Shortcut: XANGLES

Module	multicolvar
Description	Usage
Calculate the angle between an arbitrary vector and the positive x direction

Deprecated

This action has been deprecated and is no longer supported. Use DISTANCE instead.

Details and examples

Calculate the angle between an arbitrary vector and the positive x direction

As you can see if you expand the inputs below, you can achieve what this shortcut action does by using DISTANCE together with CUSTOM, BETWEEN, LESS_THAN, SUM and MEAN. We strongly encourage you to use these actions instead as using them will provide you with a clearer understanding of the equations you are using.

The following input tells plumed to calculate the angles between the x-axis and the vector connecting atom 3 to atom 5 and between the x-axis and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output

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

d1The XANGLES action with label d1 calculates the following quantities: Quantity    Type    Description  
d1_min scalar the minimum colvar: XANGLESCalculate the angle between an arbitrary vector and the positive x direction This action is a shortcut. More details ATOMS1the pairs of atoms that you would like to calculate the angles for=3,5 ATOMS2the pairs of atoms that you would like to calculate the angles for=1,2 MINcalculate the minimum value={BETA=0.1}
# PLUMED interprets the command:
# d1: XANGLES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
# as follows (Click the red comment above to revert to the short version of the input):
The XANGLES action with label d1 calculates the following quantities: Quantity    Description  
d1.min the minimum colvard1_distsThe DISTANCE action with label d1_dists calculates the following quantities: Quantity    Type    Description  
d1_dists.x vector the x-component of the vector connecting the two atoms
d1_dists.y vector the y-component of the vector connecting the two atoms
d1_dists.z vector the z-component of the vector connecting the two atoms: DISTANCECalculate the distance/s between pairs of atoms. More details COMPONENTS calculate the x, y and z components of the distance separately and store them as label ATOMS1the pair of atom that we are calculating the distance between=3,5 ATOMS2the pair of atom that we are calculating the distance between=1,2
d1_norm2The COMBINE action with label d1_norm2 calculates the following quantities: Quantity    Type    Description  
d1_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1_dists.x,d1_dists.y,d1_dists.z POWERS the powers to which you are raising each of the arguments in your function=2,2,2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_normThe CUSTOM action with label d1_norm calculates the following quantities: Quantity    Type    Description  
d1_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_norm_xThe CUSTOM action with label d1_norm_x calculates the following quantities: Quantity    Type    Description  
d1_norm_x vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1_dists.x,d1_norm 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
d1_norm_yThe CUSTOM action with label d1_norm_y calculates the following quantities: Quantity    Type    Description  
d1_norm_y vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1_dists.y,d1_norm 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
d1_norm_zThe CUSTOM action with label d1_norm_z calculates the following quantities: Quantity    Type    Description  
d1_norm_z vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1_dists.z,d1_norm 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
d1_angThe CUSTOM action with label d1_ang calculates the following quantities: Quantity    Type    Description  
d1_ang vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details FUNCthe function you wish to evaluate=acos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=d1_norm_x
d1_me_minThe CUSTOM action with label d1_me_min calculates the following quantities: Quantity    Type    Description  
d1_me_min vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1_ang FUNCthe function you wish to evaluate=exp(0.1/x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_mec_minThe SUM action with label d1_mec_min calculates the following quantities: Quantity    Type    Description  
d1_mec_min scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=d1_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_minThe CUSTOM action with label d1_min calculates the following quantities: Quantity    Type    Description  
d1_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1_mec_min FUNCthe function you wish to evaluate=0.1/log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1.min FILEthe name of the file on which to output these quantities=colvar

Notice that this command is a shortcut. You can thus learn more about how to use PLUMED by examining the expanded version of the input above.

Input

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

Keyword	Type	Description
ATOMS	atoms	the pairs of atoms that you would like to calculate the angles for

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name	Type	Keyword	Description
lessthan	scalar	LESS_THAN	the number of colvars that have a value less than a threshold
morethan	scalar	MORE_THAN	the number of colvars that have a value more than a threshold
altmin	scalar	ALT_MIN	the minimum value of the cv
min	scalar	MIN	the minimum colvar
max	scalar	MAX	the maximum colvar
between	scalar	BETWEEN	the number of colvars that have a value that lies in a particular interval
highest	scalar	HIGHEST	the largest of the colvars
lowest	scalar	LOWEST	the smallest of the colvars
sum	scalar	SUM	the sum of the colvars
mean	scalar	MEAN	the mean of the colvars

Full list of keywords

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

Keyword	Type	Default	Description
ATOMS	input	none	the pairs of atoms that you would like to calculate the angles for
LESS_THAN	optional	not used	calculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.
MORE_THAN	optional	not used	calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.
ALT_MIN	optional	not used	calculate the minimum value
MIN	optional	not used	calculate the minimum value
MAX	optional	not used	calculate the maximum value
BETWEEN	optional	not used	calculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.
HIGHEST	optional	not used	this flag allows you to recover the highest of these variables
HISTOGRAM	optional	not used	calculate a discretized histogram of the distribution of values
LOWEST	optional	not used	this flag allows you to recover the lowest of these variables
SUM	optional	not used	calculate the sum of all the quantities
MEAN	optional	not used	calculate the mean of all the quantities

Quantity	Type	Description
d1_min	scalar	the minimum colvar