ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 782 by mmeineke, Tue Sep 23 20:34:31 2003 UTC vs.
Revision 962 by tim, Mon Jan 19 18:36:21 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 –
7   #include "SimSetup.hpp"
8   #include "ReadWrite.hpp"
9   #include "parse_me.h"
# Line 22 | Line 21
21   #define NVT_ENS        1
22   #define NPTi_ENS       2
23   #define NPTf_ENS       3
24 + #define NPTxyz_ENS     4
25  
26 +
27   #define FF_DUFF 0
28   #define FF_LJ   1
29   #define FF_EAM  2
30  
31   using namespace std;
32  
33 + /**
34 + * Check whether dividend is divisble by divisor or not
35 + */
36 + bool isDivisible(double dividend, double divisor){
37 +  double tolerance = 0.000001;
38 +  double quotient;
39 +  double diff;
40 +  int intQuotient;
41 +  
42 +  quotient = dividend / divisor;
43 +
44 +  if (quotient < 0)
45 +    quotient = -quotient;
46 +
47 +  intQuotient = int (quotient + tolerance);
48 +
49 +  diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
50 +
51 +  if (diff <= tolerance)
52 +    return true;
53 +  else
54 +    return false;  
55 + }
56 +
57   SimSetup::SimSetup(){
58 +  
59 +  initSuspend = false;
60    isInfoArray = 0;
61    nInfo = 1;
62  
# Line 52 | Line 79 | void SimSetup::setSimInfo(SimInfo* the_info, int theNi
79    info = the_info;
80    nInfo = theNinfo;
81    isInfoArray = 1;
82 +  initSuspend = true;
83   }
84  
85  
# Line 90 | Line 118 | void SimSetup::createSim(void){
118   #endif // is_mpi
119  
120   void SimSetup::createSim(void){
93 –  int i, j, k, globalAtomIndex;
121  
122    // gather all of the information from the Bass file
123  
# Line 106 | Line 133 | void SimSetup::createSim(void){
133  
134    // initialize the system coordinates
135  
136 <  if (!isInfoArray){
136 >  if ( !initSuspend ){
137      initSystemCoords();
138 +
139 +    if( !(globals->getUseInitTime()) )
140 +      info[0].currentTime = 0.0;
141    }  
142  
143    // make the output filenames
# Line 129 | Line 159 | void SimSetup::makeMolecules(void){
159  
160  
161   void SimSetup::makeMolecules(void){
162 <  int k, l;
162 >  int k;
163    int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
164    molInit molInfo;
165    DirectionalAtom* dAtom;
# Line 551 | Line 581 | void SimSetup::gatherInfo(void){
581  
582  
583   void SimSetup::gatherInfo(void){
584 <  int i, j, k;
584 >  int i;
585  
586    ensembleCase = -1;
587    ffCase = -1;
# Line 602 | Line 632 | void SimSetup::gatherInfo(void){
632    else if (!strcasecmp(ensemble, "NPTf")){
633      ensembleCase = NPTf_ENS;
634    }
635 +  else if (!strcasecmp(ensemble, "NPTxyz")){
636 +    ensembleCase = NPTxyz_ENS;
637 +  }
638    else{
639      sprintf(painCave.errMsg,
640              "SimSetup Warning. Unrecognized Ensemble -> %s, "
# Line 656 | Line 689 | void SimSetup::gatherInfo(void){
689              " Please give nMol in the components.\n");
690      painCave.isFatal = 1;
691      simError();
692 +  }
693 +
694 +  //check whether sample time, status time, thermal time and reset time are divisble by dt
695 +  if (!isDivisible(globals->getSampleTime(), globals->getDt())){
696 +    sprintf(painCave.errMsg,
697 +              "Sample time is not divisible by dt \n");
698 +    painCave.isFatal = 0;
699 +    simError();    
700 +  }
701 +
702 +  if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
703 +    sprintf(painCave.errMsg,
704 +              "Status time is not divisible by dt\n");
705 +    painCave.isFatal = 0;
706 +    simError();    
707    }
708  
709 +  if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
710 +    sprintf(painCave.errMsg,
711 +              "Thermal time is not divisible by dt\n");
712 +    painCave.isFatal = 0;
713 +    simError();    
714 +  }  
715 +
716 +  if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
717 +    sprintf(painCave.errMsg,
718 +              "Reset time is not divisible by dt\n");
719 +    painCave.isFatal = 0;
720 +    simError();    
721 +  }
722 +
723    // set the status, sample, and thermal kick times
724  
725    for (i = 0; i < nInfo; i++){
# Line 687 | Line 749 | void SimSetup::gatherInfo(void){
749      }
750  
751      // check for the temperature set flag
752 <
752 >    
753      if (globals->haveTempSet())
754        info[i].setTemp = globals->getTempSet();
755  
756 <    // get some of the tricky things that may still be in the globals
756 >    // check for the extended State init
757  
758 <    double boxVector[3];
759 <    if (globals->haveBox()){
760 <      boxVector[0] = globals->getBox();
699 <      boxVector[1] = globals->getBox();
700 <      boxVector[2] = globals->getBox();
701 <
702 <      info[i].setBox(boxVector);
703 <    }
704 <    else if (globals->haveDensity()){
705 <      double vol;
706 <      vol = (double) tot_nmol / globals->getDensity();
707 <      boxVector[0] = pow(vol, (1.0 / 3.0));
708 <      boxVector[1] = boxVector[0];
709 <      boxVector[2] = boxVector[0];
710 <
711 <      info[i].setBox(boxVector);
712 <    }
713 <    else{
714 <      if (!globals->haveBoxX()){
715 <        sprintf(painCave.errMsg,
716 <                "SimSetup error, no periodic BoxX size given.\n");
717 <        painCave.isFatal = 1;
718 <        simError();
719 <      }
720 <      boxVector[0] = globals->getBoxX();
721 <
722 <      if (!globals->haveBoxY()){
723 <        sprintf(painCave.errMsg,
724 <                "SimSetup error, no periodic BoxY size given.\n");
725 <        painCave.isFatal = 1;
726 <        simError();
727 <      }
728 <      boxVector[1] = globals->getBoxY();
729 <
730 <      if (!globals->haveBoxZ()){
731 <        sprintf(painCave.errMsg,
732 <                "SimSetup error, no periodic BoxZ size given.\n");
733 <        painCave.isFatal = 1;
734 <        simError();
735 <      }
736 <      boxVector[2] = globals->getBoxZ();
737 <
738 <      info[i].setBox(boxVector);
739 <    }
758 >    info[i].useInitXSstate = globals->getUseInitXSstate();
759 >    info[i].orthoTolerance = globals->getOrthoBoxTolerance();
760 >    
761    }
762 <
762 >  
763    //setup seed for random number generator
764    int seedValue;
765  
# Line 813 | Line 834 | void SimSetup::finalInfoCheck(void){
834  
835        if (!globals->haveECR()){
836          sprintf(painCave.errMsg,
837 <                "SimSetup Warning: using default value of 1/2 the smallest "
838 <                "box length for the electrostaticCutoffRadius.\n"
818 <                "I hope you have a very fast processor!\n");
837 >                "SimSetup Warning: using default value of 15.0 angstroms"
838 >                "box length for the electrostaticCutoffRadius.\n");
839          painCave.isFatal = 0;
840          simError();
841 <        double smallest;
822 <        smallest = info[i].boxL[0];
823 <        if (info[i].boxL[1] <= smallest)
824 <          smallest = info[i].boxL[1];
825 <        if (info[i].boxL[2] <= smallest)
826 <          smallest = info[i].boxL[2];
827 <        theEcr = 0.5 * smallest;
841 >        theEcr = 15.0;
842        }
843        else{
844          theEcr = globals->getECR();
# Line 842 | Line 856 | void SimSetup::finalInfoCheck(void){
856          theEst = globals->getEST();
857        }
858  
859 <      info[i].setEcr(theEcr, theEst);
859 >      info[i].setDefaultEcr(theEcr, theEst);
860  
861        if (!globals->haveDielectric()){
862          sprintf(painCave.errMsg,
# Line 857 | Line 871 | void SimSetup::finalInfoCheck(void){
871        if (usesDipoles){
872          if (!globals->haveECR()){
873            sprintf(painCave.errMsg,
874 <                  "SimSetup Warning: using default value of 1/2 the smallest "
875 <                  "box length for the electrostaticCutoffRadius.\n"
876 <                  "I hope you have a very fast processor!\n");
877 <          painCave.isFatal = 0;
878 <          simError();
865 <          double smallest;
866 <          smallest = info[i].boxL[0];
867 <          if (info[i].boxL[1] <= smallest)
868 <            smallest = info[i].boxL[1];
869 <          if (info[i].boxL[2] <= smallest)
870 <            smallest = info[i].boxL[2];
871 <          theEcr = 0.5 * smallest;
874 >                  "SimSetup Warning: using default value of 15.0 angstroms"
875 >                  "box length for the electrostaticCutoffRadius.\n");
876 >          painCave.isFatal = 0;
877 >          simError();
878 >          theEcr = 15.0;
879          }
880          else{
881            theEcr = globals->getECR();
882          }
883 <
883 >        
884          if (!globals->haveEST()){
885            sprintf(painCave.errMsg,
886                    "SimSetup Warning: using default value of 0.05 * the "
# Line 886 | Line 893 | void SimSetup::finalInfoCheck(void){
893          else{
894            theEst = globals->getEST();
895          }
896 <
897 <        info[i].setEcr(theEcr, theEst);
896 >        
897 >        info[i].setDefaultEcr(theEcr, theEst);
898        }
899      }
900    }
894 –
901   #ifdef IS_MPI
902    strcpy(checkPointMsg, "post processing checks out");
903    MPIcheckPoint();
904   #endif // is_mpi
905   }
906 <
906 >  
907   void SimSetup::initSystemCoords(void){
908    int i;
909  
# Line 914 | Line 920 | void SimSetup::initSystemCoords(void){
920      if (worldRank == 0){
921   #endif //is_mpi
922        inName = globals->getInitialConfig();
917 –      double* tempDouble = new double[1000000];
923        fileInit = new InitializeFromFile(inName);
924   #ifdef IS_MPI
925      }
# Line 926 | Line 931 | void SimSetup::initSystemCoords(void){
931      delete fileInit;
932    }
933    else{
934 < #ifdef IS_MPI
930 <
934 >    
935      // no init from bass
936 <
936 >    
937      sprintf(painCave.errMsg,
938 <            "Cannot intialize a parallel simulation without an initial configuration file.\n");
939 <    painCave.isFatal;
938 >            "Cannot intialize a simulation without an initial configuration file.\n");
939 >    painCave.isFatal = 1;;
940      simError();
941 <
938 < #else
939 <
940 <    initFromBass();
941 <
942 <
943 < #endif
941 >    
942    }
943  
944   #ifdef IS_MPI
# Line 1158 | Line 1156 | void SimSetup::calcSysValues(void){
1156   }
1157  
1158   void SimSetup::calcSysValues(void){
1159 <  int i, j, k;
1159 >  int i;
1160  
1161    int* molMembershipArray;
1162  
# Line 1257 | Line 1255 | void SimSetup::makeSysArrays(void){
1255  
1256  
1257   void SimSetup::makeSysArrays(void){
1258 <  int i, j, k, l;
1258 >
1259 > #ifndef IS_MPI
1260 >  int k, j;
1261 > #endif // is_mpi
1262 >  int i, l;
1263  
1264    Atom** the_atoms;
1265    Molecule* the_molecules;
# Line 1344 | Line 1346 | void SimSetup::makeIntegrator(void){
1346    NVT<RealIntegrator>* myNVT = NULL;
1347    NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1348    NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1349 +  NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1350    
1351    for (k = 0; k < nInfo; k++){
1352      switch (ensembleCase){
# Line 1447 | Line 1450 | void SimSetup::makeIntegrator(void){
1450  
1451          if (globals->haveTauThermostat())
1452            myNPTf->setTauThermostat(globals->getTauThermostat());
1453 +
1454          else{
1455            sprintf(painCave.errMsg,
1456                    "SimSetup error: If you use an NPT\n"
# Line 1457 | Line 1461 | void SimSetup::makeIntegrator(void){
1461  
1462          if (globals->haveTauBarostat())
1463            myNPTf->setTauBarostat(globals->getTauBarostat());
1464 +
1465          else{
1466            sprintf(painCave.errMsg,
1467                    "SimSetup error: If you use an NPT\n"
# Line 1466 | Line 1471 | void SimSetup::makeIntegrator(void){
1471          }
1472  
1473          info->the_integrator = myNPTf;
1474 +        break;
1475 +
1476 +      case NPTxyz_ENS:
1477 +        if (globals->haveZconstraints()){
1478 +          setupZConstraint(info[k]);
1479 +          myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1480 +        }
1481 +        else
1482 +          myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1483 +
1484 +        myNPTxyz->setTargetTemp(globals->getTargetTemp());
1485 +
1486 +        if (globals->haveTargetPressure())
1487 +          myNPTxyz->setTargetPressure(globals->getTargetPressure());
1488 +        else{
1489 +          sprintf(painCave.errMsg,
1490 +                  "SimSetup error: If you use a constant pressure\n"
1491 +                  "    ensemble, you must set targetPressure in the BASS file.\n");
1492 +          painCave.isFatal = 1;
1493 +          simError();
1494 +        }    
1495 +
1496 +        if (globals->haveTauThermostat())
1497 +          myNPTxyz->setTauThermostat(globals->getTauThermostat());
1498 +        else{
1499 +          sprintf(painCave.errMsg,
1500 +                  "SimSetup error: If you use an NPT\n"
1501 +                  "    ensemble, you must set tauThermostat.\n");
1502 +          painCave.isFatal = 1;
1503 +          simError();
1504 +        }
1505 +
1506 +        if (globals->haveTauBarostat())
1507 +          myNPTxyz->setTauBarostat(globals->getTauBarostat());
1508 +        else{
1509 +          sprintf(painCave.errMsg,
1510 +                  "SimSetup error: If you use an NPT\n"
1511 +                  "    ensemble, you must set tauBarostat.\n");
1512 +          painCave.isFatal = 1;
1513 +          simError();
1514 +        }
1515 +
1516 +        info->the_integrator = myNPTxyz;
1517          break;
1518  
1519        default:

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines