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lammps
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15480 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2016-08-20 22:22:00 +00:00
parent b1829c107c
commit bfba361f65
2 changed files with 86 additions and 3 deletions
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77
src/dump.cpp
View File

@ -81,6 +81,7 @@ Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
buffer_allow = 0;
buffer_flag = 0;
padflag = 0;
pbcflag = 0;
maxbuf = maxids = maxsort = maxproc = 0;
buf = bufsort = NULL;
@ -91,6 +92,10 @@ Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
maxsbuf = 0;
sbuf = NULL;
maxpbc = 0;
xpbc = vpbc = NULL;
imagepbc = NULL;
// parse filename for special syntax
// if contains '%', write one file per proc and replace % with proc-ID
// if contains '*', write one file per timestep and replace * with timestep
@ -164,6 +169,12 @@ Dump::~Dump()
memory->destroy(sbuf);
if (pbcflag) {
memory->destroy(xpbc);
memory->destroy(vpbc);
memory->destroy(imagepbc);
}
if (multiproc) MPI_Comm_free(&clustercomm);
// XTC style sets fp to NULL since it closes file in its destructor
@ -262,6 +273,10 @@ void Dump::init()
}
}
}
// preallocation for PBC copies if requested
if (pbcflag && atom->nlocal > maxpbc) pbc_allocate();
}
/* ---------------------------------------------------------------------- */
@ -352,6 +367,28 @@ void Dump::write()
memory->create(ids,maxids,"dump:ids");
}
// apply PBC on copy of x,v,image if requested
if (pbcflag) {
int nlocal = atom->nlocal;
if (nlocal > maxpbc) pbc_allocate();
if (nlocal) {
memcpy(&xpbc[0][0],&atom->x[0][0],3*nlocal*sizeof(double));
memcpy(&vpbc[0][0],&atom->v[0][0],3*nlocal*sizeof(double));
memcpy(imagepbc,atom->image,nlocal*sizeof(imageint));
}
double **dtmp = atom->x;
atom->x = xpbc;
xpbc = dtmp;
dtmp = atom->v;
atom->v = vpbc;
vpbc = dtmp;
imageint *itmp = atom->image;
atom->image = imagepbc;
imagepbc = itmp;
domain->pbc();
}
// pack my data into buf
// if sorting on IDs also request ID list from pack()
// sort buf as needed
@ -430,6 +467,20 @@ void Dump::write()
}
}
// restore original x,v,image unaltered by PBC
if (pbcflag) {
double **dtmp = atom->x;
atom->x = xpbc;
xpbc = dtmp;
dtmp = atom->v;
atom->v = vpbc;
vpbc = dtmp;
imageint *itmp = atom->image;
atom->image = imagepbc;
imagepbc = itmp;
}
// if file per timestep, close file if I am filewriter
if (multifile) {
@ -887,6 +938,13 @@ void Dump::modify_params(int narg, char **arg)
if (padflag < 0) error->all(FLERR,"Illegal dump_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"pbc") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) pbcflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) pbcflag = 0;
else error->all(FLERR,"Illegal dump_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"sort") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"off") == 0) sort_flag = 0;
@ -919,6 +977,21 @@ void Dump::modify_params(int narg, char **arg)
return # of bytes of allocated memory
------------------------------------------------------------------------- */
void Dump::pbc_allocate()
{
memory->destroy(xpbc);
memory->destroy(vpbc);
memory->destroy(imagepbc);
maxpbc = atom->nmax;
memory->create(xpbc,maxpbc,3,"dump:xbpc");
memory->create(vpbc,maxpbc,3,"dump:vbpc");
memory->create(imagepbc,maxpbc,"dump:imagebpc");
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint Dump::memory_usage()
{
bigint bytes = memory->usage(buf,size_one*maxbuf);
@ -931,5 +1004,9 @@ bigint Dump::memory_usage()
bytes += memory->usage(proclist,maxproc);
if (irregular) bytes += irregular->memory_usage();
}
if (pbcflag) {
bytes += 6*maxpbc * sizeof(double);
bytes += maxpbc * sizeof(imageint);
}
return bytes;
}

6
src/dump.h
View File

@ -71,6 +71,7 @@ class Dump : protected Pointers {
int buffer_allow; // 1 if style allows for buffer_flag, 0 if not
int buffer_flag; // 1 if buffer output as one big string, 0 if not
int padflag; // timestep padding in filename
int pbcflag; // 1 if remap dumped atoms via PBC, 0 if not
int singlefile_opened; // 1 = one big file, already opened, else 0
int sortcol; // 0 to sort on ID, 1-N on columns
int sortcolm1; // sortcol - 1
@ -116,6 +117,10 @@ class Dump : protected Pointers {
tagint *idsort;
int *index,*proclist;
double **xpbc,**vpbc;
int *imagepbc;
int maxpbc;
class Irregular *irregular;
virtual void init_style() = 0;
@ -126,6 +131,7 @@ class Dump : protected Pointers {
virtual void pack(tagint *) = 0;
virtual int convert_string(int, double *) {return 0;}
virtual void write_data(int, double *) = 0;
void pbc_allocate();
void sort();
static int idcompare(const void *, const void *);