message: commandline args work but the program doesn't
diff: @@ -48,21 +48,40 @@ void make_mol(std::vector<atom_params>& atoms, std::vector<smt>& types,
  }
  }
  -int main() {
  +int main(int argc, char* argv[]) {
  //TODO: include progress bar?
  //set up program options
  - std::string logname("log.test");
  - auto seed = std::random_device()();
  + std::string logname;
  + unsigned seed;
  namespace po = boost::program_options;
  + po::positional_options_description positional; // remains empty
  po::options_description inputs("Input");
  inputs.add_options()
  ("seed,s", po::value<unsigned>(&seed), "seed for random number generator")
  - ("log", po::value<std::string>(&logname), "specify logfile, default is log.test");
  + ("log", po::value<std::string>(&logname), "specify logfile, default is test.log");
  po::options_description desc, desc_simple;
  desc.add(inputs);
  desc_simple.add(inputs);
  -
  - seed = 0;
  + po::variables_map vm;
  + try
  + {
  + po::store(
  + po::command_line_parser(argc, argv).options(desc)
  + .style(
  + po::command_line_style::default_style
  + ^ po::command_line_style::allow_guessing)
  + .positional(positional).run(), vm);
  + notify(vm);
  + } catch (po::error& e)
  + {
  + std::cerr << "Command line parse error: " << e.what() << '\n'
  + << "\nCorrect usage:\n" << desc_simple << '\n';
  + return 1;
  + }
  + if (!vm.count("seed"))
  + seed = std::random_device()();
  + if (!vm.count("logname"))
  + logname = "test.log";
  //set up c++11 random number engine
  std::mt19937 engine(seed);
  