forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14338 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
676cdda5aa
commit
93919c35bf
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@ -48,12 +48,16 @@ fix ttm/mod, Sergey Starikov and Vasily Pisarev (JIHT), pisarevvv at gmail.com,
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improper_style cossq, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12
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improper_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
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improper_style ring, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12
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improper_style distance, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
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pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
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pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
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pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
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pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11
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pair_style eam/cd, Alexander Stukowski, stukowski at mm.tu-darmstadt.de, 7 Nov 09
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pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
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pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
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pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13
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pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
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pair_style lj/sf, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
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pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12
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pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12
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@ -0,0 +1,262 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Paolo Raiteri (Curtin University)
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------------------------------------------------------------------------- */
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#include <mpi.h>
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#include <math.h>
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#include <stdlib.h>
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#include "improper_distance.h"
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#include "atom.h"
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#include "comm.h"
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#include "neighbor.h"
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#include "domain.h"
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#include "force.h"
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#include "update.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define TOLERANCE 0.05
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#define SMALL 0.001
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/* ---------------------------------------------------------------------- */
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ImproperDistance::ImproperDistance(LAMMPS *lmp) : Improper(lmp) {}
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/* ---------------------------------------------------------------------- */
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ImproperDistance::~ImproperDistance()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(k);
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memory->destroy(chi);
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}
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}
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/* ---------------------------------------------------------------------- */
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void ImproperDistance::compute(int eflag, int vflag)
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{
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int i1,i2,i3,i4,n,type;
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double xab, yab, zab; // bond 1-2
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double xac, yac, zac; // bond 1-3
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double xad, yad, zad; // bond 1-4
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double xbc, ybc, zbc; // bond 2-3
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double xbd, ybd, zbd; // bond 2-4
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double xna, yna, zna, rna; // normal
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double da;
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double eimproper,f1[3],f2[3],f3[3],f4[3];
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// double ss1,ss2,ss3,r1,r2,r3,c0,c1,c2,s1,s2;
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// double s12,c,s,domega,a,a11,a22,a33,a12,a13,a23;
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double domega,a;
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double sx2,sy2,sz2;
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eimproper = 0.0;
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = 0;
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double **x = atom->x;
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double **f = atom->f;
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int **improperlist = neighbor->improperlist;
