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44 #include "gromacs/fileio/confio.h"
45 #include "gromacs/legacyheaders/force.h"
46 #include "gromacs/legacyheaders/macros.h"
47 #include "gromacs/legacyheaders/names.h"
48 #include "gromacs/legacyheaders/network.h"
49 #include "gromacs/legacyheaders/nrnb.h"
50 #include "gromacs/legacyheaders/ns.h"
51 #include "gromacs/legacyheaders/qmmm.h"
52 #include "gromacs/legacyheaders/txtdump.h"
53 #include "gromacs/legacyheaders/typedefs.h"
54 #include "gromacs/math/units.h"
55 #include "gromacs/math/vec.h"
56 #include "gromacs/utility/fatalerror.h"
57 #include "gromacs/utility/smalloc.h"
59 /* ORCA interface routines */
61 void init_orca(t_QMrec *qm)
66 /* ORCA settings on the system */
67 buf = getenv("GMX_QM_ORCA_BASENAME");
70 snew(qm->orca_basename, 200);
71 sscanf(buf, "%s", qm->orca_basename);
75 gmx_fatal(FARGS, "$GMX_QM_ORCA_BASENAME is not set\n");
78 /* ORCA directory on the system */
80 buf = getenv("GMX_ORCA_PATH");
84 snew(qm->orca_dir, 200);
85 sscanf(buf, "%s", qm->orca_dir);
89 gmx_fatal(FARGS, "$GMX_ORCA_PATH not set, check manual\n");
92 fprintf(stderr, "Setting ORCA path to: %s...\n", qm->orca_dir);
93 fprintf(stderr, "ORCA initialised...\n\n");
94 /* since we append the output to the BASENAME.out file,
95 we should delete an existent old out-file here. */
96 sprintf(buf, "%s.out", qm->orca_basename);
101 void write_orca_input(t_forcerec *fr, t_QMrec *qm, t_MMrec *mm)
105 FILE *out, *pcFile, *addInputFile, *LJCoeff;
106 char *buf, *orcaInput, *addInputFilename, *LJCoeffFilename, *pcFilename, *exclInName, *exclOutName;
110 /* write the first part of the input-file */
111 snew(orcaInput, 200);
112 sprintf(orcaInput, "%s.inp", qm->orca_basename);
113 out = fopen(orcaInput, "w");
115 snew(addInputFilename, 200);
116 sprintf(addInputFilename, "%s.ORCAINFO", qm->orca_basename);
117 addInputFile = fopen(addInputFilename, "r");
119 fprintf(out, "#input-file generated by GROMACS\n");
123 fprintf(out, "!QMMMOpt TightSCF\n");
124 fprintf(out, "%s\n", "%geom TS_Search EF end");
128 fprintf(out, "!QMMMOpt TightSCF\n");
132 fprintf(out, "!EnGrad TightSCF\n");
135 /* here we include the insertion of the additional orca-input */
137 if (addInputFile != NULL)
139 while (!feof(addInputFile))
141 if (fgets(buf, 200, addInputFile) != NULL)
149 gmx_fatal(FARGS, "No information on the calculation given in %s\n", addInputFilename);
152 fclose(addInputFile);
154 if (qm->bTS || qm->bOPT)
156 /* freeze the frontier QM atoms and Link atoms. This is
157 * important only if a full QM subsystem optimization is done
158 * with a frozen MM environmeent. For dynamics, or gromacs's own
159 * optimization routines this is not important.
161 /* ORCA reads the exclusions from LJCoeffFilename.Excl,
162 * so we have to rename the file
165 for (i = 0; i < qm->nrQMatoms; i++)
167 if (qm->frontatoms[i])
171 fprintf(out, "%s\n", "%geom");
172 fprintf(out, " Constraints \n");
175 fprintf(out, " {C %d C}\n", i); /* counting from 0 */
180 fprintf(out, " end\n end\n");
182 /* make a file with information on the C6 and C12 coefficients */
183 if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
185 snew(exclInName, 200);
186 snew(exclOutName, 200);
187 sprintf(exclInName, "QMMMexcl.dat");
188 sprintf(exclOutName, "%s.LJ.Excl", qm->orca_basename);
189 rename(exclInName, exclOutName);
190 snew(LJCoeffFilename, 200);
191 sprintf(LJCoeffFilename, "%s.LJ", qm->orca_basename);
192 fprintf(out, "%s%s%s\n", "%LJCOEFFICIENTS \"", LJCoeffFilename, "\"");
193 /* make a file with information on the C6 and C12 coefficients */
194 LJCoeff = fopen(LJCoeffFilename, "w");
195 fprintf(LJCoeff, "%d\n", qm->nrQMatoms);
196 for (i = 0; i < qm->nrQMatoms; i++)
199 fprintf(LJCoeff, "%10.7lf %10.7lf\n", qm->c6[i], qm->c12[i]);
201 fprintf(LJCoeff, "%10.7f %10.7f\n", qm->c6[i], qm->c12[i]);
204 fprintf(LJCoeff, "%d\n", mm->nrMMatoms);
205 for (i = 0; i < mm->nrMMatoms; i++)
208 fprintf(LJCoeff, "%10.7lf %10.7lf\n", mm->c6[i], mm->c12[i]);
210 fprintf(LJCoeff, "%10.7f %10.7f\n", mm->c6[i], mm->c12[i]);
217 /* write charge and multiplicity */
218 fprintf(out, "*xyz %2d%2d\n", qm->QMcharge, qm->multiplicity);
220 /* write the QM coordinates */
221 for (i = 0; i < qm->nrQMatoms; i++)
224 if (qm->atomicnumberQM[i] == 0)
230 atomNr = qm->atomicnumberQM[i];
233 fprintf(out, "%3d %10.7lf %10.7lf %10.7lf\n",
239 fprintf(out, "%3d %10.7f %10.7f %10.7f\n",
248 /* write the MM point charge data */
249 if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
251 /* name of the point charge file */
252 snew(pcFilename, 200);
253 sprintf(pcFilename, "%s.pc", qm->orca_basename);
254 fprintf(out, "%s%s%s\n", "%pointcharges \"", pcFilename, "\"");
255 pcFile = fopen(pcFilename, "w");
256 fprintf(pcFile, "%d\n", mm->nrMMatoms);
257 for (i = 0; i < mm->nrMMatoms; i++)
260 fprintf(pcFile, "%8.4lf %10.7lf %10.7lf %10.7lf\n",
266 fprintf(pcFile, "%8.4f %10.7f %10.7f %10.7f\n",
273 fprintf(pcFile, "\n");
279 } /* write_orca_input */
281 real read_orca_output(rvec QMgrad[], rvec MMgrad[], t_forcerec *fr,
282 t_QMrec *qm, t_MMrec *mm)
287 buf[300], tmp[300], orca_xyzFilename[300], orca_pcgradFilename[300], orca_engradFilename[300];
291 *xyz, *pcgrad, *engrad;
296 /* in case of an optimization, the coordinates are printed in the
297 * xyz file, the energy and gradients for the QM part are stored in the engrad file
298 * and the gradients for the point charges are stored in the pc file.
301 /* we need the new xyz coordinates of the QM atoms only for separate QM-optimization
304 if (qm->bTS || qm->bOPT)
306 sprintf(orca_xyzFilename, "%s.xyz", qm->orca_basename);
307 xyz = fopen(orca_xyzFilename, "r");
308 if (fgets(buf, 300, xyz) == NULL)
310 gmx_fatal(FARGS, "Unexpected end of ORCA output");
312 if (fgets(buf, 300, xyz) == NULL)
314 gmx_fatal(FARGS, "Unexpected end of ORCA output");
316 for (i = 0; i < qm->nrQMatoms; i++)
318 if (fgets(buf, 300, xyz) == NULL)
320 gmx_fatal(FARGS, "Unexpected end of ORCA output");
323 sscanf(buf, "%s%lf%lf%lf\n",
329 sscanf(buf, "%d%f%f%f\n",
335 for (j = 0; j < DIM; j++)
337 qm->xQM[i][j] *= 0.1;
342 sprintf(orca_engradFilename, "%s.engrad", qm->orca_basename);
343 engrad = fopen(orca_engradFilename, "r");
344 /* we read the energy and the gradient for the qm-atoms from the engrad file
346 /* we can skip the first seven lines
348 for (j = 0; j < 7; j++)
350 if (fgets(buf, 300, engrad) == NULL)
352 gmx_fatal(FARGS, "Unexpected end of ORCA output");
355 /* now comes the energy
357 if (fgets(buf, 300, engrad) == NULL)
359 gmx_fatal(FARGS, "Unexpected end of ORCA output");
362 sscanf(buf, "%lf\n", &QMener);
364 sscanf(buf, "%f\n", &QMener);
366 /* we can skip the next three lines
368 for (j = 0; j < 3; j++)
370 if (fgets(buf, 300, engrad) == NULL)
372 gmx_fatal(FARGS, "Unexpected end of ORCA output");
375 /* next lines contain the gradients of the QM atoms
376 * now comes the gradient, one value per line:
377 * (atom1 x \n atom1 y \n atom1 z \n atom2 x ...
380 for (i = 0; i < 3*qm->nrQMatoms; i++)
383 if (fgets(buf, 300, engrad) == NULL)
385 gmx_fatal(FARGS, "Unexpected end of ORCA output");
390 sscanf(buf, "%lf\n", &QMgrad[k][XX]);
394 sscanf(buf, "%lf\n", &QMgrad[k][YY]);
398 sscanf(buf, "%lf\n", &QMgrad[k][ZZ]);
403 sscanf(buf, "%f\n", &QMgrad[k][XX]);
407 sscanf(buf, "%f\n", &QMgrad[k][YY]);
411 sscanf(buf, "%f\n", &QMgrad[k][ZZ]);
416 /* write the MM point charge data
418 if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
420 sprintf(orca_pcgradFilename, "%s.pcgrad", qm->orca_basename);
421 pcgrad = fopen(orca_pcgradFilename, "r");
423 /* we read the gradient for the mm-atoms from the pcgrad file
425 /* we can skip the first line
427 if (fgets(buf, 300, pcgrad) == NULL)
429 gmx_fatal(FARGS, "Unexpected end of ORCA output");
431 for (i = 0; i < mm->nrMMatoms; i++)
433 if (fgets(buf, 300, pcgrad) == NULL)
435 gmx_fatal(FARGS, "Unexpected end of ORCA output");
438 sscanf(buf, "%lf%lf%lf\n",
443 sscanf(buf, "%f%f%f\n",
454 void do_orca(char *orca_dir, char *basename)
457 /* make the call to the orca binary through system()
458 * The location of the binary is set through the
463 sprintf(buf, "%s/%s %s.inp >> %s.out",
468 fprintf(stderr, "Calling '%s'\n", buf);
469 if (system(buf) != 0)
471 gmx_fatal(FARGS, "Call to '%s' failed\n", buf);
475 real call_orca(t_forcerec *fr,
476 t_QMrec *qm, t_MMrec *mm, rvec f[], rvec fshift[])
478 /* normal orca jobs */
491 sprintf(exe, "%s", "orca");
492 snew(QMgrad, qm->nrQMatoms);
493 snew(MMgrad, mm->nrMMatoms);
495 write_orca_input(fr, qm, mm);
496 do_orca(qm->orca_dir, qm->orca_basename);
497 QMener = read_orca_output(QMgrad, MMgrad, fr, qm, mm);
498 /* put the QMMM forces in the force array and to the fshift
500 for (i = 0; i < qm->nrQMatoms; i++)
502 for (j = 0; j < DIM; j++)
504 f[i][j] = HARTREE_BOHR2MD*QMgrad[i][j];
505 fshift[i][j] = HARTREE_BOHR2MD*QMgrad[i][j];
508 for (i = 0; i < mm->nrMMatoms; i++)
510 for (j = 0; j < DIM; j++)
512 f[i+qm->nrQMatoms][j] = HARTREE_BOHR2MD*MMgrad[i][j];
513 fshift[i+qm->nrQMatoms][j] = HARTREE_BOHR2MD*MMgrad[i][j];
516 QMener = QMener*HARTREE2KJ*AVOGADRO;
522 /* end of orca sub routines */