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43 #include "gromacs/topology/ifunc.h"
44 #include "gromacs/utility/fatalerror.h"
45 #include "gromacs/utility/txtdump.h"
47 static void pr_harm(FILE *fp, const t_iparams *iparams, const char *r, const char *kr)
49 fprintf(fp, "%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e\n",
50 r, iparams->harmonic.rA, kr, iparams->harmonic.krA,
51 r, iparams->harmonic.rB, kr, iparams->harmonic.krB);
54 void pr_iparams(FILE *fp, t_functype ftype, const t_iparams *iparams)
60 pr_harm(fp, iparams, "th", "ct");
62 case F_CROSS_BOND_BONDS:
63 fprintf(fp, "r1e=%15.8e, r2e=%15.8e, krr=%15.8e\n",
64 iparams->cross_bb.r1e, iparams->cross_bb.r2e,
65 iparams->cross_bb.krr);
67 case F_CROSS_BOND_ANGLES:
68 fprintf(fp, "r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e\n",
69 iparams->cross_ba.r1e, iparams->cross_ba.r2e,
70 iparams->cross_ba.r3e, iparams->cross_ba.krt);
73 fprintf(fp, "klinA=%15.8e, aA=%15.8e, klinB=%15.8e, aB=%15.8e\n",
74 iparams->linangle.klinA, iparams->linangle.aA,
75 iparams->linangle.klinB, iparams->linangle.aB);
78 fprintf(fp, "thetaA=%15.8e, kthetaA=%15.8e, r13A=%15.8e, kUBA=%15.8e, thetaB=%15.8e, kthetaB=%15.8e, r13B=%15.8e, kUBB=%15.8e\n", iparams->u_b.thetaA, iparams->u_b.kthetaA, iparams->u_b.r13A, iparams->u_b.kUBA, iparams->u_b.thetaB, iparams->u_b.kthetaB, iparams->u_b.r13B, iparams->u_b.kUBB);
80 case F_QUARTIC_ANGLES:
81 fprintf(fp, "theta=%15.8e", iparams->qangle.theta);
82 for (int i = 0; i < 5; i++)
84 fprintf(fp, ", c%c=%15.8e", '0'+i, iparams->qangle.c[i]);
89 fprintf(fp, "a=%15.8e, b=%15.8e, c=%15.8e\n",
90 iparams->bham.a, iparams->bham.b, iparams->bham.c);
95 pr_harm(fp, iparams, "b0", "cb");
98 pr_harm(fp, iparams, "xi", "cx");
101 fprintf(fp, "b0A=%15.8e, cbA=%15.8e, betaA=%15.8e, b0B=%15.8e, cbB=%15.8e, betaB=%15.8e\n",
102 iparams->morse.b0A, iparams->morse.cbA, iparams->morse.betaA,
103 iparams->morse.b0B, iparams->morse.cbB, iparams->morse.betaB);
106 fprintf(fp, "b0=%15.8e, kb=%15.8e, kcub=%15.8e\n",
107 iparams->cubic.b0, iparams->cubic.kb, iparams->cubic.kcub);
113 fprintf(fp, "bm=%15.8e, kb=%15.8e\n", iparams->fene.bm, iparams->fene.kb);
116 fprintf(fp, "lowA=%15.8e, up1A=%15.8e, up2A=%15.8e, kA=%15.8e, lowB=%15.8e, up1B=%15.8e, up2B=%15.8e, kB=%15.8e,\n",
117 iparams->restraint.lowA, iparams->restraint.up1A,
118 iparams->restraint.up2A, iparams->restraint.kA,
119 iparams->restraint.lowB, iparams->restraint.up1B,
120 iparams->restraint.up2B, iparams->restraint.kB);
126 fprintf(fp, "tab=%d, kA=%15.8e, kB=%15.8e\n",
127 iparams->tab.table, iparams->tab.kA, iparams->tab.kB);
130 fprintf(fp, "alpha=%15.8e\n", iparams->polarize.alpha);
133 fprintf(fp, "alpha=%15.8e drcut=%15.8e khyp=%15.8e\n",
134 iparams->anharm_polarize.alpha,
135 iparams->anharm_polarize.drcut,
136 iparams->anharm_polarize.khyp);
139 fprintf(fp, "a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e\n",
140 iparams->thole.a, iparams->thole.alpha1, iparams->thole.alpha2,
141 iparams->thole.rfac);
144 fprintf(fp, "al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f\n",
145 iparams->wpol.al_x, iparams->wpol.al_y, iparams->wpol.al_z,
146 iparams->wpol.rOH, iparams->wpol.rHH, iparams->wpol.rOD);
149 fprintf(fp, "c6=%15.8e, c12=%15.8e\n", iparams->lj.c6, iparams->lj.c12);
152 fprintf(fp, "c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e\n",
153 iparams->lj14.c6A, iparams->lj14.c12A,
154 iparams->lj14.c6B, iparams->lj14.c12B);
157 fprintf(fp, "fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
159 iparams->ljc14.qi, iparams->ljc14.qj,
160 iparams->ljc14.c6, iparams->ljc14.c12);
163 fprintf(fp, "qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
164 iparams->ljcnb.qi, iparams->ljcnb.qj,
165 iparams->ljcnb.c6, iparams->ljcnb.c12);
171 fprintf(fp, "phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d\n",
172 iparams->pdihs.phiA, iparams->pdihs.cpA,
173 iparams->pdihs.phiB, iparams->pdihs.cpB,
174 iparams->pdihs.mult);
177 fprintf(fp, "label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)\n",
178 iparams->disres.label, iparams->disres.type,
179 iparams->disres.low, iparams->disres.up1,
180 iparams->disres.up2, iparams->disres.kfac);
183 fprintf(fp, "ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)\n",
184 iparams->orires.ex, iparams->orires.label, iparams->orires.power,
185 iparams->orires.c, iparams->orires.obs, iparams->orires.kfac);
188 fprintf(fp, "phiA=%15.8e, dphiA=%15.8e, kfacA=%15.8e, phiB=%15.8e, dphiB=%15.8e, kfacB=%15.8e\n",
189 iparams->dihres.phiA, iparams->dihres.dphiA, iparams->dihres.kfacA,
190 iparams->dihres.phiB, iparams->dihres.dphiB, iparams->dihres.kfacB);
193 fprintf(fp, "pos0A=(%15.8e,%15.8e,%15.8e), fcA=(%15.8e,%15.8e,%15.8e), pos0B=(%15.8e,%15.8e,%15.8e), fcB=(%15.8e,%15.8e,%15.8e)\n",
194 iparams->posres.pos0A[XX], iparams->posres.pos0A[YY],
195 iparams->posres.pos0A[ZZ], iparams->posres.fcA[XX],
196 iparams->posres.fcA[YY], iparams->posres.fcA[ZZ],
197 iparams->posres.pos0B[XX], iparams->posres.pos0B[YY],
198 iparams->posres.pos0B[ZZ], iparams->posres.fcB[XX],
199 iparams->posres.fcB[YY], iparams->posres.fcB[ZZ]);
202 fprintf(fp, "pos0=(%15.8e,%15.8e,%15.8e), geometry=%d, r=%15.8e, k=%15.8e\n",
203 iparams->fbposres.pos0[XX], iparams->fbposres.pos0[YY],
204 iparams->fbposres.pos0[ZZ], iparams->fbposres.geom,
205 iparams->fbposres.r, iparams->fbposres.k);
208 for (int i = 0; i < NR_RBDIHS; i++)
210 fprintf(fp, "%srbcA[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams->rbdihs.rbcA[i]);
213 for (int i = 0; i < NR_RBDIHS; i++)
215 fprintf(fp, "%srbcB[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams->rbdihs.rbcB[i]);
221 /* Use the OPLS -> Ryckaert-Bellemans formula backwards to get
222 * the OPLS potential constants back.
224 const real *rbcA = iparams->rbdihs.rbcA;
225 const real *rbcB = iparams->rbdihs.rbcB;
228 VA[3] = -0.25*rbcA[4];
229 VA[2] = -0.5*rbcA[3];
230 VA[1] = 4.0*VA[3]-rbcA[2];
231 VA[0] = 3.0*VA[2]-2.0*rbcA[1];
233 VB[3] = -0.25*rbcB[4];
234 VB[2] = -0.5*rbcB[3];
235 VB[1] = 4.0*VB[3]-rbcB[2];
236 VB[0] = 3.0*VB[2]-2.0*rbcB[1];
238 for (int i = 0; i < NR_FOURDIHS; i++)
240 fprintf(fp, "%sFourA[%d]=%15.8e", i == 0 ? "" : ", ", i, VA[i]);
243 for (int i = 0; i < NR_FOURDIHS; i++)
245 fprintf(fp, "%sFourB[%d]=%15.8e", i == 0 ? "" : ", ", i, VB[i]);
253 fprintf(fp, "dA=%15.8e, dB=%15.8e\n", iparams->constr.dA, iparams->constr.dB);
256 fprintf(fp, "doh=%15.8e, dhh=%15.8e\n", iparams->settle.doh,
257 iparams->settle.dhh);
260 fprintf(fp, "a=%15.8e\n", iparams->vsite.a);
265 fprintf(fp, "a=%15.8e, b=%15.8e\n", iparams->vsite.a, iparams->vsite.b);
270 fprintf(fp, "a=%15.8e, b=%15.8e, c=%15.8e\n",
271 iparams->vsite.a, iparams->vsite.b, iparams->vsite.c);
274 fprintf(fp, "n=%2d, a=%15.8e\n", iparams->vsiten.n, iparams->vsiten.a);
279 fprintf(fp, "sar=%15.8e, st=%15.8e, pi=%15.8e, gbr=%15.8e, bmlt=%15.8e\n", iparams->gb.sar, iparams->gb.st, iparams->gb.pi, iparams->gb.gbr, iparams->gb.bmlt);
282 fprintf(fp, "cmapA=%1d, cmapB=%1d\n", iparams->cmap.cmapA, iparams->cmap.cmapB);
285 pr_harm(fp, iparams, "ktheta", "costheta0");
288 fprintf(fp, "phiA=%15.8e, cpA=%15.8e",
289 iparams->pdihs.phiA, iparams->pdihs.cpA);
292 fprintf(fp, "kphi=%15.8e", iparams->cbtdihs.cbtcA[0]);
293 for (int i = 1; i < NR_CBTDIHS; i++)
295 fprintf(fp, ", cbtcA[%d]=%15.8e", i-1, iparams->cbtdihs.cbtcA[i]);
300 gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d",
301 ftype, interaction_function[ftype].name, __FILE__, __LINE__);
305 void pr_ilist(FILE *fp, int indent, const char *title,
306 const t_functype *functype, const t_ilist *ilist, gmx_bool bShowNumbers)
308 int i, j, k, type, ftype;
311 if (available(fp, ilist, indent, title) && ilist->nr > 0)
313 indent = pr_title(fp, indent, title);
314 pr_indent(fp, indent);
315 fprintf(fp, "nr: %d\n", ilist->nr);
318 pr_indent(fp, indent);
319 fprintf(fp, "iatoms:\n");
320 iatoms = ilist->iatoms;
321 for (i = j = 0; i < ilist->nr; )
324 pr_indent(fp, indent+INDENT);
326 ftype = functype[type];
327 fprintf(fp, "%d type=%d (%s)",
328 bShowNumbers ? j : -1, bShowNumbers ? type : -1,
329 interaction_function[ftype].name);
331 for (k = 0; k < interaction_function[ftype].nratoms; k++)
333 fprintf(fp, " %d", *(iatoms++));
336 i += 1+interaction_function[ftype].nratoms;
338 fprintf(fp, "%5d%5d\n", i, iatoms[i]);
346 static void pr_cmap(FILE *fp, int indent, const char *title,
347 const gmx_cmap_t *cmap_grid, gmx_bool bShowNumbers)
352 dx = 360.0 / cmap_grid->grid_spacing;
353 nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
355 if (available(fp, cmap_grid, indent, title))
357 fprintf(fp, "%s\n", title);
359 for (i = 0; i < cmap_grid->ngrid; i++)
362 fprintf(fp, "%8s %8s %8s %8s\n", "V", "dVdx", "dVdy", "d2dV");
364 fprintf(fp, "grid[%3d]={\n", bShowNumbers ? i : -1);
366 for (j = 0; j < nelem; j++)
368 if ( (j%cmap_grid->grid_spacing) == 0)
370 fprintf(fp, "%8.1f\n", idx);
374 fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4]);
375 fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4+1]);
376 fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4+2]);
377 fprintf(fp, "%8.3f\n", cmap_grid->cmapdata[i].cmap[j*4+3]);
385 void pr_ffparams(FILE *fp, int indent, const char *title,
386 const gmx_ffparams_t *ffparams,
387 gmx_bool bShowNumbers)
391 indent = pr_title(fp, indent, title);
392 pr_indent(fp, indent);
393 fprintf(fp, "atnr=%d\n", ffparams->atnr);
394 pr_indent(fp, indent);
395 fprintf(fp, "ntypes=%d\n", ffparams->ntypes);
396 for (i = 0; i < ffparams->ntypes; i++)
398 pr_indent(fp, indent+INDENT);
399 fprintf(fp, "functype[%d]=%s, ",
400 bShowNumbers ? i : -1,
401 interaction_function[ffparams->functype[i]].name);
402 pr_iparams(fp, ffparams->functype[i], &ffparams->iparams[i]);
404 pr_double(fp, indent, "reppow", ffparams->reppow);
405 pr_real(fp, indent, "fudgeQQ", ffparams->fudgeQQ);
406 pr_cmap(fp, indent, "cmap", &ffparams->cmap_grid, bShowNumbers);
409 void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef, gmx_bool bShowNumbers)
413 if (available(fp, idef, indent, title))
415 indent = pr_title(fp, indent, title);
416 pr_indent(fp, indent);
417 fprintf(fp, "atnr=%d\n", idef->atnr);
418 pr_indent(fp, indent);
419 fprintf(fp, "ntypes=%d\n", idef->ntypes);
420 for (i = 0; i < idef->ntypes; i++)
422 pr_indent(fp, indent+INDENT);
423 fprintf(fp, "functype[%d]=%s, ",
424 bShowNumbers ? i : -1,
425 interaction_function[idef->functype[i]].name);
426 pr_iparams(fp, idef->functype[i], &idef->iparams[i]);
428 pr_real(fp, indent, "fudgeQQ", idef->fudgeQQ);
430 for (j = 0; (j < F_NRE); j++)
432 pr_ilist(fp, indent, interaction_function[j].longname,
433 idef->functype, &idef->il[j], bShowNumbers);