Project ID: plumID:19.051
Source: plumed.dat
Originally used with PLUMED version: not specified
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
tested onv2.10
tested onmaster
# This input was used to compute the surface free energy excess for the 111 surface. 
# In addition to returning the metadynamics bias potential that promotes the solid-liquid transitions, 
# this PLUMED input also defines a number of restraint potentials that ensure that the central region 
# of the supercell remains in the solid, fcc structure.
UNITSThis command sets the internal units for the code. More details NATURAL use natural units
# Record the shape of the simulation cell.
cell: CELLGet the components of the simulation cell More details
# We compute the local order parameter for each atom using the cubic harmonic function “FCCUBIC”. 
# By specifying these Euler angles we ensure that the CV only identifies atoms as being in an fcc crystals if the 111 lattice direction is along the x axis of the system. 
# The sigmoid switching function “SMAP” is used to do a non-linear mapping of these symmetry function values. 
# We collect the sum of the transforced FCCCUBIC parameters for all of the atoms so the value of “cub.morethan” is proportional to the number of atoms in the fcc crystal with the specified lattice direction.
# The system contains a total of 1152 real atoms, The 1153th atom is a “ghost” atom that stays stationary at the center of the supercell. 
# This ghost atom is only used as a reference point and allows us to indicate the relative positions of the atoms in some CVs.
cub: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details ...
SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-1152 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5}
MEAN calculate the mean of all the quantities
MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={SMAP R_0=0.45 D_0=0.0 A=8 B=8}
ALPHA The alpha parameter of the angular function that is used for FCCUBIC=27 PHI The Euler rotational angle phi=-1.5708 THETA The Euler rotational angle theta=-0.61548 PSI The Euler rotational angle psi=0.785389
... 
# At undercooled conditions, the system has a strong tendency to form solids. Although the central region of the supercell is constrained to remain as an fcc crystal with the 111 lattice direction along the x axis of the system, 
# the peripheral region is likely to form twinned crystals or mis-oriented crystals with grain boundaries. As the local order parameter is not rotational-invariant, any atoms in wrongly orientated crystals usually adopt values 
# intermediate between those obtained for bulk solid and liquid. These crystals with unwanted orientations will be misidentified as partially liquid, and will be included in the computed free energy profile. When this happens, 
# the free energy profile shows bumps, which hinders the determination of the chemical potnetial and surface excess free energy. For this reason, “cub2”, “cub3”, “cub4” and “cub5” are used to identify fcc crystals with unwanted 
# orientations. Constraints are added on these CVs to prevent the formation of solid phase with an orientation incompatible with the simulation box.
cub2: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details ...
SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-1152 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5}
MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={SMAP R_0=0.05 D_0=0.4 A=16 B=8}
ALPHA The alpha parameter of the angular function that is used for FCCUBIC=27 PHI The Euler rotational angle phi=-1.5708 THETA The Euler rotational angle theta=0.61548 PSI The Euler rotational angle psi=2.35619
... 
cub3: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details ...
SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-1152 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5}
MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={SMAP R_0=0.05 D_0=0.4 A=16 B=8}
ALPHA The alpha parameter of the angular function that is used for FCCUBIC=27 PHI The Euler rotational angle phi=1.5708 THETA The Euler rotational angle theta=-1.29515 PSI The Euler rotational angle psi=0.785389
... 
cub4: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details ...
SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-1152 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5}
MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={SMAP R_0=0.05 D_0=0.4 A=16 B=8}
ALPHA The alpha parameter of the angular function that is used for FCCUBIC=27 PHI The Euler rotational angle phi=-0.2014 THETA The Euler rotational angle theta=1.84644 PSI The Euler rotational angle psi=1.71269
... 
cub5: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details ...
SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-1152 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5}
MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={SMAP R_0=0.05 D_0=0.4 A=16 B=8}
ALPHA The alpha parameter of the angular function that is used for FCCUBIC=27 PHI The Euler rotational angle phi=-0.61548 THETA The Euler rotational angle theta=-1.5708 PSI The Euler rotational angle psi=-0.785398
... 
# The 1153th ghost atom is used as a landmark. These commands allow us to calculate the value of the order parameter in the central slice of the box, in the side regions and in the border slice of the supercell. 
# Notice that the sigmoid switching function “SMAP” is tuned in order to facilitate the biasing procedures.
centercub: AROUNDThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. This action is a shortcut. More details DATAthe label of an action that calculates multicolvars=cub ATOMan alternative to ORIGIN=1153 XLOWER the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)=-1.2 XUPPER the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)=1.2 SIGMAthe width of the function to be used for kernel density estimation=0.5 MORE_THANcalcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold={SMAP R_0=0.5 D_0=0.0 A=8 B=8}
sidecub: AROUNDThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. This action is a shortcut. More details DATAthe label of an action that calculates multicolvars=cub ATOMan alternative to ORIGIN=1153 XLOWER the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)=-2.3 XUPPER the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)=2.3 SIGMAthe width of the function to be used for kernel density estimation=0.5 OUTSIDE calculate quantities for colvars that are on atoms outside the region of interest LESS_THANcalcualte the number of colvars that are inside the region of interest and that are less than a certain threshold={SMAP R_0=0.5 D_0=-0.1 A=8 B=2}
bordercub: AROUNDThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. This action is a shortcut. More details DATAthe label of an action that calculates multicolvars=cub ATOMan alternative to ORIGIN=1153 XLOWER the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)=-7.0 XUPPER the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)=7.0 SIGMAthe width of the function to be used for kernel density estimation=0.5 OUTSIDE calculate quantities for colvars that are on atoms outside the region of interest LESS_THANcalcualte the number of colvars that are inside the region of interest and that are less than a certain threshold={SMAP R_0=0.5 D_0=-0.45 A=8 B=8}
# Well-tempered metadynamics is used to induce transitions between the liquid and the fcc crystal for the region on the side of the supercell. An external history-dependent bias potential is gradually accumulated in the space of the CV 
# “sidecub.lessthan”. A Gaussian that should cover the space of 600 timesteps in the CV space is deposited every 1600 time steps, with the maximum height equal to 0.15 Lennard-Jones energy unit. The well-tempered option is activated with 
# the biasfactor set to 90. 
metad: METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=sidecub.lessthan
PACEthe frequency for hill addition=1600 HEIGHTthe heights of the Gaussian hills=0.15 SIGMAthe widths of the Gaussian hills=600 FILE a file in which the list of added hills is stored=HILLS
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=0.60 BIASFACTORuse well tempered metadynamics and use this bias factor=90
ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=50 SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.1
... 
# A restraint is used to keep the central slice of the simulation cell, near to the ghost atom, crystalline.
wall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=centercub.morethan ATthe positions of the wall=140 KAPPAthe force constant for the wall=2.0
# Several restraints are added to prevent nucleation of crystals with unwanted crystal orientations.
notwin2: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cub2.morethan ATthe positions of the wall=14 KAPPAthe force constant for the wall=0.4
notwin3: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cub3.morethan ATthe positions of the wall=14 KAPPAthe force constant for the wall=0.2
notwin4: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cub4.morethan ATthe positions of the wall=14 KAPPAthe force constant for the wall=0.2
notwin5: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cub5.morethan ATthe positions of the wall=14 KAPPAthe force constant for the wall=0.1
# A further bias is added on the atoms at the border of the simulation box far away from the ghost atom, in order to facilitate the nucleation of the melt starting from the edge of the supercell.
softliquid: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=bordercub.lessthan ATthe positions of the wall=30 KAPPAthe force constant for the wall=0.005
# Finally the instantaneous values of the CV and the biases are recorded. These are used in the re-weighting processes to construct the FES
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=10 ARGthe labels of the values that you would like to print to the file=cell.ax,cub.*,metad.bias,wall.bias,notwin2.bias,notwin3.bias,notwin4.bias,notwin5.bias,softliquid.bias FILEthe name of the file on which to output these quantities=FES
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=10 ARGthe labels of the values that you would like to print to the file=cub2.*,cub3.*,cub4.*,cub5.*,centercub.*,sidecub.*,sidecub.*,bordercub.*  FILEthe name of the file on which to output these quantities=COLVAR
ENDPLUMEDTerminate plumed input. More details