Refactor X functions

.github/CHANGELOG.md

@@ -14,8 +14,9 @@
 * Remove case sensitivity of xyz file inputs (#9)
 * Add CLI option to disable centering of molecules (#14)
 * Disable default rotation wrt inertia axis for z-matrix input and add a CLI option to force it (#14)
-* Read molecules from the standard input
-* Show infrared intensities and mode masses
+* Read molecules from the standard input (#28)
+* Show infrared intensities and mode masses (#35)
+* Improve the text-in-corner look (de242c7, #36)
 * Improve data structures and code readability
 
 ### Fixes
@@ -24,6 +25,7 @@
 * Fix NaNs when compute dihedrals (#14)
 * Fix the "readagain" (`r`) and "readmore" (`tab`) bugs (#31)
 * Fix z-matrix input with unit=bohr (8554864)
+* Fix text blinking when playing animation (80cae88, #36)
 
 ### Coming in the next version:
 * extended xyz (#16, #17)

obj/v/ac3_print.d

@@ -1,2 +1,2 @@
 obj/v/ac3_print.o obj-pic/v/ac3_print.o: src/v/ac3_print.c src/v/v.h \
- src/mol/mol.h src/mol/common.h src/v/pars.h
+ src/mol/mol.h src/mol/common.h src/v/pars.h src/math/vec3.h

obj/v/evr.d

@@ -1,3 +1,3 @@
 obj/v/evr.o obj-pic/v/evr.o: src/v/evr.c src/v/v.h src/mol/mol.h \
- src/mol/common.h src/v/pars.h src/v/x.h src/v/evr.h src/math/3d.h \
+ src/mol/common.h src/v/pars.h src/v/evr.h src/math/3d.h \
  src/math/matrix.h src/math/vecn.h src/math/vec3.h

obj/v/redraw.d

@@ -0,0 +1,3 @@
+obj/v/redraw.o obj-pic/v/redraw.o: src/v/redraw.c src/v/v.h src/mol/mol.h \
+ src/mol/common.h src/v/pars.h src/v/evr.h src/math/3d.h \
+ src/math/matrix.h src/math/vecn.h

obj/v/x.d

@@ -1,3 +1,3 @@
 obj/v/x.o obj-pic/v/x.o: src/v/x.c src/v/v.h src/mol/mol.h \
- src/mol/common.h src/v/pars.h src/v/x.h src/math/vec2.h \
- src/mol/palette_v.h src/mol/palette_cpk.h
+ src/mol/common.h src/v/pars.h src/v/x.h src/mol/palette_v.h \
+ src/mol/palette_cpk.h

python/vmol/main.py

@@ -47,7 +47,6 @@ class vibr_t(ctypes.Structure):  # noqa: N801
           double * ints;
           double * disp;
           double * mass;
-          double * r0;
           int      n;
         } vibr_t;
     ```
@@ -58,7 +57,6 @@ class vibr_t(ctypes.Structure):  # noqa: N801
             ("ints", c_double_p),
             ("disp", c_double_p),
             ("mass", c_double_p),
-            ("r0",   c_double_p),
             ("n",    c_int),
             )
 
@@ -399,13 +397,13 @@ def vib2struct(nat, vib=None):
 
     Returns:
         vibr_t: An instance of `vibr_t` with the fields set.  If missing, the optional fields are set to 0,
-            and the `r0` is set to NULL.  If the input dictionary is None, everything is set to 0/NULL.
+            If the input dictionary is None, everything is set to 0/NULL.
 
     Raises:
         TypeError: If mol is neither a dictionary nor None.
     """
     if vib is None:
-        return vibr_t(n=c_int(0), disp=None, freq=None, ints=None, mass=None, r0=None)
+        return vibr_t(n=c_int(0), disp=None, freq=None, ints=None, mass=None)
 
     if not isinstance(vib, dict):
         msg = f"vib must be None or a dictionary, but got {type(vib)}"
@@ -452,7 +450,7 @@ def check_array(key, required=True, shape=None, ndim=None, dtype=c_double):
     for key, val in vdict.items():
         vdict[key] = val.ctypes.data_as(c_double_p)
 
-    v = vibr_t(n=nvib, disp=vdict['disp'], freq=vdict['freq'], ints=vdict['ints'], mass=vdict['mass'], r0=None)
+    v = vibr_t(n=nvib, disp=vdict['disp'], freq=vdict['freq'], ints=vdict['ints'], mass=vdict['mass'])
     v._keepalive = (nvib, vdict['disp'], vdict['freq'], vdict['ints'], vdict['mass'])  # keep strong references
     return v
 

src/math/3d.h

@@ -2,10 +2,12 @@
 
 #define DEG2RAD (M_PI/180.0)
 
-void rotmx0_update(double mx[9], double mx1[9], double phi, int axis);
-void rot3d (int n, double * r, double m[9]);
+void rotmx0_update(double mx[9], double phi, int axis);
+void rot3d(int n, double * v, const double * r, const double m[9]);
+void rot3d_inplace(int n, double * r, const double m[9]);
 void rotmx (double * rot, double * u, double phi);
 void rot_around_perp(double rot[9], double dx, double dy, double factor);
+void mx3_lmultmx(const double A[9], double B[9]);
 
 int zmat2cart(int n, double r[3],
               double a[3], double b[3], double c[3],

src/math/matrix.c

@@ -11,7 +11,7 @@ void mx_id(unsigned int n, double * a){
 }
 
 void mx_multmx(unsigned int m, unsigned int n, unsigned int q,
-               double * p, double * a, double * b){
+               double * p, const double * a, const double * b){
   /* a: m*n
    * b: n*q
    * p = ab: m*q

src/math/matrix.h

@@ -15,7 +15,7 @@ static inline unsigned int mpos(unsigned int i, unsigned int j){
 #endif
 
 void     mx_id          (unsigned int n, double * a);
-void     mx_multmx      (unsigned int m, unsigned int n, unsigned int q, double * p, double * a, double * b);
+void     mx_multmx      (unsigned int m, unsigned int n, unsigned int q, double * p, const double * a, const double * b);
 int      mx_inv         (unsigned int n, unsigned int r, double * b, double * a, double eps);
 void     jacobi         (double * a, double * b, double * d, unsigned int n, double eps, unsigned int rot, FILE * f);
 

src/math/rot3d.c

@@ -1,24 +1,26 @@
 #include "3d.h"
 #include "vec3.h"
 
-void rotmx0_update(double mx[9], double mx1[9], double phi, int axis){
-
+void rotmx0_update(double mx[9], double phi, int axis){
   double c = cos(phi);
   double s = sin(phi);
   double ms[3][9]={
     { 1.0, 0.0, 0.0, 0.0, c, -s, 0.0, s, c },
     { c, 0.0, -s, 0.0, 1.0, 0.0, s, 0.0, c },
     { c, -s, 0.0, s, c, 0.0, 0.0, 0.0, 1.0 }
   };
-  veccp(9, mx1, ms[axis]);
+  mx3_lmultmx(ms[axis], mx);
+  return;
+}
 
-  double mx0[9];
-  veccp(9, mx0, mx);
-  mx_multmx(3,3,3, mx, mx1, mx0);
+void rot3d(int n, double * v, const double * r, const double m[9]){
+  for(int i=0; i<n; i++){
+    r3mx(v+3*i, r+3*i, m);
+  }
   return;
 }
 
-void rot3d(int n, double * r, double m[9]){
+void rot3d_inplace(int n, double * r, const double m[9]){
   for(int i=0; i<n; i++){
     double v[3];
     r3mx(v, r+3*i, m);
@@ -54,3 +56,11 @@ void rot_around_perp(double rot[9], double dx, double dy, double factor){
   rotmx(rot, u, factor*l);
   return;
 }
+
+void mx3_lmultmx(const double A[9], double B[9]){
+  // B := A * B
+  double t[9];
+  mx_multmx(3,3,3, t, A, B);
+  veccp(9, B, t);
+  return;
+}

src/math/vec3.h

@@ -12,14 +12,14 @@ static inline void r3set (double * u, double s){
   return;
 }
 
-static inline double r3dot (double * u, double * v){
+static inline double r3dot (const double * u, const double * v){
   return (u[0]*v[0] + u[1]*v[1] + u[2]*v[2]);
 }
 
-static inline double r3d2 (double * u, double * v){
+static inline double r3d2 (const double * u, const double * v){
   return (u[0]-v[0])*(u[0]-v[0]) +
          (u[1]-v[1])*(u[1]-v[1]) +
-	 (u[2]-v[2])*(u[2]-v[2]);
+         (u[2]-v[2])*(u[2]-v[2]);
 }
 
 static inline void r3x (double * w, double * u, double * v){
@@ -29,42 +29,49 @@ static inline void r3x (double * w, double * u, double * v){
   return;
 }
 
-static inline void r3mx (double * u, double * v, double * m){
+static inline void r3mx (double * u, const double * v, const double * m){
   u[0] =  v[0]*m[0] + v[1]*m[1] + v[2]*m[2];
   u[1] =  v[0]*m[3] + v[1]*m[4] + v[2]*m[5];
   u[2] =  v[0]*m[6] + v[1]*m[7] + v[2]*m[8];
   return;
 }
 
+static inline void r3mxt (double * u, const double * v, const double * m){
+  u[0] =  v[0]*m[0] + v[1]*m[3] + v[2]*m[6];
+  u[1] =  v[0]*m[1] + v[1]*m[4] + v[2]*m[7];
+  u[2] =  v[0]*m[2] + v[1]*m[5] + v[2]*m[8];
+  return;
+}
+
 static inline void r3scal (double * u, double c){
   u[0] *= c;
   u[1] *= c;
   u[2] *= c;
   return;
 }
 
-static inline void r3adds (double * u, double * v, double c){
+static inline void r3adds (double * u, const double * v, double c){
   u[0] += c*v[0];
   u[1] += c*v[1];
   u[2] += c*v[2];
   return;
 }
 
-static inline void r3add (double * u, double * v){
+static inline void r3add (double * u, const double * v){
   u[0] += v[0];
   u[1] += v[1];
   u[2] += v[2];
   return;
 }
 
-static inline void r3min (double * u, double * v){
+static inline void r3min (double * u, const double * v){
   u[0] -= v[0];
   u[1] -= v[1];
   u[2] -= v[2];
   return;
 }
 
-static inline void r3sum (double * w, double * u, double * v){
+static inline void r3sum (double * w, const double * u, const double * v){
   w[0] = u[0] + v[0];
   w[1] = u[1] + v[1];
   w[2] = u[2] + v[2];
@@ -78,28 +85,28 @@ static inline void r3diff (double * w, double * u, double * v){
   return;
 }
 
-static inline void r3cp (double * u, double * v){
+static inline void r3cp (double * u, const double * v){
   u[0] = v[0];
   u[1] = v[1];
   u[2] = v[2];
   return;
 }
 
-static inline void r3sums (double * w, double * u, double s, double * v, double t){
+static inline void r3sums (double * w, const double * u, double s, const double * v, double t){
   w[0] = u[0]*s + v[0]*t;
   w[1] = u[1]*s + v[1]*t;
   w[2] = u[2]*s + v[2]*t;
   return;
 }
 
-static inline void r3sums3 (double * w, double * u1, double s1, double * u2, double s2, double * u3, double s3){
+static inline void r3sums3 (double * w, const double * u1, double s1, const double * u2, double s2, const double * u3, double s3){
   w[0] = u1[0]*s1 + u2[0]*s2 + u3[0]*s3;
   w[1] = u1[1]*s1 + u2[1]*s2 + u3[1]*s3;
   w[2] = u1[2]*s1 + u2[2]*s2 + u3[2]*s3;
   return;
 }
 
-static inline void r3cpsc (double * u, double * v, double c){
+static inline void r3cpsc (double * u, const double * v, double c){
   u[0] = v[0]*c;
   u[1] = v[1]*c;
   u[2] = v[2]*c;
@@ -113,29 +120,29 @@ static inline void r3shift(double * u, double s){
   return;
 }
 
-static inline double r3sumcomp(double * u){
+static inline double r3sumcomp(const double * u){
   return u[0]+u[1]+u[2];
 }
 
-static inline double r3v(double * u){
+static inline double r3v(const double * u){
   return u[0]*u[1]*u[2];
 }
 
-static inline void r3divcomp(double * w, double * u, double * v){
+static inline void r3divcomp(double * w, const double * u, const double * v){
   w[0] = u[0] / v[0];
   w[1] = u[1] / v[1];
   w[2] = u[2] / v[2];
   return;
 }
 
-static inline void r3multcomp(double * w, double * u, double * v){
+static inline void r3multcomp(double * w, const double * u, const double * v){
   w[0] = u[0] * v[0];
   w[1] = u[1] * v[1];
   w[2] = u[2] * v[2];
   return;
 }
 
-static inline void r3outer(double * w, double * u, double * v){
+static inline void r3outer(double * w, const double * u, const double * v){
   /* w = u * v^T
    * w[i,j] = u[i]*v[j]
    */
@@ -151,7 +158,7 @@ static inline void r3outer(double * w, double * u, double * v){
   return;
 }
 
-static inline void r3outer6(double * w, double * u, double * v){
+static inline void r3outer6(double * w, const double * u, const double * v){
   w[0] = u[0] * v[0];
   w[1] = u[0] * v[1];
   w[2] = u[1] * v[1];
@@ -161,7 +168,7 @@ static inline void r3outer6(double * w, double * u, double * v){
   return;
 }
 
-static inline double mat3det(double * mat){
+static inline double mat3det(const double * mat){
   return mat[0]*mat[4]*mat[8] + mat[1]*mat[5]*mat[6] + mat[2]*mat[3]*mat[7] - mat[2]*mat[4]*mat[6] - mat[1]*mat[3]*mat[8] - mat[0]*mat[5]*mat[7];
 }