(96dae5a7) · Commits · 郑智淋 / lammps

src/USER-CG-CMM/angle_cg_cmm.cpp

+87 −4

Original line number	Diff line number	Diff line
		@@ -49,6 +49,88 @@ AngleCGCMM::~AngleCGCMM()

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

		void AngleCGCMM::ev_tally_lj13(int i, int j, int nlocal, int newton_bond,
		double evdwl, double fpair,
		double delx, double dely, double delz)
		{
		double v[6];

		if (eflag_either) {
		if (eflag_global) {
		if (newton_bond) {
		energy += evdwl;
		} else {
		if (i < nlocal)
		energy += 0.5*evdwl;
		if (j < nlocal)
		energy += 0.5*evdwl;
		}
		}
		if (eflag_atom) {
		if (newton_bond \|\| i < nlocal) eatom[i] += 0.5*evdwl;
		if (newton_bond \|\| j < nlocal) eatom[i] += 0.5*evdwl;
		}
		}

		if (vflag_either) {
		v[0] = delxdelxfpair;
		v[1] = delydelyfpair;
		v[2] = delzdelzfpair;
		v[3] = delxdelyfpair;
		v[4] = delxdelzfpair;
		v[5] = delydelzfpair;

		if (vflag_global) {
		if (newton_bond) {
		virial[0] += v[0];
		virial[1] += v[1];
		virial[2] += v[2];
		virial[3] += v[3];
		virial[4] += v[4];
		virial[5] += v[5];
		} else {
		if (i < nlocal) {
		virial[0] += 0.5*v[0];
		virial[1] += 0.5*v[1];
		virial[2] += 0.5*v[2];
		virial[3] += 0.5*v[3];
		virial[4] += 0.5*v[4];
		virial[5] += 0.5*v[5];
		}
		if (j < nlocal) {
		virial[0] += 0.5*v[0];
		virial[1] += 0.5*v[1];
		virial[2] += 0.5*v[2];
		virial[3] += 0.5*v[3];
		virial[4] += 0.5*v[4];
		virial[5] += 0.5*v[5];
		}
		}
		}

		if (vflag_atom) {
		if (newton_bond \|\| i < nlocal) {
		vatom[i][0] += 0.5*v[0];
		vatom[i][1] += 0.5*v[1];
		vatom[i][2] += 0.5*v[2];
		vatom[i][3] += 0.5*v[3];
		vatom[i][4] += 0.5*v[4];
		vatom[i][5] += 0.5*v[5];
		}
		if (newton_bond \|\| j < nlocal) {
		vatom[j][0] += 0.5*v[0];
		vatom[j][1] += 0.5*v[1];
		vatom[j][2] += 0.5*v[2];
		vatom[j][3] += 0.5*v[3];
		vatom[j][4] += 0.5*v[4];
		vatom[j][5] += 0.5*v[5];
		}
		}
		}
		}

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

		void AngleCGCMM::compute(int eflag, int vflag)
		{
		int i1,i2,i3,n,type;
		@@ -142,7 +224,7 @@ void AngleCGCMM::compute(int eflag, int vflag)
		dtheta = acos(c) - theta0[type];
		tk = k[type] * dtheta;

		if (eflag) eangle = tk*dtheta + e13;
		if (eflag) eangle = tk*dtheta;

		a = -2.0 * tk * s;
		a11 = a*c / rsq1;
		@@ -176,11 +258,12 @@ void AngleCGCMM::compute(int eflag, int vflag)
		f[i3][2] += f3[2] - f13*delz3;
		}

		// FIXME: we'll need to override this one for accurate virial.
		// for the time being, we hope that this contribution
		// is very small (it should be).
		if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
		delx1,dely1,delz1,delx2,dely2,delz2);

		if (evflag) ev_tally_lj13(i1,i3,nlocal,newton_bond,
		e13,f13,delx3,dely3,delz3);

		}
		}

src/USER-CG-CMM/angle_cg_cmm.h

+4 −0

Original line number	Diff line number	Diff line
		@@ -34,6 +34,10 @@ class AngleCGCMM : public Angle, public CGCMMParms {
		void read_restart(FILE *);
		double single(int, int, int, int);

		protected:
		void ev_tally_lj13(int, int, int, int, double, double,
		double, double, double);

		private:
		double k,theta0;
		int *cg_type;

src/USER-CG-CMM/pair_cg_cmm.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -33,7 +33,7 @@ namespace LAMMPS_NS {
		double single(int, int, int, int, double, double, double, double &);

		private:
		// disable default destructor
		// disable default constructor
		PairCGCMM();
		};
		}

src/USER-CG-CMM/pair_cmm_common.cpp

+4 −1

Original line number	Diff line number	Diff line
		@@ -259,6 +259,7 @@ double PairCMMCommon::init_one(int i, int j)

		if (allocated_coul) {
		mycut = MAX(cut_lj[i][j],cut_coul[i][j]);
		cut[i][j] = mycut;
		cut_ljsq[i][j]=cut_lj[i][j]*cut_lj[i][j];
		cut_coulsq[i][j]=cut_coul[i][j]*cut_coul[i][j];
		if (offset_flag) {
		@@ -274,6 +275,7 @@ double PairCMMCommon::init_one(int i, int j)
		lj4[j][i] = lj4[i][j];
		offset[j][i] = offset[i][j];
		cg_type[j][i] = cg_type[i][j];
		cut[j][i] = mycut;

		if (allocated_coul) {
		cut_lj[j][i]=cut_lj[i][j];
		@@ -407,6 +409,7 @@ void PairCMMCommon::read_restart_settings(FILE *fp)
		MPI_Bcast(&kappa,1,MPI_DOUBLE,0,world);
		MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
		MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
		cut_coulsq_global = cut_coul_global*cut_coul_global;
		}

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

src/USER-CG-CMM/pair_cmm_common.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -201,6 +201,7 @@ namespace LAMMPS_NS {
		const double ytmp = x[i][1];
		const double ztmp = x[i][2];
		double qtmp = (COUL_TYPE != CG_COUL_NONE) ? q[i] : 0.0;

		const int itype = type[i];
		const int * const jlist = firstneigh[i];
		const int jnum = numneigh[i];

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