From d3096fc949b0a0d03d48e1f5cfe488180608f38b Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 23 Oct 2015 00:23:02 +0000 Subject: [PATCH] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14183 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/doc2/Section_commands.html | 10 +- doc/doc2/genindex.html | 8 +- doc/doc2/pair_mgpt.html | 16 +- doc/doc2/pair_smtbq.html | 272 +++++++++++++++++++++++++++++++++ 4 files changed, 295 insertions(+), 11 deletions(-) create mode 100644 doc/doc2/pair_smtbq.html diff --git a/doc/doc2/Section_commands.html b/doc/doc2/Section_commands.html index 411376f9da..4e3e097fb2 100644 --- a/doc/doc2/Section_commands.html +++ b/doc/doc2/Section_commands.html @@ -536,11 +536,11 @@ package. listlj/charmm/coul/long/soft (o)lj/cut/coul/cut/soft (o)lj/cut/coul/long/soft (o) lj/cut/dipole/sf (go)lj/cut/soft (o)lj/cut/tip4p/long/soft (o)lj/sdk (gko) lj/sdk/coul/long (go)lj/sdk/coul/msm (o)lj/sf (o)meam/spline -meam/sw/splinequipreax/csmd/hertz -smd/tlsphsmd/triangulated/surfacesmd/ulsphsph/heatconduction -sph/idealgassph/ljsph/rhosumsph/taitwater -sph/taitwater/morrissrptersoff/table (o)thole -tip4p/long/soft (o) +meam/sw/splinemgptquipreax/c +smd/hertzsmd/tlsphsmd/triangulated/surfacesmd/ulsph +smtbqsph/heatconductionsph/idealgassph/lj +sph/rhosumsph/taitwatersph/taitwater/morrissrp +tersoff/table (o)tholetip4p/long/soft (o)
diff --git a/doc/doc2/genindex.html b/doc/doc2/genindex.html index 36d13dad48..455592789c 100644 --- a/doc/doc2/genindex.html +++ b/doc/doc2/genindex.html @@ -1795,12 +1795,12 @@
pair_style lj/smooth
- -
pair_style lj/smooth/linear
+
+
pair_style lj96/cut
@@ -1818,6 +1818,10 @@ +
pair_style mgpt +
+ +
pair_style mie/cut
diff --git a/doc/doc2/pair_mgpt.html b/doc/doc2/pair_mgpt.html index 11ec3c2fff..9d6e62defe 100644 --- a/doc/doc2/pair_mgpt.html +++ b/doc/doc2/pair_mgpt.html @@ -134,12 +134,19 @@ constant-volume calculations and simulations. It is strongly recommended that the user work through and understand these examples before proceeding to more complex simulations.

+

IMPORTANT NOTE: For good performance, LAMMPS should be built with the +compiler flags "-O3 -msse3 -funroll-loops" when including this pair +style. The src/MAKE/OPTIONS/Makefile.mpi_fastmgpt is an example +machine Makefile with these options included as part of a standard MPI +build. Note that as-is it will build with whatever low-level compiler +(g++, icc, etc) is the default for your MPI installation. +

Mixing, shift, table tail correction, restart:

-

The (mgpt) pair style does not support the -pair_modify mix, shift, table, and tail options. +

This pair style does not support the pair_modify +mix, 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 @@ -154,8 +161,9 @@ script that reads a restart file.

Restrictions:

-

The mgpt pair style is part of the USER-MGPT package and is only -enabled if LAMMPS is built with that package. +

This pair style is part of the USER-MGPT package and is only enabled +if LAMMPS is built with that package. See the Making +LAMMPS section for more info.

The MGPT potentials require the newtion setting to be "on" for pair style interactions. diff --git a/doc/doc2/pair_smtbq.html b/doc/doc2/pair_smtbq.html new file mode 100644 index 0000000000..3efce316c9 --- /dev/null +++ b/doc/doc2/pair_smtbq.html @@ -0,0 +1,272 @@ + +

LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

pair_style smtbq command +

+

Syntax: +

+
pair_style smtbq 
+
+

Examples: +

+
pair_style smtbq
+pair_coeff * * ffield.smtbq.Al2O3 O Al 
+
+

Description: +

+

This pair stylecomputes a variable charge SMTB-Q (Second-Moment +tight-Binding QEq) potential as described in SMTB-Q_1 and +SMTB-Q_2. Briefly, the energy of metallic-oxygen systems +is given by three contributions: +

+
+
+

where Etot is the total potential energy of the system, +EES is the electrostatic part of the total energy, +EOO is the interaction between oxygens and +EMO is a short-range interaction between metal and oxygen +atoms. This interactions depend on interatomic distance +rij and/or the charge Qi of atoms +i. Cut-off function enables smooth convergence to zero interaction. +

+

The parameters appearing in the upper expressions are set in the +ffield.SMTBQ.Syst file where Syst corresponds to the selected system +(e.g. field.SMTBQ.Al2O3). Exemples for TiO2, +Al2O3 are provided. A single pair_coeff command +is used with the SMTBQ styles which provides the path to the potential +file with parameters for needed elements. These are mapped to LAMMPS +atom types by specifying additional arguments after the potential +filename in the pair_coeff command. Note that atom type 1 must always +correspond to oxygen atoms. As an example, to simulate a TiO2 system, +atom type 1 has to be oxygen and atom type 2 Ti. The following +pair_coeff command should then be used: +

+
pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti 
+
+The electrostatic part of the energy consists of two components + +

self-energy of atom i in the form of a second order charge dependent +polynomial and a long-range Coulombic electrostatic interaction. The +latter uses the wolf summation method described in Wolf, +spherically truncated at a longer cutoff, Rcoul. The +charge of each ion is modeled by an orbital Slater which depends on +the principal quantum number (n) of the outer orbital shared by the +ion. +

+

Interaction between oxygen, EOO, consists of two parts, +an attractive and a repulsive part. The attractive part is effective +only at short range (< r2OO). The attractive +contribution was optimized to study surfaces reconstruction +(e.g. SMTB-Q_2 in TiO2) and is not necessary +for oxide bulk modeling. The repulsive part is the Pauli interaction +between the electron clouds of oxygen. The Pauli repulsion and the +coulombic electrostatic interaction have same cut off value. In the +ffield.SMTBQ.Syst, the keyword 'buck' allows to consider only the +repulsive O-O interactions. The keyword 'buckPlusAttr' allows to +consider the repulsive and the attractive O-O interactions. +

+

The short-range interaction between metal-oxygen, EMO is +based on the second moment approximation of the density of states with +a N-body potential for the band energy term, +Eicov, and a Born-Mayer type repulsive terms +as indicated by the keyword 'second_moment' in the +ffield.SMTBQ.Syst. The energy band term is given by: +

+
+
+

where ηi is the stoichiometry of atom i, +δQi is the charge delocalization of atom i, +compared to its formal charge +QFi. n0, the number of hybridized +orbitals, is calculated with to the atomic orbitals shared +di and the stoichiometry +ηi. rc1 and rc2 are the two +cutoff radius around the fourth neighbors in the cutoff function. +

+

In the formalism used here, ξ0 is the energy +parameter. ξ0 is in tight-binding approximation the +hopping integral between the hybridized orbitals of the cation and the +anion. In the literature we find many ways to write the hopping +integral depending on whether one takes the point of view of the anion +or cation. These are equivalent vision. The correspondence between the +two visions is explained in appendix A of the article in the +SrTiO3 SMTB-Q_3 (parameter β shown in +this article is in fact the βO). To summarize the +relationship between the hopping integral ξ0 and the +others, we have in an oxide CnOm the following +relationship: +

+
+
+

Thus parameter μ, indicated above, is given by : μ = (√n ++ √m) ⁄ 2 +

+

The potential offers the possibility to consider the polarizability of +the electron clouds of oxygen by changing the slater radius of the +charge density around the oxygens through the parameters rBB, rB and +rS in the ffield.SMTBQ.Syst. This change in radius is performed +according to the method developed by E. Maras +SMTB-Q_2. This method needs to determine the number of +nearest neighbors around the oxygen. This calculation is based on +first (r1n) and second (r2n) distances +neighbors. +

+

The SMTB-Q potential is a variable charge potential. The equilibrium +charge on each atom is calculated by the electronegativity +equalization (QEq) method. See Rick for further detail. One +can adjust the frequency, the maximum number of iterative loop and the +convergence of the equilibrium charge calculation. To obtain the +energy conservation in NVE thermodynamic ensemble, we recommend to use +a convergence parameter in the interval 10-5 - +10-6 eV. +

+

The ffield.SMTBQ.Syst files are provided for few systems. They consist +of nine parts and the lines beginning with '#' are comments (note that +the number of comment lines matter). The first sections are on the +potential parameters and others are on the simulation options and +might be modified. Keywords are character type and must be enclosed in +quotation marks (''). +

+

1) Number of different element in the oxide: +

+ +

2) Atomic parameters +

+For the anion (oxygen) + + +

For each cations (metal): +

+ +

3) Potential parameters: +

+ +

4) Tables parameters: +

+ +

5) Rick model parameter: +

+ +

6) Coordination parameter: +

+ +

7) Charge initialization mode: +

+ +8) Mode for the electronegativity equalization (Qeq) + + +9) Verbose + + +

IMPORTANT NOTE: This last option slows down the calculation +dramatically. Use only with a single processor simulation. +

+
+ +

Mixing, shift, table, tail correction, restart, rRESPA info: +

+

This pair style does not support the pair_modify +mix, 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 +needs 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. +

+
+ +

Restriction: +

+

This pair style is part of the USER-SMTBQ package and is only enabled +if LAMMPS is built with that package. See the Making +LAMMPS section for more info. +

+

This potential requires using atom type 1 for oxygen and atom type +higher than 1 for metal atoms. +

+

This pair style requires the newton setting to be "on" +for pair interactions. +

+

The SMTB-Q potential files provided with LAMMPS (see the potentials +directory) are parameterized for metal units. +

+
+ +

Citing this work: +

+

Please cite related publication: N. Salles, O. Politano, E. Amzallag +and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189 +

+
+ + + +

(SMTB-Q_1) N. Salles, O. Politano, E. Amzallag, R. Tetot, +Comput. Mater. Sci. 111 (2016) 181-189 +

+ + +

(SMTB-Q_2) E. Maras, N. Salles, R. Tetot, T. Ala-Nissila, +H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399 +

+ + +

(SMTB-Q_3) R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface +Science 616, 19-8722 28 (2013) +

+ + +

(Wolf) D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem +Phys, 110, 8254 (1999). +

+ + +

(Rick) S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141 +(1994). +

+