(d0e374e4) · Commits · 郑智淋 / lammps

src/ASPHERE/fix_npt_asphere.cpp

+3 −3

Original line number	Diff line number	Diff line
		@@ -79,7 +79,7 @@ void FixNPTASphere::initial_integrate(int vflag)
		}
		ang_factor = exp(-dthalf*eta_dot);

		// v update only for atoms in NPT group
		// v update only for atoms in group

		double **x = atom->x;
		double **v = atom->v;
		@@ -107,7 +107,7 @@ void FixNPTASphere::initial_integrate(int vflag)

		remap(0);

		// x update by full step only for atoms in NPT group
		// x update by full step only for atoms in group

		for (i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		@@ -147,7 +147,7 @@ void FixNPTASphere::final_integrate()
		{
		int i;

		// v update only for atoms in NPT group
		// v update only for atoms in group

		double **v = atom->v;
		double **f = atom->f;

src/ASPHERE/fix_nvt_asphere.cpp

+2 −2

Original line number	Diff line number	Diff line
		@@ -61,7 +61,7 @@ void FixNVTASphere::initial_integrate(int vflag)
		eta += dtv*eta_dot;
		factor = exp(-dthalf*eta_dot);

		// update v and x of only atoms in NVT group
		// update v and x of only atoms in group

		double **x = atom->x;
		double **v = atom->v;
		@@ -106,7 +106,7 @@ void FixNVTASphere::final_integrate()
		{
		double dtfm;

		// update v of only atoms in NVT group
		// update v of only atoms in group

		double **v = atom->v;
		double **f = atom->f;

src/compute.cpp

+14 −0

Original line number	Diff line number	Diff line
		@@ -60,6 +60,7 @@ 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_pre = NULL;
		timeflag = 0;
		invoked = 0;
		@@ -162,3 +163,16 @@ int Compute::matchstep(int ntimestep)
		}
		return 0;
		}

		/* ----------------------------------------------------------------------
		add back in velocity bias removed by remove_bias() to leave thermal temp
		assume remove_bias() was previously called for this atom
		------------------------------------------------------------------------- */

		void Compute::restore_bias(double *v)
		{
		v[0] += vbias[0];
		v[1] += vbias[1];
		v[2] += vbias[2];
		}

src/compute.h

+6 −0

Original line number	Diff line number	Diff line
		@@ -45,6 +45,9 @@ 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 has bias routines for isolating thermal temp
		double vbias[3]; // stored velocity bias for one atom

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

		int timeflag; // 1 if Compute stores list of timesteps it's called on
		@@ -73,6 +76,9 @@ class Compute : protected Pointers {
		virtual int pack_reverse_comm(int, int, double *) {return 0;}
		virtual void unpack_reverse_comm(int, int , double ) {}

		virtual void remove_bias(int, double *) {}
		void restore_bias(double *);

		void addstep(int);
		int matchstep(int);

src/compute_temp_com.cpp

+21 −10

Original line number	Diff line number	Diff line
		@@ -44,6 +44,8 @@ ComputeTempCOM::ComputeTempCOM(LAMMPS lmp, int narg, char *arg) :
		extscalar = 0;
		extvector = 1;
		tempflag = 1;
		tempbias = 1;
		vbias[0] = vbias[1] = vbias[2] = 0.0;

		vector = new double[6];
		}
		@@ -81,12 +83,12 @@ void ComputeTempCOM::recount()

		double ComputeTempCOM::compute_scalar()
		{
		double vcm[3],vthermal[3];
		double vthermal[3];

		invoked \|= INVOKED_SCALAR;

		if (dynamic) masstotal = group->mass(igroup);
		group->vcm(igroup,masstotal,vcm);
		group->vcm(igroup,masstotal,vbias);

		double **v = atom->v;
		double *mass = atom->mass;
		@@ -98,9 +100,9 @@ double ComputeTempCOM::compute_scalar()
		double t = 0.0;
		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		vthermal[0] = v[i][0] - vcm[0];
		vthermal[1] = v[i][1] - vcm[1];
		vthermal[2] = v[i][2] - vcm[2];
		vthermal[0] = v[i][0] - vbias[0];
		vthermal[1] = v[i][1] - vbias[1];
		vthermal[2] = v[i][2] - vbias[2];
		if (mass)
		t += (vthermal[0]vthermal[0] + vthermal[1]vthermal[1] +
		vthermal[2]vthermal[2]) mass[type[i]];
		@@ -120,12 +122,12 @@ double ComputeTempCOM::compute_scalar()
		void ComputeTempCOM::compute_vector()
		{
		int i;
		double vcm[3],vthermal[3];
		double vthermal[3];

		invoked \|= INVOKED_VECTOR;

		if (dynamic) masstotal = group->mass(igroup);
		group->vcm(igroup,masstotal,vcm);
		group->vcm(igroup,masstotal,vbias);

		double **x = atom->x;
		double **v = atom->v;
		@@ -140,9 +142,9 @@ void ComputeTempCOM::compute_vector()

		for (i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		vthermal[0] = v[i][0] - vcm[0];
		vthermal[1] = v[i][1] - vcm[1];
		vthermal[2] = v[i][2] - vcm[2];
		vthermal[0] = v[i][0] - vbias[0];
		vthermal[1] = v[i][1] - vbias[1];
		vthermal[2] = v[i][2] - vbias[2];

		if (mass) massone = mass[type[i]];
		else massone = rmass[i];
		@@ -157,3 +159,12 @@ void ComputeTempCOM::compute_vector()
		MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
		for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
		}

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

		void ComputeTempCOM::remove_bias(int i, double *v)
		{
		v[0] = v[0] - vbias[0];
		v[1] = v[1] - vbias[1];
		v[2] = v[2] - vbias[2];
		}

Admin message