void gmx_sumli_sim(int nr, gmx_large_int_t r[], const gmx_multisim_t *ms)
{
#ifndef GMX_MPI
gmx_call("gmx_sumli_sim");
#else
#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREAD_MPI)
MPI_Allreduce(MPI_IN_PLACE, r, nr, GMX_MPI_LARGE_INT, MPI_SUM,
ms->mpi_comm_masters);
#else
/* this is thread-unsafe, but it will do for now: */
int i;
if (nr > ms->mpb->libuf_alloc)
{
ms->mpb->libuf_alloc = nr;
srenew(ms->mpb->libuf, ms->mpb->libuf_alloc);
}
MPI_Allreduce(r, ms->mpb->libuf, nr, GMX_MPI_LARGE_INT, MPI_SUM,
ms->mpi_comm_masters);
for (i = 0; i < nr; i++)
{
r[i] = ms->mpb->libuf[i];
}
#endif
#endif
}
void gmx_finalize(const t_commrec *cr)
{
int ret;
#ifndef GMX_MPI
gmx_call("gmx_finalize");
#else
/* We sync the processes here to try to avoid problems
* with buggy MPI implementations that could cause
* unfinished processes to terminate.
*/
MPI_Barrier(MPI_COMM_WORLD);
/*
if (DOMAINDECOMP(cr)) {
if (cr->npmenodes > 0 || cr->dd->bCartesian)
MPI_Comm_free(&cr->mpi_comm_mygroup);
if (cr->dd->bCartesian)
MPI_Comm_free(&cr->mpi_comm_mysim);
}
*/
/* Apparently certain mpich implementations cause problems
* with MPI_Finalize. In that case comment out MPI_Finalize.
*/
if (debug)
fprintf(debug,"Will call MPI_Finalize now\n");
ret = MPI_Finalize();
if (debug)
fprintf(debug,"Return code from MPI_Finalize = %d\n",ret);
#endif
}
void gmx_abort(int noderank, int nnodes, int errorno)
{
#ifndef GMX_MPI
gmx_call("gmx_abort");
#else
#ifdef GMX_THREAD_MPI
fprintf(stderr, "Halting program %s\n", ShortProgram());
thanx(stderr);
exit(1);
#else
if (nnodes > 1)
{
fprintf(stderr, "Halting parallel program %s on CPU %d out of %d\n",
ShortProgram(), noderank, nnodes);
}
else
{
fprintf(stderr, "Halting program %s\n", ShortProgram());
}
thanx(stderr);
MPI_Abort(MPI_COMM_WORLD, errorno);
exit(1);
#endif
#endif
}
void gmx_sumi(int nr,int r[],const t_commrec *cr)
{
#ifndef GMX_MPI
gmx_call("gmx_sumi");
#else
static int *buf=NULL;
static int nalloc=0;
int i;
if (nr > nalloc) {
nalloc = nr;
srenew(buf,nalloc);
}
if (cr->nc.bUse) {
/* Use two step summing */
MPI_Allreduce(r,buf,nr,MPI_INT,MPI_SUM,cr->nc.comm_intra);
if (cr->nc.rank_intra == 0) {
/* Sum with the buffers reversed */
MPI_Allreduce(buf,r,nr,MPI_INT,MPI_SUM,cr->nc.comm_inter);
}
MPI_Bcast(r,nr,MPI_INT,0,cr->nc.comm_intra);
} else {
MPI_Allreduce(r,buf,nr,MPI_INT,MPI_SUM,cr->mpi_comm_mygroup);
for(i=0; i<nr; i++)
r[i] = buf[i];
}
#endif
}
void gmx_bcast_sim(int nbytes, void *b, const t_commrec *cr)
{
#ifndef GMX_MPI
gmx_call("gmx_bast");
#else
MPI_Bcast(b, nbytes, MPI_BYTE, MASTERRANK(cr), cr->mpi_comm_mysim);
#endif
}
void gmx_barrier(const t_commrec *cr)
{
#ifndef GMX_MPI
gmx_call("gmx_barrier");
#else
MPI_Barrier(cr->mpi_comm_mygroup);
#endif
}
void gmx_sumf_sim(int nr, float r[], const gmx_multisim_t *ms)
{
#ifndef GMX_MPI
gmx_call("gmx_sumf_sim");
#else
gmx_sumf_comm(nr, r, ms->mpi_comm_masters);
#endif
}
void gmx_sumd_sim(int nr,double r[],const gmx_multisim_t *ms)
{
#ifndef GMX_MPI
gmx_call("gmx_sumd");
#else
gmx_sumd_comm(nr,r,ms->mpi_comm_masters);
#endif
}
void gmx_sumi(int nr, int r[], const t_commrec *cr)
{
#ifndef GMX_MPI
gmx_call("gmx_sumi");
#else
#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREAD_MPI)
if (cr->nc.bUse)
{
/* Use two step summing */
if (cr->nc.rank_intra == 0)
{
MPI_Reduce(MPI_IN_PLACE, r, nr, MPI_INT, MPI_SUM, 0, cr->nc.comm_intra);
/* Sum with the buffers reversed */
MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_INT, MPI_SUM, cr->nc.comm_inter);
}
else
{
/* This is here because of the silly MPI specification
that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
MPI_Reduce(r, NULL, nr, MPI_INT, MPI_SUM, 0, cr->nc.comm_intra);
}
MPI_Bcast(r, nr, MPI_INT, 0, cr->nc.comm_intra);
}
else
{
MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_INT, MPI_SUM, cr->mpi_comm_mygroup);
}
#else
int i;
if (nr > cr->mpb->ibuf_alloc)
{
cr->mpb->ibuf_alloc = nr;
srenew(cr->mpb->ibuf, cr->mpb->ibuf_alloc);
}
if (cr->nc.bUse)
{
/* Use two step summing */
MPI_Allreduce(r, cr->mpb->ibuf, nr, MPI_INT, MPI_SUM, cr->nc.comm_intra);
if (cr->nc.rank_intra == 0)
{
/* Sum with the buffers reversed */
MPI_Allreduce(cr->mpb->ibuf, r, nr, MPI_INT, MPI_SUM, cr->nc.comm_inter);
}
MPI_Bcast(r, nr, MPI_INT, 0, cr->nc.comm_intra);
}
else
{
MPI_Allreduce(r, cr->mpb->ibuf, nr, MPI_INT, MPI_SUM, cr->mpi_comm_mygroup);
for (i = 0; i < nr; i++)
{
r[i] = cr->mpb->ibuf[i];
}
}
#endif
#endif
}
/*!
* \param[in] sym Symbol to query.
* \returns The method associated with \p sym, or NULL if \p sym is not a
* \ref SYMBOL_METHOD symbol.
*/
struct gmx_ana_selmethod_t *
_gmx_sel_sym_value_method(gmx_sel_symrec_t *sym)
{
if (sym->type != SYMBOL_METHOD)
{
gmx_call("symbol is not a method symbol");
return NULL;
}
return sym->u.meth;
}
/*!
* \param[in] sym Symbol to query.
* \returns The variable expression associated with \p sym, or NULL if
* \p sym is not a \ref SYMBOL_VARIABLE symbol.
*/
struct t_selelem *
_gmx_sel_sym_value_var(gmx_sel_symrec_t *sym)
{
if (sym->type != SYMBOL_VARIABLE)
{
gmx_call("symbol is not a variable symbol");
return NULL;
}
return sym->u.var;
}
/*!
* \param[in] d Trajectory analysis data structure.
* \param[out] nanagrps Number of analysis groups specified by the user.
* \returns 0 on success, a non-zero error code on error.
*
* If a specific number (not -1) of analysis groups has been set with
* gmx_ana_set_nanagrps(), the value is always the same value.
* Hence, you only need to call this function if gmx_ana_set_nanagrps() has
* been called with \p nanagrps set to -1.
*
* Should only be called after gmx_ana_init_selections().
*/
int
gmx_ana_get_nanagrps(gmx_ana_traj_t *d, int *nanagrps)
{
if (d->nanagrps == -1)
{
*nanagrps = 0;
gmx_call("gmx_ana_init_selections() not called");
return EINVAL;
}
*nanagrps = d->nanagrps;
return 0;
}
/*!
* \param[in] d Trajectory analysis data structure.
* \param[out] grpnames Array of selection names.
* \returns 0 on success, a non-zero error code on error.
*
* The pointer returned in \p *grpnames should not be freed.
* Should only be called after gmx_ana_init_selections().
*/
int
gmx_ana_get_grpnames(gmx_ana_traj_t *d, char ***grpnames)
{
if (!d->grpnames)
{
*grpnames = NULL;
gmx_call("gmx_ana_init_selections() not called");
return EINVAL;
}
*grpnames = d->grpnames;
return 0;
}
/*!
* \param[in,out] d Trajectory analysis data structure.
* \param[in] frflags Flags for what to read from the trajectory file.
* \returns 0 on success, an error code on error.
*
* The TRX_NEED_X flag is always set.
* If the analysis tools needs some other information (velocities, forces),
* it can call this function to load additional information from the
* trajectory.
*/
int
gmx_ana_set_frflags(gmx_ana_traj_t *d, int frflags)
{
if (d->fr)
{
gmx_call("cannot set trajectory flags after the first frame has been read");
return -1;
}
frflags |= TRX_NEED_X;
d->frflags = frflags;
return 0;
}
/*!
* \param[in] d Trajectory analysis data structure.
* \param[in] i Ordinal number of the reference selection to get.
* \param[out] sel Selection object for the \p i'th reference group.
* \returns 0 on success, a non-zero error code on error.
*
* The pointer returned in \p *sel should not be freed.
* Should only be called after gmx_ana_init_selections().
*/
int
gmx_ana_get_refsel(gmx_ana_traj_t *d, int i, gmx_ana_selection_t **sel)
{
if (i < 0 || i >= d->nrefgrps)
{
*sel = NULL;
gmx_call("invalid reference group number");
return EINVAL;
}
*sel = gmx_ana_selcollection_get_selection(d->sc, i);
if (!*sel)
{
gmx_incons("gmx_ana_init_selections() not called");
return EINVAL;
}
return 0;
}
void gmx_sumi_sim(int nr,int r[],const gmx_multisim_t *ms)
{
#ifndef GMX_MPI
gmx_call("gmx_sumd");
#else
static int *buf=NULL;
static int nalloc=0;
int i;
if (nr > nalloc) {
nalloc = nr;
srenew(buf,nalloc);
}
MPI_Allreduce(r,buf,nr,MPI_INT,MPI_SUM,ms->mpi_comm_masters);
for(i=0; i<nr; i++)
r[i] = buf[i];
#endif
}
/*!
* \param[in,out] sel Selection element to set the type for.
* \param[in] vtype Value type for the selection element.
* \returns 0 on success, EINVAL if the value type is invalid.
*
* If the new type is \ref GROUP_VALUE or \ref POS_VALUE, the
* \ref SEL_ALLOCDATA flag is also set.
*
* This function should only be called at most once for each element,
* preferably right after calling _gmx_selelem_create().
*/
int
_gmx_selelem_set_vtype(t_selelem *sel, e_selvalue_t vtype)
{
if (sel->type == SEL_BOOLEAN && vtype != GROUP_VALUE)
{
gmx_bug("internal error");
return EINVAL;
}
if (sel->v.type != NO_VALUE && vtype != sel->v.type)
{
gmx_call("_gmx_selelem_set_vtype() called more than once");
return EINVAL;
}
sel->v.type = vtype;
if (vtype == GROUP_VALUE || vtype == POS_VALUE)
{
sel->flags |= SEL_ALLOCDATA;
}
return 0;
}
int gmx_setup(int *argc, char **argv, int *nnodes)
{
#ifndef GMX_MPI
gmx_call("gmx_setup");
return 0;
#else
char buf[256];
int resultlen; /* actual length of node name */
int i, flag;
int mpi_num_nodes;
int mpi_my_rank;
char mpi_hostname[MPI_MAX_PROCESSOR_NAME];
/* Call the MPI routines */
#ifdef GMX_LIB_MPI
#ifdef GMX_FAHCORE
(void) fah_MPI_Init(argc, &argv);
#else
(void) MPI_Init(argc, &argv);
#endif
#endif
(void) MPI_Comm_size( MPI_COMM_WORLD, &mpi_num_nodes );
(void) MPI_Comm_rank( MPI_COMM_WORLD, &mpi_my_rank );
(void) MPI_Get_processor_name( mpi_hostname, &resultlen );
#ifdef GMX_LIB_MPI
if (debug)
{
fprintf(debug, "NNODES=%d, MYRANK=%d, HOSTNAME=%s\n",
mpi_num_nodes, mpi_my_rank, mpi_hostname);
}
#endif
*nnodes = mpi_num_nodes;
return mpi_my_rank;
#endif
}
void gmx_pme_send_force_vir_ener(struct gmx_pme_pp *pme_pp,
rvec gmx_unused *f,
matrix vir_q, real energy_q,
matrix vir_lj, real energy_lj,
real dvdlambda_q, real dvdlambda_lj,
float cycles)
{
#ifdef GMX_MPI
gmx_pme_comm_vir_ene_t cve;
int messages, ind_start, ind_end;
cve.cycles = cycles;
/* Now the evaluated forces have to be transferred to the PP nodes */
messages = 0;
ind_end = 0;
for (int receiver = 0; receiver < pme_pp->nnode; receiver++)
{
ind_start = ind_end;
ind_end = ind_start + pme_pp->nat[receiver];
if (MPI_Isend(f[ind_start], (ind_end-ind_start)*sizeof(rvec), MPI_BYTE,
pme_pp->node[receiver], 0,
pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]) != 0)
{
gmx_comm("MPI_Isend failed in do_pmeonly");
}
}
/* send virial and energy to our last PP node */
copy_mat(vir_q, cve.vir_q);
copy_mat(vir_lj, cve.vir_lj);
cve.energy_q = energy_q;
cve.energy_lj = energy_lj;
cve.dvdlambda_q = dvdlambda_q;
cve.dvdlambda_lj = dvdlambda_lj;
/* check for the signals to send back to a PP node */
cve.stop_cond = gmx_get_stop_condition();
cve.cycles = cycles;
if (debug)
{
fprintf(debug, "PME rank sending to PP rank %d: virial and energy\n",
pme_pp->node_peer);
}
MPI_Isend(&cve, sizeof(cve), MPI_BYTE,
pme_pp->node_peer, 1,
pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]);
/* Wait for the forces to arrive */
MPI_Waitall(messages, pme_pp->req, pme_pp->stat);
#else
gmx_call("MPI not enabled");
GMX_UNUSED_VALUE(pme_pp);
GMX_UNUSED_VALUE(f);
GMX_UNUSED_VALUE(vir_q);
GMX_UNUSED_VALUE(energy_q);
GMX_UNUSED_VALUE(vir_lj);
GMX_UNUSED_VALUE(energy_lj);
GMX_UNUSED_VALUE(dvdlambda_q);
GMX_UNUSED_VALUE(dvdlambda_lj);
GMX_UNUSED_VALUE(cycles);
#endif
}
/*! \brief Send the PME mesh force, virial and energy to the PP-only ranks. */
static void gmx_pme_send_force_vir_ener(gmx_pme_pp *pme_pp,
const rvec *f,
matrix vir_q, real energy_q,
matrix vir_lj, real energy_lj,
real dvdlambda_q, real dvdlambda_lj,
float cycles)
{
#if GMX_MPI
gmx_pme_comm_vir_ene_t cve;
int messages, ind_start, ind_end;
cve.cycles = cycles;
/* Now the evaluated forces have to be transferred to the PP nodes */
messages = 0;
ind_end = 0;
for (const auto &receiver : pme_pp->ppRanks)
{
ind_start = ind_end;
ind_end = ind_start + receiver.numAtoms;
if (MPI_Isend(const_cast<void *>(static_cast<const void *>(f[ind_start])),
(ind_end-ind_start)*sizeof(rvec), MPI_BYTE,
receiver.rankId, 0,
pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]) != 0)
{
gmx_comm("MPI_Isend failed in do_pmeonly");
}
}
/* send virial and energy to our last PP node */
copy_mat(vir_q, cve.vir_q);
copy_mat(vir_lj, cve.vir_lj);
cve.energy_q = energy_q;
cve.energy_lj = energy_lj;
cve.dvdlambda_q = dvdlambda_q;
cve.dvdlambda_lj = dvdlambda_lj;
/* check for the signals to send back to a PP node */
cve.stop_cond = gmx_get_stop_condition();
cve.cycles = cycles;
if (debug)
{
fprintf(debug, "PME rank sending to PP rank %d: virial and energy\n",
pme_pp->peerRankId);
}
MPI_Isend(&cve, sizeof(cve), MPI_BYTE,
pme_pp->peerRankId, 1,
pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]);
/* Wait for the forces to arrive */
MPI_Waitall(messages, pme_pp->req.data(), pme_pp->stat.data());
#else
gmx_call("MPI not enabled");
GMX_UNUSED_VALUE(pme_pp);
GMX_UNUSED_VALUE(f);
GMX_UNUSED_VALUE(vir_q);
GMX_UNUSED_VALUE(energy_q);
GMX_UNUSED_VALUE(vir_lj);
GMX_UNUSED_VALUE(energy_lj);
GMX_UNUSED_VALUE(dvdlambda_q);
GMX_UNUSED_VALUE(dvdlambda_lj);
GMX_UNUSED_VALUE(cycles);
#endif
}
/*!
* \param[in,out] d Trajectory analysis data structure.
* \returns 0 on success, a non-zero error code on error.
*
* Initializes the selection data in \c gmx_ana_traj_t based on
* the selection options and/or index files provided on the command line.
*
* This function is called automatically by parse_trjana_args() and should
* not be called directly unless \ref ANA_USER_SELINIT is specified.
*
* \see ANA_USER_SELINIT
*/
int
gmx_ana_init_selections(gmx_ana_traj_t *d)
{
int rc;
int i;
int nr;
gmx_ana_indexgrps_t *grps;
int natoms;
bool bStdIn;
bool bInteractive;
bool bOk;
if (d->sel)
{
gmx_call("init_selections called more than once\n"
"perhaps you forgot ANA_USER_SELINIT");
return -1;
}
/* Check if we need some information from the topology */
if (gmx_ana_selcollection_requires_top(d->sc))
{
rc = load_topology(d, TRUE);
if (rc != 0)
{
return rc;
}
}
/* Load the topology and init the index groups */
gmx_ana_indexgrps_init(&grps, d->top, d->ndxfile);
/* Parse the selection */
rc = gmx_ana_selmethod_register_defaults(d->sc);
if (rc != 0)
{
gmx_fatal(FARGS, "default selection method registration failed");
return rc;
}
bStdIn = (d->selfile && d->selfile[0] == '-' && d->selfile[1] == 0)
|| (d->selection && d->selection[0] == 0)
|| (!d->selfile && !d->selection);
bInteractive = bStdIn && isatty(fileno(stdin));
if (bStdIn && bInteractive)
{
/* Parse from stdin */
/* First we parse the reference groups if there are any */
if (d->nrefgrps > 0)
{
fprintf(stderr, "\nSpecify ");
if (d->nrefgrps == 1)
{
fprintf(stderr, "a reference selection");
}
else
{
fprintf(stderr, "%d reference selections", d->nrefgrps);
}
fprintf(stderr, ":\n");
fprintf(stderr, "(one selection per line, use \\ for line continuation)\n");
rc = gmx_ana_selcollection_parse_stdin(d->sc, d->nrefgrps, grps, TRUE);
nr = gmx_ana_selcollection_get_count(d->sc);
if (rc != 0 || nr != d->nrefgrps)
{
gmx_ana_traj_free(d);
gmx_input("unrecoverable error in selection parsing");
return rc;
}
}
/* Then, we parse the analysis groups */
fprintf(stderr, "\nSpecify ");
if (d->nanagrps == 1)
{
fprintf(stderr, "a selection");
}
else if (d->nanagrps == -1)
{
fprintf(stderr, "any number of selections");
}
else
{
fprintf(stderr, "%d selections", d->nanagrps);
}
fprintf(stderr, " for analysis:\n");
fprintf(stderr, "(one selection per line, use \\ for line continuation%s)\n",
d->nanagrps == -1 ? ", Ctrl-D to end" : "");
rc = gmx_ana_selcollection_parse_stdin(d->sc, d->nanagrps, grps, TRUE);
fprintf(stderr, "\n");
}
else if (bStdIn)
{
rc = gmx_ana_selcollection_parse_stdin(d->sc, -1, grps, FALSE);
}
else if (d->selection)
{
rc = gmx_ana_selcollection_parse_str(d->sc, d->selection, grps);
}
else
{
rc = gmx_ana_selcollection_parse_file(d->sc, d->selfile, grps);
}
gmx_ana_indexgrps_free(grps);
if (rc != 0)
{
/* Free memory for memory leak checking */
gmx_ana_traj_free(d);
gmx_input("selection(s) could not be parsed");
return rc;
}
/* Check the number of groups */
nr = gmx_ana_selcollection_get_count(d->sc);
if (nr <= d->nrefgrps)
{
gmx_input("selection does not specify enough index groups");
return -1;
}
if (d->nanagrps <= 0)
{
d->nanagrps = nr - d->nrefgrps;
}
else if (nr != d->nrefgrps + d->nanagrps)
{
gmx_input("selection does not specify the correct number of index groups");
return -1;
}
if (d->flags & ANA_DEBUG_SELECTION)
{
gmx_ana_selcollection_print_tree(stderr, d->sc, FALSE);
}
if (gmx_ana_selcollection_requires_top(d->sc))
{
rc = load_topology(d, TRUE);
if (rc != 0)
{
return rc;
}
}
if (d->top)
{
natoms = -1;
}
else
{
rc = init_first_frame(d);
if (rc != 0)
{
return rc;
}
natoms = d->fr->natoms;
}
gmx_ana_selcollection_set_topology(d->sc, d->top, natoms);
rc = gmx_ana_selcollection_compile(d->sc);
if (rc != 0)
{
/* Free memory for memory leak checking */
gmx_ana_traj_free(d);
gmx_input("selection could not be compiled");
return rc;
}
/* Create the selection array */
d->ngrps = gmx_ana_selcollection_get_count(d->sc);
if (!(d->flags & ANA_USE_FULLGRPS))
{
d->ngrps -= d->nrefgrps;
}
snew(d->sel, d->ngrps);
for (i = 0; i < d->ngrps; ++i)
{
if (d->flags & ANA_USE_FULLGRPS)
{
d->sel[i] = gmx_ana_selcollection_get_selection(d->sc, i);
}
else
{
d->sel[i] = gmx_ana_selcollection_get_selection(d->sc, i + d->nrefgrps);
}
}
if (d->flags & ANA_DEBUG_SELECTION)
{
fprintf(stderr, "\n");
gmx_ana_selcollection_print_tree(stderr, d->sc, FALSE);
fprintf(stderr, "\n");
gmx_ana_poscalc_coll_print_tree(stderr, d->pcc);
fprintf(stderr, "\n");
}
/* Initialize the position evaluation */
gmx_ana_poscalc_init_eval(d->pcc);
if (d->flags & ANA_DEBUG_SELECTION)
{
gmx_ana_poscalc_coll_print_tree(stderr, d->pcc);
fprintf(stderr, "\n");
}
/* Check that dynamic selections are not provided if not allowed */
if (d->flags & ANA_NO_DYNSEL)
{
for (i = 0; i < d->nrefgrps + d->nanagrps; ++i)
{
gmx_ana_selection_t *sel;
sel = gmx_ana_selcollection_get_selection(d->sc, i);
if (sel->bDynamic)
{
gmx_fatal(FARGS, "%s does not support dynamic selections",
ShortProgram());
return -1;
}
}
}
/* Check that non-atom positions are not provided if not allowed.
* TODO: It would be better to have these checks in the parser. */
if (d->flags & ANA_ONLY_ATOMPOS)
{
for (i = 0; i < d->nanagrps; ++i)
{
gmx_ana_selection_t *sel;
sel = gmx_ana_selcollection_get_selection(d->sc, i + d->nrefgrps);
if (sel->p.m.type != INDEX_ATOM)
{
gmx_fatal(FARGS, "%s does not support non-atom positions",
ShortProgram());
return -1;
}
}
}
/* Create the names array */
snew(d->grpnames, d->ngrps);
for (i = 0; i < d->ngrps; ++i)
{
d->grpnames[i] = gmx_ana_selection_name(d->sel[i]);
}
return 0;
}
void write_orca_input(int step ,t_forcerec *fr, t_QMrec *qm, t_MMrec *mm)
{
int
i;
t_QMMMrec
*QMMMrec;
FILE
*out, *pcFile, *addInputFile, *LJCoeff;
char
*buf,*orcaInput,*addInputFilename,*LJCoeffFilename,
*pcFilename,*exclInName,*exclOutName;
QMMMrec = fr->qr;
/* write the first part of the input-file */
snew(orcaInput,200);
sprintf(orcaInput,"%s.inp",qm->orca_basename);
out = fopen(orcaInput,"w");
snew(addInputFilename,200);
sprintf(addInputFilename,"%s.ORCAINFO",qm->orca_basename);
addInputFile = fopen(addInputFilename,"r");
fprintf(out, "#input-file generated by gromacs\n");
if(qm->bTS) {
fprintf(out,"!QMMMOpt TightSCF\n");
fprintf(out,"%s\n","%geom TS_Search EF end");
}
else if (qm->bOPT) {
fprintf(out,"!QMMMOpt TightSCF\n");
}
else {
fprintf(out,"!EnGrad TightSCF\n");
}
/* here we include the insertion of the additional orca-input */
snew(buf,200);
if (addInputFile!=NULL) {
while (!feof(addInputFile)) {
if (fgets(buf, 200, addInputFile) != NULL)
fputs(buf, out);
}
}
else {
fprintf(stderr,"No information on the calculation given in <%s>\n",addInputFilename);
gmx_call("qm_orca.c");
}
fclose(addInputFile);
if(qm->bTS||qm->bOPT) {
/* freeze the frontier QM atoms and Link atoms. This is
* important only if a full QM subsystem optimization is done
* with a frozen MM environmeent. For dynamics, or gromacs's own
* optimization routines this is not important.
*/
/* ORCA reads the exclusions from LJCoeffFilename.Excl,
*so we have to rename the file
*/
int didStart = 0;
for(i=0; i<qm->nrQMatoms; i++) {
if(qm->frontatoms[i]) {
if (!didStart) {
fprintf(out,"%s\n","%geom");
fprintf(out," Constraints \n");
didStart = 1;
}
fprintf(out," {C %d C}\n",i); /* counting from 0 */
}
}
if (didStart) fprintf(out," end\n end\n");
/* make a file with information on the C6 and C12 coefficients */
if(QMMMrec->QMMMscheme!=eQMMMschemeoniom && mm->nrMMatoms) {
snew(exclInName,200);
snew(exclOutName,200);
sprintf(exclInName,"QMMMexcl.dat");
sprintf(exclOutName,"%s.LJ.Excl",qm->orca_basename);
rename(exclInName,exclOutName);
snew(LJCoeffFilename,200);
sprintf(LJCoeffFilename,"%s.LJ",qm->orca_basename);
fprintf(out,"%s%s%s\n","%LJCOEFFICIENTS \"",LJCoeffFilename,"\"");
/* make a file with information on the C6 and C12 coefficients */
LJCoeff = fopen(LJCoeffFilename,"w");
fprintf(LJCoeff,"%d\n",qm->nrQMatoms);
for (i=0; i<qm->nrQMatoms; i++) {
#ifdef GMX_DOUBLE
fprintf(LJCoeff,"%10.7lf %10.7lf\n",qm->c6[i],qm->c12[i]);
#else
fprintf(LJCoeff,"%10.7f %10.7f\n",qm->c6[i],qm->c12[i]);
#endif
}
fprintf(LJCoeff,"%d\n",mm->nrMMatoms);
for (i=0; i<mm->nrMMatoms; i++) {
#ifdef GMX_DOUBLE
fprintf(LJCoeff,"%10.7lf %10.7lf\n",mm->c6[i],mm->c12[i]);
#else
fprintf(LJCoeff,"%10.7f %10.7f\n",mm->c6[i],mm->c12[i]);
#endif
}
fclose(LJCoeff);
}
}
/* write charge and multiplicity
*/
fprintf(out,"*xyz %2d%2d\n",qm->QMcharge,qm->multiplicity);
/* write the QM coordinates
*/
for (i=0; i<qm->nrQMatoms; i++) {
int atomNr;
if (qm->atomicnumberQM[i]==0)
atomNr = 1;
else
atomNr = qm->atomicnumberQM[i];
#ifdef GMX_DOUBLE
fprintf(out,"%3d %10.7lf %10.7lf %10.7lf\n",
atomNr,
qm->xQM[i][XX]/0.1,
qm->xQM[i][YY]/0.1,
qm->xQM[i][ZZ]/0.1);
#else
fprintf(out,"%3d %10.7f %10.7f %10.7f\n",
atomNr,
qm->xQM[i][XX]/0.1,
qm->xQM[i][YY]/0.1,
qm->xQM[i][ZZ]/0.1);
#endif
}
fprintf(out,"*\n");
/* write the MM point charge data
*/
if(QMMMrec->QMMMscheme!=eQMMMschemeoniom && mm->nrMMatoms) {
/* name of the point charge file */
snew(pcFilename,200);
sprintf(pcFilename,"%s.pc",qm->orca_basename);
fprintf(out,"%s%s%s\n","%pointcharges \"",pcFilename,"\"");
pcFile = fopen(pcFilename,"w");
fprintf(pcFile,"%d\n",mm->nrMMatoms);
for(i=0; i<mm->nrMMatoms; i++) {
#ifdef GMX_DOUBLE
fprintf(pcFile,"%8.4lf %10.7lf %10.7lf %10.7lf\n",
mm->MMcharges[i],
mm->xMM[i][XX]/0.1,
mm->xMM[i][YY]/0.1,
mm->xMM[i][ZZ]/0.1);
#else
fprintf(pcFile,"%8.4f %10.7f %10.7f %10.7f\n",
mm->MMcharges[i],
mm->xMM[i][XX]/0.1,
mm->xMM[i][YY]/0.1,
mm->xMM[i][ZZ]/0.1);
#endif
}
fprintf(pcFile,"\n");
fclose(pcFile);
}
fprintf(out,"\n");
fclose(out);
} /* write_orca_input */
int gmx_setup(int *argc,char **argv,int *nnodes)
{
#ifndef GMX_MPI
gmx_call("gmx_setup");
return 0;
#else
char buf[256];
int resultlen; /* actual length of node name */
int i,flag;
int mpi_num_nodes;
int mpi_my_rank;
char mpi_hostname[MPI_MAX_PROCESSOR_NAME];
/* Call the MPI routines */
(void) MPI_Init(argc,&argv);
(void) MPI_Comm_size( MPI_COMM_WORLD, &mpi_num_nodes );
(void) MPI_Comm_rank( MPI_COMM_WORLD, &mpi_my_rank );
(void) MPI_Get_processor_name( mpi_hostname, &resultlen );
#ifdef USE_MPE
/* MPE logging routines. Get event IDs from MPE: */
/* General events */
ev_timestep1 = MPE_Log_get_event_number( );
ev_timestep2 = MPE_Log_get_event_number( );
ev_force_start = MPE_Log_get_event_number( );
ev_force_finish = MPE_Log_get_event_number( );
ev_do_fnbf_start = MPE_Log_get_event_number( );
ev_do_fnbf_finish = MPE_Log_get_event_number( );
ev_ns_start = MPE_Log_get_event_number( );
ev_ns_finish = MPE_Log_get_event_number( );
ev_calc_bonds_start = MPE_Log_get_event_number( );
ev_calc_bonds_finish = MPE_Log_get_event_number( );
ev_global_stat_start = MPE_Log_get_event_number( );
ev_global_stat_finish = MPE_Log_get_event_number( );
ev_virial_start = MPE_Log_get_event_number( );
ev_virial_finish = MPE_Log_get_event_number( );
/* Shift related events */
ev_shift_start = MPE_Log_get_event_number( );
ev_shift_finish = MPE_Log_get_event_number( );
ev_unshift_start = MPE_Log_get_event_number( );
ev_unshift_finish = MPE_Log_get_event_number( );
ev_mk_mshift_start = MPE_Log_get_event_number( );
ev_mk_mshift_finish = MPE_Log_get_event_number( );
/* PME related events */
ev_pme_start = MPE_Log_get_event_number( );
ev_pme_finish = MPE_Log_get_event_number( );
ev_spread_on_grid_start = MPE_Log_get_event_number( );
ev_spread_on_grid_finish = MPE_Log_get_event_number( );
ev_sum_qgrid_start = MPE_Log_get_event_number( );
ev_sum_qgrid_finish = MPE_Log_get_event_number( );
ev_gmxfft3d_start = MPE_Log_get_event_number( );
ev_gmxfft3d_finish = MPE_Log_get_event_number( );
ev_solve_pme_start = MPE_Log_get_event_number( );
ev_solve_pme_finish = MPE_Log_get_event_number( );
ev_gather_f_bsplines_start = MPE_Log_get_event_number( );
ev_gather_f_bsplines_finish= MPE_Log_get_event_number( );
ev_reduce_start = MPE_Log_get_event_number( );
ev_reduce_finish = MPE_Log_get_event_number( );
ev_rscatter_start = MPE_Log_get_event_number( );
ev_rscatter_finish = MPE_Log_get_event_number( );
ev_alltoall_start = MPE_Log_get_event_number( );
ev_alltoall_finish = MPE_Log_get_event_number( );
ev_pmeredist_start = MPE_Log_get_event_number( );
ev_pmeredist_finish = MPE_Log_get_event_number( );
ev_init_pme_start = MPE_Log_get_event_number( );
ev_init_pme_finish = MPE_Log_get_event_number( );
ev_send_coordinates_start = MPE_Log_get_event_number( );
ev_send_coordinates_finish = MPE_Log_get_event_number( );
ev_update_fr_start = MPE_Log_get_event_number( );
ev_update_fr_finish = MPE_Log_get_event_number( );
ev_clear_rvecs_start = MPE_Log_get_event_number( );
ev_clear_rvecs_finish = MPE_Log_get_event_number( );
ev_update_start = MPE_Log_get_event_number( );
ev_update_finish = MPE_Log_get_event_number( );
ev_output_start = MPE_Log_get_event_number( );
ev_output_finish = MPE_Log_get_event_number( );
ev_sum_lrforces_start = MPE_Log_get_event_number( );
