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44 #include "gromacs/legacyheaders/typedefs.h"
45 #include "gromacs/legacyheaders/macros.h"
46 #include "gromacs/utility/smalloc.h"
47 #include "gromacs/math/units.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/legacyheaders/force.h"
50 #include "gromacs/fileio/confio.h"
51 #include "gromacs/legacyheaders/names.h"
52 #include "gromacs/legacyheaders/network.h"
53 #include "gromacs/legacyheaders/ns.h"
54 #include "gromacs/legacyheaders/nrnb.h"
55 #include "gromacs/legacyheaders/bondf.h"
56 #include "gromacs/legacyheaders/txtdump.h"
57 #include "gromacs/legacyheaders/qmmm.h"
58 #include "gromacs/utility/fatalerror.h"
60 /* ORCA interface routines */
62 void init_orca(t_QMrec *qm)
67 /* ORCA settings on the system */
68 buf = getenv("GMX_QM_ORCA_BASENAME");
71 snew(qm->orca_basename, 200);
72 sscanf(buf, "%s", qm->orca_basename);
76 gmx_fatal(FARGS, "$GMX_QM_ORCA_BASENAME is not set\n");
79 /* ORCA directory on the system */
81 buf = getenv("GMX_ORCA_PATH");
85 snew(qm->orca_dir, 200);
86 sscanf(buf, "%s", qm->orca_dir);
90 gmx_fatal(FARGS, "$GMX_ORCA_PATH not set, check manual\n");
93 fprintf(stderr, "Setting ORCA path to: %s...\n", qm->orca_dir);
94 fprintf(stderr, "ORCA initialised...\n\n");
95 /* since we append the output to the BASENAME.out file,
96 we should delete an existent old out-file here. */
97 sprintf(buf, "%s.out", qm->orca_basename);
102 void write_orca_input(t_forcerec *fr, t_QMrec *qm, t_MMrec *mm)
106 FILE *out, *pcFile, *addInputFile, *LJCoeff;
107 char *buf, *orcaInput, *addInputFilename, *LJCoeffFilename, *pcFilename, *exclInName, *exclOutName;
111 /* write the first part of the input-file */
112 snew(orcaInput, 200);
113 sprintf(orcaInput, "%s.inp", qm->orca_basename);
114 out = fopen(orcaInput, "w");
116 snew(addInputFilename, 200);
117 sprintf(addInputFilename, "%s.ORCAINFO", qm->orca_basename);
118 addInputFile = fopen(addInputFilename, "r");
120 fprintf(out, "#input-file generated by GROMACS\n");
124 fprintf(out, "!QMMMOpt TightSCF\n");
125 fprintf(out, "%s\n", "%geom TS_Search EF end");
129 fprintf(out, "!QMMMOpt TightSCF\n");
133 fprintf(out, "!EnGrad TightSCF\n");
136 /* here we include the insertion of the additional orca-input */
138 if (addInputFile != NULL)
140 while (!feof(addInputFile))
142 if (fgets(buf, 200, addInputFile) != NULL)
150 gmx_fatal(FARGS, "No information on the calculation given in %s\n", addInputFilename);
153 fclose(addInputFile);
155 if (qm->bTS || qm->bOPT)
157 /* freeze the frontier QM atoms and Link atoms. This is
158 * important only if a full QM subsystem optimization is done
159 * with a frozen MM environmeent. For dynamics, or gromacs's own
160 * optimization routines this is not important.
162 /* ORCA reads the exclusions from LJCoeffFilename.Excl,
163 * so we have to rename the file
166 for (i = 0; i < qm->nrQMatoms; i++)
168 if (qm->frontatoms[i])
172 fprintf(out, "%s\n", "%geom");
173 fprintf(out, " Constraints \n");
176 fprintf(out, " {C %d C}\n", i); /* counting from 0 */
181 fprintf(out, " end\n end\n");
183 /* make a file with information on the C6 and C12 coefficients */
184 if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
186 snew(exclInName, 200);
187 snew(exclOutName, 200);
188 sprintf(exclInName, "QMMMexcl.dat");
189 sprintf(exclOutName, "%s.LJ.Excl", qm->orca_basename);
190 rename(exclInName, exclOutName);
191 snew(LJCoeffFilename, 200);
192 sprintf(LJCoeffFilename, "%s.LJ", qm->orca_basename);
193 fprintf(out, "%s%s%s\n", "%LJCOEFFICIENTS \"", LJCoeffFilename, "\"");
194 /* make a file with information on the C6 and C12 coefficients */
195 LJCoeff = fopen(LJCoeffFilename, "w");
196 fprintf(LJCoeff, "%d\n", qm->nrQMatoms);
197 for (i = 0; i < qm->nrQMatoms; i++)
200 fprintf(LJCoeff, "%10.7lf %10.7lf\n", qm->c6[i], qm->c12[i]);
202 fprintf(LJCoeff, "%10.7f %10.7f\n", qm->c6[i], qm->c12[i]);
205 fprintf(LJCoeff, "%d\n", mm->nrMMatoms);
206 for (i = 0; i < mm->nrMMatoms; i++)
209 fprintf(LJCoeff, "%10.7lf %10.7lf\n", mm->c6[i], mm->c12[i]);
211 fprintf(LJCoeff, "%10.7f %10.7f\n", mm->c6[i], mm->c12[i]);
218 /* write charge and multiplicity */
219 fprintf(out, "*xyz %2d%2d\n", qm->QMcharge, qm->multiplicity);
221 /* write the QM coordinates */
222 for (i = 0; i < qm->nrQMatoms; i++)
225 if (qm->atomicnumberQM[i] == 0)
231 atomNr = qm->atomicnumberQM[i];
234 fprintf(out, "%3d %10.7lf %10.7lf %10.7lf\n",
240 fprintf(out, "%3d %10.7f %10.7f %10.7f\n",
249 /* write the MM point charge data */
250 if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
252 /* name of the point charge file */
253 snew(pcFilename, 200);
254 sprintf(pcFilename, "%s.pc", qm->orca_basename);
255 fprintf(out, "%s%s%s\n", "%pointcharges \"", pcFilename, "\"");
256 pcFile = fopen(pcFilename, "w");
257 fprintf(pcFile, "%d\n", mm->nrMMatoms);
258 for (i = 0; i < mm->nrMMatoms; i++)
261 fprintf(pcFile, "%8.4lf %10.7lf %10.7lf %10.7lf\n",
267 fprintf(pcFile, "%8.4f %10.7f %10.7f %10.7f\n",
274 fprintf(pcFile, "\n");
280 } /* write_orca_input */
282 real read_orca_output(rvec QMgrad[], rvec MMgrad[], t_forcerec *fr,
283 t_QMrec *qm, t_MMrec *mm)
288 buf[300], tmp[300], orca_xyzFilename[300], orca_pcgradFilename[300], orca_engradFilename[300];
292 *xyz, *pcgrad, *engrad;
297 /* in case of an optimization, the coordinates are printed in the
298 * xyz file, the energy and gradients for the QM part are stored in the engrad file
299 * and the gradients for the point charges are stored in the pc file.
302 /* we need the new xyz coordinates of the QM atoms only for separate QM-optimization
305 if (qm->bTS || qm->bOPT)
307 sprintf(orca_xyzFilename, "%s.xyz", qm->orca_basename);
308 xyz = fopen(orca_xyzFilename, "r");
309 if (fgets(buf, 300, xyz) == NULL)
311 gmx_fatal(FARGS, "Unexpected end of ORCA output");
313 if (fgets(buf, 300, xyz) == NULL)
315 gmx_fatal(FARGS, "Unexpected end of ORCA output");
317 for (i = 0; i < qm->nrQMatoms; i++)
319 if (fgets(buf, 300, xyz) == NULL)
321 gmx_fatal(FARGS, "Unexpected end of ORCA output");
324 sscanf(buf, "%s%lf%lf%lf\n",
330 sscanf(buf, "%d%f%f%f\n",
336 for (j = 0; j < DIM; j++)
338 qm->xQM[i][j] *= 0.1;
343 sprintf(orca_engradFilename, "%s.engrad", qm->orca_basename);
344 engrad = fopen(orca_engradFilename, "r");
345 /* we read the energy and the gradient for the qm-atoms from the engrad file
347 /* we can skip the first seven lines
349 for (j = 0; j < 7; j++)
351 if (fgets(buf, 300, engrad) == NULL)
353 gmx_fatal(FARGS, "Unexpected end of ORCA output");
356 /* now comes the energy
358 if (fgets(buf, 300, engrad) == NULL)
360 gmx_fatal(FARGS, "Unexpected end of ORCA output");
363 sscanf(buf, "%lf\n", &QMener);
365 sscanf(buf, "%f\n", &QMener);
367 /* we can skip the next three lines
369 for (j = 0; j < 3; j++)
371 if (fgets(buf, 300, engrad) == NULL)
373 gmx_fatal(FARGS, "Unexpected end of ORCA output");
376 /* next lines contain the gradients of the QM atoms
377 * now comes the gradient, one value per line:
378 * (atom1 x \n atom1 y \n atom1 z \n atom2 x ...
381 for (i = 0; i < 3*qm->nrQMatoms; i++)
384 if (fgets(buf, 300, engrad) == NULL)
386 gmx_fatal(FARGS, "Unexpected end of ORCA output");
391 sscanf(buf, "%lf\n", &QMgrad[k][XX]);
395 sscanf(buf, "%lf\n", &QMgrad[k][YY]);
399 sscanf(buf, "%lf\n", &QMgrad[k][ZZ]);
404 sscanf(buf, "%f\n", &QMgrad[k][XX]);
408 sscanf(buf, "%f\n", &QMgrad[k][YY]);
412 sscanf(buf, "%f\n", &QMgrad[k][ZZ]);
417 /* write the MM point charge data
419 if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
421 sprintf(orca_pcgradFilename, "%s.pcgrad", qm->orca_basename);
422 pcgrad = fopen(orca_pcgradFilename, "r");
424 /* we read the gradient for the mm-atoms from the pcgrad file
426 /* we can skip the first line
428 if (fgets(buf, 300, pcgrad) == NULL)
430 gmx_fatal(FARGS, "Unexpected end of ORCA output");
432 for (i = 0; i < mm->nrMMatoms; i++)
434 if (fgets(buf, 300, pcgrad) == NULL)
436 gmx_fatal(FARGS, "Unexpected end of ORCA output");
439 sscanf(buf, "%lf%lf%lf\n",
444 sscanf(buf, "%f%f%f\n",
455 void do_orca(char *orca_dir, char *basename)
458 /* make the call to the orca binary through system()
459 * The location of the binary is set through the
464 sprintf(buf, "%s/%s %s.inp >> %s.out",
469 fprintf(stderr, "Calling '%s'\n", buf);
470 if (system(buf) != 0)
472 gmx_fatal(FARGS, "Call to '%s' failed\n", buf);
476 real call_orca(t_forcerec *fr,
477 t_QMrec *qm, t_MMrec *mm, rvec f[], rvec fshift[])
479 /* normal orca jobs */
492 sprintf(exe, "%s", "orca");
493 snew(QMgrad, qm->nrQMatoms);
494 snew(MMgrad, mm->nrMMatoms);
496 write_orca_input(fr, qm, mm);
497 do_orca(qm->orca_dir, qm->orca_basename);
498 QMener = read_orca_output(QMgrad, MMgrad, fr, qm, mm);
499 /* put the QMMM forces in the force array and to the fshift
501 for (i = 0; i < qm->nrQMatoms; i++)
503 for (j = 0; j < DIM; j++)
505 f[i][j] = HARTREE_BOHR2MD*QMgrad[i][j];
506 fshift[i][j] = HARTREE_BOHR2MD*QMgrad[i][j];
509 for (i = 0; i < mm->nrMMatoms; i++)
511 for (j = 0; j < DIM; j++)
513 f[i+qm->nrQMatoms][j] = HARTREE_BOHR2MD*MMgrad[i][j];
514 fshift[i+qm->nrQMatoms][j] = HARTREE_BOHR2MD*MMgrad[i][j];
517 QMener = QMener*HARTREE2KJ*AVOGADRO;
523 /* end of orca sub routines */