106
General Questions and Answers / Re: Reason for sudden jump in stress optimization
« on: September 13, 2022, 11:39 »
Thankyou Anders Blom
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107
General Questions and Answers / Re: Reason for sudden jump in stress optimization
« on: September 9, 2022, 11:53 »
Here is an attached pic that shows sudden jumps in AIMD calculations as well. What could be possible reasons? This happened in many simulations?
108
General Questions and Answers / Re: Reason for sudden jump in stress optimization
« on: September 2, 2022, 07:19 »
Can I get your email where I can send further details?
Also, Could you explain what you mean by "scan lattice parameters..."?
Thanks
Also, Could you explain what you mean by "scan lattice parameters..."?
Thanks
109
General Questions and Answers / Reason for sudden jump in stress optimization
« on: August 20, 2022, 19:27 »
Dear All,
I am running optimization for a metal-semiconductor structure. I ran it earlier for 24 hours then it got interrupted & I took last minus 2 image from trajectory & rerun the calculation. However, I observed the following sudden increase in stress as shown in image below.
Also the simulation is converging very slowly.
Kindly provide any reason for why it is converging slowly? & why this sudden increase in stress?
I am running optimization for a metal-semiconductor structure. I ran it earlier for 24 hours then it got interrupted & I took last minus 2 image from trajectory & rerun the calculation. However, I observed the following sudden increase in stress as shown in image below.
Also the simulation is converging very slowly.
Kindly provide any reason for why it is converging slowly? & why this sudden increase in stress?
110
General Questions and Answers / 3D plots
« on: August 16, 2022, 16:15 »
Dear Admin,
How can one visualize 3D plots of band decomposed charge density? Like 3D charge accumulation & depletion regions?
How can one visualize 3D plots of band decomposed charge density? Like 3D charge accumulation & depletion regions?
111
General Questions and Answers / Re: How does QuantumATK calculate the kinetic energy?
« on: August 16, 2022, 07:01 »
Calculate total energy & look for log file. There will be all energy contributions.
112
General Questions and Answers / Re: Error when running QuantumATK on multiple nodes
« on: August 16, 2022, 07:01 »
Sometimes the terminal calls atkpython from libexec when it should be called from bin. This is one reason why you have no printing even after 10 mins.
So try this:
pathto/QuantumATK/libexec/mpiexec.hydra -n 10 /pathto/QuantumATK/bin/atkpython input.py
So try this:
pathto/QuantumATK/libexec/mpiexec.hydra -n 10 /pathto/QuantumATK/bin/atkpython input.py
113
General Questions and Answers / Using GPUCompute Nodes
« on: August 13, 2022, 08:44 »
Dear Admin,
Is it possible to run QATK on GPU compute nodes?
If so, how can I do that?
Also, will there be a speedup in comparison to running a optimization calculation on CPU?
Is it possible to run QATK on GPU compute nodes?
If so, how can I do that?
Also, will there be a speedup in comparison to running a optimization calculation on CPU?
114
General Questions and Answers / Re: Interface Relaxation
« on: August 12, 2022, 09:37 »
Thanks that was helpuful.
115
General Questions and Answers / Interface Relaxation
« on: August 6, 2022, 07:30 »
Dear Admin,
Are these methods same or different? (Kindly mention the difference if any) {Assume A & B are pre-relaxed before building interface}
Method 1: I make interface between two materials A & B using interface builder with a strain of 3%. Then I do interface relaxation using DFT keeping layers away from interface as rigid.
Method 2: I make interface between two materials A & B using interface builder with a strain of 0.8% (using large supercell). Then I do interface relaxation using DFT keeping layers away from interface as rigid.
Method 3: I just drag & drop two materials with (say) 4x4 supercell in builder & adjust interface distance to some value from experiments. Then perform a full DFT optimization.
Will all methods yield same end configuration? Also, how is method 3 different from 1 & 2 and if it is same what is then the purpose of interface builder?
Are these methods same or different? (Kindly mention the difference if any) {Assume A & B are pre-relaxed before building interface}
Method 1: I make interface between two materials A & B using interface builder with a strain of 3%. Then I do interface relaxation using DFT keeping layers away from interface as rigid.
Method 2: I make interface between two materials A & B using interface builder with a strain of 0.8% (using large supercell). Then I do interface relaxation using DFT keeping layers away from interface as rigid.
Method 3: I just drag & drop two materials with (say) 4x4 supercell in builder & adjust interface distance to some value from experiments. Then perform a full DFT optimization.
Will all methods yield same end configuration? Also, how is method 3 different from 1 & 2 and if it is same what is then the purpose of interface builder?
116
General Questions and Answers / Re: Running QATK on Multiple Nodes
« on: August 2, 2022, 13:19 »
Dear Admin,
Yes it is resolved now. Looks like it was error on the cluster.
Yes it is resolved now. Looks like it was error on the cluster.
117
General Questions and Answers / AKMC License
« on: August 2, 2022, 13:16 »
I was running adaptive kinetic monte carlo (AKMC) on 80 cores using the following command:
mpiexec.hydra -n 80 atkpython akmc_test.py > akmc_test.log
however i get this error, though we already have more than 80 licenses of ATK.
License Error: Unable to obtain a required license for the
requested license feature. It could mean there are no valid
licenses left, a problem with the connection to the license
server, or the license file does not contain the requested feature.
See below for more details.
Licensed number of users already reached.
Feature: qatk_forcefield
License path: 27020@XXXXXXXXX:
FlexNet Licensing error:-4,234
Kindly help resolve it. Also, are there separate licenses required to use AKMC module.
Also, is there a way to add external potential energy contributions in CINEB/NEB calculations? I am interested in observing how the migration barrier is affected by some external potential energy/ applied field? If it is possible how to do it?
mpiexec.hydra -n 80 atkpython akmc_test.py > akmc_test.log
however i get this error, though we already have more than 80 licenses of ATK.
License Error: Unable to obtain a required license for the
requested license feature. It could mean there are no valid
licenses left, a problem with the connection to the license
server, or the license file does not contain the requested feature.
See below for more details.
Licensed number of users already reached.
Feature: qatk_forcefield
License path: 27020@XXXXXXXXX:
FlexNet Licensing error:-4,234
Kindly help resolve it. Also, are there separate licenses required to use AKMC module.
Also, is there a way to add external potential energy contributions in CINEB/NEB calculations? I am interested in observing how the migration barrier is affected by some external potential energy/ applied field? If it is possible how to do it?
118
General Questions and Answers / Multiple Node issue
« on: July 23, 2022, 15:16 »
Dear Admin,
When using the following command for 2 node with 25 cores per node:
mpiexec -n 50 -ppn 25 atkpython test.py > test.log
I see from CPU activity all calculations run on single node.
& when I use following command (host_names is a file that contains compute node addresses):
mpiexec -f host_names -n 50 -ppn -25 atkpython test.py > test.log
I see this error:
bash: /opt/QuantumATK/QuantumATK-T-2022.03-SP1/libexec/pmi_proxy: No such file or directory
bash: /opt/QuantumATK/QuantumATK-T-2022.03-SP1/libexec/pmi_proxy: No such file or directory
Kindly help resolve this error.
When using the following command for 2 node with 25 cores per node:
mpiexec -n 50 -ppn 25 atkpython test.py > test.log
I see from CPU activity all calculations run on single node.
& when I use following command (host_names is a file that contains compute node addresses):
mpiexec -f host_names -n 50 -ppn -25 atkpython test.py > test.log
I see this error:
bash: /opt/QuantumATK/QuantumATK-T-2022.03-SP1/libexec/pmi_proxy: No such file or directory
bash: /opt/QuantumATK/QuantumATK-T-2022.03-SP1/libexec/pmi_proxy: No such file or directory
Kindly help resolve this error.
119
General Questions and Answers / Re: Running mpi job using multiple hosts
« on: July 20, 2022, 18:32 »
Did u find solution ? I face same issue. can u kindly help?
120
General Questions and Answers / Re: Running QATK on Multiple Nodes
« on: July 20, 2022, 07:03 »
Kindly look at the images below for illustration of the problem i face:
When I run mpiexec -n 200 -ppn 40 atkpython ted.py > ted.log it runs all mpis on master node while other compute nodes have 0 usage as you can see below in one of the images.
When I run mpiexec -f host_file -n 200 -ppn 40 atkpython ted.py > ted.log it gives the following error as in image.
When I run mpiexec -n 200 -ppn 40 atkpython ted.py > ted.log it runs all mpis on master node while other compute nodes have 0 usage as you can see below in one of the images.
When I run mpiexec -f host_file -n 200 -ppn 40 atkpython ted.py > ted.log it gives the following error as in image.