PLUMED-NEST

Project ID: plumID:19.081
Source: Al/02_FCC/plumed.start.dat
Originally used with PLUMED version: 2.6-dev
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

# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../../RefCV.cpp

The LOAD action with label  calculates somethingenergy: ENERGYCalculate the total potential energy of the simulation box. More details

The ENERGY action with label energy calculates somethingvol: VOLUMECalculate the volume of the simulation box. More details

The VOLUME action with label vol calculates the volume of simulation boxREFCVThis action is not part of PLUMED and was included by using a LOAD command More details ...
 SPECIES=1-256
 SIGMA=0.04
 LATTICE_CONSTANTS=0.38
 CRYSTAL_STRUCTURE=FCC
 LABEL=refcv
 MORE_THAN={RATIONAL R_0=0.5 NN=12 MM=24}
 MEAN
... REFCV

# Construct a bias potential using VES
#
# Basis functions

bf1: BF_LEGENDRELegendre polynomials basis functions. More details ORDERThe order of the basis function expansion=8 MINIMUMThe minimum of the interval on which the basis functions are defined=-80000 MAXIMUMThe maximum of the interval on which the basis functions are defined=-51000
The BF_LEGENDRE action with label bf1 calculates somethingbf2: BF_LEGENDRELegendre polynomials basis functions. More details ORDERThe order of the basis function expansion=8 MINIMUMThe minimum of the interval on which the basis functions are defined=2.9 MAXIMUMThe maximum of the interval on which the basis functions are defined=4.3
The BF_LEGENDRE action with label bf2 calculates somethingbf3: BF_LEGENDRELegendre polynomials basis functions. More details ORDERThe order of the basis function expansion=8 MINIMUMThe minimum of the interval on which the basis functions are defined=0.0 MAXIMUMThe maximum of the interval on which the basis functions are defined=256.0

# Target distribution

The BF_LEGENDRE action with label bf3 calculates somethingTD_MULTITHERMAL_MULTIBARICMultithermal-multibaric target distribution (dynamic). More details ... 
 LABELa label for the action so that its output can be referenced in the input to other actions=td_multitp
 MIN_PRESSUREMinimum pressure=12044.281714
 MAX_PRESSUREMaximum pressure=24088.563428
 MIN_TEMPMinimum energy=1800.0
 MAX_TEMPMaximum energy=2400.0
 PRESSURETarget pressure of the barostat used in the MD engine=18066.422571
 SIGMAThe standard deviation parameters of the Gaussian kernels used for smoothing the target distribution=500.0,0.05,10.0
 THRESHOLD Maximum exploration free energy in kT=20
 STEPS_TEMP Number of temperature steps=20
 STEPS_PRESSURE Number of pressure steps=20
... TD_MULTITHERMAL_MULTIBARIC

# Expansion

The TD_MULTITHERMAL_MULTIBARIC action with label td_multitp calculates somethingVES_LINEAR_EXPANSIONLinear basis set expansion bias. More details ...
 ARGthe labels of the scalars on which the bias will act=energy,vol,refcv.morethan
 BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1,bf2,bf3
 TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=2000.0
 GRID_BINSthe number of bins used for the grid=40,40,40
 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td_multitp
 LABELa label for the action so that its output can be referenced in the input to other actions=b1
... VES_LINEAR_EXPANSION

# Optimization algorithm

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 potentialOPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. More details ...
  BIASthe label of the VES bias to be optimized=b1
  STRIDEthe frequency of updating the coefficients given in the number of MD steps=500
  LABELa label for the action so that its output can be referenced in the input to other actions=o1
  STEPSIZEthe step size used for the optimization=50.
  FES_OUTPUThow often the FES(s) should be written out to file=500
  BIAS_OUTPUThow often the bias(es) should be written out to file=500
  TARGETDIST_OUTPUThow often the dynamic target distribution(s) should be written out to file=500
  COEFFS_OUTPUT how often the coefficients should be written to file=100
  TARGETDIST_STRIDEstride for updating a target distribution that is iteratively updated during the optimization=500
  #MULTIPLE_WALKERS # Commented out to pass plumed nest's test, uncomment for calculation
... OPT_AVERAGED_SGD


The OPT_AVERAGED_SGD action with label o1 calculates the following quantities:
 Quantity   
 Description  
o1.value
a scalarQ6Calculate sixth order Steinhardt parameters. More details SPECIESthis keyword is used for colvars such as coordination number=1-256 SWITCHthe switching function that it used in the construction of the contact matrix={CUBIC D_0=0.25 D_MAX=0.35} VMEAN calculate the norm of the mean vector LABELa label for the action so that its output can be referenced in the input to other actions=q6
The Q6 action with label q6 calculates the following quantities:
 Quantity   
 Description  
q6._vmean
the norm of the mean vector
q6.value
the norms of the vectors of spherical harmonic coefficientsdiff: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=q6.vmean,refcv.mean FUNCthe function you wish to evaluate=(x-0.064)/(0.461-0.064)-(y-0.251)/(0.752-0.251) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label diff calculates the following quantities:
 Quantity   
 Description  
diff.value
an arbitrary functionUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=diff ATthe positions of the wall=0.05 KAPPAthe force constant for the wall=500000 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=uwall

The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500