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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 859 by mmeineke, Mon Nov 10 21:50:36 2003 UTC vs.
Revision 1032 by tim, Fri Feb 6 19:05:07 2004 UTC

# Line 9 | Line 9
9   #include "parse_me.h"
10   #include "Integrator.hpp"
11   #include "simError.h"
12 + #include "ConjugateMinimizer.hpp"
13  
14   #ifdef IS_MPI
15   #include "mpiBASS.h"
# Line 24 | Line 25
25   #define NPTxyz_ENS     4
26  
27  
28 < #define FF_DUFF 0
29 < #define FF_LJ   1
30 < #define FF_EAM  2
28 > #define FF_DUFF  0
29 > #define FF_LJ    1
30 > #define FF_EAM   2
31 > #define FF_H2O 3
32  
33   using namespace std;
34  
35 + /**
36 + * Check whether dividend is divisble by divisor or not
37 + */
38 + bool isDivisible(double dividend, double divisor){
39 +  double tolerance = 0.000001;
40 +  double quotient;
41 +  double diff;
42 +  int intQuotient;
43 +  
44 +  quotient = dividend / divisor;
45 +
46 +  if (quotient < 0)
47 +    quotient = -quotient;
48 +
49 +  intQuotient = int (quotient + tolerance);
50 +
51 +  diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
52 +
53 +  if (diff <= tolerance)
54 +    return true;
55 +  else
56 +    return false;  
57 + }
58 +
59   SimSetup::SimSetup(){
60    
61    initSuspend = false;
# Line 120 | Line 146 | void SimSetup::createSim(void){
146  
147    makeOutNames();
148  
149 <  // make the integrator
150 <
151 <  makeIntegrator();
152 <
149 >  if (globals->haveMinimizer())
150 >    // make minimizer
151 >    makeMinimizer();
152 >  else
153 >    // make the integrator
154 >    makeIntegrator();
155 >  
156   #ifdef IS_MPI
157    mpiSim->mpiRefresh();
158   #endif
# Line 150 | Line 179 | void SimSetup::makeMolecules(void){
179    bend_set* theBends;
180    torsion_set* theTorsions;
181  
153 –
182    //init the forceField paramters
183  
184    the_ff->readParams();
# Line 158 | Line 186 | void SimSetup::makeMolecules(void){
186  
187    // init the atoms
188  
189 +  double phi, theta, psi;
190 +  double sux, suy, suz;
191 +  double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
192    double ux, uy, uz, u, uSqr;
193  
194    for (k = 0; k < nInfo; k++){
# Line 194 | Line 225 | void SimSetup::makeMolecules(void){
225            info[k].n_oriented++;
226            molInfo.myAtoms[j] = dAtom;
227  
228 <          ux = currentAtom->getOrntX();
229 <          uy = currentAtom->getOrntY();
230 <          uz = currentAtom->getOrntZ();
228 >          // Directional Atoms have standard unit vectors which are oriented
229 >          // in space using the three Euler angles.  We assume the standard
230 >          // unit vector was originally along the z axis below.
