From: Mark Abraham Date: Fri, 8 Jan 2016 01:35:59 +0000 (+0100) Subject: Merge branch release-5-1 X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=4160022f829c7e9cc546181bddab619244659329;p=alexxy%2Fgromacs.git Merge branch release-5-1 Ported the change from enum_name returning UNDEFINED to "no name defined" to the new implementation. Change-Id: I39ded9be8a49d3ff7de7c5e7c9d05eefbd385727 --- 4160022f829c7e9cc546181bddab619244659329 diff --cc src/gromacs/mdtypes/md_enums.cpp index 4ab36431d7,0000000000..e9795a8ab5 mode 100644,000000..100644 --- a/src/gromacs/mdtypes/md_enums.cpp +++ b/src/gromacs/mdtypes/md_enums.cpp @@@ -1,270 -1,0 +1,270 @@@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright (c) 1991-2000, University of Groningen, The Netherlands. + * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by + * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, + * and including many others, as listed in the AUTHORS file in the + * top-level source directory and at http://www.gromacs.org. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * http://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at http://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out http://www.gromacs.org. + */ +#include "gmxpre.h" + +#include "md_enums.h" + +const char *enum_name(int index, int max_index, const char *names[]) +{ + if (index < 0 || index >= max_index) + { - static const char *undef = "UNDEFINED"; ++ static const char *undef = "no name defined"; + return undef; + } + else + { + return names[index]; + } +} + +const char *yesno_names[BOOL_NR+1] = +{ + "no", "yes", nullptr +}; + + + +const char *ens_names[ensNR+1] = +{ + "Grid", "Simple", nullptr +}; + +const char *ei_names[eiNR+1] = +{ + "md", "steep", "cg", "bd", "sd2 - removed", "nm", "l-bfgs", "tpi", "tpic", "sd", "md-vv", "md-vv-avek", nullptr +}; + +const char *ecutscheme_names[ecutsNR+1] = { + "Verlet", "Group", nullptr +}; + +const char *erefscaling_names[erscNR+1] = { + "No", "All", "COM", nullptr +}; + +const char *eel_names[eelNR+1] = { + "Cut-off", "Reaction-Field", "Generalized-Reaction-Field", + "PME", "Ewald", "P3M-AD", "Poisson", "Switch", "Shift", "User", + "Generalized-Born", "Reaction-Field-nec", "Encad-shift", + "PME-User", "PME-Switch", "PME-User-Switch", + "Reaction-Field-zero", nullptr +}; + +const char *eewg_names[eewgNR+1] = { + "3d", "3dc", nullptr +}; + +const char *eljpme_names[eljpmeNR+1] = { + "Geometric", "Lorentz-Berthelot", nullptr +}; + +const char *evdw_names[evdwNR+1] = { + "Cut-off", "Switch", "Shift", "User", "Encad-shift", + "PME", nullptr +}; + +const char *econstr_names[econtNR+1] = { + "Lincs", "Shake", nullptr +}; + +const char *eintmod_names[eintmodNR+1] = { + "Potential-shift-Verlet", "Potential-shift", "None", "Potential-switch", "Exact-cutoff", "Force-switch", nullptr +}; + +const char *etcoupl_names[etcNR+1] = { + "No", "Berendsen", "Nose-Hoover", "yes", "Andersen", "Andersen-massive", "V-rescale", nullptr +}; /* yes is alias for berendsen */ + +const char *epcoupl_names[epcNR+1] = { + "No", "Berendsen", "Parrinello-Rahman", "Isotropic", "MTTK", nullptr +}; /* isotropic is alias for berendsen */ + +const char *epcoupltype_names[epctNR+1] = { + "Isotropic", "Semiisotropic", "Anisotropic", "Surface-Tension", nullptr +}; + +const char *edisre_names[edrNR+1] = { + "No", "Simple", "Ensemble", nullptr +}; + +const char *edisreweighting_names[edrwNR+1] = { + "Conservative", "Equal", nullptr +}; + +const char *enbf_names[eNBF_NR+1] = { + "", "LJ", "Buckingham", nullptr +}; + +const char *ecomb_names[eCOMB_NR+1] = { + "", "Geometric", "Arithmetic", "GeomSigEps", nullptr +}; + +const char *esimtemp_names[esimtempNR+1] = { + "geometric", "exponential", "linear", nullptr +}; + +const char *efep_names[efepNR+1] = { + "no", "yes", "static", "slow-growth", "expanded", nullptr +}; + +const char *efpt_names[efptNR+1] = { + "fep-lambdas", "mass-lambdas", "coul-lambdas", "vdw-lambdas", "bonded-lambdas", "restraint-lambdas", "temperature-lambdas", nullptr +}; + +const char *efpt_singular_names[efptNR+1] = { + "fep-lambda", "mass-lambda", "coul-lambda", "vdw-lambda", "bonded-lambda", "restraint-lambda", "temperature-lambda", nullptr +}; + +const char *edHdLPrintEnergy_names[edHdLPrintEnergyNR+1] = { + "no", "total", "potential", "yes", nullptr +}; + +const char *elamstats_names[elamstatsNR+1] = { + "no", "metropolis-transition", "barker-transition", "minvar", "wang-landau", "weighted-wang-landau", nullptr +}; + +const char *elmcmove_names[elmcmoveNR+1] = { + "no", "metropolis", "barker", "gibbs", "metropolized-gibbs", nullptr +}; + +const char *elmceq_names[elmceqNR+1] = { + "no", "yes", "wl-delta", "number-all-lambda", "number-steps", "number-samples", "count-ratio", nullptr +}; + +const char *separate_dhdl_file_names[esepdhdlfileNR+1] = { + "yes", "no", nullptr +}; + +const char *dhdl_derivatives_names[edhdlderivativesNR+1] = { + "yes", "no", nullptr +}; + +const char *esol_names[esolNR+1] = { + "No", "SPC", "TIP4p", nullptr +}; + +const char *edispc_names[edispcNR+1] = { + "No", "EnerPres", "Ener", "AllEnerPres", "AllEner", nullptr +}; + +const char *ecm_names[ecmNR+1] = { + "Linear", "Angular", "None", nullptr +}; + +const char *eann_names[eannNR+1] = { + "No", "Single", "Periodic", nullptr +}; + +const char *eis_names[eisNR+1] = { + "No", "GBSA", nullptr +}; + +const char *egb_names[egbNR+1] = { + "Still", "HCT", "OBC", nullptr +}; + +const char *esa_names[esaNR+1] = { + "Ace-approximation", "None", "Still", nullptr +}; + +const char *ewt_names[ewtNR+1] = { + "9-3", "10-4", "table", "12-6", nullptr +}; + +const char *epull_names[epullNR+1] = { + "umbrella", "constraint", "constant-force", "flat-bottom", nullptr +}; + +const char *epullg_names[epullgNR+1] = { + "distance", "direction", "cylinder", "direction-periodic", "direction-relative", nullptr +}; + +const char *erotg_names[erotgNR+1] = { + "iso", "iso-pf", "pm", "pm-pf", "rm", "rm-pf", "rm2", "rm2-pf", "flex", "flex-t", "flex2", "flex2-t", nullptr +}; + +const char *erotg_fitnames[erotgFitNR+1] = { + "rmsd", "norm", "potential", nullptr +}; + +const char *eSwapTypes_names[eSwapTypesNR+1] = { + "no", "X", "Y", "Z", nullptr +}; + +const char *eSwapFixedGrp_names[eSwapFixedGrpNR+1] = { + "Split0", "Split1", "Solvent", nullptr +}; + + +const char *eQMmethod_names[eQMmethodNR+1] = { + "AM1", "PM3", "RHF", + "UHF", "DFT", "B3LYP", "MP2", "CASSCF", "B3LYPLAN", + "DIRECT", nullptr +}; + +const char *eQMbasis_names[eQMbasisNR+1] = { + "STO3G", "STO-3G", "3-21G", + "3-21G*", "3-21+G*", "6-21G", + "6-31G", "6-31G*", "6-31+G*", + "6-311G", nullptr +}; + +const char *eQMMMscheme_names[eQMMMschemeNR+1] = { + "normal", "ONIOM", nullptr +}; + +const char *eMultentOpt_names[eMultentOptNR+1] = { + "multiple_entries", "no", "use_last", nullptr +}; + +const char *gmx_nblist_geometry_names[GMX_NBLIST_GEOMETRY_NR+1] = { + "Particle-Particle", "Water3-Particle", "Water3-Water3", "Water4-Particle", "Water4-Water4", "CG-CG", nullptr +}; + +const char *gmx_nblist_interaction_names[GMX_NBLIST_INTERACTION_NR+1] = { + "Standard", "Free_Energy", nullptr +}; + +const char *gmx_nbkernel_elec_names[GMX_NBKERNEL_ELEC_NR+1] = +{ + "None", "Coulomb", "Reaction-Field", "Cubic-Spline-Table", "Generalized-Born", "Ewald", nullptr +}; + +const char *gmx_nbkernel_vdw_names[GMX_NBKERNEL_VDW_NR+1] = +{ + "None", "Lennard-Jones", "Buckingham", "Cubic-Spline-Table", "LJEwald", nullptr +}; diff --cc src/gromacs/mdtypes/md_enums.h index 553de25587,0000000000..26fe09e76e mode 100644,000000..100644 --- a/src/gromacs/mdtypes/md_enums.h +++ b/src/gromacs/mdtypes/md_enums.h @@@ -1,681 -1,0 +1,681 @@@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright (c) 1991-2000, University of Groningen, The Netherlands. + * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by + * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, + * and including many others, as listed in the AUTHORS file in the + * top-level source directory and at http://www.gromacs.org. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * http://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at http://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out http://www.gromacs.org. + */ +/*! \file + * \brief + * Declares enumerated types used throughout the code. + * + * \author David van der Spoel + * \inpublicapi + * \ingroup module_mdtypes + */ +#ifndef GMX_MDTYPES_MD_ENUMS_H +#define GMX_MDTYPES_MD_ENUMS_H + +#include "gromacs/utility/basedefinitions.h" + +/*! \brief Return a string from a list of strings + * + * If index if within 0 .. max_index-1 returns the corresponding string - * or UNDEFINED otherwise, in other words this is a range-check that does ++ * or "no name defined" otherwise, in other words this is a range-check that does + * not crash. + * \param[in] index The index in the array + * \param[in] max_index The length of the array + * \param[in] names The array - * \return the correct string or UNDEFINED ++ * \return the correct string or "no name defined" + */ +const char *enum_name(int index, int max_index, const char *names[]); + +//! Boolean strings no or yes +extern const char *yesno_names[BOOL_NR+1]; + +//! \brief The two compartments for CompEL setups. +enum eCompartment { + eCompA, eCompB, eCompNR +}; + +/*! \brief The channels that define with their COM the compartment boundaries in CompEL setups. + * + * In principle one could also use modified setups with more than two channels. + */ +enum eChannel { + eChan0, eChan1, eChanNR +}; + +/*! \brief Temperature coupling type + * + * yes is an alias for berendsen + */ +enum { + etcNO, etcBERENDSEN, etcNOSEHOOVER, etcYES, etcANDERSEN, etcANDERSENMASSIVE, etcVRESCALE, etcNR +}; +//! Strings corresponding to temperatyre coupling types +extern const char *etcoupl_names[etcNR+1]; +//! Macro