--- /dev/null
+/*
+ * 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.
+ * 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
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <ctype.h>
+#include <stdlib.h>
+#include <limits.h>
+#include "sysstuff.h"
+#include "smalloc.h"
+#include "typedefs.h"
+#include "physics.h"
+#include "names.h"
+#include "gmx_fatal.h"
+#include "macros.h"
+#include "index.h"
+#include "symtab.h"
+#include "string2.h"
+#include "readinp.h"
+#include "warninp.h"
+#include "readir.h"
+#include "toputil.h"
+#include "index.h"
+#include "network.h"
+#include "vec.h"
+#include "pbc.h"
+#include "mtop_util.h"
+#include "chargegroup.h"
+#include "inputrec.h"
+#include "calc_verletbuf.h"
+
+#define MAXPTR 254
+#define NOGID 255
+
+/* Resource parameters
+ * Do not change any of these until you read the instruction
+ * in readinp.h. Some cpp's do not take spaces after the backslash
+ * (like the c-shell), which will give you a very weird compiler
+ * message.
+ */
+
+typedef struct t_inputrec_strings
+{
+ char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
+ acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
+ energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
+ couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
+ wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN];
+ char fep_lambda[efptNR][STRLEN];
+ char lambda_weights[STRLEN];
+ char **pull_grp;
+ char **rot_grp;
+ char anneal[STRLEN], anneal_npoints[STRLEN],
+ anneal_time[STRLEN], anneal_temp[STRLEN];
+ char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
+ bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
+ SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
+ char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
+ efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
+
+} gmx_inputrec_strings;
+
+static gmx_inputrec_strings *is = NULL;
+
+void init_inputrec_strings()
+{
+ if (is)
+ {
+ gmx_incons("Attempted to call init_inputrec_strings before calling done_inputrec_strings. Only one inputrec (i.e. .mdp file) can be parsed at a time.");
+ }
+ snew(is, 1);
+}
+
+void done_inputrec_strings()
+{
+ sfree(is);
+ is = NULL;
+}
+
+static char swapgrp[STRLEN], splitgrp0[STRLEN], splitgrp1[STRLEN], solgrp[STRLEN];
+
+enum {
+ egrptpALL, /* All particles have to be a member of a group. */
+ egrptpALL_GENREST, /* A rest group with name is generated for particles *
+ * that are not part of any group. */
+ egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
+ * for the rest group. */
+ egrptpONE /* Merge all selected groups into one group, *
+ * make a rest group for the remaining particles. */
+};
+
+static const char *constraints[eshNR+1] = {
+ "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
+};
+
+static const char *couple_lam[ecouplamNR+1] = {
+ "vdw-q", "vdw", "q", "none", NULL
+};
+
+void init_ir(t_inputrec *ir, t_gromppopts *opts)
+{
+ snew(opts->include, STRLEN);
+ snew(opts->define, STRLEN);
+ snew(ir->fepvals, 1);
+ snew(ir->expandedvals, 1);
+ snew(ir->simtempvals, 1);
+}
+
+static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
+{
+
+ int i;
+
+ for (i = 0; i < ntemps; i++)
+ {
+ /* simple linear scaling -- allows more control */
+ if (simtemp->eSimTempScale == esimtempLINEAR)
+ {
+ simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
+ }
+ else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
+ {
+ simtemp->temperatures[i] = simtemp->simtemp_low * pow(simtemp->simtemp_high/simtemp->simtemp_low, (1.0*i)/(ntemps-1));
+ }
+ else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
+ {
+ simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*((exp(temperature_lambdas[i])-1)/(exp(1.0)-1));
+ }
+ else
+ {
+ char errorstr[128];
+ sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
+ gmx_fatal(FARGS, errorstr);
+ }
+ }
+}
+
+
+
+static void _low_check(gmx_bool b, char *s, warninp_t wi)
+{
+ if (b)
+ {
+ warning_error(wi, s);
+ }
+}
+
+static void check_nst(const char *desc_nst, int nst,
+ const char *desc_p, int *p,
+ warninp_t wi)
+{
+ char buf[STRLEN];
+
+ if (*p > 0 && *p % nst != 0)
+ {
+ /* Round up to the next multiple of nst */
+ *p = ((*p)/nst + 1)*nst;
+ sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
+ desc_p, desc_nst, desc_p, *p);
+ warning(wi, buf);
+ }
+}
+
+static gmx_bool ir_NVE(const t_inputrec *ir)
+{
+ return ((ir->eI == eiMD || EI_VV(ir->eI)) && ir->etc == etcNO);
+}
+
+static int lcd(int n1, int n2)
+{
+ int d, i;
+
+ d = 1;
+ for (i = 2; (i <= n1 && i <= n2); i++)
+ {
+ if (n1 % i == 0 && n2 % i == 0)
+ {
+ d = i;
+ }
+ }
+
+ return d;
+}
+
+static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
+{
+ if (*eintmod == eintmodPOTSHIFT_VERLET)
+ {
+ if (ir->cutoff_scheme == ecutsVERLET)
+ {
+ *eintmod = eintmodPOTSHIFT;
+ }
+ else
+ {
+ *eintmod = eintmodNONE;
+ }
+ }
+}
+
+void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
+ warninp_t wi)
+/* Check internal consistency */
+{
+ /* Strange macro: first one fills the err_buf, and then one can check
+ * the condition, which will print the message and increase the error
+ * counter.
+ */
+#define CHECK(b) _low_check(b, err_buf, wi)
+ char err_buf[256], warn_buf[STRLEN];
+ int i, j;
+ int ns_type = 0;
+ real dt_coupl = 0;
+ real dt_pcoupl;
+ int nstcmin;
+ t_lambda *fep = ir->fepvals;
+ t_expanded *expand = ir->expandedvals;
+
+ set_warning_line(wi, mdparin, -1);
+
+ /* BASIC CUT-OFF STUFF */
+ if (ir->rcoulomb < 0)
+ {
+ warning_error(wi, "rcoulomb should be >= 0");
+ }
+ if (ir->rvdw < 0)
+ {
+ warning_error(wi, "rvdw should be >= 0");
+ }
+ if (ir->rlist < 0 &&
+ !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
+ {
+ warning_error(wi, "rlist should be >= 0");
+ }
+
+ process_interaction_modifier(ir, &ir->coulomb_modifier);
+ process_interaction_modifier(ir, &ir->vdw_modifier);
+
+ if (ir->cutoff_scheme == ecutsGROUP)
+ {
+ warning_note(wi,
+ "The group cutoff scheme is deprecated in Gromacs 5.0 and will be removed in a future "
+ "release when all interaction forms are supported for the verlet scheme. The verlet "
+ "scheme already scales better, and it is compatible with GPUs and other accelerators.");
+
+ /* BASIC CUT-OFF STUFF */
+ if (ir->rlist == 0 ||
+ !((ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > ir->rlist) ||
+ (ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > ir->rlist)))
+ {
+ /* No switched potential and/or no twin-range:
+ * we can set the long-range cut-off to the maximum of the other cut-offs.
+ */
+ ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
+ }
+ else if (ir->rlistlong < 0)
+ {
+ ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
+ sprintf(warn_buf, "rlistlong was not set, setting it to %g (no buffer)",
+ ir->rlistlong);
+ warning(wi, warn_buf);
+ }
+ if (ir->rlistlong == 0 && ir->ePBC != epbcNONE)
+ {
+ warning_error(wi, "Can not have an infinite cut-off with PBC");
+ }
+ if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist))
+ {
+ warning_error(wi, "rlistlong can not be shorter than rlist");
+ }
+ if (IR_TWINRANGE(*ir) && ir->nstlist <= 0)
+ {
+ warning_error(wi, "Can not have nstlist<=0 with twin-range interactions");
+ }
+ }
+
+ if (ir->rlistlong == ir->rlist)
+ {
+ ir->nstcalclr = 0;
+ }
+ else if (ir->rlistlong > ir->rlist && ir->nstcalclr == 0)
+ {
+ warning_error(wi, "With different cutoffs for electrostatics and VdW, nstcalclr must be -1 or a positive number");
+ }
+
+ if (ir->cutoff_scheme == ecutsVERLET)
+ {
+ real rc_max;
+
+ /* Normal Verlet type neighbor-list, currently only limited feature support */
+ if (inputrec2nboundeddim(ir) < 3)
+ {
+ warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
+ }
+ if (ir->rcoulomb != ir->rvdw)
+ {
+ warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported");
+ }
+ if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
+ {
+ if (ir->vdw_modifier == eintmodNONE ||
+ ir->vdw_modifier == eintmodPOTSHIFT)
+ {
+ ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
+
+ sprintf(warn_buf, "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
+ warning_note(wi, warn_buf);
+
+ ir->vdwtype = evdwCUT;
+ }
+ else
+ {
+ sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
+ warning_error(wi, warn_buf);
+ }
+ }
+
+ if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
+ {
+ warning_error(wi, "With Verlet lists only cut-off and PME LJ interactions are supported");
+ }
+ if (!(ir->coulombtype == eelCUT ||
+ (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC) ||
+ EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
+ {
+ warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
+ }
+ if (!(ir->coulomb_modifier == eintmodNONE ||
+ ir->coulomb_modifier == eintmodPOTSHIFT))
+ {
+ sprintf(warn_buf, "coulomb_modifier=%s is not supported with the Verlet cut-off scheme", eintmod_names[ir->coulomb_modifier]);
+ warning_error(wi, warn_buf);
+ }
+
+ if (ir->nstlist <= 0)
+ {
+ warning_error(wi, "With Verlet lists nstlist should be larger than 0");
+ }
+
+ if (ir->nstlist < 10)
+ {
+ warning_note(wi, "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation.");
+ }
+
+ rc_max = max(ir->rvdw, ir->rcoulomb);
+
+ if (ir->verletbuf_tol <= 0)
+ {
+ if (ir->verletbuf_tol == 0)
+ {
+ warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
+ }
+
+ if (ir->rlist < rc_max)
+ {
+ warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
+ }
+
+ if (ir->rlist == rc_max && ir->nstlist > 1)
+ {
+ warning_note(wi, "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet buffer. The cluster pair list does have a buffering effect, but choosing a larger rlist might be necessary for good energy conservation.");
+ }
+ }
+ else
+ {
+ if (ir->rlist > rc_max)
+ {
+ warning_note(wi, "You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance.");
+ }
+
+ if (ir->nstlist == 1)
+ {
+ /* No buffer required */
+ ir->rlist = rc_max;
+ }
+ else
+ {
+ if (EI_DYNAMICS(ir->eI))
+ {
+ if (inputrec2nboundeddim(ir) < 3)
+ {
+ warning_error(wi, "The box volume is required for calculating rlist from the energy drift with verlet-buffer-tolerance > 0. You are using at least one unbounded dimension, so no volume can be computed. Either use a finite box, or set rlist yourself together with verlet-buffer-tolerance = -1.");
+ }
+ /* Set rlist temporarily so we can continue processing */
+ ir->rlist = rc_max;
+ }
+ else
+ {
+ /* Set the buffer to 5% of the cut-off */
+ ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
+ }
+ }
+ }
+
+ /* No twin-range calculations with Verlet lists */
+ ir->rlistlong = ir->rlist;
+ }
+
+ if (ir->nstcalclr == -1)
+ {
+ /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
+ ir->nstcalclr = ir->nstlist;
+ }
+ else if (ir->nstcalclr > 0)
+ {
+ if (ir->nstlist > 0 && (ir->nstlist % ir->nstcalclr != 0))
+ {
+ warning_error(wi, "nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
+ }
+ }
+ else if (ir->nstcalclr < -1)
+ {
+ warning_error(wi, "nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
+ }
+
+ if (EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rvdw && ir->nstcalclr > 1)
+ {
+ warning_error(wi, "When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
+ }
+
+ /* GENERAL INTEGRATOR STUFF */
+ if (!(ir->eI == eiMD || EI_VV(ir->eI)))
+ {
+ ir->etc = etcNO;
+ }
+ if (ir->eI == eiVVAK)
+ {
+ sprintf(warn_buf, "Integrator method %s is implemented primarily for validation purposes; for molecular dynamics, you should probably be using %s or %s", ei_names[eiVVAK], ei_names[eiMD], ei_names[eiVV]);
+ warning_note(wi, warn_buf);
+ }
+ if (!EI_DYNAMICS(ir->eI))
+ {
+ ir->epc = epcNO;
+ }
+ if (EI_DYNAMICS(ir->eI))
+ {
+ if (ir->nstcalcenergy < 0)
+ {
+ ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
+ if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
+ {
+ /* nstcalcenergy larger than nstener does not make sense.
+ * We ideally want nstcalcenergy=nstener.
+ */
+ if (ir->nstlist > 0)
+ {
+ ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
+ }
+ else
+ {
+ ir->nstcalcenergy = ir->nstenergy;
+ }
+ }
+ }
+ else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
+ (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
+ (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
+
+ {
+ const char *nsten = "nstenergy";
+ const char *nstdh = "nstdhdl";
+ const char *min_name = nsten;
+ int min_nst = ir->nstenergy;
+
+ /* find the smallest of ( nstenergy, nstdhdl ) */
+ if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
+ (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
+ {
+ min_nst = ir->fepvals->nstdhdl;
+ min_name = nstdh;
+ }
+ /* If the user sets nstenergy small, we should respect that */
+ sprintf(warn_buf,
+ "Setting nstcalcenergy (%d) equal to %s (%d)",
+ ir->nstcalcenergy, min_name, min_nst);
+ warning_note(wi, warn_buf);
+ ir->nstcalcenergy = min_nst;
+ }
+
+ if (ir->epc != epcNO)
+ {
+ if (ir->nstpcouple < 0)
+ {
+ ir->nstpcouple = ir_optimal_nstpcouple(ir);
+ }
+ }
+ if (IR_TWINRANGE(*ir))
+ {
+ check_nst("nstlist", ir->nstlist,
+ "nstcalcenergy", &ir->nstcalcenergy, wi);
+ if (ir->epc != epcNO)
+ {
+ check_nst("nstlist", ir->nstlist,
+ "nstpcouple", &ir->nstpcouple, wi);
+ }
+ }
+
+ if (ir->nstcalcenergy > 0)
+ {
+ if (ir->efep != efepNO)
+ {
+ /* nstdhdl should be a multiple of nstcalcenergy */
+ check_nst("nstcalcenergy", ir->nstcalcenergy,
+ "nstdhdl", &ir->fepvals->nstdhdl, wi);
+ /* nstexpanded should be a multiple of nstcalcenergy */
+ check_nst("nstcalcenergy", ir->nstcalcenergy,
+ "nstexpanded", &ir->expandedvals->nstexpanded, wi);
+ }
+ /* for storing exact averages nstenergy should be
+ * a multiple of nstcalcenergy
+ */
+ check_nst("nstcalcenergy", ir->nstcalcenergy,
+ "nstenergy", &ir->nstenergy, wi);
+ }
+ }
+
+ /* LD STUFF */
+ if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
+ ir->bContinuation && ir->ld_seed != -1)
+ {
+ warning_note(wi, "You are doing a continuation with SD or BD, make sure that ld_seed is different from the previous run (using ld_seed=-1 will ensure this)");
+ }
+
+ /* TPI STUFF */
+ if (EI_TPI(ir->eI))
+ {
+ sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
+ CHECK(ir->ePBC != epbcXYZ);
+ sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
+ CHECK(ir->ns_type != ensGRID);
+ sprintf(err_buf, "with TPI nstlist should be larger than zero");
+ CHECK(ir->nstlist <= 0);
+ sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
+ CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
+ }
+
+ /* SHAKE / LINCS */
+ if ( (opts->nshake > 0) && (opts->bMorse) )
+ {
+ sprintf(warn_buf,
+ "Using morse bond-potentials while constraining bonds is useless");
+ warning(wi, warn_buf);
+ }
+
+ if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
+ ir->bContinuation && ir->ld_seed != -1)
+ {
+ warning_note(wi, "You are doing a continuation with SD or BD, make sure that ld_seed is different from the previous run (using ld_seed=-1 will ensure this)");
+ }
+ /* verify simulated tempering options */
+
+ if (ir->bSimTemp)
+ {
+ gmx_bool bAllTempZero = TRUE;
+ for (i = 0; i < fep->n_lambda; i++)
+ {
+ sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i, efpt_names[efptTEMPERATURE], fep->all_lambda[efptTEMPERATURE][i]);
+ CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
+ if (fep->all_lambda[efptTEMPERATURE][i] > 0)
+ {
+ bAllTempZero = FALSE;
+ }
+ }
+ sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
+ CHECK(bAllTempZero == TRUE);
+
+ sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
+ CHECK(ir->eI != eiVV);
+
+ /* check compatability of the temperature coupling with simulated tempering */
+
+ if (ir->etc == etcNOSEHOOVER)
+ {
+ sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
+ warning_note(wi, warn_buf);
+ }
+
+ /* check that the temperatures make sense */
+
+ sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= than the simulated tempering lower temperature (%g)", ir->simtempvals->simtemp_high, ir->simtempvals->simtemp_low);
+ CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
+
+ sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
+ CHECK(ir->simtempvals->simtemp_high <= 0);
+
+ sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
+ CHECK(ir->simtempvals->simtemp_low <= 0);
+ }
+
+ /* verify free energy options */
+
+ if (ir->efep != efepNO)
+ {
+ fep = ir->fepvals;
+ sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
+ fep->sc_power);
+ CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
+
+ sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
+ (int)fep->sc_r_power);
+ CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
+
+ sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
+ CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
+
+ sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
+ CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
+
+ sprintf(err_buf, "Can only use expanded ensemble with md-vv for now; should be supported for other integrators in 5.0");
+ CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
+
+ sprintf(err_buf, "Free-energy not implemented for Ewald");
+ CHECK(ir->coulombtype == eelEWALD);
+
+ /* check validty of lambda inputs */
+ if (fep->n_lambda == 0)
+ {
+ /* Clear output in case of no states:*/
+ sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
+ CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
+ }
+ else
+ {
+ sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
+ CHECK((fep->init_fep_state >= fep->n_lambda));
+ }
+
+ sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
+ CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
+
+ sprintf(err_buf, "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with init-lambda-state or with init-lambda, but not both",
+ fep->init_lambda, fep->init_fep_state);
+ CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
+
+
+
+ if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
+ {
+ int n_lambda_terms;
+ n_lambda_terms = 0;
+ for (i = 0; i < efptNR; i++)
+ {
+ if (fep->separate_dvdl[i])
+ {
+ n_lambda_terms++;
+ }
+ }
+ if (n_lambda_terms > 1)
+ {
+ sprintf(warn_buf, "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't use init-lambda to set lambda state (except for slow growth). Use init-lambda-state instead.");
+ warning(wi, warn_buf);
+ }
+
+ if (n_lambda_terms < 2 && fep->n_lambda > 0)
+ {
+ warning_note(wi,
+ "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
+ }
+ }
+
+ for (j = 0; j < efptNR; j++)
+ {
+ for (i = 0; i < fep->n_lambda; i++)
+ {
+ sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i, efpt_names[j], fep->all_lambda[j][i]);
+ CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
+ }
+ }
+
+ if ((fep->sc_alpha > 0) && (!fep->bScCoul))
+ {
+ for (i = 0; i < fep->n_lambda; i++)
+ {
+ sprintf(err_buf, "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to crashes, and is not supported.", i, fep->all_lambda[efptVDW][i],
+ fep->all_lambda[efptCOUL][i]);
+ CHECK((fep->sc_alpha > 0) &&
+ (((fep->all_lambda[efptCOUL][i] > 0.0) &&
+ (fep->all_lambda[efptCOUL][i] < 1.0)) &&
+ ((fep->all_lambda[efptVDW][i] > 0.0) &&
+ (fep->all_lambda[efptVDW][i] < 1.0))));
+ }
+ }
+
+ if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
+ {
+ real sigma, lambda, r_sc;
+
+ sigma = 0.34;
+ /* Maximum estimate for A and B charges equal with lambda power 1 */
+ lambda = 0.5;
+ r_sc = pow(lambda*fep->sc_alpha*pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
+ sprintf(warn_buf, "With PME there is a minor soft core effect present at the cut-off, proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on energy conservation, but usually other effects dominate. With a common sigma value of %g nm the fraction of the particle-particle potential at the cut-off at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
+ fep->sc_r_power,
+ sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
+ warning_note(wi, warn_buf);
+ }
+
+ /* Free Energy Checks -- In an ideal world, slow growth and FEP would
+ be treated differently, but that's the next step */
+
+ for (i = 0; i < efptNR; i++)
+ {
+ for (j = 0; j < fep->n_lambda; j++)
+ {
+ sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
+ CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
+ }
+ }
+ }
+
+ if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
+ {
+ fep = ir->fepvals;
+ expand = ir->expandedvals;
+
+ /* checking equilibration of weights inputs for validity */
+
+ sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
+ expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
+ CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
+
+ sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
+ expand->equil_samples, elmceq_names[elmceqSAMPLES]);
+ CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
+
+ sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
+ expand->equil_steps, elmceq_names[elmceqSTEPS]);
+ CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
+
+ sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
+ expand->equil_samples, elmceq_names[elmceqWLDELTA]);
+ CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
+
+ sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
+ expand->equil_ratio, elmceq_names[elmceqRATIO]);
+ CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
+
+ sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
+ expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
+ CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
+
+ sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
+ expand->equil_samples, elmceq_names[elmceqSAMPLES]);
+ CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
+
+ sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
+ expand->equil_steps, elmceq_names[elmceqSTEPS]);
+ CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
+
+ sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
+ expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
+ CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
+
+ sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
+ expand->equil_ratio, elmceq_names[elmceqRATIO]);
+ CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
+
+ sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
+ elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
+ CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
+
+ sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
+ CHECK((expand->lmc_repeats <= 0));
+ sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
+ CHECK((expand->minvarmin <= 0));
+ sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
+ CHECK((expand->c_range < 0));
+ sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
+ fep->init_fep_state, expand->lmc_forced_nstart);
+ CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
+ sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
+ CHECK((expand->lmc_forced_nstart < 0));
+ sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
+ CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
+
+ sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
+ CHECK((expand->init_wl_delta < 0));
+ sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
+ CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
+ sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
+ CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
+
+ /* if there is no temperature control, we need to specify an MC temperature */
+ sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
+ if (expand->nstTij > 0)
+ {
+ sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
+ expand->nstTij, ir->nstlog);
+ CHECK((mod(expand->nstTij, ir->nstlog) != 0));
+ }
+ }
+
+ /* PBC/WALLS */
+ sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
+ CHECK(ir->nwall && ir->ePBC != epbcXY);
+
+ /* VACUUM STUFF */
+ if (ir->ePBC != epbcXYZ && ir->nwall != 2)
+ {
+ if (ir->ePBC == epbcNONE)
+ {
+ if (ir->epc != epcNO)
+ {
+ warning(wi, "Turning off pressure coupling for vacuum system");
+ ir->epc = epcNO;
+ }
+ }
+ else
+ {
+ sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
+ epbc_names[ir->ePBC]);
+ CHECK(ir->epc != epcNO);
+ }
+ sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
+ CHECK(EEL_FULL(ir->coulombtype));
+
+ sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
+ epbc_names[ir->ePBC]);
+ CHECK(ir->eDispCorr != edispcNO);
+ }
+
+ if (ir->rlist == 0.0)
+ {
+ sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
+ "with coulombtype = %s or coulombtype = %s\n"
+ "without periodic boundary conditions (pbc = %s) and\n"
+ "rcoulomb and rvdw set to zero",
+ eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
+ CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
+ (ir->ePBC != epbcNONE) ||
+ (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
+
+ if (ir->nstlist < 0)
+ {
+ warning_error(wi, "Can not have heuristic neighborlist updates without cut-off");
+ }
+ if (ir->nstlist > 0)
+ {
+ warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
+ }
+ }
+
+ /* COMM STUFF */
+ if (ir->nstcomm == 0)
+ {
+ ir->comm_mode = ecmNO;
+ }
+ if (ir->comm_mode != ecmNO)
+ {
+ if (ir->nstcomm < 0)
+ {
+ warning(wi, "If you want to remove the rotation around the center of mass, you should set comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to its absolute value");
+ ir->nstcomm = abs(ir->nstcomm);
+ }
+
+ if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
+ {
+ warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
+ ir->nstcomm = ir->nstcalcenergy;
+ }
+
+ if (ir->comm_mode == ecmANGULAR)
+ {
+ sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
+ CHECK(ir->bPeriodicMols);
+ if (ir->ePBC != epbcNONE)
+ {
+ warning(wi, "Removing the rotation around the center of mass in a periodic system (this is not a problem when you have only one molecule).");
+ }
+ }
+ }
+
+ if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
+ {
+ warning_note(wi, "Tumbling and or flying ice-cubes: We are not removing rotation around center of mass in a non-periodic system. You should probably set comm_mode = ANGULAR.");
+ }
+
+ sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
+ " algorithm not implemented");
+ CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
+ && (ir->ns_type == ensSIMPLE));
+
+ /* TEMPERATURE COUPLING */
+ if (ir->etc == etcYES)
+ {
+ ir->etc = etcBERENDSEN;
+ warning_note(wi, "Old option for temperature coupling given: "
+ "changing \"yes\" to \"Berendsen\"\n");
+ }
+
+ if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
+ {
+ if (ir->opts.nhchainlength < 1)
+ {
+ sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
+ ir->opts.nhchainlength = 1;
+ warning(wi, warn_buf);
+ }
+
+ if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
+ {
+ warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
+ ir->opts.nhchainlength = 1;
+ }
+ }
+ else
+ {
+ ir->opts.nhchainlength = 0;
+ }
+
+ if (ir->eI == eiVVAK)
+ {
+ sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
+ ei_names[eiVVAK]);
+ CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
+ }
+
+ if (ETC_ANDERSEN(ir->etc))
+ {
+ sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
+ CHECK(!(EI_VV(ir->eI)));
+
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
+ CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
+ sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
+ i, ir->opts.tau_t[i]);
+ CHECK(ir->opts.tau_t[i] < 0);
+ }
+ if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
+ {
+ sprintf(warn_buf, "Center of mass removal not necessary for %s. All velocities of coupled groups are rerandomized periodically, so flying ice cube errors will not occur.", etcoupl_names[ir->etc]);
+ warning_note(wi, warn_buf);
+ }
+
+ sprintf(err_buf, "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are randomized every time step", ir->nstcomm, etcoupl_names[ir->etc]);
+ CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
+
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
+ sprintf(err_buf, "tau_t/delta_t for group %d for temperature control method %s must be a multiple of nstcomm (%d), as velocities of atoms in coupled groups are randomized every time step. The input tau_t (%8.3f) leads to %d steps per randomization", i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
+ CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
+ }
+ }
+ if (ir->etc == etcBERENDSEN)
+ {
+ sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
+ ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
+ warning_note(wi, warn_buf);
+ }
+
+ if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
+ && ir->epc == epcBERENDSEN)
+ {
+ sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
+ "true ensemble for the thermostat");
+ warning(wi, warn_buf);
+ }
+
+ /* PRESSURE COUPLING */
+ if (ir->epc == epcISOTROPIC)
+ {
+ ir->epc = epcBERENDSEN;
+ warning_note(wi, "Old option for pressure coupling given: "
+ "changing \"Isotropic\" to \"Berendsen\"\n");
+ }
+
+ if (ir->epc != epcNO)
+ {
+ dt_pcoupl = ir->nstpcouple*ir->delta_t;
+
+ sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
+ CHECK(ir->tau_p <= 0);
+
+ if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc))
+ {
+ sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
+ EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
+ warning(wi, warn_buf);
+ }
+
+ sprintf(err_buf, "compressibility must be > 0 when using pressure"
+ " coupling %s\n", EPCOUPLTYPE(ir->epc));
+ CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
+ ir->compress[ZZ][ZZ] < 0 ||
+ (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
+ ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
+
+ if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
+ {
+ sprintf(warn_buf,
+ "You are generating velocities so I am assuming you "
+ "are equilibrating a system. You are using "
+ "%s pressure coupling, but this can be "
+ "unstable for equilibration. If your system crashes, try "
+ "equilibrating first with Berendsen pressure coupling. If "
+ "you are not equilibrating the system, you can probably "
+ "ignore this warning.",
+ epcoupl_names[ir->epc]);
+ warning(wi, warn_buf);
+ }
+ }
+
+ if (EI_VV(ir->eI))
+ {
+ if (ir->epc > epcNO)
+ {
+ if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
+ {
+ warning_error(wi, "for md-vv and md-vv-avek, can only use Berendsen and Martyna-Tuckerman-Tobias-Klein (MTTK) equations for pressure control; MTTK is equivalent to Parrinello-Rahman.");
+ }
+ }
+ }
++ else
++ {
++ if (ir->epc == epcMTTK)
++ {
++ warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
++ }
++ }
+
+ /* ELECTROSTATICS */
+ /* More checks are in triple check (grompp.c) */
+
+ if (ir->coulombtype == eelSWITCH)
+ {
+ sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
+ "artifacts, advice: use coulombtype = %s",
+ eel_names[ir->coulombtype],
+ eel_names[eelRF_ZERO]);
+ warning(wi, warn_buf);
+ }
+
+ if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
+ {
+ sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
+ warning_note(wi, warn_buf);
+ }
+
+ if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
+ {
+ sprintf(warn_buf, "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old format and exchanging epsilon-r and epsilon-rf", ir->epsilon_r);
+ warning(wi, warn_buf);
+ ir->epsilon_rf = ir->epsilon_r;
+ ir->epsilon_r = 1.0;
+ }
+
+ if (getenv("GALACTIC_DYNAMICS") == NULL)
+ {
+ sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
+ CHECK(ir->epsilon_r < 0);
+ }
+
+ if (EEL_RF(ir->coulombtype))
+ {
+ /* reaction field (at the cut-off) */
+
+ if (ir->coulombtype == eelRF_ZERO)
+ {
+ sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->epsilon_rf != 0);
+ ir->epsilon_rf = 0.0;
+ }
+
+ sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
+ CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
+ (ir->epsilon_r == 0));
+ if (ir->epsilon_rf == ir->epsilon_r)
+ {
+ sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
+ eel_names[ir->coulombtype]);
+ warning(wi, warn_buf);
+ }
+ }
+ /* Allow rlist>rcoulomb for tabulated long range stuff. This just
+ * means the interaction is zero outside rcoulomb, but it helps to
+ * provide accurate energy conservation.
+ */
+ if (ir_coulomb_might_be_zero_at_cutoff(ir))
+ {
+ if (ir_coulomb_switched(ir))
+ {
+ sprintf(err_buf,
+ "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
+ }
+ }
+ else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
+ {
+ if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
+ {
+ sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->rlist > ir->rcoulomb);
+ }
+ }
+
+ if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
+ ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
+ {
+ sprintf(warn_buf,
+ "The switch/shift interaction settings are just for compatibility; you will get better "
+ "performance from applying potential modifiers to your interactions!\n");
+ warning_note(wi, warn_buf);
+ }
+
+ if (ir->coulombtype == eelPMESWITCH)
+ {
+ if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
+ {
+ sprintf(warn_buf, "The switching range for %s should be 5%% or less, energy conservation will be good anyhow, since ewald_rtol = %g",
+ eel_names[ir->coulombtype],
+ ir->ewald_rtol);
+ warning(wi, warn_buf);
+ }
+ }
+
+ if (EEL_FULL(ir->coulombtype))
+ {
+ if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
+ ir->coulombtype == eelPMEUSERSWITCH)
+ {
+ sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->rcoulomb > ir->rlist);
+ }
+ else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
+ {
+ if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
+ {
+ sprintf(err_buf,
+ "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
+ "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
+ "a potential modifier.", eel_names[ir->coulombtype]);
+ if (ir->nstcalclr == 1)
+ {
+ CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
+ }
+ else
+ {
+ CHECK(ir->rcoulomb != ir->rlist);
+ }
+ }
+ }
+ }
+
+ if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
+ {
+ if (ir->pme_order < 3)
+ {
+ warning_error(wi, "pme-order can not be smaller than 3");
+ }
+ }
+
+ if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
+ {
+ if (ir->ewald_geometry == eewg3D)
+ {
+ sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
+ epbc_names[ir->ePBC], eewg_names[eewg3DC]);
+ warning(wi, warn_buf);
+ }
+ /* This check avoids extra pbc coding for exclusion corrections */
+ sprintf(err_buf, "wall-ewald-zfac should be >= 2");
+ CHECK(ir->wall_ewald_zfac < 2);
+ }
+
+ if (ir_vdw_switched(ir))
+ {
+ sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
+ CHECK(ir->rvdw_switch >= ir->rvdw);
+
+ if (ir->rvdw_switch < 0.5*ir->rvdw)
+ {
+ sprintf(warn_buf, "You are applying a switch function to vdw forces or potentials from %g to %g nm, which is more than half the interaction range, whereas switch functions are intended to act only close to the cut-off.",
+ ir->rvdw_switch, ir->rvdw);
+ warning_note(wi, warn_buf);
+ }
+ }
+ else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
+ {
+ if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
+ {
+ sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
+ CHECK(ir->rlist > ir->rvdw);
+ }
+ }
+
+ if (ir->cutoff_scheme == ecutsGROUP)
+ {
+ if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
+ (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)) &&
+ ir->nstlist != 1)
+ {
+ warning_note(wi, "With exact cut-offs, rlist should be "
+ "larger than rcoulomb and rvdw, so that there "
+ "is a buffer region for particle motion "
+ "between neighborsearch steps");
+ }
+
+ if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
+ {
+ sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
+ IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
+ warning_note(wi, warn_buf);
+ }
+ if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
+ {
+ sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
+ IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
+ warning_note(wi, warn_buf);
+ }
+ }
+
+ if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
+ {
+ warning_note(wi, "You have selected user tables with dispersion correction, the dispersion will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction between rvdw_switch and rvdw will not be double counted). Make sure that you really want dispersion correction to -C6/r^6.");
+ }
+
+ if (ir->nstlist == -1)
+ {
+ sprintf(err_buf, "With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
+ CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
+ }
+ sprintf(err_buf, "nstlist can not be smaller than -1");
+ CHECK(ir->nstlist < -1);
+
+ if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
+ && ir->rvdw != 0)
+ {
+ warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
+ }
+
+ if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
+ {
+ warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
+ }
+
+ /* ENERGY CONSERVATION */
+ if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
+ {
+ if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
+ {
+ sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
+ evdw_names[evdwSHIFT]);
+ warning_note(wi, warn_buf);
+ }
+ if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
+ {
+ sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
+ eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
+ warning_note(wi, warn_buf);
+ }
+ }
+
+ /* IMPLICIT SOLVENT */
+ if (ir->coulombtype == eelGB_NOTUSED)
+ {
+ ir->coulombtype = eelCUT;
+ ir->implicit_solvent = eisGBSA;
+ fprintf(stderr, "Note: Old option for generalized born electrostatics given:\n"
+ "Changing coulombtype from \"generalized-born\" to \"cut-off\" and instead\n"
+ "setting implicit-solvent value to \"GBSA\" in input section.\n");
+ }
+
+ if (ir->sa_algorithm == esaSTILL)
+ {
+ sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
+ CHECK(ir->sa_algorithm == esaSTILL);
+ }
+
+ if (ir->implicit_solvent == eisGBSA)
+ {
+ sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
+ CHECK(ir->rgbradii != ir->rlist);
+
+ if (ir->coulombtype != eelCUT)
+ {
+ sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
+ CHECK(ir->coulombtype != eelCUT);
+ }
+ if (ir->vdwtype != evdwCUT)
+ {
+ sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
+ CHECK(ir->vdwtype != evdwCUT);
+ }
+ if (ir->nstgbradii < 1)
+ {
+ sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
+ warning_note(wi, warn_buf);
+ ir->nstgbradii = 1;
+ }
+ if (ir->sa_algorithm == esaNO)
+ {
+ sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
+ warning_note(wi, warn_buf);
+ }
+ if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
+ {
+ sprintf(warn_buf, "Value of sa_surface_tension is < 0. Changing it to 2.05016 or 2.25936 kJ/nm^2/mol for Still and HCT/OBC respectively\n");
+ warning_note(wi, warn_buf);
+
+ if (ir->gb_algorithm == egbSTILL)
+ {
+ ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
+ }
+ else
+ {
+ ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
+ }
+ }
+ if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
+ {
+ sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
+ CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
+ }
+
+ }
+
+ if (ir->bAdress)
+ {
+ if (ir->cutoff_scheme != ecutsGROUP)
+ {
+ warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
+ }
+ if (!EI_SD(ir->eI))
+ {
+ warning_error(wi, "AdresS simulation supports only stochastic dynamics");
+ }
+ if (ir->epc != epcNO)
+ {
+ warning_error(wi, "AdresS simulation does not support pressure coupling");
+ }
+ if (EEL_FULL(ir->coulombtype))
+ {
+ warning_error(wi, "AdresS simulation does not support long-range electrostatics");
+ }
+ }
+}
+
+/* count the number of text elemets separated by whitespace in a string.
+ str = the input string
+ maxptr = the maximum number of allowed elements
+ ptr = the output array of pointers to the first character of each element
+ returns: the number of elements. */
+int str_nelem(const char *str, int maxptr, char *ptr[])
+{
+ int np = 0;
+ char *copy0, *copy;
+
+ copy0 = strdup(str);
+ copy = copy0;
+ ltrim(copy);
+ while (*copy != '\0')
+ {
+ if (np >= maxptr)
+ {
+ gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
+ str, maxptr);
+ }
+ if (ptr)
+ {
+ ptr[np] = copy;
+ }
+ np++;
+ while ((*copy != '\0') && !isspace(*copy))
+ {
+ copy++;
+ }
+ if (*copy != '\0')
+ {
+ *copy = '\0';
+ copy++;
+ }
+ ltrim(copy);
+ }
+ if (ptr == NULL)
+ {
+ sfree(copy0);
+ }
+
+ return np;
+}
+
+/* interpret a number of doubles from a string and put them in an array,
+ after allocating space for them.
+ str = the input string
+ n = the (pre-allocated) number of doubles read
+ r = the output array of doubles. */
+static void parse_n_real(char *str, int *n, real **r)
+{
+ char *ptr[MAXPTR];
+ int i;
+
+ *n = str_nelem(str, MAXPTR, ptr);
+
+ snew(*r, *n);
+ for (i = 0; i < *n; i++)
+ {
+ (*r)[i] = strtod(ptr[i], NULL);
+ }
+}
+
+static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
+{
+
+ int i, j, max_n_lambda, nweights, nfep[efptNR];
+ t_lambda *fep = ir->fepvals;
+ t_expanded *expand = ir->expandedvals;
+ real **count_fep_lambdas;
+ gmx_bool bOneLambda = TRUE;
+
+ snew(count_fep_lambdas, efptNR);
+
+ /* FEP input processing */
+ /* first, identify the number of lambda values for each type.
+ All that are nonzero must have the same number */
+
+ for (i = 0; i < efptNR; i++)
+ {
+ parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
+ }
+
+ /* now, determine the number of components. All must be either zero, or equal. */
+
+ max_n_lambda = 0;
+ for (i = 0; i < efptNR; i++)
+ {
+ if (nfep[i] > max_n_lambda)
+ {
+ max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
+ must have the same number if its not zero.*/
+ break;
+ }
+ }
+
+ for (i = 0; i < efptNR; i++)
+ {
+ if (nfep[i] == 0)
+ {
+ ir->fepvals->separate_dvdl[i] = FALSE;
+ }
+ else if (nfep[i] == max_n_lambda)
+ {
+ if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
+ respect to the temperature currently */
+ {
+ ir->fepvals->separate_dvdl[i] = TRUE;
+ }
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
+ nfep[i], efpt_names[i], max_n_lambda);
+ }
+ }
+ /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
+ ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
+
+ /* the number of lambdas is the number we've read in, which is either zero
+ or the same for all */
+ fep->n_lambda = max_n_lambda;
+
+ /* allocate space for the array of lambda values */
+ snew(fep->all_lambda, efptNR);
+ /* if init_lambda is defined, we need to set lambda */
+ if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
+ {
+ ir->fepvals->separate_dvdl[efptFEP] = TRUE;
+ }
+ /* otherwise allocate the space for all of the lambdas, and transfer the data */
+ for (i = 0; i < efptNR; i++)
+ {
+ snew(fep->all_lambda[i], fep->n_lambda);
+ if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
+ are zero */
+ {
+ for (j = 0; j < fep->n_lambda; j++)
+ {
+ fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
+ }
+ sfree(count_fep_lambdas[i]);
+ }
+ }
+ sfree(count_fep_lambdas);
+
+ /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
+ bookkeeping -- for now, init_lambda */
+
+ if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
+ {
+ for (i = 0; i < fep->n_lambda; i++)
+ {
+ fep->all_lambda[efptFEP][i] = fep->init_lambda;
+ }
+ }
+
+ /* check to see if only a single component lambda is defined, and soft core is defined.
+ In this case, turn on coulomb soft core */
+
+ if (max_n_lambda == 0)
+ {
+ bOneLambda = TRUE;
+ }
+ else
+ {
+ for (i = 0; i < efptNR; i++)
+ {
+ if ((nfep[i] != 0) && (i != efptFEP))
+ {
+ bOneLambda = FALSE;
+ }
+ }
+ }
+ if ((bOneLambda) && (fep->sc_alpha > 0))
+ {
+ fep->bScCoul = TRUE;
+ }
+
+ /* Fill in the others with the efptFEP if they are not explicitly
+ specified (i.e. nfep[i] == 0). This means if fep is not defined,
+ they are all zero. */
+
+ for (i = 0; i < efptNR; i++)
+ {
+ if ((nfep[i] == 0) && (i != efptFEP))
+ {
+ for (j = 0; j < fep->n_lambda; j++)
+ {
+ fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
+ }
+ }
+ }
+
+
+ /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
+ if (fep->sc_r_power == 48)
+ {
+ if (fep->sc_alpha > 0.1)
+ {
+ gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
+ }
+ }
+
+ expand = ir->expandedvals;
+ /* now read in the weights */
+ parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
+ if (nweights == 0)
+ {
+ snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
+ }
+ else if (nweights != fep->n_lambda)
+ {
+ gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
+ nweights, fep->n_lambda);
+ }
+ if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
+ {
+ expand->nstexpanded = fep->nstdhdl;
+ /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
+ }
+ if ((expand->nstexpanded < 0) && ir->bSimTemp)
+ {
+ expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
+ /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
+ 2*tau_t just to be careful so it's not to frequent */
+ }
+}
+
+
+static void do_simtemp_params(t_inputrec *ir)
+{
+
+ snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
+ GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
+
+ return;
+}
+
+static void do_wall_params(t_inputrec *ir,
+ char *wall_atomtype, char *wall_density,
+ t_gromppopts *opts)
+{
+ int nstr, i;
+ char *names[MAXPTR];
+ double dbl;
+
+ opts->wall_atomtype[0] = NULL;
+ opts->wall_atomtype[1] = NULL;
+
+ ir->wall_atomtype[0] = -1;
+ ir->wall_atomtype[1] = -1;
+ ir->wall_density[0] = 0;
+ ir->wall_density[1] = 0;
+
+ if (ir->nwall > 0)
+ {
+ nstr = str_nelem(wall_atomtype, MAXPTR, names);
+ if (nstr != ir->nwall)
+ {
+ gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
+ ir->nwall, nstr);
+ }
+ for (i = 0; i < ir->nwall; i++)
+ {
+ opts->wall_atomtype[i] = strdup(names[i]);
+ }
+
+ if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
+ {
+ nstr = str_nelem(wall_density, MAXPTR, names);
+ if (nstr != ir->nwall)
+ {
+ gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
+ }
+ for (i = 0; i < ir->nwall; i++)
+ {
+ sscanf(names[i], "%lf", &dbl);
+ if (dbl <= 0)
+ {
+ gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
+ }
+ ir->wall_density[i] = dbl;
+ }
+ }
+ }
+}
+
+static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
+{
+ int i;
+ t_grps *grps;
+ char str[STRLEN];
+
+ if (nwall > 0)
+ {
+ srenew(groups->grpname, groups->ngrpname+nwall);
+ grps = &(groups->grps[egcENER]);
+ srenew(grps->nm_ind, grps->nr+nwall);
+ for (i = 0; i < nwall; i++)
+ {
+ sprintf(str, "wall%d", i);
+ groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
+ grps->nm_ind[grps->nr++] = groups->ngrpname++;
+ }
+ }
+}
+
+void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
+ t_expanded *expand, warninp_t wi)
+{
+ int ninp, nerror = 0;
+ t_inpfile *inp;
+
+ ninp = *ninp_p;
+ inp = *inp_p;
+
+ /* read expanded ensemble parameters */
+ CCTYPE ("expanded ensemble variables");
+ ITYPE ("nstexpanded", expand->nstexpanded, -1);
+ EETYPE("lmc-stats", expand->elamstats, elamstats_names);
+ EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
+ EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
+ ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
+ ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
+ ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
+ RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
+ RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
+ CCTYPE("Seed for Monte Carlo in lambda space");
+ ITYPE ("lmc-seed", expand->lmc_seed, -1);
+ RTYPE ("mc-temperature", expand->mc_temp, -1);
+ ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
+ ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
+ ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
+ EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
+ ITYPE("nst-transition-matrix", expand->nstTij, -1);
+ ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
+ ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
+ RTYPE ("wl-scale", expand->wl_scale, 0.8);
+ RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
+ RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
+ EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
+
+ *ninp_p = ninp;
+ *inp_p = inp;
+
+ return;
+}
+
+void get_ir(const char *mdparin, const char *mdparout,
+ t_inputrec *ir, t_gromppopts *opts,
+ warninp_t wi)
+{
+ char *dumstr[2];
+ double dumdub[2][6];
+ t_inpfile *inp;
+ const char *tmp;
+ int i, j, m, ninp;
+ char warn_buf[STRLEN];
+ t_lambda *fep = ir->fepvals;
+ t_expanded *expand = ir->expandedvals;
+
+ init_inputrec_strings();
+ inp = read_inpfile(mdparin, &ninp, wi);
+
+ snew(dumstr[0], STRLEN);
+ snew(dumstr[1], STRLEN);
+
+ if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
+ {
+ sprintf(warn_buf,
+ "%s did not specify a value for the .mdp option "
+ "\"cutoff-scheme\". Probably it was first intended for use "
+ "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
+ "introduced, but the group scheme was still the default. "
+ "The default is now the Verlet scheme, so you will observe "
+ "different behaviour.", mdparin);
+ warning_note(wi, warn_buf);
+ }
+
+ /* remove the following deprecated commands */
+ REM_TYPE("title");
+ REM_TYPE("cpp");
+ REM_TYPE("domain-decomposition");
+ REM_TYPE("andersen-seed");
+ REM_TYPE("dihre");
+ REM_TYPE("dihre-fc");
+ REM_TYPE("dihre-tau");
+ REM_TYPE("nstdihreout");
+ REM_TYPE("nstcheckpoint");
+
+ /* replace the following commands with the clearer new versions*/
+ REPL_TYPE("unconstrained-start", "continuation");
+ REPL_TYPE("foreign-lambda", "fep-lambdas");
+ REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
+ REPL_TYPE("nstxtcout", "nstxout-compressed");
+ REPL_TYPE("xtc-grps", "compressed-x-grps");
+ REPL_TYPE("xtc-precision", "compressed-x-precision");
+
+ CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
+ CTYPE ("Preprocessor information: use cpp syntax.");
+ CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
+ STYPE ("include", opts->include, NULL);
+ CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
+ STYPE ("define", opts->define, NULL);
+
+ CCTYPE ("RUN CONTROL PARAMETERS");
+ EETYPE("integrator", ir->eI, ei_names);
+ CTYPE ("Start time and timestep in ps");
+ RTYPE ("tinit", ir->init_t, 0.0);
+ RTYPE ("dt", ir->delta_t, 0.001);
+ STEPTYPE ("nsteps", ir->nsteps, 0);
+ CTYPE ("For exact run continuation or redoing part of a run");
+ STEPTYPE ("init-step", ir->init_step, 0);
+ CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
+ ITYPE ("simulation-part", ir->simulation_part, 1);
+ CTYPE ("mode for center of mass motion removal");
+ EETYPE("comm-mode", ir->comm_mode, ecm_names);
+ CTYPE ("number of steps for center of mass motion removal");
+ ITYPE ("nstcomm", ir->nstcomm, 100);
+ CTYPE ("group(s) for center of mass motion removal");
+ STYPE ("comm-grps", is->vcm, NULL);
+
+ CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
+ CTYPE ("Friction coefficient (amu/ps) and random seed");
+ RTYPE ("bd-fric", ir->bd_fric, 0.0);
+ STEPTYPE ("ld-seed", ir->ld_seed, -1);
+
+ /* Em stuff */
+ CCTYPE ("ENERGY MINIMIZATION OPTIONS");
+ CTYPE ("Force tolerance and initial step-size");
+ RTYPE ("emtol", ir->em_tol, 10.0);
+ RTYPE ("emstep", ir->em_stepsize, 0.01);
+ CTYPE ("Max number of iterations in relax-shells");
+ ITYPE ("niter", ir->niter, 20);
+ CTYPE ("Step size (ps^2) for minimization of flexible constraints");
+ RTYPE ("fcstep", ir->fc_stepsize, 0);
+ CTYPE ("Frequency of steepest descents steps when doing CG");
+ ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
+ ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
+
+ CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
+ RTYPE ("rtpi", ir->rtpi, 0.05);
+
+ /* Output options */
+ CCTYPE ("OUTPUT CONTROL OPTIONS");
+ CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
+ ITYPE ("nstxout", ir->nstxout, 0);
+ ITYPE ("nstvout", ir->nstvout, 0);
+ ITYPE ("nstfout", ir->nstfout, 0);
+ ir->nstcheckpoint = 1000;
+ CTYPE ("Output frequency for energies to log file and energy file");
+ ITYPE ("nstlog", ir->nstlog, 1000);
+ ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
+ ITYPE ("nstenergy", ir->nstenergy, 1000);
+ CTYPE ("Output frequency and precision for .xtc file");
+ ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
+ RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
+ CTYPE ("This selects the subset of atoms for the compressed");
+ CTYPE ("trajectory file. You can select multiple groups. By");
+ CTYPE ("default, all atoms will be written.");
+ STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
+ CTYPE ("Selection of energy groups");
+ STYPE ("energygrps", is->energy, NULL);
+
+ /* Neighbor searching */
+ CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
+ CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
+ EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
+ CTYPE ("nblist update frequency");
+ ITYPE ("nstlist", ir->nstlist, 10);
+ CTYPE ("ns algorithm (simple or grid)");
+ EETYPE("ns-type", ir->ns_type, ens_names);
+ /* set ndelta to the optimal value of 2 */
+ ir->ndelta = 2;
+ CTYPE ("Periodic boundary conditions: xyz, no, xy");
+ EETYPE("pbc", ir->ePBC, epbc_names);
+ EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
+ CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
+ CTYPE ("a value of -1 means: use rlist");
+ RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
+ CTYPE ("nblist cut-off");
+ RTYPE ("rlist", ir->rlist, 1.0);
+ CTYPE ("long-range cut-off for switched potentials");
+ RTYPE ("rlistlong", ir->rlistlong, -1);
+ ITYPE ("nstcalclr", ir->nstcalclr, -1);
+
+ /* Electrostatics */
+ CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
+ CTYPE ("Method for doing electrostatics");
+ EETYPE("coulombtype", ir->coulombtype, eel_names);
+ EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
+ CTYPE ("cut-off lengths");
+ RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
+ RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
+ CTYPE ("Relative dielectric constant for the medium and the reaction field");
+ RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
+ RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
+ CTYPE ("Method for doing Van der Waals");
+ EETYPE("vdw-type", ir->vdwtype, evdw_names);
+ EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
+ CTYPE ("cut-off lengths");
+ RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
+ RTYPE ("rvdw", ir->rvdw, 1.0);
+ CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
+ EETYPE("DispCorr", ir->eDispCorr, edispc_names);
+ CTYPE ("Extension of the potential lookup tables beyond the cut-off");
+ RTYPE ("table-extension", ir->tabext, 1.0);
+ CTYPE ("Separate tables between energy group pairs");
+ STYPE ("energygrp-table", is->egptable, NULL);
+ CTYPE ("Spacing for the PME/PPPM FFT grid");
+ RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
+ CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
+ ITYPE ("fourier-nx", ir->nkx, 0);
+ ITYPE ("fourier-ny", ir->nky, 0);
+ ITYPE ("fourier-nz", ir->nkz, 0);
+ CTYPE ("EWALD/PME/PPPM parameters");
+ ITYPE ("pme-order", ir->pme_order, 4);
+ RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
+ RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
+ EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
+ EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
+ RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
+ EETYPE("optimize-fft", ir->bOptFFT, yesno_names);
+
+ CCTYPE("IMPLICIT SOLVENT ALGORITHM");
+ EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
+
+ CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
+ CTYPE ("Algorithm for calculating Born radii");
+ EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
+ CTYPE ("Frequency of calculating the Born radii inside rlist");
+ ITYPE ("nstgbradii", ir->nstgbradii, 1);
+ CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
+ CTYPE ("between rlist and rgbradii is updated every nstlist steps");
+ RTYPE ("rgbradii", ir->rgbradii, 1.0);
+ CTYPE ("Dielectric coefficient of the implicit solvent");
+ RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
+ CTYPE ("Salt concentration in M for Generalized Born models");
+ RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
+ CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
+ RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
+ RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
+ RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
+ RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
+ EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
+ CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
+ CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
+ RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
+
+ /* Coupling stuff */
+ CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
+ CTYPE ("Temperature coupling");
+ EETYPE("tcoupl", ir->etc, etcoupl_names);
+ ITYPE ("nsttcouple", ir->nsttcouple, -1);
+ ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
+ EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
+ CTYPE ("Groups to couple separately");
+ STYPE ("tc-grps", is->tcgrps, NULL);
+ CTYPE ("Time constant (ps) and reference temperature (K)");
+ STYPE ("tau-t", is->tau_t, NULL);
+ STYPE ("ref-t", is->ref_t, NULL);
+ CTYPE ("pressure coupling");
+ EETYPE("pcoupl", ir->epc, epcoupl_names);
+ EETYPE("pcoupltype", ir->epct, epcoupltype_names);
+ ITYPE ("nstpcouple", ir->nstpcouple, -1);
+ CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
+ RTYPE ("tau-p", ir->tau_p, 1.0);
+ STYPE ("compressibility", dumstr[0], NULL);
+ STYPE ("ref-p", dumstr[1], NULL);
+ CTYPE ("Scaling of reference coordinates, No, All or COM");
+ EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
+
+ /* QMMM */
+ CCTYPE ("OPTIONS FOR QMMM calculations");
+ EETYPE("QMMM", ir->bQMMM, yesno_names);
+ CTYPE ("Groups treated Quantum Mechanically");
+ STYPE ("QMMM-grps", is->QMMM, NULL);
+ CTYPE ("QM method");
+ STYPE("QMmethod", is->QMmethod, NULL);
+ CTYPE ("QMMM scheme");
+ EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
+ CTYPE ("QM basisset");
+ STYPE("QMbasis", is->QMbasis, NULL);
+ CTYPE ("QM charge");
+ STYPE ("QMcharge", is->QMcharge, NULL);
+ CTYPE ("QM multiplicity");
+ STYPE ("QMmult", is->QMmult, NULL);
+ CTYPE ("Surface Hopping");
+ STYPE ("SH", is->bSH, NULL);
+ CTYPE ("CAS space options");
+ STYPE ("CASorbitals", is->CASorbitals, NULL);
+ STYPE ("CASelectrons", is->CASelectrons, NULL);
+ STYPE ("SAon", is->SAon, NULL);
+ STYPE ("SAoff", is->SAoff, NULL);
+ STYPE ("SAsteps", is->SAsteps, NULL);
+ CTYPE ("Scale factor for MM charges");
+ RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
+ CTYPE ("Optimization of QM subsystem");
+ STYPE ("bOPT", is->bOPT, NULL);
+ STYPE ("bTS", is->bTS, NULL);
+
+ /* Simulated annealing */
+ CCTYPE("SIMULATED ANNEALING");
+ CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
+ STYPE ("annealing", is->anneal, NULL);
+ CTYPE ("Number of time points to use for specifying annealing in each group");
+ STYPE ("annealing-npoints", is->anneal_npoints, NULL);
+ CTYPE ("List of times at the annealing points for each group");
+ STYPE ("annealing-time", is->anneal_time, NULL);
+ CTYPE ("Temp. at each annealing point, for each group.");
+ STYPE ("annealing-temp", is->anneal_temp, NULL);
+
+ /* Startup run */
+ CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
+ EETYPE("gen-vel", opts->bGenVel, yesno_names);
+ RTYPE ("gen-temp", opts->tempi, 300.0);
+ ITYPE ("gen-seed", opts->seed, -1);
+
+ /* Shake stuff */
+ CCTYPE ("OPTIONS FOR BONDS");
+ EETYPE("constraints", opts->nshake, constraints);
+ CTYPE ("Type of constraint algorithm");
+ EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
+ CTYPE ("Do not constrain the start configuration");
+ EETYPE("continuation", ir->bContinuation, yesno_names);
+ CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
+ EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
+ CTYPE ("Relative tolerance of shake");
+ RTYPE ("shake-tol", ir->shake_tol, 0.0001);
+ CTYPE ("Highest order in the expansion of the constraint coupling matrix");
+ ITYPE ("lincs-order", ir->nProjOrder, 4);
+ CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
+ CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
+ CTYPE ("For energy minimization with constraints it should be 4 to 8.");
+ ITYPE ("lincs-iter", ir->nLincsIter, 1);
+ CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
+ CTYPE ("rotates over more degrees than");
+ RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
+ CTYPE ("Convert harmonic bonds to morse potentials");
+ EETYPE("morse", opts->bMorse, yesno_names);
+
+ /* Energy group exclusions */
+ CCTYPE ("ENERGY GROUP EXCLUSIONS");
+ CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
+ STYPE ("energygrp-excl", is->egpexcl, NULL);
+
+ /* Walls */
+ CCTYPE ("WALLS");
+ CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
+ ITYPE ("nwall", ir->nwall, 0);
+ EETYPE("wall-type", ir->wall_type, ewt_names);
+ RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
+ STYPE ("wall-atomtype", is->wall_atomtype, NULL);
+ STYPE ("wall-density", is->wall_density, NULL);
+ RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
+
+ /* COM pulling */
+ CCTYPE("COM PULLING");
+ CTYPE("Pull type: no, umbrella, constraint or constant-force");
+ EETYPE("pull", ir->ePull, epull_names);
+ if (ir->ePull != epullNO)
+ {
+ snew(ir->pull, 1);
+ is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
+ }
+
+ /* Enforced rotation */
+ CCTYPE("ENFORCED ROTATION");
+ CTYPE("Enforced rotation: No or Yes");
+ EETYPE("rotation", ir->bRot, yesno_names);
+ if (ir->bRot)
+ {
+ snew(ir->rot, 1);
+ is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
+ }
+
+ /* Refinement */
+ CCTYPE("NMR refinement stuff");
+ CTYPE ("Distance restraints type: No, Simple or Ensemble");
+ EETYPE("disre", ir->eDisre, edisre_names);
+ CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
+ EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
+ CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
+ EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
+ RTYPE ("disre-fc", ir->dr_fc, 1000.0);
+ RTYPE ("disre-tau", ir->dr_tau, 0.0);
+ CTYPE ("Output frequency for pair distances to energy file");
+ ITYPE ("nstdisreout", ir->nstdisreout, 100);
+ CTYPE ("Orientation restraints: No or Yes");
+ EETYPE("orire", opts->bOrire, yesno_names);
+ CTYPE ("Orientation restraints force constant and tau for time averaging");
+ RTYPE ("orire-fc", ir->orires_fc, 0.0);
+ RTYPE ("orire-tau", ir->orires_tau, 0.0);
+ STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
+ CTYPE ("Output frequency for trace(SD) and S to energy file");
+ ITYPE ("nstorireout", ir->nstorireout, 100);
+
+ /* free energy variables */
+ CCTYPE ("Free energy variables");
+ EETYPE("free-energy", ir->efep, efep_names);
+ STYPE ("couple-moltype", is->couple_moltype, NULL);
+ EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
+ EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
+ EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
+
+ RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
+ we can recognize if
+ it was not entered */
+ ITYPE ("init-lambda-state", fep->init_fep_state, -1);
+ RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
+ ITYPE ("nstdhdl", fep->nstdhdl, 50);
+ STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
+ STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
+ STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
+ STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
+ STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
+ STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
+ STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
+ ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
+ STYPE ("init-lambda-weights", is->lambda_weights, NULL);
+ EETYPE("dhdl-print-energy", fep->bPrintEnergy, yesno_names);
+ RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
+ ITYPE ("sc-power", fep->sc_power, 1);
+ RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
+ RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
+ EETYPE("sc-coul", fep->bScCoul, yesno_names);
+ ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
+ RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
+ EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
+ separate_dhdl_file_names);
+ EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
+ ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
+ RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
+
+ /* Non-equilibrium MD stuff */
+ CCTYPE("Non-equilibrium MD stuff");
+ STYPE ("acc-grps", is->accgrps, NULL);
+ STYPE ("accelerate", is->acc, NULL);
+ STYPE ("freezegrps", is->freeze, NULL);
+ STYPE ("freezedim", is->frdim, NULL);
+ RTYPE ("cos-acceleration", ir->cos_accel, 0);
+ STYPE ("deform", is->deform, NULL);
+
+ /* simulated tempering variables */
+ CCTYPE("simulated tempering variables");
+ EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
+ EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
+ RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
+ RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
+
+ /* expanded ensemble variables */
+ if (ir->efep == efepEXPANDED || ir->bSimTemp)
+ {
+ read_expandedparams(&ninp, &inp, expand, wi);
+ }
+
+ /* Electric fields */
+ CCTYPE("Electric fields");
+ CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
+ CTYPE ("and a phase angle (real)");
+ STYPE ("E-x", is->efield_x, NULL);
+ STYPE ("E-xt", is->efield_xt, NULL);
+ STYPE ("E-y", is->efield_y, NULL);
+ STYPE ("E-yt", is->efield_yt, NULL);
+ STYPE ("E-z", is->efield_z, NULL);
+ STYPE ("E-zt", is->efield_zt, NULL);
+
+ CCTYPE("Ion/water position swapping for computational electrophysiology setups");
+ CTYPE("Swap positions along direction: no, X, Y, Z");
+ EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
+ if (ir->eSwapCoords != eswapNO)
+ {
+ snew(ir->swap, 1);
+ CTYPE("Swap attempt frequency");
+ ITYPE("swap-frequency", ir->swap->nstswap, 1);
+ CTYPE("Two index groups that contain the compartment-partitioning atoms");
+ STYPE("split-group0", splitgrp0, NULL);
+ STYPE("split-group1", splitgrp1, NULL);
+ CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
+ EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
+ EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
+
+ CTYPE("Group name of ions that can be exchanged with solvent molecules");
+ STYPE("swap-group", swapgrp, NULL);
+ CTYPE("Group name of solvent molecules");
+ STYPE("solvent-group", solgrp, NULL);
+
+ CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
+ CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
+ CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
+ RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
+ RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
+ RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
+ RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
+ RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
+ RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
+
+ CTYPE("Average the number of ions per compartment over these many swap attempt steps");
+ ITYPE("coupl-steps", ir->swap->nAverage, 10);
+ CTYPE("Requested number of anions and cations for each of the two compartments");
+ CTYPE("-1 means fix the numbers as found in time step 0");
+ ITYPE("anionsA", ir->swap->nanions[0], -1);
+ ITYPE("cationsA", ir->swap->ncations[0], -1);
+ ITYPE("anionsB", ir->swap->nanions[1], -1);
+ ITYPE("cationsB", ir->swap->ncations[1], -1);
+ CTYPE("Start to swap ions if threshold difference to requested count is reached");
+ RTYPE("threshold", ir->swap->threshold, 1.0);
+ }
+
+ /* AdResS defined thingies */
+ CCTYPE ("AdResS parameters");
+ EETYPE("adress", ir->bAdress, yesno_names);
+ if (ir->bAdress)
+ {
+ snew(ir->adress, 1);
+ read_adressparams(&ninp, &inp, ir->adress, wi);
+ }
+
+ /* User defined thingies */
+ CCTYPE ("User defined thingies");
+ STYPE ("user1-grps", is->user1, NULL);
+ STYPE ("user2-grps", is->user2, NULL);
+ ITYPE ("userint1", ir->userint1, 0);
+ ITYPE ("userint2", ir->userint2, 0);
+ ITYPE ("userint3", ir->userint3, 0);
+ ITYPE ("userint4", ir->userint4, 0);
+ RTYPE ("userreal1", ir->userreal1, 0);
+ RTYPE ("userreal2", ir->userreal2, 0);
+ RTYPE ("userreal3", ir->userreal3, 0);
+ RTYPE ("userreal4", ir->userreal4, 0);
+#undef CTYPE
+
+ write_inpfile(mdparout, ninp, inp, FALSE, wi);
+ for (i = 0; (i < ninp); i++)
+ {
+ sfree(inp[i].name);
+ sfree(inp[i].value);
+ }
+ sfree(inp);
+
+ /* Process options if necessary */
+ for (m = 0; m < 2; m++)
+ {
+ for (i = 0; i < 2*DIM; i++)
+ {
+ dumdub[m][i] = 0.0;
+ }
+ if (ir->epc)
+ {
+ switch (ir->epct)
+ {
+ case epctISOTROPIC:
+ if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
+ {
+ warning_error(wi, "Pressure coupling not enough values (I need 1)");
+ }
+ dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
+ break;
+ case epctSEMIISOTROPIC:
+ case epctSURFACETENSION:
+ if (sscanf(dumstr[m], "%lf%lf",
+ &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
+ {
+ warning_error(wi, "Pressure coupling not enough values (I need 2)");
+ }
+ dumdub[m][YY] = dumdub[m][XX];
+ break;
+ case epctANISOTROPIC:
+ if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
+ &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
+ &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
+ {
+ warning_error(wi, "Pressure coupling not enough values (I need 6)");
+ }
+ break;
+ default:
+ gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
+ epcoupltype_names[ir->epct]);
+ }
+ }
+ }
+ clear_mat(ir->ref_p);
+ clear_mat(ir->compress);
+ for (i = 0; i < DIM; i++)
+ {
+ ir->ref_p[i][i] = dumdub[1][i];
+ ir->compress[i][i] = dumdub[0][i];
+ }
+ if (ir->epct == epctANISOTROPIC)
+ {
+ ir->ref_p[XX][YY] = dumdub[1][3];
+ ir->ref_p[XX][ZZ] = dumdub[1][4];
+ ir->ref_p[YY][ZZ] = dumdub[1][5];
+ if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
+ {
+ warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
+ }
+ ir->compress[XX][YY] = dumdub[0][3];
+ ir->compress[XX][ZZ] = dumdub[0][4];
+ ir->compress[YY][ZZ] = dumdub[0][5];
+ for (i = 0; i < DIM; i++)
+ {
+ for (m = 0; m < i; m++)
+ {
+ ir->ref_p[i][m] = ir->ref_p[m][i];
+ ir->compress[i][m] = ir->compress[m][i];
+ }
+ }
+ }
+
+ if (ir->comm_mode == ecmNO)
+ {
+ ir->nstcomm = 0;
+ }
+
+ opts->couple_moltype = NULL;
+ if (strlen(is->couple_moltype) > 0)
+ {
+ if (ir->efep != efepNO)
+ {
+ opts->couple_moltype = strdup(is->couple_moltype);
+ if (opts->couple_lam0 == opts->couple_lam1)
+ {
+ warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
+ }
+ if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
+ opts->couple_lam1 == ecouplamNONE))
+ {
+ warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
+ }
+ }
+ else
+ {
+ warning(wi, "Can not couple a molecule with free_energy = no");
+ }
+ }
+ /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
+ if (ir->efep != efepNO)
+ {
+ if (fep->delta_lambda > 0)
+ {
+ ir->efep = efepSLOWGROWTH;
+ }
+ }
+
+ if (ir->bSimTemp)
+ {
+ fep->bPrintEnergy = TRUE;
+ /* always print out the energy to dhdl if we are doing expanded ensemble, since we need the total energy
+ if the temperature is changing. */
+ }
+
+ if ((ir->efep != efepNO) || ir->bSimTemp)
+ {
+ ir->bExpanded = FALSE;
+ if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
+ {
+ ir->bExpanded = TRUE;
+ }
+ do_fep_params(ir, is->fep_lambda, is->lambda_weights);
+ if (ir->bSimTemp) /* done after fep params */
+ {
+ do_simtemp_params(ir);
+ }
+ }
+ else
+ {
+ ir->fepvals->n_lambda = 0;
+ }
+
+ /* WALL PARAMETERS */
+
+ do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
+
+ /* ORIENTATION RESTRAINT PARAMETERS */
+
+ if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
+ {
+ warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
+ }
+
+ /* DEFORMATION PARAMETERS */
+
+ clear_mat(ir->deform);
+ for (i = 0; i < 6; i++)
+ {
+ dumdub[0][i] = 0;
+ }
+ m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
+ &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
+ &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
+ for (i = 0; i < 3; i++)
+ {
+ ir->deform[i][i] = dumdub[0][i];
+ }
+ ir->deform[YY][XX] = dumdub[0][3];
+ ir->deform[ZZ][XX] = dumdub[0][4];
+ ir->deform[ZZ][YY] = dumdub[0][5];
+ if (ir->epc != epcNO)
+ {
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j <= i; j++)
+ {
+ if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
+ {
+ warning_error(wi, "A box element has deform set and compressibility > 0");
+ }
+ }
+ }
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j < i; j++)
+ {
+ if (ir->deform[i][j] != 0)
+ {
+ for (m = j; m < DIM; m++)
+ {
+ if (ir->compress[m][j] != 0)
+ {
+ sprintf(warn_buf, "An off-diagonal box element has deform set while compressibility > 0 for the same component of another box vector, this might lead to spurious periodicity effects.");
+ warning(wi, warn_buf);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /* Ion/water position swapping checks */
+ if (ir->eSwapCoords != eswapNO)
+ {
+ if (ir->swap->nstswap < 1)
+ {
+ warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
+ }
+ if (ir->swap->nAverage < 1)
+ {
+ warning_error(wi, "coupl_steps must be 1 or larger.\n");
+ }
+ if (ir->swap->threshold < 1.0)
+ {
+ warning_error(wi, "Ion count threshold must be at least 1.\n");
+ }
+ }
+
+ sfree(dumstr[0]);
+ sfree(dumstr[1]);
+}
+
+static int search_QMstring(const char *s, int ng, const char *gn[])
+{
+ /* same as normal search_string, but this one searches QM strings */
+ int i;
+
+ for (i = 0; (i < ng); i++)
+ {
+ if (gmx_strcasecmp(s, gn[i]) == 0)
+ {
+ return i;
+ }
+ }
+
+ gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
+
+ return -1;
+
+} /* search_QMstring */
+
+/* We would like gn to be const as well, but C doesn't allow this */
+int search_string(const char *s, int ng, char *gn[])
+{
+ int i;
+
+ for (i = 0; (i < ng); i++)
+ {
+ if (gmx_strcasecmp(s, gn[i]) == 0)
+ {
+ return i;
+ }
+ }
+
+ gmx_fatal(FARGS,
+ "Group %s referenced in the .mdp file was not found in the index file.\n"
+ "Group names must match either [moleculetype] names or custom index group\n"
+ "names, in which case you must supply an index file to the '-n' option\n"
+ "of grompp.",
+ s);
+
+ return -1;
+}
+
+static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
+ t_blocka *block, char *gnames[],
+ int gtype, int restnm,
+ int grptp, gmx_bool bVerbose,
+ warninp_t wi)
+{
+ unsigned short *cbuf;
+ t_grps *grps = &(groups->grps[gtype]);
+ int i, j, gid, aj, ognr, ntot = 0;
+ const char *title;
+ gmx_bool bRest;
+ char warn_buf[STRLEN];
+
+ if (debug)
+ {
+ fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
+ }
+
+ title = gtypes[gtype];
+
+ snew(cbuf, natoms);
+ /* Mark all id's as not set */
+ for (i = 0; (i < natoms); i++)
+ {
+ cbuf[i] = NOGID;
+ }
+
+ snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
+ for (i = 0; (i < ng); i++)
+ {
+ /* Lookup the group name in the block structure */
+ gid = search_string(ptrs[i], block->nr, gnames);
+ if ((grptp != egrptpONE) || (i == 0))
+ {
+ grps->nm_ind[grps->nr++] = gid;
+ }
+ if (debug)
+ {
+ fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
+ }
+
+ /* Now go over the atoms in the group */
+ for (j = block->index[gid]; (j < block->index[gid+1]); j++)
+ {
+
+ aj = block->a[j];
+
+ /* Range checking */
+ if ((aj < 0) || (aj >= natoms))
+ {
+ gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
+ }
+ /* Lookup up the old group number */
+ ognr = cbuf[aj];
+ if (ognr != NOGID)
+ {
+ gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
+ aj+1, title, ognr+1, i+1);
+ }
+ else
+ {
+ /* Store the group number in buffer */
+ if (grptp == egrptpONE)
+ {
+ cbuf[aj] = 0;
+ }
+ else
+ {
+ cbuf[aj] = i;
+ }
+ ntot++;
+ }
+ }
+ }
+
+ /* Now check whether we have done all atoms */
+ bRest = FALSE;
+ if (ntot != natoms)
+ {
+ if (grptp == egrptpALL)
+ {
+ gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
+ natoms-ntot, title);
+ }
+ else if (grptp == egrptpPART)
+ {
+ sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
+ natoms-ntot, title);
+ warning_note(wi, warn_buf);
+ }
+ /* Assign all atoms currently unassigned to a rest group */
+ for (j = 0; (j < natoms); j++)
+ {
+ if (cbuf[j] == NOGID)
+ {
+ cbuf[j] = grps->nr;
+ bRest = TRUE;
+ }
+ }
+ if (grptp != egrptpPART)
+ {
+ if (bVerbose)
+ {
+ fprintf(stderr,
+ "Making dummy/rest group for %s containing %d elements\n",
+ title, natoms-ntot);
+ }
+ /* Add group name "rest" */
+ grps->nm_ind[grps->nr] = restnm;
+
+ /* Assign the rest name to all atoms not currently assigned to a group */
+ for (j = 0; (j < natoms); j++)
+ {
+ if (cbuf[j] == NOGID)
+ {
+ cbuf[j] = grps->nr;
+ }
+ }
+ grps->nr++;
+ }
+ }
+
+ if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
+ {
+ /* All atoms are part of one (or no) group, no index required */
+ groups->ngrpnr[gtype] = 0;
+ groups->grpnr[gtype] = NULL;
+ }
+ else
+ {
+ groups->ngrpnr[gtype] = natoms;
+ snew(groups->grpnr[gtype], natoms);
+ for (j = 0; (j < natoms); j++)
+ {
+ groups->grpnr[gtype][j] = cbuf[j];
+ }
+ }
+
+ sfree(cbuf);
+
+ return (bRest && grptp == egrptpPART);
+}
+
+static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
+{
+ t_grpopts *opts;
+ gmx_groups_t *groups;
+ t_pull *pull;
+ int natoms, ai, aj, i, j, d, g, imin, jmin;
+ t_iatom *ia;
+ int *nrdf2, *na_vcm, na_tot;
+ double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
+ gmx_mtop_atomloop_all_t aloop;
+ t_atom *atom;
+ int mb, mol, ftype, as;
+ gmx_molblock_t *molb;
+ gmx_moltype_t *molt;
+
+ /* Calculate nrdf.
+ * First calc 3xnr-atoms for each group
+ * then subtract half a degree of freedom for each constraint
+ *
+ * Only atoms and nuclei contribute to the degrees of freedom...
+ */
+
+ opts = &ir->opts;
+
+ groups = &mtop->groups;
+ natoms = mtop->natoms;
+
+ /* Allocate one more for a possible rest group */
+ /* We need to sum degrees of freedom into doubles,
+ * since floats give too low nrdf's above 3 million atoms.
+ */
+ snew(nrdf_tc, groups->grps[egcTC].nr+1);
+ snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
+ snew(na_vcm, groups->grps[egcVCM].nr+1);
+
+ for (i = 0; i < groups->grps[egcTC].nr; i++)
+ {
+ nrdf_tc[i] = 0;
+ }
+ for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
+ {
+ nrdf_vcm[i] = 0;
+ }
+
+ snew(nrdf2, natoms);
+ aloop = gmx_mtop_atomloop_all_init(mtop);
+ while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
+ {
+ nrdf2[i] = 0;
+ if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
+ {
+ g = ggrpnr(groups, egcFREEZE, i);
+ /* Double count nrdf for particle i */
+ for (d = 0; d < DIM; d++)
+ {
+ if (opts->nFreeze[g][d] == 0)
+ {
+ nrdf2[i] += 2;
+ }
+ }
+ nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
+ nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
+ }
+ }
+
+ as = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molb = &mtop->molblock[mb];
+ molt = &mtop->moltype[molb->type];
+ atom = molt->atoms.atom;
+ for (mol = 0; mol < molb->nmol; mol++)
+ {
+ for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
+ {
+ ia = molt->ilist[ftype].iatoms;
+ for (i = 0; i < molt->ilist[ftype].nr; )
+ {
+ /* Subtract degrees of freedom for the constraints,
+ * if the particles still have degrees of freedom left.
+ * If one of the particles is a vsite or a shell, then all
+ * constraint motion will go there, but since they do not
+ * contribute to the constraints the degrees of freedom do not
+ * change.
+ */
+ ai = as + ia[1];
+ aj = as + ia[2];
+ if (((atom[ia[1]].ptype == eptNucleus) ||
+ (atom[ia[1]].ptype == eptAtom)) &&
+ ((atom[ia[2]].ptype == eptNucleus) ||
+ (atom[ia[2]].ptype == eptAtom)))
+ {
+ if (nrdf2[ai] > 0)
+ {
+ jmin = 1;
+ }
+ else
+ {
+ jmin = 2;
+ }
+ if (nrdf2[aj] > 0)
+ {
+ imin = 1;
+ }
+ else
+ {
+ imin = 2;
+ }
+ imin = min(imin, nrdf2[ai]);
+ jmin = min(jmin, nrdf2[aj]);
+ nrdf2[ai] -= imin;
+ nrdf2[aj] -= jmin;
+ nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
+ nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
+ nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
+ nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
+ }
+ ia += interaction_function[ftype].nratoms+1;
+ i += interaction_function[ftype].nratoms+1;
+ }
+ }
+ ia = molt->ilist[F_SETTLE].iatoms;
+ for (i = 0; i < molt->ilist[F_SETTLE].nr; )
+ {
+ /* Subtract 1 dof from every atom in the SETTLE */
+ for (j = 0; j < 3; j++)
+ {
+ ai = as + ia[1+j];
+ imin = min(2, nrdf2[ai]);
+ nrdf2[ai] -= imin;
+ nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
+ nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
+ }
+ ia += 4;
+ i += 4;
+ }
+ as += molt->atoms.nr;
+ }
+ }
+
+ if (ir->ePull == epullCONSTRAINT)
+ {
+ /* Correct nrdf for the COM constraints.
+ * We correct using the TC and VCM group of the first atom
+ * in the reference and pull group. If atoms in one pull group
+ * belong to different TC or VCM groups it is anyhow difficult
+ * to determine the optimal nrdf assignment.
+ */
+ pull = ir->pull;
+
+ for (i = 0; i < pull->ncoord; i++)
+ {
+ imin = 1;
+
+ for (j = 0; j < 2; j++)
+ {
+ const t_pull_group *pgrp;
+
+ pgrp = &pull->group[pull->coord[i].group[j]];
+
+ if (pgrp->nat > 0)
+ {
+ /* Subtract 1/2 dof from each group */
+ ai = pgrp->ind[0];
+ nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
+ nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
+ if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
+ {
+ gmx_fatal(FARGS, "Center of mass pulling constraints caused the number of degrees of freedom for temperature coupling group %s to be negative", gnames[groups->grps[egcTC].nm_ind[ggrpnr(groups, egcTC, ai)]]);
+ }
+ }
+ else
+ {
+ /* We need to subtract the whole DOF from group j=1 */
+ imin += 1;
+ }
+ }
+ }
+ }
+
+ if (ir->nstcomm != 0)
+ {
+ /* Subtract 3 from the number of degrees of freedom in each vcm group
+ * when com translation is removed and 6 when rotation is removed
+ * as well.
+ */
+ switch (ir->comm_mode)
+ {
+ case ecmLINEAR:
+ n_sub = ndof_com(ir);
+ break;
+ case ecmANGULAR:
+ n_sub = 6;
+ break;
+ default:
+ n_sub = 0;
+ gmx_incons("Checking comm_mode");
+ }
+
+ for (i = 0; i < groups->grps[egcTC].nr; i++)
+ {
+ /* Count the number of atoms of TC group i for every VCM group */
+ for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
+ {
+ na_vcm[j] = 0;
+ }
+ na_tot = 0;
+ for (ai = 0; ai < natoms; ai++)
+ {
+ if (ggrpnr(groups, egcTC, ai) == i)
+ {
+ na_vcm[ggrpnr(groups, egcVCM, ai)]++;
+ na_tot++;
+ }
+ }
+ /* Correct for VCM removal according to the fraction of each VCM
+ * group present in this TC group.
+ */
+ nrdf_uc = nrdf_tc[i];
+ if (debug)
+ {
+ fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
+ i, nrdf_uc, n_sub);
+ }
+ nrdf_tc[i] = 0;
+ for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
+ {
+ if (nrdf_vcm[j] > n_sub)
+ {
+ nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
+ (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
+ }
+ if (debug)
+ {
+ fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
+ j, nrdf_vcm[j], nrdf_tc[i]);
+ }
+ }
+ }
+ }
+ for (i = 0; (i < groups->grps[egcTC].nr); i++)
+ {
+ opts->nrdf[i] = nrdf_tc[i];
+ if (opts->nrdf[i] < 0)
+ {
+ opts->nrdf[i] = 0;
+ }
+ fprintf(stderr,
+ "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
+ gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
+ }
+
+ sfree(nrdf2);
+ sfree(nrdf_tc);
+ sfree(nrdf_vcm);
+ sfree(na_vcm);
+}
+
+static void decode_cos(char *s, t_cosines *cosine)
+{
+ char *t;
+ char format[STRLEN], f1[STRLEN];
+ double a, phi;
+ int i;
+
+ t = strdup(s);
+ trim(t);
+
+ cosine->n = 0;
+ cosine->a = NULL;
+ cosine->phi = NULL;
+ if (strlen(t))
+ {
+ sscanf(t, "%d", &(cosine->n));
+ if (cosine->n <= 0)
+ {
+ cosine->n = 0;
+ }
+ else
+ {
+ snew(cosine->a, cosine->n);
+ snew(cosine->phi, cosine->n);
+
+ sprintf(format, "%%*d");
+ for (i = 0; (i < cosine->n); i++)
+ {
+ strcpy(f1, format);
+ strcat(f1, "%lf%lf");
+ if (sscanf(t, f1, &a, &phi) < 2)
+ {
+ gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
+ }
+ cosine->a[i] = a;
+ cosine->phi[i] = phi;
+ strcat(format, "%*lf%*lf");
+ }
+ }
+ }
+ sfree(t);
+}
+
+static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
+ const char *option, const char *val, int flag)
+{
+ /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
+ * But since this is much larger than STRLEN, such a line can not be parsed.
+ * The real maximum is the number of names that fit in a string: STRLEN/2.
+ */
+#define EGP_MAX (STRLEN/2)
+ int nelem, i, j, k, nr;
+ char *names[EGP_MAX];
+ char ***gnames;
+ gmx_bool bSet;
+
+ gnames = groups->grpname;
+
+ nelem = str_nelem(val, EGP_MAX, names);
+ if (nelem % 2 != 0)
+ {
+ gmx_fatal(FARGS, "The number of groups for %s is odd", option);
+ }
+ nr = groups->grps[egcENER].nr;
+ bSet = FALSE;
+ for (i = 0; i < nelem/2; i++)
+ {
+ j = 0;
+ while ((j < nr) &&
+ gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
+ {
+ j++;
+ }
+ if (j == nr)
+ {
+ gmx_fatal(FARGS, "%s in %s is not an energy group\n",
+ names[2*i], option);
+ }
+ k = 0;
+ while ((k < nr) &&
+ gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
+ {
+ k++;
+ }
+ if (k == nr)
+ {
+ gmx_fatal(FARGS, "%s in %s is not an energy group\n",
+ names[2*i+1], option);
+ }
+ if ((j < nr) && (k < nr))
+ {
+ ir->opts.egp_flags[nr*j+k] |= flag;
+ ir->opts.egp_flags[nr*k+j] |= flag;
+ bSet = TRUE;
+ }
+ }
+
+ return bSet;
+}
+
+
+static void make_swap_groups(
+ t_swapcoords *swap,
+ char *swapgname,
+ char *splitg0name,
+ char *splitg1name,
+ char *solgname,
+ t_blocka *grps,
+ char **gnames)
+{
+ int ig = -1, i = 0, j;
+ char *splitg;
+
+
+ /* Just a quick check here, more thorough checks are in mdrun */
+ if (strcmp(splitg0name, splitg1name) == 0)
+ {
+ gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
+ }
+
+ /* First get the swap group index atoms */
+ ig = search_string(swapgname, grps->nr, gnames);
+ swap->nat = grps->index[ig+1] - grps->index[ig];
+ if (swap->nat > 0)
+ {
+ fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
+ snew(swap->ind, swap->nat);
+ for (i = 0; i < swap->nat; i++)
+ {
+ swap->ind[i] = grps->a[grps->index[ig]+i];
+ }
+ }
+ else
+ {
+ gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
+ }
+
+ /* Now do so for the split groups */
+ for (j = 0; j < 2; j++)
+ {
+ if (j == 0)
+ {
+ splitg = splitg0name;
+ }
+ else
+ {
+ splitg = splitg1name;
+ }
+
+ ig = search_string(splitg, grps->nr, gnames);
+ swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
+ if (swap->nat_split[j] > 0)
+ {
+ fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
+ j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
+ snew(swap->ind_split[j], swap->nat_split[j]);
+ for (i = 0; i < swap->nat_split[j]; i++)
+ {
+ swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
+ }
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
+ }
+ }
+
+ /* Now get the solvent group index atoms */
+ ig = search_string(solgname, grps->nr, gnames);
+ swap->nat_sol = grps->index[ig+1] - grps->index[ig];
+ if (swap->nat_sol > 0)
+ {
+ fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
+ snew(swap->ind_sol, swap->nat_sol);
+ for (i = 0; i < swap->nat_sol; i++)
+ {
+ swap->ind_sol[i] = grps->a[grps->index[ig]+i];
+ }
+ }
+ else
+ {
+ gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
+ }
+}
+
+
+void do_index(const char* mdparin, const char *ndx,
+ gmx_mtop_t *mtop,
+ gmx_bool bVerbose,
+ t_inputrec *ir, rvec *v,
+ warninp_t wi)
+{
+ t_blocka *grps;
+ gmx_groups_t *groups;
+ int natoms;
+ t_symtab *symtab;
+ t_atoms atoms_all;
+ char warnbuf[STRLEN], **gnames;
+ int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
+ real tau_min;
+ int nstcmin;
+ int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
+ char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
+ int i, j, k, restnm;
+ real SAtime;
+ gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
+ int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
+ nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
+ char warn_buf[STRLEN];
+
+ if (bVerbose)
+ {
+ fprintf(stderr, "processing index file...\n");
+ }
+ debug_gmx();
+ if (ndx == NULL)
+ {
+ snew(grps, 1);
+ snew(grps->index, 1);
+ snew(gnames, 1);
+ atoms_all = gmx_mtop_global_atoms(mtop);
+ analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
+ free_t_atoms(&atoms_all, FALSE);
+ }
+ else
+ {
+ grps = init_index(ndx, &gnames);
+ }
+
+ groups = &mtop->groups;
+ natoms = mtop->natoms;
+ symtab = &mtop->symtab;
+
+ snew(groups->grpname, grps->nr+1);
+
+ for (i = 0; (i < grps->nr); i++)
+ {
+ groups->grpname[i] = put_symtab(symtab, gnames[i]);
+ }
+ groups->grpname[i] = put_symtab(symtab, "rest");
+ restnm = i;
+ srenew(gnames, grps->nr+1);
+ gnames[restnm] = *(groups->grpname[i]);
+ groups->ngrpname = grps->nr+1;
+
+ set_warning_line(wi, mdparin, -1);
+
+ ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
+ nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
+ ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
+ if ((ntau_t != ntcg) || (nref_t != ntcg))
+ {
+ gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
+ "%d tau-t values", ntcg, nref_t, ntau_t);
+ }
+
+ bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
+ do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
+ restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
+ nr = groups->grps[egcTC].nr;
+ ir->opts.ngtc = nr;
+ snew(ir->opts.nrdf, nr);
+ snew(ir->opts.tau_t, nr);
+ snew(ir->opts.ref_t, nr);
+ if (ir->eI == eiBD && ir->bd_fric == 0)
+ {
+ fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
+ }
+
+ if (bSetTCpar)
+ {
+ if (nr != nref_t)
+ {
+ gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
+ }
+
+ tau_min = 1e20;
+ for (i = 0; (i < nr); i++)
+ {
+ ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
+ if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
+ {
+ sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
+ warning_error(wi, warn_buf);
+ }
+
+ if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
+ {
+ warning_note(wi, "tau-t = -1 is the value to signal that a group should not have temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
+ }
+
+ if (ir->opts.tau_t[i] >= 0)
+ {
+ tau_min = min(tau_min, ir->opts.tau_t[i]);
+ }
+ }
+ if (ir->etc != etcNO && ir->nsttcouple == -1)
+ {
+ ir->nsttcouple = ir_optimal_nsttcouple(ir);
+ }
+
+ if (EI_VV(ir->eI))
+ {
+ if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
+ {
+ gmx_fatal(FARGS, "Cannot do Nose-Hoover temperature with Berendsen pressure control with md-vv; use either vrescale temperature with berendsen pressure or Nose-Hoover temperature with MTTK pressure");
+ }
+ if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
+ {
+ if (ir->nstpcouple != ir->nsttcouple)
+ {
+ int mincouple = min(ir->nstpcouple, ir->nsttcouple);
+ ir->nstpcouple = ir->nsttcouple = mincouple;
+ sprintf(warn_buf, "for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = %d", mincouple);
+ warning_note(wi, warn_buf);
+ }
+ }
+ }
+ /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
+ primarily for testing purposes, and does not work with temperature coupling other than 1 */
+
+ if (ETC_ANDERSEN(ir->etc))
+ {
+ if (ir->nsttcouple != 1)
+ {
+ ir->nsttcouple = 1;
+ sprintf(warn_buf, "Andersen temperature control methods assume nsttcouple = 1; there is no need for larger nsttcouple > 1, since no global parameters are computed. nsttcouple has been reset to 1");
+ warning_note(wi, warn_buf);
+ }
+ }
+ nstcmin = tcouple_min_integration_steps(ir->etc);
+ if (nstcmin > 1)
+ {
+ if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
+ {
+ sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
+ ETCOUPLTYPE(ir->etc),
+ tau_min, nstcmin,
+ ir->nsttcouple*ir->delta_t);
+ warning(wi, warn_buf);
+ }
+ }
+ for (i = 0; (i < nr); i++)
+ {
+ ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
+ if (ir->opts.ref_t[i] < 0)
+ {
+ gmx_fatal(FARGS, "ref-t for group %d negative", i);
+ }
+ }
+ /* set the lambda mc temperature to the md integrator temperature (which should be defined
+ if we are in this conditional) if mc_temp is negative */
+ if (ir->expandedvals->mc_temp < 0)
+ {
+ ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
+ }
+ }
+
+ /* Simulated annealing for each group. There are nr groups */
+ nSA = str_nelem(is->anneal, MAXPTR, ptr1);
+ if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
+ {
+ nSA = 0;
+ }
+ if (nSA > 0 && nSA != nr)
+ {
+ gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
+ }
+ else
+ {
+ snew(ir->opts.annealing, nr);
+ snew(ir->opts.anneal_npoints, nr);
+ snew(ir->opts.anneal_time, nr);
+ snew(ir->opts.anneal_temp, nr);
+ for (i = 0; i < nr; i++)
+ {
+ ir->opts.annealing[i] = eannNO;
+ ir->opts.anneal_npoints[i] = 0;
+ ir->opts.anneal_time[i] = NULL;
+ ir->opts.anneal_temp[i] = NULL;
+ }
+ if (nSA > 0)
+ {
+ bAnneal = FALSE;
+ for (i = 0; i < nr; i++)
+ {
+ if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
+ {
+ ir->opts.annealing[i] = eannNO;
+ }
+ else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
+ {
+ ir->opts.annealing[i] = eannSINGLE;
+ bAnneal = TRUE;
+ }
+ else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
+ {
+ ir->opts.annealing[i] = eannPERIODIC;
+ bAnneal = TRUE;
+ }
+ }
+ if (bAnneal)
+ {
+ /* Read the other fields too */
+ nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
+ if (nSA_points != nSA)
+ {
+ gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
+ }
+ for (k = 0, i = 0; i < nr; i++)
+ {
+ ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
+ if (ir->opts.anneal_npoints[i] == 1)
+ {
+ gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
+ }
+ snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
+ snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
+ k += ir->opts.anneal_npoints[i];
+ }
+
+ nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
+ if (nSA_time != k)
+ {
+ gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
+ }
+ nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
+ if (nSA_temp != k)
+ {
+ gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
+ }
+
+ for (i = 0, k = 0; i < nr; i++)
+ {
+
+ for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
+ {
+ ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
+ ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
+ if (j == 0)
+ {
+ if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
+ {
+ gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
+ }
+ }
+ else
+ {
+ /* j>0 */
+ if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
+ {
+ gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
+ ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
+ }
+ }
+ if (ir->opts.anneal_temp[i][j] < 0)
+ {
+ gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
+ }
+ k++;
+ }
+ }
+ /* Print out some summary information, to make sure we got it right */
+ for (i = 0, k = 0; i < nr; i++)
+ {
+ if (ir->opts.annealing[i] != eannNO)
+ {
+ j = groups->grps[egcTC].nm_ind[i];
+ fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
+ *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
+ ir->opts.anneal_npoints[i]);
+ fprintf(stderr, "Time (ps) Temperature (K)\n");
+ /* All terms except the last one */
+ for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
+ {
+ fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
+ }
+
+ /* Finally the last one */
+ j = ir->opts.anneal_npoints[i]-1;
+ if (ir->opts.annealing[i] == eannSINGLE)
+ {
+ fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
+ }
+ else
+ {
+ fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
+ if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
+ {
+ warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ if (ir->ePull != epullNO)
+ {
+ make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
+
+ make_pull_coords(ir->pull);
+ }
+
+ if (ir->bRot)
+ {
+ make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
+ }
+
+ if (ir->eSwapCoords != eswapNO)
+ {
+ make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
+ }
+
+ nacc = str_nelem(is->acc, MAXPTR, ptr1);
+ nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
+ if (nacg*DIM != nacc)
+ {
+ gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
+ nacg, nacc);
+ }
+ do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
+ restnm, egrptpALL_GENREST, bVerbose, wi);
+ nr = groups->grps[egcACC].nr;
+ snew(ir->opts.acc, nr);
+ ir->opts.ngacc = nr;
+
+ for (i = k = 0; (i < nacg); i++)
+ {
+ for (j = 0; (j < DIM); j++, k++)
+ {
+ ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
+ }
+ }
+ for (; (i < nr); i++)
+ {
+ for (j = 0; (j < DIM); j++)
+ {
+ ir->opts.acc[i][j] = 0;
+ }
+ }
+
+ nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
+ nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
+ if (nfrdim != DIM*nfreeze)
+ {
+ gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
+ nfreeze, nfrdim);
+ }
+ do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
+ restnm, egrptpALL_GENREST, bVerbose, wi);
+ nr = groups->grps[egcFREEZE].nr;
+ ir->opts.ngfrz = nr;
+ snew(ir->opts.nFreeze, nr);
+ for (i = k = 0; (i < nfreeze); i++)
+ {
+ for (j = 0; (j < DIM); j++, k++)
+ {
+ ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
+ if (!ir->opts.nFreeze[i][j])
+ {
+ if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
+ {
+ sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
+ "(not %s)", ptr1[k]);
+ warning(wi, warn_buf);
+ }
+ }
+ }
+ }
+ for (; (i < nr); i++)
+ {
+ for (j = 0; (j < DIM); j++)
+ {
+ ir->opts.nFreeze[i][j] = 0;
+ }
+ }
+
+ nenergy = str_nelem(is->energy, MAXPTR, ptr1);
+ do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
+ restnm, egrptpALL_GENREST, bVerbose, wi);
+ add_wall_energrps(groups, ir->nwall, symtab);
+ ir->opts.ngener = groups->grps[egcENER].nr;
+ nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
+ bRest =
+ do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
+ restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
+ if (bRest)
+ {
+ warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
+ "This may lead to artifacts.\n"
+ "In most cases one should use one group for the whole system.");
+ }
+
+ /* Now we have filled the freeze struct, so we can calculate NRDF */
+ calc_nrdf(mtop, ir, gnames);
+
+ if (v && NULL)
+ {
+ real fac, ntot = 0;
+
+ /* Must check per group! */
+ for (i = 0; (i < ir->opts.ngtc); i++)
+ {
+ ntot += ir->opts.nrdf[i];
+ }
+ if (ntot != (DIM*natoms))
+ {
+ fac = sqrt(ntot/(DIM*natoms));
+ if (bVerbose)
+ {
+ fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
+ "and removal of center of mass motion\n", fac);
+ }
+ for (i = 0; (i < natoms); i++)
+ {
+ svmul(fac, v[i], v[i]);
+ }
+ }
+ }
+
+ nuser = str_nelem(is->user1, MAXPTR, ptr1);
+ do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
+ restnm, egrptpALL_GENREST, bVerbose, wi);
+ nuser = str_nelem(is->user2, MAXPTR, ptr1);
+ do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
+ restnm, egrptpALL_GENREST, bVerbose, wi);
+ nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
+ do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
+ restnm, egrptpONE, bVerbose, wi);
+ nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
+ do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
+ restnm, egrptpALL_GENREST, bVerbose, wi);
+
+ /* QMMM input processing */
+ nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
+ nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
+ nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
+ if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
+ {
+ gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
+ " and %d methods\n", nQMg, nQMbasis, nQMmethod);
+ }
+ /* group rest, if any, is always MM! */
+ do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
+ restnm, egrptpALL_GENREST, bVerbose, wi);
+ nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
+ ir->opts.ngQM = nQMg;
+ snew(ir->opts.QMmethod, nr);
+ snew(ir->opts.QMbasis, nr);
+ for (i = 0; i < nr; i++)
+ {
+ /* input consists of strings: RHF CASSCF PM3 .. These need to be
+ * converted to the corresponding enum in names.c
+ */
+ ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
+ eQMmethod_names);
+ ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
+ eQMbasis_names);
+
+ }
+ nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
+ nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
+ nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
+ snew(ir->opts.QMmult, nr);
+ snew(ir->opts.QMcharge, nr);
+ snew(ir->opts.bSH, nr);
+
+ for (i = 0; i < nr; i++)
+ {
+ ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
+ ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
+ ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
+ }
+
+ nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
+ nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
+ snew(ir->opts.CASelectrons, nr);
+ snew(ir->opts.CASorbitals, nr);
+ for (i = 0; i < nr; i++)
+ {
+ ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
+ ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
+ }
+ /* special optimization options */
+
+ nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
+ nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
+ snew(ir->opts.bOPT, nr);
+ snew(ir->opts.bTS, nr);
+ for (i = 0; i < nr; i++)
+ {
+ ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
+ ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
+ }
+ nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
+ nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
+ nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
+ snew(ir->opts.SAon, nr);
+ snew(ir->opts.SAoff, nr);
+ snew(ir->opts.SAsteps, nr);
+
+ for (i = 0; i < nr; i++)
+ {
+ ir->opts.SAon[i] = strtod(ptr1[i], NULL);
+ ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
+ ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
+ }
+ /* end of QMMM input */
+
+ if (bVerbose)
+ {
+ for (i = 0; (i < egcNR); i++)
+ {
+ fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
+ for (j = 0; (j < groups->grps[i].nr); j++)
+ {
+ fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
+ }
+ fprintf(stderr, "\n");
+ }
+ }
+
+ nr = groups->grps[egcENER].nr;
+ snew(ir->opts.egp_flags, nr*nr);
+
+ bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
+ if (bExcl && ir->cutoff_scheme == ecutsVERLET)
+ {
+ warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
+ }
+ if (bExcl && EEL_FULL(ir->coulombtype))
+ {
+ warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
+ }
+
+ bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
+ if (bTable && !(ir->vdwtype == evdwUSER) &&
+ !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
+ !(ir->coulombtype == eelPMEUSERSWITCH))
+ {
+ gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
+ }
+
+ decode_cos(is->efield_x, &(ir->ex[XX]));
+ decode_cos(is->efield_xt, &(ir->et[XX]));
+ decode_cos(is->efield_y, &(ir->ex[YY]));
+ decode_cos(is->efield_yt, &(ir->et[YY]));
+ decode_cos(is->efield_z, &(ir->ex[ZZ]));
+ decode_cos(is->efield_zt, &(ir->et[ZZ]));
+
+ if (ir->bAdress)
+ {
+ do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
+ }
+
+ for (i = 0; (i < grps->nr); i++)
+ {
+ sfree(gnames[i]);
+ }
+ sfree(gnames);
+ done_blocka(grps);
+ sfree(grps);
+
+}
+
+
+
+static void check_disre(gmx_mtop_t *mtop)
+{
+ gmx_ffparams_t *ffparams;
+ t_functype *functype;
+ t_iparams *ip;
+ int i, ndouble, ftype;
+ int label, old_label;
+
+ if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
+ {
+ ffparams = &mtop->ffparams;
+ functype = ffparams->functype;
+ ip = ffparams->iparams;
+ ndouble = 0;
+ old_label = -1;
+ for (i = 0; i < ffparams->ntypes; i++)
+ {
+ ftype = functype[i];
+ if (ftype == F_DISRES)
+ {
+ label = ip[i].disres.label;
+ if (label == old_label)
+ {
+ fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
+ ndouble++;
+ }
+ old_label = label;
+ }
+ }
+ if (ndouble > 0)
+ {
+ gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
+ "probably the parameters for multiple pairs in one restraint "
+ "are not identical\n", ndouble);
+ }
+ }
+}
+
+static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
+ gmx_bool posres_only,
+ ivec AbsRef)
+{
+ int d, g, i;
+ gmx_mtop_ilistloop_t iloop;
+ t_ilist *ilist;
+ int nmol;
+ t_iparams *pr;
+
+ clear_ivec(AbsRef);
+
+ if (!posres_only)
+ {
+ /* Check the COM */
+ for (d = 0; d < DIM; d++)
+ {
+ AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
+ }
+ /* Check for freeze groups */
+ for (g = 0; g < ir->opts.ngfrz; g++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ if (ir->opts.nFreeze[g][d] != 0)
+ {
+ AbsRef[d] = 1;
+ }
+ }
+ }
+ }
+
+ /* Check for position restraints */
+ iloop = gmx_mtop_ilistloop_init(sys);
+ while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
+ {
+ if (nmol > 0 &&
+ (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
+ {
+ for (i = 0; i < ilist[F_POSRES].nr; i += 2)
+ {
+ pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
+ for (d = 0; d < DIM; d++)
+ {
+ if (pr->posres.fcA[d] != 0)
+ {
+ AbsRef[d] = 1;
+ }
+ }
+ }
+ for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
+ {
+ /* Check for flat-bottom posres */
+ pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
+ if (pr->fbposres.k != 0)
+ {
+ switch (pr->fbposres.geom)
+ {
+ case efbposresSPHERE:
+ AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
+ break;
+ case efbposresCYLINDER:
+ AbsRef[XX] = AbsRef[YY] = 1;
+ break;
+ case efbposresX: /* d=XX */
+ case efbposresY: /* d=YY */
+ case efbposresZ: /* d=ZZ */
+ d = pr->fbposres.geom - efbposresX;
+ AbsRef[d] = 1;
+ break;
+ default:
+ gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
+ "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
+ pr->fbposres.geom);
+ }
+ }
+ }
+ }
+ }
+
+ return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
+}
+
+static void
+check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
+ gmx_bool *bC6ParametersWorkWithGeometricRules,
+ gmx_bool *bC6ParametersWorkWithLBRules,
+ gmx_bool *bLBRulesPossible)
+{
+ int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
+ int *typecount;
+ real tol;
+ double geometricdiff, LBdiff;
+ double c6i, c6j, c12i, c12j;
+ double c6, c6_geometric, c6_LB;
+ double sigmai, sigmaj, epsi, epsj;
+ gmx_bool bCanDoLBRules, bCanDoGeometricRules;
+ const char *ptr;
+
+ /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
+ * force-field floating point parameters.
+ */
+ tol = 1e-5;
+ ptr = getenv("GMX_LJCOMB_TOL");
+ if (ptr != NULL)
+ {
+ double dbl;
+
+ sscanf(ptr, "%lf", &dbl);
+ tol = dbl;
+ }
+
+ *bC6ParametersWorkWithLBRules = TRUE;
+ *bC6ParametersWorkWithGeometricRules = TRUE;
+ bCanDoLBRules = TRUE;
+ bCanDoGeometricRules = TRUE;
+ ntypes = mtop->ffparams.atnr;
+ snew(typecount, ntypes);
+ gmx_mtop_count_atomtypes(mtop, state, typecount);
+ geometricdiff = LBdiff = 0.0;
+ *bLBRulesPossible = TRUE;
+ for (tpi = 0; tpi < ntypes; ++tpi)
+ {
+ c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
+ c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
+ for (tpj = tpi; tpj < ntypes; ++tpj)
+ {
+ c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
+ c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
+ c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
+ c6_geometric = sqrt(c6i * c6j);
+ if (!gmx_numzero(c6_geometric))
+ {
+ if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
+ {
+ sigmai = pow(c12i / c6i, 1.0/6.0);
+ sigmaj = pow(c12j / c6j, 1.0/6.0);
+ epsi = c6i * c6i /(4.0 * c12i);
+ epsj = c6j * c6j /(4.0 * c12j);
+ c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
+ }
+ else
+ {
+ *bLBRulesPossible = FALSE;
+ c6_LB = c6_geometric;
+ }
+ bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
+ }
+
+ if (FALSE == bCanDoLBRules)
+ {
+ *bC6ParametersWorkWithLBRules = FALSE;
+ }
+
+ bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
+
+ if (FALSE == bCanDoGeometricRules)
+ {
+ *bC6ParametersWorkWithGeometricRules = FALSE;
+ }
+ }
+ }
+ sfree(typecount);
+}
+
+static void
+check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
+ warninp_t wi)
+{
+ char err_buf[256];
+ gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
+
+ check_combination_rule_differences(mtop, 0,
+ &bC6ParametersWorkWithGeometricRules,
+ &bC6ParametersWorkWithLBRules,
+ &bLBRulesPossible);
+ if (ir->ljpme_combination_rule == eljpmeLB)
+ {
+ if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
+ {
+ warning(wi, "You are using arithmetic-geometric combination rules "
+ "in LJ-PME, but your non-bonded C6 parameters do not "
+ "follow these rules.");
+ }
+ }
+ else
+ {
+ if (FALSE == bC6ParametersWorkWithGeometricRules)
+ {
+ if (ir->eDispCorr != edispcNO)
+ {
+ warning_note(wi, "You are using geometric combination rules in "
+ "LJ-PME, but your non-bonded C6 parameters do "
+ "not follow these rules. "
+ "This will introduce very small errors in the forces and energies in "
+ "your simulations. Dispersion correction will correct total energy "
+ "and/or pressure for isotropic systems, but not forces or surface tensions.");
+ }
+ else
+ {
+ warning_note(wi, "You are using geometric combination rules in "
+ "LJ-PME, but your non-bonded C6 parameters do "
+ "not follow these rules. "
+ "This will introduce very small errors in the forces and energies in "
+ "your simulations. If your system is homogeneous, consider using dispersion correction "
+ "for the total energy and pressure.");
+ }
+ }
+ }
+}
+
+void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
+ warninp_t wi)
+{
+ char err_buf[256];
+ int i, m, c, nmol, npct;
+ gmx_bool bCharge, bAcc;
+ real gdt_max, *mgrp, mt;
+ rvec acc;
+ gmx_mtop_atomloop_block_t aloopb;
+ gmx_mtop_atomloop_all_t aloop;
+ t_atom *atom;
+ ivec AbsRef;
+ char warn_buf[STRLEN];
+
+ set_warning_line(wi, mdparin, -1);
+
+ if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
+ ir->comm_mode == ecmNO &&
+ !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
+ !ETC_ANDERSEN(ir->etc))
+ {
+ warning(wi, "You are not using center of mass motion removal (mdp option comm-mode), numerical rounding errors can lead to build up of kinetic energy of the center of mass");
+ }
+
+ /* Check for pressure coupling with absolute position restraints */
+ if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
+ {
+ absolute_reference(ir, sys, TRUE, AbsRef);
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ if (AbsRef[m] && norm2(ir->compress[m]) > 0)
+ {
+ warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
+ break;
+ }
+ }
+ }
+ }
+
+ bCharge = FALSE;
+ aloopb = gmx_mtop_atomloop_block_init(sys);
+ while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
+ {
+ if (atom->q != 0 || atom->qB != 0)
+ {
+ bCharge = TRUE;
+ }
+ }
+
+ if (!bCharge)
+ {
+ if (EEL_FULL(ir->coulombtype))
+ {
+ sprintf(err_buf,
+ "You are using full electrostatics treatment %s for a system without charges.\n"
+ "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
+ EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
+ warning(wi, err_buf);
+ }
+ }
+ else
+ {
+ if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
+ {
+ sprintf(err_buf,
+ "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
+ "You might want to consider using %s electrostatics.\n",
+ EELTYPE(eelPME));
+ warning_note(wi, err_buf);
+ }
+ }
+
+ /* Check if combination rules used in LJ-PME are the same as in the force field */
+ if (EVDW_PME(ir->vdwtype))
+ {
+ check_combination_rules(ir, sys, wi);
+ }
+
+ /* Generalized reaction field */
+ if (ir->opts.ngtc == 0)
+ {
+ sprintf(err_buf, "No temperature coupling while using coulombtype %s",
+ eel_names[eelGRF]);
+ CHECK(ir->coulombtype == eelGRF);
+ }
+ else
+ {
+ sprintf(err_buf, "When using coulombtype = %s"
+ " ref-t for temperature coupling should be > 0",
+ eel_names[eelGRF]);
+ CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
+ }
+
+ if (ir->eI == eiSD1 &&
+ (gmx_mtop_ftype_count(sys, F_CONSTR) > 0 ||
+ gmx_mtop_ftype_count(sys, F_SETTLE) > 0))
+ {
+ sprintf(warn_buf, "With constraints integrator %s is less accurate, consider using %s instead", ei_names[ir->eI], ei_names[eiSD2]);
+ warning_note(wi, warn_buf);
+ }
+
+ bAcc = FALSE;
+ for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
+ {
+ for (m = 0; (m < DIM); m++)
+ {
+ if (fabs(ir->opts.acc[i][m]) > 1e-6)
+ {
+ bAcc = TRUE;
+ }
+ }
+ }
+ if (bAcc)
+ {
+ clear_rvec(acc);
+ snew(mgrp, sys->groups.grps[egcACC].nr);
+ aloop = gmx_mtop_atomloop_all_init(sys);
+ while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
+ {
+ mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
+ }
+ mt = 0.0;
+ for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
+ {
+ for (m = 0; (m < DIM); m++)
+ {
+ acc[m] += ir->opts.acc[i][m]*mgrp[i];
+ }
+ mt += mgrp[i];
+ }
+ for (m = 0; (m < DIM); m++)
+ {
+ if (fabs(acc[m]) > 1e-6)
+ {
+ const char *dim[DIM] = { "X", "Y", "Z" };
+ fprintf(stderr,
+ "Net Acceleration in %s direction, will %s be corrected\n",
+ dim[m], ir->nstcomm != 0 ? "" : "not");
+ if (ir->nstcomm != 0 && m < ndof_com(ir))
+ {
+ acc[m] /= mt;
+ for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
+ {
+ ir->opts.acc[i][m] -= acc[m];
+ }
+ }
+ }
+ }
+ sfree(mgrp);
+ }
+
+ if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
+ !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
+ {
+ gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
+ }
+
+ if (ir->ePull != epullNO)
+ {
+ gmx_bool bPullAbsoluteRef;
+
+ bPullAbsoluteRef = FALSE;
+ for (i = 0; i < ir->pull->ncoord; i++)
+ {
+ bPullAbsoluteRef = bPullAbsoluteRef ||
+ ir->pull->coord[i].group[0] == 0 ||
+ ir->pull->coord[i].group[1] == 0;
+ }
+ if (bPullAbsoluteRef)
+ {
+ absolute_reference(ir, sys, FALSE, AbsRef);
+ for (m = 0; m < DIM; m++)
+ {
+ if (ir->pull->dim[m] && !AbsRef[m])
+ {
+ warning(wi, "You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts.");
+ break;
+ }
+ }
+ }
+
+ if (ir->pull->eGeom == epullgDIRPBC)
+ {
+ for (i = 0; i < 3; i++)
+ {
+ for (m = 0; m <= i; m++)
+ {
+ if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
+ ir->deform[i][m] != 0)
+ {
+ for (c = 0; c < ir->pull->ncoord; c++)
+ {
+ if (ir->pull->coord[c].vec[m] != 0)
+ {
+ gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ check_disre(sys);
+}
+
+void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
+{
+ real min_size;
+ gmx_bool bTWIN;
+ char warn_buf[STRLEN];
+ const char *ptr;
+
+ ptr = check_box(ir->ePBC, box);
+ if (ptr)
+ {
+ warning_error(wi, ptr);
+ }
+
+ if (bConstr && ir->eConstrAlg == econtSHAKE)
+ {
+ if (ir->shake_tol <= 0.0)
+ {
+ sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
+ ir->shake_tol);
+ warning_error(wi, warn_buf);
+ }
+
+ if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
+ {
+ sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
+ if (ir->epc == epcNO)
+ {
+ warning(wi, warn_buf);
+ }
+ else
+ {
+ warning_error(wi, warn_buf);
+ }
+ }
+ }
+
+ if ( (ir->eConstrAlg == econtLINCS) && bConstr)
+ {
+ /* If we have Lincs constraints: */
+ if (ir->eI == eiMD && ir->etc == etcNO &&
+ ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
+ {
+ sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
+ warning_note(wi, warn_buf);
+ }
+
+ if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
+ {
+ sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
+ warning_note(wi, warn_buf);
+ }
+ if (ir->epc == epcMTTK)
+ {
+ warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
+ }
+ }
+
++ if (bConstr && ir->epc == epcMTTK)
++ {
++ warning_note(wi, "MTTK with constraints is deprecated, and will be removed in GROMACS 5.1");
++ }
++
+ if (ir->LincsWarnAngle > 90.0)
+ {
+ sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
+ warning(wi, warn_buf);
+ ir->LincsWarnAngle = 90.0;
+ }
+
+ if (ir->ePBC != epbcNONE)
+ {
+ if (ir->nstlist == 0)
+ {
+ warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
+ }
+ bTWIN = (ir->rlistlong > ir->rlist);
+ if (ir->ns_type == ensGRID)
+ {
+ if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
+ {
+ sprintf(warn_buf, "ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease %s.\n",
+ bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
+ warning_error(wi, warn_buf);
+ }
+ }
+ else
+ {
+ min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
+ if (2*ir->rlistlong >= min_size)
+ {
+ sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
+ warning_error(wi, warn_buf);
+ if (TRICLINIC(box))
+ {
+ fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
+ }
+ }
+ }
+ }
+}
+
+void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
+ rvec *x,
+ warninp_t wi)
+{
+ real rvdw1, rvdw2, rcoul1, rcoul2;
+ char warn_buf[STRLEN];
+
+ calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
+
+ if (rvdw1 > 0)
+ {
+ printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
+ rvdw1, rvdw2);
+ }
+ if (rcoul1 > 0)
+ {
+ printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
+ rcoul1, rcoul2);
+ }
+
+ if (ir->rlist > 0)
+ {
+ if (rvdw1 + rvdw2 > ir->rlist ||
+ rcoul1 + rcoul2 > ir->rlist)
+ {
+ sprintf(warn_buf,
+ "The sum of the two largest charge group radii (%f) "
+ "is larger than rlist (%f)\n",
+ max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
+ warning(wi, warn_buf);
+ }
+ else
+ {
+ /* Here we do not use the zero at cut-off macro,
+ * since user defined interactions might purposely
+ * not be zero at the cut-off.
+ */
+ if (ir_vdw_is_zero_at_cutoff(ir) &&
+ rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
+ {
+ sprintf(warn_buf, "The sum of the two largest charge group "
+ "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
+ "With exact cut-offs, better performance can be "
+ "obtained with cutoff-scheme = %s, because it "
+ "does not use charge groups at all.",
+ rvdw1+rvdw2,
+ ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
+ ir->rlistlong, ir->rvdw,
+ ecutscheme_names[ecutsVERLET]);
+ if (ir_NVE(ir))
+ {
+ warning(wi, warn_buf);
+ }
+ else
+ {
+ warning_note(wi, warn_buf);
+ }
+ }
+ if (ir_coulomb_is_zero_at_cutoff(ir) &&
+ rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
+ {
+ sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
+ "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
+ rcoul1+rcoul2,
+ ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
+ ir->rlistlong, ir->rcoulomb,
+ ecutscheme_names[ecutsVERLET]);
+ if (ir_NVE(ir))
+ {
+ warning(wi, warn_buf);
+ }
+ else
+ {
+ warning_note(wi, warn_buf);
+ }
+ }
+ }
+ }
+}
--- /dev/null
- dd_move_x_constraints(cr->dd, box, xp, NULL);
+/*
+ * 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.
+ * 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
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/* This file is completely threadsafe - keep it that way! */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+#include "main.h"
+#include "constr.h"
+#include "copyrite.h"
+#include "physics.h"
+#include "vec.h"
+#include "pbc.h"
+#include "smalloc.h"
+#include "mdrun.h"
+#include "nrnb.h"
+#include "domdec.h"
+#include "mtop_util.h"
+#include "gmx_omp_nthreads.h"
+
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/utility/gmxomp.h"
+
+typedef struct {
+ int b0; /* first constraint for this thread */
+ int b1; /* b1-1 is the last constraint for this thread */
+ int nind; /* number of indices */
+ int *ind; /* constraint index for updating atom data */
+ int nind_r; /* number of indices */
+ int *ind_r; /* constraint index for updating atom data */
+ int ind_nalloc; /* allocation size of ind and ind_r */
+ tensor vir_r_m_dr; /* temporary variable for virial calculation */
+} lincs_thread_t;
+
+typedef struct gmx_lincsdata {
+ int ncg; /* the global number of constraints */
+ int ncg_flex; /* the global number of flexible constraints */
+ int ncg_triangle; /* the global number of constraints in triangles */
+ int nIter; /* the number of iterations */
+ int nOrder; /* the order of the matrix expansion */
+ int nc; /* the number of constraints */
+ int nc_alloc; /* the number we allocated memory for */
+ int ncc; /* the number of constraint connections */
+ int ncc_alloc; /* the number we allocated memory for */
+ real matlam; /* the FE lambda value used for filling blc and blmf */
+ real *bllen0; /* the reference distance in topology A */
+ real *ddist; /* the reference distance in top B - the r.d. in top A */
+ int *bla; /* the atom pairs involved in the constraints */
+ real *blc; /* 1/sqrt(invmass1 + invmass2) */
+ real *blc1; /* as blc, but with all masses 1 */
+ int *blnr; /* index into blbnb and blmf */
+ int *blbnb; /* list of constraint connections */
+ int ntriangle; /* the local number of constraints in triangles */
+ int *triangle; /* the list of triangle constraints */
+ int *tri_bits; /* the bits tell if the matrix element should be used */
+ int ncc_triangle; /* the number of constraint connections in triangles */
+ gmx_bool bCommIter; /* communicate before each LINCS interation */
+ real *blmf; /* matrix of mass factors for constraint connections */
+ real *blmf1; /* as blmf, but with all masses 1 */
+ real *bllen; /* the reference bond length */
+ int nth; /* The number of threads doing LINCS */
+ lincs_thread_t *th; /* LINCS thread division */
+ unsigned *atf; /* atom flags for thread parallelization */
+ int atf_nalloc; /* allocation size of atf */
+ /* arrays for temporary storage in the LINCS algorithm */
+ rvec *tmpv;
+ real *tmpncc;
+ real *tmp1;
+ real *tmp2;
+ real *tmp3;
+ real *tmp4;
+ real *mlambda; /* the Lagrange multipliers * -1 */
+ /* storage for the constraint RMS relative deviation output */
+ real rmsd_data[3];
+} t_gmx_lincsdata;
+
+real *lincs_rmsd_data(struct gmx_lincsdata *lincsd)
+{
+ return lincsd->rmsd_data;
+}
+
+real lincs_rmsd(struct gmx_lincsdata *lincsd, gmx_bool bSD2)
+{
+ if (lincsd->rmsd_data[0] > 0)
+ {
+ return sqrt(lincsd->rmsd_data[bSD2 ? 2 : 1]/lincsd->rmsd_data[0]);
+ }
+ else
+ {
+ return 0;
+ }
+}
+
+/* Do a set of nrec LINCS matrix multiplications.
+ * This function will return with up to date thread-local
+ * constraint data, without an OpenMP barrier.
+ */
+static void lincs_matrix_expand(const struct gmx_lincsdata *lincsd,
+ int b0, int b1,
+ const real *blcc,
+ real *rhs1, real *rhs2, real *sol)
+{
+ int nrec, rec, b, j, n, nr0, nr1;
+ real mvb, *swap;
+ int ntriangle, tb, bits;
+ const int *blnr = lincsd->blnr, *blbnb = lincsd->blbnb;
+ const int *triangle = lincsd->triangle, *tri_bits = lincsd->tri_bits;
+
+ ntriangle = lincsd->ntriangle;
+ nrec = lincsd->nOrder;
+
+ for (rec = 0; rec < nrec; rec++)
+ {
+#pragma omp barrier
+ for (b = b0; b < b1; b++)
+ {
+ mvb = 0;
+ for (n = blnr[b]; n < blnr[b+1]; n++)
+ {
+ j = blbnb[n];
+ mvb = mvb + blcc[n]*rhs1[j];
+ }
+ rhs2[b] = mvb;
+ sol[b] = sol[b] + mvb;
+ }
+ swap = rhs1;
+ rhs1 = rhs2;
+ rhs2 = swap;
+ } /* nrec*(ncons+2*nrtot) flops */
+
+ if (ntriangle > 0)
+ {
+ /* Perform an extra nrec recursions for only the constraints
+ * involved in rigid triangles.
+ * In this way their accuracy should come close to those of the other
+ * constraints, since traingles of constraints can produce eigenvalues
+ * around 0.7, while the effective eigenvalue for bond constraints
+ * is around 0.4 (and 0.7*0.7=0.5).
+ */
+ /* We need to copy the temporary array, since only the elements
+ * for constraints involved in triangles are updated and then
+ * the pointers are swapped. This saving copying the whole arrary.
+ * We need barrier as other threads might still be reading from rhs2.
+ */
+#pragma omp barrier
+ for (b = b0; b < b1; b++)
+ {
+ rhs2[b] = rhs1[b];
+ }
+#pragma omp barrier
+#pragma omp master
+ {
+ for (rec = 0; rec < nrec; rec++)
+ {
+ for (tb = 0; tb < ntriangle; tb++)
+ {
+ b = triangle[tb];
+ bits = tri_bits[tb];
+ mvb = 0;
+ nr0 = blnr[b];
+ nr1 = blnr[b+1];
+ for (n = nr0; n < nr1; n++)
+ {
+ if (bits & (1<<(n-nr0)))
+ {
+ j = blbnb[n];
+ mvb = mvb + blcc[n]*rhs1[j];
+ }
+ }
+ rhs2[b] = mvb;
+ sol[b] = sol[b] + mvb;
+ }
+ swap = rhs1;
+ rhs1 = rhs2;
+ rhs2 = swap;
+ }
+ } /* flops count is missing here */
+
+ /* We need a barrier here as the calling routine will continue
+ * to operate on the thread-local constraints without barrier.
+ */
+#pragma omp barrier
+ }
+}
+
+static void lincs_update_atoms_noind(int ncons, const int *bla,
+ real prefac,
+ const real *fac, rvec *r,
+ const real *invmass,
+ rvec *x)
+{
+ int b, i, j;
+ real mvb, im1, im2, tmp0, tmp1, tmp2;
+
+ if (invmass != NULL)
+ {
+ for (b = 0; b < ncons; b++)
+ {
+ i = bla[2*b];
+ j = bla[2*b+1];
+ mvb = prefac*fac[b];
+ im1 = invmass[i];
+ im2 = invmass[j];
+ tmp0 = r[b][0]*mvb;
+ tmp1 = r[b][1]*mvb;
+ tmp2 = r[b][2]*mvb;
+ x[i][0] -= tmp0*im1;
+ x[i][1] -= tmp1*im1;
+ x[i][2] -= tmp2*im1;
+ x[j][0] += tmp0*im2;
+ x[j][1] += tmp1*im2;
+ x[j][2] += tmp2*im2;
+ } /* 16 ncons flops */
+ }
+ else
+ {
+ for (b = 0; b < ncons; b++)
+ {
+ i = bla[2*b];
+ j = bla[2*b+1];
+ mvb = prefac*fac[b];
+ tmp0 = r[b][0]*mvb;
+ tmp1 = r[b][1]*mvb;
+ tmp2 = r[b][2]*mvb;
+ x[i][0] -= tmp0;
+ x[i][1] -= tmp1;
+ x[i][2] -= tmp2;
+ x[j][0] += tmp0;
+ x[j][1] += tmp1;
+ x[j][2] += tmp2;
+ }
+ }
+}
+
+static void lincs_update_atoms_ind(int ncons, const int *ind, const int *bla,
+ real prefac,
+ const real *fac, rvec *r,
+ const real *invmass,
+ rvec *x)
+{
+ int bi, b, i, j;
+ real mvb, im1, im2, tmp0, tmp1, tmp2;
+
+ if (invmass != NULL)
+ {
+ for (bi = 0; bi < ncons; bi++)
+ {
+ b = ind[bi];
+ i = bla[2*b];
+ j = bla[2*b+1];
+ mvb = prefac*fac[b];
+ im1 = invmass[i];
+ im2 = invmass[j];
+ tmp0 = r[b][0]*mvb;
+ tmp1 = r[b][1]*mvb;
+ tmp2 = r[b][2]*mvb;
+ x[i][0] -= tmp0*im1;
+ x[i][1] -= tmp1*im1;
+ x[i][2] -= tmp2*im1;
+ x[j][0] += tmp0*im2;
+ x[j][1] += tmp1*im2;
+ x[j][2] += tmp2*im2;
+ } /* 16 ncons flops */
+ }
+ else
+ {
+ for (bi = 0; bi < ncons; bi++)
+ {
+ b = ind[bi];
+ i = bla[2*b];
+ j = bla[2*b+1];
+ mvb = prefac*fac[b];
+ tmp0 = r[b][0]*mvb;
+ tmp1 = r[b][1]*mvb;
+ tmp2 = r[b][2]*mvb;
+ x[i][0] -= tmp0;
+ x[i][1] -= tmp1;
+ x[i][2] -= tmp2;
+ x[j][0] += tmp0;
+ x[j][1] += tmp1;
+ x[j][2] += tmp2;
+ } /* 16 ncons flops */
+ }
+}
+
+static void lincs_update_atoms(struct gmx_lincsdata *li, int th,
+ real prefac,
+ const real *fac, rvec *r,
+ const real *invmass,
+ rvec *x)
+{
+ if (li->nth == 1)
+ {
+ /* Single thread, we simply update for all constraints */
+ lincs_update_atoms_noind(li->nc, li->bla, prefac, fac, r, invmass, x);
+ }
+ else
+ {
+ /* Update the atom vector components for our thread local
+ * constraints that only access our local atom range.
+ * This can be done without a barrier.
+ */
+ lincs_update_atoms_ind(li->th[th].nind, li->th[th].ind,
+ li->bla, prefac, fac, r, invmass, x);
+
+ if (li->th[li->nth].nind > 0)
+ {
+ /* Update the constraints that operate on atoms
+ * in multiple thread atom blocks on the master thread.
+ */
+#pragma omp barrier
+#pragma omp master
+ {
+ lincs_update_atoms_ind(li->th[li->nth].nind,
+ li->th[li->nth].ind,
+ li->bla, prefac, fac, r, invmass, x);
+ }
+ }
+ }
+}
+
+/* LINCS projection, works on derivatives of the coordinates */
+static void do_lincsp(rvec *x, rvec *f, rvec *fp, t_pbc *pbc,
+ struct gmx_lincsdata *lincsd, int th,
+ real *invmass,
+ int econq, real *dvdlambda,
+ gmx_bool bCalcVir, tensor rmdf)
+{
+ int b0, b1, b, i, j, k, n;
+ real tmp0, tmp1, tmp2, im1, im2, mvb, rlen, len, wfac, lam;
+ rvec dx;
+ int *bla, *blnr, *blbnb;
+ rvec *r;
+ real *blc, *blmf, *blcc, *rhs1, *rhs2, *sol;
+
+ b0 = lincsd->th[th].b0;
+ b1 = lincsd->th[th].b1;
+
+ bla = lincsd->bla;
+ r = lincsd->tmpv;
+ blnr = lincsd->blnr;
+ blbnb = lincsd->blbnb;
+ if (econq != econqForce)
+ {
+ /* Use mass-weighted parameters */
+ blc = lincsd->blc;
+ blmf = lincsd->blmf;
+ }
+ else
+ {
+ /* Use non mass-weighted parameters */
+ blc = lincsd->blc1;
+ blmf = lincsd->blmf1;
+ }
+ blcc = lincsd->tmpncc;
+ rhs1 = lincsd->tmp1;
+ rhs2 = lincsd->tmp2;
+ sol = lincsd->tmp3;
+
+ /* Compute normalized i-j vectors */
+ if (pbc)
+ {
+ for (b = b0; b < b1; b++)
+ {
+ pbc_dx_aiuc(pbc, x[bla[2*b]], x[bla[2*b+1]], dx);
+ unitv(dx, r[b]);
+ }
+ }
+ else
+ {
+ for (b = b0; b < b1; b++)
+ {
+ rvec_sub(x[bla[2*b]], x[bla[2*b+1]], dx);
+ unitv(dx, r[b]);
+ } /* 16 ncons flops */
+ }
+
+#pragma omp barrier
+ for (b = b0; b < b1; b++)
+ {
+ tmp0 = r[b][0];
+ tmp1 = r[b][1];
+ tmp2 = r[b][2];
+ i = bla[2*b];
+ j = bla[2*b+1];
+ for (n = blnr[b]; n < blnr[b+1]; n++)
+ {
+ k = blbnb[n];
+ blcc[n] = blmf[n]*(tmp0*r[k][0] + tmp1*r[k][1] + tmp2*r[k][2]);
+ } /* 6 nr flops */
+ mvb = blc[b]*(tmp0*(f[i][0] - f[j][0]) +
+ tmp1*(f[i][1] - f[j][1]) +
+ tmp2*(f[i][2] - f[j][2]));
+ rhs1[b] = mvb;
+ sol[b] = mvb;
+ /* 7 flops */
+ }
+ /* Together: 23*ncons + 6*nrtot flops */
+
+ lincs_matrix_expand(lincsd, b0, b1, blcc, rhs1, rhs2, sol);
+ /* nrec*(ncons+2*nrtot) flops */
+
+ if (econq == econqDeriv_FlexCon)
+ {
+ /* We only want to constraint the flexible constraints,
+ * so we mask out the normal ones by setting sol to 0.
+ */
+ for (b = b0; b < b1; b++)
+ {
+ if (!(lincsd->bllen0[b] == 0 && lincsd->ddist[b] == 0))
+ {
+ sol[b] = 0;
+ }
+ }
+ }
+
+ /* We multiply sol by blc, so we can use lincs_update_atoms for OpenMP */
+ for (b = b0; b < b1; b++)
+ {
+ sol[b] *= blc[b];
+ }
+
+ /* When constraining forces, we should not use mass weighting,
+ * so we pass invmass=NULL, which results in the use of 1 for all atoms.
+ */
+ lincs_update_atoms(lincsd, th, 1.0, sol, r,
+ (econq != econqForce) ? invmass : NULL, fp);
+
+ if (dvdlambda != NULL)
+ {
+#pragma omp barrier
+ for (b = b0; b < b1; b++)
+ {
+ *dvdlambda -= sol[b]*lincsd->ddist[b];
+ }
+ /* 10 ncons flops */
+ }
+
+ if (bCalcVir)
+ {
+ /* Constraint virial,
+ * determines sum r_bond x delta f,
+ * where delta f is the constraint correction
+ * of the quantity that is being constrained.
+ */
+ for (b = b0; b < b1; b++)
+ {
+ mvb = lincsd->bllen[b]*sol[b];
+ for (i = 0; i < DIM; i++)
+ {
+ tmp1 = mvb*r[b][i];
+ for (j = 0; j < DIM; j++)
+ {
+ rmdf[i][j] += tmp1*r[b][j];
+ }
+ }
+ } /* 23 ncons flops */
+ }
+}
+
+static void do_lincs(rvec *x, rvec *xp, matrix box, t_pbc *pbc,
+ struct gmx_lincsdata *lincsd, int th,
+ real *invmass,
+ t_commrec *cr,
+ gmx_bool bCalcLambda,
+ real wangle, int *warn,
+ real invdt, rvec *v,
+ gmx_bool bCalcVir, tensor vir_r_m_dr)
+{
+ int b0, b1, b, i, j, k, n, iter;
+ real tmp0, tmp1, tmp2, im1, im2, mvb, rlen, len, len2, dlen2, wfac;
+ rvec dx;
+ int *bla, *blnr, *blbnb;
+ rvec *r;
+ real *blc, *blmf, *bllen, *blcc, *rhs1, *rhs2, *sol, *blc_sol, *mlambda;
+ int *nlocat;
+
+ b0 = lincsd->th[th].b0;
+ b1 = lincsd->th[th].b1;
+
+ bla = lincsd->bla;
+ r = lincsd->tmpv;
+ blnr = lincsd->blnr;
+ blbnb = lincsd->blbnb;
+ blc = lincsd->blc;
+ blmf = lincsd->blmf;
+ bllen = lincsd->bllen;
+ blcc = lincsd->tmpncc;
+ rhs1 = lincsd->tmp1;
+ rhs2 = lincsd->tmp2;
+ sol = lincsd->tmp3;
+ blc_sol = lincsd->tmp4;
+ mlambda = lincsd->mlambda;
+
+ if (DOMAINDECOMP(cr) && cr->dd->constraints)
+ {
+ nlocat = dd_constraints_nlocalatoms(cr->dd);
+ }
+ else
+ {
+ nlocat = NULL;
+ }
+
+ if (pbc)
+ {
+ /* Compute normalized i-j vectors */
+ for (b = b0; b < b1; b++)
+ {
+ pbc_dx_aiuc(pbc, x[bla[2*b]], x[bla[2*b+1]], dx);
+ unitv(dx, r[b]);
+ }
+#pragma omp barrier
+ for (b = b0; b < b1; b++)
+ {
+ for (n = blnr[b]; n < blnr[b+1]; n++)
+ {
+ blcc[n] = blmf[n]*iprod(r[b], r[blbnb[n]]);
+ }
+ pbc_dx_aiuc(pbc, xp[bla[2*b]], xp[bla[2*b+1]], dx);
+ mvb = blc[b]*(iprod(r[b], dx) - bllen[b]);
+ rhs1[b] = mvb;
+ sol[b] = mvb;
+ }
+ }
+ else
+ {
+ /* Compute normalized i-j vectors */
+ for (b = b0; b < b1; b++)
+ {
+ i = bla[2*b];
+ j = bla[2*b+1];
+ tmp0 = x[i][0] - x[j][0];
+ tmp1 = x[i][1] - x[j][1];
+ tmp2 = x[i][2] - x[j][2];
+ rlen = gmx_invsqrt(tmp0*tmp0+tmp1*tmp1+tmp2*tmp2);
+ r[b][0] = rlen*tmp0;
+ r[b][1] = rlen*tmp1;
+ r[b][2] = rlen*tmp2;
+ } /* 16 ncons flops */
+
+#pragma omp barrier
+ for (b = b0; b < b1; b++)
+ {
+ tmp0 = r[b][0];
+ tmp1 = r[b][1];
+ tmp2 = r[b][2];
+ len = bllen[b];
+ i = bla[2*b];
+ j = bla[2*b+1];
+ for (n = blnr[b]; n < blnr[b+1]; n++)
+ {
+ k = blbnb[n];
+ blcc[n] = blmf[n]*(tmp0*r[k][0] + tmp1*r[k][1] + tmp2*r[k][2]);
+ } /* 6 nr flops */
+ mvb = blc[b]*(tmp0*(xp[i][0] - xp[j][0]) +
+ tmp1*(xp[i][1] - xp[j][1]) +
+ tmp2*(xp[i][2] - xp[j][2]) - len);
+ rhs1[b] = mvb;
+ sol[b] = mvb;
+ /* 10 flops */
+ }
+ /* Together: 26*ncons + 6*nrtot flops */
+ }
+
+ lincs_matrix_expand(lincsd, b0, b1, blcc, rhs1, rhs2, sol);
+ /* nrec*(ncons+2*nrtot) flops */
+
+ for (b = b0; b < b1; b++)
+ {
+ mlambda[b] = blc[b]*sol[b];
+ }
+
+ /* Update the coordinates */
+ lincs_update_atoms(lincsd, th, 1.0, mlambda, r, invmass, xp);
+
+ /*
+ ******** Correction for centripetal effects ********
+ */
+
+ wfac = cos(DEG2RAD*wangle);
+ wfac = wfac*wfac;
+
+ for (iter = 0; iter < lincsd->nIter; iter++)
+ {
+ if ((lincsd->bCommIter && DOMAINDECOMP(cr) && cr->dd->constraints))
+ {
+#pragma omp barrier
+#pragma omp master
+ {
+ /* Communicate the corrected non-local coordinates */
+ if (DOMAINDECOMP(cr))
+ {
++ dd_move_x_constraints(cr->dd, box, xp, NULL, FALSE);
+ }
+ }
+ }
+
+#pragma omp barrier
+ for (b = b0; b < b1; b++)
+ {
+ len = bllen[b];
+ if (pbc)
+ {
+ pbc_dx_aiuc(pbc, xp[bla[2*b]], xp[bla[2*b+1]], dx);
+ }
+ else
+ {
+ rvec_sub(xp[bla[2*b]], xp[bla[2*b+1]], dx);
+ }
+ len2 = len*len;
+ dlen2 = 2*len2 - norm2(dx);
+ if (dlen2 < wfac*len2 && (nlocat == NULL || nlocat[b]))
+ {
+ *warn = b;
+ }
+ if (dlen2 > 0)
+ {
+ mvb = blc[b]*(len - dlen2*gmx_invsqrt(dlen2));
+ }
+ else
+ {
+ mvb = blc[b]*len;
+ }
+ rhs1[b] = mvb;
+ sol[b] = mvb;
+ } /* 20*ncons flops */
+
+ lincs_matrix_expand(lincsd, b0, b1, blcc, rhs1, rhs2, sol);
+ /* nrec*(ncons+2*nrtot) flops */
+
+ for (b = b0; b < b1; b++)
+ {
+ mvb = blc[b]*sol[b];
+ blc_sol[b] = mvb;
+ mlambda[b] += mvb;
+ }
+
+ /* Update the coordinates */
+ lincs_update_atoms(lincsd, th, 1.0, blc_sol, r, invmass, xp);
+ }
+ /* nit*ncons*(37+9*nrec) flops */
+
+ if (v != NULL)
+ {
+ /* Update the velocities */
+ lincs_update_atoms(lincsd, th, invdt, mlambda, r, invmass, v);
+ /* 16 ncons flops */
+ }
+
+ if (nlocat != NULL && bCalcLambda)
+ {
+ /* In lincs_update_atoms thread might cross-read mlambda */
+#pragma omp barrier
+
+ /* Only account for local atoms */
+ for (b = b0; b < b1; b++)
+ {
+ mlambda[b] *= 0.5*nlocat[b];
+ }
+ }
+
+ if (bCalcVir)
+ {
+ /* Constraint virial */
+ for (b = b0; b < b1; b++)
+ {
+ tmp0 = -bllen[b]*mlambda[b];
+ for (i = 0; i < DIM; i++)
+ {
+ tmp1 = tmp0*r[b][i];
+ for (j = 0; j < DIM; j++)
+ {
+ vir_r_m_dr[i][j] -= tmp1*r[b][j];
+ }
+ }
+ } /* 22 ncons flops */
+ }
+
+ /* Total:
+ * 26*ncons + 6*nrtot + nrec*(ncons+2*nrtot)
+ * + nit * (20*ncons + nrec*(ncons+2*nrtot) + 17 ncons)
+ *
+ * (26+nrec)*ncons + (6+2*nrec)*nrtot
+ * + nit * ((37+nrec)*ncons + 2*nrec*nrtot)
+ * if nit=1
+ * (63+nrec)*ncons + (6+4*nrec)*nrtot
+ */
+}
+
+void set_lincs_matrix(struct gmx_lincsdata *li, real *invmass, real lambda)
+{
+ int i, a1, a2, n, k, sign, center;
+ int end, nk, kk;
+ const real invsqrt2 = 0.7071067811865475244;
+
+ for (i = 0; (i < li->nc); i++)
+ {
+ a1 = li->bla[2*i];
+ a2 = li->bla[2*i+1];
+ li->blc[i] = gmx_invsqrt(invmass[a1] + invmass[a2]);
+ li->blc1[i] = invsqrt2;
+ }
+
+ /* Construct the coupling coefficient matrix blmf */
+ li->ntriangle = 0;
+ li->ncc_triangle = 0;
+ for (i = 0; (i < li->nc); i++)
+ {
+ a1 = li->bla[2*i];
+ a2 = li->bla[2*i+1];
+ for (n = li->blnr[i]; (n < li->blnr[i+1]); n++)
+ {
+ k = li->blbnb[n];
+ if (a1 == li->bla[2*k] || a2 == li->bla[2*k+1])
+ {
+ sign = -1;
+ }
+ else
+ {
+ sign = 1;
+ }
+ if (a1 == li->bla[2*k] || a1 == li->bla[2*k+1])
+ {
+ center = a1;
+ end = a2;
+ }
+ else
+ {
+ center = a2;
+ end = a1;
+ }
+ li->blmf[n] = sign*invmass[center]*li->blc[i]*li->blc[k];
+ li->blmf1[n] = sign*0.5;
+ if (li->ncg_triangle > 0)
+ {
+ /* Look for constraint triangles */
+ for (nk = li->blnr[k]; (nk < li->blnr[k+1]); nk++)
+ {
+ kk = li->blbnb[nk];
+ if (kk != i && kk != k &&
+ (li->bla[2*kk] == end || li->bla[2*kk+1] == end))
+ {
+ if (li->ntriangle == 0 ||
+ li->triangle[li->ntriangle-1] < i)
+ {
+ /* Add this constraint to the triangle list */
+ li->triangle[li->ntriangle] = i;
+ li->tri_bits[li->ntriangle] = 0;
+ li->ntriangle++;
+ if (li->blnr[i+1] - li->blnr[i] > sizeof(li->tri_bits[0])*8 - 1)
+ {
+ gmx_fatal(FARGS, "A constraint is connected to %d constraints, this is more than the %d allowed for constraints participating in triangles",
+ li->blnr[i+1] - li->blnr[i],
+ sizeof(li->tri_bits[0])*8-1);
+ }
+ }
+ li->tri_bits[li->ntriangle-1] |= (1<<(n-li->blnr[i]));
+ li->ncc_triangle++;
+ }
+ }
+ }
+ }
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "Of the %d constraints %d participate in triangles\n",
+ li->nc, li->ntriangle);
+ fprintf(debug, "There are %d couplings of which %d in triangles\n",
+ li->ncc, li->ncc_triangle);
+ }
+
+ /* Set matlam,
+ * so we know with which lambda value the masses have been set.
+ */
+ li->matlam = lambda;
+}
+
+static int count_triangle_constraints(t_ilist *ilist, t_blocka *at2con)
+{
+ int ncon1, ncon_tot;
+ int c0, a00, a01, n1, c1, a10, a11, ac1, n2, c2, a20, a21;
+ int ncon_triangle;
+ gmx_bool bTriangle;
+ t_iatom *ia1, *ia2, *iap;
+
+ ncon1 = ilist[F_CONSTR].nr/3;
+ ncon_tot = ncon1 + ilist[F_CONSTRNC].nr/3;
+
+ ia1 = ilist[F_CONSTR].iatoms;
+ ia2 = ilist[F_CONSTRNC].iatoms;
+
+ ncon_triangle = 0;
+ for (c0 = 0; c0 < ncon_tot; c0++)
+ {
+ bTriangle = FALSE;
+ iap = constr_iatomptr(ncon1, ia1, ia2, c0);
+ a00 = iap[1];
+ a01 = iap[2];
+ for (n1 = at2con->index[a01]; n1 < at2con->index[a01+1]; n1++)
+ {
+ c1 = at2con->a[n1];
+ if (c1 != c0)
+ {
+ iap = constr_iatomptr(ncon1, ia1, ia2, c1);
+ a10 = iap[1];
+ a11 = iap[2];
+ if (a10 == a01)
+ {
+ ac1 = a11;
+ }
+ else
+ {
+ ac1 = a10;
+ }
+ for (n2 = at2con->index[ac1]; n2 < at2con->index[ac1+1]; n2++)
+ {
+ c2 = at2con->a[n2];
+ if (c2 != c0 && c2 != c1)
+ {
+ iap = constr_iatomptr(ncon1, ia1, ia2, c2);
+ a20 = iap[1];
+ a21 = iap[2];
+ if (a20 == a00 || a21 == a00)
+ {
+ bTriangle = TRUE;
+ }
+ }
+ }
+ }
+ }
+ if (bTriangle)
+ {
+ ncon_triangle++;
+ }
+ }
+
+ return ncon_triangle;
+}
+
+static gmx_bool more_than_two_sequential_constraints(const t_ilist *ilist,
+ const t_blocka *at2con)
+{
+ t_iatom *ia1, *ia2, *iap;
+ int ncon1, ncon_tot, c;
+ int a1, a2;
+ gmx_bool bMoreThanTwoSequentialConstraints;
+
+ ncon1 = ilist[F_CONSTR].nr/3;
+ ncon_tot = ncon1 + ilist[F_CONSTRNC].nr/3;
+
+ ia1 = ilist[F_CONSTR].iatoms;
+ ia2 = ilist[F_CONSTRNC].iatoms;
+
+ bMoreThanTwoSequentialConstraints = FALSE;
+ for (c = 0; c < ncon_tot && !bMoreThanTwoSequentialConstraints; c++)
+ {
+ iap = constr_iatomptr(ncon1, ia1, ia2, c);
+ a1 = iap[1];
+ a2 = iap[2];
+ /* Check if this constraint has constraints connected at both atoms */
+ if (at2con->index[a1+1] - at2con->index[a1] > 1 &&
+ at2con->index[a2+1] - at2con->index[a2] > 1)
+ {
+ bMoreThanTwoSequentialConstraints = TRUE;
+ }
+ }
+
+ return bMoreThanTwoSequentialConstraints;
+}
+
+static int int_comp(const void *a, const void *b)
+{
+ return (*(int *)a) - (*(int *)b);
+}
+
+gmx_lincsdata_t init_lincs(FILE *fplog, gmx_mtop_t *mtop,
+ int nflexcon_global, t_blocka *at2con,
+ gmx_bool bPLINCS, int nIter, int nProjOrder)
+{
+ struct gmx_lincsdata *li;
+ int mb;
+ gmx_moltype_t *molt;
+
+ if (fplog)
+ {
+ fprintf(fplog, "\nInitializing%s LINear Constraint Solver\n",
+ bPLINCS ? " Parallel" : "");
+ }
+
+ snew(li, 1);
+
+ li->ncg =
+ gmx_mtop_ftype_count(mtop, F_CONSTR) +
+ gmx_mtop_ftype_count(mtop, F_CONSTRNC);
+ li->ncg_flex = nflexcon_global;
+
+ li->nIter = nIter;
+ li->nOrder = nProjOrder;
+
+ li->ncg_triangle = 0;
+ li->bCommIter = FALSE;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molt = &mtop->moltype[mtop->molblock[mb].type];
+ li->ncg_triangle +=
+ mtop->molblock[mb].nmol*
+ count_triangle_constraints(molt->ilist,
+ &at2con[mtop->molblock[mb].type]);
+ if (bPLINCS && li->bCommIter == FALSE)
+ {
+ /* Check if we need to communicate not only before LINCS,
+ * but also before each iteration.
+ * The check for only two sequential constraints is only
+ * useful for the common case of H-bond only constraints.
+ * With more effort we could also make it useful for small
+ * molecules with nr. sequential constraints <= nOrder-1.
+ */
+ li->bCommIter = (li->nOrder < 1 || more_than_two_sequential_constraints(molt->ilist, &at2con[mtop->molblock[mb].type]));
+ }
+ }
+ if (debug && bPLINCS)
+ {
+ fprintf(debug, "PLINCS communication before each iteration: %d\n",
+ li->bCommIter);
+ }
+
+ /* LINCS can run on any number of threads.
+ * Currently the number is fixed for the whole simulation,
+ * but it could be set in set_lincs().
+ */
+ li->nth = gmx_omp_nthreads_get(emntLINCS);
+ if (li->nth == 1)
+ {
+ snew(li->th, 1);
+ }
+ else
+ {
+ /* Allocate an extra elements for "thread-overlap" constraints */
+ snew(li->th, li->nth+1);
+ }
+ if (debug)
+ {
+ fprintf(debug, "LINCS: using %d threads\n", li->nth);
+ }
+
+ if (bPLINCS || li->ncg_triangle > 0)
+ {
+ please_cite(fplog, "Hess2008a");
+ }
+ else
+ {
+ please_cite(fplog, "Hess97a");
+ }
+
+ if (fplog)
+ {
+ fprintf(fplog, "The number of constraints is %d\n", li->ncg);
+ if (bPLINCS)
+ {
+ fprintf(fplog, "There are inter charge-group constraints,\n"
+ "will communicate selected coordinates each lincs iteration\n");
+ }
+ if (li->ncg_triangle > 0)
+ {
+ fprintf(fplog,
+ "%d constraints are involved in constraint triangles,\n"
+ "will apply an additional matrix expansion of order %d for couplings\n"
+ "between constraints inside triangles\n",
+ li->ncg_triangle, li->nOrder);
+ }
+ }
+
+ return li;
+}
+
+/* Sets up the work division over the threads */
+static void lincs_thread_setup(struct gmx_lincsdata *li, int natoms)
+{
+ lincs_thread_t *li_m;
+ int th;
+ unsigned *atf;
+ int a;
+
+ if (natoms > li->atf_nalloc)
+ {
+ li->atf_nalloc = over_alloc_large(natoms);
+ srenew(li->atf, li->atf_nalloc);
+ }
+
+ atf = li->atf;
+ /* Clear the atom flags */
+ for (a = 0; a < natoms; a++)
+ {
+ atf[a] = 0;
+ }
+
+ for (th = 0; th < li->nth; th++)
+ {
+ lincs_thread_t *li_th;
+ int b;
+
+ li_th = &li->th[th];
+
+ /* The constraints are divided equally over the threads */
+ li_th->b0 = (li->nc* th )/li->nth;
+ li_th->b1 = (li->nc*(th+1))/li->nth;
+
+ if (th < sizeof(*atf)*8)
+ {
+ /* For each atom set a flag for constraints from each */
+ for (b = li_th->b0; b < li_th->b1; b++)
+ {
+ atf[li->bla[b*2] ] |= (1U<<th);
+ atf[li->bla[b*2+1]] |= (1U<<th);
+ }
+ }
+ }
+
+#pragma omp parallel for num_threads(li->nth) schedule(static)
+ for (th = 0; th < li->nth; th++)
+ {
+ lincs_thread_t *li_th;
+ unsigned mask;
+ int b;
+
+ li_th = &li->th[th];
+
+ if (li_th->b1 - li_th->b0 > li_th->ind_nalloc)
+ {
+ li_th->ind_nalloc = over_alloc_large(li_th->b1-li_th->b0);
+ srenew(li_th->ind, li_th->ind_nalloc);
+ srenew(li_th->ind_r, li_th->ind_nalloc);
+ }
+
+ if (th < sizeof(*atf)*8)
+ {
+ mask = (1U<<th) - 1U;
+
+ li_th->nind = 0;
+ li_th->nind_r = 0;
+ for (b = li_th->b0; b < li_th->b1; b++)
+ {
+ /* We let the constraint with the lowest thread index
+ * operate on atoms with constraints from multiple threads.
+ */
+ if (((atf[li->bla[b*2]] & mask) == 0) &&
+ ((atf[li->bla[b*2+1]] & mask) == 0))
+ {
+ /* Add the constraint to the local atom update index */
+ li_th->ind[li_th->nind++] = b;
+ }
+ else
+ {
+ /* Add the constraint to the rest block */
+ li_th->ind_r[li_th->nind_r++] = b;
+ }
+ }
+ }
+ else
+ {
+ /* We are out of bits, assign all constraints to rest */
+ for (b = li_th->b0; b < li_th->b1; b++)
+ {
+ li_th->ind_r[li_th->nind_r++] = b;
+ }
+ }
+ }
+
+ /* We need to copy all constraints which have not be assigned
+ * to a thread to a separate list which will be handled by one thread.
+ */
+ li_m = &li->th[li->nth];
+
+ li_m->nind = 0;
+ for (th = 0; th < li->nth; th++)
+ {
+ lincs_thread_t *li_th;
+ int b;
+
+ li_th = &li->th[th];
+
+ if (li_m->nind + li_th->nind_r > li_m->ind_nalloc)
+ {
+ li_m->ind_nalloc = over_alloc_large(li_m->nind+li_th->nind_r);
+ srenew(li_m->ind, li_m->ind_nalloc);
+ }
+
+ for (b = 0; b < li_th->nind_r; b++)
+ {
+ li_m->ind[li_m->nind++] = li_th->ind_r[b];
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "LINCS thread %d: %d constraints\n",
+ th, li_th->nind);
+ }
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "LINCS thread r: %d constraints\n",
+ li_m->nind);
+ }
+}
+
+
+void set_lincs(t_idef *idef, t_mdatoms *md,
+ gmx_bool bDynamics, t_commrec *cr,
+ struct gmx_lincsdata *li)
+{
+ int start, natoms, nflexcon;
+ t_blocka at2con;
+ t_iatom *iatom;
+ int i, k, ncc_alloc, ni, con, nconnect, concon;
+ int type, a1, a2;
+ real lenA = 0, lenB;
+ gmx_bool bLocal;
+
+ li->nc = 0;
+ li->ncc = 0;
+ /* Zero the thread index ranges.
+ * Otherwise without local constraints we could return with old ranges.
+ */
+ for (i = 0; i < li->nth; i++)
+ {
+ li->th[i].b0 = 0;
+ li->th[i].b1 = 0;
+ li->th[i].nind = 0;
+ }
+ if (li->nth > 1)
+ {
+ li->th[li->nth].nind = 0;
+ }
+
+ /* This is the local topology, so there are only F_CONSTR constraints */
+ if (idef->il[F_CONSTR].nr == 0)
+ {
+ /* There are no constraints,
+ * we do not need to fill any data structures.
+ */
+ return;
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "Building the LINCS connectivity\n");
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ if (cr->dd->constraints)
+ {
+ dd_get_constraint_range(cr->dd, &start, &natoms);
+ }
+ else
+ {
+ natoms = cr->dd->nat_home;
+ }
+ start = 0;
+ }
+ else
+ {
+ start = 0;
+ natoms = md->homenr;
+ }
+ at2con = make_at2con(start, natoms, idef->il, idef->iparams, bDynamics,
+ &nflexcon);
+
+
+ if (idef->il[F_CONSTR].nr/3 > li->nc_alloc || li->nc_alloc == 0)
+ {
+ li->nc_alloc = over_alloc_dd(idef->il[F_CONSTR].nr/3);
+ srenew(li->bllen0, li->nc_alloc);
+ srenew(li->ddist, li->nc_alloc);
+ srenew(li->bla, 2*li->nc_alloc);
+ srenew(li->blc, li->nc_alloc);
+ srenew(li->blc1, li->nc_alloc);
+ srenew(li->blnr, li->nc_alloc+1);
+ srenew(li->bllen, li->nc_alloc);
+ srenew(li->tmpv, li->nc_alloc);
+ srenew(li->tmp1, li->nc_alloc);
+ srenew(li->tmp2, li->nc_alloc);
+ srenew(li->tmp3, li->nc_alloc);
+ srenew(li->tmp4, li->nc_alloc);
+ srenew(li->mlambda, li->nc_alloc);
+ if (li->ncg_triangle > 0)
+ {
+ /* This is allocating too much, but it is difficult to improve */
+ srenew(li->triangle, li->nc_alloc);
+ srenew(li->tri_bits, li->nc_alloc);
+ }
+ }
+
+ iatom = idef->il[F_CONSTR].iatoms;
+
+ ncc_alloc = li->ncc_alloc;
+ li->blnr[0] = 0;
+
+ ni = idef->il[F_CONSTR].nr/3;
+
+ con = 0;
+ nconnect = 0;
+ li->blnr[con] = nconnect;
+ for (i = 0; i < ni; i++)
+ {
+ bLocal = TRUE;
+ type = iatom[3*i];
+ a1 = iatom[3*i+1];
+ a2 = iatom[3*i+2];
+ lenA = idef->iparams[type].constr.dA;
+ lenB = idef->iparams[type].constr.dB;
+ /* Skip the flexible constraints when not doing dynamics */
+ if (bDynamics || lenA != 0 || lenB != 0)
+ {
+ li->bllen0[con] = lenA;
+ li->ddist[con] = lenB - lenA;
+ /* Set the length to the topology A length */
+ li->bllen[con] = li->bllen0[con];
+ li->bla[2*con] = a1;
+ li->bla[2*con+1] = a2;
+ /* Construct the constraint connection matrix blbnb */
+ for (k = at2con.index[a1-start]; k < at2con.index[a1-start+1]; k++)
+ {
+ concon = at2con.a[k];
+ if (concon != i)
+ {
+ if (nconnect >= ncc_alloc)
+ {
+ ncc_alloc = over_alloc_small(nconnect+1);
+ srenew(li->blbnb, ncc_alloc);
+ }
+ li->blbnb[nconnect++] = concon;
+ }
+ }
+ for (k = at2con.index[a2-start]; k < at2con.index[a2-start+1]; k++)
+ {
+ concon = at2con.a[k];
+ if (concon != i)
+ {
+ if (nconnect+1 > ncc_alloc)
+ {
+ ncc_alloc = over_alloc_small(nconnect+1);
+ srenew(li->blbnb, ncc_alloc);
+ }
+ li->blbnb[nconnect++] = concon;
+ }
+ }
+ li->blnr[con+1] = nconnect;
+
+ if (cr->dd == NULL)
+ {
+ /* Order the blbnb matrix to optimize memory access */
+ qsort(&(li->blbnb[li->blnr[con]]), li->blnr[con+1]-li->blnr[con],
+ sizeof(li->blbnb[0]), int_comp);
+ }
+ /* Increase the constraint count */
+ con++;
+ }
+ }
+
+ done_blocka(&at2con);
+
+ /* This is the real number of constraints,
+ * without dynamics the flexible constraints are not present.
+ */
+ li->nc = con;
+
+ li->ncc = li->blnr[con];
+ if (cr->dd == NULL)
+ {
+ /* Since the matrix is static, we can free some memory */
+ ncc_alloc = li->ncc;
+ srenew(li->blbnb, ncc_alloc);
+ }
+
+ if (ncc_alloc > li->ncc_alloc)
+ {
+ li->ncc_alloc = ncc_alloc;
+ srenew(li->blmf, li->ncc_alloc);
+ srenew(li->blmf1, li->ncc_alloc);
+ srenew(li->tmpncc, li->ncc_alloc);
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "Number of constraints is %d, couplings %d\n",
+ li->nc, li->ncc);
+ }
+
+ if (li->nth == 1)
+ {
+ li->th[0].b0 = 0;
+ li->th[0].b1 = li->nc;
+ }
+ else
+ {
+ lincs_thread_setup(li, md->nr);
+ }
+
+ set_lincs_matrix(li, md->invmass, md->lambda);
+}
+
+static void lincs_warning(FILE *fplog,
+ gmx_domdec_t *dd, rvec *x, rvec *xprime, t_pbc *pbc,
+ int ncons, int *bla, real *bllen, real wangle,
+ int maxwarn, int *warncount)
+{
+ int b, i, j;
+ rvec v0, v1;
+ real wfac, d0, d1, cosine;
+ char buf[STRLEN];
+
+ wfac = cos(DEG2RAD*wangle);
+
+ sprintf(buf, "bonds that rotated more than %g degrees:\n"
+ " atom 1 atom 2 angle previous, current, constraint length\n",
+ wangle);
+ fprintf(stderr, "%s", buf);
+ if (fplog)
+ {
+ fprintf(fplog, "%s", buf);
+ }
+
+ for (b = 0; b < ncons; b++)
+ {
+ i = bla[2*b];
+ j = bla[2*b+1];
+ if (pbc)
+ {
+ pbc_dx_aiuc(pbc, x[i], x[j], v0);
+ pbc_dx_aiuc(pbc, xprime[i], xprime[j], v1);
+ }
+ else
+ {
+ rvec_sub(x[i], x[j], v0);
+ rvec_sub(xprime[i], xprime[j], v1);
+ }
+ d0 = norm(v0);
+ d1 = norm(v1);
+ cosine = iprod(v0, v1)/(d0*d1);
+ if (cosine < wfac)
+ {
+ sprintf(buf, " %6d %6d %5.1f %8.4f %8.4f %8.4f\n",
+ ddglatnr(dd, i), ddglatnr(dd, j),
+ RAD2DEG*acos(cosine), d0, d1, bllen[b]);
+ fprintf(stderr, "%s", buf);
+ if (fplog)
+ {
+ fprintf(fplog, "%s", buf);
+ }
+ if (!gmx_isfinite(d1))
+ {
+ gmx_fatal(FARGS, "Bond length not finite.");
+ }
+
+ (*warncount)++;
+ }
+ }
+ if (*warncount > maxwarn)
+ {
+ too_many_constraint_warnings(econtLINCS, *warncount);
+ }
+}
+
+static void cconerr(gmx_domdec_t *dd,
+ int ncons, int *bla, real *bllen, rvec *x, t_pbc *pbc,
+ real *ncons_loc, real *ssd, real *max, int *imax)
+{
+ real len, d, ma, ssd2, r2;
+ int *nlocat, count, b, im;
+ rvec dx;
+
+ if (dd && dd->constraints)
+ {
+ nlocat = dd_constraints_nlocalatoms(dd);
+ }
+ else
+ {
+ nlocat = 0;
+ }
+
+ ma = 0;
+ ssd2 = 0;
+ im = 0;
+ count = 0;
+ for (b = 0; b < ncons; b++)
+ {
+ if (pbc)
+ {
+ pbc_dx_aiuc(pbc, x[bla[2*b]], x[bla[2*b+1]], dx);
+ }
+ else
+ {
+ rvec_sub(x[bla[2*b]], x[bla[2*b+1]], dx);
+ }
+ r2 = norm2(dx);
+ len = r2*gmx_invsqrt(r2);
+ d = fabs(len/bllen[b]-1);
+ if (d > ma && (nlocat == NULL || nlocat[b]))
+ {
+ ma = d;
+ im = b;
+ }
+ if (nlocat == NULL)
+ {
+ ssd2 += d*d;
+ count++;
+ }
+ else
+ {
+ ssd2 += nlocat[b]*d*d;
+ count += nlocat[b];
+ }
+ }
+
+ *ncons_loc = (nlocat ? 0.5 : 1)*count;
+ *ssd = (nlocat ? 0.5 : 1)*ssd2;
+ *max = ma;
+ *imax = im;
+}
+
+gmx_bool constrain_lincs(FILE *fplog, gmx_bool bLog, gmx_bool bEner,
+ t_inputrec *ir,
+ gmx_int64_t step,
+ struct gmx_lincsdata *lincsd, t_mdatoms *md,
+ t_commrec *cr,
+ rvec *x, rvec *xprime, rvec *min_proj,
+ matrix box, t_pbc *pbc,
+ real lambda, real *dvdlambda,
+ real invdt, rvec *v,
+ gmx_bool bCalcVir, tensor vir_r_m_dr,
+ int econq,
+ t_nrnb *nrnb,
+ int maxwarn, int *warncount)
+{
+ char buf[STRLEN], buf2[22], buf3[STRLEN];
+ int i, warn, p_imax, error;
+ real ncons_loc, p_ssd, p_max = 0;
+ rvec dx;
+ gmx_bool bOK;
+
+ bOK = TRUE;
+
+ if (lincsd->nc == 0 && cr->dd == NULL)
+ {
+ if (bLog || bEner)
+ {
+ lincsd->rmsd_data[0] = 0;
+ if (ir->eI == eiSD2 && v == NULL)
+ {
+ i = 2;
+ }
+ else
+ {
+ i = 1;
+ }
+ lincsd->rmsd_data[i] = 0;
+ }
+
+ return bOK;
+ }
+
+ if (econq == econqCoord)
+ {
+ if (ir->efep != efepNO)
+ {
+ if (md->nMassPerturbed && lincsd->matlam != md->lambda)
+ {
+ set_lincs_matrix(lincsd, md->invmass, md->lambda);
+ }
+
+ for (i = 0; i < lincsd->nc; i++)
+ {
+ lincsd->bllen[i] = lincsd->bllen0[i] + lambda*lincsd->ddist[i];
+ }
+ }
+
+ if (lincsd->ncg_flex)
+ {
+ /* Set the flexible constraint lengths to the old lengths */
+ if (pbc != NULL)
+ {
+ for (i = 0; i < lincsd->nc; i++)
+ {
+ if (lincsd->bllen[i] == 0)
+ {
+ pbc_dx_aiuc(pbc, x[lincsd->bla[2*i]], x[lincsd->bla[2*i+1]], dx);
+ lincsd->bllen[i] = norm(dx);
+ }
+ }
+ }
+ else
+ {
+ for (i = 0; i < lincsd->nc; i++)
+ {
+ if (lincsd->bllen[i] == 0)
+ {
+ lincsd->bllen[i] =
+ sqrt(distance2(x[lincsd->bla[2*i]],
+ x[lincsd->bla[2*i+1]]));
+ }
+ }
+ }
+ }
+
+ if (bLog && fplog)
+ {
+ cconerr(cr->dd, lincsd->nc, lincsd->bla, lincsd->bllen, xprime, pbc,
+ &ncons_loc, &p_ssd, &p_max, &p_imax);
+ }
+
+ /* This warn var can be updated by multiple threads
+ * at the same time. But as we only need to detect
+ * if a warning occured or not, this is not an issue.
+ */
+ warn = -1;
+
+ /* The OpenMP parallel region of constrain_lincs for coords */
+#pragma omp parallel num_threads(lincsd->nth)
+ {
+ int th = gmx_omp_get_thread_num();
+
+ clear_mat(lincsd->th[th].vir_r_m_dr);
+
+ do_lincs(x, xprime, box, pbc, lincsd, th,
+ md->invmass, cr,
+ bCalcVir || (ir->efep != efepNO),
+ ir->LincsWarnAngle, &warn,
+ invdt, v, bCalcVir,
+ th == 0 ? vir_r_m_dr : lincsd->th[th].vir_r_m_dr);
+ }
+
+ if (ir->efep != efepNO)
+ {
+ real dt_2, dvdl = 0;
+
+ dt_2 = 1.0/(ir->delta_t*ir->delta_t);
+ for (i = 0; (i < lincsd->nc); i++)
+ {
+ dvdl -= lincsd->mlambda[i]*dt_2*lincsd->ddist[i];
+ }
+ *dvdlambda += dvdl;
+ }
+
+ if (bLog && fplog && lincsd->nc > 0)
+ {
+ fprintf(fplog, " Rel. Constraint Deviation: RMS MAX between atoms\n");
+ fprintf(fplog, " Before LINCS %.6f %.6f %6d %6d\n",
+ sqrt(p_ssd/ncons_loc), p_max,
+ ddglatnr(cr->dd, lincsd->bla[2*p_imax]),
+ ddglatnr(cr->dd, lincsd->bla[2*p_imax+1]));
+ }
+ if (bLog || bEner)
+ {
+ cconerr(cr->dd, lincsd->nc, lincsd->bla, lincsd->bllen, xprime, pbc,
+ &ncons_loc, &p_ssd, &p_max, &p_imax);
+ /* Check if we are doing the second part of SD */
+ if (ir->eI == eiSD2 && v == NULL)
+ {
+ i = 2;
+ }
+ else
+ {
+ i = 1;
+ }
+ lincsd->rmsd_data[0] = ncons_loc;
+ lincsd->rmsd_data[i] = p_ssd;
+ }
+ else
+ {
+ lincsd->rmsd_data[0] = 0;
+ lincsd->rmsd_data[1] = 0;
+ lincsd->rmsd_data[2] = 0;
+ }
+ if (bLog && fplog && lincsd->nc > 0)
+ {
+ fprintf(fplog,
+ " After LINCS %.6f %.6f %6d %6d\n\n",
+ sqrt(p_ssd/ncons_loc), p_max,
+ ddglatnr(cr->dd, lincsd->bla[2*p_imax]),
+ ddglatnr(cr->dd, lincsd->bla[2*p_imax+1]));
+ }
+
+ if (warn >= 0)
+ {
+ if (maxwarn >= 0)
+ {
+ cconerr(cr->dd, lincsd->nc, lincsd->bla, lincsd->bllen, xprime, pbc,
+ &ncons_loc, &p_ssd, &p_max, &p_imax);
+ if (MULTISIM(cr))
+ {
+ sprintf(buf3, " in simulation %d", cr->ms->sim);
+ }
+ else
+ {
+ buf3[0] = 0;
+ }
+ sprintf(buf, "\nStep %s, time %g (ps) LINCS WARNING%s\n"
+ "relative constraint deviation after LINCS:\n"
+ "rms %.6f, max %.6f (between atoms %d and %d)\n",
+ gmx_step_str(step, buf2), ir->init_t+step*ir->delta_t,
+ buf3,
+ sqrt(p_ssd/ncons_loc), p_max,
+ ddglatnr(cr->dd, lincsd->bla[2*p_imax]),
+ ddglatnr(cr->dd, lincsd->bla[2*p_imax+1]));
+ if (fplog)
+ {
+ fprintf(fplog, "%s", buf);
+ }
+ fprintf(stderr, "%s", buf);
+ lincs_warning(fplog, cr->dd, x, xprime, pbc,
+ lincsd->nc, lincsd->bla, lincsd->bllen,
+ ir->LincsWarnAngle, maxwarn, warncount);
+ }
+ bOK = (p_max < 0.5);
+ }
+
+ if (lincsd->ncg_flex)
+ {
+ for (i = 0; (i < lincsd->nc); i++)
+ {
+ if (lincsd->bllen0[i] == 0 && lincsd->ddist[i] == 0)
+ {
+ lincsd->bllen[i] = 0;
+ }
+ }
+ }
+ }
+ else
+ {
+ /* The OpenMP parallel region of constrain_lincs for derivatives */
+#pragma omp parallel num_threads(lincsd->nth)
+ {
+ int th = gmx_omp_get_thread_num();
+
+ do_lincsp(x, xprime, min_proj, pbc, lincsd, th,
+ md->invmass, econq, ir->efep != efepNO ? dvdlambda : NULL,
+ bCalcVir, th == 0 ? vir_r_m_dr : lincsd->th[th].vir_r_m_dr);
+ }
+ }
+
+ if (bCalcVir && lincsd->nth > 1)
+ {
+ for (i = 1; i < lincsd->nth; i++)
+ {
+ m_add(vir_r_m_dr, lincsd->th[i].vir_r_m_dr, vir_r_m_dr);
+ }
+ }
+
+ /* count assuming nit=1 */
+ inc_nrnb(nrnb, eNR_LINCS, lincsd->nc);
+ inc_nrnb(nrnb, eNR_LINCSMAT, (2+lincsd->nOrder)*lincsd->ncc);
+ if (lincsd->ntriangle > 0)
+ {
+ inc_nrnb(nrnb, eNR_LINCSMAT, lincsd->nOrder*lincsd->ncc_triangle);
+ }
+ if (v)
+ {
+ inc_nrnb(nrnb, eNR_CONSTR_V, lincsd->nc*2);
+ }
+ if (bCalcVir)
+ {
+ inc_nrnb(nrnb, eNR_CONSTR_VIR, lincsd->nc);
+ }
+
+ return bOK;
+}
--- /dev/null
- dd_move_x_constraints(cr->dd, box, x, xprime);
+/*
+ * 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.
+ * 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
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "gromacs/fileio/confio.h"
+#include "types/commrec.h"
+#include "constr.h"
+#include "copyrite.h"
+#include "invblock.h"
+#include "main.h"
+#include "mdrun.h"
+#include "nrnb.h"
+#include "smalloc.h"
+#include "vec.h"
+#include "physics.h"
+#include "names.h"
+#include "txtdump.h"
+#include "domdec.h"
+#include "gromacs/fileio/pdbio.h"
+#include "splitter.h"
+#include "mtop_util.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "macros.h"
+#include "gmx_omp_nthreads.h"
+#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/pulling/pull.h"
+
+
+typedef struct gmx_constr {
+ int ncon_tot; /* The total number of constraints */
+ int nflexcon; /* The number of flexible constraints */
+ int n_at2con_mt; /* The size of at2con = #moltypes */
+ t_blocka *at2con_mt; /* A list of atoms to constraints */
+ int n_at2settle_mt; /* The size of at2settle = #moltypes */
+ int **at2settle_mt; /* A list of atoms to settles */
+ gmx_bool bInterCGsettles;
+ gmx_lincsdata_t lincsd; /* LINCS data */
+ gmx_shakedata_t shaked; /* SHAKE data */
+ gmx_settledata_t settled; /* SETTLE data */
+ int nblocks; /* The number of SHAKE blocks */
+ int *sblock; /* The SHAKE blocks */
+ int sblock_nalloc; /* The allocation size of sblock */
+ real *lagr; /* Lagrange multipliers for SHAKE */
+ int lagr_nalloc; /* The allocation size of lagr */
+ int maxwarn; /* The maximum number of warnings */
+ int warncount_lincs;
+ int warncount_settle;
+ gmx_edsam_t ed; /* The essential dynamics data */
+
+ tensor *vir_r_m_dr_th; /* Thread local working data */
+ int *settle_error; /* Thread local working data */
+
+ gmx_mtop_t *warn_mtop; /* Only used for printing warnings */
+} t_gmx_constr;
+
+typedef struct {
+ atom_id iatom[3];
+ atom_id blocknr;
+} t_sortblock;
+
+static void *init_vetavars(t_vetavars *vars,
+ gmx_bool constr_deriv,
+ real veta, real vetanew, t_inputrec *ir, gmx_ekindata_t *ekind, gmx_bool bPscal)
+{
+ double g;
+ int i;
+
+ /* first, set the alpha integrator variable */
+ if ((ir->opts.nrdf[0] > 0) && bPscal)
+ {
+ vars->alpha = 1.0 + DIM/((double)ir->opts.nrdf[0]);
+ }
+ else
+ {
+ vars->alpha = 1.0;
+ }
+ g = 0.5*veta*ir->delta_t;
+ vars->rscale = exp(g)*series_sinhx(g);
+ g = -0.25*vars->alpha*veta*ir->delta_t;
+ vars->vscale = exp(g)*series_sinhx(g);
+ vars->rvscale = vars->vscale*vars->rscale;
+ vars->veta = vetanew;
+
+ if (constr_deriv)
+ {
+ snew(vars->vscale_nhc, ir->opts.ngtc);
+ if ((ekind == NULL) || (!bPscal))
+ {
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ vars->vscale_nhc[i] = 1;
+ }
+ }
+ else
+ {
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ vars->vscale_nhc[i] = ekind->tcstat[i].vscale_nhc;
+ }
+ }
+ }
+ else
+ {
+ vars->vscale_nhc = NULL;
+ }
+
+ return vars;
+}
+
+static void free_vetavars(t_vetavars *vars)
+{
+ if (vars->vscale_nhc != NULL)
+ {
+ sfree(vars->vscale_nhc);
+ }
+}
+
+static int pcomp(const void *p1, const void *p2)
+{
+ int db;
+ atom_id min1, min2, max1, max2;
+ t_sortblock *a1 = (t_sortblock *)p1;
+ t_sortblock *a2 = (t_sortblock *)p2;
+
+ db = a1->blocknr-a2->blocknr;
+
+ if (db != 0)
+ {
+ return db;
+ }
+
+ min1 = min(a1->iatom[1], a1->iatom[2]);
+ max1 = max(a1->iatom[1], a1->iatom[2]);
+ min2 = min(a2->iatom[1], a2->iatom[2]);
+ max2 = max(a2->iatom[1], a2->iatom[2]);
+
+ if (min1 == min2)
+ {
+ return max1-max2;
+ }
+ else
+ {
+ return min1-min2;
+ }
+}
+
+int n_flexible_constraints(struct gmx_constr *constr)
+{
+ int nflexcon;
+
+ if (constr)
+ {
+ nflexcon = constr->nflexcon;
+ }
+ else
+ {
+ nflexcon = 0;
+ }
+
+ return nflexcon;
+}
+
+void too_many_constraint_warnings(int eConstrAlg, int warncount)
+{
+ const char *abort = "- aborting to avoid logfile runaway.\n"
+ "This normally happens when your system is not sufficiently equilibrated,"
+ "or if you are changing lambda too fast in free energy simulations.\n";
+
+ gmx_fatal(FARGS,
+ "Too many %s warnings (%d)\n"
+ "If you know what you are doing you can %s"
+ "set the environment variable GMX_MAXCONSTRWARN to -1,\n"
+ "but normally it is better to fix the problem",
+ (eConstrAlg == econtLINCS) ? "LINCS" : "SETTLE", warncount,
+ (eConstrAlg == econtLINCS) ?
+ "adjust the lincs warning threshold in your mdp file\nor " : "\n");
+}
+
+static void write_constr_pdb(const char *fn, const char *title,
+ gmx_mtop_t *mtop,
+ int start, int homenr, t_commrec *cr,
+ rvec x[], matrix box)
+{
+ char fname[STRLEN], format[STRLEN];
+ FILE *out;
+ int dd_ac0 = 0, dd_ac1 = 0, i, ii, resnr;
+ gmx_domdec_t *dd;
+ char *anm, *resnm;
+
+ dd = NULL;
+ if (DOMAINDECOMP(cr))
+ {
+ dd = cr->dd;
+ dd_get_constraint_range(dd, &dd_ac0, &dd_ac1);
+ start = 0;
+ homenr = dd_ac1;
+ }
+
+ if (PAR(cr))
+ {
+ sprintf(fname, "%s_n%d.pdb", fn, cr->sim_nodeid);
+ }
+ else
+ {
+ sprintf(fname, "%s.pdb", fn);
+ }
+ sprintf(format, "%s\n", get_pdbformat());
+
+ out = gmx_fio_fopen(fname, "w");
+
+ fprintf(out, "TITLE %s\n", title);
+ gmx_write_pdb_box(out, -1, box);
+ for (i = start; i < start+homenr; i++)
+ {
+ if (dd != NULL)
+ {
+ if (i >= dd->nat_home && i < dd_ac0)
+ {
+ continue;
+ }
+ ii = dd->gatindex[i];
+ }
+ else
+ {
+ ii = i;
+ }
+ gmx_mtop_atominfo_global(mtop, ii, &anm, &resnr, &resnm);
+ fprintf(out, format, "ATOM", (ii+1)%100000,
+ anm, resnm, ' ', resnr%10000, ' ',
+ 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ]);
+ }
+ fprintf(out, "TER\n");
+
+ gmx_fio_fclose(out);
+}
+
+static void dump_confs(FILE *fplog, gmx_int64_t step, gmx_mtop_t *mtop,
+ int start, int homenr, t_commrec *cr,
+ rvec x[], rvec xprime[], matrix box)
+{
+ char buf[256], buf2[22];
+
+ char *env = getenv("GMX_SUPPRESS_DUMP");
+ if (env)
+ {
+ return;
+ }
+
+ sprintf(buf, "step%sb", gmx_step_str(step, buf2));
+ write_constr_pdb(buf, "initial coordinates",
+ mtop, start, homenr, cr, x, box);
+ sprintf(buf, "step%sc", gmx_step_str(step, buf2));
+ write_constr_pdb(buf, "coordinates after constraining",
+ mtop, start, homenr, cr, xprime, box);
+ if (fplog)
+ {
+ fprintf(fplog, "Wrote pdb files with previous and current coordinates\n");
+ }
+ fprintf(stderr, "Wrote pdb files with previous and current coordinates\n");
+}
+
+static void pr_sortblock(FILE *fp, const char *title, int nsb, t_sortblock sb[])
+{
+ int i;
+
+ fprintf(fp, "%s\n", title);
+ for (i = 0; (i < nsb); i++)
+ {
+ fprintf(fp, "i: %5d, iatom: (%5d %5d %5d), blocknr: %5d\n",
+ i, sb[i].iatom[0], sb[i].iatom[1], sb[i].iatom[2],
+ sb[i].blocknr);
+ }
+}
+
+gmx_bool constrain(FILE *fplog, gmx_bool bLog, gmx_bool bEner,
+ struct gmx_constr *constr,
+ t_idef *idef, t_inputrec *ir, gmx_ekindata_t *ekind,
+ t_commrec *cr,
+ gmx_int64_t step, int delta_step,
+ t_mdatoms *md,
+ rvec *x, rvec *xprime, rvec *min_proj,
+ gmx_bool bMolPBC, matrix box,
+ real lambda, real *dvdlambda,
+ rvec *v, tensor *vir,
+ t_nrnb *nrnb, int econq, gmx_bool bPscal,
+ real veta, real vetanew)
+{
+ gmx_bool bOK, bDump;
+ int start, homenr, nrend;
+ int i, j, d;
+ int ncons, settle_error;
+ tensor vir_r_m_dr;
+ rvec *vstor;
+ real invdt, vir_fac, t;
+ t_ilist *settle;
+ int nsettle;
+ t_pbc pbc, *pbc_null;
+ char buf[22];
+ t_vetavars vetavar;
+ int nth, th;
+
+ if (econq == econqForceDispl && !EI_ENERGY_MINIMIZATION(ir->eI))
+ {
+ gmx_incons("constrain called for forces displacements while not doing energy minimization, can not do this while the LINCS and SETTLE constraint connection matrices are mass weighted");
+ }
+
+ bOK = TRUE;
+ bDump = FALSE;
+
+ start = 0;
+ homenr = md->homenr;
+ nrend = start+homenr;
+
+ /* set constants for pressure control integration */
+ init_vetavars(&vetavar, econq != econqCoord,
+ veta, vetanew, ir, ekind, bPscal);
+
+ if (ir->delta_t == 0)
+ {
+ invdt = 0;
+ }
+ else
+ {
+ invdt = 1/ir->delta_t;
+ }
+
+ if (ir->efep != efepNO && EI_DYNAMICS(ir->eI))
+ {
+ /* Set the constraint lengths for the step at which this configuration
+ * is meant to be. The invmasses should not be changed.
+ */
+ lambda += delta_step*ir->fepvals->delta_lambda;
+ }
+
+ if (vir != NULL)
+ {
+ clear_mat(vir_r_m_dr);
+ }
+
+ where();
+
+ settle = &idef->il[F_SETTLE];
+ nsettle = settle->nr/(1+NRAL(F_SETTLE));
+
+ if (nsettle > 0)
+ {
+ nth = gmx_omp_nthreads_get(emntSETTLE);
+ }
+ else
+ {
+ nth = 1;
+ }
+
+ if (nth > 1 && constr->vir_r_m_dr_th == NULL)
+ {
+ snew(constr->vir_r_m_dr_th, nth);
+ snew(constr->settle_error, nth);
+ }
+
+ settle_error = -1;
+
+ /* We do not need full pbc when constraints do not cross charge groups,
+ * i.e. when dd->constraint_comm==NULL.
+ * Note that PBC for constraints is different from PBC for bondeds.
+ * For constraints there is both forward and backward communication.
+ */
+ if (ir->ePBC != epbcNONE &&
+ (cr->dd || bMolPBC) && !(cr->dd && cr->dd->constraint_comm == NULL))
+ {
+ /* With pbc=screw the screw has been changed to a shift
+ * by the constraint coordinate communication routine,
+ * so that here we can use normal pbc.
+ */
+ pbc_null = set_pbc_dd(&pbc, ir->ePBC, cr->dd, FALSE, box);
+ }
+ else
+ {
+ pbc_null = NULL;
+ }
+
+ /* Communicate the coordinates required for the non-local constraints
+ * for LINCS and/or SETTLE.
+ */
+ if (cr->dd)
+ {
++ dd_move_x_constraints(cr->dd, box, x, xprime, econq == econqCoord);
+ }
+
+ if (constr->lincsd != NULL)
+ {
+ bOK = constrain_lincs(fplog, bLog, bEner, ir, step, constr->lincsd, md, cr,
+ x, xprime, min_proj,
+ box, pbc_null, lambda, dvdlambda,
+ invdt, v, vir != NULL, vir_r_m_dr,
+ econq, nrnb,
+ constr->maxwarn, &constr->warncount_lincs);
+ if (!bOK && constr->maxwarn >= 0)
+ {
+ if (fplog != NULL)
+ {
+ fprintf(fplog, "Constraint error in algorithm %s at step %s\n",
+ econstr_names[econtLINCS], gmx_step_str(step, buf));
+ }
+ bDump = TRUE;
+ }
+ }
+
+ if (constr->nblocks > 0)
+ {
+ switch (econq)
+ {
+ case (econqCoord):
+ bOK = bshakef(fplog, constr->shaked,
+ md->invmass, constr->nblocks, constr->sblock,
+ idef, ir, x, xprime, nrnb,
+ constr->lagr, lambda, dvdlambda,
+ invdt, v, vir != NULL, vir_r_m_dr,
+ constr->maxwarn >= 0, econq, &vetavar);
+ break;
+ case (econqVeloc):
+ bOK = bshakef(fplog, constr->shaked,
+ md->invmass, constr->nblocks, constr->sblock,
+ idef, ir, x, min_proj, nrnb,
+ constr->lagr, lambda, dvdlambda,
+ invdt, NULL, vir != NULL, vir_r_m_dr,
+ constr->maxwarn >= 0, econq, &vetavar);
+ break;
+ default:
+ gmx_fatal(FARGS, "Internal error, SHAKE called for constraining something else than coordinates");
+ break;
+ }
+
+ if (!bOK && constr->maxwarn >= 0)
+ {
+ if (fplog != NULL)
+ {
+ fprintf(fplog, "Constraint error in algorithm %s at step %s\n",
+ econstr_names[econtSHAKE], gmx_step_str(step, buf));
+ }
+ bDump = TRUE;
+ }
+ }
+
+ if (nsettle > 0)
+ {
+ int calcvir_atom_end;
+
+ if (vir == NULL)
+ {
+ calcvir_atom_end = 0;
+ }
+ else
+ {
+ calcvir_atom_end = md->homenr;
+ }
+
+ switch (econq)
+ {
+ case econqCoord:
+#pragma omp parallel for num_threads(nth) schedule(static)
+ for (th = 0; th < nth; th++)
+ {
+ int start_th, end_th;
+
+ if (th > 0)
+ {
+ clear_mat(constr->vir_r_m_dr_th[th]);
+ }
+
+ start_th = (nsettle* th )/nth;
+ end_th = (nsettle*(th+1))/nth;
+ if (start_th >= 0 && end_th - start_th > 0)
+ {
+ csettle(constr->settled,
+ end_th-start_th,
+ settle->iatoms+start_th*(1+NRAL(F_SETTLE)),
+ pbc_null,
+ x[0], xprime[0],
+ invdt, v ? v[0] : NULL, calcvir_atom_end,
+ th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
+ th == 0 ? &settle_error : &constr->settle_error[th],
+ &vetavar);
+ }
+ }
+ inc_nrnb(nrnb, eNR_SETTLE, nsettle);
+ if (v != NULL)
+ {
+ inc_nrnb(nrnb, eNR_CONSTR_V, nsettle*3);
+ }
+ if (vir != NULL)
+ {
+ inc_nrnb(nrnb, eNR_CONSTR_VIR, nsettle*3);
+ }
+ break;
+ case econqVeloc:
+ case econqDeriv:
+ case econqForce:
+ case econqForceDispl:
+#pragma omp parallel for num_threads(nth) schedule(static)
+ for (th = 0; th < nth; th++)
+ {
+ int start_th, end_th;
+
+ if (th > 0)
+ {
+ clear_mat(constr->vir_r_m_dr_th[th]);
+ }
+
+ start_th = (nsettle* th )/nth;
+ end_th = (nsettle*(th+1))/nth;
+
+ if (start_th >= 0 && end_th - start_th > 0)
+ {
+ settle_proj(constr->settled, econq,
+ end_th-start_th,
+ settle->iatoms+start_th*(1+NRAL(F_SETTLE)),
+ pbc_null,
+ x,
+ xprime, min_proj, calcvir_atom_end,
+ th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
+ &vetavar);
+ }
+ }
+ /* This is an overestimate */
+ inc_nrnb(nrnb, eNR_SETTLE, nsettle);
+ break;
+ case econqDeriv_FlexCon:
+ /* Nothing to do, since the are no flexible constraints in settles */
+ break;
+ default:
+ gmx_incons("Unknown constraint quantity for settle");
+ }
+ }
+
+ if (settle->nr > 0)
+ {
+ /* Combine virial and error info of the other threads */
+ for (i = 1; i < nth; i++)
+ {
+ m_add(vir_r_m_dr, constr->vir_r_m_dr_th[i], vir_r_m_dr);
+ settle_error = constr->settle_error[i];
+ }
+
+ if (econq == econqCoord && settle_error >= 0)
+ {
+ bOK = FALSE;
+ if (constr->maxwarn >= 0)
+ {
+ char buf[256];
+ sprintf(buf,
+ "\nstep " "%"GMX_PRId64 ": Water molecule starting at atom %d can not be "
+ "settled.\nCheck for bad contacts and/or reduce the timestep if appropriate.\n",
+ step, ddglatnr(cr->dd, settle->iatoms[settle_error*(1+NRAL(F_SETTLE))+1]));
+ if (fplog)
+ {
+ fprintf(fplog, "%s", buf);
+ }
+ fprintf(stderr, "%s", buf);
+ constr->warncount_settle++;
+ if (constr->warncount_settle > constr->maxwarn)
+ {
+ too_many_constraint_warnings(-1, constr->warncount_settle);
+ }
+ bDump = TRUE;
+ }
+ }
+ }
+
+ free_vetavars(&vetavar);
+
+ if (vir != NULL)
+ {
+ switch (econq)
+ {
+ case econqCoord:
+ vir_fac = 0.5/(ir->delta_t*ir->delta_t);
+ break;
+ case econqVeloc:
+ vir_fac = 0.5/ir->delta_t;
+ break;
+ case econqForce:
+ case econqForceDispl:
+ vir_fac = 0.5;
+ break;
+ default:
+ vir_fac = 0;
+ gmx_incons("Unsupported constraint quantity for virial");
+ }
+
+ if (EI_VV(ir->eI))
+ {
+ vir_fac *= 2; /* only constraining over half the distance here */
+ }
+ for (i = 0; i < DIM; i++)
+ {
+ for (j = 0; j < DIM; j++)
+ {
+ (*vir)[i][j] = vir_fac*vir_r_m_dr[i][j];
+ }
+ }
+ }
+
+ if (bDump)
+ {
+ dump_confs(fplog, step, constr->warn_mtop, start, homenr, cr, x, xprime, box);
+ }
+
+ if (econq == econqCoord)
+ {
+ if (ir->ePull == epullCONSTRAINT)
+ {
+ if (EI_DYNAMICS(ir->eI))
+ {
+ t = ir->init_t + (step + delta_step)*ir->delta_t;
+ }
+ else
+ {
+ t = ir->init_t;
+ }
+ set_pbc(&pbc, ir->ePBC, box);
+ pull_constraint(ir->pull, md, &pbc, cr, ir->delta_t, t, x, xprime, v, *vir);
+ }
+ if (constr->ed && delta_step > 0)
+ {
+ /* apply the essential dynamcs constraints here */
+ do_edsam(ir, step, cr, xprime, v, box, constr->ed);
+ }
+ }
+
+ return bOK;
+}
+
+real *constr_rmsd_data(struct gmx_constr *constr)
+{
+ if (constr->lincsd)
+ {
+ return lincs_rmsd_data(constr->lincsd);
+ }
+ else
+ {
+ return NULL;
+ }
+}
+
+real constr_rmsd(struct gmx_constr *constr, gmx_bool bSD2)
+{
+ if (constr->lincsd)
+ {
+ return lincs_rmsd(constr->lincsd, bSD2);
+ }
+ else
+ {
+ return 0;
+ }
+}
+
+static void make_shake_sblock_serial(struct gmx_constr *constr,
+ t_idef *idef, t_mdatoms *md)
+{
+ int i, j, m, ncons;
+ int bstart, bnr;
+ t_blocka sblocks;
+ t_sortblock *sb;
+ t_iatom *iatom;
+ atom_id *inv_sblock;
+
+ /* Since we are processing the local topology,
+ * the F_CONSTRNC ilist has been concatenated to the F_CONSTR ilist.
+ */
+ ncons = idef->il[F_CONSTR].nr/3;
+
+ init_blocka(&sblocks);
+ gen_sblocks(NULL, 0, md->homenr, idef, &sblocks, FALSE);
+
+ /*
+ bstart=(idef->nodeid > 0) ? blocks->multinr[idef->nodeid-1] : 0;
+ nblocks=blocks->multinr[idef->nodeid] - bstart;
+ */
+ bstart = 0;
+ constr->nblocks = sblocks.nr;
+ if (debug)
+ {
+ fprintf(debug, "ncons: %d, bstart: %d, nblocks: %d\n",
+ ncons, bstart, constr->nblocks);
+ }
+
+ /* Calculate block number for each atom */
+ inv_sblock = make_invblocka(&sblocks, md->nr);
+
+ done_blocka(&sblocks);
+
+ /* Store the block number in temp array and
+ * sort the constraints in order of the sblock number
+ * and the atom numbers, really sorting a segment of the array!
+ */
+#ifdef DEBUGIDEF
+ pr_idef(fplog, 0, "Before Sort", idef);
+#endif
+ iatom = idef->il[F_CONSTR].iatoms;
+ snew(sb, ncons);
+ for (i = 0; (i < ncons); i++, iatom += 3)
+ {
+ for (m = 0; (m < 3); m++)
+ {
+ sb[i].iatom[m] = iatom[m];
+ }
+ sb[i].blocknr = inv_sblock[iatom[1]];
+ }
+
+ /* Now sort the blocks */
+ if (debug)
+ {
+ pr_sortblock(debug, "Before sorting", ncons, sb);
+ fprintf(debug, "Going to sort constraints\n");
+ }
+
+ qsort(sb, ncons, (size_t)sizeof(*sb), pcomp);
+
+ if (debug)
+ {
+ pr_sortblock(debug, "After sorting", ncons, sb);
+ }
+
+ iatom = idef->il[F_CONSTR].iatoms;
+ for (i = 0; (i < ncons); i++, iatom += 3)
+ {
+ for (m = 0; (m < 3); m++)
+ {
+ iatom[m] = sb[i].iatom[m];
+ }
+ }
+#ifdef DEBUGIDEF
+ pr_idef(fplog, 0, "After Sort", idef);
+#endif
+
+ j = 0;
+ snew(constr->sblock, constr->nblocks+1);
+ bnr = -2;
+ for (i = 0; (i < ncons); i++)
+ {
+ if (sb[i].blocknr != bnr)
+ {
+ bnr = sb[i].blocknr;
+ constr->sblock[j++] = 3*i;
+ }
+ }
+ /* Last block... */
+ constr->sblock[j++] = 3*ncons;
+
+ if (j != (constr->nblocks+1))
+ {
+ fprintf(stderr, "bstart: %d\n", bstart);
+ fprintf(stderr, "j: %d, nblocks: %d, ncons: %d\n",
+ j, constr->nblocks, ncons);
+ for (i = 0; (i < ncons); i++)
+ {
+ fprintf(stderr, "i: %5d sb[i].blocknr: %5u\n", i, sb[i].blocknr);
+ }
+ for (j = 0; (j <= constr->nblocks); j++)
+ {
+ fprintf(stderr, "sblock[%3d]=%5d\n", j, (int)constr->sblock[j]);
+ }
+ gmx_fatal(FARGS, "DEATH HORROR: "
+ "sblocks does not match idef->il[F_CONSTR]");
+ }
+ sfree(sb);
+ sfree(inv_sblock);
+}
+
+static void make_shake_sblock_dd(struct gmx_constr *constr,
+ t_ilist *ilcon, t_block *cgs,
+ gmx_domdec_t *dd)
+{
+ int ncons, c, cg;
+ t_iatom *iatom;
+
+ if (dd->ncg_home+1 > constr->sblock_nalloc)
+ {
+ constr->sblock_nalloc = over_alloc_dd(dd->ncg_home+1);
+ srenew(constr->sblock, constr->sblock_nalloc);
+ }
+
+ ncons = ilcon->nr/3;
+ iatom = ilcon->iatoms;
+ constr->nblocks = 0;
+ cg = 0;
+ for (c = 0; c < ncons; c++)
+ {
+ if (c == 0 || iatom[1] >= cgs->index[cg+1])
+ {
+ constr->sblock[constr->nblocks++] = 3*c;
+ while (iatom[1] >= cgs->index[cg+1])
+ {
+ cg++;
+ }
+ }
+ iatom += 3;
+ }
+ constr->sblock[constr->nblocks] = 3*ncons;
+}
+
+t_blocka make_at2con(int start, int natoms,
+ t_ilist *ilist, t_iparams *iparams,
+ gmx_bool bDynamics, int *nflexiblecons)
+{
+ int *count, ncon, con, con_tot, nflexcon, ftype, i, a;
+ t_iatom *ia;
+ t_blocka at2con;
+ gmx_bool bFlexCon;
+
+ snew(count, natoms);
+ nflexcon = 0;
+ for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
+ {
+ ncon = ilist[ftype].nr/3;
+ ia = ilist[ftype].iatoms;
+ for (con = 0; con < ncon; con++)
+ {
+ bFlexCon = (iparams[ia[0]].constr.dA == 0 &&
+ iparams[ia[0]].constr.dB == 0);
+ if (bFlexCon)
+ {
+ nflexcon++;
+ }
+ if (bDynamics || !bFlexCon)
+ {
+ for (i = 1; i < 3; i++)
+ {
+ a = ia[i] - start;
+ count[a]++;
+ }
+ }
+ ia += 3;
+ }
+ }
+ *nflexiblecons = nflexcon;
+
+ at2con.nr = natoms;
+ at2con.nalloc_index = at2con.nr+1;
+ snew(at2con.index, at2con.nalloc_index);
+ at2con.index[0] = 0;
+ for (a = 0; a < natoms; a++)
+ {
+ at2con.index[a+1] = at2con.index[a] + count[a];
+ count[a] = 0;
+ }
+ at2con.nra = at2con.index[natoms];
+ at2con.nalloc_a = at2con.nra;
+ snew(at2con.a, at2con.nalloc_a);
+
+ /* The F_CONSTRNC constraints have constraint numbers
+ * that continue after the last F_CONSTR constraint.
+ */
+ con_tot = 0;
+ for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
+ {
+ ncon = ilist[ftype].nr/3;
+ ia = ilist[ftype].iatoms;
+ for (con = 0; con < ncon; con++)
+ {
+ bFlexCon = (iparams[ia[0]].constr.dA == 0 &&
+ iparams[ia[0]].constr.dB == 0);
+ if (bDynamics || !bFlexCon)
+ {
+ for (i = 1; i < 3; i++)
+ {
+ a = ia[i] - start;
+ at2con.a[at2con.index[a]+count[a]++] = con_tot;
+ }
+ }
+ con_tot++;
+ ia += 3;
+ }
+ }
+
+ sfree(count);
+
+ return at2con;
+}
+
+static int *make_at2settle(int natoms, const t_ilist *ilist)
+{
+ int *at2s;
+ int a, stride, s;
+
+ snew(at2s, natoms);
+ /* Set all to no settle */
+ for (a = 0; a < natoms; a++)
+ {
+ at2s[a] = -1;
+ }
+
+ stride = 1 + NRAL(F_SETTLE);
+
+ for (s = 0; s < ilist->nr; s += stride)
+ {
+ at2s[ilist->iatoms[s+1]] = s/stride;
+ at2s[ilist->iatoms[s+2]] = s/stride;
+ at2s[ilist->iatoms[s+3]] = s/stride;
+ }
+
+ return at2s;
+}
+
+void set_constraints(struct gmx_constr *constr,
+ gmx_localtop_t *top, t_inputrec *ir,
+ t_mdatoms *md, t_commrec *cr)
+{
+ t_idef *idef;
+ int ncons;
+ t_ilist *settle;
+ int iO, iH;
+
+ idef = &top->idef;
+
+ if (constr->ncon_tot > 0)
+ {
+ /* We are using the local topology,
+ * so there are only F_CONSTR constraints.
+ */
+ ncons = idef->il[F_CONSTR].nr/3;
+
+ /* With DD we might also need to call LINCS with ncons=0 for
+ * communicating coordinates to other nodes that do have constraints.
+ */
+ if (ir->eConstrAlg == econtLINCS)
+ {
+ set_lincs(idef, md, EI_DYNAMICS(ir->eI), cr, constr->lincsd);
+ }
+ if (ir->eConstrAlg == econtSHAKE)
+ {
+ if (cr->dd)
+ {
+ make_shake_sblock_dd(constr, &idef->il[F_CONSTR], &top->cgs, cr->dd);
+ }
+ else
+ {
+ make_shake_sblock_serial(constr, idef, md);
+ }
+ if (ncons > constr->lagr_nalloc)
+ {
+ constr->lagr_nalloc = over_alloc_dd(ncons);
+ srenew(constr->lagr, constr->lagr_nalloc);
+ }
+ }
+ }
+
+ if (idef->il[F_SETTLE].nr > 0 && constr->settled == NULL)
+ {
+ settle = &idef->il[F_SETTLE];
+ iO = settle->iatoms[1];
+ iH = settle->iatoms[2];
+ constr->settled =
+ settle_init(md->massT[iO], md->massT[iH],
+ md->invmass[iO], md->invmass[iH],
+ idef->iparams[settle->iatoms[0]].settle.doh,
+ idef->iparams[settle->iatoms[0]].settle.dhh);
+ }
+
+ /* Make a selection of the local atoms for essential dynamics */
+ if (constr->ed && cr->dd)
+ {
+ dd_make_local_ed_indices(cr->dd, constr->ed);
+ }
+}
+
+static void constr_recur(t_blocka *at2con,
+ t_ilist *ilist, t_iparams *iparams, gmx_bool bTopB,
+ int at, int depth, int nc, int *path,
+ real r0, real r1, real *r2max,
+ int *count)
+{
+ int ncon1;
+ t_iatom *ia1, *ia2;
+ int c, con, a1;
+ gmx_bool bUse;
+ t_iatom *ia;
+ real len, rn0, rn1;
+
+ (*count)++;
+
+ ncon1 = ilist[F_CONSTR].nr/3;
+ ia1 = ilist[F_CONSTR].iatoms;
+ ia2 = ilist[F_CONSTRNC].iatoms;
+
+ /* Loop over all constraints connected to this atom */
+ for (c = at2con->index[at]; c < at2con->index[at+1]; c++)
+ {
+ con = at2con->a[c];
+ /* Do not walk over already used constraints */
+ bUse = TRUE;
+ for (a1 = 0; a1 < depth; a1++)
+ {
+ if (con == path[a1])
+ {
+ bUse = FALSE;
+ }
+ }
+ if (bUse)
+ {
+ ia = constr_iatomptr(ncon1, ia1, ia2, con);
+ /* Flexible constraints currently have length 0, which is incorrect */
+ if (!bTopB)
+ {
+ len = iparams[ia[0]].constr.dA;
+ }
+ else
+ {
+ len = iparams[ia[0]].constr.dB;
+ }
+ /* In the worst case the bond directions alternate */
+ if (nc % 2 == 0)
+ {
+ rn0 = r0 + len;
+ rn1 = r1;
+ }
+ else
+ {
+ rn0 = r0;
+ rn1 = r1 + len;
+ }
+ /* Assume angles of 120 degrees between all bonds */
+ if (rn0*rn0 + rn1*rn1 + rn0*rn1 > *r2max)
+ {
+ *r2max = rn0*rn0 + rn1*rn1 + r0*rn1;
+ if (debug)
+ {
+ fprintf(debug, "Found longer constraint distance: r0 %5.3f r1 %5.3f rmax %5.3f\n", rn0, rn1, sqrt(*r2max));
+ for (a1 = 0; a1 < depth; a1++)
+ {
+ fprintf(debug, " %d %5.3f",
+ path[a1],
+ iparams[constr_iatomptr(ncon1, ia1, ia2, con)[0]].constr.dA);
+ }
+ fprintf(debug, " %d %5.3f\n", con, len);
+ }
+ }
+ /* Limit the number of recursions to 1000*nc,
+ * so a call does not take more than a second,
+ * even for highly connected systems.
+ */
+ if (depth + 1 < nc && *count < 1000*nc)
+ {
+ if (ia[1] == at)
+ {
+ a1 = ia[2];
+ }
+ else
+ {
+ a1 = ia[1];
+ }
+ /* Recursion */
+ path[depth] = con;
+ constr_recur(at2con, ilist, iparams,
+ bTopB, a1, depth+1, nc, path, rn0, rn1, r2max, count);
+ path[depth] = -1;
+ }
+ }
+ }
+}
+
+static real constr_r_max_moltype(gmx_moltype_t *molt, t_iparams *iparams,
+ t_inputrec *ir)
+{
+ int natoms, nflexcon, *path, at, count;
+
+ t_blocka at2con;
+ real r0, r1, r2maxA, r2maxB, rmax, lam0, lam1;
+
+ if (molt->ilist[F_CONSTR].nr == 0 &&
+ molt->ilist[F_CONSTRNC].nr == 0)
+ {
+ return 0;
+ }
+
+ natoms = molt->atoms.nr;
+
+ at2con = make_at2con(0, natoms, molt->ilist, iparams,
+ EI_DYNAMICS(ir->eI), &nflexcon);
+ snew(path, 1+ir->nProjOrder);
+ for (at = 0; at < 1+ir->nProjOrder; at++)
+ {
+ path[at] = -1;
+ }
+
+ r2maxA = 0;
+ for (at = 0; at < natoms; at++)
+ {
+ r0 = 0;
+ r1 = 0;
+
+ count = 0;
+ constr_recur(&at2con, molt->ilist, iparams,
+ FALSE, at, 0, 1+ir->nProjOrder, path, r0, r1, &r2maxA, &count);
+ }
+ if (ir->efep == efepNO)
+ {
+ rmax = sqrt(r2maxA);
+ }
+ else
+ {
+ r2maxB = 0;
+ for (at = 0; at < natoms; at++)
+ {
+ r0 = 0;
+ r1 = 0;
+ count = 0;
+ constr_recur(&at2con, molt->ilist, iparams,
+ TRUE, at, 0, 1+ir->nProjOrder, path, r0, r1, &r2maxB, &count);
+ }
+ lam0 = ir->fepvals->init_lambda;
+ if (EI_DYNAMICS(ir->eI))
+ {
+ lam0 += ir->init_step*ir->fepvals->delta_lambda;
+ }
+ rmax = (1 - lam0)*sqrt(r2maxA) + lam0*sqrt(r2maxB);
+ if (EI_DYNAMICS(ir->eI))
+ {
+ lam1 = ir->fepvals->init_lambda + (ir->init_step + ir->nsteps)*ir->fepvals->delta_lambda;
+ rmax = max(rmax, (1 - lam1)*sqrt(r2maxA) + lam1*sqrt(r2maxB));
+ }
+ }
+
+ done_blocka(&at2con);
+ sfree(path);
+
+ return rmax;
+}
+
+real constr_r_max(FILE *fplog, gmx_mtop_t *mtop, t_inputrec *ir)
+{
+ int mt;
+ real rmax;
+
+ rmax = 0;
+ for (mt = 0; mt < mtop->nmoltype; mt++)
+ {
+ rmax = max(rmax,
+ constr_r_max_moltype(&mtop->moltype[mt],
+ mtop->ffparams.iparams, ir));
+ }
+
+ if (fplog)
+ {
+ fprintf(fplog, "Maximum distance for %d constraints, at 120 deg. angles, all-trans: %.3f nm\n", 1+ir->nProjOrder, rmax);
+ }
+
+ return rmax;
+}
+
+gmx_constr_t init_constraints(FILE *fplog,
+ gmx_mtop_t *mtop, t_inputrec *ir,
+ gmx_edsam_t ed, t_state *state,
+ t_commrec *cr)
+{
+ int ncon, nset, nmol, settle_type, i, natoms, mt, nflexcon;
+ struct gmx_constr *constr;
+ char *env;
+ t_ilist *ilist;
+ gmx_mtop_ilistloop_t iloop;
+
+ ncon =
+ gmx_mtop_ftype_count(mtop, F_CONSTR) +
+ gmx_mtop_ftype_count(mtop, F_CONSTRNC);
+ nset = gmx_mtop_ftype_count(mtop, F_SETTLE);
+
+ if (ncon+nset == 0 && ir->ePull != epullCONSTRAINT && ed == NULL)
+ {
+ return NULL;
+ }
+
+ snew(constr, 1);
+
+ constr->ncon_tot = ncon;
+ constr->nflexcon = 0;
+ if (ncon > 0)
+ {
+ constr->n_at2con_mt = mtop->nmoltype;
+ snew(constr->at2con_mt, constr->n_at2con_mt);
+ for (mt = 0; mt < mtop->nmoltype; mt++)
+ {
+ constr->at2con_mt[mt] = make_at2con(0, mtop->moltype[mt].atoms.nr,
+ mtop->moltype[mt].ilist,
+ mtop->ffparams.iparams,
+ EI_DYNAMICS(ir->eI), &nflexcon);
+ for (i = 0; i < mtop->nmolblock; i++)
+ {
+ if (mtop->molblock[i].type == mt)
+ {
+ constr->nflexcon += mtop->molblock[i].nmol*nflexcon;
+ }
+ }
+ }
+
+ if (constr->nflexcon > 0)
+ {
+ if (fplog)
+ {
+ fprintf(fplog, "There are %d flexible constraints\n",
+ constr->nflexcon);
+ if (ir->fc_stepsize == 0)
+ {
+ fprintf(fplog, "\n"
+ "WARNING: step size for flexible constraining = 0\n"
+ " All flexible constraints will be rigid.\n"
+ " Will try to keep all flexible constraints at their original length,\n"
+ " but the lengths may exhibit some drift.\n\n");
+ constr->nflexcon = 0;
+ }
+ }
+ if (constr->nflexcon > 0)
+ {
+ please_cite(fplog, "Hess2002");
+ }
+ }
+
+ if (ir->eConstrAlg == econtLINCS)
+ {
+ constr->lincsd = init_lincs(fplog, mtop,
+ constr->nflexcon, constr->at2con_mt,
+ DOMAINDECOMP(cr) && cr->dd->bInterCGcons,
+ ir->nLincsIter, ir->nProjOrder);
+ }
+
+ if (ir->eConstrAlg == econtSHAKE)
+ {
+ if (DOMAINDECOMP(cr) && cr->dd->bInterCGcons)
+ {
+ gmx_fatal(FARGS, "SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS");
+ }
+ if (constr->nflexcon)
+ {
+ gmx_fatal(FARGS, "For this system also velocities and/or forces need to be constrained, this can not be done with SHAKE, you should select LINCS");
+ }
+ please_cite(fplog, "Ryckaert77a");
+ if (ir->bShakeSOR)
+ {
+ please_cite(fplog, "Barth95a");
+ }
+
+ constr->shaked = shake_init();
+ }
+ }
+
+ if (nset > 0)
+ {
+ please_cite(fplog, "Miyamoto92a");
+
+ constr->bInterCGsettles = inter_charge_group_settles(mtop);
+
+ /* Check that we have only one settle type */
+ settle_type = -1;
+ iloop = gmx_mtop_ilistloop_init(mtop);
+ while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
+ {
+ for (i = 0; i < ilist[F_SETTLE].nr; i += 4)
+ {
+ if (settle_type == -1)
+ {
+ settle_type = ilist[F_SETTLE].iatoms[i];
+ }
+ else if (ilist[F_SETTLE].iatoms[i] != settle_type)
+ {
+ gmx_fatal(FARGS,
+ "The [molecules] section of your topology specifies more than one block of\n"
+ "a [moleculetype] with a [settles] block. Only one such is allowed. If you\n"
+ "are trying to partition your solvent into different *groups* (e.g. for\n"
+ "freezing, T-coupling, etc.) then you are using the wrong approach. Index\n"
+ "files specify groups. Otherwise, you may wish to change the least-used\n"
+ "block of molecules with SETTLE constraints into 3 normal constraints.");
+ }
+ }
+ }
+
+ constr->n_at2settle_mt = mtop->nmoltype;
+ snew(constr->at2settle_mt, constr->n_at2settle_mt);
+ for (mt = 0; mt < mtop->nmoltype; mt++)
+ {
+ constr->at2settle_mt[mt] =
+ make_at2settle(mtop->moltype[mt].atoms.nr,
+ &mtop->moltype[mt].ilist[F_SETTLE]);
+ }
+ }
+
+ constr->maxwarn = 999;
+ env = getenv("GMX_MAXCONSTRWARN");
+ if (env)
+ {
+ constr->maxwarn = 0;
+ sscanf(env, "%d", &constr->maxwarn);
+ if (fplog)
+ {
+ fprintf(fplog,
+ "Setting the maximum number of constraint warnings to %d\n",
+ constr->maxwarn);
+ }
+ if (MASTER(cr))
+ {
+ fprintf(stderr,
+ "Setting the maximum number of constraint warnings to %d\n",
+ constr->maxwarn);
+ }
+ }
+ if (constr->maxwarn < 0 && fplog)
+ {
+ fprintf(fplog, "maxwarn < 0, will not stop on constraint errors\n");
+ }
+ constr->warncount_lincs = 0;
+ constr->warncount_settle = 0;
+
+ /* Initialize the essential dynamics sampling.
+ * Put the pointer to the ED struct in constr */
+ constr->ed = ed;
+ if (ed != NULL || state->edsamstate.nED > 0)
+ {
+ init_edsam(mtop, ir, cr, ed, state->x, state->box, &state->edsamstate);
+ }
+
+ constr->warn_mtop = mtop;
+
+ return constr;
+}
+
+const t_blocka *atom2constraints_moltype(gmx_constr_t constr)
+{
+ return constr->at2con_mt;
+}
+
+const int **atom2settle_moltype(gmx_constr_t constr)
+{
+ return (const int **)constr->at2settle_mt;
+}
+
+
+gmx_bool inter_charge_group_constraints(const gmx_mtop_t *mtop)
+{
+ const gmx_moltype_t *molt;
+ const t_block *cgs;
+ const t_ilist *il;
+ int mb;
+ int nat, *at2cg, cg, a, ftype, i;
+ gmx_bool bInterCG;
+
+ bInterCG = FALSE;
+ for (mb = 0; mb < mtop->nmolblock && !bInterCG; mb++)
+ {
+ molt = &mtop->moltype[mtop->molblock[mb].type];
+
+ if (molt->ilist[F_CONSTR].nr > 0 ||
+ molt->ilist[F_CONSTRNC].nr > 0 ||
+ molt->ilist[F_SETTLE].nr > 0)
+ {
+ cgs = &molt->cgs;
+ snew(at2cg, molt->atoms.nr);
+ for (cg = 0; cg < cgs->nr; cg++)
+ {
+ for (a = cgs->index[cg]; a < cgs->index[cg+1]; a++)
+ {
+ at2cg[a] = cg;
+ }
+ }
+
+ for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
+ {
+ il = &molt->ilist[ftype];
+ for (i = 0; i < il->nr && !bInterCG; i += 1+NRAL(ftype))
+ {
+ if (at2cg[il->iatoms[i+1]] != at2cg[il->iatoms[i+2]])
+ {
+ bInterCG = TRUE;
+ }
+ }
+ }
+
+ sfree(at2cg);
+ }
+ }
+
+ return bInterCG;
+}
+
+gmx_bool inter_charge_group_settles(const gmx_mtop_t *mtop)
+{
+ const gmx_moltype_t *molt;
+ const t_block *cgs;
+ const t_ilist *il;
+ int mb;
+ int nat, *at2cg, cg, a, ftype, i;
+ gmx_bool bInterCG;
+
+ bInterCG = FALSE;
+ for (mb = 0; mb < mtop->nmolblock && !bInterCG; mb++)
+ {
+ molt = &mtop->moltype[mtop->molblock[mb].type];
+
+ if (molt->ilist[F_SETTLE].nr > 0)
+ {
+ cgs = &molt->cgs;
+ snew(at2cg, molt->atoms.nr);
+ for (cg = 0; cg < cgs->nr; cg++)
+ {
+ for (a = cgs->index[cg]; a < cgs->index[cg+1]; a++)
+ {
+ at2cg[a] = cg;
+ }
+ }
+
+ for (ftype = F_SETTLE; ftype <= F_SETTLE; ftype++)
+ {
+ il = &molt->ilist[ftype];
+ for (i = 0; i < il->nr && !bInterCG; i += 1+NRAL(F_SETTLE))
+ {
+ if (at2cg[il->iatoms[i+1]] != at2cg[il->iatoms[i+2]] ||
+ at2cg[il->iatoms[i+1]] != at2cg[il->iatoms[i+3]])
+ {
+ bInterCG = TRUE;
+ }
+ }
+ }
+
+ sfree(at2cg);
+ }
+ }
+
+ return bInterCG;
+}
+
+/* helper functions for andersen temperature control, because the
+ * gmx_constr construct is only defined in constr.c. Return the list
+ * of blocks (get_sblock) and the number of blocks (get_nblocks). */
+
+extern int *get_sblock(struct gmx_constr *constr)
+{
+ return constr->sblock;
+}
+
+extern int get_nblocks(struct gmx_constr *constr)
+{
+ return constr->nblocks;
+}
--- /dev/null
- matrix box, rvec *x0, rvec *x1)
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2006,2007,2008,2009,2010,2012,2013,2014, 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
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+#include <assert.h>
+
+#include "smalloc.h"
+#include "vec.h"
+#include "constr.h"
+#include "types/commrec.h"
+#include "domdec.h"
+#include "domdec_network.h"
+#include "mtop_util.h"
+#include "gmx_ga2la.h"
+#include "gmx_hash.h"
+#include "gmx_omp_nthreads.h"
+#include "macros.h"
+
+typedef struct {
+ int nsend;
+ int *a;
+ int a_nalloc;
+ int nrecv;
+} gmx_specatsend_t;
+
+typedef struct {
+ int *ind;
+ int nalloc;
+ int n;
+} ind_req_t;
+
+typedef struct gmx_domdec_specat_comm {
+ /* The number of indices to receive during the setup */
+ int nreq[DIM][2][2];
+ /* The atoms to send */
+ gmx_specatsend_t spas[DIM][2];
+ gmx_bool *bSendAtom;
+ int bSendAtom_nalloc;
+ /* Send buffers */
+ int *ibuf;
+ int ibuf_nalloc;
+ rvec *vbuf;
+ int vbuf_nalloc;
+ rvec *vbuf2;
+ int vbuf2_nalloc;
+ /* The range in the local buffer(s) for received atoms */
+ int at_start;
+ int at_end;
+
+ /* The atom indices we need from the surrounding cells.
+ * We can gather the indices over nthread threads.
+ */
+ int nthread;
+ ind_req_t *ireq;
+} gmx_domdec_specat_comm_t;
+
+typedef struct gmx_domdec_constraints {
+ int *molb_con_offset;
+ int *molb_ncon_mol;
+ /* The fully local and connected constraints */
+ int ncon;
+ /* The global constraint number, only required for clearing gc_req */
+ int *con_gl;
+ int *con_nlocat;
+ int con_nalloc;
+ /* Boolean that tells if a global constraint index has been requested */
+ char *gc_req;
+ /* Global to local communicated constraint atom only index */
+ gmx_hash_t ga2la;
+
+ /* Multi-threading stuff */
+ int nthread;
+ t_ilist *ils;
+} gmx_domdec_constraints_t;
+
+
+static void dd_move_f_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
+ rvec *f, rvec *fshift)
+{
+ gmx_specatsend_t *spas;
+ rvec *vbuf;
+ int n, n0, n1, d, dim, dir, i;
+ ivec vis;
+ int is;
+ gmx_bool bPBC, bScrew;
+
+ n = spac->at_end;
+ for (d = dd->ndim-1; d >= 0; d--)
+ {
+ dim = dd->dim[d];
+ if (dd->nc[dim] > 2)
+ {
+ /* Pulse the grid forward and backward */
+ spas = spac->spas[d];
+ n0 = spas[0].nrecv;
+ n1 = spas[1].nrecv;
+ n -= n1 + n0;
+ vbuf = spac->vbuf;
+ /* Send and receive the coordinates */
+ dd_sendrecv2_rvec(dd, d,
+ f+n+n1, n0, vbuf, spas[0].nsend,
+ f+n, n1, vbuf+spas[0].nsend, spas[1].nsend);
+ for (dir = 0; dir < 2; dir++)
+ {
+ bPBC = ((dir == 0 && dd->ci[dim] == 0) ||
+ (dir == 1 && dd->ci[dim] == dd->nc[dim]-1));
+ bScrew = (bPBC && dd->bScrewPBC && dim == XX);
+
+ spas = &spac->spas[d][dir];
+ /* Sum the buffer into the required forces */
+ if (!bPBC || (!bScrew && fshift == NULL))
+ {
+ for (i = 0; i < spas->nsend; i++)
+ {
+ rvec_inc(f[spas->a[i]], *vbuf);
+ vbuf++;
+ }
+ }
+ else
+ {
+ clear_ivec(vis);
+ vis[dim] = (dir == 0 ? 1 : -1);
+ is = IVEC2IS(vis);
+ if (!bScrew)
+ {
+ /* Sum and add to shift forces */
+ for (i = 0; i < spas->nsend; i++)
+ {
+ rvec_inc(f[spas->a[i]], *vbuf);
+ rvec_inc(fshift[is], *vbuf);
+ vbuf++;
+ }
+ }
+ else
+ {
+ /* Rotate the forces */
+ for (i = 0; i < spas->nsend; i++)
+ {
+ f[spas->a[i]][XX] += (*vbuf)[XX];
+ f[spas->a[i]][YY] -= (*vbuf)[YY];
+ f[spas->a[i]][ZZ] -= (*vbuf)[ZZ];
+ if (fshift)
+ {
+ rvec_inc(fshift[is], *vbuf);
+ }
+ vbuf++;
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ /* Two cells, so we only need to communicate one way */
+ spas = &spac->spas[d][0];
+ n -= spas->nrecv;
+ /* Send and receive the coordinates */
+ dd_sendrecv_rvec(dd, d, dddirForward,
+ f+n, spas->nrecv, spac->vbuf, spas->nsend);
+ /* Sum the buffer into the required forces */
+ if (dd->bScrewPBC && dim == XX &&
+ (dd->ci[dim] == 0 ||
+ dd->ci[dim] == dd->nc[dim]-1))
+ {
+ for (i = 0; i < spas->nsend; i++)
+ {
+ /* Rotate the force */
+ f[spas->a[i]][XX] += spac->vbuf[i][XX];
+ f[spas->a[i]][YY] -= spac->vbuf[i][YY];
+ f[spas->a[i]][ZZ] -= spac->vbuf[i][ZZ];
+ }
+ }
+ else
+ {
+ for (i = 0; i < spas->nsend; i++)
+ {
+ rvec_inc(f[spas->a[i]], spac->vbuf[i]);
+ }
+ }
+ }
+ }
+}
+
+void dd_move_f_vsites(gmx_domdec_t *dd, rvec *f, rvec *fshift)
+{
+ if (dd->vsite_comm)
+ {
+ dd_move_f_specat(dd, dd->vsite_comm, f, fshift);
+ }
+}
+
+void dd_clear_f_vsites(gmx_domdec_t *dd, rvec *f)
+{
+ int i;
+
+ if (dd->vsite_comm)
+ {
+ for (i = dd->vsite_comm->at_start; i < dd->vsite_comm->at_end; i++)
+ {
+ clear_rvec(f[i]);
+ }
+ }
+}
+
+static void dd_move_x_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
- if (x1)
++ matrix box,
++ rvec *x0,
++ rvec *x1, gmx_bool bX1IsCoord)
+{
+ gmx_specatsend_t *spas;
+ rvec *x, *vbuf, *rbuf;
+ int nvec, v, n, nn, ns0, ns1, nr0, nr1, nr, d, dim, dir, i;
+ gmx_bool bPBC, bScrew = FALSE;
+ rvec shift = {0, 0, 0};
+
+ nvec = 1;
- if (!bPBC)
++ if (x1 != NULL)
+ {
+ nvec++;
+ }
+
+ n = spac->at_start;
+ for (d = 0; d < dd->ndim; d++)
+ {
+ dim = dd->dim[d];
+ if (dd->nc[dim] > 2)
+ {
+ /* Pulse the grid forward and backward */
+ vbuf = spac->vbuf;
+ for (dir = 0; dir < 2; dir++)
+ {
+ if (dir == 0 && dd->ci[dim] == 0)
+ {
+ bPBC = TRUE;
+ bScrew = (dd->bScrewPBC && dim == XX);
+ copy_rvec(box[dim], shift);
+ }
+ else if (dir == 1 && dd->ci[dim] == dd->nc[dim]-1)
+ {
+ bPBC = TRUE;
+ bScrew = (dd->bScrewPBC && dim == XX);
+ for (i = 0; i < DIM; i++)
+ {
+ shift[i] = -box[dim][i];
+ }
+ }
+ else
+ {
+ bPBC = FALSE;
+ bScrew = FALSE;
+ }
+ spas = &spac->spas[d][dir];
+ for (v = 0; v < nvec; v++)
+ {
+ x = (v == 0 ? x0 : x1);
+ /* Copy the required coordinates to the send buffer */
- void dd_move_x_constraints(gmx_domdec_t *dd, matrix box, rvec *x0, rvec *x1)
++ if (!bPBC || (v == 1 && !bX1IsCoord))
+ {
+ /* Only copy */
+ for (i = 0; i < spas->nsend; i++)
+ {
+ copy_rvec(x[spas->a[i]], *vbuf);
+ vbuf++;
+ }
+ }
+ else if (!bScrew)
+ {
+ /* Shift coordinates */
+ for (i = 0; i < spas->nsend; i++)
+ {
+ rvec_add(x[spas->a[i]], shift, *vbuf);
+ vbuf++;
+ }
+ }
+ else
+ {
+ /* Shift and rotate coordinates */
+ for (i = 0; i < spas->nsend; i++)
+ {
+ (*vbuf)[XX] = x[spas->a[i]][XX] + shift[XX];
+ (*vbuf)[YY] = box[YY][YY] - x[spas->a[i]][YY] + shift[YY];
+ (*vbuf)[ZZ] = box[ZZ][ZZ] - x[spas->a[i]][ZZ] + shift[ZZ];
+ vbuf++;
+ }
+ }
+ }
+ }
+ /* Send and receive the coordinates */
+ spas = spac->spas[d];
+ ns0 = spas[0].nsend;
+ nr0 = spas[0].nrecv;
+ ns1 = spas[1].nsend;
+ nr1 = spas[1].nrecv;
+ if (nvec == 1)
+ {
+ dd_sendrecv2_rvec(dd, d,
+ spac->vbuf+ns0, ns1, x0+n, nr1,
+ spac->vbuf, ns0, x0+n+nr1, nr0);
+ }
+ else
+ {
+ /* Communicate both vectors in one buffer */
+ rbuf = spac->vbuf2;
+ dd_sendrecv2_rvec(dd, d,
+ spac->vbuf+2*ns0, 2*ns1, rbuf, 2*nr1,
+ spac->vbuf, 2*ns0, rbuf+2*nr1, 2*nr0);
+ /* Split the buffer into the two vectors */
+ nn = n;
+ for (dir = 1; dir >= 0; dir--)
+ {
+ nr = spas[dir].nrecv;
+ for (v = 0; v < 2; v++)
+ {
+ x = (v == 0 ? x0 : x1);
+ for (i = 0; i < nr; i++)
+ {
+ copy_rvec(*rbuf, x[nn+i]);
+ rbuf++;
+ }
+ }
+ nn += nr;
+ }
+ }
+ n += nr0 + nr1;
+ }
+ else
+ {
+ spas = &spac->spas[d][0];
+ /* Copy the required coordinates to the send buffer */
+ vbuf = spac->vbuf;
+ for (v = 0; v < nvec; v++)
+ {
+ x = (v == 0 ? x0 : x1);
+ if (dd->bScrewPBC && dim == XX &&
+ (dd->ci[XX] == 0 || dd->ci[XX] == dd->nc[XX]-1))
+ {
+ /* Here we only perform the rotation, the rest of the pbc
+ * is handled in the constraint or viste routines.
+ */
+ for (i = 0; i < spas->nsend; i++)
+ {
+ (*vbuf)[XX] = x[spas->a[i]][XX];
+ (*vbuf)[YY] = box[YY][YY] - x[spas->a[i]][YY];
+ (*vbuf)[ZZ] = box[ZZ][ZZ] - x[spas->a[i]][ZZ];
+ vbuf++;
+ }
+ }
+ else
+ {
+ for (i = 0; i < spas->nsend; i++)
+ {
+ copy_rvec(x[spas->a[i]], *vbuf);
+ vbuf++;
+ }
+ }
+ }
+ /* Send and receive the coordinates */
+ if (nvec == 1)
+ {
+ dd_sendrecv_rvec(dd, d, dddirBackward,
+ spac->vbuf, spas->nsend, x0+n, spas->nrecv);
+ }
+ else
+ {
+ /* Communicate both vectors in one buffer */
+ rbuf = spac->vbuf2;
+ dd_sendrecv_rvec(dd, d, dddirBackward,
+ spac->vbuf, 2*spas->nsend, rbuf, 2*spas->nrecv);
+ /* Split the buffer into the two vectors */
+ nr = spas[0].nrecv;
+ for (v = 0; v < 2; v++)
+ {
+ x = (v == 0 ? x0 : x1);
+ for (i = 0; i < nr; i++)
+ {
+ copy_rvec(*rbuf, x[n+i]);
+ rbuf++;
+ }
+ }
+ }
+ n += spas->nrecv;
+ }
+ }
+}
+
- dd_move_x_specat(dd, dd->constraint_comm, box, x0, x1);
++void dd_move_x_constraints(gmx_domdec_t *dd, matrix box,
++ rvec *x0, rvec *x1, gmx_bool bX1IsCoord)
+{
+ if (dd->constraint_comm)
+ {
- dd_move_x_specat(dd, dd->vsite_comm, box, x, NULL);
++ dd_move_x_specat(dd, dd->constraint_comm, box, x0, x1, bX1IsCoord);
+ }
+}
+
+void dd_move_x_vsites(gmx_domdec_t *dd, matrix box, rvec *x)
+{
+ if (dd->vsite_comm)
+ {
++ dd_move_x_specat(dd, dd->vsite_comm, box, x, NULL, FALSE);
+ }
+}
+
+int *dd_constraints_nlocalatoms(gmx_domdec_t *dd)
+{
+ if (dd->constraints)
+ {
+ return dd->constraints->con_nlocat;
+ }
+ else
+ {
+ return NULL;
+ }
+}
+
+void dd_clear_local_constraint_indices(gmx_domdec_t *dd)
+{
+ gmx_domdec_constraints_t *dc;
+ int i;
+
+ dc = dd->constraints;
+
+ for (i = 0; i < dc->ncon; i++)
+ {
+ dc->gc_req[dc->con_gl[i]] = 0;
+ }
+
+ if (dd->constraint_comm)
+ {
+ gmx_hash_clear_and_optimize(dc->ga2la);
+ }
+}
+
+void dd_clear_local_vsite_indices(gmx_domdec_t *dd)
+{
+ int i;
+
+ if (dd->vsite_comm)
+ {
+ gmx_hash_clear_and_optimize(dd->ga2la_vsite);
+ }
+}
+
+static int setup_specat_communication(gmx_domdec_t *dd,
+ ind_req_t *ireq,
+ gmx_domdec_specat_comm_t *spac,
+ gmx_hash_t ga2la_specat,
+ int at_start,
+ int vbuf_fac,
+ const char *specat_type,
+ const char *add_err)
+{
+ int nsend[2], nlast, nsend_zero[2] = {0, 0}, *nsend_ptr;
+ int d, dim, ndir, dir, nr, ns, i, nrecv_local, n0, start, indr, ind, buf[2];
+ int nat_tot_specat, nat_tot_prev, nalloc_old;
+ gmx_bool bPBC, bFirst;
+ gmx_specatsend_t *spas;
+
+ if (debug)
+ {
+ fprintf(debug, "Begin setup_specat_communication for %s\n", specat_type);
+ }
+
+ /* nsend[0]: the number of atoms requested by this node only,
+ * we communicate this for more efficients checks
+ * nsend[1]: the total number of requested atoms
+ */
+ nsend[0] = ireq->n;
+ nsend[1] = nsend[0];
+ nlast = nsend[1];
+ for (d = dd->ndim-1; d >= 0; d--)
+ {
+ /* Pulse the grid forward and backward */
+ dim = dd->dim[d];
+ bPBC = (dim < dd->npbcdim);
+ if (dd->nc[dim] == 2)
+ {
+ /* Only 2 cells, so we only need to communicate once */
+ ndir = 1;
+ }
+ else
+ {
+ ndir = 2;
+ }
+ for (dir = 0; dir < ndir; dir++)
+ {
+ if (!bPBC &&
+ dd->nc[dim] > 2 &&
+ ((dir == 0 && dd->ci[dim] == dd->nc[dim] - 1) ||
+ (dir == 1 && dd->ci[dim] == 0)))
+ {
+ /* No pbc: the fist/last cell should not request atoms */
+ nsend_ptr = nsend_zero;
+ }
+ else
+ {
+ nsend_ptr = nsend;
+ }
+ /* Communicate the number of indices */
+ dd_sendrecv_int(dd, d, dir == 0 ? dddirForward : dddirBackward,
+ nsend_ptr, 2, spac->nreq[d][dir], 2);
+ nr = spac->nreq[d][dir][1];
+ if (nlast+nr > ireq->nalloc)
+ {
+ ireq->nalloc = over_alloc_dd(nlast+nr);
+ srenew(ireq->ind, ireq->nalloc);
+ }
+ /* Communicate the indices */
+ dd_sendrecv_int(dd, d, dir == 0 ? dddirForward : dddirBackward,
+ ireq->ind, nsend_ptr[1], ireq->ind+nlast, nr);
+ nlast += nr;
+ }
+ nsend[1] = nlast;
+ }
+ if (debug)
+ {
+ fprintf(debug, "Communicated the counts\n");
+ }
+
+ /* Search for the requested atoms and communicate the indices we have */
+ nat_tot_specat = at_start;
+ nrecv_local = 0;
+ for (d = 0; d < dd->ndim; d++)
+ {
+ bFirst = (d == 0);
+ /* Pulse the grid forward and backward */
+ if (dd->dim[d] >= dd->npbcdim || dd->nc[dd->dim[d]] > 2)
+ {
+ ndir = 2;
+ }
+ else
+ {
+ ndir = 1;
+ }
+ nat_tot_prev = nat_tot_specat;
+ for (dir = ndir-1; dir >= 0; dir--)
+ {
+ if (nat_tot_specat > spac->bSendAtom_nalloc)
+ {
+ nalloc_old = spac->bSendAtom_nalloc;
+ spac->bSendAtom_nalloc = over_alloc_dd(nat_tot_specat);
+ srenew(spac->bSendAtom, spac->bSendAtom_nalloc);
+ for (i = nalloc_old; i < spac->bSendAtom_nalloc; i++)
+ {
+ spac->bSendAtom[i] = FALSE;
+ }
+ }
+ spas = &spac->spas[d][dir];
+ n0 = spac->nreq[d][dir][0];
+ nr = spac->nreq[d][dir][1];
+ if (debug)
+ {
+ fprintf(debug, "dim=%d, dir=%d, searching for %d atoms\n",
+ d, dir, nr);
+ }
+ start = nlast - nr;
+ spas->nsend = 0;
+ nsend[0] = 0;
+ for (i = 0; i < nr; i++)
+ {
+ indr = ireq->ind[start+i];
+ ind = -1;
+ /* Check if this is a home atom and if so ind will be set */
+ if (!ga2la_get_home(dd->ga2la, indr, &ind))
+ {
+ /* Search in the communicated atoms */
+ ind = gmx_hash_get_minone(ga2la_specat, indr);
+ }
+ if (ind >= 0)
+ {
+ if (i < n0 || !spac->bSendAtom[ind])
+ {
+ if (spas->nsend+1 > spas->a_nalloc)
+ {
+ spas->a_nalloc = over_alloc_large(spas->nsend+1);
+ srenew(spas->a, spas->a_nalloc);
+ }
+ /* Store the local index so we know which coordinates
+ * to send out later.
+ */
+ spas->a[spas->nsend] = ind;
+ spac->bSendAtom[ind] = TRUE;
+ if (spas->nsend+1 > spac->ibuf_nalloc)
+ {
+ spac->ibuf_nalloc = over_alloc_large(spas->nsend+1);
+ srenew(spac->ibuf, spac->ibuf_nalloc);
+ }
+ /* Store the global index so we can send it now */
+ spac->ibuf[spas->nsend] = indr;
+ if (i < n0)
+ {
+ nsend[0]++;
+ }
+ spas->nsend++;
+ }
+ }
+ }
+ nlast = start;
+ /* Clear the local flags */
+ for (i = 0; i < spas->nsend; i++)
+ {
+ spac->bSendAtom[spas->a[i]] = FALSE;
+ }
+ /* Send and receive the number of indices to communicate */
+ nsend[1] = spas->nsend;
+ dd_sendrecv_int(dd, d, dir == 0 ? dddirBackward : dddirForward,
+ nsend, 2, buf, 2);
+ if (debug)
+ {
+ fprintf(debug, "Send to node %d, %d (%d) indices, "
+ "receive from node %d, %d (%d) indices\n",
+ dd->neighbor[d][1-dir], nsend[1], nsend[0],
+ dd->neighbor[d][dir], buf[1], buf[0]);
+ if (gmx_debug_at)
+ {
+ for (i = 0; i < spas->nsend; i++)
+ {
+ fprintf(debug, " %d", spac->ibuf[i]+1);
+ }
+ fprintf(debug, "\n");
+ }
+ }
+ nrecv_local += buf[0];
+ spas->nrecv = buf[1];
+ if (nat_tot_specat + spas->nrecv > dd->gatindex_nalloc)
+ {
+ dd->gatindex_nalloc =
+ over_alloc_dd(nat_tot_specat + spas->nrecv);
+ srenew(dd->gatindex, dd->gatindex_nalloc);
+ }
+ /* Send and receive the indices */
+ dd_sendrecv_int(dd, d, dir == 0 ? dddirBackward : dddirForward,
+ spac->ibuf, spas->nsend,
+ dd->gatindex+nat_tot_specat, spas->nrecv);
+ nat_tot_specat += spas->nrecv;
+ }
+
+ /* Allocate the x/f communication buffers */
+ ns = spac->spas[d][0].nsend;
+ nr = spac->spas[d][0].nrecv;
+ if (ndir == 2)
+ {
+ ns += spac->spas[d][1].nsend;
+ nr += spac->spas[d][1].nrecv;
+ }
+ if (vbuf_fac*ns > spac->vbuf_nalloc)
+ {
+ spac->vbuf_nalloc = over_alloc_dd(vbuf_fac*ns);
+ srenew(spac->vbuf, spac->vbuf_nalloc);
+ }
+ if (vbuf_fac == 2 && vbuf_fac*nr > spac->vbuf2_nalloc)
+ {
+ spac->vbuf2_nalloc = over_alloc_dd(vbuf_fac*nr);
+ srenew(spac->vbuf2, spac->vbuf2_nalloc);
+ }
+
+ /* Make a global to local index for the communication atoms */
+ for (i = nat_tot_prev; i < nat_tot_specat; i++)
+ {
+ gmx_hash_change_or_set(ga2la_specat, dd->gatindex[i], i);
+ }
+ }
+
+ /* Check that in the end we got the number of atoms we asked for */
+ if (nrecv_local != ireq->n)
+ {
+ if (debug)
+ {
+ fprintf(debug, "Requested %d, received %d (tot recv %d)\n",
+ ireq->n, nrecv_local, nat_tot_specat-at_start);
+ if (gmx_debug_at)
+ {
+ for (i = 0; i < ireq->n; i++)
+ {
+ ind = gmx_hash_get_minone(ga2la_specat, ireq->ind[i]);
+ fprintf(debug, " %s%d",
+ (ind >= 0) ? "" : "!",
+ ireq->ind[i]+1);
+ }
+ fprintf(debug, "\n");
+ }
+ }
+ fprintf(stderr, "\nDD cell %d %d %d: Neighboring cells do not have atoms:",
+ dd->ci[XX], dd->ci[YY], dd->ci[ZZ]);
+ for (i = 0; i < ireq->n; i++)
+ {
+ if (gmx_hash_get_minone(ga2la_specat, ireq->ind[i]) < 0)
+ {
+ fprintf(stderr, " %d", ireq->ind[i]+1);
+ }
+ }
+ fprintf(stderr, "\n");
+ gmx_fatal(FARGS, "DD cell %d %d %d could only obtain %d of the %d atoms that are connected via %ss from the neighboring cells. This probably means your %s lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells%s%s.",
+ dd->ci[XX], dd->ci[YY], dd->ci[ZZ],
+ nrecv_local, ireq->n, specat_type,
+ specat_type, add_err,
+ dd->bGridJump ? " or use the -rcon option of mdrun" : "");
+ }
+
+ spac->at_start = at_start;
+ spac->at_end = nat_tot_specat;
+
+ if (debug)
+ {
+ fprintf(debug, "Done setup_specat_communication\n");
+ }
+
+ return nat_tot_specat;
+}
+
+static void walk_out(int con, int con_offset, int a, int offset, int nrec,
+ int ncon1, const t_iatom *ia1, const t_iatom *ia2,
+ const t_blocka *at2con,
+ const gmx_ga2la_t ga2la, gmx_bool bHomeConnect,
+ gmx_domdec_constraints_t *dc,
+ gmx_domdec_specat_comm_t *dcc,
+ t_ilist *il_local,
+ ind_req_t *ireq)
+{
+ int a1_gl, a2_gl, a_loc, i, coni, b;
+ const t_iatom *iap;
+
+ if (dc->gc_req[con_offset+con] == 0)
+ {
+ /* Add this non-home constraint to the list */
+ if (dc->ncon+1 > dc->con_nalloc)
+ {
+ dc->con_nalloc = over_alloc_large(dc->ncon+1);
+ srenew(dc->con_gl, dc->con_nalloc);
+ srenew(dc->con_nlocat, dc->con_nalloc);
+ }
+ dc->con_gl[dc->ncon] = con_offset + con;
+ dc->con_nlocat[dc->ncon] = (bHomeConnect ? 1 : 0);
+ dc->gc_req[con_offset+con] = 1;
+ if (il_local->nr + 3 > il_local->nalloc)
+ {
+ il_local->nalloc = over_alloc_dd(il_local->nr+3);
+ srenew(il_local->iatoms, il_local->nalloc);
+ }
+ iap = constr_iatomptr(ncon1, ia1, ia2, con);
+ il_local->iatoms[il_local->nr++] = iap[0];
+ a1_gl = offset + iap[1];
+ a2_gl = offset + iap[2];
+ /* The following indexing code can probably be optizimed */
+ if (ga2la_get_home(ga2la, a1_gl, &a_loc))
+ {
+ il_local->iatoms[il_local->nr++] = a_loc;
+ }
+ else
+ {
+ /* We set this index later */
+ il_local->iatoms[il_local->nr++] = -a1_gl - 1;
+ }
+ if (ga2la_get_home(ga2la, a2_gl, &a_loc))
+ {
+ il_local->iatoms[il_local->nr++] = a_loc;
+ }
+ else
+ {
+ /* We set this index later */
+ il_local->iatoms[il_local->nr++] = -a2_gl - 1;
+ }
+ dc->ncon++;
+ }
+ /* Check to not ask for the same atom more than once */
+ if (gmx_hash_get_minone(dc->ga2la, offset+a) == -1)
+ {
+ assert(dcc);
+ /* Add this non-home atom to the list */
+ if (ireq->n+1 > ireq->nalloc)
+ {
+ ireq->nalloc = over_alloc_large(ireq->n+1);
+ srenew(ireq->ind, ireq->nalloc);
+ }
+ ireq->ind[ireq->n++] = offset + a;
+ /* Temporarily mark with -2, we get the index later */
+ gmx_hash_set(dc->ga2la, offset+a, -2);
+ }
+
+ if (nrec > 0)
+ {
+ for (i = at2con->index[a]; i < at2con->index[a+1]; i++)
+ {
+ coni = at2con->a[i];
+ if (coni != con)
+ {
+ /* Walk further */
+ iap = constr_iatomptr(ncon1, ia1, ia2, coni);
+ if (a == iap[1])
+ {
+ b = iap[2];
+ }
+ else
+ {
+ b = iap[1];
+ }
+ if (!ga2la_get_home(ga2la, offset+b, &a_loc))
+ {
+ walk_out(coni, con_offset, b, offset, nrec-1,
+ ncon1, ia1, ia2, at2con,
+ ga2la, FALSE, dc, dcc, il_local, ireq);
+ }
+ }
+ }
+ }
+}
+
+static void atoms_to_settles(gmx_domdec_t *dd,
+ const gmx_mtop_t *mtop,
+ const int *cginfo,
+ const int **at2settle_mt,
+ int cg_start, int cg_end,
+ t_ilist *ils_local,
+ ind_req_t *ireq)
+{
+ gmx_ga2la_t ga2la;
+ gmx_mtop_atomlookup_t alook;
+ int settle;
+ int nral, sa;
+ int cg, a, a_gl, a_glsa, a_gls[3], a_locs[3];
+ int mb, molnr, a_mol, offset;
+ const gmx_molblock_t *molb;
+ const t_iatom *ia1;
+ gmx_bool a_home[3];
+ int nlocal;
+ gmx_bool bAssign;
+
+ ga2la = dd->ga2la;
+
+ alook = gmx_mtop_atomlookup_settle_init(mtop);
+
+ nral = NRAL(F_SETTLE);
+
+ for (cg = cg_start; cg < cg_end; cg++)
+ {
+ if (GET_CGINFO_SETTLE(cginfo[cg]))
+ {
+ for (a = dd->cgindex[cg]; a < dd->cgindex[cg+1]; a++)
+ {
+ a_gl = dd->gatindex[a];
+
+ gmx_mtop_atomnr_to_molblock_ind(alook, a_gl, &mb, &molnr, &a_mol);
+ molb = &mtop->molblock[mb];
+
+ settle = at2settle_mt[molb->type][a_mol];
+
+ if (settle >= 0)
+ {
+ offset = a_gl - a_mol;
+
+ ia1 = mtop->moltype[molb->type].ilist[F_SETTLE].iatoms;
+
+ bAssign = FALSE;
+ nlocal = 0;
+ for (sa = 0; sa < nral; sa++)
+ {
+ a_glsa = offset + ia1[settle*(1+nral)+1+sa];
+ a_gls[sa] = a_glsa;
+ a_home[sa] = ga2la_get_home(ga2la, a_glsa, &a_locs[sa]);
+ if (a_home[sa])
+ {
+ if (nlocal == 0 && a_gl == a_glsa)
+ {
+ bAssign = TRUE;
+ }
+ nlocal++;
+ }
+ }
+
+ if (bAssign)
+ {
+ if (ils_local->nr+1+nral > ils_local->nalloc)
+ {
+ ils_local->nalloc = over_alloc_dd(ils_local->nr+1+nral);
+ srenew(ils_local->iatoms, ils_local->nalloc);
+ }
+
+ ils_local->iatoms[ils_local->nr++] = ia1[settle*4];
+
+ for (sa = 0; sa < nral; sa++)
+ {
+ if (ga2la_get_home(ga2la, a_gls[sa], &a_locs[sa]))
+ {
+ ils_local->iatoms[ils_local->nr++] = a_locs[sa];
+ }
+ else
+ {
+ ils_local->iatoms[ils_local->nr++] = -a_gls[sa] - 1;
+ /* Add this non-home atom to the list */
+ if (ireq->n+1 > ireq->nalloc)
+ {
+ ireq->nalloc = over_alloc_large(ireq->n+1);
+ srenew(ireq->ind, ireq->nalloc);
+ }
+ ireq->ind[ireq->n++] = a_gls[sa];
+ /* A check on double atom requests is
+ * not required for settle.
+ */
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ gmx_mtop_atomlookup_destroy(alook);
+}
+
+static void atoms_to_constraints(gmx_domdec_t *dd,
+ const gmx_mtop_t *mtop,
+ const int *cginfo,
+ const t_blocka *at2con_mt, int nrec,
+ t_ilist *ilc_local,
+ ind_req_t *ireq)
+{
+ const t_blocka *at2con;
+ gmx_ga2la_t ga2la;
+ gmx_mtop_atomlookup_t alook;
+ int ncon1;
+ gmx_molblock_t *molb;
+ t_iatom *ia1, *ia2, *iap;
+ int nhome, cg, a, a_gl, a_mol, a_loc, b_lo, offset, mb, molnr, b_mol, i, con, con_offset;
+ gmx_domdec_constraints_t *dc;
+ gmx_domdec_specat_comm_t *dcc;
+
+ dc = dd->constraints;
+ dcc = dd->constraint_comm;
+
+ ga2la = dd->ga2la;
+
+ alook = gmx_mtop_atomlookup_init(mtop);
+
+ nhome = 0;
+ for (cg = 0; cg < dd->ncg_home; cg++)
+ {
+ if (GET_CGINFO_CONSTR(cginfo[cg]))
+ {
+ for (a = dd->cgindex[cg]; a < dd->cgindex[cg+1]; a++)
+ {
+ a_gl = dd->gatindex[a];
+
+ gmx_mtop_atomnr_to_molblock_ind(alook, a_gl, &mb, &molnr, &a_mol);
+ molb = &mtop->molblock[mb];
+
+ ncon1 = mtop->moltype[molb->type].ilist[F_CONSTR].nr/NRAL(F_SETTLE);
+
+ ia1 = mtop->moltype[molb->type].ilist[F_CONSTR].iatoms;
+ ia2 = mtop->moltype[molb->type].ilist[F_CONSTRNC].iatoms;
+
+ /* Calculate the global constraint number offset for the molecule.
+ * This is only required for the global index to make sure
+ * that we use each constraint only once.
+ */
+ con_offset =
+ dc->molb_con_offset[mb] + molnr*dc->molb_ncon_mol[mb];
+
+ /* The global atom number offset for this molecule */
+ offset = a_gl - a_mol;
+ at2con = &at2con_mt[molb->type];
+ for (i = at2con->index[a_mol]; i < at2con->index[a_mol+1]; i++)
+ {
+ con = at2con->a[i];
+ iap = constr_iatomptr(ncon1, ia1, ia2, con);
+ if (a_mol == iap[1])
+ {
+ b_mol = iap[2];
+ }
+ else
+ {
+ b_mol = iap[1];
+ }
+ if (ga2la_get_home(ga2la, offset+b_mol, &a_loc))
+ {
+ /* Add this fully home constraint at the first atom */
+ if (a_mol < b_mol)
+ {
+ if (dc->ncon+1 > dc->con_nalloc)
+ {
+ dc->con_nalloc = over_alloc_large(dc->ncon+1);
+ srenew(dc->con_gl, dc->con_nalloc);
+ srenew(dc->con_nlocat, dc->con_nalloc);
+ }
+ dc->con_gl[dc->ncon] = con_offset + con;
+ dc->con_nlocat[dc->ncon] = 2;
+ if (ilc_local->nr + 3 > ilc_local->nalloc)
+ {
+ ilc_local->nalloc = over_alloc_dd(ilc_local->nr + 3);
+ srenew(ilc_local->iatoms, ilc_local->nalloc);
+ }
+ b_lo = a_loc;
+ ilc_local->iatoms[ilc_local->nr++] = iap[0];
+ ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? a : b_lo);
+ ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? b_lo : a );
+ dc->ncon++;
+ nhome++;
+ }
+ }
+ else
+ {
+ /* We need the nrec constraints coupled to this constraint,
+ * so we need to walk out of the home cell by nrec+1 atoms,
+ * since already atom bg is not locally present.
+ * Therefore we call walk_out with nrec recursions to go
+ * after this first call.
+ */
+ walk_out(con, con_offset, b_mol, offset, nrec,
+ ncon1, ia1, ia2, at2con,
+ dd->ga2la, TRUE, dc, dcc, ilc_local, ireq);
+ }
+ }
+ }
+ }
+ }
+
+ gmx_mtop_atomlookup_destroy(alook);
+
+ if (debug)
+ {
+ fprintf(debug,
+ "Constraints: home %3d border %3d atoms: %3d\n",
+ nhome, dc->ncon-nhome,
+ dd->constraint_comm ? ireq->n : 0);
+ }
+}
+
+int dd_make_local_constraints(gmx_domdec_t *dd, int at_start,
+ const gmx_mtop_t *mtop,
+ const int *cginfo,
+ gmx_constr_t constr, int nrec,
+ t_ilist *il_local)
+{
+ gmx_domdec_constraints_t *dc;
+ t_ilist *ilc_local, *ils_local;
+ ind_req_t *ireq;
+ const t_blocka *at2con_mt;
+ const int **at2settle_mt;
+ gmx_hash_t ga2la_specat;
+ int at_end, i, j;
+ t_iatom *iap;
+
+ dc = dd->constraints;
+
+ ilc_local = &il_local[F_CONSTR];
+ ils_local = &il_local[F_SETTLE];
+
+ dc->ncon = 0;
+ ilc_local->nr = 0;
+ if (dd->constraint_comm)
+ {
+ at2con_mt = atom2constraints_moltype(constr);
+ ireq = &dd->constraint_comm->ireq[0];
+ ireq->n = 0;
+ }
+ else
+ {
+ at2con_mt = NULL;
+ ireq = NULL;
+ }
+
+ if (dd->bInterCGsettles)
+ {
+ at2settle_mt = atom2settle_moltype(constr);
+ ils_local->nr = 0;
+ }
+ else
+ {
+ /* Settle works inside charge groups, we assigned them already */
+ at2settle_mt = NULL;
+ }
+
+ if (at2settle_mt == NULL)
+ {
+ atoms_to_constraints(dd, mtop, cginfo, at2con_mt, nrec,
+ ilc_local, ireq);
+ }
+ else
+ {
+ int t0_set;
+ int thread;
+
+ /* Do the constraints, if present, on the first thread.
+ * Do the settles on all other threads.
+ */
+ t0_set = ((at2con_mt != NULL && dc->nthread > 1) ? 1 : 0);
+
+#pragma omp parallel for num_threads(dc->nthread) schedule(static)
+ for (thread = 0; thread < dc->nthread; thread++)
+ {
+ if (at2con_mt && thread == 0)
+ {
+ atoms_to_constraints(dd, mtop, cginfo, at2con_mt, nrec,
+ ilc_local, ireq);
+ }
+
+ if (thread >= t0_set)
+ {
+ int cg0, cg1;
+ t_ilist *ilst;
+ ind_req_t *ireqt;
+
+ /* Distribute the settle check+assignments over
+ * dc->nthread or dc->nthread-1 threads.
+ */
+ cg0 = (dd->ncg_home*(thread-t0_set ))/(dc->nthread-t0_set);
+ cg1 = (dd->ncg_home*(thread-t0_set+1))/(dc->nthread-t0_set);
+
+ if (thread == t0_set)
+ {
+ ilst = ils_local;
+ }
+ else
+ {
+ ilst = &dc->ils[thread];
+ }
+ ilst->nr = 0;
+
+ ireqt = &dd->constraint_comm->ireq[thread];
+ if (thread > 0)
+ {
+ ireqt->n = 0;
+ }
+
+ atoms_to_settles(dd, mtop, cginfo, at2settle_mt,
+ cg0, cg1,
+ ilst, ireqt);
+ }
+ }
+
+ /* Combine the generate settles and requested indices */
+ for (thread = 1; thread < dc->nthread; thread++)
+ {
+ t_ilist *ilst;
+ ind_req_t *ireqt;
+ int ia;
+
+ if (thread > t0_set)
+ {
+ ilst = &dc->ils[thread];
+ if (ils_local->nr + ilst->nr > ils_local->nalloc)
+ {
+ ils_local->nalloc = over_alloc_large(ils_local->nr + ilst->nr);
+ srenew(ils_local->iatoms, ils_local->nalloc);
+ }
+ for (ia = 0; ia < ilst->nr; ia++)
+ {
+ ils_local->iatoms[ils_local->nr+ia] = ilst->iatoms[ia];
+ }
+ ils_local->nr += ilst->nr;
+ }
+
+ ireqt = &dd->constraint_comm->ireq[thread];
+ if (ireq->n+ireqt->n > ireq->nalloc)
+ {
+ ireq->nalloc = over_alloc_large(ireq->n+ireqt->n);
+ srenew(ireq->ind, ireq->nalloc);
+ }
+ for (ia = 0; ia < ireqt->n; ia++)
+ {
+ ireq->ind[ireq->n+ia] = ireqt->ind[ia];
+ }
+ ireq->n += ireqt->n;
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "Settles: total %3d\n", ils_local->nr/4);
+ }
+ }
+
+ if (dd->constraint_comm)
+ {
+ int nral1;
+
+ at_end =
+ setup_specat_communication(dd, ireq, dd->constraint_comm,
+ dd->constraints->ga2la,
+ at_start, 2,
+ "constraint", " or lincs-order");
+
+ /* Fill in the missing indices */
+ ga2la_specat = dd->constraints->ga2la;
+
+ nral1 = 1 + NRAL(F_CONSTR);
+ for (i = 0; i < ilc_local->nr; i += nral1)
+ {
+ iap = ilc_local->iatoms + i;
+ for (j = 1; j < nral1; j++)
+ {
+ if (iap[j] < 0)
+ {
+ iap[j] = gmx_hash_get_minone(ga2la_specat, -iap[j]-1);
+ }
+ }
+ }
+
+ nral1 = 1 + NRAL(F_SETTLE);
+ for (i = 0; i < ils_local->nr; i += nral1)
+ {
+ iap = ils_local->iatoms + i;
+ for (j = 1; j < nral1; j++)
+ {
+ if (iap[j] < 0)
+ {
+ iap[j] = gmx_hash_get_minone(ga2la_specat, -iap[j]-1);
+ }
+ }
+ }
+ }
+ else
+ {
+ at_end = at_start;
+ }
+
+ return at_end;
+}
+
+int dd_make_local_vsites(gmx_domdec_t *dd, int at_start, t_ilist *lil)
+{
+ gmx_domdec_specat_comm_t *spac;
+ ind_req_t *ireq;
+ gmx_hash_t ga2la_specat;
+ int ftype, nral, i, j, gat, a;
+ t_ilist *lilf;
+ t_iatom *iatoms;
+ int at_end;
+
+ spac = dd->vsite_comm;
+ ireq = &spac->ireq[0];
+ ga2la_specat = dd->ga2la_vsite;
+
+ ireq->n = 0;
+ /* Loop over all the home vsites */
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (interaction_function[ftype].flags & IF_VSITE)
+ {
+ nral = NRAL(ftype);
+ lilf = &lil[ftype];
+ for (i = 0; i < lilf->nr; i += 1+nral)
+ {
+ iatoms = lilf->iatoms + i;
+ /* Check if we have the other atoms */
+ for (j = 1; j < 1+nral; j++)
+ {
+ if (iatoms[j] < 0)
+ {
+ /* This is not a home atom,
+ * we need to ask our neighbors.
+ */
+ a = -iatoms[j] - 1;
+ /* Check to not ask for the same atom more than once */
+ if (gmx_hash_get_minone(dd->ga2la_vsite, a) == -1)
+ {
+ /* Add this non-home atom to the list */
+ if (ireq->n+1 > ireq->nalloc)
+ {
+ ireq->nalloc = over_alloc_large(ireq->n+1);
+ srenew(ireq->ind, ireq->nalloc);
+ }
+ ireq->ind[ireq->n++] = a;
+ /* Temporarily mark with -2,
+ * we get the index later.
+ */
+ gmx_hash_set(ga2la_specat, a, -2);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ at_end = setup_specat_communication(dd, ireq, dd->vsite_comm, ga2la_specat,
+ at_start, 1, "vsite", "");
+
+ /* Fill in the missing indices */
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (interaction_function[ftype].flags & IF_VSITE)
+ {
+ nral = NRAL(ftype);
+ lilf = &lil[ftype];
+ for (i = 0; i < lilf->nr; i += 1+nral)
+ {
+ iatoms = lilf->iatoms + i;
+ for (j = 1; j < 1+nral; j++)
+ {
+ if (iatoms[j] < 0)
+ {
+ iatoms[j] = gmx_hash_get_minone(ga2la_specat, -iatoms[j]-1);
+ }
+ }
+ }
+ }
+ }
+
+ return at_end;
+}
+
+static gmx_domdec_specat_comm_t *specat_comm_init(int nthread)
+{
+ gmx_domdec_specat_comm_t *spac;
+
+ snew(spac, 1);
+ spac->nthread = nthread;
+ snew(spac->ireq, spac->nthread);
+
+ return spac;
+}
+
+void init_domdec_constraints(gmx_domdec_t *dd,
+ gmx_mtop_t *mtop)
+{
+ gmx_domdec_constraints_t *dc;
+ gmx_molblock_t *molb;
+ int mb, ncon, c, a;
+
+ if (debug)
+ {
+ fprintf(debug, "Begin init_domdec_constraints\n");
+ }
+
+ snew(dd->constraints, 1);
+ dc = dd->constraints;
+
+ snew(dc->molb_con_offset, mtop->nmolblock);
+ snew(dc->molb_ncon_mol, mtop->nmolblock);
+
+ ncon = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molb = &mtop->molblock[mb];
+ dc->molb_con_offset[mb] = ncon;
+ dc->molb_ncon_mol[mb] =
+ mtop->moltype[molb->type].ilist[F_CONSTR].nr/3 +
+ mtop->moltype[molb->type].ilist[F_CONSTRNC].nr/3;
+ ncon += molb->nmol*dc->molb_ncon_mol[mb];
+ }
+
+ if (ncon > 0)
+ {
+ snew(dc->gc_req, ncon);
+ for (c = 0; c < ncon; c++)
+ {
+ dc->gc_req[c] = 0;
+ }
+ }
+
+ /* Use a hash table for the global to local index.
+ * The number of keys is a rough estimate, it will be optimized later.
+ */
+ dc->ga2la = gmx_hash_init(min(mtop->natoms/20,
+ mtop->natoms/(2*dd->nnodes)));
+
+ dc->nthread = gmx_omp_nthreads_get(emntDomdec);
+ snew(dc->ils, dc->nthread);
+
+ dd->constraint_comm = specat_comm_init(dc->nthread);
+}
+
+void init_domdec_vsites(gmx_domdec_t *dd, int n_intercg_vsite)
+{
+ int i;
+ gmx_domdec_constraints_t *dc;
+
+ if (debug)
+ {
+ fprintf(debug, "Begin init_domdec_vsites\n");
+ }
+
+ /* Use a hash table for the global to local index.
+ * The number of keys is a rough estimate, it will be optimized later.
+ */
+ dd->ga2la_vsite = gmx_hash_init(min(n_intercg_vsite/20,
+ n_intercg_vsite/(2*dd->nnodes)));
+
+ dd->vsite_comm = specat_comm_init(1);
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff