/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2017,2018,2019, 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/gmxana/gmx_ana.h"
#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
-#include "gromacs/mdlib/mdebin.h"
+#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/dir_separator.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
-#include "gromacs/mdlib/mdebin.h"
+#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/trajectory/energyframe.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
-#include "gromacs/mdlib/mdebin.h"
+#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
-#include "gromacs/mdlib/mdebin.h"
+#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/trajectoryanalysis/topologyinformation.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018,2019, 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/mdlib/mdrun.h"
#include "gromacs/mdlib/sighandler.h"
#include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdlib/update.h"
#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/basedefinitions.h"
/* This is a running averaging structure ('energy bin') for use during mdrun. */
-typedef struct {
+struct t_ebin
+{
int nener;
gmx_enxnm_t *enm;
int64_t nsteps;
int64_t nsteps_sim;
int64_t nsum_sim;
t_energy *e_sim;
-} t_ebin;
+};
enum {
eprNORMAL, eprAVER, eprRMS, eprNR
*/
#include "gmxpre.h"
-#include "mdebin.h"
+#include "energyoutput.h"
#include <cfloat>
#include <cstdlib>
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/ebin.h"
#include "gromacs/mdlib/mdebin_bar.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdtypes/energyhistory.h"
"Coul-14", "LJ-14", nullptr
};
+/* forward declaration */
+typedef struct t_mde_delta_h_coll t_mde_delta_h_coll;
+
+namespace gmx
+{
+
+namespace detail
+{
+
+/* This is the collection of energy averages collected during mdrun, and to
+ be written out to the .edr file. */
+struct t_mdebin
+{
+ double delta_t;
+ t_ebin *ebin;
+ int ie, iconrmsd, ib, ivol, idens, ipv, ienthalpy;
+ int isvir, ifvir, ipres, ivir, isurft, ipc, itemp, itc, itcb, iu, imu;
+ int ivcos, ivisc;
+ int nE, nEg, nEc, nTC, nTCP, nU, nNHC;
+ int *igrp;
+ int mde_n, mdeb_n;
+ real *tmp_r;
+ rvec *tmp_v;
+ gmx_bool bConstr;
+ gmx_bool bConstrVir;
+ gmx_bool bTricl;
+ gmx_bool bDynBox;
+ gmx_bool bNHC_trotter;
+ gmx_bool bPrintNHChains;
+ gmx_bool bMTTK;
+ gmx_bool bMu; /* true if dipole is calculated */
+ gmx_bool bDiagPres;
+ gmx_bool bPres;
+ int f_nre;
+ int epc;
+ real ref_p;
+ int etc;
+ int nCrmsd;
+ gmx_bool bEner[F_NRE];
+ gmx_bool bEInd[egNR];
+ char **print_grpnms;
+
+ FILE *fp_dhdl; /* the dhdl.xvg output file */
+ double *dE; /* energy components for dhdl.xvg output */
+ t_mde_delta_h_coll *dhc; /* the delta U components (raw data + histogram) */
+ real *temperatures;
+};
+
+} // namespace detail
+
+using detail::t_mdebin;
+
+namespace
+{
+
+//! Legacy init function
t_mdebin *init_mdebin(ener_file_t fp_ene,
const gmx_mtop_t *mtop,
const t_inputrec *ir,
return md;
}
+//! Legacy cleanup function
void done_mdebin(t_mdebin *mdebin)
{
sfree(mdebin->igrp);
sfree(mdebin);
}
+} // namespace
+} // namespace gmx
+
/* print a lambda vector to a string
fep = the inputrec's FEP input data
i = the index of the lambda vector
}
}
-
-extern FILE *open_dhdl(const char *filename, const t_inputrec *ir,
- const gmx_output_env_t *oenv)
+FILE *open_dhdl(const char *filename, const t_inputrec *ir,
+ const gmx_output_env_t *oenv)
{
FILE *fp;
const char *dhdl = "dH/d\\lambda", *deltag = "\\DeltaH", *lambda = "\\lambda",
return fp;
}
+namespace gmx
+{
+namespace
+{
+
+//! Legacy update function
void upd_mdebin(t_mdebin *md,
gmx_bool bDoDHDL,
gmx_bool bSum,
}
}
+} // namespace
-void upd_mdebin_step(t_mdebin *md)
+void EnergyOutput::recordNonEnergyStep()
{
- ebin_increase_count(md->ebin, FALSE);
+ ebin_increase_count(mdebin->ebin, false);
}
-static void npr(FILE *log, int n, char c)
+namespace
+{
+
+//! Legacy output function
+void npr(FILE *log, int n, char c)
{
for (; (n > 0); n--)
{
}
}
-static void pprint(FILE *log, const char *s, t_mdebin *md)
+//! Legacy output function
+void pprint(FILE *log, const char *s, t_mdebin *md)
{
char CHAR = '#';
int slen;
fprintf(log, "\n");
}
+} // namespace
+
void print_ebin_header(FILE *log, int64_t steps, double time)
{
char buf[22];
"Step", "Time", gmx_step_str(steps, buf), time);
}
+namespace
+{
+
// TODO It is too many responsibilities for this function to handle
// both .edr and .log output for both per-time and time-average data.
+//! Legacy ebin output function
void print_ebin(ener_file_t fp_ene, gmx_bool bEne, gmx_bool bDR, gmx_bool bOR,
FILE *log,
int64_t step, double time,
}
+//! Legacy update function
void update_energyhistory(energyhistory_t * enerhist, const t_mdebin * mdebin)
{
const t_ebin * const ebin = mdebin->ebin;
}
}
+//! Legacy restore function
void restore_energyhistory_from_state(t_mdebin * mdebin,
const energyhistory_t * enerhist)
{
mde_delta_h_coll_restore_energyhistory(mdebin->dhc, enerhist->deltaHForeignLambdas.get());
}
}
+
+} // namespace
+
+EnergyOutput::EnergyOutput()
+ : mdebin(nullptr)
+{
+}
+
+void EnergyOutput::prepare(ener_file *fp_ene,
+ const gmx_mtop_t *mtop,
+ const t_inputrec *ir,
+ FILE *fp_dhdl,
+ bool isRerun)
+{
+ mdebin = init_mdebin(fp_ene, mtop, ir, fp_dhdl, isRerun);
+}
+
+EnergyOutput::~EnergyOutput()
+{
+ done_mdebin(mdebin);
+}
+
+t_ebin *EnergyOutput::getEbin()
+{
+ return mdebin->ebin;
+}
+
+void EnergyOutput::addDataAtEnergyStep(bool bDoDHDL,
+ bool bSum,
+ double time,
+ real tmass,
+ gmx_enerdata_t *enerd,
+ t_state *state,
+ t_lambda *fep,
+ t_expanded *expand,
+ matrix box,
+ tensor svir,
+ tensor fvir,
+ tensor vir,
+ tensor pres,
+ gmx_ekindata_t *ekind,
+ rvec mu_tot,
+ const gmx::Constraints *constr)
+{
+ upd_mdebin(mdebin, bDoDHDL, bSum, time, tmass, enerd, state, fep,
+ expand, box, svir, fvir, vir, pres, ekind, mu_tot, constr);
+}
+
+void EnergyOutput::printStepToEnergyFile(ener_file *fp_ene, bool bEne, bool bDR, bool bOR,
+ FILE *log,
+ int64_t step, double time,
+ int mode,
+ t_fcdata *fcd,
+ gmx_groups_t *groups, t_grpopts *opts,
+ gmx::Awh *awh)
+{
+ print_ebin(fp_ene, bEne, bDR, bOR, log, step, time, mode,
+ mdebin, fcd, groups, opts, awh);
+}
+
+int EnergyOutput::numEnergyTerms() const
+{
+ return mdebin->ebin->nener;
+}
+
+void EnergyOutput::fillEnergyHistory(energyhistory_t *enerhist) const
+{
+ update_energyhistory(enerhist, mdebin);
+}
+
+void EnergyOutput::restoreFromEnergyHistory(const energyhistory_t &enerhist)
+{
+ restore_energyhistory_from_state(mdebin, &enerhist);
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, 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.
+ */
+#ifndef GMX_MDLIB_ENERGYOUTPUT_H
+#define GMX_MDLIB_ENERGYOUTPUT_H
+
+#include <cstdio>
+
+#include "gromacs/mdtypes/enerdata.h"
+
+class energyhistory_t;
+struct ener_file;
+struct gmx_ekindata_t;
+struct gmx_enerdata_t;
+struct gmx_groups_t;
+struct gmx_mtop_t;
+struct gmx_output_env_t;
+struct t_ebin;
+struct t_expanded;
+struct t_fcdata;
+struct t_grpopts;
+struct t_inputrec;
+struct t_lambda;
+class t_state;
+
+namespace gmx
+{
+class Awh;
+class Constraints;
+}
+
+extern const char *egrp_nm[egNR+1];
+
+/* delta_h block type enum: the kinds of energies written out. */
+enum
+{
+ dhbtDH = 0, /* delta H BAR energy difference*/
+ dhbtDHDL = 1, /* dH/dlambda derivative */
+ dhbtEN, /* System energy */
+ dhbtPV, /* pV term */
+ dhbtEXPANDED, /* expanded ensemble statistics */
+ dhbtNR
+};
+
+namespace gmx
+{
+
+// TODO remove use of detail namespace when removing t_mdebin in
+// favour of an Impl class.
+namespace detail
+{
+struct t_mdebin;
+}
+
+/* The functions & data structures here determine the content for outputting
+ the .edr file; the file format and actual writing is done with functions
+ defined in enxio.h */
+
+class EnergyOutput
+{
+ public:
+ EnergyOutput();
+ /*! \brief Initiate MD energy bin
+ *
+ * This second phase of construction is needed until we have
+ * modules that understand how to request output from
+ * EnergyOutput.
+ *
+ * \todo Refactor to separate a function to write the energy
+ * file header. Perhaps transform the remainder into a factory
+ * function.
+ */
+ void prepare(ener_file *fp_ene,
+ const gmx_mtop_t *mtop,
+ const t_inputrec *ir,
+ FILE *fp_dhdl,
+ bool isRerun = false);
+ ~EnergyOutput();
+ /*! \brief Update the averaging structures.
+ *
+ * Called every step on which the energies are evaluated. */
+ void addDataAtEnergyStep(bool bDoDHDL,
+ bool bSum,
+ double time,
+ real tmass,
+ gmx_enerdata_t *enerd,
+ t_state *state,
+ t_lambda *fep,
+ t_expanded *expand,
+ matrix lastbox,
+ tensor svir,
+ tensor fvir,
+ tensor vir,
+ tensor pres,
+ gmx_ekindata_t *ekind,
+ rvec mu_tot,
+ const gmx::Constraints *constr);
+ /*! \brief Updated the averaging structures
+ *
+ * Called every step on which the energies are not evaluated.
+ *
+ * \todo This schedule is known in advance, and should be made
+ * an intrinsic behaviour of EnergyOutput, rather than being
+ * wastefully called every step. */
+ void recordNonEnergyStep();
+
+ /*! \brief Help write quantites to the energy file
+ *
+ * \todo Perhaps this responsibility should involve some other
+ * object visiting all the contributing objects. */
+ void printStepToEnergyFile(ener_file *fp_ene, bool bEne, bool bDR, bool bOR,
+ FILE *log,
+ int64_t step, double time,
+ int mode,
+ t_fcdata *fcd,
+ gmx_groups_t *groups, t_grpopts *opts,
+ gmx::Awh *awh);
+ /*! \brief Get the number of energy terms recorded.
+ *
+ * \todo Refactor this to return the expected output size,
+ * rather than exposing the implementation details about
+ * energy terms. */
+ int numEnergyTerms() const;
+ /*! \brief Getter used for testing t_ebin
+ *
+ * \todo Find a better approach for this. */
+ t_ebin *getEbin();
+
+ /* Between .edr writes, the averages are history dependent,
+ and that history needs to be retained in checkpoints.
+ These functions set/read the energyhistory_t class
+ that is written to checkpoints in checkpoint.c */
+
+ //! Fill the energyhistory_t data.
+ void fillEnergyHistory(energyhistory_t * enerhist) const;
+ //! Restore from energyhistory_t data.
+ void restoreFromEnergyHistory(const energyhistory_t &enerhist);
+
+ private:
+ // TODO transform this into an impl class.
+ detail::t_mdebin *mdebin = nullptr;
+};
+
+} // namespace gmx
+
+//! Open the dhdl file for output
+FILE *open_dhdl(const char *filename, const t_inputrec *ir,
+ const gmx_output_env_t *oenv);
+
+namespace gmx
+{
+
+//! Print an energy-output header to the log file
+void print_ebin_header(FILE *log, int64_t steps, double time);
+
+} // namespace gmx
+
+#endif
#include "gromacs/mdlib/vcm.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/df_history.h"
+#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/energyhistory.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/group.h"
+++ /dev/null
-/*
- * 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) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * 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.
- */
-#ifndef GMX_MDLIB_MDEBIN_H
-#define GMX_MDLIB_MDEBIN_H
-
-#include <stdio.h>
-
-#include "gromacs/fileio/enxio.h"
-#include "gromacs/mdlib/ebin.h"
-#include "gromacs/mdtypes/enerdata.h"
-
-class energyhistory_t;
-struct gmx_ekindata_t;
-struct gmx_enerdata_t;
-struct gmx_mtop_t;
-struct gmx_output_env_t;
-struct t_expanded;
-struct t_fcdata;
-struct t_grpopts;
-struct t_lambda;
-class t_state;
-
-namespace gmx
-{
-class Awh;
-class Constraints;
-}
-
-extern const char *egrp_nm[egNR+1];
-
-/* The functions & data structures here determine the content for outputting
- the .edr file; the file format and actual writing is done with functions
- defined in enxio.h */
-
-/* forward declaration */
-typedef struct t_mde_delta_h_coll t_mde_delta_h_coll;
-
-
-/* This is the collection of energy averages collected during mdrun, and to
- be written out to the .edr file. */
-typedef struct t_mdebin {
- double delta_t;
- t_ebin *ebin;
- int ie, iconrmsd, ib, ivol, idens, ipv, ienthalpy;
- int isvir, ifvir, ipres, ivir, isurft, ipc, itemp, itc, itcb, iu, imu;
- int ivcos, ivisc;
- int nE, nEg, nEc, nTC, nTCP, nU, nNHC;
- int *igrp;
- int mde_n, mdeb_n;
- real *tmp_r;
- rvec *tmp_v;
- gmx_bool bConstr;
- gmx_bool bConstrVir;
- gmx_bool bTricl;
- gmx_bool bDynBox;
- gmx_bool bNHC_trotter;
- gmx_bool bPrintNHChains;
- gmx_bool bMTTK;
- gmx_bool bMu; /* true if dipole is calculated */
- gmx_bool bDiagPres;
- gmx_bool bPres;
- int f_nre;
- int epc;
- real ref_p;
- int etc;
- int nCrmsd;
- gmx_bool bEner[F_NRE];
- gmx_bool bEInd[egNR];
- char **print_grpnms;
-
- FILE *fp_dhdl; /* the dhdl.xvg output file */
- double *dE; /* energy components for dhdl.xvg output */
- t_mde_delta_h_coll *dhc; /* the delta U components (raw data + histogram) */
- real *temperatures;
-} t_mdebin;
-
-
-/* delta_h block type enum: the kinds of energies written out. */
-enum
-{
- dhbtDH = 0, /* delta H BAR energy difference*/
- dhbtDHDL = 1, /* dH/dlambda derivative */
- dhbtEN, /* System energy */
- dhbtPV, /* pV term */
- dhbtEXPANDED, /* expanded ensemble statistics */
- dhbtNR
-};
-
-
-
-t_mdebin *init_mdebin(ener_file_t fp_ene,
- const gmx_mtop_t *mtop,
- const t_inputrec *ir,
- FILE *fp_dhdl,
- bool isRerun = false);
-/* Initiate MD energy bin and write header to energy file. */
-
-//! Destroy mdebin
-void done_mdebin(t_mdebin *mdebin);
-
-FILE *open_dhdl(const char *filename, const t_inputrec *ir,
- const gmx_output_env_t *oenv);
-/* Open the dhdl file for output */
-
-/* update the averaging structures. Called every time
- the energies are evaluated. */
-void upd_mdebin(t_mdebin *md,
- gmx_bool bDoDHDL,
- gmx_bool bSum,
- double time,
- real tmass,
- gmx_enerdata_t *enerd,
- t_state *state,
- t_lambda *fep,
- t_expanded *expand,
- matrix lastbox,
- tensor svir,
- tensor fvir,
- tensor vir,
- tensor pres,
- gmx_ekindata_t *ekind,
- rvec mu_tot,
- const gmx::Constraints *constr);
-
-void upd_mdebin_step(t_mdebin *md);
-/* Updates only the step count in md */
-
-void print_ebin_header(FILE *log, int64_t steps, double time);
-
-void print_ebin(ener_file_t fp_ene, gmx_bool bEne, gmx_bool bDR, gmx_bool bOR,
- FILE *log,
- int64_t step, double time,
- int mode,
- t_mdebin *md, t_fcdata *fcd,
- gmx_groups_t *groups, t_grpopts *opts,
- gmx::Awh *awh);
-
-
-
-/* Between .edr writes, the averages are history dependent,
- and that history needs to be retained in checkpoints.
- These functions set/read the energyhistory_t class
- that is written to checkpoints in checkpoint.c */
-
-/* Set the energyhistory_t data from a mdebin structure */
-void update_energyhistory(energyhistory_t * enerhist, const t_mdebin * mdebin);
-
-/* Read the energyhistory_t data to a mdebin structure*/
-void restore_energyhistory_from_state(t_mdebin * mdebin,
- const energyhistory_t * enerhist);
-
-#endif
#include <memory>
#include "gromacs/fileio/enxio.h"
-#include "gromacs/mdlib/mdebin.h"
+#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdtypes/energyhistory.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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 _mdebin_bar_h
#define _mdebin_bar_h
-#include "gromacs/mdlib/mdebin.h"
+#include "gromacs/mdlib/energyoutput.h"
/* The functions & data structures here describe writing
energy differences (or their histogram )for use with g_bar */
class delta_h_history_t;
+struct t_enxframe;
/* Data for one foreign lambda, or derivative. */
typedef struct
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdlib/update.h"
#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/forceoutput.h"
#include "gromacs/mdtypes/iforceprovider.h"
#include "gromacs/mdtypes/inputrec.h"
#define GMX_MDLIB_SIM_UTIL_H
#include "gromacs/fileio/enxio.h"
-#include "gromacs/mdlib/mdebin.h"
#include "gromacs/mdlib/mdoutf.h"
#include "gromacs/mdlib/vcm.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/utility/arrayref.h"
+struct gmx_ekindata_t;
+struct gmx_enerdata_t;
struct gmx_output_env_t;
struct gmx_pme_t;
struct MdrunOptions;
{
class BoxDeformation;
class Constraints;
+class EnergyOutput;
class IMDOutputProvider;
class MDLogger;
class Update;
#include "gromacs/mdlib/tgroup.h"
#include "gromacs/mdlib/vcm.h"
#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
calc_verletbuf.cpp
constr.cpp
ebin.cpp
- mdebin.cpp
+ energyoutput.cpp
settle.cpp
shake.cpp
simulationsignal.cpp
*/
#include "gmxpre.h"
-#include "gromacs/mdlib/mdebin.h"
+#include "gromacs/mdlib/energyoutput.h"
#include <cstdio>
fclose(fp);
}
-class MdebinTest : public ::testing::Test
+class EnergyOutputTest : public ::testing::Test
{
public:
TestFileManager fileManager_;
- // Objects needed to make t_mdebin
+ // Objects needed to make EnergyOutput
t_inputrec inputrec_;
gmx_mtop_t mtop_;
- t_mdebin *mdebin_;
- unique_cptr<t_mdebin, done_mdebin> mdebinGuard_;
+ EnergyOutput energyOutput_;
// Objects needed for default energy output behavior.
t_mdatoms mdatoms_;
TestReferenceData refData_;
TestReferenceChecker checker_;
- MdebinTest() :
+ EnergyOutputTest() :
logFilename_(fileManager_.getTemporaryFilePath(".log")),
log_(std::fopen(logFilename_.c_str(), "w")), logFileGuard_(log_),
checker_(refData_.rootChecker())
{
- mdebin_ = init_mdebin(nullptr, &mtop_, &inputrec_, nullptr, false);
- mdebinGuard_.reset(mdebin_);
+ energyOutput_.prepare(nullptr, &mtop_, &inputrec_, nullptr, false);
constraints_ = makeConstraints(mtop_, inputrec_, false, log_, mdatoms_, nullptr,
nullptr, nullptr, nullptr, false);
}
};
-TEST_F(MdebinTest, HandlesEmptyAverages)
+TEST_F(EnergyOutputTest, HandlesEmptyAverages)
{
ASSERT_NE(log_, nullptr);
// Test printing values
- print_ebin(nullptr, false, false, false, log_,
- 0, 0, eprNORMAL, mdebin_,
- nullptr, nullptr, nullptr, nullptr);
+ energyOutput_.printStepToEnergyFile(nullptr, false, false, false, log_,
+ 0, 0, eprNORMAL,
+ nullptr, nullptr, nullptr, nullptr);
// Test printing averages
- print_ebin(nullptr, false, false, false, log_,
- 0, 0, eprAVER, mdebin_,
- nullptr, nullptr, nullptr, nullptr);
+ energyOutput_.printStepToEnergyFile(nullptr, false, false, false, log_,
+ 0, 0, eprAVER,
+ nullptr, nullptr, nullptr, nullptr);
// We need to close the file before the contents are available.
logFileGuard_.reset(nullptr);
- checker_.checkInteger(mdebin_->ebin->nener, "Number of Energy Terms");
+ checker_.checkInteger(energyOutput_.numEnergyTerms(), "Number of Energy Terms");
checker_.checkString(TextReader::readFileToString(logFilename_), "log");
}
-TEST_F(MdebinTest, HandlesSingleStep)
+TEST_F(EnergyOutputTest, HandlesSingleStep)
{
ASSERT_NE(log_, nullptr);
real time = 1.0;
real testValue = 1.0;
setStepData(testValue);
- upd_mdebin(mdebin_, false, true, time, 0.0, &enerdata_,
- nullptr, nullptr, nullptr, box_,
- nullptr, nullptr, totalVirial_, pressure_,
- nullptr, nullptr, constraints_.get());
+ energyOutput_.addDataAtEnergyStep(false, true, time, 0.0, &enerdata_,
+ nullptr, nullptr, nullptr, box_,
+ nullptr, nullptr, totalVirial_, pressure_,
+ nullptr, nullptr, constraints_.get());
// Test printing values
- print_ebin(nullptr, false, false, false, log_,
- 0, 0, eprNORMAL, mdebin_,
- nullptr, nullptr, nullptr, nullptr);
+ energyOutput_.printStepToEnergyFile(nullptr, false, false, false, log_,
+ 0, 0, eprNORMAL,
+ nullptr, nullptr, nullptr, nullptr);
// Test printing averages
- print_ebin(nullptr, false, false, false, log_,
- 0, 0, eprAVER, mdebin_,
- nullptr, nullptr, nullptr, nullptr);
+ energyOutput_.printStepToEnergyFile(nullptr, false, false, false, log_,
+ 0, 0, eprAVER,
+ nullptr, nullptr, nullptr, nullptr);
// We need to close the file before the contents are available.
logFileGuard_.reset(nullptr);
- checker_.checkInteger(mdebin_->ebin->nener, "Number of Energy Terms");
+ checker_.checkInteger(energyOutput_.numEnergyTerms(), "Number of Energy Terms");
checker_.checkString(TextReader::readFileToString(logFilename_), "log");
}
-TEST_F(MdebinTest, HandlesTwoSteps)
+TEST_F(EnergyOutputTest, HandlesTwoSteps)
{
ASSERT_NE(log_, nullptr);
real time = 1.0;
real testValue = 1.0;
setStepData(testValue);
- upd_mdebin(mdebin_, false, true, time, 0.0, &enerdata_,
- nullptr, nullptr, nullptr, box_,
- nullptr, nullptr, totalVirial_, pressure_,
- nullptr, nullptr, constraints_.get());
+ energyOutput_.addDataAtEnergyStep(false, true, time, 0.0, &enerdata_,
+ nullptr, nullptr, nullptr, box_,
+ nullptr, nullptr, totalVirial_, pressure_,
+ nullptr, nullptr, constraints_.get());
// Test printing values
- print_ebin(nullptr, false, false, false, log_,
- 0, 0, eprNORMAL, mdebin_,
- nullptr, nullptr, nullptr, nullptr);
+ energyOutput_.printStepToEnergyFile(nullptr, false, false, false, log_,
+ 0, 0, eprNORMAL,
+ nullptr, nullptr, nullptr, nullptr);
// Add synthetic data for the second step
time += 0.005;
setStepData(testValue += 1.0);
- upd_mdebin(mdebin_, false, true, time, 0.0, &enerdata_,
- nullptr, nullptr, nullptr, box_,
- nullptr, nullptr, totalVirial_, pressure_,
- nullptr, nullptr, constraints_.get());
+ energyOutput_.addDataAtEnergyStep(false, true, time, 0.0, &enerdata_,
+ nullptr, nullptr, nullptr, box_,
+ nullptr, nullptr, totalVirial_, pressure_,
+ nullptr, nullptr, constraints_.get());
// Test printing values
- print_ebin(nullptr, false, false, false, log_,
- 0, 0, eprNORMAL, mdebin_,
- nullptr, nullptr, nullptr, nullptr);
+ energyOutput_.printStepToEnergyFile(nullptr, false, false, false, log_,
+ 0, 0, eprNORMAL,
+ nullptr, nullptr, nullptr, nullptr);
// Test printing averages
- print_ebin(nullptr, false, false, false, log_,
- 0, 0, eprAVER, mdebin_,
- nullptr, nullptr, nullptr, nullptr);
+ energyOutput_.printStepToEnergyFile(nullptr, false, false, false, log_,
+ 0, 0, eprAVER,
+ nullptr, nullptr, nullptr, nullptr);
// We need to close the file before the contents are available.
logFileGuard_.reset(nullptr);
- checker_.checkInteger(mdebin_->ebin->nener, "Number of Energy Terms");
+ checker_.checkInteger(energyOutput_.numEnergyTerms(), "Number of Energy Terms");
checker_.checkString(TextReader::readFileToString(logFilename_), "log");
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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/utility/smalloc.h"
void
-do_md_trajectory_writing(FILE *fplog,
- t_commrec *cr,
- int nfile,
- const t_filenm fnm[],
- int64_t step,
- int64_t step_rel,
- double t,
- t_inputrec *ir,
- t_state *state,
- t_state *state_global,
- ObservablesHistory *observablesHistory,
- gmx_mtop_t *top_global,
- t_forcerec *fr,
- gmx_mdoutf_t outf,
- t_mdebin *mdebin,
- gmx_ekindata_t *ekind,
- gmx::ArrayRef<gmx::RVec> f,
- gmx_bool bCPT,
- gmx_bool bRerunMD,
- gmx_bool bLastStep,
- gmx_bool bDoConfOut,
- gmx_bool bSumEkinhOld
+do_md_trajectory_writing(FILE *fplog,
+ t_commrec *cr,
+ int nfile,
+ const t_filenm fnm[],
+ int64_t step,
+ int64_t step_rel,
+ double t,
+ t_inputrec *ir,
+ t_state *state,
+ t_state *state_global,
+ ObservablesHistory *observablesHistory,
+ gmx_mtop_t *top_global,
+ t_forcerec *fr,
+ gmx_mdoutf_t outf,
+ const gmx::EnergyOutput &energyOutput,
+ gmx_ekindata_t *ekind,
+ gmx::ArrayRef<gmx::RVec> f,
+ gmx_bool bCPT,
+ gmx_bool bRerunMD,
+ gmx_bool bLastStep,
+ gmx_bool bDoConfOut,
+ gmx_bool bSumEkinhOld
)
{
int mdof_flags;
state_global->ekinstate.bUpToDate = TRUE;
}
- update_energyhistory(observablesHistory->energyHistory.get(), mdebin);
+ energyOutput.fillEnergyHistory(observablesHistory->energyHistory.get());
}
}
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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 <stdio.h>
-#include "gromacs/mdlib/mdebin.h"
+#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdlib/mdoutf.h"
#include "gromacs/timing/wallcycle.h"
struct t_filenm;
struct t_forcerec;
+namespace gmx
+{
+class EnergyOutput;
+}
+
/*! \brief Wrapper routine for writing trajectories during mdrun
*
* This routine does communication (e.g. collecting distributed coordinates)
struct gmx_mtop_t *top_global,
t_forcerec *fr,
gmx_mdoutf_t outf,
- t_mdebin *mdebin,
- struct gmx_ekindata_t *ekind,
+ const gmx::EnergyOutput &energyOutput,
+ gmx_ekindata_t *ekind,
gmx::ArrayRef<gmx::RVec> f,
gmx_bool bCPT,
gmx_bool bRerunMD,
#include "gromacs/mdlib/compute_io.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/ebin.h"
+#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdlib/expanded.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdlib/md_support.h"
#include "gromacs/mdlib/mdatoms.h"
-#include "gromacs/mdlib/mdebin.h"
#include "gromacs/mdlib/mdoutf.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/mdsetup.h"
pleaseCiteCouplingAlgorithms(fplog, *ir);
}
init_nrnb(nrnb);
- gmx_mdoutf *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr,
- outputProvider, ir, top_global, oenv, wcycle);
- t_mdebin *mdebin = init_mdebin(mdrunOptions.continuationOptions.appendFiles ? nullptr : mdoutf_get_fp_ene(outf),
- top_global, ir, mdoutf_get_fp_dhdl(outf));
+ gmx_mdoutf *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, oenv, wcycle);
+ gmx::EnergyOutput energyOutput;
+ energyOutput.prepare(mdoutf_get_fp_ene(outf), top_global, ir, mdoutf_get_fp_dhdl(outf));
/* Energy terms and groups */
snew(enerd, 1);
ir->nstcalcenergy, DOMAINDECOMP(cr));
{
- double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
+ double io = compute_io(ir, top_global->natoms, groups, energyOutput.numEnergyTerms(), 1);
if ((io > 2000) && MASTER(cr))
{
fprintf(stderr,
{
if (startingFromCheckpoint)
{
- /* Update mdebin with energy history if appending to output files */
+ /* Restore from energy history if appending to output files */
if (continuationOptions.appendFiles)
{
/* If no history is available (because a checkpoint is from before
*/
if (observablesHistory->energyHistory)
{
- restore_energyhistory_from_state(mdebin, observablesHistory->energyHistory.get());
+ energyOutput.restoreFromEnergyHistory(*observablesHistory->energyHistory);
}
}
else if (observablesHistory->energyHistory)
{
observablesHistory->pullHistory = std::make_unique<PullHistory>();
}
- /* Set the initial energy history in state by updating once */
- update_energyhistory(observablesHistory->energyHistory.get(), mdebin);
+ /* Set the initial energy history */
+ energyOutput.fillEnergyHistory(observablesHistory->energyHistory.get());
}
preparePrevStepPullCom(ir, mdatoms, state, state_global, cr, startingFromCheckpoint);
do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
ir, state, state_global, observablesHistory,
top_global, fr,
- outf, mdebin, ekind, f,
+ outf, energyOutput, ekind, f,
checkpointHandler->isCheckpointingStep(),
bRerunMD, bLastStep,
mdrunOptions.writeConfout,
}
if (bCalcEner)
{
- upd_mdebin(mdebin, bDoDHDL, bCalcEnerStep,
- t, mdatoms->tmass, enerd, state,
- ir->fepvals, ir->expandedvals, lastbox,
- shake_vir, force_vir, total_vir, pres,
- ekind, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(bDoDHDL, bCalcEnerStep,
+ t, mdatoms->tmass, enerd, state,
+ ir->fepvals, ir->expandedvals, lastbox,
+ shake_vir, force_vir, total_vir, pres,
+ ekind, mu_tot, constr);
}
else
{
- upd_mdebin_step(mdebin);
+ energyOutput.recordNonEnergyStep();
}
gmx_bool do_dr = do_per_step(step, ir->nstdisreout);
gmx_bool do_or = do_per_step(step, ir->nstorireout);
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : nullptr,
- step, t,
- eprNORMAL, mdebin, fcd, groups, &(ir->opts), awh.get());
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
+ do_log ? fplog : nullptr,
+ step, t,
+ eprNORMAL, fcd, groups, &(ir->opts), awh.get());
if (ir->bPull)
{
{
if (ir->nstcalcenergy > 0)
{
- print_ebin(mdoutf_get_fp_ene(outf), FALSE, FALSE, FALSE, fplog, step, t,
- eprAVER, mdebin, fcd, groups, &(ir->opts), awh.get());
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), FALSE, FALSE, FALSE,
+ fplog, step, t,
+ eprAVER, fcd, groups, &(ir->opts), awh.get());
}
}
- done_mdebin(mdebin);
done_mdoutf(outf);
if (bPMETune)
#include "gromacs/mdlib/compute_io.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/ebin.h"
+#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdlib/expanded.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdlib/md_support.h"
#include "gromacs/mdlib/mdatoms.h"
-#include "gromacs/mdlib/mdebin.h"
#include "gromacs/mdlib/mdoutf.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/mdsetup.h"
#include "gromacs/mdtypes/awh_params.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/df_history.h"
+#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/energyhistory.h"
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/forcerec.h"
initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
init_nrnb(nrnb);
- gmx_mdoutf *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, oenv, wcycle);
- t_mdebin *mdebin = init_mdebin(mdrunOptions.continuationOptions.appendFiles ? nullptr : mdoutf_get_fp_ene(outf),
- top_global, ir, mdoutf_get_fp_dhdl(outf), true);
+ gmx_mdoutf *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, oenv, wcycle);
+ gmx::EnergyOutput energyOutput;
+ energyOutput.prepare(mdoutf_get_fp_ene(outf), top_global, ir, mdoutf_get_fp_dhdl(outf), true);
/* Energy terms and groups */
snew(enerd, 1);
ir->nstcalcenergy, DOMAINDECOMP(cr));
{
- double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
+ double io = compute_io(ir, top_global->natoms, groups, energyOutput.numEnergyTerms(), 1);
if ((io > 2000) && MASTER(cr))
{
fprintf(stderr,
do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
ir, state, state_global, observablesHistory,
top_global, fr,
- outf, mdebin, ekind, f,
+ outf, energyOutput, ekind, f,
isCheckpointingStep, doRerun, isLastStep,
mdrunOptions.writeConfout,
bSumEkinhOld);
if (MASTER(cr))
{
const bool bCalcEnerStep = true;
- upd_mdebin(mdebin, doFreeEnergyPerturbation, bCalcEnerStep,
- t, mdatoms->tmass, enerd, state,
- ir->fepvals, ir->expandedvals, state->box,
- shake_vir, force_vir, total_vir, pres,
- ekind, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep,
+ t, mdatoms->tmass, enerd, state,
+ ir->fepvals, ir->expandedvals, state->box,
+ shake_vir, force_vir, total_vir, pres,
+ ekind, mu_tot, constr);
const bool do_ene = true;
const bool do_log = true;
const bool do_dr = ir->nstdisreout != 0;
const bool do_or = ir->nstorireout != 0;
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : nullptr,
- step, t,
- eprNORMAL, mdebin, fcd, groups, &(ir->opts), awh);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
+ do_log ? fplog : nullptr,
+ step, t,
+ eprNORMAL, fcd, groups, &(ir->opts), awh);
if (do_per_step(step, ir->nstlog))
{
gmx_pme_send_finish(cr);
}
- done_mdebin(mdebin);
done_mdoutf(outf);
done_shellfc(fplog, shellfc, step_rel);
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/ebin.h"
+#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/md_support.h"
#include "gromacs/mdlib/mdatoms.h"
-#include "gromacs/mdlib/mdebin.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/mdsetup.h"
#include "gromacs/mdlib/ns.h"
gmx_mdoutf *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, inputrec, top_global, nullptr, wcycle);
snew(enerd, 1);
init_enerdata(top_global->groups.grps[egcENER].nr, inputrec->fepvals->n_lambda, enerd);
- t_mdebin *mdebin = init_mdebin(mdoutf_get_fp_ene(outf), top_global, inputrec, nullptr);
+ gmx::EnergyOutput energyOutput;
+ energyOutput.prepare(mdoutf_get_fp_ene(outf), top_global, inputrec, nullptr);
/* Print to log file */
print_em_start(fplog, cr, walltime_accounting, wcycle, CG);
{
/* Copy stuff to the energy bin for easy printing etc. */
matrix nullBox = {};
- upd_mdebin(mdebin, FALSE, FALSE, static_cast<double>(step),
- mdatoms->tmass, enerd, nullptr, nullptr, nullptr, nullBox,
- nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(false, false, static_cast<double>(step),
+ mdatoms->tmass, enerd, nullptr, nullptr, nullptr, nullBox,
+ nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
print_ebin_header(fplog, step, step);
- print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
- mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE,
+ fplog, step, step, eprNORMAL,
+ fcd, &(top_global->groups), &(inputrec->opts), nullptr);
}
/* Estimate/guess the initial stepsize */
}
/* Store the new (lower) energies */
matrix nullBox = {};
- upd_mdebin(mdebin, FALSE, FALSE, static_cast<double>(step),
- mdatoms->tmass, enerd, nullptr, nullptr, nullptr, nullBox,
- nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(false, false, static_cast<double>(step),
+ mdatoms->tmass, enerd, nullptr, nullptr, nullptr, nullBox,
+ nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
do_log = do_per_step(step, inputrec->nstlog);
do_ene = do_per_step(step, inputrec->nstenergy);
{
print_ebin_header(fplog, step, step);
}
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
- do_log ? fplog : nullptr, step, step, eprNORMAL,
- mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
+ do_log ? fplog : nullptr, step, step, eprNORMAL,
+ fcd, &(top_global->groups), &(inputrec->opts), nullptr);
}
/* Send energies and positions to the IMD client if bIMD is TRUE. */
if (!do_ene || !do_log)
{
/* Write final energy file entries */
- print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
- !do_log ? fplog : nullptr, step, step, eprNORMAL,
- mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
+ !do_log ? fplog : nullptr, step, step, eprNORMAL,
+ fcd, &(top_global->groups), &(inputrec->opts), nullptr);
}
}
gmx_mdoutf *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, inputrec, top_global, nullptr, wcycle);
snew(enerd, 1);
init_enerdata(top_global->groups.grps[egcENER].nr, inputrec->fepvals->n_lambda, enerd);
- t_mdebin *mdebin = init_mdebin(mdoutf_get_fp_ene(outf), top_global, inputrec, nullptr);
+ gmx::EnergyOutput energyOutput;
+ energyOutput.prepare(mdoutf_get_fp_ene(outf), top_global, inputrec, nullptr);
start = 0;
end = mdatoms->homenr;
{
/* Copy stuff to the energy bin for easy printing etc. */
matrix nullBox = {};
- upd_mdebin(mdebin, FALSE, FALSE, static_cast<double>(step),
- mdatoms->tmass, enerd, nullptr, nullptr, nullptr, nullBox,
- nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(false, false, static_cast<double>(step),
+ mdatoms->tmass, enerd, nullptr, nullptr, nullptr, nullBox,
+ nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
print_ebin_header(fplog, step, step);
- print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
- mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE,
+ fplog, step, step, eprNORMAL,
+ fcd, &(top_global->groups), &(inputrec->opts), nullptr);
}
/* Set the initial step.