for selecting t coupling string +#define ETCOUPLTYPE(e) enum_name(e, etcNR, etcoupl_names) +//! Return whether this is andersen coupling +#define ETC_ANDERSEN(e) (((e) == etcANDERSENMASSIVE) || ((e) == etcANDERSEN)) + +/*! \brief Pressure coupling types + * + * isotropic is an alias for berendsen + */ +enum { + epcNO, epcBERENDSEN, epcPARRINELLORAHMAN, epcISOTROPIC, epcMTTK, epcNR +}; +//! String corresponding to pressure coupling algorithm +extern const char *epcoupl_names[epcNR+1]; +//! Macro to return the correct pcoupling string +#define EPCOUPLTYPE(e) enum_name(e, epcNR, epcoupl_names) + +//! Flat-bottom posres geometries +enum { + efbposresZERO, efbposresSPHERE, efbposresCYLINDER, efbposresX, efbposresY, efbposresZ, + efbposresCYLINDERX, efbposresCYLINDERY, efbposresCYLINDERZ, efbposresNR +}; + +//! Relative coordinate scaling type for position restraints. +enum { + erscNO, erscALL, erscCOM, erscNR +}; +//! String corresponding to relativ coordinate scaling. +extern const char *erefscaling_names[erscNR+1]; +//! Macro to select correct coordinate scaling string. +#define EREFSCALINGTYPE(e) enum_name(e, erscNR, erefscaling_names) + +//! Trotter decomposition extended variable parts. +enum { + etrtNONE, etrtNHC, etrtBAROV, etrtBARONHC, etrtNHC2, etrtBAROV2, etrtBARONHC2, + etrtVELOCITY1, etrtVELOCITY2, etrtPOSITION, etrtSKIPALL, etrtNR +}; + +//! Sequenced parts of the trotter decomposition. +enum { + ettTSEQ0, ettTSEQ1, ettTSEQ2, ettTSEQ3, ettTSEQ4, ettTSEQMAX +}; + +//! Pressure coupling type +enum { + epctISOTROPIC, epctSEMIISOTROPIC, epctANISOTROPIC, + epctSURFACETENSION, epctNR +}; +//! String corresponding to pressure coupling type +extern const char *epcoupltype_names[epctNR+1]; +//! Macro to select the right string for pcoupl type +#define EPCOUPLTYPETYPE(e) enum_name(e, epctNR, epcoupltype_names) + +//! \\brief Cutoff scheme +enum { + ecutsVERLET, ecutsGROUP, ecutsNR +}; +//! String corresponding to cutoff scheme +extern const char *ecutscheme_names[ecutsNR+1]; +//! Macro to select the right string for cutoff scheme +#define ECUTSCHEME(e) enum_name(e, ecutsNR, ecutscheme_names) + +/*! \brief Coulomb / VdW interaction modifiers. + * + * grompp replaces eintmodPOTSHIFT_VERLET by eintmodPOTSHIFT or eintmodNONE. + * Exactcutoff is only used by Reaction-field-zero, and is not user-selectable. + */ +enum eintmod { + eintmodPOTSHIFT_VERLET, eintmodPOTSHIFT, eintmodNONE, eintmodPOTSWITCH, eintmodEXACTCUTOFF, eintmodFORCESWITCH, eintmodNR +}; +//! String corresponding to interaction modifiers +extern const char *eintmod_names[eintmodNR+1]; +//! Macro to select the correct string for modifiers +#define INTMODIFIER(e) enum_name(e, eintmodNR, eintmod_names) + +/*! \brief Cut-off treatment for Coulomb + * + * eelNOTUSED1 used to be GB, but to enable generalized born with different + * forms of electrostatics (RF, switch, etc.) in the future it is now selected + * separately (through the implicit_solvent option). + */ +enum { + eelCUT, eelRF, eelGRF, eelPME, eelEWALD, eelP3M_AD, + eelPOISSON, eelSWITCH, eelSHIFT, eelUSER, eelGB_NOTUSED, eelRF_NEC_UNSUPPORTED, eelENCADSHIFT, + eelPMEUSER, eelPMESWITCH, eelPMEUSERSWITCH, eelRF_ZERO, eelNR +}; +//! String corresponding to Coulomb treatment +extern const char *eel_names[eelNR+1]; +//! Macro for correct string for Coulomb treatment +#define EELTYPE(e) enum_name(e, eelNR, eel_names) + +//! Ewald geometry. +enum { + eewg3D, eewg3DC, eewgNR +}; +//! String corresponding to Ewald geometry +extern const char *eewg_names[eewgNR+1]; + +//! Macro telling us whether we use reaction field +#define EEL_RF(e) ((e) == eelRF || (e) == eelGRF || (e) == eelRF_NEC_UNSUPPORTED || (e) == eelRF_ZERO ) + +//! Macro telling us whether we use PME +#define EEL_PME(e) ((e) == eelPME || (e) == eelPMESWITCH || (e) == eelPMEUSER || (e) == eelPMEUSERSWITCH || (e) == eelP3M_AD) +//! Macro telling us whether we use PME or full Ewald +#define EEL_PME_EWALD(e) (EEL_PME(e) || (e) == eelEWALD) +//! Macro telling us whether we use full electrostatics of any sort +#define EEL_FULL(e) (EEL_PME_EWALD(e) || (e) == eelPOISSON) +//! Macro telling us whether we use user defined electrostatics +#define EEL_USER(e) ((e) == eelUSER || (e) == eelPMEUSER || (e) == (eelPMEUSERSWITCH)) + +//! Van der Waals interaction treatment +enum { + evdwCUT, evdwSWITCH, evdwSHIFT, evdwUSER, evdwENCADSHIFT, + evdwPME, evdwNR +}; +//! String corresponding to Van der Waals treatment +extern const char *evdw_names[evdwNR+1]; +//! Macro for selecting correct string for VdW treatment +#define EVDWTYPE(e) enum_name(e, evdwNR, evdw_names) + +//! Type of long-range VdW treatment of combination rules +enum { + eljpmeGEOM, eljpmeLB, eljpmeNR +}; +//! String for LJPME combination rule treatment +extern const char *eljpme_names[eljpmeNR+1]; +//! Macro for correct LJPME comb rule name +#define ELJPMECOMBNAMES(e) enum_name(e, eljpmeNR, eljpme_names) + +//! Macro to tell us whether we use LJPME +#define EVDW_PME(e) ((e) == evdwPME) + +//! Neighborsearching algorithm +enum { + ensGRID, ensSIMPLE, ensNR +}; +//! String corresponding to neighborsearching +extern const char *ens_names[ensNR+1]; +//! Macro for correct NS algorithm +#define ENS(e) enum_name(e, ensNR, ens_names) + +/*! \brief Integrator algorithm + * + * eiSD2 has been removed, but we keep a renamed enum entry, + * so we can refuse to do MD with such .tpr files. + * eiVV is normal velocity verlet + * eiVVAK uses 1/2*(KE(t-dt/2)+KE(t+dt/2)) as the kinetic energy, + * and the half step kinetic energy for temperature control + */ +enum { + eiMD, eiSteep, eiCG, eiBD, eiSD2_REMOVED, eiNM, eiLBFGS, eiTPI, eiTPIC, eiSD1, eiVV, eiVVAK, eiNR +}; +//! Name of the integrator algorithm +extern const char *ei_names[eiNR+1]; +//! Macro returning integrator string +#define EI(e) enum_name(e, eiNR, ei_names) +//! Do we use velocity Verlet +#define EI_VV(e) ((e) == eiVV || (e) == eiVVAK) +//! Do we use molecular dynamics +#define EI_MD(e) ((e) == eiMD || EI_VV(e)) +//! Do we use stochastic dynamics +#define EI_SD(e) ((e) == eiSD1) +//! Do we use any stochastic integrator +#define EI_RANDOM(e) (EI_SD(e) || (e) == eiBD) +/*above integrators may not conserve momenta*/ +//! Do we use any type of dynamics +#define EI_DYNAMICS(e) (EI_MD(e) || EI_RANDOM(e)) +//! Or do we use minimization +#define EI_ENERGY_MINIMIZATION(e) ((e) == eiSteep || (e) == eiCG || (e) == eiLBFGS) +//! Do we apply test particle insertion +#define EI_TPI(e) ((e) == eiTPI || (e) == eiTPIC) +//! Do we deal with particle velocities +#define EI_STATE_VELOCITY(e) (EI_MD(e) || EI_SD(e)) + +//! Constraint algorithm +enum { + econtLINCS, econtSHAKE, econtNR +}; +//! String corresponding to constraint algorithm +extern const char *econstr_names[econtNR+1]; +//! Macro to select the correct string +#define ECONSTRTYPE(e) enum_name(e, econtNR, econstr_names) + +//! Distance restraint refinement algorithm +enum { + edrNone, edrSimple, edrEnsemble, edrNR +}; +//! String corresponding to distance restraint algorithm +extern const char *edisre_names[edrNR+1]; +//! Macro to select the right disre algorithm string +#define EDISRETYPE(e) enum_name(e, edrNR, edisre_names) + +//! Distance restraints weighting type +enum { + edrwConservative, edrwEqual, edrwNR +}; +//! String corresponding to distance restraint weighting +extern const char *edisreweighting_names[edrwNR+1]; +//! Macro corresponding to dr weighting +#define EDISREWEIGHTING(e) enum_name(e, edrwNR, edisreweighting_names) + +//! Combination rule algorithm. +enum { + eCOMB_NONE, eCOMB_GEOMETRIC, eCOMB_ARITHMETIC, eCOMB_GEOM_SIG_EPS, eCOMB_NR +}; +//! String for combination rule algorithm +extern const char *ecomb_names[eCOMB_NR+1]; +//! Macro to select the comb rule string +#define ECOMBNAME(e) enum_name(e, eCOMB_NR, ecomb_names) + +//! Van der Waals potential. +enum { + eNBF_NONE, eNBF_LJ, eNBF_BHAM, eNBF_NR +}; +//! String corresponding to Van der Waals potential +extern const char *enbf_names[eNBF_NR+1]; +//! Macro for correct VdW potential string +#define ENBFNAME(e) enum_name(e, eNBF_NR, enbf_names) + +//! Simulated tempering methods. +enum { + esimtempGEOMETRIC, esimtempEXPONENTIAL, esimtempLINEAR, esimtempNR +}; +//! String corresponding to simulated tempering +extern const char *esimtemp_names[esimtempNR+1]; +//! Macro for correct tempering string +#define ESIMTEMP(e) enum_name(e, esimtempNR, esimtemp_names) + +/*! \brief Free energy perturbation type + * + * efepNO, there are no evaluations at other states. + * efepYES, treated equivalently to efepSTATIC. + * efepSTATIC, then lambdas do not change during the simulation. + * efepSLOWGROWTH, then the states change monotonically + * throughout the simulation. + * efepEXPANDED, then expanded ensemble simulations are occuring. + */ +enum { + efepNO, efepYES, efepSTATIC, efepSLOWGROWTH, efepEXPANDED, efepNR +}; +//! String corresponding to FEP type. +extern const char *efep_names[efepNR+1]; +//! Macro corresponding to FEP string. +#define EFEPTYPE(e) enum_name(e, efepNR, efep_names) + +//! Free energy pertubation coupling types. +enum { + efptFEP, efptMASS, efptCOUL, efptVDW, efptBONDED, efptRESTRAINT, efptTEMPERATURE, efptNR +}; +//! String for FEP coupling type +extern const char *efpt_names[efptNR+1]; +//! Long names for FEP coupling type +extern const char *efpt_singular_names[efptNR+1]; + +/*! \brief What to print for free energy calculations + * + * Printing the energy to the free energy dhdl file. + * YES is an alias to TOTAL, and + * will be converted in readir, so we never have to account for it in code. + */ +enum { + edHdLPrintEnergyNO, edHdLPrintEnergyTOTAL, edHdLPrintEnergyPOTENTIAL, edHdLPrintEnergyYES, edHdLPrintEnergyNR +}; +//! String corresponding to printing of free energy +extern const char *edHdLPrintEnergy_names[edHdLPrintEnergyNR+1]; + +/*! \brief How the lambda weights are calculated + * + * elamstatsMETROPOLIS - using the metropolis criteria + * elamstatsBARKER - using the Barker critera for transition weights, + * also called unoptimized Bennett + * elamstatsMINVAR - using Barker + minimum variance for weights + * elamstatsWL - Wang-Landu (using visitation counts) + * elamstatsWWL - Weighted Wang-Landau (using optimized Gibbs + * weighted visitation counts) + */ +enum { + elamstatsNO, elamstatsMETROPOLIS, elamstatsBARKER, elamstatsMINVAR, elamstatsWL, elamstatsWWL, elamstatsNR +}; +//! String corresponding to lambda weights +extern const char *elamstats_names[elamstatsNR+1]; +//! Macro telling us whether we use expanded ensemble +#define ELAMSTATS_EXPANDED(e) ((e) > elamstatsNO) +//! Macro telling us whether we use some kind of Wang-Landau +#define EWL(e) ((e) == elamstatsWL || (e) == elamstatsWWL) + +/*! \brief How moves in lambda are calculated + * + * elmovemcMETROPOLIS - using the Metropolis criteria, and 50% up and down + * elmovemcBARKER - using the Barker criteria, and 50% up and down + * elmovemcGIBBS - computing the transition using the marginalized + * probabilities of the lambdas + * elmovemcMETGIBBS - computing the transition using the metropolized + * version of Gibbs (Monte Carlo Strategies in + * Scientific computing, Liu, p. 134) + */ +enum { + elmcmoveNO, elmcmoveMETROPOLIS, elmcmoveBARKER, elmcmoveGIBBS, elmcmoveMETGIBBS, elmcmoveNR +}; +//! String corresponding to lambda moves +extern const char *elmcmove_names[elmcmoveNR+1]; + +/*! \brief How we decide whether weights have reached equilibrium + * + * elmceqNO - never stop, weights keep going + * elmceqYES - fix the weights from the beginning; no movement + * elmceqWLDELTA - stop when the WL-delta falls below a certain level + * elmceqNUMATLAM - stop when we have a certain number of samples at + * every step + * elmceqSTEPS - stop when we've run a certain total number of steps + * elmceqSAMPLES - stop when we've run a certain total number of samples + * elmceqRATIO - stop when the ratio of samples (lowest to highest) + * is sufficiently large + */ +enum { + elmceqNO, elmceqYES, elmceqWLDELTA, elmceqNUMATLAM, elmceqSTEPS, elmceqSAMPLES, elmceqRATIO, elmceqNR +}; +//! String corresponding to equilibrium algorithm +extern const char *elmceq_names[elmceqNR+1]; + +/*! \brief separate_dhdl_file selection + * + * NOTE: YES is the first one. Do NOT interpret this one as a gmx_bool + */ +enum +{ + esepdhdlfileYES, esepdhdlfileNO, esepdhdlfileNR +}; +//! String corresponding to separate DHDL file selection +extern const char *separate_dhdl_file_names[esepdhdlfileNR+1]; +//! Monster macro for DHDL file selection +#define SEPDHDLFILETYPE(e) enum_name(e, esepdhdlfileNR, separate_dhdl_file_names) + +/*! \brief dhdl_derivatives selection \ + * + * NOTE: YES is the first one. Do NOT interpret this one as a gmx_bool + */ +enum +{ + edhdlderivativesYES, edhdlderivativesNO, edhdlderivativesNR +}; +//! String for DHDL derivatives +extern const char *dhdl_derivatives_names[edhdlderivativesNR+1]; +//! YAMM (Yet another monster macro) +#define DHDLDERIVATIVESTYPE(e) enum_name(e, edhdlderivativesNR, dhdl_derivatives_names) + +/*! \brief Solvent model + * + * Distinguishes classical water types with 3 or 4 particles + */ +enum { + esolNO, esolSPC, esolTIP4P, esolNR +}; +//! String corresponding to solvent type +extern const char *esol_names[esolNR+1]; +//! Macro lest we print the wrong solvent model string +#define ESOLTYPE(e) enum_name(e, esolNR, esol_names) + +//! Dispersion correction. +enum { + edispcNO, edispcEnerPres, edispcEner, edispcAllEnerPres, edispcAllEner, edispcNR +}; +//! String corresponding to dispersion corrections +extern const char *edispc_names[edispcNR+1]; +//! Macro for dispcorr string +#define EDISPCORR(e) enum_name(e, edispcNR, edispc_names) + +//! Center of mass motion removal algorithm. +enum { + ecmLINEAR, ecmANGULAR, ecmNO, ecmNR +}; +//! String corresponding to COM removal +extern const char *ecm_names[ecmNR+1]; +//! Macro for COM removal string +#define ECOM(e) enum_name(e, ecmNR, ecm_names) + +//! Algorithm for simulated annealing. +enum { + eannNO, eannSINGLE, eannPERIODIC, eannNR +}; +//! String for simulated annealing +extern const char *eann_names[eannNR+1]; +//! And macro for simulated annealing string +#define EANNEAL(e) enum_name(e, eannNR, eann_names) + +//! Implicit solvent algorithms. +enum { + eisNO, eisGBSA, eisNR +}; +//! String corresponding to implicit solvent. +extern const char *eis_names[eisNR+1]; +//! Macro for implicit solvent string. +#define EIMPLICITSOL(e) enum_name(e, eisNR, eis_names) + +//! Algorithms for calculating GB radii. +enum { + egbSTILL, egbHCT, egbOBC, egbNR +}; +//! String for GB algorithm name. +extern const char *egb_names[egbNR+1]; +//! Macro for GB string. +#define EGBALGORITHM(e) enum_name(e, egbNR, egb_names) + +//! Surface area algorithm for implicit solvent. +enum { + esaAPPROX, esaNO, esaSTILL, esaNR +}; +//! String corresponding to surface area algorithm. +extern const char *esa_names[esaNR+1]; +//! brief Macro for SA algorithm string. +#define ESAALGORITHM(e) enum_name(e, esaNR, esa_names) + +//! Wall types. +enum { + ewt93, ewt104, ewtTABLE, ewt126, ewtNR +}; +//! String corresponding to wall type +extern const char *ewt_names[ewtNR+1]; +//! Macro for wall type string +#define EWALLTYPE(e) enum_name(e, ewtNR, ewt_names) + +//! Pulling algorithm. +enum { + epullUMBRELLA, epullCONSTRAINT, epullCONST_F, epullFLATBOTTOM, epullNR +}; +//! String for pulling algorithm +extern const char *epull_names[epullNR+1]; +//! Macro for pulling string +#define EPULLTYPE(e) enum_name(e, epullNR, epull_names) + +//! Control of pull groups +enum { + epullgDIST, epullgDIR, epullgCYL, epullgDIRPBC, epullgDIRRELATIVE, epullgNR +}; +//! String for pull groups +extern const char *epullg_names[epullgNR+1]; +//! Macro for pull group string +#define EPULLGEOM(e) enum_name(e, epullgNR, epullg_names) + +//! Enforced rotation groups. +enum { + erotgISO, erotgISOPF, + erotgPM, erotgPMPF, + erotgRM, erotgRMPF, + erotgRM2, erotgRM2PF, + erotgFLEX, erotgFLEXT, + erotgFLEX2, erotgFLEX2T, + erotgNR +}; +//! Rotation group names +extern const char *erotg_names[erotgNR+1]; +//! Macro for rot group names +#define EROTGEOM(e) enum_name(e, erotgNR, erotg_names) +//! String for rotation group origin names +extern const char *erotg_originnames[erotgNR+1]; +//! Macro for rot group origin names +#define EROTORIGIN(e) enum_name(e, erotgOriginNR, erotg_originnames) + +//! Rotation group fitting type +enum { + erotgFitRMSD, erotgFitNORM, erotgFitPOT, erotgFitNR +}; +//! String corresponding to rotation group fitting +extern const char *erotg_fitnames[erotgFitNR+1]; +//! Macro for rot group fit names +#define EROTFIT(e) enum_name(e, erotgFitNR, erotg_fitnames) + +/*! \brief Direction along which ion/water swaps happen + * + * Part of "Computational Electrophysiology" (CompEL) setups + */ +enum eSwaptype { + eswapNO, eswapX, eswapY, eswapZ, eSwapTypesNR +}; +//! Names for swapping +extern const char *eSwapTypes_names[eSwapTypesNR+1]; +//! Macro for swapping string +#define ESWAPTYPE(e) enum_name(e, eSwapTypesNR, eSwapTypes_names) + +/*! \brief Swap group splitting type + * + * These are just the fixed groups we need for any setup. In t_swap's grp + * entry after that follows the variable number of swap groups. + */ +enum { + eGrpSplit0, eGrpSplit1, eGrpSolvent, eSwapFixedGrpNR +}; +//! String for swap group splitting +extern const char *eSwapFixedGrp_names[eSwapFixedGrpNR+1]; + +//! QMMM methods. +enum { + eQMmethodAM1, eQMmethodPM3, eQMmethodRHF, + eQMmethodUHF, eQMmethodDFT, eQMmethodB3LYP, eQMmethodMP2, eQMmethodCASSCF, eQMmethodB3LYPLAN, + eQMmethodDIRECT, eQMmethodNR +}; +//! String corresponding to QMMM methods +extern const char *eQMmethod_names[eQMmethodNR+1]; +//! Macro to pick QMMM method name +#define EQMMETHOD(e) enum_name(e, eQMmethodNR, eQMmethod_names) + +//! QMMM basis function for QM part +enum { + eQMbasisSTO3G, eQMbasisSTO3G2, eQMbasis321G, + eQMbasis321Gp, eQMbasis321dGp, eQMbasis621G, + eQMbasis631G, eQMbasis631Gp, eQMbasis631dGp, + eQMbasis6311G, eQMbasisNR +}; +//! Name for QMMM basis function +extern const char *eQMbasis_names[eQMbasisNR+1]; +//! Macro to pick right basis function string +#define EQMBASIS(e) enum_name(e, eQMbasisNR, eQMbasis_names) + +//! QMMM scheme +enum { + eQMMMschemenormal, eQMMMschemeoniom, eQMMMschemeNR +}; +//! QMMMM scheme names +extern const char *eQMMMscheme_names[eQMMMschemeNR+1]; +//! Macro to pick QMMMM scheme name +#define EQMMMSCHEME(e) enum_name(e, eQMMMschemeNR, eQMMMscheme_names) + +//! Internal stuff for multiple value options in mdp files +enum { + eMultentOptName, eMultentOptNo, eMultentOptLast, eMultentOptNR +}; +//! Multiple value option names +extern const char *eMultentOpt_names[eMultentOptNR+1]; + +/*! \brief Neighborlist geometry type. + * + * Kernels will compute interactions between two particles, + * 3-center water, 4-center water or coarse-grained beads. + */ +enum gmx_nblist_kernel_geometry +{ + GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, + GMX_NBLIST_GEOMETRY_WATER3_PARTICLE, + GMX_NBLIST_GEOMETRY_WATER3_WATER3, + GMX_NBLIST_GEOMETRY_WATER4_PARTICLE, + GMX_NBLIST_GEOMETRY_WATER4_WATER4, + GMX_NBLIST_GEOMETRY_CG_CG, + GMX_NBLIST_GEOMETRY_NR +}; +//! String corresponding to nblist geometry names +extern const char *gmx_nblist_geometry_names[GMX_NBLIST_GEOMETRY_NR+1]; + +/*! \brief Types of electrostatics calculations + * + * Types of electrostatics calculations available inside nonbonded kernels. + * Note that these do NOT necessarily correspond to the user selections + * in the MDP file; many interactions for instance map to tabulated kernels. + */ +enum gmx_nbkernel_elec +{ + GMX_NBKERNEL_ELEC_NONE, + GMX_NBKERNEL_ELEC_COULOMB, + GMX_NBKERNEL_ELEC_REACTIONFIELD, + GMX_NBKERNEL_ELEC_CUBICSPLINETABLE, + GMX_NBKERNEL_ELEC_GENERALIZEDBORN, + GMX_NBKERNEL_ELEC_EWALD, + GMX_NBKERNEL_ELEC_NR +}; +//! String corresponding to electrostatics kernels +extern const char *gmx_nbkernel_elec_names[GMX_NBKERNEL_ELEC_NR+1]; + +/*! \brief Types of vdw calculations available + * + * Types of vdw calculations available inside nonbonded kernels. + * Note that these do NOT necessarily correspond to the user selections + * in the MDP file; many interactions for instance map to tabulated kernels. + */ +enum gmx_nbkernel_vdw +{ + GMX_NBKERNEL_VDW_NONE, + GMX_NBKERNEL_VDW_LENNARDJONES, + GMX_NBKERNEL_VDW_BUCKINGHAM, + GMX_NBKERNEL_VDW_CUBICSPLINETABLE, + GMX_NBKERNEL_VDW_LJEWALD, + GMX_NBKERNEL_VDW_NR +}; +//! String corresponding to VdW kernels +extern const char *gmx_nbkernel_vdw_names[GMX_NBKERNEL_VDW_NR+1]; + +//! \brief Types of interactions inside the neighborlist +enum gmx_nblist_interaction_type +{ + GMX_NBLIST_INTERACTION_STANDARD, + GMX_NBLIST_INTERACTION_FREE_ENERGY, + GMX_NBLIST_INTERACTION_NR +}; +//! String corresponding to interactions in neighborlist code +extern const char *gmx_nblist_interaction_names[GMX_NBLIST_INTERACTION_NR+1]; + +#endif /* GMX_MDTYPES_MD_ENUMS_H */ diff --cc src/gromacs/tools/compare.cpp index 00703d33e4,0000000000..4b3add204c mode 100644,000000..100644 --- a/src/gromacs/tools/compare.cpp +++ b/src/gromacs/tools/compare.cpp @@@ -1,1468 -1,0 +1,1447 @@@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright (c) 1991-2000, University of Groningen, The Netherlands. + * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by + * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, + * and including many others, as listed in the AUTHORS file in the + * top-level source directory and at http://www.gromacs.org. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * http://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at http://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out http://www.gromacs.org. + */ +/* This file is completely threadsafe - keep it that way! */ + +#include "gmxpre.h" + +#include +#include +#include + +#include + +#include "gromacs/fileio/enxio.h" +#include "gromacs/fileio/tpxio.h" +#include "gromacs/fileio/trxio.h" +#include "gromacs/mdtypes/inputrec.h" +#include "gromacs/mdtypes/md_enums.h" +#include "gromacs/mdtypes/pull-params.h" +#include "gromacs/topology/ifunc.h" +#include "gromacs/topology/mtop_util.h" +#include "gromacs/topology/topology.h" +#include "gromacs/trajectory/trajectoryframe.h" +#include "gromacs/utility/cstringutil.h" +#include "gromacs/utility/fatalerror.h" +#include "gromacs/utility/futil.h" +#include "gromacs/utility/smalloc.h" +#include "gromacs/utility/stringutil.h" + +static void cmp_int(FILE *fp, const char *s, int index, int i1, int i2) +{ + if (i1 != i2) + { + if (index != -1) + { + fprintf(fp, "%s[%d] (%d - %d)\n", s, index, i1, i2); + } + else + { + fprintf(fp, "%s (%d - %d)\n", s, i1, i2); + } + } +} + +static void cmp_int64(FILE *fp, const char *s, gmx_int64_t i1, gmx_int64_t i2) +{ + if (i1 != i2) + { + fprintf(fp, "%s (", s); + fprintf(fp, "%" GMX_PRId64, i1); + fprintf(fp, " - "); + fprintf(fp, "%" GMX_PRId64, i2); + fprintf(fp, ")\n"); + } +} + +static void cmp_us(FILE *fp, const char *s, int index, unsigned short i1, unsigned short i2) +{ + if (i1 != i2) + { + if (index != -1) + { + fprintf(fp, "%s[%d] (%hu - %hu)\n", s, index, i1, i2); + } + else + { + fprintf(fp, "%s (%hu - %hu)\n", s, i1, i2); + } + } +} + +static void cmp_uc(FILE *fp, const char *s, int index, unsigned char i1, unsigned char i2) +{ + if (i1 != i2) + { + if (index != -1) + { + fprintf(fp, "%s[%d] (%d - %d)\n", s, index, i1, i2); + } + else + { + fprintf(fp, "%s (%d - %d)\n", s, i1, i2); + } + } +} + +static gmx_bool cmp_bool(FILE *fp, const char *s, int index, gmx_bool b1, gmx_bool b2) +{ + if (b1) + { + b1 = 1; + } + else + { + b1 = 0; + } + if (b2) + { + b2 = 1; + } + else + { + b2 = 0; + } + if (b1 != b2) + { + if (index != -1) + { + fprintf(fp, "%s[%d] (%s - %s)\n", s, index, + gmx::boolToString(b1), gmx::boolToString(b2)); + } + else + { + fprintf(fp, "%s (%s - %s)\n", s, + gmx::boolToString(b1), gmx::boolToString(b2)); + } + } + return b1 && b2; +} + +static void cmp_str(FILE *fp, const char *s, int index, + const char *s1, const char *s2) +{ + if (std::strcmp(s1, s2) != 0) + { + if (index != -1) + { + fprintf(fp, "%s[%d] (%s - %s)\n", s, index, s1, s2); + } + else + { + fprintf(fp, "%s (%s - %s)\n", s, s1, s2); + } + } +} + +static gmx_bool equal_real(real i1, real i2, real ftol, real abstol) +{ + return ( ( 2*fabs(i1 - i2) <= (fabs(i1) + fabs(i2))*ftol ) || fabs(i1-i2) <= abstol ); +} + +static gmx_bool equal_float(float i1, float i2, float ftol, float abstol) +{ + return ( ( 2*fabs(i1 - i2) <= (fabs(i1) + fabs(i2))*ftol ) || fabs(i1-i2) <= abstol ); +} + +static gmx_bool equal_double(double i1, double i2, real ftol, real abstol) +{ + return ( ( 2*fabs(i1 - i2) <= (fabs(i1) + fabs(i2))*ftol ) || fabs(i1-i2) <= abstol ); +} + +static void +cmp_real(FILE *fp, const char *s, int index, real i1, real i2, real ftol, real abstol) +{ + if (!equal_real(i1, i2, ftol, abstol)) + { + if (index != -1) + { + fprintf(fp, "%s[%2d] (%e - %e)\n", s, index, i1, i2); + } + else + { + fprintf(fp, "%s (%e - %e)\n", s, i1, i2); + } + } +} + +static void +cmp_float(FILE *fp, const char *s, int index, float i1, float i2, float ftol, float abstol) +{ + if (!equal_float(i1, i2, ftol, abstol)) + { + if (index != -1) + { + fprintf(fp, "%s[%2d] (%e - %e)\n", s, index, i1, i2); + } + else + { + fprintf(fp, "%s (%e - %e)\n", s, i1, i2); + } + } +} + + + +static void +cmp_double(FILE *fp, const char *s, int index, double i1, double i2, double ftol, double abstol) +{ + if (!equal_double(i1, i2, ftol, abstol)) + { + if (index != -1) + { + fprintf(fp, "%s[%2d] (%16.9e - %16.9e)\n", s, index, i1, i2); + } + else + { + fprintf(fp, "%s (%16.9e - %16.9e)\n", s, i1, i2); + } + } +} + +static void cmp_rvec(FILE *fp, const char *s, int index, rvec i1, rvec i2, real ftol, real abstol) +{ + if (!equal_real(i1[XX], i2[XX], ftol, abstol) || + !equal_real(i1[YY], i2[YY], ftol, abstol) || + !equal_real(i1[ZZ], i2[ZZ], ftol, abstol)) + { + if (index != -1) + { + fprintf(fp, "%s[%5d] (%12.5e %12.5e %12.5e) - (%12.5e %12.5e %12.5e)\n", + s, index, i1[XX], i1[YY], i1[ZZ], i2[XX], i2[YY], i2[ZZ]); + } + else + { + fprintf(fp, "%s (%12.5e %12.5e %12.5e) - (%12.5e %12.5e %12.5e)\n", + s, i1[XX], i1[YY], i1[ZZ], i2[XX], i2[YY], i2[ZZ]); + } + } +} + +static void cmp_ivec(FILE *fp, const char *s, int index, ivec i1, ivec i2) +{ + if ((i1[XX] != i2[XX]) || (i1[YY] != i2[YY]) || (i1[ZZ] != i2[ZZ])) + { + if (index != -1) + { + fprintf(fp, "%s[%5d] (%8d,%8d,%8d - %8d,%8d,%8d)\n", s, index, + i1[XX], i1[YY], i1[ZZ], i2[XX], i2[YY], i2[ZZ]); + } + else + { + fprintf(fp, "%s (%8d,%8d,%8d - %8d,%8d,%8d)\n", s, + i1[XX], i1[YY], i1[ZZ], i2[XX], i2[YY], i2[ZZ]); + } + } +} + +static void cmp_ilist(FILE *fp, int ftype, t_ilist *il1, t_ilist *il2) +{ + int i; + char buf[256]; + + fprintf(fp, "comparing ilist %s\n", interaction_function[ftype].name); + sprintf(buf, "%s->nr", interaction_function[ftype].name); + cmp_int(fp, buf, -1, il1->nr, il2->nr); + sprintf(buf, "%s->iatoms", interaction_function[ftype].name); + if (((il1->nr > 0) && (!il1->iatoms)) || + ((il2->nr > 0) && (!il2->iatoms)) || + ((il1->nr != il2->nr))) + { + fprintf(fp, "Comparing radically different topologies - %s is different\n", + buf); + } + else + { + for (i = 0; (i < il1->nr); i++) + { + cmp_int(fp, buf, i, il1->iatoms[i], il2->iatoms[i]); + } + } +} + +void cmp_iparm(FILE *fp, const char *s, t_functype ft, + t_iparams ip1, t_iparams ip2, real ftol, real abstol) +{ + int i; + gmx_bool bDiff; + + bDiff = FALSE; + for (i = 0; i < MAXFORCEPARAM && !bDiff; i++) + { + bDiff = !equal_real(ip1.generic.buf[i], ip2.generic.buf[i], ftol, abstol); + } + if (bDiff) + { + fprintf(fp, "%s1: ", s); + pr_iparams(fp, ft, &ip1); + fprintf(fp, "%s2: ", s); + pr_iparams(fp, ft, &ip2); + } +} + +void cmp_iparm_AB(FILE *fp, const char *s, t_functype ft, t_iparams ip1, real ftol, real abstol) +{ + int nrfpA, nrfpB, p0, i; + gmx_bool bDiff; + + /* Normally the first parameter is perturbable */ + p0 = 0; + nrfpA = interaction_function[ft].nrfpA; + nrfpB = interaction_function[ft].nrfpB; + if (ft == F_PDIHS) + { + nrfpB = 2; + } + else if (interaction_function[ft].flags & IF_TABULATED) + { + /* For tabulated interactions only the second parameter is perturbable */ + p0 = 1; + nrfpB = 1; + } + bDiff = FALSE; + for (i = 0; i < nrfpB && !bDiff; i++) + { + bDiff = !equal_real(ip1.generic.buf[p0+i], ip1.generic.buf[nrfpA+i], ftol, abstol); + } + if (bDiff) + { + fprintf(fp, "%s: ", s); + pr_iparams(fp, ft, &ip1); + } +} + +static void cmp_idef(FILE *fp, t_idef *id1, t_idef *id2, real ftol, real abstol) +{ + int i; + char buf1[64], buf2[64]; + + fprintf(fp, "comparing idef\n"); + if (id2) + { + cmp_int(fp, "idef->ntypes", -1, id1->ntypes, id2->ntypes); + cmp_int(fp, "idef->atnr", -1, id1->atnr, id2->atnr); + for (i = 0; (i < std::min(id1->ntypes, id2->ntypes)); i++) + { + sprintf(buf1, "idef->functype[%d]", i); + sprintf(buf2, "idef->iparam[%d]", i); + cmp_int(fp, buf1, i, (int)id1->functype[i], (int)id2->functype[i]); + cmp_iparm(fp, buf2, id1->functype[i], + id1->iparams[i], id2->iparams[i], ftol, abstol); + } + cmp_real(fp, "fudgeQQ", -1, id1->fudgeQQ, id2->fudgeQQ, ftol, abstol); + for (i = 0; (i < F_NRE); i++) + { + cmp_ilist(fp, i, &(id1->il[i]), &(id2->il[i])); + } + } + else + { + for (i = 0; (i < id1->ntypes); i++) + { + cmp_iparm_AB(fp, "idef->iparam", id1->functype[i], id1->iparams[i], ftol, abstol); + } + } +} + +static void cmp_block(FILE *fp, t_block *b1, t_block *b2, const char *s) +{ + char buf[32]; + + fprintf(fp, "comparing block %s\n", s); + sprintf(buf, "%s.nr", s); + cmp_int(fp, buf, -1, b1->nr, b2->nr); +} + +static void cmp_blocka(FILE *fp, t_blocka *b1, t_blocka *b2, const char *s) +{ + char buf[32]; + + fprintf(fp, "comparing blocka %s\n", s); + sprintf(buf, "%s.nr", s); + cmp_int(fp, buf, -1, b1->nr, b2->nr); + sprintf(buf, "%s.nra", s); + cmp_int(fp, buf, -1, b1->nra, b2->nra); +} + +static void cmp_atom(FILE *fp, int index, t_atom *a1, t_atom *a2, real ftol, real abstol) +{ + if (a2) + { + cmp_us(fp, "atom.type", index, a1->type, a2->type); + cmp_us(fp, "atom.ptype", index, a1->ptype, a2->ptype); + cmp_int(fp, "atom.resind", index, a1->resind, a2->resind); + cmp_int(fp, "atom.atomnumber", index, a1->atomnumber, a2->atomnumber); + cmp_real(fp, "atom.m", index, a1->m, a2->m, ftol, abstol); + cmp_real(fp, "atom.q", index, a1->q, a2->q, ftol, abstol); + cmp_us(fp, "atom.typeB", index, a1->typeB, a2->typeB); + cmp_real(fp, "atom.mB", index, a1->mB, a2->mB, ftol, abstol); + cmp_real(fp, "atom.qB", index, a1->qB, a2->qB, ftol, abstol); + } + else + { + cmp_us(fp, "atom.type", index, a1->type, a1->typeB); + cmp_real(fp, "atom.m", index, a1->m, a1->mB, ftol, abstol); + cmp_real(fp, "atom.q", index, a1->q, a1->qB, ftol, abstol); + } +} + +static void cmp_atoms(FILE *fp, t_atoms *a1, t_atoms *a2, real ftol, real abstol) +{ + int i; + + fprintf(fp, "comparing atoms\n"); + + if (a2) + { + cmp_int(fp, "atoms->nr", -1, a1->nr, a2->nr); + for (i = 0; (i < a1->nr); i++) + { + cmp_atom(fp, i, &(a1->atom[i]), &(a2->atom[i]), ftol, abstol); + } + } + else + { + for (i = 0; (i < a1->nr); i++) + { + cmp_atom(fp, i, &(a1->atom[i]), NULL, ftol, abstol); + } + } +} + +static void cmp_top(FILE *fp, t_topology *t1, t_topology *t2, real ftol, real abstol) +{ + fprintf(fp, "comparing top\n"); + if (t2) + { + cmp_idef(fp, &(t1->idef), &(t2->idef), ftol, abstol); + cmp_atoms(fp, &(t1->atoms), &(t2->atoms), ftol, abstol); + cmp_block(fp, &t1->cgs, &t2->cgs, "cgs"); + cmp_block(fp, &t1->mols, &t2->mols, "mols"); + cmp_bool(fp, "bIntermolecularInteractions", -1, t1->bIntermolecularInteractions, t2->bIntermolecularInteractions); + cmp_blocka(fp, &t1->excls, &t2->excls, "excls"); + } + else + { + cmp_idef(fp, &(t1->idef), NULL, ftol, abstol); + cmp_atoms(fp, &(t1->atoms), NULL, ftol, abstol); + } +} + +static void cmp_groups(FILE *fp, gmx_groups_t *g0, gmx_groups_t *g1, + int natoms0, int natoms1) +{ + int i, j; + char buf[32]; + + fprintf(fp, "comparing groups\n"); + + for (i = 0; i < egcNR; i++) + { + sprintf(buf, "grps[%d].nr", i); + cmp_int(fp, buf, -1, g0->grps[i].nr, g1->grps[i].nr); + if (g0->grps[i].nr == g1->grps[i].nr) + { + for (j = 0; j < g0->grps[i].nr; j++) + { + sprintf(buf, "grps[%d].name[%d]", i, j); + cmp_str(fp, buf, -1, + *g0->grpname[g0->grps[i].nm_ind[j]], + *g1->grpname[g1->grps[i].nm_ind[j]]); + } + } + cmp_int(fp, "ngrpnr", i, g0->ngrpnr[i], g1->ngrpnr[i]); + if (g0->ngrpnr[i] == g1->ngrpnr[i] && natoms0 == natoms1 && + (g0->grpnr[i] != NULL || g1->grpnr[i] != NULL)) + { + for (j = 0; j < natoms0; j++) + { + cmp_int(fp, gtypes[i], j, ggrpnr(g0, i, j), ggrpnr(g1, i, j)); + } + } + } + /* We have compared the names in the groups lists, + * so we can skip the grpname list comparison. + */ +} + ++static void cmp_rvecs_rmstol(FILE *fp, const char *title, int n, rvec x1[], rvec x2[], ++ real ftol, real abstol) ++{ ++ int i, m; ++ double rms; ++ ++ /* For a vector you are usally not interested in a relative difference ++ * on a component that is very small compared to the other components. ++ * Therefore we do the relative comparision relative to the RMS component. ++ */ ++ rms = 0.0; ++ for (i = 0; (i < n); i++) ++ { ++ for (m = 0; m < DIM; m++) ++ { ++ rms += x1[i][m]*x1[i][m] + x2[i][m]*x2[i][m]; ++ } ++ } ++ rms = sqrt(rms/(2*n*DIM)); ++ ++ /* Convert the relative tolerance into an absolute tolerance */ ++ if (ftol*rms < abstol) ++ { ++ abstol = ftol*rms; ++ } ++ ++ /* And now do the actual comparision */ ++ for (i = 0; (i < n); i++) ++ { ++ cmp_rvec(fp, title, i, x1[i], x2[i], 0.0, abstol); ++ } ++} ++ +static void cmp_rvecs(FILE *fp, const char *title, int n, rvec x1[], rvec x2[], + gmx_bool bRMSD, real ftol, real abstol) +{ + int i, m; + double d, ssd; + + if (bRMSD) + { + ssd = 0; + for (i = 0; (i < n); i++) + { + for (m = 0; m < DIM; m++) + { + d = x1[i][m] - x2[i][m]; + ssd += d*d; + } + } + fprintf(fp, "%s RMSD %g\n", title, std::sqrt(ssd/n)); + } + else + { - for (i = 0; (i < n); i++) - { - cmp_rvec(fp, title, i, x1[i], x2[i], ftol, abstol); - } - } - } - - - /* Similar to cmp_rvecs, but this routine scales the allowed absolute tolerance - * by the RMS of the force components of x1. - */ - static void cmp_rvecs_rmstol(FILE *fp, const char *title, int n, rvec x1[], rvec x2[], - real ftol, real abstol) - { - int i, m; - double d; - double ave_x1, rms_x1; - - /* It is tricky to compare real values, in particular forces that - * are sums of lots of terms where the final value might be close to 0.0. - * To get a reference magnitude we calculate the RMS value of each - * component in x1, and then set the allowed absolute tolerance to the - * relative tolerance times this RMS magnitude. - */ - ave_x1 = 0.0; - for (i = 0; i < n; i++) - { - for (m = 0; m < DIM; m++) - { - ave_x1 += x1[i][m]; - } - } - ave_x1 /= n*DIM; - - rms_x1 = 0.0; - for (i = 0; (i < n); i++) - { - for (m = 0; m < DIM; m++) - { - d = x1[i][m] - ave_x1; - rms_x1 += d*d; - } - } - rms_x1 = std::sqrt(rms_x1/(DIM*n)); - /* And now do the actual comparision with a hopefully realistic abstol. */ - for (i = 0; (i < n); i++) - { - cmp_rvec(fp, title, i, x1[i], x2[i], ftol, abstol*rms_x1); ++ cmp_rvecs_rmstol(fp, title, n, x1, x2, ftol, abstol); + } +} + +static void cmp_grpopts(FILE *fp, t_grpopts *opt1, t_grpopts *opt2, real ftol, real abstol) +{ + int i, j; + char buf1[256], buf2[256]; + + cmp_int(fp, "inputrec->grpopts.ngtc", -1, opt1->ngtc, opt2->ngtc); + cmp_int(fp, "inputrec->grpopts.ngacc", -1, opt1->ngacc, opt2->ngacc); + cmp_int(fp, "inputrec->grpopts.ngfrz", -1, opt1->ngfrz, opt2->ngfrz); + cmp_int(fp, "inputrec->grpopts.ngener", -1, opt1->ngener, opt2->ngener); + for (i = 0; (i < std::min(opt1->ngtc, opt2->ngtc)); i++) + { + cmp_real(fp, "inputrec->grpopts.nrdf", i, opt1->nrdf[i], opt2->nrdf[i], ftol, abstol); + cmp_real(fp, "inputrec->grpopts.ref_t", i, opt1->ref_t[i], opt2->ref_t[i], ftol, abstol); + cmp_real(fp, "inputrec->grpopts.tau_t", i, opt1->tau_t[i], opt2->tau_t[i], ftol, abstol); + cmp_int(fp, "inputrec->grpopts.annealing", i, opt1->annealing[i], opt2->annealing[i]); + cmp_int(fp, "inputrec->grpopts.anneal_npoints", i, + opt1->anneal_npoints[i], opt2->anneal_npoints[i]); + if (opt1->anneal_npoints[i] == opt2->anneal_npoints[i]) + { + sprintf(buf1, "inputrec->grpopts.anneal_time[%d]", i); + sprintf(buf2, "inputrec->grpopts.anneal_temp[%d]", i); + for (j = 0; j < opt1->anneal_npoints[i]; j++) + { + cmp_real(fp, buf1, j, opt1->anneal_time[i][j], opt2->anneal_time[i][j], ftol, abstol); + cmp_real(fp, buf2, j, opt1->anneal_temp[i][j], opt2->anneal_temp[i][j], ftol, abstol); + } + } + } + if (opt1->ngener == opt2->ngener) + { + for (i = 0; i < opt1->ngener; i++) + { + for (j = i; j < opt1->ngener; j++) + { + sprintf(buf1, "inputrec->grpopts.egp_flags[%d]", i); + cmp_int(fp, buf1, j, + opt1->egp_flags[opt1->ngener*i+j], + opt2->egp_flags[opt1->ngener*i+j]); + } + } + } + for (i = 0; (i < std::min(opt1->ngacc, opt2->ngacc)); i++) + { + cmp_rvec(fp, "inputrec->grpopts.acc", i, opt1->acc[i], opt2->acc[i], ftol, abstol); + } + for (i = 0; (i < std::min(opt1->ngfrz, opt2->ngfrz)); i++) + { + cmp_ivec(fp, "inputrec->grpopts.nFreeze", i, opt1->nFreeze[i], opt2->nFreeze[i]); + } +} + +static void cmp_cosines(FILE *fp, const char *s, t_cosines c1[DIM], t_cosines c2[DIM], real ftol, real abstol) +{ + int i, m; + char buf[256]; + + for (m = 0; (m < DIM); m++) + { + sprintf(buf, "inputrec->%s[%d]", s, m); + cmp_int(fp, buf, 0, c1->n, c2->n); + for (i = 0; (i < std::min(c1->n, c2->n)); i++) + { + cmp_real(fp, buf, i, c1->a[i], c2->a[i], ftol, abstol); + cmp_real(fp, buf, i, c1->phi[i], c2->phi[i], ftol, abstol); + } + } +} +static void cmp_pull(FILE *fp) +{ + fprintf(fp, "WARNING: Both files use COM pulling, but comparing of the pull struct is not implemented (yet). The pull parameters could be the same or different.\n"); +} + +static void cmp_simtempvals(FILE *fp, t_simtemp *simtemp1, t_simtemp *simtemp2, int n_lambda, real ftol, real abstol) +{ + int i; + cmp_int(fp, "inputrec->simtempvals->eSimTempScale", -1, simtemp1->eSimTempScale, simtemp2->eSimTempScale); + cmp_real(fp, "inputrec->simtempvals->simtemp_high", -1, simtemp1->simtemp_high, simtemp2->simtemp_high, ftol, abstol); + cmp_real(fp, "inputrec->simtempvals->simtemp_low", -1, simtemp1->simtemp_low, simtemp2->simtemp_low, ftol, abstol); + for (i = 0; i < n_lambda; i++) + { + cmp_real(fp, "inputrec->simtempvals->temperatures", -1, simtemp1->temperatures[i], simtemp2->temperatures[i], ftol, abstol); + } +} + +static void cmp_expandedvals(FILE *fp, t_expanded *expand1, t_expanded *expand2, int n_lambda, real ftol, real abstol) +{ + int i; + + cmp_bool(fp, "inputrec->fepvals->bInit_weights", -1, expand1->bInit_weights, expand2->bInit_weights); + cmp_bool(fp, "inputrec->fepvals->bWLoneovert", -1, expand1->bWLoneovert, expand2->bWLoneovert); + + for (i = 0; i < n_lambda; i++) + { + cmp_real(fp, "inputrec->expandedvals->init_lambda_weights", -1, + expand1->init_lambda_weights[i], expand2->init_lambda_weights[i], ftol, abstol); + } + + cmp_int(fp, "inputrec->expandedvals->lambda-stats", -1, expand1->elamstats, expand2->elamstats); + cmp_int(fp, "inputrec->expandedvals->lambda-mc-move", -1, expand1->elmcmove, expand2->elmcmove); + cmp_int(fp, "inputrec->expandedvals->lmc-repeats", -1, expand1->lmc_repeats, expand2->lmc_repeats); + cmp_int(fp, "inputrec->expandedvals->lmc-gibbsdelta", -1, expand1->gibbsdeltalam, expand2->gibbsdeltalam); + cmp_int(fp, "inputrec->expandedvals->lmc-forced-nstart", -1, expand1->lmc_forced_nstart, expand2->lmc_forced_nstart); + cmp_int(fp, "inputrec->expandedvals->lambda-weights-equil", -1, expand1->elmceq, expand2->elmceq); + cmp_int(fp, "inputrec->expandedvals->,weight-equil-number-all-lambda", -1, expand1->equil_n_at_lam, expand2->equil_n_at_lam); + cmp_int(fp, "inputrec->expandedvals->weight-equil-number-samples", -1, expand1->equil_samples, expand2->equil_samples); + cmp_int(fp, "inputrec->expandedvals->weight-equil-number-steps", -1, expand1->equil_steps, expand2->equil_steps); + cmp_real(fp, "inputrec->expandedvals->weight-equil-wl-delta", -1, expand1->equil_wl_delta, expand2->equil_wl_delta, ftol, abstol); + cmp_real(fp, "inputrec->expandedvals->weight-equil-count-ratio", -1, expand1->equil_ratio, expand2->equil_ratio, ftol, abstol); + cmp_bool(fp, "inputrec->expandedvals->symmetrized-transition-matrix", -1, expand1->bSymmetrizedTMatrix, expand2->bSymmetrizedTMatrix); + cmp_int(fp, "inputrec->expandedvals->nstTij", -1, expand1->nstTij, expand2->nstTij); + cmp_int(fp, "inputrec->expandedvals->mininum-var-min", -1, expand1->minvarmin, expand2->minvarmin); /*default is reasonable */ + cmp_int(fp, "inputrec->expandedvals->weight-c-range", -1, expand1->c_range, expand2->c_range); /* default is just C=0 */ + cmp_real(fp, "inputrec->expandedvals->wl-scale", -1, expand1->wl_scale, expand2->wl_scale, ftol, abstol); + cmp_real(fp, "inputrec->expandedvals->init-wl-delta", -1, expand1->init_wl_delta, expand2->init_wl_delta, ftol, abstol); + cmp_real(fp, "inputrec->expandedvals->wl-ratio", -1, expand1->wl_ratio, expand2->wl_ratio, ftol, abstol); + cmp_int(fp, "inputrec->expandedvals->nstexpanded", -1, expand1->nstexpanded, expand2->nstexpanded); + cmp_int(fp, "inputrec->expandedvals->lmc-seed", -1, expand1->lmc_seed, expand2->lmc_seed); + cmp_real(fp, "inputrec->expandedvals->mc-temperature", -1, expand1->mc_temp, expand2->mc_temp, ftol, abstol); +} + +static void cmp_fepvals(FILE *fp, t_lambda *fep1, t_lambda *fep2, real ftol, real abstol) +{ + int i, j; + cmp_int(fp, "inputrec->nstdhdl", -1, fep1->nstdhdl, fep2->nstdhdl); + cmp_double(fp, "inputrec->fepvals->init_fep_state", -1, fep1->init_fep_state, fep2->init_fep_state, ftol, abstol); + cmp_double(fp, "inputrec->fepvals->delta_lambda", -1, fep1->delta_lambda, fep2->delta_lambda, ftol, abstol); + cmp_int(fp, "inputrec->fepvals->n_lambda", -1, fep1->n_lambda, fep2->n_lambda); + for (i = 0; i < efptNR; i++) + { + for (j = 0; j < std::min(fep1->n_lambda, fep2->n_lambda); j++) + { + cmp_double(fp, "inputrec->fepvals->all_lambda", -1, fep1->all_lambda[i][j], fep2->all_lambda[i][j], ftol, abstol); + } + } + cmp_int(fp, "inputrec->fepvals->lambda_neighbors", 1, fep1->lambda_neighbors, + fep2->lambda_neighbors); + cmp_real(fp, "inputrec->fepvals->sc_alpha", -1, fep1->sc_alpha, fep2->sc_alpha, ftol, abstol); + cmp_int(fp, "inputrec->fepvals->sc_power", -1, fep1->sc_power, fep2->sc_power); + cmp_real(fp, "inputrec->fepvals->sc_r_power", -1, fep1->sc_r_power, fep2->sc_r_power, ftol, abstol); + cmp_real(fp, "inputrec->fepvals->sc_sigma", -1, fep1->sc_sigma, fep2->sc_sigma, ftol, abstol); + cmp_int(fp, "inputrec->fepvals->edHdLPrintEnergy", -1, fep1->edHdLPrintEnergy, fep1->edHdLPrintEnergy); + cmp_bool(fp, "inputrec->fepvals->bScCoul", -1, fep1->bScCoul, fep1->bScCoul); + cmp_int(fp, "inputrec->separate_dhdl_file", -1, fep1->separate_dhdl_file, fep2->separate_dhdl_file); + cmp_int(fp, "inputrec->dhdl_derivatives", -1, fep1->dhdl_derivatives, fep2->dhdl_derivatives); + cmp_int(fp, "inputrec->dh_hist_size", -1, fep1->dh_hist_size, fep2->dh_hist_size); + cmp_double(fp, "inputrec->dh_hist_spacing", -1, fep1->dh_hist_spacing, fep2->dh_hist_spacing, ftol, abstol); +} + +static void cmp_inputrec(FILE *fp, t_inputrec *ir1, t_inputrec *ir2, real ftol, real abstol) +{ + fprintf(fp, "comparing inputrec\n"); + + /* gcc 2.96 doesnt like these defines at all, but issues a huge list + * of warnings. Maybe it will change in future versions, but for the + * moment I've spelled them out instead. /EL 000820 + * #define CIB(s) cmp_int(fp,"inputrec->"#s,0,ir1->##s,ir2->##s) + * #define CII(s) cmp_int(fp,"inputrec->"#s,0,ir1->##s,ir2->##s) + * #define CIR(s) cmp_real(fp,"inputrec->"#s,0,ir1->##s,ir2->##s,ftol) + */ + cmp_int(fp, "inputrec->eI", -1, ir1->eI, ir2->eI); + cmp_int64(fp, "inputrec->nsteps", ir1->nsteps, ir2->nsteps); + cmp_int64(fp, "inputrec->init_step", ir1->init_step, ir2->init_step); + cmp_int(fp, "inputrec->simulation_part", -1, ir1->simulation_part, ir2->simulation_part); + cmp_int(fp, "inputrec->ePBC", -1, ir1->ePBC, ir2->ePBC); + cmp_int(fp, "inputrec->bPeriodicMols", -1, ir1->bPeriodicMols, ir2->bPeriodicMols); + cmp_int(fp, "inputrec->cutoff_scheme", -1, ir1->cutoff_scheme, ir2->cutoff_scheme); + cmp_int(fp, "inputrec->ns_type", -1, ir1->ns_type, ir2->ns_type); + cmp_int(fp, "inputrec->nstlist", -1, ir1->nstlist, ir2->nstlist); + cmp_int(fp, "inputrec->nstcomm", -1, ir1->nstcomm, ir2->nstcomm); + cmp_int(fp, "inputrec->comm_mode", -1, ir1->comm_mode, ir2->comm_mode); + cmp_int(fp, "inputrec->nstlog", -1, ir1->nstlog, ir2->nstlog); + cmp_int(fp, "inputrec->nstxout", -1, ir1->nstxout, ir2->nstxout); + cmp_int(fp, "inputrec->nstvout", -1, ir1->nstvout, ir2->nstvout); + cmp_int(fp, "inputrec->nstfout", -1, ir1->nstfout, ir2->nstfout); + cmp_int(fp, "inputrec->nstcalcenergy", -1, ir1->nstcalcenergy, ir2->nstcalcenergy); + cmp_int(fp, "inputrec->nstenergy", -1, ir1->nstenergy, ir2->nstenergy); + cmp_int(fp, "inputrec->nstxout_compressed", -1, ir1->nstxout_compressed, ir2->nstxout_compressed); + cmp_double(fp, "inputrec->init_t", -1, ir1->init_t, ir2->init_t, ftol, abstol); + cmp_double(fp, "inputrec->delta_t", -1, ir1->delta_t, ir2->delta_t, ftol, abstol); + cmp_real(fp, "inputrec->x_compression_precision", -1, ir1->x_compression_precision, ir2->x_compression_precision, ftol, abstol); + cmp_real(fp, "inputrec->fourierspacing", -1, ir1->fourier_spacing, ir2->fourier_spacing, ftol, abstol); + cmp_int(fp, "inputrec->nkx", -1, ir1->nkx, ir2->nkx); + cmp_int(fp, "inputrec->nky", -1, ir1->nky, ir2->nky); + cmp_int(fp, "inputrec->nkz", -1, ir1->nkz, ir2->nkz); + cmp_int(fp, "inputrec->pme_order", -1, ir1->pme_order, ir2->pme_order); + cmp_real(fp, "inputrec->ewald_rtol", -1, ir1->ewald_rtol, ir2->ewald_rtol, ftol, abstol); + cmp_int(fp, "inputrec->ewald_geometry", -1, ir1->ewald_geometry, ir2->ewald_geometry); + cmp_real(fp, "inputrec->epsilon_surface", -1, ir1->epsilon_surface, ir2->epsilon_surface, ftol, abstol); + cmp_int(fp, "inputrec->bContinuation", -1, ir1->bContinuation, ir2->bContinuation); + cmp_int(fp, "inputrec->bShakeSOR", -1, ir1->bShakeSOR, ir2->bShakeSOR); + cmp_int(fp, "inputrec->etc", -1, ir1->etc, ir2->etc); + cmp_int(fp, "inputrec->bPrintNHChains", -1, ir1->bPrintNHChains, ir2->bPrintNHChains); + cmp_int(fp, "inputrec->epc", -1, ir1->epc, ir2->epc); + cmp_int(fp, "inputrec->epct", -1, ir1->epct, ir2->epct); + cmp_real(fp, "inputrec->tau_p", -1, ir1->tau_p, ir2->tau_p, ftol, abstol); + cmp_rvec(fp, "inputrec->ref_p(x)", -1, ir1->ref_p[XX], ir2->ref_p[XX], ftol, abstol); + cmp_rvec(fp, "inputrec->ref_p(y)", -1, ir1->ref_p[YY], ir2->ref_p[YY], ftol, abstol); + cmp_rvec(fp, "inputrec->ref_p(z)", -1, ir1->ref_p[ZZ], ir2->ref_p[ZZ], ftol, abstol); + cmp_rvec(fp, "inputrec->compress(x)", -1, ir1->compress[XX], ir2->compress[XX], ftol, abstol); + cmp_rvec(fp, "inputrec->compress(y)", -1, ir1->compress[YY], ir2->compress[YY], ftol, abstol); + cmp_rvec(fp, "inputrec->compress(z)", -1, ir1->compress[ZZ], ir2->compress[ZZ], ftol, abstol); + cmp_int(fp, "refcoord_scaling", -1, ir1->refcoord_scaling, ir2->refcoord_scaling); + cmp_rvec(fp, "inputrec->posres_com", -1, ir1->posres_com, ir2->posres_com, ftol, abstol); + cmp_rvec(fp, "inputrec->posres_comB", -1, ir1->posres_comB, ir2->posres_comB, ftol, abstol); + cmp_real(fp, "inputrec->verletbuf_tol", -1, ir1->verletbuf_tol, ir2->verletbuf_tol, ftol, abstol); + cmp_real(fp, "inputrec->rlist", -1, ir1->rlist, ir2->rlist, ftol, abstol); + cmp_real(fp, "inputrec->rtpi", -1, ir1->rtpi, ir2->rtpi, ftol, abstol); + cmp_int(fp, "inputrec->coulombtype", -1, ir1->coulombtype, ir2->coulombtype); + cmp_int(fp, "inputrec->coulomb_modifier", -1, ir1->coulomb_modifier, ir2->coulomb_modifier); + cmp_real(fp, "inputrec->rcoulomb_switch", -1, ir1->rcoulomb_switch, ir2->rcoulomb_switch, ftol, abstol); + cmp_real(fp, "inputrec->rcoulomb", -1, ir1->rcoulomb, ir2->rcoulomb, ftol, abstol); + cmp_int(fp, "inputrec->vdwtype", -1, ir1->vdwtype, ir2->vdwtype); + cmp_int(fp, "inputrec->vdw_modifier", -1, ir1->vdw_modifier, ir2->vdw_modifier); cmp_real(fp, "inputrec->rvdw_switch", -1, ir1->rvdw_switch, ir2->rvdw_switch, ftol, abstol); + cmp_real(fp, "inputrec->rvdw", -1, ir1->rvdw, ir2->rvdw, ftol, abstol); + cmp_real(fp, "inputrec->epsilon_r", -1, ir1->epsilon_r, ir2->epsilon_r, ftol, abstol); + cmp_real(fp, "inputrec->epsilon_rf", -1, ir1->epsilon_rf, ir2->epsilon_rf, ftol, abstol); + cmp_real(fp, "inputrec->tabext", -1, ir1->tabext, ir2->tabext, ftol, abstol); + cmp_int(fp, "inputrec->implicit_solvent", -1, ir1->implicit_solvent, ir2->implicit_solvent); + cmp_int(fp, "inputrec->gb_algorithm", -1, ir1->gb_algorithm, ir2->gb_algorithm); + cmp_int(fp, "inputrec->nstgbradii", -1, ir1->nstgbradii, ir2->nstgbradii); + cmp_real(fp, "inputrec->rgbradii", -1, ir1->rgbradii, ir2->rgbradii, ftol, abstol); + cmp_real(fp, "inputrec->gb_saltconc", -1, ir1->gb_saltconc, ir2->gb_saltconc, ftol, abstol); + cmp_real(fp, "inputrec->gb_epsilon_solvent", -1, ir1->gb_epsilon_solvent, ir2->gb_epsilon_solvent, ftol, abstol); + cmp_real(fp, "inputrec->gb_obc_alpha", -1, ir1->gb_obc_alpha, ir2->gb_obc_alpha, ftol, abstol); + cmp_real(fp, "inputrec->gb_obc_beta", -1, ir1->gb_obc_beta, ir2->gb_obc_beta, ftol, abstol); + cmp_real(fp, "inputrec->gb_obc_gamma", -1, ir1->gb_obc_gamma, ir2->gb_obc_gamma, ftol, abstol); + cmp_real(fp, "inputrec->gb_dielectric_offset", -1, ir1->gb_dielectric_offset, ir2->gb_dielectric_offset, ftol, abstol); + cmp_int(fp, "inputrec->sa_algorithm", -1, ir1->sa_algorithm, ir2->sa_algorithm); + cmp_real(fp, "inputrec->sa_surface_tension", -1, ir1->sa_surface_tension, ir2->sa_surface_tension, ftol, abstol); + + cmp_int(fp, "inputrec->eDispCorr", -1, ir1->eDispCorr, ir2->eDispCorr); + cmp_real(fp, "inputrec->shake_tol", -1, ir1->shake_tol, ir2->shake_tol, ftol, abstol); + cmp_int(fp, "inputrec->efep", -1, ir1->efep, ir2->efep); + cmp_fepvals(fp, ir1->fepvals, ir2->fepvals, ftol, abstol); + cmp_int(fp, "inputrec->bSimTemp", -1, ir1->bSimTemp, ir2->bSimTemp); + if ((ir1->bSimTemp == ir2->bSimTemp) && (ir1->bSimTemp)) + { + cmp_simtempvals(fp, ir1->simtempvals, ir2->simtempvals, std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol); + } + cmp_int(fp, "inputrec->bExpanded", -1, ir1->bExpanded, ir2->bExpanded); + if ((ir1->bExpanded == ir2->bExpanded) && (ir1->bExpanded)) + { + cmp_expandedvals(fp, ir1->expandedvals, ir2->expandedvals, std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol); + } + cmp_int(fp, "inputrec->nwall", -1, ir1->nwall, ir2->nwall); + cmp_int(fp, "inputrec->wall_type", -1, ir1->wall_type, ir2->wall_type); + cmp_int(fp, "inputrec->wall_atomtype[0]", -1, ir1->wall_atomtype[0], ir2->wall_atomtype[0]); + cmp_int(fp, "inputrec->wall_atomtype[1]", -1, ir1->wall_atomtype[1], ir2->wall_atomtype[1]); + cmp_real(fp, "inputrec->wall_density[0]", -1, ir1->wall_density[0], ir2->wall_density[0], ftol, abstol); + cmp_real(fp, "inputrec->wall_density[1]", -1, ir1->wall_density[1], ir2->wall_density[1], ftol, abstol); + cmp_real(fp, "inputrec->wall_ewald_zfac", -1, ir1->wall_ewald_zfac, ir2->wall_ewald_zfac, ftol, abstol); + + cmp_bool(fp, "inputrec->bPull", -1, ir1->bPull, ir2->bPull); + if (ir1->bPull && ir2->bPull) + { + cmp_pull(fp); + } + + cmp_int(fp, "inputrec->eDisre", -1, ir1->eDisre, ir2->eDisre); + cmp_real(fp, "inputrec->dr_fc", -1, ir1->dr_fc, ir2->dr_fc, ftol, abstol); + cmp_int(fp, "inputrec->eDisreWeighting", -1, ir1->eDisreWeighting, ir2->eDisreWeighting); + cmp_int(fp, "inputrec->bDisreMixed", -1, ir1->bDisreMixed, ir2->bDisreMixed); + cmp_int(fp, "inputrec->nstdisreout", -1, ir1->nstdisreout, ir2->nstdisreout); + cmp_real(fp, "inputrec->dr_tau", -1, ir1->dr_tau, ir2->dr_tau, ftol, abstol); + cmp_real(fp, "inputrec->orires_fc", -1, ir1->orires_fc, ir2->orires_fc, ftol, abstol); + cmp_real(fp, "inputrec->orires_tau", -1, ir1->orires_tau, ir2->orires_tau, ftol, abstol); + cmp_int(fp, "inputrec->nstorireout", -1, ir1->nstorireout, ir2->nstorireout); + cmp_real(fp, "inputrec->em_stepsize", -1, ir1->em_stepsize, ir2->em_stepsize, ftol, abstol); + cmp_real(fp, "inputrec->em_tol", -1, ir1->em_tol, ir2->em_tol, ftol, abstol); + cmp_int(fp, "inputrec->niter", -1, ir1->niter, ir2->niter); + cmp_real(fp, "inputrec->fc_stepsize", -1, ir1->fc_stepsize, ir2->fc_stepsize, ftol, abstol); + cmp_int(fp, "inputrec->nstcgsteep", -1, ir1->nstcgsteep, ir2->nstcgsteep); + cmp_int(fp, "inputrec->nbfgscorr", 0, ir1->nbfgscorr, ir2->nbfgscorr); + cmp_int(fp, "inputrec->eConstrAlg", -1, ir1->eConstrAlg, ir2->eConstrAlg); + cmp_int(fp, "inputrec->nProjOrder", -1, ir1->nProjOrder, ir2->nProjOrder); + cmp_real(fp, "inputrec->LincsWarnAngle", -1, ir1->LincsWarnAngle, ir2->LincsWarnAngle, ftol, abstol); + cmp_int(fp, "inputrec->nLincsIter", -1, ir1->nLincsIter, ir2->nLincsIter); + cmp_real(fp, "inputrec->bd_fric", -1, ir1->bd_fric, ir2->bd_fric, ftol, abstol); + cmp_int64(fp, "inputrec->ld_seed", ir1->ld_seed, ir2->ld_seed); + cmp_real(fp, "inputrec->cos_accel", -1, ir1->cos_accel, ir2->cos_accel, ftol, abstol); + cmp_rvec(fp, "inputrec->deform(a)", -1, ir1->deform[XX], ir2->deform[XX], ftol, abstol); + cmp_rvec(fp, "inputrec->deform(b)", -1, ir1->deform[YY], ir2->deform[YY], ftol, abstol); + cmp_rvec(fp, "inputrec->deform(c)", -1, ir1->deform[ZZ], ir2->deform[ZZ], ftol, abstol); + + + cmp_int(fp, "inputrec->userint1", -1, ir1->userint1, ir2->userint1); + cmp_int(fp, "inputrec->userint2", -1, ir1->userint2, ir2->userint2); + cmp_int(fp, "inputrec->userint3", -1, ir1->userint3, ir2->userint3); + cmp_int(fp, "inputrec->userint4", -1, ir1->userint4, ir2->userint4); + cmp_real(fp, "inputrec->userreal1", -1, ir1->userreal1, ir2->userreal1, ftol, abstol); + cmp_real(fp, "inputrec->userreal2", -1, ir1->userreal2, ir2->userreal2, ftol, abstol); + cmp_real(fp, "inputrec->userreal3", -1, ir1->userreal3, ir2->userreal3, ftol, abstol); + cmp_real(fp, "inputrec->userreal4", -1, ir1->userreal4, ir2->userreal4, ftol, abstol); + cmp_grpopts(fp, &(ir1->opts), &(ir2->opts), ftol, abstol); + cmp_cosines(fp, "ex", ir1->ex, ir2->ex, ftol, abstol); + cmp_cosines(fp, "et", ir1->et, ir2->et, ftol, abstol); +} + +static void comp_pull_AB(FILE *fp, pull_params_t *pull, real ftol, real abstol) +{ + int i; + + for (i = 0; i < pull->ncoord; i++) + { + fprintf(fp, "comparing pull coord %d\n", i); + cmp_real(fp, "pull-coord->k", -1, pull->coord[i].k, pull->coord[i].kB, ftol, abstol); + } +} + +static void comp_state(t_state *st1, t_state *st2, + gmx_bool bRMSD, real ftol, real abstol) +{ + int i, j, nc; + + fprintf(stdout, "comparing flags\n"); + cmp_int(stdout, "flags", -1, st1->flags, st2->flags); + fprintf(stdout, "comparing box\n"); + cmp_rvecs(stdout, "box", DIM, st1->box, st2->box, FALSE, ftol, abstol); + fprintf(stdout, "comparing box_rel\n"); + cmp_rvecs(stdout, "box_rel", DIM, st1->box_rel, st2->box_rel, FALSE, ftol, abstol); + fprintf(stdout, "comparing boxv\n"); + cmp_rvecs(stdout, "boxv", DIM, st1->boxv, st2->boxv, FALSE, ftol, abstol); + if (st1->flags & (1<svir_prev, st2->svir_prev, ftol, abstol); ++ cmp_rvecs(stdout, "svir_prev", DIM, st1->svir_prev, st2->svir_prev, FALSE, ftol, abstol); + } + if (st1->flags & (1<fvir_prev, st2->fvir_prev, ftol, abstol); ++ cmp_rvecs(stdout, "fvir_prev", DIM, st1->fvir_prev, st2->fvir_prev, FALSE, ftol, abstol); + } + if (st1->flags & (1<pres_prev, st2->pres_prev, ftol, abstol); ++ cmp_rvecs(stdout, "pres_prev", DIM, st1->pres_prev, st2->pres_prev, FALSE, ftol, abstol); + } + cmp_int(stdout, "ngtc", -1, st1->ngtc, st2->ngtc); + cmp_int(stdout, "nhchainlength", -1, st1->nhchainlength, st2->nhchainlength); + if (st1->ngtc == st2->ngtc && st1->nhchainlength == st2->nhchainlength) + { + for (i = 0; i < st1->ngtc; i++) + { + nc = i*st1->nhchainlength; + for (j = 0; j < nc; j++) + { + cmp_real(stdout, "nosehoover_xi", + i, st1->nosehoover_xi[nc+j], st2->nosehoover_xi[nc+j], ftol, abstol); + } + } + } + cmp_int(stdout, "nnhpres", -1, st1->nnhpres, st2->nnhpres); + if (st1->nnhpres == st2->nnhpres && st1->nhchainlength == st2->nhchainlength) + { + for (i = 0; i < st1->nnhpres; i++) + { + nc = i*st1->nhchainlength; + for (j = 0; j < nc; j++) + { + cmp_real(stdout, "nosehoover_xi", + i, st1->nhpres_xi[nc+j], st2->nhpres_xi[nc+j], ftol, abstol); + } + } + } + + cmp_int(stdout, "natoms", -1, st1->natoms, st2->natoms); + if (st1->natoms == st2->natoms) + { + if ((st1->flags & (1<flags & (1<natoms, st1->x, st2->x, bRMSD, ftol, abstol); + } + if ((st1->flags & (1<flags & (1<natoms, st1->v, st2->v, bRMSD, ftol, abstol); + } + } +} + +void comp_tpx(const char *fn1, const char *fn2, + gmx_bool bRMSD, real ftol, real abstol) +{ + const char *ff[2]; + t_inputrec ir[2]; + t_state state[2]; + gmx_mtop_t mtop[2]; + t_topology top[2]; + int i; + + ff[0] = fn1; + ff[1] = fn2; + for (i = 0; i < (fn2 ? 2 : 1); i++) + { + read_tpx_state(ff[i], &(ir[i]), &state[i], &(mtop[i])); + } + if (fn2) + { + cmp_inputrec(stdout, &ir[0], &ir[1], ftol, abstol); + /* Convert gmx_mtop_t to t_topology. + * We should implement direct mtop comparison, + * but it might be useful to keep t_topology comparison as an option. + */ + top[0] = gmx_mtop_t_to_t_topology(&mtop[0]); + top[1] = gmx_mtop_t_to_t_topology(&mtop[1]); + cmp_top(stdout, &top[0], &top[1], ftol, abstol); + cmp_groups(stdout, &mtop[0].groups, &mtop[1].groups, + mtop[0].natoms, mtop[1].natoms); + comp_state(&state[0], &state[1], bRMSD, ftol, abstol); + } + else + { + if (ir[0].efep == efepNO) + { + fprintf(stdout, "inputrec->efep = %s\n", efep_names[ir[0].efep]); + } + else + { + if (ir[0].bPull) + { + comp_pull_AB(stdout, ir->pull, ftol, abstol); + } + /* Convert gmx_mtop_t to t_topology. + * We should implement direct mtop comparison, + * but it might be useful to keep t_topology comparison as an option. + */ + top[0] = gmx_mtop_t_to_t_topology(&mtop[0]); + cmp_top(stdout, &top[0], NULL, ftol, abstol); + } + } +} + +void comp_frame(FILE *fp, t_trxframe *fr1, t_trxframe *fr2, + gmx_bool bRMSD, real ftol, real abstol) +{ + fprintf(fp, "\n"); + cmp_int(fp, "flags", -1, fr1->flags, fr2->flags); + cmp_int(fp, "not_ok", -1, fr1->not_ok, fr2->not_ok); + cmp_int(fp, "natoms", -1, fr1->natoms, fr2->natoms); + cmp_real(fp, "t0", -1, fr1->t0, fr2->t0, ftol, abstol); + if (cmp_bool(fp, "bTitle", -1, fr1->bTitle, fr2->bTitle)) + { + cmp_str(fp, "title", -1, fr1->title, fr2->title); + } + if (cmp_bool(fp, "bStep", -1, fr1->bStep, fr2->bStep)) + { + cmp_int(fp, "step", -1, fr1->step, fr2->step); + } + cmp_int(fp, "step", -1, fr1->step, fr2->step); + if (cmp_bool(fp, "bTime", -1, fr1->bTime, fr2->bTime)) + { + cmp_real(fp, "time", -1, fr1->time, fr2->time, ftol, abstol); + } + if (cmp_bool(fp, "bLambda", -1, fr1->bLambda, fr2->bLambda)) + { + cmp_real(fp, "lambda", -1, fr1->lambda, fr2->lambda, ftol, abstol); + } + if (cmp_bool(fp, "bAtoms", -1, fr1->bAtoms, fr2->bAtoms)) + { + cmp_atoms(fp, fr1->atoms, fr2->atoms, ftol, abstol); + } + if (cmp_bool(fp, "bPrec", -1, fr1->bPrec, fr2->bPrec)) + { + cmp_real(fp, "prec", -1, fr1->prec, fr2->prec, ftol, abstol); + } + if (cmp_bool(fp, "bX", -1, fr1->bX, fr2->bX)) + { + cmp_rvecs(fp, "x", std::min(fr1->natoms, fr2->natoms), fr1->x, fr2->x, bRMSD, ftol, abstol); + } + if (cmp_bool(fp, "bV", -1, fr1->bV, fr2->bV)) + { + cmp_rvecs(fp, "v", std::min(fr1->natoms, fr2->natoms), fr1->v, fr2->v, bRMSD, ftol, abstol); + } + if (cmp_bool(fp, "bF", -1, fr1->bF, fr2->bF)) + { - if (bRMSD) - { - cmp_rvecs(fp, "f", std::min(fr1->natoms, fr2->natoms), fr1->f, fr2->f, bRMSD, ftol, abstol); - } - else - { - cmp_rvecs_rmstol(fp, "f", std::min(fr1->natoms, fr2->natoms), fr1->f, fr2->f, ftol, abstol); - } ++ cmp_rvecs(fp, "f", std::min(fr1->natoms, fr2->natoms), fr1->f, fr2->f, bRMSD, ftol, abstol); + } + if (cmp_bool(fp, "bBox", -1, fr1->bBox, fr2->bBox)) + { + cmp_rvecs(fp, "box", 3, fr1->box, fr2->box, FALSE, ftol, abstol); + } +} + +void comp_trx(const gmx_output_env_t *oenv, const char *fn1, const char *fn2, + gmx_bool bRMSD, real ftol, real abstol) +{ + int i; + const char *fn[2]; + t_trxframe fr[2]; + t_trxstatus *status[2]; + gmx_bool b[2]; + + fn[0] = fn1; + fn[1] = fn2; + fprintf(stderr, "Comparing trajectory files %s and %s\n", fn1, fn2); + for (i = 0; i < 2; i++) + { + b[i] = read_first_frame(oenv, &status[i], fn[i], &fr[i], TRX_READ_X|TRX_READ_V|TRX_READ_F); + } + + if (b[0] && b[1]) + { + do + { + comp_frame(stdout, &(fr[0]), &(fr[1]), bRMSD, ftol, abstol); + + for (i = 0; i < 2; i++) + { + b[i] = read_next_frame(oenv, status[i], &fr[i]); + } + } + while (b[0] && b[1]); + + for (i = 0; i < 2; i++) + { + if (b[i] && !b[1-i]) + { + fprintf(stdout, "\nEnd of file on %s but not on %s\n", fn[1-i], fn[i]); + } + close_trj(status[i]); + } + } + if (!b[0] && !b[1]) + { + fprintf(stdout, "\nBoth files read correctly\n"); + } +} + +static real ener_tensor_diag(int n, int *ind1, int *ind2, + gmx_enxnm_t *enm1, + int *tensi, int i, + t_energy e1[], t_energy e2[]) +{ + int d1, d2; + int j; + real prod1, prod2; + int nfound; + size_t len; + + d1 = tensi[i]/DIM; + d2 = tensi[i] - d1*DIM; + + /* Find the diagonal elements d1 and d2 */ + len = std::strlen(enm1[ind1[i]].name); + prod1 = 1; + prod2 = 1; + nfound = 0; + for (j = 0; j < n; j++) + { + if (tensi[j] >= 0 && + std::strlen(enm1[ind1[j]].name) == len && + std::strncmp(enm1[ind1[i]].name, enm1[ind1[j]].name, len-2) == 0 && + (tensi[j] == d1*DIM+d1 || tensi[j] == d2*DIM+d2)) + { + prod1 *= fabs(e1[ind1[j]].e); + prod2 *= fabs(e2[ind2[j]].e); + nfound++; + } + } + + if (nfound == 2) + { + return 0.5*(std::sqrt(prod1) + std::sqrt(prod2)); + } + else + { + return 0; + } +} + +static gmx_bool enernm_equal(const char *nm1, const char *nm2) +{ + int len1, len2; + + len1 = std::strlen(nm1); + len2 = std::strlen(nm2); + + /* Remove " (bar)" at the end of a name */ + if (len1 > 6 && std::strcmp(nm1+len1-6, " (bar)") == 0) + { + len1 -= 6; + } + if (len2 > 6 && std::strcmp(nm2+len2-6, " (bar)") == 0) + { + len2 -= 6; + } + + return (len1 == len2 && gmx_strncasecmp(nm1, nm2, len1) == 0); +} + +static void cmp_energies(FILE *fp, int step1, int step2, + t_energy e1[], t_energy e2[], + gmx_enxnm_t *enm1, + real ftol, real abstol, + int nre, int *ind1, int *ind2, int maxener) +{ + int i, ii; + int *tensi, len, d1, d2; + real ftol_i, abstol_i; + + snew(tensi, maxener); + /* Check for tensor elements ending on "-XX", "-XY", ... , "-ZZ" */ + for (i = 0; (i < maxener); i++) + { + ii = ind1[i]; + tensi[i] = -1; + len = std::strlen(enm1[ii].name); + if (len > 3 && enm1[ii].name[len-3] == '-') + { + d1 = enm1[ii].name[len-2] - 'X'; + d2 = enm1[ii].name[len-1] - 'X'; + if (d1 >= 0 && d1 < DIM && + d2 >= 0 && d2 < DIM) + { + tensi[i] = d1*DIM + d2; + } + } + } + + for (i = 0; (i < maxener); i++) + { + /* Check if this is an off-diagonal tensor element */ + if (tensi[i] >= 0 && tensi[i] != 0 && tensi[i] != 4 && tensi[i] != 8) + { + /* Turn on the relative tolerance check (4 is maximum relative diff.) */ + ftol_i = 5; + /* Do the relative tolerance through an absolute tolerance times + * the size of diagonal components of the tensor. + */ + abstol_i = ftol*ener_tensor_diag(nre, ind1, ind2, enm1, tensi, i, e1, e2); + if (debug) + { + fprintf(debug, "tensor '%s' val %f diag %f\n", + enm1[i].name, e1[i].e, abstol_i/ftol); + } + if (abstol_i > 0) + { + /* We found a diagonal, we need to check with the minimum tolerance */ + abstol_i = std::min(abstol_i, abstol); + } + else + { + /* We did not find a diagonal, ignore the relative tolerance check */ + abstol_i = abstol; + } + } + else + { + ftol_i = ftol; + abstol_i = abstol; + } + if (!equal_real(e1[ind1[i]].e, e2[ind2[i]].e, ftol_i, abstol_i)) + { + fprintf(fp, "%-15s step %3d: %12g, step %3d: %12g\n", + enm1[ind1[i]].name, + step1, e1[ind1[i]].e, + step2, e2[ind2[i]].e); + } + } + + sfree(tensi); +} + +#if 0 +static void cmp_disres(t_enxframe *fr1, t_enxframe *fr2, real ftol, real abstol) +{ + int i; + char bav[64], bt[64], bs[22]; + + cmp_int(stdout, "ndisre", -1, fr1->ndisre, fr2->ndisre); + if ((fr1->ndisre == fr2->ndisre) && (fr1->ndisre > 0)) + { + sprintf(bav, "step %s: disre rav", gmx_step_str(fr1->step, bs)); + sprintf(bt, "step %s: disre rt", gmx_step_str(fr1->step, bs)); + for (i = 0; (i < fr1->ndisre); i++) + { + cmp_real(stdout, bav, i, fr1->disre_rm3tav[i], fr2->disre_rm3tav[i], ftol, abstol); + cmp_real(stdout, bt, i, fr1->disre_rt[i], fr2->disre_rt[i], ftol, abstol); + } + } +} +#endif + +static void cmp_eblocks(t_enxframe *fr1, t_enxframe *fr2, real ftol, real abstol) +{ + int i, j, k; + char buf[64], bs[22]; + + cmp_int(stdout, "nblock", -1, fr1->nblock, fr2->nblock); + if ((fr1->nblock == fr2->nblock) && (fr1->nblock > 0)) + { + for (j = 0; (j < fr1->nblock); j++) + { + t_enxblock *b1, *b2; /* convenience vars */ + + b1 = &(fr1->block[j]); + b2 = &(fr2->block[j]); + + sprintf(buf, "step %s: block[%d]", gmx_step_str(fr1->step, bs), j); + cmp_int(stdout, buf, -1, b1->nsub, b2->nsub); + cmp_int(stdout, buf, -1, b1->id, b2->id); + + if ( (b1->nsub == b2->nsub) && (b1->id == b2->id) ) + { + for (i = 0; i < b1->nsub; i++) + { + t_enxsubblock *s1, *s2; + + s1 = &(b1->sub[i]); + s2 = &(b2->sub[i]); + + cmp_int(stdout, buf, -1, (int)s1->type, (int)s2->type); + cmp_int64(stdout, buf, s1->nr, s2->nr); + + if ((s1->type == s2->type) && (s1->nr == s2->nr)) + { + switch (s1->type) + { + case xdr_datatype_float: + for (k = 0; k < s1->nr; k++) + { + cmp_float(stdout, buf, i, + s1->fval[k], s2->fval[k], + ftol, abstol); + } + break; + case xdr_datatype_double: + for (k = 0; k < s1->nr; k++) + { + cmp_double(stdout, buf, i, + s1->dval[k], s2->dval[k], + ftol, abstol); + } + break; + case xdr_datatype_int: + for (k = 0; k < s1->nr; k++) + { + cmp_int(stdout, buf, i, + s1->ival[k], s2->ival[k]); + } + break; + case xdr_datatype_int64: + for (k = 0; k < s1->nr; k++) + { + cmp_int64(stdout, buf, + s1->lval[k], s2->lval[k]); + } + break; + case xdr_datatype_char: + for (k = 0; k < s1->nr; k++) + { + cmp_uc(stdout, buf, i, + s1->cval[k], s2->cval[k]); + } + break; + case xdr_datatype_string: + for (k = 0; k < s1->nr; k++) + { + cmp_str(stdout, buf, i, + s1->sval[k], s2->sval[k]); + } + break; + default: + gmx_incons("Unknown data type!!"); + } + } + } + } + } + } +} + +void comp_enx(const char *fn1, const char *fn2, real ftol, real abstol, const char *lastener) +{ + int nre, nre1, nre2; + ener_file_t in1, in2; + int i, j, maxener, *ind1, *ind2, *have; + gmx_enxnm_t *enm1 = NULL, *enm2 = NULL; + t_enxframe *fr1, *fr2; + gmx_bool b1, b2; + + fprintf(stdout, "comparing energy file %s and %s\n\n", fn1, fn2); + + in1 = open_enx(fn1, "r"); + in2 = open_enx(fn2, "r"); + do_enxnms(in1, &nre1, &enm1); + do_enxnms(in2, &nre2, &enm2); + if (nre1 != nre2) + { + fprintf(stdout, "There are %d and %d terms in the energy files\n\n", + nre1, nre2); + } + else + { + fprintf(stdout, "There are %d terms in the energy files\n\n", nre1); + } + + snew(ind1, nre1); + snew(ind2, nre2); + snew(have, nre2); + nre = 0; + for (i = 0; i < nre1; i++) + { + for (j = 0; j < nre2; j++) + { + if (enernm_equal(enm1[i].name, enm2[j].name)) + { + ind1[nre] = i; + ind2[nre] = j; + have[j] = 1; + nre++; + break; + } + } + if (nre == 0 || ind1[nre-1] != i) + { + cmp_str(stdout, "enm", i, enm1[i].name, "-"); + } + } + for (i = 0; i < nre2; i++) + { + if (have[i] == 0) + { + cmp_str(stdout, "enm", i, "-", enm2[i].name); + } + } + + maxener = nre; + for (i = 0; i < nre; i++) + { + if ((lastener != NULL) && (std::strstr(enm1[i].name, lastener) != NULL)) + { + maxener = i+1; + break; + } + } + + fprintf(stdout, "There are %d terms to compare in the energy files\n\n", + maxener); + + for (i = 0; i < maxener; i++) + { + cmp_str(stdout, "unit", i, enm1[ind1[i]].unit, enm2[ind2[i]].unit); + } + + snew(fr1, 1); + snew(fr2, 1); + do + { + b1 = do_enx(in1, fr1); + b2 = do_enx(in2, fr2); + if (b1 && !b2) + { + fprintf(stdout, "\nEnd of file on %s but not on %s\n", fn2, fn1); + } + else if (!b1 && b2) + { + fprintf(stdout, "\nEnd of file on %s but not on %s\n", fn1, fn2); + } + else if (!b1 && !b2) + { + fprintf(stdout, "\nFiles read successfully\n"); + } + else + { + cmp_real(stdout, "t", -1, fr1->t, fr2->t, ftol, abstol); + cmp_int(stdout, "step", -1, fr1->step, fr2->step); + /* We don't want to print the nre mismatch for every frame */ + /* cmp_int(stdout,"nre",-1,fr1->nre,fr2->nre); */ + if ((fr1->nre >= nre) && (fr2->nre >= nre)) + { + cmp_energies(stdout, fr1->step, fr1->step, fr1->ener, fr2->ener, + enm1, ftol, abstol, nre, ind1, ind2, maxener); + } + /*cmp_disres(fr1,fr2,ftol,abstol);*/ + cmp_eblocks(fr1, fr2, ftol, abstol); + } + } + while (b1 && b2); + + close_enx(in1); + close_enx(in2); + + free_enxframe(fr2); + sfree(fr2); + free_enxframe(fr1); + sfree(fr1); +}