Added new argument r0stop to fix restrain bond (0f00bb1c) · Commits · 郑智淋 / lammps

doc/src/fix_restrain.rst

+31 −2

Original line number	Diff line number	Diff line
		@@ -17,10 +17,18 @@ Syntax

		.. parsed-literal::

		bond args = atom1 atom2 Kstart Kstop r0
		bond args = atom1 atom2 Kstart Kstop r0start r0stop
		atom1,atom2 = IDs of 2 atoms in bond
		Kstart,Kstop = restraint coefficients at start/end of run (energy units)
		r0 = equilibrium bond distance (distance units)
		r0start = equilibrium bond distance at start of run (distance units)
		r0stop = equilibrium bond distance at end of run (distance units). If not
		specified it's assumed to be equal to r0start
		lbond args = atom1 atom2 Kstart Kstop r0start r0stop
		atom1,atom2 = IDs of 2 atoms in bond
		Kstart,Kstop = restraint coefficients at start/end of run (energy units)
		r0start = equilibrium bond distance at start of run (distance units)
		r0stop = equilibrium bond distance at end of run (distance units). If not
		specified it's assumed to be equal to r0start
		angle args = atom1 atom2 atom3 Kstart Kstop theta0
		atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
		Kstart,Kstop = restraint coefficients at start/end of run (energy units)
		@@ -38,6 +46,7 @@ Examples
		.. code-block:: LAMMPS

		fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
		fix holdem all restrain lbond 45 48 2000.0 2000.0 2.75
		fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
		fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
		fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0
		@@ -141,6 +150,26 @@ is included in :math:`K`.

		----------

		The lbond keyword applies a lowerbound bond restraint to the specified atoms
		using the same functional form used by the :doc:`bond_style harmonic <bond_harmonic>` command if the distance between
		the atoms is smaller than the equilibrium bond distance and 0 otherwise. The potential associated with
		the restraint is

		.. math::

		E = K (r - r_0)^2 if r < r_0
		E = 0 if r >= r_0

		with the following coefficients:

		* :math:`K` (energy/distance\^2)
		* :math:`r_0` (distance)

		:math:`K` and :math:`r_0` are specified with the fix. Note that the usual 1/2 factor
		is included in :math:`K`.

		----------

		The angle keyword applies an angle restraint to the specified atoms
		using the same functional form used by the :doc:`angle_style harmonic <angle_harmonic>` command. The potential associated with
		the restraint is

src/fix_restrain.cpp

+126 −7

Original line number	Diff line number	Diff line
		@@ -34,7 +34,7 @@ using namespace LAMMPS_NS;
		using namespace FixConst;
		using namespace MathConst;

		enum{BOND,ANGLE,DIHEDRAL};
		enum{BOND,LBOUND,ANGLE,DIHEDRAL};

		#define TOLERANCE 0.05
		#define SMALL 0.001
		@@ -45,7 +45,7 @@ enum{BOND,ANGLE,DIHEDRAL};
		FixRestrain::FixRestrain(LAMMPS lmp, int narg, char *arg) :
		Fix(lmp, narg, arg),
		rstyle(NULL), mult(NULL), ids(NULL), kstart(NULL), kstop(NULL), target(NULL),
		cos_target(NULL), sin_target(NULL)
		deqstart(NULL), deqstop(NULL), cos_target(NULL), sin_target(NULL)
		{
		if (narg < 4) error->all(FLERR,"Illegal fix restrain command");

		@@ -72,6 +72,8 @@ FixRestrain::FixRestrain(LAMMPS lmp, int narg, char *arg) :
		memory->grow(kstart,maxrestrain,"restrain:kstart");
		memory->grow(kstop,maxrestrain,"restrain:kstop");
		memory->grow(target,maxrestrain,"restrain:target");
		memory->grow(deqstart,maxrestrain,"restrain:deqstart");
		memory->grow(deqstop,maxrestrain,"restrain:deqstop");
		memory->grow(cos_target,maxrestrain,"restrain:cos_target");
		memory->grow(sin_target,maxrestrain,"restrain:sin_target");
		}
		@@ -83,8 +85,29 @@ FixRestrain::FixRestrain(LAMMPS lmp, int narg, char *arg) :
		ids[nrestrain][1] = force->inumeric(FLERR,arg[iarg+2]);
		kstart[nrestrain] = force->numeric(FLERR,arg[iarg+3]);
		kstop[nrestrain] = force->numeric(FLERR,arg[iarg+4]);
		target[nrestrain] = force->numeric(FLERR,arg[iarg+5]);
		deqstart[nrestrain] = force->numeric(FLERR,arg[iarg+5]);
		if (iarg+6 == narg) {
		deqstop[nrestrain] = force->numeric(FLERR,arg[iarg+5]);
		iarg += 6;
		} else {
		deqstop[nrestrain] = force->numeric(FLERR,arg[iarg+6]);
		iarg += 7;
		}
		} else if (strcmp(arg[iarg],"lbound") == 0) {
		if (iarg+6 > narg) error->all(FLERR,"Illegal fix restrain command");
		rstyle[nrestrain] = LBOUND;
		ids[nrestrain][0] = force->inumeric(FLERR,arg[iarg+1]);
		ids[nrestrain][1] = force->inumeric(FLERR,arg[iarg+2]);
		kstart[nrestrain] = force->numeric(FLERR,arg[iarg+3]);
		kstop[nrestrain] = force->numeric(FLERR,arg[iarg+4]);
		deqstart[nrestrain] = force->numeric(FLERR,arg[iarg+5]);
		if (iarg+6 == narg) {
		deqstop[nrestrain] = force->numeric(FLERR,arg[iarg+5]);
		iarg += 6;
		} else {
		deqstop[nrestrain] = force->numeric(FLERR,arg[iarg+6]);
		iarg += 7;
		}
		} else if (strcmp(arg[iarg],"angle") == 0) {
		if (iarg+7 > narg) error->all(FLERR,"Illegal fix restrain command");
		rstyle[nrestrain] = ANGLE;
		@@ -139,6 +162,8 @@ FixRestrain::~FixRestrain()
		memory->destroy(kstart);
		memory->destroy(kstop);
		memory->destroy(target);
		memory->destroy(deqstart);
		memory->destroy(deqstop);
		memory->destroy(cos_target);
		memory->destroy(sin_target);
		}
		@@ -192,11 +217,13 @@ void FixRestrain::post_force(int /vflag/)
		energy = 0.0;

		ebond = 0.0;
		elbound = 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] == LBOUND) restrain_lbound(m);
		else if (rstyle[m] == ANGLE) restrain_angle(m);
		else if (rstyle[m] == DIHEDRAL) restrain_dihedral(m);
		}
		@@ -233,6 +260,7 @@ void FixRestrain::restrain_bond(int m)
		double delta = update->ntimestep - update->beginstep;
		if (delta != 0.0) delta /= update->endstep - update->beginstep;
		double k = kstart[m] + delta * (kstop[m] - kstart[m]);
		double deq = deqstart[m] + delta * (deqstop[m] - deqstart[m]);

		i1 = atom->map(ids[m][0]);
		i2 = atom->map(ids[m][1]);
		@@ -269,7 +297,7 @@ void FixRestrain::restrain_bond(int m)

		rsq = delxdelx + delydely + delz*delz;
		r = sqrt(rsq);
		dr = r - target[m];
		dr = r - deq;
		rk = k * dr;

		// force & energy
		@@ -295,6 +323,94 @@ void FixRestrain::restrain_bond(int m)
		}
		}

		/* ----------------------------------------------------------------------
		apply harmonic lower-bound bond restraints
		---------------------------------------------------------------------- */

		void FixRestrain::restrain_lbound(int m)
		{
		int i1,i2;
		double delx,dely,delz,fbond;
		double rsq,r,dr,rk;

		double **x = atom->x;
		double **f = atom->f;
		int nlocal = atom->nlocal;
		int newton_bond = force->newton_bond;

		double delta = update->ntimestep - update->beginstep;
		if (delta != 0.0) delta /= update->endstep - update->beginstep;
		double k = kstart[m] + delta * (kstop[m] - kstart[m]);
		double deq = deqstart[m] + delta * (deqstop[m] - deqstart[m]);

		i1 = atom->map(ids[m][0]);
		i2 = atom->map(ids[m][1]);

		// newton_bond on: only processor owning i2 computes restraint
		// newton_bond off: only processors owning either of i1,i2 computes restraint

		if (newton_bond) {
		if (i2 == -1 \|\| i2 >= nlocal) return;
		if (i1 == -1) {
		char str[128];
		sprintf(str,
		"Restrain atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
		ids[m][0],ids[m][1],
		comm->me,update->ntimestep);
		error->one(FLERR,str);
		}
		} else {
		if ((i1 == -1 \|\| i1 >= nlocal) && (i2 == -1 \|\| i2 >= nlocal)) return;
		if (i1 == -1 \|\| i2 == -1) {
		char str[128];
		sprintf(str,
		"Restrain atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
		ids[m][0],ids[m][1],
		comm->me,update->ntimestep);
		error->one(FLERR,str);
		}
		}

		delx = x[i1][0] - x[i2][0];
		dely = x[i1][1] - x[i2][1];
		delz = x[i1][2] - x[i2][2];
		domain->minimum_image(delx,dely,delz);

		rsq = delxdelx + delydely + delz*delz;
		r = sqrt(rsq);
		dr = r - deq;
		rk = k * dr;

		// force & energy

		if (dr < 0) {
		if (r > 0.0) fbond = -2.0*rk/r;
		else fbond = 0.0;

		elbound += rk*dr;
		energy += rk*dr;
		} else {
		fbond = 0.0;

		elbound += 0.0;
		energy += 0.0;
		}

		// apply force to each of 2 atoms

		if (newton_bond \|\| i1 < nlocal) {
		f[i1][0] += delx*fbond;
		f[i1][1] += dely*fbond;
		f[i1][2] += delz*fbond;
		}

		if (newton_bond \|\| i2 < nlocal) {
		f[i2][0] -= delx*fbond;
		f[i2][1] -= dely*fbond;
		f[i2][2] -= delz*fbond;
		}
		}

		/* ----------------------------------------------------------------------
		apply harmonic angle restraints
		---------------------------------------------------------------------- */
		@@ -655,9 +771,12 @@ double FixRestrain::compute_vector(int n)
		MPI_Allreduce(&ebond,&ebond_all,1,MPI_DOUBLE,MPI_SUM,world);
		return ebond_all;
		} else if (n == 1) {
		MPI_Allreduce(&elbound,&elbound_all,1,MPI_DOUBLE,MPI_SUM,world);
		return elbound_all;
		} else if (n == 3) {
		MPI_Allreduce(&eangle,&eangle_all,1,MPI_DOUBLE,MPI_SUM,world);
		return eangle_all;
		} else if (n == 2) {
		} else if (n == 4) {
		MPI_Allreduce(&edihed,&edihed_all,1,MPI_DOUBLE,MPI_SUM,world);
		return edihed_all;
		} else {

src/fix_restrain.h

+3 −1

Original line number	Diff line number	Diff line
		@@ -44,14 +44,16 @@ class FixRestrain : public Fix {
		int *rstyle;
		int *mult;
		int **ids;
		double kstart,kstop,*target;
		double kstart,kstop,deqstart,deqstop,*target;
		double cos_target,sin_target;
		double energy,energy_all;
		double ebond,ebond_all;
		double elbound,elbound_all;
		double eangle,eangle_all;
		double edihed,edihed_all;

		void restrain_bond(int);
		void restrain_lbound(int);
		void restrain_angle(int);
		void restrain_dihedral(int);
		};

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