Ejemplo n.º 1
0
void init_state(t_state *state,int natoms,int ngtc)
{
  int i;

  state->natoms = natoms;
  state->nrng   = 0;
  state->flags  = 0;
  state->lambda = 0;
  clear_mat(state->box);
  clear_mat(state->box_rel);
  clear_mat(state->boxv);
  clear_mat(state->pres_prev);
  init_gtc_state(state,ngtc);
  state->nalloc = state->natoms;
  if (state->nalloc > 0) {
    snew(state->x,state->nalloc);
    snew(state->v,state->nalloc);
  } else {
    state->x = NULL;
    state->v = NULL;
  }
  state->sd_X = NULL;
  state->cg_p = NULL;

  init_ekinstate(&state->ekinstate);

  init_energyhistory(&state->enerhist);

  state->ddp_count = 0;
  state->ddp_count_cg_gl = 0;
  state->cg_gl = NULL;
  state->cg_gl_nalloc = 0;
}
Ejemplo n.º 2
0
void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int dfhistNumLambda)
{
    int i;

    state->natoms    = natoms;
    state->flags     = 0;
    state->fep_state = 0;
    state->lambda    = 0;
    snew(state->lambda, efptNR);
    for (i = 0; i < efptNR; i++)
    {
        state->lambda[i] = 0;
    }
    state->veta   = 0;
    clear_mat(state->box);
    clear_mat(state->box_rel);
    clear_mat(state->boxv);
    clear_mat(state->pres_prev);
    clear_mat(state->svir_prev);
    clear_mat(state->fvir_prev);
    init_gtc_state(state, ngtc, nnhpres, nhchainlength);
    state->nalloc = state->natoms;
    if (state->nalloc > 0)
    {
        /* We need to allocate one element extra, since we might use
         * (unaligned) 4-wide SIMD loads to access rvec entries.
         */
        snew(state->x, state->nalloc + 1);
        snew(state->v, state->nalloc + 1);
    }
    else
    {
        state->x = NULL;
        state->v = NULL;
    }
    state->cg_p = NULL;
    zero_history(&state->hist);
    zero_ekinstate(&state->ekinstate);
    snew(state->enerhist, 1);
    init_energyhistory(state->enerhist);
    if (dfhistNumLambda > 0)
    {
        snew(state->dfhist, 1);
        init_df_history(state->dfhist, dfhistNumLambda);
    }
    else
    {
        state->dfhist = NULL;
    }
    state->swapstate       = NULL;
    state->edsamstate      = NULL;
    state->ddp_count       = 0;
    state->ddp_count_cg_gl = 0;
    state->cg_gl           = NULL;
    state->cg_gl_nalloc    = 0;
}
Ejemplo n.º 3
0
void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int nlambda)
{
    int i;

    state->natoms    = natoms;
    state->flags     = 0;
    state->fep_state = 0;
    state->lambda    = 0;
    snew(state->lambda, efptNR);
    for (i = 0; i < efptNR; i++)
    {
        state->lambda[i] = 0;
    }
    state->veta   = 0;
    clear_mat(state->box);
    clear_mat(state->box_rel);
    clear_mat(state->boxv);
    clear_mat(state->pres_prev);
    clear_mat(state->svir_prev);
    clear_mat(state->fvir_prev);
    init_gtc_state(state, ngtc, nnhpres, nhchainlength);
    state->nalloc = state->natoms;
    if (state->nalloc > 0)
    {
        snew(state->x, state->nalloc);
        snew(state->v, state->nalloc);
    }
    else
    {
        state->x = NULL;
        state->v = NULL;
    }
    state->sd_X = NULL;
    state->cg_p = NULL;
    zero_history(&state->hist);
    zero_ekinstate(&state->ekinstate);
    snew(state->enerhist, 1);
    init_energyhistory(state->enerhist);
    init_df_history(&state->dfhist, nlambda);
    init_swapstate(&state->swapstate);
    state->ddp_count       = 0;
    state->ddp_count_cg_gl = 0;
    state->cg_gl           = NULL;
    state->cg_gl_nalloc    = 0;
}
Ejemplo n.º 4
0
void set_state_entries(t_state *state, const t_inputrec *ir)
{
    /* The entries in the state in the tpx file might not correspond
     * with what is needed, so we correct this here.
     */
    state->flags = 0;
    if (ir->efep != efepNO || ir->bExpanded)
    {
        state->flags |= (1<<estLAMBDA);
        state->flags |= (1<<estFEPSTATE);
    }
    state->flags |= (1<<estX);
    if (state->lambda == NULL)
    {
        snew(state->lambda, efptNR);
    }
    if (state->x == NULL)
    {
        snew(state->x, state->nalloc);
    }
    if (EI_DYNAMICS(ir->eI))
    {
        state->flags |= (1<<estV);
        if (state->v == NULL)
        {
            snew(state->v, state->nalloc);
        }
    }
    if (ir->eI == eiSD2)
    {
        state->flags |= (1<<estSDX);
        if (state->sd_X == NULL)
        {
            /* sd_X is not stored in the tpx file, so we need to allocate it */
            snew(state->sd_X, state->nalloc);
        }
    }
    if (ir->eI == eiCG)
    {
        state->flags |= (1<<estCGP);
        if (state->cg_p == NULL)
        {
            /* cg_p is not stored in the tpx file, so we need to allocate it */
            snew(state->cg_p, state->nalloc);
        }
    }

    state->nnhpres = 0;
    if (ir->ePBC != epbcNONE)
    {
        state->flags |= (1<<estBOX);
        if (PRESERVE_SHAPE(*ir))
        {
            state->flags |= (1<<estBOX_REL);
        }
        if ((ir->epc == epcPARRINELLORAHMAN) || (ir->epc == epcMTTK))
        {
            state->flags |= (1<<estBOXV);
        }
        if (ir->epc != epcNO)
        {
            if (IR_NPT_TROTTER(ir) || (IR_NPH_TROTTER(ir)))
            {
                state->nnhpres = 1;
                state->flags  |= (1<<estNHPRES_XI);
                state->flags  |= (1<<estNHPRES_VXI);
                state->flags  |= (1<<estSVIR_PREV);
                state->flags  |= (1<<estFVIR_PREV);
                state->flags  |= (1<<estVETA);
                state->flags  |= (1<<estVOL0);
            }
            else
            {
                state->flags |= (1<<estPRES_PREV);
            }
        }
    }

    if (ir->etc == etcNOSEHOOVER)
    {
        state->flags |= (1<<estNH_XI);
        state->flags |= (1<<estNH_VXI);
    }

    if (ir->etc == etcVRESCALE)
    {
        state->flags |= (1<<estTC_INT);
    }

    init_gtc_state(state, state->ngtc, state->nnhpres, ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
    init_ekinstate(&state->ekinstate, ir);

    init_energyhistory(&state->enerhist);
    init_df_history(&state->dfhist, ir->fepvals->n_lambda);
    state->swapstate.eSwapCoords = ir->eSwapCoords;
}
Ejemplo n.º 5
0
static void set_state_entries(t_state *state,t_inputrec *ir,int nnodes)
{
  /* The entries in the state in the tpx file might not correspond
   * with what is needed, so we correct this here.
   */
  state->flags = 0;
  if (ir->efep != efepNO)
    state->flags |= (1<<estLAMBDA);
  state->flags |= (1<<estX);
  if (state->x == NULL)
    snew(state->x,state->nalloc);
  if (EI_DYNAMICS(ir->eI)) {
    state->flags |= (1<<estV);
    if (state->v == NULL)
      snew(state->v,state->nalloc);
  }
  if (ir->eI == eiSD2) {
    state->flags |= (1<<estSDX);
    if (state->sd_X == NULL) {
      /* sd_X is not stored in the tpx file, so we need to allocate it */
      snew(state->sd_X,state->nalloc);
    }
  }
  if (ir->eI == eiCG) {
    state->flags |= (1<<estCGP);
  }
  if (EI_SD(ir->eI) || ir->eI == eiBD || ir->etc == etcVRESCALE) {
    state->nrng  = gmx_rng_n();
    state->nrngi = 1;
    if (EI_SD(ir->eI) || ir->eI == eiBD) {
      /* This will be correct later with DD */
      state->nrng  *= nnodes;
      state->nrngi *= nnodes;
    }
    state->flags |= ((1<<estLD_RNG) | (1<<estLD_RNGI));
    snew(state->ld_rng, state->nrng);
    snew(state->ld_rngi,state->nrngi);
  } else {
    state->nrng = 0;
  }
  if (ir->ePBC != epbcNONE) {
    state->flags |= (1<<estBOX);
    if (PRESERVE_SHAPE(*ir)) {
      state->flags |= (1<<estBOX_REL);
    }
    if (ir->epc == epcPARRINELLORAHMAN) {
      state->flags |= (1<<estBOXV);
    }
    if (ir->epc != epcNO) {
      state->flags |= (1<<estPRES_PREV);
    }
    if (ir->etc == etcNOSEHOOVER) {
      state->flags |= (1<<estNH_XI);
    }
  }
  if (ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) {
    state->flags |= (1<<estTC_INT);
  }

  init_ekinstate(&state->ekinstate,ir);

  init_energyhistory(&state->enerhist);
}
Ejemplo n.º 6
0
void set_state_entries(t_state *state, const t_inputrec *ir)
{
    /* The entries in the state in the tpx file might not correspond
     * with what is needed, so we correct this here.
     */
    state->flags = 0;
    if (ir->efep != efepNO || ir->bExpanded)
    {
        state->flags |= (1<<estLAMBDA);
        state->flags |= (1<<estFEPSTATE);
    }
    state->flags |= (1<<estX);
    if (state->lambda == NULL)
    {
        snew(state->lambda, efptNR);
    }
    if (state->x == NULL)
    {
        /* We need to allocate one element extra, since we might use
         * (unaligned) 4-wide SIMD loads to access rvec entries.
         */
        snew(state->x, state->nalloc + 1);
    }
    if (EI_DYNAMICS(ir->eI))
    {
        state->flags |= (1<<estV);
        if (state->v == NULL)
        {
            snew(state->v, state->nalloc + 1);
        }
    }
    if (ir->eI == eiCG)
    {
        state->flags |= (1<<estCGP);
        if (state->cg_p == NULL)
        {
            /* cg_p is not stored in the tpx file, so we need to allocate it */
            snew(state->cg_p, state->nalloc + 1);
        }
    }

    state->nnhpres = 0;
    if (ir->ePBC != epbcNONE)
    {
        state->flags |= (1<<estBOX);
        if (inputrecPreserveShape(ir))
        {
            state->flags |= (1<<estBOX_REL);
        }
        if ((ir->epc == epcPARRINELLORAHMAN) || (ir->epc == epcMTTK))
        {
            state->flags |= (1<<estBOXV);
        }
        if (ir->epc != epcNO)
        {
            if (inputrecNptTrotter(ir) || (inputrecNphTrotter(ir)))
            {
                state->nnhpres = 1;
                state->flags  |= (1<<estNHPRES_XI);
                state->flags  |= (1<<estNHPRES_VXI);
                state->flags  |= (1<<estSVIR_PREV);
                state->flags  |= (1<<estFVIR_PREV);
                state->flags  |= (1<<estVETA);
                state->flags  |= (1<<estVOL0);
            }
            else
            {
                state->flags |= (1<<estPRES_PREV);
            }
        }
    }

    if (ir->etc == etcNOSEHOOVER)
    {
        state->flags |= (1<<estNH_XI);
        state->flags |= (1<<estNH_VXI);
    }

    if (ir->etc == etcVRESCALE)
    {
        state->flags |= (1<<estTC_INT);
    }

    init_gtc_state(state, state->ngtc, state->nnhpres, ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
    init_ekinstate(&state->ekinstate, ir);
    snew(state->enerhist, 1);
    init_energyhistory(state->enerhist);
    init_df_history(&state->dfhist, ir->fepvals->n_lambda);
    state->swapstate.eSwapCoords = ir->eSwapCoords;
}