-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * 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
+ * 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.
*
- * 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.
+ * 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.
*
- * 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.
+ * 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.
*
- * For more info, check our website at http://www.gromacs.org
+ * 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.
*
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * 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>
#include <stdlib.h>
#include <limits.h>
#include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
#include "physics.h"
#include "names.h"
#include "macros.h"
#include "index.h"
#include "symtab.h"
-#include "string2.h"
+#include "gromacs/utility/cstringutil.h"
#include "readinp.h"
#include "warninp.h"
#include "readir.h"
#include "mtop_util.h"
#include "chargegroup.h"
#include "inputrec.h"
+#include "calc_verletbuf.h"
#define MAXPTR 254
#define NOGID 255
-#define MAXLAMBDAS 1024
/* Resource parameters
* Do not change any of these until you read the instruction
* 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 fep_lambda[efptNR][STRLEN];
-static char lambda_weights[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];
+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. */
* 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)
{
void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
warninp_t wi)
-/* Check internal consistency */
+/* Check internal consistency.
+ * NOTE: index groups are not set here yet, don't check things
+ * like temperature coupling group options here, but in triple_check
+ */
{
/* Strange macro: first one fills the err_buf, and then one can check
* the condition, which will print the message and increase the error
warning_error(wi, "rvdw should be >= 0");
}
if (ir->rlist < 0 &&
- !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_drift > 0))
+ !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
{
warning_error(wi, "rlist should be >= 0");
}
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 ||
- !((EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > ir->rlist) ||
- (EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > ir->rlist)))
+ !((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.
{
warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported");
}
- if (ir->vdwtype != evdwCUT)
+ if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
{
- warning_error(wi, "With Verlet lists only cut-off LJ interactions are supported");
+ 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) ||
{
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->implicit_solvent != eisNO)
+ {
+ warning_error(wi, "Implicit solvent is not (yet) supported with the with Verlet lists.");
+ }
if (ir->nstlist <= 0)
{
rc_max = max(ir->rvdw, ir->rcoulomb);
- if (ir->verletbuf_drift <= 0)
+ if (ir->verletbuf_tol <= 0)
{
- if (ir->verletbuf_drift == 0)
+ if (ir->verletbuf_tol == 0)
{
- warning_error(wi, "Can not have an energy drift of exactly 0");
+ warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
}
if (ir->rlist < rc_max)
{
if (ir->rlist > rc_max)
{
- warning_note(wi, "You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-drift > 0. Will set rlist using verlet-buffer-drift.");
+ 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)
{
if (EI_DYNAMICS(ir->eI))
{
- if (EI_MD(ir->eI) && ir->etc == etcNO)
- {
- warning_error(wi, "Temperature coupling is required for calculating rlist using the energy drift with verlet-buffer-drift > 0. Either use temperature coupling or set rlist yourself together with verlet-buffer-drift = -1.");
- }
-
if (inputrec2nboundeddim(ir) < 3)
{
- warning_error(wi, "The box volume is required for calculating rlist from the energy drift with verlet-buffer-drift > 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-drift = -1.");
+ 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 = 1.05*rc_max;
+ ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
}
}
}
/* find the smallest of ( nstenergy, nstdhdl ) */
if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
- (ir->fepvals->nstdhdl < ir->nstenergy) )
+ (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
{
min_nst = ir->fepvals->nstdhdl;
min_name = nstdh;
}
}
+ if (ir->nsteps == 0 && !ir->bContinuation)
+ {
+ warning_note(wi, "For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates.");
+ }
+
/* LD STUFF */
if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
ir->bContinuation && ir->ld_seed != -1)
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));
+ sprintf(err_buf, "TPI does not work (yet) with the Verlet cut-off scheme");
+ CHECK(ir->cutoff_scheme == ecutsVERLET);
}
/* SHAKE / LINCS */
(int)fep->sc_r_power);
CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
- /* check validity of options */
- if (fep->n_lambda > 0 && ir->rlist < max(ir->rvdw, ir->rcoulomb))
- {
- sprintf(warn_buf,
- "For foreign lambda free energy differences it is assumed that the soft-core interactions have no effect beyond the neighborlist cut-off");
- warning(wi, warn_buf);
- }
-
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);
if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
{
- sprintf(warn_buf, "With coulomb soft core, the reciprocal space calculation will not necessarily cancel. It may be necessary to decrease the reciprocal space energy, and increase the cutoff radius to get sufficiently close matches to energies with free energy turned off.");
- warning(wi, warn_buf);
+ 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
}
if (ir->nstlist > 0)
{
- warning_note(wi, "Simulating without cut-offs is usually (slightly) faster with nstlist=0, nstype=simple and particle decomposition");
+ warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
}
}
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]);
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.",
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))
+ if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10*GMX_REAL_EPS)
{
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);
}
}
}
+ 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) */
ir->epsilon_r = 1.0;
}
- if (getenv("GALACTIC_DYNAMICS") == NULL)
+ if (getenv("GMX_DO_GALACTIC_DYNAMICS") == NULL)
{
sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
CHECK(ir->epsilon_r < 0);
* 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 (ir_coulomb_might_be_zero_at_cutoff(ir))
{
- if (EEL_SWITCHED(ir->coulombtype))
+ if (ir_coulomb_switched(ir))
{
sprintf(err_buf,
"With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
}
}
+ if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
+ {
+ sprintf(err_buf,
+ "Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier.");
+ CHECK( ir->coulomb_modifier != eintmodNONE);
+ }
+ if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
+ {
+ sprintf(err_buf,
+ "Explicit switch/shift vdw interactions cannot be used in combination with a secondary vdw-modifier.");
+ CHECK( ir->vdw_modifier != eintmodNONE);
+ }
+
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"
+ "The switch/shift interaction settings are just for compatibility; you will get better "
"performance from applying potential modifiers to your interactions!\n");
warning_note(wi, warn_buf);
}
+ if (ir->coulombtype == eelPMESWITCH || 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 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 ||
}
}
- if (EEL_PME(ir->coulombtype))
+ if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
{
if (ir->pme_order < 3)
{
CHECK(ir->wall_ewald_zfac < 2);
}
- if (EVDW_SWITCHED(ir->vdwtype))
+ if (ir_vdw_switched(ir))
{
- sprintf(err_buf, "With vdwtype = %s rvdw-switch must be < rvdw. Or, better - use a potential modifier.",
- evdw_names[ir->vdwtype]);
+ 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)
+ else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
{
if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
{
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 (EEL_IS_ZERO_AT_CUTOFF(ir->coulombtype)
- && (ir->rlistlong <= ir->rcoulomb))
+ 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 (EVDW_SWITCHED(ir->vdwtype) && (ir->rlistlong <= ir->rvdw))
+ 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");
/* ENERGY CONSERVATION */
if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
{
- if (!EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
+ 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 (!EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > 0 && ir->coulomb_modifier == eintmodNONE)
+ 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]);
}
}
+ if (EI_VV(ir->eI) && IR_TWINRANGE(*ir) && ir->nstlist > 1)
+ {
+ sprintf(warn_buf, "Twin-range multiple time stepping does not work with integrator %s.", ei_names[ir->eI]);
+ warning_error(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");
+ sprintf(warn_buf, "Invalid option %s for coulombtype",
+ eel_names[ir->coulombtype]);
+ warning_error(wi, warn_buf);
}
if (ir->sa_algorithm == esaSTILL)
parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
if (nweights == 0)
{
- expand->bInit_weights = FALSE;
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);
}
- else
- {
- expand->bInit_weights = TRUE;
- }
if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
{
expand->nstexpanded = fep->nstdhdl;
t_lambda *fep = ir->fepvals;
t_expanded *expand = ir->expandedvals;
- inp = read_inpfile(mdparin, &ninp, NULL, wi);
+ init_inputrec_strings();
+ inp = read_inpfile(mdparin, &ninp, wi);
snew(dumstr[0], STRLEN);
snew(dumstr[1], STRLEN);
- /* remove the following deprecated commands */
+ 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);
+ }
+
+ /* ignore the following deprecated commands */
REM_TYPE("title");
REM_TYPE("cpp");
REM_TYPE("domain-decomposition");
REM_TYPE("dihre-tau");
REM_TYPE("nstdihreout");
REM_TYPE("nstcheckpoint");
+ REM_TYPE("optimize-fft");
/* 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 ("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", vcm, NULL);
+ 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);
- ITYPE ("ld-seed", ir->ld_seed, 1993);
+ STEPTYPE ("ld-seed", ir->ld_seed, -1);
/* Em stuff */
CCTYPE ("ENERGY MINIMIZATION OPTIONS");
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 ("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);
+ 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", energy, NULL);
+ STYPE ("energygrps", is->energy, NULL);
/* Neighbor searching */
CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
- CTYPE ("cut-off scheme (group: using charge groups, Verlet: particle based cut-offs)");
+ 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 drift due to the Verlet buffer in kJ/mol/ps per atom,");
+ 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-drift", ir->verletbuf_drift, 0.005);
+ 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");
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", egptable, NULL);
+ 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");
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);
CTYPE ("Temperature coupling");
EETYPE("tcoupl", ir->etc, etcoupl_names);
ITYPE ("nsttcouple", ir->nsttcouple, -1);
- ITYPE("nh-chain-length", ir->opts.nhchainlength, NHCHAINLENGTH);
+ 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", tcgrps, NULL);
+ STYPE ("tc-grps", is->tcgrps, NULL);
CTYPE ("Time constant (ps) and reference temperature (K)");
- STYPE ("tau-t", tau_t, NULL);
- STYPE ("ref-t", ref_t, NULL);
+ 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);
CCTYPE ("OPTIONS FOR QMMM calculations");
EETYPE("QMMM", ir->bQMMM, yesno_names);
CTYPE ("Groups treated Quantum Mechanically");
- STYPE ("QMMM-grps", QMMM, NULL);
+ STYPE ("QMMM-grps", is->QMMM, NULL);
CTYPE ("QM method");
- STYPE("QMmethod", QMmethod, NULL);
+ STYPE("QMmethod", is->QMmethod, NULL);
CTYPE ("QMMM scheme");
EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
CTYPE ("QM basisset");
- STYPE("QMbasis", QMbasis, NULL);
+ STYPE("QMbasis", is->QMbasis, NULL);
CTYPE ("QM charge");
- STYPE ("QMcharge", QMcharge, NULL);
+ STYPE ("QMcharge", is->QMcharge, NULL);
CTYPE ("QM multiplicity");
- STYPE ("QMmult", QMmult, NULL);
+ STYPE ("QMmult", is->QMmult, NULL);
CTYPE ("Surface Hopping");
- STYPE ("SH", bSH, NULL);
+ STYPE ("SH", is->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);
+ 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", bOPT, NULL);
- STYPE ("bTS", bTS, NULL);
+ 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", anneal, NULL);
+ STYPE ("annealing", is->anneal, NULL);
CTYPE ("Number of time points to use for specifying annealing in each group");
- STYPE ("annealing-npoints", anneal_npoints, NULL);
+ STYPE ("annealing-npoints", is->anneal_npoints, NULL);
CTYPE ("List of times at the annealing points for each group");
- STYPE ("annealing-time", anneal_time, NULL);
+ STYPE ("annealing-time", is->anneal_time, NULL);
CTYPE ("Temp. at each annealing point, for each group.");
- STYPE ("annealing-temp", anneal_temp, NULL);
+ 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, 173529);
+ ITYPE ("gen-seed", opts->seed, -1);
/* Shake stuff */
CCTYPE ("OPTIONS FOR BONDS");
/* 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);
+ STYPE ("energygrp-excl", is->egpexcl, NULL);
/* Walls */
CCTYPE ("WALLS");
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);
+ 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 */
if (ir->ePull != epullNO)
{
snew(ir->pull, 1);
- pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
+ is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
}
/* Enforced rotation */
if (ir->bRot)
{
snew(ir->rot, 1);
- rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
+ 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 */
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);
+ 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", couple_moltype, NULL);
+ 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);
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", fep_lambda[efptFEP], NULL);
- STYPE ("mass-lambdas", fep_lambda[efptMASS], NULL);
- STYPE ("coul-lambdas", fep_lambda[efptCOUL], NULL);
- STYPE ("vdw-lambdas", fep_lambda[efptVDW], NULL);
- STYPE ("bonded-lambdas", fep_lambda[efptBONDED], NULL);
- STYPE ("restraint-lambdas", fep_lambda[efptRESTRAINT], NULL);
- STYPE ("temperature-lambdas", fep_lambda[efptTEMPERATURE], NULL);
+ 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", lambda_weights, NULL);
- EETYPE("dhdl-print-energy", fep->bPrintEnergy, yesno_names);
+ STYPE ("init-lambda-weights", is->lambda_weights, NULL);
+ EETYPE("dhdl-print-energy", fep->edHdLPrintEnergy, edHdLPrintEnergy_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);
/* 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);
+ 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", deform, NULL);
+ STYPE ("deform", is->deform, NULL);
/* simulated tempering variables */
CCTYPE("simulated tempering variables");
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);
+ 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");
/* User defined thingies */
CCTYPE ("User defined thingies");
- STYPE ("user1-grps", user1, NULL);
- STYPE ("user2-grps", user2, NULL);
+ 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);
}
opts->couple_moltype = NULL;
- if (strlen(couple_moltype) > 0)
+ if (strlen(is->couple_moltype) > 0)
{
if (ir->efep != efepNO)
{
- opts->couple_moltype = strdup(couple_moltype);
+ 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");
}
else
{
- warning(wi, "Can not couple a molecule with free_energy = no");
+ warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
}
}
/* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
}
}
- if (ir->bSimTemp)
+ if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
{
- 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. */
+ fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
+ warning_note(wi, "Old option for dhdl-print-energy given: "
+ "changing \"yes\" to \"total\"\n");
+ }
+
+ if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
+ {
+ /* always print out the energy to dhdl if we are doing
+ expanded ensemble, since we need the total energy for
+ analysis if the temperature is changing. In some
+ conditions one may only want the potential energy, so
+ we will allow that if the appropriate mdp setting has
+ been enabled. Otherwise, total it is:
+ */
+ fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
}
if ((ir->efep != efepNO) || ir->bSimTemp)
{
ir->bExpanded = TRUE;
}
- do_fep_params(ir, fep_lambda, lambda_weights);
+ do_fep_params(ir, is->fep_lambda, is->lambda_weights);
if (ir->bSimTemp) /* done after fep params */
{
do_simtemp_params(ir);
/* WALL PARAMETERS */
- do_wall_params(ir, wall_atomtype, wall_density, opts);
+ do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
/* ORIENTATION RESTRAINT PARAMETERS */
- if (opts->bOrire && str_nelem(orirefitgrp, MAXPTR, NULL) != 1)
+ if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
{
warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
}
{
dumdub[0][i] = 0;
}
- m = sscanf(deform, "%lf %lf %lf %lf %lf %lf",
+ 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++)
}
}
+ /* 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(char *s, int ng, const char *gn[])
+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;
} /* search_QMstring */
-
-int search_string(char *s, int ng, char *gn[])
+/* 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;
t_grpopts *opts;
gmx_groups_t *groups;
t_pull *pull;
- int natoms, ai, aj, i, j, d, g, imin, jmin, nc;
+ 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;
* to determine the optimal nrdf assignment.
*/
pull = ir->pull;
- if (pull->eGeom == epullgPOS)
+
+ for (i = 0; i < pull->ncoord; i++)
{
- nc = 0;
- for (i = 0; i < DIM; i++)
+ imin = 1;
+
+ for (j = 0; j < 2; j++)
{
- if (pull->dim[i])
+ const t_pull_group *pgrp;
+
+ pgrp = &pull->group[pull->coord[i].group[j]];
+
+ if (pgrp->nat > 0)
{
- nc++;
+ /* 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
- {
- 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)
+ else
{
- nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5;
- nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5;
- imin--;
+ /* We need to subtract the whole DOF from group j=1 */
+ imin += 1;
}
}
- /* 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)]]);
- }
}
}
sfree(na_vcm);
}
-static void decode_cos(char *s, t_cosines *cosine, gmx_bool bTime)
+static void decode_cos(char *s, t_cosines *cosine)
{
char *t;
char format[STRLEN], f1[STRLEN];
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,
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);
+ 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 "
nstcmin = tcouple_min_integration_steps(ir->etc);
if (nstcmin > 1)
{
- if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
+ if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
{
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),
}
/* Simulated annealing for each group. There are nr groups */
- nSA = str_nelem(anneal, MAXPTR, ptr1);
+ nSA = str_nelem(is->anneal, MAXPTR, ptr1);
if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
{
nSA = 0;
if (bAnneal)
{
/* Read the other fields too */
- nSA_points = str_nelem(anneal_npoints, MAXPTR, ptr1);
+ 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);
k += ir->opts.anneal_npoints[i];
}
- nSA_time = str_nelem(anneal_time, MAXPTR, ptr1);
+ 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(anneal_temp, MAXPTR, ptr2);
+ 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);
if (ir->ePull != epullNO)
{
- make_pull_groups(ir->pull, pull_grp, grps, gnames);
+ make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
+
+ make_pull_coords(ir->pull);
}
if (ir->bRot)
{
- make_rotation_groups(ir->rot, rot_grp, grps, gnames);
+ 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(acc, MAXPTR, ptr1);
- nacg = str_nelem(accgrps, MAXPTR, ptr2);
+ 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",
}
}
- nfrdim = str_nelem(frdim, MAXPTR, ptr1);
- nfreeze = str_nelem(freeze, MAXPTR, ptr2);
+ 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",
}
}
- nenergy = str_nelem(energy, MAXPTR, ptr1);
+ 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(vcm, MAXPTR, ptr1);
+ 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);
}
}
- nuser = str_nelem(user1, MAXPTR, ptr1);
+ nuser = str_nelem(is->user1, MAXPTR, ptr1);
do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
restnm, egrptpALL_GENREST, bVerbose, wi);
- nuser = str_nelem(user2, MAXPTR, ptr1);
+ nuser = str_nelem(is->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,
+ 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(orirefitgrp, MAXPTR, ptr1);
+ 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(QMMM, MAXPTR, ptr1);
- nQMmethod = str_nelem(QMmethod, MAXPTR, ptr2);
- nQMbasis = str_nelem(QMbasis, MAXPTR, ptr3);
+ 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"
eQMbasis_names);
}
- nQMmult = str_nelem(QMmult, MAXPTR, ptr1);
- nQMcharge = str_nelem(QMcharge, MAXPTR, ptr2);
- nbSH = str_nelem(bSH, MAXPTR, ptr3);
+ 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);
ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
}
- nCASelec = str_nelem(CASelectrons, MAXPTR, ptr1);
- nCASorb = str_nelem(CASorbitals, MAXPTR, ptr2);
+ 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++)
}
/* special optimization options */
- nbOPT = str_nelem(bOPT, MAXPTR, ptr1);
- nbTS = str_nelem(bTS, MAXPTR, ptr2);
+ 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(SAon, MAXPTR, ptr1);
- nSAoff = str_nelem(SAoff, MAXPTR, ptr2);
- nSAsteps = str_nelem(SAsteps, MAXPTR, ptr3);
+ 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);
nr = groups->grps[egcENER].nr;
snew(ir->opts.egp_flags, nr*nr);
- bExcl = do_egp_flag(ir, groups, "energygrp-excl", egpexcl, EGP_EXCL);
+ 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");
warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
}
- bTable = do_egp_flag(ir, groups, "energygrp-table", egptable, EGP_TABLE);
+ 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(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);
+ 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)
{
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, g, nmol, npct;
+ char err_buf[STRLEN];
+ int i, m, c, nmol, npct;
gmx_bool bCharge, bAcc;
real gdt_max, *mgrp, mt;
rvec acc;
set_warning_line(wi, mdparin, -1);
+ if (ir->cutoff_scheme == ecutsVERLET &&
+ ir->verletbuf_tol > 0 &&
+ ir->nstlist > 1 &&
+ ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
+ (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
+ {
+ /* Check if a too small Verlet buffer might potentially
+ * cause more drift than the thermostat can couple off.
+ */
+ /* Temperature error fraction for warning and suggestion */
+ const real T_error_warn = 0.002;
+ const real T_error_suggest = 0.001;
+ /* For safety: 2 DOF per atom (typical with constraints) */
+ const real nrdf_at = 2;
+ real T, tau, max_T_error;
+ int i;
+
+ T = 0;
+ tau = 0;
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ T = max(T, ir->opts.ref_t[i]);
+ tau = max(tau, ir->opts.tau_t[i]);
+ }
+ if (T > 0)
+ {
+ /* This is a worst case estimate of the temperature error,
+ * assuming perfect buffer estimation and no cancelation
+ * of errors. The factor 0.5 is because energy distributes
+ * equally over Ekin and Epot.
+ */
+ max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
+ if (max_T_error > T_error_warn)
+ {
+ sprintf(warn_buf, "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to %.0e or decrease tau_t.",
+ ir->verletbuf_tol, T, tau,
+ 100*max_T_error,
+ 100*T_error_suggest,
+ ir->verletbuf_tol*T_error_suggest/max_T_error);
+ warning(wi, warn_buf);
+ }
+ }
+ }
+
+ if (ETC_ANDERSEN(ir->etc))
+ {
+ int i;
+
+ 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);
+ }
+
+ 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 (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
ir->comm_mode == ecmNO &&
- !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10))
+ !(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 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)
{
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))
+ if (ir->eI == eiSD2)
{
- sprintf(warn_buf, "With constraints integrator %s is less accurate, consider using %s instead", ei_names[ir->eI], ei_names[eiSD2]);
+ sprintf(warn_buf, "The stochastic dynamics integrator %s is deprecated, since\n"
+ "it is slower than integrator %s and is slightly less accurate\n"
+ "with constraints. Use the %s integrator.",
+ ei_names[ir->eI], ei_names[eiSD1], ei_names[eiSD1]);
warning_note(wi, warn_buf);
}
if (ir->ePull != epullNO)
{
- if (ir->pull->grp[0].nat == 0)
+ 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->epc != epcNO && ir->compress[i][m] != 0) ||
ir->deform[i][m] != 0)
{
- for (g = 1; g < ir->pull->ngrp; g++)
+ for (c = 0; c < ir->pull->ncoord; c++)
{
- if (ir->pull->grp[g].vec[m] != 0)
+ 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);
}
}
}
+ 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");
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);
+ 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
* 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)
+ 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 rlist (%f) - rvdw (%f)\n",
+ 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->rlist, ir->rvdw);
+ ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
+ ir->rlistlong, ir->rvdw,
+ ecutscheme_names[ecutsVERLET]);
if (ir_NVE(ir))
{
warning(wi, warn_buf);
warning_note(wi, warn_buf);
}
}
- if (EEL_IS_ZERO_AT_CUTOFF(ir->coulombtype) &&
+ 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",
+ 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);
+ ir->rlistlong, ir->rcoulomb,
+ ecutscheme_names[ecutsVERLET]);
if (ir_NVE(ir))
{
warning(wi, warn_buf);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff