-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathChangeLog
285 lines (198 loc) · 10.4 KB
/
ChangeLog
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
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
2014-07-01 Potapov Ilya <elias.potapov@gmail.com>
* src/random.c (rnd_init_cond_run): Report translation to the
output of random throwing.
2014-06-30 Potapov Ilya <elias.potapov@gmail.com>
* src/random.h: Only initial condition to write to the
output. Flag for this.
2014-06-25 Potapov Ilya <elias.potapov@gmail.com>
* src/integrator.c (write_data_file): Do not proceed writing to
the file, when NaN is calculated.
2014-06-12 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.h: T-system own tolerance values: absolute and
relative.
* src/continue.c (run_extend_rnd): Continue by the parameter along
with random throwing.
* src/trajectory.c (statND_to_file): Fixed the problem with the
array of regStat structs.
(perdcty_in_stat_array): Sort by all possible unique periodicities
for all regStat structs.
2014-06-06 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.h (struct): Distinct separation between SS and OS
regimes without determination of SS through OS.
* src/trajectory.c (statND_to_file): General statistics for
multiple regStat values. Classification by all criteria.
2014-06-04 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.c (regime_stat): Output file to report and
statistics type to report. First type added.
(ss_by_frame): New function determining SS by the fact of equal
values in the trajectory for over than 50% of the time.
2014-06-03 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.c (regime_stat): Periodicity report in the regime
statistics.
(free_regime_stat): Special free-ing of the regime stat structure
regStat.
* src/random.c (rnd_init_cond_run): A single function performing
random initial conditions throwing.
2014-05-30 Potapov Ilya <elias.potapov@gmail.com>
* src/init.h (FRAME_LINE_LEN): Frame constants are in the globale
init.h.
* src/cross.c (write_autocorr_file): Autocorrelation handling
functions in cross.c.
* src/file.c (load_frame): Frame handling functions in file.c.
2014-05-29 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.c (mol_dist): Only the first frame is analyzed
for molecular species function.
(mol_dist): Correct handling of the variable for the distribution
calculation.
* src/cross.c (peak_ampl): New amplitude calculating
function. Jumps over the peaks and calculates the min of preceding
and next troughs, then amplitude is the result of subtraction from
peak value and the min value.
* src/input_interpreter.c (periods_interp): Number of bins of the
amplitude histogram can be specified from the command line.
* src/cross.c (peak_ampl): Simple function to calculate amplitudes
from the peak information (trajPeak object).
(ampl_multi_frames): Calculate amplitudes from multiple
frames. For stochastic purposes.
* src/input_interpreter.c (periods_interp): Amplitude calculation
in the Periods Menu restored.
* src/trajectory.c (mol_dist): Bug is detected in the
function. Should be fixed in the future. Only last imported frame
is analyzed and NOT a number of them.
2014-04-24 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.h (struct): Indicator of the ascending/descending
slope.
2014-04-21 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.c (get_dynamics_nd): Period for each subsystem
printed. All phase shifts are reported.
2014-04-16 Potapov Ilya <elias.potapov@gmail.com>
* src/input_interpreter.c (rand_interp): Constraints can be set
from one-line command.
(load_initials): Take the ceiling instead of round for the
discrete initial conditions.
2014-04-15 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.c (regime_stat): The In-/Out-of-phase statistic
is included.
2014-04-14 Potapov Ilya <elias.potapov@gmail.com>
* src/input_interpreter.c (load_initials): Make the round
operation when reading the initial conditions for the discrete system.
* src/din_main.c (main): Get the $PWD system variable to resolve
the current directory name instead of the previous "./" identificator.
2014-03-30 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.c (report_translate): No phase and no homogeneity
reports are shown in case of LDIM=1.
2014-03-29 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.c (get_dynamics_nd): Reformulation of the ND T-system.
2014-03-28 Potapov Ilya <elias.potapov@gmail.com>
* src/din_main.c (main): Deleting unnecessary files: make sure the
files exist.
* src/input_interpreter.c (load_initials): Copy the initial
conditions to the correspong discrete array of initial
conditions.
2014-03-27 Potapov Ilya <elias.potapov@gmail.com>
* src/init.c (din_close): More freeing at the end.
* src/lyapunov.c (lyap_free): Freeing Lyapunov entities.
* src/input_interpreter.c (rand_interp): Parameters and variables
in the header of the random throwing output file.
2014-03-26 Potapov Ilya <elias.potapov@gmail.com>
* src/input_interpreter.c (parse_command_line): The new command
line parsing system which includes the possibility of reading the
commands from the script file. The latter can be specified to the
program using -f flag.
(rand_interp): Empty args for the random throwing
constraints. Plus, no limitation for DIM number of iterations:
given the empty args there can be more than DIM iterations.
2014-03-14 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.c (find_lag_nd): The new way of determining the
sub-system lag to check the out-of-phase regimes. This way also
includes the definition of the homogeneous vs. in-homogeneous by
the nature of it.
2014-03-11 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.c (check_slope_ampl): No boom appeared treatment
in the slope amplitudes checking. Very important issue left unseen
in the code. Now fixed.
* src/read_ode.c (read_source): The new possibility to define
number of physical systems in .ode files: "%system"
directive. This will deprecate in near future old "#system"
directive, which is kept for backward compatibility.
(read_source): The same as above for "%include"
directive. "#include" is to be deprecated in near future.
2014-02-20 Potapov Ilya <elias.potapov@gmail.com>
* src/input_interpreter.c (read_next_command_wrapper): New wrapper
function starts the new shorter way of reading the user-input.
2014-02-17 Potapov Ilya <elias.potapov@gmail.com>
* src/input_interpreter.c (rand_interp): Random throwing for the
stochastic system.
* src/trajectory.c (get_dynamics_1d): Redefined the attractor
approaching rate, that is, now, showing how much (in %) of the
last slope amplitude has changed over time from slope to
slope. Defined by analogy of the derivative of a function.
2014-02-13 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.c (get_dynamics_1d): Trying to avoid returning
meaningless NULL and save the dynamics regime checking in case of
sl_ampl_size == 1.
* src/cross.c (compute_period): Appending mode for writing the
autocorrelation function to the file.
* src/input_interpreter.c (periods_interp): Plotting the
autocorrelation function.
* src/trajectory.c (get_dynamics_1d): Simple rules to overcome SS
(or not enough points) situation when all the values in the data
file are equal to each other and no peak/trough as well as slope
information can be computed.
2014-02-11 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.c (get_dynamics_1d): The iterative check of the
slope amplitudes to support OS lag value.
2014-02-10 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.c (get_dynamics_1d): Attractor approaching rate
-- how fast you need to reach the attractor.
2014-02-06 Potapov Ilya <elias.potapov@gmail.com>
* src/trajectory.c (get_dynamics_1d): Define the descending rate
before any slope comparisons. This will indicate the descending of
the slope amplitudes. NOTE: negative values will show the
ascending, which is checked in the OS regime.
* src/read_ode.c (process_odefile): Minor bugs about NLANG value
in the processing to .c file.
2014-02-04 Potapov Ilya <elias.potapov@gmail.com>
* src/read_ode.c (read_source): The new format for the langevin
amendments: "lang x=0.1,y=0.4,z=1.3" .
2014-01-31 Potapov Ilya <elias.potapov@gmail.com>
* src/cross.c (crossing): The new way to allocate tisec in the
function. It gets allocated from within the function and then gets
returned. Additionally, the memory gets allocated by the big
chunks, whose size is determined via the constant TISEC_CHUNK_SIZE
[defined in the same file]. This avoids too many calls to the
realloc function, which is advisable to avoid.
2014-01-30 Potapov Ilya <elias.potapov@gmail.com>
* src/integrator.c (analyze_traj): The new output extension. No
more information of the cross level in the output file name. The
output extension is ".do" = (d)inamica (o)utput. The cross level
information is written in the file itself anyway.
(analyze_traj): Single .do output for all cross levels (up to
three). The output is just appended to the file.
2014-01-29 Potapov Ilya <elias.potapov@gmail.com>
* src/input_interpreter.c (main_interp): Minor bugs with memory
allocation under the "Calculate" menu of the Main Menu.
2014-01-23 Potapov Ilya <elias.potapov@gmail.com>
* src/input_interpreter.c (rand_interp): Random menu receives the
new command line treatment procedures. See read_command_line and
read_next_command functions. Additionally, this menu receives the
functionality to constrain the random throwing intervals for the
specific variables set by the user.
(graphics_interp): Free-ing symbuf variable under all *_interp
function before every return statement withing those functions. Or
as a partial solution, remove all return 0; statement under all
else if conditionals in those menus and replace all of them with
one single return 0; at the end of the functions. Except for the
return 1000; statements indicating the exit from the menus.
(rand_interp): Menu for specifying the constraints for the random
throwing.
* src/random.c (random_free): First, "freeing" function. For the
Random stuff. It is invoked in the din_close() function closing
the program.
(random_init): New boundaries for the random throwing for each
variable. Which variable is limited by the special constraints is
determined in the logical array.
2014-01-21 Potapov Ilya <elias.potapov@gmail.com>
* Some declarations missing fixed. Plus, some minor mistypos in
the code as well as some headers were undefined. New compiler, when
moved to the new OS, has complained about all of this.