diff -Naur lammps-3Jun09/doc/Eqs/pair_born.jpg lammps-4Jun09/doc/Eqs/pair_born.jpg --- lammps-3Jun09/doc/Eqs/pair_born.jpg 1969-12-31 17:00:00.000000000 -0700 +++ lammps-4Jun09/doc/Eqs/pair_born.jpg 2009-06-04 10:55:32.000000000 -0600 @@ -0,0 +1,14 @@ +JFIFHHC  !"$"$ B= +!1"A#2QUaqBSV3br?JR)JR)JR)JR)JR)JRC&t\r0VZ%[3ËZ=R0kJIRR'1*OJt~Fxf<0Z\+[ZA{i!#ó)VJRl~"濸 dĊJQv'J 'Vy"\8tɐ';iaxhA= ^:JRa;u\ɑ9;9rT#Dwl+{Yfe+XAR@"Z#u6rlzTtY,.fh."Yc, VV@"R)JR+[+}o<􈥘@jpK̃-A?TyqQr ~<=Uv1-&mMʪi>LSy'ybP(o@~:C"r/{'lSʌ,1f*6}H$zU|/=LF!i mnCѼ 8^~BtZrtolVv>x*-so+okxeA`_gQ5gL}#\ZKQ/Rc?mHҕ+#%9,}}@uy:IrnKpm@Og2JƮ7n6]\n*JNs@Zw=U;:WmwCqvRysus,gdFrU7I~>Y#?+n;,ʡu,/Qx1%|vFҋ߾n,*r+9+ybngv'hIwSXic[_,9{g"*{uv?Z,f3qs,PMhߡ6HvOcs8.8h?D"RHuh,ǵZ:=_b""#E +A@|FE[Zq,"]I .1fP oR1-MIHDv_m-ഴ%cXF?Pb"7M}md1lV{kY|OJTusI;HYU\ b:l孼6@vI>ܓI~5y)yYR5L}BTh%wza]fJhh'.G*"#w +V[c8;Y!b]Ă٫ +@ >3p{'U5b$l5X.,gIR9|~=28xB"y,!J5!,:uIbS殛ϖp,VgPD:[u1s%#VVP1{;!$]%i:Ac ? +,Zg9ik[Kh!heO2Wջ^rC]MƼLe1WbĀu Q8|w\X-3q{uk!nj!SaOt+Zkon3ߑW?-L^Y $A@ҖtMWއ~?$5& w#=)TϛN93g>m8\[4ys?yoӎ}Ys[N!^ifo96F#*zvFNGDhj Ʊ]p`@^agѿCt x^IbJ:h5 ɼw2݅>;; X--#=tvSys?yo' qly&yⵚgI$ \%ܝ0b6YTk/--o"^[Cqn{1ci7K$Zb ?cMA21w%PwZ4Lzav J<Wi.Z@4PrF +.I'kׄ/+Q%ܚ)ct'\iYB + +[Ky/HiaW }#ӹ_x`ZmqC9HөdX\u/p{޶?r/gB5t|V_޻[;ys?yoӎ}YsON93gge}oy -i`eEd挕; +#U)JRi)a=$l߶Cٿ0y 1ޛE6;1\sVDuXn`QUQ +L{!{2]]Z4Q`􂒽u9r+Ҩ_>+a- +1r $m`|zfTs-o.Ny(h-LDMr:[z4=;Ҁ{j\VfnKu̲;#uji8Rvl"N7܍wJp=os/O=:/b5p{ECwۉ$'`w6\~+siRe.[Ct* !AcNҕUW+&FumΑNr@ t4}*#;{ ŮR'ignI4[;kj$)z}5pqIKı `ThQOY #JR)JRYp|X 0yfk:Xiw9=QGg OسT79Oȸv_o{OXƲ)V#D޷v88-ȅS[;gگG ȑRxhXR) zETEDPJhWRn x."hR}E`ipD +Gֺ葱[T)JR)JR)JR)JR)JR)JR)JR)JR)JR \ No newline at end of file diff -Naur lammps-3Jun09/doc/Eqs/pair_born.tex lammps-4Jun09/doc/Eqs/pair_born.tex --- lammps-3Jun09/doc/Eqs/pair_born.tex 1969-12-31 17:00:00.000000000 -0700 +++ lammps-4Jun09/doc/Eqs/pair_born.tex 2009-06-04 10:55:32.000000000 -0600 @@ -0,0 +1,10 @@ +\documentstyle[12pt]{article} + +\begin{document} + +$$ +E = A \exp \left(\frac{\sigma - r}{\rho} \right) - + \frac{C}{r^6} + \frac{D}{r^8} + \frac{kq_i q_j}{\epsilon r} +$$ + +\end{document} diff -Naur lammps-3Jun09/doc/Section_commands.html lammps-4Jun09/doc/Section_commands.html --- lammps-3Jun09/doc/Section_commands.html 2009-04-29 10:54:14.000000000 -0600 +++ lammps-4Jun09/doc/Section_commands.html 2009-06-04 10:56:59.000000000 -0600 @@ -364,19 +364,19 @@

- - - - - - - - - - - - - + + + + + + + + + + + +
nonehybridhybrid/overlayairebo
buckbuck/coul/cutbuck/coul/longcolloid
coul/cutcoul/debyecoul/longdipole/cut
dpdeameam/opteam/alloy
eam/alloy/opteam/fseam/fs/optgayberne
gran/hertz/historygran/hookegran/hooke/historylj/charmm/coul/charmm
lj/charmm/coul/charmm/implicitlj/charmm/coul/longlj/charmm/coul/long/optlj/class2
lj/class2/coul/cutlj/class2/coul/longlj/cutlj/cut/opt
lj/cut/coul/cutlj/cut/coul/debyelj/cut/coul/longlj/cut/coul/long/tip4p
lj/expandlj/gromacslj/gromacs/coul/gromacslj/smooth
lubricatemeammorsemorse/opt
peri/pmbreaxresquaredsoft
swtabletersofftersoff/zbl
yukawa +
born/coul/longbuckbuck/coul/cutbuck/coul/long
colloidcoul/cutcoul/debyecoul/long
dipole/cutdpdeameam/opt
eam/alloyeam/alloy/opteam/fseam/fs/opt
gaybernegran/hertz/historygran/hookegran/hooke/history
lj/charmm/coul/charmmlj/charmm/coul/charmm/implicitlj/charmm/coul/longlj/charmm/coul/long/opt
lj/class2lj/class2/coul/cutlj/class2/coul/longlj/cut
lj/cut/optlj/cut/coul/cutlj/cut/coul/debyelj/cut/coul/long
lj/cut/coul/long/tip4plj/expandlj/gromacslj/gromacs/coul/gromacs
lj/smoothlubricatemeammorse
morse/optperi/pmbreaxresquared
softswtabletersoff
tersoff/zblyukawa

These are pair styles contributed by users, which can be used if diff -Naur lammps-3Jun09/doc/Section_commands.txt lammps-4Jun09/doc/Section_commands.txt --- lammps-3Jun09/doc/Section_commands.txt 2009-04-29 10:54:14.000000000 -0600 +++ lammps-4Jun09/doc/Section_commands.txt 2009-06-04 10:56:59.000000000 -0600 @@ -494,6 +494,7 @@ "hybrid"_pair_hybrid.html, "hybrid/overlay"_pair_hybrid.html, "airebo"_pair_airebo.html, +"born/coul/long"_pair_born.html, "buck"_pair_buck.html, "buck/coul/cut"_pair_buck.html, "buck/coul/long"_pair_buck.html, diff -Naur lammps-3Jun09/doc/pair_born.html lammps-4Jun09/doc/pair_born.html --- lammps-3Jun09/doc/pair_born.html 1969-12-31 17:00:00.000000000 -0700 +++ lammps-4Jun09/doc/pair_born.html 2009-06-04 10:55:43.000000000 -0600 @@ -0,0 +1,124 @@ + +

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

pair_style born/coul/long command +

+

Syntax: +

+
pair_style born/coul/long cutoff (cutoff2) 
+
+
  • cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + +
  • cutoff2 = global cutoff for Coulombic (optional) (distance units) + +

    Examples: +

    +
    pair_style born/coul/long 10.0
+pair_style born/coul/long 10.0 8.0
+pair_coeff * * 6.08 0.317 2.340 24.18 11.51
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 
+
    +

    Description: +

    +

    This pair style compute the Born-Mayer-Huggins potential described in +(Fumi and Tosi), given by +

    +
    +
    +

    where sigma is an interaction-dependent length parameter, rho is an +ionic-pair dependent length parameter, and the last term represents +the usual Coulombic pairwise interaction between atoms I and J. In +the Coulombic term, k is an energy-conversion constant, Qi and Qj are +the charges on the 2 atoms, and epsilon is the dielectric constant +which can be set by the dielectric command. +

    +

    If one cutoff is specified in the pair_style command, it is used for +both the A,C,D and Coulombic terms. If two cutoffs are specified, the +first is used as the cutoff for the A,C,D terms, and the second is the +cutoff for the Coulombic term. +

    +

    Note that this potential is identical to the Buckingham +potential when sigma = D = 0. +

    +

    An additional damping factor is applied to the Coulombic term so it +can be used in conjunction with the kspace_style +command and its ewald or pppm option. The Coulombic cutoff +specified for this style means that pairwise interactions within this +distance are computed directly; interactions outside that distance are +computed in reciprocal space. +

    +

    The following coefficients must be defined for each pair of atoms +types via the pair_coeff command as in the examples +above, or in the data file or restart files read by the +read_data or read_restart +commands, or by mixing as described below: +

    +
    • A (energy units) +
    • rho (distance units) +
    • sigma (distance units) +
    • C (energy units * distance units^6) +
    • D (energy units * distance units^8) +
    • cutoff (distance units) +
    +

    The last coefficient is optional. If not specified, the global A,C,D +cutoff specified in the pair_style command is used. Only the A,C,D +cutoff can be specified since a Coulombic cutoff cannot be specified +for an individual I,J type pair. All type pairs use the same global +Coulombic cutoff specified in the pair_style command. +

    +
    + +

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

    +

    This style does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly. +

    +

    This style supports the pair_modify shift option +for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair +interaction. +

    +

    This style does not support the pair_modify +table option since a tabulation capability has not yet been added to +this potential. +

    +

    This style does not support the pair_modify tail option for +adding long-range tail corrections to energy and pressure. +

    +

    This style writes its 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. +

    +

    This style only supports the pair keyword of run_style respa. +See the run_style command for details. +

    +
    + +

    Restrictions: +

    +

    The born/coul/long style is part of the "kspace" 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. +

    +

    Related commands: +

    +

    pair_coeff, pair_style buck +

    +

    Default: none +

    +
    + + + +

    Fumi and Tosi, J Phys Chem Solids, 25, 31 (1964), +Fumi and Tosi, J Phys Chem Solids, 25, 45 (1964). +

    + diff -Naur lammps-3Jun09/doc/pair_born.txt lammps-4Jun09/doc/pair_born.txt --- lammps-3Jun09/doc/pair_born.txt 1969-12-31 17:00:00.000000000 -0700 +++ lammps-4Jun09/doc/pair_born.txt 2009-06-04 10:55:43.000000000 -0600 @@ -0,0 +1,118 @@ +"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 born/coul/long command :h3 + +[Syntax:] + +pair_style born/coul/long cutoff (cutoff2) :pre + +cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) :l +cutoff2 = global cutoff for Coulombic (optional) (distance units) :l,ule + +[Examples:] + +pair_style born/coul/long 10.0 +pair_style born/coul/long 10.0 8.0 +pair_coeff * * 6.08 0.317 2.340 24.18 11.51 +pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre + +[Description:] + +This pair style compute the Born-Mayer-Huggins potential described in +"(Fumi and Tosi)"_#FumiTosi, given by + +:c,image(Eqs/pair_born.jpg) + +where sigma is an interaction-dependent length parameter, rho is an +ionic-pair dependent length parameter, and the last term represents +the usual Coulombic pairwise interaction between atoms I and J. In +the Coulombic term, k is an energy-conversion constant, Qi and Qj are +the charges on the 2 atoms, and epsilon is the dielectric constant +which can be set by the "dielectric"_dielectric.html command. + +If one cutoff is specified in the pair_style command, it is used for +both the A,C,D and Coulombic terms. If two cutoffs are specified, the +first is used as the cutoff for the A,C,D terms, and the second is the +cutoff for the Coulombic term. + +Note that this potential is identical to the "Buckingham +potential"_pair_buck.html when sigma = D = 0. + +An additional damping factor is applied to the Coulombic term so it +can be used in conjunction with the "kspace_style"_kspace_style.html +command and its {ewald} or {pppm} option. The Coulombic cutoff +specified for this style means that pairwise interactions within this +distance are computed directly; interactions outside that distance are +computed in reciprocal space. + +The following coefficients must be defined for each pair of atoms +types via the "pair_coeff"_pair_coeff.html command as in the examples +above, or in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html +commands, or by mixing as described below: + +A (energy units) +rho (distance units) +sigma (distance units) +C (energy units * distance units^6) +D (energy units * distance units^8) +cutoff (distance units) :ul + +The last coefficient is optional. If not specified, the global A,C,D +cutoff specified in the pair_style command is used. Only the A,C,D +cutoff can be specified since a Coulombic cutoff cannot be specified +for an individual I,J type pair. All type pairs use the same global +Coulombic cutoff specified in the pair_style command. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This style does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly. + +This style supports the "pair_modify"_pair_modify.html shift option +for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair +interaction. + +This style does not support the "pair_modify"_pair_modify.html +table option since a tabulation capability has not yet been added to +this potential. + +This style does not support the pair_modify tail option for +adding long-range tail corrections to energy and pressure. + +This style writes its information to binary +"restart"_restart.html files, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. + +This style only supports the {pair} keyword of run_style respa. +See the "run_style"_run_style.html command for details. + +:line + +[Restrictions:] + +The {born/coul/long} style is part of the "kspace" 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. + +[Related commands:] + +"pair_coeff"_pair_coeff.html, "pair_style buck"_pair_buck.html + +[Default:] none + +:line + +:link(FumiTosi) +Fumi and Tosi, J Phys Chem Solids, 25, 31 (1964), +Fumi and Tosi, J Phys Chem Solids, 25, 45 (1964). diff -Naur lammps-3Jun09/doc/pair_buck.html lammps-4Jun09/doc/pair_buck.html --- lammps-3Jun09/doc/pair_buck.html 2008-01-21 11:12:34.000000000 -0700 +++ lammps-4Jun09/doc/pair_buck.html 2009-06-04 10:55:20.000000000 -0600 @@ -60,6 +60,9 @@

    The buck/coul/cut and buck/coul/long styles add a Coulombic term as described for the lj/cut pair styles.

    +

    Note that this potential is related to the Born-Mayer-Huggins +potential. +

    The following coefficients must be defined for each pair of atoms types via the pair_coeff command as in the examples above, or in the data file or restart files read by the @@ -122,7 +125,7 @@

    Related commands:

    -

    pair_coeff +

    pair_coeff, pair_style born

    Default: none

    diff -Naur lammps-3Jun09/doc/pair_buck.txt lammps-4Jun09/doc/pair_buck.txt --- lammps-3Jun09/doc/pair_buck.txt 2008-01-21 11:12:34.000000000 -0700 +++ lammps-4Jun09/doc/pair_buck.txt 2009-06-04 10:55:20.000000000 -0600 @@ -54,6 +54,9 @@ The {buck/coul/cut} and {buck/coul/long} styles add a Coulombic term as described for the "lj/cut"_pair_lj.html pair styles. +Note that this potential is related to the "Born-Mayer-Huggins +potential"_pair_born.html. + The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the @@ -116,6 +119,6 @@ [Related commands:] -"pair_coeff"_pair_coeff.html +"pair_coeff"_pair_coeff.html, "pair_style born"_pair_born.html [Default:] none diff -Naur lammps-3Jun09/doc/pair_coeff.html lammps-4Jun09/doc/pair_coeff.html --- lammps-3Jun09/doc/pair_coeff.html 2009-02-06 09:12:07.000000000 -0700 +++ lammps-4Jun09/doc/pair_coeff.html 2009-06-04 10:56:59.000000000 -0600 @@ -89,6 +89,7 @@
    • pair_style airebo - AI-REBO potential +
    • pair_style born/coul/long - Born-Mayer-Huggins with long-range Coulomb
    • pair_style buck - Buckingham potential
    • pair_style buck/coul/cut - Buckingham with cutoff Coulomb
    • pair_style buck/coul/long - Buckingham with long-range Coulomb diff -Naur lammps-3Jun09/doc/pair_coeff.txt lammps-4Jun09/doc/pair_coeff.txt --- lammps-3Jun09/doc/pair_coeff.txt 2009-02-06 09:12:07.000000000 -0700 +++ lammps-4Jun09/doc/pair_coeff.txt 2009-06-04 10:56:59.000000000 -0600 @@ -85,6 +85,7 @@ "pair_style hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions :ul "pair_style airebo"_pair_airebo.html - AI-REBO potential +"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulomb "pair_style buck"_pair_buck.html - Buckingham potential "pair_style buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb "pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb diff -Naur lammps-3Jun09/doc/pair_style.html lammps-4Jun09/doc/pair_style.html --- lammps-3Jun09/doc/pair_style.html 2009-02-06 09:12:07.000000000 -0700 +++ lammps-4Jun09/doc/pair_style.html 2009-06-04 10:56:59.000000000 -0600 @@ -91,6 +91,7 @@
      • pair_style airebo - AI-REBO potential +
      • pair_style born/coul/long - Born-Mayer-Huggins with long-range Coulomb
      • pair_style buck - Buckingham potential
      • pair_style buck/coul/cut - Buckingham with cutoff Coulomb
      • pair_style buck/coul/long - Buckingham with long-range Coulomb diff -Naur lammps-3Jun09/doc/pair_style.txt lammps-4Jun09/doc/pair_style.txt --- lammps-3Jun09/doc/pair_style.txt 2009-02-06 09:12:07.000000000 -0700 +++ lammps-4Jun09/doc/pair_style.txt 2009-06-04 10:56:59.000000000 -0600 @@ -87,6 +87,7 @@ "pair_style hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions :ul "pair_style airebo"_pair_airebo.html - AI-REBO potential +"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulomb "pair_style buck"_pair_buck.html - Buckingham potential "pair_style buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb "pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb diff -Naur lammps-3Jun09/src/KSPACE/Install.csh lammps-4Jun09/src/KSPACE/Install.csh --- lammps-3Jun09/src/KSPACE/Install.csh 2007-10-03 10:15:35.000000000 -0600 +++ lammps-4Jun09/src/KSPACE/Install.csh 2009-06-04 10:52:20.000000000 -0600 @@ -7,6 +7,7 @@ cp ewald.cpp .. cp pppm.cpp .. cp pppm_tip4p.cpp .. + cp pair_born_coul_long.cpp .. cp pair_buck_coul_long.cpp .. cp pair_coul_long.cpp .. cp pair_lj_cut_coul_long.cpp .. @@ -20,6 +21,7 @@ cp ewald.h .. cp pppm.h .. cp pppm_tip4p.h .. + cp pair_born_coul_long.h .. cp pair_buck_coul_long.h .. cp pair_coul_long.h .. cp pair_lj_cut_coul_long.h .. @@ -38,6 +40,7 @@ rm ../ewald.cpp rm ../pppm.cpp rm ../pppm_tip4p.cpp + rm ../pair_born_coul_long.cpp rm ../pair_buck_coul_long.cpp rm ../pair_coul_long.cpp rm ../pair_lj_cut_coul_long.cpp @@ -51,6 +54,7 @@ rm ../ewald.h rm ../pppm.h rm ../pppm_tip4p.h + rm ../pair_born_coul_long.h rm ../pair_buck_coul_long.h rm ../pair_coul_long.h rm ../pair_lj_cut_coul_long.h diff -Naur lammps-3Jun09/src/KSPACE/pair_born_coul_long.cpp lammps-4Jun09/src/KSPACE/pair_born_coul_long.cpp --- lammps-3Jun09/src/KSPACE/pair_born_coul_long.cpp 1969-12-31 17:00:00.000000000 -0700 +++ lammps-4Jun09/src/KSPACE/pair_born_coul_long.cpp 2009-06-04 10:53:17.000000000 -0600 @@ -0,0 +1,472 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Ahmed Ismail (SNL) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_born_coul_long.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "kspace.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define MIN(a,b) ((a) < (b) ? (a) : (b)) +#define MAX(a,b) ((a) > (b) ? (a) : (b)) + +#define EWALD_F 1.12837917 +#define EWALD_P 0.3275911 +#define A1 0.254829592 +#define A2 -0.284496736 +#define A3 1.421413741 +#define A4 -1.453152027 +#define A5 1.061405429 + +/* ---------------------------------------------------------------------- */ + +PairBornCoulLong::PairBornCoulLong(LAMMPS *lmp) : Pair(lmp) {} + +/* ---------------------------------------------------------------------- */ + +PairBornCoulLong::~PairBornCoulLong() +{ + if (allocated) { + memory->destroy_2d_int_array(setflag); + memory->destroy_2d_double_array(cutsq); + + memory->destroy_2d_double_array(cut_lj); + memory->destroy_2d_double_array(cut_ljsq); + memory->destroy_2d_double_array(a); + memory->destroy_2d_double_array(rho); + memory->destroy_2d_double_array(sigma); + memory->destroy_2d_double_array(c); + memory->destroy_2d_double_array(d); + memory->destroy_2d_double_array(rhoinv); + memory->destroy_2d_double_array(born1); + memory->destroy_2d_double_array(born2); + memory->destroy_2d_double_array(born3); + memory->destroy_2d_double_array(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairBornCoulLong::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj; + double grij,expm2,prefactor,t,erfc; + double r,rexp; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + + if (j < nall) factor_coul = factor_lj = 1.0; + else { + factor_coul = special_coul[j/nall]; + factor_lj = special_lj[j/nall]; + j %= nall; + } + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r2inv = 1.0/rsq; + + if (rsq < cut_coulsq) { + r = sqrt(rsq); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + prefactor = qqrd2e * qtmp*q[j]/r; + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + r6inv = r2inv*r2inv*r2inv; + r = sqrt(rsq); + rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]); + forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv + + born3[itype][jtype]*r2inv*r6inv; + } else forceborn = 0.0; + + fpair = (forcecoul + factor_lj*forceborn) * r2inv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + if (rsq < cut_coulsq) { + ecoul = prefactor*erfc; + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv + + d[itype][jtype]*r6inv*r2inv - offset[itype][jtype]; + evdwl *= factor_lj; + } else evdwl = 0.0; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,ecoul,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairBornCoulLong::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq"); + + cut_lj = memory->create_2d_double_array(n+1,n+1,"pair:cut_lj"); + cut_ljsq = memory->create_2d_double_array(n+1,n+1,"pair:cut_ljsq"); + a = memory->create_2d_double_array(n+1,n+1,"pair:a"); + rho = memory->create_2d_double_array(n+1,n+1,"pair:rho"); + sigma = memory->create_2d_double_array(n+1,n+1,"pair:sigma"); + c = memory->create_2d_double_array(n+1,n+1,"pair:c"); + d = memory->create_2d_double_array(n+1,n+1,"pair:d"); + rhoinv = memory->create_2d_double_array(n+1,n+1,"pair:rhoinv"); + born1 = memory->create_2d_double_array(n+1,n+1,"pair:born1"); + born2 = memory->create_2d_double_array(n+1,n+1,"pair:born2"); + born3 = memory->create_2d_double_array(n+1,n+1,"pair:born3"); + offset = memory->create_2d_double_array(n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairBornCoulLong::settings(int narg, char **arg) +{ + if (narg < 1 || narg > 2) error->all("Illegal pair_style command"); + + cut_lj_global = atof(arg[0]); + if (narg == 1) cut_coul = cut_lj_global; + else cut_coul = atof(arg[1]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) cut_lj[i][j] = cut_lj_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairBornCoulLong::coeff(int narg, char **arg) +{ + if (narg < 7 || narg > 8) error->all("Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(arg[0],atom->ntypes,ilo,ihi); + force->bounds(arg[1],atom->ntypes,jlo,jhi); + + double a_one = atof(arg[2]); + double rho_one = atof(arg[3]); + double sigma_one = atof(arg[4]); + if (rho_one <= 0) error->all("Incorrect args for pair coefficients"); + double c_one = atof(arg[5]); + double d_one = atof(arg[6]); + + double cut_lj_one = cut_lj_global; + if (narg == 8) cut_lj_one = atof(arg[7]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + a[i][j] = a_one; + rho[i][j] = rho_one; + sigma[i][j] = sigma_one; + c[i][j] = c_one; + d[i][j] = d_one; + cut_lj[i][j] = cut_lj_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all("Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairBornCoulLong::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all("All pair coeffs are not set"); + + double cut = MAX(cut_lj[i][j],cut_coul); + cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; + + rhoinv[i][j] = 1.0/rho[i][j]; + born1[i][j] = a[i][j]/rho[i][j]; + born2[i][j] = 6.0*c[i][j]; + born3[i][j] = 8.0*d[i][j]; + + if (offset_flag) { + double rexp = exp(-cut_lj[i][j]/rho[i][j]); + offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut_lj[i][j],6.0) + + d[i][j]/pow(cut_lj[i][j],8.0); + } else offset[i][j] = 0.0; + + cut_ljsq[j][i] = cut_ljsq[i][j]; + a[j][i] = a[i][j]; + c[j][i] = c[i][j]; + d[j][i] = d[i][j]; + rhoinv[j][i] = rhoinv[i][j]; + sigma[j][i] = sigma[i][j]; + born1[j][i] = born1[i][j]; + born2[j][i] = born2[i][j]; + born3[j][i] = born3[i][j]; + offset[j][i] = offset[i][j]; + + return cut; +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairBornCoulLong::init_style() +{ + if (!atom->q_flag) + error->all("Pair style born/coul/long requires atom attribute q"); + + cut_coulsq = cut_coul * cut_coul; + + // insure use of KSpace long-range solver, set g_ewald + + if (force->kspace == NULL) + error->all("Pair style is incompatible with KSpace style"); + g_ewald = force->kspace->g_ewald; + + int irequest = neighbor->request(this); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairBornCoulLong::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&a[i][j],sizeof(double),1,fp); + fwrite(&rho[i][j],sizeof(double),1,fp); + fwrite(&sigma[i][j],sizeof(double),1,fp); + fwrite(&c[i][j],sizeof(double),1,fp); + fwrite(&d[i][j],sizeof(double),1,fp); + fwrite(&cut_lj[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairBornCoulLong::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&a[i][j],sizeof(double),1,fp); + fread(&rho[i][j],sizeof(double),1,fp); + fread(&sigma[i][j],sizeof(double),1,fp); + fread(&c[i][j],sizeof(double),1,fp); + fread(&d[i][j],sizeof(double),1,fp); + fread(&cut_lj[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&d[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairBornCoulLong::write_restart_settings(FILE *fp) +{ + fwrite(&cut_lj_global,sizeof(double),1,fp); + fwrite(&cut_coul,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairBornCoulLong::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_lj_global,sizeof(double),1,fp); + fread(&cut_coul,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- */ + +double PairBornCoulLong::single(int i, int j, int itype, int jtype, + double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double r2inv,r6inv,r,rexp,grij,expm2,t,erfc,prefactor; + double forcecoul,forceborn,phicoul,phiborn; + + r2inv = 1.0/rsq; + if (rsq < cut_coulsq) { + r = sqrt(rsq); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r; + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else forcecoul = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + r6inv = r2inv*r2inv*r2inv; + r = sqrt(rsq); + rexp = exp(-r*rhoinv[itype][jtype]); + forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv + + born3[itype][jtype]*r2inv*r6inv; + } else forceborn = 0.0; + fforce = (forcecoul + factor_lj*forceborn) * r2inv; + + double eng = 0.0; + if (rsq < cut_coulsq) { + phicoul = prefactor*erfc; + if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor; + eng += phicoul; + } + if (rsq < cut_ljsq[itype][jtype]) { + phiborn = a[itype][jtype]*rexp - c[itype][jtype]*r6inv + + d[itype][jtype]*r2inv*r6inv - offset[itype][jtype]; + eng += factor_lj*phiborn; + } + return eng; +} + +/* ---------------------------------------------------------------------- */ + +void *PairBornCoulLong::extract(char *str) +{ + if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; + return NULL; +} + diff -Naur lammps-3Jun09/src/KSPACE/pair_born_coul_long.h lammps-4Jun09/src/KSPACE/pair_born_coul_long.h --- lammps-3Jun09/src/KSPACE/pair_born_coul_long.h 1969-12-31 17:00:00.000000000 -0700 +++ lammps-4Jun09/src/KSPACE/pair_born_coul_long.h 2009-06-04 10:53:17.000000000 -0600 @@ -0,0 +1,50 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef PAIR_BORN_COUL_LONG_H +#define PAIR_BORN_COUL_LONG_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairBornCoulLong : public Pair { + public: + PairBornCoulLong(class LAMMPS *); + ~PairBornCoulLong(); + void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + double single(int, int, int, int, double, double, double, double &); + void *extract(char *); + + private: + double cut_lj_global; + double **cut_lj,**cut_ljsq; + double cut_coul,cut_coulsq; + double **a,**rho,**sigma,**c,**d; + double **rhoinv,**born1,**born2,**born3,**offset; + double g_ewald; + + void allocate(); +}; + +} + +#endif diff -Naur lammps-3Jun09/src/KSPACE/style_kspace.h lammps-4Jun09/src/KSPACE/style_kspace.h --- lammps-3Jun09/src/KSPACE/style_kspace.h 2007-10-03 10:15:35.000000000 -0600 +++ lammps-4Jun09/src/KSPACE/style_kspace.h 2009-06-04 10:54:18.000000000 -0600 @@ -24,6 +24,7 @@ #endif #ifdef PairInclude +#include "pair_born_coul_long.h" #include "pair_buck_coul_long.h" #include "pair_coul_long.h" #include "pair_lj_cut_coul_long.h" @@ -32,6 +33,7 @@ #endif #ifdef PairClass +PairStyle(born/coul/long,PairBornCoulLong) PairStyle(buck/coul/long,PairBuckCoulLong) PairStyle(coul/long,PairCoulLong) PairStyle(lj/cut/coul/long,PairLJCutCoulLong)