Write your own Methods and CVs

One of the basic design goals of SSAGES is that it should be easily extensible. To this end, it provides intuitive and simple tools to implement new collective variables (CVs) and new metadynamic methods. This section covers the basic steps to implement a new CV and a new Method. Let us start first with the implementation of a new CV. The techniques to implement a new Method are covered below.

How to write a new CV

Each CV consists of two components: A header file and a schema file. The header file contains the source code for the calculation of the CV and the schema file describes the properties of the CV in a simple JSON format. Finally, you will have to make SSAGES aware of the new CV.

The CV header file

Each CV in SSAGES is implemented as a child of the class CollectiveVariable. The header file should be placed in the directory src/CVs and has to (re)implement the following functions:

void Initialize(const Snapshot&) (optional)
This method is called during the pre-simulation phase. It is typically used to allocate or reserve memory.
void Evaluate(const Snapshot&)
Evaluation of the CV based on a simulation snapshot. Together with the value, this function should also calculate the gradient of the CV. The gradient should be a vector of length n, where n is the number of atoms in the Snapshot. Each element in the vector is the derivative of the CV with respect to the corresponding atom’s coordinates. This method is called in the post-integration phase of every iteration.
double GetValue() const
Return the current value of the CV.
double GetPeriodicValue() const
Return the current value of the CV, taking periodic boundary conditions into account. An example would be an angular CV which is bound to the region \((-\pi,\pi]\). In this case, GetValue() could return any angle, while GetPeriodicValue() should return the angle mapped back into the region \((-\pi,\pi]\). If the CV does not use periodic boundaries, this function should return the same value as GetValue().
const std::vector<Vector33>& GetGradient() const
Return the gradient of the CV (see Evaluate(const Snapshot&) for how the gradient is defined).
const std::array<double, 2>& GetBoundaries() const
Return a two-element array containing the lower and the upper boundary for the CV.
double GetDifference(const double Location) const
Return the distance of the current value of the CV from a specified location, taking periodic boundary conditions into account. If the CV does not use periodic boundary conditions, the return value should simply be GetValue() - Location.

The CV schema file

Together with the header file that contains the source code of the CV, you will have to provide a schema file to make the CV accessible to the SSAGES input files. The schema file should be placed in the directory schema/CVs/. It has to be written in the JSON format and should contain the following items:

type
The value of type should be set to object.
varname
The name of your new CV.
properties
The properties contain the type which is the internal name of the CV and a set of other properties that have to be supplied to the constructor of the CV.
required
A list containing the required properties. Optional parameters to the CV constructor are not listed here.
additionalProperties
Optional properties.

Integrate the new CV into SSAGES

Once you have provided the header and the schema file, there is one more steps to do in order to make SSAGES aware of the newly included CV.

Note

We are currently working on a method to automate this step. Revisit this section in future releases. Chances are, that you no longer have to worry about this step.

To include your new CV, you have to edit the file src/CVs/CollectiveVariable.cpp, and

  1. #include your CV header file at the top of the file.
  2. Add a new else if clause in BuildCV(). The if-test checks for the CV type set as an enum in the list of properties. Within the if-clause you should parse and validate the JSON schema, read the required properties and create the CollectiveVariable. A pointer to the newly created object should be stored in the variable named cv.

How to write a new method

Each method consists of three components: A header file, a cpp file, and a schema file. The header file and cpp file contains the source code for the method and the schema file describes the properties of the method in a simple JSON format. Finally, you will have to make SSAGES aware of the new method.

The method header file

Each method in SSAGES is implemented as a child of the class Methods. The header file should be placed in the directory src/methods and has to (re)implement the following functions:

void PreSimulation(Snapshot* snapshot, const CVList& cvs)
Setup done before the method actually runs. This function will be called vefore the simulation is started.
void PostIntegration(Snapshot* snapshot, const CVList& cvs)
This is where the heart of your method should go. By using snapshot and the cvs, modify the forces, positions, velocities, etc. appropriated by the new method. This function will be called after each integration MD step.
code:void PostSimulation(Snapshot* snapshot, const CVList& cvs) This function is called at the end of the simulation run. Use it to close files your method opened, to write out data that you have been storing, etc.

The method schema file

Together with the source code of the method, you will have to provide a schema file to make the CV accessible to the SSAGES input files. The schema file should be placed in the directory schema/methods/. It has to be written in the JSON format and should contain the following items:

type
The value of type should be set to object.
varname
The name of your new method.
properties
The properties contain the type which is the internal name of the method and a set of other properties that have to be supplied to the constructor of the method.
required
A list containing the required properties. Optional parameters to the method constructor are not listed here.
additionalProperties
Optional properties.

Integrate the new method into SSAGES

Once you have provided the header and the schema file, there is one more steps to do in order to make SSAGES aware of the newly included method.

Note

We are currently working on a method to automate this step. Revisit this section in future releases. Chances are, that you no longer have to worry about this step.

To include your new method, you have to edit the file src/methods/Methods.cpp, and

  1. #include your method header file at the top of the file.
  2. Add a new else if clause in BuildMethod(). The if-test checks for the method type set as an enum in the list of properties. Within the if-clause you should parse and validate the JSON schema, read the required properties and create the method. A pointer to the newly created object should be stored in the variable named method.

Finally, add the method .cpp to CMakeLists.txt as a source.