Merge pull request #2304 from akohlmey/collected-small-changes (93e4ed97) · Commits · 郑智淋 / lammps

doc/src/fix_restrain.rst

+4 −4

Original line number	Diff line number	Diff line
		@@ -13,7 +13,7 @@ Syntax
		* ID, group-ID are documented in :doc:`fix <fix>` command
		* restrain = style name of this fix command
		* one or more keyword/arg pairs may be appended
		* keyword = bond or angle or dihedral
		* keyword = bond or lbound or angle or dihedral

		.. parsed-literal::

		@@ -23,7 +23,7 @@ Syntax
		r0start = equilibrium bond distance at start of run (distance units)
		r0stop = equilibrium bond distance at end of run (optional) (distance units). If not
		specified it is assumed to be equal to r0start
		lbond args = atom1 atom2 Kstart Kstop r0start (r0stop)
		lbound 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)
		@@ -46,7 +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 lbound 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
		@@ -150,7 +150,7 @@ is included in :math:`K`.

		----------

		The lbond keyword applies a lower bound bond restraint to the specified atoms
		The lbound keyword applies a lower bound 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

src/KSPACE/pair_buck_long_coul_long.cpp

+12 −13

Original line number	Diff line number	Diff line
		@@ -90,6 +90,8 @@ void PairBuckLongCoulLong::settings(int narg, char **arg)
		error->warning(FLERR,"Using largest cutoff for buck/long/coul/long");
		if (!*(++arg))
		error->all(FLERR,"Cutoffs missing in pair_style buck/long/coul/long");
		if (!((ewald_order^ewald_off) & (1<<6)))
		dispersionflag = 0;
		if (ewald_off & (1<<6))
		error->all(FLERR,"LJ6 off not supported in pair_style buck/long/coul/long");
		if (!((ewald_order^ewald_off) & (1<<1)))
		@@ -387,6 +389,7 @@ void PairBuckLongCoulLong::write_restart_settings(FILE *fp)
		fwrite(&ncoultablebits,sizeof(int),1,fp);
		fwrite(&tabinner,sizeof(double),1,fp);
		fwrite(&ewald_order,sizeof(int),1,fp);
		fwrite(&dispersionflag,sizeof(int),1,fp);
		}

		/* ----------------------------------------------------------------------
		@@ -403,6 +406,7 @@ void PairBuckLongCoulLong::read_restart_settings(FILE *fp)
		utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
		utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&ewald_order,sizeof(int),1,fp,NULL,error);
		utils::sfread(FLERR,&dispersionflag,sizeof(int),1,fp,NULL,error);
		}
		MPI_Bcast(&cut_buck_global,1,MPI_DOUBLE,0,world);
		MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
		@@ -411,6 +415,7 @@ void PairBuckLongCoulLong::read_restart_settings(FILE *fp)
		MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world);
		MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
		MPI_Bcast(&ewald_order,1,MPI_INT,0,world);
		MPI_Bcast(&dispersionflag,1,MPI_INT,0,world);
		}

		/* ----------------------------------------------------------------------
		@@ -529,8 +534,7 @@ void PairBuckLongCoulLong::compute(int eflag, int vflag)
		if (eflag) ecoul = qiqj(etable[k]+fdetable[k]-t.f);
		}
		}
		}
		else force_coul = ecoul = 0.0;
		} else force_coul = ecoul = 0.0;

		if (rsq < cut_bucksqi[typej]) { // buckingham
		double rn = r2invr2invr2inv,
		@@ -543,16 +547,14 @@ void PairBuckLongCoulLong::compute(int eflag, int vflag)
		force_buck =
		rexprbuck1i[typej]-g8(((6.0a2+6.0)a2+3.0)a2+1.0)x2rsq;
		if (eflag) evdwl = exprbuckai[typej]-g6((a2+1.0)a2+0.5)x2;
		}
		else { // special case
		} else { // special case
		double f = special_lj[ni], t = rn*(1.0-f);
		force_buck = frexpr*buck1i[typej]-
		g8(((6.0a2+6.0)a2+3.0)a2+1.0)x2rsq+t*buck2i[typej];
		if (eflag) evdwl = fexprbuckai[typej] -
		g6((a2+1.0)a2+0.5)x2+tbuckci[typej];
		}
		}
		else { //table real space
		} else { //table real space
		union_int_float_t disp_t;
		disp_t.f = rsq;
		const int disp_k = (disp_t.i & ndispmask)>>ndispshiftbits;
		@@ -560,21 +562,18 @@ void PairBuckLongCoulLong::compute(int eflag, int vflag)
		if (ni == 0) {
		force_buck = rexprbuck1i[typej]-(fdisptable[disp_k]+f_dispdfdisptable[disp_k])buckci[typej];
		if (eflag) evdwl = exprbuckai[typej]-(edisptable[disp_k]+f_dispdedisptable[disp_k])*buckci[typej];
		}
		else { //speial case
		} else { //special case
		double f = special_lj[ni], t = rn*(1.0-f);
		force_buck = frexprbuck1i[typej] -(fdisptable[disp_k]+f_dispdfdisptable[disp_k])buckci[typej] +tbuck2i[typej];
		if (eflag) evdwl = fexprbuckai[typej] -(edisptable[disp_k]+f_dispdedisptable[disp_k])buckci[typej]+t*buckci[typej];
		}
		}
		}
		else { // cut
		} else { // cut
		if (ni == 0) {
		force_buck = rexprbuck1i[typej]-rn*buck2i[typej];
		if (eflag) evdwl = expr*buckai[typej] -
		rn*buckci[typej]-offseti[typej];
		}
		else { // special case
		} else { // special case
		double f = special_lj[ni];
		force_buck = f(rexprbuck1i[typej]-rnbuck2i[typej]);
		if (eflag)
		@@ -1018,7 +1017,7 @@ double PairBuckLongCoulLong::single(int i, int j, int itype, int jtype,
		g6((a2+1.0)a2+0.5)x2+tbuck_c[itype][jtype];
		} else { // cut
		force_buck =
		buck1[itype][jtype]rexpr-factor_buckbuck_c[itype][jtype]r6inv;
		factor_buck(buck1[itype][jtype]rexpr-buck2[itype][jtype]r6inv);
		eng += buck_a[itype][jtype]*expr-
		factor_buck(buck_c[itype][jtype]r6inv-offset[itype][jtype]);
		}

src/KSPACE/pair_lj_long_coul_long.cpp

+5 −0

Original line number	Diff line number	Diff line
		@@ -92,6 +92,8 @@ void PairLJLongCoulLong::settings(int narg, char **arg)
		error->warning(FLERR,"Using largest cutoff for lj/long/coul/long");
		if (!*(++arg))
		error->all(FLERR,"Cutoffs missing in pair_style lj/long/coul/long");
		if (!((ewald_order^ewald_off) & (1<<6)))
		dispersionflag = 0;
		if (!((ewald_order^ewald_off) & (1<<1)))
		error->all(FLERR,
		"Coulomb cut not supported in pair_style lj/long/coul/long");
		@@ -386,6 +388,7 @@ void PairLJLongCoulLong::write_restart_settings(FILE *fp)
		fwrite(&ncoultablebits,sizeof(int),1,fp);
		fwrite(&tabinner,sizeof(double),1,fp);
		fwrite(&ewald_order,sizeof(int),1,fp);
		fwrite(&dispersionflag,sizeof(int),1,fp);
		}

		/* ----------------------------------------------------------------------
		@@ -402,6 +405,7 @@ void PairLJLongCoulLong::read_restart_settings(FILE *fp)
		utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
		utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&ewald_order,sizeof(int),1,fp,NULL,error);
		utils::sfread(FLERR,&dispersionflag,sizeof(int),1,fp,NULL,error);
		}
		MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
		MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
		@@ -410,6 +414,7 @@ void PairLJLongCoulLong::read_restart_settings(FILE *fp)
		MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world);
		MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
		MPI_Bcast(&ewald_order,1,MPI_INT,0,world);
		MPI_Bcast(&dispersionflag,1,MPI_INT,0,world);
		}

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

src/KSPACE/pair_lj_long_tip4p_long.cpp

+5 −0

Original line number	Diff line number	Diff line
		@@ -1440,6 +1440,8 @@ void PairLJLongTIP4PLong::settings(int narg, char **arg)
		if (!comm->me && ewald_order==((1<<1)\|(1<<6)))
		error->warning(FLERR,
		"Using largest cutoff for pair_style lj/long/tip4p/long");
		if (!((ewald_order^ewald_off) & (1<<6)))
		dispersionflag = 0;
		if (!((ewald_order^ewald_off)&(1<<1)))
		error->all(FLERR,
		"Coulomb cut not supported in pair_style lj/long/tip4p/long");
		@@ -1532,6 +1534,7 @@ void PairLJLongTIP4PLong::write_restart_settings(FILE *fp)
		fwrite(&ncoultablebits,sizeof(int),1,fp);
		fwrite(&tabinner,sizeof(double),1,fp);
		fwrite(&ewald_order,sizeof(int),1,fp);
		fwrite(&dispersionflag,sizeof(int),1,fp);
		}

		/* ----------------------------------------------------------------------
		@@ -1554,6 +1557,7 @@ void PairLJLongTIP4PLong::read_restart_settings(FILE *fp)
		utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
		utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&ewald_order,sizeof(int),1,fp,NULL,error);
		utils::sfread(FLERR,&dispersionflag,sizeof(int),1,fp,NULL,error);
		}

		MPI_Bcast(&typeO,1,MPI_INT,0,world);
		@@ -1569,6 +1573,7 @@ void PairLJLongTIP4PLong::read_restart_settings(FILE *fp)
		MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world);
		MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
		MPI_Bcast(&ewald_order,1,MPI_INT,0,world);
		MPI_Bcast(&dispersionflag,1,MPI_INT,0,world);
		}

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

src/image.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -651,7 +651,7 @@ void Image::draw_cylinder(double x, double y,
		double c = surface[0] * surface[0] + surface[1] * surface[1] - radsq;

		double partial = bb - 4a*c;
		if (partial < 0) continue;
		if ((partial < 0.0) \|\| (a == 0.0)) continue;
		partial = sqrt (partial);

		double t = (-b + partial) / (2*a);

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