(e13c488f) · Commits · 郑智淋 / lammps

src/compute_angle_local.cpp

+15 −10

Original line number	Diff line number	Diff line
		@@ -47,14 +47,14 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS lmp, int narg, char *arg) :
		which = new int[nvalues];
		pack_choice = new FnPtrPack[nvalues];

		dflag = eflag = 0;
		tflag = eflag = 0;

		int i;
		for (int iarg = 3; iarg < narg; iarg++) {
		i = iarg-3;

		if (strcmp(arg[iarg],"theta") == 0) {
		dflag = 1;
		tflag = 1;
		which[i] = THETA;
		pack_choice[i] = &ComputeAngleLocal::pack_theta;
		} else if (strcmp(arg[iarg],"energy") == 0) {
		@@ -124,6 +124,7 @@ void ComputeAngleLocal::compute_local()
		if angle is deleted (type = 0), do not count
		if angle is turned off (type < 0), still count
		if flag is set, compute requested info about angle
		if angle is turned off (type < 0), energy = 0.0
		------------------------------------------------------------------------- */

		int ComputeAngleLocal::compute_angles(int flag)
		@@ -143,6 +144,7 @@ int ComputeAngleLocal::compute_angles(int flag)
		int nlocal = atom->nlocal;

		Angle *angle = force->angle;
		double PI = 4.0*atan(1.0);

		int m = 0;
		for (atom2 = 0; atom2 < nlocal; atom2++) {
		@@ -153,10 +155,10 @@ int ComputeAngleLocal::compute_angles(int flag)
		if (atom1 < 0 \|\| !(mask[atom1] & groupbit)) continue;
		atom3 = atom->map(angle_atom3[atom2][i]);
		if (atom3 < 0 \|\| !(mask[atom3] & groupbit)) continue;
		if (angle_type[atom2][i] == 0) continue;

		if (flag) {

		if (dflag) {
		if (tflag) {
		delx1 = x[atom1][0] - x[atom2][0];
		dely1 = x[atom1][1] - x[atom2][1];
		delz1 = x[atom1][2] - x[atom2][2];
		@@ -179,11 +181,14 @@ int ComputeAngleLocal::compute_angles(int flag)
		c /= r1*r2;
		if (c > 1.0) c = 1.0;
		if (c < -1.0) c = -1.0;
		theta[m] = acos(c);
		theta[m] = 180.0*acos(c)/PI;
		}

		if (eflag)
		energy[m] = angle->single(angle_type[atom1][i],atom1,atom2,atom3);
		if (eflag) {
		if (angle_type[atom2][i] > 0)
		energy[m] = angle->single(angle_type[atom2][i],atom1,atom2,atom3);
		else energy[m] = 0.0;
		}
		}

		m++;
		@@ -221,7 +226,7 @@ void ComputeAngleLocal::reallocate(int n)

		while (nmax < n) nmax += DELTA;

		if (dflag) {
		if (tflag) {
		memory->sfree(theta);
		theta = (double ) memory->smalloc(nmaxsizeof(double),
		"bond/local:theta");
		@@ -233,7 +238,7 @@ void ComputeAngleLocal::reallocate(int n)
		}

		if (nvalues == 1) {
		if (dflag) vector_local = theta;
		if (tflag) vector_local = theta;
		if (eflag) vector_local = energy;
		} else {
		memory->destroy_2d_double_array(array);
		@@ -250,7 +255,7 @@ void ComputeAngleLocal::reallocate(int n)
		double ComputeAngleLocal::memory_usage()
		{
		double bytes = 0.0;
		if (dflag) bytes += nmax * sizeof(double);
		if (tflag) bytes += nmax * sizeof(double);
		if (eflag) bytes += nmax * sizeof(double);
		if (nvalues > 1) bytes += nmaxnvalues sizeof(double);
		return bytes;

src/compute_angle_local.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -27,7 +27,7 @@ class ComputeAngleLocal : public Compute {
		double memory_usage();

		private:
		int nvalues,dflag,eflag;
		int nvalues,tflag,eflag;
		int *which;
		int ncount;

src/compute_bond_local.cpp

+6 −2

Original line number	Diff line number	Diff line
		@@ -124,6 +124,7 @@ void ComputeBondLocal::compute_local()
		if bond is deleted (type = 0), do not count
		if bond is turned off (type < 0), still count
		if flag is set, compute requested info about bond
		if bond is turned off (type < 0), energy = 0.0
		------------------------------------------------------------------------- */

		int ComputeBondLocal::compute_bonds(int flag)
		@@ -158,8 +159,11 @@ int ComputeBondLocal::compute_bonds(int flag)
		domain->minimum_image(delx,dely,delz);
		rsq = delxdelx + delydely + delz*delz;
		if (dflag) distance[m] = sqrt(rsq);
		if (eflag)
		if (eflag) {
		if (bond_type[atom1][i] > 0)
		energy[m] = bond->single(bond_type[atom1][i],rsq,atom1,atom2);
		else energy[m] = 0.0;
		}
		}

		m++;

src/fix_rigid.cpp

+9 −12

Original line number	Diff line number	Diff line
		@@ -203,10 +203,11 @@ FixRigid::FixRigid(LAMMPS lmp, int narg, char *arg) :

		// initialize force/torque flags to default = 1.0

		vector_flag = 1;
		size_vector = 12*nbody;
		array_flag = 1;
		size_array_rows = nbody;
		size_array_cols = 12;
		global_freq = 1;
		extvector = 0;
		extarray = 0;

		for (i = 0; i < nbody; i++) {
		fflag[i][0] = fflag[i][1] = fflag[i][2] = 1.0;
		@@ -2139,14 +2140,10 @@ void FixRigid::reset_dt()
		xcm = 1,2,3; vcm = 4,5,6; fcm = 7,8,9; torque = 10,11,12
		------------------------------------------------------------------------- */

		double FixRigid::compute_vector(int n)
		double FixRigid::compute_array(int i, int j)
		{
		int ibody = n/12;
		int iattribute = (n % 12) / 3;
		int index = n % 3;

		if (iattribute == 0) return xcm[ibody][index];
		else if (iattribute == 1) return vcm[ibody][index];
		else if (iattribute == 2) return fcm[ibody][index];
		else return torque[ibody][index];
		if (j <= 3) return xcm[i][j];
		if (j <= 6) return vcm[i][j-3];
		if (j <= 9) return fcm[i][j-6];
		return torque[i][j-9];
		}

src/fix_rigid.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -41,7 +41,7 @@ class FixRigid : public Fix {
		int dof(int);
		void deform(int);
		void reset_dt();
		double compute_vector(int);
		double compute_array(int, int);

		private:
		double dtv,dtf,dtq;

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