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int nimproperlist = neighbor->nimproperlist;
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int nlocal = atom->nlocal;
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int newton_bond = force->newton_bond;
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for (n = 0; n < nimproperlist; n++) {
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i1 = improperlist[n][0];
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i2 = improperlist[n][1];
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i3 = improperlist[n][2];
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i4 = improperlist[n][3];
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type = improperlist[n][4];
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// geometry of 4-body
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// 1 is the central atom
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// 2-3-4 are ment to be equivalent
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// I need the bonds between 2-3 and 2-4 to get the plane normal
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// Then I need the bond 1-2 to project it onto the normal to the plane
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// bond 1->2
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xab = x[i2][0] - x[i1][0];
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yab = x[i2][1] - x[i1][1];
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zab = x[i2][2] - x[i1][2];
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domain->minimum_image(xab,yab,zab);
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// bond 1->3
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xac = x[i3][0] - x[i1][0];
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yac = x[i3][1] - x[i1][1];
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zac = x[i3][2] - x[i1][2];
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domain->minimum_image(xac,yac,zac);
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// bond 1->4
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xad = x[i4][0] - x[i1][0];
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yad = x[i4][1] - x[i1][1];
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zad = x[i4][2] - x[i1][2];
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domain->minimum_image(xad,yad,zad);
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// bond 2-3
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xbc = x[i3][0] - x[i2][0];
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ybc = x[i3][1] - x[i2][1];
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zbc = x[i3][2] - x[i2][2];
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domain->minimum_image(xbc,ybc,zbc);
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// bond 2-4
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xbd = x[i4][0] - x[i2][0];
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ybd = x[i4][1] - x[i2][1];
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zbd = x[i4][2] - x[i2][2];
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domain->minimum_image(xbd,ybd,zbd);
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xna = ybc*zbd - zbc*ybd;
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yna = -(xbc*zbd - zbc*xbd);
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zna = xbc*ybd - ybc*xbd;
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rna = 1.0 / sqrt(xna*xna+yna*yna+zna*zna);
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xna *= rna;
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yna *= rna;
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zna *= rna;
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da = xna*xab + yna*yab + zna*zab;
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domega = k[type]*da*da + chi[type]*da*da*da*da;
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//printf("%3i %3i %3i %3i %10.5f %10.5f \n",i1,i2,i3,i4,da,domega);
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a = 2.0* (k[type]*da + 2.0*chi[type]*da*da*da);
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if (eflag) eimproper = domega;
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f1[0] = a*( xna);
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f1[1] = a*( yna);
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f1[2] = a*( zna);
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f2[0] = a*( -xna -yab*(zbd-zbc)*rna +zab*(ybd-ybc)*rna -da*( -yna*(zbd-zbc) + zna*(ybd-ybc) )*rna);
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f2[1] = a*( +xab*(zbd-zbc)*rna -yna +zab*(xbc-xbd)*rna -da*( +xna*(zbd-zbc) + zna*(xbc-xbd) )*rna);
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f2[2] = a*( -xab*(ybd-ybc)*rna -yab*(xbc-xbd)*rna -zna -da*( +xna*(ybc-ybd) - yna*(xbc-xbd) )*rna);
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f3[0] = a*( ( yab*zbd -zab*ybd ) *rna +da*( -yna*zbd +zna*ybd )*rna);
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f3[1] = a*( ( -xab*zbd +zab*xbd ) *rna +da*( +xna*zbd -zna*xbd )*rna);
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f3[2] = a*( ( +xab*ybd -yab*xbd ) *rna +da*( -xna*ybd +yna*xbd )*rna);
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f4[0] = a*( ( -yab*zbc +zab*ybc ) *rna -da*( -yna*zbc +zna*ybc )*rna);
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f4[1] = a*( ( +xab*zbc -zab*xbc ) *rna -da*( +xna*zbc -zna*xbc )*rna);
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f4[2] = a*( ( -xab*ybc +yab*xbc ) *rna -da*( -xna*ybc +yna*xbc )*rna);
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//printf("%10.5f %10.5f %10.5f \n",f1[0],f1[1],f1[2]);
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//printf("%10.5f %10.5f %10.5f \n",f2[0],f2[1],f2[2]);
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//printf("%10.5f %10.5f %10.5f \n",f3[0],f3[1],f3[2]);
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//printf("%10.5f %10.5f %10.5f \n",f4[0],f4[1],f4[2]);
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// apply force to each of 4 atoms
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if (newton_bond || i1 < nlocal) {
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f[i1][0] += f1[0];
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f[i1][1] += f1[1];
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f[i1][2] += f1[2];
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}
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if (newton_bond || i2 < nlocal) {
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f[i2][0] += f2[0];
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f[i2][1] += f2[1];
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f[i2][2] += f2[2];
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}
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if (newton_bond || i3 < nlocal) {
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f[i3][0] += f3[0];
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f[i3][1] += f3[1];
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f[i3][2] += f3[2];
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}
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if (newton_bond || i4 < nlocal) {
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f[i4][0] += f4[0];
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f[i4][1] += f4[1];
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f[i4][2] += f4[2];
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}
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if (evflag)
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ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f2,f3,f4,
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xab,yab,zab,xac,yac,zac,xad-xac,yad-yac,zad-zac);
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}
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}
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/* ---------------------------------------------------------------------- */
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void ImproperDistance::allocate()
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{
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allocated = 1;
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int n = atom->nimpropertypes;
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memory->create(k,n+1,"improper:k");
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memory->create(chi,n+1,"improper:chi");
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memory->create(setflag,n+1,"improper:setflag");
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for (int i = 1; i <= n; i++) setflag[i] = 0;
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}
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/* ----------------------------------------------------------------------
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set coeffs for one type
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------------------------------------------------------------------------- */
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void ImproperDistance::coeff(int narg, char **arg)
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{
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// if (which > 0) return;
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if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients");
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if (!allocated) allocate();
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int ilo,ihi;
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force->bounds(arg[0],atom->nimpropertypes,ilo,ihi);
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double k_one = force->numeric(FLERR,arg[1]);
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double chi_one = force->numeric(FLERR,arg[2]);
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// convert chi from degrees to radians
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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k[i] = k_one;
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//chi[i] = chi_one/180.0 * PI;
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chi[i] = chi_one;
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setflag[i] = 1;
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count++;
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}
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if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients");
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}
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/* ----------------------------------------------------------------------
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proc 0 writes out coeffs to restart file
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------------------------------------------------------------------------- */
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void ImproperDistance::write_restart(FILE *fp)
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{
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fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp);
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fwrite(&chi[1],sizeof(double),atom->nimpropertypes,fp);
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}
