This is a step towards making a constructor for t_pull.
Change-Id: I24583fa32066503ccfbe0abaef6a412241974b12
if (ir->bPull)
{
- pull = set_pull_init(ir, sys, as_rvec_array(state.x.data()), state.box, state.lambda[efptMASS], oenv);
+ pull = set_pull_init(ir, sys, as_rvec_array(state.x.data()), state.box, state.lambda[efptMASS]);
}
/* Modules that supply external potential for pull coordinates
*
* 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, led by
+ * 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.
/* Process the pull coordinates after reading the pull groups */
pull_t *set_pull_init(t_inputrec *ir, const gmx_mtop_t *mtop,
- rvec *x, matrix box, real lambda,
- const gmx_output_env_t *oenv);
+ rvec *x, matrix box, real lambda);
/* Prints the initial pull group distances in x.
* If requested, adds the current distance to the initial reference location.
* Returns the pull_t pull work struct. This should be passed to finish_pull()
*
* 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, led by
+ * 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.
}
pull_t *set_pull_init(t_inputrec *ir, const gmx_mtop_t *mtop,
- rvec *x, matrix box, real lambda,
- const gmx_output_env_t *oenv)
+ rvec *x, matrix box, real lambda)
{
pull_params_t *pull;
pull_t *pull_work;
double t_start;
pull = ir->pull;
- pull_work = init_pull(nullptr, pull, ir, 0, nullptr, mtop, nullptr, oenv, lambda, FALSE, ContinuationOptions());
+ pull_work = init_pull(nullptr, pull, ir, mtop, nullptr, lambda);
auto mdAtoms = gmx::makeMDAtoms(nullptr, *mtop, *ir, false);
auto md = mdAtoms->mdatoms();
atoms2md(mtop, ir, -1, nullptr, mtop->natoms, mdAtoms.get());
struct pull_t *
init_pull(FILE *fplog, const pull_params_t *pull_params, const t_inputrec *ir,
- int nfile, const t_filenm fnm[],
const gmx_mtop_t *mtop, const t_commrec *cr,
- const gmx_output_env_t *oenv, real lambda,
- gmx_bool bOutFile,
- const ContinuationOptions &continuationOptions)
+ real lambda)
{
struct pull_t *pull;
pull_comm_t *comm;
/* We still need to initialize the PBC reference coordinates */
pull->bSetPBCatoms = TRUE;
- /* Only do I/O when we are doing dynamics and if we are the MASTER */
pull->out_x = nullptr;
pull->out_f = nullptr;
- if (bOutFile)
- {
- /* Check for px and pf filename collision, if we are writing
- both files */
- std::string px_filename, pf_filename;
- std::string px_appended, pf_appended;
- try
- {
- px_filename = std::string(opt2fn("-px", nfile, fnm));
- pf_filename = std::string(opt2fn("-pf", nfile, fnm));
- }
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ return pull;
+}
- if ((pull->params.nstxout != 0) &&
- (pull->params.nstfout != 0) &&
- (px_filename == pf_filename))
+void init_pull_output_files(pull_t *pull,
+ int nfile,
+ const t_filenm fnm[],
+ const gmx_output_env_t *oenv,
+ const ContinuationOptions &continuationOptions)
+{
+ /* Check for px and pf filename collision, if we are writing
+ both files */
+ std::string px_filename, pf_filename;
+ std::string px_appended, pf_appended;
+ try
+ {
+ px_filename = std::string(opt2fn("-px", nfile, fnm));
+ pf_filename = std::string(opt2fn("-pf", nfile, fnm));
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+
+ if ((pull->params.nstxout != 0) &&
+ (pull->params.nstfout != 0) &&
+ (px_filename == pf_filename))
+ {
+ if (!opt2bSet("-px", nfile, fnm) && !opt2bSet("-pf", nfile, fnm))
{
- if (!opt2bSet("-px", nfile, fnm) && !opt2bSet("-pf", nfile, fnm))
- {
- /* We are writing both pull files but neither set directly. */
- try
- {
- px_appended = append_before_extension(px_filename, "_pullx");
- pf_appended = append_before_extension(pf_filename, "_pullf");
- }
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
- pull->out_x = open_pull_out(px_appended.c_str(), pull, oenv,
- TRUE, continuationOptions);
- pull->out_f = open_pull_out(pf_appended.c_str(), pull, oenv,
- FALSE, continuationOptions);
- return pull;
- }
- else
+ /* We are writing both pull files but neither set directly. */
+ try
{
- /* If one of -px and -pf is set but the filenames are identical: */
- gmx_fatal(FARGS, "Identical pull_x and pull_f output filenames %s",
- px_filename.c_str());
+ px_appended = append_before_extension(px_filename, "_pullx");
+ pf_appended = append_before_extension(pf_filename, "_pullf");
}
- }
- if (pull->params.nstxout != 0)
- {
- pull->out_x = open_pull_out(opt2fn("-px", nfile, fnm), pull, oenv,
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ pull->out_x = open_pull_out(px_appended.c_str(), pull, oenv,
TRUE, continuationOptions);
+ pull->out_f = open_pull_out(pf_appended.c_str(), pull, oenv,
+ FALSE, continuationOptions);
+ return;
}
- if (pull->params.nstfout != 0)
+ else
{
- pull->out_f = open_pull_out(opt2fn("-pf", nfile, fnm), pull, oenv,
- FALSE, continuationOptions);
+ /* If at least one of -px and -pf is set but the filenames are identical: */
+ gmx_fatal(FARGS, "Identical pull_x and pull_f output filenames %s",
+ px_filename.c_str());
}
}
-
- return pull;
+ if (pull->params.nstxout != 0)
+ {
+ pull->out_x = open_pull_out(opt2fn("-px", nfile, fnm), pull, oenv,
+ TRUE, continuationOptions);
+ }
+ if (pull->params.nstfout != 0)
+ {
+ pull->out_f = open_pull_out(opt2fn("-pf", nfile, fnm), pull, oenv,
+ FALSE, continuationOptions);
+ }
}
static void destroy_pull_group(pull_group_work_t *pgrp)
* \param fplog General output file, normally md.log.
* \param pull_params The pull input parameters containing all pull settings.
* \param ir The inputrec.
- * \param nfile Number of files.
- * \param fnm Standard filename struct.
* \param mtop The topology of the whole system.
* \param cr Struct for communication info.
- * \param oenv Output options.
* \param lambda FEP lambda.
- * \param bOutFile Open output files?
- * \param continuationOptions Options for continuing from checkpoint file
*/
struct pull_t *init_pull(FILE *fplog,
const pull_params_t *pull_params,
const t_inputrec *ir,
- int nfile,
- const t_filenm fnm[],
const gmx_mtop_t *mtop,
const t_commrec *cr,
- const gmx_output_env_t *oenv,
- real lambda,
- gmx_bool bOutFile,
- const ContinuationOptions &continuationOptions);
+ real lambda);
+/*! \brief Set up and open the pull output files, when requested.
+ *
+ * NOTE: This should only be called on the master rank and only when
+ * doing dynamics (e.g. not with energy minimization).
+ *
+ * \param pull The pull work data struct
+ * \param nfile Number of files.
+ * \param fnm Standard filename struct.
+ * \param oenv Output options.
+ * \param continuationOptions Options for continuing from checkpoint file
+ */
+void init_pull_output_files(pull_t *pull,
+ int nfile,
+ const t_filenm fnm[],
+ const gmx_output_env_t *oenv,
+ const ContinuationOptions &continuationOptions);
/*! \brief Close the pull output files.
*
{
/* Initialize pull code */
inputrec->pull_work =
- init_pull(fplog, inputrec->pull, inputrec, nfile, fnm,
- mtop, cr, oenv, inputrec->fepvals->init_lambda,
- EI_DYNAMICS(inputrec->eI) && MASTER(cr),
- continuationOptions);
+ init_pull(fplog, inputrec->pull, inputrec,
+ mtop, cr, inputrec->fepvals->init_lambda);
+ if (EI_DYNAMICS(inputrec->eI) && MASTER(cr))
+ {
+ init_pull_output_files(inputrec->pull_work,
+ nfile, fnm, oenv,
+ continuationOptions);
+ }
}
if (inputrec->bRot)
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff