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root/group/trunk/OOPSE-3.0/src/brains/SimSetup.cpp
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Comparing trunk/OOPSE-3.0/src/brains/SimSetup.cpp (file contents):
Revision 1490 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1650 by gezelter, Tue Oct 26 22:24:52 2004 UTC

# Line 4 | Line 4
4   #include <math.h>
5   #include <string>
6   #include <sprng.h>
7 < #include "SimSetup.hpp"
8 < #include "ReadWrite.hpp"
9 < #include "parse_me.h"
10 < #include "Integrator.hpp"
11 < #include "simError.h"
12 < #include "RigidBody.hpp"
13 < #include "OOPSEMinimizer.hpp"
7 > #include "brains/SimSetup.hpp"
8 > #include "io/ReadWrite.hpp"
9 > #include "io/parse_me.h"
10 > #include "integrators/Integrator.hpp"
11 > #include "utils/simError.h"
12 > #include "primitives/RigidBody.hpp"
13 > #include "minimizers/OOPSEMinimizer.hpp"
14  
15   #ifdef IS_MPI
16 < #include "mpiBASS.h"
17 < #include "mpiSimulation.hpp"
16 > #include "io/mpiBASS.h"
17 > #include "brains/mpiSimulation.hpp"
18   #endif
19  
20   // some defines for ensemble and Forcefield  cases
# Line 26 | Line 26
26   #define NPTxyz_ENS     4
27  
28  
29 < #define FF_DUFF  0
30 < #define FF_LJ    1
31 < #define FF_EAM   2
32 < #define FF_H2O   3
29 > #define FF_DUFF   0
30 > #define FF_LJ     1
31 > #define FF_EAM    2
32 > #define FF_H2O    3
33 > #define FF_SHAPES 4
34  
35   using namespace std;
36 + using namespace oopse;
37  
38   /**
39   * Check whether dividend is divisble by divisor or not
# Line 713 | Line 715 | void SimSetup::gatherInfo(void){
715    }
716    else if (!strcasecmp(force_field, "WATER")){
717      ffCase = FF_H2O;
718 +  }
719 +  else if (!strcasecmp(force_field, "SHAPES")){
720 +    ffCase = FF_SHAPES;
721    }
722    else{
723      sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
724              force_field);
725 <         painCave.isFatal = 1;
726 <         simError();
725 >    painCave.isFatal = 1;
726 >    simError();
727    }
728    if (globals->haveForceFieldVariant()) {
729      strcpy(forcefield_variant, globals->getForceFieldVariant());
# Line 908 | Line 913 | void SimSetup::gatherInfo(void){
913    }
914    
915    for (i = 0; i < nInfo; i++) {
911 –    // get the mixing rule
912 –    
913 –    strcpy(info[i].mixingRule, globals->getMixingRule());
916      info[i].usePBC = globals->getPBC();
917    }
918    
# Line 1259 | Line 1261 | void SimSetup::createFF(void){
1261  
1262      case FF_H2O:
1263        the_ff = new WATER();
1264 +      break;
1265 +
1266 +    case FF_SHAPES:
1267 +      the_ff = new Shapes_FF();
1268        break;
1269  
1270      default:
# Line 1764 | Line 1770 | void SimSetup::initFortran(void){
1770   void SimSetup::initFortran(void){
1771    info[0].refreshSim();
1772  
1773 <  if (!strcmp(info[0].mixingRule, "standard")){
1768 <    the_ff->initForceField(LB_MIXING_RULE);
1769 <  }
1770 <  else if (!strcmp(info[0].mixingRule, "explicit")){
1771 <    the_ff->initForceField(EXPLICIT_MIXING_RULE);
1772 <  }
1773 <  else{
1774 <    sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1775 <            info[0].mixingRule);
1776 <    painCave.isFatal = 1;
1777 <    simError();
1778 <  }
1779 <
1773 >  the_ff->initForceField();
1774  
1775   #ifdef IS_MPI
1776 <  strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1776 >  strcpy(checkPointMsg, "Successfully intialized the fortran portion of the force field.");
1777    MPIcheckPoint();
1778   #endif // is_mpi
1779   }
# Line 1790 | Line 1784 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1784  
1785    if (globals->haveZconstraintTime()){
1786      //add sample time of z-constraint  into SimInfo's property list                    
1787 <    DoubleData* zconsTimeProp = new DoubleData();
1787 >    DoubleGenericData* zconsTimeProp = new DoubleGenericData();
1788      zconsTimeProp->setID(ZCONSTIME_ID);
1789      zconsTimeProp->setData(globals->getZconsTime());
1790      theInfo.addProperty(zconsTimeProp);
# Line 1805 | Line 1799 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1799  
1800    //push zconsTol into siminfo, if user does not specify
1801    //value for zconsTol, a default value will be used
1802 <  DoubleData* zconsTol = new DoubleData();
1802 >  DoubleGenericData* zconsTol = new DoubleGenericData();
1803    zconsTol->setID(ZCONSTOL_ID);
1804    if (globals->haveZconsTol()){
1805      zconsTol->setData(globals->getZconsTol());
# Line 1825 | Line 1819 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1819    theInfo.addProperty(zconsTol);
1820  
1821    //set Force Subtraction Policy
1822 <  StringData* zconsForcePolicy = new StringData();
1822 >  StringGenericData* zconsForcePolicy = new StringGenericData();
1823    zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1824  
1825    if (globals->haveZconsForcePolicy()){
# Line 1844 | Line 1838 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1838    theInfo.addProperty(zconsForcePolicy);
1839  
1840    //set zcons gap
1841 <  DoubleData* zconsGap = new DoubleData();
1841 >  DoubleGenericData* zconsGap = new DoubleGenericData();
1842    zconsGap->setID(ZCONSGAP_ID);
1843  
1844    if (globals->haveZConsGap()){
# Line 1853 | Line 1847 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1847    }
1848  
1849    //set zcons fixtime
1850 <  DoubleData* zconsFixtime = new DoubleData();
1850 >  DoubleGenericData* zconsFixtime = new DoubleGenericData();
1851    zconsFixtime->setID(ZCONSFIXTIME_ID);
1852  
1853    if (globals->haveZConsFixTime()){
# Line 1862 | Line 1856 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1856    }
1857  
1858    //set zconsUsingSMD
1859 <  IntData* zconsUsingSMD = new IntData();
1859 >  IntGenericData* zconsUsingSMD = new IntGenericData();
1860    zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1861  
1862    if (globals->haveZConsUsingSMD()){
# Line 1878 | Line 1872 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1872  
1873    zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1874  
1875 <  StringData* zconsFilename = new StringData();
1875 >  StringGenericData* zconsFilename = new StringGenericData();
1876    zconsFilename->setID(ZCONSFILENAME_ID);
1877    zconsFilename->setData(zconsOutput);
1878  

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