src/gromacs/mdlib/enerdata_utils.cpp

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  38 #include "gmxpre.h"
  39
  40 #include "enerdata_utils.h"
  41
  42 #include "gromacs/mdtypes/enerdata.h"
  43 #include "gromacs/mdtypes/inputrec.h"
  44 #include "gromacs/utility/fatalerror.h"
  45 #include "gromacs/utility/smalloc.h"
  46
  47 gmx_enerdata_t::gmx_enerdata_t(int numEnergyGroups, int numFepLambdas) :
  48     grpp(numEnergyGroups),
  49     enerpart_lambda(numFepLambdas == 0 ? 0 : numFepLambdas + 1),
  50     foreign_grpp(numEnergyGroups)
  51 {
  52 }
  53
  54 static real sum_v(int n, gmx::ArrayRef<const real> v)
  55 {
  56     real t;
  57     int  i;
  58
  59     t = 0.0;
  60     for (i = 0; (i < n); i++)
  61     {
  62         t = t + v[i];
  63     }
  64
  65     return t;
  66 }
  67
  68 void sum_epot(gmx_grppairener_t* grpp, real* epot)
  69 {
  70     int i;
  71
  72     /* Accumulate energies */
  73     epot[F_COUL_SR] = sum_v(grpp->nener, grpp->ener[egCOULSR]);
  74     epot[F_LJ]      = sum_v(grpp->nener, grpp->ener[egLJSR]);
  75     epot[F_LJ14]    = sum_v(grpp->nener, grpp->ener[egLJ14]);
  76     epot[F_COUL14]  = sum_v(grpp->nener, grpp->ener[egCOUL14]);
  77
  78     /* lattice part of LR doesnt belong to any group
  79      * and has been added earlier
  80      */
  81     epot[F_BHAM] = sum_v(grpp->nener, grpp->ener[egBHAMSR]);
  82
  83     epot[F_EPOT] = 0;
  84     for (i = 0; (i < F_EPOT); i++)
  85     {
  86         if (i != F_DISRESVIOL && i != F_ORIRESDEV)
  87         {
  88             epot[F_EPOT] += epot[i];
  89         }
  90     }
  91 }
  92
  93 void sum_dhdl(gmx_enerdata_t* enerd, gmx::ArrayRef<const real> lambda, const t_lambda& fepvals)
  94 {
  95     int index;
  96
  97     enerd->dvdl_lin[efptVDW] += enerd->term[F_DVDL_VDW]; /* include dispersion correction */
  98     enerd->term[F_DVDL] = 0.0;
  99     for (int i = 0; i < efptNR; i++)
 100     {
 101         if (fepvals.separate_dvdl[i])
 102         {
 103             /* could this be done more readably/compactly? */
 104             switch (i)
 105             {
 106                 case (efptMASS): index = F_DKDL; break;
 107                 case (efptCOUL): index = F_DVDL_COUL; break;
 108                 case (efptVDW): index = F_DVDL_VDW; break;
 109                 case (efptBONDED): index = F_DVDL_BONDED; break;
 110                 case (efptRESTRAINT): index = F_DVDL_RESTRAINT; break;
 111                 default: index = F_DVDL; break;
 112             }
 113             enerd->term[index] = enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
 114             if (debug)
 115             {
 116                 fprintf(debug, "dvdl-%s[%2d]: %f: non-linear %f + linear %f\n", efpt_names[i], i,
 117                         enerd->term[index], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
 118             }
 119         }
 120         else
 121         {
 122             enerd->term[F_DVDL] += enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
 123             if (debug)
 124             {
 125                 fprintf(debug, "dvd-%sl[%2d]: %f: non-linear %f + linear %f\n", efpt_names[0], i,
 126                         enerd->term[F_DVDL], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
 127             }
 128         }
 129     }
 130
 131     if (fepvals.separate_dvdl[efptBONDED])
 132     {
 133         enerd->term[F_DVDL_BONDED] += enerd->term[F_DVDL_CONSTR];
 134     }
 135     else
 136     {
 137         enerd->term[F_DVDL] += enerd->term[F_DVDL_CONSTR];
 138     }
 139
 140     for (int i = 0; i < fepvals.n_lambda; i++)
 141     {
 142         /* note we are iterating over fepvals here!
 143            For the current lam, dlam = 0 automatically,
 144            so we don't need to add anything to the
 145            enerd->enerpart_lambda[0] */
 146
 147         /* we don't need to worry about dvdl_lin contributions to dE at
 148            current lambda, because the contributions to the current
 149            lambda are automatically zeroed */
 150
 151         double& enerpart_lambda = enerd->enerpart_lambda[i + 1];
 152
 153         for (gmx::index j = 0; j < lambda.ssize(); j++)
 154         {
 155             /* Note that this loop is over all dhdl components, not just the separated ones */
 156             const double dlam = fepvals.all_lambda[j][i] - lambda[j];
 157
 158             enerpart_lambda += dlam * enerd->dvdl_lin[j];
 159
 160             /* Constraints can not be evaluated at foreign lambdas, so we add
 161              * a linear extrapolation. This is an approximation, but usually
 162              * quite accurate since constraints change little between lambdas.
 163              */
 164             if ((j == efptBONDED && fepvals.separate_dvdl[efptBONDED])
 165                 || (j == efptFEP && !fepvals.separate_dvdl[efptBONDED]))
 166             {
 167                 enerpart_lambda += dlam * enerd->term[F_DVDL_CONSTR];
 168             }
 169
 170             if (j == efptMASS && !fepvals.separate_dvdl[j])
 171             {
 172                 enerpart_lambda += dlam * enerd->term[F_DKDL];
 173             }
 174
 175             if (debug)
 176             {
 177                 fprintf(debug, "enerdiff lam %g: (%15s), non-linear %f linear %f*%f\n",
 178                         fepvals.all_lambda[j][i], efpt_names[j],
 179                         enerpart_lambda - enerd->enerpart_lambda[0], dlam, enerd->dvdl_lin[j]);
 180             }
 181         }
 182     }
 183
 184     /* The constrain contribution is now included in other terms, so clear it */
 185     enerd->term[F_DVDL_CONSTR] = 0;
 186 }
 187
 188
 189 void reset_foreign_enerdata(gmx_enerdata_t* enerd)
 190 {
 191     int i, j;
 192
 193     /* First reset all foreign energy components.  Foreign energies always called on
 194        neighbor search steps */
 195     for (i = 0; (i < egNR); i++)
 196     {
 197         for (j = 0; (j < enerd->grpp.nener); j++)
 198         {
 199             enerd->foreign_grpp.ener[i][j] = 0.0;
 200         }
 201     }
 202
 203     /* potential energy components */
 204     for (i = 0; (i <= F_EPOT); i++)
 205     {
 206         enerd->foreign_term[i] = 0.0;
 207     }
 208 }
 209
 210 void reset_enerdata(gmx_enerdata_t* enerd)
 211 {
 212     int i, j;
 213
 214     /* First reset all energy components. */
 215     for (i = 0; (i < egNR); i++)
 216     {
 217         for (j = 0; (j < enerd->grpp.nener); j++)
 218         {
 219             enerd->grpp.ener[i][j] = 0.0;
 220         }
 221     }
 222     for (i = 0; i < efptNR; i++)
 223     {
 224         enerd->dvdl_lin[i]    = 0.0;
 225         enerd->dvdl_nonlin[i] = 0.0;
 226     }
 227
 228     /* Normal potential energy components */
 229     for (i = 0; (i <= F_EPOT); i++)
 230     {
 231         enerd->term[i] = 0.0;
 232     }
 233     enerd->term[F_DVDL]           = 0.0;
 234     enerd->term[F_DVDL_COUL]      = 0.0;
 235     enerd->term[F_DVDL_VDW]       = 0.0;
 236     enerd->term[F_DVDL_BONDED]    = 0.0;
 237     enerd->term[F_DVDL_RESTRAINT] = 0.0;
 238     enerd->term[F_DKDL]           = 0.0;
 239     std::fill(enerd->enerpart_lambda.begin(), enerd->enerpart_lambda.end(), 0);
 240     /* reset foreign energy data - separate function since we also call it elsewhere */
 241     reset_foreign_enerdata(enerd);
 242 }