Action: GATHER_REPLICAS

Module	generic
Description	Usage
Create a vector that contains the copies of the input quantities from all replicas

Input

The arguments 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

Create a vector that contains the copies of the input quantities from all replicas

There are three ways that you can generate indistinguishable replicas of a system for calculating ensemble averages:

• You can take a time average.
• You can run a multiple replica simulation and average over the replicas.
• You can do a spatial average and assume that there are multiple replicas of the system in the same simulation box and average over them.

Many actions within PLUMED will perform average over more than one of these type of replica. However, since v2.10 we have tried to separate out these three ways of generating multiple replicas for averaging. There are thus many actions where you take time averages by using ACCUMULATE or COLLECT. You take spatial averages by passing working the vectors of values. You then use this action to average over replicas. The way this works in practise is illustrated by the simple example shown below.

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

#SETTINGS NREPLICAS=2
# Calculate distance between atoms 1 and 2 on for all 2 replicas
dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
# Now gather the values of this distance on all the replicas:
gThe GATHER_REPLICAS action with label g calculates the following quantities:
 Quantity   
 Type   
 Description  
g.rep-1
scalar
the input arguments for each of the replicas  This is the 1th of these quantities
g.rep-2
scalar
the input arguments for each of the replicas  This is the 2th of these quantities: GATHER_REPLICASCreate a vector that contains the copies of the input quantities from all replicas More details ARGthe argument from the various replicas that you would like to gather=d
# Now average the two distances on the two replicas
sThe COMBINE action with label s calculates the following quantities:
 Quantity   
 Type   
 Description  
s
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=g.rep-1,g.rep-2 COEFFICIENTS the coefficients of the arguments in your function=0.5,0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# And print the instaneous average for the distance on the two replicas
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=s FILEthe name of the file on which to output these quantities=colvar

Now suppose that we wanted to calculate a time average of the distance and an average over the replicas. We could use an input like this:

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

#SETTINGS NREPLICAS=2
dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
gThe GATHER_REPLICAS action with label g calculates the following quantities:
 Quantity   
 Type   
 Description  
g.rep-1
scalar
the input arguments for each of the replicas  This is the 1th of these quantities
g.rep-2
scalar
the input arguments for each of the replicas  This is the 2th of these quantities: GATHER_REPLICASCreate a vector that contains the copies of the input quantities from all replicas More details ARGthe argument from the various replicas that you would like to gather=d
sThe COMBINE action with label s calculates the following quantities:
 Quantity   
 Type   
 Description  
s
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=g.rep-1,g.rep-2 COEFFICIENTS the coefficients of the arguments in your function=0.5,0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# This does the time averaging
aThe AVERAGE action with label a calculates the following quantities:
 Quantity   
 Type   
 Description  
a
scalar
the value of the average: AVERAGECalculate the ensemble average of a collective variable This action is a shortcut and it has hidden defaults. More details ARGthe quantity that is being averaged=s
a: AVERAGECalculate the ensemble average of a collective variable This action is a shortcut and uses the defaults shown here. More details ARGthe quantity that is being averaged=s  STRIDE the frequency with which to store data for averaging=1 CLEAR the frequency with whihc to clear the data that is being averaged=0
# PLUMED interprets the command:
# a: AVERAGE ARG=s
# as follows (Click the red comment above to revert to the short version of the input):
a_weightThe CONSTANT action with label a_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
a_weight
scalar
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=1
a_denomThe ACCUMULATE action with label a_denom calculates the following quantities:
 Quantity   
 Type   
 Description  
a_denom
scalar
a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=a_weight STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0
a_prodThe CUSTOM action with label a_prod calculates the following quantities:
 Quantity   
 Type   
 Description  
a_prod
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=s,a_weight 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
a_numerThe ACCUMULATE action with label a_numer calculates the following quantities:
 Quantity   
 Type   
 Description  
a_numer
scalar
a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=a_prod STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0
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=a_numer,a_denom 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
# --- End of included input --- # And output the final average
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=a FILEthe name of the file on which to output these quantities=colvar

Syntax

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