Version 30 Sep 2016 (be4734bd) · Commits · 郑智淋 / lammps

doc/src/PDF/colvars-refman-lammps.pdf

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examples/cmap/charmm22.cmap

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Original line number	Diff line number	Diff line
		# Title: charmm correction map
		# DATE: 2016-09-26 CONTRIBUTOR: Robert Latour, latourr@clemson.edu CITATION: TBA
		# Title: charmm22/charmm27 dihedral correction map

		# alanine map, type 1

examples/tad/README

+1 −1

Original line number	Diff line number	Diff line
		Run this example as:

		mpirun -np 3 lmp_linux -partition 3x1 -in in.tad
		mpirun -np 3 lmp_g++ -partition 3x1 -in in.tad

		You should be able to use any number of replicas >= 3.

lib/colvars/colvar.cpp

+26 −28

Original line number	Diff line number	Diff line
		@@ -150,7 +150,7 @@ colvar::colvar(std::string const &conf)
		feature_states[f_cv_linear]->enabled = lin;
		}

		// Colvar is homogeneous iff:
		// Colvar is homogeneous if:
		// - it is linear (hence not scripted)
		// - all cvcs have coefficient 1 or -1
		// i.e. sum or difference of cvcs
		@@ -375,28 +375,16 @@ colvar::colvar(std::string const &conf)

		{
		bool temp;
		if (get_keyval(conf, "outputSystemForce", temp, false)) {
		cvm::error("Colvar option outputSystemForce is deprecated.\n"
		"Please use outputTotalForce, or outputSystemForce within an ABF bias.");
		if (get_keyval(conf, "outputSystemForce", temp, false, colvarparse::parse_silent)) {
		cvm::error("Option outputSystemForce is deprecated: only outputTotalForce is supported instead.\n"
		"The two are NOT identical: see http://colvars.github.io/totalforce.html.\n", INPUT_ERROR);
		return;
		}
		}

		{
		bool b_output_total_force;
		get_keyval(conf, "outputTotalForce", b_output_total_force, false);
		if (b_output_total_force) {
		enable(f_cv_output_total_force);
		}
		}

		{
		bool b_output_applied_force;
		get_keyval(conf, "outputAppliedForce", b_output_applied_force, false);
		if (b_output_applied_force) {
		enable(f_cv_output_applied_force);
		}
		}
		get_keyval_feature(this, conf, "outputTotalForce", f_cv_output_total_force, false);
		get_keyval_feature(this, conf, "outputAppliedForce", f_cv_output_applied_force, false);
		get_keyval_feature(this, conf, "subtractAppliedForce", f_cv_subtract_applied_force, false);

		// Start in active state by default
		enable(f_cv_active);
		@@ -409,6 +397,8 @@ colvar::colvar(std::string const &conf)
		fj.type(value());
		ft.type(value());
		ft_reported.type(value());
		f_old.type(value());
		f_old.reset();

		if (cvm::b_analysis)
		parse_analysis(conf);
		@@ -519,6 +509,8 @@ int colvar::init_components(std::string const &conf)
		"number", "coordNum");
		error_code \|= init_components_type<selfcoordnum>(conf, "self-coordination "
		"number", "selfCoordNum");
		error_code \|= init_components_type<groupcoordnum>(conf, "group-coordination "
		"number", "groupCoord");
		error_code \|= init_components_type<angle>(conf, "angle", "angle");
		error_code \|= init_components_type<dipole_angle>(conf, "dipole angle", "dipoleAngle");
		error_code \|= init_components_type<dihedral>(conf, "dihedral", "dihedral");
		@@ -1104,6 +1096,14 @@ int colvar::calc_colvar_properties()

		} else {

		if (is_enabled(f_cv_subtract_applied_force)) {
		// correct the total force only if it has been measured
		// TODO add a specific test instead of relying on sq norm
		if (ft.norm2() > 0.0) {
		ft -= f_old;
		}
		}

		x_reported = x;
		ft_reported = ft;
		}
		@@ -1210,6 +1210,10 @@ cvm::real colvar::update_forces_energy()
		x_old = x;
		}

		if (is_enabled(f_cv_subtract_applied_force)) {
		f_old = f;
		}

		if (cvm::debug())
		cvm::log("Done updating colvar \""+this->name+"\".\n");
		return (potential_energy + kinetic_energy);
		@@ -1640,15 +1644,9 @@ std::ostream & colvar::write_traj(std::ostream &os)
		}

		if (is_enabled(f_cv_output_applied_force)) {
		if (is_enabled(f_cv_extended_Lagrangian)) {
		os << " "
		<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
		<< fr;
		} else {
		os << " "
		<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
		<< f;
		}
		<< applied_force();
		}

		return os;

lib/colvars/colvar.h

+10 −3

Original line number	Diff line number	Diff line
		@@ -175,6 +175,9 @@ public:
		/// (if defined) contribute to it
		colvarvalue f;

		/// Applied force at the previous step (to be subtracted from total force if needed)
		colvarvalue f_old;

		/// \brief Total force, as derived from the atomic trajectory;
		/// should equal the system force plus \link f \endlink
		colvarvalue ft;
		@@ -272,10 +275,13 @@ public:
		/// \brief Calculate the quantities associated to the colvar (but not to the CVCs)
		int calc_colvar_properties();

		/// Get the current biasing force
		inline colvarvalue bias_force() const
		/// Get the current applied force
		inline colvarvalue const applied_force() const
		{
		return fb;
		if (is_enabled(f_cv_extended_Lagrangian)) {
		return fr;
		}
		return f;
		}

		/// Set the total biasing force to zero
		@@ -482,6 +488,7 @@ public:
		class dihedral;
		class coordnum;
		class selfcoordnum;
		class groupcoordnum;
		class h_bond;
		class rmsd;
		class orientation_angle;

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