update colvars library to version 2016-08-05 (77620106) · Commits · 郑智淋 / lammps

lib/colvars/colvar.cpp

+31 −34

Original line number	Diff line number	Diff line
		@@ -1187,40 +1187,6 @@ cvm::real colvar::update_forces_energy()
		f -= fj;
		}

		if (is_enabled(f_cv_extended_Lagrangian)) {

		cvm::real dt = cvm::dt();
		cvm::real f_ext;

		// the total force is applied to the fictitious mass, while the
		// atoms only feel the harmonic force
		// fr: bias force on extended coordinate (without harmonic spring), for output in trajectory
		// f_ext: total force on extended coordinate (including harmonic spring)
		// f: - initially, external biasing force
		// - after this code block, colvar force to be applied to atomic coordinates, ie. spring force
		// (note: wall potential is added to f after this block)
		fr = f;
		f_ext = f + (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
		f = (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x);

		// leapfrog: starting from x_i, f_i, v_(i-1/2)
		vr += (0.5 * dt) * f_ext / ext_mass;
		// Because of leapfrog, kinetic energy at time i is approximate
		kinetic_energy = 0.5 * ext_mass * vr * vr;
		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 += (0.5 * dt) * f_ext / ext_mass;
		xr += dt * vr;
		xr.apply_constraints();
		if (this->b_periodic) this->wrap(xr);
		}


		// Adding wall potential to "true" colvar force, whether or not an extended coordinate is in use
		if (is_enabled(f_cv_lower_wall) \|\| is_enabled(f_cv_upper_wall)) {

		// Wall force
		@@ -1257,6 +1223,37 @@ cvm::real colvar::update_forces_energy()
		}
		}

		if (is_enabled(f_cv_extended_Lagrangian)) {

		cvm::real dt = cvm::dt();
		cvm::real f_ext;

		// the total force is applied to the fictitious mass, while the
		// atoms only feel the harmonic force
		// fr: bias force on extended coordinate (without harmonic spring), for output in trajectory
		// f_ext: total force on extended coordinate (including harmonic spring)
		// f: - initially, external biasing force
		// - after this code block, colvar force to be applied to atomic coordinates, ie. spring force
		fr = f;
		f_ext = f + (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
		f = (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x);

		// leapfrog: starting from x_i, f_i, v_(i-1/2)
		vr += (0.5 * dt) * f_ext / ext_mass;
		// Because of leapfrog, kinetic energy at time i is approximate
		kinetic_energy = 0.5 * ext_mass * vr * vr;
		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 += (0.5 * dt) * f_ext / ext_mass;
		xr += dt * vr;
		xr.apply_constraints();
		if (this->b_periodic) this->wrap(xr);
		}

		f_accumulated += f;

		if (is_enabled(f_cv_fdiff_velocity)) {

lib/colvars/colvarbias_abf.cpp

+67 −11

Original line number	Diff line number	Diff line
		@@ -12,6 +12,7 @@ colvarbias_abf::colvarbias_abf(char const *key)
		samples(NULL),
		z_gradients(NULL),
		z_samples(NULL),
		czar_gradients(NULL),
		last_gradients(NULL),
		last_samples(NULL)
		{
		@@ -144,6 +145,7 @@ int colvarbias_abf::init(std::string const &conf)
		z_gradients->request_actual_value();
		z_gradients->samples = z_samples;
		z_samples->has_parent_data = true;
		czar_gradients = new colvar_grid_gradient(colvars);
		}

		// For shared ABF, we store a second set of grids.
		@@ -178,6 +180,21 @@ colvarbias_abf::~colvarbias_abf()
		gradients = NULL;
		}

		if (z_samples) {
		delete z_samples;
		z_samples = NULL;
		}

		if (z_gradients) {
		delete z_gradients;
		z_gradients = NULL;
		}

		if (czar_gradients) {
		delete czar_gradients;
		czar_gradients = NULL;
		}

		// shared ABF
		// We used to only do this if "shared" was defined,
		// but now we can call shared externally
		@@ -237,7 +254,11 @@ int colvarbias_abf::update()
		z_bin[i] = z_samples->current_bin_scalar(i);
		}
		if ( z_samples->index_ok(z_bin) ) {
		// Set increment flag to 0 to only increment
		for (size_t i=0; i<colvars.size(); i++) {
		// If we are outside the range of xi, the force has not been obtained above
		// the function is just an accessor, so cheap to call again anyway
		force[i] = colvars[i]->system_force();
		}
		z_gradients->acc_force(z_bin, force);
		}
		}
		@@ -404,14 +425,10 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
		{
		std::string samples_out_name = prefix + ".count";
		std::string gradients_out_name = prefix + ".grad";
		std::string z_gradients_out_name = prefix + ".zgrad";
		std::string z_samples_out_name = prefix + ".zcount";
		std::ios::openmode mode = (append ? std::ios::app : std::ios::out);

		cvm::ofstream samples_os;
		cvm::ofstream gradients_os;
		cvm::ofstream z_samples_os;
		cvm::ofstream z_gradients_os;

		if (!append) cvm::backup_file(samples_out_name.c_str());
		samples_os.open(samples_out_name.c_str(), mode);
		@@ -442,6 +459,14 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
		}

		if (z_gradients) {
		// Write eABF-related quantities
		std::string z_samples_out_name = prefix + ".zcount";
		std::string z_gradients_out_name = prefix + ".zgrad";
		std::string czar_gradients_out_name = prefix + ".czar";
		cvm::ofstream z_samples_os;
		cvm::ofstream z_gradients_os;
		cvm::ofstream czar_gradients_os;

		if (!append) cvm::backup_file(z_samples_out_name.c_str());
		z_samples_os.open(z_samples_out_name.c_str(), mode);
		if (!z_samples_os.is_open()) {
		@@ -458,6 +483,24 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
		z_gradients->write_multicol(z_gradients_os);
		z_gradients_os.close();

		// Calculate CZAR estimator of gradients
		for (std::vector<int> ix = czar_gradients->new_index();
		czar_gradients->index_ok(ix); czar_gradients->incr(ix)) {
		for (size_t n = 0; n < czar_gradients->multiplicity(); n++) {
		czar_gradients->set_value(ix, z_gradients->value_output(ix, n)
		- cvm::temperature() * cvm::boltzmann() * z_samples->log_gradient_finite_diff(ix, n),
		n);
		}
		}

		if (!append) cvm::backup_file(czar_gradients_out_name.c_str());
		czar_gradients_os.open(czar_gradients_out_name.c_str(), mode);
		if (!czar_gradients_os.is_open()) {
		cvm::error("Error opening CZAR gradient file " + czar_gradients_out_name + " for writing");
		}
		czar_gradients->write_multicol(czar_gradients_os);
		czar_gradients_os.close();

		if (colvars.size() == 1) {
		std::string z_pmf_out_name = prefix + ".zpmf";
		if (!append) cvm::backup_file(z_pmf_out_name.c_str());
		@@ -468,6 +511,16 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
		z_gradients->write_1D_integral(z_pmf_os);
		z_pmf_os << std::endl;
		z_pmf_os.close();

		std::string czar_pmf_out_name = prefix + ".czarpmf";
		if (!append) cvm::backup_file(czar_pmf_out_name.c_str());
		cvm::ofstream czar_pmf_os;
		// Do numerical integration and output a PMF
		czar_pmf_os.open(czar_pmf_out_name.c_str(), mode);
		if (!czar_pmf_os.is_open()) cvm::error("Error opening CZAR pmf file " + czar_pmf_out_name + " for writing");
		czar_gradients->write_1D_integral(czar_pmf_os);
		czar_pmf_os << std::endl;
		czar_pmf_os.close();
		}
		}

		@@ -545,24 +598,27 @@ std::ostream & colvarbias_abf::write_restart(std::ostream& os)
		{

		std::ios::fmtflags flags(os.flags());
		os.setf(std::ios::fmtflags(0), std::ios::floatfield); // default floating-point format

		os << "abf {\n"
		<< " configuration {\n"
		<< " name " << this->name << "\n";
		os << " }\n";

		os << "samples\n";
		os.setf(std::ios::fmtflags(0), std::ios::floatfield); // default floating-point format
		os << "\nsamples\n";
		samples->write_raw(os, 8);
		os.flags(flags);

		os << "\ngradient\n";
		gradients->write_raw(os);
		gradients->write_raw(os, 8);

		if (z_gradients) {
		os << "z_samples\n";
		os.setf(std::ios::fmtflags(0), std::ios::floatfield); // default floating-point format
		os << "\nz_samples\n";
		z_samples->write_raw(os, 8);
		os.flags(flags);
		os << "\nz_gradient\n";
		z_gradients->write_raw(os);
		z_gradients->write_raw(os, 8);
		}

		os << "}\n\n";

lib/colvars/colvarbias_abf.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -60,6 +60,8 @@ private:
		colvar_grid_gradient *z_gradients;
		/// n-dim grid of number of samples on "real" coordinate for eABF z-based estimator
		colvar_grid_count *z_samples;
		/// n-dim grid contining CZAR estimator of "real" free energy gradients
		colvar_grid_gradient *czar_gradients;

		// shared ABF
		bool shared_on;

lib/colvars/colvarbias_histogram.cpp

+5 −2

Original line number	Diff line number	Diff line
		@@ -75,13 +75,12 @@ int colvarbias_histogram::init(std::string const &conf)
		}

		grid = new colvar_grid_scalar();
		grid->init_from_colvars(colvars);

		{
		std::string grid_conf;
		if (key_lookup(conf, "grid", grid_conf)) {
		grid->parse_params(grid_conf);
		} else {
		grid->init_from_colvars(colvars);
		}
		}

		@@ -256,6 +255,9 @@ std::istream & colvarbias_histogram::read_restart(std::istream& is)

		std::ostream & colvarbias_histogram::write_restart(std::ostream& os)
		{
		std::ios::fmtflags flags(os.flags());
		os.setf(std::ios::fmtflags(0), std::ios::floatfield);

		os << "histogram {\n"
		<< " configuration {\n"
		<< " name " << this->name << "\n";
		@@ -266,5 +268,6 @@ std::ostream & colvarbias_histogram::write_restart(std::ostream& os)

		os << "}\n\n";

		os.flags(flags);
		return os;
		}

lib/colvars/colvargrid.cpp

+2 −2

Original line number	Diff line number	Diff line
		@@ -35,13 +35,13 @@ colvar_grid_scalar::colvar_grid_scalar(colvar_grid_scalar const &g)
		}

		colvar_grid_scalar::colvar_grid_scalar(std::vector<int> const &nx_i)
		: colvar_grid<cvm::real>(nx_i, 0.0, 1), samples(NULL)
		: colvar_grid<cvm::real>(nx_i, 0.0, 1), samples(NULL), grad(NULL)
		{
		grad = new cvm::real[nd];
		}

		colvar_grid_scalar::colvar_grid_scalar(std::vector<colvar *> &colvars, bool margin)
		: colvar_grid<cvm::real>(colvars, 0.0, 1, margin), samples(NULL)
		: colvar_grid<cvm::real>(colvars, 0.0, 1, margin), samples(NULL), grad(NULL)
		{
		grad = new cvm::real[nd];
		}

Admin message