Action: DUMPVECTOR

Module	generic
Description	Usage
Print a vector to a file
This action outputs data to a file. You can read more about how PLUMED manages output files here

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
ARG	vector/matrix	the labels of vectors/matrices that should be output in the file

Further details and examples

Print a vector to a file

In the following input the four distances calculated by the DISTANCE command are output to files using this command and using PRINT

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

dThe DISTANCE action with label d calculates the following quantities: Quantity    Type    Description  
d 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d FILEthe name of the file on which to output these quantities=colvar1 STRIDE the frequency with which the quantities of interest should be output=1
The PRINT action with label  calculates somethingDUMPVECTORPrint a vector to a file More details ARGthe labels of vectors/matrices that should be output in the file=d FILE the file on which to write the vetors=colvar2 STRIDE the frequency with which the grid should be output to the file=1

The PRINT command outputs the instantaneous values of the four distances on a single row. If we have a trajectory with four frames the colvar1 file will look like the one shown below:

! FIELDS time d.1 d.2 d.3 d.4
 0.000000 1.000000 1.000000 1.414214 1.000000
 1.000000 1.000000 1.000000 1.414214 1.000000
 2.000000 1.000000 1.000000 1.414214 1.000000
 3.000000 1.000000 1.000000 1.414214 1.000000
```

By contrast the DUMPVECTOR command will produce four output files - for each step of the simulation. Each of these
output files looks like this:

! FIELDS time parameter d 3.000000 0 1.000000 3.000000 1 1.000000 3.000000 2 1.414214 3.000000 3 1.000000 ```

In other words, the four elements of the vector are printed on different rows of the output. The latest file output will be called colvar2 and all earlier files will be called analysis.n.colvar where n is an integer that indicates the order in which files were produced. By adding the flag PRINT_ONE_FILE as shown below:

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

dThe DISTANCE action with label d calculates the following quantities: Quantity    Type    Description  
d 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
DUMPVECTORPrint a vector to a file More details ARGthe labels of vectors/matrices that should be output in the file=d FILE the file on which to write the vetors=colvar2 STRIDE the frequency with which the grid should be output to the file=1 PRINT_ONE_FILE output vectors one after the other in a single file

We can ensure that all the data from all four frames is concatenated to a single file that looks as follows:

#! FIELDS time parameter d
 3.000000 0 1.000000
 3.000000 1 1.000000
 3.000000 2 1.414214
 3.000000 3 1.000000
#! FIELDS time parameter d
 0.000000 0 1.000000
 0.000000 1 1.000000
 0.000000 2 1.414214
 0.000000 3 1.000000
#! FIELDS time parameter d
 1.000000 0 1.000000
 1.000000 1 1.000000
 1.000000 2 1.414214
 1.000000 3 1.000000
#! FIELDS time parameter d
 2.000000 0 1.000000
 2.000000 1 1.000000
 2.000000 2 1.414214
 2.000000 3 1.000000

This command is useful for printing out time series that have been stored using the COLLECT action or for printing out projections that have been generating using the tools in the dimred module. The following input shows how you can use it to calculate and print the time series of values for the distances between atoms 1 and 2 and atoms 3 and 4.

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

d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 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
d2The DISTANCE action with label d2 calculates the following quantities: Quantity    Type    Description  
d2 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=3,4
c1The COLLECT action with label c1 calculates the following quantities: Quantity    Type    Description  
c1 vector the time series for the input quantity: COLLECTCollect data from the trajectory for later analysis This action has hidden defaults. More details ARGthe label of the value whose time series is being stored for later analysis=d1 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1
c1: COLLECTCollect data from the trajectory for later analysis This action uses the defaults shown here. More details ARGthe label of the value whose time series is being stored for later analysis=d1 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1  TYPE required if you are collecting an object with rank>0=auto CLEAR the frequency with which to clear all the accumulated data=0
c2The COLLECT action with label c2 calculates the following quantities: Quantity    Type    Description  
c2 vector the time series for the input quantity: COLLECTCollect data from the trajectory for later analysis This action has hidden defaults. More details ARGthe label of the value whose time series is being stored for later analysis=d2 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1
c2: COLLECTCollect data from the trajectory for later analysis This action uses the defaults shown here. More details ARGthe label of the value whose time series is being stored for later analysis=d2 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1  TYPE required if you are collecting an object with rank>0=auto CLEAR the frequency with which to clear all the accumulated data=0
DUMPVECTORPrint a vector to a file More details ARGthe labels of vectors/matrices that should be output in the file=c1,c2 FILE the file on which to write the vetors=timeseries

In the example input above the time series is output at the end of the calculation.

Outputing matrices

You can also use this command to output matrices as the following input demonstrates:

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

dThe DISTANCE_MATRIX action with label d calculates the following quantities: Quantity    Type    Description  
d matrix a matrix containing the weights for the bonds between each pair of atoms: DISTANCE_MATRIXCalculate a matrix of distances between atoms. This action has hidden defaults. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=1,2 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=3-6
d: DISTANCE_MATRIXCalculate a matrix of distances between atoms. This action uses the defaults shown here. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=1,2 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=3-6  NL_CUTOFF The cutoff for the neighbor list=0.0 NL_STRIDE The frequency with which we are updating the atoms in the neighbor list=1 CUTOFF ignore distances that have a value larger than this cutoff=-1
DUMPVECTORPrint a vector to a file More details ARGthe labels of vectors/matrices that should be output in the file=d FILE the file on which to write the vetors=matrix STRIDE the frequency with which the grid should be output to the file=1

The files matrix and analysis.n.matrix that are output on each step here looks as follows:

! FIELDS time parameter d.1 d.2 d.3 d.4
 4.000000 0 2.000000 2.000000 1.000000 1.000000
 4.000000 1 1.000000 2.000000 2.000000 1.414214

In other words, the rows and columns of the file are used to display the rows and columns of the input matrix.

Further note that if your input matrix was constructed using the VSTACK and COLLECT commands as shown below:

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

d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 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
d2The DISTANCE action with label d2 calculates the following quantities: Quantity    Type    Description  
d2 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=3,4
d3The DISTANCE action with label d3 calculates the following quantities: Quantity    Type    Description  
d3 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=5,6
c1The COLLECT action with label c1 calculates the following quantities: Quantity    Type    Description  
c1 vector the time series for the input quantity: COLLECTCollect data from the trajectory for later analysis This action has hidden defaults. More details ARGthe label of the value whose time series is being stored for later analysis=d1 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1
c1: COLLECTCollect data from the trajectory for later analysis This action uses the defaults shown here. More details ARGthe label of the value whose time series is being stored for later analysis=d1 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1  TYPE required if you are collecting an object with rank>0=auto CLEAR the frequency with which to clear all the accumulated data=0
c2The COLLECT action with label c2 calculates the following quantities: Quantity    Type    Description  
c2 vector the time series for the input quantity: COLLECTCollect data from the trajectory for later analysis This action has hidden defaults. More details ARGthe label of the value whose time series is being stored for later analysis=d2 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1
c2: COLLECTCollect data from the trajectory for later analysis This action uses the defaults shown here. More details ARGthe label of the value whose time series is being stored for later analysis=d2 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1  TYPE required if you are collecting an object with rank>0=auto CLEAR the frequency with which to clear all the accumulated data=0
c3The COLLECT action with label c3 calculates the following quantities: Quantity    Type    Description  
c3 vector the time series for the input quantity: COLLECTCollect data from the trajectory for later analysis This action has hidden defaults. More details ARGthe label of the value whose time series is being stored for later analysis=d3 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1
c3: COLLECTCollect data from the trajectory for later analysis This action uses the defaults shown here. More details ARGthe label of the value whose time series is being stored for later analysis=d3 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1  TYPE required if you are collecting an object with rank>0=auto CLEAR the frequency with which to clear all the accumulated data=0
vThe VSTACK action with label v calculates the following quantities: Quantity    Type    Description  
v matrix a matrix that contains the input vectors in its columns: VSTACKCreate a matrix by stacking vectors together More details ARGthe values that you would like to stack together to construct the output matrix=c1,c2,c3
DUMPVECTORPrint a vector to a file More details ARGthe labels of vectors/matrices that should be output in the file=v FILE the file on which to write the vetors=matrix

The output file looks as follows:

#! FIELDS time parameter d1 d2 d3
 3.000000 0 1.000000 1.000000 1.414214
 3.000000 1 1.000000 1.000000 1.414214
 3.000000 2 1.000000 1.000000 1.414214

In other words, the names of the columns in the output reflect the names of the underlying variables that were collected and stacked together to form the input matrix.

Syntax

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

Keyword	Type	Default	Description
ARG	input	none	the labels of vectors/matrices that should be output in the file
STRIDE	compulsory	0	the frequency with which the grid should be output to the file
FILE	compulsory	density	the file on which to write the vetors
FMT	optional	not used	the format that should be used to output real numbers
PRINT_ONE_FILE	optional	false	output vectors one after the other in a single file

Keys	Action
`?`	Open this help
`n`	Next page
`p`	Previous page
`s`	Search

Quantity	Type	Description
d	vector	the DISTANCE for each set of specified atoms