gmx_awh.cpp File Reference

#include "gmxpre.h"
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <algorithm>
#include <array>
#include <filesystem>
#include <memory>
#include <string>
#include <utility>
#include <vector>
#include "gromacs/applied_forces/awh/read_params.h"
#include "gromacs/commandline/filenm.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/filetypes.h"
#include "gromacs/fileio/oenv.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/awh_params.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/topology/topology.h"
#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"

Include dependency graph for gmx_awh.cpp:

Description

Tool for extracting AWH (Accelerated Weight Histogram) data from energy files.

Author

Viveca Lindahl

Berk Hess

Classes
class	OutputFile
	All meta-data that is shared for one output file type for one bias. More...
struct	BiasOutputSetup
	All meta-data that is shared for all output files for one bias. More...
class	AwhReader
	All options and meta-data needed for the AWH output. More...

Enumerations
enum	anonymous_namespace{gmx_awh.cpp}::AwhGraphSelection { anonymous_namespace{gmx_awh.cpp}::AwhGraphSelection::Pmf, anonymous_namespace{gmx_awh.cpp}::AwhGraphSelection::All }
	Enum for choosing AWH graph output. More...
enum	anonymous_namespace{gmx_awh.cpp}::EnergyUnit { anonymous_namespace{gmx_awh.cpp}::EnergyUnit::KJPerMol, anonymous_namespace{gmx_awh.cpp}::EnergyUnit::KT }
	Energy unit options. More...
enum	anonymous_namespace{gmx_awh.cpp}::OutputFileType { anonymous_namespace{gmx_awh.cpp}::OutputFileType::Awh, anonymous_namespace{gmx_awh.cpp}::OutputFileType::Friction }
	Enum for selecting output file type. More...

Functions
std::vector< std::string >	anonymous_namespace{gmx_awh.cpp}::makeLegend (const AwhBiasParams &awhBiasParams, OutputFileType outputFileType, size_t numLegend)
	Constructs a legend for a standard awh output file.
int	gmx_awh (int argc, char *argv[])
	The main function for the AWH tool.

Variables
constexpr int	anonymous_namespace{gmx_awh.cpp}::maxAwhGraphs = 6
	The maximum number of observables per subblock, not including the full friction tensor. More...