--- trunk/OOPSE/libmdtools/SimSetup.cpp 2003/10/23 19:57:25 814 +++ trunk/OOPSE/libmdtools/SimSetup.cpp 2004/01/19 18:36:21 962 @@ -1,7 +1,7 @@ #include -#include +#include #include -#include +#include #include #include #include "SimSetup.hpp" @@ -29,8 +29,34 @@ using namespace std; #define FF_EAM 2 using namespace std; + +/** + * Check whether dividend is divisble by divisor or not + */ +bool isDivisible(double dividend, double divisor){ + double tolerance = 0.000001; + double quotient; + double diff; + int intQuotient; + + quotient = dividend / divisor; + + if (quotient < 0) + quotient = -quotient; + + intQuotient = int (quotient + tolerance); + + diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); + + if (diff <= tolerance) + return true; + else + return false; +} SimSetup::SimSetup(){ + + initSuspend = false; isInfoArray = 0; nInfo = 1; @@ -53,6 +79,7 @@ void SimSetup::setSimInfo(SimInfo* the_info, int theNi info = the_info; nInfo = theNinfo; isInfoArray = 1; + initSuspend = true; } @@ -106,7 +133,7 @@ void SimSetup::createSim(void){ // initialize the system coordinates - if (!isInfoArray){ + if ( !initSuspend ){ initSystemCoords(); if( !(globals->getUseInitTime()) ) @@ -664,6 +691,35 @@ void SimSetup::gatherInfo(void){ simError(); } + //check whether sample time, status time, thermal time and reset time are divisble by dt + if (!isDivisible(globals->getSampleTime(), globals->getDt())){ + sprintf(painCave.errMsg, + "Sample time is not divisible by dt \n"); + painCave.isFatal = 0; + simError(); + } + + if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ + sprintf(painCave.errMsg, + "Status time is not divisible by dt\n"); + painCave.isFatal = 0; + simError(); + } + + if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ + sprintf(painCave.errMsg, + "Thermal time is not divisible by dt\n"); + painCave.isFatal = 0; + simError(); + } + + if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ + sprintf(painCave.errMsg, + "Reset time is not divisible by dt\n"); + painCave.isFatal = 0; + simError(); + } + // set the status, sample, and thermal kick times for (i = 0; i < nInfo; i++){ @@ -693,58 +749,17 @@ void SimSetup::gatherInfo(void){ } // check for the temperature set flag - + if (globals->haveTempSet()) info[i].setTemp = globals->getTempSet(); - // get some of the tricky things that may still be in the globals + // check for the extended State init - double boxVector[3]; - if (globals->haveBox()){ - boxVector[0] = globals->getBox(); - boxVector[1] = globals->getBox(); - boxVector[2] = globals->getBox(); - - info[i].setBox(boxVector); - } - else if (globals->haveDensity()){ - double vol; - vol = (double) tot_nmol / globals->getDensity(); - boxVector[0] = pow(vol, (1.0 / 3.0)); - boxVector[1] = boxVector[0]; - boxVector[2] = boxVector[0]; - - info[i].setBox(boxVector); - } - else{ - if (!globals->haveBoxX()){ - sprintf(painCave.errMsg, - "SimSetup error, no periodic BoxX size given.\n"); - painCave.isFatal = 1; - simError(); - } - boxVector[0] = globals->getBoxX(); - - if (!globals->haveBoxY()){ - sprintf(painCave.errMsg, - "SimSetup error, no periodic BoxY size given.\n"); - painCave.isFatal = 1; - simError(); - } - boxVector[1] = globals->getBoxY(); - - if (!globals->haveBoxZ()){ - sprintf(painCave.errMsg, - "SimSetup error, no periodic BoxZ size given.\n"); - painCave.isFatal = 1; - simError(); - } - boxVector[2] = globals->getBoxZ(); - - info[i].setBox(boxVector); - } + info[i].useInitXSstate = globals->getUseInitXSstate(); + info[i].orthoTolerance = globals->getOrthoBoxTolerance(); + } - + //setup seed for random number generator int seedValue; @@ -819,18 +834,11 @@ void SimSetup::finalInfoCheck(void){ if (!globals->haveECR()){ sprintf(painCave.errMsg, - "SimSetup Warning: using default value of 1/2 the smallest " - "box length for the electrostaticCutoffRadius.\n" - "I hope you have a very fast processor!\n"); + "SimSetup Warning: using default value of 15.0 angstroms" + "box length for the electrostaticCutoffRadius.\n"); painCave.isFatal = 0; simError(); - double smallest; - smallest = info[i].boxL[0]; - if (info[i].boxL[1] <= smallest) - smallest = info[i].boxL[1]; - if (info[i].boxL[2] <= smallest) - smallest = info[i].boxL[2]; - theEcr = 0.5 * smallest; + theEcr = 15.0; } else{ theEcr = globals->getECR(); @@ -848,7 +856,7 @@ void SimSetup::finalInfoCheck(void){ theEst = globals->getEST(); } - info[i].setEcr(theEcr, theEst); + info[i].setDefaultEcr(theEcr, theEst); if (!globals->haveDielectric()){ sprintf(painCave.errMsg, @@ -863,23 +871,16 @@ void SimSetup::finalInfoCheck(void){ if (usesDipoles){ if (!globals->haveECR()){ sprintf(painCave.errMsg, - "SimSetup Warning: using default value of 1/2 the smallest " - "box length for the electrostaticCutoffRadius.\n" - "I hope you have a very fast processor!\n"); - painCave.isFatal = 0; - simError(); - double smallest; - smallest = info[i].boxL[0]; - if (info[i].boxL[1] <= smallest) - smallest = info[i].boxL[1]; - if (info[i].boxL[2] <= smallest) - smallest = info[i].boxL[2]; - theEcr = 0.5 * smallest; + "SimSetup Warning: using default value of 15.0 angstroms" + "box length for the electrostaticCutoffRadius.\n"); + painCave.isFatal = 0; + simError(); + theEcr = 15.0; } else{ theEcr = globals->getECR(); } - + if (!globals->haveEST()){ sprintf(painCave.errMsg, "SimSetup Warning: using default value of 0.05 * the " @@ -892,18 +893,17 @@ void SimSetup::finalInfoCheck(void){ else{ theEst = globals->getEST(); } - - info[i].setEcr(theEcr, theEst); + + info[i].setDefaultEcr(theEcr, theEst); } } } - #ifdef IS_MPI strcpy(checkPointMsg, "post processing checks out"); MPIcheckPoint(); #endif // is_mpi } - + void SimSetup::initSystemCoords(void){ int i; @@ -931,21 +931,14 @@ void SimSetup::initSystemCoords(void){ delete fileInit; } else{ -#ifdef IS_MPI - + // no init from bass - + sprintf(painCave.errMsg, - "Cannot intialize a parallel simulation without an initial configuration file.\n"); + "Cannot intialize a simulation without an initial configuration file.\n"); painCave.isFatal = 1;; simError(); - -#else - - initFromBass(); - - -#endif + } #ifdef IS_MPI @@ -1457,6 +1450,7 @@ void SimSetup::makeIntegrator(void){ if (globals->haveTauThermostat()) myNPTf->setTauThermostat(globals->getTauThermostat()); + else{ sprintf(painCave.errMsg, "SimSetup error: If you use an NPT\n" @@ -1467,6 +1461,7 @@ void SimSetup::makeIntegrator(void){ if (globals->haveTauBarostat()) myNPTf->setTauBarostat(globals->getTauBarostat()); + else{ sprintf(painCave.errMsg, "SimSetup error: If you use an NPT\n"