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.

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

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.

rphi1:       READ FILE=input_colvar.data  VALUES=phi1
rphi2:       READ FILE=input_colvar.data  VALUES=phi2
PRINT ARG=rphi1,rphi2 STRIDE=500  FILE=output_colvar.data

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