Show Posts

1

General Questions and Answers / ATK unexpectedly terminates

« on: June 16, 2011, 03:23 »

Dear support,

For some reason my program stops working and I do not know if this is the problem of my computer or ATK 11.2.3 problem.
I'm running iv-loop calculations for my system. Everything starts smoothly, but after a couple of days the program terminates with the message in error file:

terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc

The last message in output file is the following:

rank 3 in job 1 tmg-dl585g5-00_55054 caused collective abort of all ranks
exit status of rank 3: killed by signal 9

It happened twice. I'm using version of Fedora 14 (x86_64).

Please help me understand if this is my hardware or ATK problem.

Also, how can I resume my interrupted simulation from 'checkpoint.nc' file?

Thanks.

2

General Questions and Answers / Hydrogen bond detection

« on: March 1, 2011, 00:04 »

Dear support staff,

I have two questions.

1. I wonder if there is any reliable way to detect hydrogen bond length. I simulate a molecule covalently bonded to the left electrode and attracted to the right hydrogen-terminated carbon electrode. The way I do it is adjust the distance between molecule and the right electrode in hope to see the minimum in total energy. To get the minimum I optimize the system and get E_tot. Then to remove the influence of electrodes I perform SCF without a molecule for the same geometry of electrodes and subtract the total energies. I expect to see the minimum but the problem is that the energy difference oscillates or stays flat for larger distances. Also, even if I manage to find the minimum this way, hydrogen bond length is too large, of the order of 2.5 Angstroms or even larger.

Also, is there a way to increase the precision of the Total energy? For large systems I have only one digit after decimal point for E_tot and even if there is a minimum, I cannot see it, because E_tot does not change when I move right electrode. Can I get, let's say, three digits after decimal point regardless of how large my system is?

To sum up, is it possible to get correct H-bond length with ATK 10.8.2? Today I read that in new version ATK 11.2 the distance between electrodes can be optimized together with the central region which means automatic detection of proper bond lengths on both sides. Will it pick up the correct hydrogen bond length?

2. In new ATK 11.2 you added the new feature of calculating the complex band structure. How do you return results for it? Can I save data points and approximate particular branch by some function for imaginary k. I need it to extract effective mass of electron.

Thanks in advance.

3

General Questions and Answers / Re: vnl crash

« on: February 22, 2011, 21:33 »

Thanks Nordland, It worked. If I open About box first, after that everything works fine.

Thanks Anders. This is true. I use default driver. I'm going to install the correct one.

4

General Questions and Answers / vnl crash

« on: February 18, 2011, 20:57 »

Dear QuantumWise support,

I have a problem with VNL. I downloaded latest ATK version 10.8.2 and installed it. Pressing almost every button on the tool bar (like Builder, Custom, Database, Scripter, Viewer) results in a crash of VNL. Surprisingly, pressing Editor, Jobs and Analyzer does not crash VNL and returns appropriate windows.

I do not know what is going on. I tried to reinstall the software several times. The result is the same. Crash after crash. I can't even build the system. Please tell me which of my log files you need to see to identify the problem and where I can find these logs on my system.

My system is:

2.6.35.11-83.fc14.x86_64
Fedora release 14 (Laughlin)
RFRemix release 14 (Laughlin)

Thanks.

5

Installation and License Questions / Error while starting license server for ATK 10.8

« on: December 15, 2010, 00:04 »

Dear QuantumWise support team,

I have the following problem. I installed ATK 10.8 and now trying to run license server from license directory as specified in tutorial:

[user@alpha: license]$ ./lmx-serv-quantum -l license_file.lic

I get the following error:

LM-X License Server v3.4 (Linux_x64)
Copyright (C) 2002-2010 X-Formation. All rights reserved.

