void System<DataType,Integrator,Potential,Communicator>::simulate(int numIters, std::ostream & output) {
// MPI Comms. //
clearBuffers() ;
appendTransitionsToBuffers() ;
appendInteractionsToBuffers() ;
communicateInteractionsTransitions() ;
// Initialise the forces. //
updateForces() ;
// Prime the velocity based on the integration policy. //
for (unsigned int i = 0 ; i < positions.size() ; i+=2) {
Integrator::initialise(&positions[i], &velocities[i], &forces[i]) ;
}
// Update velocities and positions based on the integration policy. //
for (int i = 0; i < numIters ; ++i) {
updateVelocities() ;
updatePositions() ;
// MPI Comms.
clearBuffers() ;
appendTransitionsToBuffers() ;
appendInteractionsToBuffers() ;
communicateInteractionsTransitions() ;
updateForces() ;
printSystem(output,i) ;
output << std::endl << std::endl ;
}
} /* ----- end of member function simulate ----- */
int main(int argc, const char** argv)
{
printSystem("ESGI http-client version %s",VERSION);
if(argc != 2)
{
printUsage();
return 1;
}
// Send URL to URL handler
handleURL(argv[1]);
return 0;
}
int main(int argc, char **argv)
{
AnyOption *opt = new AnyOption();
opt->addUsage("");
opt->addUsage("Usage: ");
opt->addUsage("");
opt->addUsage(" -h --help Print usage ");
opt->addUsage(" -L --subsecLet Letter of Subsector (A-P) to generate, if omitted will generate entire sector ");
opt->addUsage(" -d --detail %|zero|rift|sparse|scattered|dense ");
opt->addUsage(" -m --maturity Tech level, backwater|frontier|mature|cluster ");
opt->addUsage(" -a --ac Two-letter system alignment code ");
opt->addUsage(" -s --secName Name of sector. For default output file name and sectorName_names.txt file");
opt->addUsage(" -p --path Path to sectorName_names.txt file ");
opt->addUsage(" -o --outFormat 1|2|3|4|5|6 : v1.0, v2.0, v2.1 v2.1b, v2.2, v2.5 ");
opt->addUsage(" -u --outPath Path and name of output file ");
opt->addUsage("");
opt->setCommandFlag("main", 'm');
opt->setCommandFlag("system", 'S');
opt->setCommandFlag("sector", 's');
opt->setCommandFlag("subsector", 'u');
opt->setCommandFlag("help", 'h');
opt->setCommandOption("", 'x');
opt->setCommandOption("", 'y');
opt->setCommandOption("", 'z');
opt->setCommandOption("detail", 'd');
opt->setCommandOption("seed");
//opt->setVerbose(); /* print warnings about unknown options */
//opt->autoUsagePrint(true); /* print usage for bad options */
opt->processCommandArgs(argc, argv);
#if 0
if(! opt->hasOptions()) { /* print usage if no options */
opt->printUsage();
delete opt;
return 0;
}
#endif
if(opt->getFlag("help") || opt->getFlag('h')) {
opt->printUsage();
delete opt;
return 0;
}
//long seed = 12345;
long x = 0;
long y = 10;
long z = 0;
int detail = 3;
if(opt->getValue('x') != NULL) {
x = atol(opt->getValue('x'));
}
if(opt->getValue('y') != NULL) {
y = atol(opt->getValue('y'));
}
if(opt->getValue('z') != NULL) {
z = atol(opt->getValue('z'));
}
if(opt->getValue("seed") != NULL) {
//seed = atol(opt->getValue("seed"));
}
if(opt->getValue("detail") != NULL) {
detail = atol(opt->getValue("detail"));
}
long startX, startY, startZ;
long endX, endY, endZ;
long sectorX = 8 * 4;
long sectorY = 10 * 4;
long sectorZ = 1;
if(opt->getFlag("sector")) {
startX = x / sectorX;
endX = startX + sectorX - 1;
startY = y / sectorY;
endY = startY + sectorY - 1;
startZ = z / sectorZ;
endZ = startZ + sectorZ - 1;
} else {
startX = x;
endX = x;
startY = y;
endY = y;
startZ = z;
endZ = z;
}
for(int i = startX; i <= endX; i++) {
for(int j = startY; j <= endY; j++) {
for(int k = startZ; k <= endZ; k++) {
printSystem(x, y, z, detail);
}
}
}
}
//@njz:default value removed. defined in .h file
//void AbelianEquationsSolver::findSolutions( File& file , bool out = true )
void AbelianEquationsSolver::findSolutions( File& file , bool out)
//
{
haveSol = 0;
if( !A.haveCyclicDecomposition() )
A.computeCyclicDecomposition();
if( !A.havePrimaryDecomposition() )
A.findPrimaryBasis();
if( !rawA.haveCyclicDecomposition() )
rawA.computeCyclicDecomposition();
if( !rawA.havePrimaryDecomposition() )
rawA.findPrimaryBasis();
makeSystem();
if( out )
{
if( system.length() > 1 )
file << "The system of equations: " << endl << endl;
else
file << "The equation: " << endl << endl;
printRawSystem( file );
file << endl << "can be transformed to the one: " << endl << endl;
printSystem( file );
if( system.length() > 1 )
file << endl << "Finding solutions of this system ..." << endl << endl;
else
file << endl << "Finding solutions of this equation ..." << endl << endl;
}
//@njz
// int **matrix = new (int*)[ system.length() ];
int **matrix = new int*[ system.length() ];
//
int i,j,k,i1,j1;
for( i = 0 ; i < system.length() ; i++ )
{
matrix[i] = new int[ numberOfVariables ];
for( j = 0 ; j < numberOfVariables ; j++ )
{
Integer u = (AbelianWord( numberOfVariables , system[i] ))[j];
matrix[i][j] = u.as_long();
}
}
VectorOf< VectorOf<int> > transform;
VectorOf<int> trans(3);
// diagonalization of the matrix
sysRank = 0;
for( i = 0 ; ( i < numberOfVariables && i < system.length() ) ; i++ )
{
bool flag = false;
for( j = i ; j < system.length() ; j++ )
{
for( k = i ; k < numberOfVariables ; k++ )
if( matrix[j][k] )
{
flag = true;
break;
}
if( flag ) break;
}
if( k == numberOfVariables && j == system.length() )
{
if( sysRank )
break;
int q;
for( q = 0 ; q < b.length() ; q++ )
if( !A.isTrivial( Word( b[q] ) ) )
{
haveSol = -1;
if( out )
if( system.length() > 1 )
file << "while computing the canonical form of the system it was found that this system has no solutions." << endl;
else
file << "while computing the canonical form of the equation it was found that this equation has no solutions." << endl;
return;
}
haveSol = 0;
if( out )
if( system.length() > 1 )
file << "while computing the canonical form of the system it was found that this system has all group as a set of solutions." << endl;
else
file << "while computing the canonical form of the equation it was found that this equation has all group as a set of solutions." << endl;
return;
}
int *tmp = matrix[i];
matrix[i] = matrix[j];
matrix[j] = tmp;
Word r = b[i];
b[i] = b[j];
b[j] = r;
for( j = 0 ; j < system.length() ; j++ )
{
int t = matrix[j][i];
matrix[j][i] = matrix[j][k];
matrix[j][k] = t;
}
if( i != k )
{
trans[0] = i;
trans[1] = k;
trans[2] = 0;
transform.append( trans );
}
while( true )
{
bool check;
bool flag;
int z;
bool done = false;
int count = i + 1;
while( !done )
{
for( j = count ; j < system.length() ; j++ )
if( matrix[j][i] && abs(matrix[i][i]) != abs(matrix[j][i]) )
break;
if( j == system.length() )
break;
count = j + 1;
flag = false;
while( !flag )
{
if( abs(matrix[i][i]) > abs(matrix[j][i]) )
{
z = matrix[i][i] / matrix[j][i];
for( k = i ; k < numberOfVariables ; k++ )
matrix[i][k] = matrix[i][k] - matrix[j][k] * z;
b[i] = b[i] * A.getFPGroup().raiseToPower(b[j],-z);
}
else
{
z = matrix[j][i] / matrix[i][i];
for( k = i ; k < numberOfVariables ; k++ )
matrix[j][k] = matrix[j][k] - matrix[i][k] * z;
b[j] = b[j] * A.getFPGroup().raiseToPower(b[i],-z);
}
if( !matrix[i][i] || !matrix[j][i] )
{
if( matrix[i][i] == 0 )
{
tmp = matrix[i];
matrix[i] = matrix[j];
matrix[j] = tmp;
r = b[i];
b[i] = b[j];
b[j] = r;
}
flag = true;
}
}
if( count == system.length() )
done = true;
}
check = true;
for( j = i + 1 ; j < numberOfVariables ; j++ )
if( matrix[i][j] % matrix[i][i] )
{
check = false;
break;
}
if( check )
break;
done = false;
count = i + 1;
while( !done )
{
for( j = count ; j < numberOfVariables ; j++ )
if( matrix[i][j] && abs(matrix[i][i]) != abs(matrix[i][j]) )
break;
if( j == numberOfVariables )
break;
count = j + 1;
flag = false;
while( !flag )
{
if( abs(matrix[i][i]) > abs(matrix[i][j]) )
{
z = matrix[i][i] / matrix[i][j];
for( k = i ; k < system.length() ; k++ )
matrix[k][i] = matrix[k][i] - matrix[k][j] * z;
trans[0] = j;
trans[1] = i;
trans[2] = -z;
transform.append( trans );
}
else
{
z = matrix[i][j] / matrix[i][i];
for( k = i ; k < system.length() ; k++ )
matrix[k][j] = matrix[k][j] - matrix[k][i] * z;
trans[0] = i;
trans[1] = j;
trans[2] = -z;
transform.append( trans );
}
if( !matrix[i][i] || !matrix[i][j] )
{
if( matrix[i][i] == 0 )
{
for( k = i ; k < system.length() ; k++ )
{
int a = matrix[k][i];
matrix[k][i] = matrix[k][j];
matrix[k][j] = a;
}
if( i != j )
{
trans[0] = i;
trans[1] = j;
trans[2] = 0;
transform.append( trans );
}
}
flag = true;
}
}
if( count == numberOfVariables )
done = true;
}
check = true;
for( j = i + 1 ; j < system.length() ; j++ )
if( matrix[j][i] % matrix[i][i] )
{
check = false;
break;
}
if( check )
break;
}
for( j = i + 1 ; j < system.length() ; j++ )
if( matrix[j][i] )
{
int z = matrix[j][i] / matrix[i][i];
for( k = i ; k < numberOfVariables ; k++ )
matrix[j][k] = matrix[j][k] - matrix[i][k] * z;
b[j] = b[j] * A.getFPGroup().raiseToPower(b[i],-z);
}
for( j = i + 1 ; j < numberOfVariables ; j++ )
if( matrix[i][j] )
{
int z = matrix[i][j] / matrix[i][i];
for( k = i ; k < system.length() ; k++ )
matrix[k][j] = matrix[k][j] - matrix[k][i] * z;
trans[0] = i;
trans[1] = j;
trans[2] = -z;
transform.append( trans );
}
sysRank++;
}
for( i = sysRank ; i < system.length() ; i++ )
{
if( !A.isTrivial( Word( b[i] ) ) )
{
haveSol = -1;
if( out )
if( system.length() > 1 )
file << "while computing the canonical form of the system it was found that this system has no solutions." << endl;
else
file << "while computing the canonical form of the equation it was found that this equation has no solutions." << endl;
return;
}
}
// finding solutions and output in file
if( out )
{
file << "The canonical form: ";
file << endl << endl;
}
for( int p = 0 ; p < sysRank ; p++ )
{
if( out )
{
file << "x" << p + 1;
if( matrix[p][p] != 1 )
file << "^" << matrix[p][p];
file << " = ";
}
AbelianWord w = A.oldInAbelianForm( b[p] );
w = A.oldToNewGens( w );
w = A.newToOldGens( w );
b[p] = w.getWord().freelyReduce();
if( out )
{
A.getFPGroup().printWord( file , b[p] );
file << endl;
}
}
VectorOf<int> xNums( numberOfVariables );
for( i = 0 ; i < sysRank ; i++ )
if( root( b[i] , matrix[i][i] ) )
{
x[i] = b[i];
xNums[i] = i;
if( !A.isFree() )
{
VectorOf<int> tmp(2);
tmp[0] = ( matrix[i][i] > 0 ) ? matrix[i][i] : -matrix[i][i];
tmp[1] = 1;
torsion[i].append( tmp );
}
}
else
{
haveSol = -1;
if( out )
{
if( system.length() > 1 )
file << endl << "The system is unsolvable because there are no solutions for: " << endl << endl;
else
file << endl << "The equation is unsolvable because there are no solutions for: " << endl << endl;
file << "x" << i + 1;
if( matrix[i][i] != 1 )
file << "^" << matrix[i][i];
file << " = ";
A.getFPGroup().printWord( file , b[i].freelyReduce() );
}
return;
}
for( j = sysRank ; j < numberOfVariables ; j++ )
{
x[j] = Word();
xNums[j] = j;
VectorOf<int> tmp(2);
tmp[0] = j - sysRank + 1;
tmp[1] = 1;
params[j].append( tmp );
}
for( i = transform.length() - 1 ; i >= 0 ; i-- )
{
trans = transform[i];
if( !trans[2] )
{
int ind1 = xNums.indexOf( trans[0] );
int ind2 = xNums.indexOf( trans[1] );
xNums[ind1] = trans[1];
xNums[ind2] = trans[0];
}
else
{
int ind1 = xNums.indexOf( trans[0] );
int ind2 = xNums.indexOf( trans[1] );
x[ind1] *= A.getFPGroup().raiseToPower( x[ind2] , trans[2] );
int len = torsion[ind1].length();
for( j = 0 ; j < torsion[ind2].length() ; j++ )
{
bool f = false;
for( k = 0 ; k < len ; k++ )
if( torsion[ind1][k][0] == torsion[ind2][j][0] )
{
f = true;
break;
}
if( f )
torsion[ind1][k][1] += torsion[ind2][j][1] * trans[2];
else
{
VectorOf<int> tmp = torsion[ind2][j];
tmp[1] *= trans[2];
torsion[ind1].append( tmp );
}
}
len = params[ind1].length();
for( j = 0 ; j < params[ind2].length() ; j++ )
{
bool f = false;
for( k = 0 ; k < len ; k++ )
if( params[ind1][k][0] == params[ind2][j][0] )
{
f = true;
break;
}
if( f )
params[ind1][k][1] += params[ind2][j][1] * trans[2];
else
{
VectorOf<int> tmp = params[ind2][j];
tmp[1] *= trans[2];
params[ind1].append( tmp );
}
}
}
}
for( i = 0 ; i < x.length() ; i++ )
{
AbelianWord w = A.oldInAbelianForm( x[i] );
w = A.oldToNewGens( w );
w = A.newToOldGens( w );
x[i] = w.getWord();
}
// output in file
if( out )
{
file << endl << "The set of solutions can be presented as follows: " << endl << endl;
FPGroup G = rawA.getFPGroup();
FPGroup G1 = A.getFPGroup();
for( i = 0 ; i < numberOfVariables ; i++ )
{
int n = xNums.indexOf( i );
bool flag = false;
G.printWord( file , Generator( i + 1 ) );
file << " -> ";
if( x[n].length() )
{
G1.printWord( file , x[n].freelyReduce() );
flag = true;
}
for( j = 0 ; j < torsion[n].length() ; j++ )
{
VectorOf<int> tmp = torsion[n][j];
int z = tmp[1] % tmp[0];
if( z )
if( tmp[1] > 0 )
{
if( flag )
file << " + ";
if( tmp[1] != 1 )
file << tmp[1] << " p( " << tmp[0] << " )";
else
file << "p( " << tmp[0] << " )";
flag = true;
