Merge pull request #2255 from akohlmey/charset-cleanup (ae329acd) · Commits · 郑智淋 / lammps

lib/awpmd/ivutils/include/cvector_3.h

+1 −3

Original line number	Diff line number	Diff line
		@@ -9,8 +9,6 @@
		*
		*
		*****************************************************************************/
		/*r @file vector_3.h @brief
		*/

		# ifndef CVECTOR_3A_H
		# define CVECTOR_3A_H

lib/awpmd/ivutils/include/vector_3.h

+16 −67

Original line number	Diff line number	Diff line
		@@ -72,7 +72,7 @@

		*
		*******************************************************************************/
		/*r @file vector_3.h @brief
		/*r @file vector_3.h
		*/

		# ifndef VECTOR_3_H
		@@ -92,7 +92,6 @@
		# endif

		# ifndef fmod
		//r
		# define fmod(a,b) ((a)-((long)((a)/(b))*(b)))
		# endif

		@@ -104,8 +103,6 @@ typedef double vec_type;
		typedef float vec_type;
		#endif

		//e "infinitely" large number in Vector_3 sense
		//r " " Vector_3
		//# ifndef SINGLE_PRECISION
		//# define VEC_INFTY 1.e20
		//# else
		@@ -113,8 +110,6 @@ typedef float vec_type;
		//# endif
		#define VEC_INFTY numeric_limits<vec_type>::max()

		//e "infinitely" small number in Vector_3 sense (used for vector comparisons)
		//r " " Vector_3 ( )
		//# ifndef SINGLE_PRECISION
		//# define VEC_ZERO 1.e-20
		//# else
		@@ -122,7 +117,6 @@ typedef float vec_type;
		//# endif
		#define VEC_ZERO 512*numeric_limits<vec_type>::epsilon()

		//r N- T,
		template <class T, const int N=3>
		struct Vector_Nt {
		typedef T value_type;
		@@ -160,14 +154,12 @@ struct Vector_Nt {
		for (int i=0; i<N; i++) v[i]=v1[i];
		}

		//r it
		template <class A>
		void copy_to(A *beg) const {
		for (int i=0; i<N; i++, ++beg)
		*beg=v[i];
		}

		//r
		inline T& operator[](int i) const { return (T&)v[i]; };


		@@ -177,14 +169,12 @@ struct Vector_Nt {
		return *this;
		}

		//r a.
		inline Vector_Nt& operator=(const T &a){
		for (int i=0; i<N; i++)
		v[i]=a;
		return *this;
		};

		//r . VEC_ZERO
		inline bool operator==(const Vector_Nt &vect) const{
		for (int i=0; i<N ;i++)
		if(fabs(v[i]-vect.v[i])>VEC_ZERO)return false;
		@@ -209,7 +199,6 @@ struct Vector_Nt {
		return result;
		}

		//r
		inline T operator*(const Vector_Nt& vect) const {
		T result=0;
		for (int i=0; i<N; i++)
		@@ -217,7 +206,6 @@ struct Vector_Nt {
		return result;
		}

		//r
		inline Vector_Nt operator*(const T &coeff) const {
		Vector_Nt result;
		for (int i=0; i<N; i++)
		@@ -226,7 +214,6 @@ struct Vector_Nt {
		}

		//e vector multiplication (N=3 only)
		//r
		inline Vector_Nt operator%(const Vector_Nt &r) const{ //reserved for N specializations
		if(N==3){
		return Vector_Nt(v[1]r.v[2]-v[2]r.v[1],v[2]r.v[0]-v[0]r.v[2],v[0]r.v[1]-v[1]r.v[0]);
		@@ -234,10 +221,8 @@ struct Vector_Nt {
		return *this;
		}

		//r ( ).
		// friend Vector_Nt operator*(T coeff,const Vector_Nt& vec);

		//r
		inline Vector_Nt operator/(const T &coeff) const {
		Vector_Nt result;
		for (int i=0; i<N; i++)
		@@ -245,7 +230,6 @@ struct Vector_Nt {
		return result;
		}

		//r -1
		inline Vector_Nt operator-() const {
		Vector_Nt r;
		for (int i=0; i<N; i++)
		@@ -253,35 +237,30 @@ struct Vector_Nt {
		return r;
		}

		//r
		inline Vector_Nt& operator+=(const Vector_Nt &vect){
		for (int i=0; i<N; i++)
		v[i]+=vect.v[i];
		return *this;
		}

		//r
		inline Vector_Nt& operator-=(const Vector_Nt &vect){
		for (int i=0; i<N; i++)
		v[i]-=vect.v[i];
		return *this;
		}

		//r
		inline Vector_Nt& operator*=(const T &coeff){
		for (int i=0; i<N; i++)
		v[i]*=coeff;
		return *this;
		}

		//r
		inline Vector_Nt& operator/=(const T &coeff){
		for (int i=0; i<N; i++)
		v[i]/=coeff;
		return *this;
		}

		//r
		T norm2() const {
		T result=0;
		for (int i=0; i<N; i++)
		@@ -289,12 +268,10 @@ struct Vector_Nt {
		return result;
		}

		//r
		T norm() const {
		return sqrt(norm2());
		}

		//r ( norm() newnorm).
		T normalize(T newnorm=1.){
		T norm=this->norm();
		if(norm>=VEC_ZERO){
		@@ -333,14 +310,6 @@ struct Vector_Nt {
		//e assumes that each coordinate absolute value is in the range [0,cell[i])
		//e returned vector is in the range [-cell[i]/2,cell[i]/2)
		//e flags indicate the periodicity in specific directions: 0x1 for X, 0x2 for Y, 0x4 for Z
		//r
		/*r , - ,
		, rcell,
		. this , this.\n
		, this 33 ,
		*this .\n
		, .
		*/
		Vector_Nt rcell1(const Vector_Nt &cell,int flags=0xffff) const{
		Vector_Nt ret(*this);
		int i;
		@@ -378,9 +347,6 @@ struct Vector_Nt {

		//e reduction to elementary cell [0, cell[i]) (FOR REDUCTION TO ELEMENTARY CELL)
		//e flags indicate the periodicity in specific directions: 0x1 for X, 0x2 for Y, 0x4 for Z
		//r , rcell1, *this .
		/*r , . -
		*/
		Vector_Nt rcell(const Vector_Nt &cell, int flags=0xffff) const {
		Vector_Nt ret(*this);
		for (int i=0, flag=1; i<N; i++, flag<<=1) {
		@@ -408,7 +374,6 @@ struct Vector_Nt {
		}


		//r ind
		T maxcoord(int *ind=NULL) const {
		int im=0;
		T vv=v[0];
		@@ -452,7 +417,6 @@ struct Vector_Nt {
		}


		//r ind
		T mincoord(int *ind=NULL) const {
		int im=0;
		T vv=v[0];
		@@ -466,7 +430,6 @@ struct Vector_Nt {
		return vv;
		}

		//r , (x,y,z)\\n
		void print() const{
		cout<< "(";
		for(int i=0;i<N;i++){
		@@ -515,25 +478,18 @@ class Vector_N: public Vector_Nt<vec_type, N>{


		//e finds the maximum distance between vector pairs
		//r va1[i], va2[i], i=1..n
		/*r @param va1 - Vector_3[n]
		@param n - va1 va2
		*/
		vec_type dist_max(Vector_3 va1,Vector_3 va2,int n);

		//e finds average distance between vector pairs
		//r va1[i], va2[i], i=1..n
		vec_type dist_av(Vector_3 va1,Vector_3 va2,int n);

		//e finds the average difference norm between two vector sets of the same length
		/*e optionally gives the indexes for maximal and minimal difference
		va2 can be NULL, then the norm of va1 is used */

		//r va1[i] va2[i], , , , min max
		vec_type diff_av(Vector_3 va1,Vector_3 va2,int n, int minind=0, int maxind=0);

		//e finds suitable perpendicular to a vector
		//r vAB
		Vector_3 FindPerp(const Vector_3 &vAB);


		@@ -551,13 +507,6 @@ Vector_3 GetIScopei(const Vector_3 varr,int indarr,int n,Vector_3* box_min,Vec
		// neue Funktionen

		//e clears vector array with optional integer index
		//r ,
		/*r
		Vector_3 vec[] n . ind==NULL,
		n . ind!=NULL, i=0..n-1
		vec[ind[i]]
		. @ref indexed_calculations.
		*/
		void clear_vecarri(int n,Vector_3 vec, int ind=0);

		//e reflects the vector ini+dirt+0.5force*t^2 to be inside a box limited by 0 and box sizes

lib/colvars/colvarcomp.h

+2 −2

Original line number	Diff line number	Diff line
		@@ -1442,7 +1442,7 @@ public:

		/// \brief Colvar component: alternative path collective variable using geometry, variable s
		/// For more information see https://plumed.github.io/doc-v2.5/user-doc/html/_p_a_t_h.html
		/// Díaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601.
		/// Diaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601.
		class colvar::gspath
		: public colvar::CartesianBasedPath, public GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::S>
		{
		@@ -1534,7 +1534,7 @@ public:
		/// \brief Colvar component: alternative path collective variable using geometry, variable s
		/// Allow any combination of existing (scalar) CVs
		/// For more information see https://plumed.github.io/doc-v2.5/user-doc/html/_p_a_t_h.html
		/// Díaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601.
		/// Diaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601.
		class colvar::gspathCV
		: public colvar::CVBasedPath, public GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::S>
		{

lib/gpu/lal_soft.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -65,7 +65,7 @@ class Soft : public BaseAtomic<numtyp, acctyp> {
		/// Special LJ values
		UCL_D_Vec<numtyp> sp_lj;

		/// If atom type constants fit in shared memory, use fast kßernels
		/// If atom type constants fit in shared memory, use fast kernels
		bool shared_types;

		/// Number of atom types