src/gromacs/gmxpreprocess/readadress.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2009 Christoph Junghans, Brad Lambeth.
   5  * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
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  36 #include "gmxpre.h"
  37
  38 #include <stdlib.h>
  39 #include <string.h>
  40
  41 #include "gromacs/gmxpreprocess/readir.h"
  42 #include "gromacs/legacyheaders/names.h"
  43 #include "gromacs/legacyheaders/types/inputrec.h"
  44 #include "gromacs/utility/cstringutil.h"
  45 #include "gromacs/utility/fatalerror.h"
  46 #include "gromacs/utility/smalloc.h"
  47
  48 #define MAXPTR 254
  49
  50 static char adress_refs[STRLEN], adress_tf_grp_names[STRLEN], adress_cg_grp_names[STRLEN];
  51
  52 void read_adressparams(int *ninp_p, t_inpfile **inp_p, t_adress *adress, warninp_t wi)
  53 {
  54     int         nadress_refs, i;
  55     const char *tmp;
  56     char       *ptr1[MAXPTR];
  57
  58
  59     int        ninp;
  60     t_inpfile *inp;
  61
  62     ninp   = *ninp_p;
  63     inp    = *inp_p;
  64
  65     EETYPE("adress_type",                adress->type,         eAdresstype_names);
  66     RTYPE ("adress_const_wf",            adress->const_wf,     1);
  67     RTYPE ("adress_ex_width",            adress->ex_width,     0);
  68     RTYPE ("adress_hy_width",            adress->hy_width,     0);
  69     RTYPE ("adress_ex_forcecap",         adress->ex_forcecap,     0);
  70     EETYPE("adress_interface_correction", adress->icor,         eAdressICtype_names);
  71     EETYPE("adress_site",                adress->site,         eAdressSITEtype_names);
  72     STYPE ("adress_reference_coords",    adress_refs,             NULL);
  73     STYPE ("adress_tf_grp_names",        adress_tf_grp_names,     NULL);
  74     STYPE ("adress_cg_grp_names",        adress_cg_grp_names,     NULL);
  75     EETYPE("adress_do_hybridpairs",      adress->do_hybridpairs, yesno_names);
  76
  77     nadress_refs = str_nelem(adress_refs, MAXPTR, ptr1);
  78
  79     for (i = 0; (i < nadress_refs); i++) /*read vector components*/
  80     {
  81         adress->refs[i] = strtod(ptr1[i], NULL);
  82     }
  83     for (; (i < DIM); i++) /*remaining undefined components of the vector set to zero*/
  84     {
  85         adress->refs[i] = 0;
  86     }
  87
  88     *ninp_p   = ninp;
  89     *inp_p    = inp;
  90 }
  91
  92 void do_adress_index(t_adress *adress, gmx_groups_t *groups, char **gnames, t_grpopts *opts, warninp_t wi)
  93 {
  94     int      nr, i, j, k;
  95     char    *ptr1[MAXPTR];
  96     int      nadress_cg_grp_names, nadress_tf_grp_names;
  97
  98     /* AdResS coarse grained groups input */
  99
 100     nr = groups->grps[egcENER].nr;
 101     snew(adress->group_explicit, nr);
 102     for (i = 0; i < nr; i++)
 103     {
 104         adress->group_explicit[i] = TRUE;
 105     }
 106     adress->n_energy_grps = nr;
 107
 108     nadress_cg_grp_names = str_nelem(adress_cg_grp_names, MAXPTR, ptr1);
 109
 110     if (nadress_cg_grp_names > 0)
 111     {
 112         for (i = 0; i < nadress_cg_grp_names; i++)
 113         {
 114             /* search for the group name mathching the tf group name */
 115             k = 0;
 116             while ((k < nr) &&
 117                    gmx_strcasecmp(ptr1[i], (char*)(gnames[groups->grps[egcENER].nm_ind[k]])))
 118             {
 119                 k++;
 120             }
 121             if (k == nr)
 122             {
 123                 gmx_fatal(FARGS, "Adress cg energy group %s not found\n", ptr1[i]);
 124             }
 125             adress->group_explicit[k] = FALSE;
 126             printf ("AdResS: Energy group %s is treated as coarse-grained \n",
 127                     (char*)(gnames[groups->grps[egcENER].nm_ind[k]]));
 128         }
 129         /* set energy group exclusions between all coarse-grained and explicit groups */
 130         for (j = 0; j < nr; j++)
 131         {
 132             for (k = 0; k < nr; k++)
 133             {
 134                 if (!(adress->group_explicit[k] == adress->group_explicit[j]))
 135                 {
 136                     opts->egp_flags[nr * j + k] |= EGP_EXCL;
 137                     if (debug)
 138                     {
 139                         fprintf(debug, "AdResS excl %s %s \n",
 140                                 (char*)(gnames[groups->grps[egcENER].nm_ind[j]]),
 141                                 (char*)(gnames[groups->grps[egcENER].nm_ind[k]]));
 142                     }
 143                 }
 144             }
 145         }
 146     }
 147     else
 148     {
 149         warning(wi, "For an AdResS simulation at least one coarse-grained energy group has to be specified in adress_cg_grp_names");
 150     }
 151
 152
 153     /* AdResS multiple tf tables input */
 154     nadress_tf_grp_names = str_nelem(adress_tf_grp_names, MAXPTR, ptr1);
 155     adress->n_tf_grps    = nadress_tf_grp_names;
 156     snew(adress->tf_table_index, nadress_tf_grp_names);
 157
 158     nr = groups->grps[egcENER].nr;
 159
 160     if (nadress_tf_grp_names > 0)
 161     {
 162         for (i = 0; i < nadress_tf_grp_names; i++)
 163         {
 164             /* search for the group name mathching the tf group name */
 165             k = 0;
 166             while ((k < nr) &&
 167                    gmx_strcasecmp(ptr1[i], (char*)(gnames[groups->grps[egcENER].nm_ind[k]])))
 168             {
 169                 k++;
 170             }
 171             if (k == nr)
 172             {
 173                 gmx_fatal(FARGS, "Adress tf energy group %s not found\n", ptr1[i]);
 174             }
 175
 176             adress->tf_table_index[i] = k;
 177             if (debug)
 178             {
 179                 fprintf(debug, "found tf group %s id %d \n", ptr1[i], k);
 180             }
 181             if (adress->group_explicit[k])
 182             {
 183                 gmx_fatal(FARGS, "Thermodynamic force group %s is not a coarse-grained group in adress_cg_grp_names. The thermodynamic force has to act on the coarse-grained vsite of a molecule.\n", ptr1[i]);
 184             }
 185
 186         }
 187     }
 188     /* end AdResS multiple tf tables input */
 189
 190
 191 }