231  
232 +          phi = currentAtom->getEulerPhi() * M_PI / 180.0;
233 +          theta = currentAtom->getEulerTheta() * M_PI / 180.0;
234 +          psi = currentAtom->getEulerPsi()* M_PI / 180.0;
235 +            
236 +          Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
237 +          Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
238 +          Axz = sin(theta) * sin(psi);
239 +          
240 +          Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
241 +          Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
242 +          Ayz = sin(theta) * cos(psi);
243 +          
244 +          Azx = sin(phi) * sin(theta);
245 +          Azy = -cos(phi) * sin(theta);
246 +          Azz = cos(theta);
247 +
248 +          sux = 0.0;
249 +          suy = 0.0;
250 +          suz = 1.0;
251 +
252 +          ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
253 +          uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
254 +          uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
255 +
256            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
257  
258            u = sqrt(uSqr);
# Line 584 | Line 639 | void SimSetup::gatherInfo(void){
639    }
640    else if (!strcasecmp(force_field, "EAM")){
641      ffCase = FF_EAM;
642 +  }
643 +  else if (!strcasecmp(force_field, "WATER")){
644 +    ffCase = FF_H2O;
645    }
646    else{
647      sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
# Line 613 | Line 671 | void SimSetup::gatherInfo(void){
671    }
672    else{
673      sprintf(painCave.errMsg,
674 <            "SimSetup Warning. Unrecognized Ensemble -> %s, "
675 <            "reverting to NVE for this simulation.\n",
674 >            "SimSetup Warning. Unrecognized Ensemble -> %s \n"
675 >            "\treverting to NVE for this simulation.\n",
676              ensemble);
677           painCave.isFatal = 0;
678           simError();
# Line 646 | Line 704 | void SimSetup::gatherInfo(void){
704        if (!the_components[i]->haveNMol()){
705          // we have a problem
706          sprintf(painCave.errMsg,
707 <                "SimSetup Error. No global NMol or component NMol"
708 <                " given. Cannot calculate the number of atoms.\n");
707 >                "SimSetup Error. No global NMol or component NMol given.\n"
708 >                "\tCannot calculate the number of atoms.\n");
709          painCave.isFatal = 1;
710          simError();
711        }
# Line 665 | Line 723 | void SimSetup::gatherInfo(void){
723              " Please give nMol in the components.\n");
724      painCave.isFatal = 1;
725      simError();
726 +  }
727 +
728 +  //check whether sample time, status time, thermal time and reset time are divisble by dt
729 +  if (!isDivisible(globals->getSampleTime(), globals->getDt())){
730 +    sprintf(painCave.errMsg,
731 +            "Sample time is not divisible by dt.\n"
732 +            "\tThis will result in samples that are not uniformly\n"
733 +            "\tdistributed in time.  If this is a problem, change\n"
734 +            "\tyour sampleTime variable.\n");
735 +    painCave.isFatal = 0;
736 +    simError();    
737 +  }
738 +
739 +  if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
740 +    sprintf(painCave.errMsg,
741 +            "Status time is not divisible by dt.\n"
742 +            "\tThis will result in status reports that are not uniformly\n"
743 +            "\tdistributed in time.  If this is a problem, change \n"
744 +            "\tyour statusTime variable.\n");
745 +    painCave.isFatal = 0;
746 +    simError();    
747    }
748  
749 +  if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
750 +    sprintf(painCave.errMsg,
751 +            "Thermal time is not divisible by dt.\n"
752 +            "\tThis will result in thermalizations that are not uniformly\n"
753 +            "\tdistributed in time.  If this is a problem, change \n"
754 +            "\tyour thermalTime variable.\n");
755 +    painCave.isFatal = 0;
756 +    simError();    
757 +  }  
758 +
759 +  if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
760 +    sprintf(painCave.errMsg,
761 +            "Reset time is not divisible by dt.\n"
762 +            "\tThis will result in integrator resets that are not uniformly\n"
763 +            "\tdistributed in time.  If this is a problem, change\n"
764 +            "\tyour resetTime variable.\n");
765 +    painCave.isFatal = 0;
766 +    simError();    
767 +  }
768 +
769    // set the status, sample, and thermal kick times
770  
771    for (i = 0; i < nInfo; i++){
# Line 746 | Line 845 | void SimSetup::gatherInfo(void){
845    for (int i = 0; i < nInfo; i++){
846      info[i].setSeed(seedValue);
847    }
848 <
848 >  
849   #ifdef IS_MPI
850 <  strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
850 >  strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
851    MPIcheckPoint();
852   #endif // is_mpi
853   }
# Line 781 | Line 880 | void SimSetup::finalInfoCheck(void){
880  
881        if (!globals->haveECR()){
882          sprintf(painCave.errMsg,
883 <                "SimSetup Warning: using default value of 15.0 angstroms"
884 <                "box length for the electrostaticCutoffRadius.\n");
883 >                "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
884 >                "\tOOPSE will use a default value of 15.0 angstroms"
885 >                "\tfor the electrostaticCutoffRadius.\n");
886          painCave.isFatal = 0;
887          simError();
888          theEcr = 15.0;
# Line 793 | Line 893 | void SimSetup::finalInfoCheck(void){
893  
894        if (!globals->haveEST()){
895          sprintf(painCave.errMsg,
896 <                "SimSetup Warning: using default value of 0.05 * the "
897 <                "electrostaticCutoffRadius for the electrostaticSkinThickness\n");
896 >                "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
897 >                "\tOOPSE will use a default value of\n"
898 >                "\t0.05 * electrostaticCutoffRadius\n"
899 >                "\tfor the electrostaticSkinThickness\n");
900          painCave.isFatal = 0;
901          simError();
902          theEst = 0.05 * theEcr;
# Line 807 | Line 909 | void SimSetup::finalInfoCheck(void){
909  
910        if (!globals->haveDielectric()){
911          sprintf(painCave.errMsg,
912 <                "SimSetup Error: You are trying to use Reaction Field without"
913 <                "setting a dielectric constant!\n");
912 >                "SimSetup Error: No Dielectric constant was set.\n"
913 >                "\tYou are trying to use Reaction Field without"
914 >                "\tsetting a dielectric constant!\n");
915          painCave.isFatal = 1;
916          simError();
917        }
# Line 818 | Line 921 | void SimSetup::finalInfoCheck(void){
921        if (usesDipoles){
922          if (!globals->haveECR()){
923            sprintf(painCave.errMsg,
924 <                  "SimSetup Warning: using default value of 15.0 angstroms"
925 <                  "box length for the electrostaticCutoffRadius.\n");
924 >                  "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
925 >                  "\tOOPSE will use a default value of 15.0 angstroms"
926 >                  "\tfor the electrostaticCutoffRadius.\n");
927            painCave.isFatal = 0;
928            simError();
929            theEcr = 15.0;
# Line 830 | Line 934 | void SimSetup::finalInfoCheck(void){
934          
935          if (!globals->haveEST()){
936            sprintf(painCave.errMsg,
937 <                  "SimSetup Warning: using default value of 0.05 * the "
938 <                  "electrostaticCutoffRadius for the "
939 <                  "electrostaticSkinThickness\n");
937 >                  "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
938 >                  "\tOOPSE will use a default value of\n"
939 >                  "\t0.05 * electrostaticCutoffRadius\n"
940 >                  "\tfor the electrostaticSkinThickness\n");
941            painCave.isFatal = 0;
942            simError();
943            theEst = 0.05 * theEcr;
# Line 1037 | Line 1142 | void SimSetup::createFF(void){
1142  
1143      case FF_EAM:
1144        the_ff = new EAM_FF();
1145 +      break;
1146 +
1147 +    case FF_H2O:
1148 +      the_ff = new WATER();
1149        break;
1150  
1151      default:
# Line 1181 | Line 1290 | void SimSetup::mpiMolDivide(void){
1290  
1291    if (local_atoms != info[0].n_atoms){
1292      sprintf(painCave.errMsg,
1293 <            "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1294 <            " localAtom (%d) are not equal.\n",
1293 >            "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1294 >            "\tlocalAtom (%d) are not equal.\n",
1295              info[0].n_atoms, local_atoms);
1296      painCave.isFatal = 1;
1297      simError();
# Line 1324 | Line 1433 | void SimSetup::makeIntegrator(void){
1433          else{
1434            sprintf(painCave.errMsg,
1435                    "SimSetup error: If you use the NVT\n"
1436 <                  "    ensemble, you must set tauThermostat.\n");
1436 >                  "\tensemble, you must set tauThermostat.\n");
1437            painCave.isFatal = 1;
1438            simError();
1439          }
# Line 1347 | Line 1456 | void SimSetup::makeIntegrator(void){
1456          else{
1457            sprintf(painCave.errMsg,
1458                    "SimSetup error: If you use a constant pressure\n"
1459 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1459 >                  "\tensemble, you must set targetPressure in the BASS file.\n");
1460            painCave.isFatal = 1;
1461            simError();
1462          }
# Line 1357 | Line 1466 | void SimSetup::makeIntegrator(void){
1466          else{
1467            sprintf(painCave.errMsg,
1468                    "SimSetup error: If you use an NPT\n"
1469 <                  "    ensemble, you must set tauThermostat.\n");
1469 >                  "\tensemble, you must set tauThermostat.\n");
1470            painCave.isFatal = 1;
1471            simError();
1472          }
# Line 1367 | Line 1476 | void SimSetup::makeIntegrator(void){
1476          else{
1477            sprintf(painCave.errMsg,
1478                    "SimSetup error: If you use an NPT\n"
1479 <                  "    ensemble, you must set tauBarostat.\n");
1479 >                  "\tensemble, you must set tauBarostat.\n");
1480            painCave.isFatal = 1;
1481            simError();
1482          }
# Line 1390 | Line 1499 | void SimSetup::makeIntegrator(void){
1499          else{
1500            sprintf(painCave.errMsg,
1501                    "SimSetup error: If you use a constant pressure\n"
1502 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1502 >                  "\tensemble, you must set targetPressure in the BASS file.\n");
1503            painCave.isFatal = 1;
1504            simError();
1505          }    
# Line 1401 | Line 1510 | void SimSetup::makeIntegrator(void){
1510          else{
1511            sprintf(painCave.errMsg,
1512                    "SimSetup error: If you use an NPT\n"
1513 <                  "    ensemble, you must set tauThermostat.\n");
1513 >                  "\tensemble, you must set tauThermostat.\n");
1514            painCave.isFatal = 1;
1515            simError();
1516          }
# Line 1412 | Line 1521 | void SimSetup::makeIntegrator(void){
1521          else{
1522            sprintf(painCave.errMsg,
1523                    "SimSetup error: If you use an NPT\n"
1524 <                  "    ensemble, you must set tauBarostat.\n");
1524 >                  "\tensemble, you must set tauBarostat.\n");
1525            painCave.isFatal = 1;
1526            simError();
1527          }
# Line 1435 | Line 1544 | void SimSetup::makeIntegrator(void){
1544          else{
1545            sprintf(painCave.errMsg,
1546                    "SimSetup error: If you use a constant pressure\n"
1547 <                  "    ensemble, you must set targetPressure in the BASS file.\n");
1547 >                  "\tensemble, you must set targetPressure in the BASS file.\n");
1548            painCave.isFatal = 1;
1549            simError();
1550          }    
# Line 1445 | Line 1554 | void SimSetup::makeIntegrator(void){
1554          else{
1555            sprintf(painCave.errMsg,
1556                    "SimSetup error: If you use an NPT\n"
1557 <                  "    ensemble, you must set tauThermostat.\n");
1557 >                  "\tensemble, you must set tauThermostat.\n");
1558            painCave.isFatal = 1;
1559            simError();
1560          }
# Line 1455 | Line 1564 | void SimSetup::makeIntegrator(void){
1564          else{
1565            sprintf(painCave.errMsg,
1566                    "SimSetup error: If you use an NPT\n"
1567 <                  "    ensemble, you must set tauBarostat.\n");
1567 >                  "\tensemble, you must set tauBarostat.\n");
1568            painCave.isFatal = 1;
1569            simError();
1570          }
# Line 1508 | Line 1617 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1617    }
1618    else{
1619      sprintf(painCave.errMsg,
1620 <            "ZConstraint error: If you use an ZConstraint\n"
1621 <            " , you must set sample time.\n");
1620 >            "ZConstraint error: If you use a ZConstraint,\n"
1621 >            "\tyou must set zconsTime.\n");
1622      painCave.isFatal = 1;
1623      simError();
1624    }
# Line 1524 | Line 1633 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1633    else{
1634      double defaultZConsTol = 0.01;
1635      sprintf(painCave.errMsg,
1636 <            "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1637 <            " , default value %f is used.\n",
1636 >            "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1637 >            "\tOOPSE will use a default value of %f.\n"
1638 >            "\tTo set the tolerance, use the zconsTol variable.\n",
1639              defaultZConsTol);
1640      painCave.isFatal = 0;
1641      simError();      
# Line 1543 | Line 1653 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1653    }
1654    else{
1655      sprintf(painCave.errMsg,
1656 <            "ZConstraint Warning: User does not set force Subtraction policy, "
1657 <            "PolicyByMass is used\n");
1656 >            "ZConstraint Warning: No force subtraction policy was set.\n"
1657 >            "\tOOPSE will use PolicyByMass.\n"
1658 >            "\tTo set the policy, use the zconsForcePolicy variable.\n");
1659      painCave.isFatal = 0;
1660      simError();
1661      zconsForcePolicy->setData("BYMASS");
# Line 1588 | Line 1699 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1699    //check the uniqueness of index  
1700    if(!zconsParaData->isIndexUnique()){
1701      sprintf(painCave.errMsg,
1702 <            "ZConstraint Error: molIndex is not unique\n");
1702 >            "ZConstraint Error: molIndex is not unique!\n");
1703      painCave.isFatal = 1;
1704      simError();
1705    }
# Line 1599 | Line 1710 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1710    //push data into siminfo, therefore, we can retrieve later
1711    theInfo.addProperty(zconsParaData);
1712   }
1713 +
1714 + void SimSetup::makeMinimizer(){
1715 +
1716 +  OOPSEMinimizerBase* myOOPSEMinimizerBase;
1717 +  ObjFunctor1 * objFunc;
1718 +  OutputFunctor* outputFunc;
1719 +  ConcreteNLModel1* nlp;
1720 +  MinimizerParameterSet* param;
1721 +  ConjugateMinimizerBase* minimizer;
1722 +  int dim;
1723 +  
1724 +  for (int i = 0; i < nInfo; i++){
1725 +    //creat
1726 +    myOOPSEMinimizerBase = new OOPSEMinimizerBase(&(info[i]), the_ff);
1727 +
1728 +    //creat the object functor;
1729 +    objFunc = (ObjFunctor1*) new ClassMemObjFunctor1<OOPSEMinimizerBase>
1730 +                                              (myOOPSEMinimizerBase, &OOPSEMinimizerBase::calcGradient);
1731 +
1732 +    //creat output functor;
1733 +    outputFunc =  new ClassMemOutputFunctor<OOPSEMinimizerBase>
1734 +                               (myOOPSEMinimizerBase, &OOPSEMinimizerBase::output);
1735 +
1736 +    //creat nonlinear model
1737 +    dim = myOOPSEMinimizerBase->getDim();    
1738 +    nlp = new ConcreteNLModel1(dim, objFunc);
1739 +
1740 +    //prepare parameter set for minimizer
1741 +    param = new MinimizerParameterSet();
1742 +    param->setDefaultParameter();
1743 +
1744 +    if (globals->haveMinimizer()){
1745 +      param->setFTol(globals->getMinFTol());
1746 +    }
1747 +
1748 +    if (globals->haveMinGTol()){
1749 +      param->setGTol(globals->getMinGTol());
1750 +    }
1751 +
1752 +    if (globals->haveMinMaxIter()){
1753 +      param->setMaxIteration(globals->getMinMaxIter());
1754 +    }
1755 +
1756 +    if (globals->haveMinWriteFrq()){
1757 +      param->setMaxIteration(globals->getMinMaxIter());
1758 +    }
1759 +
1760 +    if (globals->haveMinWriteFrq()){
1761 +      param->setWriteFrq(globals->getMinWriteFrq());
1762 +    }
1763 +    
1764 +    if (globals->haveMinResetFrq()){
1765 +      param->setResetFrq(globals->getMinResetFrq());
1766 +    }
1767 +
1768 +    if (globals->haveMinLSMaxIter()){
1769 +      param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1770 +    }    
1771 +
1772 +    if (globals->haveMinLSTol()){
1773 +      param->setLineSearchTol(globals->getMinLSTol());
1774 +    }    
1775 +    
1776 +     //creat the minimizer
1777 +     minimizer = new PRCGMinimizer(nlp, param);
1778 +     minimizer->setLineSearchStrategy(nlp, GoldenSection);
1779 +     minimizer->setOutputFunctor(outputFunc);
1780 +
1781 +     //store the minimizer into simInfo
1782 +     info[i].the_minimizer = minimizer;
1783 +     info[i].has_minimizer = true;
1784 +  }
1785 +
1786 + }

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