* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2011-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, 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.
#ifndef GMX_UTILITY_GMXASSERT_H
#define GMX_UTILITY_GMXASSERT_H
-#include "gromacs/utility/basedefinitions.h"
-
#include "current_function.h"
//! \addtogroup module_utility
#include <vector>
#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/arrayref.h"
#include "nblib/exception.h"
#include "nblib/simulationstate.h"
#include "nblib/simulationstateimpl.h"
*/
#include "nblib/integrator.h"
#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/arrayref.h"
#include "nblib/molecules.h"
#include "nblib/particletype.h"
#include "nblib/simulationstate.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2017,2019,2020,2021, 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.
#include <vector>
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/flags.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2019,2021, 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.
#include <vector>
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"
#include <algorithm>
#include <vector>
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/arrayref.h"
namespace gmx
* 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.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, 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.
#include <vector>
#include "gromacs/fileio/filetypes.h"
-#include "gromacs/utility/basedefinitions.h"
//! \addtogroup module_commandline
#define ftp2FILE(ftp, nfile, fnm, mode) gmx_ffopen(ftp2fn(ftp, nfile, fnm), mode)
//! Returns TRUE when this file type has been found on the cmd-line.
-gmx_bool ftp2bSet(int ftp, int nfile, const t_filenm fnm[]);
+bool ftp2bSet(int ftp, int nfile, const t_filenm fnm[]);
//! Returns TRUE when this option has been found on the cmd-line.
-gmx_bool opt2bSet(const char* opt, int nfile, const t_filenm fnm[]);
+bool opt2bSet(const char* opt, int nfile, const t_filenm fnm[]);
/*! \brief
* Returns the file name belonging top cmd-line option opt, or NULL when
const char* ftp2fn_null(int ftp, int nfile, const t_filenm fnm[]);
//! Returns whether or not this filenm is optional.
-gmx_bool is_optional(const t_filenm* fnm);
+bool is_optional(const t_filenm* fnm);
//! Returns whether or not this filenm is output.
-gmx_bool is_output(const t_filenm* fnm);
+bool is_output(const t_filenm* fnm);
//! Returns whether or not this filenm is set.
-gmx_bool is_set(const t_filenm* fnm);
+bool is_set(const t_filenm* fnm);
/*! \brief Return whether \c filename might have been produced by mdrun -noappend.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, 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.
#include "gromacs/commandline/filenm.h"
#include "gromacs/fileio/oenv.h"
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct gmx_output_env_t;
*/
const char** c;
/** Boolean value for etBOOL. */
- gmx_bool* b;
+ bool* b;
/** Vector value for etRVEC. */
rvec* rv;
} u;
*
* \p option must specify a valid argument in \p pa of the correct type.
*/
-gmx_bool opt2parg_bool(const char* option, int nparg, t_pargs pa[]);
+bool opt2parg_bool(const char* option, int nparg, t_pargs pa[]);
/*! \brief
* Returns value of an etREAL/etTIME option.
*
* \p option must specify a valid argument in \p pa.
*/
-gmx_bool opt2parg_bSet(const char* option, int nparg, const t_pargs* pa);
+bool opt2parg_bSet(const char* option, int nparg, const t_pargs* pa);
/** Add option -w to view output files (must be implemented in program). */
*
* \see gmx_run_cmain().
*/
-gmx_bool parse_common_args(int* argc,
- char* argv[],
- unsigned long Flags,
- int nfile,
- t_filenm fnm[],
- int npargs,
- t_pargs* pa,
- int ndesc,
- const char** desc,
- int nbugs,
- const char** bugs,
- gmx_output_env_t** oenv);
+bool parse_common_args(int* argc,
+ char* argv[],
+ unsigned long Flags,
+ int nfile,
+ t_filenm fnm[],
+ int npargs,
+ t_pargs* pa,
+ int ndesc,
+ const char** desc,
+ int nbugs,
+ const char** bugs,
+ gmx_output_env_t** oenv);
/*! \} */
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct cginfo_mb_t;
class MDLogger;
class RangePartitioning;
class VirtualSitesHandler;
+template<typename>
+class ArrayRef;
} // namespace gmx
/*! \brief Returns the global topology atom number belonging to local atom index i.
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/block.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/range.h"
#include "gromacs/utility/real.h"
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/gpu_utils/gpu_macros.h"
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct gmx_hw_info_t;
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/ifunc.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/classhelpers.h"
struct bonded_threading_t;
#include "gromacs/math/vec.h"
#include "gromacs/topology/ifunc.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct gmx_grppairener_t;
#include "gromacs/math/multidimarray.h"
#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
+#include "gromacs/utility/basedefinitions.h"
namespace gmx
{
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/idef.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"
int64_t step,
t_state* state,
real* dvdlambda,
- gmx_bool computeVirial,
+ bool computeVirial,
tensor constraintsVirial);
/*! \brief Constraint coordinates.
t_state* state,
ArrayRefWithPadding<RVec> xp,
real* dvdlambda,
- gmx_bool computeVirial,
+ bool computeVirial,
tensor constraintsVirial);
} // namespace gmx
#include <vector>
#include "gromacs/gpu_utils/hostallocator.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/unique_cptr.h"
of the histogram */
unsigned int maxbin[2]; /* highest bin number with data */
- int type; /* the block type according to dhbtDH, etc. */
- int derivative; /* The derivative direction (as an index in the lambda
- vector) if this delta_h contains derivatives */
- double* lambda; /* lambda vector (or NULL if not applicable) */
- int nlambda; /* length of the lambda vector */
- gmx_bool written; /* whether this data has already been written out */
+ int type; /* the block type according to dhbtDH, etc. */
+ int derivative; /* The derivative direction (as an index in the lambda
+ vector) if this delta_h contains derivatives */
+ double* lambda; /* lambda vector (or NULL if not applicable) */
+ int nlambda; /* length of the lambda vector */
+ bool written; /* whether this data has already been written out */
int64_t subblock_meta_l[5]; /* metadata for an mdebin subblock for
I/O: for histogram counts, etc.*/
t_mde_delta_h* dh_expanded; /* expanded ensemble output block (pointer
into dh) */
- double start_time; /* start time of the current dh collection */
- double delta_time; /* time difference between samples */
- gmx_bool start_time_set; /* whether the start time has been set */
- double start_lambda; /* starting lambda for continuous motion of state*/
- double delta_lambda; /* delta lambda, for continuous motion of state */
- double temperature; /* the temperature of the samples*/
+ double start_time; /* start time of the current dh collection */
+ double delta_time; /* time difference between samples */
+ bool start_time_set; /* whether the start time has been set */
+ double start_lambda; /* starting lambda for continuous motion of state*/
+ double delta_lambda; /* delta lambda, for continuous motion of state */
+ double temperature; /* the temperature of the samples*/
double* native_lambda_vec; /* The lambda vector describing the current
lambda state if it is set (NULL otherwise) */
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/idef.h"
-#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct gmx_domdec_t;
namespace gmx
{
class RangePartitioning;
+template<typename T>
+class ArrayRef;
/*! \brief The start value of the vsite indices in the ftype enum
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2021, 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.
#include <vector>
#include "gromacs/mdtypes/awh_correlation_history.h"
-#include "gromacs/utility/basedefinitions.h"
namespace gmx
{
#include <stddef.h>
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxmpi.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2018,2019,2020,2021, 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.
#include <memory>
#include <vector>
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
//! \cond INTERNAL
//! Lambda at start time
double start_lambda;
//! Whether the lambda value is set. Here for backward-compatibility.
- gmx_bool start_lambda_set;
+ bool start_lambda_set;
//! Read / write data from / to checkpoint object
template<gmx::CheckpointDataOperation operation>
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/idef.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
enum class DistanceRestraintWeighting : int;
typedef struct t_disresdata
{
DistanceRestraintWeighting dr_weighting; /* Weighting of pairs in one restraint */
- gmx_bool dr_bMixed; /* Use sqrt of the instantaneous times *
+ bool dr_bMixed; /* Use sqrt of the instantaneous times *
* the time averaged violation */
real dr_fc; /* Force constant for disres, *
* which is multiplied by a (possibly) *
#include <memory>
#include "gromacs/gpu_utils/hostallocator.h"
-#include "gromacs/math/arrayrefwithpadding.h"
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
namespace gmx
{
+template<typename T>
+class ArrayRef;
+template<typename T>
+class ArrayRefWithPadding;
enum class PinningPolicy : int;
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
#include "locality.h"
#include <vector>
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"
//! Free energy soft-core sigma for ?????
real sc_sigma_min;
//! Use softcore for the coulomb portion as well (default FALSE)
- gmx_bool bScCoul;
+ bool bScCoul;
//! Whether to print the dvdl term associated with this term; if it is not specified as separate, it is lumped with the FEP term
gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, bool> separate_dvdl;
//! Whether to write a separate dhdl.xvg file note: NOT a gmx_bool, but an enum
//! Random number seed for lambda mc switches
int lmc_seed;
//! Whether to use minumum variance weighting
- gmx_bool minvar;
+ bool minvar;
//! The number of samples needed before kicking into minvar routine
int minvarmin;
//! The offset for the variance in MinVar
//! Range of cvalues used for BAR
int c_range;
//! Whether to print symmetrized matrices
- gmx_bool bSymmetrizedTMatrix;
+ bool bSymmetrizedTMatrix;
//! How frequently to print the transition matrices
int nstTij;
//! Number of repetitions in the MC lambda jumps MRS -- VERIFY THIS
//! Starting delta for Wang-Landau
real init_wl_delta;
//! Use one over t convergence for Wang-Landau when the delta get sufficiently small
- gmx_bool bWLoneovert;
+ bool bWLoneovert;
//! Did we initialize the weights? TODO: REMOVE FOR 5.0, no longer needed with new logic
- gmx_bool bInit_weights;
+ bool bInit_weights;
//! To override the main temperature, or define it if it's not defined
real mc_temp;
//! User-specified initial weights to start with
//! Period between when a swap is attempted
int nstswap;
//! Use mass-weighted positions in split group
- gmx_bool massw_split[2];
+ bool massw_split[2];
/*! \brief Split cylinders defined by radius, upper and lower
* extension. The split cylinders define the channels and are
* each anchored in the center of the split group */
//! Periodic molecules
bool bPeriodicMols;
//! Continuation run: starting state is correct (ie. constrained)
- gmx_bool bContinuation;
+ bool bContinuation;
//! Temperature coupling
TemperatureCoupling etc;
//! Interval in steps for temperature coupling
int nsttcouple;
//! Whether to print nose-hoover chains
- gmx_bool bPrintNHChains;
+ bool bPrintNHChains;
//! Pressure coupling
PressureCoupling epc;
//! Pressure coupling type
//! Data for the FEP state
std::unique_ptr<t_lambda> fepvals;
//! Whether to do simulated tempering
- gmx_bool bSimTemp;
+ bool bSimTemp;
//! Variables for simulated tempering
std::unique_ptr<t_simtemp> simtempvals;
//! Whether expanded ensembles are used
- gmx_bool bExpanded;
+ bool bExpanded;
//! Expanded ensemble parameters
std::unique_ptr<t_expanded> expandedvals;
//! Type of distance restraining
//! Type of weighting of pairs in one restraints
DistanceRestraintWeighting eDisreWeighting;
//! Use combination of time averaged and instantaneous violations
- gmx_bool bDisreMixed;
+ bool bDisreMixed;
//! Frequency of writing pair distances to enx
int nstdisreout;
//! Time constant for memory function in disres
//! Number of iterations in the final LINCS step
int nLincsIter;
//! Use successive overrelaxation for shake
- gmx_bool bShakeSOR;
+ bool bShakeSOR;
//! Friction coefficient for BD (amu/ps)
real bd_fric;
//! Random seed for SD and BD
/* COM pulling data */
//! Do we do COM pulling?
- gmx_bool bPull;
+ bool bPull;
//! The data for center of mass pulling
std::unique_ptr<pull_params_t> pull;
/* AWH bias data */
//! Whether to use AWH biasing for PMF calculations
- gmx_bool bDoAwh;
+ bool bDoAwh;
//! AWH biasing parameters
std::unique_ptr<gmx::AwhParams> awhParams;
/* Enforced rotation data */
//! Whether to calculate enforced rotation potential(s)
- gmx_bool bRot;
+ bool bRot;
//! The data for enforced rotation potentials
t_rot* rot;
t_swapcoords* swap;
//! Whether the tpr makes an interactive MD session possible.
- gmx_bool bIMD;
+ bool bIMD;
//! Interactive molecular dynamics
t_IMD* imd;
//! Group options
t_grpopts opts;
//! QM/MM calculation
- gmx_bool bQMMM;
+ bool bQMMM;
/* Fields for removed features go here (better caching) */
//! Whether AdResS is enabled - always false if a valid .tpr was read
- gmx_bool bAdress;
+ bool bAdress;
//! Whether twin-range scheme is active - always false if a valid .tpr was read
- gmx_bool useTwinRange;
+ bool useTwinRange;
//! Whether we have constant acceleration - removed in GROMACS 2022
bool useConstantAcceleration;
int ir_optimal_nstpcouple(const t_inputrec* ir);
/* Returns if the Coulomb force or potential is switched to zero */
-gmx_bool ir_coulomb_switched(const t_inputrec* ir);
+bool ir_coulomb_switched(const t_inputrec* ir);
/* Returns if the Coulomb interactions are zero beyond the rcoulomb.
* Note: always returns TRUE for the Verlet cut-off scheme.
*/
-gmx_bool ir_coulomb_is_zero_at_cutoff(const t_inputrec* ir);
+bool ir_coulomb_is_zero_at_cutoff(const t_inputrec* ir);
/* As ir_coulomb_is_zero_at_cutoff, but also returns TRUE for user tabulated
* interactions, since these might be zero beyond rcoulomb.
*/
-gmx_bool ir_coulomb_might_be_zero_at_cutoff(const t_inputrec* ir);
+bool ir_coulomb_might_be_zero_at_cutoff(const t_inputrec* ir);
/* Returns if the Van der Waals force or potential is switched to zero */
-gmx_bool ir_vdw_switched(const t_inputrec* ir);
+bool ir_vdw_switched(const t_inputrec* ir);
/* Returns if the Van der Waals interactions are zero beyond the rvdw.
* Note: always returns TRUE for the Verlet cut-off scheme.
*/
-gmx_bool ir_vdw_is_zero_at_cutoff(const t_inputrec* ir);
+bool ir_vdw_is_zero_at_cutoff(const t_inputrec* ir);
/* As ir_vdw_is_zero_at_cutoff, but also returns TRUE for user tabulated
* interactions, since these might be zero beyond rvdw.
*/
-gmx_bool ir_vdw_might_be_zero_at_cutoff(const t_inputrec* ir);
+bool ir_vdw_might_be_zero_at_cutoff(const t_inputrec* ir);
/*! \brief Free memory from input record.
*
*/
void done_inputrec(t_inputrec* ir);
-void pr_inputrec(FILE* fp, int indent, const char* title, const t_inputrec* ir, gmx_bool bMDPformat);
+void pr_inputrec(FILE* fp, int indent, const char* title, const t_inputrec* ir, bool bMDPformat);
void cmp_inputrec(FILE* fp, const t_inputrec* ir1, const t_inputrec* ir2, real ftol, real abstol);
void comp_pull_AB(FILE* fp, const pull_params_t& pull, real ftol, real abstol);
-gmx_bool inputrecDeform(const t_inputrec* ir);
+bool inputrecDeform(const t_inputrec* ir);
-gmx_bool inputrecDynamicBox(const t_inputrec* ir);
+bool inputrecDynamicBox(const t_inputrec* ir);
-gmx_bool inputrecPreserveShape(const t_inputrec* ir);
+bool inputrecPreserveShape(const t_inputrec* ir);
-gmx_bool inputrecNeedMutot(const t_inputrec* ir);
+bool inputrecNeedMutot(const t_inputrec* ir);
-gmx_bool inputrecTwinRange(const t_inputrec* ir);
+bool inputrecTwinRange(const t_inputrec* ir);
-gmx_bool inputrecExclForces(const t_inputrec* ir);
+bool inputrecExclForces(const t_inputrec* ir);
-gmx_bool inputrecNptTrotter(const t_inputrec* ir);
+bool inputrecNptTrotter(const t_inputrec* ir);
-gmx_bool inputrecNvtTrotter(const t_inputrec* ir);
+bool inputrecNvtTrotter(const t_inputrec* ir);
-gmx_bool inputrecNphTrotter(const t_inputrec* ir);
+bool inputrecNphTrotter(const t_inputrec* ir);
/*! \brief Return true if the simulation is 2D periodic with two walls. */
bool inputrecPbcXY2Walls(const t_inputrec* ir);
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/alignedallocator.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct t_lambda;
#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
#define GMX_MDTYPES_MDATOM_H
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
enum class ParticleType : int;
//! Number of energy groups
int nenergrp;
//! Do we have multiple center of mass motion removal groups
- gmx_bool bVCMgrps;
+ bool bVCMgrps;
//! Do we have any virtual sites?
- gmx_bool haveVsites;
+ bool haveVsites;
//! Do we have atoms that are frozen along 1 or 2 (not 3) dimensions?
- gmx_bool havePartiallyFrozenAtoms;
+ bool havePartiallyFrozenAtoms;
//! Number of perturbed atoms
int nPerturbed;
//! Number of atoms for which the mass is perturbed
//! Number of atoms for which the type is perturbed
int nTypePerturbed;
//! Do we have orientation restraints
- gmx_bool bOrires;
+ bool bOrires;
//! Atomic mass in A state
real* massA;
//! Atomic mass in B state
//! Van der Waals radius sigma^3 in the B state
real* sigma3B;
//! Is this atom perturbed
- gmx_bool* bPerturbed;
+ bool* bPerturbed;
//! Type of atom in the A state
int* typeA;
//! Type of atom in the B state
#include "gromacs/math/paddedvector.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"
public:
ekinstate_t();
- gmx_bool bUpToDate; //!< Test if all data is up to date
+ bool bUpToDate; //!< Test if all data is up to date
int ekin_n; //!< The number of tensors
tensor* ekinh; //!< Half step Ekin, size \p ekin_n
tensor* ekinf; //!< Full step Ekin, size \p ekin_n
{
int nlambda; //!< total number of lambda states - for history
- gmx_bool bEquil; //!< Have we reached equilibration
- int* n_at_lam; //!< number of points observed at each lambda
- real* wl_histo; //!< histogram for WL flatness determination
- real wl_delta; //!< current wang-landau delta
+ bool bEquil; //!< Have we reached equilibration
+ int* n_at_lam; //!< number of points observed at each lambda
+ real* wl_histo; //!< histogram for WL flatness determination
+ real wl_delta; //!< current wang-landau delta
real* sum_weights; //!< weights of the states
real* sum_dg; //!< free energies of the states -- not actually used for weighting, but informational
void init_dfhist_state(t_state* state, int dfhistNumLambda);
/*! \brief Compares two states, write the differences to stdout */
-void comp_state(const t_state* st1, const t_state* st2, gmx_bool bRMSD, real ftol, real abstol);
+void comp_state(const t_state* st1, const t_state* st2, bool bRMSD, real ftol, real abstol);
/*! \brief Allocates an rvec pointer and copy the contents of v to it */
rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n);
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2016,2017 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, 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.
#include "gromacs/onlinehelp/helpwritercontext.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/basedefinitions.h"
namespace gmx
{
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, 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.
#include <string>
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"
struct gmx_domdec_t;
struct gmx_mtop_t;
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+} // namespace gmx
+
//! Enumeration that contains all supported periodic boundary setups.
enum class PbcType : int
{
* \param[in] box The simulation cell
* \return TRUE when the box was corrected.
*/
-gmx_bool correct_box(FILE* fplog, int step, tensor box);
+bool correct_box(FILE* fplog, int step, tensor box);
/*! \brief Initiate the periodic boundary condition algorithms.
*
* \param[in] box The box tensor
* \return the pbc structure when pbc operations are required, NULL otherwise.
*/
-t_pbc* set_pbc_dd(t_pbc* pbc, PbcType pbcType, const ivec domdecCells, gmx_bool bSingleDir, const matrix box);
+t_pbc* set_pbc_dd(t_pbc* pbc, PbcType pbcType, const ivec domdecCells, bool bSingleDir, const matrix box);
/*! \brief Compute distance with PBC
*
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2018,2019,2020,2021, 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.
#include <vector>
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/range.h"
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, 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.
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/ifunc.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct gmx_ffparams_t;
const char* title,
const t_functype* functype,
const InteractionList& ilist,
- gmx_bool bShowNumbers,
- gmx_bool bShowParameters,
+ bool bShowNumbers,
+ bool bShowParameters,
const t_iparams* iparams);
-void pr_idef(FILE* fp, int indent, const char* title, const t_idef* idef, gmx_bool bShowNumbers, gmx_bool bShowParameters);
+void pr_idef(FILE* fp, int indent, const char* title, const t_idef* idef, bool bShowNumbers, bool bShowParameters);
/*! \brief
* Properly initialize idef struct.
#include <boost/stl_interfaces/iterator_interface.hpp>
#include "gromacs/topology/topology.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/enumerationhelpers.h"
struct gmx_localtop_t;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2017,2018,2019,2020,2021, 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.
#include <unordered_map>
#include <vector>
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
struct t_commrec;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, 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.
#include <array>
#include <stdexcept>
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, 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.
#include <type_traits>
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff