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37 /* This file is completely threadsafe - keep it that way! */
38 #include "conformation-utilities.h"
47 #include "gmx_fatal.h"
50 static real dist2(t_pbc *pbc, rvec x, rvec y)
54 pbc_dx(pbc, x, y, dx);
59 static real distance_to_z(rvec x)
61 return (sqr(x[XX])+sqr(x[YY]));
64 static void low_rotate_conf(int natom, rvec *x, real alfa, real beta, real gamma)
69 for (i = 0; i < natom; i++)
71 copy_rvec(x[i], x_old);
72 /*calculate new x[i] by rotation alfa around the x-axis*/
74 x[i][YY] = cos(alfa)*x_old[YY] - sin(alfa)*x_old[ZZ];
75 x[i][ZZ] = sin(alfa)*x_old[YY] + cos(alfa)*x_old[ZZ];
76 copy_rvec(x[i], x_old);
77 /*calculate new x[i] by rotation beta around the y-axis*/
78 x[i][XX] = cos(beta)*x_old[XX] + sin(beta)*x_old[ZZ];
80 x[i][ZZ] = -sin(beta)*x_old[XX] + cos(beta)*x_old[ZZ];
81 copy_rvec(x[i], x_old);
82 /*calculate new x[i] by rotation gamma around the z-axis*/
83 x[i][XX] = x_old[XX]*cos(gamma) - x_old[YY]*sin(gamma);
84 x[i][YY] = x_old[XX]*sin(gamma) + x_old[YY]*cos(gamma);
89 static void low_rotate_conf_indexed(int nindex, atom_id *index, rvec *x, real alfa, real beta, real gamma)
94 for (i = 0; i < nindex; i++)
96 copy_rvec(x[index[i]], x_old);
97 /*calculate new x[index[i]] by rotation alfa around the x-axis*/
98 x[index[i]][XX] = x_old[XX];
99 x[index[i]][YY] = cos(alfa)*x_old[YY] - sin(alfa)*x_old[ZZ];
100 x[index[i]][ZZ] = sin(alfa)*x_old[YY] + cos(alfa)*x_old[ZZ];
101 copy_rvec(x[index[i]], x_old);
102 /*calculate new x[index[i]] by rotation beta around the y-axis*/
103 x[index[i]][XX] = cos(beta)*x_old[XX] + sin(beta)*x_old[ZZ];
104 x[index[i]][YY] = x_old[YY];
105 x[index[i]][ZZ] = -sin(beta)*x_old[XX] + cos(beta)*x_old[ZZ];
106 copy_rvec(x[index[i]], x_old);
107 /*calculate new x[index[i]] by rotation gamma around the z-axis*/
108 x[index[i]][XX] = x_old[XX]*cos(gamma) - x_old[YY]*sin(gamma);
109 x[index[i]][YY] = x_old[XX]*sin(gamma) + x_old[YY]*cos(gamma);
110 x[index[i]][ZZ] = x_old[ZZ];
114 void rotate_conf(int natom, rvec *x, rvec *v, real alfa, real beta, real gamma)
118 low_rotate_conf(natom, x, alfa, beta, gamma);
122 low_rotate_conf(natom, v, alfa, beta, gamma);
126 /* Make a new box around a configuration*/
127 void make_new_box(int natoms, rvec *x, matrix box, rvec box_space,
134 /*calculate minimum and maximum x[0..DIM-1]*/
135 for (m = 0; (m < DIM); m++)
137 xmin[m] = xmax[m] = x[0][m];
139 for (i = 1; (i < natoms); i++)
141 for (m = 0; m < DIM; m++)
143 xmin[m] = min(xmin[m], x[i][m]);
144 xmax[m] = max(xmax[m], x[i][m]);
148 /*calculate the new box sizes for cubic and octahedral ...*/
149 for (m = 0; (m < DIM); m++)
151 box[m][m] = xmax[m]-xmin[m]+2*box_space[m];
154 /*move the molecule to the center of the box*/
157 for (i = 0; (i < natoms); i++)
159 for (m = 0; (m < DIM); m++)
161 x[i][m] += 0.5*(box[m][m]-xmin[m]-xmax[m]);