--- trunk/OOPSE/libmdtools/SimSetup.cpp 2003/11/06 22:01:37 855 +++ trunk/OOPSE/libmdtools/SimSetup.cpp 2004/01/30 15:01:09 999 @@ -24,12 +24,37 @@ #define NPTxyz_ENS 4 -#define FF_DUFF 0 -#define FF_LJ 1 -#define FF_EAM 2 +#define FF_DUFF 0 +#define FF_LJ 1 +#define FF_EAM 2 +#define FF_H2O 3 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; @@ -103,6 +128,10 @@ void SimSetup::createSim(void){ sysObjectsCreation(); + // check on the post processing info + + finalInfoCheck(); + // initialize the system coordinates if ( !initSuspend ){ @@ -112,10 +141,6 @@ void SimSetup::createSim(void){ info[0].currentTime = 0.0; } - // check on the post processing info - - finalInfoCheck(); - // make the output filenames makeOutNames(); @@ -150,7 +175,6 @@ void SimSetup::makeMolecules(void){ bend_set* theBends; torsion_set* theTorsions; - //init the forceField paramters the_ff->readParams(); @@ -158,6 +182,9 @@ void SimSetup::makeMolecules(void){ // init the atoms + double phi, theta, psi; + double sux, suy, suz; + double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz; double ux, uy, uz, u, uSqr; for (k = 0; k < nInfo; k++){ @@ -194,10 +221,34 @@ void SimSetup::makeMolecules(void){ info[k].n_oriented++; molInfo.myAtoms[j] = dAtom; - ux = currentAtom->getOrntX(); - uy = currentAtom->getOrntY(); - uz = currentAtom->getOrntZ(); + // Directional Atoms have standard unit vectors which are oriented + // in space using the three Euler angles. We assume the standard + // unit vector was originally along the z axis below. + phi = currentAtom->getEulerPhi() * M_PI / 180.0; + theta = currentAtom->getEulerTheta() * M_PI / 180.0; + psi = currentAtom->getEulerPsi()* M_PI / 180.0; + + Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); + Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); + Axz = sin(theta) * sin(psi); + + Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); + Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); + Ayz = sin(theta) * cos(psi); + + Azx = sin(phi) * sin(theta); + Azy = -cos(phi) * sin(theta); + Azz = cos(theta); + + sux = 0.0; + suy = 0.0; + suz = 1.0; + + ux = (Axx * sux) + (Ayx * suy) + (Azx * suz); + uy = (Axy * sux) + (Ayy * suy) + (Azy * suz); + uz = (Axz * sux) + (Ayz * suy) + (Azz * suz); + uSqr = (ux * ux) + (uy * uy) + (uz * uz); u = sqrt(uSqr); @@ -585,6 +636,9 @@ void SimSetup::gatherInfo(void){ else if (!strcasecmp(force_field, "EAM")){ ffCase = FF_EAM; } + else if (!strcasecmp(force_field, "WATER")){ + ffCase = FF_H2O; + } else{ sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", force_field); @@ -613,8 +667,8 @@ void SimSetup::gatherInfo(void){ } else{ sprintf(painCave.errMsg, - "SimSetup Warning. Unrecognized Ensemble -> %s, " - "reverting to NVE for this simulation.\n", + "SimSetup Warning. Unrecognized Ensemble -> %s \n" + "\treverting to NVE for this simulation.\n", ensemble); painCave.isFatal = 0; simError(); @@ -646,8 +700,8 @@ void SimSetup::gatherInfo(void){ if (!the_components[i]->haveNMol()){ // we have a problem sprintf(painCave.errMsg, - "SimSetup Error. No global NMol or component NMol" - " given. Cannot calculate the number of atoms.\n"); + "SimSetup Error. No global NMol or component NMol given.\n" + "\tCannot calculate the number of atoms.\n"); painCave.isFatal = 1; simError(); } @@ -665,7 +719,48 @@ void SimSetup::gatherInfo(void){ " Please give nMol in the components.\n"); painCave.isFatal = 1; 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" + "\tThis will result in samples that are not uniformly\n" + "\tdistributed in time. If this is a problem, change\n" + "\tyour sampleTime variable.\n"); + painCave.isFatal = 0; + simError(); } + + if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ + sprintf(painCave.errMsg, + "Status time is not divisible by dt.\n" + "\tThis will result in status reports that are not uniformly\n" + "\tdistributed in time. If this is a problem, change \n" + "\tyour statusTime variable.\n"); + painCave.isFatal = 0; + simError(); + } + + if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ + sprintf(painCave.errMsg, + "Thermal time is not divisible by dt.\n" + "\tThis will result in thermalizations that are not uniformly\n" + "\tdistributed in time. If this is a problem, change \n" + "\tyour thermalTime variable.\n"); + painCave.isFatal = 0; + simError(); + } + + if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ + sprintf(painCave.errMsg, + "Reset time is not divisible by dt.\n" + "\tThis will result in integrator resets that are not uniformly\n" + "\tdistributed in time. If this is a problem, change\n" + "\tyour resetTime variable.\n"); + painCave.isFatal = 0; + simError(); + } // set the status, sample, and thermal kick times @@ -748,7 +843,7 @@ void SimSetup::gatherInfo(void){ } #ifdef IS_MPI - strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); + strcpy(checkPointMsg, "Successfully gathered all information from Bass\n"); MPIcheckPoint(); #endif // is_mpi } @@ -781,18 +876,12 @@ 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: No value was set for electrostaticCutoffRadius.\n" + "\tOOPSE will use a default value of 15.0 angstroms" + "\tfor 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(); @@ -800,8 +889,10 @@ void SimSetup::finalInfoCheck(void){ if (!globals->haveEST()){ sprintf(painCave.errMsg, - "SimSetup Warning: using default value of 0.05 * the " - "electrostaticCutoffRadius for the electrostaticSkinThickness\n"); + "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" + "\tOOPSE will use a default value of\n" + "\t0.05 * electrostaticCutoffRadius\n" + "\tfor the electrostaticSkinThickness\n"); painCave.isFatal = 0; simError(); theEst = 0.05 * theEcr; @@ -814,8 +905,9 @@ void SimSetup::finalInfoCheck(void){ if (!globals->haveDielectric()){ sprintf(painCave.errMsg, - "SimSetup Error: You are trying to use Reaction Field without" - "setting a dielectric constant!\n"); + "SimSetup Error: No Dielectric constant was set.\n" + "\tYou are trying to use Reaction Field without" + "\tsetting a dielectric constant!\n"); painCave.isFatal = 1; simError(); } @@ -825,28 +917,23 @@ 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: No value was set for electrostaticCutoffRadius.\n" + "\tOOPSE will use a default value of 15.0 angstroms" + "\tfor 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 " - "electrostaticCutoffRadius for the " - "electrostaticSkinThickness\n"); + "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" + "\tOOPSE will use a default value of\n" + "\t0.05 * electrostaticCutoffRadius\n" + "\tfor the electrostaticSkinThickness\n"); painCave.isFatal = 0; simError(); theEst = 0.05 * theEcr; @@ -854,21 +941,17 @@ void SimSetup::finalInfoCheck(void){ else{ theEst = globals->getEST(); } - + info[i].setDefaultEcr(theEcr, theEst); } } - - if( !initSuspend ) - info[i].checkCutOffs(); } - #ifdef IS_MPI strcpy(checkPointMsg, "post processing checks out"); MPIcheckPoint(); #endif // is_mpi } - + void SimSetup::initSystemCoords(void){ int i; @@ -896,21 +979,14 @@ 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 @@ -1064,6 +1140,10 @@ void SimSetup::createFF(void){ the_ff = new EAM_FF(); break; + case FF_H2O: + the_ff = new WATER(); + break; + default: sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field in case statement.\n"); @@ -1206,8 +1286,8 @@ void SimSetup::mpiMolDivide(void){ if (local_atoms != info[0].n_atoms){ sprintf(painCave.errMsg, - "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" - " localAtom (%d) are not equal.\n", + "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" + "\tlocalAtom (%d) are not equal.\n", info[0].n_atoms, local_atoms); painCave.isFatal = 1; simError(); @@ -1349,7 +1429,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use the NVT\n" - " ensemble, you must set tauThermostat.\n"); + "\tensemble, you must set tauThermostat.\n"); painCave.isFatal = 1; simError(); } @@ -1372,7 +1452,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use a constant pressure\n" - " ensemble, you must set targetPressure in the BASS file.\n"); + "\tensemble, you must set targetPressure in the BASS file.\n"); painCave.isFatal = 1; simError(); } @@ -1382,7 +1462,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use an NPT\n" - " ensemble, you must set tauThermostat.\n"); + "\tensemble, you must set tauThermostat.\n"); painCave.isFatal = 1; simError(); } @@ -1392,7 +1472,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use an NPT\n" - " ensemble, you must set tauBarostat.\n"); + "\tensemble, you must set tauBarostat.\n"); painCave.isFatal = 1; simError(); } @@ -1415,7 +1495,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use a constant pressure\n" - " ensemble, you must set targetPressure in the BASS file.\n"); + "\tensemble, you must set targetPressure in the BASS file.\n"); painCave.isFatal = 1; simError(); } @@ -1426,7 +1506,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use an NPT\n" - " ensemble, you must set tauThermostat.\n"); + "\tensemble, you must set tauThermostat.\n"); painCave.isFatal = 1; simError(); } @@ -1437,7 +1517,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use an NPT\n" - " ensemble, you must set tauBarostat.\n"); + "\tensemble, you must set tauBarostat.\n"); painCave.isFatal = 1; simError(); } @@ -1460,7 +1540,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use a constant pressure\n" - " ensemble, you must set targetPressure in the BASS file.\n"); + "\tensemble, you must set targetPressure in the BASS file.\n"); painCave.isFatal = 1; simError(); } @@ -1470,7 +1550,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use an NPT\n" - " ensemble, you must set tauThermostat.\n"); + "\tensemble, you must set tauThermostat.\n"); painCave.isFatal = 1; simError(); } @@ -1480,7 +1560,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use an NPT\n" - " ensemble, you must set tauBarostat.\n"); + "\tensemble, you must set tauBarostat.\n"); painCave.isFatal = 1; simError(); } @@ -1533,8 +1613,8 @@ void SimSetup::setupZConstraint(SimInfo& theInfo){ } else{ sprintf(painCave.errMsg, - "ZConstraint error: If you use an ZConstraint\n" - " , you must set sample time.\n"); + "ZConstraint error: If you use a ZConstraint,\n" + "\tyou must set zconsTime.\n"); painCave.isFatal = 1; simError(); } @@ -1549,8 +1629,9 @@ void SimSetup::setupZConstraint(SimInfo& theInfo){ else{ double defaultZConsTol = 0.01; sprintf(painCave.errMsg, - "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" - " , default value %f is used.\n", + "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" + "\tOOPSE will use a default value of %f.\n" + "\tTo set the tolerance, use the zconsTol variable.\n", defaultZConsTol); painCave.isFatal = 0; simError(); @@ -1568,8 +1649,9 @@ void SimSetup::setupZConstraint(SimInfo& theInfo){ } else{ sprintf(painCave.errMsg, - "ZConstraint Warning: User does not set force Subtraction policy, " - "PolicyByMass is used\n"); + "ZConstraint Warning: No force subtraction policy was set.\n" + "\tOOPSE will use PolicyByMass.\n" + "\tTo set the policy, use the zconsForcePolicy variable.\n"); painCave.isFatal = 0; simError(); zconsForcePolicy->setData("BYMASS"); @@ -1613,7 +1695,7 @@ void SimSetup::setupZConstraint(SimInfo& theInfo){ //check the uniqueness of index if(!zconsParaData->isIndexUnique()){ sprintf(painCave.errMsg, - "ZConstraint Error: molIndex is not unique\n"); + "ZConstraint Error: molIndex is not unique!\n"); painCave.isFatal = 1; simError(); }