Action: ARGS2VATOM

Module	vatom
Description	Usage
Create a virtual atom from the input scalars

Details and examples

Create a virtual atom from the input scalars

This action takes five scalars that are computed by other actions in input and uses them to set the x, y and z positions and the mass and charge of a virtual atom. This action is used within the CENTER shortcut to compute a center of mass. An example input that shows how you can use this command to calculate the center of mass of atoms 1-10 is as follows:

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

# Calculate the total mass of the atoms
mThe MASS action with label m calculates the following quantities: Quantity    Type    Description  
m vector the MASS of the atom/s: MASSGet the mass of one or multiple atoms More details ATOMSthe atom numbers that you would like to store the masses and charges of=1-10
massThe SUM action with label mass calculates the following quantities: Quantity    Type    Description  
mass 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=m PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Calculate the totla charge of the atoms
qThe CHARGE action with label q calculates the following quantities: Quantity    Type    Description  
q vector the CHARGE of the atom/s: CHARGEGet the charges of one or multiple atoms More details ATOMSthe atom numbers that you would like to store the masses and charges of=1-10
chargeThe SUM action with label charge calculates the following quantities: Quantity    Type    Description  
charge 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=q PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Now get the positions of the atoms
posThe POSITION action with label pos calculates the following quantities: Quantity    Type    Description  
pos.x vector the x-component of the atom position
pos.y vector the y-component of the atom position
pos.z vector the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details WHOLEMOLECULES if this is a vector of positions do you want to make the positions into a whole before ATOMSthe atom numbers that you would like to use the positions of=1-10
# Multiply each vector of positions by the masses
xwvecThe CUSTOM action with label xwvec calculates the following quantities: Quantity    Type    Description  
xwvec 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=m,pos.x 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
ywvecThe CUSTOM action with label ywvec calculates the following quantities: Quantity    Type    Description  
ywvec 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=m,pos.y 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
zwvecThe CUSTOM action with label zwvec calculates the following quantities: Quantity    Type    Description  
zwvec 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=m,pos.z 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
# Sum the numerators in the expression for the center of mass
xnumThe SUM action with label xnum calculates the following quantities: Quantity    Type    Description  
xnum 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=xwvec PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ynumThe SUM action with label ynum calculates the following quantities: Quantity    Type    Description  
ynum 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=ywvec PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
znumThe SUM action with label znum calculates the following quantities: Quantity    Type    Description  
znum 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=zwvec PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# And compute the x, y and z positions of the center of mass
xThe CUSTOM action with label x calculates the following quantities: Quantity    Type    Description  
x scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=xnum,mass 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
yThe CUSTOM action with label y calculates the following quantities: Quantity    Type    Description  
y scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ynum,mass 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
zThe CUSTOM action with label z calculates the following quantities: Quantity    Type    Description  
z scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=znum,mass 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
# And now create the virtual atom
pThe ARGS2VATOM action with label p calculates the following quantities: Quantity    Type    Description  
p.x scalar the x coordinate of the virtual atom
p.y scalar the y coordinate of the virtual atom
p.z scalar the z coordinate of the virtual atom
p.mass scalar the mass of the virtual atom
p.charge scalar the charge of the virtual atom: ARGS2VATOMCreate a virtual atom from the input scalars More details XPOSthe value to use for the x position of the atom=x YPOSthe value to use for the y position of the atom=y ZPOSthe value to use for the z position of the atom=z MASSthe value to use for the mass of the atom=mass CHARGEthe value to use for the charge of the atom=charge

In the following input by contrast we use the PHASES method that is discussed in the documentation for CENTER to calculate the position of the center of mass:

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

# Calculate the total mass of the atoms
mThe MASS action with label m calculates the following quantities: Quantity    Type    Description  
m vector the MASS of the atom/s: MASSGet the mass of one or multiple atoms More details ATOMSthe atom numbers that you would like to store the masses and charges of=1-10
massThe SUM action with label mass calculates the following quantities: Quantity    Type    Description  
mass 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=m PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Calculate the totla charge of the atoms
qThe CHARGE action with label q calculates the following quantities: Quantity    Type    Description  
q vector the CHARGE of the atom/s: CHARGEGet the charges of one or multiple atoms More details ATOMSthe atom numbers that you would like to store the masses and charges of=1-10
chargeThe SUM action with label charge calculates the following quantities: Quantity    Type    Description  
charge 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=q PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Now get the positions of the atoms
posThe POSITION action with label pos calculates the following quantities: Quantity    Type    Description  
pos.a vector the normalized projection on the first lattice vector of the atom position
pos.b vector the normalized projection on the second lattice vector of the atom position
pos.c vector the normalized projection on the third lattice vector of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label ATOMSthe atom numbers that you would like to use the positions of=1-10
# Multiply the sins and cosines of the scaled positions by the weights
sinaThe CUSTOM action with label sina calculates the following quantities: Quantity    Type    Description  
sina 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=m,pos.a FUNCthe function you wish to evaluate=x*sin(2*pi*y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cosaThe CUSTOM action with label cosa calculates the following quantities: Quantity    Type    Description  
cosa 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=m,pos.a FUNCthe function you wish to evaluate=x*cos(2*pi*y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
sinbThe CUSTOM action with label sinb calculates the following quantities: Quantity    Type    Description  
sinb 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=m,pos.b FUNCthe function you wish to evaluate=x*sin(2*pi*y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cosbThe CUSTOM action with label cosb calculates the following quantities: Quantity    Type    Description  
cosb 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=m,pos.b FUNCthe function you wish to evaluate=x*cos(2*pi*y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
sincThe CUSTOM action with label sinc calculates the following quantities: Quantity    Type    Description  
sinc 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=m,pos.c FUNCthe function you wish to evaluate=x*sin(2*pi*y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
coscThe CUSTOM action with label cosc calculates the following quantities: Quantity    Type    Description  
cosc 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=m,pos.c FUNCthe function you wish to evaluate=x*cos(2*pi*y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# And accumulate the sums
sinsumaThe SUM action with label sinsuma calculates the following quantities: Quantity    Type    Description  
sinsuma 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=sina PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cossumaThe SUM action with label cossuma calculates the following quantities: Quantity    Type    Description  
cossuma 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=cosa PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
sinsumbThe SUM action with label sinsumb calculates the following quantities: Quantity    Type    Description  
sinsumb 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=sinb PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cossumbThe SUM action with label cossumb calculates the following quantities: Quantity    Type    Description  
cossumb 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=cosb PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
sinsumcThe SUM action with label sinsumc calculates the following quantities: Quantity    Type    Description  
sinsumc 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=sinc PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cossumcThe SUM action with label cossumc calculates the following quantities: Quantity    Type    Description  
cossumc 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=cosc PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# And get the position of the center in fractional coordinates
aThe CUSTOM action with label a calculates the following quantities: Quantity    Type    Description  
a scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=sinsuma,cossuma FUNCthe function you wish to evaluate=atan2(x,y)/(2*pi) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
bThe CUSTOM action with label b calculates the following quantities: Quantity    Type    Description  
b scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=sinsumb,cossumb FUNCthe function you wish to evaluate=atan2(x,y)/(2*pi) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cThe CUSTOM action with label c calculates the following quantities: Quantity    Type    Description  
c scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=sinsumc,cossumc FUNCthe function you wish to evaluate=atan2(x,y)/(2*pi) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# And now create the virtual atom
pThe ARGS2VATOM action with label p calculates the following quantities: Quantity    Type    Description  
p.x scalar the x coordinate of the virtual atom
p.y scalar the y coordinate of the virtual atom
p.z scalar the z coordinate of the virtual atom
p.mass scalar the mass of the virtual atom
p.charge scalar the charge of the virtual atom: ARGS2VATOMCreate a virtual atom from the input scalars More details XPOSthe value to use for the x position of the atom=a YPOSthe value to use for the y position of the atom=b ZPOSthe value to use for the z position of the atom=c MASSthe value to use for the mass of the atom=mass CHARGEthe value to use for the charge of the atom=charge FRACTIONAL the input arguments are calculated in fractional coordinates so you need to multiply by the cell

These inputs provide very slow ways of computing a center of mass - PLUMED contains faster implementations that do calculations that are equivalent to both of these inputs. This type of input is nevertheless useful if you are using arbitary weights when computing the sums in the numerator and denominator of the expression for the center as is detailed in the documentation for the CENTER command.

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
XPOS	scalar	the value to use for the x position of the atom
YPOS	scalar	the value to use for the y position of the atom
ZPOS	scalar	the value to use for the z position of the atom
MASS	scalar	the value to use for the mass of the atom
CHARGE	scalar	the value to use for the charge of the atom
XBKP	scalar	x position to use in case PBC not set when using PHASES
YBKP	scalar	y position to use in case PBC not set when using PHASES
ZBKP	scalar	z position to use in case PBC not set when using PHASES

Output components

This action calculates the values in the following table. 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	Description
x	scalar	the x coordinate of the virtual atom
y	scalar	the y coordinate of the virtual atom
z	scalar	the z coordinate of the virtual atom
mass	scalar	the mass of the virtual atom
charge	scalar	the charge of the virtual atom

Full list of keywords

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

Keyword	Type	Default	Description
XPOS	input	none	the value to use for the x position of the atom
YPOS	input	none	the value to use for the y position of the atom
ZPOS	input	none	the value to use for the z position of the atom
MASS	input	none	the value to use for the mass of the atom
CHARGE	input	none	the value to use for the charge of the atom
XBKP	input	none	x position to use in case PBC not set when using PHASES
YBKP	input	none	y position to use in case PBC not set when using PHASES
ZBKP	input	none	z position to use in case PBC not set when using PHASES
FRACTIONAL	optional	false	the input arguments are calculated in fractional coordinates so you need to multiply by the cell

Quantity	Type	Description
m	vector	the MASS of the atom/s