(fcbd40eb) · Commits · 郑智淋 / lammps · GitLab

src/SRD/Install.sh

+4 −0

Original line number	Original line	Diff line number	Diff line
	@@ -3,13 +3,17 @@
	if (test $1 == 1) then		if (test $1 == 1) then

	cp fix_srd.cpp ..		cp fix_srd.cpp ..
			cp fix_wall_srd.cpp ..

	cp fix_srd.h ..		cp fix_srd.h ..
			cp fix_wall_srd.h ..

	elif (test $1 == 0) then		elif (test $1 == 0) then

	rm ../fix_srd.cpp		rm ../fix_srd.cpp
			rm ../fix_wall_srd.cpp

	rm ../fix_srd.h		rm ../fix_srd.h
			rm ../fix_wall_srd.h

	fi		fi

src/SRD/fix_srd.cpp

+704 −262

File changed.

Preview size limit exceeded, changes collapsed.

src/SRD/fix_srd.h

+31 −10

Original line number	Original line	Diff line number	Diff line
	@@ -54,7 +54,14 @@ class FixSRD : public Fix {
	double srd_per_cell;		double srd_per_cell;
	double dmax,vmax,vmaxsq;		double dmax,vmax,vmaxsq;
	double maxbigdiam,minbigdiam;		double maxbigdiam,minbigdiam;
	double dist_bigghost;		double dist_ghost,dist_srd,dist_srd_reneigh; // explained in code

			int wallexist,nwall,wallvarflag;
			class FixWallSRD *wallfix;
			int *wallwhich;
			double xwall,xwallhold,*vwall;
			double **fwall;
			double walltrigger;

	// for orthogonal box, these are in box units		// for orthogonal box, these are in box units
	// for triclinic box, these are in lamda units		// for triclinic box, these are in lamda units
	@@ -79,11 +86,11 @@ class FixSRD : public Fix {
	double **flocal; // local ptrs to atom force and torque		double **flocal; // local ptrs to atom force and torque
	double **tlocal;		double **tlocal;

	// info to store for each owned and ghost big particle		// info to store for each owned and ghost big particle and wall

	struct Big {		struct Big {
	int index; // local index or particle in atom arrays		int index; // local index of particle/wall
	int type; // SPHERE or ELLIPSOID		int type; // SPHERE or ELLIPSOID or WALL
	int typesphere; // SPHERE_SHAPE or SPHERE_RADIUS		int typesphere; // SPHERE_SHAPE or SPHERE_RADIUS
	int typeangular; // ANGULAR_OMEGA or ANGULAR_ANGMOM		int typeangular; // ANGULAR_OMEGA or ANGULAR_ANGMOM
	double radius,radsq; // radius of sphere		double radius,radsq; // radius of sphere
	@@ -95,15 +102,15 @@ class FixSRD : public Fix {
	double ex[3],ey[3],ez[3]; // current orientation vecs for ellipsoid		double ex[3],ey[3],ez[3]; // current orientation vecs for ellipsoid
	};		};

	Big *biglist; // list of info for each owned & ghost big particle		Big *biglist; // list of info for each owned & ghost big and wall
	int any_ellipsoids; // 1 if any big particles are ellipsoids		int any_ellipsoids; // 1 if any big particles are ellipsoids
	int torqueflag; // 1 if any big particle is torqued		int torqueflag; // 1 if any big particle is torqued

	// current size of particle-based arrays		// current size of particle-based arrays

	int nbig; // # of big particles, owned + ghost		int nbig; // # of owned/ghost big particles and walls
	int nmax;		int maxbig; // max number of owned/ghost big particles and walls
	int maxbig; // max number of big particles, owned + ghost		int nmax; // max number of SRD particles

	// bins for SRD velocity remap, shifting and communication		// bins for SRD velocity remap, shifting and communication
	// binsize and inv are in lamda units for triclinic		// binsize and inv are in lamda units for triclinic
	@@ -170,6 +177,8 @@ class FixSRD : public Fix {

	int inside_sphere(double , double , Big *);		int inside_sphere(double , double , Big *);
	int inside_ellipsoid(double , double , Big *);		int inside_ellipsoid(double , double , Big *);
			int inside_wall(double *, int);

	double collision_sphere_exact(double , double , double , double ,		double collision_sphere_exact(double , double , double , double ,
	Big , double , double , double );		Big , double , double , double );
	void collision_sphere_inexact(double , double ,		void collision_sphere_inexact(double , double ,
	@@ -178,22 +187,34 @@ class FixSRD : public Fix {
	Big , double , double , double );		Big , double , double , double );
	void collision_ellipsoid_inexact(double , double ,		void collision_ellipsoid_inexact(double , double ,
	Big , double , double , double );		Big , double , double , double );
			double collision_wall_exact(double , int, double ,
			double , double , double *);
			void collision_wall_inexact(double , int, double , double , double );

	void slip_sphere(double , double , double , double );		void slip_sphere(double , double , double , double );
	void slip_ellipsoid(double , double , double , Big ,		void slip_ellipsoid(double , double , double , Big ,
	double , double , double *);		double , double , double *);
			void slip_wall(double , int, double , double *);

	void noslip(double , double , double , Big ,		void noslip(double , double , double , Big ,
	double , double , double *);		double , double , double *);
			void noslip_wall(double , int, double , double , double );

	void force_torque(double , double , double *,		void force_torque(double , double , double *,
	double , double , double *);		double , double , double *);
			void force_wall(double , double , int);

	int update_srd(int, double, double , double , double , double );		int update_srd(int, double, double , double , double , double );

	void parameterize();		void parameterize();
			void setup_bounds();
	void setup_velocity_bins();		void setup_velocity_bins();
	void setup_velocity_shift(int, int);		void setup_velocity_shift(int, int);
	void setup_search_bins();		void setup_search_bins();
	void setup_search_stencil();		void setup_search_stencil();
	void big_static();		void big_static();
	void big_dynamic();		void big_dynamic();

	double point_bin_distance(double *, int, int, int);		double point_bin_distance(double *, int, int, int);
	double bin_bin_distance(int, int, int);		double bin_bin_distance(int, int, int);
	void exyz_from_q(double , double , double , double );		void exyz_from_q(double , double , double , double );
	@@ -203,7 +224,7 @@ class FixSRD : public Fix {

	double distance(int, int);		double distance(int, int);
	void print_collision(int, int, int, double, double,		void print_collision(int, int, int, double, double,
	double , double , double *);		double , double , double *, int);
	};		};

	}		}

src/SRD/fix_wall_srd.cpp

0 → 100644

+252 −0

Original line number	Original line	Diff line number	Diff line
			/* ----------------------------------------------------------------------
			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.
			------------------------------------------------------------------------- */

			#include "stdlib.h"
			#include "string.h"
			#include "fix_wall_srd.h"
			#include "atom.h"
			#include "modify.h"
			#include "fix.h"
			#include "domain.h"
			#include "lattice.h"
			#include "input.h"
			#include "modify.h"
			#include "update.h"
			#include "variable.h"
			#include "memory.h"
			#include "error.h"

			using namespace LAMMPS_NS;

			enum{XLO,XHI,YLO,YHI,ZLO,ZHI};
			enum{NONE,EDGE,CONSTANT,VARIABLE};

			/* ---------------------------------------------------------------------- */

			FixWallSRD::FixWallSRD(LAMMPS lmp, int narg, char *arg) :
			Fix(lmp, narg, arg)
			{
			if (narg < 4) error->all("Illegal fix wall/srd command");

			// parse args

			nwall = 0;
			int scaleflag = 1;

			int iarg = 3;
			while (iarg < narg) {
			if ((strcmp(arg[iarg],"xlo") == 0) \|\| (strcmp(arg[iarg],"xhi") == 0) \|\|
			(strcmp(arg[iarg],"ylo") == 0) \|\| (strcmp(arg[iarg],"yhi") == 0) \|\|
			(strcmp(arg[iarg],"zlo") == 0) \|\| (strcmp(arg[iarg],"zhi") == 0)) {
			if (iarg+2 > narg) error->all("Illegal fix wall/srd command");

			int newwall;
			if (strcmp(arg[iarg],"xlo") == 0) newwall = XLO;
			else if (strcmp(arg[iarg],"xhi") == 0) newwall = XHI;
			else if (strcmp(arg[iarg],"ylo") == 0) newwall = YLO;
			else if (strcmp(arg[iarg],"yhi") == 0) newwall = YHI;
			else if (strcmp(arg[iarg],"zlo") == 0) newwall = ZLO;
			else if (strcmp(arg[iarg],"zhi") == 0) newwall = ZHI;

			for (int m = 0; m < nwall; m++)
			if (newwall == wallwhich[m])
			error->all("Wall defined twice in fix wall/srd command");

			wallwhich[nwall] = newwall;
			if (strcmp(arg[iarg+1],"EDGE") == 0) {
			wallstyle[nwall] = EDGE;
			int dim = wallwhich[nwall] / 2;
			int side = wallwhich[nwall] % 2;
			if (side == 0) coord0[nwall] = domain->boxlo[dim];
			else coord0[nwall] = domain->boxhi[dim];
			} else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
			wallstyle[nwall] = VARIABLE;
			int n = strlen(&arg[iarg+1][2]) + 1;
			varstr[nwall] = new char[n];
			strcpy(varstr[nwall],&arg[iarg+1][2]);
			} else {
			wallstyle[nwall] = CONSTANT;
			coord0[nwall] = atof(arg[iarg+1]);
			}

			nwall++;
			iarg += 2;

			} else if (strcmp(arg[iarg],"units") == 0) {
			if (iarg+2 > narg) error->all("Illegal wall/srd command");
			if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
			else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
			else error->all("Illegal fix wall/srd command");
			iarg += 2;
			} else error->all("Illegal fix wall/srd command");
			}

			// error check

			if (nwall == 0) error->all("Illegal fix wall command");

			for (int m = 0; m < nwall; m++) {
			if ((wallwhich[m] == XLO \|\| wallwhich[m] == XHI) && domain->xperiodic)
			error->all("Cannot use fix wall/srd in periodic dimension");
			if ((wallwhich[m] == YLO \|\| wallwhich[m] == YHI) && domain->yperiodic)
			error->all("Cannot use fix wall/srd in periodic dimension");
			if ((wallwhich[m] == ZLO \|\| wallwhich[m] == ZHI) && domain->zperiodic)
			error->all("Cannot use fix wall/srd in periodic dimension");
			}

			for (int m = 0; m < nwall; m++)
			if ((wallwhich[m] == ZLO \|\| wallwhich[m] == ZHI) && domain->dimension == 2)
			error->all("Cannot use fix wall/srd zlo/zhi for a 2d simulation");

			// setup wall force array

			array_flag = 1;
			size_array_rows = nwall;
			size_array_cols = 3;
			global_freq = 1;
			extarray = 1;

			fwall = memory->create_2d_double_array(nwall,3,"wall/srd:fwall");
			fwall_all = memory->create_2d_double_array(nwall,3,"wall/srd:fwall_all");

			// scale coord for CONSTANT walls

			int flag = 0;
			for (int m = 0; m < nwall; m++)
			if (wallstyle[m] == CONSTANT) flag = 1;

			if (flag) {
			if (scaleflag && domain->lattice == NULL)
			error->all("Use of fix wall with undefined lattice");

			double xscale,yscale,zscale;
			if (scaleflag) {
			xscale = domain->lattice->xlattice;
			yscale = domain->lattice->ylattice;
			zscale = domain->lattice->zlattice;
			}
			else xscale = yscale = zscale = 1.0;

			double scale;
			for (int m = 0; m < nwall; m++) {
			if (wallwhich[m] < YLO) scale = xscale;
			else if (wallwhich[m] < ZLO) scale = yscale;
			else scale = zscale;
			if (wallstyle[m] == CONSTANT) coord0[m] *= scale;
			}
			}

			// set time_depend and varflag if any wall positions are variable

			varflag = 0;
			for (int m = 0; m < nwall; m++)
			if (wallstyle[m] == VARIABLE) time_depend = varflag = 1;
			laststep = -1;
			}

			/* ---------------------------------------------------------------------- */

			FixWallSRD::~FixWallSRD()
			{
			for (int m = 0; m < nwall; m++)
			if (wallstyle[m] == VARIABLE) delete [] varstr[m];
			memory->destroy_2d_double_array(fwall);
			memory->destroy_2d_double_array(fwall_all);
			}

			/* ---------------------------------------------------------------------- */

			int FixWallSRD::setmask()
			{
			int mask = 0;
			return mask;
			}

			/* ---------------------------------------------------------------------- */

			void FixWallSRD::init()
			{
			int flag = 0;
			for (int m = 0; m < modify->nfix; m++)
			if (strcmp(modify->fix[m]->style,"srd2") == 0) flag = 1;
			if (!flag) error->all("Cannot use fix wall/srd without fix srd");

			for (int m = 0; m < nwall; m++) {
			if (wallstyle[m] != VARIABLE) continue;
			varindex[m] = input->variable->find(varstr[m]);
			if (varindex[m] < 0)
			error->all("Variable name for fix wall/srd does not exist");
			if (!input->variable->equalstyle(varindex[m]))
			error->all("Variable for fix wall/srd is invalid style");
			}

			dt = update->dt;
			}

			/* ----------------------------------------------------------------------
			return force component on a wall
			------------------------------------------------------------------------- */

			double FixWallSRD::compute_array(int i, int j)
			{
			// only sum across procs one time

			if (force_flag == 0) {
			MPI_Allreduce(&fwall[0][0],&fwall_all[0][0],3*nwall,
			MPI_DOUBLE,MPI_SUM,world);
			force_flag = 1;
			}
			return fwall_all[i][j];
			}

			/* ----------------------------------------------------------------------
			set wall position and velocity, zero forces on walls
			evaluate variable if necessary, wrap with clear/add
			if flag, then being called on reneighbor, so archive wall positions
			------------------------------------------------------------------------- */

			void FixWallSRD::wall_params(int flag)
			{
			double xnew;

			if (varflag) modify->clearstep_compute();

			int ntimestep = update->ntimestep;

			for (int m = 0; m < nwall; m++) {
			if (wallstyle[m] == VARIABLE)
			xnew = input->variable->compute_equal(varindex[m]);
			else xnew = coord0[m];

			if (laststep < 0) {
			xwall[m] = xwalllast[m] = xnew;
			vwall[m] = 0.0;
			} else if (laststep < ntimestep) {
			xwalllast[m] = xwall[m];
			xwall[m] = xnew;
			vwall[m] = (xwall[m] - xwalllast[m]) / dt;
			}

			fwall[m][0] = fwall[m][1] = fwall[m][2] = 0.0;
			}

			laststep = ntimestep;

			if (varflag) modify->addstep_compute(update->ntimestep + 1);

			if (flag)
			for (int m = 0; m < nwall; m++)
			xwallhold[m] = xwall[m];

			force_flag = 0;
			}

src/SRD/fix_wall_srd.h

0 → 100644

+59 −0

Original line number	Original line	Diff line number	Diff line
			/* ----------------------------------------------------------------------
			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 FIX_CLASS

			FixStyle(wall/srd,FixWallSRD)

			#else

			#ifndef LMP_FIX_WALL_SRD_H
			#define LMP_FIX_WALL_SRD_H

			#include "fix.h"

			namespace LAMMPS_NS {

			class FixWallSRD : public Fix {
			public:
			int nwall,varflag;
			int wallwhich[6];
			double xwall[6],xwallhold[6],vwall[6];
			double **fwall;

			FixWallSRD(class LAMMPS , int, char *);
			~FixWallSRD();
			int setmask();
			void init();
			double compute_array(int, int);

			void wall_params(int);

			private:
			int wallstyle[6];
			double coord0[6];
			char *varstr[6];
			int varindex[6];

			double dt;
			double xwalllast[6];
			int laststep;

			double **fwall_all;
			int force_flag;
			};

			}

			#endif
			#endif

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