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#include <algorithm> |
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#include <cstdlib> |
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#include <iostream> |
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#include <cmath> |
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#include <string> |
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#include <sprng.h> |
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|
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#include "SimSetup.hpp" |
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#include "ReadWrite.hpp" |
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#include "parse_me.h" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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|
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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 NPT_ENS 2 |
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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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|
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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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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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|
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "SimSetup creation successful" ); |
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strcpy(checkPointMsg, "SimSetup creation successful"); |
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MPIcheckPoint(); |
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#endif // IS_MPI |
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} |
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delete globals; |
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} |
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|
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void SimSetup::parseFile( char* fileName ){ |
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void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){ |
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info = the_info; |
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nInfo = theNinfo; |
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isInfoArray = 1; |
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} |
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|
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|
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void SimSetup::parseFile(char* fileName){ |
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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if (worldRank == 0){ |
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#endif // is_mpi |
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|
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|
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inFileName = fileName; |
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set_interface_stamps( stamps, globals ); |
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|
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set_interface_stamps(stamps, globals); |
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|
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#ifdef IS_MPI |
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mpiEventInit(); |
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#endif |
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|
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yacc_BASS( fileName ); |
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yacc_BASS(fileName); |
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|
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#ifdef IS_MPI |
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throwMPIEvent(NULL); |
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} |
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else receiveParse(); |
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else{ |
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receiveParse(); |
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} |
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#endif |
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|
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} |
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|
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#ifdef IS_MPI |
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void SimSetup::receiveParse(void){ |
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|
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set_interface_stamps( stamps, globals ); |
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mpiEventInit(); |
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MPIcheckPoint(); |
69 |
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mpiEventLoop(); |
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|
84 |
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set_interface_stamps(stamps, globals); |
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mpiEventInit(); |
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MPIcheckPoint(); |
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mpiEventLoop(); |
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} |
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|
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#endif // is_mpi |
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|
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void SimSetup::createSim( void ){ |
92 |
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void SimSetup::createSim(void){ |
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|
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MakeStamps *the_stamps; |
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Globals* the_globals; |
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int i, j, k, globalAtomIndex; |
80 |
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|
81 |
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int ensembleCase; |
82 |
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int ffCase; |
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|
84 |
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ensembleCase = -1; |
85 |
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ffCase = -1; |
94 |
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// gather all of the information from the Bass file |
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|
96 |
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// get the stamps and globals; |
88 |
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the_stamps = stamps; |
89 |
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the_globals = globals; |
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gatherInfo(); |
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|
98 |
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// set the easy ones first |
92 |
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simnfo->target_temp = the_globals->getTargetTemp(); |
93 |
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simnfo->dt = the_globals->getDt(); |
94 |
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simnfo->run_time = the_globals->getRunTime(); |
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// creation of complex system objects |
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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() ); |
100 |
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sysObjectsCreation(); |
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|
102 |
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if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
101 |
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else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
102 |
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else{ |
103 |
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sprintf( painCave.errMsg, |
104 |
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"SimSetup Error. Unrecognized force field -> %s\n", |
105 |
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force_field ); |
106 |
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painCave.isFatal = 1; |
107 |
< |
simError(); |
108 |
< |
} |
102 |
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// check on the post processing info |
103 |
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|
104 |
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// get the ensemble: |
111 |
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strcpy( ensemble, the_globals->getEnsemble() ); |
104 |
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finalInfoCheck(); |
105 |
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|
106 |
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if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
114 |
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else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
115 |
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else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS; |
116 |
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else{ |
117 |
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sprintf( painCave.errMsg, |
118 |
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"SimSetup Warning. Unrecognized Ensemble -> %s, " |
119 |
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"reverting to NVE for this simulation.\n", |
120 |
< |
ensemble ); |
121 |
< |
painCave.isFatal = 0; |
122 |
< |
simError(); |
123 |
< |
strcpy( ensemble, "NVE" ); |
124 |
< |
ensembleCase = NVE_ENS; |
125 |
< |
} |
126 |
< |
strcpy( simnfo->ensemble, ensemble ); |
106 |
> |
// initialize the system coordinates |
107 |
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|
108 |
+ |
if (!isInfoArray){ |
109 |
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initSystemCoords(); |
110 |
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|
111 |
< |
// if( !strcasecmp( ensemble, "NPT" ) ) { |
112 |
< |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
113 |
< |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
132 |
< |
// if (the_globals->haveTargetPressure()) |
133 |
< |
// the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
134 |
< |
// else { |
135 |
< |
// sprintf( painCave.errMsg, |
136 |
< |
// "SimSetup error: If you use the constant pressure\n" |
137 |
< |
// " ensemble, you must set targetPressure.\n" |
138 |
< |
// " This was found in the BASS file.\n"); |
139 |
< |
// painCave.isFatal = 1; |
140 |
< |
// simError(); |
141 |
< |
// } |
111 |
> |
if( !(globals->getUseInitTime()) ) |
112 |
> |
info[0].currentTime = 0.0; |
113 |
> |
} |
114 |
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|
115 |
< |
// if (the_globals->haveTauThermostat()) |
144 |
< |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
145 |
< |
// else if (the_globals->haveQmass()) |
146 |
< |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
147 |
< |
// else { |
148 |
< |
// sprintf( painCave.errMsg, |
149 |
< |
// "SimSetup error: If you use one of the constant temperature\n" |
150 |
< |
// " ensembles, you must set either tauThermostat or qMass.\n" |
151 |
< |
// " Neither of these was found in the BASS file.\n"); |
152 |
< |
// painCave.isFatal = 1; |
153 |
< |
// simError(); |
154 |
< |
// } |
115 |
> |
// make the output filenames |
116 |
|
|
117 |
< |
// if (the_globals->haveTauBarostat()) |
157 |
< |
// the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
158 |
< |
// else { |
159 |
< |
// sprintf( painCave.errMsg, |
160 |
< |
// "SimSetup error: If you use the constant pressure\n" |
161 |
< |
// " ensemble, you must set tauBarostat.\n" |
162 |
< |
// " This was found in the BASS file.\n"); |
163 |
< |
// painCave.isFatal = 1; |
164 |
< |
// simError(); |
165 |
< |
// } |
117 |
> |
makeOutNames(); |
118 |
|
|
119 |
< |
// } else if ( !strcasecmp( ensemble, "NVT") ) { |
168 |
< |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
169 |
< |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
119 |
> |
// make the integrator |
120 |
|
|
121 |
< |
// if (the_globals->haveTauThermostat()) |
172 |
< |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
173 |
< |
// else if (the_globals->haveQmass()) |
174 |
< |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
175 |
< |
// else { |
176 |
< |
// sprintf( painCave.errMsg, |
177 |
< |
// "SimSetup error: If you use one of the constant temperature\n" |
178 |
< |
// " ensembles, you must set either tauThermostat or qMass.\n" |
179 |
< |
// " Neither of these was found in the BASS file.\n"); |
180 |
< |
// painCave.isFatal = 1; |
181 |
< |
// simError(); |
182 |
< |
// } |
121 |
> |
makeIntegrator(); |
122 |
|
|
123 |
< |
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
124 |
< |
simnfo->usePBC = the_globals->getPBC(); |
125 |
< |
|
187 |
< |
int usesDipoles = 0; |
188 |
< |
switch( ffCase ){ |
123 |
> |
#ifdef IS_MPI |
124 |
> |
mpiSim->mpiRefresh(); |
125 |
> |
#endif |
126 |
|
|
127 |
< |
case FF_DUFF: |
191 |
< |
the_ff = new DUFF(); |
192 |
< |
usesDipoles = 1; |
193 |
< |
break; |
127 |
> |
// initialize the Fortran |
128 |
|
|
129 |
< |
case FF_LJ: |
130 |
< |
the_ff = new LJFF(); |
197 |
< |
break; |
129 |
> |
initFortran(); |
130 |
> |
} |
131 |
|
|
199 |
– |
default: |
200 |
– |
sprintf( painCave.errMsg, |
201 |
– |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
202 |
– |
painCave.isFatal = 1; |
203 |
– |
simError(); |
204 |
– |
} |
132 |
|
|
133 |
< |
#ifdef IS_MPI |
134 |
< |
strcpy( checkPointMsg, "ForceField creation successful" ); |
135 |
< |
MPIcheckPoint(); |
136 |
< |
#endif // is_mpi |
133 |
> |
void SimSetup::makeMolecules(void){ |
134 |
> |
int k; |
135 |
> |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
136 |
> |
molInit molInfo; |
137 |
> |
DirectionalAtom* dAtom; |
138 |
> |
LinkedAssign* extras; |
139 |
> |
LinkedAssign* current_extra; |
140 |
> |
AtomStamp* currentAtom; |
141 |
> |
BondStamp* currentBond; |
142 |
> |
BendStamp* currentBend; |
143 |
> |
TorsionStamp* currentTorsion; |
144 |
|
|
145 |
< |
// get the components and calculate the tot_nMol and indvidual n_mol |
146 |
< |
the_components = the_globals->getComponents(); |
147 |
< |
components_nmol = new int[n_components]; |
214 |
< |
comp_stamps = new MoleculeStamp*[n_components]; |
145 |
> |
bond_pair* theBonds; |
146 |
> |
bend_set* theBends; |
147 |
> |
torsion_set* theTorsions; |
148 |
|
|
216 |
– |
if( !the_globals->haveNMol() ){ |
217 |
– |
// we don't have the total number of molecules, so we assume it is |
218 |
– |
// given in each component |
149 |
|
|
150 |
< |
tot_nmol = 0; |
221 |
< |
for( i=0; i<n_components; i++ ){ |
150 |
> |
//init the forceField paramters |
151 |
|
|
152 |
< |
if( !the_components[i]->haveNMol() ){ |
224 |
< |
// we have a problem |
225 |
< |
sprintf( painCave.errMsg, |
226 |
< |
"SimSetup Error. No global NMol or component NMol" |
227 |
< |
" given. Cannot calculate the number of atoms.\n" ); |
228 |
< |
painCave.isFatal = 1; |
229 |
< |
simError(); |
230 |
< |
} |
152 |
> |
the_ff->readParams(); |
153 |
|
|
232 |
– |
tot_nmol += the_components[i]->getNMol(); |
233 |
– |
components_nmol[i] = the_components[i]->getNMol(); |
234 |
– |
} |
235 |
– |
} |
236 |
– |
else{ |
237 |
– |
sprintf( painCave.errMsg, |
238 |
– |
"SimSetup error.\n" |
239 |
– |
"\tSorry, the ability to specify total" |
240 |
– |
" nMols and then give molfractions in the components\n" |
241 |
– |
"\tis not currently supported." |
242 |
– |
" Please give nMol in the components.\n" ); |
243 |
– |
painCave.isFatal = 1; |
244 |
– |
simError(); |
245 |
– |
|
246 |
– |
|
247 |
– |
// tot_nmol = the_globals->getNMol(); |
248 |
– |
|
249 |
– |
// //we have the total number of molecules, now we check for molfractions |
250 |
– |
// for( i=0; i<n_components; i++ ){ |
251 |
– |
|
252 |
– |
// if( !the_components[i]->haveMolFraction() ){ |
253 |
– |
|
254 |
– |
// if( !the_components[i]->haveNMol() ){ |
255 |
– |
// //we have a problem |
256 |
– |
// std::cerr << "SimSetup error. Neither molFraction nor " |
257 |
– |
// << " nMol was given in component |
258 |
– |
|
259 |
– |
} |
154 |
|
|
155 |
< |
#ifdef IS_MPI |
262 |
< |
strcpy( checkPointMsg, "Have the number of components" ); |
263 |
< |
MPIcheckPoint(); |
264 |
< |
#endif // is_mpi |
155 |
> |
// init the atoms |
156 |
|
|
157 |
< |
// make an array of molecule stamps that match the components used. |
267 |
< |
// also extract the used stamps out into a separate linked list |
157 |
> |
double ux, uy, uz, u, uSqr; |
158 |
|
|
159 |
< |
simnfo->nComponents = n_components; |
160 |
< |
simnfo->componentsNmol = components_nmol; |
271 |
< |
simnfo->compStamps = comp_stamps; |
272 |
< |
simnfo->headStamp = new LinkedMolStamp(); |
273 |
< |
|
274 |
< |
char* id; |
275 |
< |
LinkedMolStamp* headStamp = simnfo->headStamp; |
276 |
< |
LinkedMolStamp* currentStamp = NULL; |
277 |
< |
for( i=0; i<n_components; i++ ){ |
159 |
> |
for (k = 0; k < nInfo; k++){ |
160 |
> |
the_ff->setSimInfo(&(info[k])); |
161 |
|
|
162 |
< |
id = the_components[i]->getType(); |
163 |
< |
comp_stamps[i] = NULL; |
164 |
< |
|
165 |
< |
// check to make sure the component isn't already in the list |
162 |
> |
atomOffset = 0; |
163 |
> |
excludeOffset = 0; |
164 |
> |
for (i = 0; i < info[k].n_mol; i++){ |
165 |
> |
stampID = info[k].molecules[i].getStampID(); |
166 |
|
|
167 |
< |
comp_stamps[i] = headStamp->match( id ); |
168 |
< |
if( comp_stamps[i] == NULL ){ |
169 |
< |
|
170 |
< |
// extract the component from the list; |
171 |
< |
|
289 |
< |
currentStamp = the_stamps->extractMolStamp( id ); |
290 |
< |
if( currentStamp == NULL ){ |
291 |
< |
sprintf( painCave.errMsg, |
292 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
293 |
< |
"list of declared molecules\n", |
294 |
< |
id ); |
295 |
< |
painCave.isFatal = 1; |
296 |
< |
simError(); |
297 |
< |
} |
298 |
< |
|
299 |
< |
headStamp->add( currentStamp ); |
300 |
< |
comp_stamps[i] = headStamp->match( id ); |
301 |
< |
} |
302 |
< |
} |
167 |
> |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
168 |
> |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
169 |
> |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
170 |
> |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
171 |
> |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
172 |
|
|
173 |
< |
#ifdef IS_MPI |
174 |
< |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
175 |
< |
MPIcheckPoint(); |
176 |
< |
#endif // is_mpi |
177 |
< |
|
173 |
> |
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
174 |
> |
molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
175 |
> |
molInfo.myBonds = new Bond * [molInfo.nBonds]; |
176 |
> |
molInfo.myBends = new Bend * [molInfo.nBends]; |
177 |
> |
molInfo.myTorsions = new Torsion * [molInfo.nTorsions]; |
178 |
|
|
179 |
+ |
theBonds = new bond_pair[molInfo.nBonds]; |
180 |
+ |
theBends = new bend_set[molInfo.nBends]; |
181 |
+ |
theTorsions = new torsion_set[molInfo.nTorsions]; |
182 |
|
|
183 |
+ |
// make the Atoms |
184 |
|
|
185 |
< |
// caclulate the number of atoms, bonds, bends and torsions |
185 |
> |
for (j = 0; j < molInfo.nAtoms; j++){ |
186 |
> |
currentAtom = comp_stamps[stampID]->getAtom(j); |
187 |
> |
if (currentAtom->haveOrientation()){ |
188 |
> |
dAtom = new DirectionalAtom((j + atomOffset), |
189 |
> |
info[k].getConfiguration()); |
190 |
> |
info[k].n_oriented++; |
191 |
> |
molInfo.myAtoms[j] = dAtom; |
192 |
|
|
193 |
< |
tot_atoms = 0; |
194 |
< |
tot_bonds = 0; |
195 |
< |
tot_bends = 0; |
317 |
< |
tot_torsions = 0; |
318 |
< |
for( i=0; i<n_components; i++ ){ |
319 |
< |
|
320 |
< |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
321 |
< |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
322 |
< |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
323 |
< |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
324 |
< |
} |
193 |
> |
ux = currentAtom->getOrntX(); |
194 |
> |
uy = currentAtom->getOrntY(); |
195 |
> |
uz = currentAtom->getOrntZ(); |
196 |
|
|
197 |
< |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
197 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
198 |
|
|
199 |
< |
simnfo->n_atoms = tot_atoms; |
200 |
< |
simnfo->n_bonds = tot_bonds; |
201 |
< |
simnfo->n_bends = tot_bends; |
202 |
< |
simnfo->n_torsions = tot_torsions; |
332 |
< |
simnfo->n_SRI = tot_SRI; |
333 |
< |
simnfo->n_mol = tot_nmol; |
334 |
< |
|
335 |
< |
simnfo->molMembershipArray = new int[tot_atoms]; |
199 |
> |
u = sqrt(uSqr); |
200 |
> |
ux = ux / u; |
201 |
> |
uy = uy / u; |
202 |
> |
uz = uz / u; |
203 |
|
|
204 |
+ |
dAtom->setSUx(ux); |
205 |
+ |
dAtom->setSUy(uy); |
206 |
+ |
dAtom->setSUz(uz); |
207 |
+ |
} |
208 |
+ |
else{ |
209 |
+ |
molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
210 |
+ |
info[k].getConfiguration()); |
211 |
+ |
} |
212 |
+ |
molInfo.myAtoms[j]->setType(currentAtom->getType()); |
213 |
+ |
|
214 |
|
#ifdef IS_MPI |
215 |
|
|
216 |
< |
// divide the molecules among processors here. |
340 |
< |
|
341 |
< |
mpiSim = new mpiSimulation( simnfo ); |
342 |
< |
|
343 |
< |
globalIndex = mpiSim->divideLabor(); |
216 |
> |
molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
217 |
|
|
218 |
< |
// set up the local variables |
219 |
< |
|
347 |
< |
int localMol, allMol; |
348 |
< |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
218 |
> |
#endif // is_mpi |
219 |
> |
} |
220 |
|
|
221 |
< |
int* mol2proc = mpiSim->getMolToProcMap(); |
222 |
< |
int* molCompType = mpiSim->getMolComponentType(); |
223 |
< |
|
224 |
< |
allMol = 0; |
225 |
< |
localMol = 0; |
355 |
< |
local_atoms = 0; |
356 |
< |
local_bonds = 0; |
357 |
< |
local_bends = 0; |
358 |
< |
local_torsions = 0; |
359 |
< |
globalAtomIndex = 0; |
221 |
> |
// make the bonds |
222 |
> |
for (j = 0; j < molInfo.nBonds; j++){ |
223 |
> |
currentBond = comp_stamps[stampID]->getBond(j); |
224 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
225 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
226 |
|
|
227 |
+ |
exI = theBonds[j].a; |
228 |
+ |
exJ = theBonds[j].b; |
229 |
|
|
230 |
< |
for( i=0; i<n_components; i++ ){ |
230 |
> |
// exclude_I must always be the smaller of the pair |
231 |
> |
if (exI > exJ){ |
232 |
> |
tempEx = exI; |
233 |
> |
exI = exJ; |
234 |
> |
exJ = tempEx; |
235 |
> |
} |
236 |
> |
#ifdef IS_MPI |
237 |
> |
tempEx = exI; |
238 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
239 |
> |
tempEx = exJ; |
240 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
241 |
|
|
242 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
243 |
< |
|
244 |
< |
if( mol2proc[allMol] == worldRank ){ |
245 |
< |
|
246 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
369 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
370 |
< |
local_bends += comp_stamps[i]->getNBends(); |
371 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
372 |
< |
localMol++; |
373 |
< |
} |
374 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
375 |
< |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
376 |
< |
globalAtomIndex++; |
242 |
> |
info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
243 |
> |
#else // isn't MPI |
244 |
> |
|
245 |
> |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
246 |
> |
#endif //is_mpi |
247 |
|
} |
248 |
+ |
excludeOffset += molInfo.nBonds; |
249 |
|
|
250 |
< |
allMol++; |
251 |
< |
} |
252 |
< |
} |
253 |
< |
local_SRI = local_bonds + local_bends + local_torsions; |
254 |
< |
|
255 |
< |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
385 |
< |
|
386 |
< |
if( local_atoms != simnfo->n_atoms ){ |
387 |
< |
sprintf( painCave.errMsg, |
388 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
389 |
< |
" localAtom (%d) are not equal.\n", |
390 |
< |
simnfo->n_atoms, |
391 |
< |
local_atoms ); |
392 |
< |
painCave.isFatal = 1; |
393 |
< |
simError(); |
394 |
< |
} |
250 |
> |
//make the bends |
251 |
> |
for (j = 0; j < molInfo.nBends; j++){ |
252 |
> |
currentBend = comp_stamps[stampID]->getBend(j); |
253 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
254 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
255 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
256 |
|
|
257 |
< |
simnfo->n_bonds = local_bonds; |
258 |
< |
simnfo->n_bends = local_bends; |
259 |
< |
simnfo->n_torsions = local_torsions; |
399 |
< |
simnfo->n_SRI = local_SRI; |
400 |
< |
simnfo->n_mol = localMol; |
257 |
> |
if (currentBend->haveExtras()){ |
258 |
> |
extras = currentBend->getExtras(); |
259 |
> |
current_extra = extras; |
260 |
|
|
261 |
< |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
262 |
< |
MPIcheckPoint(); |
263 |
< |
|
264 |
< |
|
265 |
< |
#endif // is_mpi |
266 |
< |
|
261 |
> |
while (current_extra != NULL){ |
262 |
> |
if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
263 |
> |
switch (current_extra->getType()){ |
264 |
> |
case 0: |
265 |
> |
theBends[j].ghost = current_extra->getInt() + atomOffset; |
266 |
> |
theBends[j].isGhost = 1; |
267 |
> |
break; |
268 |
|
|
269 |
< |
// create the atom and short range interaction arrays |
269 |
> |
case 1: |
270 |
> |
theBends[j].ghost = (int) current_extra->getDouble() + |
271 |
> |
atomOffset; |
272 |
> |
theBends[j].isGhost = 1; |
273 |
> |
break; |
274 |
|
|
275 |
< |
Atom::createArrays(simnfo->n_atoms); |
276 |
< |
the_atoms = new Atom*[simnfo->n_atoms]; |
277 |
< |
the_molecules = new Molecule[simnfo->n_mol]; |
278 |
< |
int molIndex; |
275 |
> |
default: |
276 |
> |
sprintf(painCave.errMsg, |
277 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
278 |
> |
"double nor an int.\n" |
279 |
> |
"-->Bend[%d] in %s\n", |
280 |
> |
j, comp_stamps[stampID]->getID()); |
281 |
> |
painCave.isFatal = 1; |
282 |
> |
simError(); |
283 |
> |
} |
284 |
> |
} |
285 |
> |
else{ |
286 |
> |
sprintf(painCave.errMsg, |
287 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
288 |
> |
" -->%s in Bend[%d] in %s\n", |
289 |
> |
current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
290 |
> |
painCave.isFatal = 1; |
291 |
> |
simError(); |
292 |
> |
} |
293 |
|
|
294 |
< |
// initialize the molecule's stampID's |
294 |
> |
current_extra = current_extra->getNext(); |
295 |
> |
} |
296 |
> |
} |
297 |
|
|
298 |
+ |
if (!theBends[j].isGhost){ |
299 |
+ |
exI = theBends[j].a; |
300 |
+ |
exJ = theBends[j].c; |
301 |
+ |
} |
302 |
+ |
else{ |
303 |
+ |
exI = theBends[j].a; |
304 |
+ |
exJ = theBends[j].b; |
305 |
+ |
} |
306 |
+ |
|
307 |
+ |
// exclude_I must always be the smaller of the pair |
308 |
+ |
if (exI > exJ){ |
309 |
+ |
tempEx = exI; |
310 |
+ |
exI = exJ; |
311 |
+ |
exJ = tempEx; |
312 |
+ |
} |
313 |
|
#ifdef IS_MPI |
314 |
< |
|
314 |
> |
tempEx = exI; |
315 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
316 |
> |
tempEx = exJ; |
317 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
318 |
|
|
319 |
< |
molIndex = 0; |
320 |
< |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
321 |
< |
|
322 |
< |
if(mol2proc[i] == worldRank ){ |
323 |
< |
the_molecules[molIndex].setStampID( molCompType[i] ); |
324 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
427 |
< |
the_molecules[molIndex].setGlobalIndex( i ); |
428 |
< |
molIndex++; |
429 |
< |
} |
430 |
< |
} |
319 |
> |
info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
320 |
> |
#else // isn't MPI |
321 |
> |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
322 |
> |
#endif //is_mpi |
323 |
> |
} |
324 |
> |
excludeOffset += molInfo.nBends; |
325 |
|
|
326 |
< |
#else // is_mpi |
327 |
< |
|
328 |
< |
molIndex = 0; |
329 |
< |
globalAtomIndex = 0; |
330 |
< |
for(i=0; i<n_components; i++){ |
331 |
< |
for(j=0; j<components_nmol[i]; j++ ){ |
438 |
< |
the_molecules[molIndex].setStampID( i ); |
439 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
440 |
< |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
441 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
442 |
< |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
443 |
< |
globalAtomIndex++; |
444 |
< |
} |
445 |
< |
molIndex++; |
446 |
< |
} |
447 |
< |
} |
448 |
< |
|
326 |
> |
for (j = 0; j < molInfo.nTorsions; j++){ |
327 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion(j); |
328 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
329 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
330 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
331 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
332 |
|
|
333 |
< |
#endif // is_mpi |
333 |
> |
exI = theTorsions[j].a; |
334 |
> |
exJ = theTorsions[j].d; |
335 |
|
|
336 |
+ |
// exclude_I must always be the smaller of the pair |
337 |
+ |
if (exI > exJ){ |
338 |
+ |
tempEx = exI; |
339 |
+ |
exI = exJ; |
340 |
+ |
exJ = tempEx; |
341 |
+ |
} |
342 |
+ |
#ifdef IS_MPI |
343 |
+ |
tempEx = exI; |
344 |
+ |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
345 |
+ |
tempEx = exJ; |
346 |
+ |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
347 |
|
|
348 |
< |
if( simnfo->n_SRI ){ |
349 |
< |
|
350 |
< |
Exclude::createArray(simnfo->n_SRI); |
351 |
< |
the_excludes = new Exclude*[simnfo->n_SRI]; |
352 |
< |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
353 |
< |
simnfo->globalExcludes = new int; |
459 |
< |
simnfo->n_exclude = simnfo->n_SRI; |
460 |
< |
} |
461 |
< |
else{ |
462 |
< |
|
463 |
< |
Exclude::createArray( 1 ); |
464 |
< |
the_excludes = new Exclude*; |
465 |
< |
the_excludes[0] = new Exclude(0); |
466 |
< |
the_excludes[0]->setPair( 0,0 ); |
467 |
< |
simnfo->globalExcludes = new int; |
468 |
< |
simnfo->globalExcludes[0] = 0; |
469 |
< |
simnfo->n_exclude = 0; |
470 |
< |
} |
348 |
> |
info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
349 |
> |
#else // isn't MPI |
350 |
> |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
351 |
> |
#endif //is_mpi |
352 |
> |
} |
353 |
> |
excludeOffset += molInfo.nTorsions; |
354 |
|
|
472 |
– |
// set the arrays into the SimInfo object |
355 |
|
|
356 |
< |
simnfo->atoms = the_atoms; |
475 |
< |
simnfo->molecules = the_molecules; |
476 |
< |
simnfo->nGlobalExcludes = 0; |
477 |
< |
simnfo->excludes = the_excludes; |
356 |
> |
// send the arrays off to the forceField for init. |
357 |
|
|
358 |
+ |
the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
359 |
+ |
the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
360 |
+ |
the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
361 |
+ |
the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
362 |
+ |
theTorsions); |
363 |
|
|
480 |
– |
// get some of the tricky things that may still be in the globals |
364 |
|
|
365 |
< |
double boxVector[3]; |
483 |
< |
if( the_globals->haveBox() ){ |
484 |
< |
boxVector[0] = the_globals->getBox(); |
485 |
< |
boxVector[1] = the_globals->getBox(); |
486 |
< |
boxVector[2] = the_globals->getBox(); |
487 |
< |
|
488 |
< |
simnfo->setBox( boxVector ); |
489 |
< |
} |
490 |
< |
else if( the_globals->haveDensity() ){ |
365 |
> |
info[k].molecules[i].initialize(molInfo); |
366 |
|
|
492 |
– |
double vol; |
493 |
– |
vol = (double)tot_nmol / the_globals->getDensity(); |
494 |
– |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
495 |
– |
boxVector[1] = boxVector[0]; |
496 |
– |
boxVector[2] = boxVector[0]; |
367 |
|
|
368 |
< |
simnfo->setBox( boxVector ); |
369 |
< |
} |
370 |
< |
else{ |
371 |
< |
if( !the_globals->haveBoxX() ){ |
502 |
< |
sprintf( painCave.errMsg, |
503 |
< |
"SimSetup error, no periodic BoxX size given.\n" ); |
504 |
< |
painCave.isFatal = 1; |
505 |
< |
simError(); |
368 |
> |
atomOffset += molInfo.nAtoms; |
369 |
> |
delete[] theBonds; |
370 |
> |
delete[] theBends; |
371 |
> |
delete[] theTorsions; |
372 |
|
} |
507 |
– |
boxVector[0] = the_globals->getBoxX(); |
508 |
– |
|
509 |
– |
if( !the_globals->haveBoxY() ){ |
510 |
– |
sprintf( painCave.errMsg, |
511 |
– |
"SimSetup error, no periodic BoxY size given.\n" ); |
512 |
– |
painCave.isFatal = 1; |
513 |
– |
simError(); |
514 |
– |
} |
515 |
– |
boxVector[1] = the_globals->getBoxY(); |
516 |
– |
|
517 |
– |
if( !the_globals->haveBoxZ() ){ |
518 |
– |
sprintf( painCave.errMsg, |
519 |
– |
"SimSetup error, no periodic BoxZ size given.\n" ); |
520 |
– |
painCave.isFatal = 1; |
521 |
– |
simError(); |
522 |
– |
} |
523 |
– |
boxVector[2] = the_globals->getBoxZ(); |
524 |
– |
|
525 |
– |
simnfo->setBox( boxVector ); |
373 |
|
} |
374 |
|
|
375 |
|
#ifdef IS_MPI |
376 |
< |
strcpy( checkPointMsg, "Box size set up" ); |
376 |
> |
sprintf(checkPointMsg, "all molecules initialized succesfully"); |
377 |
|
MPIcheckPoint(); |
378 |
|
#endif // is_mpi |
379 |
|
|
380 |
+ |
// clean up the forcefield |
381 |
|
|
382 |
< |
// initialize the arrays |
382 |
> |
the_ff->calcRcut(); |
383 |
> |
the_ff->cleanMe(); |
384 |
> |
} |
385 |
|
|
386 |
< |
the_ff->setSimInfo( simnfo ); |
386 |
> |
void SimSetup::initFromBass(void){ |
387 |
> |
int i, j, k; |
388 |
> |
int n_cells; |
389 |
> |
double cellx, celly, cellz; |
390 |
> |
double temp1, temp2, temp3; |
391 |
> |
int n_per_extra; |
392 |
> |
int n_extra; |
393 |
> |
int have_extra, done; |
394 |
|
|
395 |
< |
makeMolecules(); |
396 |
< |
simnfo->identArray = new int[simnfo->n_atoms]; |
397 |
< |
for(i=0; i<simnfo->n_atoms; i++){ |
398 |
< |
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
542 |
< |
} |
543 |
< |
|
544 |
< |
if (the_globals->getUseRF() ) { |
545 |
< |
simnfo->useReactionField = 1; |
546 |
< |
|
547 |
< |
if( !the_globals->haveECR() ){ |
548 |
< |
sprintf( painCave.errMsg, |
549 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
550 |
< |
"box length for the electrostaticCutoffRadius.\n" |
551 |
< |
"I hope you have a very fast processor!\n"); |
552 |
< |
painCave.isFatal = 0; |
553 |
< |
simError(); |
554 |
< |
double smallest; |
555 |
< |
smallest = simnfo->boxLx; |
556 |
< |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
557 |
< |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
558 |
< |
simnfo->ecr = 0.5 * smallest; |
559 |
< |
} else { |
560 |
< |
simnfo->ecr = the_globals->getECR(); |
561 |
< |
} |
395 |
> |
double vel[3]; |
396 |
> |
vel[0] = 0.0; |
397 |
> |
vel[1] = 0.0; |
398 |
> |
vel[2] = 0.0; |
399 |
|
|
400 |
< |
if( !the_globals->haveEST() ){ |
401 |
< |
sprintf( painCave.errMsg, |
402 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
403 |
< |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
404 |
< |
); |
405 |
< |
painCave.isFatal = 0; |
406 |
< |
simError(); |
407 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
408 |
< |
} else { |
409 |
< |
simnfo->est = the_globals->getEST(); |
410 |
< |
} |
411 |
< |
|
412 |
< |
if(!the_globals->haveDielectric() ){ |
413 |
< |
sprintf( painCave.errMsg, |
414 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
415 |
< |
"setting a dielectric constant!\n" |
416 |
< |
); |
400 |
> |
temp1 = (double) tot_nmol / 4.0; |
401 |
> |
temp2 = pow(temp1, (1.0 / 3.0)); |
402 |
> |
temp3 = ceil(temp2); |
403 |
> |
|
404 |
> |
have_extra = 0; |
405 |
> |
if (temp2 < temp3){ |
406 |
> |
// we have a non-complete lattice |
407 |
> |
have_extra = 1; |
408 |
> |
|
409 |
> |
n_cells = (int) temp3 - 1; |
410 |
> |
cellx = info[0].boxL[0] / temp3; |
411 |
> |
celly = info[0].boxL[1] / temp3; |
412 |
> |
cellz = info[0].boxL[2] / temp3; |
413 |
> |
n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
414 |
> |
temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
415 |
> |
n_per_extra = (int) ceil(temp1); |
416 |
> |
|
417 |
> |
if (n_per_extra > 4){ |
418 |
> |
sprintf(painCave.errMsg, |
419 |
> |
"SimSetup error. There has been an error in constructing" |
420 |
> |
" the non-complete lattice.\n"); |
421 |
|
painCave.isFatal = 1; |
422 |
|
simError(); |
423 |
|
} |
424 |
< |
simnfo->dielectric = the_globals->getDielectric(); |
425 |
< |
} else { |
426 |
< |
if (usesDipoles) { |
427 |
< |
|
428 |
< |
if( !the_globals->haveECR() ){ |
429 |
< |
sprintf( painCave.errMsg, |
430 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
431 |
< |
"box length for the electrostaticCutoffRadius.\n" |
432 |
< |
"I hope you have a very fast processor!\n"); |
433 |
< |
painCave.isFatal = 0; |
434 |
< |
simError(); |
435 |
< |
double smallest; |
436 |
< |
smallest = simnfo->boxLx; |
437 |
< |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
438 |
< |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
439 |
< |
simnfo->ecr = 0.5 * smallest; |
440 |
< |
} else { |
441 |
< |
simnfo->ecr = the_globals->getECR(); |
424 |
> |
} |
425 |
> |
else{ |
426 |
> |
n_cells = (int) temp3; |
427 |
> |
cellx = info[0].boxL[0] / temp3; |
428 |
> |
celly = info[0].boxL[1] / temp3; |
429 |
> |
cellz = info[0].boxL[2] / temp3; |
430 |
> |
} |
431 |
> |
|
432 |
> |
current_mol = 0; |
433 |
> |
current_comp_mol = 0; |
434 |
> |
current_comp = 0; |
435 |
> |
current_atom_ndx = 0; |
436 |
> |
|
437 |
> |
for (i = 0; i < n_cells ; i++){ |
438 |
> |
for (j = 0; j < n_cells; j++){ |
439 |
> |
for (k = 0; k < n_cells; k++){ |
440 |
> |
makeElement(i * cellx, j * celly, k * cellz); |
441 |
> |
|
442 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
443 |
> |
|
444 |
> |
makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
445 |
> |
|
446 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
447 |
|
} |
602 |
– |
|
603 |
– |
if( !the_globals->haveEST() ){ |
604 |
– |
sprintf( painCave.errMsg, |
605 |
– |
"SimSetup Warning: using default value of 5%% of the " |
606 |
– |
"electrostaticCutoffRadius for the " |
607 |
– |
"electrostaticSkinThickness\n" |
608 |
– |
); |
609 |
– |
painCave.isFatal = 0; |
610 |
– |
simError(); |
611 |
– |
simnfo->est = 0.05 * simnfo->ecr; |
612 |
– |
} else { |
613 |
– |
simnfo->est = the_globals->getEST(); |
614 |
– |
} |
448 |
|
} |
449 |
< |
} |
449 |
> |
} |
450 |
|
|
451 |
< |
#ifdef IS_MPI |
452 |
< |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
620 |
< |
MPIcheckPoint(); |
621 |
< |
#endif // is_mpi |
451 |
> |
if (have_extra){ |
452 |
> |
done = 0; |
453 |
|
|
454 |
< |
if( the_globals->haveInitialConfig() ){ |
455 |
< |
|
456 |
< |
InitializeFromFile* fileInit; |
457 |
< |
#ifdef IS_MPI // is_mpi |
458 |
< |
if( worldRank == 0 ){ |
459 |
< |
#endif //is_mpi |
460 |
< |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
461 |
< |
#ifdef IS_MPI |
462 |
< |
}else fileInit = new InitializeFromFile( NULL ); |
463 |
< |
#endif |
464 |
< |
fileInit->read_xyz( simnfo ); // default velocities on |
454 |
> |
int start_ndx; |
455 |
> |
for (i = 0; i < (n_cells + 1) && !done; i++){ |
456 |
> |
for (j = 0; j < (n_cells + 1) && !done; j++){ |
457 |
> |
if (i < n_cells){ |
458 |
> |
if (j < n_cells){ |
459 |
> |
start_ndx = n_cells; |
460 |
> |
} |
461 |
> |
else |
462 |
> |
start_ndx = 0; |
463 |
> |
} |
464 |
> |
else |
465 |
> |
start_ndx = 0; |
466 |
|
|
467 |
< |
delete fileInit; |
468 |
< |
} |
469 |
< |
else{ |
467 |
> |
for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
468 |
> |
makeElement(i * cellx, j * celly, k * cellz); |
469 |
> |
done = (current_mol >= tot_nmol); |
470 |
|
|
471 |
< |
#ifdef IS_MPI |
471 |
> |
if (!done && n_per_extra > 1){ |
472 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
473 |
> |
k * cellz); |
474 |
> |
done = (current_mol >= tot_nmol); |
475 |
> |
} |
476 |
|
|
477 |
< |
// no init from bass |
478 |
< |
|
479 |
< |
sprintf( painCave.errMsg, |
480 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
481 |
< |
painCave.isFatal; |
646 |
< |
simError(); |
647 |
< |
|
648 |
< |
#else |
477 |
> |
if (!done && n_per_extra > 2){ |
478 |
> |
makeElement(i * cellx, j * celly + 0.5 * celly, |
479 |
> |
k * cellz + 0.5 * cellz); |
480 |
> |
done = (current_mol >= tot_nmol); |
481 |
> |
} |
482 |
|
|
483 |
< |
initFromBass(); |
484 |
< |
|
485 |
< |
|
486 |
< |
#endif |
487 |
< |
} |
488 |
< |
|
656 |
< |
#ifdef IS_MPI |
657 |
< |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
658 |
< |
MPIcheckPoint(); |
659 |
< |
#endif // is_mpi |
660 |
< |
|
661 |
< |
|
662 |
< |
|
663 |
< |
|
664 |
< |
|
665 |
< |
|
666 |
< |
|
667 |
< |
#ifdef IS_MPI |
668 |
< |
if( worldRank == 0 ){ |
669 |
< |
#endif // is_mpi |
670 |
< |
|
671 |
< |
if( the_globals->haveFinalConfig() ){ |
672 |
< |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
673 |
< |
} |
674 |
< |
else{ |
675 |
< |
strcpy( simnfo->finalName, inFileName ); |
676 |
< |
char* endTest; |
677 |
< |
int nameLength = strlen( simnfo->finalName ); |
678 |
< |
endTest = &(simnfo->finalName[nameLength - 5]); |
679 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
680 |
< |
strcpy( endTest, ".eor" ); |
483 |
> |
if (!done && n_per_extra > 3){ |
484 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly, |
485 |
> |
k * cellz + 0.5 * cellz); |
486 |
> |
done = (current_mol >= tot_nmol); |
487 |
> |
} |
488 |
> |
} |
489 |
|
} |
682 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
683 |
– |
strcpy( endTest, ".eor" ); |
684 |
– |
} |
685 |
– |
else{ |
686 |
– |
endTest = &(simnfo->finalName[nameLength - 4]); |
687 |
– |
if( !strcmp( endTest, ".bss" ) ){ |
688 |
– |
strcpy( endTest, ".eor" ); |
689 |
– |
} |
690 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
691 |
– |
strcpy( endTest, ".eor" ); |
692 |
– |
} |
693 |
– |
else{ |
694 |
– |
strcat( simnfo->finalName, ".eor" ); |
695 |
– |
} |
696 |
– |
} |
490 |
|
} |
698 |
– |
|
699 |
– |
// make the sample and status out names |
700 |
– |
|
701 |
– |
strcpy( simnfo->sampleName, inFileName ); |
702 |
– |
char* endTest; |
703 |
– |
int nameLength = strlen( simnfo->sampleName ); |
704 |
– |
endTest = &(simnfo->sampleName[nameLength - 5]); |
705 |
– |
if( !strcmp( endTest, ".bass" ) ){ |
706 |
– |
strcpy( endTest, ".dump" ); |
707 |
– |
} |
708 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
709 |
– |
strcpy( endTest, ".dump" ); |
710 |
– |
} |
711 |
– |
else{ |
712 |
– |
endTest = &(simnfo->sampleName[nameLength - 4]); |
713 |
– |
if( !strcmp( endTest, ".bss" ) ){ |
714 |
– |
strcpy( endTest, ".dump" ); |
715 |
– |
} |
716 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
717 |
– |
strcpy( endTest, ".dump" ); |
718 |
– |
} |
719 |
– |
else{ |
720 |
– |
strcat( simnfo->sampleName, ".dump" ); |
721 |
– |
} |
722 |
– |
} |
723 |
– |
|
724 |
– |
strcpy( simnfo->statusName, inFileName ); |
725 |
– |
nameLength = strlen( simnfo->statusName ); |
726 |
– |
endTest = &(simnfo->statusName[nameLength - 5]); |
727 |
– |
if( !strcmp( endTest, ".bass" ) ){ |
728 |
– |
strcpy( endTest, ".stat" ); |
729 |
– |
} |
730 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
731 |
– |
strcpy( endTest, ".stat" ); |
732 |
– |
} |
733 |
– |
else{ |
734 |
– |
endTest = &(simnfo->statusName[nameLength - 4]); |
735 |
– |
if( !strcmp( endTest, ".bss" ) ){ |
736 |
– |
strcpy( endTest, ".stat" ); |
737 |
– |
} |
738 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
739 |
– |
strcpy( endTest, ".stat" ); |
740 |
– |
} |
741 |
– |
else{ |
742 |
– |
strcat( simnfo->statusName, ".stat" ); |
743 |
– |
} |
744 |
– |
} |
745 |
– |
|
746 |
– |
#ifdef IS_MPI |
491 |
|
} |
748 |
– |
#endif // is_mpi |
749 |
– |
|
750 |
– |
// set the status, sample, and themal kick times |
751 |
– |
|
752 |
– |
if( the_globals->haveSampleTime() ){ |
753 |
– |
simnfo->sampleTime = the_globals->getSampleTime(); |
754 |
– |
simnfo->statusTime = simnfo->sampleTime; |
755 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
756 |
– |
} |
757 |
– |
else{ |
758 |
– |
simnfo->sampleTime = the_globals->getRunTime(); |
759 |
– |
simnfo->statusTime = simnfo->sampleTime; |
760 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
761 |
– |
} |
492 |
|
|
493 |
< |
if( the_globals->haveStatusTime() ){ |
494 |
< |
simnfo->statusTime = the_globals->getStatusTime(); |
493 |
> |
for (i = 0; i < info[0].n_atoms; i++){ |
494 |
> |
info[0].atoms[i]->setVel(vel); |
495 |
|
} |
496 |
+ |
} |
497 |
|
|
498 |
< |
if( the_globals->haveThermalTime() ){ |
499 |
< |
simnfo->thermalTime = the_globals->getThermalTime(); |
500 |
< |
} |
498 |
> |
void SimSetup::makeElement(double x, double y, double z){ |
499 |
> |
int k; |
500 |
> |
AtomStamp* current_atom; |
501 |
> |
DirectionalAtom* dAtom; |
502 |
> |
double rotMat[3][3]; |
503 |
> |
double pos[3]; |
504 |
|
|
505 |
< |
// check for the temperature set flag |
506 |
< |
|
507 |
< |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
508 |
< |
|
509 |
< |
|
510 |
< |
// make the integrator |
511 |
< |
|
512 |
< |
|
513 |
< |
NVT* myNVT = NULL; |
780 |
< |
switch( ensembleCase ){ |
781 |
< |
|
782 |
< |
case NVE_ENS: |
783 |
< |
new NVE( simnfo, the_ff ); |
784 |
< |
break; |
785 |
< |
|
786 |
< |
case NVT_ENS: |
787 |
< |
myNVT = new NVT( simnfo, the_ff ); |
788 |
< |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
789 |
< |
|
790 |
< |
if (the_globals->haveTauThermostat()) |
791 |
< |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
792 |
< |
// else if (the_globals->haveQmass()) |
793 |
< |
// myNVT->setQmass(the_globals->getQmass()); |
794 |
< |
else { |
795 |
< |
sprintf( painCave.errMsg, |
796 |
< |
"SimSetup error: If you use the NVT\n" |
797 |
< |
" ensemble, you must set either tauThermostat or qMass.\n" |
798 |
< |
" Neither of these was found in the BASS file.\n"); |
505 |
> |
for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
506 |
> |
current_atom = comp_stamps[current_comp]->getAtom(k); |
507 |
> |
if (!current_atom->havePosition()){ |
508 |
> |
sprintf(painCave.errMsg, |
509 |
> |
"SimSetup:initFromBass error.\n" |
510 |
> |
"\tComponent %s, atom %s does not have a position specified.\n" |
511 |
> |
"\tThe initialization routine is unable to give a start" |
512 |
> |
" position.\n", |
513 |
> |
comp_stamps[current_comp]->getID(), current_atom->getType()); |
514 |
|
painCave.isFatal = 1; |
515 |
|
simError(); |
516 |
|
} |
802 |
– |
break; |
517 |
|
|
518 |
< |
default: |
519 |
< |
sprintf( painCave.errMsg, |
520 |
< |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
807 |
< |
painCave.isFatal = 1; |
808 |
< |
simError(); |
809 |
< |
} |
518 |
> |
pos[0] = x + current_atom->getPosX(); |
519 |
> |
pos[1] = y + current_atom->getPosY(); |
520 |
> |
pos[2] = z + current_atom->getPosZ(); |
521 |
|
|
522 |
+ |
info[0].atoms[current_atom_ndx]->setPos(pos); |
523 |
|
|
524 |
< |
#ifdef IS_MPI |
525 |
< |
mpiSim->mpiRefresh(); |
814 |
< |
#endif |
524 |
> |
if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
525 |
> |
dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
526 |
|
|
527 |
< |
// initialize the Fortran |
527 |
> |
rotMat[0][0] = 1.0; |
528 |
> |
rotMat[0][1] = 0.0; |
529 |
> |
rotMat[0][2] = 0.0; |
530 |
|
|
531 |
+ |
rotMat[1][0] = 0.0; |
532 |
+ |
rotMat[1][1] = 1.0; |
533 |
+ |
rotMat[1][2] = 0.0; |
534 |
|
|
535 |
< |
simnfo->refreshSim(); |
536 |
< |
|
537 |
< |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
538 |
< |
the_ff->initForceField( LB_MIXING_RULE ); |
535 |
> |
rotMat[2][0] = 0.0; |
536 |
> |
rotMat[2][1] = 0.0; |
537 |
> |
rotMat[2][2] = 1.0; |
538 |
> |
|
539 |
> |
dAtom->setA(rotMat); |
540 |
> |
} |
541 |
> |
|
542 |
> |
current_atom_ndx++; |
543 |
|
} |
824 |
– |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
825 |
– |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
826 |
– |
} |
827 |
– |
else{ |
828 |
– |
sprintf( painCave.errMsg, |
829 |
– |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
830 |
– |
simnfo->mixingRule ); |
831 |
– |
painCave.isFatal = 1; |
832 |
– |
simError(); |
833 |
– |
} |
544 |
|
|
545 |
+ |
current_mol++; |
546 |
+ |
current_comp_mol++; |
547 |
|
|
548 |
< |
#ifdef IS_MPI |
549 |
< |
strcpy( checkPointMsg, |
550 |
< |
"Successfully intialized the mixingRule for Fortran." ); |
551 |
< |
MPIcheckPoint(); |
840 |
< |
#endif // is_mpi |
548 |
> |
if (current_comp_mol >= components_nmol[current_comp]){ |
549 |
> |
current_comp_mol = 0; |
550 |
> |
current_comp++; |
551 |
> |
} |
552 |
|
} |
553 |
|
|
554 |
|
|
555 |
< |
void SimSetup::makeMolecules( void ){ |
555 |
> |
void SimSetup::gatherInfo(void){ |
556 |
> |
int i; |
557 |
|
|
558 |
< |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
559 |
< |
molInit info; |
848 |
< |
DirectionalAtom* dAtom; |
849 |
< |
LinkedAssign* extras; |
850 |
< |
LinkedAssign* current_extra; |
851 |
< |
AtomStamp* currentAtom; |
852 |
< |
BondStamp* currentBond; |
853 |
< |
BendStamp* currentBend; |
854 |
< |
TorsionStamp* currentTorsion; |
558 |
> |
ensembleCase = -1; |
559 |
> |
ffCase = -1; |
560 |
|
|
561 |
< |
bond_pair* theBonds; |
857 |
< |
bend_set* theBends; |
858 |
< |
torsion_set* theTorsions; |
561 |
> |
// set the easy ones first |
562 |
|
|
563 |
< |
|
564 |
< |
//init the forceField paramters |
563 |
> |
for (i = 0; i < nInfo; i++){ |
564 |
> |
info[i].target_temp = globals->getTargetTemp(); |
565 |
> |
info[i].dt = globals->getDt(); |
566 |
> |
info[i].run_time = globals->getRunTime(); |
567 |
> |
} |
568 |
> |
n_components = globals->getNComponents(); |
569 |
|
|
863 |
– |
the_ff->readParams(); |
570 |
|
|
571 |
< |
|
866 |
< |
// init the atoms |
571 |
> |
// get the forceField |
572 |
|
|
573 |
< |
double ux, uy, uz, u, uSqr; |
869 |
< |
|
870 |
< |
atomOffset = 0; |
871 |
< |
excludeOffset = 0; |
872 |
< |
for(i=0; i<simnfo->n_mol; i++){ |
873 |
< |
|
874 |
< |
stampID = the_molecules[i].getStampID(); |
573 |
> |
strcpy(force_field, globals->getForceField()); |
574 |
|
|
575 |
< |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
576 |
< |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
577 |
< |
info.nBends = comp_stamps[stampID]->getNBends(); |
578 |
< |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
579 |
< |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
575 |
> |
if (!strcasecmp(force_field, "DUFF")){ |
576 |
> |
ffCase = FF_DUFF; |
577 |
> |
} |
578 |
> |
else if (!strcasecmp(force_field, "LJ")){ |
579 |
> |
ffCase = FF_LJ; |
580 |
> |
} |
581 |
> |
else if (!strcasecmp(force_field, "EAM")){ |
582 |
> |
ffCase = FF_EAM; |
583 |
> |
} |
584 |
> |
else{ |
585 |
> |
sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
586 |
> |
force_field); |
587 |
> |
painCave.isFatal = 1; |
588 |
> |
simError(); |
589 |
> |
} |
590 |
|
|
591 |
< |
info.myAtoms = &the_atoms[atomOffset]; |
883 |
< |
info.myExcludes = &the_excludes[excludeOffset]; |
884 |
< |
info.myBonds = new Bond*[info.nBonds]; |
885 |
< |
info.myBends = new Bend*[info.nBends]; |
886 |
< |
info.myTorsions = new Torsion*[info.nTorsions]; |
591 |
> |
// get the ensemble |
592 |
|
|
593 |
< |
theBonds = new bond_pair[info.nBonds]; |
889 |
< |
theBends = new bend_set[info.nBends]; |
890 |
< |
theTorsions = new torsion_set[info.nTorsions]; |
891 |
< |
|
892 |
< |
// make the Atoms |
893 |
< |
|
894 |
< |
for(j=0; j<info.nAtoms; j++){ |
895 |
< |
|
896 |
< |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
897 |
< |
if( currentAtom->haveOrientation() ){ |
898 |
< |
|
899 |
< |
dAtom = new DirectionalAtom(j + atomOffset); |
900 |
< |
simnfo->n_oriented++; |
901 |
< |
info.myAtoms[j] = dAtom; |
902 |
< |
|
903 |
< |
ux = currentAtom->getOrntX(); |
904 |
< |
uy = currentAtom->getOrntY(); |
905 |
< |
uz = currentAtom->getOrntZ(); |
906 |
< |
|
907 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
908 |
< |
|
909 |
< |
u = sqrt( uSqr ); |
910 |
< |
ux = ux / u; |
911 |
< |
uy = uy / u; |
912 |
< |
uz = uz / u; |
913 |
< |
|
914 |
< |
dAtom->setSUx( ux ); |
915 |
< |
dAtom->setSUy( uy ); |
916 |
< |
dAtom->setSUz( uz ); |
917 |
< |
} |
918 |
< |
else{ |
919 |
< |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
920 |
< |
} |
921 |
< |
info.myAtoms[j]->setType( currentAtom->getType() ); |
922 |
< |
|
923 |
< |
#ifdef IS_MPI |
924 |
< |
|
925 |
< |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
926 |
< |
|
927 |
< |
#endif // is_mpi |
928 |
< |
} |
929 |
< |
|
930 |
< |
// make the bonds |
931 |
< |
for(j=0; j<info.nBonds; j++){ |
932 |
< |
|
933 |
< |
currentBond = comp_stamps[stampID]->getBond( j ); |
934 |
< |
theBonds[j].a = currentBond->getA() + atomOffset; |
935 |
< |
theBonds[j].b = currentBond->getB() + atomOffset; |
593 |
> |
strcpy(ensemble, globals->getEnsemble()); |
594 |
|
|
595 |
< |
exI = theBonds[j].a; |
596 |
< |
exJ = theBonds[j].b; |
595 |
> |
if (!strcasecmp(ensemble, "NVE")){ |
596 |
> |
ensembleCase = NVE_ENS; |
597 |
> |
} |
598 |
> |
else if (!strcasecmp(ensemble, "NVT")){ |
599 |
> |
ensembleCase = NVT_ENS; |
600 |
> |
} |
601 |
> |
else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
602 |
> |
ensembleCase = NPTi_ENS; |
603 |
> |
} |
604 |
> |
else if (!strcasecmp(ensemble, "NPTf")){ |
605 |
> |
ensembleCase = NPTf_ENS; |
606 |
> |
} |
607 |
> |
else{ |
608 |
> |
sprintf(painCave.errMsg, |
609 |
> |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
610 |
> |
"reverting to NVE for this simulation.\n", |
611 |
> |
ensemble); |
612 |
> |
painCave.isFatal = 0; |
613 |
> |
simError(); |
614 |
> |
strcpy(ensemble, "NVE"); |
615 |
> |
ensembleCase = NVE_ENS; |
616 |
> |
} |
617 |
|
|
618 |
< |
// exclude_I must always be the smaller of the pair |
619 |
< |
if( exI > exJ ){ |
942 |
< |
tempEx = exI; |
943 |
< |
exI = exJ; |
944 |
< |
exJ = tempEx; |
945 |
< |
} |
946 |
< |
#ifdef IS_MPI |
947 |
< |
tempEx = exI; |
948 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
949 |
< |
tempEx = exJ; |
950 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
951 |
< |
|
952 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
953 |
< |
#else // isn't MPI |
618 |
> |
for (i = 0; i < nInfo; i++){ |
619 |
> |
strcpy(info[i].ensemble, ensemble); |
620 |
|
|
621 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
956 |
< |
#endif //is_mpi |
957 |
< |
} |
958 |
< |
excludeOffset += info.nBonds; |
621 |
> |
// get the mixing rule |
622 |
|
|
623 |
< |
//make the bends |
624 |
< |
for(j=0; j<info.nBends; j++){ |
625 |
< |
|
963 |
< |
currentBend = comp_stamps[stampID]->getBend( j ); |
964 |
< |
theBends[j].a = currentBend->getA() + atomOffset; |
965 |
< |
theBends[j].b = currentBend->getB() + atomOffset; |
966 |
< |
theBends[j].c = currentBend->getC() + atomOffset; |
967 |
< |
|
968 |
< |
if( currentBend->haveExtras() ){ |
969 |
< |
|
970 |
< |
extras = currentBend->getExtras(); |
971 |
< |
current_extra = extras; |
972 |
< |
|
973 |
< |
while( current_extra != NULL ){ |
974 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
975 |
< |
|
976 |
< |
switch( current_extra->getType() ){ |
977 |
< |
|
978 |
< |
case 0: |
979 |
< |
theBends[j].ghost = |
980 |
< |
current_extra->getInt() + atomOffset; |
981 |
< |
theBends[j].isGhost = 1; |
982 |
< |
break; |
983 |
< |
|
984 |
< |
case 1: |
985 |
< |
theBends[j].ghost = |
986 |
< |
(int)current_extra->getDouble() + atomOffset; |
987 |
< |
theBends[j].isGhost = 1; |
988 |
< |
break; |
989 |
< |
|
990 |
< |
default: |
991 |
< |
sprintf( painCave.errMsg, |
992 |
< |
"SimSetup Error: ghostVectorSource was neither a " |
993 |
< |
"double nor an int.\n" |
994 |
< |
"-->Bend[%d] in %s\n", |
995 |
< |
j, comp_stamps[stampID]->getID() ); |
996 |
< |
painCave.isFatal = 1; |
997 |
< |
simError(); |
998 |
< |
} |
999 |
< |
} |
1000 |
< |
|
1001 |
< |
else{ |
1002 |
< |
|
1003 |
< |
sprintf( painCave.errMsg, |
1004 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
1005 |
< |
" -->%s in Bend[%d] in %s\n", |
1006 |
< |
current_extra->getlhs(), |
1007 |
< |
j, comp_stamps[stampID]->getID() ); |
1008 |
< |
painCave.isFatal = 1; |
1009 |
< |
simError(); |
1010 |
< |
} |
1011 |
< |
|
1012 |
< |
current_extra = current_extra->getNext(); |
1013 |
< |
} |
1014 |
< |
} |
1015 |
< |
|
1016 |
< |
if( !theBends[j].isGhost ){ |
1017 |
< |
|
1018 |
< |
exI = theBends[j].a; |
1019 |
< |
exJ = theBends[j].c; |
1020 |
< |
} |
1021 |
< |
else{ |
1022 |
< |
|
1023 |
< |
exI = theBends[j].a; |
1024 |
< |
exJ = theBends[j].b; |
1025 |
< |
} |
1026 |
< |
|
1027 |
< |
// exclude_I must always be the smaller of the pair |
1028 |
< |
if( exI > exJ ){ |
1029 |
< |
tempEx = exI; |
1030 |
< |
exI = exJ; |
1031 |
< |
exJ = tempEx; |
1032 |
< |
} |
1033 |
< |
#ifdef IS_MPI |
1034 |
< |
tempEx = exI; |
1035 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1036 |
< |
tempEx = exJ; |
1037 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1038 |
< |
|
1039 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1040 |
< |
#else // isn't MPI |
1041 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1042 |
< |
#endif //is_mpi |
1043 |
< |
} |
1044 |
< |
excludeOffset += info.nBends; |
623 |
> |
strcpy(info[i].mixingRule, globals->getMixingRule()); |
624 |
> |
info[i].usePBC = globals->getPBC(); |
625 |
> |
} |
626 |
|
|
627 |
< |
for(j=0; j<info.nTorsions; j++){ |
1047 |
< |
|
1048 |
< |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1049 |
< |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1050 |
< |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1051 |
< |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1052 |
< |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1053 |
< |
|
1054 |
< |
exI = theTorsions[j].a; |
1055 |
< |
exJ = theTorsions[j].d; |
627 |
> |
// get the components and calculate the tot_nMol and indvidual n_mol |
628 |
|
|
629 |
< |
// exclude_I must always be the smaller of the pair |
630 |
< |
if( exI > exJ ){ |
1059 |
< |
tempEx = exI; |
1060 |
< |
exI = exJ; |
1061 |
< |
exJ = tempEx; |
1062 |
< |
} |
1063 |
< |
#ifdef IS_MPI |
1064 |
< |
tempEx = exI; |
1065 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1066 |
< |
tempEx = exJ; |
1067 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1068 |
< |
|
1069 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1070 |
< |
#else // isn't MPI |
1071 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1072 |
< |
#endif //is_mpi |
1073 |
< |
} |
1074 |
< |
excludeOffset += info.nTorsions; |
629 |
> |
the_components = globals->getComponents(); |
630 |
> |
components_nmol = new int[n_components]; |
631 |
|
|
1076 |
– |
|
1077 |
– |
// send the arrays off to the forceField for init. |
632 |
|
|
633 |
< |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
634 |
< |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
635 |
< |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1082 |
< |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
633 |
> |
if (!globals->haveNMol()){ |
634 |
> |
// we don't have the total number of molecules, so we assume it is |
635 |
> |
// given in each component |
636 |
|
|
637 |
+ |
tot_nmol = 0; |
638 |
+ |
for (i = 0; i < n_components; i++){ |
639 |
+ |
if (!the_components[i]->haveNMol()){ |
640 |
+ |
// we have a problem |
641 |
+ |
sprintf(painCave.errMsg, |
642 |
+ |
"SimSetup Error. No global NMol or component NMol" |
643 |
+ |
" given. Cannot calculate the number of atoms.\n"); |
644 |
+ |
painCave.isFatal = 1; |
645 |
+ |
simError(); |
646 |
+ |
} |
647 |
|
|
648 |
< |
the_molecules[i].initialize( info ); |
649 |
< |
|
650 |
< |
|
1088 |
< |
atomOffset += info.nAtoms; |
1089 |
< |
delete[] theBonds; |
1090 |
< |
delete[] theBends; |
1091 |
< |
delete[] theTorsions; |
648 |
> |
tot_nmol += the_components[i]->getNMol(); |
649 |
> |
components_nmol[i] = the_components[i]->getNMol(); |
650 |
> |
} |
651 |
|
} |
652 |
+ |
else{ |
653 |
+ |
sprintf(painCave.errMsg, |
654 |
+ |
"SimSetup error.\n" |
655 |
+ |
"\tSorry, the ability to specify total" |
656 |
+ |
" nMols and then give molfractions in the components\n" |
657 |
+ |
"\tis not currently supported." |
658 |
+ |
" Please give nMol in the components.\n"); |
659 |
+ |
painCave.isFatal = 1; |
660 |
+ |
simError(); |
661 |
+ |
} |
662 |
|
|
663 |
< |
#ifdef IS_MPI |
1095 |
< |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1096 |
< |
MPIcheckPoint(); |
1097 |
< |
#endif // is_mpi |
663 |
> |
// set the status, sample, and thermal kick times |
664 |
|
|
665 |
< |
// clean up the forcefield |
666 |
< |
the_ff->calcRcut(); |
667 |
< |
the_ff->cleanMe(); |
665 |
> |
for (i = 0; i < nInfo; i++){ |
666 |
> |
if (globals->haveSampleTime()){ |
667 |
> |
info[i].sampleTime = globals->getSampleTime(); |
668 |
> |
info[i].statusTime = info[i].sampleTime; |
669 |
> |
info[i].thermalTime = info[i].sampleTime; |
670 |
> |
} |
671 |
> |
else{ |
672 |
> |
info[i].sampleTime = globals->getRunTime(); |
673 |
> |
info[i].statusTime = info[i].sampleTime; |
674 |
> |
info[i].thermalTime = info[i].sampleTime; |
675 |
> |
} |
676 |
|
|
677 |
< |
} |
678 |
< |
|
679 |
< |
void SimSetup::initFromBass( void ){ |
677 |
> |
if (globals->haveStatusTime()){ |
678 |
> |
info[i].statusTime = globals->getStatusTime(); |
679 |
> |
} |
680 |
|
|
681 |
< |
int i, j, k; |
682 |
< |
int n_cells; |
683 |
< |
double cellx, celly, cellz; |
1110 |
< |
double temp1, temp2, temp3; |
1111 |
< |
int n_per_extra; |
1112 |
< |
int n_extra; |
1113 |
< |
int have_extra, done; |
681 |
> |
if (globals->haveThermalTime()){ |
682 |
> |
info[i].thermalTime = globals->getThermalTime(); |
683 |
> |
} |
684 |
|
|
685 |
< |
temp1 = (double)tot_nmol / 4.0; |
686 |
< |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
687 |
< |
temp3 = ceil( temp2 ); |
685 |
> |
info[i].resetIntegrator = 0; |
686 |
> |
if( globals->haveResetTime() ){ |
687 |
> |
info[i].resetTime = globals->getResetTime(); |
688 |
> |
info[i].resetIntegrator = 1; |
689 |
> |
} |
690 |
|
|
691 |
< |
have_extra =0; |
1120 |
< |
if( temp2 < temp3 ){ // we have a non-complete lattice |
1121 |
< |
have_extra =1; |
691 |
> |
// check for the temperature set flag |
692 |
|
|
693 |
< |
n_cells = (int)temp3 - 1; |
694 |
< |
cellx = simnfo->boxLx / temp3; |
1125 |
< |
celly = simnfo->boxLy / temp3; |
1126 |
< |
cellz = simnfo->boxLz / temp3; |
1127 |
< |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1128 |
< |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1129 |
< |
n_per_extra = (int)ceil( temp1 ); |
693 |
> |
if (globals->haveTempSet()) |
694 |
> |
info[i].setTemp = globals->getTempSet(); |
695 |
|
|
696 |
< |
if( n_per_extra > 4){ |
697 |
< |
sprintf( painCave.errMsg, |
698 |
< |
"SimSetup error. There has been an error in constructing" |
699 |
< |
" the non-complete lattice.\n" ); |
700 |
< |
painCave.isFatal = 1; |
701 |
< |
simError(); |
696 |
> |
// get some of the tricky things that may still be in the globals |
697 |
> |
|
698 |
> |
double boxVector[3]; |
699 |
> |
if (globals->haveBox()){ |
700 |
> |
boxVector[0] = globals->getBox(); |
701 |
> |
boxVector[1] = globals->getBox(); |
702 |
> |
boxVector[2] = globals->getBox(); |
703 |
> |
|
704 |
> |
info[i].setBox(boxVector); |
705 |
|
} |
706 |
< |
} |
707 |
< |
else{ |
708 |
< |
n_cells = (int)temp3; |
709 |
< |
cellx = simnfo->boxLx / temp3; |
710 |
< |
celly = simnfo->boxLy / temp3; |
711 |
< |
cellz = simnfo->boxLz / temp3; |
1144 |
< |
} |
706 |
> |
else if (globals->haveDensity()){ |
707 |
> |
double vol; |
708 |
> |
vol = (double) tot_nmol / globals->getDensity(); |
709 |
> |
boxVector[0] = pow(vol, (1.0 / 3.0)); |
710 |
> |
boxVector[1] = boxVector[0]; |
711 |
> |
boxVector[2] = boxVector[0]; |
712 |
|
|
713 |
< |
current_mol = 0; |
714 |
< |
current_comp_mol = 0; |
715 |
< |
current_comp = 0; |
716 |
< |
current_atom_ndx = 0; |
713 |
> |
info[i].setBox(boxVector); |
714 |
> |
} |
715 |
> |
else{ |
716 |
> |
if (!globals->haveBoxX()){ |
717 |
> |
sprintf(painCave.errMsg, |
718 |
> |
"SimSetup error, no periodic BoxX size given.\n"); |
719 |
> |
painCave.isFatal = 1; |
720 |
> |
simError(); |
721 |
> |
} |
722 |
> |
boxVector[0] = globals->getBoxX(); |
723 |
|
|
724 |
< |
for( i=0; i < n_cells ; i++ ){ |
725 |
< |
for( j=0; j < n_cells; j++ ){ |
726 |
< |
for( k=0; k < n_cells; k++ ){ |
724 |
> |
if (!globals->haveBoxY()){ |
725 |
> |
sprintf(painCave.errMsg, |
726 |
> |
"SimSetup error, no periodic BoxY size given.\n"); |
727 |
> |
painCave.isFatal = 1; |
728 |
> |
simError(); |
729 |
> |
} |
730 |
> |
boxVector[1] = globals->getBoxY(); |
731 |
|
|
732 |
< |
makeElement( i * cellx, |
733 |
< |
j * celly, |
734 |
< |
k * cellz ); |
732 |
> |
if (!globals->haveBoxZ()){ |
733 |
> |
sprintf(painCave.errMsg, |
734 |
> |
"SimSetup error, no periodic BoxZ size given.\n"); |
735 |
> |
painCave.isFatal = 1; |
736 |
> |
simError(); |
737 |
> |
} |
738 |
> |
boxVector[2] = globals->getBoxZ(); |
739 |
|
|
740 |
< |
makeElement( i * cellx + 0.5 * cellx, |
741 |
< |
j * celly + 0.5 * celly, |
742 |
< |
k * cellz ); |
740 |
> |
info[i].setBox(boxVector); |
741 |
> |
} |
742 |
> |
} |
743 |
|
|
744 |
< |
makeElement( i * cellx, |
745 |
< |
j * celly + 0.5 * celly, |
1165 |
< |
k * cellz + 0.5 * cellz ); |
744 |
> |
//setup seed for random number generator |
745 |
> |
int seedValue; |
746 |
|
|
747 |
< |
makeElement( i * cellx + 0.5 * cellx, |
748 |
< |
j * celly, |
749 |
< |
k * cellz + 0.5 * cellz ); |
747 |
> |
if (globals->haveSeed()){ |
748 |
> |
seedValue = globals->getSeed(); |
749 |
> |
|
750 |
> |
if(seedValue / 1E9 == 0){ |
751 |
> |
sprintf(painCave.errMsg, |
752 |
> |
"Seed for sprng library should contain at least 9 digits\n" |
753 |
> |
"OOPSE will generate a seed for user\n"); |
754 |
> |
painCave.isFatal = 0; |
755 |
> |
simError(); |
756 |
> |
|
757 |
> |
//using seed generated by system instead of invalid seed set by user |
758 |
> |
#ifndef IS_MPI |
759 |
> |
seedValue = make_sprng_seed(); |
760 |
> |
#else |
761 |
> |
if (worldRank == 0){ |
762 |
> |
seedValue = make_sprng_seed(); |
763 |
|
} |
764 |
+ |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
765 |
+ |
#endif |
766 |
|
} |
767 |
+ |
}//end of if branch of globals->haveSeed() |
768 |
+ |
else{ |
769 |
+ |
|
770 |
+ |
#ifndef IS_MPI |
771 |
+ |
seedValue = make_sprng_seed(); |
772 |
+ |
#else |
773 |
+ |
if (worldRank == 0){ |
774 |
+ |
seedValue = make_sprng_seed(); |
775 |
+ |
} |
776 |
+ |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
777 |
+ |
#endif |
778 |
+ |
}//end of globals->haveSeed() |
779 |
+ |
|
780 |
+ |
for (int i = 0; i < nInfo; i++){ |
781 |
+ |
info[i].setSeed(seedValue); |
782 |
|
} |
783 |
|
|
784 |
< |
if( have_extra ){ |
785 |
< |
done = 0; |
784 |
> |
#ifdef IS_MPI |
785 |
> |
strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
786 |
> |
MPIcheckPoint(); |
787 |
> |
#endif // is_mpi |
788 |
> |
} |
789 |
|
|
1177 |
– |
int start_ndx; |
1178 |
– |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
1179 |
– |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
790 |
|
|
791 |
< |
if( i < n_cells ){ |
791 |
> |
void SimSetup::finalInfoCheck(void){ |
792 |
> |
int index; |
793 |
> |
int usesDipoles; |
794 |
> |
int i; |
795 |
|
|
796 |
< |
if( j < n_cells ){ |
797 |
< |
start_ndx = n_cells; |
1185 |
< |
} |
1186 |
< |
else start_ndx = 0; |
1187 |
< |
} |
1188 |
< |
else start_ndx = 0; |
796 |
> |
for (i = 0; i < nInfo; i++){ |
797 |
> |
// check electrostatic parameters |
798 |
|
|
799 |
< |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
799 |
> |
index = 0; |
800 |
> |
usesDipoles = 0; |
801 |
> |
while ((index < info[i].n_atoms) && !usesDipoles){ |
802 |
> |
usesDipoles = (info[i].atoms[index])->hasDipole(); |
803 |
> |
index++; |
804 |
> |
} |
805 |
|
|
806 |
< |
makeElement( i * cellx, |
807 |
< |
j * celly, |
808 |
< |
k * cellz ); |
809 |
< |
done = ( current_mol >= tot_nmol ); |
806 |
> |
#ifdef IS_MPI |
807 |
> |
int myUse = usesDipoles; |
808 |
> |
MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
809 |
> |
#endif //is_mpi |
810 |
|
|
811 |
< |
if( !done && n_per_extra > 1 ){ |
1198 |
< |
makeElement( i * cellx + 0.5 * cellx, |
1199 |
< |
j * celly + 0.5 * celly, |
1200 |
< |
k * cellz ); |
1201 |
< |
done = ( current_mol >= tot_nmol ); |
1202 |
< |
} |
811 |
> |
double theEcr, theEst; |
812 |
|
|
813 |
< |
if( !done && n_per_extra > 2){ |
814 |
< |
makeElement( i * cellx, |
1206 |
< |
j * celly + 0.5 * celly, |
1207 |
< |
k * cellz + 0.5 * cellz ); |
1208 |
< |
done = ( current_mol >= tot_nmol ); |
1209 |
< |
} |
813 |
> |
if (globals->getUseRF()){ |
814 |
> |
info[i].useReactionField = 1; |
815 |
|
|
816 |
< |
if( !done && n_per_extra > 3){ |
817 |
< |
makeElement( i * cellx + 0.5 * cellx, |
818 |
< |
j * celly, |
819 |
< |
k * cellz + 0.5 * cellz ); |
820 |
< |
done = ( current_mol >= tot_nmol ); |
821 |
< |
} |
822 |
< |
} |
816 |
> |
if (!globals->haveECR()){ |
817 |
> |
sprintf(painCave.errMsg, |
818 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
819 |
> |
"box length for the electrostaticCutoffRadius.\n" |
820 |
> |
"I hope you have a very fast processor!\n"); |
821 |
> |
painCave.isFatal = 0; |
822 |
> |
simError(); |
823 |
> |
double smallest; |
824 |
> |
smallest = info[i].boxL[0]; |
825 |
> |
if (info[i].boxL[1] <= smallest) |
826 |
> |
smallest = info[i].boxL[1]; |
827 |
> |
if (info[i].boxL[2] <= smallest) |
828 |
> |
smallest = info[i].boxL[2]; |
829 |
> |
theEcr = 0.5 * smallest; |
830 |
|
} |
831 |
+ |
else{ |
832 |
+ |
theEcr = globals->getECR(); |
833 |
+ |
} |
834 |
+ |
|
835 |
+ |
if (!globals->haveEST()){ |
836 |
+ |
sprintf(painCave.errMsg, |
837 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
838 |
+ |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n"); |
839 |
+ |
painCave.isFatal = 0; |
840 |
+ |
simError(); |
841 |
+ |
theEst = 0.05 * theEcr; |
842 |
+ |
} |
843 |
+ |
else{ |
844 |
+ |
theEst = globals->getEST(); |
845 |
+ |
} |
846 |
+ |
|
847 |
+ |
info[i].setEcr(theEcr, theEst); |
848 |
+ |
|
849 |
+ |
if (!globals->haveDielectric()){ |
850 |
+ |
sprintf(painCave.errMsg, |
851 |
+ |
"SimSetup Error: You are trying to use Reaction Field without" |
852 |
+ |
"setting a dielectric constant!\n"); |
853 |
+ |
painCave.isFatal = 1; |
854 |
+ |
simError(); |
855 |
+ |
} |
856 |
+ |
info[i].dielectric = globals->getDielectric(); |
857 |
|
} |
858 |
< |
} |
858 |
> |
else{ |
859 |
> |
if (usesDipoles){ |
860 |
> |
if (!globals->haveECR()){ |
861 |
> |
sprintf(painCave.errMsg, |
862 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
863 |
> |
"box length for the electrostaticCutoffRadius.\n" |
864 |
> |
"I hope you have a very fast processor!\n"); |
865 |
> |
painCave.isFatal = 0; |
866 |
> |
simError(); |
867 |
> |
double smallest; |
868 |
> |
smallest = info[i].boxL[0]; |
869 |
> |
if (info[i].boxL[1] <= smallest) |
870 |
> |
smallest = info[i].boxL[1]; |
871 |
> |
if (info[i].boxL[2] <= smallest) |
872 |
> |
smallest = info[i].boxL[2]; |
873 |
> |
theEcr = 0.5 * smallest; |
874 |
> |
} |
875 |
> |
else{ |
876 |
> |
theEcr = globals->getECR(); |
877 |
> |
} |
878 |
|
|
879 |
+ |
if (!globals->haveEST()){ |
880 |
+ |
sprintf(painCave.errMsg, |
881 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
882 |
+ |
"electrostaticCutoffRadius for the " |
883 |
+ |
"electrostaticSkinThickness\n"); |
884 |
+ |
painCave.isFatal = 0; |
885 |
+ |
simError(); |
886 |
+ |
theEst = 0.05 * theEcr; |
887 |
+ |
} |
888 |
+ |
else{ |
889 |
+ |
theEst = globals->getEST(); |
890 |
+ |
} |
891 |
|
|
892 |
< |
for( i=0; i<simnfo->n_atoms; i++ ){ |
893 |
< |
simnfo->atoms[i]->set_vx( 0.0 ); |
894 |
< |
simnfo->atoms[i]->set_vy( 0.0 ); |
1226 |
< |
simnfo->atoms[i]->set_vz( 0.0 ); |
892 |
> |
info[i].setEcr(theEcr, theEst); |
893 |
> |
} |
894 |
> |
} |
895 |
|
} |
896 |
+ |
|
897 |
+ |
#ifdef IS_MPI |
898 |
+ |
strcpy(checkPointMsg, "post processing checks out"); |
899 |
+ |
MPIcheckPoint(); |
900 |
+ |
#endif // is_mpi |
901 |
|
} |
902 |
|
|
903 |
< |
void SimSetup::makeElement( double x, double y, double z ){ |
903 |
> |
void SimSetup::initSystemCoords(void){ |
904 |
> |
int i; |
905 |
|
|
906 |
< |
int k; |
1233 |
< |
AtomStamp* current_atom; |
1234 |
< |
DirectionalAtom* dAtom; |
1235 |
< |
double rotMat[3][3]; |
906 |
> |
char* inName; |
907 |
|
|
908 |
< |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
908 |
> |
(info[0].getConfiguration())->createArrays(info[0].n_atoms); |
909 |
|
|
910 |
< |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
911 |
< |
if( !current_atom->havePosition() ){ |
912 |
< |
sprintf( painCave.errMsg, |
913 |
< |
"SimSetup:initFromBass error.\n" |
914 |
< |
"\tComponent %s, atom %s does not have a position specified.\n" |
915 |
< |
"\tThe initialization routine is unable to give a start" |
916 |
< |
" position.\n", |
917 |
< |
comp_stamps[current_comp]->getID(), |
918 |
< |
current_atom->getType() ); |
910 |
> |
for (i = 0; i < info[0].n_atoms; i++) |
911 |
> |
info[0].atoms[i]->setCoords(); |
912 |
> |
|
913 |
> |
if (globals->haveInitialConfig()){ |
914 |
> |
InitializeFromFile* fileInit; |
915 |
> |
#ifdef IS_MPI // is_mpi |
916 |
> |
if (worldRank == 0){ |
917 |
> |
#endif //is_mpi |
918 |
> |
inName = globals->getInitialConfig(); |
919 |
> |
fileInit = new InitializeFromFile(inName); |
920 |
> |
#ifdef IS_MPI |
921 |
> |
} |
922 |
> |
else |
923 |
> |
fileInit = new InitializeFromFile(NULL); |
924 |
> |
#endif |
925 |
> |
fileInit->readInit(info); // default velocities on |
926 |
> |
|
927 |
> |
delete fileInit; |
928 |
> |
} |
929 |
> |
else{ |
930 |
> |
#ifdef IS_MPI |
931 |
> |
|
932 |
> |
// no init from bass |
933 |
> |
|
934 |
> |
sprintf(painCave.errMsg, |
935 |
> |
"Cannot intialize a parallel simulation without an initial configuration file.\n"); |
936 |
> |
painCave.isFatal = 1;; |
937 |
> |
simError(); |
938 |
> |
|
939 |
> |
#else |
940 |
> |
|
941 |
> |
initFromBass(); |
942 |
> |
|
943 |
> |
|
944 |
> |
#endif |
945 |
> |
} |
946 |
> |
|
947 |
> |
#ifdef IS_MPI |
948 |
> |
strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
949 |
> |
MPIcheckPoint(); |
950 |
> |
#endif // is_mpi |
951 |
> |
} |
952 |
> |
|
953 |
> |
|
954 |
> |
void SimSetup::makeOutNames(void){ |
955 |
> |
int k; |
956 |
> |
|
957 |
> |
|
958 |
> |
for (k = 0; k < nInfo; k++){ |
959 |
> |
#ifdef IS_MPI |
960 |
> |
if (worldRank == 0){ |
961 |
> |
#endif // is_mpi |
962 |
> |
|
963 |
> |
if (globals->haveFinalConfig()){ |
964 |
> |
strcpy(info[k].finalName, globals->getFinalConfig()); |
965 |
> |
} |
966 |
> |
else{ |
967 |
> |
strcpy(info[k].finalName, inFileName); |
968 |
> |
char* endTest; |
969 |
> |
int nameLength = strlen(info[k].finalName); |
970 |
> |
endTest = &(info[k].finalName[nameLength - 5]); |
971 |
> |
if (!strcmp(endTest, ".bass")){ |
972 |
> |
strcpy(endTest, ".eor"); |
973 |
> |
} |
974 |
> |
else if (!strcmp(endTest, ".BASS")){ |
975 |
> |
strcpy(endTest, ".eor"); |
976 |
> |
} |
977 |
> |
else{ |
978 |
> |
endTest = &(info[k].finalName[nameLength - 4]); |
979 |
> |
if (!strcmp(endTest, ".bss")){ |
980 |
> |
strcpy(endTest, ".eor"); |
981 |
> |
} |
982 |
> |
else if (!strcmp(endTest, ".mdl")){ |
983 |
> |
strcpy(endTest, ".eor"); |
984 |
> |
} |
985 |
> |
else{ |
986 |
> |
strcat(info[k].finalName, ".eor"); |
987 |
> |
} |
988 |
> |
} |
989 |
> |
} |
990 |
> |
|
991 |
> |
// make the sample and status out names |
992 |
> |
|
993 |
> |
strcpy(info[k].sampleName, inFileName); |
994 |
> |
char* endTest; |
995 |
> |
int nameLength = strlen(info[k].sampleName); |
996 |
> |
endTest = &(info[k].sampleName[nameLength - 5]); |
997 |
> |
if (!strcmp(endTest, ".bass")){ |
998 |
> |
strcpy(endTest, ".dump"); |
999 |
> |
} |
1000 |
> |
else if (!strcmp(endTest, ".BASS")){ |
1001 |
> |
strcpy(endTest, ".dump"); |
1002 |
> |
} |
1003 |
> |
else{ |
1004 |
> |
endTest = &(info[k].sampleName[nameLength - 4]); |
1005 |
> |
if (!strcmp(endTest, ".bss")){ |
1006 |
> |
strcpy(endTest, ".dump"); |
1007 |
> |
} |
1008 |
> |
else if (!strcmp(endTest, ".mdl")){ |
1009 |
> |
strcpy(endTest, ".dump"); |
1010 |
> |
} |
1011 |
> |
else{ |
1012 |
> |
strcat(info[k].sampleName, ".dump"); |
1013 |
> |
} |
1014 |
> |
} |
1015 |
> |
|
1016 |
> |
strcpy(info[k].statusName, inFileName); |
1017 |
> |
nameLength = strlen(info[k].statusName); |
1018 |
> |
endTest = &(info[k].statusName[nameLength - 5]); |
1019 |
> |
if (!strcmp(endTest, ".bass")){ |
1020 |
> |
strcpy(endTest, ".stat"); |
1021 |
> |
} |
1022 |
> |
else if (!strcmp(endTest, ".BASS")){ |
1023 |
> |
strcpy(endTest, ".stat"); |
1024 |
> |
} |
1025 |
> |
else{ |
1026 |
> |
endTest = &(info[k].statusName[nameLength - 4]); |
1027 |
> |
if (!strcmp(endTest, ".bss")){ |
1028 |
> |
strcpy(endTest, ".stat"); |
1029 |
> |
} |
1030 |
> |
else if (!strcmp(endTest, ".mdl")){ |
1031 |
> |
strcpy(endTest, ".stat"); |
1032 |
> |
} |
1033 |
> |
else{ |
1034 |
> |
strcat(info[k].statusName, ".stat"); |
1035 |
> |
} |
1036 |
> |
} |
1037 |
> |
|
1038 |
> |
#ifdef IS_MPI |
1039 |
> |
|
1040 |
> |
} |
1041 |
> |
#endif // is_mpi |
1042 |
> |
} |
1043 |
> |
} |
1044 |
> |
|
1045 |
> |
|
1046 |
> |
void SimSetup::sysObjectsCreation(void){ |
1047 |
> |
int i, k; |
1048 |
> |
|
1049 |
> |
// create the forceField |
1050 |
> |
|
1051 |
> |
createFF(); |
1052 |
> |
|
1053 |
> |
// extract componentList |
1054 |
> |
|
1055 |
> |
compList(); |
1056 |
> |
|
1057 |
> |
// calc the number of atoms, bond, bends, and torsions |
1058 |
> |
|
1059 |
> |
calcSysValues(); |
1060 |
> |
|
1061 |
> |
#ifdef IS_MPI |
1062 |
> |
// divide the molecules among the processors |
1063 |
> |
|
1064 |
> |
mpiMolDivide(); |
1065 |
> |
#endif //is_mpi |
1066 |
> |
|
1067 |
> |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1068 |
> |
|
1069 |
> |
makeSysArrays(); |
1070 |
> |
|
1071 |
> |
// make and initialize the molecules (all but atomic coordinates) |
1072 |
> |
|
1073 |
> |
makeMolecules(); |
1074 |
> |
|
1075 |
> |
for (k = 0; k < nInfo; k++){ |
1076 |
> |
info[k].identArray = new int[info[k].n_atoms]; |
1077 |
> |
for (i = 0; i < info[k].n_atoms; i++){ |
1078 |
> |
info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1079 |
> |
} |
1080 |
> |
} |
1081 |
> |
} |
1082 |
> |
|
1083 |
> |
|
1084 |
> |
void SimSetup::createFF(void){ |
1085 |
> |
switch (ffCase){ |
1086 |
> |
case FF_DUFF: |
1087 |
> |
the_ff = new DUFF(); |
1088 |
> |
break; |
1089 |
> |
|
1090 |
> |
case FF_LJ: |
1091 |
> |
the_ff = new LJFF(); |
1092 |
> |
break; |
1093 |
> |
|
1094 |
> |
case FF_EAM: |
1095 |
> |
the_ff = new EAM_FF(); |
1096 |
> |
break; |
1097 |
> |
|
1098 |
> |
default: |
1099 |
> |
sprintf(painCave.errMsg, |
1100 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1101 |
|
painCave.isFatal = 1; |
1102 |
|
simError(); |
1103 |
+ |
} |
1104 |
+ |
|
1105 |
+ |
#ifdef IS_MPI |
1106 |
+ |
strcpy(checkPointMsg, "ForceField creation successful"); |
1107 |
+ |
MPIcheckPoint(); |
1108 |
+ |
#endif // is_mpi |
1109 |
+ |
} |
1110 |
+ |
|
1111 |
+ |
|
1112 |
+ |
void SimSetup::compList(void){ |
1113 |
+ |
int i; |
1114 |
+ |
char* id; |
1115 |
+ |
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1116 |
+ |
LinkedMolStamp* currentStamp = NULL; |
1117 |
+ |
comp_stamps = new MoleculeStamp * [n_components]; |
1118 |
+ |
|
1119 |
+ |
// make an array of molecule stamps that match the components used. |
1120 |
+ |
// also extract the used stamps out into a separate linked list |
1121 |
+ |
|
1122 |
+ |
for (i = 0; i < nInfo; i++){ |
1123 |
+ |
info[i].nComponents = n_components; |
1124 |
+ |
info[i].componentsNmol = components_nmol; |
1125 |
+ |
info[i].compStamps = comp_stamps; |
1126 |
+ |
info[i].headStamp = headStamp; |
1127 |
+ |
} |
1128 |
+ |
|
1129 |
+ |
|
1130 |
+ |
for (i = 0; i < n_components; i++){ |
1131 |
+ |
id = the_components[i]->getType(); |
1132 |
+ |
comp_stamps[i] = NULL; |
1133 |
+ |
|
1134 |
+ |
// check to make sure the component isn't already in the list |
1135 |
+ |
|
1136 |
+ |
comp_stamps[i] = headStamp->match(id); |
1137 |
+ |
if (comp_stamps[i] == NULL){ |
1138 |
+ |
// extract the component from the list; |
1139 |
+ |
|
1140 |
+ |
currentStamp = stamps->extractMolStamp(id); |
1141 |
+ |
if (currentStamp == NULL){ |
1142 |
+ |
sprintf(painCave.errMsg, |
1143 |
+ |
"SimSetup error: Component \"%s\" was not found in the " |
1144 |
+ |
"list of declared molecules\n", |
1145 |
+ |
id); |
1146 |
+ |
painCave.isFatal = 1; |
1147 |
+ |
simError(); |
1148 |
+ |
} |
1149 |
+ |
|
1150 |
+ |
headStamp->add(currentStamp); |
1151 |
+ |
comp_stamps[i] = headStamp->match(id); |
1152 |
|
} |
1153 |
+ |
} |
1154 |
|
|
1155 |
< |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1156 |
< |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1157 |
< |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1155 |
> |
#ifdef IS_MPI |
1156 |
> |
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1157 |
> |
MPIcheckPoint(); |
1158 |
> |
#endif // is_mpi |
1159 |
> |
} |
1160 |
|
|
1161 |
< |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1161 |
> |
void SimSetup::calcSysValues(void){ |
1162 |
> |
int i; |
1163 |
|
|
1164 |
< |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1164 |
> |
int* molMembershipArray; |
1165 |
|
|
1166 |
< |
rotMat[0][0] = 1.0; |
1167 |
< |
rotMat[0][1] = 0.0; |
1168 |
< |
rotMat[0][2] = 0.0; |
1166 |
> |
tot_atoms = 0; |
1167 |
> |
tot_bonds = 0; |
1168 |
> |
tot_bends = 0; |
1169 |
> |
tot_torsions = 0; |
1170 |
> |
for (i = 0; i < n_components; i++){ |
1171 |
> |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1172 |
> |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1173 |
> |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1174 |
> |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1175 |
> |
} |
1176 |
|
|
1177 |
< |
rotMat[1][0] = 0.0; |
1178 |
< |
rotMat[1][1] = 1.0; |
1266 |
< |
rotMat[1][2] = 0.0; |
1177 |
> |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1178 |
> |
molMembershipArray = new int[tot_atoms]; |
1179 |
|
|
1180 |
< |
rotMat[2][0] = 0.0; |
1181 |
< |
rotMat[2][1] = 0.0; |
1182 |
< |
rotMat[2][2] = 1.0; |
1180 |
> |
for (i = 0; i < nInfo; i++){ |
1181 |
> |
info[i].n_atoms = tot_atoms; |
1182 |
> |
info[i].n_bonds = tot_bonds; |
1183 |
> |
info[i].n_bends = tot_bends; |
1184 |
> |
info[i].n_torsions = tot_torsions; |
1185 |
> |
info[i].n_SRI = tot_SRI; |
1186 |
> |
info[i].n_mol = tot_nmol; |
1187 |
|
|
1188 |
< |
dAtom->setA( rotMat ); |
1188 |
> |
info[i].molMembershipArray = molMembershipArray; |
1189 |
> |
} |
1190 |
> |
} |
1191 |
> |
|
1192 |
> |
#ifdef IS_MPI |
1193 |
> |
|
1194 |
> |
void SimSetup::mpiMolDivide(void){ |
1195 |
> |
int i, j, k; |
1196 |
> |
int localMol, allMol; |
1197 |
> |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1198 |
> |
|
1199 |
> |
mpiSim = new mpiSimulation(info); |
1200 |
> |
|
1201 |
> |
globalIndex = mpiSim->divideLabor(); |
1202 |
> |
|
1203 |
> |
// set up the local variables |
1204 |
> |
|
1205 |
> |
mol2proc = mpiSim->getMolToProcMap(); |
1206 |
> |
molCompType = mpiSim->getMolComponentType(); |
1207 |
> |
|
1208 |
> |
allMol = 0; |
1209 |
> |
localMol = 0; |
1210 |
> |
local_atoms = 0; |
1211 |
> |
local_bonds = 0; |
1212 |
> |
local_bends = 0; |
1213 |
> |
local_torsions = 0; |
1214 |
> |
globalAtomIndex = 0; |
1215 |
> |
|
1216 |
> |
|
1217 |
> |
for (i = 0; i < n_components; i++){ |
1218 |
> |
for (j = 0; j < components_nmol[i]; j++){ |
1219 |
> |
if (mol2proc[allMol] == worldRank){ |
1220 |
> |
local_atoms += comp_stamps[i]->getNAtoms(); |
1221 |
> |
local_bonds += comp_stamps[i]->getNBonds(); |
1222 |
> |
local_bends += comp_stamps[i]->getNBends(); |
1223 |
> |
local_torsions += comp_stamps[i]->getNTorsions(); |
1224 |
> |
localMol++; |
1225 |
> |
} |
1226 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1227 |
> |
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1228 |
> |
globalAtomIndex++; |
1229 |
> |
} |
1230 |
> |
|
1231 |
> |
allMol++; |
1232 |
|
} |
1233 |
+ |
} |
1234 |
+ |
local_SRI = local_bonds + local_bends + local_torsions; |
1235 |
|
|
1236 |
< |
current_atom_ndx++; |
1236 |
> |
info[0].n_atoms = mpiSim->getMyNlocal(); |
1237 |
> |
|
1238 |
> |
if (local_atoms != info[0].n_atoms){ |
1239 |
> |
sprintf(painCave.errMsg, |
1240 |
> |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1241 |
> |
" localAtom (%d) are not equal.\n", |
1242 |
> |
info[0].n_atoms, local_atoms); |
1243 |
> |
painCave.isFatal = 1; |
1244 |
> |
simError(); |
1245 |
|
} |
1246 |
|
|
1247 |
< |
current_mol++; |
1248 |
< |
current_comp_mol++; |
1247 |
> |
info[0].n_bonds = local_bonds; |
1248 |
> |
info[0].n_bends = local_bends; |
1249 |
> |
info[0].n_torsions = local_torsions; |
1250 |
> |
info[0].n_SRI = local_SRI; |
1251 |
> |
info[0].n_mol = localMol; |
1252 |
|
|
1253 |
< |
if( current_comp_mol >= components_nmol[current_comp] ){ |
1253 |
> |
strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1254 |
> |
MPIcheckPoint(); |
1255 |
> |
} |
1256 |
|
|
1257 |
< |
current_comp_mol = 0; |
1258 |
< |
current_comp++; |
1257 |
> |
#endif // is_mpi |
1258 |
> |
|
1259 |
> |
|
1260 |
> |
void SimSetup::makeSysArrays(void){ |
1261 |
> |
|
1262 |
> |
#ifndef IS_MPI |
1263 |
> |
int k, j; |
1264 |
> |
#endif // is_mpi |
1265 |
> |
int i, l; |
1266 |
> |
|
1267 |
> |
Atom** the_atoms; |
1268 |
> |
Molecule* the_molecules; |
1269 |
> |
Exclude** the_excludes; |
1270 |
> |
|
1271 |
> |
|
1272 |
> |
for (l = 0; l < nInfo; l++){ |
1273 |
> |
// create the atom and short range interaction arrays |
1274 |
> |
|
1275 |
> |
the_atoms = new Atom * [info[l].n_atoms]; |
1276 |
> |
the_molecules = new Molecule[info[l].n_mol]; |
1277 |
> |
int molIndex; |
1278 |
> |
|
1279 |
> |
// initialize the molecule's stampID's |
1280 |
> |
|
1281 |
> |
#ifdef IS_MPI |
1282 |
> |
|
1283 |
> |
|
1284 |
> |
molIndex = 0; |
1285 |
> |
for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1286 |
> |
if (mol2proc[i] == worldRank){ |
1287 |
> |
the_molecules[molIndex].setStampID(molCompType[i]); |
1288 |
> |
the_molecules[molIndex].setMyIndex(molIndex); |
1289 |
> |
the_molecules[molIndex].setGlobalIndex(i); |
1290 |
> |
molIndex++; |
1291 |
> |
} |
1292 |
> |
} |
1293 |
> |
|
1294 |
> |
#else // is_mpi |
1295 |
> |
|
1296 |
> |
molIndex = 0; |
1297 |
> |
globalAtomIndex = 0; |
1298 |
> |
for (i = 0; i < n_components; i++){ |
1299 |
> |
for (j = 0; j < components_nmol[i]; j++){ |
1300 |
> |
the_molecules[molIndex].setStampID(i); |
1301 |
> |
the_molecules[molIndex].setMyIndex(molIndex); |
1302 |
> |
the_molecules[molIndex].setGlobalIndex(molIndex); |
1303 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1304 |
> |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1305 |
> |
globalAtomIndex++; |
1306 |
> |
} |
1307 |
> |
molIndex++; |
1308 |
> |
} |
1309 |
> |
} |
1310 |
> |
|
1311 |
> |
|
1312 |
> |
#endif // is_mpi |
1313 |
> |
|
1314 |
> |
|
1315 |
> |
if (info[l].n_SRI){ |
1316 |
> |
Exclude::createArray(info[l].n_SRI); |
1317 |
> |
the_excludes = new Exclude * [info[l].n_SRI]; |
1318 |
> |
for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1319 |
> |
the_excludes[ex] = new Exclude(ex); |
1320 |
> |
} |
1321 |
> |
info[l].globalExcludes = new int; |
1322 |
> |
info[l].n_exclude = info[l].n_SRI; |
1323 |
> |
} |
1324 |
> |
else{ |
1325 |
> |
Exclude::createArray(1); |
1326 |
> |
the_excludes = new Exclude * ; |
1327 |
> |
the_excludes[0] = new Exclude(0); |
1328 |
> |
the_excludes[0]->setPair(0, 0); |
1329 |
> |
info[l].globalExcludes = new int; |
1330 |
> |
info[l].globalExcludes[0] = 0; |
1331 |
> |
info[l].n_exclude = 0; |
1332 |
> |
} |
1333 |
> |
|
1334 |
> |
// set the arrays into the SimInfo object |
1335 |
> |
|
1336 |
> |
info[l].atoms = the_atoms; |
1337 |
> |
info[l].molecules = the_molecules; |
1338 |
> |
info[l].nGlobalExcludes = 0; |
1339 |
> |
info[l].excludes = the_excludes; |
1340 |
> |
|
1341 |
> |
the_ff->setSimInfo(info); |
1342 |
|
} |
1343 |
|
} |
1344 |
+ |
|
1345 |
+ |
void SimSetup::makeIntegrator(void){ |
1346 |
+ |
int k; |
1347 |
+ |
|
1348 |
+ |
NVE<RealIntegrator>* myNVE = NULL; |
1349 |
+ |
NVT<RealIntegrator>* myNVT = NULL; |
1350 |
+ |
NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1351 |
+ |
NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1352 |
+ |
|
1353 |
+ |
for (k = 0; k < nInfo; k++){ |
1354 |
+ |
switch (ensembleCase){ |
1355 |
+ |
case NVE_ENS: |
1356 |
+ |
if (globals->haveZconstraints()){ |
1357 |
+ |
setupZConstraint(info[k]); |
1358 |
+ |
myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1359 |
+ |
} |
1360 |
+ |
else{ |
1361 |
+ |
myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1362 |
+ |
} |
1363 |
+ |
|
1364 |
+ |
info->the_integrator = myNVE; |
1365 |
+ |
break; |
1366 |
+ |
|
1367 |
+ |
case NVT_ENS: |
1368 |
+ |
if (globals->haveZconstraints()){ |
1369 |
+ |
setupZConstraint(info[k]); |
1370 |
+ |
myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1371 |
+ |
} |
1372 |
+ |
else |
1373 |
+ |
myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1374 |
+ |
|
1375 |
+ |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1376 |
+ |
|
1377 |
+ |
if (globals->haveTauThermostat()) |
1378 |
+ |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1379 |
+ |
else{ |
1380 |
+ |
sprintf(painCave.errMsg, |
1381 |
+ |
"SimSetup error: If you use the NVT\n" |
1382 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1383 |
+ |
painCave.isFatal = 1; |
1384 |
+ |
simError(); |
1385 |
+ |
} |
1386 |
+ |
|
1387 |
+ |
info->the_integrator = myNVT; |
1388 |
+ |
break; |
1389 |
+ |
|
1390 |
+ |
case NPTi_ENS: |
1391 |
+ |
if (globals->haveZconstraints()){ |
1392 |
+ |
setupZConstraint(info[k]); |
1393 |
+ |
myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1394 |
+ |
} |
1395 |
+ |
else |
1396 |
+ |
myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1397 |
+ |
|
1398 |
+ |
myNPTi->setTargetTemp(globals->getTargetTemp()); |
1399 |
+ |
|
1400 |
+ |
if (globals->haveTargetPressure()) |
1401 |
+ |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1402 |
+ |
else{ |
1403 |
+ |
sprintf(painCave.errMsg, |
1404 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1405 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1406 |
+ |
painCave.isFatal = 1; |
1407 |
+ |
simError(); |
1408 |
+ |
} |
1409 |
+ |
|
1410 |
+ |
if (globals->haveTauThermostat()) |
1411 |
+ |
myNPTi->setTauThermostat(globals->getTauThermostat()); |
1412 |
+ |
else{ |
1413 |
+ |
sprintf(painCave.errMsg, |
1414 |
+ |
"SimSetup error: If you use an NPT\n" |
1415 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1416 |
+ |
painCave.isFatal = 1; |
1417 |
+ |
simError(); |
1418 |
+ |
} |
1419 |
+ |
|
1420 |
+ |
if (globals->haveTauBarostat()) |
1421 |
+ |
myNPTi->setTauBarostat(globals->getTauBarostat()); |
1422 |
+ |
else{ |
1423 |
+ |
sprintf(painCave.errMsg, |
1424 |
+ |
"SimSetup error: If you use an NPT\n" |
1425 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1426 |
+ |
painCave.isFatal = 1; |
1427 |
+ |
simError(); |
1428 |
+ |
} |
1429 |
+ |
|
1430 |
+ |
info->the_integrator = myNPTi; |
1431 |
+ |
break; |
1432 |
+ |
|
1433 |
+ |
case NPTf_ENS: |
1434 |
+ |
if (globals->haveZconstraints()){ |
1435 |
+ |
setupZConstraint(info[k]); |
1436 |
+ |
myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1437 |
+ |
} |
1438 |
+ |
else |
1439 |
+ |
myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1440 |
+ |
|
1441 |
+ |
myNPTf->setTargetTemp(globals->getTargetTemp()); |
1442 |
+ |
|
1443 |
+ |
if (globals->haveTargetPressure()) |
1444 |
+ |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1445 |
+ |
else{ |
1446 |
+ |
sprintf(painCave.errMsg, |
1447 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1448 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1449 |
+ |
painCave.isFatal = 1; |
1450 |
+ |
simError(); |
1451 |
+ |
} |
1452 |
+ |
|
1453 |
+ |
if (globals->haveTauThermostat()) |
1454 |
+ |
myNPTf->setTauThermostat(globals->getTauThermostat()); |
1455 |
+ |
else{ |
1456 |
+ |
sprintf(painCave.errMsg, |
1457 |
+ |
"SimSetup error: If you use an NPT\n" |
1458 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1459 |
+ |
painCave.isFatal = 1; |
1460 |
+ |
simError(); |
1461 |
+ |
} |
1462 |
+ |
|
1463 |
+ |
if (globals->haveTauBarostat()) |
1464 |
+ |
myNPTf->setTauBarostat(globals->getTauBarostat()); |
1465 |
+ |
else{ |
1466 |
+ |
sprintf(painCave.errMsg, |
1467 |
+ |
"SimSetup error: If you use an NPT\n" |
1468 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1469 |
+ |
painCave.isFatal = 1; |
1470 |
+ |
simError(); |
1471 |
+ |
} |
1472 |
+ |
|
1473 |
+ |
info->the_integrator = myNPTf; |
1474 |
+ |
break; |
1475 |
+ |
|
1476 |
+ |
default: |
1477 |
+ |
sprintf(painCave.errMsg, |
1478 |
+ |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1479 |
+ |
painCave.isFatal = 1; |
1480 |
+ |
simError(); |
1481 |
+ |
} |
1482 |
+ |
} |
1483 |
+ |
} |
1484 |
+ |
|
1485 |
+ |
void SimSetup::initFortran(void){ |
1486 |
+ |
info[0].refreshSim(); |
1487 |
+ |
|
1488 |
+ |
if (!strcmp(info[0].mixingRule, "standard")){ |
1489 |
+ |
the_ff->initForceField(LB_MIXING_RULE); |
1490 |
+ |
} |
1491 |
+ |
else if (!strcmp(info[0].mixingRule, "explicit")){ |
1492 |
+ |
the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1493 |
+ |
} |
1494 |
+ |
else{ |
1495 |
+ |
sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1496 |
+ |
info[0].mixingRule); |
1497 |
+ |
painCave.isFatal = 1; |
1498 |
+ |
simError(); |
1499 |
+ |
} |
1500 |
+ |
|
1501 |
+ |
|
1502 |
+ |
#ifdef IS_MPI |
1503 |
+ |
strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1504 |
+ |
MPIcheckPoint(); |
1505 |
+ |
#endif // is_mpi |
1506 |
+ |
} |
1507 |
+ |
|
1508 |
+ |
void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1509 |
+ |
int nZConstraints; |
1510 |
+ |
ZconStamp** zconStamp; |
1511 |
+ |
|
1512 |
+ |
if (globals->haveZconstraintTime()){ |
1513 |
+ |
//add sample time of z-constraint into SimInfo's property list |
1514 |
+ |
DoubleData* zconsTimeProp = new DoubleData(); |
1515 |
+ |
zconsTimeProp->setID(ZCONSTIME_ID); |
1516 |
+ |
zconsTimeProp->setData(globals->getZconsTime()); |
1517 |
+ |
theInfo.addProperty(zconsTimeProp); |
1518 |
+ |
} |
1519 |
+ |
else{ |
1520 |
+ |
sprintf(painCave.errMsg, |
1521 |
+ |
"ZConstraint error: If you use an ZConstraint\n" |
1522 |
+ |
" , you must set sample time.\n"); |
1523 |
+ |
painCave.isFatal = 1; |
1524 |
+ |
simError(); |
1525 |
+ |
} |
1526 |
+ |
|
1527 |
+ |
//push zconsTol into siminfo, if user does not specify |
1528 |
+ |
//value for zconsTol, a default value will be used |
1529 |
+ |
DoubleData* zconsTol = new DoubleData(); |
1530 |
+ |
zconsTol->setID(ZCONSTOL_ID); |
1531 |
+ |
if (globals->haveZconsTol()){ |
1532 |
+ |
zconsTol->setData(globals->getZconsTol()); |
1533 |
+ |
} |
1534 |
+ |
else{ |
1535 |
+ |
double defaultZConsTol = 0.01; |
1536 |
+ |
sprintf(painCave.errMsg, |
1537 |
+ |
"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1538 |
+ |
" , default value %f is used.\n", |
1539 |
+ |
defaultZConsTol); |
1540 |
+ |
painCave.isFatal = 0; |
1541 |
+ |
simError(); |
1542 |
+ |
|
1543 |
+ |
zconsTol->setData(defaultZConsTol); |
1544 |
+ |
} |
1545 |
+ |
theInfo.addProperty(zconsTol); |
1546 |
+ |
|
1547 |
+ |
//set Force Subtraction Policy |
1548 |
+ |
StringData* zconsForcePolicy = new StringData(); |
1549 |
+ |
zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1550 |
+ |
|
1551 |
+ |
if (globals->haveZconsForcePolicy()){ |
1552 |
+ |
zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1553 |
+ |
} |
1554 |
+ |
else{ |
1555 |
+ |
sprintf(painCave.errMsg, |
1556 |
+ |
"ZConstraint Warning: User does not set force Subtraction policy, " |
1557 |
+ |
"PolicyByMass is used\n"); |
1558 |
+ |
painCave.isFatal = 0; |
1559 |
+ |
simError(); |
1560 |
+ |
zconsForcePolicy->setData("BYMASS"); |
1561 |
+ |
} |
1562 |
+ |
|
1563 |
+ |
theInfo.addProperty(zconsForcePolicy); |
1564 |
+ |
|
1565 |
+ |
//Determine the name of ouput file and add it into SimInfo's property list |
1566 |
+ |
//Be careful, do not use inFileName, since it is a pointer which |
1567 |
+ |
//point to a string at master node, and slave nodes do not contain that string |
1568 |
+ |
|
1569 |
+ |
string zconsOutput(theInfo.finalName); |
1570 |
+ |
|
1571 |
+ |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1572 |
+ |
|
1573 |
+ |
StringData* zconsFilename = new StringData(); |
1574 |
+ |
zconsFilename->setID(ZCONSFILENAME_ID); |
1575 |
+ |
zconsFilename->setData(zconsOutput); |
1576 |
+ |
|
1577 |
+ |
theInfo.addProperty(zconsFilename); |
1578 |
+ |
|
1579 |
+ |
//setup index, pos and other parameters of z-constraint molecules |
1580 |
+ |
nZConstraints = globals->getNzConstraints(); |
1581 |
+ |
theInfo.nZconstraints = nZConstraints; |
1582 |
+ |
|
1583 |
+ |
zconStamp = globals->getZconStamp(); |
1584 |
+ |
ZConsParaItem tempParaItem; |
1585 |
+ |
|
1586 |
+ |
ZConsParaData* zconsParaData = new ZConsParaData(); |
1587 |
+ |
zconsParaData->setID(ZCONSPARADATA_ID); |
1588 |
+ |
|
1589 |
+ |
for (int i = 0; i < nZConstraints; i++){ |
1590 |
+ |
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1591 |
+ |
tempParaItem.zPos = zconStamp[i]->getZpos(); |
1592 |
+ |
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1593 |
+ |
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1594 |
+ |
|
1595 |
+ |
zconsParaData->addItem(tempParaItem); |
1596 |
+ |
} |
1597 |
+ |
|
1598 |
+ |
//check the uniqueness of index |
1599 |
+ |
if(!zconsParaData->isIndexUnique()){ |
1600 |
+ |
sprintf(painCave.errMsg, |
1601 |
+ |
"ZConstraint Error: molIndex is not unique\n"); |
1602 |
+ |
painCave.isFatal = 1; |
1603 |
+ |
simError(); |
1604 |
+ |
} |
1605 |
+ |
|
1606 |
+ |
//sort the parameters by index of molecules |
1607 |
+ |
zconsParaData->sortByIndex(); |
1608 |
+ |
|
1609 |
+ |
//push data into siminfo, therefore, we can retrieve later |
1610 |
+ |
theInfo.addProperty(zconsParaData); |
1611 |
+ |
} |