(2e8b9cf4) · Commits · 郑智淋 / lammps

src/ASPHERE/compute_temp_asphere.cpp

+44 −44

Original line number	Diff line number	Diff line
		@@ -37,7 +37,8 @@ using namespace LAMMPS_NS;
		ComputeTempAsphere::ComputeTempAsphere(LAMMPS lmp, int narg, char *arg) :
		Compute(lmp, narg, arg)
		{
		if (narg != 3) error->all("Illegal compute temp command");
		if (narg != 3 \|\| narg != 4)
		error->all("Illegal compute temp/asphere command");

		if (!atom->quat_flag \|\| !atom->angmom_flag)
		error->all("Compute temp/asphere requires atom attributes quat, angmom");
		@@ -48,6 +49,15 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS lmp, int narg, char *arg) :
		extvector = 1;
		tempflag = 1;

		tempbias = 0;
		id_bias = NULL;
		if (narg == 4) {
		tempbias = 1;
		int n = strlen(arg[3]) + 1;
		id_bias = new char[n];
		strcpy(id_bias,arg[3]);
		}

		vector = new double[6];
		inertia =
		memory->create_2d_double_array(atom->ntypes+1,3,"fix_temp_sphere:inertia");
		@@ -57,6 +67,7 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS lmp, int narg, char *arg) :

		ComputeTempAsphere::~ComputeTempAsphere()
		{
		delete [] id_bias;
		delete [] vector;
		memory->destroy_2d_double_array(inertia);
		}
		@@ -65,20 +76,25 @@ ComputeTempAsphere::~ComputeTempAsphere()

		void ComputeTempAsphere::init()
		{
		fix_dof = 0;
		for (int i = 0; i < modify->nfix; i++)
		fix_dof += modify->fix[i]->dof(igroup);
		dof_compute();

		tempbias = 0;
		tbias = NULL;
		if (id_bias) {
		tempbias = 1;
		if (tempbias) {
		int i = modify->find_compute(id_bias);
		if (i < 0) error->all("Could not find compute ID for temperature bias");
		tbias = modify->compute[i];
		if (tbias->tempflag == 0)
		error->all("Bias compute does not calculate temperature");
		if (tbias->tempbias == 0)
		error->all("Bias compute does not calculate a velocity bias");
		if (tbias->igroup != igroup)
		error->all("Bias compute group does not match compute group");
		tbias->init();
		if (strcmp(tbias->style,"temp/region") == 0) tempbias = 2;
		}

		fix_dof = 0;
		for (int i = 0; i < modify->nfix; i++)
		fix_dof += modify->fix[i]->dof(igroup);
		dof_compute();

		calculate_inertia();
		}

		@@ -89,10 +105,10 @@ void ComputeTempAsphere::dof_compute()
		double natoms = group->count(igroup);
		int dimension = domain->dimension;
		dof = dimension * natoms;
		if (tbias) dof -= tbias->dof_remove(natoms);
		dof -= extra_dof + fix_dof;

		// add rotational degrees of freedom
		if (tempbias == 1) dof -= tbias->dof_remove(-1) * natoms;

		// rotational degrees of freedom
		// 0 for sphere, 2 for uniaxial, 3 for biaxial

		double **shape = atom->shape;
		@@ -101,27 +117,30 @@ void ComputeTempAsphere::dof_compute()
		int nlocal = atom->nlocal;

		int itype;
		int rot_dof = 0;
		int count = 0;

		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		if (tempbias == 2 && tbias->dof_remove(i)) continue;
		itype = type[i];
		if (dimension == 2) {
		if (shape[itype][0] == shape[itype][1]) continue;
		else rot_dof += 1;
		else count++;
		} else {
		if (shape[itype][0] == shape[itype][1] &&
		shape[itype][1] == shape[itype][2]) continue;
		else if (shape[itype][0] == shape[itype][1] \|\|
		shape[itype][1] == shape[itype][2] \|\|
		shape[itype][0] == shape[itype][2]) rot_dof += 2;
		else rot_dof += 3;
		shape[itype][0] == shape[itype][2]) count += 2;
		else count += 3;
		}
		}

		int rot_total;
		MPI_Allreduce(&rot_dof,&rot_total,1,MPI_INT,MPI_SUM,world);
		dof += rot_total;
		int count_all;
		MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
		dof += count_all;

		dof -= extra_dof + fix_dof;
		if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
		else tfactor = 0.0;
		}
		@@ -132,7 +151,7 @@ double ComputeTempAsphere::compute_scalar()
		{
		invoked \|= INVOKED_SCALAR;

		if (tbias) {
		if (tempbias) {
		if (!(tbias->invoked & INVOKED_SCALAR))
		double tmp = tbias->compute_scalar();
		tbias->remove_bias_all();
		@@ -179,10 +198,10 @@ double ComputeTempAsphere::compute_scalar()
		}
		}

		if (tbias) tbias->restore_bias_all();
		if (tempbias) tbias->restore_bias_all();

		MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
		if (dynamic \|\| tbias) dof_compute();
		if (dynamic \|\| tempbias == 2) dof_compute();
		scalar *= tfactor;
		return scalar;
		}
		@@ -195,7 +214,7 @@ void ComputeTempAsphere::compute_vector()

		invoked \|= INVOKED_VECTOR;

		if (tbias) {
		if (tempbias) {
		if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
		tbias->remove_bias_all();
		}
		@@ -246,7 +265,7 @@ void ComputeTempAsphere::compute_vector()
		t[5] += inertia[itype][2]wbody[1]wbody[2];
		}

		if (tbias) tbias->restore_bias_all();
		if (tempbias) tbias->restore_bias_all();

		MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
		for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
		@@ -280,15 +299,6 @@ void ComputeTempAsphere::remove_bias(int i, double *v)
		if (tbias) tbias->remove_bias(i,v);
		}

		/* ----------------------------------------------------------------------
		remove velocity bias from all atoms to leave thermal velocity
		------------------------------------------------------------------------- */

		void ComputeTempAsphere::remove_bias_all()
		{
		if (tbias) tbias->remove_bias_all();
		}

		/* ----------------------------------------------------------------------
		add back in velocity bias to atom I removed by remove_bias()
		assume remove_bias() was previously called
		@@ -298,13 +308,3 @@ void ComputeTempAsphere::restore_bias(int i, double *v)
		{
		if (tbias) tbias->restore_bias(i,v);
		}

		/* ----------------------------------------------------------------------
		add back in velocity bias to all atoms removed by remove_bias_all()
		assume remove_bias_all() was previously called
		------------------------------------------------------------------------- */

		void ComputeTempAsphere::restore_bias_all()
		{
		if (tbias) tbias->restore_bias_all();
		}

src/ASPHERE/compute_temp_asphere.h

+1 −3

Original line number	Diff line number	Diff line
		@@ -27,15 +27,13 @@ class ComputeTempAsphere : public Compute {
		void compute_vector();

		void remove_bias(int, double *);
		void remove_bias_all();
		void restore_bias(int, double *);
		void restore_bias_all();

		private:
		int fix_dof;
		double tfactor;
		double **inertia;

		char *id_bias;
		Compute *tbias; // ptr to additional bias compute

		void dof_compute();

src/compute.cpp

+0 −18

Original line number	Diff line number	Diff line
		@@ -62,9 +62,7 @@ Compute::Compute(LAMMPS lmp, int narg, char *arg) : Pointers(lmp)
		scalar_flag = vector_flag = peratom_flag = 0;
		tempflag = pressflag = peflag = 0;
		pressatomflag = peatomflag = 0;

		tempbias = 0;
		id_bias = NULL;

		id_pre = NULL;
		timeflag = 0;
		@@ -90,7 +88,6 @@ Compute::~Compute()
		{
		delete [] id;
		delete [] style;
		delete [] id_bias;
		delete [] id_pre;

		memory->sfree(tlist);
		@@ -120,21 +117,6 @@ void Compute::modify_params(int narg, char **arg)
		else if (strcmp(arg[iarg+1],"yes") == 0) thermoflag = 1;
		else error->all("Illegal compute_modify command");
		iarg += 2;
		} else if (strcmp(arg[iarg],"bias") == 0) {
		if (iarg+2 > narg) error->all("Illegal compute_modify command");
		delete [] id_bias;
		if (strcmp(arg[iarg+1],"NULL") == 0) id_bias = NULL;
		else {
		int n = strlen(arg[iarg+1]) + 1;
		id_bias = new char[n];
		strcpy(id_bias,arg[iarg+1]);
		int icompute = modify->find_compute(id_bias);
		if (icompute < 0) error->all("Could not find compute_modify bias ID");
		Compute *temperature = modify->compute[icompute];
		if (temperature->igroup != igroup && comm->me == 0)
		error->warning("Group for compute_modify bias != compute group");
		}
		iarg += 2;
		} else error->all("Illegal compute_modify command");
		}
		}

src/compute.h

+2 −4

Original line number	Diff line number	Diff line
		@@ -45,9 +45,7 @@ class Compute : protected Pointers {
		int peflag; // 1 if Compute calculates PE (uses Force energies)
		int peatomflag; // 1 if Compute calculates per-atom PE

		int tempbias; // 0/1 if Compute temp includes
		// self or extra bias via compute_modify
		char *id_bias; // ID of extra Compute temp that adds bias
		int tempbias; // 0/1 if Compute temp includes self/extra bias

		char *id_pre; // ID of pre-compute the Compute may store

		@@ -77,7 +75,7 @@ class Compute : protected Pointers {
		virtual int pack_reverse_comm(int, int, double *) {return 0;}
		virtual void unpack_reverse_comm(int, int , double ) {}

		virtual double dof_remove(double &) {return 0.0;}
		virtual int dof_remove(int) {return 0;}
		virtual void remove_bias(int, double *) {}
		virtual void remove_bias_all() {}
		virtual void restore_bias(int, double *) {}

src/compute_temp.cpp

+2 −64

Original line number	Diff line number	Diff line
		@@ -38,6 +38,7 @@ ComputeTemp::ComputeTemp(LAMMPS lmp, int narg, char *arg) :
		extscalar = 0;
		extvector = 1;
		tempflag = 1;
		tempbias = 0;

		vector = new double[6];
		}
		@@ -57,15 +58,6 @@ void ComputeTemp::init()
		for (int i = 0; i < modify->nfix; i++)
		fix_dof += modify->fix[i]->dof(igroup);
		dof_compute();

		tempbias = 0;
		tbias = NULL;
		if (id_bias) {
		tempbias = 1;
		int i = modify->find_compute(id_bias);
		if (i < 0) error->all("Could not find compute ID for temperature bias");
		tbias = modify->compute[i];
		}
		}

		/* ---------------------------------------------------------------------- */
		@@ -74,7 +66,6 @@ void ComputeTemp::dof_compute()
		{
		double natoms = group->count(igroup);
		dof = domain->dimension * natoms;
		if (tbias) dof -= tbias->dof_remove(natoms);
		dof -= extra_dof + fix_dof;
		if (dof > 0.0) tfactor = force->mvv2e / (dof * force->boltz);
		else tfactor = 0.0;
		@@ -86,12 +77,6 @@ double ComputeTemp::compute_scalar()
		{
		invoked \|= INVOKED_SCALAR;

		if (tbias) {
		if (!(tbias->invoked & INVOKED_SCALAR))
		double tmp = tbias->compute_scalar();
		tbias->remove_bias_all();
		}

		double **v = atom->v;
		double *mass = atom->mass;
		double *rmass = atom->rmass;
		@@ -112,10 +97,8 @@ double ComputeTemp::compute_scalar()
		t += (v[i][0]v[i][0] + v[i][1]v[i][1] + v[i][2]v[i][2]) rmass[i];
		}

		if (tbias) tbias->restore_bias_all();

		MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
		if (dynamic \|\| tbias) dof_compute();
		if (dynamic) dof_compute();
		scalar *= tfactor;
		return scalar;
		}
		@@ -128,11 +111,6 @@ void ComputeTemp::compute_vector()

		invoked \|= INVOKED_VECTOR;

		if (tbias) {
		if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
		tbias->remove_bias_all();
		}

		double **v = atom->v;
		double *mass = atom->mass;
		double *rmass = atom->rmass;
		@@ -155,46 +133,6 @@ void ComputeTemp::compute_vector()
		t[5] += massone * v[i][1]*v[i][2];
		}

		if (tbias) tbias->restore_bias_all();

		MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
		for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
		}

		/* ----------------------------------------------------------------------
		remove velocity bias from atom I to leave thermal velocity
		------------------------------------------------------------------------- */

		void ComputeTemp::remove_bias(int i, double *v)
		{
		if (tbias) tbias->remove_bias(i,v);
		}

		/* ----------------------------------------------------------------------
		remove velocity bias from all atoms to leave thermal velocity
		------------------------------------------------------------------------- */

		void ComputeTemp::remove_bias_all()
		{
		if (tbias) tbias->remove_bias_all();
		}

		/* ----------------------------------------------------------------------
		add back in velocity bias to atom I removed by remove_bias()
		assume remove_bias() was previously called
		------------------------------------------------------------------------- */

		void ComputeTemp::restore_bias(int i, double *v)
		{
		if (tbias) tbias->restore_bias(i,v);
		}

		/* ----------------------------------------------------------------------
		add back in velocity bias to all atoms removed by remove_bias_all()
		assume remove_bias_all() was previously called
		------------------------------------------------------------------------- */

		void ComputeTemp::restore_bias_all()
		{
		if (tbias) tbias->restore_bias_all();
		}

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