bool process_conf(CavConfig &cfg)
{
Wpi_container points;
Voids_result res(cfg.atoms.size(), cfg.out_inf); // reserve space for atoms surf, pass main log stream
build_input(cfg.atoms, cfg.radii, cfg.r_scale, cfg.r_probe, points);
if (!regular_triangulation_voids(points, res)) {
cfg.out_inf << "algorithm fatal error!" << std::endl;
return false;
}
Surf::write_header(cfg.out_stl);
cfg.out_inf << std::setprecision(12);
cfg.out_inf << "Void num : Volume Surface " << std::endl;
for (std::size_t i = 0; i < res.voids.size(); i++) {
cfg.out_inf << std::setw(8) << i+1 << " : " << std::left << std::setw(17) << res.voids[i].volume << " ";
cfg.out_inf << res.voids[i].surface << std::right << std::endl;
if (cfg.out_vol.is_open()) cfg.out_vol << res.voids[i].volume << std::endl;
if (cfg.out_stl.is_open()) { // draw surface of void
std::vector<Weighted_point> wp;
scale_cavity_atoms(res.voids[i].atoms, cfg.atoms, cfg.radii, cfg.box, cfg.r_scale, cfg.r_probe, cfg.stl_scale, wp);
Surf::write_cavity_surface(cfg.out_stl, wp.begin(), wp.end(), cfg.nSubdiv);
}
}
Surf::write_footer(cfg.out_stl);
cfg.out_inf << "Voids count : " << res.voids.size() << std::endl;
long double total_void_volume = 0.0L;
long double total_void_surface = 0.0L;
long double total_void_surface_from_atoms = std::accumulate(res.atom_surf.begin(), res.atom_surf.end(), 0.0L); // for check
for (const auto &v: res.voids) {
total_void_volume += v.volume;
total_void_surface += v.surface;
}
// accumulate per atom surfaces
std::transform(res.atom_surf.begin(), res.atom_surf.end(), cfg.atom_confs_surf.begin(), cfg.atom_confs_surf.begin(), std::plus<long double>());
cfg.out_inf << std::setprecision(std::numeric_limits<double>::digits10);
cfg.out_inf << "voids total surface : " << total_void_surface << std::endl;
cfg.out_inf << "voids surf atom sum : " << total_void_surface_from_atoms << std::endl;
cfg.out_inf << "voids total volume : " << total_void_volume << std::endl;
cfg.out_inf << std::endl;
return true;
}
int main(int argc, char *argv[])
{
/* -h flag for help */
/* -o flag for output file */
int oflag = 0;
char *ovalue = NULL;
/* -i flag for input file */
int iflag = 0;
char *ivalue = NULL;
/* -q flag for questions file */
int qflag = 0; char *qvalue = NULL;
int opt = 0;
/* process options */
while ((opt = getopt(argc, argv, "hioq:")) != -1) {
switch (opt)
{
/* input file */
case 'i':
iflag = 1;
ivalue = optarg;
break;
/* output file */
case 'o':
oflag = 1;
ovalue = optarg;
break;
/* questions file */
case 'q':
qflag = 1;
qvalue = optarg;
//printf("\nqvalue is: %s\n", qvalue);
break;
/* h flag or error then print usage */
case '?':
case 'h':
print_usage();
return 1;
default:
print_usage();
return 1;
}
}
/* Set values based in arguments. */
if ( !oflag )
ovalue = "myoutput";
if ( !qflag )
{
qvalue = "../share/pass_gen/questions";
if (!file_exists(qvalue))
{
printf("\nDefault questions file: %s\n", qvalue);
printf("\nFile not found! Try using -q flag.\n\n");
return -1;
}
}
if ( !iflag )
ivalue = "custom_input";
/* Build an input file of words if not specified. */
build_input(qvalue, ivalue);
replace_chars(ivalue, ovalue);
append_numbers(ovalue, "output_numbers1");
prepend_numbers(ovalue, "output_numbers2");
concat_with_numbers(ivalue, "output_numbers3");
append_symbols(ivalue, "output_symbols1");
prepend_symbols(ivalue, "output_symbols2");
concat_with_symbols(ivalue, "output_symbols3");
return 0;
}
//MAIN LOGIC BEGINS
int main() {
//first unsigned int=total length of the actual representation, char = first 8 digits of the actual representation,
//each KeyObject has these properties:
//unsigned int unencodedLength; the total length of the unencoded number
//unsigned int firstNDigits; the first 32 digits of the unencoded number
//unsigned int primeRepresentation; the encoded representation of the number/key
std::vector<KeyObject> keys;
for(unsigned int i=0; i < 10000; i++){
keys.push_back(KeyObject());
}
//unsigned int initialLowerBoundIndex = 0;
//recursiveFillKeys(lowerBounds,upperBounds,initialLowerBoundIndex,keys,primes);
//simple examle of generating the keys structure. (these are the numbers we will reduce the file to,
//we store them in our ultra compact representation with some identifying info)
//for (unsigned int i=6; i<10; i++){
// for (unsigned int j=6; j<10; j++){
// keys[(h-6)*16 + (i-6)*4 + (j-6)] = unsigned integerExponent(prime[0],i)*unsigned integerExponent(prime[1],j)....
// }
//}
Vvi input(build_input());
std::cout << input << "\n";
Vvi output;
cart_product(input, output);
std::cout << output << "\n";
//sample input/output
//input
// (
// (0, 1, 2, )
// (10, 11, 12, )
// (20, 21, 22, )
// )
// output
// (
// (0, 10, 20, )
// (1, 10, 20, )
// (2, 10, 20, )
// (0, 11, 20, )
// (1, 11, 20, )
// (2, 11, 20, )
// (0, 12, 20, )
// (1, 12, 20, )
// (2, 12, 20, )
// (0, 10, 21, )
// (1, 10, 21, )
// (2, 10, 21, )
// (0, 11, 21, )
// (1, 11, 21, )
// (2, 11, 21, )
// (0, 12, 21, )
// (1, 12, 21, )
// (2, 12, 21, )
// (0, 10, 22, )
// (1, 10, 22, )
// (2, 10, 22, )
// (0, 11, 22, )
// (1, 11, 22, )
// (2, 11, 22, )
// (0, 12, 22, )
// (1, 12, 22, )
// (2, 12, 22, ))
unsigned int counter = 0;
for(Vvi::iterator it = output.begin(); ; ) {
//keyExponentValues gives us a vector with all the exponents we need to use
//to create a key
//here we calculate the number represented by the exponents
mpz_t n;
mpz_init(n);
mpz_set(n,1);
for (Vi::iterator keyExponentValues = it->begin(); ; ){
mpz_t k;
mpz_init(k);
mpz_set(k,globals.primes[counter]);
mpz_mul(n,n,k);
n *= k;
mpz_clear (k);
//mpz_sizeinbase (mpz_t op, int base)
//mpz_sizeinbase (mpz_t op, int base)
//base can only be up to size 62 max!
//here we store the length of the number represented by the exponents
keys[counter].unencodedLength = 0;
//here we store the first n digits of the number represented by the exponents
keys[counter].firstNDigits = 0;
mpz_clear (n);
//this simulates log base 2
unsigned int bitsToStoreExponent= 0;
unsigned int exponentRange = globals.exponentMax - globals.exponentMin;
while (exponentRange >>= 1) ++bitsToStoreExponent;
//IMPORTANT ENCODING LOCATED RIGHT HERE IN THIS COMMENT!!!
//00 = 6th power, 01=7th, 10=8th, 11=9th,
//first 2 bits are for 2, next 2 are for 3, next 2 are for 5, etc. etc.
unsigned int exponentCounter = 0;
for(Vi::iterator keyExponentValues = it->begin(); ; ) {
for (int j=globals.exponentMin; j<globals.exponentMax; j++){
for (int k=0;k<bitsToStoreExponent;k++){
//set i'th prime number bits to appropiate value between 0 and 2^k for exponent value j
//globals.exponentMin - j want to turn this into binary representation, get appropriate number for ith place
if (k==j){
//keys[counter].primeRepresentation();
//(globals.exponentMin - j) might be useful
if (*keyExponentValues % intPow(2,k)==0){//base 10 number convert to base two, get ith digit.
keys[counter].primeRepresentation.set(globals.howManyOfFirstNBitsStoredInKey
- exponentCounter*bitsToStoreExponent,1);
}
else{
keys[counter].primeRepresentation.set(globals.howManyOfFirstNBitsStoredInKey
- exponentCounter*bitsToStoreExponent,0);
}
}
}
}
//illustrative but less general example
//switch(keyExponentValues->me[i]){
// case 6:
// keys[counter].primeRepresentation();
// keys[counter].primeRepresentation.set[32-i*2,0];
// keys[counter].primeRepresentation.set[31-i*2,0];
// break;
// case 7:
// keys[counter].primeRepresentation();
// keys[counter].primeRepresentation.set[32,0];
// keys[counter].primeRepresentation.set[31,1];
// break;
// case 8:
// keys[counter].primeRepresentation();
// keys[counter].primeRepresentation.set[32,1];
// keys[counter].primeRepresentation.set[31,0];
// break;
// case 9:
// keys[counter].primeRepresentation();
// keys[counter].primeRepresentation.set[32,1];
// keys[counter].primeRepresentation.set[31,1];
// break;
//}
exponentCounter++;
keyExponentValues++;
}
}
counter++;
it++;
}
//HERE IS WHERE WE READ THE FILE IN THAT WE WILL ENCODE
//TODO move this to a different section
//char* input = getInputFromFile();
//unsigned int i = 0;
//while (input[i] != '\0'){
//}
return 0;
}
