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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 555 by mmeineke, Tue Jun 17 21:56:15 2003 UTC vs.
Revision 604 by gezelter, Tue Jul 15 03:08:00 2003 UTC

# Line 12 | Line 12 | SimSetup::SimSetup(){
12   #include "mpiSimulation.hpp"
13   #endif
14  
15 + // some defines for ensemble and Forcefield  cases
16 +
17 + #define NVE_ENS   0
18 + #define NVT_ENS   1
19 + #define NPTi_ENS  2
20 + #define NPTf_ENS  3
21 + #define NPTim_ENS 4
22 + #define NPTfm_ENS 5
23 +
24 +
25 + #define FF_DUFF 0
26 + #define FF_LJ   1
27 +
28 +
29   SimSetup::SimSetup(){
30    stamps = new MakeStamps();
31    globals = new Globals();
# Line 66 | Line 80 | void SimSetup::createSim( void ){
80  
81    MakeStamps *the_stamps;
82    Globals* the_globals;
69 –  ExtendedSystem* the_extendedsystem;
83    int i, j, k, globalAtomIndex;
84 +  
85 +  int ensembleCase;
86 +  int ffCase;
87 +  
88 +  ensembleCase = -1;
89 +  ffCase = -1;
90  
91    // get the stamps and globals;
92    the_stamps = stamps;
# Line 82 | Line 101 | void SimSetup::createSim( void ){
101    n_components = the_globals->getNComponents();
102    strcpy( force_field, the_globals->getForceField() );
103  
104 <  // get the ensemble and set up an extended system if we need it:
104 >  if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
105 >  else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
106 >  else{
107 >    sprintf( painCave.errMsg,
108 >             "SimSetup Error. Unrecognized force field -> %s\n",
109 >             force_field );
110 >    painCave.isFatal = 1;
111 >    simError();
112 >  }
113 >
114 >  // get the ensemble:
115    strcpy( ensemble, the_globals->getEnsemble() );
87 –  if( !strcasecmp( ensemble, "NPT" ) ) {
88 –    the_extendedsystem = new ExtendedSystem( simnfo );
89 –    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90 –    if (the_globals->haveTargetPressure())
91 –      the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92 –    else {
93 –      sprintf( painCave.errMsg,
94 –               "SimSetup error: If you use the constant pressure\n"
95 –               "    ensemble, you must set targetPressure.\n"
96 –               "    This was found in the BASS file.\n");
97 –      painCave.isFatal = 1;
98 –      simError();
99 –    }
116  
117 <    if (the_globals->haveTauThermostat())
118 <      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
119 <    else if (the_globals->haveQmass())
120 <      the_extendedsystem->setQmass(the_globals->getQmass());
121 <    else {
122 <      sprintf( painCave.errMsg,
123 <               "SimSetup error: If you use one of the constant temperature\n"
124 <               "    ensembles, you must set either tauThermostat or qMass.\n"
109 <               "    Neither of these was found in the BASS file.\n");
110 <      painCave.isFatal = 1;
111 <      simError();
112 <    }
113 <
114 <    if (the_globals->haveTauBarostat())
115 <      the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116 <    else {
117 <      sprintf( painCave.errMsg,
118 <               "SimSetup error: If you use the constant pressure\n"
119 <               "    ensemble, you must set tauBarostat.\n"
120 <               "    This was found in the BASS file.\n");
121 <      painCave.isFatal = 1;
122 <      simError();
123 <    }
124 <
125 <  } else if ( !strcasecmp( ensemble, "NVT") ) {
126 <    the_extendedsystem = new ExtendedSystem( simnfo );
127 <    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
128 <
129 <    if (the_globals->haveTauThermostat())
130 <      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131 <    else if (the_globals->haveQmass())
132 <      the_extendedsystem->setQmass(the_globals->getQmass());
133 <    else {
134 <      sprintf( painCave.errMsg,
135 <               "SimSetup error: If you use one of the constant temperature\n"
136 <               "    ensembles, you must set either tauThermostat or qMass.\n"
137 <               "    Neither of these was found in the BASS file.\n");
138 <      painCave.isFatal = 1;
139 <      simError();
140 <    }
141 <
142 <  } else if ( !strcasecmp( ensemble, "NVE") ) {
143 <  } else {
117 >  if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
118 >  else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
119 >  else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
120 >    ensembleCase = NPTi_ENS;
121 >  else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
122 >  else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
123 >  else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
124 >  else{
125      sprintf( painCave.errMsg,
126               "SimSetup Warning. Unrecognized Ensemble -> %s, "
127               "reverting to NVE for this simulation.\n",
# Line 148 | Line 129 | void SimSetup::createSim( void ){
129      painCave.isFatal = 0;
130      simError();
131      strcpy( ensemble, "NVE" );
132 +    ensembleCase = NVE_ENS;
133    }  
134    strcpy( simnfo->ensemble, ensemble );
135  
136 +
137 + //   if( !strcasecmp( ensemble, "NPT" ) ) {
138 + //     the_extendedsystem = new ExtendedSystem( simnfo );
139 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
140 + //     if (the_globals->haveTargetPressure())
141 + //       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
142 + //     else {
143 + //       sprintf( painCave.errMsg,
144 + //                "SimSetup error: If you use the constant pressure\n"
145 + //                "    ensemble, you must set targetPressure.\n"
146 + //                "    This was found in the BASS file.\n");
147 + //       painCave.isFatal = 1;
148 + //       simError();
149 + //     }
150 +
151 + //     if (the_globals->haveTauThermostat())
152 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
153 + //     else if (the_globals->haveQmass())
154 + //       the_extendedsystem->setQmass(the_globals->getQmass());
155 + //     else {
156 + //       sprintf( painCave.errMsg,
157 + //                "SimSetup error: If you use one of the constant temperature\n"
158 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
159 + //                "    Neither of these was found in the BASS file.\n");
160 + //       painCave.isFatal = 1;
161 + //       simError();
162 + //     }
163 +
164 + //     if (the_globals->haveTauBarostat())
165 + //       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
166 + //     else {
167 + //       sprintf( painCave.errMsg,
168 + //                "SimSetup error: If you use the constant pressure\n"
169 + //                "    ensemble, you must set tauBarostat.\n"
170 + //                "    This was found in the BASS file.\n");
171 + //       painCave.isFatal = 1;
172 + //       simError();
173 + //     }
174 +
175 + //   } else if ( !strcasecmp( ensemble, "NVT") ) {
176 + //     the_extendedsystem = new ExtendedSystem( simnfo );
177 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
178 +
179 + //     if (the_globals->haveTauThermostat())
180 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
181 + //     else if (the_globals->haveQmass())
182 + //       the_extendedsystem->setQmass(the_globals->getQmass());
183 + //     else {
184 + //       sprintf( painCave.errMsg,
185 + //                "SimSetup error: If you use one of the constant temperature\n"
186 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
187 + //                "    Neither of these was found in the BASS file.\n");
188 + //       painCave.isFatal = 1;
189 + //       simError();
190 + //     }
191 +
192    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
193    simnfo->usePBC = the_globals->getPBC();
194            
195    int usesDipoles = 0;
196 <  if( !strcmp( force_field, "TraPPE_Ex" ) ){
197 <    the_ff = new TraPPE_ExFF();
196 >  switch( ffCase ){
197 >
198 >  case FF_DUFF:
199 >    the_ff = new DUFF();
200      usesDipoles = 1;
201 <  }
202 <  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
203 <  else{
201 >    break;
202 >
203 >  case FF_LJ:
204 >    the_ff = new LJFF();
205 >    break;
206 >
207 >  default:
208      sprintf( painCave.errMsg,
209 <             "SimSetup Error. Unrecognized force field -> %s\n",
166 <             force_field );
209 >             "SimSetup Error. Unrecognized force field in case statement.\n");
210      painCave.isFatal = 1;
211      simError();
212    }
# Line 172 | Line 215 | void SimSetup::createSim( void ){
215    strcpy( checkPointMsg, "ForceField creation successful" );
216    MPIcheckPoint();
217   #endif // is_mpi
175 –
176 –  
218  
219    // get the components and calculate the tot_nMol and indvidual n_mol
220    the_components = the_globals->getComponents();
# Line 446 | Line 487 | void SimSetup::createSim( void ){
487  
488    // get some of the tricky things that may still be in the globals
489  
490 <  
490 >  double boxVector[3];
491    if( the_globals->haveBox() ){
492 <    simnfo->box_x = the_globals->getBox();
493 <    simnfo->box_y = the_globals->getBox();
494 <    simnfo->box_z = the_globals->getBox();
492 >    boxVector[0] = the_globals->getBox();
493 >    boxVector[1] = the_globals->getBox();
494 >    boxVector[2] = the_globals->getBox();
495 >    
496 >    simnfo->setBox( boxVector );
497    }
498    else if( the_globals->haveDensity() ){
499  
500      double vol;
501      vol = (double)tot_nmol / the_globals->getDensity();
502 <    simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
503 <    simnfo->box_y = simnfo->box_x;
504 <    simnfo->box_z = simnfo->box_x;
502 >     boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
503 >     boxVector[1] = boxVector[0];
504 >     boxVector[2] = boxVector[0];
505 >
506 >    simnfo->setBox( boxVector );
507    }
508    else{
509      if( !the_globals->haveBoxX() ){
# Line 467 | Line 512 | void SimSetup::createSim( void ){
512        painCave.isFatal = 1;
513        simError();
514      }
515 <    simnfo->box_x = the_globals->getBoxX();
515 >    boxVector[0] = the_globals->getBoxX();
516  
517      if( !the_globals->haveBoxY() ){
518        sprintf( painCave.errMsg,
# Line 475 | Line 520 | void SimSetup::createSim( void ){
520        painCave.isFatal = 1;
521        simError();
522      }
523 <    simnfo->box_y = the_globals->getBoxY();
523 >    boxVector[1] = the_globals->getBoxY();
524  
525      if( !the_globals->haveBoxZ() ){
526        sprintf( painCave.errMsg,
# Line 483 | Line 528 | void SimSetup::createSim( void ){
528        painCave.isFatal = 1;
529        simError();
530      }
531 <    simnfo->box_z = the_globals->getBoxZ();
531 >    boxVector[2] = the_globals->getBoxZ();
532 >
533 >    simnfo->setBox( boxVector );
534    }
535  
536   #ifdef IS_MPI
# Line 513 | Line 560 | void SimSetup::createSim( void ){
560        painCave.isFatal = 0;
561        simError();
562        double smallest;
563 <      smallest = simnfo->box_x;
564 <      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
565 <      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
563 >      smallest = simnfo->boxLx;
564 >      if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
565 >      if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
566        simnfo->ecr = 0.5 * smallest;
567      } else {
568        simnfo->ecr        = the_globals->getECR();
# Line 553 | Line 600 | void SimSetup::createSim( void ){
600          painCave.isFatal = 0;
601          simError();
602          double smallest;
603 <        smallest = simnfo->box_x;
604 <        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
605 <        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
603 >        smallest = simnfo->boxLx;
604 >        if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
605 >        if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
606          simnfo->ecr = 0.5 * smallest;
607        } else {
608          simnfo->ecr        = the_globals->getECR();
# Line 735 | Line 782 | void SimSetup::createSim( void ){
782  
783  
784    // make the integrator
785 +  
786 +  
787 +  NVT*  myNVT = NULL;
788 +  NPTi* myNPTi = NULL;
789 +  NPTf* myNPTf = NULL;
790 +  NPTim* myNPTim = NULL;
791  
792 +  switch( ensembleCase ){
793  
794 <  if( !strcmp( ensemble, "TraPPE_Ex" ) ){
795 <    new Symplectic(simnfo, the_ff, the_extendedsystem);
796 <  }
797 <  else if( !strcmp( force_field, "LJ" ) ){
798 <    new Verlet( *simnfo, the_ff, the_extendedsystem );
794 >  case NVE_ENS:
795 >    new NVE( simnfo, the_ff );
796 >    break;
797 >
798 >  case NVT_ENS:
799 >    myNVT = new NVT( simnfo, the_ff );
800 >    myNVT->setTargetTemp(the_globals->getTargetTemp());
801 >
802 >    if (the_globals->haveTauThermostat())
803 >      myNVT->setTauThermostat(the_globals->getTauThermostat());
804 >
805 >    else {
806 >      sprintf( painCave.errMsg,
807 >               "SimSetup error: If you use the NVT\n"
808 >               "    ensemble, you must set tauThermostat.\n");
809 >      painCave.isFatal = 1;
810 >      simError();
811 >    }
812 >    break;
813 >
814 >  case NPTi_ENS:
815 >    myNPTi = new NPTi( simnfo, the_ff );
816 >    myNPTi->setTargetTemp( the_globals->getTargetTemp());
817 >
818 >    if (the_globals->haveTargetPressure())
819 >      myNPTi->setTargetPressure(the_globals->getTargetPressure());
820 >    else {
821 >      sprintf( painCave.errMsg,
822 >               "SimSetup error: If you use a constant pressure\n"
823 >               "    ensemble, you must set targetPressure in the BASS file.\n");
824 >      painCave.isFatal = 1;
825 >      simError();
826 >    }
827 >    
828 >    if( the_globals->haveTauThermostat() )
829 >      myNPTi->setTauThermostat( the_globals->getTauThermostat() );
830 >    else{
831 >      sprintf( painCave.errMsg,
832 >               "SimSetup error: If you use an NPT\n"
833 >               "    ensemble, you must set tauThermostat.\n");
834 >      painCave.isFatal = 1;
835 >      simError();
836 >    }
837 >
838 >    if( the_globals->haveTauBarostat() )
839 >      myNPTi->setTauBarostat( the_globals->getTauBarostat() );
840 >    else{
841 >      sprintf( painCave.errMsg,
842 >               "SimSetup error: If you use an NPT\n"
843 >               "    ensemble, you must set tauBarostat.\n");
844 >      painCave.isFatal = 1;
845 >      simError();
846 >    }
847 >    break;
848 >
849 >  case NPTf_ENS:
850 >    myNPTf = new NPTf( simnfo, the_ff );
851 >    myNPTf->setTargetTemp( the_globals->getTargetTemp());
852 >
853 >    if (the_globals->haveTargetPressure())
854 >      myNPTf->setTargetPressure(the_globals->getTargetPressure());
855 >    else {
856 >      sprintf( painCave.errMsg,
857 >               "SimSetup error: If you use a constant pressure\n"
858 >               "    ensemble, you must set targetPressure in the BASS file.\n");
859 >      painCave.isFatal = 1;
860 >      simError();
861 >    }    
862 >
863 >    if( the_globals->haveTauThermostat() )
864 >      myNPTf->setTauThermostat( the_globals->getTauThermostat() );
865 >    else{
866 >      sprintf( painCave.errMsg,
867 >               "SimSetup error: If you use an NPT\n"
868 >               "    ensemble, you must set tauThermostat.\n");
869 >      painCave.isFatal = 1;
870 >      simError();
871 >    }
872 >
873 >    if( the_globals->haveTauBarostat() )
874 >      myNPTf->setTauBarostat( the_globals->getTauBarostat() );
875 >    else{
876 >      sprintf( painCave.errMsg,
877 >               "SimSetup error: If you use an NPT\n"
878 >               "    ensemble, you must set tauBarostat.\n");
879 >      painCave.isFatal = 1;
880 >      simError();
881 >    }
882 >    break;
883 >    
884 >  case NPTim_ENS:
885 >    myNPTim = new NPTim( simnfo, the_ff );
886 >    myNPTim->setTargetTemp( the_globals->getTargetTemp());
887 >
888 >    if (the_globals->haveTargetPressure())
889 >      myNPTim->setTargetPressure(the_globals->getTargetPressure());
890 >    else {
891 >      sprintf( painCave.errMsg,
892 >               "SimSetup error: If you use a constant pressure\n"
893 >               "    ensemble, you must set targetPressure in the BASS file.\n");
894 >      painCave.isFatal = 1;
895 >      simError();
896 >    }
897 >    
898 >    if( the_globals->haveTauThermostat() )
899 >      myNPTim->setTauThermostat( the_globals->getTauThermostat() );
900 >    else{
901 >      sprintf( painCave.errMsg,
902 >               "SimSetup error: If you use an NPT\n"
903 >               "    ensemble, you must set tauThermostat.\n");
904 >      painCave.isFatal = 1;
905 >      simError();
906 >    }
907 >
908 >    if( the_globals->haveTauBarostat() )
909 >      myNPTim->setTauBarostat( the_globals->getTauBarostat() );
910 >    else{
911 >      sprintf( painCave.errMsg,
912 >               "SimSetup error: If you use an NPT\n"
913 >               "    ensemble, you must set tauBarostat.\n");
914 >      painCave.isFatal = 1;
915 >      simError();
916 >    }
917 >    break;
918 >
919 >    
920 >
921 >  default:
922 >    sprintf( painCave.errMsg,
923 >             "SimSetup Error. Unrecognized ensemble in case statement.\n");
924 >    painCave.isFatal = 1;
925 >    simError();
926    }
927  
928 +
929   #ifdef IS_MPI
930    mpiSim->mpiRefresh();
931   #endif
# Line 1056 | Line 1238 | void SimSetup::initFromBass( void ){
1238      have_extra =1;
1239  
1240      n_cells = (int)temp3 - 1;
1241 <    cellx = simnfo->box_x / temp3;
1242 <    celly = simnfo->box_y / temp3;
1243 <    cellz = simnfo->box_z / temp3;
1241 >    cellx = simnfo->boxLx / temp3;
1242 >    celly = simnfo->boxLy / temp3;
1243 >    cellz = simnfo->boxLz / temp3;
1244      n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1245      temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1246      n_per_extra = (int)ceil( temp1 );
# Line 1073 | Line 1255 | void SimSetup::initFromBass( void ){
1255    }
1256    else{
1257      n_cells = (int)temp3;
1258 <    cellx = simnfo->box_x / temp3;
1259 <    celly = simnfo->box_y / temp3;
1260 <    cellz = simnfo->box_z / temp3;
1258 >    cellx = simnfo->boxLx / temp3;
1259 >    celly = simnfo->boxLy / temp3;
1260 >    cellz = simnfo->boxLz / temp3;
1261    }
1262  
1263    current_mol = 0;

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