diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp
index b5b380557..78173b809 100644
--- a/src/USER-COLVARS/fix_colvars.cpp
+++ b/src/USER-COLVARS/fix_colvars.cpp
@@ -1,970 +1,921 @@
/* ----------------------------------------------------------------------
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 (Temple U)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include "fix_colvars.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "group.h"
#include "memory.h"
#include "modify.h"
#include "respa.h"
#include "update.h"
#include "colvarproxy_lammps.h"
/* re-usable integer hash table code with static linkage. */
/** hash table top level data structure */
typedef struct inthash_t {
struct inthash_node_t **bucket; /* array of hash nodes */
int size; /* size of the array */
int entries; /* number of entries in table */
int downshift; /* shift cound, used in hash function */
int mask; /* used to select bits for hashing */
} inthash_t;
/** hash table node data structure */
typedef struct inthash_node_t {
int data; /* data in hash node */
int key; /* key for hash lookup */
struct inthash_node_t *next; /* next node in hash chain */
} inthash_node_t;
#define HASH_FAIL -1
#define HASH_LIMIT 0.5
/* initialize new hash table */
static void inthash_init(inthash_t *tptr, int buckets);
/* lookup entry in hash table */
static int inthash_lookup(void *tptr, int key);
/* insert an entry into hash table. */
static int inthash_insert(inthash_t *tptr, int key, int data);
/* delete the hash table */
static void inthash_destroy(inthash_t *tptr);
/* adapted sort for in-place sorting of map indices. */
static void id_sort(int *idmap, int left, int right);
/************************************************************************
* integer hash code:
************************************************************************/
/* inthash() - 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 int inthash(const inthash_t *tptr, int key) {
int hashvalue;
hashvalue = (((key*1103515249)>>tptr->downshift) & tptr->mask);
if (hashvalue < 0) {
hashvalue = 0;
}
return hashvalue;
}
/*
* rebuild_table_int() - Create new hash table when old one fills up.
*
* tptr: Pointer to a hash table
*/
static void rebuild_table_int(inthash_t *tptr) {
inthash_node_t **old_bucket, *old_hash, *tmp;
int old_size, h, i;
old_bucket=tptr->bucket;
old_size=tptr->size;
/* create a new table and rehash old buckets */
inthash_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=inthash(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;
}
/*
* inthash_init() - Initialize a new hash table.
*
* tptr: Pointer to the hash table to initialize
* buckets: The number of initial buckets to create
*/
void inthash_init(inthash_t *tptr, int 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=(inthash_node_t **) calloc(tptr->size, sizeof(inthash_node_t *));
return;
}
/*
* inthash_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
*/
int inthash_lookup(void *ptr, int key) {
const inthash_t *tptr = (const inthash_t *) ptr;
int h;
inthash_node_t *node;
/* find the entry in the hash table */
h=inthash(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);
}
/*
* inthash_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
*/
int inthash_insert(inthash_t *tptr, int key, int data) {
int tmp;
inthash_node_t *node;
int h;
/* check to see if the entry exists */
if ((tmp=inthash_lookup(tptr, key)) != HASH_FAIL)
return(tmp);
/* expand the table if needed */
while (tptr->entries>=HASH_LIMIT*tptr->size)
rebuild_table_int(tptr);
/* insert the new entry */
h=inthash(tptr, key);
node=(struct inthash_node_t *) malloc(sizeof(inthash_node_t));
node->data=data;
node->key=key;
node->next=tptr->bucket[h];
tptr->bucket[h]=node;
tptr->entries++;
return HASH_FAIL;
}
/*
* inthash_destroy() - Delete the entire table, and all remaining entries.
*
*/
void inthash_destroy(inthash_t *tptr) {
inthash_node_t *node, *last;
int 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(inthash_t));
}
}
/************************************************************************
* integer list sort code:
************************************************************************/
/* sort for integer map. initial call id_sort(idmap, 0, natoms - 1); */
static void id_sort(int *idmap, int left, int right)
{
int 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);
}
/***************************************************************/
using namespace LAMMPS_NS;
using namespace FixConst;
// initialize static class members
int FixColvars::instances=0;
/***************************************************************
create class and parse arguments in LAMMPS script. Syntax:
fix ID group-ID colvars <config_file> [optional flags...]
optional keyword value pairs:
input <input prefix> (for restarting/continuing, defaults to
NULL, but set to <output prefix> at end)
output <output prefix> (defaults to 'out')
seed <integer> (seed for RNG, defaults to '1966')
tstat <fix label> (label of thermostatting fix)
***************************************************************/
FixColvars::FixColvars(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 4)
error->all(FLERR,"Illegal fix colvars command: too few arguments");
if (instances > 0)
error->all(FLERR,"Only one colvars fix can be active at a time");
++instances;
scalar_flag = 1;
global_freq = 1;
nevery = 1;
extscalar = 1;
restart_global = 1;
me = comm->me;
conf_file = strdup(arg[3]);
rng_seed = 1966;
unwrap_flag = 1;
inp_name = NULL;
out_name = NULL;
tmp_name = NULL;
/* parse optional arguments */
int argsdone = 4;
while (argsdone < narg) {
// we have keyword/value pairs. check if value is missing
if (argsdone+1 == narg)
error->all(FLERR,"Missing argument to keyword");
if (0 == strcmp(arg[argsdone], "input")) {
inp_name = strdup(arg[argsdone+1]);
} else if (0 == strcmp(arg[argsdone], "output")) {
out_name = strdup(arg[argsdone+1]);
} else if (0 == strcmp(arg[argsdone], "seed")) {
rng_seed = atoi(arg[argsdone+1]);
} else if (0 == strcmp(arg[argsdone], "unwrap")) {
if (0 == strcmp(arg[argsdone+1], "yes")) {
unwrap_flag = 1;
} else if (0 == strcmp(arg[argsdone+1], "no")) {
unwrap_flag = 0;
} else {
error->all(FLERR,"Incorrect fix colvars unwrap flag");
}
} else if (0 == strcmp(arg[argsdone], "tstat")) {
tmp_name = strdup(arg[argsdone+1]);
} else {
error->all(FLERR,"Unknown fix colvars parameter");
}
++argsdone; ++argsdone;
}
if (!out_name) out_name = strdup("out");
/* initialize various state variables. */
tstat_id = -1;
energy = 0.0;
nlevels_respa = 0;
init_flag = 0;
num_coords = 0;
coords = forces = oforce = NULL;
comm_buf = NULL;
force_buf = NULL;
proxy = NULL;
idmap = NULL;
/* storage required to communicate a single coordinate or force. */
size_one = sizeof(struct commdata);
}
/*********************************
* Clean up on deleting the fix. *
*********************************/
FixColvars::~FixColvars()
{
memory->sfree(conf_file);
memory->sfree(inp_name);
memory->sfree(out_name);
memory->sfree(tmp_name);
memory->sfree(comm_buf);
if (proxy) {
delete proxy;
inthash_t *hashtable = (inthash_t *)idmap;
inthash_destroy(hashtable);
delete hashtable;
}
--instances;
}
/* ---------------------------------------------------------------------- */
int FixColvars::setmask()
{
int mask = 0;
mask |= THERMO_ENERGY;
mask |= MIN_POST_FORCE;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
// initial checks for colvars run.
void FixColvars::init()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use fix colvars without atom IDs");
if (atom->map_style == 0)
error->all(FLERR,"Fix colvars requires an atom map");
if ((me == 0) && (update->whichflag == 2))
error->warning(FLERR,"Using fix colvars with minimization");
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixColvars::setup(int vflag)
{
const int * const tag = atom->tag;
const int * const type = atom->type;
int i,nme,tmp,ndata,nlocal_max,tag_max,max;
int nlocal = atom->nlocal;
MPI_Status status;
MPI_Request request;
// one time initialization
if (init_flag == 0) {
init_flag = 1;
-#if 0
-
- // collect a list of atom type by atom id for the entire system.
- // the colvar module requires this information to set masses. :-(
-
- max=0;
- for (i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
- MPI_Allreduce(&max,&tag_max,1,MPI_INT,MPI_MAX,world);
- MPI_Allreduce(&nlocal,&nlocal_max,1,MPI_INT,MPI_MAX,world);
-
- if (me == 0) {
- typemap = new int[tag_max+1];
- memset(typemap,0,sizeof(int)*tag_max);
- }
- type_buf = new int[2*nlocal_max];
-
- if (me == 0) {
- for (i=0; i<nlocal; ++i)
- typemap[tag[i]] = type[i];
-
- // loop over procs to receive and apply remote data
-
- for (i=1; i < comm->nprocs; ++i) {
- MPI_Irecv(type_buf, 2*nlocal_max, MPI_INT, i, 0, world, &request);
- MPI_Send(&tmp, 0, MPI_INT, i, 0, world);
- MPI_Wait(&request, &status);
- MPI_Get_count(&status, MPI_INT, &ndata);
-
- for (int k=0; k<ndata; k+=2)
- typemap[type_buf[k]] = type_buf[k+1];
- }
- } else { // me != 0
-
- // copy tag/type data into communication buffer
-
- nme = 0;
- for (i=0; i<nlocal; ++i) {
- type_buf[nme] = tag[i];
- type_buf[nme+1] = type[i];
- nme +=2;
- }
-
- /* blocking receive to wait until it is our turn to send data. */
- MPI_Recv(&tmp, 0, MPI_INT, 0, 0, world, &status);
- MPI_Rsend(type_buf, nme, MPI_INT, 0, 0, world);
- }
- delete type_buf;
-#endif
-
// now create and initialize the colvars proxy
if (me == 0) {
// input (= restart) name == "NULL" means, no restart.
if (inp_name) {
if (strcmp(inp_name,"NULL") == 0) {
memory->sfree(inp_name);
inp_name = NULL;
}
}
// try to determine thermostat target temperature
double t_target = 0.0;
if (tmp_name) {
if (strcmp(tmp_name,"NULL") == 0)
tstat_id = -1;
else {
tstat_id = modify->find_fix(tmp_name);
if (tstat_id < 0) error->one(FLERR,"Could not find tstat fix ID");
double *tt = (double*)modify->fix[tstat_id]->extract("t_target",tmp);
if (tt) t_target = *tt;
}
}
proxy = new colvarproxy_lammps(lmp,inp_name,out_name,rng_seed,t_target);
proxy->init(conf_file);
coords = proxy->get_coords();
forces = proxy->get_forces();
oforce = proxy->get_oforce();
num_coords = coords->size();
}
// send the list of all colvar atom IDs to all nodes.
// also initialize and build hashtable on master.
MPI_Bcast(&num_coords, 1, MPI_INT, 0, world);
memory->create(taglist,num_coords,"colvars:taglist");
memory->create(force_buf,3*num_coords,"colvars:force_buf");
if (me == 0) {
std::vector<int> *tags_list = proxy->get_tags();
std::vector<int> &tl = *tags_list;
inthash_t *hashtable=new inthash_t;
inthash_init(hashtable, num_coords);
idmap = (void *)hashtable;
for (i=0; i < num_coords; ++i) {
taglist[i] = tl[i];
inthash_insert(hashtable, tl[i], i);
}
}
MPI_Bcast(taglist, num_coords, MPI_INT, 0, world);
} // end of one time initialization
// determine size of comm buffer
nme=0;
for (i=0; i < num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal))
++nme;
}
MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
memory->create(comm_buf,nmax,"colvars:comm_buf");
const double * const * const x = atom->x;
const tagint * const image = atom->image;
const double xprd = domain->xprd;
const double yprd = domain->yprd;
const double zprd = domain->zprd;
const double xy = domain->xy;
const double xz = domain->xz;
const double yz = domain->yz;
if (me == 0) {
std::vector<struct commdata> &cd = *coords;
std::vector<struct commdata> &of = *oforce;
// store coordinate data in holding array, clear old forces
for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) {
of[i].tag = cd[i].tag = tag[k];
of[i].type = cd[i].type = type[k];
of[i].x = of[i].y = of[i].z = 0.0;
if (unwrap_flag) {
const int ix = (image[k] & IMGMASK) - IMGMAX;
const int iy = (image[k] >> IMGBITS & IMGMASK) - IMGMAX;
const int iz = (image[k] >> IMG2BITS) - IMGMAX;
cd[i].x = x[k][0] + ix * xprd + iy * xy + iz * xz;
cd[i].y = x[k][1] + iy * yprd + iz * yz;
cd[i].z = x[k][2] + iz * zprd;
} else {
cd[i].x = x[k][0];
cd[i].y = x[k][1];
cd[i].z = x[k][2];
}
if (atom->rmass_flag) {
cd[i].m = atom->rmass[k];
} else {
cd[i].m = atom->mass[type[k]];
}
}
}
// loop over procs to receive and apply remote data
for (i=1; i < comm->nprocs; ++i) {
int maxbuf = nmax*size_one;
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 (int k=0; k<ndata; ++k) {
const int j = inthash_lookup(idmap, comm_buf[k].tag);
if (j != HASH_FAIL) {
of[j].tag = cd[j].tag = comm_buf[k].tag;
of[j].type = cd[j].type = comm_buf[k].type;
cd[j].x = comm_buf[k].x;
cd[j].y = comm_buf[k].y;
cd[j].z = comm_buf[k].z;
cd[j].m = comm_buf[k].m;
of[j].x = of[j].y = of[j].z = 0.0;
}
}
}
} else { // me != 0
// copy coordinate data into communication buffer
nme = 0;
for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) {
comm_buf[nme].tag = tag[k];
comm_buf[nme].type = type[k];
if (unwrap_flag) {
const int ix = (image[k] & IMGMASK) - IMGMAX;
const int iy = (image[k] >> IMGBITS & IMGMASK) - IMGMAX;
const int iz = (image[k] >> IMG2BITS) - IMGMAX;
comm_buf[nme].x = x[k][0] + ix * xprd + iy * xy + iz * xz;
comm_buf[nme].y = x[k][1] + iy * yprd + iz * yz;
comm_buf[nme].z = x[k][2] + iz * zprd;
} else {
comm_buf[nme].x = x[k][0];
comm_buf[nme].y = x[k][1];
comm_buf[nme].z = x[k][2];
}
if (atom->rmass_flag) {
comm_buf[nme].m = atom->rmass[k];
} else {
comm_buf[nme].m = atom->mass[type[k]];
}
++nme;
}
}
/* blocking receive to wait until it is our turn to send data. */
MPI_Recv(&tmp, 0, MPI_INT, 0, 0, world, &status);
MPI_Rsend(comm_buf, nme*size_one, MPI_BYTE, 0, 0, world);
}
// run pre-run setup in colvarproxy
proxy->setup();
// initialize forces
if (strstr(update->integrate_style,"verlet") || (update->whichflag == 2))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
/* Main colvars handler:
* Send coodinates and add colvar forces to atoms. */
void FixColvars::post_force(int vflag)
{
// some housekeeping: update status of the proxy as needed.
if (me == 0) {
if (proxy->want_exit())
error->one(FLERR,"Run aborted on request from colvars module.\n");
if (tstat_id < 0) {
proxy->set_temperature(0.0);
} else {
int tmp;
// get thermostat target temperature from corresponding fix,
// if the fix supports extraction.
double *tt = (double *) modify->fix[tstat_id]->extract("t_target",tmp);
if (tt)
proxy->set_temperature(*tt);
else
proxy->set_temperature(0.0);
}
}
const int * const tag = atom->tag;
const double * const * const x = atom->x;
double * const * const f = atom->f;
const tagint * const image = atom->image;
const double xprd = domain->xprd;
const double yprd = domain->yprd;
const double zprd = domain->zprd;
const double xy = domain->xy;
const double xz = domain->xz;
const double yz = domain->yz;
const int nlocal = atom->nlocal;
/* check and potentially grow local communication buffers. */
int i,nmax_new,nme=0;
for (i=0; i < num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal))
++nme;
}
MPI_Allreduce(&nme,&nmax_new,1,MPI_INT,MPI_MAX,world);
if (nmax_new > nmax) {
nmax = nmax_new;
memory->grow(comm_buf,nmax,"colvars:comm_buf");
}
MPI_Status status;
MPI_Request request;
int tmp, ndata;
if (me == 0) {
std::vector<struct commdata> &cd = *coords;
// store coordinate data
for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) {
if (unwrap_flag) {
const int ix = (image[k] & IMGMASK) - IMGMAX;
const int iy = (image[k] >> IMGBITS & IMGMASK) - IMGMAX;
const int iz = (image[k] >> IMG2BITS) - IMGMAX;
cd[i].x = x[k][0] + ix * xprd + iy * xy + iz * xz;
cd[i].y = x[k][1] + iy * yprd + iz * yz;
cd[i].z = x[k][2] + iz * zprd;
} else {
cd[i].x = x[k][0];
cd[i].y = x[k][1];
cd[i].z = x[k][2];
}
}
}
/* loop over procs to receive remote data */
for (i=1; i < comm->nprocs; ++i) {
int maxbuf = nmax*size_one;
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 (int k=0; k<ndata; ++k) {
const int j = inthash_lookup(idmap, comm_buf[k].tag);
if (j != HASH_FAIL) {
cd[j].x = comm_buf[k].x;
cd[j].y = comm_buf[k].y;
cd[j].z = comm_buf[k].z;
}
}
}
} else { // me != 0
/* copy coordinate data into communication buffer */
nme = 0;
for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) {
comm_buf[nme].tag = tag[k];
if (unwrap_flag) {
const int ix = (image[k] & IMGMASK) - IMGMAX;
const int iy = (image[k] >> IMGBITS & IMGMASK) - IMGMAX;
const int iz = (image[k] >> IMG2BITS) - IMGMAX;
comm_buf[nme].x = x[k][0] + ix * xprd + iy * xy + iz * xz;
comm_buf[nme].y = x[k][1] + iy * yprd + iz * yz;
comm_buf[nme].z = x[k][2] + iz * zprd;
} else {
comm_buf[nme].x = x[k][0];
comm_buf[nme].y = x[k][1];
comm_buf[nme].z = x[k][2];
}
++nme;
}
}
/* blocking receive to wait until it is our turn to send data. */
MPI_Recv(&tmp, 0, MPI_INT, 0, 0, world, &status);
MPI_Rsend(comm_buf, nme*size_one, MPI_BYTE, 0, 0, world);
}
////////////////////////////////////////////////////////////////////////
// call our workhorse and retrieve additional information.
if (me == 0) {
energy = proxy->compute();
store_forces = proxy->need_system_forces();
}
////////////////////////////////////////////////////////////////////////
// broadcast store_forces flag and energy data to all processors
MPI_Bcast(&energy, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&store_forces, 1, MPI_INT, 0, world);
// broadcast and apply biasing forces
if (me == 0) {
std::vector<struct commdata> &fo = *forces;
double *fbuf = force_buf;
for (int j=0; j < num_coords; ++j) {
*fbuf++ = fo[j].x;
*fbuf++ = fo[j].y;
*fbuf++ = fo[j].z;
}
}
MPI_Bcast(force_buf, 3*num_coords, MPI_DOUBLE, 0, world);
for (int i=0; i < num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) {
f[k][0] += force_buf[3*i+0];
f[k][1] += force_buf[3*i+1];
f[k][2] += force_buf[3*i+2];
}
}
}
/* ---------------------------------------------------------------------- */
void FixColvars::min_post_force(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixColvars::post_force_respa(int vflag, int ilevel, int iloop)
{
/* only process colvar forces on the outmost RESPA level. */
if (ilevel == nlevels_respa-1) post_force(vflag);
return;
}
/* ---------------------------------------------------------------------- */
void FixColvars::end_of_step()
{
if (store_forces) {
const int * const tag = atom->tag;
double * const * const f = atom->f;
const int nlocal = atom->nlocal;
/* check and potentially grow local communication buffers. */
int i,nmax_new,nme=0;
for (i=0; i < num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal))
++nme;
}
MPI_Allreduce(&nme,&nmax_new,1,MPI_INT,MPI_MAX,world);
if (nmax_new > nmax) {
nmax = nmax_new;
memory->grow(comm_buf,nmax,"colvars:comm_buf");
}
MPI_Status status;
MPI_Request request;
int tmp, ndata;
if (me == 0) {
// store old force data
std::vector<struct commdata> &of = *oforce;
for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) {
const int j = inthash_lookup(idmap, tag[k]);
if (j != HASH_FAIL) {
of[j].x = f[k][0];
of[j].y = f[k][1];
of[j].z = f[k][2];
}
}
}
/* loop over procs to receive remote data */
for (i=1; i < comm->nprocs; ++i) {
int maxbuf = nmax*size_one;
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 (int k=0; k<ndata; ++k) {
const int j = inthash_lookup(idmap, comm_buf[k].tag);
if (j != HASH_FAIL) {
of[j].x = comm_buf[k].x;
of[j].y = comm_buf[k].y;
of[j].z = comm_buf[k].z;
}
}
}
} else { // me != 0
/* copy total force data into communication buffer */
nme = 0;
for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) {
comm_buf[nme].tag = tag[k];
comm_buf[nme].x = f[k][0];
comm_buf[nme].y = f[k][1];
comm_buf[nme].z = f[k][2];
++nme;
}
}
/* blocking receive to wait until it is our turn to send data. */
MPI_Recv(&tmp, 0, MPI_INT, 0, 0, world, &status);
MPI_Rsend(comm_buf, nme*size_one, MPI_BYTE, 0, 0, world);
}
}
}
/* ---------------------------------------------------------------------- */
void FixColvars::write_restart(FILE *fp)
{
if (me == 0) {
std::string rest_text("");
proxy->serialize_status(rest_text);
const char *cvm_state = rest_text.c_str();
int len = strlen(cvm_state) + 1; // need to include terminating NULL byte.
fwrite(&len,sizeof(int),1,fp);
fwrite(cvm_state,1,len,fp);
}
}
/* ---------------------------------------------------------------------- */
void FixColvars::restart(char *buf)
{
init();
if (me == 0) {
std::string rest_text(buf);
proxy->deserialize_status(rest_text);
}
}
/* ---------------------------------------------------------------------- */
double FixColvars::compute_scalar()
{
return energy;
}
/* ---------------------------------------------------------------------- */
/* local memory usage. approximately. */
double FixColvars::memory_usage(void)
{
double bytes = (double) (num_coords * (2*sizeof(int)+3*sizeof(double)));
bytes += (double) (nmax*size_one) + sizeof(this);
return bytes;
}