READ

This is part of the generic module

Read quantities from a colvar file.

This Action can be used with driver to read in a colvar file that was generated during an MD simulation

Description of components

The READ command will read those fields that are labelled with the text string given to the VALUE keyword. It will also read in any fields that are labeled with the text string given to the VALUE keyword followed by a dot and a further string. If a single Value is read in this value can be referenced using the label of the Action. Alternatively, if multiple quantities are read in, they can be referenced elsewhere in the input by using the label for the Action followed by a dot and the character string that appeared after the dot in the title of the field.

Examples

This input reads in data from a file called input_colvar.data that was generated in a calculation that involved PLUMED. The first command reads in the data from the column headed phi1 while the second reads in the data from the column headed phi2.

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

rphi1: READ 
FILE
compulsory keyword 
the name of the file from which to read these quantities 
=input_colvar.data 
VALUES
compulsory keyword 
the values to read from the file 
=phi1 The READ action with label rphi1 calculates a single scalar value
rphi2: READ 
FILE
compulsory keyword 
the name of the file from which to read these quantities 
=input_colvar.data 
VALUES
compulsory keyword 
the values to read from the file 
=phi2 The READ action with label rphi2 calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=rphi1,rphi2 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=500 
FILE
the name of the file on which to output these quantities 
=output_colvar.data The PRINT action with label 

The file input_colvar.data is just a normal colvar file as shown below

#! FIELDS time phi psi metad.bias metad.rbias metad.rct
#! SET min_phi -pi
#! SET max_phi pi
#! SET min_psi -pi
#! SET max_psi pi
 0.000000  -1.2379   0.8942   0.0000   0.0000   0.0000
 1.000000  -1.4839   1.0482   0.0000   0.0000   0.0089
 2.000000  -1.3243   0.6055   0.0753   0.0664   0.0184

Glossary of keywords and components

Compulsory keywords

STRIDE	( default=1 ) the frequency with which the file should be read.
EVERY	( default=1 ) only read every \(n\)th line of the colvar file. This should be used if the colvar was written more frequently than the trajectory.
VALUES	the values to read from the file
FILE	the name of the file from which to read these quantities

Options

IGNORE_TIME	( default=off ) ignore the time in the colvar file. When this flag is not present read will be quite strict about the start time of the simulation and the stride between frames
IGNORE_FORCES	( default=off ) use this flag if the forces added by any bias can be safely ignored. As an example forces can be safely ignored if you are doing post processing that does not involve outputting forces
UPDATE_FROM	Only update this action from this time
UPDATE_UNTIL	Only update this action until this time