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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10806 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-09-18 16:20:58 +00:00
parent 23da8399c0
commit d28e92e032
9 changed files with 102 additions and 62 deletions
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78
src/read_dump.cpp
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@ -38,8 +38,10 @@ using namespace LAMMPS_NS;
#define CHUNK 1024
#define EPSILON 1.0e-6
// also in reader_native.cpp
enum{ID,TYPE,X,Y,Z,VX,VY,VZ,IX,IY,IZ};
enum{UNSET,UNSCALED,SCALED};
enum{UNSET,NOSCALE_NOWRAP,NOSCALE_WRAP,SCALE_NOWRAP,SCALE_WRAP};
/* ---------------------------------------------------------------------- */
@ -298,7 +300,6 @@ bigint ReadDump::next(bigint ncurrent, bigint nlast, int nevery, int nskip)
/* ----------------------------------------------------------------------
read and broadcast and store snapshot header info
set nsnapatoms = # of atoms in snapshot
set yindex,zindex
------------------------------------------------------------------------- */
void ReadDump::header(int fieldinfo)
@ -309,7 +310,8 @@ void ReadDump::header(int fieldinfo)
if (me == 0)
nsnapatoms = reader->read_header(box,triclinic_snap,
fieldinfo,nfield,fieldtype,fieldlabel,
scaledflag,fieldflag,xflag,yflag,zflag);
scaleflag,wrapflag,fieldflag,
xflag,yflag,zflag);
MPI_Bcast(&nsnapatoms,1,MPI_LMP_BIGINT,0,world);
MPI_Bcast(&triclinic_snap,1,MPI_INT,0,world);
@ -363,30 +365,51 @@ void ReadDump::header(int fieldinfo)
error->one(FLERR,"Read_dump triclinic status does not match simulation");
}
// error check field and scaling info
// error check on requested fields exisiting in dump file
if (fieldflag < 0)
error->one(FLERR,"Read_dump field not found in dump file");
// set overall scaling of coordinates
// error if x,y,z scaling are not the same
// all explicitly requested x,y,z must have consistent scaling & wrapping
scaled = MAX(xflag,yflag);
scaled = MAX(zflag,scaled);
if ((xflag != UNSET && xflag != scaled) ||
(yflag != UNSET && yflag != scaled) ||
(zflag != UNSET && zflag != scaled))
error->one(FLERR,"Read_dump x,y,z fields do not have consistent scaling");
int value = MAX(xflag,yflag);
value = MAX(zflag,value);
if ((xflag != UNSET && xflag != value) ||
(yflag != UNSET && yflag != value) ||
(zflag != UNSET && zflag != value))
error->one(FLERR,
"Read_dump xyz fields do not have consistent scaling/wrapping");
// set scaled/wrapped based on xyz flags
value = UNSET;
if (xflag != UNSET) value = xflag;
if (yflag != UNSET) value = yflag;
if (zflag != UNSET) value = zflag;
if (value == UNSET) {
scaled = wrapped = 0;
} else if (value == NOSCALE_NOWRAP) {
scaled = wrapped = 0;
} else if (value == NOSCALE_WRAP) {
scaled = 0;
wrapped = 1;
} else if (value == SCALE_NOWRAP) {
scaled = 1;
wrapped = 0;
} else if (value == SCALE_WRAP) {
scaled = wrapped = 1;
}
// scaled, triclinic coords require all 3 x,y,z fields, to perform unscaling
// set yindex,zindex = column index of Y and Z fields in fields array
// needed for unscaling to absolute coords in xfield(), yfield(), zfield()
if (scaled == SCALED && triclinic == 1) {
if (scaled && triclinic == 1) {
int flag = 0;
if (xflag != scaled) flag = 1;
if (yflag != scaled) flag = 1;
if (dimension == 3 && zflag != scaled) flag = 1;
if (xflag == UNSET) flag = 1;
if (yflag == UNSET) flag = 1;
if (dimension == 3 && zflag == UNSET) flag = 1;
if (flag)
error->one(FLERR,"All read_dump x,y,z fields must be specified for "
"scaled, triclinic coords");
@ -597,7 +620,8 @@ int ReadDump::fields_and_keywords(int narg, char **arg)
trimflag = 0;
addflag = 0;
for (int i = 0; i < nfield; i++) fieldlabel[i] = NULL;
scaledflag = UNSCALED;
scaleflag = 0;
wrapflag = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"box") == 0) {
@ -642,8 +666,14 @@ int ReadDump::fields_and_keywords(int narg, char **arg)
iarg += 3;
} else if (strcmp(arg[iarg],"scaled") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
if (strcmp(arg[iarg+1],"yes") == 0) scaledflag = SCALED;
else if (strcmp(arg[iarg+1],"no") == 0) scaledflag = UNSCALED;
if (strcmp(arg[iarg+1],"yes") == 0) scaleflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) scaleflag = 0;
else error->all(FLERR,"Illegal read_dump command");
iarg += 2;
} else if (strcmp(arg[iarg],"wrapped") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
if (strcmp(arg[iarg+1],"yes") == 0) wrapflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) wrapflag = 0;
else error->all(FLERR,"Illegal read_dump command");
iarg += 2;
} else if (strcmp(arg[iarg],"format") == 0) {
@ -742,7 +772,9 @@ void ReadDump::process_atoms(int n)
}
}
// replace image flag in case changed by ix,iy,iz fields
// replace image flag in case changed by ix,iy,iz fields or unwrapping
if (!wrapped) xbox = ybox = zbox = 0;
image[m] = ((tagint) (xbox + IMGMAX) & IMGMASK) |
(((tagint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
@ -877,7 +909,7 @@ void ReadDump::delete_atoms()
double ReadDump::xfield(int i, int j)
{
if (scaled == UNSCALED) return fields[i][j];
if (!scaled) return fields[i][j];
else if (!triclinic) return fields[i][j]*xprd + xlo;
else if (dimension == 2)
return xprd*fields[i][j] + xy*fields[i][yindex] + xlo;
@ -886,7 +918,7 @@ double ReadDump::xfield(int i, int j)
double ReadDump::yfield(int i, int j)
{
if (scaled == UNSCALED) return fields[i][j];
if (!scaled) return fields[i][j];
else if (!triclinic) return fields[i][j]*yprd + ylo;
else if (dimension == 2) return yprd*fields[i][j] + ylo;
return yprd*fields[i][j] + yz*fields[i][zindex] + ylo;
@ -894,6 +926,6 @@ double ReadDump::yfield(int i, int j)
double ReadDump::zfield(int i, int j)
{
if (scaled == UNSCALED) return fields[i][j];
if (!scaled) return fields[i][j];
return fields[i][j]*zprd + zlo;
}