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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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|
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#include "SimSetup.hpp" |
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#include "parse_me.h" |
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#include "mpiSimulation.hpp" |
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#endif |
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|
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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 NVEZCONS_ENS 6 |
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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; |
57 |
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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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ExtendedSystem* the_extendedsystem; |
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int i, j, k, globalAtomIndex; |
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|
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// get the stamps and globals; |
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the_stamps = stamps; |
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the_globals = globals; |
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|
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// set the easy ones first |
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simnfo->target_temp = the_globals->getTargetTemp(); |
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simnfo->dt = the_globals->getDt(); |
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simnfo->run_time = the_globals->getRunTime(); |
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|
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// get the ones we know are there, yet still may need some work. |
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n_components = the_globals->getNComponents(); |
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strcpy( force_field, the_globals->getForceField() ); |
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|
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// get the ensemble and set up an extended system if we need it: |
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strcpy( ensemble, the_globals->getEnsemble() ); |
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if( !strcasecmp( ensemble, "NPT" ) ) { |
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the_extendedsystem = new ExtendedSystem( simnfo ); |
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the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
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if (the_globals->haveTargetPressure()) |
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the_extendedsystem->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 the constant pressure\n" |
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" ensemble, you must set targetPressure.\n" |
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" This was found 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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the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
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else if (the_globals->haveQmass()) |
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the_extendedsystem->setQmass(the_globals->getQmass()); |
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else { |
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sprintf( painCave.errMsg, |
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"SimSetup error: If you use one of the constant temperature\n" |
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" ensembles, you must set either tauThermostat or qMass.\n" |
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" Neither of these was found 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->haveTauBarostat()) |
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the_extendedsystem->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 the constant pressure\n" |
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" ensemble, you must set tauBarostat.\n" |
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" This was found 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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} else if ( !strcasecmp( ensemble, "NVT") ) { |
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the_extendedsystem = new ExtendedSystem( simnfo ); |
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the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
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|
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if (the_globals->haveTauThermostat()) |
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the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
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else if (the_globals->haveQmass()) |
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the_extendedsystem->setQmass(the_globals->getQmass()); |
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else { |
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sprintf( painCave.errMsg, |
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"SimSetup error: If you use one of the constant temperature\n" |
136 |
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" ensembles, you must set either tauThermostat or qMass.\n" |
137 |
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" Neither of these was found in the BASS file.\n"); |
138 |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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} else if ( !strcasecmp( ensemble, "NVE") ) { |
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} else { |
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sprintf( painCave.errMsg, |
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"SimSetup Warning. Unrecognized Ensemble -> %s, " |
146 |
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"reverting to NVE for this simulation.\n", |
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ensemble ); |
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painCave.isFatal = 0; |
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simError(); |
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strcpy( ensemble, "NVE" ); |
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} |
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strcpy( simnfo->ensemble, ensemble ); |
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|
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strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
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simnfo->usePBC = the_globals->getPBC(); |
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|
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int usesDipoles = 0; |
158 |
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if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
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the_ff = new TraPPE_ExFF(); |
160 |
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usesDipoles = 1; |
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} |
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else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
163 |
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else{ |
164 |
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sprintf( painCave.errMsg, |
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"SimSetup Error. Unrecognized force field -> %s\n", |
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force_field ); |
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painCave.isFatal = 1; |
168 |
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simError(); |
169 |
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} |
170 |
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|
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "ForceField creation successful" ); |
173 |
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MPIcheckPoint(); |
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#endif // is_mpi |
175 |
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|
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|
100 |
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// gather all of the information from the Bass file |
101 |
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|
102 |
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gatherInfo(); |
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|
104 |
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// get the components and calculate the tot_nMol and indvidual n_mol |
179 |
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the_components = the_globals->getComponents(); |
180 |
< |
components_nmol = new int[n_components]; |
181 |
< |
comp_stamps = new MoleculeStamp*[n_components]; |
104 |
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// creation of complex system objects |
105 |
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|
106 |
< |
if( !the_globals->haveNMol() ){ |
184 |
< |
// we don't have the total number of molecules, so we assume it is |
185 |
< |
// given in each component |
106 |
> |
sysObjectsCreation(); |
107 |
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|
108 |
< |
tot_nmol = 0; |
188 |
< |
for( i=0; i<n_components; i++ ){ |
189 |
< |
|
190 |
< |
if( !the_components[i]->haveNMol() ){ |
191 |
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// we have a problem |
192 |
< |
sprintf( painCave.errMsg, |
193 |
< |
"SimSetup Error. No global NMol or component NMol" |
194 |
< |
" given. Cannot calculate the number of atoms.\n" ); |
195 |
< |
painCave.isFatal = 1; |
196 |
< |
simError(); |
197 |
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} |
198 |
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|
199 |
< |
tot_nmol += the_components[i]->getNMol(); |
200 |
< |
components_nmol[i] = the_components[i]->getNMol(); |
201 |
< |
} |
202 |
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} |
203 |
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else{ |
204 |
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sprintf( painCave.errMsg, |
205 |
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"SimSetup error.\n" |
206 |
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"\tSorry, the ability to specify total" |
207 |
< |
" nMols and then give molfractions in the components\n" |
208 |
< |
"\tis not currently supported." |
209 |
< |
" Please give nMol in the components.\n" ); |
210 |
< |
painCave.isFatal = 1; |
211 |
< |
simError(); |
212 |
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|
213 |
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|
214 |
< |
// tot_nmol = the_globals->getNMol(); |
215 |
< |
|
216 |
< |
// //we have the total number of molecules, now we check for molfractions |
217 |
< |
// for( i=0; i<n_components; i++ ){ |
218 |
< |
|
219 |
< |
// if( !the_components[i]->haveMolFraction() ){ |
220 |
< |
|
221 |
< |
// if( !the_components[i]->haveNMol() ){ |
222 |
< |
// //we have a problem |
223 |
< |
// std::cerr << "SimSetup error. Neither molFraction nor " |
224 |
< |
// << " nMol was given in component |
225 |
< |
|
226 |
< |
} |
227 |
< |
|
228 |
< |
#ifdef IS_MPI |
229 |
< |
strcpy( checkPointMsg, "Have the number of components" ); |
230 |
< |
MPIcheckPoint(); |
231 |
< |
#endif // is_mpi |
232 |
< |
|
233 |
< |
// make an array of molecule stamps that match the components used. |
234 |
< |
// also extract the used stamps out into a separate linked list |
235 |
< |
|
236 |
< |
simnfo->nComponents = n_components; |
237 |
< |
simnfo->componentsNmol = components_nmol; |
238 |
< |
simnfo->compStamps = comp_stamps; |
239 |
< |
simnfo->headStamp = new LinkedMolStamp(); |
108 |
> |
// check on the post processing info |
109 |
|
|
110 |
< |
char* id; |
242 |
< |
LinkedMolStamp* headStamp = simnfo->headStamp; |
243 |
< |
LinkedMolStamp* currentStamp = NULL; |
244 |
< |
for( i=0; i<n_components; i++ ){ |
110 |
> |
finalInfoCheck(); |
111 |
|
|
112 |
< |
id = the_components[i]->getType(); |
247 |
< |
comp_stamps[i] = NULL; |
248 |
< |
|
249 |
< |
// check to make sure the component isn't already in the list |
112 |
> |
// initialize the system coordinates |
113 |
|
|
114 |
< |
comp_stamps[i] = headStamp->match( id ); |
252 |
< |
if( comp_stamps[i] == NULL ){ |
253 |
< |
|
254 |
< |
// extract the component from the list; |
255 |
< |
|
256 |
< |
currentStamp = the_stamps->extractMolStamp( id ); |
257 |
< |
if( currentStamp == NULL ){ |
258 |
< |
sprintf( painCave.errMsg, |
259 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
260 |
< |
"list of declared molecules\n", |
261 |
< |
id ); |
262 |
< |
painCave.isFatal = 1; |
263 |
< |
simError(); |
264 |
< |
} |
265 |
< |
|
266 |
< |
headStamp->add( currentStamp ); |
267 |
< |
comp_stamps[i] = headStamp->match( id ); |
268 |
< |
} |
269 |
< |
} |
270 |
< |
|
271 |
< |
#ifdef IS_MPI |
272 |
< |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
273 |
< |
MPIcheckPoint(); |
274 |
< |
#endif // is_mpi |
114 |
> |
initSystemCoords(); |
115 |
|
|
116 |
|
|
117 |
+ |
// make the output filenames |
118 |
|
|
119 |
< |
|
120 |
< |
// caclulate the number of atoms, bonds, bends and torsions |
121 |
< |
|
281 |
< |
tot_atoms = 0; |
282 |
< |
tot_bonds = 0; |
283 |
< |
tot_bends = 0; |
284 |
< |
tot_torsions = 0; |
285 |
< |
for( i=0; i<n_components; i++ ){ |
286 |
< |
|
287 |
< |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
288 |
< |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
289 |
< |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
290 |
< |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
291 |
< |
} |
292 |
< |
|
293 |
< |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
294 |
< |
|
295 |
< |
simnfo->n_atoms = tot_atoms; |
296 |
< |
simnfo->n_bonds = tot_bonds; |
297 |
< |
simnfo->n_bends = tot_bends; |
298 |
< |
simnfo->n_torsions = tot_torsions; |
299 |
< |
simnfo->n_SRI = tot_SRI; |
300 |
< |
simnfo->n_mol = tot_nmol; |
119 |
> |
makeOutNames(); |
120 |
> |
|
121 |
> |
// make the integrator |
122 |
|
|
123 |
< |
simnfo->molMembershipArray = new int[tot_atoms]; |
303 |
< |
|
304 |
< |
#ifdef IS_MPI |
305 |
< |
|
306 |
< |
// divide the molecules among processors here. |
307 |
< |
|
308 |
< |
mpiSim = new mpiSimulation( simnfo ); |
309 |
< |
|
310 |
< |
globalIndex = mpiSim->divideLabor(); |
311 |
< |
|
312 |
< |
// set up the local variables |
313 |
< |
|
314 |
< |
int localMol, allMol; |
315 |
< |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
316 |
< |
|
317 |
< |
int* mol2proc = mpiSim->getMolToProcMap(); |
318 |
< |
int* molCompType = mpiSim->getMolComponentType(); |
319 |
< |
|
320 |
< |
allMol = 0; |
321 |
< |
localMol = 0; |
322 |
< |
local_atoms = 0; |
323 |
< |
local_bonds = 0; |
324 |
< |
local_bends = 0; |
325 |
< |
local_torsions = 0; |
326 |
< |
globalAtomIndex = 0; |
327 |
< |
|
328 |
< |
|
329 |
< |
for( i=0; i<n_components; i++ ){ |
330 |
< |
|
331 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
332 |
< |
|
333 |
< |
if( mol2proc[allMol] == worldRank ){ |
334 |
< |
|
335 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
336 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
337 |
< |
local_bends += comp_stamps[i]->getNBends(); |
338 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
339 |
< |
localMol++; |
340 |
< |
} |
341 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
342 |
< |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
343 |
< |
globalAtomIndex++; |
344 |
< |
} |
345 |
< |
|
346 |
< |
allMol++; |
347 |
< |
} |
348 |
< |
} |
349 |
< |
local_SRI = local_bonds + local_bends + local_torsions; |
350 |
< |
|
351 |
< |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
352 |
< |
|
353 |
< |
if( local_atoms != simnfo->n_atoms ){ |
354 |
< |
sprintf( painCave.errMsg, |
355 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
356 |
< |
" localAtom (%d) are not equal.\n", |
357 |
< |
simnfo->n_atoms, |
358 |
< |
local_atoms ); |
359 |
< |
painCave.isFatal = 1; |
360 |
< |
simError(); |
361 |
< |
} |
362 |
< |
|
363 |
< |
simnfo->n_bonds = local_bonds; |
364 |
< |
simnfo->n_bends = local_bends; |
365 |
< |
simnfo->n_torsions = local_torsions; |
366 |
< |
simnfo->n_SRI = local_SRI; |
367 |
< |
simnfo->n_mol = localMol; |
368 |
< |
|
369 |
< |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
370 |
< |
MPIcheckPoint(); |
371 |
< |
|
372 |
< |
|
373 |
< |
#endif // is_mpi |
374 |
< |
|
375 |
< |
|
376 |
< |
// create the atom and short range interaction arrays |
377 |
< |
|
378 |
< |
Atom::createArrays(simnfo->n_atoms); |
379 |
< |
the_atoms = new Atom*[simnfo->n_atoms]; |
380 |
< |
the_molecules = new Molecule[simnfo->n_mol]; |
381 |
< |
int molIndex; |
382 |
< |
|
383 |
< |
// initialize the molecule's stampID's |
384 |
< |
|
385 |
< |
#ifdef IS_MPI |
386 |
< |
|
387 |
< |
|
388 |
< |
molIndex = 0; |
389 |
< |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
390 |
< |
|
391 |
< |
if(mol2proc[i] == worldRank ){ |
392 |
< |
the_molecules[molIndex].setStampID( molCompType[i] ); |
393 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
394 |
< |
the_molecules[molIndex].setGlobalIndex( i ); |
395 |
< |
molIndex++; |
396 |
< |
} |
397 |
< |
} |
398 |
< |
|
399 |
< |
#else // is_mpi |
400 |
< |
|
401 |
< |
molIndex = 0; |
402 |
< |
globalAtomIndex = 0; |
403 |
< |
for(i=0; i<n_components; i++){ |
404 |
< |
for(j=0; j<components_nmol[i]; j++ ){ |
405 |
< |
the_molecules[molIndex].setStampID( i ); |
406 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
407 |
< |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
408 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
409 |
< |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
410 |
< |
globalAtomIndex++; |
411 |
< |
} |
412 |
< |
molIndex++; |
413 |
< |
} |
414 |
< |
} |
415 |
< |
|
416 |
< |
|
417 |
< |
#endif // is_mpi |
418 |
< |
|
419 |
< |
|
420 |
< |
if( simnfo->n_SRI ){ |
421 |
< |
|
422 |
< |
Exclude::createArray(simnfo->n_SRI); |
423 |
< |
the_excludes = new Exclude*[simnfo->n_SRI]; |
424 |
< |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
425 |
< |
simnfo->globalExcludes = new int; |
426 |
< |
simnfo->n_exclude = simnfo->n_SRI; |
427 |
< |
} |
428 |
< |
else{ |
429 |
< |
|
430 |
< |
Exclude::createArray( 1 ); |
431 |
< |
the_excludes = new Exclude*; |
432 |
< |
the_excludes[0] = new Exclude(0); |
433 |
< |
the_excludes[0]->setPair( 0,0 ); |
434 |
< |
simnfo->globalExcludes = new int; |
435 |
< |
simnfo->globalExcludes[0] = 0; |
436 |
< |
simnfo->n_exclude = 0; |
437 |
< |
} |
438 |
< |
|
439 |
< |
// set the arrays into the SimInfo object |
440 |
< |
|
441 |
< |
simnfo->atoms = the_atoms; |
442 |
< |
simnfo->molecules = the_molecules; |
443 |
< |
simnfo->nGlobalExcludes = 0; |
444 |
< |
simnfo->excludes = the_excludes; |
445 |
< |
|
446 |
< |
|
447 |
< |
// get some of the tricky things that may still be in the globals |
448 |
< |
|
449 |
< |
|
450 |
< |
if( the_globals->haveBox() ){ |
451 |
< |
simnfo->box_x = the_globals->getBox(); |
452 |
< |
simnfo->box_y = the_globals->getBox(); |
453 |
< |
simnfo->box_z = the_globals->getBox(); |
454 |
< |
} |
455 |
< |
else if( the_globals->haveDensity() ){ |
456 |
< |
|
457 |
< |
double vol; |
458 |
< |
vol = (double)tot_nmol / the_globals->getDensity(); |
459 |
< |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
460 |
< |
simnfo->box_y = simnfo->box_x; |
461 |
< |
simnfo->box_z = simnfo->box_x; |
462 |
< |
} |
463 |
< |
else{ |
464 |
< |
if( !the_globals->haveBoxX() ){ |
465 |
< |
sprintf( painCave.errMsg, |
466 |
< |
"SimSetup error, no periodic BoxX size given.\n" ); |
467 |
< |
painCave.isFatal = 1; |
468 |
< |
simError(); |
469 |
< |
} |
470 |
< |
simnfo->box_x = the_globals->getBoxX(); |
471 |
< |
|
472 |
< |
if( !the_globals->haveBoxY() ){ |
473 |
< |
sprintf( painCave.errMsg, |
474 |
< |
"SimSetup error, no periodic BoxY size given.\n" ); |
475 |
< |
painCave.isFatal = 1; |
476 |
< |
simError(); |
477 |
< |
} |
478 |
< |
simnfo->box_y = the_globals->getBoxY(); |
479 |
< |
|
480 |
< |
if( !the_globals->haveBoxZ() ){ |
481 |
< |
sprintf( painCave.errMsg, |
482 |
< |
"SimSetup error, no periodic BoxZ size given.\n" ); |
483 |
< |
painCave.isFatal = 1; |
484 |
< |
simError(); |
485 |
< |
} |
486 |
< |
simnfo->box_z = the_globals->getBoxZ(); |
487 |
< |
} |
488 |
< |
|
489 |
< |
#ifdef IS_MPI |
490 |
< |
strcpy( checkPointMsg, "Box size set up" ); |
491 |
< |
MPIcheckPoint(); |
492 |
< |
#endif // is_mpi |
493 |
< |
|
494 |
< |
|
495 |
< |
// initialize the arrays |
496 |
< |
|
497 |
< |
the_ff->setSimInfo( simnfo ); |
498 |
< |
|
499 |
< |
makeMolecules(); |
500 |
< |
simnfo->identArray = new int[simnfo->n_atoms]; |
501 |
< |
for(i=0; i<simnfo->n_atoms; i++){ |
502 |
< |
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
503 |
< |
} |
123 |
> |
makeIntegrator(); |
124 |
|
|
505 |
– |
if (the_globals->getUseRF() ) { |
506 |
– |
simnfo->useReactionField = 1; |
507 |
– |
|
508 |
– |
if( !the_globals->haveECR() ){ |
509 |
– |
sprintf( painCave.errMsg, |
510 |
– |
"SimSetup Warning: using default value of 1/2 the smallest " |
511 |
– |
"box length for the electrostaticCutoffRadius.\n" |
512 |
– |
"I hope you have a very fast processor!\n"); |
513 |
– |
painCave.isFatal = 0; |
514 |
– |
simError(); |
515 |
– |
double smallest; |
516 |
– |
smallest = simnfo->box_x; |
517 |
– |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
518 |
– |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
519 |
– |
simnfo->ecr = 0.5 * smallest; |
520 |
– |
} else { |
521 |
– |
simnfo->ecr = the_globals->getECR(); |
522 |
– |
} |
523 |
– |
|
524 |
– |
if( !the_globals->haveEST() ){ |
525 |
– |
sprintf( painCave.errMsg, |
526 |
– |
"SimSetup Warning: using default value of 0.05 * the " |
527 |
– |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
528 |
– |
); |
529 |
– |
painCave.isFatal = 0; |
530 |
– |
simError(); |
531 |
– |
simnfo->est = 0.05 * simnfo->ecr; |
532 |
– |
} else { |
533 |
– |
simnfo->est = the_globals->getEST(); |
534 |
– |
} |
535 |
– |
|
536 |
– |
if(!the_globals->haveDielectric() ){ |
537 |
– |
sprintf( painCave.errMsg, |
538 |
– |
"SimSetup Error: You are trying to use Reaction Field without" |
539 |
– |
"setting a dielectric constant!\n" |
540 |
– |
); |
541 |
– |
painCave.isFatal = 1; |
542 |
– |
simError(); |
543 |
– |
} |
544 |
– |
simnfo->dielectric = the_globals->getDielectric(); |
545 |
– |
} else { |
546 |
– |
if (usesDipoles) { |
547 |
– |
|
548 |
– |
if( !the_globals->haveECR() ){ |
549 |
– |
sprintf( painCave.errMsg, |
550 |
– |
"SimSetup Warning: using default value of 1/2 the smallest " |
551 |
– |
"box length for the electrostaticCutoffRadius.\n" |
552 |
– |
"I hope you have a very fast processor!\n"); |
553 |
– |
painCave.isFatal = 0; |
554 |
– |
simError(); |
555 |
– |
double smallest; |
556 |
– |
smallest = simnfo->box_x; |
557 |
– |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
558 |
– |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
559 |
– |
simnfo->ecr = 0.5 * smallest; |
560 |
– |
} else { |
561 |
– |
simnfo->ecr = the_globals->getECR(); |
562 |
– |
} |
563 |
– |
|
564 |
– |
if( !the_globals->haveEST() ){ |
565 |
– |
sprintf( painCave.errMsg, |
566 |
– |
"SimSetup Warning: using default value of 5%% of the " |
567 |
– |
"electrostaticCutoffRadius for the " |
568 |
– |
"electrostaticSkinThickness\n" |
569 |
– |
); |
570 |
– |
painCave.isFatal = 0; |
571 |
– |
simError(); |
572 |
– |
simnfo->est = 0.05 * simnfo->ecr; |
573 |
– |
} else { |
574 |
– |
simnfo->est = the_globals->getEST(); |
575 |
– |
} |
576 |
– |
} |
577 |
– |
} |
578 |
– |
|
125 |
|
#ifdef IS_MPI |
580 |
– |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
581 |
– |
MPIcheckPoint(); |
582 |
– |
#endif // is_mpi |
583 |
– |
|
584 |
– |
if( the_globals->haveInitialConfig() ){ |
585 |
– |
|
586 |
– |
InitializeFromFile* fileInit; |
587 |
– |
#ifdef IS_MPI // is_mpi |
588 |
– |
if( worldRank == 0 ){ |
589 |
– |
#endif //is_mpi |
590 |
– |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
591 |
– |
#ifdef IS_MPI |
592 |
– |
}else fileInit = new InitializeFromFile( NULL ); |
593 |
– |
#endif |
594 |
– |
fileInit->read_xyz( simnfo ); // default velocities on |
595 |
– |
|
596 |
– |
delete fileInit; |
597 |
– |
} |
598 |
– |
else{ |
599 |
– |
|
600 |
– |
#ifdef IS_MPI |
601 |
– |
|
602 |
– |
// no init from bass |
603 |
– |
|
604 |
– |
sprintf( painCave.errMsg, |
605 |
– |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
606 |
– |
painCave.isFatal; |
607 |
– |
simError(); |
608 |
– |
|
609 |
– |
#else |
610 |
– |
|
611 |
– |
initFromBass(); |
612 |
– |
|
613 |
– |
|
614 |
– |
#endif |
615 |
– |
} |
616 |
– |
|
617 |
– |
#ifdef IS_MPI |
618 |
– |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
619 |
– |
MPIcheckPoint(); |
620 |
– |
#endif // is_mpi |
621 |
– |
|
622 |
– |
|
623 |
– |
|
624 |
– |
|
625 |
– |
|
626 |
– |
|
627 |
– |
|
628 |
– |
#ifdef IS_MPI |
629 |
– |
if( worldRank == 0 ){ |
630 |
– |
#endif // is_mpi |
631 |
– |
|
632 |
– |
if( the_globals->haveFinalConfig() ){ |
633 |
– |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
634 |
– |
} |
635 |
– |
else{ |
636 |
– |
strcpy( simnfo->finalName, inFileName ); |
637 |
– |
char* endTest; |
638 |
– |
int nameLength = strlen( simnfo->finalName ); |
639 |
– |
endTest = &(simnfo->finalName[nameLength - 5]); |
640 |
– |
if( !strcmp( endTest, ".bass" ) ){ |
641 |
– |
strcpy( endTest, ".eor" ); |
642 |
– |
} |
643 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
644 |
– |
strcpy( endTest, ".eor" ); |
645 |
– |
} |
646 |
– |
else{ |
647 |
– |
endTest = &(simnfo->finalName[nameLength - 4]); |
648 |
– |
if( !strcmp( endTest, ".bss" ) ){ |
649 |
– |
strcpy( endTest, ".eor" ); |
650 |
– |
} |
651 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
652 |
– |
strcpy( endTest, ".eor" ); |
653 |
– |
} |
654 |
– |
else{ |
655 |
– |
strcat( simnfo->finalName, ".eor" ); |
656 |
– |
} |
657 |
– |
} |
658 |
– |
} |
659 |
– |
|
660 |
– |
// make the sample and status out names |
661 |
– |
|
662 |
– |
strcpy( simnfo->sampleName, inFileName ); |
663 |
– |
char* endTest; |
664 |
– |
int nameLength = strlen( simnfo->sampleName ); |
665 |
– |
endTest = &(simnfo->sampleName[nameLength - 5]); |
666 |
– |
if( !strcmp( endTest, ".bass" ) ){ |
667 |
– |
strcpy( endTest, ".dump" ); |
668 |
– |
} |
669 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
670 |
– |
strcpy( endTest, ".dump" ); |
671 |
– |
} |
672 |
– |
else{ |
673 |
– |
endTest = &(simnfo->sampleName[nameLength - 4]); |
674 |
– |
if( !strcmp( endTest, ".bss" ) ){ |
675 |
– |
strcpy( endTest, ".dump" ); |
676 |
– |
} |
677 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
678 |
– |
strcpy( endTest, ".dump" ); |
679 |
– |
} |
680 |
– |
else{ |
681 |
– |
strcat( simnfo->sampleName, ".dump" ); |
682 |
– |
} |
683 |
– |
} |
684 |
– |
|
685 |
– |
strcpy( simnfo->statusName, inFileName ); |
686 |
– |
nameLength = strlen( simnfo->statusName ); |
687 |
– |
endTest = &(simnfo->statusName[nameLength - 5]); |
688 |
– |
if( !strcmp( endTest, ".bass" ) ){ |
689 |
– |
strcpy( endTest, ".stat" ); |
690 |
– |
} |
691 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
692 |
– |
strcpy( endTest, ".stat" ); |
693 |
– |
} |
694 |
– |
else{ |
695 |
– |
endTest = &(simnfo->statusName[nameLength - 4]); |
696 |
– |
if( !strcmp( endTest, ".bss" ) ){ |
697 |
– |
strcpy( endTest, ".stat" ); |
698 |
– |
} |
699 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
700 |
– |
strcpy( endTest, ".stat" ); |
701 |
– |
} |
702 |
– |
else{ |
703 |
– |
strcat( simnfo->statusName, ".stat" ); |
704 |
– |
} |
705 |
– |
} |
706 |
– |
|
707 |
– |
#ifdef IS_MPI |
708 |
– |
} |
709 |
– |
#endif // is_mpi |
710 |
– |
|
711 |
– |
// set the status, sample, and themal kick times |
712 |
– |
|
713 |
– |
if( the_globals->haveSampleTime() ){ |
714 |
– |
simnfo->sampleTime = the_globals->getSampleTime(); |
715 |
– |
simnfo->statusTime = simnfo->sampleTime; |
716 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
717 |
– |
} |
718 |
– |
else{ |
719 |
– |
simnfo->sampleTime = the_globals->getRunTime(); |
720 |
– |
simnfo->statusTime = simnfo->sampleTime; |
721 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
722 |
– |
} |
723 |
– |
|
724 |
– |
if( the_globals->haveStatusTime() ){ |
725 |
– |
simnfo->statusTime = the_globals->getStatusTime(); |
726 |
– |
} |
727 |
– |
|
728 |
– |
if( the_globals->haveThermalTime() ){ |
729 |
– |
simnfo->thermalTime = the_globals->getThermalTime(); |
730 |
– |
} |
731 |
– |
|
732 |
– |
// check for the temperature set flag |
733 |
– |
|
734 |
– |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
735 |
– |
|
736 |
– |
|
737 |
– |
// make the integrator |
738 |
– |
|
739 |
– |
|
740 |
– |
if( !strcmp( ensemble, "TraPPE_Ex" ) ){ |
741 |
– |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
742 |
– |
} |
743 |
– |
else if( !strcmp( force_field, "LJ" ) ){ |
744 |
– |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
745 |
– |
} |
746 |
– |
|
747 |
– |
#ifdef IS_MPI |
126 |
|
mpiSim->mpiRefresh(); |
127 |
|
#endif |
128 |
|
|
129 |
|
// initialize the Fortran |
130 |
|
|
131 |
+ |
initFortran(); |
132 |
|
|
754 |
– |
simnfo->refreshSim(); |
755 |
– |
|
756 |
– |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
757 |
– |
the_ff->initForceField( LB_MIXING_RULE ); |
758 |
– |
} |
759 |
– |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
760 |
– |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
761 |
– |
} |
762 |
– |
else{ |
763 |
– |
sprintf( painCave.errMsg, |
764 |
– |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
765 |
– |
simnfo->mixingRule ); |
766 |
– |
painCave.isFatal = 1; |
767 |
– |
simError(); |
768 |
– |
} |
133 |
|
|
134 |
|
|
771 |
– |
#ifdef IS_MPI |
772 |
– |
strcpy( checkPointMsg, |
773 |
– |
"Successfully intialized the mixingRule for Fortran." ); |
774 |
– |
MPIcheckPoint(); |
775 |
– |
#endif // is_mpi |
135 |
|
} |
136 |
|
|
137 |
|
|
138 |
|
void SimSetup::makeMolecules( void ){ |
139 |
|
|
140 |
|
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
141 |
< |
molInit info; |
141 |
> |
molInit molInfo; |
142 |
|
DirectionalAtom* dAtom; |
143 |
|
LinkedAssign* extras; |
144 |
|
LinkedAssign* current_extra; |
163 |
|
|
164 |
|
atomOffset = 0; |
165 |
|
excludeOffset = 0; |
166 |
< |
for(i=0; i<simnfo->n_mol; i++){ |
166 |
> |
for(i=0; i<info->n_mol; i++){ |
167 |
|
|
168 |
|
stampID = the_molecules[i].getStampID(); |
169 |
|
|
170 |
< |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
171 |
< |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
172 |
< |
info.nBends = comp_stamps[stampID]->getNBends(); |
173 |
< |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
174 |
< |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
170 |
> |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
171 |
> |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
172 |
> |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
173 |
> |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
174 |
> |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
175 |
|
|
176 |
< |
info.myAtoms = &the_atoms[atomOffset]; |
177 |
< |
info.myExcludes = &the_excludes[excludeOffset]; |
178 |
< |
info.myBonds = new Bond*[info.nBonds]; |
179 |
< |
info.myBends = new Bend*[info.nBends]; |
180 |
< |
info.myTorsions = new Torsion*[info.nTorsions]; |
176 |
> |
molInfo.myAtoms = &the_atoms[atomOffset]; |
177 |
> |
molInfo.myExcludes = &the_excludes[excludeOffset]; |
178 |
> |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
179 |
> |
molInfo.myBends = new Bend*[molInfo.nBends]; |
180 |
> |
molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
181 |
|
|
182 |
< |
theBonds = new bond_pair[info.nBonds]; |
183 |
< |
theBends = new bend_set[info.nBends]; |
184 |
< |
theTorsions = new torsion_set[info.nTorsions]; |
182 |
> |
theBonds = new bond_pair[molInfo.nBonds]; |
183 |
> |
theBends = new bend_set[molInfo.nBends]; |
184 |
> |
theTorsions = new torsion_set[molInfo.nTorsions]; |
185 |
|
|
186 |
|
// make the Atoms |
187 |
|
|
188 |
< |
for(j=0; j<info.nAtoms; j++){ |
188 |
> |
for(j=0; j<molInfo.nAtoms; j++){ |
189 |
|
|
190 |
|
currentAtom = comp_stamps[stampID]->getAtom( j ); |
191 |
|
if( currentAtom->haveOrientation() ){ |
192 |
|
|
193 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
194 |
< |
simnfo->n_oriented++; |
195 |
< |
info.myAtoms[j] = dAtom; |
194 |
> |
info->n_oriented++; |
195 |
> |
molInfo.myAtoms[j] = dAtom; |
196 |
|
|
197 |
|
ux = currentAtom->getOrntX(); |
198 |
|
uy = currentAtom->getOrntY(); |
210 |
|
dAtom->setSUz( uz ); |
211 |
|
} |
212 |
|
else{ |
213 |
< |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
213 |
> |
molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
214 |
|
} |
215 |
< |
info.myAtoms[j]->setType( currentAtom->getType() ); |
215 |
> |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
216 |
|
|
217 |
|
#ifdef IS_MPI |
218 |
|
|
219 |
< |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
219 |
> |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
220 |
|
|
221 |
|
#endif // is_mpi |
222 |
|
} |
223 |
|
|
224 |
|
// make the bonds |
225 |
< |
for(j=0; j<info.nBonds; j++){ |
225 |
> |
for(j=0; j<molInfo.nBonds; j++){ |
226 |
|
|
227 |
|
currentBond = comp_stamps[stampID]->getBond( j ); |
228 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
249 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
250 |
|
#endif //is_mpi |
251 |
|
} |
252 |
< |
excludeOffset += info.nBonds; |
252 |
> |
excludeOffset += molInfo.nBonds; |
253 |
|
|
254 |
|
//make the bends |
255 |
< |
for(j=0; j<info.nBends; j++){ |
255 |
> |
for(j=0; j<molInfo.nBends; j++){ |
256 |
|
|
257 |
|
currentBend = comp_stamps[stampID]->getBend( j ); |
258 |
|
theBends[j].a = currentBend->getA() + atomOffset; |
335 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
336 |
|
#endif //is_mpi |
337 |
|
} |
338 |
< |
excludeOffset += info.nBends; |
338 |
> |
excludeOffset += molInfo.nBends; |
339 |
|
|
340 |
< |
for(j=0; j<info.nTorsions; j++){ |
340 |
> |
for(j=0; j<molInfo.nTorsions; j++){ |
341 |
|
|
342 |
|
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
343 |
|
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
365 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
366 |
|
#endif //is_mpi |
367 |
|
} |
368 |
< |
excludeOffset += info.nTorsions; |
368 |
> |
excludeOffset += molInfo.nTorsions; |
369 |
|
|
370 |
|
|
371 |
|
// send the arrays off to the forceField for init. |
372 |
|
|
373 |
< |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
374 |
< |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
375 |
< |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
376 |
< |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
373 |
> |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
374 |
> |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
375 |
> |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
376 |
> |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
377 |
|
|
378 |
|
|
379 |
< |
the_molecules[i].initialize( info ); |
379 |
> |
the_molecules[i].initialize( molInfo ); |
380 |
|
|
381 |
|
|
382 |
< |
atomOffset += info.nAtoms; |
382 |
> |
atomOffset += molInfo.nAtoms; |
383 |
|
delete[] theBonds; |
384 |
|
delete[] theBends; |
385 |
|
delete[] theTorsions; |
415 |
|
have_extra =1; |
416 |
|
|
417 |
|
n_cells = (int)temp3 - 1; |
418 |
< |
cellx = simnfo->box_x / temp3; |
419 |
< |
celly = simnfo->box_y / temp3; |
420 |
< |
cellz = simnfo->box_z / temp3; |
418 |
> |
cellx = info->boxL[0] / temp3; |
419 |
> |
celly = info->boxL[1] / temp3; |
420 |
> |
cellz = info->boxL[2] / temp3; |
421 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
422 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
423 |
|
n_per_extra = (int)ceil( temp1 ); |
432 |
|
} |
433 |
|
else{ |
434 |
|
n_cells = (int)temp3; |
435 |
< |
cellx = simnfo->box_x / temp3; |
436 |
< |
celly = simnfo->box_y / temp3; |
437 |
< |
cellz = simnfo->box_z / temp3; |
435 |
> |
cellx = info->boxL[0] / temp3; |
436 |
> |
celly = info->boxL[1] / temp3; |
437 |
> |
cellz = info->boxL[2] / temp3; |
438 |
|
} |
439 |
|
|
440 |
|
current_mol = 0; |
514 |
|
} |
515 |
|
|
516 |
|
|
517 |
< |
for( i=0; i<simnfo->n_atoms; i++ ){ |
518 |
< |
simnfo->atoms[i]->set_vx( 0.0 ); |
519 |
< |
simnfo->atoms[i]->set_vy( 0.0 ); |
520 |
< |
simnfo->atoms[i]->set_vz( 0.0 ); |
517 |
> |
for( i=0; i<info->n_atoms; i++ ){ |
518 |
> |
info->atoms[i]->set_vx( 0.0 ); |
519 |
> |
info->atoms[i]->set_vy( 0.0 ); |
520 |
> |
info->atoms[i]->set_vz( 0.0 ); |
521 |
|
} |
522 |
|
} |
523 |
|
|
578 |
|
current_comp++; |
579 |
|
} |
580 |
|
} |
581 |
+ |
|
582 |
+ |
|
583 |
+ |
void SimSetup::gatherInfo( void ){ |
584 |
+ |
int i,j,k; |
585 |
+ |
|
586 |
+ |
ensembleCase = -1; |
587 |
+ |
ffCase = -1; |
588 |
+ |
|
589 |
+ |
// get the stamps and globals; |
590 |
+ |
stamps = stamps; |
591 |
+ |
globals = globals; |
592 |
+ |
|
593 |
+ |
// set the easy ones first |
594 |
+ |
info->target_temp = globals->getTargetTemp(); |
595 |
+ |
info->dt = globals->getDt(); |
596 |
+ |
info->run_time = globals->getRunTime(); |
597 |
+ |
n_components = globals->getNComponents(); |
598 |
+ |
|
599 |
+ |
|
600 |
+ |
// get the forceField |
601 |
+ |
|
602 |
+ |
strcpy( force_field, globals->getForceField() ); |
603 |
+ |
|
604 |
+ |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
605 |
+ |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
606 |
+ |
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
607 |
+ |
else{ |
608 |
+ |
sprintf( painCave.errMsg, |
609 |
+ |
"SimSetup Error. Unrecognized force field -> %s\n", |
610 |
+ |
force_field ); |
611 |
+ |
painCave.isFatal = 1; |
612 |
+ |
simError(); |
613 |
+ |
} |
614 |
+ |
|
615 |
+ |
// get the ensemble |
616 |
+ |
|
617 |
+ |
strcpy( ensemble, globals->getEnsemble() ); |
618 |
+ |
|
619 |
+ |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
620 |
+ |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
621 |
+ |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
622 |
+ |
ensembleCase = NPTi_ENS; |
623 |
+ |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
624 |
+ |
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
625 |
+ |
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
626 |
+ |
else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
627 |
+ |
else{ |
628 |
+ |
sprintf( painCave.errMsg, |
629 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
630 |
+ |
"reverting to NVE for this simulation.\n", |
631 |
+ |
ensemble ); |
632 |
+ |
painCave.isFatal = 0; |
633 |
+ |
simError(); |
634 |
+ |
strcpy( ensemble, "NVE" ); |
635 |
+ |
ensembleCase = NVE_ENS; |
636 |
+ |
} |
637 |
+ |
strcpy( info->ensemble, ensemble ); |
638 |
+ |
|
639 |
+ |
// get the mixing rule |
640 |
+ |
|
641 |
+ |
strcpy( info->mixingRule, globals->getMixingRule() ); |
642 |
+ |
info->usePBC = globals->getPBC(); |
643 |
+ |
|
644 |
+ |
|
645 |
+ |
// get the components and calculate the tot_nMol and indvidual n_mol |
646 |
+ |
|
647 |
+ |
the_components = globals->getComponents(); |
648 |
+ |
components_nmol = new int[n_components]; |
649 |
+ |
|
650 |
+ |
|
651 |
+ |
if( !globals->haveNMol() ){ |
652 |
+ |
// we don't have the total number of molecules, so we assume it is |
653 |
+ |
// given in each component |
654 |
+ |
|
655 |
+ |
tot_nmol = 0; |
656 |
+ |
for( i=0; i<n_components; i++ ){ |
657 |
+ |
|
658 |
+ |
if( !the_components[i]->haveNMol() ){ |
659 |
+ |
// we have a problem |
660 |
+ |
sprintf( painCave.errMsg, |
661 |
+ |
"SimSetup Error. No global NMol or component NMol" |
662 |
+ |
" given. Cannot calculate the number of atoms.\n" ); |
663 |
+ |
painCave.isFatal = 1; |
664 |
+ |
simError(); |
665 |
+ |
} |
666 |
+ |
|
667 |
+ |
tot_nmol += the_components[i]->getNMol(); |
668 |
+ |
components_nmol[i] = the_components[i]->getNMol(); |
669 |
+ |
} |
670 |
+ |
} |
671 |
+ |
else{ |
672 |
+ |
sprintf( painCave.errMsg, |
673 |
+ |
"SimSetup error.\n" |
674 |
+ |
"\tSorry, the ability to specify total" |
675 |
+ |
" nMols and then give molfractions in the components\n" |
676 |
+ |
"\tis not currently supported." |
677 |
+ |
" Please give nMol in the components.\n" ); |
678 |
+ |
painCave.isFatal = 1; |
679 |
+ |
simError(); |
680 |
+ |
} |
681 |
+ |
|
682 |
+ |
// set the status, sample, and thermal kick times |
683 |
+ |
|
684 |
+ |
if( globals->haveSampleTime() ){ |
685 |
+ |
info->sampleTime = globals->getSampleTime(); |
686 |
+ |
info->statusTime = info->sampleTime; |
687 |
+ |
info->thermalTime = info->sampleTime; |
688 |
+ |
} |
689 |
+ |
else{ |
690 |
+ |
info->sampleTime = globals->getRunTime(); |
691 |
+ |
info->statusTime = info->sampleTime; |
692 |
+ |
info->thermalTime = info->sampleTime; |
693 |
+ |
} |
694 |
+ |
|
695 |
+ |
if( globals->haveStatusTime() ){ |
696 |
+ |
info->statusTime = globals->getStatusTime(); |
697 |
+ |
} |
698 |
+ |
|
699 |
+ |
if( globals->haveThermalTime() ){ |
700 |
+ |
info->thermalTime = globals->getThermalTime(); |
701 |
+ |
} |
702 |
+ |
|
703 |
+ |
// check for the temperature set flag |
704 |
+ |
|
705 |
+ |
if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
706 |
+ |
|
707 |
+ |
// get some of the tricky things that may still be in the globals |
708 |
+ |
|
709 |
+ |
double boxVector[3]; |
710 |
+ |
if( globals->haveBox() ){ |
711 |
+ |
boxVector[0] = globals->getBox(); |
712 |
+ |
boxVector[1] = globals->getBox(); |
713 |
+ |
boxVector[2] = globals->getBox(); |
714 |
+ |
|
715 |
+ |
info->setBox( boxVector ); |
716 |
+ |
} |
717 |
+ |
else if( globals->haveDensity() ){ |
718 |
+ |
|
719 |
+ |
double vol; |
720 |
+ |
vol = (double)tot_nmol / globals->getDensity(); |
721 |
+ |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
722 |
+ |
boxVector[1] = boxVector[0]; |
723 |
+ |
boxVector[2] = boxVector[0]; |
724 |
+ |
|
725 |
+ |
info->setBox( boxVector ); |
726 |
+ |
} |
727 |
+ |
else{ |
728 |
+ |
if( !globals->haveBoxX() ){ |
729 |
+ |
sprintf( painCave.errMsg, |
730 |
+ |
"SimSetup error, no periodic BoxX size given.\n" ); |
731 |
+ |
painCave.isFatal = 1; |
732 |
+ |
simError(); |
733 |
+ |
} |
734 |
+ |
boxVector[0] = globals->getBoxX(); |
735 |
+ |
|
736 |
+ |
if( !globals->haveBoxY() ){ |
737 |
+ |
sprintf( painCave.errMsg, |
738 |
+ |
"SimSetup error, no periodic BoxY size given.\n" ); |
739 |
+ |
painCave.isFatal = 1; |
740 |
+ |
simError(); |
741 |
+ |
} |
742 |
+ |
boxVector[1] = globals->getBoxY(); |
743 |
+ |
|
744 |
+ |
if( !globals->haveBoxZ() ){ |
745 |
+ |
sprintf( painCave.errMsg, |
746 |
+ |
"SimSetup error, no periodic BoxZ size given.\n" ); |
747 |
+ |
painCave.isFatal = 1; |
748 |
+ |
simError(); |
749 |
+ |
} |
750 |
+ |
boxVector[2] = globals->getBoxZ(); |
751 |
+ |
|
752 |
+ |
info->setBox( boxVector ); |
753 |
+ |
} |
754 |
+ |
|
755 |
+ |
|
756 |
+ |
|
757 |
+ |
#ifdef IS_MPI |
758 |
+ |
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
759 |
+ |
MPIcheckPoint(); |
760 |
+ |
#endif // is_mpi |
761 |
+ |
|
762 |
+ |
} |
763 |
+ |
|
764 |
+ |
|
765 |
+ |
void SimSetup::finalInfoCheck( void ){ |
766 |
+ |
int index; |
767 |
+ |
int usesDipoles; |
768 |
+ |
|
769 |
+ |
|
770 |
+ |
// check electrostatic parameters |
771 |
+ |
|
772 |
+ |
index = 0; |
773 |
+ |
usesDipoles = 0; |
774 |
+ |
while( (index < info->n_atoms) && !usesDipoles ){ |
775 |
+ |
usesDipoles = ((info->atoms)[index])->hasDipole(); |
776 |
+ |
index++; |
777 |
+ |
} |
778 |
+ |
|
779 |
+ |
#ifdef IS_MPI |
780 |
+ |
int myUse = usesDipoles; |
781 |
+ |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
782 |
+ |
#endif //is_mpi |
783 |
+ |
|
784 |
+ |
double theEcr, theEst; |
785 |
+ |
|
786 |
+ |
if (globals->getUseRF() ) { |
787 |
+ |
info->useReactionField = 1; |
788 |
+ |
|
789 |
+ |
if( !globals->haveECR() ){ |
790 |
+ |
sprintf( painCave.errMsg, |
791 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest " |
792 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
793 |
+ |
"I hope you have a very fast processor!\n"); |
794 |
+ |
painCave.isFatal = 0; |
795 |
+ |
simError(); |
796 |
+ |
double smallest; |
797 |
+ |
smallest = info->boxL[0]; |
798 |
+ |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
799 |
+ |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
800 |
+ |
theEcr = 0.5 * smallest; |
801 |
+ |
} else { |
802 |
+ |
theEcr = globals->getECR(); |
803 |
+ |
} |
804 |
+ |
|
805 |
+ |
if( !globals->haveEST() ){ |
806 |
+ |
sprintf( painCave.errMsg, |
807 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
808 |
+ |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
809 |
+ |
); |
810 |
+ |
painCave.isFatal = 0; |
811 |
+ |
simError(); |
812 |
+ |
theEst = 0.05 * theEcr; |
813 |
+ |
} else { |
814 |
+ |
theEst= globals->getEST(); |
815 |
+ |
} |
816 |
+ |
|
817 |
+ |
info->setEcr( theEcr, theEst ); |
818 |
+ |
|
819 |
+ |
if(!globals->haveDielectric() ){ |
820 |
+ |
sprintf( painCave.errMsg, |
821 |
+ |
"SimSetup Error: You are trying to use Reaction Field without" |
822 |
+ |
"setting a dielectric constant!\n" |
823 |
+ |
); |
824 |
+ |
painCave.isFatal = 1; |
825 |
+ |
simError(); |
826 |
+ |
} |
827 |
+ |
info->dielectric = globals->getDielectric(); |
828 |
+ |
} |
829 |
+ |
else { |
830 |
+ |
if (usesDipoles) { |
831 |
+ |
|
832 |
+ |
if( !globals->haveECR() ){ |
833 |
+ |
sprintf( painCave.errMsg, |
834 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest " |
835 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
836 |
+ |
"I hope you have a very fast processor!\n"); |
837 |
+ |
painCave.isFatal = 0; |
838 |
+ |
simError(); |
839 |
+ |
double smallest; |
840 |
+ |
smallest = info->boxL[0]; |
841 |
+ |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
842 |
+ |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
843 |
+ |
theEcr = 0.5 * smallest; |
844 |
+ |
} else { |
845 |
+ |
theEcr = globals->getECR(); |
846 |
+ |
} |
847 |
+ |
|
848 |
+ |
if( !globals->haveEST() ){ |
849 |
+ |
sprintf( painCave.errMsg, |
850 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
851 |
+ |
"electrostaticCutoffRadius for the " |
852 |
+ |
"electrostaticSkinThickness\n" |
853 |
+ |
); |
854 |
+ |
painCave.isFatal = 0; |
855 |
+ |
simError(); |
856 |
+ |
theEst = 0.05 * theEcr; |
857 |
+ |
} else { |
858 |
+ |
theEst= globals->getEST(); |
859 |
+ |
} |
860 |
+ |
|
861 |
+ |
info->setEcr( theEcr, theEst ); |
862 |
+ |
} |
863 |
+ |
} |
864 |
+ |
|
865 |
+ |
#ifdef IS_MPI |
866 |
+ |
strcpy( checkPointMsg, "post processing checks out" ); |
867 |
+ |
MPIcheckPoint(); |
868 |
+ |
#endif // is_mpi |
869 |
+ |
|
870 |
+ |
} |
871 |
+ |
|
872 |
+ |
void SimSetup::initSystemCoords( void ){ |
873 |
+ |
|
874 |
+ |
if( globals->haveInitialConfig() ){ |
875 |
+ |
|
876 |
+ |
InitializeFromFile* fileInit; |
877 |
+ |
#ifdef IS_MPI // is_mpi |
878 |
+ |
if( worldRank == 0 ){ |
879 |
+ |
#endif //is_mpi |
880 |
+ |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
881 |
+ |
#ifdef IS_MPI |
882 |
+ |
}else fileInit = new InitializeFromFile( NULL ); |
883 |
+ |
#endif |
884 |
+ |
fileInit->readInit( info ); // default velocities on |
885 |
+ |
|
886 |
+ |
delete fileInit; |
887 |
+ |
} |
888 |
+ |
else{ |
889 |
+ |
|
890 |
+ |
#ifdef IS_MPI |
891 |
+ |
|
892 |
+ |
// no init from bass |
893 |
+ |
|
894 |
+ |
sprintf( painCave.errMsg, |
895 |
+ |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
896 |
+ |
painCave.isFatal; |
897 |
+ |
simError(); |
898 |
+ |
|
899 |
+ |
#else |
900 |
+ |
|
901 |
+ |
initFromBass(); |
902 |
+ |
|
903 |
+ |
|
904 |
+ |
#endif |
905 |
+ |
} |
906 |
+ |
|
907 |
+ |
#ifdef IS_MPI |
908 |
+ |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
909 |
+ |
MPIcheckPoint(); |
910 |
+ |
#endif // is_mpi |
911 |
+ |
|
912 |
+ |
} |
913 |
+ |
|
914 |
+ |
|
915 |
+ |
void SimSetup::makeOutNames( void ){ |
916 |
+ |
|
917 |
+ |
#ifdef IS_MPI |
918 |
+ |
if( worldRank == 0 ){ |
919 |
+ |
#endif // is_mpi |
920 |
+ |
|
921 |
+ |
if( globals->haveFinalConfig() ){ |
922 |
+ |
strcpy( info->finalName, globals->getFinalConfig() ); |
923 |
+ |
} |
924 |
+ |
else{ |
925 |
+ |
strcpy( info->finalName, inFileName ); |
926 |
+ |
char* endTest; |
927 |
+ |
int nameLength = strlen( info->finalName ); |
928 |
+ |
endTest = &(info->finalName[nameLength - 5]); |
929 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
930 |
+ |
strcpy( endTest, ".eor" ); |
931 |
+ |
} |
932 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
933 |
+ |
strcpy( endTest, ".eor" ); |
934 |
+ |
} |
935 |
+ |
else{ |
936 |
+ |
endTest = &(info->finalName[nameLength - 4]); |
937 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
938 |
+ |
strcpy( endTest, ".eor" ); |
939 |
+ |
} |
940 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
941 |
+ |
strcpy( endTest, ".eor" ); |
942 |
+ |
} |
943 |
+ |
else{ |
944 |
+ |
strcat( info->finalName, ".eor" ); |
945 |
+ |
} |
946 |
+ |
} |
947 |
+ |
} |
948 |
+ |
|
949 |
+ |
// make the sample and status out names |
950 |
+ |
|
951 |
+ |
strcpy( info->sampleName, inFileName ); |
952 |
+ |
char* endTest; |
953 |
+ |
int nameLength = strlen( info->sampleName ); |
954 |
+ |
endTest = &(info->sampleName[nameLength - 5]); |
955 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
956 |
+ |
strcpy( endTest, ".dump" ); |
957 |
+ |
} |
958 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
959 |
+ |
strcpy( endTest, ".dump" ); |
960 |
+ |
} |
961 |
+ |
else{ |
962 |
+ |
endTest = &(info->sampleName[nameLength - 4]); |
963 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
964 |
+ |
strcpy( endTest, ".dump" ); |
965 |
+ |
} |
966 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
967 |
+ |
strcpy( endTest, ".dump" ); |
968 |
+ |
} |
969 |
+ |
else{ |
970 |
+ |
strcat( info->sampleName, ".dump" ); |
971 |
+ |
} |
972 |
+ |
} |
973 |
+ |
|
974 |
+ |
strcpy( info->statusName, inFileName ); |
975 |
+ |
nameLength = strlen( info->statusName ); |
976 |
+ |
endTest = &(info->statusName[nameLength - 5]); |
977 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
978 |
+ |
strcpy( endTest, ".stat" ); |
979 |
+ |
} |
980 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
981 |
+ |
strcpy( endTest, ".stat" ); |
982 |
+ |
} |
983 |
+ |
else{ |
984 |
+ |
endTest = &(info->statusName[nameLength - 4]); |
985 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
986 |
+ |
strcpy( endTest, ".stat" ); |
987 |
+ |
} |
988 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
989 |
+ |
strcpy( endTest, ".stat" ); |
990 |
+ |
} |
991 |
+ |
else{ |
992 |
+ |
strcat( info->statusName, ".stat" ); |
993 |
+ |
} |
994 |
+ |
} |
995 |
+ |
|
996 |
+ |
#ifdef IS_MPI |
997 |
+ |
} |
998 |
+ |
#endif // is_mpi |
999 |
+ |
|
1000 |
+ |
} |
1001 |
+ |
|
1002 |
+ |
|
1003 |
+ |
void SimSetup::sysObjectsCreation( void ){ |
1004 |
+ |
|
1005 |
+ |
int i; |
1006 |
+ |
|
1007 |
+ |
// create the forceField |
1008 |
+ |
|
1009 |
+ |
createFF(); |
1010 |
+ |
|
1011 |
+ |
// extract componentList |
1012 |
+ |
|
1013 |
+ |
compList(); |
1014 |
+ |
|
1015 |
+ |
// calc the number of atoms, bond, bends, and torsions |
1016 |
+ |
|
1017 |
+ |
calcSysValues(); |
1018 |
+ |
|
1019 |
+ |
#ifdef IS_MPI |
1020 |
+ |
// divide the molecules among the processors |
1021 |
+ |
|
1022 |
+ |
mpiMolDivide(); |
1023 |
+ |
#endif //is_mpi |
1024 |
+ |
|
1025 |
+ |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1026 |
+ |
|
1027 |
+ |
makeSysArrays(); |
1028 |
+ |
|
1029 |
+ |
// make and initialize the molecules (all but atomic coordinates) |
1030 |
+ |
|
1031 |
+ |
makeMolecules(); |
1032 |
+ |
info->identArray = new int[info->n_atoms]; |
1033 |
+ |
for(i=0; i<info->n_atoms; i++){ |
1034 |
+ |
info->identArray[i] = the_atoms[i]->getIdent(); |
1035 |
+ |
} |
1036 |
+ |
|
1037 |
+ |
|
1038 |
+ |
|
1039 |
+ |
} |
1040 |
+ |
|
1041 |
+ |
|
1042 |
+ |
void SimSetup::createFF( void ){ |
1043 |
+ |
|
1044 |
+ |
switch( ffCase ){ |
1045 |
+ |
|
1046 |
+ |
case FF_DUFF: |
1047 |
+ |
the_ff = new DUFF(); |
1048 |
+ |
break; |
1049 |
+ |
|
1050 |
+ |
case FF_LJ: |
1051 |
+ |
the_ff = new LJFF(); |
1052 |
+ |
break; |
1053 |
+ |
|
1054 |
+ |
case FF_EAM: |
1055 |
+ |
the_ff = new EAM_FF(); |
1056 |
+ |
break; |
1057 |
+ |
|
1058 |
+ |
default: |
1059 |
+ |
sprintf( painCave.errMsg, |
1060 |
+ |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1061 |
+ |
painCave.isFatal = 1; |
1062 |
+ |
simError(); |
1063 |
+ |
} |
1064 |
+ |
|
1065 |
+ |
#ifdef IS_MPI |
1066 |
+ |
strcpy( checkPointMsg, "ForceField creation successful" ); |
1067 |
+ |
MPIcheckPoint(); |
1068 |
+ |
#endif // is_mpi |
1069 |
+ |
|
1070 |
+ |
} |
1071 |
+ |
|
1072 |
+ |
|
1073 |
+ |
void SimSetup::compList( void ){ |
1074 |
+ |
|
1075 |
+ |
int i; |
1076 |
+ |
|
1077 |
+ |
comp_stamps = new MoleculeStamp*[n_components]; |
1078 |
+ |
|
1079 |
+ |
// make an array of molecule stamps that match the components used. |
1080 |
+ |
// also extract the used stamps out into a separate linked list |
1081 |
+ |
|
1082 |
+ |
info->nComponents = n_components; |
1083 |
+ |
info->componentsNmol = components_nmol; |
1084 |
+ |
info->compStamps = comp_stamps; |
1085 |
+ |
info->headStamp = new LinkedMolStamp(); |
1086 |
+ |
|
1087 |
+ |
char* id; |
1088 |
+ |
LinkedMolStamp* headStamp = info->headStamp; |
1089 |
+ |
LinkedMolStamp* currentStamp = NULL; |
1090 |
+ |
for( i=0; i<n_components; i++ ){ |
1091 |
+ |
|
1092 |
+ |
id = the_components[i]->getType(); |
1093 |
+ |
comp_stamps[i] = NULL; |
1094 |
+ |
|
1095 |
+ |
// check to make sure the component isn't already in the list |
1096 |
+ |
|
1097 |
+ |
comp_stamps[i] = headStamp->match( id ); |
1098 |
+ |
if( comp_stamps[i] == NULL ){ |
1099 |
+ |
|
1100 |
+ |
// extract the component from the list; |
1101 |
+ |
|
1102 |
+ |
currentStamp = stamps->extractMolStamp( id ); |
1103 |
+ |
if( currentStamp == NULL ){ |
1104 |
+ |
sprintf( painCave.errMsg, |
1105 |
+ |
"SimSetup error: Component \"%s\" was not found in the " |
1106 |
+ |
"list of declared molecules\n", |
1107 |
+ |
id ); |
1108 |
+ |
painCave.isFatal = 1; |
1109 |
+ |
simError(); |
1110 |
+ |
} |
1111 |
+ |
|
1112 |
+ |
headStamp->add( currentStamp ); |
1113 |
+ |
comp_stamps[i] = headStamp->match( id ); |
1114 |
+ |
} |
1115 |
+ |
} |
1116 |
+ |
|
1117 |
+ |
#ifdef IS_MPI |
1118 |
+ |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1119 |
+ |
MPIcheckPoint(); |
1120 |
+ |
#endif // is_mpi |
1121 |
+ |
|
1122 |
+ |
|
1123 |
+ |
} |
1124 |
+ |
|
1125 |
+ |
void SimSetup::calcSysValues( void ){ |
1126 |
+ |
int i, j, k; |
1127 |
+ |
|
1128 |
+ |
|
1129 |
+ |
tot_atoms = 0; |
1130 |
+ |
tot_bonds = 0; |
1131 |
+ |
tot_bends = 0; |
1132 |
+ |
tot_torsions = 0; |
1133 |
+ |
for( i=0; i<n_components; i++ ){ |
1134 |
+ |
|
1135 |
+ |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1136 |
+ |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1137 |
+ |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1138 |
+ |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1139 |
+ |
} |
1140 |
+ |
|
1141 |
+ |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1142 |
+ |
|
1143 |
+ |
info->n_atoms = tot_atoms; |
1144 |
+ |
info->n_bonds = tot_bonds; |
1145 |
+ |
info->n_bends = tot_bends; |
1146 |
+ |
info->n_torsions = tot_torsions; |
1147 |
+ |
info->n_SRI = tot_SRI; |
1148 |
+ |
info->n_mol = tot_nmol; |
1149 |
+ |
|
1150 |
+ |
info->molMembershipArray = new int[tot_atoms]; |
1151 |
+ |
} |
1152 |
+ |
|
1153 |
+ |
|
1154 |
+ |
#ifdef IS_MPI |
1155 |
+ |
|
1156 |
+ |
void SimSetup::mpiMolDivide( void ){ |
1157 |
+ |
|
1158 |
+ |
int i, j, k; |
1159 |
+ |
int localMol, allMol; |
1160 |
+ |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1161 |
+ |
|
1162 |
+ |
mpiSim = new mpiSimulation( info ); |
1163 |
+ |
|
1164 |
+ |
globalIndex = mpiSim->divideLabor(); |
1165 |
+ |
|
1166 |
+ |
// set up the local variables |
1167 |
+ |
|
1168 |
+ |
mol2proc = mpiSim->getMolToProcMap(); |
1169 |
+ |
molCompType = mpiSim->getMolComponentType(); |
1170 |
+ |
|
1171 |
+ |
allMol = 0; |
1172 |
+ |
localMol = 0; |
1173 |
+ |
local_atoms = 0; |
1174 |
+ |
local_bonds = 0; |
1175 |
+ |
local_bends = 0; |
1176 |
+ |
local_torsions = 0; |
1177 |
+ |
globalAtomIndex = 0; |
1178 |
+ |
|
1179 |
+ |
|
1180 |
+ |
for( i=0; i<n_components; i++ ){ |
1181 |
+ |
|
1182 |
+ |
for( j=0; j<components_nmol[i]; j++ ){ |
1183 |
+ |
|
1184 |
+ |
if( mol2proc[allMol] == worldRank ){ |
1185 |
+ |
|
1186 |
+ |
local_atoms += comp_stamps[i]->getNAtoms(); |
1187 |
+ |
local_bonds += comp_stamps[i]->getNBonds(); |
1188 |
+ |
local_bends += comp_stamps[i]->getNBends(); |
1189 |
+ |
local_torsions += comp_stamps[i]->getNTorsions(); |
1190 |
+ |
localMol++; |
1191 |
+ |
} |
1192 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1193 |
+ |
info->molMembershipArray[globalAtomIndex] = allMol; |
1194 |
+ |
globalAtomIndex++; |
1195 |
+ |
} |
1196 |
+ |
|
1197 |
+ |
allMol++; |
1198 |
+ |
} |
1199 |
+ |
} |
1200 |
+ |
local_SRI = local_bonds + local_bends + local_torsions; |
1201 |
+ |
|
1202 |
+ |
info->n_atoms = mpiSim->getMyNlocal(); |
1203 |
+ |
|
1204 |
+ |
if( local_atoms != info->n_atoms ){ |
1205 |
+ |
sprintf( painCave.errMsg, |
1206 |
+ |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1207 |
+ |
" localAtom (%d) are not equal.\n", |
1208 |
+ |
info->n_atoms, |
1209 |
+ |
local_atoms ); |
1210 |
+ |
painCave.isFatal = 1; |
1211 |
+ |
simError(); |
1212 |
+ |
} |
1213 |
+ |
|
1214 |
+ |
info->n_bonds = local_bonds; |
1215 |
+ |
info->n_bends = local_bends; |
1216 |
+ |
info->n_torsions = local_torsions; |
1217 |
+ |
info->n_SRI = local_SRI; |
1218 |
+ |
info->n_mol = localMol; |
1219 |
+ |
|
1220 |
+ |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1221 |
+ |
MPIcheckPoint(); |
1222 |
+ |
} |
1223 |
+ |
|
1224 |
+ |
#endif // is_mpi |
1225 |
+ |
|
1226 |
+ |
|
1227 |
+ |
void SimSetup::makeSysArrays( void ){ |
1228 |
+ |
int i, j, k; |
1229 |
+ |
|
1230 |
+ |
|
1231 |
+ |
// create the atom and short range interaction arrays |
1232 |
+ |
|
1233 |
+ |
Atom::createArrays(info->n_atoms); |
1234 |
+ |
the_atoms = new Atom*[info->n_atoms]; |
1235 |
+ |
the_molecules = new Molecule[info->n_mol]; |
1236 |
+ |
int molIndex; |
1237 |
+ |
|
1238 |
+ |
// initialize the molecule's stampID's |
1239 |
+ |
|
1240 |
+ |
#ifdef IS_MPI |
1241 |
+ |
|
1242 |
+ |
|
1243 |
+ |
molIndex = 0; |
1244 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1245 |
+ |
|
1246 |
+ |
if(mol2proc[i] == worldRank ){ |
1247 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1248 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
1249 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
1250 |
+ |
molIndex++; |
1251 |
+ |
} |
1252 |
+ |
} |
1253 |
+ |
|
1254 |
+ |
#else // is_mpi |
1255 |
+ |
|
1256 |
+ |
molIndex = 0; |
1257 |
+ |
globalAtomIndex = 0; |
1258 |
+ |
for(i=0; i<n_components; i++){ |
1259 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
1260 |
+ |
the_molecules[molIndex].setStampID( i ); |
1261 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
1262 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1263 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1264 |
+ |
info->molMembershipArray[globalAtomIndex] = molIndex; |
1265 |
+ |
globalAtomIndex++; |
1266 |
+ |
} |
1267 |
+ |
molIndex++; |
1268 |
+ |
} |
1269 |
+ |
} |
1270 |
+ |
|
1271 |
+ |
|
1272 |
+ |
#endif // is_mpi |
1273 |
+ |
|
1274 |
+ |
|
1275 |
+ |
if( info->n_SRI ){ |
1276 |
+ |
|
1277 |
+ |
Exclude::createArray(info->n_SRI); |
1278 |
+ |
the_excludes = new Exclude*[info->n_SRI]; |
1279 |
+ |
for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1280 |
+ |
info->globalExcludes = new int; |
1281 |
+ |
info->n_exclude = info->n_SRI; |
1282 |
+ |
} |
1283 |
+ |
else{ |
1284 |
+ |
|
1285 |
+ |
Exclude::createArray( 1 ); |
1286 |
+ |
the_excludes = new Exclude*; |
1287 |
+ |
the_excludes[0] = new Exclude(0); |
1288 |
+ |
the_excludes[0]->setPair( 0,0 ); |
1289 |
+ |
info->globalExcludes = new int; |
1290 |
+ |
info->globalExcludes[0] = 0; |
1291 |
+ |
info->n_exclude = 0; |
1292 |
+ |
} |
1293 |
+ |
|
1294 |
+ |
// set the arrays into the SimInfo object |
1295 |
+ |
|
1296 |
+ |
info->atoms = the_atoms; |
1297 |
+ |
info->molecules = the_molecules; |
1298 |
+ |
info->nGlobalExcludes = 0; |
1299 |
+ |
info->excludes = the_excludes; |
1300 |
+ |
|
1301 |
+ |
the_ff->setSimInfo( info ); |
1302 |
+ |
|
1303 |
+ |
} |
1304 |
+ |
|
1305 |
+ |
void SimSetup::makeIntegrator( void ){ |
1306 |
+ |
|
1307 |
+ |
NVT<RealIntegrator>* myNVT = NULL; |
1308 |
+ |
NPTi<RealIntegrator>* myNPTi = NULL; |
1309 |
+ |
NPTf<RealIntegrator>* myNPTf = NULL; |
1310 |
+ |
NPTim<RealIntegrator>* myNPTim = NULL; |
1311 |
+ |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1312 |
+ |
ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
1313 |
+ |
|
1314 |
+ |
cerr << "setting integrator" <<endl; |
1315 |
+ |
|
1316 |
+ |
switch( ensembleCase ){ |
1317 |
+ |
|
1318 |
+ |
case NVE_ENS: |
1319 |
+ |
new NVE<RealIntegrator>( info, the_ff ); |
1320 |
+ |
break; |
1321 |
+ |
|
1322 |
+ |
case NVT_ENS: |
1323 |
+ |
myNVT = new NVT<RealIntegrator>( info, the_ff ); |
1324 |
+ |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1325 |
+ |
|
1326 |
+ |
if (globals->haveTauThermostat()) |
1327 |
+ |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1328 |
+ |
|
1329 |
+ |
else { |
1330 |
+ |
sprintf( painCave.errMsg, |
1331 |
+ |
"SimSetup error: If you use the NVT\n" |
1332 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1333 |
+ |
painCave.isFatal = 1; |
1334 |
+ |
simError(); |
1335 |
+ |
} |
1336 |
+ |
break; |
1337 |
+ |
|
1338 |
+ |
case NPTi_ENS: |
1339 |
+ |
myNPTi = new NPTi<RealIntegrator>( info, the_ff ); |
1340 |
+ |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1341 |
+ |
|
1342 |
+ |
if (globals->haveTargetPressure()) |
1343 |
+ |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1344 |
+ |
else { |
1345 |
+ |
sprintf( painCave.errMsg, |
1346 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1347 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1348 |
+ |
painCave.isFatal = 1; |
1349 |
+ |
simError(); |
1350 |
+ |
} |
1351 |
+ |
|
1352 |
+ |
if( globals->haveTauThermostat() ) |
1353 |
+ |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1354 |
+ |
else{ |
1355 |
+ |
sprintf( painCave.errMsg, |
1356 |
+ |
"SimSetup error: If you use an NPT\n" |
1357 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1358 |
+ |
painCave.isFatal = 1; |
1359 |
+ |
simError(); |
1360 |
+ |
} |
1361 |
+ |
|
1362 |
+ |
if( globals->haveTauBarostat() ) |
1363 |
+ |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1364 |
+ |
else{ |
1365 |
+ |
sprintf( painCave.errMsg, |
1366 |
+ |
"SimSetup error: If you use an NPT\n" |
1367 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1368 |
+ |
painCave.isFatal = 1; |
1369 |
+ |
simError(); |
1370 |
+ |
} |
1371 |
+ |
break; |
1372 |
+ |
|
1373 |
+ |
case NPTf_ENS: |
1374 |
+ |
myNPTf = new NPTf<RealIntegrator>( info, the_ff ); |
1375 |
+ |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1376 |
+ |
|
1377 |
+ |
if (globals->haveTargetPressure()) |
1378 |
+ |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1379 |
+ |
else { |
1380 |
+ |
sprintf( painCave.errMsg, |
1381 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1382 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1383 |
+ |
painCave.isFatal = 1; |
1384 |
+ |
simError(); |
1385 |
+ |
} |
1386 |
+ |
|
1387 |
+ |
if( globals->haveTauThermostat() ) |
1388 |
+ |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1389 |
+ |
else{ |
1390 |
+ |
sprintf( painCave.errMsg, |
1391 |
+ |
"SimSetup error: If you use an NPT\n" |
1392 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1393 |
+ |
painCave.isFatal = 1; |
1394 |
+ |
simError(); |
1395 |
+ |
} |
1396 |
+ |
|
1397 |
+ |
if( globals->haveTauBarostat() ) |
1398 |
+ |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1399 |
+ |
else{ |
1400 |
+ |
sprintf( painCave.errMsg, |
1401 |
+ |
"SimSetup error: If you use an NPT\n" |
1402 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1403 |
+ |
painCave.isFatal = 1; |
1404 |
+ |
simError(); |
1405 |
+ |
} |
1406 |
+ |
break; |
1407 |
+ |
|
1408 |
+ |
case NPTim_ENS: |
1409 |
+ |
myNPTim = new NPTim<RealIntegrator>( info, the_ff ); |
1410 |
+ |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1411 |
+ |
|
1412 |
+ |
if (globals->haveTargetPressure()) |
1413 |
+ |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1414 |
+ |
else { |
1415 |
+ |
sprintf( painCave.errMsg, |
1416 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1417 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1418 |
+ |
painCave.isFatal = 1; |
1419 |
+ |
simError(); |
1420 |
+ |
} |
1421 |
+ |
|
1422 |
+ |
if( globals->haveTauThermostat() ) |
1423 |
+ |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1424 |
+ |
else{ |
1425 |
+ |
sprintf( painCave.errMsg, |
1426 |
+ |
"SimSetup error: If you use an NPT\n" |
1427 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1428 |
+ |
painCave.isFatal = 1; |
1429 |
+ |
simError(); |
1430 |
+ |
} |
1431 |
+ |
|
1432 |
+ |
if( globals->haveTauBarostat() ) |
1433 |
+ |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1434 |
+ |
else{ |
1435 |
+ |
sprintf( painCave.errMsg, |
1436 |
+ |
"SimSetup error: If you use an NPT\n" |
1437 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1438 |
+ |
painCave.isFatal = 1; |
1439 |
+ |
simError(); |
1440 |
+ |
} |
1441 |
+ |
break; |
1442 |
+ |
|
1443 |
+ |
case NPTfm_ENS: |
1444 |
+ |
myNPTfm = new NPTfm<RealIntegrator>( info, the_ff ); |
1445 |
+ |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1446 |
+ |
|
1447 |
+ |
if (globals->haveTargetPressure()) |
1448 |
+ |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1449 |
+ |
else { |
1450 |
+ |
sprintf( painCave.errMsg, |
1451 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1452 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1453 |
+ |
painCave.isFatal = 1; |
1454 |
+ |
simError(); |
1455 |
+ |
} |
1456 |
+ |
|
1457 |
+ |
if( globals->haveTauThermostat() ) |
1458 |
+ |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1459 |
+ |
else{ |
1460 |
+ |
sprintf( painCave.errMsg, |
1461 |
+ |
"SimSetup error: If you use an NPT\n" |
1462 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1463 |
+ |
painCave.isFatal = 1; |
1464 |
+ |
simError(); |
1465 |
+ |
} |
1466 |
+ |
|
1467 |
+ |
if( globals->haveTauBarostat() ) |
1468 |
+ |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1469 |
+ |
else{ |
1470 |
+ |
sprintf( painCave.errMsg, |
1471 |
+ |
"SimSetup error: If you use an NPT\n" |
1472 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1473 |
+ |
painCave.isFatal = 1; |
1474 |
+ |
simError(); |
1475 |
+ |
} |
1476 |
+ |
break; |
1477 |
+ |
|
1478 |
+ |
case NVEZCONS_ENS: |
1479 |
+ |
{ |
1480 |
+ |
|
1481 |
+ |
if(globals->haveZConsTime()){ |
1482 |
+ |
|
1483 |
+ |
//add sample time of z-constraint into SimInfo's property list |
1484 |
+ |
DoubleData* zconsTimeProp = new DoubleData(); |
1485 |
+ |
zconsTimeProp->setID("zconstime"); |
1486 |
+ |
zconsTimeProp->setData(globals->getZConsTime()); |
1487 |
+ |
info->addProperty(zconsTimeProp); |
1488 |
+ |
} |
1489 |
+ |
else{ |
1490 |
+ |
sprintf( painCave.errMsg, |
1491 |
+ |
"ZConstraint error: If you use an ZConstraint\n" |
1492 |
+ |
" , you must set sample time.\n"); |
1493 |
+ |
painCave.isFatal = 1; |
1494 |
+ |
simError(); |
1495 |
+ |
} |
1496 |
+ |
|
1497 |
+ |
if(globals->haveIndexOfAllZConsMols()){ |
1498 |
+ |
|
1499 |
+ |
//add index of z-constraint molecules into SimInfo's property list |
1500 |
+ |
vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1501 |
+ |
sort(tempIndex.begin(), tempIndex.end()); |
1502 |
+ |
|
1503 |
+ |
IndexData* zconsIndex = new IndexData(); |
1504 |
+ |
zconsIndex->setID("zconsindex"); |
1505 |
+ |
zconsIndex->setIndexData(tempIndex); |
1506 |
+ |
info->addProperty(zconsIndex); |
1507 |
+ |
} |
1508 |
+ |
else{ |
1509 |
+ |
sprintf( painCave.errMsg, |
1510 |
+ |
"SimSetup error: If you use an ZConstraint\n" |
1511 |
+ |
" , you must set index of z-constraint molecules.\n"); |
1512 |
+ |
painCave.isFatal = 1; |
1513 |
+ |
simError(); |
1514 |
+ |
|
1515 |
+ |
} |
1516 |
+ |
|
1517 |
+ |
//Determine the name of ouput file and add it into SimInfo's property list |
1518 |
+ |
//Be careful, do not use inFileName, since it is a pointer which |
1519 |
+ |
//point to a string at master node, and slave nodes do not contain that string |
1520 |
+ |
|
1521 |
+ |
string zconsOutput(info->finalName); |
1522 |
+ |
|
1523 |
+ |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1524 |
+ |
|
1525 |
+ |
StringData* zconsFilename = new StringData(); |
1526 |
+ |
zconsFilename->setID("zconsfilename"); |
1527 |
+ |
zconsFilename->setData(zconsOutput); |
1528 |
+ |
|
1529 |
+ |
info->addProperty(zconsFilename); |
1530 |
+ |
|
1531 |
+ |
myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff ); |
1532 |
+ |
|
1533 |
+ |
break; |
1534 |
+ |
} |
1535 |
+ |
|
1536 |
+ |
default: |
1537 |
+ |
sprintf( painCave.errMsg, |
1538 |
+ |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1539 |
+ |
painCave.isFatal = 1; |
1540 |
+ |
simError(); |
1541 |
+ |
} |
1542 |
+ |
|
1543 |
+ |
} |
1544 |
+ |
|
1545 |
+ |
void SimSetup::initFortran( void ){ |
1546 |
+ |
|
1547 |
+ |
info->refreshSim(); |
1548 |
+ |
|
1549 |
+ |
if( !strcmp( info->mixingRule, "standard") ){ |
1550 |
+ |
the_ff->initForceField( LB_MIXING_RULE ); |
1551 |
+ |
} |
1552 |
+ |
else if( !strcmp( info->mixingRule, "explicit") ){ |
1553 |
+ |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1554 |
+ |
} |
1555 |
+ |
else{ |
1556 |
+ |
sprintf( painCave.errMsg, |
1557 |
+ |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1558 |
+ |
info->mixingRule ); |
1559 |
+ |
painCave.isFatal = 1; |
1560 |
+ |
simError(); |
1561 |
+ |
} |
1562 |
+ |
|
1563 |
+ |
|
1564 |
+ |
#ifdef IS_MPI |
1565 |
+ |
strcpy( checkPointMsg, |
1566 |
+ |
"Successfully intialized the mixingRule for Fortran." ); |
1567 |
+ |
MPIcheckPoint(); |
1568 |
+ |
#endif // is_mpi |
1569 |
+ |
|
1570 |
+ |
} |