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/* ----------------------------------------------------------------------
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proc 0 reads coeffs from restart file, bcasts them
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------------------------------------------------------------------------- */
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void ImproperDistance::read_restart(FILE *fp)
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{
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allocate();
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if (comm->me == 0) {
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fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
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fread(&chi[1],sizeof(double),atom->nimpropertypes,fp);
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}
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MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
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for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
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}
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@ -0,0 +1,47 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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||||
the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef IMPROPER_CLASS
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ImproperStyle(distance,ImproperDistance)
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#else
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#ifndef LMP_IMPROPER_DISTANCE_H
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#define LMP_IMPROPER_DISTANCE_H
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#include <stdio.h>
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#include "improper.h"
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namespace LAMMPS_NS {
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class ImproperDistance : public Improper {
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public:
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ImproperDistance(class LAMMPS *);
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~ImproperDistance();
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void compute(int, int);
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void coeff(int, char **);
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void write_restart(FILE *);
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void read_restart(FILE *);
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private:
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double *k,*chi;
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void allocate();
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};
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}
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#endif
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#endif
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@ -0,0 +1,433 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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|
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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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.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Paolo Raiteri (Curtin University)
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------------------------------------------------------------------------- */
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#include <math.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include "pair_buck_mdf.h"
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#include "atom.h"
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#include "comm.h"
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#include "force.h"
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#include "neigh_list.h"
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#include "math_const.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace MathConst;
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/* ---------------------------------------------------------------------- */
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PairBuckMDF::PairBuckMDF(LAMMPS *lmp) : Pair(lmp) {}
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/* ---------------------------------------------------------------------- */
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PairBuckMDF::~PairBuckMDF()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(cutsq);
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memory->destroy(cut);
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memory->destroy(cut_inner);
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memory->destroy(cut_inner_sq);
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memory->destroy(a);
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memory->destroy(rho);
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memory->destroy(c);
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memory->destroy(rhoinv);
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memory->destroy(buck1);
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memory->destroy(buck2);
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memory->destroy(offset);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairBuckMDF::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
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double rsq,r2inv,r6inv,forcebuck,factor_lj;
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double r,rexp,phibuck;
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int *ilist,*jlist,*numneigh,**firstneigh;
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double dp, d, tt, dt, dd;
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evdwl = 0.0;
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = vflag_fdotr = 0;
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double **x = atom->x;
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double **f = atom->f;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// loop over neighbors of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
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;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
r = sqrt(rsq);
|
||||
rexp = exp(-r*rhoinv[itype][jtype]);
|
||||
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
|
||||
if (rsq > cut_inner_sq[itype][jtype]) {
|
||||
phibuck = a[itype][jtype]*rexp - c[itype][jtype]*r6inv;
|
||||
dp = (cut[itype][jtype] - cut_inner[itype][jtype]);
|
||||
d = (r-cut_inner[itype][jtype]) / dp;
|
||||
dd = 1.-d;
|
||||
// taperig function - mdf style
|
||||
tt = (1. + 3.*d + 6.*d*d)*dd*dd*dd;
|
||||
// minus the derivative of the tapering function
|
||||
dt = 30.* d*d * dd*dd * r / dp;
|
||||
|
||||
forcebuck = forcebuck*tt + phibuck*dt;
|
||||
} else {
|
||||
tt = 1;
|
||||
}
|
||||
|
||||
fpair = factor_lj*forcebuck*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) {
|
||||
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv;
|
||||
if (rsq > cut_inner_sq[itype][jtype]) evdwl *= tt;
|
||||
|
||||
evdwl *= factor_lj;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,0.0,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBuckMDF::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
|
||||
memory->create(cut,n+1,n+1,"pair:cut_lj");
|
||||
memory->create(cut_inner,n+1,n+1,"pair:cut_inner");
|
||||
memory->create(cut_inner_sq,n+1,n+1,"pair:cut_inner_sq");
|
||||
memory->create(a,n+1,n+1,"pair:a");
|
||||
memory->create(rho,n+1,n+1,"pair:rho");
|
||||
memory->create(c,n+1,n+1,"pair:c");
|
||||
memory->create(rhoinv,n+1,n+1,"pair:rhoinv");
|
||||
memory->create(buck1,n+1,n+1,"pair:buck1");
|
||||
memory->create(buck2,n+1,n+1,"pair:buck2");
|
||||
memory->create(offset,n+1,n+1,"pair:offset");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBuckMDF::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
cut_inner_global = force->numeric(FLERR,arg[0]);
|
||||
cut_global = force->numeric(FLERR,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[i][j] = cut_global;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBuckMDF::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 5 && narg != 7) error->all(FLERR,"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 = force->numeric(FLERR,arg[2]);
|
||||
double rho_one = force->numeric(FLERR,arg[3]);
|
||||
if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
double c_one = force->numeric(FLERR,arg[4]);
|
||||
|
||||
double cut_inner_one = cut_inner_global;
|
||||
double cut_one = cut_global;
|
||||
if (narg == 7) {
|
||||
cut_inner_one = force->numeric(FLERR,arg[5]);
|
||||
cut_one = force->numeric(FLERR,arg[6]);
|
||||
}
|
||||
if (cut_inner_global <= 0.0 || cut_inner_global > cut_global)
|
||||
error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
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;
|
||||
c[i][j] = c_one;
|
||||
cut[i][j] = cut_one;
|
||||
cut[j][i] = cut_one;
|
||||
cut_inner[i][j] = cut_inner_one;
|
||||
cut_inner[j][i] = cut_inner_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairBuckMDF::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
|
||||
|
||||
rhoinv[i][j] = 1.0/rho[i][j];
|
||||
buck1[i][j] = a[i][j]/rho[i][j];
|
||||
buck2[i][j] = 6.0*c[i][j];
|
||||
|
||||
if (offset_flag) {
|
||||
double rexp = exp(-cut[i][j]/rho[i][j]);
|
||||
offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut[i][j],6.0);
|
||||
} else offset[i][j] = 0.0;
|
||||
|
||||
cut_inner[j][i] = cut_inner[i][j];
|
||||
cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][j];
|
||||
cut_inner_sq[j][i] = cut_inner_sq[i][j];
|
||||
|
||||
a[j][i] = a[i][j];
|
||||
c[j][i] = c[i][j];
|
||||
rhoinv[j][i] = rhoinv[i][j];
|
||||
buck1[j][i] = buck1[i][j];
|
||||
buck2[j][i] = buck2[i][j];
|
||||
offset[j][i] = offset[i][j];
|
||||
|
||||
// compute I,J contribution to long-range tail correction
|
||||
// count total # of atoms of type I and J via Allreduce
|
||||
|
||||
if (tail_flag) {
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double count[2],all[2];
|
||||
count[0] = count[1] = 0.0;
|
||||
for (int k = 0; k < nlocal; k++) {
|
||||
if (type[k] == i) count[0] += 1.0;
|
||||
if (type[k] == j) count[1] += 1.0;
|
||||
}
|
||||
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
double rho1 = rho[i][j];
|
||||
double rho2 = rho1*rho1;
|
||||
double rho3 = rho2*rho1;
|
||||
double rc = cut[i][j];
|
||||
double rc2 = rc*rc;
|
||||
double rc3 = rc2*rc;
|
||||
etail_ij = 2.0*MY_PI*all[0]*all[1]*
|
||||
(a[i][j]*exp(-rc/rho1)*rho1*(rc2 + 2.0*rho1*rc + 2.0*rho2) -
|
||||
c[i][j]/(3.0*rc3));
|
||||
ptail_ij = (-1/3.0)*2.0*MY_PI*all[0]*all[1]*
|
||||
(-a[i][j]*exp(-rc/rho1)*
|
||||
(rc3 + 3.0*rho1*rc2 + 6.0*rho2*rc + 6.0*rho3) + 2.0*c[i][j]/rc3);
|
||||
}
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBuckMDF::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(&c[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBuckMDF::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(&c[i][j],sizeof(double),1,fp);
|
||||
fread(&cut[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(&c[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBuckMDF::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&cut_global,sizeof(double),1,fp);
|
||||
fwrite(&offset_flag,sizeof(int),1,fp);
|
||||
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||
fwrite(&tail_flag,sizeof(int),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBuckMDF::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
fread(&cut_global,sizeof(double),1,fp);
|
||||
fread(&offset_flag,sizeof(int),1,fp);
|
||||
fread(&mix_flag,sizeof(int),1,fp);
|
||||
fread(&tail_flag,sizeof(int),1,fp);
|
||||
}
|
||||
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairBuckMDF::single(int i, int j, int itype, int jtype,
|
||||
double rsq, double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double r2inv,r6inv,r,rexp,forcebuck,phibuck;
|
||||
double dp, d, tt, dt, dd;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
r = sqrt(rsq);
|
||||
rexp = exp(-r*rhoinv[itype][jtype]);
|
||||
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
|
||||
phibuck = a[itype][jtype]*rexp - c[itype][jtype]*r6inv;
|
||||
|
||||
if (rsq > cut_inner_sq[itype][jtype]) {
|
||||
|
||||
dp = (cut[itype][jtype] - cut_inner[itype][jtype]);
|
||||
d = (r - cut_inner[itype][jtype]) / dp;
|
||||
dd = 1-d;
|
||||
tt = (1. + 3.*d + 6.*d*d)* dd*dd*dd;
|
||||
dt = 30.* d*d * dd*dd * r / dp;
|
||||
|
||||
forcebuck = forcebuck*tt + phibuck*dt;
|
||||
phibuck *= tt;
|
||||
}
|
||||
|
||||
fforce = factor_lj*forcebuck*r2inv;
|
||||
|
||||
return factor_lj*phibuck;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairBuckMDF::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 2;
|
||||
if (strcmp(str,"aparm") == 0) return (void *) a;
|
||||
if (strcmp(str,"cparm") == 0) return (void *) c;
|
||||
return NULL;
|
||||
}
|
||||
|
|
@ -0,0 +1,73 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(buck/mdf,PairBuckMDF)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_BUCK_MDF_H
|
||||
#define LMP_PAIR_BUCK_MDF_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairBuckMDF : public Pair {
|
||||
public:
|
||||
PairBuckMDF(class LAMMPS *);
|
||||
virtual ~PairBuckMDF();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
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(const char *, int &);
|
||||
|
||||
protected:
|
||||
double cut_global,cut_inner_global;
|
||||
double **cut,**cut_inner,**cut_inner_sq;
|
||||
double **a,**rho,**c;
|
||||
double **rhoinv,**buck1,**buck2,**offset;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: All pair coeffs are not set
|
||||
|
||||
All pair coefficients must be set in the data file or by the
|
||||
pair_coeff command before running a simulation.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,395 @@
|
|||
|
||||
/* ----------------------------------------------------------------------
|
||||
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: Paolo Raiteri (Curtin University)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "pair_lennard_mdf.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJ_AB_MDF::PairLJ_AB_MDF(LAMMPS *lmp) : Pair(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJ_AB_MDF::~PairLJ_AB_MDF()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut);
|
||||
memory->destroy(cut_inner);
|
||||
memory->destroy(cut_inner_sq);
|
||||
memory->destroy(aparm);
|
||||
memory->destroy(bparm);
|
||||
memory->destroy(lj1);
|
||||
memory->destroy(lj2);
|
||||
memory->destroy(lj3);
|
||||
memory->destroy(lj4);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJ_AB_MDF::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||
double rsq,r2inv,r6inv,forcelj,factor_lj;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
double rr, d, dd, tt, dt, dp, philj;
|
||||
|
||||
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];
|
||||
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];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
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;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||
|
||||
if (rsq > cut_inner_sq[itype][jtype]) {
|
||||
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
|
||||
|
||||
rr = sqrt(rsq);
|
||||
dp = (cut[itype][jtype] - cut_inner[itype][jtype]);
|
||||
d = (rr-cut_inner[itype][jtype]) / dp;
|
||||
dd = 1.-d;
|
||||
// taperig function - mdf style
|
||||
tt = (1. + 3.*d + 6.*d*d)*dd*dd*dd;
|
||||
// minus the derivative of the tapering function
|
||||
dt = 30.* d*d * dd*dd * rr / dp;
|
||||
|
||||
forcelj = forcelj*tt + philj*dt;
|
||||
} else {
|
||||
tt = 1;
|
||||
}
|
||||
fpair = factor_lj*forcelj*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) {
|
||||
evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
|
||||
if (rsq > cut_inner_sq[itype][jtype]) evdwl *= tt;
|
||||
|
||||
evdwl *= factor_lj;
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,0.0,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJ_AB_MDF::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
|
||||
memory->create(cut,n+1,n+1,"pair:cut");
|
||||
memory->create(cut_inner,n+1,n+1,"pair:cut_inner");
|
||||
memory->create(cut_inner_sq,n+1,n+1,"pair:cut_inner_sq");
|
||||
memory->create(aparm,n+1,n+1,"pair:aparm");
|
||||
memory->create(bparm,n+1,n+1,"pair:bparm");
|
||||
memory->create(lj1,n+1,n+1,"pair:lj1");
|
||||
memory->create(lj2,n+1,n+1,"pair:lj2");
|
||||
memory->create(lj3,n+1,n+1,"pair:lj3");
|
||||
memory->create(lj4,n+1,n+1,"pair:lj4");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJ_AB_MDF::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
cut_inner_global = force->numeric(FLERR,arg[0]);
|
||||
cut_global = force->numeric(FLERR,arg[1]);
|
||||
|
||||
if (cut_inner_global <= 0.0 || cut_inner_global > cut_global)
|
||||
error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
// 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_inner[i][j] = cut_inner_global;
|
||||
cut[i][j] = cut_global;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJ_AB_MDF::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4 && narg != 6)
|
||||
error->all(FLERR,"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 aparm_one = force->numeric(FLERR,arg[2]);
|
||||
double bparm_one = force->numeric(FLERR,arg[3]);
|
||||
|
||||
double cut_inner_one = cut_inner_global;
|
||||
double cut_one = cut_global;
|
||||
if (narg == 6) {
|
||||
cut_inner_one = force->numeric(FLERR,arg[4]);
|
||||
cut_one = force->numeric(FLERR,arg[5]);
|
||||
}
|
||||
if (cut_inner_global <= 0.0 || cut_inner_global > cut_global)
|
||||
error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
aparm[i][j] = aparm_one;
|
||||
bparm[i][j] = bparm_one;
|
||||
cut_inner[i][j] = cut_inner_one;
|
||||
cut[i][j] = cut_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairLJ_AB_MDF::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) {
|
||||
aparm[i][j] = mix_energy(aparm[i][i],aparm[j][j],
|
||||
bparm[i][i],bparm[j][j]);
|
||||
bparm[i][j] = mix_distance(bparm[i][i],bparm[j][j]);
|
||||
cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]);
|
||||
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
|
||||
}
|
||||
|
||||
cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][j];
|
||||
|
||||
lj1[i][j] = 12.0 * aparm[i][j];
|
||||
lj2[i][j] = 6.0 * bparm[i][j];
|
||||
lj3[i][j] = aparm[i][j];
|
||||
lj4[i][j] = bparm[i][j];
|
||||
|
||||
cut_inner[j][i] = cut_inner[i][j];
|
||||
cut_inner_sq[j][i] = cut_inner_sq[i][j];
|
||||
lj1[j][i] = lj1[i][j];
|
||||
lj2[j][i] = lj2[i][j];
|
||||
lj3[j][i] = lj3[i][j];
|
||||
lj4[j][i] = lj4[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJ_AB_MDF::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(&aparm[i][j],sizeof(double),1,fp);
|
||||
fwrite(&bparm[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut_inner[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJ_AB_MDF::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(&aparm[i][j],sizeof(double),1,fp);
|
||||
fread(&bparm[i][j],sizeof(double),1,fp);
|
||||
fread(&cut_inner[i][j],sizeof(double),1,fp);
|
||||
fread(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&aparm[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&bparm[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJ_AB_MDF::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJ_AB_MDF::read_restart_settings(FILE *fp)
|
||||
{
|
||||
int me = comm->me;
|
||||
if (me == 0) {
|
||||
fread(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJ_AB_MDF::single(int i, int j, int itype, int jtype,
|
||||
double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double r2inv,r6inv,forcelj,philj;
|
||||
double rr, dp, d, tt, dt, dd;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
|
||||
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||
|
||||
if (rsq > cut_inner_sq[itype][jtype]) {
|
||||
|
||||
rr = sqrt(rsq);
|
||||
dp = (cut[itype][jtype] - cut_inner[itype][jtype]);
|
||||
d = (rr - cut_inner[itype][jtype]) / dp;
|
||||
dd = 1-d;
|
||||
tt = (1. + 3.*d + 6.*d*d)* dd*dd*dd;
|
||||
dt = 30.* d*d * dd*dd * rr / dp;
|
||||
|
||||
forcelj = forcelj*tt + philj*dt;
|
||||
philj *= dt;
|
||||
}
|
||||
|
||||
fforce = factor_lj*forcelj*r2inv;
|
||||
|
||||
return factor_lj*philj;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairLJ_AB_MDF::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 2;
|
||||
if (strcmp(str,"aparm") == 0) return (void *) aparm;
|
||||
if (strcmp(str,"bparm") == 0) return (void *) bparm;
|
||||
return NULL;
|
||||
}
|
||||
|
|
@ -0,0 +1,69 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lennard/mdf,PairLJ_AB_MDF)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_AB_MDF_H
|
||||
#define LMP_PAIR_LJ_AB_MDF_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJ_AB_MDF : public Pair {
|
||||
public:
|
||||
PairLJ_AB_MDF(class LAMMPS *);
|
||||
virtual ~PairLJ_AB_MDF();
|
||||
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
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(const char *, int &);
|
||||
|
||||
protected:
|
||||
double cut_global,cut_inner_global;
|
||||
double **cut,**cut_inner,**cut_inner_sq;
|
||||
double **aparm,**bparm;
|
||||
double **lj1,**lj2,**lj3,**lj4;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,395 @@
|
|||
|
||||
/* ----------------------------------------------------------------------
|
||||
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: Paolo Raiteri (Curtin University)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "pair_lj_mdf.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJMDF::PairLJMDF(LAMMPS *lmp) : Pair(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJMDF::~PairLJMDF()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut);
|
||||
memory->destroy(cut_inner);
|
||||
memory->destroy(cut_inner_sq);
|
||||
memory->destroy(epsilon);
|
||||
memory->destroy(sigma);
|
||||
memory->destroy(lj1);
|
||||
memory->destroy(lj2);
|
||||
memory->destroy(lj3);
|
||||
memory->destroy(lj4);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJMDF::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||
double rsq,r2inv,r6inv,forcelj,factor_lj;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
double rr, d, dd, tt, dt, dp, philj;
|
||||
|
||||
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];
|
||||
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];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
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;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||
|
||||
if (rsq > cut_inner_sq[itype][jtype]) {
|
||||
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
|
||||
|
||||
rr = sqrt(rsq);
|
||||
dp = (cut[itype][jtype] - cut_inner[itype][jtype]);
|
||||
d = (rr-cut_inner[itype][jtype]) / dp;
|
||||
dd = 1.-d;
|
||||
// taperig function - mdf style
|
||||
tt = (1. + 3.*d + 6.*d*d)*dd*dd*dd;
|
||||
// minus the derivative of the tapering function
|
||||
dt = 30.* d*d * dd*dd * rr / dp;
|
||||
|
||||
forcelj = forcelj*tt + philj*dt;
|
||||
} else {
|
||||
tt = 1;
|
||||
}
|
||||
fpair = factor_lj*forcelj*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) {
|
||||
evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
|
||||
if (rsq > cut_inner_sq[itype][jtype]) evdwl *= tt;
|
||||
|
||||
evdwl *= factor_lj;
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,0.0,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJMDF::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
|
||||
memory->create(cut,n+1,n+1,"pair:cut");
|
||||
memory->create(cut_inner,n+1,n+1,"pair:cut_inner");
|
||||
memory->create(cut_inner_sq,n+1,n+1,"pair:cut_inner_sq");
|
||||
memory->create(epsilon,n+1,n+1,"pair:epsilon");
|
||||
memory->create(sigma,n+1,n+1,"pair:sigma");
|
||||
memory->create(lj1,n+1,n+1,"pair:lj1");
|
||||
memory->create(lj2,n+1,n+1,"pair:lj2");
|
||||
memory->create(lj3,n+1,n+1,"pair:lj3");
|
||||
memory->create(lj4,n+1,n+1,"pair:lj4");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJMDF::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
cut_inner_global = force->numeric(FLERR,arg[0]);
|
||||
cut_global = force->numeric(FLERR,arg[1]);
|
||||
|
||||
if (cut_inner_global <= 0.0 || cut_inner_global > cut_global)
|
||||
error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
// 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_inner[i][j] = cut_inner_global;
|
||||
cut[i][j] = cut_global;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJMDF::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4 && narg != 6)
|
||||
error->all(FLERR,"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 epsilon_one = force->numeric(FLERR,arg[2]);
|
||||
double sigma_one = force->numeric(FLERR,arg[3]);
|
||||
|
||||
double cut_inner_one = cut_inner_global;
|
||||
double cut_one = cut_global;
|
||||
if (narg == 6) {
|
||||
cut_inner_one = force->numeric(FLERR,arg[4]);
|
||||
cut_one = force->numeric(FLERR,arg[5]);
|
||||
}
|
||||
if (cut_inner_global <= 0.0 || cut_inner_global > cut_global)
|
||||
error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
epsilon[i][j] = epsilon_one;
|
||||
sigma[i][j] = sigma_one;
|
||||
cut_inner[i][j] = cut_inner_one;
|
||||
cut[i][j] = cut_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairLJMDF::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) {
|
||||
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
|
||||
sigma[i][i],sigma[j][j]);
|
||||
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
|
||||
cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]);
|
||||
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
|
||||
}
|
||||
|
||||
cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][j];
|
||||
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
|
||||
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
|
||||
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
|
||||
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
|
||||
|
||||
cut[j][i] = cut[i][j]; // BUG FIX
|
||||
cut_inner[j][i] = cut_inner[i][j];
|
||||
cut_inner_sq[j][i] = cut_inner_sq[i][j];
|
||||
lj1[j][i] = lj1[i][j];
|
||||
lj2[j][i] = lj2[i][j];
|
||||
lj3[j][i] = lj3[i][j];
|
||||
lj4[j][i] = lj4[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJMDF::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(&epsilon[i][j],sizeof(double),1,fp);
|
||||
fwrite(&sigma[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut_inner[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJMDF::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(&epsilon[i][j],sizeof(double),1,fp);
|
||||
fread(&sigma[i][j],sizeof(double),1,fp);
|
||||
fread(&cut_inner[i][j],sizeof(double),1,fp);
|
||||
fread(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJMDF::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJMDF::read_restart_settings(FILE *fp)
|
||||
{
|
||||
int me = comm->me;
|
||||
if (me == 0) {
|
||||
fread(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJMDF::single(int i, int j, int itype, int jtype,
|
||||
double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double r2inv,r6inv,forcelj,philj;
|
||||
double rr, dp, d, tt, dt, dd;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
|
||||
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||
|
||||
if (rsq > cut_inner_sq[itype][jtype]) {
|
||||
|
||||
rr = sqrt(rsq);
|
||||
dp = (cut[itype][jtype] - cut_inner[itype][jtype]);
|
||||
d = (rr - cut_inner[itype][jtype]) / dp;
|
||||
dd = 1-d;
|
||||
tt = (1. + 3.*d + 6.*d*d)* dd*dd*dd;
|
||||
dt = 30.* d*d * dd*dd * rr / dp;
|
||||
|
||||
forcelj = forcelj*tt + philj*dt;
|
||||
philj *= tt;
|
||||
}
|
||||
|
||||
fforce = factor_lj*forcelj*r2inv;
|
||||
|
||||
return factor_lj*philj;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairLJMDF::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 2;
|
||||
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
|
||||
if (strcmp(str,"sigma") == 0) return (void *) sigma;
|
||||
return NULL;
|
||||
}
|
||||
|
|
@ -0,0 +1,69 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/mdf,PairLJMDF)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_MDF_H
|
||||
#define LMP_PAIR_LJ_MDF_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJMDF : public Pair {
|
||||
public:
|
||||
PairLJMDF(class LAMMPS *);
|
||||
virtual ~PairLJMDF();
|
||||
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
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(const char *, int &);
|
||||
|
||||
protected:
|
||||
double cut_global,cut_inner_global;
|
||||
double **cut,**cut_inner,**cut_inner_sq;
|
||||
double **epsilon,**sigma;
|
||||
double **lj1,**lj2,**lj3,**lj4;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue