* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \internal \file
+ *
+ * \brief This file defines integrators for energy minimization
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \author Erik Lindahl <erik@kth.se>
+ * \ingroup module_mdlib
+ */
#include "gmxpre.h"
+#include "minimize.h"
+
#include "config.h"
-#include <math.h>
-#include <string.h>
-#include <time.h>
+#include <cmath>
+#include <cstring>
+#include <ctime>
#include <algorithm>
+#include <vector>
+#include "gromacs/commandline/filenm.h"
#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/mtxio.h"
-#include "gromacs/fileio/trajectory_writing.h"
+#include "gromacs/gmxlib/md_logging.h"
+#include "gromacs/gmxlib/network.h"
+#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/imd/imd.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/md_support.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/mdebin.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/sim_util.h"
-#include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/linearalgebra/sparsematrix.h"
#include "gromacs/listed-forces/manage-threading.h"
+#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/constr.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/ns.h"
+#include "gromacs/mdlib/shellfc.h"
+#include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdlib/tgroup.h"
+#include "gromacs/mdlib/trajectory_writing.h"
+#include "gromacs/mdlib/update.h"
+#include "gromacs/mdlib/vsite.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
+//! Utility structure for manipulating states during EM
typedef struct {
+ //! Copy of the global state
t_state s;
+ //! Force array
rvec *f;
+ //! Potential energy
real epot;
+ //! Norm of the force
real fnorm;
+ //! Maximum force
real fmax;
+ //! Direction
int a_fmax;
} em_state_t;
+//! Initiate em_state_t structure and return pointer to it
static em_state_t *init_em_state()
{
em_state_t *ems;
return ems;
}
+//! Print the EM starting conditions
static void print_em_start(FILE *fplog,
t_commrec *cr,
gmx_walltime_accounting_t walltime_accounting,
wallcycle_start(wcycle, ewcRUN);
print_start(fplog, cr, walltime_accounting, name);
}
+
+//! Stop counting time for EM
static void em_time_end(gmx_walltime_accounting_t walltime_accounting,
gmx_wallcycle_t wcycle)
{
walltime_accounting_end(walltime_accounting);
}
+//! Printing a log file and console header
static void sp_header(FILE *out, const char *minimizer, real ftol, int nsteps)
{
fprintf(out, "\n");
fprintf(out, " Number of steps = %12d\n", nsteps);
}
+//! Print warning message
static void warn_step(FILE *fp, real ftol, gmx_bool bLastStep, gmx_bool bConstrain)
{
char buffer[2048];
fputs(wrap_lines(buffer, 78, 0, FALSE), fp);
}
-
-
+//! Print message about convergence of the EM
static void print_converged(FILE *fp, const char *alg, real ftol,
gmx_int64_t count, gmx_bool bDone, gmx_int64_t nsteps,
real epot, real fmax, int nfmax, real fnorm)
alg, ftol, gmx_step_str(count, buf));
}
-#ifdef GMX_DOUBLE
+#if GMX_DOUBLE
fprintf(fp, "Potential Energy = %21.14e\n", epot);
fprintf(fp, "Maximum force = %21.14e on atom %d\n", fmax, nfmax+1);
fprintf(fp, "Norm of force = %21.14e\n", fnorm);
#endif
}
+//! Compute the norm and max of the force array in parallel
static void get_f_norm_max(t_commrec *cr,
t_grpopts *opts, t_mdatoms *mdatoms, rvec *f,
real *fnorm, real *fmax, int *a_fmax)
{
if (!opts->nFreeze[gf][m])
{
- fam += sqr(f[i][m]);
+ fam += gmx::square(f[i][m]);
}
}
fnorm2 += fam;
}
}
+//! Compute the norm of the force
static void get_state_f_norm_max(t_commrec *cr,
t_grpopts *opts, t_mdatoms *mdatoms,
em_state_t *ems)
get_f_norm_max(cr, opts, mdatoms, ems->f, &ems->fnorm, &ems->fmax, &ems->a_fmax);
}
+//! Initialize the energy minimization
void init_em(FILE *fplog, const char *title,
t_commrec *cr, t_inputrec *ir,
t_state *state_global, gmx_mtop_t *top_global,
em_state_t *ems, gmx_localtop_t **top,
- rvec **f, rvec **f_global,
+ rvec **f,
t_nrnb *nrnb, rvec mu_tot,
t_forcerec *fr, gmx_enerdata_t **enerd,
t_graph **graph, t_mdatoms *mdatoms, gmx_global_stat_t *gstat,
dd_partition_system(fplog, ir->init_step, cr, TRUE, 1,
state_global, top_global, ir,
&ems->s, &ems->f, mdatoms, *top,
- fr, vsite, NULL, constr,
+ fr, vsite, constr,
nrnb, NULL, FALSE);
dd_store_state(cr->dd, &ems->s);
- if (ir->nstfout)
- {
- snew(*f_global, top_global->natoms);
- }
- else
- {
- *f_global = NULL;
- }
*graph = NULL;
}
else
/* Just copy the state */
ems->s = *state_global;
- snew(ems->s.x, ems->s.nalloc);
- snew(ems->f, ems->s.nalloc);
+ /* We need to allocate one element extra, since we might use
+ * (unaligned) 4-wide SIMD loads to access rvec entries.
