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

This commit is contained in:
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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16
src/USER-MOLFILE/reader_molfile.cpp
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@ -185,7 +185,7 @@ void ReaderMolfile::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 = from input scaleflag & wrapflag
if fieldflag set:
match Nfield fields to per-atom column labels
allocate and set fieldindex = which column each field maps to
@ -198,7 +198,7 @@ void ReaderMolfile::skip()
bigint ReaderMolfile::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)
{
nid = 0;
@ -279,13 +279,15 @@ bigint ReaderMolfile::read_header(double box[3][3], int &triclinic,
memory->create(fieldindex,nfield,"read_dump:fieldindex");
// we know nothing about the scaling style of coordinates,
// so the caller has to set the proper flag.
xflag = scaledflag;
yflag = scaledflag;
zflag = scaledflag;
// we know nothing about the style of coordinates,
// so caller has to set the proper flags
xflag = 2*scaleflag + wrapflag + 1;
yflag = 2*scaleflag + wrapflag + 1;
zflag = 2*scaleflag + wrapflag + 1;
// copy fieldtype list for supported fields
fieldflag = 0;
needvels = 0;
for (int i = 0; i < nfield; i++) {

2
src/USER-MOLFILE/reader_molfile.h
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@ -36,7 +36,7 @@ class ReaderMolfile : public Reader {
virtual int read_time(bigint &);
virtual void skip();
virtual bigint read_header(double [3][3], int &, int, int, int *, char **,
int, int &, int &, int &, int &);
int, int, int &, int &, int &, int &);
virtual void read_atoms(int, int, double **);
virtual void open_file(const char *);

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;
}

7
src/read_dump.h
View File

@ -55,8 +55,8 @@ private:
int boxflag; // overwrite simulation with dump file box params
int replaceflag,addflag; // flags for processing dump snapshot atoms
int trimflag,purgeflag;
int scaledflag; // user setting for coordinate scaling
int scaled; // actual setting for coordinate scaling
int scaleflag; // user 0/1 if dump file coords are unscaled/scaled
int wrapflag; // user 0/1 if dump file coords are unwrapped/wrapped
char *readerstyle; // style of dump files to read
int nfield; // # of fields to extract from dump file
@ -64,6 +64,9 @@ private:
char **fieldlabel; // user specified label for field
double **fields; // per-atom field values
int scaled; // 0/1 if dump file coords are unscaled/scaled
int wrapped; // 0/1 if dump file coords are unwrapped/wrapped
double box[3][3]; // dump file box parameters
double xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz; // dump snapshot box params
double xprd,yprd,zprd;

2
src/reader.h
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@ -30,7 +30,7 @@ class Reader : protected Pointers {
virtual int read_time(bigint &) = 0;
virtual void skip() = 0;
virtual bigint read_header(double [3][3], int &, int, int, int *, char **,
int, int &, int &, int &, int &) = 0;
int, int, int &, int &, int &, int &) = 0;
virtual void read_atoms(int, int, double **) = 0;
virtual void open_file(const char *);

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;

2
src/reader_native.h
View File

@ -34,7 +34,7 @@ class ReaderNative : public Reader {
int read_time(bigint &);
void skip();
bigint read_header(double [3][3], int &, int, int, int *, char **,
int, int &, int &, int &, int &);
int, int, int &, int &, int &, int &);
void read_atoms(int, int, double **);
private:

12
src/reader_xyz.cpp
View File

@ -98,7 +98,7 @@ void ReaderXYZ::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 = from input scaleflag & wrapflag
if fieldflag set:
match Nfield fields to per-atom column labels
allocate and set fieldindex = which column each field maps to
@ -111,7 +111,7 @@ void ReaderXYZ::skip()
bigint ReaderXYZ::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)
{
@ -128,11 +128,11 @@ bigint ReaderXYZ::read_header(double box[3][3], int &triclinic,
memory->create(fieldindex,nfield,"read_dump:fieldindex");
// for xyz we know nothing about the style of coordinates,
// so the caller has to set the proper flag.
// so caller has to set the proper flags
xflag = scaledflag;
yflag = scaledflag;
zflag = scaledflag;
xflag = 2*scaleflag + wrapflag + 1;
yflag = 2*scaleflag + wrapflag + 1;
zflag = 2*scaleflag + wrapflag + 1;
// copy fieldtype list for supported fields

2
src/reader_xyz.h
View File

@ -34,7 +34,7 @@ class ReaderXYZ : public Reader {
int read_time(bigint &);
void skip();
bigint read_header(double [3][3], int &, int, int, int *, char **,
int, int &, int &, int &, int &);
int, int, int &, int &, int &, int &);
void read_atoms(int, int, double **);
private: