CELL

This is part of the colvar module

Calculate the components of the simulation cell

Examples

The following input tells plumed to print the squared modulo of each of the three lattice vectors

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

contract shortcuts

cell: CELL The CELL action with label cell calculates the following quantities:

 Quantity   
 Description  
cell.ax
the ax component of the cell matrix
cell.ay
the ay component of the cell matrix
cell.az
the az component of the cell matrix
cell.bx
the bx component of the cell matrix
cell.by
the by component of the cell matrix
cell.bz
the bz component of the cell matrix
cell.cx
the cx component of the cell matrix
cell.cy
the cy component of the cell matrix
cell.cz
the cz component of the cell matrix


aaa: COMBINE 
ARG
the input to this function. 
=cell.ax,cell.ay,cell.az 
POWERS
compulsory keyword ( default=1.0 )
the powers to which you are raising each of the arguments in your function 
=2,2,2 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The COMBINE action with label aaa calculates a single scalar value
bbb: COMBINE 
ARG
the input to this function. 
=cell.bx,cell.by,cell.bz 
POWERS
compulsory keyword ( default=1.0 )
the powers to which you are raising each of the arguments in your function 
=2,2,2 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The COMBINE action with label bbb calculates a single scalar value
ccc: COMBINE 
ARG
the input to this function. 
=cell.cx,cell.cy,cell.cz 
POWERS
compulsory keyword ( default=1.0 )
the powers to which you are raising each of the arguments in your function 
=2,2,2 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The COMBINE action with label ccc calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=aaa,bbb,ccc The PRINT action with label 

cell: CELL The CELL action with label cell calculates the following quantities:

 Quantity   
 Description  
cell.ax
the ax component of the cell matrix
cell.ay
the ay component of the cell matrix
cell.az
the az component of the cell matrix
cell.bx
the bx component of the cell matrix
cell.by
the by component of the cell matrix
cell.bz
the bz component of the cell matrix
cell.cx
the cx component of the cell matrix
cell.cy
the cy component of the cell matrix
cell.cz
the cz component of the cell matrix


aaa: COMBINE_SCALAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=cell.ax,cell.ay,cell.az 
POWERS
compulsory keyword ( default=1.0 )
the powers to which you are raising each of the arguments in your function 
=2,2,2 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The COMBINE_SCALAR action with label aaa calculates a single scalar value
bbb: COMBINE_SCALAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=cell.bx,cell.by,cell.bz 
POWERS
compulsory keyword ( default=1.0 )
the powers to which you are raising each of the arguments in your function 
=2,2,2 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The COMBINE_SCALAR action with label bbb calculates a single scalar value
ccc: COMBINE_SCALAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=cell.cx,cell.cy,cell.cz 
POWERS
compulsory keyword ( default=1.0 )
the powers to which you are raising each of the arguments in your function 
=2,2,2 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The COMBINE_SCALAR action with label ccc calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=aaa,bbb,ccc The PRINT action with label 

Glossary of keywords and components

Description of components

By default this Action calculates the following quantities. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
ax	the ax component of the cell matrix
ay	the ay component of the cell matrix
az	the az component of the cell matrix
bx	the bx component of the cell matrix
by	the by component of the cell matrix
bz	the bz component of the cell matrix
cx	the cx component of the cell matrix
cy	the cy component of the cell matrix
cz	the cz component of the cell matrix

Options

NUMERICAL_DERIVATIVES

( default=off ) calculate the derivatives for these quantities numerically