#include <stdio.h>
-#include "simple.h"
-#include "enums.h"
-#include "../../swap/enums.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/swap/enums.h"
#ifdef __cplusplus
extern "C" {
valid value if positive) */
int init_fep_state; /* the initial number of the state */
double delta_lambda; /* change of lambda per time step (fraction of (0.1) */
- gmx_bool bPrintEnergy; /* Whether to print the energy in the dhdl */
+ int edHdLPrintEnergy; /* print no, total or potential energies in dhdl */
int n_lambda; /* The number of foreign lambda points */
double **all_lambda; /* The array of all lambda values */
int lambda_neighbors; /* The number of neighboring lambda states to
t_pull_coord *coord; /* the pull coordinates */
/* Variables not present in mdp, but used at run time */
- t_pull_group *dyna; /* dynamic groups for use with local constraints */
- rvec *rbuf; /* COM calculation buffer */
- dvec *dbuf; /* COM calculation buffer */
- double *dbuf_cyl; /* cylinder ref. groups COM calculation buffer */
+ t_pull_group *dyna; /* dynamic groups for use with local constraints */
+ gmx_bool bSetPBCatoms; /* Do we need to set x_pbc for the groups? */
- FILE *out_x; /* output file for pull data */
- FILE *out_f; /* output file for pull data */
+ rvec *rbuf; /* COM calculation buffer */
+ dvec *dbuf; /* COM calculation buffer */
+ double *dbuf_cyl; /* cylinder ref. groups COM calculation buffer */
+
+ FILE *out_x; /* output file for pull data */
+ FILE *out_f; /* output file for pull data */
} t_pull;
int nstlist; /* number of steps before pairlist is generated */
int ndelta; /* number of cells per rlong */
int nstcomm; /* number of steps after which center of mass */
- /* motion is removed */
+ /* motion is removed */
int comm_mode; /* Center of mass motion removal algorithm */
- int nstcheckpoint; /* checkpointing frequency */
int nstlog; /* number of steps after which print to logfile */
int nstxout; /* number of steps after which X is output */
int nstvout; /* id. for V */
real ewald_rtol_lj; /* Real space tolerance for LJ-Ewald */
int ewald_geometry; /* normal/3d ewald, or pseudo-2d LR corrections */
real epsilon_surface; /* Epsilon for PME dipole correction */
- gmx_bool bOptFFT; /* optimize the fft plan at start */
int ljpme_combination_rule; /* Type of combination rule in LJ-PME */
int ePBC; /* Type of periodic boundary conditions */
int bPeriodicMols; /* Periodic molecules */
real orires_fc; /* force constant for orientational restraints */
real orires_tau; /* time constant for memory function in orires */
int nstorireout; /* frequency of writing tr(SD) to enx */
- real dihre_fc; /* force constant for dihedral restraints (obsolete) */
real em_stepsize; /* The stepsize for updating */
real em_tol; /* The tolerance */
int niter; /* Number of iterations for convergence of */