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# Computational Simulation - Science topic

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Questions related to Computational Simulation

I am working on impact of a high speed metal particle on a substrate by FEA using Abaqus. The model is axisymmetric as shown in figure 1. I am using Coupled Euler- Lagrangian method for simulation. The substrate and particle is modeled as a Lagrangian body and the particle is placed in a Eulerian domain. I have created a discrete field for material assignment using volume fraction tool. The particle is then excluded from the simulation. The analysis procedure is Dynamics, temperature, explicit. The particle size is 25 microns. When I am using mesh size 1.5 microns for the particle, substrate and eulerian domain I am getting expected results as shown in animation1. But whenever I am changing the mesh size (increasing or decreasing) I am getting results as the particle is scattered or broken and impacting the substrate very randomly as shown in animation 2. Does anyone have ideas why this is happening?

The reference of the article I am using is

Xie, J., Nélias, D., Walter-Le Berre, H., Ogawa, K., and Ichikawa, Y. (October 1, 2015). "Simulation of the Cold Spray Particle Deposition Process." ASME.

*J. Tribol*. October 2015; 137(4): 041101. https://doi.org/10.1115/1.4030257Hello dear researchers

I am working with a cubic structure and I want to substitute some atoms, but I have to take a 5×4×4 supercell. Will this affect the calculations, because my elementary cell is cubic and the supercell I just generated is not cubic? Are the results I had obtained correct?

I am New to MDS simulation which software will be open source and free tutorial available for beginners?

It's my first time using NAMD and I don't know how to continue my interrupted MD Simulation which was set up for

**50 ns**. I have my output.dcd and output.xst files and also log files.Firstly I want to know how many steps have been completed? secondly, how to continue it to the total steps i.e

**25000000**in the original namd file?please provide the steps or command line needed during the restart of the simulation!

I really appreciate any help you can provide.

Regards,

Vinay

Manuscript is related to computational simulations of plant-microbe interactions.

I am using Abaqus UMAT subroutine to model wear damage between two contacting steel surfaces. I need to get the absolute maximum shear stress as it is a function of my wear damage model. I have tried using a utility routine called CALL SPRINC to get the 3 principal stresses (

*σ*1,2,3). Since abs max shear stress = (*σ1-**σ*2)/2, (*σ*1-*σ*3)/2, (*σ*2-*σ*3)/2 (the numerically largest of these).However, it gives me principal stresses for each number of element and increment (which are thousands or maybe more than that), and I do not know how to assign the values to different variables in order to calculate the abs max shear stress using the eq. above. How do I assign the values in different variables?

I have also tried using the trigonometry (with the calculation of discriminant) to solve the cubic formulation to get the principal stresses manually but there is an error in trying to run the program as follow: The executable standard.exe aborted with system error code 1073741676.

1. Is there any way to directly get the abs max shear stress in UMAT subroutine?

2. How do I assign principal stress values in different variables?

Thank you!

Which of the above two-mentioned softwares (i.e., COMSOL, or ANSYS Maxwell) are better in obtaining close results in the case of permanent magnets?

Also, what are the governing equations which are used in both these software? Are they same for both or different?

What are the boundary conditions, that are employed in each software for PM simulations?

Can anyone please guide me how we can proceed step-by-step, by employing governing equations and boundary conditions, etc.?

Any sort of calculations involved? Please help with that as well.

Thanx.

Let's say we docked Protein X with Ligand A, Ligand B and Ligand C respectively.

Meanwhile, we have three different desktops, i.e. Desktops 1-3 for molecular dynamic (MD) simulation. Can we make use of the desktops using the following way in speed up the process of getting the results from MD simulation?

First round of MD simulation:

Desktop 1 - Protein X-Ligand 1 complex

Desktop 2 - Protein X-Ligand 2 complex

Desktop 3 - Protein X-Ligand 3 complex

Second round of MD simulation:

Desktop 1 - Protein X-Ligand 3 complex

Desktop 2 - Protein X-Ligand 1 complex

Desktop 3 - Protein X-Ligand 2 complex

Third round of MD simulation:

Desktop 1 - Protein X-Ligand 2 complex

Desktop 2 - Protein X-Ligand 3 complex

Desktop 3 - Protein X-Ligand 1 complex

Thank you.

Hello, I have attached an interval to alter the deposition of energy with time. How can we write this code using the expression language in FLUENT or CFX ?

Thank you very much !

Dear All:
I am wondering if someone have an R codes (R functions) to run the test
procedures described in the paper titled “ESTIMATION AND COMPARISON OF
LOGNORMAL PARAMETERS IN THE PRESENCE OF CENSORED DATA” by STAVROS POULOUKAS
2004, Journal of Statistical Computation & Simulation, Vol. 74, No. 3,
March 2004, pp. 157–169.
I can send a copy of the paper if necessary.
with many thanks
abou

Dear Researchers :

Recently I asked an official quotation (with all the requiered concepts) from ANSYS and from COMSOL to implement the same type of License and the same set of modules, the scheme of the License are not exactly the same , but very close ,

For both software I'm interested in being able to solve applications with the Structural Mechanics Module and the Electromagnetic Module

But in general, If I place both final prices in the same footage, I realise ANSYS is always more expensive (at least today) than COMSOL (roughly between 35 - 40 % more)

Does anyone with experience in this may know one of the reasons why this is so ?

Regards !

Hello.

I am running a molecular dynamic simulation of a peptide on the membrane for 1000ns. At the end of the simulation time my membrane looks weird, kind of wavy at the bottom bilayer membrane. I am not sure if this is normal or the problem that occurred during the simulation.

I have attached some figures . I really appreciate all opinion and explanation.

Thank you!

Hi Everyone,
Hope you are doing well. I am trying to model the free standing mode of TENG in Comsol. As a beginner, I request you to please guide me if there is any free standing simulation model or tutorial video which I can follow to model this mode. I will be very grateful to you. Thank you

As a 2nd-year PhD researcher, I have been curious about the number of simulation-only PhD theses that exist in fields such as Engineering as well as unrelated fields as well. There is of course value in lab-testing, given how a simulation cannot always account for every boundary condition or factor. Usually, from my limited but growing experience, simulation, in the case of Additive Manufacturing and mechanical testing, is normally used as a validating tool; to help prove in a non-virtual environment what may be seen and tested in the lab, before any kind of scaling or future work is done using simulation (for cost-effectiveness and resource-saving etc.).

But in fields where in-situ testing is normally done, are there PhD theses that "Jump the gun" as it were, and go straight to simulation? Any information on this will be most appreciated given how, in some locations/countries where interaction and access to tools on campus and labs are minimal still due to Covid, improvisations must be made.

I am simulating cyclohexanone oxidation from a paper. I got the input files from supplementary data.

But when I am simulating, and generating Excel file at different temperatures the reactant Concentration is remaining the same and not decreasing neither the products composition is changing.

There is no reaction taking place. Please tell me how to resolve this.?

I have a case, which is about internal flow with constant heat flux. Although the inlet boundary condition is laminar, the flow is passing transition and turbulent regime along the tube. As known, the intermittency term is 1 (so, admitted as turbulent inlet BC) for freestream velocity for external flow, I would like to learn that whether using the transitional SST model by laminar inlet boundary condition in the pipe is the corrects way or not.

Best regards,

I want to learn theoretical research for energy applications. Please guide me for possible computational/simulation programming or software packages for research. Thank you.

**In experimental, the bond energy per atom rises quadratically with the number of bonds**

**then why in simulations**

**this bond energy per atom rises linearly with the number of bonds per atoms?**

What is the proper course of action to be followed in solar cell device simulation?

I am trying to carry out the molecular dynamic simulation. Is there free software?

I want to know that which is better in terms of graphics, modelling, dynamic simulation, and user friendly.

I would like to know if it is possible to do MD calculations for protein on a regular PC? If it is possible, then what are some of the software that can be used and if there is anything i need to take in consideration before running the simulation.

Hi,

I am trying to model Lamb waves propagation in an Aluminum plate using Abaqus. If I choose the frequency of 5-cycle Hanning excitation source is 0.2 MHz (to make sure that only 2 modes S0 and A0 appear in the result), the result showing good (see Fig.1) and the amplitudes of displacements does not decrease along measuring points (which have been proven by analytical approach). When I increase the frequency to 1.5 MHz (still have only 2 modes A0 and S0 depend on the dispersion curves in Fig.2) the results become disorder and instability, and the amplitude decrease along these measuring points.

Mesh size has been chosen to satisfy CFL conditions (= 1/15 x wavelength) and the time incrementation has been chosen to ensure that the fastest wave mode can propagate through element size (= element size / longitudinal wave speed).

So why the results become inaccurate?

Thank you for reading this post.

Dear all,

I have experimental data for the effect of time at different feed concentration on the permeate flux of the hybrid adsorption membrane process for the removal of dye from wastewater. I would like to get a mathematical model.

I have a question please how to calculate the concentration at the adsorbent surface?

Would please help me to understand the calculation of concentration at the adsorbent surface?

I would appreciate your reply.

I am writing to inquire if there is a way to create a time-varying temperature field and apply it to a part on ABAQUS.

I am trying to model a cylindrical tank using the coupled temperature-displacement approach for thermomechanical stress analysis during the heating/cooling cycle (i.e., thermal ratcheting).

The model, solely composed of tank shell, will be heated up using a time-varying temp. field on the part’s surface. To this end I prepared the Spatial temp. data (X, Y, Z, Field value) at each time step “t”. But I am having trouble implementing this data on the ABAQUS platform. Could you advise on this matter?

FYI, the temperature data was calculated using the STAR-CCM program. In this regard, will my issue require the STAR-CCM-ABAQUS co-simulation process? I ask because I hope my issue is solvable just on ABAQUS with simple manipulations.

Sometimes we hear somethings on stiffness problem of solution for chemical reaction modeling.

There is an option in Fluent software to figure it out.

Have you guys used it so far? tell us when and why did you use it?

Hello, everyone!

I've been trying to study the effects of some N-glycosylations in a sugar transporter. The in vivo experiments have already been performed, but I've been trying to add some N-glycans to this transporter in silico as well. I have successfully modelled some of the mutants, but there is a particular one that I've been struggling with. This mutant has 2 N-glycosylations in buried positions, and the in vivo experiments showed that these glycosylations greatly impair the transporter function. The problem is that I've been successfully adding the superficial carbohydrates, but I cannot add them in 2 buried sites. Could anyone help me with ideas on how these sugars could be added? Computer programs that can do that, or ways that I could unfold the protein, add the N-glycan and refold the protein would be extremely useful as well!

Thank you very much!

Guys,
Sometimes after initializing the problem in Fluent and triggering the calculate button, a residual/residuals start from a big non-zero magnitude. For instance, to me, it in many cases happens for some convection-diffusion equation when I'm simulating combustion. Interesting point is that the results looks ok and have good agreement with experimental results. In this page:

It's said that:

"For most problems, the default convergence criterion in

**ANSYS FLUENT**is sufficient. This criterion requires that the scaled residuals defined by Equation 26.13-4 or 26.13-9 decrease to 10^{-3}for all equations except the energy and P-1 equations, for which the criterion is 10^{-6}."As it is said, the residuals need DECREASE TO 10

^{-3}. Then it means that it doesn't matter from where the residual starts, it should finally decrease to 10^{-3}.- Am I right?
- What's your opinion?

Another question:

3. Why does it happans? (I mean why does the residual start from a non-zero magnitude?) and How to figure it out?

I've attached two screenshots of the residual of a project for instance.

I just started studying about computational chemistry. In particularly, I am interesting in calculating molecular properties by computational simulation.

Regarding to coupling constant between 2 atoms in a particular molecule, I have read some materials about DFT and Hartree-Fock approach. Both of them just use the coordinates (x, y, z) and charges of atoms as the input to calculate the properties. Did I understand it correctly?

Is there any other factors (e.g, hybridization, type of bonds,...) which affect to the calculation?

Could you please suggest any materials (papers or books) for this problem?

I am planning to measure pressure and temperature variations in and around a metal vapour deposition chamber. The substrate is a steel strip, and I wanted to experimentally measure pressure and temperature variations, as you introduce the metal vapour in the chamber. I would aim to put these gauges in different locations of the vacuum chamber. I have been advised that because of the metallic vapour being introduced in the system, the gauge gets contaminated by the vapour and renders the gauges useless. Does anyone have any suggestions of pressure gauges that may work?

This is being undertaken as a form of validation for a computational simulation of a similar scenario.

CHARMM and AMBER are the force fields used in the computational simulation for the properties of dna, protein, etc. I'd like to know that, when to use CHARMM or AMBER force field. Also is it necessary to do MD Simulation via both of them.

Thank You.

Hello,

Molecular simulation can narrow down the search for the most promising structures by predicting and providing a detailed picture on the molecular scale.

Is there any paper have tested and proved experimentally the results that have been already predicted using molecular simulation for adsorption of gases in porous materials?

**"Not the other way around"**I'm looking for reference literature.

*Thanks in advance*I want to simulate electromagnetic stirring of aluminium casting in which heat transfer and solidification of casting are observed. Is there any open source software simulating electromagnetic stirring of casting?

I am simulating crystal structures of tricalcium silicate, dicalcium silicate, etc. to obtain the IR spectra of the molecules using CASTEP. When I do the Anaylsis of the IR spectrum, I can see all the vibrational modes. I want to understand the bending/stretching modes in the MIR/FIR frequency region - such as symmetric/asymmetric or in-plane/out-of-plane.

But, I don't want to confirm the type of modes only from vizualization, I want to quantify the type of modes, from the change in bond angle, amplitude of vector, direction etc. For this purpose, I want to know vectors for each atom of all the vibrational modes. I couldn't find this information in the CASTEP output file. I found a file .phonons file which was hidden but in that file, but the values are not matching with the IR frequencies and amplitudes as seen in the CASTEP output file or in the IR spectra window where I see the vibrational modes. I am not sure why they are different.

I would be obligded if I can get some help regarding this.

I want to start studies in ideal MHD computational simulations. e.g. MHD instabilities in cylindrical Plasmas in a 2D approximation to start. Can anyone share with me some information (papers, books, websites and so on) to develope succesfully this activitie?

I wish to generate some random numbers for simulation.I have an equation for rutherford scattering of electrons.I wish to simulate electrons at random angles for which i need different values of cos(Theta).

How can i write a program and plot the graph of such a distribution where the theta takes random values from 0-180 and plots it against the energy?

Hi all,

Can any one please tell me how can I calculate the S parameters in cst when I use the plane wave?

Thanks

I'm currently doing a set of simulations on penetration depth of ions in electronic devices, and I'm wondering whether or not the crystal structure of the materials in the backend (dielectrics, metallization) in a typical Silicon process has an effect on stopping power of these compounds. The most impact I'd expect for Silicon dioxide, which in the case of PVD and/or CVD deposition tends to be pretty amorphous, while a thermal oxide seems to be much closer to a crystalline form. Now the question is how much of a difference should I expect? My gut feeling is that for a deposited amorphous oxide layer, the density should be somewhat less than that of a perfect crystal. But is the difference large enough to actually make a difference in stopping power of the oxide?

I'm aware that stopping of ions in itself is somewhat of a stochastic process such that the resulting range of the ions is subject to a statistical distribution already on its own, therefore I wonder if it actually would make a noticeable change if the density of the oxide layer would lower by a few percent...

Need to simulate coastal wave using ansys fluent on levee structure. As well as sediment. So, its gonna be three phase flow. I have been using VOF of fluid method but no success.

Does anyone come across research paper in which flow past square cylinder is analysed for different angle of incidence and flow is in vertical direction?

**Please tell me Research paper Title with author name.**

**Thanks in advance.**

Dear all,

I was trying poseview server for calculating 2D interaction of my compound with receptor. I recognize hydrophobic interaction and hydrogen bonds. In addition I also note another interaction depicted as a green line connecting two green dots. Please see attached figure. I am sure it is Pi stacking interaction. I just need to confirm it by you people... Please comment on it..

I am doing a research for alternatives of animal-testing and I need to know the challenges for in-sillico model

I really wish to know if there is any good and detailed practical material on L-System for plant growth and development apart from the Algorithmic beauty of plants?

I want to simulate the growth of waterleaf plant (Talinum triangulare) and see the effect of environment and other factors on the plant.

I have tried to use cpfg in L-Studio and I recently saw few articles on Blender, but all these seem not good for me to get the work done.

I will appreciate your comments and supports to find a solution to this task.

I want to simulate multi-pass moving heat source using DFLUX. I understand that I should use for loop but couldn't get to work, so is there any example or similar case to it?

Cloud analyst simulator has three inbuilt load balancing strategies. If we want to add some new strategies, is this possible and how is it possible?

How to mesh a shell spherical crown area with only triangular plate element in ANSYS APDL?

Now I have one problem about a shell spherical crown, a part of a shell unit sphere cutted by z = a plane, eg:a=0.5, to be meshed with only triangular plate element in ANSYS APDL.

If anyone willing to guide me a step by step procedure to mesh this part of a shell sphere area problem with only triangular plate element in ANSYS APDL, it will be much appreciated.

Your response will be highly appreciated.

You can also post your reply or private

Thanking you in advance

I am planning to generate a microalgal specific growth rate as a function of environmental factors. The thing is that I have chosen the existing models and I only want to find the models constants for each single function. The question is for example, if I want to model the specific growth rate as a function of light intensity, how do I have to do the experiments? What I have in mind is as follows:

1-setting the light intensity on different values (e.g, 50,100,150,...)

2-starting the experiments with the same initial cell concentration and constant values of other factors

3- stopping the experiment the day after

4-calculating the specific growth rate for each light intensity

5-plotting the specific growth rate vs light intensity and finding the models constants

I have this problem with the time of the growth. Is 1 day enough or I have to continue or what? I don't have any idea about how long to continue the growth

I need to need to evaluate the field along a curve for a large number of curves in CST, for a large number of files and would like to create a macro that will automatically create the full results template required, but I can't find a way to do this.

Notice: A wall has been placed at portion(s) of an OUTLET boundary condition (at 13.3% of the faces, 1.3% of the area) to prevent fluid from flowing into the domain. The boundary condition name is: R1 Outlet. The fluid name is: Air Ideal Gas. If this situation persists, consider switching to an opening type boundary condition instead.

I can see a significant cytoprotection in the combination(1:10) drug doses than the individual doses (approx. >17%, MTT assay values). I now need to find the CI values and DRI values along with relevant plots for further study. Can compusyn assist me with the job?

This the deal , when I try to run siesta, e.g.:

mpirun -np 4 /home/guilherme/siesta-3.2/Obj/siesta < AlFeO3.fdf | tee saida.out

appeared the mensage:

mpirun noticed that process rank 1 with PID 17811 on node guilherme-Inspiron-N5010 exited on signal 6 (Aborted).

And when I change -np 4 to -np 1 like:

mpirun -np 1 /home/guilherme/siesta-3.2/Obj/siesta < AlFeO3.fdf | tee saida.out

it's ok... but this way it's a normal way... without parallel mode!!

Anyone know what is going on?!

If so, which tool can I use?

What tools are used for implementing cloud security concepts like encryption and digital signatures?

Tools especially for trust evaluation based on the log details and feedbacks.

I am conducting thermodynamic research on TRNSYS modelling of thermal solar parabolic dish systems and wish to compare our model with existing TRNSYS or Matlab Simulink models for thermal parabolic dish components. There are limited models on STEC TESS libraries and I was hoping to get in contact with researchers with Solar Thermal Parabolic Dish Component models (.m or .tmf model files).

We would like to simulate the motion of a magnetic bead that is immersed in water and is subjected to an external magnetic field at the same time.

At the moment, we are trying to use COMSOL to simulate it.

Can anyone help me on what Physics module that I have to use?

Simulation computing of simple shapes.

Hello,

I am performing docking simulations with Vina. I chose 32 (max) torsion angles (that move largest number of atoms) on the ligand to be flexible. This results in very good binding pose and large affinities (~ -9.0 kcal/mol). However, when I see the ligand structure alone, its secondary structure is completely destroyed. The alpha-helix is unwound completely.

Is this considered normal, that the ligand secondary structure completely vanishes after successful docking? Or am I doing something terribly wrong.

Any help is appreciated.

Thanks

Kindly tell me which function or code would be used to stop the working of a water heating system, built in TRANSYS, for 3-4 months. The system will remain in working condition for the remaining months.

Any comments about its graphical interface, simulation and optimization resources, graphs, toolboxes, interfaces with other languages and applications?

What are the main limitations and difficulties in its use?

How can I create this file (if nobody can send it?)

Recently I've decided to change the output of my code from ASCII tab-separated files to binary ones, obviously for better performance.This code extracts EM field data in the form of 1D, 2D even 3D matrices, with an appropriate header referring to the variable name (e.g. Length(m) EM field value etc.). I would like to use a binary format for the same purpose, to store this kind of data (if possible in the same format) and import output files in popular statistical and data manipulation software. Searching around I found HDF, CDF and SDF file formats. HDF and CDF are more popular than the last one but I think difficult to use in such an easy problem like mine. Which one do you prefer or have you used before? Any kind of help is appreciated.

I simulated my sample but I just recognized that I input the data in degree unit. Or do I need to change into radian and run again?

I would like to know if is possible to run FullProf in Parallel?

Because of the software Siesta, I already have the mpirun that I can run the siesta using 2 core only typing mpirun -np 2 siesta.

Is it possible to do the same in fullprof, such as:

mpirun -np 2 fp2k Sample?

I have a protein-ligand complex. When I run the grompp program, I am encounter with this error: Ignoring obsolete mdp entry 'title'

What's this error about, and how I can solve it?

Another question: my topology file lacked a position restrained section, what do you think about this?

If these values are validated with simulation in a simple geometry like tube flow, it would be helpful.

There are various simulation methods available such as Monte Carlo etc. How to start with any material for simulation of its defects and impurities? How can we use simulation in synthesizing any material?

I would like to use GPU's to run micromagnetic simulations. What factors should I consider before buying one? Does anybody know of good source of info on the subject?

Which potential is the best choice for considering the interaction between copper nanoparticles dispersed in water and which one is the best for interaction between water-copper nanoparticles?