myprojects-hg-reborn

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I updated plot_statistics.py: it now also works out the radius of
gyration of the aggregate.

I added the cose test_interaction.tcl which includes an interaction
potential in the system (see test.tcl for an idea of the corresponding
case without interaction potential).

I updated plot_statistics.py; now the code is also able to calculate the
velocity autocorrelation function.

I added test-section2.py, basically the same as test-section.py but it
also shows how to read files from the output of the DNS code.

I added a code which is able to generate some random (scalar) velocity
and plot it on a circular domain.

I added the code plot-vector.R. It is taken from R mailing list and it
shows how to draw a vector field using R.

I added plot_statistics.py which reads and takes some basic statistics
of the output of test.tcl and read_test.tcl.

I added the code read_test.tcl which specifically reads the output
(velocities and positions) of test.tcl.

Now test.tcl uses a blockfile to save both the velocities and the
positions which are read and manipulated simultaneaously.

Now test.tcl saves also the initial particle configuration and does
start saving the results after evolving the system for the 1st time
step.

I modified read_1_particle_kind.tcl which is now able to read and save
(from the configuration blockfiles) all the particles coordinates at
different times in a format suitable for R and Python.

I modified mytest_1_particle_kind.tcl (cleaned up a bit the code, but
not 100% sure of what I did...in case revert to the previous version to
find out what happened) and added test.tcl, which evolves and saves some
statistics for a set of Brownian particles.

I modified the labels along the y axis in the code
statistic_and_arrows.R.

I introduced the scientific notation in the plots in
lognormal_binning.R.

I added 3D_R_plotting_quick.R which implements also the scientific
notation along the y axis.

I added some features to plot_potential.py which are mainly related to
some quanties of the Lennard Jones potential (minimum, time scale,
etc...).

I added the code dolfin_demo.py which solves Poisson equation on a 2D
box using the finite-element code dolfin.

I corrected some SERIOUS bugs in the code smoluchowski2.py. Some air
properties, e.g. cond_air(t) are defined as a function of t, though they
depend on T(t), but were called in the code as cond_air(T(t)), which was
leading to some serious problems.

I added the code plot_potential.py which calculates and plots some of
the interaction potentials used by Espresso.

I modified mytest_1_particle_kind.tcl. I changed the parameters of the
lennard-jones potential, the time-step, the thermal noise etc...to be
able to use the lennard-jones potential to study agglomeration.
Now, I see complex structures not necessarily sphericals.

I added the code mytest_3_particle_kind.tcl which simulates the dynamics
of two particles estabilishing a fene bond when they are close.

I added new files in which I experiment with different potentials and
read the saved configurations.

I added a linear interpolation on the boundary to estimate where the
particle gets deposited and also wrote a routine which saves only 2
positions (present and immediately precedent one) of a Brownian particle
to save memory.

I modified some of the figures generated by
read_results_smoluchowsky_single_simulation.R. The modifications are
trivial and they involve simply a vertical line for the end of the
dynamical evolution of the number distribution for a 5m-long anaconda.

I added some trivial modifications to 3D_R_plotting.R (they mainly
involve the figures I generate).

I added the code sde.py which solves the Brownian motion of a particle
in a 2D box and keeps track of the escaped particles and of the
statistics of where they leave.

I added a code which takes some statistic on the configurations saved by
mytest2.tcl.

I added the code statistic_and_arrows.R which shows how to add arrows to
an R plot and how to generate plots with 2 different scales on the y
axis.

I corrected a few typos and went on developing the code. The aim is to
calculate the time-dependent radial density function.

I added a TCL code mytest2.tcl to calculate (as a test) the dynamic of
salt particles and visualize the results.