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Comparing trunk/OOPSE-2.0/src/io/Globals.cpp (file contents):
Revision 1490 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 2204 by gezelter, Fri Apr 15 22:04:00 2005 UTC

# Line 1 | Line 1
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   /*
53   * The following section lists all of the defined tokens for the
54 < * gloabal assignment statements. All are prefixed with a G_ to avoid
54 > * global assignment statements. All are prefixed with a G_ to avoid
55   * stepping on any previously defined enumerations.
56   *
57   * NOTE: tokens start at 1, 0 is a resrved token number
# Line 71 | Line 112
112   #define G_THERM_INT_LAMBDA  50
113   #define G_THERM_INT_K       51
114   #define G_FORCEFIELD_VARIANT 52
115 + #define G_FORCEFIELD_FILENAME 53
116 + #define G_THERM_INT_DIST_SPRING  54
117 + #define G_THERM_INT_THETA_SPRING 55
118 + #define G_THERM_INT_OMEGA_SPRING 56
119  
120   Globals::Globals(){
121    initalize();
# Line 78 | Line 123 | Globals::~Globals(){
123  
124   Globals::~Globals(){
125    int i;
81 –
82 –  for( i=0; i<hash_size; i++ ){
83 –    if( command_table[i] != NULL ) delete command_table[i];
84 –  }
85 –  delete[] command_table;
86 –
126    if( components != NULL ){
127      for( i=0; i<n_components; i++ ) delete components[i];
128      delete[] components;
# Line 93 | Line 132 | void Globals::initalize(){
132   void Globals::initalize(){
133    int i;
134    
96 –  hash_size = 23;
97 –  hash_shift = 4;
98 –  
135    components = NULL;
136    
137 <  command_table = new LinkedCommand*[hash_size];
138 <  for( i=0; i<hash_size; i++ ) command_table[i] = NULL;
139 <  
140 <  addHash( "forceField",    G_FORCEFIELD );
141 <  addHash( "nComponents",   G_NCOMPONENTS );
142 <  addHash( "targetTemp",    G_TARGETTEMP );
143 <  addHash( "ensemble",      G_ENSEMBLE );
144 <  
145 <  addHash( "dt",            G_DT );
146 <  addHash( "runTime",       G_RUNTIME );
147 <  
148 <  addHash( "initialConfig", G_INITIALCONFIG );
149 <  addHash( "finalConfig",   G_FINALCONFIG );
150 <  addHash( "nMol",          G_NMOL );
151 <  addHash( "density",       G_DENSITY );
152 <  addHash( "box",           G_BOX );
153 <  addHash( "boxX",          G_BOXX );
154 <  addHash( "boxY",          G_BOXY );
155 <  addHash( "boxZ",          G_BOXZ );
156 <  addHash( "sampleTime",    G_SAMPLETIME );
157 <  addHash( "resetTime",     G_RESETTIME );
158 <  addHash( "statusTime",    G_STATUSTIME );
159 <  addHash( "cutoffRadius",  G_RCUT );
160 <  addHash( "switchingRadius",  G_RSW );
161 <  addHash( "dielectric",    G_DIELECTRIC );
162 <  addHash( "tempSet",       G_TEMPSET );
163 <  addHash( "thermalTime",   G_THERMALTIME );
164 <  addHash( "mixingRule",    G_MIXINGRULE);
165 <  addHash( "usePeriodicBoundaryConditions",        G_USEPBC);
166 <  addHash( "useReactionField",                     G_USERF );
167 <  addHash( "targetPressure",                       G_TARGETPRESSURE);
168 <  addHash( "tauThermostat",                        G_TAUTHERMOSTAT);
169 <  addHash( "tauBarostat",                          G_TAUBAROSTAT);
170 <  addHash( "zconsTime",                            G_ZCONSTIME);
171 <  addHash( "nZconstraints",                        G_NZCONSTRAINTS);
172 <  addHash( "zconsTol",                             G_ZCONSTOL);
173 <  addHash( "zconsForcePolicy",                     G_ZCONSFORCEPOLICY);
174 <  addHash( "seed",                                 G_SEED);
175 <  addHash( "useInitialTime",                       G_USEINITTIME);
176 <  addHash( "useInitialExtendedSystemState",        G_USEINIT_XS_STATE);
177 <  addHash( "orthoBoxTolerance",                    G_ORTHOBOXTOLERANCE);
178 <  addHash( "minimizer",                            G_MINIMIZER);
179 <  addHash( "minimizerMaxIter",                     G_MIN_MAXITER);
180 <  addHash( "minimizerWriteFrq",                    G_MIN_WRITEFRQ);
181 <  addHash( "minimizerStepSize",                    G_MIN_STEPSIZE);
182 <  addHash( "minimizerFTol",                        G_MIN_FTOL);
183 <  addHash( "minimizerGTol",                        G_MIN_GTOL);
184 <  addHash( "minimizerLSTol",                       G_MIN_LSTOL);
185 <  addHash( "minimizerLSMaxIter",                   G_MIN_LSMAXITER);
186 <  addHash( "zconsGap",                             G_ZCONSGAP);
187 <  addHash( "zconsFixtime",                         G_ZCONSFIXTIME);
188 <  addHash( "zconsUsingSMD",                        G_ZCONSUSINGSMD);
189 <  addHash( "useSolidThermInt",                     G_USE_SOLID_THERM_INT);
190 <  addHash( "useLiquidThermInt",                    G_USE_LIQUID_THERM_INT);
191 <  addHash( "thermodynamicIntegrationLambda",       G_THERM_INT_LAMBDA);
192 <  addHash( "thermodynamicIntegrationK",            G_THERM_INT_K);
157 <  addHash( "forceFieldVariant",                    G_FORCEFIELD_VARIANT);
137 >  command_table.insert(CommandMapType::value_type("forceField", G_FORCEFIELD));
138 >  command_table.insert(CommandMapType::value_type("nComponents", G_NCOMPONENTS));
139 >  command_table.insert(CommandMapType::value_type("targetTemp", G_TARGETTEMP));
140 >  command_table.insert(CommandMapType::value_type("ensemble", G_ENSEMBLE));
141 >  command_table.insert(CommandMapType::value_type("dt", G_DT));
142 >  command_table.insert(CommandMapType::value_type("runTime", G_RUNTIME));
143 >  command_table.insert(CommandMapType::value_type("initialConfig", G_INITIALCONFIG));
144 >  command_table.insert(CommandMapType::value_type("finalConfig", G_FINALCONFIG));
145 >  command_table.insert(CommandMapType::value_type("nMol", G_NMOL));
146 >  command_table.insert(CommandMapType::value_type("density", G_DENSITY));
147 >  command_table.insert(CommandMapType::value_type("box", G_BOX));
148 >  command_table.insert(CommandMapType::value_type("boxX", G_BOXX));
149 >  command_table.insert(CommandMapType::value_type("boxY", G_BOXY));
150 >  command_table.insert(CommandMapType::value_type("boxZ", G_BOXZ));
151 >  command_table.insert(CommandMapType::value_type("sampleTime", G_SAMPLETIME));
152 >  command_table.insert(CommandMapType::value_type("resetTime", G_RESETTIME));
153 >  command_table.insert(CommandMapType::value_type("statusTime", G_STATUSTIME));
154 >  command_table.insert(CommandMapType::value_type("cutoffRadius", G_RCUT));
155 >  command_table.insert(CommandMapType::value_type("switchingRadius", G_RSW));
156 >  command_table.insert(CommandMapType::value_type("dielectric", G_DIELECTRIC));
157 >  command_table.insert(CommandMapType::value_type("tempSet", G_TEMPSET));
158 >  command_table.insert(CommandMapType::value_type("thermalTime", G_THERMALTIME));
159 >  command_table.insert(CommandMapType::value_type("mixingRule", G_MIXINGRULE));
160 >  command_table.insert(CommandMapType::value_type("usePeriodicBoundaryConditions", G_USEPBC));
161 >  command_table.insert(CommandMapType::value_type("useReactionField", G_USERF));
162 >  command_table.insert(CommandMapType::value_type("targetPressure", G_TARGETPRESSURE));
163 >  command_table.insert(CommandMapType::value_type("tauThermostat", G_TAUTHERMOSTAT));
164 >  command_table.insert(CommandMapType::value_type("tauBarostat", G_TAUBAROSTAT));
165 >  command_table.insert(CommandMapType::value_type("zconsTime", G_ZCONSTIME));
166 >  command_table.insert(CommandMapType::value_type("nZconstraints", G_NZCONSTRAINTS));
167 >  command_table.insert(CommandMapType::value_type("zconsTol", G_ZCONSTOL));
168 >  command_table.insert(CommandMapType::value_type("zconsForcePolicy", G_ZCONSFORCEPOLICY));
169 >  command_table.insert(CommandMapType::value_type("seed", G_SEED));
170 >  command_table.insert(CommandMapType::value_type("useInitialTime", G_USEINITTIME));
171 >  command_table.insert(CommandMapType::value_type("useInitialExtendedSystemState", G_USEINIT_XS_STATE));
172 >  command_table.insert(CommandMapType::value_type("orthoBoxTolerance", G_ORTHOBOXTOLERANCE));
173 >  command_table.insert(CommandMapType::value_type("minimizer", G_MINIMIZER));
174 >  command_table.insert(CommandMapType::value_type("minimizerMaxIter", G_MIN_MAXITER));
175 >  command_table.insert(CommandMapType::value_type("minimizerWriteFrq", G_MIN_WRITEFRQ));
176 >  command_table.insert(CommandMapType::value_type("minimizerStepSize", G_MIN_STEPSIZE));
177 >  command_table.insert(CommandMapType::value_type("minimizerFTol", G_MIN_FTOL));
178 >  command_table.insert(CommandMapType::value_type("minimizerGTol", G_MIN_GTOL));
179 >  command_table.insert(CommandMapType::value_type("minimizerLSTol", G_MIN_LSTOL));
180 >  command_table.insert(CommandMapType::value_type("minimizerLSMaxIter", G_MIN_LSMAXITER));
181 >  command_table.insert(CommandMapType::value_type("zconsGap", G_ZCONSGAP));
182 >  command_table.insert(CommandMapType::value_type("zconsFixtime", G_ZCONSFIXTIME));
183 >  command_table.insert(CommandMapType::value_type("zconsUsingSMD", G_ZCONSUSINGSMD));
184 >  command_table.insert(CommandMapType::value_type("useSolidThermInt", G_USE_SOLID_THERM_INT));
185 >  command_table.insert(CommandMapType::value_type("useLiquidThermInt", G_USE_LIQUID_THERM_INT));
186 >  command_table.insert(CommandMapType::value_type("thermodynamicIntegrationLambda", G_THERM_INT_LAMBDA));
187 >  command_table.insert(CommandMapType::value_type("thermodynamicIntegrationK", G_THERM_INT_K));
188 >  command_table.insert(CommandMapType::value_type("forceFieldVariant", G_FORCEFIELD_VARIANT));
189 >  command_table.insert(CommandMapType::value_type("forceFieldFileName", G_FORCEFIELD_FILENAME));
190 >  command_table.insert(CommandMapType::value_type("thermIntDistSpringConst", G_THERM_INT_DIST_SPRING));
191 >  command_table.insert(CommandMapType::value_type("thermIntThetaSpringConst", G_THERM_INT_THETA_SPRING));
192 >  command_table.insert(CommandMapType::value_type("thermIntOmegaSpringConst", G_THERM_INT_OMEGA_SPRING));
193  
194 +
195    strcpy( mixingRule,"standard");  //default mixing rules to standard.
196    usePBC = 1; //default  periodic boundry conditions to on
197    useRF  = 0;
# Line 212 | Line 248 | void Globals::initalize(){
248    have_thermodynamic_integration_lambda = 0;
249    have_thermodynamic_integration_k = 0;
250    have_forcefield_variant = 0;
251 <
251 >  have_forcefield_filename = 0;
252 >  have_dist_spring_constant =  0;
253 >  have_theta_spring_constant = 0;
254 >  have_omega_spring_constant = 0;
255   }
256  
257   int Globals::newComponent( event* the_event ){
# Line 360 | Line 399 | int Globals::globalAssign( event* the_event ){
399    char err[300];
400    
401    token = 0;
402 <  key = hash( lhs );
403 <  if( command_table[key] != NULL ) token = command_table[key]->match( lhs );
402 >
403 >  CommandMapType::iterator iter;
404 >  std::string keyword(lhs);
405 >  iter = command_table.find(keyword);
406 >  if (iter != command_table.end()) {
407 >    token = iter->second;
408 >  }
409    
410    if( token ){
411      
# Line 1205 | Line 1249 | int Globals::globalAssign( event* the_event ){
1249        switch( the_type ){
1250          
1251        case STRING:
1252 <   strcpy(zconsForcePolicy, the_event->evt.asmt.rhs.sval);
1252 >        strcpy(zconsForcePolicy, the_event->evt.asmt.rhs.sval);
1253  
1254 <   for(int i = 0; zconsForcePolicy[i] != '\0'; i++)
1255 <        {
1256 <      zconsForcePolicy[i] = toupper(zconsForcePolicy[i]);
1257 <   }
1254 >        for(int i = 0; zconsForcePolicy[i] != '\0'; i++)
1255 >          {
1256 >            zconsForcePolicy[i] = toupper(zconsForcePolicy[i]);
1257 >          }
1258          have_zcons_force_policy = 1;
1259 <   return 1;
1259 >        return 1;
1260          break;
1261          
1262        case DOUBLE:
# Line 1389 | Line 1433 | int Globals::globalAssign( event* the_event ){
1433  
1434        case STRING:
1435          the_event->err_msg =
1436 <          strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not a double or int.\n" );
1436 >          strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not an int.\n" );
1437          return 1;
1438          break;
1439          
1440        case DOUBLE:
1441 <        minimizer_writefrq= the_event->evt.asmt.rhs.dval;
1442 <        have_minimizer_writefrq = 1;
1441 >        the_event->err_msg =
1442 >          strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not an  int.\n" );
1443          return 1;
1444          break;
1445          
# Line 1505 | Line 1549 | int Globals::globalAssign( event* the_event ){
1549  
1550        case STRING:
1551          the_event->err_msg =
1552 <          strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not a double or int.\n" );
1552 >          strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not an int.\n" );
1553          return 1;
1554          break;
1555          
1556        case DOUBLE:
1557 <        minimizer_ls_maxiteration = the_event->evt.asmt.rhs.dval;
1558 <        have_minimizer_ls_maxiteration = 1;
1557 >        the_event->err_msg =
1558 >          strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not an int.\n" );
1559          return 1;
1560          break;
1561          
# Line 1563 | Line 1607 | int Globals::globalAssign( event* the_event ){
1607        switch( the_type ){
1608          
1609        case STRING:
1610 <   the_event->err_msg =
1610 >        the_event->err_msg =
1611            strdup( "Error in parsing meta-data file!\n\tseed is not a string.\n" );
1612          return 0;
1613 <   return 0;
1613 >        return 0;
1614          break;
1615          
1616        case DOUBLE:
1617 <   have_seed = 1;
1618 <   seed = (int)the_event->evt.asmt.rhs.dval;
1617 >        have_seed = 1;
1618 >        seed = (int)the_event->evt.asmt.rhs.dval;
1619          return 1;
1620          break;
1621          
1622        case INT:
1623 <   have_seed = 1;
1624 <   seed =  the_event->evt.asmt.rhs.ival ;
1623 >        have_seed = 1;
1624 >        seed =  the_event->evt.asmt.rhs.ival ;
1625          return 1;
1626          break;
1627          
# Line 1681 | Line 1725 | int Globals::globalAssign( event* the_event ){
1725          return 0;
1726          break;
1727        }
1728 <      break;      
1728 >      break;  
1729 >  
1730      case G_FORCEFIELD_VARIANT:
1731        if( the_type == STRING ){
1732          strcpy( forcefield_variant, the_event->evt.asmt.rhs.sval );
# Line 1693 | Line 1738 | int Globals::globalAssign( event* the_event ){
1738          strdup( "Error in parsing meta-data file!\n\tforceFieldVariant was not a string assignment.\n" );
1739        return 0;
1740        break;      
1741 +      // add more token cases here.      
1742 +
1743 +    case G_FORCEFIELD_FILENAME:
1744 +      if( the_type == STRING ){
1745 +        strcpy( forcefield_filename, the_event->evt.asmt.rhs.sval );
1746 +        have_forcefield_filename = 1;
1747 +        return 1;
1748 +      }
1749 +      
1750 +      the_event->err_msg =
1751 +        strdup( "Error in parsing meta-data file!\n\tforceFieldFileName was not a string assignment.\n" );
1752 +      return 0;
1753 +      break;      
1754 +
1755 +    case G_THERM_INT_DIST_SPRING:
1756 +      switch( the_type ){
1757 +        
1758 +      case STRING:
1759 +        the_event->err_msg =
1760 +          strdup( "Error in parsing meta-data file!\n\tthermIntDistSpringConst is not a double or int.\n" );
1761 +        return 1;
1762 +        break;
1763 +        
1764 +      case DOUBLE:
1765 +        therm_int_dist_spring = the_event->evt.asmt.rhs.dval;
1766 +        have_dist_spring_constant = 1;
1767 +        return 1;
1768 +        break;
1769 +        
1770 +      case INT:
1771 +        therm_int_dist_spring = (double)the_event->evt.asmt.rhs.dval;
1772 +        have_dist_spring_constant = 1;
1773 +        return 1;
1774 +        break;
1775 +        
1776 +      default:
1777 +        the_event->err_msg =
1778 +          strdup( "Error in parsing meta-data file!\n\tthermIntDistSpringConst unrecognized.\n" );
1779 +        return 0;
1780 +        break;
1781 +      }
1782 +      break;  
1783 +
1784 +    case G_THERM_INT_THETA_SPRING:
1785 +      switch( the_type ){
1786 +        
1787 +      case STRING:
1788 +        the_event->err_msg =
1789 +          strdup( "Error in parsing meta-data file!\n\tthermIntThetaSpringConst is not a double or int.\n" );
1790 +        return 1;
1791 +        break;
1792 +        
1793 +      case DOUBLE:
1794 +        therm_int_theta_spring = the_event->evt.asmt.rhs.dval;
1795 +        have_theta_spring_constant = 1;
1796 +        return 1;
1797 +        break;
1798 +        
1799 +      case INT:
1800 +        therm_int_theta_spring = (double)the_event->evt.asmt.rhs.dval;
1801 +        have_theta_spring_constant = 1;
1802 +        return 1;
1803 +        break;
1804 +        
1805 +      default:
1806 +        the_event->err_msg =
1807 +          strdup( "Error in parsing meta-data file!\n\tthermIntThetaSpringConst unrecognized.\n" );
1808 +        return 0;
1809 +        break;
1810 +      }
1811 +      break;
1812 +
1813 +    case G_THERM_INT_OMEGA_SPRING:
1814 +      switch( the_type ){
1815 +        
1816 +      case STRING:
1817 +        the_event->err_msg =
1818 +          strdup( "Error in parsing meta-data file!\n\tthermIntOmegaSpringConst is not a double or int.\n" );
1819 +        return 1;
1820 +        break;
1821 +        
1822 +      case DOUBLE:
1823 +        therm_int_omega_spring = the_event->evt.asmt.rhs.dval;
1824 +        have_omega_spring_constant = 1;
1825 +        return 1;
1826 +        break;
1827 +        
1828 +      case INT:
1829 +        therm_int_omega_spring = (double)the_event->evt.asmt.rhs.dval;
1830 +        have_omega_spring_constant = 1;
1831 +        return 1;
1832 +        break;
1833 +        
1834 +      default:
1835 +        the_event->err_msg =
1836 +          strdup( "Error in parsing meta-data file!\n\tthermIntOmegaSpringConst unrecognized.\n" );
1837 +        return 0;
1838 +        break;
1839 +      }
1840 +      break;  
1841        // add more token cases here.      
1842      }
1843    }
# Line 1784 | Line 1929 | int Globals::hash( char* text ){
1929    return 1;
1930   }
1931  
1787 – int Globals::hash( char* text ){
1788 –
1789 –  register unsigned short int i = 0; // loop counter
1790 –  int key = 0; // the hash key
1791 –  
1792 –  while( text[i] != '\0' ){
1793 –    
1794 –    key = ( ( key << hash_shift ) + text[i] ) % hash_size;
1795 –    
1796 –    i++;
1797 –  }
1798 –  
1799 –  if( key < 0 ){
1800 –
1801 –    // if the key is less than zero, we've had an overflow error
1802 –
1803 –    sprintf( painCave.errMsg,
1804 –             "There has been an overflow error in the Globals' hash key.");
1805 –    painCave.isFatal = 1;
1806 –    simError();
1807 – #ifdef IS_MPI
1808 –    if( painCave.isEventLoop ){
1809 –      if( worldRank == 0 ) mpiInterfaceExit();
1810 –    }
1811 – #endif //is_mpi
1812 –  }
1813 –  
1814 –  return key;
1815 – }
1816 –
1817 – void Globals::addHash( char* text, int token ){
1818 –
1819 –  int key;
1820 –  LinkedCommand* the_element;
1821 –
1822 –  the_element = new LinkedCommand;
1823 –  the_element->setValues( text, token );
1824 –
1825 –  key = hash( text );
1826 –
1827 –  the_element->setNext( command_table[key] );
1828 –  command_table[key] = the_element;
1829 – }

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