forked from lijiext/lammps
coding style and whitespace cleanup to match LAMMPS style
This commit is contained in:
Axel Kohlmeyer
parent
9fa4588eb7
commit
6eddc1a2ee
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@ -11,13 +11,25 @@
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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/* ----------------------------------------------------------------------
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Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com
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------------------------------------------------------------------------- */
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#include <math.h>
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#include "math_extra.h"
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#include "fix_wall_ees.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "atom_vec_ellipsoid.h"
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#include "domain.h"
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#include "region.h"
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#include "force.h"
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#include "lattice.h"
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#include "update.h"
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#include "output.h"
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#include "respa.h"
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#include "error.h"
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#include "math_extra.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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@ -96,13 +108,13 @@ void FixWallEES::wall_particle(int m, int which, double coord)
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (side < 0)
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delta = x[i][dim] - coord;
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if (side < 0)
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delta = x[i][dim] - coord;
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else
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delta = coord - x[i][dim];
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delta = coord - x[i][dim];
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if (delta >= cutoff[m])
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continue;
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continue;
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double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}};
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double tempvec[3]= {0,0,0};
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@ -168,37 +180,37 @@ void FixWallEES::wall_particle(int m, int which, double coord)
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hms = delta - sigman;
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fwall = side*(
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-1*coeff4[m]/hhss2 +
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coeff3[m] * ( 21*delta6 + 63*delta4*sigman2 + 27*delta2*sigman4 + sigman6 ) / hhss8
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);
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f[i][dim] -= fwall;
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-1*coeff4[m]/hhss2 +
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coeff3[m] * ( 21*delta6 + 63*delta4*sigman2 + 27*delta2*sigman4 + sigman6 ) / hhss8
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);
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f[i][dim] -= fwall;
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ewall[0] += -1*coeff2[m] * ( 4*delta/sigman2/hhss + 2*log(hms/hps)/sigman3 ) +
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coeff1[m] * ( 35*delta5 + 70*delta3*sigman2 + 15*delta*sigman4 ) / hhss7;
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ewall[0] += -1*coeff2[m] * ( 4*delta/sigman2/hhss + 2*log(hms/hps)/sigman3 ) +
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coeff1[m] * ( 35*delta5 + 70*delta3*sigman2 + 15*delta*sigman4 ) / hhss7;
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ewall[m+1] += fwall;
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ewall[m+1] += fwall;
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twall = coeff6[m] * ( 6.*delta3/sigman4/hhss2 - 10.*delta/sigman2/hhss2 + 3.*log(hms/hps)/sigman5 ) +
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coeff5[m] * ( 21.*delta5 + 30.*delta3*sigman2 + 5.*delta*sigman4 ) / hhss8 ;
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twall = coeff6[m] * ( 6.*delta3/sigman4/hhss2 - 10.*delta/sigman2/hhss2 + 3.*log(hms/hps)/sigman5 ) +
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coeff5[m] * ( 21.*delta5 + 30.*delta3*sigman2 + 5.*delta*sigman4 ) / hhss8 ;
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MathExtra::matvec(Lx,nhat,tempvec);
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MathExtra::transpose_matvec(A,tempvec,tempvec2);
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for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
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that[0] = MathExtra::dot3(SAn,tempvec2);
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MathExtra::matvec(Lx,nhat,tempvec);
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MathExtra::transpose_matvec(A,tempvec,tempvec2);
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for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
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that[0] = MathExtra::dot3(SAn,tempvec2);
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MathExtra::matvec(Ly,nhat,tempvec);
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MathExtra::transpose_matvec(A,tempvec,tempvec2);
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for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
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that[1] = MathExtra::dot3(SAn,tempvec2);
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MathExtra::matvec(Ly,nhat,tempvec);
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MathExtra::transpose_matvec(A,tempvec,tempvec2);
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for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
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that[1] = MathExtra::dot3(SAn,tempvec2);
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MathExtra::matvec(Lz,nhat,tempvec);
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MathExtra::transpose_matvec(A,tempvec,tempvec2);
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for(int k = 0; k < 3; k++) tempvec2[k] *= shape[k];
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that[2] = MathExtra::dot3(SAn,tempvec2);
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MathExtra::matvec(Lz,nhat,tempvec);
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MathExtra::transpose_matvec(A,tempvec,tempvec2);
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for(int k = 0; k < 3; k++) tempvec2[k] *= shape[k];
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that[2] = MathExtra::dot3(SAn,tempvec2);
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for(int j = 0; j<3 ; j++)
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for(int j = 0; j<3 ; j++)
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tor[i][j] += twall * that[j];
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}
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@ -1,4 +1,4 @@
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/* -*- c++ -*- ----------------------------------------------------------
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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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@ -10,10 +10,14 @@
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include <iostream>
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#include "math.h"
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#include "stdlib.h"
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#include "string.h"
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/* ----------------------------------------------------------------------
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Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com
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------------------------------------------------------------------------- */
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#include <math.h>
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#include <stdlib.h>
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#include <string.h>
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#include "fix_wall_region_ees.h"
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#include "atom.h"
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#include "atom_vec.h"
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@ -31,117 +35,109 @@
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using namespace LAMMPS_NS;
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using namespace FixConst;
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enum{LJ93,LJ126,COLLOID,HARMONIC,EES};//me
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/* ---------------------------------------------------------------------- */
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/// USAGE:
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/// fix ID group-ID wall/region/ees region-ID epsilon sigma cutoff
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///
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FixWallRegionEES::FixWallRegionEES(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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Fix(lmp, narg, arg)
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{
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if (narg != 7) error->all(FLERR,"Illegal fix wall/region/ees command");
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scalar_flag = 1;
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vector_flag = 1;
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size_vector = 3;
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global_freq = 1;
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extscalar = 1;
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extvector = 1;
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if (narg != 7) error->all(FLERR,"Illegal fix wall/region/ees command");
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scalar_flag = 1;
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vector_flag = 1;
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size_vector = 3;
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global_freq = 1;
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extscalar = 1;
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extvector = 1;
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// parse args
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// parse args
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iregion = domain->find_region(arg[3]);
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix wall/region/ees does not exist");
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int n = strlen(arg[3]) + 1;
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idregion = new char[n];
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strcpy(idregion,arg[3]);
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iregion = domain->find_region(arg[3]);
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix wall/region/ees does not exist");
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int n = strlen(arg[3]) + 1;
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idregion = new char[n];
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strcpy(idregion,arg[3]);
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epsilon = force->numeric(FLERR,arg[4]);
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sigma = force->numeric(FLERR,arg[5]);
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cutoff = force->numeric(FLERR,arg[6]);
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if (cutoff <= 0.0) error->all(FLERR,"Fix wall/region/ees cutoff <= 0.0");
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epsilon = force->numeric(FLERR,arg[4]);
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sigma = force->numeric(FLERR,arg[5]);
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cutoff = force->numeric(FLERR,arg[6]);
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if (cutoff <= 0.0) error->all(FLERR,"Fix wall/region/ees cutoff <= 0.0");
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eflag = 0;
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ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
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eflag = 0;
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ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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FixWallRegionEES::~FixWallRegionEES()
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{
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delete [] idregion;
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delete [] idregion;
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}
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/* ---------------------------------------------------------------------- */
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int FixWallRegionEES::setmask()
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{
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int mask = 0;
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mask |= POST_FORCE;
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mask |= THERMO_ENERGY;
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mask |= POST_FORCE_RESPA;
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mask |= MIN_POST_FORCE;
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return mask;
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int mask = 0;
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mask |= POST_FORCE;
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mask |= THERMO_ENERGY;
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mask |= POST_FORCE_RESPA;
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mask |= MIN_POST_FORCE;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixWallRegionEES::init()
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{
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// set index and check validity of region
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// set index and check validity of region
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iregion = domain->find_region(idregion);
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix wall/region/ees does not exist");
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iregion = domain->find_region(idregion);
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix wall/region/ees does not exist");
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avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
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if (!avec)
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error->all(FLERR,"Fix wall/region/ees requires atom style ellipsoid");
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// check that all particles are finite-size ellipsoids
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// no point particles allowed, spherical is OK
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int *ellipsoid = atom->ellipsoid;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (ellipsoid[i] < 0)
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error->one(FLERR,"Fix wall/region/ees requires extended particles");
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// setup coefficients
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coeff1 = ( 2. / 4725. ) * epsilon * pow(sigma,12.0);
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coeff2 = ( 1. / 24. ) * epsilon * pow(sigma,6.0);
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coeff3 = ( 2. / 315. ) * epsilon * pow(sigma,12.0);
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coeff4 = ( 1. / 3. ) * epsilon * pow(sigma,6.0);
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coeff5 = ( 4. / 315. ) * epsilon * pow(sigma,12.0);
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coeff6 = ( 1. / 12. ) * epsilon * pow(sigma,6.0);
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offset = 0;
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avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
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if (!avec)
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error->all(FLERR,"Fix wall/region/ees requires atom style ellipsoid");
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// check that all particles are finite-size ellipsoids
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// no point particles allowed, spherical is OK
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int *ellipsoid = atom->ellipsoid;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (ellipsoid[i] < 0)
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error->one(FLERR,"Fix wall/region/ees requires extended particles");
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// setup coefficients for each style
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coeff1 = ( 2. / 4725. ) * epsilon * pow(sigma,12.0);
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coeff2 = ( 1. / 24. ) * epsilon * pow(sigma,6.0);
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coeff3 = ( 2. / 315. ) * epsilon * pow(sigma,12.0);
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coeff4 = ( 1. / 3. ) * epsilon * pow(sigma,6.0);
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coeff5 = ( 4. / 315. ) * epsilon * pow(sigma,12.0);
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coeff6 = ( 1. / 12. ) * epsilon * pow(sigma,6.0);
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offset = 0;
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if (strstr(update->integrate_style,"respa"))
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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if (strstr(update->integrate_style,"respa"))
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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}
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/* ---------------------------------------------------------------------- */
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void FixWallRegionEES::setup(int vflag)
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{
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if (strstr(update->integrate_style,"verlet"))
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post_force(vflag);
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else {
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((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
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post_force_respa(vflag,nlevels_respa-1,0);
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((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
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}
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if (strstr(update->integrate_style,"verlet"))
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post_force(vflag);
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else {
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((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
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post_force_respa(vflag,nlevels_respa-1,0);
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((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
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}
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}
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/* ---------------------------------------------------------------------- */
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@ -155,121 +151,111 @@ void FixWallRegionEES::min_setup(int vflag)
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void FixWallRegionEES::post_force(int vflag)
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{
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//me
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//sth is needed here, but I dont know what
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//that is calculation of sn
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//sth is needed here, but I dont know what
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//that is calculation of sn
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int i,m,n;
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double rinv,fx,fy,fz,tooclose[3];//me
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double sn;//me
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int i,m,n;
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double rinv,fx,fy,fz,sn,tooclose[3];
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eflag = 0;
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ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
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eflag = 0;
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ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
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double **x = atom->x;
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double **f = atom->f;
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double *radius = atom->radius;
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double **x = atom->x;
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double **f = atom->f;
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double **tor = atom->torque;
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double **tor = atom->torque; //me
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AtomVecEllipsoid::Bonus *bonus = avec->bonus;
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int *ellipsoid = atom->ellipsoid;
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//avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");//me
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AtomVecEllipsoid::Bonus *bonus = avec->bonus;//me
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int *ellipsoid = atom->ellipsoid;//me
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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Region *region = domain->regions[iregion];
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region->prematch();
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Region *region = domain->regions[iregion];
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region->prematch();
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int onflag = 0;
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int onflag = 0;
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// region->match() insures particle is in region or on surface, else error
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// if returned contact dist r = 0, is on surface, also an error
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// in COLLOID case, r <= radius is an error
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// region->match() insures particle is in region or on surface, else error
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// if returned contact dist r = 0, is on surface, also an error
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// in COLLOID case, r <= radius is an error
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (!region->match(x[i][0],x[i][1],x[i][2])) {
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onflag = 1;
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continue;
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}
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (!region->match(x[i][0],x[i][1],x[i][2])) {
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onflag = 1;
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continue;
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}
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double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}};
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double tempvec[3]= {0,0,0};
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double sn2 = 0.0;
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double nhat[3] = {0,0,0};
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double* shape = bonus[ellipsoid[i]].shape;;
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MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);
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double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}};
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double tempvec[3]= {0,0,0};
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double sn2 = 0.0;
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double nhat[3] = {0,0,0};
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double* shape = bonus[ellipsoid[i]].shape;;
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MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);
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for(int which = 0 ; which < 3; which ++){//me
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nhat[which]=1;
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nhat[(which+1)%3] = 0 ;
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nhat[(which+2)%3] = 0 ;
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sn2 = 0 ;
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MathExtra::transpose_matvec(A,nhat,tempvec);
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for(int k = 0; k<3; k++) tempvec[k] *= shape[k];
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for(int k = 0; k<3 ; k++) sn2 += tempvec[k]*tempvec[k];
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sn = sqrt(sn2);
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tooclose[which] = sn;
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}
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for(int which = 0 ; which < 3; which ++){//me
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nhat[which]=1;
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nhat[(which+1)%3] = 0 ;
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nhat[(which+2)%3] = 0 ;
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sn2 = 0 ;
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MathExtra::transpose_matvec(A,nhat,tempvec);
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for(int k = 0; k<3; k++) tempvec[k] *= shape[k];
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for(int k = 0; k<3 ; k++) sn2 += tempvec[k]*tempvec[k];
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sn = sqrt(sn2);
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tooclose[which] = sn;
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}
|
||||
n = region->surface(x[i][0],x[i][1],x[i][2],cutoff);
|
||||
|
||||
for (m = 0; m < n; m++) {
|
||||
|
||||
if (region->contact[m].delx != 0 && region->contact[m].r <= tooclose[0]){
|
||||
onflag = 1;
|
||||
continue;
|
||||
} else if (region->contact[m].dely != 0 && region->contact[m].r <= tooclose[1]){
|
||||
onflag = 1;
|
||||
continue;
|
||||
} else if (region->contact[m].delz !=0 && region->contact[m].r <= tooclose[2]){
|
||||
onflag = 1;
|
||||
continue;
|
||||
} else rinv = 1.0/region->contact[m].r;
|
||||
|
||||
n = region->surface(x[i][0],x[i][1],x[i][2],cutoff);
|
||||
ees(m,i);
|
||||
|
||||
for (m = 0; m < n; m++) {
|
||||
ewall[0] += eng;
|
||||
fx = fwall * region->contact[m].delx * rinv;
|
||||
fy = fwall * region->contact[m].dely * rinv;
|
||||
fz = fwall * region->contact[m].delz * rinv;
|
||||
f[i][0] += fx;
|
||||
f[i][1] += fy;
|
||||
f[i][2] += fz;
|
||||
|
||||
if(region->contact[m].delx != 0 && region->contact[m].r <= tooclose[0] ){
|
||||
onflag = 1;
|
||||
continue;
|
||||
ewall[1] -= fx;
|
||||
ewall[2] -= fy;
|
||||
ewall[3] -= fz;
|
||||
|
||||
}else if (region->contact[m].dely != 0 && region->contact[m].r <= tooclose[1]){
|
||||
onflag = 1;
|
||||
continue;
|
||||
}else if (region->contact[m].delz !=0 && region->contact[m].r <= tooclose[2]){
|
||||
onflag = 1;
|
||||
continue;
|
||||
}
|
||||
else rinv = 1.0/region->contact[m].r;
|
||||
tor[i][0] += torque[0];
|
||||
tor[i][1] += torque[1];
|
||||
tor[i][2] += torque[2];
|
||||
}
|
||||
}
|
||||
|
||||
ees(m,i);//me
|
||||
|
||||
ewall[0] += eng;
|
||||
fx = fwall * region->contact[m].delx * rinv;
|
||||
fy = fwall * region->contact[m].dely * rinv;
|
||||
fz = fwall * region->contact[m].delz * rinv;
|
||||
f[i][0] += fx;
|
||||
f[i][1] += fy;
|
||||
f[i][2] += fz;
|
||||
|
||||
ewall[1] -= fx;
|
||||
ewall[2] -= fy;
|
||||
ewall[3] -= fz;
|
||||
|
||||
tor[i][0] += torque[0];
|
||||
tor[i][1] += torque[1];
|
||||
tor[i][2] += torque[2];
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
if (onflag) error->one(FLERR,"Particle on or inside surface of region "
|
||||
"used in fix wall/region/ees");
|
||||
if (onflag) error->one(FLERR,"Particle on or inside surface of region "
|
||||
"used in fix wall/region/ees");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallRegionEES::post_force_respa(int vflag, int ilevel, int iloop)
|
||||
{
|
||||
if (ilevel == nlevels_respa-1) post_force(vflag);
|
||||
if (ilevel == nlevels_respa-1) post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallRegionEES::min_post_force(int vflag)
|
||||
{
|
||||
post_force(vflag);
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -278,13 +264,13 @@ void FixWallRegionEES::min_post_force(int vflag)
|
|||
|
||||
double FixWallRegionEES::compute_scalar()
|
||||
{
|
||||
// only sum across procs one time
|
||||
// only sum across procs one time
|
||||
|
||||
if (eflag == 0) {
|
||||
MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
|
||||
eflag = 1;
|
||||
}
|
||||
return ewall_all[0];
|
||||
if (eflag == 0) {
|
||||
MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
|
||||
eflag = 1;
|
||||
}
|
||||
return ewall_all[0];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -293,18 +279,15 @@ double FixWallRegionEES::compute_scalar()
|
|||
|
||||
double FixWallRegionEES::compute_vector(int n)
|
||||
{
|
||||
// only sum across procs one time
|
||||
// only sum across procs one time
|
||||
|
||||
if (eflag == 0) {
|
||||
MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
|
||||
eflag = 1;
|
||||
}
|
||||
return ewall_all[n+1];
|
||||
if (eflag == 0) {
|
||||
MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
|
||||
eflag = 1;
|
||||
}
|
||||
return ewall_all[n+1];
|
||||
}
|
||||
|
||||
|
||||
|
||||
//me
|
||||
/* ----------------------------------------------------------------------
|
||||
EES interaction for ellipsoid particle with wall
|
||||
compute eng and fwall and twall = magnitude of wall force and torque
|
||||
|
|
@ -312,94 +295,89 @@ double FixWallRegionEES::compute_vector(int n)
|
|||
|
||||
void FixWallRegionEES::ees(int m, int i)
|
||||
{
|
||||
Region *region = domain->regions[iregion];
|
||||
region->prematch();
|
||||
Region *region = domain->regions[iregion];
|
||||
region->prematch();
|
||||
|
||||
double delta = 0.0, delta2 = 0.0, delta3 = 0.0, delta4 = 0.0, delta5 = 0.0, delta6 = 0.0;
|
||||
double sigman = 0.0, sigman2 = 0.0 , sigman3 = 0.0, sigman4 = 0.0, sigman5 = 0.0, sigman6 = 0.0;
|
||||
double hhss = 0.0, hhss2 = 0.0, hhss4 = 0.0, hhss7 = 0.0, hhss8 = 0.0; //h^2 - s_n^2
|
||||
double hps = 0.0; //h+s_n
|
||||
double hms = 0.0; //h-s_n
|
||||
double twall = 0.0;
|
||||
double tempvec[3]={0,0,0};
|
||||
double tempvec2[3]= {0,0,0};
|
||||
double delta, delta2, delta3, delta4, delta5, delta6;
|
||||
double sigman, sigman2 , sigman3, sigman4, sigman5, sigman6;
|
||||
double hhss, hhss2, hhss4, hhss7, hhss8; //h^2 - s_n^2
|
||||
double hps; //h+s_n
|
||||
double hms; //h-s_n
|
||||
double twall;
|
||||
|
||||
double SAn[3] = {0,0,0};
|
||||
double that[3] = {0,0,0};
|
||||
double A[3][3], nhat[3], SAn[3], that[3];
|
||||
|
||||
double Lx[3][3] = {{0,0,0},{0,0,-1},{0,1,0}};
|
||||
double Ly[3][3] = {{0,0,1},{0,0,0},{-1,0,0}};
|
||||
double Lz[3][3] = {{0,-1,0},{1,0,0},{0,0,0}};
|
||||
double tempvec[3]= {0,0,0};
|
||||
double tempvec2[3]= {0,0,0};
|
||||
|
||||
double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}};
|
||||
double nhat[3] = {0,0,0};
|
||||
double Lx[3][3] = {{0,0,0},{0,0,-1},{0,1,0}};
|
||||
double Ly[3][3] = {{0,0,1},{0,0,0},{-1,0,0}};
|
||||
double Lz[3][3] = {{0,-1,0},{1,0,0},{0,0,0}};
|
||||
|
||||
nhat[0] = region->contact[m].delx / region->contact[m].r;
|
||||
nhat[1] = region->contact[m].dely / region->contact[m].r;
|
||||
nhat[2] = region->contact[m].delz / region->contact[m].r;
|
||||
nhat[0] = region->contact[m].delx / region->contact[m].r;
|
||||
nhat[1] = region->contact[m].dely / region->contact[m].r;
|
||||
nhat[2] = region->contact[m].delz / region->contact[m].r;
|
||||
|
||||
//avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
|
||||
int *ellipsoid = atom->ellipsoid;//me
|
||||
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
|
||||
int *ellipsoid = atom->ellipsoid;
|
||||
|
||||
double* shape = bonus[ellipsoid[i]].shape;;
|
||||
MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);
|
||||
double* shape = bonus[ellipsoid[i]].shape;;
|
||||
MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);
|
||||
|
||||
MathExtra::transpose_matvec(A,nhat,tempvec);
|
||||
for(int k = 0; k<3; k++) tempvec[k] *= shape[k];
|
||||
for(int k = 0; k<3 ; k++) sigman2 += tempvec[k]*tempvec[k];
|
||||
for(int k = 0; k<3; k++) SAn[k] = tempvec[k];
|
||||
sigman2 = 0.0;
|
||||
MathExtra::transpose_matvec(A,nhat,tempvec);
|
||||
for(int k = 0; k<3; k++) tempvec[k] *= shape[k];
|
||||
for(int k = 0; k<3; k++) sigman2 += tempvec[k]*tempvec[k];
|
||||
for(int k = 0; k<3; k++) SAn[k] = tempvec[k];
|
||||
|
||||
sigman = sqrt(sigman2);
|
||||
delta = fabs(region->contact[m].r);
|
||||
|
||||
sigman = sqrt(sigman2);
|
||||
delta = fabs(region->contact[m].r);
|
||||
sigman3 = sigman2 * sigman;
|
||||
sigman4 = sigman2 * sigman2;
|
||||
sigman5 = sigman4 * sigman;
|
||||
sigman6 = sigman3 * sigman3;
|
||||
|
||||
sigman3 = sigman2 * sigman;
|
||||
sigman4 = sigman2 * sigman2;
|
||||
sigman5 = sigman4 * sigman;
|
||||
sigman6 = sigman3 * sigman3;
|
||||
delta2 = delta * delta;
|
||||
delta3 = delta2 * delta;
|
||||
delta4 = delta2 * delta2;
|
||||
delta5 = delta3 * delta2;
|
||||
delta6 = delta3 * delta3;
|
||||
|
||||
delta2 = delta * delta;
|
||||
delta3 = delta2 * delta;
|
||||
delta4 = delta2 * delta2;
|
||||
delta5 = delta3 * delta2;
|
||||
delta6 = delta3 * delta3;
|
||||
hhss = delta2 - sigman2;
|
||||
hhss2 = hhss * hhss;
|
||||
hhss4 = hhss2 * hhss2;
|
||||
hhss8 = hhss4 * hhss4;
|
||||
hhss7 = hhss4 * hhss2 * hhss;
|
||||
|
||||
hhss = delta2 - sigman2;
|
||||
hhss2 = hhss * hhss;
|
||||
hhss4 = hhss2 * hhss2;
|
||||
hhss8 = hhss4 * hhss4;
|
||||
hhss7 = hhss4 * hhss2 * hhss;
|
||||
hps = delta + sigman;
|
||||
hms = delta - sigman;
|
||||
|
||||
hps = delta + sigman;
|
||||
hms = delta - sigman;
|
||||
fwall = -1*coeff4/hhss2 + coeff3
|
||||
* (21*delta6 + 63*delta4*sigman2 + 27*delta2*sigman4 + sigman6) / hhss8;
|
||||
|
||||
fwall = -1*coeff4/hhss2 +
|
||||
coeff3 * ( 21*delta6 + 63*delta4*sigman2 + 27*delta2*sigman4 + sigman6 ) / hhss8
|
||||
;
|
||||
eng = -1*coeff2 * (4*delta/sigman2/hhss + 2*log(hms/hps)/sigman3) +
|
||||
coeff1 * (35*delta5 + 70*delta3*sigman2 + 15*delta*sigman4) / hhss7;
|
||||
|
||||
eng = -1*coeff2 * ( 4*delta/sigman2/hhss + 2*log(hms/hps)/sigman3 ) +
|
||||
coeff1 * ( 35*delta5 + 70*delta3*sigman2 + 15*delta*sigman4 ) / hhss7;
|
||||
twall = coeff6 * (6*delta3/sigman4/hhss2 - 10*delta/sigman2/hhss2
|
||||
+ 3*log(hms/hps)/sigman5)
|
||||
+ coeff5 * (21.*delta5 + 30.*delta3*sigman2 + 5.*delta*sigman4) / hhss8;
|
||||
|
||||
twall = coeff6 * ( 6.*delta3/sigman4/hhss2 - 10.*delta/sigman2/hhss2 + 3.*log(hms/hps)/sigman5 ) +
|
||||
coeff5 * ( 21.*delta5 + 30.*delta3*sigman2 + 5.*delta*sigman4 ) / hhss8 ;
|
||||
MathExtra::matvec(Lx,nhat,tempvec);
|
||||
MathExtra::transpose_matvec(A,tempvec,tempvec2);
|
||||
for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
|
||||
that[0] = MathExtra::dot3(SAn,tempvec2);
|
||||
|
||||
MathExtra::matvec(Lx,nhat,tempvec);
|
||||
MathExtra::transpose_matvec(A,tempvec,tempvec2);
|
||||
for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
|
||||
that[0] = MathExtra::dot3(SAn,tempvec2);
|
||||
MathExtra::matvec(Ly,nhat,tempvec);
|
||||
MathExtra::transpose_matvec(A,tempvec,tempvec2);
|
||||
for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
|
||||
that[1] = MathExtra::dot3(SAn,tempvec2);
|
||||
|
||||
MathExtra::matvec(Ly,nhat,tempvec);
|
||||
MathExtra::transpose_matvec(A,tempvec,tempvec2);
|
||||
for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
|
||||
that[1] = MathExtra::dot3(SAn,tempvec2);
|
||||
|
||||
MathExtra::matvec(Lz,nhat,tempvec);
|
||||
MathExtra::transpose_matvec(A,tempvec,tempvec2);
|
||||
for(int k = 0; k < 3; k++) tempvec2[k] *= shape[k];
|
||||
that[2] = MathExtra::dot3(SAn,tempvec2);
|
||||
|
||||
for(int j = 0; j<3 ; j++)
|
||||
torque[j] = twall * that[j];
|
||||
MathExtra::matvec(Lz,nhat,tempvec);
|
||||
MathExtra::transpose_matvec(A,tempvec,tempvec2);
|
||||
for(int k = 0; k < 3; k++) tempvec2[k] *= shape[k];
|
||||
that[2] = MathExtra::dot3(SAn,tempvec2);
|
||||
|
||||
for(int j = 0; j<3 ; j++)
|
||||
torque[j] = twall * that[j];
|
||||
}
|
||||
|
|
|
|||
|
|
@ -40,7 +40,7 @@ class FixWallRegionEES : public Fix {
|
|||
double compute_vector(int);
|
||||
|
||||
private:
|
||||
class AtomVecEllipsoid *avec;//me
|
||||
class AtomVecEllipsoid *avec;
|
||||
|
||||
int iregion;
|
||||
double epsilon,sigma,cutoff;
|
||||
|
|
@ -50,11 +50,11 @@ class FixWallRegionEES : public Fix {
|
|||
char *idregion;
|
||||
|
||||
double coeff1,coeff2,coeff3,coeff4,offset;
|
||||
double coeff5, coeff6;//me
|
||||
double coeff5, coeff6;
|
||||
double eng,fwall;
|
||||
double torque[3];//me
|
||||
double torque[3];
|
||||
|
||||
void ees(int, int);//me
|
||||
void ees(int, int);
|
||||
};
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue