bool
RegisterContextPOSIXProcessMonitor_arm64::ReadAllRegisterValues(lldb::DataBufferSP &data_sp)
{
bool success = false;
data_sp.reset (new lldb_private::DataBufferHeap (REG_CONTEXT_SIZE, 0));
if (data_sp && ReadGPR () && ReadFPR ())
{
uint8_t *dst = data_sp->GetBytes();
success = dst != 0;
if (success)
{
::memcpy (dst, &m_gpr_arm64, GetGPRSize());
dst += GetGPRSize();
::memcpy (dst, &m_fpr, sizeof m_fpr);
}
}
return success;
}
int main(int argc, char ** argv)
{
print_lib_intro_notice(cout);
print_copyright_notice(cout);
cout << endl;
// example #2: open a file, run a geometry optimization, and save a file.
// ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
char infile_name[1048];
char outfile_name[1048];
DWORD nFilterIndex;
if (OpenFileDlg(0, "Ghemical Project File (*.gpr)\0*.gpr\0All files \0*.*\0",
infile_name, nFilterIndex)
!= S_OK)
{
return -1;
}
// check that we have got both file names from the command line.
/*if (argc != 3)
{
cout << "usage : example2 infile.gpr outfile.gpr" << endl;
exit(1);
}
char * infile_name = argv[1];
char * outfile_name = argv[2];
*/
// create a model object, and read in a file.
model * mdl = new model();
cout << "trying to open a file " << infile_name << " ; ";
ifstream ifile;
ifile.open(infile_name, ios::in);
if (ifile.fail())
{
cout << "failed!!!" << endl;
ifile.close();
delete mdl;
return -1;
}
cout << "ok!!!" << endl;
ReadGPR(* mdl, ifile, false, false);
ifile.close();
printf(
"mdl->use_periodic_boundary_conditions = %d\n",
mdl->use_periodic_boundary_conditions);
printf(
"mdl->periodic_box_HALFdim[0] = %f\n",
mdl->periodic_box_HALFdim[0]);
printf(
"mdl->periodic_box_HALFdim[1] = %f\n",
mdl->periodic_box_HALFdim[1]);
printf(
"mdl->periodic_box_HALFdim[2] = %f\n",
mdl->periodic_box_HALFdim[2]);
// if everything went fine, then create a computation engine object, initialize it,
// and create a geometry optimizer object using the computation engine object.
engine * eng = mdl->GetCurrentSetup()->CreateEngineByIDNumber(CURRENT_ENG1_MM);
// engine * eng = mdl->GetCurrentSetup()->CreateEngineByIDNumber(ENG1_MM_TRIPOS52);
// engine * eng = mdl->GetCurrentSetup()->CreateEngineByIDNumber(ENG1_MM_DEFAULT);
// eng_pbc != NULL if we will use a system with periodic boundary conditions...
// engine_pbc * eng_pbc = dynamic_cast<engine_pbc *>(eng);
#if USE_ENGINE_PBC_TST
engine_pbc_tst * eng_pbc = dynamic_cast<engine_pbc_tst *>(eng);
#else
engine_pbc * eng_pbc = dynamic_cast<engine_pbc *>(eng);
#endif /*USE_ENGINE_PBC_TST*/
CopyCRD(mdl, eng, 0);
CopyLockedCRD(mdl, eng, 0);
printf("\n%f %f %f %f %f %f\n",
mdl->maxCRD[0],
mdl->minCRD[0],
mdl->maxCRD[1],
mdl->minCRD[1],
mdl->maxCRD[2],
mdl->minCRD[2]);
mdl->periodic_box_HALFdim[0] = (mdl->maxCRD[0] - mdl->minCRD[0]+0.14) / 2.;
mdl->periodic_box_HALFdim[1] = (mdl->maxCRD[1] - mdl->minCRD[1]+0.12) / 2.;
mdl->periodic_box_HALFdim[0] = (mdl->maxCRD[0] - mdl->minCRD[0]) / 2. + 0.14;
mdl->periodic_box_HALFdim[1] = (mdl->maxCRD[1] - mdl->minCRD[1]) / 2. + 0.12;
printf(
"mdl->use_periodic_boundary_conditions = %d\n",
mdl->use_periodic_boundary_conditions);
printf(
"mdl->periodic_box_HALFdim[0] = %f\n",
mdl->periodic_box_HALFdim[0]);
printf(
"mdl->periodic_box_HALFdim[1] = %f\n",
mdl->periodic_box_HALFdim[1]);
printf(
"mdl->periodic_box_HALFdim[2] = %f\n",
mdl->periodic_box_HALFdim[2]);
geomopt * opt = new geomopt(eng, 100, 0.025, 10.0);
// then take 100 geometry optimization steps, and print out some data about progess.
for (int n1 = 0;n1 < 100;n1++)
{
opt->TakeCGStep(conjugate_gradient::Newton2An);
eng_pbc->CheckLocations();
cout << "step = " << (n1 + 1) << " ";
cout << "energy = " << opt->optval << " ";
cout << "step length = " << opt->optstp << endl;
}
// now copy the optimized coordinates back to the model object, and save the file.
CopyCRD(eng, mdl, 0);
delete opt; opt = NULL;
delete eng; eng = NULL;
//------------------------------------------------------------------
TCHAR filter[] = TEXT("Ghemical Project File (*.gpr)\0*.gpr\0")
TEXT("All Files (*.*)\0*.*\0");
sprintf(outfile_name, "\0");
if (SaveFileDlg(0, outfile_name, filter, nFilterIndex) == S_OK)
{
cout << "now saving file " << outfile_name << endl;
ofstream ofile;
ofile.open(outfile_name, ios::out);
WriteGPR_v100(* mdl, ofile);
ofile.close();
}
// finally release all allocated memory and leave.
delete mdl; mdl = NULL;
return 0;
}
void Load_traj(int ind1, int ind2, int dim, vector<double> & X)
{
//print_lib_intro_notice(cout);
//print_copyright_notice(cout);
cout << endl;
// example #2: open a file, run a geometry optimization, and save a file.
// ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
char infile_name[1048];
DWORD nFilterIndex;
if (OpenFileDlg(0, "Ghemical Project File (*.gpr)\0*.gpr\0All files \0*.*\0",
infile_name, nFilterIndex)
!= S_OK)
{
return;
}
cout << "trying to open a file " << infile_name << " ; ";
ifstream ifile;
ifile.open(infile_name, ios::in);
if (ifile.fail())
{
cout << "failed!!!" << endl;
ifile.close();
return;
}
cout << "ok!!!" << endl;
#if _USE_WINGHEMICAL_
//готовим классы для 3D визуализации
hInst = GetModuleHandle(NULL);
singleton_cleaner<win_app> app_cleaner;
win_app * app = win_app::GetInstance();
// new win_app() here
// -> SetNewProject();
// -> new win_project(* win_class_factory::GetInstance());
// -> new win_class_factory() : graphics_class_factory()
//
// win_project()
// -> CreateProjectView() -> new win_project_view(prj2) -> LightAdded(); ObjectAdded();
// win_project()
// -> AddGraphicsView(NULL, false);
// project::AddGraphicsView()
// -> win_class_factory::ProduceGraphicsView()
// -> new win_graphics_view(prj2, cam);
// -> BeginWinGhemical(); view_widget = CreateWinGhemical(this); SendMessage(view_widget, WM_COMMAND, ID_FILE_INITOG2, 0); ConfigureHandler(view_widget);
app_cleaner.SetInstance(app);
app->GetWinProject()->SetApp(app);
//app->work(argc, argv); //
ReadGPR(* app->GetWinProject(), ifile, false, false);
ifile.close();
{
HANDLE hThread = NULL;
{
setup * su = app->GetWinProject()->GetCurrentSetup();
static jobinfo_MolDyn_tst ji;
ji.prj = app->GetWinProject();
ji.md = moldyn_tst_param(su);
app->GetWinProject()->start_job_MolDyn_tst(& ji);
}
}
StartWinGhemical(NULL);
#else
model * mdl = new model();
ReadGPR(* mdl, ifile, false, false);
ifile.close();
#endif
char fn[512];
if (OpenFileDlg(NULL, "Ghemical Trajectory File (*.traj)\0*.traj\0All files \0*.*\0", fn, nFilterIndex) == S_OK)
{
cout << "trying to open \"" << fn << "\"." << endl;
ifstream * trajfile;
//mdl->OpenTrajectory(filename);
//{
i32s traj_num_atoms = mdl->GetAtomCount();
/* for (iter_al it1 = GetAtomsBegin();it1 != GetAtomsEnd();it1++)
{
if (!((* it1).flags & ATOMFLAG_IS_HIDDEN)) traj_num_atoms++;
}
*/
trajfile = new ifstream(fn, ios::in | ios::binary);
//trajfile->seekg(8, ios::beg); // skip the file id...
char file_id[10];
trajfile->read((char *) file_id, 8);
bool extended_trajectory = false;
if (0 == ::strncmp(file_id, "traj_v11", 8))
extended_trajectory = true;
int natoms;
trajfile->read((char *) & natoms, sizeof(natoms));
if (natoms != traj_num_atoms)
{
printf("natoms %d != traj_num_atoms %d\n", natoms, traj_num_atoms);
// ErrorMessage("The trajectory is incompatible with the current structure/setup!!!");
// PrintToLog("incompatible file : different number of atoms!\n");
goto e_close_traj;
}
i32s total_traj_frames;
trajfile->read((char *) & total_traj_frames, sizeof(total_traj_frames));
float tstep = 0.0;
if (extended_trajectory)
trajfile->read((char *) & tstep, sizeof(tstep));
//char mbuff1[256]; strstream str1(mbuff1, sizeof(mbuff1));
//str1 << "the trajectory file contains " << total_traj_frames << " frames." << endl << ends;
//PrintToLog(mbuff1);
//current_traj_frame = 0;
//}
atom * mt_a1; // measure_tool
atom * mt_a2; // measure_tool
atom * mt_a3; // measure_tool
float ekin;
float epot;
X.resize(total_traj_frames);
//i32s max_frames = app->GetWinProject()->GetTotalFrames();
for (i32s loop = 0;loop < total_traj_frames; loop++)
{
//app->GetWinProject()->SetCurrentFrame(loop);
//this->ReadFrame();
//void project::ReadFrame(void)
//{
i32s place = GetTrajectoryHeaderSize(extended_trajectory); // skip the header...
place += GetTrajectoryFrameSize(extended_trajectory, natoms) * loop; // get the correct frame...
//place += GetTrajectoryEnergySize(); // skip epot and ekin...
trajfile->seekg(place, ios::beg);
trajfile->read((char *) & ekin, sizeof(ekin));
trajfile->read((char *) & epot, sizeof(epot));
i32s ind = 0;
mt_a1 = mt_a2 = mt_a3 = NULL;
for (iter_al it1 = mdl->GetAtomsBegin(); it1 != mdl->GetAtomsEnd(); it1++)
{
// if ((* it1).flags & ATOMFLAG_IS_HIDDEN) continue; // currently all coordinates are written...
float t1a;
fGL cdata[3];
for (i32s t4 = 0;t4 < 3;t4++)
{
trajfile->read((char *) & t1a, sizeof(t1a));
cdata[t4] = t1a;
}
if (extended_trajectory)
{
for (i32s t4 = 0;t4 < 3;t4++){
trajfile->read((char *) & t1a, sizeof(t1a));
//vdata[t4] = t1a;
}
for (i32s t4 = 0;t4 < 3;t4++){
trajfile->read((char *) & t1a, sizeof(t1a));
//adata[t4] = t1a;
}
for (i32s t4 = 0;t4 < 3;t4++){
trajfile->read((char *) & t1a, sizeof(t1a));
//fdata[t4] = t1a;
}
}
(* it1).SetCRD(0, cdata[0], cdata[1], cdata[2]);
if (ind == ind1)
{
mt_a1 = &(* it1);
}
if (ind == ind2)
{
mt_a2 = &(* it1);
}
/*if (ind == indc)
{
mt_a3 = &(* it1);
}*/
ind++;
}
//this->UpdateAllGraphicsViews();
//}
fGL coordinate;
if (mt_a1 && mt_a2 && dim >=0 && dim < 3)
{
const fGL * p1 = mt_a1->GetCRD(0);
const fGL * p2 = mt_a2->GetCRD(0);
// my measure
//cout << "el = " << mt_a1->el.GetSymbol() << " " << mt_a1->el.GetAtomicNumber() << " x = " << p1[0] << " y = " << p1[1] << " z = " << p1[2] << endl;
coordinate = p1[dim]-p2[dim];
}
else
coordinate = 0;
X[loop] = coordinate;
//ref->this->UpdateAllGraphicsViews(true);
//::Sleep(100);
//void * udata = convert_cset_to_plotting_udata(this, 0);
//f64 value = coordinate;
//plot->AddData(loop, value, udata);
//mt_a1 = mt_a2 = mt_a3 = NULL;
}
e_close_traj:
//app->GetWinProject()->CloseTrajectory();
if (trajfile != NULL)
{
trajfile->close();
delete trajfile;
trajfile = NULL;
}
}
}
