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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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161
src/USER-MISC/fix_imd.cpp
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@ -5,7 +5,7 @@
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
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.
@ -13,37 +13,37 @@
/* ----------------------------------------------------------------------
The FixIMD class contains code from VMD and NAMD which is copyrighted
by the Board of Trustees of the University of Illinois and is free to
by the Board of Trustees of the University of Illinois and is free to
use with LAMMPS according to point 2 of the UIUC license (10% clause):
" Licensee may, at its own expense, create and freely distribute
complimentary works that interoperate with the Software, directing others to
the TCBG server to license and obtain the Software itself. Licensee may, at
its own expense, modify the Software to make derivative works. Except as
explicitly provided below, this License shall apply to any derivative work
as it does to the original Software distributed by Illinois. Any derivative
work should be clearly marked and renamed to notify users that it is a
modified version and not the original Software distributed by Illinois.
Licensee agrees to reproduce the copyright notice and other proprietary
markings on any derivative work and to include in the documentation of such
" Licensee may, at its own expense, create and freely distribute
complimentary works that interoperate with the Software, directing others to
the TCBG server to license and obtain the Software itself. Licensee may, at
its own expense, modify the Software to make derivative works. Except as
explicitly provided below, this License shall apply to any derivative work
as it does to the original Software distributed by Illinois. Any derivative
work should be clearly marked and renamed to notify users that it is a
modified version and not the original Software distributed by Illinois.
Licensee agrees to reproduce the copyright notice and other proprietary
markings on any derivative work and to include in the documentation of such
work the acknowledgement:
"This software includes code developed by the Theoretical and Computational
Biophysics Group in the Beckman Institute for Advanced Science and
"This software includes code developed by the Theoretical and Computational
Biophysics Group in the Beckman Institute for Advanced Science and
Technology at the University of Illinois at Urbana-Champaign."
Licensee may redistribute without restriction works with up to 1/2 of their
non-comment source code derived from at most 1/10 of the non-comment source
code developed by Illinois and contained in the Software, provided that the
above directions for notice and acknowledgement are observed. Any other
distribution of the Software or any derivative work requires a separate
license with Illinois. Licensee may contact Illinois (vmd@ks.uiuc.edu) to
Licensee may redistribute without restriction works with up to 1/2 of their
non-comment source code derived from at most 1/10 of the non-comment source
code developed by Illinois and contained in the Software, provided that the
above directions for notice and acknowledgement are observed. Any other
distribution of the Software or any derivative work requires a separate
license with Illinois. Licensee may contact Illinois (vmd@ks.uiuc.edu) to
negotiate an appropriate license for such distribution."
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (TempleU)
IMD API, hash, and socket code written by: John E. Stone,
IMD API, hash, and socket code written by: John E. Stone,
Justin Gullingsrud, and James Phillips, (TCBG, Beckman Institute, UIUC)
------------------------------------------------------------------------- */
@ -124,7 +124,7 @@ static int inthash(const inthash_t *tptr, int key) {
hashvalue = (((key*1103515249)>>tptr->downshift) & tptr->mask);
if (hashvalue < 0) {
hashvalue = 0;
}
}
return hashvalue;
}
@ -224,15 +224,15 @@ int *inthash_keys(inthash_t *tptr) {
int *keys;
inthash_node_t *node;
keys = (int *)calloc(tptr->entries, sizeof(int));
for (int i=0; i < tptr->size; ++i) {
for (node=tptr->bucket[i]; node != NULL; node=node->next) {
keys[node->data] = node->key;
}
}
return keys;
}
@ -271,7 +271,7 @@ int inthash_insert(inthash_t *tptr, int key, int data) {
/*
* inthash_destroy() - Delete the entire table, and all remaining entries.
*
*
*/
void inthash_destroy(inthash_t *tptr) {
inthash_node_t *node, *last;
@ -279,12 +279,12 @@ void inthash_destroy(inthash_t *tptr) {
for (i=0; i<tptr->size; i++) {
node = tptr->bucket[i];
while (node != NULL) {
last = node;
while (node != NULL) {
last = node;
node = node->next;
free(last);
}
}
}
/* free the entire array of buckets */
if (tptr->bucket != NULL) {
@ -432,22 +432,22 @@ using namespace LAMMPS_NS;
using namespace FixConst;
/* struct for packed data communication of coordinates and forces. */
struct commdata {
int tag;
float x,y,z;
struct commdata {
int tag;
float x,y,z;
};
/***************************************************************
* create class and parse arguments in LAMMPS script. Syntax:
* fix ID group-ID imd <imd_trate> <imd_port> [unwrap (on|off)] [fscale <imd_fscale>]
* create class and parse arguments in LAMMPS script. Syntax:
* fix ID group-ID imd <imd_trate> <imd_port> [unwrap (on|off)] [fscale <imd_fscale>]
***************************************************************/
FixIMD::FixIMD(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 4)
if (narg < 4)
error->all(FLERR,"Illegal fix imd command");
imd_port = atoi(arg[3]);
imd_port = atoi(arg[3]);
if (imd_port < 1024)
error->all(FLERR,"Illegal fix imd parameter: port < 1024");
@ -457,18 +457,18 @@ FixIMD::FixIMD(LAMMPS *lmp, int narg, char **arg) :
connect_msg = 1;
imd_fscale = 1.0;
imd_trate = 1;
/* parse optional arguments */
int argsdone = 4;
while (argsdone+1 < narg) {
if (0 == strcmp(arg[argsdone], "unwrap")) {
if (0 == strcmp(arg[argsdone+1], "on")) {
if (0 == strcmp(arg[argsdone+1], "on")) {
unwrap_flag = 1;
} else {
unwrap_flag = 0;
}
} else if (0 == strcmp(arg[argsdone], "nowait")) {
if (0 == strcmp(arg[argsdone+1], "on")) {
if (0 == strcmp(arg[argsdone+1], "on")) {
nowait_flag = 1;
} else {
nowait_flag = 0;
@ -507,7 +507,7 @@ FixIMD::FixIMD(LAMMPS *lmp, int narg, char **arg) :
comm_buf = NULL;
idmap = NULL;
rev_idmap = NULL;
if (me == 0) {
/* set up incoming socket on MPI rank 0. */
imdsock_init();
@ -524,7 +524,7 @@ FixIMD::FixIMD(LAMMPS *lmp, int narg, char **arg) :
MPI_Bcast(&imd_terminate, 1, MPI_INT, 0, world);
if (imd_terminate)
error->all(FLERR,"LAMMPS Terminated on error in IMD.");
/* storage required to communicate a single coordinate or force. */
size_one = sizeof(struct commdata);
@ -618,7 +618,7 @@ int FixIMD::reconnect()
/* set up IMD communication, but only if needed. */
imd_inactive = 0;
imd_terminate = 0;
if (me == 0) {
if (clientsock) return 1;
if (screen && connect_msg)
@ -626,7 +626,7 @@ int FixIMD::reconnect()
fprintf(screen,"Listening for IMD connection on port %d. Transfer rate %d.\n",imd_port, imd_trate);
else
fprintf(screen,"Waiting for IMD connection on port %d. Transfer rate %d.\n",imd_port, imd_trate);
connect_msg = 0;
clientsock = NULL;
if (nowait_flag) {
@ -644,7 +644,7 @@ int FixIMD::reconnect()
} while (retval <= 0);
clientsock = imdsock_accept(localsock);
}
if (!imd_inactive && !clientsock) {
if (screen)
fprintf(screen, "IMD socket accept error. Dropping connection.\n");
@ -677,7 +677,7 @@ int FixIMD::reconnect()
}
/* ---------------------------------------------------------------------- */
/* wait for IMD client (e.g. VMD) to respond, initialize communication
/* wait for IMD client (e.g. VMD) to respond, initialize communication
* buffers and collect tag/id maps. */
void FixIMD::setup(int)
{
@ -709,7 +709,7 @@ void FixIMD::setup(int)
inthash_t *hashtable=new inthash_t;
inthash_init(hashtable, num_coords);
idmap = (void *)hashtable;
MPI_Status status;
MPI_Request request;
int tmp, ndata;
@ -718,14 +718,14 @@ void FixIMD::setup(int)
if (me == 0) {
int *taglist = new int[num_coords];
int numtag=0; /* counter to map atom tags to a 0-based consecutive index list */
for (i=0; i < nlocal; ++i) {
if (mask[i] & groupbit) {
taglist[numtag] = tag[i];
++numtag;
}
}
/* 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);
@ -740,7 +740,7 @@ void FixIMD::setup(int)
}
}
/* sort list of tags by value to have consistently the
/* sort list of tags by value to have consistently the
* same list when running in parallel and build hash table. */
id_sort(taglist, 0, num_coords-1);
for (i=0; i < num_coords; ++i) {
@ -748,7 +748,7 @@ void FixIMD::setup(int)
}
delete[] taglist;
/* generate reverse index-to-tag map for communicating
/* generate reverse index-to-tag map for communicating
* IMD forces back to the proper atoms */
rev_idmap=inthash_keys(hashtable);
} else {
@ -763,7 +763,7 @@ void FixIMD::setup(int)
MPI_Recv(&tmp, 0, MPI_INT, 0, 0, world, &status);
MPI_Rsend(comm_buf, nme*size_one, MPI_BYTE, 0, 0, world);
}
return;
}
@ -834,7 +834,7 @@ void FixIMD::post_force(int vflag)
while ((imdsock_selread(clientsock, 0) > 0) || imd_paused) {
/* if something requested to turn off IMD while paused get out */
if (imd_inactive) break;
int32 length;
int msg = imd_recv_header(clientsock, &length);
@ -881,7 +881,7 @@ void FixIMD::post_force(int vflag)
case IMD_PAUSE:
/* pause the running simulation. wait for second IMD_PAUSE to continue. */
if (imd_paused) {
if (screen)
if (screen)
fprintf(screen, "Continuing run on IMD client request.\n");
imd_paused = 0;
} else {
@ -893,9 +893,9 @@ void FixIMD::post_force(int vflag)
case IMD_TRATE:
/* change the IMD transmission data rate */
if (length > 0)
if (length > 0)
imd_trate = length;
if (screen)
if (screen)
fprintf(screen, "IMD client requested change of transfer rate. Now it is %d.\n", imd_trate);
break;
@ -904,7 +904,7 @@ void FixIMD::post_force(int vflag)
imd_recv_energies(clientsock, &dummy_energies);
break;
}
case IMD_FCOORDS: {
float *dummy_coords = new float[3*length];
imd_recv_fcoords(clientsock, length, dummy_coords);
@ -924,7 +924,7 @@ void FixIMD::post_force(int vflag)
}
imd_forces = length;
buf = static_cast<struct commdata *>(force_buf);
/* compare data to hash table */
for (int ii=0; ii < length; ++ii) {
buf[ii].tag = rev_idmap[imd_tags[ii]];
@ -936,7 +936,7 @@ void FixIMD::post_force(int vflag)
delete[] imd_fdat;
break;
}
default:
if (screen)
fprintf(screen, "Unhandled incoming IMD message #%d. length=%d\n", msg, length);
@ -944,11 +944,11 @@ void FixIMD::post_force(int vflag)
}
}
}
/* update all tasks with current settings. */
int old_imd_forces = imd_forces;
MPI_Bcast(&imd_trate, 1, MPI_INT, 0, world);
MPI_Bcast(&imd_inactive, 1, MPI_INT, 0, world);
MPI_Bcast(&imd_inactive, 1, MPI_INT, 0, world);
MPI_Bcast(&imd_forces, 1, MPI_INT, 0, world);
MPI_Bcast(&imd_terminate, 1, MPI_INT, 0, world);
if (imd_terminate)
@ -958,7 +958,7 @@ void FixIMD::post_force(int vflag)
/* check if we need to readjust the forces comm buffer on the receiving nodes. */
if (me != 0) {
if (old_imd_forces < imd_forces) { /* grow holding space for forces, if needed. */
if (force_buf != NULL)
if (force_buf != NULL)
memory->sfree(force_buf);
force_buf = memory->smalloc(imd_forces*size_one, "imd:force_buf");
}
@ -971,16 +971,16 @@ void FixIMD::post_force(int vflag)
* at the expense of a more jumpy display. Rather than using
* end_of_step() we do everything here in one go.
*
* If we don't communicate, only check if we have forces
* If we don't communicate, only check if we have forces
* stored away and apply them. */
if (update->ntimestep % imd_trate) {
if (imd_forces > 0) {
double **f = atom->f;
buf = static_cast<struct commdata *>(force_buf);
/* XXX. this is in principle O(N**2) == not good.
* however we assume for now that the number of atoms
* that we manipulate via IMD will be small compared
/* XXX. this is in principle O(N**2) == not good.
* however we assume for now that the number of atoms
* that we manipulate via IMD will be small compared
* to the total system size, so we don't hurt too much. */
for (int j=0; j < imd_forces; ++j) {
for (int i=0; i < nlocal; ++i) {
@ -996,7 +996,7 @@ void FixIMD::post_force(int vflag)
}
return;
}
/* check and potentially grow local communication buffers. */
int i, k, nmax, nme=0;
for (i=0; i < nlocal; ++i)
@ -1013,7 +1013,7 @@ void FixIMD::post_force(int vflag)
MPI_Request request;
int tmp, ndata;
buf = static_cast<struct commdata *>(comm_buf);
if (me == 0) {
/* collect data into new array. we bypass the IMD API to save
* us one extra copy of the data. */
@ -1072,7 +1072,7 @@ void FixIMD::post_force(int vflag)
MPI_Wait(&request, &status);
MPI_Get_count(&status, MPI_BYTE, &ndata);
ndata /= size_one;
for (k=0; k<ndata; ++k) {
const int j = 3*inthash_lookup((inthash_t *)idmap, buf[k].tag);
if (j != HASH_FAIL) {
@ -1169,12 +1169,12 @@ double FixIMD::memory_usage(void)
/***************************************************************************/
/* NOTE: the following code is the based on the example implementation
* of the IMD protocol API from VMD and NAMD. The UIUC license allows
* of the IMD protocol API from VMD and NAMD. The UIUC license allows
* to re-use up to 10% of a project's code to be used in other software */
/***************************************************************************
* DESCRIPTION:
* Socket interface, abstracts machine dependent APIs/routines.
* Socket interface, abstracts machine dependent APIs/routines.
***************************************************************************/
int imdsock_init(void) {
@ -1190,7 +1190,7 @@ int imdsock_init(void) {
}
return rc;
#else
#else
return 0;
#endif
}
@ -1201,7 +1201,7 @@ void * imdsock_create(void) {
s = (imdsocket *) malloc(sizeof(imdsocket));
if (s != NULL)
memset(s, 0, sizeof(imdsocket));
memset(s, 0, sizeof(imdsocket));
if ((s->sd = socket(PF_INET, SOCK_STREAM, 0)) == -1) {
printf("Failed to open socket.");
@ -1214,7 +1214,7 @@ void * imdsock_create(void) {
int imdsock_bind(void * v, int port) {
imdsocket *s = (imdsocket *) v;
memset(&(s->addr), 0, sizeof(s->addr));
memset(&(s->addr), 0, sizeof(s->addr));
s->addr.sin_family = PF_INET;
s->addr.sin_port = htons(port);
@ -1296,7 +1296,7 @@ void imdsock_destroy(void * v) {
#else
close(s->sd);
#endif
free(s);
free(s);
}
int imdsock_selread(void *v, int sec) {
@ -1304,9 +1304,9 @@ int imdsock_selread(void *v, int sec) {
fd_set rfd;
struct timeval tv;
int rc;
if (v == NULL) return 0;
FD_ZERO(&rfd);
FD_SET(s->sd, &rfd);
memset((void *)&tv, 0, sizeof(struct timeval));
@ -1317,13 +1317,13 @@ int imdsock_selread(void *v, int sec) {
return rc;
}
int imdsock_selwrite(void *v, int sec) {
imdsocket *s = (imdsocket *)v;
fd_set wfd;
struct timeval tv;
int rc;
if (v == NULL) return 0;
FD_ZERO(&wfd);
@ -1394,7 +1394,7 @@ static void swap_header(IMDheader *header) {
static int32 imd_readn(void *s, char *ptr, int32 n) {
int32 nleft;
int32 nread;
nleft = n;
while (nleft > 0) {
if ((nread = imdsock_read(s, ptr, nleft)) < 0) {
@ -1449,7 +1449,7 @@ IMDType imd_recv_header(void *s, int32 *length) {
return IMD_IOERROR;
swap_header(&header);
*length = header.length;
return IMDType(header.type);
return IMDType(header.type);
}
int imd_recv_mdcomm(void *s, int32 n, int32 *indices, float *forces) {
@ -1474,4 +1474,3 @@ int imd_recv_fcoords(void *s, int32 n, float *coords) {
// fill-column: 76
// indent-tabs-mode: nil
// End: