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#include <cstdlib> |
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#include <algorithm> |
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#include <stdlib.h> |
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#include <iostream> |
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#include <cmath> |
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|
4 |
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#include <math.h> |
5 |
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#include <string> |
6 |
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#include <sprng.h> |
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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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#include "RigidBody.hpp" |
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//#include "ConjugateMinimizer.hpp" |
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#include "OOPSEMinimizer.hpp" |
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|
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#ifdef IS_MPI |
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#include "mpiBASS.h" |
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#include "mpiSimulation.hpp" |
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#endif |
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|
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// some defines for ensemble and Forcefield cases |
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|
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#define NVE_ENS 0 |
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#define NVT_ENS 1 |
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#define NPTi_ENS 2 |
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#define NPTf_ENS 3 |
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#define NPTxyz_ENS 4 |
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|
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|
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#define FF_DUFF 0 |
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#define FF_LJ 1 |
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#define FF_EAM 2 |
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#define FF_H2O 3 |
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|
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using namespace std; |
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|
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/** |
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* Check whether dividend is divisble by divisor or not |
39 |
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*/ |
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bool isDivisible(double dividend, double divisor){ |
41 |
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double tolerance = 0.000001; |
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double quotient; |
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double diff; |
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int intQuotient; |
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|
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quotient = dividend / divisor; |
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|
48 |
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if (quotient < 0) |
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quotient = -quotient; |
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|
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intQuotient = int (quotient + tolerance); |
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|
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diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); |
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|
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if (diff <= tolerance) |
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return true; |
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else |
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return false; |
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} |
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|
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SimSetup::SimSetup(){ |
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|
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initSuspend = false; |
64 |
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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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initSuspend = true; |
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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 |
94 |
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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(); |
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mpiEventLoop(); |
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|
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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 ){ |
124 |
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void SimSetup::createSim(void){ |
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|
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MakeStamps *the_stamps; |
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Globals* the_globals; |
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ExtendedSystem* the_extendedsystem; |
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int i, j; |
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// gather all of the information from the Bass file |
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|
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// get the stamps and globals; |
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the_stamps = stamps; |
74 |
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the_globals = globals; |
128 |
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gatherInfo(); |
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|
|
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// set the easy ones first |
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simnfo->target_temp = the_globals->getTargetTemp(); |
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simnfo->dt = the_globals->getDt(); |
79 |
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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. |
82 |
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n_components = the_globals->getNComponents(); |
83 |
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strcpy( force_field, the_globals->getForceField() ); |
132 |
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sysObjectsCreation(); |
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|
|
134 |
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// get the ensemble and set up an extended system if we need it: |
86 |
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strcpy( ensemble, the_globals->getEnsemble() ); |
87 |
< |
if( !strcasecmp( ensemble, "NPT" ) ) { |
88 |
< |
the_extendedsystem = new ExtendedSystem( simnfo ); |
89 |
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the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
90 |
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if (the_globals->haveTargetPressure()) |
91 |
< |
the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
92 |
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else { |
93 |
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sprintf( painCave.errMsg, |
94 |
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"SimSetup error: If you use the constant pressure\n" |
95 |
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" ensemble, you must set targetPressure.\n" |
96 |
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" This was found in the BASS file.\n"); |
97 |
< |
painCave.isFatal = 1; |
98 |
< |
simError(); |
99 |
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} |
134 |
> |
// check on the post processing info |
135 |
|
|
136 |
< |
if (the_globals->haveTauThermostat()) |
102 |
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the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
103 |
< |
else if (the_globals->haveQmass()) |
104 |
< |
the_extendedsystem->setQmass(the_globals->getQmass()); |
105 |
< |
else { |
106 |
< |
sprintf( painCave.errMsg, |
107 |
< |
"SimSetup error: If you use one of the constant temperature\n" |
108 |
< |
" ensembles, you must set either tauThermostat or qMass.\n" |
109 |
< |
" Neither of these was found in the BASS file.\n"); |
110 |
< |
painCave.isFatal = 1; |
111 |
< |
simError(); |
112 |
< |
} |
136 |
> |
finalInfoCheck(); |
137 |
|
|
138 |
< |
if (the_globals->haveTauBarostat()) |
115 |
< |
the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
116 |
< |
else { |
117 |
< |
sprintf( painCave.errMsg, |
118 |
< |
"SimSetup error: If you use the constant pressure\n" |
119 |
< |
" ensemble, you must set tauBarostat.\n" |
120 |
< |
" This was found in the BASS file.\n"); |
121 |
< |
painCave.isFatal = 1; |
122 |
< |
simError(); |
123 |
< |
} |
138 |
> |
// initialize the system coordinates |
139 |
|
|
140 |
< |
} else if ( !strcasecmp( ensemble, "NVT") ) { |
141 |
< |
the_extendedsystem = new ExtendedSystem( simnfo ); |
127 |
< |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
140 |
> |
if ( !initSuspend ){ |
141 |
> |
initSystemCoords(); |
142 |
|
|
143 |
< |
if (the_globals->haveTauThermostat()) |
144 |
< |
the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
131 |
< |
else if (the_globals->haveQmass()) |
132 |
< |
the_extendedsystem->setQmass(the_globals->getQmass()); |
133 |
< |
else { |
134 |
< |
sprintf( painCave.errMsg, |
135 |
< |
"SimSetup error: If you use one of the constant temperature\n" |
136 |
< |
" ensembles, you must set either tauThermostat or qMass.\n" |
137 |
< |
" Neither of these was found in the BASS file.\n"); |
138 |
< |
painCave.isFatal = 1; |
139 |
< |
simError(); |
140 |
< |
} |
141 |
< |
|
142 |
< |
} else if ( !strcasecmp( ensemble, "NVE") ) { |
143 |
< |
} else { |
144 |
< |
sprintf( painCave.errMsg, |
145 |
< |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
146 |
< |
"reverting to NVE for this simulation.\n", |
147 |
< |
ensemble ); |
148 |
< |
painCave.isFatal = 0; |
149 |
< |
simError(); |
150 |
< |
strcpy( ensemble, "NVE" ); |
143 |
> |
if( !(globals->getUseInitTime()) ) |
144 |
> |
info[0].currentTime = 0.0; |
145 |
|
} |
152 |
– |
strcpy( simnfo->ensemble, ensemble ); |
146 |
|
|
147 |
< |
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
155 |
< |
simnfo->usePBC = the_globals->getPBC(); |
156 |
< |
|
157 |
< |
int usesDipoles = 0; |
158 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
159 |
< |
the_ff = new TraPPE_ExFF(); |
160 |
< |
usesDipoles = 1; |
161 |
< |
} |
162 |
< |
else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
163 |
< |
else{ |
164 |
< |
sprintf( painCave.errMsg, |
165 |
< |
"SimSetup Error. Unrecognized force field -> %s\n", |
166 |
< |
force_field ); |
167 |
< |
painCave.isFatal = 1; |
168 |
< |
simError(); |
169 |
< |
} |
147 |
> |
// make the output filenames |
148 |
|
|
149 |
< |
#ifdef IS_MPI |
172 |
< |
strcpy( checkPointMsg, "ForceField creation successful" ); |
173 |
< |
MPIcheckPoint(); |
174 |
< |
#endif // is_mpi |
149 |
> |
makeOutNames(); |
150 |
|
|
151 |
+ |
if (globals->haveMinimizer()) |
152 |
+ |
// make minimizer |
153 |
+ |
makeMinimizer(); |
154 |
+ |
else |
155 |
+ |
// make the integrator |
156 |
+ |
makeIntegrator(); |
157 |
|
|
158 |
+ |
#ifdef IS_MPI |
159 |
+ |
mpiSim->mpiRefresh(); |
160 |
+ |
#endif |
161 |
|
|
162 |
< |
// get the components and calculate the tot_nMol and indvidual n_mol |
179 |
< |
the_components = the_globals->getComponents(); |
180 |
< |
components_nmol = new int[n_components]; |
181 |
< |
comp_stamps = new MoleculeStamp*[n_components]; |
162 |
> |
// initialize the Fortran |
163 |
|
|
164 |
< |
if( !the_globals->haveNMol() ){ |
165 |
< |
// we don't have the total number of molecules, so we assume it is |
185 |
< |
// given in each component |
164 |
> |
initFortran(); |
165 |
> |
} |
166 |
|
|
187 |
– |
tot_nmol = 0; |
188 |
– |
for( i=0; i<n_components; i++ ){ |
167 |
|
|
168 |
< |
if( !the_components[i]->haveNMol() ){ |
169 |
< |
// we have a problem |
170 |
< |
sprintf( painCave.errMsg, |
171 |
< |
"SimSetup Error. No global NMol or component NMol" |
172 |
< |
" given. Cannot calculate the number of atoms.\n" ); |
173 |
< |
painCave.isFatal = 1; |
174 |
< |
simError(); |
175 |
< |
} |
168 |
> |
void SimSetup::makeMolecules(void){ |
169 |
> |
int i, j, k; |
170 |
> |
int exI, exJ, exK, exL, slI; |
171 |
> |
int tempI, tempJ, tempK, tempL; |
172 |
> |
int molI; |
173 |
> |
int stampID, atomOffset, rbOffset; |
174 |
> |
molInit molInfo; |
175 |
> |
DirectionalAtom* dAtom; |
176 |
> |
RigidBody* myRB; |
177 |
> |
StuntDouble* mySD; |
178 |
> |
LinkedAssign* extras; |
179 |
> |
LinkedAssign* current_extra; |
180 |
> |
AtomStamp* currentAtom; |
181 |
> |
BondStamp* currentBond; |
182 |
> |
BendStamp* currentBend; |
183 |
> |
TorsionStamp* currentTorsion; |
184 |
> |
RigidBodyStamp* currentRigidBody; |
185 |
|
|
186 |
< |
tot_nmol += the_components[i]->getNMol(); |
187 |
< |
components_nmol[i] = the_components[i]->getNMol(); |
188 |
< |
} |
189 |
< |
} |
190 |
< |
else{ |
191 |
< |
sprintf( painCave.errMsg, |
192 |
< |
"SimSetup error.\n" |
193 |
< |
"\tSorry, the ability to specify total" |
194 |
< |
" nMols and then give molfractions in the components\n" |
195 |
< |
"\tis not currently supported." |
196 |
< |
" Please give nMol in the components.\n" ); |
197 |
< |
painCave.isFatal = 1; |
198 |
< |
simError(); |
199 |
< |
|
200 |
< |
|
214 |
< |
// tot_nmol = the_globals->getNMol(); |
215 |
< |
|
216 |
< |
// //we have the total number of molecules, now we check for molfractions |
217 |
< |
// for( i=0; i<n_components; i++ ){ |
218 |
< |
|
219 |
< |
// if( !the_components[i]->haveMolFraction() ){ |
220 |
< |
|
221 |
< |
// if( !the_components[i]->haveNMol() ){ |
222 |
< |
// //we have a problem |
223 |
< |
// std::cerr << "SimSetup error. Neither molFraction nor " |
224 |
< |
// << " nMol was given in component |
225 |
< |
|
226 |
< |
} |
186 |
> |
bond_pair* theBonds; |
187 |
> |
bend_set* theBends; |
188 |
> |
torsion_set* theTorsions; |
189 |
> |
|
190 |
> |
set<int> skipList; |
191 |
> |
|
192 |
> |
double phi, theta, psi; |
193 |
> |
|
194 |
> |
//init the forceField paramters |
195 |
> |
|
196 |
> |
the_ff->readParams(); |
197 |
> |
|
198 |
> |
// init the atoms |
199 |
> |
|
200 |
> |
int nMembers, nNew, rb1, rb2; |
201 |
|
|
202 |
< |
#ifdef IS_MPI |
203 |
< |
strcpy( checkPointMsg, "Have the number of components" ); |
230 |
< |
MPIcheckPoint(); |
231 |
< |
#endif // is_mpi |
202 |
> |
for (k = 0; k < nInfo; k++){ |
203 |
> |
the_ff->setSimInfo(&(info[k])); |
204 |
|
|
205 |
< |
// make an array of molecule stamps that match the components used. |
234 |
< |
// also extract the used stamps out into a separate linked list |
205 |
> |
atomOffset = 0; |
206 |
|
|
207 |
< |
simnfo->nComponents = n_components; |
208 |
< |
simnfo->componentsNmol = components_nmol; |
238 |
< |
simnfo->compStamps = comp_stamps; |
239 |
< |
simnfo->headStamp = new LinkedMolStamp(); |
240 |
< |
|
241 |
< |
char* id; |
242 |
< |
LinkedMolStamp* headStamp = simnfo->headStamp; |
243 |
< |
LinkedMolStamp* currentStamp = NULL; |
244 |
< |
for( i=0; i<n_components; i++ ){ |
207 |
> |
for (i = 0; i < info[k].n_mol; i++){ |
208 |
> |
stampID = info[k].molecules[i].getStampID(); |
209 |
|
|
210 |
< |
id = the_components[i]->getType(); |
211 |
< |
comp_stamps[i] = NULL; |
212 |
< |
|
213 |
< |
// check to make sure the component isn't already in the list |
210 |
> |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
211 |
> |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
212 |
> |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
213 |
> |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
214 |
> |
molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies(); |
215 |
> |
|
216 |
> |
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
217 |
|
|
218 |
< |
comp_stamps[i] = headStamp->match( id ); |
219 |
< |
if( comp_stamps[i] == NULL ){ |
218 |
> |
if (molInfo.nBonds > 0) |
219 |
> |
molInfo.myBonds = new (Bond *) [molInfo.nBonds]; |
220 |
> |
else |
221 |
> |
molInfo.myBonds = NULL; |
222 |
> |
|
223 |
> |
if (molInfo.nBends > 0) |
224 |
> |
molInfo.myBends = new (Bend *) [molInfo.nBends]; |
225 |
> |
else |
226 |
> |
molInfo.myBends = NULL; |
227 |
> |
|
228 |
> |
if (molInfo.nTorsions > 0) |
229 |
> |
molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions]; |
230 |
> |
else |
231 |
> |
molInfo.myTorsions = NULL; |
232 |
> |
|
233 |
> |
theBonds = new bond_pair[molInfo.nBonds]; |
234 |
> |
theBends = new bend_set[molInfo.nBends]; |
235 |
> |
theTorsions = new torsion_set[molInfo.nTorsions]; |
236 |
|
|
237 |
< |
// extract the component from the list; |
255 |
< |
|
256 |
< |
currentStamp = the_stamps->extractMolStamp( id ); |
257 |
< |
if( currentStamp == NULL ){ |
258 |
< |
sprintf( painCave.errMsg, |
259 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
260 |
< |
"list of declared molecules\n", |
261 |
< |
id ); |
262 |
< |
painCave.isFatal = 1; |
263 |
< |
simError(); |
264 |
< |
} |
265 |
< |
|
266 |
< |
headStamp->add( currentStamp ); |
267 |
< |
comp_stamps[i] = headStamp->match( id ); |
268 |
< |
} |
269 |
< |
} |
237 |
> |
// make the Atoms |
238 |
|
|
239 |
< |
#ifdef IS_MPI |
240 |
< |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
273 |
< |
MPIcheckPoint(); |
274 |
< |
#endif // is_mpi |
275 |
< |
|
239 |
> |
for (j = 0; j < molInfo.nAtoms; j++){ |
240 |
> |
currentAtom = comp_stamps[stampID]->getAtom(j); |
241 |
|
|
242 |
+ |
if (currentAtom->haveOrientation()){ |
243 |
+ |
dAtom = new DirectionalAtom((j + atomOffset), |
244 |
+ |
info[k].getConfiguration()); |
245 |
+ |
info[k].n_oriented++; |
246 |
+ |
molInfo.myAtoms[j] = dAtom; |
247 |
|
|
248 |
+ |
// Directional Atoms have standard unit vectors which are oriented |
249 |
+ |
// in space using the three Euler angles. We assume the standard |
250 |
+ |
// unit vector was originally along the z axis below. |
251 |
|
|
252 |
< |
// caclulate the number of atoms, bonds, bends and torsions |
252 |
> |
phi = currentAtom->getEulerPhi() * M_PI / 180.0; |
253 |
> |
theta = currentAtom->getEulerTheta() * M_PI / 180.0; |
254 |
> |
psi = currentAtom->getEulerPsi()* M_PI / 180.0; |
255 |
|
|
256 |
< |
tot_atoms = 0; |
257 |
< |
tot_bonds = 0; |
258 |
< |
tot_bends = 0; |
259 |
< |
tot_torsions = 0; |
285 |
< |
for( i=0; i<n_components; i++ ){ |
286 |
< |
|
287 |
< |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
288 |
< |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
289 |
< |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
290 |
< |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
291 |
< |
} |
256 |
> |
dAtom->setUnitFrameFromEuler(phi, theta, psi); |
257 |
> |
|
258 |
> |
} |
259 |
> |
else{ |
260 |
|
|
261 |
< |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
261 |
> |
molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration()); |
262 |
> |
} |
263 |
|
|
264 |
< |
simnfo->n_atoms = tot_atoms; |
296 |
< |
simnfo->n_bonds = tot_bonds; |
297 |
< |
simnfo->n_bends = tot_bends; |
298 |
< |
simnfo->n_torsions = tot_torsions; |
299 |
< |
simnfo->n_SRI = tot_SRI; |
300 |
< |
simnfo->n_mol = tot_nmol; |
264 |
> |
molInfo.myAtoms[j]->setType(currentAtom->getType()); |
265 |
|
|
302 |
– |
|
266 |
|
#ifdef IS_MPI |
267 |
|
|
268 |
< |
// divide the molecules among processors here. |
306 |
< |
|
307 |
< |
mpiSim = new mpiSimulation( simnfo ); |
308 |
< |
|
309 |
< |
|
268 |
> |
molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
269 |
|
|
270 |
< |
globalIndex = mpiSim->divideLabor(); |
270 |
> |
#endif // is_mpi |
271 |
> |
} |
272 |
|
|
273 |
< |
// set up the local variables |
274 |
< |
|
275 |
< |
int localMol, allMol; |
276 |
< |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
273 |
> |
// make the bonds |
274 |
> |
for (j = 0; j < molInfo.nBonds; j++){ |
275 |
> |
currentBond = comp_stamps[stampID]->getBond(j); |
276 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
277 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
278 |
|
|
279 |
< |
int* mol2proc = mpiSim->getMolToProcMap(); |
280 |
< |
int* molCompType = mpiSim->getMolComponentType(); |
320 |
< |
|
321 |
< |
allMol = 0; |
322 |
< |
localMol = 0; |
323 |
< |
local_atoms = 0; |
324 |
< |
local_bonds = 0; |
325 |
< |
local_bends = 0; |
326 |
< |
local_torsions = 0; |
327 |
< |
for( i=0; i<n_components; i++ ){ |
279 |
> |
tempI = theBonds[j].a; |
280 |
> |
tempJ = theBonds[j].b; |
281 |
|
|
282 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
283 |
< |
|
284 |
< |
if( mol2proc[j] == worldRank ){ |
285 |
< |
|
286 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
287 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
288 |
< |
local_bends += comp_stamps[i]->getNBends(); |
336 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
337 |
< |
localMol++; |
338 |
< |
} |
339 |
< |
allMol++; |
340 |
< |
} |
341 |
< |
} |
342 |
< |
local_SRI = local_bonds + local_bends + local_torsions; |
343 |
< |
|
282 |
> |
#ifdef IS_MPI |
283 |
> |
exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
284 |
> |
exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
285 |
> |
#else |
286 |
> |
exI = tempI + 1; |
287 |
> |
exJ = tempJ + 1; |
288 |
> |
#endif |
289 |
|
|
290 |
< |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
291 |
< |
|
347 |
< |
if( local_atoms != simnfo->n_atoms ){ |
348 |
< |
sprintf( painCave.errMsg, |
349 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
350 |
< |
" localAtom (%d) are not equal.\n", |
351 |
< |
simnfo->n_atoms, |
352 |
< |
local_atoms ); |
353 |
< |
painCave.isFatal = 1; |
354 |
< |
simError(); |
355 |
< |
} |
290 |
> |
info[k].excludes->addPair(exI, exJ); |
291 |
> |
} |
292 |
|
|
293 |
< |
simnfo->n_bonds = local_bonds; |
294 |
< |
simnfo->n_bends = local_bends; |
295 |
< |
simnfo->n_torsions = local_torsions; |
296 |
< |
simnfo->n_SRI = local_SRI; |
297 |
< |
simnfo->n_mol = localMol; |
293 |
> |
//make the bends |
294 |
> |
for (j = 0; j < molInfo.nBends; j++){ |
295 |
> |
currentBend = comp_stamps[stampID]->getBend(j); |
296 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
297 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
298 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
299 |
|
|
300 |
< |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
301 |
< |
MPIcheckPoint(); |
302 |
< |
|
366 |
< |
|
367 |
< |
#endif // is_mpi |
368 |
< |
|
300 |
> |
if (currentBend->haveExtras()){ |
301 |
> |
extras = currentBend->getExtras(); |
302 |
> |
current_extra = extras; |
303 |
|
|
304 |
< |
// create the atom and short range interaction arrays |
304 |
> |
while (current_extra != NULL){ |
305 |
> |
if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
306 |
> |
switch (current_extra->getType()){ |
307 |
> |
case 0: |
308 |
> |
theBends[j].ghost = current_extra->getInt() + atomOffset; |
309 |
> |
theBends[j].isGhost = 1; |
310 |
> |
break; |
311 |
|
|
312 |
< |
Atom::createArrays(simnfo->n_atoms); |
313 |
< |
the_atoms = new Atom*[simnfo->n_atoms]; |
314 |
< |
the_molecules = new Molecule[simnfo->n_mol]; |
315 |
< |
int molIndex; |
312 |
> |
case 1: |
313 |
> |
theBends[j].ghost = (int) current_extra->getDouble() + |
314 |
> |
atomOffset; |
315 |
> |
theBends[j].isGhost = 1; |
316 |
> |
break; |
317 |
|
|
318 |
< |
// initialize the molecule's stampID's |
318 |
> |
default: |
319 |
> |
sprintf(painCave.errMsg, |
320 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
321 |
> |
"double nor an int.\n" |
322 |
> |
"-->Bend[%d] in %s\n", |
323 |
> |
j, comp_stamps[stampID]->getID()); |
324 |
> |
painCave.isFatal = 1; |
325 |
> |
simError(); |
326 |
> |
} |
327 |
> |
} |
328 |
> |
else{ |
329 |
> |
sprintf(painCave.errMsg, |
330 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
331 |
> |
" -->%s in Bend[%d] in %s\n", |
332 |
> |
current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
333 |
> |
painCave.isFatal = 1; |
334 |
> |
simError(); |
335 |
> |
} |
336 |
|
|
337 |
< |
#ifdef IS_MPI |
338 |
< |
|
337 |
> |
current_extra = current_extra->getNext(); |
338 |
> |
} |
339 |
> |
} |
340 |
|
|
341 |
< |
molIndex = 0; |
342 |
< |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
343 |
< |
|
344 |
< |
if(mol2proc[i] == worldRank ){ |
345 |
< |
the_molecules[molIndex].setStampID( molCompType[i] ); |
346 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
347 |
< |
molIndex++; |
348 |
< |
} |
349 |
< |
} |
341 |
> |
if (theBends[j].isGhost) { |
342 |
> |
|
343 |
> |
tempI = theBends[j].a; |
344 |
> |
tempJ = theBends[j].b; |
345 |
> |
|
346 |
> |
#ifdef IS_MPI |
347 |
> |
exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
348 |
> |
exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
349 |
> |
#else |
350 |
> |
exI = tempI + 1; |
351 |
> |
exJ = tempJ + 1; |
352 |
> |
#endif |
353 |
> |
info[k].excludes->addPair(exI, exJ); |
354 |
|
|
355 |
< |
#else // is_mpi |
393 |
< |
|
394 |
< |
molIndex = 0; |
395 |
< |
for(i=0; i<n_components; i++){ |
396 |
< |
for(j=0; j<components_nmol[i]; j++ ){ |
397 |
< |
the_molecules[molIndex].setStampID( i ); |
398 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
399 |
< |
molIndex++; |
400 |
< |
} |
401 |
< |
} |
402 |
< |
|
355 |
> |
} else { |
356 |
|
|
357 |
< |
#endif // is_mpi |
357 |
> |
tempI = theBends[j].a; |
358 |
> |
tempJ = theBends[j].b; |
359 |
> |
tempK = theBends[j].c; |
360 |
> |
|
361 |
> |
#ifdef IS_MPI |
362 |
> |
exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
363 |
> |
exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
364 |
> |
exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
365 |
> |
#else |
366 |
> |
exI = tempI + 1; |
367 |
> |
exJ = tempJ + 1; |
368 |
> |
exK = tempK + 1; |
369 |
> |
#endif |
370 |
> |
|
371 |
> |
info[k].excludes->addPair(exI, exK); |
372 |
> |
info[k].excludes->addPair(exI, exJ); |
373 |
> |
info[k].excludes->addPair(exJ, exK); |
374 |
> |
} |
375 |
> |
} |
376 |
|
|
377 |
+ |
for (j = 0; j < molInfo.nTorsions; j++){ |
378 |
+ |
currentTorsion = comp_stamps[stampID]->getTorsion(j); |
379 |
+ |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
380 |
+ |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
381 |
+ |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
382 |
+ |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
383 |
|
|
384 |
< |
if( simnfo->n_SRI ){ |
385 |
< |
|
386 |
< |
Exclude::createArray(simnfo->n_SRI); |
387 |
< |
the_excludes = new Exclude*[simnfo->n_SRI]; |
411 |
< |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
412 |
< |
simnfo->globalExcludes = new int; |
413 |
< |
simnfo->n_exclude = simnfo->n_SRI; |
414 |
< |
} |
415 |
< |
else{ |
416 |
< |
|
417 |
< |
Exclude::createArray( 1 ); |
418 |
< |
the_excludes = new Exclude*; |
419 |
< |
the_excludes[0] = new Exclude(0); |
420 |
< |
the_excludes[0]->setPair( 0,0 ); |
421 |
< |
simnfo->globalExcludes = new int; |
422 |
< |
simnfo->globalExcludes[0] = 0; |
423 |
< |
simnfo->n_exclude = 0; |
424 |
< |
} |
384 |
> |
tempI = theTorsions[j].a; |
385 |
> |
tempJ = theTorsions[j].b; |
386 |
> |
tempK = theTorsions[j].c; |
387 |
> |
tempL = theTorsions[j].d; |
388 |
|
|
389 |
< |
// set the arrays into the SimInfo object |
389 |
> |
#ifdef IS_MPI |
390 |
> |
exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
391 |
> |
exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
392 |
> |
exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
393 |
> |
exL = info[k].atoms[tempL]->getGlobalIndex() + 1; |
394 |
> |
#else |
395 |
> |
exI = tempI + 1; |
396 |
> |
exJ = tempJ + 1; |
397 |
> |
exK = tempK + 1; |
398 |
> |
exL = tempL + 1; |
399 |
> |
#endif |
400 |
|
|
401 |
< |
simnfo->atoms = the_atoms; |
402 |
< |
simnfo->molecules = the_molecules; |
403 |
< |
simnfo->nGlobalExcludes = 0; |
404 |
< |
simnfo->excludes = the_excludes; |
401 |
> |
info[k].excludes->addPair(exI, exJ); |
402 |
> |
info[k].excludes->addPair(exI, exK); |
403 |
> |
info[k].excludes->addPair(exI, exL); |
404 |
> |
info[k].excludes->addPair(exJ, exK); |
405 |
> |
info[k].excludes->addPair(exJ, exL); |
406 |
> |
info[k].excludes->addPair(exK, exL); |
407 |
> |
} |
408 |
|
|
409 |
+ |
for (j = 0; j < molInfo.nRigidBodies; j++){ |
410 |
|
|
411 |
< |
// get some of the tricky things that may still be in the globals |
411 |
> |
currentRigidBody = comp_stamps[stampID]->getRigidBody(j); |
412 |
> |
nMembers = currentRigidBody->getNMembers(); |
413 |
|
|
414 |
< |
|
437 |
< |
if( the_globals->haveBox() ){ |
438 |
< |
simnfo->box_x = the_globals->getBox(); |
439 |
< |
simnfo->box_y = the_globals->getBox(); |
440 |
< |
simnfo->box_z = the_globals->getBox(); |
441 |
< |
} |
442 |
< |
else if( the_globals->haveDensity() ){ |
414 |
> |
// Create the Rigid Body: |
415 |
|
|
416 |
< |
double vol; |
417 |
< |
vol = (double)tot_nmol / the_globals->getDensity(); |
418 |
< |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
447 |
< |
simnfo->box_y = simnfo->box_x; |
448 |
< |
simnfo->box_z = simnfo->box_x; |
449 |
< |
} |
450 |
< |
else{ |
451 |
< |
if( !the_globals->haveBoxX() ){ |
452 |
< |
sprintf( painCave.errMsg, |
453 |
< |
"SimSetup error, no periodic BoxX size given.\n" ); |
454 |
< |
painCave.isFatal = 1; |
455 |
< |
simError(); |
456 |
< |
} |
457 |
< |
simnfo->box_x = the_globals->getBoxX(); |
416 |
> |
myRB = new RigidBody(); |
417 |
> |
|
418 |
> |
for (rb1 = 0; rb1 < nMembers; rb1++) { |
419 |
|
|
420 |
< |
if( !the_globals->haveBoxY() ){ |
421 |
< |
sprintf( painCave.errMsg, |
422 |
< |
"SimSetup error, no periodic BoxY size given.\n" ); |
423 |
< |
painCave.isFatal = 1; |
424 |
< |
simError(); |
420 |
> |
// molI is atom numbering inside this molecule |
421 |
> |
molI = currentRigidBody->getMember(rb1); |
422 |
> |
|
423 |
> |
// tempI is atom numbering on local processor |
424 |
> |
tempI = molI + atomOffset; |
425 |
> |
|
426 |
> |
// currentAtom is the AtomStamp (which we need for |
427 |
> |
// rigid body reference positions) |
428 |
> |
currentAtom = comp_stamps[stampID]->getAtom(molI); |
429 |
> |
|
430 |
> |
// When we add to the rigid body, add the atom itself and |
431 |
> |
// the stamp info: |
432 |
> |
|
433 |
> |
myRB->addAtom(info[k].atoms[tempI], currentAtom); |
434 |
> |
|
435 |
> |
// Add this atom to the Skip List for the integrators |
436 |
> |
#ifdef IS_MPI |
437 |
> |
slI = info[k].atoms[tempI]->getGlobalIndex(); |
438 |
> |
#else |
439 |
> |
slI = tempI; |
440 |
> |
#endif |
441 |
> |
skipList.insert(slI); |
442 |
> |
|
443 |
> |
} |
444 |
> |
|
445 |
> |
for(rb1 = 0; rb1 < nMembers - 1; rb1++) { |
446 |
> |
for(rb2 = rb1+1; rb2 < nMembers; rb2++) { |
447 |
> |
|
448 |
> |
tempI = currentRigidBody->getMember(rb1); |
449 |
> |
tempJ = currentRigidBody->getMember(rb2); |
450 |
> |
|
451 |
> |
// Some explanation is required here. |
452 |
> |
// Fortran indexing starts at 1, while c indexing starts at 0 |
453 |
> |
// Also, in parallel computations, the GlobalIndex is |
454 |
> |
// used for the exclude list: |
455 |
> |
|
456 |
> |
#ifdef IS_MPI |
457 |
> |
exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
458 |
> |
exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
459 |
> |
#else |
460 |
> |
exI = tempI + 1; |
461 |
> |
exJ = tempJ + 1; |
462 |
> |
#endif |
463 |
> |
|
464 |
> |
info[k].excludes->addPair(exI, exJ); |
465 |
> |
|
466 |
> |
} |
467 |
> |
} |
468 |
> |
} |
469 |
> |
|
470 |
> |
// send the arrays off to the forceField for init. |
471 |
> |
|
472 |
> |
the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
473 |
> |
the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
474 |
> |
the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
475 |
> |
the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
476 |
> |
theTorsions); |
477 |
> |
|
478 |
> |
info[k].molecules[i].initialize(molInfo); |
479 |
> |
|
480 |
> |
|
481 |
> |
atomOffset += molInfo.nAtoms; |
482 |
> |
delete[] theBonds; |
483 |
> |
delete[] theBends; |
484 |
> |
delete[] theTorsions; |
485 |
|
} |
465 |
– |
simnfo->box_y = the_globals->getBoxY(); |
486 |
|
|
487 |
< |
if( !the_globals->haveBoxZ() ){ |
488 |
< |
sprintf( painCave.errMsg, |
489 |
< |
"SimSetup error, no periodic BoxZ size given.\n" ); |
490 |
< |
painCave.isFatal = 1; |
491 |
< |
simError(); |
487 |
> |
// build up the integrableObjects vector: |
488 |
> |
|
489 |
> |
for (i = 0; i < info[k].n_atoms; i++) { |
490 |
> |
|
491 |
> |
#ifdef IS_MPI |
492 |
> |
slI = info[k].atoms[i]->getGlobalIndex(); |
493 |
> |
#else |
494 |
> |
slI = i; |
495 |
> |
#endif |
496 |
> |
|
497 |
> |
if (skipList.find(slI) == skipList.end()) { |
498 |
> |
mySD = (StuntDouble *) info[k].atoms[i]; |
499 |
> |
info[k].integrableObjects.push_back(mySD); |
500 |
> |
} |
501 |
|
} |
502 |
< |
simnfo->box_z = the_globals->getBoxZ(); |
502 |
> |
for (i = 0; i < info[k].rigidBodies.size(); i++) { |
503 |
> |
mySD = (StuntDouble *) info[k].rigidBodies[i]; |
504 |
> |
info[k].integrableObjects.push_back(mySD); |
505 |
> |
} |
506 |
> |
|
507 |
|
} |
508 |
|
|
509 |
|
#ifdef IS_MPI |
510 |
< |
strcpy( checkPointMsg, "Box size set up" ); |
510 |
> |
sprintf(checkPointMsg, "all molecules initialized succesfully"); |
511 |
|
MPIcheckPoint(); |
512 |
|
#endif // is_mpi |
513 |
|
|
514 |
+ |
// clean up the forcefield |
515 |
|
|
516 |
< |
// initialize the arrays |
516 |
> |
if (!globals->haveLJrcut()){ |
517 |
|
|
518 |
< |
the_ff->setSimInfo( simnfo ); |
518 |
> |
the_ff->calcRcut(); |
519 |
|
|
520 |
< |
makeMolecules(); |
521 |
< |
simnfo->identArray = new int[simnfo->n_atoms]; |
522 |
< |
simnfo->molMembershipArray = new int[simnfo->n_atoms]; |
489 |
< |
for(i=0; i<simnfo->n_atoms; i++){ |
490 |
< |
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
520 |
> |
} else { |
521 |
> |
|
522 |
> |
the_ff->setRcut( globals->getLJrcut() ); |
523 |
|
} |
524 |
< |
for(i=0; i< simnfo->n_mol; i++) { |
525 |
< |
the_molecules[i].atomicRollCall(simnfo->molMembershipArray); |
526 |
< |
} |
527 |
< |
|
528 |
< |
if (the_globals->getUseRF() ) { |
529 |
< |
simnfo->useReactionField = 1; |
530 |
< |
|
531 |
< |
if( !the_globals->haveECR() ){ |
532 |
< |
sprintf( painCave.errMsg, |
533 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
534 |
< |
"box length for the electrostaticCutoffRadius.\n" |
535 |
< |
"I hope you have a very fast processor!\n"); |
504 |
< |
painCave.isFatal = 0; |
505 |
< |
simError(); |
506 |
< |
double smallest; |
507 |
< |
smallest = simnfo->box_x; |
508 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
509 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
510 |
< |
simnfo->ecr = 0.5 * smallest; |
511 |
< |
} else { |
512 |
< |
simnfo->ecr = the_globals->getECR(); |
513 |
< |
} |
524 |
> |
|
525 |
> |
the_ff->cleanMe(); |
526 |
> |
} |
527 |
> |
|
528 |
> |
void SimSetup::initFromBass(void){ |
529 |
> |
int i, j, k; |
530 |
> |
int n_cells; |
531 |
> |
double cellx, celly, cellz; |
532 |
> |
double temp1, temp2, temp3; |
533 |
> |
int n_per_extra; |
534 |
> |
int n_extra; |
535 |
> |
int have_extra, done; |
536 |
|
|
537 |
< |
if( !the_globals->haveEST() ){ |
538 |
< |
sprintf( painCave.errMsg, |
539 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
540 |
< |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
541 |
< |
); |
542 |
< |
painCave.isFatal = 0; |
543 |
< |
simError(); |
544 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
545 |
< |
} else { |
546 |
< |
simnfo->est = the_globals->getEST(); |
547 |
< |
} |
548 |
< |
|
549 |
< |
if(!the_globals->haveDielectric() ){ |
550 |
< |
sprintf( painCave.errMsg, |
551 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
552 |
< |
"setting a dielectric constant!\n" |
553 |
< |
); |
537 |
> |
double vel[3]; |
538 |
> |
vel[0] = 0.0; |
539 |
> |
vel[1] = 0.0; |
540 |
> |
vel[2] = 0.0; |
541 |
> |
|
542 |
> |
temp1 = (double) tot_nmol / 4.0; |
543 |
> |
temp2 = pow(temp1, (1.0 / 3.0)); |
544 |
> |
temp3 = ceil(temp2); |
545 |
> |
|
546 |
> |
have_extra = 0; |
547 |
> |
if (temp2 < temp3){ |
548 |
> |
// we have a non-complete lattice |
549 |
> |
have_extra = 1; |
550 |
> |
|
551 |
> |
n_cells = (int) temp3 - 1; |
552 |
> |
cellx = info[0].boxL[0] / temp3; |
553 |
> |
celly = info[0].boxL[1] / temp3; |
554 |
> |
cellz = info[0].boxL[2] / temp3; |
555 |
> |
n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
556 |
> |
temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
557 |
> |
n_per_extra = (int) ceil(temp1); |
558 |
> |
|
559 |
> |
if (n_per_extra > 4){ |
560 |
> |
sprintf(painCave.errMsg, |
561 |
> |
"SimSetup error. There has been an error in constructing" |
562 |
> |
" the non-complete lattice.\n"); |
563 |
|
painCave.isFatal = 1; |
564 |
|
simError(); |
565 |
|
} |
566 |
< |
simnfo->dielectric = the_globals->getDielectric(); |
567 |
< |
} else { |
568 |
< |
if (usesDipoles) { |
569 |
< |
|
570 |
< |
if( !the_globals->haveECR() ){ |
571 |
< |
sprintf( painCave.errMsg, |
572 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
573 |
< |
"box length for the electrostaticCutoffRadius.\n" |
574 |
< |
"I hope you have a very fast processor!\n"); |
575 |
< |
painCave.isFatal = 0; |
576 |
< |
simError(); |
577 |
< |
double smallest; |
578 |
< |
smallest = simnfo->box_x; |
579 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
580 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
581 |
< |
simnfo->ecr = 0.5 * smallest; |
582 |
< |
} else { |
583 |
< |
simnfo->ecr = the_globals->getECR(); |
566 |
> |
} |
567 |
> |
else{ |
568 |
> |
n_cells = (int) temp3; |
569 |
> |
cellx = info[0].boxL[0] / temp3; |
570 |
> |
celly = info[0].boxL[1] / temp3; |
571 |
> |
cellz = info[0].boxL[2] / temp3; |
572 |
> |
} |
573 |
> |
|
574 |
> |
current_mol = 0; |
575 |
> |
current_comp_mol = 0; |
576 |
> |
current_comp = 0; |
577 |
> |
current_atom_ndx = 0; |
578 |
> |
|
579 |
> |
for (i = 0; i < n_cells ; i++){ |
580 |
> |
for (j = 0; j < n_cells; j++){ |
581 |
> |
for (k = 0; k < n_cells; k++){ |
582 |
> |
makeElement(i * cellx, j * celly, k * cellz); |
583 |
> |
|
584 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
585 |
> |
|
586 |
> |
makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
587 |
> |
|
588 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
589 |
|
} |
590 |
< |
|
591 |
< |
if( !the_globals->haveEST() ){ |
592 |
< |
sprintf( painCave.errMsg, |
593 |
< |
"SimSetup Warning: using default value of 5%% of the " |
594 |
< |
"electrostaticCutoffRadius for the " |
595 |
< |
"electrostaticSkinThickness\n" |
596 |
< |
); |
597 |
< |
painCave.isFatal = 0; |
598 |
< |
simError(); |
599 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
600 |
< |
} else { |
601 |
< |
simnfo->est = the_globals->getEST(); |
590 |
> |
} |
591 |
> |
} |
592 |
> |
|
593 |
> |
if (have_extra){ |
594 |
> |
done = 0; |
595 |
> |
|
596 |
> |
int start_ndx; |
597 |
> |
for (i = 0; i < (n_cells + 1) && !done; i++){ |
598 |
> |
for (j = 0; j < (n_cells + 1) && !done; j++){ |
599 |
> |
if (i < n_cells){ |
600 |
> |
if (j < n_cells){ |
601 |
> |
start_ndx = n_cells; |
602 |
> |
} |
603 |
> |
else |
604 |
> |
start_ndx = 0; |
605 |
> |
} |
606 |
> |
else |
607 |
> |
start_ndx = 0; |
608 |
> |
|
609 |
> |
for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
610 |
> |
makeElement(i * cellx, j * celly, k * cellz); |
611 |
> |
done = (current_mol >= tot_nmol); |
612 |
> |
|
613 |
> |
if (!done && n_per_extra > 1){ |
614 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
615 |
> |
k * cellz); |
616 |
> |
done = (current_mol >= tot_nmol); |
617 |
> |
} |
618 |
> |
|
619 |
> |
if (!done && n_per_extra > 2){ |
620 |
> |
makeElement(i * cellx, j * celly + 0.5 * celly, |
621 |
> |
k * cellz + 0.5 * cellz); |
622 |
> |
done = (current_mol >= tot_nmol); |
623 |
> |
} |
624 |
> |
|
625 |
> |
if (!done && n_per_extra > 3){ |
626 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly, |
627 |
> |
k * cellz + 0.5 * cellz); |
628 |
> |
done = (current_mol >= tot_nmol); |
629 |
> |
} |
630 |
> |
} |
631 |
|
} |
632 |
|
} |
633 |
< |
} |
633 |
> |
} |
634 |
|
|
635 |
< |
#ifdef IS_MPI |
636 |
< |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
637 |
< |
MPIcheckPoint(); |
638 |
< |
#endif // is_mpi |
635 |
> |
for (i = 0; i < info[0].n_atoms; i++){ |
636 |
> |
info[0].atoms[i]->setVel(vel); |
637 |
> |
} |
638 |
> |
} |
639 |
|
|
640 |
< |
if( the_globals->haveInitialConfig() ){ |
641 |
< |
|
642 |
< |
InitializeFromFile* fileInit; |
643 |
< |
#ifdef IS_MPI // is_mpi |
644 |
< |
if( worldRank == 0 ){ |
645 |
< |
#endif //is_mpi |
581 |
< |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
582 |
< |
#ifdef IS_MPI |
583 |
< |
}else fileInit = new InitializeFromFile( NULL ); |
584 |
< |
#endif |
585 |
< |
fileInit->read_xyz( simnfo ); // default velocities on |
640 |
> |
void SimSetup::makeElement(double x, double y, double z){ |
641 |
> |
int k; |
642 |
> |
AtomStamp* current_atom; |
643 |
> |
DirectionalAtom* dAtom; |
644 |
> |
double rotMat[3][3]; |
645 |
> |
double pos[3]; |
646 |
|
|
647 |
< |
delete fileInit; |
648 |
< |
} |
649 |
< |
else{ |
647 |
> |
for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
648 |
> |
current_atom = comp_stamps[current_comp]->getAtom(k); |
649 |
> |
if (!current_atom->havePosition()){ |
650 |
> |
sprintf(painCave.errMsg, |
651 |
> |
"SimSetup:initFromBass error.\n" |
652 |
> |
"\tComponent %s, atom %s does not have a position specified.\n" |
653 |
> |
"\tThe initialization routine is unable to give a start" |
654 |
> |
" position.\n", |
655 |
> |
comp_stamps[current_comp]->getID(), current_atom->getType()); |
656 |
> |
painCave.isFatal = 1; |
657 |
> |
simError(); |
658 |
> |
} |
659 |
|
|
660 |
< |
#ifdef IS_MPI |
660 |
> |
pos[0] = x + current_atom->getPosX(); |
661 |
> |
pos[1] = y + current_atom->getPosY(); |
662 |
> |
pos[2] = z + current_atom->getPosZ(); |
663 |
|
|
664 |
< |
// no init from bass |
594 |
< |
|
595 |
< |
sprintf( painCave.errMsg, |
596 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
597 |
< |
painCave.isFatal; |
598 |
< |
simError(); |
599 |
< |
|
600 |
< |
#else |
664 |
> |
info[0].atoms[current_atom_ndx]->setPos(pos); |
665 |
|
|
666 |
< |
initFromBass(); |
666 |
> |
if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
667 |
> |
dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
668 |
|
|
669 |
+ |
rotMat[0][0] = 1.0; |
670 |
+ |
rotMat[0][1] = 0.0; |
671 |
+ |
rotMat[0][2] = 0.0; |
672 |
|
|
673 |
< |
#endif |
674 |
< |
} |
673 |
> |
rotMat[1][0] = 0.0; |
674 |
> |
rotMat[1][1] = 1.0; |
675 |
> |
rotMat[1][2] = 0.0; |
676 |
|
|
677 |
< |
#ifdef IS_MPI |
678 |
< |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
679 |
< |
MPIcheckPoint(); |
611 |
< |
#endif // is_mpi |
677 |
> |
rotMat[2][0] = 0.0; |
678 |
> |
rotMat[2][1] = 0.0; |
679 |
> |
rotMat[2][2] = 1.0; |
680 |
|
|
681 |
+ |
dAtom->setA(rotMat); |
682 |
+ |
} |
683 |
|
|
684 |
< |
|
685 |
< |
|
686 |
< |
|
684 |
> |
current_atom_ndx++; |
685 |
> |
} |
686 |
> |
|
687 |
> |
current_mol++; |
688 |
> |
current_comp_mol++; |
689 |
> |
|
690 |
> |
if (current_comp_mol >= components_nmol[current_comp]){ |
691 |
> |
current_comp_mol = 0; |
692 |
> |
current_comp++; |
693 |
> |
} |
694 |
> |
} |
695 |
> |
|
696 |
|
|
697 |
< |
|
698 |
< |
#ifdef IS_MPI |
620 |
< |
if( worldRank == 0 ){ |
621 |
< |
#endif // is_mpi |
622 |
< |
|
623 |
< |
if( the_globals->haveFinalConfig() ){ |
624 |
< |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
625 |
< |
} |
626 |
< |
else{ |
627 |
< |
strcpy( simnfo->finalName, inFileName ); |
628 |
< |
char* endTest; |
629 |
< |
int nameLength = strlen( simnfo->finalName ); |
630 |
< |
endTest = &(simnfo->finalName[nameLength - 5]); |
631 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
632 |
< |
strcpy( endTest, ".eor" ); |
633 |
< |
} |
634 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
635 |
< |
strcpy( endTest, ".eor" ); |
636 |
< |
} |
637 |
< |
else{ |
638 |
< |
endTest = &(simnfo->finalName[nameLength - 4]); |
639 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
640 |
< |
strcpy( endTest, ".eor" ); |
641 |
< |
} |
642 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
643 |
< |
strcpy( endTest, ".eor" ); |
644 |
< |
} |
645 |
< |
else{ |
646 |
< |
strcat( simnfo->finalName, ".eor" ); |
647 |
< |
} |
648 |
< |
} |
649 |
< |
} |
650 |
< |
|
651 |
< |
// make the sample and status out names |
652 |
< |
|
653 |
< |
strcpy( simnfo->sampleName, inFileName ); |
654 |
< |
char* endTest; |
655 |
< |
int nameLength = strlen( simnfo->sampleName ); |
656 |
< |
endTest = &(simnfo->sampleName[nameLength - 5]); |
657 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
658 |
< |
strcpy( endTest, ".dump" ); |
659 |
< |
} |
660 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
661 |
< |
strcpy( endTest, ".dump" ); |
662 |
< |
} |
663 |
< |
else{ |
664 |
< |
endTest = &(simnfo->sampleName[nameLength - 4]); |
665 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
666 |
< |
strcpy( endTest, ".dump" ); |
667 |
< |
} |
668 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
669 |
< |
strcpy( endTest, ".dump" ); |
670 |
< |
} |
671 |
< |
else{ |
672 |
< |
strcat( simnfo->sampleName, ".dump" ); |
673 |
< |
} |
674 |
< |
} |
675 |
< |
|
676 |
< |
strcpy( simnfo->statusName, inFileName ); |
677 |
< |
nameLength = strlen( simnfo->statusName ); |
678 |
< |
endTest = &(simnfo->statusName[nameLength - 5]); |
679 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
680 |
< |
strcpy( endTest, ".stat" ); |
681 |
< |
} |
682 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
683 |
< |
strcpy( endTest, ".stat" ); |
684 |
< |
} |
685 |
< |
else{ |
686 |
< |
endTest = &(simnfo->statusName[nameLength - 4]); |
687 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
688 |
< |
strcpy( endTest, ".stat" ); |
689 |
< |
} |
690 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
691 |
< |
strcpy( endTest, ".stat" ); |
692 |
< |
} |
693 |
< |
else{ |
694 |
< |
strcat( simnfo->statusName, ".stat" ); |
695 |
< |
} |
696 |
< |
} |
697 |
< |
|
698 |
< |
#ifdef IS_MPI |
699 |
< |
} |
700 |
< |
#endif // is_mpi |
701 |
< |
|
702 |
< |
// set the status, sample, and themal kick times |
703 |
< |
|
704 |
< |
if( the_globals->haveSampleTime() ){ |
705 |
< |
simnfo->sampleTime = the_globals->getSampleTime(); |
706 |
< |
simnfo->statusTime = simnfo->sampleTime; |
707 |
< |
simnfo->thermalTime = simnfo->sampleTime; |
708 |
< |
} |
709 |
< |
else{ |
710 |
< |
simnfo->sampleTime = the_globals->getRunTime(); |
711 |
< |
simnfo->statusTime = simnfo->sampleTime; |
712 |
< |
simnfo->thermalTime = simnfo->sampleTime; |
713 |
< |
} |
697 |
> |
void SimSetup::gatherInfo(void){ |
698 |
> |
int i; |
699 |
|
|
700 |
< |
if( the_globals->haveStatusTime() ){ |
701 |
< |
simnfo->statusTime = the_globals->getStatusTime(); |
717 |
< |
} |
700 |
> |
ensembleCase = -1; |
701 |
> |
ffCase = -1; |
702 |
|
|
703 |
< |
if( the_globals->haveThermalTime() ){ |
704 |
< |
simnfo->thermalTime = the_globals->getThermalTime(); |
703 |
> |
// set the easy ones first |
704 |
> |
|
705 |
> |
for (i = 0; i < nInfo; i++){ |
706 |
> |
info[i].target_temp = globals->getTargetTemp(); |
707 |
> |
info[i].dt = globals->getDt(); |
708 |
> |
info[i].run_time = globals->getRunTime(); |
709 |
|
} |
710 |
+ |
n_components = globals->getNComponents(); |
711 |
|
|
723 |
– |
// check for the temperature set flag |
712 |
|
|
713 |
< |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
713 |
> |
// get the forceField |
714 |
|
|
715 |
+ |
strcpy(force_field, globals->getForceField()); |
716 |
|
|
717 |
< |
// // make the longe range forces and the integrator |
717 |
> |
if (!strcasecmp(force_field, "DUFF")){ |
718 |
> |
ffCase = FF_DUFF; |
719 |
> |
} |
720 |
> |
else if (!strcasecmp(force_field, "LJ")){ |
721 |
> |
ffCase = FF_LJ; |
722 |
> |
} |
723 |
> |
else if (!strcasecmp(force_field, "EAM")){ |
724 |
> |
ffCase = FF_EAM; |
725 |
> |
} |
726 |
> |
else if (!strcasecmp(force_field, "WATER")){ |
727 |
> |
ffCase = FF_H2O; |
728 |
> |
} |
729 |
> |
else{ |
730 |
> |
sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
731 |
> |
force_field); |
732 |
> |
painCave.isFatal = 1; |
733 |
> |
simError(); |
734 |
> |
} |
735 |
|
|
736 |
< |
// new AllLong( simnfo ); |
736 |
> |
// get the ensemble |
737 |
|
|
738 |
+ |
strcpy(ensemble, globals->getEnsemble()); |
739 |
|
|
740 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
741 |
< |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
740 |
> |
if (!strcasecmp(ensemble, "NVE")){ |
741 |
> |
ensembleCase = NVE_ENS; |
742 |
|
} |
743 |
< |
else if( !strcmp( force_field, "LJ" ) ){ |
744 |
< |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
743 |
> |
else if (!strcasecmp(ensemble, "NVT")){ |
744 |
> |
ensembleCase = NVT_ENS; |
745 |
|
} |
746 |
< |
else { |
747 |
< |
std::cerr << "I'm a bug.\n"; |
741 |
< |
fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
746 |
> |
else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
747 |
> |
ensembleCase = NPTi_ENS; |
748 |
|
} |
749 |
< |
#ifdef IS_MPI |
750 |
< |
mpiSim->mpiRefresh(); |
751 |
< |
#endif |
749 |
> |
else if (!strcasecmp(ensemble, "NPTf")){ |
750 |
> |
ensembleCase = NPTf_ENS; |
751 |
> |
} |
752 |
> |
else if (!strcasecmp(ensemble, "NPTxyz")){ |
753 |
> |
ensembleCase = NPTxyz_ENS; |
754 |
> |
} |
755 |
> |
else{ |
756 |
> |
sprintf(painCave.errMsg, |
757 |
> |
"SimSetup Warning. Unrecognized Ensemble -> %s \n" |
758 |
> |
"\treverting to NVE for this simulation.\n", |
759 |
> |
ensemble); |
760 |
> |
painCave.isFatal = 0; |
761 |
> |
simError(); |
762 |
> |
strcpy(ensemble, "NVE"); |
763 |
> |
ensembleCase = NVE_ENS; |
764 |
> |
} |
765 |
|
|
766 |
< |
// initialize the Fortran |
766 |
> |
for (i = 0; i < nInfo; i++){ |
767 |
> |
strcpy(info[i].ensemble, ensemble); |
768 |
|
|
769 |
+ |
// get the mixing rule |
770 |
|
|
771 |
< |
simnfo->refreshSim(); |
772 |
< |
|
752 |
< |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
753 |
< |
the_ff->initForceField( LB_MIXING_RULE ); |
771 |
> |
strcpy(info[i].mixingRule, globals->getMixingRule()); |
772 |
> |
info[i].usePBC = globals->getPBC(); |
773 |
|
} |
774 |
< |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
775 |
< |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
774 |
> |
|
775 |
> |
// get the components and calculate the tot_nMol and indvidual n_mol |
776 |
> |
|
777 |
> |
the_components = globals->getComponents(); |
778 |
> |
components_nmol = new int[n_components]; |
779 |
> |
|
780 |
> |
|
781 |
> |
if (!globals->haveNMol()){ |
782 |
> |
// we don't have the total number of molecules, so we assume it is |
783 |
> |
// given in each component |
784 |
> |
|
785 |
> |
tot_nmol = 0; |
786 |
> |
for (i = 0; i < n_components; i++){ |
787 |
> |
if (!the_components[i]->haveNMol()){ |
788 |
> |
// we have a problem |
789 |
> |
sprintf(painCave.errMsg, |
790 |
> |
"SimSetup Error. No global NMol or component NMol given.\n" |
791 |
> |
"\tCannot calculate the number of atoms.\n"); |
792 |
> |
painCave.isFatal = 1; |
793 |
> |
simError(); |
794 |
> |
} |
795 |
> |
|
796 |
> |
tot_nmol += the_components[i]->getNMol(); |
797 |
> |
components_nmol[i] = the_components[i]->getNMol(); |
798 |
> |
} |
799 |
|
} |
800 |
|
else{ |
801 |
< |
sprintf( painCave.errMsg, |
802 |
< |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
803 |
< |
simnfo->mixingRule ); |
801 |
> |
sprintf(painCave.errMsg, |
802 |
> |
"SimSetup error.\n" |
803 |
> |
"\tSorry, the ability to specify total" |
804 |
> |
" nMols and then give molfractions in the components\n" |
805 |
> |
"\tis not currently supported." |
806 |
> |
" Please give nMol in the components.\n"); |
807 |
|
painCave.isFatal = 1; |
808 |
|
simError(); |
809 |
|
} |
810 |
|
|
811 |
+ |
//check whether sample time, status time, thermal time and reset time are divisble by dt |
812 |
+ |
if (!isDivisible(globals->getSampleTime(), globals->getDt())){ |
813 |
+ |
sprintf(painCave.errMsg, |
814 |
+ |
"Sample time is not divisible by dt.\n" |
815 |
+ |
"\tThis will result in samples that are not uniformly\n" |
816 |
+ |
"\tdistributed in time. If this is a problem, change\n" |
817 |
+ |
"\tyour sampleTime variable.\n"); |
818 |
+ |
painCave.isFatal = 0; |
819 |
+ |
simError(); |
820 |
+ |
} |
821 |
|
|
822 |
< |
#ifdef IS_MPI |
823 |
< |
strcpy( checkPointMsg, |
824 |
< |
"Successfully intialized the mixingRule for Fortran." ); |
825 |
< |
MPIcheckPoint(); |
826 |
< |
#endif // is_mpi |
827 |
< |
} |
822 |
> |
if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
823 |
> |
sprintf(painCave.errMsg, |
824 |
> |
"Status time is not divisible by dt.\n" |
825 |
> |
"\tThis will result in status reports that are not uniformly\n" |
826 |
> |
"\tdistributed in time. If this is a problem, change \n" |
827 |
> |
"\tyour statusTime variable.\n"); |
828 |
> |
painCave.isFatal = 0; |
829 |
> |
simError(); |
830 |
> |
} |
831 |
|
|
832 |
+ |
if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
833 |
+ |
sprintf(painCave.errMsg, |
834 |
+ |
"Thermal time is not divisible by dt.\n" |
835 |
+ |
"\tThis will result in thermalizations that are not uniformly\n" |
836 |
+ |
"\tdistributed in time. If this is a problem, change \n" |
837 |
+ |
"\tyour thermalTime variable.\n"); |
838 |
+ |
painCave.isFatal = 0; |
839 |
+ |
simError(); |
840 |
+ |
} |
841 |
|
|
842 |
< |
void SimSetup::makeMolecules( void ){ |
842 |
> |
if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
843 |
> |
sprintf(painCave.errMsg, |
844 |
> |
"Reset time is not divisible by dt.\n" |
845 |
> |
"\tThis will result in integrator resets that are not uniformly\n" |
846 |
> |
"\tdistributed in time. If this is a problem, change\n" |
847 |
> |
"\tyour resetTime variable.\n"); |
848 |
> |
painCave.isFatal = 0; |
849 |
> |
simError(); |
850 |
> |
} |
851 |
|
|
852 |
< |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
778 |
< |
molInit info; |
779 |
< |
DirectionalAtom* dAtom; |
780 |
< |
LinkedAssign* extras; |
781 |
< |
LinkedAssign* current_extra; |
782 |
< |
AtomStamp* currentAtom; |
783 |
< |
BondStamp* currentBond; |
784 |
< |
BendStamp* currentBend; |
785 |
< |
TorsionStamp* currentTorsion; |
852 |
> |
// set the status, sample, and thermal kick times |
853 |
|
|
854 |
< |
bond_pair* theBonds; |
855 |
< |
bend_set* theBends; |
856 |
< |
torsion_set* theTorsions; |
854 |
> |
for (i = 0; i < nInfo; i++){ |
855 |
> |
if (globals->haveSampleTime()){ |
856 |
> |
info[i].sampleTime = globals->getSampleTime(); |
857 |
> |
info[i].statusTime = info[i].sampleTime; |
858 |
> |
info[i].thermalTime = info[i].sampleTime; |
859 |
> |
} |
860 |
> |
else{ |
861 |
> |
info[i].sampleTime = globals->getRunTime(); |
862 |
> |
info[i].statusTime = info[i].sampleTime; |
863 |
> |
info[i].thermalTime = info[i].sampleTime; |
864 |
> |
} |
865 |
|
|
866 |
< |
|
867 |
< |
//init the forceField paramters |
866 |
> |
if (globals->haveStatusTime()){ |
867 |
> |
info[i].statusTime = globals->getStatusTime(); |
868 |
> |
} |
869 |
|
|
870 |
< |
the_ff->readParams(); |
870 |
> |
if (globals->haveThermalTime()){ |
871 |
> |
info[i].thermalTime = globals->getThermalTime(); |
872 |
> |
} |
873 |
|
|
874 |
< |
|
875 |
< |
// init the atoms |
874 |
> |
info[i].resetIntegrator = 0; |
875 |
> |
if( globals->haveResetTime() ){ |
876 |
> |
info[i].resetTime = globals->getResetTime(); |
877 |
> |
info[i].resetIntegrator = 1; |
878 |
> |
} |
879 |
|
|
880 |
< |
double ux, uy, uz, u, uSqr; |
800 |
< |
|
801 |
< |
atomOffset = 0; |
802 |
< |
excludeOffset = 0; |
803 |
< |
for(i=0; i<simnfo->n_mol; i++){ |
880 |
> |
// check for the temperature set flag |
881 |
|
|
882 |
< |
stampID = the_molecules[i].getStampID(); |
882 |
> |
if (globals->haveTempSet()) |
883 |
> |
info[i].setTemp = globals->getTempSet(); |
884 |
|
|
885 |
< |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
808 |
< |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
809 |
< |
info.nBends = comp_stamps[stampID]->getNBends(); |
810 |
< |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
811 |
< |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
885 |
> |
// check for the extended State init |
886 |
|
|
887 |
< |
info.myAtoms = &the_atoms[atomOffset]; |
888 |
< |
info.myExcludes = &the_excludes[excludeOffset]; |
815 |
< |
info.myBonds = new Bond*[info.nBonds]; |
816 |
< |
info.myBends = new Bend*[info.nBends]; |
817 |
< |
info.myTorsions = new Torsion*[info.nTorsions]; |
818 |
< |
|
819 |
< |
theBonds = new bond_pair[info.nBonds]; |
820 |
< |
theBends = new bend_set[info.nBends]; |
821 |
< |
theTorsions = new torsion_set[info.nTorsions]; |
887 |
> |
info[i].useInitXSstate = globals->getUseInitXSstate(); |
888 |
> |
info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
889 |
|
|
890 |
< |
// make the Atoms |
891 |
< |
|
892 |
< |
for(j=0; j<info.nAtoms; j++){ |
893 |
< |
|
894 |
< |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
895 |
< |
if( currentAtom->haveOrientation() ){ |
896 |
< |
|
897 |
< |
dAtom = new DirectionalAtom(j + atomOffset); |
898 |
< |
simnfo->n_oriented++; |
899 |
< |
info.myAtoms[j] = dAtom; |
900 |
< |
|
901 |
< |
ux = currentAtom->getOrntX(); |
902 |
< |
uy = currentAtom->getOrntY(); |
903 |
< |
uz = currentAtom->getOrntZ(); |
904 |
< |
|
905 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
906 |
< |
|
907 |
< |
u = sqrt( uSqr ); |
908 |
< |
ux = ux / u; |
909 |
< |
uy = uy / u; |
910 |
< |
uz = uz / u; |
844 |
< |
|
845 |
< |
dAtom->setSUx( ux ); |
846 |
< |
dAtom->setSUy( uy ); |
847 |
< |
dAtom->setSUz( uz ); |
890 |
> |
} |
891 |
> |
|
892 |
> |
//setup seed for random number generator |
893 |
> |
int seedValue; |
894 |
> |
|
895 |
> |
if (globals->haveSeed()){ |
896 |
> |
seedValue = globals->getSeed(); |
897 |
> |
|
898 |
> |
if(seedValue / 1E9 == 0){ |
899 |
> |
sprintf(painCave.errMsg, |
900 |
> |
"Seed for sprng library should contain at least 9 digits\n" |
901 |
> |
"OOPSE will generate a seed for user\n"); |
902 |
> |
painCave.isFatal = 0; |
903 |
> |
simError(); |
904 |
> |
|
905 |
> |
//using seed generated by system instead of invalid seed set by user |
906 |
> |
#ifndef IS_MPI |
907 |
> |
seedValue = make_sprng_seed(); |
908 |
> |
#else |
909 |
> |
if (worldRank == 0){ |
910 |
> |
seedValue = make_sprng_seed(); |
911 |
|
} |
912 |
< |
else{ |
913 |
< |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
914 |
< |
} |
915 |
< |
info.myAtoms[j]->setType( currentAtom->getType() ); |
912 |
> |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
913 |
> |
#endif |
914 |
> |
} |
915 |
> |
}//end of if branch of globals->haveSeed() |
916 |
> |
else{ |
917 |
|
|
918 |
+ |
#ifndef IS_MPI |
919 |
+ |
seedValue = make_sprng_seed(); |
920 |
+ |
#else |
921 |
+ |
if (worldRank == 0){ |
922 |
+ |
seedValue = make_sprng_seed(); |
923 |
+ |
} |
924 |
+ |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
925 |
+ |
#endif |
926 |
+ |
}//end of globals->haveSeed() |
927 |
+ |
|
928 |
+ |
for (int i = 0; i < nInfo; i++){ |
929 |
+ |
info[i].setSeed(seedValue); |
930 |
+ |
} |
931 |
+ |
|
932 |
|
#ifdef IS_MPI |
933 |
< |
|
934 |
< |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
857 |
< |
|
933 |
> |
strcpy(checkPointMsg, "Successfully gathered all information from Bass\n"); |
934 |
> |
MPIcheckPoint(); |
935 |
|
#endif // is_mpi |
936 |
< |
} |
860 |
< |
|
861 |
< |
// make the bonds |
862 |
< |
for(j=0; j<info.nBonds; j++){ |
863 |
< |
|
864 |
< |
currentBond = comp_stamps[stampID]->getBond( j ); |
865 |
< |
theBonds[j].a = currentBond->getA() + atomOffset; |
866 |
< |
theBonds[j].b = currentBond->getB() + atomOffset; |
936 |
> |
} |
937 |
|
|
868 |
– |
exI = theBonds[j].a; |
869 |
– |
exJ = theBonds[j].b; |
938 |
|
|
939 |
< |
// exclude_I must always be the smaller of the pair |
940 |
< |
if( exI > exJ ){ |
941 |
< |
tempEx = exI; |
942 |
< |
exI = exJ; |
943 |
< |
exJ = tempEx; |
944 |
< |
} |
945 |
< |
#ifdef IS_MPI |
878 |
< |
tempEx = exI; |
879 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
880 |
< |
tempEx = exJ; |
881 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
882 |
< |
|
883 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
884 |
< |
#else // isn't MPI |
939 |
> |
void SimSetup::finalInfoCheck(void){ |
940 |
> |
int index; |
941 |
> |
int usesDipoles; |
942 |
> |
int i; |
943 |
> |
|
944 |
> |
for (i = 0; i < nInfo; i++){ |
945 |
> |
// check electrostatic parameters |
946 |
|
|
947 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
948 |
< |
#endif //is_mpi |
947 |
> |
index = 0; |
948 |
> |
usesDipoles = 0; |
949 |
> |
while ((index < info[i].n_atoms) && !usesDipoles){ |
950 |
> |
usesDipoles = (info[i].atoms[index])->hasDipole(); |
951 |
> |
index++; |
952 |
|
} |
889 |
– |
excludeOffset += info.nBonds; |
953 |
|
|
954 |
< |
//make the bends |
955 |
< |
for(j=0; j<info.nBends; j++){ |
956 |
< |
|
957 |
< |
currentBend = comp_stamps[stampID]->getBend( j ); |
958 |
< |
theBends[j].a = currentBend->getA() + atomOffset; |
959 |
< |
theBends[j].b = currentBend->getB() + atomOffset; |
960 |
< |
theBends[j].c = currentBend->getC() + atomOffset; |
961 |
< |
|
962 |
< |
if( currentBend->haveExtras() ){ |
963 |
< |
|
964 |
< |
extras = currentBend->getExtras(); |
965 |
< |
current_extra = extras; |
966 |
< |
|
967 |
< |
while( current_extra != NULL ){ |
968 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
969 |
< |
|
970 |
< |
switch( current_extra->getType() ){ |
971 |
< |
|
909 |
< |
case 0: |
910 |
< |
theBends[j].ghost = |
911 |
< |
current_extra->getInt() + atomOffset; |
912 |
< |
theBends[j].isGhost = 1; |
913 |
< |
break; |
914 |
< |
|
915 |
< |
case 1: |
916 |
< |
theBends[j].ghost = |
917 |
< |
(int)current_extra->getDouble() + atomOffset; |
918 |
< |
theBends[j].isGhost = 1; |
919 |
< |
break; |
920 |
< |
|
921 |
< |
default: |
922 |
< |
sprintf( painCave.errMsg, |
923 |
< |
"SimSetup Error: ghostVectorSource was neither a " |
924 |
< |
"double nor an int.\n" |
925 |
< |
"-->Bend[%d] in %s\n", |
926 |
< |
j, comp_stamps[stampID]->getID() ); |
927 |
< |
painCave.isFatal = 1; |
928 |
< |
simError(); |
929 |
< |
} |
930 |
< |
} |
931 |
< |
|
932 |
< |
else{ |
933 |
< |
|
934 |
< |
sprintf( painCave.errMsg, |
935 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
936 |
< |
" -->%s in Bend[%d] in %s\n", |
937 |
< |
current_extra->getlhs(), |
938 |
< |
j, comp_stamps[stampID]->getID() ); |
939 |
< |
painCave.isFatal = 1; |
940 |
< |
simError(); |
941 |
< |
} |
942 |
< |
|
943 |
< |
current_extra = current_extra->getNext(); |
944 |
< |
} |
954 |
> |
#ifdef IS_MPI |
955 |
> |
int myUse = usesDipoles; |
956 |
> |
MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
957 |
> |
#endif //is_mpi |
958 |
> |
|
959 |
> |
double theEcr, theEst; |
960 |
> |
|
961 |
> |
if (globals->getUseRF()){ |
962 |
> |
info[i].useReactionField = 1; |
963 |
> |
|
964 |
> |
if (!globals->haveECR()){ |
965 |
> |
sprintf(painCave.errMsg, |
966 |
> |
"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
967 |
> |
"\tOOPSE will use a default value of 15.0 angstroms" |
968 |
> |
"\tfor the electrostaticCutoffRadius.\n"); |
969 |
> |
painCave.isFatal = 0; |
970 |
> |
simError(); |
971 |
> |
theEcr = 15.0; |
972 |
|
} |
973 |
< |
|
974 |
< |
if( !theBends[j].isGhost ){ |
948 |
< |
|
949 |
< |
exI = theBends[j].a; |
950 |
< |
exJ = theBends[j].c; |
973 |
> |
else{ |
974 |
> |
theEcr = globals->getECR(); |
975 |
|
} |
976 |
+ |
|
977 |
+ |
if (!globals->haveEST()){ |
978 |
+ |
sprintf(painCave.errMsg, |
979 |
+ |
"SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
980 |
+ |
"\tOOPSE will use a default value of\n" |
981 |
+ |
"\t0.05 * electrostaticCutoffRadius\n" |
982 |
+ |
"\tfor the electrostaticSkinThickness\n"); |
983 |
+ |
painCave.isFatal = 0; |
984 |
+ |
simError(); |
985 |
+ |
theEst = 0.05 * theEcr; |
986 |
+ |
} |
987 |
|
else{ |
988 |
< |
|
954 |
< |
exI = theBends[j].a; |
955 |
< |
exJ = theBends[j].b; |
988 |
> |
theEst = globals->getEST(); |
989 |
|
} |
990 |
< |
|
991 |
< |
// exclude_I must always be the smaller of the pair |
992 |
< |
if( exI > exJ ){ |
993 |
< |
tempEx = exI; |
994 |
< |
exI = exJ; |
995 |
< |
exJ = tempEx; |
990 |
> |
|
991 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
992 |
> |
|
993 |
> |
if (!globals->haveDielectric()){ |
994 |
> |
sprintf(painCave.errMsg, |
995 |
> |
"SimSetup Error: No Dielectric constant was set.\n" |
996 |
> |
"\tYou are trying to use Reaction Field without" |
997 |
> |
"\tsetting a dielectric constant!\n"); |
998 |
> |
painCave.isFatal = 1; |
999 |
> |
simError(); |
1000 |
|
} |
1001 |
< |
#ifdef IS_MPI |
965 |
< |
tempEx = exI; |
966 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
967 |
< |
tempEx = exJ; |
968 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
969 |
< |
|
970 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
971 |
< |
#else // isn't MPI |
972 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
973 |
< |
#endif //is_mpi |
1001 |
> |
info[i].dielectric = globals->getDielectric(); |
1002 |
|
} |
1003 |
< |
excludeOffset += info.nBends; |
1003 |
> |
else{ |
1004 |
> |
if (usesDipoles){ |
1005 |
> |
if (!globals->haveECR()){ |
1006 |
> |
sprintf(painCave.errMsg, |
1007 |
> |
"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
1008 |
> |
"\tOOPSE will use a default value of 15.0 angstroms" |
1009 |
> |
"\tfor the electrostaticCutoffRadius.\n"); |
1010 |
> |
painCave.isFatal = 0; |
1011 |
> |
simError(); |
1012 |
> |
theEcr = 15.0; |
1013 |
> |
} |
1014 |
> |
else{ |
1015 |
> |
theEcr = globals->getECR(); |
1016 |
> |
} |
1017 |
> |
|
1018 |
> |
if (!globals->haveEST()){ |
1019 |
> |
sprintf(painCave.errMsg, |
1020 |
> |
"SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
1021 |
> |
"\tOOPSE will use a default value of\n" |
1022 |
> |
"\t0.05 * electrostaticCutoffRadius\n" |
1023 |
> |
"\tfor the electrostaticSkinThickness\n"); |
1024 |
> |
painCave.isFatal = 0; |
1025 |
> |
simError(); |
1026 |
> |
theEst = 0.05 * theEcr; |
1027 |
> |
} |
1028 |
> |
else{ |
1029 |
> |
theEst = globals->getEST(); |
1030 |
> |
} |
1031 |
> |
|
1032 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
1033 |
> |
} |
1034 |
> |
} |
1035 |
> |
} |
1036 |
> |
#ifdef IS_MPI |
1037 |
> |
strcpy(checkPointMsg, "post processing checks out"); |
1038 |
> |
MPIcheckPoint(); |
1039 |
> |
#endif // is_mpi |
1040 |
> |
} |
1041 |
> |
|
1042 |
> |
void SimSetup::initSystemCoords(void){ |
1043 |
> |
int i; |
1044 |
|
|
1045 |
< |
for(j=0; j<info.nTorsions; j++){ |
978 |
< |
|
979 |
< |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
980 |
< |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
981 |
< |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
982 |
< |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
983 |
< |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
984 |
< |
|
985 |
< |
exI = theTorsions[j].a; |
986 |
< |
exJ = theTorsions[j].d; |
1045 |
> |
char* inName; |
1046 |
|
|
1047 |
< |
// exclude_I must always be the smaller of the pair |
1048 |
< |
if( exI > exJ ){ |
1049 |
< |
tempEx = exI; |
1050 |
< |
exI = exJ; |
1051 |
< |
exJ = tempEx; |
1052 |
< |
} |
1047 |
> |
(info[0].getConfiguration())->createArrays(info[0].n_atoms); |
1048 |
> |
|
1049 |
> |
for (i = 0; i < info[0].n_atoms; i++) |
1050 |
> |
info[0].atoms[i]->setCoords(); |
1051 |
> |
|
1052 |
> |
if (globals->haveInitialConfig()){ |
1053 |
> |
InitializeFromFile* fileInit; |
1054 |
> |
#ifdef IS_MPI // is_mpi |
1055 |
> |
if (worldRank == 0){ |
1056 |
> |
#endif //is_mpi |
1057 |
> |
inName = globals->getInitialConfig(); |
1058 |
> |
fileInit = new InitializeFromFile(inName); |
1059 |
|
#ifdef IS_MPI |
995 |
– |
tempEx = exI; |
996 |
– |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
997 |
– |
tempEx = exJ; |
998 |
– |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
999 |
– |
|
1000 |
– |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1001 |
– |
#else // isn't MPI |
1002 |
– |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1003 |
– |
#endif //is_mpi |
1060 |
|
} |
1061 |
< |
excludeOffset += info.nTorsions; |
1061 |
> |
else |
1062 |
> |
fileInit = new InitializeFromFile(NULL); |
1063 |
> |
#endif |
1064 |
> |
fileInit->readInit(info); // default velocities on |
1065 |
|
|
1066 |
+ |
delete fileInit; |
1067 |
+ |
} |
1068 |
+ |
else{ |
1069 |
|
|
1070 |
< |
// send the arrays off to the forceField for init. |
1070 |
> |
// no init from bass |
1071 |
> |
|
1072 |
> |
sprintf(painCave.errMsg, |
1073 |
> |
"Cannot intialize a simulation without an initial configuration file.\n"); |
1074 |
> |
painCave.isFatal = 1;; |
1075 |
> |
simError(); |
1076 |
> |
|
1077 |
> |
} |
1078 |
|
|
1079 |
< |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1080 |
< |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1081 |
< |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1082 |
< |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1079 |
> |
#ifdef IS_MPI |
1080 |
> |
strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
1081 |
> |
MPIcheckPoint(); |
1082 |
> |
#endif // is_mpi |
1083 |
> |
} |
1084 |
|
|
1085 |
|
|
1086 |
< |
the_molecules[i].initialize( info ); |
1086 |
> |
void SimSetup::makeOutNames(void){ |
1087 |
> |
int k; |
1088 |
|
|
1089 |
|
|
1090 |
< |
atomOffset += info.nAtoms; |
1020 |
< |
delete[] theBonds; |
1021 |
< |
delete[] theBends; |
1022 |
< |
delete[] theTorsions; |
1023 |
< |
} |
1024 |
< |
|
1090 |
> |
for (k = 0; k < nInfo; k++){ |
1091 |
|
#ifdef IS_MPI |
1092 |
< |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1027 |
< |
MPIcheckPoint(); |
1092 |
> |
if (worldRank == 0){ |
1093 |
|
#endif // is_mpi |
1094 |
|
|
1095 |
< |
// clean up the forcefield |
1096 |
< |
the_ff->calcRcut(); |
1097 |
< |
the_ff->cleanMe(); |
1095 |
> |
if (globals->haveFinalConfig()){ |
1096 |
> |
strcpy(info[k].finalName, globals->getFinalConfig()); |
1097 |
> |
} |
1098 |
> |
else{ |
1099 |
> |
strcpy(info[k].finalName, inFileName); |
1100 |
> |
char* endTest; |
1101 |
> |
int nameLength = strlen(info[k].finalName); |
1102 |
> |
endTest = &(info[k].finalName[nameLength - 5]); |
1103 |
> |
if (!strcmp(endTest, ".bass")){ |
1104 |
> |
strcpy(endTest, ".eor"); |
1105 |
> |
} |
1106 |
> |
else if (!strcmp(endTest, ".BASS")){ |
1107 |
> |
strcpy(endTest, ".eor"); |
1108 |
> |
} |
1109 |
> |
else{ |
1110 |
> |
endTest = &(info[k].finalName[nameLength - 4]); |
1111 |
> |
if (!strcmp(endTest, ".bss")){ |
1112 |
> |
strcpy(endTest, ".eor"); |
1113 |
> |
} |
1114 |
> |
else if (!strcmp(endTest, ".mdl")){ |
1115 |
> |
strcpy(endTest, ".eor"); |
1116 |
> |
} |
1117 |
> |
else{ |
1118 |
> |
strcat(info[k].finalName, ".eor"); |
1119 |
> |
} |
1120 |
> |
} |
1121 |
> |
} |
1122 |
|
|
1123 |
+ |
// make the sample and status out names |
1124 |
+ |
|
1125 |
+ |
strcpy(info[k].sampleName, inFileName); |
1126 |
+ |
char* endTest; |
1127 |
+ |
int nameLength = strlen(info[k].sampleName); |
1128 |
+ |
endTest = &(info[k].sampleName[nameLength - 5]); |
1129 |
+ |
if (!strcmp(endTest, ".bass")){ |
1130 |
+ |
strcpy(endTest, ".dump"); |
1131 |
+ |
} |
1132 |
+ |
else if (!strcmp(endTest, ".BASS")){ |
1133 |
+ |
strcpy(endTest, ".dump"); |
1134 |
+ |
} |
1135 |
+ |
else{ |
1136 |
+ |
endTest = &(info[k].sampleName[nameLength - 4]); |
1137 |
+ |
if (!strcmp(endTest, ".bss")){ |
1138 |
+ |
strcpy(endTest, ".dump"); |
1139 |
+ |
} |
1140 |
+ |
else if (!strcmp(endTest, ".mdl")){ |
1141 |
+ |
strcpy(endTest, ".dump"); |
1142 |
+ |
} |
1143 |
+ |
else{ |
1144 |
+ |
strcat(info[k].sampleName, ".dump"); |
1145 |
+ |
} |
1146 |
+ |
} |
1147 |
+ |
|
1148 |
+ |
strcpy(info[k].statusName, inFileName); |
1149 |
+ |
nameLength = strlen(info[k].statusName); |
1150 |
+ |
endTest = &(info[k].statusName[nameLength - 5]); |
1151 |
+ |
if (!strcmp(endTest, ".bass")){ |
1152 |
+ |
strcpy(endTest, ".stat"); |
1153 |
+ |
} |
1154 |
+ |
else if (!strcmp(endTest, ".BASS")){ |
1155 |
+ |
strcpy(endTest, ".stat"); |
1156 |
+ |
} |
1157 |
+ |
else{ |
1158 |
+ |
endTest = &(info[k].statusName[nameLength - 4]); |
1159 |
+ |
if (!strcmp(endTest, ".bss")){ |
1160 |
+ |
strcpy(endTest, ".stat"); |
1161 |
+ |
} |
1162 |
+ |
else if (!strcmp(endTest, ".mdl")){ |
1163 |
+ |
strcpy(endTest, ".stat"); |
1164 |
+ |
} |
1165 |
+ |
else{ |
1166 |
+ |
strcat(info[k].statusName, ".stat"); |
1167 |
+ |
} |
1168 |
+ |
} |
1169 |
+ |
|
1170 |
+ |
#ifdef IS_MPI |
1171 |
+ |
|
1172 |
+ |
} |
1173 |
+ |
#endif // is_mpi |
1174 |
+ |
} |
1175 |
|
} |
1176 |
|
|
1036 |
– |
void SimSetup::initFromBass( void ){ |
1177 |
|
|
1178 |
< |
int i, j, k; |
1179 |
< |
int n_cells; |
1040 |
< |
double cellx, celly, cellz; |
1041 |
< |
double temp1, temp2, temp3; |
1042 |
< |
int n_per_extra; |
1043 |
< |
int n_extra; |
1044 |
< |
int have_extra, done; |
1178 |
> |
void SimSetup::sysObjectsCreation(void){ |
1179 |
> |
int i, k; |
1180 |
|
|
1181 |
< |
temp1 = (double)tot_nmol / 4.0; |
1047 |
< |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1048 |
< |
temp3 = ceil( temp2 ); |
1181 |
> |
// create the forceField |
1182 |
|
|
1183 |
< |
have_extra =0; |
1051 |
< |
if( temp2 < temp3 ){ // we have a non-complete lattice |
1052 |
< |
have_extra =1; |
1183 |
> |
createFF(); |
1184 |
|
|
1185 |
< |
n_cells = (int)temp3 - 1; |
1055 |
< |
cellx = simnfo->box_x / temp3; |
1056 |
< |
celly = simnfo->box_y / temp3; |
1057 |
< |
cellz = simnfo->box_z / temp3; |
1058 |
< |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1059 |
< |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1060 |
< |
n_per_extra = (int)ceil( temp1 ); |
1185 |
> |
// extract componentList |
1186 |
|
|
1187 |
< |
if( n_per_extra > 4){ |
1188 |
< |
sprintf( painCave.errMsg, |
1189 |
< |
"SimSetup error. There has been an error in constructing" |
1190 |
< |
" the non-complete lattice.\n" ); |
1187 |
> |
compList(); |
1188 |
> |
|
1189 |
> |
// calc the number of atoms, bond, bends, and torsions |
1190 |
> |
|
1191 |
> |
calcSysValues(); |
1192 |
> |
|
1193 |
> |
#ifdef IS_MPI |
1194 |
> |
// divide the molecules among the processors |
1195 |
> |
|
1196 |
> |
mpiMolDivide(); |
1197 |
> |
#endif //is_mpi |
1198 |
> |
|
1199 |
> |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1200 |
> |
|
1201 |
> |
makeSysArrays(); |
1202 |
> |
|
1203 |
> |
// make and initialize the molecules (all but atomic coordinates) |
1204 |
> |
|
1205 |
> |
makeMolecules(); |
1206 |
> |
|
1207 |
> |
for (k = 0; k < nInfo; k++){ |
1208 |
> |
info[k].identArray = new int[info[k].n_atoms]; |
1209 |
> |
for (i = 0; i < info[k].n_atoms; i++){ |
1210 |
> |
info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1211 |
> |
} |
1212 |
> |
} |
1213 |
> |
} |
1214 |
> |
|
1215 |
> |
|
1216 |
> |
void SimSetup::createFF(void){ |
1217 |
> |
switch (ffCase){ |
1218 |
> |
case FF_DUFF: |
1219 |
> |
the_ff = new DUFF(); |
1220 |
> |
break; |
1221 |
> |
|
1222 |
> |
case FF_LJ: |
1223 |
> |
the_ff = new LJFF(); |
1224 |
> |
break; |
1225 |
> |
|
1226 |
> |
case FF_EAM: |
1227 |
> |
the_ff = new EAM_FF(); |
1228 |
> |
break; |
1229 |
> |
|
1230 |
> |
case FF_H2O: |
1231 |
> |
the_ff = new WATER(); |
1232 |
> |
break; |
1233 |
> |
|
1234 |
> |
default: |
1235 |
> |
sprintf(painCave.errMsg, |
1236 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1237 |
|
painCave.isFatal = 1; |
1238 |
|
simError(); |
1068 |
– |
} |
1239 |
|
} |
1070 |
– |
else{ |
1071 |
– |
n_cells = (int)temp3; |
1072 |
– |
cellx = simnfo->box_x / temp3; |
1073 |
– |
celly = simnfo->box_y / temp3; |
1074 |
– |
cellz = simnfo->box_z / temp3; |
1075 |
– |
} |
1240 |
|
|
1241 |
< |
current_mol = 0; |
1242 |
< |
current_comp_mol = 0; |
1243 |
< |
current_comp = 0; |
1244 |
< |
current_atom_ndx = 0; |
1241 |
> |
#ifdef IS_MPI |
1242 |
> |
strcpy(checkPointMsg, "ForceField creation successful"); |
1243 |
> |
MPIcheckPoint(); |
1244 |
> |
#endif // is_mpi |
1245 |
> |
} |
1246 |
|
|
1082 |
– |
for( i=0; i < n_cells ; i++ ){ |
1083 |
– |
for( j=0; j < n_cells; j++ ){ |
1084 |
– |
for( k=0; k < n_cells; k++ ){ |
1247 |
|
|
1248 |
< |
makeElement( i * cellx, |
1249 |
< |
j * celly, |
1250 |
< |
k * cellz ); |
1248 |
> |
void SimSetup::compList(void){ |
1249 |
> |
int i; |
1250 |
> |
char* id; |
1251 |
> |
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1252 |
> |
LinkedMolStamp* currentStamp = NULL; |
1253 |
> |
comp_stamps = new MoleculeStamp * [n_components]; |
1254 |
|
|
1255 |
< |
makeElement( i * cellx + 0.5 * cellx, |
1256 |
< |
j * celly + 0.5 * celly, |
1092 |
< |
k * cellz ); |
1255 |
> |
// make an array of molecule stamps that match the components used. |
1256 |
> |
// also extract the used stamps out into a separate linked list |
1257 |
|
|
1258 |
< |
makeElement( i * cellx, |
1259 |
< |
j * celly + 0.5 * celly, |
1260 |
< |
k * cellz + 0.5 * cellz ); |
1258 |
> |
for (i = 0; i < nInfo; i++){ |
