(83ec8fbd) · Commits · 郑智淋 / lammps

tools/pymol_asphere/src/cartesian.cpp

+0 −46

Original line number	Diff line number	Diff line
		@@ -169,12 +169,6 @@ TwoD<numtyp> TwoD<numtyp>::normal() {
		return TwoD(y,x*numtyp(-1));
		}

		template<class numtyp>
		numtyp TwoD<numtyp>::dist(const TwoD<numtyp> &two) const {
		TwoD diff=*this-two;
		return numtyp(sqrt(double(diff.dot(diff))));
		}

		template<class numtyp>
		numtyp TwoD<numtyp>::dist2(const TwoD<numtyp> &two) const {
		TwoD diff=*this-two;
		@@ -293,26 +287,6 @@ template<class numtyp>
		ThreeD<numtyp>::ThreeD() {
		}

		template<class numtyp>
		numtyp & ThreeD<numtyp>::operator[](unsigned i) {
		switch(i) {
		case X: return x;
		case Y: return y;
		case Z: return z;
		}
		return x;
		}

		template<class numtyp>
		numtyp ThreeD<numtyp>::operator[](unsigned i) const {
		switch(i) {
		case X: return x;
		case Y: return y;
		case Z: return z;
		}
		return x;
		}

		template<class numtyp>
		void ThreeD<numtyp>::operator = (const ThreeD &two) {
		#ifdef NANCHECK
		@@ -396,11 +370,6 @@ numtyp ThreeD<numtyp>::dot(const ThreeD<numtyp> &two) const {
		return (xtwo.x+ytwo.y+z*two.z);
		}

		template<class numtyp>
		void ThreeD<numtyp>::operator *= (const numtyp &two) {
		x=two; y=two; z*=two;
		}

		// Move coordinates into array
		template<class numtyp>
		void ThreeD<numtyp>::to_array(numtyp *array) {
		@@ -499,27 +468,12 @@ numtyp ThreeD<numtyp>::norm2() const {
		return xx+yy+z*z;
		}

		template <class numtyp>
		numtyp ThreeD<numtyp>::dist(const ThreeD<numtyp> &two) {
		return (*this-two).norm();
		}

		template <class numtyp>
		numtyp ThreeD<numtyp>::dist2(const ThreeD<numtyp> &two) {
		ThreeD diff=*this-two;
		return diff.dot(diff);
		}

		// For normalizing a vector
		template<class numtyp>
		void ThreeD<numtyp>::normalize() {
		numtyp temp=norm();
		#ifdef NANCHECK
		assert(temp!=0);
		#endif
		*this/=temp;
		}

		// Return unit vector
		template<class numtyp>
		ThreeD<numtyp> ThreeD<numtyp>::unit() {

tools/pymol_asphere/src/cartesian.h

+32 −5

Original line number	Diff line number	Diff line
		@@ -204,8 +204,23 @@ class ThreeD {
		friend ThreeD<numtyp> operator* <>(const numtyp, const ThreeD<numtyp> &two);
		friend ThreeD<numtyp> operator/ <>(const numtyp, const ThreeD<numtyp> &two);

		numtyp &operator[](unsigned i);
		numtyp operator[](unsigned i) const;
		inline numtyp &operator[](unsigned i) {
		switch(i) {
		case X: return x;
		case Y: return y;
		case Z: return z;
		}
		return x;
		}

		inline numtyp operator[](unsigned i) const {
		switch(i) {
		case X: return x;
		case Y: return y;
		case Z: return z;
		}
		return x;
		}

		bool operator == (const ThreeD<numtyp> &two) const;
		bool operator != (const ThreeD<numtyp> &two) const;
		@@ -222,7 +237,10 @@ class ThreeD {
		void operator += (const ThreeD &two);
		void operator -= (const numtyp &two);
		void operator -= (const ThreeD &two);
		void operator *= (const numtyp &two);
		inline void operator *= (const numtyp &two) {
		x=two; y=two; z*=two;
		}

		void operator /= (const numtyp &two);

		/// Move coordinates into array
		@@ -253,11 +271,20 @@ class ThreeD {
		/// Magnitude of vector
		numtyp hypot() const;
		/// Distance between two points
		numtyp dist(const ThreeD<numtyp> &two);
		inline numtyp dist(const ThreeD<numtyp> &two) {
		return (*this-two).norm();
		}
		/// Distance squared between two points
		numtyp dist2(const ThreeD<numtyp> &two);
		/// Converts \b *this to the unit vector
		void normalize();
		inline void normalize() {
		numtyp temp=norm();
		#ifdef NANCHECK
		assert(temp!=0);
		#endif
		*this/=temp;
		}

		/// Return the unit vector of \b *this
		ThreeD<numtyp> unit();

tools/pymol_asphere/src/glsurface.cpp

+4 −2

Original line number	Diff line number	Diff line
		@@ -333,7 +333,8 @@ void GLSurface::write_vspheres(ofstream &out, const string &objname,
		writepymolheader(out);
		for (i=0; i<vertices.size(); i++) {
		// Output coords, colors, and normals of points
		// if (vertices[i].transparency!=1)
		if (vertices[i].transparency==0)
		continue;
		out << "ALPHA," << vertices[i].transparency << ",";
		out << "COLOR,";
		for (k=X; k<=Z; k++)
		@@ -353,7 +354,8 @@ void GLSurface::writespheres(ofstream &out, const string &objname) {
		writepymolheader(out);
		for (i=0; i<spheres.size(); i++) {
		// Output coords, colors, and normals of points
		// if (vertices[i].transparency!=1)
		if (vertices[i].transparency==0)
		continue;
		out << "ALPHA," << vertices[spheres[i].i].transparency << ",";
		out << "COLOR,";
		for (k=X; k<=Z; k++)

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