Commit 9c6ef167 authored by Silvia Chiacchiera's avatar Silvia Chiacchiera

test 3 (on dimers) added

parent 08132146
DL_MESO charged harmonic dimers with dpd repulsion
volume 64.0
temperature 1.0
cutoff 1.0
timestep 0.01
steps 70000
equilibration steps 20000
traj 20000 100
stats every 100
stack size 100
print every 100
job time 7200.0
close time 100.0
ensemble nvt mdvv
ewald sum 1.0 5 5 5
bjerrum 42.0
smear gauss equal
finish
DL_MESO charged harmonic dimers with dpd repulsion
SPECIES 2
solp 1.0 0.46 0
solm 1.0 -0.46 0
MOLECULES 1
DIMER
nummols 96
beads 2
solp 0.0 0.0 0.0
solm 0.1 0.0 0.0
bonds 1
harm 1 2 5.0 0.0
finish
INTERACTIONS 3
solp solp dpd 25.0 1.0 4.5
solm solm dpd 25.0 1.0 4.5
solp solm dpd 25.0 1.0 4.5
CLOSE
Number of nodes used in calculations ?
nchist: 0 96 0 0 0 0 0 0 0 0
Charges for SPECIES type solp :
Charges for SPECIES type solm :
chg= 0.4600 -0.4600
Number of snapshots: 501
<P_x>, <P_y>, <P_z>:
-3.627184E-02 -1.790324E-01 5.466988E-02
error:
9.792086E-02 1.066997E-01 9.685359E-02
<P^2>/V:
2.381825E-01
error:
8.641061E-03
<p^2>:
1.419998E-01
error:
4.556992E-04
kirkwood factor:
1.118229E+00
error:
4.415698E-02
Bjerrum length?
epsilon_r:
4.290325E+01
error:
1.520215E+00
......@@ -95,7 +95,10 @@ To input the user-defined parameters one can enter them from the keyboard or wri
``gen_dipoleaf.exe < input.txt``
As a test, we suggest two examples involving two (toy) molecular species: a
We propose two tests to familiarize with the utility and a third one on a
physically relevant system.
The first two tests involve two (toy) molecular species: a
branched one (four beads, T-shaped) and a simple dimer. All the beads carry charges.
In the first case 10 molecules of each type are present and are followed for a few time steps.
In the second case it is suggested to analyze a single snapshot with just two
......@@ -182,6 +185,45 @@ and the `dipole_BRANCH` one is
The results of this test do not depend on the number of nodes used to run the simulation.
**Third test: water in oil**
Here we suggest to consider a fluid made of harmonically bonded dimers
:math:`(+q,-q)`. Fixing appropriately the partial charge :math:`q`
and the Bjerrum length :math:`l_B` this system
mimics water in an oil background, as long as the dielectric properties
are concerned. For more details about this model, please see the page :ref:`dimers`.
Run DL_MESO_DPD using for the CONTROL file
.. literalinclude:: ./CONTROL-3
and for the FIELD file
.. literalinclude:: ./FIELD-3
Analyzing the HISTORY file with `gen_dipole.exe`, this output is printed on
the standard output
.. literalinclude:: ./out-3
In particular, we see that:
- :math:`\vec{P}=(0.0 \pm 0.1, 0.2 \pm 0.1, 0.1 \pm 0.1)`
- :math:`\epsilon_r= 43 \pm 2`
- :math:`g_k = 1.12 \pm 0.04`
Please notice that the error estimates are done assuming all the samples are
independent. From the results obtained in the testing case of the
module `gen_dipoleaf.f90`, one sees that the auto-correlation time of
:math:`\vec{P}` in this system is about 1-2 DPD time units, so the sampling choice
done here (trajectories are written every 100 time steps, i.e., every 1 DPD
time units) seems reasonable, even if a bit optimistic.
To confirm the reliability of the error estimate one can do
another run with a different random number sequence (see the directive `seed` of
DL_MESO) and see if the two results are compatible within error bars.
Source Code
___________
.. literalinclude:: ./gen_dipole.f90
......
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