*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, 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.
tpxv_PullExternalPotential, /**< Added pull type external potential */
tpxv_GenericParamsForElectricField, /**< Introduced KeyValueTree and moved electric field parameters */
tpxv_AcceleratedWeightHistogram, /**< sampling with accelerated weight histogram method (AWH) */
+ tpxv_RemoveImplicitSolvation, /**< removed support for implicit solvation */
tpxv_Count /**< the total number of tpxv versions */
};
} t_ftupd;
/*
+ * TODO The following three lines make little sense, please clarify if
+ * you've had to work out how ftupd works.
+ *
* The entries should be ordered in:
* 1. ascending function type number
* 2. ascending file version number
+ *
+ * Because we support reading of old .tpr file versions (even when
+ * mdrun can no longer run the simulation), we need to be able to read
+ * obsolete t_interaction_function types. Any data read from such
+ * fields is discarded. Their names have _NOLONGERUSED appended to
+ * them to make things clear.
*/
static const t_ftupd ftupd[] = {
{ 34, F_FENEBONDS },
{ tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_CBTDIHS },
{ 43, F_TABDIHS },
{ 65, F_CMAP },
- { 60, F_GB12 },
- { 61, F_GB13 },
- { 61, F_GB14 },
- { 72, F_GBPOL },
- { 72, F_NPSOLVATION },
+ { 60, F_GB12_NOLONGERUSED },
+ { 61, F_GB13_NOLONGERUSED },
+ { 61, F_GB14_NOLONGERUSED },
+ { 72, F_GBPOL_NOLONGERUSED },
+ { 72, F_NPSOLVATION_NOLONGERUSED },
{ 41, F_LJC14_Q },
{ 41, F_LJC_PAIRS_NB },
{ 32, F_BHAM_LR_NOLONGERUSED },
}
gmx_fio_do_real(fio, ir->tabext);
- gmx_fio_do_int(fio, ir->gb_algorithm);
- gmx_fio_do_int(fio, ir->nstgbradii);
- gmx_fio_do_real(fio, ir->rgbradii);
- gmx_fio_do_real(fio, ir->gb_saltconc);
- gmx_fio_do_int(fio, ir->implicit_solvent);
- if (file_version >= 55)
+ // This permits reading a .tpr file that used implicit solvent,
+ // and later permitting mdrun to refuse to run it.
+ if (bRead)
{
- gmx_fio_do_real(fio, ir->gb_epsilon_solvent);
- gmx_fio_do_real(fio, ir->gb_obc_alpha);
- gmx_fio_do_real(fio, ir->gb_obc_beta);
- gmx_fio_do_real(fio, ir->gb_obc_gamma);
- if (file_version >= 60)
+ if (file_version < tpxv_RemoveImplicitSolvation)
{
- gmx_fio_do_real(fio, ir->gb_dielectric_offset);
- gmx_fio_do_int(fio, ir->sa_algorithm);
+ gmx_fio_do_int(fio, idum);
+ gmx_fio_do_int(fio, idum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_int(fio, idum);
+ ir->implicit_solvent = (idum > 0);
}
else
{
- ir->gb_dielectric_offset = 0.009;
- ir->sa_algorithm = esaAPPROX;
+ ir->implicit_solvent = false;
}
- gmx_fio_do_real(fio, ir->sa_surface_tension);
-
- /* Override sa_surface_tension if it is not changed in the mpd-file */
- if (ir->sa_surface_tension < 0)
+ if (file_version >= 55 && file_version < tpxv_RemoveImplicitSolvation)
{
- if (ir->gb_algorithm == egbSTILL)
- {
- ir->sa_surface_tension = 0.0049 * 100 * CAL2JOULE;
- }
- else if (ir->gb_algorithm == egbHCT || ir->gb_algorithm == egbOBC)
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ if (file_version >= 60)
{
- ir->sa_surface_tension = 0.0054 * 100 * CAL2JOULE;
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_int(fio, idum);
}
+ gmx_fio_do_real(fio, rdum);
}
-
- }
- else
- {
- /* Better use sensible values than insane (0.0) ones... */
- ir->gb_epsilon_solvent = 80;
- ir->gb_obc_alpha = 1.0;
- ir->gb_obc_beta = 0.8;
- ir->gb_obc_gamma = 4.85;
- ir->sa_surface_tension = 2.092;
}
-
if (file_version >= 81)
{
gmx_fio_do_real(fio, ir->fourier_spacing);
gmx_fio_do_int(fio, iparams->vsiten.n);
gmx_fio_do_real(fio, iparams->vsiten.a);
break;
- case F_GB12:
- case F_GB13:
- case F_GB14:
- /* We got rid of some parameters in version 68 */
- if (bRead && file_version < 68)
+ case F_GB12_NOLONGERUSED:
+ case F_GB13_NOLONGERUSED:
+ case F_GB14_NOLONGERUSED:
+ // Implicit solvent parameters can still be read, but never used
+ if (bRead)
{
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
+ if (file_version < 68)
+ {
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ }
+ if (file_version < tpxv_RemoveImplicitSolvation)
+ {
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ }
}
- gmx_fio_do_real(fio, iparams->gb.sar);
- gmx_fio_do_real(fio, iparams->gb.st);
- gmx_fio_do_real(fio, iparams->gb.pi);
- gmx_fio_do_real(fio, iparams->gb.gbr);
- gmx_fio_do_real(fio, iparams->gb.bmlt);
break;
case F_CMAP:
gmx_fio_do_int(fio, iparams->cmap.cmapA);
j = atomtypes->nr;
if (bRead)
{
- snew(atomtypes->radius, j);
- snew(atomtypes->vol, j);
- snew(atomtypes->surftens, j);
snew(atomtypes->atomnumber, j);
- snew(atomtypes->gb_radius, j);
- snew(atomtypes->S_hct, j);
}
- gmx_fio_ndo_real(fio, atomtypes->radius, j);
- gmx_fio_ndo_real(fio, atomtypes->vol, j);
- gmx_fio_ndo_real(fio, atomtypes->surftens, j);
+ if (bRead && file_version < tpxv_RemoveImplicitSolvation)
+ {
+ std::vector<real> dummy(atomtypes->nr, 0);
+ gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
+ gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
+ gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
+ }
if (file_version >= 40)
{
gmx_fio_ndo_int(fio, atomtypes->atomnumber, j);
}
- if (file_version >= 60)
+ if (bRead && file_version >= 60 && file_version < tpxv_RemoveImplicitSolvation)
{
- gmx_fio_ndo_real(fio, atomtypes->gb_radius, j);
- gmx_fio_ndo_real(fio, atomtypes->S_hct, j);
+ std::vector<real> dummy(atomtypes->nr, 0);
+ gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
+ gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff