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support variables for more region properties 

add code to allow the center of a spherical or cylindrical
region to be determined as variables and thus change over time.
This commit is contained in:
Axel Kohlmeyer 2018-12-13 14:06:12 -05:00
parent 5b0c43108d
commit deb21ad4e2
5 changed files with 226 additions and 46 deletions
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13
doc/src/region.txt
View File

@ -26,7 +26,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp
dim = {x} or {y} or {z} = axis of cylinder
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
radius = cylinder radius (distance units)
radius can be a variable (see below)
c1,c2, and radius can be a variable (see below)
lo,hi = bounds of cylinder in dim (distance units)
{plane} args = px py pz nx ny nz
px,py,pz = point on the plane (distance units)
@ -39,7 +39,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp
{sphere} args = x y z radius
x,y,z = center of sphere (distance units)
radius = radius of sphere (distance units)
radius can be a variable (see below)
x,y,z, and radius can be a variable (see below)
{union} args = N reg-ID1 reg-ID2 ...
N = # of regions to follow, must be 2 or greater
reg-ID1,reg-ID2, ... = IDs of regions to join together
@ -179,12 +179,17 @@ The {radius} value for style {sphere} and {cylinder} can be specified
as an equal-style "variable"_variable.html. If the value is a
variable, it should be specified as v_name, where name is the variable
name. In this case, the variable will be evaluated each timestep, and
its value used to determine the radius of the region.
its value used to determine the radius of the region. For style {sphere}
also the x-, y-, and z- coordinate of the center of the sphere and for
style {cylinder} the two center positions c1 and c2 for the location of
the cylinder axes can be a variable with the same kind of effect and
requirements than for the radius.
Equal-style variables can specify formulas with various mathematical
functions, and include "thermo_style"_thermo_style.html command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent radius.
time. Thus it is easy to specify a time-dependent radius or have
a time dependent position of the sphere or cylinder region.
See the "Howto tricilinc"_Howto_triclinic.html doc page for a
geometric description of triclinic boxes, as defined by LAMMPS, and

141
src/region_cylinder.cpp
View File

@ -30,7 +30,7 @@ enum{CONSTANT,VARIABLE};
/* ---------------------------------------------------------------------- */
RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) :
Region(lmp, narg, arg), rstr(NULL)
Region(lmp, narg, arg), c1str(NULL), c2str(NULL), rstr(NULL)
{
options(narg-8,&arg[8]);
@ -44,17 +44,76 @@ RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) :
axis = arg[2][0];
if (axis == 'x') {
c1 = yscale*force->numeric(FLERR,arg[3]);
c2 = zscale*force->numeric(FLERR,arg[4]);
if (strstr(arg[3],"v_") == arg[3]) {
int n = strlen(arg[3]+2) + 1;
c1str = new char[n];
strcpy(c1str,arg[3]+2);
c1 = 0.0;
c1style = VARIABLE;
varshape = 1;
} else {
c1 = yscale*force->numeric(FLERR,arg[3]);
c1style = CONSTANT;
}
if (strstr(arg[4],"v_") == arg[4]) {
int n = strlen(arg[4]+2) + 1;
c2str = new char[n];
strcpy(c2str,arg[4]+2);
c2 = 0.0;
c2style = VARIABLE;
varshape = 1;
} else {
c2 = zscale*force->numeric(FLERR,arg[4]);
c2style = CONSTANT;
}
} else if (axis == 'y') {
c1 = xscale*force->numeric(FLERR,arg[3]);
c2 = zscale*force->numeric(FLERR,arg[4]);
if (strstr(arg[3],"v_") == arg[3]) {
int n = strlen(arg[3]+2) + 1;
c1str = new char[n];
strcpy(c1str,arg[3]+2);
c1 = 0.0;
c1style = VARIABLE;
varshape = 1;
} else {
c1 = xscale*force->numeric(FLERR,arg[3]);
c1style = CONSTANT;
}
if (strstr(arg[4],"v_") == arg[4]) {
int n = strlen(arg[4]+2) + 1;
c2str = new char[n];
strcpy(c2str,arg[4]+2);
c2 = 0.0;
c2style = VARIABLE;
varshape = 1;
} else {
c2 = zscale*force->numeric(FLERR,arg[4]);
c2style = CONSTANT;
}
} else if (axis == 'z') {
c1 = xscale*force->numeric(FLERR,arg[3]);
c2 = yscale*force->numeric(FLERR,arg[4]);
if (strstr(arg[3],"v_") == arg[3]) {
int n = strlen(arg[3]+2) + 1;
c1str = new char[n];
strcpy(c1str,arg[3]+2);
c1 = 0.0;
c1style = VARIABLE;
varshape = 1;
} else {
c1 = xscale*force->numeric(FLERR,arg[3]);
c1style = CONSTANT;
}
if (strstr(arg[4],"v_") == arg[4]) {
int n = strlen(arg[4]+2) + 1;
c2str = new char[n];
strcpy(c2str,arg[4]+2);
c2 = 0.0;
c2style = VARIABLE;
varshape = 1;
} else {
c2 = yscale*force->numeric(FLERR,arg[4]);
c2style = CONSTANT;
}
}
rstr = NULL;
if (strstr(arg[5],"v_") == arg[5]) {
int n = strlen(&arg[5][2]) + 1;
rstr = new char[n];
@ -62,8 +121,6 @@ RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) :
radius = 0.0;
rstyle = VARIABLE;
varshape = 1;
variable_check();
shape_update();
} else {
radius = force->numeric(FLERR,arg[5]);
if (axis == 'x') radius *= yscale;
@ -71,6 +128,11 @@ RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) :
rstyle = CONSTANT;
}
if (varshape) {
variable_check();
shape_update();
}
if (strcmp(arg[6],"INF") == 0 || strcmp(arg[6],"EDGE") == 0) {
if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
@ -167,6 +229,8 @@ RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) :
RegCylinder::~RegCylinder()
{
delete [] c1str;
delete [] c2str;
delete [] rstr;
delete [] contact;
}
@ -176,7 +240,7 @@ RegCylinder::~RegCylinder()
void RegCylinder::init()
{
Region::init();
if (rstr) variable_check();
if (varshape) variable_check();
}
/* ----------------------------------------------------------------------
@ -667,12 +731,27 @@ int RegCylinder::surface_exterior(double *x, double cutoff)
void RegCylinder::shape_update()
{
radius = input->variable->compute_equal(rvar);
if (radius < 0.0)
error->one(FLERR,"Variable evaluation in region gave bad value");
if (axis == 'x') radius *= xscale;
else if (axis == 'y') radius*= yscale;
else radius *= zscale;
if (c1style == VARIABLE) c1 = input->variable->compute_equal(c1var);
if (c2style == VARIABLE) c2 = input->variable->compute_equal(c2var);
if (rstyle == VARIABLE) {
radius = input->variable->compute_equal(rvar);
if (radius < 0.0)
error->one(FLERR,"Variable evaluation in region gave bad value");
}
if (axis == 'x') {
if (c1style == VARIABLE) c1 *= yscale;
if (c2style == VARIABLE) c2 *= zscale;
if (rstyle == VARIABLE) radius *= yscale;
} else if (axis == 'y') {
if (c1style == VARIABLE) c1 *= xscale;
if (c2style == VARIABLE) c2 *= zscale;
if (rstyle == VARIABLE) radius *= xscale;
} else { // axis == 'z'
if (c1style == VARIABLE) c1 *= xscale;
if (c2style == VARIABLE) c2 *= yscale;
if (rstyle == VARIABLE) radius *= xscale;
}
}
/* ----------------------------------------------------------------------
@ -681,11 +760,29 @@ void RegCylinder::shape_update()
void RegCylinder::variable_check()
{
rvar = input->variable->find(rstr);
if (rvar < 0)
error->all(FLERR,"Variable name for region cylinder does not exist");
if (!input->variable->equalstyle(rvar))
error->all(FLERR,"Variable for region cylinder is invalid style");
if (c1style == VARIABLE) {
c1var = input->variable->find(c1str);
if (c1var < 0)
error->all(FLERR,"Variable name for region cylinder does not exist");
if (!input->variable->equalstyle(c1var))
error->all(FLERR,"Variable for region cylinder is invalid style");
}
if (c2style == VARIABLE) {
c2var = input->variable->find(c2str);
if (c2var < 0)
error->all(FLERR,"Variable name for region cylinder does not exist");
if (!input->variable->equalstyle(c2var))
error->all(FLERR,"Variable for region cylinder is invalid style");
}
if (rstyle == VARIABLE) {
rvar = input->variable->find(rstr);
if (rvar < 0)
error->all(FLERR,"Variable name for region cylinder does not exist");
if (!input->variable->equalstyle(rvar))
error->all(FLERR,"Variable for region cylinder is invalid style");
}
}

4
src/region_cylinder.h
View File

@ -43,8 +43,10 @@ class RegCylinder : public Region {
double c1,c2;
double radius;
double lo,hi;
int c1style,c1var;
int c2style,c2var;
int rstyle,rvar;
char *rstr;
char *c1str,*c2str,*rstr;
void variable_check();

109
src/region_sphere.cpp
View File

@ -28,15 +28,46 @@ enum{CONSTANT,VARIABLE};
/* ---------------------------------------------------------------------- */
RegSphere::RegSphere(LAMMPS *lmp, int narg, char **arg) :
Region(lmp, narg, arg)
Region(lmp, narg, arg), xstr(NULL), ystr(NULL), zstr(NULL), rstr(NULL)
{
options(narg-6,&arg[6]);
xc = xscale*force->numeric(FLERR,arg[2]);
yc = yscale*force->numeric(FLERR,arg[3]);
zc = zscale*force->numeric(FLERR,arg[4]);
if (strstr(arg[2],"v_") == arg[2]) {
int n = strlen(arg[2]+2) + 1;
xstr = new char[n];
strcpy(xstr,arg[2]+2);
xc = 0.0;
xstyle = VARIABLE;
varshape = 1;
} else {
xc = xscale*force->numeric(FLERR,arg[2]);
xstyle = CONSTANT;
}
if (strstr(arg[3],"v_") == arg[3]) {
int n = strlen(arg[3]+2) + 1;
ystr = new char[n];
strcpy(ystr,arg[3]+2);
yc = 0.0;
ystyle = VARIABLE;
varshape = 1;
} else {
yc = yscale*force->numeric(FLERR,arg[3]);
ystyle = CONSTANT;
}
if (strstr(arg[4],"v_") == arg[4]) {
int n = strlen(arg[4]+2) + 1;
zstr = new char[n];
strcpy(zstr,arg[4]+2);
zc = 0.0;
zstyle = VARIABLE;
varshape = 1;
} else {
zc = zscale*force->numeric(FLERR,arg[4]);
zstyle = CONSTANT;
}
rstr = NULL;
if (strstr(arg[5],"v_") == arg[5]) {
int n = strlen(&arg[5][2]) + 1;
rstr = new char[n];
@ -44,19 +75,22 @@ RegSphere::RegSphere(LAMMPS *lmp, int narg, char **arg) :
radius = 0.0;
rstyle = VARIABLE;
varshape = 1;
variable_check();
shape_update();
} else {
radius = xscale*force->numeric(FLERR,arg[5]);
rstyle = CONSTANT;
}
if (varshape) {
variable_check();
shape_update();
}
// error check
if (radius < 0.0) error->all(FLERR,"Illegal region sphere command");
// extent of sphere
// for variable radius, uses initial radius
// for variable radius, uses initial radius and origin for variable center
if (interior) {
bboxflag = 1;
@ -77,6 +111,9 @@ RegSphere::RegSphere(LAMMPS *lmp, int narg, char **arg) :
RegSphere::~RegSphere()
{
delete [] xstr;
delete [] ystr;
delete [] zstr;
delete [] rstr;
delete [] contact;
}
@ -86,7 +123,7 @@ RegSphere::~RegSphere()
void RegSphere::init()
{
Region::init();
if (rstr) variable_check();
if (varshape) variable_check();
}
/* ----------------------------------------------------------------------
@ -168,9 +205,20 @@ int RegSphere::surface_exterior(double *x, double cutoff)
void RegSphere::shape_update()
{
radius = xscale * input->variable->compute_equal(rvar);
if (radius < 0.0)
error->one(FLERR,"Variable evaluation in region gave bad value");
if (xstyle == VARIABLE)
xc = xscale * input->variable->compute_equal(xvar);
if (ystyle == VARIABLE)
yc = yscale * input->variable->compute_equal(yvar);
if (zstyle == VARIABLE)
zc = zscale * input->variable->compute_equal(zvar);
if (rstyle == VARIABLE) {
radius = xscale * input->variable->compute_equal(rvar);
if (radius < 0.0)
error->one(FLERR,"Variable evaluation in region gave bad value");
}
}
/* ----------------------------------------------------------------------
@ -179,13 +227,38 @@ void RegSphere::shape_update()
void RegSphere::variable_check()
{
rvar = input->variable->find(rstr);
if (rvar < 0)
error->all(FLERR,"Variable name for region sphere does not exist");
if (!input->variable->equalstyle(rvar))
error->all(FLERR,"Variable for region sphere is invalid style");
}
if (xstyle == VARIABLE) {
xvar = input->variable->find(xstr);
if (xvar < 0)
error->all(FLERR,"Variable name for region sphere does not exist");
if (!input->variable->equalstyle(xvar))
error->all(FLERR,"Variable for region sphere is invalid style");
}
if (ystyle == VARIABLE) {
yvar = input->variable->find(ystr);
if (yvar < 0)
error->all(FLERR,"Variable name for region sphere does not exist");
if (!input->variable->equalstyle(yvar))
error->all(FLERR,"Variable for region sphere is invalid style");
}
if (zstyle == VARIABLE) {
zvar = input->variable->find(zstr);
if (zvar < 0)
error->all(FLERR,"Variable name for region sphere does not exist");
if (!input->variable->equalstyle(zvar))
error->all(FLERR,"Variable for region sphere is invalid style");
}
if (rstyle == VARIABLE) {
rvar = input->variable->find(rstr);
if (rvar < 0)
error->all(FLERR,"Variable name for region sphere does not exist");
if (!input->variable->equalstyle(rvar))
error->all(FLERR,"Variable for region sphere is invalid style");
}
}
/* ----------------------------------------------------------------------
Set values needed to calculate velocity due to shape changes.

5
src/region_sphere.h
View File

@ -40,8 +40,11 @@ class RegSphere : public Region {
private:
double xc,yc,zc;
double radius;
int xstyle,xvar;
int ystyle,yvar;
int zstyle,zvar;
int rstyle,rvar;
char *rstr;
char *xstr,*ystr,*zstr,*rstr;
void variable_check();
};