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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 823 by mmeineke, Mon Oct 27 22:07:48 2003 UTC vs.
Revision 999 by chrisfen, Fri Jan 30 15:01:09 2004 UTC

# Line 1 | Line 1
1   #include <algorithm>
2 < #include <cstdlib>
2 > #include <stdlib.h>
3   #include <iostream>
4 < #include <cmath>
4 > #include <math.h>
5   #include <string>
6   #include <sprng.h>
7   #include "SimSetup.hpp"
# Line 24 | Line 24
24   #define NPTxyz_ENS     4
25  
26  
27 < #define FF_DUFF 0
28 < #define FF_LJ   1
29 < #define FF_EAM  2
27 > #define FF_DUFF  0
28 > #define FF_LJ    1
29 > #define FF_EAM   2
30 > #define FF_H2O 3
31  
32   using namespace std;
33  
34 + /**
35 + * Check whether dividend is divisble by divisor or not
36 + */
37 + bool isDivisible(double dividend, double divisor){
38 +  double tolerance = 0.000001;
39 +  double quotient;
40 +  double diff;
41 +  int intQuotient;
42 +  
43 +  quotient = dividend / divisor;
44 +
45 +  if (quotient < 0)
46 +    quotient = -quotient;
47 +
48 +  intQuotient = int (quotient + tolerance);
49 +
50 +  diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
51 +
52 +  if (diff <= tolerance)
53 +    return true;
54 +  else
55 +    return false;  
56 + }
57 +
58   SimSetup::SimSetup(){
59    
60    initSuspend = false;
# Line 150 | Line 175 | void SimSetup::makeMolecules(void){
175    bend_set* theBends;
176    torsion_set* theTorsions;
177  
153 –
178    //init the forceField paramters
179  
180    the_ff->readParams();
# Line 158 | Line 182 | void SimSetup::makeMolecules(void){
182  
183    // init the atoms
184  
185 +  double phi, theta, psi;
186 +  double sux, suy, suz;
187 +  double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
188    double ux, uy, uz, u, uSqr;
189  
190    for (k = 0; k < nInfo; k++){
# Line 194 | Line 221 | void SimSetup::makeMolecules(void){
221            info[k].n_oriented++;
222            molInfo.myAtoms[j] = dAtom;
223  
224 <          ux = currentAtom->getOrntX();
225 <          uy = currentAtom->getOrntY();
226 <          uz = currentAtom->getOrntZ();
224 >          // Directional Atoms have standard unit vectors which are oriented
225 >          // in space using the three Euler angles.  We assume the standard
226 >          // unit vector was originally along the z axis below.
227  
228 +          phi = currentAtom->getEulerPhi() * M_PI / 180.0;
229 +          theta = currentAtom->getEulerTheta() * M_PI / 180.0;
230 +          psi = currentAtom->getEulerPsi()* M_PI / 180.0;
231 +            
232 +          Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
233 +          Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
234 +          Axz = sin(theta) * sin(psi);
235 +          
236 +          Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
237 +          Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
238 +          Ayz = sin(theta) * cos(psi);
239 +          
240 +          Azx = sin(phi) * sin(theta);
241 +          Azy = -cos(phi) * sin(theta);
242 +          Azz = cos(theta);
243 +
244 +          sux = 0.0;
245 +          suy = 0.0;
246 +          suz = 1.0;
247 +
248 +          ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
249 +          uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
250 +          uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
251 +
252            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
253  
254            u = sqrt(uSqr);
# Line 584 | Line 635 | void SimSetup::gatherInfo(void){
635    }
636    else if (!strcasecmp(force_field, "EAM")){
637      ffCase = FF_EAM;
638 +  }
639 +  else if (!strcasecmp(force_field, "WATER")){
640 +    ffCase = FF_H2O;
641    }
642    else{
643      sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
# Line 613 | Line 667 | void SimSetup::gatherInfo(void){
667    }
668    else{
669      sprintf(painCave.errMsg,
670 <            "SimSetup Warning. Unrecognized Ensemble -> %s, "
671 <            "reverting to NVE for this simulation.\n",
670 >            "SimSetup Warning. Unrecognized Ensemble -> %s \n"
671 >            "\treverting to NVE for this simulation.\n",
672              ensemble);
673           painCave.isFatal = 0;
674           simError();
# Line 646 | Line 700 | void SimSetup::gatherInfo(void){
700        if (!the_components[i]->haveNMol()){
701          // we have a problem
702          sprintf(painCave.errMsg,
703 <                "SimSetup Error. No global NMol or component NMol"
704 <                " given. Cannot calculate the number of atoms.\n");
703 >                "SimSetup Error. No global NMol or component NMol given.\n"
704 >                "\tCannot calculate the number of atoms.\n");
705          painCave.isFatal = 1;
706          simError();
707        }
# Line 667 | Line 721 | void SimSetup::gatherInfo(void){
721      simError();
722    }
723  
724 +  //check whether sample time, status time, thermal time and reset time are divisble by dt
725 +  if (!isDivisible(globals->getSampleTime(), globals->getDt())){
726 +    sprintf(painCave.errMsg,
727 +            "Sample time is not divisible by dt.\n"
728 +            "\tThis will result in samples that are not uniformly\n"
729 +            "\tdistributed in time.  If this is a problem, change\n"
730 +            "\tyour sampleTime variable.\n");
731 +    painCave.isFatal = 0;
732 +    simError();    
733 +  }
734 +
735 +  if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
736 +    sprintf(painCave.errMsg,
737 +            "Status time is not divisible by dt.\n"
738 +            "\tThis will result in status reports that are not uniformly\n"
739 +            "\tdistributed in time.  If this is a problem, change \n"
740 +            "\tyour statusTime variable.\n");
741 +    painCave.isFatal = 0;
742 +    simError();    
743 +  }
744 +
745 +  if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
746 +    sprintf(painCave.errMsg,
747 +            "Thermal time is not divisible by dt.\n"
748 +            "\tThis will result in thermalizations that are not uniformly\n"
749 +            "\tdistributed in time.  If this is a problem, change \n"
750 +            "\tyour thermalTime variable.\n");
751 +    painCave.isFatal = 0;
752 +    simError();    
753 +  }  
754 +
755 +  if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
756 +    sprintf(painCave.errMsg,
757 +            "Reset time is not divisible by dt.\n"
758 +            "\tThis will result in integrator resets that are not uniformly\n"
759 +            "\tdistributed in time.  If this is a problem, change\n"
760 +            "\tyour resetTime variable.\n");
761 +    painCave.isFatal = 0;
762 +    simError();    
763 +  }
764 +
765    // set the status, sample, and thermal kick times
766  
767    for (i = 0; i < nInfo; i++){
# Line 696 | Line 791 | void SimSetup::gatherInfo(void){
791      }
792  
793      // check for the temperature set flag
794 <
794 >    
795      if (globals->haveTempSet())
796        info[i].setTemp = globals->getTempSet();
797  
798 <    // get some of the tricky things that may still be in the globals
798 >    // check for the extended State init
799  
800 <    double boxVector[3];
801 <    if (globals->haveBox()){
802 <      boxVector[0] = globals->getBox();
708 <      boxVector[1] = globals->getBox();
709 <      boxVector[2] = globals->getBox();
710 <
711 <      info[i].setBox(boxVector);
712 <    }
713 <    else if (globals->haveDensity()){
714 <      double vol;
715 <      vol = (double) tot_nmol / globals->getDensity();
716 <      boxVector[0] = pow(vol, (1.0 / 3.0));
717 <      boxVector[1] = boxVector[0];
718 <      boxVector[2] = boxVector[0];
719 <
720 <      info[i].setBox(boxVector);
721 <    }
722 <    else{
723 <      if (!globals->haveBoxX()){
724 <        sprintf(painCave.errMsg,
725 <                "SimSetup error, no periodic BoxX size given.\n");
726 <        painCave.isFatal = 1;
727 <        simError();
728 <      }
729 <      boxVector[0] = globals->getBoxX();
730 <
731 <      if (!globals->haveBoxY()){
732 <        sprintf(painCave.errMsg,
733 <                "SimSetup error, no periodic BoxY size given.\n");
734 <        painCave.isFatal = 1;
735 <        simError();
736 <      }
737 <      boxVector[1] = globals->getBoxY();
738 <
739 <      if (!globals->haveBoxZ()){
740 <        sprintf(painCave.errMsg,
741 <                "SimSetup error, no periodic BoxZ size given.\n");
742 <        painCave.isFatal = 1;
743 <        simError();
744 <      }
745 <      boxVector[2] = globals->getBoxZ();
746 <
747 <      info[i].setBox(boxVector);
748 <    }
800 >    info[i].useInitXSstate = globals->getUseInitXSstate();
801 >    info[i].orthoTolerance = globals->getOrthoBoxTolerance();
802 >    
803    }
804 <
804 >  
805    //setup seed for random number generator
806    int seedValue;
807  
# Line 789 | Line 843 | void SimSetup::gatherInfo(void){
843    }
844  
845   #ifdef IS_MPI
846 <  strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
846 >  strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
847    MPIcheckPoint();
848   #endif // is_mpi
849   }
# Line 822 | Line 876 | void SimSetup::finalInfoCheck(void){
876  
877        if (!globals->haveECR()){
878          sprintf(painCave.errMsg,
879 <                "SimSetup Warning: using default value of 1/2 the smallest "
880 <                "box length for the electrostaticCutoffRadius.\n"
881 <                "I hope you have a very fast processor!\n");
879 >                "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
880 >                "\tOOPSE will use a default value of 15.0 angstroms"
881 >                "\tfor the electrostaticCutoffRadius.\n");
882          painCave.isFatal = 0;
883          simError();
884 <        double smallest;
831 <        smallest = info[i].boxL[0];
832 <        if (info[i].boxL[1] <= smallest)
833 <          smallest = info[i].boxL[1];
834 <        if (info[i].boxL[2] <= smallest)
835 <          smallest = info[i].boxL[2];
836 <        theEcr = 0.5 * smallest;
884 >        theEcr = 15.0;
885        }
886        else{
887          theEcr = globals->getECR();
# Line 841 | Line 889 | void SimSetup::finalInfoCheck(void){
889  
890        if (!globals->haveEST()){
891          sprintf(painCave.errMsg,
892 <                "SimSetup Warning: using default value of 0.05 * the "
893 <                "electrostaticCutoffRadius for the electrostaticSkinThickness\n");
892 >                "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
893 >                "\tOOPSE will use a default value of\n"
894 >                "\t0.05 * electrostaticCutoffRadius\n"
895 >                "\tfor the electrostaticSkinThickness\n");
896          painCave.isFatal = 0;
897          simError();
898          theEst = 0.05 * theEcr;
# Line 851 | Line 901 | void SimSetup::finalInfoCheck(void){
901          theEst = globals->getEST();
902        }
903  
904 <      info[i].setEcr(theEcr, theEst);
904 >      info[i].setDefaultEcr(theEcr, theEst);
905  
906        if (!globals->haveDielectric()){
907          sprintf(painCave.errMsg,
908 <                "SimSetup Error: You are trying to use Reaction Field without"
909 <                "setting a dielectric constant!\n");
908 >                "SimSetup Error: No Dielectric constant was set.\n"
909 >                "\tYou are trying to use Reaction Field without"
910 >                "\tsetting a dielectric constant!\n");
911          painCave.isFatal = 1;
912          simError();
913        }
# Line 866 | Line 917 | void SimSetup::finalInfoCheck(void){
917        if (usesDipoles){
918          if (!globals->haveECR()){
919            sprintf(painCave.errMsg,
920 <                  "SimSetup Warning: using default value of 1/2 the smallest "
921 <                  "box length for the electrostaticCutoffRadius.\n"
922 <                  "I hope you have a very fast processor!\n");
923 <          painCave.isFatal = 0;
924 <          simError();
925 <          double smallest;
875 <          smallest = info[i].boxL[0];
876 <          if (info[i].boxL[1] <= smallest)
877 <            smallest = info[i].boxL[1];
878 <          if (info[i].boxL[2] <= smallest)
879 <            smallest = info[i].boxL[2];
880 <          theEcr = 0.5 * smallest;
920 >                  "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
921 >                  "\tOOPSE will use a default value of 15.0 angstroms"
922 >                  "\tfor the electrostaticCutoffRadius.\n");
923 >          painCave.isFatal = 0;
924 >          simError();
925 >          theEcr = 15.0;
926          }
927          else{
928            theEcr = globals->getECR();
929          }
930 <
930 >        
931          if (!globals->haveEST()){
932            sprintf(painCave.errMsg,
933 <                  "SimSetup Warning: using default value of 0.05 * the "
934 <                  "electrostaticCutoffRadius for the "
935 <                  "electrostaticSkinThickness\n");
933 >                  "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
934 >                  "\tOOPSE will use a default value of\n"
935 >                  "\t0.05 * electrostaticCutoffRadius\n"
936 >                  "\tfor the electrostaticSkinThickness\n");
937            painCave.isFatal = 0;
938            simError();
939            theEst = 0.05 * theEcr;
# Line 895 | Line 941 | void SimSetup::finalInfoCheck(void){
941          else{
942            theEst = globals->getEST();
943          }
944 <
945 <        info[i].setEcr(theEcr, theEst);
944 >        
945 >        info[i].setDefaultEcr(theEcr, theEst);
946        }
947      }
948    }
903 –
949   #ifdef IS_MPI
950    strcpy(checkPointMsg, "post processing checks out");
951    MPIcheckPoint();
952   #endif // is_mpi
953   }
954 <
954 >  
955   void SimSetup::initSystemCoords(void){
956    int i;
957  
# Line 934 | Line 979 | void SimSetup::initSystemCoords(void){
979      delete fileInit;
980    }
981    else{
982 < #ifdef IS_MPI
938 <
982 >    
983      // no init from bass
984 <
984 >    
985      sprintf(painCave.errMsg,
986 <            "Cannot intialize a parallel simulation without an initial configuration file.\n");
986 >            "Cannot intialize a simulation without an initial configuration file.\n");
987      painCave.isFatal = 1;;
988      simError();
989 <
946 < #else
947 <
948 <    initFromBass();
949 <
950 <
951 < #endif
989 >    
990    }
991  
992   #ifdef IS_MPI
# Line 1102 | Line 1140 | void SimSetup::createFF(void){
1140        the_ff = new EAM_FF();
1141        break;
1142  
1143 +    case FF_H2O:
1144 +      the_ff = new WATER();
1145 +      break;
1146 +
1147      default:
1148        sprintf(painCave.errMsg,
1149                "SimSetup Error. Unrecognized force field in case statement.\n");
# Line 1244 | Line 1286 | void SimSetup::mpiMolDivide(void){
1286  
1287    if (local_atoms != info[0].n_atoms){
1288      sprintf(painCave.errMsg,
1289 <            "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1290 <            " localAtom (%d) are not equal.\n",
1289 >            "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1290 >            "\tlocalAtom (%d) are not equal.\n",
1291              info[0].n_atoms, local_atoms);
1292      painCave.isFatal = 1;
1293      simError();
# Line 1387 | Line 1429 | void SimSetup::makeIntegrator(void){
1429          else{
1430            sprintf(painCave.errMsg,
1431                    "SimSetup error: If you use the NVT\n"
1432 <                  "    ensemble, you must set tauThermostat.\n");
1432 >                  "\tensemble, you must set tauThermostat.\n");
1433            painCave.isFatal = 1;
1434            simError();
1435          }
# Line 1410 | Line 1452 | void SimSetup::makeIntegrator(void){
1452          else{
1453            sprintf(painCave.errMsg,
1454                    "SimSetup error: If you use a constant pressure\n"
1455 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1455 >                  "\tensemble, you must set targetPressure in the BASS file.\n");
1456            painCave.isFatal = 1;
1457            simError();
1458          }
# Line 1420 | Line 1462 | void SimSetup::makeIntegrator(void){
1462          else{
1463            sprintf(painCave.errMsg,
1464                    "SimSetup error: If you use an NPT\n"
1465 <                  "    ensemble, you must set tauThermostat.\n");
1465 >                  "\tensemble, you must set tauThermostat.\n");
1466            painCave.isFatal = 1;
1467            simError();
1468          }
# Line 1430 | Line 1472 | void SimSetup::makeIntegrator(void){
1472          else{
1473            sprintf(painCave.errMsg,
1474                    "SimSetup error: If you use an NPT\n"
1475 <                  "    ensemble, you must set tauBarostat.\n");
1475 >                  "\tensemble, you must set tauBarostat.\n");
1476            painCave.isFatal = 1;
1477            simError();
1478          }
# Line 1453 | Line 1495 | void SimSetup::makeIntegrator(void){
1495          else{
1496            sprintf(painCave.errMsg,
1497                    "SimSetup error: If you use a constant pressure\n"
1498 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1498 >                  "\tensemble, you must set targetPressure in the BASS file.\n");
1499            painCave.isFatal = 1;
1500            simError();
1501          }    
1502  
1503          if (globals->haveTauThermostat())
1504            myNPTf->setTauThermostat(globals->getTauThermostat());
1505 +
1506          else{
1507            sprintf(painCave.errMsg,
1508                    "SimSetup error: If you use an NPT\n"
1509 <                  "    ensemble, you must set tauThermostat.\n");
1509 >                  "\tensemble, you must set tauThermostat.\n");
1510            painCave.isFatal = 1;
1511            simError();
1512          }
1513  
1514          if (globals->haveTauBarostat())
1515            myNPTf->setTauBarostat(globals->getTauBarostat());
1516 +
1517          else{
1518            sprintf(painCave.errMsg,
1519                    "SimSetup error: If you use an NPT\n"
1520 <                  "    ensemble, you must set tauBarostat.\n");
1520 >                  "\tensemble, you must set tauBarostat.\n");
1521            painCave.isFatal = 1;
1522            simError();
1523          }
# Line 1496 | Line 1540 | void SimSetup::makeIntegrator(void){
1540          else{
1541            sprintf(painCave.errMsg,
1542                    "SimSetup error: If you use a constant pressure\n"
1543 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1543 >                  "\tensemble, you must set targetPressure in the BASS file.\n");
1544            painCave.isFatal = 1;
1545            simError();
1546          }    
# Line 1506 | Line 1550 | void SimSetup::makeIntegrator(void){
1550          else{
1551            sprintf(painCave.errMsg,
1552                    "SimSetup error: If you use an NPT\n"
1553 <                  "    ensemble, you must set tauThermostat.\n");
1553 >                  "\tensemble, you must set tauThermostat.\n");
1554            painCave.isFatal = 1;
1555            simError();
1556          }
# Line 1516 | Line 1560 | void SimSetup::makeIntegrator(void){
1560          else{
1561            sprintf(painCave.errMsg,
1562                    "SimSetup error: If you use an NPT\n"
1563 <                  "    ensemble, you must set tauBarostat.\n");
1563 >                  "\tensemble, you must set tauBarostat.\n");
1564            painCave.isFatal = 1;
1565            simError();
1566          }
# Line 1569 | Line 1613 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1613    }
1614    else{
1615      sprintf(painCave.errMsg,
1616 <            "ZConstraint error: If you use an ZConstraint\n"
1617 <            " , you must set sample time.\n");
1616 >            "ZConstraint error: If you use a ZConstraint,\n"
1617 >            "\tyou must set zconsTime.\n");
1618      painCave.isFatal = 1;
1619      simError();
1620    }
# Line 1585 | Line 1629 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1629    else{
1630      double defaultZConsTol = 0.01;
1631      sprintf(painCave.errMsg,
1632 <            "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1633 <            " , default value %f is used.\n",
1632 >            "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1633 >            "\tOOPSE will use a default value of %f.\n"
1634 >            "\tTo set the tolerance, use the zconsTol variable.\n",
1635              defaultZConsTol);
1636      painCave.isFatal = 0;
1637      simError();      
# Line 1604 | Line 1649 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1649    }
1650    else{
1651      sprintf(painCave.errMsg,
1652 <            "ZConstraint Warning: User does not set force Subtraction policy, "
1653 <            "PolicyByMass is used\n");
1652 >            "ZConstraint Warning: No force subtraction policy was set.\n"
1653 >            "\tOOPSE will use PolicyByMass.\n"
1654 >            "\tTo set the policy, use the zconsForcePolicy variable.\n");
1655      painCave.isFatal = 0;
1656      simError();
1657      zconsForcePolicy->setData("BYMASS");
# Line 1649 | Line 1695 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1695    //check the uniqueness of index  
1696    if(!zconsParaData->isIndexUnique()){
1697      sprintf(painCave.errMsg,
1698 <            "ZConstraint Error: molIndex is not unique\n");
1698 >            "ZConstraint Error: molIndex is not unique!\n");
1699      painCave.isFatal = 1;
1700      simError();
1701    }

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