lammps/src/USER-MANIFOLD4f65214374a5efficient_neuronet
USER-MANIFOLD
README
+==============================================================================+ This file is a part of the USER-MANIFOLD package.
This package allows LAMMPS to perform MD simulations of particles constrained on a manifold (i.e., a 2D subspace of the 3D simulation box). It achieves this using the RATTLE constraint algorithm applied to single-particle constraint functions g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold) n = grad(g).
Stefan Paquay, s.paquay@tue.nl Applied Physics/Theory of Polymers and Soft Matter, Eindhoven University of Technology (TU/e), The Netherlands
Thanks to Remy Kusters at TU/e for testing.
This software is distributed under the GNU General Public License. +==============================================================================+
At the moment we have a few manifolds available, extending them is very easy: To add a new manifold, do the following in the "USER-MANIFOLD" directory:
0. Create a new pair of source/header files, and name them "manifold_*.cpp/h",
where you should replace '*' with some (descriptive) name.
- In the header file, add the following: a. Include guards. b. Make sure you #include "manifold.h" c. In namespace LAMMPS_NS, add a new class that inherits publicly from manifold and protectedly from Pointers. d. The constructor has to take ( LAMMPS*, int, char ** ) as arguments, and should initialise Pointers. e. The header file has to contain somewhere the macro ManifoldStyle with as first argument the name of the manifold and as second argument the name of the class implementing this manifold. The macro expands into some code that registers the manifold during static initialisation, before main is entered.
- In the source file, make sure you implement the following (of course, you can also implement these in the header):
+====================================+=========================================+
| Function signature | Purpose |
+====================================+=========================================+
| destructor | Free space (can be empty) |
| constructor | Has to take (LAMMPS *lmp, int, char **) |
| as arguments and has to initialise | |
| Pointers with lmp. | |
| double g( double *x ) | A function that is 0 if the 3-vector |
| x is on the manifold. | |
| void n( double *x, double *n ) | Stores the normal of position x in the |
| 3-vector n. | |
| static const char *type() | Returns text that identifies the |
| manifold in LAMMPS input scripts. | |
| const char *id() | Should return whatever type() returns. |
| static int expected_argc() | Returns the number of arguments needed |
| for the construction/initialisation of | |
| your manifold. Example: Sphere only | |
| needs a radius, so it returns 1. The | |
| spine needs 5 parameters, so it | |
| returns 5. | |
| int nparams() | Should return same as expected_argc() |
+====================================+=========================================+
If the above instructions seem a bit intimidating, you can get by just fine by copying an existing manifold and modifying it. See e.g. manifold_sphere for a relatively simple manifold.
With those things in place, the install script should be able to add your manifold to LAMMPS without any extra work, so just running make yes-user-manifold make <your_architecture> should (re)compile LAMMPS with the manifolds added.
+==============================================================================+ Obviously, you need some parameters to represent the surface, such as the radius in the case of a sphere. These should be passed to the nve/manifold/rattle fix, with the following syntax: fix ID group-ID nve/manifold/rattle tol maxit manifold_style args
tol = tolerance to which RATTLE tries to satisfy the constraints maxit = maximum number of iterations RATTLE uses each time step manifold_style = manifold style, should equal what type() of the desired
manifold returns
args = parameters for the manifold, order is manifold-dependent.
can be equal style variables
+==============================================================================+