* \author Carsten Kutzner <ckutzne@gwdg.de>
* \ingroup module_swap
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
-#include "typedefs.h"
-#include "string2.h"
-#include "smalloc.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
#include "gromacs/mdlib/groupcoord.h"
-#include "mtop_util.h"
-#include "macros.h"
-#include "vec.h"
-#include "names.h"
-#include "network.h"
-#include "mdrun.h"
-#include "xvgr.h"
-#include "copyrite.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/timing/wallcycle.h"
#include "swapcoords.h"
+#include "gromacs/pbcutil/pbc.h"
+
static char *SwS = {"SWAP:"}; /**< For output that comes from the swap module */
static char *SwSEmpty = {" "}; /**< Placeholder for multi-line output */
static char* IonString[eIonNR] = {"anion", "cation" }; /**< Type of ion, used for verbose output */
/*! \internal \brief
- * Structure containing compartment-specific data
+ * Structure containing compartment-specific data.
*/
typedef struct swap_compartment
{
/*! \internal \brief
* This structure contains data needed for each of the groups involved in swapping: ions, water,
- * and channels
+ * and channels.
*/
typedef struct swap_group
{
-/*! Check whether point is in channel. Channel is a cylinder defined by a disc
+/*! \brief Check whether point is in channel.
+ *
+ * A channel is a cylinder defined by a disc
* with radius r around its center c. The thickness of the cylinder is
* d_up - d_down.
*
}
-/*! Prints to swap output file which ions are in which compartments. */
+/*! \brief Prints to swap output file which ions are in which compartment. */
static void print_ionlist(
t_swap *s,
double time,
}
-/*! Get the center of a group of nat atoms. Since with PBC an atom group might
- * not be whole, Use the first atom as the reference atom and determine the
- * center with respect to this reference. */
+/*! \brief Get the center of a group of nat atoms.
+ *
+ * Since with PBC an atom group might not be whole, use the first atom as the
+ * reference atom and determine the center with respect to this reference.
+ */
static void get_molecule_center(
rvec x[],
int nat,
-/*! Returns TRUE if x is between (w1+gap) and (w2-gap)
+/*! \brief Return TRUE if ion is found in the compartment.
+ *
+ * Returns TRUE if x is between (w1+gap) and (w2-gap)
*
* \code
*
}
-/*! Updates the time-averaged number of ions in a compartment. */
+/*! \brief Updates the time-averaged number of ions in a compartment. */
static void update_time_window(t_compartment *comp, int values, int replace)
{
real average;
}
-/*! Add atom with collective index ci to the list 'comp' */
+/*! \brief Add atom with collective index ci to the list 'comp'. */
static void add_to_list(
int ci, /* index of this ion in the collective array xc, qc */
t_compartment *comp, /* Compartment to add this atom to */
}
-/*! Determine the compartment boundaries from the channel centers. */
+/*! \brief Determine the compartment boundaries from the channel centers. */
static void get_compartment_boundaries(
int c,
t_swap *s,
}
-/*! To determine the flux through the individual channels, we
+/*! \brief Determine the per-channel ion flux.
+ *
+ * To determine the flux through the individual channels, we
* remember the compartment and channel history of each ion. An ion can be
* either in channel0 or channel1, or in the remaining volume of compartment
* A or B.
}
-/*! Get the lists of ions for the two compartments */
+/*! \brief Get the lists of ions for the two compartments */
static void compartmentalize_ions(
t_commrec *cr,
t_swapcoords *sc,
}
else
{
- fprintf(stderr, "%s node %d: Inconsistency during ion compartmentalization. !inA: %d, !inB: %d, total ions %d\n",
+ fprintf(stderr, "%s rank %d: Inconsistency during ion compartmentalization. !inA: %d, !inB: %d, total ions %d\n",
SwS, cr->nodeid, not_in_comp[eCompA], not_in_comp[eCompB], iong->nat);
}
}
else
{
- fprintf(stderr, "%s node %d: %d atoms are in the ion group, but altogether %d have been assigned to the compartments.\n",
+ fprintf(stderr, "%s rank %d: %d atoms are in the ion group, but altogether %d have been assigned to the compartments.\n",
SwS, cr->nodeid, iong->nat, sum);
}
}
}
-/*! Set up the compartments and get lists of solvent atoms in each compartment */
+/*! \brief Set up the compartments and get lists of solvent atoms in each compartment */
static void compartmentalize_solvent(
t_commrec *cr,
t_swapcoords *sc,
}
else
{
- fprintf(stderr, "%s node %d: Inconsistency during solvent compartmentalization. !inA: %d, !inB: %d, solvent atoms %d\n",
+ fprintf(stderr, "%s rank %d: Inconsistency during solvent compartmentalization. !inA: %d, !inB: %d, solvent atoms %d\n",
SwS, cr->nodeid, not_in_comp[eCompA], not_in_comp[eCompB], solg->nat);
}
}
}
else
{
- fprintf(stderr, "%s node %d: %d atoms in solvent group, but %d have been assigned to the compartments.\n",
+ fprintf(stderr, "%s rank %d: %d atoms in solvent group, but %d have been assigned to the compartments.\n",
SwS, cr->nodeid, solg->nat, sum);
}
}
}
-/*! Find out how many group atoms are in the compartments initially */
+/*! \brief Find out how many group atoms are in the compartments initially */
static void get_initial_ioncounts(
t_inputrec *ir,
rvec x[], /* the initial positions */
}
-/*! When called, the checkpoint file has already been read in. Here we copy
+/*! \brief Copy history of ion counts from checkpoint file.
