Hello,
I am trying to simulate blood flow in Lammps. I tried to use Hongyan Yuan & Ralph Kfoury code to base on it (blood cell in membrane) - attachment. I’m using latest version of Lammps mpi.
I’m working on Linux and I have problem to compile those codes because of atom_style. On Lammps web site page you posted that Blood flow simulations are possible to do.
Could you share me an example or get any tips how it should be done in Lammps and if it is possible to do that? Is there any sample in Lammps package?
Thank you in advance.
Regards,
in_example (7.55 KB)
Hello,
I am trying to simulate blood flow in Lammps. I tried to use Hongyan Yuan & Ralph Kfoury code to base on it (blood cell in membrane) - attachment. I’m using latest version of Lammps mpi.
I’m working on Linux and I have problem to compile those codes because of atom_style. On Lammps web site page you posted that Blood flow simulations are possible to do.
in order to get help, you have to be more specific as to what it is exactly what you are doing and where you are getting the error and what the error message is. there is not enough information here to make any accurate suggestion. i can only guess that you are use source code that is not part of the LAMMPS distribution and also not compatible with the specific LAMMPS version you are using. if that guess is correct, you have to either revert to the authors of that source code for advice or download/install a compatible version of the LAMMPS sources or adapt the source code to be compatible with your version of LAMMPS.
axel.
Thank you for your response.
I want to make simulation of soldify blood realted to surface (in my case wall). I need to base on some examples where any blood simaltion has been done but I didn’t find anythink usless.
Error dump from running porgram in example file:
LAMMPS (16 Mar 2018)
ERROR: Invalid atom_style command (…/atom_vec.cpp:71)
Regards,
Pawel
Thank you for your response.
I want to make simulation of soldify blood realted to surface (in my case wall). I need to base on some examples where any blood simaltion has been done but I didn’t find anythink usless.
you need to do what everybody does in this case: look up some publications that have done this before and see how you can implement that with LAMMPS. LAMMPS is such a flexible software, you cannot expect ready-to-use examples for “everything” bundled with the code and documentation explaining how to do all kinds of research. the LAMMPS documentation is like a driver’s manual for a car: it shows you where the knobs and switches are, but does not teach you how to drive. that is far beyond its scope and purpose.
Error dump from running porgram in example file:
LAMMPS (16 Mar 2018)
ERROR: Invalid atom_style command (…/atom_vec.cpp:71)
well, so have you looked up what this error means? there is a whole section of the manual dedicated to error messages and warnings with general and specific notes.
axel.
Of course yes. If I change atom style to atom that’s fine. But I don’t expect this result.
Belive me that I’m not expect to get full solution and do nothing. I spent a lot of hours on that and I made a lot of other simulations but with metals.
I have a problem with “atom_style hybrid ellipsoid peri molecular” with multiple parameters. I had a lot of other problems and to reslove them I had to compile:
make yes-MOLECULE
make yes-CLASS2
make yes-USER-MISC
make yes-KSPACE
make yes-USER-3SPN2
make yes-omp
and as you mentoined change some code in Lammps to make it runnable on new version of Lammps.
Currently I have an issue with multiple atomic style and I tried to resolve it in many cases. ‘Make’ some packages, find out other atom style (single) to repleace mentioned multiple atom style.
Of course I forgot to mentoined - I’m working on Linux Ubuntu 18.04.1
I was asking about examples beacuse I want to see anything related to blood in Lammps. Till now I was doing only metal simulations.
I was searching for publications and to find out any source code in Lammps realted to blood flow or anything with blood is really hard. I agree - there are many publications but without examples. A lot of theory - less practise.
Of course yes. If I change atom style to atom that’s fine. But I don’t expect this result.
Belive me that I’m not expect to get full solution and do nothing. I spent a lot of hours on that and I made a lot of other simulations but with metals.
I have a problem with “atom_style hybrid ellipsoid peri molecular” with multiple parameters. I had a lot of other problems and to reslove them I had to compile:
you may have spent many hours, but you have not spent it the right way.
make yes-MOLECULE
make yes-CLASS2
make yes-USER-MISC
make yes-KSPACE
this does not include the package for atom style peri or ellipsoid. please study the LAMMPS manual more carefully.
make yes-USER-3SPN2
this is not a package included with LAMMPS, so for this you are on your own.
make yes-omp
this also does not exist as a package.
and as you mentoined change some code in Lammps to make it runnable on new version of Lammps.
Currently I have an issue with multiple atomic style and I tried to resolve it in many cases. ‘Make’ some packages, find out other atom style (single) to repleace mentioned multiple atom style.
Of course I forgot to mentoined - I’m working on Linux Ubuntu 18.04.1
these issues are independent from the OS. these are conceptual problems.
I was asking about examples beacuse I want to see anything related to blood in Lammps. Till now I was doing only metal simulations.
I was searching for publications and to find out any source code in Lammps realted to blood flow or anything with blood is really hard. I agree - there are many publications but without examples. A lot of theory - less practise.
yes, but as i was stating before, this is not a problem to bug the LAMMPS folks with, but you need to get suitable information from the authors of those publications. you cannot always expect ready to use inputs, but just descriptions of how to set things up. if you struggle with translating this, perhaps you need to first practice simpler problems with LAMMPS and build your skills more systematically until you can handle the problems you want to handle.
axel.
Of course yes. If I change atom style to atom that's fine. But I don't
expect this result.
Belive me that I'm not expect to get full solution and do nothing. I spent
a lot of hours on that and I made a lot of other simulations but with
metals.
I have a problem with "atom_style hybrid ellipsoid peri molecular" with
multiple parameters. I had a lot of other problems and to reslove them I
had to compile:
make yes-MOLECULE
make yes-CLASS2
make yes-USER-MISC
make yes-KSPACE
make yes-USER-3SPN2
make yes-omp
You forgot to include:
make yes-peri
(I'm not sure if you need peridynamics, but if you do, you need to enable
it.)
I think part of the confusion here is that the error message is misleading in this case.
For this command in your script:
atom_style hybrid ellipsoid peri molecular
Normally, if you did not build LAMMPS with a needed package (that contained a style),
you’d get an error like Unknown atom style.
But for atom_style hybrid it doesn’t know if the extra style names
are unknown or bad args to a known style. The ellipsoid style
is always available; it’s not in a package. So when it
processes ellipsoid it think peri is an invalid arg to it,
and gives the Invalid atom_style command error.
Axel, any ideas on how to make the error message more clear?
Or maybe it should state both possibilities.
Big picture, Axel is correct. You will need to communicate
with the authors to get their additions to LAMMPS, if you
want to run their models.
Steve