// ============================================================================
// DrawBox::draw()
// convert particles from 3D space to 2D screen coordinates
// compute blending values for particles and texture
void DrawBox::draw( GLBox * glbox, const ParticlesData * part_data,
const ParticlesSelectVector * _psv, const GlobalOptions * _store_options,
QString shot_name)
{
const double * mProj = glbox->getProjMatrix();
double * mMod = const_cast<double*>
(glbox->getModelMatrix());
// get data pointers
viewport = glbox->getViewPort();
store_options = _store_options;
psv = _psv;
#define MP(row,col) mProj[col*4+row]
#define MM(row,col) mMod[col*4+row]
// get windows size
width = viewport[2];
height= viewport[3];
// set windows size
setGeometry(viewport[0],viewport[1],viewport[2],viewport[3]);
//QPainter paint(this);
//paint.eraseRect(viewport[0],viewport[1],viewport[2],viewport[3]);
clearBuffer();
if (psv->size()) {
// Zoom is located in ModelView matrix at coordinates MM(2,3)
// loop on all object
for (int i=0; i< (int ) psv->size(); i++ ) {
// loop on all visible object selected particles
//std::cerr << "----------\n";
if ((*psv)[i].vps->is_visible ) {
for (int j = 0;
j < (*psv)[i].vps->ni_index;
j ++) {
int jndex= (*psv)[i].vps->index_tab[j];
float
x=part_data->pos[jndex*3 ],
y=part_data->pos[jndex*3+1],
z=part_data->pos[jndex*3+2],
w=1;
// do the product Mmodel X point = mxyzw
float myzw0 = MM(0,1)*y + MM(0,2)*z + MM(0,3)*w;
float mx = MM(0,0)*x + myzw0;
float mx1= mx + store_options->texture_size/2.; // move X from half a texture
float myzw1 = MM(1,1)*y + MM(1,2)*z + MM(1,3)*w;
float my = MM(1,0)*x + myzw1;
float MmzG = MM(2,1)*y + MM(2,2)*z;
float Mmz = MM(2,0)*x + MmzG;
float mz = Mmz + MM(2,3)*w;
float mwG= MM(3,1)*y + MM(3,2)*z + MM(3,3)*w;
float mw = MM(3,0)*x + mwG;
// do the product Mproj X mxyzw = pxyzw
float Ppx = MP(0,0)*mx + MP(0,1)*my + MP(0,3)*mw;
float px = Ppx + MP(0,2)*mz;
float px1 = MP(0,0)*mx1 + MP(0,1)*my + MP(0,3)*mw + MP(0,2)*mz;
float Ppy= MP(1,0)*mx + MP(1,1)*my + MP(1,3)*mw;
float py = Ppy + MP(1,2)*mz;
float Ppz= MP(2,0)*mx + MP(2,1)*my + MP(2,3)*mw;
float pz = Ppz + MP(2,2)*mz;
float Ppw= MP(3,0)*mx + MP(3,1)*my + MP(3,3)*mw;
float pw = Ppw + MP(3,2)*mz;
float pw1 = MP(3,0)*mx1 + MP(3,1)*my + MP(3,3)*mw + MP(3,2)*mz;
// normalyze
//std::cerr << px << " " << py << " " << pz << "\n";
px /= pw;
px1/= pw1;
py /= pw;
pz /= pw;
//std::cerr << px << " " << py << " " << pz << "\n";
// compute screen coordinates
float winx =viewport[0] + (1 + px) * viewport[2] / 2;
float winx1=viewport[0] + (1 + px1) * viewport[2] / 2;
float winy =viewport[1] + (1 + py) * viewport[3] / 2;
// paint particles
//paint.setPen(red);
//paint.drawPoint((int) (winx), viewport[3]-(int) (winy));
#define MMAX(A,B) ((A)>(B)?(A):(B))
#define MMIN(A,B) ((A)<(B)?(A):(B))
//if (winx >= 0. && winy >= 0 && winx < 1024 && winy < 1024) {
if (winx >= 0. && winy >= 0 && winx < width && winy < height && pz<1.0) {
float size_texture = (int) fabs(winx1-winx);
//std::cerr << "x=" << winx << " x1=" << winx1 << " size="<<size_texture<< "\n";
//color_rgba[(int) (winx)][(int) (winy)].blend(psv[i].vps->col,(float) (alpha)/255.);
if (store_options->show_part) {
//color_rgba[(int) (winx)][viewport[3]-1-(int) (winy)].blend((*psv)[i].vps->col,
//(float) (store_options->particles_alpha)/255.);
filterPoint( winx,winy,(*psv)[i].vps->col,(float) (store_options->particles_alpha)/255.);
}
//paint.drawPoint((int) (winx), (int) (winy));
if (store_options->show_poly) {
float s4 = size_texture*4.;
float ratio_texture = s4 - floor(s4);
float ceil_texture = ceil(s4);
texture->draw(this,psv,i,winx,winy,(int)(ceil_texture), ratio_texture);
}
}
}
}
}
}
paintBuffer(shot_name);
}
MP MP::new_ptr( MP model ) {
return MP( 0, new Ptr( (qint64)model.m ) );
}
MP MP::operator[]( int index ) const {
return MP( c, m and not p.size() ? m->attr( index ) : 0 );
}
MP MP::new_obj( QString type ) {
return MP( 0, new ModelWithAttrAndName( type ) );
}
MP MP::new_lst() {
return MP( 0, new Lst );
}
// 起点开始搜索
int dfs_large(int id, bool inload[], int cnt, int &best_cost, bool flag = false)
{
//cout << "dfs(" << id << "," << cnt << ")" << endl;
if(id == eid)
{
best_cost = update_ans(ans_sum,ans);
//update_good(ans_sum,ans);
return FIND_SOLVE;
}
if(is_timeout())
{
return TIME_OUT; // time out
}
// start bfs
int (&last)[MAX_NODE_NUM] = g_last[cnt];
int (&w)[MAX_NODE_NUM] = g_w[cnt];
int (&dis)[MAX_NODE_NUM] = g_dis[cnt];
for(int i=0;i<node_size;i++)
{
last[i] = w[i] = dis[i] = -1;
}
int (&que)[MAX_NODE_NUM] = g_que[cnt];
int front = 0;
int rear = 0;
int find_cnt = 0;
int find_cnt_limit = find_cnt_up;
if(cnt == must_node_cnt)
find_cnt_limit = 3;
if(cnt == 1)
find_cnt_limit = node_size*8;
w[id] = 0;
dis[id] = 0;
que[rear++] = id;
// 只剩下最后一个节点 , spfa
if(cnt == 0)
{
int que_tag[MAX_NODE_NUM] = {0};
que_tag[id] = true;
while(front != rear)
{
int now_id = que[front++];
if(front == MAX_NODE_NUM)
front = 0;
for(int i=0; i<node_next[now_id].size(); i++)
{
int r_node = edge_set[node_next[now_id][i]].r;
if(inload[r_node])
continue;
if(w[r_node] == -1 || w[now_id] + edge_set[node_next[now_id][i]].cost < w[r_node])
{
w[r_node] = w[now_id] + edge_set[node_next[now_id][i]].cost;
last[r_node] = now_id;
if(!que_tag[r_node])
{
que_tag[r_node] = true;
que[rear++] = r_node;
if(rear==MAX_NODE_NUM)
rear = 0;
}
}
}
que_tag[now_id] = false;
}
if(w[eid] == -1)
return cnt+1;
int t_ans_sum = ans_sum;
vector<int> load_nodes;
load_nodes.push_back(eid);
int tmp_id = eid;
while(last[tmp_id] != -1)
{
tmp_id = last[tmp_id];
load_nodes.push_back(tmp_id);
}
reverse(load_nodes.begin(),load_nodes.end());
for(int i=0;i<load_nodes.size();i++)
{
//inload[load_nodes[i]] = true;
if(i < load_nodes.size() - 1)
{
add_edge(load_nodes[i],load_nodes[i+1],ans_sum,ans);
}
}
best_cost = update_ans(ans_sum,ans);
//update_good(ans_sum,ans);
ans_sum = t_ans_sum;
return FIND_SOLVE;
}
int fin_res = cnt;
int t_best_cost = 2000000;
while(front < rear && find_cnt < find_cnt_limit)
{
if(cnt >= must_node_cnt - 5 && front > 0 && w[que[front]] != w[que[front-1]])
{
vector<pair<int,int> > pp;
for(int i=front;i<rear;i++)
pp.push_back(MP(dis[que[i]],que[i]));
sort(pp.begin(),pp.end());
for(int i=front;i<rear;i++)
que[i] = pp[i-front].second;
}
int now_id = que[front++];
for(int i=0; i<node_next[now_id].size(); i++)
{
int r_node = edge_set[node_next[now_id][i]].r;
if(inload[r_node] || w[r_node] != -1)
continue;
if(must_node[r_node] || (cnt == 0 && r_node == eid) )
{
int t_ans_sum = ans_sum;
//vector<int> load_nodes;
vector<int> edge_nodes;
//load_nodes.push_back(r_node);
//load_nodes.push_back(now_id);
edge_nodes.push_back(node_next[now_id][i]);
int tmp_id = now_id;
while(last[tmp_id] != -1)
{
tmp_id = last[tmp_id];
//load_nodes.push_back(tmp_id);
edge_nodes.push_back(tmp_id);
tmp_id = edge_set[tmp_id].l;
}
reverse(edge_nodes.begin(),edge_nodes.end());
for(int i=0;i<edge_nodes.size();i++)
{
//inload[load_nodes[i]] = true;
inload[edge_set[edge_nodes[i]].r] = true;
/*
if(i < load_nodes.size() - 1)
{
add_edge(load_nodes[i],load_nodes[i+1],ans_sum,ans);
}
*/
ans[ans_sum++] = edge_nodes[i];
}
find_cnt ++;
int t_t_best_cost = 2000000;
int res = dfs_large(r_node, inload, cnt - 1, t_t_best_cost, flag);
//find_cnt --;
t_best_cost = min(t_best_cost,t_t_best_cost);
best_cost = min(t_best_cost,best_cost);
ans_sum = t_ans_sum;
for(int i=0;i<edge_nodes.size();i++)
{
inload[edge_set[edge_nodes[i]].r] = false;
}
if(res == END_OUT)
return res;
fin_res = min(res, fin_res);
int min_l = 8;
int min_g = 8;
if(!flag)
{
if(good_cost < INF_COST)
{
min_l = 5;
min_g = 13;
}
if(cnt > min_l && cnt < must_node_cnt - min_g)
return fin_res;
//else if((cnt > min_l) && cnt < must_node_cnt - min_g + 3 && (fin_res > 0 || t_best_cost - 20 > good_cost))
else if(cnt > min_l - 1 && cnt < must_node_cnt - min_g + 5 && (fin_res > 0 || t_best_cost - 3 > good_cost))
return fin_res;
}
else
{
min_l = 6;
min_g = 10;
if(must_node_cnt > 22)
{
min_l = 8;
min_g = 10;
}
if(good_cost < INF_COST)
{
if(node_size >= 300)
{
min_l = 6;
min_g = 12;
}
else
{
min_l = 6;
min_g = 10;
}
if(must_node_cnt > 22)
{
min_l = 8;
min_g = 6;
}
}
if(cnt > min_l && cnt < must_node_cnt - min_g )//&& t_best_cost > good_cost)
return fin_res;
else if(cnt < must_node_cnt - min_g - 2 && (t_best_cost - 3 > good_cost || cnt > 0) )
return fin_res;
}
}
else
{
w[r_node] = w[now_id] + 1;
dis[r_node] = dis[now_id] + edge_set[node_next[now_id][i]].cost;
//last[r_node] = now_id;
last[r_node] = node_next[now_id][i];
que[rear++] = r_node;
}
}
}
return fin_res;
}
void addEdge(int u, int v, int id) {
//cout << u << "<->" << v << endl;
graph[u].PB(MP(v, id));
graph[v].PB(MP(u, id));
}
LL cross(PII a,PII b, PII c){
PII ab = MP(b.first-a.first,b.second-a.second);
PII ac = MP(c.first-a.first,c.second-a.second);
return ab.first*ac.second - ab.second*ac.first;
}
int
ProcessShowIml(
PINSTALLATION_MODIFICATION_LOGFILE pIml
)
{
PIML_FILE_RECORD pFile;
PIML_FILE_RECORD_CONTENTS pOldFile;
PIML_FILE_RECORD_CONTENTS pNewFile;
PIML_KEY_RECORD pKey;
PIML_VALUE_RECORD pValue;
PIML_VALUE_RECORD_CONTENTS pOldValue;
PIML_VALUE_RECORD_CONTENTS pNewValue;
PIML_INI_RECORD pIni;
PIML_INISECTION_RECORD pSection;
PIML_INIVARIABLE_RECORD pVariable;
BOOLEAN FileNameShown;
BOOLEAN SectionNameShown;
if (pIml->NumberOfFileRecords > 0) {
printf( "File Modifications:\n" );
pFile = MP( PIML_FILE_RECORD, pIml, pIml->FileRecords );
while (pFile != NULL) {
pOldFile = MP( PIML_FILE_RECORD_CONTENTS, pIml, pFile->OldFile );
pNewFile = MP( PIML_FILE_RECORD_CONTENTS, pIml, pFile->NewFile );
printf( " %ws - ", MP( PWSTR, pIml, pFile->Name ) );
switch( pFile->Action ) {
case CreateNewFile:
printf( "created\n" );
break;
case ModifyOldFile:
printf( "overwritten\n" );
if (pOldFile != NULL) {
printf( " Old size is %u bytes\n", pOldFile->FileSize );
}
break;
case DeleteOldFile:
printf( "deleted\n" );
if (pOldFile != NULL) {
printf( " Old size is %u bytes\n", pOldFile->FileSize );
}
break;
case ModifyFileDateTime:
printf( "date/time modified\n" );
break;
case ModifyFileAttributes:
printf( "attributes modified\n" );
break;
}
pFile = MP( PIML_FILE_RECORD, pIml, pFile->Next );
}
printf( "\n" );
}
if (pIml->NumberOfKeyRecords > 0) {
printf( "Registry Modifications:\n" );
pKey = MP( PIML_KEY_RECORD, pIml, pIml->KeyRecords );
while (pKey != NULL) {
printf( " %ws - ", MP( PWSTR, pIml, pKey->Name ) );
switch( pKey->Action ) {
case CreateNewKey:
printf( "created\n" );
break;
case DeleteOldKey:
printf( "deleted\n" );
break;
case ModifyKeyValues:
printf( "modified\n" );
break;
}
pValue = MP( PIML_VALUE_RECORD, pIml, pKey->Values );
while (pValue != NULL) {
pOldValue = MP( PIML_VALUE_RECORD_CONTENTS, pIml, pValue->OldValue );
pNewValue = MP( PIML_VALUE_RECORD_CONTENTS, pIml, pValue->NewValue );
printf( " %ws - ", MP( PWSTR, pIml, pValue->Name ) );
if (pValue->Action != DeleteOldValue) {
printf( "%s [%x]",
FormatEnumType( 0, ValueDataTypeNames, pNewValue->Type, FALSE ),
pNewValue->Length
);
if (pNewValue->Type == REG_SZ ||
pNewValue->Type == REG_EXPAND_SZ
) {
printf( " '%ws'", MP( PWSTR, pIml, pNewValue->Data ) );
}
else
if (pNewValue->Type == REG_DWORD) {
printf( " 0x%x", *MP( PULONG, pIml, pNewValue->Data ) );
}
}
if (pValue->Action == CreateNewValue) {
printf( " (created)\n" );
}
else {
if (pValue->Action == DeleteOldValue) {
printf( " (deleted" );
}
else {
printf( " (modified" );
}
printf( " - was %s [%x]",
FormatEnumType( 0, ValueDataTypeNames, pOldValue->Type, FALSE ),
pOldValue->Length
);
if (pOldValue->Type == REG_SZ ||
pOldValue->Type == REG_EXPAND_SZ
) {
printf( " '%ws'", MP( PWSTR, pIml, pOldValue->Data ) );
}
else
if (pOldValue->Type == REG_DWORD) {
printf( " 0x%x", *MP( PULONG, pIml, pOldValue->Data ) );
}
printf( " )\n" );
}
pValue = MP( PIML_VALUE_RECORD, pIml, pValue->Next );
}
pKey = MP( PIML_KEY_RECORD, pIml, pKey->Next );
}
printf( "\n" );
}
if (pIml->NumberOfIniRecords > 0) {
printf( ".INI File modifications:\n" );
pIni = MP( PIML_INI_RECORD, pIml, pIml->IniRecords );
while (pIni != NULL) {
FileNameShown = FALSE;
pSection = MP( PIML_INISECTION_RECORD, pIml, pIni->Sections );
while (pSection != NULL) {
SectionNameShown = FALSE;
pVariable = MP( PIML_INIVARIABLE_RECORD, pIml, pSection->Variables );
while (pVariable != NULL) {
if (!FileNameShown) {
printf( "%ws", MP( PWSTR, pIml, pIni->Name ) );
if (pIni->Action == CreateNewIniFile) {
printf( " (created)" );
}
printf( "\n" );
FileNameShown = TRUE;
}
if (!SectionNameShown) {
printf( " [%ws]", MP( PWSTR, pIml, pSection->Name ) );
if (pSection->Action == CreateNewSection) {
printf( " (created)" );
}
else
if (pSection->Action == DeleteOldSection) {
printf( " (deleted)" );
}
printf( "\n" );
SectionNameShown = TRUE;
}
printf( " %ws = ", MP( PWSTR, pIml, pVariable->Name ) );
if (pVariable->Action == CreateNewVariable) {
printf( "'%ws' (created)\n", MP( PWSTR, pIml, pVariable->NewValue ) );
}
else
if (pVariable->Action == DeleteOldVariable) {
printf( " (deleted - was '%ws')\n", MP( PWSTR, pIml, pVariable->OldValue ) );
}
else {
printf( "'%ws' (modified - was '%ws')\n",
MP( PWSTR, pIml, pVariable->NewValue ),
MP( PWSTR, pIml, pVariable->OldValue )
);
}
pVariable = MP( PIML_INIVARIABLE_RECORD, pIml, pVariable->Next );
}
pSection = MP( PIML_INISECTION_RECORD, pIml, pSection->Next );
}
if (FileNameShown) {
printf( "\n" );
}
pIni = MP( PIML_INI_RECORD, pIml, pIni->Next );
}
}
return 0;
}
inline void Trace::commit_memory(Clnum clnum, Address a, uint8_t d) {
pair<map<Address, MemoryCell>::iterator, bool> ret = memory_.insert(MP(a, MemoryCell()));
ret.first->second[clnum] = d;
}
pair<float,float> getCentre(){
return MP(cx,cy);
}
void Trace::process() {
MUTEX_LOCK(backing_mutex_);
EntryNumber entry_count = *((EntryNumber*)backing_); // don't let this change under me
MUTEX_UNLOCK(backing_mutex_);
if (entries_done_ >= entry_count) return; // handle the > case better
remap_backing(sizeof(struct change)*entry_count); // what if this fails?
printf("on %u going from %u to %u...", trace_index_, entries_done_, entry_count);
fflush(stdout);
#ifndef _WIN32
struct timeval tv_start, tv_end;
gettimeofday(&tv_start, NULL);
#endif
// clamping
if ((entries_done_ + 1000000) < entry_count) {
entry_count = entries_done_ + 1000000;
}
while (entries_done_ != entry_count) {
// no need to lock this here, because this is the only thread that changes it
const struct change *c = &backing_[entries_done_];
char type = get_type_from_flags(c->flags);
RWLOCK_WRLOCK(db_lock_);
// clnum_to_entry_number_, instruction_pages_
if (type == 'I') {
if (clnum_to_entry_number_.size() < c->clnum) {
// there really shouldn't be holes
clnum_to_entry_number_.resize(c->clnum);
}
clnum_to_entry_number_.push_back(entries_done_);
pages_[c->address & PAGE_MASK] |= PAGE_INSTRUCTION;
}
// addresstype_to_clnums_
// ** this is 75% of the perf, real unordered_map should improve, but c++11 is hard to build
pair<unordered_map<pair<Address, char>, set<Clnum> >::iterator, bool> ret =
addresstype_to_clnums_.insert(MP(MP(c->address, type), set<Clnum>()));
ret.first->second.insert(c->clnum);
// registers_
if (type == 'W' && (c->address < (unsigned int)(register_size_ * register_count_))) {
registers_[c->address / register_size_][c->clnum] = c->data;
}
// memory_, data_pages_
if (type == 'L' || type == 'S') {
if (type == 'L') {
pages_[c->address & PAGE_MASK] |= PAGE_READ;
}
if (type == 'S') {
pages_[c->address & PAGE_MASK] |= PAGE_WRITE;
}
// no harm in doing the memory commit every time there's a load, right?
int byte_count = (c->flags&SIZE_MASK)/8;
uint64_t data = c->data;
if (is_big_endian_) {
for (int i = byte_count-1; i >= 0; --i) {
commit_memory(c->clnum, c->address+i, data&0xFF);
data >>= 8;
}
} else {
// little endian
for (int i = 0; i < byte_count; i++) {
commit_memory(c->clnum, c->address+i, data&0xFF);
data >>= 8;
}
}
}
RWLOCK_WRUNLOCK(db_lock_);
// max_clnum_
if (max_clnum_ < c->clnum && c->clnum != INVALID_CLNUM) {
max_clnum_ = c->clnum;
}
if (min_clnum_ == INVALID_CLNUM || c->clnum < min_clnum_) {
min_clnum_ = c->clnum;
}
entries_done_++;
}
static int
big_bitp(object x, ufixnum p)
{
return mpz_tstbit(MP(x),p);
}
static object
integer_log_op2(fixnum op,object x,enum type tx,object y,enum type ty) {
object u=big_fixnum1;
object ux=tx==t_bignum ? x : (mpz_set_si(MP(big_fixnum2),fix(x)), big_fixnum2);
object uy=ty==t_bignum ? y : (mpz_set_si(MP(big_fixnum3),fix(y)), big_fixnum3);
switch(op) {
case BOOLCLR: mpz_set_si(MP(u),0);break;
case BOOLSET: mpz_set_si(MP(u),-1);break;
case BOOL1: mpz_set(MP(u),MP(ux));break;
case BOOL2: mpz_set(MP(u),MP(uy));break;
case BOOLC1: mpz_com(MP(u),MP(ux));break;
case BOOLC2: mpz_com(MP(u),MP(uy));break;
case BOOLAND: mpz_and(MP(u),MP(ux),MP(uy));break;
case BOOLIOR: mpz_ior(MP(u),MP(ux),MP(uy));break;
case BOOLXOR: mpz_xor(MP(u),MP(ux),MP(uy));break;
case BOOLEQV: mpz_xor(MP(u),MP(ux),MP(uy));mpz_com(MP(u),MP(u));break;
case BOOLNAND: mpz_and(MP(u),MP(ux),MP(uy));mpz_com(MP(u),MP(u));break;
case BOOLNOR: mpz_ior(MP(u),MP(ux),MP(uy));mpz_com(MP(u),MP(u));break;
case BOOLANDC1:mpz_com(MP(u),MP(ux));mpz_and(MP(u),MP(u),MP(uy));break;
case BOOLANDC2:mpz_com(MP(u),MP(uy));mpz_and(MP(u),MP(ux),MP(u));break;
case BOOLORC1: mpz_com(MP(u),MP(ux));mpz_ior(MP(u),MP(u),MP(uy));break;
case BOOLORC2: mpz_com(MP(u),MP(uy));mpz_ior(MP(u),MP(ux),MP(u));break;
default:break;/*FIXME error*/
}
return u;
}
pLL operator * (pLL a,pLL b) {return MP(a.X*b.Y-a.Y*b.X,a.X*b.X+a.Y*b.Y);}
PDD at(PDD & a, PDD & b, double t) {
return MP(a.F * t + b.F * (1 - t), a.S * t + b.S * (1 - t));
}
int main(int argc, char * argv[])
{
try
{
libmaus2::util::ArgInfo const arginfo(argc,argv);
// free list for alignments
libmaus2::util::GrowingFreeList<libmaus2::bambam::BamAlignment> BAFL;
// insert size
int64_t const insertsize = arginfo.getValue<int64_t>("insertsize",800);
// container for bam decoders
DecoderContainer deccont;
while ( std::cin )
{
// eof?
if ( std::cin.peek() < 0 )
break;
// get next instance line
InstanceLine IS(&deccont,std::cin);
std::cout << IS << '\n';
uint64_t ilow = 0;
while ( ilow != IS.size() )
{
uint64_t ihigh = ilow;
// get interval for one type of instance
while ( ihigh != IS.size() && IS.instances[ihigh].type == IS.instances[ilow].type )
++ihigh;
// if type is split, improper or samestrand
if (
IS.instances[ilow].type == Instance::instance_type_split
||
IS.instances[ilow].type == Instance::instance_type_improper
||
IS.instances[ilow].type == Instance::instance_type_samestrand
)
{
// key is maxcnt,num
std::map<SubInstKey, std::vector<std::string>, std::greater<SubInstKey> > subinst;
for ( uint64_t i = ilow; i < ihigh; ++i )
{
std::vector<libmaus2::bambam::BamAlignment *> retlist;
// map from read name to vector of alignments
std::map<std::string, std::vector<libmaus2::bambam::BamAlignment *> > amap;
libmaus2::bambam::BamHeader::unique_ptr_type uheader;
// get alignments from A file marked with gene A
{
libmaus2::bambam::BamAlignmentDecoder & deca = IS.getInstanceDecoderA(i);
libmaus2::bambam::BamAlignment & algna = deca.getAlignment();
libmaus2::bambam::BamHeader const & headera = deca.getHeader();
libmaus2::bambam::BamHeader::unique_ptr_type theader(headera.uclone());
uheader = UNIQUE_PTR_MOVE(theader);
while ( deca.readAlignment() )
if ( algna.isMapped() && hasGeneComment(&algna,IS.geneA.name) )
{
// std::cerr << algna.formatAlignment(headera) << std::endl;
libmaus2::bambam::BamAlignment * palgn = BAFL.get();
retlist.push_back(palgn);
amap[algna.getName()].push_back(palgn);
palgn->swap(algna);
}
}
// get alignments from B file marked with gene B
{
libmaus2::bambam::BamAlignmentDecoder & decb = IS.getInstanceDecoderB(i);
libmaus2::bambam::BamAlignment & algnb = decb.getAlignment();
// libmaus2::bambam::BamHeader const & headerb = decb->getHeader();
while ( decb.readAlignment() )
if ( algnb.isMapped() && hasGeneComment(&algnb,IS.geneB.name) )
{
// std::cerr << algna.formatAlignment(headera) << std::endl;
libmaus2::bambam::BamAlignment * palgn = BAFL.get();
retlist.push_back(palgn);
amap[algnb.getName()].push_back(palgn);
palgn->swap(algnb);
}
}
// pair map intervals
std::vector<MappedPair> pairs;
// count read pairs for gene pair
uint64_t cnt = 0;
// iterate over names
for ( std::map<std::string, std::vector<libmaus2::bambam::BamAlignment *> >::iterator ita = amap.begin(); ita != amap.end(); ++ita )
{
// get vector of alignments for name
std::vector<libmaus2::bambam::BamAlignment *> & V = ita->second;
// sort by (refid,pos,read1)
std::sort(V.begin(),V.end(),PosComparator());
// remove multiple copies of same alignment
uint64_t o = 0;
uint64_t rcnt[2] = {0,0};
for ( uint64_t l = 0; l < V.size(); )
{
// skip over multiple copies of same alignment
uint64_t h = l;
while ( h != V.size() && sameAlignment(V[l],V[h]) )
++h;
// count read 1
if ( V[l]->isRead1() )
rcnt[0]++;
// count read 2
if ( V[l]->isRead2() )
rcnt[1]++;
// copy alignment pointer
if ( V[l]->isRead1() || V[l]->isRead2() )
V[o++] = V[l];
l = h;
}
V.resize(o);
// if we have read1 and read2
if ( V.size() > 1 && rcnt[0] && rcnt[1] )
{
// iterate over read 1
for ( uint64_t r1 = 0; r1 < rcnt[0]; ++r1 )
// iterate over read 2
for ( uint64_t r2 = rcnt[0]; r2 < o; ++r2 )
{
// get alignment for read 1
libmaus2::bambam::BamAlignment const * algn1 = V[r1];
// get alignment for read 2
libmaus2::bambam::BamAlignment const * algn2 = V[r2];
// if pair is marked with gene pair we are looking for
if (
(
hasGeneComment(algn1,IS.geneA.name)
&&
hasGeneComment(algn2,IS.geneB.name)
)
||
(
hasGeneComment(algn1,IS.geneB.name)
&&
hasGeneComment(algn2,IS.geneA.name)
)
)
{
#if 0
std::cerr << "\n --- \n";
std::cerr << algn1->formatAlignment(*uheader) << std::endl;
std::cerr << algn2->formatAlignment(*uheader) << std::endl;
++cnt;
std::cerr << "subcnt=" << V.size() << std::endl;
#endif
// increment number of read pairs found
cnt += 1;
// determine smaller and larger alignment (by position)
bool const smal1 = PosComparator::compare(algn1,algn2);
libmaus2::bambam::BamAlignment const * algnl = smal1 ? algn1 : algn2;
libmaus2::bambam::BamAlignment const * algnr = smal1 ? algn2 : algn1;
// "left" interval
libmaus2::math::IntegerInterval<int64_t> intl(
algnl->getPos(),
algnl->getAlignmentEnd()
);
// "right" interval
libmaus2::math::IntegerInterval<int64_t> intr(
algnr->getPos(),
algnr->getAlignmentEnd()
);
// construct mapped pair of aligned intervals
MappedPair MP(intl,intr);
// see if this interval (modulo insert size) already exists
bool existing = false;
for ( uint64_t i = 0; (!existing) && i < pairs.size(); ++i )
// already seen?
if ( MappedPair::isInsertSizeOverlap(pairs[i],MP,insertsize) )
{
// update from for left
pairs[i].first.from = std::min(
MP.first.from,
pairs[i].first.from
);
// update to for left
pairs[i].first.to = std::max(
MP.first.to,
pairs[i].first.to
);
// update from for right
pairs[i].second.from = std::min(
MP.second.from,
pairs[i].second.from
);
// update to for right
pairs[i].second.to = std::max(
MP.second.to,
pairs[i].second.to
);
// update number of supporting pair for this "break point"
pairs[i].cnt += 1;
// note that this break point already existed
existing = true;
}
#if 0
else
{
std::cerr << "no overlap" << std::endl;
std::cerr << MP << std::endl;
std::cerr << pairs[i] << std::endl;
}
#endif
// push new pair if break point did not exist yet
if ( ! existing )
pairs.push_back(MP);
}
}
}
}
// std::cerr << IS.instances[i] << " gcnt=" << cnt << ((IS.instances[i].num != cnt) ? "___" : "") << std::endl;
std::ostringstream ostr;
ostr << "\t" << IS.instances[i];
// sort by number of supporting read pairs
std::sort(pairs.begin(),pairs.end(),MappedPairCountComparator());
// maximum count
uint64_t const maxcnt = pairs.size() ? pairs.front().cnt : 0;
ostr << "\t" << maxcnt;
// output break points
for ( uint64_t j = 0; j < pairs.size();++j )
ostr << "\t" << pairs[j];
// sub instances map ordered by number of read pairs supporting break point
subinst[SubInstKey(maxcnt,IS.instances[i].num)].push_back(ostr.str());
// return alignment to free list
for ( uint64_t i = 0; i < retlist.size(); ++i )
BAFL.put(retlist[i]);
}
// output instance lines
for (
std::map<SubInstKey, std::vector<std::string>, std::greater<SubInstKey> >::const_iterator ita = subinst.begin();
ita != subinst.end(); ++ita
)
{
std::vector<std::string> const & V = ita->second;
for ( uint64_t i = 0; i < V.size(); ++i )
std::cout << V[i] << "\n";
}
}
ilow = ihigh;
}
}
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}
I rk(I f,A r,A a,A w)
{
A z=0,*p=0;
if(w)ND2 else ND1;
{
XA;
C *pp=0,*ap,*wp;
I wt=0,wr=0,wn=0,*wd=0;
I n=0,t=0,i,j,k,d[9],rw,ra,ri,ir,iw=0,ia=0,ii=0,
e=!w&&f==MP(9),h=QP(f)&&f!=MP(71)&&!e;
Q(!QA(r),9);
Q(r->t,6);
Q(r->n<1||r->n>3,8);
ar-=ra=raw(ar,*r->p);
if(!w) mv(d,ad,ra),ir=tr(ra,ad),ad+=ra;
else
{
wt=w->t,wr=w->r,wd=w->d;
wr-=rw=raw(wr,r->p[r->n>1]),ri=r->n>2?r->p[2]:9;
Q(ri<0,9);
if(ri>ra)ri=ra;
if(ri>rw)ri=rw;
mv(d,ad,ra-=ri);
ia=tr(ra,ad),mv(d+ra,wd,rw),iw=tr(rw-=ri,wd);
Q(cm(ad+=ra,wd+=rw,ri),11);
ii=tr(ri,ad),ra+=rw+ri,ir=ia*iw*ii,wn=tr(wr,wd+=ri),ad+=ri;
if(h&&ir>iw&&(f==MP(21)||f==MP(25)||f==MP(26)||f==MP(32)||f==MP(33)))
h=0;
}
an=tr(ar,ad);
if(h)
{
g=0;
aw_c[0]=a->c;
aw_c[1]=w&&w->c;
r=(A)fa(f,gC(at,ar,an,ad,a->n?a->p:0),w?gC(wt,wr,wn,wd,w->n?w->p:0):0);
aw_c[0]=aw_c[1]=1;
if(!r)R 0;
r=un(&r);
mv(d+ra,r->d,j=r->r);
if((j+=ra)>MAXR)R q=13,(I)r;
n=r->n;t=r->t;
if(ir<2) R mv(r->d,d,r->r=j),r->n*=ir,(I)r;
dc(r);
if(g==(I (*)())rsh) R rsh(w?w:a,j,d);
if(!g){h=0;}
else
{
if(at=atOnExit,w) wt=wtOnExit;
if(at!=a->t&&!(a=at?ep_cf(1):ci(1))) R 0;
if(w&&wt!=w->t&&!(w=wt?ep_cf(2):ci(2))) R 0;
OF(i,ir,n);
W(ga(t,j,i,d));
pp=(C*)z->p;
}
}
if(!h)
{
W(ga(Et,ra,ir,d));
*--Y=zr(z),p=(A*)z->p;
}
if(!w)
{
for(ap=(C*)a->p;ir--;ap+=Tt(at,an))
if(h) (*(I(*)(C*,C*,I))g)(pp,ap,an),pp+=Tt(t,n);
else a=gc(at,ar,an,ad,(I*)ap),*p++=e?a:(A)fa(f,(I)a,0);
}
else
{
for(i=0;i<ia;++i)for(j=0;j<iw;++j)
for(k=0;k<ii;++k){
ap=(C*)a->p+Tt(at,(i*ii+k)*an);
wp=(C*)w->p+Tt(wt,(j*ii+k)*wn);
if(h)
{
(*(I(*)(C*,C*,C*,I))g)(pp,ap,wp,n),pp+=Tt(t,n);
if(q==1)*--Y=(I)z,aplus_err(q,(A)Y[1]),++Y;
}
else
{
*p++=(A)fa(f,(I)gc(at,ar,an,ad,(I*)ap),(I)gc(wt,wr,wn,wd,(I*)wp));
}
}
}
if(h)R(I)z;
if(!e)z=(A)dis(r=z),dc(r);
R ++Y,(I)z;
}
}
int BlockDACG::reSolve(int numEigen, Epetra_MultiVector &Q, double *lambda, int startingEV) {
// Computes the smallest eigenvalues and the corresponding eigenvectors
// of the generalized eigenvalue problem
//
// K X = M X Lambda
//
// using a Block Deflation Accelerated Conjugate Gradient algorithm.
//
// Note that if M is not specified, then K X = X Lambda is solved.
//
// Ref: P. Arbenz & R. Lehoucq, "A comparison of algorithms for modal analysis in the
// absence of a sparse direct method", SNL, Technical Report SAND2003-1028J
// With the notations of this report, the coefficient beta is defined as
// diag( H^T_{k} G_{k} ) / diag( H^T_{k-1} G_{k-1} )
//
// Input variables:
//
// numEigen (integer) = Number of eigenmodes requested
//
// Q (Epetra_MultiVector) = Converged eigenvectors
// The number of columns of Q must be equal to numEigen + blockSize.
// The rows of Q are distributed across processors.
// At exit, the first numEigen columns contain the eigenvectors requested.
//
// lambda (array of doubles) = Converged eigenvalues
// At input, it must be of size numEigen + blockSize.
// At exit, the first numEigen locations contain the eigenvalues requested.
//
// startingEV (integer) = Number of existing converged eigenmodes
//
// Return information on status of computation
//
// info >= 0 >> Number of converged eigenpairs at the end of computation
//
// // Failure due to input arguments
//
// info = - 1 >> The stiffness matrix K has not been specified.
// info = - 2 >> The maps for the matrix K and the matrix M differ.
// info = - 3 >> The maps for the matrix K and the preconditioner P differ.
// info = - 4 >> The maps for the vectors and the matrix K differ.
// info = - 5 >> Q is too small for the number of eigenvalues requested.
// info = - 6 >> Q is too small for the computation parameters.
//
// info = - 10 >> Failure during the mass orthonormalization
//
// info = - 20 >> Error in LAPACK during the local eigensolve
//
// info = - 30 >> MEMORY
//
// Check the input parameters
if (numEigen <= startingEV) {
return startingEV;
}
int info = myVerify.inputArguments(numEigen, K, M, Prec, Q, numEigen + blockSize);
if (info < 0)
return info;
int myPid = MyComm.MyPID();
// Get the weight for approximating the M-inverse norm
Epetra_Vector *vectWeight = 0;
if (normWeight) {
vectWeight = new Epetra_Vector(View, Q.Map(), normWeight);
}
int knownEV = startingEV;
int localVerbose = verbose*(myPid==0);
// Define local block vectors
//
// MX = Working vectors (storing M*X if M is specified, else pointing to X)
// KX = Working vectors (storing K*X)
//
// R = Residuals
//
// H = Preconditioned residuals
//
// P = Search directions
// MP = Working vectors (storing M*P if M is specified, else pointing to P)
// KP = Working vectors (storing K*P)
int xr = Q.MyLength();
Epetra_MultiVector X(View, Q, numEigen, blockSize);
X.Random();
int tmp;
tmp = (M == 0) ? 5*blockSize*xr : 7*blockSize*xr;
double *work1 = new (nothrow) double[tmp];
if (work1 == 0) {
if (vectWeight)
delete vectWeight;
info = -30;
return info;
}
memRequested += sizeof(double)*tmp/(1024.0*1024.0);
highMem = (highMem > currentSize()) ? highMem : currentSize();
double *tmpD = work1;
Epetra_MultiVector KX(View, Q.Map(), tmpD, xr, blockSize);
tmpD = tmpD + xr*blockSize;
Epetra_MultiVector MX(View, Q.Map(), (M) ? tmpD : X.Values(), xr, blockSize);
tmpD = (M) ? tmpD + xr*blockSize : tmpD;
Epetra_MultiVector R(View, Q.Map(), tmpD, xr, blockSize);
tmpD = tmpD + xr*blockSize;
Epetra_MultiVector H(View, Q.Map(), tmpD, xr, blockSize);
tmpD = tmpD + xr*blockSize;
Epetra_MultiVector P(View, Q.Map(), tmpD, xr, blockSize);
tmpD = tmpD + xr*blockSize;
Epetra_MultiVector KP(View, Q.Map(), tmpD, xr, blockSize);
tmpD = tmpD + xr*blockSize;
Epetra_MultiVector MP(View, Q.Map(), (M) ? tmpD : P.Values(), xr, blockSize);
// Define arrays
//
// theta = Store the local eigenvalues (size: 2*blockSize)
// normR = Store the norm of residuals (size: blockSize)
//
// oldHtR = Store the previous H_i^T*R_i (size: blockSize)
// currentHtR = Store the current H_i^T*R_i (size: blockSize)
//
// MM = Local mass matrix (size: 2*blockSize x 2*blockSize)
// KK = Local stiffness matrix (size: 2*blockSize x 2*blockSize)
//
// S = Local eigenvectors (size: 2*blockSize x 2*blockSize)
int lwork2;
lwork2 = 5*blockSize + 12*blockSize*blockSize;
double *work2 = new (nothrow) double[lwork2];
if (work2 == 0) {
if (vectWeight)
delete vectWeight;
delete[] work1;
info = -30;
return info;
}
highMem = (highMem > currentSize()) ? highMem : currentSize();
tmpD = work2;
double *theta = tmpD;
tmpD = tmpD + 2*blockSize;
double *normR = tmpD;
tmpD = tmpD + blockSize;
double *oldHtR = tmpD;
tmpD = tmpD + blockSize;
double *currentHtR = tmpD;
tmpD = tmpD + blockSize;
memset(currentHtR, 0, blockSize*sizeof(double));
double *MM = tmpD;
tmpD = tmpD + 4*blockSize*blockSize;
double *KK = tmpD;
tmpD = tmpD + 4*blockSize*blockSize;
double *S = tmpD;
memRequested += sizeof(double)*lwork2/(1024.0*1024.0);
// Define an array to store the residuals history
if (localVerbose > 2) {
resHistory = new (nothrow) double[maxIterEigenSolve*blockSize];
if (resHistory == 0) {
if (vectWeight)
delete vectWeight;
delete[] work1;
delete[] work2;
info = -30;
return info;
}
historyCount = 0;
}
// Miscellaneous definitions
bool reStart = false;
numRestart = 0;
int localSize;
int twoBlocks = 2*blockSize;
int nFound = blockSize;
int i, j;
if (localVerbose > 0) {
cout << endl;
cout << " *|* Problem: ";
if (M)
cout << "K*Q = M*Q D ";
else
cout << "K*Q = Q D ";
if (Prec)
cout << " with preconditioner";
cout << endl;
cout << " *|* Algorithm = DACG (block version)" << endl;
cout << " *|* Size of blocks = " << blockSize << endl;
cout << " *|* Number of requested eigenvalues = " << numEigen << endl;
cout.precision(2);
cout.setf(ios::scientific, ios::floatfield);
cout << " *|* Tolerance for convergence = " << tolEigenSolve << endl;
cout << " *|* Norm used for convergence: ";
if (normWeight)
cout << "weighted L2-norm with user-provided weights" << endl;
else
cout << "L^2-norm" << endl;
if (startingEV > 0)
cout << " *|* Input converged eigenvectors = " << startingEV << endl;
cout << "\n -- Start iterations -- \n";
}
timeOuterLoop -= MyWatch.WallTime();
for (outerIter = 1; outerIter <= maxIterEigenSolve; ++outerIter) {
highMem = (highMem > currentSize()) ? highMem : currentSize();
if ((outerIter == 1) || (reStart == true)) {
reStart = false;
localSize = blockSize;
if (nFound > 0) {
Epetra_MultiVector X2(View, X, blockSize-nFound, nFound);
Epetra_MultiVector MX2(View, MX, blockSize-nFound, nFound);
Epetra_MultiVector KX2(View, KX, blockSize-nFound, nFound);
// Apply the mass matrix to X
timeMassOp -= MyWatch.WallTime();
if (M)
M->Apply(X2, MX2);
timeMassOp += MyWatch.WallTime();
massOp += nFound;
if (knownEV > 0) {
// Orthonormalize X against the known eigenvectors with Gram-Schmidt
// Note: Use R as a temporary work space
Epetra_MultiVector copyQ(View, Q, 0, knownEV);
timeOrtho -= MyWatch.WallTime();
info = modalTool.massOrthonormalize(X, MX, M, copyQ, nFound, 0, R.Values());
timeOrtho += MyWatch.WallTime();
// Exit the code if the orthogonalization did not succeed
if (info < 0) {
info = -10;
delete[] work1;
delete[] work2;
if (vectWeight)
delete vectWeight;
return info;
}
}
// Apply the stiffness matrix to X
timeStifOp -= MyWatch.WallTime();
K->Apply(X2, KX2);
timeStifOp += MyWatch.WallTime();
stifOp += nFound;
} // if (nFound > 0)
} // if ((outerIter == 1) || (reStart == true))
else {
// Apply the preconditioner on the residuals
if (Prec != 0) {
timePrecOp -= MyWatch.WallTime();
Prec->ApplyInverse(R, H);
timePrecOp += MyWatch.WallTime();
precOp += blockSize;
}
else {
memcpy(H.Values(), R.Values(), xr*blockSize*sizeof(double));
}
// Compute the product H^T*R
timeSearchP -= MyWatch.WallTime();
memcpy(oldHtR, currentHtR, blockSize*sizeof(double));
H.Dot(R, currentHtR);
// Define the new search directions
if (localSize == blockSize) {
P.Scale(-1.0, H);
localSize = twoBlocks;
} // if (localSize == blockSize)
else {
bool hasZeroDot = false;
for (j = 0; j < blockSize; ++j) {
if (oldHtR[j] == 0.0) {
hasZeroDot = true;
break;
}
callBLAS.SCAL(xr, currentHtR[j]/oldHtR[j], P.Values() + j*xr);
}
if (hasZeroDot == true) {
// Restart the computation when there is a null dot product
if (localVerbose > 0) {
cout << endl;
cout << " !! Null dot product -- Restart the search space !!\n";
cout << endl;
}
if (blockSize == 1) {
X.Random();
nFound = blockSize;
}
else {
Epetra_MultiVector Xinit(View, X, j, blockSize-j);
Xinit.Random();
nFound = blockSize - j;
} // if (blockSize == 1)
reStart = true;
numRestart += 1;
info = 0;
continue;
}
callBLAS.AXPY(xr*blockSize, -1.0, H.Values(), P.Values());
} // if (localSize == blockSize)
timeSearchP += MyWatch.WallTime();
// Apply the mass matrix on P
timeMassOp -= MyWatch.WallTime();
if (M)
M->Apply(P, MP);
timeMassOp += MyWatch.WallTime();
massOp += blockSize;
if (knownEV > 0) {
// Orthogonalize P against the known eigenvectors
// Note: Use R as a temporary work space
Epetra_MultiVector copyQ(View, Q, 0, knownEV);
timeOrtho -= MyWatch.WallTime();
modalTool.massOrthonormalize(P, MP, M, copyQ, blockSize, 1, R.Values());
timeOrtho += MyWatch.WallTime();
}
// Apply the stiffness matrix to P
timeStifOp -= MyWatch.WallTime();
K->Apply(P, KP);
timeStifOp += MyWatch.WallTime();
stifOp += blockSize;
} // if ((outerIter == 1) || (reStart == true))
// Form "local" mass and stiffness matrices
// Note: Use S as a temporary workspace
timeLocalProj -= MyWatch.WallTime();
modalTool.localProjection(blockSize, blockSize, xr, X.Values(), xr, KX.Values(), xr,
KK, localSize, S);
modalTool.localProjection(blockSize, blockSize, xr, X.Values(), xr, MX.Values(), xr,
MM, localSize, S);
if (localSize > blockSize) {
modalTool.localProjection(blockSize, blockSize, xr, X.Values(), xr, KP.Values(), xr,
KK + blockSize*localSize, localSize, S);
modalTool.localProjection(blockSize, blockSize, xr, P.Values(), xr, KP.Values(), xr,
KK + blockSize*localSize + blockSize, localSize, S);
modalTool.localProjection(blockSize, blockSize, xr, X.Values(), xr, MP.Values(), xr,
MM + blockSize*localSize, localSize, S);
modalTool.localProjection(blockSize, blockSize, xr, P.Values(), xr, MP.Values(), xr,
MM + blockSize*localSize + blockSize, localSize, S);
} // if (localSize > blockSize)
timeLocalProj += MyWatch.WallTime();
// Perform a spectral decomposition
timeLocalSolve -= MyWatch.WallTime();
int nevLocal = localSize;
info = modalTool.directSolver(localSize, KK, localSize, MM, localSize, nevLocal,
S, localSize, theta, localVerbose,
(blockSize == 1) ? 1: 0);
timeLocalSolve += MyWatch.WallTime();
if (info < 0) {
// Stop when spectral decomposition has a critical failure
break;
}
// Check for restarting
if ((theta[0] < 0.0) || (nevLocal < blockSize)) {
if (localVerbose > 0) {
cout << " Iteration " << outerIter;
cout << "- Failure for spectral decomposition - RESTART with new random search\n";
}
if (blockSize == 1) {
X.Random();
nFound = blockSize;
}
else {
Epetra_MultiVector Xinit(View, X, 1, blockSize-1);
Xinit.Random();
nFound = blockSize - 1;
} // if (blockSize == 1)
reStart = true;
numRestart += 1;
info = 0;
continue;
} // if ((theta[0] < 0.0) || (nevLocal < blockSize))
if ((localSize == twoBlocks) && (nevLocal == blockSize)) {
for (j = 0; j < nevLocal; ++j)
memcpy(S + j*blockSize, S + j*twoBlocks, blockSize*sizeof(double));
localSize = blockSize;
}
// Check the direction of eigenvectors
// Note: This sign check is important for convergence
for (j = 0; j < nevLocal; ++j) {
double coeff = S[j + j*localSize];
if (coeff < 0.0)
callBLAS.SCAL(localSize, -1.0, S + j*localSize);
}
// Compute the residuals
timeResidual -= MyWatch.WallTime();
callBLAS.GEMM('N', 'N', xr, blockSize, blockSize, 1.0, KX.Values(), xr,
S, localSize, 0.0, R.Values(), xr);
if (localSize == twoBlocks) {
callBLAS.GEMM('N', 'N', xr, blockSize, blockSize, 1.0, KP.Values(), xr,
S + blockSize, localSize, 1.0, R.Values(), xr);
}
for (j = 0; j < blockSize; ++j)
callBLAS.SCAL(localSize, theta[j], S + j*localSize);
callBLAS.GEMM('N', 'N', xr, blockSize, blockSize, -1.0, MX.Values(), xr,
S, localSize, 1.0, R.Values(), xr);
if (localSize == twoBlocks) {
callBLAS.GEMM('N', 'N', xr, blockSize, blockSize, -1.0, MP.Values(), xr,
S + blockSize, localSize, 1.0, R.Values(), xr);
}
for (j = 0; j < blockSize; ++j)
callBLAS.SCAL(localSize, 1.0/theta[j], S + j*localSize);
timeResidual += MyWatch.WallTime();
// Compute the norms of the residuals
timeNorm -= MyWatch.WallTime();
if (vectWeight)
R.NormWeighted(*vectWeight, normR);
else
R.Norm2(normR);
// Scale the norms of residuals with the eigenvalues
// Count the converged eigenvectors
nFound = 0;
for (j = 0; j < blockSize; ++j) {
normR[j] = (theta[j] == 0.0) ? normR[j] : normR[j]/theta[j];
if (normR[j] < tolEigenSolve)
nFound += 1;
}
timeNorm += MyWatch.WallTime();
// Store the residual history
if (localVerbose > 2) {
memcpy(resHistory + historyCount*blockSize, normR, blockSize*sizeof(double));
historyCount += 1;
}
// Print information on current iteration
if (localVerbose > 0) {
cout << " Iteration " << outerIter << " - Number of converged eigenvectors ";
cout << knownEV + nFound << endl;
}
if (localVerbose > 1) {
cout << endl;
cout.precision(2);
cout.setf(ios::scientific, ios::floatfield);
for (i=0; i<blockSize; ++i) {
cout << " Iteration " << outerIter << " - Scaled Norm of Residual " << i;
cout << " = " << normR[i] << endl;
}
cout << endl;
cout.precision(2);
for (i=0; i<blockSize; ++i) {
cout << " Iteration " << outerIter << " - Ritz eigenvalue " << i;
cout.setf((fabs(theta[i]) < 0.01) ? ios::scientific : ios::fixed, ios::floatfield);
cout << " = " << theta[i] << endl;
}
cout << endl;
}
if (nFound == 0) {
// Update the spaces
// Note: Use H as a temporary work space
timeLocalUpdate -= MyWatch.WallTime();
memcpy(H.Values(), X.Values(), xr*blockSize*sizeof(double));
callBLAS.GEMM('N', 'N', xr, blockSize, blockSize, 1.0, H.Values(), xr, S, localSize,
0.0, X.Values(), xr);
memcpy(H.Values(), KX.Values(), xr*blockSize*sizeof(double));
callBLAS.GEMM('N', 'N', xr, blockSize, blockSize, 1.0, H.Values(), xr, S, localSize,
0.0, KX.Values(), xr);
if (M) {
memcpy(H.Values(), MX.Values(), xr*blockSize*sizeof(double));
callBLAS.GEMM('N', 'N', xr, blockSize, blockSize, 1.0, H.Values(), xr, S, localSize,
0.0, MX.Values(), xr);
}
if (localSize == twoBlocks) {
callBLAS.GEMM('N', 'N', xr, blockSize, blockSize, 1.0, P.Values(), xr,
S + blockSize, localSize, 1.0, X.Values(), xr);
callBLAS.GEMM('N', 'N', xr, blockSize, blockSize, 1.0, KP.Values(), xr,
S + blockSize, localSize, 1.0, KX.Values(), xr);
if (M) {
callBLAS.GEMM('N', 'N', xr, blockSize, blockSize, 1.0, MP.Values(), xr,
S + blockSize, localSize, 1.0, MX.Values(), xr);
}
} // if (localSize == twoBlocks)
timeLocalUpdate += MyWatch.WallTime();
// When required, monitor some orthogonalities
if (verbose > 2) {
if (knownEV == 0) {
accuracyCheck(&X, &MX, &R, 0, (localSize>blockSize) ? &P : 0);
}
else {
Epetra_MultiVector copyQ(View, Q, 0, knownEV);
accuracyCheck(&X, &MX, &R, ©Q, (localSize>blockSize) ? &P : 0);
}
} // if (verbose > 2)
continue;
} // if (nFound == 0)
// Order the Ritz eigenvectors by putting the converged vectors at the beginning
int firstIndex = blockSize;
for (j = 0; j < blockSize; ++j) {
if (normR[j] >= tolEigenSolve) {
firstIndex = j;
break;
}
} // for (j = 0; j < blockSize; ++j)
while (firstIndex < nFound) {
for (j = firstIndex; j < blockSize; ++j) {
if (normR[j] < tolEigenSolve) {
// Swap the j-th and firstIndex-th position
callFortran.SWAP(localSize, S + j*localSize, 1, S + firstIndex*localSize, 1);
callFortran.SWAP(1, theta + j, 1, theta + firstIndex, 1);
callFortran.SWAP(1, normR + j, 1, normR + firstIndex, 1);
break;
}
} // for (j = firstIndex; j < blockSize; ++j)
for (j = 0; j < blockSize; ++j) {
if (normR[j] >= tolEigenSolve) {
firstIndex = j;
break;
}
} // for (j = 0; j < blockSize; ++j)
} // while (firstIndex < nFound)
// Copy the converged eigenvalues
memcpy(lambda + knownEV, theta, nFound*sizeof(double));
// Convergence test
if (knownEV + nFound >= numEigen) {
callBLAS.GEMM('N', 'N', xr, nFound, blockSize, 1.0, X.Values(), xr,
S, localSize, 0.0, R.Values(), xr);
if (localSize > blockSize) {
callBLAS.GEMM('N', 'N', xr, nFound, blockSize, 1.0, P.Values(), xr,
S + blockSize, localSize, 1.0, R.Values(), xr);
}
memcpy(Q.Values() + knownEV*xr, R.Values(), nFound*xr*sizeof(double));
knownEV += nFound;
if (localVerbose == 1) {
cout << endl;
cout.precision(2);
cout.setf(ios::scientific, ios::floatfield);
for (i=0; i<blockSize; ++i) {
cout << " Iteration " << outerIter << " - Scaled Norm of Residual " << i;
cout << " = " << normR[i] << endl;
}
cout << endl;
}
break;
}
// Store the converged eigenvalues and eigenvectors
callBLAS.GEMM('N', 'N', xr, nFound, blockSize, 1.0, X.Values(), xr,
S, localSize, 0.0, Q.Values() + knownEV*xr, xr);
if (localSize == twoBlocks) {
callBLAS.GEMM('N', 'N', xr, nFound, blockSize, 1.0, P.Values(), xr,
S + blockSize, localSize, 1.0, Q.Values() + knownEV*xr, xr);
}
knownEV += nFound;
// Define the restarting vectors
timeRestart -= MyWatch.WallTime();
int leftOver = (nevLocal < blockSize + nFound) ? nevLocal - nFound : blockSize;
double *Snew = S + nFound*localSize;
memcpy(H.Values(), X.Values(), blockSize*xr*sizeof(double));
callBLAS.GEMM('N', 'N', xr, leftOver, blockSize, 1.0, H.Values(), xr,
Snew, localSize, 0.0, X.Values(), xr);
memcpy(H.Values(), KX.Values(), blockSize*xr*sizeof(double));
callBLAS.GEMM('N', 'N', xr, leftOver, blockSize, 1.0, H.Values(), xr,
Snew, localSize, 0.0, KX.Values(), xr);
if (M) {
memcpy(H.Values(), MX.Values(), blockSize*xr*sizeof(double));
callBLAS.GEMM('N', 'N', xr, leftOver, blockSize, 1.0, H.Values(), xr,
Snew, localSize, 0.0, MX.Values(), xr);
}
if (localSize == twoBlocks) {
callBLAS.GEMM('N', 'N', xr, leftOver, blockSize, 1.0, P.Values(), xr,
Snew+blockSize, localSize, 1.0, X.Values(), xr);
callBLAS.GEMM('N', 'N', xr, leftOver, blockSize, 1.0, KP.Values(), xr,
Snew+blockSize, localSize, 1.0, KX.Values(), xr);
if (M) {
callBLAS.GEMM('N', 'N', xr, leftOver, blockSize, 1.0, MP.Values(), xr,
Snew+blockSize, localSize, 1.0, MX.Values(), xr);
}
} // if (localSize == twoBlocks)
if (nevLocal < blockSize + nFound) {
// Put new random vectors at the end of the block
Epetra_MultiVector Xtmp(View, X, leftOver, blockSize - leftOver);
Xtmp.Random();
}
else {
nFound = 0;
} // if (nevLocal < blockSize + nFound)
reStart = true;
timeRestart += MyWatch.WallTime();
} // for (outerIter = 1; outerIter <= maxIterEigenSolve; ++outerIter)
timeOuterLoop += MyWatch.WallTime();
highMem = (highMem > currentSize()) ? highMem : currentSize();
// Clean memory
delete[] work1;
delete[] work2;
if (vectWeight)
delete vectWeight;
// Sort the eigenpairs
timePostProce -= MyWatch.WallTime();
if ((info == 0) && (knownEV > 0)) {
mySort.sortScalars_Vectors(knownEV, lambda, Q.Values(), Q.MyLength());
}
timePostProce += MyWatch.WallTime();
return (info == 0) ? knownEV : info;
}
pii getpos(int x)
{
return MP(x/len,x%len);
}
TEST_F(VirtualTableTests, test_constraints_stacking) {
// Add two testing tables to the registry.
Registry::add<pTablePlugin>("table", "p");
Registry::add<kTablePlugin>("table", "k");
auto dbc = SQLiteDBManager::get();
{
// To simplify the attach, just access the column definition directly.
auto p = std::make_shared<pTablePlugin>();
attachTableInternal("p", p->columnDefinition(), dbc->db());
auto k = std::make_shared<kTablePlugin>();
attachTableInternal("k", k->columnDefinition(), dbc->db());
}
QueryData results;
std::string statement;
std::map<std::string, std::string> expected;
std::vector<std::pair<std::string, QueryData> > constraint_tests = {
MP("select k.x from p, k", makeResult("x", {"1", "2", "1", "2"})),
MP("select k.x from (select * from k) k2, p, k where k.x = p.x",
makeResult("k.x", {"1", "1", "2", "2"})),
MP("select k.x from (select * from k where z = 1) k2, p, k where k.x = "
"p.x",
makeResult("k.x", {"1", "2"})),
MP("select k.x from k k1, (select * from p) p1, k where k.x = p1.x",
makeResult("k.x", {"1", "1", "2", "2"})),
MP("select k.x from (select * from p) p1, k, (select * from k) k2 where "
"k.x = p1.x",
makeResult("k.x", {"1", "1", "2", "2"})),
MP("select k.x from (select * from p) p1, k, (select * from k where z = "
"2) k2 where k.x = p1.x",
makeResult("k.x", {"1", "2"})),
MP("select k.x from k, (select * from p) p1, k k2, (select * from k "
"where z = 1) k3 where k.x = p1.x",
makeResult("k.x", {"1", "1", "2", "2"})),
MP("select p.x from (select * from k where z = 1) k1, (select * from k "
"where z != 1) k2, p where p.x = k2.x",
makeResult("p.x", {"1"})),
MP("select p.x from (select * from k, (select x as xx from k where x = "
"1) k2 where z = 1) k1, (select * from k where z != 1) k2, p, k as k3 "
"where p.x = k2.x",
makeResult("p.x", {"1", "1"})),
};
for (const auto& test : constraint_tests) {
QueryData results;
queryInternal(test.first, results, dbc->db());
EXPECT_EQ(results, test.second);
}
std::vector<QueryData> union_results = {
makeResult("x", {"1", "2"}), makeResult("k.x", {"1", "2"}),
makeResult("k.x", {"1", "2"}), makeResult("k.x", {"1", "2"}),
makeResult("k.x", {"1", "2"}), makeResult("k.x", {"1", "2"}),
makeResult("k.x", {"1", "2"}), makeResult("p.x", {"1"}),
makeResult("p.x", {"1"}),
};
size_t index = 0;
for (const auto& test : constraint_tests) {
QueryData results;
queryInternal(test.first + " union " + test.first, results, dbc->db());
EXPECT_EQ(results, union_results[index++]);
}
}
void set_levels()
{
loop(i,1,11) loop(j,1,11) level[0].board[i][j]=1;
level[0].start = MP(3,3);
level[0].des = MP(8,8);
loop(i,0,50) loop(j,0,50) level[1].board[i][j]=0;
loop(i,0,50) loop(j,0,50) level[2].board[i][j]=0;
loop(i,1,4) level[1].board[1][i]=1;
loop(i,1,7) level[1].board[2][i]=1;
loop(i,1,10) level[1].board[3][i]=1;
loop(i,2,11) level[1].board[4][i]=1;
loop(i,6,11) level[1].board[5][i]=1;
loop(i,7,10) level[1].board[6][i]=1;
level[1].start = MP(2,2);
level[1].des = MP(5,8);
loop(i,7,14) level[2].board[1][i]=1;
loop(i,1,5) level[2].board[2][i]=1; loop(i,7,14) level[2].board[2][i]=1;
loop(i,1,10) level[2].board[3][i]=1; loop(i,12,16) level[2].board[3][i]=1;
loop(i,1,5) level[2].board[4][i]=1; loop(i,12,16) level[2].board[4][i]=1;
loop(i,1,5) level[2].board[5][i]=1; loop(i,12,16) level[2].board[5][i]=1;
loop(i,13,16) level[2].board[6][i]=1;
level[2].start = MP(4,2);
level[2].des = MP(4,14);
loop(i,2,7) loop(j,1,5) level[3].board[i][j]=1;
loop(i,1,7) loop(j,7,11) level[3].board[i][j]=1;
loop(i,1,6) loop(j,13,16) level[3].board[i][j]=1;
level[3].start = MP(4,2);
level[3].des = MP(2,14);
level[3].hbridge.pb(MP(3,3)); level[3].vbridge.pb(MP(2,9));
vector< pair<int,int> > temp; temp.pb(MP(5,5)); temp.pb(MP(5,6)); level[3].hbridge_value.pb(temp);
temp.clear(); temp.pb(MP(5,11)); temp.pb(MP(5,12)); level[3].vbridge_value.pb(temp);
loop(i,1,4) loop(j,12,16) level[4].board[i][j]=1;
loop(j,2,6) level[4].board[2][j]=1; loop(j,8,12) level[4].board[2][j]=1;
loop(i,3,6) loop(j,2,6) level[4].board[i][j]=1;
loop(i,6,7) loop(j,4,14) level[4].board[i][j]=1;
loop(i,7,10) loop(j,11,14) level[4].board[i][j]=1;
loop(i,7,9) loop(j,14,16) level[4].board[i][j]=1;
loop(j,8,12) level[4].board[9][j]=1;loop(j,5,6) level[4].board[9][j]=1;
loop(i,8,11) loop(j,1,4) level[4].board[i][j]=1; level[4].board[9][4]=1; level[4].board[10][4]=1;
level[4].start = MP(2,14); level[4].des = MP(9,2);
level[4].hbridge.pb(MP(2,9)); level[4].hbridge.pb(MP(7,15));
temp.clear(); temp.pb(MP(2,6)); temp.pb(MP(2,7)); level[4].hbridge_value.pb(temp);
temp.clear(); temp.pb(MP(9,6)) ; temp.pb(MP(9,7)); level[4].hbridge_value.pb(temp);
level[5].start = MP(6,2); level[5].des = MP(8,8);
loop(i,3,8) loop(j,1,4) level[5].board[i][j]=1; level[5].board[3][4]=1;
level[5].board[3][11]=1; loop(i,3,6) loop(j,12,14) level[5].board[i][j]=1;
level[5].board[6][10]=1; level[5].board[7][10]=1; level[5].board_light[6][11]=1; level[5].board_light[7][11]=1;
loop(i,6,10) loop(j,7,10) level[5].board[i][j]=1;
loop(i,1,3) loop(j,4,12) level[5].board_light[i][j]=1;
loop(i,6,10) loop(j,12,16) level[5].board_light[i][j]=1; level[5].board_light[8][14]=0; level[5].board[8][14]=1;
}
MP MP::new_lst( QString type ) {
return MP( 0, new LstWithType( type ) );
}
int main(int argc, char **argv)
{
// first build our error handler
g3ErrorHandler = new ConsoleErrorHandler();
//
// now create a domain and a modelbuilder
// and build the model
//
// Domain *theDomain = new Domain();
MapOfTaggedObjects theStorage;
// ArrayOfTaggedObjects theStorage(32);
Domain *theDomain = new Domain(theStorage);
// create the nodes using constructor:
// Node(tag, ndof, crd1, crd2)
// and then add them to the domain
Node *node1 = new Node(1, 3, 1.0, 1.0, 0.0 );
Node *node2 = new Node(2, 3, 0.0, 1.0, 0.0 );
Node *node3 = new Node(3, 3, 0.0, 0.0, 0.0 );
Node *node4 = new Node(4, 3, 1.0, 0.0, 0.0 );
Node *node5 = new Node(5, 3, 1.0, 1.0, 1.0 );
Node *node6 = new Node(6, 3, 0.0, 1.0, 1.0 );
Node *node7 = new Node(7, 3, 0.0, 0.0, 1.0 );
Node *node8 = new Node(8, 3, 1.0, 0.0, 1.0 );
theDomain->addNode(node1);
theDomain->addNode(node2);
theDomain->addNode(node3);
theDomain->addNode(node4);
theDomain->addNode(node5);
theDomain->addNode(node6);
theDomain->addNode(node7);
theDomain->addNode(node8);
// create an elastic material using constriuctor:
// ElasticMaterialModel(tag, E)
//UniaxialMaterial *theMaterial = new ElasticMaterial(1, 3000);
double PIo3 = PI/3.0;
PIo3 = 0.0;
//Drucker-Prager Model
DPYieldSurface DP_YS;
DPPotentialSurface DP_PS(0.05);
//EvolutionLaw_NL_Eeq DP_ELS1;
EvolutionLaw_L_Eeq DP_ELS1(10.0);
EvolutionLaw_T DP_ELT;
double scalars[] = {0.3, 0.0}; //alfa1, k
double NOS = 2; //Number of scalar vars
double NOT = 1; //Number of tensorial vars
stresstensor startstress;
straintensor startstrain, otherstrain;
startstrain = startstrain.pqtheta2strain( 0.000, 0.0000, 0.0);
otherstrain = otherstrain.pqtheta2strain( 0.000, 0.0000, 0.0);
stresstensor *tensors = new stresstensor[1];
EPState EPS(3000.0, 3000.0, 0.3, 0.0, startstress, otherstrain,
otherstrain, otherstrain, NOS, scalars, NOT, tensors);
Template3Dep MP(1, &DP_YS, &DP_PS, &EPS, &DP_ELS1, &DP_ELT);
NDMaterial *theMaterial = &MP;
//NDMaterial *theMaterial = new ElasticIsotropic3D(1, 3000, 0.3);
// create the truss elements using constructor:
// Truss(tag, dim, nd1, nd2, Material &,A)
// and then add them to the domain
//Truss *truss1 = new Truss(1, 2, 1, 4, *theMaterial, 10.0);
//Truss *truss2 = new Truss(2, 2, 2, 4, *theMaterial, 5.0);
//EPState *eps = 0;
EightNodeBrick *brick = new EightNodeBrick(1, 5, 6, 7, 8, 1, 2, 3, 4,
theMaterial, "Template3Dep",
0.0, 0.0, 0.0, 1.8, &EPS);
//theDomain->addElement(truss1);
//theDomain->addElement(truss2);
theDomain->addElement( brick );
// create the single-point constraint objects using constructor:
// SP_Constraint(tag, nodeTag, dofID, value)
// and then add them to the domain
SP_Constraint *sp1 = new SP_Constraint(1, 1, 0, 0.0259999);
SP_Constraint *sp2 = new SP_Constraint(2, 1, 1, 0.0259999);
SP_Constraint *sp3 = new SP_Constraint(3, 1, 2, -0.1213350);
SP_Constraint *sp4 = new SP_Constraint(4, 2, 0, -0.0259999);
SP_Constraint *sp5 = new SP_Constraint(5, 2, 1, 0.0259999);
SP_Constraint *sp6 = new SP_Constraint(6, 2, 2, -0.1213350);
SP_Constraint *sp7 = new SP_Constraint(7, 3, 0, -0.0259999);
SP_Constraint *sp8 = new SP_Constraint(8, 3, 1, -0.0259999);
SP_Constraint *sp9 = new SP_Constraint(9, 3, 2, -0.1213350);
SP_Constraint *sp10 = new SP_Constraint(10, 4, 0, 0.0259999);
SP_Constraint *sp11 = new SP_Constraint(11, 4, 1, -0.0259999);
SP_Constraint *sp12 = new SP_Constraint(12, 4, 2, -0.1213350);
SP_Constraint *sp13 = new SP_Constraint(13, 5, 0, 0.0);
SP_Constraint *sp14 = new SP_Constraint(14, 5, 1, 0.0);
SP_Constraint *sp15 = new SP_Constraint(15, 5, 2, 0.0);
SP_Constraint *sp16 = new SP_Constraint(16, 6, 0, 0.0);
SP_Constraint *sp17 = new SP_Constraint(17, 6, 1, 0.0);
SP_Constraint *sp18 = new SP_Constraint(18, 6, 2, 0.0);
SP_Constraint *sp19 = new SP_Constraint(19, 7, 0, 0.0);
SP_Constraint *sp20 = new SP_Constraint(20, 7, 1, 0.0);
SP_Constraint *sp21 = new SP_Constraint(21, 7, 2, 0.0);
SP_Constraint *sp22 = new SP_Constraint(22, 8, 0, 0.0);
SP_Constraint *sp23 = new SP_Constraint(23, 8, 1, 0.0);
SP_Constraint *sp24 = new SP_Constraint(24, 8, 2, 0.0);
//Add penalty constraint
theDomain->addSP_Constraint(sp1 );
theDomain->addSP_Constraint(sp2 );
theDomain->addSP_Constraint(sp3 );
theDomain->addSP_Constraint(sp4 );
theDomain->addSP_Constraint(sp5 );
theDomain->addSP_Constraint(sp6 );
theDomain->addSP_Constraint(sp7 );
theDomain->addSP_Constraint(sp8 );
theDomain->addSP_Constraint(sp9 );
theDomain->addSP_Constraint(sp10);
theDomain->addSP_Constraint(sp11);
theDomain->addSP_Constraint(sp12);
theDomain->addSP_Constraint(sp13);
theDomain->addSP_Constraint(sp14);
theDomain->addSP_Constraint(sp15);
theDomain->addSP_Constraint(sp16);
theDomain->addSP_Constraint(sp17);
theDomain->addSP_Constraint(sp18);
theDomain->addSP_Constraint(sp19);
theDomain->addSP_Constraint(sp20);
theDomain->addSP_Constraint(sp21);
theDomain->addSP_Constraint(sp22);
theDomain->addSP_Constraint(sp23);
theDomain->addSP_Constraint(sp24);
// construct a linear time series object using constructor:
// LinearSeries()
TimeSeries *theSeries = new LinearSeries();
// construct a load pattren using constructor:
// LoadPattern(tag)
// and then set it's TimeSeries and add it to the domain
LoadPattern *theLoadPattern = new LoadPattern(1);
theLoadPattern->setTimeSeries(theSeries);
theDomain->addLoadPattern(theLoadPattern);
// construct a nodal load using constructor:
// NodalLoad(tag, nodeID, Vector &)
// first construct a Vector of size 2 and set the values NOTE C INDEXING
// then construct the load and add it to the domain
Vector theLoadValues(3);
theLoadValues(0) = 0.0;
theLoadValues(1) = 0.0;
//theLoadValues(2) = -100.0;
theLoadValues(2) = 0.0;
NodalLoad *theLoad = new NodalLoad(1, 5, theLoadValues);
theDomain->addNodalLoad(theLoad, 1);
theLoad = new NodalLoad(2, 6, theLoadValues);
theDomain->addNodalLoad(theLoad, 1);
theLoad = new NodalLoad(3, 7, theLoadValues);
theDomain->addNodalLoad(theLoad, 1);
theLoad = new NodalLoad(4, 8, theLoadValues);
theDomain->addNodalLoad(theLoad, 1);
// create an Analysis object to perform a static analysis of the model
// - constructs:
// AnalysisModel of type AnalysisModel,
// EquiSolnAlgo of type Linear
// StaticIntegrator of type LoadControl
// ConstraintHandler of type Penalty
// DOF_Numberer which uses RCM
// LinearSOE of type Band SPD
// and then the StaticAnalysis object
AnalysisModel *theModel = new AnalysisModel();
EquiSolnAlgo *theSolnAlgo = new Linear();
StaticIntegrator *theIntegrator = new LoadControl(1.0, 1.0, 1.0, 1.0);
ConstraintHandler *theHandler = new PenaltyConstraintHandler(1.0e8,1.0e8);
RCM *theRCM = new RCM();
DOF_Numberer *theNumberer = new DOF_Numberer(*theRCM);
BandSPDLinSolver *theSolver = new BandSPDLinLapackSolver();
LinearSOE *theSOE = new BandSPDLinSOE(*theSolver);
StaticAnalysis theAnalysis(*theDomain,
*theHandler,
*theNumberer,
*theModel,
*theSolnAlgo,
*theSOE,
*theIntegrator);
// perform the analysis & print out the results for the domain
int numSteps = 1;
theAnalysis.analyze(numSteps);
cerr << *theDomain;
//brick->displaySelf();
exit(0);
}
MP MP::new_path( QString filename ) {
return MP( 0, new Path( filename ) );
}
pii operator -( const pii & a,const pii & b){
return MP(a.X-b.X,a.Y-b.Y);
}
MP MP::new_typed_array_qint32() {
return MP( 0, new TypedArray<qint32> );
}
pLL operator - (pLL a,pLL b) {return MP(a.X-b.X,a.Y-b.Y);}
TEST(ARRAY, Capacity) {
EXPECT_TRUE(kPackedCapCodeThreshold == 0x10000);
#define MP(a, b) std::make_pair(a, b)
// Update the numbers if we change kPackedCapCodeThreshold
#if (LG_SMART_SIZES_PER_DOUBLING == 1)
std::pair<uint32_t, uint32_t> caps [] = {
MP(3, 0),
MP(4, 5),
MP(5, 0),
MP(6, 7),
MP(7, 0),
MP(8, 11),
MP(12, 15),
MP(127, 0),
MP(128, 191),
MP(0xFFFF, 0),
MP(0x10000, 0x17F00),
MP(0x10001, 0)
};
#elif (LG_SMART_SIZES_PER_DOUBLING == 2)
std::pair<uint32_t, uint32_t> caps [] = {
MP(3, 0),
MP(4, 0),
MP(5, 0),
MP(6, 0),
MP(7, 0),
MP(8, 9),
MP(12, 13),
MP(127, 0),
MP(128, 159),
MP(0xFFFF, 0),
MP(0x10000, 0x13F00),
MP(0x10001, 0)
};
#else
#error Unknown LG_SMART_SIZES_PER_DOUBLING
#endif
#undef MP
for (size_t i = 0; i != sizeof(caps) / sizeof(caps[0]); ++i) {
EXPECT_TRUE(PackedArray::getMaxCapInPlaceFast(caps[i].first) ==
caps[i].second);
}
}
POINT3D normal=((p[v[i].t[1]]-p[v[i].t[0]])^(p[v[i].t[2]]-p[v[i].t[0]]));
LL il=(normal*(p[x]-p[v[i].t[0]]));
vis[i]=0;
if (il>0) vis[i]=1;
else if (il==0){
if ((normal*((p[v[i].t[1]]-p[v[i].t[0]])^(p[x]-p[v[i].t[0]]))>=0
&& normal*((p[v[i].t[2]]-p[v[i].t[1]])^(p[x]-p[v[i].t[1]]))>=0
&& normal*((p[v[i].t[0]]-p[v[i].t[2]])^(p[x]-p[v[i].t[2]]))>=0))
return; /*ODKOMENTUJ*/
vis[i]=1;
}
}
int ile=SZ(v);
REP(i,ile) if (vis[i])
REP(j,3) if (!vis[t[v[i].t[(j+1)%3]][v[i].t[j]]])
pom.PB(MP(v[i].t[j],v[i].t[(j+1)%3]));
REP(i,ile) if (vis[i]){
swap(v[i],v.back());
v.pop_back();
REP(j,3) t[v[i].t[j]][v[i].t[(j+1)%3]]=i;
vis[i--]=vis[--ile];
}
FORE(it,pom){
t[it->X][it->Y]=t[it->Y][x]=t[x][it->X]=SZ(v);
v.PB(sciana(it->X,it->Y,x));
}
}
void CH3D(){ //n>=3, oblicza wektor trojkatnych scian v (mozliwe powtorzenia)
int i=2;
POINT3D normal;
while (i<n && (normal=((p[1]-p[0])^(p[i]-p[0])))==POINT3D(0,0,0)) i++;
