Action: GET

Module	core
Description	Usage
Get data from PLUMED for another code
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.

Further details and examples

Get data from PLUMED for another code

The GET command takes in the label of a Value and transfers the contents of the Value to to a void pointer that is accessible in the code that called PLUMED. As the calling code does not know the shape of the Value in advance, we provide the functionality to get the data rank and shape. The following Python snippet illustrates how this works in practice:

import plumed

# Create a PLUMED object
p = plumed.Plumed()
# Setup PLUMED
num_atoms = 10
p.cmd("setNatoms",num_atoms)
p.cmd("setLogFile","test.log")
p.cmd("init")
# Tell PLUMED to calculate the distance between two atoms
p.cmd("readInputLine", "d1: DISTANCE ATOMS=1,2")
# Get the rank of the PLMD::Value that holds the distance
# This command sets up the GET object
rank = np.zeros( 1, dtype=np.int_ )
p.cmd("getDataRank d1", rank )
# Now get the shape of the PLMD::Value d1 that we are asking for in the GET object
shape = np.zeros( rank, dtype=np.int_ )
p.cmd("getDataShape d1", shape )
# And now set the void pointer that the data in PLMD::Value d1 should be
# transferred to so it can be accessed in our python script when asking PLMD to do a calculation
d1 = np.zeros( shape )
p.cmd("setMemoryForData d1", data )

# if we now transfer some atomic positions to plumed and call calc the variable d1 is set equal to the distance between atom 1 and atom 2.

Notice that you can have as many GET actions as you need. The data is transferred from the PLMD::Value to the void pointer when the calculate method of GET is called. Transferring variables is thus seamlessly integrated into the PLUMED calculation cycle.

You would only use the GET command if you were calling PLUMED from python or an MD code. The equivalent commands that you would use for this action in a conventional PLUMED input file as follows.

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
GETGet data from PLUMED for another code More details ARGthe label of the value that you would like to GET=d

Syntax

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