| 1 | 
+ | 
 /* | 
| 2 | 
+ | 
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. | 
| 3 | 
+ | 
 * | 
| 4 | 
+ | 
 * The University of Notre Dame grants you ("Licensee") a | 
| 5 | 
+ | 
 * non-exclusive, royalty free, license to use, modify and | 
| 6 | 
+ | 
 * redistribute this software in source and binary code form, provided | 
| 7 | 
+ | 
 * that the following conditions are met: | 
| 8 | 
+ | 
 * | 
| 9 | 
+ | 
 * 1. Acknowledgement of the program authors must be made in any | 
| 10 | 
+ | 
 *    publication of scientific results based in part on use of the | 
| 11 | 
+ | 
 *    program.  An acceptable form of acknowledgement is citation of | 
| 12 | 
+ | 
 *    the article in which the program was described (Matthew | 
| 13 | 
+ | 
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher | 
| 14 | 
+ | 
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented | 
| 15 | 
+ | 
 *    Parallel Simulation Engine for Molecular Dynamics," | 
| 16 | 
+ | 
 *    J. Comput. Chem. 26, pp. 252-271 (2005)) | 
| 17 | 
+ | 
 * | 
| 18 | 
+ | 
 * 2. Redistributions of source code must retain the above copyright | 
| 19 | 
+ | 
 *    notice, this list of conditions and the following disclaimer. | 
| 20 | 
+ | 
 * | 
| 21 | 
+ | 
 * 3. Redistributions in binary form must reproduce the above copyright | 
| 22 | 
+ | 
 *    notice, this list of conditions and the following disclaimer in the | 
| 23 | 
+ | 
 *    documentation and/or other materials provided with the | 
| 24 | 
+ | 
 *    distribution. | 
| 25 | 
+ | 
 * | 
| 26 | 
+ | 
 * This software is provided "AS IS," without a warranty of any | 
| 27 | 
+ | 
 * kind. All express or implied conditions, representations and | 
| 28 | 
+ | 
 * warranties, including any implied warranty of merchantability, | 
| 29 | 
+ | 
 * fitness for a particular purpose or non-infringement, are hereby | 
| 30 | 
+ | 
 * excluded.  The University of Notre Dame and its licensors shall not | 
| 31 | 
+ | 
 * be liable for any damages suffered by licensee as a result of | 
| 32 | 
+ | 
 * using, modifying or distributing the software or its | 
| 33 | 
+ | 
 * derivatives. In no event will the University of Notre Dame or its | 
| 34 | 
+ | 
 * licensors be liable for any lost revenue, profit or data, or for | 
| 35 | 
+ | 
 * direct, indirect, special, consequential, incidental or punitive | 
| 36 | 
+ | 
 * damages, however caused and regardless of the theory of liability, | 
| 37 | 
+ | 
 * arising out of the use of or inability to use software, even if the | 
| 38 | 
+ | 
 * University of Notre Dame has been advised of the possibility of | 
| 39 | 
+ | 
 * such damages. | 
| 40 | 
+ | 
 */ | 
| 41 | 
+ | 
  | 
| 42 | 
  | 
#include <stdlib.h> | 
| 43 | 
  | 
#include <stdio.h> | 
| 44 | 
  | 
#include <string.h> | 
| 45 | 
  | 
 | 
| 46 | 
< | 
#include "Globals.hpp" | 
| 47 | 
< | 
#include "simError.h" | 
| 46 | 
> | 
#include "io/Globals.hpp" | 
| 47 | 
> | 
#include "utils/simError.h" | 
| 48 | 
  | 
#ifdef IS_MPI | 
| 49 | 
< | 
#include "mpiBASS.h" | 
| 49 | 
> | 
#include "io/mpiBASS.h" | 
| 50 | 
  | 
#endif // is_mpi | 
| 51 | 
  | 
 | 
| 52 | 
  | 
/* | 
| 112 | 
  | 
#define G_THERM_INT_LAMBDA  50 | 
| 113 | 
  | 
#define G_THERM_INT_K       51 | 
| 114 | 
  | 
#define G_FORCEFIELD_VARIANT 52 | 
| 115 | 
< | 
 | 
| 115 | 
> | 
#define G_FORCEFIELD_FILENAME 53 | 
| 116 | 
  | 
Globals::Globals(){ | 
| 117 | 
  | 
  initalize(); | 
| 118 | 
  | 
} | 
| 196 | 
  | 
  addHash( "thermodynamicIntegrationLambda",       G_THERM_INT_LAMBDA); | 
| 197 | 
  | 
  addHash( "thermodynamicIntegrationK",            G_THERM_INT_K); | 
| 198 | 
  | 
  addHash( "forceFieldVariant",                    G_FORCEFIELD_VARIANT); | 
| 199 | 
< | 
 | 
| 199 | 
> | 
  addHash( "forceFieldFileName",                    G_FORCEFIELD_FILENAME); | 
| 200 | 
> | 
   | 
| 201 | 
  | 
  strcpy( mixingRule,"standard");  //default mixing rules to standard. | 
| 202 | 
  | 
  usePBC = 1; //default  periodic boundry conditions to on | 
| 203 | 
  | 
  useRF  = 0; | 
| 254 | 
  | 
  have_thermodynamic_integration_lambda = 0; | 
| 255 | 
  | 
  have_thermodynamic_integration_k = 0; | 
| 256 | 
  | 
  have_forcefield_variant = 0; | 
| 257 | 
+ | 
  have_forcefield_filename = 0;  | 
| 258 | 
  | 
 | 
| 259 | 
  | 
} | 
| 260 | 
  | 
 | 
| 1432 | 
  | 
 | 
| 1433 | 
  | 
      case STRING: | 
| 1434 | 
  | 
        the_event->err_msg =  | 
| 1435 | 
< | 
          strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not a double or int.\n" ); | 
| 1435 | 
> | 
          strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not an int.\n" ); | 
| 1436 | 
  | 
        return 1; | 
| 1437 | 
  | 
        break; | 
| 1438 | 
  | 
         | 
| 1439 | 
  | 
      case DOUBLE: | 
| 1440 | 
< | 
        minimizer_writefrq= the_event->evt.asmt.rhs.dval; | 
| 1441 | 
< | 
        have_minimizer_writefrq = 1; | 
| 1440 | 
> | 
        the_event->err_msg =  | 
| 1441 | 
> | 
          strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not an  int.\n" ); | 
| 1442 | 
  | 
        return 1; | 
| 1443 | 
  | 
        break; | 
| 1444 | 
  | 
         | 
| 1548 | 
  | 
 | 
| 1549 | 
  | 
      case STRING: | 
| 1550 | 
  | 
        the_event->err_msg =  | 
| 1551 | 
< | 
          strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not a double or int.\n" ); | 
| 1551 | 
> | 
          strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not an int.\n" ); | 
| 1552 | 
  | 
        return 1; | 
| 1553 | 
  | 
        break; | 
| 1554 | 
  | 
         | 
| 1555 | 
  | 
      case DOUBLE: | 
| 1556 | 
< | 
        minimizer_ls_maxiteration = the_event->evt.asmt.rhs.dval; | 
| 1557 | 
< | 
        have_minimizer_ls_maxiteration = 1; | 
| 1556 | 
> | 
        the_event->err_msg =  | 
| 1557 | 
> | 
          strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not an int.\n" ); | 
| 1558 | 
  | 
        return 1; | 
| 1559 | 
  | 
        break; | 
| 1560 | 
  | 
         | 
| 1734 | 
  | 
       | 
| 1735 | 
  | 
      the_event->err_msg =  | 
| 1736 | 
  | 
        strdup( "Error in parsing meta-data file!\n\tforceFieldVariant was not a string assignment.\n" ); | 
| 1737 | 
+ | 
      return 0; | 
| 1738 | 
+ | 
      break;       | 
| 1739 | 
+ | 
      // add more token cases here.       | 
| 1740 | 
+ | 
 | 
| 1741 | 
+ | 
    case G_FORCEFIELD_FILENAME: | 
| 1742 | 
+ | 
      if( the_type == STRING ){ | 
| 1743 | 
+ | 
        strcpy( forcefield_filename, the_event->evt.asmt.rhs.sval ); | 
| 1744 | 
+ | 
        have_forcefield_filename = 1; | 
| 1745 | 
+ | 
        return 1; | 
| 1746 | 
+ | 
      } | 
| 1747 | 
+ | 
       | 
| 1748 | 
+ | 
      the_event->err_msg =  | 
| 1749 | 
+ | 
        strdup( "Error in parsing meta-data file!\n\tforceFieldFileName was not a string assignment.\n" ); | 
| 1750 | 
  | 
      return 0; | 
| 1751 | 
  | 
      break;       | 
| 1752 | 
  | 
      // add more token cases here.       |