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lammps/src/USER-QMMM/fix_qmmm.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (ICTP)
------------------------------------------------------------------------- */
#include "fix_qmmm.h"
#include "atom.h"
#include "domain.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "error.h"
#include "group.h"
#include "memory.h"
#include <stdlib.h>
#include <string.h>
#include "libqmmm.h"
// message tags for QM/MM inter communicator communication
// have to match with those from the QM code
enum {QMMM_TAG_OTHER=0, QMMM_TAG_SIZE=1, QMMM_TAG_COORD=2,
QMMM_TAG_FORCE=3, QMMM_TAG_FORCE2=4, QMMM_TAG_CELL=5,
QMMM_TAG_RADII=6, QMMM_TAG_CHARGE=7, QMMM_TAG_TYPE=8,
QMMM_TAG_MASS=9};
using namespace LAMMPS_NS;
using namespace FixConst;
/****************************************************************************/
/* re-usable integer hash table code with static linkage. */
/** hash table top level data structure */
typedef struct taginthash_t {
struct taginthash_node_t **bucket; /* array of hash nodes */
tagint size; /* size of the array */
tagint entries; /* number of entries in table */
tagint downshift; /* shift cound, used in hash function */
tagint mask; /* used to select bits for hashing */
} taginthash_t;
/** hash table node data structure */
typedef struct taginthash_node_t {
tagint data; /* data in hash node */
tagint key; /* key for hash lookup */
struct taginthash_node_t *next; /* next node in hash chain */
} taginthash_node_t;
#define HASH_FAIL -1
#define HASH_LIMIT 0.5
/* initialize new hash table */
static void taginthash_init(taginthash_t *tptr, tagint buckets);
/* lookup entry in hash table */
static tagint taginthash_lookup(const taginthash_t *tptr, tagint key);
/* generate list of keys for reverse lookups. */
static tagint *taginthash_keys(taginthash_t *tptr);
/* insert an entry into hash table. */
static tagint taginthash_insert(taginthash_t *tptr, tagint key, tagint data);
/* delete the hash table */
static void taginthash_destroy(taginthash_t *tptr);
/* adapted sort for in-place sorting of map indices. */
static void id_sort(tagint *idmap, tagint left, tagint right);
/************************************************************************
* integer hash code:
************************************************************************/
/* taginthash() - Hash function returns a hash number for a given key.
* tptr: Pointer to a hash table, key: The key to create a hash number for */
static tagint taginthash(const taginthash_t *tptr, tagint key) {
tagint hashvalue;
hashvalue = (((key*1103515249)>>tptr->downshift) & tptr->mask);
if (hashvalue < 0) {
hashvalue = 0;
}
return hashvalue;
}
/*
* rebuild_table_tagint() - Create new hash table when old one fills up.
*
* tptr: Pointer to a hash table
*/
static void rebuild_table_tagint(taginthash_t *tptr) {
taginthash_node_t **old_bucket, *old_hash, *tmp;
tagint old_size, h, i;
old_bucket=tptr->bucket;
old_size=tptr->size;
/* create a new table and rehash old buckets */
taginthash_init(tptr, old_size<<1);
for (i=0; i<old_size; i++) {
old_hash=old_bucket[i];
while(old_hash) {
tmp=old_hash;
old_hash=old_hash->next;
h=taginthash(tptr, tmp->key);
tmp->next=tptr->bucket[h];
tptr->bucket[h]=tmp;
tptr->entries++;
} /* while */
} /* for */
/* free memory used by old table */
free(old_bucket);
return;
}
/*
* taginthash_init() - Initialize a new hash table.
*
* tptr: Pointer to the hash table to initialize
* buckets: The number of initial buckets to create
*/
void taginthash_init(taginthash_t *tptr, tagint buckets) {
/* make sure we allocate something */
if (buckets==0)
buckets=16;
/* initialize the table */
tptr->entries=0;
tptr->size=2;
tptr->mask=1;
tptr->downshift=29;
/* ensure buckets is a power of 2 */
while (tptr->size<buckets) {
tptr->size<<=1;
tptr->mask=(tptr->mask<<1)+1;
tptr->downshift--;
} /* while */
/* allocate memory for table */
tptr->bucket=(taginthash_node_t **) calloc(tptr->size, sizeof(taginthash_node_t *));
return;
}
/*
* taginthash_lookup() - Lookup an entry in the hash table and return a pointer to
* it or HASH_FAIL if it wasn't found.
*
* tptr: Pointer to the hash table
* key: The key to lookup
*/
tagint taginthash_lookup(const taginthash_t *tptr, tagint key) {
tagint h;
taginthash_node_t *node;
/* find the entry in the hash table */
h=taginthash(tptr, key);
for (node=tptr->bucket[h]; node!=NULL; node=node->next) {
if (node->key == key)
break;
}
/* return the entry if it exists, or HASH_FAIL */
return(node ? node->data : HASH_FAIL);
}
/*
* taginthash_keys() - Return a list of keys.
* NOTE: the returned list must be freed with free(3).
*/
tagint *taginthash_keys(taginthash_t *tptr) {
tagint *keys;
taginthash_node_t *node;
keys = (tagint *)calloc(tptr->entries, sizeof(tagint));
for (tagint i=0; i < tptr->size; ++i) {
for (node=tptr->bucket[i]; node != NULL; node=node->next) {
keys[node->data] = node->key;
}
}
return keys;
}
/*
* taginthash_insert() - Insert an entry into the hash table. If the entry already
* exists return a pointer to it, otherwise return HASH_FAIL.
*
* tptr: A pointer to the hash table
* key: The key to insert into the hash table
* data: A pointer to the data to insert into the hash table
*/
tagint taginthash_insert(taginthash_t *tptr, tagint key, tagint data) {
tagint tmp;
taginthash_node_t *node;
tagint h;
/* check to see if the entry exists */
if ((tmp=taginthash_lookup(tptr, key)) != HASH_FAIL)
return(tmp);
/* expand the table if needed */
while (tptr->entries>=HASH_LIMIT*tptr->size)
rebuild_table_tagint(tptr);
/* insert the new entry */
h=taginthash(tptr, key);
node=(struct taginthash_node_t *) malloc(sizeof(taginthash_node_t));
node->data=data;
node->key=key;
node->next=tptr->bucket[h];
tptr->bucket[h]=node;
tptr->entries++;
return HASH_FAIL;
}
/*
* taginthash_destroy() - Delete the entire table, and all remaining entries.
*
*/
void taginthash_destroy(taginthash_t *tptr) {
taginthash_node_t *node, *last;
tagint i;
for (i=0; i<tptr->size; i++) {
node = tptr->bucket[i];
while (node != NULL) {
last = node;
node = node->next;
free(last);
}
}
/* free the entire array of buckets */
if (tptr->bucket != NULL) {
free(tptr->bucket);
memset(tptr, 0, sizeof(taginthash_t));
}
}
/************************************************************************
* integer list sort code:
************************************************************************/
/* sort for integer map. initial call id_sort(idmap, 0, natoms - 1); */
static void id_sort(tagint *idmap, tagint left, tagint right)
{
tagint pivot, l_hold, r_hold;
l_hold = left;
r_hold = right;
pivot = idmap[left];
while (left < right) {
while ((idmap[right] >= pivot) && (left < right))
right--;
if (left != right) {
idmap[left] = idmap[right];
left++;
}
while ((idmap[left] <= pivot) && (left < right))
left++;
if (left != right) {
idmap[right] = idmap[left];
right--;
}
}
idmap[left] = pivot;
pivot = left;
left = l_hold;
right = r_hold;
if (left < pivot)
id_sort(idmap, left, pivot-1);
if (right > pivot)
id_sort(idmap, pivot+1, right);
}
/****************************************************************************/
/* struct for packed data communication of coordinates and forces. */
struct commdata {
tagint tag;
float x,y,z;
float q;
};
/***************************************************************
* create class and parse arguments in LAMMPS script. Syntax:
* fix ID group-ID qmmm [couple <group-ID>]
***************************************************************/
FixQMMM::FixQMMM(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg > 5)
error->all(FLERR,"Illegal fix qmmm command");
if (strcmp(update->unit_style,"metal") == 0) {
qmmm_fscale = 1.0/23.0609;
} else if (strcmp(update->unit_style,"real") == 0) {
qmmm_fscale = 1.0;
} else error->all(FLERR,"Fix qmmm requires real or metal units");
if (atom->tag_enable == 0)
error->all(FLERR,"Fix qmmm requires atom IDs");
if (atom->tag_consecutive() == 0)
error->all(FLERR,"Fix qmmm requires consecutive atom IDs");
/* define ec coupling group */
mm_group = group->find("all");
if ((narg == 5) && (0 == strcmp(arg[0],"couple"))) {
#if 0 /* ignore ES coupling group for now */
mm_group = group->find(arg[4]);
#endif
} else if (narg != 3) error->all(FLERR,"Illegal fix qmmm command");
if (mm_group == -1)
error->all(FLERR,"Could not find fix qmmm couple group ID");
/* retrieve settings from global QM/MM configuration struct */
comm_mode = qmmmcfg.comm_mode;
qmmm_mode = qmmmcfg.qmmm_mode;
qmmm_role = qmmmcfg.role;
verbose = qmmmcfg.verbose;
if (comm_mode != QMMM_COMM_MPI)
error->all(FLERR,"Only MPI communication mode is currently supported");
if ((qmmm_role != QMMM_ROLE_MASTER) && (qmmm_role != QMMM_ROLE_SLAVE))
error->all(FLERR,"LAMMPS can only function as MM master or MM slave");
qm_comm = MPI_Comm_f2c(qmmmcfg.qm_comm);
mm_comm = MPI_Comm_f2c(qmmmcfg.mm_comm);
/* initialize storage */
qm_idmap = mm_idmap = NULL;
qm_remap = mm_remap = NULL;
qm_coord = mm_coord = qm_force = mm_force = NULL;
qm_charge =NULL;
mm_type = NULL;
do_init = 1;
/* storage required to communicate a single coordinate or force. */
size_one = sizeof(struct commdata);
maxbuf = -1;
}
/*********************************
* Clean up on deleting the fix. *
*********************************/
FixQMMM::~FixQMMM()
{
if (qm_idmap) {
taginthash_t *hashtable = (taginthash_t *)qm_idmap;
taginthash_destroy(hashtable);
delete hashtable;
free(qm_remap);
}
memory->destroy(comm_buf);
memory->destroy(qm_coord);
memory->destroy(qm_force);
memory->destroy(qm_charge);
}
/* ---------------------------------------------------------------------- */
int FixQMMM::setmask()
{
int mask = 0;
mask |= POST_INTEGRATE;
mask |= POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixQMMM::exchange_positions()
{
double **x = atom->x;
double *charge = atom->q;
int * const mask = atom->mask;
int * const type = atom->type;
double * const mass = atom->mass;
tagint * const tag = atom->tag;
const int nlocal = atom->nlocal;
const int ntypes = atom->ntypes;
const int natoms = (int) atom->natoms;
if (atom->natoms > MAXSMALLINT)
error->all(FLERR,"Too many MM atoms for fix qmmmm");
/*
* CHECK
* AK: this is not good. atom->natoms can be huge. instead:
- collect list of atom tags (from local and remoted full MM procs) that
match fix qmmm group
- sort list -> master list of QM/MM interacting atoms
- create hash table that connects master list index with tag
- collect necessary data and get master list index via hash table
*/
if (comm->me == 0) {
// Pack various cell dimension properties into one chunk.
double celldata[9];
celldata[0] = domain->boxlo[0];
celldata[1] = domain->boxlo[1];
celldata[2] = domain->boxlo[2];
celldata[3] = domain->boxhi[0];
celldata[4] = domain->boxhi[1];
celldata[5] = domain->boxhi[2];
celldata[6] = domain->xy;
celldata[7] = domain->xz;
celldata[8] = domain->yz;
if (qmmm_role == QMMM_ROLE_MASTER) {
int isend_buf[4];
isend_buf[0] = natoms;
isend_buf[1] = num_qm;
isend_buf[2] = num_mm;
isend_buf[3] = ntypes;
MPI_Send(isend_buf, 4, MPI_INT, 1, QMMM_TAG_SIZE, qm_comm);
MPI_Send(celldata, 9, MPI_DOUBLE, 1, QMMM_TAG_CELL, qm_comm);
}
if (verbose > 0) {
if (screen) fputs("QMMM: exchange positions\n",screen);
if (logfile) fputs("QMMM: exchange positions\n",logfile);
}
}
if (qmmm_role == QMMM_ROLE_MASTER) {
int i;
double *mm_coord_all = (double *) calloc(3*natoms, sizeof(double));
double *mm_charge_all = (double *) calloc(natoms, sizeof(double));
int *mm_mask_all = (int *) calloc(natoms, sizeof(int));
/* check and potentially grow local communication buffers. */
if (atom->nmax*size_one > maxbuf) {
memory->destroy(comm_buf);
maxbuf = atom->nmax*size_one;
comm_buf = memory->smalloc(maxbuf,"qmmm:comm_buf");
}
if (comm->me == 0) {
// insert local atoms into comm buffer and global arrays
for (i=0; i<nlocal; ++i) {
const int k = (int) tag[i]-1;
mm_mask_all[ k ] = -1;
if (mask[i] & groupbit) {
const int j = 3*taginthash_lookup((taginthash_t *)qm_idmap, tag[i]);
if (j != 3*HASH_FAIL) {
qm_coord[j] = x[i][0];
qm_coord[j+1] = x[i][1];
qm_coord[j+2] = x[i][2];
qm_charge[j/3] = charge[i];
mm_mask_all[k] = type[i];
}
}
mm_coord_all[3*k + 0] = x[i][0];
mm_coord_all[3*k + 1] = x[i][1];
mm_coord_all[3*k + 2] = x[i][2];
mm_charge_all[k] = charge[i];
}
/* done collecting coordinates, send it to dependent codes */
/* to QM code */
MPI_Send(qm_coord, 3*num_qm, MPI_DOUBLE, 1, QMMM_TAG_COORD, qm_comm);
MPI_Send(qm_charge, num_qm, MPI_DOUBLE, 1, QMMM_TAG_CHARGE, qm_comm);
MPI_Send(mm_charge_all, natoms, MPI_DOUBLE, 1, QMMM_TAG_COORD, qm_comm);
MPI_Send(mm_coord_all, 3*natoms, MPI_DOUBLE, 1, QMMM_TAG_COORD, qm_comm);
MPI_Send(mm_mask_all, natoms, MPI_INT, 1, QMMM_TAG_COORD, qm_comm);
MPI_Send(type, natoms, MPI_INT, 1, QMMM_TAG_TYPE, qm_comm);
MPI_Send(mass, ntypes+1, MPI_DOUBLE, 1, QMMM_TAG_MASS, qm_comm);
/* to MM slave code */
MPI_Send(qm_coord, 3*num_qm, MPI_DOUBLE, 1, QMMM_TAG_COORD, mm_comm);
free(mm_coord_all);
free(mm_charge_all);
free(mm_mask_all);
} else {
error->one(FLERR,"Cannot handle parallel MM (yet)");
}
} else if (qmmm_role == QMMM_ROLE_SLAVE) {
MPI_Recv(qm_coord, 3*num_qm, MPI_DOUBLE, 0, QMMM_TAG_COORD, mm_comm, MPI_STATUS_IGNORE);
// not needed for as long as we allow only one MPI task as slave
MPI_Bcast(qm_coord, 3*num_qm, MPI_DOUBLE,0,world);
/* update coordinates of (QM) atoms */
