1
General Questions and Answers / Re: ModuleNotFoundError: No module named 'pwd'
« on: November 4, 2020, 03:24 »
Oddly, I restarted the software again after 2 days, and it is working fine now....
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2
General Questions and Answers / ModuleNotFoundError: No module named 'pwd'
« on: November 2, 2020, 08:00 »
Dear all,
I ran into this error when the program was starting. The program still ran smoothly the last time I used it, which is 3 days ago.
Do you have any idea what cause the problem, and how can I fix this?
Thank you so much!
Thi
-----------
Traceback (most recent call last):
File "build\lib\site-packages\parmed\gromacs\gromacstop.py", line 40, in <module>
ModuleNotFoundError: No module named 'pwd'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "zipdir\NL\GUI\Main\Main.py", line 280, in main
File "zipdir\NL\GUI\MainWindow\MainStack.py", line 10, in <module>
File "zipdir\NL\GUI\MainWindow\MainWindow.py", line 24, in <module>
File "zipdir\NL\GUI\Actions\ToolFactory.py", line 7, in <module>
File "zipdir\NL\GUI\Tools\ScriptGenerator\ScriptGenerator.py", line 47, in <module>
File "zipdir\NL\GUI\Tools\ScriptGenerator\ScriptBoard.py", line 26, in <module>
File "zipdir\NL\GUI\Tools\ScriptGenerator\ScriptBoardBase.py", line 7, in <module>
File "zipdir\NL\GUI\Tools\ScriptGenerator\ScriptBlocks\PolymerBuilder.py", line 5, in <module>
File "zipdir\NL\GUI\Tools\ScriptGenerator\ScriptBlocks\BuilderWidgets\PolymerBuilder\PolymerState.py", line 21, in <module>
File "zipdir\NL\Calculators\ExternalCalculators\ClassicalCalculators\DreidingPotentialBuilder.py", line 9, in <module>
File "zipdir\NL\Calculators\ExternalCalculators\ClassicalCalculators\PotentialBuilder.py", line 11, in <module>
File "build\lib\site-packages\foyer\atomtyper.py", line 4, in <module>
File "build\lib\site-packages\foyer\smarts_graph.py", line 6, in <module>
File "build\lib\site-packages\parmed\__init__.py", line 25, in <module>
File "build\lib\site-packages\parmed\gromacs\__init__.py", line 45, in <module>
File "build\lib\site-packages\parmed\gromacs\gromacstop.py", line 49, in <module>
File "build\lib\getpass.py", line 168, in getuser
ModuleNotFoundError: No module named 'pwd'
I ran into this error when the program was starting. The program still ran smoothly the last time I used it, which is 3 days ago.
Do you have any idea what cause the problem, and how can I fix this?
Thank you so much!
Thi
-----------
Traceback (most recent call last):
File "build\lib\site-packages\parmed\gromacs\gromacstop.py", line 40, in <module>
ModuleNotFoundError: No module named 'pwd'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "zipdir\NL\GUI\Main\Main.py", line 280, in main
File "zipdir\NL\GUI\MainWindow\MainStack.py", line 10, in <module>
File "zipdir\NL\GUI\MainWindow\MainWindow.py", line 24, in <module>
File "zipdir\NL\GUI\Actions\ToolFactory.py", line 7, in <module>
File "zipdir\NL\GUI\Tools\ScriptGenerator\ScriptGenerator.py", line 47, in <module>
File "zipdir\NL\GUI\Tools\ScriptGenerator\ScriptBoard.py", line 26, in <module>
File "zipdir\NL\GUI\Tools\ScriptGenerator\ScriptBoardBase.py", line 7, in <module>
File "zipdir\NL\GUI\Tools\ScriptGenerator\ScriptBlocks\PolymerBuilder.py", line 5, in <module>
File "zipdir\NL\GUI\Tools\ScriptGenerator\ScriptBlocks\BuilderWidgets\PolymerBuilder\PolymerState.py", line 21, in <module>
File "zipdir\NL\Calculators\ExternalCalculators\ClassicalCalculators\DreidingPotentialBuilder.py", line 9, in <module>
File "zipdir\NL\Calculators\ExternalCalculators\ClassicalCalculators\PotentialBuilder.py", line 11, in <module>
File "build\lib\site-packages\foyer\atomtyper.py", line 4, in <module>
File "build\lib\site-packages\foyer\smarts_graph.py", line 6, in <module>
File "build\lib\site-packages\parmed\__init__.py", line 25, in <module>
File "build\lib\site-packages\parmed\gromacs\__init__.py", line 45, in <module>
File "build\lib\site-packages\parmed\gromacs\gromacstop.py", line 49, in <module>
File "build\lib\getpass.py", line 168, in getuser
ModuleNotFoundError: No module named 'pwd'
3
General Questions and Answers / Re: NEB return zero value of activation energy
« on: October 30, 2020, 10:53 »
Yes, I check that it a reasonable path. Some how the problem was solved when I change to another functional.
4
General Questions and Answers / NEB return zero value of activation energy
« on: October 16, 2020, 06:52 »
Dear all,
I am running the NEB calculation for oxygen moving in a bismuth oxide lattice. Suprisingly, it returns me with the activation energy equal zero like this.
| NEB Optimization using the LBFGS optimizer |
+------------------------------------------------------------------------------+
| Iteration Step Length Max. Force Max. Energy Image Max. Energy |
| (Ang) (eV/Ang) (eV) |
+------------------------------------------------------------------------------+
| 0 0.000e+00 2.042e+00 4 1.038190 |
| 1 1.460e-01 1.527e+00 4 0.661239 |
| 2 5.897e-02 4.990e-01 4 0.447937 |
| 3 9.809e-02 4.334e-01 4 0.299187 |
| 4 7.313e-02 9.043e-01 4 0.212851 |
| 5 1.039e-01 5.077e-01 4 0.125279 |
| 6 4.990e-02 2.254e-01 4 0.076003 |
| 7 3.500e-02 2.416e-01 4 0.046288 |
| 8 6.624e-02 2.665e-01 4 0.015152 |
| 9 7.631e-02 2.870e-01 0 0.000000 |
| 10 3.436e-02 1.971e-01 0 0.000000 |
| 11 3.680e-02 2.193e-01 0 0.000000 |
| 12 5.603e-02 2.288e-01 0 0.000000 |
| 13 6.008e-02 1.451e-01 0 0.000000 |
| 14 3.966e-02 1.537e-01 0 0.000000 |
| 15 3.536e-02 1.405e-01 0 0.000000 |
| 16 3.526e-02 1.247e-01 0 0.000000 |
| 17 2.366e-02 8.175e-02 0 0.000000 |
| 18 2.393e-02 9.213e-02 0 0.000000 |
| 19 3.350e-02 1.147e-01 0 0.000000 |
| 20 3.306e-02 1.099e-01 0 0.000000 |
| 21 2.371e-02 1.107e-01 0 0.000000 |
| 22 1.409e-02 9.503e-02 0 0.000000 |
| 23 1.235e-02 7.594e-02 0 0.000000 |
| 24 1.256e-02 9.409e-02 0 0.000000 |
| 25 2.238e-02 1.023e-01 0 0.000000 |
| 26 3.851e-02 1.285e-01 0 0.000000 |
| 27 1.008e-01 2.813e-01 0 0.000000 |
| 28 7.897e-03 2.026e-01 0 0.000000 |
| 29 2.958e-02 1.504e-01 0 0.000000 |
| 30 2.162e-02 1.437e-01 0 0.000000 |
| 31 1.036e-02 1.164e-01 0 0.000000 |
| 32 1.354e-02 9.935e-02 0 0.000000 |
| 33 2.134e-02 1.151e-01 0 0.000000 |
| 34 2.581e-02 1.108e-01 0 0.000000 |
| 35 1.162e-02 9.312e-02 0 0.000000 |
| 36 6.608e-03 7.186e-02 0 0.000000 |
| 37 6.804e-03 4.837e-02 0 0.000000 |
+------------------------------------------------------------------------------+
| NEB optimization converged after 37 steps. |
+------------------------------------------------------------------------------+
<NL.CommonConcepts.Configurations.NudgedElasticBand.NudgedElasticBand object at 0x2b33e99594a8>
Is this because of some sort of error from my set up, or is there any other explanation for this situation?
I am running the NEB calculation for oxygen moving in a bismuth oxide lattice. Suprisingly, it returns me with the activation energy equal zero like this.
| NEB Optimization using the LBFGS optimizer |
+------------------------------------------------------------------------------+
| Iteration Step Length Max. Force Max. Energy Image Max. Energy |
| (Ang) (eV/Ang) (eV) |
+------------------------------------------------------------------------------+
| 0 0.000e+00 2.042e+00 4 1.038190 |
| 1 1.460e-01 1.527e+00 4 0.661239 |
| 2 5.897e-02 4.990e-01 4 0.447937 |
| 3 9.809e-02 4.334e-01 4 0.299187 |
| 4 7.313e-02 9.043e-01 4 0.212851 |
| 5 1.039e-01 5.077e-01 4 0.125279 |
| 6 4.990e-02 2.254e-01 4 0.076003 |
| 7 3.500e-02 2.416e-01 4 0.046288 |
| 8 6.624e-02 2.665e-01 4 0.015152 |
| 9 7.631e-02 2.870e-01 0 0.000000 |
| 10 3.436e-02 1.971e-01 0 0.000000 |
| 11 3.680e-02 2.193e-01 0 0.000000 |
| 12 5.603e-02 2.288e-01 0 0.000000 |
| 13 6.008e-02 1.451e-01 0 0.000000 |
| 14 3.966e-02 1.537e-01 0 0.000000 |
| 15 3.536e-02 1.405e-01 0 0.000000 |
| 16 3.526e-02 1.247e-01 0 0.000000 |
| 17 2.366e-02 8.175e-02 0 0.000000 |
| 18 2.393e-02 9.213e-02 0 0.000000 |
| 19 3.350e-02 1.147e-01 0 0.000000 |
| 20 3.306e-02 1.099e-01 0 0.000000 |
| 21 2.371e-02 1.107e-01 0 0.000000 |
| 22 1.409e-02 9.503e-02 0 0.000000 |
| 23 1.235e-02 7.594e-02 0 0.000000 |
| 24 1.256e-02 9.409e-02 0 0.000000 |
| 25 2.238e-02 1.023e-01 0 0.000000 |
| 26 3.851e-02 1.285e-01 0 0.000000 |
| 27 1.008e-01 2.813e-01 0 0.000000 |
| 28 7.897e-03 2.026e-01 0 0.000000 |
| 29 2.958e-02 1.504e-01 0 0.000000 |
| 30 2.162e-02 1.437e-01 0 0.000000 |
| 31 1.036e-02 1.164e-01 0 0.000000 |
| 32 1.354e-02 9.935e-02 0 0.000000 |
| 33 2.134e-02 1.151e-01 0 0.000000 |
| 34 2.581e-02 1.108e-01 0 0.000000 |
| 35 1.162e-02 9.312e-02 0 0.000000 |
| 36 6.608e-03 7.186e-02 0 0.000000 |
| 37 6.804e-03 4.837e-02 0 0.000000 |
+------------------------------------------------------------------------------+
| NEB optimization converged after 37 steps. |
+------------------------------------------------------------------------------+
<NL.CommonConcepts.Configurations.NudgedElasticBand.NudgedElasticBand object at 0x2b33e99594a8>
Is this because of some sort of error from my set up, or is there any other explanation for this situation?
5
General Questions and Answers / Re: Error on AnalysisBar Add-on : singular primitive lattice vectors
« on: October 16, 2020, 06:43 »
Thank you for your reply! I have figured out the problems.
6
General Questions and Answers / Idle process
« on: September 16, 2020, 04:48 »
Dear all,
I was trying to optimize the geometry of δ bismuth oxide, but it keep failing.
I keep receiving this error message. Could you please tell me the possible causes of this error?
The error message:
+------------------------------------------------------------------------------+
| WARNING: Some processes are idle. |
+------------------------------------------------------------------------------+
Thank you very much.
I was trying to optimize the geometry of δ bismuth oxide, but it keep failing.
I keep receiving this error message. Could you please tell me the possible causes of this error?
The error message:
+------------------------------------------------------------------------------+
| WARNING: Some processes are idle. |
+------------------------------------------------------------------------------+
Thank you very much.
7
General Questions and Answers / Error on AnalysisBar Add-on : singular primitive lattice vectors
« on: August 28, 2020, 04:15 »
Hi,
An error panel keeps showing up everytime I open QuantumATK, and the program just shut down if I try to open builder. The error message image is attached below. The detail error message is:
[Exception message:
Traceback (most recent call last):
File "zipdir\NL\GUI\MainWindow\AnalysisBar\AnalysisBar.py", line 350, in labFloorChanged
File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12-SP1\Lib\site-packages\AddOns\OldAnalysisReplacement\InfoPanelPlugin.py", line 119, in labFloorChanged
self.setFromItems(items)
File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12-SP1\Lib\site-packages\AddOns\OldAnalysisReplacement\InfoPanelPlugin.py", line 134, in setFromItems
supported, info = digestItem(items[0], self.labFloor(), self.__formatter)
File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12-SP1\Lib\site-packages\AddOns\OldAnalysisReplacement\Digester.py", line 118, in digestItem
info = generateInfo(item, lab_floor_model, fingerprint, formatter)
File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12-SP1\Lib\site-packages\AddOns\OldAnalysisReplacement\Digester.py", line 191, in generateInfo
calculator_info = calculatorInfo(configuration)
File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12-SP1\Lib\site-packages\AddOns\OldAnalysisReplacement\Digester.py", line 262, in calculatorInfo
density_mesh_cutoff_info = densityMeshCutoffInfo(configuration)
File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12-SP1\Lib\site-packages\AddOns\OldAnalysisReplacement\Digester.py", line 315, in densityMeshCutoffInfo
ccp_configuration = setupConfiguration(configuration, 0.0)
File "zipdir\NL\CommonConcepts\Configurations\AtomicConfigurationUtilities.py", line 114, in setupConfiguration
File "zipdir\NL\CommonConcepts\Configurations\Utilities.py", line 298, in wrapConfiguration
File "zipdir\NL\CommonConcepts\Configurations\Utilities.py", line 358, in wrapConfigurationFractional
File "zipdir\NL\CommonConcepts\Configurations\Utilities.py", line 1185, in cartesianToleranceToFractional
File "zipdir\NL\CommonConcepts\Configurations\Utilities.py", line 1211, in cartesianToFractional
NL.ComputerScienceUtilities.Exceptions.NLValueError: The primitive lattice vectors are nearly singular. ]
It would be very helpful if I can know why I am having this error, and how to fix it.
Thank you very much
An error panel keeps showing up everytime I open QuantumATK, and the program just shut down if I try to open builder. The error message image is attached below. The detail error message is:
[Exception message:
Traceback (most recent call last):
File "zipdir\NL\GUI\MainWindow\AnalysisBar\AnalysisBar.py", line 350, in labFloorChanged
File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12-SP1\Lib\site-packages\AddOns\OldAnalysisReplacement\InfoPanelPlugin.py", line 119, in labFloorChanged
self.setFromItems(items)
File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12-SP1\Lib\site-packages\AddOns\OldAnalysisReplacement\InfoPanelPlugin.py", line 134, in setFromItems
supported, info = digestItem(items[0], self.labFloor(), self.__formatter)
File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12-SP1\Lib\site-packages\AddOns\OldAnalysisReplacement\Digester.py", line 118, in digestItem
info = generateInfo(item, lab_floor_model, fingerprint, formatter)
File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12-SP1\Lib\site-packages\AddOns\OldAnalysisReplacement\Digester.py", line 191, in generateInfo
calculator_info = calculatorInfo(configuration)
File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12-SP1\Lib\site-packages\AddOns\OldAnalysisReplacement\Digester.py", line 262, in calculatorInfo
density_mesh_cutoff_info = densityMeshCutoffInfo(configuration)
File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12-SP1\Lib\site-packages\AddOns\OldAnalysisReplacement\Digester.py", line 315, in densityMeshCutoffInfo
ccp_configuration = setupConfiguration(configuration, 0.0)
File "zipdir\NL\CommonConcepts\Configurations\AtomicConfigurationUtilities.py", line 114, in setupConfiguration
File "zipdir\NL\CommonConcepts\Configurations\Utilities.py", line 298, in wrapConfiguration
File "zipdir\NL\CommonConcepts\Configurations\Utilities.py", line 358, in wrapConfigurationFractional
File "zipdir\NL\CommonConcepts\Configurations\Utilities.py", line 1185, in cartesianToleranceToFractional
File "zipdir\NL\CommonConcepts\Configurations\Utilities.py", line 1211, in cartesianToFractional
NL.ComputerScienceUtilities.Exceptions.NLValueError: The primitive lattice vectors are nearly singular. ]
It would be very helpful if I can know why I am having this error, and how to fix it.
Thank you very much
Pages: [1]