// zexit with error message
void zexit(std::string message){
// check calling of routine if error checking is activated
if(err::check==true){std::cout << "err::zexit(std::string) has been called" << std::endl;}
// Abort MPI processes for parallel execution
#ifdef MPICF
std::cerr << "Fatal error on rank " << vmpi::my_rank << ": " << message << std::endl;
std::cerr << "Aborting program." << std::endl;
zlog << zTs() << "Fatal error on rank " << vmpi::my_rank << ": " << message << std::endl;
zlog << zTs() << "Aborting program." << std::endl;
// concatenate log and sort
#ifdef WIN_COMPILE
system("type log.* 2>NUL | sort > log");
#else
system("ls log.* | xargs cat | sort -n > log");
#endif
MPI::COMM_WORLD.Abort(EXIT_FAILURE);
// MPI program dies ungracefully here
#else
// Print Error message to screen and log
std::cerr << "Fatal error: " << message << std::endl;
zlog << zTs() << "Fatal error: " << message << std::endl;
#endif
// Print error message to screen and log
zlog << zTs() << "Aborting program." << std::endl;
std::cout << "Aborting program. See log file for details." << std::endl;
// Now exit program disgracefully
exit(EXIT_FAILURE);
}
//------------------------------------------------------------------------------------------------------
// Function to initialize data structures
//------------------------------------------------------------------------------------------------------
void susceptibility_statistic_t::initialize(stats::magnetization_statistic_t& mag_stat) {
// Check that magnetization statistic is properly initialized
if(!mag_stat.is_initialized()){
terminaltextcolor(RED);
std::cerr << "Programmer Error - Uninitialized magnetization statistic passed to susceptibility statistic - please initialize first." << std::endl;
terminaltextcolor(WHITE);
zlog << zTs() << "Programmer Error - Uninitialized magnetization statistic passed to susceptibility statistic - please initialize first." << std::endl;
err::vexit();
}
// Determine number of magnetization statistics*4
std::vector<double> temp = mag_stat.get_magnetization();
num_elements = temp.size()/4;
// Now set number of susceptibility values to match
mean_susceptibility.resize(4*num_elements,0.0);
mean_susceptibility_squared.resize(4*num_elements,0.0);
mean_absolute_susceptibility.resize(4*num_elements,0.0);
mean_absolute_susceptibility_squared.resize(4*num_elements,0.0);
// copy saturation data
saturation = mag_stat.saturation;
// initialize mean counter
mean_counter = 0.0;
// Set flag indicating correct initialization
initialized=true;
}
//---------------------------------------------------------------------------
// Function to process material parameters
//---------------------------------------------------------------------------
bool match_material_parameter(std::string const word, std::string const value, std::string const unit, int const line, int const super_index, const int sub_index, const int max_materials){
// add prefix string
std::string prefix="material:";
// Check for empty material parameter array and resize to avoid segmentation fault
if(internal::mp.size() == 0){
internal::mp.resize(max_materials);
}
//------------------------------------------------------------
// Check for material properties
//------------------------------------------------------------
std::string test = "dmi-constant"; // short form
std::string test2 = "dzyaloshinskii-moriya-interaction-constant"; // long form
if( (word == test) || (word == test2) ){
double dmi = atof(value.c_str());
vin::check_for_valid_value(dmi, word, line, prefix, unit, "energy", -1e-17, 1e-17,"material"," < +/- 1.0e17");
internal::mp[super_index].dmi[sub_index] = dmi;
internal::enable_dmi = true; // Switch on dmi calculation and fully unrolled tensorial anisotropy
return true;
}
test = "exchange-matrix";
if(word==test){
// extract comma separated values from string
std::vector<double> Jij = vin::doubles_from_string(value);
if(Jij.size() == 1){
vin::check_for_valid_value(Jij[0], word, line, prefix, unit, "energy", -1e-18, 1e-18,"material"," < +/- 1.0e18");
// set all components in case vectorial form is needed later
vin::read_material[super_index].Jij_matrix_SI[sub_index][0] = Jij[0]; // Import exchange as field
vin::read_material[super_index].Jij_matrix_SI[sub_index][1] = Jij[0];
vin::read_material[super_index].Jij_matrix_SI[sub_index][2] = Jij[0];
return true;
}
else if(Jij.size() == 3){
vin::check_for_valid_vector(Jij, word, line, prefix, unit, "energy", -1e-18, 1e-18,"material"," < +/- 1.0e18");
vin::read_material[super_index].Jij_matrix_SI[sub_index][0] = Jij[0]; // Import exchange as field
vin::read_material[super_index].Jij_matrix_SI[sub_index][1] = Jij[1];
vin::read_material[super_index].Jij_matrix_SI[sub_index][2] = Jij[2];
// set vectorial anisotropy
internal::exchange_type = internal::vectorial;
return true;
}
else{
terminaltextcolor(RED);
std::cerr << "Error in input file - material[" << super_index << "]:exchange_matrix[" << sub_index << "] must have one or three values." << std::endl;
terminaltextcolor(WHITE);
zlog << zTs() << "Error in input file - material[" << super_index << "]:exchange_matrix[" << sub_index << "] must have one or three values." << std::endl;
err::vexit();
return false;
}
}
//--------------------------------------------------------------------
// Keyword not found
//--------------------------------------------------------------------
return false;
}
//-------------------------------------------------------------------------------
// Function to initialize create module
//-------------------------------------------------------------------------------
void initialize(){
// If create material parameters uninitialised then initialise with default parameters
if(create::internal::mp.size() == 0){
create::internal::mp.resize(mp::num_materials);
}
// Loop over materials to check for invalid input and warn appropriately
for(int mat=0;mat<mp::num_materials;mat++){
const double lmin=create::internal::mp[mat].min;
const double lmax=create::internal::mp[mat].max;
for(int nmat=0;nmat<mp::num_materials;nmat++){
if(nmat!=mat){
double min=create::internal::mp[nmat].min;
double max=create::internal::mp[nmat].max;
if(((lmin>min) && (lmin<max)) || ((lmax>min) && (lmax<max))){
terminaltextcolor(RED);
std::cerr << "Warning: Overlapping material heights found. Check log for details." << std::endl;
terminaltextcolor(WHITE);
zlog << zTs() << "Warning: material " << mat+1 << " overlaps material " << nmat+1 << "." << std::endl;
zlog << zTs() << "If you have defined geometry then this may be OK, or possibly you meant to specify alloy keyword instead." << std::endl;
zlog << zTs() << "----------------------------------------------------" << std::endl;
zlog << zTs() << " Material "<< mat+1 << ":minimum-height = " << lmin << std::endl;
zlog << zTs() << " Material "<< mat+1 << ":maximum-height = " << lmax << std::endl;
zlog << zTs() << " Material "<< nmat+1 << ":minimum-height = " << min << std::endl;
zlog << zTs() << " Material "<< nmat+1 << ":maximum-height = " << max << std::endl;
}
}
}
}
return;
}
//--------------------------------------------------
// Add point to list of input points
//
void lattice_anis_t::add_point(double temperature, double anisotropy){
// check for valid temperature value
if( temperature < 0.0 && temperature > 10000.0 ){
std::cerr << "Error: Temperature value " << temperature << " in lattice anisotropy file is invalid. Temperature values must be in the range 0 - 10000 K. Exiting." << std::endl;
zlog << zTs() << "Error: Temperature value " << temperature << " in lattice anisotropy file is invalid. Temperature values must be in the range 0 - 10000 K. Exiting." << std::endl;
err::vexit();
}
// add values to list
T.push_back(temperature);
k.push_back(anisotropy);
return;
}
/// Main function for vampire
/// Prints out program header and calls main program routines
int main(int argc, char* argv[]){
//=============================================================
// Check for valid command-line arguments
//=============================================================
std::string infile="input";
for(int arg = 1; arg < argc; arg++){
std::string sw=argv[arg];
// input file
if(sw=="-f"){
// check number of args not exceeded
if(arg+1 < argc){
arg++;
infile=string(argv[arg]);
}
else{
std::cerr << "Error - no file specified for \'-f\' command line option" << std::endl;
return EXIT_FAILURE;
}
}
else{
std::cerr << "Error - unknown command line parameter \'" << sw << "\'" << std::endl;
return EXIT_FAILURE;
}
}
// For parallel execution intialise MPI
#ifdef MPICF
vmpi::initialise();
#endif
// Initialise log file
vout::zLogTsInit(std::string(argv[0]));
// Output Program Header
if(vmpi::my_rank==0){
std::cout << " _ " << std::endl;
std::cout << " (_) " << std::endl;
std::cout << " __ ____ _ _ __ ___ _ __ _ _ __ ___ " << std::endl;
std::cout << " \\ \\ / / _` | '_ ` _ \\| '_ \\| | '__/ _ \\" << std::endl;
std::cout << " \\ V / (_| | | | | | | |_) | | | | __/" << std::endl;
std::cout << " \\_/ \\__,_|_| |_| |_| .__/|_|_| \\___|" << std::endl;
std::cout << " | | " << std::endl;
std::cout << " |_| " << std::endl;
std::cout << std::endl;
std::cout << " Version 3.0.3 " << __DATE__ << " " << __TIME__ << std::endl;
std::cout << std::endl;
std::cout << " Licensed under the GNU Public License(v2). See licence file for details." << std::endl;
std::cout << std::endl;
std::cout << " Lead Developer: Richard F L Evans <*****@*****.**>" << std::endl;
std::cout << std::endl;
std::cout << " Contributors: Weijia Fan, Phanwadee Chureemart, Joe Barker, " << std::endl;
std::cout << " Thomas Ostler, Andreas Biternas, Roy W Chantrell" << std::endl;
std::cout << " " << std::endl;
#ifdef COMP
std::cout << " Compiled with: " << COMP << std::endl;
#endif
std::cout << " Compiler Flags: ";
#ifdef CUDA
std::cout << "CUDA ";
#endif
#ifdef MPICF
std::cout << "MPI ";
#endif
std::cout << std::endl;
std::cout << std::endl;
std::cout << "================================================================================" << std::endl;
time_t rawtime = time(NULL);
struct tm * timeinfo = localtime(&rawtime);
std::cout<<asctime(timeinfo);
}
#ifdef MPICF
vmpi::hosts();
#endif
#ifdef MPICF
// nullify non root cout stream
if(vmpi::my_rank!=0){
vout::nullify(std::cout);
}
#endif
// Initialise system
mp::initialise(infile);
// Create system
cs::create();
// Simulate system
sim::run();
// Finalise MPI
#ifdef MPICF
vmpi::finalise();
// concatenate log, sort, and append departure message.
#ifdef WIN_COMPILE
if(vmpi::num_processors!=1 && vmpi::my_rank==0) system("type log.* 2>NUL | sort > log");
#else
if(vmpi::num_processors!=1 && vmpi::my_rank==0) system("ls log.* | xargs cat | sort -n > log");
#endif
#endif
zlog << zTs() << "Simulation ended gracefully." << std::endl;
std::cout << "Simulation ended gracefully." << std::endl;
return EXIT_SUCCESS;
}
int voronoi_film(std::vector<cs::catom_t> & catom_array){
// check calling of routine if error checking is activated
if(err::check==true){
terminaltextcolor(RED);
std::cerr << "cs::voronoi_film has been called" << std::endl;
terminaltextcolor(WHITE);
}
//====================================================================================
//
// voronoi
//
// Subroutine to create granular system using qhull voronoi generator
//
// Version 1.0 R Evans 16/07/2009
//
//====================================================================================
//
// Locally allocated variables: init_grain_coord_array
// init_grain_pointx_array
// init_grain_pointy_array
// init_num_assoc_vertices_array
//
//=====================================================================================
//---------------------------------------------------
// Local constants
//---------------------------------------------------
const int max_vertices=50;
double grain_sd=create_voronoi::voronoi_sd;
// Set number of particles in x and y directions
double size = create::internal::voronoi_grain_size + create::internal::voronoi_grain_spacing;
double grain_cell_size_x = size;
double grain_cell_size_y = sqrt(3.0)*size;
int num_x_particle = 4+2*vmath::iround(cs::system_dimensions[0]/(grain_cell_size_x));
int num_y_particle = 4+2*vmath::iround(cs::system_dimensions[1]/(grain_cell_size_y));
int init_num_grains = num_x_particle*num_y_particle*2;
// Define initial grain arrays
std::vector <std::vector <double> > grain_coord_array;
std::vector <std::vector <std::vector <double> > > grain_vertices_array;
// Reserve space for pointers
grain_coord_array.reserve(init_num_grains);
grain_vertices_array.reserve(init_num_grains);
// Calculate pointers
for(int grain=0;grain<init_num_grains;grain++){
grain_coord_array.push_back(std::vector <double>());
grain_coord_array[grain].reserve(2);
grain_vertices_array.push_back(std::vector <std::vector <double> >());
//for(int vertex=0;vertex<max_vertices;vertex++){
// grain_vertices_array[grain].push_back(std::vector <double>());
// grain_vertices_array[grain][vertex].reserve(2);
//}
//std::cout << grain_vertices_array[grain].size() << " " << grain_vertices_array[grain].capacity() << std::endl;
}
//std::cin.get();
double delta_particle_x = grain_cell_size_x;
double delta_particle_y = grain_cell_size_y;
double delta_particle_x_parity = delta_particle_x*0.5;
double delta_particle_y_parity = delta_particle_y*0.5;
// Set voronoi seed;
mtrandom::grnd.seed(mtrandom::voronoi_seed);
// Loop to generate hexagonal lattice points
double particle_coords[2];
int vp=int(create_voronoi::parity);
int grain=0;
for (int x_particle=0;x_particle < num_x_particle;x_particle++){
for (int y_particle=0;y_particle < num_y_particle;y_particle++){
for (int particle_parity=0;particle_parity<2;particle_parity++){
//particle_coords[0] = (particle_parity)*delta_particle_x_parity + delta_particle_x*x_particle-size + vp*double(1-2*particle_parity)*delta_particle_x_parity;
//particle_coords[1] = (particle_parity)*delta_particle_y_parity + delta_particle_y*y_particle-size;
particle_coords[0] = (particle_parity)*delta_particle_x_parity + delta_particle_x*x_particle + vp*double(1-2*particle_parity)*delta_particle_x_parity;
particle_coords[1] = (particle_parity)*delta_particle_y_parity + delta_particle_y*y_particle;
grain_coord_array[grain].push_back(particle_coords[0]+grain_sd*mtrandom::gaussian()*delta_particle_x);
grain_coord_array[grain].push_back(particle_coords[1]+grain_sd*mtrandom::gaussian()*delta_particle_y);
grain++;
}
}
}
//-----------------------
// Check for grains >=1
//-----------------------
if(grain<1){
terminaltextcolor(RED);
std::cerr << "Error! - No grains found in structure - Increase system dimensions" << std::endl;
terminaltextcolor(WHITE);
zlog << zTs() << "Error! - No grains found in structure - Increase system dimensions" << std::endl;
err::vexit();
}
// Calculate Voronoi construction using qhull removing boundary grains (false)
create::internal::populate_vertex_points(grain_coord_array, grain_vertices_array, false);
// Shrink Voronoi vertices in reduced coordinates to get spacing
double shrink_factor = create::internal::voronoi_grain_size/(create::internal::voronoi_grain_size+create::internal::voronoi_grain_spacing);
// Reduce vertices to relative coordinates
for(unsigned int grain=0;grain<grain_coord_array.size();grain++){
//grain_coord_array[grain][0]=0.0;
//grain_coord_array[grain][1]=0.0;
const int nv = grain_vertices_array[grain].size();
// Exclude grains with zero vertices
if(nv!=0){
for(int vertex=0;vertex<nv;vertex++){
double vc[2]; // vertex coordinates
vc[0]=shrink_factor*(grain_vertices_array[grain][vertex][0]-grain_coord_array[grain][0]);
vc[1]=shrink_factor*(grain_vertices_array[grain][vertex][1]-grain_coord_array[grain][1]);
grain_vertices_array[grain][vertex][0]=vc[0];
grain_vertices_array[grain][vertex][1]=vc[1];
}
}
}
// round grains if necessary
if(create_voronoi::rounded) create::internal::voronoi_grain_rounding(grain_coord_array, grain_vertices_array);
// Create a 2D supercell array of atom numbers to improve performance for systems with many grains
std::vector < std::vector < std::vector < int > > > supercell_array;
int min_bounds[3];
int max_bounds[3];
min_bounds[0]=0;
min_bounds[1]=0;
min_bounds[2]=0;
max_bounds[0]=cs::total_num_unit_cells[0];
max_bounds[1]=cs::total_num_unit_cells[1];
max_bounds[2]=cs::total_num_unit_cells[2];
// allocate supercell array
int dx = max_bounds[0]-min_bounds[0];
int dy = max_bounds[1]-min_bounds[1];
supercell_array.resize(dx);
for(int i=0;i<dx;i++) supercell_array[i].resize(dy);
// loop over atoms and populate supercell array
for(unsigned int atom=0;atom<catom_array.size();atom++){
int cx = int (catom_array[atom].x/unit_cell.dimensions[0]);
int cy = int (catom_array[atom].y/unit_cell.dimensions[1]);
supercell_array.at(cx).at(cy).push_back(atom);
}
// Determine order for core-shell grains
std::list<create::internal::core_radius_t> material_order(0);
for(int mat=0;mat<mp::num_materials;mat++){
create::internal::core_radius_t tmp;
tmp.mat=mat;
tmp.radius=mp::material[mat].core_shell_size;
material_order.push_back(tmp);
}
// sort by increasing radius
material_order.sort(create::internal::compare_radius);
std::cout <<"Generating Voronoi Grains";
zlog << zTs() << "Generating Voronoi Grains";
// arrays to store list of grain vertices
double tmp_grain_pointx_array[max_vertices];
double tmp_grain_pointy_array[max_vertices];
// loop over all grains with vertices
for(unsigned int grain=0;grain<grain_coord_array.size();grain++){
// Exclude grains with zero vertices
if((grain%(grain_coord_array.size()/10))==0){
std::cout << "." << std::flush;
zlog << "." << std::flush;
}
if(grain_vertices_array[grain].size()!=0){
// initialise minimum and max supercell coordinates for grain
int minx=10000000;
int maxx=0;
int miny=10000000;
int maxy=0;
// Set temporary vertex coordinates (real) and compute cell ranges
int num_vertices = grain_vertices_array[grain].size();
for(int vertex=0;vertex<num_vertices;vertex++){
// determine vertex coordinates
tmp_grain_pointx_array[vertex]=grain_vertices_array[grain][vertex][0];
tmp_grain_pointy_array[vertex]=grain_vertices_array[grain][vertex][1];
// determine unit cell coordinates encompassed by grain
int x = int((tmp_grain_pointx_array[vertex]+grain_coord_array[grain][0])/unit_cell.dimensions[0]);
int y = int((tmp_grain_pointy_array[vertex]+grain_coord_array[grain][1])/unit_cell.dimensions[1]);
if(x < minx) minx = x;
if(x > maxx) maxx = x;
if(y < miny) miny = y;
if(y > maxy) maxy = y;
}
// determine coordinate offset for grains
const double x0 = grain_coord_array[grain][0];
const double y0 = grain_coord_array[grain][1];
// loopover cells
for(int i=minx;i<=maxx;i++){
for(int j=miny;j<=maxy;j++){
// loop over atoms in cells;
for(unsigned int id=0;id<supercell_array[i][j].size();id++){
int atom = supercell_array[i][j][id];
// Get atomic position
double x = catom_array[atom].x;
double y = catom_array[atom].y;
if(mp::material[catom_array[atom].material].core_shell_size>0.0){
// Iterate over materials
for(std::list<create::internal::core_radius_t>::iterator it = material_order.begin(); it != material_order.end(); it++){
int mat = (it)->mat;
double factor = mp::material[mat].core_shell_size;
double maxz=create::internal::mp[mat].max*cs::system_dimensions[2];
double minz=create::internal::mp[mat].min*cs::system_dimensions[2];
double cz=catom_array[atom].z;
const int atom_uc_cat = catom_array[atom].uc_category;
const int mat_uc_cat = create::internal::mp[mat].unit_cell_category;
// check for within core shell range
if(vmath::point_in_polygon_factor(x-x0,y-y0,factor, tmp_grain_pointx_array,tmp_grain_pointy_array,num_vertices)==true){
if((cz>=minz) && (cz<maxz) && (atom_uc_cat == mat_uc_cat) ){
catom_array[atom].include=true;
catom_array[atom].material=mat;
catom_array[atom].grain=grain;
}
// if set to clear atoms then remove atoms within radius
else if(cs::fill_core_shell==false){
catom_array[atom].include=false;
}
}
}
}
// Check to see if site is within polygon
else if(vmath::point_in_polygon_factor(x-x0,y-y0,1.0,tmp_grain_pointx_array,tmp_grain_pointy_array,num_vertices)==true){
catom_array[atom].include=true;
catom_array[atom].grain=grain;
}
}
}
}
}
}
terminaltextcolor(GREEN);
std::cout << "done!" << std::endl;
terminaltextcolor(WHITE);
zlog << "done!" << std::endl;
// add final grain for continuous layer
grain_coord_array.push_back(std::vector <double>());
grain_coord_array[grain_coord_array.size()-1].push_back(0.0); // x
grain_coord_array[grain_coord_array.size()-1].push_back(0.0); // y
// check for continuous layer
for(unsigned int atom=0; atom < catom_array.size(); atom++){
if(mp::material[catom_array[atom].material].continuous==true && catom_array[atom].include == false ){
catom_array[atom].include=true;
catom_array[atom].grain=int(grain_coord_array.size()-1);
}
}
// set number of grains
grains::num_grains = int(grain_coord_array.size());
// sort atoms by grain number
sort_atoms_by_grain(catom_array);
return EXIT_SUCCESS;
}
//--------------------------------------------------
// Creates a lookup table of interpolated functions
// to calculate lattice anisotropy
//
void lattice_anis_t::set_interpolation_table(){
// Output informative message to log
zlog << zTs() << "Determining interpolation variables for tabulated lattice anisotropy." << std::endl;
// Check for undefined lattice anisotropy
if(T.size()==0){
Tmax=0;
k_Tmax=0.0;
return;
}
// check T(i+1) > T(i)
for(unsigned int i=1; i<T.size(); i++){
if(T[i]<T[i-1]){
std::cerr << "Error: temperature value "<< T[i] <<" on line " << i+2 << " is less than the previous value " << T[i-1] << " and must be given in ascending order. Exiting" << std::endl;
zlog << zTs() << "Error: temperature value "<< T[i] <<" on line " << i+2 << " is less than the previous value " << T[i-1] << " and must be given in ascending order. Exiting" << std::endl;
err::vexit();
}
}
// loop over all temperatures up to Tmax and create temporary list of min, max, m and c values
std::vector<double> tmin;
std::vector<double> tmax;
std::vector<double> tm;
std::vector<double> tc;
// start from i+1
for(unsigned int i=1; i<T.size(); i++){
tmin.push_back(T[i-1]);
tmax.push_back(T[i]);
tm.push_back(vmath::interpolate_m(T[i-1],k[i-1],T[i],k[i]));
tc.push_back(vmath::interpolate_c(T[i-1],k[i-1],T[i],k[i]));
}
// determine maximum temperature specified in interpolation table
Tmax=int(T[T.size()-1]);
// resize interpolation array to size Tmax
m.resize(Tmax,0.0);
c.resize(Tmax,0.0);
// determine last value of k at Tmax
k_Tmax = k[k.size()-1];
// determine first value of k
double k_Tmin = k[0];
double Tmin = T[0];
// loop over all values up to Tmax and substitute m and c interpolation
for(unsigned int Ti=0; Ti<Tmax; Ti++){ // 1 Kelvin resolution
bool found_mc=false;
// Check for T<Tmin
if(double(Ti)<double(Tmin)){
m[Ti] = 0;
c[Ti] = k_Tmin;
//mark valid value found
found_mc = true;
// move to next temperature value
continue;
}
// loop over all possible values
for(unsigned int mm=0; mm<tmin.size(); mm++){
double min = tmin[mm];
double max = tmax[mm];
// check if Ti is in temperature range
if( double(Ti) >= min && double(Ti) < max ){
// copy interpolation values
m[Ti] = tm[mm];
c[Ti] = tc[mm];
// mark valid function found
found_mc = true;
// move to next temperature value Ti
break;
}
}
// check for value not in range
if(found_mc==false){
std::cerr << "Code error: Temperature value " << Ti << " in interpolation function is not within range specified in lattice-anisotropy-file. Exiting" << std::endl;
zlog << zTs() << "Code error: Temperature value " << Ti << " in interpolation function is not within range specified in lattice-anisotropy-file. Exiting" << std::endl;
err::vexit();
}
}
return;
}
//---------------------------------------------------------------------------------------------------------------------
// Setting algorithm for exchange bias in IrMn3
//---------------------------------------------------------------------------------------------------------------------
void setting_process(){
//Arrays to determine the 8 possible ground state spin orientations configurations
double Configurations[8][3] = {
{0, 0, -1},
{-0.94, 0, 0.3},
{0.44, -0.845, 0.3},
{0.44, 0.845, 0.3},
{0, 0, 1},
{0.94, 0, -0.3},
{-0.44, 0.845, -0.3},
{-0.44, -0.845, -0.3}
};
// List the 8 possible combinations of spin orientation
double Possible_Arrays[8][4] = {
{0,1,2,3},
{1,0,3,2},
{2,3,0,1},
{3,2,1,0},
{4,5,6,7},
{5,4,7,6},
{6,7,4,5},
{7,6,5,4}
};
std::vector< std::vector <int> > No_in_Sublattice;
// Number sublattices in each grain
No_in_Sublattice.resize(4);
// resize array for correct number of atoms in each grain
// std::cout << grains::num_grains <<std::endl;
for(int i = 0; i < 4; i++) No_in_Sublattice[i].resize(grains::num_grains,0.0);
std::vector <int> Local_Sub (grains::num_grains*4,0);
std::vector <int> Chosen_array(grains::num_grains,0);
std::vector <int> Largest_Sublattice(grains::num_grains,0);
std::vector <int> Max_atoms(grains::num_grains,0);
#ifdef MPICF
stats::num_atoms = vmpi::num_core_atoms+vmpi::num_bdry_atoms;
#else
stats::num_atoms = atoms::num_atoms;
#endif
std::cerr << "A" << stats::num_atoms << "\t" << grains::num_grains << std::endl;
//Calculates how many atoms are in the top layer of each sublattice in each grain.
for (int atom = 0; atom < stats::num_atoms; atom++){
for (int neighbour = atoms::neighbour_list_start_index[atom]; neighbour < atoms::neighbour_list_end_index[atom]; neighbour ++){
// explain what if statement is testing - yes Sarah...
//std::cout << atom << "\t" << neighbour <<atoms::type_array[atom] << '\t' << atoms::type_array[atoms::neighbour_list_array[neighbour]] << std::endl;
if ((atoms::type_array[atom] >3) && (atoms::type_array[atoms::neighbour_list_array[neighbour]] < 4)){
// std::cerr << atoms::grain_array[atom] << "\t"<< atoms::type_array[atoms::neighbour_list_array[neighbour]] << "\t" << atoms::type_array[atom] <<endl;
No_in_Sublattice[atoms::type_array[atoms::neighbour_list_array[neighbour]]][atoms::grain_array[atom]]++;
// cerr << No_in_Sublattice[atoms::type_array[atoms::neighbour_list_array[neighbour]]][atoms::grain_array[atom]]<<endl;
}
}
}
int k = 0;
for (int j = 0; j < grains::num_grains; j ++){
for (int i = 0; i < 4; i ++){
Local_Sub[k] = No_in_Sublattice[i][j];
k++;
}
}
std::cerr << "before" << Local_Sub[0] << '\t' << Local_Sub[1] << '\t' << Local_Sub[2] << '\t' << Local_Sub[3] << std::endl;
#ifdef MPICF
MPI_Allreduce(MPI_IN_PLACE, &Local_Sub[0],grains::num_grains*4,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
#endif
std::cerr<< "after" << Local_Sub[0] << '\t' << Local_Sub[1] << '\t' << Local_Sub[2] << '\t' << Local_Sub[3] << std::endl;
int l =0;
//calculates which sublattice contains the most atoms for each grain.
for (int j = 0; j < grains::num_grains; j++){
for( int i = 0; i <4; i ++){
// std::cout << Local_Sub[l] << "\t" << Local_Sub[l] << std::endl;
if ((Local_Sub[l] > Max_atoms[j]) & (Local_Sub[l] != 0)){
Largest_Sublattice[j] = i;
Max_atoms[j] =Local_Sub[l];
}
l++;
}
if (Local_Sub[l-1] !=0 ) cerr << Largest_Sublattice[j] <<endl;
}
int j = 0;
for (int i = 0; i < grains::num_grains*4; i= i +4){
if (Local_Sub[i] != 0){
cerr <<"number in each sublattice for grain" << j << ";" << Local_Sub[i] << "\t" << Local_Sub[i +1] << "\t" << Local_Sub[i+2] << "\t" << Local_Sub[i+3] << "\t" << std::endl;
zlog << zTs() <<"number in each sublattice for grain" << j << ";" << Local_Sub[i] << "\t" << Local_Sub[i +1] << "\t" << Local_Sub[i+2] << "\t" << Local_Sub[i+3] << "\t" << std::endl;
j++;
}
}
double result,angle;
double min_angle = 1000;
double Direction_Closest_to_Field;
//Loop over all possible combinations to calculate which possible vector is closest to the applied field.
for (int i = 0; i < 8; i ++){
result = Configurations[i][0]*sim::H_vec[0] + Configurations[i][1]*sim::H_vec[1] + Configurations[i][2]*sim::H_vec[2];
angle = acos(result);
//Calculates the minimum angle between the applied field and the spin directions.
if ( angle< min_angle){
Direction_Closest_to_Field = i;
min_angle = angle;
}
}
// std::cout << Direction_Closest_to_Field <<std::endl;
//Sets the sublattice with the largest number of atoms along the direction nearest the field
//This minimises S.H
for (int j = 0; j < grains::num_grains; j ++){
for (int i = 0; i <8; i ++){
if (Possible_Arrays[i][Largest_Sublattice[j]] == Direction_Closest_to_Field){
// std::cout << i <<std::endl;
Chosen_array[j] = i;
break;
}
}
}
std::cout << "a" <<std::endl;
for (int i = 0; i <stats::num_atoms; i++){
// std::cout << atoms::type_array[i] << "\t" << atoms::z_spin_array[i] <<std::endl;
if(atoms::type_array[i] > 3){
atoms::x_spin_array[i] = sim::H_vec[0];
atoms::y_spin_array[i] = sim::H_vec[1];
atoms::z_spin_array[i] = sim::H_vec[2];
}
else {
int Array = Possible_Arrays[Chosen_array[atoms::grain_array[i]]][atoms::type_array[i]];
atoms::x_spin_array[i] = Configurations[Array][0];
atoms::y_spin_array[i] = Configurations[Array][1];
atoms::z_spin_array[i] = Configurations[Array][2];
}
}
// Calculate magnetisation statistics
stats::mag_m();
// Output data
vout::data();
}
/// @brief Cell initialiser function /// /// @details Determines number of cells, assigns atoms to cells, and sets up cell arrays /// /// @section License /// Use of this code, either in source or compiled form, is subject to license from the authors. /// Copyright \htmlonly © \endhtmlonly Richard Evans, 2009-2011. All Rights Reserved. /// /// @section Information /// @author Richard Evans, [email protected] /// @version 1.0 /// @date 28/03/2011 /// /// @return EXIT_SUCCESS /// /// @internal /// Created: 05/02/2011 /// Revision: --- ///===================================================================================== /// int initialise(){ // check calling of routine if error checking is activated if(err::check==true) std::cout << "cells::initialise has been called" << std::endl; cells::num_cells=0; cells::num_local_cells=0; zlog << zTs() << "Cell size = " << cells::size << std::endl; // determine number of cells in each direction (with small shift to prevent the fence post problem) unsigned int ncellx = static_cast<unsigned int>(ceil((cs::system_dimensions[0]+0.01)/cells::size)); unsigned int ncelly = static_cast<unsigned int>(ceil((cs::system_dimensions[1]+0.01)/cells::size)); unsigned int ncellz = static_cast<unsigned int>(ceil((cs::system_dimensions[2]+0.01)/cells::size)); //update total number of cells cells::num_cells=ncellx*ncelly*ncellz; zlog << zTs() << "Cells in x,y,z: " << ncellx << "\t" << ncelly << "\t" << ncellz << std::endl; zlog << zTs() << "Total number of cells: " << cells::num_cells << std::endl; zlog << zTs() << "Memory required for cell arrays: " << 80.0*double(cells::num_cells)/1.0e6 << " MB" << std::endl; // Determine number of cells in x,y,z const int d[3]={ncellx,ncelly,ncellz}; // Set cell counter int cell=0; // Declare array for create space for 3D supercell array int*** supercell_array; //std::cout << "Memory required for cell list calculation:" << 8.0*double(d[0])*double(d[1])*double(d[2])/1.0e6 << " MB" << std::endl; try{supercell_array=new int**[d[0]]; for(int i=0; i<d[0] ; i++){ supercell_array[i]=new int*[d[1]]; for(int j=0; j<d[1] ; j++){ supercell_array[i][j]=new int[d[2]]; for(int k=0; k<d[2] ; k++){ supercell_array[i][j][k]=cell; cell++; } } } } catch(...){std::cerr << "Error allocating supercell_array for cell list calculation" << std::endl;err::vexit();} // slightly offset atomic coordinates to prevent fence post problem double atom_offset[3]={0.01,0.01,0.01}; // For MPI version, only add local atoms #ifdef MPICF int num_local_atoms = vmpi::num_core_atoms+vmpi::num_bdry_atoms; #else int num_local_atoms = atoms::num_atoms; #endif // Assign atoms to cells for(int atom=0;atom<num_local_atoms;atom++){ double c[3]={atoms::x_coord_array[atom]+atom_offset[0],atoms::y_coord_array[atom]+atom_offset[1],atoms::z_coord_array[atom]+atom_offset[2]}; int scc[3]={0,0,0}; // super cell coordinates for(int i=0;i<3;i++){ scc[i]=int(c[i]/cells::size); // Always round down for supercell coordinates // Always check cell in range if(scc[i]<0 || scc[i]>= d[i]){ std::cerr << "Error - atom out of supercell range in neighbourlist calculation!" << std::endl; #ifdef MPICF std::cerr << "\tCPU Rank: " << vmpi::my_rank << std::endl; #endif std::cerr << "\tAtom number: " << atom << std::endl; std::cerr << "\tAtom coordinates: " << c[0] << "\t" << c[1] << "\t" << c[2] << "\t" << std::endl; std::cerr << "\tCell coordinates: " << scc[0] << "\t" << scc[1] << "\t" << scc[2] << "\t" << std::endl; std::cerr << "\tCell maxima: " << d[0] << "\t" << d[1] << "\t" << d[2] << std::endl; err::vexit(); } } // If no error for range then assign atom to cell. atoms::cell_array[atom]=supercell_array[scc[0]][scc[1]][scc[2]]; } // Deallocate supercell array try{ for(int i=0; i<d[0] ; i++){ for(int j=0; j<d[1] ;j++){ delete [] supercell_array[i][j]; } delete [] supercell_array[i]; } delete [] supercell_array; supercell_array=NULL; } catch(...){zlog << zTs() << "error deallocating supercell_array" << std::endl; err::vexit();} // Resize new cell arrays cells::x_coord_array.resize(cells::num_cells,0.0); cells::y_coord_array.resize(cells::num_cells,0.0); cells::z_coord_array.resize(cells::num_cells,0.0); cells::x_mag_array.resize(cells::num_cells,0.0); cells::y_mag_array.resize(cells::num_cells,0.0); cells::z_mag_array.resize(cells::num_cells,0.0); cells::x_field_array.resize(cells::num_cells,0.0); cells::y_field_array.resize(cells::num_cells,0.0); cells::z_field_array.resize(cells::num_cells,0.0); cells::num_atoms_in_cell.resize(cells::num_cells,0); cells::volume_array.resize(cells::num_cells,0.0); std::vector<double> total_moment_array(cells::num_cells,0.0); // Now add atoms to each cell as magnetic 'centre of mass' for(int atom=0;atom<num_local_atoms;atom++){ int local_cell=atoms::cell_array[atom]; int type = atoms::type_array[atom]; const double mus = mp::material[type].mu_s_SI; cells::x_coord_array[local_cell]+=atoms::x_coord_array[atom]*mus; cells::y_coord_array[local_cell]+=atoms::y_coord_array[atom]*mus; cells::z_coord_array[local_cell]+=atoms::z_coord_array[atom]*mus; total_moment_array[local_cell]+=mus; cells::num_atoms_in_cell[local_cell]++; } // For MPI sum coordinates from all CPUs #ifdef MPICF MPI::COMM_WORLD.Allreduce(MPI_IN_PLACE,&cells::num_atoms_in_cell[0],cells::num_cells,MPI_INT,MPI_SUM); MPI::COMM_WORLD.Allreduce(MPI_IN_PLACE,&cells::x_coord_array[0],cells::num_cells,MPI_DOUBLE,MPI_SUM); MPI::COMM_WORLD.Allreduce(MPI_IN_PLACE,&cells::y_coord_array[0],cells::num_cells,MPI_DOUBLE,MPI_SUM); MPI::COMM_WORLD.Allreduce(MPI_IN_PLACE,&cells::z_coord_array[0],cells::num_cells,MPI_DOUBLE,MPI_SUM); MPI::COMM_WORLD.Allreduce(MPI_IN_PLACE,&total_moment_array[0],cells::num_cells,MPI_DOUBLE,MPI_SUM); #endif //if(vmpi::my_rank==0){ //vinfo << "=========================================================================" << std::endl; //vinfo << "Number of atoms/cell: cell number, num atoms, coord" << std::endl; //vinfo << "=========================================================================" << std::endl; //} // Used to calculate magnetisation in each cell. Poor approximation when unit cell size ~ system size. const double atomic_volume = cs::unit_cell.dimensions[0]*cs::unit_cell.dimensions[1]*cs::unit_cell.dimensions[2]/cells::num_atoms_in_unit_cell; // Now find mean coordinates via magnetic 'centre of mass' for(int local_cell=0;local_cell<cells::num_cells;local_cell++){ if(cells::num_atoms_in_cell[local_cell]>0){ cells::x_coord_array[local_cell] = cells::x_coord_array[local_cell]/(total_moment_array[local_cell]); cells::y_coord_array[local_cell] = cells::y_coord_array[local_cell]/(total_moment_array[local_cell]); cells::z_coord_array[local_cell] = cells::z_coord_array[local_cell]/(total_moment_array[local_cell]); cells::volume_array[local_cell] = double(cells::num_atoms_in_cell[local_cell])*atomic_volume; } //if(vmpi::my_rank==0){ //vinfo << local_cell << "\t" << cells::num_atoms_in_cell[local_cell] << "\t"; //vinfo << cells::x_coord_array[local_cell] << "\t" << cells::y_coord_array[local_cell]; //vinfo << "\t" << cells::z_coord_array[local_cell] << "\t" << std::endl; //} } //Set number of atoms in cell to zero for(int cell=0;cell<cells::num_cells;cell++){ cells::num_atoms_in_cell[cell]=0; } // Now re-update num_atoms in cell for local atoms only for(int atom=0;atom<num_local_atoms;atom++){ int local_cell=atoms::cell_array[atom]; cells::num_atoms_in_cell[local_cell]++; } // Calculate number of local cells for(int cell=0;cell<cells::num_cells;cell++){ if(cells::num_atoms_in_cell[cell]!=0){ cells::local_cell_array.push_back(cell); cells::num_local_cells++; } } zlog << zTs() << "Number of local cells on rank " << vmpi::my_rank << ": " << cells::num_local_cells << std::endl; cells::initialised=true; // Precalculate cell magnetisation cells::mag(); return EXIT_SUCCESS; }
//------------------------------------------------------------------------------
// Function to calculate neighbour interactions assuming fractional unit cell
//------------------------------------------------------------------------------
void calculate_interactions(unit_cell_t& unit_cell){
// determine neighbour range
const double rcut = unit_cell.cutoff_radius*exchange_interaction_range*1.001; // reduced to unit cell units
const double rcutsq = rcut*rcut; // reduced to unit cell units
// temporary for unit cell size
const double ucsx = unit_cell.dimensions[0];
const double ucsy = unit_cell.dimensions[1];
const double ucsz = unit_cell.dimensions[2];
// determine number of unit cells in x,y and z
const int nx = 1 + 2*ceil(rcut); // number of replicated cells in x,y,z
const int ny = 1 + 2*ceil(rcut);
const int nz = 1 + 2*ceil(rcut);
zlog << zTs() << "Generating neighbour interactions for a lattice of " << nx << " x " << ny << " x " << nz << " unit cells for neighbour calculation" << std::endl;
// temporary array for replicated atoms
std::vector<local::atom_t> ratoms;
// replicate in x,y,z
for(int x = 0; x < nx; ++x){
for(int y = 0; y < ny; ++y){
for(int z = 0; z < nz; ++z){
for(int a=0; a < unit_cell.atom.size(); ++a){
local::atom_t tmp;
tmp.mat = unit_cell.atom[a].mat;
tmp.x = (unit_cell.atom[a].x + double(x))*ucsx;
tmp.y = (unit_cell.atom[a].y + double(y))*ucsy;
tmp.z = (unit_cell.atom[a].z + double(z))*ucsz;
tmp.id = a;
tmp.idx = x; // unit cell id
tmp.idy = y;
tmp.idz = z;
ratoms.push_back(tmp);
}
}
}
}
// calculate neighbours and exchange for central cell
int mid_cell_x = (nx-1)/2;
int mid_cell_y = (ny-1)/2;
int mid_cell_z = (nz-1)/2;
const double nnrcut_sq = unit_cell.cutoff_radius*unit_cell.cutoff_radius*1.001*1.001; // nearest neighbour cutoff radius
// loop over all i atoms
for(int i=0; i < ratoms.size(); ++i){
// check for i atoms only in central cell
if( (ratoms[i].idx == mid_cell_x) && (ratoms[i].idy == mid_cell_y) && (ratoms[i].idz == mid_cell_z) ){
// loop over all j atoms
for(int j=0; j < ratoms.size(); ++j){
// calculate interatomic radius_sq
const double rx = ratoms[j].x - ratoms[i].x;
const double ry = ratoms[j].y - ratoms[i].y;
const double rz = ratoms[j].z - ratoms[i].z;
double range_sq = rx*rx + ry*ry + rz*rz;
// check for rij < rcut and i!= j
if( range_sq < rcutsq && i != j ){
// Neighbour found
uc::interaction_t tmp;
// Determine unit cell id for i and j atoms
tmp.i = ratoms[i].id;
tmp.j = ratoms[j].id;
// Determine unit cell offsets
tmp.dx = ratoms[j].idx - ratoms[i].idx;
tmp.dy = ratoms[j].idy - ratoms[i].idy;
tmp.dz = ratoms[j].idz - ratoms[i].idz;
// save interaction range
tmp.rij = sqrt(range_sq);
// Determine normalised exchange constants
tmp.Jij[0][0] = uc::internal::exchange(range_sq, nnrcut_sq); // xx
tmp.Jij[0][1] = 0.0; // xy
tmp.Jij[0][2] = 0.0; // xz
tmp.Jij[1][0] = 0.0; // yx
tmp.Jij[1][1] = uc::internal::exchange(range_sq, nnrcut_sq); // yy
tmp.Jij[1][2] = 0.0; // yz
tmp.Jij[2][0] = 0.0; // zx
tmp.Jij[2][1] = 0.0; // zy
tmp.Jij[2][2] = uc::internal::exchange(range_sq, nnrcut_sq); // zz
unit_cell.interaction.push_back(tmp);
}
}
}
}
// Set calculated interactions range
int interaction_range=0;
for(int i=0; i<unit_cell.interaction.size(); i++){
if(abs(unit_cell.interaction[i].dx)>interaction_range) interaction_range=abs(unit_cell.interaction[i].dx);
if(abs(unit_cell.interaction[i].dy)>interaction_range) interaction_range=abs(unit_cell.interaction[i].dy);
if(abs(unit_cell.interaction[i].dz)>interaction_range) interaction_range=abs(unit_cell.interaction[i].dz);
}
unit_cell.interaction_range = interaction_range;
// Normalise exchange interactions
uc::internal::normalise_exchange(unit_cell);
// Output interactions to screen
/*for(int i=0; i<unit_cell.interaction.size(); i++){
std::cerr << i << "\t" << unit_cell.interaction[i].i << "\t"
<< unit_cell.interaction[i].j << "\t"
<< unit_cell.interaction[i].dx << "\t"
<< unit_cell.interaction[i].dy << "\t"
<< unit_cell.interaction[i].dz << "\t"
<< unit_cell.interaction[i].rij << "\t"
<< unit_cell.interaction[i].Jij[0][0] << std::endl;
}*/
// Check for interactions
if(unit_cell.interaction.size()==0){
terminaltextcolor(RED);
std::cerr << "Error! No interactions generated for " << uc::internal::crystal_structure << " crystal structure. Try increasing the interaction range. Aborting." << std::endl;
terminaltextcolor(WHITE);
zlog << zTs() << "Error! No interactions generated for " << uc::internal::crystal_structure << " crystal structure. Try increasing the interaction range. Aborting." << std::endl;
err::vexit();
}
// Determine exchange type
if(uc::internal::exchange_type == isotropic) unit_cell.exchange_type=-1;
else if(uc::internal::exchange_type == vectorial) unit_cell.exchange_type=3;
else{
terminaltextcolor(RED);
std::cerr << "Programmer error! Exchange type " << uc::internal::exchange_type << " is not a recognised value!" << std::endl;
terminaltextcolor(WHITE);
zlog << zTs() << "Programmer error! Exchange type " << uc::internal::exchange_type << " is not a recognised value!" << std::endl;
err::vexit();
}
return;
}
//------------------------------------------------------------------------------
// Function to output non-magnetic atomic positions to disk
//------------------------------------------------------------------------------
void atoms_non_magnetic(){
//------------------------------------------------------------
// Determine non magnetic atoms to be outputted to coord list
//------------------------------------------------------------
// array of atom numbers to be outputted
std::vector<uint64_t> atom_list(0);
// get output bounds
const double minB[3] = {atoms_output_min[0] * cs::system_dimensions[0],
atoms_output_min[1] * cs::system_dimensions[1],
atoms_output_min[2] * cs::system_dimensions[2]};
const double maxB[3] = {atoms_output_max[0] * cs::system_dimensions[0],
atoms_output_max[1] * cs::system_dimensions[1],
atoms_output_max[2] * cs::system_dimensions[2]};
// Determine non magnetic atoms to be outputted to coord list
for (uint64_t atom = 0; atom < cs::non_magnetic_atoms_array.size(); atom++){
const double cc[3] = {cs::non_magnetic_atoms_array[atom].x, cs::non_magnetic_atoms_array[atom].y, cs::non_magnetic_atoms_array[atom].z};
// check atom within output bounds
if ( (cc[0] >= minB[0]) && (cc[0] <= maxB[0]) ){
if ( (cc[1] >= minB[1]) && (cc[1] <= maxB[1]) ){
if ( (cc[2] >= minB[2]) && (cc[2] <= maxB[2]) ){
atom_list.push_back(atom); //non-magnetic atoms
}
}
}
}
//------------------------------------------------
// Create temporary buffers for atom information
//------------------------------------------------
uint64_t num_local_atoms = atom_list.size();
uint64_t num_total_atoms = 0; // number of atoms across all processors
#ifdef MPICF
// calculate number of atoms to be output on all processors
MPI_Allreduce(&num_local_atoms, &num_total_atoms, 1, MPI_UINT64_T, MPI_SUM, MPI_COMM_WORLD);
#else
num_total_atoms = num_local_atoms;
#endif
std::vector<int> atom_type_buffer(num_local_atoms);
for(unsigned int atom = 0; atom < num_local_atoms; atom++) atom_type_buffer[atom] = cs::non_magnetic_atoms_array[ atom_list[atom] ].mat;
std::vector<int> atom_category_buffer(num_local_atoms);
for(unsigned int atom = 0; atom < num_local_atoms; atom++) atom_category_buffer[atom] = cs::non_magnetic_atoms_array[ atom_list[atom] ].cat;
std::vector<double> atom_coord_buffer(3*num_local_atoms);
for(unsigned int atom = 0; atom < num_local_atoms; atom++){
const uint64_t atom_id = atom_list[atom]; // get atom array index
atom_coord_buffer[3*atom + 0] = cs::non_magnetic_atoms_array[atom_id].x;
atom_coord_buffer[3*atom + 1] = cs::non_magnetic_atoms_array[atom_id].y;
atom_coord_buffer[3*atom + 2] = cs::non_magnetic_atoms_array[atom_id].z;
}
//------------------------------------------
// Output Meta Data from root process
//------------------------------------------
// set number of files
// const int files = config::internal::num_io_groups; // unused variable
if(config::internal::mode != legacy && vmpi::my_rank == 0){
config::internal::write_non_magnetic_meta(num_total_atoms);
}
//------------------------------------------
// Output coordinate data
//------------------------------------------
// Determine output filename
std::stringstream file_sstr;
// set simple file name for single file output
if(config::internal::num_io_groups == 1) file_sstr << "non-magnetic-atoms.data";
// otherwise set indexed files
else file_sstr << "non-magnetic-atoms-" << std::setfill('0') << std::setw(6) << config::internal::io_group_id << ".data";
// convert string stream to string
std::string filename = file_sstr.str();
// Calculate number of bytes to be written to disk
const double data_size = double(num_total_atoms) * 1.0e-9 * (3.0*double(sizeof(double) + 2.0*double(sizeof(int)) ) );
// Output informative messages of actual data size to be outputed to disk (in binary mode)
zlog << zTs() << "Total non-magnetic data filesize: " << 1000.0 * data_size << " MB" << std::endl;
// Output informative message to log file on root process
zlog << zTs() << "Outputting non-magnetic atomic coordinate file to disk ";
// Variable for calculating output bandwidth
double io_time = 1.0e-12;
//-----------------------------------------------------
// Parallel mode output
//-----------------------------------------------------
#ifdef MPICF
// Determine io mode and call appropriate function for data
switch(config::internal::mode){
// legacy
case config::internal::legacy:
break;
case config::internal::mpi_io:{
vutil::vtimer_t timer; // instantiate timer
MPI_File fh; // MPI file handle
MPI_Status status; // MPI io status
// convert filename to character string for output
char *cfilename = (char*)filename.c_str();
// Open file on all processors
MPI_File_open(MPI_COMM_WORLD, cfilename, MPI_MODE_WRONLY | MPI_MODE_CREATE, MPI_INFO_NULL, &fh);
// write number of atoms on root process
if(vmpi::my_rank == 0) MPI_File_write(fh, &num_total_atoms, 1, MPI_UINT64_T, &status);
// Calculate local byte offsets since MPI-IO is simple and doesn't update the file handle pointer after I/O
MPI_Offset type_offset = config::internal::linear_offset + sizeof(uint64_t);
MPI_Offset category_offset = config::internal::linear_offset + num_total_atoms * sizeof(int) + sizeof(uint64_t);
MPI_Offset data_offset = config::internal::buffer_offset + 2 * num_total_atoms * sizeof(int) + sizeof(uint64_t);
timer.start(); // start timer
// Write data to disk
MPI_File_write_at_all(fh, type_offset, &atom_type_buffer[0], atom_type_buffer.size(), MPI_INT, &status);
MPI_File_write_at_all(fh, category_offset, &atom_category_buffer[0], atom_category_buffer.size(), MPI_INT, &status);
MPI_File_write_at_all(fh, data_offset, &atom_coord_buffer[0], atom_coord_buffer.size(), MPI_DOUBLE, &status);
timer.stop(); // Stop timer
// Calculate elapsed time
io_time = timer.elapsed_time();
// Close file
MPI_File_close(&fh);
break;
}
case config::internal::fpprocess:
io_time = write_coord_data(filename, atom_coord_buffer, atom_type_buffer, atom_category_buffer);
break;
case config::internal::fpnode:{
// Gather data from all processors in io group
std::vector<int> collated_atom_type_buffer(0);
collate_int_data(atom_type_buffer, collated_atom_type_buffer);
std::vector<int> collated_atom_category_buffer(0);
collate_int_data(atom_category_buffer, collated_atom_category_buffer);
std::vector<double> collated_atom_coord_buffer(0);
collate_double_data(atom_coord_buffer, collated_atom_coord_buffer);
// output data on master io processes
if(config::internal::io_group_master) io_time = write_coord_data(filename, collated_atom_coord_buffer, collated_atom_type_buffer, collated_atom_category_buffer);
// find longest time in all io nodes
double max_io_time = 0.0;
// calculate actual bandwidth on root process
MPI_Reduce(&io_time, &max_io_time, 1, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
io_time = max_io_time;
break;
}
}
#else
//-----------------------------------------------------
// Serial mode output (ignores most io directives)
//-----------------------------------------------------
// if new output (not legacy) then output non magnetic atoms
if(config::internal::mode != config::internal::legacy) io_time = write_coord_data(filename, atom_coord_buffer, atom_type_buffer, atom_category_buffer);
#endif
// Output bandwidth to log file
zlog << data_size/io_time << " GB/s in " << io_time << " s" << std::endl;
return;
}
int create_crystal_structure(std::vector<cs::catom_t> & catom_array){
//----------------------------------------------------------
// check calling of routine if error checking is activated
//----------------------------------------------------------
if(err::check==true){std::cout << "cs::create_crystal_structure has been called" << std::endl;}
int min_bounds[3];
int max_bounds[3];
#ifdef MPICF
if(vmpi::mpi_mode==0){
min_bounds[0] = int(vmpi::min_dimensions[0]/unit_cell.dimensions[0]);
min_bounds[1] = int(vmpi::min_dimensions[1]/unit_cell.dimensions[1]);
min_bounds[2] = int(vmpi::min_dimensions[2]/unit_cell.dimensions[2]);
max_bounds[0] = vmath::iceil(vmpi::max_dimensions[0]/unit_cell.dimensions[0]);
max_bounds[1] = vmath::iceil(vmpi::max_dimensions[1]/unit_cell.dimensions[1]);
max_bounds[2] = vmath::iceil(vmpi::max_dimensions[2]/unit_cell.dimensions[2]);
}
else{
min_bounds[0]=0;
min_bounds[1]=0;
min_bounds[2]=0;
max_bounds[0]=cs::total_num_unit_cells[0];
max_bounds[1]=cs::total_num_unit_cells[1];
max_bounds[2]=cs::total_num_unit_cells[2];
}
#else
min_bounds[0]=0;
min_bounds[1]=0;
min_bounds[2]=0;
max_bounds[0]=cs::total_num_unit_cells[0];
max_bounds[1]=cs::total_num_unit_cells[1];
max_bounds[2]=cs::total_num_unit_cells[2];
#endif
cs::local_num_unit_cells[0]=max_bounds[0]-min_bounds[0];
cs::local_num_unit_cells[1]=max_bounds[1]-min_bounds[1];
cs::local_num_unit_cells[2]=max_bounds[2]-min_bounds[2];
int num_atoms=cs::local_num_unit_cells[0]*cs::local_num_unit_cells[1]*cs::local_num_unit_cells[2]*unit_cell.atom.size();
// set catom_array size
catom_array.reserve(num_atoms);
// Initialise atoms number
int atom=0;
// find maximum height lh_category
unsigned int maxlh=0;
for(unsigned int uca=0;uca<unit_cell.atom.size();uca++) if(unit_cell.atom[uca].hc > maxlh) maxlh = unit_cell.atom[uca].hc;
maxlh+=1;
const double cff = 1.e-9; // Small numerical correction for atoms exactly on the borderline between processors
// Duplicate unit cell
for(int z=min_bounds[2];z<max_bounds[2];z++){
for(int y=min_bounds[1];y<max_bounds[1];y++){
for(int x=min_bounds[0];x<max_bounds[0];x++){
// need to change this to accept non-orthogonal lattices
// Loop over atoms in unit cell
for(unsigned int uca=0;uca<unit_cell.atom.size();uca++){
double cx = (double(x)+unit_cell.atom[uca].x)*unit_cell.dimensions[0]+cff;
double cy = (double(y)+unit_cell.atom[uca].y)*unit_cell.dimensions[1]+cff;
double cz = (double(z)+unit_cell.atom[uca].z)*unit_cell.dimensions[2]+cff;
#ifdef MPICF
if(vmpi::mpi_mode==0){
// only generate atoms within allowed dimensions
if( (cx>=vmpi::min_dimensions[0] && cx<vmpi::max_dimensions[0]) &&
(cy>=vmpi::min_dimensions[1] && cy<vmpi::max_dimensions[1]) &&
(cz>=vmpi::min_dimensions[2] && cz<vmpi::max_dimensions[2])){
#endif
if((cx<cs::system_dimensions[0]) && (cy<cs::system_dimensions[1]) && (cz<cs::system_dimensions[2])){
catom_array.push_back(cs::catom_t());
catom_array[atom].x=cx;
catom_array[atom].y=cy;
catom_array[atom].z=cz;
//std::cout << atom << "\t" << cx << "\t" << cy <<"\t" << cz << std::endl;
catom_array[atom].material=unit_cell.atom[uca].mat;
catom_array[atom].uc_id=uca;
catom_array[atom].lh_category=unit_cell.atom[uca].hc+z*maxlh;
catom_array[atom].uc_category=unit_cell.atom[uca].lc;
catom_array[atom].scx=x;
catom_array[atom].scy=y;
catom_array[atom].scz=z;
atom++;
}
#ifdef MPICF
}
}
else{
if((cx<cs::system_dimensions[0]) && (cy<cs::system_dimensions[1]) && (cz<cs::system_dimensions[2])){
catom_array.push_back(cs::catom_t());
catom_array[atom].x=cx;
catom_array[atom].y=cy;
catom_array[atom].z=cz;
catom_array[atom].material=unit_cell.atom[uca].mat;
catom_array[atom].uc_id=uca;
catom_array[atom].lh_category=unit_cell.atom[uca].hc+z*maxlh;
catom_array[atom].uc_category=unit_cell.atom[uca].lc;
catom_array[atom].scx=x;
catom_array[atom].scy=y;
catom_array[atom].scz=z;
catom_array[atom].include=false; // assume no atoms until classification complete
atom++;
}
}
#endif
}
}
}
}
// Check to see if actual and expected number of atoms agree, if not trim the excess
if(atom!=num_atoms){
std::vector<cs::catom_t> tmp_catom_array(num_atoms);
tmp_catom_array=catom_array;
catom_array.resize(atom);
for(int a=0;a<atom;a++){
catom_array[a]=tmp_catom_array[a];
}
tmp_catom_array.resize(0);
}
// If z-height material selection is enabled then do so
if(cs::SelectMaterialByZHeight==true){
// Check for interfacial roughness and call custom material assignment routine
if(cs::interfacial_roughness==true) cs::roughness(catom_array);
// Check for multilayer system and if required generate multilayers
else if(cs::multilayers) cs::generate_multilayers(catom_array);
// Otherwise perform normal assignement of materials
else{
// determine z-bounds for materials
std::vector<double> mat_min(mp::num_materials);
std::vector<double> mat_max(mp::num_materials);
std::vector<bool> mat_fill(mp::num_materials);
// Unroll min, max and fill for performance
for(int mat=0;mat<mp::num_materials;mat++){
mat_min[mat]=mp::material[mat].min*cs::system_dimensions[2];
mat_max[mat]=mp::material[mat].max*cs::system_dimensions[2];
// alloys generally are not defined by height, and so have max = 0.0
if(mat_max[mat]<0.0000001) mat_max[mat]=-0.1;
mat_fill[mat]=mp::material[mat].fill;
}
// Assign materials to generated atoms
for(unsigned int atom=0;atom<catom_array.size();atom++){
for(int mat=0;mat<mp::num_materials;mat++){
const double cz=catom_array[atom].z;
if((cz>=mat_min[mat]) && (cz<mat_max[mat]) && (mat_fill[mat]==false)){
catom_array[atom].material=mat;
catom_array[atom].include=true;
}
}
}
}
// Delete unneeded atoms
clear_atoms(catom_array);
}
// Check to see if any atoms have been generated
if(atom==0){
terminaltextcolor(RED);
std::cout << "Error - no atoms have been generated, increase system dimensions!" << std::endl;
terminaltextcolor(WHITE);
zlog << zTs() << "Error: No atoms have been generated. Increase system dimensions." << std::endl;
err::vexit();
}
// Now unselect all atoms by default for particle shape cutting
for(unsigned int atom=0;atom<catom_array.size();atom++){
catom_array[atom].include=false;
}
return EXIT_SUCCESS;
}
///
/// @brief Initialise Constrained Monte Carlo module
///
/// Creates the rotation matices for the given angle and computes the
/// Boltzmann factor for the given temperature.
///
/// @return void
///
void CMCMCinit(){
// Check for calling of function
if(err::check==true) std::cout << "sim::CMCMCinit has been called" << std::endl;
// Create rotational matrices for cmc
cmc::mat_polar_rot_matrix();
cmc::atom_list.resize(mp::num_materials);
// create list of matching materials
for(int atom=0;atom<atoms::num_atoms;atom++){
int mat=atoms::type_array[atom];
cmc::atom_list[mat].push_back(atom);
}
// Check for rotational update
if(sim::constraint_rotation==false || (sim::constraint_theta_changed==false && sim::constraint_phi_changed==false)){
// Output message showing constraint direction re-initialisation
zlog << zTs() << "Initialising spins in all materials to new constraint directions." << std::endl;
// Initialise all spins along the constraint direction(s).
for(int atom =0;atom<atoms::num_atoms;atom++){
int imat=atoms::type_array[atom];
if(mp::material[imat].constrained==true){
double sx=sin(cmc::cmc_mat[imat].constraint_phi*M_PI/180.0)*cos(cmc::cmc_mat[imat].constraint_theta*M_PI/180.0);
double sy=sin(cmc::cmc_mat[imat].constraint_phi*M_PI/180.0)*sin(cmc::cmc_mat[imat].constraint_theta*M_PI/180.0);
double sz=cos(cmc::cmc_mat[imat].constraint_phi*M_PI/180.0);
atoms::x_spin_array[atom]=sx;
atoms::y_spin_array[atom]=sy;
atoms::z_spin_array[atom]=sz;
}
}
}
else{
// Output message showing constraint direction re-initialisation
zlog << zTs() << "Initialising spins in material " << cmc::active_material << " by rotation to new constraint direction (phi, theta) "
<< cmc::cmc_mat[cmc::active_material].constraint_phi << " , " << cmc::cmc_mat[cmc::active_material].constraint_theta << std::endl;
// Rotate spins from old to new constraint direction
// Determine angles to rotate spins by
double theta_old = cmc::cmc_mat[cmc::active_material].constraint_theta;
double theta_new = cmc::cmc_mat[cmc::active_material].constraint_theta;
double phi_old = cmc::cmc_mat[cmc::active_material].constraint_phi;
double phi_new = cmc::cmc_mat[cmc::active_material].constraint_phi;
// note - sim::constraint_phi, sim::constraint_theta are already at new angle
if(sim::constraint_theta_changed) theta_old = cmc::cmc_mat[cmc::active_material].constraint_theta - cmc::cmc_mat[cmc::active_material].constraint_theta_delta;
if(sim::constraint_phi_changed) phi_old = cmc::cmc_mat[cmc::active_material].constraint_phi - cmc::cmc_mat[cmc::active_material].constraint_phi_delta;
// Rotate all spins in active material from theta_old to theta = 0 (reference direction along x)
cmc::rotate_material_spins_around_z_axis(-theta_old, cmc::active_material);
// Rotate all spins in active material from phi_old to phi_new
cmc::rotate_material_spins_around_x_axis(phi_new-phi_old, cmc::active_material);
// Rotate all spins in active material from theta = 0 to theta = theta_new
cmc::rotate_material_spins_around_z_axis(theta_new, cmc::active_material);
// reset rotation flags
sim::constraint_theta_changed = false;
sim::constraint_phi_changed = false;
}
// disable thermal field calculation
sim::hamiltonian_simulation_flags[3]=0;
// set initialised flag to true
cmc::is_initialised=true;
return;
}
void zLogTsInit(std::string tmp){
// Get program name and process ID
std::string tmprev;
int linelength = tmp.length();
// set character triggers
const char* key="/"; /// Word identifier
// copy characters after last /
for(int i=linelength-1;i>=0;i--){
char c=tmp.at(i);
if(c != *key){
tmprev.push_back(c);
}
else break;
}
//reverse read into program name
linelength=tmprev.size();
for(int i=linelength-1;i>=0;i--){
char c=tmprev.at(i);
zLogProgramName.push_back(c);
}
// Get hostname
char loghostname [80];
#ifdef WIN_COMPILE
DWORD sizelhn = sizeof ( loghostname );
int GHS=!GetComputerName(loghostname, &sizelhn); //GetComputerName returns true when retrieves hostname
#else
int GHS=gethostname(loghostname, 80);
#endif
terminaltextcolor(YELLOW);
if(GHS!=0) std::cerr << "Warning: Unable to retrieve hostname for zlog file." << std::endl;
terminaltextcolor(WHITE);
zLogHostName = loghostname;
// Now get process ID
#ifdef WIN_COMPILE
zLogPid = _getpid();
#else
zLogPid = getpid();
#endif
// Open log filename
if(vmpi::my_rank==0) zlog.open("log");
// Mark as initialised;
zLogInitialised=true;
zlog << zTs() << "Logfile opened" << std::endl;
//------------------------------------
// Determine current directory
//------------------------------------
char directory [256];
#ifdef WIN_COMPILE
_getcwd(directory, sizeof(directory));
#else
getcwd(directory, sizeof(directory));
#endif
// write system and version information
zlog << zTs() << "Executable : " << vout::zLogProgramName << std::endl;
zlog << zTs() << "Host name : " << vout::zLogHostName << ":" << std::endl;
zlog << zTs() << "Directory : " << directory << std::endl;
zlog << zTs() << "Process ID : " << vout::zLogPid << std::endl;
zlog << zTs() << "Version : " << vinfo::version() << std::endl;
zlog << zTs() << "Githash : " << vinfo::githash() << std::endl;
return;
}
//----------------------------------------------------------------------
//
// Function to generate rough surfaces (optionally unique) between
// multiple materials at the interface of min/max.
//
// A local height is defined which overrides the min/max values of
// the extent of the material as defined in the material file. No
// atoms are added or removed by the process, but this will override
// structural effects such as core-shell systems.
//
// The roughness is generated by creating seed points with a random
// radius with a flat distribution around the mean. Within this
// radius a stepwise change in the local height is defined, again
// Gaussian distributed with a mean step height of zero. A maximum
// Height is specified which truncates outlying values. Typical
// values of the maximum step height would be 1-5 monolayers.
//
// The seed points are used to generate a 2D array defining the local
// height for any point in space. A loop over all atoms then reassigns
// atoms to materials according to the local height, overriding the
// materials set in the crsytal.
//
//------------------------------------------------------------------------
//
void roughness(std::vector<cs::catom_t> & catom_array){
// Output instructuve message to log file
zlog << zTs() << "Calculating interfacial roughness for generated system." << std::endl;
// Construct a 2D array of height according to roughness resoution
const double resolution=cs::interfacial_roughness_height_field_resolution; // Angstroms
const unsigned int seed_density=cs::interfacial_roughness_seed_count;
const double seed_radius=cs::interfacial_roughness_mean_seed_radius;
const double seed_height_mean=cs::interfacial_roughness_mean_seed_height;
const double seed_height_max=cs::interfacial_roughness_seed_height_max;
const double seed_radius_variance=cs::interfacial_roughness_seed_radius_variance;
// Declare array to store height field
std::vector<std::vector<double> >height_field(0);
// Calculate size of height_field array
double nx = int(vmath::iceil(cs::system_dimensions[0]/resolution));
double ny = int(vmath::iceil(cs::system_dimensions[1]/resolution));
// Resize height_field array
height_field.resize(nx);
for(int i=0; i<nx; i++) height_field.at(i).resize(ny);
// Generate seed points and radii
std::vector<seed_point_t> seed_points(0);
// Define local random generator for surface roughness
MTRand rgrnd;
// Initialise random number generator
rgrnd.seed(cs::interfacial_roughness_random_seed);
for(unsigned int p=0; p < seed_density ; p++){
// Generate random point coordinates
double x=rgrnd()*cs::system_dimensions[0];
double y=rgrnd()*cs::system_dimensions[1];
// Generate random radius with flat profile r = r0 +/- variance*rnd()
double r=seed_radius*(1.0+seed_radius_variance*(2.0*rgrnd()-1.0));
// Generate random height with gaussian profile
double h=seed_height_mean*mtrandom::gaussianc(rgrnd);
// Overwrite generated height if greater than maximum
if(fabs(h)>seed_height_max) h=vmath::sign(h)*seed_height_max;
// Check for type of roughness
// Troughs
if(cs::interfacial_roughness_type==-1) h = -1.0*fabs(h);
// Peaks
else if(cs::interfacial_roughness_type==1) h = fabs(h);
// Save point characteristics to array
seed_point_t tmp;
tmp.x = x;
tmp.y = y;
tmp.radius = r;
tmp.height = h;
seed_points.push_back(tmp);
}
// Now apply seed points to generate local height field
// Loop over all height field coordinates
for(int ix = 0; ix < nx; ix++){
for(int iy = 0; iy < ny; iy++){
const double x = double(ix)*resolution; // real space coordinates
const double y = double(iy)*resolution;
// Loop over all seed points
for(unsigned int p=0; p < seed_density ; p++){
double rx=x-seed_points.at(p).x;
double ry=y-seed_points.at(p).y;
// Check for point in range
if(rx*rx+ry*ry <= seed_points.at(p).radius*seed_points.at(p).radius) height_field.at(ix).at(iy)=seed_points.at(p).height;
}
}
}
// Assign materials to generated atoms
for(unsigned int atom=0;atom<catom_array.size();atom++){
// Determine height field coordinates
const int hx = int(catom_array[atom].x/resolution);
const int hy = int(catom_array[atom].y/resolution);
// Loop over all materials and determine local height
for(int mat=0;mat<mp::num_materials;mat++){
double min=create::internal::mp[mat].min*cs::system_dimensions[2];
double max=create::internal::mp[mat].max*cs::system_dimensions[2];
double local_height = height_field.at(hx).at(hy);
bool fill = mp::material[mat].fill;
// optionally specify a material specific height here -- not yet implemented
//if(cs::interfacial_roughness_local_height_field==true){
//double local_height = height_field.at(mat).at(hx).at(hy);
//}
const int atom_uc_cat = catom_array[atom].uc_category;
const int mat_uc_cat = create::internal::mp[mat].unit_cell_category;
// Include atoms if within material height
const double cz=catom_array[atom].z;
if((cz>=min+local_height) && (cz<max+local_height) && (fill==false) && (atom_uc_cat == mat_uc_cat) ){
catom_array[atom].material=mat;
catom_array[atom].include=true;
}
}
}
return;
}
///
/// @brief Initialise Constrained Monte Carlo module
///
/// Creates the rotation matices for the given angle and computes the
/// Boltzmann factor for the given temperature.
///
/// @return void
///
void CMCinit(){
// Check for calling of function
if(err::check==true) std::cout << "sim::CMCinit has been called" << std::endl;
// Create rotational matrices for cmc
cmc::polar_rot_matrix(sim::constraint_phi,sim::constraint_theta, cmc::polar_matrix, cmc::polar_matrix_tp, cmc::polar_vector);
// Check for rotational update
if((sim::constraint_rotation==false || (sim::constraint_theta_changed==false && sim::constraint_phi_changed==false)) && sim::checkpoint_loaded_flag==false){
// Output message showing constraint direction re-initialisation
zlog << zTs() << "Initialising spins to new constraint direction (phi, theta) " << sim::constraint_phi << " , " << sim::constraint_theta << std::endl;
// Initialise all spins along the constraint direction.
double sx=sin(sim::constraint_phi*M_PI/180.0)*cos(sim::constraint_theta*M_PI/180.0);
double sy=sin(sim::constraint_phi*M_PI/180.0)*sin(sim::constraint_theta*M_PI/180.0);
double sz=cos(sim::constraint_phi*M_PI/180.0);
for(int atom =0;atom<atoms::num_atoms;atom++){
atoms::x_spin_array[atom]=sx;
atoms::y_spin_array[atom]=sy;
atoms::z_spin_array[atom]=sz;
}
}
// If the simulation is restarted from within the temperature loop, then the spin configurations must not be reinitialised
else if(sim::checkpoint_loaded_flag==true){
zlog << zTs() << "Not re-initialising spins to constraint directions since still in temperature loop" << std::endl;
}
else{
// Output message showing constraint direction re-initialisation
zlog << zTs() << "Initialising spins by rotation from last constraint direction to new constraint direction (phi, theta) "
<< sim::constraint_phi << " , " << sim::constraint_theta << std::endl;
// Rotate spins from old to new constraint direction
// Determine angles to rotate spins by
double theta_old = sim::constraint_theta;
double theta_new = sim::constraint_theta;
double phi_old = sim::constraint_phi;
double phi_new = sim::constraint_phi;
// note - sim::constraint_phi, sim::constraint_theta are already at new angle
if(sim::constraint_theta_changed) theta_old = sim::constraint_theta - sim::constraint_theta_delta;
if(sim::constraint_phi_changed) phi_old = sim::constraint_phi - sim::constraint_phi_delta;
// Rotate all spins from theta_old to theta = 0 (reference direction along x)
cmc::rotate_spins_around_z_axis(-theta_old);
// Rotate all spins from phi_old to phi_new
cmc::rotate_spins_around_x_axis(phi_new-phi_old);
// Rotate all spins from theta = 0 to theta = theta_new
cmc::rotate_spins_around_z_axis(theta_new);
// reset rotation flags
sim::constraint_theta_changed = false;
sim::constraint_phi_changed = false;
}
// disable thermal field calculation
sim::hamiltonian_simulation_flags[3]=0;
// set initialised flag to true
cmc::is_initialised=true;
return;
}
/// @brief Cells output function /// /// @details Outputs formatted data snapshot for visualisation /// /// //------------------------------------------------------ /// // Atomistic coordinate configuration file for vampire /// //------------------------------------------------------ /// // Date: xx/xx/xxxx xx.xx.xx /// //------------------------------------------------------ /// Number of cells: $n_cells /// //------------------------------------------------------ /// Number of atom files: $n_files /// atoms-coords-00CPU0.cfg /// atoms-coords-00CPU1.cfg /// atoms-coords-00CPU2.cfg /// //------------------------------------------------------ /// Number of local cells: $n_loc_cells /// $material $category $x $y $z $species /// $material $category $x $y $z $species /// $material $category $x ... /// /// @section License /// Use of this code, either in source or compiled form, is subject to license from the authors. /// Copyright \htmlonly © \endhtmlonly Richard Evans, 2009-2011. All Rights Reserved. /// /// @section Information /// @author Richard Evans, [email protected] /// @version 1.0 /// @date 31/05/2011 /// /// @internal /// Created: 31/05/2011 /// Revision: --- ///===================================================================================== /// void legacy_cells_coords() { // wait for all processes vmpi::barrier(); // instantiate timer vutil::vtimer_t timer; // Set local output filename std::stringstream file_sstr; file_sstr << "cells-coords"; file_sstr << ".cfg"; std::string cfg_file = file_sstr.str(); const char *cfg_filec = cfg_file.c_str(); // start timer timer.start(); // Output masterfile header on root process if (vmpi::my_rank == 0) { zlog << zTs() << "Outputting cell coordinates to disk" << std::flush; // Declare and open output file std::ofstream cfg_file_ofstr; cfg_file_ofstr.open(cfg_filec); // Get system date time_t rawtime = time(NULL); struct tm *timeinfo = localtime(&rawtime); cfg_file_ofstr << "#------------------------------------------------------" << std::endl; cfg_file_ofstr << "# Cell coordinates configuration file for vampire" << std::endl; cfg_file_ofstr << "#------------------------------------------------------" << std::endl; cfg_file_ofstr << "# Date: " << asctime(timeinfo); cfg_file_ofstr << "#------------------------------------------------------" << std::endl; cfg_file_ofstr << "# Number of cells: " << cells::num_cells << std::endl; cfg_file_ofstr << "#------------------------------------------------------" << std::endl; cfg_file_ofstr << "#" << std::endl; cfg_file_ofstr << "#" << std::endl; cfg_file_ofstr << "#" << std::endl; cfg_file_ofstr << "#" << std::endl; cfg_file_ofstr << "#" << std::endl; cfg_file_ofstr << "#------------------------------------------------------" << std::endl; config::internal::total_output_cells = 0; for (int cell = 0; cell < cells::num_cells; cell++){ if (cells::num_atoms_in_cell_global[cell] > 0){ cfg_file_ofstr << cell << "\t" << cells::num_atoms_in_cell_global[cell] << "\t" << cells::pos_and_mom_array[4 * cell + 0] << "\t" << cells::pos_and_mom_array[4 * cell + 1] << "\t" << cells::pos_and_mom_array[4 * cell + 2] << std::endl; config::internal::total_output_cells++; } } cfg_file_ofstr.close(); } // stop the timer timer.stop(); const double data_size = double(config::internal::total_output_cells) * 2.0 * sizeof(int) * 3.0 * sizeof(double); const double io_time = timer.elapsed_time(); zlog << " of size " << data_size*1.0e-6 << " MB [ " << data_size*1.0e-9/timer.elapsed_time() << " GB/s in " << io_time << " s ]" << std::endl; // wait for all processes vmpi::barrier(); return; }
/// @brief Cell output function /// /// @details Outputs formatted data snapshot for visualisation /// /// #------------------------------------------------------ /// # Cell configuration file for vampire /// #------------------------------------------------------ /// # Date: xx/xx/xxxx xx.xx.xx /// #------------------------------------------------------ /// Number of cells: $n_cells /// System dimensions: $max_x $max_y $max_z /// Coordinates-file: $coord_file /// Time: $t /// Field: $H /// Temperature: $T /// Magnetisation: $mx $my $mz /// Number of Materials: $n_mat /// Material Properties 1: $mu_s $mmx $mmy $mmz $mm /// Material Properties 2: $mu_s $mmx $mmy $mmz ... /// #------------------------------------------------------ /// /// @section License /// Use of this code, either in source or compiled form, is subject to license from the authors. /// Copyright \htmlonly © \endhtmlonly Richard Evans, 2009-2011. All Rights Reserved. /// /// @section Information /// @author Richard Evans, [email protected] /// @version 1.0 /// @date 26/04/2013 /// /// @internal /// Created: 26/04/2013 /// Revision: --- ///===================================================================================== /// void legacy_cells() { // wait for all processes vmpi::barrier(); // instantiate timer vutil::vtimer_t timer; // Set local output filename std::stringstream file_sstr; file_sstr << "cells-"; file_sstr << std::setfill('0') << std::setw(8) << sim::output_cells_file_counter; file_sstr << ".cfg"; std::string cfg_file = file_sstr.str(); const char *cfg_filec = cfg_file.c_str(); #ifdef MPICF // if flag to print cells field is active, all cpus send cells field to root proc if(dipole::activated) dipole::send_cells_field(cells::cell_id_array, dipole::cells_field_array_x, dipole::cells_field_array_y, dipole::cells_field_array_z, cells::num_local_cells); #endif // start timer timer.start(); // Output masterfile header on root process if (vmpi::my_rank == 0) { zlog << zTs() << "Outputting cell configuration " << sim::output_cells_file_counter << " to disk" << std::flush; // Declare and open output file std::ofstream cfg_file_ofstr; cfg_file_ofstr.open(cfg_filec); // Get system date time_t rawtime = time(NULL); struct tm *timeinfo = localtime(&rawtime); cfg_file_ofstr << "#------------------------------------------------------" << std::endl; cfg_file_ofstr << "# Cell configuration file for vampire" << std::endl; cfg_file_ofstr << "#------------------------------------------------------" << std::endl; cfg_file_ofstr << "# Date: " << asctime(timeinfo); cfg_file_ofstr << "#------------------------------------------------------" << std::endl; cfg_file_ofstr << "# Number of spins: " << cells::num_cells << std::endl; cfg_file_ofstr << "# System dimensions:" << cs::system_dimensions[0] << "\t" << cs::system_dimensions[1] << "\t" << cs::system_dimensions[2] << std::endl; cfg_file_ofstr << "# Coordinates-file: cells-coord.cfg" << std::endl; cfg_file_ofstr << "# Time: " << double(sim::time) * mp::dt_SI << std::endl; cfg_file_ofstr << "# Field: " << sim::H_applied << std::endl; cfg_file_ofstr << "# Temperature: " << sim::temperature << std::endl; cfg_file_ofstr << "# Magnetisation: " << stats::system_magnetization.output_normalized_magnetization() << std::endl; cfg_file_ofstr << "#------------------------------------------------------" << std::endl; // Root process now outputs the cell magnetisations for (int cell = 0; cell < cells::num_cells; cell++){ if (cells::num_atoms_in_cell_global[cell] > 0){ cfg_file_ofstr << cells::mag_array_x[cell] << "\t" << cells::mag_array_y[cell] << "\t" << cells::mag_array_z[cell] << "\t"; if(dipole::activated) cfg_file_ofstr << dipole::cells_field_array_x[cell] << "\t" << dipole::cells_field_array_y[cell] << "\t" << dipole::cells_field_array_z[cell] << "\n"; else cfg_file_ofstr << "\n"; } } cfg_file_ofstr.close(); } // stop the timer timer.stop(); double data_size = double(config::internal::total_output_cells) * 3.0 * sizeof(double); if(dipole::activated) data_size = data_size * 2.0; const double io_time = timer.elapsed_time(); zlog << " of size " << data_size*1.0e-6 << " MB [ " << data_size*1.0e-9/timer.elapsed_time() << " GB/s in " << io_time << " s ]" << std::endl; sim::output_cells_file_counter++; // wait for all processes vmpi::barrier(); return; }
//------------------------------------------------------------------------------
//
// Function to set the type of exchange used in the code from a string
// processed from the unit cell file. Default is normalised isotropic
// exchange where the values of the exchange are set from the material
// file.
//
// Function returns the number of exchange interactions specified in the
// unit cell file.
//
//------------------------------------------------------------------------------
unsigned int set_exchange_type(std::string exchange_type_string){
//----------------------------------------
// check for standard isotropic exchange
//----------------------------------------
const std::string isotropic_str = "isotropic";
if(isotropic_str == exchange_type_string){
// set exchange type
exchange::internal::exchange_type = internal::isotropic;
// unset normalization flag
exchange::internal::use_material_exchange_constants = false;
return 1; // number of exchange interactions
}
//----------------------------------------
// check for standard vectorial exchange
//----------------------------------------
const std::string vectorial_str = "vectorial";
if(vectorial_str == exchange_type_string){
// set exchange type
exchange::internal::exchange_type = internal::vectorial;
// unset normalization flag
exchange::internal::use_material_exchange_constants = false;
return 3; // number of exchange interactions
}
//----------------------------------------
// check for standard tensorial exchange
//----------------------------------------
const std::string tensorial_str = "tensorial";
if(tensorial_str == exchange_type_string){
// set exchange type
exchange::internal::exchange_type = internal::tensorial;
// unset normalization flag
exchange::internal::use_material_exchange_constants = false;
return 9; // number of exchange interactions
}
//-----------------------------------------
// check for normalised isotropic exchange
//-----------------------------------------
const std::string norm_isotropic_str = "normalised-isotropic";
if(norm_isotropic_str == exchange_type_string){
// set exchange type
exchange::internal::exchange_type = internal::isotropic;
// unset normalization flag
exchange::internal::use_material_exchange_constants = true;
return 1; // number of exchange interactions
}
//-----------------------------------------
// check for normalised vectorial exchange
//-----------------------------------------
const std::string norm_vectorial_str = "normalised-vectorial";
if(norm_vectorial_str == exchange_type_string){
// set exchange type
exchange::internal::exchange_type = internal::vectorial;
// unset normalization flag
exchange::internal::use_material_exchange_constants = true;
return 3; // number of exchange interactions
}
//-----------------------------------------
// check for normalised tensorial exchange
//-----------------------------------------
const std::string norm_tensorial_str = "normalised-tensorial";
if(norm_tensorial_str == exchange_type_string){
// set exchange type
exchange::internal::exchange_type = internal::tensorial;
// unset normalization flag
exchange::internal::use_material_exchange_constants = true;
return 9; // number of exchange interactions
}
terminaltextcolor(RED);
zlog << zTs() << "\nError: Unkown exchange type \"" << exchange_type_string << "\" in unit cell file. Exiting!" << std::endl;
std::cerr << "\nError: Unkown exchange type \"" << exchange_type_string << "\" in unit cell file. Exiting!" << std::endl;
terminaltextcolor(WHITE);
// exit program
err::vexit();
return 0;
}
/// @brief Function to run one a single program /// /// @callgraph /// @callergraph /// /// @section License /// Use of this code, either in source or compiled form, is subject to license from the authors. /// Copyright \htmlonly © \endhtmlonly Richard Evans, 2009-2011. All Rights Reserved. /// /// @section Information /// @author Richard Evans, [email protected] /// @version 1.1 /// @date 09/03/2011 /// /// @return EXIT_SUCCESS /// /// @internal /// Created: 02/10/2008 /// Revision: 1.1 09/03/2011 ///===================================================================================== /// int run(){ // Check for calling of function if(err::check==true) std::cout << "sim::run has been called" << std::endl; // Initialise simulation data structures sim::initialize(mp::num_materials); anisotropy::initialize(atoms::num_atoms, atoms::type_array, mp::mu_s_array); // now seed generator mtrandom::grnd.seed(vmpi::parallel_rng_seed(mtrandom::integration_seed)); // Check for load spin configurations from checkpoint if(sim::load_checkpoint_flag) load_checkpoint(); { // Set up statistical data sets #ifdef MPICF int num_atoms_for_statistics = vmpi::num_core_atoms+vmpi::num_bdry_atoms; #else int num_atoms_for_statistics = atoms::num_atoms; #endif // unroll list of non-magnetic materials std::vector<bool> non_magnetic_materials_array(mp::num_materials, false); for(int m = 0; m < mp::num_materials; m++){ if( mp::material[m].non_magnetic == 2 ) non_magnetic_materials_array[m] = true; } stats::initialize(num_atoms_for_statistics, mp::num_materials, atoms::m_spin_array, atoms::type_array, atoms::category_array, non_magnetic_materials_array); } // Precalculate initial statistics stats::update(atoms::x_spin_array, atoms::y_spin_array, atoms::z_spin_array, atoms::m_spin_array); // initialise dipole field calculation dipole::initialize(cells::num_atoms_in_unit_cell, cells::num_cells, cells::num_local_cells, cells::macro_cell_size, cells::local_cell_array, cells::num_atoms_in_cell, cells::num_atoms_in_cell_global, // <---- cells::index_atoms_array, cells::volume_array, cells::pos_and_mom_array, cells::atom_in_cell_coords_array_x, cells::atom_in_cell_coords_array_y, cells::atom_in_cell_coords_array_z, atoms::type_array, cells::atom_cell_id_array, atoms::x_coord_array, atoms::y_coord_array, atoms::z_coord_array, atoms::num_atoms ); // Initialize GPU acceleration if enabled if(gpu::acceleration) gpu::initialize(); // For MPI version, calculate initialisation time if(vmpi::my_rank==0){ #ifdef MPICF std::cout << "Time for initialisation: " << MPI_Wtime()-vmpi::start_time << std::endl; zlog << zTs() << "Time for initialisation: " << MPI_Wtime()-vmpi::start_time << std::endl; vmpi::start_time=MPI_Wtime(); // reset timer #endif } // Set timer for runtime stopwatch_t stopwatch; stopwatch.start(); // Precondition spins at equilibration temperature sim::internal::monte_carlo_preconditioning(); // For MPI version, calculate initialisation time if(vmpi::my_rank==0){ std::cout << "Starting Simulation with Program "; zlog << zTs() << "Starting Simulation with Program "; } // Now set initial compute time #ifdef MPICF vmpi::ComputeTime=MPI_Wtime(); vmpi::WaitTime=MPI_Wtime(); vmpi::TotalComputeTime=0.0; vmpi::TotalWaitTime=0.0; #endif // Select program to run switch(sim::program){ case 0: if(vmpi::my_rank==0){ std::cout << "Benchmark..." << std::endl; zlog << "Benchmark..." << std::endl; } program::bmark(); break; case 1: if(vmpi::my_rank==0){ std::cout << "Time-Series..." << std::endl; zlog << "Time-Series..." << std::endl; } program::time_series(); break; case 2: if(vmpi::my_rank==0){ std::cout << "Hysteresis-Loop..." << std::endl; zlog << "Hysteresis-Loop..." << std::endl; } program::hysteresis(); break; case 3: if(vmpi::my_rank==0){ std::cout << "Static-Hysteresis-Loop..." << std::endl; zlog << "Static-Hysteresis-Loop..." << std::endl; } program::static_hysteresis(); break; case 4: if(vmpi::my_rank==0){ std::cout << "Curie-Temperature..." << std::endl; zlog << "Curie-Temperature..." << std::endl; } program::curie_temperature(); break; case 5: if(vmpi::my_rank==0){ std::cout << "Field-Cool..." << std::endl; zlog << "Field-Cool..." << std::endl; } program::field_cool(); break; case 6: if(vmpi::my_rank==0){ std::cout << "Temperature-Pulse..." << std::endl; zlog << "Temperature-Pulse..." << std::endl; } program::temperature_pulse(); break; case 7: if(vmpi::my_rank==0){ std::cout << "HAMR-Simulation..." << std::endl; zlog << "HAMR-Simulation..." << std::endl; } program::hamr(); break; case 8: if(vmpi::my_rank==0){ std::cout << "CMC-Anisotropy..." << std::endl; zlog << "CMC-Anisotropy..." << std::endl; } program::cmc_anisotropy(); break; case 9: if(vmpi::my_rank==0){ std::cout << "Hybrid-CMC..." << std::endl; zlog << "Hybrid-CMC..." << std::endl; } program::hybrid_cmc(); break; case 10: if(vmpi::my_rank==0){ std::cout << "Reverse-Hybrid-CMC..." << std::endl; zlog << "Reverse-Hybrid-CMC..." << std::endl; } program::reverse_hybrid_cmc(); break; case 11: if(vmpi::my_rank==0){ std::cout << "LaGrange-Multiplier..." << std::endl; zlog << "LaGrange-Multiplier..." << std::endl; } program::lagrange_multiplier(); break; case 12: if(vmpi::my_rank==0){ std::cout << "partial-hysteresis-loop..." << std::endl; zlog << "partial-hysteresis-loop..." << std::endl; } program::partial_hysteresis_loop(); break; case 13: if(vmpi::my_rank==0){ std::cout << "localised-temperature-pulse..." << std::endl; zlog << "localised-temperature-pulse..." << std::endl; } program::localised_temperature_pulse(); break; case 14: if(vmpi::my_rank==0){ std::cout << "effective-damping..." << std::endl; zlog << "effective-damping..." << std::endl; } program::effective_damping(); break; case 15: if(vmpi::my_rank==0){ std::cout << "fmr..." << std::endl; zlog << "fmr..." << std::endl; } program::fmr(); break; case 16: if(vmpi::my_rank==0){ std::cout << "localised-field-cool..." << std::endl; zlog << "localised-field-cool..." << std::endl; } program::local_field_cool(); break; case 50: if(vmpi::my_rank==0){ std::cout << "Diagnostic-Boltzmann..." << std::endl; zlog << "Diagnostic-Boltzmann..." << std::endl; } program::boltzmann_dist(); break; case 51: if(vmpi::my_rank==0){ std::cout << "Setting..." << std::endl; zlog << "Setting..." << std::endl; } program::setting_process(); break; default:{ std::cerr << "Unknown Internal Program ID "<< sim::program << " requested, exiting" << std::endl; zlog << "Unknown Internal Program ID "<< sim::program << " requested, exiting" << std::endl; exit (EXIT_FAILURE); } } std::cout << "Simulation run time [s]: " << stopwatch.elapsed_seconds() << std::endl; zlog << zTs() << "Simulation run time [s]: " << stopwatch.elapsed_seconds() << std::endl; //------------------------------------------------ // Output Monte Carlo statistics if applicable //------------------------------------------------ if(sim::integrator==1){ std::cout << "Monte Carlo statistics:" << std::endl; std::cout << "\tTotal moves: " << long(sim::mc_statistics_moves) << std::endl; std::cout << "\t" << ((sim::mc_statistics_moves - sim::mc_statistics_reject)/sim::mc_statistics_moves)*100.0 << "% Accepted" << std::endl; std::cout << "\t" << (sim::mc_statistics_reject/sim::mc_statistics_moves)*100.0 << "% Rejected" << std::endl; zlog << zTs() << "Monte Carlo statistics:" << std::endl; zlog << zTs() << "\tTotal moves: " << sim::mc_statistics_moves << std::endl; zlog << zTs() << "\t" << ((sim::mc_statistics_moves - sim::mc_statistics_reject)/sim::mc_statistics_moves)*100.0 << "% Accepted" << std::endl; zlog << zTs() << "\t" << (sim::mc_statistics_reject/sim::mc_statistics_moves)*100.0 << "% Rejected" << std::endl; } if(sim::integrator==3 || sim::integrator==4){ std::cout << "Constrained Monte Carlo statistics:" << std::endl; std::cout << "\tTotal moves: " << cmc::mc_total << std::endl; std::cout << "\t" << (cmc::mc_success/cmc::mc_total)*100.0 << "% Accepted" << std::endl; std::cout << "\t" << (cmc::energy_reject/cmc::mc_total)*100.0 << "% Rejected (Energy)" << std::endl; std::cout << "\t" << (cmc::sphere_reject/cmc::mc_total)*100.0 << "% Rejected (Sphere)" << std::endl; zlog << zTs() << "Constrained Monte Carlo statistics:" << std::endl; zlog << zTs() << "\tTotal moves: " << cmc::mc_total << std::endl; zlog << zTs() << "\t" << (cmc::mc_success/cmc::mc_total)*100.0 << "% Accepted" << std::endl; zlog << zTs() << "\t" << (cmc::energy_reject/cmc::mc_total)*100.0 << "% Rejected (Energy)" << std::endl; zlog << zTs() << "\t" << (cmc::sphere_reject/cmc::mc_total)*100.0 << "% Rejected (Sphere)" << std::endl; } //program::LLB_Boltzmann(); // De-initialize GPU if(gpu::acceleration) gpu::finalize(); // optionally save checkpoint file if(sim::save_checkpoint_flag && !sim::save_checkpoint_continuous_flag) save_checkpoint(); return EXIT_SUCCESS; }
