* 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.
#ifndef GMX_GMXPREPROCESS_READIR_H
#define GMX_GMXPREPROCESS_READIR_H
+#include <string>
+
#include "gromacs/fileio/readinp.h"
#include "gromacs/math/vectypes.h"
+#include "gromacs/mdtypes/multipletimestepping.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/real.h"
namespace gmx
{
class MDModules;
-struct MdModulesNotifier;
+struct MDModulesNotifiers;
} // namespace gmx
struct gmx_mtop_t;
struct t_grpopts;
struct t_inpfile;
struct t_inputrec;
+struct t_pull_group;
+struct t_pull_coord;
struct t_rot;
struct warninp;
typedef warninp* warninp_t;
struct t_gromppopts
{
- int warnings;
- int nshake;
- char* include;
- char* define;
- bool bGenVel;
- bool bGenPairs;
- real tempi;
- int seed;
- bool bOrire;
- bool bMorse;
- char* wall_atomtype[2];
- char* couple_moltype;
- int couple_lam0;
- int couple_lam1;
- bool bCoupleIntra;
+ int warnings = 0;
+ int nshake = 0;
+ char* include = nullptr;
+ char* define = nullptr;
+ bool bGenVel = false;
+ bool bGenPairs = false;
+ real tempi = 0;
+ int seed = 0;
+ gmx::GromppMtsOpts mtsOpts;
+ bool bOrire = false;
+ bool bMorse = false;
+ char* wall_atomtype[2] = { nullptr, nullptr };
+ char* couple_moltype = nullptr;
+ int couple_lam0 = 0;
+ int couple_lam1 = 0;
+ bool bCoupleIntra = false;
};
/*! \brief Initialise object to hold strings parsed from an .mdp file */
/*! \brief Clean up object that holds strings parsed from an .mdp file */
void done_inputrec_strings();
-void check_ir(const char* mdparin,
- const gmx::MdModulesNotifier& mdModulesNotifier,
- t_inputrec* ir,
- t_gromppopts* opts,
- warninp_t wi);
-/* Validate inputrec data.
- * Fatal errors will be added to nerror.
+/*! \brief Performs all validation on \p ir that can be done without index groups and topology
+ *
+ * Any errors, warnings or notes are added to \p wi
*/
-int search_string(const char* s, int ng, char* gn[]);
-/* Returns the index of string s in the index groups */
+void check_ir(const char* mdparin,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
+ t_inputrec* ir,
+ t_gromppopts* opts,
+ warninp_t wi);
+
+//! Returns the index of string \p s in \p gn or exit with a verbose fatal error when not found
+int search_string(const char* s, int ng, char* const gn[]);
void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi);
/* Do more checks */
* function is called. Also prints the input file back to mdparout.
*/
-void do_index(const char* mdparin,
- const char* ndx,
- gmx_mtop_t* mtop,
- bool bVerbose,
- const gmx::MdModulesNotifier& notifier,
- t_inputrec* ir,
- warninp_t wi);
+void do_index(const char* mdparin,
+ const char* ndx,
+ gmx_mtop_t* mtop,
+ bool bVerbose,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
+ t_inputrec* ir,
+ warninp_t wi);
/* Read the index file and assign grp numbers to atoms.
*/
std::vector<std::string> read_pullparams(std::vector<t_inpfile>* inp, pull_params_t* pull, warninp_t wi);
/* Reads the pull parameters, returns a list of the pull group names */
-
-void make_pull_groups(pull_params_t* pull,
- gmx::ArrayRef<const std::string> pullGroupNames,
- const t_blocka* grps,
- char** gnames);
+void process_pull_groups(gmx::ArrayRef<t_pull_group> pullGroups,
+ gmx::ArrayRef<const std::string> pullGroupNames,
+ const t_blocka* grps,
+ char** gnames);
/* Process the pull group parameters after reading the index groups */
-void make_pull_coords(pull_params_t* pull);
+void checkPullCoords(gmx::ArrayRef<const t_pull_group> pullGroups,
+ gmx::ArrayRef<const t_pull_coord> pullCoords);
/* 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, warninp_t wi);
+pull_t* set_pull_init(t_inputrec* ir,
+ const gmx_mtop_t& mtop,
+ gmx::ArrayRef<const gmx::RVec> x,
+ matrix box,
+ real lambda,
+ warninp_t wi);
/* 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()
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff