src/gromacs/mdlib/qm_orca.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "qm_orca.h"
  40
  41 #include <stdio.h>
  42 #include <stdlib.h>
  43 #include <string.h>
  44
  45 #include <cmath>
  46
  47 #include "gromacs/fileio/confio.h"
  48 #include "gromacs/gmxlib/network.h"
  49 #include "gromacs/gmxlib/nrnb.h"
  50 #include "gromacs/math/units.h"
  51 #include "gromacs/math/vec.h"
  52 #include "gromacs/mdlib/ns.h"
  53 #include "gromacs/mdlib/qmmm.h"
  54 #include "gromacs/mdtypes/forcerec.h"
  55 #include "gromacs/mdtypes/md_enums.h"
  56 #include "gromacs/utility/fatalerror.h"
  57 #include "gromacs/utility/smalloc.h"
  58
  59 /* ORCA interface routines */
  60
  61 void init_orca(t_QMrec *qm)
  62 {
  63     char *buf;
  64     snew(buf, 200);
  65
  66     /* ORCA settings on the system */
  67     buf = getenv("GMX_QM_ORCA_BASENAME");
  68     if (buf)
  69     {
  70         snew(qm->orca_basename, 200);
  71         sscanf(buf, "%s", qm->orca_basename);
  72     }
  73     else
  74     {
  75         gmx_fatal(FARGS, "$GMX_QM_ORCA_BASENAME is not set\n");
  76     }
  77
  78     /* ORCA directory on the system */
  79     snew(buf, 200);
  80     buf = getenv("GMX_ORCA_PATH");
  81
  82     if (buf)
  83     {
  84         snew(qm->orca_dir, 200);
  85         sscanf(buf, "%s", qm->orca_dir);
  86     }
  87     else
  88     {
  89         gmx_fatal(FARGS, "$GMX_ORCA_PATH not set, check manual\n");
  90     }
  91
  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);
  97     remove(buf);
  98 }
  99
 100
 101 static void write_orca_input(t_forcerec *fr, t_QMrec *qm, t_MMrec *mm)
 102 {
 103     int        i;
 104     t_QMMMrec *QMMMrec;
 105     FILE      *out, *pcFile, *addInputFile;
 106     char      *buf, *orcaInput, *addInputFilename, *pcFilename;
 107
 108     QMMMrec = fr->qr;
 109
 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");
 114
 115     snew(addInputFilename, 200);
 116     sprintf(addInputFilename, "%s.ORCAINFO", qm->orca_basename);
 117     addInputFile = fopen(addInputFilename, "r");
 118
 119     fprintf(out, "#input-file generated by GROMACS\n");
 120
 121     fprintf(out, "!EnGrad TightSCF\n");
 122
 123     /* here we include the insertion of the additional orca-input */
 124     snew(buf, 200);
 125     if (addInputFile != nullptr)
 126     {
 127         while (!feof(addInputFile))
 128         {
 129             if (fgets(buf, 200, addInputFile) != nullptr)
 130             {
 131                 fputs(buf, out);
 132             }
 133         }
 134     }
 135     else
 136     {
 137         gmx_fatal(FARGS, "No information on the calculation given in %s\n", addInputFilename);
 138     }
 139
 140     fclose(addInputFile);
 141
 142     /* write charge and multiplicity */
 143     fprintf(out, "*xyz %2d%2d\n", qm->QMcharge, qm->multiplicity);
 144
 145     /* write the QM coordinates */
 146     for (i = 0; i < qm->nrQMatoms; i++)
 147     {
 148         int atomNr;
 149         if (qm->atomicnumberQM[i] == 0)
 150         {
 151             atomNr = 1;
 152         }
 153         else
 154         {
 155             atomNr = qm->atomicnumberQM[i];
 156         }
 157         fprintf(out, "%3d %10.7f  %10.7f  %10.7f\n",
 158                 atomNr,
 159                 qm->xQM[i][XX]/0.1,
 160                 qm->xQM[i][YY]/0.1,
 161                 qm->xQM[i][ZZ]/0.1);
 162     }
 163     fprintf(out, "*\n");
 164
 165     /* write the MM point charge data */
 166     if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
 167     {
 168         /* name of the point charge file */
 169         snew(pcFilename, 200);
 170         sprintf(pcFilename, "%s.pc", qm->orca_basename);
 171         fprintf(out, "%s%s%s\n", "%pointcharges \"", pcFilename, "\"");
 172         pcFile = fopen(pcFilename, "w");
 173         fprintf(pcFile, "%d\n", mm->nrMMatoms);
 174         for (i = 0; i < mm->nrMMatoms; i++)
 175         {
 176             fprintf(pcFile, "%8.4f %10.7f  %10.7f  %10.7f\n",
 177                     mm->MMcharges[i],
 178                     mm->xMM[i][XX]/0.1,
 179                     mm->xMM[i][YY]/0.1,
 180                     mm->xMM[i][ZZ]/0.1);
 181         }
 182         fprintf(pcFile, "\n");
 183         fclose(pcFile);
 184     }
 185     fprintf(out, "\n");
 186
 187     fclose(out);
 188 }  /* write_orca_input */
 189
 190 static real read_orca_output(rvec QMgrad[], rvec MMgrad[], t_forcerec *fr,
 191                              t_QMrec *qm, t_MMrec *mm)
 192 {
 193     int
 194         i, j;
 195     char
 196         buf[300], orca_pcgradFilename[300], orca_engradFilename[300];
 197     real
 198         QMener;
 199     FILE
 200        *pcgrad, *engrad;
 201     int k;
 202     t_QMMMrec
 203        *QMMMrec;
 204     QMMMrec = fr->qr;
 205
 206     /* the energy and gradients for the QM part are stored in the engrad file
 207      * and the gradients for the point charges are stored in the pc file.
 208      */
 209     sprintf(orca_engradFilename, "%s.engrad", qm->orca_basename);
 210     engrad = fopen(orca_engradFilename, "r");
 211     /* we read the energy and the gradient for the qm-atoms from the engrad file
 212      */
 213     /* we can skip the first seven lines
 214      */
 215     for (j = 0; j < 7; j++)
 216     {
 217         if (fgets(buf, 300, engrad) == nullptr)
 218         {
 219             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 220         }
 221     }
 222     /* now comes the energy
 223      */
 224     if (fgets(buf, 300, engrad) == nullptr)
 225     {
 226         gmx_fatal(FARGS, "Unexpected end of ORCA output");
 227     }
 228 #if GMX_DOUBLE
 229     sscanf(buf, "%lf\n", &QMener);
 230 #else
 231     sscanf(buf, "%f\n", &QMener);
 232 #endif
 233     /* we can skip the next three lines
 234      */
 235     for (j = 0; j < 3; j++)
 236     {
 237         if (fgets(buf, 300, engrad) == nullptr)
 238         {
 239             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 240         }
 241     }
 242     /* next lines contain the gradients of the QM atoms
 243      * now comes the gradient, one value per line:
 244      * (atom1 x \n atom1 y \n atom1 z \n atom2 x ...
 245      */
 246
 247     for (i = 0; i < 3*qm->nrQMatoms; i++)
 248     {
 249         k = i/3;
 250         if (fgets(buf, 300, engrad) == nullptr)
 251         {
 252             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 253         }
 254 #if GMX_DOUBLE
 255         if (i%3 == 0)
 256         {
 257             sscanf(buf, "%lf\n", &QMgrad[k][XX]);
 258         }
 259         else if (i%3 == 1)
 260         {
 261             sscanf(buf, "%lf\n", &QMgrad[k][YY]);
 262         }
 263         else if (i%3 == 2)
 264         {
 265             sscanf(buf, "%lf\n", &QMgrad[k][ZZ]);
 266         }
 267 #else
 268         if (i%3 == 0)
 269         {
 270             sscanf(buf, "%f\n", &QMgrad[k][XX]);
 271         }
 272         else if (i%3 == 1)
 273         {
 274             sscanf(buf, "%f\n", &QMgrad[k][YY]);
 275         }
 276         else if (i%3 == 2)
 277         {
 278             sscanf(buf, "%f\n", &QMgrad[k][ZZ]);
 279         }
 280 #endif
 281     }
 282     fclose(engrad);
 283     /* write the MM point charge data
 284      */
 285     if (QMMMrec->QMMMscheme != eQMMMschemeoniom && mm->nrMMatoms)
 286     {
 287         sprintf(orca_pcgradFilename, "%s.pcgrad", qm->orca_basename);
 288         pcgrad = fopen(orca_pcgradFilename, "r");
 289
 290         /* we read the gradient for the mm-atoms from the pcgrad file
 291          */
 292         /* we can skip the first line
 293          */
 294         if (fgets(buf, 300, pcgrad) == nullptr)
 295         {
 296             gmx_fatal(FARGS, "Unexpected end of ORCA output");
 297         }
 298         for (i = 0; i < mm->nrMMatoms; i++)
 299         {
 300             if (fgets(buf, 300, pcgrad) == nullptr)
 301             {
 302                 gmx_fatal(FARGS, "Unexpected end of ORCA output");
 303             }
 304     #if GMX_DOUBLE
 305             sscanf(buf, "%lf%lf%lf\n",
 306                    &MMgrad[i][XX],
 307                    &MMgrad[i][YY],
 308                    &MMgrad[i][ZZ]);
 309     #else
 310             sscanf(buf, "%f%f%f\n",
 311                    &MMgrad[i][XX],
 312                    &MMgrad[i][YY],
 313                    &MMgrad[i][ZZ]);
 314     #endif
 315         }
 316         fclose(pcgrad);
 317     }
 318     return(QMener);
 319 }
 320
 321 static void do_orca(char *orca_dir, char *basename)
 322 {
 323
 324     /* make the call to the orca binary through system()
 325      * The location of the binary is set through the
 326      * environment.
 327      */
 328     char
 329         buf[100];
 330     sprintf(buf, "%s/%s %s.inp >> %s.out",
 331             orca_dir,
 332             "orca",
 333             basename,
 334             basename);
 335     fprintf(stderr, "Calling '%s'\n", buf);
 336     if (system(buf) != 0)
 337     {
 338         gmx_fatal(FARGS, "Call to '%s' failed\n", buf);
 339     }
 340 }
 341
 342 real call_orca(t_forcerec *fr,
 343                t_QMrec *qm, t_MMrec *mm, rvec f[], rvec fshift[])
 344 {
 345     /* normal orca jobs */
 346     static int
 347         step = 0;
 348     int
 349         i, j;
 350     real
 351         QMener;
 352     rvec
 353        *QMgrad, *MMgrad;
 354     char
 355        *exe;
 356
 357     snew(exe, 30);
 358     sprintf(exe, "%s", "orca");
 359     snew(QMgrad, qm->nrQMatoms);
 360     snew(MMgrad, mm->nrMMatoms);
 361
 362     write_orca_input(fr, qm, mm);
 363     do_orca(qm->orca_dir, qm->orca_basename);
 364     QMener = read_orca_output(QMgrad, MMgrad, fr, qm, mm);
 365     /* put the QMMM forces in the force array and to the fshift
 366      */
 367     for (i = 0; i < qm->nrQMatoms; i++)
 368     {
 369         for (j = 0; j < DIM; j++)
 370         {
 371             f[i][j]      = HARTREE_BOHR2MD*QMgrad[i][j];
 372             fshift[i][j] = HARTREE_BOHR2MD*QMgrad[i][j];
 373         }
 374     }
 375     for (i = 0; i < mm->nrMMatoms; i++)
 376     {
 377         for (j = 0; j < DIM; j++)
 378         {
 379             f[i+qm->nrQMatoms][j]      = HARTREE_BOHR2MD*MMgrad[i][j];
 380             fshift[i+qm->nrQMatoms][j] = HARTREE_BOHR2MD*MMgrad[i][j];
 381         }
 382     }
 383     QMener = QMener*HARTREE2KJ*AVOGADRO;
 384     step++;
 385     free(exe);
 386     return(QMener);
 387 } /* call_orca */
 388
 389 /* end of orca sub routines */