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HADRESS_Version_24_Jun_2016

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<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix lambdah command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID lambdah/calc N<sub>H-mol</sub> L<sub>HY</sub> L<sub>AT</sub> P<sub>flag</sub> &#948;&#955; dT<sub>p</sub> T<sub>p</sub><sup>Start</sup> T<sub>p</sub><sup>End</sup> HY<sub>Shape</sub> D<sub>flag</sub> &Delta;x dT<sub>d</sub> T<sub>d</sub><sup>Start</sup> T<sub>d</sub><sup>End</sup> &#963; R &#961;<sub>0</sub> c file<sub>flag</sub>
</PRE>
<UL><LI>ID is documented in <A HREF = "fix.html">fix</A> command
<LI>group-ID has to be all
<LI>lambdaH/calc = style name of this fix command
<LI>N<sub>H-mol</sub> = Number of molecular types within the low resolution
<LI>L<sub>HY</sub> = Length of Hybrid region
<LI>L<sub>AT</sub> = Length of Atomistic (high resolution) region
<LI>P<sub>flag</sub> = <I>0</I> or <I>1</I>
<PRE> <I>0</I> Constant-pressure route is off
<I>1</I> Constant-pressure route is on
</PRE>
<LI>&#948;&#955; = Bin size in constant-pressure route
<LI>dT<sub>p</sub> = Time step interval of constant-pressure route
<LI>T<sub>p</sub><sup>Start</sup> = Starting time step of constant-pressure route
<LI>T<sub>p</sub><sup>End</sup> = Ending time step of constant-pressure route
<LI>HY<sub>Shape</sub> = Shape of Hybrid region : <I>slab</I>, <I>sphere</I>, <I>cylinder</I>
<PRE> <I>slab</I> is for rectangular hybrid region
<I>sphere</I> is for spherical hybrid region
<I>cylinder</I> is for cylinderical hybrid region
</PRE>
<LI>D<sub>flag</sub> = <I>0</I> or <I>1</I>
<PRE> <I>0</I> Constant-density route is off
<I>1</I> Constant-density route is on
</PRE>
<LI>&Delta;x = Bin size in constant-density route (length unit)
<LI>dT<sub>d</sub> = Time step interval of constant-density route
<LI>T<sub>d</sub><sup>Start</sup> = Starting time step of constant-density route
<LI>T<sub>d</sub><sup>End</sup> = Ending time step of constant-density route
<LI>&#963; = Width of gaussian function in constant-density route (length unit)
<LI>R = Range of gaussian function in constant-density route (length unit)
<LI>&#961;<sub>0</sub> = Reference number density in constant-density route
<LI>c = Prefactor in constant-density route (energy unit)
<LI>file<sub>flag</sub> = <I>0</I> or <I>1</I>
<PRE> <I>0</I> Do not employ density-balancing file
<I>1</I> Employ density-balancing file
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>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
</PRE>
<P><B>Description:</B>
</P>
<P>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 <A HREF = "#Potestio2013_1">(Potestio2013_1)</A>, <A HREF = "#Potestio2013_2">(Potestio2013_2)</A>, <A HREF = "#Heidari2016">(Heidari2016)</A>.
</P>
<P>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 [-0.5L<sub>AT</sub> 0.5L<sub>AT</sub>]:
</P>
<CENTER><IMG SRC = "Eqs/HADRESS_Switching_Function_Slab.png">
</CENTER>
<P>The following switching function is defined for a spherical/cylinderical atomistic region located at the middle of the simulation box:
</P>
<CENTER><IMG SRC = "Eqs/HADRESS_Switching_Function_Sphere.png">
</CENTER>
<P>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 &#955; represented above the simulation snapshot.
</P>
<CENTER><IMG SRC = "JPG/HADRESS_MODEL_LAMMPS.png">
</CENTER>
<P><I>N<sub>H-mol</sub></I> 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.
</P>
<P>The <I>L<sub>HY</sub></I> specifies the length of the Hybrid region. For the cases of cylinderical or spherical hybrid regions, this quantity denotes <I>r<sub>HY</sub></I>.
</P>
<P>The <I>L<sub>AT</sub></I> determines the length of Atomistic region. For the cases of cylinderical or spherical hybrid regions, this quantity denotes <I>r<sub>AT</sub></I>.
</P>
<P>The <I>P<sub>flag</sub></I> switches off and on the constant-pressure route.
</P>
<P>The <I>&#948;&#955;</I> 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 &#955; bins of <I>&#948;&#955;</I> side.
</P>
<P>The <I>dT<sub>p</sub></I> denotes the time intervals in constant-pressure route at which the averaged drift forces are applied on the molecules of the hybrid region.
</P>
<P>The <I>T<sub>p</sub><sup>Start</sup></I> denotes the time step at which the simulation of the constant-pressure route is started.
</P>
<P>The <I>T<sub>p</sub><sup>End</sup></I> specifies the ending time step of the constant-pressure route.
</P>
<P>The <I>HY<sub>Shape</sub></I> specifies the geometry of the Hybrid region. This could be <I>slab</I>, <I>sphere</I>, <I>cylinder</I>.
</P>
<P><I>D<sub>flag</sub></I> switches off and on the constant-pressure route.
</P>
<P><I>&Delta;x</I> is the bin size by which the simulation box is descritized in the constant-density route.
</P>
<P><I>dT<sub>d</sub></I> is the time interval in constant-density route at which the averaged thermodynamic forces are applied.
</P>
<P><I>T<sub>d</sub><sup>Start</sup></I> is the starting time step of constant-density route.
</P>
<P><I>T<sub>d</sub><sup>End</sup></I> is the ending time step of constant-density route.
</P>
<P><I>&#963;</I> is the width of Gaussian function in the constant-density route.
</P>
<P><I>R</I> is the range of Gaussian function in the constant-density route.
</P>
<P><I>&#961;<sub>0</sub></I> is the reference density in the constant-density route.
</P>
<P><I>c</I> is the prefactor in the constant-density route.
</P>
<P><I>file<sub>flag</sub></I> denotes a flag whether the file containing the density-balancing force is employed or not.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>.
</P>
<P>This fix creates a file named "Mean_Comp_Density.txt" in which the compensation forces are printed.
This file is created at <I>T<sub>d</sub><sup>Start</sup></I> and is updated every <I>dT<sub>d</sub></I>.
The updating process of the file is finished at time step <I>T<sub>d</sub><sup>End</sup></I>.
For those equillibrated simulations starting at time step larger than <I>T<sub>d</sub><sup>End</sup></I>,
the file "Mean_Comp_Density.txt" is loaded in this fix.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>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.
</P>
<P>To employ the H-AdResS scheme, the full/hars atom style has to be used:
</P>
<PRE> atom_style full/hars
</PRE>
<P>To perform HAdResS, Data File should contain the following extra information with respect to the Data File defined in full atom style:
</P>
<P>[1] <B>mol_H</B> determines the number of molecular types in the low resolution (coarse-grained) region.
</P>
<P>[2] <B>representative_flag</B> determines which atom carries the molecule's information
(center of mass, molecule's resolution, ...) in the low resolution (coarse-grained) region.
</P>
<P>[3] <B>mol_type</B> denotes the type of the molecule in the low resolution (coarse-grained) region.
</P>
<P>The following example is extracted from a Data File in which the simulation box contains water molecules and the ions of sodium and cholorine:
</P>
<PRE>30720 atoms
20480 bonds
10240 angles
</PRE>
<PRE>4 atom types
<B>1 mol_H types</B>
1 bond types
1 angle types
</PRE>
<PRE>-99.968000 99.968000 xlo xhi
-20.793600 20.793600 ylo yhi
-20.793600 20.793600 zlo zhi
</PRE>
<PRE>Masses
</PRE>
<PRE>1 15.999400
2 1.007940
3 22.9898
4 35.453
</PRE>
<PRE>Atoms
#atomID molecule-tag atom-type q <B>representative_flag mol_type</B> 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
.
.
.
</PRE>
<P>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).
