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.

UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units

# Record the shape of the simulation cell.
cell: 
CELL
Calculate 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: 
FCCUBIC
Measure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details
 ...

SPECIES
this keyword is used for colvars such as coordination number
=1-1152 
SWITCH
the switching function that it used in the construction of the contact matrix
={CUBIC D_0=1.2 D_MAX=1.5}

MEAN
 calculate the mean of all the quantities


MORE_THAN
calculate the number of variables that are more than a certain target value
={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: 
FCCUBIC
Measure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details
 ...

SPECIES
this keyword is used for colvars such as coordination number
=1-1152 
SWITCH
the switching function that it used in the construction of the contact matrix
={CUBIC D_0=1.2 D_MAX=1.5}

MORE_THAN
calculate the number of variables that are more than a certain target value
={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: 
FCCUBIC
Measure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details
 ...

SPECIES
this keyword is used for colvars such as coordination number
=1-1152 
SWITCH
the switching function that it used in the construction of the contact matrix
={CUBIC D_0=1.2 D_MAX=1.5}

MORE_THAN
calculate the number of variables that are more than a certain target value
={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: 
FCCUBIC
Measure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details
 ...

SPECIES
this keyword is used for colvars such as coordination number
=1-1152 
SWITCH
the switching function that it used in the construction of the contact matrix
={CUBIC D_0=1.2 D_MAX=1.5}

MORE_THAN
calculate the number of variables that are more than a certain target value
={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: 
FCCUBIC
Measure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details
 ...

SPECIES
this keyword is used for colvars such as coordination number
=1-1152 
SWITCH
the switching function that it used in the construction of the contact matrix
={CUBIC D_0=1.2 D_MAX=1.5}

MORE_THAN
calculate the number of variables that are more than a certain target value
={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: 
AROUND
This 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
 
DATA
the label of an action that calculates multicolvars
=cub 
ATOM
an 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 
SIGMA
the width of the function to be used for kernel density estimation
=0.5 
MORE_THAN
calcualte 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: 
AROUND
This 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
 
DATA
the label of an action that calculates multicolvars
=cub 
ATOM
an 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 
SIGMA
the 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_THAN
calcualte 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: 
AROUND
This 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
 
DATA
the label of an action that calculates multicolvars
=cub 
ATOM
an 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 
SIGMA
the 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_THAN
calcualte 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: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...

ARG
the input for this action is the scalar output from one or more other actions
=sidecub.lessthan

PACE
the frequency for hill addition
=1600 
HEIGHT
the heights of the Gaussian hills
=0.15 
SIGMA
the widths of the Gaussian hills
=600 
FILE
 a file in which the list of added hills is stored
=HILLS

TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=0.60 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=90

ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=DIFF 
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=50 
SIGMA_MIN
the 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_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=centercub.morethan 
AT
the positions of the wall
=140 
KAPPA
the force constant for the wall
=2.0
# Several restraints are added to prevent nucleation of crystals with unwanted crystal orientations.
notwin2: 
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
=cub2.morethan 
AT
the positions of the wall
=14 
KAPPA
the force constant for the wall
=0.4
notwin3: 
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
=cub3.morethan 
AT
the positions of the wall
=14 
KAPPA
the force constant for the wall
=0.2
notwin4: 
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
=cub4.morethan 
AT
the positions of the wall
=14 
KAPPA
the force constant for the wall
=0.2
notwin5: 
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
=cub5.morethan 
AT
the positions of the wall
=14 
KAPPA
the 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_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=bordercub.lessthan 
AT
the positions of the wall
=30 
KAPPA
the 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

PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=10 
ARG
the input for this action is the scalar output from one or more other actions
=cell.ax,cub.*,metad.bias,wall.bias,notwin2.bias,notwin3.bias,notwin4.bias,notwin5.bias,softliquid.bias 
FILE
the name of the file on which to output these quantities
=FES

PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=10 
ARG
the input for this action is the scalar output from one or more other actions
=cub2.*,cub3.*,cub4.*,cub5.*,centercub.*,sidecub.*,sidecub.*,bordercub  
FILE
the name of the file on which to output these quantities
=COLVAR

ENDPLUMED
Terminate plumed input. More details