src/gromacs/mdlib/qm_orca.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2008, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  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 != nullptr)
 135     {
 136         while (!feof(addInputFile))
 137         {
 138             if (fgets(buf, 200, addInputFile) != nullptr)
 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                 fprintf(LJCoeff, "%10.7f  %10.7f\n", qm->c6[i], qm->c12[i]);
 196             }
 197             fprintf(LJCoeff, "%d\n", mm->nrMMatoms);
 198             for (i = 0; i < mm->nrMMatoms; i++)
 199             {
 200                 fprintf(LJCoeff, "%10.7f  %10.7f\n", mm->c6[i], mm->c12[i]);
 201             }
 202             fclose(LJCoeff);
 203         }
 204     }
 205
 206     /* write charge and multiplicity */
 207     fprintf(out, "*xyz %2d%2d\n", qm->QMcharge, qm->multiplicity);
 208
 209     /* write the QM coordinates */
 210     for (i = 0; i < qm->nrQMatoms; i++)
 211     {
 212         int atomNr;
 213         if (qm->atomicnumberQM[i] == 0)
 214         {
 215             atomNr = 1;
 216         }
 217         else
 218         {
 219             atomNr = qm->atomicnumberQM[i];
 220         }
 221         fprintf(out, "%3d %10.7f  %10.7f  %10.7f\n",
 222                 atomNr,
 223                 qm->xQM[i][XX]/0.1,
 224                 qm->xQM[i][YY]/0.1,
 225                 qm->xQM[i][ZZ]/0.1);
 226     }
 227     fprintf(out, "*\n");
 228
 229     /* write the MM point charge data */
 230     if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
 231     {
 232         /* name of the point charge file */
 233         snew(pcFilename, 200);
 234         sprintf(pcFilename, "%s.pc", qm->orca_basename);
 235         fprintf(out, "%s%s%s\n", "%pointcharges \"", pcFilename, "\"");
 236         pcFile = fopen(pcFilename, "w");
 237         fprintf(pcFile, "%d\n", mm->nrMMatoms);
 238         for (i = 0; i < mm->nrMMatoms; i++)
 239         {
 240             fprintf(pcFile, "%8.4f %10.7f  %10.7f  %10.7f\n",
 241                     mm->MMcharges[i],
 242                     mm->xMM[i][XX]/0.1,
 243                     mm->xMM[i][YY]/0.1,
 244                     mm->xMM[i][ZZ]/0.1);
 245         }
 246         fprintf(pcFile, "\n");
 247         fclose(pcFile);
 248     }
 249     fprintf(out, "\n");
 250
 251     fclose(out);
 252 }  /* write_orca_input */
 253
 254 real read_orca_output(rvec QMgrad[], rvec MMgrad[], t_forcerec *fr,
 255                       t_QMrec *qm, t_MMrec *mm)
 256 {
 257     int
 258         i, j, atnum;
 259     char
 260         buf[300], orca_xyzFilename[300], orca_pcgradFilename[300], orca_engradFilename[300];
 261     real
 262         QMener;
 263     FILE
 264        *xyz, *pcgrad, *engrad;
 265     int k;
 266     t_QMMMrec
 267        *QMMMrec;
 268     QMMMrec = fr->qr;
 269     /* in case of an optimization, the coordinates are printed in the
 270      * xyz file, the energy and gradients for the QM part are stored in the engrad file
 271      * and the gradients for the point charges are stored in the pc file.
 272      */
 273
 274     /* we need the new xyz coordinates of the QM atoms only for separate QM-optimization
 275      */
 276
 277     if (qm->bTS || qm->bOPT)
 278     {
 279         sprintf(orca_xyzFilename, "%s.xyz", qm->orca_basename);
 280         xyz = fopen(orca_xyzFilename, "r");
 281         if (fgets(buf, 300, xyz) == nullptr)
 282         {
 283             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 284         }
 285         if (fgets(buf, 300, xyz) == nullptr)
 286         {
 287             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 288         }
 289         for (i = 0; i < qm->nrQMatoms; i++)
 290         {
 291             if (fgets(buf, 300, xyz) == nullptr)
 292             {
 293                 gmx_fatal(FARGS, "Unexpected end of ORCA output");
 294             }
 295 #if GMX_DOUBLE
 296             sscanf(buf, "%d%lf%lf%lf\n",
 297                    &atnum,
 298                    &qm->xQM[i][XX],
 299                    &qm->xQM[i][YY],
 300                    &qm->xQM[i][ZZ]);
 301 #else
 302             sscanf(buf, "%d%f%f%f\n",
 303                    &atnum,
 304                    &qm->xQM[i][XX],
 305                    &qm->xQM[i][YY],
 306                    &qm->xQM[i][ZZ]);
 307 #endif
 308             for (j = 0; j < DIM; j++)
 309             {
 310                 qm->xQM[i][j] *= 0.1;
 311             }
 312         }
 313         fclose(xyz);
 314     }
 315     sprintf(orca_engradFilename, "%s.engrad", qm->orca_basename);
 316     engrad = fopen(orca_engradFilename, "r");
 317     /* we read the energy and the gradient for the qm-atoms from the engrad file
 318      */
 319     /* we can skip the first seven lines
 320      */
 321     for (j = 0; j < 7; j++)
 322     {
 323         if (fgets(buf, 300, engrad) == nullptr)
 324         {
 325             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 326         }
 327     }
 328     /* now comes the energy
 329      */
 330     if (fgets(buf, 300, engrad) == nullptr)
 331     {
 332         gmx_fatal(FARGS, "Unexpected end of ORCA output");
 333     }
 334 #if GMX_DOUBLE
 335     sscanf(buf, "%lf\n", &QMener);
 336 #else
 337     sscanf(buf, "%f\n", &QMener);
 338 #endif
 339     /* we can skip the next three lines
 340      */
 341     for (j = 0; j < 3; j++)
 342     {
 343         if (fgets(buf, 300, engrad) == nullptr)
 344         {
 345             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 346         }
 347     }
 348     /* next lines contain the gradients of the QM atoms
 349      * now comes the gradient, one value per line:
 350      * (atom1 x \n atom1 y \n atom1 z \n atom2 x ...
 351      */
 352
 353     for (i = 0; i < 3*qm->nrQMatoms; i++)
 354     {
 355         k = i/3;
 356         if (fgets(buf, 300, engrad) == nullptr)
 357         {
 358             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 359         }
 360 #if GMX_DOUBLE
 361         if (i%3 == 0)
 362         {
 363             sscanf(buf, "%lf\n", &QMgrad[k][XX]);
 364         }
 365         else if (i%3 == 1)
 366         {
 367             sscanf(buf, "%lf\n", &QMgrad[k][YY]);
 368         }
 369         else if (i%3 == 2)
 370         {
 371             sscanf(buf, "%lf\n", &QMgrad[k][ZZ]);
 372         }
 373 #else
 374         if (i%3 == 0)
 375         {
 376             sscanf(buf, "%f\n", &QMgrad[k][XX]);
 377         }
 378         else if (i%3 == 1)
 379         {
 380             sscanf(buf, "%f\n", &QMgrad[k][YY]);
 381         }
 382         else if (i%3 == 2)
 383         {
 384             sscanf(buf, "%f\n", &QMgrad[k][ZZ]);
 385         }
 386 #endif
 387     }
 388     fclose(engrad);
 389     /* write the MM point charge data
 390      */
 391     if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
 392     {
 393         sprintf(orca_pcgradFilename, "%s.pcgrad", qm->orca_basename);
 394         pcgrad = fopen(orca_pcgradFilename, "r");
 395
 396         /* we read the gradient for the mm-atoms from the pcgrad file
 397          */
 398         /* we can skip the first line
 399          */
 400         if (fgets(buf, 300, pcgrad) == nullptr)
 401         {
 402             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 403         }
 404         for (i = 0; i < mm->nrMMatoms; i++)
 405         {
 406             if (fgets(buf, 300, pcgrad) == nullptr)
 407             {
 408                 gmx_fatal(FARGS, "Unexpected end of ORCA output");
 409             }
 410     #if GMX_DOUBLE
 411             sscanf(buf, "%lf%lf%lf\n",
 412                    &MMgrad[i][XX],
 413                    &MMgrad[i][YY],
 414                    &MMgrad[i][ZZ]);
 415     #else
 416             sscanf(buf, "%f%f%f\n",
 417                    &MMgrad[i][XX],
 418                    &MMgrad[i][YY],
 419                    &MMgrad[i][ZZ]);
 420     #endif
 421         }
 422         fclose(pcgrad);
 423     }
 424     return(QMener);
 425 }
 426
 427 void do_orca(char *orca_dir, char *basename)
 428 {
 429
 430     /* make the call to the orca binary through system()
 431      * The location of the binary is set through the
 432      * environment.
 433      */
 434     char
 435         buf[100];
 436     sprintf(buf, "%s/%s %s.inp >> %s.out",
 437             orca_dir,
 438             "orca",
 439             basename,
 440             basename);
 441     fprintf(stderr, "Calling '%s'\n", buf);
 442     if (system(buf) != 0)
 443     {
 444         gmx_fatal(FARGS, "Call to '%s' failed\n", buf);
 445     }
 446 }
 447
 448 real call_orca(t_forcerec *fr,
 449                t_QMrec *qm, t_MMrec *mm, rvec f[], rvec fshift[])
 450 {
 451     /* normal orca jobs */
 452     static int
 453         step = 0;
 454     int
 455         i, j;
 456     real
 457         QMener;
 458     rvec
 459        *QMgrad, *MMgrad;
 460     char
 461        *exe;
 462
 463     snew(exe, 30);
 464     sprintf(exe, "%s", "orca");
 465     snew(QMgrad, qm->nrQMatoms);
 466     snew(MMgrad, mm->nrMMatoms);
 467
 468     write_orca_input(fr, qm, mm);
 469     do_orca(qm->orca_dir, qm->orca_basename);
 470     QMener = read_orca_output(QMgrad, MMgrad, fr, qm, mm);
 471     /* put the QMMM forces in the force array and to the fshift
 472      */
 473     for (i = 0; i < qm->nrQMatoms; i++)
 474     {
 475         for (j = 0; j < DIM; j++)
 476         {
 477             f[i][j]      = HARTREE_BOHR2MD*QMgrad[i][j];
 478             fshift[i][j] = HARTREE_BOHR2MD*QMgrad[i][j];
 479         }
 480     }
 481     for (i = 0; i < mm->nrMMatoms; i++)
 482     {
 483         for (j = 0; j < DIM; j++)
 484         {
 485             f[i+qm->nrQMatoms][j]      = HARTREE_BOHR2MD*MMgrad[i][j];
 486             fshift[i+qm->nrQMatoms][j] = HARTREE_BOHR2MD*MMgrad[i][j];
 487         }
 488     }
 489     QMener = QMener*HARTREE2KJ*AVOGADRO;
 490     step++;
 491     free(exe);
 492     return(QMener);
 493 } /* call_orca */
 494
 495 /* end of orca sub routines */