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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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#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; |
38 |
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|
39 |
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stamps = new MakeStamps(); |
40 |
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globals = new Globals(); |
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|
42 |
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|
43 |
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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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|
96 |
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void SimSetup::createSim( void ){ |
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|
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MakeStamps *the_stamps; |
82 |
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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]; |
101 |
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for(i=0; i<info->n_atoms; i++){ |
102 |
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info->identArray[i] = the_atoms[i]->getIdent(); |
103 |
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} |
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|
105 |
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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 ){ |
140 |
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|
141 |
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case NVE_ENS: |
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new NVE( info, the_ff ); |
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break; |
144 |
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|
145 |
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case NVT_ENS: |
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myNVT = new NVT( info, the_ff ); |
147 |
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myNVT->setTargetTemp(the_globals->getTargetTemp()); |
148 |
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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 { |
153 |
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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() ); |
164 |
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|
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if (the_globals->haveTargetPressure()) |
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myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
167 |
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else { |
168 |
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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, |
179 |
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"SimSetup error: If you use an NPT\n" |
180 |
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" ensemble, you must set tauThermostat.\n"); |
181 |
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painCave.isFatal = 1; |
182 |
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simError(); |
183 |
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} |
184 |
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|
185 |
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if( the_globals->haveTauBarostat() ) |
186 |
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myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
187 |
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else{ |
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sprintf( painCave.errMsg, |
189 |
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"SimSetup error: If you use an NPT\n" |
190 |
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" ensemble, you must set tauBarostat.\n"); |
191 |
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painCave.isFatal = 1; |
192 |
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simError(); |
193 |
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} |
194 |
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break; |
195 |
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|
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case NPTf_ENS: |
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myNPTf = new NPTf( info, the_ff ); |
198 |
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myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
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|
200 |
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if (the_globals->haveTargetPressure()) |
201 |
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myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
202 |
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else { |
203 |
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sprintf( painCave.errMsg, |
204 |
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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"); |
206 |
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painCave.isFatal = 1; |
207 |
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simError(); |
208 |
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} |
209 |
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|
210 |
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if( the_globals->haveTauThermostat() ) |
211 |
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myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
212 |
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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() ); |
222 |
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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"); |
226 |
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painCave.isFatal = 1; |
227 |
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simError(); |
228 |
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} |
229 |
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break; |
230 |
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|
231 |
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case NPTim_ENS: |
232 |
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myNPTim = new NPTim( info, the_ff ); |
233 |
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myNPTim->setTargetTemp( the_globals->getTargetTemp()); |
234 |
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|
235 |
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if (the_globals->haveTargetPressure()) |
236 |
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myNPTim->setTargetPressure(the_globals->getTargetPressure()); |
237 |
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else { |
238 |
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sprintf( painCave.errMsg, |
239 |
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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"); |
241 |
– |
painCave.isFatal = 1; |
242 |
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simError(); |
243 |
– |
} |
244 |
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|
245 |
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if( the_globals->haveTauThermostat() ) |
246 |
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myNPTim->setTauThermostat( the_globals->getTauThermostat() ); |
247 |
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else{ |
248 |
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sprintf( painCave.errMsg, |
249 |
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"SimSetup error: If you use an NPT\n" |
250 |
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" ensemble, you must set tauThermostat.\n"); |
251 |
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painCave.isFatal = 1; |
252 |
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simError(); |
253 |
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} |
254 |
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|
255 |
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if( the_globals->haveTauBarostat() ) |
256 |
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myNPTim->setTauBarostat( the_globals->getTauBarostat() ); |
257 |
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else{ |
258 |
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sprintf( painCave.errMsg, |
259 |
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"SimSetup error: If you use an NPT\n" |
260 |
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" ensemble, you must set tauBarostat.\n"); |
261 |
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painCave.isFatal = 1; |
262 |
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simError(); |
263 |
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} |
264 |
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break; |
265 |
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|
266 |
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case NPTfm_ENS: |
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myNPTfm = new NPTfm( info, the_ff ); |
268 |
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myNPTfm->setTargetTemp( the_globals->getTargetTemp()); |
269 |
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|
270 |
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if (the_globals->haveTargetPressure()) |
271 |
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myNPTfm->setTargetPressure(the_globals->getTargetPressure()); |
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else { |
273 |
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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; |
277 |
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simError(); |
278 |
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} |
279 |
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|
280 |
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if( the_globals->haveTauThermostat() ) |
281 |
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myNPTfm->setTauThermostat( the_globals->getTauThermostat() ); |
282 |
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else{ |
283 |
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sprintf( painCave.errMsg, |
284 |
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"SimSetup error: If you use an NPT\n" |
285 |
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" ensemble, you must set tauThermostat.\n"); |
286 |
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painCave.isFatal = 1; |
287 |
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simError(); |
288 |
– |
} |
289 |
– |
|
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 |
– |
" 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, |
303 |
– |
"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 |
– |
|
125 |
|
#ifdef IS_MPI |
126 |
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mpiSim->mpiRefresh(); |
127 |
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#endif |
128 |
|
|
129 |
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// initialize the Fortran |
130 |
|
|
131 |
+ |
initFortran(); |
132 |
|
|
316 |
– |
info->refreshSim(); |
317 |
– |
|
318 |
– |
if( !strcmp( info->mixingRule, "standard") ){ |
319 |
– |
the_ff->initForceField( LB_MIXING_RULE ); |
320 |
– |
} |
321 |
– |
else if( !strcmp( info->mixingRule, "explicit") ){ |
322 |
– |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
323 |
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} |
324 |
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else{ |
325 |
– |
sprintf( painCave.errMsg, |
326 |
– |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
327 |
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info->mixingRule ); |
328 |
– |
painCave.isFatal = 1; |
329 |
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simError(); |
330 |
– |
} |
133 |
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|
134 |
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|
333 |
– |
#ifdef IS_MPI |
334 |
– |
strcpy( checkPointMsg, |
335 |
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"Successfully intialized the mixingRule for Fortran." ); |
336 |
– |
MPIcheckPoint(); |
337 |
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#endif // is_mpi |
135 |
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} |
136 |
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|
137 |
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|
138 |
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void SimSetup::makeMolecules( void ){ |
139 |
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|
140 |
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int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
141 |
< |
molInit info; |
141 |
> |
molInit molInfo; |
142 |
|
DirectionalAtom* dAtom; |
143 |
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LinkedAssign* extras; |
144 |
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LinkedAssign* current_extra; |
167 |
|
|
168 |
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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 |
|
info->n_oriented++; |
195 |
< |
info.myAtoms[j] = dAtom; |
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 = info->boxLx / temp3; |
419 |
< |
celly = info->boxLy / temp3; |
420 |
< |
cellz = info->boxLz / 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 = info->boxLx / temp3; |
436 |
< |
celly = info->boxLy / temp3; |
437 |
< |
cellz = info->boxLz / 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; |
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 |
< |
the_stamps = stamps; |
591 |
< |
the_globals = globals; |
590 |
> |
stamps = stamps; |
591 |
> |
globals = globals; |
592 |
|
|
593 |
|
// set the easy ones first |
594 |
< |
info->target_temp = the_globals->getTargetTemp(); |
595 |
< |
info->dt = the_globals->getDt(); |
596 |
< |
info->run_time = the_globals->getRunTime(); |
597 |
< |
n_components = the_globals->getNComponents(); |
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, the_globals->getForceField() ); |
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", |
614 |
|
|
615 |
|
// get the ensemble |
616 |
|
|
617 |
< |
strcpy( ensemble, the_globals->getEnsemble() ); |
617 |
> |
strcpy( ensemble, globals->getEnsemble() ); |
618 |
|
|
619 |
|
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
620 |
|
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_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, " |
638 |
|
|
639 |
|
// get the mixing rule |
640 |
|
|
641 |
< |
strcpy( info->mixingRule, the_globals->getMixingRule() ); |
642 |
< |
info->usePBC = the_globals->getPBC(); |
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 = the_globals->getComponents(); |
647 |
> |
the_components = globals->getComponents(); |
648 |
|
components_nmol = new int[n_components]; |
649 |
|
|
650 |
|
|
651 |
< |
if( !the_globals->haveNMol() ){ |
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 |
|
|
681 |
|
|
682 |
|
// set the status, sample, and thermal kick times |
683 |
|
|
684 |
< |
if( the_globals->haveSampleTime() ){ |
685 |
< |
info->sampleTime = the_globals->getSampleTime(); |
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 = the_globals->getRunTime(); |
690 |
> |
info->sampleTime = globals->getRunTime(); |
691 |
|
info->statusTime = info->sampleTime; |
692 |
|
info->thermalTime = info->sampleTime; |
693 |
|
} |
694 |
|
|
695 |
< |
if( the_globals->haveStatusTime() ){ |
696 |
< |
info->statusTime = the_globals->getStatusTime(); |
695 |
> |
if( globals->haveStatusTime() ){ |
696 |
> |
info->statusTime = globals->getStatusTime(); |
697 |
|
} |
698 |
|
|
699 |
< |
if( the_globals->haveThermalTime() ){ |
700 |
< |
info->thermalTime = the_globals->getThermalTime(); |
699 |
> |
if( globals->haveThermalTime() ){ |
700 |
> |
info->thermalTime = globals->getThermalTime(); |
701 |
|
} |
702 |
|
|
703 |
|
// check for the temperature set flag |
704 |
|
|
705 |
< |
if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet(); |
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( the_globals->haveBox() ){ |
711 |
< |
boxVector[0] = the_globals->getBox(); |
712 |
< |
boxVector[1] = the_globals->getBox(); |
713 |
< |
boxVector[2] = the_globals->getBox(); |
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( the_globals->haveDensity() ){ |
717 |
> |
else if( globals->haveDensity() ){ |
718 |
|
|
719 |
|
double vol; |
720 |
< |
vol = (double)tot_nmol / the_globals->getDensity(); |
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]; |
725 |
|
info->setBox( boxVector ); |
726 |
|
} |
727 |
|
else{ |
728 |
< |
if( !the_globals->haveBoxX() ){ |
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] = the_globals->getBoxX(); |
734 |
> |
boxVector[0] = globals->getBoxX(); |
735 |
|
|
736 |
< |
if( !the_globals->haveBoxY() ){ |
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] = the_globals->getBoxY(); |
742 |
> |
boxVector[1] = globals->getBoxY(); |
743 |
|
|
744 |
< |
if( !the_globals->haveBoxZ() ){ |
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] = the_globals->getBoxZ(); |
750 |
> |
boxVector[2] = globals->getBoxZ(); |
751 |
|
|
752 |
|
info->setBox( boxVector ); |
753 |
|
} |
777 |
|
} |
778 |
|
|
779 |
|
#ifdef IS_MPI |
780 |
< |
int myUse = usesDipoles |
781 |
< |
MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
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 (the_globals->getUseRF() ) { |
786 |
> |
if (globals->getUseRF() ) { |
787 |
|
info->useReactionField = 1; |
788 |
|
|
789 |
< |
if( !the_globals->haveECR() ){ |
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" |
794 |
|
painCave.isFatal = 0; |
795 |
|
simError(); |
796 |
|
double smallest; |
797 |
< |
smallest = info->boxLx; |
798 |
< |
if (info->boxLy <= smallest) smallest = info->boxLy; |
799 |
< |
if (info->boxLz <= smallest) smallest = info->boxLz; |
800 |
< |
info->ecr = 0.5 * 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 |
< |
info->ecr = the_globals->getECR(); |
802 |
> |
theEcr = globals->getECR(); |
803 |
|
} |
804 |
|
|
805 |
< |
if( !the_globals->haveEST() ){ |
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 |
< |
info->est = 0.05 * info->ecr; |
812 |
> |
theEst = 0.05 * theEcr; |
813 |
|
} else { |
814 |
< |
info->est = the_globals->getEST(); |
814 |
> |
theEst= globals->getEST(); |
815 |
|
} |
816 |
+ |
|
817 |
+ |
info->setEcr( theEcr, theEst ); |
818 |
|
|
819 |
< |
if(!the_globals->haveDielectric() ){ |
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" |
824 |
|
painCave.isFatal = 1; |
825 |
|
simError(); |
826 |
|
} |
827 |
< |
info->dielectric = the_globals->getDielectric(); |
827 |
> |
info->dielectric = globals->getDielectric(); |
828 |
|
} |
829 |
|
else { |
830 |
|
if (usesDipoles) { |
831 |
|
|
832 |
< |
if( !the_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->boxLx; |
841 |
< |
if (info->boxLy <= smallest) smallest = info->boxLy; |
842 |
< |
if (info->boxLz <= smallest) smallest = info->boxLz; |
843 |
< |
info->ecr = 0.5 * smallest; |
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 |
< |
info->ecr = the_globals->getECR(); |
845 |
> |
theEcr = globals->getECR(); |
846 |
|
} |
847 |
|
|
848 |
< |
if( !the_globals->haveEST() ){ |
849 |
< |
sprintf( painCave.errMsg, |
850 |
< |
"SimSetup Warning: using default value of 5%% of the " |
851 |
< |
"electrostaticCutoffRadius for the " |
852 |
< |
"electrostaticSkinThickness\n" |
853 |
< |
); |
854 |
< |
painCave.isFatal = 0; |
855 |
< |
simError(); |
856 |
< |
info->est = 0.05 * info->ecr; |
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 |
< |
info->est = the_globals->getEST(); |
858 |
> |
theEst= globals->getEST(); |
859 |
|
} |
860 |
+ |
|
861 |
+ |
info->setEcr( theEcr, theEst ); |
862 |
|
} |
863 |
|
} |
864 |
|
|
871 |
|
|
872 |
|
void SimSetup::initSystemCoords( void ){ |
873 |
|
|
874 |
< |
if( the_globals->haveInitialConfig() ){ |
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( the_globals->getInitialConfig() ); |
880 |
> |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
881 |
|
#ifdef IS_MPI |
882 |
|
}else fileInit = new InitializeFromFile( NULL ); |
883 |
|
#endif |
884 |
< |
fileInit->read_xyz( info ); // default velocities on |
884 |
> |
fileInit->readInit( info ); // default velocities on |
885 |
|
|
886 |
|
delete fileInit; |
887 |
|
} |
918 |
|
if( worldRank == 0 ){ |
919 |
|
#endif // is_mpi |
920 |
|
|
921 |
< |
if( the_globals->haveFinalConfig() ){ |
922 |
< |
strcpy( info->finalName, the_globals->getFinalConfig() ); |
921 |
> |
if( globals->haveFinalConfig() ){ |
922 |
> |
strcpy( info->finalName, globals->getFinalConfig() ); |
923 |
|
} |
924 |
|
else{ |
925 |
|
strcpy( info->finalName, inFileName ); |
1002 |
|
|
1003 |
|
void SimSetup::sysObjectsCreation( void ){ |
1004 |
|
|
1005 |
+ |
int i; |
1006 |
+ |
|
1007 |
|
// create the forceField |
1008 |
|
|
1009 |
|
createFF(); |
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 |
|
|
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"); |
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. |
1099 |
|
|
1100 |
|
// extract the component from the list; |
1101 |
|
|
1102 |
< |
currentStamp = the_stamps->extractMolStamp( id ); |
1102 |
> |
currentStamp = stamps->extractMolStamp( id ); |
1103 |
|
if( currentStamp == NULL ){ |
1104 |
|
sprintf( painCave.errMsg, |
1105 |
|
"SimSetup error: Component \"%s\" was not found in the " |
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; |
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 |
|
|
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); |
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 |
+ |
} |