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# Geometry - Science topic

Explore the latest questions and answers in Geometry, and find Geometry experts.

Questions related to Geometry

Einstein's 1905 theory derives a relativistic geometry for spacetime in the

*absence*of matter, and then applies it in the*presence*of matter, to derive rules for how that matter behaves at high relative velocities.Einstein does not seem to explain, hypothesise or justify why the behaviour of matter should obey a geometry that presupposes that no matter is present. To turn a two-postulate relativistic theory of empty space into a physical theory (that applies to matter) requires an additional (third) postulate, addressing how the presence and motion of matter does (or doesn't!) affect the shape of the region's ligthbeam geometry.

It seems difficult to come up with a specific "postulate #3" to complete SR's derivation that does not then invalidate the whole theory. This is presumably why Einstein never completed the process.

Preprint Einstein's Missing Third Postulate

Is there way way to complete SR's derivation

*without*the necessary third postulate being in disagreement with known principles or evidence? If not, do we need to reassess the case for special relativity?Euclidean 3 dimensional geometry is taught in engineering school.

How can there be variation in the models of interpreting 3D?

Hi, I'm trying to assign different material to this geometry (attached), cortical bone for external part (and internal 'islands') and bone marrow for internal part (no islands), but the section is empty while trying to assign materials. Do anyone know what problem is occuring?

Appreciate every advice

Thanks

My study area is extremely large (multiple valleys) and precipitation is close to zero. Streams are often dry, but runoff almost solely comes from glacier melt and is heterogenous throughout the valleys. I have extracted stream boundaries for hundreds of basins using a machine learning algorithm and I can get channel geometry such as width/depth/cross sectional area (at any point along the stream), wetted perimeter etc. Is there any way I can get approximate velocity, discharge, etc at bankfull using stream geometry and a corresponding DEM? Maybe using slope and geometry?

I have tried changing the lattice parameter using this formula: a2 - a1/a1 where a1 and a2 are unstrained and strained lattice parameter after full geometry optimization. Problem is...suppose I have optimized the compound on which I want to apply strain and got lattice parameter 5. Now I want to apply 1% strain on it...So I set the lattice parameter 5.05 and start full cell optimization again. After optimization it's showing lattice parameter..5.001( closer to 5)..It's pretty normal I know. But then How can I apply exactly 1% strain on a certain compound?

I want to define a contact between two bodies. Due to the geometry, both bodies do not touch. The gravity would cause both bodies to touch.

I am working on material studio 2020, CASTEP module, when I optimize the geometry, I am getting this message at each job failure

[mpiexec@Rahat-Saqfi] ..\hydra\pm\pmiserv\pmiserv_cb.c (863): connection to proxy 0 at host Rahat-Saqfi failed

[mpiexec@Rahat-Saqfi] ..\hydra\tools\demux\demux_select.c (103): callback returned error status

[mpiexec@Rahat-Saqfi] ..\hydra\pm\pmiserv\pmiserv_pmci.c (520): error waiting for event

[mpiexec@Rahat-Saqfi] ..\hydra\ui\mpich\mpiexec.c (1149): process manager error waiting for completion

How to resolve it?

When I am using

**MOLUSCE**, a QGIS plugin, it displays a**warning message: the geometry of different rasters does not match**. Raster geometry generally means raster cell size, number of rows and columns, and projection. S**o how can I generate two or multiple rasters that have the exact same geometry?***Does anyone have any helpful advice on how I can get past this error message?*I would greatly appreciate any suggestions or feedback.

"There are no empty bands for at least one k point and spin; this may slow the convergence and/or lead to an inaccurate ground state. If this warning persists, you should consider increasing n extra bands and/or reducing smearing width in the param file. Recommend using n extra bands of 8 to 18". In every step of geometry optimisation result for a particular material this notification is shown. How can I solve this problem?

I'm performing a geometry optimization on cyclopentanol and I want to constrain a planar geometry on the five-membered ring. Can anyone explain briefly how this is achieved? Perhaps sharing a sample Gaussian input file would help.

Dear all,

I have a small query regarding the equivalency of the 2D and 3D cohesive zone models.
I have designed a 2D square geometry tied with a cohesive element in the middle in ABAQUS. I am trying the validate my load-displacement response with an equivalent 3D model geometry using a suitable out-of-plane thickness. However, the results are not the same at all.
The same can perfectly validate for a model without a cohesive zone. Will anyone please help me to resolve the issue?

The model geometry is attached herewith for a clear understanding.

Hi,

I am doing a single-point SA-CASSCF calculation on the azobenzene derivative, and once the calculation is completed I got energies corresponding to S0 and S1 states, however, no structural data corresponding to the S1 is found in the output file. Do I need to specify extra keywords/options to get the geometry of the S1 state?

Here is the route section for the mentioned calcultion,

#p casscf(6,4,nroot=2,stateaverage)/6-31+g(d) nosymm scf=(maxcyc=500) Guess=(read,Alter) pop=full geom=connectivity

Thanks in advance...

I work usually with idealized geometry, but this time I want to use patient specific geometry of blood arteries. Is there any way to upload/implement such type of geometry to a Matlab code?

I am running simulation in damask on the mesh solver example that damask developers provided in dasmask documentation. The problem which i am facing is that how to control the maximum iteration number? because the simulation is running from morning till evening and has reached to 125 iteration and then gives message of cut back and started simulation from start. how to control iteration number?

I'm learning to do a simulation in Gaussian. The objective is to simulate the molecules that I study in my master's degree. For that, I did the geometry optimization along with the frequency calculation to confirm the geometry, then I did the TD-DFT calculation to get the electronic transitions.

The transition results coincide very well with the spectral region of the experimental results. However, molar absorptivity is a few orders of magnitude higher. I would like to know if this is normal or if the calculations may be wrong? if it is normal, is there any reference that discusses this difference?

I need to store molecular geometries in redundant internal coordinates (RICs) and have so far been able to get all of the information I need aside from what the d.o.f.s correspond to. I presume that the "Redundant internal coordinate indices" hold this information but I cannot find information on them anywhere in Gaussian documentation or other forums, etc. It doesn't seem to be a connectivity matrix, but the numbers clearly correspond to each atom and it is not clear to me from analyzing the geometry visually either. I would really like to avoid having to write and validate code from scratch to backtrack this information from cartesian coordinates or pulling connectivity from a different output file format.

I have attached an example of the formchk file output from Gaussian optimization and frequency analysis for a basic case (methanol) but here is the crucial information for easy viewing:

Atomic numbers I N= 6

6 1 1 1 8 1

...

...

Redundant internal dimensions I N= 4

15 5 7 3

Redundant internal coordinate indices I N= 60

1 2 0 0 1 3

0 0 1 4 0 0

1 5 0 0 5 6

0 0 2 1 3 0

2 1 4 0 2 1

5 0 3 1 4 0

3 1 5 0 4 1

5 0 1 5 6 0

2 1 5 6 3 1

5 6 4 1 5 6

Redundant internal coordinates R N= 15

2.06335755E+00 2.07679249E+00 2.07679461E+00 2.73743812E+00 1.83354933E+00

1.90516186E+00 1.90518195E+00 1.84167462E+00 1.91434964E+00 1.94775283E+00

1.94775582E+00 1.96310537E+00 -3.14097002E+00 -1.07379153E+00 1.07501112E+00

Thank you for any and all insight!

Hello everyone,

I have multiple projects, where the only thing that needs to be changed is the geometry (mechanical model) the transient thermal and the static structural will stay the same. However if i want to copy the whole project (all 3) it gives a error: The given data container reference is null. If i want to duplicate them separately then each analysis will create its own tree which means that they are not connected anymore. How can i copy all 3 projects and only modify the geometry?

Help would be much appreciated!

Kind regards Thomas

I want to specify natural convection boundary condition at the top of the wall. I am trying to reproduce some results. Author didn't specify value of h (heat transfer coefficient). He gave an expression for it. You can see it in attachment. I don't know how to incorporate this equation in my boundary. I am attaching geometry and equation that I want to apply at the top wall. Can anyone please help me in it?

In ABAQUS, I want to model a bent tube with varying thicknesses and diameter (continuous linear function) from one end to the other. I have attached a sketch with the question for better understanding.

Later I want to hydroform it into an even more complicated shape, therefore meshing, surface definition, and boundary condition definition are important. It is not a challenge for modeling tools like SolidWorks, CATIA or ProE but importing part from there is a mess and even if somehow import is successful, meshing, surface interaction definition, and BC definition is problematic. Therefore, it would be great if I can directly model it in ABAQUS.

I tried 3D/Shell deformable sweep command but it only asks for a sweep geometry at then sweeps the geometry along the defined path continuously, while I want to vary the thickness and diameter linearly.

Is there a possibility to do that?

For example a square unit cell in xy plane to be tilted in the same plane by 45 degrees

Hi all,

I have worked on CFD simulations/analysis of a diffuser turbocharger compressor geometry for a typical engine passenger car. Also, I have completed optimisation process of the diffuser geometry using Adjoint Method.

In the numerical CFD simulation chapters, I need to justify why a high-fidelity simulations is required for the optimisation process. What are the alternative methods? How my results will be different if used, for example; semi-empirical correlations to estimate the efficiency of the compressor stage?

Any idea, suggestion, comments or recommendations, I would much appreciate.

Thank you in advance for your time and cooperation.

I need to find this distance for complete the modeling of reflection-absorption of light in Si solar cell.

Good afternoon,

I am currently simulating a combustion in CFD on ANSYS FLUENT and I am trying to get the best mesh possible out of this geometry. It is a rather simple one, with four inlets that lead to the combustion chamber. My question is, since I am quite new to ANSYS, what is the best way to mesh this geometry? Of course the inlets will have to be more refined than the rest of the mesh but I was asking the best methods to approach this. I am having trouble meshing the inside of the furnace because I am always getting really insconsistent tetrahedral cells.

Thank you very much.

- I am preparing to submit a manuscript in field of materials science. Is there a new rapid peer-reviewed, open access journal of materials science and geometry?

How can I import

**2D**sketches from**CATIA**into**COMSOL Multiphysics**?The formats that COMSOL reads in 2D geometry are not available in CATIA.

Hi everyone, is there a way to link Matlab with Abaqus?

Specifically I have done a geometry in Matlab, and then I want to import this geometry in Abaqus for mechanical analysis, but I don't work how it works.

Every advice will be appreciated

I would like to simulate a copolymer with 25 units of PE and 25 units of PEG in MS. During this task I was troubled with an convergence issue regarding the mesocite geometry optimization. Hence I need some advice in order to solve this problem for a further DPD calculation.

For this reason I tried to write down all the steps that a have been working on until this issue (pls see the attached MS-file):

1.) Define a copolymere with an ethylene and ethylenglycol repeating unit

2.) Perform a forcite geometry optimization

3.) Define the coarse grain under mesostructure as well as the bead type (see file)

4.) Calculate the repulsions parameter a = 104 + 3.5 X between PE and PEG

(while X represents the Flory-Huggins interaction parameter which I calculated beforehand)

5.) Define a DPD forcefield where you enter the repulsions parameter in a table

(a = 104 for same block interaction like PE/PE and PEG/PEG and a = 195 for different block interaction like PE/PEG)

6.) Define a mesostructure template (120•120•120 A)

7.) Fill the template with the .xcd-files from the copolymers

8.) add the forcefield to the file

9.) run the geometry optimization (COVERGENCE FAILURE)

...

10.) Perform the DPD calculation (intented GOAL)

Link to google drive file (because the zip file wont upload for some reason):

I would like to create a porous geometry. I am looking for your suggestions on any open-source software which can help me to create the geometry. It would be idle if I can control or define the porosity of my created geometry.

Dear all

While doing geometry optimization using materials studio - Castep for mixture atoms,

I'm receiving an error as follows

"Error geom_precon_exp_get_r_NN: increased r_cut to twice system extent without finding neighbours for all atoms. This can happen if your system is too small; try setting r_cut manually"

how to rectify it?

Thanks in advance

I have done an analysis of residual stresses in a composite plate structure in ABAQUS. I need to take a section of the plate (a rectangular patch which represents a tensile sample) and apply tensile loads to it WITH THE RESIDUAL STRESSES from the first model BEING ITS INITIAL STRESS STATE.

I know that it is possible to do this if the

*geometries are same*and I can take the final stress state of the first model as the initial condition for the second model. But since the*second geometry is a subset of the first*, I am not able to map the results**ONLY**in that region as the transfer takes place based on node numbering and the node numbers in both the models do not match.Any info on whether this is possible on ABAQUS would be welcome. Is there any technique that I can use to solve this problem?

Many analytical approaches have been developed over the years , and comprehensive bibliographic studies have been published on the prediction of E2,G12,Poisson's ratio of unidirectional composites. in The Halpin-Tsai equation 𝜉 is an empirical factor, which measures the reinforcement of the fibers of the composite material which depends on the geometry of the fiber, the arrangement of the fibers and the loading conditions. In generally, 𝜉 may vary from zero to infinity. taking 𝜉=2 to calculate E2 and 𝜉=1 to calculate the shear modulus G12

I am looking for the value or the equation to determine 𝜉 to determine the Poisson's ratio v23 ?

LIGO and cooperating institutions obviously determine distance r of their hypothetical gravitational wave sources on the basis of a 1/r dependence of related spatial strain, see on page 9 of reference below. Fall-off by 1/r in fact applies in case of gravitational potential V

_{g}= - GM/r of a single source. Shouldn’t any additional effect of a binary system with internal separation s - just for geometrical reasons - additionally reduce by s/r ?Does any one have some experience with creating 3D geometries with FreeCAD and subsequently editing it to the OpenFOAM CFD software? Could you share any tutorial or demo links with me?

I came across a document where the authors have generated 2d terrain from an experimental flume. Images are attached. I would like to generate 2D geometry of a tilting flume for 2d analysis. I have dimension/1d geometry of the flume.

I am working on geometry of banach spces and applications in metric fixed point theory , especially my interesting is renorming of Banach spaces, Is anyone interested in collaboration

I am not able to import the parameters in ANSYS which are necessary for optimization. I tried different file types like step, sat and iges . I am using fusion360 for CAD. How should i import the design with parameters?

Hi,

I am looking for recommendations of any open source geodynamic modelling software that could help me model how the style of subduction initiation impacts the geometry of the resulting slab?

By "style of subduction initiation", I mean spontaneous (e.g. mantle plume, passive margin or transform collapse) or induced (transference or polarity reversal). So theoretically, I want to input the characteristics of these styles and see the geometry of the slab produced.

Thanks,

Shane

Image from Stern and Gerya (2018)

I am currently working on a project that includes pencil geometry Cs-137 sources and lattice geometry. I try to obtain the voxel dose by using the f6 tally and my simulation was successful but my dose distribution is not looking homogeneous. Geometry and source to surface distance are symmetrically created. So, I should have homogeneous distributions. I used this source definition below. Is there anything wrong or can you advise me of a physics card in order to get more homogeneous dose distributions?

**sdef pos=d4 par=2 rad=d1 ext=d2 axs=0 1 0 erg=0.662**

**c**

**c RADIAL DISTRIBUTION OF THE SOURCE**

**si1 0 0.5375**

**sp1 -21 1**

**c**

**c VERTICAL DISTRIBUTION OF THE SOURCE**

**si2 -4.40 4.40**

**sp2 -21 0**

**c**

**si4 L 7.2 -8.98825 0**

**7.2 0.00275 0**

**7.2 8.98925 0**

**sp4 D 1 1 1**

**phys:p 100 0 0 0 0 J 0**

Hello everyone

Can I use Vina to dock analogues of nucleotides triphosphates into a polymerase active site coordinating Mg ions?

The ions are also typically in coordination with water molecules to satisfy their proper geometry.

Is it possible to do such docking while, at least, Mg ions are kept at the active site?

If not, is there any open-source docking tool to to such docking?

Hi,

I am having problems optimizing already computed excited states.
This is my input:
#rb3lyp/Gen pseudo=read scf=(maxcycle=400, conver=6) opt TD=(Read, Root=7)

My problem:
How do I refer to the output file with the computed excited states?
I put it in the same folder and tried adding the file name to the headline:
#rb3lyp/Gen pseudo=read scf=(maxcycle=400, conver=6) opt TD=(Read, Root=7) NA_T_50states.log

but it didn’t work.

How do I compute the height of tallest skyscraper of Wuhan (Wuhan Greenland center) from S1A images using radar geometry?

Dear all,

I have a Abaqus script that repeats a lattice structure in two dimension. I am modeling lattice cells as solids with their wall thickness. And geometry is a plate-like structure with a smaller out of plane thickness compared to other lengths.

However, i want to roll this structure into a tube like geometry. The result I'm trying to achieve is actually a tube with lattice walls. I want to write this Abaqus script parametrically in terms of mesh repetitions and relative density.

If anyone has any ideas on how to do this and can help I'd be very happy.

I have imported a structure on ABAQUS that was designed on SOLIDWORKS, after importing the structure opens but there are invalid geometries that appear on the structure making meshing impossible. I would like to know what to do to solve this problem so that meshing can be done.

thank you for your attention

Hi all. I want to create mapped mesh ( same nodes on opposite sides mapped and aligned with each other) for different geometry on opposite surfaces of a cuboid in y direction (top and bottom surface are having different features ) as shown in two figures ? Any help will be appreciated. Thanks all.

Hello all,

I am currently presenting a problem on a model that has among its contact interactions, one that is of special interest.

I am modelling human bone in contact with a metal implant. The contact interaction is defined with normal and tangential behaviors and with a 0.5 friction coefficient. The process that I am doing is removing bone from the contact interaction zone. Hence I have 6 different models with a different volume removed on each of them.

As a result of this action, I would expect Von Mises stress and contact pressure to increase in the implant, and the contact area to decrease. Interestingly, that behavior is presented in the first model that I cut. Nevertheless, as I increase the deepness of the cut (or remove more bone section) , Von Mises starts to decrease and contact area starts to increase despite contact pressure increasing.

I was suggested to check my mesh. Nonetheless, I performed a mesh analysis test on the geometry before being cut and selected the best matching mesh with a 1% difference criteria. Thus, I am unsure about what could be happening as the only thing changing in my models is the geometry based on my cuts.

I attach an image of the numerical behaviour experiencing.

Thanks for the help.

The translation surfaces parametrized r(x,y)=(x,y,f(x)+g(y)) are obtained by translating two curves lying in orthonogal planes. What about the affine translation surfaces parametrized R(x,y)=(x,y,f(x)+g(y+ax)) for nonzero constant a ? Could the affine translation surfaces be geometrically described such as that of translation surfaces?

Hi all

I am trying to simulate soft elastohydrodynamic lubrication is rubber seals. In this case I have to prestress the seal by compressing it between housing and the shaft. I want to use this deformed geometry along with its residual stress to run a fluid-structure interaction(FSI) simulation. I know how to export the deformed geometry but does anyone know how to export the deformed geometry along with its residual stresses?

Thank you

Hi, how can I define the Casimir force which acts between plates of a parallel plate capacitor while performing electrostatic - solid mechanics simulation in COMSOL Multiphysics?

The specialty of the Casimir force is that it varies with the plate displacement. It is inversely proportional to the fourth-power of the distance between two plates:

**[**

*Force*_{Casimir}_{ }*~ 1/(initial separation between plates - plate displacement)*]^{4}It acts only when spacing between two plates is of few nanometers.

Hi everyone,

Is there a method to divide the imported part into multiple parts within Abaqus CAE?

I am working on a model in Abaqus CAE with a geometry imported from a .STEP file. I need to define non-design regions by defining parts which are

**separate from the design region**. For example, the design region must be named Part-1, while the remaining of the geometry is divided into Part-2, Part-3, etc. However, the whole geometry is imported as a single part from the .STEP file even though I check the "**create individual parts**" option during the import process.Please note that, since I need the non-design regions to be in different parts, I cannot use the partitioning methods (e.g. cell partitioning).

I will be grateful for your comments and insights.

I am simulating a hydraulic jump in a rectangular flume that has an inlet and an tailgate at outlet. I need to adjust the tail gate opening to get the desired hydraulic jump. So i simulated the case for few time steps but now I want to drop the tail-gate further to obstruct the flow.

I have duplicated the geometry,mesh and setup , then i changed the dimension of my tail-gate (there by closing the outlet opening below the tail-gate further) .

**I have initialised the case with the existing .cdat file from the previous simulation.**But the console shows me DIVERGENCE immediately after running the calculations.I even updated the mesh and re-cheked the setup Could help me with this?Is there any mathematical equation that relates the shape/geometry of metasurfaces with their light confinement properties? Why does C-shaped metasurface behave differently than L-shaped?

There are multiple methods to calculate cold and hot outlet temperatures, e.g.

**LMTD**and**P-NTU.****P-NTU**directly calculates both the hot and cold outlet temperatures using two linear equations based on (a) exchangers geometry (b) flow and (c) heat-capacity of the fluids.**LMTD**based method requires (a) exchangers geometry (b) flow (c) heat-capacity of the fluids and (d) one of the outlet temperatures to calculate the remaining outlet temperature.

(Note : LMTD method can find both the outlet temperatures, if heat exchanger is single-pass)

Both the methods give same answers (while designing and rating heat exchangers) !

My question is as follows:

**Is recursive type calculations in LMTD can be considered as a drawback of LMTD method? , Particularly in heat exchanger networks?**

So my geometry has two solids which I have to rotate in a certain angle for every simulation with the mesh, so I choose fluent meshing where I can rotate my geometry but after rotating the geometry the mesh nodes doesn't match in the connecting points of the geometry, how can I match the nodes.

In first order watersheds, can the shape index (Ff=A/Lb²) and the elongation ratio (Er=(2/Lb)*(A/Pi^0.5) return values >= 1?

Working with large watersheds, these values tend to be < or = unity. However, working on small hydrographic basins (1st order) I find some volers above the unit.

Is there any convention that the values of Ff and Er cannot exceed unity?

Thanks.

Hi,

I have determined the velocity profile of fluid in my geometry (both 2D and 3D). However, from here, I do not know how to proceed to find the wall shear stress in my geometry.

Can anyone provide me step by step details please. I am not well-versed with Matlab, however, I can try if I have been given few leads.

Kindly help.

Thanks

I am trying to analyse a large structure with multiple loading scenarios (independent - different loading directions), while considering geometric non-linearity. Using different steps is not sufficient, since each step starts off with the geometry shaped as it was at the end of the previous step.

I tried creating a dummy step just to deactivate all the loads from the previous step, but the non-linearity causes some distortion to remain even without any loads.

One obvious solution is to run each step in a separate analysis, but the model is quite large and the input file processing takes about about as much time as it takes the solver to solve a step, which would immediately double the time required to obtain the entire solution and there would also be redundant information in the result files (mesh data repeated in each result file). So creating a separate analysis for each step is something that I am trying to avoid for the moment.

Tech laptop specs:

Asus Rogue Strix G

Video card: 4 Gb

Intel CORE I7 9TH Gen Turing Architecture

Ram 24GB

At the bottom part o the comsol windows screen show 3.1Gb / 3.8Gb I know this is Physical /Virtual Memory

1. How could be possible that use more virtual memory than physical? "it is frustrating"

2. But The computing time is taking Too much time (45 minutes ), why COMSOL does not take more memory from my 24Gb of RAM?

3. Can configure Comsol four using a specific amount of memory?

Different geometry of unique nanomaterials

Hi ,

My name is Ömer and I'm doing a research which involve a simulation in ansys fluent of an single stage axial compressor.

Idont know how to criated a blade geometry in bladegen for axial compressor. I made a meanline analysis with criate an EXCEL program to look literature.

I'm also beginner in simulations, so I want to know how to use cfx for criate my compressors map and another analysis things.

If you help me about it, I will be really happy because I dont have too much time for learn.

Does anyone know of any image analysis software that can be used to determine the geometry changes before and after working and compare their sizes, I am looking for alternative methods to CMM?

ZnO samples are being synthesized at 400 C

Hello,

I am running airflow simulation through a model of lungs. I want to find the velocities and pressures at certain locations. I tried creating ISO-surfaces but this surface cuts through the whole geometry and I want only specific locations on the geometry as shown by the colored lines in the figure. Is there a way to create a plane at the location of these lines exactly that will give only this branch? I want to find the velocities and pressures at the end of each branch.

Thank you in advance

I was doing the calculation of the excited state of the molecule in gaussian but each time after some intermediate geometries my link die. I am unable to get the excited state geometry of the molecule. Can anyone provide me a solution?

During optimization the geometries tend to change from one symmetry group to another, therefore the output file does not produce the intended structure because of change of symmetry. I want to fix the symmetry in Gaussian so that the structure remains the same during optimization. Any one to help me please.

The molecules contain Fe, B,C,H, F. The scf energies are very close to converging but they just don't converge. I tried increasing the scf cycles, changing the input geometry etc. I am using the basis set of def2tzvpd.

In the Comsol reference manual moving mesh is suggested for solving RF MEMS switches. But the problem is more consistent with deforming geometry because usually the space between membrane and substrate is filled with air and the strain is not important here. is this interpretation correct? and can be deforming geometry can be used for this problem?

Hi,

I am running MD simulations of a Gold-chelate compound with square planar geometry of Au (III). I parametrized the missing force field parameters for Au and its four neighboring atoms using MCPB and VFFDT properly. The issue is that after the full minimization step (without restraint) in MD simulations, the geometry of Au (III) changes from square planar to tetrahedral which is undesired. Could you please guide me on how to solve the issue?

Thanks

Wing geometry analysis usually involves wing detachment to avoid capture bias. I am curious if analysis of wing geometry can be done without detaching the wings. This is sometimes important when it comes to preserved specimens. Mosquito specimens are very valuable yet so fragile. An intact mosquito specimen is needed for further morphological identification in the future. If it is possible what is the treatment or technical suggestion to capture the wing geometry without detaching it to avoid bias?