Shortcut: YANGLES

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

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.

Input

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

Further details and examples

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

The following input tells plumed to calculate the angles between the y-axis and the vector connecting atom 3 to atom 5 and between the y-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 YANGLES action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1_min
scalar
the minimum colvar: YANGLESCalculate the angle between an arbitrary vector and the positive y 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: YANGLES 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 YANGLES 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 compbination 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_y
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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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.

Syntax

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