</P>
<HR>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_lj_hars.html">pair_lj_hars.html</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Potestio2013_1"></A>
<P><B>(Potestio2013_1)</B> R. Potestio, S. Fritsch, P. Espanol, R. Delgado-Buscalioni, K. Kremer, R. Everaers, and D. Donadio, <I>Hamiltonian Adaptive Resolution Simulation for Molecular Liquids</I>, <A HREF = "http://dx.doi.org/10.1103/PhysRevLett.110.108301">Phys. Rev. Lett. [110],
108301 (2013)</A>
</P>
<A NAME = "Potestio2013_2"></A>
<P><B>(Potestio2013_2)</B> R. Potestio, S. Fritsch, P. Espanol, R. Delgado-Buscalioni, K. Kremer, R. Everaers, and D. Donadio, <I>Monte Carlo Adaptive Resolution Simulation of Multicomponent Molecular Liquids</I>, <A HREF = "http://dx.doi.org/10.1103/PhysRevLett.111.060601">Phys. Rev. Lett. [111],
060601 (2013)</A>
</P>
<A NAME = "Heidari2016"></A>
<P><B>(Heidari2016)</B> M. Heidari, R. Cortes-Huerto, D. Donadio and R. Potestio, <I>Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations</I>, "EPJST (2016)"
</P>
</HTML>

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<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lj/cut/hars/at command
</H3>
<H3>pair_style lj/cut/coul/dsf/hars/at command
</H3>
<H3>pair_style lj/cut/hars/cg command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
</PRE>
<LI>style =
<PRE> <I>lj/cut/hars/at</I> or
<I>lj/cut/coul/dsf/hars/at</I> or
<I>lj/cut/hars/cg</I>
</PRE>
<LI>args = list of arguments for a particular style
<PRE> <I>lj/cut/hars/at</I> args = cutoff All_AT Flag_Load_File
cutoff = global cutoff for Lennard Jones interactions (distance units)
All_AT = Fully atomic simulation flag, = <I>0</I> or <I>1</I>
<I>0</I> Fully atomic simulation is off and HAdResS is on
<I>1</I> Fully atomic simulation is on and HAdResS is off
Flag_Load_File = Flag of employing compensation energy file, = <I>0</I> or <I>1</I>
<I>0</I> Do not employ compensation energy until T<sub>p</sub><sup>Start</sup>
<I>1</I> Employ compensation energy file immediately
</PRE>
<PRE> <I>lj/cut/coul/dsf/hars/at</I> 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, = <I>0</I> or <I>1</I>
<I>0</I> Fully atomic simulation is off and HAdResS is on
<I>1</I> Fully atomic simulation is on and HAdResS is off
Flag_Load_File = Flag of employing compensation energy file, = <I>0</I> or <I>1</I>
<I>0</I> Do not employ compensation energy until T<sub>p</sub><sup>Start</sup>
<I>1</I> Employ compensation energy file immediately
</PRE>
<PRE> <I>lj/cut/hars/cg</I> args = cutoff All_CG Flag_Load_File
cutoff = global cutoff for Lennard Jones interactions (distance units)
All_CG = Fully coarse-grained simulation flag, = <I>0</I> or <I>1</I>
<I>0</I> Fully coarse-grained simulation is off and HAdResS is on
<I>1</I> Fully coarse-grained simulation is on and HAdResS is off
Flag_Load_File = Flag of employing compensation energy file, = <I>0</I> or <I>1</I>
<I>0</I> Do not employ compensation energy until T<sub>p</sub><sup>Start</sup>
<I>1</I> Employ compensation energy file immediately
</PRE>
<P><B>Examples:</B>
</P>
<PRE>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
</PRE>
<P><B>Description:</B>
</P>
<P>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 <A HREF = "#Potestio2013_1">(Potestio2013_1)</A>, <A HREF = "#Potestio2013_2">(Potestio2013_2)</A>, <A HREF = "#Heidari2016">(Heidari2016)</A>:
</P>
<CENTER><IMG SRC = "Eqs/HADRESS_System_Hamiltonian.png">
</CENTER>
<P>The term K is the atomistic kinetic energy, and V<sup>int</sup> consists of all the intramolecular bonded interactions (e.g. bond stretching).
The value of the switching function is determined by the sizes L<sub>AT</sub>
L<sub>HY</sub> of the atomistic and hybrid regions, respectively, and of the specific geometry of the atomistic region.
</P>
<P>In the Hamiltonian, the non-bonded potential energy contribution of each molecule is given by a weighted sum of two terms
V<sub>&#945;</sub><sup>CG</sup> and V<sub>&#945;</sub><sup>AT</sup>, defined as:
</P>
<CENTER><IMG SRC = "Eqs/HADRESS_System_Potentials.png">
</CENTER>
<P>The <I>lj/cut/hars/at</I> 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
</P>
<CENTER><IMG SRC = "Eqs/HADRESS_AT_pair_lj.png">
</CENTER>
<P>rc is the cutoff.
</P>
<P>Style <I>lj/cut/coul/dsf/hars/at</I> 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 <A HREF = "#Fennell">Fennell et al.</A>, given by:
</P>
<CENTER><IMG SRC = "Eqs/HADRESS_AT_pair_coul_dsf.jpg">
</CENTER>
<P>where <I>alpha</I> is the damping parameter and erfc() is the complementary
error-function. This potential is essentially a short-range,
spherically-truncated, charge-neutralized, shifted, pairwise <I>1/r</I>
summation.
</P>
<P>The <I>lj/cut/hars/cg</I> 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
</P>
<CENTER><IMG SRC = "Eqs/HADRESS_CG_pair_lj.png">
</CENTER>
<P>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.
</P>
<P>Important Note: For dual resolution simulations, it is required to use hybrid/overlay to include
both resolution pair-styles.
</P>
<P>For all of dual resolution pair styles, the following coefficients must
be defined for each pair of atoms types via the
<A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples below
</P>
<LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>cutoff (distance units)
<P>For examples:
</P>
<PRE> 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
</PRE>
<P>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.
</P>
<P>All potentials have to be shifted at the cutoff through the command
</P>
<PRE> pair_modify shift yes
</PRE>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>All of the <I>lj/cut</I> pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> shift option for the energy of the
Lennard-Jones portion of the pair interaction.
</P>
<P>All of the <I>lj/cut</I> pair styles write their information to <A HREF = "restart.html">binary
restart files</A>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
</P>
<P>The pair styles do not support the use of the rRESPA hierarchy.
</P>
<P>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 (&#955;) is printed. Each file is created at <I>T<sub>p</sub><sup>Start</sup></I> and is updated every <I>dT<sub>p</sub></I>.
The updating process of the files is finished at time step <I>T<sub>p</sub><sup>End</sup></I>.
For those equilibrated simulations starting at time step larger than <I>T<sub>p</sub><sup>End</sup></I>, the file "Mean_Comp_Energy_XX.txt" is loaded in each pair styles. For more information,
see <A HREF = "fix_lambdah_calc.html">fix_lambdah_calc</A>.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>In HAdResS, it is required to include both high resolution (atomistic)
and low resolution (coarse-grained) force fields together through
</P>
<PRE> pair_style hybrid/overlay
</PRE>
<P>An example of such setup is given above.
</P>
<P>To employ the H-AdResS scheme, the full/hars atom style as well as <A HREF = "fix_lambdah_calc.html">(fix_lambdah_calc)</A> have to be used:
</P>
<PRE> atom_style full/hars
</PRE>
<PRE> fix ID group-ID lambdah/calc ...
</PRE>
<HR>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_lambdah_calc.html">fix_lambdah_calc</A>, <A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Potestio2013_1"></A>
<P><B>(Potestio2013_1)</B> R. Potestio, S. Fritsch, P. Espanol, R. Delgado-Buscalioni, K. Kremer, R. Everaers, and D. Donadio, <I>Hamiltonian Adaptive Resolution Simulation for Molecular Liquids</I>, <A HREF = "http://dx.doi.org/10.1103/PhysRevLett.110.108301">Phys. Rev. Lett. [110],
108301 (2013)</A>
</P>
<A NAME = "Potestio2013_2"></A>
<P><B>(Potestio2013_2)</B> R. Potestio, S. Fritsch, P. Espanol, R. Delgado-Buscalioni, K. Kremer, R. Everaers, and D. Donadio, <I>Monte Carlo Adaptive Resolution Simulation of Multicomponent Molecular Liquids</I>, <A HREF = "http://dx.doi.org/10.1103/PhysRevLett.111.060601">Phys. Rev. Lett. [111],
060601 (2013)</A>
</P>
<A NAME = "Heidari2016"></A>
<P><B>(Heidari2016)</B> M. Heidari, R. Cortes-Huerto, D. Donadio and R. Potestio, <I>Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations</I>, "EPJST (2016)"
</P>
<A NAME = "Fennell"></A>
<P><B>(Fennell)</B> C. J. Fennell, J. D. Gezelter, J Chem Phys, 124,
234104 (2006).
</P>
</HTML>