+ *
+ * When called, the checkpoint file has already been read in. Here we copy
* over the values from .cpt file to the swap data structure.
*/
static void get_initial_ioncounts_from_cpt(
}
-/*! Master node lets all other nodes know about the initial ion counts. */
+/*! \brief The master lets all others know about the initial ion counts. */
static void bc_initial_concentrations(
t_commrec *cr,
t_swapcoords *swap)
}
-/*! Ensure that each atom belongs to at most one of the swap groups. */
+/*! \brief Ensure that each atom belongs to at most one of the swap groups. */
static void check_swap_groups(t_swap *s, int nat, gmx_bool bVerbose)
{
t_group *g;
}
-/*! Get the number of atoms per molecule for this group.
- * Also ensure that all the molecules in this group have this number of atoms. */
+/*! \brief Get the number of atoms per molecule for this group.
+ *
+ * Also ensure that all the molecules in this group have this number of atoms.
+ */
static int get_group_apm_check(
int group,
t_swap *s,
}
-/*! Print the legend to the swapcoords output file as well as the
- * initial ion counts */
+/*! \brief Print the legend to the swap output file.
+ *
+ * Also print the initial ion counts
+ */
static void print_ionlist_legend(t_inputrec *ir, const output_env_t oenv)
{
const char **legend;
}
-/*! Initialize arrays that keep track of where the ions come from and where
- * they go */
+/*! \brief Initialize channel ion flux detection routine.
+ *
+ * Initialize arrays that keep track of where the ions come from and where
+ * they go.
+ */
static void detect_flux_per_channel_init(
t_commrec *cr,
t_swap *s,
}
-/*! Output the starting structure so that in case of multimeric channels
+/*! \brief Outputs the initial structure to PDB file for debugging reasons.
+ *
+ * Output the starting structure so that in case of multimeric channels
* the user can check whether we have the correct PBC image for all atoms.
* If this is not correct, the ion counts per channel will be very likely
- * wrong. */
+ * wrong.
+ */
static void outputStartStructureIfWanted(gmx_mtop_t *mtop, rvec *x, int ePBC, matrix box)
{
char *env = getenv("GMX_COMPELDUMP");
}
-/*! The swapstate struct stores the information we need to make the channels
- * whole again after restarts from a checkpoint file. Here we do the following:
+/*! \brief Initialize the swapstate structure, used for checkpoint writing.
+ *
+ * The swapstate struct stores the information we need to make the channels
+ * whole again after restarts from a checkpoint file. Here we do the following:\n
* a) If we did not start from .cpt, we prepare the struct for proper .cpt writing,\n
* b) if we did start from .cpt, we copy over the last whole structures from .cpt,\n
* c) in any case, for subsequent checkpoint writing, we set the pointers in\n
* swapstate to the x_old arrays, which contain the correct PBC representation of
- * multimeric channels at the last time step. */
+ * multimeric channels at the last time step.
+ */
static void init_swapstate(
swapstate_t *swapstate,
t_swapcoords *sc,
}
-/*! From the requested and average ion counts we determine whether a swap is needed
- * at this time step. */
+/*! \brief Do we need to swap ions with water molecules at this step?
+ *
+ * From the requested and average ion counts we determine whether a swap is needed
+ * at this time step.
+ */
static gmx_bool need_swap(t_swapcoords *sc)
{
t_swap *s;
}
-/*! Returns the index of an atom that is far off the compartment boundaries.
+/*! \brief Return index of atom that we can use for swapping.
+ *
+ * Returns the index of an atom that is far off the compartment boundaries.
* Other atoms of the molecule (if any) will directly follow the returned index
*/
static int get_index_of_distant_atom(
}
-/*! Swaps centers of mass and makes molecule whole if broken */
+/*! \brief Swaps centers of mass and makes molecule whole if broken */
static void translate_positions(
rvec *x,
int apm,
}
-/*! Write back the the modified local positions from the collective array to the official coordinates */
+/*! \brief Write back the the modified local positions from the collective array to the official positions. */
static void apply_modified_positions(
t_group *g,
rvec x[])
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