(ed9f1366) · Commits · 郑智淋 / lammps

src/USER-MISC/fix_ti_rs.cpp

deleted100755 → 0

+0 −199

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

		/* -------------------------------------------------------------------------
		Contributing authors:
		Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
		Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
		------------------------------------------------------------------------- */

		#include <stdlib.h>
		#include <string.h>
		#include <math.h>
		#include "fix_ti_rs.h"
		#include "atom.h"
		#include "update.h"
		#include "respa.h"
		#include "error.h"
		#include "force.h"

		using namespace LAMMPS_NS;
		using namespace FixConst;

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

		// Class constructor initialize all variables.

		FixTIRS::FixTIRS(LAMMPS lmp, int narg, char *arg) : Fix(lmp, narg, arg)
		{
		// Checking the input information.
		if (narg < 7 \|\| narg > 9) error->all(FLERR,"Illegal fix ti/rs command");

		// Fix flags.
		vector_flag = 1;
		size_vector = 2;
		global_freq = 1;
		extvector = 1;

		// Time variables.
		t_switch = force->bnumeric(FLERR,arg[5]);
		t_equil = force->bnumeric(FLERR,arg[6]);
		t0 = update->ntimestep;
		if (t_switch <= 0) error->all(FLERR,"Illegal fix ti/rs command");
		if (t_equil <= 0) error->all(FLERR,"Illegal fix ti/rs command");

		// Coupling parameter limits and initialization.
		l_initial = force->numeric(FLERR,arg[3]);
		l_final = force->numeric(FLERR,arg[4]);
		sf = 1;
		if (narg > 7) {
		if (strcmp(arg[7], "function") == 0) sf = force->inumeric(FLERR,arg[8]);
		else error->all(FLERR,"Illegal fix ti/rs switching function");
		if ((sf<1) \|\| (sf>3))
		error->all(FLERR,"Illegal fix ti/rs switching function");
		}
		lambda = switch_func(0);
		dlambda = dswitch_func(0);
		}

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

		FixTIRS::~FixTIRS()
		{
		// unregister callbacks to this fix from Atom class
		atom->delete_callback(id,0);
		atom->delete_callback(id,1);
		}

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

		int FixTIRS::setmask()
		{
		int mask = 0;
		mask \|= INITIAL_INTEGRATE;
		mask \|= POST_FORCE;
		return mask;
		}

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

		void FixTIRS::init()
		{
		if (strstr(update->integrate_style,"respa"))
		nlevels_respa = ((Respa *) update->integrate)->nlevels;
		}

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

		void FixTIRS::setup(int vflag)
		{
		if (strstr(update->integrate_style,"verlet"))
		post_force(vflag);
		else {
		((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
		post_force_respa(vflag,nlevels_respa-1,0);
		((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
		}
		}

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

		void FixTIRS::min_setup(int vflag)
		{
		post_force(vflag);
		}


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

		void FixTIRS::post_force(int vflag)
		{

		int *mask = atom->mask;
		int nlocal = atom->nlocal;
		double **f = atom->f;

		// Scaling forces.
		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		f[i][0] = lambda * f[i][0];
		f[i][1] = lambda * f[i][1];
		f[i][2] = lambda * f[i][2];
		}
		}
		}

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

		void FixTIRS::post_force_respa(int vflag, int ilevel, int iloop)
		{
		if (ilevel == nlevels_respa-1) post_force(vflag);
		}

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

		void FixTIRS::min_post_force(int vflag)
		{
		post_force(vflag);
		}

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

		void FixTIRS::initial_integrate(int vflag)
		{
		// Update the coupling parameter value.
		const bigint t = update->ntimestep - (t0+t_equil);
		const double r_switch = 1.0/t_switch;

		if( (t >= 0) && (t <= t_switch) ) {
		lambda = switch_func(t*r_switch);
		dlambda = dswitch_func(t*r_switch);
		}

		if( (t >= t_equil+t_switch) && (t <= (t_equil+2*t_switch)) ) {
		lambda = switch_func(1.0 - (t - t_switch - t_equil)*r_switch);
		dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)*r_switch);
		}
		}

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

		double FixTIRS::compute_vector(int n)
		{
		linfo[0] = lambda;
		linfo[1] = dlambda;
		return linfo[n];
		}

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

		double FixTIRS::switch_func(double t)
		{
		if (sf == 2) return l_initial / (1 + t * (l_initial/l_final - 1));
		if (sf == 3) return l_initial / (1 + log2(1+t) * (l_initial/l_final - 1));

		// Default option is sf = 1.
		return l_initial + (l_final - l_initial) * t;
		}

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

		double FixTIRS::dswitch_func(double t)
		{
		double aux = (1.0/l_initial - 1.0/l_final);
		if (sf == 2) return lambda * lambda * aux / t_switch;
		if (sf == 3) return lambda * lambda * aux / (t_switch * log(2) * (1 + t));

		// Default option is sf = 1.
		return (l_final-l_initial)/t_switch;
		}

src/USER-MISC/fix_ti_rs.h

deleted100755 → 0

+0 −66

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

		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 authors:
		Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
		Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
		------------------------------------------------------------------------- */

		#ifdef FIX_CLASS

		FixStyle(ti/rs,FixTIRS)

		#else

		#ifndef LMP_FIX_TI_RS_H
		#define LMP_FIX_TI_RS_H

		#include "fix.h"

		namespace LAMMPS_NS {

		class FixTIRS : public Fix {
		public:
		FixTIRS(class LAMMPS , int, char *);
		~FixTIRS();
		int setmask();
		void init();
		void setup(int);
		void min_setup(int);
		void post_force(int);
		void post_force_respa(int, int, int);
		void min_post_force(int);
		virtual void initial_integrate(int);
		double compute_vector(int);

		private:
		double switch_func(double);
		double dswitch_func(double);

		double lambda; // Coupling parameter.
		double dlambda; // Lambda variation with t.
		double l_initial; // Lambda initial value.
		double l_final; // Lambda final value.
		double linfo[2]; // Current lambda status.
		bigint t_switch; // Total switching steps.
		bigint t_equil; // Equilibration time.
		bigint t0; // Initial time.
		int sf; // Switching function option.
		int nlevels_respa;
		};

		}

		#endif
		#endif

src/USER-MISC/fix_ti_spring.cpp

+44 −32

Original line number	Diff line number	Diff line
		@@ -13,12 +13,13 @@

		/* -------------------------------------------------------------------------
		Contributing authors:
		Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
		Rodrigo Freitas (UC Berkeley) - rodrigof@berkeley.edu
		Mark Asta (UC Berkeley) - mdasta@berkeley.edu
		Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
		------------------------------------------------------------------------- */

		#include <stdlib.h>
		#include <string.h>
		#include "stdlib.h"
		#include "string.h"
		#include "fix_ti_spring.h"
		#include "atom.h"
		#include "update.h"
		@@ -31,6 +32,18 @@
		using namespace LAMMPS_NS;
		using namespace FixConst;

		static const char cite_ti_spring[] =
		"ti/spring command:\n\n"
		"@article{freitas2016,\n"
		" author={Freitas, Rodrigo and Asta, Mark and de Koning, Maurice},\n"
		" title={Nonequilibrium free-energy calculation of solids using LAMMPS},\n"
		" journal={Computational Materials Science},\n"
		" volume={112},\n"
		" pages={333--341},\n"
		" year={2016},\n"
		" publisher={Elsevier}\n"
		"}\n\n";

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

		FixTISpring::FixTISpring(LAMMPS lmp, int narg, char *arg) :
		@@ -64,7 +77,7 @@ FixTISpring::FixTISpring(LAMMPS lmp, int narg, char *arg) :

		double **x = atom->x;
		int *mask = atom->mask;
		imageint *image = atom->image;
		tagint *image = atom->image;
		int nlocal = atom->nlocal;

		for (int i = 0; i < nlocal; i++) {
		@@ -73,16 +86,16 @@ FixTISpring::FixTISpring(LAMMPS lmp, int narg, char *arg) :
		}

		// Time variables.
		t_switch = force->bnumeric(FLERR,arg[4]); // Number of steps for switching.
		t_equil = force->bnumeric(FLERR,arg[5]); // Number of steps for equilibration.
		t_switch = atoi(arg[4]); // Switching time.
		t_equil = atoi(arg[5]); // Equilibration time.
		t0 = update->ntimestep; // Initial time.
		if (t_switch <= 0) error->all(FLERR,"Illegal fix ti/spring command");
		if (t_equil <= 0) error->all(FLERR,"Illegal fix ti/spring command");
		if (t_switch < 0.0) error->all(FLERR,"Illegal fix ti/spring command");
		if (t_equil < 0.0) error->all(FLERR,"Illegal fix ti/spring command");

		// Coupling parameter initialization.
		sf = 1;
		if (narg > 6) {
		if (strcmp(arg[6], "function") == 0) sf = force->inumeric(FLERR,arg[7]);
		if (strcmp(arg[6], "function") == 0) sf = atoi(arg[7]);
		else error->all(FLERR,"Illegal fix ti/spring switching function");
		if ((sf!=1) && (sf!=2))
		error->all(FLERR,"Illegal fix ti/spring switching function");
		@@ -151,13 +164,13 @@ void FixTISpring::min_setup(int vflag)
		void FixTISpring::post_force(int vflag)
		{
		// If on the first equilibration do not calculate forces.
		bigint t = update->ntimestep - t0;
		int t = update->ntimestep - t0;
		if(t < t_equil) return;

		double **x = atom->x;
		double **f = atom->f;
		int *mask = atom->mask;
		imageint *image = atom->image;
		tagint *image = atom->image;
		int nlocal = atom->nlocal;

		double dx, dy, dz;
		@@ -199,17 +212,16 @@ void FixTISpring::min_post_force(int vflag)
		void FixTISpring::initial_integrate(int vflag)
		{
		// Update the coupling parameter value.
		const bigint t = update->ntimestep - (t0+t_equil);
		const double r_switch = 1.0/t_switch;
		double t = update->ntimestep - (t0+t_equil);

		if( (t >= 0) && (t <= t_switch) ) {
		lambda = switch_func(t*r_switch);
		dlambda = dswitch_func(t*r_switch);
		lambda = switch_func(t/t_switch);
		dlambda = dswitch_func(t/t_switch);
		}

		if( (t >= t_equil+t_switch) && (t <= (t_equil+2*t_switch)) ) {
		lambda = switch_func(1.0 - (t - t_switch - t_equil)*r_switch);
		dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)*r_switch);
		lambda = switch_func(1.0 - (t - t_switch - t_equil)/t_switch );
		dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)/t_switch );
		}
		}

src/USER-MISC/fix_ti_spring.h

+8 −7

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
		@@ -13,7 +13,8 @@

		/* ----------------------------------------------------------------------
		Contributing authors:
		Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
		Rodrigo Freitas (UC Berkeley) - rodrigof@berkeley.edu
		Mark Asta (UC Berkeley) - mdasta@berkeley.edu
		Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
		------------------------------------------------------------------------- */

		@@ -65,9 +66,9 @@ class FixTISpring : public Fix {
		double lambda; // Coupling parameter.
		double dlambda; // Lambda variation with t.
		double linfo[2]; // Current lambda status.
		bigint t_switch; // Total switching steps.
		bigint t_equil; // Equilibration time.
		bigint t0; // Initial time.
		int t_switch; // Total switching steps.
		int t_equil; // Equilibration time.
		int t0; // Initial time.
		int sf; // Switching function option.
		int nlevels_respa;
		};

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