AddNewPotential

The aim of the tutorial is to implement a new interaction potential in ESPResSo++. We start with the Gromos fourth-power bond-stretching potential, because its functional form is simple and its implementation is somewhat similar to other potentials already implemented in ESPResSo++. Everything you learn in this tutorial will then be relevent for implementing any other more complicated potential.

Make sure you have a working, compiled version of ESPResSo++ before starting the tutorial.

For those who are not so familiar with C++ or interfacing python and C++, you will find some helpful notes in the appendix.

Steps for adding a new interaction potential

  1. Choose the potential and derive the force.

  2. Choose the appropriate interaction template from those in $ESPRESSOHOME/src/interaction, e.g. VerletListInteractionTemplate.hpp, FixedTripleListInteractionTemplate.hpp

  3. Create the .cpp, .hpp and .py files for your potential, place them in $ESPRESSOHOME/src/interaction and modify $ESPRESSOHOME/src/interaction/bindings.cpp and $ESPRESSOHOME/src/interaction/__init__.py

  4. Compile.

These steps are described in more detail below for our tutorial example potential.

Today’s tutorial exercise

Step 1

The potential we are implementing today is a two-body bonded potential with the form

\[V(r_{ij})=\frac{1}{4}k_{ij}(r^2_{ij}-r^2_{0,ij})^2\]

noindent where \(r_{ij}\) is the distance between particles i and j. The potential has two input parameters \(r_{0}\) and \(k\).

Derive the force.

Step 2

This is a 2-body interaction between a predefined (fixed) list of atom pairs. What is the appropriate interaction template to use? Choose one in $ESPRESSOHOME/src/interaction

Open the interaction template file. (When you close the file later, close it without saving, or else later on your compile time will be very long, because of the number of dependencies on the interaction template!) Identify the functions addForces() and computeEnergy(). Many interaction templates also contain functions such as computeVirial(), computeVirialX() (for calculating the virial in slabs along the x-direction) etc.

Find the function calls:

potential->_computeForce(force, dist)

in addForces() and

potential->_computeEnergy(r21)

in computeEnergy().

An interaction template can be combined with many different potentials (e.g. harmonic potential, Lennard Jones potential, etc.) Each potential will have its own C++ class containing functions to compute the energy and forces for that particular potential (see e.g. Harmonic.cpp/hpp, LennardJones.cpp/hpp) In turn, each potential can be combined with many different interaction templates.

You don’t need to modify the interaction template file today. (Close it without saving!)

Step 3

In this step we create the .cpp, .hpp and .py files for our potential. Let’s call the potential FourthPower. The FourthPower.py file will contain the end-user python interface, and in the FourthPower.cpp and FourthPower.hpp files we will create a C++ class for our potential. We will also write a wrapper which will allow the user to call the C++ code from the python interface.

3(a) Interfacing potential class and interaction template

In many cases, it’s not necessary to understand the contents of this section in order to implement a new potential. If you like, you can skip directly to Section 3(b) Creating the new potential class.

Now we need to understand how the interaction template will interface with our new class. This is done via a class template, e.g. in Potential.hpp, AnglePotential.hpp, DihedralPotential.hpp etc.

Still in $ESPRESSOHOME/src/interaction, open the file Potential.hpp. (When you close the file later, close it without saving, or else later on your compile time will be very long, because of the number of dependencies on the file!)

Find the functions _computeForce(Real3D& force, const Real3D& dist) and _computeEnergy(real dist) which you identified in the interaction template. Note that _computeForce(Real3D& force, const Real3D& dist) calls the function _computeForceRaw(force, dist, distSqr) and _computeEnergy(real dist) calls _computeEnergySqr(dist*dist) which calls _computeEnergySqrRaw(distSqr). The functions _computeForceRaw() and _computeEnergySqrRaw() are the new functions we need to write for our new potential. They will be member methods of our new C++ class FourthPower.

You don’t need to modify anything in Potential.hpp today. (Close it without saving!)

3(b) Creating the new potential class

An easy way to implement the new C++ class is to identify a previously implemented potential which somewhat resembles your new potential, e.g. here we could take the Harmonic potential, which is also a 2-body potential, and which has also been interfaced with the FixedPairListInteractionTemplate.

Still in $ESPRESSOHOME/src/interaction, copy the files Harmonic.py, Harmonic.cpp and Harmonic.hpp to new files FourthPower.py, FourthPower.cpp and FourthPower.hpp. In the new files, find and replace all occurences of ‘Harmonic’ with ‘FourthPower’, and ‘HARMONIC’ with ‘FOURTHPOWER’.

First modify FourthPower.hpp.

Note the #include statement for FixedPairListInteractionTemplate.hpp and Potential.hpp, the files you examined in Step 2 and Step 3(a) Interfacing potential class and interaction template.

The Harmonic potential had parameters called K and r0. You can reuse these for the FourthPower potential, along with the setters and getters setK, getK, setR0 and getR0. For better efficiency, you could also create a new variable which contains the square of r0.

Now we need functions _computeForceRaw() and _computeEnergySqrRaw(), as explained in Step 3(a) Interfacing potential class and interaction template. Modify these functions to use the functional form of the fourth power potential as derived in Step 1. Note that Real3D dist, which contains the vector between the two particles, has been defined as \(r_{p1} - r_{p2}\) (see addForces() in FixedPairListInteractionTemplate.hpp).

Next open Harmonic.py and FourthPower.py.

Here is an example of an end-user’s python script to add an interaction using the harmonic potential:

harmonicbondslist = espresso.FixedPairList(system.storage)
harmonicbondslist.addBonds(bond_list) #bond_list is a list of tuples [(particleindex_i,particleindex_j),...]
harmonic_potential = espresso.interaction.Harmonic(K=10.0, r0=1.0, cutoff = 5.0, shift = 0.0)
harmonic_interaction = espresso.interaction.FixedPairListHarmonic(system, harmonicbondslist, potential=harmonic_potential)
system.addInteraction(harmonic_interaction)

Compare this to the contents of Harmonic.py to understand the python source code.

Our new potential FourthPower can be called by the end-user in a similar way. Since the Harmonic and FourthPower potentials have similar input parameters (K, r0) and both use the FixedPairListInteractionTemplate, you don’t need to make any further modifications to the file FourthPower.py, besides replacing ‘Harmonic’ with ‘FourthPower’.

Next open FourthPower.cpp.

Here you will find the C++/python interface, in the function registerPython(). If you want to understand this function, you will find details in Exposing a C++ class or struct to python using boost. You don’t need to make any further modifications to this file, besides replacing ‘Harmonic’ with ‘FourthPower’.

3(c) Including the new class in espressopp

Finally, update the files $ESPRESSOHOME/src/interaction/bindings.cpp and $ESPRESSOHOME/src/interaction/__init__.py (for example by copying and modifying all the lines referring to the Harmonic potential so that they now refer to the FourthPower potential). You need to make three modifications: to include the new .hpp file, to call the new registerPython() wrapper, and to import everything in the new python module.

Step 4

Move to the directory $ESPRESSOHOME. Update the makefiles and compile using the commands:

cmake .
make

Advanced exercise

For an interaction potential of your choosing, follow the steps above to implement it, e.g. a non-bonded two-body interaction, probably using VerletListInteractionTemplate and based on the LennardJones potential, or a bonded three-body interaction, probably using FixedTripleListInteractionTemplate.hpp and based on the AngularHarmonic potential.

You will probably have to write setters and getters for the parameters in your potential in your .hpp file, and make the corresponding modifications to the function registerPython() in the .cpp file and the python user interface in the .py file.

Appendices

Exposing a C++ class or struct to python using boost

(See http://www.boost.org/doc/libs/1_56_0/libs/python/doc/tutorial/doc/html/python/exposing.html)

Say we have a C++ struct called World:

struct World
{
    World(std::string msg): msg(msg) {}              // constructor
    void set(std::string msg) { this->msg = msg; }   // function set
    std::string greet() { return msg; }              // function greet
    std::string msg;                                 // member variable
};

Now we write the C++ class wrapper for struct World to expose the constructor and the functions greet and set to python:

{
    class_<World>("World", init<std::string>())
        .def("greet", &World::greet)
        .def("set", &World::set)
    ;
}

If there are additional constructors we can also expose them using def(), e.g. for an additional constructor which takes two doubles:

class_<World>("World", init<std::string>())
    .def(init<double, double>())
    .def("greet", &World::greet)
    .def("set", &World::set)
;

We can also expose the data members of the C++ class or struct and the associated access (getter and setter) functions using add_property(), e.g. for the variable myValue with access functions getMyValue and setMyValue:

.add_property("myValue",&World::getMyValue,&World::setMyValue)

C++ classes and structs may be derived from other classes. Say we have the C++ struct myDerivedStruct which is derived from the struct myBaseStruct:

struct myBaseStruct { virtual ~myBaseStruct(); };
struct myDerivedStruct : myBaseStruct {};

We can wrap the base class myBaseStruct as explained above:

<Base>("Base")
   /*...*/
   ;

Now when we want to wrap the class myDerivedStruct, we tell boost that it is derived from the base class myBaseStruct:

class_<myDerivedStruct, bases<myBaseStruct> >("myDerivedStruct")
    /*...*/
    ;

typedef

typedef declaration allows you to create an alias that can be used anywhere in place of a (possibly complex) type name

typedef DataType AliasName;

Python notes

Syntax for classes in python

(See also https://docs.python.org/2/tutorial/classes.html)

Here is a python class called DerivedClassName which is derived from two other base classes (BaseClassName1 and BaseClassName1), is initialised with two variables x and y which have default values 1 and 2, and contains a function myFunction.

class DerivedClassName(BaseClassName1, BaseClassName2):
    """docstring"""          #a way of providing some documentation for the class
    def __init__(self,x=1,y=2): #takes two variable which have default values 1 and 2
        self.x = x
        self.y = y
    def myFunction(self):
        return self.x * self.y

PMI

PMI = parallel method invocation. For more details see the file $ESPRESSOHOME/src/pmi.py