/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
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* of the License, or (at your option) any later version.
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+ * consider code for inclusion in the official distribution, but
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+ * in the README & COPYING files - if they are missing, get the
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#ifdef GMX_QMMM_GAMESS
#include <math.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "smalloc.h"
-#include "physics.h"
-#include "macros.h"
-#include "vec.h"
-#include "force.h"
-#include "invblock.h"
-#include "confio.h"
-#include "names.h"
-#include "network.h"
-#include "pbc.h"
-#include "ns.h"
-#include "nrnb.h"
-#include "bondf.h"
-#include "mshift.h"
-#include "txtdump.h"
-#include "copyrite.h"
-#include "qmmm.h"
#include <stdio.h>
-#include <string.h>
-#include "gmx_fatal.h"
-#include "typedefs.h"
#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* QMMM sub routines */
/* mopac interface routines */
-#ifndef F77_FUNC
-#define F77_FUNC(name,NAME) name ## _
-#endif
-
+void
+F77_FUNC(inigms, IMIGMS) (void);
-void
-F77_FUNC(inigms,IMIGMS)(void);
+void
+F77_FUNC(endgms, ENDGMS) (void);
-void
-F77_FUNC(endgms,ENDGMS)(void);
+void
+F77_FUNC(grads, GRADS) (int *nrqmat, real *qmcrd, int *nrmmat, real *mmchrg,
+ real *mmcrd, real *qmgrad, real *mmgrad, real *energy);
-void
-F77_FUNC(grads,GRADS)(int *nrqmat,real *qmcrd,int *nrmmat, real *mmchrg,
- real *mmcrd, real *qmgrad,real *mmgrad, real *energy);
+void init_gamess(t_commrec *cr, t_QMrec *qm, t_MMrec *mm)
+{
+ /* it works hopelessly complicated :-)
+ * first a file is written. Then the standard gamess input/output
+ * routine is called (no system()!) to set up all fortran arrays.
+ * this routine writes a punch file, like in a normal gamess run.
+ * via this punch file the other games routines, needed for gradient
+ * and energy evaluations are called. This setup works fine for
+ * dynamics simulations. 7-6-2002 (London)
+ */
+ int
+ i, j, rank;
+ FILE
+ *out;
+ char
+ periodic_system[37][3] = {
+ "XX", "H ", "He", "Li", "Be", "B ", "C ", "N ",
+ "O ", "F ", "Ne", "Na", "Mg", "Al", "Si", "P ",
+ "S ", "Cl", "Ar", "K ", "Ca", "Sc", "Ti", "V ",
+ "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga",
+ "Ge", "As", "Se", "Br", "Kr"
+ };
-void init_gamess(t_commrec *cr,t_QMrec *qm, t_MMrec *mm){
- /* it works hopelessly complicated :-)
- * first a file is written. Then the standard gamess input/output
- * routine is called (no system()!) to set up all fortran arrays.
- * this routine writes a punch file, like in a normal gamess run.
- * via this punch file the other games routines, needed for gradient
- * and energy evaluations are called. This setup works fine for
- * dynamics simulations. 7-6-2002 (London)
- */
- int
- i,j,rank;
- FILE
- *out;
- char
- periodic_system[37][3]={"XX","H ","He","Li","Be","B ","C ","N ",
- "O ","F ","Ne","Na","Mg","Al","Si","P ",
- "S ","Cl","Ar","K ","Ca","Sc","Ti","V ",
- "Cr","Mn","Fe","Co","Ni","Cu","Zn","Ga",
- "Ge","As","Se","Br","Kr"};
-
- if (PAR(cr)){
+ if (PAR(cr))
+ {
- if MASTER(cr){
- out=fopen("FOR009","w");
- /* of these options I am not completely sure.... the overall
- * preformance on more than 4 cpu's is rather poor at the moment.
- */
- fprintf(out,"memory 48000000\nPARALLEL IOMODE SCREENED\n");
- fprintf(out,"ELEC %d\nMULT %d\nSUPER ON\nNOSYM\nGEOMETRY ANGSTROM\n",
- qm->nelectrons,qm->multiplicity);
- for (i=0;i<qm->nrQMatoms;i++){
+ if (MASTER(cr))
+ {
+ out = fopen("FOR009", "w");
+ /* of these options I am not completely sure.... the overall
+ * preformance on more than 4 cpu's is rather poor at the moment.
+ */
+ fprintf(out, "memory 48000000\nPARALLEL IOMODE SCREENED\n");
+ fprintf(out, "ELEC %d\nMULT %d\nSUPER ON\nNOSYM\nGEOMETRY ANGSTROM\n",
+ qm->nelectrons, qm->multiplicity);
+ for (i = 0; i < qm->nrQMatoms; i++)
+ {
#ifdef DOUBLE
- fprintf(out,"%10.7lf %10.7lf %10.7lf %5.3lf %2s\n",
- i/2.,
- i/3.,
- i/4.,
- qm->atomicnumberQM[i]*1.0,
- periodic_system[qm->atomicnumberQM[i]]);
+ fprintf(out, "%10.7lf %10.7lf %10.7lf %5.3lf %2s\n",
+ i/2.,
+ i/3.,
+ i/4.,
+ qm->atomicnumberQM[i]*1.0,
+ periodic_system[qm->atomicnumberQM[i]]);
#else
- fprintf(out,"%10.7f %10.7f %10.7f %5.3f %2s\n",
- i/2.,
- i/3.,
- i/4.,
- qm->atomicnumberQM[i]*1.0,
- periodic_system[qm->atomicnumberQM[i]]);
+ fprintf(out, "%10.7f %10.7f %10.7f %5.3f %2s\n",
+ i/2.,
+ i/3.,
+ i/4.,
+ qm->atomicnumberQM[i]*1.0,
+ periodic_system[qm->atomicnumberQM[i]]);
#endif
- }
- if(mm->nrMMatoms){
- for (j=i;j<i+2;j++){
+ }
+ if (mm->nrMMatoms)
+ {
+ for (j = i; j < i+2; j++)
+ {
#ifdef DOUBLE
- fprintf(out,"%10.7lf %10.7lf %10.7lf %5.3lf BQ\n",
- j/5.,
- j/6.,
- j/7.,
- 1.0);
+ fprintf(out, "%10.7lf %10.7lf %10.7lf %5.3lf BQ\n",
+ j/5.,
+ j/6.,
+ j/7.,
+ 1.0);
#else
- fprintf(out,"%10.7f %10.7f %10.7f %5.3f BQ\n",
- j/5.,
- j/6.,
- j/7.,
- 2.0);
+ fprintf(out, "%10.7f %10.7f %10.7f %5.3f BQ\n",
+ j/5.,
+ j/6.,
+ j/7.,
+ 2.0);
#endif
- }
- }
- if(!qm->bTS)
- fprintf(out,"END\nBASIS %s\nRUNTYPE GRADIENT\nSCFTYPE %s\n",
- eQMbasis_names[qm->QMbasis],
- eQMmethod_names[qm->QMmethod]); /* see enum.h */
- else
- fprintf(out,"END\nBASIS %s\nRUNTYPE SADDLE\nSCFTYPE %s\n",
- eQMbasis_names[qm->QMbasis],
- eQMmethod_names[qm->QMmethod]); /* see enum.h */
- fclose(out);
+ }
+ }
+ if (!qm->bTS)
+ {
+ fprintf(out, "END\nBASIS %s\nRUNTYPE GRADIENT\nSCFTYPE %s\n",
+ eQMbasis_names[qm->QMbasis],
+ eQMmethod_names[qm->QMmethod]); /* see enum.h */
+ }
+ else
+ {
+ fprintf(out, "END\nBASIS %s\nRUNTYPE SADDLE\nSCFTYPE %s\n",
+ eQMbasis_names[qm->QMbasis],
+ eQMmethod_names[qm->QMmethod]); /* see enum.h */
+ }
+ fclose(out);
+ }
+ gmx_barrier(cr);
+ F77_FUNC(inigms, IMIGMS) ();
}
- gmx_barrier(cr);
- F77_FUNC(inigms,IMIGMS)();
- }
- else{ /* normal serial run */
-
- out=fopen("FOR009","w");
- /* of these options I am not completely sure.... the overall
- * preformance on more than 4 cpu's is rather poor at the moment.
- */
- fprintf(out,"ELEC %d\nMULT %d\nSUPER ON\nNOSYM\nGEOMETRY ANGSTROM\n",
- qm->nelectrons,qm->multiplicity);
- for (i=0;i<qm->nrQMatoms;i++){
+ else /* normal serial run */
+
+ {
+ out = fopen("FOR009", "w");
+ /* of these options I am not completely sure.... the overall
+ * preformance on more than 4 cpu's is rather poor at the moment.
+ */
+ fprintf(out, "ELEC %d\nMULT %d\nSUPER ON\nNOSYM\nGEOMETRY ANGSTROM\n",
+ qm->nelectrons, qm->multiplicity);
+ for (i = 0; i < qm->nrQMatoms; i++)
+ {
#ifdef DOUBLE
- fprintf(out,"%10.7lf %10.7lf %10.7lf %5.3lf %2s\n",
- i/2.,
- i/3.,
- i/4.,
- qm->atomicnumberQM[i]*1.0,
- periodic_system[qm->atomicnumberQM[i]]);
+ fprintf(out, "%10.7lf %10.7lf %10.7lf %5.3lf %2s\n",
+ i/2.,
+ i/3.,
+ i/4.,
+ qm->atomicnumberQM[i]*1.0,
+ periodic_system[qm->atomicnumberQM[i]]);
#else
- fprintf(out,"%10.7f %10.7f %10.7f %5.3f %2s\n",
- i/2.,
- i/3.,
- i/4.,
- qm->atomicnumberQM[i]*1.0,
- periodic_system[qm->atomicnumberQM[i]]);
+ fprintf(out, "%10.7f %10.7f %10.7f %5.3f %2s\n",
+ i/2.,
+ i/3.,
+ i/4.,
+ qm->atomicnumberQM[i]*1.0,
+ periodic_system[qm->atomicnumberQM[i]]);
#endif
- }
- if(mm->nrMMatoms){
- for (j=i;j<i+2;j++){
+ }
+ if (mm->nrMMatoms)
+ {
+ for (j = i; j < i+2; j++)
+ {
#ifdef DOUBLE
- fprintf(out,"%10.7lf %10.7lf %10.7lf %5.3lf BQ\n",
- j/5.,
- j/6.,
- j/7.,
- 1.0);
+ fprintf(out, "%10.7lf %10.7lf %10.7lf %5.3lf BQ\n",
+ j/5.,
+ j/6.,
+ j/7.,
+ 1.0);
#else
- fprintf(out,"%10.7f %10.7f %10.7f %5.3f BQ\n",
- j/5.,
- j/6.,
- j/7.,
- 2.0);
+ fprintf(out, "%10.7f %10.7f %10.7f %5.3f BQ\n",
+ j/5.,
+ j/6.,
+ j/7.,
+ 2.0);
#endif
- }
+ }
+ }
+ if (!qm->bTS)
+ {
+ fprintf(out, "END\nBASIS %s\nRUNTYPE GRADIENT\nSCFTYPE %s\n",
+ eQMbasis_names[qm->QMbasis],
+ eQMmethod_names[qm->QMmethod]); /* see enum.h */
+ }
+ else
+ {
+ fprintf(out, "END\nBASIS %s\nRUNTYPE SADDLE\nSCFTYPE %s\n",
+ eQMbasis_names[qm->QMbasis],
+ eQMmethod_names[qm->QMmethod]); /* see enum.h */
+ }
+ F77_FUNC(inigms, IMIGMS) ();
}
- if(!qm->bTS)
- fprintf(out,"END\nBASIS %s\nRUNTYPE GRADIENT\nSCFTYPE %s\n",
- eQMbasis_names[qm->QMbasis],
- eQMmethod_names[qm->QMmethod]); /* see enum.h */
- else
- fprintf(out,"END\nBASIS %s\nRUNTYPE SADDLE\nSCFTYPE %s\n",
- eQMbasis_names[qm->QMbasis],
- eQMmethod_names[qm->QMmethod]); /* see enum.h */
- F77_FUNC(inigms,IMIGMS)();
- }
}
-real call_gamess(t_commrec *cr, t_forcerec *fr, t_QMrec *qm, t_MMrec *mm,
- rvec f[], rvec fshift[])
+real call_gamess(t_commrec *cr, t_forcerec *fr, t_QMrec *qm, t_MMrec *mm,
+ rvec f[], rvec fshift[])
{
- /* do the actual QMMM calculation using GAMESS-UK. In this
- * implementation (3-2001) a system call is made to the GAMESS-UK
- * binary. Now we are working to get the electron integral, SCF, and
- * gradient routines linked directly
- */
- int
- i,j,rank;
- real
- QMener=0.0,*qmgrad,*mmgrad,*mmcrd,*qmcrd,energy;
- t_QMMMrec
- *qr;
+ /* do the actual QMMM calculation using GAMESS-UK. In this
+ * implementation (3-2001) a system call is made to the GAMESS-UK
+ * binary. Now we are working to get the electron integral, SCF, and
+ * gradient routines linked directly
+ */
+ int
+ i, j, rank;
+ real
+ QMener = 0.0, *qmgrad, *mmgrad, *mmcrd, *qmcrd, energy;
+ t_QMMMrec
+ *qr;
- /* copy the QMMMrec pointer */
- qr = fr->qr;
- snew(qmcrd, 3*(qm->nrQMatoms));
- snew(mmcrd,3*(mm->nrMMatoms));
- snew(qmgrad,3*(qm->nrQMatoms));
- snew(mmgrad,3*(mm->nrMMatoms));
-
- /* copy the data from qr into the arrays that are going to be used
- * in the fortran routines of gamess
- */
- for(i=0;i<qm->nrQMatoms;i++){
- for (j=0;j<DIM;j++){
- qmcrd[DIM*i+j] = 1/BOHR2NM*qm->xQM[i][j];
+ /* copy the QMMMrec pointer */
+ qr = fr->qr;
+ snew(qmcrd, 3*(qm->nrQMatoms));
+ snew(mmcrd, 3*(mm->nrMMatoms));
+ snew(qmgrad, 3*(qm->nrQMatoms));
+ snew(mmgrad, 3*(mm->nrMMatoms));
+
+ /* copy the data from qr into the arrays that are going to be used
+ * in the fortran routines of gamess
+ */
+ for (i = 0; i < qm->nrQMatoms; i++)
+ {
+ for (j = 0; j < DIM; j++)
+ {
+ qmcrd[DIM*i+j] = 1/BOHR2NM*qm->xQM[i][j];
+ }
}
- }
- for(i=0;i<mm->nrMMatoms;i++){
- for (j=0;j<DIM;j++){
- mmcrd[DIM*i+j] = 1/BOHR2NM*mm->xMM[i][j];
+ for (i = 0; i < mm->nrMMatoms; i++)
+ {
+ for (j = 0; j < DIM; j++)
+ {
+ mmcrd[DIM*i+j] = 1/BOHR2NM*mm->xMM[i][j];
+ }
+ }
+ for (i = 0; i < 3*qm->nrQMatoms; i += 3)
+ {
+ fprintf(stderr, "%8.5f, %8.5f, %8.5f\n",
+ qmcrd[i],
+ qmcrd[i+1],
+ qmcrd[i+2]);
}
- }
- for (i=0;i<3*qm->nrQMatoms;i+=3){
- fprintf(stderr,"%8.5f, %8.5f, %8.5f\n",
- qmcrd[i],
- qmcrd[i+1],
- qmcrd[i+2]);
- }
- F77_FUNC(grads,GRADS)(&qm->nrQMatoms,qmcrd,&mm->nrMMatoms,mm->MMcharges,
- mmcrd,qmgrad,mmgrad,&energy);
+ F77_FUNC(grads, GRADS) (&qm->nrQMatoms, qmcrd, &mm->nrMMatoms, mm->MMcharges,
+ mmcrd, qmgrad, mmgrad, &energy);
- for(i=0;i<qm->nrQMatoms;i++){
- for(j=0;j<DIM;j++){
- f[i][j] = HARTREE_BOHR2MD*qmgrad[3*i+j];
- fshift[i][j] = HARTREE_BOHR2MD*qmgrad[3*i+j];
+ for (i = 0; i < qm->nrQMatoms; i++)
+ {
+ for (j = 0; j < DIM; j++)
+ {
+ f[i][j] = HARTREE_BOHR2MD*qmgrad[3*i+j];
+ fshift[i][j] = HARTREE_BOHR2MD*qmgrad[3*i+j];
+ }
}
- }
- for(i=0;i<mm->nrMMatoms;i++){
- for(j=0;j<DIM;j++){
- f[i][j] = HARTREE_BOHR2MD*mmgrad[3*i+j];
- fshift[i][j] = HARTREE_BOHR2MD*mmgrad[3*i+j];
+ for (i = 0; i < mm->nrMMatoms; i++)
+ {
+ for (j = 0; j < DIM; j++)
+ {
+ f[i][j] = HARTREE_BOHR2MD*mmgrad[3*i+j];
+ fshift[i][j] = HARTREE_BOHR2MD*mmgrad[3*i+j];
+ }
}
- }
- /* convert a.u to kJ/mol */
- QMener=energy*HARTREE2KJ*AVOGADRO;
- return(QMener);
+ /* convert a.u to kJ/mol */
+ QMener = energy*HARTREE2KJ*AVOGADRO;
+ return(QMener);
}
#else
int
-gmx_qmmm_gamess_empty;
+ gmx_qmmm_gamess_empty;
#endif
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff