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
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# 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 detailsNATURAL# Record the shape of the simulation cell. cell:use natural unitsCELL# 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:Calculate the components of the simulation cell More detailsFCCUBIC...Measure how similar the environment around atoms is to that found in a FCC structure. More detailsSPECIES=1-1152this keyword is used for colvars such as coordination numberSWITCH={CUBIC D_0=1.2 D_MAX=1.5}the switching function that it used in the construction of the contact matrixMEANcalculate the mean of all the quantitiesMORE_THAN={SMAP R_0=0.45 D_0=0.0 A=8 B=8}calculate the number of variables that are more than a certain target valueALPHA=27The alpha parameter of the angular function that is used for FCCUBICPHI=-1.5708The Euler rotational angle phiTHETA=-0.61548The Euler rotational angle thetaPSI=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:The Euler rotational angle psiFCCUBIC...Measure how similar the environment around atoms is to that found in a FCC structure. More detailsSPECIES=1-1152this keyword is used for colvars such as coordination numberSWITCH={CUBIC D_0=1.2 D_MAX=1.5}the switching function that it used in the construction of the contact matrixMORE_THAN={SMAP R_0=0.05 D_0=0.4 A=16 B=8}calculate the number of variables that are more than a certain target valueALPHA=27The alpha parameter of the angular function that is used for FCCUBICPHI=-1.5708The Euler rotational angle phiTHETA=0.61548The Euler rotational angle thetaPSI=2.35619 ... cub3:The Euler rotational angle psiFCCUBIC...Measure how similar the environment around atoms is to that found in a FCC structure. More detailsSPECIES=1-1152this keyword is used for colvars such as coordination numberSWITCH={CUBIC D_0=1.2 D_MAX=1.5}the switching function that it used in the construction of the contact matrixMORE_THAN={SMAP R_0=0.05 D_0=0.4 A=16 B=8}calculate the number of variables that are more than a certain target valueALPHA=27The alpha parameter of the angular function that is used for FCCUBICPHI=1.5708The Euler rotational angle phiTHETA=-1.29515The Euler rotational angle thetaPSI=0.785389 ... cub4:The Euler rotational angle psiFCCUBIC...Measure how similar the environment around atoms is to that found in a FCC structure. More detailsSPECIES=1-1152this keyword is used for colvars such as coordination numberSWITCH={CUBIC D_0=1.2 D_MAX=1.5}the switching function that it used in the construction of the contact matrixMORE_THAN={SMAP R_0=0.05 D_0=0.4 A=16 B=8}calculate the number of variables that are more than a certain target valueALPHA=27The alpha parameter of the angular function that is used for FCCUBICPHI=-0.2014The Euler rotational angle phiTHETA=1.84644The Euler rotational angle thetaPSI=1.71269 ... cub5:The Euler rotational angle psiFCCUBIC...Measure how similar the environment around atoms is to that found in a FCC structure. More detailsSPECIES=1-1152this keyword is used for colvars such as coordination numberSWITCH={CUBIC D_0=1.2 D_MAX=1.5}the switching function that it used in the construction of the contact matrixMORE_THAN={SMAP R_0=0.05 D_0=0.4 A=16 B=8}calculate the number of variables that are more than a certain target valueALPHA=27The alpha parameter of the angular function that is used for FCCUBICPHI=-0.61548The Euler rotational angle phiTHETA=-1.5708The Euler rotational angle thetaPSI=-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:The Euler rotational angle psiAROUNDThis 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. More detailsDATA=cubthe label of an action that calculates multicolvarsATOM=1153an alternative to ORIGINXLOWER=-1.2the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)XUPPER=1.2the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)SIGMA=0.5the width of the function to be used for kernel density estimationMORE_THAN={SMAP R_0=0.5 D_0=0.0 A=8 B=8} sidecub:calcualte the number of colvars that are inside the region of interest and that are greater that a certain thresholdAROUNDThis 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. More detailsDATA=cubthe label of an action that calculates multicolvarsATOM=1153an alternative to ORIGINXLOWER=-2.3the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)XUPPER=2.3the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)SIGMA=0.5the width of the function to be used for kernel density estimationOUTSIDEcalculate quantities for colvars that are on atoms outside the region of interestLESS_THAN={SMAP R_0=0.5 D_0=-0.1 A=8 B=2} bordercub:calcualte the number of colvars that are inside the region of interest and that are less than a certain thresholdAROUNDThis 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. More detailsDATA=cubthe label of an action that calculates multicolvarsATOM=1153an alternative to ORIGINXLOWER=-7.0the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)XUPPER=7.0the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)SIGMA=0.5the width of the function to be used for kernel density estimationOUTSIDEcalculate quantities for colvars that are on atoms outside the region of interestLESS_THAN={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:calcualte the number of colvars that are inside the region of interest and that are less than a certain thresholdMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=sidecub.lessthanthe input for this action is the scalar output from one or more other actionsPACE=1600the frequency for hill additionHEIGHT=0.15the heights of the Gaussian hillsSIGMA=600the widths of the Gaussian hillsFILE=HILLSa file in which the list of added hills is storedTEMP=0.60the system temperature - this is only needed if you are doing well-tempered metadynamicsBIASFACTOR=90use well tempered metadynamics and use this bias factorADAPTIVE=DIFFuse a geometric (=GEOM) or diffusion (=DIFF) based hills width schemeSIGMA_MAX=50the upper bounds for the sigmas (in CV units) when using adaptive hillsSIGMA_MIN=0.1 ... # A restraint is used to keep the central slice of the simulation cell, near to the ghost atom, crystalline. wall:the lower bounds for the sigmas (in CV units) when using adaptive hillsLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=centercub.morethanthe arguments on which the bias is actingAT=140the positions of the wallKAPPA=2.0 # Several restraints are added to prevent nucleation of crystals with unwanted crystal orientations. notwin2:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=cub2.morethanthe arguments on which the bias is actingAT=14the positions of the wallKAPPA=0.4 notwin3:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=cub3.morethanthe arguments on which the bias is actingAT=14the positions of the wallKAPPA=0.2 notwin4:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=cub4.morethanthe arguments on which the bias is actingAT=14the positions of the wallKAPPA=0.2 notwin5:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=cub5.morethanthe arguments on which the bias is actingAT=14the positions of the wallKAPPA=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:the force constant for the wallLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=bordercub.lessthanthe arguments on which the bias is actingAT=30the positions of the wallKAPPA=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 FESthe force constant for the wallPrint quantities to a file. More detailsSTRIDE=10the frequency with which the quantities of interest should be outputARG=cell.ax,cub.*,metad.bias,wall.bias,notwin2.bias,notwin3.bias,notwin4.bias,notwin5.bias,softliquid.biasthe input for this action is the scalar output from one or more other actionsFILE=FESthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsSTRIDE=10the frequency with which the quantities of interest should be outputARG=cub2.*,cub3.*,cub4.*,cub5.*,centercub.*,sidecub.*,sidecub.*,bordercubthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantitiesENDPLUMEDTerminate plumed input. More details