(5d667835) · Commits · 郑智淋 / lammps

src/atom.cpp

+8 −1

Original line number	Diff line number	Diff line
		@@ -76,6 +76,8 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
		spin = NULL;
		eradius = ervel = erforce = NULL;

		length = theta = NULL;

		maxspecial = 1;
		nspecial = NULL;
		special = NULL;
		@@ -102,6 +104,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
		quat_flag = omega_flag = angmom_flag = torque_flag = 0;
		radius_flag = density_flag = rmass_flag = vfrac_flag = 0;
		spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
		line_flag = 0;

		// ntype-length arrays

		@@ -185,6 +188,9 @@ Atom::~Atom()
		memory->sfree(ervel);
		memory->sfree(erforce);

		memory->sfree(length);
		memory->sfree(theta);

		memory->sfree(molecule);

		memory->destroy_2d_int_array(nspecial);
		@@ -262,6 +268,7 @@ void Atom::create_avec(const char style, int narg, char *arg)
		quat_flag = omega_flag = angmom_flag = torque_flag = 0;
		radius_flag = density_flag = rmass_flag = vfrac_flag = 0;
		spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
		line_flag = 0;

		avec = new_avec(style,narg,arg);
		int n = strlen(style) + 1;

src/atom.h

+3 −0

Original line number	Diff line number	Diff line
		@@ -55,6 +55,8 @@ class Atom : protected Pointers {
		int *spin;
		double eradius,ervel,*erforce;

		double length,theta;

		int **nspecial; // 0,1,2 = cummulative # of 1-2,1-3,1-4 neighs
		int **special; // IDs of 1-2,1-3,1-4 neighs of each atom
		int maxspecial; // special[nlocal][maxspecial]
		@@ -84,6 +86,7 @@ class Atom : protected Pointers {
		int quat_flag,omega_flag,angmom_flag,torque_flag;
		int radius_flag,density_flag,rmass_flag,vfrac_flag;
		int spin_flag,eradius_flag,ervel_flag,erforce_flag;
		int line_flag;

		// extra peratom info in restart file destined for fix & diag

src/compute_erotate_sphere.cpp

+13 −1

Original line number	Diff line number	Diff line
		@@ -23,7 +23,8 @@

		using namespace LAMMPS_NS;

		#define INERTIA 0.4 // moment of inertia for sphere
		//#define INERTIA 0.4 // moment of inertia for sphere
		#define INERTIA (1.0/12.0) // moment of inertia for sphere

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

		@@ -37,11 +38,13 @@ ComputeERotateSphere::ComputeERotateSphere(LAMMPS lmp, int narg, char *arg) :

		// error checks

		/*
		if (!atom->omega_flag)
		error->all("Compute erotate/sphere requires atom attribute omega");
		if (!atom->radius_flag && !atom->avec->shape_type)
		error->all("Compute erotate/sphere requires atom attribute "
		"radius or shape");
		*/
		}

		/* ---------------------------------------------------------------------- */
		@@ -53,6 +56,7 @@ void ComputeERotateSphere::init()
		// if shape used, check that all particles are spherical
		// point particles are allowed

		/*
		if (atom->radius == NULL) {
		double **shape = atom->shape;
		int *type = atom->type;
		@@ -68,6 +72,7 @@ void ComputeERotateSphere::init()
		"spherical particle shapes");
		}
		}
		*/

		pfactor = 0.5 * force->mvv2e * INERTIA;
		}
		@@ -112,6 +117,13 @@ double ComputeERotateSphere::compute_scalar()

		} else {
		if (rmass) {
		for (i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		erotate += (omega[i][0]omega[i][0] + omega[i][1]omega[i][1] +
		omega[i][2]omega[i][2])
		atom->length[i]atom->length[i]rmass[i];
		}
		} else if (rmass) {
		for (i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		itype = type[i];

src/compute_property_atom.cpp

+131 −0

Original line number	Diff line number	Diff line
		@@ -11,6 +11,7 @@
		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		#include "math.h"
		#include "string.h"
		#include "compute_property_atom.h"
		#include "atom.h"
		@@ -218,6 +219,37 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS lmp, int narg, char *arg) :
		"atom property that isn't allocated");
		pack_choice[i] = &ComputePropertyAtom::pack_erforce;

		} else if (strcmp(arg[iarg],"end1x") == 0) {
		if (!atom->line_flag)
		error->all("Compute property/atom for "
		"atom property that isn't allocated");
		pack_choice[i] = &ComputePropertyAtom::pack_end1x;
		} else if (strcmp(arg[iarg],"end1y") == 0) {
		if (!atom->line_flag)
		error->all("Compute property/atom for "
		"atom property that isn't allocated");
		pack_choice[i] = &ComputePropertyAtom::pack_end1y;
		} else if (strcmp(arg[iarg],"end1z") == 0) {
		if (!atom->line_flag)
		error->all("Compute property/atom for "
		"atom property that isn't allocated");
		pack_choice[i] = &ComputePropertyAtom::pack_end1z;
		} else if (strcmp(arg[iarg],"end2x") == 0) {
		if (!atom->line_flag)
		error->all("Compute property/atom for "
		"atom property that isn't allocated");
		pack_choice[i] = &ComputePropertyAtom::pack_end2x;
		} else if (strcmp(arg[iarg],"end2y") == 0) {
		if (!atom->line_flag)
		error->all("Compute property/atom for "
		"atom property that isn't allocated");
		pack_choice[i] = &ComputePropertyAtom::pack_end2y;
		} else if (strcmp(arg[iarg],"end2z") == 0) {
		if (!atom->line_flag)
		error->all("Compute property/atom for "
		"atom property that isn't allocated");
		pack_choice[i] = &ComputePropertyAtom::pack_end2z;

		} else error->all("Invalid keyword in compute property/atom command");
		}

		@@ -1100,3 +1132,102 @@ void ComputePropertyAtom::pack_erforce(int n)
		n += nvalues;
		}
		}

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

		void ComputePropertyAtom::pack_end1x(int n)
		{
		double **x = atom->x;
		double *length = atom->length;
		double *theta = atom->theta;
		int *mask = atom->mask;
		int nlocal = atom->nlocal;

		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) buf[n] = x[i][0] - 0.5length[i]cos(theta[i]);
		else buf[n] = 0.0;
		n += nvalues;
		}
		}

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

		void ComputePropertyAtom::pack_end1y(int n)
		{
		double **x = atom->x;
		double *length = atom->length;
		double *theta = atom->theta;
		int *mask = atom->mask;
		int nlocal = atom->nlocal;

		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) buf[n] = x[i][1] - 0.5length[i]sin(theta[i]);
		else buf[n] = 0.0;
		n += nvalues;
		}
		}

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

		void ComputePropertyAtom::pack_end1z(int n)
		{
		double **x = atom->x;
		int *mask = atom->mask;
		int nlocal = atom->nlocal;

		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) buf[n] = x[i][2];
		else buf[n] = 0.0;
		n += nvalues;
		}
		}

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

		void ComputePropertyAtom::pack_end2x(int n)
		{
		double **x = atom->x;
		double *length = atom->length;
		double *theta = atom->theta;
		int *mask = atom->mask;
		int nlocal = atom->nlocal;

		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) buf[n] = x[i][0] + 0.5length[i]cos(theta[i]);
		else buf[n] = 0.0;
		n += nvalues;
		}
		}

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

		void ComputePropertyAtom::pack_end2y(int n)
		{
		double **x = atom->x;
		double *length = atom->length;
		double *theta = atom->theta;
		int *mask = atom->mask;
		int nlocal = atom->nlocal;

		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) buf[n] = x[i][1] + 0.5length[i]sin(theta[i]);
		else buf[n] = 0.0;
		n += nvalues;
		}
		}

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

		void ComputePropertyAtom::pack_end2z(int n)
		{
		double **x = atom->x;
		int *mask = atom->mask;
		int nlocal = atom->nlocal;

		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) buf[n] = x[i][2];
		else buf[n] = 0.0;
		n += nvalues;
		}
		}

src/compute_property_atom.h

+6 −0

Original line number	Diff line number	Diff line
		@@ -94,6 +94,12 @@ class ComputePropertyAtom : public Compute {
		void pack_eradius(int);
		void pack_ervel(int);
		void pack_erforce(int);
		void pack_end1x(int);
		void pack_end1y(int);
		void pack_end1z(int);
		void pack_end2x(int);
		void pack_end2y(int);
		void pack_end2z(int);
		};

		}

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