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38 /* This file is completely threadsafe - keep it that way! */
39 #include "gmxpre.h"
40
41 #include "ebin.h"
42
43 #include <cmath>
44 #include <cstring>
45
46 #include <algorithm>
47
48 #include "gromacs/math/units.h"
49 #include "gromacs/math/utilities.h"
50 #include "gromacs/math/vec.h"
51 #include "gromacs/topology/ifunc.h"
52 #include "gromacs/trajectory/energyframe.h"
53 #include "gromacs/utility/arrayref.h"
54 #include "gromacs/utility/basedefinitions.h"
55 #include "gromacs/utility/cstringutil.h"
56 #include "gromacs/utility/fatalerror.h"
57 #include "gromacs/utility/smalloc.h"
58 #include "gromacs/utility/stringutil.h"
59
mk_ebin()60 t_ebin* mk_ebin()
61 {
62 t_ebin* eb;
63
64 snew(eb, 1);
65
66 return eb;
67 }
68
done_ebin(t_ebin * eb)69 void done_ebin(t_ebin* eb)
70 {
71 for (int i = 0; i < eb->nener; i++)
72 {
73 sfree(eb->enm[i].name);
74 sfree(eb->enm[i].unit);
75 }
76 sfree(eb->e);
77 sfree(eb->e_sim);
78 sfree(eb->enm);
79 sfree(eb);
80 }
81
get_ebin_space(t_ebin * eb,int nener,const char * const enm[],const char * unit)82 int get_ebin_space(t_ebin* eb, int nener, const char* const enm[], const char* unit)
83 {
84 int index;
85 int i, f;
86 const char* u;
87
88 index = eb->nener;
89 eb->nener += nener;
90 srenew(eb->e, eb->nener);
91 srenew(eb->e_sim, eb->nener);
92 srenew(eb->enm, eb->nener);
93 for (i = index; (i < eb->nener); i++)
94 {
95 eb->e[i].e = 0;
96 eb->e[i].eav = 0;
97 eb->e[i].esum = 0;
98 eb->e_sim[i].e = 0;
99 eb->e_sim[i].eav = 0;
100 eb->e_sim[i].esum = 0;
101 eb->enm[i].name = gmx_strdup(enm[i - index]);
102 if (unit != nullptr)
103 {
104 eb->enm[i].unit = gmx_strdup(unit);
105 }
106 else
107 {
108 /* Determine the unit from the longname.
109 * These units should have been defined in ifunc.c
110 * But even better would be if all interactions functions
111 * return energies and all non-interaction function
112 * entries would be removed from the ifunc array.
113 */
114 u = unit_energy;
115 for (f = 0; f < F_NRE; f++)
116 {
117 if (strcmp(eb->enm[i].name, interaction_function[f].longname) == 0)
118 {
119 /* Only the terms in this list are not energies */
120 switch (f)
121 {
122 case F_DISRESVIOL: u = unit_length; break;
123 case F_ORIRESDEV: u = "obs"; break;
124 case F_TEMP: u = unit_temp_K; break;
125 case F_PDISPCORR:
126 case F_PRES: u = unit_pres_bar; break;
127 }
128 }
129 }
130 eb->enm[i].unit = gmx_strdup(u);
131 }
132 }
133
134 return index;
135 }
136
137 // ICC 19 -O3 -msse2 generates wrong code. Lower optimization levels
138 // and other SIMD levels seem fine, however.
139 #if defined __ICC
140 # pragma intel optimization_level 2
141 #endif
add_ebin(t_ebin * eb,int entryIndex,int nener,const real ener[],gmx_bool bSum)142 void add_ebin(t_ebin* eb, int entryIndex, int nener, const real ener[], gmx_bool bSum)
143 {
144 int i, m;
145 double e, invmm, diff;
146 t_energy *eg, *egs;
147
148 if ((entryIndex + nener > eb->nener) || (entryIndex < 0))
149 {
150 gmx_fatal(FARGS, "%s-%d: Energies out of range: entryIndex=%d nener=%d maxener=%d",
151 __FILE__, __LINE__, entryIndex, nener, eb->nener);
152 }
153
154 eg = &(eb->e[entryIndex]);
155
156 for (i = 0; (i < nener); i++)
157 {
158 eg[i].e = ener[i];
159 }
160
161 if (bSum)
162 {
163 egs = &(eb->e_sim[entryIndex]);
164
165 m = eb->nsum;
166
167 if (m == 0)
168 {
169 for (i = 0; (i < nener); i++)
170 {
171 eg[i].eav = 0;
172 eg[i].esum = ener[i];
173 egs[i].esum += ener[i];
174 }
175 }
176 else
177 {
178 invmm = (1.0 / m) / (m + 1.0);
179
180 for (i = 0; (i < nener); i++)
181 {
182 /* Value for this component */
183 e = ener[i];
184
185 /* first update sigma, then sum */
186 diff = eg[i].esum - m * e;
187 eg[i].eav += diff * diff * invmm;
188 eg[i].esum += e;
189 egs[i].esum += e;
190 }
191 }
192 }
193 }
194
195 // TODO It would be faster if this function was templated on both bSum
196 // and whether eb->nsum was zero, to lift the branches out of the loop
197 // over all possible energy terms, but that is true for a lot of the
198 // ebin and mdebin functionality, so we should do it all or nothing.
add_ebin_indexed(t_ebin * eb,int entryIndex,gmx::ArrayRef<bool> shouldUse,gmx::ArrayRef<const real> ener,gmx_bool bSum)199 void add_ebin_indexed(t_ebin* eb,
200 int entryIndex,
201 gmx::ArrayRef<bool> shouldUse,
202 gmx::ArrayRef<const real> ener,
203 gmx_bool bSum)
204 {
205
206 GMX_ASSERT(shouldUse.size() == ener.size(), "View sizes must match");
207 GMX_ASSERT(entryIndex + std::count(shouldUse.begin(), shouldUse.end(), true) <= eb->nener,
208 gmx::formatString("Energies out of range: entryIndex=%d nener=%td maxener=%d", entryIndex,
209 std::count(shouldUse.begin(), shouldUse.end(), true), eb->nener)
210 .c_str());
211 GMX_ASSERT(entryIndex >= 0, "Must have non-negative entry");
212
213 const int m = eb->nsum;
214 const double invmm = (m == 0) ? 0 : (1.0 / m) / (m + 1.0);
215 t_energy* energyEntry = &(eb->e[entryIndex]);
216 t_energy* simEnergyEntry = &(eb->e_sim[entryIndex]);
217 auto shouldUseIter = shouldUse.begin();
218 for (const auto& theEnergy : ener)
219 {
220 if (*shouldUseIter)
221 {
222 energyEntry->e = theEnergy;
223 if (bSum)
224 {
225 if (m == 0)
226 {
227 energyEntry->eav = 0;
228 energyEntry->esum = theEnergy;
229 simEnergyEntry->esum += theEnergy;
230 }
231 else
232 {
233 /* first update sigma, then sum */
234 double diff = energyEntry->esum - m * theEnergy;
235 energyEntry->eav += diff * diff * invmm;
236 energyEntry->esum += theEnergy;
237 simEnergyEntry->esum += theEnergy;
238 }
239 ++simEnergyEntry;
240 }
241 ++energyEntry;
242 }
243 ++shouldUseIter;
244 }
245 }
246
ebin_increase_count(int increment,t_ebin * eb,gmx_bool bSum)247 void ebin_increase_count(int increment, t_ebin* eb, gmx_bool bSum)
248 {
249 eb->nsteps += increment;
250 eb->nsteps_sim += increment;
251
252 if (bSum)
253 {
254 eb->nsum += increment;
255 eb->nsum_sim += increment;
256 }
257 }
258
reset_ebin_sums(t_ebin * eb)259 void reset_ebin_sums(t_ebin* eb)
260 {
261 eb->nsteps = 0;
262 eb->nsum = 0;
263 /* The actual sums are cleared when the next frame is stored */
264 }
265
pr_ebin(FILE * fp,t_ebin * eb,int entryIndex,int nener,int nperline,int prmode,gmx_bool bPrHead)266 void pr_ebin(FILE* fp, t_ebin* eb, int entryIndex, int nener, int nperline, int prmode, gmx_bool bPrHead)
267 {
268 int i, j, i0;
269 int rc;
270 char buf[30];
271
272 rc = 0;
273
274 if (entryIndex < 0 || entryIndex > eb->nener)
275 {
276 gmx_fatal(FARGS, "Invalid entryIndex in pr_ebin: %d", entryIndex);
277 }
278 int start = entryIndex;
279 if (nener > eb->nener)
280 {
281 gmx_fatal(FARGS, "Invalid nener in pr_ebin: %d", nener);
282 }
283 int end = eb->nener;
284 if (nener != -1)
285 {
286 end = entryIndex + nener;
287 }
288 for (i = start; (i < end) && rc >= 0;)
289 {
290 if (bPrHead)
291 {
292 i0 = i;
293 for (j = 0; (j < nperline) && (i < end) && rc >= 0; j++, i++)
294 {
295 if (strncmp(eb->enm[i].name, "Pres", 4) == 0)
296 {
297 /* Print the pressure unit to avoid confusion */
298 sprintf(buf, "%s (%s)", eb->enm[i].name, unit_pres_bar);
299 rc = fprintf(fp, "%15s", buf);
300 }
301 else
302 {
303 rc = fprintf(fp, "%15s", eb->enm[i].name);
304 }
305 }
306
307 if (rc >= 0)
308 {
309 rc = fprintf(fp, "\n");
310 }
311
312 i = i0;
313 }
314 for (j = 0; (j < nperline) && (i < end) && rc >= 0; j++, i++)
315 {
316 switch (prmode)
317 {
318 case eprNORMAL: rc = fprintf(fp, " %12.5e", eb->e[i].e); break;
319 case eprAVER:
320 if (eb->nsum_sim > 0)
321 {
322 rc = fprintf(fp, " %12.5e", eb->e_sim[i].esum / eb->nsum_sim);
323 }
324 else
325 {
326 rc = fprintf(fp, " %-12s", "N/A");
327 }
328 break;
329 default: gmx_fatal(FARGS, "Invalid print mode %d in pr_ebin", prmode);
330 }
331 }
332 if (rc >= 0)
333 {
334 rc = fprintf(fp, "\n");
335 }
336 }
337 if (rc < 0)
338 {
339 gmx_fatal(FARGS, "Cannot write to logfile; maybe you are out of disk space?");
340 }
341 }
342