--- /dev/null
- if (ir->coulombtype == eelPMESWITCH)
+/*
+ * 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 "gromacs/utility/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 "gromacs/utility/cstringutil.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],
+ imd_grp[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);
+ }
+
- 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);
++ if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
+ {
+ if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
+ {
++ real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
++ sprintf(warn_buf, "The switching range for should be 5%% or less (currently %.2f%% using a switching range of %4f-%4f) for accurate electrostatic energies, energy conservation will be good regardless, since ewald_rtol = %g.",
++ percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
++ warning(wi, warn_buf);
++ }
++ }
++
++ if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
++ {
++ if (ir->rvdw_switch == 0)
++ {
++ sprintf(warn_buf, "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones potential. This suggests it was not set in the mdp, which can lead to large energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw switching range.");
+ 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->vdwtype == evdwPME)
+ {
+ if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
+ {
+ sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s a\
+nd %s",
+ evdw_names[ir->vdwtype],
+ eintmod_names[eintmodPOTSHIFT],
+ eintmod_names[eintmodNONE]);
+ }
+ }
+
+ 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);
+ }
+
+ /* Interactive MD */
+ ir->bIMD = FALSE;
+ CCTYPE("Group to display and/or manipulate in interactive MD session");
+ STYPE ("IMD-group", is->imd_grp, NULL);
+ if (is->imd_grp[0] != '\0')
+ {
+ snew(ir->imd, 1);
+ ir->bIMD = TRUE;
+ }
+
+ /* 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 make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
+{
+ int ig = -1, i;
+
+
+ ig = search_string(IMDgname, grps->nr, gnames);
+ IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
+
+ if (IMDgroup->nat > 0)
+ {
+ fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
+ IMDgname, IMDgroup->nat);
+ snew(IMDgroup->ind, IMDgroup->nat);
+ for (i = 0; i < IMDgroup->nat; i++)
+ {
+ IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
+ }
+ }
+}
+
+
+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);
+ }
+
+ /* Make indices for IMD session */
+ if (ir->bIMD)
+ {
+ make_IMD_group(ir->imd, is->imd_grp, 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
- static real vrescale_gamdev(int ia,
+/*
+ * 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 <assert.h>
+
+#include "typedefs.h"
+#include "types/commrec.h"
+#include "gromacs/utility/smalloc.h"
+#include "update.h"
+#include "vec.h"
+#include "macros.h"
+#include "physics.h"
+#include "names.h"
+#include "gmx_fatal.h"
+#include "txtdump.h"
+#include "nrnb.h"
+#include "gromacs/random/random.h"
+#include "update.h"
+#include "mdrun.h"
+
+#define NTROTTERPARTS 3
+
+/* Suzuki-Yoshida Constants, for n=3 and n=5, for symplectic integration */
+/* for n=1, w0 = 1 */
+/* for n=3, w0 = w2 = 1/(2-2^-(1/3)), w1 = 1-2*w0 */
+/* for n=5, w0 = w1 = w3 = w4 = 1/(4-4^-(1/3)), w1 = 1-4*w0 */
+
+#define MAX_SUZUKI_YOSHIDA_NUM 5
+#define SUZUKI_YOSHIDA_NUM 5
+
+static const double sy_const_1[] = { 1. };
+static const double sy_const_3[] = { 0.828981543588751, -0.657963087177502, 0.828981543588751 };
+static const double sy_const_5[] = { 0.2967324292201065, 0.2967324292201065, -0.186929716880426, 0.2967324292201065, 0.2967324292201065 };
+
+static const double* sy_const[] = {
+ NULL,
+ sy_const_1,
+ NULL,
+ sy_const_3,
+ NULL,
+ sy_const_5
+};
+
+/*
+ static const double sy_const[MAX_SUZUKI_YOSHIDA_NUM+1][MAX_SUZUKI_YOSHIDA_NUM+1] = {
+ {},
+ {1},
+ {},
+ {0.828981543588751,-0.657963087177502,0.828981543588751},
+ {},
+ {0.2967324292201065,0.2967324292201065,-0.186929716880426,0.2967324292201065,0.2967324292201065}
+ };*/
+
+/* these integration routines are only referenced inside this file */
+static void NHC_trotter(t_grpopts *opts, int nvar, gmx_ekindata_t *ekind, real dtfull,
+ double xi[], double vxi[], double scalefac[], real *veta, t_extmass *MassQ, gmx_bool bEkinAveVel)
+
+{
+ /* general routine for both barostat and thermostat nose hoover chains */
+
+ int i, j, mi, mj, jmax;
+ double Ekin, Efac, reft, kT, nd;
+ double dt;
+ t_grp_tcstat *tcstat;
+ double *ivxi, *ixi;
+ double *iQinv;
+ double *GQ;
+ gmx_bool bBarostat;
+ int mstepsi, mstepsj;
+ int ns = SUZUKI_YOSHIDA_NUM; /* set the degree of integration in the types/state.h file */
+ int nh = opts->nhchainlength;
+
+ snew(GQ, nh);
+ mstepsi = mstepsj = ns;
+
+/* if scalefac is NULL, we are doing the NHC of the barostat */
+
+ bBarostat = FALSE;
+ if (scalefac == NULL)
+ {
+ bBarostat = TRUE;
+ }
+
+ for (i = 0; i < nvar; i++)
+ {
+
+ /* make it easier to iterate by selecting
+ out the sub-array that corresponds to this T group */
+
+ ivxi = &vxi[i*nh];
+ ixi = &xi[i*nh];
+ if (bBarostat)
+ {
+ iQinv = &(MassQ->QPinv[i*nh]);
+ nd = 1.0; /* THIS WILL CHANGE IF NOT ISOTROPIC */
+ reft = max(0.0, opts->ref_t[0]);
+ Ekin = sqr(*veta)/MassQ->Winv;
+ }
+ else
+ {
+ iQinv = &(MassQ->Qinv[i*nh]);
+ tcstat = &ekind->tcstat[i];
+ nd = opts->nrdf[i];
+ reft = max(0.0, opts->ref_t[i]);
+ if (bEkinAveVel)
+ {
+ Ekin = 2*trace(tcstat->ekinf)*tcstat->ekinscalef_nhc;
+ }
+ else
+ {
+ Ekin = 2*trace(tcstat->ekinh)*tcstat->ekinscaleh_nhc;
+ }
+ }
+ kT = BOLTZ*reft;
+
+ for (mi = 0; mi < mstepsi; mi++)
+ {
+ for (mj = 0; mj < mstepsj; mj++)
+ {
+ /* weighting for this step using Suzuki-Yoshida integration - fixed at 5 */
+ dt = sy_const[ns][mj] * dtfull / mstepsi;
+
+ /* compute the thermal forces */
+ GQ[0] = iQinv[0]*(Ekin - nd*kT);
+
+ for (j = 0; j < nh-1; j++)
+ {
+ if (iQinv[j+1] > 0)
+ {
+ /* we actually don't need to update here if we save the
+ state of the GQ, but it's easier to just recompute*/
+ GQ[j+1] = iQinv[j+1]*((sqr(ivxi[j])/iQinv[j])-kT);
+ }
+ else
+ {
+ GQ[j+1] = 0;
+ }
+ }
+
+ ivxi[nh-1] += 0.25*dt*GQ[nh-1];
+ for (j = nh-1; j > 0; j--)
+ {
+ Efac = exp(-0.125*dt*ivxi[j]);
+ ivxi[j-1] = Efac*(ivxi[j-1]*Efac + 0.25*dt*GQ[j-1]);
+ }
+
+ Efac = exp(-0.5*dt*ivxi[0]);
+ if (bBarostat)
+ {
+ *veta *= Efac;
+ }
+ else
+ {
+ scalefac[i] *= Efac;
+ }
+ Ekin *= (Efac*Efac);
+
+ /* Issue - if the KE is an average of the last and the current temperatures, then we might not be
+ able to scale the kinetic energy directly with this factor. Might take more bookkeeping -- have to
+ think about this a bit more . . . */
+
+ GQ[0] = iQinv[0]*(Ekin - nd*kT);
+
+ /* update thermostat positions */
+ for (j = 0; j < nh; j++)
+ {
+ ixi[j] += 0.5*dt*ivxi[j];
+ }
+
+ for (j = 0; j < nh-1; j++)
+ {
+ Efac = exp(-0.125*dt*ivxi[j+1]);
+ ivxi[j] = Efac*(ivxi[j]*Efac + 0.25*dt*GQ[j]);
+ if (iQinv[j+1] > 0)
+ {
+ GQ[j+1] = iQinv[j+1]*((sqr(ivxi[j])/iQinv[j])-kT);
+ }
+ else
+ {
+ GQ[j+1] = 0;
+ }
+ }
+ ivxi[nh-1] += 0.25*dt*GQ[nh-1];
+ }
+ }
+ }
+ sfree(GQ);
+}
+
+static void boxv_trotter(t_inputrec *ir, real *veta, real dt, tensor box,
+ gmx_ekindata_t *ekind, tensor vir, real pcorr, t_extmass *MassQ)
+{
+
+ real pscal;
+ double alpha;
+ int i, j, d, n, nwall;
+ real T, GW, vol;
+ tensor Winvm, ekinmod, localpres;
+
+ /* The heat bath is coupled to a separate barostat, the last temperature group. In the
+ 2006 Tuckerman et al paper., the order is iL_{T_baro} iL {T_part}
+ */
+
+ if (ir->epct == epctSEMIISOTROPIC)
+ {
+ nwall = 2;
+ }
+ else
+ {
+ nwall = 3;
+ }
+
+ /* eta is in pure units. veta is in units of ps^-1. GW is in
+ units of ps^-2. However, eta has a reference of 1 nm^3, so care must be
+ taken to use only RATIOS of eta in updating the volume. */
+
+ /* we take the partial pressure tensors, modify the
+ kinetic energy tensor, and recovert to pressure */
+
+ if (ir->opts.nrdf[0] == 0)
+ {
+ gmx_fatal(FARGS, "Barostat is coupled to a T-group with no degrees of freedom\n");
+ }
+ /* alpha factor for phase space volume, then multiply by the ekin scaling factor. */
+ alpha = 1.0 + DIM/((double)ir->opts.nrdf[0]);
+ alpha *= ekind->tcstat[0].ekinscalef_nhc;
+ msmul(ekind->ekin, alpha, ekinmod);
+ /* for now, we use Elr = 0, because if you want to get it right, you
+ really should be using PME. Maybe print a warning? */
+
+ pscal = calc_pres(ir->ePBC, nwall, box, ekinmod, vir, localpres)+pcorr;
+
+ vol = det(box);
+ GW = (vol*(MassQ->Winv/PRESFAC))*(DIM*pscal - trace(ir->ref_p)); /* W is in ps^2 * bar * nm^3 */
+
+ *veta += 0.5*dt*GW;
+}
+
+/*
+ * This file implements temperature and pressure coupling algorithms:
+ * For now only the Weak coupling and the modified weak coupling.
+ *
+ * Furthermore computation of pressure and temperature is done here
+ *
+ */
+
+real calc_pres(int ePBC, int nwall, matrix box, tensor ekin, tensor vir,
+ tensor pres)
+{
+ int n, m;
+ real fac;
+
+ if (ePBC == epbcNONE || (ePBC == epbcXY && nwall != 2))
+ {
+ clear_mat(pres);
+ }
+ else
+ {
+ /* Uitzoeken welke ekin hier van toepassing is, zie Evans & Morris - E.
+ * Wrs. moet de druktensor gecorrigeerd worden voor de netto stroom in
+ * het systeem...
+ */
+
+ fac = PRESFAC*2.0/det(box);
+ for (n = 0; (n < DIM); n++)
+ {
+ for (m = 0; (m < DIM); m++)
+ {
+ pres[n][m] = (ekin[n][m] - vir[n][m])*fac;
+ }
+ }
+
+ if (debug)
+ {
+ pr_rvecs(debug, 0, "PC: pres", pres, DIM);
+ pr_rvecs(debug, 0, "PC: ekin", ekin, DIM);
+ pr_rvecs(debug, 0, "PC: vir ", vir, DIM);
+ pr_rvecs(debug, 0, "PC: box ", box, DIM);
+ }
+ }
+ return trace(pres)/DIM;
+}
+
+real calc_temp(real ekin, real nrdf)
+{
+ if (nrdf > 0)
+ {
+ return (2.0*ekin)/(nrdf*BOLTZ);
+ }
+ else
+ {
+ return 0;
+ }
+}
+
+void parrinellorahman_pcoupl(FILE *fplog, gmx_int64_t step,
+ t_inputrec *ir, real dt, tensor pres,
+ tensor box, tensor box_rel, tensor boxv,
+ tensor M, matrix mu, gmx_bool bFirstStep)
+{
+ /* This doesn't do any coordinate updating. It just
+ * integrates the box vector equations from the calculated
+ * acceleration due to pressure difference. We also compute
+ * the tensor M which is used in update to couple the particle
+ * coordinates to the box vectors.
+ *
+ * In Nose and Klein (Mol.Phys 50 (1983) no 5., p 1055) this is
+ * given as
+ * -1 . . -1
+ * M_nk = (h') * (h' * h + h' h) * h
+ *
+ * with the dots denoting time derivatives and h is the transformation from
+ * the scaled frame to the real frame, i.e. the TRANSPOSE of the box.
+ * This also goes for the pressure and M tensors - they are transposed relative
+ * to ours. Our equation thus becomes:
+ *
+ * -1 . . -1
+ * M_gmx = M_nk' = b * (b * b' + b * b') * b'
+ *
+ * where b is the gromacs box matrix.
+ * Our box accelerations are given by
+ * .. ..
+ * b = vol/W inv(box') * (P-ref_P) (=h')
+ */
+
+ int d, n;
+ tensor winv;
+ real vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
+ real atot, arel, change, maxchange, xy_pressure;
+ tensor invbox, pdiff, t1, t2;
+
+ real maxl;
+
+ m_inv_ur0(box, invbox);
+
+ if (!bFirstStep)
+ {
+ /* Note that PRESFAC does not occur here.
+ * The pressure and compressibility always occur as a product,
+ * therefore the pressure unit drops out.
+ */
+ maxl = max(box[XX][XX], box[YY][YY]);
+ maxl = max(maxl, box[ZZ][ZZ]);
+ for (d = 0; d < DIM; d++)
+ {
+ for (n = 0; n < DIM; n++)
+ {
+ winv[d][n] =
+ (4*M_PI*M_PI*ir->compress[d][n])/(3*ir->tau_p*ir->tau_p*maxl);
+ }
+ }
+
+ m_sub(pres, ir->ref_p, pdiff);
+
+ if (ir->epct == epctSURFACETENSION)
+ {
+ /* Unlike Berendsen coupling it might not be trivial to include a z
+ * pressure correction here? On the other hand we don't scale the
+ * box momentarily, but change accelerations, so it might not be crucial.
+ */
+ xy_pressure = 0.5*(pres[XX][XX]+pres[YY][YY]);
+ for (d = 0; d < ZZ; d++)
+ {
+ pdiff[d][d] = (xy_pressure-(pres[ZZ][ZZ]-ir->ref_p[d][d]/box[d][d]));
+ }
+ }
+
+ tmmul(invbox, pdiff, t1);
+ /* Move the off-diagonal elements of the 'force' to one side to ensure
+ * that we obey the box constraints.
+ */
+ for (d = 0; d < DIM; d++)
+ {
+ for (n = 0; n < d; n++)
+ {
+ t1[d][n] += t1[n][d];
+ t1[n][d] = 0;
+ }
+ }
+
+ switch (ir->epct)
+ {
+ case epctANISOTROPIC:
+ for (d = 0; d < DIM; d++)
+ {
+ for (n = 0; n <= d; n++)
+ {
+ t1[d][n] *= winv[d][n]*vol;
+ }
+ }
+ break;
+ case epctISOTROPIC:
+ /* calculate total volume acceleration */
+ atot = box[XX][XX]*box[YY][YY]*t1[ZZ][ZZ]+
+ box[XX][XX]*t1[YY][YY]*box[ZZ][ZZ]+
+ t1[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
+ arel = atot/(3*vol);
+ /* set all RELATIVE box accelerations equal, and maintain total V
+ * change speed */
+ for (d = 0; d < DIM; d++)
+ {
+ for (n = 0; n <= d; n++)
+ {
+ t1[d][n] = winv[0][0]*vol*arel*box[d][n];
+ }
+ }
+ break;
+ case epctSEMIISOTROPIC:
+ case epctSURFACETENSION:
+ /* Note the correction to pdiff above for surftens. coupling */
+
+ /* calculate total XY volume acceleration */
+ atot = box[XX][XX]*t1[YY][YY]+t1[XX][XX]*box[YY][YY];
+ arel = atot/(2*box[XX][XX]*box[YY][YY]);
+ /* set RELATIVE XY box accelerations equal, and maintain total V
+ * change speed. Dont change the third box vector accelerations */
+ for (d = 0; d < ZZ; d++)
+ {
+ for (n = 0; n <= d; n++)
+ {
+ t1[d][n] = winv[d][n]*vol*arel*box[d][n];
+ }
+ }
+ for (n = 0; n < DIM; n++)
+ {
+ t1[ZZ][n] *= winv[d][n]*vol;
+ }
+ break;
+ default:
+ gmx_fatal(FARGS, "Parrinello-Rahman pressure coupling type %s "
+ "not supported yet\n", EPCOUPLTYPETYPE(ir->epct));
+ break;
+ }
+
+ maxchange = 0;
+ for (d = 0; d < DIM; d++)
+ {
+ for (n = 0; n <= d; n++)
+ {
+ boxv[d][n] += dt*t1[d][n];
+
+ /* We do NOT update the box vectors themselves here, since
+ * we need them for shifting later. It is instead done last
+ * in the update() routine.
+ */
+
+ /* Calculate the change relative to diagonal elements-
+ since it's perfectly ok for the off-diagonal ones to
+ be zero it doesn't make sense to check the change relative
+ to its current size.
+ */
+
+ change = fabs(dt*boxv[d][n]/box[d][d]);
+
+ if (change > maxchange)
+ {
+ maxchange = change;
+ }
+ }
+ }
+
+ if (maxchange > 0.01 && fplog)
+ {
+ char buf[22];
+ fprintf(fplog,
+ "\nStep %s Warning: Pressure scaling more than 1%%. "
+ "This may mean your system\n is not yet equilibrated. "
+ "Use of Parrinello-Rahman pressure coupling during\n"
+ "equilibration can lead to simulation instability, "
+ "and is discouraged.\n",
+ gmx_step_str(step, buf));
+ }
+ }
+
+ preserve_box_shape(ir, box_rel, boxv);
+
+ mtmul(boxv, box, t1); /* t1=boxv * b' */
+ mmul(invbox, t1, t2);
+ mtmul(t2, invbox, M);
+
+ /* Determine the scaling matrix mu for the coordinates */
+ for (d = 0; d < DIM; d++)
+ {
+ for (n = 0; n <= d; n++)
+ {
+ t1[d][n] = box[d][n] + dt*boxv[d][n];
+ }
+ }
+ preserve_box_shape(ir, box_rel, t1);
+ /* t1 is the box at t+dt, determine mu as the relative change */
+ mmul_ur0(invbox, t1, mu);
+}
+
+void berendsen_pcoupl(FILE *fplog, gmx_int64_t step,
+ t_inputrec *ir, real dt, tensor pres, matrix box,
+ matrix mu)
+{
+ int d, n;
+ real scalar_pressure, xy_pressure, p_corr_z;
+ char *ptr, buf[STRLEN];
+
+ /*
+ * Calculate the scaling matrix mu
+ */
+ scalar_pressure = 0;
+ xy_pressure = 0;
+ for (d = 0; d < DIM; d++)
+ {
+ scalar_pressure += pres[d][d]/DIM;
+ if (d != ZZ)
+ {
+ xy_pressure += pres[d][d]/(DIM-1);
+ }
+ }
+ /* Pressure is now in bar, everywhere. */
+#define factor(d, m) (ir->compress[d][m]*dt/ir->tau_p)
+
+ /* mu has been changed from pow(1+...,1/3) to 1+.../3, since this is
+ * necessary for triclinic scaling
+ */
+ clear_mat(mu);
+ switch (ir->epct)
+ {
+ case epctISOTROPIC:
+ for (d = 0; d < DIM; d++)
+ {
+ mu[d][d] = 1.0 - factor(d, d)*(ir->ref_p[d][d] - scalar_pressure) /DIM;
+ }
+ break;
+ case epctSEMIISOTROPIC:
+ for (d = 0; d < ZZ; d++)
+ {
+ mu[d][d] = 1.0 - factor(d, d)*(ir->ref_p[d][d]-xy_pressure)/DIM;
+ }
+ mu[ZZ][ZZ] =
+ 1.0 - factor(ZZ, ZZ)*(ir->ref_p[ZZ][ZZ] - pres[ZZ][ZZ])/DIM;
+ break;
+ case epctANISOTROPIC:
+ for (d = 0; d < DIM; d++)
+ {
+ for (n = 0; n < DIM; n++)
+ {
+ mu[d][n] = (d == n ? 1.0 : 0.0)
+ -factor(d, n)*(ir->ref_p[d][n] - pres[d][n])/DIM;
+ }
+ }
+ break;
+ case epctSURFACETENSION:
+ /* ir->ref_p[0/1] is the reference surface-tension times *
+ * the number of surfaces */
+ if (ir->compress[ZZ][ZZ])
+ {
+ p_corr_z = dt/ir->tau_p*(ir->ref_p[ZZ][ZZ] - pres[ZZ][ZZ]);
+ }
+ else
+ {
+ /* when the compressibity is zero, set the pressure correction *
+ * in the z-direction to zero to get the correct surface tension */
+ p_corr_z = 0;
+ }
+ mu[ZZ][ZZ] = 1.0 - ir->compress[ZZ][ZZ]*p_corr_z;
+ for (d = 0; d < DIM-1; d++)
+ {
+ mu[d][d] = 1.0 + factor(d, d)*(ir->ref_p[d][d]/(mu[ZZ][ZZ]*box[ZZ][ZZ])
+ - (pres[ZZ][ZZ]+p_corr_z - xy_pressure))/(DIM-1);
+ }
+ break;
+ default:
+ gmx_fatal(FARGS, "Berendsen pressure coupling type %s not supported yet\n",
+ EPCOUPLTYPETYPE(ir->epct));
+ break;
+ }
+ /* To fullfill the orientation restrictions on triclinic boxes
+ * we will set mu_yx, mu_zx and mu_zy to 0 and correct
+ * the other elements of mu to first order.
+ */
+ mu[YY][XX] += mu[XX][YY];
+ mu[ZZ][XX] += mu[XX][ZZ];
+ mu[ZZ][YY] += mu[YY][ZZ];
+ mu[XX][YY] = 0;
+ mu[XX][ZZ] = 0;
+ mu[YY][ZZ] = 0;
+
+ if (debug)
+ {
+ pr_rvecs(debug, 0, "PC: pres ", pres, 3);
+ pr_rvecs(debug, 0, "PC: mu ", mu, 3);
+ }
+
+ if (mu[XX][XX] < 0.99 || mu[XX][XX] > 1.01 ||
+ mu[YY][YY] < 0.99 || mu[YY][YY] > 1.01 ||
+ mu[ZZ][ZZ] < 0.99 || mu[ZZ][ZZ] > 1.01)
+ {
+ char buf2[22];
+ sprintf(buf, "\nStep %s Warning: pressure scaling more than 1%%, "
+ "mu: %g %g %g\n",
+ gmx_step_str(step, buf2), mu[XX][XX], mu[YY][YY], mu[ZZ][ZZ]);
+ if (fplog)
+ {
+ fprintf(fplog, "%s", buf);
+ }
+ fprintf(stderr, "%s", buf);
+ }
+}
+
+void berendsen_pscale(t_inputrec *ir, matrix mu,
+ matrix box, matrix box_rel,
+ int start, int nr_atoms,
+ rvec x[], unsigned short cFREEZE[],
+ t_nrnb *nrnb)
+{
+ ivec *nFreeze = ir->opts.nFreeze;
+ int n, d, g = 0;
+
+ /* Scale the positions */
+ for (n = start; n < start+nr_atoms; n++)
+ {
+ if (cFREEZE)
+ {
+ g = cFREEZE[n];
+ }
+
+ if (!nFreeze[g][XX])
+ {
+ x[n][XX] = mu[XX][XX]*x[n][XX]+mu[YY][XX]*x[n][YY]+mu[ZZ][XX]*x[n][ZZ];
+ }
+ if (!nFreeze[g][YY])
+ {
+ x[n][YY] = mu[YY][YY]*x[n][YY]+mu[ZZ][YY]*x[n][ZZ];
+ }
+ if (!nFreeze[g][ZZ])
+ {
+ x[n][ZZ] = mu[ZZ][ZZ]*x[n][ZZ];
+ }
+ }
+ /* compute final boxlengths */
+ for (d = 0; d < DIM; d++)
+ {
+ box[d][XX] = mu[XX][XX]*box[d][XX]+mu[YY][XX]*box[d][YY]+mu[ZZ][XX]*box[d][ZZ];
+ box[d][YY] = mu[YY][YY]*box[d][YY]+mu[ZZ][YY]*box[d][ZZ];
+ box[d][ZZ] = mu[ZZ][ZZ]*box[d][ZZ];
+ }
+
+ preserve_box_shape(ir, box_rel, box);
+
+ /* (un)shifting should NOT be done after this,
+ * since the box vectors might have changed
+ */
+ inc_nrnb(nrnb, eNR_PCOUPL, nr_atoms);
+}
+
+void berendsen_tcoupl(t_inputrec *ir, gmx_ekindata_t *ekind, real dt)
+{
+ t_grpopts *opts;
+ int i;
+ real T, reft = 0, lll;
+
+ opts = &ir->opts;
+
+ for (i = 0; (i < opts->ngtc); i++)
+ {
+ if (ir->eI == eiVV)
+ {
+ T = ekind->tcstat[i].T;
+ }
+ else
+ {
+ T = ekind->tcstat[i].Th;
+ }
+
+ if ((opts->tau_t[i] > 0) && (T > 0.0))
+ {
+ reft = max(0.0, opts->ref_t[i]);
+ lll = sqrt(1.0 + (dt/opts->tau_t[i])*(reft/T-1.0));
+ ekind->tcstat[i].lambda = max(min(lll, 1.25), 0.8);
+ }
+ else
+ {
+ ekind->tcstat[i].lambda = 1.0;
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "TC: group %d: T: %g, Lambda: %g\n",
+ i, T, ekind->tcstat[i].lambda);
+ }
+ }
+}
+
+void andersen_tcoupl(t_inputrec *ir, gmx_int64_t step,
+ const t_commrec *cr, const t_mdatoms *md, t_state *state, real rate, const gmx_bool *randomize, const real *boltzfac)
+{
+ const int *gatindex = (DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
+ int i;
+ int gc = 0;
+
+ /* randomize the velocities of the selected particles */
+
+ for (i = 0; i < md->homenr; i++) /* now loop over the list of atoms */
+ {
+ int ng = gatindex ? gatindex[i] : i;
+ gmx_bool bRandomize;
+
+ if (md->cTC)
+ {
+ gc = md->cTC[i]; /* assign the atom to a temperature group if there are more than one */
+ }
+ if (randomize[gc])
+ {
+ if (ir->etc == etcANDERSEN)
+ {
+ bRandomize = TRUE;
+ }
+ else
+ {
+ double uniform[2];
+
+ gmx_rng_cycle_2uniform(step*2, ng, ir->andersen_seed, RND_SEED_ANDERSEN, uniform);
+ bRandomize = (uniform[0] < rate);
+ }
+ if (bRandomize)
+ {
+ real scal, gauss[3];
+ int d;
+
+ scal = sqrt(boltzfac[gc]*md->invmass[i]);
+ gmx_rng_cycle_3gaussian_table(step*2+1, ng, ir->andersen_seed, RND_SEED_ANDERSEN, gauss);
+ for (d = 0; d < DIM; d++)
+ {
+ state->v[i][d] = scal*gauss[d];
+ }
+ }
+ }
+ }
+}
+
+
+void nosehoover_tcoupl(t_grpopts *opts, gmx_ekindata_t *ekind, real dt,
+ double xi[], double vxi[], t_extmass *MassQ)
+{
+ int i;
+ real reft, oldvxi;
+
+ /* note that this routine does not include Nose-hoover chains yet. Should be easy to add. */
+
+ for (i = 0; (i < opts->ngtc); i++)
+ {
+ reft = max(0.0, opts->ref_t[i]);
+ oldvxi = vxi[i];
+ vxi[i] += dt*MassQ->Qinv[i]*(ekind->tcstat[i].Th - reft);
+ xi[i] += dt*(oldvxi + vxi[i])*0.5;
+ }
+}
+
+t_state *init_bufstate(const t_state *template_state)
+{
+ t_state *state;
+ int nc = template_state->nhchainlength;
+ snew(state, 1);
+ snew(state->nosehoover_xi, nc*template_state->ngtc);
+ snew(state->nosehoover_vxi, nc*template_state->ngtc);
+ snew(state->therm_integral, template_state->ngtc);
+ snew(state->nhpres_xi, nc*template_state->nnhpres);
+ snew(state->nhpres_vxi, nc*template_state->nnhpres);
+
+ return state;
+}
+
+void destroy_bufstate(t_state *state)
+{
+ sfree(state->x);
+ sfree(state->v);
+ sfree(state->nosehoover_xi);
+ sfree(state->nosehoover_vxi);
+ sfree(state->therm_integral);
+ sfree(state->nhpres_xi);
+ sfree(state->nhpres_vxi);
+ sfree(state);
+}
+
+void trotter_update(t_inputrec *ir, gmx_int64_t step, gmx_ekindata_t *ekind,
+ gmx_enerdata_t *enerd, t_state *state,
+ tensor vir, t_mdatoms *md,
+ t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno)
+{
+
+ int n, i, j, d, ntgrp, ngtc, gc = 0;
+ t_grp_tcstat *tcstat;
+ t_grpopts *opts;
+ gmx_int64_t step_eff;
+ real ecorr, pcorr, dvdlcorr;
+ real bmass, qmass, reft, kT, dt, nd;
+ tensor dumpres, dumvir;
+ double *scalefac, dtc;
+ int *trotter_seq;
+ rvec sumv = {0, 0, 0}, consk;
+ gmx_bool bCouple;
+
+ if (trotter_seqno <= ettTSEQ2)
+ {
+ step_eff = step-1; /* the velocity verlet calls are actually out of order -- the first half step
+ is actually the last half step from the previous step. Thus the first half step
+ actually corresponds to the n-1 step*/
+
+ }
+ else
+ {
+ step_eff = step;
+ }
+
+ bCouple = (ir->nsttcouple == 1 ||
+ do_per_step(step_eff+ir->nsttcouple, ir->nsttcouple));
+
+ trotter_seq = trotter_seqlist[trotter_seqno];
+
+ if ((trotter_seq[0] == etrtSKIPALL) || (!bCouple))
+ {
+ return;
+ }
+ dtc = ir->nsttcouple*ir->delta_t; /* This is OK for NPT, because nsttcouple == nstpcouple is enforcesd */
+ opts = &(ir->opts); /* just for ease of referencing */
+ ngtc = opts->ngtc;
+ assert(ngtc > 0);
+ snew(scalefac, opts->ngtc);
+ for (i = 0; i < ngtc; i++)
+ {
+ scalefac[i] = 1;
+ }
+ /* execute the series of trotter updates specified in the trotterpart array */
+
+ for (i = 0; i < NTROTTERPARTS; i++)
+ {
+ /* allow for doubled intgrators by doubling dt instead of making 2 calls */
+ if ((trotter_seq[i] == etrtBAROV2) || (trotter_seq[i] == etrtBARONHC2) || (trotter_seq[i] == etrtNHC2))
+ {
+ dt = 2 * dtc;
+ }
+ else
+ {
+ dt = dtc;
+ }
+
+ switch (trotter_seq[i])
+ {
+ case etrtBAROV:
+ case etrtBAROV2:
+ boxv_trotter(ir, &(state->veta), dt, state->box, ekind, vir,
+ enerd->term[F_PDISPCORR], MassQ);
+ break;
+ case etrtBARONHC:
+ case etrtBARONHC2:
+ NHC_trotter(opts, state->nnhpres, ekind, dt, state->nhpres_xi,
+ state->nhpres_vxi, NULL, &(state->veta), MassQ, FALSE);
+ break;
+ case etrtNHC:
+ case etrtNHC2:
+ NHC_trotter(opts, opts->ngtc, ekind, dt, state->nosehoover_xi,
+ state->nosehoover_vxi, scalefac, NULL, MassQ, (ir->eI == eiVV));
+ /* need to rescale the kinetic energies and velocities here. Could
+ scale the velocities later, but we need them scaled in order to
+ produce the correct outputs, so we'll scale them here. */
+
+ for (i = 0; i < ngtc; i++)
+ {
+ tcstat = &ekind->tcstat[i];
+ tcstat->vscale_nhc = scalefac[i];
+ tcstat->ekinscaleh_nhc *= (scalefac[i]*scalefac[i]);
+ tcstat->ekinscalef_nhc *= (scalefac[i]*scalefac[i]);
+ }
+ /* now that we've scaled the groupwise velocities, we can add them up to get the total */
+ /* but do we actually need the total? */
+
+ /* modify the velocities as well */
+ for (n = 0; n < md->homenr; n++)
+ {
+ if (md->cTC) /* does this conditional need to be here? is this always true?*/
+ {
+ gc = md->cTC[n];
+ }
+ for (d = 0; d < DIM; d++)
+ {
+ state->v[n][d] *= scalefac[gc];
+ }
+
+ if (debug)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ sumv[d] += (state->v[n][d])/md->invmass[n];
+ }
+ }
+ }
+ break;
+ default:
+ break;
+ }
+ }
+ /* check for conserved momentum -- worth looking at this again eventually, but not working right now.*/
+#if 0
+ if (debug)
+ {
+ if (bFirstHalf)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ consk[d] = sumv[d]*exp((1 + 1.0/opts->nrdf[0])*((1.0/DIM)*log(det(state->box)/state->vol0)) + state->nosehoover_xi[0]);
+ }
+ fprintf(debug, "Conserved kappa: %15.8f %15.8f %15.8f\n", consk[0], consk[1], consk[2]);
+ }
+ }
+#endif
+ sfree(scalefac);
+}
+
+
+extern void init_npt_masses(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bInit)
+{
+ int n, i, j, d, ntgrp, ngtc, nnhpres, nh, gc = 0;
+ t_grp_tcstat *tcstat;
+ t_grpopts *opts;
+ real ecorr, pcorr, dvdlcorr;
+ real bmass, qmass, reft, kT, dt, ndj, nd;
+ tensor dumpres, dumvir;
+
+ opts = &(ir->opts); /* just for ease of referencing */
+ ngtc = ir->opts.ngtc;
+ nnhpres = state->nnhpres;
+ nh = state->nhchainlength;
+
+ if (ir->eI == eiMD)
+ {
+ if (bInit)
+ {
+ snew(MassQ->Qinv, ngtc);
+ }
+ for (i = 0; (i < ngtc); i++)
+ {
+ if ((opts->tau_t[i] > 0) && (opts->ref_t[i] > 0))
+ {
+ MassQ->Qinv[i] = 1.0/(sqr(opts->tau_t[i]/M_2PI)*opts->ref_t[i]);
+ }
+ else
+ {
+ MassQ->Qinv[i] = 0.0;
+ }
+ }
+ }
+ else if (EI_VV(ir->eI))
+ {
+ /* Set pressure variables */
+
+ if (bInit)
+ {
+ if (state->vol0 == 0)
+ {
+ state->vol0 = det(state->box);
+ /* because we start by defining a fixed
+ compressibility, we need the volume at this
+ compressibility to solve the problem. */
+ }
+ }
+
+ /* units are nm^3 * ns^2 / (nm^3 * bar / kJ/mol) = kJ/mol */
+ /* Consider evaluating eventually if this the right mass to use. All are correct, some might be more stable */
+ MassQ->Winv = (PRESFAC*trace(ir->compress)*BOLTZ*opts->ref_t[0])/(DIM*state->vol0*sqr(ir->tau_p/M_2PI));
+ /* An alternate mass definition, from Tuckerman et al. */
+ /* MassQ->Winv = 1.0/(sqr(ir->tau_p/M_2PI)*(opts->nrdf[0]+DIM)*BOLTZ*opts->ref_t[0]); */
+ for (d = 0; d < DIM; d++)
+ {
+ for (n = 0; n < DIM; n++)
+ {
+ MassQ->Winvm[d][n] = PRESFAC*ir->compress[d][n]/(state->vol0*sqr(ir->tau_p/M_2PI));
+ /* not clear this is correct yet for the anisotropic case. Will need to reevaluate
+ before using MTTK for anisotropic states.*/
+ }
+ }
+ /* Allocate space for thermostat variables */
+ if (bInit)
+ {
+ snew(MassQ->Qinv, ngtc*nh);
+ }
+
+ /* now, set temperature variables */
+ for (i = 0; i < ngtc; i++)
+ {
+ if ((opts->tau_t[i] > 0) && (opts->ref_t[i] > 0))
+ {
+ reft = max(0.0, opts->ref_t[i]);
+ nd = opts->nrdf[i];
+ kT = BOLTZ*reft;
+ for (j = 0; j < nh; j++)
+ {
+ if (j == 0)
+ {
+ ndj = nd;
+ }
+ else
+ {
+ ndj = 1;
+ }
+ MassQ->Qinv[i*nh+j] = 1.0/(sqr(opts->tau_t[i]/M_2PI)*ndj*kT);
+ }
+ }
+ else
+ {
+ reft = 0.0;
+ for (j = 0; j < nh; j++)
+ {
+ MassQ->Qinv[i*nh+j] = 0.0;
+ }
+ }
+ }
+ }
+}
+
+int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bTrotter)
+{
+ int n, i, j, d, ntgrp, ngtc, nnhpres, nh, gc = 0;
+ t_grp_tcstat *tcstat;
+ t_grpopts *opts;
+ real ecorr, pcorr, dvdlcorr;
+ real bmass, qmass, reft, kT, dt, ndj, nd;
+ tensor dumpres, dumvir;
+ int **trotter_seq;
+
+ opts = &(ir->opts); /* just for ease of referencing */
+ ngtc = state->ngtc;
+ nnhpres = state->nnhpres;
+ nh = state->nhchainlength;
+
+ init_npt_masses(ir, state, MassQ, TRUE);
+
+ /* first, initialize clear all the trotter calls */
+ snew(trotter_seq, ettTSEQMAX);
+ for (i = 0; i < ettTSEQMAX; i++)
+ {
+ snew(trotter_seq[i], NTROTTERPARTS);
+ for (j = 0; j < NTROTTERPARTS; j++)
+ {
+ trotter_seq[i][j] = etrtNONE;
+ }
+ trotter_seq[i][0] = etrtSKIPALL;
+ }
+
+ if (!bTrotter)
+ {
+ /* no trotter calls, so we never use the values in the array.
+ * We access them (so we need to define them, but ignore
+ * then.*/
+
+ return trotter_seq;
+ }
+
+ /* compute the kinetic energy by using the half step velocities or
+ * the kinetic energies, depending on the order of the trotter calls */
+
+ if (ir->eI == eiVV)
+ {
+ if (IR_NPT_TROTTER(ir))
+ {
+ /* This is the complicated version - there are 4 possible calls, depending on ordering.
+ We start with the initial one. */
+ /* first, a round that estimates veta. */
+ trotter_seq[0][0] = etrtBAROV;
+
+ /* trotter_seq[1] is etrtNHC for 1/2 step velocities - leave zero */
+
+ /* The first half trotter update */
+ trotter_seq[2][0] = etrtBAROV;
+ trotter_seq[2][1] = etrtNHC;
+ trotter_seq[2][2] = etrtBARONHC;
+
+ /* The second half trotter update */
+ trotter_seq[3][0] = etrtBARONHC;
+ trotter_seq[3][1] = etrtNHC;
+ trotter_seq[3][2] = etrtBAROV;
+
+ /* trotter_seq[4] is etrtNHC for second 1/2 step velocities - leave zero */
+
+ }
+ else if (IR_NVT_TROTTER(ir))
+ {
+ /* This is the easy version - there are only two calls, both the same.
+ Otherwise, even easier -- no calls */
+ trotter_seq[2][0] = etrtNHC;
+ trotter_seq[3][0] = etrtNHC;
+ }
+ else if (IR_NPH_TROTTER(ir))
+ {
+ /* This is the complicated version - there are 4 possible calls, depending on ordering.
+ We start with the initial one. */
+ /* first, a round that estimates veta. */
+ trotter_seq[0][0] = etrtBAROV;
+
+ /* trotter_seq[1] is etrtNHC for 1/2 step velocities - leave zero */
+
+ /* The first half trotter update */
+ trotter_seq[2][0] = etrtBAROV;
+ trotter_seq[2][1] = etrtBARONHC;
+
+ /* The second half trotter update */
+ trotter_seq[3][0] = etrtBARONHC;
+ trotter_seq[3][1] = etrtBAROV;
+
+ /* trotter_seq[4] is etrtNHC for second 1/2 step velocities - leave zero */
+ }
+ }
+ else if (ir->eI == eiVVAK)
+ {
+ if (IR_NPT_TROTTER(ir))
+ {
+ /* This is the complicated version - there are 4 possible calls, depending on ordering.
+ We start with the initial one. */
+ /* first, a round that estimates veta. */
+ trotter_seq[0][0] = etrtBAROV;
+
+ /* The first half trotter update, part 1 -- double update, because it commutes */
+ trotter_seq[1][0] = etrtNHC;
+
+ /* The first half trotter update, part 2 */
+ trotter_seq[2][0] = etrtBAROV;
+ trotter_seq[2][1] = etrtBARONHC;
+
+ /* The second half trotter update, part 1 */
+ trotter_seq[3][0] = etrtBARONHC;
+ trotter_seq[3][1] = etrtBAROV;
+
+ /* The second half trotter update */
+ trotter_seq[4][0] = etrtNHC;
+ }
+ else if (IR_NVT_TROTTER(ir))
+ {
+ /* This is the easy version - there is only one call, both the same.
+ Otherwise, even easier -- no calls */
+ trotter_seq[1][0] = etrtNHC;
+ trotter_seq[4][0] = etrtNHC;
+ }
+ else if (IR_NPH_TROTTER(ir))
+ {
+ /* This is the complicated version - there are 4 possible calls, depending on ordering.
+ We start with the initial one. */
+ /* first, a round that estimates veta. */
+ trotter_seq[0][0] = etrtBAROV;
+
+ /* The first half trotter update, part 1 -- leave zero */
+ trotter_seq[1][0] = etrtNHC;
+
+ /* The first half trotter update, part 2 */
+ trotter_seq[2][0] = etrtBAROV;
+ trotter_seq[2][1] = etrtBARONHC;
+
+ /* The second half trotter update, part 1 */
+ trotter_seq[3][0] = etrtBARONHC;
+ trotter_seq[3][1] = etrtBAROV;
+
+ /* The second half trotter update -- blank for now */
+ }
+ }
+
+ switch (ir->epct)
+ {
+ case epctISOTROPIC:
+ default:
+ bmass = DIM*DIM; /* recommended mass parameters for isotropic barostat */
+ }
+
+ snew(MassQ->QPinv, nnhpres*opts->nhchainlength);
+
+ /* barostat temperature */
+ if ((ir->tau_p > 0) && (opts->ref_t[0] > 0))
+ {
+ reft = max(0.0, opts->ref_t[0]);
+ kT = BOLTZ*reft;
+ for (i = 0; i < nnhpres; i++)
+ {
+ for (j = 0; j < nh; j++)
+ {
+ if (j == 0)
+ {
+ qmass = bmass;
+ }
+ else
+ {
+ qmass = 1;
+ }
+ MassQ->QPinv[i*opts->nhchainlength+j] = 1.0/(sqr(opts->tau_t[0]/M_2PI)*qmass*kT);
+ }
+ }
+ }
+ else
+ {
+ for (i = 0; i < nnhpres; i++)
+ {
+ for (j = 0; j < nh; j++)
+ {
+ MassQ->QPinv[i*nh+j] = 0.0;
+ }
+ }
+ }
+ return trotter_seq;
+}
+
+real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ)
+{
+ int i, j, nd, ndj, bmass, qmass, ngtcall;
+ real ener_npt, reft, eta, kT, tau;
+ double *ivxi, *ixi;
+ double *iQinv;
+ real vol, dbaro, W, Q;
+ int nh = state->nhchainlength;
+
+ ener_npt = 0;
+
+ /* now we compute the contribution of the pressure to the conserved quantity*/
+
+ if (ir->epc == epcMTTK)
+ {
+ /* find the volume, and the kinetic energy of the volume */
+
+ switch (ir->epct)
+ {
+
+ case epctISOTROPIC:
+ /* contribution from the pressure momenenta */
+ ener_npt += 0.5*sqr(state->veta)/MassQ->Winv;
+
+ /* contribution from the PV term */
+ vol = det(state->box);
+ ener_npt += vol*trace(ir->ref_p)/(DIM*PRESFAC);
+
+ break;
+ case epctANISOTROPIC:
+
+ break;
+
+ case epctSURFACETENSION:
+
+ break;
+ case epctSEMIISOTROPIC:
+
+ break;
+ default:
+ break;
+ }
+ }
+
+ if (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir))
+ {
+ /* add the energy from the barostat thermostat chain */
+ for (i = 0; i < state->nnhpres; i++)
+ {
+
+ /* note -- assumes only one degree of freedom that is thermostatted in barostat */
+ ivxi = &state->nhpres_vxi[i*nh];
+ ixi = &state->nhpres_xi[i*nh];
+ iQinv = &(MassQ->QPinv[i*nh]);
+ reft = max(ir->opts.ref_t[0], 0); /* using 'System' temperature */
+ kT = BOLTZ * reft;
+
+ for (j = 0; j < nh; j++)
+ {
+ if (iQinv[j] > 0)
+ {
+ ener_npt += 0.5*sqr(ivxi[j])/iQinv[j];
+ /* contribution from the thermal variable of the NH chain */
+ ener_npt += ixi[j]*kT;
+ }
+ if (debug)
+ {
+ fprintf(debug, "P-T-group: %10d Chain %4d ThermV: %15.8f ThermX: %15.8f", i, j, ivxi[j], ixi[j]);
+ }
+ }
+ }
+ }
+
+ if (ir->etc)
+ {
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ ixi = &state->nosehoover_xi[i*nh];
+ ivxi = &state->nosehoover_vxi[i*nh];
+ iQinv = &(MassQ->Qinv[i*nh]);
+
+ nd = ir->opts.nrdf[i];
+ reft = max(ir->opts.ref_t[i], 0);
+ kT = BOLTZ * reft;
+
+ if (nd > 0)
+ {
+ if (IR_NVT_TROTTER(ir))
+ {
+ /* contribution from the thermal momenta of the NH chain */
+ for (j = 0; j < nh; j++)
+ {
+ if (iQinv[j] > 0)
+ {
+ ener_npt += 0.5*sqr(ivxi[j])/iQinv[j];
+ /* contribution from the thermal variable of the NH chain */
+ if (j == 0)
+ {
+ ndj = nd;
+ }
+ else
+ {
+ ndj = 1;
+ }
+ ener_npt += ndj*ixi[j]*kT;
+ }
+ }
+ }
+ else /* Other non Trotter temperature NH control -- no chains yet. */
+ {
+ ener_npt += 0.5*BOLTZ*nd*sqr(ivxi[0])/iQinv[0];
+ ener_npt += nd*ixi[0]*kT;
+ }
+ }
+ }
+ }
+ return ener_npt;
+}
+
- int j;
++static real vrescale_gamdev(real ia,
+ gmx_int64_t step, gmx_int64_t *count,
+ gmx_int64_t seed1, gmx_int64_t seed2)
+/* Gamma distribution, adapted from numerical recipes */
+{
- if (ia < 6)
+ real am, e, s, v1, v2, x, y;
+ double rnd[2];
+
- x = 1.0;
- for (j = 1; j <= ia; j++)
++ assert(ia > 1);
++
++ do
+ {
+ do
+ {
- x *= rnd[0];
++ do
+ {
+ gmx_rng_cycle_2uniform(step, (*count)++, seed1, seed2, rnd);
- while (x == 0);
- x = -log(x);
- }
- else
- {
- do
- {
- do
- {
- do
- {
- gmx_rng_cycle_2uniform(step, (*count)++, seed1, seed2, rnd);
- v1 = rnd[0];
- v2 = 2.0*rnd[1] - 1.0;
- }
- while (v1*v1 + v2*v2 > 1.0 ||
- v1*v1*GMX_REAL_MAX < 3.0*ia);
- /* The last check above ensures that both x (3.0 > 2.0 in s)
- * and the pre-factor for e do not go out of range.
- */
- y = v2/v1;
- am = ia - 1;
- s = sqrt(2.0*am + 1.0);
- x = s*y + am;
- }
- while (x <= 0.0);
- e = (1.0 + y*y)*exp(am*log(x/am) - s*y);
++ v1 = rnd[0];
++ v2 = 2.0*rnd[1] - 1.0;
+ }
++ while (v1*v1 + v2*v2 > 1.0 ||
++ v1*v1*GMX_REAL_MAX < 3.0*ia);
++ /* The last check above ensures that both x (3.0 > 2.0 in s)
++ * and the pre-factor for e do not go out of range.
++ */
++ y = v2/v1;
++ am = ia - 1;
++ s = sqrt(2.0*am + 1.0);
++ x = s*y + am;
+ }
- gmx_rng_cycle_2uniform(step, (*count)++, seed1, seed2, rnd);
- }
- while (rnd[0] > e);
++ while (x <= 0.0);
+
- static real vrescale_sumnoises(int nn,
++ e = (1.0 + y*y)*exp(am*log(x/am) - s*y);
++
++ gmx_rng_cycle_2uniform(step, (*count)++, seed1, seed2, rnd);
+ }
++ while (rnd[0] > e);
+
+ return x;
+}
+
+static real gaussian_count(gmx_int64_t step, gmx_int64_t *count,
+ gmx_int64_t seed1, gmx_int64_t seed2)
+{
+ double rnd[2], x, y, r;
+
+ do
+ {
+ gmx_rng_cycle_2uniform(step, (*count)++, seed1, seed2, rnd);
+ x = 2.0*rnd[0] - 1.0;
+ y = 2.0*rnd[1] - 1.0;
+ r = x*x + y*y;
+ }
+ while (r > 1.0 || r == 0.0);
+
+ r = sqrt(-2.0*log(r)/r);
+
+ return x*r;
+}
+
- * Returns the sum of n independent gaussian noises squared
++static real vrescale_sumnoises(real nn,
+ gmx_int64_t step, gmx_int64_t *count,
+ gmx_int64_t seed1, gmx_int64_t seed2)
+{
+/*
- * of nn calls to gmx_rng_gaussian_real).xs
++ * Returns the sum of nn independent gaussian noises squared
+ * (i.e. equivalent to summing the square of the return values
- real r, gauss;
-
- r = 2.0*vrescale_gamdev(nn/2, step, count, seed1, seed2);
++ * of nn calls to gmx_rng_gaussian_real).
+ */
- if (nn % 2 == 1)
++ const real ndeg_tol = 0.0001;
++ real r;
+
- gauss = gaussian_count(step, count, seed1, seed2);
++ if (nn < 2 + ndeg_tol)
+ {
- r += gauss*gauss;
++ int nn_int, i;
++ real gauss;
++
++ nn_int = (int)(nn + 0.5);
++
++ if (nn - nn_int < -ndeg_tol || nn - nn_int > ndeg_tol)
++ {
++ gmx_fatal(FARGS, "The v-rescale thermostat was called with a group with #DOF=%f, but for #DOF<3 only integer #DOF are supported", nn + 1);
++ }
++
++ r = 0;
++ for (i = 0; i < nn_int; i++)
++ {
++ gauss = gaussian_count(step, count, seed1, seed2);
+
- static real vrescale_resamplekin(real kk, real sigma, int ndeg, real taut,
++ r += gauss*gauss;
++ }
++ }
++ else
++ {
++ /* Use a gamma distribution for any real nn > 2 */
++ r = 2.0*vrescale_gamdev(0.5*nn, step, count, seed1, seed2);
+ }
+
+ return r;
+}
+
++static real vrescale_resamplekin(real kk, real sigma, real ndeg, real taut,
+ gmx_int64_t step, gmx_int64_t seed)
+{
+/*
+ * Generates a new value for the kinetic energy,
+ * according to Bussi et al JCP (2007), Eq. (A7)
+ * kk: present value of the kinetic energy of the atoms to be thermalized (in arbitrary units)
+ * sigma: target average value of the kinetic energy (ndeg k_b T/2) (in the same units as kk)
+ * ndeg: number of degrees of freedom of the atoms to be thermalized
+ * taut: relaxation time of the thermostat, in units of 'how often this routine is called'
+ */
+ /* rnd_count tracks the step-local state for the cycle random
+ * number generator.
+ */
+ gmx_int64_t rnd_count = 0;
+ real factor, rr, ekin_new;
+
+ if (taut > 0.1)
+ {
+ factor = exp(-1.0/taut);
+ }
+ else
+ {
+ factor = 0.0;
+ }
+
+ rr = gaussian_count(step, &rnd_count, seed, RND_SEED_VRESCALE);
+
+ ekin_new =
+ kk +
+ (1.0 - factor)*(sigma*(vrescale_sumnoises(ndeg-1, step, &rnd_count, seed, RND_SEED_VRESCALE) + rr*rr)/ndeg - kk) +
+ 2.0*rr*sqrt(kk*sigma/ndeg*(1.0 - factor)*factor);
+
+ return ekin_new;
+}
+
+void vrescale_tcoupl(t_inputrec *ir, gmx_int64_t step,
+ gmx_ekindata_t *ekind, real dt,
+ double therm_integral[])
+{
+ t_grpopts *opts;
+ int i;
+ real Ek, Ek_ref1, Ek_ref, Ek_new;
+
+ opts = &ir->opts;
+
+ for (i = 0; (i < opts->ngtc); i++)
+ {
+ if (ir->eI == eiVV)
+ {
+ Ek = trace(ekind->tcstat[i].ekinf);
+ }
+ else
+ {
+ Ek = trace(ekind->tcstat[i].ekinh);
+ }
+
+ if (opts->tau_t[i] >= 0 && opts->nrdf[i] > 0 && Ek > 0)
+ {
+ Ek_ref1 = 0.5*opts->ref_t[i]*BOLTZ;
+ Ek_ref = Ek_ref1*opts->nrdf[i];
+
+ Ek_new = vrescale_resamplekin(Ek, Ek_ref, opts->nrdf[i],
+ opts->tau_t[i]/dt,
+ ir->ld_seed, step);
+
+ /* Analytically Ek_new>=0, but we check for rounding errors */
+ if (Ek_new <= 0)
+ {
+ ekind->tcstat[i].lambda = 0.0;
+ }
+ else
+ {
+ ekind->tcstat[i].lambda = sqrt(Ek_new/Ek);
+ }
+
+ therm_integral[i] -= Ek_new - Ek;
+
+ if (debug)
+ {
+ fprintf(debug, "TC: group %d: Ekr %g, Ek %g, Ek_new %g, Lambda: %g\n",
+ i, Ek_ref, Ek, Ek_new, ekind->tcstat[i].lambda);
+ }
+ }
+ else
+ {
+ ekind->tcstat[i].lambda = 1.0;
+ }
+ }
+}
+
+real vrescale_energy(t_grpopts *opts, double therm_integral[])
+{
+ int i;
+ real ener;
+
+ ener = 0;
+ for (i = 0; i < opts->ngtc; i++)
+ {
+ ener += therm_integral[i];
+ }
+
+ return ener;
+}
+
+void rescale_velocities(gmx_ekindata_t *ekind, t_mdatoms *mdatoms,
+ int start, int end, rvec v[])
+{
+ t_grp_acc *gstat;
+ t_grp_tcstat *tcstat;
+ unsigned short *cACC, *cTC;
+ int ga, gt, n, d;
+ real lg;
+ rvec vrel;
+
+ tcstat = ekind->tcstat;
+ cTC = mdatoms->cTC;
+
+ if (ekind->bNEMD)
+ {
+ gstat = ekind->grpstat;
+ cACC = mdatoms->cACC;
+
+ ga = 0;
+ gt = 0;
+ for (n = start; n < end; n++)
+ {
+ if (cACC)
+ {
+ ga = cACC[n];
+ }
+ if (cTC)
+ {
+ gt = cTC[n];
+ }
+ /* Only scale the velocity component relative to the COM velocity */
+ rvec_sub(v[n], gstat[ga].u, vrel);
+ lg = tcstat[gt].lambda;
+ for (d = 0; d < DIM; d++)
+ {
+ v[n][d] = gstat[ga].u[d] + lg*vrel[d];
+ }
+ }
+ }
+ else
+ {
+ gt = 0;
+ for (n = start; n < end; n++)
+ {
+ if (cTC)
+ {
+ gt = cTC[n];
+ }
+ lg = tcstat[gt].lambda;
+ for (d = 0; d < DIM; d++)
+ {
+ v[n][d] *= lg;
+ }
+ }
+ }
+}
+
+
+/* set target temperatures if we are annealing */
+void update_annealing_target_temp(t_grpopts *opts, real t)
+{
+ int i, j, n, npoints;
+ real pert, thist = 0, x;
+
+ for (i = 0; i < opts->ngtc; i++)
+ {
+ npoints = opts->anneal_npoints[i];
+ switch (opts->annealing[i])
+ {
+ case eannNO:
+ continue;
+ case eannPERIODIC:
+ /* calculate time modulo the period */
+ pert = opts->anneal_time[i][npoints-1];
+ n = t / pert;
+ thist = t - n*pert; /* modulo time */
+ /* Make sure rounding didn't get us outside the interval */
+ if (fabs(thist-pert) < GMX_REAL_EPS*100)
+ {
+ thist = 0;
+ }
+ break;
+ case eannSINGLE:
+ thist = t;
+ break;
+ default:
+ gmx_fatal(FARGS, "Death horror in update_annealing_target_temp (i=%d/%d npoints=%d)", i, opts->ngtc, npoints);
+ }
+ /* We are doing annealing for this group if we got here,
+ * and we have the (relative) time as thist.
+ * calculate target temp */
+ j = 0;
+ while ((j < npoints-1) && (thist > (opts->anneal_time[i][j+1])))
+ {
+ j++;
+ }
+ if (j < npoints-1)
+ {
+ /* Found our position between points j and j+1.
+ * Interpolate: x is the amount from j+1, (1-x) from point j
+ * First treat possible jumps in temperature as a special case.
+ */
+ if ((opts->anneal_time[i][j+1]-opts->anneal_time[i][j]) < GMX_REAL_EPS*100)
+ {
+ opts->ref_t[i] = opts->anneal_temp[i][j+1];
+ }
+ else
+ {
+ x = ((thist-opts->anneal_time[i][j])/
+ (opts->anneal_time[i][j+1]-opts->anneal_time[i][j]));
+ opts->ref_t[i] = x*opts->anneal_temp[i][j+1]+(1-x)*opts->anneal_temp[i][j];
+ }
+ }
+ else
+ {
+ opts->ref_t[i] = opts->anneal_temp[i][npoints-1];
+ }
+ }
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff