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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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43
src/reader_native.cpp
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@ -22,8 +22,10 @@ using namespace LAMMPS_NS;
#define MAXLINE 1024 // max line length in dump file
// also in read_dump.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};
/* ---------------------------------------------------------------------- */
@ -90,20 +92,21 @@ void ReaderNative::skip()
read remaining header info:
return natoms
box bounds, triclinic (inferred), fieldflag (1 if any fields not found),
xyz flag = UNSET (not a requested field), SCALED, UNSCALED
xyz flags = UNSET (not a requested field), SCALE/WRAP as in enum
if fieldflag set:
match Nfield fields to per-atom column labels
allocate and set fieldindex = which column each field maps to
fieldtype = X,VX,IZ etc
fieldlabel = user-specified label or NULL if use fieldtype default
xyz flag = scaledflag if has fieldlabel name, else set by x,xs,xu,xsu
xyz flags = scaleflag+wrapflag if has fieldlabel name,
else set by x,xs,xu,xsu
only called by proc 0
------------------------------------------------------------------------- */
bigint ReaderNative::read_header(double box[3][3], int &triclinic,
int fieldinfo, int nfield,
int *fieldtype, char **fieldlabel,
int scaledflag, int &fieldflag,
int scaleflag, int wrapflag, int &fieldflag,
int &xflag, int &yflag, int &zflag)
{
bigint natoms;
@ -147,7 +150,7 @@ bigint ReaderNative::read_header(double box[3][3], int &triclinic,
// match each field with a column of per-atom data
// if fieldlabel set, match with explicit column
// else infer one or more column matches from fieldtype
// xyz flag set by scaledflag (if fieldlabel set) or column label
// xyz flag set by scaleflag + wrapflag (if fieldlabel set) or column label
memory->create(fieldindex,nfield,"read_dump:fieldindex");
@ -159,9 +162,9 @@ bigint ReaderNative::read_header(double box[3][3], int &triclinic,
for (int i = 0; i < nfield; i++) {
if (fieldlabel[i]) {
fieldindex[i] = find_label(fieldlabel[i],nwords,labels);
if (fieldtype[i] == X) xflag = scaledflag;
else if (fieldtype[i] == Y) yflag = scaledflag;
else if (fieldtype[i] == Z) zflag = scaledflag;
if (fieldtype[i] == X) xflag = 2*scaleflag + wrapflag + 1;
else if (fieldtype[i] == Y) yflag = 2*scaleflag + wrapflag + 1;
else if (fieldtype[i] == Z) zflag = 2*scaleflag + wrapflag + 1;
}
else if (fieldtype[i] == ID)
@ -171,7 +174,7 @@ bigint ReaderNative::read_header(double box[3][3], int &triclinic,
else if (fieldtype[i] == X) {
fieldindex[i] = find_label("x",nwords,labels);
xflag = UNSCALED;
xflag = NOSCALE_WRAP;
if (fieldindex[i] < 0) {
fieldindex[i] = nwords;
s_index = find_label("xs",nwords,labels);
@ -179,22 +182,22 @@ bigint ReaderNative::read_header(double box[3][3], int &triclinic,
su_index = find_label("xsu",nwords,labels);
if (s_index >= 0 && s_index < fieldindex[i]) {
fieldindex[i] = s_index;
xflag = SCALED;
xflag = SCALE_WRAP;
}
if (u_index >= 0 && u_index < fieldindex[i]) {
fieldindex[i] = u_index;
xflag = UNSCALED;
xflag = NOSCALE_NOWRAP;
}
if (su_index >= 0 && su_index < fieldindex[i]) {
fieldindex[i] = su_index;
xflag = SCALED;
xflag = SCALE_NOWRAP;
}
}
if (fieldindex[i] == nwords) fieldindex[i] = -1;
} else if (fieldtype[i] == Y) {
fieldindex[i] = find_label("y",nwords,labels);
yflag = UNSCALED;
yflag = NOSCALE_WRAP;
if (fieldindex[i] < 0) {
fieldindex[i] = nwords;
s_index = find_label("ys",nwords,labels);
@ -202,22 +205,22 @@ bigint ReaderNative::read_header(double box[3][3], int &triclinic,
su_index = find_label("ysu",nwords,labels);
if (s_index >= 0 && s_index < fieldindex[i]) {
fieldindex[i] = s_index;
yflag = SCALED;
yflag = SCALE_WRAP;
}
if (u_index >= 0 && u_index < fieldindex[i]) {
fieldindex[i] = u_index;
yflag = UNSCALED;
yflag = NOSCALE_NOWRAP;
}
if (su_index >= 0 && su_index < fieldindex[i]) {
fieldindex[i] = su_index;
yflag = SCALED;
yflag = SCALE_NOWRAP;
}
}
if (fieldindex[i] == nwords) fieldindex[i] = -1;
} else if (fieldtype[i] == Z) {
fieldindex[i] = find_label("z",nwords,labels);
zflag = UNSCALED;
zflag = NOSCALE_WRAP;
if (fieldindex[i] < 0) {
fieldindex[i] = nwords;
s_index = find_label("zs",nwords,labels);
@ -225,15 +228,15 @@ bigint ReaderNative::read_header(double box[3][3], int &triclinic,
su_index = find_label("zsu",nwords,labels);
if (s_index >= 0 && s_index < fieldindex[i]) {
fieldindex[i] = s_index;
zflag = SCALED;
zflag = SCALE_WRAP;
}
if (u_index >= 0 && u_index < fieldindex[i]) {
fieldindex[i] = u_index;
zflag = UNSCALED;
zflag = NOSCALE_NOWRAP;
}
if (su_index >= 0 && su_index < fieldindex[i]) {
fieldindex[i] = su_index;
zflag = SCALED;
zflag = SCALE_NOWRAP;
}
}
if (fieldindex[i] == nwords) fieldindex[i] = -1;