myprojects-hg-reborn

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Now I re-added the plotting of the mean x position in
plot_statistics.py.

I updated test_interaction.tcl; now the code saves the time in time.dat
and it properly closes some files it creates to save the results.

I simply made more explicit the syntax to calculate the radius of
gyration in Espresso (by adding 0 1 $n_part), but the returned value is
exactly the same as before.

Now plot_statistics.py reads the time from a data file and I also
corrected the way in which I was "folding" the particles into the box.

Now test.tcl also saves in a .dat file the time along the simulation and
it explicitely close the generated data files (which can now be read
only when the simulation is finished).

Now plot_statistics.py compares the radius of gyration calculated by
espresso with mine.

I corrected a bug in test.tcl: now the code correctly places the
particles in the middle of the box and saves the radius of gyration.

Now plot_statistics.py also reads and plots the radius of gyration
calculated by espresso.

Now the code test_interaction.tcl is able to calculate the radius of
gyration using Espresso's in-built function, but there is probably
something wrong in the calculation.

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.