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#include <algorithm> |
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#include <cstdlib> |
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#include <iostream> |
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#include <cmath> |
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#include <string> |
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#include "SimSetup.hpp" |
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#include "parse_me.h" |
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// some defines for ensemble and Forcefield cases |
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|
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#define NVE_ENS 0 |
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#define NVT_ENS 1 |
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#define NPTi_ENS 2 |
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#define NPTf_ENS 3 |
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#define NPTim_ENS 4 |
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#define NPTfm_ENS 5 |
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#define NVE_ENS 0 |
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#define NVT_ENS 1 |
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#define NPTi_ENS 2 |
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#define NPTf_ENS 3 |
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#define NPTim_ENS 4 |
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#define NPTfm_ENS 5 |
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#define NVEZCONS_ENS 6 |
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#define NVTZCONS_ENS 7 |
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#define NPTiZCONS_ENS 8 |
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#define NPTfZCONS_ENS 9 |
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#define NPTimZCONS_ENS 10 |
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#define NPTfmZCONS_ENS 11 |
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|
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|
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#define FF_DUFF 0 |
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#define FF_LJ 1 |
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#define FF_EAM 2 |
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|
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using namespace std; |
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|
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SimSetup::SimSetup(){ |
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|
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isInfoArray = 0; |
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nInfo = 1; |
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|
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stamps = new MakeStamps(); |
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globals = new Globals(); |
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|
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|
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "SimSetup creation successful" ); |
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MPIcheckPoint(); |
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delete globals; |
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} |
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|
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void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
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info = the_info; |
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nInfo = theNinfo; |
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isInfoArray = 1; |
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} |
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|
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|
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void SimSetup::parseFile( char* fileName ){ |
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|
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#ifdef IS_MPI |
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|
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void SimSetup::createSim( void ){ |
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|
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MakeStamps *the_stamps; |
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Globals* the_globals; |
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int i, j, k, globalAtomIndex; |
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|
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// gather all of the information from the Bass file |
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|
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sysObjectsCreation(); |
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|
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|
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|
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// initialize the arrays |
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|
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|
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|
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makeMolecules(); |
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info->identArray = new int[info->n_atoms]; |
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for(i=0; i<info->n_atoms; i++){ |
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info->identArray[i] = the_atoms[i]->getIdent(); |
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} |
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|
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|
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// check on the post processing info |
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|
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finalInfoCheck(); |
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|
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|
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|
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|
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// initialize the system coordinates |
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|
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initSystemCoords(); |
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|
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makeOutNames(); |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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// make the integrator |
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|
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makeIntegrator(); |
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|
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NVT* myNVT = NULL; |
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NPTi* myNPTi = NULL; |
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NPTf* myNPTf = NULL; |
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NPTim* myNPTim = NULL; |
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NPTfm* myNPTfm = NULL; |
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|
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switch( ensembleCase ){ |
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|
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case NVE_ENS: |
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new NVE( info, the_ff ); |
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break; |
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|
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case NVT_ENS: |
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myNVT = new NVT( info, the_ff ); |
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myNVT->setTargetTemp(the_globals->getTargetTemp()); |
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|
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if (the_globals->haveTauThermostat()) |
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myNVT->setTauThermostat(the_globals->getTauThermostat()); |
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|
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else { |
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sprintf( painCave.errMsg, |
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"SimSetup error: If you use the NVT\n" |
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" ensemble, you must set tauThermostat.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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break; |
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|
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case NPTi_ENS: |
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myNPTi = new NPTi( info, the_ff ); |
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myNPTi->setTargetTemp( the_globals->getTargetTemp() ); |
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|
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if (the_globals->haveTargetPressure()) |
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myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
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else { |
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sprintf( painCave.errMsg, |
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"SimSetup error: If you use a constant pressure\n" |
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" ensemble, you must set targetPressure in the BASS file.\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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if( the_globals->haveTauThermostat() ) |
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myNPTi->setTauThermostat( the_globals->getTauThermostat() ); |
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else{ |
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sprintf( painCave.errMsg, |
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"SimSetup error: If you use an NPT\n" |
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" ensemble, you must set tauThermostat.\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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if( the_globals->haveTauBarostat() ) |
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myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
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else{ |
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sprintf( painCave.errMsg, |
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"SimSetup error: If you use an NPT\n" |
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" ensemble, you must set tauBarostat.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
194 |
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break; |
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|
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case NPTf_ENS: |
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myNPTf = new NPTf( info, the_ff ); |
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myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
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|
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if (the_globals->haveTargetPressure()) |
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myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
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else { |
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sprintf( painCave.errMsg, |
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"SimSetup error: If you use a constant pressure\n" |
205 |
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" ensemble, you must set targetPressure in the BASS file.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
209 |
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|
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if( the_globals->haveTauThermostat() ) |
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myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
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else{ |
213 |
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sprintf( painCave.errMsg, |
214 |
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"SimSetup error: If you use an NPT\n" |
215 |
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" ensemble, you must set tauThermostat.\n"); |
216 |
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painCave.isFatal = 1; |
217 |
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simError(); |
218 |
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} |
219 |
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|
220 |
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if( the_globals->haveTauBarostat() ) |
221 |
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myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
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else{ |
223 |
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sprintf( painCave.errMsg, |
224 |
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"SimSetup error: If you use an NPT\n" |
225 |
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" ensemble, you must set tauBarostat.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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break; |
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|
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case NPTim_ENS: |
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myNPTim = new NPTim( info, the_ff ); |
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myNPTim->setTargetTemp( the_globals->getTargetTemp()); |
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|
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if (the_globals->haveTargetPressure()) |
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myNPTim->setTargetPressure(the_globals->getTargetPressure()); |
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else { |
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sprintf( painCave.errMsg, |
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"SimSetup error: If you use a constant pressure\n" |
240 |
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" ensemble, you must set targetPressure in the BASS file.\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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if( the_globals->haveTauThermostat() ) |
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myNPTim->setTauThermostat( the_globals->getTauThermostat() ); |
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else{ |
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sprintf( painCave.errMsg, |
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"SimSetup error: If you use an NPT\n" |
250 |
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" ensemble, you must set tauThermostat.\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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if( the_globals->haveTauBarostat() ) |
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myNPTim->setTauBarostat( the_globals->getTauBarostat() ); |
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else{ |
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sprintf( painCave.errMsg, |
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"SimSetup error: If you use an NPT\n" |
260 |
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" ensemble, you must set tauBarostat.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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break; |
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|
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case NPTfm_ENS: |
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myNPTfm = new NPTfm( info, the_ff ); |
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myNPTfm->setTargetTemp( the_globals->getTargetTemp()); |
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|
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if (the_globals->haveTargetPressure()) |
271 |
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myNPTfm->setTargetPressure(the_globals->getTargetPressure()); |
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else { |
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sprintf( painCave.errMsg, |
274 |
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"SimSetup error: If you use a constant pressure\n" |
275 |
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" ensemble, you must set targetPressure in the BASS file.\n"); |
276 |
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painCave.isFatal = 1; |
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simError(); |
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} |
279 |
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|
280 |
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if( the_globals->haveTauThermostat() ) |
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myNPTfm->setTauThermostat( the_globals->getTauThermostat() ); |
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else{ |
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sprintf( painCave.errMsg, |
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"SimSetup error: If you use an NPT\n" |
285 |
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" ensemble, you must set tauThermostat.\n"); |
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painCave.isFatal = 1; |
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simError(); |
288 |
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} |
289 |
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|
290 |
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if( the_globals->haveTauBarostat() ) |
291 |
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myNPTfm->setTauBarostat( the_globals->getTauBarostat() ); |
292 |
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else{ |
293 |
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sprintf( painCave.errMsg, |
294 |
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"SimSetup error: If you use an NPT\n" |
295 |
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" ensemble, you must set tauBarostat.\n"); |
296 |
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painCave.isFatal = 1; |
297 |
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simError(); |
298 |
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} |
299 |
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break; |
300 |
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|
301 |
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default: |
302 |
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sprintf( painCave.errMsg, |
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"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
304 |
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painCave.isFatal = 1; |
305 |
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simError(); |
306 |
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} |
307 |
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|
308 |
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|
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#ifdef IS_MPI |
130 |
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mpiSim->mpiRefresh(); |
131 |
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#endif |
132 |
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|
133 |
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// initialize the Fortran |
134 |
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|
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+ |
initFortran(); |
136 |
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|
316 |
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info->refreshSim(); |
317 |
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|
318 |
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if( !strcmp( info->mixingRule, "standard") ){ |
319 |
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the_ff->initForceField( LB_MIXING_RULE ); |
320 |
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} |
321 |
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else if( !strcmp( info->mixingRule, "explicit") ){ |
322 |
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the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
323 |
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} |
324 |
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else{ |
325 |
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sprintf( painCave.errMsg, |
326 |
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"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
327 |
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info->mixingRule ); |
328 |
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painCave.isFatal = 1; |
329 |
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simError(); |
330 |
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} |
137 |
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|
138 |
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|
333 |
– |
#ifdef IS_MPI |
334 |
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strcpy( checkPointMsg, |
335 |
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"Successfully intialized the mixingRule for Fortran." ); |
336 |
– |
MPIcheckPoint(); |
337 |
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#endif // is_mpi |
139 |
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} |
140 |
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|
141 |
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|
142 |
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void SimSetup::makeMolecules( void ){ |
143 |
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|
144 |
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int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
145 |
< |
molInit info; |
145 |
> |
molInit molInfo; |
146 |
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DirectionalAtom* dAtom; |
147 |
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LinkedAssign* extras; |
148 |
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LinkedAssign* current_extra; |
171 |
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|
172 |
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stampID = the_molecules[i].getStampID(); |
173 |
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|
174 |
< |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
175 |
< |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
176 |
< |
info.nBends = comp_stamps[stampID]->getNBends(); |
177 |
< |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
178 |
< |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
174 |
> |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
175 |
> |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
176 |
> |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
177 |
> |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
178 |
> |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
179 |
|
|
180 |
< |
info.myAtoms = &the_atoms[atomOffset]; |
181 |
< |
info.myExcludes = &the_excludes[excludeOffset]; |
182 |
< |
info.myBonds = new Bond*[info.nBonds]; |
183 |
< |
info.myBends = new Bend*[info.nBends]; |
184 |
< |
info.myTorsions = new Torsion*[info.nTorsions]; |
180 |
> |
molInfo.myAtoms = &the_atoms[atomOffset]; |
181 |
> |
molInfo.myExcludes = &the_excludes[excludeOffset]; |
182 |
> |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
183 |
> |
molInfo.myBends = new Bend*[molInfo.nBends]; |
184 |
> |
molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
185 |
|
|
186 |
< |
theBonds = new bond_pair[info.nBonds]; |
187 |
< |
theBends = new bend_set[info.nBends]; |
188 |
< |
theTorsions = new torsion_set[info.nTorsions]; |
186 |
> |
theBonds = new bond_pair[molInfo.nBonds]; |
187 |
> |
theBends = new bend_set[molInfo.nBends]; |
188 |
> |
theTorsions = new torsion_set[molInfo.nTorsions]; |
189 |
|
|
190 |
|
// make the Atoms |
191 |
|
|
192 |
< |
for(j=0; j<info.nAtoms; j++){ |
192 |
> |
for(j=0; j<molInfo.nAtoms; j++){ |
193 |
|
|
194 |
|
currentAtom = comp_stamps[stampID]->getAtom( j ); |
195 |
|
if( currentAtom->haveOrientation() ){ |
196 |
|
|
197 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
198 |
|
info->n_oriented++; |
199 |
< |
info.myAtoms[j] = dAtom; |
199 |
> |
molInfo.myAtoms[j] = dAtom; |
200 |
|
|
201 |
|
ux = currentAtom->getOrntX(); |
202 |
|
uy = currentAtom->getOrntY(); |
214 |
|
dAtom->setSUz( uz ); |
215 |
|
} |
216 |
|
else{ |
217 |
< |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
217 |
> |
molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
218 |
|
} |
219 |
< |
info.myAtoms[j]->setType( currentAtom->getType() ); |
219 |
> |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
220 |
|
|
221 |
|
#ifdef IS_MPI |
222 |
|
|
223 |
< |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
223 |
> |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
224 |
|
|
225 |
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#endif // is_mpi |
226 |
|
} |
227 |
|
|
228 |
|
// make the bonds |
229 |
< |
for(j=0; j<info.nBonds; j++){ |
229 |
> |
for(j=0; j<molInfo.nBonds; j++){ |
230 |
|
|
231 |
|
currentBond = comp_stamps[stampID]->getBond( j ); |
232 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
253 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
254 |
|
#endif //is_mpi |
255 |
|
} |
256 |
< |
excludeOffset += info.nBonds; |
256 |
> |
excludeOffset += molInfo.nBonds; |
257 |
|
|
258 |
|
//make the bends |
259 |
< |
for(j=0; j<info.nBends; j++){ |
259 |
> |
for(j=0; j<molInfo.nBends; j++){ |
260 |
|
|
261 |
|
currentBend = comp_stamps[stampID]->getBend( j ); |
262 |
|
theBends[j].a = currentBend->getA() + atomOffset; |
339 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
340 |
|
#endif //is_mpi |
341 |
|
} |
342 |
< |
excludeOffset += info.nBends; |
342 |
> |
excludeOffset += molInfo.nBends; |
343 |
|
|
344 |
< |
for(j=0; j<info.nTorsions; j++){ |
344 |
> |
for(j=0; j<molInfo.nTorsions; j++){ |
345 |
|
|
346 |
|
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
347 |
|
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
369 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
370 |
|
#endif //is_mpi |
371 |
|
} |
372 |
< |
excludeOffset += info.nTorsions; |
372 |
> |
excludeOffset += molInfo.nTorsions; |
373 |
|
|
374 |
|
|
375 |
|
// send the arrays off to the forceField for init. |
376 |
|
|
377 |
< |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
378 |
< |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
379 |
< |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
380 |
< |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
377 |
> |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
378 |
> |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
379 |
> |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
380 |
> |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
381 |
|
|
382 |
|
|
383 |
< |
the_molecules[i].initialize( info ); |
383 |
> |
the_molecules[i].initialize( molInfo ); |
384 |
|
|
385 |
|
|
386 |
< |
atomOffset += info.nAtoms; |
386 |
> |
atomOffset += molInfo.nAtoms; |
387 |
|
delete[] theBonds; |
388 |
|
delete[] theBends; |
389 |
|
delete[] theTorsions; |
419 |
|
have_extra =1; |
420 |
|
|
421 |
|
n_cells = (int)temp3 - 1; |
422 |
< |
cellx = info->boxLx / temp3; |
423 |
< |
celly = info->boxLy / temp3; |
424 |
< |
cellz = info->boxLz / temp3; |
422 |
> |
cellx = info->boxL[0] / temp3; |
423 |
> |
celly = info->boxL[1] / temp3; |
424 |
> |
cellz = info->boxL[2] / temp3; |
425 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
426 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
427 |
|
n_per_extra = (int)ceil( temp1 ); |
436 |
|
} |
437 |
|
else{ |
438 |
|
n_cells = (int)temp3; |
439 |
< |
cellx = info->boxLx / temp3; |
440 |
< |
celly = info->boxLy / temp3; |
441 |
< |
cellz = info->boxLz / temp3; |
439 |
> |
cellx = info->boxL[0] / temp3; |
440 |
> |
celly = info->boxL[1] / temp3; |
441 |
> |
cellz = info->boxL[2] / temp3; |
442 |
|
} |
443 |
|
|
444 |
|
current_mol = 0; |
585 |
|
|
586 |
|
|
587 |
|
void SimSetup::gatherInfo( void ){ |
588 |
+ |
int i,j,k; |
589 |
|
|
590 |
|
ensembleCase = -1; |
591 |
|
ffCase = -1; |
592 |
|
|
593 |
|
// get the stamps and globals; |
594 |
< |
the_stamps = stamps; |
595 |
< |
the_globals = globals; |
594 |
> |
stamps = stamps; |
595 |
> |
globals = globals; |
596 |
|
|
597 |
|
// set the easy ones first |
598 |
< |
info->target_temp = the_globals->getTargetTemp(); |
599 |
< |
info->dt = the_globals->getDt(); |
600 |
< |
info->run_time = the_globals->getRunTime(); |
601 |
< |
n_components = the_globals->getNComponents(); |
598 |
> |
info->target_temp = globals->getTargetTemp(); |
599 |
> |
info->dt = globals->getDt(); |
600 |
> |
info->run_time = globals->getRunTime(); |
601 |
> |
n_components = globals->getNComponents(); |
602 |
|
|
603 |
|
|
604 |
|
// get the forceField |
605 |
|
|
606 |
< |
strcpy( force_field, the_globals->getForceField() ); |
606 |
> |
strcpy( force_field, globals->getForceField() ); |
607 |
|
|
608 |
|
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
609 |
|
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
610 |
+ |
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
611 |
|
else{ |
612 |
|
sprintf( painCave.errMsg, |
613 |
|
"SimSetup Error. Unrecognized force field -> %s\n", |
618 |
|
|
619 |
|
// get the ensemble |
620 |
|
|
621 |
< |
strcpy( ensemble, the_globals->getEnsemble() ); |
621 |
> |
strcpy( ensemble, globals->getEnsemble() ); |
622 |
|
|
623 |
|
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
624 |
|
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
627 |
|
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
628 |
|
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
629 |
|
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
630 |
+ |
|
631 |
+ |
else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
632 |
+ |
else if( !strcasecmp( ensemble, "NVTZCONS")) ensembleCase = NVTZCONS_ENS; |
633 |
+ |
else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPT")) |
634 |
+ |
ensembleCase = NPTiZCONS_ENS; |
635 |
+ |
else if( !strcasecmp( ensemble, "NPTfCONS")) ensembleCase = NPTfZCONS_ENS; |
636 |
+ |
else if( !strcasecmp( ensemble, "NPTimZCONS")) ensembleCase = NPTimZCONS_ENS; |
637 |
+ |
else if( !strcasecmp( ensemble, "NPTfmCONS")) ensembleCase = NPTfmZCONS_ENS; |
638 |
+ |
|
639 |
|
else{ |
640 |
|
sprintf( painCave.errMsg, |
641 |
|
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
650 |
|
|
651 |
|
// get the mixing rule |
652 |
|
|
653 |
< |
strcpy( info->mixingRule, the_globals->getMixingRule() ); |
654 |
< |
info->usePBC = the_globals->getPBC(); |
653 |
> |
strcpy( info->mixingRule, globals->getMixingRule() ); |
654 |
> |
info->usePBC = globals->getPBC(); |
655 |
|
|
656 |
|
|
657 |
|
// get the components and calculate the tot_nMol and indvidual n_mol |
658 |
|
|
659 |
< |
the_components = the_globals->getComponents(); |
659 |
> |
the_components = globals->getComponents(); |
660 |
|
components_nmol = new int[n_components]; |
661 |
|
|
662 |
|
|
663 |
< |
if( !the_globals->haveNMol() ){ |
663 |
> |
if( !globals->haveNMol() ){ |
664 |
|
// we don't have the total number of molecules, so we assume it is |
665 |
|
// given in each component |
666 |
|
|
693 |
|
|
694 |
|
// set the status, sample, and thermal kick times |
695 |
|
|
696 |
< |
if( the_globals->haveSampleTime() ){ |
697 |
< |
info->sampleTime = the_globals->getSampleTime(); |
696 |
> |
if( globals->haveSampleTime() ){ |
697 |
> |
info->sampleTime = globals->getSampleTime(); |
698 |
|
info->statusTime = info->sampleTime; |
699 |
|
info->thermalTime = info->sampleTime; |
700 |
|
} |
701 |
|
else{ |
702 |
< |
info->sampleTime = the_globals->getRunTime(); |
702 |
> |
info->sampleTime = globals->getRunTime(); |
703 |
|
info->statusTime = info->sampleTime; |
704 |
|
info->thermalTime = info->sampleTime; |
705 |
|
} |
706 |
|
|
707 |
< |
if( the_globals->haveStatusTime() ){ |
708 |
< |
info->statusTime = the_globals->getStatusTime(); |
707 |
> |
if( globals->haveStatusTime() ){ |
708 |
> |
info->statusTime = globals->getStatusTime(); |
709 |
|
} |
710 |
|
|
711 |
< |
if( the_globals->haveThermalTime() ){ |
712 |
< |
info->thermalTime = the_globals->getThermalTime(); |
711 |
> |
if( globals->haveThermalTime() ){ |
712 |
> |
info->thermalTime = globals->getThermalTime(); |
713 |
|
} |
714 |
|
|
715 |
|
// check for the temperature set flag |
716 |
|
|
717 |
< |
if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet(); |
717 |
> |
if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
718 |
|
|
719 |
|
// get some of the tricky things that may still be in the globals |
720 |
|
|
721 |
|
double boxVector[3]; |
722 |
< |
if( the_globals->haveBox() ){ |
723 |
< |
boxVector[0] = the_globals->getBox(); |
724 |
< |
boxVector[1] = the_globals->getBox(); |
725 |
< |
boxVector[2] = the_globals->getBox(); |
722 |
> |
if( globals->haveBox() ){ |
723 |
> |
boxVector[0] = globals->getBox(); |
724 |
> |
boxVector[1] = globals->getBox(); |
725 |
> |
boxVector[2] = globals->getBox(); |
726 |
|
|
727 |
|
info->setBox( boxVector ); |
728 |
|
} |
729 |
< |
else if( the_globals->haveDensity() ){ |
729 |
> |
else if( globals->haveDensity() ){ |
730 |
|
|
731 |
|
double vol; |
732 |
< |
vol = (double)tot_nmol / the_globals->getDensity(); |
732 |
> |
vol = (double)tot_nmol / globals->getDensity(); |
733 |
|
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
734 |
|
boxVector[1] = boxVector[0]; |
735 |
|
boxVector[2] = boxVector[0]; |
737 |
|
info->setBox( boxVector ); |
738 |
|
} |
739 |
|
else{ |
740 |
< |
if( !the_globals->haveBoxX() ){ |
740 |
> |
if( !globals->haveBoxX() ){ |
741 |
|
sprintf( painCave.errMsg, |
742 |
|
"SimSetup error, no periodic BoxX size given.\n" ); |
743 |
|
painCave.isFatal = 1; |
744 |
|
simError(); |
745 |
|
} |
746 |
< |
boxVector[0] = the_globals->getBoxX(); |
746 |
> |
boxVector[0] = globals->getBoxX(); |
747 |
|
|
748 |
< |
if( !the_globals->haveBoxY() ){ |
748 |
> |
if( !globals->haveBoxY() ){ |
749 |
|
sprintf( painCave.errMsg, |
750 |
|
"SimSetup error, no periodic BoxY size given.\n" ); |
751 |
|
painCave.isFatal = 1; |
752 |
|
simError(); |
753 |
|
} |
754 |
< |
boxVector[1] = the_globals->getBoxY(); |
754 |
> |
boxVector[1] = globals->getBoxY(); |
755 |
|
|
756 |
< |
if( !the_globals->haveBoxZ() ){ |
756 |
> |
if( !globals->haveBoxZ() ){ |
757 |
|
sprintf( painCave.errMsg, |
758 |
|
"SimSetup error, no periodic BoxZ size given.\n" ); |
759 |
|
painCave.isFatal = 1; |
760 |
|
simError(); |
761 |
|
} |
762 |
< |
boxVector[2] = the_globals->getBoxZ(); |
762 |
> |
boxVector[2] = globals->getBoxZ(); |
763 |
|
|
764 |
|
info->setBox( boxVector ); |
765 |
|
} |
789 |
|
} |
790 |
|
|
791 |
|
#ifdef IS_MPI |
792 |
< |
int myUse = usesDipoles |
793 |
< |
MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
792 |
> |
int myUse = usesDipoles; |
793 |
> |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
794 |
|
#endif //is_mpi |
795 |
|
|
796 |
+ |
double theEcr, theEst; |
797 |
|
|
798 |
< |
if (the_globals->getUseRF() ) { |
798 |
> |
if (globals->getUseRF() ) { |
799 |
|
info->useReactionField = 1; |
800 |
|
|
801 |
< |
if( !the_globals->haveECR() ){ |
801 |
> |
if( !globals->haveECR() ){ |
802 |
|
sprintf( painCave.errMsg, |
803 |
|
"SimSetup Warning: using default value of 1/2 the smallest " |
804 |
|
"box length for the electrostaticCutoffRadius.\n" |
806 |
|
painCave.isFatal = 0; |
807 |
|
simError(); |
808 |
|
double smallest; |
809 |
< |
smallest = info->boxLx; |
810 |
< |
if (info->boxLy <= smallest) smallest = info->boxLy; |
811 |
< |
if (info->boxLz <= smallest) smallest = info->boxLz; |
812 |
< |
info->ecr = 0.5 * smallest; |
809 |
> |
smallest = info->boxL[0]; |
810 |
> |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
811 |
> |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
812 |
> |
theEcr = 0.5 * smallest; |
813 |
|
} else { |
814 |
< |
info->ecr = the_globals->getECR(); |
814 |
> |
theEcr = globals->getECR(); |
815 |
|
} |
816 |
|
|
817 |
< |
if( !the_globals->haveEST() ){ |
817 |
> |
if( !globals->haveEST() ){ |
818 |
|
sprintf( painCave.errMsg, |
819 |
|
"SimSetup Warning: using default value of 0.05 * the " |
820 |
|
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
821 |
|
); |
822 |
|
painCave.isFatal = 0; |
823 |
|
simError(); |
824 |
< |
info->est = 0.05 * info->ecr; |
824 |
> |
theEst = 0.05 * theEcr; |
825 |
|
} else { |
826 |
< |
info->est = the_globals->getEST(); |
826 |
> |
theEst= globals->getEST(); |
827 |
|
} |
828 |
+ |
|
829 |
+ |
info->setEcr( theEcr, theEst ); |
830 |
|
|
831 |
< |
if(!the_globals->haveDielectric() ){ |
831 |
> |
if(!globals->haveDielectric() ){ |
832 |
|
sprintf( painCave.errMsg, |
833 |
|
"SimSetup Error: You are trying to use Reaction Field without" |
834 |
|
"setting a dielectric constant!\n" |
836 |
|
painCave.isFatal = 1; |
837 |
|
simError(); |
838 |
|
} |
839 |
< |
info->dielectric = the_globals->getDielectric(); |
839 |
> |
info->dielectric = globals->getDielectric(); |
840 |
|
} |
841 |
|
else { |
842 |
|
if (usesDipoles) { |
843 |
|
|
844 |
< |
if( !the_globals->haveECR() ){ |
845 |
< |
sprintf( painCave.errMsg, |
846 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
847 |
< |
"box length for the electrostaticCutoffRadius.\n" |
848 |
< |
"I hope you have a very fast processor!\n"); |
849 |
< |
painCave.isFatal = 0; |
850 |
< |
simError(); |
851 |
< |
double smallest; |
852 |
< |
smallest = info->boxLx; |
853 |
< |
if (info->boxLy <= smallest) smallest = info->boxLy; |
854 |
< |
if (info->boxLz <= smallest) smallest = info->boxLz; |
855 |
< |
info->ecr = 0.5 * smallest; |
844 |
> |
if( !globals->haveECR() ){ |
845 |
> |
sprintf( painCave.errMsg, |
846 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
847 |
> |
"box length for the electrostaticCutoffRadius.\n" |
848 |
> |
"I hope you have a very fast processor!\n"); |
849 |
> |
painCave.isFatal = 0; |
850 |
> |
simError(); |
851 |
> |
double smallest; |
852 |
> |
smallest = info->boxL[0]; |
853 |
> |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
854 |
> |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
855 |
> |
theEcr = 0.5 * smallest; |
856 |
|
} else { |
857 |
< |
info->ecr = the_globals->getECR(); |
857 |
> |
theEcr = globals->getECR(); |
858 |
|
} |
859 |
|
|
860 |
< |
if( !the_globals->haveEST() ){ |
861 |
< |
sprintf( painCave.errMsg, |
862 |
< |
"SimSetup Warning: using default value of 5%% of the " |
863 |
< |
"electrostaticCutoffRadius for the " |
864 |
< |
"electrostaticSkinThickness\n" |
865 |
< |
); |
866 |
< |
painCave.isFatal = 0; |
867 |
< |
simError(); |
868 |
< |
info->est = 0.05 * info->ecr; |
860 |
> |
if( !globals->haveEST() ){ |
861 |
> |
sprintf( painCave.errMsg, |
862 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
863 |
> |
"electrostaticCutoffRadius for the " |
864 |
> |
"electrostaticSkinThickness\n" |
865 |
> |
); |
866 |
> |
painCave.isFatal = 0; |
867 |
> |
simError(); |
868 |
> |
theEst = 0.05 * theEcr; |
869 |
|
} else { |
870 |
< |
info->est = the_globals->getEST(); |
870 |
> |
theEst= globals->getEST(); |
871 |
|
} |
872 |
+ |
|
873 |
+ |
info->setEcr( theEcr, theEst ); |
874 |
|
} |
875 |
|
} |
876 |
|
|
883 |
|
|
884 |
|
void SimSetup::initSystemCoords( void ){ |
885 |
|
|
886 |
< |
if( the_globals->haveInitialConfig() ){ |
886 |
> |
if( globals->haveInitialConfig() ){ |
887 |
|
|
888 |
|
InitializeFromFile* fileInit; |
889 |
|
#ifdef IS_MPI // is_mpi |
890 |
|
if( worldRank == 0 ){ |
891 |
|
#endif //is_mpi |
892 |
< |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
892 |
> |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
893 |
|
#ifdef IS_MPI |
894 |
|
}else fileInit = new InitializeFromFile( NULL ); |
895 |
|
#endif |
896 |
< |
fileInit->read_xyz( info ); // default velocities on |
896 |
> |
fileInit->readInit( info ); // default velocities on |
897 |
|
|
898 |
|
delete fileInit; |
899 |
|
} |
930 |
|
if( worldRank == 0 ){ |
931 |
|
#endif // is_mpi |
932 |
|
|
933 |
< |
if( the_globals->haveFinalConfig() ){ |
934 |
< |
strcpy( info->finalName, the_globals->getFinalConfig() ); |
933 |
> |
if( globals->haveFinalConfig() ){ |
934 |
> |
strcpy( info->finalName, globals->getFinalConfig() ); |
935 |
|
} |
936 |
|
else{ |
937 |
|
strcpy( info->finalName, inFileName ); |
1014 |
|
|
1015 |
|
void SimSetup::sysObjectsCreation( void ){ |
1016 |
|
|
1017 |
+ |
int i; |
1018 |
+ |
|
1019 |
|
// create the forceField |
1020 |
|
|
1021 |
|
createFF(); |
1038 |
|
|
1039 |
|
makeSysArrays(); |
1040 |
|
|
1041 |
+ |
// make and initialize the molecules (all but atomic coordinates) |
1042 |
+ |
|
1043 |
+ |
makeMolecules(); |
1044 |
+ |
info->identArray = new int[info->n_atoms]; |
1045 |
+ |
for(i=0; i<info->n_atoms; i++){ |
1046 |
+ |
info->identArray[i] = the_atoms[i]->getIdent(); |
1047 |
+ |
} |
1048 |
|
|
1049 |
|
|
1050 |
|
|
1063 |
|
the_ff = new LJFF(); |
1064 |
|
break; |
1065 |
|
|
1066 |
+ |
case FF_EAM: |
1067 |
+ |
the_ff = new EAM_FF(); |
1068 |
+ |
break; |
1069 |
+ |
|
1070 |
|
default: |
1071 |
|
sprintf( painCave.errMsg, |
1072 |
|
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1083 |
|
|
1084 |
|
|
1085 |
|
void SimSetup::compList( void ){ |
1086 |
+ |
|
1087 |
+ |
int i; |
1088 |
|
|
1089 |
|
comp_stamps = new MoleculeStamp*[n_components]; |
1090 |
|
|
1111 |
|
|
1112 |
|
// extract the component from the list; |
1113 |
|
|
1114 |
< |
currentStamp = the_stamps->extractMolStamp( id ); |
1114 |
> |
currentStamp = stamps->extractMolStamp( id ); |
1115 |
|
if( currentStamp == NULL ){ |
1116 |
|
sprintf( painCave.errMsg, |
1117 |
|
"SimSetup error: Component \"%s\" was not found in the " |
1135 |
|
} |
1136 |
|
|
1137 |
|
void SimSetup::calcSysValues( void ){ |
1138 |
+ |
int i, j, k; |
1139 |
|
|
1140 |
+ |
|
1141 |
|
tot_atoms = 0; |
1142 |
|
tot_bonds = 0; |
1143 |
|
tot_bends = 0; |
1167 |
|
|
1168 |
|
void SimSetup::mpiMolDivide( void ){ |
1169 |
|
|
1170 |
+ |
int i, j, k; |
1171 |
|
int localMol, allMol; |
1172 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1173 |
|
|
1237 |
|
|
1238 |
|
|
1239 |
|
void SimSetup::makeSysArrays( void ){ |
1240 |
+ |
int i, j, k; |
1241 |
|
|
1242 |
+ |
|
1243 |
|
// create the atom and short range interaction arrays |
1244 |
|
|
1245 |
|
Atom::createArrays(info->n_atoms); |
1313 |
|
the_ff->setSimInfo( info ); |
1314 |
|
|
1315 |
|
} |
1316 |
+ |
|
1317 |
+ |
void SimSetup::makeIntegrator( void ){ |
1318 |
+ |
|
1319 |
+ |
NVT<RealIntegrator>* myNVT = NULL; |
1320 |
+ |
NPTi<RealIntegrator>* myNPTi = NULL; |
1321 |
+ |
NPTf<RealIntegrator>* myNPTf = NULL; |
1322 |
+ |
NPTim<RealIntegrator>* myNPTim = NULL; |
1323 |
+ |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1324 |
+ |
ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
1325 |
+ |
ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL; |
1326 |
+ |
ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL; |
1327 |
+ |
ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL; |
1328 |
+ |
ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL; |
1329 |
+ |
ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL; |
1330 |
+ |
|
1331 |
+ |
cerr << "setting integrator" <<endl; |
1332 |
+ |
|
1333 |
+ |
switch( ensembleCase ){ |
1334 |
+ |
|
1335 |
+ |
case NVE_ENS: |
1336 |
+ |
new NVE<RealIntegrator>( info, the_ff ); |
1337 |
+ |
break; |
1338 |
+ |
|
1339 |
+ |
case NVT_ENS: |
1340 |
+ |
myNVT = new NVT<RealIntegrator>( info, the_ff ); |
1341 |
+ |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1342 |
+ |
|
1343 |
+ |
if (globals->haveTauThermostat()) |
1344 |
+ |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1345 |
+ |
|
1346 |
+ |
else { |
1347 |
+ |
sprintf( painCave.errMsg, |
1348 |
+ |
"SimSetup error: If you use the NVT\n" |
1349 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1350 |
+ |
painCave.isFatal = 1; |
1351 |
+ |
simError(); |
1352 |
+ |
} |
1353 |
+ |
break; |
1354 |
+ |
|
1355 |
+ |
case NPTi_ENS: |
1356 |
+ |
myNPTi = new NPTi<RealIntegrator>( info, the_ff ); |
1357 |
+ |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1358 |
+ |
|
1359 |
+ |
if (globals->haveTargetPressure()) |
1360 |
+ |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1361 |
+ |
else { |
1362 |
+ |
sprintf( painCave.errMsg, |
1363 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1364 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1365 |
+ |
painCave.isFatal = 1; |
1366 |
+ |
simError(); |
1367 |
+ |
} |
1368 |
+ |
|
1369 |
+ |
if( globals->haveTauThermostat() ) |
1370 |
+ |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1371 |
+ |
else{ |
1372 |
+ |
sprintf( painCave.errMsg, |
1373 |
+ |
"SimSetup error: If you use an NPT\n" |
1374 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1375 |
+ |
painCave.isFatal = 1; |
1376 |
+ |
simError(); |
1377 |
+ |
} |
1378 |
+ |
|
1379 |
+ |
if( globals->haveTauBarostat() ) |
1380 |
+ |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1381 |
+ |
else{ |
1382 |
+ |
sprintf( painCave.errMsg, |
1383 |
+ |
"SimSetup error: If you use an NPT\n" |
1384 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1385 |
+ |
painCave.isFatal = 1; |
1386 |
+ |
simError(); |
1387 |
+ |
} |
1388 |
+ |
break; |
1389 |
+ |
|
1390 |
+ |
case NPTf_ENS: |
1391 |
+ |
myNPTf = new NPTf<RealIntegrator>( info, the_ff ); |
1392 |
+ |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1393 |
+ |
|
1394 |
+ |
if (globals->haveTargetPressure()) |
1395 |
+ |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1396 |
+ |
else { |
1397 |
+ |
sprintf( painCave.errMsg, |
1398 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1399 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1400 |
+ |
painCave.isFatal = 1; |
1401 |
+ |
simError(); |
1402 |
+ |
} |
1403 |
+ |
|
1404 |
+ |
if( globals->haveTauThermostat() ) |
1405 |
+ |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1406 |
+ |
else{ |
1407 |
+ |
sprintf( painCave.errMsg, |
1408 |
+ |
"SimSetup error: If you use an NPT\n" |
1409 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1410 |
+ |
painCave.isFatal = 1; |
1411 |
+ |
simError(); |
1412 |
+ |
} |
1413 |
+ |
|
1414 |
+ |
if( globals->haveTauBarostat() ) |
1415 |
+ |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1416 |
+ |
else{ |
1417 |
+ |
sprintf( painCave.errMsg, |
1418 |
+ |
"SimSetup error: If you use an NPT\n" |
1419 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1420 |
+ |
painCave.isFatal = 1; |
1421 |
+ |
simError(); |
1422 |
+ |
} |
1423 |
+ |
break; |
1424 |
+ |
|
1425 |
+ |
case NPTim_ENS: |
1426 |
+ |
myNPTim = new NPTim<RealIntegrator>( info, the_ff ); |
1427 |
+ |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1428 |
+ |
|
1429 |
+ |
if (globals->haveTargetPressure()) |
1430 |
+ |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1431 |
+ |
else { |
1432 |
+ |
sprintf( painCave.errMsg, |
1433 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1434 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1435 |
+ |
painCave.isFatal = 1; |
1436 |
+ |
simError(); |
1437 |
+ |
} |
1438 |
+ |
|
1439 |
+ |
if( globals->haveTauThermostat() ) |
1440 |
+ |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1441 |
+ |
else{ |
1442 |
+ |
sprintf( painCave.errMsg, |
1443 |
+ |
"SimSetup error: If you use an NPT\n" |
1444 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1445 |
+ |
painCave.isFatal = 1; |
1446 |
+ |
simError(); |
1447 |
+ |
} |
1448 |
+ |
|
1449 |
+ |
if( globals->haveTauBarostat() ) |
1450 |
+ |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1451 |
+ |
else{ |
1452 |
+ |
sprintf( painCave.errMsg, |
1453 |
+ |
"SimSetup error: If you use an NPT\n" |
1454 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1455 |
+ |
painCave.isFatal = 1; |
1456 |
+ |
simError(); |
1457 |
+ |
} |
1458 |
+ |
break; |
1459 |
+ |
|
1460 |
+ |
case NPTfm_ENS: |
1461 |
+ |
myNPTfm = new NPTfm<RealIntegrator>( info, the_ff ); |
1462 |
+ |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1463 |
+ |
|
1464 |
+ |
if (globals->haveTargetPressure()) |
1465 |
+ |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1466 |
+ |
else { |
1467 |
+ |
sprintf( painCave.errMsg, |
1468 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1469 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1470 |
+ |
painCave.isFatal = 1; |
1471 |
+ |
simError(); |
1472 |
+ |
} |
1473 |
+ |
|
1474 |
+ |
if( globals->haveTauThermostat() ) |
1475 |
+ |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1476 |
+ |
else{ |
1477 |
+ |
sprintf( painCave.errMsg, |
1478 |
+ |
"SimSetup error: If you use an NPT\n" |
1479 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1480 |
+ |
painCave.isFatal = 1; |
1481 |
+ |
simError(); |
1482 |
+ |
} |
1483 |
+ |
|
1484 |
+ |
if( globals->haveTauBarostat() ) |
1485 |
+ |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1486 |
+ |
else{ |
1487 |
+ |
sprintf( painCave.errMsg, |
1488 |
+ |
"SimSetup error: If you use an NPT\n" |
1489 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1490 |
+ |
painCave.isFatal = 1; |
1491 |
+ |
simError(); |
1492 |
+ |
} |
1493 |
+ |
break; |
1494 |
+ |
|
1495 |
+ |
case NVEZCONS_ENS: |
1496 |
+ |
|
1497 |
+ |
|
1498 |
+ |
//setup index of z-constraint molecules, z-constraint sampel time |
1499 |
+ |
//and z-constraint force output name. These parameter should be known |
1500 |
+ |
//before constructing the z-constraint integrator |
1501 |
+ |
setupZConstraint(); |
1502 |
+ |
|
1503 |
+ |
myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff ); |
1504 |
+ |
|
1505 |
+ |
break; |
1506 |
+ |
|
1507 |
+ |
|
1508 |
+ |
case NVTZCONS_ENS: |
1509 |
+ |
|
1510 |
+ |
setupZConstraint(); |
1511 |
+ |
|
1512 |
+ |
myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff ); |
1513 |
+ |
myNVTZCons->setTargetTemp(globals->getTargetTemp()); |
1514 |
+ |
|
1515 |
+ |
if (globals->haveTauThermostat()) |
1516 |
+ |
myNVTZCons->setTauThermostat(globals->getTauThermostat()); |
1517 |
+ |
|
1518 |
+ |
else { |
1519 |
+ |
sprintf( painCave.errMsg, |
1520 |
+ |
"SimSetup error: If you use the NVT\n" |
1521 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1522 |
+ |
painCave.isFatal = 1; |
1523 |
+ |
simError(); |
1524 |
+ |
} |
1525 |
+ |
break; |
1526 |
+ |
|
1527 |
+ |
case NPTiZCONS_ENS: |
1528 |
+ |
|
1529 |
+ |
setupZConstraint(); |
1530 |
+ |
|
1531 |
+ |
myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff ); |
1532 |
+ |
myNPTiZCons->setTargetTemp( globals->getTargetTemp() ); |
1533 |
+ |
|
1534 |
+ |
if (globals->haveTargetPressure()) |
1535 |
+ |
myNPTiZCons->setTargetPressure(globals->getTargetPressure()); |
1536 |
+ |
else { |
1537 |
+ |
sprintf( painCave.errMsg, |
1538 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1539 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1540 |
+ |
painCave.isFatal = 1; |
1541 |
+ |
simError(); |
1542 |
+ |
} |
1543 |
+ |
|
1544 |
+ |
if( globals->haveTauThermostat() ) |
1545 |
+ |
myNPTiZCons->setTauThermostat( globals->getTauThermostat() ); |
1546 |
+ |
else{ |
1547 |
+ |
sprintf( painCave.errMsg, |
1548 |
+ |
"SimSetup error: If you use an NPT\n" |
1549 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1550 |
+ |
painCave.isFatal = 1; |
1551 |
+ |
simError(); |
1552 |
+ |
} |
1553 |
+ |
|
1554 |
+ |
if( globals->haveTauBarostat() ) |
1555 |
+ |
myNPTiZCons->setTauBarostat( globals->getTauBarostat() ); |
1556 |
+ |
else{ |
1557 |
+ |
sprintf( painCave.errMsg, |
1558 |
+ |
"SimSetup error: If you use an NPT\n" |
1559 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1560 |
+ |
painCave.isFatal = 1; |
1561 |
+ |
simError(); |
1562 |
+ |
} |
1563 |
+ |
|
1564 |
+ |
break; |
1565 |
+ |
|
1566 |
+ |
case NPTfZCONS_ENS: |
1567 |
+ |
|
1568 |
+ |
setupZConstraint(); |
1569 |
+ |
|
1570 |
+ |
myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff ); |
1571 |
+ |
myNPTfZCons->setTargetTemp( globals->getTargetTemp()); |
1572 |
+ |
|
1573 |
+ |
if (globals->haveTargetPressure()) |
1574 |
+ |
myNPTfZCons->setTargetPressure(globals->getTargetPressure()); |
1575 |
+ |
else { |
1576 |
+ |
sprintf( painCave.errMsg, |
1577 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1578 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1579 |
+ |
painCave.isFatal = 1; |
1580 |
+ |
simError(); |
1581 |
+ |
} |
1582 |
+ |
|
1583 |
+ |
if( globals->haveTauThermostat() ) |
1584 |
+ |
myNPTfZCons->setTauThermostat( globals->getTauThermostat() ); |
1585 |
+ |
else{ |
1586 |
+ |
sprintf( painCave.errMsg, |
1587 |
+ |
"SimSetup error: If you use an NPT\n" |
1588 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1589 |
+ |
painCave.isFatal = 1; |
1590 |
+ |
simError(); |
1591 |
+ |
} |
1592 |
+ |
|
1593 |
+ |
if( globals->haveTauBarostat() ) |
1594 |
+ |
myNPTfZCons->setTauBarostat( globals->getTauBarostat() ); |
1595 |
+ |
else{ |
1596 |
+ |
sprintf( painCave.errMsg, |
1597 |
+ |
"SimSetup error: If you use an NPT\n" |
1598 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1599 |
+ |
painCave.isFatal = 1; |
1600 |
+ |
simError(); |
1601 |
+ |
} |
1602 |
+ |
|
1603 |
+ |
break; |
1604 |
+ |
|
1605 |
+ |
case NPTimZCONS_ENS: |
1606 |
+ |
|
1607 |
+ |
setupZConstraint(); |
1608 |
+ |
|
1609 |
+ |
myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff ); |
1610 |
+ |
myNPTimZCons->setTargetTemp( globals->getTargetTemp()); |
1611 |
+ |
|
1612 |
+ |
if (globals->haveTargetPressure()) |
1613 |
+ |
myNPTimZCons->setTargetPressure(globals->getTargetPressure()); |
1614 |
+ |
else { |
1615 |
+ |
sprintf( painCave.errMsg, |
1616 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1617 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1618 |
+ |
painCave.isFatal = 1; |
1619 |
+ |
simError(); |
1620 |
+ |
} |
1621 |
+ |
|
1622 |
+ |
if( globals->haveTauThermostat() ) |
1623 |
+ |
myNPTimZCons->setTauThermostat( globals->getTauThermostat() ); |
1624 |
+ |
else{ |
1625 |
+ |
sprintf( painCave.errMsg, |
1626 |
+ |
"SimSetup error: If you use an NPT\n" |
1627 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1628 |
+ |
painCave.isFatal = 1; |
1629 |
+ |
simError(); |
1630 |
+ |
} |
1631 |
+ |
|
1632 |
+ |
if( globals->haveTauBarostat() ) |
1633 |
+ |
myNPTimZCons->setTauBarostat( globals->getTauBarostat() ); |
1634 |
+ |
else{ |
1635 |
+ |
sprintf( painCave.errMsg, |
1636 |
+ |
"SimSetup error: If you use an NPT\n" |
1637 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1638 |
+ |
painCave.isFatal = 1; |
1639 |
+ |
simError(); |
1640 |
+ |
} |
1641 |
+ |
|
1642 |
+ |
break; |
1643 |
+ |
|
1644 |
+ |
case NPTfmZCONS_ENS: |
1645 |
+ |
|
1646 |
+ |
setupZConstraint(); |
1647 |
+ |
|
1648 |
+ |
myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff ); |
1649 |
+ |
myNPTfmZCons->setTargetTemp( globals->getTargetTemp()); |
1650 |
+ |
|
1651 |
+ |
if (globals->haveTargetPressure()) |
1652 |
+ |
myNPTfmZCons->setTargetPressure(globals->getTargetPressure()); |
1653 |
+ |
else { |
1654 |
+ |
sprintf( painCave.errMsg, |
1655 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1656 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1657 |
+ |
painCave.isFatal = 1; |
1658 |
+ |
simError(); |
1659 |
+ |
} |
1660 |
+ |
|
1661 |
+ |
if( globals->haveTauThermostat() ) |
1662 |
+ |
myNPTfmZCons->setTauThermostat( globals->getTauThermostat() ); |
1663 |
+ |
else{ |
1664 |
+ |
sprintf( painCave.errMsg, |
1665 |
+ |
"SimSetup error: If you use an NPT\n" |
1666 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1667 |
+ |
painCave.isFatal = 1; |
1668 |
+ |
simError(); |
1669 |
+ |
} |
1670 |
+ |
|
1671 |
+ |
if( globals->haveTauBarostat() ) |
1672 |
+ |
myNPTfmZCons->setTauBarostat( globals->getTauBarostat() ); |
1673 |
+ |
else{ |
1674 |
+ |
sprintf( painCave.errMsg, |
1675 |
+ |
"SimSetup error: If you use an NPT\n" |
1676 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1677 |
+ |
painCave.isFatal = 1; |
1678 |
+ |
simError(); |
1679 |
+ |
} |
1680 |
+ |
break; |
1681 |
+ |
|
1682 |
+ |
|
1683 |
+ |
|
1684 |
+ |
default: |
1685 |
+ |
sprintf( painCave.errMsg, |
1686 |
+ |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1687 |
+ |
painCave.isFatal = 1; |
1688 |
+ |
simError(); |
1689 |
+ |
} |
1690 |
+ |
|
1691 |
+ |
} |
1692 |
+ |
|
1693 |
+ |
void SimSetup::initFortran( void ){ |
1694 |
+ |
|
1695 |
+ |
info->refreshSim(); |
1696 |
+ |
|
1697 |
+ |
if( !strcmp( info->mixingRule, "standard") ){ |
1698 |
+ |
the_ff->initForceField( LB_MIXING_RULE ); |
1699 |
+ |
} |
1700 |
+ |
else if( !strcmp( info->mixingRule, "explicit") ){ |
1701 |
+ |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1702 |
+ |
} |
1703 |
+ |
else{ |
1704 |
+ |
sprintf( painCave.errMsg, |
1705 |
+ |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1706 |
+ |
info->mixingRule ); |
1707 |
+ |
painCave.isFatal = 1; |
1708 |
+ |
simError(); |
1709 |
+ |
} |
1710 |
+ |
|
1711 |
+ |
|
1712 |
+ |
#ifdef IS_MPI |
1713 |
+ |
strcpy( checkPointMsg, |
1714 |
+ |
"Successfully intialized the mixingRule for Fortran." ); |
1715 |
+ |
MPIcheckPoint(); |
1716 |
+ |
#endif // is_mpi |
1717 |
+ |
|
1718 |
+ |
} |
1719 |
+ |
|
1720 |
+ |
void SimSetup::setupZConstraint() |
1721 |
+ |
{ |
1722 |
+ |
if(globals->haveZConsTime()){ |
1723 |
+ |
|
1724 |
+ |
//add sample time of z-constraint into SimInfo's property list |
1725 |
+ |
DoubleData* zconsTimeProp = new DoubleData(); |
1726 |
+ |
zconsTimeProp->setID("zconstime"); |
1727 |
+ |
zconsTimeProp->setData(globals->getZConsTime()); |
1728 |
+ |
info->addProperty(zconsTimeProp); |
1729 |
+ |
} |
1730 |
+ |
else{ |
1731 |
+ |
sprintf( painCave.errMsg, |
1732 |
+ |
"ZConstraint error: If you use an ZConstraint\n" |
1733 |
+ |
" , you must set sample time.\n"); |
1734 |
+ |
painCave.isFatal = 1; |
1735 |
+ |
simError(); |
1736 |
+ |
} |
1737 |
+ |
|
1738 |
+ |
if(globals->haveIndexOfAllZConsMols()){ |
1739 |
+ |
|
1740 |
+ |
//add index of z-constraint molecules into SimInfo's property list |
1741 |
+ |
vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1742 |
+ |
|
1743 |
+ |
//sort the index |
1744 |
+ |
sort(tempIndex.begin(), tempIndex.end()); |
1745 |
+ |
|
1746 |
+ |
IndexData* zconsIndex = new IndexData(); |
1747 |
+ |
zconsIndex->setID("zconsindex"); |
1748 |
+ |
zconsIndex->setIndexData(tempIndex); |
1749 |
+ |
info->addProperty(zconsIndex); |
1750 |
+ |
} |
1751 |
+ |
else{ |
1752 |
+ |
sprintf( painCave.errMsg, |
1753 |
+ |
"SimSetup error: If you use an ZConstraint\n" |
1754 |
+ |
" , you must set index of z-constraint molecules.\n"); |
1755 |
+ |
painCave.isFatal = 1; |
1756 |
+ |
simError(); |
1757 |
+ |
|
1758 |
+ |
} |
1759 |
+ |
|
1760 |
+ |
//Determine the name of ouput file and add it into SimInfo's property list |
1761 |
+ |
//Be careful, do not use inFileName, since it is a pointer which |
1762 |
+ |
//point to a string at master node, and slave nodes do not contain that string |
1763 |
+ |
|
1764 |
+ |
string zconsOutput(info->finalName); |
1765 |
+ |
|
1766 |
+ |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1767 |
+ |
|
1768 |
+ |
StringData* zconsFilename = new StringData(); |
1769 |
+ |
zconsFilename->setID("zconsfilename"); |
1770 |
+ |
zconsFilename->setData(zconsOutput); |
1771 |
+ |
|
1772 |
+ |
info->addProperty(zconsFilename); |
1773 |
+ |
|
1774 |
+ |
} |