Merge pull request #702 from giacomofiorin/colvars-fix-the-fix (260bbc6f) · Commits · 郑智淋 / lammps

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

−143 B (586 KiB)

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+5 −5

Original line number	Diff line number	Diff line
		@@ -1145,7 +1145,7 @@ int colvar::collect_cvc_values()
		if (!cvcs[i]->is_enabled()) continue;
		x += (cvcs[i])->sup_coeff *
		( ((cvcs[i])->sup_np != 1) ?
		std::pow((cvcs[i])->value().real_value, (cvcs[i])->sup_np) :
		cvm::integer_power((cvcs[i])->value().real_value, (cvcs[i])->sup_np) :
		(cvcs[i])->value().real_value );
		}
		} else {
		@@ -1226,7 +1226,7 @@ int colvar::collect_cvc_gradients()
		if (!cvcs[i]->is_enabled()) continue;
		// Coefficient: d(a * x^n) = a * n * x^(n-1) * dx
		cvm::real coeff = (cvcs[i])->sup_coeff * cvm::real((cvcs[i])->sup_np) *
		std::pow((cvcs[i])->value().real_value, (cvcs[i])->sup_np-1);
		cvm::integer_power((cvcs[i])->value().real_value, (cvcs[i])->sup_np-1);

		for (size_t j = 0; j < cvcs[i]->atom_groups.size(); j++) {

		@@ -1594,7 +1594,7 @@ void colvar::communicate_forces()
		if (!cvcs[i]->is_enabled()) continue;
		(cvcs[i])->apply_force(f * (cvcs[i])->sup_coeff *
		cvm::real((cvcs[i])->sup_np) *
		(std::pow((cvcs[i])->value().real_value,
		(cvm::integer_power((cvcs[i])->value().real_value,
		(cvcs[i])->sup_np-1)) );
		}

+2 −2

Original line number	Diff line number	Diff line
		@@ -45,7 +45,7 @@ namespace UIestimator {
		this->width = width;
		this->dimension = lowerboundary.size();
		this->y_size = y_size; // keep in mind the internal (spare) matrix is stored in diagonal form
		this->y_total_size = int(pow(y_size, dimension) + EPSILON);
		this->y_total_size = int(pow(double(y_size), dimension) + EPSILON);

		// the range of the matrix is [lowerboundary, upperboundary]
		x_total_size = 1;
		@@ -121,7 +121,7 @@ namespace UIestimator {
		int index = 0;
		for (i = 0; i < dimension; i++) {
		if (i + 1 < dimension)
		index += temp[i] * int(pow(y_size, dimension - i - 1) + EPSILON);
		index += temp[i] * int(pow(double(y_size), dimension - i - 1) + EPSILON);
		else
		index += temp[i];
		}

+16 −5

Original line number	Diff line number	Diff line
		@@ -524,9 +524,18 @@ int colvarbias_ti::update_system_forces(std::vector<colvarvalue> const
		cvm::log("Updating system forces for bias "+this->name+"\n");
		}

		// Collect total colvar forces from the previous step
		colvarproxy *proxy = cvm::main()->proxy;

		size_t i;
		if (cvm::step_relative() > 0) {

		if (proxy->total_forces_same_step()) {
		for (i = 0; i < num_variables(); i++) {
		ti_bin[i] = ti_avg_forces->current_bin_scalar(i);
		}
		}

		// Collect total colvar forces
		if ((cvm::step_relative() > 0) \|\| proxy->total_forces_same_step()) {
		if (ti_avg_forces->index_ok(ti_bin)) {
		for (i = 0; i < num_variables(); i++) {
		if (variables(i)->is_enabled(f_cv_subtract_applied_force)) {
		@@ -542,10 +551,12 @@ int colvarbias_ti::update_system_forces(std::vector<colvarvalue> const
		}
		}

		// Set the index to be used in the next iteration, when total forces come in
		if (!proxy->total_forces_same_step()) {
		// Set the index for use in the next iteration, when total forces come in
		for (i = 0; i < num_variables(); i++) {
		ti_bin[i] = ti_avg_forces->current_bin_scalar(i);
		}
		}

		return COLVARS_OK;
		}

+9 −2

Original line number	Diff line number	Diff line
		@@ -304,6 +304,10 @@ int colvarbias_abf::update()
		// and subtract previous ABF force if necessary
		update_system_force(i);
		}
		if (cvm::proxy->total_forces_same_step()) {
		// e.g. in LAMMPS, total forces are current
		force_bin = bin;
		}
		gradients->acc_force(force_bin, system_force);
		}
		if ( z_gradients && update_bias ) {
		@@ -321,8 +325,11 @@ int colvarbias_abf::update()
		}
		}

		// save bin for next timestep
		if (!cvm::proxy->total_forces_same_step()) {
		// e.g. in NAMD, total forces will be available for next timestep
		// hence we store the current colvar bin
		force_bin = bin;
		}

		// Reset biasing forces from previous timestep
		for (size_t i = 0; i < colvars.size(); i++) {