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37 /* This file is completely threadsafe - keep it that way! */
38 #include "conformation-utilities.h"
44 #include "gromacs/math/vec.h"
45 #include "gromacs/pbcutil/pbc.h"
47 static real dist2(t_pbc *pbc, rvec x, rvec y)
51 pbc_dx(pbc, x, y, dx);
56 static real distance_to_z(rvec x)
58 return (sqr(x[XX])+sqr(x[YY]));
61 static void low_rotate_conf(int natom, rvec *x, real alfa, real beta, real gamma)
66 for (i = 0; i < natom; i++)
68 copy_rvec(x[i], x_old);
69 /*calculate new x[i] by rotation alfa around the x-axis*/
71 x[i][YY] = cos(alfa)*x_old[YY] - sin(alfa)*x_old[ZZ];
72 x[i][ZZ] = sin(alfa)*x_old[YY] + cos(alfa)*x_old[ZZ];
73 copy_rvec(x[i], x_old);
74 /*calculate new x[i] by rotation beta around the y-axis*/
75 x[i][XX] = cos(beta)*x_old[XX] + sin(beta)*x_old[ZZ];
77 x[i][ZZ] = -sin(beta)*x_old[XX] + cos(beta)*x_old[ZZ];
78 copy_rvec(x[i], x_old);
79 /*calculate new x[i] by rotation gamma around the z-axis*/
80 x[i][XX] = x_old[XX]*cos(gamma) - x_old[YY]*sin(gamma);
81 x[i][YY] = x_old[XX]*sin(gamma) + x_old[YY]*cos(gamma);
86 static void low_rotate_conf_indexed(int nindex, atom_id *index, rvec *x, real alfa, real beta, real gamma)
91 for (i = 0; i < nindex; i++)
93 copy_rvec(x[index[i]], x_old);
94 /*calculate new x[index[i]] by rotation alfa around the x-axis*/
95 x[index[i]][XX] = x_old[XX];
96 x[index[i]][YY] = cos(alfa)*x_old[YY] - sin(alfa)*x_old[ZZ];
97 x[index[i]][ZZ] = sin(alfa)*x_old[YY] + cos(alfa)*x_old[ZZ];
98 copy_rvec(x[index[i]], x_old);
99 /*calculate new x[index[i]] by rotation beta around the y-axis*/
100 x[index[i]][XX] = cos(beta)*x_old[XX] + sin(beta)*x_old[ZZ];
101 x[index[i]][YY] = x_old[YY];
102 x[index[i]][ZZ] = -sin(beta)*x_old[XX] + cos(beta)*x_old[ZZ];
103 copy_rvec(x[index[i]], x_old);
104 /*calculate new x[index[i]] by rotation gamma around the z-axis*/
105 x[index[i]][XX] = x_old[XX]*cos(gamma) - x_old[YY]*sin(gamma);
106 x[index[i]][YY] = x_old[XX]*sin(gamma) + x_old[YY]*cos(gamma);
107 x[index[i]][ZZ] = x_old[ZZ];
111 void rotate_conf(int natom, rvec *x, rvec *v, real alfa, real beta, real gamma)
115 low_rotate_conf(natom, x, alfa, beta, gamma);
119 low_rotate_conf(natom, v, alfa, beta, gamma);
123 /* Make a new box around a configuration*/
124 void make_new_box(int natoms, rvec *x, matrix box, rvec box_space,
131 /*calculate minimum and maximum x[0..DIM-1]*/
132 for (m = 0; (m < DIM); m++)
134 xmin[m] = xmax[m] = x[0][m];
136 for (i = 1; (i < natoms); i++)
138 for (m = 0; m < DIM; m++)
140 xmin[m] = min(xmin[m], x[i][m]);
141 xmax[m] = max(xmax[m], x[i][m]);
145 /*calculate the new box sizes for cubic and octahedral ...*/
146 for (m = 0; (m < DIM); m++)
148 box[m][m] = xmax[m]-xmin[m]+2*box_space[m];
151 /*move the molecule to the center of the box*/
154 for (i = 0; (i < natoms); i++)
156 for (m = 0; (m < DIM); m++)
158 x[i][m] += 0.5*(box[m][m]-xmin[m]-xmax[m]);