I am at a bit of a loss. I have instantiated an std::array <int,9> acceptances with 9 zeros manually plugged.
This is kind of a long snippet of code, but I do not know what else to do. I have highlighted everywhere I have printed out acceptances. For some reasons, acceptances[1] = garbage. I do not see why this is happening. Right now, I am simply reassigning the value, but now I am worried stuff like this might happen elsewhere.
Here is the code:
// INSTANTIATE SIMULATIONS VARIABLES
int step_number {0};
int move_number {0};
double sysEnergy {0};
bool IMP_BOOL {true};
std::array <int,9> attempts = {0,0,0,0,0,0,0,0,0};
std::array <int,9> acceptances = {0,0,0,0,0,0,0,0,0};
std::array <double,8> contacts = {0,0,0,0,0,0,0,0};
std::cout << "acceptances[1] = " << acceptances[1] << std::endl;
//~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#
// Parse inputs...
// This command will take all of the above inputs and make sure they are valid.
InputParser ( dfreq, max_iter, r, positions, topology, dfile, efile, mfile, stats_file, lattice_file_read );
//~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#
//~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#
// ExtractNumberOfPolymers extracts the total number of chains in the input file. used to reserve vector [line 171]
const int N = ExtractNumberOfPolymers(positions);
// EXTRACT TOPOLOGY FROM FILE
std::array <double,13> info_vec {ExtractTopologyFromFile(topology)};
// info_vec is the vector with all the information that constitutes the toplogy of the simulation
// assign values from info vec to relevant variables
const int x = info_vec[0] ;
const int y = info_vec[1] ;
const int z = info_vec[2] ;
const double T = info_vec[3] ;
const double frac = info_vec[12];
std::array <double,8> E = {info_vec[4], info_vec[5], info_vec[6], info_vec[7], info_vec[8], info_vec[9], info_vec[10], info_vec[11]};
// initialize custom data structures
std::vector <Polymer> Polymers;
Polymers.reserve(N);
std::vector <Particle*> LATTICE;
LATTICE.reserve (x*y*z);
std::vector <int> solvation_shells;
solvation_shells.reserve(26*26*N);
//~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#
// OPENING TILES
std::cout << std::endl;
std::cout << "Preparing for take-off...\n\n" ;
std::cout << "Chemical information: " << std::endl;
std::cout << "Number of polymers is " << N << ".\n\n";
std::cout << "Geometric information about simulation cell: " << std::endl;
std::cout << "x = " << x <<", y = " << y << ", z = "<< z << "." << std::endl << std::endl;
std::cout << "Thermodynamic and energetic information about simulation: " << std::endl;
std::cout << "Temperature = " << T << "." << std::endl;
std::cout << "Emm_a = " << E[0] <<", Emm_n = " << E[1] << ", Ems1_a = "<< E[2] << ", Ems1_n = " << E[3] <<".\n";
std::cout << "Ems2_a = " << E[4] <<", Ems2_n = " << E[5] << ", Es1s2_a = "<< E[6] << ", Es1s2_n = " << E[7] <<".\n";
std::cout << "Off to a good start. \n\n";
std::cout << "--------------------------------------------------------------------\n" << std::endl;
std::cout << "Running some more checks on input... \n\n" ;
std::cout << "acceptances[1] = " << acceptances[1] << std::endl;
//~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#
// set timers for simulation set-up.
auto start = std::chrono::high_resolution_clock::now();
auto stop = std::chrono::high_resolution_clock::now();
auto duration = std::chrono::duration_cast<std::chrono::milliseconds> (stop-start);
if ( !r ){
std::cout << "Setting up the lattice from scratch! " << std::endl;
SetUpLatticeFromScratch (&Polymers, &LATTICE, positions, frac, x, y, z);
stop = std::chrono::high_resolution_clock::now();
duration = std::chrono::duration_cast<std::chrono::milliseconds> (stop-start);
std::cout << "Solvation took " << duration.count () << " milliseconds." << std::endl;
std::cout << "Cell has been solvated! \n\n" ;
dumpPositionsOfPolymers(&Polymers, step_number, dfile);
}
//~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#
else {
std::cout << "Setting up system from a restart file!" << std::endl;
SetUpLatticeFromRestart (x, y, z, &Polymers, &LATTICE, &step_number, lattice_file_read, dfile, positions );
stop = std::chrono::high_resolution_clock::now();
duration = std::chrono::duration_cast<std::chrono::milliseconds> (stop-start);
std::cout << "System set-up took " << duration.count () << " milliseconds." << std::endl;
std::cout << "Simulation cell has been made! \n\n" ;
}
//~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#
//~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#
// THERMODYNAMICS OF SET-UP
std::cout <<"\nCalculating energy..." << std::endl;
sysEnergy = CalculateEnergy(&Polymers, &LATTICE, &solvation_shells, &E, &contacts, x, y, z);
std::cout << "Energy of system is " << sysEnergy << ".\n" << std::endl;
// if i am not restarting, i do not need to dump anything. All the information is already present.
if (!r) {
dumpEnergy (sysEnergy, step_number, &contacts, efile);
dumpOrientation (&Polymers, &LATTICE, step_number, mfile, x, y, z);
}
else {
dumpOrientation (&Polymers, &LATTICE, step_number, mfile, x, y, z);
}
std::cout << "Initiation complete. We are ready to go. The engine will output information every " << dfreq << " configuration(s)." << std::endl;
std::cout << "Number of iteration to perform: " << max_iter << "." << std::endl;
// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!
std::cout << "acceptances[1] = " << acceptances[1] << std::endl;
acceptances[1] = 0;
std::cout << "acceptances[1] = " << acceptances[1] << std::endl;
// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
The output reads:
acceptances[1] = 0
.
.
.
acceptances[1] = 1079214080
acceptances[1] = 0
I don't get it. I am not touching acceptances, yet, somehow it is being corrupted in there somewhere. Why is this happening? I am using clang, an Apple M1, -mcpu=apple-m1.