There are also additional pair styles submitted by users which are diff --git a/doc/pair_style.txt b/doc/pair_style.txt index 35c0f2bf0b..f96bc89f84 100644 --- a/doc/pair_style.txt +++ b/doc/pair_style.txt @@ -133,6 +133,7 @@ the pair_style command, and coefficients specified by the associated "pair_style sw"_pair_sw.html - Stillinger-Weber 3-body potential "pair_style table"_pair_table.html - tabulated pair potential "pair_style tersoff"_pair_tersoff.html - Tersoff 3-body potential +"pair_style tersoff/zbl"_pair_tersoff.html - Tersoff/ZBL 3-body potential "pair_style yukawa"_pair_yukawa.html - Yukawa potential :ul There are also additional pair styles submitted by users which are diff --git a/doc/pair_tersoff.html b/doc/pair_tersoff.html index b7dc86acf9..fbfbfdf5cd 100644 --- a/doc/pair_tersoff.html +++ b/doc/pair_tersoff.html @@ -18,7 +18,7 @@
Examples:
pair_style tersoff -pair_coeff * * si.tersoff Si +pair_coeff * * Si.tersoff Si pair_coeff * * SiC.tersoff Si C Si
Description: @@ -124,7 +124,7 @@ specified as either 3 or 1. Tersoff used a slightly different but equivalent form for alloys, which we will refer to as Tersoff_2 potential (Tersoff_2).
-LAMMPS parameter values for Tersoff_2 can be obtained as follows. +
LAMMPS parameter values for Tersoff_2 can be obtained as follows: gamma = 1, just as for Tersoff_1, but now lambda3 = 0 and the value of m has no effect. The parameters for species i and j can be calculated using the Tersoff_2 mixing rules: diff --git a/doc/pair_tersoff.txt b/doc/pair_tersoff.txt index 85cf3831aa..1325f7618e 100644 --- a/doc/pair_tersoff.txt +++ b/doc/pair_tersoff.txt @@ -15,7 +15,7 @@ pair_style tersoff :pre [Examples:] pair_style tersoff -pair_coeff * * si.tersoff Si +pair_coeff * * Si.tersoff Si pair_coeff * * SiC.tersoff Si C Si :pre [Description:] @@ -121,7 +121,7 @@ specified as either 3 or 1. Tersoff used a slightly different but equivalent form for alloys, which we will refer to as Tersoff_2 potential "(Tersoff_2)"_#Tersoff_2. -LAMMPS parameter values for Tersoff_2 can be obtained as follows. +LAMMPS parameter values for Tersoff_2 can be obtained as follows: gamma = 1, just as for Tersoff_1, but now lambda3 = 0 and the value of m has no effect. The parameters for species i and j can be calculated using the Tersoff_2 mixing rules: diff --git a/doc/pair_tersoff_zbl.html b/doc/pair_tersoff_zbl.html new file mode 100644 index 0000000000..5c32d6079e --- /dev/null +++ b/doc/pair_tersoff_zbl.html @@ -0,0 +1,243 @@ + +
+ +
pair_style tersoff/zbl command +
+Syntax: +
+pair_style tersoff/zbl ++
Examples: +
+pair_style tersoff/zbl +pair_coeff * * SiC.tersoff.zbl Si C Si ++
Description: +
+The tersoff/zbl style computes a 3-body Tersoff potential +(Tersoff_1) with a close-separation pairwise modification +based on a Coulomb potential and the Ziegler-Biersack-Littmark +universal screening function (ZBL), giving the energy E of a +system of atoms as +
+
+The f_F term is a fermi-like function used to smoothly connect the ZBL +repulsive potential with the Tersoff potential. There are 2 +parameters used to adjust it: A_F and r_C. A_F controls how "sharp" +the transition is between the two, and r_C is essentially the cutoff +for the ZBL potential. +
+For the ZBL portion, there are two terms. The first is the Coulomb +repulsive term, with Z1, Z2 as the number of protons in each nucleus, +e as the electron charge (1 for metal and real units) and epsilon0 as +the permittivity of vacuum. The second part is the ZBL universal +screening function, with a0 being the Bohr radius (typically 0.529 +Angstroms), and the remainder of the coefficients provided by the +original paper. This screening function should be applicable to most +systems. However, it is only accurate for small separations +(i.e. less than 1 Angstrom). +
+For the Tersoff portion, f_R is a two-body term and f_A includes +three-body interactions. The summations in the formula are over all +neighbors J and K of atom I within a cutoff distance = R + D. +
+Only a single pair_coeff command is used with the tersoff/zbl style +which specifies a Tersoff/ZBL potential file with parameters for all +needed elements. These are mapped to LAMMPS atom types by specifying +N additional arguments after the filename in the pair_coeff command, +where N is the number of LAMMPS atom types: +
+- filename +
- N element names = mapping of Tersoff/ZBL elements to atom types +
As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values +for Si and C. If your LAMMPS simulation has 4 atoms types and you +want the 1st 3 to be Si, and the 4th to be C, you would use the +following pair_coeff command: +
+pair_coeff * * SiC.tersoff Si Si Si C ++
The 1st 2 arguments must be * * so as to span all LAMMPS atom types. +The first three Si arguments map LAMMPS atom types 1,2,3 to the Si +element in the Tersoff/ZBL file. The final C argument maps LAMMPS +atom type 4 to the C element in the Tersoff/ZBL file. If a mapping +value is specified as NULL, the mapping is not performed. This can be +used when a tersoff/zbl 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. +
+Tersoff/ZBL files in the potentials directory of the LAMMPS +distribution have a ".tersoff.zbl" suffix. Lines that are not blank +or comments (starting with #) define parameters for a triplet of +elements. The parameters in a single entry correspond to coefficients +in the formula above: +
+- 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 +
- gamma +
- lambda3 (1/distance units) +
- c +
- d +
- costheta0 (can be a value < -1 or > 1) +
- n +
- beta +
- lambda2 (1/distance units) +
- B (energy units) +
- R (distance units) +
- D (distance units) +
- lambda1 (1/distance units) +
- A (energy units) +
- Z_i +
- Z_j +
- ZBLcut (distance units) +
- ZBLexpscale (1/distance units) +
The n, beta, lambda2, B, lambda1, and A parameters are only used for +two-body interactions. The m, gamma, lambda3, c, d, and costheta0 +parameters are only used for three-body interactions. The R and D +parameters are used for both two-body and three-body interactions. The +Z_i,Z_j, ZBLcut, ZBLexpscale parameters are used in the ZBL repulsive +portion of the potential and in the Fermi-like function. The +non-annotated parameters are unitless. The value of m must be 3 or 1. +
+The Tersoff/ZBL potential file must contain entries for all the +elements listed in the pair_coeff command. It can also contain +entries for additional elements not being used in a particular +simulation; LAMMPS ignores those entries. +
+For a single-element simulation, only a single entry is required +(e.g. SiSiSi). For a two-element simulation, the file must contain 8 +entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that +specify Tersoff parameters for all permutations of the two elements +interacting in three-body configurations. Thus for 3 elements, 27 +entries would be required, etc. +
+As annotated above, the first element in the entry is the center atom +in a three-body interaction and it is bonded to the 2nd atom and the +bond is influenced by the 3rd atom. Thus an entry for SiCC means Si +bonded to a C with another C atom influencing the bond. Thus +three-body parameters for SiCSi and SiSiC entries will not, in +general, be the same. The parameters used for the two-body +interaction come from the entry where the 2nd element is repeated. +Thus the two-body parameters for Si interacting with C, comes from the +SiCC entry. By symmetry, the twobody parameters in the SiCC and CSiSi +entries should thus be the same. The parameters used for a particular +three-body interaction come from the entry with the corresponding +three elements. The parameters used only for two-body interactions +(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd +element are different (e.g. SiCSi) are not used for anything and can +be set to 0.0 if desired. +
+We chose the above form so as to enable users to define all commonly +used variants of the Tersoff portion of the potential. In particular, +our form reduces to the original Tersoff form when m = 3 and gamma = +1, while it reduces to the form of Albe et al. when beta = 1 +and m = 1. Note that in the current Tersoff implementation in LAMMPS, +m must be specified as either 3 or 1. Tersoff used a slightly +different but equivalent form for alloys, which we will refer to as +Tersoff_2 potential (Tersoff_2). +
+LAMMPS parameter values for Tersoff_2 can be obtained as follows: +gamma = 1, just as for Tersoff_1, but now lambda3 = 0 and the value of +m has no effect. The parameters for species i and j can be calculated +using the Tersoff_2 mixing rules: +
+
+Values not shown are determined by the first atom type. Finally, the +Tersoff_2 parameters R and S must be converted to the LAMMPS +parameters R and D (R is different in both forms), using the following +relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the +Tersoff_2 parameters. +
+In the potentials directory, the file SiCGe.tersoff provides the +LAMMPS parameters for Tersoff's various versions of Si, as well as his +alloy parameters for Si, C, and Ge. This file can be used for pure Si, +(three different versions), pure C, pure Ge, binary SiC, and binary +SiGe. LAMMPS will generate an error if this file is used with any +combination involving C and Ge, since there are no entries for the GeC +interactions (Tersoff did not publish parameters for this +cross-interaction.) Tersoff files are also provided for the SiC alloy +(SiC.tersoff) and the GaN (GaN.tersoff) alloys. +
+Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou +for helping clarify how Tersoff parameters for alloys have been +defined in various papers. Also thanks to Ram Devanathan for +providing the base ZBL implementation. +
++ +
Mixing, shift, table, tail correction, restart, rRESPA info: +
+For atom type pairs I,J and I != J, where types I and J correspond to +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 +shift, table, and tail options. +
