Merge pull request #693 from giacomofiorin/colvars-update (f8f13d92) · Commits · 郑智淋 / lammps

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

+8.94 KiB (566 KiB)

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lib/colvars/Makefile.common

+1 −2

Original line number	Diff line number	Diff line
		@@ -59,8 +59,7 @@ LEPTON_OBJS = \
		COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o) $(LEPTON_OBJS)

		%.o: %.cpp
		$(CXX) $(CXXFLAGS) $(COLVARS_INCFLAGS) \
		-Ilepton/include -DLEPTON -c -o $@ $<
		$(CXX) $(CXXFLAGS) $(COLVARS_INCFLAGS) -Ilepton/include -DLEPTON -c -o $@ $<

		$(COLVARS_LIB): Makefile.deps $(COLVARS_OBJS)
		$(AR) $(ARFLAGS) $(COLVARS_LIB) $(COLVARS_OBJS) $(LEPTON_OBJS)

lib/colvars/Makefile.deps

+6 −5

Original line number	Diff line number	Diff line
		@@ -14,7 +14,7 @@ $(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \
		lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
		lepton/include/lepton/Exception.h \
		lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
		colvarbias_abf.h colvarbias.h colvargrid.h
		colvarbias_abf.h colvarbias.h colvargrid.h colvar_UIestimator.h
		$(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \
		colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \
		colvarbias_alb.h colvar.h colvarparse.h colvardeps.h \
		@@ -39,7 +39,8 @@ $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
		lepton/include/lepton/ExpressionTreeNode.h \
		lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
		lepton/include/lepton/Exception.h \
		lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h
		lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
		colvargrid.h
		$(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
		colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \
		colvarvalue.h colvar.h colvarparse.h colvardeps.h \
		@@ -198,9 +199,9 @@ $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
		lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
		lepton/include/lepton/Exception.h \
		lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
		colvarbias.h colvarbias_abf.h colvargrid.h colvarbias_alb.h \
		colvarbias_histogram.h colvarbias_meta.h colvarbias_restraint.h \
		colvarscript.h colvaratoms.h
		colvarbias.h colvarbias_abf.h colvargrid.h colvar_UIestimator.h \
		colvarbias_alb.h colvarbias_histogram.h colvarbias_meta.h \
		colvarbias_restraint.h colvarscript.h colvaratoms.h colvarcomp.h
		$(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \
		colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \
		colvarparse.h

lib/colvars/colvar.cpp

+18 −5

Original line number	Diff line number	Diff line
		@@ -1008,6 +1008,8 @@ int colvar::calc()

		int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
		{
		colvarproxy *proxy = cvm::main()->proxy;

		int error_code = COLVARS_OK;
		if (cvm::debug())
		cvm::log("Calculating colvar \""+this->name+"\", components "+
		@@ -1018,14 +1020,18 @@ int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
		return error_code;
		}

		if (cvm::step_relative() > 0) {
		// Total force depends on Jacobian derivative from previous timestep
		if ((cvm::step_relative() > 0) && (!proxy->total_forces_same_step())){
		// Use Jacobian derivative from previous timestep
		error_code \|= calc_cvc_total_force(first_cvc, num_cvcs);
		}
		// atom coordinates are updated by the next line
		error_code \|= calc_cvc_values(first_cvc, num_cvcs);
		error_code \|= calc_cvc_gradients(first_cvc, num_cvcs);
		error_code \|= calc_cvc_Jacobians(first_cvc, num_cvcs);
		if (proxy->total_forces_same_step()){
		// Use Jacobian derivative from this timestep
		error_code \|= calc_cvc_total_force(first_cvc, num_cvcs);
		}

		if (cvm::debug())
		cvm::log("Done calculating colvar \""+this->name+"\".\n");
		@@ -1043,6 +1049,7 @@ int colvar::collect_cvc_data()

		if (cvm::step_relative() > 0) {
		// Total force depends on Jacobian derivative from previous timestep
		// collect_cvc_total_forces() uses the previous value of jd
		error_code \|= collect_cvc_total_forces();
		}
		error_code \|= collect_cvc_values();
		@@ -1471,9 +1478,15 @@ cvm::real colvar::update_forces_energy()
		// Coupling force is a slow force, to be applied to atomic coords impulse-style
		f *= cvm::real(time_step_factor);

		if (is_enabled(f_cv_subtract_applied_force)) {
		// Report a "system" force without the biases on this colvar
		// that is, just the spring force
		ft_reported = (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
		} else {
		// The total force acting on the extended variable is f_ext
		// This will be used in the next timestep
		ft_reported = f_ext;
		}

		// leapfrog: starting from x_i, f_i, v_(i-1/2)
		vr += (0.5 * dt) * f_ext / ext_mass;

lib/colvars/colvar.h

+14 −1

Original line number	Diff line number	Diff line
		@@ -61,6 +61,9 @@ public:
		/// \brief Current actual value (not extended DOF)
		colvarvalue const & actual_value() const;

		/// \brief Force constant of the spring
		cvm::real const & force_constant() const;

		/// \brief Current velocity (previously set by calc() or by read_traj())
		colvarvalue const & velocity() const;

		@@ -96,6 +99,12 @@ public:
		{
		return cv_features;
		}
		static void delete_features() {
		for (size_t i=0; i < cv_features.size(); i++) {
		delete cv_features[i];
		}
		cv_features.clear();
		}

		/// Implements possible actions to be carried out
		/// when a given feature is enabled
		@@ -592,6 +601,10 @@ public:
		}
		};

		inline cvm::real const & colvar::force_constant() const
		{
		return ext_force_k;
		}

		inline colvarvalue const & colvar::value() const
		{

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