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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 490 by gezelter, Fri Apr 11 15:16:59 2003 UTC vs.
Revision 586 by mmeineke, Wed Jul 9 22:14:06 2003 UTC

# Line 12 | Line 12
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 +
22 +
23 + #define FF_DUFF 0
24 + #define FF_LJ   1
25 +
26 +
27   SimSetup::SimSetup(){
28    stamps = new MakeStamps();
29    globals = new Globals();
# Line 66 | Line 78 | void SimSetup::createSim( void ){
78  
79    MakeStamps *the_stamps;
80    Globals* the_globals;
69 –  ExtendedSystem* the_extendedsystem;
81    int i, j, k, globalAtomIndex;
82 +  
83 +  int ensembleCase;
84 +  int ffCase;
85 +  
86 +  ensembleCase = -1;
87 +  ffCase = -1;
88  
89    // get the stamps and globals;
90    the_stamps = stamps;
# Line 82 | Line 99 | void SimSetup::createSim( void ){
99    n_components = the_globals->getNComponents();
100    strcpy( force_field, the_globals->getForceField() );
101  
102 <  // get the ensemble and set up an extended system if we need it:
102 >  if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
103 >  else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
104 >  else{
105 >    sprintf( painCave.errMsg,
106 >             "SimSetup Error. Unrecognized force field -> %s\n",
107 >             force_field );
108 >    painCave.isFatal = 1;
109 >    simError();
110 >  }
111 >
112 >  // get the ensemble:
113    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 –    }
114  
115 <    if (the_globals->haveTauThermostat())
116 <      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
117 <    else if (the_globals->haveQmass())
118 <      the_extendedsystem->setQmass(the_globals->getQmass());
119 <    else {
120 <      sprintf( painCave.errMsg,
107 <               "SimSetup error: If you use one of the constant temperature\n"
108 <               "    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 {
115 >  if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
116 >  else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
117 >  else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
118 >    ensembleCase = NPTi_ENS;
119 >  else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
120 >  else{
121      sprintf( painCave.errMsg,
122               "SimSetup Warning. Unrecognized Ensemble -> %s, "
123               "reverting to NVE for this simulation.\n",
# Line 148 | Line 125 | void SimSetup::createSim( void ){
125      painCave.isFatal = 0;
126      simError();
127      strcpy( ensemble, "NVE" );
128 +    ensembleCase = NVE_ENS;
129    }  
130    strcpy( simnfo->ensemble, ensemble );
131  
132 +
133 + //   if( !strcasecmp( ensemble, "NPT" ) ) {
134 + //     the_extendedsystem = new ExtendedSystem( simnfo );
135 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
136 + //     if (the_globals->haveTargetPressure())
137 + //       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
138 + //     else {
139 + //       sprintf( painCave.errMsg,
140 + //                "SimSetup error: If you use the constant pressure\n"
141 + //                "    ensemble, you must set targetPressure.\n"
142 + //                "    This was found in the BASS file.\n");
143 + //       painCave.isFatal = 1;
144 + //       simError();
145 + //     }
146 +
147 + //     if (the_globals->haveTauThermostat())
148 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
149 + //     else if (the_globals->haveQmass())
150 + //       the_extendedsystem->setQmass(the_globals->getQmass());
151 + //     else {
152 + //       sprintf( painCave.errMsg,
153 + //                "SimSetup error: If you use one of the constant temperature\n"
154 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
155 + //                "    Neither of these was found in the BASS file.\n");
156 + //       painCave.isFatal = 1;
157 + //       simError();
158 + //     }
159 +
160 + //     if (the_globals->haveTauBarostat())
161 + //       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
162 + //     else {
163 + //       sprintf( painCave.errMsg,
164 + //                "SimSetup error: If you use the constant pressure\n"
165 + //                "    ensemble, you must set tauBarostat.\n"
166 + //                "    This was found in the BASS file.\n");
167 + //       painCave.isFatal = 1;
168 + //       simError();
169 + //     }
170 +
171 + //   } else if ( !strcasecmp( ensemble, "NVT") ) {
172 + //     the_extendedsystem = new ExtendedSystem( simnfo );
173 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
174 +
175 + //     if (the_globals->haveTauThermostat())
176 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
177 + //     else if (the_globals->haveQmass())
178 + //       the_extendedsystem->setQmass(the_globals->getQmass());
179 + //     else {
180 + //       sprintf( painCave.errMsg,
181 + //                "SimSetup error: If you use one of the constant temperature\n"
182 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
183 + //                "    Neither of these was found in the BASS file.\n");
184 + //       painCave.isFatal = 1;
185 + //       simError();
186 + //     }
187 +
188    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
189    simnfo->usePBC = the_globals->getPBC();
190            
191    int usesDipoles = 0;
192 <  if( !strcmp( force_field, "TraPPE_Ex" ) ){
193 <    the_ff = new TraPPE_ExFF();
192 >  switch( ffCase ){
193 >
194 >  case FF_DUFF:
195 >    the_ff = new DUFF();
196      usesDipoles = 1;
197 <  }
198 <  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
199 <  else{
197 >    break;
198 >
199 >  case FF_LJ:
200 >    the_ff = new LJFF();
201 >    break;
202 >
203 >  default:
204      sprintf( painCave.errMsg,
205 <             "SimSetup Error. Unrecognized force field -> %s\n",
166 <             force_field );
205 >             "SimSetup Error. Unrecognized force field in case statement.\n");
206      painCave.isFatal = 1;
207      simError();
208    }
# Line 173 | Line 212 | void SimSetup::createSim( void ){
212    MPIcheckPoint();
213   #endif // is_mpi
214  
176 –  
177 –
215    // get the components and calculate the tot_nMol and indvidual n_mol
216    the_components = the_globals->getComponents();
217    components_nmol = new int[n_components];
# Line 298 | Line 335 | void SimSetup::createSim( void ){
335    simnfo->n_torsions = tot_torsions;
336    simnfo->n_SRI = tot_SRI;
337    simnfo->n_mol = tot_nmol;
338 +  
339    simnfo->molMembershipArray = new int[tot_atoms];
340  
341   #ifdef IS_MPI
# Line 347 | Line 385 | void SimSetup::createSim( void ){
385    }
386    local_SRI = local_bonds + local_bends + local_torsions;
387    
350 –  if (worldRank != 0) {
351 –    for (i =0; i < tot_atoms; i++){
352 –      std::cerr << "i = " << i << " molMembershipArray[i] = " << simnfo->molMembershipArray[i] << "\n";
353 –    }
354 –  }
355 –
388    simnfo->n_atoms = mpiSim->getMyNlocal();  
389    
390    if( local_atoms != simnfo->n_atoms ){
# Line 451 | Line 483 | void SimSetup::createSim( void ){
483  
484    // get some of the tricky things that may still be in the globals
485  
486 <  
486 >  double boxVector[3];
487    if( the_globals->haveBox() ){
488 <    simnfo->box_x = the_globals->getBox();
489 <    simnfo->box_y = the_globals->getBox();
490 <    simnfo->box_z = the_globals->getBox();
488 >    boxVector[0] = the_globals->getBox();
489 >    boxVector[1] = the_globals->getBox();
490 >    boxVector[2] = the_globals->getBox();
491 >    
492 >    simnfo->setBox( boxVector );
493    }
494    else if( the_globals->haveDensity() ){
495  
496      double vol;
497      vol = (double)tot_nmol / the_globals->getDensity();
498 <    simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
499 <    simnfo->box_y = simnfo->box_x;
500 <    simnfo->box_z = simnfo->box_x;
498 >     boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
499 >     boxVector[1] = boxVector[0];
500 >     boxVector[2] = boxVector[0];
501 >
502 >    simnfo->setBox( boxVector );
503    }
504    else{
505      if( !the_globals->haveBoxX() ){
# Line 472 | Line 508 | void SimSetup::createSim( void ){
508        painCave.isFatal = 1;
509        simError();
510      }
511 <    simnfo->box_x = the_globals->getBoxX();
511 >    boxVector[0] = the_globals->getBoxX();
512  
513      if( !the_globals->haveBoxY() ){
514        sprintf( painCave.errMsg,
# Line 480 | Line 516 | void SimSetup::createSim( void ){
516        painCave.isFatal = 1;
517        simError();
518      }
519 <    simnfo->box_y = the_globals->getBoxY();
519 >    boxVector[1] = the_globals->getBoxY();
520  
521      if( !the_globals->haveBoxZ() ){
522        sprintf( painCave.errMsg,
# Line 488 | Line 524 | void SimSetup::createSim( void ){
524        painCave.isFatal = 1;
525        simError();
526      }
527 <    simnfo->box_z = the_globals->getBoxZ();
527 >    boxVector[2] = the_globals->getBoxZ();
528 >
529 >    simnfo->setBox( boxVector );
530    }
531  
532   #ifdef IS_MPI
# Line 518 | Line 556 | void SimSetup::createSim( void ){
556        painCave.isFatal = 0;
557        simError();
558        double smallest;
559 <      smallest = simnfo->box_x;
560 <      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
561 <      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
559 >      smallest = simnfo->boxLx;
560 >      if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
561 >      if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
562        simnfo->ecr = 0.5 * smallest;
563      } else {
564        simnfo->ecr        = the_globals->getECR();
# Line 558 | Line 596 | void SimSetup::createSim( void ){
596          painCave.isFatal = 0;
597          simError();
598          double smallest;
599 <        smallest = simnfo->box_x;
600 <        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
601 <        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
599 >        smallest = simnfo->boxLx;
600 >        if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
601 >        if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
602          simnfo->ecr = 0.5 * smallest;
603        } else {
604          simnfo->ecr        = the_globals->getECR();
# Line 739 | Line 777 | void SimSetup::createSim( void ){
777    if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
778  
779  
780 < //   // make the longe range forces and the integrator
781 <
782 < //   new AllLong( simnfo );
780 >  // make the integrator
781 >  
782 >  
783 >  NVT*  myNVT = NULL;
784 >  NPTi* myNPTi = NULL;
785 >  NPTf* myNPTf = NULL;
786 >  switch( ensembleCase ){
787  
788 +  case NVE_ENS:
789 +    new NVE( simnfo, the_ff );
790 +    break;
791  
792 <  if( !strcmp( force_field, "TraPPE_Ex" ) ){
793 <    new Symplectic(simnfo, the_ff, the_extendedsystem);
794 <  }
795 <  else if( !strcmp( force_field, "LJ" ) ){
796 <    new Verlet( *simnfo, the_ff, the_extendedsystem );
797 <  }
798 <  else {
799 <    std::cerr << "I'm a bug.\n";
800 <    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
792 >  case NVT_ENS:
793 >    myNVT = new NVT( simnfo, the_ff );
794 >    myNVT->setTargetTemp(the_globals->getTargetTemp());
795 >
796 >    if (the_globals->haveTauThermostat())
797 >      myNVT->setTauThermostat(the_globals->getTauThermostat());
798 >
799 >    else {
800 >      sprintf( painCave.errMsg,
801 >               "SimSetup error: If you use the NVT\n"
802 >               "    ensemble, you must set tauThermostat.\n");
803 >      painCave.isFatal = 1;
804 >      simError();
805 >    }
806 >    break;
807 >
808 >  case NPTi_ENS:
809 >    myNPTi = new NPTi( simnfo, the_ff );
810 >    myNPTi->setTargetTemp( the_globals->getTargetTemp());
811 >
812 >    if (the_globals->haveTargetPressure())
813 >      myNPTi->setTargetPressure(the_globals->getTargetPressure());
814 >    else {
815 >      sprintf( painCave.errMsg,
816 >               "SimSetup error: If you use a constant pressure\n"
817 >               "    ensemble, you must set targetPressure in the BASS file.\n");
818 >      painCave.isFatal = 1;
819 >      simError();
820 >    }
821 >    
822 >    if( the_globals->haveTauThermostat() )
823 >      myNPTi->setTauThermostat( the_globals->getTauThermostat() );
824 >    else{
825 >      sprintf( painCave.errMsg,
826 >               "SimSetup error: If you use an NPT\n"
827 >               "    ensemble, you must set tauThermostat.\n");
828 >      painCave.isFatal = 1;
829 >      simError();
830 >    }
831 >
832 >    if( the_globals->haveTauBarostat() )
833 >      myNPTi->setTauBarostat( the_globals->getTauBarostat() );
834 >    else{
835 >      sprintf( painCave.errMsg,
836 >               "SimSetup error: If you use an NPT\n"
837 >               "    ensemble, you must set tauBarostat.\n");
838 >      painCave.isFatal = 1;
839 >      simError();
840 >    }
841 >    break;
842 >
843 >  case NPTf_ENS:
844 >    myNPTf = new NPTf( simnfo, the_ff );
845 >    myNPTf->setTargetTemp( the_globals->getTargetTemp());
846 >
847 >    if (the_globals->haveTargetPressure())
848 >      myNPTf->setTargetPressure(the_globals->getTargetPressure());
849 >    else {
850 >      sprintf( painCave.errMsg,
851 >               "SimSetup error: If you use a constant pressure\n"
852 >               "    ensemble, you must set targetPressure in the BASS file.\n");
853 >      painCave.isFatal = 1;
854 >      simError();
855 >    }    
856 >
857 >    if( the_globals->haveTauThermostat() )
858 >      myNPTf->setTauThermostat( the_globals->getTauThermostat() );
859 >    else{
860 >      sprintf( painCave.errMsg,
861 >               "SimSetup error: If you use an NPT\n"
862 >               "    ensemble, you must set tauThermostat.\n");
863 >      painCave.isFatal = 1;
864 >      simError();
865 >    }
866 >
867 >    if( the_globals->haveTauBarostat() )
868 >      myNPTf->setTauBarostat( the_globals->getTauBarostat() );
869 >    else{
870 >      sprintf( painCave.errMsg,
871 >               "SimSetup error: If you use an NPT\n"
872 >               "    ensemble, you must set tauBarostat.\n");
873 >      painCave.isFatal = 1;
874 >      simError();
875 >    }
876 >    break;
877 >    
878 >    
879 >
880 >  default:
881 >    sprintf( painCave.errMsg,
882 >             "SimSetup Error. Unrecognized ensemble in case statement.\n");
883 >    painCave.isFatal = 1;
884 >    simError();
885    }
886 +
887 +
888   #ifdef IS_MPI
889    mpiSim->mpiRefresh();
890   #endif
# Line 1066 | Line 1197 | void SimSetup::initFromBass( void ){
1197      have_extra =1;
1198  
1199      n_cells = (int)temp3 - 1;
1200 <    cellx = simnfo->box_x / temp3;
1201 <    celly = simnfo->box_y / temp3;
1202 <    cellz = simnfo->box_z / temp3;
1200 >    cellx = simnfo->boxLx / temp3;
1201 >    celly = simnfo->boxLy / temp3;
1202 >    cellz = simnfo->boxLz / temp3;
1203      n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1204      temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1205      n_per_extra = (int)ceil( temp1 );
# Line 1083 | Line 1214 | void SimSetup::initFromBass( void ){
1214    }
1215    else{
1216      n_cells = (int)temp3;
1217 <    cellx = simnfo->box_x / temp3;
1218 <    celly = simnfo->box_y / temp3;
1219 <    cellz = simnfo->box_z / temp3;
1217 >    cellx = simnfo->boxLx / temp3;
1218 >    celly = simnfo->boxLy / temp3;
1219 >    cellz = simnfo->boxLz / temp3;
1220    }
1221  
1222    current_mol = 0;

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