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Messages - coraline

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1
Oddly, I restarted the software again after 2 days, and it is working fine now....

2
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'

3
Yes, I check that it a reasonable path. Some how the problem was solved when I change to another functional.

4
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?

5
Thank you for your reply! I have figured out the problems.

6
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.

7
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

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