3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
9 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
10 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
11 * Copyright (c) 2001-2008, The GROMACS development team,
12 * check out http://www.gromacs.org for more information.
14 * This program is free software; you can redistribute it and/or
15 * modify it under the terms of the GNU General Public License
16 * as published by the Free Software Foundation; either version 2
17 * of the License, or (at your option) any later version.
19 * If you want to redistribute modifications, please consider that
20 * scientific software is very special. Version control is crucial -
21 * bugs must be traceable. We will be happy to consider code for
22 * inclusion in the official distribution, but derived work must not
23 * be called official GROMACS. Details are found in the README & COPYING
24 * files - if they are missing, get the official version at www.gromacs.org.
26 * To help us fund GROMACS development, we humbly ask that you cite
27 * the papers on the package - you can find them in the top README file.
29 * For more info, check our website at http://www.gromacs.org
32 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
43 int nrQMatoms; /* total nr of QM atoms */
44 rvec *xQM; /* shifted to center of box */
45 int *indexQM; /* atom i = atom indexQM[i] in mdrun */
46 int *atomicnumberQM;/* atomic numbers of QM atoms */
47 real *QMcharges; /* atomic charges of QM atoms(ONIOM) */
49 int QMcharge; /* charge of the QM system */
50 int multiplicity; /* multipicity (no of unpaired eln) */
51 int QMmethod; /* see enums.h for all methods */
52 int QMbasis; /* see enums.h for all bases */
53 int nelectrons; /* total number of elecs in QM region*/
54 gmx_bool bTS; /* Optimize a TS, only steep, no md */
55 gmx_bool bOPT; /* Optimize QM subsys, only steep, no md */
56 gmx_bool *frontatoms; /* qm atoms on the QM side of a QM-MM bond */
57 /* Gaussian specific stuff */
58 int nQMcpus; /* no. of CPUs used for the QM calc. */
59 int QMmem; /* memory for the gaussian calc. */
60 int accuracy; /* convergence criterium (E(-x)) */
61 gmx_bool cpmcscf; /* using cpmcscf(l1003)*/
65 char *orca_basename; /* basename for I/O with orca */
66 char *orca_dir; /* directory for ORCA */
69 /* Surface hopping stuff */
70 gmx_bool bSH; /* surface hopping (diabatic only) */
71 real SAon; /* at which energy gap the SA starts */
72 real SAoff; /* at which energy gap the SA stops */
73 int SAsteps; /* stepwise switchinng on the SA */
74 int SAstep; /* current state of SA */
86 int nrMMatoms; /* nr of MM atoms, updated every step*/
87 rvec *xMM; /* shifted to center of box */
88 int *indexMM; /* atom i = atom indexMM[I] in mdrun */
89 real *MMcharges; /* MM point charges in std QMMM calc.*/
91 int *MMatomtype; /* only important for semi-emp. */
93 /* gaussian specific stuff */
100 int QMMMscheme; /* ONIOM (multi-layer) or normal */
101 int nrQMlayers; /* number of QM layers (total layers +1 (MM)) */
102 t_QMrec **qm; /* atoms and run params for each QM group */
103 t_MMrec *mm; /* there can only be one MM subsystem ! */