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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@679 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-06-26 21:47:46 +00:00
parent e9bbd83ca9
commit e361598ce7
4 changed files with 118 additions and 46 deletions
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48
doc/fix_ave_spatial.html
View File

@ -43,7 +43,7 @@
<PRE>keyword = <I>norm</I> or <I>units</I>
<I>norm</I> value = <I>all</I> or <I>sample</I>
<I>units</I> value = <I>box</I> or <I>lattice</I>
<I>units</I> value = <I>box</I> or <I>lattice</I> or <I>reduced</I>
</PRE>
</UL>
@ -51,7 +51,7 @@
</P>
<PRE>fix 1 all ave/spatial 10000 10000 z lower 2.0 centro.profile compute myCentro
fix 1 flow ave/spatial 100 1000 y 0.0 1.0 vel.profile atom vx norm sample
fix 1 flow ave/spatial 100 1000 y 0.0 1.0 dens.profile density mass
fix 1 flow ave/spatial 100 1000 y 0.0 2.5 dens.profile density mass
</PRE>
<P><B>Description:</B>
</P>
@ -94,13 +94,41 @@ the box. On subsequent timesteps every atom is mapped to one of the
layers. Atoms beyond the lowermost/uppermost layer are counted in the
first/last layer.
</P>
<P>For orthogonal simulation boxes, the layers are slices aligned with
the xyz coordinate axes. For non-orthogonal (triclinic) simulation
boxes, the layers are tilted slices that align with the tilted faces
of the box. See the <A HREF = "region.html">region prism</A> command for a
discussion of the geometry of tilted boxes in LAMMPS. As described
there, a tilted simulation box has edge vectors a,b,c. In that
nomenclature, layers in the x dimension have faces with normals in the
"b" cross "c" direction. Layers in y have faces normal to the "a"
cross "c" direction. And layers in z have faces normal to the "a"
cross "b" direction. Note that in order to define the thickness and
position of these tilted layers in an unambiguous fashion, the <I>units</I>
option must be set to <I>reduced</I>.
</P>
<P>The <I>units</I> keyword determines the meaning of the distance units used
for the layer thickness <I>delta</I> and <I>origin</I> if it is a coordinate
value. A <I>box</I> value selects standard distance units as defined by
the <A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or
metal. A <I>lattice</I> value means the distance units are in lattice
spacings. The <A HREF = "lattice.html">lattice</A> command must have been
previously used to define the lattice spacing.
for the layer thickness <I>delta</I> and for <I>origin</I> if it is a coordinate
value. For orthogonal simulation boxes, any of the 3 options may be
used. For non-orthongal (triclinic) simulation boxes, only the
<I>reduced</I> option may be used.
</P>
<P>A <I>box</I> value selects standard distance units as defined by the
<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal.
A <I>lattice</I> value means the distance units are in lattice spacings.
The <A HREF = "lattice.html">lattice</A> command must have been previously used to
define the lattice spacing. A <I>reduced</I> value means normalized
unitless values between 0 and 1, which represent the lower and upper
faces of the simulation box respectively. Thus an <I>origin</I> value of
0.5 means the center of the box in any dimension. A <I>delta</I> value of
0.1 means 10 layers span the box in any dimension.
</P>
<P>Consider a non-orthogonal box, with layers in the x dimension. No
matter how the box is tilted, an <I>origin</I> of 0.0 means start layers at
the lower "b" cross "c" plane of the simulation box and an <I>origin</I> of
1.0 means to start layers at the upper "b" cross "c" face of the box.
A <I>delta</I> value of 0.1 means there will be 10 layers from 0.0 to 1.0,
regardless of the current size or shape of the simulation box.
</P>
<P>The <I>Nevery</I> and <I>Nfreq</I> arguments specify how the property calculated
for each layer is time-averaged. The property is calculated once each
@ -126,7 +154,9 @@ A line with the timestep and number of layers is written. Then one
line per layer is written, containing the layer ID (1-N), the
coordinate of the center of the layer, the number of atoms in the
layer, and one or more calculated values. The number of atoms and the
value(s) are average quantities.
value(s) are average quantities. Note that for non-orthogonal
(triclinic) simulation boxes, the "coord" of the layer will be a
normalized value between 0 and 1.
</P>
<P>If the <I>density</I> or <I>atom</I> keyword is used, or the <I>compute</I> keyword
with a compute that calculates a single quantity per atom, then a

51
doc/fix_ave_spatial.txt
View File

@ -30,7 +30,7 @@ style = {density} or {atom} or {compute} :l
zero or more keyword/value pairs may be appended to the args :l
keyword = {norm} or {units}
{norm} value = {all} or {sample}
{units} value = {box} or {lattice} :pre
{units} value = {box} or {lattice} or {reduced} :pre
:ule
@ -38,7 +38,7 @@ keyword = {norm} or {units}
fix 1 all ave/spatial 10000 10000 z lower 2.0 centro.profile compute myCentro
fix 1 flow ave/spatial 100 1000 y 0.0 1.0 vel.profile atom vx norm sample
fix 1 flow ave/spatial 100 1000 y 0.0 1.0 dens.profile density mass :pre
fix 1 flow ave/spatial 100 1000 y 0.0 2.5 dens.profile density mass :pre
[Description:]
@ -81,13 +81,41 @@ the box. On subsequent timesteps every atom is mapped to one of the
layers. Atoms beyond the lowermost/uppermost layer are counted in the
first/last layer.
For orthogonal simulation boxes, the layers are "slices" aligned with
the xyz coordinate axes. For non-orthogonal (triclinic) simulation
boxes, the layers are "tilted slices" that align with the tilted faces
of the box. See the "region prism"_region.html command for a
discussion of the geometry of tilted boxes in LAMMPS. As described
there, a tilted simulation box has edge vectors a,b,c. In that
nomenclature, layers in the x dimension have faces with normals in the
"b" cross "c" direction. Layers in y have faces normal to the "a"
cross "c" direction. And layers in z have faces normal to the "a"
cross "b" direction. Note that in order to define the thickness and
position of these tilted layers in an unambiguous fashion, the {units}
option must be set to {reduced}.
The {units} keyword determines the meaning of the distance units used
for the layer thickness {delta} and {origin} if it is a coordinate
value. A {box} value selects standard distance units as defined by
the "units"_units.html command, e.g. Angstroms for units = real or
metal. A {lattice} value means the distance units are in lattice
spacings. The "lattice"_lattice.html command must have been
previously used to define the lattice spacing.
for the layer thickness {delta} and for {origin} if it is a coordinate
value. For orthogonal simulation boxes, any of the 3 options may be
used. For non-orthongal (triclinic) simulation boxes, only the
{reduced} option may be used.
A {box} value selects standard distance units as defined by the
"units"_units.html command, e.g. Angstroms for units = real or metal.
A {lattice} value means the distance units are in lattice spacings.
The "lattice"_lattice.html command must have been previously used to
define the lattice spacing. A {reduced} value means normalized
unitless values between 0 and 1, which represent the lower and upper
faces of the simulation box respectively. Thus an {origin} value of
0.5 means the center of the box in any dimension. A {delta} value of
0.1 means 10 layers span the box in any dimension.
Consider a non-orthogonal box, with layers in the x dimension. No
matter how the box is tilted, an {origin} of 0.0 means start layers at
the lower "b" cross "c" plane of the simulation box and an {origin} of
1.0 means to start layers at the upper "b" cross "c" face of the box.
A {delta} value of 0.1 means there will be 10 layers from 0.0 to 1.0,
regardless of the current size or shape of the simulation box.
The {Nevery} and {Nfreq} arguments specify how the property calculated
for each layer is time-averaged. The property is calculated once each
@ -113,7 +141,11 @@ A line with the timestep and number of layers is written. Then one
line per layer is written, containing the layer ID (1-N), the
coordinate of the center of the layer, the number of atoms in the
layer, and one or more calculated values. The number of atoms and the
value(s) are average quantities.
value(s) are average quantities. For orthogonal simulation boxes,
"coord" is printed in box units, whether the {units} keyword has a
value of {box} or {lattice}. For non-orthogonal (triclinic)
simulation boxes, "coord" is printed in reduced units (0-1) which is
the required value for the {units} keyword.
If the {density} or {atom} keyword is used, or the {compute} keyword
with a compute that calculates a single quantity per atom, then a
@ -149,4 +181,3 @@ minimization"_minimize.html.
[Default:]
The option defaults are norm = all and units = lattice.

63
src/fix_ave_spatial.cpp
View File

@ -33,6 +33,7 @@ using namespace LAMMPS_NS;
enum{LOWER,CENTER,UPPER,COORD};
enum{DENSITY_MASS,DENSITY_NUM,VX,VY,VZ,FX,FY,FZ,COMPUTE};
enum{SAMPLE,ALL};
enum{BOX,LATTICE,REDUCED};
/* ---------------------------------------------------------------------- */
@ -92,7 +93,7 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
// parse optional args
normflag = ALL;
int scaleflag = 1;
scaleflag = BOX;
int iarg = 11;
while (iarg < narg) {
@ -104,8 +105,9 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = BOX;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = LATTICE;
else if (strcmp(arg[iarg+1],"reduced") == 0) scaleflag = REDUCED;
else error->all("Illegal fix ave/spatial command");
iarg += 2;
} else error->all("Illegal fix ave/spatial command");
@ -119,10 +121,14 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
// setup scaling
if (scaleflag && domain->lattice == NULL)
int triclinic = domain->triclinic;
if (triclinic == 1 && scaleflag != REDUCED)
error->all("Fix ave/spatial for triclinic boxes requires units reduced");
if (scaleflag == LATTICE && domain->lattice == NULL)
error->all("Use of fix ave/spatial with undefined lattice");
if (scaleflag) {
if (scaleflag == LATTICE) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
@ -147,15 +153,6 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
if (delta <= 0.0) error->all("Illegal fix ave/spatial command");
invdelta = 1.0/delta;
if (domain->triclinic) {
if (dim == 0 && (domain->xy != 0.0 || domain->xz != 0.0))
error->all("Cannot (yet) use fix ave/spatial with triclinic box");
if (dim == 1 && (domain->xy != 0.0 || domain->yz != 0.0))
error->all("Cannot (yet) use fix ave/spatial with triclinic box");
if (dim == 2 && (domain->xz != 0.0 || domain->yz != 0.0))
error->all("Cannot (yet) use fix ave/spatial with triclinic box");
}
nvalues = 1;
if (which == COMPUTE) {
int icompute = modify->find_compute(id_compute);
@ -240,34 +237,42 @@ void FixAveSpatial::end_of_step()
// allocate and initialize arrays based on new layer count
if (nsum == 0) {
double *boxlo = domain->boxlo;
double *boxhi = domain->boxhi;
double *boxlo,*boxhi,*prd;
if (scaleflag == REDUCED) {
boxlo = domain->boxlo_lamda;
boxhi = domain->boxhi_lamda;
prd = domain->prd_lamda;
} else {
boxlo = domain->boxlo;
boxhi = domain->boxhi;
prd = domain->prd;
}
if (originflag == LOWER) origin = boxlo[dim];
else if (originflag == UPPER) origin = boxhi[dim];
else if (originflag == CENTER)
origin = 0.5 * (boxlo[dim] + boxhi[dim]);
else if (originflag == CENTER) origin = 0.5 * (boxlo[dim] + boxhi[dim]);
if (origin < domain->boxlo[dim]) {
m = static_cast<int> ((domain->boxlo[dim] - origin) * invdelta);
if (origin < boxlo[dim]) {
m = static_cast<int> ((boxlo[dim] - origin) * invdelta);
lo = origin + m*delta;
} else {
m = static_cast<int> ((origin - domain->boxlo[dim]) * invdelta);
m = static_cast<int> ((origin - boxlo[dim]) * invdelta);
lo = origin - m*delta;
if (lo > domain->boxlo[dim]) lo -= delta;
if (lo > boxlo[dim]) lo -= delta;
}
if (origin < domain->boxhi[dim]) {
m = static_cast<int> ((domain->boxhi[dim] - origin) * invdelta);
if (origin < boxhi[dim]) {
m = static_cast<int> ((boxhi[dim] - origin) * invdelta);
hi = origin + m*delta;
if (hi < boxhi[dim]) hi += delta;
} else {
m = static_cast<int> ((origin - domain->boxhi[dim]) * invdelta);
m = static_cast<int> ((origin - boxhi[dim]) * invdelta);
hi = origin - m*delta;
}
offset = lo;
nlayers = static_cast<int> ((hi-lo) * invdelta + 0.5);
double volume = domain->xprd * domain->yprd * domain->zprd;
layer_volume = delta * volume/domain->prd[dim];
layer_volume = delta * volume/prd[dim];
if (nlayers > maxlayer) {
maxlayer = nlayers;
@ -307,6 +312,8 @@ void FixAveSpatial::end_of_step()
// perform the computation for one sample
// sum within each layer, only include atoms in fix group
// insure array index is within bounds (since atoms can be outside box)
// if scaleflag = REDUCED, convert box coords to lamda coords
// DENSITY_MASS adds mass to values
// DENSITY_NUM adds 1 to values
// ATOM adds atom vector to values
@ -316,6 +323,8 @@ void FixAveSpatial::end_of_step()
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
if (which == DENSITY_MASS) {
int *type = atom->type;
double *mass = atom->mass;
@ -386,6 +395,8 @@ void FixAveSpatial::end_of_step()
}
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
// average a single sample
if (normflag == ALL) {

2
src/fix_ave_spatial.h
View File

@ -35,7 +35,7 @@ class FixAveSpatial : public Fix {
char *id_compute;
FILE *fp;
int nlayers,nvalues,nsum,maxlayer;
int nlayers,nvalues,nsum,maxlayer,scaleflag;
int compute_size_peratom;
double xscale,yscale,zscale;
double layer_volume;