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Use proper doxygen tags in modular simulator
[gromacs.git] / src / gromacs / topology / idef.cpp
bloba82e6e5754bbb112fe7d8f2fab1953dd5827c9df
1 /*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
7 * Copyright (c) 2019,2020, by the GROMACS development team, led by
8 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
9 * and including many others, as listed in the AUTHORS file in the
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37 */
38 #include "gmxpre.h"
39
40 #include "idef.h"
41
42 #include <cstdio>
43
44 #include "gromacs/topology/forcefieldparameters.h"
45 #include "gromacs/topology/ifunc.h"
46 #include "gromacs/utility/fatalerror.h"
47 #include "gromacs/utility/smalloc.h"
48 #include "gromacs/utility/stringstream.h"
49 #include "gromacs/utility/textwriter.h"
50 #include "gromacs/utility/txtdump.h"
51
52 static void printHarmonicInteraction(gmx::TextWriter* writer,
53 const t_iparams& iparams,
54 const char* r,
55 const char* kr)
56 {
57 writer->writeLineFormatted("%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e", r,
58 iparams.harmonic.rA, kr, iparams.harmonic.krA, r,
59 iparams.harmonic.rB, kr, iparams.harmonic.krB);
60 }
61
62 void pr_iparams(FILE* fp, t_functype ftype, const t_iparams& iparams)
63 {
64 gmx::StringOutputStream stream;
65 {
66 gmx::TextWriter writer(&stream);
67 printInteractionParameters(&writer, ftype, iparams);
68 }
69 fputs(stream.toString().c_str(), fp);
70 }
71
72 void printInteractionParameters(gmx::TextWriter* writer, t_functype ftype, const t_iparams& iparams)
73 {
74 switch (ftype)
75 {
76 case F_ANGLES:
77 case F_G96ANGLES: printHarmonicInteraction(writer, iparams, "th", "ct"); break;
78 case F_CROSS_BOND_BONDS:
79 writer->writeLineFormatted("r1e=%15.8e, r2e=%15.8e, krr=%15.8e", iparams.cross_bb.r1e,
80 iparams.cross_bb.r2e, iparams.cross_bb.krr);
81 break;
82 case F_CROSS_BOND_ANGLES:
83 writer->writeLineFormatted("r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e",
84 iparams.cross_ba.r1e, iparams.cross_ba.r2e,
85 iparams.cross_ba.r3e, iparams.cross_ba.krt);
86 break;
87 case F_LINEAR_ANGLES:
88 writer->writeLineFormatted("klinA=%15.8e, aA=%15.8e, klinB=%15.8e, aB=%15.8e",
89 iparams.linangle.klinA, iparams.linangle.aA,
90 iparams.linangle.klinB, iparams.linangle.aB);
91 break;
92 case F_UREY_BRADLEY:
93 writer->writeLineFormatted(
94 "thetaA=%15.8e, kthetaA=%15.8e, r13A=%15.8e, kUBA=%15.8e, thetaB=%15.8e, "
95 "kthetaB=%15.8e, r13B=%15.8e, kUBB=%15.8e",
96 iparams.u_b.thetaA, iparams.u_b.kthetaA, iparams.u_b.r13A, iparams.u_b.kUBA,
97 iparams.u_b.thetaB, iparams.u_b.kthetaB, iparams.u_b.r13B, iparams.u_b.kUBB);
98 break;
99 case F_QUARTIC_ANGLES:
100 writer->writeStringFormatted("theta=%15.8e", iparams.qangle.theta);
101 for (int i = 0; i < 5; i++)
102 {
103 writer->writeStringFormatted(", c%c=%15.8e", '0' + i, iparams.qangle.c[i]);
104 }
105 writer->ensureLineBreak();
106 break;
107 case F_BHAM:
108 writer->writeLineFormatted("a=%15.8e, b=%15.8e, c=%15.8e", iparams.bham.a,
109 iparams.bham.b, iparams.bham.c);
110 break;
111 case F_BONDS:
112 case F_G96BONDS:
113 case F_HARMONIC: printHarmonicInteraction(writer, iparams, "b0", "cb"); break;
114 case F_IDIHS: printHarmonicInteraction(writer, iparams, "xi", "cx"); break;
115 case F_MORSE:
116 writer->writeLineFormatted(
117 "b0A=%15.8e, cbA=%15.8e, betaA=%15.8e, b0B=%15.8e, cbB=%15.8e, betaB=%15.8e",
118 iparams.morse.b0A, iparams.morse.cbA, iparams.morse.betaA, iparams.morse.b0B,
119 iparams.morse.cbB, iparams.morse.betaB);
120 break;
121 case F_CUBICBONDS:
122 writer->writeLineFormatted("b0=%15.8e, kb=%15.8e, kcub=%15.8e", iparams.cubic.b0,
123 iparams.cubic.kb, iparams.cubic.kcub);
124 break;
125 case F_CONNBONDS: writer->ensureEmptyLine(); break;
126 case F_FENEBONDS:
127 writer->writeLineFormatted("bm=%15.8e, kb=%15.8e", iparams.fene.bm, iparams.fene.kb);
128 break;
129 case F_RESTRBONDS:
130 writer->writeLineFormatted(
131 "lowA=%15.8e, up1A=%15.8e, up2A=%15.8e, kA=%15.8e, lowB=%15.8e, up1B=%15.8e, "
132 "up2B=%15.8e, kB=%15.8e,",
133 iparams.restraint.lowA, iparams.restraint.up1A, iparams.restraint.up2A,
134 iparams.restraint.kA, iparams.restraint.lowB, iparams.restraint.up1B,
135 iparams.restraint.up2B, iparams.restraint.kB);
136 break;
137 case F_TABBONDS:
138 case F_TABBONDSNC:
139 case F_TABANGLES:
140 case F_TABDIHS:
141 writer->writeLineFormatted("tab=%d, kA=%15.8e, kB=%15.8e", iparams.tab.table,
142 iparams.tab.kA, iparams.tab.kB);
143 break;
144 case F_POLARIZATION:
145 writer->writeLineFormatted("alpha=%15.8e", iparams.polarize.alpha);
146 break;
147 case F_ANHARM_POL:
148 writer->writeLineFormatted("alpha=%15.8e drcut=%15.8e khyp=%15.8e",
149 iparams.anharm_polarize.alpha, iparams.anharm_polarize.drcut,
150 iparams.anharm_polarize.khyp);
151 break;
152 case F_THOLE_POL:
153 writer->writeLineFormatted("a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e",
154 iparams.thole.a, iparams.thole.alpha1, iparams.thole.alpha2,
155 iparams.thole.rfac);
156 break;
157 case F_WATER_POL:
158 writer->writeLineFormatted(
159 "al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f",
160 iparams.wpol.al_x, iparams.wpol.al_y, iparams.wpol.al_z, iparams.wpol.rOH,
161 iparams.wpol.rHH, iparams.wpol.rOD);
162 break;
163 case F_LJ:
164 writer->writeLineFormatted("c6=%15.8e, c12=%15.8e", iparams.lj.c6, iparams.lj.c12);
165 break;
166 case F_LJ14:
167 writer->writeLineFormatted("c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e",
168 iparams.lj14.c6A, iparams.lj14.c12A, iparams.lj14.c6B,
169 iparams.lj14.c12B);
170 break;
171 case F_LJC14_Q:
172 writer->writeLineFormatted("fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e",
173 iparams.ljc14.fqq, iparams.ljc14.qi, iparams.ljc14.qj,
174 iparams.ljc14.c6, iparams.ljc14.c12);
175 break;
176 case F_LJC_PAIRS_NB:
177 writer->writeLineFormatted("qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e", iparams.ljcnb.qi,
178 iparams.ljcnb.qj, iparams.ljcnb.c6, iparams.ljcnb.c12);
179 break;
180 case F_PDIHS:
181 case F_PIDIHS:
182 case F_ANGRES:
183 case F_ANGRESZ:
184 writer->writeLineFormatted("phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d",
185 iparams.pdihs.phiA, iparams.pdihs.cpA, iparams.pdihs.phiB,
186 iparams.pdihs.cpB, iparams.pdihs.mult);
187 break;
188 case F_DISRES:
189 writer->writeLineFormatted(
190 "label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)",
191 iparams.disres.label, iparams.disres.type, iparams.disres.low,
192 iparams.disres.up1, iparams.disres.up2, iparams.disres.kfac);
193 break;
194 case F_ORIRES:
195 writer->writeLineFormatted(
196 "ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)",
197 iparams.orires.ex, iparams.orires.label, iparams.orires.power, iparams.orires.c,
198 iparams.orires.obs, iparams.orires.kfac);
199 break;
200 case F_DIHRES:
201 writer->writeLineFormatted(
202 "phiA=%15.8e, dphiA=%15.8e, kfacA=%15.8e, phiB=%15.8e, dphiB=%15.8e, "
203 "kfacB=%15.8e",
204 iparams.dihres.phiA, iparams.dihres.dphiA, iparams.dihres.kfacA,
205 iparams.dihres.phiB, iparams.dihres.dphiB, iparams.dihres.kfacB);
206 break;
207 case F_POSRES:
208 writer->writeLineFormatted(
209 "pos0A=(%15.8e,%15.8e,%15.8e), fcA=(%15.8e,%15.8e,%15.8e), "
210 "pos0B=(%15.8e,%15.8e,%15.8e), fcB=(%15.8e,%15.8e,%15.8e)",
211 iparams.posres.pos0A[XX], iparams.posres.pos0A[YY], iparams.posres.pos0A[ZZ],
212 iparams.posres.fcA[XX], iparams.posres.fcA[YY], iparams.posres.fcA[ZZ],
213 iparams.posres.pos0B[XX], iparams.posres.pos0B[YY], iparams.posres.pos0B[ZZ],
214 iparams.posres.fcB[XX], iparams.posres.fcB[YY], iparams.posres.fcB[ZZ]);
215 break;
216 case F_FBPOSRES:
217 writer->writeLineFormatted(
218 "pos0=(%15.8e,%15.8e,%15.8e), geometry=%d, r=%15.8e, k=%15.8e",
219 iparams.fbposres.pos0[XX], iparams.fbposres.pos0[YY], iparams.fbposres.pos0[ZZ],
220 iparams.fbposres.geom, iparams.fbposres.r, iparams.fbposres.k);
221 break;
222 case F_RBDIHS:
223 for (int i = 0; i < NR_RBDIHS; i++)
224 {
225 writer->writeStringFormatted("%srbcA[%d]=%15.8e", i == 0 ? "" : ", ", i,
226 iparams.rbdihs.rbcA[i]);
227 }
228 writer->ensureLineBreak();
229 for (int i = 0; i < NR_RBDIHS; i++)
230 {
231 writer->writeStringFormatted("%srbcB[%d]=%15.8e", i == 0 ? "" : ", ", i,
232 iparams.rbdihs.rbcB[i]);
233 }
234 writer->ensureLineBreak();
235 break;
236 case F_FOURDIHS:
237 {
238 /* Use the OPLS -> Ryckaert-Bellemans formula backwards to get
239 * the OPLS potential constants back.
240 */
241 const real* rbcA = iparams.rbdihs.rbcA;
242 const real* rbcB = iparams.rbdihs.rbcB;
243 real VA[4], VB[4];
244
245 VA[3] = -0.25 * rbcA[4];
246 VA[2] = -0.5 * rbcA[3];
247 VA[1] = 4.0 * VA[3] - rbcA[2];
248 VA[0] = 3.0 * VA[2] - 2.0 * rbcA[1];
249
250 VB[3] = -0.25 * rbcB[4];
251 VB[2] = -0.5 * rbcB[3];
252 VB[1] = 4.0 * VB[3] - rbcB[2];
253 VB[0] = 3.0 * VB[2] - 2.0 * rbcB[1];
254
255 for (int i = 0; i < NR_FOURDIHS; i++)
256 {
257 writer->writeStringFormatted("%sFourA[%d]=%15.8e", i == 0 ? "" : ", ", i, VA[i]);
258 }
259 writer->ensureLineBreak();
260 for (int i = 0; i < NR_FOURDIHS; i++)
261 {
262 writer->writeStringFormatted("%sFourB[%d]=%15.8e", i == 0 ? "" : ", ", i, VB[i]);
263 }
264 writer->ensureLineBreak();
265 break;
266 }
267
268 case F_CONSTR:
269 case F_CONSTRNC:
270 writer->writeLineFormatted("dA=%15.8e, dB=%15.8e", iparams.constr.dA, iparams.constr.dB);
271 break;
272 case F_SETTLE:
273 writer->writeLineFormatted("doh=%15.8e, dhh=%15.8e", iparams.settle.doh, iparams.settle.dhh);
274 break;
275 case F_VSITE2: writer->writeLineFormatted("a=%15.8e", iparams.vsite.a); break;
276 case F_VSITE3:
277 case F_VSITE3FD:
278 case F_VSITE3FAD:
279 writer->writeLineFormatted("a=%15.8e, b=%15.8e", iparams.vsite.a, iparams.vsite.b);
280 break;
281 case F_VSITE3OUT:
282 case F_VSITE4FD:
283 case F_VSITE4FDN:
284 writer->writeLineFormatted("a=%15.8e, b=%15.8e, c=%15.8e", iparams.vsite.a,
285 iparams.vsite.b, iparams.vsite.c);
286 break;
287 case F_VSITEN:
288 writer->writeLineFormatted("n=%2d, a=%15.8e", iparams.vsiten.n, iparams.vsiten.a);
289 break;
290 case F_GB12_NOLONGERUSED:
291 case F_GB13_NOLONGERUSED:
292 case F_GB14_NOLONGERUSED:
293 // These could only be generated by grompp, not written in
294 // a .top file. Now that implicit solvent is not
295 // supported, they can't be generated, and the values are
296 // ignored if read from an old .tpr file. So there is
297 // nothing to print.
298 break;
299 case F_CMAP:
300 writer->writeLineFormatted("cmapA=%1d, cmapB=%1d", iparams.cmap.cmapA, iparams.cmap.cmapB);
301 break;
302 case F_RESTRANGLES: printHarmonicInteraction(writer, iparams, "ktheta", "costheta0"); break;
303 case F_RESTRDIHS:
304 writer->writeLineFormatted("phiA=%15.8e, cpA=%15.8e", iparams.pdihs.phiA, iparams.pdihs.cpA);
305 break;
306 case F_CBTDIHS:
307 writer->writeLineFormatted("kphi=%15.8e", iparams.cbtdihs.cbtcA[0]);
308 for (int i = 1; i < NR_CBTDIHS; i++)
309 {
310 writer->writeStringFormatted(", cbtcA[%d]=%15.8e", i - 1, iparams.cbtdihs.cbtcA[i]);
311 }
312 writer->ensureLineBreak();
313 break;
314 default:
315 gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d", ftype,
316 interaction_function[ftype].name, __FILE__, __LINE__);
317 }
318 }
319
320 template<typename T>
321 static void printIlist(FILE* fp,
322 int indent,
323 const char* title,
324 const t_functype* functype,
325 const T& ilist,
326 gmx_bool bShowNumbers,
327 gmx_bool bShowParameters,
328 const t_iparams* iparams)
329 {
330 int i, j, k, type, ftype;
331
332 indent = pr_title(fp, indent, title);
333 pr_indent(fp, indent);
334 fprintf(fp, "nr: %d\n", ilist.size());
335 if (!ilist.empty())
336 {
337 pr_indent(fp, indent);
338 fprintf(fp, "iatoms:\n");
339 for (i = j = 0; i < ilist.size();)
340 {
341 pr_indent(fp, indent + INDENT);
342 type = ilist.iatoms[i];
343 ftype = functype[type];
344 if (bShowNumbers)
345 {
346 fprintf(fp, "%d type=%d ", j, type);
347 }
348 j++;
349 printf("(%s)", interaction_function[ftype].name);
350 for (k = 0; k < interaction_function[ftype].nratoms; k++)
351 {
352 fprintf(fp, " %3d", ilist.iatoms[i + 1 + k]);
353 }
354 if (bShowParameters)
355 {
356 fprintf(fp, " ");
357 pr_iparams(fp, ftype, iparams[type]);
358 }
359 fprintf(fp, "\n");
360 i += 1 + interaction_function[ftype].nratoms;
361 }
362 }
363 }
364
365 void pr_ilist(FILE* fp,
366 int indent,
367 const char* title,
368 const t_functype* functype,
369 const InteractionList& ilist,
370 gmx_bool bShowNumbers,
371 gmx_bool bShowParameters,
372 const t_iparams* iparams)
373 {
374 printIlist(fp, indent, title, functype, ilist, bShowNumbers, bShowParameters, iparams);
375 }
376
377 void pr_idef(FILE* fp, int indent, const char* title, const t_idef* idef, gmx_bool bShowNumbers, gmx_bool bShowParameters)
378 {
379 int i, j;
380
381 if (available(fp, idef, indent, title))
382 {
383 indent = pr_title(fp, indent, title);
384 pr_indent(fp, indent);
385 fprintf(fp, "atnr=%d\n", idef->atnr);
386 pr_indent(fp, indent);
387 fprintf(fp, "ntypes=%d\n", idef->ntypes);
388 for (i = 0; i < idef->ntypes; i++)
389 {
390 pr_indent(fp, indent + INDENT);
391 fprintf(fp, "functype[%d]=%s, ", bShowNumbers ? i : -1,
392 interaction_function[idef->functype[i]].name);
393 pr_iparams(fp, idef->functype[i], idef->iparams[i]);
394 }
395 pr_real(fp, indent, "fudgeQQ", idef->fudgeQQ);
396
397 for (j = 0; (j < F_NRE); j++)
398 {
399 printIlist(fp, indent, interaction_function[j].longname, idef->functype, idef->il[j],
400 bShowNumbers, bShowParameters, idef->iparams);
401 }
402 }
403 }
404
405 void init_idef(t_idef* idef)
406 {
407 idef->ntypes = 0;
408 idef->atnr = 0;
409 idef->functype = nullptr;
410 idef->iparams = nullptr;
411 idef->fudgeQQ = 0.0;
412 idef->iparams_posres = nullptr;
413 idef->iparams_fbposres = nullptr;
414 for (int f = 0; f < F_NRE; ++f)
415 {
416 idef->il[f].iatoms = nullptr;
417 idef->il[f].nalloc = 0;
418 idef->il[f].nr = 0;
419 }
420 }
421
422 InteractionDefinitions::InteractionDefinitions(const gmx_ffparams_t& ffparams) :
423 iparams(ffparams.iparams),
424 functype(ffparams.functype),
425 cmap_grid(ffparams.cmap_grid)
426 {
427 }
428
429 void InteractionDefinitions::clear()
430 {
431 /* Clear the counts */
432 for (auto& ilist : il)
433 {
434 ilist.clear();
435 }
436 iparams_posres.clear();
437 iparams_fbposres.clear();
438 }
439
440 void done_idef(t_idef* idef)
441 {
442 sfree(idef->functype);
443 sfree(idef->iparams);
444 sfree(idef->iparams_posres);
445 sfree(idef->iparams_fbposres);
446 for (int f = 0; f < F_NRE; ++f)
447 {
448 sfree(idef->il[f].iatoms);
449 }
450
451 init_idef(idef);
452 }
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