}
/* Store the new (lower) energies */
matrix nullBox = {};
- upd_mdebin(mdebin, FALSE, FALSE, static_cast<double>(step),
- mdatoms->tmass, enerd, nullptr, nullptr, nullptr, nullBox,
- nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(false, false, static_cast<double>(step),
+ mdatoms->tmass, enerd, nullptr, nullptr, nullptr, nullBox,
+ nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
+
do_log = do_per_step(step, inputrec->nstlog);
do_ene = do_per_step(step, inputrec->nstenergy);
+
+ /* Prepare IMD energy record, if bIMD is TRUE. */
+ IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, step, TRUE);
+
if (do_log)
{
print_ebin_header(fplog, step, step);
}
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
- do_log ? fplog : nullptr, step, step, eprNORMAL,
- mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
+ do_log ? fplog : nullptr, step, step, eprNORMAL,
+ fcd, &(top_global->groups), &(inputrec->opts), nullptr);
}
/* Send x and E to IMD client, if bIMD is TRUE. */
}
if (!do_ene || !do_log) /* Write final energy file entries */
{
- print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
- !do_log ? fplog : nullptr, step, step, eprNORMAL,
- mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
+ !do_log ? fplog : nullptr, step, step, eprNORMAL,
+ fcd, &(top_global->groups), &(inputrec->opts), nullptr);
}
/* Print some stuff... */
gmx_mdoutf *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, inputrec, top_global, nullptr, wcycle);
snew(enerd, 1);
init_enerdata(top_global->groups.grps[egcENER].nr, inputrec->fepvals->n_lambda, enerd);
- t_mdebin *mdebin = init_mdebin(mdoutf_get_fp_ene(outf), top_global, inputrec, nullptr);
+ gmx::EnergyOutput energyOutput;
+ energyOutput.prepare(mdoutf_get_fp_ene(outf), top_global, inputrec, nullptr);
/* Print to log file */
print_em_start(fplog, cr, walltime_accounting, wcycle, SD);
{
/* Store the new (lower) energies */
matrix nullBox = {};
- upd_mdebin(mdebin, FALSE, FALSE, static_cast<double>(count),
- mdatoms->tmass, enerd, nullptr, nullptr, nullptr,
- nullBox, nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(false, false, static_cast<double>(count),
+ mdatoms->tmass, enerd, nullptr, nullptr, nullptr, nullBox,
+ nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
/* Prepare IMD energy record, if bIMD is TRUE. */
IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, count, TRUE);
- print_ebin(mdoutf_get_fp_ene(outf), TRUE,
- do_per_step(steps_accepted, inputrec->nstdisreout),
- do_per_step(steps_accepted, inputrec->nstorireout),
- fplog, count, count, eprNORMAL,
- mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
+ const bool do_dr = do_per_step(steps_accepted, inputrec->nstdisreout);
+ const bool do_or = do_per_step(steps_accepted, inputrec->nstorireout);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), TRUE,
+ do_dr, do_or,
+ fplog, count, count, eprNORMAL,
+ fcd, &(top_global->groups),
+ &(inputrec->opts), nullptr);
fflush(fplog);
}
}
#include "gromacs/mdlib/compute_io.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/ebin.h"
+#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdlib/expanded.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdlib/md_support.h"
#include "gromacs/mdlib/mdatoms.h"
-#include "gromacs/mdlib/mdebin.h"
#include "gromacs/mdlib/mdoutf.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/mdsetup.h"
initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
init_nrnb(nrnb);
-
- gmx_mdoutf *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, oenv, wcycle);
- t_mdebin *mdebin = init_mdebin(mdrunOptions.continuationOptions.appendFiles ? nullptr : mdoutf_get_fp_ene(outf),
- top_global, ir, mdoutf_get_fp_dhdl(outf), true);
+ gmx_mdoutf *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, oenv, wcycle);
+ gmx::EnergyOutput energyOutput;
+ energyOutput.prepare(mdoutf_get_fp_ene(outf), top_global, ir, mdoutf_get_fp_dhdl(outf), true);
/* Energy terms and groups */
snew(enerd, 1);
ir->nstcalcenergy, DOMAINDECOMP(cr));
{
- double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
+ double io = compute_io(ir, top_global->natoms, groups, energyOutput.numEnergyTerms(), 1);
if ((io > 2000) && MASTER(cr))
{
fprintf(stderr,
do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
ir, state, state_global, observablesHistory,
top_global, fr,
- outf, mdebin, ekind, f,
+ outf, energyOutput, ekind, f,
isCheckpointingStep, doRerun, isLastStep,
mdrunOptions.writeConfout,
bSumEkinhOld);
if (MASTER(cr))
{
const bool bCalcEnerStep = true;
- upd_mdebin(mdebin, doFreeEnergyPerturbation, bCalcEnerStep,
- t, mdatoms->tmass, enerd, state,
- ir->fepvals, ir->expandedvals, rerun_fr.box,
- shake_vir, force_vir, total_vir, pres,
- ekind, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep,
+ t, mdatoms->tmass, enerd, state,
+ ir->fepvals, ir->expandedvals, state->box,
+ shake_vir, force_vir, total_vir, pres,
+ ekind, mu_tot, constr);
const bool do_ene = true;
const bool do_log = true;
const bool do_dr = ir->nstdisreout != 0;
const bool do_or = ir->nstorireout != 0;
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : nullptr,
- step, t,
- eprNORMAL, mdebin, fcd, groups, &(ir->opts), awh);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
+ do_log ? fplog : nullptr,
+ step, t,
+ eprNORMAL, fcd, groups, &(ir->opts), awh);
if (do_per_step(step, ir->nstlog))
{
gmx_pme_send_finish(cr);
}
- done_mdebin(mdebin);
done_mdoutf(outf);
done_shellfc(fplog, shellfc, step_rel);
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/mdlib/mdatoms.h"
-#include "gromacs/mdlib/mdebin.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/ns.h"
#include "gromacs/mdlib/sim_util.h"
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff