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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 962 by tim, Mon Jan 19 18:36:21 2004 UTC vs.
Revision 983 by gezelter, Mon Jan 26 21:45:03 2004 UTC

# Line 174 | Line 174 | void SimSetup::makeMolecules(void){
174    bend_set* theBends;
175    torsion_set* theTorsions;
176  
177 –
177    //init the forceField paramters
178  
179    the_ff->readParams();
# Line 182 | Line 181 | void SimSetup::makeMolecules(void){
181  
182    // init the atoms
183  
184 +  double phi, theta, psi;
185 +  double sux, suy, suz;
186 +  double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
187    double ux, uy, uz, u, uSqr;
188  
189    for (k = 0; k < nInfo; k++){
# Line 218 | Line 220 | void SimSetup::makeMolecules(void){
220            info[k].n_oriented++;
221            molInfo.myAtoms[j] = dAtom;
222  
223 <          ux = currentAtom->getOrntX();
224 <          uy = currentAtom->getOrntY();
225 <          uz = currentAtom->getOrntZ();
223 >          // Directional Atoms have standard unit vectors which are oriented
224 >          // in space using the three Euler angles.  We assume the standard
225 >          // unit vector was originally along the z axis below.
226  
227 +          phi = currentAtom->getEulerPhi();
228 +          theta = currentAtom->getEulerTheta();
229 +          psi = currentAtom->getEulerPsi();
230 +            
231 +          Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
232 +          Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
233 +          Axz = sin(theta) * sin(psi);
234 +          
235 +          Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
236 +          Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
237 +          Ayz = sin(theta) * cos(psi);
238 +          
239 +          Azx = sin(phi) * sin(theta);
240 +          Azy = -cos(phi) * sin(theta);
241 +          Azz = cos(theta);
242 +
243 +          sux = 0.0;
244 +          suy = 0.0;
245 +          suz = 1.0;
246 +
247 +          ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
248 +          uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
249 +          uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
250 +
251            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
252  
253            u = sqrt(uSqr);
# Line 637 | Line 663 | void SimSetup::gatherInfo(void){
663    }
664    else{
665      sprintf(painCave.errMsg,
666 <            "SimSetup Warning. Unrecognized Ensemble -> %s, "
667 <            "reverting to NVE for this simulation.\n",
666 >            "SimSetup Warning. Unrecognized Ensemble -> %s \n"
667 >            "\treverting to NVE for this simulation.\n",
668              ensemble);
669           painCave.isFatal = 0;
670           simError();
# Line 670 | Line 696 | void SimSetup::gatherInfo(void){
696        if (!the_components[i]->haveNMol()){
697          // we have a problem
698          sprintf(painCave.errMsg,
699 <                "SimSetup Error. No global NMol or component NMol"
700 <                " given. Cannot calculate the number of atoms.\n");
699 >                "SimSetup Error. No global NMol or component NMol given.\n"
700 >                "\tCannot calculate the number of atoms.\n");
701          painCave.isFatal = 1;
702          simError();
703        }
# Line 694 | Line 720 | void SimSetup::gatherInfo(void){
720    //check whether sample time, status time, thermal time and reset time are divisble by dt
721    if (!isDivisible(globals->getSampleTime(), globals->getDt())){
722      sprintf(painCave.errMsg,
723 <              "Sample time is not divisible by dt \n");
723 >            "Sample time is not divisible by dt.\n"
724 >            "\tThis will result in samples that are not uniformly\n"
725 >            "\tdistributed in time.  If this is a problem, change\n"
726 >            "\tyour sampleTime variable.\n");
727      painCave.isFatal = 0;
728      simError();    
729    }
730  
731    if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
732      sprintf(painCave.errMsg,
733 <              "Status time is not divisible by dt\n");
733 >            "Status time is not divisible by dt.\n"
734 >            "\tThis will result in status reports that are not uniformly\n"
735 >            "\tdistributed in time.  If this is a problem, change \n"
736 >            "\tyour statusTime variable.\n");
737      painCave.isFatal = 0;
738      simError();    
739    }
740  
741    if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
742      sprintf(painCave.errMsg,
743 <              "Thermal time is not divisible by dt\n");
743 >            "Thermal time is not divisible by dt.\n"
744 >            "\tThis will result in thermalizations that are not uniformly\n"
745 >            "\tdistributed in time.  If this is a problem, change \n"
746 >            "\tyour thermalTime variable.\n");
747      painCave.isFatal = 0;
748      simError();    
749    }  
750  
751    if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
752      sprintf(painCave.errMsg,
753 <              "Reset time is not divisible by dt\n");
753 >            "Reset time is not divisible by dt.\n"
754 >            "\tThis will result in integrator resets that are not uniformly\n"
755 >            "\tdistributed in time.  If this is a problem, change\n"
756 >            "\tyour resetTime variable.\n");
757      painCave.isFatal = 0;
758      simError();    
759    }
# Line 834 | Line 872 | void SimSetup::finalInfoCheck(void){
872  
873        if (!globals->haveECR()){
874          sprintf(painCave.errMsg,
875 <                "SimSetup Warning: using default value of 15.0 angstroms"
876 <                "box length for the electrostaticCutoffRadius.\n");
875 >                "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
876 >                "\tOOPSE will use a default value of 15.0 angstroms"
877 >                "\tfor the electrostaticCutoffRadius.\n");
878          painCave.isFatal = 0;
879          simError();
880          theEcr = 15.0;
# Line 846 | Line 885 | void SimSetup::finalInfoCheck(void){
885  
886        if (!globals->haveEST()){
887          sprintf(painCave.errMsg,
888 <                "SimSetup Warning: using default value of 0.05 * the "
889 <                "electrostaticCutoffRadius for the electrostaticSkinThickness\n");
888 >                "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
889 >                "\tOOPSE will use a default value of\n"
890 >                "\t0.05 * electrostaticCutoffRadius\n"
891 >                "\tfor the electrostaticSkinThickness\n");
892          painCave.isFatal = 0;
893          simError();
894          theEst = 0.05 * theEcr;
# Line 860 | Line 901 | void SimSetup::finalInfoCheck(void){
901  
902        if (!globals->haveDielectric()){
903          sprintf(painCave.errMsg,
904 <                "SimSetup Error: You are trying to use Reaction Field without"
905 <                "setting a dielectric constant!\n");
904 >                "SimSetup Error: No Dielectric constant was set.\n"
905 >                "\tYou are trying to use Reaction Field without"
906 >                "\tsetting a dielectric constant!\n");
907          painCave.isFatal = 1;
908          simError();
909        }
# Line 871 | Line 913 | void SimSetup::finalInfoCheck(void){
913        if (usesDipoles){
914          if (!globals->haveECR()){
915            sprintf(painCave.errMsg,
916 <                  "SimSetup Warning: using default value of 15.0 angstroms"
917 <                  "box length for the electrostaticCutoffRadius.\n");
916 >                  "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
917 >                  "\tOOPSE will use a default value of 15.0 angstroms"
918 >                  "\tfor the electrostaticCutoffRadius.\n");
919            painCave.isFatal = 0;
920            simError();
921            theEcr = 15.0;
# Line 883 | Line 926 | void SimSetup::finalInfoCheck(void){
926          
927          if (!globals->haveEST()){
928            sprintf(painCave.errMsg,
929 <                  "SimSetup Warning: using default value of 0.05 * the "
930 <                  "electrostaticCutoffRadius for the "
931 <                  "electrostaticSkinThickness\n");
929 >                  "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
930 >                  "\tOOPSE will use a default value of\n"
931 >                  "\t0.05 * electrostaticCutoffRadius\n"
932 >                  "\tfor the electrostaticSkinThickness\n");
933            painCave.isFatal = 0;
934            simError();
935            theEst = 0.05 * theEcr;
# Line 1234 | Line 1278 | void SimSetup::mpiMolDivide(void){
1278  
1279    if (local_atoms != info[0].n_atoms){
1280      sprintf(painCave.errMsg,
1281 <            "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1282 <            " localAtom (%d) are not equal.\n",
1281 >            "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1282 >            "\tlocalAtom (%d) are not equal.\n",
1283              info[0].n_atoms, local_atoms);
1284      painCave.isFatal = 1;
1285      simError();
# Line 1377 | Line 1421 | void SimSetup::makeIntegrator(void){
1421          else{
1422            sprintf(painCave.errMsg,
1423                    "SimSetup error: If you use the NVT\n"
1424 <                  "    ensemble, you must set tauThermostat.\n");
1424 >                  "\tensemble, you must set tauThermostat.\n");
1425            painCave.isFatal = 1;
1426            simError();
1427          }
# Line 1400 | Line 1444 | void SimSetup::makeIntegrator(void){
1444          else{
1445            sprintf(painCave.errMsg,
1446                    "SimSetup error: If you use a constant pressure\n"
1447 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1447 >                  "\tensemble, you must set targetPressure in the BASS file.\n");
1448            painCave.isFatal = 1;
1449            simError();
1450          }
# Line 1410 | Line 1454 | void SimSetup::makeIntegrator(void){
1454          else{
1455            sprintf(painCave.errMsg,
1456                    "SimSetup error: If you use an NPT\n"
1457 <                  "    ensemble, you must set tauThermostat.\n");
1457 >                  "\tensemble, you must set tauThermostat.\n");
1458            painCave.isFatal = 1;
1459            simError();
1460          }
# Line 1420 | Line 1464 | void SimSetup::makeIntegrator(void){
1464          else{
1465            sprintf(painCave.errMsg,
1466                    "SimSetup error: If you use an NPT\n"
1467 <                  "    ensemble, you must set tauBarostat.\n");
1467 >                  "\tensemble, you must set tauBarostat.\n");
1468            painCave.isFatal = 1;
1469            simError();
1470          }
# Line 1443 | Line 1487 | void SimSetup::makeIntegrator(void){
1487          else{
1488            sprintf(painCave.errMsg,
1489                    "SimSetup error: If you use a constant pressure\n"
1490 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1490 >                  "\tensemble, you must set targetPressure in the BASS file.\n");
1491            painCave.isFatal = 1;
1492            simError();
1493          }    
# Line 1454 | Line 1498 | void SimSetup::makeIntegrator(void){
1498          else{
1499            sprintf(painCave.errMsg,
1500                    "SimSetup error: If you use an NPT\n"
1501 <                  "    ensemble, you must set tauThermostat.\n");
1501 >                  "\tensemble, you must set tauThermostat.\n");
1502            painCave.isFatal = 1;
1503            simError();
1504          }
# Line 1465 | Line 1509 | void SimSetup::makeIntegrator(void){
1509          else{
1510            sprintf(painCave.errMsg,
1511                    "SimSetup error: If you use an NPT\n"
1512 <                  "    ensemble, you must set tauBarostat.\n");
1512 >                  "\tensemble, you must set tauBarostat.\n");
1513            painCave.isFatal = 1;
1514            simError();
1515          }
# Line 1488 | Line 1532 | void SimSetup::makeIntegrator(void){
1532          else{
1533            sprintf(painCave.errMsg,
1534                    "SimSetup error: If you use a constant pressure\n"
1535 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1535 >                  "\tensemble, you must set targetPressure in the BASS file.\n");
1536            painCave.isFatal = 1;
1537            simError();
1538          }    
# Line 1498 | Line 1542 | void SimSetup::makeIntegrator(void){
1542          else{
1543            sprintf(painCave.errMsg,
1544                    "SimSetup error: If you use an NPT\n"
1545 <                  "    ensemble, you must set tauThermostat.\n");
1545 >                  "\tensemble, you must set tauThermostat.\n");
1546            painCave.isFatal = 1;
1547            simError();
1548          }
# Line 1508 | Line 1552 | void SimSetup::makeIntegrator(void){
1552          else{
1553            sprintf(painCave.errMsg,
1554                    "SimSetup error: If you use an NPT\n"
1555 <                  "    ensemble, you must set tauBarostat.\n");
1555 >                  "\tensemble, you must set tauBarostat.\n");
1556            painCave.isFatal = 1;
1557            simError();
1558          }
# Line 1561 | Line 1605 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1605    }
1606    else{
1607      sprintf(painCave.errMsg,
1608 <            "ZConstraint error: If you use an ZConstraint\n"
1609 <            " , you must set sample time.\n");
1608 >            "ZConstraint error: If you use a ZConstraint,\n"
1609 >            "\tyou must set zconsTime.\n");
1610      painCave.isFatal = 1;
1611      simError();
1612    }
# Line 1577 | Line 1621 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1621    else{
1622      double defaultZConsTol = 0.01;
1623      sprintf(painCave.errMsg,
1624 <            "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1625 <            " , default value %f is used.\n",
1624 >            "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1625 >            "\tOOPSE will use a default value of %f.\n"
1626 >            "\tTo set the tolerance, use the zconsTol variable.\n",
1627              defaultZConsTol);
1628      painCave.isFatal = 0;
1629      simError();      
# Line 1596 | Line 1641 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1641    }
1642    else{
1643      sprintf(painCave.errMsg,
1644 <            "ZConstraint Warning: User does not set force Subtraction policy, "
1645 <            "PolicyByMass is used\n");
1644 >            "ZConstraint Warning: No force subtraction policy was set.\n"
1645 >            "\tOOPSE will use PolicyByMass.\n"
1646 >            "\tTo set the policy, use the zconsForcePolicy variable.\n");
1647      painCave.isFatal = 0;
1648      simError();
1649      zconsForcePolicy->setData("BYMASS");
# Line 1641 | Line 1687 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1687    //check the uniqueness of index  
1688    if(!zconsParaData->isIndexUnique()){
1689      sprintf(painCave.errMsg,
1690 <            "ZConstraint Error: molIndex is not unique\n");
1690 >            "ZConstraint Error: molIndex is not unique!\n");
1691      painCave.isFatal = 1;
1692      simError();
1693    }

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