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This commit is contained in:
Axel Kohlmeyer
2020-07-27 17:15:29 -04:00
parent 634f274a04
commit 2bb5c53a47
3 changed files with 19 additions and 70 deletions
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83
lib/awpmd/ivutils/include/vector_3.h
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@ -2,9 +2,9 @@
* *
* Copyright (c), Ilya Valuev 2005 All Rights Reserved. * Copyright (c), Ilya Valuev 2005 All Rights Reserved.
* *
* Author : Ilya Valuev, MIPT, Moscow, Russia * Author : Ilya Valuev, MIPT, Moscow, Russia
* *
* Project : GridMD, ivutils * Project : GridMD, ivutils
* *
*****************************************************************************/ *****************************************************************************/
@ -69,11 +69,11 @@
* Revision 1.11 2008/04/15 13:11:41 valuev * Revision 1.11 2008/04/15 13:11:41 valuev
* Added antisymmetrized wave packets * Added antisymmetrized wave packets
* *
* *
*******************************************************************************/ *******************************************************************************/
/*r @file vector_3.h @brief <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> /*r @file vector_3.h
*/ */
# ifndef VECTOR_3_H # ifndef VECTOR_3_H
@ -92,7 +92,6 @@
# endif # endif
# ifndef fmod # ifndef fmod
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
# define fmod(a,b) ((a)-((long)((a)/(b))*(b))) # define fmod(a,b) ((a)-((long)((a)/(b))*(b)))
# endif # endif
@ -104,8 +103,6 @@ typedef double vec_type;
typedef float vec_type; typedef float vec_type;
#endif #endif
//e "infinitely" large number in Vector_3 sense
//r "<22><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>" <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> Vector_3
//# ifndef SINGLE_PRECISION //# ifndef SINGLE_PRECISION
//# define VEC_INFTY 1.e20 //# define VEC_INFTY 1.e20
//# else //# else
@ -113,8 +110,6 @@ typedef float vec_type;
//# endif //# endif
#define VEC_INFTY numeric_limits<vec_type>::max() #define VEC_INFTY numeric_limits<vec_type>::max()
//e "infinitely" small number in Vector_3 sense (used for vector comparisons)
//r "<22><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD>" <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> Vector_3 (<28><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>)
//# ifndef SINGLE_PRECISION //# ifndef SINGLE_PRECISION
//# define VEC_ZERO 1.e-20 //# define VEC_ZERO 1.e-20
//# else //# else
@ -122,11 +117,10 @@ typedef float vec_type;
//# endif //# endif
#define VEC_ZERO 512*numeric_limits<vec_type>::epsilon() #define VEC_ZERO 512*numeric_limits<vec_type>::epsilon()
//r N-<2D><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> T, <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> template <class T, const int N=3>
template <class T, const int N=3>
struct Vector_Nt { struct Vector_Nt {
typedef T value_type; typedef T value_type;
T v[N]; T v[N];
Vector_Nt(const T &a=0){ Vector_Nt(const T &a=0){
@ -134,7 +128,7 @@ struct Vector_Nt {
v[i]=a; v[i]=a;
} }
explicit Vector_Nt(const T &a1, const T &a2) { explicit Vector_Nt(const T &a1, const T &a2) {
if(N>0)v[0]=a1; if(N>0)v[0]=a1;
if(N>1)v[1]=a2; if(N>1)v[1]=a2;
@ -160,14 +154,12 @@ struct Vector_Nt {
for (int i=0; i<N; i++) v[i]=v1[i]; for (int i=0; i<N; i++) v[i]=v1[i];
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> it
template <class A> template <class A>
void copy_to(A *beg) const { void copy_to(A *beg) const {
for (int i=0; i<N; i++, ++beg) for (int i=0; i<N; i++, ++beg)
*beg=v[i]; *beg=v[i];
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
inline T& operator[](int i) const { return (T&)v[i]; }; inline T& operator[](int i) const { return (T&)v[i]; };
@ -177,14 +169,12 @@ struct Vector_Nt {
return *this; return *this;
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> a.
inline Vector_Nt& operator=(const T &a){ inline Vector_Nt& operator=(const T &a){
for (int i=0; i<N; i++) for (int i=0; i<N; i++)
v[i]=a; v[i]=a;
return *this; return *this;
}; };
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>. <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><> VEC_ZERO <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
inline bool operator==(const Vector_Nt &vect) const{ inline bool operator==(const Vector_Nt &vect) const{
for (int i=0; i<N ;i++) for (int i=0; i<N ;i++)
if(fabs(v[i]-vect.v[i])>VEC_ZERO)return false; if(fabs(v[i]-vect.v[i])>VEC_ZERO)return false;
@ -208,8 +198,7 @@ struct Vector_Nt {
result.v[i]=v[i]-vect.v[i]; result.v[i]=v[i]-vect.v[i];
return result; return result;
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
inline T operator*(const Vector_Nt& vect) const { inline T operator*(const Vector_Nt& vect) const {
T result=0; T result=0;
for (int i=0; i<N; i++) for (int i=0; i<N; i++)
@ -217,7 +206,6 @@ struct Vector_Nt {
return result; return result;
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
inline Vector_Nt operator*(const T &coeff) const { inline Vector_Nt operator*(const T &coeff) const {
Vector_Nt result; Vector_Nt result;
for (int i=0; i<N; i++) for (int i=0; i<N; i++)
@ -226,7 +214,6 @@ struct Vector_Nt {
} }
//e vector multiplication (N=3 only) //e vector multiplication (N=3 only)
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
inline Vector_Nt operator%(const Vector_Nt &r) const{ //reserved for N specializations inline Vector_Nt operator%(const Vector_Nt &r) const{ //reserved for N specializations
if(N==3){ 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]); 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; return *this;
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> (<28><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>).
// friend Vector_Nt operator*(T coeff,const Vector_Nt& vec); // friend Vector_Nt operator*(T coeff,const Vector_Nt& vec);
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
inline Vector_Nt operator/(const T &coeff) const { inline Vector_Nt operator/(const T &coeff) const {
Vector_Nt result; Vector_Nt result;
for (int i=0; i<N; i++) for (int i=0; i<N; i++)
@ -245,7 +230,6 @@ struct Vector_Nt {
return result; return result;
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> -1
inline Vector_Nt operator-() const { inline Vector_Nt operator-() const {
Vector_Nt r; Vector_Nt r;
for (int i=0; i<N; i++) for (int i=0; i<N; i++)
@ -253,48 +237,41 @@ struct Vector_Nt {
return r; return r;
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
inline Vector_Nt& operator+=(const Vector_Nt &vect){ inline Vector_Nt& operator+=(const Vector_Nt &vect){
for (int i=0; i<N; i++) for (int i=0; i<N; i++)
v[i]+=vect.v[i]; v[i]+=vect.v[i];
return *this; return *this;
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
inline Vector_Nt& operator-=(const Vector_Nt &vect){ inline Vector_Nt& operator-=(const Vector_Nt &vect){
for (int i=0; i<N; i++) for (int i=0; i<N; i++)
v[i]-=vect.v[i]; v[i]-=vect.v[i];
return *this; return *this;
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
inline Vector_Nt& operator*=(const T &coeff){ inline Vector_Nt& operator*=(const T &coeff){
for (int i=0; i<N; i++) for (int i=0; i<N; i++)
v[i]*=coeff; v[i]*=coeff;
return *this; return *this;
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
inline Vector_Nt& operator/=(const T &coeff){ inline Vector_Nt& operator/=(const T &coeff){
for (int i=0; i<N; i++) for (int i=0; i<N; i++)
v[i]/=coeff; v[i]/=coeff;
return *this; return *this;
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
T norm2() const { T norm2() const {
T result=0; T result=0;
for (int i=0; i<N; i++) for (int i=0; i<N; i++)
result+=v[i]*v[i]; result+=v[i]*v[i];
return result; return result;
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
T norm() const { T norm() const {
return sqrt(norm2()); return sqrt(norm2());
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> (<28><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> norm() <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> newnorm).
T normalize(T newnorm=1.){ T normalize(T newnorm=1.){
T norm=this->norm(); T norm=this->norm();
if(norm>=VEC_ZERO){ if(norm>=VEC_ZERO){
@ -325,22 +302,14 @@ struct Vector_Nt {
newnorm/=sqrt(fabs(result)); newnorm/=sqrt(fabs(result));
for (int i=0; i<N; i++) for (int i=0; i<N; i++)
v[i]*=newnorm; v[i]*=newnorm;
return result<0 ? VEC_INFTY : result; return result<0 ? VEC_INFTY : result;
} }
//e nearest image distance within rectangular cell (FOR DISTANCE MEASUREMENTS) //e nearest image distance within rectangular cell (FOR DISTANCE MEASUREMENTS)
//e assumes that each coordinate absolute value is in the range [0,cell[i]) //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 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 //e flags indicate the periodicity in specific directions: 0x1 for X, 0x2 for Y, 0x4 for Z
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
/*r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
<20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> rcell, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
<20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD>. <20><><EFBFBD><EFBFBD> *this <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> *this.\n
<20><><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD> *this <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD> 3*3 <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD>
*this <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>.\n
<20><><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>.
*/
Vector_Nt rcell1(const Vector_Nt &cell,int flags=0xffff) const{ Vector_Nt rcell1(const Vector_Nt &cell,int flags=0xffff) const{
Vector_Nt ret(*this); Vector_Nt ret(*this);
int i; int i;
@ -378,9 +347,6 @@ struct Vector_Nt {
//e reduction to elementary cell [0, cell[i]) (FOR REDUCTION TO ELEMENTARY CELL) //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 //e flags indicate the periodicity in specific directions: 0x1 for X, 0x2 for Y, 0x4 for Z
//r <20><><EFBFBD><EFBFBD><EFBFBD> <20><> <20><>, <20><><EFBFBD> <20> rcell1, <20><> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> *this <20> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD>.
/*r <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20> <20><> <20><><EFBFBD><EFBFBD>. <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><>-<2D><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
<20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> */
Vector_Nt rcell(const Vector_Nt &cell, int flags=0xffff) const { Vector_Nt rcell(const Vector_Nt &cell, int flags=0xffff) const {
Vector_Nt ret(*this); Vector_Nt ret(*this);
for (int i=0, flag=1; i<N; i++, flag<<=1) { for (int i=0, flag=1; i<N; i++, flag<<=1) {
@ -406,9 +372,8 @@ struct Vector_Nt {
} }
return ret; return ret;
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> ind
T maxcoord(int *ind=NULL) const { T maxcoord(int *ind=NULL) const {
int im=0; int im=0;
T vv=v[0]; T vv=v[0];
@ -452,7 +417,6 @@ struct Vector_Nt {
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> ind
T mincoord(int *ind=NULL) const { T mincoord(int *ind=NULL) const {
int im=0; int im=0;
T vv=v[0]; T vv=v[0];
@ -466,7 +430,6 @@ struct Vector_Nt {
return vv; return vv;
} }
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> (x,y,z)\\n
void print() const{ void print() const{
cout<< "("; cout<< "(";
for(int i=0;i<N;i++){ for(int i=0;i<N;i++){
@ -505,7 +468,7 @@ typedef Vector_3 *Vector_3P;
typedef Vector_Nt<vec_type, 2> Vector_2; typedef Vector_Nt<vec_type, 2> Vector_2;
typedef Vector_2 *Vector_2P; typedef Vector_2 *Vector_2P;
template <int N> template <int N>
class Vector_N: public Vector_Nt<vec_type, N>{ class Vector_N: public Vector_Nt<vec_type, N>{
}; };
@ -515,25 +478,18 @@ class Vector_N: public Vector_Nt<vec_type, N>{
//e finds the maximum distance between vector pairs //e finds the maximum distance between vector pairs
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> va1[i], va2[i], i=1..n
/*r @param va1 - <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> Vector_3[n]
@param n - <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> va1 <20> va2
*/
vec_type dist_max(Vector_3 *va1,Vector_3 *va2,int n); vec_type dist_max(Vector_3 *va1,Vector_3 *va2,int n);
//e finds average distance between vector pairs //e finds average distance between vector pairs
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> va1[i], va2[i], i=1..n
vec_type dist_av(Vector_3 *va1,Vector_3 *va2,int 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 finds the average difference norm between two vector sets of the same length
/*e optionally gives the indexes for maximal and minimal difference /*e optionally gives the indexes for maximal and minimal difference
va2 can be NULL, then the norm of va1 is used */ va2 can be NULL, then the norm of va1 is used */
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> va1[i] <20> va2[i], <20> <20><><EFBFBD><EFBFBD><EFBFBD>, <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> min <20> max <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
vec_type diff_av(Vector_3 *va1,Vector_3 *va2,int n, int *minind=0, int *maxind=0); 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 //e finds suitable perpendicular to a vector
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> vAB
Vector_3 FindPerp(const Vector_3 &vAB); Vector_3 FindPerp(const Vector_3 &vAB);
@ -551,19 +507,12 @@ Vector_3 GetIScopei(const Vector_3 *varr,int *indarr,int n,Vector_3* box_min,Vec
// neue Funktionen // neue Funktionen
//e clears vector array with optional integer index //e clears vector array with optional integer index
//r <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
/*r
<EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> Vector_3 vec[] <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> n <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>. <20><><EFBFBD><EFBFBD> ind==NULL, <20><>
<EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> n <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>. <20><><EFBFBD><EFBFBD> ind!=NULL, <20><> <20><><EFBFBD> i=0..n-1
<EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> vec[ind[i]]
<EFBFBD><EFBFBD>. @ref indexed_calculations.
*/
void clear_vecarri(int n,Vector_3 *vec, int *ind=0); void clear_vecarri(int n,Vector_3 *vec, int *ind=0);
//e reflects the vector ini+dir*t+0.5*force*t^2 to be inside a box limited by 0 and box sizes //e reflects the vector ini+dir*t+0.5*force*t^2 to be inside a box limited by 0 and box sizes
//e changes dir according to the final state //e changes dir according to the final state
//e fills crossed dir with bit flags corresponding directions along which the walls were crossed //e fills crossed dir with bit flags corresponding directions along which the walls were crossed
Vector_3 Reflect(Vector_3& ini, double t,Vector_3 &dir, double *box, int flag=0x7, const Vector_3 &force=Vector_3()); Vector_3 Reflect(Vector_3& ini, double t,Vector_3 &dir, double *box, int flag=0x7, const Vector_3 &force=Vector_3());
inline vec_type vec_area(const Vector_2 &vect1, const Vector_2 &vect2) { inline vec_type vec_area(const Vector_2 &vect1, const Vector_2 &vect2) {

4
lib/colvars/colvarcomp.h
View File

@ -1442,7 +1442,7 @@ public:
/// \brief Colvar component: alternative path collective variable using geometry, variable s /// \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 /// 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 class colvar::gspath
: public colvar::CartesianBasedPath, public GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::S> : 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 /// \brief Colvar component: alternative path collective variable using geometry, variable s
/// Allow any combination of existing (scalar) CVs /// 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 /// 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 class colvar::gspathCV
: public colvar::CVBasedPath, public GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::S> : public colvar::CVBasedPath, public GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::S>
{ {

2
lib/gpu/lal_soft.h
View File

@ -65,7 +65,7 @@ class Soft : public BaseAtomic<numtyp, acctyp> {
/// Special LJ values /// Special LJ values
UCL_D_Vec<numtyp> sp_lj; 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; bool shared_types;
/// Number of atom types /// Number of atom types