diff --git a/doc/Eqs/pair_comb1.jpg b/doc/Eqs/pair_comb1.jpg
index 0e7fc4e352..d92f37be1c 100644
Binary files a/doc/Eqs/pair_comb1.jpg and b/doc/Eqs/pair_comb1.jpg differ
diff --git a/doc/Eqs/pair_comb1.tex b/doc/Eqs/pair_comb1.tex
index 880445299b..aab7c8d2d4 100644
--- a/doc/Eqs/pair_comb1.tex
+++ b/doc/Eqs/pair_comb1.tex
@@ -1,12 +1,7 @@
\documentclass[12pt]{article}
-
-\begin{document}
-
+\begin{document} \large
\begin{eqnarray*}
-E_T & = & \sum_i [ E_i^S + \frac{1}{2} \sum_{j \neq i} V_{ij}
- (r_{ij},q_i,q_j) + E_i^{BB} ] \\
-V_{ij}(r_{ij},q_i,q_j) & = & U_{ij}^R(r_{ij}) + U_{ij}^A(r_{ij},
- q_i,q_j) + U_{ij}^I(r_{ij},q_i,q_j) + U_{ij}^V(r_{ij}) \\
+E_T & = & \sum_i [ E_i^{self} (q_i) + \sum_{j>i} [E_{ij}^{short} (r_{ij}, q_i, q_j) + E_{ij}^{Coul} (r_{ij}, q_i, q_j)] + \\
+&& E^{polar} (q_i, r_{ij}) + E^{vdW} (r_{ij}) + E^{barr} (q_i) + E^{corr} (r_{ij}, \theta_{jik})] \\
\end{eqnarray*}
-
\end{document}
diff --git a/doc/Eqs/pair_comb2.jpg b/doc/Eqs/pair_comb2.jpg
index 206046000a..c73a174ac2 100644
Binary files a/doc/Eqs/pair_comb2.jpg and b/doc/Eqs/pair_comb2.jpg differ
diff --git a/doc/Eqs/pair_comb2.tex b/doc/Eqs/pair_comb2.tex
index 07822d119c..faa664ef09 100644
--- a/doc/Eqs/pair_comb2.tex
+++ b/doc/Eqs/pair_comb2.tex
@@ -2,11 +2,21 @@
\begin{document}
-\begin{eqnarray*}
-U_{ij}^R(r_{ij}) & = & f_{S_{ij}} A_{ij} \exp (-\lambda_{ij} r_{ij}) \\
-U_{ij}^A(r_{ij},q_i,q_j) & = & -f_{S_{ij}} b_{ij} B_{ij} \exp (-\alpha_{ij} r_{ij}) \\
-U_{ij}^I(r_{ij},q_i,q_j) & = & J_{ij} (r_{ij}) q_i q_j \\
-U_{ij}^V(r_{ij}) & = & f_{L_{ij}} (C_{VDW_i}C_{VDW_j})^\frac{1}{2}/r_{ij}^6 \\
-\end{eqnarray*}
+\begin{table}[h]
+\begin{tabular}{|c|c|c|c|c|c|c|c|}
+\hline
+ & $O$ & $Cu$ & $N$ & $C$ & $H$ & $Ti$ & $Zn$ \\ \hline
+$O$ & F & F & F & F & F & F & F \\ \hline
+$Cu$ & F & F & P & F & F & P & F \\ \hline
+$N$ & F & P & F & M & F & P & P \\ \hline
+$C$ & F & F & M & F & F & M & M \\ \hline
+$H$ & F & F & F & F & F & M & M \\ \hline
+$Ti$ & F & P & P & M & M & F & P \\ \hline
+$Zn$ & F & F & P & M & M & P & F \\ \hline
+\multicolumn{8}{l}{F: Fully optimized} \\
+\multicolumn{8}{l}{M: Only optimized for dimer molecule} \\
+\multicolumn{8}{l}{P: in Progress but have it from mixing rule} \\
+\end{tabular}
+\end{table}
\end{document}
diff --git a/doc/Section_commands.html b/doc/Section_commands.html
index 0e4209b95d..51cbc24029 100644
--- a/doc/Section_commands.html
+++ b/doc/Section_commands.html
@@ -482,12 +482,12 @@ potentials. Click on the style itself for a full description:
| lj/long/coul/long | lj/long/dipole/long | lj/long/tip4p/long | lj/smooth |
| lj/smooth/linear | lj96/cut | lubricate | lubricate/poly |
| lubricateU | lubricateU/poly | meam | mie/cut |
-| morse | nm/cut | nm/cut/coul/cut | nm/cut/coul/long |
-| peri/lps | peri/pmb | peri/ves | reax |
-| rebo | resquared | soft | sw |
-| table | tersoff | tersoff/mod | tersoff/zbl |
-| tip4p/cut | tip4p/long | tri/lj | yukawa |
-| yukawa/colloid | zbl
+ |
| morse | nb3b/harmonic | nm/cut | nm/cut/coul/cut |
+| nm/cut/coul/long | peri/lps | peri/pmb | peri/ves |
+| reax | rebo | resquared | soft |
+| sw | table | tersoff | tersoff/mod |
+| tersoff/zbl | tip4p/cut | tip4p/long | tri/lj |
+| yukawa | yukawa/colloid | zbl
|
These are pair styles contributed by users, which can be used if
@@ -498,9 +498,9 @@ package.
| awpmd/cut | coul/diel | eam/cd | edip |
| eff/cut | gauss/cut | list | lj/cut/dipole/sf |
| lj/sdk | lj/sdk/coul/long | lj/sdk/coul/msm | lj/sf |
-| meam/spline | meam/sw/spline | nb3b/harmonic | reax/c |
-| sph/heatconduction | sph/idealgas | sph/lj | sph/rhosum |
-| sph/taitwater | sph/taitwater/morris | tersoff/table
+ |
| meam/spline | meam/sw/spline | reax/c | sph/heatconduction |
+| sph/idealgas | sph/lj | sph/rhosum | sph/taitwater |
+| sph/taitwater/morris | tersoff/table
|
These are accelerated pair styles, which can be used if LAMMPS is
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index 71ee898ae0..fd89ea9609 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -778,6 +778,7 @@ potentials. Click on the style itself for a full description:
"meam"_pair_meam.html,
"mie/cut"_pair_mie.html,
"morse"_pair_morse.html,
+"nb3b/harmonic"_pair_nb3b_harmonic.html,
"nm/cut"_pair_nm.html,
"nm/cut/coul/cut"_pair_nm.html,
"nm/cut/coul/long"_pair_nm.html,
@@ -818,7 +819,6 @@ package"_Section_start.html#start_3.
"lj/sf"_pair_lj_sf.html,
"meam/spline"_pair_meam_spline.html,
"meam/sw/spline"_pair_meam_sw_spline.html,
-"nb3b/harmonic"_pair_nb3b_harmonic.html,
"reax/c"_pair_reax_c.html,
"sph/heatconduction"_pair_sph_heatconduction.html,
"sph/idealgas"_pair_sph_idealgas.html,
diff --git a/doc/pair_comb.html b/doc/pair_comb.html
index b140b639a7..8d46099968 100644
--- a/doc/pair_comb.html
+++ b/doc/pair_comb.html
@@ -13,51 +13,50 @@
pair_style comb/omp command
+pair_style comb3 command
+
Syntax:
-pair_style comb
+pair_style comb
+pair_style comb3 keyword
+keyword = polar
+ polar value = polar_on or polar_off = whether or not to include atomic polarization
+
+
+
Examples:
pair_style comb
pair_coeff * * ../potentials/ffield.comb Si
pair_coeff * * ../potentials/ffield.comb Hf Si O
+pair_style comb3 polar_off
+pair_coeff * * ../potentials/ffield.comb3 O Cu N C O
+
Description:
-Style comb computes a variable charge COMB (Charge-Optimized
-Many-Body) potential as described in (COMB_1) and
-(COMB_2). The energy E of a system of atoms
-is given by
+
Style comb computes the second-generation variable charge COMB
+(Charge-Optimized Many-Body) potential. Style comb3 computes
+the third-generation COMB potential. These COMB potentials are
+described in (COMB1) and (COMB2). Briefly,
+the total energy ET of a system of atoms is given by
-where ET is the total potential energy of the system,
-ESi is the self-energy term of atom i,
-Vij is the interatomic potential between the ith and
-jth atoms, rij is the distance of the atoms i and
-j, and qi and qj are charges of the atoms,
-and EBBi is the bond-bending term of atom i.
+
where Eiself is the self-energy of atom i
+(including atomic ionization energies and electron affinities),
+Eijshort is the bond-order potential between
+atoms i and j,
+EijCoul is the Coulomb interactions,
+Epolar is the polarization term for organic systems
+(style comb3 only),
+EvdW is the van der Waals energy (style comb3 only),
+Ebarr is a charge barrier function, and
+Ecorr are angular correction terms.
-The interatomic potential energy Vij consists of four
-components: two-body short-range repulsion,
-URij, many-body short-range attraction,
-UAij, long-range Coulombic electrostatic
-interaction, UIij, and van der Waals energy,
-UVij, which are defined as:
-
-
-
-The short-range repulsion and attraction are based on the
-Tersoff potential (see the pair_style
-tersoff command); thus for a zero-charge pure
-element system with no van der Waals interaction, the COMB potential
-reduces to Tersoff potential, typically truncated at a short cutoff,
-e.g. 3 to 4 Angstroms. The long-range Coulombic term uses the Wolf
-summation method described in Wolf, spherically truncated at a
-longer cutoff, e.g. 12 Angstroms.
-
-The COMB potential is a variable charge potential. The equilibrium
+
The COMB potentials (styles comb and comb3) are variable
+charge potentials. The equilibrium
charge on each atom is calculated by the electronegativity
equalization (QEq) method. See Rick for further details.
This is implemented by the fix qeq/comb command,
@@ -67,14 +66,11 @@ command has options that determine how often charge equilibration is
performed, its convergence criterion, and which atoms are included in
the calculation.
-Only a single pair_coeff command is used with the comb style which
-specifies the COMB potential file with parameters for all needed
-elements. These are mapped to LAMMPS atom types by specifying N
-additional arguments after the potential file in the pair_coeff
-command, where N is the number of LAMMPS atom types. The provided
-potential file ffield.comb contains all currently-available COMB
-parameterizations: for Si, Cu, Hf, Ti, O, their oxides and Zr, Zn and
-U metals.
+
Only a single pair_coeff command is used with the comb and comb3
+styles which specifies the COMB potential file with parameters for
+all needed elements. These are mapped to LAMMPS atom types by
+specifying N additional arguments after the potential file in the
+pair_coeff command, where N is the number of LAMMPS atom types.
For example, if your LAMMPS simulation of a Si/SiO2/
HfO2 interface has 4 atom types, and you want the 1st and
@@ -93,80 +89,28 @@ This can be used when a comb potential is used as part of the
hybrid pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
-The ffield.comb potential file is in the potentials directory of
-the LAMMPS distribution. See the pair_coeff doc page
-for alternate ways to specify the path for the potential file. Lines
-that are not blank or comments (starting with #) define parameters for
-a triplet of elements. The 49 parameters in a single entry correspond
-to coefficients in the formula above:
+
For style comb, the provided potential file ffield.comb contains
+all currently-available 2nd generation COMB parameterizations:
+for Si, Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals.
+For style comb3, the potential file ffield.comb3 contains all
+currently-available 3rd generation COMB paramterizations:
+O, Cu, N, C, H, Ti and Zn.
+The status of the optimization of the compounds, for example
+Cu2O, TiN and hydrocarbons, are given in the
+following table:
-
- element 1 (the center atom in a 3-body interaction)
-
- element 2 (the atom bonded to the center atom)
-
- element 3 (the atom influencing the 1-2 bond in a bond-order sense)
-
- m
-
- c
-
- d
-
- h (cos_theta0 (can be a value -1 or 1))
-
- n
-
- beta
-
- lambda21, lambda2 of element 1 (1/distance units)
-
- lambda22, lambda2 of element 2 (1/distance units)
-
- B of element 1 (energy units)
-
- B of element 2 (energy units)
-
- R (cutoff, distance units, 0.5*(r_outer + r_inner))
-
- D (cutoff, distance units, R - r_inner)
-
- lambda11, lambda1 of element 1 (1/distance units)
-
- lambda12, lambda1 of element 2 (1/distance units)
-
- A of element 1 (energy units)
-
- A of element 2 (energy units)
-
- K_LP_1 (energy units, 1st order Legendre polynomial coefficient)
-
- K_LP_3 (energy units, 3rd order Legendre polynomial coefficient)
-
- K_LP_6 (energy units, 6th order Legendre polynomial coefficient)
-
- A123 (cos_theta, theta = equilibrium MOM or OMO bond angles)
-
- Aconf (cos_theta, theta = equilibrium MOM or OMO bond-bending coefficient)
-
- addrep (energy units, additional repulsion)
-
- R_omiga_a (unit-less scaler for A)
-
- R_omiga_b (unit-less scaler for B)
-
- R_omiga_c (unit-less scaler for 0.5*(lambda21+lambda22))
-
- R_omiga_d (unit-less scaler for 0.5*(lambda11+lambda12))
-
- QL1 (charge units, lower charge limit for element 1)
-
- QU1 (charge units, upper charge limit for element 1)
-
- DL1 (distance units, ion radius of element 1 with charge QL1)
-
- DU1 (distance units, ion radius of element 1 with charge QU1)
-
- QL2 (charge units, lower charge limit for element 2)
-
- QU2 (charge units, upper charge limit for element 2)
-
- DL2 (distance units, ion radius of element 2 with charge QL2)
-
- DU2 (distance units, ion radius of element 2 with charge QU2)
-
- chi (energy units, self energy 1st power term)
-
- dJ (energy units, self energy 2nd power term)
-
- dK (energy units, self energy 3rd power term)
-
- dL (energy units, self energy 4th power term)
-
- dM (energy units, self energy 6th power term)
-
- esm (distance units, orbital exponent)
-
- cmn1 (self energy penalty, rho 1 of element 1)
-
- cml1 (self energy penalty, rho 1 of element 2)
-
- cmn2 (self energy penalty, rho 2 of element 1)
-
- cmn2 (self energy penalty, rho 2 of element 2)
-
- coulcut (long range Coulombic cutoff, distance units)
-
- hfocor (coordination term)
-
-The parameterization of COMB potentials start with a pure element
-(e.g. Si, Cu) then extend to its oxide and polymorphs
-(e.g. SiO2, Cu2O). For interactions not
-involving oxygen (e.g. Si-Cu or Hf-Zr), the COMB potential uses a
-mixing rule to generate these parameters. For furthur details on the
-parameterization and parameters, see the Tersoff
-doc page and the COMB publications (COMB_1) and
-(COMB_2). For more details on 3-body interaction types
-(e.g. SiSiO vs SiOSi), the mixing rule, and how to generate the
-potential file, please see the Tersoff doc page.
+
+
+For style comb3, in addition to ffield.comb3, a special
+parameter file, lib.comb3,
+that is exclusively used for C/O/H systems, will be automatically
+loaded if carbon atom is detected in LAMMPS input structure.
+Keyword polar indicates whether the force field includes the atomic
+polarization. Since the equilibration of the polarization has not
+yet been implemented, it can only set polar_off at present.
-In the potentials directory, the file ffield.comb provides the
-LAMMPS parameters for COMB's Si, Cu, Ti, Hf and their oxides, as well
-as pure U, Zn and Zr metals. This file can be used for pure elements
-(e.g. Si, Zr), binary oxides, binary alloys (e.g. SiCu, TiZr), and
-complex systems. Note that alloys and complex systems require all
-3-body entries be pre-defined in the potential file.
+
IMPORTANT NOTE: You can not use potential file ffield.comb with
+style comb3, nor file ffield.comb3 with style comb.
@@ -198,16 +142,16 @@ more instructions on how to use the accelerated styles effectively.
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.
-This pair style does not support the pair_modify
+
These pair styles does not support the pair_modify
shift, table, and tail options.
-This pair style does not write its information to binary restart
+These pair styles do not write its information to binary restart
files, since it is stored in potential files. Thus, you
need to re-specify the pair_style, pair_coeff, and fix
qeq/comb commands in an input script that reads a
restart file.
-This pair style can only be used via the pair keyword of the
+
These pair styles can only be used via the pair keyword of the
run_style respa command. It does not support the
inner, middle, outer keywords.
@@ -215,15 +159,15 @@ restart file.
Restrictions:
-This pair style is part of the MANYBODY package. It is only enabled
+
These pair styles are part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the Making LAMMPS section for more info.
-This pair style requires the newton setting to be "on"
+
These pair styles requires the newton setting to be "on"
for pair interactions.
-The COMB potentials in the ffield.comb file provided with LAMMPS
-(see the potentials directory) are parameterized for metal
+
The COMB potentials in the ffield.comb and ffield.comb3 files provided
+with LAMMPS (see the potentials directory) are parameterized for metal
units. You can use the COMB potential with any LAMMPS
units, but you would need to create your own COMB potential file with
coefficients listed in the appropriate units if your simulation
@@ -238,27 +182,19 @@ doesn't use "metal" units.
-
+
-
(COMB_1) J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
+
(COMB1) S. R. Phillpot and S. B. Sinnott, Science 325, 1634-1635 (2009)
-
+
-(COMB_2) T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, S. R.
-Phillpot, Phys Rev B, 81, 125328 (2010).
-
-
-
-(Tersoff) J. Tersoff, Phys Rev B, 37, 6991 (1988).
+
(COMB2) T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek,
+Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R,
+in press (DOI: 10.1016/j.mser.2013.07.001)
(Rick) S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
(1994).
-
-
-(Wolf) D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
-Phys, 110, 8254 (1999).
-