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AnimeshAnimesh 
I am doing PhD ( mechanical engineering ) on impact analysis of Graphene reinforced polyurethane nanocomposite using Accelrys Material studio 7. For impact analysis constraint is very very important. Can anybody discuss various type of constraint used in material studio???when we used atom,length and lattice constraints??? During impact analysis is it possible to give velocity on the impactor or striker in material studio????
Best Answer chosen by Animesh
CarstenCarsten (Accelrys) 
This should be possible:
  1. Build Graphene starting from Graphite.
  2. Optimize a and b vector with the method you want to use, fix c and the angles.
  3. Build the Graphene superstructure you want to use.
  4. Add enough vacuum space to the model.
  5. Build and optimize the cluster you want to impact onto the Graphene layer.
  6. Add it at 6-7\AA on top of the Graphene onto which you want to fire it.
  7. Do a 1step MD with the method you want to use at the temperature you want to use. this is just to get the velocity property for the atoms.
  8. Download the results.
  9. Select the added atoms and edit the relative velocity of he added atoms and set it to a velocties that way that they fly towards the Graphene layer (typically, x,y=0 and z to a certain value).
  10. Do an NVE run with Current velocities.
The attached *.xsd file should be hopefully be ready to be used in an NVE run with velocities set to Current in Materials Studio 7.0.

The trajectory of the complete run (Cl2 as the molecule to which the velocities wre assigned) is too large to be attached and was done with DFTB+ in Materials Studio 2017.
deepsdeeps 
Dear All,

User-added image
I am trying to calculate the solubility parameter for a single chain of polymer.The above expression is given in a reference(link).Could someone tell me how to calculate Es and Eb given in the equation.Es the single chain energy; Eb the energy of the same chain in periodic system; Vc the volume of the cell in cubic angstrom, C the unit conversion factor.
How do I calculate Es and Eb from the trajectory file of the dynamic run?

Thank you so much for your time and consideration.

 
Best Answer chosen by deeps
reinierreinier
The easiest would be to run Forcite Cohesive Energy Density task, which will do this calculation for you.

In principle you could simulate a single molecule in vacuum at a given temperature, and obtain Es as the average total energy. Then run a liquid simulation at the same temperature and obtain Eb as the average total energy per molecule. Since the temperatures are the same, the kinetic energy cancels. You’ll need to divide by the volume per molecule to obtain the cohesive energy density.

In practice for small molecules the vacuum energy equals the intramolecular energy in the liquid, and you can obtain Es – Eb directly as the average intermolecular energy, without simulating the vapor. For polymers simulating the vapor is not realistic as experimentally they decompose.
 
SousaSousa 
Hello dear MS users,
Could anyone tell me how i can construct a nonowire with the structure shown in the following picture?User-added image
Best Regards
Sousa
Best Answer chosen by Sousa
reinierreinier
Hi Sousa,
 
Below are two posts with scripts to build icosahedron and dodecahedron shaped nanoclusters. The basic idea is to carve the required shape out of a block of material. You could something similar for your nanowire.
Good luck,
Reinier

 
武汉理工大学武汉理工大学 
Hi every one
I used Amorphous Cell to bulit cell containing 100 molecules and the geometry optimization has been performed after construction.Then the system went through NVT dynamics in Forcite with thermostat Nose.However,lots of molecules went out of the cell after the dynamics finished, so I think the boundary condition does not work,but I do not know what is wrong with my caculation.I come across the same problem when using GULP for dynamics.Picture is  finall frame.

Any help will be appreciated.
Thanks in advance 


Sincerely 
Li
Best Answer chosen by 武汉理工大学
reinierreinier
Hi Li,

Did you check "Recalculate atom visibility every frame" on the Animation Options dialog? This will effectively change the display style of the Lattice to "In-Cell" for each frame, and hence keeps atoms in the box during the animation.

Best,
Reinier
NicolNicol 
Hi,
I'm new here. I have a question regarding geometry optimization-Forcite module. I tried every forcefield available in the module but still the end result is not converge after the iteration finished. Increasing the iteration is also not working. I'm trying to find g(r) using this module.
Thank you

Nicol
Best Answer chosen by Nicol
Simon MillerSimon Miller
Hi

When you choose a forcefield you need to do so carefully, as it needs to describe the potential energy surface of your structure reasonably accurately. In general COMPASS is usually the first choice, but if you have some exotic structure containing say metal complexes then Universal might be a better choice. Your Geom. Opt. may fail to converge, because the forcefield does not provide a good description of the potential energy surface. Usually when that is the case then there are warnings or errors messages about missing or automatic parameters and / or the resulting optimized structure is far from the experimental one. If you use rigid bodies and they are internally strained this can result in a failure to converge. Also if the tolerances are too tight then they may never be met! However, if may be that you can ignore these messages, but do so with caution. i.e. check to see if the final structure is reasonable; for example are bond lengths, cell parameters, etc about right? Are rings that should be planar actually planar or are they distorted etc.

BTW Normally the g(r) is computed from a trajectory produced in a dynamics run otherwise you will not take into account temperature effects and will be difficult to compare to experiment.

Regards
Simon
faruqfaruq 
Dear All
I have recently updated Materials studio 2016 to my windows machine. We have a licence for CASTEP and ONETEP as well.  It works absolutely ok with CASTEP using single core along with parallel calculations but with ONETEP, It does not work  for even a single machine.   Please update me what to do. here i have copied the warning .............

Thanks 
Faruq

Job started: 27-04-2016 10:41 (+0100)
 
License checkout of MS_onetep successful
 
Reading parameters from file "Al.dat" ...... done

Checking processes and threads...
   Running with 2 MPI processes.
   There are 2 MPI processes running on the same node as the root process.
   This binary does not support OpenMP threading.
... done

''''''''''''''''''''''''
ONETEP terminated abnormally due to the following error:

Error in parallel_strategy_list_overlaps: spheres exceed cell size.      
... detected on MPI rank #0.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

ONETEP execution aborted
  
Checked out license feature: MS_onetep <v2015.10> [for 4804:219863:2:THE UNIVERSITY OF BOLTON] (1 copy)

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
 
Best Answer chosen by faruq
victor.milmanvictor.milman
Hi,

The error is described in the lines that say "error". OpenMP is a warning. 
The error comes from ONETEP's dislike of small cells. If atom-centered spheres overalp with their periodic images, ONETEP cannot operate. This code is designed for large systems; in fact, the crossover in terms of performance between ONETEP (linear scaling) and CASTEP (quadratic to cubic scaling) happens for systems with hundreds of atoms. Smaller systems are faster with CASTEP. Anyway, if you want to use ONETEP, please make a bigger supercell - look at atomic radii in ONETEP setup options to get an idea of how big it should e to avoid spheres overlap.
Cheers
deepsdeeps 
Dear All,
I have used COMPASS force field to estimate the cohesive energy density(CED) of ethanol.It gives a value close to the experimental result.I have also checked this with the Dreiding potential,the result predicted is not close to the experimental value.Could someone explain why there is a difference in result?
Is it necessary to use COMPASS for predicting liquid properties?

Thanks for your time and consideration.
Best Answer chosen by deeps
reinierreinier
COMPASS is fitted to experimental CED data, so it is likely that it will do a better job than Dreiding, which is fitted to crystal structure and sublimation energy. Moreover Dreiding does not provide charges, and the result depends on the way these were calculated.
mostafamostafa 
Hello all,
I need to build a big Zeolite (100 and 800 nanometer) structure, but in materials studio system hangs and i can't bild my structure. Is there any other possibility to build this structure???????
thanks all,
regards.
Best Answer chosen by mostafa
reinierreinier
A typical zeolite has 50 atoms per nm3. So a box with length 100 nm contains 50 million atoms, storage of which is beyond the memory in most desktops. Moreover the size would be impractical for any subsequent calculation.
Enxi PengEnxi Peng 
Hello Everyone

I'm seeking some information on how COMPASS II in Forcite assigns charges to a system when the option is selected as "force field assigned". 
My questions are 
1. Does COMPASS II automatically assigns and equilibrates the charges throughout the system to make the net-charge of the system zero? (Like how QEq does it)
2. Do I have to use QEq prior to running MD in Forcite to obtain a net-charge of zero?

Thanks 
 
Best Answer chosen by Enxi Peng
reinierreinier
Hi Enxi Peng,

The charge assigment of COMPASS II is similar to that of pcff, based on bond increments.

If you open pcff in the force field viewer (Modules | Forcite | Forcefield Manager | Select pcff | Press >>), open the Interactions tab, and set Show interaction to Bond increments, you should see a long list of values for each pair of force field types, e.g. -/+ 0.1268 e for (c=,h):

pcff

This means that an atom of type c= bonded to an atom of type h will be incremented by -0.1268. The net charge of an atom follows by summing over all its bonds.

In most cases the bond increments add up to 0, and consequently the whole system will be charge neutral.

Hope this helps,
Reinier
shining_sirshining_sir 
Hello Everyone,

First thanks for your attention on this question.

I built a mixture in Amorphous cell, with 50 A molecules (CxHyOz) and 50 B molecules (CxHyNz).

My question is, if I would like to calculate RDF between A and B, what should I do?

My current method is to select all A molecules as Set 1, and select all B molecules as Set 2, then using Forcite-RDF module. Is it correct, and this RDF is atoms-atoms RDF or centroid-centroid RDF?  do I have to creat a centroid any more?

By the way, If I want to study A-A interaction/structure, when I choose set 1 and set 1 in Sets, do I have to check "Include intra-intermolecular components"? 

Thanks in advance,
best,
Guangji

 
Best Answer chosen by shining_sir
reinierreinier
You are right, there is no difference between the "total" and "AA". Somewhat confusingly when you analyze AB you also get AA and BB; there is no option to just get AB without the others unfortunately.