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37 /* This file is completely threadsafe - keep it that way! */
46 #include "gromacs/math/units.h"
47 #include "gromacs/math/utilities.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/topology/ifunc.h"
50 #include "gromacs/trajectory/energyframe.h"
51 #include "gromacs/utility/cstringutil.h"
52 #include "gromacs/utility/fatalerror.h"
53 #include "gromacs/utility/smalloc.h"
64 void done_ebin(t_ebin *eb)
66 for (int i = 0; i < eb->nener; i++)
68 sfree(eb->enm[i].name);
69 sfree(eb->enm[i].unit);
76 int get_ebin_space(t_ebin *eb, int nener, const char *const enm[], const char *unit)
84 srenew(eb->e, eb->nener);
85 srenew(eb->e_sim, eb->nener);
86 srenew(eb->enm, eb->nener);
87 for (i = index; (i < eb->nener); i++)
94 eb->e_sim[i].esum = 0;
95 eb->enm[i].name = gmx_strdup(enm[i-index]);
98 eb->enm[i].unit = gmx_strdup(unit);
102 /* Determine the unit from the longname.
103 * These units should have been defined in ifunc.c
104 * But even better would be if all interactions functions
105 * return energies and all non-interaction function
106 * entries would be removed from the ifunc array.
109 for (f = 0; f < F_NRE; f++)
111 if (strcmp(eb->enm[i].name,
112 interaction_function[f].longname) == 0)
114 /* Only the terms in this list are not energies */
117 case F_DISRESVIOL: u = unit_length; break;
118 case F_ORIRESDEV: u = "obs"; break;
119 case F_TEMP: u = unit_temp_K; break;
121 case F_PRES: u = unit_pres_bar; break;
125 eb->enm[i].unit = gmx_strdup(u);
132 void add_ebin(t_ebin *eb, int index, int nener, const real ener[], gmx_bool bSum)
135 double e, invmm, diff;
138 if ((index+nener > eb->nener) || (index < 0))
140 gmx_fatal(FARGS, "%s-%d: Energies out of range: index=%d nener=%d maxener=%d",
141 __FILE__, __LINE__, index, nener, eb->nener);
144 eg = &(eb->e[index]);
146 for (i = 0; (i < nener); i++)
153 egs = &(eb->e_sim[index]);
159 for (i = 0; (i < nener); i++)
162 eg[i].esum = ener[i];
163 egs[i].esum += ener[i];
168 invmm = (1.0/m)/(m+1.0);
170 for (i = 0; (i < nener); i++)
172 /* Value for this component */
175 /* first update sigma, then sum */
176 diff = eg[i].esum - m*e;
177 eg[i].eav += diff*diff*invmm;
185 void ebin_increase_count(t_ebin *eb, gmx_bool bSum)
197 void reset_ebin_sums(t_ebin *eb)
201 /* The actual sums are cleared when the next frame is stored */
204 void pr_ebin(FILE *fp, t_ebin *eb, int index, int nener, int nperline,
205 int prmode, gmx_bool bPrHead)
213 if (index < 0 || index > eb->nener)
215 gmx_fatal(FARGS, "Invalid index in pr_ebin: %d", index);
218 if (nener > eb->nener)
220 gmx_fatal(FARGS, "Invalid nener in pr_ebin: %d", nener);
227 for (i = start; (i < end) && rc >= 0; )
232 for (j = 0; (j < nperline) && (i < end) && rc >= 0; j++, i++)
234 if (strncmp(eb->enm[i].name, "Pres", 4) == 0)
236 /* Print the pressure unit to avoid confusion */
237 sprintf(buf, "%s (%s)", eb->enm[i].name, unit_pres_bar);
238 rc = fprintf(fp, "%15s", buf);
242 rc = fprintf(fp, "%15s", eb->enm[i].name);
248 rc = fprintf(fp, "\n");
253 for (j = 0; (j < nperline) && (i < end) && rc >= 0; j++, i++)
258 rc = fprintf(fp, " %12.5e", eb->e[i].e);
261 if (eb->nsum_sim > 0)
263 rc = fprintf(fp, " %12.5e", eb->e_sim[i].esum/eb->nsum_sim);
267 rc = fprintf(fp, " %-12s", "N/A");
270 default: gmx_fatal(FARGS, "Invalid print mode %d in pr_ebin",
277 rc = fprintf(fp, "\n");
282 gmx_fatal(FARGS, "Cannot write to logfile; maybe you are out of disk space?");