148 (2 threads) |
| Process ID 7 at s148 (2 threads) |
+------------------------------------------------------------------------------+
|--------------------------------------------------|
Calculating Kinetic Matrix : ==================================================
|--------------------------------------------------|
Calculating Nonlocal Part : ==================================================
|--------------------------------------------------|
Calculating Nonlocal Part : ==================================================
|--------------------------------------------------|
Calculating Nonlocal Part : ==================================================
+------------------------------------------------------------------------------+
| |
| SCF Loop Information |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| K-point grid: 1 x 1 x 7 |
| Number of irreducible k-points: 7 |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Real space grid sampling is (505, 505, 150) in a, b, and c directions. |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Memory requirements for the calculation |
+------------------------------------------------------------------------------+
| Dense matrices: 157 MB per matrix [Matrix dimensions 4550 x 4550] |
| Total memory required per k-point: 473 MB |
| |
| Storage of real-space orbitals: Disabled |
| Storage requires 720 MB |
| |
| Total memory required per real-space grid: 1.17 GB |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| SCF History |
+------------------------------------------------------------------------------+
| Memory required to store SCF history: 5.86 GB |
| Number of history steps: 20 |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Checkpoint Handler |
+------------------------------------------------------------------------------+
| Filename : /W/sb255620/VNL/checkpointraw.hdf5 |
| Interval : 0.5 h |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Diagonalization solver parallelization report |
+------------------------------------------------------------------------------+
| Total number of processes: 8 |
| Total number of k-points: 7 |
| Processes per k-point: 1 |
+------------------------------------------------------------------------------+
| Process occupation |
+------------------------------------------------------------------------------+
| Process 0: |===============================================================| |
| Process 1: |===============================================================| |
| Process 2: |===============================================================| |
| Process 3: |===============================================================| |
| Process 4: |===============================================================| |
| Process 5: |===============================================================| |
| Process 6: |===============================================================| |
| Process 7: | | |
+------------------------------------------------------------------------------+
| WARNING: Some processes are idle. |
+------------------------------------------------------------------------------+
|--------------------------------------------------|
Calculating Eigenvalues : ==================================================
Calculating Density Matrix : ==================================================
+------------------------------------------------------------------------------+
| Density Matrix Report DM[U] DM[D] DD |
+------------------------------------------------------------------------------+
| 0 Bi [ 20.000 , 6.876 , 2.285 ] 7.94291 6.93789 -0.11920 |
| 1 Bi [ 13.180 , 10.813 , 2.285 ] 7.81446 7.11966 -0.06589 |
| 2 Bi [ 17.727 , 10.813 , 2.285 ] 7.75630 7.30821 0.06451 |
| 3 Bi [ 22.273 , 10.813 , 2.285 ] 7.75630 7.30821 0.06451 |
[...]
| 179 Bi [ 29.093 , 27.874 , -0.000 ] 7.80852 7.14572 -0.04576 |
| 180 Bi [ 17.727 , 31.812 , -0.000 ] 7.82164 7.13865 -0.03971 |
| 181 Bi [ 22.273 , 31.812 , -0.000 ] 7.82164 7.13865 -0.03971 |
+------------------------------------------------------------------------------+
| 0 E = -2132.12 dE = 3.444100e+01 dH = 1.077753e-01 |
+------------------------------------------------------------------------------+
[...]
+------------------------------------------------------------------------------+
| Calculation Converged in 29 steps |
| |
| Fermi Level = -4.274652 eV |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| DFT Calculation [Finished Thu Jul 12 13:25:20 2018] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Bandstructure Analysis |
| |
+------------------------------------------------------------------------------+
|--------------------------------------------------|
Calculating Bandstructure : ==================================================
Timing: Total Per Step %
--------------------------------------------------------------------------------
Diagonalization : 61221.98 s 2111.10 s 74.48% |=============|
Real Space Integral : 5636.02 s 187.87 s 6.86% ||
Valence Density : 2679.99 s 89.33 s 3.26% ||
Exchange-Correlation : 1902.03 s 63.40 s 2.31% |
Hartree Potential : 191.05 s 6.37 s 0.23% |
Core Density : 91.54 s 91.54 s 0.11% |
Setting Density Matrix : 88.10 s 88.10 s 0.11% |
Mixing : 69.65 s 2.40 s 0.08% |
Constant Terms : 35.20 s 35.20 s 0.04% |
Difference Density : 30.93 s 1.00 s 0.04% |
Loading Modules + MPI : 18.39 s 18.39 s 0.02% |
Real Space Basis : 9.26 s 9.26 s 0.01% |
Neutral Atom Potential : 7.30 s 7.30 s 0.01% |
Hubbard Term : 0.00 s 0.00 s 0.00% |
Fixed Spins Term : 0.00 s 0.00 s 0.00% |
Basis Set Generation : 0.00 s 0.00 s 0.00% |
--------------------------------------------------------------------------------
Total : 82194.93 s (22h49m54.93s)As for the error message, it is as such :
Code
Traceback (most recent call last):
File "zipdir\NL\GUI\MainWindow\LabFloor\LabFloorModel.py", line 327, in load
File "C:\Program Files\QuantumATK\QuantumATK-2018.06\Lib\site-packages\AddOns\ATKDataReader\ATKDataReader.py", line 291, in load
filename, object_id=object_id, read_state=read_full, lightweight=lightweight)[0]
File "zipdir\NL\IO\NLSaveUtilities.py", line 847, in nlread
File "zipdir\NL\IO\HDF5.py", line 490, in readHDF5
File "zipdir\NL\IO\HDF5.py", line 576, in readHDF5Group
File "zipdir\NL\IO\HDF5.py", line 537, in readHDF5Dict
File "zipdir\NL\IO\HDF5.py", line 609, in readHDF5Group
File "zipdir\NL\IO\HDF5.py", line 537, in readHDF5Dict
File "zipdir\NL\IO\HDF5.py", line 597, in readHDF5Group
File "zipdir\NL\IO\Serializable.py", line 318, in _fromVersionedData
File "zipdir\NL\CommonConcepts\Calculator.py", line 68, in _createObject
File "zipdir\NL\QuantumATK\ScopeExecuter.py", line 214, in scope_execute
NLScopeExecutionError: The checkpoint file /W/sb255620/VNL/checkpointraw.hdf5 is not writable. Please make sure that a writable directory is selected, or disable checkpoint_handler on the calculator.
3
General Questions and Answers / Checkpoint handler and remote jobs
« on: July 12, 2018, 15:50 »
Hello, I am working with VNL on a local windows machine, and running the calculations on a remote Linux cluster.
I haven't found a clear indication on how to use checkpoint files in a remote configuration.
So far, what I've tried is :
- Create a script file specifying a local path for the checkpoint file (i.e. u’C:\User\[...]\Bi_nw\checkpointraw.hdf5’)
- Go into the script editor and change it to an absolute path on the server (i.e. u’/W/sb255620/VNL/checkpointraw.hdf5’)
- Create a blank “checkpoint.hdf5” file at the specified location on the server, and make it writable for all users (otherwise atk will throw an error when I start the calculation)
When I do this, the calculations finish, but once I download the result file on my local machine and try to read the band structure, I get the error shown in the picture below.
Apparently the results in the final hdf5 file are dependent on the checkpoint file.
What should I do instead ? Should I use the same file for results and checkpoint ? Or is there something to do with the I/O window in the job manager when I submit the job ?
I haven't found a clear indication on how to use checkpoint files in a remote configuration.
So far, what I've tried is :
- Create a script file specifying a local path for the checkpoint file (i.e. u’C:\User\[...]\Bi_nw\checkpointraw.hdf5’)
- Go into the script editor and change it to an absolute path on the server (i.e. u’/W/sb255620/VNL/checkpointraw.hdf5’)
- Create a blank “checkpoint.hdf5” file at the specified location on the server, and make it writable for all users (otherwise atk will throw an error when I start the calculation)
When I do this, the calculations finish, but once I download the result file on my local machine and try to read the band structure, I get the error shown in the picture below.
Apparently the results in the final hdf5 file are dependent on the checkpoint file.
What should I do instead ? Should I use the same file for results and checkpoint ? Or is there something to do with the I/O window in the job manager when I submit the job ?
4
General Questions and Answers / Re: Relaxation of Bismuth
« on: July 3, 2018, 16:17 »
Thanks for the suggestion, I'll try fitting it.
I am trying to characterize surface states in those nanowires, so I do need to perform a relaxation.
I am trying to characterize surface states in those nanowires, so I do need to perform a relaxation.
5
General Questions and Answers / Relaxation of Bismuth
« on: July 3, 2018, 14:21 »
So, I'm trying to relax H-passivated bismuth nanowires in ATK, however doing DFT-based relaxation is quite time-consuming. Thus I've been trying to perform some ForceField based calculations, at least to get a first approximation before doing DFT iterations.
There are however no TremoloX/Brenner/EMT parameters available for bismuth and bismuth compounds. Since we can add custom potentials now, I've tried using a naive Lennard-Jones potential for Bi-Bi and Bi-H potentials. This fails and results in a massive spaghetti ball, as seen in the attached picture.
Here is my question then, for people who are more familiar with molecular dynamics: is there some more appropriate pseudopotential that would be suited for quick-but-accurate relaxation of Bi nanowires ?
There are however no TremoloX/Brenner/EMT parameters available for bismuth and bismuth compounds. Since we can add custom potentials now, I've tried using a naive Lennard-Jones potential for Bi-Bi and Bi-H potentials. This fails and results in a massive spaghetti ball, as seen in the attached picture.
Here is my question then, for people who are more familiar with molecular dynamics: is there some more appropriate pseudopotential that would be suited for quick-but-accurate relaxation of Bi nanowires ?
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