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PLUMED manual

Shortcut: DIFFERENCE

Shortcut: DIFFERENCE

Module	refdist
Description	Usage
Calculate the differences between two scalars or vectors
output value	type
a function that measures the difference	scalar/vector

Details and examples

Calculate the differences between two scalars or vectors

This action can be used to calculate the difference between two values. For example, if we want to calculate the difference between the distances between atoms 1 and 2 and 3 and 4 we can use an input like the one shown 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
diffThe DIFFERENCE action with label diff calculates the following quantities: Quantity    Type    Description  
diff scalar a function that measures the difference: DIFFERENCECalculate the differences between two scalars or vectors 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=diff FILEthe name of the file on which to output these quantities=colvar

At first sight this action appears pointless as you can achieve the same result with 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
diffThe CUSTOM action with label diff calculates the following quantities: Quantity    Type    Description  
diff scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1,d2 FUNCthe function you wish to evaluate=x-y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=diff FILEthe name of the file on which to output these quantities=colvar

However, this second example will not give an equivalent result to the following input:

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

t1The TORSION action with label t1 calculates the following quantities: Quantity    Type    Description  
t1 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,3,4
t2The TORSION action with label t2 calculates the following quantities: Quantity    Type    Description  
t2 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,6,7,8
diffThe DIFFERENCE action with label diff calculates the following quantities: Quantity    Type    Description  
diff scalar a function that measures the difference: DIFFERENCECalculate the differences between two scalars or vectors More details ARGthe values input to this function=t1,t2
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=diff FILEthe name of the file on which to output these quantities=colvar

as the CUSTOM command cannot caclulate differences between periodic input variables. In this case you have to use DIFFERENCE to ensure that the periodic boundary conditions are applied when the final difference is calculated.

Difference from reference value/s

The DIFFERENCE command is frequently used to determine the difference between the instantaneous value of a quantity and a reference value as illustrated in the example below:

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

ref_psiThe CONSTANT action with label ref_psi calculates the following quantities: Quantity    Type    Description  
ref_psi 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 VALUESthe numbers that are in your constant value=2.25029540
ref_psi: 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=2.25029540  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
tThe TORSION action with label t calculates the following quantities: Quantity    Type    Description  
t scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,3,4
diffThe DIFFERENCE action with label diff calculates the following quantities: Quantity    Type    Description  
diff scalar a function that measures the difference: DIFFERENCECalculate the differences between two scalars or vectors More details ARGthe values input to this function=t,ref_psi
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=diff FILEthe name of the file on which to output these quantities=colvar

You can also use this action to calculate the difference between the instaneous values of a vector of quantities and a reference vector as illustrated in the example below:

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

refThe CONSTANT action with label ref calculates the following quantities: Quantity    Type    Description  
ref 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=1.387980,1.126120,1.269380,1.321120,1.212420
ref: 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=1.387980,1.126120,1.269380,1.321120,1.212420  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
dThe DISTANCES action with label d calculates the following quantities: Quantity    Type    Description  
d vector the DISTANCES between the each pair of atoms that were specified: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details ATOMS1the pairs of atoms that you would like to calculate the angles for=1,2 ATOMS2the pairs of atoms that you would like to calculate the angles for=3,4 ATOMS3the pairs of atoms that you would like to calculate the angles for=5,6 ATOMS4the pairs of atoms that you would like to calculate the angles for=7,8 ATOMS5the pairs of atoms that you would like to calculate the angles for=9,10
# PLUMED interprets the command:
# d: DISTANCES ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 ATOMS4=7,8 ATOMS5=9,10
# as follows (Click the red comment above to revert to the short version of the input):
d_vatom1The CENTER_FAST action with label d_vatom1 calculates the following quantities: Quantity    Type    Description  
d_vatom1 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1,2
d_vatom2The CENTER_FAST action with label d_vatom2 calculates the following quantities: Quantity    Type    Description  
d_vatom2 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=3,4
d_vatom3The CENTER_FAST action with label d_vatom3 calculates the following quantities: Quantity    Type    Description  
d_vatom3 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=5,6
d_vatom4The CENTER_FAST action with label d_vatom4 calculates the following quantities: Quantity    Type    Description  
d_vatom4 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=7,8
d_vatom5The CENTER_FAST action with label d_vatom5 calculates the following quantities: Quantity    Type    Description  
d_vatom5 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=9,10
d_grpThe GROUP action with label d_grp calculates the following quantities: Quantity    Type    Description  
d_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=d_vatom1,d_vatom2,d_vatom3,d_vatom4,d_vatom5
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 ATOMS3the pair of atom that we are calculating the distance between=5,6 ATOMS4the pair of atom that we are calculating the distance between=7,8 ATOMS5the pair of atom that we are calculating the distance between=9,10
# --- End of included input --- diffThe DIFFERENCE action with label diff calculates the following quantities: Quantity    Type    Description  
diff vector the vector obtained by doing an element-wise application of a function that measures the difference to the input vectors: DIFFERENCECalculate the differences between two scalars or vectors More details ARGthe values input to this function=d,ref
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=diff FILEthe name of the file on which to output these quantities=colvar

The output in this case is a five dimensional vector. Each element of this vector contains the difference between the corresponding elements of the two input vectors.

Notice that you cannot use a mixture of scalars and vectors in the input for this action. Only two values can be input to this action and these two input values must have the same rank and the same number of elements.

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

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