logo
Tags down

shadow

Simulation of molecular dynamics in Python


By : user3850978
Date : October 18 2020, 11:12 AM
will be helpful for those in need Have you considered SimPy? SimPy is a rather generic Discrete Event Simulation package, but could feasibly meet your needs.
Better yet the Molecular Modelling ToolKit (MMTK) seems more specialized...
code :


Share : facebook icon twitter icon

Best language for Molecular Dynamics Simulator, to be run in production. (Python+Numpy?)


By : amcphall
Date : March 29 2020, 07:55 AM
I wish this helpful for you The high performing MD implementations tend to be decidedly imperative (as opposed to functional) with big arrays of data trumping object-oriented design. I've worked with LAMMPS, and while it has its warts, it does get the job done. A perhaps more appealing option is HOOMD, which has been optimized from the beginning for Nvidia GPUs with CUDA. HOOMD doesn't have all the features of LAMMPS, but the interface seems a bit nicer (it's scriptable from Python) and it's very high performance.
I've actually implemented my own MD code a couple times (Java and Scala) using a high level object oriented design, and have found disappointing performance compared to the popular MD implementations that are heavily tuned and use C++/CUDA. These days, it seems few scientists write their own MD implementations, but it is useful to be able to modify existing ones.

Runaway Velocities when implementing Velocity Verlet Algorithm in Periodic Molecular Dynamics Simulation


By : Jack
Date : March 29 2020, 07:55 AM
wish of those help Maybe you figured it out already, but I think the mistake is in the checkBoundaries code for the periodic boundaries. I might be wrong, but I don't think you can use the % operator on floats/doubles. I think the code should be (see also https://en.wikipedia.org/wiki/Periodic_boundary_conditions )
code :
Vector3d op = a.getPosition(); //old position
double w = getWidth();
position.setX( op.getX() - w*((int)(2*op.getX()-1)) );
position.setX( op.getY() - w*((int)(2*op.getY()-1)) );
position.setX( op.getZ() - w*((int)(2*op.getZ()-1)) );

I need help for N-body molecular simulation performance!!(java applet)


By : Carlos Romero
Date : March 29 2020, 07:55 AM
This might help you Instead of using a lookup tables, try using Chebyshev polynomials. Remember that you can exponentiate x^k in only ln(k) steps.
It may seem like a lot of operations, but the fact that in can be done without hitting memory (and therefore not affecting the cache) can make it significantly faster than a lookup table.

OpenMP and OOP (Molecular Dynamics Simulation)


By : Heatwave
Date : March 29 2020, 07:55 AM
To fix this issue Without further details on your simulation type I can only speculate, so here are my speculations.
Did you look into the issue of load balancing? I guess the loop distributes the particles among threads but if you have some kind of a restricted range potential, then the computational time might differ from particle to particle in the different regions of the simulation volume, depending on the spatial density. This is a very common problem in molecular dynamics and one that is very hard to solve properly in distributed memory (MPI in most cases) codes. Fortunately with OpenMP you get direct access to all particles at each computing element and so the load balancing is much easier to achieve. It is not only easier, but it is also built-in, so to speak - simply change the scheduling of the for directive with the schedule(dynamic,chunk) clause, where chunk is a small number whose optimal value might vary from simulation to simulation. You might make chunk part of the input data to the program or you might instead write schedule(runtime) and then play with different scheduling classes by setting the OMP_SCHEDULE environment variable to values like "static", "dynamic,1", "dynamic,10", "guided", etc.

Questions about Molecular dynamics code in "Understanding Molecular Simulation: From Algorithms to Applications&quo


By : J.K.
Date : March 29 2020, 07:55 AM
this will help The example code in "Understanding Molecular Simulation: From Algorithms to Applications", as in many other textbooks, is pseudocode. It is not complete (lack of declarations, for instance) and meant to illustrate the algorithms a bit more explicitly than "just the mathematics". In this book, it is confusing because they write incomplete Fortran for the pseudocode.
This is still a good "general problem": understand how old-fashioned textbook material with Fortran can be used :-)
Related Posts Related Posts :
  • Avoiding unnecessary slice copying in Python
  • Outlook contacts using Python client
  • ctypes loading a c shared library that has dependencies
  • Where should sys.path.append('...') statement go?
  • How to set target hosts in Fabric file
  • MATLAB to Python Code conversion (NumPy, SciPy, MatplotLib?)
  • Feedparser-basics how to
  • In Python with sqlite is it necessary to close a cursor?
  • libxml2 install error: command 'gcc' failed with exit status 1? What are the dependencies of libxml2?
  • customize the django admin panel?
  • How to decode JSON with Python
  • Modify excel file in python on linux enviroment
  • Jython image manipulation
  • Python Drawing Portion of Image When Mouse Hover
  • How do I make a command line program that takes arguments?
  • Python and NGREP
  • How can I make URLs in Django similar to stackoverflow?
  • how to make python to return floating point?
  • how are pgp keys formatted?
  • Why does += behave unexpectedly on lists?
  • memory location of dictionary in python 2.6.4 only?
  • Accessing a ServerFactory from the Service in Twisted
  • Scraping for a "preview" of a webpage - Python
  • Installing PIL on Snow Leopard
  • App Engine (Python) Datastore Precall API Hooks
  • python switch by class name?
  • Running Python With STDIN From Bash
  • Automate Windows GUI operations with Python
  • Concurrent downloads - Python
  • Python directory list returned to Django template
  • Google App Engine with Eclipse?
  • Can't import numpy into embedded ironpython engine
  • Secure Python Markdown Library
  • How can I implement a tree in Python?
  • How to get parameters of fail case in Python unittest?
  • How to make a count in python so that the program ends after a particular number of counts?
  • How can I create an ODBC connection to SAS?
  • Creating a global function, accessible from all classes, with Python + Pylons
  • How can I access a function from FORTRAN which is writen in Python?
  • How can i capture the UDP packet and find the TTL Values from the packet using python
  • Match start and end of file in python with regex
  • How to switch axes in matplotlib?
  • django error :1146, "Table 'basic_project.topics_topic' doesn't exist"
  • Python and Memory Consumption
  • Can you go to a line with the file operations in python?
  • Python Boto S3 to work with Custom Domains in Amazon S3
  • Where can i get exercises for 'Dive into Python'?
  • merging Python dictionaries
  • Urlretrieve and User-Agent? - Python
  • pyxmpp: quick tutorial for creating a muc client?
  • append new row to old csv file python
  • Teaching Python to a Law Student
  • How do I drop a bash shell from within Python?
  • mod_wsgi excessively slow at startup?
  • How to convert from unicode with python
  • In Django, how do I make my sessions persist through http://mydomain.com and http://www.mydomain.com?
  • Is there a way to create a python object that will be not sortable?
  • Listing names of available Virtualbox VMs using Python
  • Regex redefinition error
  • Set database connection timeout in Python
  • shadow
    Privacy Policy - Terms - Contact Us © bighow.org