Merge pull request #816 from giacomofiorin/colvars-update-2018-02-23 (812a4545) · Commits · 郑智淋 / lammps

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

+7.51 KiB (594 KiB)

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+1 −1

Original line number	Diff line number	Diff line
		@@ -195,7 +195,7 @@ int colvar::init(std::string const &conf)
		// - it is homogeneous
		// - all cvcs are periodic
		// - all cvcs have the same period
		if (cvcs[0]->b_periodic) { // TODO make this a CVC feature
		if (is_enabled(f_cv_homogeneous) && cvcs[0]->b_periodic) { // TODO make this a CVC feature
		bool b_periodic = true;
		period = cvcs[0]->period;
		for (i = 1; i < cvcs.size(); i++) {

+10 −6

Original line number	Diff line number	Diff line
		@@ -11,8 +11,6 @@
		#define COLVAR_H

		#include <iostream>
		#include <iomanip>
		#include <cmath>

		#include "colvarmodule.h"
		#include "colvarvalue.h"
		@@ -61,6 +59,9 @@ public:
		/// \brief Current actual value (not extended DOF)
		colvarvalue const & actual_value() const;

		/// \brief Current running average (if calculated as set by analysis flag)
		colvarvalue const & run_ave() const;

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

		@@ -516,7 +517,7 @@ public:
		// collective variable component base class
		class cvc;

		// currently available collective variable components
		// list of available collective variable components

		// scalar colvar components
		class distance;
		@@ -611,12 +612,15 @@ inline colvarvalue const & colvar::value() const
		return x_reported;
		}


		inline colvarvalue const & colvar::actual_value() const
		{
		return x;
		}

		inline colvarvalue const & colvar::run_ave() const
		{
		return runave;
		}

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

+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(double(y_size), dimension) + EPSILON);
		this->y_total_size = int(std::pow(double(y_size), double(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(double(y_size), dimension - i - 1) + EPSILON);
		index += temp[i] * int(std::pow(double(y_size), double(dimension - i - 1)) + EPSILON);
		else
		index += temp[i];
		}

+2 −0

Original line number	Diff line number	Diff line
		@@ -8,9 +8,11 @@
		// Colvars repository at GitHub.

		#include "colvarmodule.h"
		#include "colvarproxy.h"
		#include "colvarparse.h"
		#include "colvaratoms.h"


		cvm::atom::atom()
		{
		index = -1;