[2010-12-14 15:09:45] LM-X License Server v3.4 build 6106 on tmg-dl585g5-00 (Linux_x64)
[2010-12-14 15:09:45] Copyright (C) 2002-2010 X-Formation. All rights reserved.
[2010-12-14 15:09:45] Website: http://www.lm-x.com http://www.x-formation.com
[2010-12-14 15:09:45] License server has pid 27457.
[2010-12-14 15:09:45] Serving licenses for QUANTUM.
[2010-12-14 15:09:45]
[2010-12-14 15:09:45] FAIL: Unable to create lockfile /var/tmp/quantum.lock!

Could you explain me what this is and how I fix it? I'm trying to run license server NOT as a root. I'm a regular user. Is it because I do not have sufficient privileges?

I use the following linux:

Scientific Linux SL release 5.2
x86_64 GNU/Linux

Thanks.

6

General Questions and Answers / Centering the system in unit cell

« on: October 22, 2010, 23:29 »

Hello everyone,

My question is addressed to the ATK 2010 developers. When building a device just for convenience I usually move the atoms in the unit cell to the left so the leftmost atom has zero z-component. After inserting the molecule, as recommended, I center the system in the unit cell before switching into the "device mode". One day I forgot to do it. As a result I obtained huge values for DD and DM in the output file for left electrode. Here is the typical values:

+------------------------------------------------------------------------------+
| Density Matrix Report DM DD |
+------------------------------------------------------------------------------+
| 0 C [ 5.000 , 1.231 , 0.000 ] 145.93467 141.93467 |
| 1 C [ 5.000 , 3.692 , 0.000 ] 145.35013 141.35013 |
| 2 C [ 5.000 , 6.153 , 0.000 ] 145.93382 141.93382 |
| 3 C [ 5.000 , 0.000 , 0.710 ] 3.44331 -0.55669 |
| 4 C [ 5.000 , 2.461 , 0.710 ] 3.44260 -0.55740 |
| 5 C [ 5.000 , 4.922 , 0.710 ] 3.44260 -0.55740 |
| 6 C [ 5.000 , 0.000 , 2.131 ] 4.00128 0.00128 |
| 7 C [ 5.000 , 2.461 , 2.131 ] 4.00044 0.00044 |
| 8 C [ 5.000 , 4.922 , 2.131 ] 4.00044 0.00044 |
| 9 C [ 5.000 , 1.231 , 2.842 ] 3.70081 -0.29919 |
| 10 C [ 5.000 , 3.692 , 2.842 ] 3.70013 -0.29987 |
| 11 C [ 5.000 , 6.153 , 2.842 ] 3.70081 -0.29919 |
| 12 C [ 5.000 , 6.153 , 4.263 ] -137.07787 -141.07787 |
| 13 C [ 5.000 , 3.692 , 4.263 ] -136.49443 -140.49443 |
| 14 C [ 5.000 , 1.231 , 4.263 ] -137.07872 -141.07872 |
+------------------------------------------------------------------------------+
| 3 E = -45.6314 dE = 1.205925e+00 dH = 2.830564e-01 |
+------------------------------------------------------------------------------+

Also, starting from some iteration I get abnormally large forces on some atoms in the central region:

