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PLUMED manual

Action: DUMPFORCES

Action: DUMPFORCES

Module	generic
Description	Usage
Dump the force acting on one of a values in a file.
This action outputs data to a file. You can read more about how PLUMED manages output files here

Details and examples

Dump the force acting on one of a values in a file.

Consider the following PLUMED input:

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

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=1,2
VThe RESTRAINT action with label V calculates the following quantities: Quantity    Type    Description  
V.bias scalar the instantaneous value of the bias potential
V.force2 scalar the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=r ATthe position of the restraint=0.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100
V: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=r ATthe position of the restraint=0.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0

This input will ultimately apply forces on the $x$ , $y$ and $z$ components of two atoms as well as the 9 cell vectors. The force on the $i$ th of these 15 quantities is given by:

$F_i = - \frac{\textrm{d}V}{\textrm{d}r}\frac{\partial r}{\partial x_i}$

where $x_i$ is the $x$ , $y$ or $z$ component of the position of one of the two atoms or one of the cell vectors. If we modify the input above by adding the DUMPFORCES command as shown below:

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

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=1,2
VThe RESTRAINT action with label V calculates the following quantities: Quantity    Type    Description  
V.bias scalar the instantaneous value of the bias potential
V.force2 scalar the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=r ATthe position of the restraint=0.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100
V: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=r ATthe position of the restraint=0.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
DUMPFORCESDump the force acting on one of a values in a file. More details ARGthe labels of the values whose forces should be output=r FILEthe name of the file on which to output the forces=forces STRIDE the frequency with which the forces should be output=5 FMT the format with which the derivatives should be output=%10.5f

we can then monitor the value of $-\frac{\textrm{d}V}{\textrm{d}r}$ in the output file forces. As explained by the equation above to get the forces on the atom this 'input force' needs to be multiplied by $\frac{\partial r}{\partial x_i}$ . To view the various components of the $\frac{\partial r}{\partial x_i}$ you would use the DUMPDERIVATIVES command. To control the buffering of output you use the FLUSH command.

DUMPFORCES 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

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=1,2
VThe RESTRAINT action with label V calculates the following quantities: Quantity    Type    Description  
V.bias scalar the instantaneous value of the bias potential
V.force2 scalar the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=r ATthe position of the restraint=0.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100
V: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=r ATthe position of the restraint=0.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
DUMPFORCESDump the force acting on one of a values in a file. More details ARGthe labels of the values whose forces should be output=r FILEthe name of the file on which to output the forces=forces

and a file called forces is already present in the directory where the calculation is running, the existing file is backed up and renamed to bck.0.forces so that new data can be output to a new file called forces. 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

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=1,2
VThe RESTRAINT action with label V calculates the following quantities: Quantity    Type    Description  
V.bias scalar the instantaneous value of the bias potential
V.force2 scalar the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=r ATthe position of the restraint=0.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100
V: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=r ATthe position of the restraint=0.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
DUMPFORCESDump the force acting on one of a values in a file. More details ARGthe labels of the values whose forces should be output=r FILEthe name of the file on which to output the forces=forces 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 somethingrThe 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=1,2
VThe RESTRAINT action with label V calculates the following quantities: Quantity    Type    Description  
V.bias scalar the instantaneous value of the bias potential
V.force2 scalar the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=r ATthe position of the restraint=0.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100
V: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=r ATthe position of the restraint=0.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
DUMPFORCESDump the force acting on one of a values in a file. More details ARGthe labels of the values whose forces should be output=r FILEthe name of the file on which to output the forces=forces

However, the advantage of using the RESTART keyword is that you can apped to some files and back up others. If you use the RESTART action instead data will be appended to all output files.

Switching printing on and off

You can use the UPDATE_FROM and UPDATE_UNTIL flags to make the DUMPFORCES 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

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=1,2
VThe RESTRAINT action with label V calculates the following quantities: Quantity    Type    Description  
V.bias scalar the instantaneous value of the bias potential
V.force2 scalar the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=r ATthe position of the restraint=0.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100
V: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=r ATthe position of the restraint=0.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
DUMPFORCESDump the force acting on one of a values in a file. More details ...
  ARGthe labels of the values whose forces should be output=r FILEthe name of the file on which to output the forces=forces
  UPDATE_FROMOnly update this action from this time=100 UPDATE_UNTILOnly update this action until this time=500
  STRIDE the frequency with which the forces should be output=1
...

During the first 100 ps of the simulation with this input the force is not output to the file called forces. The force is instead first output after the first 100 ps of trajectory have elapsed. Furthermore, output of the force stops once the trajectory is longer than 500 ps. In other words, the force 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/grid	the labels of the values whose forces should be output

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 forces should be output
STRIDE	compulsory	1	the frequency with which the forces should be output
FILE	compulsory	none	the name of the file on which to output the forces
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