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PLUMED manual

Shortcut: LOWEST

Shortcut: LOWEST

Module	function
Description	Usage
This function can be used to find the lowest colvar by magnitude in a set.
output value	type
the highest of the input values	scalar

Details and examples

This function can be used to find the lowest colvar by magnitude in a set.

This action allows you to find the lowest of the input arguments. As a first example of how it might be used consider the following input:

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

d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
d2The DISTANCE action with label d2 calculates the following quantities: Quantity    Type    Description  
d2 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,4
l1The LOWEST action with label l1 calculates the following quantities: Quantity    Type    Description  
l1 scalar the highest of the input values: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d1,d2
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=l1 FILEthe name of the file on which to output these quantities=colvar

The value, l1, that is output to the file colvar here will be equal to d1 if d1<d2 and will be equal to d2 if d2<d1. In other words, if all the arguments input to a LOWEST action are scalars then the output value will be a scalar that is equal to the smallest of the input arguments. Notice that you can also use this command with more than two arguments as illustrated below:

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

d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
d2The DISTANCE action with label d2 calculates the following quantities: Quantity    Type    Description  
d2 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,4
d3The DISTANCE action with label d3 calculates the following quantities: Quantity    Type    Description  
d3 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,6
d4The DISTANCE action with label d4 calculates the following quantities: Quantity    Type    Description  
d4 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,8
l1The LOWEST action with label l1 calculates the following quantities: Quantity    Type    Description  
l1 scalar the highest of the input values: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d1,d2,d3,d4
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=l1 FILEthe name of the file on which to output these quantities=colvar

Using a single vector as input

Instead of inputting multiple scalars you can input a single vector to this action instead as is illustrated below:

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

dThe DISTANCE action with label d calculates the following quantities: Quantity    Type    Description  
d vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1,2 ATOMS2the pair of atom that we are calculating the distance between=3,4
l1The LOWEST action with label l1 calculates the following quantities: Quantity    Type    Description  
l1 scalar the highest of the input values: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=l1 FILEthe name of the file on which to output these quantities=colvar

The output from this action is a single scalar once again. This single scalar is equal to the smallest element of the input vector.

Using multiple vectors in input

If you input multiple vectors with the same numbers of elements to this action, as shown below, the output will be a vector.

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

d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1,2 ATOMS2the pair of atom that we are calculating the distance between=3,4
d2The DISTANCE action with label d2 calculates the following quantities: Quantity    Type    Description  
d2 vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=5,6 ATOMS2the pair of atom that we are calculating the distance between=7,8
d3The DISTANCE action with label d3 calculates the following quantities: Quantity    Type    Description  
d3 vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=9,10 ATOMS2the pair of atom that we are calculating the distance between=11,12
l2The LOWEST action with label l2 calculates the following quantities: Quantity    Type    Description  
l2 vector the smallest element in the input vector if one vector specified.  If multiple vectors of the same size specified the largest elements of these vector computed elementwise.: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d1,d2,d3
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=l2 FILEthe name of the file on which to output these quantities=colvar

The elements of the output vector here are determined by doing an elementwise comparison of the elements in the input vectors. In the above input the first element of h2 is equal to the distance between atoms 1 and 2 if this distance is smaller than the distances between atoms 5 and 6 and the distance between atoms 9 and 10. By the same token the second element of h2 is equal to the distance between atoms 3 and 4 if this is smaller than the distance between atoms 7 and 8 and the distance between atoms 11 and 12. In other words, if the elements of the $j$ th input vector are given by $v_i^{(j)}$ then the elements of the output vector, $h_i$ are given by:

$h_i = \min_j v_i^{(j)}$

Notice that you can also use a combination of scalars and vectors in the input to this action as shown below:

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

cThe CONSTANT action with label c calculates the following quantities: Quantity    Type    Description  
c scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUEthe single number that you would like to store=0.5
c: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUEthe single number that you would like to store=0.5  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
dThe DISTANCE action with label d calculates the following quantities: Quantity    Type    Description  
d vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1,2 ATOMS2the pair of atom that we are calculating the distance between=3,4
hThe LOWEST action with label h calculates the following quantities: Quantity    Type    Description  
h vector the smallest element in the input vector if one vector specified.  If multiple vectors of the same size specified the largest elements of these vector computed elementwise.: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d,c
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=h FILEthe name of the file on which to output these quantities=colvar

For the input above the LOWEST action outputs a vector with two elements. The elements of this vector are equal to the distances between the pairs of atoms that are specified in the DISTANCE command as long as those distances are less than 0.5 nm. If either of the two input distances is more than 0.5 nm then the corresponding value in the vector h is set equal to 0.5 nm.

The MASK keyword

You should only use the MASK keyword for this action if you are using multiple arguments and at least one vector in the input to this action. The following input illustrates how this keyword works:

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

mThe CONSTANT action with label m calculates the following quantities: Quantity    Type    Description  
m vector the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1,0
m: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1,0  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1,2 ATOMS2the pair of atom that we are calculating the distance between=3,4
d2The DISTANCE action with label d2 calculates the following quantities: Quantity    Type    Description  
d2 vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=5,6 ATOMS2the pair of atom that we are calculating the distance between=7,8
d3The DISTANCE action with label d3 calculates the following quantities: Quantity    Type    Description  
d3 vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=9,10 ATOMS2the pair of atom that we are calculating the distance between=11,12
h2The LOWEST action with label h2 calculates the following quantities: Quantity    Type    Description  
h2 vector the smallest element in the input vector if one vector specified.  If multiple vectors of the same size specified the largest elements of these vector computed elementwise.: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d1,d2,d3 MASKthe label for a sparse vector/matrix that should be used to determine which elements of the vector/matrix should be computed=m

By using the MASK keyword here you ensure that only the first element of the output vector for h2 is calculated. This element of the output vector is evaluated as the corresponding element of the vector that is passed in the input to the MASK keyword is one. By the same logic the second element of the output vector is not computed because the corresponding element in the mask vector is 0.

The input above illustrates the key idea for the MASK keyword and is probably not very useful. To see an example where using a MASK for this type of action is useful you should look at the expanded shortcuts in the documentation for PARABETARMSD.

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
ARG	scalar/vector/matrix	the values input to this function
MASK	vector/matrix	the label for a sparse vector/matrix that should be used to determine which elements of the vector/matrix should be computed

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ARG	input	none	the values input to this function
MASK	input	none	the label for a sparse vector/matrix that should be used to determine which elements of the vector/matrix should be computed