+------------------------------------------------------------------------------+
| Density Matrix Report DM DD |
+------------------------------------------------------------------------------+
| 0 C [ 5.000 , 1.231 , 0.000 ] -1938964.66509 -1938968.66509 |
| 1 C [ 5.000 , 3.692 , 0.000 ] -1939052.45277 -1939056.45277 |
| 2 C [ 5.000 , 6.153 , 0.000 ] -1938967.28253 -1938971.28253 |
| 3 C [ 5.000 , 0.000 , 0.710 ] -1232.68324 -1236.68324 |
| 4 C [ 5.000 , 2.461 , 0.710 ] -1233.05722 -1237.05722 |
| 5 C [ 5.000 , 4.922 , 0.710 ] -1233.05763 -1237.05763 |
| 6 C [ 5.000 , 0.000 , 2.131 ] -85.32339 -89.32339 |
| 7 C [ 5.000 , 2.461 , 2.131 ] -85.24910 -89.24910 |
| 8 C [ 5.000 , 4.922 , 2.131 ] -85.24915 -89.24915 |
| 9 C [ 5.000 , 1.231 , 2.842 ] 26.94666 22.94666 |
| 10 C [ 5.000 , 3.692 , 2.842 ] 26.93101 22.93101 |
| 11 C [ 5.000 , 6.153 , 2.842 ] 26.94667 22.94667 |
| 12 C [ 5.000 , 6.153 , 4.263 ] -17.30353 -21.30353 |
| 13 C [ 5.000 , 3.692 , 4.263 ] -17.28189 -21.28189 |
| 14 C [ 5.000 , 1.231 , 4.263 ] -17.30349 -21.30349 |
| 15 C [ 5.000 , 0.000 , 4.973 ] 0.00000 -4.00000 |
| 16 C [ 5.000 , 2.461 , 4.973 ] 0.00000 -4.00000 |
| 17 C [ 5.000 , 4.922 , 4.973 ] 0.00000 -4.00000 |
| 18 C [ 5.000 , 2.461 , 6.394 ] 0.00000 -4.00000 |
.......

After I center the system, this problem disappears.

My question is why forgetting to center the system leads to so large forces? It's just centering, and periodicity should take care of everything. Note that after switching to the device mode I picked the correct left and right electrode length (4.2626 A in my case). In documentation the centering operation is mentioned rather as a suggestion for correct detection of the periodicity, not as a requirement. In the end, I can always manually type in correct size of the unit cell in the device mode.

Another question is if there is a bigger problem behind it and centering eliminates it only partially?

Just in case if you need it, here is my test system:

Thanks in advance.

###############################################################
# TwoProbe configuration
###############################################################

###############################################################
# Left electrode
###############################################################

# Set up lattice
vector_a = [10.0, 0.0, 0.0]*Angstrom
vector_b = [0.0, 7.38300513133, 0.0]*Angstrom
vector_c = [0.0, 0.0, 4.2626]*Angstrom
left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
left_electrode_elements = [Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon]

# Define coordinates
left_electrode_coordinates = [[ 5. , 1.23050086, 0. ],
[ 5. , 3.69150257, 0. ],
[ 5. , 6.15250428, 0. ],
[ 5. , 0. , 0.71043 ],
[ 5. , 2.46100171, 0.71043 ],
[ 5. , 4.92200342, 0.71043 ],
[ 5. , 0. , 2.13129 ],
[ 5. , 2.46100171, 2.13129 ],
[ 5. , 4.92200342, 2.13129 ],
[ 5. , 1.23050086, 2.84172 ],
[ 5. , 3.69150257, 2.84172 ],
[ 5. , 6.15250428, 2.84172 ],
[ 5. , 6.15250428, 4.26258 ],
[ 5. , 3.69150257, 4.26258 ],
[ 5. , 1.23050086, 4.26258 ]]*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 = [10.0, 0.0, 0.0]*Angstrom
vector_b = [0.0, 7.38300513133, 0.0]*Angstrom
vector_c = [0.0, 0.0, 4.2626]*Angstrom
right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
right_electrode_elements = [Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon]

# Define coordinates
right_electrode_coordinates = [[ 5.00000000e+00, 3.69150257e+00, -2.00000000e-05],
[ 5.00000000e+00, 1.23050086e+00, -2.00000000e-05],
[ 5.00000000e+00, 6.15250428e+00, -2.00000000e-05],
[ 5.00000000e+00, 0.00000000e+00, 7.10410000e-01],
[ 5.00000000e+00, 4.92200342e+00, 7.10410000e-01],
[ 5.00000000e+00, 2.46100171e+00, 7.10410000e-01],
[ 5.00000000e+00, 0.00000000e+00, 2.13127000e+00],
[ 5.00000000e+00, 4.92200342e+00, 2.13127000e+00],
[ 5.00000000e+00, 2.46100171e+00, 2.13127000e+00],
[ 5.00000000e+00, 3.69150257e+00, 2.84170000e+00],
[ 5.00000000e+00, 6.15250428e+00, 2.84170000e+00],
[ 5.00000000e+00, 1.23050086e+00, 2.84170000e+00]]*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 = [10.0, 0.0, 0.0]*Angstrom
vector_b = [0.0, 7.38300513133, 0.0]*Angstrom
vector_c = [0.0, 0.0, 21.3939]*Angstrom
central_region_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
central_region_elements = [Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Hydrogen, Hydrogen, Carbon, Hydrogen, Hydrogen, Carbon, Carbon,
Carbon, Carbon, Hydrogen, Hydrogen, Carbon, Hydrogen, Hydrogen,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon]

# Define coordinates
central_region_coordinates = [[ 5. , 1.23050086, 0. ],
[ 5. , 3.69150257, 0. ],
[ 5. , 6.15250428, 0. ],
[ 5. , 0. , 0.71043 ],
[ 5. , 2.46100171, 0.71043 ],
[ 5. , 4.92200342, 0.71043 ],
[ 5. , 0. , 2.13129 ],
[ 5. , 2.46100171, 2.13129 ],
[ 5. , 4.92200342, 2.13129 ],
[ 5. , 1.23050086, 2.84172 ],
[ 5. , 3.69150257, 2.84172 ],
[ 5. , 6.15250428, 2.84172 ],
[ 5. , 6.15250428, 4.26258 ],
[ 5. , 3.69150257, 4.26258 ],
[ 5. , 1.23050086, 4.26258 ],
[ 5. , 0. , 4.97301 ],
[ 5. , 2.46100171, 4.97301 ],
[ 5. , 4.92200342, 4.97301 ],
[ 5. , 2.46100171, 6.39387 ],
[ 5. , 4.92200342, 6.39387 ],
[ 5. , 0. , 6.39387 ],
[ 5. , 3.6915 , 7.1043 ],
[ 5. , 6.15250428, 7.1043 ],
[ 5. , 1.23050086, 7.1043 ],
[ 5. , 1.23050087, 8.2053 ],
[ 5. , 6.15250429, 8.2053 ],
[ 5. , 3.6915 , 8.5788 ],
[ 2.8813 , 3.23562028, 8.726333 ],
[ 7.118674 , 4.14747328, 8.726334 ],
[ 3.806231 , 3.42960428, 9.285847 ],
[ 6.193767 , 3.95342128, 9.285857 ],
[ 6.193768 , 3.95342528, 10.687147 ],
[ 3.806234 , 3.42960828, 10.687157 ],
[ 7.118675 , 4.14747728, 11.246667 ],
[ 2.881305 , 3.23561728, 11.246667 ],
[ 5.000008 , 3.69149728, 11.3942 ],
[ 5. , 6.15250429, 11.7677 ],
[ 5. , 1.23050087, 11.7677 ],
[ 5. , 1.23050086, 12.8687 ],
[ 5. , 3.69150257, 12.8687 ],
[ 5. , 6.15250428, 12.8687 ],
[ 5. , 2.46100171, 13.57913 ],
[ 5. , 0. , 13.57913 ],
[ 5. , 4.92200342, 13.57913 ],
[ 5. , 4.92200342, 14.99999 ],
[ 5. , 0. , 14.99999 ],
[ 5. , 2.46100171, 14.99999 ],
[ 5. , 3.69150257, 15.71042 ],
[ 5. , 6.15250428, 15.71042 ],
[ 5. , 1.23050086, 15.71042 ],
[ 5. , 3.69150257, 17.13128 ],
[ 5. , 1.23050086, 17.13128 ],
[ 5. , 6.15250428, 17.13128 ],
[ 5. , 0. , 17.84171 ],
[ 5. , 4.92200342, 17.84171 ],
[ 5. , 2.46100171, 17.84171 ],
[ 5. , 0. , 19.26257 ],
[ 5. , 4.92200342, 19.26257 ],
[ 5. , 2.46100171, 19.26257 ],
[ 5. , 3.69150257, 19.973 ],
[ 5. , 6.15250428, 19.973 ],
[ 5. , 1.23050086, 19.973 ]]*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]
)

7

General Questions and Answers / Re: Help error

« on: August 31, 2010, 02:39 »

Hey guys,

I have similar problem. I perform geometry optimization. After some time (half an hour or so) my calculation crashes. Here is how I run my job and the log from xterm after the crash:

[user@dirac: parallel_test]$ mpiexec -n 4 /home/user/QuantumWise/atk-10.8.0/atkpython/bin/atkpython run_file.py > run_file.out
Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(773)................: MPI_Allreduce(sbuf=0x107c51e0, rbuf=0x108277f0, count=318, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD) failed
MPIR_Reduce(759)..................:
MPIR_Reduce_redscat_gather(485)...:
MPIDI_CH3U_Receive_data_found(129): Message from rank 3 and tag 11 truncated; 1280 bytes received but buffer size is 1264
Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(773)................: MPI_Allreduce(sbuf=0x15df8b20, rbuf=0x10e33900, count=318, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD) failed
MPIR_Reduce(759)..................:
MPIR_Reduce_redscat_gather(485)...:
MPIDI_CH3U_Receive_data_found(129): Message from rank 3 and tag 11 truncated; 640 bytes received but buffer size is 632

And here are the error lines from output file:

rank 1 in job 3 dirac_57726 caused collective abort of all ranks
exit status of rank 1: killed by signal 9

I'm running Suse Linux on AMD 64 with 4 cores. My calculator parameters are:

basis_set = GGABasis.DoubleZetaPolarized
exchange_correlation = GGA.PBE
electron_temperature=800.0*Kelvin
k_point_sampling=(1, 1, 100)

The contacts and molecule are composed of carbon and hydrogen with total number of molecules about 100.

8

General Questions and Answers / Re: Resturt from previous run in atk 2010

« on: August 24, 2010, 20:49 »

Thanks a lot Anders.

9

General Questions and Answers / Resturt from previous run in atk 2010

« on: August 23, 2010, 21:58 »

Dear all,

I'm a new user. I started from 2010 version and know nothing about previous 2008 one. I'd like to ask you how to start a new job from a previous run or possibly from interrupted run in ATK 2010. What I'm trying to do is get I/V curve for 2 probe system with a small organic molecule between the leads. The leads and the molecule are composed of Carbon and Hydrogen with the total number of atoms about 100.

I used the bias loop script provided here: http://www.quantumwise.com/documents/tutorials/GrapheneJunctionDevice/XHTML/chap.current.html

Even though the script mentions the "use the self consistent state of the old calculation as starting input", I have a strong suspicion that it only picks up the geometry configuration and previous calculator parameters with modified bias, but not the self consistent field state from the previous run. I tried to nlprint the "device_configuration" object in the manual mode and got the geometry of the system. The restarting from previous run is important because my calculations of current do not converge even when I raise the temperature up to 1000 (I used extended Huckel method), so the restarting from previous run could possibly solve my problem of convergence.

I found some tips how to restart from previous run in 2008 version (http://www.quantumwise.com/documents/manuals/ATK-2008.10/chap.tipstricks.html), but I guess it won't work in 2010. I searched the atk 2010 manual and didn't find anything like "runtimeParameters" or "checkpoint_filename" parameters.

In sum,

1. I would appreciate if anybody tells me a legitimate way to start my calculations from the previous or interrupted run in atk 2010 (or proves me wrong about my suspicion regarding the "device_configuration" functionality).
2. Could you suggest something how to improve the convergence apart form raising the temperature?

Thanks.

QuantumATK Forum

News:

Messages - alex_z