(a62fdded) · Commits · 郑智淋 / lammps

src/ASPHERE/Install.csh

+4 −0

Original line number	Diff line number	Diff line
		@@ -5,6 +5,7 @@ if ($1 == 1) then
		cp style_asphere.h ..

		cp atom_vec_ellipsoid.cpp ..
		cp compute_erotate_asphere.cpp ..
		cp compute_temp_asphere.cpp ..
		cp fix_npt_asphere.cpp ..
		cp fix_nve_asphere.cpp ..
		@@ -13,6 +14,7 @@ if ($1 == 1) then
		cp pair_resquared.cpp ..

		cp atom_vec_ellipsoid.h ..
		cp compute_erotate_asphere.h ..
		cp compute_temp_asphere.h ..
		cp fix_npt_asphere.h ..
		cp fix_nve_asphere.h ..
		@@ -26,6 +28,7 @@ else if ($1 == 0) then
		touch ../style_asphere.h

		rm ../atom_vec_ellipsoid.cpp
		rm ../compute_erotate_asphere.cpp
		rm ../compute_temp_asphere.cpp
		rm ../fix_npt_asphere.cpp
		rm ../fix_nve_asphere.cpp
		@@ -34,6 +37,7 @@ else if ($1 == 0) then
		rm ../pair_resquared.cpp

		rm ../atom_vec_ellipsoid.h
		rm ../compute_erotate_asphere.h
		rm ../compute_temp_asphere.h
		rm ../fix_npt_asphere.h
		rm ../fix_nve_asphere.h

src/ASPHERE/compute_erotate_asphere.cpp

0 → 100644

+118 −0

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.
		------------------------------------------------------------------------- */

		#include "mpi.h"
		#include "compute_erotate_asphere.h"
		#include "math_extra.h"
		#include "atom.h"
		#include "force.h"
		#include "memory.h"
		#include "error.h"

		using namespace LAMMPS_NS;

		#define INVOKED_SCALAR 1

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

		ComputeERotateASphere::ComputeERotateASphere(LAMMPS lmp, int narg, char *arg) :
		Compute(lmp, narg, arg)
		{
		if (narg != 3) error->all("Illegal compute erotate/asphere command");

		if (!atom->angmom_flag \|\| !atom->quat_flag)
		error->all("Compute erotate/asphere requires atom attributes angmom, quat");

		scalar_flag = 1;
		extscalar = 1;

		inertia =
		memory->create_2d_double_array(atom->ntypes+1,3,"fix_temp_sphere:inertia");
		}

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

		ComputeERotateASphere::~ComputeERotateASphere()
		{
		memory->destroy_2d_double_array(inertia);
		}

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

		void ComputeERotateASphere::init()
		{
		pfactor = 0.5 * force->mvv2e;

		if (!atom->shape)
		error->all("Compute erotate/asphere requires atom attribute shape");

		calculate_inertia();
		}

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

		double ComputeERotateASphere::compute_scalar()
		{
		invoked \|= INVOKED_SCALAR;

		double **quat = atom->quat;
		double **angmom = atom->angmom;
		int *mask = atom->mask;
		int *type = atom->type;
		int nlocal = atom->nlocal;

		int itype;
		double wbody[3];
		double rot[3][3];
		double erotate = 0.0;

		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		itype = type[i];

		// wbody = angular velocity in body frame

		MathExtra::quat_to_mat(quat[i],rot);
		MathExtra::transpose_times_column3(rot,angmom[i],wbody);
		wbody[0] /= inertia[itype][0];
		wbody[1] /= inertia[itype][1];
		wbody[2] /= inertia[itype][2];

		erotate += inertia[itype][0]wbody[0]wbody[0]+
		inertia[itype][1]wbody[1]wbody[1]+
		inertia[itype][2]wbody[2]wbody[2];
		}

		MPI_Allreduce(&erotate,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
		scalar *= pfactor;
		return scalar;
		}

		/* ----------------------------------------------------------------------
		principal moments of inertia for ellipsoids
		------------------------------------------------------------------------- */

		void ComputeERotateASphere::calculate_inertia()
		{
		double *mass = atom->mass;
		double **shape = atom->shape;

		for (int i = 1; i <= atom->ntypes; i++) {
		inertia[i][0] = mass[i] *
		(shape[i][1]shape[i][1]+shape[i][2]shape[i][2]) / 5.0;
		inertia[i][1] = mass[i] *
		(shape[i][0]shape[i][0]+shape[i][2]shape[i][2]) / 5.0;
		inertia[i][2] = mass[i] *
		(shape[i][0]shape[i][0]+shape[i][1]shape[i][1]) / 5.0;
		}
		}

src/ASPHERE/compute_erotate_asphere.h

0 → 100644

+37 −0

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.
		------------------------------------------------------------------------- */

		#ifndef COMPUTE_EROTATE_ASPHERE_H
		#define COMPUTE_EROTATE_ASPHERE_H

		#include "compute.h"

		namespace LAMMPS_NS {

		class ComputeERotateASphere : public Compute {
		public:
		ComputeERotateASphere(class LAMMPS , int, char *);
		~ComputeERotateASphere();
		void init();
		double compute_scalar();

		private:
		double pfactor;
		double **inertia;

		void calculate_inertia();
		};

		}

		#endif

src/ASPHERE/style_asphere.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -20,10 +20,12 @@ AtomStyle(ellipsoid,AtomVecEllipsoid)
		# endif

		#ifdef ComputeInclude
		#include "compute_erotate_asphere.h"
		#include "compute_temp_asphere.h"
		#endif

		#ifdef ComputeClass
		ComputeStyle(erotate/asphere,ComputeERotateASphere)
		ComputeStyle(temp/asphere,ComputeTempAsphere)
		#endif

Admin message