#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
-using gmx::AwhParams;
using gmx::AwhBiasParams;
+using gmx::AwhParams;
namespace
{
/*! \brief All meta-data that is shared for one output file type for one bias */
class OutputFile
{
- public:
- /*! \brief Constructor, Set the output base file name and title.
- *
- * Result is a valid object, but will produce empty output files.
- *
- * \param[in] filename The name for output files, frame time, and possibly bias number, will be added per file/frame.
- * \param[in] baseTitle The base title of the plot, the bias number might be added.
- * \param[in] numBias The total number of AWH biases in the system.
- * \param[in] biasIndex The index of this bias.
- */
- OutputFile(const std::string &filename,
- const std::string &baseTitle,
- int numBias,
- int biasIndex);
-
- /*! \brief Initializes the output file setup for the AWH output.
- *
- * \param[in] subBlockStart Index of the first sub-block to write in the energy frame.
- * \param[in] numSubBlocks The total number of sub-blocks in the framw.
- * \param[in] awhBiasParams The AWH bias parameters.
- * \param[in] graphSelection Selects which graphs to plot.
- * \param[in] energyUnit Requested energy unit in output.
- * \param[in] kTValue kB*T in kJ/mol.
- */
- void initializeAwhOutputFile(int subBlockStart,
- int numSubBlocks,
- const AwhBiasParams *awhBiasParams,
- AwhGraphSelection graphSelection,
- EnergyUnit energyUnit,
- real kTValue);
-
- /*! \brief Initializes the output file setup for the fricion output.
- *
- * \param[in] subBlockStart Index of the first sub-block to write in the energy frame.
- * \param[in] numSubBlocks The total number of sub-blocks in the framw.
- * \param[in] awhBiasParams The AWH bias parameters.
- * \param[in] energyUnit Requested energy unit in output.
- * \param[in] kTValue kB*T in kJ/mol.
- */
- void initializeFrictionOutputFile(int subBlockStart,
- int numSubBlocks,
- const AwhBiasParams *awhBiasParams,
- EnergyUnit energyUnit,
- real kTValue);
-
- /*! \brief Opens a single output file for a bias, prints title and legends.
- *
- * \param[in] time The time for of frame to be written.
- * \param[in] oenv The output environment.
- * \returns the file pointer.
- */
- FILE * openBiasOutputFile(double time,
- const gmx_output_env_t *oenv) const;
-
- /*! \brief Writes data selected from \p block to file.
- *
- * \param[in] block The energy block with the data to write.
- * \param[in] subBlockStart The sub-block start index.
- * \param[in] fp The file pointer.
- */
- void writeData(const t_enxblock &block,
- int subBlockStart,
- FILE *fp) const;
-
- private:
- std::string baseFilename_; /**< Base of the output file name. */
- std::string title_; /**< Title for the graph. */
- int numDim_; /**< Number of dimensions. */
- int firstGraphSubBlock_; /**< Index in the energy sub-blocks for the first graph. */
- int numGraph_; /**< Number of actual graphs. */
- bool useKTForEnergy_; /**< Whether to use kT instead of kJ/mol for energy. */
- std::vector<real> scaleFactor_; /**< Scale factors from energy file data to output for each of the numGraph quantities. */
-
- std::vector<std::string> legend_; /**< Legends for the output */
- std::string xLabel_; /**< Label for the x-axis. */
- std::string yLabel_; /**< Label for the y-axis. */
+public:
+ /*! \brief Constructor, Set the output base file name and title.
+ *
+ * Result is a valid object, but will produce empty output files.
+ *
+ * \param[in] filename The name for output files, frame time, and possibly bias number, will be added per file/frame.
+ * \param[in] baseTitle The base title of the plot, the bias number might be added.
+ * \param[in] numBias The total number of AWH biases in the system.
+ * \param[in] biasIndex The index of this bias.
+ */
+ OutputFile(const std::string& filename, const std::string& baseTitle, int numBias, int biasIndex);
+
+ /*! \brief Initializes the output file setup for the AWH output.
+ *
+ * \param[in] subBlockStart Index of the first sub-block to write in the energy frame.
+ * \param[in] numSubBlocks The total number of sub-blocks in the framw.
+ * \param[in] awhBiasParams The AWH bias parameters.
+ * \param[in] graphSelection Selects which graphs to plot.
+ * \param[in] energyUnit Requested energy unit in output.
+ * \param[in] kTValue kB*T in kJ/mol.
+ */
+ void initializeAwhOutputFile(int subBlockStart,
+ int numSubBlocks,
+ const AwhBiasParams* awhBiasParams,
+ AwhGraphSelection graphSelection,
+ EnergyUnit energyUnit,
+ real kTValue);
+
+ /*! \brief Initializes the output file setup for the fricion output.
+ *
+ * \param[in] subBlockStart Index of the first sub-block to write in the energy frame.
+ * \param[in] numSubBlocks The total number of sub-blocks in the framw.
+ * \param[in] awhBiasParams The AWH bias parameters.
+ * \param[in] energyUnit Requested energy unit in output.
+ * \param[in] kTValue kB*T in kJ/mol.
+ */
+ void initializeFrictionOutputFile(int subBlockStart,
+ int numSubBlocks,
+ const AwhBiasParams* awhBiasParams,
+ EnergyUnit energyUnit,
+ real kTValue);
+
+ /*! \brief Opens a single output file for a bias, prints title and legends.
+ *
+ * \param[in] time The time for of frame to be written.
+ * \param[in] oenv The output environment.
+ * \returns the file pointer.
+ */
+ FILE* openBiasOutputFile(double time, const gmx_output_env_t* oenv) const;
+
+ /*! \brief Writes data selected from \p block to file.
+ *
+ * \param[in] block The energy block with the data to write.
+ * \param[in] subBlockStart The sub-block start index.
+ * \param[in] fp The file pointer.
+ */
+ void writeData(const t_enxblock& block, int subBlockStart, FILE* fp) const;
+
+private:
+ std::string baseFilename_; /**< Base of the output file name. */
+ std::string title_; /**< Title for the graph. */
+ int numDim_; /**< Number of dimensions. */
+ int firstGraphSubBlock_; /**< Index in the energy sub-blocks for the first graph. */
+ int numGraph_; /**< Number of actual graphs. */
+ bool useKTForEnergy_; /**< Whether to use kT instead of kJ/mol for energy. */
+ std::vector<real> scaleFactor_; /**< Scale factors from energy file data to output for each of the numGraph quantities. */
+
+ std::vector<std::string> legend_; /**< Legends for the output */
+ std::string xLabel_; /**< Label for the x-axis. */
+ std::string yLabel_; /**< Label for the y-axis. */
};
/*! \brief All meta-data that is shared for all output files for one bias */
}
//! Return the AWH output file data.
- const OutputFile &awhOutputFile() const
+ const OutputFile& awhOutputFile() const
{
- GMX_RELEASE_ASSERT(awhOutputFile_ != nullptr, "awhOutputFile() called without initialized AWH output file");
+ GMX_RELEASE_ASSERT(awhOutputFile_ != nullptr,
+ "awhOutputFile() called without initialized AWH output file");
return *awhOutputFile_;
}
//! Return the a pointer to the friction output file data, can return nullptr
- const OutputFile *frictionOutputFile() const
- {
- return frictionOutputFile_.get();
- }
+ const OutputFile* frictionOutputFile() const { return frictionOutputFile_.get(); }
//! Return the starting subblock.
- int subblockStart() const
- {
- return subblockStart_;
- }
+ int subblockStart() const { return subblockStart_; }
- private:
- const int subblockStart_; /**< The start index of the subblocks to read. */
- std::unique_ptr<OutputFile> awhOutputFile_; /**< The standard AWH output file data. */
- std::unique_ptr<OutputFile> frictionOutputFile_; /**< The friction/metric tensor output file data */
+private:
+ const int subblockStart_; /**< The start index of the subblocks to read. */
+ std::unique_ptr<OutputFile> awhOutputFile_; /**< The standard AWH output file data. */
+ std::unique_ptr<OutputFile> frictionOutputFile_; /**< The friction/metric tensor output file data */
};
/*! \brief All options and meta-data needed for the AWH output */
class AwhReader
{
- public:
- //! Constructor
- AwhReader(const AwhParams *awhParams,
- int numFileOptions,
- const t_filenm *filenames,
- AwhGraphSelection awhGraphSelection,
- EnergyUnit energyUnit,
- real kT,
- const t_enxblock *block);
-
- //! Extract and print AWH data for an AWH block of one energy frame
- void processAwhFrame(const t_enxblock &block,
- double time,
- const gmx_output_env_t *oenv) const;
-
- private:
- std::vector<BiasOutputSetup> biasOutputSetups_; /**< The output setups, one for each AWH bias. */
- public:
- const real kT_; /**< kB*T in kJ/mol. */
+public:
+ //! Constructor
+ AwhReader(const AwhParams* awhParams,
+ int numFileOptions,
+ const t_filenm* filenames,
+ AwhGraphSelection awhGraphSelection,
+ EnergyUnit energyUnit,
+ real kT,
+ const t_enxblock* block);
+
+ //! Extract and print AWH data for an AWH block of one energy frame
+ void processAwhFrame(const t_enxblock& block, double time, const gmx_output_env_t* oenv) const;
+
+private:
+ std::vector<BiasOutputSetup> biasOutputSetups_; /**< The output setups, one for each AWH bias. */
+public:
+ const real kT_; /**< kB*T in kJ/mol. */
};
namespace
//! Enum for selecting output file type.
enum class OutputFileType
{
- Awh, //!< AWH, all data except friction tensor.
- Friction //!< The full friction tensor.
+ Awh, //!< AWH, all data except friction tensor.
+ Friction //!< The full friction tensor.
};
/*! \brief The maximum number of observables per subblock, not including the full friction tensor.
constexpr int maxAwhGraphs = 6;
/*! \brief Constructs a legend for a standard awh output file */
-std::vector<std::string>makeLegend(const AwhBiasParams *awhBiasParams,
- OutputFileType outputFileType,
- size_t numLegend)
+std::vector<std::string> makeLegend(const AwhBiasParams* awhBiasParams,
+ OutputFileType outputFileType,
+ size_t numLegend)
{
- const std::array<std::string, maxAwhGraphs> legendBase =
- {
- { "PMF",
- "Coord bias",
- "Coord distr",
- "Ref value distr",
- "Target ref value distr",
+ const std::array<std::string, maxAwhGraphs> legendBase = {
+ { "PMF", "Coord bias", "Coord distr", "Ref value distr", "Target ref value distr",
"Friction metric" }
};
- std::vector<std::string> legend;
+ std::vector<std::string> legend;
/* Give legends to dimensions higher than the first */
for (int d = 1; d < awhBiasParams->ndim; d++)
{
break;
}
- GMX_RELEASE_ASSERT(legend.size() == numLegend, "The number of legends requested for printing and the number generated should be the same");
+ GMX_RELEASE_ASSERT(legend.size() == numLegend,
+ "The number of legends requested for printing and the number generated "
+ "should be the same");
return legend;
}
} // namespace
-OutputFile::OutputFile(const std::string &filename,
- const std::string &baseTitle,
- int numBias,
- int biasIndex) :
+OutputFile::OutputFile(const std::string& filename, const std::string& baseTitle, int numBias, int biasIndex) :
numDim_(0),
firstGraphSubBlock_(0),
numGraph_(0),
if (numBias > 1)
{
baseFilename_ += gmx::formatString("%d", biasIndex + 1);
- title_ += gmx::formatString(" %d", biasIndex + 1);
+ title_ += gmx::formatString(" %d", biasIndex + 1);
}
}
void OutputFile::initializeAwhOutputFile(int subblockStart,
int numSubBlocks,
- const AwhBiasParams *awhBiasParams,
+ const AwhBiasParams* awhBiasParams,
AwhGraphSelection graphSelection,
EnergyUnit energyUnit,
real kTValue)
if (graphSelection == AwhGraphSelection::All)
{
/* There are one metadata and ndim coordinate blocks */
- numGraph_ = std::min(numSubBlocks - 1 - numDim_,
- maxAwhGraphs);
+ numGraph_ = std::min(numSubBlocks - 1 - numDim_, maxAwhGraphs);
}
else
{
- numGraph_ = 1;
+ numGraph_ = 1;
}
- useKTForEnergy_ = (energyUnit == EnergyUnit::KT);
+ useKTForEnergy_ = (energyUnit == EnergyUnit::KT);
scaleFactor_.resize(numGraph_, 1);
if (!useKTForEnergy_)
{
int numLegend = numDim_ - 1 + numGraph_;
legend_ = makeLegend(awhBiasParams, OutputFileType::Awh, numLegend);
/* We could have both length and angle coordinates in a single bias */
- xLabel_ = "(nm or deg)";
- yLabel_ = useKTForEnergy_ ? "(k\\sB\\NT)" : "(kJ/mol)";
+ xLabel_ = "(nm or deg)";
+ yLabel_ = useKTForEnergy_ ? "(k\\sB\\NT)" : "(kJ/mol)";
if (graphSelection == AwhGraphSelection::All)
{
- yLabel_ += gmx::formatString(", (nm\\S-%d\\N or rad\\S-%d\\N), (-)",
- awhBiasParams->ndim, awhBiasParams->ndim);
+ yLabel_ += gmx::formatString(", (nm\\S-%d\\N or rad\\S-%d\\N), (-)", awhBiasParams->ndim,
+ awhBiasParams->ndim);
}
}
/*! \brief Initializes the output file setup for the fricion output (note that the filename is not set here). */
void OutputFile::initializeFrictionOutputFile(int subBlockStart,
int numSubBlocks,
- const AwhBiasParams *awhBiasParams,
+ const AwhBiasParams* awhBiasParams,
EnergyUnit energyUnit,
real kTValue)
{
/* The first subblock with actual graph y-values is index 1 + ndim */
numDim_ = awhBiasParams->ndim;
- int numTensorElements = (numDim_*(numDim_ + 1))/2;
+ int numTensorElements = (numDim_ * (numDim_ + 1)) / 2;
/* The friction tensor elements are always the last subblocks */
if (numSubBlocks < 1 + numDim_ + maxAwhGraphs + numTensorElements)
{
- gmx_fatal(FARGS, "You requested friction tensor output, but the AWH data in the energy file does not contain the friction tensor");
+ gmx_fatal(FARGS,
+ "You requested friction tensor output, but the AWH data in the energy file does "
+ "not contain the friction tensor");
}
- GMX_ASSERT(numSubBlocks == 1 + numDim_ + maxAwhGraphs + numTensorElements, "The number of sub-blocks per bias should be 1 + ndim + maxAwhGraphs + (ndim*(ndim + 1))/2");
+ GMX_ASSERT(numSubBlocks == 1 + numDim_ + maxAwhGraphs + numTensorElements,
+ "The number of sub-blocks per bias should be 1 + ndim + maxAwhGraphs + (ndim*(ndim "
+ "+ 1))/2");
firstGraphSubBlock_ = subBlockStart + numSubBlocks - numTensorElements;
numGraph_ = numTensorElements;
useKTForEnergy_ = (energyUnit == EnergyUnit::KT);
scaleFactor_.resize(numGraph_, useKTForEnergy_ ? 1 : kTValue);
- int numLegend = numDim_ - 1 + numGraph_;
- legend_ = makeLegend(awhBiasParams, OutputFileType::Friction, numLegend);
- xLabel_ = "(nm or deg)";
+ int numLegend = numDim_ - 1 + numGraph_;
+ legend_ = makeLegend(awhBiasParams, OutputFileType::Friction, numLegend);
+ xLabel_ = "(nm or deg)";
if (useKTForEnergy_)
{
- yLabel_ = "friction/k\\sB\\NT (nm\\S-2\\Nps or rad\\S-2\\Nps)";
+ yLabel_ = "friction/k\\sB\\NT (nm\\S-2\\Nps or rad\\S-2\\Nps)";
}
else
{
- yLabel_ = "friction (kJ mol\\S-1\\Nnm\\S-2\\Nps or kJ mol\\S-1\\Nrad\\S-2\\Nps)";
+ yLabel_ = "friction (kJ mol\\S-1\\Nnm\\S-2\\Nps or kJ mol\\S-1\\Nrad\\S-2\\Nps)";
}
}
-AwhReader::AwhReader(const AwhParams *awhParams,
+AwhReader::AwhReader(const AwhParams* awhParams,
int numFileOptions,
- const t_filenm *filenames,
+ const t_filenm* filenames,
AwhGraphSelection awhGraphSelection,
EnergyUnit energyUnit,
real kT,
- const t_enxblock *block) :
+ const t_enxblock* block) :
kT_(kT)
{
GMX_RELEASE_ASSERT(block != nullptr, "NULL pointer passed to initAwhReader");
int subblockStart = 0;
for (int k = 0; k < awhParams->numBias; k++)
{
- AwhBiasParams *awhBiasParams = &awhParams->awhBiasParams[k];
+ AwhBiasParams* awhBiasParams = &awhParams->awhBiasParams[k];
- int numSubBlocks = static_cast<int>(block->sub[subblockStart].fval[0]);
+ int numSubBlocks = static_cast<int>(block->sub[subblockStart].fval[0]);
- std::unique_ptr<OutputFile> awhOutputFile(new OutputFile(opt2fn("-o", numFileOptions, filenames), "AWH", awhParams->numBias, k));
+ std::unique_ptr<OutputFile> awhOutputFile(new OutputFile(
+ opt2fn("-o", numFileOptions, filenames), "AWH", awhParams->numBias, k));
- awhOutputFile->initializeAwhOutputFile(subblockStart, numSubBlocks,
- awhBiasParams, awhGraphSelection,
- energyUnit, kT);
+ awhOutputFile->initializeAwhOutputFile(subblockStart, numSubBlocks, awhBiasParams,
+ awhGraphSelection, energyUnit, kT);
std::unique_ptr<OutputFile> frictionOutputFile;
if (outputFriction)
{
- frictionOutputFile = std::make_unique<OutputFile>(opt2fn("-fric", numFileOptions, filenames), "Friction tensor", awhParams->numBias, k);
+ frictionOutputFile = std::make_unique<OutputFile>(
+ opt2fn("-fric", numFileOptions, filenames), "Friction tensor", awhParams->numBias, k);
- frictionOutputFile->initializeFrictionOutputFile(subblockStart, numSubBlocks, awhBiasParams, energyUnit, kT);
+ frictionOutputFile->initializeFrictionOutputFile(subblockStart, numSubBlocks,
+ awhBiasParams, energyUnit, kT);
}
- biasOutputSetups_.emplace_back(BiasOutputSetup(subblockStart,
- std::move(awhOutputFile),
+ biasOutputSetups_.emplace_back(BiasOutputSetup(subblockStart, std::move(awhOutputFile),
std::move(frictionOutputFile)));
subblockStart += numSubBlocks;
}
}
-FILE * OutputFile::openBiasOutputFile(double time,
- const gmx_output_env_t *oenv) const
+FILE* OutputFile::openBiasOutputFile(double time, const gmx_output_env_t* oenv) const
{
std::string filename = baseFilename_ + gmx::formatString("_t%g.xvg", time);
- FILE *fp = xvgropen(filename.c_str(), title_.c_str(), xLabel_, yLabel_, oenv);
+ FILE* fp = xvgropen(filename.c_str(), title_.c_str(), xLabel_, yLabel_, oenv);
xvgrLegend(fp, legend_, oenv);
return fp;
}
/*! \brief Prints data selected by \p outputFile from \p block to \p fp */
-void OutputFile::writeData(const t_enxblock &block,
- int subBlockStart,
- FILE *fp) const
+void OutputFile::writeData(const t_enxblock& block, int subBlockStart, FILE* fp) const
{
int numPoints = block.sub[subBlockStart + 1].nr;
for (int j = 0; j < numPoints; j++)
/* Print numGraph observables */
for (int i = 0; i < numGraph_; i++)
{
- fprintf(fp, " %g", block.sub[firstGraphSubBlock_ + i].fval[j]*scaleFactor_[i]);
+ fprintf(fp, " %g", block.sub[firstGraphSubBlock_ + i].fval[j] * scaleFactor_[i]);
}
fprintf(fp, "\n");
}
}
-void AwhReader::processAwhFrame(const t_enxblock &block,
- double time,
- const gmx_output_env_t *oenv) const
+void AwhReader::processAwhFrame(const t_enxblock& block, double time, const gmx_output_env_t* oenv) const
{
/* We look for AWH data every energy frame and count the no of AWH frames found. We only extract every 'skip' AWH frame. */
- for (const auto &setup : biasOutputSetups_)
+ for (const auto& setup : biasOutputSetups_)
{
const int subStart = setup.subblockStart();
/* Each frame and AWH instance extracted generates one xvg file. */
{
- const OutputFile &awhOutputFile = setup.awhOutputFile();
+ const OutputFile& awhOutputFile = setup.awhOutputFile();
- FILE *fpAwh = awhOutputFile.openBiasOutputFile(time, oenv);
+ FILE* fpAwh = awhOutputFile.openBiasOutputFile(time, oenv);
/* Now do the actual printing. Metadata in first subblock is treated separately. */
fprintf(fpAwh, "# AWH metadata: target error = %.2f kT = %.2f kJ/mol\n",
- block.sub[subStart].fval[1],
- block.sub[subStart].fval[1]*kT_);
+ block.sub[subStart].fval[1], block.sub[subStart].fval[1] * kT_);
- fprintf(fpAwh, "# AWH metadata: log sample weight = %4.2f\n",
- block.sub[subStart].fval[2]);
+ fprintf(fpAwh, "# AWH metadata: log sample weight = %4.2f\n", block.sub[subStart].fval[2]);
awhOutputFile.writeData(block, subStart, fpAwh);
gmx_ffclose(fpAwh);
}
- const OutputFile *frictionOutputFile = setup.frictionOutputFile();
+ const OutputFile* frictionOutputFile = setup.frictionOutputFile();
if (frictionOutputFile != nullptr)
{
- FILE *fpFriction = frictionOutputFile->openBiasOutputFile(time, oenv);
+ FILE* fpFriction = frictionOutputFile->openBiasOutputFile(time, oenv);
frictionOutputFile->writeData(block, subStart, fpFriction);
}
/*! \brief The main function for the AWH tool */
-int gmx_awh(int argc, char *argv[])
+int gmx_awh(int argc, char* argv[])
{
- const char *desc[] = {
- "[THISMODULE] extracts AWH data from an energy file.",
- "One or two files are written per AWH bias per time frame.",
- "The bias index, if more than one, is appended to the file, as well as",
- "the time of the frame. By default only the PMF is printed.",
- "With [TT]-more[tt] the bias, target and coordinate distributions",
- "are also printed.",
- "With [TT]-more[tt] the bias, target and coordinate distributions",
- "are also printed, as well as the metric sqrt(det(friction_tensor))",
- "normalized such that the average is 1.",
- "Option [TT]-fric[tt] prints all components of the friction tensor",
- "to an additional set of files."
- };
- static gmx_bool moreGraphs = FALSE;
- static int skip = 0;
- static gmx_bool kTUnit = FALSE;
- t_pargs pa[] = {
- { "-skip", FALSE, etINT, {&skip},
- "Skip number of frames between data points" },
- { "-more", FALSE, etBOOL, {&moreGraphs},
- "Print more output" },
- { "-kt", FALSE, etBOOL, {&kTUnit},
+ const char* desc[] = { "[THISMODULE] extracts AWH data from an energy file.",
+ "One or two files are written per AWH bias per time frame.",
+ "The bias index, if more than one, is appended to the file, as well as",
+ "the time of the frame. By default only the PMF is printed.",
+ "With [TT]-more[tt] the bias, target and coordinate distributions",
+ "are also printed.",
+ "With [TT]-more[tt] the bias, target and coordinate distributions",
+ "are also printed, as well as the metric sqrt(det(friction_tensor))",
+ "normalized such that the average is 1.",
+ "Option [TT]-fric[tt] prints all components of the friction tensor",
+ "to an additional set of files." };
+ static gmx_bool moreGraphs = FALSE;
+ static int skip = 0;
+ static gmx_bool kTUnit = FALSE;
+ t_pargs pa[] = {
+ { "-skip", FALSE, etINT, { &skip }, "Skip number of frames between data points" },
+ { "-more", FALSE, etBOOL, { &moreGraphs }, "Print more output" },
+ { "-kt",
+ FALSE,
+ etBOOL,
+ { &kTUnit },
"Print free energy output in units of kT instead of kJ/mol" }
};
- ener_file_t fp;
- t_inputrec ir;
- gmx_enxnm_t *enm = nullptr;
- t_enxframe *frame;
- int nre;
- gmx_output_env_t *oenv;
-
- t_filenm fnm[] = {
- { efEDR, "-f", nullptr, ffREAD },
- { efTPR, "-s", nullptr, ffREAD },
- { efXVG, "-o", "awh", ffWRITE },
- { efXVG, "-fric", "friction", ffOPTWR }
- };
- const int nfile = asize(fnm);
- if (!parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END,
- nfile, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ ener_file_t fp;
+ t_inputrec ir;
+ gmx_enxnm_t* enm = nullptr;
+ t_enxframe* frame;
+ int nre;
+ gmx_output_env_t* oenv;
+
+ t_filenm fnm[] = { { efEDR, "-f", nullptr, ffREAD },
+ { efTPR, "-s", nullptr, ffREAD },
+ { efXVG, "-o", "awh", ffWRITE },
+ { efXVG, "-fric", "friction", ffOPTWR } };
+ const int nfile = asize(fnm);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END, nfile, fnm,
+ asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
std::unique_ptr<AwhReader> awhReader;
/* Initiate counters */
- gmx_bool haveFrame;
- int awhFrameCounter = 0;
- int timeCheck = 0;
+ gmx_bool haveFrame;
+ int awhFrameCounter = 0;
+ int timeCheck = 0;
do
{
haveFrame = do_enx(fp, frame);
- bool useFrame = false;
+ bool useFrame = false;
- t_enxblock *block = nullptr;
+ t_enxblock* block = nullptr;
if (haveFrame)
{
*/
if (awhReader == nullptr)
{
- AwhGraphSelection awhGraphSelection = (moreGraphs ? AwhGraphSelection::All : AwhGraphSelection::Pmf);
- EnergyUnit energyUnit = (kTUnit ? EnergyUnit::KT : EnergyUnit::KJPerMol);
- awhReader =
- std::make_unique<AwhReader>(ir.awhParams,
- nfile, fnm,
- awhGraphSelection,
- energyUnit, BOLTZ*ir.opts.ref_t[0],
- block);
+ AwhGraphSelection awhGraphSelection =
+ (moreGraphs ? AwhGraphSelection::All : AwhGraphSelection::Pmf);
+ EnergyUnit energyUnit = (kTUnit ? EnergyUnit::KT : EnergyUnit::KJPerMol);
+ awhReader = std::make_unique<AwhReader>(ir.awhParams, nfile, fnm, awhGraphSelection,
+ energyUnit, BOLTZ * ir.opts.ref_t[0], block);
}
awhReader->processAwhFrame(*block, frame->t, oenv);
}
- }
- while (haveFrame && (timeCheck <= 0));
+ } while (haveFrame && (timeCheck <= 0));
fprintf(stderr, "\n");
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff