PLUMED-NEST

Project ID: plumID:22.001
Source: lammps/CaCO3/sym10/plumed.dat
Originally used with PLUMED version: 2.8
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

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

#SETTINGS NREPLICAS=2
# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A 
ENERGY
the units of energy
=eV

# CVs
dist:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7345,7346

The DISTANCE action with label dist calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=coord
  
GROUPA
First list of atoms
=7345
  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=2-7343:3
  
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=1.0 D_0=2.1 NN=4 MM=8}
  
NLIST
 Use a neighbor list to speed up the calculation
  
NL_CUTOFF
The cutoff for the neighbor list
=10
  
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=10
... COORDINATION

# Target distribution
The COORDINATION action with label coord calculates a scalar quantitytd_wt: 
TD_WELLTEMPERED
Well-tempered target distribution (dynamic). More details
 
BIASFACTOR
The bias factor used for the well-tempered distribution
=5


# Basisset
BF_WAVELETS
Daubechies Wavelets basis functions. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=bfdist
  
ORDER
The order of the basis function expansion
=10
  
MINIMUM
The minimum of the interval on which the basis functions are defined
=2
  
MAXIMUM
The maximum of the interval on which the basis functions are defined
=12
  
FUNCTION_LENGTH
The domain size of the individual basis functions
=3.65
  
TYPE
Specify the wavelet type
=SYMLETS
  
TAILS_THRESHOLD
The threshold for cutting off tail wavelets as a fraction of the maximum value
=0.01
... BF_WAVELETS

BF_WAVELETS
Daubechies Wavelets basis functions. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=bfcoord
  
ORDER
The order of the basis function expansion
=10
  
MINIMUM
The minimum of the interval on which the basis functions are defined
=5
  
MAXIMUM
The maximum of the interval on which the basis functions are defined
=9
  
FUNCTION_LENGTH
The domain size of the individual basis functions
=3.5
  
TYPE
Specify the wavelet type
=SYMLETS
  
TAILS_THRESHOLD
The threshold for cutting off tail wavelets as a fraction of the maximum value
=0.01
... BF_WAVELETS


VES_LINEAR_EXPANSION
Linear basis set expansion bias. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=b1
  
ARG
the input for this action is the scalar output from one or more other actions
=dist,coord
  
BASIS_FUNCTIONS
the label of the one dimensional basis functions that should be used
=bfdist,bfcoord
  
TEMP
the system temperature - this is needed if the MD code does not pass the temperature to PLUMED
=300.0
  
GRID_BINS
the number of bins used for the grid
=300,300
  
OPTIMIZATION_THRESHOLD
Threshold value to turn off optimization of localized basis functions
=0.000001
  
TARGET_DISTRIBUTION
the label of the target distribution to be used
=td_wt
... VES_LINEAR_EXPANSION

The VES_LINEAR_EXPANSION action with label b1 calculates the following quantities:
 Quantity   
 Description  
b1.bias
the instantaneous value of the bias potential
b1.force2
the instantaneous value of the squared force due to this bias potential
OPT_AVERAGED_SGD
Averaged stochastic gradient decent with fixed step size. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=o1
  
BIAS
the label of the VES bias to be optimized
=b1
  
STRIDE
the frequency of updating the coefficients given in the number of MD steps
=10
  
STEPSIZE
the step size used for the optimization
=0.001
  
FES_OUTPUT
how often the FES(s) should be written out to file
=100
  
BIAS_OUTPUT
how often the bias(es) should be written out to file
=100
  
COEFFS_OUTPUT
 how often the coefficients should be written to file
=10
  
TARGETDIST_STRIDE
stride for updating a target distribution that is iteratively updated during the optimization
=100
  
TARGETDIST_OUTPUT
how often the dynamic target distribution(s) should be written out to file
=100
  
MULTIPLE_WALKERS
 if optimization is to be performed using multiple walkers connected via MPI
... OPT_AVERAGED_SGD

The OPT_AVERAGED_SGD action with label o1 calculates a scalar quantity
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 ...
  
ARG
the arguments on which the bias is acting
=dist
  
AT
the positions of the wall
=12
  
KAPPA
the force constant for the wall
=12.0
  
EXP
 the powers for the walls
=2
  
EPS
 the values for s_i in the expression for a wall
=1
  
OFFSET
 the offset for the start of the wall
=0
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wall
... UPPER_WALLS

FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=100
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=COLVAR