From 6394161a7cd66e3058a0cd3eb6f67a4ab456228d Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Tue, 23 Oct 2012 15:51:01 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8992
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/atom.cpp | 1 -
src/atom.h | 4 ++--
src/atom_map.cpp | 8 +++++++-
src/read_dump.cpp | 27 +++++++++++++++++++++------
src/rerun.cpp | 4 ++--
5 files changed, 32 insertions(+), 12 deletions(-)
diff --git a/src/atom.cpp b/src/atom.cpp
index c7067abc16..0eee4269e0 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -237,7 +237,6 @@ Atom::~Atom()
// delete mapping data structures
- memory->destroy(sametag);
map_delete();
}
diff --git a/src/atom.h b/src/atom.h
index 33ab918af2..bc49b11382 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -116,6 +116,7 @@ class Atom : protected Pointers {
int map_style; // default or user-specified style of map
// 0 = none, 1 = array, 2 = hash
+ int map_tag_max; // max atom ID that map() is setup for
// spatial sorting of atoms
@@ -198,8 +199,7 @@ class Atom : protected Pointers {
// global to local ID mapping
- int map_tag_max; // size of map_array
- int *map_array; // direct map of length max atom ID + 1
+ int *map_array; // direct map of length map_tag_max + 1
int smax; // max size of sametag
struct HashElem {
diff --git a/src/atom_map.cpp b/src/atom_map.cpp
index 33caa87062..93c377b81e 100644
--- a/src/atom_map.cpp
+++ b/src/atom_map.cpp
@@ -244,12 +244,18 @@ void Atom::map_one(int global, int local)
void Atom::map_delete()
{
+ memory->destroy(sametag);
+ sametag = NULL;
+
if (map_style == 1) {
- if (map_tag_max) memory->destroy(map_array);
+ memory->destroy(map_array);
+ map_array = NULL;
} else {
if (map_nhash) {
delete [] map_bucket;
delete [] map_hash;
+ map_bucket = NULL;
+ map_hash = NULL;
}
map_nhash = 0;
}
diff --git a/src/read_dump.cpp b/src/read_dump.cpp
index f1691ab443..268165c17e 100644
--- a/src/read_dump.cpp
+++ b/src/read_dump.cpp
@@ -86,6 +86,9 @@ ReadDump::~ReadDump()
void ReadDump::command(int narg, char **arg)
{
+ if (domain->box_exist == 0)
+ error->all(FLERR,"Read_dump command before simulation box is defined");
+
if (narg < 2) error->all(FLERR,"Illegal read_dump command");
store_files(1,&arg[0]);
@@ -321,14 +324,24 @@ void ReadDump::header(int fieldinfo)
yhi = box[1][1];
zlo = box[2][0];
zhi = box[2][1];
- xprd = xhi - xlo;
- yprd = yhi - ylo;
- zprd = zhi - zlo;
if (triclinic_snap) {
xy = box[0][2];
xz = box[1][2];
yz = box[2][2];
+ double xdelta = MIN(0.0,xy);
+ xdelta = MIN(xdelta,xz);
+ xdelta = MIN(xdelta,xy+xz);
+ xlo = xlo - xdelta;
+ xdelta = MAX(0.0,xy);
+ xdelta = MAX(xdelta,xz);
+ xdelta = MAX(xdelta,xy+xz);
+ xhi = xhi - xdelta;
+ ylo = ylo - MIN(0.0,yz);
+ yhi = yhi - MAX(0.0,yz);
}
+ xprd = xhi - xlo;
+ yprd = yhi - ylo;
+ zprd = zhi - zlo;
// done if not checking fields
@@ -662,21 +675,23 @@ int ReadDump::fields_and_keywords(int narg, char **arg)
void ReadDump::process_atoms(int n)
{
- int i,m,ifield,itype;
+ int i,m,ifield,itype,itag;;
int xbox,ybox,zbox;
double **x = atom->x;
double **v = atom->v;
tagint *image = atom->image;
int nlocal = atom->nlocal;
+ int map_tag_max = atom->map_tag_max;
for (i = 0; i < n; i++) {
ucflag[i] = 0;
- // map() call is invalid if purged all atoms
+ // check if new atom matches one I own
// setting m = -1 forces new atom not to match
- if (!purgeflag) m = atom->map(static_cast<int> (fields[i][0]));
+ itag = static_cast<int> (fields[i][0]);
+ if (itag <= map_tag_max) m = atom->map(static_cast<int> (fields[i][0]));
else m = -1;
if (m < 0 || m >= nlocal) continue;
diff --git a/src/rerun.cpp b/src/rerun.cpp
index 38078e7626..4edcd70676 100644
--- a/src/rerun.cpp
+++ b/src/rerun.cpp
@@ -35,11 +35,11 @@ Rerun::Rerun(LAMMPS *lmp) : Pointers(lmp) {}
void Rerun::command(int narg, char **arg)
{
- if (narg < 2) error->all(FLERR,"Illegal rerun command");
-
if (domain->box_exist == 0)
error->all(FLERR,"Rerun command before simulation box is defined");
+ if (narg < 2) error->all(FLERR,"Illegal rerun command");
+
// list of dump files = args until a keyword
int iarg = 0;
--
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