Action: DUMPPROJECTIONS

Module	generic
Description	Usage
Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases).
This action outputs data to a file. You can read more about how PLUMED manages output files here

Details and examples

Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases).

Consider the following PLUMED input:

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

x1The CENTER_FAST action with label x1 calculates the following quantities:
 Quantity   
 Type   
 Description  
x1
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1-10
x2The CENTER_FAST action with label x2 calculates the following quantities:
 Quantity   
 Type   
 Description  
x2
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=11-20
rThe DISTANCE action with label r calculates the following quantities:
 Quantity   
 Type   
 Description  
r
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=x1,x2

The derivatives of the distance r with respect to the atomic positions, $X_i$, are given by:

$$\frac{\partial r}{\partial X_i} = \frac{\partial r}{\partial x_1}\frac{\partial r}{\partial x_2}\frac{\partial x_1}{\partial X_i}\frac{\partial x_2}{\partial X_i}$$

For the input above there are 69 of these derivatives in total. These include the derivatives of $r$ with respect to the $x$, $y$ and $z$ components of the 10 atomic positions that are used to calculate $x_1$, the derivatives of $r$ with respect to the $x$, $y$ and $z$ components of the 10 atomic positions that are used to calculate $x_2$ and the 9 derivatives of $r$ with respect to the cell vectors.

If we add a DUMPROJECTIONS command to the above input as shown below:

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

x1The CENTER_FAST action with label x1 calculates the following quantities:
 Quantity   
 Type   
 Description  
x1
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1-10
x2The CENTER_FAST action with label x2 calculates the following quantities:
 Quantity   
 Type   
 Description  
x2
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=11-20
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=x1,x2
DUMPPROJECTIONSDump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases). More details ARGthe labels of the values whose gradients should be outpu=d FILEthe name of the file on which to output the derivatives=proj STRIDE the frequency with which the derivatives should be output=20

PLUMED will output these 69 derivatives to the proj file.

only works for scalars

This action cannot be used if non rank zero objects are passed between actions that are used to calculate the quantity (d in the above examples) whose projections are being output using the DUMPPROJECTIONS command

RESTART, UPDATE_FROM and UPDATE_UNTIL

Notice that the RESTART, UPDATE_FROM and UPDATE_UNTIL keywords keywords can be used in this action in the same way as they are used for PRINT. Consequently, if you would like to append derivatives to an existing file called proj instead of backing that file up at the start of the calculation and outputting the data from the calculation on a new file called proj you would use an input like the one shown below:

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

x1The CENTER_FAST action with label x1 calculates the following quantities:
 Quantity   
 Type   
 Description  
x1
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1-10
x2The CENTER_FAST action with label x2 calculates the following quantities:
 Quantity   
 Type   
 Description  
x2
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=11-20
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=x1,x2
DUMPPROJECTIONSDump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases). More details ARGthe labels of the values whose gradients should be outpu=d STRIDE the frequency with which the derivatives should be output=1 FILEthe name of the file on which to output the derivatives=proj FMT the format with which the derivatives should be output=%10.6f RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES

Similarly, if you want to only output the derivatives during the 400 ps time interval after the first 100 ps of the simulation you would use an input like the one shown below:

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

x1The CENTER_FAST action with label x1 calculates the following quantities:
 Quantity   
 Type   
 Description  
x1
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1-10
x2The CENTER_FAST action with label x2 calculates the following quantities:
 Quantity   
 Type   
 Description  
x2
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=11-20
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=x1,x2
DUMPPROJECTIONSDump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases). More details ARGthe labels of the values whose gradients should be outpu=d STRIDE the frequency with which the derivatives should be output=1 FILEthe name of the file on which to output the derivatives=d UPDATE_FROMOnly update this action from this time=100 UPDATE_UNTILOnly update this action until this time=500

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	the labels of the values whose gradients should be outpu

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 whose gradients should be outpu
STRIDE	compulsory	1	the frequency with which the derivatives should be output
FILE	compulsory	none	the name of the file on which to output the derivatives
FMT	compulsory	%15.10f	the format with which the derivatives should be output
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