for (int i=0; i < nlocal; ++i) {
if (mask[i] & groupbit) {
for (int j=0; j < num_qm; ++j) {
if (tag[i] == qm_remap[j]) {
x[i][0] = qm_coord[3*j];
x[i][1] = qm_coord[3*j+1];
x[i][2] = qm_coord[3*j+2];
}
}
}
}
}
return;
}
/* ---------------------------------------------------------------------- */
void FixQMMM::exchange_forces()
{
double **f = atom->f;
const int * const mask = atom->mask;
const tagint * const tag = atom->tag;
const int nlocal = atom->nlocal;
const int natoms = (int) atom->natoms;
if ((comm->me) == 0 && (verbose > 0)) {
if (screen) fputs("QMMM: exchange forces\n",screen);
if (logfile) fputs("QMMM: exchange forces\n",logfile);
}
if (qmmm_role == QMMM_ROLE_MASTER) {
struct commdata *buf = static_cast<struct commdata *>(comm_buf);
double *mm_force_all = (double *) calloc(natoms*3, sizeof(double));
double *mm_force_on_qm_atoms = qm_coord; // use qm_coord as a buffer
if (comm->me == 0) {
// receive QM forces from QE
MPI_Recv(qm_force,3*num_qm,MPI_DOUBLE,1,QMMM_TAG_FORCE,qm_comm,MPI_STATUS_IGNORE);
// receive ec contribution to MM forces from QE
MPI_Recv(mm_force_all,3*natoms,MPI_DOUBLE,1,QMMM_TAG_FORCE2,qm_comm,MPI_STATUS_IGNORE);
// receive MM forces from LAMMPS
MPI_Recv( mm_force_on_qm_atoms, 3*num_qm,MPI_DOUBLE,1,QMMM_TAG_FORCE,mm_comm,MPI_STATUS_IGNORE);
// subtract MM forces from QM forces to get the delta
// NOTE: QM forces are always sent in "real" units,
// so we need to apply the scaling factor to get to the
// supported internal units ("metal" or "real")
for (int i=0; i < num_qm; ++i) {
if (verbose > 1) {
const char fmt[] = "[" TAGINT_FORMAT "]: QM(%g %g %g) MM(%g %g %g) /\\(%g %g %g)\n";
if (screen) fprintf(screen, fmt, qm_remap[i],
qmmm_fscale*qm_force[3*i+0], qmmm_fscale*qm_force[3*i+1], qmmm_fscale*qm_force[3*i+2],
mm_force_on_qm_atoms[3*i+0], mm_force_on_qm_atoms[3*i+1], mm_force_on_qm_atoms[3*i+2],
qmmm_fscale*qm_force[3*i+0] - mm_force_on_qm_atoms[3*i+0],
qmmm_fscale*qm_force[3*i+1] - mm_force_on_qm_atoms[3*i+1],
qmmm_fscale*qm_force[3*i+2] - mm_force_on_qm_atoms[3*i+2]);
if (logfile) fprintf(logfile, fmt, qm_remap[i],
qmmm_fscale*qm_force[3*i+0], qmmm_fscale*qm_force[3*i+1], qmmm_fscale*qm_force[3*i+2],
mm_force_on_qm_atoms[3*i+0], mm_force_on_qm_atoms[3*i+1], mm_force_on_qm_atoms[3*i+2],
qmmm_fscale*qm_force[3*i+0] - mm_force_on_qm_atoms[3*i+0],
qmmm_fscale*qm_force[3*i+1] - mm_force_on_qm_atoms[3*i+1],
qmmm_fscale*qm_force[3*i+2] - mm_force_on_qm_atoms[3*i+2]);
}
buf[i].tag = qm_remap[i];
buf[i].x = qmmm_fscale*qm_force[3*i+0] - mm_force_on_qm_atoms[3*i+0];
buf[i].y = qmmm_fscale*qm_force[3*i+1] - mm_force_on_qm_atoms[3*i+1];
buf[i].z = qmmm_fscale*qm_force[3*i+2] - mm_force_on_qm_atoms[3*i+2];
}
}
MPI_Bcast(comm_buf,num_qm*size_one,MPI_BYTE,0,world);
// Inefficient... use buffers.
MPI_Bcast(mm_force_all,natoms*3,MPI_DOUBLE,0,world);
/* apply forces resulting from QM/MM coupling */
if (qmmm_mode == QMMM_MODE_MECH) {
for (int i=0; i < nlocal; ++i) {
if (mask[i] & groupbit) {
for (int j=0; j < num_qm; ++j) {
if (tag[i] == buf[j].tag) {
f[i][0] += buf[j].x;
f[i][1] += buf[j].y;
f[i][2] += buf[j].z;
}
}
}
}
} else if (qmmm_mode == QMMM_MODE_ELEC) {
for (int i=0; i < nlocal; ++i) {
if (mask[i] & groupbit) {
for (int j=0; j < num_qm; ++j) {
if (tag[i] == buf[j].tag) {
f[i][0] += buf[j].x;
f[i][1] += buf[j].y;
f[i][2] += buf[j].z;
}
}
} else {
const int k = (int) tag[i]-1;
f[i][0] += qmmm_fscale * mm_force_all[ 3*k + 0 ];
f[i][1] += qmmm_fscale * mm_force_all[ 3*k + 1 ];
f[i][2] += qmmm_fscale * mm_force_all[ 3*k + 2 ];
}
}
}
free(mm_force_all);
} else if (qmmm_role == QMMM_ROLE_SLAVE) {
// use qm_force and qm_coord as communication buffer
double * mm_force_on_qm_atoms = qm_force;
double * reduced_mm_force_on_qm_atoms = qm_coord;
memset( mm_force_on_qm_atoms, 0, 3*num_qm*sizeof(double) );
for (int i=0; i < nlocal; ++i) {
if (mask[i] & groupbit) {
const int j = 3*taginthash_lookup((taginthash_t *)qm_idmap, tag[i]);
if (j != 3*HASH_FAIL) {
mm_force_on_qm_atoms[j] = f[i][0];
mm_force_on_qm_atoms[j+1] = f[i][1];
mm_force_on_qm_atoms[j+2] = f[i][2];
}
}
}
// collect and send MM slave forces to MM master
// the reduction is not really needed with only one rank (for now)
MPI_Reduce(mm_force_on_qm_atoms, reduced_mm_force_on_qm_atoms, 3*num_qm, MPI_DOUBLE, MPI_SUM, 0, world);
// use qm_coord array as a communication buffer
MPI_Send(reduced_mm_force_on_qm_atoms, 3*num_qm, MPI_DOUBLE, 0, QMMM_TAG_FORCE, mm_comm);
}
return;
}
/* ---------------------------------------------------------------------- */
void FixQMMM::init()
{
if (strstr(update->integrate_style,"respa"))
error->all(FLERR,"Fix qmmm does not currently support r-RESPA");
if (do_init) {
int me = comm->me;
do_init = 0;
if (qmmm_role == QMMM_ROLE_MASTER) {
MPI_Request req[2];
int nat[2];
if (me == 0) {
// receive number of QM atoms from QE
MPI_Irecv(nat, 1, MPI_INT, 1, QMMM_TAG_SIZE, qm_comm, req);
// receive number of QM atoms from MM slave
MPI_Irecv(nat+1, 1, MPI_INT, 1, QMMM_TAG_SIZE, mm_comm, req+1);
MPI_Waitall(2,req,MPI_STATUS_IGNORE);
}
// broadcast across MM master processes
MPI_Bcast(nat, 2, MPI_INT, 0, world);
num_qm = group->count(igroup);
num_mm = group->count(mm_group);
// consistency check. the fix group and the QM and MM slave
if ((num_qm != nat[0]) || (num_qm != nat[1]))
error->all(FLERR,"Inconsistent number of QM/MM atoms");
memory->create(qm_coord,3*num_qm,"qmmm:qm_coord");
memory->create(qm_charge,num_qm,"qmmm:qm_charge");
memory->create(qm_force,3*num_qm,"qmmm:qm_force");
const char fmt1[] = "Initializing QM/MM master with %d QM atoms\n";
const char fmt2[] = "Initializing QM/MM master with %d MM atoms\n";
const char fmt3[] = "Electrostatic coupling with %d atoms\n";
if (screen) {
fprintf(screen,fmt1,num_qm);
fprintf(screen,fmt2,num_mm);
if (qmmm_mode == QMMM_MODE_ELEC) fprintf(screen,fmt3,num_mm-num_qm);
}
if (logfile) {
fprintf(logfile,fmt1,num_qm);
fprintf(logfile,fmt2,num_mm);
if (qmmm_mode == QMMM_MODE_ELEC) fprintf(logfile,fmt3,num_mm-num_qm);
}
} else if (qmmm_role == QMMM_ROLE_SLAVE) {
num_qm = group->count(igroup);
if (me == 0) {
/* send number of QM atoms to MM-master for confirmation */
MPI_Send(&num_qm, 1, MPI_INT, 0, QMMM_TAG_SIZE, mm_comm);
}
memory->create(qm_coord,3*num_qm,"qmmm:qm_coord");
memory->create(qm_force,3*num_qm,"qmmm:qm_force");
const char fmt[] = "Initializing QM/MM slave with %d QM atoms\n";
if (screen) fprintf(screen,fmt,num_qm);
if (logfile) fprintf(logfile,fmt,num_qm);
}
// communication buffer
maxbuf = atom->nmax*size_one;
comm_buf = (void *) memory->smalloc(maxbuf,"qmmm:comm_buf");
/* initialize and build hashtable to map QM atoms */
taginthash_t *qm_hash=new taginthash_t;
taginthash_init(qm_hash, num_qm);
qm_idmap = (void *)qm_hash;
const int nlocal = atom->nlocal;
int i, j, tmp, ndata, qm_ntag;
tagint *tag = atom->tag;
int *mask = atom->mask;
struct commdata *buf = static_cast<struct commdata *>(comm_buf);
if (me == 0) {
MPI_Status status;
MPI_Request request;
tagint *qm_taglist = new tagint[num_qm];
qm_ntag = 0;
for (i=0; i < nlocal; ++i) {
if (mask[i] & groupbit)
qm_taglist[qm_ntag++] = tag[i];
}
/* loop over procs to receive remote data */
for (i=1; i < comm->nprocs; ++i) {
MPI_Irecv(comm_buf, maxbuf, MPI_BYTE, i, 0, world, &request);
MPI_Send(&tmp, 0, MPI_INT, i, 0, world);
MPI_Wait(&request, &status);
MPI_Get_count(&status, MPI_BYTE, &ndata);
ndata /= size_one;
for (j=0; j < ndata; ++j) {
qm_taglist[qm_ntag++] = buf[j].tag;
}
}
/* sort list of tags by value to have consistently the
* same list when running in parallel and build hash table. */
id_sort(qm_taglist, 0, num_qm-1);
for (i=0; i < num_qm; ++i) {
taginthash_insert(qm_hash, qm_taglist[i], i);
}
delete[] qm_taglist;
/* generate reverse index-to-tag map for communicating
* qm/mm forces back to the proper atoms */
qm_remap=taginthash_keys(qm_hash);
if (verbose > 1) {
const char fmt[] = "qm_remap[%d]=" TAGINT_FORMAT
" qm_hash[" TAGINT_FORMAT "]=" TAGINT_FORMAT "\n";
// print hashtable and reverse mapping
for (i=0; i < num_qm; ++i) {
if (screen) fprintf(screen,fmt,i,qm_remap[i],qm_remap[i],
taginthash_lookup(qm_hash, qm_remap[i]));
if (logfile) fprintf(logfile,fmt,i,qm_remap[i],qm_remap[i],
taginthash_lookup(qm_hash, qm_remap[i]));
}
}
} else {
j = 0;
for (i=0; i < nlocal; ++i) {
if (mask[i] & groupbit) {
buf[j].x = -1.0;
buf[j].tag = tag[i];
++j;
}
}
/* blocking receive to wait until it is our turn to send data. */
MPI_Recv(&tmp, 0, MPI_INT, 0, 0, world, MPI_STATUS_IGNORE);
MPI_Rsend(comm_buf, j*size_one, MPI_BYTE, 0, 0, world);
}
// finally, after all is set up, do a first position synchronization
exchange_positions();
}
}
/* ---------------------------------------------------------------------- */
void FixQMMM::post_integrate()
{
exchange_positions();
}
/* ---------------------------------------------------------------------- */
void FixQMMM::setup(int)
{
exchange_forces();
}
/* ---------------------------------------------------------------------- */
void FixQMMM::post_force(int vflag)
{
exchange_forces();
}
/* ---------------------------------------------------------------------- */
/* local memory usage. approximately. */
double FixQMMM::memory_usage(void)
{
double bytes;
bytes = sizeof(FixQMMM);
bytes += maxbuf;
bytes += 6*num_qm*sizeof(double);
return bytes;
}
// Local Variables:
// mode: c++
// compile-command: "make -j4 openmpi"
// c-basic-offset: 2
// fill-column: 76
// indent-tabs-mode: nil
// End:
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