src/gromacs/mdlib/qm_orca.cpp

   1 /*
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  37 #include "gmxpre.h"
  38
  39 #include <math.h>
  40 #include <stdio.h>
  41 #include <stdlib.h>
  42 #include <string.h>
  43
  44 #include "gromacs/fileio/confio.h"
  45 #include "gromacs/gmxlib/network.h"
  46 #include "gromacs/gmxlib/nrnb.h"
  47 #include "gromacs/math/units.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/mdlib/force.h"
  50 #include "gromacs/mdlib/ns.h"
  51 #include "gromacs/mdlib/qmmm.h"
  52 #include "gromacs/mdtypes/md_enums.h"
  53 #include "gromacs/utility/fatalerror.h"
  54 #include "gromacs/utility/smalloc.h"
  55
  56 /* ORCA interface routines */
  57
  58 void init_orca(t_QMrec *qm)
  59 {
  60     char *buf;
  61     snew(buf, 200);
  62
  63     /* ORCA settings on the system */
  64     buf = getenv("GMX_QM_ORCA_BASENAME");
  65     if (buf)
  66     {
  67         snew(qm->orca_basename, 200);
  68         sscanf(buf, "%s", qm->orca_basename);
  69     }
  70     else
  71     {
  72         gmx_fatal(FARGS, "$GMX_QM_ORCA_BASENAME is not set\n");
  73     }
  74
  75     /* ORCA directory on the system */
  76     snew(buf, 200);
  77     buf = getenv("GMX_ORCA_PATH");
  78
  79     if (buf)
  80     {
  81         snew(qm->orca_dir, 200);
  82         sscanf(buf, "%s", qm->orca_dir);
  83     }
  84     else
  85     {
  86         gmx_fatal(FARGS, "$GMX_ORCA_PATH not set, check manual\n");
  87     }
  88
  89     fprintf(stderr, "Setting ORCA path to: %s...\n", qm->orca_dir);
  90     fprintf(stderr, "ORCA initialised...\n\n");
  91     /* since we append the output to the BASENAME.out file,
  92        we should delete an existent old out-file here. */
  93     sprintf(buf, "%s.out", qm->orca_basename);
  94     remove(buf);
  95 }
  96
  97
  98 void write_orca_input(t_forcerec *fr, t_QMrec *qm, t_MMrec *mm)
  99 {
 100     int        i;
 101     t_QMMMrec *QMMMrec;
 102     FILE      *out, *pcFile, *addInputFile, *LJCoeff;
 103     char      *buf, *orcaInput, *addInputFilename, *LJCoeffFilename, *pcFilename, *exclInName, *exclOutName;
 104
 105     QMMMrec = fr->qr;
 106
 107     /* write the first part of the input-file */
 108     snew(orcaInput, 200);
 109     sprintf(orcaInput, "%s.inp", qm->orca_basename);
 110     out = fopen(orcaInput, "w");
 111
 112     snew(addInputFilename, 200);
 113     sprintf(addInputFilename, "%s.ORCAINFO", qm->orca_basename);
 114     addInputFile = fopen(addInputFilename, "r");
 115
 116     fprintf(out, "#input-file generated by GROMACS\n");
 117
 118     if (qm->bTS)
 119     {
 120         fprintf(out, "!QMMMOpt TightSCF\n");
 121         fprintf(out, "%s\n", "%geom TS_Search EF end");
 122     }
 123     else if (qm->bOPT)
 124     {
 125         fprintf(out, "!QMMMOpt TightSCF\n");
 126     }
 127     else
 128     {
 129         fprintf(out, "!EnGrad TightSCF\n");
 130     }
 131
 132     /* here we include the insertion of the additional orca-input */
 133     snew(buf, 200);
 134     if (addInputFile != NULL)
 135     {
 136         while (!feof(addInputFile))
 137         {
 138             if (fgets(buf, 200, addInputFile) != NULL)
 139             {
 140                 fputs(buf, out);
 141             }
 142         }
 143     }
 144     else
 145     {
 146         gmx_fatal(FARGS, "No information on the calculation given in %s\n", addInputFilename);
 147     }
 148
 149     fclose(addInputFile);
 150
 151     if (qm->bTS || qm->bOPT)
 152     {
 153         /* freeze the frontier QM atoms and Link atoms. This is
 154          * important only if a full QM subsystem optimization is done
 155          * with a frozen MM environmeent. For dynamics, or gromacs's own
 156          * optimization routines this is not important.
 157          */
 158         /* ORCA reads the exclusions from LJCoeffFilename.Excl,
 159          * so we have to rename the file
 160          */
 161         int didStart = 0;
 162         for (i = 0; i < qm->nrQMatoms; i++)
 163         {
 164             if (qm->frontatoms[i])
 165             {
 166                 if (!didStart)
 167                 {
 168                     fprintf(out, "%s\n", "%geom");
 169                     fprintf(out, "   Constraints \n");
 170                     didStart = 1;
 171                 }
 172                 fprintf(out, "        {C %d C}\n", i); /* counting from 0 */
 173             }
 174         }
 175         if (didStart)
 176         {
 177             fprintf(out, "     end\n   end\n");
 178         }
 179         /* make a file with information on the C6 and C12 coefficients */
 180         if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
 181         {
 182             snew(exclInName, 200);
 183             snew(exclOutName, 200);
 184             sprintf(exclInName, "QMMMexcl.dat");
 185             sprintf(exclOutName, "%s.LJ.Excl", qm->orca_basename);
 186             rename(exclInName, exclOutName);
 187             snew(LJCoeffFilename, 200);
 188             sprintf(LJCoeffFilename, "%s.LJ", qm->orca_basename);
 189             fprintf(out, "%s%s%s\n", "%LJCOEFFICIENTS \"", LJCoeffFilename, "\"");
 190             /* make a file with information on the C6 and C12 coefficients */
 191             LJCoeff = fopen(LJCoeffFilename, "w");
 192             fprintf(LJCoeff, "%d\n", qm->nrQMatoms);
 193             for (i = 0; i < qm->nrQMatoms; i++)
 194             {
 195 #ifdef GMX_DOUBLE
 196                 fprintf(LJCoeff, "%10.7lf  %10.7lf\n", qm->c6[i], qm->c12[i]);
 197 #else
 198                 fprintf(LJCoeff, "%10.7f  %10.7f\n", qm->c6[i], qm->c12[i]);
 199 #endif
 200             }
 201             fprintf(LJCoeff, "%d\n", mm->nrMMatoms);
 202             for (i = 0; i < mm->nrMMatoms; i++)
 203             {
 204 #ifdef GMX_DOUBLE
 205                 fprintf(LJCoeff, "%10.7lf  %10.7lf\n", mm->c6[i], mm->c12[i]);
 206 #else
 207                 fprintf(LJCoeff, "%10.7f  %10.7f\n", mm->c6[i], mm->c12[i]);
 208 #endif
 209             }
 210             fclose(LJCoeff);
 211         }
 212     }
 213
 214     /* write charge and multiplicity */
 215     fprintf(out, "*xyz %2d%2d\n", qm->QMcharge, qm->multiplicity);
 216
 217     /* write the QM coordinates */
 218     for (i = 0; i < qm->nrQMatoms; i++)
 219     {
 220         int atomNr;
 221         if (qm->atomicnumberQM[i] == 0)
 222         {
 223             atomNr = 1;
 224         }
 225         else
 226         {
 227             atomNr = qm->atomicnumberQM[i];
 228         }
 229 #ifdef GMX_DOUBLE
 230         fprintf(out, "%3d %10.7lf  %10.7lf  %10.7lf\n",
 231                 atomNr,
 232                 qm->xQM[i][XX]/0.1,
 233                 qm->xQM[i][YY]/0.1,
 234                 qm->xQM[i][ZZ]/0.1);
 235 #else
 236         fprintf(out, "%3d %10.7f  %10.7f  %10.7f\n",
 237                 atomNr,
 238                 qm->xQM[i][XX]/0.1,
 239                 qm->xQM[i][YY]/0.1,
 240                 qm->xQM[i][ZZ]/0.1);
 241 #endif
 242     }
 243     fprintf(out, "*\n");
 244
 245     /* write the MM point charge data */
 246     if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
 247     {
 248         /* name of the point charge file */
 249         snew(pcFilename, 200);
 250         sprintf(pcFilename, "%s.pc", qm->orca_basename);
 251         fprintf(out, "%s%s%s\n", "%pointcharges \"", pcFilename, "\"");
 252         pcFile = fopen(pcFilename, "w");
 253         fprintf(pcFile, "%d\n", mm->nrMMatoms);
 254         for (i = 0; i < mm->nrMMatoms; i++)
 255         {
 256 #ifdef GMX_DOUBLE
 257             fprintf(pcFile, "%8.4lf %10.7lf  %10.7lf  %10.7lf\n",
 258                     mm->MMcharges[i],
 259                     mm->xMM[i][XX]/0.1,
 260                     mm->xMM[i][YY]/0.1,
 261                     mm->xMM[i][ZZ]/0.1);
 262 #else
 263             fprintf(pcFile, "%8.4f %10.7f  %10.7f  %10.7f\n",
 264                     mm->MMcharges[i],
 265                     mm->xMM[i][XX]/0.1,
 266                     mm->xMM[i][YY]/0.1,
 267                     mm->xMM[i][ZZ]/0.1);
 268 #endif
 269         }
 270         fprintf(pcFile, "\n");
 271         fclose(pcFile);
 272     }
 273     fprintf(out, "\n");
 274
 275     fclose(out);
 276 }  /* write_orca_input */
 277
 278 real read_orca_output(rvec QMgrad[], rvec MMgrad[], t_forcerec *fr,
 279                       t_QMrec *qm, t_MMrec *mm)
 280 {
 281     int
 282         i, j, atnum;
 283     char
 284         buf[300], orca_xyzFilename[300], orca_pcgradFilename[300], orca_engradFilename[300];
 285     real
 286         QMener;
 287     FILE
 288        *xyz, *pcgrad, *engrad;
 289     int k;
 290     t_QMMMrec
 291        *QMMMrec;
 292     QMMMrec = fr->qr;
 293     /* in case of an optimization, the coordinates are printed in the
 294      * xyz file, the energy and gradients for the QM part are stored in the engrad file
 295      * and the gradients for the point charges are stored in the pc file.
 296      */
 297
 298     /* we need the new xyz coordinates of the QM atoms only for separate QM-optimization
 299      */
 300
 301     if (qm->bTS || qm->bOPT)
 302     {
 303         sprintf(orca_xyzFilename, "%s.xyz", qm->orca_basename);
 304         xyz = fopen(orca_xyzFilename, "r");
 305         if (fgets(buf, 300, xyz) == NULL)
 306         {
 307             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 308         }
 309         if (fgets(buf, 300, xyz) == NULL)
 310         {
 311             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 312         }
 313         for (i = 0; i < qm->nrQMatoms; i++)
 314         {
 315             if (fgets(buf, 300, xyz) == NULL)
 316             {
 317                 gmx_fatal(FARGS, "Unexpected end of ORCA output");
 318             }
 319 #ifdef GMX_DOUBLE
 320             sscanf(buf, "%d%lf%lf%lf\n",
 321                    &atnum,
 322                    &qm->xQM[i][XX],
 323                    &qm->xQM[i][YY],
 324                    &qm->xQM[i][ZZ]);
 325 #else
 326             sscanf(buf, "%d%f%f%f\n",
 327                    &atnum,
 328                    &qm->xQM[i][XX],
 329                    &qm->xQM[i][YY],
 330                    &qm->xQM[i][ZZ]);
 331 #endif
 332             for (j = 0; j < DIM; j++)
 333             {
 334                 qm->xQM[i][j] *= 0.1;
 335             }
 336         }
 337         fclose(xyz);
 338     }
 339     sprintf(orca_engradFilename, "%s.engrad", qm->orca_basename);
 340     engrad = fopen(orca_engradFilename, "r");
 341     /* we read the energy and the gradient for the qm-atoms from the engrad file
 342      */
 343     /* we can skip the first seven lines
 344      */
 345     for (j = 0; j < 7; j++)
 346     {
 347         if (fgets(buf, 300, engrad) == NULL)
 348         {
 349             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 350         }
 351     }
 352     /* now comes the energy
 353      */
 354     if (fgets(buf, 300, engrad) == NULL)
 355     {
 356         gmx_fatal(FARGS, "Unexpected end of ORCA output");
 357     }
 358 #ifdef GMX_DOUBLE
 359     sscanf(buf, "%lf\n", &QMener);
 360 #else
 361     sscanf(buf, "%f\n", &QMener);
 362 #endif
 363     /* we can skip the next three lines
 364      */
 365     for (j = 0; j < 3; j++)
 366     {
 367         if (fgets(buf, 300, engrad) == NULL)
 368         {
 369             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 370         }
 371     }
 372     /* next lines contain the gradients of the QM atoms
 373      * now comes the gradient, one value per line:
 374      * (atom1 x \n atom1 y \n atom1 z \n atom2 x ...
 375      */
 376
 377     for (i = 0; i < 3*qm->nrQMatoms; i++)
 378     {
 379         k = i/3;
 380         if (fgets(buf, 300, engrad) == NULL)
 381         {
 382             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 383         }
 384 #ifdef GMX_DOUBLE
 385         if (i%3 == 0)
 386         {
 387             sscanf(buf, "%lf\n", &QMgrad[k][XX]);
 388         }
 389         else if (i%3 == 1)
 390         {
 391             sscanf(buf, "%lf\n", &QMgrad[k][YY]);
 392         }
 393         else if (i%3 == 2)
 394         {
 395             sscanf(buf, "%lf\n", &QMgrad[k][ZZ]);
 396         }
 397 #else
 398         if (i%3 == 0)
 399         {
 400             sscanf(buf, "%f\n", &QMgrad[k][XX]);
 401         }
 402         else if (i%3 == 1)
 403         {
 404             sscanf(buf, "%f\n", &QMgrad[k][YY]);
 405         }
 406         else if (i%3 == 2)
 407         {
 408             sscanf(buf, "%f\n", &QMgrad[k][ZZ]);
 409         }
 410 #endif
 411     }
 412     fclose(engrad);
 413     /* write the MM point charge data
 414      */
 415     if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
 416     {
 417         sprintf(orca_pcgradFilename, "%s.pcgrad", qm->orca_basename);
 418         pcgrad = fopen(orca_pcgradFilename, "r");
 419
 420         /* we read the gradient for the mm-atoms from the pcgrad file
 421          */
 422         /* we can skip the first line
 423          */
 424         if (fgets(buf, 300, pcgrad) == NULL)
 425         {
 426             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 427         }
 428         for (i = 0; i < mm->nrMMatoms; i++)
 429         {
 430             if (fgets(buf, 300, pcgrad) == NULL)
 431             {
 432                 gmx_fatal(FARGS, "Unexpected end of ORCA output");
 433             }
 434     #ifdef GMX_DOUBLE
 435             sscanf(buf, "%lf%lf%lf\n",
 436                    &MMgrad[i][XX],
 437                    &MMgrad[i][YY],
 438                    &MMgrad[i][ZZ]);
 439     #else
 440             sscanf(buf, "%f%f%f\n",
 441                    &MMgrad[i][XX],
 442                    &MMgrad[i][YY],
 443                    &MMgrad[i][ZZ]);
 444     #endif
 445         }
 446         fclose(pcgrad);
 447     }
 448     return(QMener);
 449 }
 450
 451 void do_orca(char *orca_dir, char *basename)
 452 {
 453
 454     /* make the call to the orca binary through system()
 455      * The location of the binary is set through the
 456      * environment.
 457      */
 458     char
 459         buf[100];
 460     sprintf(buf, "%s/%s %s.inp >> %s.out",
 461             orca_dir,
 462             "orca",
 463             basename,
 464             basename);
 465     fprintf(stderr, "Calling '%s'\n", buf);
 466     if (system(buf) != 0)
 467     {
 468         gmx_fatal(FARGS, "Call to '%s' failed\n", buf);
 469     }
 470 }
 471
 472 real call_orca(t_forcerec *fr,
 473                t_QMrec *qm, t_MMrec *mm, rvec f[], rvec fshift[])
 474 {
 475     /* normal orca jobs */
 476     static int
 477         step = 0;
 478     int
 479         i, j;
 480     real
 481         QMener;
 482     rvec
 483        *QMgrad, *MMgrad;
 484     char
 485        *exe;
 486
 487     snew(exe, 30);
 488     sprintf(exe, "%s", "orca");
 489     snew(QMgrad, qm->nrQMatoms);
 490     snew(MMgrad, mm->nrMMatoms);
 491
 492     write_orca_input(fr, qm, mm);
 493     do_orca(qm->orca_dir, qm->orca_basename);
 494     QMener = read_orca_output(QMgrad, MMgrad, fr, qm, mm);
 495     /* put the QMMM forces in the force array and to the fshift
 496      */
 497     for (i = 0; i < qm->nrQMatoms; i++)
 498     {
 499         for (j = 0; j < DIM; j++)
 500         {
 501             f[i][j]      = HARTREE_BOHR2MD*QMgrad[i][j];
 502             fshift[i][j] = HARTREE_BOHR2MD*QMgrad[i][j];
 503         }
 504     }
 505     for (i = 0; i < mm->nrMMatoms; i++)
 506     {
 507         for (j = 0; j < DIM; j++)
 508         {
 509             f[i+qm->nrQMatoms][j]      = HARTREE_BOHR2MD*MMgrad[i][j];
 510             fshift[i+qm->nrQMatoms][j] = HARTREE_BOHR2MD*MMgrad[i][j];
 511         }
 512     }
 513     QMener = QMener*HARTREE2KJ*AVOGADRO;
 514     step++;
 515     free(exe);
 516     return(QMener);
 517 } /* call_orca */
 518
 519 /* end of orca sub routines */