Re: [ESPResSo-users] Using two different Lennard-Jones potentials for same particles

[David Sean]

I may be late in the game here, but could one not exploit the
LENNARD_JONES_GENERIC feature (provided the exponents 6 and 12 are
chosen) to obtain two LJ interactions with different parameters ?

David

2018-03-03 4:50 GMT+01:00 Henri Menke <address@hidden>:
> Hi Reza,
>
> Sorry to hear that it doesn't work.  I must have remembered it incorrectly.
>
> In the tabulated interaction the parameters 'energy' and 'force' take arrays,
> i.e. you have to read in the files 'potential.dat' and 'force.dat' first.  On
> the other hand you don't even need to save them as files in this case at all
> because you can compute the arrays using numpy on the fly.
>
> The Lennard-Jones interaction with the parameters
>
>     system.non_bonded_inter[0,0].lennard_jones.set_params(
>         epsilon=0.1, sigma=0.1, cutoff=1.0, shift=0.0)
>
> can be reproduced with a tabulated potential of the form
>
>     import numpy as np
>
>     epsilon = 0.1
>     sigma = 0.1
>     def V(r):
>         return 4*epsilon*((sigma/r)**12 - (sigma/r)**6)
>     def F(r):
>         return -48*epsilon*((sigma/r)**12 - .5*(sigma/r)**6)/r
>
>     rmin, rmax = 1e-16, 1.0
>     r = np.linspace(rmin,rmax,10000)
>
>     system.non_bonded_inter[0,0].tabulated.set_params(
>         min=rmin, max=rmax, energy=V(r), force=F(r))
>
> If you need to include shifts and offsets, just modify the functions V(r) and
> F(r) according to the documentation at
> http://espressomd.org/html/doc/inter_non-bonded.html#lennard-jones-interaction
>
> Kind regards,
> Henri
>
> On Fri, 2018-03-02 at 23:54 +0330, Mohammadreza Niknam Hamidabad wrote:
>> Hello all,
>>
>> I did this for using two different LJ potential for same particles:
>>
>> system.non_bonded_inter[1, 2].lennard_jones.set_params(
>>     epsilon=ep1, sigma=1.0,
>>     cutoff=1.1225, shift="auto", offset=0.0, min=0.0)
>>
>> system.non_bonded_inter[2, 1].lennard_jones.set_params(
>>     epsilon=ep2, sigma=1.0,
>>     cutoff=2.5, shift="auto", offset=0.0, min=1.1225)
>>
>> then I used :
>>
>> print (system.non_bonded_inter[1,2].lennard_jones.get_params())
>> print (system.non_bonded_inter[2,1].lennard_jones.get_params())
>>
>> and I got the same things and this trick didn't work for me (the second
>> potential overwrites the first one) so I tried writing a tabulated 
>> interaction
>> for them sth like this:
>>
>> system.non_bonded_inter[1, 2].tabulated.set_params(min=0, max=2.5002,
>> energy='potential.dat', force='force.dat')
>>
>> Then I got this error: TypeError: a float is required
>> Could you help me with this tabulated interaction? I've attached force.dat 
>> and
>> potential.dat.
>> Is it possible I use just one file with couple of columns in it for force and
>> potential? Could you help me with its format?
>>
>> And the other thing, I use visualization_opengl for visualizing my
>> constraints. It's very good But is it possible I can do the same thing with
>> VMD. I think in Tcl version, ESPResSo had this feature.
>> I know you guys are so busy I appreciate any help you can provide. Thank you
>> so much for your time.
>>
>> Best regards,
>> Reza
>>
>>
>> On Tue, Feb 27, 2018 at 3:12 AM, Henri Menke <address@hidden> wrote:
>> > Hi Reza,
>> >
>> > In your current interaction setup the second one will overwrite the first.
>> > But
>> > you can work around it by simply reversing the numbers in the second call.
>> >
>> > system.non_bonded_inter[1, 2].lennard_jones.set_params(
>> >     epsilon=ep1, sigma=1.0,
>> >     cutoff=1.1225, shift="auto", offset=0.0, min=0.0)
>> >
>> > system.non_bonded_inter[2, 1].lennard_jones.set_params(
>> >     epsilon=ep2, sigma=1.0,
>> >     cutoff=2.5, shift="auto", offset=0.0, min=1.1225)
>> >
>> > The compiler error is not reproducible for me on Ubuntu 16.04 with 
>> > libraries
>> > and
>> > tools from the official repositories.  Do you happen to have a version of
>> > FFTW3
>> > which you compiled yourself?  In that case it could be that you originally
>> > built
>> > it without the -fPIC flag but after a system updated (or whatever) your
>> > linker
>> > is now enforcing position independent executables to mitigate recent Intel
>> > processor security bugs.
>> > https://en.wikipedia.org/wiki/Position-independent_code
>> >
>> > Currently the ESPResSo build system does not have a switch to disable
>> > algorithms
>> > using FFTW3 because they are an integral part of ESPResSo's feature set.
>> > You
>> > could try removing the FFTW3 paths from the CMake configurations file by
>> > hand or
>> > using the ccmake command line tool.
>> >
>> > Kind regards,
>> > Henri
>> >
>> > On Tue, 2018-02-27 at 01:36 +0330, Mohammadreza Niknam Hamidabad wrote:
>> > > Hello all,
>> > >
>> > > I'm working on behavior of some proteins and I need to use two different
>> > LJ
>> > > potentials for the same types. some thing like this:
>> > >
>> > > system.non_bonded_inter[1, 2].lennard_jones.set_params(
>> > >     epsilon=ep1, sigma=1.0,
>> > >     cutoff=1.1225, shift="auto", offset=0.0, min=0.0)
>> > >
>> > > system.non_bonded_inter[1, 2].lennard_jones.set_params(
>> > >     epsilon=ep2, sigma=1.0,
>> > >     cutoff=2.5, shift="auto", offset=0.0, min=1.1225)
>> > >
>> > > Is it possible? Does the second potential overwrite the first one? If 
>> > > not,
>> > > except tabulated interaction, you guys have any suggestion?
>> > >
>> > > Also I want to compile newer development version, but every time I
>> > encounter
>> > > some errors about fftw3 and recompile with -fPIC.
>> > >
>> > > Do you know how can I solve it? or how can I turn off and disable fftw3?
>> > (I
>> > > don't need any algorithm for electrostatics or p3m)
>> > > I couldn't find options for make command in installation process to
>> > disable
>> > > it:
>> > > mkdir build
>> > > cd build
>> > > cmake ..
>> > > make
>> > >
>> > > Best regards,
>> > > Reza
>> > >
>> > >
>> >
>