+ */
+ snew(ems->s.x, ems->s.nalloc + 1);
+ snew(ems->f, ems->s.nalloc+1);
+ snew(ems->s.v, ems->s.nalloc+1);
for (i = 0; i < state_global->natoms; i++)
{
copy_rvec(state_global->x[i], ems->s.x[i]);
}
copy_mat(state_global->box, ems->s.box);
- *top = gmx_mtop_generate_local_top(top_global, ir);
- *f_global = *f;
+ *top = gmx_mtop_generate_local_top(top_global, ir->efep != efepNO);
setup_bonded_threading(fr, &(*top)->idef);
calc_shifts(ems->s.box, fr->shift_vec);
}
+//! Finalize the minimization
static void finish_em(t_commrec *cr, gmx_mdoutf_t outf,
gmx_walltime_accounting_t walltime_accounting,
gmx_wallcycle_t wcycle)
em_time_end(walltime_accounting, wcycle);
}
+//! Swap two different EM states during minimization
static void swap_em_state(em_state_t *ems1, em_state_t *ems2)
{
em_state_t tmp;
*ems2 = tmp;
}
+//! Copy coordinate from an EM state to a "normal" state structure
static void copy_em_coords(em_state_t *ems, t_state *state)
{
int i;
}
}
+//! Save the EM trajectory
static void write_em_traj(FILE *fplog, t_commrec *cr,
gmx_mdoutf_t outf,
gmx_bool bX, gmx_bool bF, const char *confout,
gmx_mtop_t *top_global,
t_inputrec *ir, gmx_int64_t step,
em_state_t *state,
- t_state *state_global, rvec *f_global)
+ t_state *state_global)
{
int mdof_flags;
gmx_bool bIMDout = FALSE;
if ((bX || bF || bIMDout || confout != NULL) && !DOMAINDECOMP(cr))
{
copy_em_coords(state, state_global);
- f_global = state->f;
}
mdof_flags = 0;
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
top_global, step, (double)step,
- &state->s, state_global, state->f, f_global);
+ &state->s, state_global, state->f);
if (confout != NULL && MASTER(cr))
{
}
}
-static void do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
+//! \brief Do one minimization step
+//
+// \returns true when the step succeeded, false when a constraint error occurred
+static bool do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
gmx_bool bMolPBC,
em_state_t *ems1, real a, rvec *f, em_state_t *ems2,
gmx_constr_t constr, gmx_localtop_t *top,
real dvdl_constr;
int nthreads gmx_unused;
+ bool validStep = true;
+
s1 = &ems1->s;
s2 = &ems2->s;
if (s2->nalloc != s1->nalloc)
{
s2->nalloc = s1->nalloc;
- srenew(s2->x, s1->nalloc);
+ /* We need to allocate one element extra, since we might use
+ * (unaligned) 4-wide SIMD loads to access rvec entries.
+ */
+ srenew(s2->x, s1->nalloc + 1);
srenew(ems2->f, s1->nalloc);
if (s2->flags & (1<<estCGP))
{
- srenew(s2->cg_p, s1->nalloc);
+ srenew(s2->cg_p, s1->nalloc + 1);
}
}
#pragma omp for schedule(static) nowait
for (int i = start; i < end; i++)
{
- if (md->cFREEZE)
- {
- gf = md->cFREEZE[i];
- }
- for (int m = 0; m < DIM; m++)
+ try
{
- if (ir->opts.nFreeze[gf][m])
+ if (md->cFREEZE)
{
- x2[i][m] = x1[i][m];
+ gf = md->cFREEZE[i];
}
- else
+ for (int m = 0; m < DIM; m++)
{
- x2[i][m] = x1[i][m] + a*f[i][m];
+ if (ir->opts.nFreeze[gf][m])
+ {
+ x2[i][m] = x1[i][m];
+ }
+ else
+ {
+ x2[i][m] = x1[i][m] + a*f[i][m];
+ }
}
}
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
if (s2->flags & (1<<estCGP))
#pragma omp for schedule(static) nowait
for (int i = start; i < end; i++)
{
+ // Trivial OpenMP block that does not throw
copy_rvec(p1[i], p2[i]);
}
}
{
#pragma omp barrier
s2->cg_gl_nalloc = s1->cg_gl_nalloc;
- srenew(s2->cg_gl, s2->cg_gl_nalloc);
+ try
+ {
+ /* We need to allocate one element extra, since we might use
+ * (unaligned) 4-wide SIMD loads to access rvec entries.
+ */
+ srenew(s2->cg_gl, s2->cg_gl_nalloc + 1);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
#pragma omp barrier
}
s2->ncg_gl = s1->ncg_gl;
{
wallcycle_start(wcycle, ewcCONSTR);
dvdl_constr = 0;
- constrain(NULL, TRUE, TRUE, constr, &top->idef,
- ir, cr, count, 0, 1.0, md,
- s1->x, s2->x, NULL, bMolPBC, s2->box,
- s2->lambda[efptBONDED], &dvdl_constr,
- NULL, NULL, nrnb, econqCoord);
+ validStep =
+ constrain(NULL, TRUE, TRUE, constr, &top->idef,
+ ir, cr, count, 0, 1.0, md,
+ s1->x, s2->x, NULL, bMolPBC, s2->box,
+ s2->lambda[efptBONDED], &dvdl_constr,
+ NULL, NULL, nrnb, econqCoord);
wallcycle_stop(wcycle, ewcCONSTR);
+
+ // We should move this check to the different minimizers
+ if (!validStep && ir->eI != eiSteep)
+ {
+ gmx_fatal(FARGS, "The coordinates could not be constrained. Minimizer '%s' can not handle constraint failures, use minimizer '%s' before using '%s'.",
+ EI(ir->eI), EI(eiSteep), EI(ir->eI));
+ }
}
+
+ return validStep;
}
+//! Prepare EM for using domain decomposition parallellization
static void em_dd_partition_system(FILE *fplog, int step, t_commrec *cr,
gmx_mtop_t *top_global, t_inputrec *ir,
em_state_t *ems, gmx_localtop_t *top,
dd_partition_system(fplog, step, cr, FALSE, 1,
NULL, top_global, ir,
&ems->s, &ems->f,
- mdatoms, top, fr, vsite, NULL, constr,
+ mdatoms, top, fr, vsite, constr,
nrnb, wcycle, FALSE);
dd_store_state(cr->dd, &ems->s);
}
+//! De one energy evaluation
static void evaluate_energy(FILE *fplog, t_commrec *cr,
gmx_mtop_t *top_global,
em_state_t *ems, gmx_localtop_t *top,
ems->s.lambda, graph, fr, vsite, mu_tot, t, NULL, NULL, TRUE,
GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES |
GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY |
- (bNS ? GMX_FORCE_NS | GMX_FORCE_DO_LR : 0));
+ (bNS ? GMX_FORCE_NS : 0));
/* Clear the unused shake virial and pressure */
clear_mat(shake_vir);
{
wallcycle_start(wcycle, ewcMoveE);
- global_stat(fplog, gstat, cr, enerd, force_vir, shake_vir, mu_tot,
+ global_stat(gstat, cr, enerd, force_vir, shake_vir, mu_tot,
inputrec, NULL, NULL, NULL, 1, &terminate,
- top_global, &ems->s, FALSE,
+ NULL, FALSE,
CGLO_ENERGY |
CGLO_PRESSURE |
CGLO_CONSTRAINT);
}
/* Calculate long range corrections to pressure and energy */
- calc_dispcorr(inputrec, fr, top_global->natoms, ems->s.box, ems->s.lambda[efptVDW],
+ calc_dispcorr(inputrec, fr, ems->s.box, ems->s.lambda[efptVDW],
pres, force_vir, &prescorr, &enercorr, &dvdlcorr);
enerd->term[F_DISPCORR] = enercorr;
enerd->term[F_EPOT] += enercorr;
}
}
+//! Parallel utility summing energies and forces
static double reorder_partsum(t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms,
- gmx_mtop_t *mtop,
+ gmx_mtop_t *top_global,
em_state_t *s_min, em_state_t *s_b)
{
rvec *fm, *fb, *fmg;
* This conflicts with the spirit of domain decomposition,
* but to fully optimize this a much more complicated algorithm is required.
*/
- snew(fmg, mtop->natoms);
+ snew(fmg, top_global->natoms);
ncg = s_min->s.ncg_gl;
cg_gl = s_min->s.cg_gl;
i++;
}
}
- gmx_sum(mtop->natoms*3, fmg[0], cr);
+ gmx_sum(top_global->natoms*3, fmg[0], cr);
/* Now we will determine the part of the sum for the cgs in state s_b */
ncg = s_b->s.ncg_gl;
partsum = 0;
i = 0;
gf = 0;
- grpnrFREEZE = mtop->groups.grpnr[egcFREEZE];
+ grpnrFREEZE = top_global->groups.grpnr[egcFREEZE];
for (c = 0; c < ncg; c++)
{
cg = cg_gl[c];
return partsum;
}
+//! Print some stuff, like beta, whatever that means.
static real pr_beta(t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms,
- gmx_mtop_t *mtop,
+ gmx_mtop_t *top_global,
em_state_t *s_min, em_state_t *s_b)
{
rvec *fm, *fb;
else
{
/* We need to reorder cgs while summing */
- sum = reorder_partsum(cr, opts, mdatoms, mtop, s_min, s_b);
+ sum = reorder_partsum(cr, opts, mdatoms, top_global, s_min, s_b);
}
if (PAR(cr))
{
gmx_sumd(1, &sum, cr);
}
- return sum/sqr(s_min->fnorm);
+ return sum/gmx::square(s_min->fnorm);
}
+namespace gmx
+{
+
+/*! \brief Do conjugate gradients minimization
+ \copydoc integrator_t (FILE *fplog, t_commrec *cr,
+ int nfile, const t_filenm fnm[],
+ const gmx_output_env_t *oenv, gmx_bool bVerbose,
+ int nstglobalcomm,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ int stepout,
+ t_inputrec *inputrec,
+ gmx_mtop_t *top_global, t_fcdata *fcd,
+ t_state *state_global,
+ t_mdatoms *mdatoms,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_edsam_t ed,
+ t_forcerec *fr,
+ int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
+ gmx_membed_t gmx_unused *membed,
+ real cpt_period, real max_hours,
+ int imdport,
+ unsigned long Flags,
+ gmx_walltime_accounting_t walltime_accounting)
+ */
double do_cg(FILE *fplog, t_commrec *cr,
int nfile, const t_filenm fnm[],
- const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
+ const gmx_output_env_t gmx_unused *oenv, gmx_bool bVerbose,
int gmx_unused nstglobalcomm,
gmx_vsite_t *vsite, gmx_constr_t constr,
int gmx_unused stepout,
gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
- gmx_membed_t gmx_unused membed,
+ gmx_membed_t gmx_unused *membed,
real gmx_unused cpt_period, real gmx_unused max_hours,
int imdport,
unsigned long gmx_unused Flags,
rvec *f;
gmx_global_stat_t gstat;
t_graph *graph;
- rvec *f_global, *p, *sf;
+ rvec *p, *sf;
double gpa, gpb, gpc, tmp, minstep;
real fnormn;
real stepsize;
/* Init em and store the local state in s_min */
init_em(fplog, CG, cr, inputrec,
- state_global, top_global, s_min, &top, &f, &f_global,
+ state_global, top_global, s_min, &top, &f,
nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
mdatoms->tmass, enerd, &s_min->s, inputrec->fepvals, inputrec->expandedvals, s_min->s.box,
NULL, NULL, vir, pres, NULL, mu_tot, constr);
- print_ebin_header(fplog, step, step, s_min->s.lambda[efptFEP]);
+ print_ebin_header(fplog, step, step);
print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+ mdebin, fcd, &(top_global->groups), &(inputrec->opts));
}
where();
* we either converge or reach the max number of steps.
*/
converged = FALSE;
- for (step = 0; (number_steps < 0 || (number_steps >= 0 && step <= number_steps)) && !converged; step++)
+ for (step = 0; (number_steps < 0 || step <= number_steps) && !converged; step++)
{
/* start taking steps in a new direction
write_em_traj(fplog, cr, outf, do_x, do_f, NULL,
top_global, inputrec, step,
- s_min, state_global, f_global);
+ s_min, state_global);
/* Take a step downhill.
* In theory, we should minimize the function along this direction.
fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
step, s_min->epot, s_min->fnorm/sqrtNumAtoms,
s_min->fmax, s_min->a_fmax+1);
+ fflush(stderr);
}
/* Store the new (lower) energies */
upd_mdebin(mdebin, FALSE, FALSE, (double)step,
if (do_log)
{
- print_ebin_header(fplog, step, step, s_min->s.lambda[efptFEP]);
+ print_ebin_header(fplog, step, step);
}
print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
do_log ? fplog : NULL, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+ mdebin, fcd, &(top_global->groups), &(inputrec->opts));
}
/* Send energies and positions to the IMD client if bIMD is TRUE. */
*/
converged = converged || (s_min->fmax < inputrec->em_tol);
- } /* End of the loop */
+ } /* End of the loop */
/* IMD cleanup, if bIMD is TRUE. */
IMD_finalize(inputrec->bIMD, inputrec->imd);
if (!do_log)
{
/* Write final value to log since we didn't do anything the last step */
- print_ebin_header(fplog, step, step, s_min->s.lambda[efptFEP]);
+ print_ebin_header(fplog, step, step);
}
if (!do_ene || !do_log)
{
/* Write final energy file entries */
print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
!do_log ? fplog : NULL, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+ mdebin, fcd, &(top_global->groups), &(inputrec->opts));
}
}
write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm),
top_global, inputrec, step,
- s_min, state_global, f_global);
+ s_min, state_global);
if (MASTER(cr))
walltime_accounting_set_nsteps_done(walltime_accounting, step);
return 0;
-} /* That's all folks */
-
-
+} /* That's all folks */
+
+
+/*! \brief Do L-BFGS conjugate gradients minimization
+ \copydoc integrator_t (FILE *fplog, t_commrec *cr,
+ int nfile, const t_filenm fnm[],
+ const gmx_output_env_t *oenv, gmx_bool bVerbose,
+ int nstglobalcomm,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ int stepout,
+ t_inputrec *inputrec,
+ gmx_mtop_t *top_global, t_fcdata *fcd,
+ t_state *state_global,
+ t_mdatoms *mdatoms,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_edsam_t ed,
+ t_forcerec *fr,
+ int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
+ real cpt_period, real max_hours,
+ int imdport,
+ unsigned long Flags,
+ gmx_walltime_accounting_t walltime_accounting)
+ */
double do_lbfgs(FILE *fplog, t_commrec *cr,
int nfile, const t_filenm fnm[],
- const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
+ const gmx_output_env_t gmx_unused *oenv, gmx_bool bVerbose,
int gmx_unused nstglobalcomm,
gmx_vsite_t *vsite, gmx_constr_t constr,
int gmx_unused stepout,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
- t_state *state,
+ t_state *state_global,
t_mdatoms *mdatoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
- gmx_membed_t gmx_unused membed,
+ gmx_membed_t gmx_unused *membed,
real gmx_unused cpt_period, real gmx_unused max_hours,
int imdport,
unsigned long gmx_unused Flags,
rvec *f;
gmx_global_stat_t gstat;
t_graph *graph;
- rvec *f_global;
int ncorr, nmaxcorr, point, cp, neval, nminstep;
double stepsize, step_taken, gpa, gpb, gpc, tmp, minstep;
real *rho, *alpha, *ff, *xx, *p, *s, *lastx, *lastf, **dx, **dg;
gmx_fatal(FARGS, "The combination of constraints and L-BFGS minimization is not implemented. Either do not use constraints, or use another minimizer (e.g. steepest descent).");
}
- n = 3*state->natoms;
+ n = 3*state_global->natoms;
nmaxcorr = inputrec->nbfgscorr;
/* Allocate memory */
/* Init em */
init_em(fplog, LBFGS, cr, inputrec,
- state, top_global, &ems, &top, &f, &f_global,
+ state_global, top_global, &ems, &top, &f,
nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
/* Do_lbfgs is not completely updated like do_steep and do_cg,
sfree(ems.s.x);
sfree(ems.f);
- xx = (real *)state->x;
+ xx = (real *)state_global->x;
ff = (real *)f;
start = 0;
if (vsite)
{
- construct_vsites(vsite, state->x, 1, NULL,
+ construct_vsites(vsite, state_global->x, 1, NULL,
top->idef.iparams, top->idef.il,
- fr->ePBC, fr->bMolPBC, cr, state->box);
+ fr->ePBC, fr->bMolPBC, cr, state_global->box);
}
/* Call the force routine and some auxiliary (neighboursearching etc.) */
* We do not unshift, so molecules are always whole
*/
neval++;
- ems.s.x = state->x;
+ ems.s.x = state_global->x;
ems.f = f;
evaluate_energy(fplog, cr,
top_global, &ems, top,
{
/* Copy stuff to the energy bin for easy printing etc. */
upd_mdebin(mdebin, FALSE, FALSE, (double)step,
- mdatoms->tmass, enerd, state, inputrec->fepvals, inputrec->expandedvals, state->box,
+ mdatoms->tmass, enerd, state_global, inputrec->fepvals, inputrec->expandedvals, state_global->box,
NULL, NULL, vir, pres, NULL, mu_tot, constr);
- print_ebin_header(fplog, step, step, state->lambda[efptFEP]);
+ print_ebin_header(fplog, step, step);
print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+ mdebin, fcd, &(top_global->groups), &(inputrec->opts));
}
where();
if (MASTER(cr))
{
- double sqrtNumAtoms = sqrt(static_cast<double>(state->natoms));
+ double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
fprintf(stderr, "Using %d BFGS correction steps.\n\n", nmaxcorr);
fprintf(stderr, " F-max = %12.5e on atom %d\n", fmax, nfmax+1);
fprintf(stderr, " F-Norm = %12.5e\n", fnorm/sqrtNumAtoms);
/* Set the gradient from the force */
converged = FALSE;
- for (step = 0; (number_steps < 0 || (number_steps >= 0 && step <= number_steps)) && !converged; step++)
+ for (step = 0; (number_steps < 0 || step <= number_steps) && !converged; step++)
{
/* Write coordinates if necessary */
}
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
- top_global, step, (real)step, state, state, f, f);
+ top_global, step, (real)step, state_global, state_global, f);
/* Do the linesearching in the direction dx[point][0..(n-1)] */
{
if (bVerbose)
{
- double sqrtNumAtoms = sqrt(static_cast<double>(state->natoms));
+ double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
step, Epot, fnorm/sqrtNumAtoms, fmax, nfmax+1);
+ fflush(stderr);
}
/* Store the new (lower) energies */
upd_mdebin(mdebin, FALSE, FALSE, (double)step,
- mdatoms->tmass, enerd, state, inputrec->fepvals, inputrec->expandedvals, state->box,
+ mdatoms->tmass, enerd, state_global, inputrec->fepvals, inputrec->expandedvals, state_global->box,
NULL, NULL, vir, pres, NULL, mu_tot, constr);
do_log = do_per_step(step, inputrec->nstlog);
do_ene = do_per_step(step, inputrec->nstenergy);
if (do_log)
{
- print_ebin_header(fplog, step, step, state->lambda[efptFEP]);
+ print_ebin_header(fplog, step, step);
}
print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
do_log ? fplog : NULL, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+ mdebin, fcd, &(top_global->groups), &(inputrec->opts));
}
/* Send x and E to IMD client, if bIMD is TRUE. */
- if (do_IMD(inputrec->bIMD, step, cr, TRUE, state->box, state->x, inputrec, 0, wcycle) && MASTER(cr))
+ if (do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, state_global->x, inputrec, 0, wcycle) && MASTER(cr))
{
IMD_send_positions(inputrec->imd);
}
*/
converged = converged || (fmax < inputrec->em_tol);
- } /* End of the loop */
+ } /* End of the loop */
/* IMD cleanup, if bIMD is TRUE. */
IMD_finalize(inputrec->bIMD, inputrec->imd);
*/
if (!do_log) /* Write final value to log since we didn't do anythin last step */
{
- print_ebin_header(fplog, step, step, state->lambda[efptFEP]);
+ print_ebin_header(fplog, step, step);
}
if (!do_ene || !do_log) /* Write final energy file entries */
{
print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
!do_log ? fplog : NULL, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+ mdebin, fcd, &(top_global->groups), &(inputrec->opts));
}
/* Print some stuff... */
do_f = !do_per_step(step, inputrec->nstfout);
write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm),
top_global, inputrec, step,
- &ems, state, f);
+ &ems, state_global);
if (MASTER(cr))
{
- double sqrtNumAtoms = sqrt(static_cast<double>(state->natoms));
+ double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
print_converged(stderr, LBFGS, inputrec->em_tol, step, converged,
number_steps, Epot, fmax, nfmax, fnorm/sqrtNumAtoms);
print_converged(fplog, LBFGS, inputrec->em_tol, step, converged,
walltime_accounting_set_nsteps_done(walltime_accounting, step);
return 0;
-} /* That's all folks */
-
-
+} /* That's all folks */
+
+/*! \brief Do steepest descents minimization
+ \copydoc integrator_t (FILE *fplog, t_commrec *cr,
+ int nfile, const t_filenm fnm[],
+ const gmx_output_env_t *oenv, gmx_bool bVerbose,
+ int nstglobalcomm,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ int stepout,
+ t_inputrec *inputrec,
+ gmx_mtop_t *top_global, t_fcdata *fcd,
+ t_state *state_global,
+ t_mdatoms *mdatoms,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_edsam_t ed,
+ t_forcerec *fr,
+ int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
+ real cpt_period, real max_hours,
+ int imdport,
+ unsigned long Flags,
+ gmx_walltime_accounting_t walltime_accounting)
+ */
double do_steep(FILE *fplog, t_commrec *cr,
int nfile, const t_filenm fnm[],
- const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
+ const gmx_output_env_t gmx_unused *oenv, gmx_bool bVerbose,
int gmx_unused nstglobalcomm,
gmx_vsite_t *vsite, gmx_constr_t constr,
int gmx_unused stepout,
gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
- gmx_membed_t gmx_unused membed,
+ gmx_membed_t gmx_unused *membed,
real gmx_unused cpt_period, real gmx_unused max_hours,
int imdport,
unsigned long gmx_unused Flags,
{
const char *SD = "Steepest Descents";
em_state_t *s_min, *s_try;
- rvec *f_global;
gmx_localtop_t *top;
gmx_enerdata_t *enerd;
rvec *f;
/* Init em and store the local state in s_try */
init_em(fplog, SD, cr, inputrec,
- state_global, top_global, s_try, &top, &f, &f_global,
+ state_global, top_global, s_try, &top, &f,
nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
bAbort = (nsteps >= 0) && (count == nsteps);
/* set new coordinates, except for first step */
+ bool validStep = true;
if (count > 0)
{
- do_em_step(cr, inputrec, mdatoms, fr->bMolPBC,
- s_min, stepsize, s_min->f, s_try,
- constr, top, nrnb, wcycle, count);
+ validStep =
+ do_em_step(cr, inputrec, mdatoms, fr->bMolPBC,
+ s_min, stepsize, s_min->f, s_try,
+ constr, top, nrnb, wcycle, count);
}
- evaluate_energy(fplog, cr,
- top_global, s_try, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, count, count == 0);
+ if (validStep)
+ {
+ evaluate_energy(fplog, cr,
+ top_global, s_try, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph, mdatoms, fr,
+ mu_tot, enerd, vir, pres, count, count == 0);
+ }
+ else
+ {
+ // Signal constraint error during stepping with energy=inf
+ s_try->epot = std::numeric_limits<real>::infinity();
+ }
if (MASTER(cr))
{
- print_ebin_header(fplog, count, count, s_try->s.lambda[efptFEP]);
+ print_ebin_header(fplog, count, count);
}
if (count == 0)
fprintf(stderr, "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
count, ustep, s_try->epot, s_try->fmax, s_try->a_fmax+1,
( (count == 0) || (s_try->epot < s_min->epot) ) ? '\n' : '\r');
+ fflush(stderr);
}
if ( (count == 0) || (s_try->epot < s_min->epot) )
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, TRUE,
+ fplog, count, count, eprNORMAL,
mdebin, fcd, &(top_global->groups), &(inputrec->opts));
fflush(fplog);
}
do_f = do_per_step(steps_accepted, inputrec->nstfout);
write_em_traj(fplog, cr, outf, do_x, do_f, NULL,
top_global, inputrec, count,
- s_min, state_global, f_global);
+ s_min, state_global);
}
else
{
stepsize = ustep/s_min->fmax;
/* Check if stepsize is too small, with 1 nm as a characteristic length */
-#ifdef GMX_DOUBLE
+#if GMX_DOUBLE
if (count == nsteps || ustep < 1e-12)
#else
if (count == nsteps || ustep < 1e-6)
}
count++;
- } /* End of the loop */
+ } /* End of the loop */
/* IMD cleanup, if bIMD is TRUE. */
IMD_finalize(inputrec->bIMD, inputrec->imd);
}
write_em_traj(fplog, cr, outf, TRUE, inputrec->nstfout, ftp2fn(efSTO, nfile, fnm),
top_global, inputrec, count,
- s_min, state_global, f_global);
+ s_min, state_global);
if (MASTER(cr))
{
walltime_accounting_set_nsteps_done(walltime_accounting, count);
return 0;
-} /* That's all folks */
-
-
+} /* That's all folks */
+
+/*! \brief Do normal modes analysis
+ \copydoc integrator_t (FILE *fplog, t_commrec *cr,
+ int nfile, const t_filenm fnm[],
+ const gmx_output_env_t *oenv, gmx_bool bVerbose,
+ int nstglobalcomm,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ int stepout,
+ t_inputrec *inputrec,
+ gmx_mtop_t *top_global, t_fcdata *fcd,
+ t_state *state_global,
+ t_mdatoms *mdatoms,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_edsam_t ed,
+ t_forcerec *fr,
+ int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
+ real cpt_period, real max_hours,
+ int imdport,
+ unsigned long Flags,
+ gmx_walltime_accounting_t walltime_accounting)
+ */
double do_nm(FILE *fplog, t_commrec *cr,
int nfile, const t_filenm fnm[],
- const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
+ const gmx_output_env_t gmx_unused *oenv, gmx_bool bVerbose,
int gmx_unused nstglobalcomm,
gmx_vsite_t *vsite, gmx_constr_t constr,
int gmx_unused stepout,
gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
- gmx_membed_t gmx_unused membed,
+ gmx_membed_t gmx_unused *membed,
real gmx_unused cpt_period, real gmx_unused max_hours,
int imdport,
unsigned long gmx_unused Flags,
{
const char *NM = "Normal Mode Analysis";
gmx_mdoutf_t outf;
- int natoms, atom, d;
int nnodes, node;
- rvec *f_global;
gmx_localtop_t *top;
gmx_enerdata_t *enerd;
rvec *f;
rvec mu_tot;
rvec *fneg, *dfdx;
gmx_bool bSparse; /* use sparse matrix storage format */
- size_t sz = 0;
+ size_t sz;
gmx_sparsematrix_t * sparse_matrix = NULL;
real * full_matrix = NULL;
em_state_t * state_work;
/* added with respect to mdrun */
- int i, j, k, row, col;
- real der_range = 10.0*sqrt(GMX_REAL_EPS);
- real x_min;
- bool bIsMaster = MASTER(cr);
+ int row, col;
+ real der_range = 10.0*sqrt(GMX_REAL_EPS);
+ real x_min;
+ bool bIsMaster = MASTER(cr);
if (constr != NULL)
{
/* Init em and store the local state in state_minimum */
init_em(fplog, NM, cr, inputrec,
state_global, top_global, state_work, &top,
- &f, &f_global,
+ &f,
nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
nfile, fnm, &outf, NULL, imdport, Flags, wcycle);
- natoms = top_global->natoms;
- snew(fneg, natoms);
- snew(dfdx, natoms);
+ gmx_shellfc_t *shellfc = init_shell_flexcon(stdout,
+ top_global,
+ n_flexible_constraints(constr),
+ inputrec->nstcalcenergy,
+ DOMAINDECOMP(cr));
-#ifndef GMX_DOUBLE
+ if (shellfc)
+ {
+ make_local_shells(cr, mdatoms, shellfc);
+ }
+ std::vector<size_t> atom_index = get_atom_index(top_global);
+ snew(fneg, atom_index.size());
+ snew(dfdx, atom_index.size());
+
+#if !GMX_DOUBLE
if (bIsMaster)
{
fprintf(stderr,
md_print_info(cr, fplog, "Non-cutoff electrostatics used, forcing full Hessian format.\n");
bSparse = FALSE;
}
- else if (top_global->natoms < 1000)
+ else if (atom_index.size() < 1000)
{
- md_print_info(cr, fplog, "Small system size (N=%d), using full Hessian format.\n", top_global->natoms);
+ md_print_info(cr, fplog, "Small system size (N=%d), using full Hessian format.\n", atom_index.size());
bSparse = FALSE;
}
else
bSparse = TRUE;
}
- if (bIsMaster)
- {
- sz = DIM*top_global->natoms;
+ /* Number of dimensions, based on real atoms, that is not vsites or shell */
+ sz = DIM*atom_index.size();
- fprintf(stderr, "Allocating Hessian memory...\n\n");
+ fprintf(stderr, "Allocating Hessian memory...\n\n");
- if (bSparse)
- {
- sparse_matrix = gmx_sparsematrix_init(sz);
- sparse_matrix->compressed_symmetric = TRUE;
- }
- else
- {
- snew(full_matrix, sz*sz);
- }
+ if (bSparse)
+ {
+ sparse_matrix = gmx_sparsematrix_init(sz);
+ sparse_matrix->compressed_symmetric = TRUE;
+ }
+ else
+ {
+ snew(full_matrix, sz*sz);
}
init_nrnb(nrnb);
print_em_start(fplog, cr, walltime_accounting, wcycle, NM);
/* fudge nr of steps to nr of atoms */
- inputrec->nsteps = natoms*2;
+ inputrec->nsteps = atom_index.size()*2;
if (bIsMaster)
{
************************************************************/
/* Steps are divided one by one over the nodes */
- for (atom = cr->nodeid; atom < natoms; atom += nnodes)
+ bool bNS = true;
+ for (unsigned int aid = cr->nodeid; aid < atom_index.size(); aid += nnodes)
{
-
- for (d = 0; d < DIM; d++)
+ size_t atom = atom_index[aid];
+ for (size_t d = 0; d < DIM; d++)
{
- x_min = state_work->s.x[atom][d];
+ gmx_bool bBornRadii = FALSE;
+ gmx_int64_t step = 0;
+ int force_flags = GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES;
+ double t = 0;
- state_work->s.x[atom][d] = x_min - der_range;
-
- /* Make evaluate_energy do a single node force calculation */
- cr->nnodes = 1;
- evaluate_energy(fplog, cr,
- top_global, state_work, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, atom*2, FALSE);
+ x_min = state_work->s.x[atom][d];
- for (i = 0; i < natoms; i++)
+ for (unsigned int dx = 0; (dx < 2); dx++)
{
- copy_rvec(state_work->f[i], fneg[i]);
- }
+ if (dx == 0)
+ {
+ state_work->s.x[atom][d] = x_min - der_range;
+ }
+ else
+ {
+ state_work->s.x[atom][d] = x_min + der_range;
+ }
- state_work->s.x[atom][d] = x_min + der_range;
+ /* Make evaluate_energy do a single node force calculation */
+ cr->nnodes = 1;
+ if (shellfc)
+ {
+ /* Now is the time to relax the shells */
+ (void) relax_shell_flexcon(fplog, cr, bVerbose, step,
+ inputrec, bNS, force_flags,
+ top,
+ constr, enerd, fcd,
+ &state_work->s, state_work->f, vir, mdatoms,
+ nrnb, wcycle, graph, &top_global->groups,
+ shellfc, fr, bBornRadii, t, mu_tot,
+ vsite, NULL);
+ bNS = false;
+ step++;
+ }
+ else
+ {
+ evaluate_energy(fplog, cr,
+ top_global, state_work, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph, mdatoms, fr,
+ mu_tot, enerd, vir, pres, atom*2+dx, FALSE);
+ }
- evaluate_energy(fplog, cr,
- top_global, state_work, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, atom*2+1, FALSE);
- cr->nnodes = nnodes;
+ cr->nnodes = nnodes;
+
+ if (dx == 0)
+ {
+ for (size_t i = 0; i < atom_index.size(); i++)
+ {
+ copy_rvec(state_work->f[atom_index[i]], fneg[i]);
+ }
+ }
+ }
/* x is restored to original */
state_work->s.x[atom][d] = x_min;
- for (j = 0; j < natoms; j++)
+ for (size_t j = 0; j < atom_index.size(); j++)
{
- for (k = 0; (k < DIM); k++)
+ for (size_t k = 0; (k < DIM); k++)
{
dfdx[j][k] =
- -(state_work->f[j][k] - fneg[j][k])/(2*der_range);
+ -(state_work->f[atom_index[j]][k] - fneg[j][k])/(2*der_range);
}
}
if (!bIsMaster)
{
-#ifdef GMX_MPI
-#ifdef GMX_DOUBLE
-#define mpi_type MPI_DOUBLE
-#else
-#define mpi_type MPI_FLOAT
-#endif
- MPI_Send(dfdx[0], natoms*DIM, mpi_type, MASTERNODE(cr), cr->nodeid,
- cr->mpi_comm_mygroup);
+#if GMX_MPI
+#define mpi_type GMX_MPI_REAL
+ MPI_Send(dfdx[0], atom_index.size()*DIM, mpi_type, MASTER(cr),
+ cr->nodeid, cr->mpi_comm_mygroup);
#endif
}
else
{
- for (node = 0; (node < nnodes && atom+node < natoms); node++)
+ for (node = 0; (node < nnodes && atom+node < atom_index.size()); node++)
{
if (node > 0)
{
-#ifdef GMX_MPI
+#if GMX_MPI
MPI_Status stat;
- MPI_Recv(dfdx[0], natoms*DIM, mpi_type, node, node,
+ MPI_Recv(dfdx[0], atom_index.size()*DIM, mpi_type, node, node,
cr->mpi_comm_mygroup, &stat);
#undef mpi_type
#endif
row = (atom + node)*DIM + d;
- for (j = 0; j < natoms; j++)
+ for (size_t j = 0; j < atom_index.size(); j++)
{
- for (k = 0; k < DIM; k++)
+ for (size_t k = 0; k < DIM; k++)
{
col = j*DIM + k;
if (bIsMaster && bVerbose)
{
fprintf(stderr, "\rFinished step %d out of %d",
- std::min(atom+nnodes, natoms), natoms);
+ static_cast<int>(std::min(atom+nnodes, atom_index.size())),
+ static_cast<int>(atom_index.size()));
fflush(stderr);
}
}
finish_em(cr, outf, walltime_accounting, wcycle);
- walltime_accounting_set_nsteps_done(walltime_accounting, natoms*2);
+ walltime_accounting_set_nsteps_done(walltime_accounting, atom_index.size()*2);
return 0;
}
+
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff