Allow extended Lagrangian on non-scalar collective variables (7a45c72b) · Commits · 郑智淋 / lammps

lib/colvars/colvar.cpp

+7 −4

Original line number	Diff line number	Diff line
		@@ -1085,7 +1085,7 @@ int colvar::calc_colvar_properties()
		// TODO: put it in the restart information
		if (cvm::step_relative() == 0) {
		xr = x;
		vr = 0.0; // (already 0; added for clarity)
		vr.reset(); // (already 0; added for clarity)
		}

		// report the restraint center as "value"
		@@ -1171,7 +1171,8 @@ cvm::real colvar::update_forces_energy()
		if (is_enabled(f_cv_extended_Lagrangian)) {

		cvm::real dt = cvm::dt();
		cvm::real f_ext;
		colvarvalue f_ext(fr.type());
		f_ext.reset();

		// the total force is applied to the fictitious mass, while the
		// atoms only feel the harmonic force
		@@ -1200,8 +1201,10 @@ cvm::real colvar::update_forces_energy()
		potential_energy = 0.5 * ext_force_k * this->dist2(xr, x);
		// leap to v_(i+1/2)
		if (is_enabled(f_cv_Langevin)) {
		vr -= dt * ext_gamma * vr.real_value;
		vr += dt * ext_sigma * cvm::rand_gaussian() / ext_mass;
		vr -= dt * ext_gamma * vr;
		colvarvalue rnd(x);
		rnd.set_random();
		vr += dt * ext_sigma * rnd / ext_mass;
		}
		vr += (0.5 * dt) * f_ext / ext_mass;
		xr += dt * vr;

+1 −1

Original line number	Diff line number	Diff line
		@@ -404,7 +404,7 @@ int colvarbias_meta::update()

		if (ebmeta) {
		hills_scale *= 1.0/target_dist->value(target_dist->get_colvars_index());
		if(cvm::step_absolute() <= ebmeta_equil_steps) {
		if(cvm::step_absolute() <= long(ebmeta_equil_steps)) {
		cvm::real const hills_lambda=(cvm::real(ebmeta_equil_steps - cvm::step_absolute()))/(cvm::real(ebmeta_equil_steps));
		hills_scale = hills_lambda + (1-hills_lambda)*hills_scale;
		}

+3 −3

Original line number	Diff line number	Diff line
		@@ -1071,7 +1071,7 @@ public:
		{
		// write the header
		os << "object 1 class gridpositions counts";
		int icv;
		size_t icv;
		for (icv = 0; icv < number_of_colvars(); icv++) {
		os << " " << number_of_points(icv);
		}
		@@ -1166,7 +1166,7 @@ public:

		/// \brief Return the log-gradient from finite differences
		/// on the same grid for dimension n
		inline const cvm::real log_gradient_finite_diff( const std::vector<int> &ix0,
		inline cvm::real log_gradient_finite_diff(const std::vector<int> &ix0,
		int n = 0)
		{
		cvm::real A0, A1;

+2 −2

Original line number	Diff line number	Diff line
		@@ -4,7 +4,7 @@
		#define COLVARMODULE_H

		#ifndef COLVARS_VERSION
		#define COLVARS_VERSION "2016-10-21"
		#define COLVARS_VERSION "2016-10-27"
		#endif

		#ifndef COLVARS_DEBUG
		@@ -198,7 +198,7 @@ public:
		}

		/// \brief How many objects are configured yet?
		inline size_t const size() const
		inline size_t size() const
		{
		return colvars.size() + biases.size();
		}

+1 −1

Original line number	Diff line number	Diff line
		@@ -25,7 +25,7 @@ public:
		colvarmodule *colvars;

		/// Default constructor
		inline colvarproxy() : script(NULL), b_smp_active(true) {}
		inline colvarproxy() : b_smp_active(true), script(NULL) {}

		/// Default destructor
		virtual ~colvarproxy() {}