/
_util.c
232 lines (213 loc) · 7.16 KB
/
_util.c
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
/*
* This file is part of thermotools.
*
* Copyright 2015-2017 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
*
* thermotools is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include "_util.h"
inline double wrap(double x, const double width, const double inverse_width) {
if(width > 0.0) {
return x - nearbyint(x * inverse_width) * width;
} else return x;
}
/***************************************************************************************************
* sorting
***************************************************************************************************/
extern void _mixed_sort(double *array, int L, int R)
/* _mixed_sort() is based on examples from http://www.linux-related.de (2004) */
{
int l, r;
double swap;
if(R - L > 25) /* use quicksort */
{
l = L - 1;
r = R;
for(;;)
{
while(array[++l] < array[R]);
while((array[--r] > array[R]) && (r > l));
if(l >= r) break;
swap = array[l];
array[l] = array[r];
array[r] = swap;
}
swap = array[l];
array[l] = array[R];
array[R] = swap;
_mixed_sort(array, L, l - 1);
_mixed_sort(array, l + 1, R);
}
else /* use insertion sort */
{
for(l=L+1; l<=R; ++l)
{
swap = array[l];
for(r=l-1; (r >= L) && (swap < array[r]); --r)
array[r + 1] = array[r];
array[r + 1] = swap;
}
}
}
/***************************************************************************************************
* direct summation schemes
***************************************************************************************************/
extern void _kahan_summation_step(
double new_value, double *sum, double *err, double *loc, double *tmp)
{
*loc = new_value - *err;
*tmp = *sum + *loc;
*err = (*tmp - *sum) - *loc;
*sum = *tmp;
}
extern double _kahan_summation(double *array, int size)
{
int i;
double sum = 0.0, err = 0.0, loc, tmp;
for(i=0; i<size; ++i)
{
loc = array[i] - err;
tmp = sum + loc;
err = (tmp - sum) - loc;
sum = tmp;
}
return sum;
}
/***************************************************************************************************
* logspace summation schemes
***************************************************************************************************/
extern double _logsumexp(double *array, int size, double array_max)
{
int i;
double sum = 0.0;
if(0 == size) return -INFINITY;
if(-INFINITY == array_max)
return -INFINITY;
for(i=0; i<size; ++i)
sum += exp(array[i] - array_max);
return array_max + log(sum);
}
extern double _logsumexp_kahan_inplace(double *array, int size, double array_max)
{
int i;
if(0 == size) return -INFINITY;
if(-INFINITY == array_max)
return -INFINITY;
for(i=0; i<size; ++i)
array[i] = exp(array[i] - array_max);
return array_max + log(_kahan_summation(array, size));
}
extern double _logsumexp_sort_inplace(double *array, int size)
{
if(0 == size) return -INFINITY;
_mixed_sort(array, 0, size - 1);
return _logsumexp(array, size, array[size - 1]);
}
extern double _logsumexp_sort_kahan_inplace(double *array, int size)
{
if(0 == size) return -INFINITY;
_mixed_sort(array, 0, size - 1);
return _logsumexp_kahan_inplace(array, size, array[size - 1]);
}
extern double _logsumexp_pair(double a, double b)
{
if((-INFINITY == a) && (-INFINITY == b))
return -INFINITY;
if(b > a)
return b + log(1.0 + exp(a - b));
return a + log(1.0 + exp(b - a));
}
/***************************************************************************************************
* counting states and transitions
***************************************************************************************************/
extern int _get_therm_state_break_points(int *T_x, int seq_length, int *break_points)
{
int i, K, o = 1;
break_points[0] = 0;
K = T_x[0];
for(i=1; i<seq_length; ++i)
{
if(T_x[i] != K)
{
K = T_x[i];
break_points[o++] = i;
}
}
return o;
}
/***************************************************************************************************
* bias calculation tools
***************************************************************************************************/
extern void _get_umbrella_bias(
double *traj, double *umbrella_centers, double *force_constants,
double *width, double *inverse_width,
int nsamples, int nthermo, int ndim, double *bias)
{
int i, j, s, k;
int dd = ndim * ndim, kdd, kdim, sdim;
double sum, isum, fc;
for(s=0; s<nsamples; ++s)
{
sdim = s * ndim;
for(k=0; k<nthermo; ++k)
{
sum = 0.0;
kdd = k * dd;
kdim = k * ndim;
for(i=0; i<ndim; ++i)
{
isum = 0.0;
for(j=0; j<ndim; ++j)
{
fc = force_constants[kdd + i * ndim + j];
if(0.0 == fc)
continue;
isum += fc
* wrap(traj[sdim + i] - umbrella_centers[kdim + i], width[i], inverse_width[i])
* wrap(traj[sdim + j] - umbrella_centers[kdim + j], width[j], inverse_width[j]);
}
sum += isum;
}
bias[s * nthermo + k] = 0.5 * sum;
}
}
}
/***************************************************************************************************
* transition matrix renormalization
***************************************************************************************************/
extern void _renormalize_transition_matrix(double *p, int n_conf_states, double *scratch_M)
{
int i, j;
double sum, max_sum = 0.0;
for(i=0; i<n_conf_states; ++i)
{
for(j=0; j<n_conf_states; ++j)
scratch_M[j] = p[i * n_conf_states + j];
_mixed_sort(scratch_M, 0, n_conf_states - 1);
sum = _kahan_summation(scratch_M, n_conf_states);
max_sum = (max_sum > sum) ? max_sum : sum;
}
if(0.0 >= max_sum) return;
for(i=0; i<n_conf_states; ++i)
{
for(j=0; j<n_conf_states; ++j)
{
p[i * n_conf_states + j] /= max_sum;
if(i == j) scratch_M[i] = 0.0;
else scratch_M[i] = p[i * n_conf_states + j];
}
_mixed_sort(scratch_M, 0, n_conf_states - 1);
p[i * n_conf_states + i] = 1.0 - _kahan_summation(scratch_M, n_conf_states);
}
}