coding style and whitespace cleanup to match LAMMPS style (6eddc1a2) · Commits · 郑智淋 / lammps

src/USER-MISC/fix_wall_ees.cpp

+39 −27

Original line number	Diff line number	Diff line
		@@ -11,13 +11,25 @@
		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		#include "math.h"
		/* ----------------------------------------------------------------------
		Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com
		------------------------------------------------------------------------- */

		#include <math.h>
		#include "math_extra.h"
		#include "fix_wall_ees.h"
		#include "atom.h"
		#include "atom_vec.h"
		#include "atom_vec_ellipsoid.h"
		#include "domain.h"
		#include "region.h"
		#include "force.h"
		#include "lattice.h"
		#include "update.h"
		#include "output.h"
		#include "respa.h"
		#include "error.h"
		#include "math_extra.h"

		using namespace LAMMPS_NS;
		using namespace FixConst;

src/USER-MISC/fix_wall_region_ees.cpp

+266 −288

Original line number	Diff line number	Diff line
		/* -- c++ -- ----------------------------------------------------------
		/* ----------------------------------------------------------------------
		LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
		http://lammps.sandia.gov, Sandia National Laboratories
		Steve Plimpton, sjplimp@sandia.gov
		@@ -10,10 +10,14 @@

		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */
		#include <iostream>
		#include "math.h"
		#include "stdlib.h"
		#include "string.h"

		/* ----------------------------------------------------------------------
		Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com
		------------------------------------------------------------------------- */

		#include <math.h>
		#include <stdlib.h>
		#include <string.h>
		#include "fix_wall_region_ees.h"
		#include "atom.h"
		#include "atom_vec.h"
		@@ -31,12 +35,8 @@
		using namespace LAMMPS_NS;
		using namespace FixConst;

		enum{LJ93,LJ126,COLLOID,HARMONIC,EES};//me

		/* ---------------------------------------------------------------------- */
		/// USAGE:
		/// fix ID group-ID wall/region/ees region-ID epsilon sigma cutoff
		///

		FixWallRegionEES::FixWallRegionEES(LAMMPS lmp, int narg, char *arg) :
		Fix(lmp, narg, arg)
		{
		@@ -57,8 +57,6 @@ FixWallRegionEES::FixWallRegionEES(LAMMPS lmp, int narg, char *arg) :
		idregion = new char[n];
		strcpy(idregion,arg[3]);



		epsilon = force->numeric(FLERR,arg[4]);
		sigma = force->numeric(FLERR,arg[5]);
		cutoff = force->numeric(FLERR,arg[6]);
		@@ -98,7 +96,6 @@ void FixWallRegionEES::init()
		if (iregion == -1)
		error->all(FLERR,"Region ID for fix wall/region/ees does not exist");


		avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
		if (!avec)
		error->all(FLERR,"Fix wall/region/ees requires atom style ellipsoid");
		@@ -115,8 +112,7 @@ void FixWallRegionEES::init()
		if (ellipsoid[i] < 0)
		error->one(FLERR,"Fix wall/region/ees requires extended particles");


		// setup coefficients for each style
		// setup coefficients

		coeff1 = ( 2. / 4725. ) * epsilon * pow(sigma,12.0);
		coeff2 = ( 1. / 24. ) * epsilon * pow(sigma,6.0);
		@@ -155,26 +151,21 @@ void FixWallRegionEES::min_setup(int vflag)

		void FixWallRegionEES::post_force(int vflag)
		{
		//me
		//sth is needed here, but I dont know what
		//that is calculation of sn

		int i,m,n;
		double rinv,fx,fy,fz,tooclose[3];//me
		double sn;//me
		double rinv,fx,fy,fz,sn,tooclose[3];

		eflag = 0;
		ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;

		double **x = atom->x;
		double **f = atom->f;
		double *radius = atom->radius;

		double **tor = atom->torque; //me
		double **tor = atom->torque;

		//avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");//me
		AtomVecEllipsoid::Bonus *bonus = avec->bonus;//me
		int *ellipsoid = atom->ellipsoid;//me
		AtomVecEllipsoid::Bonus *bonus = avec->bonus;
		int *ellipsoid = atom->ellipsoid;

		int *mask = atom->mask;
		int nlocal = atom->nlocal;
		@@ -214,8 +205,6 @@ void FixWallRegionEES::post_force(int vflag)
		tooclose[which] = sn;
		}



		n = region->surface(x[i][0],x[i][1],x[i][2],cutoff);

		for (m = 0; m < n; m++) {
		@@ -223,17 +212,15 @@ void FixWallRegionEES::post_force(int vflag)
		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;
		} else rinv = 1.0/region->contact[m].r;

		ees(m,i);//me
		ees(m,i);

		ewall[0] += eng;
		fx = fwall * region->contact[m].delx * rinv;
		@@ -250,7 +237,6 @@ void FixWallRegionEES::post_force(int vflag)
		tor[i][0] += torque[0];
		tor[i][1] += torque[1];
		tor[i][2] += torque[2];

		}
		}

		@@ -302,9 +288,6 @@ double FixWallRegionEES::compute_vector(int n)
		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
		@@ -315,42 +298,38 @@ void FixWallRegionEES::ees(int m, int i)
		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 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 A[3][3], nhat[3], SAn[3], that[3];

		double tempvec[3]= {0,0,0};
		double tempvec2[3]= {0,0,0};

		double SAn[3] = {0,0,0};
		double that[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}};

		double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}};
		double nhat[3] = {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;

		//avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
		AtomVecEllipsoid::Bonus *bonus = avec->bonus;
		int *ellipsoid = atom->ellipsoid;//me
		int *ellipsoid = atom->ellipsoid;

		double* shape = bonus[ellipsoid[i]].shape;;
		MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);

		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);

		@@ -374,15 +353,15 @@ void FixWallRegionEES::ees(int m, int i)
		hps = delta + sigman;
		hms = delta - sigman;

		fwall = -1*coeff4/hhss2 +
		coeff3 * ( 21delta6 + 63delta4sigman2 + 27delta2*sigman4 + sigman6 ) / hhss8
		;
		fwall = -1*coeff4/hhss2 + coeff3
		* (21delta6 + 63delta4sigman2 + 27delta2*sigman4 + sigman6) / hhss8;

		eng = -1coeff2 (4delta/sigman2/hhss + 2log(hms/hps)/sigman3) +
		coeff1 * (35delta5 + 70delta3sigman2 + 15delta*sigman4) / hhss7;

		twall = coeff6 * ( 6.delta3/sigman4/hhss2 - 10.delta/sigman2/hhss2 + 3.*log(hms/hps)/sigman5 ) +
		coeff5 * ( 21.delta5 + 30.delta3sigman2 + 5.delta*sigman4 ) / hhss8 ;
		twall = coeff6 * (6delta3/sigman4/hhss2 - 10delta/sigman2/hhss2
		+ 3*log(hms/hps)/sigman5)
		+ coeff5 * (21.delta5 + 30.delta3sigman2 + 5.delta*sigman4) / hhss8;

		MathExtra::matvec(Lx,nhat,tempvec);
		MathExtra::transpose_matvec(A,tempvec,tempvec2);
		@@ -401,5 +380,4 @@ void FixWallRegionEES::ees(int m, int i)

		for(int j = 0; j<3 ; j++)
		torque[j] = twall * that[j];

		}

src/USER-MISC/fix_wall_region_ees.h

+4 −4

Original line number	Diff line number	Diff line
		@@ -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);
		};

		}

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