Shortcuts
Many of the commands in a PLUMED input file are shortcuts. When PLUMED reads one of these shortcuts replaces it with multiple lines of PLUMED input and then reads
in all the actions that are defiend in this longer and more complicated input. The reason for implementing these commands in this way is twofold:
- It ensures that there is less code within PLUMED to maintain.
- It allows users of PLUMED to understand how various methods are implemented within PLUMED.
We believe that the second item in this list is a particularly important objective. We cannot guarantee that PLUMED contains the fastest implementations of these methods
on all the various architectures that are available to the modern simulator. We hope, however, that users can read the manual, understand our shortcut implementations and use that understanding when implementing
faster versions of these methods that may be required to run a particular system with a particular computer architecture. In this way we hope that PLUMED serves as a textbook about
the various methods that are implemented within it as well as a simulation code.
Visualising how shortcuts work
You can see an example of a shortcut in the following input:
Click on the labels of the actions for more information on what each action computes
c1The COORDINATIONNUMBER action with label c1 calculates the following quantities:| Quantity | Type | Description |
| c1 | vector | the coordination numbers of the specified atoms |
| c1_mean | scalar | the mean of the colvars |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-100 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2} MEAN calculate the mean of all the quantities
# c1: COORDINATIONNUMBER SPECIES=1-100 SWITCH={RATIONAL R_0=0.2} MEAN
c1_grpThe GROUP action with label c1_grp calculates the following quantities:| Quantity | Type | Description |
| c1_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=1-100
c1_matThe CONTACT_MATRIX action with label c1_mat calculates the following quantities:| Quantity | Type | Description |
| c1_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-100 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}
c1_onesThe CONSTANT action with label c1_ones calculates the following quantities:| Quantity | Type | Description |
| c1_ones | vector | the constant value that was read from the plumed input |
: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=100
c1The MATRIX_VECTOR_PRODUCT action with label c1 calculates the following quantities:| Quantity | Type | Description |
| c1 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=c1_mat,c1_ones
c1_caverageThe MEAN action with label c1_caverage calculates the following quantities:| Quantity | Type | Description |
| c1_caverage | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=c1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c1_meanThe MEAN action with label c1_mean calculates the following quantities:| Quantity | Type | Description |
| c1_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=c1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
Whenever shortcuts are used in example inputs in this manual, the nest or the tutorials site you have the option to expand the shortcut and see all the various constituent actions
that are used in the expanded input that evlauates the final quantity of interest. To expand the input you simply hover over the name of the action and use the approriate link
from the tooltip that appears.
Values from shortcuts
In the manual pages for shortcuts you will see that these commands define values just like actions. The values calculated by shortcuts that are
specified in the manual can be referenced in other parts of the PLUMED input in the usual ways. Notice, however, that the name of the value that appears in the
output file may differ from the name of the component. For example, if you use the following input:
Click on the labels of the actions for more information on what each action computes
d1The DISTANCES action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | vector | the DISTANCES between the each pair of atoms that were specified |
| d1_lessthan | scalar | the number of colvars that have a value less than a threshold |
: 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 LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.1}
# d1: DISTANCES ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 ATOMS4=7,8 ATOMS5=9,10 LESS_THAN={RATIONAL R_0=0.1}
d1_vatom1The CENTER_FAST action with label d1_vatom1 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=1,2
d1_vatom2The CENTER_FAST action with label d1_vatom2 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=3,4
d1_vatom3The CENTER_FAST action with label d1_vatom3 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=5,6
d1_vatom4The CENTER_FAST action with label d1_vatom4 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=7,8
d1_vatom5The CENTER_FAST action with label d1_vatom5 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=9,10
d1_grpThe GROUP action with label d1_grp calculates the following quantities:| Quantity | Type | Description |
| d1_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=d1_vatom1,d1_vatom2,d1_vatom3,d1_vatom4,d1_vatom5
d1The DISTANCE action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | 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
d1_ltThe LESS_THAN action with label d1_lt calculates the following quantities:| Quantity | Type | Description |
| d1_lt | vector | the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors |
: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=d1 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.1}
d1_lessthanThe SUM action with label d1_lessthan calculates the following quantities:| Quantity | Type | Description |
| d1_lessthan | 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_lt 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.lessthan FILEthe name of the file on which to output these quantities=colvar1
The output values in the output colvar1 file will be in a column with the heading d1_lessthan rather than d1.lessthan as d1_lessthan is the label of the action that actually calculates the
quantity of interest.
PLUMED only allows you access the subset of the values that defined in the manual from the shortcut input using the label.component syntax. So if we take the input above:
Click on the labels of the actions for more information on what each action computes
d1The DISTANCES action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | vector | the DISTANCES between the each pair of atoms that were specified |
| d1_lessthan | scalar | the number of colvars that have a value less than a threshold |
: 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 LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.1}
# d1: DISTANCES ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 ATOMS4=7,8 ATOMS5=9,10 LESS_THAN={RATIONAL R_0=0.1}
d1_vatom1The CENTER_FAST action with label d1_vatom1 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=1,2
d1_vatom2The CENTER_FAST action with label d1_vatom2 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=3,4
d1_vatom3The CENTER_FAST action with label d1_vatom3 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=5,6
d1_vatom4The CENTER_FAST action with label d1_vatom4 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=7,8
d1_vatom5The CENTER_FAST action with label d1_vatom5 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=9,10
d1_grpThe GROUP action with label d1_grp calculates the following quantities:| Quantity | Type | Description |
| d1_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=d1_vatom1,d1_vatom2,d1_vatom3,d1_vatom4,d1_vatom5
d1The DISTANCE action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | 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
d1_ltThe LESS_THAN action with label d1_lt calculates the following quantities:| Quantity | Type | Description |
| d1_lt | vector | the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors |
: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=d1 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.1}
d1_lessthanThe SUM action with label d1_lessthan calculates the following quantities:| Quantity | Type | Description |
| d1_lessthan | 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_lt 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.lessthan FILEthe name of the file on which to output these quantities=colvar1
The PRINT action with label calculates somethingPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1_lessthan FILEthe name of the file on which to output these quantities=colvar2
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1_lt FILEthe name of the file on which to output these quantities=colvar4
Shortcuts and wildcards
If you have the following input:
Click on the labels of the actions for more information on what each action computes
d1The DISTANCES action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | vector | the DISTANCES between the each pair of atoms that were specified |
| d1_lessthan | scalar | the number of colvars that have a value less than a threshold |
| d1_mean | scalar | the mean of the colvars |
: 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 LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.1} MEAN calculate the mean of all the quantities
# d1: DISTANCES ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 ATOMS4=7,8 ATOMS5=9,10 LESS_THAN={RATIONAL R_0=0.1} MEAN
d1_vatom1The CENTER_FAST action with label d1_vatom1 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=1,2
d1_vatom2The CENTER_FAST action with label d1_vatom2 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=3,4
d1_vatom3The CENTER_FAST action with label d1_vatom3 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=5,6
d1_vatom4The CENTER_FAST action with label d1_vatom4 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=7,8
d1_vatom5The CENTER_FAST action with label d1_vatom5 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=9,10
d1_grpThe GROUP action with label d1_grp calculates the following quantities:| Quantity | Type | Description |
| d1_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=d1_vatom1,d1_vatom2,d1_vatom3,d1_vatom4,d1_vatom5
d1The DISTANCE action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | 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
d1_ltThe LESS_THAN action with label d1_lt calculates the following quantities:| Quantity | Type | Description |
| d1_lt | vector | the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors |
: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=d1 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.1}
d1_lessthanThe SUM action with label d1_lessthan calculates the following quantities:| Quantity | Type | Description |
| d1_lessthan | 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_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_meanThe MEAN action with label d1_mean calculates the following quantities:| Quantity | Type | Description |
| d1_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=d1 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.* FILEthe name of the file on which to output these quantities=colvar2
The values d1_lessthan and d1_mean will be output in the colvar2 file as these are the components of the DISTANCES shortcut that are defined in the manual. d1_lt is not output as this is an intermediate value that is not defined in the manual.
The same result can be obtained using the following input:
Click on the labels of the actions for more information on what each action computes
d1The DISTANCES action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | vector | the DISTANCES between the each pair of atoms that were specified |
| d1_lessthan | scalar | the number of colvars that have a value less than a threshold |
| d1_mean | scalar | the mean of the colvars |
: 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 LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.1} MEAN calculate the mean of all the quantities
# d1: DISTANCES ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 ATOMS4=7,8 ATOMS5=9,10 LESS_THAN={RATIONAL R_0=0.1} MEAN
d1_vatom1The CENTER_FAST action with label d1_vatom1 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=1,2
d1_vatom2The CENTER_FAST action with label d1_vatom2 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=3,4
d1_vatom3The CENTER_FAST action with label d1_vatom3 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=5,6
d1_vatom4The CENTER_FAST action with label d1_vatom4 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=7,8
d1_vatom5The CENTER_FAST action with label d1_vatom5 calculates the following quantities:| Quantity | Type | Description |
| d1_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 you are calculating the Gyration Tensor for=9,10
d1_grpThe GROUP action with label d1_grp calculates the following quantities:| Quantity | Type | Description |
| d1_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=d1_vatom1,d1_vatom2,d1_vatom3,d1_vatom4,d1_vatom5
d1The DISTANCE action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | 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
d1_ltThe LESS_THAN action with label d1_lt calculates the following quantities:| Quantity | Type | Description |
| d1_lt | vector | the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors |
: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=d1 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.1}
d1_lessthanThe SUM action with label d1_lessthan calculates the following quantities:| Quantity | Type | Description |
| d1_lessthan | 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_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_meanThe MEAN action with label d1_mean calculates the following quantities:| Quantity | Type | Description |
| d1_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=d1 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=* FILEthe name of the file on which to output these quantities=colvar
as the * wildcard instructs PLUMED to output values from all the shortcuts in the input file that are described in the manual. However, if you use a . wildcard everything (including the value of d1_lt and all the other intermediate values) will
be output.
