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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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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++){ |
