Functions

When performing biased dynamics or analyzing a trajectory you may wish to analyze/bias the value of some function of a set of collective variables rather than the values of the collective variables directly. You can do this with PLUMED by using any one of the following list of functions.

Notice that in many functions you should explicitly say to PLUMED whether the result is a periodic variable or not using the keyword PERIODIC. This is crucial to allow a variable to be properly based. To know if a function is periodic of not you should answer to the following question:

• Can my function change with a discontinuity when I move my atoms in a continuous manner?

In case the answer is no, than you should use PERIODIC=NO. In case the answer is yes, then you should consider the following question:

• Are the values of the function at the discontinuity always the same or do they change?

In case the answer is that they are the same, you should use PERIODIC=A,B where A is the smallest value and B is the largest value. In case the answer is that the values at the discontinuity are not always the same, then you cannot construct a variable that can be biased with PLUMED. Consider the following examples:

Click on the labels of the actions for more information on what each action computes

contract shortcuts

t: TORSION 
ATOMS
the four atoms involved in the torsional angle 
=1,2,3,4 The TORSION action with label t calculates a single scalar value
# When atoms are moved, t could jump suddenly from -pi to +pi
c: MATHEVAL 
ARG
the input to this function. 
=t 
FUNC
compulsory keyword 
the function you wish to evaluate 
=x*x*x 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=-31.0062766802998,31.0062766802998 The MATHEVAL action with label c calculates a single scalar value
# When atoms are moved, c could jump suddenly from -pi**3 to +pi**3
# equivalently, we could have used:
# c: COMBINE ARG=t POWERS=3 PERIODIC=-31.0062766802998,31.0062766802998
# compute x/y/z components of the distance between atoms 1 and 10
d: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,10 
COMPONENTS
( default=off ) calculate the x, y and z components of the distance separately and
store them as label.x, 
 The DISTANCE action with label d calculates the following quantities:

 Quantity   
 Description  
d.x
the x-component of the vector connecting the two atoms
d.y
the y-component of the vector connecting the two atoms
d.z
the z-component of the vector connecting the two atoms


# make a new variable equal to d.z but with the correct periodicity
dz: COMBINE 
ARG
the input to this function. 
=d.z 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=-10,10 The COMBINE action with label dz calculates a single scalar value
# here we assumed the system is in a orthorhombic box with z side = 20

t: TORSION 
ATOMS
the four atoms involved in the torsional angle 
=1,2,3,4 The TORSION action with label t calculates a single scalar value
# When atoms are moved, t could jump suddenly from -pi to +pi
c: MATHEVAL_SCALAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=t 
FUNC
compulsory keyword 
the function you wish to evaluate 
=x*x*x 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=-31.0062766802998,31.0062766802998 The MATHEVAL_SCALAR action with label c calculates a single scalar value
# When atoms are moved, c could jump suddenly from -pi**3 to +pi**3
# equivalently, we could have used:
# c: COMBINE ARG=t POWERS=3 PERIODIC=-31.0062766802998,31.0062766802998
# compute x/y/z components of the distance between atoms 1 and 10
d: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,10 
COMPONENTS
( default=off ) calculate the x, y and z components of the distance separately and
store them as label.x, 
 The DISTANCE action with label d calculates the following quantities:

 Quantity   
 Description  
d.x
the x-component of the vector connecting the two atoms
d.y
the y-component of the vector connecting the two atoms
d.z
the z-component of the vector connecting the two atoms


# make a new variable equal to d.z but with the correct periodicity
dz: COMBINE_SCALAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=d.z 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=-10,10 The COMBINE_SCALAR action with label dz calculates a single scalar value
# here we assumed the system is in a orthorhombic box with z side = 20

BESSEL	Calculate the value of a Bessel function.
BESSEL_SCALAR	Calculate the value of a Bessel function.
BESSEL_VECTOR	Calculate the bessel function for all the elements in a vector
BETWEEN	Use a switching function to determine how many of the input variables are within a certain range.
BETWEEN_VECTOR	Use a switching function to determine how many of the input components are within a certain range
COMBINE	Calculate a polynomial combination of a set of other variables.
COMBINE_SCALAR	Calculate a polynomial combination of a set of other variables.
COMBINE_VECTOR	Add together the elements of a set of vectors elementwise
CUSTOM	Calculate a combination of variables using a custom expression.
CUSTOM_SCALAR	Calculate a function of a set of input scalars
CUSTOM_VECTOR	Calculate a function of a set of input vectors elementwise
DIFFERENCE	Calculate the differences between two scalars
DIFFERENCE_SCALAR	Calculate the differences between two scalars
DIFFERENCE_VECTOR	Calculate the differences between the elements of two vectors
ENSEMBLE	Calculates the replica averaging of a collective variable over multiple replicas.
FLATTEN	Convert a matrix into a vector
FUNCPATHGENERAL	This function calculates path collective variables (PCVs) using an arbitrary combination of collective variables.
FUNCPATHMSD	This function calculates path collective variables.
FUNCSUMHILLS	This function is intended to be called by the command line tool sum_hills. It is meant to integrate a HILLS file or an HILLS file interpreted as a histogram in a variety of ways. It is, therefore, not expected that you use this during your dynamics (it will crash!)
HIGHEST	This function can be used to find the highest colvar by magnitude in a set.
KERNEL	Use a switching function to determine how many of the input variables are less than a certain cutoff.
LESS_THAN	Use a switching function to determine how many of the input variables are less than a certain cutoff.
LESS_THAN_VECTOR	Use a switching function to determine how many components of the vector are less than a certain cutoff.
LOCALENSEMBLE	Calculates the average over multiple arguments.
LOWEST	This function can be used to find the lowest colvar by magnitude in a set.
MAHALANOBIS_DISTANCE	Calculate the mahalanobis distance between two points in CV space
MATHEVAL	An alias to the CUSTOM function.
MATHEVAL_SCALAR	Calculate a function of a set of input scalars
MATHEVAL_VECTOR	Calculate a function of a set of input vectors elementwise
MATRIX_PRODUCT_DIAGONAL	Calculate the product of two matrices and return a vector that contains the diagonal elements of the ouptut vector
MOMENTS	Calculate the moments of the distribution of input quantities
MOMENTS_SCALAR	Calculate the moments of the distribution of input quantities
MOMENTS_VECTOR	Calculate the moments of the distribution of input vectors
MORE_THAN	Use a switching function to determine how many of the input variables are more than a certain cutoff.
MORE_THAN_VECTOR	Use a switching function to determine how many of elements in the input vector are more than a certain cutoff.
NORMALIZED_EUCLIDEAN_DISTANCE	Calculate the normalised euclidean distance between two points in CV space
PIECEWISE	Compute a piece wise straight line through its arguments that passes through a set of ordered control points.
PIECEWISE_SCALAR	Compute a piece wise straight line through its arguments that passes through a set of ordered control points.
PRODUCT	Calculate the product of the input quantities
PYTHONFUNCTION	Define collective variables in the Python language.
SORT	This function can be used to sort colvars according to their magnitudes.
SORT_SCALAR	Sort the input scalars in a vector according to their magnitudes
SORT_VECTOR	Sort the elements in a vector according to their magnitudes
STATS	Calculates statistical properties of a set of collective variables with respect to a set of reference values.

In addition to the keywords above, by enabling optional modules you can access to the following keywords:

PYTORCH_MODEL	(from PYTORCH module) Load a PyTorch model compiled with TorchScript.
SELECT	(from PLUMED-ISDB module) Selects an argument based on the value of a SELECTOR.