1259 |
> |
info[i].nComponents = n_components; |
1260 |
> |
info[i].componentsNmol = components_nmol; |
1261 |
> |
info[i].compStamps = comp_stamps; |
1262 |
> |
info[i].headStamp = headStamp; |
1263 |
> |
} |
1264 |
|
|
1265 |
< |
makeElement( i * cellx + 0.5 * cellx, |
1266 |
< |
j * celly, |
1267 |
< |
k * cellz + 0.5 * cellz ); |
1265 |
> |
|
1266 |
> |
for (i = 0; i < n_components; i++){ |
1267 |
> |
id = the_components[i]->getType(); |
1268 |
> |
comp_stamps[i] = NULL; |
1269 |
> |
|
1270 |
> |
// check to make sure the component isn't already in the list |
1271 |
> |
|
1272 |
> |
comp_stamps[i] = headStamp->match(id); |
1273 |
> |
if (comp_stamps[i] == NULL){ |
1274 |
> |
// extract the component from the list; |
1275 |
> |
|
1276 |
> |
currentStamp = stamps->extractMolStamp(id); |
1277 |
> |
if (currentStamp == NULL){ |
1278 |
> |
sprintf(painCave.errMsg, |
1279 |
> |
"SimSetup error: Component \"%s\" was not found in the " |
1280 |
> |
"list of declared molecules\n", |
1281 |
> |
id); |
1282 |
> |
painCave.isFatal = 1; |
1283 |
> |
simError(); |
1284 |
|
} |
1285 |
+ |
|
1286 |
+ |
headStamp->add(currentStamp); |
1287 |
+ |
comp_stamps[i] = headStamp->match(id); |
1288 |
|
} |
1289 |
|
} |
1290 |
|
|
1291 |
< |
if( have_extra ){ |
1292 |
< |
done = 0; |
1291 |
> |
#ifdef IS_MPI |
1292 |
> |
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1293 |
> |
MPIcheckPoint(); |
1294 |
> |
#endif // is_mpi |
1295 |
> |
} |
1296 |
|
|
1297 |
< |
int start_ndx; |
1298 |
< |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
1110 |
< |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
1297 |
> |
void SimSetup::calcSysValues(void){ |
1298 |
> |
int i; |
1299 |
|
|
1300 |
< |
if( i < n_cells ){ |
1300 |
> |
int* molMembershipArray; |
1301 |
|
|
1302 |
< |
if( j < n_cells ){ |
1303 |
< |
start_ndx = n_cells; |
1304 |
< |
} |
1305 |
< |
else start_ndx = 0; |
1306 |
< |
} |
1307 |
< |
else start_ndx = 0; |
1302 |
> |
tot_atoms = 0; |
1303 |
> |
tot_bonds = 0; |
1304 |
> |
tot_bends = 0; |
1305 |
> |
tot_torsions = 0; |
1306 |
> |
tot_rigid = 0; |
1307 |
> |
for (i = 0; i < n_components; i++){ |
1308 |
> |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1309 |
> |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1310 |
> |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1311 |
> |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1312 |
> |
tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies(); |
1313 |
> |
} |
1314 |
> |
|
1315 |
> |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1316 |
> |
molMembershipArray = new int[tot_atoms]; |
1317 |
|
|
1318 |
< |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1318 |
> |
for (i = 0; i < nInfo; i++){ |
1319 |
> |
info[i].n_atoms = tot_atoms; |
1320 |
> |
info[i].n_bonds = tot_bonds; |
1321 |
> |
info[i].n_bends = tot_bends; |
1322 |
> |
info[i].n_torsions = tot_torsions; |
1323 |
> |
info[i].n_SRI = tot_SRI; |
1324 |
> |
info[i].n_mol = tot_nmol; |
1325 |
|
|
1326 |
< |
makeElement( i * cellx, |
1327 |
< |
j * celly, |
1328 |
< |
k * cellz ); |
1126 |
< |
done = ( current_mol >= tot_nmol ); |
1326 |
> |
info[i].molMembershipArray = molMembershipArray; |
1327 |
> |
} |
1328 |
> |
} |
1329 |
|
|
1330 |
< |
if( !done && n_per_extra > 1 ){ |
1129 |
< |
makeElement( i * cellx + 0.5 * cellx, |
1130 |
< |
j * celly + 0.5 * celly, |
1131 |
< |
k * cellz ); |
1132 |
< |
done = ( current_mol >= tot_nmol ); |
1133 |
< |
} |
1330 |
> |
#ifdef IS_MPI |
1331 |
|
|
1332 |
< |
if( !done && n_per_extra > 2){ |
1333 |
< |
makeElement( i * cellx, |
1334 |
< |
j * celly + 0.5 * celly, |
1335 |
< |
k * cellz + 0.5 * cellz ); |
1336 |
< |
done = ( current_mol >= tot_nmol ); |
1140 |
< |
} |
1332 |
> |
void SimSetup::mpiMolDivide(void){ |
1333 |
> |
int i, j, k; |
1334 |
> |
int localMol, allMol; |
1335 |
> |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1336 |
> |
int local_rigid; |
1337 |
|
|
1338 |
< |
if( !done && n_per_extra > 3){ |
1339 |
< |
makeElement( i * cellx + 0.5 * cellx, |
1340 |
< |
j * celly, |
1341 |
< |
k * cellz + 0.5 * cellz ); |
1342 |
< |
done = ( current_mol >= tot_nmol ); |
1343 |
< |
} |
1344 |
< |
} |
1338 |
> |
mpiSim = new mpiSimulation(info); |
1339 |
> |
|
1340 |
> |
globalIndex = mpiSim->divideLabor(); |
1341 |
> |
|
1342 |
> |
// set up the local variables |
1343 |
> |
|
1344 |
> |
mol2proc = mpiSim->getMolToProcMap(); |
1345 |
> |
molCompType = mpiSim->getMolComponentType(); |
1346 |
> |
|
1347 |
> |
allMol = 0; |
1348 |
> |
localMol = 0; |
1349 |
> |
local_atoms = 0; |
1350 |
> |
local_bonds = 0; |
1351 |
> |
local_bends = 0; |
1352 |
> |
local_torsions = 0; |
1353 |
> |
local_rigid = 0; |
1354 |
> |
globalAtomIndex = 0; |
1355 |
> |
|
1356 |
> |
for (i = 0; i < n_components; i++){ |
1357 |
> |
for (j = 0; j < components_nmol[i]; j++){ |
1358 |
> |
if (mol2proc[allMol] == worldRank){ |
1359 |
> |
local_atoms += comp_stamps[i]->getNAtoms(); |
1360 |
> |
local_bonds += comp_stamps[i]->getNBonds(); |
1361 |
> |
local_bends += comp_stamps[i]->getNBends(); |
1362 |
> |
local_torsions += comp_stamps[i]->getNTorsions(); |
1363 |
> |
local_rigid += comp_stamps[i]->getNRigidBodies(); |
1364 |
> |
localMol++; |
1365 |
> |
} |
1366 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1367 |
> |
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1368 |
> |
globalAtomIndex++; |
1369 |
|
} |
1370 |
+ |
|
1371 |
+ |
allMol++; |
1372 |
|
} |
1373 |
|
} |
1374 |
+ |
local_SRI = local_bonds + local_bends + local_torsions; |
1375 |
|
|
1376 |
+ |
info[0].n_atoms = mpiSim->getMyNlocal(); |
1377 |
+ |
|
1378 |
|
|
1379 |
< |
for( i=0; i<simnfo->n_atoms; i++ ){ |
1380 |
< |
simnfo->atoms[i]->set_vx( 0.0 ); |
1381 |
< |
simnfo->atoms[i]->set_vy( 0.0 ); |
1382 |
< |
simnfo->atoms[i]->set_vz( 0.0 ); |
1379 |
> |
if (local_atoms != info[0].n_atoms){ |
1380 |
> |
sprintf(painCave.errMsg, |
1381 |
> |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1382 |
> |
"\tlocalAtom (%d) are not equal.\n", |
1383 |
> |
info[0].n_atoms, local_atoms); |
1384 |
> |
painCave.isFatal = 1; |
1385 |
> |
simError(); |
1386 |
|
} |
1387 |
+ |
|
1388 |
+ |
info[0].n_bonds = local_bonds; |
1389 |
+ |
info[0].n_bends = local_bends; |
1390 |
+ |
info[0].n_torsions = local_torsions; |
1391 |
+ |
info[0].n_SRI = local_SRI; |
1392 |
+ |
info[0].n_mol = localMol; |
1393 |
+ |
|
1394 |
+ |
strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1395 |
+ |
MPIcheckPoint(); |
1396 |
|
} |
1397 |
|
|
1398 |
< |
void SimSetup::makeElement( double x, double y, double z ){ |
1398 |
> |
#endif // is_mpi |
1399 |
|
|
1163 |
– |
int k; |
1164 |
– |
AtomStamp* current_atom; |
1165 |
– |
DirectionalAtom* dAtom; |
1166 |
– |
double rotMat[3][3]; |
1400 |
|
|
1401 |
< |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1401 |
> |
void SimSetup::makeSysArrays(void){ |
1402 |
> |
|
1403 |
> |
#ifndef IS_MPI |
1404 |
> |
int k, j; |
1405 |
> |
#endif // is_mpi |
1406 |
> |
int i, l; |
1407 |
|
|
1408 |
< |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
1409 |
< |
if( !current_atom->havePosition() ){ |
1172 |
< |
sprintf( painCave.errMsg, |
1173 |
< |
"SimSetup:initFromBass error.\n" |
1174 |
< |
"\tComponent %s, atom %s does not have a position specified.\n" |
1175 |
< |
"\tThe initialization routine is unable to give a start" |
1176 |
< |
" position.\n", |
1177 |
< |
comp_stamps[current_comp]->getID(), |
1178 |
< |
current_atom->getType() ); |
1179 |
< |
painCave.isFatal = 1; |
1180 |
< |
simError(); |
1181 |
< |
} |
1408 |
> |
Atom** the_atoms; |
1409 |
> |
Molecule* the_molecules; |
1410 |
|
|
1411 |
< |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1412 |
< |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1185 |
< |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1411 |
> |
for (l = 0; l < nInfo; l++){ |
1412 |
> |
// create the atom and short range interaction arrays |
1413 |
|
|
1414 |
< |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1414 |
> |
the_atoms = new Atom * [info[l].n_atoms]; |
1415 |
> |
the_molecules = new Molecule[info[l].n_mol]; |
1416 |
> |
int molIndex; |
1417 |
|
|
1418 |
< |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1418 |
> |
// initialize the molecule's stampID's |
1419 |
|
|
1420 |
< |
rotMat[0][0] = 1.0; |
1192 |
< |
rotMat[0][1] = 0.0; |
1193 |
< |
rotMat[0][2] = 0.0; |
1420 |
> |
#ifdef IS_MPI |
1421 |
|
|
1195 |
– |
rotMat[1][0] = 0.0; |
1196 |
– |
rotMat[1][1] = 1.0; |
1197 |
– |
rotMat[1][2] = 0.0; |
1422 |
|
|
1423 |
< |
rotMat[2][0] = 0.0; |
1424 |
< |
rotMat[2][1] = 0.0; |
1425 |
< |
rotMat[2][2] = 1.0; |
1423 |
> |
molIndex = 0; |
1424 |
> |
for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1425 |
> |
if (mol2proc[i] == worldRank){ |
1426 |
> |
the_molecules[molIndex].setStampID(molCompType[i]); |
1427 |
> |
the_molecules[molIndex].setMyIndex(molIndex); |
1428 |
> |
the_molecules[molIndex].setGlobalIndex(i); |
1429 |
> |
molIndex++; |
1430 |
> |
} |
1431 |
> |
} |
1432 |
|
|
1433 |
< |
dAtom->setA( rotMat ); |
1433 |
> |
#else // is_mpi |
1434 |
> |
|
1435 |
> |
molIndex = 0; |
1436 |
> |
globalAtomIndex = 0; |
1437 |
> |
for (i = 0; i < n_components; i++){ |
1438 |
> |
for (j = 0; j < components_nmol[i]; j++){ |
1439 |
> |
the_molecules[molIndex].setStampID(i); |
1440 |
> |
the_molecules[molIndex].setMyIndex(molIndex); |
1441 |
> |
the_molecules[molIndex].setGlobalIndex(molIndex); |
1442 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1443 |
> |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1444 |
> |
globalAtomIndex++; |
1445 |
> |
} |
1446 |
> |
molIndex++; |
1447 |
> |
} |
1448 |
|
} |
1449 |
|
|
1450 |
< |
current_atom_ndx++; |
1450 |
> |
|
1451 |
> |
#endif // is_mpi |
1452 |
> |
|
1453 |
> |
info[l].globalExcludes = new int; |
1454 |
> |
info[l].globalExcludes[0] = 0; |
1455 |
> |
|
1456 |
> |
// set the arrays into the SimInfo object |
1457 |
> |
|
1458 |
> |
info[l].atoms = the_atoms; |
1459 |
> |
info[l].molecules = the_molecules; |
1460 |
> |
info[l].nGlobalExcludes = 0; |
1461 |
> |
|
1462 |
> |
the_ff->setSimInfo(info); |
1463 |
|
} |
1464 |
+ |
} |
1465 |
|
|
1466 |
< |
current_mol++; |
1467 |
< |
current_comp_mol++; |
1466 |
> |
void SimSetup::makeIntegrator(void){ |
1467 |
> |
int k; |
1468 |
|
|
1469 |
< |
if( current_comp_mol >= components_nmol[current_comp] ){ |
1469 |
> |
NVE<RealIntegrator>* myNVE = NULL; |
1470 |
> |
NVT<RealIntegrator>* myNVT = NULL; |
1471 |
> |
NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1472 |
> |
NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1473 |
> |
NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1474 |
> |
|
1475 |
> |
for (k = 0; k < nInfo; k++){ |
1476 |
> |
switch (ensembleCase){ |
1477 |
> |
case NVE_ENS: |
1478 |
> |
if (globals->haveZconstraints()){ |
1479 |
> |
setupZConstraint(info[k]); |
1480 |
> |
myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1481 |
> |
} |
1482 |
> |
else{ |
1483 |
> |
myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1484 |
> |
} |
1485 |
> |
|
1486 |
> |
info->the_integrator = myNVE; |
1487 |
> |
break; |
1488 |
|
|
1489 |
< |
current_comp_mol = 0; |
1490 |
< |
current_comp++; |
1489 |
> |
case NVT_ENS: |
1490 |
> |
if (globals->haveZconstraints()){ |
1491 |
> |
setupZConstraint(info[k]); |
1492 |
> |
myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1493 |
> |
} |
1494 |
> |
else |
1495 |
> |
myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1496 |
> |
|
1497 |
> |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1498 |
> |
|
1499 |
> |
if (globals->haveTauThermostat()) |
1500 |
> |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1501 |
> |
else{ |
1502 |
> |
sprintf(painCave.errMsg, |
1503 |
> |
"SimSetup error: If you use the NVT\n" |
1504 |
> |
"\tensemble, you must set tauThermostat.\n"); |
1505 |
> |
painCave.isFatal = 1; |
1506 |
> |
simError(); |
1507 |
> |
} |
1508 |
> |
|
1509 |
> |
info->the_integrator = myNVT; |
1510 |
> |
break; |
1511 |
> |
|
1512 |
> |
case NPTi_ENS: |
1513 |
> |
if (globals->haveZconstraints()){ |
1514 |
> |
setupZConstraint(info[k]); |
1515 |
> |
myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1516 |
> |
} |
1517 |
> |
else |
1518 |
> |
myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1519 |
> |
|
1520 |
> |
myNPTi->setTargetTemp(globals->getTargetTemp()); |
1521 |
> |
|
1522 |
> |
if (globals->haveTargetPressure()) |
1523 |
> |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1524 |
> |
else{ |
1525 |
> |
sprintf(painCave.errMsg, |
1526 |
> |
"SimSetup error: If you use a constant pressure\n" |
1527 |
> |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1528 |
> |
painCave.isFatal = 1; |
1529 |
> |
simError(); |
1530 |
> |
} |
1531 |
> |
|
1532 |
> |
if (globals->haveTauThermostat()) |
1533 |
> |
myNPTi->setTauThermostat(globals->getTauThermostat()); |
1534 |
> |
else{ |
1535 |
> |
sprintf(painCave.errMsg, |
1536 |
> |
"SimSetup error: If you use an NPT\n" |
1537 |
> |
"\tensemble, you must set tauThermostat.\n"); |
1538 |
> |
painCave.isFatal = 1; |
1539 |
> |
simError(); |
1540 |
> |
} |
1541 |
> |
|
1542 |
> |
if (globals->haveTauBarostat()) |
1543 |
> |
myNPTi->setTauBarostat(globals->getTauBarostat()); |
1544 |
> |
else{ |
1545 |
> |
sprintf(painCave.errMsg, |
1546 |
> |
"SimSetup error: If you use an NPT\n" |
1547 |
> |
"\tensemble, you must set tauBarostat.\n"); |
1548 |
> |
painCave.isFatal = 1; |
1549 |
> |
simError(); |
1550 |
> |
} |
1551 |
> |
|
1552 |
> |
info->the_integrator = myNPTi; |
1553 |
> |
break; |
1554 |
> |
|
1555 |
> |
case NPTf_ENS: |
1556 |
> |
if (globals->haveZconstraints()){ |
1557 |
> |
setupZConstraint(info[k]); |
1558 |
> |
myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1559 |
> |
} |
1560 |
> |
else |
1561 |
> |
myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1562 |
> |
|
1563 |
> |
myNPTf->setTargetTemp(globals->getTargetTemp()); |
1564 |
> |
|
1565 |
> |
if (globals->haveTargetPressure()) |
1566 |
> |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1567 |
> |
else{ |
1568 |
> |
sprintf(painCave.errMsg, |
1569 |
> |
"SimSetup error: If you use a constant pressure\n" |
1570 |
> |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1571 |
> |
painCave.isFatal = 1; |
1572 |
> |
simError(); |
1573 |
> |
} |
1574 |
> |
|
1575 |
> |
if (globals->haveTauThermostat()) |
1576 |
> |
myNPTf->setTauThermostat(globals->getTauThermostat()); |
1577 |
> |
|
1578 |
> |
else{ |
1579 |
> |
sprintf(painCave.errMsg, |
1580 |
> |
"SimSetup error: If you use an NPT\n" |
1581 |
> |
"\tensemble, you must set tauThermostat.\n"); |
1582 |
> |
painCave.isFatal = 1; |
1583 |
> |
simError(); |
1584 |
> |
} |
1585 |
> |
|
1586 |
> |
if (globals->haveTauBarostat()) |
1587 |
> |
myNPTf->setTauBarostat(globals->getTauBarostat()); |
1588 |
> |
|
1589 |
> |
else{ |
1590 |
> |
sprintf(painCave.errMsg, |
1591 |
> |
"SimSetup error: If you use an NPT\n" |
1592 |
> |
"\tensemble, you must set tauBarostat.\n"); |
1593 |
> |
painCave.isFatal = 1; |
1594 |
> |
simError(); |
1595 |
> |
} |
1596 |
> |
|
1597 |
> |
info->the_integrator = myNPTf; |
1598 |
> |
break; |
1599 |
> |
|
1600 |
> |
case NPTxyz_ENS: |
1601 |
> |
if (globals->haveZconstraints()){ |
1602 |
> |
setupZConstraint(info[k]); |
1603 |
> |
myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1604 |
> |
} |
1605 |
> |
else |
1606 |
> |
myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1607 |
> |
|
1608 |
> |
myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1609 |
> |
|
1610 |
> |
if (globals->haveTargetPressure()) |
1611 |
> |
myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1612 |
> |
else{ |
1613 |
> |
sprintf(painCave.errMsg, |
1614 |
> |
"SimSetup error: If you use a constant pressure\n" |
1615 |
> |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1616 |
> |
painCave.isFatal = 1; |
1617 |
> |
simError(); |
1618 |
> |
} |
1619 |
> |
|
1620 |
> |
if (globals->haveTauThermostat()) |
1621 |
> |
myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1622 |
> |
else{ |
1623 |
> |
sprintf(painCave.errMsg, |
1624 |
> |
"SimSetup error: If you use an NPT\n" |
1625 |
> |
"\tensemble, you must set tauThermostat.\n"); |
1626 |
> |
painCave.isFatal = 1; |
1627 |
> |
simError(); |
1628 |
> |
} |
1629 |
> |
|
1630 |
> |
if (globals->haveTauBarostat()) |
1631 |
> |
myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1632 |
> |
else{ |
1633 |
> |
sprintf(painCave.errMsg, |
1634 |
> |
"SimSetup error: If you use an NPT\n" |
1635 |
> |
"\tensemble, you must set tauBarostat.\n"); |
1636 |
> |
painCave.isFatal = 1; |
1637 |
> |
simError(); |
1638 |
> |
} |
1639 |
> |
|
1640 |
> |
info->the_integrator = myNPTxyz; |
1641 |
> |
break; |
1642 |
> |
|
1643 |
> |
default: |
1644 |
> |
sprintf(painCave.errMsg, |
1645 |
> |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1646 |
> |
painCave.isFatal = 1; |
1647 |
> |
simError(); |
1648 |
> |
} |
1649 |
|
} |
1650 |
|
} |
1651 |
+ |
|
1652 |
+ |
void SimSetup::initFortran(void){ |
1653 |
+ |
info[0].refreshSim(); |
1654 |
+ |
|
1655 |
+ |
if (!strcmp(info[0].mixingRule, "standard")){ |
1656 |
+ |
the_ff->initForceField(LB_MIXING_RULE); |
1657 |
+ |
} |
1658 |
+ |
else if (!strcmp(info[0].mixingRule, "explicit")){ |
1659 |
+ |
the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1660 |
+ |
} |
1661 |
+ |
else{ |
1662 |
+ |
sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1663 |
+ |
info[0].mixingRule); |
1664 |
+ |
painCave.isFatal = 1; |
1665 |
+ |
simError(); |
1666 |
+ |
} |
1667 |
+ |
|
1668 |
+ |
|
1669 |
+ |
#ifdef IS_MPI |
1670 |
+ |
strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1671 |
+ |
MPIcheckPoint(); |
1672 |
+ |
#endif // is_mpi |
1673 |
+ |
} |
1674 |
+ |
|
1675 |
+ |
void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1676 |
+ |
int nZConstraints; |
1677 |
+ |
ZconStamp** zconStamp; |
1678 |
+ |
|
1679 |
+ |
if (globals->haveZconstraintTime()){ |
1680 |
+ |
//add sample time of z-constraint into SimInfo's property list |
1681 |
+ |
DoubleData* zconsTimeProp = new DoubleData(); |
1682 |
+ |
zconsTimeProp->setID(ZCONSTIME_ID); |
1683 |
+ |
zconsTimeProp->setData(globals->getZconsTime()); |
1684 |
+ |
theInfo.addProperty(zconsTimeProp); |
1685 |
+ |
} |
1686 |
+ |
else{ |
1687 |
+ |
sprintf(painCave.errMsg, |
1688 |
+ |
"ZConstraint error: If you use a ZConstraint,\n" |
1689 |
+ |
"\tyou must set zconsTime.\n"); |
1690 |
+ |
painCave.isFatal = 1; |
1691 |
+ |
simError(); |
1692 |
+ |
} |
1693 |
+ |
|
1694 |
+ |
//push zconsTol into siminfo, if user does not specify |
1695 |
+ |
//value for zconsTol, a default value will be used |
1696 |
+ |
DoubleData* zconsTol = new DoubleData(); |
1697 |
+ |
zconsTol->setID(ZCONSTOL_ID); |
1698 |
+ |
if (globals->haveZconsTol()){ |
1699 |
+ |
zconsTol->setData(globals->getZconsTol()); |
1700 |
+ |
} |
1701 |
+ |
else{ |
1702 |
+ |
double defaultZConsTol = 0.01; |
1703 |
+ |
sprintf(painCave.errMsg, |
1704 |
+ |
"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
1705 |
+ |
"\tOOPSE will use a default value of %f.\n" |
1706 |
+ |
"\tTo set the tolerance, use the zconsTol variable.\n", |
1707 |
+ |
defaultZConsTol); |
1708 |
+ |
painCave.isFatal = 0; |
1709 |
+ |
simError(); |
1710 |
+ |
|
1711 |
+ |
zconsTol->setData(defaultZConsTol); |
1712 |
+ |
} |
1713 |
+ |
theInfo.addProperty(zconsTol); |
1714 |
+ |
|
1715 |
+ |
//set Force Subtraction Policy |
1716 |
+ |
StringData* zconsForcePolicy = new StringData(); |
1717 |
+ |
zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1718 |
+ |
|
1719 |
+ |
if (globals->haveZconsForcePolicy()){ |
1720 |
+ |
zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1721 |
+ |
} |
1722 |
+ |
else{ |
1723 |
+ |
sprintf(painCave.errMsg, |
1724 |
+ |
"ZConstraint Warning: No force subtraction policy was set.\n" |
1725 |
+ |
"\tOOPSE will use PolicyByMass.\n" |
1726 |
+ |
"\tTo set the policy, use the zconsForcePolicy variable.\n"); |
1727 |
+ |
painCave.isFatal = 0; |
1728 |
+ |
simError(); |
1729 |
+ |
zconsForcePolicy->setData("BYMASS"); |
1730 |
+ |
} |
1731 |
+ |
|
1732 |
+ |
theInfo.addProperty(zconsForcePolicy); |
1733 |
+ |
|
1734 |
+ |
//set zcons gap |
1735 |
+ |
DoubleData* zconsGap = new DoubleData(); |
1736 |
+ |
zconsGap->setID(ZCONSGAP_ID); |
1737 |
+ |
|
1738 |
+ |
if (globals->haveZConsGap()){ |
1739 |
+ |
zconsGap->setData(globals->getZconsGap()); |
1740 |
+ |
theInfo.addProperty(zconsGap); |
1741 |
+ |
} |
1742 |
+ |
|
1743 |
+ |
//set zcons fixtime |
1744 |
+ |
DoubleData* zconsFixtime = new DoubleData(); |
1745 |
+ |
zconsFixtime->setID(ZCONSFIXTIME_ID); |
1746 |
+ |
|
1747 |
+ |
if (globals->haveZConsFixTime()){ |
1748 |
+ |
zconsFixtime->setData(globals->getZconsFixtime()); |
1749 |
+ |
theInfo.addProperty(zconsFixtime); |
1750 |
+ |
} |
1751 |
+ |
|
1752 |
+ |
//set zconsUsingSMD |
1753 |
+ |
IntData* zconsUsingSMD = new IntData(); |
1754 |
+ |
zconsUsingSMD->setID(ZCONSUSINGSMD_ID); |
1755 |
+ |
|
1756 |
+ |
if (globals->haveZConsUsingSMD()){ |
1757 |
+ |
zconsUsingSMD->setData(globals->getZconsUsingSMD()); |
1758 |
+ |
theInfo.addProperty(zconsUsingSMD); |
1759 |
+ |
} |
1760 |
+ |
|
1761 |
+ |
//Determine the name of ouput file and add it into SimInfo's property list |
1762 |
+ |
//Be careful, do not use inFileName, since it is a pointer which |
1763 |
+ |
//point to a string at master node, and slave nodes do not contain that string |
1764 |
+ |
|
1765 |
+ |
string zconsOutput(theInfo.finalName); |
1766 |
+ |
|
1767 |
+ |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1768 |
+ |
|
1769 |
+ |
StringData* zconsFilename = new StringData(); |
1770 |
+ |
zconsFilename->setID(ZCONSFILENAME_ID); |
1771 |
+ |
zconsFilename->setData(zconsOutput); |
1772 |
+ |
|
1773 |
+ |
theInfo.addProperty(zconsFilename); |
1774 |
+ |
|
1775 |
+ |
//setup index, pos and other parameters of z-constraint molecules |
1776 |
+ |
nZConstraints = globals->getNzConstraints(); |
1777 |
+ |
theInfo.nZconstraints = nZConstraints; |
1778 |
+ |
|
1779 |
+ |
zconStamp = globals->getZconStamp(); |
1780 |
+ |
ZConsParaItem tempParaItem; |
1781 |
+ |
|
1782 |
+ |
ZConsParaData* zconsParaData = new ZConsParaData(); |
1783 |
+ |
zconsParaData->setID(ZCONSPARADATA_ID); |
1784 |
+ |
|
1785 |
+ |
for (int i = 0; i < nZConstraints; i++){ |
1786 |
+ |
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1787 |
+ |
tempParaItem.zPos = zconStamp[i]->getZpos(); |
1788 |
+ |
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1789 |
+ |
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1790 |
+ |
tempParaItem.havingCantVel = zconStamp[i]->haveCantVel(); |
1791 |
+ |
tempParaItem.cantVel = zconStamp[i]->getCantVel(); |
1792 |
+ |
zconsParaData->addItem(tempParaItem); |
1793 |
+ |
} |
1794 |
+ |
|
1795 |
+ |
//check the uniqueness of index |
1796 |
+ |
if(!zconsParaData->isIndexUnique()){ |
1797 |
+ |
sprintf(painCave.errMsg, |
1798 |
+ |
"ZConstraint Error: molIndex is not unique!\n"); |
1799 |
+ |
painCave.isFatal = 1; |
1800 |
+ |
simError(); |
1801 |
+ |
} |
1802 |
+ |
|
1803 |
+ |
//sort the parameters by index of molecules |
1804 |
+ |
zconsParaData->sortByIndex(); |
1805 |
+ |
|
1806 |
+ |
//push data into siminfo, therefore, we can retrieve later |
1807 |
+ |
theInfo.addProperty(zconsParaData); |
1808 |
+ |
} |
1809 |
+ |
|
1810 |
+ |
void SimSetup::makeMinimizer(){ |
1811 |
+ |
|
1812 |
+ |
OOPSEMinimizer* myOOPSEMinimizer; |
1813 |
+ |
MinimizerParameterSet* param; |
1814 |
+ |
char minimizerName[100]; |
1815 |
+ |
|
1816 |
+ |
for (int i = 0; i < nInfo; i++){ |
1817 |
+ |
|
1818 |
+ |
//prepare parameter set for minimizer |
1819 |
+ |
param = new MinimizerParameterSet(); |
1820 |
+ |
param->setDefaultParameter(); |
1821 |
+ |
|
1822 |
+ |
if (globals->haveMinimizer()){ |
1823 |
+ |
param->setFTol(globals->getMinFTol()); |
1824 |
+ |
} |
1825 |
+ |
|
1826 |
+ |
if (globals->haveMinGTol()){ |
1827 |
+ |
param->setGTol(globals->getMinGTol()); |
1828 |
+ |
} |
1829 |
+ |
|
1830 |
+ |
if (globals->haveMinMaxIter()){ |
1831 |
+ |
param->setMaxIteration(globals->getMinMaxIter()); |
1832 |
+ |
} |
1833 |
+ |
|
1834 |
+ |
if (globals->haveMinWriteFrq()){ |
1835 |
+ |
param->setMaxIteration(globals->getMinMaxIter()); |
1836 |
+ |
} |
1837 |
+ |
|
1838 |
+ |
if (globals->haveMinWriteFrq()){ |
1839 |
+ |
param->setWriteFrq(globals->getMinWriteFrq()); |
1840 |
+ |
} |
1841 |
+ |
|
1842 |
+ |
if (globals->haveMinStepSize()){ |
1843 |
+ |
param->setStepSize(globals->getMinStepSize()); |
1844 |
+ |
} |
1845 |
+ |
|
1846 |
+ |
if (globals->haveMinLSMaxIter()){ |
1847 |
+ |
param->setLineSearchMaxIteration(globals->getMinLSMaxIter()); |
1848 |
+ |
} |
1849 |
+ |
|
1850 |
+ |
if (globals->haveMinLSTol()){ |
1851 |
+ |
param->setLineSearchTol(globals->getMinLSTol()); |
1852 |
+ |
} |
1853 |
+ |
|
1854 |
+ |
strcpy(minimizerName, globals->getMinimizer()); |
1855 |
+ |
|
1856 |
+ |
if (!strcasecmp(minimizerName, "CG")){ |
1857 |
+ |
myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
1858 |
+ |
} |
1859 |
+ |
else if (!strcasecmp(minimizerName, "SD")){ |
1860 |
+ |
//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param); |
1861 |
+ |
myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param); |
1862 |
+ |
} |
1863 |
+ |
else{ |
1864 |
+ |
sprintf(painCave.errMsg, |
1865 |
+ |
"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n"); |
1866 |
+ |
painCave.isFatal = 0; |
1867 |
+ |
simError(); |
1868 |
+ |
|
1869 |
+ |
myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
1870 |
+ |
} |
1871 |
+ |
info[i].the_integrator = myOOPSEMinimizer; |
1872 |
+ |
|
1873 |
+ |
//store the minimizer into simInfo |
1874 |
+ |
info[i].the_minimizer = myOOPSEMinimizer; |
1875 |
+ |
info[i].has_minimizer = true; |
1876 |
+ |
} |
1877 |
+ |
|
1878 |
+ |
} |