forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14428 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
05240f9467
commit
fbd03b390f
|
|
@ -14,10 +14,12 @@
|
|||
#include <string.h>
|
||||
#include "compute_msd_chunk.h"
|
||||
#include "atom.h"
|
||||
#include "group.h"
|
||||
#include "update.h"
|
||||
#include "modify.h"
|
||||
#include "compute_chunk_atom.h"
|
||||
#include "domain.h"
|
||||
#include "fix_store.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
|
|
@ -42,25 +44,51 @@ ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
|
|||
idchunk = new char[n];
|
||||
strcpy(idchunk,arg[3]);
|
||||
|
||||
firstflag = 1;
|
||||
init();
|
||||
|
||||
massproc = masstotal = NULL;
|
||||
com = comall = cominit = NULL;
|
||||
com = comall = NULL;
|
||||
msd = NULL;
|
||||
|
||||
firstflag = 1;
|
||||
// create a new fix STORE style for reference positions
|
||||
// id = compute-ID + COMPUTE_STORE, fix group = compute group
|
||||
// do not know size of array at this point, just allocate 1x3 array
|
||||
// fix creation must be done now so that a restart run can
|
||||
// potentially re-populate the fix array (and change it to correct size)
|
||||
// otherwise size reset and init will be done in setup()
|
||||
|
||||
n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
|
||||
id_fix = new char[n];
|
||||
strcpy(id_fix,id);
|
||||
strcat(id_fix,"_COMPUTE_STORE");
|
||||
|
||||
char **newarg = new char*[6];
|
||||
newarg[0] = id_fix;
|
||||
newarg[1] = group->names[igroup];
|
||||
newarg[2] = (char *) "STORE";
|
||||
newarg[3] = (char *) "global";
|
||||
newarg[4] = (char *) "1";
|
||||
newarg[5] = (char *) "1";
|
||||
modify->add_fix(6,newarg);
|
||||
fix = (FixStore *) modify->fix[modify->nfix-1];
|
||||
delete [] newarg;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeMSDChunk::~ComputeMSDChunk()
|
||||
{
|
||||
// check nfix in case all fixes have already been deleted
|
||||
|
||||
if (modify->nfix) modify->delete_fix(id_fix);
|
||||
|
||||
delete [] id_fix;
|
||||
delete [] idchunk;
|
||||
memory->destroy(massproc);
|
||||
memory->destroy(masstotal);
|
||||
memory->destroy(com);
|
||||
memory->destroy(comall);
|
||||
memory->destroy(cominit);
|
||||
memory->destroy(msd);
|
||||
}
|
||||
|
||||
|
|
@ -74,6 +102,15 @@ void ComputeMSDChunk::init()
|
|||
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
|
||||
if (strcmp(cchunk->style,"chunk/atom") != 0)
|
||||
error->all(FLERR,"Compute msd/chunk does not use chunk/atom compute");
|
||||
|
||||
// set fix which stores reference atom coords
|
||||
// if firstflag, will be created in setup()
|
||||
|
||||
if (!firstflag) {
|
||||
int ifix = modify->find_fix(id_fix);
|
||||
if (ifix < 0) error->all(FLERR,"Could not find compute msd/chunk fix ID");
|
||||
fix = (FixStore *) modify->fix[ifix];
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -87,6 +124,13 @@ void ComputeMSDChunk::setup()
|
|||
compute_array();
|
||||
firstflag = 0;
|
||||
|
||||
// if fix->astore is already correct size, restart file set it up
|
||||
// otherwise reset its size now and initialize to current COM
|
||||
|
||||
if (fix->nrow == nchunk && fix->ncol == 3) return;
|
||||
fix->reset_global(nchunk,3);
|
||||
|
||||
double **cominit = fix->astore;
|
||||
for (int i = 0; i < nchunk; i++) {
|
||||
cominit[i][0] = comall[i][0];
|
||||
cominit[i][1] = comall[i][1];
|
||||
|
|
@ -163,11 +207,12 @@ void ComputeMSDChunk::compute_array()
|
|||
}
|
||||
|
||||
// MSD is difference between current and initial COM
|
||||
// cominit does not yet exist when called first time from setup()
|
||||
// cominit is initilialized by setup() when firstflag is set
|
||||
|
||||
if (firstflag) return;
|
||||
|
||||
double dx,dy,dz;
|
||||
double **cominit = fix->astore;
|
||||
|
||||
for (int i = 0; i < nchunk; i++) {
|
||||
dx = comall[i][0] - cominit[i][0];
|
||||
|
|
@ -246,7 +291,6 @@ void ComputeMSDChunk::allocate()
|
|||
memory->create(masstotal,nchunk,"msd/chunk:masstotal");
|
||||
memory->create(com,nchunk,3,"msd/chunk:com");
|
||||
memory->create(comall,nchunk,3,"msd/chunk:comall");
|
||||
memory->create(cominit,nchunk,3,"msd/chunk:cominit");
|
||||
memory->create(msd,nchunk,4,"msd/chunk:msd");
|
||||
array = msd;
|
||||
}
|
||||
|
|
@ -258,7 +302,7 @@ void ComputeMSDChunk::allocate()
|
|||
double ComputeMSDChunk::memory_usage()
|
||||
{
|
||||
double bytes = (bigint) nchunk * 2 * sizeof(double);
|
||||
bytes += (bigint) nchunk * 3*3 * sizeof(double);
|
||||
bytes += (bigint) nchunk * 2*3 * sizeof(double);
|
||||
bytes += (bigint) nchunk * 4 * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -44,13 +44,14 @@ class ComputeMSDChunk : public Compute {
|
|||
int nchunk;
|
||||
char *idchunk;
|
||||
class ComputeChunkAtom *cchunk;
|
||||
char *id_fix;
|
||||
class FixStore *fix;
|
||||
int firstflag;
|
||||
|
||||
double *massproc,*masstotal;
|
||||
double **com,**comall,**cominit;
|
||||
double **com,**comall;
|
||||
double **msd;
|
||||
|
||||
int firstflag;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
|
|
|
|||
|
|
@ -32,15 +32,15 @@ FixStore::FixStore(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
|||
if (narg != 6) error->all(FLERR,"Illegal fix store command");
|
||||
|
||||
// 4th arg determines GLOBAL vs PERATOM values
|
||||
// syntax: id group style peratom 0/1 nvalue
|
||||
// 0/1 flag = not-store or store peratom values in restart file
|
||||
// nvalue = # of peratom values, N=1 is vector, N>1 is array
|
||||
// syntax: id group style global nrow ncol
|
||||
// Nrow by Ncol array of global values
|
||||
// Ncol=1 is vector, Nrow>1 is array
|
||||
// syntax: id group style peratom 0/1 nvalue
|
||||
// 0/1 flag = not-store or store peratom values in restart file
|
||||
// nvalue = # of peratom values, N=1 is vector, N>1 is array
|
||||
|
||||
if (strcmp(arg[3],"peratom") == 0) flavor = PERATOM;
|
||||
else if (strcmp(arg[3],"global") == 0) flavor = GLOBAL;
|
||||
if (strcmp(arg[3],"global") == 0) flavor = GLOBAL;
|
||||
else if (strcmp(arg[3],"peratom") == 0) flavor = PERATOM;
|
||||
else error->all(FLERR,"Invalid fix store command");
|
||||
|
||||
// GLOBAL values are always written to restart file
|
||||
|
|
@ -54,7 +54,8 @@ FixStore::FixStore(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
|||
error->all(FLERR,"Invalid fix store command");
|
||||
vecflag = 0;
|
||||
if (ncol == 1) vecflag = 1;
|
||||
} else {
|
||||
}
|
||||
if (flavor == PERATOM) {
|
||||
restart_peratom = force->inumeric(FLERR,arg[4]);
|
||||
nvalues = force->inumeric(FLERR,arg[5]);
|
||||
if (restart_peratom < 0 or restart_peratom > 1 || nvalues <= 0)
|
||||
|
|
@ -66,21 +67,23 @@ FixStore::FixStore(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
|||
vstore = NULL;
|
||||
astore = NULL;
|
||||
|
||||
// allocate vector or array
|
||||
// allocate vector or array and restart buffer rbuf
|
||||
// for PERATOM, register with Atom class
|
||||
|
||||
if (flavor == GLOBAL) {
|
||||
if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
|
||||
else memory->create(astore,nrow,ncol,"fix/store:astore");
|
||||
memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
|
||||
}
|
||||
if (flavor == PERATOM) {
|
||||
grow_arrays(atom->nmax);
|
||||
atom->add_callback(0);
|
||||
if (restart_peratom) atom->add_callback(1);
|
||||
rbuf = NULL;
|
||||
}
|
||||
|
||||
// zero the storage
|
||||
// PERATOM may be exchanged before filled by caller
|
||||
// PERATOM may be comm->exchanged before filled by caller
|
||||
|
||||
if (flavor == GLOBAL) {
|
||||
if (vecflag)
|
||||
|
|
@ -99,6 +102,7 @@ FixStore::FixStore(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
|||
for (int j = 0; j < nvalues; j++)
|
||||
astore[i][j] = 0.0;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
@ -114,6 +118,7 @@ FixStore::~FixStore()
|
|||
|
||||
memory->destroy(vstore);
|
||||
memory->destroy(astore);
|
||||
memory->destroy(rbuf);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
@ -124,18 +129,47 @@ int FixStore::setmask()
|
|||
return mask;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
reset size of global vector/array
|
||||
invoked by caller if size is unknown at time this fix is instantiated
|
||||
caller will do subsequent initialization
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixStore::reset_global(int nrow_caller, int ncol_caller)
|
||||
{
|
||||
memory->destroy(vstore);
|
||||
memory->destroy(astore);
|
||||
memory->destroy(rbuf);
|
||||
vstore = NULL;
|
||||
astore = NULL;
|
||||
|
||||
vecflag = 0;
|
||||
if (ncol_caller == 1) vecflag = 1;
|
||||
nrow = nrow_caller;
|
||||
ncol = ncol_caller;
|
||||
if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
|
||||
else memory->create(astore,nrow,ncol,"fix/store:astore");
|
||||
memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
write global array to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixStore::write_restart(FILE *fp)
|
||||
{
|
||||
int n = nrow*ncol;
|
||||
// fill rbuf with size and vec/array values
|
||||
|
||||
rbuf[0] = nrow;
|
||||
rbuf[1] = ncol;
|
||||
if (vecflag) memcpy(&rbuf[2],vstore,nrow*sizeof(double));
|
||||
else memcpy(&rbuf[2],&astore[0][0],nrow*ncol*sizeof(double));
|
||||
|
||||
int n = nrow*ncol + 2;
|
||||
if (comm->me == 0) {
|
||||
int size = n * sizeof(double);
|
||||
fwrite(&size,sizeof(int),1,fp);
|
||||
if (vecflag) fwrite(vstore,sizeof(double),n,fp);
|
||||
else fwrite(&astore[0][0],sizeof(double),n,fp);
|
||||
fwrite(rbuf,sizeof(double),n,fp);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -145,12 +179,36 @@ void FixStore::write_restart(FILE *fp)
|
|||
|
||||
void FixStore::restart(char *buf)
|
||||
{
|
||||
// HOWTO insure size of buf is the same
|
||||
// first 2 values in buf are vec/array sizes
|
||||
|
||||
double *dbuf = (double *) buf;
|
||||
int nrow_restart = dbuf[0];
|
||||
int ncol_restart = dbuf[1];
|
||||
|
||||
// if size of vec/array has changed,
|
||||
// means the restart file is setting size of vec or array and doing init
|
||||
// because caller did not know size at time this fix was instantiated
|
||||
// reallocate vstore or astore accordingly
|
||||
|
||||
if (nrow != nrow_restart || ncol != ncol_restart) {
|
||||
memory->destroy(vstore);
|
||||
memory->destroy(astore);
|
||||
memory->destroy(rbuf);
|
||||
vstore = NULL;
|
||||
astore = NULL;
|
||||
|
||||
vecflag = 0;
|
||||
if (ncol_restart == 1) vecflag = 1;
|
||||
nrow = nrow_restart;
|
||||
ncol = ncol_restart;
|
||||
if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
|
||||
else memory->create(astore,nrow,ncol,"fix/store:astore");
|
||||
memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
|
||||
}
|
||||
|
||||
int n = nrow*ncol;
|
||||
double *dbuf = (double *) buf;
|
||||
if (vecflag) memcpy(vstore,dbuf,n*sizeof(double));
|
||||
else memcpy(&astore[0][0],dbuf,n*sizeof(double));
|
||||
if (vecflag) memcpy(vstore,&dbuf[2],n*sizeof(double));
|
||||
else memcpy(&astore[0][0],&dbuf[2],n*sizeof(double));
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -31,6 +31,7 @@ class FixStore : public Fix {
|
|||
int nvalues; // number of per-atom values
|
||||
double *vstore; // vector storage for GLOBAL or PERATOM
|
||||
double **astore; // array storage for GLOBAL or PERATOM
|
||||
double *rbuf; // restart buffer for GLOBAL vec/array
|
||||
|
||||
FixStore(class LAMMPS *, int, char **);
|
||||
~FixStore();
|
||||
|
|
@ -50,9 +51,12 @@ class FixStore : public Fix {
|
|||
|
||||
double memory_usage();
|
||||
|
||||
void reset_global(int, int);
|
||||
|
||||
private:
|
||||
int flavor; // GLOBAL or PERATOM
|
||||
int vecflag; // 1 if ncol=1 or nvalues=1
|
||||
|
||||
};
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue