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