## Thursday, April 9, 2015

### LAMMPS temperature increase nvt : Noose-Hoover thermostating

The format of the most basic NVT instruction in LAMMPS is:
fix fix-ID group-ID nvt temp Tstart Tstop Tdamp
Example:
fix 1 all nvt temp 20.0 1200.0 0.05
[the units used here is 'units metal', i.e., T is in kelvin, time is in picosecond].
Here, the highlighted texts are the keywords one needs to use. In LAMMPS, 'fix' is a task, and thus fix-ID is the task ID. This ID can be used later to extract information from the output of the task (i.e., fix). The group-ID is the ID of the group of atoms on which the task will be applied. In the example, by 'all' it means the fix is applied to all the atoms.
Tstart is the starting temperature, and Tstop is the 'target' temperature (indeed not 'stopping' temperature. 'Tstop' is a confusing name used in LAMMPS manual). If the simulation is not run for for sufficient no. of timesteps, the temperature may not reach the targeted temperature. In that case, one can restart a run (for that one has to generate a restart file while doing the nvt run with the command 'write_restart').
The parameter Tdamp is related to Noose-Hoover thermostating that takes place during nvt run. The value of Tdamp has to be optimized: too small a value will cause erratic temperature fluctuation, and a large value will delay the equilibration. LAMMPS manual says a good choice for many models is Tdamp = 100 * timesteps. Thus, if the timestep is 0.001 ps (= 1 fs), then Tdamp = 100 * 0.001 ps = 0.1 ps. Note that Tdamp is not equal to 100 * time units, which for 'units metal' would be 100 ps.

Ref: http://mycomputinglogs.blogspot.fr/2013/04/nvt-run-with-lammps.html

## Wednesday, April 8, 2015

### Scientific visualization and analysis software for atomistic simulation data and molecular dynamics: ovito (and VMD)

There are a lot of software for this purpose. I select here only two softs.

## OVITO

OVITO : http://www.ovito.org/
is a scientific visualization and analysis software for atomistic simulation data developed by Alexander Stukowski at Darmstadt University of Technology, Germany. The program is Open Source and freely available for all major platforms.
Molecular dynamics (MD), molecular statics and Monte-Carlo based simulations are nowadays standard methods for modeling materials with atomic-scale resolution. Such atomistic simulation models generate three-dimensional atomic configurations or trajectories, which usually need to be further analyzed in order to generate new scientific insights. Powerful analysis and visualization techniques play a key role in this process as simulated systems become larger and more complex. Without the right software tools, key information would remain undiscovered, inaccessible and unused. The task of visualization packages such as OVITO is to translate the raw atomic coordinates into a meaningful graphical representation and enable an interpretation by the scientist.

It looks like the current version of OVITO only supports atom_style
atomic.
Here are a list of alternative programs which can generate bonds,
angles, dihedrals, and impropers:


http://lammps.sandia.gov/threads/msg45535.html
http://montecarlo.sourceforge.net/emc/Welcome.html   (EMC)
http://sourceforge.net/projects/moleculardynami/
http://lammps.sandia.gov/prepost.html


## VMD

The simple VMDhttp://www.ks.uiuc.edu/Research/vmd/
VMD is designed for modeling, visualization, and analysis of systems (such as proteins, nucleic acids, lipid bilayer assemblies, etc.)  It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.
• Support for all major computer platforms
• Support for multicore processors
• Support for GPU accelerated computation
• Many excellent VMD tutorials developed locally, and by the research community at large
• No limits on the number of molecules, atoms, residues or number of trajectory frames, except available memory

## Tuesday, April 7, 2015

### MPICH2and error "using credential" and LAMMPS

LAMMPS and MPI.

LAMMPS for windows : http://rpm.lammps.org/windows.html

Only the lmp_mpi executable supports parallel execution via MPI (which can be combined with OpenMPI multi-threading).
For that you also need to install MPICH2 from Argonne lab. The installer does not contain it and does not check for it.
After the installation of the MPICH software, it needs to be integrated into the system.
You install MPICH2 from Argonne lab but if you try directly to use LAMMPS_mpi. It doesn't work:
"user credentials needed to launch processes"...

Use a terminal emulator, for example PowerShell and write:
smpd -install

after
cd c:\mydirectory
where the file "in.colloid" is.

and at the end
mpiexec -localonly 4 lmp_mpi -in in.colloid

for 4 processors.