-Syntax: -
-fix ID group-ID lambdah/calc NH-mol LHY LAT Pflag δλ dTp TpStart TpEnd HYShape Dflag Δx dTd TdStart TdEnd σ R ρ0 c fileflag --
0 Constant-pressure route is off - 1 Constant-pressure route is on --
slab is for rectangular hybrid region - sphere is for spherical hybrid region - cylinder is for cylinderical hybrid region --
0 Constant-density route is off - 1 Constant-density route is on --
0 Do not employ density-balancing file - 1 Employ density-balancing file -- -
Examples: -
-fix 1 all lambdah/calc 1 25 60 1 0.02 1000 150000 300000 slab 1 1.5 500 400000 700000 6 2 0.1 2 0 -fix 1 all lambdah/calc 1 25 60 1 0.02 1000 100000 200000 sphere 1 1.5 500 300000 700000 6 2 0.1 2 0 --
Description: -
-The Hamiltonian adaptive resolution simulation scheme (H-AdResS) is a dual-resolution simulation method that -joins models with different levels of complexity for the same system within a global Hamiltonian framework (Potestio2013_1), (Potestio2013_2), (Heidari2016). -
-Depending on the shape of the Hybrid region which might be either slab, sphere or cynlinder, this fix calculates -the resolution of every atom based on the center of mass of its molecule. -The following switching function is defined for a simulation box whose atomistic region is limited to [-0.5LAT 0.5LAT]: -
-
-The following switching function is defined for a spherical/cylinderical atomistic region located at the middle of the simulation box: -
-
-A setup of a Hamiltonian Adaptive Resolution Simulation is shown below. The box is partitioned into three - different region types, namely: Coarse-grained (CG), Hybrid (HY), and Atomistic (AT). In each region, - the resolution of each molecule (here water) is determined by the instantaneous value of the - smooth function λ represented above the simulation snapshot. -
-
-NH-mol determines the number of molecular types within the low resolution. For instance, for a system containing -coarse-grained water molecules in the coarse-grained region, this number equals one. However, for a sytem containing -water molecules and ions such as Na and Cl and they interact differently in the coarse-grained region, -this number is 3. -
-The LHY specifies the length of the Hybrid region. For the cases of cylinderical or spherical hybrid regions, this quantity denotes rHY. -
-The LAT determines the length of Atomistic region. For the cases of cylinderical or spherical hybrid regions, this quantity denotes rAT. -
-The Pflag switches off and on the constant-pressure route. -
-The δλ denotes the bin size over the hybrid region. In the on-the-fly method of averaging the drift forces, -particles are sorted into uniformly spaced λ bins of δλ side. -
-The dTp denotes the time intervals in constant-pressure route at which the averaged drift forces are applied on the molecules of the hybrid region. -
-The TpStart denotes the time step at which the simulation of the constant-pressure route is started. -
-The TpEnd specifies the ending time step of the constant-pressure route. -
-The HYShape specifies the geometry of the Hybrid region. This could be slab, sphere, cylinder. -
-Dflag switches off and on the constant-pressure route. -
-Δx is the bin size by which the simulation box is descritized in the constant-density route. -
-dTd is the time interval in constant-density route at which the averaged thermodynamic forces are applied. -
-TdStart is the starting time step of constant-density route. -
-TdEnd is the ending time step of constant-density route. -
-σ is the width of Gaussian function in the constant-density route. -
-R is the range of Gaussian function in the constant-density route. -
-ρ0 is the reference density in the constant-density route. -
-c is the prefactor in the constant-density route. -
-fileflag denotes a flag whether the file containing the density-balancing force is employed or not. -
-Restart, fix_modify, output, run start/stop, minimize info: -
-No information about this fix is written to binary restart -files. -
-This fix creates a file named "Mean_Comp_Density.txt" in which the compensation forces are printed. -This file is created at TdStart and is updated every dTd. -The updating process of the file is finished at time step TdEnd. -For those equillibrated simulations starting at time step larger than TdEnd, -the file "Mean_Comp_Density.txt" is loaded in this fix. -
-Restrictions: -
-This fix calculates the center of mass of the particles. Thus at the beginning of the calculation, -it is required that all atoms belonging to a molecule are on the same side of the box. -
-To employ the H-AdResS scheme, the full/hars atom style has to be used: -
-atom_style full/hars --
To perform HAdResS, Data File should contain the following extra information with respect to the Data File defined in full atom style: -
-[1] mol_H determines the number of molecular types in the low resolution (coarse-grained) region. -
-[2] representative_flag determines which atom carries the molecule's information -(center of mass, molecule's resolution, ...) in the low resolution (coarse-grained) region. -
-[3] mol_type denotes the type of the molecule in the low resolution (coarse-grained) region. -
-The following example is extracted from a Data File in which the simulation box contains water molecules and the ions of sodium and cholorine: -
-30720 atoms -20480 bonds -10240 angles --
4 atom types -1 mol_H types -1 bond types -1 angle types --
-99.968000 99.968000 xlo xhi --20.793600 20.793600 ylo yhi --20.793600 20.793600 zlo zhi --
Masses --
1 15.999400 -2 1.007940 -3 22.9898 -4 35.453 --
Atoms -#atomID molecule-tag atom-type q representative_flag mol_type x y z -1 1 1 -0.847200 1 1 -99.654503 -19.897600 -20.192101 -2 1 2 0.423600 0 1 -100.568001 -19.999300 -20.586599 -3 1 2 0.423600 0 1 -99.777702 -20.103100 -19.221300 -4 2 1 -0.847200 1 1 -97.826401 -17.709900 -20.127100 -5 2 2 0.423600 0 1 -96.938400 -18.071301 -19.842800 -6 2 2 0.423600 0 1 -97.735100 -16.718800 -20.030100 -7 3 3 1.0 1 1 -97.429398 -20.402201 -17.494900 -8 3 4 -1.0 1 1 -96.834000 -19.671400 -17.160999 -. -. -. --
As it is shown, the representative_flag of the oxygen atoms is equal 1, and -since the soldium and cholorine are single atom ions, their representative_flags are also equals 1. -The interactions of water molecules and ions are the same in the coarse-grained region, -thus they all carry the same molecular type (mol_type). -
-Related commands: -
- -Default: none -
-(Potestio2013_1) R. Potestio, S. Fritsch, P. Espanol, R. Delgado-Buscalioni, K. Kremer, R. Everaers, and D. Donadio, Hamiltonian Adaptive Resolution Simulation for Molecular Liquids, Phys. Rev. Lett. [110], -108301 (2013) -
- - -(Potestio2013_2) R. Potestio, S. Fritsch, P. Espanol, R. Delgado-Buscalioni, K. Kremer, R. Everaers, and D. Donadio, Monte Carlo Adaptive Resolution Simulation of Multicomponent Molecular Liquids, Phys. Rev. Lett. [111], -060601 (2013) -
- - -(Heidari2016) M. Heidari, R. Cortes-Huerto, D. Donadio and R. Potestio, Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations, "EPJST (2016)" -
- diff --git a/doc/pair_lj_hars.html b/doc/pair_lj_hars.html deleted file mode 100644 index 50596c9d30..0000000000 --- a/doc/pair_lj_hars.html +++ /dev/null @@ -1,198 +0,0 @@ - -Syntax: -
-pair_style style args --
lj/cut/hars/at or - lj/cut/coul/dsf/hars/at or - lj/cut/hars/cg --
lj/cut/hars/at args = cutoff All_AT Flag_Load_File - cutoff = global cutoff for Lennard Jones interactions (distance units) - All_AT = Fully atomic simulation flag, = 0 or 1 - 0 Fully atomic simulation is off and HAdResS is on - 1 Fully atomic simulation is on and HAdResS is off - Flag_Load_File = Flag of employing compensation energy file, = 0 or 1 - 0 Do not employ compensation energy until TpStart - 1 Employ compensation energy file immediately --
lj/cut/coul/dsf/hars/at args = Alpha LJcutoff Coulcutoff All_AT Flag_Load_File - Alpha = Damping coefficient in DSF potential (1.0/distance units) - LJcutoff = global cutoff for Lennard Jones interactions (distance units) - Coulcutoff = global cutoff for DSF coulombic interactions (distance units) - All_AT = Fully atomic simulation flag, = 0 or 1 - 0 Fully atomic simulation is off and HAdResS is on - 1 Fully atomic simulation is on and HAdResS is off - Flag_Load_File = Flag of employing compensation energy file, = 0 or 1 - 0 Do not employ compensation energy until TpStart - 1 Employ compensation energy file immediately --
lj/cut/hars/cg args = cutoff All_CG Flag_Load_File - cutoff = global cutoff for Lennard Jones interactions (distance units) - All_CG = Fully coarse-grained simulation flag, = 0 or 1 - 0 Fully coarse-grained simulation is off and HAdResS is on - 1 Fully coarse-grained simulation is on and HAdResS is off - Flag_Load_File = Flag of employing compensation energy file, = 0 or 1 - 0 Do not employ compensation energy until TpStart - 1 Employ compensation energy file immediately --
Examples: -
-pair_style hybrid/overlay lj/cut/hars/cg 2.469416506 0 0 lj/cut/hars/at 0.2 10.0 12.0 0 0 -pair_style hybrid/overlay lj/cut/hars/cg 1.1224 1 0 lj/cut/hars/at 1.5 1 0 --
Description: -
-In the H-AdResS scheme, the description of the interactions within a system of particles is given in terms -of a global Hamiltonian function H, which has the following form (Potestio2013_1), (Potestio2013_2), (Heidari2016): -
-
-The term K is the atomistic kinetic energy, and Vint consists of all the intramolecular bonded interactions (e.g. bond stretching). -The value of the switching function is determined by the sizes LAT -LHY of the atomistic and hybrid regions, respectively, and of the specific geometry of the atomistic region. -
-In the Hamiltonian, the non-bonded potential energy contribution of each molecule is given by a weighted sum of two terms -VαCG and VαAT, defined as: -
-
-The lj/cut/hars/at styles compute the standard 12/6 Lennard-Jones potential for the atoms located in atomistic (high resolution) and hybrid region. -The general formula is given by -
-
-rc is the cutoff. -
-Style lj/cut/coul/dsf/hars/at computes the standard 12/6 Lennard-Jones and Coulomb interactions for atoms of atomistic (high resolution) and hybrid region. -The Coulombic term is computed via the damped shifted force model introduced by Fennell et al., given by: -
-
-where alpha is the damping parameter and erfc() is the complementary -error-function. This potential is essentially a short-range, -spherically-truncated, charge-neutralized, shifted, pairwise 1/r -summation. -
-The lj/cut/hars/cg styles compute the standard 12/6 Lennard-Jones potential for the atoms located in the low resolution (coarse-grained) and hybrid region. -The general formula is given by -
-
-rc is the cutoff. -As mentioned above, the interactions in the coarse-grained region are computed based on the center of mass of the particles. -
-Important Note: For dual resolution simulations, it is required to use hybrid/overlay to include -both resolution pair-styles. -
-For all of dual resolution pair styles, the following coefficients must -be defined for each pair of atoms types via the -pair_coeff command as in the examples below -
-For examples: -
-pair_coeff * * lj/cut/hars/cg 1.0 2.2 - pair_coeff 1 1 lj/cut/coul/dsf/hars/at 0.15535 3.166 - pair_coeff * 2 lj/cut/coul/dsf/hars/at 0.0000 0.0000 --
Note that sigma is defined in the LJ formula as the zero-crossing -distance for the potential, not as the energy minimum at 2^(1/6) -sigma. -
-All potentials have to be shifted at the cutoff through the command -
-pair_modify shift yes --
Mixing, shift, table, tail correction, restart, rRESPA info: -
-All of the lj/cut pair styles support the -pair_modify shift option for the energy of the -Lennard-Jones portion of the pair interaction. -
-All of the lj/cut pair styles write their information to binary -restart files, so pair_style and pair_coeff commands do -not need to be specified in an input script that reads a restart file. -
-The pair styles do not support the use of the rRESPA hierarchy. -
-Each pair styles creates a file named as "Mean_Comp_Energy_XX.txt", where the file name's suffix "XX", is replaced by "AT" and "CG" for atomistic and coarse-grained pairwise interactions respectively. -In these files the averaged compensation energy as function of the resolution (λ) is printed. Each file is created at TpStart and is updated every dTp. -The updating process of the files is finished at time step TpEnd. -For those equilibrated simulations starting at time step larger than TpEnd, the file "Mean_Comp_Energy_XX.txt" is loaded in each pair styles. For more information, -see fix_lambdah_calc. -
-Restrictions: -
-In HAdResS, it is required to include both high resolution (atomistic) -and low resolution (coarse-grained) force fields together through -
-pair_style hybrid/overlay --
An example of such setup is given above. -
-To employ the H-AdResS scheme, the full/hars atom style as well as (fix_lambdah_calc) have to be used: -
-atom_style full/hars --
fix ID group-ID lambdah/calc ... --
Related commands: -
-fix_lambdah_calc, pair_coeff -
-Default: none -
-(Potestio2013_1) R. Potestio, S. Fritsch, P. Espanol, R. Delgado-Buscalioni, K. Kremer, R. Everaers, and D. Donadio, Hamiltonian Adaptive Resolution Simulation for Molecular Liquids, Phys. Rev. Lett. [110], -108301 (2013) -
- - -(Potestio2013_2) R. Potestio, S. Fritsch, P. Espanol, R. Delgado-Buscalioni, K. Kremer, R. Everaers, and D. Donadio, Monte Carlo Adaptive Resolution Simulation of Multicomponent Molecular Liquids, Phys. Rev. Lett. [111], -060601 (2013) -
- - -(Heidari2016) M. Heidari, R. Cortes-Huerto, D. Donadio and R. Potestio, Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations, "EPJST (2016)" -
- - -(Fennell) C. J. Fennell, J. D. Gezelter, J Chem Phys, 124, -234104 (2006). -
-