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ATC version 2.0, date: Nov20

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12757 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
jatempl
2014-11-20 18:59:03 +00:00
parent 2fecb0f4b8
commit ac5973073f
69 changed files with 5895 additions and 2159 deletions
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259
lib/atc/FE_Mesh.cpp
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@ -24,6 +24,7 @@ using ATC_Utility::split_values;
using ATC_Utility::plane_coords;
using ATC_Utility::norm3;
using ATC_Utility::to_string;
using ATC_Utility::tolerance;
@ -113,55 +114,24 @@ namespace ATC {
if (strcmp(arg[argIdx],"plane")==0)
{
argIdx++;
string n(arg[argIdx++]);
int idir = -1, isgn = 0;
int i2dir = -1, i3dir = -1;
double x2min = 0.0, x2max = 0.0, x3min = 0.0, x3max = 0.0;
string_to_index(n, idir, isgn);
double x = parse_minmax(arg[argIdx++]);
if (narg > argIdx ) {
if (string_to_index(arg[argIdx],i2dir)) {
argIdx++;
x2min = parse_min(arg[argIdx++]);
x2max = parse_max(arg[argIdx++]);
}
}
if (narg > argIdx ) {
if (string_to_index(arg[argIdx],i3dir)) {
argIdx++;
x3min = parse_min(arg[argIdx++]);
x3max = parse_max(arg[argIdx++]);
}
}
if (i2dir >= 0 &&
((i2dir == idir) || (i2dir == idir) || (i2dir == idir) ) )
{
throw ATC_Error( "inconsistent directions in create_faceset plane");
}
if (narg > argIdx && (strcmp(arg[argIdx++],"units") == 0))
{}
else
{
if (idir == 0) { x *= xscale_; }
else if (idir == 1) { x *= yscale_; }
else if (idir == 2) { x *= zscale_; }
if (i2dir >=0) {
if (i2dir == 0) { x2min *= xscale_; x2max *= xscale_; }
else if (i2dir == 1) { x2min *= yscale_; x2max *= yscale_; }
else if (i2dir == 2) { x2min *= zscale_; x2max *= zscale_; }
}
if (i3dir >=0) {
if (i3dir == 0) { x3min *= xscale_; x2max *= xscale_; }
else if (i3dir == 1) { x3min *= yscale_; x3max *= yscale_; }
else if (i3dir == 2) { x3min *= zscale_; x3max *= zscale_; }
}
}
if (i2dir >=0) {
create_faceset(tag, x, idir, isgn, i2dir, x2min, x2max,
i3dir, x3min, x3max);
int ndir, idir[3], isgn;
double xlimits[3][2];
parse_plane(argIdx, narg, arg, ndir, idir, isgn, xlimits);
if (xlimits[idir[1]][0] == xlimits[idir[1]][1])
split_values(xlimits[idir[1]][0],xlimits[idir[1]][1]);
if (xlimits[idir[2]][0] == xlimits[idir[2]][1])
split_values(xlimits[idir[2]][0],xlimits[idir[2]][1]);
parse_units(argIdx,narg,arg,
xlimits[0][0],xlimits[0][1],
xlimits[1][0],xlimits[1][1],
xlimits[2][0],xlimits[2][1]);
if (ndir > 1) {
create_faceset(tag, xlimits[idir[0]][0], idir[0], isgn,
idir[1], xlimits[idir[1]][0], xlimits[idir[1]][1],
idir[2], xlimits[idir[2]][0], xlimits[idir[2]][1]);
}
else {
create_faceset(tag, x, idir, isgn);
create_faceset(tag, xlimits[idir[0]][0], idir[0], isgn);
}
match = true;
}
@ -178,18 +148,7 @@ namespace ATC {
bool outward = true;
if (narg > argIdx && (strcmp(arg[argIdx++],"in") == 0))
outward = false;
if (narg > argIdx && (strcmp(arg[argIdx++],"units") == 0)) {}
else
{ // scale from lattice units to physical units
xmin *= xscale_;
xmax *= xscale_;
ymin *= yscale_;
ymax *= yscale_;
zmin *= zscale_;
zmax *= zscale_;
}
parse_units(argIdx,narg,arg, xmin,xmax,ymin,ymax,zmin,zmax);
create_faceset(tag, xmin, xmax, ymin, ymax, zmin, zmax, outward);
match = true;
}
@ -212,13 +171,33 @@ namespace ATC {
Coordinates are assumed to be in lattice units.
*/
else if (strcmp(arg[1],"create_nodeset")==0) {
string tag = arg[2];
double xmin = parse_min(arg[3]);
double xmax = parse_max(arg[4]);
double ymin = parse_min(arg[5]);
double ymax = parse_max(arg[6]);
double zmin = parse_min(arg[7]);
double zmax = parse_max(arg[8]);
int argIdx = 2;
string tag = arg[argIdx++];
double xmin, xmax, ymin, ymax, zmin, zmax;
if (strcmp(arg[argIdx],"plane")==0) {
argIdx++;
int ndir, idir[3], isgn;
double xlimits[3][2];
parse_plane(argIdx, narg, arg, ndir, idir, isgn, xlimits);
xmin = xlimits[0][0];
xmax = xlimits[0][1];
ymin = xlimits[1][0];
ymax = xlimits[1][1];
zmin = xlimits[2][0];
zmax = xlimits[2][1];
}
else {
xmin = parse_min(arg[argIdx++]);
xmax = parse_max(arg[argIdx++]);
ymin = parse_min(arg[argIdx++]);
ymax = parse_max(arg[argIdx++]);
zmin = parse_min(arg[argIdx++]);
zmax = parse_max(arg[argIdx++]);
}
if (xmin == xmax) split_values(xmin,xmax);
if (ymin == ymax) split_values(ymin,ymax);
if (zmin == zmax) split_values(zmin,zmax);
parse_units(argIdx,narg,arg, xmin,xmax,ymin,ymax,zmin,zmax);
create_nodeset(tag, xmin, xmax, ymin, ymax, zmin, zmax);
match = true;
}
@ -268,7 +247,8 @@ namespace ATC {
Coordinates are assumed to be in lattice units.
*/
else if (strcmp(arg[1],"create_elementset")==0) {
string tag = arg[2];
int argIdx = 2;
string tag = arg[argIdx++];
double xmin = 0;
double xmax = 0;
double ymin = 0;
@ -276,15 +256,19 @@ namespace ATC {
double zmin = 0;
double zmax = 0;
if (narg > 4) {
xmin = parse_min(arg[3]);
xmax = parse_max(arg[4]);
ymin = parse_min(arg[5]);
ymax = parse_max(arg[6]);
zmin = parse_min(arg[7]);
zmax = parse_max(arg[8]);
xmin = parse_min(arg[argIdx++]);
xmax = parse_max(arg[argIdx++]);
ymin = parse_min(arg[argIdx++]);
ymax = parse_max(arg[argIdx++]);
zmin = parse_min(arg[argIdx++]);
zmax = parse_max(arg[argIdx++]);
if (xmin == xmax) split_values(xmin,xmax);
if (ymin == ymax) split_values(ymin,ymax);
if (zmin == zmax) split_values(zmin,zmax);
parse_units(argIdx,narg,arg, xmin,xmax,ymin,ymax,zmin,zmax);
}
else {
string regionName = arg[3];
string regionName = arg[argIdx++];
LammpsInterface::instance()->
region_bounds(regionName.c_str(),xmin,xmax,ymin,ymax,zmin,zmax);
}
@ -355,16 +339,86 @@ namespace ATC {
return match;
}
// -------------------------------------------------------------
void FE_Mesh::parse_units(int & argIdx, int narg, char ** arg,
double & xmin, double & xmax, double & ymin, double & ymax,
double & zmin, double & zmax)
{
if (narg > argIdx && (strcmp(arg[argIdx++],"units") == 0)) {}
else
{ // scale from lattice units to physical units
xmin *= xscale_; xmax *= xscale_;
ymin *= yscale_; ymax *= yscale_;
zmin *= zscale_; zmax *= zscale_;
}
}
// -------------------------------------------------------------
// parse plane
// -------------------------------------------------------------
void FE_Mesh::parse_plane(int & argIdx, int narg, char ** arg,
int & ndir, int * idir, int & isgn, double xlimits[][2])
{
ndir = 0;
xlimits[0][0] = parse_min("-INF");
xlimits[0][1] = parse_max("INF");
xlimits[1][0] = parse_min("-INF");
xlimits[1][1] = parse_max("INF");
xlimits[2][0] = parse_min("-INF");
xlimits[2][1] = parse_max("INF");
string n(arg[argIdx++]);
int i1dir = -1, i2dir = -1, i3dir = -1;
string_to_index(n, i1dir, isgn);
idir[ndir++] = i1dir;
idir[ndir] = (i1dir+1) % 3;
idir[ndir+1] = (i1dir+2) % 3;
xlimits[i1dir][0] = parse_minmax(arg[argIdx++]);
xlimits[i1dir][1] = xlimits[i1dir][0];
if (narg > argIdx ) {
if (string_to_index(arg[argIdx],i2dir)) {
argIdx++;
xlimits[i2dir][0] = parse_min(arg[argIdx++]);
xlimits[i2dir][1] = parse_max(arg[argIdx++]);
idir[ndir++] = i2dir;
}
if (narg > argIdx ) {
if (string_to_index(arg[argIdx],i3dir)) {
argIdx++;
xlimits[i3dir][0] = parse_min(arg[argIdx++]);
xlimits[i3dir][1] = parse_max(arg[argIdx++]);
}
}
else {
i3dir = 0;
if ((i1dir == 0 && i2dir == 1) || (i1dir == 1 && i2dir == 0) ) {
i3dir = 2;
}
else if ((i1dir == 0 && i2dir == 2) || (i1dir == 2 && i2dir == 0) ) {
i3dir = 1;
}
}
idir[ndir++] = i3dir;
}
if ((idir[0]==idir[1]) || (idir[0]==idir[2]) || (idir[1]==idir[2]) ) {
throw ATC_Error( "inconsistent directions in plane:"+to_string(idir[0]+1)+" "+to_string(idir[1]+1)+" "+to_string(idir[2]+1));
}
}
// -------------------------------------------------------------
// initialize
// -------------------------------------------------------------
void FE_Mesh::initialize(void)
{
bool aligned = is_aligned();
if (!aligned) {
feElement_->set_projection_guess(CENTROID_LINEARIZED);
ATC::LammpsInterface::instance()->print_msg_once("WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive");
// if HEX8 -> orient();
}
bool twoD = is_two_dimensional();
if (twoD) {
feElement_->set_projection_guess(TWOD_ANALYTIC);
if (feElement_->order()< 3) hasPlanarFaces_ = true;
ATC::LammpsInterface::instance()->print_msg_once(" mesh is two dimensional");
}
}
//-----------------------------------------------------------------
@ -702,7 +756,7 @@ namespace ATC {
// elementset_to_nodeset
// -------------------------------------------------------------
void FE_Mesh::elementset_to_nodeset
(const set<int> & elemSet, set<int> & nodeSet) const
(const set<int> & elemSet, set<int> nodeSet) const
{
int npe = num_nodes_per_element();
set<int>::const_iterator itr;
@ -721,7 +775,7 @@ namespace ATC {
// elementset_to_nodeset
// -------------------------------------------------------------
void FE_Mesh::elementset_to_nodeset
(const string & name, set<int> & nodeSet) const
(const string & name, set<int> nodeSet) const
{
if (name == "all")
for (int ielem = 0; ielem < nElts_; ielem++)
@ -748,6 +802,13 @@ namespace ATC {
}
}
}
set<int> FE_Mesh::elementset_to_nodeset
(const string & name) const
{
set<int> nset;
elementset_to_nodeset(name,nset);
return nset;
}
// -------------------------------------------------------------
// elementset_to_minimal_nodeset
@ -944,17 +1005,6 @@ namespace ATC {
throw ATC_Error( message);
}
if (xmin == xmax) split_values(xmin,xmax);
if (ymin == ymax) split_values(ymin,ymax);
if (zmin == zmax) split_values(zmin,zmax);
xmin *= xscale_;
xmax *= xscale_;
ymin *= yscale_;
ymax *= yscale_;
zmin *= zscale_;
zmax *= zscale_;
set<int> nodeSet;
// Loop over nodes and add their unique id's to the set if they're
@ -1003,17 +1053,6 @@ namespace ATC {
throw ATC_Error( message);
}
if (xmin == xmax) split_values(xmin,xmax);
if (ymin == ymax) split_values(ymin,ymax);
if (zmin == zmax) split_values(zmin,zmax);
xmin *= xscale_;
xmax *= xscale_;
ymin *= yscale_;
ymax *= yscale_;
zmin *= zscale_;
zmax *= zscale_;
set<int> nodeSet;
// Loop over nodes and add their unique id's to the set if they're
@ -1060,10 +1099,6 @@ namespace ATC {
if (iter != faceSetMap_.end())
throw ATC_Error( "A faceset with name " + name + " is already defined.");
if (xmin == xmax) split_values(xmin,xmax);
if (ymin == ymax) split_values(ymin,ymax);
if (zmin == zmax) split_values(zmin,zmax);
set<PAIR> faceSet;
// Loop over face and add their unique id's to the set if they concide
// with region
@ -1147,7 +1182,7 @@ namespace ATC {
int nIdx2, double x2lo, double x2hi,
int nIdx3, double x3lo, double x3hi)
{
// note scaling done by caller and split_values is tricky with orientation
double xtol = tolerance(xRef);
// Make sure we don't already have a faceset with this name
FACE_SET_MAP::iterator iter = faceSetMap_.find(name);
if (iter != faceSetMap_.end())
@ -1170,7 +1205,7 @@ namespace ATC {
for (int inode = 0; inode < npf; inode++) {
int node = connectivity_(face_conn(iface,inode),ielem);
double x = nodalCoords_(nIdx,node);
if ( fabs(x-xRef) > tol){ in = false; break;}
if ( fabs(x-xRef) > xtol){ in = false; break;}
if (finite2) {
double y = nodalCoords_(nIdx2,node);
if ( y < x2lo || y > x2hi){ in = false; break;}
@ -1227,17 +1262,6 @@ namespace ATC {
throw ATC_Error( message);
}
if (xmin == xmax) split_values(xmin,xmax);
if (ymin == ymax) split_values(ymin,ymax);
if (zmin == zmax) split_values(zmin,zmax);
xmin *= xscale_;
xmax *= xscale_;
ymin *= yscale_;
ymax *= yscale_;
zmin *= zscale_;
zmax *= zscale_;
set<int> nodeSet;
// Loop over nodes and add their unique id's to the set if they're
@ -1758,9 +1782,7 @@ namespace ATC {
}
FE_3DMesh::~FE_3DMesh() {
//if (tree_) delete tree_;
// not sure why, commenting out for now - JZ 2/28/13
if (tree_) delete tree_;
}
// -------------------------------------------------------------
@ -2498,6 +2520,7 @@ namespace ATC {
const double zscale)
: hx_(hx), hy_(hy), hz_(hz)
{
tree_ = NULL;
hasPlanarFaces_ = true;
xscale_ = xscale;
yscale_ = yscale;