--- /dev/null
-
- gmx_fatal(FARGS,"Group %s not found in indexfile.\nMaybe you have non-default goups in your .mdp file, while not using the '-n' option of grompp.\nIn that case use the '-n' option.\n",s);
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <ctype.h>
+#include <stdlib.h>
+#include <limits.h>
+#include "sysstuff.h"
+#include "smalloc.h"
+#include "typedefs.h"
+#include "physics.h"
+#include "names.h"
+#include "gmx_fatal.h"
+#include "macros.h"
+#include "index.h"
+#include "symtab.h"
+#include "string2.h"
+#include "readinp.h"
+#include "warninp.h"
+#include "readir.h"
+#include "toputil.h"
+#include "index.h"
+#include "network.h"
+#include "vec.h"
+#include "pbc.h"
+#include "mtop_util.h"
+#include "chargegroup.h"
+#include "inputrec.h"
+
+#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.
+ */
+
+static 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],xtc_grps[STRLEN],
+ couple_moltype[STRLEN],orirefitgrp[STRLEN],egptable[STRLEN],egpexcl[STRLEN],
+ wall_atomtype[STRLEN],wall_density[STRLEN],deform[STRLEN],QMMM[STRLEN];
+static char foreign_lambda[STRLEN];
+static char **pull_grp;
+static char **rot_grp;
+static char anneal[STRLEN],anneal_npoints[STRLEN],
+ anneal_time[STRLEN],anneal_temp[STRLEN];
+static 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];
+static char efield_x[STRLEN],efield_xt[STRLEN],efield_y[STRLEN],
+ efield_yt[STRLEN],efield_z[STRLEN],efield_zt[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. */
+};
+
+
+void init_ir(t_inputrec *ir, t_gromppopts *opts)
+{
+ snew(opts->include,STRLEN);
+ snew(opts->define,STRLEN);
+}
+
+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;
+}
+
+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 ns_type=0;
+ real dt_pcoupl;
+
+ set_warning_line(wi,mdparin,-1);
+
+ /* BASIC CUT-OFF STUFF */
+ if (ir->rlist == 0 ||
+ !((EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > ir->rlist) ||
+ (EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && 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");
+ }
+
+ /* GENERAL INTEGRATOR STUFF */
+ if (!(ir->eI == eiMD || EI_VV(ir->eI)))
+ {
+ ir->etc = etcNO;
+ }
+ 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;
+ }
+ }
+ }
+ 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 > 1)
+ {
+ /* for storing exact averages nstenergy should be
+ * a multiple of nstcalcenergy
+ */
+ check_nst("nstcalcenergy",ir->nstcalcenergy,
+ "nstenergy",&ir->nstenergy,wi);
+ if (ir->efep != efepNO)
+ {
+ /* nstdhdl should be a multiple of nstcalcenergy */
+ check_nst("nstcalcenergy",ir->nstcalcenergy,
+ "nstdhdl",&ir->nstdhdl,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);
+ }
+
+ sprintf(err_buf,"shake_tol must be > 0 instead of %g while using shake",
+ ir->shake_tol);
+ CHECK(((ir->shake_tol <= 0.0) && (opts->nshake>0) &&
+ (ir->eConstrAlg == econtSHAKE)));
+
+ /* 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 is usually (slightly) faster with nstlist=0, nstype=simple and particle decomposition");
+ }
+ }
+
+ /* 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,"Free-energy not implemented for Ewald and PPPM");
+ CHECK((ir->coulombtype==eelEWALD || ir->coulombtype==eelPPPM)
+ && (ir->efep!=efepNO));
+
+ 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)
+ {
+ 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->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 || ir->etc==etcANDERSEN || ir->etc==etcANDERSENINTERVAL)
+ && 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));
+
+ sprintf(err_buf,"pressure coupling with PPPM not implemented, use PME");
+ CHECK(ir->coulombtype == eelPPPM);
+
+ }
+ else if (ir->coulombtype == eelPPPM)
+ {
+ sprintf(warn_buf,"The pressure with PPPM is incorrect, if you need the pressure use PME");
+ warning(wi,warn_buf);
+ }
+
+ if (EI_VV(ir->eI))
+ {
+ if (ir->epc > epcNO)
+ {
+ if (ir->epc!=epcMTTK)
+ {
+ warning_error(wi,"NPT only defined for vv using Martyna-Tuckerman-Tobias-Klein equations");
+ }
+ }
+ }
+
+ /* ELECTROSTATICS */
+ /* More checks are in triple check (grompp.c) */
+ if (ir->coulombtype == eelPPPM)
+ {
+ warning_error(wi,"PPPM is not functional in the current version, we plan to implement PPPM through a small modification of the PME code");
+ }
+
+ 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, 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(err_buf,"With coulombtype = %s, epsilon_rf must be 0",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->epsilon_rf != 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 (EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype)) {
+ if (EEL_SWITCHED(ir->coulombtype)) {
+ sprintf(err_buf,
+ "With coulombtype = %s rcoulomb_switch must be < rcoulomb",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
+ }
+ } else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype)) {
+ sprintf(err_buf,"With coulombtype = %s, rcoulomb must be >= rlist",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->rlist > ir->rcoulomb);
+ }
+
+ 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->coulombtype == eelPME) {
+ sprintf(err_buf,
+ "With coulombtype = %s, rcoulomb must be equal to rlist\n"
+ "If you want optimal energy conservation or exact integration use %s",
+ eel_names[ir->coulombtype],eel_names[eelPMESWITCH]);
+ } else {
+ sprintf(err_buf,
+ "With coulombtype = %s, rcoulomb must be equal to rlist",
+ eel_names[ir->coulombtype]);
+ }
+ CHECK(ir->rcoulomb != ir->rlist);
+ }
+ }
+
+ if (EEL_PME(ir->coulombtype)) {
+ 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 (EVDW_SWITCHED(ir->vdwtype)) {
+ sprintf(err_buf,"With vdwtype = %s rvdw_switch must be < rvdw",
+ evdw_names[ir->vdwtype]);
+ CHECK(ir->rvdw_switch >= ir->rvdw);
+ } else if (ir->vdwtype == evdwCUT) {
+ sprintf(err_buf,"With vdwtype = %s, rvdw must be >= rlist",evdw_names[ir->vdwtype]);
+ CHECK(ir->rlist > ir->rvdw);
+ }
+ if (EEL_IS_ZERO_AT_CUTOFF(ir->coulombtype)
+ && (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 (EVDW_SWITCHED(ir->vdwtype) && (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,
+ "nstlist=-1 only works with switched or shifted potentials,\n"
+ "suggestion: use vdw-type=%s and coulomb-type=%s",
+ evdw_names[evdwSHIFT],eel_names[eelPMESWITCH]);
+ CHECK(!(EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) &&
+ EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype)));
+
+ 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.");
+ }
+
+ /* FREE ENERGY */
+ if (ir->efep != efepNO) {
+ sprintf(err_buf,"The soft-core power is %d and can only be 1 or 2",
+ ir->sc_power);
+ CHECK(ir->sc_alpha!=0 && ir->sc_power!=1 && ir->sc_power!=2);
+ }
+
+ /* ENERGY CONSERVATION */
+ if (ir_NVE(ir))
+ {
+ if (!EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > 0)
+ {
+ 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 (!EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && 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);
+ }
+
+ }
+}
+
+static 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;
+}
+
+static void parse_n_double(char *str,int *n,double **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_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 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];
+
+ inp = read_inpfile(mdparin, &ninp, NULL, wi);
+
+ snew(dumstr[0],STRLEN);
+ snew(dumstr[1],STRLEN);
+
+ REM_TYPE("title");
+ REM_TYPE("cpp");
+ REM_TYPE("domain-decomposition");
+ REPL_TYPE("unconstrained-start","continuation");
+ REM_TYPE("dihre-tau");
+ REM_TYPE("nstdihreout");
+ REM_TYPE("nstcheckpoint");
+
+ 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, 10);
+ CTYPE ("group(s) for center of mass motion removal");
+ STYPE ("comm-grps", vcm, NULL);
+
+ CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
+ CTYPE ("Friction coefficient (amu/ps) and random seed");
+ RTYPE ("bd-fric", ir->bd_fric, 0.0);
+ ITYPE ("ld-seed", ir->ld_seed, 1993);
+
+ /* 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, 100);
+ ITYPE ("nstvout", ir->nstvout, 100);
+ ITYPE ("nstfout", ir->nstfout, 0);
+ ir->nstcheckpoint = 1000;
+ CTYPE ("Output frequency for energies to log file and energy file");
+ ITYPE ("nstlog", ir->nstlog, 100);
+ ITYPE ("nstcalcenergy",ir->nstcalcenergy, -1);
+ ITYPE ("nstenergy", ir->nstenergy, 100);
+ CTYPE ("Output frequency and precision for .xtc file");
+ ITYPE ("nstxtcout", ir->nstxtcout, 0);
+ RTYPE ("xtc-precision",ir->xtcprec, 1000.0);
+ CTYPE ("This selects the subset of atoms for the .xtc file. You can");
+ CTYPE ("select multiple groups. By default all atoms will be written.");
+ STYPE ("xtc-grps", xtc_grps, NULL);
+ CTYPE ("Selection of energy groups");
+ STYPE ("energygrps", energy, NULL);
+
+ /* Neighbor searching */
+ CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
+ 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 ("nblist cut-off");
+ RTYPE ("rlist", ir->rlist, 1.0);
+ CTYPE ("long-range cut-off for switched potentials");
+ RTYPE ("rlistlong", ir->rlistlong, -1);
+
+ /* Electrostatics */
+ CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
+ CTYPE ("Method for doing electrostatics");
+ EETYPE("coulombtype", ir->coulombtype, eel_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, 1.0);
+ CTYPE ("Method for doing Van der Waals");
+ EETYPE("vdw-type", ir->vdwtype, evdw_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 ("Seperate tables between energy group pairs");
+ STYPE ("energygrp_table", egptable, NULL);
+ CTYPE ("Spacing for the PME/PPPM FFT grid");
+ RTYPE ("fourierspacing", opts->fourierspacing,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);
+ 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, NHCHAINLENGTH);
+ CTYPE ("Groups to couple separately");
+ STYPE ("tc-grps", tcgrps, NULL);
+ CTYPE ("Time constant (ps) and reference temperature (K)");
+ STYPE ("tau-t", tau_t, NULL);
+ STYPE ("ref-t", 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);
+
+ CTYPE ("Random seed for Andersen thermostat");
+ ITYPE ("andersen_seed", ir->andersen_seed, 815131);
+
+ /* QMMM */
+ CCTYPE ("OPTIONS FOR QMMM calculations");
+ EETYPE("QMMM", ir->bQMMM, yesno_names);
+ CTYPE ("Groups treated Quantum Mechanically");
+ STYPE ("QMMM-grps", QMMM, NULL);
+ CTYPE ("QM method");
+ STYPE("QMmethod", QMmethod, NULL);
+ CTYPE ("QMMM scheme");
+ EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
+ CTYPE ("QM basisset");
+ STYPE("QMbasis", QMbasis, NULL);
+ CTYPE ("QM charge");
+ STYPE ("QMcharge", QMcharge,NULL);
+ CTYPE ("QM multiplicity");
+ STYPE ("QMmult", QMmult,NULL);
+ CTYPE ("Surface Hopping");
+ STYPE ("SH", bSH, NULL);
+ CTYPE ("CAS space options");
+ STYPE ("CASorbitals", CASorbitals, NULL);
+ STYPE ("CASelectrons", CASelectrons, NULL);
+ STYPE ("SAon", SAon, NULL);
+ STYPE ("SAoff",SAoff,NULL);
+ STYPE ("SAsteps", SAsteps, NULL);
+ CTYPE ("Scale factor for MM charges");
+ RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
+ CTYPE ("Optimization of QM subsystem");
+ STYPE ("bOPT", bOPT, NULL);
+ STYPE ("bTS", bTS, NULL);
+
+ /* Simulated annealing */
+ CCTYPE("SIMULATED ANNEALING");
+ CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
+ STYPE ("annealing", anneal, NULL);
+ CTYPE ("Number of time points to use for specifying annealing in each group");
+ STYPE ("annealing_npoints", anneal_npoints, NULL);
+ CTYPE ("List of times at the annealing points for each group");
+ STYPE ("annealing_time", anneal_time, NULL);
+ CTYPE ("Temp. at each annealing point, for each group.");
+ STYPE ("annealing_temp", 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, 173529);
+
+ /* 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", 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", wall_atomtype, NULL);
+ STYPE ("wall_density", 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);
+ 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);
+ rot_grp = read_rotparams(&ninp,&inp,ir->rot,wi);
+ }
+
+ /* Refinement */
+ CCTYPE("NMR refinement stuff");
+ CTYPE ("Distance restraints type: No, Simple or Ensemble");
+ EETYPE("disre", ir->eDisre, edisre_names);
+ CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
+ EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
+ CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
+ EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
+ RTYPE ("disre-fc", ir->dr_fc, 1000.0);
+ RTYPE ("disre-tau", ir->dr_tau, 0.0);
+ CTYPE ("Output frequency for pair distances to energy file");
+ ITYPE ("nstdisreout", ir->nstdisreout, 100);
+ CTYPE ("Orientation restraints: No or Yes");
+ EETYPE("orire", opts->bOrire, yesno_names);
+ CTYPE ("Orientation restraints force constant and tau for time averaging");
+ RTYPE ("orire-fc", ir->orires_fc, 0.0);
+ RTYPE ("orire-tau", ir->orires_tau, 0.0);
+ STYPE ("orire-fitgrp",orirefitgrp, NULL);
+ CTYPE ("Output frequency for trace(SD) and S to energy file");
+ ITYPE ("nstorireout", ir->nstorireout, 100);
+ CTYPE ("Dihedral angle restraints: No or Yes");
+ EETYPE("dihre", opts->bDihre, yesno_names);
+ RTYPE ("dihre-fc", ir->dihre_fc, 1000.0);
+
+ /* Free energy stuff */
+ CCTYPE ("Free energy control stuff");
+ EETYPE("free-energy", ir->efep, efep_names);
+ RTYPE ("init-lambda", ir->init_lambda,0.0);
+ RTYPE ("delta-lambda",ir->delta_lambda,0.0);
+ STYPE ("foreign_lambda", foreign_lambda, NULL);
+ RTYPE ("sc-alpha",ir->sc_alpha,0.0);
+ ITYPE ("sc-power",ir->sc_power,0);
+ RTYPE ("sc-sigma",ir->sc_sigma,0.3);
+ ITYPE ("nstdhdl", ir->nstdhdl, 10);
+ EETYPE("separate-dhdl-file", ir->separate_dhdl_file,
+ separate_dhdl_file_names);
+ EETYPE("dhdl-derivatives", ir->dhdl_derivatives, dhdl_derivatives_names);
+ ITYPE ("dh_hist_size", ir->dh_hist_size, 0);
+ RTYPE ("dh_hist_spacing", ir->dh_hist_spacing, 0.1);
+ STYPE ("couple-moltype", 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);
+
+ /* Non-equilibrium MD stuff */
+ CCTYPE("Non-equilibrium MD stuff");
+ STYPE ("acc-grps", accgrps, NULL);
+ STYPE ("accelerate", acc, NULL);
+ STYPE ("freezegrps", freeze, NULL);
+ STYPE ("freezedim", frdim, NULL);
+ RTYPE ("cos-acceleration", ir->cos_accel, 0);
+ STYPE ("deform", deform, NULL);
+
+ /* 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", efield_x, NULL);
+ STYPE ("E-xt", efield_xt, NULL);
+ STYPE ("E-y", efield_y, NULL);
+ STYPE ("E-yt", efield_yt, NULL);
+ STYPE ("E-z", efield_z, NULL);
+ STYPE ("E-zt", efield_zt, NULL);
+
+ /* User defined thingies */
+ CCTYPE ("User defined thingies");
+ STYPE ("user1-grps", user1, NULL);
+ STYPE ("user2-grps", 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(couple_moltype) > 0) {
+ if (ir->efep != efepNO) {
+ opts->couple_moltype = strdup(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");
+ }
+ }
+
+ do_wall_params(ir,wall_atomtype,wall_density,opts);
+
+ if (opts->bOrire && str_nelem(orirefitgrp,MAXPTR,NULL)!=1) {
+ warning_error(wi,"ERROR: Need one orientation restraint fit group\n");
+ }
+
+ clear_mat(ir->deform);
+ for(i=0; i<6; i++)
+ dumdub[0][i] = 0;
+ m = sscanf(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);
+ }
+ }
+ }
+
+ if (ir->efep != efepNO) {
+ parse_n_double(foreign_lambda,&ir->n_flambda,&ir->flambda);
+ if (ir->n_flambda > 0 && ir->rlist < max(ir->rvdw,ir->rcoulomb)) {
+ warning_note(wi,"For foreign lambda free energy differences it is assumed that the soft-core interactions have no effect beyond the neighborlist cut-off");
+ }
+ } else {
+ ir->n_flambda = 0;
+ }
+
+ sfree(dumstr[0]);
+ sfree(dumstr[1]);
+}
+
+static int search_QMstring(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 */
+
+
+int search_string(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 not found in index file.\nGroup names must match either [moleculetype] names\nor custom index group names,in which case you\nmust supply an index file to the '-n' option 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)
+ {
+ 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,nc;
+ 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(ai=as+ia[1]; ai<as+ia[1]+3; ai++) {
+ 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 += 2;
+ i += 2;
+ }
+ 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;
+ if (pull->eGeom == epullgPOS) {
+ nc = 0;
+ for(i=0; i<DIM; i++) {
+ if (pull->dim[i])
+ nc++;
+ }
+ } else {
+ nc = 1;
+ }
+ for(i=0; i<pull->ngrp; i++) {
+ imin = 2*nc;
+ if (pull->grp[0].nat > 0) {
+ /* Subtract 1/2 dof from the reference group */
+ ai = pull->grp[0].ind[0];
+ if (nrdf_tc[ggrpnr(groups,egcTC,ai)] > 1) {
+ nrdf_tc [ggrpnr(groups,egcTC ,ai)] -= 0.5;
+ nrdf_vcm[ggrpnr(groups,egcVCM,ai)] -= 0.5;
+ imin--;
+ }
+ }
+ /* Subtract 1/2 dof from the pulled group */
+ ai = pull->grp[1+i].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)]]);
+ }
+ }
+
+ 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,gmx_bool bTime)
+{
+ 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;
+}
+
+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(tau_t,MAXPTR,ptr1);
+ nref_t = str_nelem(ref_t,MAXPTR,ptr2);
+ ntcg = str_nelem(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) ||
+ (ir->etc != etcVRESCALE && 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->epc==epcMTTK) && (ir->etc>etcNO))
+ {
+ int mincouple;
+ mincouple = ir->nsttcouple;
+ if (ir->nstpcouple < mincouple)
+ {
+ mincouple = ir->nstpcouple;
+ }
+ ir->nstpcouple = mincouple;
+ ir->nsttcouple = mincouple;
+ warning_note(wi,"for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple)");
+ }
+ }
+ 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);
+ }
+ }
+ }
+
+ /* Simulated annealing for each group. There are nr groups */
+ nSA = str_nelem(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(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(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(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,pull_grp,grps,gnames);
+ }
+
+ if (ir->bRot) {
+ make_rotation_groups(ir->rot,rot_grp,grps,gnames);
+ }
+
+ nacc = str_nelem(acc,MAXPTR,ptr1);
+ nacg = str_nelem(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(frdim,MAXPTR,ptr1);
+ nfreeze = str_nelem(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(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(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(user1,MAXPTR,ptr1);
+ do_numbering(natoms,groups,nuser,ptr1,grps,gnames,egcUser1,
+ restnm,egrptpALL_GENREST,bVerbose,wi);
+ nuser=str_nelem(user2,MAXPTR,ptr1);
+ do_numbering(natoms,groups,nuser,ptr1,grps,gnames,egcUser2,
+ restnm,egrptpALL_GENREST,bVerbose,wi);
+ nuser=str_nelem(xtc_grps,MAXPTR,ptr1);
+ do_numbering(natoms,groups,nuser,ptr1,grps,gnames,egcXTC,
+ restnm,egrptpONE,bVerbose,wi);
+ nofg = str_nelem(orirefitgrp,MAXPTR,ptr1);
+ do_numbering(natoms,groups,nofg,ptr1,grps,gnames,egcORFIT,
+ restnm,egrptpALL_GENREST,bVerbose,wi);
+
+ /* QMMM input processing */
+ nQMg = str_nelem(QMMM,MAXPTR,ptr1);
+ nQMmethod = str_nelem(QMmethod,MAXPTR,ptr2);
+ nQMbasis = str_nelem(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(QMmult,MAXPTR,ptr1);
+ nQMcharge = str_nelem(QMcharge,MAXPTR,ptr2);
+ nbSH = str_nelem(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(CASelectrons,MAXPTR,ptr1);
+ nCASorb = str_nelem(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(bOPT,MAXPTR,ptr1);
+ nbTS = str_nelem(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(SAon,MAXPTR,ptr1);
+ nSAoff = str_nelem(SAoff,MAXPTR,ptr2);
+ nSAsteps = str_nelem(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",egpexcl,EGP_EXCL);
+ 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",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(efield_x,&(ir->ex[XX]),FALSE);
+ decode_cos(efield_xt,&(ir->et[XX]),TRUE);
+ decode_cos(efield_y,&(ir->ex[YY]),FALSE);
+ decode_cos(efield_yt,&(ir->et[YY]),TRUE);
+ decode_cos(efield_z,&(ir->ex[ZZ]),FALSE);
+ decode_cos(efield_zt,&(ir->et[ZZ]),TRUE);
+
+ 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,ivec AbsRef)
+{
+ int d,g,i;
+ gmx_mtop_ilistloop_t iloop;
+ t_ilist *ilist;
+ int nmol;
+ t_iparams *pr;
+
+ /* 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) {
+ 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;
+ }
+ }
+ }
+ }
+ }
+
+ return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
+}
+
+void triple_check(const char *mdparin,t_inputrec *ir,gmx_mtop_t *sys,
+ warninp_t wi)
+{
+ char err_buf[256];
+ int i,m,g,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,AbsRef) || ir->nsteps <= 10)) {
+ 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");
+ }
+
+ 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);
+ }
+ }
+
+ /* 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) {
+ gdt_max = 0;
+ for(i=0; (i<ir->opts.ngtc); i++)
+ gdt_max = max(gdt_max,ir->delta_t/ir->opts.tau_t[i]);
+ if (0.5*gdt_max > 0.0015) {
+ sprintf(warn_buf,"The relative error with integrator %s is 0.5*delta_t/tau_t = %g, you might want to switch to integrator %s\n",
+ ei_names[ir->eI],0.5*gdt_max,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->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) {
+ if (ir->pull->grp[0].nat == 0) {
+ absolute_reference(ir,sys,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(g=1; g<ir->pull->ngrp; g++) {
+ if (ir->pull->grp[g].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 (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 (EVDW_IS_ZERO_AT_CUTOFF(ir->vdwtype) &&
+ rvdw1 + rvdw2 > ir->rlist - ir->rvdw)
+ {
+ sprintf(warn_buf,"The sum of the two largest charge group radii (%f) is larger than rlist (%f) - rvdw (%f)\n",
+ rvdw1+rvdw2,
+ ir->rlist,ir->rvdw);
+ if (ir_NVE(ir))
+ {
+ warning(wi,warn_buf);
+ }
+ else
+ {
+ warning_note(wi,warn_buf);
+ }
+ }
+ if (EEL_IS_ZERO_AT_CUTOFF(ir->coulombtype) &&
+ 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",
+ rcoul1+rcoul2,
+ ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
+ ir->rlistlong,ir->rcoulomb);
+ if (ir_NVE(ir))
+ {
+ warning(wi,warn_buf);
+ }
+ else
+ {
+ warning_note(wi,warn_buf);
+ }
+ }
+ }
+ }
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff