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#include <string> |
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#include "SimSetup.hpp" |
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#include "ReadWrite.hpp" |
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#include "parse_me.h" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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int i, j, k, globalAtomIndex; |
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// gather all of the information from the Bass file |
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gatherInfo(); |
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// creation of complex system objects |
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sysObjectsCreation(); |
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// check on the post processing info |
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finalInfoCheck(); |
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// initialize the system coordinates |
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void SimSetup::initSystemCoords( void ){ |
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int i; |
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std::cerr << "Setting atom Coords\n"; |
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char* inName; |
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(info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
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for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
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#ifdef IS_MPI // is_mpi |
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if( worldRank == 0 ){ |
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#endif //is_mpi |
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fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
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inName = globals->getInitialConfig(); |
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double* tempDouble = new double[1000000]; |
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fileInit = new InitializeFromFile( inName ); |
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#ifdef IS_MPI |
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}else fileInit = new InitializeFromFile( NULL ); |
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#endif |
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int i,k; |
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// create the forceField |
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createFF(); |
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// extract componentList |
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#endif //is_mpi |
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// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
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makeSysArrays(); |
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// make and initialize the molecules (all but atomic coordinates) |
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makeMolecules(); |
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for(k=0; k<nInfo; k++){ |
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" , you must set sample time.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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// |
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nZConstraints = globals->getNzConstraints(); |
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zconStamp = globals->getZconStamp(); |
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ZConsParaItem tempParaItem; |
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|
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ZConsParaData* zconsParaData = new ZConsParaData(); |
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zconsParaData->setID(ZCONSPARADATA_ID); |
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|
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for(int i = 0; i < nZConstraints; i++){ |
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tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
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tempParaItem.zPos = zconStamp[i]->getZpos(); |
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tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
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tempParaItem.kRatio = zconStamp[i]->getKratio(); |
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zconsParaData->addItem(tempParaItem); |
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} |
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//sort the parameters by index of molecules |
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zconsParaData->sortByIndex(); |
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//push data into siminfo, therefore, we can retrieve later |
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theInfo.addProperty(zconsParaData); |
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//push zconsTol into siminfo, if user does not specify |
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//value for zconsTol, a default value will be used |
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DoubleData* zconsTol = new DoubleData(); |
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zconsTol->setData(globals->getZconsTol()); |
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} |
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else{ |
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double defaultZConsTol = 1E-6; |
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double defaultZConsTol = 0.01; |
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sprintf( painCave.errMsg, |
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"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
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" , default value %f is used.\n", defaultZConsTol); |
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zconsTol->setData(defaultZConsTol); |
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} |
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theInfo.addProperty(zconsTol); |
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|
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//set Force Substraction Policy |
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StringData* zconsForcePolicy = new StringData(); |
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zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
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|
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if(globals->haveZconsForcePolicy()){ |
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zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
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} |
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else{ |
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sprintf( painCave.errMsg, |
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"ZConstraint Warning: User does not set force substraction policy, " |
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"average force substraction policy is used\n"); |
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painCave.isFatal = 0; |
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simError(); |
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zconsForcePolicy->setData("BYNUMBER"); |
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} |
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theInfo.addProperty(zconsForcePolicy); |
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//Determine the name of ouput file and add it into SimInfo's property list |
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//Be careful, do not use inFileName, since it is a pointer which |
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//point to a string at master node, and slave nodes do not contain that string |
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zconsFilename->setID(ZCONSFILENAME_ID); |
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zconsFilename->setData(zconsOutput); |
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theInfo.addProperty(zconsFilename); |
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theInfo.addProperty(zconsFilename); |
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|
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//setup index, pos and other parameters of z-constraint molecules |
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nZConstraints = globals->getNzConstraints(); |
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theInfo.nZconstraints = nZConstraints; |
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|
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zconStamp = globals->getZconStamp(); |
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ZConsParaItem tempParaItem; |
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|
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ZConsParaData* zconsParaData = new ZConsParaData(); |
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zconsParaData->setID(ZCONSPARADATA_ID); |
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|
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for(int i = 0; i < nZConstraints; i++){ |
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tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
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tempParaItem.zPos = zconStamp[i]->getZpos(); |
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tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
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tempParaItem.kRatio = zconStamp[i]->getKratio(); |
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zconsParaData->addItem(tempParaItem); |
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} |
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//sort the parameters by index of molecules |
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zconsParaData->sortByIndex(); |
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|
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//push data into siminfo, therefore, we can retrieve later |
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theInfo.addProperty(zconsParaData); |
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} |