Merge pull request #898 from robeme/fix_restrain_individual_energies (e5a589e0) · Commits · 郑智淋 / lammps

doc/src/fix_restrain.txt

+11 −4

Original line number	Diff line number	Diff line
		@@ -187,10 +187,17 @@ added forces to be included in the total potential energy of the
		system (the quantity being minimized), you MUST enable the
		"fix_modify"_fix_modify.html {energy} option for this fix.

		This fix computes a global scalar, which can be accessed by various
		"output commands"_Section_howto.html#howto_15. The scalar is the
		potential energy for all the restraints as discussed above. The scalar
		value calculated by this fix is "extensive".
		This fix computes a global scalar and a global vector of length 3, which
		can be accessed by various "output commands"_Section_howto.html#howto_15.
		The scalar is the total potential energy for {all} the restraints as
		discussed above. The vector values are the sum of contributions to the
		following individual categories:

		1 = bond energy
		2 = angle energy
		3 = dihedral energy :ul

		The scalar and vector values calculated by this fix are "extensive".

		No parameter of this fix can be used with the {start/stop} keywords of
		the "run"_run.html command.

src/fix_restrain.cpp

+30 −0

Original line number	Diff line number	Diff line
		@@ -53,6 +53,9 @@ FixRestrain::FixRestrain(LAMMPS lmp, int narg, char *arg) :
		scalar_flag = 1;
		global_freq = 1;
		extscalar = 1;
		vector_flag = 1;
		size_vector = 3;
		extvector = 1;
		respa_level_support = 1;
		ilevel_respa = 0;

		@@ -189,6 +192,10 @@ void FixRestrain::post_force(int vflag)
		{
		energy = 0.0;

		ebond = 0.0;
		eangle = 0.0;
		edihed = 0.0;

		for (int m = 0; m < nrestrain; m++)
		if (rstyle[m] == BOND) restrain_bond(m);
		else if (rstyle[m] == ANGLE) restrain_angle(m);
		@@ -271,6 +278,7 @@ void FixRestrain::restrain_bond(int m)
		if (r > 0.0) fbond = -2.0*rk/r;
		else fbond = 0.0;

		ebond += rk*dr;
		energy += rk*dr;

		// apply force to each of 2 atoms
		@@ -378,6 +386,7 @@ void FixRestrain::restrain_angle(int m)
		dtheta = acos(c) - target[m];
		tk = k * dtheta;

		eangle += tk*dtheta;
		energy += tk*dtheta;

		a = -2.0 * tk * s;
		@@ -558,6 +567,7 @@ void FixRestrain::restrain_dihedral(int m)
		df1 *= -mult[m];
		p += 1.0;

		edihed += k * p;
		energy += k * p;

		fg = vb1xvb2xm + vb1yvb2ym + vb1z*vb2zm;
		@@ -635,3 +645,23 @@ double FixRestrain::compute_scalar()
		MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
		return energy_all;
		}

		/* ----------------------------------------------------------------------
		return individual energy contributions
		------------------------------------------------------------------------- */

		double FixRestrain::compute_vector(int n)
		{
		if (n == 0) {
		MPI_Allreduce(&ebond,&ebond_all,1,MPI_DOUBLE,MPI_SUM,world);
		return ebond_all;
		} else if (n == 1) {
		MPI_Allreduce(&eangle,&eangle_all,1,MPI_DOUBLE,MPI_SUM,world);
		return eangle_all;
		} else if (n == 2) {
		MPI_Allreduce(&edihed,&edihed_all,1,MPI_DOUBLE,MPI_SUM,world);
		return edihed_all;
		} else {
		return 0.0;
		}
		}

src/fix_restrain.h

+4 −0

Original line number	Diff line number	Diff line
		@@ -36,6 +36,7 @@ class FixRestrain : public Fix {
		void post_force_respa(int, int, int);
		void min_post_force(int);
		double compute_scalar();
		double compute_vector(int);

		private:
		int ilevel_respa;
		@@ -46,6 +47,9 @@ class FixRestrain : public Fix {
		double kstart,kstop,*target;
		double cos_target,sin_target;
		double energy,energy_all;
		double ebond,ebond_all;
		double eangle,eangle_all;
		double edihed,edihed_all;

		void restrain_bond(int);
		void restrain_angle(int);

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