}
else
{
file << " - ";
if( tmp[1] != -1 )
file << -tmp[1] << " p( " << tmp[0] << " )";
else
file << "p( " << tmp[0] << " )";
flag = true;
}
}
for( j = 0 ; j < params[n].length() ; j++ )
{
VectorOf<int> tmp = params[n][j];
if( tmp[1] )
if( tmp[1] > 0 )
{
if( flag )
file << " + ";
if( tmp[1] != 1 )
file << tmp[1] << " t" << tmp[0];
else
file << "t" << tmp[0];
flag = true;
}
else
{
file << " - ";
if( tmp[1] != -1 )
file << -tmp[1] << " t" << tmp[0];
else
file << "t" << tmp[0];
flag = true;
}
}
if( !flag )
file << "1 ";
if( i != numberOfVariables )
file << ",";
file << endl;
}
file << endl << "where p( n ) is any element of n-heigth and t_i - any element of the group." << endl;
}
VectorOf< VectorOf< VectorOf<int> > > t( numberOfVariables );
VectorOf< VectorOf< VectorOf<int> > > p( numberOfVariables );
VectorOf<Word> x1( numberOfVariables );
for( i = 0 ; i < numberOfVariables ; i++ )
{
int n = xNums.indexOf( i );
x1[i] = x[n];
t[i] = torsion[n];
p[i] = params[n];
}
torsion = t;
params = p;
x = x1;
for( i = 0 ; i < system.length() ; i++ )
delete [] matrix[i];
delete [] matrix;
}
int main(int argc, char* argv[])
{
int program = 0;
// Get input file from first command line argument
if(argc < 2){ // No input file given
std::cerr << "Usage: ./main [input_file]\n";
program = -1;
} else {
std::string ifname = argv[1]; // Input filename
std::string ofname = ifname; // Output file prefix
std::size_t pos = ofname.find('.');
if (pos != std::string::npos) { // Cut off extension
ofname.erase(pos, ofname.length());
}
// Open the input file
std::ifstream input(ifname);
// Check it opened successfully
if (!input.is_open()){
std::cerr << "Failed to open input file.\n";
program = -1;
} else {
// Make the system
System sys = makeSystem(input);
// Calculate the overlap integrals
sys.calcOverlap();
// Open main output file and print system details
std::ofstream output(ofname + ".out");
printSystem(sys, output, true);
// Do all the optional commands
int lastcmd = 0;
int flag = 1;
int orthog = 0;
std::vector<int> currcmd;
Eigen::MatrixXd f;
while(flag > 0){
currcmd = getNextCmd(input, lastcmd);
switch(currcmd[0]){
case 1: { // Print the overlap integrals
std::ofstream intout(ofname + ".ints");
printIntegrals(sys, intout);
intout.close();
break;
}
case 2: { // Print the sparse graph data
std::ofstream sparseout(ofname + ".sparse");
printSparseGraph(sys, sparseout, currcmd[1]);
sparseout.close();
break;
}
case 3: { // Canonical orthogonalisation
f = orthogonalise(sys, currcmd[1], CANONICAL);
orthog = 1;
break;
}
case 4: { // Gram-Schmidt orthogonalisation
f = orthogonalise(sys, currcmd[1], GRAM_SCHMIDT);
orthog = 2;
break;
}
case 5: { // Symmetric Lowdin orthogonalisation
f = orthogonalise(sys, currcmd[1], SYM_LOWDIN);
orthog = 3;
break;
}
case -1: { // Error
output << "\nErroneous command given.\n";
flag = 0;
program = -1;
break;
}
default: { // No more commands
output << "\nProgram finished.\n";
flag = 0;
}
}
lastcmd++;
}
// Print orthogonalisation data if needed
if (orthog > 0) {
std::ofstream orthogout(ofname + ".orthog");
printOrthog(sys, orthogout, f, orthog);
orthogout.close();
}
output.close();
}
}
return program;
}