ev_sum_lrforces_finish = MPE_Log_get_event_number( );
ev_sort_start = MPE_Log_get_event_number( );
ev_sort_finish = MPE_Log_get_event_number( );
ev_sum_qgrid_start = MPE_Log_get_event_number( );
ev_sum_qgrid_finish = MPE_Log_get_event_number( );
/* Essential dynamics related events */
ev_edsam_start = MPE_Log_get_event_number( );
ev_edsam_finish = MPE_Log_get_event_number( );
ev_get_coords_start = MPE_Log_get_event_number( );
ev_get_coords_finish = MPE_Log_get_event_number( );
ev_ed_apply_cons_start = MPE_Log_get_event_number( );
ev_ed_apply_cons_finish = MPE_Log_get_event_number( );
ev_fit_to_reference_start = MPE_Log_get_event_number( );
ev_fit_to_reference_finish = MPE_Log_get_event_number( );
/* describe events: */
if ( mpi_my_rank == 0 )
{
/* General events */
MPE_Describe_state(ev_timestep1, ev_timestep2, "timestep START", "magenta" );
MPE_Describe_state(ev_force_start, ev_force_finish, "force", "cornflower blue" );
MPE_Describe_state(ev_do_fnbf_start, ev_do_fnbf_finish, "do_fnbf", "navy" );
MPE_Describe_state(ev_ns_start, ev_ns_finish, "neighbor search", "tomato" );
MPE_Describe_state(ev_calc_bonds_start, ev_calc_bonds_finish, "bonded forces", "slate blue" );
MPE_Describe_state(ev_global_stat_start, ev_global_stat_finish, "global stat", "firebrick3");
MPE_Describe_state(ev_update_fr_start, ev_update_fr_finish, "update forcerec", "goldenrod");
MPE_Describe_state(ev_clear_rvecs_start, ev_clear_rvecs_finish, "clear rvecs", "bisque");
MPE_Describe_state(ev_update_start, ev_update_finish, "update", "cornsilk");
MPE_Describe_state(ev_output_start, ev_output_finish, "output", "black");
MPE_Describe_state(ev_virial_start, ev_virial_finish, "calc_virial", "thistle4");
/* PME related events */
MPE_Describe_state(ev_pme_start, ev_pme_finish, "doing PME", "grey" );
MPE_Describe_state(ev_spread_on_grid_start, ev_spread_on_grid_finish, "spread", "dark orange" );
MPE_Describe_state(ev_sum_qgrid_start, ev_sum_qgrid_finish, "sum qgrid", "slate blue");
MPE_Describe_state(ev_gmxfft3d_start, ev_gmxfft3d_finish, "fft3d", "snow2" );
MPE_Describe_state(ev_solve_pme_start, ev_solve_pme_finish, "solve PME", "indian red" );
MPE_Describe_state(ev_gather_f_bsplines_start, ev_gather_f_bsplines_finish, "bsplines", "light sea green" );
MPE_Describe_state(ev_reduce_start, ev_reduce_finish, "reduce", "cyan1" );
MPE_Describe_state(ev_rscatter_start, ev_rscatter_finish, "rscatter", "cyan3" );
MPE_Describe_state(ev_alltoall_start, ev_alltoall_finish, "alltoall", "LightCyan4" );
MPE_Describe_state(ev_pmeredist_start, ev_pmeredist_finish, "pmeredist", "thistle" );
MPE_Describe_state(ev_init_pme_start, ev_init_pme_finish, "init PME", "snow4");
MPE_Describe_state(ev_send_coordinates_start, ev_send_coordinates_finish, "send_coordinates","blue");
MPE_Describe_state(ev_sum_lrforces_start, ev_sum_lrforces_finish, "sum_LRforces", "lime green");
MPE_Describe_state(ev_sort_start, ev_sort_finish, "sort pme atoms", "brown");
MPE_Describe_state(ev_sum_qgrid_start, ev_sum_qgrid_finish, "sum charge grid", "medium orchid");
/* Shift related events */
MPE_Describe_state(ev_shift_start, ev_shift_finish, "shift", "orange");
MPE_Describe_state(ev_unshift_start, ev_unshift_finish, "unshift", "dark orange");
MPE_Describe_state(ev_mk_mshift_start, ev_mk_mshift_finish, "mk_mshift", "maroon");
/* Essential dynamics related events */
MPE_Describe_state(ev_edsam_start, ev_edsam_finish, "EDSAM", "deep sky blue");
MPE_Describe_state(ev_get_coords_start, ev_get_coords_finish, "ED get coords", "steel blue");
MPE_Describe_state(ev_ed_apply_cons_start, ev_ed_apply_cons_finish, "ED apply constr", "forest green");
MPE_Describe_state(ev_fit_to_reference_start, ev_fit_to_reference_finish, "ED fit to ref", "lavender");
}
MPE_Init_log();
#endif
fprintf(stderr,"NNODES=%d, MYRANK=%d, HOSTNAME=%s\n",
mpi_num_nodes,mpi_my_rank,mpi_hostname);
*nnodes=mpi_num_nodes;
return mpi_my_rank;
#endif
}