+This pair style does not write its information to binary restart +files, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. +
+This pair style can only be used via the pair keyword of the +run_style respa command. It does not support the +inner, middle, outer keywords. +
++ +
Restrictions: +
+This pair style is 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" +for pair interactions. +
+The Tersoff/ZBL potential files provided with LAMMPS (see the +potentials directory) are parameterized for metal units. +You can use the Tersoff potential with any LAMMPS units, but you would +need to create your own Tersoff potential file with coefficients +listed in the appropriate units if your simulation doesn't use "metal" +units. +
+Related commands: +
+ +Default: none +
++ + + +
(Tersoff_1) J. Tersoff, Phys Rev B, 37, 6991 (1988). +
+ + +(ZBL) J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges +of Ions in Matter' Vol 1, 1985, Pergamon Press. +
+ + +(Albe) J. Nord, K. Albe, P. Erhartand K. Nordlund, J. Phys.: +Condens. Matter, 15, 5649(2003). +
+ + +(Tersoff_2) J. Tersoff, Phys Rev B, 39, 5566 (1989) +
+ diff --git a/doc/pair_tersoff_zbl.txt b/doc/pair_tersoff_zbl.txt new file mode 100644 index 0000000000..7f1b95541f --- /dev/null +++ b/doc/pair_tersoff_zbl.txt @@ -0,0 +1,234 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style tersoff/zbl command :h3 + +[Syntax:] + +pair_style tersoff/zbl :pre + +[Examples:] + +pair_style tersoff/zbl +pair_coeff * * SiC.tersoff.zbl Si C Si :pre + +[Description:] + +The {tersoff/zbl} style computes a 3-body Tersoff potential +"(Tersoff_1)"_#Tersoff_1 with a close-separation pairwise modification +based on a Coulomb potential and the Ziegler-Biersack-Littmark +universal screening function "(ZBL)"_#ZBL, giving the energy E of a +system of atoms as + +:c,image(Eqs/pair_tersoff_zbl.jpg) + +The f_F term is a fermi-like function used to smoothly connect the ZBL +repulsive potential with the Tersoff potential. There are 2 +parameters used to adjust it: A_F and r_C. A_F controls how "sharp" +the transition is between the two, and r_C is essentially the cutoff +for the ZBL potential. + +For the ZBL portion, there are two terms. The first is the Coulomb +repulsive term, with Z1, Z2 as the number of protons in each nucleus, +e as the electron charge (1 for metal and real units) and epsilon0 as +the permittivity of vacuum. The second part is the ZBL universal +screening function, with a0 being the Bohr radius (typically 0.529 +Angstroms), and the remainder of the coefficients provided by the +original paper. This screening function should be applicable to most +systems. However, it is only accurate for small separations +(i.e. less than 1 Angstrom). + +For the Tersoff portion, f_R is a two-body term and f_A includes +three-body interactions. The summations in the formula are over all +neighbors J and K of atom I within a cutoff distance = R + D. + +Only a single pair_coeff command is used with the {tersoff/zbl} style +which specifies a Tersoff/ZBL potential file with parameters for all +needed elements. These are mapped to LAMMPS atom types by specifying +N additional arguments after the filename in the pair_coeff command, +where N is the number of LAMMPS atom types: + +filename +N element names = mapping of Tersoff/ZBL elements to atom types :ul + +As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values +for Si and C. If your LAMMPS simulation has 4 atoms types and you +want the 1st 3 to be Si, and the 4th to be C, you would use the +following pair_coeff command: + +pair_coeff * * SiC.tersoff Si Si Si C :pre + +The 1st 2 arguments must be * * so as to span all LAMMPS atom types. +The first three Si arguments map LAMMPS atom types 1,2,3 to the Si +element in the Tersoff/ZBL file. The final C argument maps LAMMPS +atom type 4 to the C element in the Tersoff/ZBL file. If a mapping +value is specified as NULL, the mapping is not performed. This can be +used when a {tersoff/zbl} 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. + +Tersoff/ZBL files in the {potentials} directory of the LAMMPS +distribution have a ".tersoff.zbl" suffix. Lines that are not blank +or comments (starting with #) define parameters for a triplet of +elements. The parameters in a single entry correspond to coefficients +in the formula above: + +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 +gamma +lambda3 (1/distance units) +c +d +costheta0 (can be a value < -1 or > 1) +n +beta +lambda2 (1/distance units) +B (energy units) +R (distance units) +D (distance units) +lambda1 (1/distance units) +A (energy units) +Z_i +Z_j +ZBLcut (distance units) +ZBLexpscale (1/distance units) :ul + +The n, beta, lambda2, B, lambda1, and A parameters are only used for +two-body interactions. The m, gamma, lambda3, c, d, and costheta0 +parameters are only used for three-body interactions. The R and D +parameters are used for both two-body and three-body interactions. The +Z_i,Z_j, ZBLcut, ZBLexpscale parameters are used in the ZBL repulsive +portion of the potential and in the Fermi-like function. The +non-annotated parameters are unitless. The value of m must be 3 or 1. + +The Tersoff/ZBL potential file must contain entries for all the +elements listed in the pair_coeff command. It can also contain +entries for additional elements not being used in a particular +simulation; LAMMPS ignores those entries. + +For a single-element simulation, only a single entry is required +(e.g. SiSiSi). For a two-element simulation, the file must contain 8 +entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that +specify Tersoff parameters for all permutations of the two elements +interacting in three-body configurations. Thus for 3 elements, 27 +entries would be required, etc. + +As annotated above, the first element in the entry is the center atom +in a three-body interaction and it is bonded to the 2nd atom and the +bond is influenced by the 3rd atom. Thus an entry for SiCC means Si +bonded to a C with another C atom influencing the bond. Thus +three-body parameters for SiCSi and SiSiC entries will not, in +general, be the same. The parameters used for the two-body +interaction come from the entry where the 2nd element is repeated. +Thus the two-body parameters for Si interacting with C, comes from the +SiCC entry. By symmetry, the twobody parameters in the SiCC and CSiSi +entries should thus be the same. The parameters used for a particular +three-body interaction come from the entry with the corresponding +three elements. The parameters used only for two-body interactions +(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd +element are different (e.g. SiCSi) are not used for anything and can +be set to 0.0 if desired. + +We chose the above form so as to enable users to define all commonly +used variants of the Tersoff portion of the potential. In particular, +our form reduces to the original Tersoff form when m = 3 and gamma = +1, while it reduces to the form of "Albe et al."_#Albe when beta = 1 +and m = 1. Note that in the current Tersoff implementation in LAMMPS, +m must be specified as either 3 or 1. Tersoff used a slightly +different but equivalent form for alloys, which we will refer to as +Tersoff_2 potential "(Tersoff_2)"_#Tersoff_2. + +LAMMPS parameter values for Tersoff_2 can be obtained as follows: +gamma = 1, just as for Tersoff_1, but now lambda3 = 0 and the value of +m has no effect. The parameters for species i and j can be calculated +using the Tersoff_2 mixing rules: + +:c,image(Eqs/pair_tersoff_2.jpg) + +Values not shown are determined by the first atom type. Finally, the +Tersoff_2 parameters R and S must be converted to the LAMMPS +parameters R and D (R is different in both forms), using the following +relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the +Tersoff_2 parameters. + +In the potentials directory, the file SiCGe.tersoff provides the +LAMMPS parameters for Tersoff's various versions of Si, as well as his +alloy parameters for Si, C, and Ge. This file can be used for pure Si, +(three different versions), pure C, pure Ge, binary SiC, and binary +SiGe. LAMMPS will generate an error if this file is used with any +combination involving C and Ge, since there are no entries for the GeC +interactions (Tersoff did not publish parameters for this +cross-interaction.) Tersoff files are also provided for the SiC alloy +(SiC.tersoff) and the GaN (GaN.tersoff) alloys. + +Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou +for helping clarify how Tersoff parameters for alloys have been +defined in various papers. Also thanks to Ram Devanathan for +providing the base ZBL implementation. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +For atom type pairs I,J and I != J, where types I and J correspond to +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"_pair_modify.html +shift, table, and tail options. + +This pair style does not write its information to "binary restart +files"_restart.html, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +:line + +[Restrictions:] + +This pair style is 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_start.html#2_3 section for more info. + +This pair style requires the "newton"_newton.html setting to be "on" +for pair interactions. + +The Tersoff/ZBL potential files provided with LAMMPS (see the +potentials directory) are parameterized for metal "units"_units.html. +You can use the Tersoff potential with any LAMMPS units, but you would +need to create your own Tersoff potential file with coefficients +listed in the appropriate units if your simulation doesn't use "metal" +units. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:line + +:link(Tersoff_1) +[(Tersoff_1)] J. Tersoff, Phys Rev B, 37, 6991 (1988). + +:link(ZBL) +[(ZBL)] J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges +of Ions in Matter' Vol 1, 1985, Pergamon Press. + +:link(Albe) +[(Albe)] J. Nord, K. Albe, P. Erhartand K. Nordlund, J. Phys.: +Condens. Matter, 15, 5649(2003). + +:link(Tersoff_2) +[(Tersoff_2)] J. Tersoff, Phys Rev B, 39, 5566 (1989)