src/gromacs/mdlib/qm_orca.c

   1 /*
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   5  * Copyright (c) 2001-2008, The GROMACS development team.
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  37 #include "config.h"
  38
  39 #include <math.h>
  40 #include <stdio.h>
  41 #include <stdlib.h>
  42 #include <string.h>
  43
  44 #include "typedefs.h"
  45 #include "macros.h"
  46 #include "gromacs/utility/smalloc.h"
  47 #include "gromacs/math/units.h"
  48 #include "gromacs/math/vec.h"
  49 #include "force.h"
  50 #include "gromacs/fileio/confio.h"
  51 #include "names.h"
  52 #include "network.h"
  53 #include "ns.h"
  54 #include "nrnb.h"
  55 #include "bondf.h"
  56 #include "txtdump.h"
  57 #include "qmmm.h"
  58 #include "gromacs/utility/fatalerror.h"
  59
  60 /* ORCA interface routines */
  61
  62 void init_orca(t_QMrec *qm)
  63 {
  64     char *buf;
  65     snew(buf, 200);
  66
  67     /* ORCA settings on the system */
  68     buf = getenv("GMX_QM_ORCA_BASENAME");
  69     if (buf)
  70     {
  71         snew(qm->orca_basename, 200);
  72         sscanf(buf, "%s", qm->orca_basename);
  73     }
  74     else
  75     {
  76         gmx_fatal(FARGS, "$GMX_QM_ORCA_BASENAME is not set\n");
  77     }
  78
  79     /* ORCA directory on the system */
  80     snew(buf, 200);
  81     buf = getenv("GMX_ORCA_PATH");
  82
  83     if (buf)
  84     {
  85         snew(qm->orca_dir, 200);
  86         sscanf(buf, "%s", qm->orca_dir);
  87     }
  88     else
  89     {
  90         gmx_fatal(FARGS, "$GMX_ORCA_PATH not set, check manual\n");
  91     }
  92
  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);
  98     remove(buf);
  99 }
 100
 101
 102 void write_orca_input(t_forcerec *fr, t_QMrec *qm, t_MMrec *mm)
 103 {
 104     int        i;
 105     t_QMMMrec *QMMMrec;
 106     FILE      *out, *pcFile, *addInputFile, *LJCoeff;
 107     char      *buf, *orcaInput, *addInputFilename, *LJCoeffFilename, *pcFilename, *exclInName, *exclOutName;
 108
 109     QMMMrec = fr->qr;
 110
 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");
 115
 116     snew(addInputFilename, 200);
 117     sprintf(addInputFilename, "%s.ORCAINFO", qm->orca_basename);
 118     addInputFile = fopen(addInputFilename, "r");
 119
 120     fprintf(out, "#input-file generated by GROMACS\n");
 121
 122     if (qm->bTS)
 123     {
 124         fprintf(out, "!QMMMOpt TightSCF\n");
 125         fprintf(out, "%s\n", "%geom TS_Search EF end");
 126     }
 127     else if (qm->bOPT)
 128     {
 129         fprintf(out, "!QMMMOpt TightSCF\n");
 130     }
 131     else
 132     {
 133         fprintf(out, "!EnGrad TightSCF\n");
 134     }
 135
 136     /* here we include the insertion of the additional orca-input */
 137     snew(buf, 200);
 138     if (addInputFile != NULL)
 139     {
 140         while (!feof(addInputFile))
 141         {
 142             if (fgets(buf, 200, addInputFile) != NULL)
 143             {
 144                 fputs(buf, out);
 145             }
 146         }
 147     }
 148     else
 149     {
 150         gmx_fatal(FARGS, "No information on the calculation given in %s\n", addInputFilename);
 151     }
 152
 153     fclose(addInputFile);
 154
 155     if (qm->bTS || qm->bOPT)
 156     {
 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.
 161          */
 162         /* ORCA reads the exclusions from LJCoeffFilename.Excl,
 163          * so we have to rename the file
 164          */
 165         int didStart = 0;
 166         for (i = 0; i < qm->nrQMatoms; i++)
 167         {
 168             if (qm->frontatoms[i])
 169             {
 170                 if (!didStart)
 171                 {
 172                     fprintf(out, "%s\n", "%geom");
 173                     fprintf(out, "   Constraints \n");
 174                     didStart = 1;
 175                 }
 176                 fprintf(out, "        {C %d C}\n", i); /* counting from 0 */
 177             }
 178         }
 179         if (didStart)
 180         {
 181             fprintf(out, "     end\n   end\n");
 182         }
 183         /* make a file with information on the C6 and C12 coefficients */
 184         if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
 185         {
 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++)
 198             {
 199 #ifdef GMX_DOUBLE
 200                 fprintf(LJCoeff, "%10.7lf  %10.7lf\n", qm->c6[i], qm->c12[i]);
 201 #else
 202                 fprintf(LJCoeff, "%10.7f  %10.7f\n", qm->c6[i], qm->c12[i]);
 203 #endif
 204             }
 205             fprintf(LJCoeff, "%d\n", mm->nrMMatoms);
 206             for (i = 0; i < mm->nrMMatoms; i++)
 207             {
 208 #ifdef GMX_DOUBLE
 209                 fprintf(LJCoeff, "%10.7lf  %10.7lf\n", mm->c6[i], mm->c12[i]);
 210 #else
 211                 fprintf(LJCoeff, "%10.7f  %10.7f\n", mm->c6[i], mm->c12[i]);
 212 #endif
 213             }
 214             fclose(LJCoeff);
 215         }
 216     }
 217
 218     /* write charge and multiplicity */
 219     fprintf(out, "*xyz %2d%2d\n", qm->QMcharge, qm->multiplicity);
 220
 221     /* write the QM coordinates */
 222     for (i = 0; i < qm->nrQMatoms; i++)
 223     {
 224         int atomNr;
 225         if (qm->atomicnumberQM[i] == 0)
 226         {
 227             atomNr = 1;
 228         }
 229         else
 230         {
 231             atomNr = qm->atomicnumberQM[i];
 232         }
 233 #ifdef GMX_DOUBLE
 234         fprintf(out, "%3d %10.7lf  %10.7lf  %10.7lf\n",
 235                 atomNr,
 236                 qm->xQM[i][XX]/0.1,
 237                 qm->xQM[i][YY]/0.1,
 238                 qm->xQM[i][ZZ]/0.1);
 239 #else
 240         fprintf(out, "%3d %10.7f  %10.7f  %10.7f\n",
 241                 atomNr,
 242                 qm->xQM[i][XX]/0.1,
 243                 qm->xQM[i][YY]/0.1,
 244                 qm->xQM[i][ZZ]/0.1);
 245 #endif
 246     }
 247     fprintf(out, "*\n");
 248
 249     /* write the MM point charge data */
 250     if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
 251     {
 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++)
 259         {
 260 #ifdef GMX_DOUBLE
 261             fprintf(pcFile, "%8.4lf %10.7lf  %10.7lf  %10.7lf\n",
 262                     mm->MMcharges[i],
 263                     mm->xMM[i][XX]/0.1,
 264                     mm->xMM[i][YY]/0.1,
 265                     mm->xMM[i][ZZ]/0.1);
 266 #else
 267             fprintf(pcFile, "%8.4f %10.7f  %10.7f  %10.7f\n",
 268                     mm->MMcharges[i],
 269                     mm->xMM[i][XX]/0.1,
 270                     mm->xMM[i][YY]/0.1,
 271                     mm->xMM[i][ZZ]/0.1);
 272 #endif
 273         }
 274         fprintf(pcFile, "\n");
 275         fclose(pcFile);
 276     }
 277     fprintf(out, "\n");
 278
 279     fclose(out);
 280 }  /* write_orca_input */
 281
 282 real read_orca_output(rvec QMgrad[], rvec MMgrad[], t_forcerec *fr,
 283                       t_QMrec *qm, t_MMrec *mm)
 284 {
 285     int
 286         i, j, atnum;
 287     char
 288         buf[300], tmp[300], orca_xyzFilename[300], orca_pcgradFilename[300], orca_engradFilename[300];
 289     real
 290         QMener;
 291     FILE
 292        *xyz, *pcgrad, *engrad;
 293     int k;
 294     t_QMMMrec
 295        *QMMMrec;
 296     QMMMrec = fr->qr;
 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.
 300      */
 301
 302     /* we need the new xyz coordinates of the QM atoms only for separate QM-optimization
 303      */
 304
 305     if (qm->bTS || qm->bOPT)
 306     {
 307         sprintf(orca_xyzFilename, "%s.xyz", qm->orca_basename);
 308         xyz = fopen(orca_xyzFilename, "r");
 309         if (fgets(buf, 300, xyz) == NULL)
 310         {
 311             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 312         }
 313         if (fgets(buf, 300, xyz) == NULL)
 314         {
 315             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 316         }
 317         for (i = 0; i < qm->nrQMatoms; i++)
 318         {
 319             if (fgets(buf, 300, xyz) == NULL)
 320             {
 321                 gmx_fatal(FARGS, "Unexpected end of ORCA output");
 322             }
 323 #ifdef GMX_DOUBLE
 324             sscanf(buf, "%s%lf%lf%lf\n",
 325                    tmp,
 326                    &qm->xQM[i][XX],
 327                    &qm->xQM[i][YY],
 328                    &qm->xQM[i][ZZ]);
 329 #else
 330             sscanf(buf, "%d%f%f%f\n",
 331                    &atnum,
 332                    &qm->xQM[i][XX],
 333                    &qm->xQM[i][YY],
 334                    &qm->xQM[i][ZZ]);
 335 #endif
 336             for (j = 0; j < DIM; j++)
 337             {
 338                 qm->xQM[i][j] *= 0.1;
 339             }
 340         }
 341         fclose(xyz);
 342     }
 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
 346      */
 347     /* we can skip the first seven lines
 348      */
 349     for (j = 0; j < 7; j++)
 350     {
 351         if (fgets(buf, 300, engrad) == NULL)
 352         {
 353             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 354         }
 355     }
 356     /* now comes the energy
 357      */
 358     if (fgets(buf, 300, engrad) == NULL)
 359     {
 360         gmx_fatal(FARGS, "Unexpected end of ORCA output");
 361     }
 362 #ifdef GMX_DOUBLE
 363     sscanf(buf, "%lf\n", &QMener);
 364 #else
 365     sscanf(buf, "%f\n", &QMener);
 366 #endif
 367     /* we can skip the next three lines
 368      */
 369     for (j = 0; j < 3; j++)
 370     {
 371         if (fgets(buf, 300, engrad) == NULL)
 372         {
 373             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 374         }
 375     }
 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 ...
 379      */
 380
 381     for (i = 0; i < 3*qm->nrQMatoms; i++)
 382     {
 383         k = i/3;
 384         if (fgets(buf, 300, engrad) == NULL)
 385         {
 386             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 387         }
 388 #ifdef GMX_DOUBLE
 389         if (i%3 == 0)
 390         {
 391             sscanf(buf, "%lf\n", &QMgrad[k][XX]);
 392         }
 393         else if (i%3 == 1)
 394         {
 395             sscanf(buf, "%lf\n", &QMgrad[k][YY]);
 396         }
 397         else if (i%3 == 2)
 398         {
 399             sscanf(buf, "%lf\n", &QMgrad[k][ZZ]);
 400         }
 401 #else
 402         if (i%3 == 0)
 403         {
 404             sscanf(buf, "%f\n", &QMgrad[k][XX]);
 405         }
 406         else if (i%3 == 1)
 407         {
 408             sscanf(buf, "%f\n", &QMgrad[k][YY]);
 409         }
 410         else if (i%3 == 2)
 411         {
 412             sscanf(buf, "%f\n", &QMgrad[k][ZZ]);
 413         }
 414 #endif
 415     }
 416     fclose(engrad);
 417     /* write the MM point charge data
 418      */
 419     if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
 420     {
 421         sprintf(orca_pcgradFilename, "%s.pcgrad", qm->orca_basename);
 422         pcgrad = fopen(orca_pcgradFilename, "r");
 423
 424         /* we read the gradient for the mm-atoms from the pcgrad file
 425          */
 426         /* we can skip the first line
 427          */
 428         if (fgets(buf, 300, pcgrad) == NULL)
 429         {
 430             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 431         }
 432         for (i = 0; i < mm->nrMMatoms; i++)
 433         {
 434             if (fgets(buf, 300, pcgrad) == NULL)
 435             {
 436                 gmx_fatal(FARGS, "Unexpected end of ORCA output");
 437             }
 438     #ifdef GMX_DOUBLE
 439             sscanf(buf, "%lf%lf%lf\n",
 440                    &MMgrad[i][XX],
 441                    &MMgrad[i][YY],
 442                    &MMgrad[i][ZZ]);
 443     #else
 444             sscanf(buf, "%f%f%f\n",
 445                    &MMgrad[i][XX],
 446                    &MMgrad[i][YY],
 447                    &MMgrad[i][ZZ]);
 448     #endif
 449         }
 450         fclose(pcgrad);
 451     }
 452     return(QMener);
 453 }
 454
 455 void do_orca(char *orca_dir, char *basename)
 456 {
 457
 458     /* make the call to the orca binary through system()
 459      * The location of the binary is set through the
 460      * environment.
 461      */
 462     char
 463         buf[100];
 464     sprintf(buf, "%s/%s %s.inp >> %s.out",
 465             orca_dir,
 466             "orca",
 467             basename,
 468             basename);
 469     fprintf(stderr, "Calling '%s'\n", buf);
 470     if (system(buf) != 0)
 471     {
 472         gmx_fatal(FARGS, "Call to '%s' failed\n", buf);
 473     }
 474 }
 475
 476 real call_orca(t_forcerec *fr,
 477                t_QMrec *qm, t_MMrec *mm, rvec f[], rvec fshift[])
 478 {
 479     /* normal orca jobs */
 480     static int
 481         step = 0;
 482     int
 483         i, j;
 484     real
 485         QMener;
 486     rvec
 487        *QMgrad, *MMgrad;
 488     char
 489        *exe;
 490
 491     snew(exe, 30);
 492     sprintf(exe, "%s", "orca");
 493     snew(QMgrad, qm->nrQMatoms);
 494     snew(MMgrad, mm->nrMMatoms);
 495
 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
 500      */
 501     for (i = 0; i < qm->nrQMatoms; i++)
 502     {
 503         for (j = 0; j < DIM; j++)
 504         {
 505             f[i][j]      = HARTREE_BOHR2MD*QMgrad[i][j];
 506             fshift[i][j] = HARTREE_BOHR2MD*QMgrad[i][j];
 507         }
 508     }
 509     for (i = 0; i < mm->nrMMatoms; i++)
 510     {
 511         for (j = 0; j < DIM; j++)
 512         {
 513             f[i+qm->nrQMatoms][j]      = HARTREE_BOHR2MD*MMgrad[i][j];
 514             fshift[i+qm->nrQMatoms][j] = HARTREE_BOHR2MD*MMgrad[i][j];
 515         }
 516     }
 517     QMener = QMener*HARTREE2KJ*AVOGADRO;
 518     step++;
 519     free(exe);
 520     return(QMener);
 521 } /* call_orca */
 522
 523 /* end of orca sub routines */