Unanswered Questions
68 questions with no upvoted or accepted answers
22
votes
0
answers
248
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Is there a software that can do derivatives with respect to user defined vibrational modes?
I'm doing some property calculations that depend on a sum of derivatives of some quantity with respect to normal vibrational modes. I was hoping to find some physical intuition relating the type of ...
- 15.9k
7
votes
0
answers
231
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Apparent conservation of potential energy in NPT simulation?
I was examining a system with a problematic equilibration (more details given at the end, but probably unnecessary to answer the question), and came upon what is presumably a pretty basic conceptual ...
6
votes
0
answers
67
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Resolving issue with Atoms Not Assigned Properly using atom_style full
Greetings Matter Modeling,
I'm getting an error when using atom_style full. 25 out of 30 atoms import properly. I recently started using atom_style full building up the model.
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- 24.2k
6
votes
0
answers
105
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What are the parameters in PySCF's Selected Configuration Interaction code
Dear StackExchange Members,
I'm using the native PySCF implementation of selected configuration interaction (SCI). However, I can't seem to find any documentation detailing the algorithm or various ...
- 20.1k
6
votes
0
answers
77
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Benchmarking DFT vs Experimental Gaps - Confusion over Fundamental and Optical Gaps
Recently, I've come across discussions about the differences between fundamental (or electronic) bandgaps and optical bandgaps, with the two quantities differing mainly by the electron-hole binding ...
- 1,366
5
votes
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answers
205
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Significant differences between NPT and NVT equilibrated simulations
I am performing a set of classical MD simulations using a type of ReaxFF description to study aluminate Oligomerization. I have performed two sets of simulations, one where the system is equilibrated ...
4
votes
0
answers
79
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How to extract Lindemann Index from LAMMPS dump files?
I used a python code to extract Lindemann index from dump files. But the problem is the code works fine with dump files with little amount of data and atoms. When I use large files if shows overflow ...
- 1,694
4
votes
0
answers
66
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How to create a water droplet (half-sphere) on a rock (quartz) surface
I am to Equilibrate a uniformly distributed spc water molecules at 300k in 50x50x50 box. Water density is taken to be 1000kg/m3. Simulate the system in the NVT ensemble. The spc water is modeled using ...
4
votes
0
answers
72
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What kinds of calculations have to execute for obtaining the velocity of the chemical precipitation of some salt on a thread from a water-salt mix?
Some salt ($\ce{NaCl}$ or another one) of $m$ grams is dissolved in some water of $V$ liters. After mixing up, the substance looks transparent or to put it more exact as a chemical solution. Then a ...
- 1,027
3
votes
0
answers
36
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How to correctly set the high-symmetry point path block when there are breakpoints in the recommended path?
I watched Dr. Mohan's tutorial video, and the settings he provided are as follows:
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- 31
3
votes
0
answers
61
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Which ensemble to use for annealing?
I am trying to do a simulation for solid Mg dopes GaN in LAMMPS where I follow the following procedure:
Energy minimization at 0K
Heating to 873K
Holding at 873K
Quenching to 300K
For this I am ...
3
votes
0
answers
73
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LAMMPS: Start NVE simulation with different initial energies
I am new to LAMMPS and am using it to conduct microcanonical (NVE) MD simulations. I am able to run NVE simulations using the fix NVE command, but I want to start a series of simulations in parallel ...
- 161
3
votes
0
answers
57
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How to compute molar Gibbs free energy (chemical potential) for single molecule using gaussian09?
I want to calculate the Gibbs free energy of single gas molecule (AsH3) using Gaussian 09, but I am confused between "Thermal correction to Gibbs Free Energy" and "Sum of electronic and ...
- 71
3
votes
0
answers
53
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Why does the streitz and eam/alloy potential setting fail?
I used the following input file with streitz and eam/alloy potential settings for the simulation with LAMMPS.
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- 833
3
votes
0
answers
59
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Structure breaks down in the MD simulation with LAMMPS
I used the following input file to simulate the thermal conductance of the Al2O3/Bilayer Graphene/Al2O3 structure along the z axis.
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