Action: PRINT

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

Details and examples

Print quantities to a file.

This command can be used to output quantities to a file. The following demonstrates a very simple example:

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
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
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=colvar

This command outputs the distance between atom 1 and 2 to a file called colvar every step of trajectory. If you want to output the distance less frequently you can use the STRIDE keyword as illustrated 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
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
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=colvar STRIDE the frequency with which the quantities of interest should be output=10

With the input above the distance is only output on every 10th step. Notice this distance will only be calculated on every step as this quantity is not used on every other step.

You can also control the format of the numbers that are output by using the FMT keyword 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
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
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=colvar FMT the format that should be used to output real numbers=%10.6f

The FMT key takes a C format specifiers in input, which is what determines the appearance of the numbers output.

You can also use the PRINT command to output objects that have a rank that is greater than zero. For example, the following input calculates a vector of three distances. These three distances are then output to the output colvar file every step.

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
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=colvar

Alterantively, we can output a matrix by using an input like the one shown below:

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 GROUPthe atoms for which you would like to calculate the adjacency matrix=1-4
d: DISTANCE_MATRIXCalculate a matrix of distances between atoms. This action uses the defaults shown here. More details GROUPthe atoms for which you would like to calculate the adjacency matrix=1-4  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
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=colvar

The output colvar file here will contain the 16 elements of the matrix on each line output. You can also use PRINT to output functions on grids. However, you are probably better using DUMPGRID or DUMPCUBE to output functions on grids.

The PRINT directive can be used multiple times in the input so you can print files with different strides or print different quantities to different files as illustrated in the example input below:

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

# compute distance:
distanceThe DISTANCE action with label distance calculates the following quantities:
 Quantity   
 Type   
 Description  
distance
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=2,5
# compute total energy (potential)
energyThe ENERGY action with label energy calculates the following quantities:
 Quantity   
 Type   
 Description  
energy
scalar
the internal energy: ENERGYCalculate the total potential energy of the simulation box. More details
# print distance on a file
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=distance          STRIDE the frequency with which the quantities of interest should be output=10   FILEthe name of the file on which to output these quantities=COLVAR
# print both variables on another file
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=distance,energy   STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=COLVAR_ALL

The input above instructs plumed to print the distance between atoms 3 and 5 on a file called COLVAR every 10 steps, and the distance and total energy on a file called COLVAR_ALL every 1000 steps.

You can control the buffering of output using the FLUSH keyword. Furthermore, whether the output file is appended or backed up depends on whetehr or not the RESTART action is present on the file. If you add RESTART=yes on the line containing the PRINT directive the file will be appended also.

Printing happens in the so-called "update" phase. This implies that printing is affected by the presence of UPDATE_IF actions. One can thus decide to start and stop printing at preassigned values of time using the UPDATE_FROM and UPDATE_UNTIL keywords. Keep into account that even on steps when the action is not updated (and thus the file is not printed) the argument will be activated. In other words, if you use UPDATE_FROM to start printing at a given time, the collective variables this PRINT statement depends on will be computed also before that time.

PRINT and RESTART

If you run a calculation with the following input:

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
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
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=colvar

and a file called colvar is already present in the directory where the calculation is running, the existing file is backed up and renamed to bck.0.colvar so that new data can be output to a new file called colvar. If you would like to append to the existing file you can use the RESTART command 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
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
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=colvar RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES

You can achieve the same result by using the RESTART action as shown below:

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

RESTARTActivate restart. More details
The RESTART action with label  calculates somethingdThe 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
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=colvar

However, the advantage of using the RESTART keyword is that you can apped to some files and back up others as illustrated 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
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=colvar1
The PRINT action with label  calculates somethingd2The 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d2 FILEthe name of the file on which to output these quantities=colvar2 RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES

If you use the input above the file colvar1 is backed up, while new data will be appended to the file colvar2. If you use the RESTART action instead data will be appended to both colvar files.

Switching printing on and off

You can use the UPDATE_FROM and UPDATE_UNTIL flags to make the PRINT command only output data at certain points during the trajectory. To see how this works consider the following example:

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
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
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=colvar UPDATE_FROMOnly update this action from this time=100 UPDATE_UNTILOnly update this action until this time=500 STRIDE the frequency with which the quantities of interest should be output=1

During the first 100 ps of the simulation with this input the distance between atoms 1 and 2 is not output to the file called colvar. The distance is instead first output after the first 100 ps of trajectory have elapsed. Furthermore, output of the distance stops once the trajectory is longer than 500 ps. In other words, the distance is only output during the 400 ps time interval after the first 100 ps of the simulation.

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	scalar/vector/matrix	the labels of the values that you would like to print to the file

Full list of keywords

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 the values that you would like to print to the file
STRIDE	compulsory	1	the frequency with which the quantities of interest should be output
FMT	compulsory	%f	the format that should be used to output real numbers
FILE	optional	not used	the name of the file on which to output these quantities
RESTART	optional	not used	allows per-action setting of restart (YES/NO/AUTO)
UPDATE_FROM	optional	not used	Only update this action from this time
UPDATE_UNTIL	optional	not used	Only update this action until this time